Multiple sequence alignment - TraesCS7A01G436600

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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 TraesCS7A01G436600 chr7A 100.000 2750 0 0 1 2750 631364047 631366796 0.000000e+00 5079.0
1 TraesCS7A01G436600 chr7D 89.153 2268 112 57 136 2321 547459111 547456896 0.000000e+00 2702.0
2 TraesCS7A01G436600 chr7D 89.848 197 4 4 2564 2750 547456696 547456506 3.540000e-59 239.0
3 TraesCS7A01G436600 chr7B 88.404 1880 105 45 502 2321 590501647 590499821 0.000000e+00 2159.0
4 TraesCS7A01G436600 chr7B 87.834 337 26 11 2309 2643 590499806 590499483 5.560000e-102 381.0
5 TraesCS7A01G436600 chr7B 88.959 317 21 4 177 484 590501942 590501631 2.000000e-101 379.0
6 TraesCS7A01G436600 chr7B 96.078 102 4 0 2649 2750 590498939 590498838 1.690000e-37 167.0
7 TraesCS7A01G436600 chr5D 72.944 462 90 27 1302 1738 520910224 520910675 7.990000e-26 128.0
8 TraesCS7A01G436600 chr5D 72.143 560 107 35 1202 1746 424033433 424033958 1.030000e-24 124.0
9 TraesCS7A01G436600 chr4D 72.014 561 110 33 1200 1738 386831292 386831827 3.720000e-24 122.0
10 TraesCS7A01G436600 chr4D 76.037 217 40 11 1202 1412 121970953 121971163 4.850000e-18 102.0
11 TraesCS7A01G436600 chr4B 72.435 497 92 34 1271 1737 494692158 494691677 1.730000e-22 117.0
12 TraesCS7A01G436600 chr4B 77.376 221 30 17 1202 1412 184865085 184865295 2.240000e-21 113.0
13 TraesCS7A01G436600 chr4A 71.658 561 112 34 1200 1738 68141578 68142113 8.050000e-21 111.0
14 TraesCS7A01G436600 chr4A 76.442 208 37 11 1211 1412 449117542 449117341 4.850000e-18 102.0
15 TraesCS7A01G436600 chr5A 76.636 214 41 7 1531 1738 649441940 649442150 2.900000e-20 110.0
16 TraesCS7A01G436600 chr5B 78.378 111 19 5 1302 1411 656926020 656926126 1.770000e-07 67.6


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 TraesCS7A01G436600 chr7A 631364047 631366796 2749 False 5079.0 5079 100.00000 1 2750 1 chr7A.!!$F1 2749
1 TraesCS7A01G436600 chr7D 547456506 547459111 2605 True 1470.5 2702 89.50050 136 2750 2 chr7D.!!$R1 2614
2 TraesCS7A01G436600 chr7B 590498838 590501942 3104 True 771.5 2159 90.31875 177 2750 4 chr7B.!!$R1 2573

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
172 173 0.033781 TTTGACGTTGGTCCCGGTAG 59.966 55.0 0.0 0.0 42.73 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1902 0.457166 CAACAATGCCATGCACCGAG 60.457 55.0 0.0 0.0 43.04 4.63 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
26 27 8.293699 TGAGAGAGTATATTAAACACAGCTCA 57.706 34.615 0.00 0.00 0.00 4.26
27 28 8.918116 TGAGAGAGTATATTAAACACAGCTCAT 58.082 33.333 0.00 0.00 0.00 2.90
53 54 3.383092 TTTTTGCGGGTCGTGTAGT 57.617 47.368 0.00 0.00 0.00 2.73
54 55 2.522836 TTTTTGCGGGTCGTGTAGTA 57.477 45.000 0.00 0.00 0.00 1.82
55 56 2.068837 TTTTGCGGGTCGTGTAGTAG 57.931 50.000 0.00 0.00 0.00 2.57
56 57 0.961019 TTTGCGGGTCGTGTAGTAGT 59.039 50.000 0.00 0.00 0.00 2.73
57 58 1.819928 TTGCGGGTCGTGTAGTAGTA 58.180 50.000 0.00 0.00 0.00 1.82
58 59 1.372582 TGCGGGTCGTGTAGTAGTAG 58.627 55.000 0.00 0.00 0.00 2.57
59 60 1.339055 TGCGGGTCGTGTAGTAGTAGT 60.339 52.381 0.00 0.00 0.00 2.73
60 61 2.093711 TGCGGGTCGTGTAGTAGTAGTA 60.094 50.000 0.00 0.00 0.00 1.82
61 62 2.285488 GCGGGTCGTGTAGTAGTAGTAC 59.715 54.545 8.04 8.04 0.00 2.73
62 63 3.521560 CGGGTCGTGTAGTAGTAGTACA 58.478 50.000 12.90 12.90 32.00 2.90
63 64 4.122776 CGGGTCGTGTAGTAGTAGTACAT 58.877 47.826 18.56 0.00 36.51 2.29
64 65 4.025396 CGGGTCGTGTAGTAGTAGTACATG 60.025 50.000 23.33 23.33 40.61 3.21
65 66 5.118990 GGGTCGTGTAGTAGTAGTACATGA 58.881 45.833 26.13 26.13 43.81 3.07
66 67 5.236047 GGGTCGTGTAGTAGTAGTACATGAG 59.764 48.000 28.76 19.03 45.51 2.90
67 68 5.814705 GGTCGTGTAGTAGTAGTACATGAGT 59.185 44.000 28.76 0.00 45.51 3.41
68 69 6.019156 GGTCGTGTAGTAGTAGTACATGAGTC 60.019 46.154 28.76 22.19 45.51 3.36
69 70 6.533012 GTCGTGTAGTAGTAGTACATGAGTCA 59.467 42.308 28.76 13.40 45.51 3.41
70 71 7.063898 GTCGTGTAGTAGTAGTACATGAGTCAA 59.936 40.741 28.76 13.12 45.51 3.18
71 72 7.603784 TCGTGTAGTAGTAGTACATGAGTCAAA 59.396 37.037 26.13 11.10 42.17 2.69
72 73 8.396390 CGTGTAGTAGTAGTACATGAGTCAAAT 58.604 37.037 24.39 0.00 41.36 2.32
77 78 9.682465 AGTAGTAGTACATGAGTCAAATACAGA 57.318 33.333 15.73 4.65 0.00 3.41
80 81 9.862371 AGTAGTACATGAGTCAAATACAGAAAG 57.138 33.333 15.73 0.00 0.00 2.62
81 82 9.856488 GTAGTACATGAGTCAAATACAGAAAGA 57.144 33.333 15.73 0.00 0.00 2.52
82 83 8.764524 AGTACATGAGTCAAATACAGAAAGAC 57.235 34.615 15.73 0.00 0.00 3.01
83 84 8.589338 AGTACATGAGTCAAATACAGAAAGACT 58.411 33.333 15.73 0.00 41.84 3.24
94 95 2.662700 CAGAAAGACTGTCGCGTAACT 58.337 47.619 5.77 0.00 41.30 2.24
95 96 2.657372 CAGAAAGACTGTCGCGTAACTC 59.343 50.000 5.77 0.00 41.30 3.01
96 97 1.642843 GAAAGACTGTCGCGTAACTCG 59.357 52.381 5.77 0.00 43.12 4.18
97 98 0.590195 AAGACTGTCGCGTAACTCGT 59.410 50.000 5.77 0.00 42.13 4.18
98 99 0.590195 AGACTGTCGCGTAACTCGTT 59.410 50.000 5.77 0.00 42.13 3.85
99 100 1.002033 AGACTGTCGCGTAACTCGTTT 60.002 47.619 5.77 0.00 42.13 3.60
100 101 1.121967 GACTGTCGCGTAACTCGTTTG 59.878 52.381 5.77 0.00 42.13 2.93
101 102 1.126079 CTGTCGCGTAACTCGTTTGT 58.874 50.000 5.77 0.00 42.13 2.83
102 103 1.519758 CTGTCGCGTAACTCGTTTGTT 59.480 47.619 5.77 0.00 42.13 2.83
103 104 1.518102 TGTCGCGTAACTCGTTTGTTC 59.482 47.619 5.77 0.00 42.13 3.18
104 105 0.771756 TCGCGTAACTCGTTTGTTCG 59.228 50.000 5.77 0.00 42.13 3.95
105 106 0.499761 CGCGTAACTCGTTTGTTCGT 59.500 50.000 0.00 0.00 42.13 3.85
106 107 1.071959 CGCGTAACTCGTTTGTTCGTT 60.072 47.619 0.00 0.00 42.13 3.85
107 108 2.543646 GCGTAACTCGTTTGTTCGTTC 58.456 47.619 0.00 0.00 42.13 3.95
108 109 2.791485 CGTAACTCGTTTGTTCGTTCG 58.209 47.619 0.00 0.00 34.52 3.95
109 110 2.543646 GTAACTCGTTTGTTCGTTCGC 58.456 47.619 0.00 0.00 0.00 4.70
110 111 1.000884 AACTCGTTTGTTCGTTCGCA 58.999 45.000 0.00 0.00 0.00 5.10
111 112 1.000884 ACTCGTTTGTTCGTTCGCAA 58.999 45.000 0.00 0.00 0.00 4.85
112 113 1.394227 ACTCGTTTGTTCGTTCGCAAA 59.606 42.857 0.00 0.00 32.89 3.68
113 114 2.159680 ACTCGTTTGTTCGTTCGCAAAA 60.160 40.909 0.00 0.00 36.51 2.44
114 115 2.841329 CTCGTTTGTTCGTTCGCAAAAA 59.159 40.909 0.00 0.00 36.51 1.94
167 168 0.179040 TCCTGTTTGACGTTGGTCCC 60.179 55.000 0.00 0.00 42.73 4.46
168 169 1.503818 CCTGTTTGACGTTGGTCCCG 61.504 60.000 0.00 0.00 42.73 5.14
172 173 0.033781 TTTGACGTTGGTCCCGGTAG 59.966 55.000 0.00 0.00 42.73 3.18
186 187 1.142465 CCGGTAGGAGTAGGCTGAGTA 59.858 57.143 0.00 0.00 41.02 2.59
206 207 1.294659 GAGTTGACTTGCCAGCTCGG 61.295 60.000 0.00 0.00 35.33 4.63
209 210 1.758440 TTGACTTGCCAGCTCGGTCT 61.758 55.000 4.45 0.00 36.97 3.85
237 238 4.019983 TCCGTGAAGGAGAGGAGC 57.980 61.111 0.00 0.00 45.98 4.70
255 256 1.673665 CTTGTGGGAGCAGTGGAGC 60.674 63.158 0.00 0.00 0.00 4.70
323 327 1.294780 CAGACCAGAGTGCCACTCC 59.705 63.158 20.90 6.00 46.18 3.85
344 357 0.609957 TCCCTTCGTACGCAGGAGAA 60.610 55.000 31.68 15.70 29.89 2.87
353 366 1.227089 CGCAGGAGAATGGAGTCGG 60.227 63.158 0.00 0.00 0.00 4.79
393 406 0.251297 TCAATCCAACACTGGGCAGG 60.251 55.000 0.00 0.00 43.71 4.85
394 407 1.077265 AATCCAACACTGGGCAGGG 59.923 57.895 0.00 0.00 43.71 4.45
395 408 3.590466 ATCCAACACTGGGCAGGGC 62.590 63.158 0.00 0.00 43.71 5.19
467 489 3.822594 TGCATTCAATACAACGTGTCC 57.177 42.857 0.00 0.00 0.00 4.02
485 507 4.803613 GTGTCCAAACATGGTTTTTGTCTC 59.196 41.667 0.00 0.00 37.81 3.36
490 512 6.816140 TCCAAACATGGTTTTTGTCTCTTTTC 59.184 34.615 0.00 0.00 32.92 2.29
496 526 7.877612 ACATGGTTTTTGTCTCTTTTCTTTTGT 59.122 29.630 0.00 0.00 0.00 2.83
640 676 2.207788 GAACCGCCCGTCCCAAAATG 62.208 60.000 0.00 0.00 0.00 2.32
693 754 6.399249 CGCAGTAGATTTTCTCGTTTTTACGA 60.399 38.462 0.20 0.20 40.06 3.43
694 755 7.453838 GCAGTAGATTTTCTCGTTTTTACGAT 58.546 34.615 0.49 0.00 41.56 3.73
696 757 7.835066 CAGTAGATTTTCTCGTTTTTACGATCG 59.165 37.037 14.88 14.88 41.56 3.69
698 759 5.636543 AGATTTTCTCGTTTTTACGATCGGT 59.363 36.000 20.98 7.72 41.56 4.69
699 760 6.808212 AGATTTTCTCGTTTTTACGATCGGTA 59.192 34.615 20.98 6.69 41.56 4.02
700 761 5.997732 TTTCTCGTTTTTACGATCGGTAG 57.002 39.130 20.98 4.74 41.56 3.18
701 762 4.019919 TCTCGTTTTTACGATCGGTAGG 57.980 45.455 20.98 5.46 41.56 3.18
702 763 3.689161 TCTCGTTTTTACGATCGGTAGGA 59.311 43.478 20.98 9.20 41.56 2.94
703 764 4.019919 TCGTTTTTACGATCGGTAGGAG 57.980 45.455 20.98 5.26 37.20 3.69
704 765 3.440173 TCGTTTTTACGATCGGTAGGAGT 59.560 43.478 20.98 0.00 37.20 3.85
705 766 4.634004 TCGTTTTTACGATCGGTAGGAGTA 59.366 41.667 20.98 0.00 37.20 2.59
706 767 4.966366 CGTTTTTACGATCGGTAGGAGTAG 59.034 45.833 20.98 0.00 34.64 2.57
707 768 5.277047 GTTTTTACGATCGGTAGGAGTAGG 58.723 45.833 20.98 0.00 31.46 3.18
708 769 4.422073 TTTACGATCGGTAGGAGTAGGA 57.578 45.455 20.98 0.00 31.46 2.94
709 770 2.547299 ACGATCGGTAGGAGTAGGAG 57.453 55.000 20.98 0.00 0.00 3.69
710 771 1.767681 ACGATCGGTAGGAGTAGGAGT 59.232 52.381 20.98 0.00 0.00 3.85
711 772 2.968574 ACGATCGGTAGGAGTAGGAGTA 59.031 50.000 20.98 0.00 0.00 2.59
712 773 3.006752 ACGATCGGTAGGAGTAGGAGTAG 59.993 52.174 20.98 0.00 0.00 2.57
713 774 3.006752 CGATCGGTAGGAGTAGGAGTAGT 59.993 52.174 7.38 0.00 0.00 2.73
714 775 4.219507 CGATCGGTAGGAGTAGGAGTAGTA 59.780 50.000 7.38 0.00 0.00 1.82
757 825 2.009042 GCTCTGTACCACCTCACATGC 61.009 57.143 0.00 0.00 0.00 4.06
830 899 2.747855 GCCAGCCTTTCACTCGGG 60.748 66.667 0.00 0.00 0.00 5.14
885 955 4.098807 CCCCCAAAACCCTCATTAAATACG 59.901 45.833 0.00 0.00 0.00 3.06
1005 1082 3.190849 CGCACACAGGAGATGGCG 61.191 66.667 0.00 0.00 38.45 5.69
1353 1430 2.279120 CTGGCCGAGATCACGCTC 60.279 66.667 7.06 2.15 0.00 5.03
1784 1867 2.032302 CACGGATCTAGACCTGAAGACG 59.968 54.545 0.00 0.00 0.00 4.18
1799 1882 3.575256 TGAAGACGGTGGTAGTATGTTGT 59.425 43.478 0.00 0.00 0.00 3.32
1801 1884 3.921677 AGACGGTGGTAGTATGTTGTTG 58.078 45.455 0.00 0.00 0.00 3.33
1802 1885 3.322828 AGACGGTGGTAGTATGTTGTTGT 59.677 43.478 0.00 0.00 0.00 3.32
1803 1886 4.060205 GACGGTGGTAGTATGTTGTTGTT 58.940 43.478 0.00 0.00 0.00 2.83
1804 1887 4.453751 ACGGTGGTAGTATGTTGTTGTTT 58.546 39.130 0.00 0.00 0.00 2.83
1805 1888 4.512571 ACGGTGGTAGTATGTTGTTGTTTC 59.487 41.667 0.00 0.00 0.00 2.78
1806 1889 4.512198 CGGTGGTAGTATGTTGTTGTTTCA 59.488 41.667 0.00 0.00 0.00 2.69
1808 1891 5.529800 GGTGGTAGTATGTTGTTGTTTCAGT 59.470 40.000 0.00 0.00 0.00 3.41
1809 1892 6.038936 GGTGGTAGTATGTTGTTGTTTCAGTT 59.961 38.462 0.00 0.00 0.00 3.16
1810 1893 6.910433 GTGGTAGTATGTTGTTGTTTCAGTTG 59.090 38.462 0.00 0.00 0.00 3.16
1811 1894 6.824196 TGGTAGTATGTTGTTGTTTCAGTTGA 59.176 34.615 0.00 0.00 0.00 3.18
1812 1895 7.011950 TGGTAGTATGTTGTTGTTTCAGTTGAG 59.988 37.037 0.00 0.00 0.00 3.02
1813 1896 5.821204 AGTATGTTGTTGTTTCAGTTGAGC 58.179 37.500 0.00 0.00 0.00 4.26
1814 1897 3.502191 TGTTGTTGTTTCAGTTGAGCC 57.498 42.857 0.00 0.00 0.00 4.70
1815 1898 2.159448 TGTTGTTGTTTCAGTTGAGCCG 60.159 45.455 0.00 0.00 0.00 5.52
1816 1899 1.021202 TGTTGTTTCAGTTGAGCCGG 58.979 50.000 0.00 0.00 0.00 6.13
1817 1900 1.021968 GTTGTTTCAGTTGAGCCGGT 58.978 50.000 1.90 0.00 0.00 5.28
1818 1901 1.021202 TTGTTTCAGTTGAGCCGGTG 58.979 50.000 1.90 0.00 0.00 4.94
1819 1902 1.282875 GTTTCAGTTGAGCCGGTGC 59.717 57.895 1.90 0.00 37.95 5.01
1852 1935 3.618150 GCATTGTTGCTGTGTTGTTCTTT 59.382 39.130 0.00 0.00 45.77 2.52
1919 2017 2.403252 ACAATAGTGGTAGTGGCAGC 57.597 50.000 0.00 0.00 0.00 5.25
1956 2054 1.463674 GTTTGTGGTAGGCCTGGATG 58.536 55.000 17.99 0.00 35.27 3.51
1958 2056 0.548926 TTGTGGTAGGCCTGGATGGA 60.549 55.000 17.99 0.00 38.35 3.41
1977 2075 8.356027 TGGATGGATGGGTATAATAGTATGGTA 58.644 37.037 0.00 0.00 0.00 3.25
1979 2077 9.435570 GATGGATGGGTATAATAGTATGGTAGT 57.564 37.037 0.00 0.00 0.00 2.73
2029 2127 9.542462 TCGAACTACTTATATTTTTCATCTGGG 57.458 33.333 0.00 0.00 0.00 4.45
2056 2154 0.716108 GTTGATTCTGTCCTCGTGCG 59.284 55.000 0.00 0.00 0.00 5.34
2057 2155 0.601057 TTGATTCTGTCCTCGTGCGA 59.399 50.000 0.00 0.00 0.00 5.10
2058 2156 0.171231 TGATTCTGTCCTCGTGCGAG 59.829 55.000 13.99 13.99 41.63 5.03
2060 2158 1.599606 ATTCTGTCCTCGTGCGAGCT 61.600 55.000 15.32 0.00 40.69 4.09
2062 2160 2.049156 TGTCCTCGTGCGAGCTTG 60.049 61.111 15.32 0.00 40.69 4.01
2063 2161 3.482783 GTCCTCGTGCGAGCTTGC 61.483 66.667 19.70 19.70 40.69 4.01
2097 2206 6.194796 TCATTTTTCCTGCATTGCTAGTAC 57.805 37.500 10.49 0.00 0.00 2.73
2098 2207 5.945784 TCATTTTTCCTGCATTGCTAGTACT 59.054 36.000 10.49 0.00 0.00 2.73
2099 2208 7.109501 TCATTTTTCCTGCATTGCTAGTACTA 58.890 34.615 10.49 1.89 0.00 1.82
2101 2210 7.553881 TTTTTCCTGCATTGCTAGTACTATC 57.446 36.000 10.49 0.00 0.00 2.08
2102 2211 6.485830 TTTCCTGCATTGCTAGTACTATCT 57.514 37.500 10.49 0.00 0.00 1.98
2103 2212 6.485830 TTCCTGCATTGCTAGTACTATCTT 57.514 37.500 10.49 0.00 0.00 2.40
2104 2213 5.847304 TCCTGCATTGCTAGTACTATCTTG 58.153 41.667 10.49 3.44 0.00 3.02
2127 2237 5.355071 TGGATTGATTTCTTGATCGTTCAGG 59.645 40.000 0.00 0.00 32.27 3.86
2206 2316 4.864334 GGGCGGTGCTCCTGGATG 62.864 72.222 0.00 0.00 0.00 3.51
2207 2317 3.785859 GGCGGTGCTCCTGGATGA 61.786 66.667 0.00 0.00 0.00 2.92
2208 2318 2.268920 GCGGTGCTCCTGGATGAA 59.731 61.111 0.00 0.00 0.00 2.57
2210 2320 1.900351 CGGTGCTCCTGGATGAAGA 59.100 57.895 0.00 0.00 0.00 2.87
2284 2408 3.736213 CTTTTGTCACGGAACATCATCG 58.264 45.455 0.00 0.00 0.00 3.84
2341 2497 1.140252 AGTTTGTACTCCGGTGCAACT 59.860 47.619 0.00 3.38 45.03 3.16
2353 2509 2.437359 GCAACTGAGGCGCTGGAT 60.437 61.111 7.64 0.00 0.00 3.41
2386 2542 2.498481 TCGTTGGATACTTGGATTCCGT 59.502 45.455 0.00 0.00 37.61 4.69
2387 2543 2.864343 CGTTGGATACTTGGATTCCGTC 59.136 50.000 0.00 0.00 37.61 4.79
2388 2544 3.430374 CGTTGGATACTTGGATTCCGTCT 60.430 47.826 0.00 0.00 37.61 4.18
2389 2545 4.120589 GTTGGATACTTGGATTCCGTCTC 58.879 47.826 0.00 0.00 37.61 3.36
2405 2561 1.658095 GTCTCAATGCAGCGACTCTTC 59.342 52.381 0.00 0.00 0.00 2.87
2409 2565 2.231235 TCAATGCAGCGACTCTTCTACA 59.769 45.455 0.00 0.00 0.00 2.74
2414 2570 2.477189 GCAGCGACTCTTCTACAGTCTC 60.477 54.545 0.00 0.00 38.55 3.36
2419 2575 1.717077 ACTCTTCTACAGTCTCCCCCA 59.283 52.381 0.00 0.00 0.00 4.96
2420 2576 2.104170 CTCTTCTACAGTCTCCCCCAC 58.896 57.143 0.00 0.00 0.00 4.61
2421 2577 0.818296 CTTCTACAGTCTCCCCCACG 59.182 60.000 0.00 0.00 0.00 4.94
2426 2582 1.186267 ACAGTCTCCCCCACGAAGAC 61.186 60.000 0.00 0.00 39.76 3.01
2427 2583 1.977544 AGTCTCCCCCACGAAGACG 60.978 63.158 0.00 0.00 43.30 4.18
2470 2626 7.277098 TGAAACGCTGAAGAAATACCAGTATAC 59.723 37.037 0.00 0.00 0.00 1.47
2474 2630 8.585881 ACGCTGAAGAAATACCAGTATACATAT 58.414 33.333 5.50 0.00 0.00 1.78
2500 2656 9.958180 TTCATCTTTGTTTGTAGATATTCTGGA 57.042 29.630 0.00 0.00 30.20 3.86
2502 2658 9.994432 CATCTTTGTTTGTAGATATTCTGGAAC 57.006 33.333 0.00 0.00 30.20 3.62
2554 2711 6.600882 AAAGCTCACCTCATTCATTTCATT 57.399 33.333 0.00 0.00 0.00 2.57
2557 2714 5.713389 AGCTCACCTCATTCATTTCATTTCA 59.287 36.000 0.00 0.00 0.00 2.69
2558 2715 6.209986 AGCTCACCTCATTCATTTCATTTCAA 59.790 34.615 0.00 0.00 0.00 2.69
2559 2716 6.530534 GCTCACCTCATTCATTTCATTTCAAG 59.469 38.462 0.00 0.00 0.00 3.02
2560 2717 6.392354 TCACCTCATTCATTTCATTTCAAGC 58.608 36.000 0.00 0.00 0.00 4.01
2578 2741 3.005539 TCACTCCTGCCTGCCCTC 61.006 66.667 0.00 0.00 0.00 4.30
2579 2742 3.007920 CACTCCTGCCTGCCCTCT 61.008 66.667 0.00 0.00 0.00 3.69
2580 2743 1.687146 CACTCCTGCCTGCCCTCTA 60.687 63.158 0.00 0.00 0.00 2.43
2647 3361 1.705256 TTCACGTCGCAGTTATGGAC 58.295 50.000 0.00 0.00 0.00 4.02
2648 3362 0.455464 TCACGTCGCAGTTATGGACG 60.455 55.000 10.80 10.80 46.52 4.79
2649 3363 0.455464 CACGTCGCAGTTATGGACGA 60.455 55.000 18.15 0.00 45.25 4.20
2709 3423 1.471684 CTGGCAATCACTCCAGCTTTC 59.528 52.381 0.00 0.00 42.79 2.62
2715 3429 2.359230 ACTCCAGCTTTCGCCTGC 60.359 61.111 0.00 0.00 36.60 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.293699 TGAGCTGTGTTTAATATACTCTCTCA 57.706 34.615 0.00 0.00 0.00 3.27
35 36 2.224018 ACTACTACACGACCCGCAAAAA 60.224 45.455 0.00 0.00 0.00 1.94
36 37 1.340889 ACTACTACACGACCCGCAAAA 59.659 47.619 0.00 0.00 0.00 2.44
37 38 0.961019 ACTACTACACGACCCGCAAA 59.039 50.000 0.00 0.00 0.00 3.68
38 39 1.739466 CTACTACTACACGACCCGCAA 59.261 52.381 0.00 0.00 0.00 4.85
39 40 1.339055 ACTACTACTACACGACCCGCA 60.339 52.381 0.00 0.00 0.00 5.69
40 41 1.373570 ACTACTACTACACGACCCGC 58.626 55.000 0.00 0.00 0.00 6.13
41 42 3.521560 TGTACTACTACTACACGACCCG 58.478 50.000 0.00 0.00 0.00 5.28
42 43 5.118990 TCATGTACTACTACTACACGACCC 58.881 45.833 0.00 0.00 0.00 4.46
43 44 5.814705 ACTCATGTACTACTACTACACGACC 59.185 44.000 0.00 0.00 0.00 4.79
44 45 6.533012 TGACTCATGTACTACTACTACACGAC 59.467 42.308 0.00 0.00 0.00 4.34
45 46 6.633856 TGACTCATGTACTACTACTACACGA 58.366 40.000 0.00 0.00 0.00 4.35
46 47 6.898912 TGACTCATGTACTACTACTACACG 57.101 41.667 0.00 0.00 0.00 4.49
51 52 9.682465 TCTGTATTTGACTCATGTACTACTACT 57.318 33.333 0.00 0.00 0.00 2.57
54 55 9.862371 CTTTCTGTATTTGACTCATGTACTACT 57.138 33.333 0.00 0.00 0.00 2.57
55 56 9.856488 TCTTTCTGTATTTGACTCATGTACTAC 57.144 33.333 0.00 0.00 0.00 2.73
56 57 9.856488 GTCTTTCTGTATTTGACTCATGTACTA 57.144 33.333 0.00 0.00 0.00 1.82
57 58 8.589338 AGTCTTTCTGTATTTGACTCATGTACT 58.411 33.333 0.00 0.00 33.31 2.73
58 59 8.651588 CAGTCTTTCTGTATTTGACTCATGTAC 58.348 37.037 0.00 0.00 39.17 2.90
59 60 8.763049 CAGTCTTTCTGTATTTGACTCATGTA 57.237 34.615 0.00 0.00 39.17 2.29
60 61 7.664082 CAGTCTTTCTGTATTTGACTCATGT 57.336 36.000 0.00 0.00 39.17 3.21
71 72 8.991287 CGAGTTACGCGACAGTCTTTCTGTAT 62.991 46.154 15.93 0.00 45.25 2.29
72 73 7.791763 CGAGTTACGCGACAGTCTTTCTGTA 62.792 48.000 15.93 0.00 45.25 2.74
74 75 4.734434 CGAGTTACGCGACAGTCTTTCTG 61.734 52.174 15.93 0.00 41.53 3.02
75 76 2.664971 CGAGTTACGCGACAGTCTTTCT 60.665 50.000 15.93 0.00 34.51 2.52
76 77 1.642843 CGAGTTACGCGACAGTCTTTC 59.357 52.381 15.93 0.00 34.51 2.62
77 78 1.002033 ACGAGTTACGCGACAGTCTTT 60.002 47.619 15.93 0.00 46.94 2.52
78 79 0.590195 ACGAGTTACGCGACAGTCTT 59.410 50.000 15.93 1.39 46.94 3.01
79 80 0.590195 AACGAGTTACGCGACAGTCT 59.410 50.000 15.93 3.23 46.94 3.24
80 81 1.121967 CAAACGAGTTACGCGACAGTC 59.878 52.381 15.93 10.12 46.94 3.51
81 82 1.126079 CAAACGAGTTACGCGACAGT 58.874 50.000 15.93 0.06 46.94 3.55
82 83 1.126079 ACAAACGAGTTACGCGACAG 58.874 50.000 15.93 6.41 46.94 3.51
83 84 1.518102 GAACAAACGAGTTACGCGACA 59.482 47.619 15.93 0.00 46.94 4.35
84 85 1.457554 CGAACAAACGAGTTACGCGAC 60.458 52.381 15.93 0.00 46.94 5.19
85 86 0.771756 CGAACAAACGAGTTACGCGA 59.228 50.000 15.93 0.00 46.94 5.87
86 87 0.499761 ACGAACAAACGAGTTACGCG 59.500 50.000 3.53 3.53 46.94 6.01
87 88 2.543646 GAACGAACAAACGAGTTACGC 58.456 47.619 0.00 0.00 46.94 4.42
89 90 2.034675 TGCGAACGAACAAACGAGTTAC 60.035 45.455 0.00 0.00 37.03 2.50
90 91 2.191802 TGCGAACGAACAAACGAGTTA 58.808 42.857 0.00 0.00 37.03 2.24
91 92 1.000884 TGCGAACGAACAAACGAGTT 58.999 45.000 0.00 0.00 37.03 3.01
92 93 1.000884 TTGCGAACGAACAAACGAGT 58.999 45.000 0.00 0.00 37.03 4.18
93 94 2.079941 TTTGCGAACGAACAAACGAG 57.920 45.000 0.00 0.00 37.03 4.18
94 95 2.522372 TTTTGCGAACGAACAAACGA 57.478 40.000 0.00 0.00 35.60 3.85
135 136 0.182775 AACAGGAACAAGACGCCCTT 59.817 50.000 0.00 0.00 34.91 3.95
136 137 0.182775 AAACAGGAACAAGACGCCCT 59.817 50.000 0.00 0.00 0.00 5.19
137 138 0.310854 CAAACAGGAACAAGACGCCC 59.689 55.000 0.00 0.00 0.00 6.13
138 139 1.002792 GTCAAACAGGAACAAGACGCC 60.003 52.381 0.00 0.00 0.00 5.68
139 140 1.332904 CGTCAAACAGGAACAAGACGC 60.333 52.381 0.00 0.00 41.59 5.19
140 141 2.645628 CGTCAAACAGGAACAAGACG 57.354 50.000 0.00 0.00 42.00 4.18
141 142 3.486875 CCAACGTCAAACAGGAACAAGAC 60.487 47.826 0.00 0.00 0.00 3.01
142 143 2.680841 CCAACGTCAAACAGGAACAAGA 59.319 45.455 0.00 0.00 0.00 3.02
143 144 2.422127 ACCAACGTCAAACAGGAACAAG 59.578 45.455 0.00 0.00 0.00 3.16
144 145 2.420722 GACCAACGTCAAACAGGAACAA 59.579 45.455 0.00 0.00 38.99 2.83
167 168 2.104451 TCTACTCAGCCTACTCCTACCG 59.896 54.545 0.00 0.00 0.00 4.02
168 169 3.136992 ACTCTACTCAGCCTACTCCTACC 59.863 52.174 0.00 0.00 0.00 3.18
172 173 3.379057 GTCAACTCTACTCAGCCTACTCC 59.621 52.174 0.00 0.00 0.00 3.85
179 180 2.289072 TGGCAAGTCAACTCTACTCAGC 60.289 50.000 0.00 0.00 0.00 4.26
180 181 3.583806 CTGGCAAGTCAACTCTACTCAG 58.416 50.000 0.00 0.00 0.00 3.35
186 187 0.320247 CGAGCTGGCAAGTCAACTCT 60.320 55.000 0.00 0.00 30.16 3.24
206 207 3.032609 CGGATCGGCGCATGAGAC 61.033 66.667 10.83 0.00 0.00 3.36
209 210 3.363844 TTCACGGATCGGCGCATGA 62.364 57.895 10.83 6.93 0.00 3.07
237 238 1.673665 GCTCCACTGCTCCCACAAG 60.674 63.158 0.00 0.00 0.00 3.16
304 308 1.294780 GAGTGGCACTCTGGTCTGG 59.705 63.158 34.49 0.00 41.88 3.86
318 322 1.807886 CGTACGAAGGGAGGGAGTG 59.192 63.158 10.44 0.00 0.00 3.51
323 327 2.494918 CCTGCGTACGAAGGGAGG 59.505 66.667 31.73 16.65 41.80 4.30
344 357 2.502492 CCGATCTGCCCGACTCCAT 61.502 63.158 0.00 0.00 0.00 3.41
353 366 2.818132 CTCCTGGACCGATCTGCC 59.182 66.667 0.00 0.00 0.00 4.85
393 406 3.236618 GAGTGTTGTTGTCGCGGCC 62.237 63.158 8.89 0.00 0.00 6.13
394 407 2.042520 TTGAGTGTTGTTGTCGCGGC 62.043 55.000 2.29 2.29 0.00 6.53
395 408 0.375454 TTTGAGTGTTGTTGTCGCGG 59.625 50.000 6.13 0.00 0.00 6.46
396 409 1.062002 AGTTTGAGTGTTGTTGTCGCG 59.938 47.619 0.00 0.00 0.00 5.87
397 410 2.705154 GAGTTTGAGTGTTGTTGTCGC 58.295 47.619 0.00 0.00 0.00 5.19
467 489 7.832503 AGAAAAGAGACAAAAACCATGTTTG 57.167 32.000 5.89 5.89 40.95 2.93
496 526 7.010923 GTGCTGACAAAAACCATGTTTAATTCA 59.989 33.333 0.00 0.00 0.00 2.57
545 575 0.331278 AAATGGGAAGGTGATGCGGA 59.669 50.000 0.00 0.00 0.00 5.54
582 618 1.543429 GGAAAGATAGGATGGGCGGTG 60.543 57.143 0.00 0.00 0.00 4.94
640 676 0.942252 AAACTTTCGCCTTCACCGAC 59.058 50.000 0.00 0.00 34.01 4.79
693 754 6.728164 TGTATACTACTCCTACTCCTACCGAT 59.272 42.308 4.17 0.00 0.00 4.18
694 755 6.077993 TGTATACTACTCCTACTCCTACCGA 58.922 44.000 4.17 0.00 0.00 4.69
696 757 9.585369 AAAATGTATACTACTCCTACTCCTACC 57.415 37.037 4.17 0.00 0.00 3.18
724 785 2.749044 AGAGCGAGACCGGCGTAA 60.749 61.111 6.01 0.00 36.06 3.18
727 788 3.506096 TACAGAGCGAGACCGGCG 61.506 66.667 0.00 0.00 36.06 6.46
728 789 2.102553 GTACAGAGCGAGACCGGC 59.897 66.667 0.00 0.00 36.06 6.13
729 790 2.044555 TGGTACAGAGCGAGACCGG 61.045 63.158 0.00 0.00 34.49 5.28
731 792 0.966370 AGGTGGTACAGAGCGAGACC 60.966 60.000 0.00 0.00 41.80 3.85
732 793 0.452585 GAGGTGGTACAGAGCGAGAC 59.547 60.000 0.00 0.00 41.80 3.36
845 914 1.266178 GGGTGAAAAAGGTGGATGGG 58.734 55.000 0.00 0.00 0.00 4.00
853 922 1.142060 GGGTTTTGGGGGTGAAAAAGG 59.858 52.381 0.00 0.00 0.00 3.11
978 1055 3.259425 CTGTGTGCGCTTCTTGGCC 62.259 63.158 9.73 0.00 0.00 5.36
1366 1443 2.789917 GTAGAAGTCGAGCGCGGA 59.210 61.111 10.69 0.00 38.28 5.54
1368 1445 1.928769 GTCGTAGAAGTCGAGCGCG 60.929 63.158 2.41 2.41 39.69 6.86
1771 1854 2.040813 ACTACCACCGTCTTCAGGTCTA 59.959 50.000 0.00 0.00 40.59 2.59
1773 1856 1.254954 ACTACCACCGTCTTCAGGTC 58.745 55.000 0.00 0.00 40.59 3.85
1784 1867 5.529800 ACTGAAACAACAACATACTACCACC 59.470 40.000 0.00 0.00 0.00 4.61
1799 1882 1.021202 CACCGGCTCAACTGAAACAA 58.979 50.000 0.00 0.00 0.00 2.83
1801 1884 1.282875 GCACCGGCTCAACTGAAAC 59.717 57.895 0.00 0.00 36.96 2.78
1802 1885 3.744559 GCACCGGCTCAACTGAAA 58.255 55.556 0.00 0.00 36.96 2.69
1818 1901 2.103538 CAATGCCATGCACCGAGC 59.896 61.111 0.00 0.00 43.04 5.03
1819 1902 0.457166 CAACAATGCCATGCACCGAG 60.457 55.000 0.00 0.00 43.04 4.63
1820 1903 1.585517 CAACAATGCCATGCACCGA 59.414 52.632 0.00 0.00 43.04 4.69
1821 1904 4.172346 CAACAATGCCATGCACCG 57.828 55.556 0.00 0.00 43.04 4.94
1852 1935 1.771073 CGCAACGACAGCAAGAACCA 61.771 55.000 0.00 0.00 0.00 3.67
1956 2054 9.933240 ACTACTACCATACTATTATACCCATCC 57.067 37.037 0.00 0.00 0.00 3.51
2025 2123 2.893682 GAATCAACCGGGGAGCCCAG 62.894 65.000 6.32 2.98 45.83 4.45
2029 2127 0.744771 GACAGAATCAACCGGGGAGC 60.745 60.000 6.32 0.00 0.00 4.70
2056 2154 6.903883 AAATGAATGAATGAATGCAAGCTC 57.096 33.333 0.00 0.00 0.00 4.09
2057 2155 7.148306 GGAAAAATGAATGAATGAATGCAAGCT 60.148 33.333 0.00 0.00 0.00 3.74
2058 2156 6.964934 GGAAAAATGAATGAATGAATGCAAGC 59.035 34.615 0.00 0.00 0.00 4.01
2060 2158 7.361371 GCAGGAAAAATGAATGAATGAATGCAA 60.361 33.333 0.00 0.00 0.00 4.08
2062 2160 6.092944 TGCAGGAAAAATGAATGAATGAATGC 59.907 34.615 0.00 0.00 0.00 3.56
2063 2161 7.603963 TGCAGGAAAAATGAATGAATGAATG 57.396 32.000 0.00 0.00 0.00 2.67
2065 2163 7.361371 GCAATGCAGGAAAAATGAATGAATGAA 60.361 33.333 0.00 0.00 0.00 2.57
2066 2164 6.092944 GCAATGCAGGAAAAATGAATGAATGA 59.907 34.615 0.00 0.00 0.00 2.57
2097 2206 8.375608 ACGATCAAGAAATCAATCCAAGATAG 57.624 34.615 0.00 0.00 0.00 2.08
2098 2207 8.737168 AACGATCAAGAAATCAATCCAAGATA 57.263 30.769 0.00 0.00 0.00 1.98
2099 2208 7.337689 TGAACGATCAAGAAATCAATCCAAGAT 59.662 33.333 0.00 0.00 30.99 2.40
2101 2210 6.845302 TGAACGATCAAGAAATCAATCCAAG 58.155 36.000 0.00 0.00 30.99 3.61
2102 2211 6.127925 CCTGAACGATCAAGAAATCAATCCAA 60.128 38.462 0.00 0.00 34.49 3.53
2103 2212 5.355071 CCTGAACGATCAAGAAATCAATCCA 59.645 40.000 0.00 0.00 34.49 3.41
2104 2213 5.355350 ACCTGAACGATCAAGAAATCAATCC 59.645 40.000 0.00 0.00 34.49 3.01
2127 2237 2.350522 ACAGCGATCAACCATTCAGAC 58.649 47.619 0.00 0.00 0.00 3.51
2136 2246 6.086371 GCACTTTTTAAAGTACAGCGATCAAC 59.914 38.462 7.49 0.00 46.89 3.18
2193 2303 1.198713 TCTCTTCATCCAGGAGCACC 58.801 55.000 0.00 0.00 0.00 5.01
2194 2304 2.499289 TCTTCTCTTCATCCAGGAGCAC 59.501 50.000 0.00 0.00 0.00 4.40
2202 2312 3.729462 CGACAGTCGTCTTCTCTTCATCC 60.729 52.174 15.21 0.00 40.23 3.51
2203 2313 3.421741 CGACAGTCGTCTTCTCTTCATC 58.578 50.000 15.21 0.00 40.23 2.92
2204 2314 3.479505 CGACAGTCGTCTTCTCTTCAT 57.520 47.619 15.21 0.00 40.23 2.57
2205 2315 2.971430 CGACAGTCGTCTTCTCTTCA 57.029 50.000 15.21 0.00 40.23 3.02
2246 2357 1.967343 AAGCTCCCTCCCCTCCCTAG 61.967 65.000 0.00 0.00 0.00 3.02
2247 2358 1.537478 AAAGCTCCCTCCCCTCCCTA 61.537 60.000 0.00 0.00 0.00 3.53
2248 2359 2.438666 AAAAGCTCCCTCCCCTCCCT 62.439 60.000 0.00 0.00 0.00 4.20
2284 2408 3.712091 ATCCTTCACGTCCTCGATTAC 57.288 47.619 0.00 0.00 40.62 1.89
2311 2436 3.740141 CGGAGTACAAACTGGAGTGTGTT 60.740 47.826 7.91 0.00 43.58 3.32
2341 2497 4.166888 GCTCCATCCAGCGCCTCA 62.167 66.667 2.29 0.00 0.00 3.86
2386 2542 1.547820 AGAAGAGTCGCTGCATTGAGA 59.452 47.619 0.00 0.00 0.00 3.27
2387 2543 2.007360 AGAAGAGTCGCTGCATTGAG 57.993 50.000 0.00 0.00 0.00 3.02
2388 2544 2.231235 TGTAGAAGAGTCGCTGCATTGA 59.769 45.455 0.00 0.00 0.00 2.57
2389 2545 2.602211 CTGTAGAAGAGTCGCTGCATTG 59.398 50.000 0.00 0.00 0.00 2.82
2405 2561 0.818296 CTTCGTGGGGGAGACTGTAG 59.182 60.000 0.00 0.00 0.00 2.74
2409 2565 1.977544 CGTCTTCGTGGGGGAGACT 60.978 63.158 1.09 0.00 0.00 3.24
2420 2576 5.973565 ACGGGAAATTTATACTACGTCTTCG 59.026 40.000 0.00 0.00 43.34 3.79
2421 2577 6.974622 TCACGGGAAATTTATACTACGTCTTC 59.025 38.462 0.00 0.00 0.00 2.87
2426 2582 6.405216 CGTTTCACGGGAAATTTATACTACG 58.595 40.000 17.22 8.59 44.32 3.51
2427 2583 6.036408 AGCGTTTCACGGGAAATTTATACTAC 59.964 38.462 17.22 0.00 44.32 2.73
2428 2584 6.036300 CAGCGTTTCACGGGAAATTTATACTA 59.964 38.462 17.22 0.00 44.32 1.82
2429 2585 4.939439 AGCGTTTCACGGGAAATTTATACT 59.061 37.500 17.22 5.07 44.32 2.12
2442 2598 3.185594 TGGTATTTCTTCAGCGTTTCACG 59.814 43.478 0.00 0.00 45.88 4.35
2443 2599 4.213482 ACTGGTATTTCTTCAGCGTTTCAC 59.787 41.667 0.00 0.00 32.19 3.18
2474 2630 9.958180 TCCAGAATATCTACAAACAAAGATGAA 57.042 29.630 0.00 0.00 34.36 2.57
2483 2639 7.201652 GCTTCAGGTTCCAGAATATCTACAAAC 60.202 40.741 0.00 0.00 0.00 2.93
2494 2650 1.338107 TCGAGCTTCAGGTTCCAGAA 58.662 50.000 0.00 0.00 0.00 3.02
2498 2654 2.289133 ACTCTTTCGAGCTTCAGGTTCC 60.289 50.000 0.00 0.00 41.09 3.62
2500 2656 3.477210 AACTCTTTCGAGCTTCAGGTT 57.523 42.857 0.00 0.00 41.09 3.50
2502 2658 3.365220 CGTAAACTCTTTCGAGCTTCAGG 59.635 47.826 0.00 0.00 41.09 3.86
2554 2711 0.035881 CAGGCAGGAGTGAGCTTGAA 59.964 55.000 0.00 0.00 39.88 2.69
2557 2714 2.350514 GCAGGCAGGAGTGAGCTT 59.649 61.111 0.00 0.00 0.00 3.74
2558 2715 3.715097 GGCAGGCAGGAGTGAGCT 61.715 66.667 0.00 0.00 0.00 4.09
2559 2716 4.792804 GGGCAGGCAGGAGTGAGC 62.793 72.222 0.00 0.00 0.00 4.26
2560 2717 3.007920 AGGGCAGGCAGGAGTGAG 61.008 66.667 0.00 0.00 0.00 3.51
2578 2741 1.475682 GTGGACTCCGGTTGGTAGTAG 59.524 57.143 0.00 0.00 36.30 2.57
2579 2742 1.549203 GTGGACTCCGGTTGGTAGTA 58.451 55.000 0.00 0.00 36.30 1.82
2580 2743 1.530013 CGTGGACTCCGGTTGGTAGT 61.530 60.000 0.00 0.00 36.30 2.73
2648 3362 5.480642 TTTCAGCAGAGGATCCTATGATC 57.519 43.478 35.22 20.51 45.61 2.92
2649 3363 4.262981 GCTTTCAGCAGAGGATCCTATGAT 60.263 45.833 35.22 28.76 41.89 2.45
2715 3429 1.671054 TGCTCCGGAAAGCGGAAAG 60.671 57.895 5.23 0.00 45.54 2.62


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

AutoCloner maintained by Alex Coulton.