Multiple sequence alignment - TraesCS7A01G408300

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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 TraesCS7A01G408300 chr7A 100.000 2921 0 0 1 2921 594451519 594454439 0.000000e+00 5395.0
1 TraesCS7A01G408300 chr7A 93.568 2410 130 9 461 2847 628652620 628655027 0.000000e+00 3568.0
2 TraesCS7A01G408300 chr7A 87.003 1762 218 6 1098 2850 628867155 628865396 0.000000e+00 1975.0
3 TraesCS7A01G408300 chr7A 97.107 242 7 0 1 242 13882738 13882497 2.710000e-110 409.0
4 TraesCS7A01G408300 chr7D 96.590 2317 47 8 245 2541 518776736 518779040 0.000000e+00 3812.0
5 TraesCS7A01G408300 chr7D 93.400 2409 136 7 461 2847 545654205 545656612 0.000000e+00 3546.0
6 TraesCS7A01G408300 chr7D 87.535 1797 211 8 1061 2847 545660102 545661895 0.000000e+00 2065.0
7 TraesCS7A01G408300 chr7D 87.070 1802 220 8 1059 2850 546129865 546128067 0.000000e+00 2025.0
8 TraesCS7A01G408300 chr7D 97.959 392 4 1 2534 2921 518779182 518779573 0.000000e+00 676.0
9 TraesCS7A01G408300 chr7D 97.934 242 5 0 1 242 27010003 27009762 1.250000e-113 420.0
10 TraesCS7A01G408300 chr7B 91.168 2389 152 14 243 2606 589939134 589941488 0.000000e+00 3188.0
11 TraesCS7A01G408300 chr7B 86.090 1826 243 6 1040 2856 590107498 590105675 0.000000e+00 1954.0
12 TraesCS7A01G408300 chr7B 85.516 1802 241 14 1058 2847 589899221 589901014 0.000000e+00 1864.0
13 TraesCS7A01G408300 chr7B 92.672 232 13 1 2620 2847 589942917 589943148 6.030000e-87 331.0
14 TraesCS7A01G408300 chr7B 86.567 67 6 2 2854 2920 552115284 552115347 1.450000e-08 71.3
15 TraesCS7A01G408300 chr5B 96.694 242 8 0 1 242 545884412 545884653 1.260000e-108 403.0
16 TraesCS7A01G408300 chr2B 97.071 239 7 0 1 239 25413162 25413400 1.260000e-108 403.0
17 TraesCS7A01G408300 chr2B 96.281 242 9 0 1 242 117720935 117721176 5.870000e-107 398.0
18 TraesCS7A01G408300 chr6B 96.281 242 9 0 1 242 706981406 706981647 5.870000e-107 398.0
19 TraesCS7A01G408300 chr6A 96.281 242 9 0 1 242 41483495 41483254 5.870000e-107 398.0
20 TraesCS7A01G408300 chr1A 96.281 242 9 0 1 242 366122526 366122285 5.870000e-107 398.0
21 TraesCS7A01G408300 chr1A 96.266 241 9 0 2 242 586093813 586093573 2.110000e-106 396.0


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 TraesCS7A01G408300 chr7A 594451519 594454439 2920 False 5395.0 5395 100.0000 1 2921 1 chr7A.!!$F1 2920
1 TraesCS7A01G408300 chr7A 628652620 628655027 2407 False 3568.0 3568 93.5680 461 2847 1 chr7A.!!$F2 2386
2 TraesCS7A01G408300 chr7A 628865396 628867155 1759 True 1975.0 1975 87.0030 1098 2850 1 chr7A.!!$R2 1752
3 TraesCS7A01G408300 chr7D 545654205 545661895 7690 False 2805.5 3546 90.4675 461 2847 2 chr7D.!!$F2 2386
4 TraesCS7A01G408300 chr7D 518776736 518779573 2837 False 2244.0 3812 97.2745 245 2921 2 chr7D.!!$F1 2676
5 TraesCS7A01G408300 chr7D 546128067 546129865 1798 True 2025.0 2025 87.0700 1059 2850 1 chr7D.!!$R2 1791
6 TraesCS7A01G408300 chr7B 590105675 590107498 1823 True 1954.0 1954 86.0900 1040 2856 1 chr7B.!!$R1 1816
7 TraesCS7A01G408300 chr7B 589899221 589901014 1793 False 1864.0 1864 85.5160 1058 2847 1 chr7B.!!$F2 1789
8 TraesCS7A01G408300 chr7B 589939134 589943148 4014 False 1759.5 3188 91.9200 243 2847 2 chr7B.!!$F3 2604


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
136 137 0.188587 TACCTGAGGCTCCCGATGAT 59.811 55.0 12.86 0.0 0.0 2.45 F
145 146 0.244721 CTCCCGATGATGCTGCGATA 59.755 55.0 0.00 0.0 0.0 2.92 F
1467 1493 0.113190 CAAACCCCAGCCTTCCTCTT 59.887 55.0 0.00 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1427 1.131638 TGAGGTGGTTGAAGCTGACT 58.868 50.000 0.0 0.0 0.00 3.41 R
1779 1806 6.165700 AGAACTCCTTGCAAATCATTGTTT 57.834 33.333 0.0 0.0 38.85 2.83 R
2468 2502 1.918262 AGCCCAGTTCATCAATCCAGA 59.082 47.619 0.0 0.0 0.00 3.86 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
17 18 2.960129 CCCGCGATGTACCGAAGC 60.960 66.667 8.23 0.00 0.00 3.86
18 19 2.202690 CCGCGATGTACCGAAGCA 60.203 61.111 8.23 0.00 0.00 3.91
19 20 2.230940 CCGCGATGTACCGAAGCAG 61.231 63.158 8.23 0.00 0.00 4.24
20 21 2.230940 CGCGATGTACCGAAGCAGG 61.231 63.158 0.00 0.00 37.30 4.85
22 23 1.421410 GCGATGTACCGAAGCAGGTG 61.421 60.000 8.53 0.00 45.54 4.00
23 24 1.421410 CGATGTACCGAAGCAGGTGC 61.421 60.000 8.53 7.76 45.54 5.01
33 34 3.730761 GCAGGTGCTTGACGGCAG 61.731 66.667 0.00 0.00 43.25 4.85
37 38 3.782244 GTGCTTGACGGCAGCGAG 61.782 66.667 7.96 0.00 43.25 5.03
38 39 3.989787 TGCTTGACGGCAGCGAGA 61.990 61.111 7.96 0.00 37.29 4.04
39 40 2.510238 GCTTGACGGCAGCGAGAT 60.510 61.111 0.00 0.00 0.00 2.75
40 41 2.806856 GCTTGACGGCAGCGAGATG 61.807 63.158 0.00 0.00 0.00 2.90
41 42 1.153765 CTTGACGGCAGCGAGATGA 60.154 57.895 0.00 0.00 0.00 2.92
42 43 0.529337 CTTGACGGCAGCGAGATGAT 60.529 55.000 0.00 0.00 0.00 2.45
43 44 0.528466 TTGACGGCAGCGAGATGATC 60.528 55.000 0.00 0.00 0.00 2.92
51 52 3.228624 CGAGATGATCGCTTGCCG 58.771 61.111 0.00 0.00 45.98 5.69
52 53 2.305853 CGAGATGATCGCTTGCCGG 61.306 63.158 0.00 0.00 45.98 6.13
53 54 1.958205 GAGATGATCGCTTGCCGGG 60.958 63.158 2.18 0.00 37.59 5.73
54 55 2.974698 GATGATCGCTTGCCGGGG 60.975 66.667 2.18 0.00 37.59 5.73
62 63 3.142838 CTTGCCGGGGCTTCCATG 61.143 66.667 11.55 0.00 42.51 3.66
63 64 3.643595 CTTGCCGGGGCTTCCATGA 62.644 63.158 11.55 0.00 42.51 3.07
64 65 3.216985 TTGCCGGGGCTTCCATGAA 62.217 57.895 11.55 0.00 42.51 2.57
65 66 3.140814 GCCGGGGCTTCCATGAAC 61.141 66.667 2.18 0.00 38.26 3.18
66 67 2.440247 CCGGGGCTTCCATGAACC 60.440 66.667 0.00 0.00 34.36 3.62
67 68 2.677228 CGGGGCTTCCATGAACCT 59.323 61.111 0.00 0.00 34.36 3.50
68 69 1.632018 CCGGGGCTTCCATGAACCTA 61.632 60.000 0.00 0.00 34.36 3.08
69 70 0.463833 CGGGGCTTCCATGAACCTAC 60.464 60.000 0.00 0.00 34.36 3.18
70 71 0.919710 GGGGCTTCCATGAACCTACT 59.080 55.000 0.00 0.00 35.00 2.57
71 72 1.134068 GGGGCTTCCATGAACCTACTC 60.134 57.143 0.00 0.00 35.00 2.59
72 73 1.559682 GGGCTTCCATGAACCTACTCA 59.440 52.381 0.00 0.00 0.00 3.41
73 74 2.420687 GGGCTTCCATGAACCTACTCAG 60.421 54.545 0.00 0.00 0.00 3.35
83 84 3.583054 CCTACTCAGGTACCCGACA 57.417 57.895 8.74 0.00 37.15 4.35
84 85 1.843368 CCTACTCAGGTACCCGACAA 58.157 55.000 8.74 0.00 37.15 3.18
85 86 1.475682 CCTACTCAGGTACCCGACAAC 59.524 57.143 8.74 0.00 37.15 3.32
86 87 1.131883 CTACTCAGGTACCCGACAACG 59.868 57.143 8.74 0.00 39.43 4.10
87 88 0.538057 ACTCAGGTACCCGACAACGA 60.538 55.000 8.74 0.00 42.66 3.85
88 89 0.599558 CTCAGGTACCCGACAACGAA 59.400 55.000 8.74 0.00 42.66 3.85
89 90 0.314935 TCAGGTACCCGACAACGAAC 59.685 55.000 8.74 0.00 42.66 3.95
90 91 1.005294 CAGGTACCCGACAACGAACG 61.005 60.000 8.74 0.00 42.66 3.95
91 92 1.007387 GGTACCCGACAACGAACGT 60.007 57.895 0.00 0.00 42.66 3.99
92 93 1.277495 GGTACCCGACAACGAACGTG 61.277 60.000 0.00 0.00 42.66 4.49
93 94 0.317770 GTACCCGACAACGAACGTGA 60.318 55.000 0.00 0.00 42.66 4.35
94 95 0.597568 TACCCGACAACGAACGTGAT 59.402 50.000 0.00 0.00 42.66 3.06
95 96 0.942410 ACCCGACAACGAACGTGATG 60.942 55.000 0.00 0.00 42.66 3.07
96 97 0.942410 CCCGACAACGAACGTGATGT 60.942 55.000 0.00 2.52 42.66 3.06
97 98 0.433492 CCGACAACGAACGTGATGTC 59.567 55.000 16.89 16.89 42.66 3.06
98 99 0.433492 CGACAACGAACGTGATGTCC 59.567 55.000 19.34 8.15 42.66 4.02
99 100 0.433492 GACAACGAACGTGATGTCCG 59.567 55.000 16.34 0.00 36.94 4.79
100 101 0.942410 ACAACGAACGTGATGTCCGG 60.942 55.000 0.00 0.00 0.00 5.14
101 102 0.942410 CAACGAACGTGATGTCCGGT 60.942 55.000 0.00 0.00 0.00 5.28
102 103 0.665369 AACGAACGTGATGTCCGGTC 60.665 55.000 0.00 0.00 38.63 4.79
103 104 3.763319 GAACGTGATGTCCGGTCG 58.237 61.111 0.00 1.01 31.71 4.79
104 105 1.804326 GAACGTGATGTCCGGTCGG 60.804 63.158 0.00 2.52 31.71 4.79
105 106 3.291101 AACGTGATGTCCGGTCGGG 62.291 63.158 9.68 0.00 35.59 5.14
106 107 3.755628 CGTGATGTCCGGTCGGGT 61.756 66.667 9.68 0.00 37.00 5.28
107 108 2.125673 GTGATGTCCGGTCGGGTG 60.126 66.667 9.68 0.00 37.00 4.61
108 109 2.602267 TGATGTCCGGTCGGGTGT 60.602 61.111 9.68 0.00 37.00 4.16
109 110 2.125673 GATGTCCGGTCGGGTGTG 60.126 66.667 9.68 0.00 37.00 3.82
110 111 4.388499 ATGTCCGGTCGGGTGTGC 62.388 66.667 9.68 0.00 37.00 4.57
118 119 2.598099 TCGGGTGTGCACGAGGTA 60.598 61.111 13.13 0.00 46.67 3.08
119 120 2.431942 CGGGTGTGCACGAGGTAC 60.432 66.667 13.13 3.88 45.97 3.34
120 121 2.047560 GGGTGTGCACGAGGTACC 60.048 66.667 13.13 13.36 0.00 3.34
121 122 2.580601 GGGTGTGCACGAGGTACCT 61.581 63.158 16.26 16.26 0.00 3.08
122 123 1.374252 GGTGTGCACGAGGTACCTG 60.374 63.158 22.10 14.16 0.00 4.00
123 124 1.663739 GTGTGCACGAGGTACCTGA 59.336 57.895 22.10 0.00 0.00 3.86
124 125 0.388649 GTGTGCACGAGGTACCTGAG 60.389 60.000 22.10 15.64 0.00 3.35
125 126 1.215647 GTGCACGAGGTACCTGAGG 59.784 63.158 22.10 10.90 0.00 3.86
126 127 2.184579 GCACGAGGTACCTGAGGC 59.815 66.667 22.10 15.50 0.00 4.70
127 128 2.352032 GCACGAGGTACCTGAGGCT 61.352 63.158 22.10 0.00 0.00 4.58
128 129 1.810532 CACGAGGTACCTGAGGCTC 59.189 63.158 22.10 7.79 0.00 4.70
129 130 1.380112 ACGAGGTACCTGAGGCTCC 60.380 63.158 22.10 1.21 0.00 4.70
130 131 2.128507 CGAGGTACCTGAGGCTCCC 61.129 68.421 22.10 5.29 0.00 4.30
131 132 2.042843 AGGTACCTGAGGCTCCCG 60.043 66.667 15.42 4.12 0.00 5.14
132 133 2.043248 GGTACCTGAGGCTCCCGA 60.043 66.667 12.86 0.00 0.00 5.14
133 134 1.457831 GGTACCTGAGGCTCCCGAT 60.458 63.158 12.86 0.00 0.00 4.18
134 135 1.742768 GTACCTGAGGCTCCCGATG 59.257 63.158 12.86 0.00 0.00 3.84
135 136 0.755698 GTACCTGAGGCTCCCGATGA 60.756 60.000 12.86 0.00 0.00 2.92
136 137 0.188587 TACCTGAGGCTCCCGATGAT 59.811 55.000 12.86 0.00 0.00 2.45
137 138 1.370437 CCTGAGGCTCCCGATGATG 59.630 63.158 12.86 0.00 0.00 3.07
138 139 1.301558 CTGAGGCTCCCGATGATGC 60.302 63.158 12.86 0.00 0.00 3.91
139 140 1.756408 CTGAGGCTCCCGATGATGCT 61.756 60.000 12.86 0.00 0.00 3.79
140 141 1.301558 GAGGCTCCCGATGATGCTG 60.302 63.158 2.15 0.00 0.00 4.41
141 142 2.976903 GGCTCCCGATGATGCTGC 60.977 66.667 0.00 0.00 0.00 5.25
142 143 3.344215 GCTCCCGATGATGCTGCG 61.344 66.667 0.00 0.00 0.00 5.18
143 144 2.418777 CTCCCGATGATGCTGCGA 59.581 61.111 0.00 0.00 0.00 5.10
144 145 1.005275 CTCCCGATGATGCTGCGAT 60.005 57.895 0.00 0.00 0.00 4.58
145 146 0.244721 CTCCCGATGATGCTGCGATA 59.755 55.000 0.00 0.00 0.00 2.92
146 147 0.244721 TCCCGATGATGCTGCGATAG 59.755 55.000 0.00 0.00 0.00 2.08
147 148 0.244721 CCCGATGATGCTGCGATAGA 59.755 55.000 0.00 0.00 39.76 1.98
148 149 1.626747 CCGATGATGCTGCGATAGAG 58.373 55.000 0.00 0.00 39.76 2.43
149 150 1.067985 CCGATGATGCTGCGATAGAGT 60.068 52.381 0.00 0.00 39.76 3.24
150 151 1.984297 CGATGATGCTGCGATAGAGTG 59.016 52.381 0.00 0.00 39.76 3.51
151 152 2.606551 CGATGATGCTGCGATAGAGTGT 60.607 50.000 0.00 0.00 39.76 3.55
152 153 3.365364 CGATGATGCTGCGATAGAGTGTA 60.365 47.826 0.00 0.00 39.76 2.90
153 154 3.632855 TGATGCTGCGATAGAGTGTAG 57.367 47.619 0.00 0.00 39.76 2.74
154 155 2.287849 TGATGCTGCGATAGAGTGTAGC 60.288 50.000 0.00 0.00 39.76 3.58
155 156 1.102978 TGCTGCGATAGAGTGTAGCA 58.897 50.000 0.85 0.85 38.68 3.49
156 157 1.683385 TGCTGCGATAGAGTGTAGCAT 59.317 47.619 0.85 0.00 36.37 3.79
157 158 2.287849 TGCTGCGATAGAGTGTAGCATC 60.288 50.000 0.85 0.00 36.37 3.91
158 159 2.924454 GCTGCGATAGAGTGTAGCATCC 60.924 54.545 0.00 0.00 37.20 3.51
159 160 2.294512 CTGCGATAGAGTGTAGCATCCA 59.705 50.000 0.00 0.00 37.20 3.41
160 161 2.034685 TGCGATAGAGTGTAGCATCCAC 59.965 50.000 0.00 0.00 39.76 4.02
161 162 2.608261 GCGATAGAGTGTAGCATCCACC 60.608 54.545 0.00 0.00 39.76 4.61
162 163 2.350868 CGATAGAGTGTAGCATCCACCG 60.351 54.545 0.00 0.00 39.76 4.94
163 164 0.744874 TAGAGTGTAGCATCCACCGC 59.255 55.000 0.00 0.00 33.20 5.68
164 165 1.521681 GAGTGTAGCATCCACCGCC 60.522 63.158 0.00 0.00 33.20 6.13
165 166 1.961180 GAGTGTAGCATCCACCGCCT 61.961 60.000 0.00 0.00 33.20 5.52
166 167 1.078426 GTGTAGCATCCACCGCCTT 60.078 57.895 0.00 0.00 0.00 4.35
167 168 1.090052 GTGTAGCATCCACCGCCTTC 61.090 60.000 0.00 0.00 0.00 3.46
168 169 1.264749 TGTAGCATCCACCGCCTTCT 61.265 55.000 0.00 0.00 0.00 2.85
169 170 0.530870 GTAGCATCCACCGCCTTCTC 60.531 60.000 0.00 0.00 0.00 2.87
170 171 2.016393 TAGCATCCACCGCCTTCTCG 62.016 60.000 0.00 0.00 0.00 4.04
178 179 4.955089 CGCCTTCTCGGAGCTATC 57.045 61.111 0.00 0.00 33.16 2.08
179 180 1.287503 CGCCTTCTCGGAGCTATCC 59.712 63.158 0.00 0.00 42.81 2.59
180 181 1.175983 CGCCTTCTCGGAGCTATCCT 61.176 60.000 0.00 0.00 44.22 3.24
181 182 1.044611 GCCTTCTCGGAGCTATCCTT 58.955 55.000 0.00 0.00 44.22 3.36
182 183 1.270041 GCCTTCTCGGAGCTATCCTTG 60.270 57.143 0.00 0.00 44.22 3.61
183 184 1.270041 CCTTCTCGGAGCTATCCTTGC 60.270 57.143 0.00 0.00 44.22 4.01
184 185 1.686052 CTTCTCGGAGCTATCCTTGCT 59.314 52.381 0.00 0.00 44.22 3.91
185 186 1.035923 TCTCGGAGCTATCCTTGCTG 58.964 55.000 0.00 0.00 44.22 4.41
186 187 1.035923 CTCGGAGCTATCCTTGCTGA 58.964 55.000 0.00 0.00 44.22 4.26
187 188 1.000385 CTCGGAGCTATCCTTGCTGAG 60.000 57.143 0.00 0.00 44.22 3.35
188 189 0.599728 CGGAGCTATCCTTGCTGAGC 60.600 60.000 0.00 0.00 44.22 4.26
190 191 1.140652 GGAGCTATCCTTGCTGAGCTT 59.859 52.381 5.83 0.00 45.15 3.74
191 192 2.482864 GAGCTATCCTTGCTGAGCTTC 58.517 52.381 5.83 0.00 45.15 3.86
192 193 1.836166 AGCTATCCTTGCTGAGCTTCA 59.164 47.619 5.83 0.00 42.59 3.02
193 194 2.158928 AGCTATCCTTGCTGAGCTTCAG 60.159 50.000 5.83 8.34 46.90 3.02
200 201 3.123620 CTGAGCTTCAGCCGTGCC 61.124 66.667 0.00 0.00 43.38 5.01
201 202 3.602513 CTGAGCTTCAGCCGTGCCT 62.603 63.158 0.00 0.00 43.38 4.75
202 203 2.817396 GAGCTTCAGCCGTGCCTC 60.817 66.667 0.00 0.00 43.38 4.70
203 204 4.400961 AGCTTCAGCCGTGCCTCC 62.401 66.667 0.00 0.00 43.38 4.30
204 205 4.704833 GCTTCAGCCGTGCCTCCA 62.705 66.667 0.00 0.00 34.31 3.86
205 206 2.270205 CTTCAGCCGTGCCTCCAT 59.730 61.111 0.00 0.00 0.00 3.41
206 207 1.377725 CTTCAGCCGTGCCTCCATT 60.378 57.895 0.00 0.00 0.00 3.16
207 208 1.651240 CTTCAGCCGTGCCTCCATTG 61.651 60.000 0.00 0.00 0.00 2.82
208 209 3.136123 CAGCCGTGCCTCCATTGG 61.136 66.667 0.00 0.00 0.00 3.16
209 210 3.329889 AGCCGTGCCTCCATTGGA 61.330 61.111 5.05 5.05 0.00 3.53
217 218 3.181367 CTCCATTGGAGCGTGCAC 58.819 61.111 19.49 6.82 43.29 4.57
218 219 2.741985 TCCATTGGAGCGTGCACG 60.742 61.111 34.01 34.01 43.27 5.34
219 220 3.803082 CCATTGGAGCGTGCACGG 61.803 66.667 37.47 20.19 40.23 4.94
220 221 4.465512 CATTGGAGCGTGCACGGC 62.466 66.667 37.47 28.57 40.23 5.68
229 230 4.107051 GTGCACGGCATGGCAGTC 62.107 66.667 20.37 7.34 41.91 3.51
232 233 2.360350 CACGGCATGGCAGTCCTT 60.360 61.111 20.37 0.00 34.30 3.36
233 234 2.045926 ACGGCATGGCAGTCCTTC 60.046 61.111 20.37 0.00 29.95 3.46
234 235 2.046023 CGGCATGGCAGTCCTTCA 60.046 61.111 20.37 0.00 0.00 3.02
235 236 1.452651 CGGCATGGCAGTCCTTCAT 60.453 57.895 20.37 0.00 0.00 2.57
236 237 1.721664 CGGCATGGCAGTCCTTCATG 61.722 60.000 20.37 0.00 40.66 3.07
241 242 3.194719 GCAGTCCTTCATGCCTGC 58.805 61.111 0.00 0.00 42.94 4.85
344 347 3.307480 CCCCGATTCAGTCCACTTAACTT 60.307 47.826 0.00 0.00 0.00 2.66
348 351 4.559251 CGATTCAGTCCACTTAACTTCTCG 59.441 45.833 0.00 0.00 0.00 4.04
493 501 0.339859 ACCAGGGCTCTCTCCACATA 59.660 55.000 0.00 0.00 0.00 2.29
568 576 5.993106 AACAGCAGAGAAACTTGTACTTC 57.007 39.130 0.00 0.00 0.00 3.01
649 658 2.099756 ACCCGCGTATTCTTGTAGGTAC 59.900 50.000 4.92 0.00 0.00 3.34
900 912 1.480545 TGAGTACCACACCATCATCCG 59.519 52.381 0.00 0.00 0.00 4.18
945 957 4.222145 TCAGTACTAAAAATCTCAGGCGGT 59.778 41.667 0.00 0.00 0.00 5.68
1066 1092 1.538950 CTTTCCTTGGACTTGCTGCTC 59.461 52.381 0.00 0.00 0.00 4.26
1074 1100 1.949847 GACTTGCTGCTCGCCTCCTA 61.950 60.000 0.00 0.00 38.05 2.94
1100 1126 1.280421 CTTTGCCTCTCCTACCAGCTT 59.720 52.381 0.00 0.00 0.00 3.74
1401 1427 2.945008 CAGAAGCATTATTGGCCTCGAA 59.055 45.455 3.32 0.00 0.00 3.71
1467 1493 0.113190 CAAACCCCAGCCTTCCTCTT 59.887 55.000 0.00 0.00 0.00 2.85
1620 1646 0.460722 TCAATGCCCCATCATTTGCG 59.539 50.000 0.00 0.00 34.68 4.85
1779 1806 2.568956 ACTGGAGCACATCTCTTTAGCA 59.431 45.455 0.00 0.00 41.60 3.49
1787 1814 5.474532 AGCACATCTCTTTAGCAAACAATGA 59.525 36.000 0.00 0.00 0.00 2.57
2172 2199 0.770499 TTCATGGCCAGTTCTCACCA 59.230 50.000 13.05 0.00 36.43 4.17
2308 2341 3.942130 GGAACCAATTTCAAGGGTGAG 57.058 47.619 0.00 0.00 35.70 3.51
2362 2395 6.968131 TTTGAGAATCTTCAGGTATTGACG 57.032 37.500 0.00 0.00 34.94 4.35
2369 2402 9.521841 AGAATCTTCAGGTATTGACGATAGATA 57.478 33.333 0.00 0.00 42.19 1.98
2465 2499 8.684386 TTAAATCAACTCACTGGACAAATACA 57.316 30.769 0.00 0.00 0.00 2.29
2468 2502 7.765695 ATCAACTCACTGGACAAATACAATT 57.234 32.000 0.00 0.00 0.00 2.32
2900 4502 8.947055 AACTGCATTTTAAACTTCTTTGTCAT 57.053 26.923 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.202690 TGCTTCGGTACATCGCGG 60.203 61.111 6.13 0.00 0.00 6.46
2 3 2.230940 CCTGCTTCGGTACATCGCG 61.231 63.158 0.00 0.00 0.00 5.87
4 5 1.421410 GCACCTGCTTCGGTACATCG 61.421 60.000 0.00 0.00 34.94 3.84
6 7 4.617875 GCACCTGCTTCGGTACAT 57.382 55.556 0.00 0.00 34.94 2.29
16 17 3.730761 CTGCCGTCAAGCACCTGC 61.731 66.667 0.00 0.00 38.00 4.85
17 18 3.730761 GCTGCCGTCAAGCACCTG 61.731 66.667 0.00 0.00 38.00 4.00
20 21 3.782244 CTCGCTGCCGTCAAGCAC 61.782 66.667 0.00 0.00 38.00 4.40
21 22 3.300934 ATCTCGCTGCCGTCAAGCA 62.301 57.895 0.00 0.00 41.46 3.91
22 23 2.510238 ATCTCGCTGCCGTCAAGC 60.510 61.111 0.00 0.00 35.54 4.01
23 24 0.529337 ATCATCTCGCTGCCGTCAAG 60.529 55.000 0.00 0.00 35.54 3.02
24 25 0.528466 GATCATCTCGCTGCCGTCAA 60.528 55.000 0.00 0.00 35.54 3.18
25 26 1.066422 GATCATCTCGCTGCCGTCA 59.934 57.895 0.00 0.00 35.54 4.35
26 27 2.013483 CGATCATCTCGCTGCCGTC 61.013 63.158 0.00 0.00 41.14 4.79
27 28 2.026734 CGATCATCTCGCTGCCGT 59.973 61.111 0.00 0.00 41.14 5.68
35 36 1.958205 CCCGGCAAGCGATCATCTC 60.958 63.158 0.00 0.00 0.00 2.75
36 37 2.109799 CCCGGCAAGCGATCATCT 59.890 61.111 0.00 0.00 0.00 2.90
37 38 2.974698 CCCCGGCAAGCGATCATC 60.975 66.667 0.00 0.00 0.00 2.92
45 46 3.142838 CATGGAAGCCCCGGCAAG 61.143 66.667 8.74 0.00 44.88 4.01
46 47 3.216985 TTCATGGAAGCCCCGGCAA 62.217 57.895 8.74 0.00 44.88 4.52
47 48 3.656280 TTCATGGAAGCCCCGGCA 61.656 61.111 8.74 0.00 44.88 5.69
48 49 3.140814 GTTCATGGAAGCCCCGGC 61.141 66.667 0.00 0.00 42.33 6.13
49 50 1.632018 TAGGTTCATGGAAGCCCCGG 61.632 60.000 0.00 0.00 40.41 5.73
50 51 0.463833 GTAGGTTCATGGAAGCCCCG 60.464 60.000 4.69 0.00 40.41 5.73
51 52 0.919710 AGTAGGTTCATGGAAGCCCC 59.080 55.000 4.69 0.00 40.41 5.80
52 53 1.559682 TGAGTAGGTTCATGGAAGCCC 59.440 52.381 4.69 0.00 40.41 5.19
53 54 2.420687 CCTGAGTAGGTTCATGGAAGCC 60.421 54.545 4.69 0.00 40.41 4.35
54 55 2.911484 CCTGAGTAGGTTCATGGAAGC 58.089 52.381 0.00 0.15 39.39 3.86
74 75 0.317770 TCACGTTCGTTGTCGGGTAC 60.318 55.000 0.00 0.00 37.69 3.34
75 76 0.597568 ATCACGTTCGTTGTCGGGTA 59.402 50.000 0.00 0.00 37.69 3.69
76 77 0.942410 CATCACGTTCGTTGTCGGGT 60.942 55.000 0.00 0.00 37.69 5.28
77 78 0.942410 ACATCACGTTCGTTGTCGGG 60.942 55.000 0.00 0.00 37.69 5.14
78 79 0.433492 GACATCACGTTCGTTGTCGG 59.567 55.000 12.20 0.00 37.69 4.79
79 80 0.433492 GGACATCACGTTCGTTGTCG 59.567 55.000 17.70 0.69 39.45 4.35
80 81 0.433492 CGGACATCACGTTCGTTGTC 59.567 55.000 16.70 16.70 42.07 3.18
81 82 0.942410 CCGGACATCACGTTCGTTGT 60.942 55.000 0.00 2.96 45.89 3.32
82 83 0.942410 ACCGGACATCACGTTCGTTG 60.942 55.000 9.46 0.00 45.89 4.10
83 84 0.665369 GACCGGACATCACGTTCGTT 60.665 55.000 9.46 0.00 45.89 3.85
84 85 1.080974 GACCGGACATCACGTTCGT 60.081 57.895 9.46 0.00 45.89 3.85
85 86 2.150218 CGACCGGACATCACGTTCG 61.150 63.158 9.46 0.00 46.97 3.95
86 87 1.804326 CCGACCGGACATCACGTTC 60.804 63.158 9.46 0.00 37.50 3.95
87 88 2.260434 CCGACCGGACATCACGTT 59.740 61.111 9.46 0.00 37.50 3.99
88 89 3.755628 CCCGACCGGACATCACGT 61.756 66.667 9.46 0.00 37.50 4.49
89 90 3.755628 ACCCGACCGGACATCACG 61.756 66.667 9.46 3.72 37.50 4.35
90 91 2.125673 CACCCGACCGGACATCAC 60.126 66.667 9.46 0.00 37.50 3.06
91 92 2.602267 ACACCCGACCGGACATCA 60.602 61.111 9.46 0.00 37.50 3.07
92 93 2.125673 CACACCCGACCGGACATC 60.126 66.667 9.46 0.00 37.50 3.06
93 94 4.388499 GCACACCCGACCGGACAT 62.388 66.667 9.46 0.00 37.50 3.06
100 101 2.922950 TACCTCGTGCACACCCGAC 61.923 63.158 18.64 0.00 0.00 4.79
101 102 2.598099 TACCTCGTGCACACCCGA 60.598 61.111 18.64 7.34 0.00 5.14
102 103 2.431942 GTACCTCGTGCACACCCG 60.432 66.667 18.64 2.38 0.00 5.28
103 104 2.047560 GGTACCTCGTGCACACCC 60.048 66.667 18.64 2.77 0.00 4.61
104 105 1.374252 CAGGTACCTCGTGCACACC 60.374 63.158 18.64 16.01 0.00 4.16
105 106 0.388649 CTCAGGTACCTCGTGCACAC 60.389 60.000 18.64 6.69 32.68 3.82
106 107 1.532604 CCTCAGGTACCTCGTGCACA 61.533 60.000 18.64 3.15 32.68 4.57
107 108 1.215647 CCTCAGGTACCTCGTGCAC 59.784 63.158 12.84 6.82 32.68 4.57
108 109 2.646175 GCCTCAGGTACCTCGTGCA 61.646 63.158 12.84 0.00 32.68 4.57
109 110 2.184579 GCCTCAGGTACCTCGTGC 59.815 66.667 12.84 10.84 32.68 5.34
110 111 1.668101 GGAGCCTCAGGTACCTCGTG 61.668 65.000 12.84 8.71 0.00 4.35
111 112 1.380112 GGAGCCTCAGGTACCTCGT 60.380 63.158 12.84 0.00 0.00 4.18
112 113 2.128507 GGGAGCCTCAGGTACCTCG 61.129 68.421 12.84 8.23 41.76 4.63
113 114 2.128507 CGGGAGCCTCAGGTACCTC 61.129 68.421 12.84 0.00 42.96 3.85
114 115 1.950748 ATCGGGAGCCTCAGGTACCT 61.951 60.000 9.21 9.21 42.96 3.08
115 116 1.457831 ATCGGGAGCCTCAGGTACC 60.458 63.158 2.73 2.73 41.56 3.34
116 117 0.755698 TCATCGGGAGCCTCAGGTAC 60.756 60.000 0.00 0.00 0.00 3.34
117 118 0.188587 ATCATCGGGAGCCTCAGGTA 59.811 55.000 0.00 0.00 0.00 3.08
118 119 1.074926 ATCATCGGGAGCCTCAGGT 60.075 57.895 0.00 0.00 0.00 4.00
119 120 1.370437 CATCATCGGGAGCCTCAGG 59.630 63.158 0.00 0.00 0.00 3.86
120 121 1.301558 GCATCATCGGGAGCCTCAG 60.302 63.158 0.00 0.00 0.00 3.35
121 122 1.763655 AGCATCATCGGGAGCCTCA 60.764 57.895 0.00 0.00 0.00 3.86
122 123 1.301558 CAGCATCATCGGGAGCCTC 60.302 63.158 0.00 0.00 0.00 4.70
123 124 2.827423 CAGCATCATCGGGAGCCT 59.173 61.111 0.00 0.00 0.00 4.58
124 125 2.976903 GCAGCATCATCGGGAGCC 60.977 66.667 0.00 0.00 0.00 4.70
125 126 3.344215 CGCAGCATCATCGGGAGC 61.344 66.667 0.00 0.00 0.00 4.70
126 127 0.244721 TATCGCAGCATCATCGGGAG 59.755 55.000 0.00 0.00 0.00 4.30
127 128 0.244721 CTATCGCAGCATCATCGGGA 59.755 55.000 0.00 0.00 0.00 5.14
128 129 0.244721 TCTATCGCAGCATCATCGGG 59.755 55.000 0.00 0.00 0.00 5.14
129 130 1.067985 ACTCTATCGCAGCATCATCGG 60.068 52.381 0.00 0.00 0.00 4.18
130 131 1.984297 CACTCTATCGCAGCATCATCG 59.016 52.381 0.00 0.00 0.00 3.84
131 132 3.023946 ACACTCTATCGCAGCATCATC 57.976 47.619 0.00 0.00 0.00 2.92
132 133 3.613671 GCTACACTCTATCGCAGCATCAT 60.614 47.826 0.00 0.00 0.00 2.45
133 134 2.287849 GCTACACTCTATCGCAGCATCA 60.288 50.000 0.00 0.00 0.00 3.07
134 135 2.287849 TGCTACACTCTATCGCAGCATC 60.288 50.000 0.00 0.00 34.30 3.91
135 136 1.683385 TGCTACACTCTATCGCAGCAT 59.317 47.619 0.00 0.00 34.30 3.79
136 137 1.102978 TGCTACACTCTATCGCAGCA 58.897 50.000 0.00 0.00 36.72 4.41
137 138 2.323959 GATGCTACACTCTATCGCAGC 58.676 52.381 0.00 0.00 33.72 5.25
138 139 2.294512 TGGATGCTACACTCTATCGCAG 59.705 50.000 0.00 0.00 33.72 5.18
139 140 2.034685 GTGGATGCTACACTCTATCGCA 59.965 50.000 0.00 0.00 35.98 5.10
140 141 2.608261 GGTGGATGCTACACTCTATCGC 60.608 54.545 6.09 0.00 38.83 4.58
141 142 2.350868 CGGTGGATGCTACACTCTATCG 60.351 54.545 6.09 0.00 38.83 2.92
142 143 2.608261 GCGGTGGATGCTACACTCTATC 60.608 54.545 6.09 0.00 38.83 2.08
143 144 1.341531 GCGGTGGATGCTACACTCTAT 59.658 52.381 6.09 0.00 38.83 1.98
144 145 0.744874 GCGGTGGATGCTACACTCTA 59.255 55.000 6.09 0.00 38.83 2.43
145 146 1.517832 GCGGTGGATGCTACACTCT 59.482 57.895 6.09 0.00 38.83 3.24
146 147 1.521681 GGCGGTGGATGCTACACTC 60.522 63.158 6.09 0.46 38.83 3.51
147 148 1.553690 AAGGCGGTGGATGCTACACT 61.554 55.000 6.09 0.00 38.83 3.55
148 149 1.078426 AAGGCGGTGGATGCTACAC 60.078 57.895 0.00 0.00 38.10 2.90
149 150 1.220749 GAAGGCGGTGGATGCTACA 59.779 57.895 0.00 0.00 0.00 2.74
150 151 0.530870 GAGAAGGCGGTGGATGCTAC 60.531 60.000 0.00 0.00 0.00 3.58
151 152 1.823295 GAGAAGGCGGTGGATGCTA 59.177 57.895 0.00 0.00 0.00 3.49
152 153 2.586792 GAGAAGGCGGTGGATGCT 59.413 61.111 0.00 0.00 0.00 3.79
153 154 2.892425 CGAGAAGGCGGTGGATGC 60.892 66.667 0.00 0.00 0.00 3.91
154 155 2.202932 CCGAGAAGGCGGTGGATG 60.203 66.667 0.00 0.00 46.07 3.51
161 162 1.287503 GGATAGCTCCGAGAAGGCG 59.712 63.158 0.00 0.00 40.77 5.52
170 171 0.758123 AGCTCAGCAAGGATAGCTCC 59.242 55.000 0.00 0.00 41.35 4.70
171 172 2.158986 TGAAGCTCAGCAAGGATAGCTC 60.159 50.000 0.00 0.00 44.30 4.09
172 173 1.836166 TGAAGCTCAGCAAGGATAGCT 59.164 47.619 0.00 0.00 46.96 3.32
173 174 2.211806 CTGAAGCTCAGCAAGGATAGC 58.788 52.381 0.00 0.00 37.72 2.97
183 184 3.123620 GGCACGGCTGAAGCTCAG 61.124 66.667 0.00 8.34 46.90 3.35
184 185 3.596066 GAGGCACGGCTGAAGCTCA 62.596 63.158 0.00 0.00 41.70 4.26
185 186 2.817396 GAGGCACGGCTGAAGCTC 60.817 66.667 0.00 0.00 41.70 4.09
186 187 4.400961 GGAGGCACGGCTGAAGCT 62.401 66.667 0.00 0.00 41.70 3.74
187 188 3.984193 ATGGAGGCACGGCTGAAGC 62.984 63.158 0.00 2.39 41.14 3.86
188 189 1.377725 AATGGAGGCACGGCTGAAG 60.378 57.895 0.00 0.00 0.00 3.02
189 190 1.675310 CAATGGAGGCACGGCTGAA 60.675 57.895 0.00 0.00 0.00 3.02
190 191 2.046023 CAATGGAGGCACGGCTGA 60.046 61.111 0.00 0.00 0.00 4.26
191 192 3.136123 CCAATGGAGGCACGGCTG 61.136 66.667 0.00 0.00 0.00 4.85
192 193 3.329889 TCCAATGGAGGCACGGCT 61.330 61.111 0.00 0.00 0.00 5.52
193 194 2.825836 CTCCAATGGAGGCACGGC 60.826 66.667 21.25 0.00 45.43 5.68
201 202 2.741985 CGTGCACGCTCCAATGGA 60.742 61.111 28.16 0.48 0.00 3.41
202 203 3.803082 CCGTGCACGCTCCAATGG 61.803 66.667 33.17 13.44 38.18 3.16
203 204 4.465512 GCCGTGCACGCTCCAATG 62.466 66.667 33.17 18.44 38.18 2.82
212 213 4.107051 GACTGCCATGCCGTGCAC 62.107 66.667 6.82 6.82 43.04 4.57
215 216 2.360350 AAGGACTGCCATGCCGTG 60.360 61.111 0.00 0.00 36.29 4.94
216 217 2.045926 GAAGGACTGCCATGCCGT 60.046 61.111 0.00 0.00 36.29 5.68
217 218 1.452651 ATGAAGGACTGCCATGCCG 60.453 57.895 0.00 0.00 36.29 5.69
218 219 2.112898 CATGAAGGACTGCCATGCC 58.887 57.895 0.00 0.00 36.29 4.40
226 227 0.395311 CATGGCAGGCATGAAGGACT 60.395 55.000 28.95 0.00 32.09 3.85
227 228 0.682209 ACATGGCAGGCATGAAGGAC 60.682 55.000 36.69 0.00 34.39 3.85
228 229 0.681887 CACATGGCAGGCATGAAGGA 60.682 55.000 36.69 0.00 34.39 3.36
229 230 1.672854 CCACATGGCAGGCATGAAGG 61.673 60.000 36.69 30.91 34.39 3.46
230 231 0.968901 ACCACATGGCAGGCATGAAG 60.969 55.000 36.69 28.14 39.32 3.02
231 232 0.966875 GACCACATGGCAGGCATGAA 60.967 55.000 36.69 0.00 39.32 2.57
232 233 1.378911 GACCACATGGCAGGCATGA 60.379 57.895 36.69 0.00 39.32 3.07
233 234 2.767445 CGACCACATGGCAGGCATG 61.767 63.158 30.44 30.44 39.32 4.06
234 235 2.438975 CGACCACATGGCAGGCAT 60.439 61.111 2.93 2.93 39.32 4.40
235 236 3.610619 CTCGACCACATGGCAGGCA 62.611 63.158 0.00 0.00 39.32 4.75
236 237 2.821366 CTCGACCACATGGCAGGC 60.821 66.667 0.00 0.00 39.32 4.85
237 238 1.742880 CACTCGACCACATGGCAGG 60.743 63.158 0.00 0.00 39.32 4.85
238 239 1.742880 CCACTCGACCACATGGCAG 60.743 63.158 0.00 0.00 39.32 4.85
239 240 2.347114 CCACTCGACCACATGGCA 59.653 61.111 0.00 0.00 39.32 4.92
240 241 2.436646 CCCACTCGACCACATGGC 60.437 66.667 0.00 0.00 39.32 4.40
241 242 2.436646 GCCCACTCGACCACATGG 60.437 66.667 0.00 0.00 42.17 3.66
493 501 2.911636 TGGCCATTTTGATTGGAACCAT 59.088 40.909 0.00 0.00 36.26 3.55
568 576 9.793259 ATTTTATCCTACCACCAGTATGTATTG 57.207 33.333 0.00 0.00 0.00 1.90
649 658 4.615588 AAGTCAACTCTTGAGAGAAGGG 57.384 45.455 14.61 1.86 44.74 3.95
900 912 3.359950 AGCCATGAGGAAAACAGGAATC 58.640 45.455 0.00 0.00 36.89 2.52
945 957 8.896320 TGTACTGCTCTGAACAATACTAAAAA 57.104 30.769 2.02 0.00 0.00 1.94
1066 1092 1.646189 GCAAAGAAGAGTAGGAGGCG 58.354 55.000 0.00 0.00 0.00 5.52
1074 1100 2.835156 GGTAGGAGAGGCAAAGAAGAGT 59.165 50.000 0.00 0.00 0.00 3.24
1194 1220 1.350684 TCCCATTTGCAGCAGTCTGTA 59.649 47.619 0.93 0.00 42.29 2.74
1401 1427 1.131638 TGAGGTGGTTGAAGCTGACT 58.868 50.000 0.00 0.00 0.00 3.41
1467 1493 6.544928 TTGCTTGAGATATTCAGTACCTGA 57.455 37.500 0.00 0.00 38.87 3.86
1620 1646 8.789825 ATTGGTTATATGAGAGATCAAGCATC 57.210 34.615 0.00 0.00 0.00 3.91
1779 1806 6.165700 AGAACTCCTTGCAAATCATTGTTT 57.834 33.333 0.00 0.00 38.85 2.83
2172 2199 3.766051 GGACCTGAGATTTCCAATGCTTT 59.234 43.478 0.00 0.00 0.00 3.51
2308 2341 6.455360 AATGTTTCATCATGTGGTATGGTC 57.545 37.500 0.00 0.00 0.00 4.02
2362 2395 6.506500 CCAGTCAATGGGCAATTATCTATC 57.493 41.667 0.00 0.00 46.36 2.08
2465 2499 3.703052 GCCCAGTTCATCAATCCAGAATT 59.297 43.478 0.00 0.00 0.00 2.17
2468 2502 1.918262 AGCCCAGTTCATCAATCCAGA 59.082 47.619 0.00 0.00 0.00 3.86
2872 4474 8.196802 ACAAAGAAGTTTAAAATGCAGTTTCC 57.803 30.769 16.40 5.65 0.00 3.13



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

AutoCloner maintained by Alex Coulton.