Multiple sequence alignment - TraesCS1B01G115200

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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 TraesCS1B01G115200 chr1B 100.000 6573 0 0 1 6573 135811936 135818508 0.000000e+00 12139.0
1 TraesCS1B01G115200 chr4D 94.831 2515 92 19 3479 5968 329139363 329136862 0.000000e+00 3890.0
2 TraesCS1B01G115200 chr4D 95.632 1099 20 6 2331 3401 329140478 329139380 0.000000e+00 1738.0
3 TraesCS1B01G115200 chr4D 94.952 1050 31 9 1 1031 329179465 329178419 0.000000e+00 1626.0
4 TraesCS1B01G115200 chr4D 88.785 856 51 22 1027 1852 329143788 329142948 0.000000e+00 1007.0
5 TraesCS1B01G115200 chr4D 95.687 371 14 1 1849 2219 329142919 329142551 4.390000e-166 595.0
6 TraesCS1B01G115200 chr4D 89.297 327 21 7 6252 6573 329136450 329136133 1.330000e-106 398.0
7 TraesCS1B01G115200 chr4D 78.378 222 22 16 5967 6180 329136655 329136452 3.220000e-23 121.0
8 TraesCS1B01G115200 chr4D 82.857 105 2 4 2237 2334 329140636 329140541 5.460000e-11 80.5
9 TraesCS1B01G115200 chr4A 95.226 1927 75 11 3937 5862 140978051 140979961 0.000000e+00 3033.0
10 TraesCS1B01G115200 chr4A 95.492 732 32 1 2331 3061 140975983 140976714 0.000000e+00 1168.0
11 TraesCS1B01G115200 chr4A 95.690 464 20 0 4413 4876 253273776 253274239 0.000000e+00 747.0
12 TraesCS1B01G115200 chr4A 88.608 474 25 9 3479 3951 140977485 140977930 3.460000e-152 549.0
13 TraesCS1B01G115200 chr4A 87.927 439 20 11 3059 3472 140976971 140977401 2.760000e-133 486.0
14 TraesCS1B01G115200 chr4A 87.500 392 43 4 1851 2240 140974697 140975084 1.300000e-121 448.0
15 TraesCS1B01G115200 chr4A 79.895 572 52 31 6006 6573 140980364 140980876 1.740000e-95 361.0
16 TraesCS1B01G115200 chr4A 85.455 110 4 7 5869 5968 140980030 140980137 3.240000e-18 104.0
17 TraesCS1B01G115200 chr4B 96.233 1407 51 2 4431 5836 408980732 408979327 0.000000e+00 2303.0
18 TraesCS1B01G115200 chr4B 93.545 1100 34 9 2331 3401 408984427 408983336 0.000000e+00 1604.0
19 TraesCS1B01G115200 chr4B 91.467 961 50 16 3479 4435 408983319 408982387 0.000000e+00 1291.0
20 TraesCS1B01G115200 chr4B 79.092 617 53 32 5967 6573 408978890 408978340 8.110000e-94 355.0
21 TraesCS1B01G115200 chr7B 86.176 1577 169 31 4016 5574 629581295 629579750 0.000000e+00 1659.0
22 TraesCS1B01G115200 chr7B 83.658 667 79 19 2496 3142 629582717 629582061 9.430000e-168 601.0
23 TraesCS1B01G115200 chr7B 86.245 269 23 7 3269 3535 629581583 629581327 5.020000e-71 279.0
24 TraesCS1B01G115200 chr7B 81.739 115 17 4 2078 2190 649855056 649855168 7.020000e-15 93.5
25 TraesCS1B01G115200 chr7D 81.827 2047 255 75 2487 4478 572549022 572551006 0.000000e+00 1611.0
26 TraesCS1B01G115200 chr7D 85.505 1228 138 26 4492 5708 572553697 572554895 0.000000e+00 1245.0
27 TraesCS1B01G115200 chr7A 84.645 1296 158 28 4426 5708 661594034 661595301 0.000000e+00 1253.0
28 TraesCS1B01G115200 chr7A 82.523 761 103 18 2392 3142 661589247 661589987 5.560000e-180 641.0
29 TraesCS1B01G115200 chr7A 86.538 364 32 11 3226 3584 661590315 661590666 1.030000e-102 385.0
30 TraesCS1B01G115200 chr7A 81.087 460 59 13 3762 4215 661590686 661591123 6.310000e-90 342.0
31 TraesCS1B01G115200 chr3A 87.143 140 8 5 6430 6569 55173387 55173516 4.110000e-32 150.0
32 TraesCS1B01G115200 chr5B 86.429 140 9 5 6430 6569 544815064 544815193 1.910000e-30 145.0


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 TraesCS1B01G115200 chr1B 135811936 135818508 6572 False 12139.000000 12139 100.000000 1 6573 1 chr1B.!!$F1 6572
1 TraesCS1B01G115200 chr4D 329178419 329179465 1046 True 1626.000000 1626 94.952000 1 1031 1 chr4D.!!$R1 1030
2 TraesCS1B01G115200 chr4D 329136133 329143788 7655 True 1118.500000 3890 89.352429 1027 6573 7 chr4D.!!$R2 5546
3 TraesCS1B01G115200 chr4A 140974697 140980876 6179 False 878.428571 3033 88.586143 1851 6573 7 chr4A.!!$F2 4722
4 TraesCS1B01G115200 chr4B 408978340 408984427 6087 True 1388.250000 2303 90.084250 2331 6573 4 chr4B.!!$R1 4242
5 TraesCS1B01G115200 chr7B 629579750 629582717 2967 True 846.333333 1659 85.359667 2496 5574 3 chr7B.!!$R1 3078
6 TraesCS1B01G115200 chr7D 572549022 572554895 5873 False 1428.000000 1611 83.666000 2487 5708 2 chr7D.!!$F1 3221
7 TraesCS1B01G115200 chr7A 661589247 661595301 6054 False 655.250000 1253 83.698250 2392 5708 4 chr7A.!!$F1 3316

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
288 289 0.668706 CACTGTGCTTCCCGAGTCAG 60.669 60.000 0.00 0.0 36.38 3.51 F
962 970 1.072331 ACAGGAGTGGAACGAGCAAAT 59.928 47.619 0.00 0.0 45.86 2.32 F
1751 1833 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
1752 1834 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82 F
1754 1836 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82 F
1757 1839 1.001974 ACACACACACACACACACTCT 59.998 47.619 0.00 0.0 0.00 3.24 F
3618 7107 0.890542 GAGACTGCACATGTGGCCAA 60.891 55.000 26.55 0.0 0.00 4.52 F
5260 15953 0.464193 TGTGCACTGCTGCTTCTCAA 60.464 50.000 19.41 0.0 44.57 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1630 0.038526 AAACAGAGCGTCGGTACCTG 60.039 55.000 10.90 10.56 0.00 4.00 R
2630 5397 1.108776 ACAGTACATGTATCGGCGGT 58.891 50.000 9.18 0.65 41.60 5.68 R
3594 7069 0.322648 CACATGTGCAGTCTCCTCCA 59.677 55.000 13.94 0.00 0.00 3.86 R
3603 7078 0.390124 AGTTTTGGCCACATGTGCAG 59.610 50.000 20.81 9.00 0.00 4.41 R
3611 7100 3.118905 TGGCATTTTAGTTTTGGCCAC 57.881 42.857 3.88 0.00 45.69 5.01 R
3652 7142 5.776173 TGGATTAAAAGAAAAAGGTCGCA 57.224 34.783 0.00 0.00 0.00 5.10 R
5536 16229 0.109551 TCAGTCTTCTCGCAGCTTCG 60.110 55.000 0.00 0.00 0.00 3.79 R
6197 17317 0.879400 CGACAGGATGATGCTGGAGC 60.879 60.000 18.22 6.32 40.38 4.70 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
54 55 5.070446 TCCACTATCACTTGGGTATCACATC 59.930 44.000 0.00 0.00 33.25 3.06
114 115 1.745653 GCACTTCCTTAATGAGGCCAC 59.254 52.381 5.01 0.00 45.87 5.01
116 117 1.065418 ACTTCCTTAATGAGGCCACCG 60.065 52.381 5.01 0.00 45.87 4.94
170 171 4.127171 TCAGACTTGGTTGCTTGAGTAAC 58.873 43.478 3.72 3.72 39.44 2.50
288 289 0.668706 CACTGTGCTTCCCGAGTCAG 60.669 60.000 0.00 0.00 36.38 3.51
384 385 1.339610 CTCAAATTTCCCACAACGGCA 59.660 47.619 0.00 0.00 0.00 5.69
464 471 3.326747 GGTTGACTACCAAGTGCTACTG 58.673 50.000 0.76 0.00 46.92 2.74
520 527 4.935352 AGCTGTTGTAGATCTCTCATCC 57.065 45.455 0.00 0.00 0.00 3.51
547 554 7.872483 ACAGTTTGGAAACATTCAAATATGGTC 59.128 33.333 5.11 0.00 42.32 4.02
640 647 9.119512 TCCCTTTTAATAGTTTTTCCTCCTCTA 57.880 33.333 0.00 0.00 0.00 2.43
772 780 8.993121 CATATTGAGCCTTTTCTAATACACGAT 58.007 33.333 0.00 0.00 0.00 3.73
819 827 9.605275 TGAACAAATTTGGATTACACAATGAAA 57.395 25.926 21.74 0.00 0.00 2.69
962 970 1.072331 ACAGGAGTGGAACGAGCAAAT 59.928 47.619 0.00 0.00 45.86 2.32
1011 1031 3.425162 ACCTTCAAGATGGTTCTGGTC 57.575 47.619 2.07 0.00 35.58 4.02
1062 1082 5.274015 TGGTTTCTTTTAGTGGGTTCCTTT 58.726 37.500 0.00 0.00 0.00 3.11
1079 1099 8.649591 GGGTTCCTTTGGGTTATTTTAACTTTA 58.350 33.333 0.00 0.00 0.00 1.85
1304 1332 9.540431 CAAAACAAAAATTCAGAAAATGTTCGT 57.460 25.926 6.66 0.00 38.90 3.85
1310 1338 8.661352 AAAATTCAGAAAATGTTCGTGGATTT 57.339 26.923 7.81 7.81 38.90 2.17
1495 1537 3.794270 CCGGCTGGTACAATGACG 58.206 61.111 2.29 0.00 38.70 4.35
1500 1542 1.076332 GCTGGTACAATGACGTGGTC 58.924 55.000 0.00 0.00 38.70 4.02
1549 1591 7.554211 AGATACAGTGGACGATCGATATAGTA 58.446 38.462 24.34 15.99 0.00 1.82
1643 1685 5.895636 TTTGACTCACAAAAGTGTCACAT 57.104 34.783 5.62 0.00 44.16 3.21
1644 1686 5.484173 TTGACTCACAAAAGTGTCACATC 57.516 39.130 5.62 0.00 40.48 3.06
1645 1687 4.769688 TGACTCACAAAAGTGTCACATCT 58.230 39.130 5.62 0.00 37.17 2.90
1686 1735 4.547671 TCTCCCTGATTCTCTATCCGTTT 58.452 43.478 0.00 0.00 31.87 3.60
1687 1736 4.585162 TCTCCCTGATTCTCTATCCGTTTC 59.415 45.833 0.00 0.00 31.87 2.78
1688 1737 4.547671 TCCCTGATTCTCTATCCGTTTCT 58.452 43.478 0.00 0.00 31.87 2.52
1689 1738 4.585162 TCCCTGATTCTCTATCCGTTTCTC 59.415 45.833 0.00 0.00 31.87 2.87
1690 1739 4.586841 CCCTGATTCTCTATCCGTTTCTCT 59.413 45.833 0.00 0.00 31.87 3.10
1692 1741 5.278758 CCTGATTCTCTATCCGTTTCTCTCC 60.279 48.000 0.00 0.00 31.87 3.71
1693 1742 4.585162 TGATTCTCTATCCGTTTCTCTCCC 59.415 45.833 0.00 0.00 31.87 4.30
1694 1743 3.664551 TCTCTATCCGTTTCTCTCCCA 57.335 47.619 0.00 0.00 0.00 4.37
1695 1744 4.186077 TCTCTATCCGTTTCTCTCCCAT 57.814 45.455 0.00 0.00 0.00 4.00
1731 1813 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1732 1814 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1733 1815 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
1734 1816 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
1735 1817 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
1736 1818 4.160439 TCTCTCTCTCTCTCTCTCTCACAC 59.840 50.000 0.00 0.00 0.00 3.82
1737 1819 3.837731 TCTCTCTCTCTCTCTCTCACACA 59.162 47.826 0.00 0.00 0.00 3.72
1738 1820 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
1739 1821 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
1740 1822 3.407698 TCTCTCTCTCTCTCACACACAC 58.592 50.000 0.00 0.00 0.00 3.82
1741 1823 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
1742 1824 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
1743 1825 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
1744 1826 2.359214 TCTCTCTCTCACACACACACAC 59.641 50.000 0.00 0.00 0.00 3.82
1745 1827 2.099405 TCTCTCTCACACACACACACA 58.901 47.619 0.00 0.00 0.00 3.72
1746 1828 2.159240 TCTCTCTCACACACACACACAC 60.159 50.000 0.00 0.00 0.00 3.82
1747 1829 1.548269 TCTCTCACACACACACACACA 59.452 47.619 0.00 0.00 0.00 3.72
1748 1830 1.660607 CTCTCACACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
1749 1831 1.001406 TCTCACACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
1750 1832 1.128507 CTCACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
1751 1833 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1752 1834 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1753 1835 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1754 1836 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1755 1837 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
1756 1838 1.128507 CACACACACACACACACACTC 59.871 52.381 0.00 0.00 0.00 3.51
1757 1839 1.001974 ACACACACACACACACACTCT 59.998 47.619 0.00 0.00 0.00 3.24
1758 1840 1.660607 CACACACACACACACACTCTC 59.339 52.381 0.00 0.00 0.00 3.20
1759 1841 1.550524 ACACACACACACACACTCTCT 59.449 47.619 0.00 0.00 0.00 3.10
1760 1842 2.196749 CACACACACACACACTCTCTC 58.803 52.381 0.00 0.00 0.00 3.20
1761 1843 2.103373 ACACACACACACACTCTCTCT 58.897 47.619 0.00 0.00 0.00 3.10
1762 1844 2.159184 ACACACACACACACTCTCTCTG 60.159 50.000 0.00 0.00 0.00 3.35
1763 1845 2.103373 ACACACACACACTCTCTCTGT 58.897 47.619 0.00 0.00 0.00 3.41
1764 1846 2.099921 ACACACACACACTCTCTCTGTC 59.900 50.000 0.00 0.00 0.00 3.51
1765 1847 1.683917 ACACACACACTCTCTCTGTCC 59.316 52.381 0.00 0.00 0.00 4.02
1766 1848 1.959985 CACACACACTCTCTCTGTCCT 59.040 52.381 0.00 0.00 0.00 3.85
1767 1849 2.030363 CACACACACTCTCTCTGTCCTC 60.030 54.545 0.00 0.00 0.00 3.71
1768 1850 2.158534 ACACACACTCTCTCTGTCCTCT 60.159 50.000 0.00 0.00 0.00 3.69
1769 1851 2.890311 CACACACTCTCTCTGTCCTCTT 59.110 50.000 0.00 0.00 0.00 2.85
1770 1852 3.320541 CACACACTCTCTCTGTCCTCTTT 59.679 47.826 0.00 0.00 0.00 2.52
1771 1853 3.572255 ACACACTCTCTCTGTCCTCTTTC 59.428 47.826 0.00 0.00 0.00 2.62
1772 1854 3.826157 CACACTCTCTCTGTCCTCTTTCT 59.174 47.826 0.00 0.00 0.00 2.52
1773 1855 4.079253 ACACTCTCTCTGTCCTCTTTCTC 58.921 47.826 0.00 0.00 0.00 2.87
1774 1856 4.202567 ACACTCTCTCTGTCCTCTTTCTCT 60.203 45.833 0.00 0.00 0.00 3.10
1775 1857 4.396166 CACTCTCTCTGTCCTCTTTCTCTC 59.604 50.000 0.00 0.00 0.00 3.20
1839 1921 3.253677 AGTCGTTTCCTCTCTGTGTAGTG 59.746 47.826 0.00 0.00 0.00 2.74
1857 1971 3.840991 AGTGGCGATGTAGGATTAGGTA 58.159 45.455 0.00 0.00 0.00 3.08
1934 2048 4.200283 CGGCGGAGGAGTCAGCTC 62.200 72.222 0.00 0.00 42.93 4.09
2004 2118 1.302511 CCACTCTTGGGTTGACGGG 60.303 63.158 0.00 0.00 39.57 5.28
2028 2142 2.180204 GGTGCACGACAACACTGCT 61.180 57.895 11.45 0.00 35.37 4.24
2105 2219 7.859325 TTACTCTGCATATAAGTTTTGACCC 57.141 36.000 0.00 0.00 0.00 4.46
2266 4278 3.584406 TGCAGCTAACTGTCTTCTCTC 57.416 47.619 0.00 0.00 46.30 3.20
2306 4995 2.813908 GGTAACACGGAGCAGCGG 60.814 66.667 0.00 0.00 0.00 5.52
2455 5214 2.764547 CTCCCCGGTCCTTCCTCC 60.765 72.222 0.00 0.00 0.00 4.30
2618 5385 1.012671 GTTAATGTACGCTGCGCCG 60.013 57.895 23.51 4.34 0.00 6.46
2922 5697 1.989620 CCAGAAGAAGGGCAGCTCT 59.010 57.895 0.00 0.00 0.00 4.09
3010 5785 3.381272 CGGAGGTCATAACAAATGCCATT 59.619 43.478 0.00 0.00 0.00 3.16
3175 6444 5.185442 TCTTGGCAAAATGTTCATGCTCATA 59.815 36.000 0.00 0.00 39.94 2.15
3227 6496 6.973474 GCTACTCAAATATTCGACACAGTACT 59.027 38.462 0.00 0.00 0.00 2.73
3279 6670 4.776743 CATAATTCCTCTTTCGCAATCCG 58.223 43.478 0.00 0.00 38.61 4.18
3300 6692 3.122948 CGTATTGTTCTTTGACGGGTCTG 59.877 47.826 0.00 0.00 0.00 3.51
3321 6713 3.865164 TGCATATAAACACAGAGAGCACG 59.135 43.478 0.00 0.00 0.00 5.34
3402 6794 9.982651 GGTAATATTGCTTCTCACTTCACTATA 57.017 33.333 3.46 0.00 0.00 1.31
3405 6797 8.894768 ATATTGCTTCTCACTTCACTATAACC 57.105 34.615 0.00 0.00 0.00 2.85
3406 6798 6.360370 TTGCTTCTCACTTCACTATAACCT 57.640 37.500 0.00 0.00 0.00 3.50
3407 6799 5.967088 TGCTTCTCACTTCACTATAACCTC 58.033 41.667 0.00 0.00 0.00 3.85
3408 6800 5.105310 TGCTTCTCACTTCACTATAACCTCC 60.105 44.000 0.00 0.00 0.00 4.30
3618 7107 0.890542 GAGACTGCACATGTGGCCAA 60.891 55.000 26.55 0.00 0.00 4.52
3652 7142 8.574251 TGCCATATGTTTCTGTTTACTAATGT 57.426 30.769 1.24 0.00 0.00 2.71
3655 7145 7.639850 CCATATGTTTCTGTTTACTAATGTGCG 59.360 37.037 1.24 0.00 0.00 5.34
3666 7157 6.870971 TTACTAATGTGCGACCTTTTTCTT 57.129 33.333 0.00 0.00 0.00 2.52
3794 7285 5.610982 AGGAAAGATGGTATGCTAACCCATA 59.389 40.000 5.71 0.00 39.06 2.74
3859 7350 8.702438 CATTTAGTTATGGCTTTTGAACTGTTG 58.298 33.333 0.00 0.00 34.15 3.33
3869 7360 3.557577 TTGAACTGTTGATTCCATGCG 57.442 42.857 0.00 0.00 0.00 4.73
3888 7379 3.994392 TGCGTTAGATTTTCTGTCTGGAC 59.006 43.478 0.00 0.00 0.00 4.02
3954 7580 4.399303 ACTGGCTTATCCAAATACTTGTGC 59.601 41.667 0.00 0.00 46.01 4.57
4274 8293 8.816640 TTTTATGCTTCAAATTTCAGGTTCTC 57.183 30.769 0.00 0.00 0.00 2.87
4304 8323 7.094634 GGATCTAAAGTGAAGATTGCAGTTCAA 60.095 37.037 9.14 0.00 39.32 2.69
4305 8324 7.194607 TCTAAAGTGAAGATTGCAGTTCAAG 57.805 36.000 9.14 4.89 38.22 3.02
4371 8391 9.810545 TTAAACTTCAGTTGTTTTTCCCTTATG 57.189 29.630 0.00 0.00 38.44 1.90
4580 15263 3.049708 TCAGCAGGATGTTCAGAAGTG 57.950 47.619 0.00 0.00 39.31 3.16
4600 15283 8.408601 AGAAGTGTGGAAATATTGAATACATGC 58.591 33.333 0.00 0.00 0.00 4.06
4647 15330 1.918957 CCTGATCTTTCCAAGGTCCCT 59.081 52.381 0.00 0.00 37.87 4.20
4813 15496 1.851304 TGACAGCCCAAAATCCATCC 58.149 50.000 0.00 0.00 0.00 3.51
4982 15674 6.119536 TGGACCTGTATCATTATGGTTTGTC 58.880 40.000 0.00 0.00 0.00 3.18
5260 15953 0.464193 TGTGCACTGCTGCTTCTCAA 60.464 50.000 19.41 0.00 44.57 3.02
5317 16010 3.830178 TCGGATTCTACAAGGAGAACACA 59.170 43.478 0.00 0.00 38.25 3.72
5536 16229 4.142609 TGGCCACAGAGAGAACATTATC 57.857 45.455 0.00 0.00 0.00 1.75
5574 16267 5.738909 ACTGAAGCAGCTATACAAATGAGT 58.261 37.500 0.00 0.00 34.37 3.41
5631 16324 1.340991 GCCAGGCAATAAGAACCCAGA 60.341 52.381 6.55 0.00 0.00 3.86
5645 16338 1.272872 ACCCAGAAGCATTTGGAGCAT 60.273 47.619 0.00 0.00 36.55 3.79
5649 16342 2.753452 CAGAAGCATTTGGAGCATGAGT 59.247 45.455 0.00 0.00 0.00 3.41
5692 16385 3.577919 AGTGTTAGAACAGAGACAGGGT 58.422 45.455 0.00 0.00 40.05 4.34
5708 16401 1.136110 AGGGTTGTTGTTTTTGCTCCG 59.864 47.619 0.00 0.00 0.00 4.63
5731 16424 6.019318 CCGTTCGTAACCATTTAATACTGGAG 60.019 42.308 6.31 0.00 36.35 3.86
5778 16471 7.869937 CGGAGTCTATCATGATGTATTTGTCTT 59.130 37.037 18.72 0.00 0.00 3.01
5807 16500 0.373716 CGTTGACGGCCTTATGCTTC 59.626 55.000 0.00 0.00 40.92 3.86
5819 16512 4.371786 CCTTATGCTTCTTGCTACGATGA 58.628 43.478 0.00 0.00 43.37 2.92
5836 16529 1.367346 TGATGTGCACCTCCCCTTTA 58.633 50.000 15.69 0.00 0.00 1.85
5863 16556 8.152898 TCTCCTACTGCATATCTAAAGTACGTA 58.847 37.037 0.00 0.00 0.00 3.57
5929 16685 1.755179 GGTAGACCAAGTGCATGCAT 58.245 50.000 25.64 7.13 35.64 3.96
5930 16686 1.402968 GGTAGACCAAGTGCATGCATG 59.597 52.381 25.64 22.70 35.64 4.06
5931 16687 2.086869 GTAGACCAAGTGCATGCATGT 58.913 47.619 25.64 18.05 0.00 3.21
5933 16689 0.883153 GACCAAGTGCATGCATGTGA 59.117 50.000 25.64 12.10 0.00 3.58
5934 16690 1.270274 GACCAAGTGCATGCATGTGAA 59.730 47.619 25.64 11.22 0.00 3.18
5935 16691 1.687660 ACCAAGTGCATGCATGTGAAA 59.312 42.857 25.64 8.76 0.00 2.69
5963 16727 0.749454 AGACCGATCCATTGCTTGCC 60.749 55.000 0.00 0.00 0.00 4.52
5983 17092 1.452833 CAGCTAAGGCCAAGGCTCC 60.453 63.158 5.01 0.00 37.50 4.70
5984 17093 1.617839 AGCTAAGGCCAAGGCTCCT 60.618 57.895 5.01 0.00 37.50 3.69
5985 17094 1.153066 GCTAAGGCCAAGGCTCCTC 60.153 63.158 5.01 0.00 37.50 3.71
5986 17095 1.144936 CTAAGGCCAAGGCTCCTCG 59.855 63.158 5.01 0.00 37.50 4.63
6019 17128 7.492669 TCCAGCTGTCTCTTTTATAATTCTTCG 59.507 37.037 13.81 0.00 0.00 3.79
6020 17129 7.492669 CCAGCTGTCTCTTTTATAATTCTTCGA 59.507 37.037 13.81 0.00 0.00 3.71
6049 17167 3.340814 TCTTCTTCCATGTCTGCTTCC 57.659 47.619 0.00 0.00 0.00 3.46
6051 17169 3.328931 TCTTCTTCCATGTCTGCTTCCTT 59.671 43.478 0.00 0.00 0.00 3.36
6073 17191 2.290367 TGTTGCATCACCTGTTTCTTCG 59.710 45.455 0.00 0.00 0.00 3.79
6079 17197 0.859232 CACCTGTTTCTTCGTCACCG 59.141 55.000 0.00 0.00 0.00 4.94
6091 17211 3.311110 TCACCGTCAGCTCCACCC 61.311 66.667 0.00 0.00 0.00 4.61
6092 17212 3.314331 CACCGTCAGCTCCACCCT 61.314 66.667 0.00 0.00 0.00 4.34
6093 17213 2.997897 ACCGTCAGCTCCACCCTC 60.998 66.667 0.00 0.00 0.00 4.30
6094 17214 2.997315 CCGTCAGCTCCACCCTCA 60.997 66.667 0.00 0.00 0.00 3.86
6095 17215 2.362369 CCGTCAGCTCCACCCTCAT 61.362 63.158 0.00 0.00 0.00 2.90
6097 17217 1.451028 GTCAGCTCCACCCTCATGC 60.451 63.158 0.00 0.00 0.00 4.06
6099 17219 4.479993 AGCTCCACCCTCATGCGC 62.480 66.667 0.00 0.00 0.00 6.09
6100 17220 4.783621 GCTCCACCCTCATGCGCA 62.784 66.667 14.96 14.96 0.00 6.09
6101 17221 2.513204 CTCCACCCTCATGCGCAG 60.513 66.667 18.32 8.46 0.00 5.18
6121 17241 1.788258 CATTGTCTGCAGTGAGTCGT 58.212 50.000 14.67 0.00 34.71 4.34
6122 17242 2.946564 CATTGTCTGCAGTGAGTCGTA 58.053 47.619 14.67 0.00 34.71 3.43
6123 17243 2.706555 TTGTCTGCAGTGAGTCGTAG 57.293 50.000 14.67 0.00 0.00 3.51
6124 17244 1.892209 TGTCTGCAGTGAGTCGTAGA 58.108 50.000 14.67 0.00 0.00 2.59
6125 17245 1.807142 TGTCTGCAGTGAGTCGTAGAG 59.193 52.381 14.67 0.00 36.95 2.43
6126 17246 1.807742 GTCTGCAGTGAGTCGTAGAGT 59.192 52.381 14.67 0.00 46.63 3.24
6127 17247 2.226912 GTCTGCAGTGAGTCGTAGAGTT 59.773 50.000 14.67 0.00 42.24 3.01
6128 17248 2.885266 TCTGCAGTGAGTCGTAGAGTTT 59.115 45.455 14.67 0.00 42.24 2.66
6129 17249 3.318275 TCTGCAGTGAGTCGTAGAGTTTT 59.682 43.478 14.67 0.00 42.24 2.43
6149 17269 7.840931 AGTTTTCTCCTTCATTTTCACAAGTT 58.159 30.769 0.00 0.00 0.00 2.66
6154 17274 6.550854 TCTCCTTCATTTTCACAAGTTCCATT 59.449 34.615 0.00 0.00 0.00 3.16
6161 17281 6.403866 TTTTCACAAGTTCCATTAGCATGT 57.596 33.333 0.00 0.00 0.00 3.21
6180 17300 1.114722 TTTGTGCCAAAGCCTCCTGG 61.115 55.000 0.00 0.00 38.69 4.45
6183 17303 2.753446 GCCAAAGCCTCCTGGAGC 60.753 66.667 18.51 13.29 34.35 4.70
6184 17304 2.759114 CCAAAGCCTCCTGGAGCA 59.241 61.111 18.51 0.00 34.35 4.26
6185 17305 1.378250 CCAAAGCCTCCTGGAGCAG 60.378 63.158 18.51 6.89 34.35 4.24
6186 17306 2.045131 CAAAGCCTCCTGGAGCAGC 61.045 63.158 18.51 16.43 34.57 5.25
6187 17307 2.229928 AAAGCCTCCTGGAGCAGCT 61.230 57.895 18.51 18.38 30.67 4.24
6188 17308 2.195692 AAAGCCTCCTGGAGCAGCTC 62.196 60.000 22.43 14.69 28.71 4.09
6189 17309 3.082701 GCCTCCTGGAGCAGCTCT 61.083 66.667 21.99 0.00 34.57 4.09
6190 17310 2.901813 CCTCCTGGAGCAGCTCTG 59.098 66.667 21.99 14.36 34.57 3.35
6200 17320 4.205287 CAGCTCTGCTCCTTGCTC 57.795 61.111 0.00 0.00 43.37 4.26
6201 17321 1.449956 CAGCTCTGCTCCTTGCTCC 60.450 63.158 0.00 0.00 43.37 4.70
6216 17336 0.879400 GCTCCAGCATCATCCTGTCG 60.879 60.000 0.00 0.00 41.59 4.35
6217 17337 0.879400 CTCCAGCATCATCCTGTCGC 60.879 60.000 0.00 0.00 0.00 5.19
6221 17341 1.144716 GCATCATCCTGTCGCCAGA 59.855 57.895 0.00 0.00 41.50 3.86
6247 17367 0.396435 CAGGCCTGCCCAATATCGTA 59.604 55.000 22.33 0.00 36.58 3.43
6248 17368 0.396811 AGGCCTGCCCAATATCGTAC 59.603 55.000 3.11 0.00 36.58 3.67
6249 17369 0.396811 GGCCTGCCCAATATCGTACT 59.603 55.000 0.00 0.00 0.00 2.73
6252 17372 3.495453 GGCCTGCCCAATATCGTACTAAA 60.495 47.826 0.00 0.00 0.00 1.85
6253 17373 4.131596 GCCTGCCCAATATCGTACTAAAA 58.868 43.478 0.00 0.00 0.00 1.52
6255 17375 5.277828 GCCTGCCCAATATCGTACTAAAAAG 60.278 44.000 0.00 0.00 0.00 2.27
6256 17376 5.238650 CCTGCCCAATATCGTACTAAAAAGG 59.761 44.000 0.00 0.00 0.00 3.11
6259 17379 7.057894 TGCCCAATATCGTACTAAAAAGGAAT 58.942 34.615 0.00 0.00 0.00 3.01
6260 17380 8.212312 TGCCCAATATCGTACTAAAAAGGAATA 58.788 33.333 0.00 0.00 0.00 1.75
6286 17406 5.474532 GCATAACATATGAATTCAGCAGGGA 59.525 40.000 14.54 0.00 0.00 4.20
6294 17414 2.322355 ATTCAGCAGGGAATCTCACG 57.678 50.000 0.00 0.00 32.09 4.35
6319 17439 5.915196 AGCTTTTTATCGAAACAAGCTTGAC 59.085 36.000 32.50 19.91 41.26 3.18
6321 17441 6.129352 GCTTTTTATCGAAACAAGCTTGACTG 60.129 38.462 32.50 17.74 36.63 3.51
6339 17459 4.281941 TGACTGCGAATCTTCCATATAGCT 59.718 41.667 0.00 0.00 0.00 3.32
6340 17460 4.815269 ACTGCGAATCTTCCATATAGCTC 58.185 43.478 0.00 0.00 0.00 4.09
6376 17496 6.817641 TGCAAGCCCAACAATTTCAATATTAG 59.182 34.615 0.00 0.00 0.00 1.73
6385 17505 8.567948 CAACAATTTCAATATTAGGGCGACTAT 58.432 33.333 0.00 0.00 0.00 2.12
6387 17507 8.567948 ACAATTTCAATATTAGGGCGACTATTG 58.432 33.333 2.35 2.35 34.41 1.90
6479 17601 1.949547 GCAGCAGAGCACTGGAAGAAT 60.950 52.381 13.26 0.00 43.62 2.40
6485 17607 4.378774 CAGAGCACTGGAAGAATAGATGG 58.621 47.826 2.82 0.00 40.14 3.51
6488 17610 3.776969 AGCACTGGAAGAATAGATGGTGA 59.223 43.478 0.00 0.00 37.43 4.02
6505 17627 6.610830 AGATGGTGAATACTCTCAGATTCAGT 59.389 38.462 0.00 0.00 41.51 3.41
6506 17628 6.214191 TGGTGAATACTCTCAGATTCAGTC 57.786 41.667 0.00 0.00 41.51 3.51
6507 17629 5.716703 TGGTGAATACTCTCAGATTCAGTCA 59.283 40.000 0.00 0.00 41.51 3.41
6508 17630 6.382282 TGGTGAATACTCTCAGATTCAGTCAT 59.618 38.462 0.00 0.00 41.51 3.06
6509 17631 7.093156 TGGTGAATACTCTCAGATTCAGTCATT 60.093 37.037 0.00 0.00 41.51 2.57
6510 17632 7.437862 GGTGAATACTCTCAGATTCAGTCATTC 59.562 40.741 0.00 0.00 41.51 2.67
6511 17633 7.978414 GTGAATACTCTCAGATTCAGTCATTCA 59.022 37.037 0.00 0.00 41.51 2.57
6512 17634 8.196103 TGAATACTCTCAGATTCAGTCATTCAG 58.804 37.037 0.00 0.00 37.19 3.02
6513 17635 7.894753 ATACTCTCAGATTCAGTCATTCAGA 57.105 36.000 0.00 0.00 0.00 3.27
6514 17636 6.602410 ACTCTCAGATTCAGTCATTCAGAA 57.398 37.500 0.00 0.00 0.00 3.02
6515 17637 6.397272 ACTCTCAGATTCAGTCATTCAGAAC 58.603 40.000 0.00 0.00 0.00 3.01
6516 17638 6.014755 ACTCTCAGATTCAGTCATTCAGAACA 60.015 38.462 0.00 0.00 0.00 3.18
6517 17639 6.762333 TCTCAGATTCAGTCATTCAGAACAA 58.238 36.000 0.00 0.00 0.00 2.83
6518 17640 6.872547 TCTCAGATTCAGTCATTCAGAACAAG 59.127 38.462 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.880027 GTGAAAGTAACCTGGTGCTGG 59.120 52.381 0.00 0.00 0.00 4.85
114 115 3.485463 TTTAGTGGATAATGCCCTCGG 57.515 47.619 0.00 0.00 0.00 4.63
116 117 6.998673 ACTGTATTTTAGTGGATAATGCCCTC 59.001 38.462 0.00 0.00 0.00 4.30
170 171 8.980143 ATTGTCGTACAAATTTGGGAATTTAG 57.020 30.769 21.74 5.07 42.14 1.85
231 232 8.519799 AATAGTTCTCAAAGGAAAGTTGTTGA 57.480 30.769 0.00 0.00 0.00 3.18
273 274 0.109039 GAGACTGACTCGGGAAGCAC 60.109 60.000 0.00 0.00 35.84 4.40
288 289 7.867403 TGCAAGAACATTTCATTTTAAGGAGAC 59.133 33.333 0.00 0.00 0.00 3.36
334 335 6.594788 AGGATTATGTGATTTGTGCTTTGT 57.405 33.333 0.00 0.00 0.00 2.83
336 337 9.807649 GAATAAGGATTATGTGATTTGTGCTTT 57.192 29.630 0.00 0.00 41.21 3.51
475 482 9.482627 GCTTATGCTAGAGTACTAAATGTCAAT 57.517 33.333 0.00 0.00 36.03 2.57
520 527 7.656948 ACCATATTTGAATGTTTCCAAACTGTG 59.343 33.333 3.92 0.00 39.59 3.66
547 554 7.722363 AGAAATAAAAACAGGTTTACACCCAG 58.278 34.615 0.00 0.00 45.63 4.45
610 617 9.485206 GGAGGAAAAACTATTAAAAGGGAAAAC 57.515 33.333 0.00 0.00 0.00 2.43
754 762 6.092259 AGTGTTCATCGTGTATTAGAAAAGGC 59.908 38.462 0.00 0.00 0.00 4.35
834 842 8.958119 TCACCATGTATATAGGAAAAGTTCAC 57.042 34.615 0.00 0.00 0.00 3.18
835 843 9.391006 GTTCACCATGTATATAGGAAAAGTTCA 57.609 33.333 0.00 0.00 0.00 3.18
870 878 9.775854 TGTAATCCAAAAATGTTCATCATGTTT 57.224 25.926 0.00 0.00 42.68 2.83
949 957 7.604927 ACTTAAATAGTACATTTGCTCGTTCCA 59.395 33.333 11.29 0.00 34.56 3.53
962 970 7.041235 CCAAAACCGGACAACTTAAATAGTACA 60.041 37.037 9.46 0.00 35.54 2.90
1011 1031 6.465439 AAAGGGAAAACCAGTAAAAGACAG 57.535 37.500 0.00 0.00 43.89 3.51
1495 1537 1.142314 TAATGTAGCGGCCGACCAC 59.858 57.895 33.48 22.36 34.57 4.16
1500 1542 1.426041 GGTGTGTAATGTAGCGGCCG 61.426 60.000 24.05 24.05 0.00 6.13
1558 1600 5.222048 ACCCAACTAGAAGAAATAGCAACCA 60.222 40.000 0.00 0.00 0.00 3.67
1588 1630 0.038526 AAACAGAGCGTCGGTACCTG 60.039 55.000 10.90 10.56 0.00 4.00
1686 1735 3.648067 GAGAGAGAGAGAGATGGGAGAGA 59.352 52.174 0.00 0.00 0.00 3.10
1687 1736 3.649981 AGAGAGAGAGAGAGATGGGAGAG 59.350 52.174 0.00 0.00 0.00 3.20
1688 1737 3.648067 GAGAGAGAGAGAGAGATGGGAGA 59.352 52.174 0.00 0.00 0.00 3.71
1689 1738 3.649981 AGAGAGAGAGAGAGAGATGGGAG 59.350 52.174 0.00 0.00 0.00 4.30
1690 1739 3.648067 GAGAGAGAGAGAGAGAGATGGGA 59.352 52.174 0.00 0.00 0.00 4.37
1692 1741 4.592351 AGAGAGAGAGAGAGAGAGAGATGG 59.408 50.000 0.00 0.00 0.00 3.51
1693 1742 5.539574 AGAGAGAGAGAGAGAGAGAGAGATG 59.460 48.000 0.00 0.00 0.00 2.90
1694 1743 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
1695 1744 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1731 1813 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
1732 1814 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1733 1815 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1734 1816 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1735 1817 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1736 1818 1.128507 GAGTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1737 1819 1.001974 AGAGTGTGTGTGTGTGTGTGT 59.998 47.619 0.00 0.00 0.00 3.72
1738 1820 1.660607 GAGAGTGTGTGTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
1739 1821 1.550524 AGAGAGTGTGTGTGTGTGTGT 59.449 47.619 0.00 0.00 0.00 3.72
1740 1822 2.159184 AGAGAGAGTGTGTGTGTGTGTG 60.159 50.000 0.00 0.00 0.00 3.82
1741 1823 2.103373 AGAGAGAGTGTGTGTGTGTGT 58.897 47.619 0.00 0.00 0.00 3.72
1742 1824 2.159184 ACAGAGAGAGTGTGTGTGTGTG 60.159 50.000 0.00 0.00 29.56 3.82
1743 1825 2.099921 GACAGAGAGAGTGTGTGTGTGT 59.900 50.000 0.00 0.00 31.30 3.72
1744 1826 2.544694 GGACAGAGAGAGTGTGTGTGTG 60.545 54.545 0.00 0.00 31.30 3.82
1745 1827 1.683917 GGACAGAGAGAGTGTGTGTGT 59.316 52.381 0.00 0.00 31.30 3.72
1746 1828 1.959985 AGGACAGAGAGAGTGTGTGTG 59.040 52.381 0.00 0.00 31.30 3.82
1747 1829 2.158534 AGAGGACAGAGAGAGTGTGTGT 60.159 50.000 0.00 0.00 31.30 3.72
1748 1830 2.513753 AGAGGACAGAGAGAGTGTGTG 58.486 52.381 0.00 0.00 31.30 3.82
1749 1831 2.969821 AGAGGACAGAGAGAGTGTGT 57.030 50.000 0.00 0.00 34.69 3.72
1750 1832 3.826157 AGAAAGAGGACAGAGAGAGTGTG 59.174 47.826 0.00 0.00 0.00 3.82
1751 1833 4.079253 GAGAAAGAGGACAGAGAGAGTGT 58.921 47.826 0.00 0.00 0.00 3.55
1752 1834 4.335416 AGAGAAAGAGGACAGAGAGAGTG 58.665 47.826 0.00 0.00 0.00 3.51
1753 1835 4.567747 GGAGAGAAAGAGGACAGAGAGAGT 60.568 50.000 0.00 0.00 0.00 3.24
1754 1836 3.947834 GGAGAGAAAGAGGACAGAGAGAG 59.052 52.174 0.00 0.00 0.00 3.20
1755 1837 3.621214 CGGAGAGAAAGAGGACAGAGAGA 60.621 52.174 0.00 0.00 0.00 3.10
1756 1838 2.682856 CGGAGAGAAAGAGGACAGAGAG 59.317 54.545 0.00 0.00 0.00 3.20
1757 1839 2.040545 ACGGAGAGAAAGAGGACAGAGA 59.959 50.000 0.00 0.00 0.00 3.10
1758 1840 2.442413 ACGGAGAGAAAGAGGACAGAG 58.558 52.381 0.00 0.00 0.00 3.35
1759 1841 2.588464 ACGGAGAGAAAGAGGACAGA 57.412 50.000 0.00 0.00 0.00 3.41
1760 1842 2.096174 CGTACGGAGAGAAAGAGGACAG 59.904 54.545 7.57 0.00 0.00 3.51
1761 1843 2.082231 CGTACGGAGAGAAAGAGGACA 58.918 52.381 7.57 0.00 0.00 4.02
1762 1844 2.083002 ACGTACGGAGAGAAAGAGGAC 58.917 52.381 21.06 0.00 0.00 3.85
1763 1845 2.486472 ACGTACGGAGAGAAAGAGGA 57.514 50.000 21.06 0.00 0.00 3.71
1764 1846 3.269178 AGTACGTACGGAGAGAAAGAGG 58.731 50.000 21.06 0.00 0.00 3.69
1765 1847 6.414408 TTTAGTACGTACGGAGAGAAAGAG 57.586 41.667 21.06 0.00 0.00 2.85
1766 1848 6.801539 TTTTAGTACGTACGGAGAGAAAGA 57.198 37.500 21.06 0.00 0.00 2.52
1767 1849 7.752239 TGATTTTTAGTACGTACGGAGAGAAAG 59.248 37.037 21.06 0.00 0.00 2.62
1768 1850 7.592938 TGATTTTTAGTACGTACGGAGAGAAA 58.407 34.615 21.06 14.81 0.00 2.52
1769 1851 7.144722 TGATTTTTAGTACGTACGGAGAGAA 57.855 36.000 21.06 11.27 0.00 2.87
1770 1852 6.741992 TGATTTTTAGTACGTACGGAGAGA 57.258 37.500 21.06 6.63 0.00 3.10
1771 1853 7.416022 AGATGATTTTTAGTACGTACGGAGAG 58.584 38.462 21.06 0.00 0.00 3.20
1772 1854 7.325660 AGATGATTTTTAGTACGTACGGAGA 57.674 36.000 21.06 5.07 0.00 3.71
1773 1855 6.356452 CGAGATGATTTTTAGTACGTACGGAG 59.644 42.308 21.06 0.00 0.00 4.63
1774 1856 6.183360 ACGAGATGATTTTTAGTACGTACGGA 60.183 38.462 21.06 8.59 0.00 4.69
1775 1857 5.967674 ACGAGATGATTTTTAGTACGTACGG 59.032 40.000 21.06 1.43 0.00 4.02
1839 1921 4.321824 GGACTTACCTAATCCTACATCGCC 60.322 50.000 0.00 0.00 35.41 5.54
1857 1971 2.096248 GATCTCGTGAGGAGTGGACTT 58.904 52.381 1.79 0.00 43.60 3.01
1934 2048 1.767289 ACGCACAGAACACTCTTACG 58.233 50.000 0.00 0.00 0.00 3.18
2004 2118 2.110213 TTGTCGTGCACCCTCACC 59.890 61.111 12.15 0.00 33.57 4.02
2028 2142 7.526918 AGAAAGAAAAATAACAGAGGGGAGAA 58.473 34.615 0.00 0.00 0.00 2.87
2234 3186 8.204160 AGACAGTTAGCTGCATATTACAACATA 58.796 33.333 6.48 0.00 46.30 2.29
2266 4278 2.869801 TGAAACTTCCGCAACACTGTAG 59.130 45.455 0.00 0.00 0.00 2.74
2306 4995 2.748058 TTTGAAGGCCAGCTCCGGTC 62.748 60.000 5.01 0.00 0.00 4.79
2315 5004 3.373001 CCTCCCAATATCTTTGAAGGCCA 60.373 47.826 5.01 0.00 0.00 5.36
2398 5157 1.876714 CGGTAGTTGCCATCGTCGG 60.877 63.158 0.00 0.00 0.00 4.79
2455 5214 2.184579 GGAGAAGGAAGGCGACGG 59.815 66.667 0.00 0.00 0.00 4.79
2630 5397 1.108776 ACAGTACATGTATCGGCGGT 58.891 50.000 9.18 0.65 41.60 5.68
3010 5785 2.362397 GGAACGATGAGATACCTCTGCA 59.638 50.000 0.00 0.00 40.10 4.41
3227 6496 7.916977 CACAGAATGAAAACATGAACTTTCTGA 59.083 33.333 26.10 11.57 42.06 3.27
3279 6670 3.120304 GCAGACCCGTCAAAGAACAATAC 60.120 47.826 0.00 0.00 0.00 1.89
3300 6692 3.865745 ACGTGCTCTCTGTGTTTATATGC 59.134 43.478 0.00 0.00 0.00 3.14
3584 7059 6.100279 TGTGCAGTCTCCTCCATAAGAATATT 59.900 38.462 0.00 0.00 0.00 1.28
3585 7060 5.604231 TGTGCAGTCTCCTCCATAAGAATAT 59.396 40.000 0.00 0.00 0.00 1.28
3588 7063 3.173151 TGTGCAGTCTCCTCCATAAGAA 58.827 45.455 0.00 0.00 0.00 2.52
3591 7066 2.840038 ACATGTGCAGTCTCCTCCATAA 59.160 45.455 0.00 0.00 0.00 1.90
3593 7068 1.065636 CACATGTGCAGTCTCCTCCAT 60.066 52.381 13.94 0.00 0.00 3.41
3594 7069 0.322648 CACATGTGCAGTCTCCTCCA 59.677 55.000 13.94 0.00 0.00 3.86
3595 7070 0.392193 CCACATGTGCAGTCTCCTCC 60.392 60.000 20.81 0.00 0.00 4.30
3597 7072 1.002868 GCCACATGTGCAGTCTCCT 60.003 57.895 20.81 0.00 0.00 3.69
3598 7073 2.042831 GGCCACATGTGCAGTCTCC 61.043 63.158 20.81 9.49 0.00 3.71
3599 7074 0.890542 TTGGCCACATGTGCAGTCTC 60.891 55.000 20.81 5.95 0.00 3.36
3603 7078 0.390124 AGTTTTGGCCACATGTGCAG 59.610 50.000 20.81 9.00 0.00 4.41
3611 7100 3.118905 TGGCATTTTAGTTTTGGCCAC 57.881 42.857 3.88 0.00 45.69 5.01
3618 7107 9.777297 AAACAGAAACATATGGCATTTTAGTTT 57.223 25.926 4.78 11.52 0.00 2.66
3652 7142 5.776173 TGGATTAAAAGAAAAAGGTCGCA 57.224 34.783 0.00 0.00 0.00 5.10
3750 7241 6.405278 TCCTAGTCAAATAATCTGCGATCA 57.595 37.500 0.00 0.00 0.00 2.92
3794 7285 9.561069 GATGTCATTAGATGTTGGTAAACCTAT 57.439 33.333 0.02 0.00 35.25 2.57
3854 7345 5.490139 AATCTAACGCATGGAATCAACAG 57.510 39.130 0.00 0.00 0.00 3.16
3859 7350 6.037610 AGACAGAAAATCTAACGCATGGAATC 59.962 38.462 0.00 0.00 0.00 2.52
3888 7379 6.598457 CAGCCCATTAAGAGATTATGGATCTG 59.402 42.308 0.00 0.00 45.17 2.90
3954 7580 5.401376 TCGTTGTAGACAAAATCAAGAGTCG 59.599 40.000 0.00 0.00 37.63 4.18
4118 7756 3.181478 GGTTTCGTCGATACCAAGATCCT 60.181 47.826 24.59 0.00 34.56 3.24
4274 8293 7.094463 ACTGCAATCTTCACTTTAGATCCAAAG 60.094 37.037 11.50 11.50 40.62 2.77
4304 8323 2.704190 ACGGGATATGATGGGTCTCT 57.296 50.000 0.00 0.00 0.00 3.10
4305 8324 6.540438 TTATTACGGGATATGATGGGTCTC 57.460 41.667 0.00 0.00 0.00 3.36
4371 8391 7.175990 TCACTTAGGTTTGGGAATCACAAATAC 59.824 37.037 14.22 10.24 39.68 1.89
4580 15263 6.306356 GCATCGCATGTATTCAATATTTCCAC 59.694 38.462 0.00 0.00 0.00 4.02
4600 15283 2.358957 TCCATTTTCAGGACTGCATCG 58.641 47.619 0.00 0.00 0.00 3.84
4647 15330 9.261180 GAACAAAAGAATATGATATCTGTCCGA 57.739 33.333 3.98 0.00 0.00 4.55
4813 15496 2.027837 CCTTTGCCCCAGGAATTTCAAG 60.028 50.000 0.00 0.00 32.41 3.02
4890 15579 3.244770 ACTGGACCGAACATGTTGGTAAT 60.245 43.478 23.86 9.80 35.75 1.89
4949 15641 2.028112 TGATACAGGTCCAGCTTGACAC 60.028 50.000 18.74 8.86 36.97 3.67
5317 16010 5.574082 TCAAACGTGTCGACAATGATTTTT 58.426 33.333 21.95 10.13 0.00 1.94
5405 16098 2.149973 AAGACATCCCAGGAATTGCC 57.850 50.000 0.00 0.00 0.00 4.52
5536 16229 0.109551 TCAGTCTTCTCGCAGCTTCG 60.110 55.000 0.00 0.00 0.00 3.79
5574 16267 1.075374 AGGCCATCTGCTAAACCAACA 59.925 47.619 5.01 0.00 40.92 3.33
5631 16324 4.312443 CAAAACTCATGCTCCAAATGCTT 58.688 39.130 0.00 0.00 0.00 3.91
5645 16338 2.154462 GCAGCCTAGAAGCAAAACTCA 58.846 47.619 0.00 0.00 34.23 3.41
5649 16342 1.538047 CCAGCAGCCTAGAAGCAAAA 58.462 50.000 0.00 0.00 34.23 2.44
5659 16352 0.326264 CTAACACTTCCCAGCAGCCT 59.674 55.000 0.00 0.00 0.00 4.58
5692 16385 2.095161 ACGAACGGAGCAAAAACAACAA 60.095 40.909 0.00 0.00 0.00 2.83
5708 16401 8.658499 ATCTCCAGTATTAAATGGTTACGAAC 57.342 34.615 0.00 0.00 37.84 3.95
5731 16424 3.422603 CGCAGCAATTGAACAAGCAAATC 60.423 43.478 10.34 0.00 0.00 2.17
5778 16471 1.670674 GGCCGTCAACGAACAGATGTA 60.671 52.381 3.71 0.00 43.02 2.29
5786 16479 0.036765 AGCATAAGGCCGTCAACGAA 60.037 50.000 3.71 0.00 46.50 3.85
5807 16500 1.328680 GGTGCACATCATCGTAGCAAG 59.671 52.381 20.43 0.00 36.91 4.01
5819 16512 2.173569 GAGATAAAGGGGAGGTGCACAT 59.826 50.000 20.43 12.71 0.00 3.21
5836 16529 7.666388 ACGTACTTTAGATATGCAGTAGGAGAT 59.334 37.037 0.00 0.00 33.68 2.75
5863 16556 6.710597 TGAGTGACTGTAGAAAGTAAGTGT 57.289 37.500 0.00 0.00 0.00 3.55
5929 16685 5.642063 GGATCGGTCTAAACTCAATTTCACA 59.358 40.000 0.00 0.00 0.00 3.58
5930 16686 5.642063 TGGATCGGTCTAAACTCAATTTCAC 59.358 40.000 0.00 0.00 0.00 3.18
5931 16687 5.800296 TGGATCGGTCTAAACTCAATTTCA 58.200 37.500 0.00 0.00 0.00 2.69
5933 16689 6.404734 GCAATGGATCGGTCTAAACTCAATTT 60.405 38.462 0.00 0.00 0.00 1.82
5934 16690 5.066505 GCAATGGATCGGTCTAAACTCAATT 59.933 40.000 0.00 0.00 0.00 2.32
5935 16691 4.576463 GCAATGGATCGGTCTAAACTCAAT 59.424 41.667 0.00 0.00 0.00 2.57
5963 16727 2.440980 GCCTTGGCCTTAGCTGGG 60.441 66.667 3.32 0.00 39.73 4.45
5983 17092 2.670414 GAGACAGCTGGAAATTGACGAG 59.330 50.000 19.93 0.00 0.00 4.18
5984 17093 2.300152 AGAGACAGCTGGAAATTGACGA 59.700 45.455 19.93 0.00 0.00 4.20
5985 17094 2.693069 AGAGACAGCTGGAAATTGACG 58.307 47.619 19.93 0.00 0.00 4.35
5986 17095 5.444663 AAAAGAGACAGCTGGAAATTGAC 57.555 39.130 19.93 0.61 0.00 3.18
6019 17128 6.811170 CAGACATGGAAGAAGAAAGACTAGTC 59.189 42.308 15.41 15.41 0.00 2.59
6020 17129 6.696411 CAGACATGGAAGAAGAAAGACTAGT 58.304 40.000 0.00 0.00 0.00 2.57
6049 17167 4.311816 AGAAACAGGTGATGCAACAAAG 57.688 40.909 0.00 0.00 0.00 2.77
6051 17169 3.243035 CGAAGAAACAGGTGATGCAACAA 60.243 43.478 0.00 0.00 0.00 2.83
6073 17191 2.048127 GGTGGAGCTGACGGTGAC 60.048 66.667 0.00 0.00 0.00 3.67
6079 17197 1.451028 GCATGAGGGTGGAGCTGAC 60.451 63.158 0.00 0.00 0.00 3.51
6102 17222 1.788258 ACGACTCACTGCAGACAATG 58.212 50.000 23.35 8.36 0.00 2.82
6103 17223 2.820197 TCTACGACTCACTGCAGACAAT 59.180 45.455 23.35 2.50 0.00 2.71
6104 17224 2.226674 CTCTACGACTCACTGCAGACAA 59.773 50.000 23.35 3.91 0.00 3.18
6105 17225 1.807142 CTCTACGACTCACTGCAGACA 59.193 52.381 23.35 4.83 0.00 3.41
6106 17226 1.807742 ACTCTACGACTCACTGCAGAC 59.192 52.381 23.35 5.24 0.00 3.51
6107 17227 2.186532 ACTCTACGACTCACTGCAGA 57.813 50.000 23.35 0.00 0.00 4.26
6108 17228 2.999507 AACTCTACGACTCACTGCAG 57.000 50.000 13.48 13.48 0.00 4.41
6109 17229 3.318275 AGAAAACTCTACGACTCACTGCA 59.682 43.478 0.00 0.00 0.00 4.41
6110 17230 3.903360 AGAAAACTCTACGACTCACTGC 58.097 45.455 0.00 0.00 0.00 4.40
6111 17231 4.216687 AGGAGAAAACTCTACGACTCACTG 59.783 45.833 0.00 0.00 0.00 3.66
6112 17232 4.400120 AGGAGAAAACTCTACGACTCACT 58.600 43.478 0.00 0.00 0.00 3.41
6113 17233 4.769859 AGGAGAAAACTCTACGACTCAC 57.230 45.455 0.00 0.00 0.00 3.51
6114 17234 4.825634 TGAAGGAGAAAACTCTACGACTCA 59.174 41.667 0.00 0.00 0.00 3.41
6115 17235 5.373981 TGAAGGAGAAAACTCTACGACTC 57.626 43.478 0.00 0.00 0.00 3.36
6116 17236 5.986501 ATGAAGGAGAAAACTCTACGACT 57.013 39.130 0.00 0.00 0.00 4.18
6120 17240 8.154649 TGTGAAAATGAAGGAGAAAACTCTAC 57.845 34.615 0.00 0.00 0.00 2.59
6121 17241 8.746052 TTGTGAAAATGAAGGAGAAAACTCTA 57.254 30.769 0.00 0.00 0.00 2.43
6122 17242 7.340487 ACTTGTGAAAATGAAGGAGAAAACTCT 59.660 33.333 0.00 0.00 0.00 3.24
6123 17243 7.484140 ACTTGTGAAAATGAAGGAGAAAACTC 58.516 34.615 0.00 0.00 0.00 3.01
6124 17244 7.410120 ACTTGTGAAAATGAAGGAGAAAACT 57.590 32.000 0.00 0.00 0.00 2.66
6125 17245 7.222805 GGAACTTGTGAAAATGAAGGAGAAAAC 59.777 37.037 0.00 0.00 0.00 2.43
6126 17246 7.093552 TGGAACTTGTGAAAATGAAGGAGAAAA 60.094 33.333 0.00 0.00 0.00 2.29
6127 17247 6.379703 TGGAACTTGTGAAAATGAAGGAGAAA 59.620 34.615 0.00 0.00 0.00 2.52
6128 17248 5.890985 TGGAACTTGTGAAAATGAAGGAGAA 59.109 36.000 0.00 0.00 0.00 2.87
6129 17249 5.445069 TGGAACTTGTGAAAATGAAGGAGA 58.555 37.500 0.00 0.00 0.00 3.71
6143 17263 5.531634 CACAAACATGCTAATGGAACTTGT 58.468 37.500 0.00 0.00 38.19 3.16
6145 17265 4.559153 GCACAAACATGCTAATGGAACTT 58.441 39.130 0.00 0.00 42.62 2.66
6149 17269 2.523245 TGGCACAAACATGCTAATGGA 58.477 42.857 0.00 0.00 45.38 3.41
6161 17281 3.499158 TCCAGGAGGCTTTGGCACAAA 62.499 52.381 12.65 0.00 38.21 2.83
6197 17317 0.879400 CGACAGGATGATGCTGGAGC 60.879 60.000 18.22 6.32 40.38 4.70
6198 17318 0.879400 GCGACAGGATGATGCTGGAG 60.879 60.000 18.22 11.87 40.38 3.86
6199 17319 1.144716 GCGACAGGATGATGCTGGA 59.855 57.895 18.22 0.00 40.38 3.86
6200 17320 1.890979 GGCGACAGGATGATGCTGG 60.891 63.158 18.22 2.54 40.38 4.85
6201 17321 1.153309 TGGCGACAGGATGATGCTG 60.153 57.895 12.62 12.62 41.93 4.41
6216 17336 1.905354 AGGCCTGCAAAACTCTGGC 60.905 57.895 3.11 2.37 44.64 4.85
6217 17337 1.962144 CAGGCCTGCAAAACTCTGG 59.038 57.895 22.33 0.00 0.00 3.86
6255 17375 9.565213 GCTGAATTCATATGTTATGCTTATTCC 57.435 33.333 8.96 0.00 0.00 3.01
6259 17379 7.175467 CCCTGCTGAATTCATATGTTATGCTTA 59.825 37.037 8.96 0.00 0.00 3.09
6260 17380 6.015688 CCCTGCTGAATTCATATGTTATGCTT 60.016 38.462 8.96 0.00 0.00 3.91
6262 17382 5.474532 TCCCTGCTGAATTCATATGTTATGC 59.525 40.000 8.96 6.84 0.00 3.14
6263 17383 7.514784 TTCCCTGCTGAATTCATATGTTATG 57.485 36.000 8.96 0.00 0.00 1.90
6265 17385 7.520798 AGATTCCCTGCTGAATTCATATGTTA 58.479 34.615 8.96 0.00 35.15 2.41
6283 17403 4.025647 CGATAAAAAGCTCGTGAGATTCCC 60.026 45.833 0.27 0.00 35.80 3.97
6286 17406 6.147164 TGTTTCGATAAAAAGCTCGTGAGATT 59.853 34.615 0.00 0.00 38.92 2.40
6294 17414 6.086896 GTCAAGCTTGTTTCGATAAAAAGCTC 59.913 38.462 24.96 15.72 42.09 4.09
6319 17439 4.814147 TGAGCTATATGGAAGATTCGCAG 58.186 43.478 0.00 0.00 0.00 5.18
6321 17441 3.616379 GCTGAGCTATATGGAAGATTCGC 59.384 47.826 0.00 0.00 0.00 4.70
6368 17488 4.946784 GGCAATAGTCGCCCTAATATTG 57.053 45.455 0.00 0.00 44.22 1.90
6385 17505 8.526978 TGACTGTATTGCTAAATTTATTGGCAA 58.473 29.630 19.57 19.57 40.64 4.52
6387 17507 8.925161 TTGACTGTATTGCTAAATTTATTGGC 57.075 30.769 0.00 0.00 0.00 4.52
6479 17601 7.782168 ACTGAATCTGAGAGTATTCACCATCTA 59.218 37.037 0.00 0.00 37.23 1.98
6485 17607 7.978414 TGAATGACTGAATCTGAGAGTATTCAC 59.022 37.037 2.10 0.00 37.23 3.18
6488 17610 8.303780 TCTGAATGACTGAATCTGAGAGTATT 57.696 34.615 0.00 0.00 0.00 1.89
6505 17627 6.318396 TGTGTGTCAATTCTTGTTCTGAATGA 59.682 34.615 0.00 0.00 34.74 2.57
6506 17628 6.497437 TGTGTGTCAATTCTTGTTCTGAATG 58.503 36.000 0.00 0.00 34.74 2.67
6507 17629 6.238842 CCTGTGTGTCAATTCTTGTTCTGAAT 60.239 38.462 0.00 0.00 35.88 2.57
6508 17630 5.066375 CCTGTGTGTCAATTCTTGTTCTGAA 59.934 40.000 0.00 0.00 0.00 3.02
6509 17631 4.576053 CCTGTGTGTCAATTCTTGTTCTGA 59.424 41.667 0.00 0.00 0.00 3.27
6510 17632 4.261322 CCCTGTGTGTCAATTCTTGTTCTG 60.261 45.833 0.00 0.00 0.00 3.02
6511 17633 3.885297 CCCTGTGTGTCAATTCTTGTTCT 59.115 43.478 0.00 0.00 0.00 3.01
6512 17634 3.632145 ACCCTGTGTGTCAATTCTTGTTC 59.368 43.478 0.00 0.00 0.00 3.18
6513 17635 3.631250 ACCCTGTGTGTCAATTCTTGTT 58.369 40.909 0.00 0.00 0.00 2.83
6514 17636 3.297134 ACCCTGTGTGTCAATTCTTGT 57.703 42.857 0.00 0.00 0.00 3.16
6515 17637 3.004734 GGAACCCTGTGTGTCAATTCTTG 59.995 47.826 0.00 0.00 0.00 3.02
6516 17638 3.222603 GGAACCCTGTGTGTCAATTCTT 58.777 45.455 0.00 0.00 0.00 2.52
6517 17639 2.174639 TGGAACCCTGTGTGTCAATTCT 59.825 45.455 0.00 0.00 0.00 2.40
6518 17640 2.582052 TGGAACCCTGTGTGTCAATTC 58.418 47.619 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.