Multiple sequence alignment - TraesCS4D01G231400

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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 TraesCS4D01G231400 chr4D 100.000 3994 0 0 1 3994 391040718 391036725 0.000000e+00 7376.0
1 TraesCS4D01G231400 chr4D 91.875 160 11 2 1677 1836 90391247 90391404 5.200000e-54 222.0
2 TraesCS4D01G231400 chr4D 87.568 185 19 4 1651 1833 455756856 455756674 1.120000e-50 211.0
3 TraesCS4D01G231400 chr4D 82.482 137 24 0 1699 1835 115068571 115068435 1.950000e-23 121.0
4 TraesCS4D01G231400 chr4A 93.845 2177 109 15 1831 3994 72924514 72922350 0.000000e+00 3254.0
5 TraesCS4D01G231400 chr4A 89.254 1675 94 34 41 1649 72926171 72924517 0.000000e+00 2017.0
6 TraesCS4D01G231400 chr4B 92.734 2202 102 28 1831 3994 480925053 480922872 0.000000e+00 3127.0
7 TraesCS4D01G231400 chr4B 91.563 1612 85 25 66 1652 480926637 480925052 0.000000e+00 2176.0
8 TraesCS4D01G231400 chr6D 91.875 160 11 2 1677 1836 286157151 286157308 5.200000e-54 222.0
9 TraesCS4D01G231400 chr5D 91.875 160 11 2 1677 1836 8845827 8845984 5.200000e-54 222.0
10 TraesCS4D01G231400 chr5D 91.875 160 11 2 1677 1836 124138866 124139023 5.200000e-54 222.0
11 TraesCS4D01G231400 chr5D 91.875 160 11 2 1677 1836 365042900 365042743 5.200000e-54 222.0
12 TraesCS4D01G231400 chr5D 91.875 160 11 2 1677 1836 440541837 440541994 5.200000e-54 222.0
13 TraesCS4D01G231400 chr5D 91.875 160 11 2 1677 1836 470364289 470364446 5.200000e-54 222.0
14 TraesCS4D01G231400 chr1D 91.875 160 11 2 1677 1836 383864853 383864696 5.200000e-54 222.0
15 TraesCS4D01G231400 chr1D 88.667 150 16 1 1684 1833 301948781 301948633 8.820000e-42 182.0
16 TraesCS4D01G231400 chr1D 88.462 130 15 0 1704 1833 71286470 71286341 1.490000e-34 158.0
17 TraesCS4D01G231400 chr3D 86.928 153 20 0 1684 1836 471664443 471664291 5.310000e-39 172.0
18 TraesCS4D01G231400 chr5A 85.437 103 14 1 1730 1832 585148175 585148276 5.460000e-19 106.0
19 TraesCS4D01G231400 chrUn 79.231 130 15 6 1704 1833 194986581 194986464 3.310000e-11 80.5
20 TraesCS4D01G231400 chr7A 89.286 56 4 2 1636 1691 655447181 655447128 7.160000e-08 69.4
21 TraesCS4D01G231400 chr5B 93.182 44 2 1 1648 1691 620651841 620651883 3.330000e-06 63.9


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 TraesCS4D01G231400 chr4D 391036725 391040718 3993 True 7376.0 7376 100.0000 1 3994 1 chr4D.!!$R2 3993
1 TraesCS4D01G231400 chr4A 72922350 72926171 3821 True 2635.5 3254 91.5495 41 3994 2 chr4A.!!$R1 3953
2 TraesCS4D01G231400 chr4B 480922872 480926637 3765 True 2651.5 3127 92.1485 66 3994 2 chr4B.!!$R1 3928

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
502 550 0.038435 CAATGCGTGCCACATGGAAA 60.038 50.0 0.87 0.00 37.39 3.13 F
2295 2394 0.109153 ATCTGCTGAAGGTGCACACA 59.891 50.0 20.43 13.97 36.37 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2566 0.039326 AGCAATTGCAGGAGCTCCTT 59.961 50.0 33.33 16.15 46.65 3.36 R
3553 3675 0.463474 GGGCCTCTGCAATCTGAGTC 60.463 60.0 0.84 0.00 40.13 3.36 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.131326 TGCTACCGTGTGTATGCAC 57.869 52.632 7.03 7.03 45.44 4.57
28 29 2.900122 GTGTATGCACGCTTGTCAAT 57.100 45.000 0.00 0.00 35.75 2.57
29 30 2.774007 GTGTATGCACGCTTGTCAATC 58.226 47.619 0.00 0.00 35.75 2.67
30 31 1.393196 TGTATGCACGCTTGTCAATCG 59.607 47.619 7.25 7.25 0.00 3.34
31 32 1.393539 GTATGCACGCTTGTCAATCGT 59.606 47.619 8.58 8.58 36.84 3.73
35 36 2.383298 CACGCTTGTCAATCGTGTTT 57.617 45.000 26.08 0.00 45.75 2.83
36 37 2.036217 CACGCTTGTCAATCGTGTTTG 58.964 47.619 26.08 7.93 45.75 2.93
37 38 1.044725 CGCTTGTCAATCGTGTTTGC 58.955 50.000 0.67 0.00 0.00 3.68
38 39 1.408422 GCTTGTCAATCGTGTTTGCC 58.592 50.000 0.00 0.00 0.00 4.52
39 40 1.001378 GCTTGTCAATCGTGTTTGCCT 60.001 47.619 0.00 0.00 0.00 4.75
64 65 5.438117 GCAACTTCACCTTTTAACTCGTAC 58.562 41.667 0.00 0.00 0.00 3.67
74 75 8.271487 CACCTTTTAACTCGTACTACAAGAAAC 58.729 37.037 0.00 0.00 0.00 2.78
89 90 0.505655 GAAACGTACGTGGACACTGC 59.494 55.000 23.57 0.00 0.00 4.40
160 161 2.508887 CTGCGAGCTCTGTCCTGC 60.509 66.667 12.85 7.12 0.00 4.85
168 169 0.676151 GCTCTGTCCTGCCCAAGAAG 60.676 60.000 0.00 0.00 0.00 2.85
199 203 1.537638 CGATGTACTAGCGAGCCTCAT 59.462 52.381 0.00 0.00 41.60 2.90
317 321 8.598075 GTCAGTAAGAAAAGAGTTCGTAAAACA 58.402 33.333 0.00 0.00 0.00 2.83
354 365 2.888534 CGGATTGGCCCGTACGTG 60.889 66.667 15.21 3.42 44.23 4.49
356 367 1.078988 GGATTGGCCCGTACGTGAA 60.079 57.895 15.21 1.38 0.00 3.18
357 368 1.363885 GGATTGGCCCGTACGTGAAC 61.364 60.000 15.21 0.09 0.00 3.18
358 369 1.363885 GATTGGCCCGTACGTGAACC 61.364 60.000 15.21 10.03 0.00 3.62
372 383 4.825546 CGTGAACCGTATGGAGTACTAT 57.174 45.455 8.33 0.00 39.21 2.12
373 384 5.179045 CGTGAACCGTATGGAGTACTATT 57.821 43.478 8.33 0.00 39.21 1.73
414 457 1.769733 TTACGTGACGGGAAAACTCG 58.230 50.000 10.66 0.00 0.00 4.18
415 458 0.664166 TACGTGACGGGAAAACTCGC 60.664 55.000 10.66 0.00 0.00 5.03
431 479 3.490890 GCCCAAGTCATGAGCGAC 58.509 61.111 0.00 0.00 36.08 5.19
456 504 3.118454 GTCATCACCACCCGTGCG 61.118 66.667 0.00 0.00 42.69 5.34
502 550 0.038435 CAATGCGTGCCACATGGAAA 60.038 50.000 0.87 0.00 37.39 3.13
551 599 5.296813 CTGTAGATTAACAGCAACCCAAC 57.703 43.478 0.00 0.00 40.40 3.77
552 600 4.720046 TGTAGATTAACAGCAACCCAACA 58.280 39.130 0.00 0.00 0.00 3.33
553 601 5.133941 TGTAGATTAACAGCAACCCAACAA 58.866 37.500 0.00 0.00 0.00 2.83
554 602 5.594725 TGTAGATTAACAGCAACCCAACAAA 59.405 36.000 0.00 0.00 0.00 2.83
645 703 1.270094 CCCAAACGGAAAAGAAAGGCC 60.270 52.381 0.00 0.00 0.00 5.19
722 786 1.063190 TCTCGCATCCTTCCTTCCCTA 60.063 52.381 0.00 0.00 0.00 3.53
723 787 1.069358 CTCGCATCCTTCCTTCCCTAC 59.931 57.143 0.00 0.00 0.00 3.18
724 788 1.123928 CGCATCCTTCCTTCCCTACT 58.876 55.000 0.00 0.00 0.00 2.57
725 789 2.091499 TCGCATCCTTCCTTCCCTACTA 60.091 50.000 0.00 0.00 0.00 1.82
790 854 2.588034 GGCACCTAATCGGCGTCC 60.588 66.667 6.85 0.00 35.61 4.79
917 981 1.317431 TGGCCGCTATATATCCGCGT 61.317 55.000 20.86 0.00 44.92 6.01
957 1021 3.311106 TCTCGCTACACCTTTGTTAACG 58.689 45.455 0.26 0.00 37.15 3.18
1182 1246 2.511600 CAATCCAGGGTCGCGGAC 60.512 66.667 6.13 2.87 33.05 4.79
1205 1269 0.316854 GTACGCGACGATCCTTCCTC 60.317 60.000 15.93 0.00 0.00 3.71
1231 1295 2.360801 CGATCTCCTCTTCCTCTTGGTC 59.639 54.545 0.00 0.00 34.23 4.02
1244 1308 0.541863 CTTGGTCCGCCAGTAGGATT 59.458 55.000 0.00 0.00 46.91 3.01
1257 1321 5.393896 GCCAGTAGGATTGTACTACGACTTT 60.394 44.000 0.00 0.00 44.20 2.66
1324 1407 1.215382 GGAATGAAAACCGCCTGGC 59.785 57.895 9.11 9.11 39.70 4.85
1359 1442 7.009174 CACTTGGCATTTCGGTTATTGTTTATC 59.991 37.037 0.00 0.00 0.00 1.75
1392 1477 1.205655 CGTCTTGATCTTCTGCCTCCA 59.794 52.381 0.00 0.00 0.00 3.86
1462 1547 0.481567 ATGGCCTCATGGGGATTCTG 59.518 55.000 18.46 0.00 35.12 3.02
1474 1559 1.963515 GGGATTCTGCTTTGTTGGTGT 59.036 47.619 0.00 0.00 0.00 4.16
1543 1628 0.797249 CGGCGACAACTTCTACGAGG 60.797 60.000 0.00 0.00 0.00 4.63
1575 1660 0.166814 GCGTTCATGACCAGCAGTTC 59.833 55.000 0.00 0.00 0.00 3.01
1578 1663 1.728971 GTTCATGACCAGCAGTTCGAG 59.271 52.381 0.00 0.00 0.00 4.04
1629 1714 3.159298 CTTGCAGAAGCCGTGGTAT 57.841 52.632 0.00 0.00 41.13 2.73
1644 1729 3.243434 CGTGGTATCTCGGTAAGCTTCAT 60.243 47.826 0.00 0.00 0.00 2.57
1649 1734 5.635700 GGTATCTCGGTAAGCTTCATTGATC 59.364 44.000 0.00 0.00 0.00 2.92
1651 1736 6.656632 ATCTCGGTAAGCTTCATTGATCTA 57.343 37.500 0.00 0.00 0.00 1.98
1652 1737 5.833082 TCTCGGTAAGCTTCATTGATCTAC 58.167 41.667 0.00 0.00 0.00 2.59
1653 1738 5.594725 TCTCGGTAAGCTTCATTGATCTACT 59.405 40.000 0.00 0.00 0.00 2.57
1654 1739 5.833082 TCGGTAAGCTTCATTGATCTACTC 58.167 41.667 0.00 0.00 0.00 2.59
1655 1740 4.985409 CGGTAAGCTTCATTGATCTACTCC 59.015 45.833 0.00 0.00 0.00 3.85
1656 1741 5.301555 GGTAAGCTTCATTGATCTACTCCC 58.698 45.833 0.00 0.00 0.00 4.30
1657 1742 5.071115 GGTAAGCTTCATTGATCTACTCCCT 59.929 44.000 0.00 0.00 0.00 4.20
1658 1743 4.953940 AGCTTCATTGATCTACTCCCTC 57.046 45.455 0.00 0.00 0.00 4.30
1659 1744 3.645687 AGCTTCATTGATCTACTCCCTCC 59.354 47.826 0.00 0.00 0.00 4.30
1660 1745 3.553922 GCTTCATTGATCTACTCCCTCCG 60.554 52.174 0.00 0.00 0.00 4.63
1661 1746 3.314307 TCATTGATCTACTCCCTCCGT 57.686 47.619 0.00 0.00 0.00 4.69
1662 1747 3.643237 TCATTGATCTACTCCCTCCGTT 58.357 45.455 0.00 0.00 0.00 4.44
1663 1748 3.637229 TCATTGATCTACTCCCTCCGTTC 59.363 47.826 0.00 0.00 0.00 3.95
1664 1749 2.068834 TGATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
1665 1750 1.569548 TGATCTACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36
1666 1751 2.781757 TGATCTACTCCCTCCGTTCCTA 59.218 50.000 0.00 0.00 0.00 2.94
1667 1752 3.203710 TGATCTACTCCCTCCGTTCCTAA 59.796 47.826 0.00 0.00 0.00 2.69
1668 1753 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
1669 1754 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
1670 1755 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
1671 1756 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
1672 1757 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
1673 1758 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1674 1759 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1675 1760 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1676 1761 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1677 1762 4.510340 CCCTCCGTTCCTAAATATTTGTCG 59.490 45.833 11.05 7.80 0.00 4.35
1678 1763 5.114081 CCTCCGTTCCTAAATATTTGTCGT 58.886 41.667 11.05 0.00 0.00 4.34
1679 1764 5.583457 CCTCCGTTCCTAAATATTTGTCGTT 59.417 40.000 11.05 0.00 0.00 3.85
1680 1765 6.238022 CCTCCGTTCCTAAATATTTGTCGTTC 60.238 42.308 11.05 0.00 0.00 3.95
1681 1766 5.581874 TCCGTTCCTAAATATTTGTCGTTCC 59.418 40.000 11.05 0.00 0.00 3.62
1682 1767 5.220719 CCGTTCCTAAATATTTGTCGTTCCC 60.221 44.000 11.05 0.00 0.00 3.97
1683 1768 5.352016 CGTTCCTAAATATTTGTCGTTCCCA 59.648 40.000 11.05 0.00 0.00 4.37
1684 1769 6.128227 CGTTCCTAAATATTTGTCGTTCCCAA 60.128 38.462 11.05 0.00 0.00 4.12
1685 1770 7.573469 CGTTCCTAAATATTTGTCGTTCCCAAA 60.573 37.037 11.05 0.00 36.34 3.28
1686 1771 7.948034 TCCTAAATATTTGTCGTTCCCAAAT 57.052 32.000 11.05 0.00 43.14 2.32
1687 1772 9.463902 TTCCTAAATATTTGTCGTTCCCAAATA 57.536 29.630 11.05 7.73 44.45 1.40
1694 1779 6.642707 TTTGTCGTTCCCAAATATTTGTCT 57.357 33.333 23.24 0.00 36.45 3.41
1695 1780 6.642707 TTGTCGTTCCCAAATATTTGTCTT 57.357 33.333 23.24 0.00 36.45 3.01
1696 1781 6.642707 TGTCGTTCCCAAATATTTGTCTTT 57.357 33.333 23.24 0.00 36.45 2.52
1697 1782 6.674066 TGTCGTTCCCAAATATTTGTCTTTC 58.326 36.000 23.24 10.84 36.45 2.62
1698 1783 6.488683 TGTCGTTCCCAAATATTTGTCTTTCT 59.511 34.615 23.24 0.00 36.45 2.52
1699 1784 7.662258 TGTCGTTCCCAAATATTTGTCTTTCTA 59.338 33.333 23.24 4.37 36.45 2.10
1700 1785 8.175716 GTCGTTCCCAAATATTTGTCTTTCTAG 58.824 37.037 23.24 8.23 36.45 2.43
1701 1786 8.098286 TCGTTCCCAAATATTTGTCTTTCTAGA 58.902 33.333 23.24 11.23 36.45 2.43
1702 1787 8.726988 CGTTCCCAAATATTTGTCTTTCTAGAA 58.273 33.333 23.24 0.00 36.45 2.10
1788 1873 7.905604 CATACATCCGTATGTTGTAATCCAT 57.094 36.000 0.00 0.00 46.70 3.41
1789 1874 8.322906 CATACATCCGTATGTTGTAATCCATT 57.677 34.615 0.00 0.00 46.70 3.16
1790 1875 8.783093 CATACATCCGTATGTTGTAATCCATTT 58.217 33.333 0.00 0.00 46.70 2.32
1791 1876 7.026631 ACATCCGTATGTTGTAATCCATTTG 57.973 36.000 0.00 0.00 44.07 2.32
1792 1877 6.826231 ACATCCGTATGTTGTAATCCATTTGA 59.174 34.615 0.00 0.00 44.07 2.69
1793 1878 7.338196 ACATCCGTATGTTGTAATCCATTTGAA 59.662 33.333 0.00 0.00 44.07 2.69
1794 1879 7.689446 TCCGTATGTTGTAATCCATTTGAAA 57.311 32.000 0.00 0.00 0.00 2.69
1795 1880 8.287439 TCCGTATGTTGTAATCCATTTGAAAT 57.713 30.769 0.00 0.00 0.00 2.17
1796 1881 8.187480 TCCGTATGTTGTAATCCATTTGAAATG 58.813 33.333 10.84 10.84 0.00 2.32
1797 1882 7.043458 CCGTATGTTGTAATCCATTTGAAATGC 60.043 37.037 12.26 0.00 0.00 3.56
1798 1883 7.701924 CGTATGTTGTAATCCATTTGAAATGCT 59.298 33.333 12.26 2.15 0.00 3.79
1799 1884 9.369904 GTATGTTGTAATCCATTTGAAATGCTT 57.630 29.630 12.26 9.97 0.00 3.91
1801 1886 8.984891 TGTTGTAATCCATTTGAAATGCTTAG 57.015 30.769 12.26 0.00 0.00 2.18
1802 1887 8.801299 TGTTGTAATCCATTTGAAATGCTTAGA 58.199 29.630 12.26 7.93 0.00 2.10
1803 1888 9.638239 GTTGTAATCCATTTGAAATGCTTAGAA 57.362 29.630 12.26 12.47 0.00 2.10
1805 1890 9.859427 TGTAATCCATTTGAAATGCTTAGAAAG 57.141 29.630 12.26 0.00 0.00 2.62
1807 1892 8.992835 AATCCATTTGAAATGCTTAGAAAGAC 57.007 30.769 12.26 0.00 0.00 3.01
1808 1893 7.523293 TCCATTTGAAATGCTTAGAAAGACA 57.477 32.000 12.26 0.00 0.00 3.41
1809 1894 7.950512 TCCATTTGAAATGCTTAGAAAGACAA 58.049 30.769 12.26 0.00 0.00 3.18
1810 1895 8.420222 TCCATTTGAAATGCTTAGAAAGACAAA 58.580 29.630 12.26 0.00 0.00 2.83
1811 1896 9.211485 CCATTTGAAATGCTTAGAAAGACAAAT 57.789 29.630 12.26 0.00 36.38 2.32
1822 1907 9.267096 GCTTAGAAAGACAAATATTTGAGAACG 57.733 33.333 30.18 7.22 40.55 3.95
1826 1911 8.507249 AGAAAGACAAATATTTGAGAACGAAGG 58.493 33.333 30.18 4.51 40.55 3.46
1827 1912 6.743575 AGACAAATATTTGAGAACGAAGGG 57.256 37.500 30.18 4.03 40.55 3.95
1828 1913 6.472887 AGACAAATATTTGAGAACGAAGGGA 58.527 36.000 30.18 0.00 40.55 4.20
1829 1914 6.595716 AGACAAATATTTGAGAACGAAGGGAG 59.404 38.462 30.18 3.44 40.55 4.30
1870 1957 4.082125 TCAGAGAAATGGGAAGCTTTTCC 58.918 43.478 0.00 6.63 40.38 3.13
1948 2040 1.493854 AAACCATGACTACCGGGGCA 61.494 55.000 6.32 0.00 0.00 5.36
1956 2048 4.418328 TACCGGGGCAATGCGCTT 62.418 61.111 21.29 9.14 41.33 4.68
1971 2063 2.195567 GCTTGCACAGCTTGACCCA 61.196 57.895 11.98 0.00 46.27 4.51
2016 2108 4.902448 CGATTCGTTTGCATGAGATCATTC 59.098 41.667 0.00 0.00 33.61 2.67
2017 2109 5.502869 CGATTCGTTTGCATGAGATCATTCA 60.503 40.000 0.00 0.00 33.61 2.57
2055 2147 8.303876 GGTACATGGTCATATTTTGTTTGAACT 58.696 33.333 0.00 0.00 0.00 3.01
2187 2286 3.574396 TGGAGTTCTTCTTCATCGACACT 59.426 43.478 0.00 0.00 0.00 3.55
2199 2298 3.381590 TCATCGACACTACTCCATTCCAG 59.618 47.826 0.00 0.00 0.00 3.86
2235 2334 5.334421 ACTCACCCTAAAGACAGTCACTAT 58.666 41.667 2.66 0.00 0.00 2.12
2295 2394 0.109153 ATCTGCTGAAGGTGCACACA 59.891 50.000 20.43 13.97 36.37 3.72
2297 2396 0.956633 CTGCTGAAGGTGCACACATT 59.043 50.000 20.43 10.06 38.10 2.71
2415 2517 5.382618 AATCAACTGCAAAGTGGAAGATC 57.617 39.130 0.00 0.00 0.00 2.75
2436 2538 2.679837 CGCTATTGGGCATCATACCATC 59.320 50.000 0.00 0.00 36.48 3.51
2442 2544 1.612726 GGGCATCATACCATCAGGAGC 60.613 57.143 0.00 0.00 38.69 4.70
2451 2553 0.463204 CCATCAGGAGCGTCAGTGAT 59.537 55.000 0.00 0.00 36.89 3.06
2520 2622 7.272978 TCAAGGTAATTCATAAGTAGCCTCAC 58.727 38.462 0.00 0.00 30.44 3.51
2553 2655 7.840931 ACTATATCAAAAAGCCCAGAAAAAGG 58.159 34.615 0.00 0.00 0.00 3.11
2557 2659 4.040339 TCAAAAAGCCCAGAAAAAGGATCC 59.960 41.667 2.48 2.48 0.00 3.36
2661 2763 2.417933 GCAGCAGAGACAGGTTAACATG 59.582 50.000 18.17 18.17 0.00 3.21
2714 2816 5.065218 AGAGCAGTAAGGCATTAAATTCACG 59.935 40.000 0.00 0.00 35.83 4.35
2745 2847 1.421382 TGTCTAACCTTAACGCACGC 58.579 50.000 0.00 0.00 0.00 5.34
2765 2867 1.429463 GCTTCTGTTGTACCAGTCCG 58.571 55.000 0.00 0.00 34.02 4.79
3046 3148 4.678509 TTGGTAGCGCTATTTGTGAAAG 57.321 40.909 21.96 0.00 0.00 2.62
3213 3324 5.049828 TGGTTCTGATGCATACATAAGTCG 58.950 41.667 0.00 0.00 36.29 4.18
3284 3395 5.196341 TCTAATATTGTACCCTGCACTCG 57.804 43.478 0.00 0.00 0.00 4.18
3301 3412 7.148918 CCTGCACTCGAAAAATTAAATGAACTG 60.149 37.037 0.00 0.00 0.00 3.16
3328 3439 0.958382 TGGCGGTGACCTTTGCATAC 60.958 55.000 0.00 0.00 0.00 2.39
3360 3471 4.540824 GATTCAACAAGAGTGCAAAGACC 58.459 43.478 0.00 0.00 0.00 3.85
3537 3659 2.362717 GAGAGATCCCCTTAACAGGTCG 59.637 54.545 0.00 0.00 38.79 4.79
3552 3674 2.811431 CAGGTCGTGCATTAAGTTTGGA 59.189 45.455 0.00 0.00 0.00 3.53
3553 3675 3.074412 AGGTCGTGCATTAAGTTTGGAG 58.926 45.455 0.00 0.00 0.00 3.86
3709 3833 6.072508 TGCCAAGAAAATATCACTTCAGACAC 60.073 38.462 0.00 0.00 0.00 3.67
3718 3842 3.120792 TCACTTCAGACACGCAAACTAC 58.879 45.455 0.00 0.00 0.00 2.73
3748 3872 6.317789 CAGAATAACTCTGGCAAAAACTCA 57.682 37.500 0.00 0.00 46.89 3.41
3849 3973 7.878127 GGTCTATATTAAGCCACATGAAAGCTA 59.122 37.037 0.00 0.00 35.30 3.32
3912 4036 7.721842 TGTTTTAACACCAGTGAATCCATCTTA 59.278 33.333 4.48 0.00 33.17 2.10
3913 4037 7.921786 TTTAACACCAGTGAATCCATCTTAG 57.078 36.000 4.48 0.00 0.00 2.18
3945 4071 4.220382 CCCCAATGAGCAACAGTTAAATCA 59.780 41.667 0.00 0.00 0.00 2.57
3962 4088 0.472471 TCAAAAACTCTCCACGGCCT 59.528 50.000 0.00 0.00 0.00 5.19
3984 4110 4.627611 TGTCAGACGTAATGCTACCTAC 57.372 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.131326 GTGCATACACACGGTAGCA 57.869 52.632 0.00 0.00 46.61 3.49
9 10 2.774007 GATTGACAAGCGTGCATACAC 58.226 47.619 0.00 0.00 43.76 2.90
10 11 1.393196 CGATTGACAAGCGTGCATACA 59.607 47.619 17.29 0.00 35.23 2.29
11 12 2.077155 CGATTGACAAGCGTGCATAC 57.923 50.000 17.29 0.00 35.23 2.39
19 20 1.001378 AGGCAAACACGATTGACAAGC 60.001 47.619 8.46 0.00 40.96 4.01
20 21 2.605338 CCAGGCAAACACGATTGACAAG 60.605 50.000 8.46 1.99 40.96 3.16
21 22 1.336440 CCAGGCAAACACGATTGACAA 59.664 47.619 8.46 0.00 40.96 3.18
22 23 0.950836 CCAGGCAAACACGATTGACA 59.049 50.000 8.46 0.00 40.96 3.58
23 24 0.387239 GCCAGGCAAACACGATTGAC 60.387 55.000 6.55 0.00 38.68 3.18
24 25 0.821301 TGCCAGGCAAACACGATTGA 60.821 50.000 13.33 0.00 34.76 2.57
25 26 0.031857 TTGCCAGGCAAACACGATTG 59.968 50.000 25.43 0.00 45.96 2.67
26 27 2.424474 TTGCCAGGCAAACACGATT 58.576 47.368 25.43 0.00 45.96 3.34
27 28 4.172625 TTGCCAGGCAAACACGAT 57.827 50.000 25.43 0.00 45.96 3.73
34 35 0.396974 AAGGTGAAGTTGCCAGGCAA 60.397 50.000 23.88 23.88 46.80 4.52
35 36 0.396974 AAAGGTGAAGTTGCCAGGCA 60.397 50.000 11.22 11.22 36.47 4.75
36 37 0.752658 AAAAGGTGAAGTTGCCAGGC 59.247 50.000 3.66 3.66 0.00 4.85
37 38 3.636764 AGTTAAAAGGTGAAGTTGCCAGG 59.363 43.478 0.00 0.00 0.00 4.45
38 39 4.554723 CGAGTTAAAAGGTGAAGTTGCCAG 60.555 45.833 0.00 0.00 0.00 4.85
39 40 3.314080 CGAGTTAAAAGGTGAAGTTGCCA 59.686 43.478 0.00 0.00 0.00 4.92
50 51 7.168135 ACGTTTCTTGTAGTACGAGTTAAAAGG 59.832 37.037 15.80 15.32 37.44 3.11
64 65 3.423206 GTGTCCACGTACGTTTCTTGTAG 59.577 47.826 20.23 4.56 0.00 2.74
74 75 2.803670 CCGCAGTGTCCACGTACG 60.804 66.667 15.01 15.01 36.20 3.67
89 90 0.673985 TGAACTGTCTCACTCACCCG 59.326 55.000 0.00 0.00 0.00 5.28
155 156 2.347490 GCGTCTTCTTGGGCAGGA 59.653 61.111 0.00 0.00 0.00 3.86
160 161 4.735132 TCGCGGCGTCTTCTTGGG 62.735 66.667 22.90 0.00 0.00 4.12
168 169 2.051614 TACATCGATCGCGGCGTC 60.052 61.111 22.90 16.94 38.28 5.19
317 321 1.541310 TTTCGTGGATCTCCGGTGCT 61.541 55.000 0.00 0.00 39.43 4.40
368 379 9.463902 ACCACGATGAGCTTATAGTATAATAGT 57.536 33.333 3.95 0.00 0.00 2.12
372 383 9.903682 GTAAACCACGATGAGCTTATAGTATAA 57.096 33.333 3.95 2.65 0.00 0.98
414 457 1.078848 AGTCGCTCATGACTTGGGC 60.079 57.895 3.09 3.09 46.85 5.36
415 458 0.742281 CCAGTCGCTCATGACTTGGG 60.742 60.000 0.00 0.00 46.85 4.12
431 479 1.134280 GGGTGGTGATGACTGATCCAG 60.134 57.143 0.00 0.00 37.52 3.86
432 480 0.911769 GGGTGGTGATGACTGATCCA 59.088 55.000 0.00 0.00 0.00 3.41
456 504 2.031157 GGAGAGATTCGAGCAGCTAGTC 60.031 54.545 0.00 0.00 0.00 2.59
466 514 4.507756 CGCATTGTTATTGGAGAGATTCGA 59.492 41.667 0.00 0.00 0.00 3.71
591 639 5.924475 TTCTGCTTACTTTTGTGCTACTC 57.076 39.130 0.00 0.00 0.00 2.59
701 765 0.179070 GGGAAGGAAGGATGCGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
722 786 1.380112 GGTGGGCGAGGAGAGTAGT 60.380 63.158 0.00 0.00 0.00 2.73
723 787 1.076632 AGGTGGGCGAGGAGAGTAG 60.077 63.158 0.00 0.00 0.00 2.57
724 788 1.076923 GAGGTGGGCGAGGAGAGTA 60.077 63.158 0.00 0.00 0.00 2.59
725 789 2.363147 GAGGTGGGCGAGGAGAGT 60.363 66.667 0.00 0.00 0.00 3.24
1182 1246 2.001361 AAGGATCGTCGCGTACCTGG 62.001 60.000 5.77 0.00 35.12 4.45
1194 1258 4.286320 CGGGCCGAGGAAGGATCG 62.286 72.222 24.41 0.00 39.86 3.69
1205 1269 2.731374 GAAGAGGAGATCGGGCCG 59.269 66.667 22.51 22.51 0.00 6.13
1231 1295 2.287427 CGTAGTACAATCCTACTGGCGG 60.287 54.545 0.38 0.00 34.04 6.13
1324 1407 1.178534 AATGCCAAGTGGACCAACCG 61.179 55.000 0.18 0.00 42.61 4.44
1359 1442 1.982938 AAGACGACCCCTTCCTCCG 60.983 63.158 0.00 0.00 0.00 4.63
1462 1547 1.818674 CCCCATCTACACCAACAAAGC 59.181 52.381 0.00 0.00 0.00 3.51
1474 1559 1.074775 CCCCGACCTTCCCCATCTA 60.075 63.158 0.00 0.00 0.00 1.98
1560 1645 0.247460 CCTCGAACTGCTGGTCATGA 59.753 55.000 9.48 0.00 0.00 3.07
1575 1660 5.220710 AGATATTGGTGAAGGATTCCTCG 57.779 43.478 5.48 0.00 46.93 4.63
1578 1663 5.998363 GGTGTAGATATTGGTGAAGGATTCC 59.002 44.000 0.00 0.00 46.93 3.01
1629 1714 5.594725 AGTAGATCAATGAAGCTTACCGAGA 59.405 40.000 0.00 0.00 0.00 4.04
1644 1729 2.024273 AGGAACGGAGGGAGTAGATCAA 60.024 50.000 0.00 0.00 0.00 2.57
1649 1734 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
1651 1736 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
1652 1737 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1653 1738 5.677567 GACAAATATTTAGGAACGGAGGGA 58.322 41.667 0.00 0.00 0.00 4.20
1654 1739 4.510340 CGACAAATATTTAGGAACGGAGGG 59.490 45.833 0.00 0.00 0.00 4.30
1655 1740 5.114081 ACGACAAATATTTAGGAACGGAGG 58.886 41.667 0.00 0.00 0.00 4.30
1656 1741 6.238022 GGAACGACAAATATTTAGGAACGGAG 60.238 42.308 0.00 0.00 0.00 4.63
1657 1742 5.581874 GGAACGACAAATATTTAGGAACGGA 59.418 40.000 0.00 0.00 0.00 4.69
1658 1743 5.220719 GGGAACGACAAATATTTAGGAACGG 60.221 44.000 0.00 0.00 0.00 4.44
1659 1744 5.352016 TGGGAACGACAAATATTTAGGAACG 59.648 40.000 0.00 5.49 0.00 3.95
1660 1745 6.746745 TGGGAACGACAAATATTTAGGAAC 57.253 37.500 0.00 0.00 0.00 3.62
1661 1746 7.762588 TTTGGGAACGACAAATATTTAGGAA 57.237 32.000 0.00 0.00 33.26 3.36
1662 1747 7.948034 ATTTGGGAACGACAAATATTTAGGA 57.052 32.000 0.00 0.00 44.27 2.94
1670 1755 7.227049 AGACAAATATTTGGGAACGACAAAT 57.773 32.000 27.43 6.24 46.76 2.32
1671 1756 6.642707 AGACAAATATTTGGGAACGACAAA 57.357 33.333 27.43 0.00 42.34 2.83
1672 1757 6.642707 AAGACAAATATTTGGGAACGACAA 57.357 33.333 27.43 0.00 42.34 3.18
1673 1758 6.488683 AGAAAGACAAATATTTGGGAACGACA 59.511 34.615 27.43 0.00 42.34 4.35
1674 1759 6.909909 AGAAAGACAAATATTTGGGAACGAC 58.090 36.000 27.43 14.30 42.34 4.34
1675 1760 8.098286 TCTAGAAAGACAAATATTTGGGAACGA 58.902 33.333 27.43 12.84 42.34 3.85
1676 1761 8.263940 TCTAGAAAGACAAATATTTGGGAACG 57.736 34.615 27.43 11.14 42.34 3.95
1765 1850 8.783093 CAAATGGATTACAACATACGGATGTAT 58.217 33.333 15.10 8.21 45.93 2.29
1766 1851 7.988028 TCAAATGGATTACAACATACGGATGTA 59.012 33.333 15.10 0.00 45.93 2.29
1768 1853 7.258022 TCAAATGGATTACAACATACGGATG 57.742 36.000 5.94 5.94 39.16 3.51
1769 1854 7.873719 TTCAAATGGATTACAACATACGGAT 57.126 32.000 0.00 0.00 0.00 4.18
1770 1855 7.689446 TTTCAAATGGATTACAACATACGGA 57.311 32.000 0.00 0.00 0.00 4.69
1771 1856 7.043458 GCATTTCAAATGGATTACAACATACGG 60.043 37.037 12.14 0.00 0.00 4.02
1772 1857 7.701924 AGCATTTCAAATGGATTACAACATACG 59.298 33.333 12.14 0.00 0.00 3.06
1773 1858 8.931385 AGCATTTCAAATGGATTACAACATAC 57.069 30.769 12.14 0.00 0.00 2.39
1775 1860 9.590451 CTAAGCATTTCAAATGGATTACAACAT 57.410 29.630 12.14 0.00 0.00 2.71
1776 1861 8.801299 TCTAAGCATTTCAAATGGATTACAACA 58.199 29.630 12.14 0.00 0.00 3.33
1777 1862 9.638239 TTCTAAGCATTTCAAATGGATTACAAC 57.362 29.630 12.14 0.00 0.00 3.32
1779 1864 9.859427 CTTTCTAAGCATTTCAAATGGATTACA 57.141 29.630 12.14 0.00 0.00 2.41
1782 1867 8.587608 TGTCTTTCTAAGCATTTCAAATGGATT 58.412 29.630 12.14 1.03 0.00 3.01
1783 1868 8.125978 TGTCTTTCTAAGCATTTCAAATGGAT 57.874 30.769 12.14 0.00 0.00 3.41
1784 1869 7.523293 TGTCTTTCTAAGCATTTCAAATGGA 57.477 32.000 12.14 0.00 0.00 3.41
1785 1870 8.592105 TTTGTCTTTCTAAGCATTTCAAATGG 57.408 30.769 12.14 0.00 0.00 3.16
1796 1881 9.267096 CGTTCTCAAATATTTGTCTTTCTAAGC 57.733 33.333 23.95 7.30 39.18 3.09
1800 1885 8.507249 CCTTCGTTCTCAAATATTTGTCTTTCT 58.493 33.333 23.95 0.00 39.18 2.52
1801 1886 7.750903 CCCTTCGTTCTCAAATATTTGTCTTTC 59.249 37.037 23.95 12.84 39.18 2.62
1802 1887 7.447238 TCCCTTCGTTCTCAAATATTTGTCTTT 59.553 33.333 23.95 0.00 39.18 2.52
1803 1888 6.940298 TCCCTTCGTTCTCAAATATTTGTCTT 59.060 34.615 23.95 0.00 39.18 3.01
1804 1889 6.472887 TCCCTTCGTTCTCAAATATTTGTCT 58.527 36.000 23.95 0.00 39.18 3.41
1805 1890 6.371825 ACTCCCTTCGTTCTCAAATATTTGTC 59.628 38.462 23.95 13.65 39.18 3.18
1806 1891 6.238648 ACTCCCTTCGTTCTCAAATATTTGT 58.761 36.000 23.95 1.02 39.18 2.83
1807 1892 6.743575 ACTCCCTTCGTTCTCAAATATTTG 57.256 37.500 20.13 20.13 39.48 2.32
1808 1893 8.265055 TGATACTCCCTTCGTTCTCAAATATTT 58.735 33.333 0.00 0.00 0.00 1.40
1809 1894 7.792032 TGATACTCCCTTCGTTCTCAAATATT 58.208 34.615 0.00 0.00 0.00 1.28
1810 1895 7.361457 TGATACTCCCTTCGTTCTCAAATAT 57.639 36.000 0.00 0.00 0.00 1.28
1811 1896 6.785337 TGATACTCCCTTCGTTCTCAAATA 57.215 37.500 0.00 0.00 0.00 1.40
1812 1897 5.677319 TGATACTCCCTTCGTTCTCAAAT 57.323 39.130 0.00 0.00 0.00 2.32
1813 1898 5.422331 AGATGATACTCCCTTCGTTCTCAAA 59.578 40.000 0.00 0.00 0.00 2.69
1814 1899 4.956700 AGATGATACTCCCTTCGTTCTCAA 59.043 41.667 0.00 0.00 0.00 3.02
1815 1900 4.537751 AGATGATACTCCCTTCGTTCTCA 58.462 43.478 0.00 0.00 0.00 3.27
1816 1901 5.116069 GAGATGATACTCCCTTCGTTCTC 57.884 47.826 0.00 0.00 0.00 2.87
1956 2048 1.227943 GACTGGGTCAAGCTGTGCA 60.228 57.895 0.00 0.00 32.09 4.57
1971 2063 1.153489 ATCGAGCTTGCGCATGACT 60.153 52.632 25.77 20.36 39.10 3.41
2016 2108 3.444742 ACCATGTACCTGCATTGACAATG 59.555 43.478 21.56 21.56 41.85 2.82
2017 2109 3.696051 GACCATGTACCTGCATTGACAAT 59.304 43.478 0.00 0.00 0.00 2.71
2118 2217 7.389232 TGAATGATAGTCAAGTCTCATGTTGT 58.611 34.615 0.00 0.00 0.00 3.32
2121 2220 7.215789 GGATGAATGATAGTCAAGTCTCATGT 58.784 38.462 0.00 0.00 0.00 3.21
2125 2224 6.183360 ACAGGGATGAATGATAGTCAAGTCTC 60.183 42.308 0.00 0.00 0.00 3.36
2187 2286 4.160439 CAGTACTTGAGCTGGAATGGAGTA 59.840 45.833 0.00 0.00 0.00 2.59
2199 2298 1.066787 GGGTGAGTCCAGTACTTGAGC 60.067 57.143 0.00 0.00 39.07 4.26
2235 2334 1.979155 CGCCACTCCTCTCCAGTCA 60.979 63.158 0.00 0.00 0.00 3.41
2415 2517 2.183478 TGGTATGATGCCCAATAGCG 57.817 50.000 0.00 0.00 34.65 4.26
2436 2538 1.568606 CATGATCACTGACGCTCCTG 58.431 55.000 0.00 0.00 0.00 3.86
2442 2544 0.536724 TGTCCCCATGATCACTGACG 59.463 55.000 0.00 0.00 0.00 4.35
2451 2553 1.852157 GCTCCTTGGTGTCCCCATGA 61.852 60.000 0.00 0.00 44.74 3.07
2464 2566 0.039326 AGCAATTGCAGGAGCTCCTT 59.961 50.000 33.33 16.15 46.65 3.36
2528 2630 7.673926 TCCTTTTTCTGGGCTTTTTGATATAGT 59.326 33.333 0.00 0.00 0.00 2.12
2529 2631 8.066612 TCCTTTTTCTGGGCTTTTTGATATAG 57.933 34.615 0.00 0.00 0.00 1.31
2531 2633 6.933514 TCCTTTTTCTGGGCTTTTTGATAT 57.066 33.333 0.00 0.00 0.00 1.63
2532 2634 6.070824 GGATCCTTTTTCTGGGCTTTTTGATA 60.071 38.462 3.84 0.00 0.00 2.15
2533 2635 5.280164 GGATCCTTTTTCTGGGCTTTTTGAT 60.280 40.000 3.84 0.00 0.00 2.57
2534 2636 4.040339 GGATCCTTTTTCTGGGCTTTTTGA 59.960 41.667 3.84 0.00 0.00 2.69
2535 2637 4.040829 AGGATCCTTTTTCTGGGCTTTTTG 59.959 41.667 9.02 0.00 0.00 2.44
2553 2655 6.268566 GGCATGAAAGTGTCATAAAAGGATC 58.731 40.000 0.00 0.00 45.69 3.36
2557 2659 5.649782 AGGGCATGAAAGTGTCATAAAAG 57.350 39.130 0.00 0.00 45.69 2.27
2687 2789 7.065803 GTGAATTTAATGCCTTACTGCTCTGTA 59.934 37.037 0.00 0.00 0.00 2.74
2714 2816 5.500645 AAGGTTAGACAACTTCAACAAGC 57.499 39.130 0.00 0.00 34.88 4.01
2745 2847 1.429463 GGACTGGTACAACAGAAGCG 58.571 55.000 0.24 0.00 40.97 4.68
2765 2867 4.551388 CTCCGCTAGTGAAGTATTGGATC 58.449 47.826 4.44 0.00 0.00 3.36
3046 3148 3.243839 ACCACAGTGGCACATTCAATTTC 60.244 43.478 20.48 0.00 42.67 2.17
3213 3324 2.462456 TCGCATCAATAGATCCCTGC 57.538 50.000 0.00 0.00 30.20 4.85
3301 3412 1.400737 AGGTCACCGCCAGATACTAC 58.599 55.000 0.00 0.00 0.00 2.73
3328 3439 5.583854 CACTCTTGTTGAATCCTGATACCAG 59.416 44.000 0.00 0.00 40.09 4.00
3498 3620 6.857437 TCTCTCTGATGGTCTGAAACATTA 57.143 37.500 0.00 0.00 0.00 1.90
3537 3659 4.997395 TCTGAGTCTCCAAACTTAATGCAC 59.003 41.667 0.00 0.00 0.00 4.57
3552 3674 0.540923 GGCCTCTGCAATCTGAGTCT 59.459 55.000 0.00 0.00 40.13 3.24
3553 3675 0.463474 GGGCCTCTGCAATCTGAGTC 60.463 60.000 0.84 0.00 40.13 3.36
3709 3833 6.367969 AGTTATTCTGGTACTTGTAGTTTGCG 59.632 38.462 0.00 0.00 0.00 4.85
3849 3973 9.658799 CCGTTCCTTGATATATGTATTTCAGAT 57.341 33.333 0.00 0.00 0.00 2.90
3912 4036 3.387962 TGCTCATTGGGGTAATCTCTCT 58.612 45.455 0.00 0.00 0.00 3.10
3913 4037 3.845781 TGCTCATTGGGGTAATCTCTC 57.154 47.619 0.00 0.00 0.00 3.20
3945 4071 1.318576 CAAGGCCGTGGAGAGTTTTT 58.681 50.000 11.31 0.00 0.00 1.94
3962 4088 4.142315 GGTAGGTAGCATTACGTCTGACAA 60.142 45.833 8.73 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.