Multiple sequence alignment - TraesCS3B01G261700

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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 TraesCS3B01G261700 chr3B 100.000 2507 0 0 1 2507 419796460 419798966 0.000000e+00 4630.0
1 TraesCS3B01G261700 chr3B 94.330 194 8 1 2314 2507 166174092 166173902 6.780000e-76 294.0
2 TraesCS3B01G261700 chr3B 93.299 194 13 0 2314 2507 692958255 692958062 1.130000e-73 287.0
3 TraesCS3B01G261700 chr3B 94.444 36 2 0 2086 2121 261636245 261636280 3.480000e-04 56.5
4 TraesCS3B01G261700 chr3B 96.970 33 0 1 2033 2064 220728080 220728048 1.000000e-03 54.7
5 TraesCS3B01G261700 chr3D 92.065 2218 97 36 144 2314 301422093 301419908 0.000000e+00 3048.0
6 TraesCS3B01G261700 chr3D 83.146 89 15 0 2033 2121 614088030 614088118 5.750000e-12 82.4
7 TraesCS3B01G261700 chr3A 92.616 1747 62 27 272 1993 434004779 434006483 0.000000e+00 2449.0
8 TraesCS3B01G261700 chr3A 94.764 191 9 1 2125 2314 434042968 434043158 1.890000e-76 296.0
9 TraesCS3B01G261700 chr1B 94.359 195 9 2 2313 2507 592491918 592492110 5.240000e-77 298.0
10 TraesCS3B01G261700 chr2A 94.330 194 6 3 2315 2507 220370675 220370486 2.440000e-75 292.0
11 TraesCS3B01G261700 chrUn 93.846 195 8 2 2314 2507 315220557 315220748 8.770000e-75 291.0
12 TraesCS3B01G261700 chrUn 93.846 195 8 2 2314 2507 315224214 315224405 8.770000e-75 291.0
13 TraesCS3B01G261700 chrUn 93.846 195 8 2 2314 2507 332867683 332867492 8.770000e-75 291.0
14 TraesCS3B01G261700 chr2D 93.367 196 12 1 2313 2507 151419505 151419310 3.160000e-74 289.0
15 TraesCS3B01G261700 chr2D 86.517 89 12 0 2033 2121 125112757 125112669 5.710000e-17 99.0
16 TraesCS3B01G261700 chr1D 93.367 196 10 2 2312 2507 253098459 253098651 1.130000e-73 287.0
17 TraesCS3B01G261700 chr7A 97.452 157 3 1 1 156 689690452 689690608 1.480000e-67 267.0
18 TraesCS3B01G261700 chr7A 85.393 89 13 0 2036 2124 561709818 561709730 2.660000e-15 93.5
19 TraesCS3B01G261700 chr6B 94.268 157 8 1 1 156 716589937 716590093 3.220000e-59 239.0
20 TraesCS3B01G261700 chr6B 96.970 33 0 1 2033 2064 43346364 43346332 1.000000e-03 54.7
21 TraesCS3B01G261700 chr4A 88.991 109 11 1 53 160 708325430 708325538 1.560000e-27 134.0
22 TraesCS3B01G261700 chr4A 96.970 33 0 1 2033 2064 703667547 703667579 1.000000e-03 54.7
23 TraesCS3B01G261700 chr5A 94.595 37 2 0 2029 2065 95572111 95572075 9.690000e-05 58.4
24 TraesCS3B01G261700 chr2B 96.970 33 0 1 2033 2064 697010677 697010709 1.000000e-03 54.7


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 TraesCS3B01G261700 chr3B 419796460 419798966 2506 False 4630 4630 100.000 1 2507 1 chr3B.!!$F2 2506
1 TraesCS3B01G261700 chr3D 301419908 301422093 2185 True 3048 3048 92.065 144 2314 1 chr3D.!!$R1 2170
2 TraesCS3B01G261700 chr3A 434004779 434006483 1704 False 2449 2449 92.616 272 1993 1 chr3A.!!$F1 1721
3 TraesCS3B01G261700 chrUn 315220557 315224405 3848 False 291 291 93.846 2314 2507 2 chrUn.!!$F1 193

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
118 119 0.173255 TAACGACCGGGAAATCGACC 59.827 55.0 17.93 0.0 40.86 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2066 0.034896 TTTTGAGACGGAGGGAGCAC 59.965 55.0 0.0 0.0 0.0 4.4 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
62 63 4.851114 CTTTGCGCGGCATCGACG 62.851 66.667 8.83 0.00 38.76 5.12
70 71 3.918220 GGCATCGACGCAAGCGAG 61.918 66.667 22.30 14.05 45.72 5.03
71 72 2.880879 GCATCGACGCAAGCGAGA 60.881 61.111 22.30 18.62 45.72 4.04
72 73 2.233654 GCATCGACGCAAGCGAGAT 61.234 57.895 22.30 19.91 45.72 2.75
73 74 1.756375 GCATCGACGCAAGCGAGATT 61.756 55.000 22.30 0.00 45.72 2.40
74 75 0.228238 CATCGACGCAAGCGAGATTC 59.772 55.000 22.30 7.08 45.72 2.52
75 76 0.872021 ATCGACGCAAGCGAGATTCC 60.872 55.000 22.30 2.21 45.72 3.01
76 77 2.517450 CGACGCAAGCGAGATTCCC 61.517 63.158 22.30 0.58 42.83 3.97
77 78 2.125106 ACGCAAGCGAGATTCCCC 60.125 61.111 22.30 0.00 42.83 4.81
78 79 3.264897 CGCAAGCGAGATTCCCCG 61.265 66.667 9.11 0.00 42.83 5.73
79 80 2.125106 GCAAGCGAGATTCCCCGT 60.125 61.111 0.00 0.00 0.00 5.28
80 81 2.174319 GCAAGCGAGATTCCCCGTC 61.174 63.158 0.00 0.00 0.00 4.79
81 82 1.517832 CAAGCGAGATTCCCCGTCT 59.482 57.895 0.00 0.00 0.00 4.18
82 83 0.528684 CAAGCGAGATTCCCCGTCTC 60.529 60.000 0.00 0.00 38.95 3.36
93 94 2.499685 CCGTCTCGGGTGGGAATC 59.500 66.667 0.00 0.00 44.15 2.52
94 95 2.104331 CGTCTCGGGTGGGAATCG 59.896 66.667 0.00 0.00 0.00 3.34
95 96 2.499685 GTCTCGGGTGGGAATCGG 59.500 66.667 0.00 0.00 0.00 4.18
96 97 2.762459 TCTCGGGTGGGAATCGGG 60.762 66.667 0.00 0.00 0.00 5.14
97 98 4.547367 CTCGGGTGGGAATCGGGC 62.547 72.222 0.00 0.00 0.00 6.13
99 100 4.189580 CGGGTGGGAATCGGGCAT 62.190 66.667 0.00 0.00 0.00 4.40
100 101 2.813726 CGGGTGGGAATCGGGCATA 61.814 63.158 0.00 0.00 0.00 3.14
101 102 1.534697 GGGTGGGAATCGGGCATAA 59.465 57.895 0.00 0.00 0.00 1.90
102 103 0.822121 GGGTGGGAATCGGGCATAAC 60.822 60.000 0.00 0.00 0.00 1.89
103 104 1.164041 GGTGGGAATCGGGCATAACG 61.164 60.000 0.00 0.00 0.00 3.18
104 105 0.179067 GTGGGAATCGGGCATAACGA 60.179 55.000 0.00 0.00 45.19 3.85
105 106 0.179067 TGGGAATCGGGCATAACGAC 60.179 55.000 0.00 0.00 43.78 4.34
106 107 0.883370 GGGAATCGGGCATAACGACC 60.883 60.000 0.00 0.00 43.78 4.79
111 112 2.585698 GGGCATAACGACCGGGAA 59.414 61.111 6.32 0.00 27.65 3.97
112 113 1.078285 GGGCATAACGACCGGGAAA 60.078 57.895 6.32 0.00 27.65 3.13
113 114 0.464916 GGGCATAACGACCGGGAAAT 60.465 55.000 6.32 0.00 27.65 2.17
114 115 0.942252 GGCATAACGACCGGGAAATC 59.058 55.000 6.32 0.00 0.00 2.17
115 116 0.580104 GCATAACGACCGGGAAATCG 59.420 55.000 6.32 8.75 43.97 3.34
116 117 1.803625 GCATAACGACCGGGAAATCGA 60.804 52.381 17.93 0.00 40.86 3.59
117 118 1.856597 CATAACGACCGGGAAATCGAC 59.143 52.381 17.93 0.00 40.86 4.20
118 119 0.173255 TAACGACCGGGAAATCGACC 59.827 55.000 17.93 0.00 40.86 4.79
119 120 2.202837 CGACCGGGAAATCGACCC 60.203 66.667 6.32 0.00 40.86 4.46
120 121 2.718073 CGACCGGGAAATCGACCCT 61.718 63.158 6.32 0.00 44.72 4.34
121 122 1.153429 GACCGGGAAATCGACCCTG 60.153 63.158 6.32 4.01 44.72 4.45
122 123 2.189521 CCGGGAAATCGACCCTGG 59.810 66.667 12.23 12.23 44.72 4.45
123 124 2.513897 CGGGAAATCGACCCTGGC 60.514 66.667 7.90 0.00 44.72 4.85
124 125 2.513897 GGGAAATCGACCCTGGCG 60.514 66.667 2.32 0.00 43.65 5.69
125 126 2.267961 GGAAATCGACCCTGGCGT 59.732 61.111 0.00 0.00 0.00 5.68
126 127 1.814169 GGAAATCGACCCTGGCGTC 60.814 63.158 0.00 5.53 0.00 5.19
132 133 3.823330 GACCCTGGCGTCGATCGT 61.823 66.667 15.94 0.00 42.13 3.73
133 134 3.352338 GACCCTGGCGTCGATCGTT 62.352 63.158 15.94 0.00 42.13 3.85
134 135 1.996786 GACCCTGGCGTCGATCGTTA 61.997 60.000 15.94 0.00 42.13 3.18
135 136 1.299165 CCCTGGCGTCGATCGTTAG 60.299 63.158 15.94 8.78 42.13 2.34
136 137 1.944676 CCTGGCGTCGATCGTTAGC 60.945 63.158 15.94 17.51 42.13 3.09
137 138 2.277692 TGGCGTCGATCGTTAGCG 60.278 61.111 15.94 15.57 42.13 4.26
138 139 2.277756 GGCGTCGATCGTTAGCGT 60.278 61.111 15.94 0.00 42.13 5.07
139 140 2.284456 GGCGTCGATCGTTAGCGTC 61.284 63.158 15.94 13.01 42.13 5.19
140 141 2.284456 GCGTCGATCGTTAGCGTCC 61.284 63.158 15.94 1.46 42.13 4.79
141 142 1.997227 CGTCGATCGTTAGCGTCCG 60.997 63.158 15.94 4.32 39.49 4.79
142 143 2.023741 TCGATCGTTAGCGTCCGC 59.976 61.111 15.94 2.94 42.33 5.54
154 155 2.789249 GTCCGCGTGTAAATGCCC 59.211 61.111 4.92 0.00 0.00 5.36
179 183 4.723309 AGAACTTCCACAAAGATGCTTCT 58.277 39.130 0.00 0.00 38.44 2.85
180 184 5.869579 AGAACTTCCACAAAGATGCTTCTA 58.130 37.500 2.02 0.00 38.44 2.10
305 310 1.153369 ATGATTGCTGACCCCGACG 60.153 57.895 0.00 0.00 0.00 5.12
594 601 0.387367 CCGAGTTCTGACCGTGACTG 60.387 60.000 0.00 0.00 0.00 3.51
638 645 1.430632 CGAGCGCCAATGCAAATCT 59.569 52.632 2.29 0.00 37.32 2.40
694 701 5.807011 GCCATGTCAAGTTGAATAATTGGTC 59.193 40.000 7.25 4.08 0.00 4.02
739 746 2.299297 CCCTTCTCGGTAACTTGTGAGT 59.701 50.000 0.00 0.00 37.87 3.41
756 763 6.161855 TGTGAGTTGAGACAAGAATACACT 57.838 37.500 0.00 0.00 0.00 3.55
773 780 6.791867 ATACACTTCATCTAACACCTGCTA 57.208 37.500 0.00 0.00 0.00 3.49
821 834 9.357652 CACCTTCCATGAAATGTTTATTACAAG 57.642 33.333 0.00 0.00 44.81 3.16
827 840 8.810427 CCATGAAATGTTTATTACAAGCATGTC 58.190 33.333 0.00 0.00 44.81 3.06
838 851 3.775202 ACAAGCATGTCTAGACGATCAC 58.225 45.455 17.85 5.84 33.41 3.06
890 903 2.219458 TCGTGAACGGGTGCATAAAAA 58.781 42.857 2.59 0.00 40.29 1.94
896 913 4.155826 TGAACGGGTGCATAAAAAGAGATG 59.844 41.667 0.00 0.00 0.00 2.90
897 914 3.950397 ACGGGTGCATAAAAAGAGATGA 58.050 40.909 0.00 0.00 0.00 2.92
909 926 9.277783 CATAAAAAGAGATGAAGGTCGGATTAT 57.722 33.333 0.00 0.00 0.00 1.28
925 942 5.879777 TCGGATTATCATTCAGCAACAGAAA 59.120 36.000 0.00 0.00 0.00 2.52
929 946 7.650903 GGATTATCATTCAGCAACAGAAATTCC 59.349 37.037 0.00 0.00 0.00 3.01
931 948 6.600882 ATCATTCAGCAACAGAAATTCCTT 57.399 33.333 0.00 0.00 0.00 3.36
940 957 3.139077 ACAGAAATTCCTTCGTGTCACC 58.861 45.455 0.00 0.00 39.22 4.02
1607 1634 7.414098 GGTGATGTGTAATCTGTTCATAACCAC 60.414 40.741 0.00 0.00 38.93 4.16
1684 1719 4.329256 GGTATGACGCTTAGGAAAGTGAAC 59.671 45.833 5.74 1.18 44.46 3.18
1691 1726 5.212934 CGCTTAGGAAAGTGAACCTTTTTC 58.787 41.667 0.00 0.00 44.46 2.29
1826 1861 5.617187 GCACATATCTACAAATTTTCTCGCG 59.383 40.000 0.00 0.00 0.00 5.87
1828 1863 7.180079 CACATATCTACAAATTTTCTCGCGTT 58.820 34.615 5.77 0.00 0.00 4.84
1844 1879 2.031919 TTTCATGTGCGCCTCCGT 59.968 55.556 4.18 0.00 36.67 4.69
1919 1954 2.683362 CCTCCCGCCAATTCTTTTAGAC 59.317 50.000 0.00 0.00 0.00 2.59
1943 1980 2.200373 AGCATGTCCGGCTTTAAAGT 57.800 45.000 16.38 0.00 38.81 2.66
1946 1983 4.270008 AGCATGTCCGGCTTTAAAGTTAT 58.730 39.130 16.38 0.85 38.81 1.89
1947 1984 5.433526 AGCATGTCCGGCTTTAAAGTTATA 58.566 37.500 16.38 0.00 38.81 0.98
1948 1985 5.296035 AGCATGTCCGGCTTTAAAGTTATAC 59.704 40.000 16.38 10.45 38.81 1.47
2029 2066 8.251750 TCAGTCTCAAATTGGATTAAACGTAG 57.748 34.615 0.00 0.00 0.00 3.51
2031 2068 7.957484 CAGTCTCAAATTGGATTAAACGTAGTG 59.043 37.037 0.00 0.00 45.00 2.74
2042 2079 1.593296 AACGTAGTGCTCCCTCCGTC 61.593 60.000 0.00 0.00 45.00 4.79
2043 2080 1.749638 CGTAGTGCTCCCTCCGTCT 60.750 63.158 0.00 0.00 0.00 4.18
2044 2081 1.716826 CGTAGTGCTCCCTCCGTCTC 61.717 65.000 0.00 0.00 0.00 3.36
2045 2082 0.680280 GTAGTGCTCCCTCCGTCTCA 60.680 60.000 0.00 0.00 0.00 3.27
2048 2085 0.034896 GTGCTCCCTCCGTCTCAAAA 59.965 55.000 0.00 0.00 0.00 2.44
2051 2088 2.569853 TGCTCCCTCCGTCTCAAAATAA 59.430 45.455 0.00 0.00 0.00 1.40
2052 2089 2.937149 GCTCCCTCCGTCTCAAAATAAC 59.063 50.000 0.00 0.00 0.00 1.89
2059 2096 5.462530 TCCGTCTCAAAATAACTGTCTCA 57.537 39.130 0.00 0.00 0.00 3.27
2060 2097 5.849510 TCCGTCTCAAAATAACTGTCTCAA 58.150 37.500 0.00 0.00 0.00 3.02
2061 2098 5.694910 TCCGTCTCAAAATAACTGTCTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
2062 2099 5.696724 CCGTCTCAAAATAACTGTCTCAACT 59.303 40.000 0.00 0.00 0.00 3.16
2063 2100 6.202954 CCGTCTCAAAATAACTGTCTCAACTT 59.797 38.462 0.00 0.00 0.00 2.66
2065 2102 7.794349 CGTCTCAAAATAACTGTCTCAACTTTC 59.206 37.037 0.00 0.00 0.00 2.62
2066 2103 8.831550 GTCTCAAAATAACTGTCTCAACTTTCT 58.168 33.333 0.00 0.00 0.00 2.52
2067 2104 8.830580 TCTCAAAATAACTGTCTCAACTTTCTG 58.169 33.333 0.00 0.00 0.00 3.02
2068 2105 7.417612 TCAAAATAACTGTCTCAACTTTCTGC 58.582 34.615 0.00 0.00 0.00 4.26
2069 2106 7.283127 TCAAAATAACTGTCTCAACTTTCTGCT 59.717 33.333 0.00 0.00 0.00 4.24
2070 2107 8.559536 CAAAATAACTGTCTCAACTTTCTGCTA 58.440 33.333 0.00 0.00 0.00 3.49
2071 2108 7.897575 AATAACTGTCTCAACTTTCTGCTAG 57.102 36.000 0.00 0.00 0.00 3.42
2073 2110 5.283457 ACTGTCTCAACTTTCTGCTAGTT 57.717 39.130 0.00 0.00 36.31 2.24
2075 2112 6.116126 ACTGTCTCAACTTTCTGCTAGTTTT 58.884 36.000 0.00 0.00 33.73 2.43
2076 2113 7.272978 ACTGTCTCAACTTTCTGCTAGTTTTA 58.727 34.615 0.00 0.00 33.73 1.52
2078 2115 8.677148 TGTCTCAACTTTCTGCTAGTTTTAAT 57.323 30.769 0.00 0.00 33.73 1.40
2079 2116 9.772973 TGTCTCAACTTTCTGCTAGTTTTAATA 57.227 29.630 0.00 0.00 33.73 0.98
2118 2155 8.078060 AGGTTAAGACATTTATTTTGGGATGG 57.922 34.615 0.00 0.00 0.00 3.51
2119 2156 7.898636 AGGTTAAGACATTTATTTTGGGATGGA 59.101 33.333 0.00 0.00 0.00 3.41
2153 2202 6.731164 ACAAGACCAAACATAAAACTAACGG 58.269 36.000 0.00 0.00 0.00 4.44
2155 2204 5.623169 AGACCAAACATAAAACTAACGGGA 58.377 37.500 0.00 0.00 0.00 5.14
2199 2248 5.994054 GGTATTGCTTCTCTTGATAGCATGA 59.006 40.000 0.00 0.00 43.72 3.07
2249 2298 4.170723 CGCCTCACGGTCTTCTTC 57.829 61.111 0.00 0.00 38.44 2.87
2251 2300 0.038159 CGCCTCACGGTCTTCTTCTT 60.038 55.000 0.00 0.00 38.44 2.52
2252 2301 1.605712 CGCCTCACGGTCTTCTTCTTT 60.606 52.381 0.00 0.00 38.44 2.52
2253 2302 2.352421 CGCCTCACGGTCTTCTTCTTTA 60.352 50.000 0.00 0.00 38.44 1.85
2254 2303 2.994578 GCCTCACGGTCTTCTTCTTTAC 59.005 50.000 0.00 0.00 0.00 2.01
2255 2304 3.586892 CCTCACGGTCTTCTTCTTTACC 58.413 50.000 0.00 0.00 0.00 2.85
2259 2308 4.342951 TCACGGTCTTCTTCTTTACCAAGA 59.657 41.667 0.00 0.00 37.24 3.02
2260 2309 5.011738 TCACGGTCTTCTTCTTTACCAAGAT 59.988 40.000 0.00 0.00 38.89 2.40
2261 2310 5.120830 CACGGTCTTCTTCTTTACCAAGATG 59.879 44.000 0.00 0.00 38.89 2.90
2262 2311 5.221661 ACGGTCTTCTTCTTTACCAAGATGT 60.222 40.000 0.00 0.00 38.89 3.06
2263 2312 5.701290 CGGTCTTCTTCTTTACCAAGATGTT 59.299 40.000 0.00 0.00 38.89 2.71
2264 2313 6.872020 CGGTCTTCTTCTTTACCAAGATGTTA 59.128 38.462 0.00 0.00 38.89 2.41
2265 2314 7.549488 CGGTCTTCTTCTTTACCAAGATGTTAT 59.451 37.037 0.00 0.00 38.89 1.89
2266 2315 9.232473 GGTCTTCTTCTTTACCAAGATGTTATT 57.768 33.333 0.00 0.00 38.89 1.40
2268 2317 8.730680 TCTTCTTCTTTACCAAGATGTTATTGC 58.269 33.333 0.00 0.00 38.89 3.56
2269 2318 8.635765 TTCTTCTTTACCAAGATGTTATTGCT 57.364 30.769 0.00 0.00 38.89 3.91
2270 2319 8.044060 TCTTCTTTACCAAGATGTTATTGCTG 57.956 34.615 0.00 0.00 38.89 4.41
2271 2320 7.882791 TCTTCTTTACCAAGATGTTATTGCTGA 59.117 33.333 0.00 0.00 38.89 4.26
2272 2321 7.377766 TCTTTACCAAGATGTTATTGCTGAC 57.622 36.000 0.00 0.00 33.80 3.51
2273 2322 6.939730 TCTTTACCAAGATGTTATTGCTGACA 59.060 34.615 0.00 0.00 33.80 3.58
2286 2335 4.686191 TTGCTGACAAAAATGGACCATT 57.314 36.364 14.28 14.28 35.39 3.16
2322 2371 5.012664 TCAGCAGGGTGATTAGTGTTAGAAA 59.987 40.000 0.00 0.00 0.00 2.52
2324 2373 4.636206 GCAGGGTGATTAGTGTTAGAAAGG 59.364 45.833 0.00 0.00 0.00 3.11
2328 2377 6.500751 AGGGTGATTAGTGTTAGAAAGGAGAA 59.499 38.462 0.00 0.00 0.00 2.87
2334 2383 7.569599 TTAGTGTTAGAAAGGAGAAAGGGAT 57.430 36.000 0.00 0.00 0.00 3.85
2349 2399 7.417911 GGAGAAAGGGATTTGGTGGAATAATTC 60.418 40.741 0.00 0.00 0.00 2.17
2372 6076 3.632643 TGATGTATTGCTTGAGCCTCA 57.367 42.857 0.00 0.00 41.18 3.86
2415 6119 8.893727 AGTACATGATTTATTTGGAGTACAAGC 58.106 33.333 0.00 0.00 40.82 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.359848 CCGCTCGATGCAAAGTAACT 58.640 50.000 0.00 0.00 43.06 2.24
1 2 0.373716 CCCGCTCGATGCAAAGTAAC 59.626 55.000 0.00 0.00 43.06 2.50
2 3 0.248012 TCCCGCTCGATGCAAAGTAA 59.752 50.000 0.00 0.00 43.06 2.24
3 4 0.248012 TTCCCGCTCGATGCAAAGTA 59.752 50.000 0.00 0.00 43.06 2.24
4 5 0.605319 TTTCCCGCTCGATGCAAAGT 60.605 50.000 0.00 0.00 43.06 2.66
5 6 0.521291 TTTTCCCGCTCGATGCAAAG 59.479 50.000 0.00 0.00 43.06 2.77
6 7 0.955178 TTTTTCCCGCTCGATGCAAA 59.045 45.000 0.00 0.00 43.06 3.68
7 8 2.635079 TTTTTCCCGCTCGATGCAA 58.365 47.368 0.00 0.00 43.06 4.08
8 9 4.388229 TTTTTCCCGCTCGATGCA 57.612 50.000 0.00 0.00 43.06 3.96
45 46 4.851114 CGTCGATGCCGCGCAAAG 62.851 66.667 8.75 0.00 43.62 2.77
53 54 3.918220 CTCGCTTGCGTCGATGCC 61.918 66.667 26.06 10.48 35.25 4.40
54 55 1.756375 AATCTCGCTTGCGTCGATGC 61.756 55.000 22.77 22.77 35.25 3.91
55 56 0.228238 GAATCTCGCTTGCGTCGATG 59.772 55.000 14.70 0.00 35.25 3.84
56 57 0.872021 GGAATCTCGCTTGCGTCGAT 60.872 55.000 14.70 13.89 35.25 3.59
57 58 1.516386 GGAATCTCGCTTGCGTCGA 60.516 57.895 14.70 12.36 34.52 4.20
58 59 2.517450 GGGAATCTCGCTTGCGTCG 61.517 63.158 14.70 7.65 0.00 5.12
59 60 2.174319 GGGGAATCTCGCTTGCGTC 61.174 63.158 14.70 4.98 0.00 5.19
60 61 2.125106 GGGGAATCTCGCTTGCGT 60.125 61.111 14.70 0.00 0.00 5.24
61 62 3.264897 CGGGGAATCTCGCTTGCG 61.265 66.667 8.87 8.87 0.00 4.85
62 63 2.125106 ACGGGGAATCTCGCTTGC 60.125 61.111 0.00 0.00 0.00 4.01
63 64 0.528684 GAGACGGGGAATCTCGCTTG 60.529 60.000 0.00 0.00 33.68 4.01
64 65 1.817209 GAGACGGGGAATCTCGCTT 59.183 57.895 0.00 0.00 33.68 4.68
65 66 3.527641 GAGACGGGGAATCTCGCT 58.472 61.111 0.00 0.00 33.68 4.93
77 78 2.104331 CGATTCCCACCCGAGACG 59.896 66.667 0.00 0.00 0.00 4.18
78 79 2.499685 CCGATTCCCACCCGAGAC 59.500 66.667 0.00 0.00 0.00 3.36
79 80 2.762459 CCCGATTCCCACCCGAGA 60.762 66.667 0.00 0.00 0.00 4.04
80 81 4.547367 GCCCGATTCCCACCCGAG 62.547 72.222 0.00 0.00 0.00 4.63
82 83 2.332312 TTATGCCCGATTCCCACCCG 62.332 60.000 0.00 0.00 0.00 5.28
83 84 0.822121 GTTATGCCCGATTCCCACCC 60.822 60.000 0.00 0.00 0.00 4.61
84 85 1.164041 CGTTATGCCCGATTCCCACC 61.164 60.000 0.00 0.00 0.00 4.61
85 86 0.179067 TCGTTATGCCCGATTCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
86 87 0.179067 GTCGTTATGCCCGATTCCCA 60.179 55.000 0.00 0.00 36.62 4.37
87 88 0.883370 GGTCGTTATGCCCGATTCCC 60.883 60.000 0.00 0.00 36.62 3.97
88 89 1.219522 CGGTCGTTATGCCCGATTCC 61.220 60.000 0.00 0.00 44.41 3.01
89 90 1.219522 CCGGTCGTTATGCCCGATTC 61.220 60.000 0.00 0.00 44.41 2.52
90 91 1.227438 CCGGTCGTTATGCCCGATT 60.227 57.895 0.00 0.00 44.41 3.34
91 92 2.420043 CCGGTCGTTATGCCCGAT 59.580 61.111 0.00 0.00 44.41 4.18
92 93 3.840594 CCCGGTCGTTATGCCCGA 61.841 66.667 0.00 0.00 44.41 5.14
93 94 2.855880 TTTCCCGGTCGTTATGCCCG 62.856 60.000 0.00 0.00 41.37 6.13
94 95 0.464916 ATTTCCCGGTCGTTATGCCC 60.465 55.000 0.00 0.00 0.00 5.36
95 96 0.942252 GATTTCCCGGTCGTTATGCC 59.058 55.000 0.00 0.00 0.00 4.40
96 97 0.580104 CGATTTCCCGGTCGTTATGC 59.420 55.000 0.00 0.00 33.42 3.14
97 98 1.856597 GTCGATTTCCCGGTCGTTATG 59.143 52.381 11.42 0.00 38.85 1.90
98 99 1.202452 GGTCGATTTCCCGGTCGTTAT 60.202 52.381 11.42 0.00 38.85 1.89
99 100 0.173255 GGTCGATTTCCCGGTCGTTA 59.827 55.000 11.42 0.00 38.85 3.18
100 101 1.079612 GGTCGATTTCCCGGTCGTT 60.080 57.895 11.42 0.00 38.85 3.85
101 102 2.575461 GGTCGATTTCCCGGTCGT 59.425 61.111 11.42 0.00 38.85 4.34
102 103 2.202837 GGGTCGATTTCCCGGTCG 60.203 66.667 5.87 5.87 39.11 4.79
107 108 2.513897 CGCCAGGGTCGATTTCCC 60.514 66.667 1.23 1.23 44.90 3.97
108 109 1.814169 GACGCCAGGGTCGATTTCC 60.814 63.158 8.69 0.00 0.00 3.13
109 110 3.795638 GACGCCAGGGTCGATTTC 58.204 61.111 8.69 0.00 0.00 2.17
115 116 1.996786 TAACGATCGACGCCAGGGTC 61.997 60.000 24.34 4.85 46.94 4.46
116 117 2.001361 CTAACGATCGACGCCAGGGT 62.001 60.000 24.34 0.00 46.94 4.34
117 118 1.299165 CTAACGATCGACGCCAGGG 60.299 63.158 24.34 0.00 46.94 4.45
118 119 1.944676 GCTAACGATCGACGCCAGG 60.945 63.158 24.34 5.48 46.94 4.45
119 120 2.286559 CGCTAACGATCGACGCCAG 61.287 63.158 24.34 11.33 46.94 4.85
120 121 2.277692 CGCTAACGATCGACGCCA 60.278 61.111 24.34 0.47 46.94 5.69
121 122 2.277756 ACGCTAACGATCGACGCC 60.278 61.111 24.34 6.33 46.94 5.68
122 123 2.284456 GGACGCTAACGATCGACGC 61.284 63.158 24.34 18.35 46.94 5.19
124 125 2.284456 GCGGACGCTAACGATCGAC 61.284 63.158 24.34 7.11 43.93 4.20
125 126 2.023741 GCGGACGCTAACGATCGA 59.976 61.111 24.34 0.00 43.93 3.59
126 127 3.376464 CGCGGACGCTAACGATCG 61.376 66.667 14.88 14.88 43.93 3.69
127 128 2.277756 ACGCGGACGCTAACGATC 60.278 61.111 12.47 0.00 45.53 3.69
128 129 1.980951 TACACGCGGACGCTAACGAT 61.981 55.000 12.47 0.00 45.53 3.73
129 130 2.181372 TTACACGCGGACGCTAACGA 62.181 55.000 12.47 0.00 45.53 3.85
130 131 1.336403 TTTACACGCGGACGCTAACG 61.336 55.000 12.47 1.49 45.53 3.18
131 132 0.994263 ATTTACACGCGGACGCTAAC 59.006 50.000 12.47 0.00 45.53 2.34
132 133 0.993532 CATTTACACGCGGACGCTAA 59.006 50.000 12.47 4.12 45.53 3.09
133 134 1.415288 GCATTTACACGCGGACGCTA 61.415 55.000 12.47 0.00 45.53 4.26
134 135 2.736682 GCATTTACACGCGGACGCT 61.737 57.895 12.47 0.00 45.53 5.07
135 136 2.276430 GCATTTACACGCGGACGC 60.276 61.111 12.47 6.63 45.53 5.19
137 138 1.303091 AAGGGCATTTACACGCGGAC 61.303 55.000 12.47 0.00 0.00 4.79
138 139 0.249676 TAAGGGCATTTACACGCGGA 59.750 50.000 12.47 0.00 0.00 5.54
139 140 0.655733 CTAAGGGCATTTACACGCGG 59.344 55.000 12.47 1.27 0.00 6.46
140 141 1.647346 TCTAAGGGCATTTACACGCG 58.353 50.000 3.53 3.53 0.00 6.01
141 142 3.007635 AGTTCTAAGGGCATTTACACGC 58.992 45.455 0.00 0.00 0.00 5.34
142 143 4.094442 GGAAGTTCTAAGGGCATTTACACG 59.906 45.833 2.25 0.00 0.00 4.49
146 147 5.249780 TGTGGAAGTTCTAAGGGCATTTA 57.750 39.130 2.25 0.00 0.00 1.40
154 155 6.429385 AGAAGCATCTTTGTGGAAGTTCTAAG 59.571 38.462 2.25 2.73 36.70 2.18
179 183 2.637382 TCTAATGAAGCGATGGGGCATA 59.363 45.455 0.00 0.00 34.64 3.14
180 184 1.421268 TCTAATGAAGCGATGGGGCAT 59.579 47.619 0.00 0.00 34.64 4.40
265 269 5.484173 TCAGCTAATGGCAAATAGTTTCG 57.516 39.130 11.03 0.00 44.79 3.46
305 310 6.507023 TCCTTTCAGCAGAGATTTTGTTTTC 58.493 36.000 0.00 0.00 0.00 2.29
473 479 2.464865 CGTATGTCTGACTAAGCTGCC 58.535 52.381 9.51 0.00 0.00 4.85
474 480 1.855360 GCGTATGTCTGACTAAGCTGC 59.145 52.381 9.51 0.00 0.00 5.25
475 481 2.112522 CGCGTATGTCTGACTAAGCTG 58.887 52.381 9.51 6.18 0.00 4.24
476 482 2.014857 TCGCGTATGTCTGACTAAGCT 58.985 47.619 5.77 0.00 0.00 3.74
594 601 6.455646 GCATATATGATAAGCTACGGTTGCAC 60.456 42.308 17.10 5.91 0.00 4.57
638 645 2.787601 ACAAGTCGTTCGTAGCTCAA 57.212 45.000 0.00 0.00 0.00 3.02
694 701 1.033574 GTATCTGACCTCCGGACCAG 58.966 60.000 0.00 8.75 31.94 4.00
739 746 9.424319 GTTAGATGAAGTGTATTCTTGTCTCAA 57.576 33.333 0.00 0.00 0.00 3.02
751 758 6.791867 ATAGCAGGTGTTAGATGAAGTGTA 57.208 37.500 0.00 0.00 0.00 2.90
756 763 5.661312 AGGTGTATAGCAGGTGTTAGATGAA 59.339 40.000 0.00 0.00 0.00 2.57
773 780 1.276622 GGGTGAGTGTGGAGGTGTAT 58.723 55.000 0.00 0.00 0.00 2.29
821 834 5.725110 AAAATGTGATCGTCTAGACATGC 57.275 39.130 22.37 10.66 0.00 4.06
827 840 6.019881 TGCGAACATAAAATGTGATCGTCTAG 60.020 38.462 12.89 0.00 44.07 2.43
838 851 2.832178 CGTCACGTGCGAACATAAAATG 59.168 45.455 22.18 0.00 0.00 2.32
890 903 6.268617 TGAATGATAATCCGACCTTCATCTCT 59.731 38.462 0.00 0.00 0.00 3.10
896 913 4.380531 TGCTGAATGATAATCCGACCTTC 58.619 43.478 0.00 0.00 0.00 3.46
897 914 4.422073 TGCTGAATGATAATCCGACCTT 57.578 40.909 0.00 0.00 0.00 3.50
909 926 5.335113 CGAAGGAATTTCTGTTGCTGAATGA 60.335 40.000 0.00 0.00 33.44 2.57
925 942 2.925724 TGTTTGGTGACACGAAGGAAT 58.074 42.857 3.17 0.00 42.67 3.01
929 946 3.059188 GGTGTATGTTTGGTGACACGAAG 60.059 47.826 3.17 0.00 42.50 3.79
931 948 2.158943 TGGTGTATGTTTGGTGACACGA 60.159 45.455 0.00 0.00 42.50 4.35
940 957 2.288763 GGCTGGGTTTGGTGTATGTTTG 60.289 50.000 0.00 0.00 0.00 2.93
1293 1311 3.491652 GCCGCCGAGTGCTTCTTC 61.492 66.667 0.00 0.00 38.05 2.87
1532 1555 3.262420 ACACTAACACATCATTCGCCTC 58.738 45.455 0.00 0.00 0.00 4.70
1576 1603 6.764379 TGAACAGATTACACATCACCAACTA 58.236 36.000 0.00 0.00 0.00 2.24
1587 1614 4.331717 CCCGTGGTTATGAACAGATTACAC 59.668 45.833 0.00 0.00 0.00 2.90
1607 1634 2.803155 TACAGCAGAGCAAAGCCCCG 62.803 60.000 0.00 0.00 0.00 5.73
1684 1719 1.136336 GCACAGCGTAGACGAAAAAGG 60.136 52.381 6.19 0.00 43.02 3.11
1691 1726 0.642291 CAATCAGCACAGCGTAGACG 59.358 55.000 0.00 0.00 43.27 4.18
1759 1794 4.081972 GGCCATTCTTTCTCTTTTCTTCCC 60.082 45.833 0.00 0.00 0.00 3.97
1826 1861 1.017177 TACGGAGGCGCACATGAAAC 61.017 55.000 10.83 0.00 0.00 2.78
1828 1863 1.447140 GTACGGAGGCGCACATGAA 60.447 57.895 10.83 0.00 0.00 2.57
1844 1879 3.516300 AGGAGAGTCGAGAGTCAAGAGTA 59.484 47.826 10.20 0.00 33.26 2.59
1919 1954 3.892200 AAGCCGGACATGCTTTTTG 57.108 47.368 5.05 0.00 46.47 2.44
2029 2066 0.034896 TTTTGAGACGGAGGGAGCAC 59.965 55.000 0.00 0.00 0.00 4.40
2031 2068 2.937149 GTTATTTTGAGACGGAGGGAGC 59.063 50.000 0.00 0.00 0.00 4.70
2042 2079 7.589221 GCAGAAAGTTGAGACAGTTATTTTGAG 59.411 37.037 0.00 0.00 0.00 3.02
2043 2080 7.283127 AGCAGAAAGTTGAGACAGTTATTTTGA 59.717 33.333 0.00 0.00 0.00 2.69
2044 2081 7.420800 AGCAGAAAGTTGAGACAGTTATTTTG 58.579 34.615 0.00 0.00 0.00 2.44
2045 2082 7.573968 AGCAGAAAGTTGAGACAGTTATTTT 57.426 32.000 0.00 0.00 0.00 1.82
2048 2085 6.998802 ACTAGCAGAAAGTTGAGACAGTTAT 58.001 36.000 0.00 0.00 0.00 1.89
2051 2088 4.946478 ACTAGCAGAAAGTTGAGACAGT 57.054 40.909 0.00 0.00 0.00 3.55
2052 2089 6.610741 AAAACTAGCAGAAAGTTGAGACAG 57.389 37.500 0.00 0.00 37.26 3.51
2092 2129 9.196139 CCATCCCAAAATAAATGTCTTAACCTA 57.804 33.333 0.00 0.00 0.00 3.08
2093 2130 7.898636 TCCATCCCAAAATAAATGTCTTAACCT 59.101 33.333 0.00 0.00 0.00 3.50
2094 2131 8.073467 TCCATCCCAAAATAAATGTCTTAACC 57.927 34.615 0.00 0.00 0.00 2.85
2095 2132 8.966868 TCTCCATCCCAAAATAAATGTCTTAAC 58.033 33.333 0.00 0.00 0.00 2.01
2096 2133 9.189156 CTCTCCATCCCAAAATAAATGTCTTAA 57.811 33.333 0.00 0.00 0.00 1.85
2097 2134 8.336235 ACTCTCCATCCCAAAATAAATGTCTTA 58.664 33.333 0.00 0.00 0.00 2.10
2099 2136 6.735556 ACTCTCCATCCCAAAATAAATGTCT 58.264 36.000 0.00 0.00 0.00 3.41
2100 2137 7.556275 TGTACTCTCCATCCCAAAATAAATGTC 59.444 37.037 0.00 0.00 0.00 3.06
2101 2138 7.410174 TGTACTCTCCATCCCAAAATAAATGT 58.590 34.615 0.00 0.00 0.00 2.71
2102 2139 7.880160 TGTACTCTCCATCCCAAAATAAATG 57.120 36.000 0.00 0.00 0.00 2.32
2106 2143 8.096621 TGTAATGTACTCTCCATCCCAAAATA 57.903 34.615 0.00 0.00 0.00 1.40
2107 2144 6.969043 TGTAATGTACTCTCCATCCCAAAAT 58.031 36.000 0.00 0.00 0.00 1.82
2108 2145 6.381498 TGTAATGTACTCTCCATCCCAAAA 57.619 37.500 0.00 0.00 0.00 2.44
2110 2147 5.724370 TCTTGTAATGTACTCTCCATCCCAA 59.276 40.000 0.00 0.00 0.00 4.12
2111 2148 5.128827 GTCTTGTAATGTACTCTCCATCCCA 59.871 44.000 0.00 0.00 0.00 4.37
2112 2149 5.453480 GGTCTTGTAATGTACTCTCCATCCC 60.453 48.000 0.00 0.00 0.00 3.85
2113 2150 5.128827 TGGTCTTGTAATGTACTCTCCATCC 59.871 44.000 0.00 0.00 0.00 3.51
2114 2151 6.222038 TGGTCTTGTAATGTACTCTCCATC 57.778 41.667 0.00 0.00 0.00 3.51
2115 2152 6.620877 TTGGTCTTGTAATGTACTCTCCAT 57.379 37.500 0.00 0.00 0.00 3.41
2117 2154 6.228258 TGTTTGGTCTTGTAATGTACTCTCC 58.772 40.000 0.00 0.00 0.00 3.71
2118 2155 7.907214 ATGTTTGGTCTTGTAATGTACTCTC 57.093 36.000 0.00 0.00 0.00 3.20
2119 2156 9.787435 TTTATGTTTGGTCTTGTAATGTACTCT 57.213 29.630 0.00 0.00 0.00 3.24
2199 2248 4.242602 GCCAAGATTAAGGGCGCT 57.757 55.556 7.64 0.00 38.04 5.92
2249 2298 7.144722 TGTCAGCAATAACATCTTGGTAAAG 57.855 36.000 0.00 0.00 33.32 1.85
2251 2300 7.517614 TTTGTCAGCAATAACATCTTGGTAA 57.482 32.000 0.00 0.00 33.32 2.85
2252 2301 7.517614 TTTTGTCAGCAATAACATCTTGGTA 57.482 32.000 0.00 0.00 33.32 3.25
2253 2302 6.403866 TTTTGTCAGCAATAACATCTTGGT 57.596 33.333 0.00 0.00 34.84 3.67
2254 2303 7.148540 CCATTTTTGTCAGCAATAACATCTTGG 60.149 37.037 0.00 0.00 34.18 3.61
2255 2304 7.599621 TCCATTTTTGTCAGCAATAACATCTTG 59.400 33.333 0.00 0.00 34.18 3.02
2259 2308 6.165577 GGTCCATTTTTGTCAGCAATAACAT 58.834 36.000 0.00 0.00 34.18 2.71
2260 2309 5.069648 TGGTCCATTTTTGTCAGCAATAACA 59.930 36.000 0.00 0.00 34.18 2.41
2261 2310 5.537188 TGGTCCATTTTTGTCAGCAATAAC 58.463 37.500 0.00 0.00 34.18 1.89
2262 2311 5.798125 TGGTCCATTTTTGTCAGCAATAA 57.202 34.783 0.00 0.00 34.18 1.40
2263 2312 5.999205 ATGGTCCATTTTTGTCAGCAATA 57.001 34.783 0.00 0.00 34.18 1.90
2264 2313 4.895668 ATGGTCCATTTTTGTCAGCAAT 57.104 36.364 0.00 0.00 34.18 3.56
2265 2314 4.686191 AATGGTCCATTTTTGTCAGCAA 57.314 36.364 11.59 0.00 28.76 3.91
2266 2315 4.686191 AAATGGTCCATTTTTGTCAGCA 57.314 36.364 22.00 0.00 40.60 4.41
2267 2316 7.489574 TTTTAAATGGTCCATTTTTGTCAGC 57.510 32.000 30.15 0.00 40.60 4.26
2322 2371 2.358258 TCCACCAAATCCCTTTCTCCT 58.642 47.619 0.00 0.00 0.00 3.69
2324 2373 7.423844 AATTATTCCACCAAATCCCTTTCTC 57.576 36.000 0.00 0.00 0.00 2.87
2328 2377 5.269189 ACGAATTATTCCACCAAATCCCTT 58.731 37.500 0.00 0.00 0.00 3.95
2334 2383 6.582677 ACATCAACGAATTATTCCACCAAA 57.417 33.333 0.00 0.00 0.00 3.28
2349 2399 2.679837 AGGCTCAAGCAATACATCAACG 59.320 45.455 4.13 0.00 44.36 4.10
2372 6076 6.902974 TCATGTACTCCTACATATATGCCCAT 59.097 38.462 12.79 0.00 40.99 4.00
2402 6106 1.133637 TGGCTTGGCTTGTACTCCAAA 60.134 47.619 13.18 0.86 41.35 3.28
2415 6119 5.934781 AGACTAGGAAATATTCTGGCTTGG 58.065 41.667 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.