Multiple sequence alignment - TraesCS4A01G050000

Loading Multiple Alignment...

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 TraesCS4A01G050000 chr4A 100.000 3377 0 0 1 3377 40859014 40862390 0.000000e+00 6237.0
1 TraesCS4A01G050000 chr4D 92.081 2374 92 41 345 2667 423430728 423428400 0.000000e+00 3254.0
2 TraesCS4A01G050000 chr4D 91.268 710 48 8 2676 3374 423428366 423427660 0.000000e+00 955.0
3 TraesCS4A01G050000 chr4B 91.513 1956 105 34 1463 3371 519824327 519822386 0.000000e+00 2636.0
4 TraesCS4A01G050000 chr4B 87.967 1205 67 30 292 1468 519825521 519824367 0.000000e+00 1351.0
5 TraesCS4A01G050000 chr5A 82.584 178 27 3 1242 1417 592638837 592638662 1.620000e-33 154.0
6 TraesCS4A01G050000 chr5B 83.041 171 25 3 1242 1410 580366673 580366505 5.840000e-33 152.0
7 TraesCS4A01G050000 chr5D 81.667 180 29 3 1242 1419 473003387 473003210 2.720000e-31 147.0
8 TraesCS4A01G050000 chr2D 83.607 122 16 4 1262 1381 564384036 564384155 9.910000e-21 111.0
9 TraesCS4A01G050000 chr2B 78.333 180 29 8 1207 1381 675514517 675514691 1.280000e-19 108.0
10 TraesCS4A01G050000 chr2A 77.778 180 30 9 1207 1381 705068455 705068629 5.960000e-18 102.0
11 TraesCS4A01G050000 chr7B 83.721 86 12 2 2741 2825 291577693 291577609 2.790000e-11 80.5
12 TraesCS4A01G050000 chr3D 91.379 58 5 0 1327 1384 613780056 613780113 2.790000e-11 80.5
13 TraesCS4A01G050000 chr7A 80.851 94 18 0 2732 2825 206949948 206950041 1.300000e-09 75.0


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 TraesCS4A01G050000 chr4A 40859014 40862390 3376 False 6237.0 6237 100.0000 1 3377 1 chr4A.!!$F1 3376
1 TraesCS4A01G050000 chr4D 423427660 423430728 3068 True 2104.5 3254 91.6745 345 3374 2 chr4D.!!$R1 3029
2 TraesCS4A01G050000 chr4B 519822386 519825521 3135 True 1993.5 2636 89.7400 292 3371 2 chr4B.!!$R1 3079

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
499 500 0.036732 TGCCAGACCAGACCACATTC 59.963 55.0 0.0 0.0 0.00 2.67 F
1098 1131 0.251341 GCTCTTTCACACCACCCCAT 60.251 55.0 0.0 0.0 0.00 4.00 F
1592 1677 0.256752 TTCATGGGCATGGTGGAGAG 59.743 55.0 0.0 0.0 39.24 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1656 0.033796 CTCCACCATGCCCATGAACT 60.034 55.0 9.73 0.0 41.2 3.01 R
2022 2107 0.179000 AGATGATGAACTGGTCGCCC 59.821 55.0 0.00 0.0 0.0 6.13 R
3177 3328 0.185416 CTCTAAGCCCCGTCCTCCTA 59.815 60.0 0.00 0.0 0.0 2.94 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
18 19 2.819477 TGCTTTGGTTGGAGGTTGG 58.181 52.632 0.00 0.00 0.00 3.77
19 20 0.260230 TGCTTTGGTTGGAGGTTGGA 59.740 50.000 0.00 0.00 0.00 3.53
20 21 0.961753 GCTTTGGTTGGAGGTTGGAG 59.038 55.000 0.00 0.00 0.00 3.86
21 22 1.754201 GCTTTGGTTGGAGGTTGGAGT 60.754 52.381 0.00 0.00 0.00 3.85
22 23 2.666317 CTTTGGTTGGAGGTTGGAGTT 58.334 47.619 0.00 0.00 0.00 3.01
23 24 2.358322 TTGGTTGGAGGTTGGAGTTC 57.642 50.000 0.00 0.00 0.00 3.01
24 25 0.476771 TGGTTGGAGGTTGGAGTTCC 59.523 55.000 0.00 0.00 0.00 3.62
25 26 0.251209 GGTTGGAGGTTGGAGTTCCC 60.251 60.000 0.00 0.00 34.29 3.97
26 27 0.251209 GTTGGAGGTTGGAGTTCCCC 60.251 60.000 0.00 0.00 34.29 4.81
27 28 1.432023 TTGGAGGTTGGAGTTCCCCC 61.432 60.000 0.00 0.00 34.29 5.40
28 29 1.541620 GGAGGTTGGAGTTCCCCCT 60.542 63.158 6.27 6.27 38.58 4.79
29 30 1.563577 GGAGGTTGGAGTTCCCCCTC 61.564 65.000 18.76 18.76 45.35 4.30
30 31 0.547954 GAGGTTGGAGTTCCCCCTCT 60.548 60.000 19.31 4.28 43.95 3.69
31 32 0.842467 AGGTTGGAGTTCCCCCTCTG 60.842 60.000 0.00 0.00 32.72 3.35
32 33 1.685820 GTTGGAGTTCCCCCTCTGG 59.314 63.158 0.00 0.00 34.29 3.86
33 34 2.231380 TTGGAGTTCCCCCTCTGGC 61.231 63.158 0.00 0.00 34.29 4.85
34 35 3.412408 GGAGTTCCCCCTCTGGCC 61.412 72.222 0.00 0.00 0.00 5.36
35 36 3.787001 GAGTTCCCCCTCTGGCCG 61.787 72.222 0.00 0.00 0.00 6.13
52 53 2.819595 GGCGACGATGGTGCATGT 60.820 61.111 0.00 0.00 0.00 3.21
53 54 2.703409 GCGACGATGGTGCATGTC 59.297 61.111 0.00 0.00 0.00 3.06
54 55 2.100031 GCGACGATGGTGCATGTCA 61.100 57.895 0.00 0.00 0.00 3.58
55 56 2.001357 CGACGATGGTGCATGTCAG 58.999 57.895 0.00 0.00 0.00 3.51
56 57 1.423721 CGACGATGGTGCATGTCAGG 61.424 60.000 0.00 0.00 0.00 3.86
57 58 1.709147 GACGATGGTGCATGTCAGGC 61.709 60.000 1.65 1.65 0.00 4.85
58 59 1.746239 CGATGGTGCATGTCAGGCA 60.746 57.895 8.34 8.34 39.32 4.75
63 64 2.110835 TGCATGTCAGGCACGTGT 59.889 55.556 18.38 0.00 43.24 4.49
64 65 2.253051 TGCATGTCAGGCACGTGTG 61.253 57.895 18.38 8.70 43.24 3.82
74 75 2.052237 CACGTGTGCAGCGGTTTC 60.052 61.111 7.58 0.00 0.00 2.78
75 76 3.636043 ACGTGTGCAGCGGTTTCG 61.636 61.111 13.99 2.47 39.81 3.46
76 77 4.368808 CGTGTGCAGCGGTTTCGG 62.369 66.667 2.96 0.00 36.79 4.30
77 78 4.683334 GTGTGCAGCGGTTTCGGC 62.683 66.667 0.00 0.00 36.79 5.54
78 79 4.927782 TGTGCAGCGGTTTCGGCT 62.928 61.111 0.00 0.00 42.61 5.52
79 80 2.740826 GTGCAGCGGTTTCGGCTA 60.741 61.111 0.00 0.00 39.08 3.93
80 81 2.031314 TGCAGCGGTTTCGGCTAA 59.969 55.556 1.84 0.00 39.08 3.09
81 82 2.032634 TGCAGCGGTTTCGGCTAAG 61.033 57.895 1.84 0.00 39.08 2.18
82 83 2.033194 GCAGCGGTTTCGGCTAAGT 61.033 57.895 1.84 0.00 39.08 2.24
83 84 1.787847 CAGCGGTTTCGGCTAAGTG 59.212 57.895 1.84 0.00 39.08 3.16
84 85 1.375523 AGCGGTTTCGGCTAAGTGG 60.376 57.895 0.21 0.00 39.39 4.00
85 86 3.035576 GCGGTTTCGGCTAAGTGGC 62.036 63.158 0.00 0.00 36.79 5.01
86 87 1.669760 CGGTTTCGGCTAAGTGGCA 60.670 57.895 0.00 0.00 41.89 4.92
87 88 1.024579 CGGTTTCGGCTAAGTGGCAT 61.025 55.000 0.00 0.00 41.89 4.40
88 89 0.733150 GGTTTCGGCTAAGTGGCATC 59.267 55.000 0.00 0.00 41.89 3.91
89 90 0.733150 GTTTCGGCTAAGTGGCATCC 59.267 55.000 0.00 0.00 41.89 3.51
90 91 0.393808 TTTCGGCTAAGTGGCATCCC 60.394 55.000 0.00 0.00 41.89 3.85
91 92 2.203209 CGGCTAAGTGGCATCCCC 60.203 66.667 0.00 0.00 41.89 4.81
92 93 2.746375 CGGCTAAGTGGCATCCCCT 61.746 63.158 0.00 0.00 41.89 4.79
93 94 1.149401 GGCTAAGTGGCATCCCCTC 59.851 63.158 0.00 0.00 41.37 4.30
94 95 1.227674 GCTAAGTGGCATCCCCTCG 60.228 63.158 0.00 0.00 32.31 4.63
95 96 1.686325 GCTAAGTGGCATCCCCTCGA 61.686 60.000 0.00 0.00 32.31 4.04
96 97 0.390860 CTAAGTGGCATCCCCTCGAG 59.609 60.000 5.13 5.13 32.31 4.04
97 98 1.686325 TAAGTGGCATCCCCTCGAGC 61.686 60.000 6.99 0.00 32.31 5.03
100 101 3.564218 GGCATCCCCTCGAGCCAT 61.564 66.667 6.99 0.00 46.26 4.40
101 102 2.512896 GCATCCCCTCGAGCCATT 59.487 61.111 6.99 0.00 0.00 3.16
102 103 1.152881 GCATCCCCTCGAGCCATTT 60.153 57.895 6.99 0.00 0.00 2.32
103 104 0.108585 GCATCCCCTCGAGCCATTTA 59.891 55.000 6.99 0.00 0.00 1.40
104 105 1.271597 GCATCCCCTCGAGCCATTTAT 60.272 52.381 6.99 0.00 0.00 1.40
105 106 2.815589 GCATCCCCTCGAGCCATTTATT 60.816 50.000 6.99 0.00 0.00 1.40
106 107 3.490348 CATCCCCTCGAGCCATTTATTT 58.510 45.455 6.99 0.00 0.00 1.40
107 108 4.651778 CATCCCCTCGAGCCATTTATTTA 58.348 43.478 6.99 0.00 0.00 1.40
108 109 4.081322 TCCCCTCGAGCCATTTATTTAC 57.919 45.455 6.99 0.00 0.00 2.01
109 110 2.806244 CCCCTCGAGCCATTTATTTACG 59.194 50.000 6.99 0.00 0.00 3.18
110 111 2.223377 CCCTCGAGCCATTTATTTACGC 59.777 50.000 6.99 0.00 0.00 4.42
111 112 2.096909 CCTCGAGCCATTTATTTACGCG 60.097 50.000 6.99 3.53 0.00 6.01
112 113 2.538449 CTCGAGCCATTTATTTACGCGT 59.462 45.455 19.17 19.17 0.00 6.01
113 114 2.283086 TCGAGCCATTTATTTACGCGTG 59.717 45.455 24.59 1.96 0.00 5.34
114 115 2.598907 CGAGCCATTTATTTACGCGTGG 60.599 50.000 24.59 13.14 0.00 4.94
115 116 1.472990 GCCATTTATTTACGCGTGGC 58.527 50.000 24.59 19.59 44.37 5.01
116 117 2.834574 CCATTTATTTACGCGTGGCA 57.165 45.000 24.59 5.55 0.00 4.92
117 118 3.138205 CCATTTATTTACGCGTGGCAA 57.862 42.857 24.59 12.44 0.00 4.52
118 119 2.849473 CCATTTATTTACGCGTGGCAAC 59.151 45.455 24.59 0.00 0.00 4.17
119 120 3.426963 CCATTTATTTACGCGTGGCAACT 60.427 43.478 24.59 5.10 37.61 3.16
120 121 3.458779 TTTATTTACGCGTGGCAACTC 57.541 42.857 24.59 0.00 37.61 3.01
121 122 1.361793 TATTTACGCGTGGCAACTCC 58.638 50.000 24.59 0.00 37.61 3.85
122 123 0.321298 ATTTACGCGTGGCAACTCCT 60.321 50.000 24.59 0.00 35.26 3.69
123 124 0.533308 TTTACGCGTGGCAACTCCTT 60.533 50.000 24.59 0.00 35.26 3.36
124 125 0.533308 TTACGCGTGGCAACTCCTTT 60.533 50.000 24.59 0.00 35.26 3.11
125 126 0.317799 TACGCGTGGCAACTCCTTTA 59.682 50.000 24.59 0.00 35.26 1.85
126 127 0.949105 ACGCGTGGCAACTCCTTTAG 60.949 55.000 12.93 0.00 35.26 1.85
127 128 1.635663 CGCGTGGCAACTCCTTTAGG 61.636 60.000 0.00 0.00 35.26 2.69
128 129 1.923227 GCGTGGCAACTCCTTTAGGC 61.923 60.000 0.00 0.00 35.26 3.93
129 130 1.635663 CGTGGCAACTCCTTTAGGCG 61.636 60.000 0.00 0.00 35.26 5.52
130 131 1.002624 TGGCAACTCCTTTAGGCGG 60.003 57.895 0.00 0.00 35.26 6.13
131 132 1.002502 GGCAACTCCTTTAGGCGGT 60.003 57.895 0.00 0.00 34.44 5.68
132 133 0.608308 GGCAACTCCTTTAGGCGGTT 60.608 55.000 0.00 0.00 33.56 4.44
133 134 1.244816 GCAACTCCTTTAGGCGGTTT 58.755 50.000 4.88 0.00 31.97 3.27
134 135 1.611977 GCAACTCCTTTAGGCGGTTTT 59.388 47.619 4.88 0.00 31.97 2.43
135 136 2.815503 GCAACTCCTTTAGGCGGTTTTA 59.184 45.455 4.88 0.00 31.97 1.52
136 137 3.119955 GCAACTCCTTTAGGCGGTTTTAG 60.120 47.826 4.88 0.00 31.97 1.85
137 138 4.320870 CAACTCCTTTAGGCGGTTTTAGA 58.679 43.478 4.88 0.00 31.97 2.10
138 139 3.935315 ACTCCTTTAGGCGGTTTTAGAC 58.065 45.455 0.00 0.00 34.44 2.59
139 140 3.325716 ACTCCTTTAGGCGGTTTTAGACA 59.674 43.478 0.00 0.00 34.44 3.41
140 141 3.667360 TCCTTTAGGCGGTTTTAGACAC 58.333 45.455 0.00 0.00 34.44 3.67
141 142 3.071312 TCCTTTAGGCGGTTTTAGACACA 59.929 43.478 0.00 0.00 34.44 3.72
142 143 3.187842 CCTTTAGGCGGTTTTAGACACAC 59.812 47.826 0.00 0.00 0.00 3.82
143 144 2.068837 TAGGCGGTTTTAGACACACG 57.931 50.000 0.00 0.00 0.00 4.49
144 145 0.105408 AGGCGGTTTTAGACACACGT 59.895 50.000 0.00 0.00 0.00 4.49
145 146 0.509929 GGCGGTTTTAGACACACGTC 59.490 55.000 0.00 0.00 42.95 4.34
146 147 1.210870 GCGGTTTTAGACACACGTCA 58.789 50.000 0.00 0.00 45.23 4.35
147 148 1.796459 GCGGTTTTAGACACACGTCAT 59.204 47.619 0.00 0.00 45.23 3.06
148 149 2.222445 GCGGTTTTAGACACACGTCATT 59.778 45.455 0.00 0.00 45.23 2.57
149 150 3.303526 GCGGTTTTAGACACACGTCATTT 60.304 43.478 0.00 0.00 45.23 2.32
150 151 4.084433 GCGGTTTTAGACACACGTCATTTA 60.084 41.667 0.00 0.00 45.23 1.40
151 152 5.558653 GCGGTTTTAGACACACGTCATTTAA 60.559 40.000 0.00 0.00 45.23 1.52
152 153 6.420588 CGGTTTTAGACACACGTCATTTAAA 58.579 36.000 0.00 0.00 45.23 1.52
153 154 6.572254 CGGTTTTAGACACACGTCATTTAAAG 59.428 38.462 0.00 0.00 45.23 1.85
154 155 6.854381 GGTTTTAGACACACGTCATTTAAAGG 59.146 38.462 0.00 0.00 45.23 3.11
155 156 5.600908 TTAGACACACGTCATTTAAAGGC 57.399 39.130 0.00 0.00 45.23 4.35
156 157 2.478894 AGACACACGTCATTTAAAGGCG 59.521 45.455 12.68 12.68 45.23 5.52
157 158 1.533731 ACACACGTCATTTAAAGGCGG 59.466 47.619 16.63 10.39 0.00 6.13
158 159 1.533731 CACACGTCATTTAAAGGCGGT 59.466 47.619 16.63 10.82 0.00 5.68
159 160 2.031508 CACACGTCATTTAAAGGCGGTT 60.032 45.455 16.63 4.86 0.00 4.44
160 161 2.619646 ACACGTCATTTAAAGGCGGTTT 59.380 40.909 16.63 0.68 0.00 3.27
161 162 3.067040 ACACGTCATTTAAAGGCGGTTTT 59.933 39.130 16.63 0.00 0.00 2.43
162 163 4.045783 CACGTCATTTAAAGGCGGTTTTT 58.954 39.130 16.63 0.00 0.00 1.94
233 234 6.791867 TCTATGGGATATAATCTTCCGTGG 57.208 41.667 0.00 0.00 32.48 4.94
234 235 4.844349 ATGGGATATAATCTTCCGTGGG 57.156 45.455 0.00 0.00 32.48 4.61
235 236 2.304761 TGGGATATAATCTTCCGTGGGC 59.695 50.000 0.00 0.00 32.48 5.36
236 237 2.572104 GGGATATAATCTTCCGTGGGCT 59.428 50.000 0.00 0.00 32.48 5.19
237 238 3.773119 GGGATATAATCTTCCGTGGGCTA 59.227 47.826 0.00 0.00 32.48 3.93
238 239 4.409247 GGGATATAATCTTCCGTGGGCTAT 59.591 45.833 0.00 0.00 32.48 2.97
239 240 5.104485 GGGATATAATCTTCCGTGGGCTATT 60.104 44.000 0.00 0.00 32.48 1.73
240 241 6.415573 GGATATAATCTTCCGTGGGCTATTT 58.584 40.000 0.00 0.00 0.00 1.40
241 242 6.884836 GGATATAATCTTCCGTGGGCTATTTT 59.115 38.462 0.00 0.00 0.00 1.82
242 243 8.044908 GGATATAATCTTCCGTGGGCTATTTTA 58.955 37.037 0.00 0.00 0.00 1.52
243 244 9.099454 GATATAATCTTCCGTGGGCTATTTTAG 57.901 37.037 0.00 0.00 0.00 1.85
252 253 2.715536 GCTATTTTAGCCCCACCGG 58.284 57.895 0.00 0.00 45.95 5.28
253 254 0.181824 GCTATTTTAGCCCCACCGGA 59.818 55.000 9.46 0.00 45.95 5.14
254 255 1.202891 GCTATTTTAGCCCCACCGGAT 60.203 52.381 9.46 0.00 45.95 4.18
255 256 2.504367 CTATTTTAGCCCCACCGGATG 58.496 52.381 9.46 2.15 0.00 3.51
256 257 0.629058 ATTTTAGCCCCACCGGATGT 59.371 50.000 9.46 0.00 0.00 3.06
257 258 0.322997 TTTTAGCCCCACCGGATGTG 60.323 55.000 9.46 0.00 45.01 3.21
267 268 4.277239 CGGATGTGAACGGAAGCA 57.723 55.556 0.00 0.00 0.00 3.91
268 269 2.081526 CGGATGTGAACGGAAGCAG 58.918 57.895 0.00 0.00 0.00 4.24
269 270 1.361668 CGGATGTGAACGGAAGCAGG 61.362 60.000 0.00 0.00 0.00 4.85
270 271 1.026718 GGATGTGAACGGAAGCAGGG 61.027 60.000 0.00 0.00 0.00 4.45
271 272 0.321653 GATGTGAACGGAAGCAGGGT 60.322 55.000 0.00 0.00 0.00 4.34
272 273 0.110486 ATGTGAACGGAAGCAGGGTT 59.890 50.000 0.00 0.00 0.00 4.11
273 274 0.106918 TGTGAACGGAAGCAGGGTTT 60.107 50.000 0.00 0.00 0.00 3.27
274 275 1.029681 GTGAACGGAAGCAGGGTTTT 58.970 50.000 0.00 0.00 0.00 2.43
275 276 2.223745 GTGAACGGAAGCAGGGTTTTA 58.776 47.619 0.00 0.00 0.00 1.52
276 277 2.817844 GTGAACGGAAGCAGGGTTTTAT 59.182 45.455 0.00 0.00 0.00 1.40
277 278 3.254903 GTGAACGGAAGCAGGGTTTTATT 59.745 43.478 0.00 0.00 0.00 1.40
278 279 4.456566 GTGAACGGAAGCAGGGTTTTATTA 59.543 41.667 0.00 0.00 0.00 0.98
279 280 4.698304 TGAACGGAAGCAGGGTTTTATTAG 59.302 41.667 0.00 0.00 0.00 1.73
280 281 4.296621 ACGGAAGCAGGGTTTTATTAGT 57.703 40.909 0.00 0.00 0.00 2.24
281 282 4.659115 ACGGAAGCAGGGTTTTATTAGTT 58.341 39.130 0.00 0.00 0.00 2.24
282 283 5.074804 ACGGAAGCAGGGTTTTATTAGTTT 58.925 37.500 0.00 0.00 0.00 2.66
283 284 5.048294 ACGGAAGCAGGGTTTTATTAGTTTG 60.048 40.000 0.00 0.00 0.00 2.93
284 285 5.621329 CGGAAGCAGGGTTTTATTAGTTTGG 60.621 44.000 0.00 0.00 0.00 3.28
285 286 4.801330 AGCAGGGTTTTATTAGTTTGGC 57.199 40.909 0.00 0.00 0.00 4.52
286 287 4.156477 AGCAGGGTTTTATTAGTTTGGCA 58.844 39.130 0.00 0.00 0.00 4.92
287 288 4.591072 AGCAGGGTTTTATTAGTTTGGCAA 59.409 37.500 0.00 0.00 0.00 4.52
288 289 5.071115 AGCAGGGTTTTATTAGTTTGGCAAA 59.929 36.000 8.93 8.93 0.00 3.68
289 290 5.760743 GCAGGGTTTTATTAGTTTGGCAAAA 59.239 36.000 15.29 0.00 0.00 2.44
290 291 6.261158 GCAGGGTTTTATTAGTTTGGCAAAAA 59.739 34.615 15.29 6.90 0.00 1.94
323 324 3.119849 GGTTGCATATATAGCGGCAAAGG 60.120 47.826 16.28 0.00 46.50 3.11
329 330 1.682451 TATAGCGGCAAAGGGAGCGT 61.682 55.000 1.45 0.00 34.34 5.07
339 340 2.543687 AAGGGAGCGTCGTGTCATCG 62.544 60.000 0.00 0.00 0.00 3.84
348 349 0.249699 TCGTGTCATCGCAAAGTGGT 60.250 50.000 0.00 0.00 0.00 4.16
362 363 4.728534 CAAAGTGGTCGTTTTGAGTTTGA 58.271 39.130 0.00 0.00 36.61 2.69
365 366 3.754323 AGTGGTCGTTTTGAGTTTGACAA 59.246 39.130 0.00 0.00 0.00 3.18
392 393 5.980116 CGATTGAGGAAATAGAGACGAACAT 59.020 40.000 0.00 0.00 0.00 2.71
441 442 1.002468 CCGATCCGATGGCATTGAAAC 60.002 52.381 16.49 5.76 0.00 2.78
465 466 4.380867 CCAATTTCCATTCTCAAGGAACGG 60.381 45.833 0.00 0.00 43.23 4.44
470 471 2.552155 CCATTCTCAAGGAACGGGAACA 60.552 50.000 0.00 0.00 34.02 3.18
472 473 3.284793 TTCTCAAGGAACGGGAACAAA 57.715 42.857 0.00 0.00 0.00 2.83
473 474 2.567985 TCTCAAGGAACGGGAACAAAC 58.432 47.619 0.00 0.00 0.00 2.93
474 475 2.171870 TCTCAAGGAACGGGAACAAACT 59.828 45.455 0.00 0.00 0.00 2.66
490 491 2.359602 CTGTGCCTGCCAGACCAG 60.360 66.667 0.00 0.00 31.38 4.00
499 500 0.036732 TGCCAGACCAGACCACATTC 59.963 55.000 0.00 0.00 0.00 2.67
503 504 1.349026 CAGACCAGACCACATTCCAGT 59.651 52.381 0.00 0.00 0.00 4.00
538 544 4.460263 TGAGAGATTCCAGAGACTAGAGC 58.540 47.826 0.00 0.00 0.00 4.09
562 568 2.126888 GCCGCATTCCACACAACG 60.127 61.111 0.00 0.00 0.00 4.10
590 596 2.915463 GGAGTAAACGATGACACGACAG 59.085 50.000 0.00 0.00 37.03 3.51
604 610 1.068474 CGACAGAACTAAAGCCGTGG 58.932 55.000 0.00 0.00 0.00 4.94
616 622 2.431942 CCGTGGTATATCGGCGCC 60.432 66.667 19.07 19.07 40.28 6.53
617 623 2.431942 CGTGGTATATCGGCGCCC 60.432 66.667 23.46 4.99 0.00 6.13
618 624 2.927580 CGTGGTATATCGGCGCCCT 61.928 63.158 23.46 11.53 0.00 5.19
640 646 5.340439 TCCCTTTTCCTCGAAAGTCTATC 57.660 43.478 0.00 0.00 35.37 2.08
669 675 1.351080 ACCGATCCTCCCTCCTACGA 61.351 60.000 0.00 0.00 0.00 3.43
786 819 2.048503 AGGCCGAGGAAACGAACG 60.049 61.111 0.00 0.00 35.09 3.95
853 886 1.704582 GCGTCGTTGAGATGTCTGC 59.295 57.895 0.00 0.00 38.14 4.26
871 904 2.537560 CCATCCGGTTCGCATGAGC 61.538 63.158 0.00 0.00 37.42 4.26
883 916 1.005340 GCATGAGCGAGACTGGAAAG 58.995 55.000 0.00 0.00 0.00 2.62
1011 1044 1.362717 CCCGCCTATGAGTACACCG 59.637 63.158 0.00 0.00 0.00 4.94
1051 1084 3.108289 CACACTCGCGCTCCACAG 61.108 66.667 5.56 0.00 0.00 3.66
1094 1127 1.845809 CGCAGCTCTTTCACACCACC 61.846 60.000 0.00 0.00 0.00 4.61
1095 1128 1.518903 GCAGCTCTTTCACACCACCC 61.519 60.000 0.00 0.00 0.00 4.61
1096 1129 0.890996 CAGCTCTTTCACACCACCCC 60.891 60.000 0.00 0.00 0.00 4.95
1097 1130 1.150536 GCTCTTTCACACCACCCCA 59.849 57.895 0.00 0.00 0.00 4.96
1098 1131 0.251341 GCTCTTTCACACCACCCCAT 60.251 55.000 0.00 0.00 0.00 4.00
1415 1454 2.840651 TCTTCTCCCTCATCCAAGGTTC 59.159 50.000 0.00 0.00 34.34 3.62
1439 1478 1.000506 TGCCTCCTACACTCGTTCAAC 59.999 52.381 0.00 0.00 0.00 3.18
1440 1479 1.978542 CCTCCTACACTCGTTCAACG 58.021 55.000 2.64 2.64 44.19 4.10
1441 1480 1.337821 CTCCTACACTCGTTCAACGC 58.662 55.000 4.63 0.00 42.21 4.84
1442 1481 0.386352 TCCTACACTCGTTCAACGCG 60.386 55.000 4.63 3.53 42.21 6.01
1489 1574 0.460722 TTGTTGACTCGTGGGTTCGA 59.539 50.000 0.00 0.00 38.19 3.71
1490 1575 0.460722 TGTTGACTCGTGGGTTCGAA 59.539 50.000 0.00 0.00 39.34 3.71
1491 1576 1.134759 TGTTGACTCGTGGGTTCGAAA 60.135 47.619 0.00 0.00 39.34 3.46
1592 1677 0.256752 TTCATGGGCATGGTGGAGAG 59.743 55.000 0.00 0.00 39.24 3.20
2049 2134 1.590238 CAGTTCATCATCTTCGCGTCC 59.410 52.381 5.77 0.00 0.00 4.79
2103 2188 3.788766 GTGGGCATCGTGTCACGC 61.789 66.667 20.56 6.64 42.21 5.34
2211 2296 4.918201 GCCATCGAGAAGGGCCGG 62.918 72.222 0.00 0.00 41.90 6.13
2212 2297 3.154473 CCATCGAGAAGGGCCGGA 61.154 66.667 5.05 0.00 0.00 5.14
2214 2299 2.127869 CATCGAGAAGGGCCGGAGA 61.128 63.158 5.05 0.00 0.00 3.71
2215 2300 1.381327 ATCGAGAAGGGCCGGAGAA 60.381 57.895 5.05 0.00 0.00 2.87
2381 2481 2.398429 CGTGCTGCGCTGAATCAG 59.602 61.111 19.32 5.78 34.12 2.90
2431 2531 2.740714 GATGCTCACCGAACGTGGC 61.741 63.158 0.00 0.00 43.23 5.01
2534 2634 1.065102 TCCGCGTCGAATTAAGAGGAG 59.935 52.381 4.92 4.33 0.00 3.69
2535 2635 1.478137 CGCGTCGAATTAAGAGGAGG 58.522 55.000 0.00 0.00 0.00 4.30
2537 2637 2.287668 CGCGTCGAATTAAGAGGAGGAT 60.288 50.000 0.00 0.00 0.00 3.24
2538 2638 3.718815 GCGTCGAATTAAGAGGAGGATT 58.281 45.455 0.00 0.00 0.00 3.01
2539 2639 4.556104 CGCGTCGAATTAAGAGGAGGATTA 60.556 45.833 0.00 0.00 0.00 1.75
2540 2640 5.471257 GCGTCGAATTAAGAGGAGGATTAT 58.529 41.667 0.00 0.00 0.00 1.28
2600 2709 4.035208 GTCGTGTTGGTGTGAAGAGAATTT 59.965 41.667 0.00 0.00 0.00 1.82
2619 2728 6.428159 AGAATTTAAGTGGTACTCTGTGCTTG 59.572 38.462 0.00 0.00 30.14 4.01
2668 2777 0.904649 CTTTGCCCCCTCCAATTTCC 59.095 55.000 0.00 0.00 0.00 3.13
2687 2821 1.071385 CCTGTCTGTTCTGTTCTGCCT 59.929 52.381 0.00 0.00 0.00 4.75
2692 2826 4.997395 TGTCTGTTCTGTTCTGCCTATTTC 59.003 41.667 0.00 0.00 0.00 2.17
2700 2834 3.500680 TGTTCTGCCTATTTCCGTGTTTC 59.499 43.478 0.00 0.00 0.00 2.78
2757 2891 2.094762 AATCTTAGCTGGCGAACGTT 57.905 45.000 0.00 0.00 0.00 3.99
2786 2920 1.285950 GTTTTGCCAGCGAACCCTC 59.714 57.895 0.00 0.00 0.00 4.30
2885 3019 0.180406 CTAATAACCGCCACCCTGCT 59.820 55.000 0.00 0.00 0.00 4.24
2887 3021 0.843984 AATAACCGCCACCCTGCTAT 59.156 50.000 0.00 0.00 0.00 2.97
2928 3062 1.452108 GCCGTCTCCCCCATTCTTG 60.452 63.158 0.00 0.00 0.00 3.02
2929 3063 1.452108 CCGTCTCCCCCATTCTTGC 60.452 63.158 0.00 0.00 0.00 4.01
3006 3157 4.311816 GTCAACGGACGAAGGGATATAA 57.688 45.455 0.00 0.00 33.68 0.98
3019 3170 9.675464 ACGAAGGGATATAATGTAAAGAAACAA 57.325 29.630 0.00 0.00 32.02 2.83
3046 3197 3.875134 GCTATTTACTAGGCGCCTGAAAA 59.125 43.478 38.98 30.76 0.00 2.29
3082 3233 6.164176 CCAAACGAGTTAGAATGAGTAGGTT 58.836 40.000 0.00 0.00 0.00 3.50
3177 3328 1.364171 GGCTGGTCGATGACGCTAT 59.636 57.895 0.00 0.00 39.58 2.97
3232 3383 3.006537 AGCGCTAAACTGGTAGAGAACAA 59.993 43.478 8.99 0.00 0.00 2.83
3237 3388 3.814005 AACTGGTAGAGAACAACGTGT 57.186 42.857 0.00 0.00 0.00 4.49
3266 3423 3.673597 TGAGAGAGAGGGGGCGGT 61.674 66.667 0.00 0.00 0.00 5.68
3288 3448 2.130821 TTTGGCCAGCGGTACATGGA 62.131 55.000 5.11 0.00 39.02 3.41
3290 3450 2.897350 GCCAGCGGTACATGGAGC 60.897 66.667 13.52 0.00 39.02 4.70
3292 3452 1.078497 CCAGCGGTACATGGAGCAA 60.078 57.895 8.09 0.00 39.02 3.91
3300 3461 1.072266 TACATGGAGCAAGGGGTGTT 58.928 50.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.260230 TCCAACCTCCAACCAAAGCA 59.740 50.000 0.00 0.00 0.00 3.91
1 2 0.961753 CTCCAACCTCCAACCAAAGC 59.038 55.000 0.00 0.00 0.00 3.51
2 3 2.364972 ACTCCAACCTCCAACCAAAG 57.635 50.000 0.00 0.00 0.00 2.77
3 4 2.661718 GAACTCCAACCTCCAACCAAA 58.338 47.619 0.00 0.00 0.00 3.28
4 5 1.133606 GGAACTCCAACCTCCAACCAA 60.134 52.381 0.00 0.00 35.64 3.67
5 6 0.476771 GGAACTCCAACCTCCAACCA 59.523 55.000 0.00 0.00 35.64 3.67
6 7 0.251209 GGGAACTCCAACCTCCAACC 60.251 60.000 0.00 0.00 37.91 3.77
7 8 0.251209 GGGGAACTCCAACCTCCAAC 60.251 60.000 0.00 0.00 37.91 3.77
8 9 1.432023 GGGGGAACTCCAACCTCCAA 61.432 60.000 0.00 0.00 45.53 3.53
9 10 1.850755 GGGGGAACTCCAACCTCCA 60.851 63.158 0.00 0.00 45.53 3.86
10 11 1.541620 AGGGGGAACTCCAACCTCC 60.542 63.158 5.62 0.00 46.51 4.30
11 12 1.992037 GAGGGGGAACTCCAACCTC 59.008 63.158 17.81 17.81 46.83 3.85
12 13 0.842467 CAGAGGGGGAACTCCAACCT 60.842 60.000 10.15 10.15 44.38 3.50
13 14 1.685820 CAGAGGGGGAACTCCAACC 59.314 63.158 0.00 0.00 38.26 3.77
14 15 1.685820 CCAGAGGGGGAACTCCAAC 59.314 63.158 0.00 0.00 38.26 3.77
15 16 2.231380 GCCAGAGGGGGAACTCCAA 61.231 63.158 0.00 0.00 38.26 3.53
16 17 2.610859 GCCAGAGGGGGAACTCCA 60.611 66.667 0.00 0.00 38.26 3.86
17 18 3.412408 GGCCAGAGGGGGAACTCC 61.412 72.222 0.00 0.00 38.26 3.85
18 19 3.787001 CGGCCAGAGGGGGAACTC 61.787 72.222 2.24 0.00 37.04 3.01
34 35 3.928769 CATGCACCATCGTCGCCG 61.929 66.667 0.00 0.00 0.00 6.46
35 36 2.813179 GACATGCACCATCGTCGCC 61.813 63.158 0.00 0.00 0.00 5.54
36 37 2.028766 CTGACATGCACCATCGTCGC 62.029 60.000 0.00 0.00 30.46 5.19
37 38 1.423721 CCTGACATGCACCATCGTCG 61.424 60.000 0.00 0.00 30.46 5.12
38 39 1.709147 GCCTGACATGCACCATCGTC 61.709 60.000 0.00 0.00 0.00 4.20
39 40 1.746615 GCCTGACATGCACCATCGT 60.747 57.895 0.00 0.00 0.00 3.73
40 41 1.746239 TGCCTGACATGCACCATCG 60.746 57.895 0.78 0.00 32.85 3.84
41 42 4.324471 TGCCTGACATGCACCATC 57.676 55.556 0.78 0.00 32.85 3.51
46 47 2.110835 ACACGTGCCTGACATGCA 59.889 55.556 17.22 0.78 39.03 3.96
47 48 2.557805 CACACGTGCCTGACATGC 59.442 61.111 17.22 0.00 39.03 4.06
57 58 2.052237 GAAACCGCTGCACACGTG 60.052 61.111 15.48 15.48 0.00 4.49
58 59 3.636043 CGAAACCGCTGCACACGT 61.636 61.111 0.00 0.00 0.00 4.49
59 60 4.368808 CCGAAACCGCTGCACACG 62.369 66.667 0.00 0.00 0.00 4.49
60 61 4.683334 GCCGAAACCGCTGCACAC 62.683 66.667 0.00 0.00 0.00 3.82
61 62 2.997952 TTAGCCGAAACCGCTGCACA 62.998 55.000 0.00 0.00 37.12 4.57
62 63 2.240612 CTTAGCCGAAACCGCTGCAC 62.241 60.000 0.00 0.00 37.12 4.57
63 64 2.031314 TTAGCCGAAACCGCTGCA 59.969 55.556 0.00 0.00 37.12 4.41
64 65 2.033194 ACTTAGCCGAAACCGCTGC 61.033 57.895 0.00 0.00 37.12 5.25
65 66 1.635663 CCACTTAGCCGAAACCGCTG 61.636 60.000 0.00 0.00 37.12 5.18
66 67 1.375523 CCACTTAGCCGAAACCGCT 60.376 57.895 0.00 0.00 40.45 5.52
67 68 3.035576 GCCACTTAGCCGAAACCGC 62.036 63.158 0.00 0.00 0.00 5.68
68 69 1.024579 ATGCCACTTAGCCGAAACCG 61.025 55.000 0.00 0.00 0.00 4.44
69 70 0.733150 GATGCCACTTAGCCGAAACC 59.267 55.000 0.00 0.00 0.00 3.27
70 71 0.733150 GGATGCCACTTAGCCGAAAC 59.267 55.000 0.00 0.00 0.00 2.78
71 72 0.393808 GGGATGCCACTTAGCCGAAA 60.394 55.000 0.00 0.00 0.00 3.46
72 73 1.223487 GGGATGCCACTTAGCCGAA 59.777 57.895 0.00 0.00 0.00 4.30
73 74 2.742116 GGGGATGCCACTTAGCCGA 61.742 63.158 5.30 0.00 0.00 5.54
74 75 2.203209 GGGGATGCCACTTAGCCG 60.203 66.667 5.30 0.00 0.00 5.52
75 76 1.149401 GAGGGGATGCCACTTAGCC 59.851 63.158 5.30 0.00 37.42 3.93
76 77 1.227674 CGAGGGGATGCCACTTAGC 60.228 63.158 5.30 0.00 37.42 3.09
77 78 0.390860 CTCGAGGGGATGCCACTTAG 59.609 60.000 5.30 0.00 37.42 2.18
78 79 1.686325 GCTCGAGGGGATGCCACTTA 61.686 60.000 15.58 0.00 37.42 2.24
79 80 3.036429 GCTCGAGGGGATGCCACTT 62.036 63.158 15.58 0.00 37.42 3.16
80 81 3.474570 GCTCGAGGGGATGCCACT 61.475 66.667 15.58 0.00 41.79 4.00
81 82 4.554036 GGCTCGAGGGGATGCCAC 62.554 72.222 15.58 0.00 44.34 5.01
83 84 2.631012 AAATGGCTCGAGGGGATGCC 62.631 60.000 15.58 9.48 45.10 4.40
84 85 0.108585 TAAATGGCTCGAGGGGATGC 59.891 55.000 15.58 0.00 0.00 3.91
85 86 2.867109 ATAAATGGCTCGAGGGGATG 57.133 50.000 15.58 0.00 0.00 3.51
86 87 3.884037 AAATAAATGGCTCGAGGGGAT 57.116 42.857 15.58 0.00 0.00 3.85
87 88 3.493699 CGTAAATAAATGGCTCGAGGGGA 60.494 47.826 15.58 0.00 0.00 4.81
88 89 2.806244 CGTAAATAAATGGCTCGAGGGG 59.194 50.000 15.58 0.00 0.00 4.79
89 90 2.223377 GCGTAAATAAATGGCTCGAGGG 59.777 50.000 15.58 0.00 0.00 4.30
90 91 2.096909 CGCGTAAATAAATGGCTCGAGG 60.097 50.000 15.58 0.00 0.00 4.63
91 92 2.538449 ACGCGTAAATAAATGGCTCGAG 59.462 45.455 11.67 8.45 0.00 4.04
92 93 2.283086 CACGCGTAAATAAATGGCTCGA 59.717 45.455 13.44 0.00 0.00 4.04
93 94 2.598907 CCACGCGTAAATAAATGGCTCG 60.599 50.000 13.44 0.00 0.00 5.03
94 95 2.981875 CCACGCGTAAATAAATGGCTC 58.018 47.619 13.44 0.00 0.00 4.70
96 97 1.472990 GCCACGCGTAAATAAATGGC 58.527 50.000 13.44 14.96 45.26 4.40
97 98 2.834574 TGCCACGCGTAAATAAATGG 57.165 45.000 13.44 7.72 0.00 3.16
98 99 3.753842 AGTTGCCACGCGTAAATAAATG 58.246 40.909 13.44 0.00 0.00 2.32
99 100 3.181504 GGAGTTGCCACGCGTAAATAAAT 60.182 43.478 13.44 4.27 36.34 1.40
100 101 2.160022 GGAGTTGCCACGCGTAAATAAA 59.840 45.455 13.44 0.00 36.34 1.40
101 102 1.733360 GGAGTTGCCACGCGTAAATAA 59.267 47.619 13.44 1.99 36.34 1.40
102 103 1.066716 AGGAGTTGCCACGCGTAAATA 60.067 47.619 13.44 0.00 40.02 1.40
103 104 0.321298 AGGAGTTGCCACGCGTAAAT 60.321 50.000 13.44 1.02 40.02 1.40
104 105 0.533308 AAGGAGTTGCCACGCGTAAA 60.533 50.000 13.44 3.97 40.02 2.01
105 106 0.533308 AAAGGAGTTGCCACGCGTAA 60.533 50.000 13.44 0.00 40.02 3.18
106 107 0.317799 TAAAGGAGTTGCCACGCGTA 59.682 50.000 13.44 0.00 40.02 4.42
107 108 0.949105 CTAAAGGAGTTGCCACGCGT 60.949 55.000 5.58 5.58 40.02 6.01
108 109 1.635663 CCTAAAGGAGTTGCCACGCG 61.636 60.000 3.53 3.53 40.02 6.01
109 110 1.923227 GCCTAAAGGAGTTGCCACGC 61.923 60.000 0.00 0.00 40.02 5.34
110 111 1.635663 CGCCTAAAGGAGTTGCCACG 61.636 60.000 0.00 0.00 40.02 4.94
111 112 1.305930 CCGCCTAAAGGAGTTGCCAC 61.306 60.000 0.00 0.00 40.02 5.01
112 113 1.002624 CCGCCTAAAGGAGTTGCCA 60.003 57.895 0.00 0.00 40.02 4.92
113 114 0.608308 AACCGCCTAAAGGAGTTGCC 60.608 55.000 0.00 0.00 37.39 4.52
114 115 1.244816 AAACCGCCTAAAGGAGTTGC 58.755 50.000 0.00 0.00 34.68 4.17
115 116 4.153655 GTCTAAAACCGCCTAAAGGAGTTG 59.846 45.833 0.00 0.00 34.68 3.16
116 117 4.202388 TGTCTAAAACCGCCTAAAGGAGTT 60.202 41.667 0.00 0.00 37.39 3.01
117 118 3.325716 TGTCTAAAACCGCCTAAAGGAGT 59.674 43.478 0.00 0.00 37.39 3.85
118 119 3.683340 GTGTCTAAAACCGCCTAAAGGAG 59.317 47.826 0.00 0.00 37.39 3.69
119 120 3.071312 TGTGTCTAAAACCGCCTAAAGGA 59.929 43.478 0.00 0.00 37.39 3.36
120 121 3.187842 GTGTGTCTAAAACCGCCTAAAGG 59.812 47.826 0.00 0.00 38.53 3.11
121 122 3.120786 CGTGTGTCTAAAACCGCCTAAAG 60.121 47.826 0.00 0.00 0.00 1.85
122 123 2.801679 CGTGTGTCTAAAACCGCCTAAA 59.198 45.455 0.00 0.00 0.00 1.85
123 124 2.224018 ACGTGTGTCTAAAACCGCCTAA 60.224 45.455 0.00 0.00 0.00 2.69
124 125 1.340889 ACGTGTGTCTAAAACCGCCTA 59.659 47.619 0.00 0.00 0.00 3.93
125 126 0.105408 ACGTGTGTCTAAAACCGCCT 59.895 50.000 0.00 0.00 0.00 5.52
126 127 0.509929 GACGTGTGTCTAAAACCGCC 59.490 55.000 0.00 0.00 42.08 6.13
127 128 1.210870 TGACGTGTGTCTAAAACCGC 58.789 50.000 0.00 0.00 45.70 5.68
128 129 4.461992 AAATGACGTGTGTCTAAAACCG 57.538 40.909 0.00 0.00 45.70 4.44
129 130 6.854381 CCTTTAAATGACGTGTGTCTAAAACC 59.146 38.462 0.00 0.00 45.70 3.27
130 131 6.358822 GCCTTTAAATGACGTGTGTCTAAAAC 59.641 38.462 0.00 0.00 45.70 2.43
131 132 6.432107 GCCTTTAAATGACGTGTGTCTAAAA 58.568 36.000 0.00 0.00 45.70 1.52
132 133 5.333492 CGCCTTTAAATGACGTGTGTCTAAA 60.333 40.000 0.00 0.00 45.70 1.85
133 134 4.150980 CGCCTTTAAATGACGTGTGTCTAA 59.849 41.667 0.00 0.00 45.70 2.10
134 135 3.676172 CGCCTTTAAATGACGTGTGTCTA 59.324 43.478 0.00 0.00 45.70 2.59
135 136 2.478894 CGCCTTTAAATGACGTGTGTCT 59.521 45.455 0.00 0.00 45.70 3.41
136 137 2.412325 CCGCCTTTAAATGACGTGTGTC 60.412 50.000 0.00 0.00 45.71 3.67
137 138 1.533731 CCGCCTTTAAATGACGTGTGT 59.466 47.619 0.00 0.00 0.00 3.72
138 139 1.533731 ACCGCCTTTAAATGACGTGTG 59.466 47.619 0.00 0.00 0.00 3.82
139 140 1.886886 ACCGCCTTTAAATGACGTGT 58.113 45.000 0.00 0.00 0.00 4.49
140 141 2.981400 AACCGCCTTTAAATGACGTG 57.019 45.000 0.00 0.00 0.00 4.49
141 142 3.994204 AAAACCGCCTTTAAATGACGT 57.006 38.095 0.00 0.00 0.00 4.34
208 209 7.509318 CCCACGGAAGATTATATCCCATAGATA 59.491 40.741 0.00 0.00 41.73 1.98
209 210 6.327626 CCCACGGAAGATTATATCCCATAGAT 59.672 42.308 0.00 0.00 39.15 1.98
210 211 5.661312 CCCACGGAAGATTATATCCCATAGA 59.339 44.000 0.00 0.00 31.73 1.98
211 212 5.685075 GCCCACGGAAGATTATATCCCATAG 60.685 48.000 0.00 0.00 31.73 2.23
212 213 4.163458 GCCCACGGAAGATTATATCCCATA 59.837 45.833 0.00 0.00 31.73 2.74
213 214 3.054361 GCCCACGGAAGATTATATCCCAT 60.054 47.826 0.00 0.00 31.73 4.00
214 215 2.304761 GCCCACGGAAGATTATATCCCA 59.695 50.000 0.00 0.00 31.73 4.37
215 216 2.572104 AGCCCACGGAAGATTATATCCC 59.428 50.000 0.00 0.00 31.73 3.85
216 217 3.983044 AGCCCACGGAAGATTATATCC 57.017 47.619 0.00 0.00 0.00 2.59
217 218 7.923414 AAAATAGCCCACGGAAGATTATATC 57.077 36.000 0.00 0.00 0.00 1.63
218 219 7.553044 GCTAAAATAGCCCACGGAAGATTATAT 59.447 37.037 0.00 0.00 45.95 0.86
219 220 6.877322 GCTAAAATAGCCCACGGAAGATTATA 59.123 38.462 0.00 0.00 45.95 0.98
220 221 5.705905 GCTAAAATAGCCCACGGAAGATTAT 59.294 40.000 0.00 0.00 45.95 1.28
221 222 5.061179 GCTAAAATAGCCCACGGAAGATTA 58.939 41.667 0.00 0.00 45.95 1.75
222 223 3.883489 GCTAAAATAGCCCACGGAAGATT 59.117 43.478 0.00 0.00 45.95 2.40
223 224 3.477530 GCTAAAATAGCCCACGGAAGAT 58.522 45.455 0.00 0.00 45.95 2.40
224 225 2.914059 GCTAAAATAGCCCACGGAAGA 58.086 47.619 0.00 0.00 45.95 2.87
235 236 2.158667 ACATCCGGTGGGGCTAAAATAG 60.159 50.000 0.00 0.00 34.94 1.73
236 237 1.847737 ACATCCGGTGGGGCTAAAATA 59.152 47.619 0.00 0.00 34.94 1.40
237 238 0.629058 ACATCCGGTGGGGCTAAAAT 59.371 50.000 0.00 0.00 34.94 1.82
238 239 0.322997 CACATCCGGTGGGGCTAAAA 60.323 55.000 0.00 0.00 44.04 1.52
239 240 1.301623 CACATCCGGTGGGGCTAAA 59.698 57.895 0.00 0.00 44.04 1.85
240 241 2.994699 CACATCCGGTGGGGCTAA 59.005 61.111 0.00 0.00 44.04 3.09
248 249 1.375523 GCTTCCGTTCACATCCGGT 60.376 57.895 0.00 0.00 44.51 5.28
249 250 1.361668 CTGCTTCCGTTCACATCCGG 61.362 60.000 0.00 0.00 45.55 5.14
250 251 1.361668 CCTGCTTCCGTTCACATCCG 61.362 60.000 0.00 0.00 0.00 4.18
251 252 1.026718 CCCTGCTTCCGTTCACATCC 61.027 60.000 0.00 0.00 0.00 3.51
252 253 0.321653 ACCCTGCTTCCGTTCACATC 60.322 55.000 0.00 0.00 0.00 3.06
253 254 0.110486 AACCCTGCTTCCGTTCACAT 59.890 50.000 0.00 0.00 0.00 3.21
254 255 0.106918 AAACCCTGCTTCCGTTCACA 60.107 50.000 0.00 0.00 0.00 3.58
255 256 1.029681 AAAACCCTGCTTCCGTTCAC 58.970 50.000 0.00 0.00 0.00 3.18
256 257 2.642154 TAAAACCCTGCTTCCGTTCA 57.358 45.000 0.00 0.00 0.00 3.18
257 258 4.698780 ACTAATAAAACCCTGCTTCCGTTC 59.301 41.667 0.00 0.00 0.00 3.95
258 259 4.659115 ACTAATAAAACCCTGCTTCCGTT 58.341 39.130 0.00 0.00 0.00 4.44
259 260 4.296621 ACTAATAAAACCCTGCTTCCGT 57.703 40.909 0.00 0.00 0.00 4.69
260 261 5.399013 CAAACTAATAAAACCCTGCTTCCG 58.601 41.667 0.00 0.00 0.00 4.30
261 262 5.720202 CCAAACTAATAAAACCCTGCTTCC 58.280 41.667 0.00 0.00 0.00 3.46
262 263 5.168569 GCCAAACTAATAAAACCCTGCTTC 58.831 41.667 0.00 0.00 0.00 3.86
263 264 4.591072 TGCCAAACTAATAAAACCCTGCTT 59.409 37.500 0.00 0.00 0.00 3.91
264 265 4.156477 TGCCAAACTAATAAAACCCTGCT 58.844 39.130 0.00 0.00 0.00 4.24
265 266 4.529109 TGCCAAACTAATAAAACCCTGC 57.471 40.909 0.00 0.00 0.00 4.85
266 267 7.793927 TTTTTGCCAAACTAATAAAACCCTG 57.206 32.000 0.00 0.00 0.00 4.45
302 303 3.119849 CCCTTTGCCGCTATATATGCAAC 60.120 47.826 7.49 0.67 42.84 4.17
312 313 3.659089 GACGCTCCCTTTGCCGCTA 62.659 63.158 0.00 0.00 0.00 4.26
329 330 0.249699 ACCACTTTGCGATGACACGA 60.250 50.000 0.00 0.00 35.09 4.35
339 340 2.844122 ACTCAAAACGACCACTTTGC 57.156 45.000 0.00 0.00 33.45 3.68
362 363 6.334202 GTCTCTATTTCCTCAATCGAGTTGT 58.666 40.000 0.00 0.00 36.49 3.32
365 366 4.882427 TCGTCTCTATTTCCTCAATCGAGT 59.118 41.667 0.00 0.00 36.49 4.18
371 372 7.122204 TGTCTATGTTCGTCTCTATTTCCTCAA 59.878 37.037 0.00 0.00 0.00 3.02
380 381 8.502105 TGTAATCTTGTCTATGTTCGTCTCTA 57.498 34.615 0.00 0.00 0.00 2.43
392 393 5.468746 GTGCCAACACTTGTAATCTTGTCTA 59.531 40.000 0.00 0.00 43.85 2.59
441 442 4.380867 CGTTCCTTGAGAATGGAAATTGGG 60.381 45.833 0.00 0.00 43.06 4.12
465 466 1.363807 GGCAGGCACAGTTTGTTCC 59.636 57.895 0.00 0.00 33.72 3.62
470 471 1.529244 GGTCTGGCAGGCACAGTTT 60.529 57.895 22.23 0.00 37.25 2.66
472 473 3.170672 TGGTCTGGCAGGCACAGT 61.171 61.111 22.23 0.00 37.25 3.55
473 474 2.359602 CTGGTCTGGCAGGCACAG 60.360 66.667 22.23 20.08 37.30 3.66
474 475 2.848679 TCTGGTCTGGCAGGCACA 60.849 61.111 22.23 14.94 0.00 4.57
490 491 0.883833 CCTTGCACTGGAATGTGGTC 59.116 55.000 0.00 0.00 38.31 4.02
521 524 3.317993 GTGGAGCTCTAGTCTCTGGAATC 59.682 52.174 14.64 0.00 0.00 2.52
525 528 2.023673 CAGTGGAGCTCTAGTCTCTGG 58.976 57.143 14.64 0.00 0.00 3.86
538 544 2.046023 TGGAATGCGGCAGTGGAG 60.046 61.111 8.01 0.00 0.00 3.86
562 568 3.126514 TGTCATCGTTTACTCCGAGAGAC 59.873 47.826 1.33 0.00 40.60 3.36
590 596 3.985925 CCGATATACCACGGCTTTAGTTC 59.014 47.826 0.00 0.00 42.55 3.01
604 610 1.542187 AAGGGAGGGCGCCGATATAC 61.542 60.000 22.54 6.81 0.00 1.47
613 619 2.125106 CGAGGAAAAGGGAGGGCG 60.125 66.667 0.00 0.00 0.00 6.13
615 621 1.351350 ACTTTCGAGGAAAAGGGAGGG 59.649 52.381 0.07 0.00 39.96 4.30
616 622 2.303311 AGACTTTCGAGGAAAAGGGAGG 59.697 50.000 0.07 0.00 39.96 4.30
617 623 3.686916 AGACTTTCGAGGAAAAGGGAG 57.313 47.619 0.07 0.00 39.96 4.30
618 624 4.775780 TGATAGACTTTCGAGGAAAAGGGA 59.224 41.667 0.07 0.00 39.96 4.20
640 646 2.232452 GGGAGGATCGGTCACATATCTG 59.768 54.545 0.00 0.00 34.37 2.90
706 712 6.612456 AGAAATTGATATGGCTGATGGGAAAA 59.388 34.615 0.00 0.00 0.00 2.29
786 819 3.110178 CCGTCTGAACCCGAACGC 61.110 66.667 0.00 0.00 0.00 4.84
834 867 1.983907 CAGACATCTCAACGACGCG 59.016 57.895 3.53 3.53 0.00 6.01
871 904 4.244425 TCAAACTCTCTTTCCAGTCTCG 57.756 45.455 0.00 0.00 0.00 4.04
872 905 5.360591 TGTTCAAACTCTCTTTCCAGTCTC 58.639 41.667 0.00 0.00 0.00 3.36
873 906 5.359194 TGTTCAAACTCTCTTTCCAGTCT 57.641 39.130 0.00 0.00 0.00 3.24
874 907 4.024472 GCTGTTCAAACTCTCTTTCCAGTC 60.024 45.833 0.00 0.00 0.00 3.51
1051 1084 3.462678 GAGGCCGAGGGAGTGTCC 61.463 72.222 0.00 0.00 35.23 4.02
1094 1127 4.157120 GGTCGACCGTGGGATGGG 62.157 72.222 20.85 0.00 0.00 4.00
1415 1454 2.496817 GAGTGTAGGAGGCAGGCG 59.503 66.667 0.00 0.00 0.00 5.52
1422 1461 1.337821 GCGTTGAACGAGTGTAGGAG 58.662 55.000 23.12 0.00 46.05 3.69
1423 1462 0.386352 CGCGTTGAACGAGTGTAGGA 60.386 55.000 23.12 0.00 46.05 2.94
1424 1463 1.941476 GCGCGTTGAACGAGTGTAGG 61.941 60.000 23.12 1.95 46.05 3.18
1427 1466 3.688330 CGCGCGTTGAACGAGTGT 61.688 61.111 24.19 0.00 46.05 3.55
1463 1502 2.031683 CCCACGAGTCAACAAACAAGTC 59.968 50.000 0.00 0.00 0.00 3.01
1489 1574 1.334960 CGCGAACTCTGCAACCAATTT 60.335 47.619 0.00 0.00 0.00 1.82
1490 1575 0.238289 CGCGAACTCTGCAACCAATT 59.762 50.000 0.00 0.00 0.00 2.32
1491 1576 0.884704 ACGCGAACTCTGCAACCAAT 60.885 50.000 15.93 0.00 0.00 3.16
1571 1656 0.033796 CTCCACCATGCCCATGAACT 60.034 55.000 9.73 0.00 41.20 3.01
2022 2107 0.179000 AGATGATGAACTGGTCGCCC 59.821 55.000 0.00 0.00 0.00 6.13
2211 2296 2.095252 GTCGTGGAAGCGCCTTCTC 61.095 63.158 2.29 0.00 40.07 2.87
2212 2297 2.048127 GTCGTGGAAGCGCCTTCT 60.048 61.111 2.29 0.00 40.07 2.85
2214 2299 3.986006 TCGTCGTGGAAGCGCCTT 61.986 61.111 2.29 0.00 37.63 4.35
2215 2300 4.719369 GTCGTCGTGGAAGCGCCT 62.719 66.667 2.29 0.00 37.63 5.52
2431 2531 1.680105 CCGCTAGCACGTTTACGGTG 61.680 60.000 16.45 4.25 44.95 4.94
2600 2709 3.306088 GCTCAAGCACAGAGTACCACTTA 60.306 47.826 0.00 0.00 41.59 2.24
2619 2728 5.873712 TCTGAATTGATCACAGAAGAAGCTC 59.126 40.000 11.08 0.00 37.66 4.09
2668 2777 2.540265 AGGCAGAACAGAACAGACAG 57.460 50.000 0.00 0.00 0.00 3.51
2757 2891 1.962306 GGCAAAACGTCCGTGGCTA 60.962 57.895 11.02 0.00 35.12 3.93
2786 2920 0.529992 GGAGATCGTGCGGTTTAGGG 60.530 60.000 0.00 0.00 0.00 3.53
2859 2993 3.340928 GGTGGCGGTTATTAGAAACTGT 58.659 45.455 0.00 0.00 37.91 3.55
2870 3004 1.692173 GGATAGCAGGGTGGCGGTTA 61.692 60.000 0.00 0.00 39.27 2.85
2885 3019 6.404513 CGGTTTTTAATGCGTTTAAGGGGATA 60.405 38.462 0.00 0.00 31.57 2.59
2887 3021 4.321082 CGGTTTTTAATGCGTTTAAGGGGA 60.321 41.667 0.00 0.00 31.57 4.81
2928 3062 0.524180 CGTAACTAGGGTCCGTTCGC 60.524 60.000 0.00 0.00 0.00 4.70
2929 3063 0.524180 GCGTAACTAGGGTCCGTTCG 60.524 60.000 0.00 0.00 0.00 3.95
3019 3170 5.046591 TCAGGCGCCTAGTAAATAGCATATT 60.047 40.000 32.30 0.00 0.00 1.28
3046 3197 0.671251 TCGTTTGGCGCTTGGAAAAT 59.329 45.000 7.64 0.00 41.07 1.82
3082 3233 0.462225 CCTCACCGTCTCTAGCTCGA 60.462 60.000 0.00 0.00 0.00 4.04
3177 3328 0.185416 CTCTAAGCCCCGTCCTCCTA 59.815 60.000 0.00 0.00 0.00 2.94
3237 3388 4.056125 CTCTCACGCACGCCTCCA 62.056 66.667 0.00 0.00 0.00 3.86
3288 3448 2.845345 CCTCCCAACACCCCTTGCT 61.845 63.158 0.00 0.00 0.00 3.91
3290 3450 1.295020 TATCCTCCCAACACCCCTTG 58.705 55.000 0.00 0.00 0.00 3.61
3292 3452 2.068831 TTTATCCTCCCAACACCCCT 57.931 50.000 0.00 0.00 0.00 4.79
3300 3461 9.540538 TTTTCTTCATTTGTATTTATCCTCCCA 57.459 29.630 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.