Multiple sequence alignment - TraesCS3D01G176500

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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 TraesCS3D01G176500 chr3D 100.000 2540 0 0 1 2540 157754561 157757100 0.000000e+00 4691
1 TraesCS3D01G176500 chr3B 90.821 1852 118 21 1 1823 229161266 229163094 0.000000e+00 2431
2 TraesCS3D01G176500 chr3B 86.478 673 50 21 1876 2539 229163220 229163860 0.000000e+00 701
3 TraesCS3D01G176500 chr6D 88.212 1527 150 21 193 1709 438529634 438528128 0.000000e+00 1796
4 TraesCS3D01G176500 chr6D 86.713 1287 132 20 193 1471 438526692 438527947 0.000000e+00 1393
5 TraesCS3D01G176500 chr6D 96.429 84 3 0 16 99 438529713 438529630 3.410000e-29 139
6 TraesCS3D01G176500 chr6D 95.181 83 4 0 16 98 438526612 438526694 5.700000e-27 132
7 TraesCS3D01G176500 chr3A 94.018 1003 52 6 712 1709 170384412 170383413 0.000000e+00 1513
8 TraesCS3D01G176500 chr3A 93.156 716 42 4 1 713 170385205 170384494 0.000000e+00 1044
9 TraesCS3D01G176500 chr3A 85.627 654 56 25 1892 2540 170304889 170304269 0.000000e+00 652
10 TraesCS3D01G176500 chr3A 85.627 654 56 25 1892 2540 170356034 170355414 0.000000e+00 652
11 TraesCS3D01G176500 chr3A 85.627 654 56 25 1892 2540 170383128 170382508 0.000000e+00 652
12 TraesCS3D01G176500 chrUn 94.498 927 44 5 712 1634 336469380 336470303 0.000000e+00 1423
13 TraesCS3D01G176500 chrUn 93.296 716 41 4 1 713 336468587 336469298 0.000000e+00 1050
14 TraesCS3D01G176500 chrUn 93.296 716 41 4 1 713 397151262 397151973 0.000000e+00 1050
15 TraesCS3D01G176500 chrUn 96.000 425 14 2 712 1133 397152055 397152479 0.000000e+00 688
16 TraesCS3D01G176500 chrUn 93.548 372 23 1 1 371 392970165 392970536 1.030000e-153 553


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 TraesCS3D01G176500 chr3D 157754561 157757100 2539 False 4691.000000 4691 100.000000 1 2540 1 chr3D.!!$F1 2539
1 TraesCS3D01G176500 chr3B 229161266 229163860 2594 False 1566.000000 2431 88.649500 1 2539 2 chr3B.!!$F1 2538
2 TraesCS3D01G176500 chr6D 438528128 438529713 1585 True 967.500000 1796 92.320500 16 1709 2 chr6D.!!$R1 1693
3 TraesCS3D01G176500 chr6D 438526612 438527947 1335 False 762.500000 1393 90.947000 16 1471 2 chr6D.!!$F1 1455
4 TraesCS3D01G176500 chr3A 170382508 170385205 2697 True 1069.666667 1513 90.933667 1 2540 3 chr3A.!!$R3 2539
5 TraesCS3D01G176500 chr3A 170304269 170304889 620 True 652.000000 652 85.627000 1892 2540 1 chr3A.!!$R1 648
6 TraesCS3D01G176500 chr3A 170355414 170356034 620 True 652.000000 652 85.627000 1892 2540 1 chr3A.!!$R2 648
7 TraesCS3D01G176500 chrUn 336468587 336470303 1716 False 1236.500000 1423 93.897000 1 1634 2 chrUn.!!$F2 1633
8 TraesCS3D01G176500 chrUn 397151262 397152479 1217 False 869.000000 1050 94.648000 1 1133 2 chrUn.!!$F3 1132

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
627 635 2.573009 TCATTCTTCTGGAGCATGGACA 59.427 45.455 0.0 0.0 30.97 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1773 0.038983 AACAAAATTACGGCGCCCAC 60.039 50.0 23.46 0.0 0.0 4.61 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
44 45 6.122277 TCAATAGAATGGAGAATTGTGGGTC 58.878 40.000 0.00 0.00 32.43 4.46
108 109 7.998383 TGTGAATATGGTAAAATAGCATGTCCT 59.002 33.333 11.25 0.00 45.56 3.85
176 177 9.330063 CAACTTAGACAATAATCAGGCAGAATA 57.670 33.333 0.00 0.00 0.00 1.75
191 192 7.386025 TCAGGCAGAATATCTTTCATTATGACG 59.614 37.037 0.00 0.00 37.63 4.35
267 268 7.005902 TGACCAGGACAAATTATGCATCATAT 58.994 34.615 0.19 0.00 0.00 1.78
268 269 7.040271 TGACCAGGACAAATTATGCATCATATG 60.040 37.037 0.19 1.45 0.00 1.78
390 393 3.589988 CCGTGCTGTGTTCTCTAATCTT 58.410 45.455 0.00 0.00 0.00 2.40
395 398 6.366332 CGTGCTGTGTTCTCTAATCTTTACTT 59.634 38.462 0.00 0.00 0.00 2.24
562 569 6.368805 AGAAGAACTTCCACTTCCTTTGAAT 58.631 36.000 10.41 0.00 42.09 2.57
627 635 2.573009 TCATTCTTCTGGAGCATGGACA 59.427 45.455 0.00 0.00 30.97 4.02
662 670 8.374327 AGTTTGTAGTGTGTTACTGTAAATCC 57.626 34.615 1.10 0.00 40.65 3.01
788 881 5.221986 TGCATTCATTATCCTATCAGGCAGT 60.222 40.000 0.00 0.00 34.61 4.40
999 1095 6.964464 TCTATCACCAAATAAAAGGGCTGTA 58.036 36.000 0.00 0.00 0.00 2.74
1305 1403 2.584835 TGGCCTTGTCATTAGCAGTT 57.415 45.000 3.32 0.00 0.00 3.16
1334 1432 2.666317 CTTTTGGGTGTTGGTCCTTCT 58.334 47.619 0.00 0.00 0.00 2.85
1345 1443 5.183904 GTGTTGGTCCTTCTAAGCAATTCAT 59.816 40.000 0.00 0.00 36.60 2.57
1347 1445 6.374333 TGTTGGTCCTTCTAAGCAATTCATAC 59.626 38.462 0.00 0.00 36.60 2.39
1353 1451 7.011857 GTCCTTCTAAGCAATTCATACCTGAAG 59.988 40.741 0.00 0.00 44.32 3.02
1369 1467 0.675837 GAAGGTAGTTTGCCGACCCC 60.676 60.000 0.00 0.00 33.40 4.95
1370 1468 1.131928 AAGGTAGTTTGCCGACCCCT 61.132 55.000 0.00 0.00 33.40 4.79
1371 1469 1.078637 GGTAGTTTGCCGACCCCTC 60.079 63.158 0.00 0.00 0.00 4.30
1375 1473 0.537371 AGTTTGCCGACCCCTCTTTG 60.537 55.000 0.00 0.00 0.00 2.77
1382 1480 2.810767 GCCGACCCCTCTTTGATTATCC 60.811 54.545 0.00 0.00 0.00 2.59
1425 1523 0.980231 GGAGTCTCAGGTGGGCATCT 60.980 60.000 1.47 0.00 0.00 2.90
1526 1624 3.070018 CAGCTTTCGACAGACCTGAATT 58.930 45.455 1.94 0.00 0.00 2.17
1567 1665 2.420687 GGAAATCCAGTGCCAGGTCTAG 60.421 54.545 0.00 0.00 35.64 2.43
1599 1697 2.435938 GTTCGCTGATTCGGCCCA 60.436 61.111 11.82 0.00 31.00 5.36
1601 1699 0.531974 GTTCGCTGATTCGGCCCATA 60.532 55.000 11.82 0.00 31.00 2.74
1608 1706 3.447586 GCTGATTCGGCCCATAGTATCTA 59.552 47.826 6.17 0.00 0.00 1.98
1615 1713 2.027100 GGCCCATAGTATCTACCTTGCC 60.027 54.545 0.00 0.00 0.00 4.52
1616 1714 2.907042 GCCCATAGTATCTACCTTGCCT 59.093 50.000 0.00 0.00 0.00 4.75
1635 1733 6.712179 TGCCTGATGTTTATGCATAAATGA 57.288 33.333 29.36 20.79 35.02 2.57
1667 1766 5.411361 TGAAATTGGACACCTCTATGTTTCG 59.589 40.000 0.00 0.00 31.24 3.46
1674 1773 5.291128 GGACACCTCTATGTTTCGTACATTG 59.709 44.000 10.32 9.02 45.19 2.82
1678 1777 4.570772 CCTCTATGTTTCGTACATTGTGGG 59.429 45.833 18.17 14.44 45.19 4.61
1685 1784 1.448189 GTACATTGTGGGCGCCGTA 60.448 57.895 22.54 13.03 0.00 4.02
1695 1794 0.241481 GGGCGCCGTAATTTTGTTCA 59.759 50.000 22.54 0.00 0.00 3.18
1709 1808 6.566197 ATTTTGTTCAGAAACTAGGAGCTG 57.434 37.500 0.00 0.00 36.30 4.24
1710 1809 3.685139 TGTTCAGAAACTAGGAGCTGG 57.315 47.619 0.00 0.00 36.30 4.85
1712 1811 4.157246 TGTTCAGAAACTAGGAGCTGGTA 58.843 43.478 0.00 0.00 36.30 3.25
1720 1838 3.633418 ACTAGGAGCTGGTAGTACCTTG 58.367 50.000 20.07 13.41 39.58 3.61
1721 1839 2.921834 AGGAGCTGGTAGTACCTTGA 57.078 50.000 20.07 0.00 39.58 3.02
1746 1864 5.410067 CATCAAATTTGGTATCCGTTGCTT 58.590 37.500 17.90 0.00 0.00 3.91
1752 1870 1.268352 TGGTATCCGTTGCTTGCAAAC 59.732 47.619 9.75 0.00 0.00 2.93
1757 1875 0.662619 CCGTTGCTTGCAAACTGAGA 59.337 50.000 9.75 0.00 0.00 3.27
1763 1881 2.485426 TGCTTGCAAACTGAGATAGTGC 59.515 45.455 0.00 0.00 40.26 4.40
1770 1888 6.639563 TGCAAACTGAGATAGTGCTGTATTA 58.360 36.000 0.00 0.00 40.26 0.98
1775 1893 5.201713 TGAGATAGTGCTGTATTACTGGC 57.798 43.478 3.30 4.64 0.00 4.85
1776 1894 4.895889 TGAGATAGTGCTGTATTACTGGCT 59.104 41.667 11.44 0.00 0.00 4.75
1782 1900 5.360591 AGTGCTGTATTACTGGCTACATTC 58.639 41.667 11.44 0.00 0.00 2.67
1790 1908 2.648059 ACTGGCTACATTCTGAATGCC 58.352 47.619 25.96 21.90 42.69 4.40
1791 1909 2.025981 ACTGGCTACATTCTGAATGCCA 60.026 45.455 25.96 24.58 46.59 4.92
1792 1910 3.084536 TGGCTACATTCTGAATGCCAA 57.915 42.857 25.96 13.40 45.92 4.52
1793 1911 3.018856 TGGCTACATTCTGAATGCCAAG 58.981 45.455 25.96 20.95 45.92 3.61
1794 1912 3.282021 GGCTACATTCTGAATGCCAAGA 58.718 45.455 25.96 9.07 42.69 3.02
1795 1913 3.696051 GGCTACATTCTGAATGCCAAGAA 59.304 43.478 25.96 7.76 42.69 2.52
1796 1914 4.201990 GGCTACATTCTGAATGCCAAGAAG 60.202 45.833 25.96 15.66 42.69 2.85
1797 1915 4.397417 GCTACATTCTGAATGCCAAGAAGT 59.603 41.667 25.96 9.93 42.69 3.01
1798 1916 5.105997 GCTACATTCTGAATGCCAAGAAGTT 60.106 40.000 25.96 9.30 42.69 2.66
1799 1917 5.130292 ACATTCTGAATGCCAAGAAGTTG 57.870 39.130 25.96 4.30 42.69 3.16
1800 1918 4.586001 ACATTCTGAATGCCAAGAAGTTGT 59.414 37.500 25.96 4.90 42.69 3.32
1801 1919 5.769662 ACATTCTGAATGCCAAGAAGTTGTA 59.230 36.000 25.96 0.00 42.69 2.41
1802 1920 5.689383 TTCTGAATGCCAAGAAGTTGTAC 57.311 39.130 0.00 0.00 30.95 2.90
1803 1921 4.713553 TCTGAATGCCAAGAAGTTGTACA 58.286 39.130 0.00 0.00 30.95 2.90
1804 1922 5.316167 TCTGAATGCCAAGAAGTTGTACAT 58.684 37.500 0.00 0.00 32.58 2.29
1805 1923 5.769662 TCTGAATGCCAAGAAGTTGTACATT 59.230 36.000 0.00 0.00 39.47 2.71
1806 1924 6.012658 TGAATGCCAAGAAGTTGTACATTC 57.987 37.500 16.56 16.56 45.16 2.67
1807 1925 6.012658 GAATGCCAAGAAGTTGTACATTCA 57.987 37.500 17.60 0.00 44.79 2.57
1808 1926 5.633830 ATGCCAAGAAGTTGTACATTCAG 57.366 39.130 10.93 4.14 28.82 3.02
1809 1927 4.460263 TGCCAAGAAGTTGTACATTCAGT 58.540 39.130 10.93 0.00 30.95 3.41
1810 1928 4.515191 TGCCAAGAAGTTGTACATTCAGTC 59.485 41.667 10.93 4.04 30.95 3.51
1811 1929 4.515191 GCCAAGAAGTTGTACATTCAGTCA 59.485 41.667 10.93 0.00 30.95 3.41
1812 1930 5.008613 GCCAAGAAGTTGTACATTCAGTCAA 59.991 40.000 10.93 0.00 30.95 3.18
1813 1931 6.430451 CCAAGAAGTTGTACATTCAGTCAAC 58.570 40.000 10.93 0.00 37.95 3.18
1814 1932 6.430451 CAAGAAGTTGTACATTCAGTCAACC 58.570 40.000 10.93 0.00 38.19 3.77
1815 1933 5.930135 AGAAGTTGTACATTCAGTCAACCT 58.070 37.500 10.93 0.00 38.19 3.50
1816 1934 5.760253 AGAAGTTGTACATTCAGTCAACCTG 59.240 40.000 10.93 0.00 42.97 4.00
1834 1952 9.726438 GTCAACCTGATGGCTAATAAGTTATAT 57.274 33.333 0.00 0.00 36.63 0.86
1860 1978 8.547967 TCAGTTAACCTGATGACTGTTTATTC 57.452 34.615 0.88 0.00 45.34 1.75
1861 1979 8.375506 TCAGTTAACCTGATGACTGTTTATTCT 58.624 33.333 0.88 0.00 45.34 2.40
1862 1980 8.446273 CAGTTAACCTGATGACTGTTTATTCTG 58.554 37.037 0.88 0.00 44.49 3.02
1863 1981 8.157476 AGTTAACCTGATGACTGTTTATTCTGT 58.843 33.333 0.88 0.00 0.00 3.41
1864 1982 6.808008 AACCTGATGACTGTTTATTCTGTG 57.192 37.500 0.00 0.00 0.00 3.66
1865 1983 4.697352 ACCTGATGACTGTTTATTCTGTGC 59.303 41.667 0.00 0.00 0.00 4.57
1866 1984 4.696877 CCTGATGACTGTTTATTCTGTGCA 59.303 41.667 0.00 0.00 0.00 4.57
1867 1985 5.391310 CCTGATGACTGTTTATTCTGTGCAC 60.391 44.000 10.75 10.75 0.00 4.57
1868 1986 5.308014 TGATGACTGTTTATTCTGTGCACT 58.692 37.500 19.41 0.00 0.00 4.40
1869 1987 5.179929 TGATGACTGTTTATTCTGTGCACTG 59.820 40.000 19.41 18.10 0.00 3.66
1871 1989 2.554032 ACTGTTTATTCTGTGCACTGCC 59.446 45.455 19.41 3.01 0.00 4.85
1873 1991 3.221771 TGTTTATTCTGTGCACTGCCTT 58.778 40.909 19.41 8.06 0.00 4.35
1882 2103 3.637432 TGTGCACTGCCTTTTATTTTCG 58.363 40.909 19.41 0.00 0.00 3.46
1884 2105 4.022416 TGTGCACTGCCTTTTATTTTCGAT 60.022 37.500 19.41 0.00 0.00 3.59
1906 2171 0.386478 GCTGAAGGCAAGCTCGTTTG 60.386 55.000 0.00 0.00 41.35 2.93
1931 2196 3.082619 TCCGTCTGGGACAAGGATT 57.917 52.632 0.00 0.00 40.94 3.01
1944 2209 3.005554 ACAAGGATTCGAGTTGATGCTG 58.994 45.455 6.05 0.00 0.00 4.41
1963 2228 5.472148 TGCTGATCTTTTGGCAGTTATTTG 58.528 37.500 0.00 0.00 32.39 2.32
1965 2230 5.928264 GCTGATCTTTTGGCAGTTATTTGTT 59.072 36.000 0.00 0.00 32.39 2.83
1969 2236 5.841810 TCTTTTGGCAGTTATTTGTTCCTG 58.158 37.500 0.00 0.00 0.00 3.86
2031 2298 6.541278 GGTTACTTGCTTCTAATTAATCCGGT 59.459 38.462 0.00 0.00 0.00 5.28
2050 2317 8.828688 ATCCGGTATATGTTTTAAGAACTAGC 57.171 34.615 0.00 0.00 0.00 3.42
2081 2348 3.324268 TGGTGTTGGTATCGGACTTTGTA 59.676 43.478 0.00 0.00 0.00 2.41
2082 2349 4.020039 TGGTGTTGGTATCGGACTTTGTAT 60.020 41.667 0.00 0.00 0.00 2.29
2083 2350 5.187381 TGGTGTTGGTATCGGACTTTGTATA 59.813 40.000 0.00 0.00 0.00 1.47
2084 2351 5.521372 GGTGTTGGTATCGGACTTTGTATAC 59.479 44.000 0.00 0.00 0.00 1.47
2085 2352 5.230726 GTGTTGGTATCGGACTTTGTATACG 59.769 44.000 0.00 0.00 0.00 3.06
2086 2353 3.968649 TGGTATCGGACTTTGTATACGC 58.031 45.455 0.00 0.00 0.00 4.42
2087 2354 2.975851 GGTATCGGACTTTGTATACGCG 59.024 50.000 3.53 3.53 0.00 6.01
2090 2357 0.835740 CGGACTTTGTATACGCGACG 59.164 55.000 15.93 0.00 0.00 5.12
2098 2365 1.518515 TGTATACGCGACGAGTCTACG 59.481 52.381 15.93 11.94 39.31 3.51
2103 2370 2.398498 ACGCGACGAGTCTACGTATAT 58.602 47.619 15.93 0.00 46.52 0.86
2119 2390 4.037208 ACGTATATTTCCATCGTCGGAACT 59.963 41.667 7.65 5.93 44.80 3.01
2120 2391 4.615961 CGTATATTTCCATCGTCGGAACTC 59.384 45.833 7.65 0.00 44.80 3.01
2121 2392 1.922570 ATTTCCATCGTCGGAACTCG 58.077 50.000 7.65 0.00 44.80 4.18
2122 2393 0.734942 TTTCCATCGTCGGAACTCGC 60.735 55.000 7.65 0.00 44.80 5.03
2123 2394 1.868987 TTCCATCGTCGGAACTCGCA 61.869 55.000 4.49 0.00 40.20 5.10
2125 2396 1.011968 CCATCGTCGGAACTCGCAAA 61.012 55.000 0.00 0.00 39.05 3.68
2127 2398 1.005975 CATCGTCGGAACTCGCAAATC 60.006 52.381 0.00 0.00 39.05 2.17
2128 2399 0.038983 TCGTCGGAACTCGCAAATCA 60.039 50.000 0.00 0.00 39.05 2.57
2129 2400 0.093026 CGTCGGAACTCGCAAATCAC 59.907 55.000 0.00 0.00 39.05 3.06
2132 2403 0.179250 CGGAACTCGCAAATCACGTG 60.179 55.000 9.94 9.94 0.00 4.49
2140 2411 1.865725 GCAAATCACGTGCGTACTTC 58.134 50.000 11.67 0.00 31.20 3.01
2141 2412 1.193650 GCAAATCACGTGCGTACTTCA 59.806 47.619 11.67 0.00 31.20 3.02
2142 2413 2.159707 GCAAATCACGTGCGTACTTCAT 60.160 45.455 11.67 0.00 31.20 2.57
2143 2414 3.659735 CAAATCACGTGCGTACTTCATC 58.340 45.455 11.67 0.00 0.00 2.92
2144 2415 2.647529 ATCACGTGCGTACTTCATCA 57.352 45.000 11.67 0.00 0.00 3.07
2145 2416 1.693467 TCACGTGCGTACTTCATCAC 58.307 50.000 11.67 0.00 0.00 3.06
2146 2417 0.713883 CACGTGCGTACTTCATCACC 59.286 55.000 0.82 0.00 0.00 4.02
2155 2426 4.096382 GCGTACTTCATCACCCATCAAATT 59.904 41.667 0.00 0.00 0.00 1.82
2157 2428 6.258160 CGTACTTCATCACCCATCAAATTTC 58.742 40.000 0.00 0.00 0.00 2.17
2175 2446 0.031043 TCTCCTTTGTTTCGCGTCGA 59.969 50.000 5.77 0.00 0.00 4.20
2179 2450 0.232303 CTTTGTTTCGCGTCGAAGCT 59.768 50.000 20.83 0.00 46.43 3.74
2180 2451 0.042535 TTTGTTTCGCGTCGAAGCTG 60.043 50.000 20.83 14.03 46.43 4.24
2181 2452 2.202058 GTTTCGCGTCGAAGCTGC 60.202 61.111 20.83 5.99 46.43 5.25
2191 2462 0.109551 TCGAAGCTGCAACGAGAGAG 60.110 55.000 14.78 0.00 0.00 3.20
2192 2463 0.387878 CGAAGCTGCAACGAGAGAGT 60.388 55.000 11.72 0.00 0.00 3.24
2202 2473 3.892122 GAGAGAGTCGAGACGCCA 58.108 61.111 3.43 0.00 36.20 5.69
2203 2474 1.426223 GAGAGAGTCGAGACGCCAC 59.574 63.158 3.43 0.00 36.20 5.01
2204 2475 1.299562 GAGAGAGTCGAGACGCCACA 61.300 60.000 3.43 0.00 36.20 4.17
2205 2476 0.889638 AGAGAGTCGAGACGCCACAA 60.890 55.000 3.43 0.00 36.20 3.33
2206 2477 0.039437 GAGAGTCGAGACGCCACAAA 60.039 55.000 3.43 0.00 36.20 2.83
2207 2478 0.318784 AGAGTCGAGACGCCACAAAC 60.319 55.000 3.43 0.00 36.20 2.93
2284 2555 4.530857 GCAGACGGCGGCCACTAT 62.531 66.667 20.71 0.20 0.00 2.12
2408 2685 4.363990 CCGTGGAGCAGCTGACGT 62.364 66.667 20.43 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.208355 CACTGTTTTGGTCGTTATGTTCG 58.792 43.478 0.00 0.00 0.00 3.95
176 177 6.599244 TCTGCCTTTTCGTCATAATGAAAGAT 59.401 34.615 0.00 0.00 40.54 2.40
191 192 6.347160 GCAAATCAAAGACATTCTGCCTTTTC 60.347 38.462 0.00 0.00 27.35 2.29
267 268 9.342308 AGAACTGTAGATTTCAAAAATGAGACA 57.658 29.630 0.00 0.00 0.00 3.41
297 298 5.126222 TGGCAGTTGTAGAACAATGTCAAAA 59.874 36.000 5.45 0.00 40.59 2.44
390 393 7.402071 ACATTAGTTATCAGGGAGGACAAGTAA 59.598 37.037 0.00 0.00 0.00 2.24
395 398 4.408921 CCACATTAGTTATCAGGGAGGACA 59.591 45.833 0.00 0.00 0.00 4.02
562 569 1.472082 CCACTGATGCGTATTTTGGCA 59.528 47.619 0.00 0.00 44.29 4.92
576 583 6.169557 ACTAGAATTGTGTGTTACCACTGA 57.830 37.500 0.00 0.00 42.34 3.41
662 670 7.544566 AGAATTTCACAGCAGCTAATCAATTTG 59.455 33.333 0.00 0.00 0.00 2.32
728 820 7.140048 GCTCTGATTTGATTTCTCATGGATTC 58.860 38.462 0.00 0.00 0.00 2.52
818 911 8.188139 CAGAAAGTAACAAATAATATTGGCGGT 58.812 33.333 0.00 0.00 34.56 5.68
1347 1445 1.439679 GTCGGCAAACTACCTTCAGG 58.560 55.000 0.00 0.00 42.17 3.86
1353 1451 1.078637 GAGGGGTCGGCAAACTACC 60.079 63.158 0.00 0.00 0.00 3.18
1357 1455 0.536460 TCAAAGAGGGGTCGGCAAAC 60.536 55.000 0.00 0.00 0.00 2.93
1363 1461 3.495100 CCTGGATAATCAAAGAGGGGTCG 60.495 52.174 0.00 0.00 0.00 4.79
1369 1467 5.104360 TCCTTGGACCTGGATAATCAAAGAG 60.104 44.000 0.00 0.00 0.00 2.85
1370 1468 4.788075 TCCTTGGACCTGGATAATCAAAGA 59.212 41.667 0.00 0.00 0.00 2.52
1371 1469 5.116084 TCCTTGGACCTGGATAATCAAAG 57.884 43.478 0.00 0.00 0.00 2.77
1382 1480 2.629051 GAACCGTTATCCTTGGACCTG 58.371 52.381 0.00 0.00 0.00 4.00
1425 1523 2.359850 GTGCCCATCGCTCCACAA 60.360 61.111 0.00 0.00 38.78 3.33
1452 1550 2.412323 CCGCACAAGCATGGCTGAT 61.412 57.895 0.00 0.00 39.62 2.90
1453 1551 3.057548 CCGCACAAGCATGGCTGA 61.058 61.111 0.00 0.00 39.62 4.26
1526 1624 2.635714 CATGACACTATGCAGGCTTGA 58.364 47.619 0.00 0.00 0.00 3.02
1567 1665 1.766143 CGAACTCGCATAGGGCTTGC 61.766 60.000 0.00 0.00 41.67 4.01
1585 1683 0.317160 TACTATGGGCCGAATCAGCG 59.683 55.000 0.00 0.00 0.00 5.18
1599 1697 7.380423 AAACATCAGGCAAGGTAGATACTAT 57.620 36.000 0.00 0.00 0.00 2.12
1601 1699 5.700402 AAACATCAGGCAAGGTAGATACT 57.300 39.130 0.00 0.00 0.00 2.12
1608 1706 2.806434 TGCATAAACATCAGGCAAGGT 58.194 42.857 0.00 0.00 28.32 3.50
1615 1713 7.864379 GGAGGTTCATTTATGCATAAACATCAG 59.136 37.037 29.32 17.94 35.31 2.90
1616 1714 7.201902 GGGAGGTTCATTTATGCATAAACATCA 60.202 37.037 29.32 11.56 35.31 3.07
1635 1733 2.490902 GGTGTCCAATTTCAGGGAGGTT 60.491 50.000 0.00 0.00 32.85 3.50
1667 1766 1.020333 TTACGGCGCCCACAATGTAC 61.020 55.000 23.46 0.00 0.00 2.90
1672 1771 0.039074 CAAAATTACGGCGCCCACAA 60.039 50.000 23.46 12.84 0.00 3.33
1674 1773 0.038983 AACAAAATTACGGCGCCCAC 60.039 50.000 23.46 0.00 0.00 4.61
1678 1777 2.604969 TCTGAACAAAATTACGGCGC 57.395 45.000 6.90 0.00 0.00 6.53
1685 1784 6.015940 CCAGCTCCTAGTTTCTGAACAAAATT 60.016 38.462 0.00 0.00 38.26 1.82
1695 1794 4.017314 AGGTACTACCAGCTCCTAGTTTCT 60.017 45.833 8.01 2.35 41.95 2.52
1709 1808 6.404734 CCAAATTTGATGCTCAAGGTACTACC 60.405 42.308 19.86 0.00 38.49 3.18
1710 1809 6.151144 ACCAAATTTGATGCTCAAGGTACTAC 59.849 38.462 19.86 0.00 38.49 2.73
1720 1838 4.900635 ACGGATACCAAATTTGATGCTC 57.099 40.909 19.86 9.88 0.00 4.26
1721 1839 4.677779 GCAACGGATACCAAATTTGATGCT 60.678 41.667 19.86 1.27 0.00 3.79
1736 1854 1.267806 CTCAGTTTGCAAGCAACGGAT 59.732 47.619 16.04 0.00 35.46 4.18
1746 1864 3.407424 ACAGCACTATCTCAGTTTGCA 57.593 42.857 0.00 0.00 34.26 4.08
1752 1870 5.010516 AGCCAGTAATACAGCACTATCTCAG 59.989 44.000 7.92 0.00 0.00 3.35
1757 1875 6.672266 ATGTAGCCAGTAATACAGCACTAT 57.328 37.500 7.92 0.00 35.49 2.12
1763 1881 7.307632 GCATTCAGAATGTAGCCAGTAATACAG 60.308 40.741 21.82 0.00 41.01 2.74
1770 1888 2.025981 TGGCATTCAGAATGTAGCCAGT 60.026 45.455 21.82 0.00 46.81 4.00
1775 1893 6.072286 ACAACTTCTTGGCATTCAGAATGTAG 60.072 38.462 21.82 16.44 41.01 2.74
1776 1894 5.769662 ACAACTTCTTGGCATTCAGAATGTA 59.230 36.000 21.82 10.65 41.01 2.29
1782 1900 5.633830 ATGTACAACTTCTTGGCATTCAG 57.366 39.130 0.00 0.00 0.00 3.02
1790 1908 6.260936 AGGTTGACTGAATGTACAACTTCTTG 59.739 38.462 0.00 1.08 41.23 3.02
1791 1909 6.357367 AGGTTGACTGAATGTACAACTTCTT 58.643 36.000 0.00 0.00 41.23 2.52
1792 1910 5.930135 AGGTTGACTGAATGTACAACTTCT 58.070 37.500 0.00 0.00 41.23 2.85
1807 1925 5.700402 ACTTATTAGCCATCAGGTTGACT 57.300 39.130 0.00 0.00 37.19 3.41
1808 1926 9.726438 ATATAACTTATTAGCCATCAGGTTGAC 57.274 33.333 0.00 0.00 37.19 3.18
1812 1930 9.950496 CTGAATATAACTTATTAGCCATCAGGT 57.050 33.333 0.00 0.00 37.19 4.00
1813 1931 9.950496 ACTGAATATAACTTATTAGCCATCAGG 57.050 33.333 0.00 0.00 38.23 3.86
1853 1971 3.923017 AAGGCAGTGCACAGAATAAAC 57.077 42.857 21.04 0.00 0.00 2.01
1854 1972 4.935352 AAAAGGCAGTGCACAGAATAAA 57.065 36.364 21.04 0.00 0.00 1.40
1855 1973 6.588719 AATAAAAGGCAGTGCACAGAATAA 57.411 33.333 21.04 0.00 0.00 1.40
1856 1974 6.588719 AAATAAAAGGCAGTGCACAGAATA 57.411 33.333 21.04 3.05 0.00 1.75
1857 1975 5.473066 AAATAAAAGGCAGTGCACAGAAT 57.527 34.783 21.04 0.00 0.00 2.40
1858 1976 4.935352 AAATAAAAGGCAGTGCACAGAA 57.065 36.364 21.04 0.00 0.00 3.02
1859 1977 4.556501 CGAAAATAAAAGGCAGTGCACAGA 60.557 41.667 21.04 0.00 0.00 3.41
1860 1978 3.670055 CGAAAATAAAAGGCAGTGCACAG 59.330 43.478 21.04 12.97 0.00 3.66
1861 1979 3.316588 TCGAAAATAAAAGGCAGTGCACA 59.683 39.130 21.04 0.00 0.00 4.57
1862 1980 3.896122 TCGAAAATAAAAGGCAGTGCAC 58.104 40.909 18.61 9.40 0.00 4.57
1863 1981 4.458989 AGATCGAAAATAAAAGGCAGTGCA 59.541 37.500 18.61 0.00 0.00 4.57
1864 1982 4.795278 CAGATCGAAAATAAAAGGCAGTGC 59.205 41.667 6.55 6.55 0.00 4.40
1865 1983 4.795278 GCAGATCGAAAATAAAAGGCAGTG 59.205 41.667 0.00 0.00 0.00 3.66
1866 1984 4.702131 AGCAGATCGAAAATAAAAGGCAGT 59.298 37.500 0.00 0.00 0.00 4.40
1867 1985 5.032863 CAGCAGATCGAAAATAAAAGGCAG 58.967 41.667 0.00 0.00 0.00 4.85
1868 1986 4.699735 TCAGCAGATCGAAAATAAAAGGCA 59.300 37.500 0.00 0.00 0.00 4.75
1869 1987 5.235305 TCAGCAGATCGAAAATAAAAGGC 57.765 39.130 0.00 0.00 0.00 4.35
1871 1989 5.741040 GCCTTCAGCAGATCGAAAATAAAAG 59.259 40.000 0.00 0.00 42.97 2.27
1873 1991 5.235305 GCCTTCAGCAGATCGAAAATAAA 57.765 39.130 0.00 0.00 42.97 1.40
1906 2171 2.741092 TCCCAGACGGACAGTTGC 59.259 61.111 0.00 0.00 34.86 4.17
1931 2196 3.686241 CCAAAAGATCAGCATCAACTCGA 59.314 43.478 0.00 0.00 0.00 4.04
1944 2209 6.587608 CAGGAACAAATAACTGCCAAAAGATC 59.412 38.462 0.00 0.00 0.00 2.75
1986 2253 9.227777 AGTAACCGTAATTTTCTTTAGCAGATT 57.772 29.630 0.00 0.00 0.00 2.40
1987 2254 8.788325 AGTAACCGTAATTTTCTTTAGCAGAT 57.212 30.769 0.00 0.00 0.00 2.90
1989 2256 7.270579 GCAAGTAACCGTAATTTTCTTTAGCAG 59.729 37.037 0.00 0.00 0.00 4.24
1990 2257 7.040961 AGCAAGTAACCGTAATTTTCTTTAGCA 60.041 33.333 0.00 0.00 0.00 3.49
1991 2258 7.303261 AGCAAGTAACCGTAATTTTCTTTAGC 58.697 34.615 0.00 0.00 0.00 3.09
1992 2259 9.326339 GAAGCAAGTAACCGTAATTTTCTTTAG 57.674 33.333 0.00 0.00 0.00 1.85
1994 2261 7.937649 AGAAGCAAGTAACCGTAATTTTCTTT 58.062 30.769 0.00 0.00 0.00 2.52
1995 2262 7.506328 AGAAGCAAGTAACCGTAATTTTCTT 57.494 32.000 0.00 0.00 0.00 2.52
1996 2263 8.611654 TTAGAAGCAAGTAACCGTAATTTTCT 57.388 30.769 0.00 0.00 0.00 2.52
1997 2264 9.836076 AATTAGAAGCAAGTAACCGTAATTTTC 57.164 29.630 0.00 0.00 0.00 2.29
2006 2273 6.541278 ACCGGATTAATTAGAAGCAAGTAACC 59.459 38.462 9.46 0.00 0.00 2.85
2050 2317 4.174009 CGATACCAACACCAAGTCTACTG 58.826 47.826 0.00 0.00 0.00 2.74
2059 2326 2.105134 ACAAAGTCCGATACCAACACCA 59.895 45.455 0.00 0.00 0.00 4.17
2081 2348 1.840181 TACGTAGACTCGTCGCGTAT 58.160 50.000 18.36 0.00 43.12 3.06
2082 2349 1.840181 ATACGTAGACTCGTCGCGTA 58.160 50.000 21.77 21.77 44.75 4.42
2083 2350 1.840181 TATACGTAGACTCGTCGCGT 58.160 50.000 19.78 19.78 43.12 6.01
2084 2351 3.430609 AATATACGTAGACTCGTCGCG 57.569 47.619 0.00 0.00 43.12 5.87
2085 2352 4.147443 GGAAATATACGTAGACTCGTCGC 58.853 47.826 0.08 0.00 43.12 5.19
2086 2353 5.334435 TGGAAATATACGTAGACTCGTCG 57.666 43.478 0.08 0.00 43.12 5.12
2087 2354 6.014293 CGATGGAAATATACGTAGACTCGTC 58.986 44.000 0.08 0.00 43.12 4.20
2090 2357 6.014293 CGACGATGGAAATATACGTAGACTC 58.986 44.000 0.08 0.00 37.32 3.36
2121 2392 1.193650 TGAAGTACGCACGTGATTTGC 59.806 47.619 22.23 1.50 36.57 3.68
2122 2393 3.122780 TGATGAAGTACGCACGTGATTTG 59.877 43.478 22.23 7.87 0.00 2.32
2123 2394 3.122948 GTGATGAAGTACGCACGTGATTT 59.877 43.478 22.23 0.82 0.00 2.17
2125 2396 2.259618 GTGATGAAGTACGCACGTGAT 58.740 47.619 22.23 9.02 0.00 3.06
2127 2398 0.713883 GGTGATGAAGTACGCACGTG 59.286 55.000 12.28 12.28 32.24 4.49
2128 2399 0.389426 GGGTGATGAAGTACGCACGT 60.389 55.000 0.00 0.00 32.24 4.49
2129 2400 0.389296 TGGGTGATGAAGTACGCACG 60.389 55.000 0.00 0.00 35.24 5.34
2132 2403 2.309528 TGATGGGTGATGAAGTACGC 57.690 50.000 0.00 0.00 0.00 4.42
2134 2405 7.396540 AGAAATTTGATGGGTGATGAAGTAC 57.603 36.000 0.00 0.00 0.00 2.73
2135 2406 6.603201 GGAGAAATTTGATGGGTGATGAAGTA 59.397 38.462 0.00 0.00 0.00 2.24
2137 2408 5.655532 AGGAGAAATTTGATGGGTGATGAAG 59.344 40.000 0.00 0.00 0.00 3.02
2138 2409 5.582953 AGGAGAAATTTGATGGGTGATGAA 58.417 37.500 0.00 0.00 0.00 2.57
2139 2410 5.197224 AGGAGAAATTTGATGGGTGATGA 57.803 39.130 0.00 0.00 0.00 2.92
2140 2411 5.927281 AAGGAGAAATTTGATGGGTGATG 57.073 39.130 0.00 0.00 0.00 3.07
2141 2412 5.781818 ACAAAGGAGAAATTTGATGGGTGAT 59.218 36.000 0.00 0.00 39.50 3.06
2142 2413 5.147032 ACAAAGGAGAAATTTGATGGGTGA 58.853 37.500 0.00 0.00 39.50 4.02
2143 2414 5.473066 ACAAAGGAGAAATTTGATGGGTG 57.527 39.130 0.00 0.00 39.50 4.61
2144 2415 6.499106 AAACAAAGGAGAAATTTGATGGGT 57.501 33.333 0.00 0.00 39.50 4.51
2145 2416 5.634859 CGAAACAAAGGAGAAATTTGATGGG 59.365 40.000 0.00 0.00 39.50 4.00
2146 2417 5.119125 GCGAAACAAAGGAGAAATTTGATGG 59.881 40.000 0.00 0.00 39.50 3.51
2155 2426 0.856641 CGACGCGAAACAAAGGAGAA 59.143 50.000 15.93 0.00 0.00 2.87
2157 2428 0.856641 TTCGACGCGAAACAAAGGAG 59.143 50.000 15.93 0.00 43.00 3.69
2175 2446 0.387878 CGACTCTCTCGTTGCAGCTT 60.388 55.000 0.00 0.00 37.64 3.74
2179 2450 0.517755 GTCTCGACTCTCTCGTTGCA 59.482 55.000 0.00 0.00 43.45 4.08
2180 2451 0.519586 CGTCTCGACTCTCTCGTTGC 60.520 60.000 0.00 0.00 43.45 4.17
2181 2452 0.519586 GCGTCTCGACTCTCTCGTTG 60.520 60.000 0.00 0.00 43.45 4.10
2191 2462 2.142641 GAGTTTGTGGCGTCTCGAC 58.857 57.895 0.00 0.00 34.27 4.20
2192 2463 4.647654 GAGTTTGTGGCGTCTCGA 57.352 55.556 0.00 0.00 0.00 4.04
2194 2465 1.495584 TTGCGAGTTTGTGGCGTCTC 61.496 55.000 0.00 0.00 31.05 3.36
2195 2466 0.884704 ATTGCGAGTTTGTGGCGTCT 60.885 50.000 0.00 0.00 31.05 4.18
2196 2467 0.725784 CATTGCGAGTTTGTGGCGTC 60.726 55.000 0.00 0.00 31.05 5.19
2197 2468 1.282570 CATTGCGAGTTTGTGGCGT 59.717 52.632 0.00 0.00 31.05 5.68
2198 2469 2.082366 GCATTGCGAGTTTGTGGCG 61.082 57.895 0.00 0.00 31.05 5.69
2199 2470 1.005294 CTGCATTGCGAGTTTGTGGC 61.005 55.000 3.84 0.00 0.00 5.01
2201 2472 0.039798 AGCTGCATTGCGAGTTTGTG 60.040 50.000 1.02 0.00 38.13 3.33
2202 2473 0.039798 CAGCTGCATTGCGAGTTTGT 60.040 50.000 0.00 0.00 38.13 2.83
2203 2474 0.731514 CCAGCTGCATTGCGAGTTTG 60.732 55.000 8.66 6.12 38.13 2.93
2204 2475 1.174712 ACCAGCTGCATTGCGAGTTT 61.175 50.000 8.66 0.00 38.13 2.66
2205 2476 1.601759 ACCAGCTGCATTGCGAGTT 60.602 52.632 8.66 0.00 38.13 3.01
2206 2477 2.033141 ACCAGCTGCATTGCGAGT 59.967 55.556 8.66 0.00 38.13 4.18
2207 2478 2.483745 CACCAGCTGCATTGCGAG 59.516 61.111 8.66 4.16 38.13 5.03
2269 2540 2.758327 TCATAGTGGCCGCCGTCT 60.758 61.111 14.07 8.44 0.00 4.18
2284 2555 3.695606 GACACCGGCAGCTCCTCA 61.696 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.