Multiple sequence alignment - TraesCS2D01G097400

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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 TraesCS2D01G097400 chr2D 100.000 4007 0 0 1 4007 49871042 49875048 0.000000e+00 7400
1 TraesCS2D01G097400 chr2D 85.688 538 57 7 33 552 579485262 579485797 2.110000e-152 549
2 TraesCS2D01G097400 chr2B 93.062 1427 75 13 1892 3310 77165662 77167072 0.000000e+00 2065
3 TraesCS2D01G097400 chr2B 90.481 977 53 19 833 1793 77164698 77165650 0.000000e+00 1253
4 TraesCS2D01G097400 chr2B 87.536 698 34 21 3327 4007 77167126 77167787 0.000000e+00 758
5 TraesCS2D01G097400 chr2B 84.183 569 42 16 33 578 42270404 42269861 3.570000e-140 508
6 TraesCS2D01G097400 chr2B 90.214 327 19 3 320 633 587408172 587408498 8.010000e-112 414
7 TraesCS2D01G097400 chr2B 95.000 80 4 0 554 633 397577550 397577629 4.200000e-25 126
8 TraesCS2D01G097400 chr2B 87.963 108 5 3 693 799 77158666 77158766 1.960000e-23 121
9 TraesCS2D01G097400 chr2B 94.805 77 4 0 557 633 712594848 712594772 1.960000e-23 121
10 TraesCS2D01G097400 chr2B 94.805 77 4 0 557 633 775068704 775068628 1.960000e-23 121
11 TraesCS2D01G097400 chr2B 91.667 84 7 0 557 640 695679806 695679723 2.530000e-22 117
12 TraesCS2D01G097400 chr2A 94.564 699 34 3 1925 2622 51579311 51580006 0.000000e+00 1077
13 TraesCS2D01G097400 chr2A 89.413 869 50 18 693 1555 51578184 51579016 0.000000e+00 1057
14 TraesCS2D01G097400 chr2A 92.273 660 43 7 2620 3276 51580042 51580696 0.000000e+00 929
15 TraesCS2D01G097400 chr2A 81.949 554 72 19 3331 3871 51580778 51581316 1.020000e-120 444
16 TraesCS2D01G097400 chr2A 83.391 289 37 5 1514 1793 51579018 51579304 1.430000e-64 257
17 TraesCS2D01G097400 chr2A 96.667 90 3 0 1790 1879 4211353 4211264 2.490000e-32 150
18 TraesCS2D01G097400 chr1B 88.872 647 33 14 33 640 555751536 555752182 0.000000e+00 760
19 TraesCS2D01G097400 chr3B 88.480 625 37 7 48 640 736459513 736460134 0.000000e+00 723
20 TraesCS2D01G097400 chr3B 85.918 632 50 10 33 638 15210574 15211192 4.370000e-179 638
21 TraesCS2D01G097400 chr3B 85.407 651 50 9 33 638 15403156 15403806 5.650000e-178 634
22 TraesCS2D01G097400 chr3B 85.945 619 50 22 30 630 522581655 522582254 9.450000e-176 627
23 TraesCS2D01G097400 chr3B 87.524 529 44 10 33 544 583327250 583327773 3.450000e-165 592
24 TraesCS2D01G097400 chr3B 93.243 148 7 1 496 640 320863463 320863316 8.720000e-52 215
25 TraesCS2D01G097400 chr3B 96.629 89 3 0 1788 1876 569062506 569062594 8.970000e-32 148
26 TraesCS2D01G097400 chr3B 92.929 99 6 1 1790 1888 807575428 807575525 4.170000e-30 143
27 TraesCS2D01G097400 chr5B 87.780 491 24 20 33 487 607294501 607294991 3.520000e-150 542
28 TraesCS2D01G097400 chr5B 84.826 547 40 16 33 552 252359884 252359354 9.930000e-141 510
29 TraesCS2D01G097400 chr7D 85.448 536 58 8 33 552 221270067 221269536 1.270000e-149 540
30 TraesCS2D01G097400 chr7D 96.703 91 3 0 1787 1877 599718438 599718528 6.940000e-33 152
31 TraesCS2D01G097400 chr6B 87.344 482 45 8 33 500 132196217 132195738 4.560000e-149 538
32 TraesCS2D01G097400 chr6B 80.660 212 26 7 299 504 113530597 113530395 2.490000e-32 150
33 TraesCS2D01G097400 chr3D 84.369 531 62 11 33 544 26390582 26390054 5.980000e-138 501
34 TraesCS2D01G097400 chr6A 87.566 378 24 9 33 389 39268651 39269026 2.230000e-112 416
35 TraesCS2D01G097400 chr1D 81.031 543 77 14 33 552 213169969 213169430 3.730000e-110 409
36 TraesCS2D01G097400 chr5A 83.043 460 56 10 33 471 675315186 675314728 8.070000e-107 398
37 TraesCS2D01G097400 chr4D 83.777 413 45 12 156 552 172121828 172122234 4.890000e-99 372
38 TraesCS2D01G097400 chr4D 86.179 123 14 3 1758 1878 301528758 301528637 3.250000e-26 130
39 TraesCS2D01G097400 chr6D 94.894 235 9 1 409 640 333485904 333485670 8.180000e-97 364
40 TraesCS2D01G097400 chr1A 93.069 101 5 2 1786 1885 584082902 584082803 3.230000e-31 147
41 TraesCS2D01G097400 chr1A 93.684 95 4 2 1790 1883 133417547 133417454 1.500000e-29 141
42 TraesCS2D01G097400 chr7A 90.476 105 9 1 1787 1891 213151262 213151365 1.940000e-28 137
43 TraesCS2D01G097400 chr5D 88.288 111 11 2 1778 1888 475843304 475843412 9.040000e-27 132


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 TraesCS2D01G097400 chr2D 49871042 49875048 4006 False 7400.000000 7400 100.000000 1 4007 1 chr2D.!!$F1 4006
1 TraesCS2D01G097400 chr2D 579485262 579485797 535 False 549.000000 549 85.688000 33 552 1 chr2D.!!$F2 519
2 TraesCS2D01G097400 chr2B 77164698 77167787 3089 False 1358.666667 2065 90.359667 833 4007 3 chr2B.!!$F4 3174
3 TraesCS2D01G097400 chr2B 42269861 42270404 543 True 508.000000 508 84.183000 33 578 1 chr2B.!!$R1 545
4 TraesCS2D01G097400 chr2A 51578184 51581316 3132 False 752.800000 1077 88.318000 693 3871 5 chr2A.!!$F1 3178
5 TraesCS2D01G097400 chr1B 555751536 555752182 646 False 760.000000 760 88.872000 33 640 1 chr1B.!!$F1 607
6 TraesCS2D01G097400 chr3B 736459513 736460134 621 False 723.000000 723 88.480000 48 640 1 chr3B.!!$F6 592
7 TraesCS2D01G097400 chr3B 15210574 15211192 618 False 638.000000 638 85.918000 33 638 1 chr3B.!!$F1 605
8 TraesCS2D01G097400 chr3B 15403156 15403806 650 False 634.000000 634 85.407000 33 638 1 chr3B.!!$F2 605
9 TraesCS2D01G097400 chr3B 522581655 522582254 599 False 627.000000 627 85.945000 30 630 1 chr3B.!!$F3 600
10 TraesCS2D01G097400 chr3B 583327250 583327773 523 False 592.000000 592 87.524000 33 544 1 chr3B.!!$F5 511
11 TraesCS2D01G097400 chr5B 252359354 252359884 530 True 510.000000 510 84.826000 33 552 1 chr5B.!!$R1 519
12 TraesCS2D01G097400 chr7D 221269536 221270067 531 True 540.000000 540 85.448000 33 552 1 chr7D.!!$R1 519
13 TraesCS2D01G097400 chr3D 26390054 26390582 528 True 501.000000 501 84.369000 33 544 1 chr3D.!!$R1 511
14 TraesCS2D01G097400 chr1D 213169430 213169969 539 True 409.000000 409 81.031000 33 552 1 chr1D.!!$R1 519

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
31 32 0.807667 GCATGTGTCCGGCTCACTAG 60.808 60.0 22.95 17.63 36.83 2.57 F
1478 1571 0.179034 CCCTTGGCTATCTGTCTGCC 60.179 60.0 0.00 0.00 46.26 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1835 1.069227 GTGTGATCGCCAAAGTTGACC 60.069 52.381 3.31 0.0 0.0 4.02 R
3319 3505 0.327191 CTGGGCTACCCTCCCCTTTA 60.327 60.000 3.93 0.0 45.7 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.485677 GGATGGACACCTGCATGTG 58.514 57.895 19.12 19.12 42.05 3.21
23 24 2.032528 ACACCTGCATGTGTCCGG 59.967 61.111 20.45 3.07 46.15 5.14
24 25 3.434319 CACCTGCATGTGTCCGGC 61.434 66.667 13.40 0.00 0.00 6.13
25 26 3.640407 ACCTGCATGTGTCCGGCT 61.640 61.111 0.00 0.00 0.00 5.52
26 27 2.821366 CCTGCATGTGTCCGGCTC 60.821 66.667 0.00 0.00 0.00 4.70
27 28 2.046988 CTGCATGTGTCCGGCTCA 60.047 61.111 0.00 0.00 0.00 4.26
28 29 2.358615 TGCATGTGTCCGGCTCAC 60.359 61.111 18.28 18.28 36.48 3.51
31 32 0.807667 GCATGTGTCCGGCTCACTAG 60.808 60.000 22.95 17.63 36.83 2.57
302 332 7.724305 ATTGTCGTTGTACAGTACTTTCATT 57.276 32.000 12.07 0.00 0.00 2.57
360 392 3.811083 ACAGTGGGTGAAATAAACGTGA 58.189 40.909 0.00 0.00 0.00 4.35
379 413 5.163301 ACGTGAATTAGATTAGTGGAGGCAT 60.163 40.000 0.00 0.00 0.00 4.40
440 501 7.400599 TGGATTAGTAGTACTTTCGATGTGT 57.599 36.000 8.40 0.00 0.00 3.72
487 548 4.881273 TCTAATCCATGTTCATTTCACCCG 59.119 41.667 0.00 0.00 0.00 5.28
574 645 2.423185 TGGTCATCATTTTCGTCCATGC 59.577 45.455 0.00 0.00 0.00 4.06
641 715 8.657712 TCCTCATCATCATCATCAACTCTAATT 58.342 33.333 0.00 0.00 0.00 1.40
642 716 8.937884 CCTCATCATCATCATCAACTCTAATTC 58.062 37.037 0.00 0.00 0.00 2.17
643 717 8.530269 TCATCATCATCATCAACTCTAATTCG 57.470 34.615 0.00 0.00 0.00 3.34
644 718 8.362639 TCATCATCATCATCAACTCTAATTCGA 58.637 33.333 0.00 0.00 0.00 3.71
645 719 8.985805 CATCATCATCATCAACTCTAATTCGAA 58.014 33.333 0.00 0.00 0.00 3.71
646 720 8.947055 TCATCATCATCAACTCTAATTCGAAA 57.053 30.769 0.00 0.00 0.00 3.46
647 721 8.820933 TCATCATCATCAACTCTAATTCGAAAC 58.179 33.333 0.00 0.00 0.00 2.78
648 722 8.606602 CATCATCATCAACTCTAATTCGAAACA 58.393 33.333 0.00 0.00 0.00 2.83
649 723 8.189709 TCATCATCAACTCTAATTCGAAACAG 57.810 34.615 0.00 2.22 0.00 3.16
650 724 6.408858 TCATCAACTCTAATTCGAAACAGC 57.591 37.500 0.00 0.00 0.00 4.40
651 725 5.351465 TCATCAACTCTAATTCGAAACAGCC 59.649 40.000 0.00 0.00 0.00 4.85
652 726 4.894784 TCAACTCTAATTCGAAACAGCCT 58.105 39.130 0.00 0.00 0.00 4.58
653 727 6.032956 TCAACTCTAATTCGAAACAGCCTA 57.967 37.500 0.00 0.00 0.00 3.93
654 728 5.867716 TCAACTCTAATTCGAAACAGCCTAC 59.132 40.000 0.00 0.00 0.00 3.18
655 729 5.662674 ACTCTAATTCGAAACAGCCTACT 57.337 39.130 0.00 0.00 0.00 2.57
700 774 2.031616 ATGGGCATCGATGGAGCG 59.968 61.111 26.00 1.16 0.00 5.03
701 775 3.541950 ATGGGCATCGATGGAGCGG 62.542 63.158 26.00 0.38 0.00 5.52
718 792 1.933307 CGGGGGAAACTAATGGGCCT 61.933 60.000 4.53 0.00 0.00 5.19
777 851 3.726517 CCTGGGCTCGTGCGTTTG 61.727 66.667 3.02 0.00 40.82 2.93
868 942 1.228124 ATCGCCCTCCTCTCTCTCG 60.228 63.158 0.00 0.00 0.00 4.04
870 944 2.123897 GCCCTCCTCTCTCTCGCT 60.124 66.667 0.00 0.00 0.00 4.93
953 1029 1.696884 CCTGGCCTCCCTCTAGATTTC 59.303 57.143 3.32 0.00 0.00 2.17
954 1030 1.696884 CTGGCCTCCCTCTAGATTTCC 59.303 57.143 3.32 0.00 0.00 3.13
1236 1329 1.850441 GATCACGCACGTACACATACC 59.150 52.381 0.00 0.00 0.00 2.73
1265 1358 1.490490 TCAAATCCTCCCCTGAATCCG 59.510 52.381 0.00 0.00 0.00 4.18
1285 1378 1.155424 GCGCCCGGTTTCGAATCATA 61.155 55.000 11.42 0.00 39.00 2.15
1295 1388 2.423926 TCGAATCATAGCGAGCTTCC 57.576 50.000 1.86 0.00 32.13 3.46
1307 1400 1.844687 GAGCTTCCTGCCTCCAAATT 58.155 50.000 0.00 0.00 44.23 1.82
1318 1411 0.804989 CTCCAAATTCCCAGTGCGAC 59.195 55.000 0.00 0.00 0.00 5.19
1477 1570 0.833287 TCCCTTGGCTATCTGTCTGC 59.167 55.000 0.00 0.00 0.00 4.26
1478 1571 0.179034 CCCTTGGCTATCTGTCTGCC 60.179 60.000 0.00 0.00 46.26 4.85
1479 1572 0.835941 CCTTGGCTATCTGTCTGCCT 59.164 55.000 0.00 0.00 46.23 4.75
1480 1573 1.474677 CCTTGGCTATCTGTCTGCCTG 60.475 57.143 0.00 0.00 46.23 4.85
1503 1596 2.045926 ACCGTGAGCCTCCATTGC 60.046 61.111 0.00 0.00 0.00 3.56
1512 1605 3.137533 GAGCCTCCATTGCTATCTGAAC 58.862 50.000 0.00 0.00 39.69 3.18
1522 1651 4.727507 TGCTATCTGAACTCTGAAGACC 57.272 45.455 0.00 0.00 0.00 3.85
1579 1708 5.327732 ACAGATGAATGATTGGTTCAGGTT 58.672 37.500 0.00 0.00 38.81 3.50
1581 1710 7.121382 ACAGATGAATGATTGGTTCAGGTTAT 58.879 34.615 0.00 0.00 38.81 1.89
1589 1718 7.252612 TGATTGGTTCAGGTTATAGTTGAGA 57.747 36.000 0.00 0.00 0.00 3.27
1643 1778 8.180267 GTGAGATTGAAATACTGAACAGATTGG 58.820 37.037 8.87 0.00 0.00 3.16
1655 1790 1.707427 ACAGATTGGCTTCACCTTCCT 59.293 47.619 0.00 0.00 40.22 3.36
1660 1795 0.832135 TGGCTTCACCTTCCTCGACT 60.832 55.000 0.00 0.00 40.22 4.18
1712 1847 2.561037 CCCACCGGTCAACTTTGGC 61.561 63.158 2.59 0.00 0.00 4.52
1716 1851 0.953960 ACCGGTCAACTTTGGCGATC 60.954 55.000 0.00 0.00 32.44 3.69
1717 1852 0.953471 CCGGTCAACTTTGGCGATCA 60.953 55.000 0.00 0.00 32.44 2.92
1721 1856 1.601903 GTCAACTTTGGCGATCACACA 59.398 47.619 0.00 0.00 0.00 3.72
1766 1904 2.480073 CCACTGGCAGTTTGTGTCTTTG 60.480 50.000 19.43 2.23 0.00 2.77
1767 1905 1.134946 ACTGGCAGTTTGTGTCTTTGC 59.865 47.619 15.88 0.00 0.00 3.68
1793 1932 8.470040 TTGATGTGTTTATTACCGAACTACTC 57.530 34.615 0.00 0.00 0.00 2.59
1794 1933 7.833786 TGATGTGTTTATTACCGAACTACTCT 58.166 34.615 0.00 0.00 0.00 3.24
1796 1935 7.458409 TGTGTTTATTACCGAACTACTCTCT 57.542 36.000 0.00 0.00 0.00 3.10
1797 1936 7.533426 TGTGTTTATTACCGAACTACTCTCTC 58.467 38.462 0.00 0.00 0.00 3.20
1798 1937 7.392673 TGTGTTTATTACCGAACTACTCTCTCT 59.607 37.037 0.00 0.00 0.00 3.10
1799 1938 7.697291 GTGTTTATTACCGAACTACTCTCTCTG 59.303 40.741 0.00 0.00 0.00 3.35
1800 1939 7.392673 TGTTTATTACCGAACTACTCTCTCTGT 59.607 37.037 0.00 0.00 0.00 3.41
1801 1940 8.887717 GTTTATTACCGAACTACTCTCTCTGTA 58.112 37.037 0.00 0.00 0.00 2.74
1802 1941 9.453572 TTTATTACCGAACTACTCTCTCTGTAA 57.546 33.333 0.00 0.00 0.00 2.41
1803 1942 7.934855 ATTACCGAACTACTCTCTCTGTAAA 57.065 36.000 0.00 0.00 0.00 2.01
1804 1943 5.625921 ACCGAACTACTCTCTCTGTAAAC 57.374 43.478 0.00 0.00 0.00 2.01
1805 1944 5.315348 ACCGAACTACTCTCTCTGTAAACT 58.685 41.667 0.00 0.00 0.00 2.66
1806 1945 6.471146 ACCGAACTACTCTCTCTGTAAACTA 58.529 40.000 0.00 0.00 0.00 2.24
1807 1946 6.939163 ACCGAACTACTCTCTCTGTAAACTAA 59.061 38.462 0.00 0.00 0.00 2.24
1808 1947 7.611079 ACCGAACTACTCTCTCTGTAAACTAAT 59.389 37.037 0.00 0.00 0.00 1.73
1809 1948 9.107177 CCGAACTACTCTCTCTGTAAACTAATA 57.893 37.037 0.00 0.00 0.00 0.98
1817 1956 9.820229 CTCTCTCTGTAAACTAATATAAGAGCG 57.180 37.037 0.00 0.00 0.00 5.03
1818 1957 9.339850 TCTCTCTGTAAACTAATATAAGAGCGT 57.660 33.333 0.00 0.00 0.00 5.07
1819 1958 9.953697 CTCTCTGTAAACTAATATAAGAGCGTT 57.046 33.333 0.00 0.00 0.00 4.84
1835 1974 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
1836 1975 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
1868 2007 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
1869 2008 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
1870 2009 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
1871 2010 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
1872 2011 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
1873 2012 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1874 2013 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
1875 2014 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
1878 2017 7.757941 ATTAGTTTACGGAGGGAGTACTATC 57.242 40.000 0.00 0.00 0.00 2.08
1879 2018 4.133078 AGTTTACGGAGGGAGTACTATCG 58.867 47.826 0.00 0.00 0.00 2.92
1880 2019 4.130118 GTTTACGGAGGGAGTACTATCGA 58.870 47.826 0.00 0.00 0.00 3.59
1881 2020 4.422073 TTACGGAGGGAGTACTATCGAA 57.578 45.455 0.00 0.00 0.00 3.71
1882 2021 3.287867 ACGGAGGGAGTACTATCGAAA 57.712 47.619 0.00 0.00 0.00 3.46
1883 2022 3.212685 ACGGAGGGAGTACTATCGAAAG 58.787 50.000 0.00 0.00 0.00 2.62
1884 2023 3.212685 CGGAGGGAGTACTATCGAAAGT 58.787 50.000 0.00 0.00 0.00 2.66
1885 2024 3.250521 CGGAGGGAGTACTATCGAAAGTC 59.749 52.174 0.00 0.00 0.00 3.01
1886 2025 4.463070 GGAGGGAGTACTATCGAAAGTCT 58.537 47.826 0.00 0.00 0.00 3.24
1887 2026 4.888823 GGAGGGAGTACTATCGAAAGTCTT 59.111 45.833 0.00 0.00 0.00 3.01
1888 2027 5.360429 GGAGGGAGTACTATCGAAAGTCTTT 59.640 44.000 0.00 0.00 0.00 2.52
1889 2028 6.545298 GGAGGGAGTACTATCGAAAGTCTTTA 59.455 42.308 0.00 0.00 0.00 1.85
1890 2029 7.067981 GGAGGGAGTACTATCGAAAGTCTTTAA 59.932 40.741 0.00 0.00 0.00 1.52
1961 2100 3.347958 TGCACAAAGAACAATTCGGTC 57.652 42.857 0.00 0.00 34.02 4.79
2012 2157 7.032580 TGAAAATTTCGTGGCATATTTGGTAG 58.967 34.615 0.97 0.00 0.00 3.18
2112 2258 7.095857 GCATATACAGCTCTTCTTACACATGAC 60.096 40.741 0.00 0.00 0.00 3.06
2114 2260 3.324846 ACAGCTCTTCTTACACATGACCA 59.675 43.478 0.00 0.00 0.00 4.02
2119 2265 6.989169 AGCTCTTCTTACACATGACCATTATC 59.011 38.462 0.00 0.00 0.00 1.75
2129 2275 7.549839 ACACATGACCATTATCAATTCTTTGG 58.450 34.615 0.00 0.00 33.44 3.28
2293 2439 3.287867 CCTCATGGAGGCAAGTGTATT 57.712 47.619 0.00 0.00 43.29 1.89
2369 2515 1.272147 GCAGTGACCTTTTCTCCCCAT 60.272 52.381 0.00 0.00 0.00 4.00
2390 2536 8.408601 CCCCATAACTGAAACTTGATGAAATAG 58.591 37.037 0.00 0.00 0.00 1.73
2393 2539 9.499585 CATAACTGAAACTTGATGAAATAGCAG 57.500 33.333 0.00 0.00 0.00 4.24
2439 2585 1.816074 TACATGGCAGGAAAACCGTC 58.184 50.000 5.99 0.00 0.00 4.79
2478 2624 2.766263 CCACACCATCCTGTTAGAGCTA 59.234 50.000 0.00 0.00 0.00 3.32
2494 2640 4.353777 AGAGCTACCATCAGGAGTTTACA 58.646 43.478 0.00 0.00 38.69 2.41
2514 2660 3.632604 ACAGGTACAGATTCATCGTCGAT 59.367 43.478 0.75 0.75 0.00 3.59
2517 2663 3.004419 GGTACAGATTCATCGTCGATGGA 59.996 47.826 29.72 24.59 40.15 3.41
2676 2861 2.399916 TGATCATCGGTGATGCAACA 57.600 45.000 17.68 4.66 44.96 3.33
2683 2868 1.269174 TCGGTGATGCAACACAATTGG 59.731 47.619 25.93 11.02 41.88 3.16
2700 2885 2.564721 GGTGCAGGACTTTGTGCCC 61.565 63.158 0.00 0.00 39.04 5.36
2706 2891 0.182775 AGGACTTTGTGCCCGAAAGT 59.817 50.000 0.00 0.00 44.51 2.66
2823 3008 2.797278 CCTCCCGGCGCAACTCTAT 61.797 63.158 10.83 0.00 0.00 1.98
2826 3011 1.592669 CCCGGCGCAACTCTATCTG 60.593 63.158 10.83 0.00 0.00 2.90
3061 3246 0.025513 CGCAAGCGAGAGGATTTTCG 59.974 55.000 9.11 0.00 42.83 3.46
3121 3307 8.654230 TTGCATAAACAAGCTGTAATTTTCAA 57.346 26.923 0.00 0.00 0.00 2.69
3263 3449 4.746115 TCAACTGCTCATGAACAAAATTGC 59.254 37.500 0.00 0.00 0.00 3.56
3272 3458 4.861389 TGAACAAAATTGCTGCTGTTTG 57.139 36.364 16.29 16.29 37.08 2.93
3273 3459 4.252073 TGAACAAAATTGCTGCTGTTTGT 58.748 34.783 17.22 17.22 44.01 2.83
3280 3466 6.544038 AAATTGCTGCTGTTTGTAAAATCC 57.456 33.333 0.00 0.00 0.00 3.01
3289 3475 8.865590 TGCTGTTTGTAAAATCCTAAGAAAAC 57.134 30.769 0.00 0.00 0.00 2.43
3294 3480 8.761497 GTTTGTAAAATCCTAAGAAAACTTGCC 58.239 33.333 0.00 0.00 0.00 4.52
3295 3481 7.589958 TGTAAAATCCTAAGAAAACTTGCCA 57.410 32.000 0.00 0.00 0.00 4.92
3297 3483 5.728637 AAATCCTAAGAAAACTTGCCAGG 57.271 39.130 0.00 0.00 0.00 4.45
3358 3579 3.064324 GCCCAACAATGAGCGGCT 61.064 61.111 0.00 0.00 36.65 5.52
3397 3627 3.809832 CAGTGTCCTGACGAGTGAAAATT 59.190 43.478 0.00 0.00 41.50 1.82
3477 3707 1.408822 GCATTCCCGTCATTTCTCCCT 60.409 52.381 0.00 0.00 0.00 4.20
3586 3816 1.303806 GCCTTTGGCCCTAACGGAA 60.304 57.895 0.00 0.00 44.06 4.30
3604 3834 1.536331 GAACGCCCGATGTTACCAAAA 59.464 47.619 0.00 0.00 0.00 2.44
3611 3841 1.136110 CGATGTTACCAAAATGCCCCC 59.864 52.381 0.00 0.00 0.00 5.40
3612 3842 2.466846 GATGTTACCAAAATGCCCCCT 58.533 47.619 0.00 0.00 0.00 4.79
3613 3843 1.931635 TGTTACCAAAATGCCCCCTC 58.068 50.000 0.00 0.00 0.00 4.30
3616 3846 0.406361 TACCAAAATGCCCCCTCGTT 59.594 50.000 0.00 0.00 0.00 3.85
3618 3848 1.591183 CAAAATGCCCCCTCGTTGG 59.409 57.895 0.00 0.00 0.00 3.77
3630 3860 0.930310 CTCGTTGGGCATGATACGTG 59.070 55.000 0.00 0.00 35.63 4.49
3654 3884 7.587028 GTGTATTTGCAAATTTCCATGTGTTTG 59.413 33.333 28.45 0.00 35.30 2.93
3659 3889 4.378666 GCAAATTTCCATGTGTTTGCCATC 60.379 41.667 16.81 0.00 46.42 3.51
3661 3891 4.895668 ATTTCCATGTGTTTGCCATCTT 57.104 36.364 0.00 0.00 0.00 2.40
3662 3892 3.940209 TTCCATGTGTTTGCCATCTTC 57.060 42.857 0.00 0.00 0.00 2.87
3663 3893 3.159213 TCCATGTGTTTGCCATCTTCT 57.841 42.857 0.00 0.00 0.00 2.85
3664 3894 4.299586 TCCATGTGTTTGCCATCTTCTA 57.700 40.909 0.00 0.00 0.00 2.10
3665 3895 4.009675 TCCATGTGTTTGCCATCTTCTAC 58.990 43.478 0.00 0.00 0.00 2.59
3666 3896 4.012374 CCATGTGTTTGCCATCTTCTACT 58.988 43.478 0.00 0.00 0.00 2.57
3667 3897 5.045942 TCCATGTGTTTGCCATCTTCTACTA 60.046 40.000 0.00 0.00 0.00 1.82
3678 3908 8.948631 TGCCATCTTCTACTATAACTCTTTTG 57.051 34.615 0.00 0.00 0.00 2.44
3714 3946 8.314751 TCTTTTATCTTCTAGTATATGCTGGGC 58.685 37.037 3.24 0.00 0.00 5.36
3716 3948 7.798710 TTATCTTCTAGTATATGCTGGGCTT 57.201 36.000 3.24 0.00 0.00 4.35
3717 3949 5.730296 TCTTCTAGTATATGCTGGGCTTC 57.270 43.478 3.24 0.00 0.00 3.86
3718 3950 5.147767 TCTTCTAGTATATGCTGGGCTTCA 58.852 41.667 3.24 0.00 0.00 3.02
3742 3974 5.684704 TGGGGATTGATCTTCTATGTTGTC 58.315 41.667 0.00 0.00 0.00 3.18
3749 3981 5.532557 TGATCTTCTATGTTGTCCGCTATG 58.467 41.667 0.00 0.00 0.00 2.23
3757 3989 5.734855 ATGTTGTCCGCTATGTACATTTC 57.265 39.130 14.77 5.38 0.00 2.17
3762 3994 4.051922 GTCCGCTATGTACATTTCTCAGG 58.948 47.826 14.77 9.42 0.00 3.86
3769 4001 4.808414 TGTACATTTCTCAGGAGGTCTG 57.192 45.455 0.00 0.00 44.68 3.51
3771 4003 1.066573 ACATTTCTCAGGAGGTCTGCG 60.067 52.381 0.00 0.00 43.06 5.18
3778 4010 2.680352 GGAGGTCTGCGGTGGAGA 60.680 66.667 0.00 0.00 0.00 3.71
3871 4105 4.365723 TGGAAGACTTTTAGACGTGTGAC 58.634 43.478 0.00 0.00 0.00 3.67
3872 4106 3.739810 GGAAGACTTTTAGACGTGTGACC 59.260 47.826 0.00 0.00 0.00 4.02
3873 4107 4.501058 GGAAGACTTTTAGACGTGTGACCT 60.501 45.833 0.00 0.00 0.00 3.85
3917 4167 5.408604 AGAAGCCGTGTATTTGTTCTTACAG 59.591 40.000 0.00 0.00 35.28 2.74
3973 4223 2.758089 GCCACAATCGAGCAGCTGG 61.758 63.158 17.12 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.485677 CACATGCAGGTGTCCATCC 58.514 57.895 22.84 0.00 34.09 3.51
7 8 3.434319 GCCGGACACATGCAGGTG 61.434 66.667 28.54 28.54 44.35 4.00
8 9 3.612247 GAGCCGGACACATGCAGGT 62.612 63.158 5.05 0.00 0.00 4.00
9 10 2.821366 GAGCCGGACACATGCAGG 60.821 66.667 5.05 0.00 0.00 4.85
10 11 2.046988 TGAGCCGGACACATGCAG 60.047 61.111 5.05 0.00 0.00 4.41
11 12 1.540435 TAGTGAGCCGGACACATGCA 61.540 55.000 25.87 11.20 40.25 3.96
12 13 0.807667 CTAGTGAGCCGGACACATGC 60.808 60.000 25.87 2.57 40.25 4.06
13 14 0.807667 GCTAGTGAGCCGGACACATG 60.808 60.000 25.87 19.78 43.49 3.21
14 15 1.517832 GCTAGTGAGCCGGACACAT 59.482 57.895 25.87 16.58 43.49 3.21
15 16 2.970639 GCTAGTGAGCCGGACACA 59.029 61.111 25.87 12.02 43.49 3.72
23 24 9.342035 GGGTTATTCCTAGTAGTGCTAGTGAGC 62.342 48.148 13.45 3.05 44.37 4.26
24 25 6.016108 GGGTTATTCCTAGTAGTGCTAGTGAG 60.016 46.154 13.45 0.01 44.37 3.51
25 26 5.832060 GGGTTATTCCTAGTAGTGCTAGTGA 59.168 44.000 13.45 8.06 44.37 3.41
26 27 5.834204 AGGGTTATTCCTAGTAGTGCTAGTG 59.166 44.000 13.45 6.09 44.37 2.74
27 28 6.028258 AGGGTTATTCCTAGTAGTGCTAGT 57.972 41.667 13.45 0.00 44.37 2.57
28 29 7.690952 CTAGGGTTATTCCTAGTAGTGCTAG 57.309 44.000 8.22 8.22 47.00 3.42
42 43 4.648307 ACAAGCGCTACTACTAGGGTTATT 59.352 41.667 12.05 0.00 35.73 1.40
162 166 2.431057 ACCAAGCGCTACTGCTAACTAT 59.569 45.455 12.05 0.00 46.60 2.12
360 392 6.713903 CACATGATGCCTCCACTAATCTAATT 59.286 38.462 0.00 0.00 0.00 1.40
440 501 1.064003 AGTGGAGGCAACATGTGGTA 58.936 50.000 0.00 0.00 41.41 3.25
574 645 6.535150 AGTGACCAAGTTGTTATATGATGTCG 59.465 38.462 1.45 0.00 0.00 4.35
677 751 2.689471 CTCCATCGATGCCCATGAAAAA 59.311 45.455 20.25 0.00 0.00 1.94
678 752 2.300433 CTCCATCGATGCCCATGAAAA 58.700 47.619 20.25 0.00 0.00 2.29
679 753 1.971481 CTCCATCGATGCCCATGAAA 58.029 50.000 20.25 0.00 0.00 2.69
680 754 0.535780 GCTCCATCGATGCCCATGAA 60.536 55.000 20.25 0.00 0.00 2.57
681 755 1.071987 GCTCCATCGATGCCCATGA 59.928 57.895 20.25 10.18 0.00 3.07
682 756 2.322830 CGCTCCATCGATGCCCATG 61.323 63.158 20.25 6.08 0.00 3.66
683 757 2.031616 CGCTCCATCGATGCCCAT 59.968 61.111 20.25 0.00 0.00 4.00
684 758 4.240103 CCGCTCCATCGATGCCCA 62.240 66.667 20.25 4.92 0.00 5.36
685 759 4.996434 CCCGCTCCATCGATGCCC 62.996 72.222 20.25 8.74 0.00 5.36
686 760 4.996434 CCCCGCTCCATCGATGCC 62.996 72.222 20.25 9.08 0.00 4.40
687 761 4.996434 CCCCCGCTCCATCGATGC 62.996 72.222 20.25 8.02 0.00 3.91
688 762 2.324014 TTTCCCCCGCTCCATCGATG 62.324 60.000 18.76 18.76 0.00 3.84
689 763 2.070039 TTTCCCCCGCTCCATCGAT 61.070 57.895 0.00 0.00 0.00 3.59
690 764 2.685743 TTTCCCCCGCTCCATCGA 60.686 61.111 0.00 0.00 0.00 3.59
691 765 1.682451 TAGTTTCCCCCGCTCCATCG 61.682 60.000 0.00 0.00 0.00 3.84
700 774 0.338467 AAGGCCCATTAGTTTCCCCC 59.662 55.000 0.00 0.00 0.00 5.40
701 775 1.485124 CAAGGCCCATTAGTTTCCCC 58.515 55.000 0.00 0.00 0.00 4.81
776 850 4.966787 GGGTTTGTCTGCCCGGCA 62.967 66.667 12.67 12.67 34.90 5.69
785 859 1.891919 TGCTGCGACTGGGTTTGTC 60.892 57.895 0.00 0.00 0.00 3.18
953 1029 2.445654 GGGCAGAGGAGGAGAGGG 60.446 72.222 0.00 0.00 0.00 4.30
954 1030 2.445654 GGGGCAGAGGAGGAGAGG 60.446 72.222 0.00 0.00 0.00 3.69
1130 1218 4.354943 ACCCTCCACCCCCTCCTG 62.355 72.222 0.00 0.00 0.00 3.86
1236 1329 8.766994 TTCAGGGGAGGATTTGATTAAATTAG 57.233 34.615 0.00 0.00 36.66 1.73
1265 1358 3.872728 GATTCGAAACCGGGCGCC 61.873 66.667 21.18 21.18 0.00 6.53
1285 1378 3.780173 GGAGGCAGGAAGCTCGCT 61.780 66.667 0.00 0.00 44.79 4.93
1295 1388 1.180029 CACTGGGAATTTGGAGGCAG 58.820 55.000 0.00 0.00 0.00 4.85
1503 1596 5.913137 ACAGGTCTTCAGAGTTCAGATAG 57.087 43.478 0.00 0.00 0.00 2.08
1643 1778 1.819903 ACTAGTCGAGGAAGGTGAAGC 59.180 52.381 0.00 0.00 0.00 3.86
1655 1790 4.524053 TCTAGATGAAAGCCACTAGTCGA 58.476 43.478 0.00 0.00 35.34 4.20
1700 1835 1.069227 GTGTGATCGCCAAAGTTGACC 60.069 52.381 3.31 0.00 0.00 4.02
1766 1904 6.178239 AGTTCGGTAATAAACACATCAAGC 57.822 37.500 0.00 0.00 0.00 4.01
1767 1905 8.475331 AGTAGTTCGGTAATAAACACATCAAG 57.525 34.615 0.00 0.00 0.00 3.02
1793 1932 9.953697 AACGCTCTTATATTAGTTTACAGAGAG 57.046 33.333 0.00 0.00 34.15 3.20
1809 1948 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
1810 1949 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
1811 1950 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
1812 1951 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
1842 1981 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
1843 1982 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
1844 1983 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
1845 1984 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
1846 1985 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
1847 1986 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1848 1987 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1849 1988 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
1852 1991 9.460019 GATAGTACTCCCTCCGTAAACTAATAT 57.540 37.037 0.00 0.00 0.00 1.28
1853 1992 7.604164 CGATAGTACTCCCTCCGTAAACTAATA 59.396 40.741 0.00 0.00 0.00 0.98
1854 1993 6.429385 CGATAGTACTCCCTCCGTAAACTAAT 59.571 42.308 0.00 0.00 0.00 1.73
1855 1994 5.760253 CGATAGTACTCCCTCCGTAAACTAA 59.240 44.000 0.00 0.00 0.00 2.24
1856 1995 5.070446 TCGATAGTACTCCCTCCGTAAACTA 59.930 44.000 0.00 0.00 37.40 2.24
1857 1996 4.133078 CGATAGTACTCCCTCCGTAAACT 58.867 47.826 0.00 0.00 0.00 2.66
1858 1997 4.130118 TCGATAGTACTCCCTCCGTAAAC 58.870 47.826 0.00 0.00 37.40 2.01
1859 1998 4.422073 TCGATAGTACTCCCTCCGTAAA 57.578 45.455 0.00 0.00 37.40 2.01
1860 1999 4.422073 TTCGATAGTACTCCCTCCGTAA 57.578 45.455 0.00 0.00 37.40 3.18
1861 2000 4.141620 ACTTTCGATAGTACTCCCTCCGTA 60.142 45.833 6.75 0.00 37.40 4.02
1862 2001 3.212685 CTTTCGATAGTACTCCCTCCGT 58.787 50.000 0.00 0.00 37.40 4.69
1863 2002 3.212685 ACTTTCGATAGTACTCCCTCCG 58.787 50.000 6.75 0.00 37.40 4.63
1864 2003 4.463070 AGACTTTCGATAGTACTCCCTCC 58.537 47.826 8.59 0.00 37.40 4.30
1865 2004 6.453926 AAAGACTTTCGATAGTACTCCCTC 57.546 41.667 8.59 0.00 37.40 4.30
1866 2005 7.951347 TTAAAGACTTTCGATAGTACTCCCT 57.049 36.000 8.59 0.00 37.40 4.20
1944 2083 7.010183 CAGATATACGACCGAATTGTTCTTTGT 59.990 37.037 0.00 0.00 0.00 2.83
1961 2100 6.247727 ACAGATGCTACTGACAGATATACG 57.752 41.667 10.08 0.00 40.63 3.06
2012 2157 2.164422 GGTAGGCATTCAGACTTTTGGC 59.836 50.000 0.00 0.00 36.54 4.52
2129 2275 5.641209 CAGGGCTCTGCAATACAAGATATAC 59.359 44.000 0.00 0.00 33.86 1.47
2207 2353 2.985957 TCATCCTGATCACGCATCAA 57.014 45.000 0.00 0.00 41.25 2.57
2293 2439 1.912731 TCCCATGATCCTTCCACGAAA 59.087 47.619 0.00 0.00 0.00 3.46
2369 2515 7.362056 GCCTGCTATTTCATCAAGTTTCAGTTA 60.362 37.037 0.00 0.00 0.00 2.24
2390 2536 3.077359 ACTGTCAGTATTTCAAGCCTGC 58.923 45.455 2.87 0.00 0.00 4.85
2393 2539 2.162408 GGCACTGTCAGTATTTCAAGCC 59.838 50.000 4.85 8.74 0.00 4.35
2478 2624 4.164981 TGTACCTGTAAACTCCTGATGGT 58.835 43.478 0.00 0.00 34.23 3.55
2494 2640 3.004839 CCATCGACGATGAATCTGTACCT 59.995 47.826 33.73 0.00 42.09 3.08
2514 2660 3.385115 GGGGAGGTATCTTCTTTCTCCA 58.615 50.000 9.49 0.00 44.17 3.86
2517 2663 3.399952 TCGGGGAGGTATCTTCTTTCT 57.600 47.619 0.00 0.00 0.00 2.52
2676 2861 2.101249 CACAAAGTCCTGCACCAATTGT 59.899 45.455 4.43 0.00 30.71 2.71
2683 2868 2.908073 CGGGCACAAAGTCCTGCAC 61.908 63.158 0.00 0.00 40.99 4.57
2700 2885 0.597637 ACACGCTCTCCACACTTTCG 60.598 55.000 0.00 0.00 0.00 3.46
2706 2891 2.596338 TCCGACACGCTCTCCACA 60.596 61.111 0.00 0.00 0.00 4.17
2808 2993 1.592669 CAGATAGAGTTGCGCCGGG 60.593 63.158 4.18 0.00 0.00 5.73
2817 3002 0.684479 TGAGCACGCCCAGATAGAGT 60.684 55.000 0.00 0.00 0.00 3.24
2823 3008 2.343758 GAGTTGAGCACGCCCAGA 59.656 61.111 0.00 0.00 0.00 3.86
3043 3228 3.885777 CGAAAATCCTCTCGCTTGC 57.114 52.632 0.00 0.00 0.00 4.01
3155 3341 6.882610 TTATTCTTGACAAATGACTGCAGT 57.117 33.333 21.88 21.88 0.00 4.40
3263 3449 8.968242 GTTTTCTTAGGATTTTACAAACAGCAG 58.032 33.333 0.00 0.00 0.00 4.24
3272 3458 7.039993 TCCTGGCAAGTTTTCTTAGGATTTTAC 60.040 37.037 0.00 0.00 37.31 2.01
3273 3459 7.007723 TCCTGGCAAGTTTTCTTAGGATTTTA 58.992 34.615 0.00 0.00 37.31 1.52
3305 3491 6.296836 CCCTCCCCTTTACACTTGTATAAGTT 60.297 42.308 1.55 0.00 44.57 2.66
3309 3495 4.702196 ACCCTCCCCTTTACACTTGTATA 58.298 43.478 0.00 0.00 0.00 1.47
3313 3499 2.355818 GCTACCCTCCCCTTTACACTTG 60.356 54.545 0.00 0.00 0.00 3.16
3316 3502 0.545171 GGCTACCCTCCCCTTTACAC 59.455 60.000 0.00 0.00 0.00 2.90
3318 3504 0.622446 TGGGCTACCCTCCCCTTTAC 60.622 60.000 3.93 0.00 45.70 2.01
3319 3505 0.327191 CTGGGCTACCCTCCCCTTTA 60.327 60.000 3.93 0.00 45.70 1.85
3323 3509 2.446802 CTCTGGGCTACCCTCCCC 60.447 72.222 3.93 0.00 45.70 4.81
3324 3510 2.446802 CCTCTGGGCTACCCTCCC 60.447 72.222 3.93 0.00 45.70 4.30
3370 3591 3.314331 CGTCAGGACACTGGGCCT 61.314 66.667 4.53 0.00 44.99 5.19
3397 3627 0.833409 TCAGTCCTCCAGCTCTGCAA 60.833 55.000 0.00 0.00 0.00 4.08
3477 3707 1.000385 CCGCTGGCATCTTTCAAACAA 60.000 47.619 0.00 0.00 0.00 2.83
3611 3841 0.930310 CACGTATCATGCCCAACGAG 59.070 55.000 13.37 4.67 38.64 4.18
3612 3842 0.248012 ACACGTATCATGCCCAACGA 59.752 50.000 13.37 0.00 38.64 3.85
3613 3843 1.929230 TACACGTATCATGCCCAACG 58.071 50.000 0.00 7.20 40.99 4.10
3616 3846 2.616376 GCAAATACACGTATCATGCCCA 59.384 45.455 13.14 0.00 34.72 5.36
3618 3848 3.961477 TGCAAATACACGTATCATGCC 57.039 42.857 18.00 7.40 37.43 4.40
3626 3856 5.404968 CACATGGAAATTTGCAAATACACGT 59.595 36.000 24.35 18.08 30.51 4.49
3654 3884 7.988028 ACCAAAAGAGTTATAGTAGAAGATGGC 59.012 37.037 0.00 0.00 0.00 4.40
3702 3934 2.440409 CCCATGAAGCCCAGCATATAC 58.560 52.381 0.00 0.00 0.00 1.47
3703 3935 1.355381 CCCCATGAAGCCCAGCATATA 59.645 52.381 0.00 0.00 0.00 0.86
3704 3936 0.113776 CCCCATGAAGCCCAGCATAT 59.886 55.000 0.00 0.00 0.00 1.78
3705 3937 0.992970 TCCCCATGAAGCCCAGCATA 60.993 55.000 0.00 0.00 0.00 3.14
3706 3938 1.661990 ATCCCCATGAAGCCCAGCAT 61.662 55.000 0.00 0.00 0.00 3.79
3707 3939 1.877672 AATCCCCATGAAGCCCAGCA 61.878 55.000 0.00 0.00 0.00 4.41
3708 3940 1.075748 AATCCCCATGAAGCCCAGC 60.076 57.895 0.00 0.00 0.00 4.85
3709 3941 0.259647 TCAATCCCCATGAAGCCCAG 59.740 55.000 0.00 0.00 0.00 4.45
3710 3942 0.935942 ATCAATCCCCATGAAGCCCA 59.064 50.000 0.00 0.00 0.00 5.36
3712 3944 2.671896 AGATCAATCCCCATGAAGCC 57.328 50.000 0.00 0.00 0.00 4.35
3713 3945 3.830121 AGAAGATCAATCCCCATGAAGC 58.170 45.455 0.00 0.00 0.00 3.86
3714 3946 6.540995 ACATAGAAGATCAATCCCCATGAAG 58.459 40.000 0.00 0.00 0.00 3.02
3716 3948 6.126390 ACAACATAGAAGATCAATCCCCATGA 60.126 38.462 0.00 0.00 0.00 3.07
3717 3949 6.066690 ACAACATAGAAGATCAATCCCCATG 58.933 40.000 0.00 0.66 0.00 3.66
3718 3950 6.271585 ACAACATAGAAGATCAATCCCCAT 57.728 37.500 0.00 0.00 0.00 4.00
3742 3974 4.302455 CTCCTGAGAAATGTACATAGCGG 58.698 47.826 9.21 4.73 0.00 5.52
3749 3981 3.526534 GCAGACCTCCTGAGAAATGTAC 58.473 50.000 0.00 0.00 45.78 2.90
3757 3989 2.575993 CACCGCAGACCTCCTGAG 59.424 66.667 0.00 0.00 45.78 3.35
3762 3994 1.142748 CATCTCCACCGCAGACCTC 59.857 63.158 0.00 0.00 0.00 3.85
3769 4001 7.298122 CACAATTATATTTACATCTCCACCGC 58.702 38.462 0.00 0.00 0.00 5.68
3771 4003 8.396272 AGCACAATTATATTTACATCTCCACC 57.604 34.615 0.00 0.00 0.00 4.61
3800 4032 5.021458 AGGTGTCCTTTCTTAACGAGGATA 58.979 41.667 0.00 0.00 41.33 2.59
3871 4105 5.981315 TCTACGCGTATGGAATCTTTTTAGG 59.019 40.000 20.91 1.98 0.00 2.69
3872 4106 7.459394 TTCTACGCGTATGGAATCTTTTTAG 57.541 36.000 20.91 4.38 0.00 1.85
3873 4107 6.019318 GCTTCTACGCGTATGGAATCTTTTTA 60.019 38.462 20.91 0.00 0.00 1.52
3917 4167 9.400638 GATAGGCGTCATAGCATAGTATTATTC 57.599 37.037 0.00 0.00 36.81 1.75
3973 4223 7.095270 TCCTTCTCTAAAACAACGATAAGGTC 58.905 38.462 0.00 0.00 34.48 3.85


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

AutoCloner maintained by Alex Coulton.