Multiple sequence alignment - TraesCS4A01G048500

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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 TraesCS4A01G048500 chr4A 100.000 2515 0 0 619 3133 39270419 39272933 0.000000e+00 4645
1 TraesCS4A01G048500 chr4A 100.000 202 0 0 1 202 39269801 39270002 1.200000e-99 374
2 TraesCS4A01G048500 chr4A 86.170 188 26 0 8 195 143696093 143695906 1.670000e-48 204
3 TraesCS4A01G048500 chr4A 100.000 98 0 0 3449 3546 39273249 39273346 7.820000e-42 182
4 TraesCS4A01G048500 chr4D 93.047 2517 123 28 619 3127 425698496 425696024 0.000000e+00 3631
5 TraesCS4A01G048500 chr4D 87.151 179 23 0 8 186 327384892 327385070 1.670000e-48 204
6 TraesCS4A01G048500 chr4B 94.792 2304 96 14 693 2982 521712929 521710636 0.000000e+00 3568
7 TraesCS4A01G048500 chr4B 94.574 129 7 0 3001 3129 521710128 521710000 2.160000e-47 200
8 TraesCS4A01G048500 chr1A 81.633 294 44 7 619 908 568569846 568569559 5.920000e-58 235
9 TraesCS4A01G048500 chrUn 86.316 190 23 3 1 188 102117568 102117380 1.670000e-48 204
10 TraesCS4A01G048500 chrUn 86.170 188 24 2 1 187 250117083 250116897 6.000000e-48 202
11 TraesCS4A01G048500 chr7A 87.222 180 21 2 1 179 94424412 94424234 1.670000e-48 204
12 TraesCS4A01G048500 chr6D 87.222 180 21 2 1 179 284869415 284869237 1.670000e-48 204
13 TraesCS4A01G048500 chr3A 87.222 180 21 2 1 179 129523270 129523092 1.670000e-48 204
14 TraesCS4A01G048500 chr3A 79.538 303 46 13 631 922 663683748 663684045 6.000000e-48 202
15 TraesCS4A01G048500 chr3A 84.615 169 18 6 2681 2845 267044914 267045078 1.020000e-35 161
16 TraesCS4A01G048500 chr3A 84.375 160 16 6 2681 2836 675873028 675873182 7.930000e-32 148
17 TraesCS4A01G048500 chr3D 80.351 285 40 11 631 911 555757955 555758227 6.000000e-48 202
18 TraesCS4A01G048500 chr3D 83.436 163 19 5 2681 2839 540569244 540569086 1.030000e-30 145
19 TraesCS4A01G048500 chr1B 79.730 296 47 10 619 908 659582830 659582542 6.000000e-48 202
20 TraesCS4A01G048500 chr1D 85.638 188 25 2 1 187 17288401 17288587 2.790000e-46 196
21 TraesCS4A01G048500 chr1D 85.638 188 25 2 1 187 17300090 17300276 2.790000e-46 196
22 TraesCS4A01G048500 chr1D 79.522 293 42 10 619 908 474142045 474141768 3.610000e-45 193
23 TraesCS4A01G048500 chr5D 84.524 168 20 4 2681 2844 399614677 399614512 1.020000e-35 161
24 TraesCS4A01G048500 chr5B 84.524 168 20 4 2681 2844 479726990 479726825 1.020000e-35 161
25 TraesCS4A01G048500 chr3B 84.024 169 18 7 2681 2844 276481904 276481740 1.700000e-33 154
26 TraesCS4A01G048500 chr2D 85.906 149 13 5 2681 2824 337850053 337850198 6.130000e-33 152


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 TraesCS4A01G048500 chr4A 39269801 39273346 3545 False 1733.666667 4645 100.000 1 3546 3 chr4A.!!$F1 3545
1 TraesCS4A01G048500 chr4D 425696024 425698496 2472 True 3631.000000 3631 93.047 619 3127 1 chr4D.!!$R1 2508
2 TraesCS4A01G048500 chr4B 521710000 521712929 2929 True 1884.000000 3568 94.683 693 3129 2 chr4B.!!$R1 2436

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
911 922 1.039068 CCATTTTGCACACCCTGACA 58.961 50.000 0.0 0.0 0.00 3.58 F
1858 1870 1.541233 CCAACGTCAGAAGCTTGGAGT 60.541 52.381 2.1 0.0 36.06 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2028 0.46729 GGCCAAGGAACACCAAGTGA 60.467 55.0 0.0 0.0 36.96 3.41 R
3458 3986 0.03254 CGCAAGCTTTTGGAGGCTTT 59.967 50.0 0.0 0.0 45.03 3.51 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
22 23 3.889196 TTCTCGTTTGATTCGGTTTGG 57.111 42.857 0.00 0.00 0.00 3.28
23 24 2.841215 TCTCGTTTGATTCGGTTTGGT 58.159 42.857 0.00 0.00 0.00 3.67
24 25 3.207778 TCTCGTTTGATTCGGTTTGGTT 58.792 40.909 0.00 0.00 0.00 3.67
25 26 3.628487 TCTCGTTTGATTCGGTTTGGTTT 59.372 39.130 0.00 0.00 0.00 3.27
26 27 4.815308 TCTCGTTTGATTCGGTTTGGTTTA 59.185 37.500 0.00 0.00 0.00 2.01
27 28 5.470777 TCTCGTTTGATTCGGTTTGGTTTAT 59.529 36.000 0.00 0.00 0.00 1.40
28 29 6.649973 TCTCGTTTGATTCGGTTTGGTTTATA 59.350 34.615 0.00 0.00 0.00 0.98
29 30 6.601264 TCGTTTGATTCGGTTTGGTTTATAC 58.399 36.000 0.00 0.00 0.00 1.47
30 31 5.505446 CGTTTGATTCGGTTTGGTTTATACG 59.495 40.000 0.00 0.00 0.00 3.06
31 32 5.548706 TTGATTCGGTTTGGTTTATACGG 57.451 39.130 0.00 0.00 0.00 4.02
32 33 3.940221 TGATTCGGTTTGGTTTATACGGG 59.060 43.478 0.00 0.00 0.00 5.28
33 34 3.415457 TTCGGTTTGGTTTATACGGGT 57.585 42.857 0.00 0.00 0.00 5.28
34 35 3.415457 TCGGTTTGGTTTATACGGGTT 57.585 42.857 0.00 0.00 0.00 4.11
35 36 3.072944 TCGGTTTGGTTTATACGGGTTG 58.927 45.455 0.00 0.00 0.00 3.77
36 37 2.813172 CGGTTTGGTTTATACGGGTTGT 59.187 45.455 0.00 0.00 0.00 3.32
37 38 3.365164 CGGTTTGGTTTATACGGGTTGTG 60.365 47.826 0.00 0.00 0.00 3.33
38 39 3.057386 GGTTTGGTTTATACGGGTTGTGG 60.057 47.826 0.00 0.00 0.00 4.17
39 40 3.505480 TTGGTTTATACGGGTTGTGGT 57.495 42.857 0.00 0.00 0.00 4.16
40 41 3.505480 TGGTTTATACGGGTTGTGGTT 57.495 42.857 0.00 0.00 0.00 3.67
41 42 3.830121 TGGTTTATACGGGTTGTGGTTT 58.170 40.909 0.00 0.00 0.00 3.27
42 43 4.978099 TGGTTTATACGGGTTGTGGTTTA 58.022 39.130 0.00 0.00 0.00 2.01
43 44 5.568392 TGGTTTATACGGGTTGTGGTTTAT 58.432 37.500 0.00 0.00 0.00 1.40
44 45 6.715280 TGGTTTATACGGGTTGTGGTTTATA 58.285 36.000 0.00 0.00 0.00 0.98
45 46 7.344913 TGGTTTATACGGGTTGTGGTTTATAT 58.655 34.615 0.00 0.00 0.00 0.86
46 47 7.282675 TGGTTTATACGGGTTGTGGTTTATATG 59.717 37.037 0.00 0.00 0.00 1.78
47 48 7.282901 GGTTTATACGGGTTGTGGTTTATATGT 59.717 37.037 0.00 0.00 0.00 2.29
48 49 8.337532 GTTTATACGGGTTGTGGTTTATATGTC 58.662 37.037 0.00 0.00 0.00 3.06
49 50 4.563140 ACGGGTTGTGGTTTATATGTCT 57.437 40.909 0.00 0.00 0.00 3.41
50 51 4.913784 ACGGGTTGTGGTTTATATGTCTT 58.086 39.130 0.00 0.00 0.00 3.01
51 52 5.318630 ACGGGTTGTGGTTTATATGTCTTT 58.681 37.500 0.00 0.00 0.00 2.52
52 53 5.771165 ACGGGTTGTGGTTTATATGTCTTTT 59.229 36.000 0.00 0.00 0.00 2.27
53 54 6.941436 ACGGGTTGTGGTTTATATGTCTTTTA 59.059 34.615 0.00 0.00 0.00 1.52
54 55 7.612633 ACGGGTTGTGGTTTATATGTCTTTTAT 59.387 33.333 0.00 0.00 0.00 1.40
55 56 9.111613 CGGGTTGTGGTTTATATGTCTTTTATA 57.888 33.333 0.00 0.00 0.00 0.98
71 72 9.723601 TGTCTTTTATACTTTGGTTTATACGGT 57.276 29.630 0.00 0.00 0.00 4.83
91 92 9.846248 ATACGGTTTTATACATAGATACGGTTC 57.154 33.333 0.00 0.00 0.00 3.62
92 93 7.715657 ACGGTTTTATACATAGATACGGTTCA 58.284 34.615 0.00 0.00 0.00 3.18
93 94 7.864379 ACGGTTTTATACATAGATACGGTTCAG 59.136 37.037 0.00 0.00 0.00 3.02
94 95 7.864379 CGGTTTTATACATAGATACGGTTCAGT 59.136 37.037 0.00 0.00 0.00 3.41
95 96 9.538508 GGTTTTATACATAGATACGGTTCAGTT 57.461 33.333 0.00 0.00 0.00 3.16
98 99 9.454585 TTTATACATAGATACGGTTCAGTTTCG 57.545 33.333 0.00 0.00 0.00 3.46
99 100 4.679662 ACATAGATACGGTTCAGTTTCGG 58.320 43.478 0.00 0.00 0.00 4.30
100 101 4.159135 ACATAGATACGGTTCAGTTTCGGT 59.841 41.667 0.00 0.00 0.00 4.69
101 102 5.357878 ACATAGATACGGTTCAGTTTCGGTA 59.642 40.000 0.00 0.00 0.00 4.02
102 103 4.789012 AGATACGGTTCAGTTTCGGTAA 57.211 40.909 0.00 0.00 0.00 2.85
103 104 5.334724 AGATACGGTTCAGTTTCGGTAAT 57.665 39.130 0.00 0.00 0.00 1.89
104 105 6.455360 AGATACGGTTCAGTTTCGGTAATA 57.545 37.500 0.00 0.00 0.00 0.98
105 106 6.866480 AGATACGGTTCAGTTTCGGTAATAA 58.134 36.000 0.00 0.00 0.00 1.40
106 107 6.976925 AGATACGGTTCAGTTTCGGTAATAAG 59.023 38.462 0.00 0.00 0.00 1.73
107 108 3.681417 ACGGTTCAGTTTCGGTAATAAGC 59.319 43.478 0.00 0.00 0.00 3.09
108 109 3.680937 CGGTTCAGTTTCGGTAATAAGCA 59.319 43.478 0.00 0.00 0.00 3.91
109 110 4.331717 CGGTTCAGTTTCGGTAATAAGCAT 59.668 41.667 0.00 0.00 0.00 3.79
110 111 5.163794 CGGTTCAGTTTCGGTAATAAGCATT 60.164 40.000 0.00 0.00 0.00 3.56
111 112 6.617879 GGTTCAGTTTCGGTAATAAGCATTT 58.382 36.000 0.00 0.00 0.00 2.32
112 113 7.413219 CGGTTCAGTTTCGGTAATAAGCATTTA 60.413 37.037 0.00 0.00 0.00 1.40
113 114 7.695201 GGTTCAGTTTCGGTAATAAGCATTTAC 59.305 37.037 0.00 0.00 0.00 2.01
114 115 8.448615 GTTCAGTTTCGGTAATAAGCATTTACT 58.551 33.333 0.00 0.00 31.62 2.24
115 116 8.556213 TCAGTTTCGGTAATAAGCATTTACTT 57.444 30.769 0.00 0.00 31.62 2.24
116 117 9.005777 TCAGTTTCGGTAATAAGCATTTACTTT 57.994 29.630 0.00 0.00 31.62 2.66
117 118 9.274065 CAGTTTCGGTAATAAGCATTTACTTTC 57.726 33.333 0.00 0.00 31.62 2.62
118 119 8.173130 AGTTTCGGTAATAAGCATTTACTTTCG 58.827 33.333 0.00 0.00 31.62 3.46
119 120 6.592798 TCGGTAATAAGCATTTACTTTCGG 57.407 37.500 0.00 0.00 31.62 4.30
120 121 6.108015 TCGGTAATAAGCATTTACTTTCGGT 58.892 36.000 0.00 0.00 31.62 4.69
121 122 6.594937 TCGGTAATAAGCATTTACTTTCGGTT 59.405 34.615 0.00 0.00 31.62 4.44
122 123 6.903479 CGGTAATAAGCATTTACTTTCGGTTC 59.097 38.462 0.00 0.00 31.62 3.62
123 124 6.903479 GGTAATAAGCATTTACTTTCGGTTCG 59.097 38.462 0.00 0.00 31.62 3.95
124 125 6.730960 AATAAGCATTTACTTTCGGTTCGA 57.269 33.333 0.00 0.00 0.00 3.71
125 126 6.920569 ATAAGCATTTACTTTCGGTTCGAT 57.079 33.333 0.00 0.00 35.23 3.59
126 127 5.622770 AAGCATTTACTTTCGGTTCGATT 57.377 34.783 0.00 0.00 35.23 3.34
127 128 5.622770 AGCATTTACTTTCGGTTCGATTT 57.377 34.783 0.00 0.00 35.23 2.17
128 129 5.628134 AGCATTTACTTTCGGTTCGATTTC 58.372 37.500 0.00 0.00 35.23 2.17
129 130 5.180492 AGCATTTACTTTCGGTTCGATTTCA 59.820 36.000 0.00 0.00 35.23 2.69
130 131 5.508224 GCATTTACTTTCGGTTCGATTTCAG 59.492 40.000 0.00 0.00 35.23 3.02
131 132 6.599437 CATTTACTTTCGGTTCGATTTCAGT 58.401 36.000 0.00 0.00 35.23 3.41
132 133 7.622672 GCATTTACTTTCGGTTCGATTTCAGTA 60.623 37.037 0.00 0.00 35.23 2.74
133 134 7.712264 TTTACTTTCGGTTCGATTTCAGTAA 57.288 32.000 0.00 0.00 35.23 2.24
134 135 7.894376 TTACTTTCGGTTCGATTTCAGTAAT 57.106 32.000 0.00 0.00 35.23 1.89
135 136 8.984891 TTACTTTCGGTTCGATTTCAGTAATA 57.015 30.769 0.00 0.00 35.23 0.98
136 137 7.894376 ACTTTCGGTTCGATTTCAGTAATAA 57.106 32.000 0.00 0.00 35.23 1.40
137 138 7.736447 ACTTTCGGTTCGATTTCAGTAATAAC 58.264 34.615 0.00 0.00 35.23 1.89
138 139 6.651755 TTCGGTTCGATTTCAGTAATAACC 57.348 37.500 0.00 0.00 35.23 2.85
139 140 5.722263 TCGGTTCGATTTCAGTAATAACCA 58.278 37.500 0.00 0.00 35.74 3.67
140 141 6.164876 TCGGTTCGATTTCAGTAATAACCAA 58.835 36.000 0.00 0.00 35.74 3.67
141 142 6.649973 TCGGTTCGATTTCAGTAATAACCAAA 59.350 34.615 0.00 0.00 35.74 3.28
142 143 7.334921 TCGGTTCGATTTCAGTAATAACCAAAT 59.665 33.333 0.00 0.00 35.74 2.32
143 144 7.966204 CGGTTCGATTTCAGTAATAACCAAATT 59.034 33.333 0.00 0.00 35.74 1.82
175 176 9.892130 AAGTTGGTGTAAATTTTTAATCCAACA 57.108 25.926 28.23 14.28 46.50 3.33
176 177 9.320352 AGTTGGTGTAAATTTTTAATCCAACAC 57.680 29.630 28.23 18.76 46.50 3.32
177 178 9.099454 GTTGGTGTAAATTTTTAATCCAACACA 57.901 29.630 25.44 8.08 45.31 3.72
178 179 9.838339 TTGGTGTAAATTTTTAATCCAACACAT 57.162 25.926 14.99 0.00 35.14 3.21
190 191 8.789881 TTAATCCAACACATAACTTTTTCACG 57.210 30.769 0.00 0.00 0.00 4.35
191 192 5.821516 TCCAACACATAACTTTTTCACGT 57.178 34.783 0.00 0.00 0.00 4.49
192 193 5.574082 TCCAACACATAACTTTTTCACGTG 58.426 37.500 9.94 9.94 0.00 4.49
193 194 5.124138 TCCAACACATAACTTTTTCACGTGT 59.876 36.000 16.51 0.00 37.71 4.49
194 195 6.315642 TCCAACACATAACTTTTTCACGTGTA 59.684 34.615 16.51 2.27 35.20 2.90
195 196 7.012515 TCCAACACATAACTTTTTCACGTGTAT 59.987 33.333 16.51 0.92 35.20 2.29
196 197 8.283992 CCAACACATAACTTTTTCACGTGTATA 58.716 33.333 16.51 0.00 35.20 1.47
197 198 9.098746 CAACACATAACTTTTTCACGTGTATAC 57.901 33.333 16.51 0.00 35.20 1.47
198 199 8.367943 ACACATAACTTTTTCACGTGTATACA 57.632 30.769 16.51 0.08 34.55 2.29
199 200 8.995220 ACACATAACTTTTTCACGTGTATACAT 58.005 29.630 16.51 0.82 34.55 2.29
200 201 9.820229 CACATAACTTTTTCACGTGTATACATT 57.180 29.630 16.51 7.62 0.00 2.71
644 645 1.227999 TGCACGTTGGCTAAGCAGTC 61.228 55.000 0.00 0.00 34.04 3.51
646 647 1.442769 CACGTTGGCTAAGCAGTCAT 58.557 50.000 0.00 0.00 35.97 3.06
679 681 9.443283 CACATAAAATGAAGCACTAAATAGCTC 57.557 33.333 0.00 0.00 40.90 4.09
691 693 7.010552 AGCACTAAATAGCTCGAAAGTATTGTG 59.989 37.037 0.00 0.00 36.00 3.33
911 922 1.039068 CCATTTTGCACACCCTGACA 58.961 50.000 0.00 0.00 0.00 3.58
944 955 3.659364 CGAGAAAAGAAGTTGAAGACGCG 60.659 47.826 3.53 3.53 0.00 6.01
980 992 3.970842 AGGGTAATCTTCTCAGTCGACT 58.029 45.455 13.58 13.58 0.00 4.18
984 996 4.142643 GGTAATCTTCTCAGTCGACTCGTT 60.143 45.833 16.96 5.58 0.00 3.85
1054 1066 4.007644 CGGACTGCCTGCTCCACA 62.008 66.667 0.00 0.00 0.00 4.17
1378 1390 2.678934 TTAGCCGTGGCCTCGAGT 60.679 61.111 27.84 16.21 43.17 4.18
1497 1509 3.012518 CCACAAGGATTTCGAGAAGCAT 58.987 45.455 0.00 0.00 36.89 3.79
1545 1557 3.439154 AGACTTGGAGATCAGAAGCTCA 58.561 45.455 0.00 0.00 39.77 4.26
1702 1714 1.544691 GAGCCTTCTCTGTCACCGTAA 59.455 52.381 0.00 0.00 36.42 3.18
1760 1772 3.637273 GGACAACCCTCTGCCGGT 61.637 66.667 1.90 0.00 34.07 5.28
1766 1778 2.045926 CCCTCTGCCGGTGAAAGG 60.046 66.667 1.90 5.31 0.00 3.11
1792 1804 3.129638 TCCCTTTGTTTTTCAACAGGACG 59.870 43.478 0.00 0.00 43.92 4.79
1796 1808 3.577649 TGTTTTTCAACAGGACGCAAA 57.422 38.095 0.00 0.00 38.03 3.68
1828 1840 4.926238 CACCGATGCTATGTAGATTTCTCC 59.074 45.833 0.00 0.00 0.00 3.71
1848 1860 1.671328 CGCTCTCTATCCAACGTCAGA 59.329 52.381 0.00 0.00 0.00 3.27
1858 1870 1.541233 CCAACGTCAGAAGCTTGGAGT 60.541 52.381 2.10 0.00 36.06 3.85
1869 1881 3.515602 AGCTTGGAGTTGTCAGGATTT 57.484 42.857 0.00 0.00 0.00 2.17
1890 1906 6.642707 TTTCGTGATATGGTTTGTTCCTTT 57.357 33.333 0.00 0.00 0.00 3.11
1895 1911 6.455113 CGTGATATGGTTTGTTCCTTTAGTCG 60.455 42.308 0.00 0.00 0.00 4.18
1974 1990 4.213482 CACACTAACTAACCCTGTTCTTGC 59.787 45.833 0.00 0.00 0.00 4.01
1977 1993 4.842380 ACTAACTAACCCTGTTCTTGCCTA 59.158 41.667 0.00 0.00 0.00 3.93
2012 2028 3.016736 CAACATATTTCGCCACCTCCTT 58.983 45.455 0.00 0.00 0.00 3.36
2016 2032 0.693049 ATTTCGCCACCTCCTTCACT 59.307 50.000 0.00 0.00 0.00 3.41
2051 2067 3.016736 CCTGCCGAGTACCAATTTCAAT 58.983 45.455 0.00 0.00 0.00 2.57
2299 2315 8.606830 ACTTGATTTATCTAACTGAAGGACCTT 58.393 33.333 6.40 6.40 0.00 3.50
2301 2317 9.886132 TTGATTTATCTAACTGAAGGACCTTAC 57.114 33.333 6.75 1.80 0.00 2.34
2302 2318 8.483758 TGATTTATCTAACTGAAGGACCTTACC 58.516 37.037 6.75 0.00 0.00 2.85
2347 2363 2.549754 CTCCTGTGTGTAGTGCCAAAAG 59.450 50.000 0.00 0.00 0.00 2.27
2356 2372 1.632589 AGTGCCAAAAGGTTCCATCC 58.367 50.000 0.00 0.00 0.00 3.51
2433 2449 6.032956 AGTACAAATCCAGTACGATGACAA 57.967 37.500 0.00 0.00 44.92 3.18
2460 2476 1.559682 TCATGAAGGCCAAGGTACTCC 59.440 52.381 5.01 0.00 38.49 3.85
2645 2662 8.794335 AATAGAGTTTACTCCACTTTTCATCC 57.206 34.615 6.28 0.00 43.88 3.51
2653 2670 4.907269 ACTCCACTTTTCATCCCCAAAAAT 59.093 37.500 0.00 0.00 0.00 1.82
2679 2699 1.031029 TTACGCATTTTACCCGGCCC 61.031 55.000 0.00 0.00 0.00 5.80
2683 2703 4.049817 ATTTTACCCGGCCCGGCA 62.050 61.111 19.21 3.04 46.86 5.69
2801 2825 1.217916 TTTCCTTCACAGACCCCACA 58.782 50.000 0.00 0.00 0.00 4.17
2839 2863 6.040209 TCAACACTAGATACGCCCTTTTAA 57.960 37.500 0.00 0.00 0.00 1.52
2846 2870 7.713942 CACTAGATACGCCCTTTTAATTTACCT 59.286 37.037 0.00 0.00 0.00 3.08
2851 2875 2.169769 GCCCTTTTAATTTACCTGGCCC 59.830 50.000 0.00 0.00 0.00 5.80
2867 2891 2.224917 TGGCCCCGAAGTTTAATCTTGT 60.225 45.455 0.00 0.00 0.00 3.16
2947 2971 3.126858 CCATGTGACTCCATTTTGGTACG 59.873 47.826 0.00 0.00 39.03 3.67
2982 3510 1.202710 ACATGCCCTTTGTACGTGTCA 60.203 47.619 0.00 0.00 0.00 3.58
2983 3511 1.196808 CATGCCCTTTGTACGTGTCAC 59.803 52.381 0.00 0.00 0.00 3.67
2984 3512 0.533308 TGCCCTTTGTACGTGTCACC 60.533 55.000 0.00 0.00 0.00 4.02
2985 3513 1.232621 GCCCTTTGTACGTGTCACCC 61.233 60.000 0.00 0.00 0.00 4.61
2986 3514 0.947180 CCCTTTGTACGTGTCACCCG 60.947 60.000 0.00 0.00 0.00 5.28
2987 3515 1.562575 CCTTTGTACGTGTCACCCGC 61.563 60.000 0.00 0.00 0.00 6.13
2988 3516 0.876777 CTTTGTACGTGTCACCCGCA 60.877 55.000 0.00 0.00 0.00 5.69
2989 3517 0.249953 TTTGTACGTGTCACCCGCAT 60.250 50.000 0.00 0.00 0.00 4.73
2990 3518 0.946700 TTGTACGTGTCACCCGCATG 60.947 55.000 0.00 0.00 0.00 4.06
2991 3519 2.098233 GTACGTGTCACCCGCATGG 61.098 63.158 0.00 0.00 41.37 3.66
2992 3520 3.943479 TACGTGTCACCCGCATGGC 62.943 63.158 0.00 0.00 37.83 4.40
2995 3523 3.952508 TGTCACCCGCATGGCACT 61.953 61.111 0.00 0.00 37.83 4.40
2996 3524 3.434319 GTCACCCGCATGGCACTG 61.434 66.667 0.00 0.00 37.83 3.66
3047 3575 1.216064 TCAGGATGGTCAGAATGGGG 58.784 55.000 0.00 0.00 33.82 4.96
3112 3640 3.209410 AGAGTGACCAAGCTTGAACTTG 58.791 45.455 28.05 12.76 45.42 3.16
3477 4005 3.359002 AGCCTCCAAAAGCTTGCG 58.641 55.556 0.00 0.00 35.22 4.85
3478 4006 1.529244 AGCCTCCAAAAGCTTGCGT 60.529 52.632 0.00 0.00 35.22 5.24
3479 4007 0.250727 AGCCTCCAAAAGCTTGCGTA 60.251 50.000 0.00 0.00 35.22 4.42
3480 4008 0.596082 GCCTCCAAAAGCTTGCGTAA 59.404 50.000 0.00 0.00 0.00 3.18
3481 4009 1.000717 GCCTCCAAAAGCTTGCGTAAA 60.001 47.619 0.00 0.00 0.00 2.01
3482 4010 2.661594 CCTCCAAAAGCTTGCGTAAAC 58.338 47.619 0.00 0.00 0.00 2.01
3483 4011 2.607038 CCTCCAAAAGCTTGCGTAAACC 60.607 50.000 0.00 0.00 0.00 3.27
3484 4012 1.002251 TCCAAAAGCTTGCGTAAACCG 60.002 47.619 0.00 0.00 40.40 4.44
3485 4013 1.002251 CCAAAAGCTTGCGTAAACCGA 60.002 47.619 0.00 0.00 39.56 4.69
3486 4014 2.351350 CCAAAAGCTTGCGTAAACCGAT 60.351 45.455 0.00 0.00 39.56 4.18
3487 4015 2.894307 AAAGCTTGCGTAAACCGATC 57.106 45.000 0.00 0.00 39.56 3.69
3488 4016 1.084289 AAGCTTGCGTAAACCGATCC 58.916 50.000 0.00 0.00 39.56 3.36
3489 4017 0.743345 AGCTTGCGTAAACCGATCCC 60.743 55.000 0.00 0.00 39.56 3.85
3490 4018 2.003672 CTTGCGTAAACCGATCCCG 58.996 57.895 0.00 0.00 39.56 5.14
3491 4019 0.738412 CTTGCGTAAACCGATCCCGT 60.738 55.000 0.00 0.00 39.56 5.28
3492 4020 0.529833 TTGCGTAAACCGATCCCGTA 59.470 50.000 0.00 0.00 39.56 4.02
3493 4021 0.529833 TGCGTAAACCGATCCCGTAA 59.470 50.000 0.00 0.00 39.56 3.18
3494 4022 1.067283 TGCGTAAACCGATCCCGTAAA 60.067 47.619 0.00 0.00 39.56 2.01
3495 4023 1.999024 GCGTAAACCGATCCCGTAAAA 59.001 47.619 0.00 0.00 39.56 1.52
3496 4024 2.414825 GCGTAAACCGATCCCGTAAAAA 59.585 45.455 0.00 0.00 39.56 1.94
3497 4025 3.724716 GCGTAAACCGATCCCGTAAAAAC 60.725 47.826 0.00 0.00 39.56 2.43
3498 4026 3.431572 CGTAAACCGATCCCGTAAAAACA 59.568 43.478 0.00 0.00 39.56 2.83
3499 4027 3.902261 AAACCGATCCCGTAAAAACAC 57.098 42.857 0.00 0.00 0.00 3.32
3500 4028 1.812235 ACCGATCCCGTAAAAACACC 58.188 50.000 0.00 0.00 0.00 4.16
3501 4029 1.089112 CCGATCCCGTAAAAACACCC 58.911 55.000 0.00 0.00 0.00 4.61
3502 4030 1.089112 CGATCCCGTAAAAACACCCC 58.911 55.000 0.00 0.00 0.00 4.95
3503 4031 1.466856 GATCCCGTAAAAACACCCCC 58.533 55.000 0.00 0.00 0.00 5.40
3504 4032 1.005097 GATCCCGTAAAAACACCCCCT 59.995 52.381 0.00 0.00 0.00 4.79
3505 4033 0.401356 TCCCGTAAAAACACCCCCTC 59.599 55.000 0.00 0.00 0.00 4.30
3506 4034 0.402887 CCCGTAAAAACACCCCCTCT 59.597 55.000 0.00 0.00 0.00 3.69
3507 4035 1.530323 CCGTAAAAACACCCCCTCTG 58.470 55.000 0.00 0.00 0.00 3.35
3508 4036 1.202842 CCGTAAAAACACCCCCTCTGT 60.203 52.381 0.00 0.00 0.00 3.41
3509 4037 2.148768 CGTAAAAACACCCCCTCTGTC 58.851 52.381 0.00 0.00 0.00 3.51
3510 4038 2.511659 GTAAAAACACCCCCTCTGTCC 58.488 52.381 0.00 0.00 0.00 4.02
3511 4039 1.231963 AAAAACACCCCCTCTGTCCT 58.768 50.000 0.00 0.00 0.00 3.85
3512 4040 0.478507 AAAACACCCCCTCTGTCCTG 59.521 55.000 0.00 0.00 0.00 3.86
3513 4041 0.697854 AAACACCCCCTCTGTCCTGT 60.698 55.000 0.00 0.00 0.00 4.00
3514 4042 0.192566 AACACCCCCTCTGTCCTGTA 59.807 55.000 0.00 0.00 0.00 2.74
3515 4043 0.417841 ACACCCCCTCTGTCCTGTAT 59.582 55.000 0.00 0.00 0.00 2.29
3516 4044 1.649633 ACACCCCCTCTGTCCTGTATA 59.350 52.381 0.00 0.00 0.00 1.47
3517 4045 2.045326 ACACCCCCTCTGTCCTGTATAA 59.955 50.000 0.00 0.00 0.00 0.98
3518 4046 3.311402 ACACCCCCTCTGTCCTGTATAAT 60.311 47.826 0.00 0.00 0.00 1.28
3519 4047 3.716872 CACCCCCTCTGTCCTGTATAATT 59.283 47.826 0.00 0.00 0.00 1.40
3520 4048 4.166144 CACCCCCTCTGTCCTGTATAATTT 59.834 45.833 0.00 0.00 0.00 1.82
3521 4049 5.368523 CACCCCCTCTGTCCTGTATAATTTA 59.631 44.000 0.00 0.00 0.00 1.40
3522 4050 5.368816 ACCCCCTCTGTCCTGTATAATTTAC 59.631 44.000 0.00 0.00 0.00 2.01
3523 4051 5.510861 CCCCCTCTGTCCTGTATAATTTACG 60.511 48.000 0.00 0.00 0.00 3.18
3524 4052 5.510861 CCCCTCTGTCCTGTATAATTTACGG 60.511 48.000 0.00 0.00 0.00 4.02
3525 4053 5.510861 CCCTCTGTCCTGTATAATTTACGGG 60.511 48.000 14.63 14.63 43.61 5.28
3532 4060 6.765403 TCCTGTATAATTTACGGGAAGATGG 58.235 40.000 18.39 0.00 46.70 3.51
3533 4061 5.411669 CCTGTATAATTTACGGGAAGATGGC 59.588 44.000 15.27 0.00 44.72 4.40
3534 4062 5.310451 TGTATAATTTACGGGAAGATGGCC 58.690 41.667 0.00 0.00 0.00 5.36
3535 4063 4.724279 ATAATTTACGGGAAGATGGCCT 57.276 40.909 3.32 0.00 0.00 5.19
3536 4064 3.382083 AATTTACGGGAAGATGGCCTT 57.618 42.857 3.32 0.00 37.93 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.096682 ACCAAACCGAATCAAACGAGAAAA 59.903 37.500 0.00 0.00 0.00 2.29
1 2 3.628487 ACCAAACCGAATCAAACGAGAAA 59.372 39.130 0.00 0.00 0.00 2.52
2 3 3.207778 ACCAAACCGAATCAAACGAGAA 58.792 40.909 0.00 0.00 0.00 2.87
3 4 2.841215 ACCAAACCGAATCAAACGAGA 58.159 42.857 0.00 0.00 0.00 4.04
4 5 3.619233 AACCAAACCGAATCAAACGAG 57.381 42.857 0.00 0.00 0.00 4.18
5 6 5.692613 ATAAACCAAACCGAATCAAACGA 57.307 34.783 0.00 0.00 0.00 3.85
6 7 5.505446 CGTATAAACCAAACCGAATCAAACG 59.495 40.000 0.00 0.00 0.00 3.60
7 8 5.796437 CCGTATAAACCAAACCGAATCAAAC 59.204 40.000 0.00 0.00 0.00 2.93
8 9 5.106237 CCCGTATAAACCAAACCGAATCAAA 60.106 40.000 0.00 0.00 0.00 2.69
9 10 4.395542 CCCGTATAAACCAAACCGAATCAA 59.604 41.667 0.00 0.00 0.00 2.57
10 11 3.940221 CCCGTATAAACCAAACCGAATCA 59.060 43.478 0.00 0.00 0.00 2.57
11 12 3.940852 ACCCGTATAAACCAAACCGAATC 59.059 43.478 0.00 0.00 0.00 2.52
12 13 3.954200 ACCCGTATAAACCAAACCGAAT 58.046 40.909 0.00 0.00 0.00 3.34
13 14 3.415457 ACCCGTATAAACCAAACCGAA 57.585 42.857 0.00 0.00 0.00 4.30
14 15 3.072944 CAACCCGTATAAACCAAACCGA 58.927 45.455 0.00 0.00 0.00 4.69
15 16 2.813172 ACAACCCGTATAAACCAAACCG 59.187 45.455 0.00 0.00 0.00 4.44
16 17 3.057386 CCACAACCCGTATAAACCAAACC 60.057 47.826 0.00 0.00 0.00 3.27
17 18 3.569277 ACCACAACCCGTATAAACCAAAC 59.431 43.478 0.00 0.00 0.00 2.93
18 19 3.830121 ACCACAACCCGTATAAACCAAA 58.170 40.909 0.00 0.00 0.00 3.28
19 20 3.505480 ACCACAACCCGTATAAACCAA 57.495 42.857 0.00 0.00 0.00 3.67
20 21 3.505480 AACCACAACCCGTATAAACCA 57.495 42.857 0.00 0.00 0.00 3.67
21 22 7.282901 ACATATAAACCACAACCCGTATAAACC 59.717 37.037 0.00 0.00 0.00 3.27
22 23 8.212317 ACATATAAACCACAACCCGTATAAAC 57.788 34.615 0.00 0.00 0.00 2.01
23 24 8.266473 AGACATATAAACCACAACCCGTATAAA 58.734 33.333 0.00 0.00 0.00 1.40
24 25 7.794041 AGACATATAAACCACAACCCGTATAA 58.206 34.615 0.00 0.00 0.00 0.98
25 26 7.364149 AGACATATAAACCACAACCCGTATA 57.636 36.000 0.00 0.00 0.00 1.47
26 27 6.243216 AGACATATAAACCACAACCCGTAT 57.757 37.500 0.00 0.00 0.00 3.06
27 28 5.680594 AGACATATAAACCACAACCCGTA 57.319 39.130 0.00 0.00 0.00 4.02
28 29 4.563140 AGACATATAAACCACAACCCGT 57.437 40.909 0.00 0.00 0.00 5.28
29 30 5.890424 AAAGACATATAAACCACAACCCG 57.110 39.130 0.00 0.00 0.00 5.28
45 46 9.723601 ACCGTATAAACCAAAGTATAAAAGACA 57.276 29.630 0.00 0.00 0.00 3.41
65 66 9.846248 GAACCGTATCTATGTATAAAACCGTAT 57.154 33.333 0.00 0.00 0.00 3.06
66 67 8.845227 TGAACCGTATCTATGTATAAAACCGTA 58.155 33.333 0.00 0.00 0.00 4.02
67 68 7.715657 TGAACCGTATCTATGTATAAAACCGT 58.284 34.615 0.00 0.00 0.00 4.83
68 69 7.864379 ACTGAACCGTATCTATGTATAAAACCG 59.136 37.037 0.00 0.00 0.00 4.44
69 70 9.538508 AACTGAACCGTATCTATGTATAAAACC 57.461 33.333 0.00 0.00 0.00 3.27
72 73 9.454585 CGAAACTGAACCGTATCTATGTATAAA 57.545 33.333 0.00 0.00 0.00 1.40
73 74 8.077991 CCGAAACTGAACCGTATCTATGTATAA 58.922 37.037 0.00 0.00 0.00 0.98
74 75 7.229306 ACCGAAACTGAACCGTATCTATGTATA 59.771 37.037 0.00 0.00 0.00 1.47
75 76 6.040166 ACCGAAACTGAACCGTATCTATGTAT 59.960 38.462 0.00 0.00 0.00 2.29
76 77 5.357878 ACCGAAACTGAACCGTATCTATGTA 59.642 40.000 0.00 0.00 0.00 2.29
77 78 4.159135 ACCGAAACTGAACCGTATCTATGT 59.841 41.667 0.00 0.00 0.00 2.29
78 79 4.679662 ACCGAAACTGAACCGTATCTATG 58.320 43.478 0.00 0.00 0.00 2.23
79 80 4.996788 ACCGAAACTGAACCGTATCTAT 57.003 40.909 0.00 0.00 0.00 1.98
80 81 5.895636 TTACCGAAACTGAACCGTATCTA 57.104 39.130 0.00 0.00 0.00 1.98
81 82 4.789012 TTACCGAAACTGAACCGTATCT 57.211 40.909 0.00 0.00 0.00 1.98
82 83 6.292008 GCTTATTACCGAAACTGAACCGTATC 60.292 42.308 0.00 0.00 0.00 2.24
83 84 5.521372 GCTTATTACCGAAACTGAACCGTAT 59.479 40.000 0.00 0.00 0.00 3.06
84 85 4.864247 GCTTATTACCGAAACTGAACCGTA 59.136 41.667 0.00 0.00 0.00 4.02
85 86 3.681417 GCTTATTACCGAAACTGAACCGT 59.319 43.478 0.00 0.00 0.00 4.83
86 87 3.680937 TGCTTATTACCGAAACTGAACCG 59.319 43.478 0.00 0.00 0.00 4.44
87 88 5.813080 ATGCTTATTACCGAAACTGAACC 57.187 39.130 0.00 0.00 0.00 3.62
88 89 8.448615 AGTAAATGCTTATTACCGAAACTGAAC 58.551 33.333 0.00 0.00 34.50 3.18
89 90 8.556213 AGTAAATGCTTATTACCGAAACTGAA 57.444 30.769 0.00 0.00 34.50 3.02
90 91 8.556213 AAGTAAATGCTTATTACCGAAACTGA 57.444 30.769 0.00 0.00 34.50 3.41
91 92 9.274065 GAAAGTAAATGCTTATTACCGAAACTG 57.726 33.333 0.00 0.00 34.50 3.16
92 93 8.173130 CGAAAGTAAATGCTTATTACCGAAACT 58.827 33.333 0.00 0.00 34.50 2.66
93 94 7.427318 CCGAAAGTAAATGCTTATTACCGAAAC 59.573 37.037 0.00 0.00 34.50 2.78
94 95 7.119553 ACCGAAAGTAAATGCTTATTACCGAAA 59.880 33.333 0.00 0.00 34.50 3.46
95 96 6.594937 ACCGAAAGTAAATGCTTATTACCGAA 59.405 34.615 0.00 0.00 34.50 4.30
96 97 6.108015 ACCGAAAGTAAATGCTTATTACCGA 58.892 36.000 0.00 0.00 34.50 4.69
97 98 6.354039 ACCGAAAGTAAATGCTTATTACCG 57.646 37.500 0.00 0.00 34.50 4.02
98 99 6.903479 CGAACCGAAAGTAAATGCTTATTACC 59.097 38.462 0.00 0.00 34.50 2.85
99 100 7.678226 TCGAACCGAAAGTAAATGCTTATTAC 58.322 34.615 0.00 0.00 31.77 1.89
100 101 7.830940 TCGAACCGAAAGTAAATGCTTATTA 57.169 32.000 0.00 0.00 31.06 0.98
101 102 6.730960 TCGAACCGAAAGTAAATGCTTATT 57.269 33.333 0.00 0.00 31.06 1.40
102 103 6.920569 ATCGAACCGAAAGTAAATGCTTAT 57.079 33.333 0.00 0.00 39.99 1.73
103 104 6.730960 AATCGAACCGAAAGTAAATGCTTA 57.269 33.333 0.00 0.00 39.99 3.09
104 105 5.622770 AATCGAACCGAAAGTAAATGCTT 57.377 34.783 0.00 0.00 39.99 3.91
105 106 5.180492 TGAAATCGAACCGAAAGTAAATGCT 59.820 36.000 0.00 0.00 39.99 3.79
106 107 5.387279 TGAAATCGAACCGAAAGTAAATGC 58.613 37.500 0.00 0.00 39.99 3.56
107 108 6.599437 ACTGAAATCGAACCGAAAGTAAATG 58.401 36.000 0.00 0.00 39.99 2.32
108 109 6.796705 ACTGAAATCGAACCGAAAGTAAAT 57.203 33.333 0.00 0.00 39.99 1.40
109 110 7.712264 TTACTGAAATCGAACCGAAAGTAAA 57.288 32.000 0.00 0.00 39.99 2.01
110 111 7.894376 ATTACTGAAATCGAACCGAAAGTAA 57.106 32.000 13.90 13.90 39.99 2.24
111 112 8.863049 GTTATTACTGAAATCGAACCGAAAGTA 58.137 33.333 0.00 0.00 39.99 2.24
112 113 7.148523 GGTTATTACTGAAATCGAACCGAAAGT 60.149 37.037 0.00 0.00 39.99 2.66
113 114 7.148540 TGGTTATTACTGAAATCGAACCGAAAG 60.149 37.037 0.00 0.00 38.35 2.62
114 115 6.649973 TGGTTATTACTGAAATCGAACCGAAA 59.350 34.615 0.00 0.00 38.35 3.46
115 116 6.164876 TGGTTATTACTGAAATCGAACCGAA 58.835 36.000 0.00 0.00 38.35 4.30
116 117 5.722263 TGGTTATTACTGAAATCGAACCGA 58.278 37.500 0.00 0.00 38.35 4.69
117 118 6.411630 TTGGTTATTACTGAAATCGAACCG 57.588 37.500 0.00 0.00 38.35 4.44
149 150 9.892130 TGTTGGATTAAAAATTTACACCAACTT 57.108 25.926 28.76 8.85 45.87 2.66
150 151 9.320352 GTGTTGGATTAAAAATTTACACCAACT 57.680 29.630 28.76 0.17 45.87 3.16
151 152 9.099454 TGTGTTGGATTAAAAATTTACACCAAC 57.901 29.630 26.00 26.00 45.88 3.77
152 153 9.838339 ATGTGTTGGATTAAAAATTTACACCAA 57.162 25.926 11.92 13.90 36.57 3.67
164 165 9.239002 CGTGAAAAAGTTATGTGTTGGATTAAA 57.761 29.630 0.00 0.00 0.00 1.52
165 166 8.407064 ACGTGAAAAAGTTATGTGTTGGATTAA 58.593 29.630 0.00 0.00 0.00 1.40
166 167 7.858382 CACGTGAAAAAGTTATGTGTTGGATTA 59.142 33.333 10.90 0.00 0.00 1.75
167 168 6.695278 CACGTGAAAAAGTTATGTGTTGGATT 59.305 34.615 10.90 0.00 0.00 3.01
168 169 6.183360 ACACGTGAAAAAGTTATGTGTTGGAT 60.183 34.615 25.01 0.00 35.74 3.41
169 170 5.124138 ACACGTGAAAAAGTTATGTGTTGGA 59.876 36.000 25.01 0.00 35.74 3.53
170 171 5.336744 ACACGTGAAAAAGTTATGTGTTGG 58.663 37.500 25.01 0.00 35.74 3.77
171 172 9.098746 GTATACACGTGAAAAAGTTATGTGTTG 57.901 33.333 25.01 0.00 39.53 3.33
172 173 8.828644 TGTATACACGTGAAAAAGTTATGTGTT 58.171 29.630 25.01 0.00 39.53 3.32
173 174 8.367943 TGTATACACGTGAAAAAGTTATGTGT 57.632 30.769 25.01 0.00 41.47 3.72
174 175 9.820229 AATGTATACACGTGAAAAAGTTATGTG 57.180 29.630 25.01 0.00 0.00 3.21
622 623 1.737236 CTGCTTAGCCAACGTGCATTA 59.263 47.619 0.29 0.00 33.02 1.90
644 645 7.919091 AGTGCTTCATTTTATGTGATTAGCATG 59.081 33.333 0.00 0.00 0.00 4.06
646 647 7.395190 AGTGCTTCATTTTATGTGATTAGCA 57.605 32.000 0.00 0.00 0.00 3.49
656 657 8.662781 TCGAGCTATTTAGTGCTTCATTTTAT 57.337 30.769 0.00 0.00 39.91 1.40
661 662 6.109359 ACTTTCGAGCTATTTAGTGCTTCAT 58.891 36.000 0.00 0.00 39.91 2.57
675 676 4.034510 GCAATAGCACAATACTTTCGAGCT 59.965 41.667 0.00 0.00 41.58 4.09
873 884 8.940952 CAAAATGGAACTGAAAACCAAAAACTA 58.059 29.630 0.00 0.00 37.24 2.24
888 899 1.688197 CAGGGTGTGCAAAATGGAACT 59.312 47.619 0.00 0.00 0.00 3.01
911 922 6.809976 ACTTCTTTTCTCGAAGGGGTATAT 57.190 37.500 4.98 0.00 41.61 0.86
944 955 1.685148 ACCCTAGATCCGTTCCGTAC 58.315 55.000 0.00 0.00 0.00 3.67
984 996 4.803924 GCATCCATGTATTTCAGATCGGGA 60.804 45.833 0.00 0.00 0.00 5.14
1054 1066 2.765807 CAGGCGGGAGAGGATGGT 60.766 66.667 0.00 0.00 0.00 3.55
1497 1509 0.529833 CTCTGAGCCAAGCGAAGAGA 59.470 55.000 13.21 0.00 41.83 3.10
1506 1518 0.979665 CTTGGAGGACTCTGAGCCAA 59.020 55.000 16.74 14.43 37.13 4.52
1545 1557 4.099633 TCCTTGAGAGATTGGACATGTCT 58.900 43.478 24.50 5.76 0.00 3.41
1607 1619 4.039973 TGACCTCGAAGTTTAAGATGGTGT 59.960 41.667 0.00 0.00 0.00 4.16
1702 1714 1.147824 CAAGATCAGGCGCATCCCT 59.852 57.895 10.83 0.00 34.93 4.20
1707 1719 0.674581 CTTGGACAAGATCAGGCGCA 60.675 55.000 10.83 0.00 40.79 6.09
1766 1778 7.090808 GTCCTGTTGAAAAACAAAGGGATATC 58.909 38.462 0.00 0.00 40.54 1.63
1828 1840 1.671328 TCTGACGTTGGATAGAGAGCG 59.329 52.381 0.00 0.00 0.00 5.03
1848 1860 3.515602 AATCCTGACAACTCCAAGCTT 57.484 42.857 0.00 0.00 0.00 3.74
1858 1870 5.097742 ACCATATCACGAAATCCTGACAA 57.902 39.130 0.00 0.00 0.00 3.18
1869 1881 6.469410 ACTAAAGGAACAAACCATATCACGA 58.531 36.000 0.00 0.00 0.00 4.35
1890 1906 2.455674 ATGAAGCAAGCACACGACTA 57.544 45.000 0.00 0.00 0.00 2.59
1895 1911 4.549458 ACATACAAATGAAGCAAGCACAC 58.451 39.130 0.00 0.00 36.54 3.82
1974 1990 3.016031 TGTTGTGCCTACATTGCATAGG 58.984 45.455 7.40 7.40 41.46 2.57
1977 1993 5.857471 AATATGTTGTGCCTACATTGCAT 57.143 34.783 7.35 2.70 41.46 3.96
2012 2028 0.467290 GGCCAAGGAACACCAAGTGA 60.467 55.000 0.00 0.00 36.96 3.41
2016 2032 1.832167 GCAGGCCAAGGAACACCAA 60.832 57.895 5.01 0.00 0.00 3.67
2051 2067 1.675310 CACTTCCTGGCGCCATCAA 60.675 57.895 32.87 23.39 0.00 2.57
2282 2298 5.898397 GGTAGGTAAGGTCCTTCAGTTAGAT 59.102 44.000 7.61 0.00 38.86 1.98
2347 2363 2.087646 GAAGCTGAACTGGATGGAACC 58.912 52.381 0.00 0.00 0.00 3.62
2433 2449 2.158505 CCTTGGCCTTCATGATCATCCT 60.159 50.000 4.86 0.00 0.00 3.24
2460 2476 4.104776 GGACACAACATTGTCAACTTGTG 58.895 43.478 24.03 24.03 46.68 3.33
2541 2557 6.590292 TGAACAGCTAAAACGAGGATTCTAAG 59.410 38.462 0.00 0.00 0.00 2.18
2683 2703 0.972983 AGACTCTACCACTGCGCCAT 60.973 55.000 4.18 0.00 0.00 4.40
2839 2863 0.702316 AACTTCGGGGCCAGGTAAAT 59.298 50.000 4.39 0.00 0.00 1.40
2846 2870 2.224917 ACAAGATTAAACTTCGGGGCCA 60.225 45.455 4.39 0.00 0.00 5.36
2851 2875 6.743575 ATCCTGAACAAGATTAAACTTCGG 57.256 37.500 0.00 0.00 0.00 4.30
2892 2916 4.714308 TCGGGGATAATTCTTGCCAAAATT 59.286 37.500 2.04 4.04 0.00 1.82
2947 2971 2.543653 GGCATGTGTCTGGTTTGTTGAC 60.544 50.000 0.00 0.00 0.00 3.18
2991 3519 2.042686 TCAATCCTATGTGGCAGTGC 57.957 50.000 6.55 6.55 35.26 4.40
2992 3520 6.592994 CACTATATCAATCCTATGTGGCAGTG 59.407 42.308 0.00 0.00 35.26 3.66
2993 3521 6.296087 CCACTATATCAATCCTATGTGGCAGT 60.296 42.308 0.00 0.00 37.49 4.40
2994 3522 6.111382 CCACTATATCAATCCTATGTGGCAG 58.889 44.000 0.00 0.00 37.49 4.85
2995 3523 5.547666 ACCACTATATCAATCCTATGTGGCA 59.452 40.000 0.00 0.00 45.18 4.92
2996 3524 6.054860 ACCACTATATCAATCCTATGTGGC 57.945 41.667 0.00 0.00 45.18 5.01
3007 3535 8.112822 TCCTGAATTTTGGAACCACTATATCAA 58.887 33.333 0.00 0.00 0.00 2.57
3009 3537 8.571336 CATCCTGAATTTTGGAACCACTATATC 58.429 37.037 4.78 0.00 35.81 1.63
3047 3575 1.931635 TACCCCCTGGCAAAATTGTC 58.068 50.000 0.00 0.00 33.59 3.18
3050 3578 2.984672 ACTTTACCCCCTGGCAAAATT 58.015 42.857 0.00 0.00 33.59 1.82
3456 3984 2.564771 GCAAGCTTTTGGAGGCTTTTT 58.435 42.857 0.00 0.00 45.03 1.94
3457 3985 1.538849 CGCAAGCTTTTGGAGGCTTTT 60.539 47.619 0.00 0.00 45.03 2.27
3458 3986 0.032540 CGCAAGCTTTTGGAGGCTTT 59.967 50.000 0.00 0.00 45.03 3.51
3460 3988 0.250727 TACGCAAGCTTTTGGAGGCT 60.251 50.000 0.00 0.00 45.62 4.58
3461 3989 0.596082 TTACGCAAGCTTTTGGAGGC 59.404 50.000 0.00 0.00 45.62 4.70
3462 3990 2.607038 GGTTTACGCAAGCTTTTGGAGG 60.607 50.000 0.00 0.00 45.62 4.30
3463 3991 2.661594 GGTTTACGCAAGCTTTTGGAG 58.338 47.619 0.00 0.00 45.62 3.86
3464 3992 1.002251 CGGTTTACGCAAGCTTTTGGA 60.002 47.619 0.00 0.00 45.62 3.53
3465 3993 1.002251 TCGGTTTACGCAAGCTTTTGG 60.002 47.619 0.00 0.00 43.86 3.28
3466 3994 2.392933 TCGGTTTACGCAAGCTTTTG 57.607 45.000 0.00 0.00 43.86 2.44
3467 3995 2.095415 GGATCGGTTTACGCAAGCTTTT 60.095 45.455 0.00 0.00 43.86 2.27
3468 3996 1.467342 GGATCGGTTTACGCAAGCTTT 59.533 47.619 0.00 0.00 43.86 3.51
3469 3997 1.084289 GGATCGGTTTACGCAAGCTT 58.916 50.000 0.00 0.00 43.86 3.74
3470 3998 0.743345 GGGATCGGTTTACGCAAGCT 60.743 55.000 0.00 0.00 43.86 3.74
3471 3999 1.719709 GGGATCGGTTTACGCAAGC 59.280 57.895 0.00 0.00 43.86 4.01
3472 4000 0.738412 ACGGGATCGGTTTACGCAAG 60.738 55.000 0.00 0.00 43.86 4.01
3473 4001 0.529833 TACGGGATCGGTTTACGCAA 59.470 50.000 0.00 0.00 43.86 4.85
3474 4002 0.529833 TTACGGGATCGGTTTACGCA 59.470 50.000 0.00 0.00 43.86 5.24
3475 4003 1.639280 TTTACGGGATCGGTTTACGC 58.361 50.000 0.00 0.00 43.86 4.42
3476 4004 3.431572 TGTTTTTACGGGATCGGTTTACG 59.568 43.478 0.00 0.00 46.11 3.18
3477 4005 4.378356 GGTGTTTTTACGGGATCGGTTTAC 60.378 45.833 0.00 0.00 41.39 2.01
3478 4006 3.750652 GGTGTTTTTACGGGATCGGTTTA 59.249 43.478 0.00 0.00 41.39 2.01
3479 4007 2.553602 GGTGTTTTTACGGGATCGGTTT 59.446 45.455 0.00 0.00 41.39 3.27
3480 4008 2.153645 GGTGTTTTTACGGGATCGGTT 58.846 47.619 0.00 0.00 41.39 4.44
3481 4009 1.611410 GGGTGTTTTTACGGGATCGGT 60.611 52.381 0.00 0.00 41.39 4.69
3482 4010 1.089112 GGGTGTTTTTACGGGATCGG 58.911 55.000 0.00 0.00 41.39 4.18
3483 4011 1.089112 GGGGTGTTTTTACGGGATCG 58.911 55.000 0.00 0.00 43.02 3.69
3484 4012 1.005097 AGGGGGTGTTTTTACGGGATC 59.995 52.381 0.00 0.00 0.00 3.36
3485 4013 1.005097 GAGGGGGTGTTTTTACGGGAT 59.995 52.381 0.00 0.00 0.00 3.85
3486 4014 0.401356 GAGGGGGTGTTTTTACGGGA 59.599 55.000 0.00 0.00 0.00 5.14
3487 4015 0.402887 AGAGGGGGTGTTTTTACGGG 59.597 55.000 0.00 0.00 0.00 5.28
3488 4016 1.202842 ACAGAGGGGGTGTTTTTACGG 60.203 52.381 0.00 0.00 0.00 4.02
3489 4017 2.148768 GACAGAGGGGGTGTTTTTACG 58.851 52.381 0.00 0.00 0.00 3.18
3490 4018 2.107726 AGGACAGAGGGGGTGTTTTTAC 59.892 50.000 0.00 0.00 0.00 2.01
3491 4019 2.107552 CAGGACAGAGGGGGTGTTTTTA 59.892 50.000 0.00 0.00 0.00 1.52
3492 4020 1.133482 CAGGACAGAGGGGGTGTTTTT 60.133 52.381 0.00 0.00 0.00 1.94
3493 4021 0.478507 CAGGACAGAGGGGGTGTTTT 59.521 55.000 0.00 0.00 0.00 2.43
3494 4022 0.697854 ACAGGACAGAGGGGGTGTTT 60.698 55.000 0.00 0.00 0.00 2.83
3495 4023 0.192566 TACAGGACAGAGGGGGTGTT 59.807 55.000 0.00 0.00 0.00 3.32
3496 4024 0.417841 ATACAGGACAGAGGGGGTGT 59.582 55.000 0.00 0.00 0.00 4.16
3497 4025 2.471815 TATACAGGACAGAGGGGGTG 57.528 55.000 0.00 0.00 0.00 4.61
3498 4026 3.726837 ATTATACAGGACAGAGGGGGT 57.273 47.619 0.00 0.00 0.00 4.95
3499 4027 5.510861 CGTAAATTATACAGGACAGAGGGGG 60.511 48.000 0.00 0.00 0.00 5.40
3500 4028 5.510861 CCGTAAATTATACAGGACAGAGGGG 60.511 48.000 0.00 0.00 0.00 4.79
3501 4029 5.510861 CCCGTAAATTATACAGGACAGAGGG 60.511 48.000 0.00 0.00 0.00 4.30
3502 4030 5.303589 TCCCGTAAATTATACAGGACAGAGG 59.696 44.000 0.00 0.00 0.00 3.69
3503 4031 6.401047 TCCCGTAAATTATACAGGACAGAG 57.599 41.667 0.00 0.00 0.00 3.35
3504 4032 6.608405 TCTTCCCGTAAATTATACAGGACAGA 59.392 38.462 3.60 6.57 0.00 3.41
3505 4033 6.812998 TCTTCCCGTAAATTATACAGGACAG 58.187 40.000 3.60 5.17 0.00 3.51
3506 4034 6.795144 TCTTCCCGTAAATTATACAGGACA 57.205 37.500 3.60 0.00 0.00 4.02
3507 4035 6.649557 CCATCTTCCCGTAAATTATACAGGAC 59.350 42.308 3.60 0.00 0.00 3.85
3508 4036 6.743208 GCCATCTTCCCGTAAATTATACAGGA 60.743 42.308 0.00 0.00 0.00 3.86
3509 4037 5.411669 GCCATCTTCCCGTAAATTATACAGG 59.588 44.000 0.00 0.00 0.00 4.00
3510 4038 5.411669 GGCCATCTTCCCGTAAATTATACAG 59.588 44.000 0.00 0.00 0.00 2.74
3511 4039 5.072600 AGGCCATCTTCCCGTAAATTATACA 59.927 40.000 5.01 0.00 0.00 2.29
3512 4040 5.557866 AGGCCATCTTCCCGTAAATTATAC 58.442 41.667 5.01 0.00 0.00 1.47
3513 4041 5.836024 AGGCCATCTTCCCGTAAATTATA 57.164 39.130 5.01 0.00 0.00 0.98
3514 4042 4.724279 AGGCCATCTTCCCGTAAATTAT 57.276 40.909 5.01 0.00 0.00 1.28
3515 4043 4.457466 GAAGGCCATCTTCCCGTAAATTA 58.543 43.478 5.01 0.00 44.60 1.40
3516 4044 3.288092 GAAGGCCATCTTCCCGTAAATT 58.712 45.455 5.01 0.00 44.60 1.82
3517 4045 2.932261 GAAGGCCATCTTCCCGTAAAT 58.068 47.619 5.01 0.00 44.60 1.40
3518 4046 2.413310 GAAGGCCATCTTCCCGTAAA 57.587 50.000 5.01 0.00 44.60 2.01


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

AutoCloner maintained by Alex Coulton.