Multiple sequence alignment - TraesCS3A01G432200

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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 TraesCS3A01G432200 chr3A 100.000 5408 0 0 1 5408 673449647 673444240 0.000000e+00 9987.0
1 TraesCS3A01G432200 chr3A 93.907 755 22 2 1 734 84664162 84664913 0.000000e+00 1118.0
2 TraesCS3A01G432200 chr3B 94.528 4697 194 37 736 5408 712573659 712569002 0.000000e+00 7191.0
3 TraesCS3A01G432200 chr3B 94.324 740 23 10 1 734 452748546 452747820 0.000000e+00 1116.0
4 TraesCS3A01G432200 chr3D 94.121 3776 174 27 736 4491 537918758 537915011 0.000000e+00 5699.0
5 TraesCS3A01G432200 chr3D 89.901 406 35 5 4510 4914 537914867 537914467 8.030000e-143 518.0
6 TraesCS3A01G432200 chr3D 88.387 310 28 6 4916 5224 537914431 537914129 3.080000e-97 366.0
7 TraesCS3A01G432200 chr7A 96.866 734 23 0 1 734 689959764 689960497 0.000000e+00 1229.0
8 TraesCS3A01G432200 chr1A 96.866 734 23 0 1 734 286245639 286244906 0.000000e+00 1229.0
9 TraesCS3A01G432200 chr1A 96.594 734 25 0 1 734 287786275 287785542 0.000000e+00 1218.0
10 TraesCS3A01G432200 chr5A 96.467 736 25 1 1 736 535685504 535686238 0.000000e+00 1214.0
11 TraesCS3A01G432200 chr5A 94.591 758 19 2 1 737 510261272 510260516 0.000000e+00 1153.0
12 TraesCS3A01G432200 chr1B 96.049 734 29 0 1 734 365464483 365465216 0.000000e+00 1195.0
13 TraesCS3A01G432200 chr1B 95.510 735 33 0 1 735 111683793 111684527 0.000000e+00 1175.0
14 TraesCS3A01G432200 chr1B 85.965 57 8 0 3096 3152 474447084 474447140 1.630000e-05 62.1
15 TraesCS3A01G432200 chr2B 95.640 734 32 0 1 734 54336629 54335896 0.000000e+00 1179.0
16 TraesCS3A01G432200 chr4A 94.054 740 25 10 1 734 135352838 135353564 0.000000e+00 1105.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G432200 chr3A 673444240 673449647 5407 True 9987.000000 9987 100.000 1 5408 1 chr3A.!!$R1 5407
1 TraesCS3A01G432200 chr3A 84664162 84664913 751 False 1118.000000 1118 93.907 1 734 1 chr3A.!!$F1 733
2 TraesCS3A01G432200 chr3B 712569002 712573659 4657 True 7191.000000 7191 94.528 736 5408 1 chr3B.!!$R2 4672
3 TraesCS3A01G432200 chr3B 452747820 452748546 726 True 1116.000000 1116 94.324 1 734 1 chr3B.!!$R1 733
4 TraesCS3A01G432200 chr3D 537914129 537918758 4629 True 2194.333333 5699 90.803 736 5224 3 chr3D.!!$R1 4488
5 TraesCS3A01G432200 chr7A 689959764 689960497 733 False 1229.000000 1229 96.866 1 734 1 chr7A.!!$F1 733
6 TraesCS3A01G432200 chr1A 286244906 286245639 733 True 1229.000000 1229 96.866 1 734 1 chr1A.!!$R1 733
7 TraesCS3A01G432200 chr1A 287785542 287786275 733 True 1218.000000 1218 96.594 1 734 1 chr1A.!!$R2 733
8 TraesCS3A01G432200 chr5A 535685504 535686238 734 False 1214.000000 1214 96.467 1 736 1 chr5A.!!$F1 735
9 TraesCS3A01G432200 chr5A 510260516 510261272 756 True 1153.000000 1153 94.591 1 737 1 chr5A.!!$R1 736
10 TraesCS3A01G432200 chr1B 365464483 365465216 733 False 1195.000000 1195 96.049 1 734 1 chr1B.!!$F2 733
11 TraesCS3A01G432200 chr1B 111683793 111684527 734 False 1175.000000 1175 95.510 1 735 1 chr1B.!!$F1 734
12 TraesCS3A01G432200 chr2B 54335896 54336629 733 True 1179.000000 1179 95.640 1 734 1 chr2B.!!$R1 733
13 TraesCS3A01G432200 chr4A 135352838 135353564 726 False 1105.000000 1105 94.054 1 734 1 chr4A.!!$F1 733


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
779 832 0.100503 CCCAACGAAATTCCCGATGC 59.899 55.0 7.12 0.0 0.00 3.91 F
1378 1435 0.033991 CCTCGACTTCTCCCTCTCCA 60.034 60.0 0.00 0.0 0.00 3.86 F
1539 1596 0.179108 GCAACGAATCGGCTACCTCT 60.179 55.0 7.80 0.0 0.00 3.69 F
1769 1832 0.248825 CAGGCTCACTTCGATCTCCG 60.249 60.0 0.00 0.0 40.25 4.63 F
1984 2056 0.320374 TTGGCAGAACGTAGACCAGG 59.680 55.0 0.00 0.0 0.00 4.45 F
1991 2063 0.323957 AACGTAGACCAGGGGAAAGC 59.676 55.0 0.00 0.0 0.00 3.51 F
1992 2064 0.544595 ACGTAGACCAGGGGAAAGCT 60.545 55.0 0.00 0.0 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 2335 0.035056 CAATCCCTTGCCCTTCGAGT 60.035 55.000 0.00 0.0 0.00 4.18 R
2264 2336 0.749454 CCAATCCCTTGCCCTTCGAG 60.749 60.000 0.00 0.0 0.00 4.04 R
3451 3523 1.621672 CCCAGAGGAGGAAGCCACTC 61.622 65.000 0.00 0.0 33.47 3.51 R
4049 4121 1.064017 ACCTTGAACCAACTGGCAAGA 60.064 47.619 14.32 0.0 37.43 3.02 R
4256 4328 1.202879 TCGGCAATGACTGAAACCCTT 60.203 47.619 0.00 0.0 0.00 3.95 R
4320 4392 1.613925 CCTTCAGTCAACCTCGAGTCA 59.386 52.381 12.31 0.0 0.00 3.41 R
4416 4488 3.057456 ACCGTGCAACAAACTAACACAAA 60.057 39.130 0.00 0.0 35.74 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
124 125 0.388294 TCATCTGCTGCCTCATCGAG 59.612 55.000 0.00 0.00 0.00 4.04
169 170 9.499479 CAATCTTTACCTCATTACATAGCTCAT 57.501 33.333 0.00 0.00 0.00 2.90
218 219 3.487372 TGATCTATCCTACACCTCCACG 58.513 50.000 0.00 0.00 0.00 4.94
477 526 1.021390 GGAGGTTGGTCGATGCACAG 61.021 60.000 0.00 0.00 0.00 3.66
486 535 1.811266 CGATGCACAGGGACCGAAG 60.811 63.158 0.00 0.00 0.00 3.79
595 644 4.042187 AGCAAGGAGACTAGTCAAAACCAT 59.958 41.667 24.44 11.77 42.68 3.55
642 694 4.226394 TGGAGGAGAATTGATCCGGTTTTA 59.774 41.667 0.00 0.00 42.02 1.52
645 697 6.152154 GGAGGAGAATTGATCCGGTTTTAAAA 59.848 38.462 0.00 0.00 42.02 1.52
666 718 4.591321 AAGTTTAGGGGCTGATTGATCA 57.409 40.909 0.00 0.00 35.16 2.92
684 736 2.871453 TCAGGTTTTAGACTTTGGGGC 58.129 47.619 0.00 0.00 0.00 5.80
739 791 5.106673 GGAAAACGATACTTTCCTCAAGGTG 60.107 44.000 7.02 0.00 45.66 4.00
751 803 0.111446 TCAAGGTGAATTGGCCGGAA 59.889 50.000 5.05 0.00 0.00 4.30
779 832 0.100503 CCCAACGAAATTCCCGATGC 59.899 55.000 7.12 0.00 0.00 3.91
791 846 1.084370 CCCGATGCGAACCTCTTGTC 61.084 60.000 0.00 0.00 0.00 3.18
817 872 1.699343 GTGACGAACGAGAAAGGAGG 58.301 55.000 0.14 0.00 0.00 4.30
1009 1066 4.489771 CCCCCGACATGGCTCCAC 62.490 72.222 0.00 0.00 35.87 4.02
1012 1069 4.082523 CCGACATGGCTCCACCGT 62.083 66.667 0.00 0.00 43.94 4.83
1080 1137 4.790962 CTGCAGTGCCTGGGCGAT 62.791 66.667 13.72 0.00 45.51 4.58
1378 1435 0.033991 CCTCGACTTCTCCCTCTCCA 60.034 60.000 0.00 0.00 0.00 3.86
1415 1472 3.068691 CTCCGACGAGCCCCTCAA 61.069 66.667 0.00 0.00 0.00 3.02
1444 1501 1.669604 CTCCGTCCTCGAGAATCTCA 58.330 55.000 15.71 0.00 39.71 3.27
1445 1502 1.332375 CTCCGTCCTCGAGAATCTCAC 59.668 57.143 15.71 0.00 39.71 3.51
1448 1505 1.380524 GTCCTCGAGAATCTCACCGA 58.619 55.000 15.71 1.80 0.00 4.69
1473 1530 1.589993 CGCGGCCTACACAGAGATG 60.590 63.158 0.00 0.00 0.00 2.90
1481 1538 1.613317 TACACAGAGATGGCCCACCG 61.613 60.000 0.00 0.00 39.70 4.94
1521 1578 3.435186 GCCTCTTCGTGGCTTGGC 61.435 66.667 0.00 0.00 46.38 4.52
1533 1590 2.690778 GCTTGGCAACGAATCGGCT 61.691 57.895 7.80 0.00 42.51 5.52
1534 1591 1.366111 GCTTGGCAACGAATCGGCTA 61.366 55.000 7.80 0.00 42.51 3.93
1535 1592 0.373716 CTTGGCAACGAATCGGCTAC 59.626 55.000 7.80 0.00 42.51 3.58
1536 1593 1.022451 TTGGCAACGAATCGGCTACC 61.022 55.000 7.80 3.49 42.51 3.18
1537 1594 1.153429 GGCAACGAATCGGCTACCT 60.153 57.895 7.80 0.00 0.00 3.08
1538 1595 1.152383 GGCAACGAATCGGCTACCTC 61.152 60.000 7.80 0.00 0.00 3.85
1539 1596 0.179108 GCAACGAATCGGCTACCTCT 60.179 55.000 7.80 0.00 0.00 3.69
1540 1597 1.841450 CAACGAATCGGCTACCTCTC 58.159 55.000 7.80 0.00 0.00 3.20
1541 1598 0.745468 AACGAATCGGCTACCTCTCC 59.255 55.000 7.80 0.00 0.00 3.71
1542 1599 1.283181 CGAATCGGCTACCTCTCCG 59.717 63.158 0.00 0.00 46.52 4.63
1543 1600 1.007154 GAATCGGCTACCTCTCCGC 60.007 63.158 0.00 0.00 44.91 5.54
1544 1601 2.734756 GAATCGGCTACCTCTCCGCG 62.735 65.000 0.00 0.00 44.91 6.46
1548 1605 3.839432 GCTACCTCTCCGCGGCTT 61.839 66.667 23.51 4.54 0.00 4.35
1549 1606 2.105128 CTACCTCTCCGCGGCTTG 59.895 66.667 23.51 13.37 0.00 4.01
1550 1607 3.432051 CTACCTCTCCGCGGCTTGG 62.432 68.421 23.51 22.77 0.00 3.61
1563 1620 2.007608 CGGCTTGGTAACTTTAGCTCC 58.992 52.381 0.00 0.00 36.74 4.70
1567 1624 0.251073 TGGTAACTTTAGCTCCGCCC 59.749 55.000 0.00 0.00 37.61 6.13
1572 1629 2.285069 TTTAGCTCCGCCCTCCCA 60.285 61.111 0.00 0.00 0.00 4.37
1580 1637 4.135153 CGCCCTCCCAGTCGACAG 62.135 72.222 19.50 10.04 0.00 3.51
1584 1641 2.262915 CTCCCAGTCGACAGCACC 59.737 66.667 19.50 0.00 0.00 5.01
1585 1642 2.203640 TCCCAGTCGACAGCACCT 60.204 61.111 19.50 0.00 0.00 4.00
1596 1653 2.985847 AGCACCTTCTTTGGCCGC 60.986 61.111 0.00 0.00 0.00 6.53
1635 1692 1.275291 CTGCTGGAAAGGTTAGTCGGA 59.725 52.381 0.00 0.00 0.00 4.55
1638 1695 2.280628 CTGGAAAGGTTAGTCGGATGC 58.719 52.381 0.00 0.00 0.00 3.91
1640 1697 2.039216 TGGAAAGGTTAGTCGGATGCAA 59.961 45.455 0.00 0.00 0.00 4.08
1769 1832 0.248825 CAGGCTCACTTCGATCTCCG 60.249 60.000 0.00 0.00 40.25 4.63
1780 1843 1.676678 CGATCTCCGGATGTGGGTGT 61.677 60.000 3.57 0.00 31.46 4.16
1788 1851 1.005037 GATGTGGGTGTGCGTCTCA 60.005 57.895 0.00 0.00 0.00 3.27
1798 1861 0.371645 GTGCGTCTCAAGCTGTATGC 59.628 55.000 0.00 0.00 43.29 3.14
1801 1864 1.004185 GCGTCTCAAGCTGTATGCATG 60.004 52.381 10.16 0.00 45.94 4.06
1803 1866 2.030091 CGTCTCAAGCTGTATGCATGTG 59.970 50.000 10.16 0.04 45.94 3.21
1807 1870 2.946990 TCAAGCTGTATGCATGTGATGG 59.053 45.455 10.16 0.00 45.94 3.51
1825 1888 5.955355 GTGATGGAGCTTACTAGGGAGATAT 59.045 44.000 0.00 0.00 0.00 1.63
1831 1894 4.020662 AGCTTACTAGGGAGATATTGCAGC 60.021 45.833 0.00 0.00 0.00 5.25
1832 1895 4.020662 GCTTACTAGGGAGATATTGCAGCT 60.021 45.833 0.00 0.00 0.00 4.24
1836 1899 0.892814 GGGAGATATTGCAGCTGGCC 60.893 60.000 17.12 0.00 43.89 5.36
1838 1901 1.683943 GAGATATTGCAGCTGGCCAA 58.316 50.000 17.12 12.46 43.89 4.52
1840 1903 2.029623 AGATATTGCAGCTGGCCAAAG 58.970 47.619 17.12 0.00 43.89 2.77
1856 1928 2.103263 CCAAAGAGGGGAAGGACTATCG 59.897 54.545 0.00 0.00 0.00 2.92
1860 1932 0.338814 AGGGGAAGGACTATCGTGGT 59.661 55.000 0.00 0.00 0.00 4.16
1861 1933 0.464452 GGGGAAGGACTATCGTGGTG 59.536 60.000 0.00 0.00 0.00 4.17
1864 1936 2.100418 GGGAAGGACTATCGTGGTGTAC 59.900 54.545 0.00 0.00 0.00 2.90
1873 1945 7.037438 GGACTATCGTGGTGTACTCAATTTTA 58.963 38.462 0.00 0.00 0.00 1.52
1884 1956 9.722056 GGTGTACTCAATTTTAATTATCTGCAG 57.278 33.333 7.63 7.63 0.00 4.41
1886 1958 9.679661 TGTACTCAATTTTAATTATCTGCAGGA 57.320 29.630 15.13 0.57 0.00 3.86
1889 1961 8.897752 ACTCAATTTTAATTATCTGCAGGAGTC 58.102 33.333 15.13 0.00 0.00 3.36
1894 1966 0.461548 TTATCTGCAGGAGTCGCTGG 59.538 55.000 15.13 0.00 0.00 4.85
1895 1967 0.684479 TATCTGCAGGAGTCGCTGGT 60.684 55.000 15.13 0.68 0.00 4.00
1907 1979 2.050077 GCTGGTTTCTGCCGTTGC 60.050 61.111 0.00 0.00 38.26 4.17
1945 2017 3.949754 GCTCATCCTTGATGATGTTTGGA 59.050 43.478 7.19 0.00 46.16 3.53
1950 2022 5.902613 TCCTTGATGATGTTTGGAATGAC 57.097 39.130 0.00 0.00 0.00 3.06
1952 2024 5.774184 TCCTTGATGATGTTTGGAATGACAA 59.226 36.000 0.00 0.00 0.00 3.18
1953 2025 5.865552 CCTTGATGATGTTTGGAATGACAAC 59.134 40.000 0.00 0.00 0.00 3.32
1960 2032 1.890876 TTGGAATGACAACGGGAGTG 58.109 50.000 0.00 0.00 46.69 3.51
1963 2035 1.079503 GAATGACAACGGGAGTGAGC 58.920 55.000 0.00 0.00 46.69 4.26
1977 2049 1.070134 AGTGAGCTTTGGCAGAACGTA 59.930 47.619 0.00 0.00 41.70 3.57
1984 2056 0.320374 TTGGCAGAACGTAGACCAGG 59.680 55.000 0.00 0.00 0.00 4.45
1989 2061 1.621814 CAGAACGTAGACCAGGGGAAA 59.378 52.381 0.00 0.00 0.00 3.13
1991 2063 0.323957 AACGTAGACCAGGGGAAAGC 59.676 55.000 0.00 0.00 0.00 3.51
1992 2064 0.544595 ACGTAGACCAGGGGAAAGCT 60.545 55.000 0.00 0.00 0.00 3.74
1993 2065 0.613777 CGTAGACCAGGGGAAAGCTT 59.386 55.000 0.00 0.00 0.00 3.74
2008 2080 4.572795 GGAAAGCTTTACTATCACCTCTGC 59.427 45.833 14.53 0.00 0.00 4.26
2024 2096 0.809385 CTGCAGAATGGTCAGCAAGG 59.191 55.000 8.42 0.00 44.64 3.61
2037 2109 4.116238 GTCAGCAAGGTAGCAGAATAGTC 58.884 47.826 0.00 0.00 36.85 2.59
2099 2171 3.763557 AAGGATCCCAATGATGTTGGT 57.236 42.857 8.55 0.00 37.88 3.67
2110 2182 2.246469 TGATGTTGGTTGGATTGGGTG 58.754 47.619 0.00 0.00 0.00 4.61
2150 2222 1.498865 CTCAAGAAGCACGCGTTGGT 61.499 55.000 10.22 8.43 37.63 3.67
2158 2230 1.010125 CACGCGTTGGTTTGTGAGG 60.010 57.895 10.22 0.00 34.29 3.86
2165 2237 2.544267 CGTTGGTTTGTGAGGAGAGTTC 59.456 50.000 0.00 0.00 0.00 3.01
2168 2240 2.104792 TGGTTTGTGAGGAGAGTTCTGG 59.895 50.000 0.00 0.00 0.00 3.86
2173 2245 6.410540 GTTTGTGAGGAGAGTTCTGGATATT 58.589 40.000 0.00 0.00 0.00 1.28
2174 2246 5.860941 TGTGAGGAGAGTTCTGGATATTC 57.139 43.478 0.00 0.00 0.00 1.75
2175 2247 5.523588 TGTGAGGAGAGTTCTGGATATTCT 58.476 41.667 0.00 0.00 0.00 2.40
2182 2254 6.097554 GGAGAGTTCTGGATATTCTCAGTTGA 59.902 42.308 2.68 0.00 36.79 3.18
2252 2324 2.354821 CAGCTAAAGTTATTGGCGGGAC 59.645 50.000 0.00 0.00 0.00 4.46
2278 2350 1.221021 GGTACTCGAAGGGCAAGGG 59.779 63.158 0.00 0.00 0.00 3.95
2317 2389 4.716287 TGGAGACAGATATTCATGGTGACA 59.284 41.667 0.00 0.00 40.01 3.58
2403 2475 7.746475 GCATATTGCAGTATATTTCCGAAGAAC 59.254 37.037 0.87 0.00 44.26 3.01
2538 2610 5.296151 TGTTGAGGTCATTCTTTCAGACT 57.704 39.130 0.00 0.00 32.98 3.24
2820 2892 3.930229 AGATAAAGAATGTGCGCACGTTA 59.070 39.130 39.66 27.74 40.35 3.18
2853 2925 6.106673 CGGATGTGATATATCCAAGTTACCC 58.893 44.000 10.25 0.97 43.46 3.69
2964 3036 6.885918 TGCATCTTCAGACTTTTGATATTCCA 59.114 34.615 0.00 0.00 0.00 3.53
3022 3094 1.571460 CAGTTGACCAGCTTGCGAC 59.429 57.895 0.00 0.00 0.00 5.19
3138 3210 1.652947 AGGGGCGAACCTTAGAAGAA 58.347 50.000 0.00 0.00 37.69 2.52
3152 3224 9.844257 AACCTTAGAAGAATTGAAGGATATGAG 57.156 33.333 6.52 0.00 39.17 2.90
3216 3288 2.029649 TCAATGCAAAGAGGAAGCTTGC 60.030 45.455 10.41 10.41 0.00 4.01
3451 3523 2.134789 AGCTAATTGCAGAAGGTGGG 57.865 50.000 0.00 0.00 45.94 4.61
4049 4121 8.525316 TGACTGCAAGAATATCAAATCATTTGT 58.475 29.630 9.98 0.88 38.56 2.83
4213 4285 3.011821 AGTGTCCCTACCTTCTGAGATGA 59.988 47.826 0.00 0.00 0.00 2.92
4256 4328 5.420725 AAACTGAGTATATCACACTGCCA 57.579 39.130 0.00 0.00 33.22 4.92
4320 4392 5.454613 GGAATTTCTTCATTTGGTTGGGTGT 60.455 40.000 0.00 0.00 32.70 4.16
4664 4861 2.182825 GTTCCACACACTAGCGTATCG 58.817 52.381 0.00 0.00 0.00 2.92
4665 4862 1.456296 TCCACACACTAGCGTATCGT 58.544 50.000 0.00 0.00 0.00 3.73
4801 4998 3.700863 ATTAGGGTCCACTAGCTGGTA 57.299 47.619 0.95 0.00 41.52 3.25
4995 5226 1.780919 AGTATGCCCCAGTTTATCCCC 59.219 52.381 0.00 0.00 0.00 4.81
5310 5542 1.283029 CTGGACCATGGTGTTCCTCAT 59.717 52.381 25.52 0.00 34.23 2.90
5324 5556 5.293079 GTGTTCCTCATAGTTCATCTTCTGC 59.707 44.000 0.00 0.00 0.00 4.26
5346 5578 3.467776 CCTCTGCTAGGTTTCTGCC 57.532 57.895 0.00 0.00 40.94 4.85
5347 5579 0.460987 CCTCTGCTAGGTTTCTGCCG 60.461 60.000 0.00 0.00 40.94 5.69
5348 5580 0.532573 CTCTGCTAGGTTTCTGCCGA 59.467 55.000 0.00 0.00 0.00 5.54
5349 5581 1.137872 CTCTGCTAGGTTTCTGCCGAT 59.862 52.381 0.00 0.00 0.00 4.18
5350 5582 2.362397 CTCTGCTAGGTTTCTGCCGATA 59.638 50.000 0.00 0.00 0.00 2.92
5351 5583 2.362397 TCTGCTAGGTTTCTGCCGATAG 59.638 50.000 0.00 0.00 0.00 2.08
5352 5584 2.101582 CTGCTAGGTTTCTGCCGATAGT 59.898 50.000 0.00 0.00 0.00 2.12
5353 5585 2.500098 TGCTAGGTTTCTGCCGATAGTT 59.500 45.455 0.00 0.00 0.00 2.24
5354 5586 3.055385 TGCTAGGTTTCTGCCGATAGTTT 60.055 43.478 0.00 0.00 0.00 2.66
5355 5587 3.309954 GCTAGGTTTCTGCCGATAGTTTG 59.690 47.826 0.00 0.00 0.00 2.93
5356 5588 3.418684 AGGTTTCTGCCGATAGTTTGT 57.581 42.857 0.00 0.00 0.00 2.83
5357 5589 3.074412 AGGTTTCTGCCGATAGTTTGTG 58.926 45.455 0.00 0.00 0.00 3.33
5358 5590 2.812011 GGTTTCTGCCGATAGTTTGTGT 59.188 45.455 0.00 0.00 0.00 3.72
5359 5591 3.364964 GGTTTCTGCCGATAGTTTGTGTG 60.365 47.826 0.00 0.00 0.00 3.82
5360 5592 2.831685 TCTGCCGATAGTTTGTGTGT 57.168 45.000 0.00 0.00 0.00 3.72
5361 5593 2.683968 TCTGCCGATAGTTTGTGTGTC 58.316 47.619 0.00 0.00 0.00 3.67
5400 5632 9.887629 ATATCTGGATTTCATACATGAAGCTAG 57.112 33.333 0.00 8.57 46.34 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 6.661805 GGAAGATTGTTTTTATGGGTAGGTCA 59.338 38.462 0.00 0.00 0.00 4.02
204 205 1.763968 CAGATCGTGGAGGTGTAGGA 58.236 55.000 0.00 0.00 0.00 2.94
477 526 0.613777 ATTCAGGTGACTTCGGTCCC 59.386 55.000 0.00 0.00 43.85 4.46
486 535 0.967380 CAGCCCCCAATTCAGGTGAC 60.967 60.000 0.00 0.00 0.00 3.67
616 668 2.551721 CCGGATCAATTCTCCTCCATGG 60.552 54.545 4.97 4.97 37.10 3.66
617 669 2.105477 ACCGGATCAATTCTCCTCCATG 59.895 50.000 9.46 0.00 0.00 3.66
618 670 2.412591 ACCGGATCAATTCTCCTCCAT 58.587 47.619 9.46 0.00 0.00 3.41
622 674 7.232737 ACTTTTTAAAACCGGATCAATTCTCCT 59.767 33.333 9.46 0.00 0.00 3.69
642 694 5.779771 TGATCAATCAGCCCCTAAACTTTTT 59.220 36.000 0.00 0.00 32.11 1.94
645 697 4.530875 CTGATCAATCAGCCCCTAAACTT 58.469 43.478 7.05 0.00 46.63 2.66
666 718 1.422402 TCGCCCCAAAGTCTAAAACCT 59.578 47.619 0.00 0.00 0.00 3.50
684 736 3.123804 CCTGTCTAATGGACCGATTTCG 58.876 50.000 0.00 0.00 43.89 3.46
739 791 1.090052 CGGTCTCTTCCGGCCAATTC 61.090 60.000 2.24 0.00 45.88 2.17
751 803 1.838073 ATTTCGTTGGGCCGGTCTCT 61.838 55.000 5.77 0.00 0.00 3.10
779 832 1.749634 ACGATAGGGACAAGAGGTTCG 59.250 52.381 0.00 0.00 43.77 3.95
815 870 1.244697 TTCGCTGCTTCTCGTCTCCT 61.245 55.000 0.00 0.00 0.00 3.69
816 871 0.388649 TTTCGCTGCTTCTCGTCTCC 60.389 55.000 0.00 0.00 0.00 3.71
817 872 0.711118 GTTTCGCTGCTTCTCGTCTC 59.289 55.000 0.00 0.00 0.00 3.36
1434 1491 1.586564 GGCGTCGGTGAGATTCTCG 60.587 63.158 9.07 0.00 32.35 4.04
1465 1522 4.101448 GCGGTGGGCCATCTCTGT 62.101 66.667 16.16 0.00 34.80 3.41
1513 1570 2.331893 CCGATTCGTTGCCAAGCCA 61.332 57.895 5.20 0.00 0.00 4.75
1521 1578 1.536284 GGAGAGGTAGCCGATTCGTTG 60.536 57.143 5.20 0.00 0.00 4.10
1536 1593 1.810030 GTTACCAAGCCGCGGAGAG 60.810 63.158 33.48 16.97 0.00 3.20
1537 1594 1.823169 AAGTTACCAAGCCGCGGAGA 61.823 55.000 33.48 2.73 0.00 3.71
1538 1595 0.953960 AAAGTTACCAAGCCGCGGAG 60.954 55.000 33.48 17.79 0.00 4.63
1539 1596 0.321021 TAAAGTTACCAAGCCGCGGA 59.679 50.000 33.48 2.66 0.00 5.54
1540 1597 0.725117 CTAAAGTTACCAAGCCGCGG 59.275 55.000 24.05 24.05 0.00 6.46
1541 1598 0.096454 GCTAAAGTTACCAAGCCGCG 59.904 55.000 0.00 0.00 0.00 6.46
1542 1599 1.397343 GAGCTAAAGTTACCAAGCCGC 59.603 52.381 0.00 0.00 35.54 6.53
1543 1600 2.007608 GGAGCTAAAGTTACCAAGCCG 58.992 52.381 0.00 0.00 35.54 5.52
1544 1601 2.007608 CGGAGCTAAAGTTACCAAGCC 58.992 52.381 0.00 0.00 35.54 4.35
1563 1620 4.135153 CTGTCGACTGGGAGGGCG 62.135 72.222 17.92 0.00 0.00 6.13
1567 1624 1.821061 AAGGTGCTGTCGACTGGGAG 61.821 60.000 21.94 10.08 0.00 4.30
1572 1629 1.541233 CCAAAGAAGGTGCTGTCGACT 60.541 52.381 17.92 0.00 0.00 4.18
1579 1636 2.985847 GCGGCCAAAGAAGGTGCT 60.986 61.111 2.24 0.00 31.97 4.40
1580 1637 4.404654 CGCGGCCAAAGAAGGTGC 62.405 66.667 2.24 0.00 0.00 5.01
1611 1668 3.368427 CGACTAACCTTTCCAGCAGATCA 60.368 47.826 0.00 0.00 0.00 2.92
1614 1671 1.275291 CCGACTAACCTTTCCAGCAGA 59.725 52.381 0.00 0.00 0.00 4.26
1618 1675 2.280628 GCATCCGACTAACCTTTCCAG 58.719 52.381 0.00 0.00 0.00 3.86
1635 1692 1.305465 TTGAGCAGGGCCATTGCAT 60.305 52.632 27.09 15.49 43.92 3.96
1638 1695 1.651240 CGAGTTGAGCAGGGCCATTG 61.651 60.000 6.18 3.11 0.00 2.82
1640 1697 2.270205 CGAGTTGAGCAGGGCCAT 59.730 61.111 6.18 0.00 0.00 4.40
1698 1761 3.554692 GTCGTCTTGCCGATGCCG 61.555 66.667 0.00 0.00 39.34 5.69
1769 1832 1.741770 GAGACGCACACCCACATCC 60.742 63.158 0.00 0.00 0.00 3.51
1780 1843 0.037419 TGCATACAGCTTGAGACGCA 60.037 50.000 0.00 0.00 45.94 5.24
1788 1851 3.211865 CTCCATCACATGCATACAGCTT 58.788 45.455 0.00 0.00 45.94 3.74
1798 1861 3.643320 TCCCTAGTAAGCTCCATCACATG 59.357 47.826 0.00 0.00 0.00 3.21
1801 1864 3.567397 TCTCCCTAGTAAGCTCCATCAC 58.433 50.000 0.00 0.00 0.00 3.06
1803 1866 6.629291 GCAATATCTCCCTAGTAAGCTCCATC 60.629 46.154 0.00 0.00 0.00 3.51
1807 1870 5.719173 CTGCAATATCTCCCTAGTAAGCTC 58.281 45.833 0.00 0.00 0.00 4.09
1825 1888 1.904865 CCTCTTTGGCCAGCTGCAA 60.905 57.895 8.66 5.34 43.89 4.08
1831 1894 1.000396 CCTTCCCCTCTTTGGCCAG 60.000 63.158 5.11 0.00 0.00 4.85
1832 1895 1.465188 TCCTTCCCCTCTTTGGCCA 60.465 57.895 0.00 0.00 0.00 5.36
1836 1899 3.460857 CGATAGTCCTTCCCCTCTTTG 57.539 52.381 0.00 0.00 0.00 2.77
1856 1928 9.503427 GCAGATAATTAAAATTGAGTACACCAC 57.497 33.333 0.00 0.00 0.00 4.16
1860 1932 9.679661 TCCTGCAGATAATTAAAATTGAGTACA 57.320 29.630 17.39 0.00 0.00 2.90
1864 1936 8.066595 CGACTCCTGCAGATAATTAAAATTGAG 58.933 37.037 17.39 10.52 0.00 3.02
1873 1945 2.484417 CCAGCGACTCCTGCAGATAATT 60.484 50.000 17.39 0.00 33.85 1.40
1877 1949 1.548357 AACCAGCGACTCCTGCAGAT 61.548 55.000 17.39 0.00 33.85 2.90
1884 1956 2.035442 GGCAGAAACCAGCGACTCC 61.035 63.158 0.00 0.00 0.00 3.85
1886 1958 2.357517 CGGCAGAAACCAGCGACT 60.358 61.111 0.00 0.00 0.00 4.18
1887 1959 2.251642 AACGGCAGAAACCAGCGAC 61.252 57.895 0.00 0.00 0.00 5.19
1889 1961 2.252260 CAACGGCAGAAACCAGCG 59.748 61.111 0.00 0.00 0.00 5.18
1907 1979 1.349026 TGAGCAAGAACCTCTTCCCTG 59.651 52.381 0.00 0.00 33.78 4.45
1945 2017 0.687354 AGCTCACTCCCGTTGTCATT 59.313 50.000 0.00 0.00 0.00 2.57
1950 2022 1.856265 GCCAAAGCTCACTCCCGTTG 61.856 60.000 0.00 0.00 35.50 4.10
1952 2024 2.032681 GCCAAAGCTCACTCCCGT 59.967 61.111 0.00 0.00 35.50 5.28
1953 2025 2.032528 TGCCAAAGCTCACTCCCG 59.967 61.111 0.00 0.00 40.80 5.14
1959 2031 1.343142 TCTACGTTCTGCCAAAGCTCA 59.657 47.619 0.00 0.00 40.80 4.26
1960 2032 1.727335 GTCTACGTTCTGCCAAAGCTC 59.273 52.381 0.00 0.00 40.80 4.09
1963 2035 2.069273 CTGGTCTACGTTCTGCCAAAG 58.931 52.381 0.00 0.00 0.00 2.77
1977 2049 2.349445 AGTAAAGCTTTCCCCTGGTCT 58.651 47.619 16.57 0.38 0.00 3.85
1984 2056 5.119694 CAGAGGTGATAGTAAAGCTTTCCC 58.880 45.833 16.57 7.82 0.00 3.97
1989 2061 4.026744 TCTGCAGAGGTGATAGTAAAGCT 58.973 43.478 13.74 0.00 0.00 3.74
1991 2063 5.757320 CCATTCTGCAGAGGTGATAGTAAAG 59.243 44.000 24.63 8.33 0.00 1.85
1992 2064 5.189736 ACCATTCTGCAGAGGTGATAGTAAA 59.810 40.000 23.10 3.00 32.04 2.01
1993 2065 4.716784 ACCATTCTGCAGAGGTGATAGTAA 59.283 41.667 23.10 3.51 32.04 2.24
2008 2080 2.012673 GCTACCTTGCTGACCATTCTG 58.987 52.381 0.00 0.00 0.00 3.02
2024 2096 5.264712 GTGTAGTCACGACTATTCTGCTAC 58.735 45.833 9.99 0.00 44.73 3.58
2051 2123 1.012086 CATGTCAGCCACCATCTTCG 58.988 55.000 0.00 0.00 0.00 3.79
2099 2171 0.322456 CTCTTCGGCACCCAATCCAA 60.322 55.000 0.00 0.00 0.00 3.53
2110 2182 0.598065 AACAACCAATGCTCTTCGGC 59.402 50.000 0.00 0.00 0.00 5.54
2145 2217 3.561725 CAGAACTCTCCTCACAAACCAAC 59.438 47.826 0.00 0.00 0.00 3.77
2150 2222 6.441924 AGAATATCCAGAACTCTCCTCACAAA 59.558 38.462 0.00 0.00 0.00 2.83
2158 2230 7.106439 TCAACTGAGAATATCCAGAACTCTC 57.894 40.000 0.00 0.39 34.65 3.20
2165 2237 6.477053 TCTCCTTCAACTGAGAATATCCAG 57.523 41.667 0.00 0.00 34.79 3.86
2168 2240 6.709846 CCCAATCTCCTTCAACTGAGAATATC 59.290 42.308 0.00 0.00 40.75 1.63
2173 2245 3.517100 CTCCCAATCTCCTTCAACTGAGA 59.483 47.826 0.00 0.00 41.55 3.27
2174 2246 3.517100 TCTCCCAATCTCCTTCAACTGAG 59.483 47.826 0.00 0.00 0.00 3.35
2175 2247 3.520696 TCTCCCAATCTCCTTCAACTGA 58.479 45.455 0.00 0.00 0.00 3.41
2182 2254 4.017683 AGCAATCTTTCTCCCAATCTCCTT 60.018 41.667 0.00 0.00 0.00 3.36
2223 2295 4.433615 CAATAACTTTAGCTGCGAGAGGA 58.566 43.478 0.00 0.00 0.00 3.71
2252 2324 1.202268 CCCTTCGAGTACCACTAAGCG 60.202 57.143 0.00 0.00 0.00 4.68
2258 2330 0.391263 CCTTGCCCTTCGAGTACCAC 60.391 60.000 0.00 0.00 0.00 4.16
2263 2335 0.035056 CAATCCCTTGCCCTTCGAGT 60.035 55.000 0.00 0.00 0.00 4.18
2264 2336 0.749454 CCAATCCCTTGCCCTTCGAG 60.749 60.000 0.00 0.00 0.00 4.04
2278 2350 5.734720 TGTCTCCAAGATACTGTTCCAATC 58.265 41.667 0.00 0.00 0.00 2.67
2317 2389 2.020720 TGACAAAAGTGTGGCGACAAT 58.979 42.857 2.03 0.00 46.06 2.71
2323 2395 3.923017 ATAGCTTGACAAAAGTGTGGC 57.077 42.857 0.00 0.00 38.41 5.01
2403 2475 4.098501 AGTTTCTTTGGCTCAAACTTCCAG 59.901 41.667 0.00 0.00 37.09 3.86
2418 2490 9.178758 GATATCCACATCCTAACAAGTTTCTTT 57.821 33.333 0.00 0.00 0.00 2.52
2538 2610 3.678529 GCCTTTTGTTTCCTTGCTTGACA 60.679 43.478 0.00 0.00 0.00 3.58
2709 2781 9.877178 GTCCTTAATCTCTTCAGATAGTTTTGA 57.123 33.333 0.00 0.00 38.55 2.69
2713 2785 8.474025 CAGTGTCCTTAATCTCTTCAGATAGTT 58.526 37.037 0.00 0.00 38.55 2.24
2715 2787 8.231692 TCAGTGTCCTTAATCTCTTCAGATAG 57.768 38.462 0.00 0.00 38.55 2.08
2716 2788 8.774546 ATCAGTGTCCTTAATCTCTTCAGATA 57.225 34.615 0.00 0.00 38.55 1.98
2820 2892 8.146053 TGGATATATCACATCCGGTAAAATCT 57.854 34.615 14.60 0.00 44.27 2.40
2853 2925 4.619760 TGAGTTAGTACGTCAATTGCTTCG 59.380 41.667 0.00 8.10 0.00 3.79
2964 3036 1.891150 CCATCAAGCTGGCACTTCTTT 59.109 47.619 0.00 0.00 0.00 2.52
3022 3094 4.627611 ATTTTGACTCGATGCCAAGATG 57.372 40.909 0.00 0.00 0.00 2.90
3138 3210 7.403671 CATGAAGATCCCTCATATCCTTCAAT 58.596 38.462 0.00 0.00 34.06 2.57
3152 3224 2.744352 AAGAAGCCCATGAAGATCCC 57.256 50.000 0.00 0.00 0.00 3.85
3216 3288 3.549070 GCTTATTTGCCAATTGAGCTTCG 59.451 43.478 7.12 0.00 31.99 3.79
3451 3523 1.621672 CCCAGAGGAGGAAGCCACTC 61.622 65.000 0.00 0.00 33.47 3.51
4049 4121 1.064017 ACCTTGAACCAACTGGCAAGA 60.064 47.619 14.32 0.00 37.43 3.02
4256 4328 1.202879 TCGGCAATGACTGAAACCCTT 60.203 47.619 0.00 0.00 0.00 3.95
4320 4392 1.613925 CCTTCAGTCAACCTCGAGTCA 59.386 52.381 12.31 0.00 0.00 3.41
4416 4488 3.057456 ACCGTGCAACAAACTAACACAAA 60.057 39.130 0.00 0.00 35.74 2.83
4426 4498 3.472652 AGAGAACATACCGTGCAACAAA 58.527 40.909 0.00 0.00 35.74 2.83
4664 4861 6.541111 AAAGATTCGAAGTAAACACAGGAC 57.459 37.500 3.35 0.00 0.00 3.85
4665 4862 7.384115 CAGTAAAGATTCGAAGTAAACACAGGA 59.616 37.037 3.35 0.00 0.00 3.86
4744 4941 3.068307 CCCAAGACAGTAATCCTAGTCGG 59.932 52.174 0.00 0.00 36.18 4.79
4801 4998 3.818773 CACGGAGGTAAAACAACAATCCT 59.181 43.478 0.00 0.00 0.00 3.24
4974 5205 2.983898 GGGGATAAACTGGGGCATACTA 59.016 50.000 0.00 0.00 0.00 1.82
4995 5226 2.854777 CAGCTATCGAAGACCAAAGACG 59.145 50.000 0.00 0.00 42.51 4.18
5187 5419 2.181954 TTGCATTGCCAAATGGAACC 57.818 45.000 6.12 0.00 45.73 3.62
5310 5542 4.159321 CAGAGGTGAGCAGAAGATGAACTA 59.841 45.833 0.00 0.00 0.00 2.24
5342 5574 1.390123 CGACACACAAACTATCGGCAG 59.610 52.381 0.00 0.00 0.00 4.85
5345 5577 4.032445 CCATAACGACACACAAACTATCGG 59.968 45.833 0.00 0.00 37.11 4.18
5346 5578 4.860352 TCCATAACGACACACAAACTATCG 59.140 41.667 0.00 0.00 38.71 2.92
5347 5579 5.220416 GCTCCATAACGACACACAAACTATC 60.220 44.000 0.00 0.00 0.00 2.08
5348 5580 4.630069 GCTCCATAACGACACACAAACTAT 59.370 41.667 0.00 0.00 0.00 2.12
5349 5581 3.991773 GCTCCATAACGACACACAAACTA 59.008 43.478 0.00 0.00 0.00 2.24
5350 5582 2.806244 GCTCCATAACGACACACAAACT 59.194 45.455 0.00 0.00 0.00 2.66
5351 5583 2.095919 GGCTCCATAACGACACACAAAC 60.096 50.000 0.00 0.00 0.00 2.93
5352 5584 2.147958 GGCTCCATAACGACACACAAA 58.852 47.619 0.00 0.00 0.00 2.83
5353 5585 1.070914 TGGCTCCATAACGACACACAA 59.929 47.619 0.00 0.00 0.00 3.33
5354 5586 0.682292 TGGCTCCATAACGACACACA 59.318 50.000 0.00 0.00 0.00 3.72
5355 5587 1.803334 TTGGCTCCATAACGACACAC 58.197 50.000 0.00 0.00 0.00 3.82
5356 5588 2.779755 ATTGGCTCCATAACGACACA 57.220 45.000 0.00 0.00 0.00 3.72
5357 5589 4.449068 CAGATATTGGCTCCATAACGACAC 59.551 45.833 0.00 0.00 0.00 3.67
5358 5590 4.503123 CCAGATATTGGCTCCATAACGACA 60.503 45.833 0.00 0.00 40.87 4.35
5359 5591 3.997021 CCAGATATTGGCTCCATAACGAC 59.003 47.826 0.00 0.00 40.87 4.34
5360 5592 4.271696 CCAGATATTGGCTCCATAACGA 57.728 45.455 0.00 0.00 40.87 3.85



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

AutoCloner maintained by Alex Coulton.