Multiple sequence alignment - TraesCS7A01G392600

Loading Multiple Alignment...

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 TraesCS7A01G392600 chr7A 100.000 2201 0 0 1 2201 569404997 569402797 0.000000e+00 4065.0
1 TraesCS7A01G392600 chr7B 93.481 1672 53 18 4 1651 531613035 531611396 0.000000e+00 2433.0
2 TraesCS7A01G392600 chr7B 86.697 218 29 0 1984 2201 531611221 531611004 2.180000e-60 243.0
3 TraesCS7A01G392600 chr7B 89.375 160 13 2 1779 1935 531611393 531611235 4.790000e-47 198.0
4 TraesCS7A01G392600 chr7B 91.429 140 10 2 1646 1784 140609535 140609397 8.020000e-45 191.0
5 TraesCS7A01G392600 chr7D 92.868 1332 40 21 2 1311 501901250 501899952 0.000000e+00 1882.0
6 TraesCS7A01G392600 chr7D 92.414 435 16 11 894 1327 501842029 501842447 2.420000e-169 604.0
7 TraesCS7A01G392600 chr7D 85.047 321 9 11 1340 1651 501899957 501899667 7.690000e-75 291.0
8 TraesCS7A01G392600 chr7D 89.427 227 24 0 1975 2201 501899539 501899313 9.940000e-74 287.0
9 TraesCS7A01G392600 chr3A 92.754 138 10 0 1649 1786 110030183 110030046 1.330000e-47 200.0
10 TraesCS7A01G392600 chr3A 92.701 137 10 0 1650 1786 469077433 469077569 4.790000e-47 198.0
11 TraesCS7A01G392600 chr2D 93.985 133 6 1 1649 1781 100314158 100314028 1.330000e-47 200.0
12 TraesCS7A01G392600 chr2D 88.636 88 6 3 1895 1980 323075512 323075597 1.070000e-18 104.0
13 TraesCS7A01G392600 chr2A 93.893 131 6 2 1648 1777 674600045 674599916 1.720000e-46 196.0
14 TraesCS7A01G392600 chr2A 93.893 131 6 2 1648 1777 674715018 674714889 1.720000e-46 196.0
15 TraesCS7A01G392600 chr6D 92.593 135 10 0 1650 1784 35022452 35022318 6.200000e-46 195.0
16 TraesCS7A01G392600 chr6D 85.263 95 10 4 1894 1985 297523584 297523491 6.470000e-16 95.3
17 TraesCS7A01G392600 chr4B 92.086 139 9 2 1649 1786 25944471 25944334 6.200000e-46 195.0
18 TraesCS7A01G392600 chr3B 92.029 138 10 1 1648 1785 407477763 407477899 2.230000e-45 193.0
19 TraesCS7A01G392600 chr3D 89.535 86 6 3 1896 1980 312907591 312907508 2.990000e-19 106.0
20 TraesCS7A01G392600 chr5A 88.506 87 8 2 1895 1980 473843860 473843775 1.070000e-18 104.0
21 TraesCS7A01G392600 chr6A 87.209 86 9 2 1896 1980 463531082 463531166 1.800000e-16 97.1
22 TraesCS7A01G392600 chr4D 87.356 87 7 3 1896 1980 77021574 77021658 1.800000e-16 97.1
23 TraesCS7A01G392600 chr4A 87.356 87 7 3 1896 1980 440964907 440964823 1.800000e-16 97.1
24 TraesCS7A01G392600 chr1A 86.517 89 10 2 1896 1983 588495266 588495179 1.800000e-16 97.1
25 TraesCS7A01G392600 chr2B 85.263 95 10 3 1889 1981 362021231 362021139 6.470000e-16 95.3


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 TraesCS7A01G392600 chr7A 569402797 569404997 2200 True 4065 4065 100.000 1 2201 1 chr7A.!!$R1 2200
1 TraesCS7A01G392600 chr7B 531611004 531613035 2031 True 958 2433 89.851 4 2201 3 chr7B.!!$R2 2197
2 TraesCS7A01G392600 chr7D 501899313 501901250 1937 True 820 1882 89.114 2 2201 3 chr7D.!!$R1 2199

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
181 182 0.320771 CTAGCTGTCCCGCAAGTTGT 60.321 55.0 4.48 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 1811 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
94 95 9.745018 ATGCATCTTATTACTGGCATAATTACT 57.255 29.630 0.00 0.00 39.92 2.24
151 152 2.050077 GCGGCACTGCTTGGAAAC 60.050 61.111 0.00 0.00 0.00 2.78
179 180 1.376037 GCTAGCTGTCCCGCAAGTT 60.376 57.895 7.70 0.00 0.00 2.66
180 181 1.639298 GCTAGCTGTCCCGCAAGTTG 61.639 60.000 7.70 0.00 0.00 3.16
181 182 0.320771 CTAGCTGTCCCGCAAGTTGT 60.321 55.000 4.48 0.00 0.00 3.32
182 183 0.602638 TAGCTGTCCCGCAAGTTGTG 60.603 55.000 9.54 9.54 0.00 3.33
424 426 9.204337 TGAATTACATCATCATCCCAGAAAAAT 57.796 29.630 0.00 0.00 0.00 1.82
476 480 3.277142 ACCTTAAAACGATGGGCTAGG 57.723 47.619 0.00 0.00 0.00 3.02
510 514 0.375454 TTTCGCCACAATTATCGCCG 59.625 50.000 0.00 0.00 0.00 6.46
560 568 1.364901 CCCGATCCATGCATTTGCC 59.635 57.895 0.00 0.00 41.18 4.52
736 744 2.941720 CAAGAATCCTTCAGGTAGCAGC 59.058 50.000 0.00 0.00 36.34 5.25
737 745 2.191400 AGAATCCTTCAGGTAGCAGCA 58.809 47.619 0.00 0.00 36.34 4.41
738 746 2.170187 AGAATCCTTCAGGTAGCAGCAG 59.830 50.000 0.00 0.00 36.34 4.24
1010 1041 1.034292 GCTGCAAGAATGGGAGGGAC 61.034 60.000 0.00 0.00 34.07 4.46
1209 1240 1.740905 GGCTACCTAGGCTCGGTTC 59.259 63.158 16.61 8.58 44.61 3.62
1215 1246 3.028094 ACCTAGGCTCGGTTCATCTTA 57.972 47.619 9.30 0.00 0.00 2.10
1306 1337 2.362077 GCTTGGTTAATCGGCCATTGAT 59.638 45.455 2.24 0.00 34.37 2.57
1316 1347 2.955660 TCGGCCATTGATTTGTTATCCC 59.044 45.455 2.24 0.00 0.00 3.85
1329 1360 2.027192 TGTTATCCCGCTGCTCTCTTTT 60.027 45.455 0.00 0.00 0.00 2.27
1438 1476 3.824810 GCTGGAGGCATGAGCTTC 58.175 61.111 0.00 0.00 45.35 3.86
1443 1481 2.104451 CTGGAGGCATGAGCTTCTGTAT 59.896 50.000 0.00 0.00 45.39 2.29
1449 1487 3.881688 GGCATGAGCTTCTGTATGTGAAT 59.118 43.478 0.00 0.00 41.70 2.57
1598 1654 4.456911 GCATATGCCTACAGTTGCACATAT 59.543 41.667 17.26 2.40 40.88 1.78
1651 1709 7.253817 CGTCTCTAAGCTTAAAGTTGCTCATAC 60.254 40.741 7.74 0.00 38.75 2.39
1653 1711 7.976734 TCTCTAAGCTTAAAGTTGCTCATACTC 59.023 37.037 7.74 0.00 38.75 2.59
1654 1712 7.042335 TCTAAGCTTAAAGTTGCTCATACTCC 58.958 38.462 7.74 0.00 38.75 3.85
1655 1713 4.518249 AGCTTAAAGTTGCTCATACTCCC 58.482 43.478 0.00 0.00 33.90 4.30
1656 1714 4.226168 AGCTTAAAGTTGCTCATACTCCCT 59.774 41.667 0.00 0.00 33.90 4.20
1657 1715 4.572795 GCTTAAAGTTGCTCATACTCCCTC 59.427 45.833 0.00 0.00 0.00 4.30
1658 1716 3.636153 AAAGTTGCTCATACTCCCTCC 57.364 47.619 0.00 0.00 0.00 4.30
1659 1717 2.254152 AGTTGCTCATACTCCCTCCA 57.746 50.000 0.00 0.00 0.00 3.86
1660 1718 2.769209 AGTTGCTCATACTCCCTCCAT 58.231 47.619 0.00 0.00 0.00 3.41
1661 1719 2.703007 AGTTGCTCATACTCCCTCCATC 59.297 50.000 0.00 0.00 0.00 3.51
1662 1720 1.722034 TGCTCATACTCCCTCCATCC 58.278 55.000 0.00 0.00 0.00 3.51
1663 1721 0.605589 GCTCATACTCCCTCCATCCG 59.394 60.000 0.00 0.00 0.00 4.18
1664 1722 1.261480 CTCATACTCCCTCCATCCGG 58.739 60.000 0.00 0.00 0.00 5.14
1665 1723 0.857675 TCATACTCCCTCCATCCGGA 59.142 55.000 6.61 6.61 39.79 5.14
1666 1724 1.219469 TCATACTCCCTCCATCCGGAA 59.781 52.381 9.01 0.00 42.21 4.30
1667 1725 2.047061 CATACTCCCTCCATCCGGAAA 58.953 52.381 9.01 0.00 42.21 3.13
1668 1726 2.489528 TACTCCCTCCATCCGGAAAT 57.510 50.000 9.01 0.00 42.21 2.17
1669 1727 2.489528 ACTCCCTCCATCCGGAAATA 57.510 50.000 9.01 0.00 42.21 1.40
1670 1728 2.047830 ACTCCCTCCATCCGGAAATAC 58.952 52.381 9.01 0.00 42.21 1.89
1671 1729 2.330216 CTCCCTCCATCCGGAAATACT 58.670 52.381 9.01 0.00 42.21 2.12
1672 1730 2.706190 CTCCCTCCATCCGGAAATACTT 59.294 50.000 9.01 0.00 42.21 2.24
1673 1731 2.438021 TCCCTCCATCCGGAAATACTTG 59.562 50.000 9.01 0.00 42.21 3.16
1674 1732 2.172717 CCCTCCATCCGGAAATACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
1675 1733 3.467803 CCTCCATCCGGAAATACTTGTC 58.532 50.000 9.01 0.00 42.21 3.18
1676 1734 3.118408 CCTCCATCCGGAAATACTTGTCA 60.118 47.826 9.01 0.00 42.21 3.58
1677 1735 4.444876 CCTCCATCCGGAAATACTTGTCAT 60.445 45.833 9.01 0.00 42.21 3.06
1678 1736 5.110814 TCCATCCGGAAATACTTGTCATT 57.889 39.130 9.01 0.00 38.83 2.57
1679 1737 6.241882 TCCATCCGGAAATACTTGTCATTA 57.758 37.500 9.01 0.00 38.83 1.90
1680 1738 6.654959 TCCATCCGGAAATACTTGTCATTAA 58.345 36.000 9.01 0.00 38.83 1.40
1681 1739 7.113437 TCCATCCGGAAATACTTGTCATTAAA 58.887 34.615 9.01 0.00 38.83 1.52
1682 1740 7.612244 TCCATCCGGAAATACTTGTCATTAAAA 59.388 33.333 9.01 0.00 38.83 1.52
1683 1741 8.413229 CCATCCGGAAATACTTGTCATTAAAAT 58.587 33.333 9.01 0.00 0.00 1.82
1684 1742 9.236691 CATCCGGAAATACTTGTCATTAAAATG 57.763 33.333 9.01 0.00 37.75 2.32
1685 1743 7.767261 TCCGGAAATACTTGTCATTAAAATGG 58.233 34.615 0.00 0.00 37.03 3.16
1686 1744 7.612244 TCCGGAAATACTTGTCATTAAAATGGA 59.388 33.333 0.00 0.00 37.03 3.41
1687 1745 8.413229 CCGGAAATACTTGTCATTAAAATGGAT 58.587 33.333 0.00 0.00 37.03 3.41
1708 1766 9.968870 ATGGATAGAAAAGAACGTATCTAGAAC 57.031 33.333 0.00 0.00 37.42 3.01
1709 1767 8.127327 TGGATAGAAAAGAACGTATCTAGAACG 58.873 37.037 19.25 19.25 45.64 3.95
1710 1768 8.341173 GGATAGAAAAGAACGTATCTAGAACGA 58.659 37.037 24.46 2.19 42.90 3.85
1711 1769 9.713740 GATAGAAAAGAACGTATCTAGAACGAA 57.286 33.333 24.46 0.22 42.90 3.85
1713 1771 8.807667 AGAAAAGAACGTATCTAGAACGAAAA 57.192 30.769 24.46 0.00 42.90 2.29
1714 1772 9.420551 AGAAAAGAACGTATCTAGAACGAAAAT 57.579 29.630 24.46 12.92 42.90 1.82
1717 1775 9.630098 AAAGAACGTATCTAGAACGAAAATACA 57.370 29.630 24.46 0.00 42.90 2.29
1718 1776 9.798994 AAGAACGTATCTAGAACGAAAATACAT 57.201 29.630 24.46 4.31 42.90 2.29
1719 1777 9.448294 AGAACGTATCTAGAACGAAAATACATC 57.552 33.333 24.46 10.95 42.90 3.06
1720 1778 9.448294 GAACGTATCTAGAACGAAAATACATCT 57.552 33.333 24.46 5.02 42.90 2.90
1730 1788 9.915629 AGAACGAAAATACATCTAGATACATCC 57.084 33.333 4.54 0.00 0.00 3.51
1731 1789 9.141400 GAACGAAAATACATCTAGATACATCCC 57.859 37.037 4.54 0.00 0.00 3.85
1732 1790 7.612677 ACGAAAATACATCTAGATACATCCCC 58.387 38.462 4.54 0.00 0.00 4.81
1733 1791 7.455008 ACGAAAATACATCTAGATACATCCCCT 59.545 37.037 4.54 0.00 0.00 4.79
1734 1792 8.314751 CGAAAATACATCTAGATACATCCCCTT 58.685 37.037 4.54 0.00 0.00 3.95
1741 1799 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
1747 1805 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
1750 1808 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
1751 1809 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
1752 1810 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
1753 1811 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
1754 1812 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
1755 1813 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
1762 1820 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
1763 1821 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
1764 1822 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
1765 1823 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1766 1824 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1767 1825 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1768 1826 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1769 1827 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1770 1828 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1771 1829 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1772 1830 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1773 1831 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1774 1832 1.397390 TATTTCCGGACGGAGGGAGC 61.397 60.000 13.64 0.00 46.06 4.70
1775 1833 4.689549 TTCCGGACGGAGGGAGCA 62.690 66.667 13.64 0.00 46.06 4.26
1776 1834 3.976490 TTCCGGACGGAGGGAGCAT 62.976 63.158 13.64 0.00 46.06 3.79
1777 1835 2.520982 CCGGACGGAGGGAGCATA 60.521 66.667 4.40 0.00 37.50 3.14
1882 1943 5.920840 TCATTCAAGTAAAGACTGACACTCG 59.079 40.000 0.00 0.00 35.52 4.18
1905 1966 5.008712 CGTATGTTGCTATGTACTCTCTCCA 59.991 44.000 0.00 0.00 0.00 3.86
1915 1976 7.561722 GCTATGTACTCTCTCCATCCCATAATA 59.438 40.741 0.00 0.00 0.00 0.98
1926 1987 7.618117 TCTCCATCCCATAATATAAGAGCGTTA 59.382 37.037 0.00 0.00 0.00 3.18
1929 1990 9.396022 CCATCCCATAATATAAGAGCGTTATTT 57.604 33.333 0.40 0.00 0.00 1.40
1941 2002 7.829378 AAGAGCGTTATTTTACACTAAGAGG 57.171 36.000 0.00 0.00 0.00 3.69
1942 2003 6.932947 AGAGCGTTATTTTACACTAAGAGGT 58.067 36.000 0.00 0.00 0.00 3.85
1945 2006 6.589139 AGCGTTATTTTACACTAAGAGGTGTC 59.411 38.462 3.48 0.00 45.94 3.67
1946 2007 6.366877 GCGTTATTTTACACTAAGAGGTGTCA 59.633 38.462 3.48 0.00 45.94 3.58
1947 2008 7.095523 GCGTTATTTTACACTAAGAGGTGTCAA 60.096 37.037 3.48 0.00 45.94 3.18
1948 2009 8.767085 CGTTATTTTACACTAAGAGGTGTCAAA 58.233 33.333 3.48 6.56 45.94 2.69
1952 2013 7.962964 TTTACACTAAGAGGTGTCAAAGATG 57.037 36.000 3.48 0.00 45.94 2.90
1953 2014 4.319177 ACACTAAGAGGTGTCAAAGATGC 58.681 43.478 0.00 0.00 45.94 3.91
1954 2015 4.040952 ACACTAAGAGGTGTCAAAGATGCT 59.959 41.667 0.00 0.00 45.94 3.79
1955 2016 4.629200 CACTAAGAGGTGTCAAAGATGCTC 59.371 45.833 0.00 0.00 33.04 4.26
1956 2017 4.530161 ACTAAGAGGTGTCAAAGATGCTCT 59.470 41.667 0.00 0.00 0.00 4.09
1957 2018 4.363991 AAGAGGTGTCAAAGATGCTCTT 57.636 40.909 0.00 0.00 38.59 2.85
1958 2019 5.489792 AAGAGGTGTCAAAGATGCTCTTA 57.510 39.130 0.00 0.00 35.27 2.10
1959 2020 5.690464 AGAGGTGTCAAAGATGCTCTTAT 57.310 39.130 0.00 0.00 35.27 1.73
1960 2021 6.798427 AGAGGTGTCAAAGATGCTCTTATA 57.202 37.500 0.00 0.00 35.27 0.98
1961 2022 7.372260 AGAGGTGTCAAAGATGCTCTTATAT 57.628 36.000 0.00 0.00 35.27 0.86
1962 2023 7.800092 AGAGGTGTCAAAGATGCTCTTATATT 58.200 34.615 0.00 0.00 35.27 1.28
1963 2024 8.928448 AGAGGTGTCAAAGATGCTCTTATATTA 58.072 33.333 0.00 0.00 35.27 0.98
1964 2025 9.717942 GAGGTGTCAAAGATGCTCTTATATTAT 57.282 33.333 0.00 0.00 35.27 1.28
1965 2026 9.499479 AGGTGTCAAAGATGCTCTTATATTATG 57.501 33.333 0.00 0.00 35.27 1.90
1966 2027 8.725148 GGTGTCAAAGATGCTCTTATATTATGG 58.275 37.037 0.00 0.00 35.27 2.74
1967 2028 8.725148 GTGTCAAAGATGCTCTTATATTATGGG 58.275 37.037 0.00 0.00 35.27 4.00
1968 2029 8.659527 TGTCAAAGATGCTCTTATATTATGGGA 58.340 33.333 0.00 0.00 35.27 4.37
1969 2030 8.940952 GTCAAAGATGCTCTTATATTATGGGAC 58.059 37.037 0.00 0.00 35.27 4.46
1970 2031 8.884323 TCAAAGATGCTCTTATATTATGGGACT 58.116 33.333 0.00 0.00 35.27 3.85
1971 2032 8.944029 CAAAGATGCTCTTATATTATGGGACTG 58.056 37.037 0.00 0.00 35.27 3.51
1972 2033 8.441311 AAGATGCTCTTATATTATGGGACTGA 57.559 34.615 0.00 0.00 34.42 3.41
1973 2034 8.076910 AGATGCTCTTATATTATGGGACTGAG 57.923 38.462 0.00 0.00 0.00 3.35
1981 2042 6.936968 ATATTATGGGACTGAGGGAGTAAC 57.063 41.667 0.00 0.00 33.83 2.50
1992 2053 7.123847 GGACTGAGGGAGTAACTCTAAATGTAA 59.876 40.741 0.00 0.00 33.83 2.41
1999 2060 9.281371 GGGAGTAACTCTAAATGTAAACAGTTT 57.719 33.333 3.49 3.49 35.62 2.66
2009 2070 7.581213 AAATGTAAACAGTTTCAGTGATGGA 57.419 32.000 0.48 0.00 28.91 3.41
2011 2072 6.371809 TGTAAACAGTTTCAGTGATGGAAC 57.628 37.500 0.48 0.00 0.00 3.62
2040 2101 3.697166 CCAATAGGGTTAGTGGCAAAGT 58.303 45.455 0.00 0.00 38.11 2.66
2048 2109 2.163818 TAGTGGCAAAGTCGTGAAGG 57.836 50.000 0.00 0.00 0.00 3.46
2074 2135 0.689623 AGCAGGAGCAAGCTACAAGT 59.310 50.000 7.10 0.00 45.49 3.16
2080 2141 4.399618 CAGGAGCAAGCTACAAGTCTAGTA 59.600 45.833 7.10 0.00 0.00 1.82
2150 2211 0.896226 GCCCCGAAACTGAGAGTAGT 59.104 55.000 0.00 0.00 0.00 2.73
2151 2212 1.404315 GCCCCGAAACTGAGAGTAGTG 60.404 57.143 0.00 0.00 0.00 2.74
2159 2220 5.411977 CGAAACTGAGAGTAGTGACTTCCTA 59.588 44.000 0.00 0.00 35.45 2.94
2198 2259 4.983215 TTGTGTTGTTATCGTACTGCAG 57.017 40.909 13.48 13.48 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.119316 CCACTTGGTTGTTGCACTGTTTA 60.119 43.478 0.00 0.00 0.00 2.01
5 6 1.204467 CCACTTGGTTGTTGCACTGTT 59.796 47.619 0.00 0.00 0.00 3.16
7 8 3.646650 CCACTTGGTTGTTGCACTG 57.353 52.632 0.00 0.00 0.00 3.66
93 94 4.095483 CACTTGCTGCCCAAAGTAGAATAG 59.905 45.833 3.87 0.00 31.94 1.73
94 95 4.009675 CACTTGCTGCCCAAAGTAGAATA 58.990 43.478 3.87 0.00 31.94 1.75
95 96 2.821969 CACTTGCTGCCCAAAGTAGAAT 59.178 45.455 3.87 0.00 31.94 2.40
212 213 1.268083 CGATCACTACACTGCGTCGAT 60.268 52.381 0.00 0.00 0.00 3.59
476 480 3.186909 GGCGAAATGCTATTTTGGGTTC 58.813 45.455 9.49 0.00 45.43 3.62
486 490 3.303725 GCGATAATTGTGGCGAAATGCTA 60.304 43.478 0.00 0.00 45.43 3.49
822 836 2.498078 CGATTTATAGGGGAGGGAGAGC 59.502 54.545 0.00 0.00 0.00 4.09
1010 1041 3.853330 CGCCGAAGCACGACATGG 61.853 66.667 0.00 0.00 45.77 3.66
1104 1135 3.687102 CCGACGTACCACAGCCCA 61.687 66.667 0.00 0.00 0.00 5.36
1206 1237 3.599046 CGGAAGCAGCATAAGATGAAC 57.401 47.619 0.00 0.00 31.30 3.18
1306 1337 1.555075 AGAGAGCAGCGGGATAACAAA 59.445 47.619 0.00 0.00 0.00 2.83
1316 1347 4.241681 AGAACTAGAAAAAGAGAGCAGCG 58.758 43.478 0.00 0.00 0.00 5.18
1443 1481 7.404104 AGGCCAATATCTCTCCATATATTCACA 59.596 37.037 5.01 0.00 0.00 3.58
1449 1487 7.574021 ACAAAGGCCAATATCTCTCCATATA 57.426 36.000 5.01 0.00 0.00 0.86
1558 1604 2.551355 TGCTTCGATCGACTCTGAAG 57.449 50.000 19.26 12.52 37.47 3.02
1598 1654 4.780815 ACTGGAGTTGTTCATCAAACTCA 58.219 39.130 15.25 3.75 38.76 3.41
1656 1714 4.771114 ATGACAAGTATTTCCGGATGGA 57.229 40.909 4.15 0.00 44.61 3.41
1657 1715 6.935741 TTAATGACAAGTATTTCCGGATGG 57.064 37.500 4.15 0.00 0.00 3.51
1658 1716 9.236691 CATTTTAATGACAAGTATTTCCGGATG 57.763 33.333 4.15 0.97 38.70 3.51
1659 1717 8.413229 CCATTTTAATGACAAGTATTTCCGGAT 58.587 33.333 4.15 0.00 38.70 4.18
1660 1718 7.612244 TCCATTTTAATGACAAGTATTTCCGGA 59.388 33.333 0.00 0.00 38.70 5.14
1661 1719 7.767261 TCCATTTTAATGACAAGTATTTCCGG 58.233 34.615 0.00 0.00 38.70 5.14
1682 1740 9.968870 GTTCTAGATACGTTCTTTTCTATCCAT 57.031 33.333 0.00 0.00 35.79 3.41
1683 1741 8.127327 CGTTCTAGATACGTTCTTTTCTATCCA 58.873 37.037 15.11 0.00 35.79 3.41
1684 1742 8.341173 TCGTTCTAGATACGTTCTTTTCTATCC 58.659 37.037 19.69 0.00 39.84 2.59
1685 1743 9.713740 TTCGTTCTAGATACGTTCTTTTCTATC 57.286 33.333 19.69 0.00 39.84 2.08
1687 1745 9.897744 TTTTCGTTCTAGATACGTTCTTTTCTA 57.102 29.630 19.69 0.00 39.84 2.10
1688 1746 8.807667 TTTTCGTTCTAGATACGTTCTTTTCT 57.192 30.769 19.69 0.00 39.84 2.52
1691 1749 9.630098 TGTATTTTCGTTCTAGATACGTTCTTT 57.370 29.630 19.69 10.09 39.84 2.52
1692 1750 9.798994 ATGTATTTTCGTTCTAGATACGTTCTT 57.201 29.630 19.69 10.99 39.84 2.52
1693 1751 9.448294 GATGTATTTTCGTTCTAGATACGTTCT 57.552 33.333 19.69 0.00 39.84 3.01
1694 1752 9.448294 AGATGTATTTTCGTTCTAGATACGTTC 57.552 33.333 19.69 8.60 39.84 3.95
1704 1762 9.915629 GGATGTATCTAGATGTATTTTCGTTCT 57.084 33.333 15.79 0.00 0.00 3.01
1705 1763 9.141400 GGGATGTATCTAGATGTATTTTCGTTC 57.859 37.037 15.79 0.00 0.00 3.95
1706 1764 8.095169 GGGGATGTATCTAGATGTATTTTCGTT 58.905 37.037 15.79 0.00 0.00 3.85
1707 1765 7.455008 AGGGGATGTATCTAGATGTATTTTCGT 59.545 37.037 15.79 0.00 0.00 3.85
1708 1766 7.841956 AGGGGATGTATCTAGATGTATTTTCG 58.158 38.462 15.79 0.00 0.00 3.46
1715 1773 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
1721 1779 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
1724 1782 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
1725 1783 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
1726 1784 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
1727 1785 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
1728 1786 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
1729 1787 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
1737 1795 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
1738 1796 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
1739 1797 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
1740 1798 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1741 1799 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1742 1800 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1743 1801 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1744 1802 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1745 1803 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1746 1804 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1747 1805 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1748 1806 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1749 1807 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1750 1808 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1751 1809 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1752 1810 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1753 1811 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1754 1812 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1755 1813 1.397390 GCTCCCTCCGTCCGGAAATA 61.397 60.000 5.23 0.00 44.66 1.40
1756 1814 2.732619 GCTCCCTCCGTCCGGAAAT 61.733 63.158 5.23 0.00 44.66 2.17
1757 1815 3.387947 GCTCCCTCCGTCCGGAAA 61.388 66.667 5.23 0.00 44.66 3.13
1758 1816 2.577020 TATGCTCCCTCCGTCCGGAA 62.577 60.000 5.23 0.00 44.66 4.30
1759 1817 2.577020 TTATGCTCCCTCCGTCCGGA 62.577 60.000 0.00 0.00 42.90 5.14
1760 1818 2.131709 TTATGCTCCCTCCGTCCGG 61.132 63.158 0.00 0.00 0.00 5.14
1761 1819 1.067582 GTTATGCTCCCTCCGTCCG 59.932 63.158 0.00 0.00 0.00 4.79
1762 1820 0.759346 ATGTTATGCTCCCTCCGTCC 59.241 55.000 0.00 0.00 0.00 4.79
1763 1821 3.321111 TCTTATGTTATGCTCCCTCCGTC 59.679 47.826 0.00 0.00 0.00 4.79
1764 1822 3.305720 TCTTATGTTATGCTCCCTCCGT 58.694 45.455 0.00 0.00 0.00 4.69
1765 1823 4.248859 CATCTTATGTTATGCTCCCTCCG 58.751 47.826 0.00 0.00 0.00 4.63
1766 1824 5.234466 ACATCTTATGTTATGCTCCCTCC 57.766 43.478 0.00 0.00 41.63 4.30
1789 1847 5.856156 TCTAACGGTCAATTAAGTGGTTGA 58.144 37.500 2.65 0.00 32.31 3.18
1871 1932 2.947852 AGCAACATACGAGTGTCAGTC 58.052 47.619 0.00 0.00 0.00 3.51
1874 1935 4.450082 ACATAGCAACATACGAGTGTCA 57.550 40.909 0.00 0.00 0.00 3.58
1882 1943 6.392625 TGGAGAGAGTACATAGCAACATAC 57.607 41.667 0.00 0.00 0.00 2.39
1915 1976 9.530633 CCTCTTAGTGTAAAATAACGCTCTTAT 57.469 33.333 0.00 0.00 40.56 1.73
1932 1993 4.573900 AGCATCTTTGACACCTCTTAGTG 58.426 43.478 0.00 0.00 43.65 2.74
1933 1994 4.826556 GAGCATCTTTGACACCTCTTAGT 58.173 43.478 0.00 0.00 0.00 2.24
1949 2010 7.271511 CCTCAGTCCCATAATATAAGAGCATC 58.728 42.308 0.00 0.00 0.00 3.91
1950 2011 6.157645 CCCTCAGTCCCATAATATAAGAGCAT 59.842 42.308 0.00 0.00 0.00 3.79
1951 2012 5.485353 CCCTCAGTCCCATAATATAAGAGCA 59.515 44.000 0.00 0.00 0.00 4.26
1952 2013 5.721960 TCCCTCAGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
1953 2014 6.957020 ACTCCCTCAGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
1954 2015 6.875469 ACTCCCTCAGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
1955 2016 8.532819 GTTACTCCCTCAGTCCCATAATATAAG 58.467 40.741 0.00 0.00 36.43 1.73
1956 2017 8.239478 AGTTACTCCCTCAGTCCCATAATATAA 58.761 37.037 0.00 0.00 36.43 0.98
1957 2018 7.776745 AGTTACTCCCTCAGTCCCATAATATA 58.223 38.462 0.00 0.00 36.43 0.86
1958 2019 6.635021 AGTTACTCCCTCAGTCCCATAATAT 58.365 40.000 0.00 0.00 36.43 1.28
1959 2020 6.039415 AGTTACTCCCTCAGTCCCATAATA 57.961 41.667 0.00 0.00 36.43 0.98
1960 2021 4.897051 AGTTACTCCCTCAGTCCCATAAT 58.103 43.478 0.00 0.00 36.43 1.28
1961 2022 4.016479 AGAGTTACTCCCTCAGTCCCATAA 60.016 45.833 8.96 0.00 36.43 1.90
1962 2023 3.532232 AGAGTTACTCCCTCAGTCCCATA 59.468 47.826 8.96 0.00 36.43 2.74
1963 2024 2.316372 AGAGTTACTCCCTCAGTCCCAT 59.684 50.000 8.96 0.00 36.43 4.00
1964 2025 1.717077 AGAGTTACTCCCTCAGTCCCA 59.283 52.381 8.96 0.00 36.43 4.37
1965 2026 2.535836 AGAGTTACTCCCTCAGTCCC 57.464 55.000 8.96 0.00 36.43 4.46
1966 2027 5.422650 ACATTTAGAGTTACTCCCTCAGTCC 59.577 44.000 8.96 0.00 36.43 3.85
1967 2028 6.532988 ACATTTAGAGTTACTCCCTCAGTC 57.467 41.667 8.96 0.00 36.43 3.51
1968 2029 8.312564 GTTTACATTTAGAGTTACTCCCTCAGT 58.687 37.037 8.96 5.79 39.41 3.41
1969 2030 8.311836 TGTTTACATTTAGAGTTACTCCCTCAG 58.688 37.037 8.96 0.00 0.00 3.35
1970 2031 8.197592 TGTTTACATTTAGAGTTACTCCCTCA 57.802 34.615 8.96 0.00 0.00 3.86
1971 2032 8.312564 ACTGTTTACATTTAGAGTTACTCCCTC 58.687 37.037 8.96 0.00 0.00 4.30
1972 2033 8.203681 ACTGTTTACATTTAGAGTTACTCCCT 57.796 34.615 8.96 0.00 0.00 4.20
1973 2034 8.843885 AACTGTTTACATTTAGAGTTACTCCC 57.156 34.615 8.96 0.00 0.00 4.30
1981 2042 9.817365 CATCACTGAAACTGTTTACATTTAGAG 57.183 33.333 5.64 0.00 0.00 2.43
1992 2053 3.804036 TCGTTCCATCACTGAAACTGTT 58.196 40.909 0.00 0.00 0.00 3.16
1999 2060 2.362397 GGCTCTATCGTTCCATCACTGA 59.638 50.000 0.00 0.00 0.00 3.41
2009 2070 4.900054 ACTAACCCTATTGGCTCTATCGTT 59.100 41.667 0.00 0.00 37.83 3.85
2011 2072 4.322049 CCACTAACCCTATTGGCTCTATCG 60.322 50.000 0.00 0.00 37.83 2.92
2036 2097 3.181469 TGCTCAAGTACCTTCACGACTTT 60.181 43.478 0.00 0.00 31.04 2.66
2040 2101 1.272490 CCTGCTCAAGTACCTTCACGA 59.728 52.381 0.00 0.00 0.00 4.35
2048 2109 1.082690 GCTTGCTCCTGCTCAAGTAC 58.917 55.000 0.00 0.00 41.15 2.73
2085 2146 1.803334 TCTGAGCGCGGTTTGTAAAT 58.197 45.000 14.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.