Multiple sequence alignment - TraesCS5D01G174300

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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 TraesCS5D01G174300 chr5D 100.000 2674 0 0 1 2674 273115855 273113182 0.000000e+00 4939.0
1 TraesCS5D01G174300 chr5D 81.132 212 27 7 1548 1756 457659263 457659464 9.910000e-35 158.0
2 TraesCS5D01G174300 chr5D 93.333 45 3 0 1890 1934 67695203 67695247 1.720000e-07 67.6
3 TraesCS5D01G174300 chr5D 93.333 45 3 0 1890 1934 266350424 266350468 1.720000e-07 67.6
4 TraesCS5D01G174300 chr5B 88.719 2030 111 54 16 2001 308924062 308922107 0.000000e+00 2372.0
5 TraesCS5D01G174300 chr5B 86.957 460 58 2 2216 2674 308921895 308921437 1.420000e-142 516.0
6 TraesCS5D01G174300 chr5A 90.542 1586 70 31 16 1558 362416275 362414727 0.000000e+00 2025.0
7 TraesCS5D01G174300 chr2B 79.227 207 27 11 1545 1746 444613242 444613047 2.160000e-26 130.0
8 TraesCS5D01G174300 chr6D 84.615 117 15 3 2538 2653 386107781 386107895 2.180000e-21 113.0
9 TraesCS5D01G174300 chr6D 93.333 45 3 0 1890 1934 59564327 59564371 1.720000e-07 67.6
10 TraesCS5D01G174300 chr6D 93.333 45 3 0 1890 1934 185341868 185341824 1.720000e-07 67.6
11 TraesCS5D01G174300 chr7D 83.761 117 19 0 1550 1666 235571405 235571521 7.830000e-21 111.0
12 TraesCS5D01G174300 chr7D 97.727 44 1 0 1891 1934 634901965 634902008 2.850000e-10 76.8
13 TraesCS5D01G174300 chr7D 95.455 44 1 1 1891 1934 164373376 164373334 4.780000e-08 69.4
14 TraesCS5D01G174300 chr3A 82.258 124 20 2 2547 2669 63853819 63853941 3.640000e-19 106.0
15 TraesCS5D01G174300 chr4D 87.640 89 8 3 2546 2633 507879675 507879589 1.690000e-17 100.0
16 TraesCS5D01G174300 chr3D 88.000 75 8 1 2526 2599 4676972 4677046 1.320000e-13 87.9
17 TraesCS5D01G174300 chr3D 95.652 46 2 0 1630 1675 2305999 2306044 1.030000e-09 75.0
18 TraesCS5D01G174300 chr4A 79.508 122 22 3 2485 2605 679262131 679262250 1.710000e-12 84.2
19 TraesCS5D01G174300 chr7A 84.524 84 10 2 2535 2615 206924415 206924498 2.210000e-11 80.5
20 TraesCS5D01G174300 chr7B 86.301 73 7 2 2535 2604 162091331 162091403 2.850000e-10 76.8
21 TraesCS5D01G174300 chr7B 91.228 57 4 1 2246 2301 699932755 699932811 2.850000e-10 76.8
22 TraesCS5D01G174300 chr7B 95.455 44 2 0 1891 1934 600573675 600573718 1.330000e-08 71.3
23 TraesCS5D01G174300 chr2D 85.294 68 9 1 2535 2601 21623531 21623464 4.780000e-08 69.4
24 TraesCS5D01G174300 chr1D 93.333 45 3 0 1890 1934 101750600 101750556 1.720000e-07 67.6
25 TraesCS5D01G174300 chr1A 86.207 58 8 0 1607 1664 243605761 243605704 2.220000e-06 63.9
26 TraesCS5D01G174300 chr3B 96.970 33 1 0 2180 2212 169251651 169251683 3.720000e-04 56.5


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 TraesCS5D01G174300 chr5D 273113182 273115855 2673 True 4939 4939 100.000 1 2674 1 chr5D.!!$R1 2673
1 TraesCS5D01G174300 chr5B 308921437 308924062 2625 True 1444 2372 87.838 16 2674 2 chr5B.!!$R1 2658
2 TraesCS5D01G174300 chr5A 362414727 362416275 1548 True 2025 2025 90.542 16 1558 1 chr5A.!!$R1 1542

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
468 479 1.002792 TGCTCGTATCCAAGATCGTCG 60.003 52.381 0.0 0.0 0.0 5.12 F
1082 1128 0.962489 CGTCTCCTGTGTCACCTTCT 59.038 55.000 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 1492 0.093026 GAACATGCAGTCACGTACGC 59.907 55.0 16.72 0.0 0.0 4.42 R
2628 2761 0.179094 ACGTGGACAGAGCGAAACAA 60.179 50.0 0.00 0.0 0.0 2.83 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
91 99 3.057315 CACATTGGCGAGGTTTCTGATTT 60.057 43.478 0.00 0.00 0.00 2.17
92 100 3.057315 ACATTGGCGAGGTTTCTGATTTG 60.057 43.478 0.00 0.00 0.00 2.32
210 220 3.268330 TGAAGTCGACTGCTACTCGTAT 58.732 45.455 24.00 1.68 32.77 3.06
213 223 3.468770 AGTCGACTGCTACTCGTATGAT 58.531 45.455 19.30 0.00 32.77 2.45
374 384 1.533033 TCCAGTCGGAGCTCCACAA 60.533 57.895 31.67 14.17 35.91 3.33
384 394 1.303643 GCTCCACAACCTCAAGGGG 60.304 63.158 0.29 0.00 40.27 4.79
437 447 3.304829 TCACCATCGAAGGTCCATGATA 58.695 45.455 9.89 0.00 40.77 2.15
438 448 3.903714 TCACCATCGAAGGTCCATGATAT 59.096 43.478 9.89 0.00 40.77 1.63
453 464 6.312426 GTCCATGATATCTTATTTCCTGCTCG 59.688 42.308 3.98 0.00 0.00 5.03
468 479 1.002792 TGCTCGTATCCAAGATCGTCG 60.003 52.381 0.00 0.00 0.00 5.12
548 559 8.342634 GCTTATTTTATCTTATTTGACGCCAGA 58.657 33.333 0.00 0.00 0.00 3.86
571 582 8.774586 CAGAAGATTATTCTGGGGTTTATAACG 58.225 37.037 12.27 0.00 41.54 3.18
584 595 3.733024 TTATAACGGTTCTTGCTTGCG 57.267 42.857 0.00 0.00 0.00 4.85
624 640 5.565637 GCAAAGCTCGAGTAGGATCATATCA 60.566 44.000 15.13 0.00 0.00 2.15
638 660 6.889722 AGGATCATATCAGTAGAGGAAGTAGC 59.110 42.308 0.00 0.00 0.00 3.58
641 663 5.475220 TCATATCAGTAGAGGAAGTAGCAGC 59.525 44.000 0.00 0.00 0.00 5.25
683 716 1.064208 CCGAGTGAGTCTGTATCGTGG 59.936 57.143 0.00 0.00 0.00 4.94
777 819 2.159142 GCTTCTCATGGCAGGGAAATTG 60.159 50.000 0.00 0.00 0.00 2.32
799 841 2.171237 CCATGCTCCCAGACATGAGTAA 59.829 50.000 0.00 0.00 45.23 2.24
807 849 2.289631 CCAGACATGAGTAACACCAGCA 60.290 50.000 0.00 0.00 0.00 4.41
818 860 2.890808 ACACCAGCACTATGTATCGG 57.109 50.000 0.00 0.00 0.00 4.18
820 862 2.100916 ACACCAGCACTATGTATCGGAC 59.899 50.000 0.00 0.00 0.00 4.79
921 967 4.281435 TGATGTTACCTGAACCACGACTTA 59.719 41.667 0.00 0.00 37.22 2.24
948 994 4.276926 AGAAATCTGCTGTCTGTTTCAACC 59.723 41.667 0.00 0.00 32.66 3.77
1082 1128 0.962489 CGTCTCCTGTGTCACCTTCT 59.038 55.000 0.00 0.00 0.00 2.85
1091 1137 4.263068 CCTGTGTCACCTTCTATTCACCTT 60.263 45.833 0.00 0.00 0.00 3.50
1093 1139 6.352222 CCTGTGTCACCTTCTATTCACCTTAT 60.352 42.308 0.00 0.00 0.00 1.73
1098 1144 6.981559 GTCACCTTCTATTCACCTTATCTCAC 59.018 42.308 0.00 0.00 0.00 3.51
1348 1395 1.444119 GGAAACGTCAGGCTGCACAA 61.444 55.000 10.34 0.00 0.00 3.33
1410 1458 7.672239 AGAAAGAGAGAGATAGGTGTTAACTGT 59.328 37.037 7.22 0.00 0.00 3.55
1411 1459 6.767524 AGAGAGAGATAGGTGTTAACTGTG 57.232 41.667 7.22 0.00 0.00 3.66
1412 1460 5.654650 AGAGAGAGATAGGTGTTAACTGTGG 59.345 44.000 7.22 0.00 0.00 4.17
1413 1461 5.580998 AGAGAGATAGGTGTTAACTGTGGA 58.419 41.667 7.22 0.00 0.00 4.02
1437 1485 3.571401 GGATGGATGGATGATTGAACCAC 59.429 47.826 0.00 0.00 36.49 4.16
1440 1488 5.385628 TGGATGGATGATTGAACCACATA 57.614 39.130 0.00 0.00 36.49 2.29
1441 1489 5.955944 TGGATGGATGATTGAACCACATAT 58.044 37.500 0.00 0.00 36.49 1.78
1443 1491 7.701815 TGGATGGATGATTGAACCACATATAT 58.298 34.615 0.00 0.00 36.49 0.86
1444 1492 7.612633 TGGATGGATGATTGAACCACATATATG 59.387 37.037 11.29 11.29 36.49 1.78
1445 1493 6.822667 TGGATGATTGAACCACATATATGC 57.177 37.500 12.79 0.00 0.00 3.14
1467 1516 0.588252 ACGTGACTGCATGTTCTTGC 59.412 50.000 0.00 4.14 41.35 4.01
1486 1535 3.020274 TGCTTTACCGGGTGTACGTATA 58.980 45.455 10.66 0.00 0.00 1.47
1487 1536 3.636300 TGCTTTACCGGGTGTACGTATAT 59.364 43.478 10.66 0.00 0.00 0.86
1490 1539 6.030228 GCTTTACCGGGTGTACGTATATATC 58.970 44.000 10.66 0.00 0.00 1.63
1530 1587 7.122799 GGGAACAAAATTGCTATTCCTACTCTT 59.877 37.037 11.52 0.00 39.09 2.85
1558 1615 4.563184 TGTGCAAACAAATTACGGAAACAC 59.437 37.500 0.00 0.00 0.00 3.32
1559 1616 4.801516 GTGCAAACAAATTACGGAAACACT 59.198 37.500 0.00 0.00 0.00 3.55
1571 1628 5.338614 ACGGAAACACTAAAAATCTGACG 57.661 39.130 0.00 0.00 0.00 4.35
1572 1629 4.812626 ACGGAAACACTAAAAATCTGACGT 59.187 37.500 0.00 0.00 0.00 4.34
1573 1630 5.050567 ACGGAAACACTAAAAATCTGACGTC 60.051 40.000 9.11 9.11 0.00 4.34
1585 1642 3.947910 TCTGACGTCGGATTTTTAGGT 57.052 42.857 23.11 0.00 0.00 3.08
1586 1643 5.587388 ATCTGACGTCGGATTTTTAGGTA 57.413 39.130 30.05 5.84 38.77 3.08
1590 1647 5.104374 TGACGTCGGATTTTTAGGTATGAC 58.896 41.667 11.62 0.00 0.00 3.06
1592 1649 5.107133 ACGTCGGATTTTTAGGTATGACAG 58.893 41.667 0.00 0.00 0.00 3.51
1597 1654 8.358148 GTCGGATTTTTAGGTATGACAGATCTA 58.642 37.037 0.00 0.00 0.00 1.98
1600 1657 9.832445 GGATTTTTAGGTATGACAGATCTAACA 57.168 33.333 2.25 0.00 0.00 2.41
1611 1668 7.658179 TGACAGATCTAACACTTTTCATGAC 57.342 36.000 0.00 0.00 0.00 3.06
1612 1669 7.216494 TGACAGATCTAACACTTTTCATGACA 58.784 34.615 0.00 0.00 0.00 3.58
1624 1681 9.077885 ACACTTTTCATGACAGTTTATATTGGT 57.922 29.630 0.00 0.00 0.00 3.67
1626 1683 9.295825 ACTTTTCATGACAGTTTATATTGGTGA 57.704 29.630 0.00 0.00 0.00 4.02
1634 1691 8.485392 TGACAGTTTATATTGGTGAGATGATGA 58.515 33.333 0.00 0.00 0.00 2.92
1635 1692 9.330063 GACAGTTTATATTGGTGAGATGATGAA 57.670 33.333 0.00 0.00 0.00 2.57
1656 1713 5.807520 TGAAAAATTTAGTTTGCAAGCACGA 59.192 32.000 16.04 0.00 0.00 4.35
1666 1723 4.560136 TTGCAAGCACGACAATTTTCTA 57.440 36.364 0.00 0.00 0.00 2.10
1670 1727 4.737765 GCAAGCACGACAATTTTCTAACAA 59.262 37.500 0.00 0.00 0.00 2.83
1701 1760 8.628882 AAAATAATAAACTCAGGCGTATTTGC 57.371 30.769 0.00 0.00 0.00 3.68
1721 1782 3.818210 TGCCATGTTCGTCAACTAAATGT 59.182 39.130 0.00 0.00 33.17 2.71
1729 1790 5.400066 TCGTCAACTAAATGTCATCCTCA 57.600 39.130 0.00 0.00 0.00 3.86
1732 1793 6.708502 TCGTCAACTAAATGTCATCCTCAAAA 59.291 34.615 0.00 0.00 0.00 2.44
1790 1852 7.451255 TCAGATTTACAATGGAGTCCACAAATT 59.549 33.333 15.86 1.27 35.80 1.82
1792 1854 9.308000 AGATTTACAATGGAGTCCACAAATTAA 57.692 29.630 15.86 5.51 35.80 1.40
1793 1855 9.573133 GATTTACAATGGAGTCCACAAATTAAG 57.427 33.333 15.86 0.97 35.80 1.85
1794 1856 8.472007 TTTACAATGGAGTCCACAAATTAAGT 57.528 30.769 15.86 6.91 35.80 2.24
1795 1857 9.575868 TTTACAATGGAGTCCACAAATTAAGTA 57.424 29.630 15.86 5.97 35.80 2.24
1796 1858 7.448748 ACAATGGAGTCCACAAATTAAGTAC 57.551 36.000 15.86 0.00 35.80 2.73
1797 1859 6.433093 ACAATGGAGTCCACAAATTAAGTACC 59.567 38.462 15.86 0.00 35.80 3.34
1798 1860 4.571919 TGGAGTCCACAAATTAAGTACCG 58.428 43.478 8.12 0.00 0.00 4.02
1799 1861 4.040706 TGGAGTCCACAAATTAAGTACCGT 59.959 41.667 8.12 0.00 0.00 4.83
1800 1862 4.390909 GGAGTCCACAAATTAAGTACCGTG 59.609 45.833 3.60 0.00 0.00 4.94
1801 1863 5.217978 AGTCCACAAATTAAGTACCGTGA 57.782 39.130 0.00 0.00 0.00 4.35
1802 1864 5.235516 AGTCCACAAATTAAGTACCGTGAG 58.764 41.667 0.00 0.00 0.00 3.51
1803 1865 5.011329 AGTCCACAAATTAAGTACCGTGAGA 59.989 40.000 0.00 0.00 0.00 3.27
1804 1866 5.347907 GTCCACAAATTAAGTACCGTGAGAG 59.652 44.000 0.00 0.00 0.00 3.20
1805 1867 5.244402 TCCACAAATTAAGTACCGTGAGAGA 59.756 40.000 0.00 0.00 0.00 3.10
1806 1868 5.929992 CCACAAATTAAGTACCGTGAGAGAA 59.070 40.000 0.00 0.00 0.00 2.87
1807 1869 6.425721 CCACAAATTAAGTACCGTGAGAGAAA 59.574 38.462 0.00 0.00 0.00 2.52
1808 1870 7.360101 CCACAAATTAAGTACCGTGAGAGAAAG 60.360 40.741 0.00 0.00 0.00 2.62
1809 1871 6.147328 ACAAATTAAGTACCGTGAGAGAAAGC 59.853 38.462 0.00 0.00 0.00 3.51
1810 1872 4.859304 TTAAGTACCGTGAGAGAAAGCA 57.141 40.909 0.00 0.00 0.00 3.91
1811 1873 3.746045 AAGTACCGTGAGAGAAAGCAA 57.254 42.857 0.00 0.00 0.00 3.91
1812 1874 3.963428 AGTACCGTGAGAGAAAGCAAT 57.037 42.857 0.00 0.00 0.00 3.56
1813 1875 5.401531 AAGTACCGTGAGAGAAAGCAATA 57.598 39.130 0.00 0.00 0.00 1.90
1814 1876 5.401531 AGTACCGTGAGAGAAAGCAATAA 57.598 39.130 0.00 0.00 0.00 1.40
1815 1877 5.978814 AGTACCGTGAGAGAAAGCAATAAT 58.021 37.500 0.00 0.00 0.00 1.28
1816 1878 6.043411 AGTACCGTGAGAGAAAGCAATAATC 58.957 40.000 0.00 0.00 0.00 1.75
1842 1904 4.612943 TGAAAGAAAACGTGGCAATAACC 58.387 39.130 0.00 0.00 0.00 2.85
1857 1919 2.634815 TAACCGGGTGTTGTAAAGCA 57.365 45.000 0.00 0.00 37.83 3.91
1858 1920 1.765230 AACCGGGTGTTGTAAAGCAA 58.235 45.000 6.32 0.00 35.31 3.91
1877 1945 4.020839 AGCAAGTACGTACTTATGGGTGTT 60.021 41.667 34.03 20.00 44.19 3.32
1881 1949 3.531934 ACGTACTTATGGGTGTTAGGC 57.468 47.619 0.00 0.00 0.00 3.93
1890 1958 1.279025 GGGTGTTAGGCTCCCCATGA 61.279 60.000 0.00 0.00 43.42 3.07
1920 1988 3.728718 CGAAAACCAACATTCGGTGAAAG 59.271 43.478 0.27 0.00 43.41 2.62
1934 2002 2.351738 GGTGAAAGCCGATGAAAACCAG 60.352 50.000 0.00 0.00 0.00 4.00
1936 2004 1.202348 GAAAGCCGATGAAAACCAGGG 59.798 52.381 0.00 0.00 0.00 4.45
1937 2005 0.112412 AAGCCGATGAAAACCAGGGT 59.888 50.000 0.00 0.00 0.00 4.34
1942 2010 4.141251 AGCCGATGAAAACCAGGGTATATT 60.141 41.667 0.00 0.00 0.00 1.28
1943 2011 5.072600 AGCCGATGAAAACCAGGGTATATTA 59.927 40.000 0.00 0.00 0.00 0.98
1945 2013 6.293790 GCCGATGAAAACCAGGGTATATTAAC 60.294 42.308 0.00 0.00 0.00 2.01
1946 2014 6.768861 CCGATGAAAACCAGGGTATATTAACA 59.231 38.462 0.00 0.00 0.00 2.41
1948 2016 7.255001 CGATGAAAACCAGGGTATATTAACACC 60.255 40.741 0.00 0.00 0.00 4.16
1949 2017 6.791371 TGAAAACCAGGGTATATTAACACCA 58.209 36.000 0.00 0.00 36.48 4.17
1950 2018 7.415086 TGAAAACCAGGGTATATTAACACCAT 58.585 34.615 0.00 0.00 36.48 3.55
1951 2019 7.340743 TGAAAACCAGGGTATATTAACACCATG 59.659 37.037 9.35 9.35 44.29 3.66
1954 2022 6.975949 ACCAGGGTATATTAACACCATGAAA 58.024 36.000 15.31 0.00 46.90 2.69
1955 2023 7.060421 ACCAGGGTATATTAACACCATGAAAG 58.940 38.462 15.31 5.35 46.90 2.62
1986 2054 4.506654 GCTTTCGTTAAGAGACAGACACAA 59.493 41.667 4.59 0.00 35.80 3.33
1990 2058 5.597806 TCGTTAAGAGACAGACACAAACAT 58.402 37.500 0.00 0.00 0.00 2.71
2006 2099 4.953579 ACAAACATAGAGAGAGAGGAGGAC 59.046 45.833 0.00 0.00 0.00 3.85
2009 2102 3.181458 ACATAGAGAGAGAGGAGGACGAC 60.181 52.174 0.00 0.00 0.00 4.34
2018 2111 3.063084 GAGGACGACGACCAGGCT 61.063 66.667 18.31 0.00 0.00 4.58
2051 2172 6.400091 CGATGAACTAAACTAGGCGCATATTC 60.400 42.308 10.83 6.82 0.00 1.75
2060 2181 2.149578 AGGCGCATATTCTGAGAATGC 58.850 47.619 17.50 13.50 42.02 3.56
2068 2189 6.072838 CGCATATTCTGAGAATGCCACTTAAT 60.073 38.462 17.50 0.00 42.37 1.40
2070 2191 8.449397 GCATATTCTGAGAATGCCACTTAATAG 58.551 37.037 17.50 0.00 40.06 1.73
2103 2236 3.750639 CAAATGATGCATTTTGGCCAC 57.249 42.857 3.88 0.00 40.60 5.01
2104 2237 2.406596 AATGATGCATTTTGGCCACC 57.593 45.000 3.88 0.00 28.76 4.61
2105 2238 0.176219 ATGATGCATTTTGGCCACCG 59.824 50.000 3.88 0.00 0.00 4.94
2106 2239 0.897401 TGATGCATTTTGGCCACCGA 60.897 50.000 3.88 0.00 0.00 4.69
2107 2240 0.246086 GATGCATTTTGGCCACCGAA 59.754 50.000 3.88 0.41 0.00 4.30
2108 2241 0.903942 ATGCATTTTGGCCACCGAAT 59.096 45.000 3.88 3.32 0.00 3.34
2109 2242 1.550327 TGCATTTTGGCCACCGAATA 58.450 45.000 3.88 0.00 0.00 1.75
2110 2243 2.106566 TGCATTTTGGCCACCGAATAT 58.893 42.857 3.88 0.00 0.00 1.28
2111 2244 3.291584 TGCATTTTGGCCACCGAATATA 58.708 40.909 3.88 0.00 0.00 0.86
2112 2245 3.894427 TGCATTTTGGCCACCGAATATAT 59.106 39.130 3.88 0.00 0.00 0.86
2113 2246 4.236935 GCATTTTGGCCACCGAATATATG 58.763 43.478 3.88 1.57 0.00 1.78
2114 2247 4.236935 CATTTTGGCCACCGAATATATGC 58.763 43.478 3.88 0.00 0.00 3.14
2115 2248 2.647683 TTGGCCACCGAATATATGCA 57.352 45.000 3.88 0.00 0.00 3.96
2116 2249 1.890876 TGGCCACCGAATATATGCAC 58.109 50.000 0.00 0.00 0.00 4.57
2117 2250 1.419762 TGGCCACCGAATATATGCACT 59.580 47.619 0.00 0.00 0.00 4.40
2118 2251 2.635427 TGGCCACCGAATATATGCACTA 59.365 45.455 0.00 0.00 0.00 2.74
2119 2252 3.263170 TGGCCACCGAATATATGCACTAT 59.737 43.478 0.00 0.00 0.00 2.12
2120 2253 4.468153 TGGCCACCGAATATATGCACTATA 59.532 41.667 0.00 0.00 0.00 1.31
2121 2254 5.050490 GGCCACCGAATATATGCACTATAG 58.950 45.833 0.00 0.00 0.00 1.31
2122 2255 5.395324 GGCCACCGAATATATGCACTATAGT 60.395 44.000 0.00 0.00 0.00 2.12
2123 2256 5.749109 GCCACCGAATATATGCACTATAGTC 59.251 44.000 1.26 1.35 35.17 2.59
2281 2414 7.275183 AGATTAAATTCAGCTTAAATTGCCCC 58.725 34.615 4.92 0.00 0.00 5.80
2291 2424 6.598850 CAGCTTAAATTGCCCCATAAATTTGT 59.401 34.615 0.00 0.00 36.80 2.83
2303 2436 7.491682 CCCCATAAATTTGTAGGAAATGACAG 58.508 38.462 0.00 0.00 0.00 3.51
2304 2437 6.980397 CCCATAAATTTGTAGGAAATGACAGC 59.020 38.462 0.00 0.00 0.00 4.40
2307 2440 9.421806 CATAAATTTGTAGGAAATGACAGCAAA 57.578 29.630 0.00 0.00 0.00 3.68
2309 2442 7.951530 AATTTGTAGGAAATGACAGCAAAAG 57.048 32.000 0.00 0.00 0.00 2.27
2312 2445 6.317789 TGTAGGAAATGACAGCAAAAGAAG 57.682 37.500 0.00 0.00 0.00 2.85
2313 2446 6.061441 TGTAGGAAATGACAGCAAAAGAAGA 58.939 36.000 0.00 0.00 0.00 2.87
2315 2448 6.081872 AGGAAATGACAGCAAAAGAAGAAG 57.918 37.500 0.00 0.00 0.00 2.85
2317 2450 3.930634 ATGACAGCAAAAGAAGAAGGC 57.069 42.857 0.00 0.00 0.00 4.35
2318 2451 2.653726 TGACAGCAAAAGAAGAAGGCA 58.346 42.857 0.00 0.00 0.00 4.75
2319 2452 2.620115 TGACAGCAAAAGAAGAAGGCAG 59.380 45.455 0.00 0.00 0.00 4.85
2320 2453 1.339291 ACAGCAAAAGAAGAAGGCAGC 59.661 47.619 0.00 0.00 0.00 5.25
2322 2455 0.387750 GCAAAAGAAGAAGGCAGCCG 60.388 55.000 5.55 0.00 0.00 5.52
2323 2456 0.954452 CAAAAGAAGAAGGCAGCCGT 59.046 50.000 5.55 1.27 0.00 5.68
2393 2526 0.240145 TGGATGGCGATCGACGATAC 59.760 55.000 21.57 13.61 45.77 2.24
2405 2538 1.589076 GACGATACGGCGAATCTACG 58.411 55.000 16.62 12.42 34.83 3.51
2406 2539 0.236711 ACGATACGGCGAATCTACGG 59.763 55.000 16.62 0.00 34.83 4.02
2407 2540 0.236711 CGATACGGCGAATCTACGGT 59.763 55.000 16.62 0.00 0.00 4.83
2420 2553 6.565623 GCGAATCTACGGTAGTTAGTCTTAGG 60.566 46.154 14.45 0.00 0.00 2.69
2456 2589 4.898320 AGCATCTACAATCACAACTCACA 58.102 39.130 0.00 0.00 0.00 3.58
2467 2600 4.468713 TCACAACTCACAAATTCCATCCA 58.531 39.130 0.00 0.00 0.00 3.41
2468 2601 4.892345 TCACAACTCACAAATTCCATCCAA 59.108 37.500 0.00 0.00 0.00 3.53
2476 2609 3.069443 ACAAATTCCATCCAACAAACGCT 59.931 39.130 0.00 0.00 0.00 5.07
2483 2616 2.677003 CCAACAAACGCTCGCGGAT 61.677 57.895 16.18 1.09 44.69 4.18
2484 2617 1.509787 CAACAAACGCTCGCGGATG 60.510 57.895 16.18 15.03 44.69 3.51
2513 2646 1.375396 CTTCCGCGGACAATGACCA 60.375 57.895 31.19 9.90 0.00 4.02
2529 2662 6.183360 ACAATGACCAGACAACACACTAAAAG 60.183 38.462 0.00 0.00 0.00 2.27
2533 2666 4.080526 ACCAGACAACACACTAAAAGTCCT 60.081 41.667 0.00 0.00 0.00 3.85
2534 2667 4.881850 CCAGACAACACACTAAAAGTCCTT 59.118 41.667 0.00 0.00 0.00 3.36
2540 2673 3.875134 ACACACTAAAAGTCCTTTCCACG 59.125 43.478 0.00 0.00 31.45 4.94
2542 2675 4.025145 CACACTAAAAGTCCTTTCCACGAC 60.025 45.833 0.00 0.00 31.45 4.34
2544 2677 2.721425 AAAAGTCCTTTCCACGACCA 57.279 45.000 0.00 0.00 31.45 4.02
2546 2679 1.420430 AAGTCCTTTCCACGACCAGA 58.580 50.000 0.00 0.00 0.00 3.86
2552 2685 2.159085 CCTTTCCACGACCAGATACCTC 60.159 54.545 0.00 0.00 0.00 3.85
2557 2690 3.517901 TCCACGACCAGATACCTCATTTT 59.482 43.478 0.00 0.00 0.00 1.82
2558 2691 3.871594 CCACGACCAGATACCTCATTTTC 59.128 47.826 0.00 0.00 0.00 2.29
2561 2694 4.045104 CGACCAGATACCTCATTTTCGAG 58.955 47.826 0.00 0.00 0.00 4.04
2577 2710 7.552330 TCATTTTCGAGTCATCAAATCCATACA 59.448 33.333 0.00 0.00 0.00 2.29
2590 2723 6.971756 TCAAATCCATACAATTACATGCAACG 59.028 34.615 0.00 0.00 0.00 4.10
2606 2739 6.877322 ACATGCAACGTAAACCTAGTCTAAAT 59.123 34.615 0.00 0.00 0.00 1.40
2607 2740 8.036575 ACATGCAACGTAAACCTAGTCTAAATA 58.963 33.333 0.00 0.00 0.00 1.40
2610 2743 7.010738 TGCAACGTAAACCTAGTCTAAATATGC 59.989 37.037 0.00 0.00 0.00 3.14
2616 2749 3.319972 ACCTAGTCTAAATATGCGCCGAA 59.680 43.478 4.18 0.00 0.00 4.30
2628 2761 2.342648 GCCGAAGACCGTCCTTGT 59.657 61.111 0.00 0.00 36.31 3.16
2633 2766 1.937899 CGAAGACCGTCCTTGTTGTTT 59.062 47.619 0.00 0.00 0.00 2.83
2638 2771 0.234884 CCGTCCTTGTTGTTTCGCTC 59.765 55.000 0.00 0.00 0.00 5.03
2645 2778 1.295792 TGTTGTTTCGCTCTGTCCAC 58.704 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.039856 CCACCACCCCAAAAAGTCAG 58.960 55.000 0.00 0.00 0.00 3.51
1 2 0.336737 ACCACCACCCCAAAAAGTCA 59.663 50.000 0.00 0.00 0.00 3.41
2 3 1.037493 GACCACCACCCCAAAAAGTC 58.963 55.000 0.00 0.00 0.00 3.01
3 4 0.397957 GGACCACCACCCCAAAAAGT 60.398 55.000 0.00 0.00 35.97 2.66
4 5 0.397816 TGGACCACCACCCCAAAAAG 60.398 55.000 0.00 0.00 41.77 2.27
5 6 0.397816 CTGGACCACCACCCCAAAAA 60.398 55.000 0.00 0.00 41.77 1.94
6 7 1.231641 CTGGACCACCACCCCAAAA 59.768 57.895 0.00 0.00 41.77 2.44
7 8 1.585651 AACTGGACCACCACCCCAAA 61.586 55.000 0.00 0.00 41.77 3.28
8 9 2.009882 AACTGGACCACCACCCCAA 61.010 57.895 0.00 0.00 41.77 4.12
9 10 2.369015 AACTGGACCACCACCCCA 60.369 61.111 0.00 0.00 41.77 4.96
10 11 1.789576 ATCAACTGGACCACCACCCC 61.790 60.000 0.00 0.00 41.77 4.95
11 12 0.322546 GATCAACTGGACCACCACCC 60.323 60.000 0.00 0.00 41.77 4.61
12 13 0.693049 AGATCAACTGGACCACCACC 59.307 55.000 0.00 0.00 41.77 4.61
13 14 1.347707 TCAGATCAACTGGACCACCAC 59.652 52.381 0.00 0.00 45.76 4.16
14 15 1.347707 GTCAGATCAACTGGACCACCA 59.652 52.381 0.00 0.00 45.76 4.17
80 88 7.923414 ATACAGTAGGTTCAAATCAGAAACC 57.077 36.000 0.00 0.00 35.83 3.27
91 99 3.343617 GCCAGCAAATACAGTAGGTTCA 58.656 45.455 0.00 0.00 0.00 3.18
92 100 2.683362 GGCCAGCAAATACAGTAGGTTC 59.317 50.000 0.00 0.00 0.00 3.62
210 220 2.440627 CTCCTGGTGGAATGGATGATCA 59.559 50.000 0.00 0.00 42.66 2.92
213 223 0.548031 GCTCCTGGTGGAATGGATGA 59.452 55.000 0.00 0.00 42.66 2.92
437 447 5.808366 TGGATACGAGCAGGAAATAAGAT 57.192 39.130 0.00 0.00 42.51 2.40
438 448 5.601662 CTTGGATACGAGCAGGAAATAAGA 58.398 41.667 0.00 0.00 42.41 2.10
548 559 7.580007 ACCGTTATAAACCCCAGAATAATCTT 58.420 34.615 0.00 0.00 32.03 2.40
550 561 7.718314 AGAACCGTTATAAACCCCAGAATAATC 59.282 37.037 0.00 0.00 0.00 1.75
569 580 1.355210 CAACGCAAGCAAGAACCGT 59.645 52.632 0.00 0.00 45.62 4.83
571 582 2.381589 GTTACAACGCAAGCAAGAACC 58.618 47.619 0.00 0.00 45.62 3.62
584 595 2.561373 GCAGCCAGCGGTTACAAC 59.439 61.111 0.00 0.00 0.00 3.32
624 640 3.094484 ACTGCTGCTACTTCCTCTACT 57.906 47.619 0.00 0.00 0.00 2.57
638 660 2.522836 AGAATCCGATGCTACTGCTG 57.477 50.000 0.00 0.00 40.48 4.41
641 663 5.573282 CGGTTATTAGAATCCGATGCTACTG 59.427 44.000 0.00 0.00 44.86 2.74
683 716 8.592998 CAAACTAATTACTACCATCTTCGACAC 58.407 37.037 0.00 0.00 0.00 3.67
777 819 0.818445 CTCATGTCTGGGAGCATGGC 60.818 60.000 0.00 0.00 41.83 4.40
799 841 2.100916 GTCCGATACATAGTGCTGGTGT 59.899 50.000 0.00 0.00 0.00 4.16
807 849 8.824756 ATATACTGATTGGTCCGATACATAGT 57.175 34.615 0.00 0.00 0.00 2.12
859 904 6.413892 TGATATACCAGTTGCAACATCAGAA 58.586 36.000 30.11 12.46 0.00 3.02
897 943 3.070446 AGTCGTGGTTCAGGTAACATCAA 59.930 43.478 0.00 0.00 40.08 2.57
898 944 2.631062 AGTCGTGGTTCAGGTAACATCA 59.369 45.455 0.00 0.00 40.08 3.07
899 945 3.314541 AGTCGTGGTTCAGGTAACATC 57.685 47.619 0.00 0.00 40.08 3.06
900 946 3.764237 AAGTCGTGGTTCAGGTAACAT 57.236 42.857 0.00 0.00 40.08 2.71
901 947 4.669206 TTAAGTCGTGGTTCAGGTAACA 57.331 40.909 0.00 0.00 40.08 2.41
921 967 6.866480 TGAAACAGACAGCAGATTTCTTTTT 58.134 32.000 0.00 0.00 31.86 1.94
948 994 3.206964 AGATCTGATTCAGTGCATGCAG 58.793 45.455 23.41 10.99 32.61 4.41
1064 1110 4.220821 TGAATAGAAGGTGACACAGGAGAC 59.779 45.833 8.08 0.00 0.00 3.36
1082 1128 5.529289 AGGTGAGGTGAGATAAGGTGAATA 58.471 41.667 0.00 0.00 0.00 1.75
1091 1137 3.138468 TGCTAGCTAGGTGAGGTGAGATA 59.862 47.826 22.10 0.00 37.09 1.98
1093 1139 1.285078 TGCTAGCTAGGTGAGGTGAGA 59.715 52.381 22.10 0.00 37.09 3.27
1098 1144 2.100584 CTCTGTTGCTAGCTAGGTGAGG 59.899 54.545 22.10 0.00 0.00 3.86
1410 1458 3.658705 TCAATCATCCATCCATCCATCCA 59.341 43.478 0.00 0.00 0.00 3.41
1411 1459 4.311520 TCAATCATCCATCCATCCATCC 57.688 45.455 0.00 0.00 0.00 3.51
1412 1460 4.461781 GGTTCAATCATCCATCCATCCATC 59.538 45.833 0.00 0.00 0.00 3.51
1413 1461 4.140876 TGGTTCAATCATCCATCCATCCAT 60.141 41.667 0.00 0.00 0.00 3.41
1437 1485 3.305110 TGCAGTCACGTACGCATATATG 58.695 45.455 16.72 8.45 34.31 1.78
1440 1488 2.127251 CATGCAGTCACGTACGCATAT 58.873 47.619 16.72 0.00 42.43 1.78
1441 1489 1.135228 ACATGCAGTCACGTACGCATA 60.135 47.619 16.72 0.00 42.43 3.14
1443 1491 0.598942 AACATGCAGTCACGTACGCA 60.599 50.000 16.72 4.03 40.25 5.24
1444 1492 0.093026 GAACATGCAGTCACGTACGC 59.907 55.000 16.72 0.00 0.00 4.42
1445 1493 1.698165 AGAACATGCAGTCACGTACG 58.302 50.000 15.01 15.01 0.00 3.67
1467 1516 7.383102 AGATATATACGTACACCCGGTAAAG 57.617 40.000 0.00 0.00 32.72 1.85
1490 1539 9.467258 CAATTTTGTTCCCATAAGCATATGTAG 57.533 33.333 8.07 0.00 37.75 2.74
1530 1587 6.132791 TCCGTAATTTGTTTGCACAAGTTA 57.867 33.333 0.00 0.00 43.92 2.24
1571 1628 7.210873 AGATCTGTCATACCTAAAAATCCGAC 58.789 38.462 0.00 0.00 0.00 4.79
1572 1629 7.361457 AGATCTGTCATACCTAAAAATCCGA 57.639 36.000 0.00 0.00 0.00 4.55
1573 1630 8.979574 GTTAGATCTGTCATACCTAAAAATCCG 58.020 37.037 5.18 0.00 0.00 4.18
1585 1642 9.371136 GTCATGAAAAGTGTTAGATCTGTCATA 57.629 33.333 5.18 0.00 0.00 2.15
1586 1643 7.879677 TGTCATGAAAAGTGTTAGATCTGTCAT 59.120 33.333 5.18 0.00 0.00 3.06
1590 1647 7.664082 ACTGTCATGAAAAGTGTTAGATCTG 57.336 36.000 5.18 0.00 0.00 2.90
1597 1654 9.912634 CCAATATAAACTGTCATGAAAAGTGTT 57.087 29.630 11.93 10.65 0.00 3.32
1600 1657 9.295825 TCACCAATATAAACTGTCATGAAAAGT 57.704 29.630 0.00 1.20 0.00 2.66
1624 1681 9.761504 TTGCAAACTAAATTTTTCATCATCTCA 57.238 25.926 0.00 0.00 0.00 3.27
1626 1683 8.715088 GCTTGCAAACTAAATTTTTCATCATCT 58.285 29.630 0.00 0.00 0.00 2.90
1634 1691 5.578727 TGTCGTGCTTGCAAACTAAATTTTT 59.421 32.000 0.00 0.00 0.00 1.94
1635 1692 5.105752 TGTCGTGCTTGCAAACTAAATTTT 58.894 33.333 0.00 0.00 0.00 1.82
1640 1697 3.980646 ATTGTCGTGCTTGCAAACTAA 57.019 38.095 0.00 0.00 0.00 2.24
1692 1751 1.129624 TGACGAACATGGCAAATACGC 59.870 47.619 0.00 0.00 0.00 4.42
1701 1760 5.605564 TGACATTTAGTTGACGAACATGG 57.394 39.130 0.00 0.00 34.17 3.66
1763 1825 5.245531 TGTGGACTCCATTGTAAATCTGAC 58.754 41.667 0.00 0.00 35.28 3.51
1765 1827 6.573664 TTTGTGGACTCCATTGTAAATCTG 57.426 37.500 0.00 0.00 35.28 2.90
1773 1835 6.403200 CGGTACTTAATTTGTGGACTCCATTG 60.403 42.308 0.00 0.00 35.28 2.82
1775 1837 5.183228 CGGTACTTAATTTGTGGACTCCAT 58.817 41.667 0.00 0.00 35.28 3.41
1790 1852 4.859304 TTGCTTTCTCTCACGGTACTTA 57.141 40.909 0.00 0.00 0.00 2.24
1792 1854 3.963428 ATTGCTTTCTCTCACGGTACT 57.037 42.857 0.00 0.00 0.00 2.73
1793 1855 5.810587 TGATTATTGCTTTCTCTCACGGTAC 59.189 40.000 0.00 0.00 0.00 3.34
1794 1856 5.972935 TGATTATTGCTTTCTCTCACGGTA 58.027 37.500 0.00 0.00 0.00 4.02
1795 1857 4.832248 TGATTATTGCTTTCTCTCACGGT 58.168 39.130 0.00 0.00 0.00 4.83
1796 1858 5.757320 AGATGATTATTGCTTTCTCTCACGG 59.243 40.000 0.00 0.00 0.00 4.94
1797 1859 6.478016 TCAGATGATTATTGCTTTCTCTCACG 59.522 38.462 0.00 0.00 0.00 4.35
1798 1860 7.783090 TCAGATGATTATTGCTTTCTCTCAC 57.217 36.000 0.00 0.00 0.00 3.51
1799 1861 8.797350 TTTCAGATGATTATTGCTTTCTCTCA 57.203 30.769 0.00 0.00 0.00 3.27
1800 1862 9.107177 TCTTTCAGATGATTATTGCTTTCTCTC 57.893 33.333 0.00 0.00 0.00 3.20
1801 1863 9.458727 TTCTTTCAGATGATTATTGCTTTCTCT 57.541 29.630 0.00 0.00 0.00 3.10
1805 1867 9.132521 CGTTTTCTTTCAGATGATTATTGCTTT 57.867 29.630 0.00 0.00 0.00 3.51
1806 1868 8.299570 ACGTTTTCTTTCAGATGATTATTGCTT 58.700 29.630 0.00 0.00 0.00 3.91
1807 1869 7.752239 CACGTTTTCTTTCAGATGATTATTGCT 59.248 33.333 0.00 0.00 0.00 3.91
1808 1870 7.008628 CCACGTTTTCTTTCAGATGATTATTGC 59.991 37.037 0.00 0.00 0.00 3.56
1809 1871 7.008628 GCCACGTTTTCTTTCAGATGATTATTG 59.991 37.037 0.00 0.00 0.00 1.90
1810 1872 7.029563 GCCACGTTTTCTTTCAGATGATTATT 58.970 34.615 0.00 0.00 0.00 1.40
1811 1873 6.150976 TGCCACGTTTTCTTTCAGATGATTAT 59.849 34.615 0.00 0.00 0.00 1.28
1812 1874 5.471797 TGCCACGTTTTCTTTCAGATGATTA 59.528 36.000 0.00 0.00 0.00 1.75
1813 1875 4.278170 TGCCACGTTTTCTTTCAGATGATT 59.722 37.500 0.00 0.00 0.00 2.57
1814 1876 3.820467 TGCCACGTTTTCTTTCAGATGAT 59.180 39.130 0.00 0.00 0.00 2.45
1815 1877 3.210227 TGCCACGTTTTCTTTCAGATGA 58.790 40.909 0.00 0.00 0.00 2.92
1816 1878 3.624326 TGCCACGTTTTCTTTCAGATG 57.376 42.857 0.00 0.00 0.00 2.90
1831 1893 0.242555 CAACACCCGGTTATTGCCAC 59.757 55.000 0.00 0.00 37.72 5.01
1835 1897 3.253677 TGCTTTACAACACCCGGTTATTG 59.746 43.478 0.00 9.06 37.72 1.90
1842 1904 2.096614 CGTACTTGCTTTACAACACCCG 60.097 50.000 0.00 0.00 33.68 5.28
1858 1920 4.098501 GCCTAACACCCATAAGTACGTACT 59.901 45.833 22.45 22.45 38.39 2.73
1877 1945 3.960755 CGTATGATATCATGGGGAGCCTA 59.039 47.826 25.44 1.98 37.15 3.93
1881 1949 5.643777 GGTTTTCGTATGATATCATGGGGAG 59.356 44.000 25.44 12.88 37.15 4.30
1887 1955 8.282592 CGAATGTTGGTTTTCGTATGATATCAT 58.717 33.333 21.50 21.50 39.77 2.45
1890 1958 6.540914 ACCGAATGTTGGTTTTCGTATGATAT 59.459 34.615 4.62 0.00 42.31 1.63
1914 1982 2.351738 CCTGGTTTTCATCGGCTTTCAC 60.352 50.000 0.00 0.00 0.00 3.18
1920 1988 2.052782 ATACCCTGGTTTTCATCGGC 57.947 50.000 0.00 0.00 0.00 5.54
1924 1992 7.415086 TGGTGTTAATATACCCTGGTTTTCAT 58.585 34.615 0.00 0.00 34.81 2.57
1925 1993 6.791371 TGGTGTTAATATACCCTGGTTTTCA 58.209 36.000 0.00 0.00 34.81 2.69
1926 1994 7.558444 TCATGGTGTTAATATACCCTGGTTTTC 59.442 37.037 0.00 0.00 34.81 2.29
1942 2010 5.250200 AGCGGTATTTCTTTCATGGTGTTA 58.750 37.500 0.00 0.00 0.00 2.41
1943 2011 4.079253 AGCGGTATTTCTTTCATGGTGTT 58.921 39.130 0.00 0.00 0.00 3.32
1945 2013 4.701956 AAGCGGTATTTCTTTCATGGTG 57.298 40.909 0.00 0.00 0.00 4.17
1946 2014 4.142687 CGAAAGCGGTATTTCTTTCATGGT 60.143 41.667 13.09 0.00 45.01 3.55
1948 2016 4.969816 ACGAAAGCGGTATTTCTTTCATG 58.030 39.130 13.09 0.00 45.01 3.07
1949 2017 5.622770 AACGAAAGCGGTATTTCTTTCAT 57.377 34.783 13.09 0.00 45.01 2.57
1950 2018 6.424509 TCTTAACGAAAGCGGTATTTCTTTCA 59.575 34.615 13.09 0.00 45.01 2.69
1951 2019 6.824557 TCTTAACGAAAGCGGTATTTCTTTC 58.175 36.000 0.00 5.02 39.80 2.62
1954 2022 5.575995 GTCTCTTAACGAAAGCGGTATTTCT 59.424 40.000 0.00 0.00 39.80 2.52
1955 2023 5.346822 TGTCTCTTAACGAAAGCGGTATTTC 59.653 40.000 0.00 0.00 39.80 2.17
1986 2054 3.456644 TCGTCCTCCTCTCTCTCTATGTT 59.543 47.826 0.00 0.00 0.00 2.71
1990 2058 1.409790 CGTCGTCCTCCTCTCTCTCTA 59.590 57.143 0.00 0.00 0.00 2.43
2018 2111 3.650907 TTAGTTCATCGCCGGCGCA 62.651 57.895 42.78 30.59 39.59 6.09
2020 2113 1.082117 AGTTTAGTTCATCGCCGGCG 61.082 55.000 42.13 42.13 41.35 6.46
2021 2114 1.859080 CTAGTTTAGTTCATCGCCGGC 59.141 52.381 19.07 19.07 0.00 6.13
2022 2115 2.470821 CCTAGTTTAGTTCATCGCCGG 58.529 52.381 0.00 0.00 0.00 6.13
2024 2117 1.859080 CGCCTAGTTTAGTTCATCGCC 59.141 52.381 0.00 0.00 0.00 5.54
2025 2118 1.258197 GCGCCTAGTTTAGTTCATCGC 59.742 52.381 0.00 0.00 0.00 4.58
2028 2121 6.425114 CAGAATATGCGCCTAGTTTAGTTCAT 59.575 38.462 4.18 0.00 0.00 2.57
2029 2122 5.753438 CAGAATATGCGCCTAGTTTAGTTCA 59.247 40.000 4.18 0.00 0.00 3.18
2030 2123 5.983720 TCAGAATATGCGCCTAGTTTAGTTC 59.016 40.000 4.18 0.00 0.00 3.01
2031 2124 5.914033 TCAGAATATGCGCCTAGTTTAGTT 58.086 37.500 4.18 0.00 0.00 2.24
2060 2181 5.295787 TGCGACCTAAAATGCTATTAAGTGG 59.704 40.000 0.00 0.00 0.00 4.00
2068 2189 5.733091 GCATCATTTGCGACCTAAAATGCTA 60.733 40.000 3.77 0.00 42.54 3.49
2070 2191 3.243643 GCATCATTTGCGACCTAAAATGC 59.756 43.478 3.77 0.00 42.54 3.56
2098 2231 2.185004 AGTGCATATATTCGGTGGCC 57.815 50.000 0.00 0.00 0.00 5.36
2099 2232 5.661458 ACTATAGTGCATATATTCGGTGGC 58.339 41.667 4.10 0.00 0.00 5.01
2100 2233 5.971792 CGACTATAGTGCATATATTCGGTGG 59.028 44.000 10.90 7.92 41.90 4.61
2101 2234 6.552629 ACGACTATAGTGCATATATTCGGTG 58.447 40.000 23.36 9.99 46.14 4.94
2102 2235 6.754702 ACGACTATAGTGCATATATTCGGT 57.245 37.500 23.36 14.62 46.14 4.69
2103 2236 9.007252 GTTAACGACTATAGTGCATATATTCGG 57.993 37.037 23.36 14.27 46.14 4.30
2104 2237 9.770503 AGTTAACGACTATAGTGCATATATTCG 57.229 33.333 10.90 20.84 46.74 3.34
2281 2414 8.984891 TTGCTGTCATTTCCTACAAATTTATG 57.015 30.769 0.00 0.00 0.00 1.90
2291 2424 6.207417 CCTTCTTCTTTTGCTGTCATTTCCTA 59.793 38.462 0.00 0.00 0.00 2.94
2303 2436 0.387750 CGGCTGCCTTCTTCTTTTGC 60.388 55.000 17.92 0.00 0.00 3.68
2304 2437 0.954452 ACGGCTGCCTTCTTCTTTTG 59.046 50.000 17.92 0.00 0.00 2.44
2307 2440 0.954452 CAAACGGCTGCCTTCTTCTT 59.046 50.000 17.92 0.00 0.00 2.52
2309 2442 1.581447 CCAAACGGCTGCCTTCTTC 59.419 57.895 17.92 0.00 0.00 2.87
2320 2453 3.363341 AAATACAGTGTTGCCAAACGG 57.637 42.857 0.00 0.00 39.30 4.44
2322 2455 5.457473 GTGTGTAAATACAGTGTTGCCAAAC 59.543 40.000 0.00 0.00 36.78 2.93
2323 2456 5.125578 TGTGTGTAAATACAGTGTTGCCAAA 59.874 36.000 0.00 0.00 36.78 3.28
2329 2462 5.070001 AGGCATGTGTGTAAATACAGTGTT 58.930 37.500 0.00 0.00 36.78 3.32
2393 2526 2.289002 ACTAACTACCGTAGATTCGCCG 59.711 50.000 12.66 0.00 0.00 6.46
2399 2532 5.688807 TGCCTAAGACTAACTACCGTAGAT 58.311 41.667 12.66 3.02 0.00 1.98
2405 2538 8.462589 AGTAGTATTGCCTAAGACTAACTACC 57.537 38.462 0.00 0.00 40.96 3.18
2420 2553 9.134734 GATTGTAGATGCTCTAAGTAGTATTGC 57.865 37.037 0.00 0.00 29.58 3.56
2442 2575 5.865552 GGATGGAATTTGTGAGTTGTGATTG 59.134 40.000 0.00 0.00 0.00 2.67
2454 2587 3.069443 AGCGTTTGTTGGATGGAATTTGT 59.931 39.130 0.00 0.00 0.00 2.83
2456 2589 3.611530 CGAGCGTTTGTTGGATGGAATTT 60.612 43.478 0.00 0.00 0.00 1.82
2467 2600 2.860293 CATCCGCGAGCGTTTGTT 59.140 55.556 8.23 0.00 37.81 2.83
2468 2601 3.788766 GCATCCGCGAGCGTTTGT 61.789 61.111 8.23 0.00 37.81 2.83
2498 2631 2.100631 GTCTGGTCATTGTCCGCGG 61.101 63.158 22.12 22.12 0.00 6.46
2507 2640 5.437060 ACTTTTAGTGTGTTGTCTGGTCAT 58.563 37.500 0.00 0.00 0.00 3.06
2509 2642 4.272748 GGACTTTTAGTGTGTTGTCTGGTC 59.727 45.833 0.00 0.00 0.00 4.02
2513 2646 5.589050 GGAAAGGACTTTTAGTGTGTTGTCT 59.411 40.000 0.00 0.00 32.11 3.41
2529 2662 2.418334 GGTATCTGGTCGTGGAAAGGAC 60.418 54.545 0.00 0.00 0.00 3.85
2533 2666 2.531771 TGAGGTATCTGGTCGTGGAAA 58.468 47.619 0.00 0.00 0.00 3.13
2534 2667 2.225382 TGAGGTATCTGGTCGTGGAA 57.775 50.000 0.00 0.00 0.00 3.53
2540 2673 5.012328 ACTCGAAAATGAGGTATCTGGTC 57.988 43.478 0.00 0.00 40.39 4.02
2542 2675 5.011090 TGACTCGAAAATGAGGTATCTGG 57.989 43.478 0.00 0.00 40.39 3.86
2544 2677 6.471233 TGATGACTCGAAAATGAGGTATCT 57.529 37.500 0.00 0.00 40.39 1.98
2546 2679 7.227512 GGATTTGATGACTCGAAAATGAGGTAT 59.772 37.037 0.00 0.00 40.39 2.73
2552 2685 7.696755 TGTATGGATTTGATGACTCGAAAATG 58.303 34.615 0.00 0.00 0.00 2.32
2557 2690 7.984617 TGTAATTGTATGGATTTGATGACTCGA 59.015 33.333 0.00 0.00 0.00 4.04
2558 2691 8.141835 TGTAATTGTATGGATTTGATGACTCG 57.858 34.615 0.00 0.00 0.00 4.18
2561 2694 8.136800 TGCATGTAATTGTATGGATTTGATGAC 58.863 33.333 0.00 0.00 0.00 3.06
2577 2710 6.877322 AGACTAGGTTTACGTTGCATGTAATT 59.123 34.615 11.49 0.00 30.49 1.40
2590 2723 5.118203 CGGCGCATATTTAGACTAGGTTTAC 59.882 44.000 10.83 0.00 0.00 2.01
2606 2739 2.103538 GACGGTCTTCGGCGCATA 59.896 61.111 10.83 0.00 44.45 3.14
2616 2749 1.578583 CGAAACAACAAGGACGGTCT 58.421 50.000 8.23 0.00 0.00 3.85
2628 2761 0.179094 ACGTGGACAGAGCGAAACAA 60.179 50.000 0.00 0.00 0.00 2.83
2633 2766 1.599797 TCAGACGTGGACAGAGCGA 60.600 57.895 0.00 0.00 0.00 4.93
2638 2771 0.456824 CATCCGTCAGACGTGGACAG 60.457 60.000 21.34 5.32 40.58 3.51
2645 2778 0.527817 GCTTACCCATCCGTCAGACG 60.528 60.000 16.50 16.50 42.11 4.18


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

AutoCloner maintained by Alex Coulton.