Multiple sequence alignment - TraesCS1D01G267900

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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 TraesCS1D01G267900 chr1D 100.000 2515 0 0 1 2515 363796197 363793683 0.000000e+00 4645
1 TraesCS1D01G267900 chr1D 94.618 706 35 3 1812 2515 480194172 480194876 0.000000e+00 1090
2 TraesCS1D01G267900 chr1D 94.579 701 37 1 1816 2515 91504600 91503900 0.000000e+00 1083
3 TraesCS1D01G267900 chr1D 78.368 809 117 33 970 1724 363801542 363800738 2.930000e-129 472
4 TraesCS1D01G267900 chr1D 88.034 234 27 1 255 487 363803823 363803590 2.460000e-70 276
5 TraesCS1D01G267900 chr1A 90.904 1627 89 28 232 1815 463031368 463029758 0.000000e+00 2130
6 TraesCS1D01G267900 chr1A 85.150 633 71 16 1 625 463030328 463029711 5.910000e-176 627
7 TraesCS1D01G267900 chr1A 96.053 228 7 2 1 227 463031633 463031407 1.100000e-98 370
8 TraesCS1D01G267900 chr1A 79.806 515 79 14 970 1461 463031926 463031414 3.980000e-93 351
9 TraesCS1D01G267900 chr1A 79.671 487 79 14 1254 1724 463037975 463037493 1.440000e-87 333
10 TraesCS1D01G267900 chr1B 93.625 847 24 14 232 1052 487011970 487011128 0.000000e+00 1238
11 TraesCS1D01G267900 chr1B 94.415 752 35 5 1049 1795 487011048 487010299 0.000000e+00 1149
12 TraesCS1D01G267900 chr1B 83.394 548 80 9 16 558 487010840 487010299 4.830000e-137 497
13 TraesCS1D01G267900 chr1B 80.194 515 76 14 970 1461 487012527 487012016 1.840000e-96 363
14 TraesCS1D01G267900 chr1B 94.444 234 12 1 1 233 487012236 487012003 2.380000e-95 359
15 TraesCS1D01G267900 chr5D 95.720 701 28 2 1816 2515 559142498 559141799 0.000000e+00 1127
16 TraesCS1D01G267900 chr6D 95.467 706 30 2 1812 2515 23413892 23414597 0.000000e+00 1125
17 TraesCS1D01G267900 chr6D 94.901 706 34 2 1812 2515 122819590 122820295 0.000000e+00 1103
18 TraesCS1D01G267900 chr3D 95.184 706 32 2 1812 2515 71811329 71812034 0.000000e+00 1114
19 TraesCS1D01G267900 chr3D 94.334 706 38 2 1812 2515 488466185 488466890 0.000000e+00 1081
20 TraesCS1D01G267900 chr7D 94.729 702 35 2 1816 2515 543268089 543268790 0.000000e+00 1090
21 TraesCS1D01G267900 chr2D 94.476 706 37 2 1812 2515 483929176 483928471 0.000000e+00 1086


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 TraesCS1D01G267900 chr1D 363793683 363796197 2514 True 4645.0 4645 100.00000 1 2515 1 chr1D.!!$R2 2514
1 TraesCS1D01G267900 chr1D 480194172 480194876 704 False 1090.0 1090 94.61800 1812 2515 1 chr1D.!!$F1 703
2 TraesCS1D01G267900 chr1D 91503900 91504600 700 True 1083.0 1083 94.57900 1816 2515 1 chr1D.!!$R1 699
3 TraesCS1D01G267900 chr1D 363800738 363803823 3085 True 374.0 472 83.20100 255 1724 2 chr1D.!!$R3 1469
4 TraesCS1D01G267900 chr1A 463029711 463031926 2215 True 869.5 2130 87.97825 1 1815 4 chr1A.!!$R2 1814
5 TraesCS1D01G267900 chr1B 487010299 487012527 2228 True 721.2 1238 89.21440 1 1795 5 chr1B.!!$R1 1794
6 TraesCS1D01G267900 chr5D 559141799 559142498 699 True 1127.0 1127 95.72000 1816 2515 1 chr5D.!!$R1 699
7 TraesCS1D01G267900 chr6D 23413892 23414597 705 False 1125.0 1125 95.46700 1812 2515 1 chr6D.!!$F1 703
8 TraesCS1D01G267900 chr6D 122819590 122820295 705 False 1103.0 1103 94.90100 1812 2515 1 chr6D.!!$F2 703
9 TraesCS1D01G267900 chr3D 71811329 71812034 705 False 1114.0 1114 95.18400 1812 2515 1 chr3D.!!$F1 703
10 TraesCS1D01G267900 chr3D 488466185 488466890 705 False 1081.0 1081 94.33400 1812 2515 1 chr3D.!!$F2 703
11 TraesCS1D01G267900 chr7D 543268089 543268790 701 False 1090.0 1090 94.72900 1816 2515 1 chr7D.!!$F1 699
12 TraesCS1D01G267900 chr2D 483928471 483929176 705 True 1086.0 1086 94.47600 1812 2515 1 chr2D.!!$R1 703

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
107 108 0.035317 CTGTGTAGGCTTCCTGTGCA 59.965 55.0 0.0 0.0 34.61 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 4605 0.11456 TCGAAGAGTCAGGGGGAGTT 59.885 55.0 0.0 0.0 0.0 3.01 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
49 50 4.171663 ACATGCATGTTAATTCGTTGCA 57.828 36.364 26.61 7.46 37.90 4.08
50 51 4.168014 ACATGCATGTTAATTCGTTGCAG 58.832 39.130 26.61 0.00 37.90 4.41
52 53 4.495911 TGCATGTTAATTCGTTGCAGAA 57.504 36.364 0.00 0.00 34.31 3.02
53 54 4.864633 TGCATGTTAATTCGTTGCAGAAA 58.135 34.783 0.00 0.00 33.43 2.52
54 55 5.284864 TGCATGTTAATTCGTTGCAGAAAA 58.715 33.333 0.00 0.00 33.43 2.29
55 56 5.401972 TGCATGTTAATTCGTTGCAGAAAAG 59.598 36.000 0.00 0.00 33.43 2.27
57 58 6.143758 GCATGTTAATTCGTTGCAGAAAAGAA 59.856 34.615 0.00 0.00 39.98 2.52
58 59 7.617935 GCATGTTAATTCGTTGCAGAAAAGAAG 60.618 37.037 0.00 0.00 39.22 2.85
59 60 6.791303 TGTTAATTCGTTGCAGAAAAGAAGT 58.209 32.000 0.00 0.00 39.22 3.01
60 61 6.690957 TGTTAATTCGTTGCAGAAAAGAAGTG 59.309 34.615 0.46 0.00 39.22 3.16
61 62 2.755836 TCGTTGCAGAAAAGAAGTGC 57.244 45.000 0.00 0.00 37.73 4.40
62 63 2.288666 TCGTTGCAGAAAAGAAGTGCT 58.711 42.857 0.00 0.00 38.09 4.40
65 66 1.321474 TGCAGAAAAGAAGTGCTGGG 58.679 50.000 0.00 0.00 38.09 4.45
68 69 2.586425 CAGAAAAGAAGTGCTGGGGAA 58.414 47.619 0.00 0.00 0.00 3.97
69 70 2.958355 CAGAAAAGAAGTGCTGGGGAAA 59.042 45.455 0.00 0.00 0.00 3.13
71 72 4.766891 CAGAAAAGAAGTGCTGGGGAAATA 59.233 41.667 0.00 0.00 0.00 1.40
72 73 4.767409 AGAAAAGAAGTGCTGGGGAAATAC 59.233 41.667 0.00 0.00 0.00 1.89
73 74 2.808906 AGAAGTGCTGGGGAAATACC 57.191 50.000 0.00 0.00 38.08 2.73
74 75 2.279173 AGAAGTGCTGGGGAAATACCT 58.721 47.619 0.00 0.00 38.98 3.08
75 76 2.239907 AGAAGTGCTGGGGAAATACCTC 59.760 50.000 0.00 0.00 40.19 3.85
78 79 0.918983 TGCTGGGGAAATACCTCTGG 59.081 55.000 0.00 0.00 40.48 3.86
79 80 1.213296 GCTGGGGAAATACCTCTGGA 58.787 55.000 0.00 0.00 40.48 3.86
80 81 1.564348 GCTGGGGAAATACCTCTGGAA 59.436 52.381 0.00 0.00 40.48 3.53
81 82 2.422093 GCTGGGGAAATACCTCTGGAAG 60.422 54.545 0.00 0.00 40.48 3.46
82 83 2.846827 CTGGGGAAATACCTCTGGAAGT 59.153 50.000 0.00 0.00 40.48 3.01
83 84 2.844348 TGGGGAAATACCTCTGGAAGTC 59.156 50.000 0.00 0.00 40.48 3.01
84 85 2.172930 GGGGAAATACCTCTGGAAGTCC 59.827 54.545 0.00 0.00 35.94 3.85
85 86 2.844348 GGGAAATACCTCTGGAAGTCCA 59.156 50.000 0.00 0.00 40.41 4.02
86 87 3.370633 GGGAAATACCTCTGGAAGTCCAC 60.371 52.174 0.00 0.00 38.89 4.02
88 89 4.383226 GGAAATACCTCTGGAAGTCCACTC 60.383 50.000 0.00 0.00 37.05 3.51
89 90 3.767309 ATACCTCTGGAAGTCCACTCT 57.233 47.619 0.00 0.00 42.01 3.24
90 91 1.638529 ACCTCTGGAAGTCCACTCTG 58.361 55.000 0.00 0.00 42.01 3.35
91 92 1.133009 ACCTCTGGAAGTCCACTCTGT 60.133 52.381 0.00 0.00 42.01 3.41
92 93 1.274728 CCTCTGGAAGTCCACTCTGTG 59.725 57.143 0.00 0.00 42.01 3.66
93 94 1.967066 CTCTGGAAGTCCACTCTGTGT 59.033 52.381 0.00 0.00 42.01 3.72
94 95 3.157881 CTCTGGAAGTCCACTCTGTGTA 58.842 50.000 0.00 0.00 42.01 2.90
95 96 3.157881 TCTGGAAGTCCACTCTGTGTAG 58.842 50.000 0.00 0.00 42.01 2.74
96 97 2.232452 CTGGAAGTCCACTCTGTGTAGG 59.768 54.545 0.00 0.00 42.01 3.18
97 98 1.066787 GGAAGTCCACTCTGTGTAGGC 60.067 57.143 0.00 0.00 35.64 3.93
99 100 2.016905 AGTCCACTCTGTGTAGGCTT 57.983 50.000 0.00 0.00 0.00 4.35
101 102 1.066787 GTCCACTCTGTGTAGGCTTCC 60.067 57.143 0.00 0.00 0.00 3.46
103 104 1.066573 CCACTCTGTGTAGGCTTCCTG 60.067 57.143 0.00 0.00 34.61 3.86
104 105 1.620819 CACTCTGTGTAGGCTTCCTGT 59.379 52.381 0.00 0.00 34.61 4.00
105 106 1.620819 ACTCTGTGTAGGCTTCCTGTG 59.379 52.381 0.00 0.00 34.61 3.66
106 107 0.321671 TCTGTGTAGGCTTCCTGTGC 59.678 55.000 0.00 0.00 34.61 4.57
107 108 0.035317 CTGTGTAGGCTTCCTGTGCA 59.965 55.000 0.00 0.00 34.61 4.57
108 109 0.472044 TGTGTAGGCTTCCTGTGCAA 59.528 50.000 0.00 0.00 34.61 4.08
109 110 1.160137 GTGTAGGCTTCCTGTGCAAG 58.840 55.000 0.00 0.00 34.61 4.01
112 113 1.778017 TAGGCTTCCTGTGCAAGGCA 61.778 55.000 11.05 0.30 46.92 4.75
116 117 0.963962 CTTCCTGTGCAAGGCAACAT 59.036 50.000 9.35 0.00 46.92 2.71
117 118 0.675083 TTCCTGTGCAAGGCAACATG 59.325 50.000 9.35 0.00 46.92 3.21
126 127 2.343101 CAAGGCAACATGCTTGATTGG 58.657 47.619 6.60 0.00 44.28 3.16
127 128 1.927487 AGGCAACATGCTTGATTGGA 58.073 45.000 6.60 0.00 44.28 3.53
128 129 1.822990 AGGCAACATGCTTGATTGGAG 59.177 47.619 6.60 0.00 44.28 3.86
130 131 1.738030 GCAACATGCTTGATTGGAGGC 60.738 52.381 6.60 0.00 40.96 4.70
131 132 1.546923 CAACATGCTTGATTGGAGGCA 59.453 47.619 6.60 0.00 39.06 4.75
132 133 1.927487 ACATGCTTGATTGGAGGCAA 58.073 45.000 6.60 0.00 38.21 4.52
133 134 2.250031 ACATGCTTGATTGGAGGCAAA 58.750 42.857 6.60 0.00 38.21 3.68
134 135 2.633967 ACATGCTTGATTGGAGGCAAAA 59.366 40.909 6.60 0.00 38.21 2.44
136 137 3.322211 TGCTTGATTGGAGGCAAAATG 57.678 42.857 0.00 0.00 0.00 2.32
137 138 2.633967 TGCTTGATTGGAGGCAAAATGT 59.366 40.909 0.00 0.00 0.00 2.71
139 140 4.067192 GCTTGATTGGAGGCAAAATGTTT 58.933 39.130 0.00 0.00 0.00 2.83
140 141 5.221601 TGCTTGATTGGAGGCAAAATGTTTA 60.222 36.000 0.00 0.00 0.00 2.01
141 142 5.700373 GCTTGATTGGAGGCAAAATGTTTAA 59.300 36.000 0.00 0.00 0.00 1.52
142 143 6.347644 GCTTGATTGGAGGCAAAATGTTTAAC 60.348 38.462 0.00 0.00 0.00 2.01
143 144 5.226396 TGATTGGAGGCAAAATGTTTAACG 58.774 37.500 0.00 0.00 0.00 3.18
144 145 3.019933 TGGAGGCAAAATGTTTAACGC 57.980 42.857 0.00 0.00 0.00 4.84
145 146 2.288518 TGGAGGCAAAATGTTTAACGCC 60.289 45.455 3.33 3.33 39.90 5.68
146 147 2.288518 GGAGGCAAAATGTTTAACGCCA 60.289 45.455 12.13 0.00 42.10 5.69
148 149 3.584834 AGGCAAAATGTTTAACGCCATC 58.415 40.909 12.13 0.00 42.10 3.51
149 150 2.344142 GGCAAAATGTTTAACGCCATCG 59.656 45.455 6.17 0.00 39.38 3.84
162 163 1.801771 CGCCATCGTAAAGGAACACAA 59.198 47.619 0.00 0.00 0.00 3.33
163 164 2.159707 CGCCATCGTAAAGGAACACAAG 60.160 50.000 0.00 0.00 0.00 3.16
164 165 2.812011 GCCATCGTAAAGGAACACAAGT 59.188 45.455 0.00 0.00 0.00 3.16
165 166 3.364964 GCCATCGTAAAGGAACACAAGTG 60.365 47.826 0.00 0.00 0.00 3.16
167 168 4.992319 CCATCGTAAAGGAACACAAGTGTA 59.008 41.667 6.24 0.00 44.13 2.90
168 169 5.642063 CCATCGTAAAGGAACACAAGTGTAT 59.358 40.000 6.24 0.00 44.13 2.29
173 174 3.629142 AGGAACACAAGTGTATAGGGC 57.371 47.619 6.24 0.00 44.13 5.19
174 175 2.238898 AGGAACACAAGTGTATAGGGCC 59.761 50.000 6.24 0.00 44.13 5.80
175 176 2.026636 GGAACACAAGTGTATAGGGCCA 60.027 50.000 6.18 0.00 44.13 5.36
176 177 3.270877 GAACACAAGTGTATAGGGCCAG 58.729 50.000 6.18 0.00 44.13 4.85
177 178 1.065418 ACACAAGTGTATAGGGCCAGC 60.065 52.381 6.18 0.00 42.90 4.85
179 180 1.846439 ACAAGTGTATAGGGCCAGCAT 59.154 47.619 6.18 0.00 0.00 3.79
180 181 2.242196 ACAAGTGTATAGGGCCAGCATT 59.758 45.455 6.18 0.00 0.00 3.56
181 182 2.620115 CAAGTGTATAGGGCCAGCATTG 59.380 50.000 6.18 0.00 0.00 2.82
184 185 2.618709 GTGTATAGGGCCAGCATTGAAC 59.381 50.000 6.18 0.00 0.00 3.18
185 186 2.240921 TGTATAGGGCCAGCATTGAACA 59.759 45.455 6.18 0.00 0.00 3.18
187 188 0.680921 TAGGGCCAGCATTGAACAGC 60.681 55.000 6.18 0.00 0.00 4.40
188 189 2.180017 GGCCAGCATTGAACAGCG 59.820 61.111 0.00 0.00 35.48 5.18
189 190 2.334946 GGCCAGCATTGAACAGCGA 61.335 57.895 0.00 0.00 35.48 4.93
192 193 1.904144 CCAGCATTGAACAGCGAATG 58.096 50.000 0.00 0.00 35.48 2.67
208 209 3.557595 GCGAATGCTACTGCTATTTCTGT 59.442 43.478 0.00 0.00 40.48 3.41
209 210 4.551603 GCGAATGCTACTGCTATTTCTGTG 60.552 45.833 0.00 0.00 40.48 3.66
210 211 4.805719 CGAATGCTACTGCTATTTCTGTGA 59.194 41.667 0.00 0.00 40.48 3.58
211 212 5.276584 CGAATGCTACTGCTATTTCTGTGAC 60.277 44.000 0.00 0.00 40.48 3.67
212 213 4.535526 TGCTACTGCTATTTCTGTGACA 57.464 40.909 0.00 0.00 40.48 3.58
214 215 5.304778 TGCTACTGCTATTTCTGTGACAAA 58.695 37.500 0.00 0.00 40.48 2.83
215 216 5.939883 TGCTACTGCTATTTCTGTGACAAAT 59.060 36.000 0.00 0.00 40.48 2.32
216 217 7.102993 TGCTACTGCTATTTCTGTGACAAATA 58.897 34.615 0.00 0.00 40.48 1.40
217 218 7.278646 TGCTACTGCTATTTCTGTGACAAATAG 59.721 37.037 11.02 11.02 42.86 1.73
218 219 7.278868 GCTACTGCTATTTCTGTGACAAATAGT 59.721 37.037 14.89 4.78 42.34 2.12
219 220 7.986085 ACTGCTATTTCTGTGACAAATAGTT 57.014 32.000 14.89 2.47 42.34 2.24
220 221 8.396272 ACTGCTATTTCTGTGACAAATAGTTT 57.604 30.769 14.89 2.21 42.34 2.66
221 222 8.292448 ACTGCTATTTCTGTGACAAATAGTTTG 58.708 33.333 14.89 9.71 42.34 2.93
231 232 3.733024 CAAATAGTTTGTTAGCGCGGA 57.267 42.857 8.83 0.00 35.94 5.54
232 233 3.670203 CAAATAGTTTGTTAGCGCGGAG 58.330 45.455 8.83 0.00 35.94 4.63
234 235 2.728690 TAGTTTGTTAGCGCGGAGAA 57.271 45.000 8.83 0.00 0.00 2.87
235 236 1.873698 AGTTTGTTAGCGCGGAGAAA 58.126 45.000 8.83 2.81 0.00 2.52
236 237 1.529865 AGTTTGTTAGCGCGGAGAAAC 59.470 47.619 22.16 22.16 31.40 2.78
237 238 0.869730 TTTGTTAGCGCGGAGAAACC 59.130 50.000 8.83 0.00 0.00 3.27
238 239 0.249953 TTGTTAGCGCGGAGAAACCA 60.250 50.000 8.83 0.00 38.90 3.67
239 240 0.669318 TGTTAGCGCGGAGAAACCAG 60.669 55.000 8.83 0.00 38.90 4.00
241 242 0.108804 TTAGCGCGGAGAAACCAGAG 60.109 55.000 8.83 0.00 38.90 3.35
242 243 1.945354 TAGCGCGGAGAAACCAGAGG 61.945 60.000 8.83 0.00 38.90 3.69
243 244 2.815647 CGCGGAGAAACCAGAGGC 60.816 66.667 0.00 0.00 38.90 4.70
245 246 1.302511 GCGGAGAAACCAGAGGCAA 60.303 57.895 0.00 0.00 38.90 4.52
247 248 1.406887 GCGGAGAAACCAGAGGCAATA 60.407 52.381 0.00 0.00 38.90 1.90
248 249 2.555199 CGGAGAAACCAGAGGCAATAG 58.445 52.381 0.00 0.00 38.90 1.73
249 250 2.093447 CGGAGAAACCAGAGGCAATAGT 60.093 50.000 0.00 0.00 38.90 2.12
250 251 3.619979 CGGAGAAACCAGAGGCAATAGTT 60.620 47.826 0.00 0.00 38.90 2.24
251 252 3.942115 GGAGAAACCAGAGGCAATAGTTC 59.058 47.826 0.00 0.00 38.79 3.01
252 253 3.600388 AGAAACCAGAGGCAATAGTTCG 58.400 45.455 0.00 0.00 0.00 3.95
253 254 3.008049 AGAAACCAGAGGCAATAGTTCGT 59.992 43.478 0.00 0.00 0.00 3.85
255 256 1.899814 ACCAGAGGCAATAGTTCGTGA 59.100 47.619 0.00 0.00 0.00 4.35
256 257 2.501723 ACCAGAGGCAATAGTTCGTGAT 59.498 45.455 0.00 0.00 0.00 3.06
402 3030 9.620660 GTCCATTGATTTGTAATCGTAAAAGTT 57.379 29.630 0.00 0.00 0.00 2.66
567 3196 3.266772 TGCCCTCATTTGAGTTGGACTAT 59.733 43.478 6.81 0.00 40.48 2.12
601 3230 6.828273 TCATACATCATGGGGTTTCACTTAAG 59.172 38.462 0.00 0.00 35.16 1.85
609 3238 2.604614 GGGTTTCACTTAAGCTGCGTTG 60.605 50.000 1.29 0.00 0.00 4.10
702 3333 6.266168 TGAGAACGGATTGCAACAAATATT 57.734 33.333 0.00 0.00 0.00 1.28
704 3335 7.151308 TGAGAACGGATTGCAACAAATATTTT 58.849 30.769 0.00 0.00 0.00 1.82
781 3412 0.250338 GCTGACTCCGAGTTTGGGTT 60.250 55.000 1.71 0.00 0.00 4.11
1121 3861 5.772825 ATGTGTTTTGTGCTGATACTTGT 57.227 34.783 0.00 0.00 0.00 3.16
1123 3863 4.202000 TGTGTTTTGTGCTGATACTTGTGG 60.202 41.667 0.00 0.00 0.00 4.17
1217 3969 3.192212 GGCAACAATTCTCTTCTTCTGGG 59.808 47.826 0.00 0.00 0.00 4.45
1219 3971 4.279420 GCAACAATTCTCTTCTTCTGGGTT 59.721 41.667 0.00 0.00 0.00 4.11
1245 3997 8.647143 TTGTGATTTTTCATGTTTTCTCTTCC 57.353 30.769 0.00 0.00 0.00 3.46
1246 3998 7.780064 TGTGATTTTTCATGTTTTCTCTTCCA 58.220 30.769 0.00 0.00 0.00 3.53
1318 4072 0.690762 GTGCTGGGAAAGGACCACTA 59.309 55.000 0.00 0.00 41.20 2.74
1354 4108 2.256461 GCTTTCTGTGCAAGGCGG 59.744 61.111 0.00 0.00 0.00 6.13
1367 4121 2.567564 AAGGCGGCATGCTTGATTGC 62.568 55.000 18.92 11.62 45.43 3.56
1573 4330 5.313520 TCAGCAATGTTGTAATGATGTGG 57.686 39.130 0.00 0.00 32.59 4.17
1637 4395 6.634436 GTCCATTGATTTCTGATCGTAAATGC 59.366 38.462 9.18 3.76 0.00 3.56
1703 4461 0.673644 CGGTCCCTTGTTAGCACTGG 60.674 60.000 0.00 0.00 0.00 4.00
1806 4564 9.606631 ACTATCCTCATTTGAGTTTGAACTATC 57.393 33.333 6.81 0.00 39.88 2.08
1811 4569 7.824289 CCTCATTTGAGTTTGAACTATCACCTA 59.176 37.037 6.81 0.00 39.88 3.08
1814 4572 8.660373 CATTTGAGTTTGAACTATCACCTACTC 58.340 37.037 0.00 0.00 39.88 2.59
1836 4594 1.219664 CGGAGTAAATGGCCACGGA 59.780 57.895 8.16 0.00 0.00 4.69
1847 4605 1.692173 GGCCACGGATAGCCTAACCA 61.692 60.000 0.00 0.00 46.14 3.67
1858 4616 1.205460 GCCTAACCAACTCCCCCTGA 61.205 60.000 0.00 0.00 0.00 3.86
1902 4660 0.324614 TCGAGCCTTCAAGCATCCAA 59.675 50.000 0.00 0.00 34.23 3.53
1934 4692 1.700042 CCTTCCTCTGGCCGCCTATT 61.700 60.000 11.61 0.00 0.00 1.73
1941 4699 3.168528 GGCCGCCTATTCCCAGGA 61.169 66.667 0.71 0.00 38.00 3.86
1952 4710 0.178926 TTCCCAGGACCGACTACCAA 60.179 55.000 0.00 0.00 0.00 3.67
2070 4828 1.613630 AAGATGGCCGACTCCCAGT 60.614 57.895 0.00 0.00 35.48 4.00
2157 4915 2.109799 CGAATCCCGGAGCATGCT 59.890 61.111 22.92 22.92 33.91 3.79
2324 5083 4.475444 CCCCTAGTCGGCCTGGGA 62.475 72.222 15.58 0.00 44.45 4.37
2360 5119 1.946063 TAGCCGGCTACCTCCCTTCT 61.946 60.000 32.24 6.88 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.537192 CATGCATGTTTATATCCATGAAAACTT 57.463 29.630 18.91 0.00 40.70 2.66
11 12 8.698210 ACATGCATGTTTATATCCATGAAAACT 58.302 29.630 26.61 0.00 40.70 2.66
12 13 8.876275 ACATGCATGTTTATATCCATGAAAAC 57.124 30.769 26.61 2.87 40.70 2.43
28 29 4.082841 TCTGCAACGAATTAACATGCATGT 60.083 37.500 26.61 26.61 45.03 3.21
29 30 4.413969 TCTGCAACGAATTAACATGCATG 58.586 39.130 25.09 25.09 45.03 4.06
30 31 4.700268 TCTGCAACGAATTAACATGCAT 57.300 36.364 0.00 0.00 45.03 3.96
31 32 4.495911 TTCTGCAACGAATTAACATGCA 57.504 36.364 0.00 0.00 44.07 3.96
32 33 5.629020 TCTTTTCTGCAACGAATTAACATGC 59.371 36.000 0.00 0.00 37.52 4.06
33 34 7.379529 ACTTCTTTTCTGCAACGAATTAACATG 59.620 33.333 0.00 0.00 0.00 3.21
36 37 6.345015 GCACTTCTTTTCTGCAACGAATTAAC 60.345 38.462 0.00 0.00 0.00 2.01
38 39 5.008613 AGCACTTCTTTTCTGCAACGAATTA 59.991 36.000 0.00 0.00 33.06 1.40
39 40 4.044426 GCACTTCTTTTCTGCAACGAATT 58.956 39.130 0.00 0.00 0.00 2.17
40 41 3.316308 AGCACTTCTTTTCTGCAACGAAT 59.684 39.130 0.00 0.00 33.06 3.34
41 42 2.682856 AGCACTTCTTTTCTGCAACGAA 59.317 40.909 0.00 0.00 33.06 3.85
48 49 2.276732 TCCCCAGCACTTCTTTTCTG 57.723 50.000 0.00 0.00 0.00 3.02
49 50 3.312736 TTTCCCCAGCACTTCTTTTCT 57.687 42.857 0.00 0.00 0.00 2.52
50 51 4.082190 GGTATTTCCCCAGCACTTCTTTTC 60.082 45.833 0.00 0.00 0.00 2.29
52 53 3.076032 AGGTATTTCCCCAGCACTTCTTT 59.924 43.478 0.00 0.00 36.75 2.52
53 54 2.649816 AGGTATTTCCCCAGCACTTCTT 59.350 45.455 0.00 0.00 36.75 2.52
54 55 2.239907 GAGGTATTTCCCCAGCACTTCT 59.760 50.000 0.00 0.00 36.75 2.85
55 56 2.239907 AGAGGTATTTCCCCAGCACTTC 59.760 50.000 0.00 0.00 36.75 3.01
57 58 1.561542 CAGAGGTATTTCCCCAGCACT 59.438 52.381 0.00 0.00 36.75 4.40
58 59 1.408822 CCAGAGGTATTTCCCCAGCAC 60.409 57.143 0.00 0.00 36.75 4.40
59 60 0.918983 CCAGAGGTATTTCCCCAGCA 59.081 55.000 0.00 0.00 36.75 4.41
60 61 1.213296 TCCAGAGGTATTTCCCCAGC 58.787 55.000 0.00 0.00 36.75 4.85
61 62 2.846827 ACTTCCAGAGGTATTTCCCCAG 59.153 50.000 0.00 0.00 36.75 4.45
62 63 2.844348 GACTTCCAGAGGTATTTCCCCA 59.156 50.000 0.00 0.00 36.75 4.96
78 79 1.896465 AGCCTACACAGAGTGGACTTC 59.104 52.381 1.93 0.00 37.94 3.01
79 80 2.016905 AGCCTACACAGAGTGGACTT 57.983 50.000 1.93 0.00 37.94 3.01
80 81 1.896465 GAAGCCTACACAGAGTGGACT 59.104 52.381 1.93 0.00 37.94 3.85
81 82 1.066787 GGAAGCCTACACAGAGTGGAC 60.067 57.143 1.93 0.00 37.94 4.02
82 83 1.203187 AGGAAGCCTACACAGAGTGGA 60.203 52.381 1.93 0.00 37.94 4.02
83 84 1.066573 CAGGAAGCCTACACAGAGTGG 60.067 57.143 1.93 0.00 37.94 4.00
84 85 1.620819 ACAGGAAGCCTACACAGAGTG 59.379 52.381 0.00 0.00 39.75 3.51
85 86 1.620819 CACAGGAAGCCTACACAGAGT 59.379 52.381 0.00 0.00 29.64 3.24
86 87 1.674221 GCACAGGAAGCCTACACAGAG 60.674 57.143 0.00 0.00 29.64 3.35
88 89 0.035317 TGCACAGGAAGCCTACACAG 59.965 55.000 0.00 0.00 29.64 3.66
89 90 0.472044 TTGCACAGGAAGCCTACACA 59.528 50.000 0.00 0.00 29.64 3.72
90 91 1.160137 CTTGCACAGGAAGCCTACAC 58.840 55.000 0.00 0.00 29.64 2.90
91 92 3.631453 CTTGCACAGGAAGCCTACA 57.369 52.632 0.00 0.00 29.64 2.74
101 102 0.032952 AAGCATGTTGCCTTGCACAG 59.967 50.000 0.00 0.00 46.52 3.66
103 104 0.032403 TCAAGCATGTTGCCTTGCAC 59.968 50.000 6.06 0.00 46.52 4.57
104 105 0.970640 ATCAAGCATGTTGCCTTGCA 59.029 45.000 6.06 0.00 46.52 4.08
105 106 1.730064 CAATCAAGCATGTTGCCTTGC 59.270 47.619 6.06 0.00 46.52 4.01
106 107 2.028839 TCCAATCAAGCATGTTGCCTTG 60.029 45.455 4.85 4.85 46.52 3.61
107 108 2.232941 CTCCAATCAAGCATGTTGCCTT 59.767 45.455 0.00 0.00 46.52 4.35
108 109 1.822990 CTCCAATCAAGCATGTTGCCT 59.177 47.619 0.00 0.00 46.52 4.75
109 110 1.134907 CCTCCAATCAAGCATGTTGCC 60.135 52.381 0.00 0.00 46.52 4.52
110 111 1.738030 GCCTCCAATCAAGCATGTTGC 60.738 52.381 0.00 0.00 45.46 4.17
112 113 1.927487 TGCCTCCAATCAAGCATGTT 58.073 45.000 0.00 0.00 0.00 2.71
116 117 2.633967 ACATTTTGCCTCCAATCAAGCA 59.366 40.909 0.00 0.00 0.00 3.91
117 118 3.323751 ACATTTTGCCTCCAATCAAGC 57.676 42.857 0.00 0.00 0.00 4.01
118 119 6.128849 CGTTAAACATTTTGCCTCCAATCAAG 60.129 38.462 0.00 0.00 0.00 3.02
119 120 5.694006 CGTTAAACATTTTGCCTCCAATCAA 59.306 36.000 0.00 0.00 0.00 2.57
120 121 5.226396 CGTTAAACATTTTGCCTCCAATCA 58.774 37.500 0.00 0.00 0.00 2.57
121 122 4.091365 GCGTTAAACATTTTGCCTCCAATC 59.909 41.667 0.00 0.00 0.00 2.67
122 123 3.993736 GCGTTAAACATTTTGCCTCCAAT 59.006 39.130 0.00 0.00 0.00 3.16
124 125 2.288518 GGCGTTAAACATTTTGCCTCCA 60.289 45.455 7.37 0.00 39.38 3.86
125 126 2.288518 TGGCGTTAAACATTTTGCCTCC 60.289 45.455 12.99 0.00 42.87 4.30
126 127 3.019933 TGGCGTTAAACATTTTGCCTC 57.980 42.857 12.99 0.00 42.87 4.70
127 128 3.584834 GATGGCGTTAAACATTTTGCCT 58.415 40.909 12.99 3.36 42.87 4.75
128 129 2.344142 CGATGGCGTTAAACATTTTGCC 59.656 45.455 7.59 7.59 42.76 4.52
142 143 1.434555 TGTGTTCCTTTACGATGGCG 58.565 50.000 0.00 0.00 44.79 5.69
143 144 2.812011 ACTTGTGTTCCTTTACGATGGC 59.188 45.455 0.00 0.00 0.00 4.40
144 145 3.813166 ACACTTGTGTTCCTTTACGATGG 59.187 43.478 0.00 0.00 0.00 3.51
145 146 6.721571 ATACACTTGTGTTCCTTTACGATG 57.278 37.500 11.80 0.00 0.00 3.84
146 147 7.039882 CCTATACACTTGTGTTCCTTTACGAT 58.960 38.462 11.80 0.00 0.00 3.73
148 149 5.579511 CCCTATACACTTGTGTTCCTTTACG 59.420 44.000 11.80 0.00 0.00 3.18
149 150 5.353400 GCCCTATACACTTGTGTTCCTTTAC 59.647 44.000 11.80 0.00 0.00 2.01
150 151 5.493809 GCCCTATACACTTGTGTTCCTTTA 58.506 41.667 11.80 0.00 0.00 1.85
151 152 4.332828 GCCCTATACACTTGTGTTCCTTT 58.667 43.478 11.80 0.00 0.00 3.11
152 153 3.308188 GGCCCTATACACTTGTGTTCCTT 60.308 47.826 11.80 0.00 0.00 3.36
154 155 2.026636 TGGCCCTATACACTTGTGTTCC 60.027 50.000 11.80 5.28 0.00 3.62
156 157 2.618045 GCTGGCCCTATACACTTGTGTT 60.618 50.000 11.80 3.35 0.00 3.32
157 158 1.065418 GCTGGCCCTATACACTTGTGT 60.065 52.381 11.30 11.30 0.00 3.72
159 160 1.285280 TGCTGGCCCTATACACTTGT 58.715 50.000 0.00 0.00 0.00 3.16
160 161 2.620115 CAATGCTGGCCCTATACACTTG 59.380 50.000 0.00 0.00 0.00 3.16
162 163 2.126882 TCAATGCTGGCCCTATACACT 58.873 47.619 0.00 0.00 0.00 3.55
163 164 2.618709 GTTCAATGCTGGCCCTATACAC 59.381 50.000 0.00 0.00 0.00 2.90
164 165 2.240921 TGTTCAATGCTGGCCCTATACA 59.759 45.455 0.00 0.00 0.00 2.29
165 166 2.880890 CTGTTCAATGCTGGCCCTATAC 59.119 50.000 0.00 0.00 0.00 1.47
166 167 2.749466 GCTGTTCAATGCTGGCCCTATA 60.749 50.000 0.00 0.00 0.00 1.31
167 168 2.025863 GCTGTTCAATGCTGGCCCTAT 61.026 52.381 0.00 0.00 0.00 2.57
168 169 0.680921 GCTGTTCAATGCTGGCCCTA 60.681 55.000 0.00 0.00 0.00 3.53
173 174 1.904144 CATTCGCTGTTCAATGCTGG 58.096 50.000 0.00 0.00 0.00 4.85
187 188 4.805719 TCACAGAAATAGCAGTAGCATTCG 59.194 41.667 0.00 0.00 45.49 3.34
188 189 5.582269 TGTCACAGAAATAGCAGTAGCATTC 59.418 40.000 0.00 0.00 45.49 2.67
189 190 5.491070 TGTCACAGAAATAGCAGTAGCATT 58.509 37.500 0.00 0.00 45.49 3.56
192 193 5.862924 TTTGTCACAGAAATAGCAGTAGC 57.137 39.130 0.00 0.00 42.56 3.58
194 195 9.502091 AAACTATTTGTCACAGAAATAGCAGTA 57.498 29.630 8.58 0.00 43.07 2.74
195 196 7.986085 AACTATTTGTCACAGAAATAGCAGT 57.014 32.000 8.58 0.00 43.07 4.40
196 197 8.665175 CAAACTATTTGTCACAGAAATAGCAG 57.335 34.615 8.58 0.00 43.07 4.24
211 212 3.369756 TCTCCGCGCTAACAAACTATTTG 59.630 43.478 5.56 0.00 45.95 2.32
212 213 3.592059 TCTCCGCGCTAACAAACTATTT 58.408 40.909 5.56 0.00 0.00 1.40
214 215 2.953466 TCTCCGCGCTAACAAACTAT 57.047 45.000 5.56 0.00 0.00 2.12
215 216 2.728690 TTCTCCGCGCTAACAAACTA 57.271 45.000 5.56 0.00 0.00 2.24
216 217 1.529865 GTTTCTCCGCGCTAACAAACT 59.470 47.619 5.56 0.00 0.00 2.66
217 218 1.399343 GGTTTCTCCGCGCTAACAAAC 60.399 52.381 5.56 9.37 0.00 2.93
218 219 0.869730 GGTTTCTCCGCGCTAACAAA 59.130 50.000 5.56 0.00 0.00 2.83
219 220 0.249953 TGGTTTCTCCGCGCTAACAA 60.250 50.000 5.56 0.00 39.52 2.83
220 221 0.669318 CTGGTTTCTCCGCGCTAACA 60.669 55.000 5.56 0.00 39.52 2.41
221 222 0.389426 TCTGGTTTCTCCGCGCTAAC 60.389 55.000 5.56 1.28 39.52 2.34
222 223 0.108804 CTCTGGTTTCTCCGCGCTAA 60.109 55.000 5.56 0.00 39.52 3.09
223 224 1.511305 CTCTGGTTTCTCCGCGCTA 59.489 57.895 5.56 0.00 39.52 4.26
224 225 2.262915 CTCTGGTTTCTCCGCGCT 59.737 61.111 5.56 0.00 39.52 5.92
225 226 2.815647 CCTCTGGTTTCTCCGCGC 60.816 66.667 0.00 0.00 39.52 6.86
227 228 0.678048 ATTGCCTCTGGTTTCTCCGC 60.678 55.000 0.00 0.00 39.52 5.54
228 229 2.093447 ACTATTGCCTCTGGTTTCTCCG 60.093 50.000 0.00 0.00 39.52 4.63
229 230 3.636153 ACTATTGCCTCTGGTTTCTCC 57.364 47.619 0.00 0.00 0.00 3.71
231 232 3.008049 ACGAACTATTGCCTCTGGTTTCT 59.992 43.478 0.00 0.00 0.00 2.52
232 233 3.125316 CACGAACTATTGCCTCTGGTTTC 59.875 47.826 0.00 0.00 0.00 2.78
234 235 2.301870 TCACGAACTATTGCCTCTGGTT 59.698 45.455 0.00 0.00 0.00 3.67
235 236 1.899814 TCACGAACTATTGCCTCTGGT 59.100 47.619 0.00 0.00 0.00 4.00
236 237 2.672961 TCACGAACTATTGCCTCTGG 57.327 50.000 0.00 0.00 0.00 3.86
237 238 4.872691 AGAAATCACGAACTATTGCCTCTG 59.127 41.667 0.00 0.00 0.00 3.35
238 239 5.091261 AGAAATCACGAACTATTGCCTCT 57.909 39.130 0.00 0.00 0.00 3.69
239 240 5.447818 CCAAGAAATCACGAACTATTGCCTC 60.448 44.000 0.00 0.00 0.00 4.70
241 242 4.156008 ACCAAGAAATCACGAACTATTGCC 59.844 41.667 0.00 0.00 0.00 4.52
242 243 5.296813 ACCAAGAAATCACGAACTATTGC 57.703 39.130 0.00 0.00 0.00 3.56
243 244 7.481798 GCTAAACCAAGAAATCACGAACTATTG 59.518 37.037 0.00 0.00 0.00 1.90
245 246 6.653320 TGCTAAACCAAGAAATCACGAACTAT 59.347 34.615 0.00 0.00 0.00 2.12
247 248 4.819630 TGCTAAACCAAGAAATCACGAACT 59.180 37.500 0.00 0.00 0.00 3.01
248 249 5.103290 TGCTAAACCAAGAAATCACGAAC 57.897 39.130 0.00 0.00 0.00 3.95
249 250 5.957842 ATGCTAAACCAAGAAATCACGAA 57.042 34.783 0.00 0.00 0.00 3.85
250 251 8.725405 TTATATGCTAAACCAAGAAATCACGA 57.275 30.769 0.00 0.00 0.00 4.35
251 252 9.438291 CTTTATATGCTAAACCAAGAAATCACG 57.562 33.333 0.00 0.00 0.00 4.35
252 253 9.736023 CCTTTATATGCTAAACCAAGAAATCAC 57.264 33.333 0.00 0.00 0.00 3.06
253 254 8.912988 CCCTTTATATGCTAAACCAAGAAATCA 58.087 33.333 0.00 0.00 0.00 2.57
255 256 8.065007 TCCCCTTTATATGCTAAACCAAGAAAT 58.935 33.333 0.00 0.00 0.00 2.17
256 257 7.415086 TCCCCTTTATATGCTAAACCAAGAAA 58.585 34.615 0.00 0.00 0.00 2.52
402 3030 5.069119 ACCTGAGACGATTAGCACATCATAA 59.931 40.000 0.00 0.00 0.00 1.90
567 3196 5.908831 ACCCCATGATGTATGAGTAGGTTAA 59.091 40.000 0.00 0.00 39.21 2.01
578 3207 5.594317 GCTTAAGTGAAACCCCATGATGTAT 59.406 40.000 4.02 0.00 37.80 2.29
601 3230 2.159801 GGATTTCAAAATGCAACGCAGC 60.160 45.455 0.00 0.00 43.65 5.25
609 3238 5.121142 CAGAACACCATGGATTTCAAAATGC 59.879 40.000 21.47 0.52 37.27 3.56
704 3335 3.121019 CCCGAACGTGGCCAAAAA 58.879 55.556 7.24 0.00 0.00 1.94
781 3412 3.067180 CCTTTCTTTCTGCAAGCTGTTGA 59.933 43.478 0.00 0.00 35.46 3.18
1061 3801 2.457323 ATGGTCGGTGGTGTTGGGT 61.457 57.895 0.00 0.00 0.00 4.51
1121 3861 1.614996 ACCATGATTCGCAAACACCA 58.385 45.000 0.00 0.00 0.00 4.17
1123 3863 2.595386 GGAACCATGATTCGCAAACAC 58.405 47.619 0.00 0.00 0.00 3.32
1219 3971 9.097257 GGAAGAGAAAACATGAAAAATCACAAA 57.903 29.630 0.00 0.00 0.00 2.83
1354 4108 4.104143 GCCTGCAATCAAGCATGC 57.896 55.556 10.51 10.51 46.00 4.06
1367 4121 1.125270 GGCGTTAAACGTTTTGCCTG 58.875 50.000 29.31 15.12 44.73 4.85
1602 4359 7.954835 TCAGAAATCAATGGACATCTTTTGTT 58.045 30.769 0.00 0.00 39.18 2.83
1637 4395 5.522824 CCTGAGACGATTGGCATATCATATG 59.477 44.000 0.00 0.00 0.00 1.78
1703 4461 9.956720 CAATTCTAACAGGGAATCATTTCATAC 57.043 33.333 0.00 0.00 32.96 2.39
1814 4572 1.369625 GTGGCCATTTACTCCGACAG 58.630 55.000 9.72 0.00 0.00 3.51
1836 4594 1.010917 AGGGGGAGTTGGTTAGGCTAT 59.989 52.381 0.00 0.00 0.00 2.97
1847 4605 0.114560 TCGAAGAGTCAGGGGGAGTT 59.885 55.000 0.00 0.00 0.00 3.01
1858 4616 5.253330 TGGCCTGATAATTTTTCGAAGAGT 58.747 37.500 3.32 0.00 38.43 3.24
1902 4660 2.439156 GAAGGCGGCTCCATGCTT 60.439 61.111 13.70 0.00 42.39 3.91
1929 4687 1.962100 GTAGTCGGTCCTGGGAATAGG 59.038 57.143 0.00 0.00 39.29 2.57
1934 4692 0.178926 TTTGGTAGTCGGTCCTGGGA 60.179 55.000 0.00 0.00 0.00 4.37
1941 4699 0.320160 GTCGCCTTTTGGTAGTCGGT 60.320 55.000 0.00 0.00 42.99 4.69
2070 4828 3.318384 TGCAGTCTTGGCCGGCTA 61.318 61.111 28.56 19.98 0.00 3.93
2128 4886 1.691689 GGATTCGGGGGTGGTAGGT 60.692 63.158 0.00 0.00 0.00 3.08
2324 5083 1.745320 CTATTGGGAGCCGGCTACGT 61.745 60.000 32.11 21.93 38.78 3.57
2360 5119 6.252967 ACTTAATGATGCACATGTTTCGAA 57.747 33.333 0.00 0.00 39.39 3.71


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

AutoCloner maintained by Alex Coulton.