Multiple sequence alignment - TraesCS6B01G183400

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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 TraesCS6B01G183400 chr6B 100.000 5843 0 0 1 5843 204928712 204922870 0.000000e+00 10791.0
1 TraesCS6B01G183400 chr6B 87.101 721 73 12 5 711 159696117 159696831 0.000000e+00 798.0
2 TraesCS6B01G183400 chr6D 92.520 2206 92 34 750 2936 115550154 115548003 0.000000e+00 3092.0
3 TraesCS6B01G183400 chr6D 94.546 1742 63 11 4130 5843 115546785 115545048 0.000000e+00 2662.0
4 TraesCS6B01G183400 chr6D 93.683 1124 48 11 3019 4130 115547976 115546864 0.000000e+00 1661.0
5 TraesCS6B01G183400 chr6D 90.000 610 57 2 5 614 90121995 90121390 0.000000e+00 785.0
6 TraesCS6B01G183400 chr6D 95.935 246 9 1 4356 4601 162229148 162228904 1.180000e-106 398.0
7 TraesCS6B01G183400 chr6D 100.000 37 0 0 2961 2997 115548017 115547981 1.050000e-07 69.4
8 TraesCS6B01G183400 chr6A 92.090 2187 96 34 774 2936 143969829 143967696 0.000000e+00 3009.0
9 TraesCS6B01G183400 chr6A 94.440 1331 43 11 4130 5440 143966425 143965106 0.000000e+00 2019.0
10 TraesCS6B01G183400 chr6A 90.726 744 45 13 3015 3751 143967673 143966947 0.000000e+00 970.0
11 TraesCS6B01G183400 chr6A 89.344 610 63 2 5 614 108937947 108938554 0.000000e+00 765.0
12 TraesCS6B01G183400 chr6A 92.308 455 22 4 3677 4130 143966946 143966504 8.260000e-178 634.0
13 TraesCS6B01G183400 chr6A 95.405 370 17 0 5474 5843 143965109 143964740 1.810000e-164 590.0
14 TraesCS6B01G183400 chr6A 100.000 60 0 0 2961 3020 143967710 143967651 1.720000e-20 111.0
15 TraesCS6B01G183400 chr2D 88.579 718 68 8 5 710 119074993 119074278 0.000000e+00 859.0
16 TraesCS6B01G183400 chr2D 100.000 31 0 0 3640 3670 163017708 163017678 2.270000e-04 58.4
17 TraesCS6B01G183400 chr2B 87.483 719 77 6 5 711 733975423 733974706 0.000000e+00 817.0
18 TraesCS6B01G183400 chr5D 87.115 714 77 9 5 705 407010053 407010764 0.000000e+00 795.0
19 TraesCS6B01G183400 chr1D 86.630 718 81 9 5 711 52739670 52738957 0.000000e+00 780.0
20 TraesCS6B01G183400 chr3D 86.528 720 82 8 5 711 317092009 317091292 0.000000e+00 778.0
21 TraesCS6B01G183400 chr5B 86.536 713 82 8 5 705 488118420 488117710 0.000000e+00 773.0
22 TraesCS6B01G183400 chr2A 82.964 722 98 16 5 705 618264435 618265152 3.840000e-176 628.0
23 TraesCS6B01G183400 chr4D 86.957 46 6 0 3441 3486 123099038 123099083 1.100000e-02 52.8


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 TraesCS6B01G183400 chr6B 204922870 204928712 5842 True 10791.000000 10791 100.00000 1 5843 1 chr6B.!!$R1 5842
1 TraesCS6B01G183400 chr6B 159696117 159696831 714 False 798.000000 798 87.10100 5 711 1 chr6B.!!$F1 706
2 TraesCS6B01G183400 chr6D 115545048 115550154 5106 True 1871.100000 3092 95.18725 750 5843 4 chr6D.!!$R3 5093
3 TraesCS6B01G183400 chr6D 90121390 90121995 605 True 785.000000 785 90.00000 5 614 1 chr6D.!!$R1 609
4 TraesCS6B01G183400 chr6A 143964740 143969829 5089 True 1222.166667 3009 94.16150 774 5843 6 chr6A.!!$R1 5069
5 TraesCS6B01G183400 chr6A 108937947 108938554 607 False 765.000000 765 89.34400 5 614 1 chr6A.!!$F1 609
6 TraesCS6B01G183400 chr2D 119074278 119074993 715 True 859.000000 859 88.57900 5 710 1 chr2D.!!$R1 705
7 TraesCS6B01G183400 chr2B 733974706 733975423 717 True 817.000000 817 87.48300 5 711 1 chr2B.!!$R1 706
8 TraesCS6B01G183400 chr5D 407010053 407010764 711 False 795.000000 795 87.11500 5 705 1 chr5D.!!$F1 700
9 TraesCS6B01G183400 chr1D 52738957 52739670 713 True 780.000000 780 86.63000 5 711 1 chr1D.!!$R1 706
10 TraesCS6B01G183400 chr3D 317091292 317092009 717 True 778.000000 778 86.52800 5 711 1 chr3D.!!$R1 706
11 TraesCS6B01G183400 chr5B 488117710 488118420 710 True 773.000000 773 86.53600 5 705 1 chr5B.!!$R1 700
12 TraesCS6B01G183400 chr2A 618264435 618265152 717 False 628.000000 628 82.96400 5 705 1 chr2A.!!$F1 700

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
714 737 0.038892 GTCCGACGAGTGTGCCTTAA 60.039 55.0 0.00 0.0 0.00 1.85 F
1454 1505 0.037326 TCGACCTTTCTGCGATTGCT 60.037 50.0 6.47 0.0 43.34 3.91 F
1795 1859 0.168128 GAACGGCTGTGCAATACCAC 59.832 55.0 0.00 0.0 36.28 4.16 F
3206 3272 0.234884 GTTCGGAAAAGTCGGCACTG 59.765 55.0 0.00 0.0 31.06 3.66 F
3245 3311 0.833834 CCACTCCACCCACTCAGACT 60.834 60.0 0.00 0.0 0.00 3.24 F
4677 4913 0.396435 TCGTCCAATTCACTGGTGCT 59.604 50.0 0.00 0.0 37.74 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1875 0.032540 CAAGTGCCCTGCCAAAAGTC 59.967 55.000 0.00 0.0 0.00 3.01 R
3221 3287 0.035458 GAGTGGGTGGAGTGGAAGTG 59.965 60.000 0.00 0.0 0.00 3.16 R
3224 3290 0.105194 TCTGAGTGGGTGGAGTGGAA 60.105 55.000 0.00 0.0 0.00 3.53 R
4277 4513 0.100861 CCTCTCCTCGTCCGCTTAAC 59.899 60.000 0.00 0.0 0.00 2.01 R
4770 5006 0.601576 CGTCCATGGTGAAACGGACA 60.602 55.000 12.58 0.0 42.69 4.02 R
5714 5974 1.600164 GCATTTGCGTGCTCTTGTTCA 60.600 47.619 1.76 0.0 41.82 3.18 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
76 77 3.744530 GCGGGGCTGTATCTTCAATAGTT 60.745 47.826 0.00 0.00 0.00 2.24
114 115 2.037511 CAGGGCCAAACACAACAATCAT 59.962 45.455 6.18 0.00 0.00 2.45
180 181 4.735822 GCTCATACAGACGTACTCATCAAC 59.264 45.833 0.00 0.00 0.00 3.18
188 189 4.576873 AGACGTACTCATCAACGAGATCAT 59.423 41.667 1.45 0.00 41.55 2.45
211 212 0.734889 GCACTCCGTATGCAAGCATT 59.265 50.000 13.32 0.00 42.88 3.56
224 225 3.430862 GCATTCGGACGGCTGCAA 61.431 61.111 0.50 0.00 34.77 4.08
244 245 7.284919 TGCAATGCATTTCTGATAAGATGAT 57.715 32.000 9.83 0.00 31.71 2.45
292 293 6.373774 CCTCTTTGCACTCAAAATAGTCATCT 59.626 38.462 0.00 0.00 41.22 2.90
317 318 3.723681 TCCGACTACCCCCTCTCTAATAA 59.276 47.826 0.00 0.00 0.00 1.40
337 338 9.178758 CTAATAAGGTTGAAAAGATGCCTACTT 57.821 33.333 0.00 0.00 0.00 2.24
384 388 2.335011 GTTGAACAGCGGGTTGGC 59.665 61.111 1.39 0.00 40.63 4.52
467 475 1.224003 AAGGTGCCCTGGGATGGATT 61.224 55.000 19.27 0.57 32.13 3.01
483 491 1.504359 GATTCACGGAACAACGACCA 58.496 50.000 0.00 0.00 37.61 4.02
487 495 0.528901 CACGGAACAACGACCACTGA 60.529 55.000 0.00 0.00 37.61 3.41
543 551 1.824230 GATCTCCTCCTCATCATCGGG 59.176 57.143 0.00 0.00 0.00 5.14
548 556 1.152756 TCCTCATCATCGGGCGAGA 60.153 57.895 0.00 0.00 0.00 4.04
649 670 1.592400 ATCGACGAAGAAGCCGACCA 61.592 55.000 0.00 0.00 33.69 4.02
656 679 0.610687 AAGAAGCCGACCAGAAGAGG 59.389 55.000 0.00 0.00 0.00 3.69
676 699 1.842010 GCCCGCCTCCCTTATACCT 60.842 63.158 0.00 0.00 0.00 3.08
711 734 2.910479 TGTCCGACGAGTGTGCCT 60.910 61.111 0.00 0.00 0.00 4.75
712 735 2.338984 GTCCGACGAGTGTGCCTT 59.661 61.111 0.00 0.00 0.00 4.35
713 736 1.174078 TGTCCGACGAGTGTGCCTTA 61.174 55.000 0.00 0.00 0.00 2.69
714 737 0.038892 GTCCGACGAGTGTGCCTTAA 60.039 55.000 0.00 0.00 0.00 1.85
715 738 0.675083 TCCGACGAGTGTGCCTTAAA 59.325 50.000 0.00 0.00 0.00 1.52
716 739 0.788391 CCGACGAGTGTGCCTTAAAC 59.212 55.000 0.00 0.00 0.00 2.01
717 740 1.493772 CGACGAGTGTGCCTTAAACA 58.506 50.000 0.00 0.00 0.00 2.83
718 741 2.066262 CGACGAGTGTGCCTTAAACAT 58.934 47.619 0.00 0.00 0.00 2.71
719 742 2.478894 CGACGAGTGTGCCTTAAACATT 59.521 45.455 0.00 0.00 0.00 2.71
720 743 3.664276 CGACGAGTGTGCCTTAAACATTG 60.664 47.826 0.00 0.00 0.00 2.82
721 744 3.472652 ACGAGTGTGCCTTAAACATTGA 58.527 40.909 0.00 0.00 0.00 2.57
722 745 3.880490 ACGAGTGTGCCTTAAACATTGAA 59.120 39.130 0.00 0.00 0.00 2.69
723 746 4.518970 ACGAGTGTGCCTTAAACATTGAAT 59.481 37.500 0.00 0.00 0.00 2.57
724 747 5.703592 ACGAGTGTGCCTTAAACATTGAATA 59.296 36.000 0.00 0.00 0.00 1.75
725 748 6.205853 ACGAGTGTGCCTTAAACATTGAATAA 59.794 34.615 0.00 0.00 0.00 1.40
726 749 7.081349 CGAGTGTGCCTTAAACATTGAATAAA 58.919 34.615 0.00 0.00 0.00 1.40
727 750 7.271223 CGAGTGTGCCTTAAACATTGAATAAAG 59.729 37.037 0.00 0.00 0.00 1.85
728 751 6.868339 AGTGTGCCTTAAACATTGAATAAAGC 59.132 34.615 0.00 0.00 0.00 3.51
729 752 6.644592 GTGTGCCTTAAACATTGAATAAAGCA 59.355 34.615 0.00 0.00 0.00 3.91
730 753 6.867816 TGTGCCTTAAACATTGAATAAAGCAG 59.132 34.615 8.63 0.00 29.38 4.24
731 754 5.868801 TGCCTTAAACATTGAATAAAGCAGC 59.131 36.000 0.00 0.00 0.00 5.25
732 755 5.868801 GCCTTAAACATTGAATAAAGCAGCA 59.131 36.000 0.00 0.00 0.00 4.41
733 756 6.368516 GCCTTAAACATTGAATAAAGCAGCAA 59.631 34.615 0.00 0.00 0.00 3.91
734 757 7.622048 GCCTTAAACATTGAATAAAGCAGCAAC 60.622 37.037 0.00 0.00 0.00 4.17
735 758 5.827568 AAACATTGAATAAAGCAGCAACG 57.172 34.783 0.00 0.00 0.00 4.10
736 759 4.503741 ACATTGAATAAAGCAGCAACGT 57.496 36.364 0.00 0.00 0.00 3.99
737 760 4.870363 ACATTGAATAAAGCAGCAACGTT 58.130 34.783 0.00 0.00 0.00 3.99
738 761 4.917415 ACATTGAATAAAGCAGCAACGTTC 59.083 37.500 0.00 0.00 0.00 3.95
739 762 3.552604 TGAATAAAGCAGCAACGTTCC 57.447 42.857 0.00 0.00 0.00 3.62
740 763 2.227865 TGAATAAAGCAGCAACGTTCCC 59.772 45.455 0.00 0.00 0.00 3.97
741 764 1.173913 ATAAAGCAGCAACGTTCCCC 58.826 50.000 0.00 0.00 0.00 4.81
742 765 0.109723 TAAAGCAGCAACGTTCCCCT 59.890 50.000 0.00 0.00 0.00 4.79
743 766 1.172812 AAAGCAGCAACGTTCCCCTC 61.173 55.000 0.00 0.00 0.00 4.30
744 767 2.281484 GCAGCAACGTTCCCCTCA 60.281 61.111 0.00 0.00 0.00 3.86
745 768 1.896660 GCAGCAACGTTCCCCTCAA 60.897 57.895 0.00 0.00 0.00 3.02
746 769 1.452145 GCAGCAACGTTCCCCTCAAA 61.452 55.000 0.00 0.00 0.00 2.69
747 770 1.028905 CAGCAACGTTCCCCTCAAAA 58.971 50.000 0.00 0.00 0.00 2.44
748 771 1.407258 CAGCAACGTTCCCCTCAAAAA 59.593 47.619 0.00 0.00 0.00 1.94
781 804 3.674997 TCTGTTTCCAGCTATCCACAAC 58.325 45.455 0.00 0.00 38.66 3.32
988 1011 0.178992 CCCAAGCTGACCAACCAAGA 60.179 55.000 0.00 0.00 0.00 3.02
1262 1291 2.358737 CGAGGCCCACACCAAGTC 60.359 66.667 0.00 0.00 0.00 3.01
1333 1362 1.170290 CCGGTGGGTGTTTCTTGACC 61.170 60.000 0.00 0.00 0.00 4.02
1338 1367 3.341263 GGTGTTTCTTGACCCTCCC 57.659 57.895 0.00 0.00 0.00 4.30
1341 1370 1.420138 GTGTTTCTTGACCCTCCCAGA 59.580 52.381 0.00 0.00 0.00 3.86
1351 1380 1.452108 CCTCCCAGATTGTTCGCCC 60.452 63.158 0.00 0.00 0.00 6.13
1355 1384 1.079127 CCAGATTGTTCGCCCGAGT 60.079 57.895 0.00 0.00 0.00 4.18
1373 1402 2.427095 GAGTTTTGTTCTTGCACCCTGT 59.573 45.455 0.00 0.00 0.00 4.00
1383 1412 3.365265 CACCCTGTTTGCTCGCCC 61.365 66.667 0.00 0.00 0.00 6.13
1445 1496 3.223661 CTGCAAGCTCGACCTTTCT 57.776 52.632 0.00 0.00 0.00 2.52
1446 1497 0.795085 CTGCAAGCTCGACCTTTCTG 59.205 55.000 0.00 0.00 0.00 3.02
1447 1498 1.230635 TGCAAGCTCGACCTTTCTGC 61.231 55.000 0.00 0.00 0.00 4.26
1448 1499 1.784062 CAAGCTCGACCTTTCTGCG 59.216 57.895 0.00 0.00 0.00 5.18
1449 1500 0.667487 CAAGCTCGACCTTTCTGCGA 60.667 55.000 0.00 0.00 0.00 5.10
1450 1501 0.247736 AAGCTCGACCTTTCTGCGAT 59.752 50.000 0.00 0.00 33.20 4.58
1451 1502 0.247736 AGCTCGACCTTTCTGCGATT 59.752 50.000 0.00 0.00 33.20 3.34
1452 1503 0.371645 GCTCGACCTTTCTGCGATTG 59.628 55.000 0.00 0.00 33.20 2.67
1453 1504 0.371645 CTCGACCTTTCTGCGATTGC 59.628 55.000 0.00 0.00 43.20 3.56
1454 1505 0.037326 TCGACCTTTCTGCGATTGCT 60.037 50.000 6.47 0.00 43.34 3.91
1455 1506 0.798776 CGACCTTTCTGCGATTGCTT 59.201 50.000 6.47 0.00 43.34 3.91
1456 1507 1.197721 CGACCTTTCTGCGATTGCTTT 59.802 47.619 6.47 0.00 43.34 3.51
1457 1508 2.350772 CGACCTTTCTGCGATTGCTTTT 60.351 45.455 6.47 0.00 43.34 2.27
1458 1509 3.642705 GACCTTTCTGCGATTGCTTTTT 58.357 40.909 6.47 0.00 43.34 1.94
1490 1541 5.940192 TTCTTTTTCTGCGATTGCTCTTA 57.060 34.783 6.47 0.00 43.34 2.10
1500 1551 3.551250 GCGATTGCTCTTACTCTACTCCC 60.551 52.174 0.00 0.00 38.39 4.30
1501 1552 3.886505 CGATTGCTCTTACTCTACTCCCT 59.113 47.826 0.00 0.00 0.00 4.20
1504 1555 2.024846 TGCTCTTACTCTACTCCCTGCT 60.025 50.000 0.00 0.00 0.00 4.24
1505 1556 2.621526 GCTCTTACTCTACTCCCTGCTC 59.378 54.545 0.00 0.00 0.00 4.26
1508 1559 2.803030 TACTCTACTCCCTGCTCGTT 57.197 50.000 0.00 0.00 0.00 3.85
1509 1560 2.803030 ACTCTACTCCCTGCTCGTTA 57.197 50.000 0.00 0.00 0.00 3.18
1523 1574 3.430895 TGCTCGTTATTCGTTCTTGGAAC 59.569 43.478 0.82 0.82 40.80 3.62
1547 1598 1.373570 GGAAGCAGGAGATTCAACGG 58.626 55.000 0.00 0.00 41.82 4.44
1548 1599 1.373570 GAAGCAGGAGATTCAACGGG 58.626 55.000 0.00 0.00 39.86 5.28
1573 1624 0.959553 TCTTTCCGACTGCGAACTCT 59.040 50.000 0.00 0.00 40.82 3.24
1587 1638 3.506810 CGAACTCTGCACTTCCTTAGAG 58.493 50.000 0.00 0.00 41.78 2.43
1590 1641 2.028567 ACTCTGCACTTCCTTAGAGCAC 60.029 50.000 0.00 0.00 44.09 4.40
1592 1643 0.679505 TGCACTTCCTTAGAGCACGT 59.320 50.000 0.00 0.00 44.09 4.49
1680 1744 0.973632 ACTGTGGTTATCCTGTGCGA 59.026 50.000 0.00 0.00 34.23 5.10
1790 1854 2.629656 GGCTGAACGGCTGTGCAAT 61.630 57.895 8.00 0.00 31.62 3.56
1794 1858 0.250510 TGAACGGCTGTGCAATACCA 60.251 50.000 2.98 0.00 27.70 3.25
1795 1859 0.168128 GAACGGCTGTGCAATACCAC 59.832 55.000 0.00 0.00 36.28 4.16
1796 1860 1.241315 AACGGCTGTGCAATACCACC 61.241 55.000 0.00 0.00 34.85 4.61
1798 1862 1.647545 CGGCTGTGCAATACCACCTG 61.648 60.000 0.00 0.00 34.85 4.00
1799 1863 0.609131 GGCTGTGCAATACCACCTGT 60.609 55.000 0.00 0.00 34.85 4.00
1800 1864 1.247567 GCTGTGCAATACCACCTGTT 58.752 50.000 0.00 0.00 34.85 3.16
1801 1865 1.613437 GCTGTGCAATACCACCTGTTT 59.387 47.619 0.00 0.00 34.85 2.83
1802 1866 2.351738 GCTGTGCAATACCACCTGTTTC 60.352 50.000 0.00 0.00 34.85 2.78
1803 1867 2.228822 CTGTGCAATACCACCTGTTTCC 59.771 50.000 0.00 0.00 34.85 3.13
1804 1868 2.235016 GTGCAATACCACCTGTTTCCA 58.765 47.619 0.00 0.00 0.00 3.53
1805 1869 2.228822 GTGCAATACCACCTGTTTCCAG 59.771 50.000 0.00 0.00 38.50 3.86
1806 1870 2.158534 TGCAATACCACCTGTTTCCAGT 60.159 45.455 0.00 0.00 36.95 4.00
1807 1871 2.890945 GCAATACCACCTGTTTCCAGTT 59.109 45.455 0.00 0.00 36.95 3.16
1808 1872 3.320826 GCAATACCACCTGTTTCCAGTTT 59.679 43.478 0.00 0.00 36.95 2.66
1809 1873 4.202212 GCAATACCACCTGTTTCCAGTTTT 60.202 41.667 0.00 0.00 36.95 2.43
1810 1874 5.288804 CAATACCACCTGTTTCCAGTTTTG 58.711 41.667 0.00 0.00 36.95 2.44
1811 1875 2.107366 ACCACCTGTTTCCAGTTTTGG 58.893 47.619 0.00 0.00 46.49 3.28
1842 1906 4.885426 CACTTGTCCCTGTGCTGT 57.115 55.556 0.00 0.00 0.00 4.40
1845 1909 1.128200 ACTTGTCCCTGTGCTGTGTA 58.872 50.000 0.00 0.00 0.00 2.90
1876 1941 2.942804 TGGGCTGAAATTCTGTTGTGA 58.057 42.857 2.00 0.00 0.00 3.58
1956 2021 9.924010 ACTCTTAGATCTTAGTTGGTACATACT 57.076 33.333 0.00 0.00 39.30 2.12
1960 2025 7.826918 AGATCTTAGTTGGTACATACTCTCC 57.173 40.000 2.74 0.00 39.30 3.71
2005 2070 4.460263 ACTGTCTGTGGTTTTGCTGATTA 58.540 39.130 0.00 0.00 0.00 1.75
2034 2099 2.512692 TGGTGATCAAGGTTCCATGG 57.487 50.000 4.97 4.97 0.00 3.66
2200 2265 8.275758 TCCATACTTTAAGTGGGTAATTATGCA 58.724 33.333 8.00 0.00 33.78 3.96
2207 2272 9.702253 TTTAAGTGGGTAATTATGCAGGATTTA 57.298 29.630 0.00 0.00 0.00 1.40
2235 2300 1.546323 CCTTGCTCTCCACACCACATT 60.546 52.381 0.00 0.00 0.00 2.71
2251 2316 4.755123 ACCACATTGTACTGAAACTACTGC 59.245 41.667 0.00 0.00 0.00 4.40
2256 2321 7.598869 CACATTGTACTGAAACTACTGCTCTTA 59.401 37.037 0.00 0.00 0.00 2.10
2258 2323 8.651588 CATTGTACTGAAACTACTGCTCTTAAG 58.348 37.037 0.00 0.00 0.00 1.85
2294 2359 6.292596 GCTAGTTGTGAGTTGAACTTCTTCAG 60.293 42.308 0.00 0.00 37.70 3.02
2347 2412 3.047796 GCTTTCGCTAATGCCATGATTG 58.952 45.455 0.00 0.00 35.36 2.67
2395 2460 8.614469 TGATATATGAGATGATAGCTAGTCGG 57.386 38.462 0.00 0.00 0.00 4.79
2508 2574 7.725844 AGTTTTGTCTGGAATAAAGATCCACTT 59.274 33.333 0.00 0.00 41.98 3.16
2511 2577 7.496346 TGTCTGGAATAAAGATCCACTTAGT 57.504 36.000 0.00 0.00 41.98 2.24
2516 2582 7.282585 TGGAATAAAGATCCACTTAGTCATGG 58.717 38.462 0.00 0.00 41.98 3.66
2665 2731 3.118992 TCCAGCACTGAGTCATGACATAC 60.119 47.826 27.02 17.28 0.00 2.39
2713 2779 9.722056 GTATGATTTGTCAGTCATTTTGTATCC 57.278 33.333 7.77 0.00 36.53 2.59
2728 2794 3.872696 TGTATCCATCGCAGTTCACATT 58.127 40.909 0.00 0.00 0.00 2.71
2853 2919 4.379813 CGTGGGATTCCAAAAACATCAGAG 60.380 45.833 4.80 0.00 46.04 3.35
3013 3079 6.015519 CCCAACTGGTTTGAGTCAATTGATTA 60.016 38.462 12.12 0.00 37.39 1.75
3014 3080 7.309990 CCCAACTGGTTTGAGTCAATTGATTAT 60.310 37.037 12.12 0.75 37.39 1.28
3015 3081 8.090214 CCAACTGGTTTGAGTCAATTGATTATT 58.910 33.333 12.12 0.00 37.39 1.40
3016 3082 9.480053 CAACTGGTTTGAGTCAATTGATTATTT 57.520 29.630 12.12 0.00 37.39 1.40
3106 3172 4.925054 CCTACAAATTGAACAACCAGCATG 59.075 41.667 0.00 0.00 0.00 4.06
3140 3206 8.610248 TCTTGAGGATGACAAACGTATAAAAA 57.390 30.769 0.00 0.00 0.00 1.94
3175 3241 2.935201 CCTTGAATCGGAGAGAGCAAAG 59.065 50.000 0.00 0.00 43.63 2.77
3206 3272 0.234884 GTTCGGAAAAGTCGGCACTG 59.765 55.000 0.00 0.00 31.06 3.66
3221 3287 3.649073 GGCACTGTAAAAATGTGGTTCC 58.351 45.455 0.00 0.00 32.85 3.62
3222 3288 3.068873 GGCACTGTAAAAATGTGGTTCCA 59.931 43.478 0.00 0.00 32.85 3.53
3223 3289 4.048504 GCACTGTAAAAATGTGGTTCCAC 58.951 43.478 14.31 14.31 37.46 4.02
3224 3290 4.202111 GCACTGTAAAAATGTGGTTCCACT 60.202 41.667 20.48 5.00 37.78 4.00
3225 3291 5.681179 GCACTGTAAAAATGTGGTTCCACTT 60.681 40.000 20.48 12.88 37.78 3.16
3226 3292 5.977129 CACTGTAAAAATGTGGTTCCACTTC 59.023 40.000 20.48 5.40 37.78 3.01
3245 3311 0.833834 CCACTCCACCCACTCAGACT 60.834 60.000 0.00 0.00 0.00 3.24
3260 3326 1.005215 CAGACTGAGGGGGATGCTTTT 59.995 52.381 0.00 0.00 0.00 2.27
3312 3378 8.896320 TGTGAATCTTACACTACAAAGCTTAA 57.104 30.769 0.00 0.00 38.81 1.85
3342 3408 1.397343 GCTAGGCGCTGTTTAGGTTTC 59.603 52.381 7.64 0.00 35.14 2.78
3347 3413 0.953960 CGCTGTTTAGGTTTCCGCCT 60.954 55.000 0.00 0.00 42.43 5.52
3368 3434 3.343617 TGGTTTTCCTTGATAAGCCGAG 58.656 45.455 0.00 0.00 41.38 4.63
3387 3453 1.082104 CAGCCCGCGTTTTCACTTC 60.082 57.895 4.92 0.00 0.00 3.01
3424 3495 2.046023 TGCGGTGCATTCCTCCTG 60.046 61.111 0.00 0.00 31.71 3.86
3425 3496 2.825836 GCGGTGCATTCCTCCTGG 60.826 66.667 0.00 0.00 0.00 4.45
3426 3497 2.825836 CGGTGCATTCCTCCTGGC 60.826 66.667 0.00 0.00 0.00 4.85
3427 3498 2.356278 GGTGCATTCCTCCTGGCA 59.644 61.111 0.00 0.00 0.00 4.92
3454 3528 3.553828 TGTAAGGCCCCTTTCTAATCG 57.446 47.619 4.68 0.00 37.47 3.34
3457 3531 4.903049 TGTAAGGCCCCTTTCTAATCGATA 59.097 41.667 4.68 0.00 37.47 2.92
3486 3560 1.284198 AGCTCTCCTGCCAACATTCAT 59.716 47.619 0.00 0.00 0.00 2.57
3620 3697 5.168569 TCACAAATGTAAAACGTTTTGGCA 58.831 33.333 31.26 27.43 35.31 4.92
3842 3993 2.027745 TCAGCCTGAGGTGATTTGACTC 60.028 50.000 0.00 0.00 45.34 3.36
3863 4014 8.397906 TGACTCAAGTTGTTTTTCAGTATTGAG 58.602 33.333 2.11 9.41 41.69 3.02
3894 4045 5.978814 ACTAGTTTTCCTGCACCTACATAG 58.021 41.667 0.00 0.00 0.00 2.23
3900 4051 1.933853 CCTGCACCTACATAGAAACGC 59.066 52.381 0.00 0.00 0.00 4.84
3932 4083 9.845740 TGCAACACTTGGATATATGTAGTTATT 57.154 29.630 0.00 0.00 0.00 1.40
3997 4148 5.880054 ACTATGAATTTCCGTTGGAACAG 57.120 39.130 0.00 0.00 41.87 3.16
4098 4250 9.689976 TGATAAAAACCAACATCACACATTTAG 57.310 29.630 0.00 0.00 0.00 1.85
4146 4378 4.440525 GGTTAGAATGGTGTCATGGCAATG 60.441 45.833 0.00 0.00 33.18 2.82
4172 4404 8.352942 GCTTTTGGTAATATGCATAAGTAAGCT 58.647 33.333 11.13 0.00 31.63 3.74
4211 4444 7.364056 CCAATTCACTTTGGTATGTCCATTCAT 60.364 37.037 0.00 0.00 46.60 2.57
4277 4513 6.183360 GCCTCAAAACAGTTAAAACCAAAAGG 60.183 38.462 0.00 0.00 0.00 3.11
4284 4520 6.037726 ACAGTTAAAACCAAAAGGTTAAGCG 58.962 36.000 0.00 0.00 0.00 4.68
4293 4529 0.531200 AAGGTTAAGCGGACGAGGAG 59.469 55.000 0.00 0.00 0.00 3.69
4324 4560 9.013229 GGGCAATATACTCATAATTCAACATGA 57.987 33.333 0.00 0.00 0.00 3.07
4396 4632 4.549458 ACTGCTCAATTGTTTTTGATCGG 58.451 39.130 5.13 0.00 35.20 4.18
4433 4669 3.566742 GCATATGAGCCACATGATGTTCA 59.433 43.478 6.97 3.93 39.77 3.18
4465 4701 3.726607 CAGATATCTCTGCTCCCAACAC 58.273 50.000 1.03 0.00 42.36 3.32
4529 4765 5.801947 CCTTTTGATTGACCGATTGATGAAC 59.198 40.000 0.00 0.00 0.00 3.18
4677 4913 0.396435 TCGTCCAATTCACTGGTGCT 59.604 50.000 0.00 0.00 37.74 4.40
4727 4963 4.057943 AGGTAGCCCTCCGTCGGT 62.058 66.667 11.88 0.00 35.62 4.69
4853 5090 1.594397 GATGAATTGATGCGCGAGACA 59.406 47.619 12.10 2.32 0.00 3.41
4857 5094 0.670239 ATTGATGCGCGAGACACACA 60.670 50.000 12.10 0.00 0.00 3.72
4861 5098 3.038417 GCGCGAGACACACAAGCT 61.038 61.111 12.10 0.00 0.00 3.74
5091 5344 2.089980 CTTCTCCCTGACAAGCCATTG 58.910 52.381 0.00 0.00 42.46 2.82
5092 5345 0.322816 TCTCCCTGACAAGCCATTGC 60.323 55.000 0.00 0.00 40.27 3.56
5093 5346 0.609957 CTCCCTGACAAGCCATTGCA 60.610 55.000 0.00 0.00 40.27 4.08
5094 5347 0.895100 TCCCTGACAAGCCATTGCAC 60.895 55.000 0.00 0.00 40.27 4.57
5248 5502 5.941788 AGGGAACAGTCTAATTTGACTTGT 58.058 37.500 18.22 15.97 44.01 3.16
5364 5624 1.882623 CCTGTCTCCTCAAAGCAAACC 59.117 52.381 0.00 0.00 0.00 3.27
5542 5802 3.159213 TGAAATCACCAGCTGGATTGT 57.841 42.857 39.19 18.93 38.94 2.71
5709 5969 4.000325 CCGACACCACAGAAATCAACATA 59.000 43.478 0.00 0.00 0.00 2.29
5714 5974 7.414429 CGACACCACAGAAATCAACATAATGAT 60.414 37.037 0.00 0.00 41.74 2.45
5752 6012 3.620615 CGAAGCACAAACTTGCACA 57.379 47.368 0.00 0.00 45.62 4.57
5802 6062 2.289565 CGGAAAAGCTCCATTAGGTCC 58.710 52.381 0.00 0.00 45.74 4.46
5833 6093 5.107453 GCATACAAGGCAACATCTATACGAC 60.107 44.000 0.00 0.00 41.41 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 5.363939 AGAGCCAACTATTGAAGATACAGC 58.636 41.667 0.00 0.00 0.00 4.40
76 77 2.451490 CCTGAGTACTTGAGAGAGCCA 58.549 52.381 0.00 0.00 0.00 4.75
114 115 5.482526 TCCATGTACAAGTTCTACAAGGCTA 59.517 40.000 0.00 0.00 34.37 3.93
211 212 3.974835 ATGCATTGCAGCCGTCCGA 62.975 57.895 17.52 0.00 43.65 4.55
224 225 7.668469 TGGCTTATCATCTTATCAGAAATGCAT 59.332 33.333 0.00 0.00 30.76 3.96
244 245 1.816224 GCCGTTGGAAAGATTGGCTTA 59.184 47.619 0.00 0.00 39.38 3.09
292 293 2.141911 AGAGAGGGGGTAGTCGGATAA 58.858 52.381 0.00 0.00 0.00 1.75
317 318 6.761714 CGTATAAGTAGGCATCTTTTCAACCT 59.238 38.462 0.08 0.00 34.42 3.50
337 338 3.194116 AGTTTCAGAGGCGTTTCCGTATA 59.806 43.478 0.00 0.00 40.77 1.47
358 361 1.466167 CCGCTGTTCAACCATCAGAAG 59.534 52.381 0.00 0.00 0.00 2.85
384 388 6.936900 TCTTTGGAAGGACTATTTTGACTCAG 59.063 38.462 0.00 0.00 0.00 3.35
412 420 1.450312 CCGAGAGAGCGGCCATTTT 60.450 57.895 2.24 0.00 45.38 1.82
467 475 0.528901 CAGTGGTCGTTGTTCCGTGA 60.529 55.000 0.00 0.00 0.00 4.35
483 491 5.030147 TCCATCACCACCTTAATAGTCAGT 58.970 41.667 0.00 0.00 0.00 3.41
487 495 4.772886 GGTCCATCACCACCTTAATAGT 57.227 45.455 0.00 0.00 45.98 2.12
548 556 2.875933 TCTTTTGCGACTCCAACGATTT 59.124 40.909 0.00 0.00 0.00 2.17
656 679 3.622826 TATAAGGGAGGCGGGCGC 61.623 66.667 0.00 0.00 41.06 6.53
671 694 2.286425 AGGCCAGCCACCAGGTAT 60.286 61.111 12.03 0.00 38.92 2.73
672 695 3.329889 CAGGCCAGCCACCAGGTA 61.330 66.667 12.03 0.00 38.92 3.08
694 717 1.174078 TAAGGCACACTCGTCGGACA 61.174 55.000 9.10 0.00 0.00 4.02
705 728 6.753180 TGCTTTATTCAATGTTTAAGGCACA 58.247 32.000 9.30 0.00 34.33 4.57
711 734 6.920758 ACGTTGCTGCTTTATTCAATGTTTAA 59.079 30.769 0.00 0.00 35.78 1.52
712 735 6.442952 ACGTTGCTGCTTTATTCAATGTTTA 58.557 32.000 0.00 0.00 35.78 2.01
713 736 5.288804 ACGTTGCTGCTTTATTCAATGTTT 58.711 33.333 0.00 0.00 35.78 2.83
714 737 4.870363 ACGTTGCTGCTTTATTCAATGTT 58.130 34.783 0.00 0.00 35.78 2.71
715 738 4.503741 ACGTTGCTGCTTTATTCAATGT 57.496 36.364 0.00 0.00 34.81 2.71
716 739 4.324402 GGAACGTTGCTGCTTTATTCAATG 59.676 41.667 13.06 0.00 0.00 2.82
717 740 4.485163 GGAACGTTGCTGCTTTATTCAAT 58.515 39.130 13.06 0.00 0.00 2.57
718 741 3.305064 GGGAACGTTGCTGCTTTATTCAA 60.305 43.478 19.59 0.00 0.00 2.69
719 742 2.227865 GGGAACGTTGCTGCTTTATTCA 59.772 45.455 19.59 0.00 0.00 2.57
720 743 2.415491 GGGGAACGTTGCTGCTTTATTC 60.415 50.000 19.59 0.00 0.00 1.75
721 744 1.544246 GGGGAACGTTGCTGCTTTATT 59.456 47.619 19.59 0.00 0.00 1.40
722 745 1.173913 GGGGAACGTTGCTGCTTTAT 58.826 50.000 19.59 0.00 0.00 1.40
723 746 0.109723 AGGGGAACGTTGCTGCTTTA 59.890 50.000 19.59 0.00 0.00 1.85
724 747 1.152756 AGGGGAACGTTGCTGCTTT 60.153 52.632 19.59 0.00 0.00 3.51
725 748 1.600916 GAGGGGAACGTTGCTGCTT 60.601 57.895 19.59 0.00 0.00 3.91
726 749 2.032681 GAGGGGAACGTTGCTGCT 59.967 61.111 19.59 0.00 0.00 4.24
727 750 1.452145 TTTGAGGGGAACGTTGCTGC 61.452 55.000 19.59 9.52 0.00 5.25
728 751 1.028905 TTTTGAGGGGAACGTTGCTG 58.971 50.000 19.59 0.00 0.00 4.41
729 752 1.770294 TTTTTGAGGGGAACGTTGCT 58.230 45.000 19.59 0.00 0.00 3.91
781 804 0.819582 CTTGGCTTGCCATAAGTGGG 59.180 55.000 15.58 0.00 46.14 4.61
875 898 4.849518 AGAGACTTGGAATAGAAAAGGCC 58.150 43.478 0.00 0.00 28.45 5.19
1152 1181 3.039526 CCCCCTCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1153 1182 4.890306 GCCCCCTCCTCCTCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
1333 1362 1.452108 GGGCGAACAATCTGGGAGG 60.452 63.158 0.00 0.00 0.00 4.30
1338 1367 1.156736 AAACTCGGGCGAACAATCTG 58.843 50.000 0.00 0.00 0.00 2.90
1341 1370 1.314730 ACAAAACTCGGGCGAACAAT 58.685 45.000 0.00 0.00 0.00 2.71
1351 1380 1.676006 AGGGTGCAAGAACAAAACTCG 59.324 47.619 0.00 0.00 0.00 4.18
1355 1384 3.594134 CAAACAGGGTGCAAGAACAAAA 58.406 40.909 0.00 0.00 0.00 2.44
1383 1412 0.586319 TCAAAGAAAAGCACGGCTCG 59.414 50.000 0.00 0.00 38.25 5.03
1455 1506 8.983724 TCGCAGAAAAAGAAAAGAAAAGAAAAA 58.016 25.926 0.00 0.00 0.00 1.94
1456 1507 8.527567 TCGCAGAAAAAGAAAAGAAAAGAAAA 57.472 26.923 0.00 0.00 0.00 2.29
1457 1508 8.702163 ATCGCAGAAAAAGAAAAGAAAAGAAA 57.298 26.923 0.00 0.00 43.58 2.52
1458 1509 8.594687 CAATCGCAGAAAAAGAAAAGAAAAGAA 58.405 29.630 0.00 0.00 43.58 2.52
1459 1510 7.254084 GCAATCGCAGAAAAAGAAAAGAAAAGA 60.254 33.333 0.00 0.00 43.58 2.52
1460 1511 6.842780 GCAATCGCAGAAAAAGAAAAGAAAAG 59.157 34.615 0.00 0.00 43.58 2.27
1461 1512 6.534793 AGCAATCGCAGAAAAAGAAAAGAAAA 59.465 30.769 0.00 0.00 43.58 2.29
1462 1513 6.042143 AGCAATCGCAGAAAAAGAAAAGAAA 58.958 32.000 0.00 0.00 43.58 2.52
1463 1514 5.591099 AGCAATCGCAGAAAAAGAAAAGAA 58.409 33.333 0.00 0.00 43.58 2.52
1464 1515 5.009010 AGAGCAATCGCAGAAAAAGAAAAGA 59.991 36.000 0.00 0.00 43.58 2.52
1465 1516 5.218139 AGAGCAATCGCAGAAAAAGAAAAG 58.782 37.500 0.00 0.00 43.58 2.27
1466 1517 5.186996 AGAGCAATCGCAGAAAAAGAAAA 57.813 34.783 0.00 0.00 43.58 2.29
1467 1518 4.836125 AGAGCAATCGCAGAAAAAGAAA 57.164 36.364 0.00 0.00 43.58 2.52
1468 1519 4.836125 AAGAGCAATCGCAGAAAAAGAA 57.164 36.364 0.00 0.00 43.58 2.52
1469 1520 4.997395 AGTAAGAGCAATCGCAGAAAAAGA 59.003 37.500 0.00 0.00 43.58 2.52
1470 1521 5.121454 AGAGTAAGAGCAATCGCAGAAAAAG 59.879 40.000 0.00 0.00 43.58 2.27
1471 1522 4.997395 AGAGTAAGAGCAATCGCAGAAAAA 59.003 37.500 0.00 0.00 43.58 1.94
1490 1541 2.803030 TAACGAGCAGGGAGTAGAGT 57.197 50.000 0.00 0.00 0.00 3.24
1500 1551 3.250744 TCCAAGAACGAATAACGAGCAG 58.749 45.455 0.00 0.00 45.77 4.24
1501 1552 3.306917 TCCAAGAACGAATAACGAGCA 57.693 42.857 0.00 0.00 45.77 4.26
1504 1555 4.240096 GGAGTTCCAAGAACGAATAACGA 58.760 43.478 2.04 0.00 39.66 3.85
1505 1556 3.060363 CGGAGTTCCAAGAACGAATAACG 59.940 47.826 2.04 0.00 41.36 3.18
1508 1559 2.093869 CCCGGAGTTCCAAGAACGAATA 60.094 50.000 0.73 0.00 35.14 1.75
1509 1560 1.338769 CCCGGAGTTCCAAGAACGAAT 60.339 52.381 0.73 0.00 35.14 3.34
1523 1574 0.105778 GAATCTCCTGCTTCCCGGAG 59.894 60.000 0.73 0.00 46.52 4.63
1554 1605 0.959553 AGAGTTCGCAGTCGGAAAGA 59.040 50.000 0.00 0.00 36.13 2.52
1555 1606 1.063806 CAGAGTTCGCAGTCGGAAAG 58.936 55.000 0.00 0.00 36.13 2.62
1556 1607 0.944311 GCAGAGTTCGCAGTCGGAAA 60.944 55.000 0.00 0.00 36.13 3.13
1558 1609 2.258591 GCAGAGTTCGCAGTCGGA 59.741 61.111 0.00 0.00 36.13 4.55
1559 1610 2.049156 TGCAGAGTTCGCAGTCGG 60.049 61.111 0.00 0.00 33.55 4.79
1560 1611 0.941463 AAGTGCAGAGTTCGCAGTCG 60.941 55.000 0.00 0.00 42.15 4.18
1561 1612 0.787183 GAAGTGCAGAGTTCGCAGTC 59.213 55.000 0.00 0.00 42.15 3.51
1562 1613 0.601311 GGAAGTGCAGAGTTCGCAGT 60.601 55.000 0.00 0.00 44.86 4.40
1654 1718 1.280998 AGGATAACCACAGTTTCCGGG 59.719 52.381 0.00 0.00 37.81 5.73
1680 1744 0.611714 ATCGGGAAACAAGCCGTACT 59.388 50.000 0.00 0.00 0.00 2.73
1798 1862 3.621268 GCCAAAAGTCCAAAACTGGAAAC 59.379 43.478 0.00 0.00 40.06 2.78
1799 1863 3.261897 TGCCAAAAGTCCAAAACTGGAAA 59.738 39.130 0.00 0.00 40.06 3.13
1800 1864 2.834549 TGCCAAAAGTCCAAAACTGGAA 59.165 40.909 0.00 0.00 40.06 3.53
1801 1865 2.430332 CTGCCAAAAGTCCAAAACTGGA 59.570 45.455 0.00 0.00 38.58 3.86
1802 1866 2.483538 CCTGCCAAAAGTCCAAAACTGG 60.484 50.000 0.00 0.00 38.58 4.00
1803 1867 2.483538 CCCTGCCAAAAGTCCAAAACTG 60.484 50.000 0.00 0.00 38.58 3.16
1804 1868 1.762370 CCCTGCCAAAAGTCCAAAACT 59.238 47.619 0.00 0.00 41.10 2.66
1805 1869 1.810031 GCCCTGCCAAAAGTCCAAAAC 60.810 52.381 0.00 0.00 0.00 2.43
1806 1870 0.467804 GCCCTGCCAAAAGTCCAAAA 59.532 50.000 0.00 0.00 0.00 2.44
1807 1871 0.689080 TGCCCTGCCAAAAGTCCAAA 60.689 50.000 0.00 0.00 0.00 3.28
1808 1872 1.075674 TGCCCTGCCAAAAGTCCAA 60.076 52.632 0.00 0.00 0.00 3.53
1809 1873 1.832167 GTGCCCTGCCAAAAGTCCA 60.832 57.895 0.00 0.00 0.00 4.02
1810 1874 1.115326 AAGTGCCCTGCCAAAAGTCC 61.115 55.000 0.00 0.00 0.00 3.85
1811 1875 0.032540 CAAGTGCCCTGCCAAAAGTC 59.967 55.000 0.00 0.00 0.00 3.01
1812 1876 0.687427 ACAAGTGCCCTGCCAAAAGT 60.687 50.000 0.00 0.00 0.00 2.66
1813 1877 0.032540 GACAAGTGCCCTGCCAAAAG 59.967 55.000 0.00 0.00 0.00 2.27
1837 1901 2.034432 CCAAAAGTGCACATACACAGCA 59.966 45.455 21.04 0.00 43.23 4.41
1838 1902 2.607771 CCCAAAAGTGCACATACACAGC 60.608 50.000 21.04 0.00 43.23 4.40
1839 1903 2.607771 GCCCAAAAGTGCACATACACAG 60.608 50.000 21.04 2.96 43.23 3.66
1840 1904 1.339610 GCCCAAAAGTGCACATACACA 59.660 47.619 21.04 0.00 43.23 3.72
1841 1905 1.613437 AGCCCAAAAGTGCACATACAC 59.387 47.619 21.04 1.85 41.02 2.90
1842 1906 1.612950 CAGCCCAAAAGTGCACATACA 59.387 47.619 21.04 0.00 0.00 2.29
1845 1909 1.412079 TTCAGCCCAAAAGTGCACAT 58.588 45.000 21.04 3.48 0.00 3.21
2005 2070 2.242043 CTTGATCACCAAAAGCCAGGT 58.758 47.619 0.00 0.00 39.10 4.00
2200 2265 6.012945 GGAGAGCAAGGGAGAATATAAATCCT 60.013 42.308 0.00 0.00 33.40 3.24
2207 2272 3.135530 GTGTGGAGAGCAAGGGAGAATAT 59.864 47.826 0.00 0.00 0.00 1.28
2212 2277 1.298014 GGTGTGGAGAGCAAGGGAG 59.702 63.158 0.00 0.00 0.00 4.30
2214 2279 1.302832 GTGGTGTGGAGAGCAAGGG 60.303 63.158 0.00 0.00 0.00 3.95
2251 2316 9.331282 ACAACTAGCCAATTATAAGCTTAAGAG 57.669 33.333 10.85 0.00 38.06 2.85
2256 2321 7.112779 ACTCACAACTAGCCAATTATAAGCTT 58.887 34.615 3.48 3.48 38.06 3.74
2258 2323 6.927294 ACTCACAACTAGCCAATTATAAGC 57.073 37.500 0.00 0.00 0.00 3.09
2259 2324 8.492673 TCAACTCACAACTAGCCAATTATAAG 57.507 34.615 0.00 0.00 0.00 1.73
2260 2325 8.726988 GTTCAACTCACAACTAGCCAATTATAA 58.273 33.333 0.00 0.00 0.00 0.98
2262 2327 6.942576 AGTTCAACTCACAACTAGCCAATTAT 59.057 34.615 0.00 0.00 30.80 1.28
2272 2337 5.491982 ACTGAAGAAGTTCAACTCACAACT 58.508 37.500 5.50 0.00 42.27 3.16
2294 2359 8.263940 TCATACCTAGCTCAAACACAATTTAC 57.736 34.615 0.00 0.00 0.00 2.01
2421 2487 8.967664 AAGCATTTATTATCGGTACAAAGGTA 57.032 30.769 0.00 0.00 0.00 3.08
2422 2488 7.875327 AAGCATTTATTATCGGTACAAAGGT 57.125 32.000 0.00 0.00 0.00 3.50
2423 2489 9.019764 CAAAAGCATTTATTATCGGTACAAAGG 57.980 33.333 0.00 0.00 37.28 3.11
2424 2490 8.531530 GCAAAAGCATTTATTATCGGTACAAAG 58.468 33.333 0.00 0.00 37.28 2.77
2425 2491 7.489757 GGCAAAAGCATTTATTATCGGTACAAA 59.510 33.333 0.00 0.00 37.28 2.83
2426 2492 6.975772 GGCAAAAGCATTTATTATCGGTACAA 59.024 34.615 0.00 0.00 37.28 2.41
2427 2493 6.095580 TGGCAAAAGCATTTATTATCGGTACA 59.904 34.615 0.00 0.00 37.28 2.90
2428 2494 6.500041 TGGCAAAAGCATTTATTATCGGTAC 58.500 36.000 0.00 0.00 37.28 3.34
2516 2582 2.095461 GAGAACATGGGAAAGGCCTTC 58.905 52.381 20.79 12.24 36.66 3.46
2604 2670 9.798994 AGATGAGATTTATCAAAATGAACTTGC 57.201 29.630 0.00 0.00 35.41 4.01
2665 2731 2.408271 TTCATTGGTAGCAGCTCAGG 57.592 50.000 0.00 0.00 0.00 3.86
2713 2779 4.345271 TTCATCAATGTGAACTGCGATG 57.655 40.909 0.00 0.00 33.41 3.84
2853 2919 4.864704 TTACAATCCAACTTTTCCCTGC 57.135 40.909 0.00 0.00 0.00 4.85
2971 3037 8.904963 ACCAGTTGGGATGATTCCTATATTATT 58.095 33.333 2.79 0.00 42.20 1.40
2972 3038 8.468547 ACCAGTTGGGATGATTCCTATATTAT 57.531 34.615 2.79 0.00 42.20 1.28
3028 3094 9.886132 GGTCTTCTGTACTCCATTCTAAAATAA 57.114 33.333 0.00 0.00 0.00 1.40
3029 3095 9.268282 AGGTCTTCTGTACTCCATTCTAAAATA 57.732 33.333 0.00 0.00 0.00 1.40
3073 3139 7.825331 TGTTCAATTTGTAGGATTGTAACCA 57.175 32.000 0.00 0.00 36.23 3.67
3140 3206 7.290061 TCCGATTCAAGGATTTTCATAGGAAT 58.710 34.615 0.00 0.00 30.36 3.01
3175 3241 2.814280 TTCCGAACAGAGAACCAGAC 57.186 50.000 0.00 0.00 0.00 3.51
3221 3287 0.035458 GAGTGGGTGGAGTGGAAGTG 59.965 60.000 0.00 0.00 0.00 3.16
3222 3288 0.399949 TGAGTGGGTGGAGTGGAAGT 60.400 55.000 0.00 0.00 0.00 3.01
3223 3289 0.322975 CTGAGTGGGTGGAGTGGAAG 59.677 60.000 0.00 0.00 0.00 3.46
3224 3290 0.105194 TCTGAGTGGGTGGAGTGGAA 60.105 55.000 0.00 0.00 0.00 3.53
3225 3291 0.832135 GTCTGAGTGGGTGGAGTGGA 60.832 60.000 0.00 0.00 0.00 4.02
3226 3292 0.833834 AGTCTGAGTGGGTGGAGTGG 60.834 60.000 0.00 0.00 0.00 4.00
3260 3326 3.795688 AGAGATTGAGTGAAGGCCAAA 57.204 42.857 5.01 0.00 0.00 3.28
3342 3408 2.122783 TATCAAGGAAAACCAGGCGG 57.877 50.000 0.00 0.00 38.77 6.13
3347 3413 3.343617 CTCGGCTTATCAAGGAAAACCA 58.656 45.455 0.00 0.00 0.00 3.67
3368 3434 3.194272 AAGTGAAAACGCGGGCTGC 62.194 57.895 12.47 8.64 41.47 5.25
3424 3495 0.817654 GGGCCTTACAAGAACATGCC 59.182 55.000 0.84 0.00 36.68 4.40
3425 3496 0.817654 GGGGCCTTACAAGAACATGC 59.182 55.000 0.84 0.00 0.00 4.06
3426 3497 2.514458 AGGGGCCTTACAAGAACATG 57.486 50.000 0.84 0.00 0.00 3.21
3427 3498 3.076032 AGAAAGGGGCCTTACAAGAACAT 59.924 43.478 0.84 0.00 34.84 2.71
3454 3528 3.401182 CAGGAGAGCTGCCAAATCTATC 58.599 50.000 0.00 0.00 0.00 2.08
3457 3531 0.394080 GCAGGAGAGCTGCCAAATCT 60.394 55.000 0.00 0.00 41.58 2.40
3518 3593 6.071391 CCACTTGTTGGGAACTATAAATGCTT 60.071 38.462 0.00 0.00 42.54 3.91
3566 3641 9.104713 AGGGAGTATATACATCAATGATGACAA 57.895 33.333 27.86 13.71 42.09 3.18
3580 3655 8.204836 ACATTTGTGAACAGAGGGAGTATATAC 58.795 37.037 4.60 4.60 0.00 1.47
3589 3666 5.212194 CGTTTTACATTTGTGAACAGAGGG 58.788 41.667 10.39 0.00 0.00 4.30
3620 3697 9.816354 ATGTAAGACATTTTTGCAGTTTAAACT 57.184 25.926 15.22 15.22 34.67 2.66
3647 3724 3.322254 ACAACTACTCCCTCTGTTCACAG 59.678 47.826 0.02 0.02 45.08 3.66
3697 3774 6.528321 TGATTCCTAAATGTAGAGCCATCAG 58.472 40.000 0.00 0.00 0.00 2.90
3729 3880 9.840427 CCAGTTCATTTAATCTACAACGATTTT 57.160 29.630 0.00 0.00 35.40 1.82
3730 3881 9.226606 TCCAGTTCATTTAATCTACAACGATTT 57.773 29.630 0.00 0.00 35.40 2.17
3735 3886 8.324163 ACAGTCCAGTTCATTTAATCTACAAC 57.676 34.615 0.00 0.00 0.00 3.32
3863 4014 7.445945 AGGTGCAGGAAAACTAGTCATATATC 58.554 38.462 0.00 0.00 0.00 1.63
3870 4021 4.267349 TGTAGGTGCAGGAAAACTAGTC 57.733 45.455 0.00 0.00 0.00 2.59
3894 4045 4.394795 CAAGTGTTGCATACTAGCGTTTC 58.605 43.478 4.75 0.00 37.31 2.78
4078 4230 7.346751 AGTTCTAAATGTGTGATGTTGGTTT 57.653 32.000 0.00 0.00 0.00 3.27
4082 4234 9.546909 GATTGTAGTTCTAAATGTGTGATGTTG 57.453 33.333 0.00 0.00 0.00 3.33
4098 4250 8.607459 CCACAAGATCACTATTGATTGTAGTTC 58.393 37.037 0.00 0.00 42.95 3.01
4146 4378 8.352942 AGCTTACTTATGCATATTACCAAAAGC 58.647 33.333 7.36 14.31 34.73 3.51
4172 4404 7.396055 CCAAAGTGAATTGGGAGTTCCTAATAA 59.604 37.037 9.79 0.54 44.98 1.40
4173 4405 6.889722 CCAAAGTGAATTGGGAGTTCCTAATA 59.110 38.462 9.79 0.00 44.98 0.98
4277 4513 0.100861 CCTCTCCTCGTCCGCTTAAC 59.899 60.000 0.00 0.00 0.00 2.01
4284 4520 3.462678 GCCCACCTCTCCTCGTCC 61.463 72.222 0.00 0.00 0.00 4.79
4293 4529 7.168219 TGAATTATGAGTATATTGCCCACCTC 58.832 38.462 0.00 0.00 0.00 3.85
4390 4626 6.207691 TGCATTCGAGATATATTCCGATCA 57.792 37.500 10.00 7.16 30.58 2.92
4396 4632 7.654923 TGGCTCATATGCATTCGAGATATATTC 59.345 37.037 22.56 8.01 34.04 1.75
4465 4701 4.136796 TGGACACTCAAGAACATCCAAAG 58.863 43.478 0.00 0.00 33.34 2.77
4529 4765 2.772691 GCGTCCGGACCTACAGGAG 61.773 68.421 28.52 12.90 42.99 3.69
4677 4913 2.034999 CCCCGGCTGTTTTGGCTA 59.965 61.111 0.00 0.00 0.00 3.93
4713 4949 2.753043 GACACCGACGGAGGGCTA 60.753 66.667 23.38 0.00 35.02 3.93
4770 5006 0.601576 CGTCCATGGTGAAACGGACA 60.602 55.000 12.58 0.00 42.69 4.02
4853 5090 4.024048 CCAAAATCGTACAGAAGCTTGTGT 60.024 41.667 29.43 29.43 38.34 3.72
4857 5094 5.491982 AGATCCAAAATCGTACAGAAGCTT 58.508 37.500 0.00 0.00 0.00 3.74
4861 5098 5.810587 GCTGTAGATCCAAAATCGTACAGAA 59.189 40.000 15.06 0.00 39.73 3.02
5057 5309 7.180229 TGTCAGGGAGAAGAAATATACAAGTCA 59.820 37.037 0.00 0.00 0.00 3.41
5147 5401 4.726035 TCGTCTATGATACCCCTCTTCT 57.274 45.455 0.00 0.00 0.00 2.85
5364 5624 1.061131 CTAACGCGAGCTGTTTGGATG 59.939 52.381 15.93 0.00 0.00 3.51
5420 5680 8.442632 TTCAGGCTGATTTATATTGAAGACAG 57.557 34.615 19.50 0.00 0.00 3.51
5527 5787 2.885135 ATGAACAATCCAGCTGGTGA 57.115 45.000 31.58 14.98 36.34 4.02
5709 5969 2.153645 TGCGTGCTCTTGTTCATCATT 58.846 42.857 0.00 0.00 0.00 2.57
5714 5974 1.600164 GCATTTGCGTGCTCTTGTTCA 60.600 47.619 1.76 0.00 41.82 3.18
5752 6012 2.770164 ATCCGCTTGCTCTTGTACTT 57.230 45.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.