Multiple sequence alignment - TraesCS5A01G546600

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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 TraesCS5A01G546600 chr5A 100.000 4145 0 0 1 4145 700662257 700666401 0.000000e+00 7655.0
1 TraesCS5A01G546600 chr5A 96.203 474 17 1 1 473 261823740 261824213 0.000000e+00 774.0
2 TraesCS5A01G546600 chr5A 94.231 104 6 0 575 678 261824210 261824313 4.290000e-35 159.0
3 TraesCS5A01G546600 chrUn 88.895 1693 78 37 726 2377 110657634 110659257 0.000000e+00 1984.0
4 TraesCS5A01G546600 chrUn 91.100 1191 81 13 2509 3696 110659336 110660504 0.000000e+00 1589.0
5 TraesCS5A01G546600 chrUn 91.646 395 30 3 3754 4145 110660728 110661122 1.010000e-150 544.0
6 TraesCS5A01G546600 chrUn 95.370 108 3 1 3681 3786 110660624 110660731 1.980000e-38 171.0
7 TraesCS5A01G546600 chr4B 88.157 1579 76 49 797 2336 660661340 660662846 0.000000e+00 1777.0
8 TraesCS5A01G546600 chr4B 88.293 1418 118 28 2509 3907 660664144 660665532 0.000000e+00 1655.0
9 TraesCS5A01G546600 chr4B 97.561 41 1 0 773 813 660661283 660661323 2.070000e-08 71.3
10 TraesCS5A01G546600 chr1A 97.938 679 14 0 1 679 64904370 64905048 0.000000e+00 1177.0
11 TraesCS5A01G546600 chr1A 98.358 670 10 1 1 670 144631131 144630463 0.000000e+00 1175.0
12 TraesCS5A01G546600 chr1A 87.500 360 37 7 1243 1595 368802317 368801959 3.860000e-110 409.0
13 TraesCS5A01G546600 chr1A 84.615 260 37 2 2029 2285 368801859 368801600 5.320000e-64 255.0
14 TraesCS5A01G546600 chr1A 95.327 107 5 0 472 578 202083501 202083395 1.980000e-38 171.0
15 TraesCS5A01G546600 chr1A 100.000 29 0 0 650 678 505492691 505492719 2.000000e-03 54.7
16 TraesCS5A01G546600 chr6A 97.085 686 12 3 1 678 4565754 4566439 0.000000e+00 1149.0
17 TraesCS5A01G546600 chr6A 93.458 107 7 0 472 578 124313135 124313241 4.290000e-35 159.0
18 TraesCS5A01G546600 chr6D 91.507 471 35 3 1 466 455273119 455272649 0.000000e+00 643.0
19 TraesCS5A01G546600 chr3A 91.045 469 38 3 1 466 701879286 701878819 7.560000e-177 630.0
20 TraesCS5A01G546600 chr3A 98.324 358 5 1 1 357 48398103 48398460 9.780000e-176 627.0
21 TraesCS5A01G546600 chr3A 96.667 360 10 1 1 358 48327529 48327888 7.670000e-167 597.0
22 TraesCS5A01G546600 chr3A 95.575 339 12 2 353 691 48364293 48364628 1.310000e-149 540.0
23 TraesCS5A01G546600 chr3A 94.690 339 15 2 353 691 48442180 48442515 1.320000e-144 523.0
24 TraesCS5A01G546600 chr3A 92.523 107 8 0 472 578 739292878 739292984 2.000000e-33 154.0
25 TraesCS5A01G546600 chr2D 86.749 483 46 8 1 473 35527295 35526821 4.750000e-144 521.0
26 TraesCS5A01G546600 chr1D 86.104 367 42 8 1237 1595 295541400 295541035 1.810000e-103 387.0
27 TraesCS5A01G546600 chr1D 85.769 260 34 2 2029 2285 295540951 295540692 5.280000e-69 272.0
28 TraesCS5A01G546600 chr1B 86.141 368 40 10 1237 1595 397056900 397056535 1.810000e-103 387.0
29 TraesCS5A01G546600 chr2A 90.598 117 9 2 465 579 71629232 71629116 2.000000e-33 154.0
30 TraesCS5A01G546600 chr7D 87.273 55 7 0 1514 1568 89867661 89867607 3.460000e-06 63.9
31 TraesCS5A01G546600 chr7D 87.273 55 7 0 1514 1568 89893816 89893762 3.460000e-06 63.9
32 TraesCS5A01G546600 chr7B 87.273 55 7 0 1514 1568 41031646 41031592 3.460000e-06 63.9
33 TraesCS5A01G546600 chr7A 87.273 55 7 0 1514 1568 91492992 91492938 3.460000e-06 63.9


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 TraesCS5A01G546600 chr5A 700662257 700666401 4144 False 7655.000000 7655 100.00000 1 4145 1 chr5A.!!$F1 4144
1 TraesCS5A01G546600 chr5A 261823740 261824313 573 False 466.500000 774 95.21700 1 678 2 chr5A.!!$F2 677
2 TraesCS5A01G546600 chrUn 110657634 110661122 3488 False 1072.000000 1984 91.75275 726 4145 4 chrUn.!!$F1 3419
3 TraesCS5A01G546600 chr4B 660661283 660665532 4249 False 1167.766667 1777 91.33700 773 3907 3 chr4B.!!$F1 3134
4 TraesCS5A01G546600 chr1A 64904370 64905048 678 False 1177.000000 1177 97.93800 1 679 1 chr1A.!!$F1 678
5 TraesCS5A01G546600 chr1A 144630463 144631131 668 True 1175.000000 1175 98.35800 1 670 1 chr1A.!!$R1 669
6 TraesCS5A01G546600 chr1A 368801600 368802317 717 True 332.000000 409 86.05750 1243 2285 2 chr1A.!!$R3 1042
7 TraesCS5A01G546600 chr6A 4565754 4566439 685 False 1149.000000 1149 97.08500 1 678 1 chr6A.!!$F1 677
8 TraesCS5A01G546600 chr1D 295540692 295541400 708 True 329.500000 387 85.93650 1237 2285 2 chr1D.!!$R1 1048

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
717 727 0.179111 TAGATTCGGCAGTTGCGAGG 60.179 55.0 0.0 0.0 43.26 4.63 F
1762 1834 0.036010 ATGGCAAGGAACCGAGTGAG 60.036 55.0 0.0 0.0 0.00 3.51 F
1867 1971 0.102481 AGTATAGCCAACTGTCCGCG 59.898 55.0 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2134 0.108207 GATGGCCACATCCTCCTGAG 59.892 60.0 8.16 0.0 46.23 3.35 R
3070 4340 0.108585 AACGCTTCAAGCTCCCTCAA 59.891 50.0 8.02 0.0 39.60 3.02 R
3151 4421 0.893727 CTTGGCGGTTGGCTTTACCT 60.894 55.0 0.00 0.0 42.94 3.08 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
163 165 7.776107 TCAGTAATATATGAGCTATCTGGCAC 58.224 38.462 0.00 0.00 34.17 5.01
273 275 7.284944 TGGGAAAAGTTGAATTTTGAAATGCAT 59.715 29.630 0.00 0.00 34.03 3.96
375 377 1.704641 AGGCCCTTTGTTTGTCTTCC 58.295 50.000 0.00 0.00 0.00 3.46
506 508 7.043590 CGTTCCGAATTACTCGTCATAGAAATT 60.044 37.037 0.00 0.00 46.65 1.82
564 566 6.227522 TCCACTTCTGTGACGAATAATTTGA 58.772 36.000 0.00 0.00 46.55 2.69
604 614 5.948162 AGATGATATTTCTGGCAACACACTT 59.052 36.000 0.00 0.00 46.17 3.16
679 689 2.736081 CGCACGGGCATACAACTAGTAA 60.736 50.000 11.77 0.00 41.24 2.24
680 690 2.864343 GCACGGGCATACAACTAGTAAG 59.136 50.000 3.77 0.00 40.72 2.34
681 691 3.454375 CACGGGCATACAACTAGTAAGG 58.546 50.000 0.00 0.00 36.05 2.69
682 692 3.131577 CACGGGCATACAACTAGTAAGGA 59.868 47.826 0.00 0.00 36.05 3.36
683 693 3.965347 ACGGGCATACAACTAGTAAGGAT 59.035 43.478 0.00 0.00 36.05 3.24
684 694 4.407945 ACGGGCATACAACTAGTAAGGATT 59.592 41.667 0.00 0.00 36.05 3.01
685 695 5.599656 ACGGGCATACAACTAGTAAGGATTA 59.400 40.000 0.00 0.00 36.05 1.75
686 696 6.157211 CGGGCATACAACTAGTAAGGATTAG 58.843 44.000 0.00 0.00 36.05 1.73
687 697 6.465084 GGGCATACAACTAGTAAGGATTAGG 58.535 44.000 0.00 0.00 36.05 2.69
688 698 6.269307 GGGCATACAACTAGTAAGGATTAGGA 59.731 42.308 0.00 0.00 36.05 2.94
689 699 7.379750 GGCATACAACTAGTAAGGATTAGGAG 58.620 42.308 0.00 0.00 36.05 3.69
690 700 7.232941 GGCATACAACTAGTAAGGATTAGGAGA 59.767 40.741 0.00 0.00 36.05 3.71
691 701 8.301002 GCATACAACTAGTAAGGATTAGGAGAG 58.699 40.741 0.00 0.00 36.05 3.20
692 702 6.718522 ACAACTAGTAAGGATTAGGAGAGC 57.281 41.667 0.00 0.00 0.00 4.09
693 703 6.436890 ACAACTAGTAAGGATTAGGAGAGCT 58.563 40.000 0.00 0.00 0.00 4.09
694 704 7.584532 ACAACTAGTAAGGATTAGGAGAGCTA 58.415 38.462 0.00 0.00 0.00 3.32
695 705 7.503230 ACAACTAGTAAGGATTAGGAGAGCTAC 59.497 40.741 0.00 0.00 0.00 3.58
696 706 7.396906 ACTAGTAAGGATTAGGAGAGCTACT 57.603 40.000 0.00 0.00 0.00 2.57
697 707 7.818469 ACTAGTAAGGATTAGGAGAGCTACTT 58.182 38.462 0.00 0.00 0.00 2.24
698 708 8.283708 ACTAGTAAGGATTAGGAGAGCTACTTT 58.716 37.037 0.00 0.00 0.00 2.66
699 709 9.796180 CTAGTAAGGATTAGGAGAGCTACTTTA 57.204 37.037 0.00 0.00 0.00 1.85
700 710 8.700439 AGTAAGGATTAGGAGAGCTACTTTAG 57.300 38.462 0.00 0.00 0.00 1.85
701 711 8.504409 AGTAAGGATTAGGAGAGCTACTTTAGA 58.496 37.037 0.00 0.00 0.00 2.10
702 712 9.304335 GTAAGGATTAGGAGAGCTACTTTAGAT 57.696 37.037 0.00 0.00 0.00 1.98
703 713 8.791298 AAGGATTAGGAGAGCTACTTTAGATT 57.209 34.615 0.00 0.00 0.00 2.40
704 714 8.417273 AGGATTAGGAGAGCTACTTTAGATTC 57.583 38.462 0.00 0.00 0.00 2.52
705 715 7.175990 AGGATTAGGAGAGCTACTTTAGATTCG 59.824 40.741 0.00 0.00 0.00 3.34
706 716 6.636562 TTAGGAGAGCTACTTTAGATTCGG 57.363 41.667 0.00 0.00 0.00 4.30
707 717 3.319689 AGGAGAGCTACTTTAGATTCGGC 59.680 47.826 0.00 0.00 0.00 5.54
708 718 3.068307 GGAGAGCTACTTTAGATTCGGCA 59.932 47.826 0.00 0.00 0.00 5.69
709 719 4.295051 GAGAGCTACTTTAGATTCGGCAG 58.705 47.826 0.00 0.00 0.00 4.85
710 720 3.702045 AGAGCTACTTTAGATTCGGCAGT 59.298 43.478 0.00 0.00 0.00 4.40
711 721 4.160626 AGAGCTACTTTAGATTCGGCAGTT 59.839 41.667 0.00 0.00 0.00 3.16
712 722 4.184629 AGCTACTTTAGATTCGGCAGTTG 58.815 43.478 0.00 0.00 0.00 3.16
713 723 3.242446 GCTACTTTAGATTCGGCAGTTGC 60.242 47.826 0.00 0.00 41.14 4.17
714 724 1.732259 ACTTTAGATTCGGCAGTTGCG 59.268 47.619 0.00 0.00 43.26 4.85
715 725 1.999735 CTTTAGATTCGGCAGTTGCGA 59.000 47.619 0.00 0.00 43.26 5.10
716 726 1.640428 TTAGATTCGGCAGTTGCGAG 58.360 50.000 0.00 0.00 43.26 5.03
717 727 0.179111 TAGATTCGGCAGTTGCGAGG 60.179 55.000 0.00 0.00 43.26 4.63
718 728 2.436646 ATTCGGCAGTTGCGAGGG 60.437 61.111 0.00 0.00 43.26 4.30
719 729 2.852495 GATTCGGCAGTTGCGAGGGA 62.852 60.000 0.00 0.00 43.26 4.20
720 730 2.257409 ATTCGGCAGTTGCGAGGGAT 62.257 55.000 0.00 0.00 43.26 3.85
721 731 2.436646 CGGCAGTTGCGAGGGATT 60.437 61.111 0.00 0.00 43.26 3.01
722 732 2.753966 CGGCAGTTGCGAGGGATTG 61.754 63.158 0.00 0.00 43.26 2.67
723 733 1.377202 GGCAGTTGCGAGGGATTGA 60.377 57.895 0.00 0.00 43.26 2.57
724 734 0.749454 GGCAGTTGCGAGGGATTGAT 60.749 55.000 0.00 0.00 43.26 2.57
728 738 2.119495 AGTTGCGAGGGATTGATACCT 58.881 47.619 0.00 0.00 46.30 3.08
730 740 3.069729 AGTTGCGAGGGATTGATACCTAC 59.930 47.826 0.00 0.00 42.67 3.18
741 751 6.935208 GGGATTGATACCTACTAATCACCAAC 59.065 42.308 0.00 0.00 31.99 3.77
767 777 2.204237 GCACTTGCCAAAGAAACCTTG 58.796 47.619 0.00 0.00 36.84 3.61
768 778 2.418609 GCACTTGCCAAAGAAACCTTGT 60.419 45.455 0.00 0.00 36.84 3.16
769 779 3.860641 CACTTGCCAAAGAAACCTTGTT 58.139 40.909 0.00 0.00 36.84 2.83
770 780 3.618150 CACTTGCCAAAGAAACCTTGTTG 59.382 43.478 0.00 0.00 36.84 3.33
771 781 3.513515 ACTTGCCAAAGAAACCTTGTTGA 59.486 39.130 0.00 0.00 36.84 3.18
850 890 2.012673 CTTGTTAGACAGCCCATCTGC 58.987 52.381 0.00 0.00 46.76 4.26
851 891 0.253044 TGTTAGACAGCCCATCTGCC 59.747 55.000 0.00 0.00 46.76 4.85
871 911 0.245539 CCATCCAGCAAAGCCACTTG 59.754 55.000 0.00 0.00 0.00 3.16
907 952 0.318955 GGAGACGGACGGAAAAACGA 60.319 55.000 0.00 0.00 37.61 3.85
1600 1672 3.826282 ACCCCATGGTGAGTCCTG 58.174 61.111 11.73 0.00 45.58 3.86
1601 1673 1.160870 ACCCCATGGTGAGTCCTGA 59.839 57.895 11.73 0.00 45.58 3.86
1602 1674 0.253347 ACCCCATGGTGAGTCCTGAT 60.253 55.000 11.73 0.00 45.58 2.90
1603 1675 0.471617 CCCCATGGTGAGTCCTGATC 59.528 60.000 11.73 0.00 37.07 2.92
1604 1676 0.105593 CCCATGGTGAGTCCTGATCG 59.894 60.000 11.73 0.00 37.07 3.69
1605 1677 0.826715 CCATGGTGAGTCCTGATCGT 59.173 55.000 2.57 0.00 37.07 3.73
1606 1678 1.208052 CCATGGTGAGTCCTGATCGTT 59.792 52.381 2.57 0.00 37.07 3.85
1607 1679 2.544685 CATGGTGAGTCCTGATCGTTC 58.455 52.381 0.00 0.00 37.07 3.95
1608 1680 0.526211 TGGTGAGTCCTGATCGTTCG 59.474 55.000 0.00 0.00 37.07 3.95
1609 1681 0.526662 GGTGAGTCCTGATCGTTCGT 59.473 55.000 0.00 0.00 0.00 3.85
1610 1682 1.467713 GGTGAGTCCTGATCGTTCGTC 60.468 57.143 0.00 0.00 0.00 4.20
1611 1683 0.809385 TGAGTCCTGATCGTTCGTCC 59.191 55.000 0.00 0.00 0.00 4.79
1612 1684 0.100861 GAGTCCTGATCGTTCGTCCC 59.899 60.000 0.00 0.00 0.00 4.46
1613 1685 1.141234 GTCCTGATCGTTCGTCCCC 59.859 63.158 0.00 0.00 0.00 4.81
1614 1686 1.304630 TCCTGATCGTTCGTCCCCA 60.305 57.895 0.00 0.00 0.00 4.96
1615 1687 0.686441 TCCTGATCGTTCGTCCCCAT 60.686 55.000 0.00 0.00 0.00 4.00
1616 1688 0.530650 CCTGATCGTTCGTCCCCATG 60.531 60.000 0.00 0.00 0.00 3.66
1617 1689 0.530650 CTGATCGTTCGTCCCCATGG 60.531 60.000 4.14 4.14 0.00 3.66
1618 1690 1.261938 TGATCGTTCGTCCCCATGGT 61.262 55.000 11.73 0.00 0.00 3.55
1619 1691 0.810031 GATCGTTCGTCCCCATGGTG 60.810 60.000 11.73 0.00 0.00 4.17
1620 1692 2.252072 ATCGTTCGTCCCCATGGTGG 62.252 60.000 11.73 11.84 37.25 4.61
1646 1718 2.746277 GTGCGGGTTAGGTGCCTG 60.746 66.667 0.12 0.00 35.53 4.85
1649 1721 3.717294 CGGGTTAGGTGCCTGCCT 61.717 66.667 0.12 0.00 42.43 4.75
1650 1722 2.272471 GGGTTAGGTGCCTGCCTC 59.728 66.667 0.12 0.00 39.94 4.70
1651 1723 2.272471 GGTTAGGTGCCTGCCTCC 59.728 66.667 0.12 0.00 39.94 4.30
1652 1724 2.125106 GTTAGGTGCCTGCCTCCG 60.125 66.667 0.12 0.00 39.94 4.63
1653 1725 3.399181 TTAGGTGCCTGCCTCCGG 61.399 66.667 0.00 0.00 39.94 5.14
1668 1740 1.161563 TCCGGTTCTTGCGTCCAAAC 61.162 55.000 0.00 0.00 0.00 2.93
1718 1790 1.963338 GCAGCTGCGTCTTCTTGGT 60.963 57.895 25.23 0.00 0.00 3.67
1722 1794 1.901650 GCTGCGTCTTCTTGGTTCCG 61.902 60.000 0.00 0.00 0.00 4.30
1734 1806 1.374560 TGGTTCCGAAATGGCATACG 58.625 50.000 16.33 16.33 37.80 3.06
1735 1807 1.339247 TGGTTCCGAAATGGCATACGT 60.339 47.619 19.79 0.00 37.80 3.57
1737 1809 1.735571 GTTCCGAAATGGCATACGTGT 59.264 47.619 19.79 0.00 37.80 4.49
1746 1818 1.809547 TGGCATACGTGTTGTTCATGG 59.190 47.619 0.00 0.00 37.38 3.66
1750 1822 3.491356 CATACGTGTTGTTCATGGCAAG 58.509 45.455 0.00 0.00 37.38 4.01
1753 1825 1.336440 CGTGTTGTTCATGGCAAGGAA 59.664 47.619 0.00 0.00 0.00 3.36
1755 1827 1.686052 TGTTGTTCATGGCAAGGAACC 59.314 47.619 23.90 14.57 44.57 3.62
1757 1829 0.109532 TGTTCATGGCAAGGAACCGA 59.890 50.000 23.90 10.51 44.57 4.69
1758 1830 0.804989 GTTCATGGCAAGGAACCGAG 59.195 55.000 19.07 0.00 40.42 4.63
1759 1831 0.400213 TTCATGGCAAGGAACCGAGT 59.600 50.000 0.00 0.00 0.00 4.18
1761 1833 0.321564 CATGGCAAGGAACCGAGTGA 60.322 55.000 0.00 0.00 0.00 3.41
1762 1834 0.036010 ATGGCAAGGAACCGAGTGAG 60.036 55.000 0.00 0.00 0.00 3.51
1763 1835 2.035442 GGCAAGGAACCGAGTGAGC 61.035 63.158 0.00 0.00 0.00 4.26
1790 1887 7.138692 AGTTCAATCAATAGTTCTTGCTGTC 57.861 36.000 0.00 0.00 0.00 3.51
1804 1901 5.916318 TCTTGCTGTCAAATTGACCAATTT 58.084 33.333 21.75 13.26 46.40 1.82
1842 1942 2.760634 TTTCTCTTGTGCTATGCCGA 57.239 45.000 0.00 0.00 0.00 5.54
1845 1945 3.266510 TCTCTTGTGCTATGCCGAATT 57.733 42.857 0.00 0.00 0.00 2.17
1854 1958 5.696270 TGTGCTATGCCGAATTTCAGTATAG 59.304 40.000 11.34 11.34 0.00 1.31
1855 1959 4.690748 TGCTATGCCGAATTTCAGTATAGC 59.309 41.667 24.39 24.39 40.95 2.97
1856 1960 4.093556 GCTATGCCGAATTTCAGTATAGCC 59.906 45.833 22.27 11.16 36.93 3.93
1857 1961 3.552132 TGCCGAATTTCAGTATAGCCA 57.448 42.857 0.00 0.00 0.00 4.75
1858 1962 3.879998 TGCCGAATTTCAGTATAGCCAA 58.120 40.909 0.00 0.00 0.00 4.52
1859 1963 3.625764 TGCCGAATTTCAGTATAGCCAAC 59.374 43.478 0.00 0.00 0.00 3.77
1860 1964 3.877508 GCCGAATTTCAGTATAGCCAACT 59.122 43.478 0.00 0.00 0.00 3.16
1861 1965 4.260784 GCCGAATTTCAGTATAGCCAACTG 60.261 45.833 4.70 4.70 44.66 3.16
1862 1966 4.876107 CCGAATTTCAGTATAGCCAACTGT 59.124 41.667 9.69 0.00 43.88 3.55
1863 1967 5.006746 CCGAATTTCAGTATAGCCAACTGTC 59.993 44.000 9.69 1.56 43.88 3.51
1864 1968 5.006746 CGAATTTCAGTATAGCCAACTGTCC 59.993 44.000 9.69 0.00 43.88 4.02
1865 1969 3.520290 TTCAGTATAGCCAACTGTCCG 57.480 47.619 9.69 0.00 43.88 4.79
1866 1970 1.136305 TCAGTATAGCCAACTGTCCGC 59.864 52.381 9.69 0.00 43.88 5.54
1867 1971 0.102481 AGTATAGCCAACTGTCCGCG 59.898 55.000 0.00 0.00 0.00 6.46
1868 1972 0.179119 GTATAGCCAACTGTCCGCGT 60.179 55.000 4.92 0.00 0.00 6.01
1869 1973 1.066002 GTATAGCCAACTGTCCGCGTA 59.934 52.381 4.92 0.00 0.00 4.42
1897 2001 5.826643 TGGAAGCTACTTATCCAACCATTT 58.173 37.500 1.42 0.00 40.19 2.32
1916 2020 7.959689 CCATTTAAATTCATGGTTGTTGTCA 57.040 32.000 0.00 0.00 36.01 3.58
1917 2021 8.375608 CCATTTAAATTCATGGTTGTTGTCAA 57.624 30.769 0.00 0.00 36.01 3.18
1935 2039 5.863965 TGTCAACTTGTCATGATGGAACTA 58.136 37.500 0.00 0.00 0.00 2.24
1936 2040 5.934043 TGTCAACTTGTCATGATGGAACTAG 59.066 40.000 0.00 0.00 0.00 2.57
1942 2046 2.866762 GTCATGATGGAACTAGGTTCGC 59.133 50.000 0.00 0.00 42.78 4.70
1943 2047 2.499693 TCATGATGGAACTAGGTTCGCA 59.500 45.455 0.00 4.77 42.78 5.10
1945 2049 3.179443 TGATGGAACTAGGTTCGCATC 57.821 47.619 21.12 21.12 42.78 3.91
1986 2092 5.340528 GGTTCCCCAACCCATAAGAGATTTA 60.341 44.000 0.00 0.00 46.01 1.40
2027 2134 5.722863 GCACTAAAGTTTCGGTTTGTTTTGC 60.723 40.000 0.00 0.00 0.00 3.68
2046 2153 0.108207 CTCAGGAGGATGTGGCCATC 59.892 60.000 9.72 2.39 45.65 3.51
2395 3665 4.926832 GTCTCACTTTAGTTCTGCCTTCTC 59.073 45.833 0.00 0.00 0.00 2.87
2404 3674 2.732412 TCTGCCTTCTCAGAAACTCG 57.268 50.000 0.00 0.00 39.89 4.18
2420 3690 5.982516 AGAAACTCGATGCTATCTGATTGAC 59.017 40.000 3.25 0.00 0.00 3.18
2421 3691 4.250116 ACTCGATGCTATCTGATTGACC 57.750 45.455 3.25 0.00 0.00 4.02
2430 3700 5.716228 TGCTATCTGATTGACCCATTTGTTT 59.284 36.000 3.25 0.00 0.00 2.83
2431 3701 6.038356 GCTATCTGATTGACCCATTTGTTTG 58.962 40.000 3.25 0.00 0.00 2.93
2433 3703 5.710513 TCTGATTGACCCATTTGTTTGAG 57.289 39.130 0.00 0.00 0.00 3.02
2438 3708 5.964958 TTGACCCATTTGTTTGAGATCTC 57.035 39.130 16.21 16.21 0.00 2.75
2442 3712 5.501156 ACCCATTTGTTTGAGATCTCTACC 58.499 41.667 22.95 9.42 0.00 3.18
2444 3714 5.500234 CCATTTGTTTGAGATCTCTACCCA 58.500 41.667 22.95 11.91 0.00 4.51
2445 3715 5.355350 CCATTTGTTTGAGATCTCTACCCAC 59.645 44.000 22.95 11.53 0.00 4.61
2447 3717 5.407407 TTGTTTGAGATCTCTACCCACTC 57.593 43.478 22.95 6.35 0.00 3.51
2448 3718 3.769844 TGTTTGAGATCTCTACCCACTCC 59.230 47.826 22.95 2.65 0.00 3.85
2451 3721 1.950909 GAGATCTCTACCCACTCCACG 59.049 57.143 15.80 0.00 0.00 4.94
2452 3722 1.285373 AGATCTCTACCCACTCCACGT 59.715 52.381 0.00 0.00 0.00 4.49
2453 3723 1.405821 GATCTCTACCCACTCCACGTG 59.594 57.143 9.08 9.08 43.41 4.49
2460 3730 4.278956 CACTCCACGTGGCTAACC 57.721 61.111 30.25 0.00 40.02 2.85
2461 3731 1.671742 CACTCCACGTGGCTAACCT 59.328 57.895 30.25 4.76 40.02 3.50
2462 3732 0.892755 CACTCCACGTGGCTAACCTA 59.107 55.000 30.25 9.81 40.02 3.08
2465 3735 2.570302 ACTCCACGTGGCTAACCTAAAT 59.430 45.455 30.25 0.00 36.63 1.40
2467 3737 4.142004 ACTCCACGTGGCTAACCTAAATAG 60.142 45.833 30.25 18.44 36.63 1.73
2468 3738 2.870411 CCACGTGGCTAACCTAAATAGC 59.130 50.000 24.02 0.00 43.99 2.97
2479 3749 8.446599 GCTAACCTAAATAGCCTGTTATGAAA 57.553 34.615 0.00 0.00 39.87 2.69
2480 3750 9.067986 GCTAACCTAAATAGCCTGTTATGAAAT 57.932 33.333 0.00 0.00 39.87 2.17
2523 3793 6.062258 TGAAATAGTTTAGCTGCCTAGGTT 57.938 37.500 11.31 0.00 35.90 3.50
2537 3807 3.041946 CCTAGGTTAGGCAAGGACTCAT 58.958 50.000 0.00 0.00 39.48 2.90
2595 3865 7.661847 ACATATAAGGCTAGCAGGATAACAAAC 59.338 37.037 18.24 0.00 0.00 2.93
2599 3869 3.375299 GGCTAGCAGGATAACAAACAGTG 59.625 47.826 18.24 0.00 0.00 3.66
2605 3875 7.145932 AGCAGGATAACAAACAGTGAATTAC 57.854 36.000 0.00 0.00 0.00 1.89
2615 3885 9.744468 AACAAACAGTGAATTACATTTAACTCC 57.256 29.630 0.00 0.00 0.00 3.85
2616 3886 8.908903 ACAAACAGTGAATTACATTTAACTCCA 58.091 29.630 0.00 0.00 0.00 3.86
2617 3887 9.912634 CAAACAGTGAATTACATTTAACTCCAT 57.087 29.630 0.00 0.00 0.00 3.41
2652 3922 6.068670 ACTTGCAATTTACTGGTTCTTACCT 58.931 36.000 0.00 0.00 45.27 3.08
2689 3959 3.741245 AGGTGAGGACTGAGCTACTAA 57.259 47.619 0.00 0.00 0.00 2.24
2725 3995 8.186821 GTCGTAATAGCAAGTTCTACCTTAAGA 58.813 37.037 3.36 0.00 0.00 2.10
2760 4030 2.235016 GACTACCGATCAGAGATGGCT 58.765 52.381 0.00 0.00 0.00 4.75
2835 4105 1.522580 GGAATCAGTCCTGCTCGGC 60.523 63.158 0.00 0.00 43.98 5.54
2838 4108 1.548357 AATCAGTCCTGCTCGGCTGT 61.548 55.000 5.33 0.00 37.82 4.40
2883 4153 2.265467 TACGCCTGCCATTCCCTTCC 62.265 60.000 0.00 0.00 0.00 3.46
2955 4225 0.247736 GTCTTGAGACGGTGCTGGAT 59.752 55.000 0.00 0.00 35.12 3.41
3122 4392 3.332187 TCTCAGAGAAGGAGAAGGAGTCA 59.668 47.826 0.00 0.00 38.40 3.41
3148 4418 2.695666 GGATCATCGAGGAGGTGAAGAA 59.304 50.000 5.80 0.00 44.24 2.52
3173 4443 0.891904 TAAAGCCAACCGCCAAGGAC 60.892 55.000 0.00 0.00 45.00 3.85
3186 4456 0.750249 CAAGGACCTTTTGGCGGTTT 59.250 50.000 3.21 0.00 45.59 3.27
3213 4483 2.174360 TCTACTCTGCTGCATCTGTGT 58.826 47.619 1.31 1.54 0.00 3.72
3214 4484 2.094338 TCTACTCTGCTGCATCTGTGTG 60.094 50.000 1.31 0.00 0.00 3.82
3290 4560 1.295423 GCACTACCGGTGGTCATGT 59.705 57.895 22.17 5.08 45.44 3.21
3357 4627 3.903090 TCCCAATTTTTGATGGTGAAGCT 59.097 39.130 0.00 0.00 34.79 3.74
3376 4646 2.862530 GCTGACAGTTTGCGAGTCTGTA 60.863 50.000 11.99 3.66 41.58 2.74
3432 4702 4.202357 ACAAAGTGGCAATCTCTGTACAGA 60.202 41.667 23.80 23.80 35.85 3.41
3502 4775 5.440610 AGAGGCTGATATTTAGGTGGTTTG 58.559 41.667 0.00 0.00 0.00 2.93
3622 4900 9.874215 CATATGTGCAATCTTGTTGTATAGAAG 57.126 33.333 0.00 0.00 0.00 2.85
3655 4934 8.287439 TCTGTTTCAGTTATGTTCAGGAAAAA 57.713 30.769 0.00 0.00 32.61 1.94
3656 4935 8.405531 TCTGTTTCAGTTATGTTCAGGAAAAAG 58.594 33.333 0.00 0.00 33.13 2.27
3771 5191 6.620678 TCTTTGCAAATTCCAGTAATGTAGC 58.379 36.000 13.23 0.00 0.00 3.58
3928 5378 2.042686 ACACACAGAGCAGCAAAAGA 57.957 45.000 0.00 0.00 0.00 2.52
4007 5457 6.844696 TCAGAATGATATACAAACGGAAGC 57.155 37.500 0.00 0.00 42.56 3.86
4023 5473 6.183309 ACGGAAGCTTCATTAGAAAATCAC 57.817 37.500 27.02 4.77 32.35 3.06
4025 5475 5.030936 GGAAGCTTCATTAGAAAATCACGC 58.969 41.667 27.02 0.85 32.35 5.34
4050 5500 5.746307 TGCATATGAATCAGCAAAGAGTC 57.254 39.130 6.97 0.00 33.48 3.36
4067 5517 1.603802 AGTCACCGCAACAAAGTGATG 59.396 47.619 0.00 0.00 42.14 3.07
4073 5523 1.415374 GCAACAAAGTGATGCTGCAG 58.585 50.000 10.11 10.11 42.03 4.41
4086 5536 5.684626 GTGATGCTGCAGATATTAGTTTTGC 59.315 40.000 20.43 0.00 35.42 3.68
4087 5537 4.637483 TGCTGCAGATATTAGTTTTGCC 57.363 40.909 20.43 0.00 33.98 4.52
4090 5540 5.127519 TGCTGCAGATATTAGTTTTGCCATT 59.872 36.000 20.43 0.00 33.98 3.16
4133 5585 1.068588 AGCAGCCAAGCATGCATATTG 59.931 47.619 21.98 15.35 45.01 1.90
4141 5593 3.947910 AGCATGCATATTGGCCATTAC 57.052 42.857 21.98 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 165 9.927668 AGAAAAGTTTCCAATGGTATAATTGTG 57.072 29.630 0.00 0.00 37.92 3.33
273 275 6.541907 TCTATCCTAATTTACATGGCATGCA 58.458 36.000 26.70 12.32 0.00 3.96
604 614 2.296792 ACATTGCACATGCGGCTTATA 58.703 42.857 10.82 0.00 45.83 0.98
679 689 7.175990 CGAATCTAAAGTAGCTCTCCTAATCCT 59.824 40.741 0.00 0.00 0.00 3.24
680 690 7.309920 CGAATCTAAAGTAGCTCTCCTAATCC 58.690 42.308 0.00 0.00 0.00 3.01
681 691 7.309920 CCGAATCTAAAGTAGCTCTCCTAATC 58.690 42.308 0.00 0.00 0.00 1.75
682 692 6.294843 GCCGAATCTAAAGTAGCTCTCCTAAT 60.295 42.308 0.00 0.00 0.00 1.73
683 693 5.009811 GCCGAATCTAAAGTAGCTCTCCTAA 59.990 44.000 0.00 0.00 0.00 2.69
684 694 4.519730 GCCGAATCTAAAGTAGCTCTCCTA 59.480 45.833 0.00 0.00 0.00 2.94
685 695 3.319689 GCCGAATCTAAAGTAGCTCTCCT 59.680 47.826 0.00 0.00 0.00 3.69
686 696 3.068307 TGCCGAATCTAAAGTAGCTCTCC 59.932 47.826 0.00 0.00 0.00 3.71
687 697 4.202070 ACTGCCGAATCTAAAGTAGCTCTC 60.202 45.833 0.00 0.00 0.00 3.20
688 698 3.702045 ACTGCCGAATCTAAAGTAGCTCT 59.298 43.478 0.00 0.00 0.00 4.09
689 699 4.048241 ACTGCCGAATCTAAAGTAGCTC 57.952 45.455 0.00 0.00 0.00 4.09
690 700 4.184629 CAACTGCCGAATCTAAAGTAGCT 58.815 43.478 0.00 0.00 0.00 3.32
691 701 3.242446 GCAACTGCCGAATCTAAAGTAGC 60.242 47.826 0.00 0.00 34.31 3.58
692 702 3.000322 CGCAACTGCCGAATCTAAAGTAG 60.000 47.826 0.00 0.00 37.91 2.57
693 703 2.927477 CGCAACTGCCGAATCTAAAGTA 59.073 45.455 0.00 0.00 37.91 2.24
694 704 1.732259 CGCAACTGCCGAATCTAAAGT 59.268 47.619 0.00 0.00 37.91 2.66
695 705 1.999735 TCGCAACTGCCGAATCTAAAG 59.000 47.619 0.00 0.00 37.91 1.85
696 706 1.999735 CTCGCAACTGCCGAATCTAAA 59.000 47.619 0.00 0.00 37.91 1.85
697 707 1.640428 CTCGCAACTGCCGAATCTAA 58.360 50.000 0.00 0.00 37.91 2.10
698 708 0.179111 CCTCGCAACTGCCGAATCTA 60.179 55.000 0.00 0.00 37.91 1.98
699 709 1.448540 CCTCGCAACTGCCGAATCT 60.449 57.895 0.00 0.00 37.91 2.40
700 710 2.464459 CCCTCGCAACTGCCGAATC 61.464 63.158 0.00 0.00 37.91 2.52
701 711 2.257409 ATCCCTCGCAACTGCCGAAT 62.257 55.000 0.00 0.00 37.91 3.34
702 712 2.463589 AATCCCTCGCAACTGCCGAA 62.464 55.000 0.00 0.00 37.91 4.30
703 713 2.954684 AATCCCTCGCAACTGCCGA 61.955 57.895 0.00 0.00 37.91 5.54
704 714 2.436646 AATCCCTCGCAACTGCCG 60.437 61.111 0.00 0.00 37.91 5.69
705 715 0.749454 ATCAATCCCTCGCAACTGCC 60.749 55.000 0.00 0.00 37.91 4.85
706 716 1.599542 GTATCAATCCCTCGCAACTGC 59.400 52.381 0.00 0.00 37.78 4.40
707 717 2.158900 AGGTATCAATCCCTCGCAACTG 60.159 50.000 0.00 0.00 0.00 3.16
708 718 2.119495 AGGTATCAATCCCTCGCAACT 58.881 47.619 0.00 0.00 0.00 3.16
709 719 2.622064 AGGTATCAATCCCTCGCAAC 57.378 50.000 0.00 0.00 0.00 4.17
710 720 3.305720 AGTAGGTATCAATCCCTCGCAA 58.694 45.455 0.00 0.00 32.08 4.85
711 721 2.958818 AGTAGGTATCAATCCCTCGCA 58.041 47.619 0.00 0.00 32.08 5.10
712 722 5.185249 TGATTAGTAGGTATCAATCCCTCGC 59.815 44.000 0.00 0.00 32.08 5.03
713 723 6.350277 GGTGATTAGTAGGTATCAATCCCTCG 60.350 46.154 0.00 0.00 32.94 4.63
714 724 6.497259 TGGTGATTAGTAGGTATCAATCCCTC 59.503 42.308 0.00 0.00 32.94 4.30
715 725 6.390504 TGGTGATTAGTAGGTATCAATCCCT 58.609 40.000 0.00 0.00 32.94 4.20
716 726 6.681729 TGGTGATTAGTAGGTATCAATCCC 57.318 41.667 0.00 0.00 32.94 3.85
717 727 7.506114 TGTTGGTGATTAGTAGGTATCAATCC 58.494 38.462 0.00 0.00 32.94 3.01
718 728 8.958119 TTGTTGGTGATTAGTAGGTATCAATC 57.042 34.615 0.00 0.00 32.94 2.67
719 729 9.747898 TTTTGTTGGTGATTAGTAGGTATCAAT 57.252 29.630 0.00 0.00 32.94 2.57
720 730 9.226606 CTTTTGTTGGTGATTAGTAGGTATCAA 57.773 33.333 0.00 0.00 32.94 2.57
721 731 7.827236 CCTTTTGTTGGTGATTAGTAGGTATCA 59.173 37.037 0.00 0.00 0.00 2.15
722 732 7.201705 GCCTTTTGTTGGTGATTAGTAGGTATC 60.202 40.741 0.00 0.00 0.00 2.24
723 733 6.602009 GCCTTTTGTTGGTGATTAGTAGGTAT 59.398 38.462 0.00 0.00 0.00 2.73
724 734 5.941647 GCCTTTTGTTGGTGATTAGTAGGTA 59.058 40.000 0.00 0.00 0.00 3.08
728 738 5.381757 AGTGCCTTTTGTTGGTGATTAGTA 58.618 37.500 0.00 0.00 0.00 1.82
730 740 4.853924 AGTGCCTTTTGTTGGTGATTAG 57.146 40.909 0.00 0.00 0.00 1.73
755 765 6.813152 ACTCAACAATCAACAAGGTTTCTTTG 59.187 34.615 0.00 0.00 0.00 2.77
757 767 6.530019 ACTCAACAATCAACAAGGTTTCTT 57.470 33.333 0.00 0.00 0.00 2.52
759 769 8.871686 ATTAACTCAACAATCAACAAGGTTTC 57.128 30.769 0.00 0.00 0.00 2.78
762 772 7.581213 TGATTAACTCAACAATCAACAAGGT 57.419 32.000 0.00 0.00 38.02 3.50
763 773 8.298854 TCATGATTAACTCAACAATCAACAAGG 58.701 33.333 0.00 0.00 42.67 3.61
765 775 9.844790 GATCATGATTAACTCAACAATCAACAA 57.155 29.630 10.14 0.00 42.67 2.83
767 777 9.844790 TTGATCATGATTAACTCAACAATCAAC 57.155 29.630 10.14 0.00 42.67 3.18
849 889 3.464494 GGCTTTGCTGGATGGGGC 61.464 66.667 0.00 0.00 0.00 5.80
850 890 2.037687 TGGCTTTGCTGGATGGGG 59.962 61.111 0.00 0.00 0.00 4.96
851 891 0.901580 AAGTGGCTTTGCTGGATGGG 60.902 55.000 0.00 0.00 0.00 4.00
871 911 1.051556 TCCCCCACCTTGTTTTTGGC 61.052 55.000 0.00 0.00 0.00 4.52
924 969 0.336737 TGGGTTTGGTGGGTTGACTT 59.663 50.000 0.00 0.00 0.00 3.01
1224 1285 2.035783 GGGGGCTTGGAGGTTGTC 59.964 66.667 0.00 0.00 0.00 3.18
1597 1669 0.530650 CATGGGGACGAACGATCAGG 60.531 60.000 0.14 0.00 0.00 3.86
1600 1672 0.810031 CACCATGGGGACGAACGATC 60.810 60.000 18.09 0.00 38.05 3.69
1601 1673 1.220749 CACCATGGGGACGAACGAT 59.779 57.895 18.09 0.00 38.05 3.73
1602 1674 2.660206 CACCATGGGGACGAACGA 59.340 61.111 18.09 0.00 38.05 3.85
1603 1675 2.435938 CCACCATGGGGACGAACG 60.436 66.667 18.14 0.00 38.05 3.95
1612 1684 3.372730 CGCAACCACCCACCATGG 61.373 66.667 11.19 11.19 43.43 3.66
1613 1685 2.597217 ACGCAACCACCCACCATG 60.597 61.111 0.00 0.00 0.00 3.66
1614 1686 2.597217 CACGCAACCACCCACCAT 60.597 61.111 0.00 0.00 0.00 3.55
1621 1693 2.961669 CTAACCCGCACGCAACCAC 61.962 63.158 0.00 0.00 0.00 4.16
1622 1694 2.666862 CTAACCCGCACGCAACCA 60.667 61.111 0.00 0.00 0.00 3.67
1623 1695 3.428282 CCTAACCCGCACGCAACC 61.428 66.667 0.00 0.00 0.00 3.77
1648 1720 0.882927 TTTGGACGCAAGAACCGGAG 60.883 55.000 9.46 0.00 43.62 4.63
1649 1721 1.146485 TTTGGACGCAAGAACCGGA 59.854 52.632 9.46 0.00 43.62 5.14
1650 1722 1.281656 GTTTGGACGCAAGAACCGG 59.718 57.895 0.00 0.00 43.62 5.28
1651 1723 1.083015 CGTTTGGACGCAAGAACCG 60.083 57.895 0.00 0.00 43.03 4.44
1652 1724 4.914291 CGTTTGGACGCAAGAACC 57.086 55.556 0.00 0.00 43.03 3.62
1668 1740 2.282887 CCACCTTGGAAACCCCCG 60.283 66.667 0.00 0.00 40.96 5.73
1687 1759 0.320771 CAGCTGCTAACTTCCACGGT 60.321 55.000 0.00 0.00 0.00 4.83
1697 1769 1.432514 CAAGAAGACGCAGCTGCTAA 58.567 50.000 34.22 0.00 39.32 3.09
1710 1782 1.885887 TGCCATTTCGGAACCAAGAAG 59.114 47.619 0.00 0.00 36.56 2.85
1718 1790 2.102070 ACACGTATGCCATTTCGGAA 57.898 45.000 0.00 0.00 36.56 4.30
1722 1794 4.153958 TGAACAACACGTATGCCATTTC 57.846 40.909 0.00 0.00 0.00 2.17
1734 1806 2.545742 GGTTCCTTGCCATGAACAACAC 60.546 50.000 7.96 0.00 42.04 3.32
1735 1807 1.686052 GGTTCCTTGCCATGAACAACA 59.314 47.619 7.96 0.00 42.04 3.33
1737 1809 0.958091 CGGTTCCTTGCCATGAACAA 59.042 50.000 7.96 0.00 42.04 2.83
1746 1818 2.035442 GGCTCACTCGGTTCCTTGC 61.035 63.158 0.00 0.00 0.00 4.01
1750 1822 2.156051 AACTCGGCTCACTCGGTTCC 62.156 60.000 0.00 0.00 0.00 3.62
1753 1825 1.461091 TTGAACTCGGCTCACTCGGT 61.461 55.000 0.00 0.00 0.00 4.69
1755 1827 1.272781 GATTGAACTCGGCTCACTCG 58.727 55.000 0.00 0.00 0.00 4.18
1757 1829 2.839486 TTGATTGAACTCGGCTCACT 57.161 45.000 0.00 0.00 0.00 3.41
1758 1830 4.184629 ACTATTGATTGAACTCGGCTCAC 58.815 43.478 0.00 0.00 0.00 3.51
1759 1831 4.471904 ACTATTGATTGAACTCGGCTCA 57.528 40.909 0.00 0.00 0.00 4.26
1761 1833 5.091261 AGAACTATTGATTGAACTCGGCT 57.909 39.130 0.00 0.00 0.00 5.52
1762 1834 5.563842 CAAGAACTATTGATTGAACTCGGC 58.436 41.667 0.00 0.00 31.55 5.54
1763 1835 5.352569 AGCAAGAACTATTGATTGAACTCGG 59.647 40.000 0.00 0.00 31.55 4.63
1836 1936 4.085357 TGGCTATACTGAAATTCGGCAT 57.915 40.909 1.01 0.00 0.00 4.40
1842 1942 4.876107 CGGACAGTTGGCTATACTGAAATT 59.124 41.667 17.53 0.63 44.52 1.82
1845 1945 2.418197 GCGGACAGTTGGCTATACTGAA 60.418 50.000 17.53 0.00 44.52 3.02
1854 1958 0.388907 TAAGTACGCGGACAGTTGGC 60.389 55.000 25.94 0.00 0.00 4.52
1855 1959 1.924524 CATAAGTACGCGGACAGTTGG 59.075 52.381 25.94 4.94 0.00 3.77
1856 1960 1.924524 CCATAAGTACGCGGACAGTTG 59.075 52.381 25.94 16.53 0.00 3.16
1857 1961 1.820519 TCCATAAGTACGCGGACAGTT 59.179 47.619 25.94 12.94 0.00 3.16
1858 1962 1.466856 TCCATAAGTACGCGGACAGT 58.533 50.000 25.94 13.79 0.00 3.55
1859 1963 2.460918 CTTCCATAAGTACGCGGACAG 58.539 52.381 25.94 10.20 0.00 3.51
1860 1964 1.470285 GCTTCCATAAGTACGCGGACA 60.470 52.381 25.94 3.54 34.99 4.02
1861 1965 1.202382 AGCTTCCATAAGTACGCGGAC 60.202 52.381 15.35 15.35 34.99 4.79
1862 1966 1.108776 AGCTTCCATAAGTACGCGGA 58.891 50.000 12.47 0.00 34.99 5.54
1863 1967 2.034305 AGTAGCTTCCATAAGTACGCGG 59.966 50.000 12.47 0.00 34.99 6.46
1864 1968 3.351020 AGTAGCTTCCATAAGTACGCG 57.649 47.619 3.53 3.53 34.99 6.01
1865 1969 5.862860 GGATAAGTAGCTTCCATAAGTACGC 59.137 44.000 0.00 0.00 34.99 4.42
1866 1970 6.978338 TGGATAAGTAGCTTCCATAAGTACG 58.022 40.000 0.00 0.00 34.65 3.67
1867 1971 7.656542 GGTTGGATAAGTAGCTTCCATAAGTAC 59.343 40.741 4.93 0.62 39.22 2.73
1868 1972 7.346175 TGGTTGGATAAGTAGCTTCCATAAGTA 59.654 37.037 4.93 0.00 39.22 2.24
1869 1973 6.157994 TGGTTGGATAAGTAGCTTCCATAAGT 59.842 38.462 4.93 0.00 39.22 2.24
1911 2015 5.132502 AGTTCCATCATGACAAGTTGACAA 58.867 37.500 10.54 0.00 0.00 3.18
1912 2016 4.717877 AGTTCCATCATGACAAGTTGACA 58.282 39.130 10.54 10.45 0.00 3.58
1913 2017 5.352569 CCTAGTTCCATCATGACAAGTTGAC 59.647 44.000 10.54 3.81 0.00 3.18
1914 2018 5.013079 ACCTAGTTCCATCATGACAAGTTGA 59.987 40.000 10.54 0.00 0.00 3.18
1915 2019 5.248640 ACCTAGTTCCATCATGACAAGTTG 58.751 41.667 0.00 0.00 0.00 3.16
1916 2020 5.505181 ACCTAGTTCCATCATGACAAGTT 57.495 39.130 0.00 0.00 0.00 2.66
1917 2021 5.491982 GAACCTAGTTCCATCATGACAAGT 58.508 41.667 0.00 0.00 36.65 3.16
1918 2022 4.568359 CGAACCTAGTTCCATCATGACAAG 59.432 45.833 0.00 0.00 39.14 3.16
1943 2047 5.448632 GGAACCGCATTGAAGTAAATTCGAT 60.449 40.000 0.00 0.00 41.93 3.59
1945 2049 4.095610 GGAACCGCATTGAAGTAAATTCG 58.904 43.478 0.00 0.00 41.14 3.34
1973 2077 8.705594 TGAGTAGTTCCCTTAAATCTCTTATGG 58.294 37.037 0.00 0.00 0.00 2.74
1986 2092 3.127425 GTGCAACTGAGTAGTTCCCTT 57.873 47.619 0.00 0.00 45.12 3.95
2010 2117 3.428862 CCTGAGCAAAACAAACCGAAACT 60.429 43.478 0.00 0.00 0.00 2.66
2027 2134 0.108207 GATGGCCACATCCTCCTGAG 59.892 60.000 8.16 0.00 46.23 3.35
2046 2153 4.293648 TCCGGTATGCCATCCGCG 62.294 66.667 0.00 0.00 44.63 6.46
2079 2186 2.501723 ACCGAATGTCTGTAGCAGGATT 59.498 45.455 0.00 0.00 31.51 3.01
2395 3665 5.981915 TCAATCAGATAGCATCGAGTTTCTG 59.018 40.000 0.00 0.00 33.55 3.02
2401 3671 3.006217 TGGGTCAATCAGATAGCATCGAG 59.994 47.826 0.00 0.00 0.00 4.04
2404 3674 5.533903 ACAAATGGGTCAATCAGATAGCATC 59.466 40.000 0.00 0.00 0.00 3.91
2420 3690 4.884164 GGGTAGAGATCTCAAACAAATGGG 59.116 45.833 24.39 0.00 0.00 4.00
2421 3691 5.355350 GTGGGTAGAGATCTCAAACAAATGG 59.645 44.000 24.39 0.00 0.00 3.16
2430 3700 2.684038 CGTGGAGTGGGTAGAGATCTCA 60.684 54.545 24.39 8.03 0.00 3.27
2431 3701 1.950909 CGTGGAGTGGGTAGAGATCTC 59.049 57.143 15.29 15.29 0.00 2.75
2433 3703 1.405821 CACGTGGAGTGGGTAGAGATC 59.594 57.143 7.95 0.00 46.77 2.75
2444 3714 1.636148 TTAGGTTAGCCACGTGGAGT 58.364 50.000 38.30 25.08 37.39 3.85
2445 3715 2.754946 TTTAGGTTAGCCACGTGGAG 57.245 50.000 38.30 13.43 37.39 3.86
2447 3717 2.870411 GCTATTTAGGTTAGCCACGTGG 59.130 50.000 30.66 30.66 36.82 4.94
2454 3724 8.446599 TTTCATAACAGGCTATTTAGGTTAGC 57.553 34.615 0.00 0.00 41.08 3.09
2495 3765 8.470002 CCTAGGCAGCTAAACTATTTCATTTTT 58.530 33.333 0.00 0.00 0.00 1.94
2496 3766 7.615757 ACCTAGGCAGCTAAACTATTTCATTTT 59.384 33.333 9.30 0.00 0.00 1.82
2497 3767 7.119387 ACCTAGGCAGCTAAACTATTTCATTT 58.881 34.615 9.30 0.00 0.00 2.32
2498 3768 6.663734 ACCTAGGCAGCTAAACTATTTCATT 58.336 36.000 9.30 0.00 0.00 2.57
2499 3769 6.253946 ACCTAGGCAGCTAAACTATTTCAT 57.746 37.500 9.30 0.00 0.00 2.57
2500 3770 5.693769 ACCTAGGCAGCTAAACTATTTCA 57.306 39.130 9.30 0.00 0.00 2.69
2501 3771 6.706716 CCTAACCTAGGCAGCTAAACTATTTC 59.293 42.308 9.30 0.00 39.48 2.17
2502 3772 6.592870 CCTAACCTAGGCAGCTAAACTATTT 58.407 40.000 9.30 0.00 39.48 1.40
2503 3773 6.176014 CCTAACCTAGGCAGCTAAACTATT 57.824 41.667 9.30 0.00 39.48 1.73
2504 3774 5.810080 CCTAACCTAGGCAGCTAAACTAT 57.190 43.478 9.30 0.00 39.48 2.12
2523 3793 5.132648 ACAATTATGGATGAGTCCTTGCCTA 59.867 40.000 0.00 0.00 45.32 3.93
2564 3834 6.935240 TCCTGCTAGCCTTATATGTACAAT 57.065 37.500 13.29 0.00 0.00 2.71
2565 3835 6.935240 ATCCTGCTAGCCTTATATGTACAA 57.065 37.500 13.29 0.00 0.00 2.41
2580 3850 7.880713 TGTAATTCACTGTTTGTTATCCTGCTA 59.119 33.333 0.00 0.00 0.00 3.49
2583 3853 9.912634 AAATGTAATTCACTGTTTGTTATCCTG 57.087 29.630 0.00 0.00 33.67 3.86
2621 3891 9.461312 AGAACCAGTAAATTGCAAGTATATGAA 57.539 29.630 4.94 0.00 0.00 2.57
2622 3892 9.461312 AAGAACCAGTAAATTGCAAGTATATGA 57.539 29.630 4.94 0.00 0.00 2.15
2625 3895 9.169592 GGTAAGAACCAGTAAATTGCAAGTATA 57.830 33.333 4.94 0.00 45.98 1.47
2689 3959 4.389890 TGCTATTACGACCATACCGTTT 57.610 40.909 0.00 0.00 40.95 3.60
2725 3995 2.553172 GGTAGTCATCGTATCGCTTCCT 59.447 50.000 0.00 0.00 0.00 3.36
2760 4030 1.270826 CAGAGGCAGAACAGAGAACGA 59.729 52.381 0.00 0.00 0.00 3.85
2835 4105 3.181507 CGGCAATTATGACAGGAACACAG 60.182 47.826 0.00 0.00 32.33 3.66
2838 4108 3.342377 TCGGCAATTATGACAGGAACA 57.658 42.857 0.00 0.00 32.33 3.18
2955 4225 1.674359 AGTTCGTTGCCACAACATGA 58.326 45.000 10.74 0.00 0.00 3.07
3039 4309 0.627451 TGGCATCTCCCTCTTGCAAT 59.373 50.000 0.00 0.00 38.12 3.56
3070 4340 0.108585 AACGCTTCAAGCTCCCTCAA 59.891 50.000 8.02 0.00 39.60 3.02
3087 4357 1.133407 CTCTGAGACCGGTCTAGCAAC 59.867 57.143 36.38 23.35 40.61 4.17
3122 4392 1.252175 CCTCCTCGATGATCCGACAT 58.748 55.000 0.00 0.00 34.56 3.06
3148 4418 1.602605 GCGGTTGGCTTTACCTGGT 60.603 57.895 4.05 4.05 40.22 4.00
3151 4421 0.893727 CTTGGCGGTTGGCTTTACCT 60.894 55.000 0.00 0.00 42.94 3.08
3152 4422 1.584495 CTTGGCGGTTGGCTTTACC 59.416 57.895 0.00 0.00 42.94 2.85
3155 4425 2.197324 TCCTTGGCGGTTGGCTTT 59.803 55.556 0.00 0.00 42.94 3.51
3173 4443 1.028905 TGTCAGAAACCGCCAAAAGG 58.971 50.000 0.00 0.00 0.00 3.11
3181 4451 3.119316 AGCAGAGTAGATGTCAGAAACCG 60.119 47.826 0.00 0.00 0.00 4.44
3186 4456 2.450476 TGCAGCAGAGTAGATGTCAGA 58.550 47.619 0.00 0.00 0.00 3.27
3213 4483 1.229428 GTAAGTTGCAGCTGCTGTCA 58.771 50.000 36.61 22.95 42.66 3.58
3214 4484 1.196354 CTGTAAGTTGCAGCTGCTGTC 59.804 52.381 36.61 25.30 42.66 3.51
3285 4555 5.245531 ACTTCTGGCGAGAAAAATACATGA 58.754 37.500 12.50 0.00 37.77 3.07
3290 4560 5.547465 TCTGAACTTCTGGCGAGAAAAATA 58.453 37.500 12.50 0.00 37.77 1.40
3357 4627 3.660501 ATACAGACTCGCAAACTGTCA 57.339 42.857 0.00 0.00 42.65 3.58
3376 4646 4.962995 ACTGCCTCTGTTGGTACACTATAT 59.037 41.667 0.00 0.00 39.29 0.86
3459 4732 5.997746 CCTCTTCACAACACCAATAAGAGAA 59.002 40.000 10.61 0.00 41.46 2.87
3460 4733 5.551233 CCTCTTCACAACACCAATAAGAGA 58.449 41.667 10.61 0.00 41.46 3.10
3461 4734 4.154918 GCCTCTTCACAACACCAATAAGAG 59.845 45.833 0.00 0.00 39.61 2.85
3462 4735 4.072131 GCCTCTTCACAACACCAATAAGA 58.928 43.478 0.00 0.00 0.00 2.10
3463 4736 4.074970 AGCCTCTTCACAACACCAATAAG 58.925 43.478 0.00 0.00 0.00 1.73
3502 4775 9.109393 TCTGTAATACAATCTTTAATCACCAGC 57.891 33.333 0.00 0.00 0.00 4.85
3622 4900 4.757149 ACATAACTGAAACAGAAGCACCTC 59.243 41.667 5.76 0.00 35.18 3.85
3655 4934 3.532641 AACTGGAGCCATCTTTTTCCT 57.467 42.857 0.00 0.00 0.00 3.36
3656 4935 3.829026 AGAAACTGGAGCCATCTTTTTCC 59.171 43.478 0.00 0.00 0.00 3.13
3771 5191 8.044060 TCTTCCTGTTATTTGTGCTGAATTAG 57.956 34.615 0.00 0.00 0.00 1.73
3855 5305 3.561310 GCATAGAAACCAATCTGATGCGA 59.439 43.478 0.00 0.00 32.32 5.10
3856 5306 3.562973 AGCATAGAAACCAATCTGATGCG 59.437 43.478 0.00 0.00 39.16 4.73
3993 5443 8.780846 TTTCTAATGAAGCTTCCGTTTGTATA 57.219 30.769 23.42 1.79 33.28 1.47
4001 5451 5.258622 CGTGATTTTCTAATGAAGCTTCCG 58.741 41.667 23.42 10.73 33.28 4.30
4007 5457 6.718388 TGCATAGCGTGATTTTCTAATGAAG 58.282 36.000 0.00 0.00 33.28 3.02
4023 5473 4.673534 TTGCTGATTCATATGCATAGCG 57.326 40.909 12.79 6.10 35.27 4.26
4025 5475 7.172703 TGACTCTTTGCTGATTCATATGCATAG 59.827 37.037 12.79 4.87 36.38 2.23
4050 5500 0.311790 AGCATCACTTTGTTGCGGTG 59.688 50.000 4.09 0.00 45.11 4.94
4067 5517 4.637483 TGGCAAAACTAATATCTGCAGC 57.363 40.909 9.47 0.00 34.66 5.25
4098 5548 1.402787 CTGCTTGTTTCTTGTGGGGT 58.597 50.000 0.00 0.00 0.00 4.95
4099 5549 0.032540 GCTGCTTGTTTCTTGTGGGG 59.967 55.000 0.00 0.00 0.00 4.96
4100 5550 0.032540 GGCTGCTTGTTTCTTGTGGG 59.967 55.000 0.00 0.00 0.00 4.61
4101 5551 0.746063 TGGCTGCTTGTTTCTTGTGG 59.254 50.000 0.00 0.00 0.00 4.17
4102 5552 2.466846 CTTGGCTGCTTGTTTCTTGTG 58.533 47.619 0.00 0.00 0.00 3.33
4104 5554 1.202440 TGCTTGGCTGCTTGTTTCTTG 60.202 47.619 0.00 0.00 0.00 3.02
4105 5555 1.113788 TGCTTGGCTGCTTGTTTCTT 58.886 45.000 0.00 0.00 0.00 2.52
4107 5557 1.425412 CATGCTTGGCTGCTTGTTTC 58.575 50.000 0.00 0.00 34.64 2.78
4108 5558 0.601841 GCATGCTTGGCTGCTTGTTT 60.602 50.000 11.37 0.00 39.38 2.83
4109 5559 1.005394 GCATGCTTGGCTGCTTGTT 60.005 52.632 11.37 0.00 39.38 2.83


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

AutoCloner maintained by Alex Coulton.