Multiple sequence alignment - TraesCS5B01G353000

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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 TraesCS5B01G353000 chr5B 100.000 2198 0 0 1 2198 532769557 532767360 0.000000e+00 4060
1 TraesCS5B01G353000 chr5B 94.915 649 33 0 1539 2187 149382156 149382804 0.000000e+00 1016
2 TraesCS5B01G353000 chr5B 84.127 126 15 4 2 125 511299870 511299748 1.380000e-22 117
3 TraesCS5B01G353000 chr5D 93.053 1166 51 9 368 1529 438178410 438177271 0.000000e+00 1677
4 TraesCS5B01G353000 chr5D 81.385 231 35 4 989 1218 47531855 47531632 4.820000e-42 182
5 TraesCS5B01G353000 chr3B 94.915 649 30 3 1539 2187 814498754 814498109 0.000000e+00 1013
6 TraesCS5B01G353000 chr3B 94.615 650 35 0 1538 2187 819924955 819924306 0.000000e+00 1007
7 TraesCS5B01G353000 chr3A 94.325 652 33 4 1538 2187 662617780 662617131 0.000000e+00 996
8 TraesCS5B01G353000 chr2B 94.308 650 34 3 1539 2187 51079452 51080099 0.000000e+00 992
9 TraesCS5B01G353000 chr6D 94.281 647 36 1 1541 2187 464577415 464578060 0.000000e+00 989
10 TraesCS5B01G353000 chr6D 76.710 614 123 15 609 1207 464653465 464652857 7.570000e-85 324
11 TraesCS5B01G353000 chr6B 94.145 649 36 2 1539 2187 44245841 44245195 0.000000e+00 987
12 TraesCS5B01G353000 chr6B 94.145 649 35 3 1539 2187 320542816 320542171 0.000000e+00 985
13 TraesCS5B01G353000 chr6B 74.832 596 136 11 621 1209 718257295 718256707 7.790000e-65 257
14 TraesCS5B01G353000 chr6B 78.988 257 49 4 949 1200 718240542 718240286 1.040000e-38 171
15 TraesCS5B01G353000 chr2A 94.009 651 36 3 1538 2187 644222272 644222920 0.000000e+00 983
16 TraesCS5B01G353000 chr5A 92.654 667 36 4 368 1030 553166793 553166136 0.000000e+00 948
17 TraesCS5B01G353000 chr5A 93.582 483 22 4 1047 1529 553146192 553145719 0.000000e+00 712
18 TraesCS5B01G353000 chr5A 80.870 230 38 2 989 1218 37935908 37935685 2.240000e-40 176
19 TraesCS5B01G353000 chr7A 80.952 231 36 5 986 1215 674139788 674140011 2.240000e-40 176
20 TraesCS5B01G353000 chr6A 79.556 225 45 1 989 1213 616794809 616794586 2.260000e-35 159
21 TraesCS5B01G353000 chrUn 81.818 132 24 0 1087 1218 221378233 221378102 6.410000e-21 111


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 TraesCS5B01G353000 chr5B 532767360 532769557 2197 True 4060 4060 100.000 1 2198 1 chr5B.!!$R2 2197
1 TraesCS5B01G353000 chr5B 149382156 149382804 648 False 1016 1016 94.915 1539 2187 1 chr5B.!!$F1 648
2 TraesCS5B01G353000 chr5D 438177271 438178410 1139 True 1677 1677 93.053 368 1529 1 chr5D.!!$R2 1161
3 TraesCS5B01G353000 chr3B 814498109 814498754 645 True 1013 1013 94.915 1539 2187 1 chr3B.!!$R1 648
4 TraesCS5B01G353000 chr3B 819924306 819924955 649 True 1007 1007 94.615 1538 2187 1 chr3B.!!$R2 649
5 TraesCS5B01G353000 chr3A 662617131 662617780 649 True 996 996 94.325 1538 2187 1 chr3A.!!$R1 649
6 TraesCS5B01G353000 chr2B 51079452 51080099 647 False 992 992 94.308 1539 2187 1 chr2B.!!$F1 648
7 TraesCS5B01G353000 chr6D 464577415 464578060 645 False 989 989 94.281 1541 2187 1 chr6D.!!$F1 646
8 TraesCS5B01G353000 chr6D 464652857 464653465 608 True 324 324 76.710 609 1207 1 chr6D.!!$R1 598
9 TraesCS5B01G353000 chr6B 44245195 44245841 646 True 987 987 94.145 1539 2187 1 chr6B.!!$R1 648
10 TraesCS5B01G353000 chr6B 320542171 320542816 645 True 985 985 94.145 1539 2187 1 chr6B.!!$R2 648
11 TraesCS5B01G353000 chr6B 718256707 718257295 588 True 257 257 74.832 621 1209 1 chr6B.!!$R4 588
12 TraesCS5B01G353000 chr2A 644222272 644222920 648 False 983 983 94.009 1538 2187 1 chr2A.!!$F1 649
13 TraesCS5B01G353000 chr5A 553166136 553166793 657 True 948 948 92.654 368 1030 1 chr5A.!!$R3 662

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
313 314 0.032952 CACCGTCCGAGTTGAAGGAA 59.967 55.0 0.02 0.0 38.41 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2168 0.032615 TGGGAGCTGTTTGGTTGGTT 60.033 50.0 0.0 0.0 0.0 3.67 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
32 33 3.585247 CCATGGGATGGGAGGGAG 58.415 66.667 2.85 0.00 46.86 4.30
33 34 1.073474 CCATGGGATGGGAGGGAGA 60.073 63.158 2.85 0.00 46.86 3.71
34 35 0.698886 CCATGGGATGGGAGGGAGAA 60.699 60.000 2.85 0.00 46.86 2.87
35 36 1.225373 CATGGGATGGGAGGGAGAAA 58.775 55.000 0.00 0.00 0.00 2.52
36 37 1.144503 CATGGGATGGGAGGGAGAAAG 59.855 57.143 0.00 0.00 0.00 2.62
37 38 0.421495 TGGGATGGGAGGGAGAAAGA 59.579 55.000 0.00 0.00 0.00 2.52
38 39 1.203557 TGGGATGGGAGGGAGAAAGAA 60.204 52.381 0.00 0.00 0.00 2.52
39 40 1.923148 GGGATGGGAGGGAGAAAGAAA 59.077 52.381 0.00 0.00 0.00 2.52
40 41 2.515853 GGGATGGGAGGGAGAAAGAAAT 59.484 50.000 0.00 0.00 0.00 2.17
41 42 3.560105 GGATGGGAGGGAGAAAGAAATG 58.440 50.000 0.00 0.00 0.00 2.32
42 43 2.514458 TGGGAGGGAGAAAGAAATGC 57.486 50.000 0.00 0.00 0.00 3.56
43 44 1.005924 TGGGAGGGAGAAAGAAATGCC 59.994 52.381 0.00 0.00 0.00 4.40
44 45 1.005924 GGGAGGGAGAAAGAAATGCCA 59.994 52.381 0.00 0.00 0.00 4.92
45 46 2.373224 GGAGGGAGAAAGAAATGCCAG 58.627 52.381 0.00 0.00 0.00 4.85
46 47 2.291217 GGAGGGAGAAAGAAATGCCAGT 60.291 50.000 0.00 0.00 0.00 4.00
47 48 3.425659 GAGGGAGAAAGAAATGCCAGTT 58.574 45.455 0.00 0.00 0.00 3.16
48 49 3.425659 AGGGAGAAAGAAATGCCAGTTC 58.574 45.455 0.00 0.00 0.00 3.01
49 50 3.157087 GGGAGAAAGAAATGCCAGTTCA 58.843 45.455 7.70 0.00 0.00 3.18
50 51 3.766051 GGGAGAAAGAAATGCCAGTTCAT 59.234 43.478 7.70 0.00 0.00 2.57
51 52 4.949856 GGGAGAAAGAAATGCCAGTTCATA 59.050 41.667 7.70 0.00 0.00 2.15
52 53 5.163612 GGGAGAAAGAAATGCCAGTTCATAC 60.164 44.000 7.70 0.00 0.00 2.39
53 54 5.415701 GGAGAAAGAAATGCCAGTTCATACA 59.584 40.000 7.70 0.00 0.00 2.29
54 55 6.071952 GGAGAAAGAAATGCCAGTTCATACAA 60.072 38.462 7.70 0.00 0.00 2.41
55 56 7.363268 GGAGAAAGAAATGCCAGTTCATACAAT 60.363 37.037 7.70 0.00 0.00 2.71
56 57 7.542025 AGAAAGAAATGCCAGTTCATACAATC 58.458 34.615 7.70 0.00 0.00 2.67
57 58 6.839124 AAGAAATGCCAGTTCATACAATCA 57.161 33.333 7.70 0.00 0.00 2.57
58 59 6.446781 AGAAATGCCAGTTCATACAATCAG 57.553 37.500 7.70 0.00 0.00 2.90
59 60 5.359009 AGAAATGCCAGTTCATACAATCAGG 59.641 40.000 7.70 0.00 0.00 3.86
60 61 3.998913 TGCCAGTTCATACAATCAGGA 57.001 42.857 0.00 0.00 0.00 3.86
61 62 3.877559 TGCCAGTTCATACAATCAGGAG 58.122 45.455 0.00 0.00 0.00 3.69
62 63 3.519107 TGCCAGTTCATACAATCAGGAGA 59.481 43.478 0.00 0.00 0.00 3.71
63 64 4.125703 GCCAGTTCATACAATCAGGAGAG 58.874 47.826 0.00 0.00 0.00 3.20
64 65 4.141846 GCCAGTTCATACAATCAGGAGAGA 60.142 45.833 0.00 0.00 0.00 3.10
65 66 5.599732 CCAGTTCATACAATCAGGAGAGAG 58.400 45.833 0.00 0.00 0.00 3.20
66 67 5.128499 CCAGTTCATACAATCAGGAGAGAGT 59.872 44.000 0.00 0.00 0.00 3.24
67 68 6.351711 CCAGTTCATACAATCAGGAGAGAGTT 60.352 42.308 0.00 0.00 0.00 3.01
68 69 7.102346 CAGTTCATACAATCAGGAGAGAGTTT 58.898 38.462 0.00 0.00 0.00 2.66
69 70 8.253810 CAGTTCATACAATCAGGAGAGAGTTTA 58.746 37.037 0.00 0.00 0.00 2.01
70 71 8.986991 AGTTCATACAATCAGGAGAGAGTTTAT 58.013 33.333 0.00 0.00 0.00 1.40
71 72 9.606631 GTTCATACAATCAGGAGAGAGTTTATT 57.393 33.333 0.00 0.00 0.00 1.40
95 96 6.973700 TTTTTACTACCTTCCTATTGGGGA 57.026 37.500 0.00 0.00 35.33 4.81
96 97 5.963214 TTTACTACCTTCCTATTGGGGAC 57.037 43.478 0.00 0.00 34.78 4.46
97 98 3.797671 ACTACCTTCCTATTGGGGACT 57.202 47.619 0.00 0.00 34.78 3.85
98 99 4.913154 ACTACCTTCCTATTGGGGACTA 57.087 45.455 0.00 0.00 34.78 2.59
99 100 4.554683 ACTACCTTCCTATTGGGGACTAC 58.445 47.826 0.00 0.00 34.78 2.73
100 101 2.395619 ACCTTCCTATTGGGGACTACG 58.604 52.381 0.00 0.00 34.78 3.51
101 102 2.292719 ACCTTCCTATTGGGGACTACGT 60.293 50.000 0.00 0.00 34.78 3.57
102 103 2.102588 CCTTCCTATTGGGGACTACGTG 59.897 54.545 0.00 0.00 34.78 4.49
103 104 1.117150 TCCTATTGGGGACTACGTGC 58.883 55.000 0.00 0.00 35.33 5.34
104 105 1.120530 CCTATTGGGGACTACGTGCT 58.879 55.000 0.00 0.00 0.00 4.40
105 106 2.091720 TCCTATTGGGGACTACGTGCTA 60.092 50.000 0.00 0.00 35.33 3.49
106 107 2.035576 CCTATTGGGGACTACGTGCTAC 59.964 54.545 0.00 0.00 0.00 3.58
107 108 1.861982 ATTGGGGACTACGTGCTACT 58.138 50.000 0.00 0.00 0.00 2.57
108 109 1.636148 TTGGGGACTACGTGCTACTT 58.364 50.000 0.00 0.00 0.00 2.24
109 110 1.636148 TGGGGACTACGTGCTACTTT 58.364 50.000 0.00 0.00 0.00 2.66
110 111 1.972795 TGGGGACTACGTGCTACTTTT 59.027 47.619 0.00 0.00 0.00 2.27
111 112 2.369532 TGGGGACTACGTGCTACTTTTT 59.630 45.455 0.00 0.00 0.00 1.94
112 113 3.577848 TGGGGACTACGTGCTACTTTTTA 59.422 43.478 0.00 0.00 0.00 1.52
113 114 4.223477 TGGGGACTACGTGCTACTTTTTAT 59.777 41.667 0.00 0.00 0.00 1.40
114 115 4.807834 GGGGACTACGTGCTACTTTTTATC 59.192 45.833 0.00 0.00 0.00 1.75
115 116 5.394993 GGGGACTACGTGCTACTTTTTATCT 60.395 44.000 0.00 0.00 0.00 1.98
116 117 6.183360 GGGGACTACGTGCTACTTTTTATCTA 60.183 42.308 0.00 0.00 0.00 1.98
117 118 7.260603 GGGACTACGTGCTACTTTTTATCTAA 58.739 38.462 0.00 0.00 0.00 2.10
118 119 7.434602 GGGACTACGTGCTACTTTTTATCTAAG 59.565 40.741 0.00 0.00 0.00 2.18
119 120 7.434602 GGACTACGTGCTACTTTTTATCTAAGG 59.565 40.741 0.00 0.00 0.00 2.69
120 121 6.755607 ACTACGTGCTACTTTTTATCTAAGGC 59.244 38.462 0.00 0.00 0.00 4.35
121 122 5.484715 ACGTGCTACTTTTTATCTAAGGCA 58.515 37.500 0.00 0.00 0.00 4.75
122 123 5.350640 ACGTGCTACTTTTTATCTAAGGCAC 59.649 40.000 0.00 0.00 37.40 5.01
123 124 5.500290 CGTGCTACTTTTTATCTAAGGCACG 60.500 44.000 18.92 18.92 46.74 5.34
124 125 5.350640 GTGCTACTTTTTATCTAAGGCACGT 59.649 40.000 0.00 0.00 33.95 4.49
125 126 5.350365 TGCTACTTTTTATCTAAGGCACGTG 59.650 40.000 12.28 12.28 0.00 4.49
126 127 4.680171 ACTTTTTATCTAAGGCACGTGC 57.320 40.909 32.15 32.15 41.14 5.34
127 128 4.324267 ACTTTTTATCTAAGGCACGTGCT 58.676 39.130 36.84 22.72 41.70 4.40
128 129 4.154195 ACTTTTTATCTAAGGCACGTGCTG 59.846 41.667 36.84 23.95 41.70 4.41
129 130 2.309528 TTATCTAAGGCACGTGCTGG 57.690 50.000 36.84 21.90 41.70 4.85
130 131 1.480789 TATCTAAGGCACGTGCTGGA 58.519 50.000 36.84 26.12 41.70 3.86
131 132 0.833287 ATCTAAGGCACGTGCTGGAT 59.167 50.000 36.84 27.06 41.70 3.41
132 133 0.108186 TCTAAGGCACGTGCTGGATG 60.108 55.000 36.84 23.00 41.70 3.51
133 134 1.078497 TAAGGCACGTGCTGGATGG 60.078 57.895 36.84 0.00 41.70 3.51
134 135 1.836999 TAAGGCACGTGCTGGATGGT 61.837 55.000 36.84 17.62 41.70 3.55
135 136 3.434319 GGCACGTGCTGGATGGTG 61.434 66.667 36.84 0.00 41.70 4.17
136 137 2.358615 GCACGTGCTGGATGGTGA 60.359 61.111 32.55 0.00 38.21 4.02
137 138 1.965930 GCACGTGCTGGATGGTGAA 60.966 57.895 32.55 0.00 38.21 3.18
138 139 1.514678 GCACGTGCTGGATGGTGAAA 61.515 55.000 32.55 0.00 38.21 2.69
139 140 0.518636 CACGTGCTGGATGGTGAAAG 59.481 55.000 0.82 0.00 32.23 2.62
140 141 0.606401 ACGTGCTGGATGGTGAAAGG 60.606 55.000 0.00 0.00 0.00 3.11
141 142 1.308069 CGTGCTGGATGGTGAAAGGG 61.308 60.000 0.00 0.00 0.00 3.95
142 143 1.304381 TGCTGGATGGTGAAAGGGC 60.304 57.895 0.00 0.00 0.00 5.19
143 144 1.304381 GCTGGATGGTGAAAGGGCA 60.304 57.895 0.00 0.00 0.00 5.36
144 145 1.598701 GCTGGATGGTGAAAGGGCAC 61.599 60.000 0.00 0.00 38.05 5.01
145 146 1.303236 TGGATGGTGAAAGGGCACG 60.303 57.895 0.00 0.00 39.66 5.34
146 147 2.700773 GGATGGTGAAAGGGCACGC 61.701 63.158 0.00 0.00 39.66 5.34
147 148 1.971167 GATGGTGAAAGGGCACGCA 60.971 57.895 0.00 0.00 39.66 5.24
148 149 2.200170 GATGGTGAAAGGGCACGCAC 62.200 60.000 1.67 1.67 39.66 5.34
149 150 2.904866 GGTGAAAGGGCACGCACA 60.905 61.111 10.90 0.00 39.66 4.57
150 151 2.485795 GGTGAAAGGGCACGCACAA 61.486 57.895 10.90 0.00 39.66 3.33
151 152 1.435515 GTGAAAGGGCACGCACAAA 59.564 52.632 5.03 0.00 0.00 2.83
152 153 0.179124 GTGAAAGGGCACGCACAAAA 60.179 50.000 5.03 0.00 0.00 2.44
153 154 0.532573 TGAAAGGGCACGCACAAAAA 59.467 45.000 0.00 0.00 0.00 1.94
218 219 4.879014 GCCAAAAGCAAATACACGTTAC 57.121 40.909 0.00 0.00 42.97 2.50
219 220 4.542735 GCCAAAAGCAAATACACGTTACT 58.457 39.130 0.00 0.00 42.97 2.24
220 221 4.979815 GCCAAAAGCAAATACACGTTACTT 59.020 37.500 0.00 0.00 42.97 2.24
221 222 6.144175 GCCAAAAGCAAATACACGTTACTTA 58.856 36.000 0.00 0.00 42.97 2.24
222 223 6.804783 GCCAAAAGCAAATACACGTTACTTAT 59.195 34.615 0.00 0.00 42.97 1.73
223 224 7.327518 GCCAAAAGCAAATACACGTTACTTATT 59.672 33.333 0.00 0.00 42.97 1.40
224 225 9.828852 CCAAAAGCAAATACACGTTACTTATTA 57.171 29.630 0.00 0.00 0.00 0.98
252 253 7.948278 ACAACAGTCAGACAAAGTAATAGAC 57.052 36.000 2.66 0.00 0.00 2.59
253 254 7.497595 ACAACAGTCAGACAAAGTAATAGACA 58.502 34.615 2.66 0.00 0.00 3.41
254 255 8.150945 ACAACAGTCAGACAAAGTAATAGACAT 58.849 33.333 2.66 0.00 0.00 3.06
255 256 9.639601 CAACAGTCAGACAAAGTAATAGACATA 57.360 33.333 2.66 0.00 0.00 2.29
257 258 9.809096 ACAGTCAGACAAAGTAATAGACATATG 57.191 33.333 2.66 0.00 0.00 1.78
266 267 9.425893 CAAAGTAATAGACATATGAACTTTGCG 57.574 33.333 10.38 2.13 42.22 4.85
267 268 8.942338 AAGTAATAGACATATGAACTTTGCGA 57.058 30.769 10.38 0.00 30.08 5.10
268 269 8.581057 AGTAATAGACATATGAACTTTGCGAG 57.419 34.615 10.38 0.00 0.00 5.03
269 270 5.914085 ATAGACATATGAACTTTGCGAGC 57.086 39.130 10.38 0.00 0.00 5.03
270 271 2.604914 AGACATATGAACTTTGCGAGCG 59.395 45.455 10.38 0.00 0.00 5.03
271 272 2.603110 GACATATGAACTTTGCGAGCGA 59.397 45.455 10.38 0.00 0.00 4.93
272 273 2.604914 ACATATGAACTTTGCGAGCGAG 59.395 45.455 10.38 0.00 0.00 5.03
273 274 2.647529 TATGAACTTTGCGAGCGAGA 57.352 45.000 5.50 0.00 0.00 4.04
274 275 1.795768 ATGAACTTTGCGAGCGAGAA 58.204 45.000 5.50 0.00 0.00 2.87
275 276 1.795768 TGAACTTTGCGAGCGAGAAT 58.204 45.000 5.50 0.00 0.00 2.40
276 277 2.954316 TGAACTTTGCGAGCGAGAATA 58.046 42.857 5.50 0.00 0.00 1.75
277 278 3.521560 TGAACTTTGCGAGCGAGAATAT 58.478 40.909 5.50 0.00 0.00 1.28
278 279 4.678622 TGAACTTTGCGAGCGAGAATATA 58.321 39.130 5.50 0.00 0.00 0.86
279 280 5.106442 TGAACTTTGCGAGCGAGAATATAA 58.894 37.500 5.50 0.00 0.00 0.98
280 281 5.579119 TGAACTTTGCGAGCGAGAATATAAA 59.421 36.000 5.50 0.00 0.00 1.40
281 282 6.257849 TGAACTTTGCGAGCGAGAATATAAAT 59.742 34.615 5.50 0.00 0.00 1.40
282 283 7.436970 TGAACTTTGCGAGCGAGAATATAAATA 59.563 33.333 5.50 0.00 0.00 1.40
283 284 7.709269 ACTTTGCGAGCGAGAATATAAATAA 57.291 32.000 5.50 0.00 0.00 1.40
284 285 7.564988 ACTTTGCGAGCGAGAATATAAATAAC 58.435 34.615 5.50 0.00 0.00 1.89
285 286 6.462073 TTGCGAGCGAGAATATAAATAACC 57.538 37.500 0.00 0.00 0.00 2.85
286 287 5.534407 TGCGAGCGAGAATATAAATAACCA 58.466 37.500 0.00 0.00 0.00 3.67
287 288 5.633601 TGCGAGCGAGAATATAAATAACCAG 59.366 40.000 0.00 0.00 0.00 4.00
288 289 5.634020 GCGAGCGAGAATATAAATAACCAGT 59.366 40.000 0.00 0.00 0.00 4.00
289 290 6.805271 GCGAGCGAGAATATAAATAACCAGTA 59.195 38.462 0.00 0.00 0.00 2.74
290 291 7.488471 GCGAGCGAGAATATAAATAACCAGTAT 59.512 37.037 0.00 0.00 0.00 2.12
291 292 9.999009 CGAGCGAGAATATAAATAACCAGTATA 57.001 33.333 0.00 0.00 0.00 1.47
293 294 9.804758 AGCGAGAATATAAATAACCAGTATAGC 57.195 33.333 0.00 0.00 0.00 2.97
294 295 9.032420 GCGAGAATATAAATAACCAGTATAGCC 57.968 37.037 0.00 0.00 0.00 3.93
298 299 9.095065 GAATATAAATAACCAGTATAGCCACCG 57.905 37.037 0.00 0.00 0.00 4.94
299 300 4.765813 AAATAACCAGTATAGCCACCGT 57.234 40.909 0.00 0.00 0.00 4.83
300 301 4.332428 AATAACCAGTATAGCCACCGTC 57.668 45.455 0.00 0.00 0.00 4.79
301 302 0.828677 AACCAGTATAGCCACCGTCC 59.171 55.000 0.00 0.00 0.00 4.79
302 303 1.362717 CCAGTATAGCCACCGTCCG 59.637 63.158 0.00 0.00 0.00 4.79
303 304 1.105167 CCAGTATAGCCACCGTCCGA 61.105 60.000 0.00 0.00 0.00 4.55
304 305 0.311165 CAGTATAGCCACCGTCCGAG 59.689 60.000 0.00 0.00 0.00 4.63
305 306 0.106819 AGTATAGCCACCGTCCGAGT 60.107 55.000 0.00 0.00 0.00 4.18
306 307 0.743097 GTATAGCCACCGTCCGAGTT 59.257 55.000 0.00 0.00 0.00 3.01
307 308 0.742505 TATAGCCACCGTCCGAGTTG 59.257 55.000 0.00 0.00 0.00 3.16
308 309 0.968901 ATAGCCACCGTCCGAGTTGA 60.969 55.000 0.00 0.00 0.00 3.18
309 310 1.180456 TAGCCACCGTCCGAGTTGAA 61.180 55.000 0.00 0.00 0.00 2.69
310 311 2.027625 GCCACCGTCCGAGTTGAAG 61.028 63.158 0.00 0.00 0.00 3.02
311 312 1.374252 CCACCGTCCGAGTTGAAGG 60.374 63.158 0.00 0.00 39.47 3.46
312 313 1.663739 CACCGTCCGAGTTGAAGGA 59.336 57.895 0.02 0.00 37.34 3.36
313 314 0.032952 CACCGTCCGAGTTGAAGGAA 59.967 55.000 0.02 0.00 38.41 3.36
314 315 0.033090 ACCGTCCGAGTTGAAGGAAC 59.967 55.000 0.02 0.00 38.41 3.62
315 316 0.032952 CCGTCCGAGTTGAAGGAACA 59.967 55.000 0.00 0.00 38.41 3.18
316 317 1.539496 CCGTCCGAGTTGAAGGAACAA 60.539 52.381 0.00 0.00 38.41 2.83
317 318 2.413837 CGTCCGAGTTGAAGGAACAAT 58.586 47.619 0.00 0.00 38.41 2.71
318 319 2.157668 CGTCCGAGTTGAAGGAACAATG 59.842 50.000 0.00 0.00 38.41 2.82
319 320 3.139077 GTCCGAGTTGAAGGAACAATGT 58.861 45.455 0.00 0.00 38.41 2.71
320 321 4.312443 GTCCGAGTTGAAGGAACAATGTA 58.688 43.478 0.00 0.00 38.41 2.29
321 322 4.151867 GTCCGAGTTGAAGGAACAATGTAC 59.848 45.833 0.00 0.00 38.41 2.90
322 323 3.122948 CCGAGTTGAAGGAACAATGTACG 59.877 47.826 0.00 0.00 36.98 3.67
323 324 3.985279 CGAGTTGAAGGAACAATGTACGA 59.015 43.478 0.00 0.00 36.98 3.43
324 325 4.143389 CGAGTTGAAGGAACAATGTACGAC 60.143 45.833 0.00 0.00 36.98 4.34
325 326 4.699637 AGTTGAAGGAACAATGTACGACA 58.300 39.130 0.00 0.00 36.98 4.35
326 327 5.305585 AGTTGAAGGAACAATGTACGACAT 58.694 37.500 0.00 0.00 36.98 3.06
327 328 5.179368 AGTTGAAGGAACAATGTACGACATG 59.821 40.000 0.00 0.00 35.73 3.21
328 329 4.888917 TGAAGGAACAATGTACGACATGA 58.111 39.130 0.00 0.00 37.97 3.07
329 330 5.487433 TGAAGGAACAATGTACGACATGAT 58.513 37.500 0.00 0.00 37.97 2.45
330 331 5.937540 TGAAGGAACAATGTACGACATGATT 59.062 36.000 0.00 0.00 37.97 2.57
331 332 7.100409 TGAAGGAACAATGTACGACATGATTA 58.900 34.615 0.00 0.00 37.97 1.75
332 333 7.604545 TGAAGGAACAATGTACGACATGATTAA 59.395 33.333 0.00 0.00 37.97 1.40
333 334 8.506168 AAGGAACAATGTACGACATGATTAAT 57.494 30.769 0.00 0.00 37.97 1.40
334 335 8.142994 AGGAACAATGTACGACATGATTAATC 57.857 34.615 8.60 8.60 37.97 1.75
335 336 7.226720 AGGAACAATGTACGACATGATTAATCC 59.773 37.037 12.90 0.00 37.97 3.01
336 337 7.011950 GGAACAATGTACGACATGATTAATCCA 59.988 37.037 12.90 1.54 37.97 3.41
337 338 7.246674 ACAATGTACGACATGATTAATCCAC 57.753 36.000 12.90 1.51 37.97 4.02
338 339 6.019075 ACAATGTACGACATGATTAATCCACG 60.019 38.462 12.90 13.79 37.97 4.94
339 340 4.364860 TGTACGACATGATTAATCCACGG 58.635 43.478 12.90 2.67 0.00 4.94
340 341 3.812156 ACGACATGATTAATCCACGGA 57.188 42.857 12.90 0.00 0.00 4.69
341 342 3.717707 ACGACATGATTAATCCACGGAG 58.282 45.455 12.90 3.27 0.00 4.63
342 343 3.383505 ACGACATGATTAATCCACGGAGA 59.616 43.478 12.90 0.00 0.00 3.71
343 344 4.142026 ACGACATGATTAATCCACGGAGAA 60.142 41.667 12.90 0.00 0.00 2.87
344 345 4.808895 CGACATGATTAATCCACGGAGAAA 59.191 41.667 12.90 0.00 0.00 2.52
345 346 5.466728 CGACATGATTAATCCACGGAGAAAT 59.533 40.000 12.90 0.00 0.00 2.17
346 347 6.346919 CGACATGATTAATCCACGGAGAAATC 60.347 42.308 12.90 12.87 33.48 2.17
347 348 5.765182 ACATGATTAATCCACGGAGAAATCC 59.235 40.000 12.90 0.00 32.66 3.01
348 349 5.366482 TGATTAATCCACGGAGAAATCCA 57.634 39.130 12.90 6.22 32.66 3.41
349 350 5.123227 TGATTAATCCACGGAGAAATCCAC 58.877 41.667 12.90 0.19 32.66 4.02
350 351 4.837093 TTAATCCACGGAGAAATCCACT 57.163 40.909 0.00 0.00 0.00 4.00
351 352 2.990066 ATCCACGGAGAAATCCACTC 57.010 50.000 0.00 0.00 0.00 3.51
352 353 0.530744 TCCACGGAGAAATCCACTCG 59.469 55.000 0.00 0.00 35.49 4.18
353 354 1.084370 CCACGGAGAAATCCACTCGC 61.084 60.000 0.00 0.00 35.49 5.03
354 355 0.389817 CACGGAGAAATCCACTCGCA 60.390 55.000 0.00 0.00 35.49 5.10
355 356 0.320374 ACGGAGAAATCCACTCGCAA 59.680 50.000 0.00 0.00 35.49 4.85
356 357 1.270625 ACGGAGAAATCCACTCGCAAA 60.271 47.619 0.00 0.00 35.49 3.68
357 358 1.804151 CGGAGAAATCCACTCGCAAAA 59.196 47.619 0.00 0.00 35.49 2.44
358 359 2.225491 CGGAGAAATCCACTCGCAAAAA 59.775 45.455 0.00 0.00 35.49 1.94
539 544 6.795593 CACGTAACTATATAGGATCACACACG 59.204 42.308 14.25 11.86 0.00 4.49
546 551 2.170985 GATCACACACGCACACGC 59.829 61.111 0.00 0.00 45.53 5.34
547 552 2.587473 ATCACACACGCACACGCA 60.587 55.556 0.00 0.00 45.53 5.24
548 553 2.748546 GATCACACACGCACACGCAC 62.749 60.000 0.00 0.00 45.53 5.34
549 554 4.589700 CACACACGCACACGCACC 62.590 66.667 0.00 0.00 45.53 5.01
587 592 4.202567 ACCTCTCTCATCTAGCTCTAAGGG 60.203 50.000 0.00 0.00 0.00 3.95
598 603 1.138266 GCTCTAAGGGTCCATGCGTAA 59.862 52.381 0.00 0.00 0.00 3.18
599 604 2.419574 GCTCTAAGGGTCCATGCGTAAA 60.420 50.000 0.00 0.00 0.00 2.01
673 681 3.874383 TCAAAACAGAGGGATTGGTCA 57.126 42.857 0.00 0.00 0.00 4.02
686 694 6.676558 AGGGATTGGTCATGATCAAATACTT 58.323 36.000 24.54 8.45 34.74 2.24
835 843 0.526662 CACGTGTACCTCCTCAGACC 59.473 60.000 7.58 0.00 0.00 3.85
865 873 3.006940 TCACATATGAACTTGAACCGCC 58.993 45.455 10.38 0.00 0.00 6.13
885 893 1.335415 CGGAGGTCATATCTGTCTGCG 60.335 57.143 0.00 0.00 34.65 5.18
940 960 4.937620 TCATTTCATCCTCTTCTTCAACGG 59.062 41.667 0.00 0.00 0.00 4.44
982 1002 4.820716 CCATGTCATCCTTCTCCATTTCTC 59.179 45.833 0.00 0.00 0.00 2.87
1207 1228 4.342092 CCACCTTGGTTTGAAGAAGATTGT 59.658 41.667 0.00 0.00 31.35 2.71
1208 1229 5.163416 CCACCTTGGTTTGAAGAAGATTGTT 60.163 40.000 0.00 0.00 31.35 2.83
1215 1236 7.555087 TGGTTTGAAGAAGATTGTTGAAATGT 58.445 30.769 0.00 0.00 0.00 2.71
1232 1253 9.888878 GTTGAAATGTTGACATATATCATGAGG 57.111 33.333 0.09 0.00 35.10 3.86
1237 1258 6.772605 TGTTGACATATATCATGAGGAAGGG 58.227 40.000 0.09 0.00 0.00 3.95
1265 1286 2.277084 GACCTCGGTATTGCAAACGAT 58.723 47.619 19.69 9.90 34.60 3.73
1291 1312 1.465689 CGCATCGGATGTTGAAACCAC 60.466 52.381 18.54 0.00 0.00 4.16
1345 1366 3.869065 TCTTTCCTTGTGAACTTGTCGT 58.131 40.909 0.00 0.00 31.05 4.34
1393 1414 4.464597 AGAAGCTGTAGGTCTTAGTTCCAG 59.535 45.833 0.00 0.00 0.00 3.86
1419 1440 0.181114 ACACTGGCTTGTGCTTCTCA 59.819 50.000 10.25 0.00 41.30 3.27
1421 1442 1.884579 CACTGGCTTGTGCTTCTCAAT 59.115 47.619 0.00 0.00 39.59 2.57
1473 1494 2.489722 CTCCACAGTCTCGTCTTCATCA 59.510 50.000 0.00 0.00 0.00 3.07
1474 1495 3.092301 TCCACAGTCTCGTCTTCATCAT 58.908 45.455 0.00 0.00 0.00 2.45
1475 1496 3.129462 TCCACAGTCTCGTCTTCATCATC 59.871 47.826 0.00 0.00 0.00 2.92
1476 1497 3.104470 CACAGTCTCGTCTTCATCATCG 58.896 50.000 0.00 0.00 0.00 3.84
1477 1498 2.115595 CAGTCTCGTCTTCATCATCGC 58.884 52.381 0.00 0.00 0.00 4.58
1478 1499 2.020720 AGTCTCGTCTTCATCATCGCT 58.979 47.619 0.00 0.00 0.00 4.93
1479 1500 2.115595 GTCTCGTCTTCATCATCGCTG 58.884 52.381 0.00 0.00 0.00 5.18
1480 1501 1.745653 TCTCGTCTTCATCATCGCTGT 59.254 47.619 0.00 0.00 0.00 4.40
1481 1502 2.115595 CTCGTCTTCATCATCGCTGTC 58.884 52.381 0.00 0.00 0.00 3.51
1482 1503 1.472480 TCGTCTTCATCATCGCTGTCA 59.528 47.619 0.00 0.00 0.00 3.58
1491 1512 0.523335 CATCGCTGTCATCGTCGTCA 60.523 55.000 0.00 0.00 0.00 4.35
1499 1520 2.870411 TGTCATCGTCGTCATCGTCTAT 59.130 45.455 0.00 0.00 38.33 1.98
1520 1541 4.017177 TGAGACGACAAAGGTAGAGAGA 57.983 45.455 0.00 0.00 0.00 3.10
1529 1550 7.122948 ACGACAAAGGTAGAGAGATATGAAGTT 59.877 37.037 0.00 0.00 0.00 2.66
1530 1551 8.622157 CGACAAAGGTAGAGAGATATGAAGTTA 58.378 37.037 0.00 0.00 0.00 2.24
1531 1552 9.959749 GACAAAGGTAGAGAGATATGAAGTTAG 57.040 37.037 0.00 0.00 0.00 2.34
1532 1553 9.482175 ACAAAGGTAGAGAGATATGAAGTTAGT 57.518 33.333 0.00 0.00 0.00 2.24
1533 1554 9.743057 CAAAGGTAGAGAGATATGAAGTTAGTG 57.257 37.037 0.00 0.00 0.00 2.74
1534 1555 7.519032 AGGTAGAGAGATATGAAGTTAGTGC 57.481 40.000 0.00 0.00 0.00 4.40
1535 1556 7.063593 AGGTAGAGAGATATGAAGTTAGTGCA 58.936 38.462 0.00 0.00 0.00 4.57
1536 1557 7.230510 AGGTAGAGAGATATGAAGTTAGTGCAG 59.769 40.741 0.00 0.00 0.00 4.41
1634 1655 3.101437 TCAACCGGCTAGGATTACAGAA 58.899 45.455 0.00 0.00 45.00 3.02
1652 1673 6.339587 ACAGAACACAAGAACCAAAGAAAA 57.660 33.333 0.00 0.00 0.00 2.29
1715 1737 4.625607 AACTAGCCTCAAAGCTACAAGT 57.374 40.909 0.00 0.00 42.70 3.16
1916 1939 0.853530 AAGAAGGCCACAACCTCCTT 59.146 50.000 5.01 0.00 39.93 3.36
1945 1968 2.513065 GAAAGGCGTCGTACCGTCGA 62.513 60.000 7.40 0.00 40.28 4.20
1952 1975 2.600792 GCGTCGTACCGTCGAAAGATAT 60.601 50.000 7.40 0.00 45.19 1.63
2021 2044 3.917760 GAGGATCCCCGCACTCCG 61.918 72.222 8.55 0.00 37.58 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.144503 CTTTCTCCCTCCCATCCCATG 59.855 57.143 0.00 0.00 0.00 3.66
17 18 1.011293 TCTTTCTCCCTCCCATCCCAT 59.989 52.381 0.00 0.00 0.00 4.00
18 19 0.421495 TCTTTCTCCCTCCCATCCCA 59.579 55.000 0.00 0.00 0.00 4.37
19 20 1.596496 TTCTTTCTCCCTCCCATCCC 58.404 55.000 0.00 0.00 0.00 3.85
20 21 3.560105 CATTTCTTTCTCCCTCCCATCC 58.440 50.000 0.00 0.00 0.00 3.51
21 22 2.954989 GCATTTCTTTCTCCCTCCCATC 59.045 50.000 0.00 0.00 0.00 3.51
22 23 2.358615 GGCATTTCTTTCTCCCTCCCAT 60.359 50.000 0.00 0.00 0.00 4.00
23 24 1.005924 GGCATTTCTTTCTCCCTCCCA 59.994 52.381 0.00 0.00 0.00 4.37
24 25 1.005924 TGGCATTTCTTTCTCCCTCCC 59.994 52.381 0.00 0.00 0.00 4.30
25 26 2.291217 ACTGGCATTTCTTTCTCCCTCC 60.291 50.000 0.00 0.00 0.00 4.30
26 27 3.078891 ACTGGCATTTCTTTCTCCCTC 57.921 47.619 0.00 0.00 0.00 4.30
27 28 3.181429 TGAACTGGCATTTCTTTCTCCCT 60.181 43.478 17.05 0.00 0.00 4.20
28 29 3.157087 TGAACTGGCATTTCTTTCTCCC 58.843 45.455 17.05 0.00 0.00 4.30
29 30 5.415701 TGTATGAACTGGCATTTCTTTCTCC 59.584 40.000 17.05 2.54 0.00 3.71
30 31 6.500684 TGTATGAACTGGCATTTCTTTCTC 57.499 37.500 17.05 7.29 0.00 2.87
31 32 6.899393 TTGTATGAACTGGCATTTCTTTCT 57.101 33.333 17.05 4.18 0.00 2.52
32 33 7.315142 TGATTGTATGAACTGGCATTTCTTTC 58.685 34.615 17.05 10.11 0.00 2.62
33 34 7.230849 TGATTGTATGAACTGGCATTTCTTT 57.769 32.000 17.05 8.46 0.00 2.52
34 35 6.127535 CCTGATTGTATGAACTGGCATTTCTT 60.128 38.462 17.05 13.47 0.00 2.52
35 36 5.359009 CCTGATTGTATGAACTGGCATTTCT 59.641 40.000 17.05 6.88 0.00 2.52
36 37 5.357878 TCCTGATTGTATGAACTGGCATTTC 59.642 40.000 10.36 10.36 0.00 2.17
37 38 5.263599 TCCTGATTGTATGAACTGGCATTT 58.736 37.500 0.00 0.00 0.00 2.32
38 39 4.858850 TCCTGATTGTATGAACTGGCATT 58.141 39.130 0.00 0.00 0.00 3.56
39 40 4.164796 TCTCCTGATTGTATGAACTGGCAT 59.835 41.667 0.00 0.00 0.00 4.40
40 41 3.519107 TCTCCTGATTGTATGAACTGGCA 59.481 43.478 0.00 0.00 0.00 4.92
41 42 4.125703 CTCTCCTGATTGTATGAACTGGC 58.874 47.826 0.00 0.00 0.00 4.85
42 43 5.128499 ACTCTCTCCTGATTGTATGAACTGG 59.872 44.000 0.00 0.00 0.00 4.00
43 44 6.219417 ACTCTCTCCTGATTGTATGAACTG 57.781 41.667 0.00 0.00 0.00 3.16
44 45 6.865834 AACTCTCTCCTGATTGTATGAACT 57.134 37.500 0.00 0.00 0.00 3.01
45 46 9.606631 AATAAACTCTCTCCTGATTGTATGAAC 57.393 33.333 0.00 0.00 0.00 3.18
72 73 6.506413 AGTCCCCAATAGGAAGGTAGTAAAAA 59.494 38.462 0.00 0.00 37.78 1.94
73 74 6.034003 AGTCCCCAATAGGAAGGTAGTAAAA 58.966 40.000 0.00 0.00 37.78 1.52
74 75 5.606761 AGTCCCCAATAGGAAGGTAGTAAA 58.393 41.667 0.00 0.00 37.78 2.01
75 76 5.230746 AGTCCCCAATAGGAAGGTAGTAA 57.769 43.478 0.00 0.00 37.78 2.24
76 77 4.913154 AGTCCCCAATAGGAAGGTAGTA 57.087 45.455 0.00 0.00 37.78 1.82
77 78 3.797671 AGTCCCCAATAGGAAGGTAGT 57.202 47.619 0.00 0.00 37.78 2.73
78 79 3.573110 CGTAGTCCCCAATAGGAAGGTAG 59.427 52.174 0.00 0.00 37.78 3.18
79 80 3.052642 ACGTAGTCCCCAATAGGAAGGTA 60.053 47.826 0.00 0.00 29.74 3.08
80 81 2.292719 ACGTAGTCCCCAATAGGAAGGT 60.293 50.000 0.00 0.00 29.74 3.50
81 82 2.102588 CACGTAGTCCCCAATAGGAAGG 59.897 54.545 0.00 0.00 41.61 3.46
82 83 2.483188 GCACGTAGTCCCCAATAGGAAG 60.483 54.545 0.00 0.00 41.61 3.46
83 84 1.483415 GCACGTAGTCCCCAATAGGAA 59.517 52.381 0.00 0.00 41.61 3.36
84 85 1.117150 GCACGTAGTCCCCAATAGGA 58.883 55.000 0.00 0.00 41.61 2.94
85 86 1.120530 AGCACGTAGTCCCCAATAGG 58.879 55.000 0.00 0.00 41.61 2.57
86 87 2.957006 AGTAGCACGTAGTCCCCAATAG 59.043 50.000 0.00 0.00 41.61 1.73
87 88 3.022557 AGTAGCACGTAGTCCCCAATA 57.977 47.619 0.00 0.00 41.61 1.90
88 89 1.861982 AGTAGCACGTAGTCCCCAAT 58.138 50.000 0.00 0.00 41.61 3.16
89 90 1.636148 AAGTAGCACGTAGTCCCCAA 58.364 50.000 0.00 0.00 41.61 4.12
90 91 1.636148 AAAGTAGCACGTAGTCCCCA 58.364 50.000 0.00 0.00 41.61 4.96
91 92 2.756840 AAAAGTAGCACGTAGTCCCC 57.243 50.000 0.00 0.00 41.61 4.81
92 93 5.658468 AGATAAAAAGTAGCACGTAGTCCC 58.342 41.667 0.00 0.00 41.61 4.46
93 94 7.434602 CCTTAGATAAAAAGTAGCACGTAGTCC 59.565 40.741 0.00 0.00 41.61 3.85
94 95 7.043524 GCCTTAGATAAAAAGTAGCACGTAGTC 60.044 40.741 0.00 0.00 41.61 2.59
96 97 6.755141 TGCCTTAGATAAAAAGTAGCACGTAG 59.245 38.462 0.00 0.00 0.00 3.51
97 98 6.532657 GTGCCTTAGATAAAAAGTAGCACGTA 59.467 38.462 0.00 0.00 34.63 3.57
98 99 5.350640 GTGCCTTAGATAAAAAGTAGCACGT 59.649 40.000 0.00 0.00 34.63 4.49
99 100 5.796813 GTGCCTTAGATAAAAAGTAGCACG 58.203 41.667 0.00 0.00 34.63 5.34
100 101 5.350640 ACGTGCCTTAGATAAAAAGTAGCAC 59.649 40.000 0.00 0.00 38.08 4.40
101 102 5.350365 CACGTGCCTTAGATAAAAAGTAGCA 59.650 40.000 0.82 0.00 0.00 3.49
102 103 5.726963 GCACGTGCCTTAGATAAAAAGTAGC 60.727 44.000 30.12 0.00 34.31 3.58
103 104 5.581085 AGCACGTGCCTTAGATAAAAAGTAG 59.419 40.000 35.51 0.00 43.38 2.57
104 105 5.350365 CAGCACGTGCCTTAGATAAAAAGTA 59.650 40.000 35.51 0.00 43.38 2.24
105 106 4.154195 CAGCACGTGCCTTAGATAAAAAGT 59.846 41.667 35.51 10.19 43.38 2.66
106 107 4.437390 CCAGCACGTGCCTTAGATAAAAAG 60.437 45.833 35.51 9.96 43.38 2.27
107 108 3.438781 CCAGCACGTGCCTTAGATAAAAA 59.561 43.478 35.51 0.00 43.38 1.94
108 109 3.006940 CCAGCACGTGCCTTAGATAAAA 58.993 45.455 35.51 0.00 43.38 1.52
109 110 2.235155 TCCAGCACGTGCCTTAGATAAA 59.765 45.455 35.51 9.37 43.38 1.40
110 111 1.828595 TCCAGCACGTGCCTTAGATAA 59.171 47.619 35.51 10.98 43.38 1.75
111 112 1.480789 TCCAGCACGTGCCTTAGATA 58.519 50.000 35.51 12.57 43.38 1.98
112 113 0.833287 ATCCAGCACGTGCCTTAGAT 59.167 50.000 35.51 26.58 43.38 1.98
113 114 0.108186 CATCCAGCACGTGCCTTAGA 60.108 55.000 35.51 25.65 43.38 2.10
114 115 1.091771 CCATCCAGCACGTGCCTTAG 61.092 60.000 35.51 22.27 43.38 2.18
115 116 1.078497 CCATCCAGCACGTGCCTTA 60.078 57.895 35.51 21.46 43.38 2.69
116 117 2.360350 CCATCCAGCACGTGCCTT 60.360 61.111 35.51 17.12 43.38 4.35
117 118 3.640407 ACCATCCAGCACGTGCCT 61.640 61.111 35.51 20.51 43.38 4.75
118 119 3.434319 CACCATCCAGCACGTGCC 61.434 66.667 35.51 18.54 43.38 5.01
119 120 1.514678 TTTCACCATCCAGCACGTGC 61.515 55.000 32.79 32.79 42.49 5.34
120 121 0.518636 CTTTCACCATCCAGCACGTG 59.481 55.000 12.28 12.28 0.00 4.49
121 122 0.606401 CCTTTCACCATCCAGCACGT 60.606 55.000 0.00 0.00 0.00 4.49
122 123 1.308069 CCCTTTCACCATCCAGCACG 61.308 60.000 0.00 0.00 0.00 5.34
123 124 1.598701 GCCCTTTCACCATCCAGCAC 61.599 60.000 0.00 0.00 0.00 4.40
124 125 1.304381 GCCCTTTCACCATCCAGCA 60.304 57.895 0.00 0.00 0.00 4.41
125 126 1.304381 TGCCCTTTCACCATCCAGC 60.304 57.895 0.00 0.00 0.00 4.85
126 127 1.308069 CGTGCCCTTTCACCATCCAG 61.308 60.000 0.00 0.00 33.57 3.86
127 128 1.303236 CGTGCCCTTTCACCATCCA 60.303 57.895 0.00 0.00 33.57 3.41
128 129 2.700773 GCGTGCCCTTTCACCATCC 61.701 63.158 0.00 0.00 33.57 3.51
129 130 1.971167 TGCGTGCCCTTTCACCATC 60.971 57.895 0.00 0.00 33.57 3.51
130 131 2.115052 TGCGTGCCCTTTCACCAT 59.885 55.556 0.00 0.00 33.57 3.55
131 132 2.904866 GTGCGTGCCCTTTCACCA 60.905 61.111 0.00 0.00 33.57 4.17
132 133 2.010582 TTTGTGCGTGCCCTTTCACC 62.011 55.000 0.00 0.00 33.57 4.02
133 134 0.179124 TTTTGTGCGTGCCCTTTCAC 60.179 50.000 0.00 0.00 0.00 3.18
134 135 0.532573 TTTTTGTGCGTGCCCTTTCA 59.467 45.000 0.00 0.00 0.00 2.69
135 136 3.354131 TTTTTGTGCGTGCCCTTTC 57.646 47.368 0.00 0.00 0.00 2.62
197 198 4.542735 AGTAACGTGTATTTGCTTTTGGC 58.457 39.130 0.00 0.00 42.22 4.52
198 199 8.736751 AATAAGTAACGTGTATTTGCTTTTGG 57.263 30.769 0.00 0.00 32.10 3.28
226 227 9.640963 GTCTATTACTTTGTCTGACTGTTGTAT 57.359 33.333 9.51 0.00 0.00 2.29
227 228 8.635328 TGTCTATTACTTTGTCTGACTGTTGTA 58.365 33.333 9.51 4.76 0.00 2.41
228 229 7.497595 TGTCTATTACTTTGTCTGACTGTTGT 58.502 34.615 9.51 5.64 0.00 3.32
229 230 7.946655 TGTCTATTACTTTGTCTGACTGTTG 57.053 36.000 9.51 0.00 0.00 3.33
231 232 9.809096 CATATGTCTATTACTTTGTCTGACTGT 57.191 33.333 9.51 7.90 0.00 3.55
240 241 9.425893 CGCAAAGTTCATATGTCTATTACTTTG 57.574 33.333 22.99 22.99 42.36 2.77
241 242 9.378551 TCGCAAAGTTCATATGTCTATTACTTT 57.621 29.630 1.90 7.52 33.78 2.66
242 243 8.942338 TCGCAAAGTTCATATGTCTATTACTT 57.058 30.769 1.90 2.37 0.00 2.24
243 244 7.169982 GCTCGCAAAGTTCATATGTCTATTACT 59.830 37.037 1.90 0.00 0.00 2.24
244 245 7.284351 GCTCGCAAAGTTCATATGTCTATTAC 58.716 38.462 1.90 0.00 0.00 1.89
245 246 6.143919 CGCTCGCAAAGTTCATATGTCTATTA 59.856 38.462 1.90 0.00 0.00 0.98
246 247 5.050769 CGCTCGCAAAGTTCATATGTCTATT 60.051 40.000 1.90 0.00 0.00 1.73
247 248 4.445718 CGCTCGCAAAGTTCATATGTCTAT 59.554 41.667 1.90 0.00 0.00 1.98
248 249 3.796717 CGCTCGCAAAGTTCATATGTCTA 59.203 43.478 1.90 0.00 0.00 2.59
249 250 2.604914 CGCTCGCAAAGTTCATATGTCT 59.395 45.455 1.90 0.24 0.00 3.41
250 251 2.603110 TCGCTCGCAAAGTTCATATGTC 59.397 45.455 1.90 0.00 0.00 3.06
251 252 2.604914 CTCGCTCGCAAAGTTCATATGT 59.395 45.455 1.90 0.00 0.00 2.29
252 253 2.860136 TCTCGCTCGCAAAGTTCATATG 59.140 45.455 0.00 0.00 0.00 1.78
253 254 3.165058 TCTCGCTCGCAAAGTTCATAT 57.835 42.857 0.00 0.00 0.00 1.78
254 255 2.647529 TCTCGCTCGCAAAGTTCATA 57.352 45.000 0.00 0.00 0.00 2.15
255 256 1.795768 TTCTCGCTCGCAAAGTTCAT 58.204 45.000 0.00 0.00 0.00 2.57
256 257 1.795768 ATTCTCGCTCGCAAAGTTCA 58.204 45.000 0.00 0.00 0.00 3.18
257 258 5.637104 TTATATTCTCGCTCGCAAAGTTC 57.363 39.130 0.00 0.00 0.00 3.01
258 259 6.604735 ATTTATATTCTCGCTCGCAAAGTT 57.395 33.333 0.00 0.00 0.00 2.66
259 260 7.307219 GGTTATTTATATTCTCGCTCGCAAAGT 60.307 37.037 0.00 0.00 0.00 2.66
260 261 7.010023 GGTTATTTATATTCTCGCTCGCAAAG 58.990 38.462 0.00 0.00 0.00 2.77
261 262 6.480651 TGGTTATTTATATTCTCGCTCGCAAA 59.519 34.615 0.00 0.00 0.00 3.68
262 263 5.986741 TGGTTATTTATATTCTCGCTCGCAA 59.013 36.000 0.00 0.00 0.00 4.85
263 264 5.534407 TGGTTATTTATATTCTCGCTCGCA 58.466 37.500 0.00 0.00 0.00 5.10
264 265 5.634020 ACTGGTTATTTATATTCTCGCTCGC 59.366 40.000 0.00 0.00 0.00 5.03
265 266 8.912787 ATACTGGTTATTTATATTCTCGCTCG 57.087 34.615 0.00 0.00 0.00 5.03
267 268 9.804758 GCTATACTGGTTATTTATATTCTCGCT 57.195 33.333 0.00 0.00 0.00 4.93
268 269 9.032420 GGCTATACTGGTTATTTATATTCTCGC 57.968 37.037 0.00 0.00 0.00 5.03
272 273 9.095065 CGGTGGCTATACTGGTTATTTATATTC 57.905 37.037 0.00 0.00 0.00 1.75
273 274 8.599792 ACGGTGGCTATACTGGTTATTTATATT 58.400 33.333 0.00 0.00 0.00 1.28
274 275 8.142485 ACGGTGGCTATACTGGTTATTTATAT 57.858 34.615 0.00 0.00 0.00 0.86
275 276 7.309990 GGACGGTGGCTATACTGGTTATTTATA 60.310 40.741 0.00 0.00 0.00 0.98
276 277 6.429521 ACGGTGGCTATACTGGTTATTTAT 57.570 37.500 0.00 0.00 0.00 1.40
277 278 5.221501 GGACGGTGGCTATACTGGTTATTTA 60.222 44.000 0.00 0.00 0.00 1.40
278 279 4.443881 GGACGGTGGCTATACTGGTTATTT 60.444 45.833 0.00 0.00 0.00 1.40
279 280 3.070590 GGACGGTGGCTATACTGGTTATT 59.929 47.826 0.00 0.00 0.00 1.40
280 281 2.631545 GGACGGTGGCTATACTGGTTAT 59.368 50.000 0.00 0.00 0.00 1.89
281 282 2.034124 GGACGGTGGCTATACTGGTTA 58.966 52.381 0.00 0.00 0.00 2.85
282 283 0.828677 GGACGGTGGCTATACTGGTT 59.171 55.000 0.00 0.00 0.00 3.67
283 284 1.389609 CGGACGGTGGCTATACTGGT 61.390 60.000 0.00 0.00 0.00 4.00
284 285 1.105167 TCGGACGGTGGCTATACTGG 61.105 60.000 0.00 0.00 0.00 4.00
285 286 0.311165 CTCGGACGGTGGCTATACTG 59.689 60.000 0.00 0.00 0.00 2.74
286 287 0.106819 ACTCGGACGGTGGCTATACT 60.107 55.000 0.00 0.00 0.00 2.12
287 288 0.743097 AACTCGGACGGTGGCTATAC 59.257 55.000 0.00 0.00 0.00 1.47
288 289 0.742505 CAACTCGGACGGTGGCTATA 59.257 55.000 0.00 0.00 0.00 1.31
289 290 0.968901 TCAACTCGGACGGTGGCTAT 60.969 55.000 0.00 0.00 0.00 2.97
290 291 1.180456 TTCAACTCGGACGGTGGCTA 61.180 55.000 0.00 0.00 0.00 3.93
291 292 2.436087 CTTCAACTCGGACGGTGGCT 62.436 60.000 0.00 0.00 0.00 4.75
292 293 2.027625 CTTCAACTCGGACGGTGGC 61.028 63.158 0.00 0.00 0.00 5.01
293 294 1.374252 CCTTCAACTCGGACGGTGG 60.374 63.158 0.00 0.00 0.00 4.61
294 295 0.032952 TTCCTTCAACTCGGACGGTG 59.967 55.000 0.00 0.00 0.00 4.94
295 296 0.033090 GTTCCTTCAACTCGGACGGT 59.967 55.000 0.00 0.00 31.50 4.83
296 297 0.032952 TGTTCCTTCAACTCGGACGG 59.967 55.000 0.00 0.00 35.79 4.79
297 298 1.860676 TTGTTCCTTCAACTCGGACG 58.139 50.000 0.00 0.00 35.79 4.79
298 299 3.139077 ACATTGTTCCTTCAACTCGGAC 58.861 45.455 0.00 0.00 35.79 4.79
299 300 3.485463 ACATTGTTCCTTCAACTCGGA 57.515 42.857 0.00 0.00 35.79 4.55
300 301 3.122948 CGTACATTGTTCCTTCAACTCGG 59.877 47.826 0.00 0.00 35.79 4.63
301 302 3.985279 TCGTACATTGTTCCTTCAACTCG 59.015 43.478 0.00 0.00 35.79 4.18
302 303 4.748102 TGTCGTACATTGTTCCTTCAACTC 59.252 41.667 0.00 0.00 35.79 3.01
303 304 4.699637 TGTCGTACATTGTTCCTTCAACT 58.300 39.130 0.00 0.00 35.79 3.16
304 305 5.178623 TCATGTCGTACATTGTTCCTTCAAC 59.821 40.000 0.00 0.00 36.53 3.18
305 306 5.301555 TCATGTCGTACATTGTTCCTTCAA 58.698 37.500 0.00 0.00 36.53 2.69
306 307 4.888917 TCATGTCGTACATTGTTCCTTCA 58.111 39.130 0.00 0.00 36.53 3.02
307 308 6.422776 AATCATGTCGTACATTGTTCCTTC 57.577 37.500 0.00 0.00 36.53 3.46
308 309 7.915293 TTAATCATGTCGTACATTGTTCCTT 57.085 32.000 0.00 0.00 36.53 3.36
309 310 7.226720 GGATTAATCATGTCGTACATTGTTCCT 59.773 37.037 17.07 0.00 36.53 3.36
310 311 7.011950 TGGATTAATCATGTCGTACATTGTTCC 59.988 37.037 17.07 0.00 36.53 3.62
311 312 7.850982 GTGGATTAATCATGTCGTACATTGTTC 59.149 37.037 17.07 0.00 36.53 3.18
312 313 7.465379 CGTGGATTAATCATGTCGTACATTGTT 60.465 37.037 17.07 0.00 36.53 2.83
313 314 6.019075 CGTGGATTAATCATGTCGTACATTGT 60.019 38.462 17.07 0.00 36.53 2.71
314 315 6.354858 CGTGGATTAATCATGTCGTACATTG 58.645 40.000 17.07 0.00 36.53 2.82
315 316 5.465390 CCGTGGATTAATCATGTCGTACATT 59.535 40.000 17.07 0.00 36.53 2.71
316 317 4.988540 CCGTGGATTAATCATGTCGTACAT 59.011 41.667 17.07 0.00 39.91 2.29
317 318 4.098196 TCCGTGGATTAATCATGTCGTACA 59.902 41.667 17.07 0.70 0.00 2.90
318 319 4.613944 TCCGTGGATTAATCATGTCGTAC 58.386 43.478 17.07 3.83 0.00 3.67
319 320 4.581409 TCTCCGTGGATTAATCATGTCGTA 59.419 41.667 17.07 2.77 0.00 3.43
320 321 3.383505 TCTCCGTGGATTAATCATGTCGT 59.616 43.478 17.07 0.00 0.00 4.34
321 322 3.977427 TCTCCGTGGATTAATCATGTCG 58.023 45.455 17.07 13.55 0.00 4.35
322 323 6.073003 GGATTTCTCCGTGGATTAATCATGTC 60.073 42.308 17.07 0.49 31.35 3.06
323 324 5.765182 GGATTTCTCCGTGGATTAATCATGT 59.235 40.000 17.07 0.00 31.35 3.21
324 325 5.764686 TGGATTTCTCCGTGGATTAATCATG 59.235 40.000 17.07 8.49 45.37 3.07
325 326 5.765182 GTGGATTTCTCCGTGGATTAATCAT 59.235 40.000 17.07 0.00 45.37 2.45
326 327 5.104527 AGTGGATTTCTCCGTGGATTAATCA 60.105 40.000 17.07 1.07 45.37 2.57
327 328 5.368989 AGTGGATTTCTCCGTGGATTAATC 58.631 41.667 6.93 6.93 45.37 1.75
328 329 5.368989 GAGTGGATTTCTCCGTGGATTAAT 58.631 41.667 0.00 0.00 45.37 1.40
329 330 4.679639 CGAGTGGATTTCTCCGTGGATTAA 60.680 45.833 0.00 0.00 45.37 1.40
330 331 3.181479 CGAGTGGATTTCTCCGTGGATTA 60.181 47.826 0.00 0.00 45.37 1.75
331 332 2.418746 CGAGTGGATTTCTCCGTGGATT 60.419 50.000 0.00 0.00 45.37 3.01
332 333 1.137086 CGAGTGGATTTCTCCGTGGAT 59.863 52.381 0.00 0.00 45.37 3.41
333 334 0.530744 CGAGTGGATTTCTCCGTGGA 59.469 55.000 0.00 0.00 45.37 4.02
334 335 1.084370 GCGAGTGGATTTCTCCGTGG 61.084 60.000 0.00 0.00 45.37 4.94
335 336 0.389817 TGCGAGTGGATTTCTCCGTG 60.390 55.000 0.00 0.00 45.37 4.94
336 337 0.320374 TTGCGAGTGGATTTCTCCGT 59.680 50.000 0.00 0.00 45.37 4.69
337 338 1.438651 TTTGCGAGTGGATTTCTCCG 58.561 50.000 0.00 0.00 45.37 4.63
338 339 3.915437 TTTTTGCGAGTGGATTTCTCC 57.085 42.857 0.00 0.00 42.45 3.71
356 357 2.593346 TGCAAGTTCCGTGCATTTTT 57.407 40.000 0.70 0.00 46.76 1.94
362 363 1.009675 CACAGTGCAAGTTCCGTGC 60.010 57.895 0.00 0.00 42.55 5.34
363 364 1.009675 GCACAGTGCAAGTTCCGTG 60.010 57.895 21.22 0.00 44.26 4.94
364 365 3.420943 GCACAGTGCAAGTTCCGT 58.579 55.556 21.22 0.00 44.26 4.69
551 556 3.660111 GAGGTTGTGTGTGCGGGC 61.660 66.667 0.00 0.00 0.00 6.13
552 557 1.961277 GAGAGGTTGTGTGTGCGGG 60.961 63.158 0.00 0.00 0.00 6.13
553 558 0.946221 GAGAGAGGTTGTGTGTGCGG 60.946 60.000 0.00 0.00 0.00 5.69
565 570 4.202567 ACCCTTAGAGCTAGATGAGAGAGG 60.203 50.000 0.00 0.00 0.00 3.69
587 592 7.545965 AGCACTCTATATATTTTACGCATGGAC 59.454 37.037 0.00 0.00 0.00 4.02
598 603 7.065085 CCAGCGCAAATAGCACTCTATATATTT 59.935 37.037 11.47 0.00 46.13 1.40
599 604 6.536582 CCAGCGCAAATAGCACTCTATATATT 59.463 38.462 11.47 0.00 46.13 1.28
673 681 7.293073 ACTAATGGCTGGAAGTATTTGATCAT 58.707 34.615 0.00 0.00 35.30 2.45
686 694 6.672593 AGAATAATGGAAACTAATGGCTGGA 58.327 36.000 0.00 0.00 0.00 3.86
820 828 1.924731 CACTGGTCTGAGGAGGTACA 58.075 55.000 0.00 0.00 0.00 2.90
860 868 1.152525 AGATATGACCTCCGGCGGT 60.153 57.895 27.32 18.04 40.80 5.68
865 873 1.335415 CGCAGACAGATATGACCTCCG 60.335 57.143 0.00 0.00 0.00 4.63
885 893 2.605580 GCTACAAGACTTGTTTGCAGCC 60.606 50.000 25.10 9.51 42.22 4.85
940 960 1.004440 AGGAGGACGAAGCACAAGC 60.004 57.895 0.00 0.00 42.56 4.01
982 1002 4.079665 TCATCTACACTGACTCGTTTCG 57.920 45.455 0.00 0.00 0.00 3.46
1207 1228 9.850198 TCCTCATGATATATGTCAACATTTCAA 57.150 29.630 6.23 0.00 37.76 2.69
1208 1229 9.850198 TTCCTCATGATATATGTCAACATTTCA 57.150 29.630 6.23 3.81 37.76 2.69
1215 1236 6.239973 CCACCCTTCCTCATGATATATGTCAA 60.240 42.308 6.23 0.00 0.00 3.18
1245 1266 1.717194 TCGTTTGCAATACCGAGGTC 58.283 50.000 0.00 0.00 0.00 3.85
1282 1303 6.072948 CGTAATATGAAGTGTGGTGGTTTCAA 60.073 38.462 0.00 0.00 33.71 2.69
1291 1312 6.662414 ACAATCACGTAATATGAAGTGTGG 57.338 37.500 6.09 1.04 36.16 4.17
1345 1366 2.525629 TGAGACGTCCCAGGGCAA 60.526 61.111 13.01 0.00 0.00 4.52
1393 1414 1.200020 GCACAAGCCAGTGTACATTCC 59.800 52.381 0.00 0.00 41.52 3.01
1419 1440 6.934645 TCAGTTTTAGTTTCATCGACCAGATT 59.065 34.615 0.00 0.00 37.52 2.40
1421 1442 5.849510 TCAGTTTTAGTTTCATCGACCAGA 58.150 37.500 0.00 0.00 0.00 3.86
1473 1494 0.382158 ATGACGACGATGACAGCGAT 59.618 50.000 21.46 3.86 0.00 4.58
1474 1495 0.248094 GATGACGACGATGACAGCGA 60.248 55.000 21.46 0.00 0.00 4.93
1475 1496 1.524179 CGATGACGACGATGACAGCG 61.524 60.000 12.26 12.26 42.66 5.18
1476 1497 0.523546 ACGATGACGACGATGACAGC 60.524 55.000 0.00 0.00 42.66 4.40
1477 1498 1.062733 AGACGATGACGACGATGACAG 59.937 52.381 0.00 0.00 42.66 3.51
1478 1499 1.084289 AGACGATGACGACGATGACA 58.916 50.000 0.00 0.00 42.66 3.58
1479 1500 3.059800 TCATAGACGATGACGACGATGAC 60.060 47.826 0.00 0.00 44.59 3.06
1480 1501 3.128349 TCATAGACGATGACGACGATGA 58.872 45.455 0.00 11.50 45.95 2.92
1481 1502 3.184581 TCTCATAGACGATGACGACGATG 59.815 47.826 0.00 0.00 43.39 3.84
1482 1503 3.184783 GTCTCATAGACGATGACGACGAT 59.815 47.826 0.00 0.00 39.78 3.73
1499 1520 4.017177 TCTCTCTACCTTTGTCGTCTCA 57.983 45.455 0.00 0.00 0.00 3.27
1610 1631 3.035363 TGTAATCCTAGCCGGTTGATGA 58.965 45.455 1.90 0.00 0.00 2.92
1691 1713 5.480772 ACTTGTAGCTTTGAGGCTAGTTAGA 59.519 40.000 0.00 0.00 44.17 2.10
1715 1737 9.719355 TGTGTGCTTATCTGTTTTATCTTCTAA 57.281 29.630 0.00 0.00 0.00 2.10
1877 1900 2.407562 TCGGAGATGGAATTGGATGGA 58.592 47.619 0.00 0.00 0.00 3.41
1952 1975 9.442062 TCCATTATAGTTCTAGGTGGAACATTA 57.558 33.333 8.69 0.00 45.52 1.90
1972 1995 2.425592 CTCCGGCGGCATCCATTA 59.574 61.111 23.83 0.00 0.00 1.90
2145 2168 0.032615 TGGGAGCTGTTTGGTTGGTT 60.033 50.000 0.00 0.00 0.00 3.67
2173 2196 5.642165 TCTACTAGTGTCCTTCTTGAAGGT 58.358 41.667 23.78 11.09 40.81 3.50


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

AutoCloner maintained by Alex Coulton.