Multiple sequence alignment - TraesCS2D01G225900

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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 TraesCS2D01G225900 chr2D 100.000 3164 0 0 1 3164 194048112 194044949 0.000000e+00 5843.0
1 TraesCS2D01G225900 chr2B 93.182 1540 51 12 723 2221 249670400 249668874 0.000000e+00 2213.0
2 TraesCS2D01G225900 chr2B 94.271 384 10 7 327 698 249670775 249670392 7.610000e-161 577.0
3 TraesCS2D01G225900 chr2B 94.194 155 9 0 179 333 249670954 249670800 1.470000e-58 237.0
4 TraesCS2D01G225900 chr2A 95.070 1420 34 8 802 2218 207654950 207653564 0.000000e+00 2202.0
5 TraesCS2D01G225900 chr2A 95.539 964 23 6 2219 3164 207653495 207652534 0.000000e+00 1524.0
6 TraesCS2D01G225900 chr2A 95.767 378 10 3 327 698 207657880 207657503 3.490000e-169 604.0
7 TraesCS2D01G225900 chr2A 93.985 133 8 0 201 333 207658037 207657905 5.350000e-48 202.0
8 TraesCS2D01G225900 chr1D 95.000 40 2 0 2134 2173 7895621 7895660 2.630000e-06 63.9


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 TraesCS2D01G225900 chr2D 194044949 194048112 3163 True 5843 5843 100.000000 1 3164 1 chr2D.!!$R1 3163
1 TraesCS2D01G225900 chr2B 249668874 249670954 2080 True 1009 2213 93.882333 179 2221 3 chr2B.!!$R1 2042
2 TraesCS2D01G225900 chr2A 207652534 207658037 5503 True 1133 2202 95.090250 201 3164 4 chr2A.!!$R1 2963

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
158 159 0.032815 CCAAACGGGCGGACAAAATT 59.967 50.0 0.0 0.0 0.0 1.82 F
169 170 0.386731 GACAAAATTGGTCGCCCGTG 60.387 55.0 0.0 0.0 0.0 4.94 F
1988 4543 0.609662 GCCCTGTGTTTGGAATGCAT 59.390 50.0 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 4613 0.958091 TTCATGTTTGGAACGCAGGG 59.042 50.0 0.00 0.00 0.00 4.45 R
2117 4676 5.752955 GCACACTGTATGTTTTGGTCAATTT 59.247 36.0 0.00 0.00 40.64 1.82 R
2864 5508 0.386476 CTAATGCATGGCCATTGCGT 59.614 50.0 25.25 23.61 36.21 5.24 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
24 25 4.065281 GGACACCGAGGGGACACG 62.065 72.222 0.00 0.00 44.43 4.49
25 26 4.736896 GACACCGAGGGGACACGC 62.737 72.222 0.00 0.00 43.43 5.34
47 48 2.736995 CGTCCGCACCGACACATT 60.737 61.111 0.00 0.00 32.74 2.71
48 49 2.314647 CGTCCGCACCGACACATTT 61.315 57.895 0.00 0.00 32.74 2.32
49 50 1.206578 GTCCGCACCGACACATTTG 59.793 57.895 0.00 0.00 32.74 2.32
50 51 1.069935 TCCGCACCGACACATTTGA 59.930 52.632 0.00 0.00 0.00 2.69
51 52 0.948623 TCCGCACCGACACATTTGAG 60.949 55.000 0.00 0.00 0.00 3.02
52 53 1.154413 CGCACCGACACATTTGAGC 60.154 57.895 0.00 0.00 0.00 4.26
53 54 1.210155 GCACCGACACATTTGAGCC 59.790 57.895 0.00 0.00 0.00 4.70
54 55 1.497278 CACCGACACATTTGAGCCG 59.503 57.895 0.00 0.00 0.00 5.52
55 56 1.070786 ACCGACACATTTGAGCCGT 59.929 52.632 0.00 0.00 0.00 5.68
56 57 0.319083 ACCGACACATTTGAGCCGTA 59.681 50.000 0.00 0.00 0.00 4.02
57 58 1.270412 ACCGACACATTTGAGCCGTAA 60.270 47.619 0.00 0.00 0.00 3.18
58 59 1.801771 CCGACACATTTGAGCCGTAAA 59.198 47.619 0.00 0.00 0.00 2.01
59 60 2.418628 CCGACACATTTGAGCCGTAAAT 59.581 45.455 0.00 0.00 0.00 1.40
60 61 3.119990 CCGACACATTTGAGCCGTAAATT 60.120 43.478 0.00 0.00 0.00 1.82
61 62 4.472286 CGACACATTTGAGCCGTAAATTT 58.528 39.130 0.00 0.00 0.00 1.82
62 63 4.320690 CGACACATTTGAGCCGTAAATTTG 59.679 41.667 0.00 0.00 33.59 2.32
63 64 5.446143 ACACATTTGAGCCGTAAATTTGA 57.554 34.783 0.00 0.00 32.42 2.69
64 65 5.460646 ACACATTTGAGCCGTAAATTTGAG 58.539 37.500 0.00 0.00 32.42 3.02
65 66 4.324402 CACATTTGAGCCGTAAATTTGAGC 59.676 41.667 0.00 0.90 30.58 4.26
66 67 3.569250 TTTGAGCCGTAAATTTGAGCC 57.431 42.857 0.00 0.00 0.00 4.70
67 68 1.083489 TGAGCCGTAAATTTGAGCCG 58.917 50.000 0.00 0.00 0.00 5.52
68 69 0.377203 GAGCCGTAAATTTGAGCCGG 59.623 55.000 0.00 0.00 41.50 6.13
69 70 0.035820 AGCCGTAAATTTGAGCCGGA 60.036 50.000 5.05 0.00 41.08 5.14
70 71 0.806241 GCCGTAAATTTGAGCCGGAA 59.194 50.000 5.05 0.00 41.08 4.30
71 72 1.200484 GCCGTAAATTTGAGCCGGAAA 59.800 47.619 5.05 0.00 41.08 3.13
72 73 2.159296 GCCGTAAATTTGAGCCGGAAAT 60.159 45.455 5.05 0.00 41.08 2.17
73 74 3.434637 CCGTAAATTTGAGCCGGAAATG 58.565 45.455 5.05 0.00 41.08 2.32
74 75 3.434637 CGTAAATTTGAGCCGGAAATGG 58.565 45.455 5.05 0.00 0.00 3.16
75 76 3.733684 CGTAAATTTGAGCCGGAAATGGG 60.734 47.826 5.05 0.00 0.00 4.00
76 77 1.937191 AATTTGAGCCGGAAATGGGT 58.063 45.000 5.05 0.00 43.87 4.51
77 78 1.937191 ATTTGAGCCGGAAATGGGTT 58.063 45.000 5.05 0.00 40.53 4.11
78 79 1.253100 TTTGAGCCGGAAATGGGTTC 58.747 50.000 5.05 0.00 40.53 3.62
79 80 0.958382 TTGAGCCGGAAATGGGTTCG 60.958 55.000 5.05 0.00 40.53 3.95
80 81 1.376812 GAGCCGGAAATGGGTTCGT 60.377 57.895 5.05 0.00 40.53 3.85
81 82 1.644786 GAGCCGGAAATGGGTTCGTG 61.645 60.000 5.05 0.00 40.53 4.35
82 83 2.874751 CCGGAAATGGGTTCGTGC 59.125 61.111 0.00 0.00 37.08 5.34
83 84 2.478746 CGGAAATGGGTTCGTGCG 59.521 61.111 0.00 0.00 37.08 5.34
84 85 2.874751 GGAAATGGGTTCGTGCGG 59.125 61.111 0.00 0.00 37.08 5.69
85 86 1.673009 GGAAATGGGTTCGTGCGGA 60.673 57.895 0.00 0.00 37.08 5.54
86 87 1.500396 GAAATGGGTTCGTGCGGAC 59.500 57.895 0.00 0.00 0.00 4.79
87 88 1.228003 AAATGGGTTCGTGCGGACA 60.228 52.632 8.11 0.00 0.00 4.02
88 89 1.512156 AAATGGGTTCGTGCGGACAC 61.512 55.000 8.11 1.49 43.76 3.67
96 97 2.330041 GTGCGGACACGTTTTGGG 59.670 61.111 0.63 0.00 43.45 4.12
97 98 2.181521 GTGCGGACACGTTTTGGGA 61.182 57.895 0.63 0.00 43.45 4.37
98 99 1.451567 TGCGGACACGTTTTGGGAA 60.452 52.632 0.00 0.00 43.45 3.97
99 100 0.820074 TGCGGACACGTTTTGGGAAT 60.820 50.000 0.00 0.00 43.45 3.01
100 101 0.386731 GCGGACACGTTTTGGGAATG 60.387 55.000 0.00 0.00 43.45 2.67
101 102 0.239879 CGGACACGTTTTGGGAATGG 59.760 55.000 0.00 0.00 34.81 3.16
102 103 0.601057 GGACACGTTTTGGGAATGGG 59.399 55.000 0.00 0.00 0.00 4.00
103 104 1.324383 GACACGTTTTGGGAATGGGT 58.676 50.000 0.00 0.00 0.00 4.51
104 105 1.268625 GACACGTTTTGGGAATGGGTC 59.731 52.381 0.00 0.00 0.00 4.46
105 106 0.239879 CACGTTTTGGGAATGGGTCG 59.760 55.000 0.00 0.00 0.00 4.79
106 107 0.108963 ACGTTTTGGGAATGGGTCGA 59.891 50.000 0.00 0.00 0.00 4.20
107 108 1.271707 ACGTTTTGGGAATGGGTCGAT 60.272 47.619 0.00 0.00 0.00 3.59
108 109 1.132262 CGTTTTGGGAATGGGTCGATG 59.868 52.381 0.00 0.00 0.00 3.84
109 110 1.135112 GTTTTGGGAATGGGTCGATGC 60.135 52.381 0.00 0.00 0.00 3.91
110 111 0.038890 TTTGGGAATGGGTCGATGCA 59.961 50.000 0.00 0.00 0.00 3.96
111 112 0.258484 TTGGGAATGGGTCGATGCAT 59.742 50.000 0.00 0.00 0.00 3.96
112 113 0.258484 TGGGAATGGGTCGATGCATT 59.742 50.000 0.00 0.00 0.00 3.56
113 114 0.954452 GGGAATGGGTCGATGCATTC 59.046 55.000 0.00 0.00 34.37 2.67
119 120 3.736483 GTCGATGCATTCGGCCAT 58.264 55.556 2.24 0.00 46.75 4.40
120 121 2.024918 GTCGATGCATTCGGCCATT 58.975 52.632 2.24 0.00 46.75 3.16
121 122 1.225855 GTCGATGCATTCGGCCATTA 58.774 50.000 2.24 0.00 46.75 1.90
122 123 1.069906 GTCGATGCATTCGGCCATTAC 60.070 52.381 2.24 5.02 46.75 1.89
123 124 1.229428 CGATGCATTCGGCCATTACT 58.771 50.000 2.24 0.00 44.28 2.24
124 125 1.603802 CGATGCATTCGGCCATTACTT 59.396 47.619 2.24 0.00 44.28 2.24
125 126 2.033299 CGATGCATTCGGCCATTACTTT 59.967 45.455 2.24 0.00 44.28 2.66
126 127 3.489059 CGATGCATTCGGCCATTACTTTT 60.489 43.478 2.24 0.00 44.28 2.27
127 128 3.229276 TGCATTCGGCCATTACTTTTG 57.771 42.857 2.24 0.00 43.89 2.44
128 129 2.560542 TGCATTCGGCCATTACTTTTGT 59.439 40.909 2.24 0.00 43.89 2.83
129 130 3.179048 GCATTCGGCCATTACTTTTGTC 58.821 45.455 2.24 0.00 36.11 3.18
130 131 3.769536 CATTCGGCCATTACTTTTGTCC 58.230 45.455 2.24 0.00 0.00 4.02
131 132 2.570415 TCGGCCATTACTTTTGTCCA 57.430 45.000 2.24 0.00 0.00 4.02
132 133 2.156098 TCGGCCATTACTTTTGTCCAC 58.844 47.619 2.24 0.00 0.00 4.02
133 134 1.135803 CGGCCATTACTTTTGTCCACG 60.136 52.381 2.24 0.00 0.00 4.94
134 135 1.883926 GGCCATTACTTTTGTCCACGT 59.116 47.619 0.00 0.00 0.00 4.49
135 136 2.095415 GGCCATTACTTTTGTCCACGTC 60.095 50.000 0.00 0.00 0.00 4.34
136 137 2.412325 GCCATTACTTTTGTCCACGTCG 60.412 50.000 0.00 0.00 0.00 5.12
137 138 3.061322 CCATTACTTTTGTCCACGTCGA 58.939 45.455 0.00 0.00 0.00 4.20
138 139 3.120786 CCATTACTTTTGTCCACGTCGAC 60.121 47.826 6.34 6.34 0.00 4.20
139 140 2.138596 TACTTTTGTCCACGTCGACC 57.861 50.000 10.91 0.00 31.35 4.79
140 141 0.531311 ACTTTTGTCCACGTCGACCC 60.531 55.000 10.91 0.00 31.35 4.46
141 142 0.531090 CTTTTGTCCACGTCGACCCA 60.531 55.000 10.91 0.00 31.35 4.51
142 143 0.107800 TTTTGTCCACGTCGACCCAA 60.108 50.000 10.91 1.19 31.35 4.12
143 144 0.107800 TTTGTCCACGTCGACCCAAA 60.108 50.000 10.91 8.61 31.35 3.28
144 145 0.810823 TTGTCCACGTCGACCCAAAC 60.811 55.000 10.91 4.50 31.35 2.93
145 146 2.027897 TCCACGTCGACCCAAACG 59.972 61.111 10.58 0.00 44.22 3.60
146 147 3.039588 CCACGTCGACCCAAACGG 61.040 66.667 10.58 0.00 42.99 4.44
155 156 2.907917 CCCAAACGGGCGGACAAA 60.908 61.111 0.00 0.00 36.72 2.83
156 157 2.491022 CCCAAACGGGCGGACAAAA 61.491 57.895 0.00 0.00 36.72 2.44
157 158 1.663173 CCAAACGGGCGGACAAAAT 59.337 52.632 0.00 0.00 0.00 1.82
158 159 0.032815 CCAAACGGGCGGACAAAATT 59.967 50.000 0.00 0.00 0.00 1.82
159 160 1.135867 CAAACGGGCGGACAAAATTG 58.864 50.000 0.00 0.00 0.00 2.32
160 161 0.032815 AAACGGGCGGACAAAATTGG 59.967 50.000 0.00 0.00 0.00 3.16
161 162 1.110518 AACGGGCGGACAAAATTGGT 61.111 50.000 0.00 0.00 0.00 3.67
162 163 1.211709 CGGGCGGACAAAATTGGTC 59.788 57.895 0.00 0.00 34.52 4.02
163 164 1.211709 GGGCGGACAAAATTGGTCG 59.788 57.895 0.00 2.66 36.12 4.79
164 165 1.443702 GGCGGACAAAATTGGTCGC 60.444 57.895 19.55 19.55 45.65 5.19
165 166 1.443702 GCGGACAAAATTGGTCGCC 60.444 57.895 18.02 5.70 42.98 5.54
166 167 1.211709 CGGACAAAATTGGTCGCCC 59.788 57.895 0.00 0.00 36.12 6.13
167 168 1.211709 GGACAAAATTGGTCGCCCG 59.788 57.895 0.00 0.00 36.12 6.13
168 169 1.520600 GGACAAAATTGGTCGCCCGT 61.521 55.000 0.00 0.00 36.12 5.28
169 170 0.386731 GACAAAATTGGTCGCCCGTG 60.387 55.000 0.00 0.00 0.00 4.94
170 171 1.080839 CAAAATTGGTCGCCCGTGG 60.081 57.895 0.00 0.00 0.00 4.94
171 172 1.228306 AAAATTGGTCGCCCGTGGA 60.228 52.632 0.00 0.00 0.00 4.02
172 173 1.241315 AAAATTGGTCGCCCGTGGAG 61.241 55.000 0.00 0.00 0.00 3.86
173 174 2.406002 AAATTGGTCGCCCGTGGAGT 62.406 55.000 0.00 0.00 0.00 3.85
174 175 1.546589 AATTGGTCGCCCGTGGAGTA 61.547 55.000 0.00 0.00 0.00 2.59
175 176 1.956629 ATTGGTCGCCCGTGGAGTAG 61.957 60.000 0.00 0.00 0.00 2.57
176 177 4.509737 GGTCGCCCGTGGAGTAGC 62.510 72.222 0.00 0.00 0.00 3.58
177 178 3.450115 GTCGCCCGTGGAGTAGCT 61.450 66.667 0.00 0.00 0.00 3.32
226 227 1.335496 ACACATGTGGCACCGTAAAAC 59.665 47.619 28.64 0.00 34.19 2.43
245 246 5.629079 AAACGGAAGGTTTGAGATTGATC 57.371 39.130 0.00 0.00 46.81 2.92
274 275 1.471684 GGCCACTCAATTCTTGCTGAG 59.528 52.381 0.00 0.00 43.90 3.35
294 295 4.202567 TGAGATTTGGGAAACTGTTAGCCT 60.203 41.667 10.85 0.00 0.00 4.58
297 298 6.122964 AGATTTGGGAAACTGTTAGCCTATC 58.877 40.000 10.85 10.77 0.00 2.08
330 331 7.847487 TCGTTTACTGAAGAATAGTGTTTGTG 58.153 34.615 0.00 0.00 0.00 3.33
362 395 1.005867 CACCTGCACCAAACCATGC 60.006 57.895 0.00 0.00 42.40 4.06
410 443 6.239204 CCCCGGAAGTTTCTCTTAACAAAAAT 60.239 38.462 0.73 0.00 36.40 1.82
688 732 3.440522 GCTAAGGAGGTAAACCAAGCTTG 59.559 47.826 19.93 19.93 38.89 4.01
701 745 4.505313 CCAAGCTTGGGAGTTAACTTTC 57.495 45.455 34.08 5.93 44.70 2.62
702 746 3.255888 CCAAGCTTGGGAGTTAACTTTCC 59.744 47.826 34.08 14.51 44.70 3.13
703 747 4.145052 CAAGCTTGGGAGTTAACTTTCCT 58.855 43.478 19.14 7.86 33.85 3.36
704 748 4.022413 AGCTTGGGAGTTAACTTTCCTC 57.978 45.455 21.73 7.78 33.85 3.71
705 749 3.394606 AGCTTGGGAGTTAACTTTCCTCA 59.605 43.478 21.73 9.92 33.85 3.86
706 750 4.141251 AGCTTGGGAGTTAACTTTCCTCAA 60.141 41.667 21.73 15.35 33.85 3.02
707 751 4.583073 GCTTGGGAGTTAACTTTCCTCAAA 59.417 41.667 21.73 12.03 33.85 2.69
708 752 5.068591 GCTTGGGAGTTAACTTTCCTCAAAA 59.931 40.000 21.73 11.78 33.85 2.44
709 753 6.406512 GCTTGGGAGTTAACTTTCCTCAAAAA 60.407 38.462 21.73 11.54 33.85 1.94
755 799 2.820037 GCCGGCTCCAAGTGCTAC 60.820 66.667 22.15 0.00 0.00 3.58
760 804 1.067142 CGGCTCCAAGTGCTACTACAA 60.067 52.381 0.00 0.00 0.00 2.41
842 3368 6.516718 ACACTGCTACGCAAGATAAAGATAT 58.483 36.000 0.00 0.00 38.41 1.63
881 3407 1.311651 GGCCAGCTTCTGAAAGGCTC 61.312 60.000 20.48 11.60 44.60 4.70
886 3412 1.876156 AGCTTCTGAAAGGCTCAAACG 59.124 47.619 0.00 0.00 32.17 3.60
887 3413 1.068954 GCTTCTGAAAGGCTCAAACGG 60.069 52.381 0.00 0.00 32.17 4.44
978 3528 2.562296 ACCACCTCTCTCTCTCTCTCT 58.438 52.381 0.00 0.00 0.00 3.10
979 3529 2.505819 ACCACCTCTCTCTCTCTCTCTC 59.494 54.545 0.00 0.00 0.00 3.20
994 3544 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
995 3545 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1273 3828 4.631377 TCGTATTGCACTTTTGATCAGGAG 59.369 41.667 0.00 0.57 0.00 3.69
1276 3831 3.063510 TGCACTTTTGATCAGGAGGAG 57.936 47.619 10.89 5.52 0.00 3.69
1277 3832 1.742268 GCACTTTTGATCAGGAGGAGC 59.258 52.381 10.89 10.17 0.00 4.70
1278 3833 2.617532 GCACTTTTGATCAGGAGGAGCT 60.618 50.000 10.89 0.00 31.67 4.09
1279 3834 3.008330 CACTTTTGATCAGGAGGAGCTG 58.992 50.000 0.00 0.00 31.67 4.24
1280 3835 2.026449 ACTTTTGATCAGGAGGAGCTGG 60.026 50.000 0.00 0.00 31.67 4.85
1581 4136 2.483876 GTCAGTGCTTTGTCACAGCTA 58.516 47.619 12.06 0.00 39.35 3.32
1733 4288 3.719268 ATTGTGGATCTTGTGCCTACA 57.281 42.857 0.00 0.00 34.31 2.74
1734 4289 3.719268 TTGTGGATCTTGTGCCTACAT 57.281 42.857 0.00 0.00 36.53 2.29
1850 4405 2.011046 GCAGTGATGGAAGGAGTGAGC 61.011 57.143 0.00 0.00 0.00 4.26
1967 4522 6.387220 ACCAGGGCTAACTTTGAGACTTATAT 59.613 38.462 0.00 0.00 0.00 0.86
1988 4543 0.609662 GCCCTGTGTTTGGAATGCAT 59.390 50.000 0.00 0.00 0.00 3.96
2054 4613 7.889589 ATTCCTTCAAAATTTCCGTGAAATC 57.110 32.000 10.88 0.00 40.77 2.17
2311 4938 6.995091 AGAACAAAATCTACTAGATGGATGGC 59.005 38.462 0.00 0.00 34.65 4.40
2312 4939 6.252599 ACAAAATCTACTAGATGGATGGCA 57.747 37.500 0.00 0.00 34.65 4.92
2327 4954 5.096521 TGGATGGCATTCTACTGGATATCT 58.903 41.667 7.41 0.00 0.00 1.98
2378 5005 4.657814 AGAGGTGATGTGGTACCAAATT 57.342 40.909 18.98 2.68 39.46 1.82
2452 5079 6.014499 CGTCCAGGGATATAACATAAGTCCTT 60.014 42.308 0.00 0.00 0.00 3.36
2455 5082 6.210784 CCAGGGATATAACATAAGTCCTTCGA 59.789 42.308 0.00 0.00 0.00 3.71
2540 5167 0.037590 TTGTTTCCATAGCGGCTGGT 59.962 50.000 13.86 1.35 35.19 4.00
2612 5239 8.824159 ACTCACTTGTGTTCATCATATATAGC 57.176 34.615 0.46 0.00 0.00 2.97
2625 5252 9.067986 TCATCATATATAGCTACCTTACCATCG 57.932 37.037 0.00 0.00 0.00 3.84
2638 5265 0.537188 ACCATCGATGAGTGGGTCAC 59.463 55.000 26.86 0.00 38.28 3.67
2675 5303 5.104527 TCCCTCTGTTAATCTTACACCCATG 60.105 44.000 0.00 0.00 0.00 3.66
2767 5411 6.971184 GTGCTATTGAAATCATGAAGAACAGG 59.029 38.462 0.00 0.00 0.00 4.00
2780 5424 5.010933 TGAAGAACAGGTCGAGTTATCTCT 58.989 41.667 0.00 0.00 38.45 3.10
2781 5425 5.124138 TGAAGAACAGGTCGAGTTATCTCTC 59.876 44.000 0.00 0.00 38.45 3.20
2782 5426 4.850680 AGAACAGGTCGAGTTATCTCTCT 58.149 43.478 0.00 0.00 38.45 3.10
2864 5508 9.676861 GAATAGATTGTGGATAATCATGGATCA 57.323 33.333 0.00 0.00 39.08 2.92
2866 5510 5.936372 AGATTGTGGATAATCATGGATCACG 59.064 40.000 0.00 0.00 39.08 4.35
2957 5601 3.699038 AGTTAAAGGCTTGACTGTTGCAA 59.301 39.130 13.76 0.00 30.60 4.08
3148 5792 4.522789 TGTGGCCTCTGGTTATTCTTTTTC 59.477 41.667 3.32 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.065281 CGTGTCCCCTCGGTGTCC 62.065 72.222 0.00 0.00 0.00 4.02
8 9 4.736896 GCGTGTCCCCTCGGTGTC 62.737 72.222 0.00 0.00 0.00 3.67
30 31 2.314647 AAATGTGTCGGTGCGGACG 61.315 57.895 0.00 0.00 39.83 4.79
31 32 1.206578 CAAATGTGTCGGTGCGGAC 59.793 57.895 0.00 0.00 37.45 4.79
32 33 0.948623 CTCAAATGTGTCGGTGCGGA 60.949 55.000 0.00 0.00 0.00 5.54
33 34 1.497278 CTCAAATGTGTCGGTGCGG 59.503 57.895 0.00 0.00 0.00 5.69
34 35 1.154413 GCTCAAATGTGTCGGTGCG 60.154 57.895 0.00 0.00 0.00 5.34
35 36 1.210155 GGCTCAAATGTGTCGGTGC 59.790 57.895 0.00 0.00 0.00 5.01
36 37 1.227999 ACGGCTCAAATGTGTCGGTG 61.228 55.000 13.12 0.00 40.42 4.94
37 38 0.319083 TACGGCTCAAATGTGTCGGT 59.681 50.000 13.12 3.12 40.42 4.69
38 39 1.434555 TTACGGCTCAAATGTGTCGG 58.565 50.000 13.12 0.00 40.42 4.79
39 40 3.740044 ATTTACGGCTCAAATGTGTCG 57.260 42.857 7.80 7.80 41.65 4.35
40 41 5.457140 TCAAATTTACGGCTCAAATGTGTC 58.543 37.500 9.38 0.00 33.89 3.67
41 42 5.446143 TCAAATTTACGGCTCAAATGTGT 57.554 34.783 9.38 0.00 33.89 3.72
42 43 4.324402 GCTCAAATTTACGGCTCAAATGTG 59.676 41.667 0.00 5.08 33.60 3.21
43 44 4.485163 GCTCAAATTTACGGCTCAAATGT 58.515 39.130 0.00 0.00 0.00 2.71
44 45 3.859386 GGCTCAAATTTACGGCTCAAATG 59.141 43.478 0.00 0.00 0.00 2.32
45 46 3.427503 CGGCTCAAATTTACGGCTCAAAT 60.428 43.478 9.66 0.00 0.00 2.32
46 47 2.095466 CGGCTCAAATTTACGGCTCAAA 60.095 45.455 9.66 0.00 0.00 2.69
47 48 1.466950 CGGCTCAAATTTACGGCTCAA 59.533 47.619 9.66 0.00 0.00 3.02
48 49 1.083489 CGGCTCAAATTTACGGCTCA 58.917 50.000 9.66 0.00 0.00 4.26
49 50 0.377203 CCGGCTCAAATTTACGGCTC 59.623 55.000 9.01 1.24 37.93 4.70
50 51 0.035820 TCCGGCTCAAATTTACGGCT 60.036 50.000 14.33 0.00 43.93 5.52
51 52 0.806241 TTCCGGCTCAAATTTACGGC 59.194 50.000 14.33 9.19 43.93 5.68
52 53 3.434637 CATTTCCGGCTCAAATTTACGG 58.565 45.455 13.43 13.43 45.52 4.02
53 54 3.434637 CCATTTCCGGCTCAAATTTACG 58.565 45.455 0.00 0.00 0.00 3.18
54 55 3.194755 ACCCATTTCCGGCTCAAATTTAC 59.805 43.478 0.00 0.00 0.00 2.01
55 56 3.436243 ACCCATTTCCGGCTCAAATTTA 58.564 40.909 0.00 0.00 0.00 1.40
56 57 2.256306 ACCCATTTCCGGCTCAAATTT 58.744 42.857 0.00 0.00 0.00 1.82
57 58 1.937191 ACCCATTTCCGGCTCAAATT 58.063 45.000 0.00 0.00 0.00 1.82
58 59 1.824852 GAACCCATTTCCGGCTCAAAT 59.175 47.619 0.00 0.00 0.00 2.32
59 60 1.253100 GAACCCATTTCCGGCTCAAA 58.747 50.000 0.00 0.00 0.00 2.69
60 61 0.958382 CGAACCCATTTCCGGCTCAA 60.958 55.000 0.00 0.00 0.00 3.02
61 62 1.376683 CGAACCCATTTCCGGCTCA 60.377 57.895 0.00 0.00 0.00 4.26
62 63 1.376812 ACGAACCCATTTCCGGCTC 60.377 57.895 0.00 0.00 0.00 4.70
63 64 1.674322 CACGAACCCATTTCCGGCT 60.674 57.895 0.00 0.00 0.00 5.52
64 65 2.874751 CACGAACCCATTTCCGGC 59.125 61.111 0.00 0.00 0.00 6.13
65 66 2.874751 GCACGAACCCATTTCCGG 59.125 61.111 0.00 0.00 0.00 5.14
66 67 2.478746 CGCACGAACCCATTTCCG 59.521 61.111 0.00 0.00 0.00 4.30
67 68 1.673009 TCCGCACGAACCCATTTCC 60.673 57.895 0.00 0.00 0.00 3.13
68 69 1.231958 TGTCCGCACGAACCCATTTC 61.232 55.000 0.00 0.00 0.00 2.17
69 70 1.228003 TGTCCGCACGAACCCATTT 60.228 52.632 0.00 0.00 0.00 2.32
70 71 1.964373 GTGTCCGCACGAACCCATT 60.964 57.895 0.00 0.00 35.75 3.16
71 72 2.358247 GTGTCCGCACGAACCCAT 60.358 61.111 0.00 0.00 35.75 4.00
79 80 1.716826 TTCCCAAAACGTGTCCGCAC 61.717 55.000 0.00 0.00 41.97 5.34
80 81 0.820074 ATTCCCAAAACGTGTCCGCA 60.820 50.000 0.00 0.00 37.70 5.69
81 82 0.386731 CATTCCCAAAACGTGTCCGC 60.387 55.000 0.00 0.00 37.70 5.54
82 83 0.239879 CCATTCCCAAAACGTGTCCG 59.760 55.000 0.00 0.00 40.83 4.79
83 84 0.601057 CCCATTCCCAAAACGTGTCC 59.399 55.000 0.00 0.00 0.00 4.02
84 85 1.268625 GACCCATTCCCAAAACGTGTC 59.731 52.381 0.00 0.00 0.00 3.67
85 86 1.324383 GACCCATTCCCAAAACGTGT 58.676 50.000 0.00 0.00 0.00 4.49
86 87 0.239879 CGACCCATTCCCAAAACGTG 59.760 55.000 0.00 0.00 0.00 4.49
87 88 0.108963 TCGACCCATTCCCAAAACGT 59.891 50.000 0.00 0.00 0.00 3.99
88 89 1.132262 CATCGACCCATTCCCAAAACG 59.868 52.381 0.00 0.00 0.00 3.60
89 90 1.135112 GCATCGACCCATTCCCAAAAC 60.135 52.381 0.00 0.00 0.00 2.43
90 91 1.181786 GCATCGACCCATTCCCAAAA 58.818 50.000 0.00 0.00 0.00 2.44
91 92 0.038890 TGCATCGACCCATTCCCAAA 59.961 50.000 0.00 0.00 0.00 3.28
92 93 0.258484 ATGCATCGACCCATTCCCAA 59.742 50.000 0.00 0.00 0.00 4.12
93 94 0.258484 AATGCATCGACCCATTCCCA 59.742 50.000 0.00 0.00 0.00 4.37
94 95 0.954452 GAATGCATCGACCCATTCCC 59.046 55.000 20.87 5.98 40.73 3.97
105 106 3.715628 AAAGTAATGGCCGAATGCATC 57.284 42.857 0.00 0.00 43.89 3.91
106 107 3.195396 ACAAAAGTAATGGCCGAATGCAT 59.805 39.130 0.00 0.00 43.89 3.96
107 108 2.560542 ACAAAAGTAATGGCCGAATGCA 59.439 40.909 0.00 0.00 43.89 3.96
108 109 3.179048 GACAAAAGTAATGGCCGAATGC 58.821 45.455 0.00 0.00 40.16 3.56
109 110 3.769536 GGACAAAAGTAATGGCCGAATG 58.230 45.455 0.00 0.00 35.93 2.67
114 115 1.883926 ACGTGGACAAAAGTAATGGCC 59.116 47.619 0.00 0.00 46.87 5.36
115 116 2.412325 CGACGTGGACAAAAGTAATGGC 60.412 50.000 0.00 0.00 0.00 4.40
116 117 3.061322 TCGACGTGGACAAAAGTAATGG 58.939 45.455 0.00 0.00 0.00 3.16
117 118 3.120786 GGTCGACGTGGACAAAAGTAATG 60.121 47.826 28.33 0.00 38.70 1.90
118 119 3.062042 GGTCGACGTGGACAAAAGTAAT 58.938 45.455 28.33 0.00 38.70 1.89
119 120 2.472816 GGTCGACGTGGACAAAAGTAA 58.527 47.619 28.33 0.00 38.70 2.24
120 121 1.269726 GGGTCGACGTGGACAAAAGTA 60.270 52.381 28.33 0.00 38.70 2.24
121 122 0.531311 GGGTCGACGTGGACAAAAGT 60.531 55.000 28.33 0.00 38.70 2.66
122 123 0.531090 TGGGTCGACGTGGACAAAAG 60.531 55.000 28.33 0.00 38.70 2.27
123 124 0.107800 TTGGGTCGACGTGGACAAAA 60.108 50.000 28.33 19.45 38.70 2.44
124 125 0.107800 TTTGGGTCGACGTGGACAAA 60.108 50.000 28.33 19.14 38.70 2.83
125 126 0.810823 GTTTGGGTCGACGTGGACAA 60.811 55.000 28.33 14.78 38.70 3.18
126 127 1.227321 GTTTGGGTCGACGTGGACA 60.227 57.895 28.33 9.65 38.70 4.02
127 128 2.305127 CGTTTGGGTCGACGTGGAC 61.305 63.158 21.05 21.05 34.75 4.02
128 129 2.027897 CGTTTGGGTCGACGTGGA 59.972 61.111 9.92 0.00 34.75 4.02
129 130 3.039588 CCGTTTGGGTCGACGTGG 61.040 66.667 9.92 0.00 37.56 4.94
139 140 0.032815 AATTTTGTCCGCCCGTTTGG 59.967 50.000 0.00 0.00 37.09 3.28
140 141 1.135867 CAATTTTGTCCGCCCGTTTG 58.864 50.000 0.00 0.00 0.00 2.93
141 142 0.032815 CCAATTTTGTCCGCCCGTTT 59.967 50.000 0.00 0.00 0.00 3.60
142 143 1.110518 ACCAATTTTGTCCGCCCGTT 61.111 50.000 0.00 0.00 0.00 4.44
143 144 1.520600 GACCAATTTTGTCCGCCCGT 61.521 55.000 0.00 0.00 0.00 5.28
144 145 1.211709 GACCAATTTTGTCCGCCCG 59.788 57.895 0.00 0.00 0.00 6.13
145 146 1.211709 CGACCAATTTTGTCCGCCC 59.788 57.895 0.47 0.00 0.00 6.13
146 147 1.443702 GCGACCAATTTTGTCCGCC 60.444 57.895 12.50 0.70 39.48 6.13
147 148 1.443702 GGCGACCAATTTTGTCCGC 60.444 57.895 14.19 14.19 42.33 5.54
148 149 4.859784 GGCGACCAATTTTGTCCG 57.140 55.556 0.00 0.00 0.00 4.79
160 161 3.412879 GAGCTACTCCACGGGCGAC 62.413 68.421 0.00 0.00 0.00 5.19
161 162 2.261430 TAGAGCTACTCCACGGGCGA 62.261 60.000 0.00 0.00 0.00 5.54
162 163 1.381928 TTAGAGCTACTCCACGGGCG 61.382 60.000 0.00 0.00 0.00 6.13
163 164 0.102663 GTTAGAGCTACTCCACGGGC 59.897 60.000 0.00 0.00 0.00 6.13
164 165 1.471119 TGTTAGAGCTACTCCACGGG 58.529 55.000 0.00 0.00 0.00 5.28
165 166 2.799917 GCATGTTAGAGCTACTCCACGG 60.800 54.545 0.00 0.00 0.00 4.94
166 167 2.159240 TGCATGTTAGAGCTACTCCACG 60.159 50.000 0.00 0.00 0.00 4.94
167 168 3.190874 GTGCATGTTAGAGCTACTCCAC 58.809 50.000 0.00 0.00 0.00 4.02
168 169 2.831526 TGTGCATGTTAGAGCTACTCCA 59.168 45.455 0.00 0.00 0.00 3.86
169 170 3.526931 TGTGCATGTTAGAGCTACTCC 57.473 47.619 0.00 0.00 0.00 3.85
245 246 5.559148 AGAATTGAGTGGCCTAATAGGAG 57.441 43.478 11.13 0.00 37.67 3.69
274 275 5.007724 CGATAGGCTAACAGTTTCCCAAATC 59.992 44.000 0.00 0.39 0.00 2.17
294 295 4.880886 TCAGTAAACGAACGATCCGATA 57.119 40.909 0.14 0.00 0.00 2.92
297 298 3.495193 TCTTCAGTAAACGAACGATCCG 58.505 45.455 0.14 0.00 0.00 4.18
330 331 3.252701 GTGCAGGTGAATGGATCATCATC 59.747 47.826 0.00 0.00 41.98 2.92
362 395 5.048504 GGTTGGTATAGGTGAATGCATCATG 60.049 44.000 0.00 0.00 40.97 3.07
410 443 6.015350 TGTGGTTGTCCAAAAGTGTTCTTTAA 60.015 34.615 0.00 0.00 46.15 1.52
415 448 3.859411 TGTGGTTGTCCAAAAGTGTTC 57.141 42.857 0.00 0.00 46.15 3.18
712 756 4.215613 CGCTAGTTAACTCCCAAGCTTTTT 59.784 41.667 20.42 0.00 0.00 1.94
713 757 3.751698 CGCTAGTTAACTCCCAAGCTTTT 59.248 43.478 20.42 0.00 0.00 2.27
714 758 3.335579 CGCTAGTTAACTCCCAAGCTTT 58.664 45.455 20.42 0.00 0.00 3.51
715 759 2.354805 CCGCTAGTTAACTCCCAAGCTT 60.355 50.000 20.42 0.00 0.00 3.74
716 760 1.207329 CCGCTAGTTAACTCCCAAGCT 59.793 52.381 20.42 0.00 0.00 3.74
717 761 1.066358 ACCGCTAGTTAACTCCCAAGC 60.066 52.381 12.39 14.17 0.00 4.01
718 762 2.618053 CACCGCTAGTTAACTCCCAAG 58.382 52.381 12.39 5.03 0.00 3.61
719 763 1.338389 GCACCGCTAGTTAACTCCCAA 60.338 52.381 12.39 0.00 0.00 4.12
720 764 0.248289 GCACCGCTAGTTAACTCCCA 59.752 55.000 12.39 0.00 0.00 4.37
721 765 0.461516 GGCACCGCTAGTTAACTCCC 60.462 60.000 12.39 3.41 0.00 4.30
766 810 2.414994 TGGGTACGTTGTGTTGGAAA 57.585 45.000 0.00 0.00 0.00 3.13
767 811 2.619177 CAATGGGTACGTTGTGTTGGAA 59.381 45.455 0.00 0.00 38.51 3.53
768 812 2.158798 TCAATGGGTACGTTGTGTTGGA 60.159 45.455 0.00 0.00 42.80 3.53
770 814 2.350388 GCTCAATGGGTACGTTGTGTTG 60.350 50.000 0.00 0.00 42.80 3.33
780 824 2.546899 ACAGTACCAGCTCAATGGGTA 58.453 47.619 0.00 0.00 45.25 3.69
842 3368 2.105821 CCGGCCTAATCAATAACCTCCA 59.894 50.000 0.00 0.00 0.00 3.86
881 3407 8.600625 TCGAAGAATATTTCATACTTCCGTTTG 58.399 33.333 0.00 0.00 35.14 2.93
978 3528 3.096852 ACACGAGAGAGAGAGAGAGAGA 58.903 50.000 0.00 0.00 0.00 3.10
979 3529 3.526931 ACACGAGAGAGAGAGAGAGAG 57.473 52.381 0.00 0.00 0.00 3.20
994 3544 4.770531 ACAGCCTGGCTTATATATACACGA 59.229 41.667 20.79 0.00 36.40 4.35
995 3545 5.073311 ACAGCCTGGCTTATATATACACG 57.927 43.478 20.79 5.54 36.40 4.49
1252 3807 4.943705 TCCTCCTGATCAAAAGTGCAATAC 59.056 41.667 0.00 0.00 0.00 1.89
1273 3828 1.457455 CTCCTCCTCCTCCAGCTCC 60.457 68.421 0.00 0.00 0.00 4.70
1276 3831 1.457455 CTCCTCCTCCTCCTCCAGC 60.457 68.421 0.00 0.00 0.00 4.85
1277 3832 1.232792 CCTCCTCCTCCTCCTCCAG 59.767 68.421 0.00 0.00 0.00 3.86
1278 3833 2.328589 CCCTCCTCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
1279 3834 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1280 3835 2.123033 GCCCTCCTCCTCCTCCTC 60.123 72.222 0.00 0.00 0.00 3.71
1581 4136 5.012893 CACCTTCTTTTAGGGCTGAATTCT 58.987 41.667 7.05 0.00 39.76 2.40
1651 4206 6.668323 ACCATTTCAAGAAAACACGTATCAG 58.332 36.000 0.00 0.00 33.56 2.90
1686 4241 8.956426 TCCAAAGAAAAATATCGCTCAAGTATT 58.044 29.630 0.00 0.00 0.00 1.89
1763 4318 2.441532 CCAGCCCCCTTCATGCAG 60.442 66.667 0.00 0.00 0.00 4.41
1832 4387 1.949799 AGCTCACTCCTTCCATCACT 58.050 50.000 0.00 0.00 0.00 3.41
1967 4522 1.470996 GCATTCCAAACACAGGGCCA 61.471 55.000 6.18 0.00 0.00 5.36
2054 4613 0.958091 TTCATGTTTGGAACGCAGGG 59.042 50.000 0.00 0.00 0.00 4.45
2117 4676 5.752955 GCACACTGTATGTTTTGGTCAATTT 59.247 36.000 0.00 0.00 40.64 1.82
2236 4863 3.622630 AGTGAGTGAACTATACCGAGCT 58.377 45.455 0.00 0.00 0.00 4.09
2311 4938 7.179872 TGAATGAGGGAGATATCCAGTAGAATG 59.820 40.741 8.98 0.00 0.00 2.67
2312 4939 7.251936 TGAATGAGGGAGATATCCAGTAGAAT 58.748 38.462 8.98 0.00 0.00 2.40
2327 4954 3.758425 CACCATATGCATGAATGAGGGA 58.242 45.455 10.16 0.00 33.67 4.20
2426 5053 5.245526 GGACTTATGTTATATCCCTGGACGT 59.754 44.000 0.00 0.00 0.00 4.34
2452 5079 5.838529 ACAACATATATTCACCACGATCGA 58.161 37.500 24.34 0.00 0.00 3.59
2455 5082 6.042093 AGAGGACAACATATATTCACCACGAT 59.958 38.462 0.00 0.00 0.00 3.73
2540 5167 3.825143 TCATGCTGATAAGCTAGTGCA 57.175 42.857 3.06 0.00 42.74 4.57
2612 5239 3.005897 CCCACTCATCGATGGTAAGGTAG 59.994 52.174 24.61 14.81 33.80 3.18
2625 5252 1.168714 GGCAAAGTGACCCACTCATC 58.831 55.000 0.00 0.00 44.62 2.92
2638 5265 2.695147 ACAGAGGGAAAGTTTGGCAAAG 59.305 45.455 13.94 0.00 0.00 2.77
2675 5303 1.379642 GCCCTGTGCAGCCATAAGTC 61.380 60.000 0.00 0.00 40.77 3.01
2801 5445 6.827727 TGCTTACTCCTATAAACCCTGAATC 58.172 40.000 0.00 0.00 0.00 2.52
2835 5479 8.105197 TCCATGATTATCCACAATCTATTCCAG 58.895 37.037 0.00 0.00 36.16 3.86
2864 5508 0.386476 CTAATGCATGGCCATTGCGT 59.614 50.000 25.25 23.61 36.21 5.24
2866 5510 0.391597 AGCTAATGCATGGCCATTGC 59.608 50.000 24.69 24.69 42.74 3.56
2957 5601 4.476479 AGTCATCTAGCCTTTTCAATCCCT 59.524 41.667 0.00 0.00 0.00 4.20
3012 5656 5.221722 GGTGAAGCTGTCAATCAGGGATATA 60.222 44.000 0.00 0.00 43.78 0.86
3016 5660 1.003580 GGTGAAGCTGTCAATCAGGGA 59.996 52.381 0.00 0.00 43.78 4.20
3131 5775 8.367156 TGGAAAATGGAAAAAGAATAACCAGAG 58.633 33.333 0.00 0.00 34.08 3.35


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

AutoCloner maintained by Alex Coulton.