Multiple sequence alignment - TraesCS4A01G327800

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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 TraesCS4A01G327800 chr4A 100.000 2759 0 0 1 2759 614000892 613998134 0.000000e+00 5096.0
1 TraesCS4A01G327800 chr4A 94.820 2606 98 8 175 2759 519796235 519798824 0.000000e+00 4030.0
2 TraesCS4A01G327800 chr3A 96.315 2361 52 13 175 2534 57514754 57512428 0.000000e+00 3845.0
3 TraesCS4A01G327800 chr3A 87.624 1810 174 32 948 2735 110461902 110460121 0.000000e+00 2056.0
4 TraesCS4A01G327800 chr2B 92.993 2626 113 28 175 2759 527660582 527663177 0.000000e+00 3764.0
5 TraesCS4A01G327800 chr5A 89.453 1811 151 23 976 2759 556702765 556704562 0.000000e+00 2250.0
6 TraesCS4A01G327800 chr5A 89.177 1811 156 23 976 2759 556697850 556699647 0.000000e+00 2222.0
7 TraesCS4A01G327800 chr5A 88.913 1813 158 26 976 2759 709482231 709480433 0.000000e+00 2194.0
8 TraesCS4A01G327800 chr5A 88.791 1811 162 24 976 2759 465388412 465390208 0.000000e+00 2182.0
9 TraesCS4A01G327800 chr5A 88.435 441 35 5 992 1423 553373705 553373272 4.070000e-143 518.0
10 TraesCS4A01G327800 chr7A 89.288 1811 151 28 976 2759 60710846 60709052 0.000000e+00 2230.0
11 TraesCS4A01G327800 chr7A 89.177 1811 156 23 976 2759 689399101 689397304 0.000000e+00 2222.0
12 TraesCS4A01G327800 chr2A 96.443 1265 38 3 175 1439 181791401 181790144 0.000000e+00 2080.0
13 TraesCS4A01G327800 chr2A 96.716 1218 36 2 1543 2759 717806061 717807275 0.000000e+00 2025.0
14 TraesCS4A01G327800 chr2A 92.515 815 40 5 175 980 717805231 717806033 0.000000e+00 1147.0
15 TraesCS4A01G327800 chr3D 87.002 1831 184 27 958 2759 611435444 611437249 0.000000e+00 2013.0
16 TraesCS4A01G327800 chr3D 86.645 1827 184 34 958 2759 611423333 611425124 0.000000e+00 1967.0
17 TraesCS4A01G327800 chr6A 87.702 1732 174 21 976 2682 316458806 316460523 0.000000e+00 1982.0
18 TraesCS4A01G327800 chr1B 91.581 1069 38 16 167 1230 112758411 112757390 0.000000e+00 1428.0
19 TraesCS4A01G327800 chr1B 92.440 582 30 5 634 1202 25833083 25833663 0.000000e+00 819.0
20 TraesCS4A01G327800 chr1B 94.828 58 3 0 581 638 25824896 25824953 1.050000e-14 91.6
21 TraesCS4A01G327800 chr5B 87.448 1211 117 19 976 2160 320401310 320402511 0.000000e+00 1362.0
22 TraesCS4A01G327800 chr5B 87.528 441 39 5 992 1423 532863599 532863166 1.910000e-136 496.0
23 TraesCS4A01G327800 chr5B 92.683 41 3 0 79 119 580850422 580850382 2.970000e-05 60.2
24 TraesCS4A01G327800 chr1A 89.788 1038 61 16 175 1202 19934534 19935536 0.000000e+00 1288.0
25 TraesCS4A01G327800 chr1A 89.306 1038 64 18 175 1202 19984887 19985887 0.000000e+00 1258.0
26 TraesCS4A01G327800 chr4B 86.667 960 93 19 976 1910 16676616 16677565 0.000000e+00 1031.0
27 TraesCS4A01G327800 chr4B 87.446 231 22 5 900 1123 27406095 27405865 2.730000e-65 259.0
28 TraesCS4A01G327800 chr5D 88.662 441 34 5 992 1423 438355883 438355450 8.750000e-145 523.0


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 TraesCS4A01G327800 chr4A 613998134 614000892 2758 True 5096 5096 100.0000 1 2759 1 chr4A.!!$R1 2758
1 TraesCS4A01G327800 chr4A 519796235 519798824 2589 False 4030 4030 94.8200 175 2759 1 chr4A.!!$F1 2584
2 TraesCS4A01G327800 chr3A 57512428 57514754 2326 True 3845 3845 96.3150 175 2534 1 chr3A.!!$R1 2359
3 TraesCS4A01G327800 chr3A 110460121 110461902 1781 True 2056 2056 87.6240 948 2735 1 chr3A.!!$R2 1787
4 TraesCS4A01G327800 chr2B 527660582 527663177 2595 False 3764 3764 92.9930 175 2759 1 chr2B.!!$F1 2584
5 TraesCS4A01G327800 chr5A 556697850 556704562 6712 False 2236 2250 89.3150 976 2759 2 chr5A.!!$F2 1783
6 TraesCS4A01G327800 chr5A 709480433 709482231 1798 True 2194 2194 88.9130 976 2759 1 chr5A.!!$R2 1783
7 TraesCS4A01G327800 chr5A 465388412 465390208 1796 False 2182 2182 88.7910 976 2759 1 chr5A.!!$F1 1783
8 TraesCS4A01G327800 chr7A 60709052 60710846 1794 True 2230 2230 89.2880 976 2759 1 chr7A.!!$R1 1783
9 TraesCS4A01G327800 chr7A 689397304 689399101 1797 True 2222 2222 89.1770 976 2759 1 chr7A.!!$R2 1783
10 TraesCS4A01G327800 chr2A 181790144 181791401 1257 True 2080 2080 96.4430 175 1439 1 chr2A.!!$R1 1264
11 TraesCS4A01G327800 chr2A 717805231 717807275 2044 False 1586 2025 94.6155 175 2759 2 chr2A.!!$F1 2584
12 TraesCS4A01G327800 chr3D 611435444 611437249 1805 False 2013 2013 87.0020 958 2759 1 chr3D.!!$F2 1801
13 TraesCS4A01G327800 chr3D 611423333 611425124 1791 False 1967 1967 86.6450 958 2759 1 chr3D.!!$F1 1801
14 TraesCS4A01G327800 chr6A 316458806 316460523 1717 False 1982 1982 87.7020 976 2682 1 chr6A.!!$F1 1706
15 TraesCS4A01G327800 chr1B 112757390 112758411 1021 True 1428 1428 91.5810 167 1230 1 chr1B.!!$R1 1063
16 TraesCS4A01G327800 chr1B 25833083 25833663 580 False 819 819 92.4400 634 1202 1 chr1B.!!$F2 568
17 TraesCS4A01G327800 chr5B 320401310 320402511 1201 False 1362 1362 87.4480 976 2160 1 chr5B.!!$F1 1184
18 TraesCS4A01G327800 chr1A 19934534 19935536 1002 False 1288 1288 89.7880 175 1202 1 chr1A.!!$F1 1027
19 TraesCS4A01G327800 chr1A 19984887 19985887 1000 False 1258 1258 89.3060 175 1202 1 chr1A.!!$F2 1027
20 TraesCS4A01G327800 chr4B 16676616 16677565 949 False 1031 1031 86.6670 976 1910 1 chr4B.!!$F1 934

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
147 148 0.035458 CCGTGAGTTTCTTGGAGCCT 59.965 55.0 0.00 0.00 0.0 4.58 F
150 151 0.250901 TGAGTTTCTTGGAGCCTGGC 60.251 55.0 11.65 11.65 0.0 4.85 F
165 166 0.251916 CTGGCCGGAATAAGACCACA 59.748 55.0 5.28 0.00 0.0 4.17 F
166 167 0.693622 TGGCCGGAATAAGACCACAA 59.306 50.0 5.05 0.00 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 6362 2.836981 GGTGATAGGCTCATATGGCTCT 59.163 50.000 13.6 11.58 42.90 4.09 R
1491 6512 3.392616 CCACATCTAAGGGCATAGGTTCT 59.607 47.826 0.0 0.00 0.00 3.01 R
1703 6755 3.953612 TGCCAACTTGAACTCTTTCATGT 59.046 39.130 0.0 1.24 46.74 3.21 R
1976 7036 4.701765 ACTAGAGCAATCATGACCACATC 58.298 43.478 0.0 0.00 34.15 3.06 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
25 26 2.125952 GCAAAATGCAGGGTCGGC 60.126 61.111 0.00 0.00 44.26 5.54
26 27 2.639327 GCAAAATGCAGGGTCGGCT 61.639 57.895 0.00 0.00 44.26 5.52
27 28 1.312371 GCAAAATGCAGGGTCGGCTA 61.312 55.000 0.00 0.00 44.26 3.93
28 29 0.734889 CAAAATGCAGGGTCGGCTAG 59.265 55.000 0.00 0.00 0.00 3.42
29 30 0.618458 AAAATGCAGGGTCGGCTAGA 59.382 50.000 0.00 0.00 0.00 2.43
30 31 0.179000 AAATGCAGGGTCGGCTAGAG 59.821 55.000 0.00 0.00 0.00 2.43
31 32 0.978146 AATGCAGGGTCGGCTAGAGT 60.978 55.000 0.00 0.00 0.00 3.24
32 33 0.978146 ATGCAGGGTCGGCTAGAGTT 60.978 55.000 0.00 0.00 0.00 3.01
33 34 1.153549 GCAGGGTCGGCTAGAGTTG 60.154 63.158 0.00 0.00 0.00 3.16
34 35 1.153549 CAGGGTCGGCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
35 36 1.305381 AGGGTCGGCTAGAGTTGCT 60.305 57.895 0.00 0.00 0.00 3.91
36 37 1.142097 GGGTCGGCTAGAGTTGCTC 59.858 63.158 0.00 0.00 0.00 4.26
37 38 1.324005 GGGTCGGCTAGAGTTGCTCT 61.324 60.000 4.02 4.02 43.83 4.09
38 39 0.533032 GGTCGGCTAGAGTTGCTCTT 59.467 55.000 3.87 0.00 41.50 2.85
39 40 1.749634 GGTCGGCTAGAGTTGCTCTTA 59.250 52.381 3.87 0.00 41.50 2.10
40 41 2.223618 GGTCGGCTAGAGTTGCTCTTAG 60.224 54.545 3.87 2.21 41.50 2.18
41 42 2.025155 TCGGCTAGAGTTGCTCTTAGG 58.975 52.381 3.87 0.00 41.50 2.69
42 43 2.025155 CGGCTAGAGTTGCTCTTAGGA 58.975 52.381 3.87 0.00 41.50 2.94
43 44 2.034053 CGGCTAGAGTTGCTCTTAGGAG 59.966 54.545 3.87 0.00 41.50 3.69
57 58 3.527641 GGAGCTACCTGGAGACCG 58.472 66.667 0.00 0.00 35.41 4.79
58 59 2.128507 GGAGCTACCTGGAGACCGG 61.129 68.421 0.00 0.00 35.41 5.28
59 60 2.760385 AGCTACCTGGAGACCGGC 60.760 66.667 0.00 0.00 0.00 6.13
60 61 3.851128 GCTACCTGGAGACCGGCC 61.851 72.222 0.00 0.00 0.00 6.13
61 62 2.042843 CTACCTGGAGACCGGCCT 60.043 66.667 0.00 0.00 0.00 5.19
62 63 2.043248 TACCTGGAGACCGGCCTC 60.043 66.667 9.66 9.66 0.00 4.70
63 64 2.575455 CTACCTGGAGACCGGCCTCT 62.575 65.000 17.91 5.95 33.79 3.69
64 65 2.856039 TACCTGGAGACCGGCCTCTG 62.856 65.000 17.91 10.53 33.79 3.35
65 66 4.154347 CTGGAGACCGGCCTCTGC 62.154 72.222 17.91 11.96 33.79 4.26
67 68 3.706373 GGAGACCGGCCTCTGCAA 61.706 66.667 17.91 0.00 40.13 4.08
68 69 2.435059 GAGACCGGCCTCTGCAAC 60.435 66.667 11.00 0.00 40.13 4.17
69 70 4.379243 AGACCGGCCTCTGCAACG 62.379 66.667 0.00 0.00 40.13 4.10
73 74 3.357079 CGGCCTCTGCAACGCTTT 61.357 61.111 0.00 0.00 40.13 3.51
74 75 2.908073 CGGCCTCTGCAACGCTTTT 61.908 57.895 0.00 0.00 40.13 2.27
75 76 1.363807 GGCCTCTGCAACGCTTTTT 59.636 52.632 0.00 0.00 40.13 1.94
76 77 0.664466 GGCCTCTGCAACGCTTTTTC 60.664 55.000 0.00 0.00 40.13 2.29
77 78 0.998727 GCCTCTGCAACGCTTTTTCG 60.999 55.000 0.00 0.00 37.47 3.46
78 79 0.307760 CCTCTGCAACGCTTTTTCGT 59.692 50.000 0.00 0.00 45.58 3.85
79 80 1.529438 CCTCTGCAACGCTTTTTCGTA 59.471 47.619 0.00 0.00 42.46 3.43
80 81 2.032377 CCTCTGCAACGCTTTTTCGTAA 60.032 45.455 0.00 0.00 42.46 3.18
81 82 3.364964 CCTCTGCAACGCTTTTTCGTAAT 60.365 43.478 0.00 0.00 42.46 1.89
82 83 4.142988 CCTCTGCAACGCTTTTTCGTAATA 60.143 41.667 0.00 0.00 42.46 0.98
83 84 4.704457 TCTGCAACGCTTTTTCGTAATAC 58.296 39.130 0.00 0.00 42.46 1.89
84 85 4.449743 TCTGCAACGCTTTTTCGTAATACT 59.550 37.500 0.00 0.00 42.46 2.12
85 86 4.704457 TGCAACGCTTTTTCGTAATACTC 58.296 39.130 0.00 0.00 42.46 2.59
86 87 4.086574 GCAACGCTTTTTCGTAATACTCC 58.913 43.478 0.00 0.00 42.46 3.85
87 88 4.644954 CAACGCTTTTTCGTAATACTCCC 58.355 43.478 0.00 0.00 42.46 4.30
88 89 4.198028 ACGCTTTTTCGTAATACTCCCT 57.802 40.909 0.00 0.00 41.36 4.20
89 90 4.179298 ACGCTTTTTCGTAATACTCCCTC 58.821 43.478 0.00 0.00 41.36 4.30
90 91 3.554731 CGCTTTTTCGTAATACTCCCTCC 59.445 47.826 0.00 0.00 0.00 4.30
91 92 3.554731 GCTTTTTCGTAATACTCCCTCCG 59.445 47.826 0.00 0.00 0.00 4.63
92 93 4.752146 CTTTTTCGTAATACTCCCTCCGT 58.248 43.478 0.00 0.00 0.00 4.69
93 94 4.806640 TTTTCGTAATACTCCCTCCGTT 57.193 40.909 0.00 0.00 0.00 4.44
94 95 4.376340 TTTCGTAATACTCCCTCCGTTC 57.624 45.455 0.00 0.00 0.00 3.95
95 96 2.301346 TCGTAATACTCCCTCCGTTCC 58.699 52.381 0.00 0.00 0.00 3.62
96 97 2.026641 CGTAATACTCCCTCCGTTCCA 58.973 52.381 0.00 0.00 0.00 3.53
97 98 2.626743 CGTAATACTCCCTCCGTTCCAT 59.373 50.000 0.00 0.00 0.00 3.41
98 99 3.822735 CGTAATACTCCCTCCGTTCCATA 59.177 47.826 0.00 0.00 0.00 2.74
99 100 4.279169 CGTAATACTCCCTCCGTTCCATAA 59.721 45.833 0.00 0.00 0.00 1.90
100 101 4.684484 AATACTCCCTCCGTTCCATAAC 57.316 45.455 0.00 0.00 0.00 1.89
125 126 8.857216 ACGTAGTACATTTAGATTTTCTGAACG 58.143 33.333 0.38 0.00 41.94 3.95
126 127 7.839837 CGTAGTACATTTAGATTTTCTGAACGC 59.160 37.037 0.38 0.00 0.00 4.84
127 128 7.667043 AGTACATTTAGATTTTCTGAACGCA 57.333 32.000 0.00 0.00 0.00 5.24
128 129 7.519002 AGTACATTTAGATTTTCTGAACGCAC 58.481 34.615 0.00 0.00 0.00 5.34
129 130 5.699839 ACATTTAGATTTTCTGAACGCACC 58.300 37.500 0.00 0.00 0.00 5.01
130 131 4.398549 TTTAGATTTTCTGAACGCACCG 57.601 40.909 0.00 0.00 0.00 4.94
131 132 1.878953 AGATTTTCTGAACGCACCGT 58.121 45.000 0.00 0.00 43.97 4.83
132 133 1.531149 AGATTTTCTGAACGCACCGTG 59.469 47.619 0.00 0.00 39.99 4.94
133 134 1.529438 GATTTTCTGAACGCACCGTGA 59.471 47.619 1.65 0.00 39.99 4.35
134 135 0.934496 TTTTCTGAACGCACCGTGAG 59.066 50.000 1.65 0.82 39.99 3.51
135 136 0.179094 TTTCTGAACGCACCGTGAGT 60.179 50.000 1.65 1.61 39.99 3.41
136 137 0.179094 TTCTGAACGCACCGTGAGTT 60.179 50.000 19.05 19.05 42.92 3.01
137 138 0.179094 TCTGAACGCACCGTGAGTTT 60.179 50.000 19.80 6.05 40.39 2.66
138 139 0.232303 CTGAACGCACCGTGAGTTTC 59.768 55.000 19.80 13.72 40.39 2.78
139 140 0.179094 TGAACGCACCGTGAGTTTCT 60.179 50.000 19.80 0.13 40.39 2.52
140 141 0.935196 GAACGCACCGTGAGTTTCTT 59.065 50.000 19.80 0.00 40.39 2.52
141 142 0.655733 AACGCACCGTGAGTTTCTTG 59.344 50.000 14.13 0.00 37.06 3.02
142 143 1.157870 ACGCACCGTGAGTTTCTTGG 61.158 55.000 1.65 0.00 39.18 3.61
143 144 0.878523 CGCACCGTGAGTTTCTTGGA 60.879 55.000 1.65 0.00 0.00 3.53
144 145 0.868406 GCACCGTGAGTTTCTTGGAG 59.132 55.000 1.65 0.00 0.00 3.86
145 146 0.868406 CACCGTGAGTTTCTTGGAGC 59.132 55.000 0.00 0.00 0.00 4.70
146 147 0.250338 ACCGTGAGTTTCTTGGAGCC 60.250 55.000 0.00 0.00 0.00 4.70
147 148 0.035458 CCGTGAGTTTCTTGGAGCCT 59.965 55.000 0.00 0.00 0.00 4.58
148 149 1.151668 CGTGAGTTTCTTGGAGCCTG 58.848 55.000 0.00 0.00 0.00 4.85
149 150 1.528129 GTGAGTTTCTTGGAGCCTGG 58.472 55.000 0.00 0.00 0.00 4.45
150 151 0.250901 TGAGTTTCTTGGAGCCTGGC 60.251 55.000 11.65 11.65 0.00 4.85
151 152 0.962855 GAGTTTCTTGGAGCCTGGCC 60.963 60.000 16.57 6.85 0.00 5.36
152 153 2.034066 TTTCTTGGAGCCTGGCCG 59.966 61.111 16.57 0.00 0.00 6.13
153 154 3.567579 TTTCTTGGAGCCTGGCCGG 62.568 63.158 16.57 3.88 0.00 6.13
155 156 4.033776 CTTGGAGCCTGGCCGGAA 62.034 66.667 15.09 4.37 33.16 4.30
156 157 3.338250 TTGGAGCCTGGCCGGAAT 61.338 61.111 15.09 0.00 33.16 3.01
157 158 1.983119 CTTGGAGCCTGGCCGGAATA 61.983 60.000 15.09 0.00 33.16 1.75
158 159 1.567208 TTGGAGCCTGGCCGGAATAA 61.567 55.000 15.09 0.00 33.16 1.40
159 160 1.227973 GGAGCCTGGCCGGAATAAG 60.228 63.158 15.09 0.00 33.16 1.73
160 161 1.696097 GGAGCCTGGCCGGAATAAGA 61.696 60.000 15.09 0.00 33.16 2.10
161 162 0.533085 GAGCCTGGCCGGAATAAGAC 60.533 60.000 15.09 0.00 33.16 3.01
162 163 1.526225 GCCTGGCCGGAATAAGACC 60.526 63.158 15.09 0.00 33.16 3.85
163 164 1.912220 CCTGGCCGGAATAAGACCA 59.088 57.895 15.09 0.00 33.16 4.02
164 165 0.463833 CCTGGCCGGAATAAGACCAC 60.464 60.000 15.09 0.00 33.16 4.16
165 166 0.251916 CTGGCCGGAATAAGACCACA 59.748 55.000 5.28 0.00 0.00 4.17
166 167 0.693622 TGGCCGGAATAAGACCACAA 59.306 50.000 5.05 0.00 0.00 3.33
167 168 1.074084 TGGCCGGAATAAGACCACAAA 59.926 47.619 5.05 0.00 0.00 2.83
168 169 1.471287 GGCCGGAATAAGACCACAAAC 59.529 52.381 5.05 0.00 0.00 2.93
169 170 2.433436 GCCGGAATAAGACCACAAACT 58.567 47.619 5.05 0.00 0.00 2.66
170 171 2.817844 GCCGGAATAAGACCACAAACTT 59.182 45.455 5.05 0.00 0.00 2.66
171 172 3.254903 GCCGGAATAAGACCACAAACTTT 59.745 43.478 5.05 0.00 0.00 2.66
172 173 4.615223 GCCGGAATAAGACCACAAACTTTC 60.615 45.833 5.05 0.00 0.00 2.62
173 174 4.517453 CCGGAATAAGACCACAAACTTTCA 59.483 41.667 0.00 0.00 0.00 2.69
215 216 7.604657 ACACTGTTTTAAATATTGGTTCCCA 57.395 32.000 0.00 0.00 0.00 4.37
352 354 4.336889 TGTCAGTCTTTTCTCGTTGGAT 57.663 40.909 0.00 0.00 0.00 3.41
540 592 0.965866 AGTTCTGCGGATGGAGACGA 60.966 55.000 0.00 0.00 42.81 4.20
550 602 3.823330 GGAGACGACGCCACGGAT 61.823 66.667 2.39 0.00 36.03 4.18
832 906 1.303074 CTTGGCAGCAGCTTCAGGA 60.303 57.895 0.00 0.00 41.70 3.86
954 1037 6.798427 AGCTGTGTATTTGAGGAAGAGATA 57.202 37.500 0.00 0.00 0.00 1.98
1356 6362 7.232910 TGATTATTGCATATTGTGATCCCTCA 58.767 34.615 0.00 0.00 0.00 3.86
1491 6512 7.675161 TGAGGAGAATATGTATGAAGTGGAA 57.325 36.000 0.00 0.00 0.00 3.53
1703 6755 6.013379 TGACAAAAGGCTTTACATATCCCAA 58.987 36.000 13.77 0.00 0.00 4.12
1756 6808 6.428465 TCAGCATGCAATCAAACATGAATTTT 59.572 30.769 21.98 0.00 45.23 1.82
1976 7036 7.030768 TCTCTTTTTAAGGTGAACAAAAACCG 58.969 34.615 0.00 0.00 41.61 4.44
2216 7277 4.527816 TGGGATAGCAGCTTTGACAATTTT 59.472 37.500 0.00 0.00 0.00 1.82
2217 7278 4.866486 GGGATAGCAGCTTTGACAATTTTG 59.134 41.667 0.00 0.00 0.00 2.44
2221 7282 7.975616 GGATAGCAGCTTTGACAATTTTGATAA 59.024 33.333 0.00 0.00 0.00 1.75
2338 7400 3.784338 TCTTTGCTTTGAAACCTTGCAG 58.216 40.909 0.00 0.00 35.02 4.41
2670 7732 8.735315 TGTCAAACTTCAAGAAAAAGTATCACA 58.265 29.630 0.00 0.00 35.96 3.58
2671 7733 9.736023 GTCAAACTTCAAGAAAAAGTATCACAT 57.264 29.630 0.00 0.00 35.96 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.444895 CTGCATTTTGCCGACCTGC 60.445 57.895 0.00 0.00 44.23 4.85
1 2 1.213537 CCTGCATTTTGCCGACCTG 59.786 57.895 0.00 0.00 44.23 4.00
2 3 1.978617 CCCTGCATTTTGCCGACCT 60.979 57.895 0.00 0.00 44.23 3.85
3 4 2.212900 GACCCTGCATTTTGCCGACC 62.213 60.000 0.00 0.00 44.23 4.79
6 7 2.179018 CGACCCTGCATTTTGCCG 59.821 61.111 0.00 0.00 44.23 5.69
7 8 2.573340 CCGACCCTGCATTTTGCC 59.427 61.111 0.00 0.00 44.23 4.52
8 9 1.312371 TAGCCGACCCTGCATTTTGC 61.312 55.000 0.00 0.00 45.29 3.68
9 10 0.734889 CTAGCCGACCCTGCATTTTG 59.265 55.000 0.00 0.00 0.00 2.44
10 11 0.618458 TCTAGCCGACCCTGCATTTT 59.382 50.000 0.00 0.00 0.00 1.82
11 12 0.179000 CTCTAGCCGACCCTGCATTT 59.821 55.000 0.00 0.00 0.00 2.32
12 13 0.978146 ACTCTAGCCGACCCTGCATT 60.978 55.000 0.00 0.00 0.00 3.56
13 14 0.978146 AACTCTAGCCGACCCTGCAT 60.978 55.000 0.00 0.00 0.00 3.96
14 15 1.609501 AACTCTAGCCGACCCTGCA 60.610 57.895 0.00 0.00 0.00 4.41
15 16 1.153549 CAACTCTAGCCGACCCTGC 60.154 63.158 0.00 0.00 0.00 4.85
16 17 1.153549 GCAACTCTAGCCGACCCTG 60.154 63.158 0.00 0.00 0.00 4.45
17 18 1.305381 AGCAACTCTAGCCGACCCT 60.305 57.895 0.00 0.00 0.00 4.34
18 19 1.142097 GAGCAACTCTAGCCGACCC 59.858 63.158 0.00 0.00 0.00 4.46
19 20 0.533032 AAGAGCAACTCTAGCCGACC 59.467 55.000 0.00 0.00 40.28 4.79
20 21 2.223618 CCTAAGAGCAACTCTAGCCGAC 60.224 54.545 0.00 0.00 40.28 4.79
21 22 2.025155 CCTAAGAGCAACTCTAGCCGA 58.975 52.381 0.00 0.00 40.28 5.54
22 23 2.025155 TCCTAAGAGCAACTCTAGCCG 58.975 52.381 0.00 0.00 40.28 5.52
23 24 3.726291 CTCCTAAGAGCAACTCTAGCC 57.274 52.381 0.00 0.00 40.28 3.93
34 35 3.219281 GTCTCCAGGTAGCTCCTAAGAG 58.781 54.545 16.88 16.88 46.24 2.85
35 36 2.091775 GGTCTCCAGGTAGCTCCTAAGA 60.092 54.545 0.00 1.23 46.24 2.10
36 37 2.312390 GGTCTCCAGGTAGCTCCTAAG 58.688 57.143 0.00 0.00 46.24 2.18
37 38 1.409802 CGGTCTCCAGGTAGCTCCTAA 60.410 57.143 0.00 0.00 46.24 2.69
38 39 0.183014 CGGTCTCCAGGTAGCTCCTA 59.817 60.000 0.00 0.00 46.24 2.94
40 41 2.128507 CCGGTCTCCAGGTAGCTCC 61.129 68.421 0.00 0.00 0.00 4.70
41 42 2.787567 GCCGGTCTCCAGGTAGCTC 61.788 68.421 1.90 0.00 0.00 4.09
42 43 2.760385 GCCGGTCTCCAGGTAGCT 60.760 66.667 1.90 0.00 0.00 3.32
43 44 3.851128 GGCCGGTCTCCAGGTAGC 61.851 72.222 1.90 0.00 0.00 3.58
44 45 2.042843 AGGCCGGTCTCCAGGTAG 60.043 66.667 0.35 0.00 0.00 3.18
45 46 2.043248 GAGGCCGGTCTCCAGGTA 60.043 66.667 26.14 0.00 0.00 3.08
46 47 3.999285 AGAGGCCGGTCTCCAGGT 61.999 66.667 32.04 11.42 34.46 4.00
47 48 3.465403 CAGAGGCCGGTCTCCAGG 61.465 72.222 32.04 18.22 34.46 4.45
48 49 4.154347 GCAGAGGCCGGTCTCCAG 62.154 72.222 32.04 24.86 34.46 3.86
50 51 3.706373 TTGCAGAGGCCGGTCTCC 61.706 66.667 32.04 18.40 40.13 3.71
51 52 2.435059 GTTGCAGAGGCCGGTCTC 60.435 66.667 29.00 29.00 40.13 3.36
52 53 4.379243 CGTTGCAGAGGCCGGTCT 62.379 66.667 9.26 9.26 40.13 3.85
56 57 2.406452 AAAAAGCGTTGCAGAGGCCG 62.406 55.000 0.00 0.00 39.95 6.13
57 58 0.664466 GAAAAAGCGTTGCAGAGGCC 60.664 55.000 0.00 0.00 39.95 5.19
58 59 0.998727 CGAAAAAGCGTTGCAGAGGC 60.999 55.000 5.72 5.72 39.41 4.70
59 60 0.307760 ACGAAAAAGCGTTGCAGAGG 59.692 50.000 0.00 0.00 42.71 3.69
60 61 2.941891 TACGAAAAAGCGTTGCAGAG 57.058 45.000 0.00 0.00 42.71 3.35
61 62 3.889196 ATTACGAAAAAGCGTTGCAGA 57.111 38.095 0.00 0.00 42.71 4.26
62 63 4.708601 AGTATTACGAAAAAGCGTTGCAG 58.291 39.130 0.00 0.00 42.71 4.41
63 64 4.377635 GGAGTATTACGAAAAAGCGTTGCA 60.378 41.667 0.00 0.00 42.71 4.08
64 65 4.086574 GGAGTATTACGAAAAAGCGTTGC 58.913 43.478 0.00 0.00 42.71 4.17
65 66 4.390909 AGGGAGTATTACGAAAAAGCGTTG 59.609 41.667 0.00 0.00 42.71 4.10
66 67 4.572909 AGGGAGTATTACGAAAAAGCGTT 58.427 39.130 0.00 0.00 42.71 4.84
68 69 3.554731 GGAGGGAGTATTACGAAAAAGCG 59.445 47.826 0.00 0.00 37.29 4.68
69 70 3.554731 CGGAGGGAGTATTACGAAAAAGC 59.445 47.826 0.00 0.00 0.00 3.51
70 71 4.752146 ACGGAGGGAGTATTACGAAAAAG 58.248 43.478 0.00 0.00 0.00 2.27
71 72 4.806640 ACGGAGGGAGTATTACGAAAAA 57.193 40.909 0.00 0.00 0.00 1.94
72 73 4.381932 GGAACGGAGGGAGTATTACGAAAA 60.382 45.833 0.00 0.00 0.00 2.29
73 74 3.131046 GGAACGGAGGGAGTATTACGAAA 59.869 47.826 0.00 0.00 0.00 3.46
74 75 2.689983 GGAACGGAGGGAGTATTACGAA 59.310 50.000 0.00 0.00 0.00 3.85
75 76 2.301346 GGAACGGAGGGAGTATTACGA 58.699 52.381 0.00 0.00 0.00 3.43
76 77 2.026641 TGGAACGGAGGGAGTATTACG 58.973 52.381 0.00 0.00 0.00 3.18
77 78 5.536260 GTTATGGAACGGAGGGAGTATTAC 58.464 45.833 0.00 0.00 0.00 1.89
78 79 5.796424 GTTATGGAACGGAGGGAGTATTA 57.204 43.478 0.00 0.00 0.00 0.98
79 80 4.684484 GTTATGGAACGGAGGGAGTATT 57.316 45.455 0.00 0.00 0.00 1.89
99 100 8.857216 CGTTCAGAAAATCTAAATGTACTACGT 58.143 33.333 0.00 0.00 0.00 3.57
100 101 7.839837 GCGTTCAGAAAATCTAAATGTACTACG 59.160 37.037 0.00 0.00 0.00 3.51
101 102 8.653338 TGCGTTCAGAAAATCTAAATGTACTAC 58.347 33.333 0.00 0.00 0.00 2.73
102 103 8.653338 GTGCGTTCAGAAAATCTAAATGTACTA 58.347 33.333 0.00 0.00 0.00 1.82
103 104 7.360946 GGTGCGTTCAGAAAATCTAAATGTACT 60.361 37.037 4.43 0.00 0.00 2.73
104 105 6.741358 GGTGCGTTCAGAAAATCTAAATGTAC 59.259 38.462 0.00 0.00 0.00 2.90
105 106 6.401688 CGGTGCGTTCAGAAAATCTAAATGTA 60.402 38.462 0.00 0.00 0.00 2.29
106 107 5.616866 CGGTGCGTTCAGAAAATCTAAATGT 60.617 40.000 0.00 0.00 0.00 2.71
107 108 4.788100 CGGTGCGTTCAGAAAATCTAAATG 59.212 41.667 0.00 0.00 0.00 2.32
108 109 4.454504 ACGGTGCGTTCAGAAAATCTAAAT 59.545 37.500 0.00 0.00 36.35 1.40
109 110 3.810941 ACGGTGCGTTCAGAAAATCTAAA 59.189 39.130 0.00 0.00 36.35 1.85
110 111 3.185594 CACGGTGCGTTCAGAAAATCTAA 59.814 43.478 0.00 0.00 38.32 2.10
111 112 2.734606 CACGGTGCGTTCAGAAAATCTA 59.265 45.455 0.00 0.00 38.32 1.98
112 113 1.531149 CACGGTGCGTTCAGAAAATCT 59.469 47.619 0.00 0.00 38.32 2.40
113 114 1.529438 TCACGGTGCGTTCAGAAAATC 59.471 47.619 2.51 0.00 38.32 2.17
114 115 1.531149 CTCACGGTGCGTTCAGAAAAT 59.469 47.619 2.51 0.00 38.32 1.82
115 116 0.934496 CTCACGGTGCGTTCAGAAAA 59.066 50.000 2.51 0.00 38.32 2.29
116 117 0.179094 ACTCACGGTGCGTTCAGAAA 60.179 50.000 2.51 0.00 38.32 2.52
117 118 0.179094 AACTCACGGTGCGTTCAGAA 60.179 50.000 10.50 0.00 38.32 3.02
118 119 0.179094 AAACTCACGGTGCGTTCAGA 60.179 50.000 15.98 0.00 38.32 3.27
119 120 0.232303 GAAACTCACGGTGCGTTCAG 59.768 55.000 15.98 4.76 38.32 3.02
120 121 0.179094 AGAAACTCACGGTGCGTTCA 60.179 50.000 15.98 0.00 38.32 3.18
121 122 0.935196 AAGAAACTCACGGTGCGTTC 59.065 50.000 15.98 12.05 38.32 3.95
122 123 0.655733 CAAGAAACTCACGGTGCGTT 59.344 50.000 10.50 10.50 38.32 4.84
123 124 1.157870 CCAAGAAACTCACGGTGCGT 61.158 55.000 2.51 0.00 42.36 5.24
124 125 0.878523 TCCAAGAAACTCACGGTGCG 60.879 55.000 2.51 0.00 0.00 5.34
125 126 0.868406 CTCCAAGAAACTCACGGTGC 59.132 55.000 2.51 0.00 0.00 5.01
126 127 0.868406 GCTCCAAGAAACTCACGGTG 59.132 55.000 0.56 0.56 0.00 4.94
127 128 0.250338 GGCTCCAAGAAACTCACGGT 60.250 55.000 0.00 0.00 0.00 4.83
128 129 0.035458 AGGCTCCAAGAAACTCACGG 59.965 55.000 0.00 0.00 0.00 4.94
129 130 1.151668 CAGGCTCCAAGAAACTCACG 58.848 55.000 0.00 0.00 0.00 4.35
130 131 1.528129 CCAGGCTCCAAGAAACTCAC 58.472 55.000 0.00 0.00 0.00 3.51
131 132 0.250901 GCCAGGCTCCAAGAAACTCA 60.251 55.000 3.29 0.00 0.00 3.41
132 133 0.962855 GGCCAGGCTCCAAGAAACTC 60.963 60.000 12.43 0.00 0.00 3.01
133 134 1.075659 GGCCAGGCTCCAAGAAACT 59.924 57.895 12.43 0.00 0.00 2.66
134 135 2.335712 CGGCCAGGCTCCAAGAAAC 61.336 63.158 12.43 0.00 0.00 2.78
135 136 2.034066 CGGCCAGGCTCCAAGAAA 59.966 61.111 12.43 0.00 0.00 2.52
136 137 4.033776 CCGGCCAGGCTCCAAGAA 62.034 66.667 12.43 0.00 0.00 2.52
138 139 1.983119 TATTCCGGCCAGGCTCCAAG 61.983 60.000 12.43 0.00 40.77 3.61
139 140 1.567208 TTATTCCGGCCAGGCTCCAA 61.567 55.000 12.43 1.46 40.77 3.53
140 141 1.983119 CTTATTCCGGCCAGGCTCCA 61.983 60.000 12.43 0.00 40.77 3.86
141 142 1.227973 CTTATTCCGGCCAGGCTCC 60.228 63.158 12.43 0.00 40.77 4.70
142 143 0.533085 GTCTTATTCCGGCCAGGCTC 60.533 60.000 12.43 0.00 40.77 4.70
143 144 1.527370 GTCTTATTCCGGCCAGGCT 59.473 57.895 12.43 0.00 40.77 4.58
144 145 1.526225 GGTCTTATTCCGGCCAGGC 60.526 63.158 1.26 1.26 40.77 4.85
145 146 0.463833 GTGGTCTTATTCCGGCCAGG 60.464 60.000 2.24 5.27 42.97 4.45
146 147 0.251916 TGTGGTCTTATTCCGGCCAG 59.748 55.000 2.24 0.00 0.00 4.85
147 148 0.693622 TTGTGGTCTTATTCCGGCCA 59.306 50.000 2.24 0.00 0.00 5.36
148 149 1.471287 GTTTGTGGTCTTATTCCGGCC 59.529 52.381 0.00 0.00 0.00 6.13
149 150 2.433436 AGTTTGTGGTCTTATTCCGGC 58.567 47.619 0.00 0.00 0.00 6.13
150 151 4.517453 TGAAAGTTTGTGGTCTTATTCCGG 59.483 41.667 0.00 0.00 0.00 5.14
151 152 5.682943 TGAAAGTTTGTGGTCTTATTCCG 57.317 39.130 0.00 0.00 0.00 4.30
152 153 7.272037 TCTTGAAAGTTTGTGGTCTTATTCC 57.728 36.000 0.00 0.00 0.00 3.01
153 154 9.581099 TTTTCTTGAAAGTTTGTGGTCTTATTC 57.419 29.630 0.00 0.00 0.00 1.75
156 157 9.581099 GAATTTTCTTGAAAGTTTGTGGTCTTA 57.419 29.630 0.00 0.00 0.00 2.10
157 158 7.549134 GGAATTTTCTTGAAAGTTTGTGGTCTT 59.451 33.333 0.00 0.00 0.00 3.01
158 159 7.041721 GGAATTTTCTTGAAAGTTTGTGGTCT 58.958 34.615 0.00 0.00 0.00 3.85
159 160 7.041721 AGGAATTTTCTTGAAAGTTTGTGGTC 58.958 34.615 0.00 0.00 0.00 4.02
160 161 6.946340 AGGAATTTTCTTGAAAGTTTGTGGT 58.054 32.000 0.00 0.00 0.00 4.16
161 162 7.848223 AAGGAATTTTCTTGAAAGTTTGTGG 57.152 32.000 0.00 0.00 0.00 4.17
338 340 6.322491 GGGTAATTTCATCCAACGAGAAAAG 58.678 40.000 0.00 0.00 35.20 2.27
352 354 6.841755 TCTTTTTCCTCAAAGGGGTAATTTCA 59.158 34.615 0.00 0.00 35.59 2.69
496 548 3.612247 ATCCATAGCCATCCGCCGC 62.612 63.158 0.00 0.00 38.78 6.53
497 549 1.742880 CATCCATAGCCATCCGCCG 60.743 63.158 0.00 0.00 38.78 6.46
498 550 1.377725 CCATCCATAGCCATCCGCC 60.378 63.158 0.00 0.00 38.78 6.13
499 551 2.042831 GCCATCCATAGCCATCCGC 61.043 63.158 0.00 0.00 37.98 5.54
504 556 3.480679 CTGCCGCCATCCATAGCCA 62.481 63.158 0.00 0.00 0.00 4.75
545 597 4.856801 GCCATGGCCGTCATCCGT 62.857 66.667 27.24 0.00 32.92 4.69
624 694 4.640690 ACCTGACCTCAGCCCCGT 62.641 66.667 0.00 0.00 42.47 5.28
803 877 1.071471 CTGCCAAGAACGACCCAGT 59.929 57.895 0.00 0.00 0.00 4.00
832 906 1.671742 CAACTGAGTACCGCCCTGT 59.328 57.895 0.00 0.00 0.00 4.00
960 1043 8.615211 CAATCTGATCATCAACCGAAATTAAGA 58.385 33.333 0.00 0.00 0.00 2.10
1356 6362 2.836981 GGTGATAGGCTCATATGGCTCT 59.163 50.000 13.60 11.58 42.90 4.09
1491 6512 3.392616 CCACATCTAAGGGCATAGGTTCT 59.607 47.826 0.00 0.00 0.00 3.01
1703 6755 3.953612 TGCCAACTTGAACTCTTTCATGT 59.046 39.130 0.00 1.24 46.74 3.21
1756 6808 8.651389 AGGTGTACTATACTCGGTGTTATACTA 58.349 37.037 0.00 0.00 0.00 1.82
1976 7036 4.701765 ACTAGAGCAATCATGACCACATC 58.298 43.478 0.00 0.00 34.15 3.06
2216 7277 9.906660 ATTTCAACTTGCGATTTAAACTTATCA 57.093 25.926 0.00 0.00 0.00 2.15
2221 7282 7.875971 AGAGATTTCAACTTGCGATTTAAACT 58.124 30.769 0.00 0.00 0.00 2.66
2251 7312 4.694760 TCAATCTGCACTATGCTACCAT 57.305 40.909 2.02 0.00 45.31 3.55
2296 7358 8.633561 CAAAGAAGAACCTTCTAAACCTGATTT 58.366 33.333 9.36 0.00 36.28 2.17
2297 7359 7.255625 GCAAAGAAGAACCTTCTAAACCTGATT 60.256 37.037 9.36 0.00 36.28 2.57
2338 7400 3.879892 GCAACCACTAAGGAATCCATCTC 59.120 47.826 0.61 0.00 41.22 2.75
2537 7599 2.044555 GGCTAAACCCCTTGGCGAC 61.045 63.158 0.00 0.00 42.24 5.19
2608 7670 6.569127 TGCATTCCCTATGTTTTACCTCTA 57.431 37.500 0.00 0.00 36.57 2.43
2670 7732 8.917088 CCAAAGATGGTCATCAAATACCTTTAT 58.083 33.333 12.75 0.00 42.18 1.40
2671 7733 7.341769 CCCAAAGATGGTCATCAAATACCTTTA 59.658 37.037 12.75 0.00 46.01 1.85


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

AutoCloner maintained by Alex Coulton.