Multiple sequence alignment - TraesCS1B01G421400

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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 TraesCS1B01G421400 chr1B 100.000 2261 0 0 1 2261 645279128 645281388 0.000000e+00 4176.0
1 TraesCS1B01G421400 chr1B 76.258 775 135 33 793 1545 645303452 645304199 1.280000e-97 366.0
2 TraesCS1B01G421400 chr1B 79.135 532 79 19 793 1299 645275506 645274982 2.780000e-89 339.0
3 TraesCS1B01G421400 chr1B 74.938 810 139 34 1448 2244 645300813 645301571 1.690000e-81 313.0
4 TraesCS1B01G421400 chr1B 84.192 291 40 5 1426 1714 645274859 645274573 6.150000e-71 278.0
5 TraesCS1B01G421400 chr1B 77.532 316 57 12 956 1260 645319855 645320167 6.420000e-41 178.0
6 TraesCS1B01G421400 chr1D 85.973 1490 118 38 414 1856 467457728 467459173 0.000000e+00 1509.0
7 TraesCS1B01G421400 chr1D 80.614 521 73 21 794 1297 467467149 467467658 5.890000e-101 377.0
8 TraesCS1B01G421400 chr1D 89.655 261 24 3 2001 2259 467459374 467459633 1.670000e-86 329.0
9 TraesCS1B01G421400 chr1D 86.174 311 36 6 1426 1733 467467768 467468074 1.670000e-86 329.0
10 TraesCS1B01G421400 chr1D 82.609 299 44 2 970 1262 467487491 467487787 8.010000e-65 257.0
11 TraesCS1B01G421400 chr1D 76.031 509 88 23 1562 2061 467474483 467474966 1.350000e-57 233.0
12 TraesCS1B01G421400 chr1D 76.573 286 29 14 538 801 467466856 467467125 3.050000e-24 122.0
13 TraesCS1B01G421400 chr1D 76.307 287 33 14 538 801 467487036 467487310 1.100000e-23 121.0
14 TraesCS1B01G421400 chr1A 87.050 834 65 18 449 1262 559799884 559800694 0.000000e+00 902.0
15 TraesCS1B01G421400 chr1A 77.688 744 117 34 1426 2139 559837452 559838176 2.090000e-110 409.0
16 TraesCS1B01G421400 chr1A 79.696 527 76 19 793 1299 559836802 559837317 3.570000e-93 351.0
17 TraesCS1B01G421400 chr1A 80.872 413 50 17 793 1192 559808770 559809166 4.720000e-77 298.0
18 TraesCS1B01G421400 chr1A 76.829 246 25 10 538 764 559805861 559806093 2.370000e-20 110.0
19 TraesCS1B01G421400 chr1A 83.761 117 11 5 693 801 559836663 559836779 1.100000e-18 104.0
20 TraesCS1B01G421400 chr2D 81.275 251 38 8 24 272 588738368 588738611 6.370000e-46 195.0
21 TraesCS1B01G421400 chr7A 79.310 174 28 7 94 265 403189242 403189409 5.100000e-22 115.0
22 TraesCS1B01G421400 chrUn 83.333 108 18 0 158 265 85096759 85096866 1.430000e-17 100.0
23 TraesCS1B01G421400 chrUn 83.333 108 18 0 158 265 351964688 351964795 1.430000e-17 100.0
24 TraesCS1B01G421400 chrUn 92.857 56 4 0 211 266 88406723 88406668 5.180000e-12 82.4
25 TraesCS1B01G421400 chrUn 92.857 56 4 0 211 266 88458923 88458868 5.180000e-12 82.4
26 TraesCS1B01G421400 chr7B 92.857 56 4 0 211 266 732355686 732355741 5.180000e-12 82.4
27 TraesCS1B01G421400 chr7B 96.875 32 1 0 239 270 95339316 95339347 1.000000e-03 54.7
28 TraesCS1B01G421400 chr7B 100.000 29 0 0 239 267 640520838 640520866 1.000000e-03 54.7


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 TraesCS1B01G421400 chr1B 645279128 645281388 2260 False 4176.0 4176 100.000000 1 2261 1 chr1B.!!$F1 2260
1 TraesCS1B01G421400 chr1B 645300813 645304199 3386 False 339.5 366 75.598000 793 2244 2 chr1B.!!$F3 1451
2 TraesCS1B01G421400 chr1B 645274573 645275506 933 True 308.5 339 81.663500 793 1714 2 chr1B.!!$R1 921
3 TraesCS1B01G421400 chr1D 467457728 467459633 1905 False 919.0 1509 87.814000 414 2259 2 chr1D.!!$F2 1845
4 TraesCS1B01G421400 chr1D 467466856 467468074 1218 False 276.0 377 81.120333 538 1733 3 chr1D.!!$F3 1195
5 TraesCS1B01G421400 chr1A 559799884 559800694 810 False 902.0 902 87.050000 449 1262 1 chr1A.!!$F1 813
6 TraesCS1B01G421400 chr1A 559836663 559838176 1513 False 288.0 409 80.381667 693 2139 3 chr1A.!!$F3 1446
7 TraesCS1B01G421400 chr1A 559805861 559809166 3305 False 204.0 298 78.850500 538 1192 2 chr1A.!!$F2 654

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
913 3084 0.394565 ATATCGAGCCTCAACCTGCC 59.605 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 4582 0.24691 TGCCACCTTCGCGTGTATAA 59.753 50.0 5.77 0.0 31.47 0.98 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
29 30 4.356436 AGGGAGATTTTCTTCAAATGGGG 58.644 43.478 0.00 0.00 35.02 4.96
31 32 4.403752 GGGAGATTTTCTTCAAATGGGGAG 59.596 45.833 0.00 0.00 35.02 4.30
32 33 4.403752 GGAGATTTTCTTCAAATGGGGAGG 59.596 45.833 0.00 0.00 35.02 4.30
33 34 5.264395 GAGATTTTCTTCAAATGGGGAGGA 58.736 41.667 0.00 0.00 35.02 3.71
34 35 5.267587 AGATTTTCTTCAAATGGGGAGGAG 58.732 41.667 0.00 0.00 35.02 3.69
35 36 4.469469 TTTTCTTCAAATGGGGAGGAGT 57.531 40.909 0.00 0.00 0.00 3.85
37 38 5.592587 TTTCTTCAAATGGGGAGGAGTTA 57.407 39.130 0.00 0.00 0.00 2.24
40 41 5.509498 TCTTCAAATGGGGAGGAGTTATTG 58.491 41.667 0.00 0.00 0.00 1.90
41 42 4.249638 TCAAATGGGGAGGAGTTATTGG 57.750 45.455 0.00 0.00 0.00 3.16
46 47 2.110899 TGGGGAGGAGTTATTGGCAAAA 59.889 45.455 3.01 0.00 0.00 2.44
48 49 3.195610 GGGGAGGAGTTATTGGCAAAAAG 59.804 47.826 3.01 0.00 0.00 2.27
49 50 4.086457 GGGAGGAGTTATTGGCAAAAAGA 58.914 43.478 3.01 0.00 0.00 2.52
50 51 4.158579 GGGAGGAGTTATTGGCAAAAAGAG 59.841 45.833 3.01 0.00 0.00 2.85
51 52 4.380973 GGAGGAGTTATTGGCAAAAAGAGC 60.381 45.833 3.01 0.00 0.00 4.09
59 60 2.804697 GGCAAAAAGAGCCCGTTTAA 57.195 45.000 0.00 0.00 46.50 1.52
61 62 2.609491 GGCAAAAAGAGCCCGTTTAAGG 60.609 50.000 0.00 0.00 46.50 2.69
66 67 0.683412 AGAGCCCGTTTAAGGTCGTT 59.317 50.000 0.00 0.00 35.67 3.85
67 68 1.071228 AGAGCCCGTTTAAGGTCGTTT 59.929 47.619 0.00 0.00 35.67 3.60
70 71 3.264947 AGCCCGTTTAAGGTCGTTTATC 58.735 45.455 0.00 0.00 0.00 1.75
71 72 2.029606 GCCCGTTTAAGGTCGTTTATCG 59.970 50.000 0.00 0.00 41.41 2.92
72 73 3.253230 CCCGTTTAAGGTCGTTTATCGT 58.747 45.455 0.00 0.00 40.80 3.73
75 76 4.385447 CCGTTTAAGGTCGTTTATCGTGAA 59.615 41.667 0.00 0.00 40.80 3.18
78 79 1.986698 AGGTCGTTTATCGTGAACCG 58.013 50.000 0.00 0.00 38.45 4.44
79 80 1.270550 AGGTCGTTTATCGTGAACCGT 59.729 47.619 0.00 0.00 38.45 4.83
80 81 2.061028 GGTCGTTTATCGTGAACCGTT 58.939 47.619 0.00 0.00 40.80 4.44
81 82 3.057596 AGGTCGTTTATCGTGAACCGTTA 60.058 43.478 0.00 0.00 38.45 3.18
83 84 3.668191 GTCGTTTATCGTGAACCGTTACA 59.332 43.478 0.00 0.00 40.80 2.41
84 85 3.668191 TCGTTTATCGTGAACCGTTACAC 59.332 43.478 0.00 0.00 40.80 2.90
86 87 3.657015 TTATCGTGAACCGTTACACCA 57.343 42.857 0.00 0.00 37.94 4.17
87 88 2.754946 ATCGTGAACCGTTACACCAT 57.245 45.000 0.00 0.00 37.94 3.55
88 89 1.785768 TCGTGAACCGTTACACCATG 58.214 50.000 0.00 0.00 37.94 3.66
90 91 1.458064 CGTGAACCGTTACACCATGTC 59.542 52.381 0.00 0.00 34.05 3.06
91 92 2.762745 GTGAACCGTTACACCATGTCT 58.237 47.619 0.00 0.00 0.00 3.41
92 93 3.612241 CGTGAACCGTTACACCATGTCTA 60.612 47.826 0.00 0.00 34.05 2.59
94 95 3.321396 TGAACCGTTACACCATGTCTACA 59.679 43.478 0.00 0.00 0.00 2.74
95 96 4.202233 TGAACCGTTACACCATGTCTACAA 60.202 41.667 0.00 0.00 0.00 2.41
97 98 4.901868 ACCGTTACACCATGTCTACAAAT 58.098 39.130 0.00 0.00 0.00 2.32
101 102 6.456853 CCGTTACACCATGTCTACAAATGATG 60.457 42.308 0.00 0.00 0.00 3.07
102 103 6.456853 CGTTACACCATGTCTACAAATGATGG 60.457 42.308 0.00 0.00 39.66 3.51
104 105 3.067180 CACCATGTCTACAAATGATGGGC 59.933 47.826 0.00 0.00 38.33 5.36
105 106 3.053395 ACCATGTCTACAAATGATGGGCT 60.053 43.478 0.00 0.00 38.33 5.19
106 107 3.956199 CCATGTCTACAAATGATGGGCTT 59.044 43.478 0.00 0.00 31.56 4.35
107 108 4.037208 CCATGTCTACAAATGATGGGCTTC 59.963 45.833 0.00 0.00 31.56 3.86
121 122 3.732212 TGGGCTTCATCTGTCATAATCG 58.268 45.455 0.00 0.00 0.00 3.34
122 123 3.134623 TGGGCTTCATCTGTCATAATCGT 59.865 43.478 0.00 0.00 0.00 3.73
123 124 3.743396 GGGCTTCATCTGTCATAATCGTC 59.257 47.826 0.00 0.00 0.00 4.20
124 125 4.371786 GGCTTCATCTGTCATAATCGTCA 58.628 43.478 0.00 0.00 0.00 4.35
126 127 5.119898 GGCTTCATCTGTCATAATCGTCATC 59.880 44.000 0.00 0.00 0.00 2.92
127 128 5.693555 GCTTCATCTGTCATAATCGTCATCA 59.306 40.000 0.00 0.00 0.00 3.07
128 129 6.201615 GCTTCATCTGTCATAATCGTCATCAA 59.798 38.462 0.00 0.00 0.00 2.57
129 130 7.254556 GCTTCATCTGTCATAATCGTCATCAAA 60.255 37.037 0.00 0.00 0.00 2.69
131 132 8.080083 TCATCTGTCATAATCGTCATCAAATG 57.920 34.615 0.00 0.00 0.00 2.32
135 136 7.386025 TCTGTCATAATCGTCATCAAATGGATC 59.614 37.037 0.00 0.00 32.57 3.36
136 137 6.991531 TGTCATAATCGTCATCAAATGGATCA 59.008 34.615 0.00 0.00 32.57 2.92
137 138 7.498570 TGTCATAATCGTCATCAAATGGATCAA 59.501 33.333 0.00 0.00 32.57 2.57
138 139 8.344831 GTCATAATCGTCATCAAATGGATCAAA 58.655 33.333 0.00 0.00 32.57 2.69
139 140 8.562052 TCATAATCGTCATCAAATGGATCAAAG 58.438 33.333 0.00 0.00 32.57 2.77
140 141 6.764308 AATCGTCATCAAATGGATCAAAGT 57.236 33.333 0.00 0.00 32.57 2.66
141 142 6.764308 ATCGTCATCAAATGGATCAAAGTT 57.236 33.333 0.00 0.00 32.57 2.66
142 143 5.941733 TCGTCATCAAATGGATCAAAGTTG 58.058 37.500 0.00 0.00 32.57 3.16
143 144 5.473162 TCGTCATCAAATGGATCAAAGTTGT 59.527 36.000 7.44 0.00 32.57 3.32
146 147 7.147312 GTCATCAAATGGATCAAAGTTGTCAA 58.853 34.615 7.44 0.00 32.57 3.18
147 148 7.115378 GTCATCAAATGGATCAAAGTTGTCAAC 59.885 37.037 7.68 7.68 32.57 3.18
149 150 4.503741 AATGGATCAAAGTTGTCAACCG 57.496 40.909 12.17 1.90 0.00 4.44
151 152 3.546724 TGGATCAAAGTTGTCAACCGAA 58.453 40.909 12.17 0.00 0.00 4.30
152 153 3.563808 TGGATCAAAGTTGTCAACCGAAG 59.436 43.478 12.17 0.96 0.00 3.79
153 154 3.564225 GGATCAAAGTTGTCAACCGAAGT 59.436 43.478 12.17 0.00 0.00 3.01
188 189 9.033481 TGCAAAAGATTAAGTCAAAAATCTGTG 57.967 29.630 0.00 2.69 40.66 3.66
196 197 5.520376 AGTCAAAAATCTGTGGTTTCTGG 57.480 39.130 0.00 0.00 0.00 3.86
197 198 4.051237 GTCAAAAATCTGTGGTTTCTGGC 58.949 43.478 0.00 0.00 0.00 4.85
199 200 4.161189 TCAAAAATCTGTGGTTTCTGGCAA 59.839 37.500 0.00 0.00 0.00 4.52
220 221 4.776795 AAAAATCGCATACCGGAGTTTT 57.223 36.364 9.46 0.00 37.59 2.43
222 223 6.445357 AAAAATCGCATACCGGAGTTTTAT 57.555 33.333 9.46 0.00 37.59 1.40
223 224 5.418310 AAATCGCATACCGGAGTTTTATG 57.582 39.130 9.46 6.55 37.59 1.90
224 225 2.206750 TCGCATACCGGAGTTTTATGC 58.793 47.619 19.13 19.13 39.86 3.14
225 226 1.937223 CGCATACCGGAGTTTTATGCA 59.063 47.619 25.13 0.00 42.43 3.96
226 227 2.353269 CGCATACCGGAGTTTTATGCAA 59.647 45.455 25.13 0.00 42.43 4.08
227 228 3.181505 CGCATACCGGAGTTTTATGCAAA 60.182 43.478 25.13 0.00 42.43 3.68
228 229 4.102649 GCATACCGGAGTTTTATGCAAAC 58.897 43.478 22.44 0.00 44.73 2.93
243 244 4.177165 TGCAAACTTAGGCATCAATGTG 57.823 40.909 0.00 0.00 34.58 3.21
244 245 3.056678 TGCAAACTTAGGCATCAATGTGG 60.057 43.478 0.00 0.00 34.58 4.17
247 248 2.726821 ACTTAGGCATCAATGTGGTGG 58.273 47.619 0.00 0.00 0.00 4.61
249 250 2.897271 TAGGCATCAATGTGGTGGTT 57.103 45.000 0.00 0.00 0.00 3.67
250 251 2.014010 AGGCATCAATGTGGTGGTTT 57.986 45.000 0.00 0.00 0.00 3.27
251 252 2.328319 AGGCATCAATGTGGTGGTTTT 58.672 42.857 0.00 0.00 0.00 2.43
252 253 3.505386 AGGCATCAATGTGGTGGTTTTA 58.495 40.909 0.00 0.00 0.00 1.52
253 254 4.095946 AGGCATCAATGTGGTGGTTTTAT 58.904 39.130 0.00 0.00 0.00 1.40
254 255 4.081531 AGGCATCAATGTGGTGGTTTTATG 60.082 41.667 0.00 0.00 0.00 1.90
255 256 3.618150 GCATCAATGTGGTGGTTTTATGC 59.382 43.478 0.00 0.00 0.00 3.14
259 260 5.862845 TCAATGTGGTGGTTTTATGCAATT 58.137 33.333 0.00 0.00 0.00 2.32
261 262 4.944619 TGTGGTGGTTTTATGCAATTCA 57.055 36.364 0.00 0.00 0.00 2.57
262 263 4.626042 TGTGGTGGTTTTATGCAATTCAC 58.374 39.130 0.00 0.00 0.00 3.18
263 264 4.343526 TGTGGTGGTTTTATGCAATTCACT 59.656 37.500 0.00 0.00 0.00 3.41
264 265 4.923281 GTGGTGGTTTTATGCAATTCACTC 59.077 41.667 0.00 0.00 0.00 3.51
265 266 4.021544 TGGTGGTTTTATGCAATTCACTCC 60.022 41.667 0.00 0.00 0.00 3.85
266 267 4.021544 GGTGGTTTTATGCAATTCACTCCA 60.022 41.667 0.00 0.00 0.00 3.86
267 268 5.337491 GGTGGTTTTATGCAATTCACTCCAT 60.337 40.000 0.00 0.00 0.00 3.41
268 269 5.577945 GTGGTTTTATGCAATTCACTCCATG 59.422 40.000 0.00 0.00 0.00 3.66
269 270 5.245751 TGGTTTTATGCAATTCACTCCATGT 59.754 36.000 0.00 0.00 0.00 3.21
270 271 6.435591 TGGTTTTATGCAATTCACTCCATGTA 59.564 34.615 0.00 0.00 0.00 2.29
273 274 8.810427 GTTTTATGCAATTCACTCCATGTATTG 58.190 33.333 0.00 2.85 44.67 1.90
275 276 8.744568 TTATGCAATTCACTCCATGTATTGTA 57.255 30.769 0.00 4.48 44.07 2.41
276 277 7.828508 ATGCAATTCACTCCATGTATTGTAT 57.171 32.000 0.00 6.22 44.07 2.29
278 279 6.602803 TGCAATTCACTCCATGTATTGTATGT 59.397 34.615 7.72 0.00 44.07 2.29
279 280 7.772757 TGCAATTCACTCCATGTATTGTATGTA 59.227 33.333 7.72 0.00 44.07 2.29
287 288 9.712305 ACTCCATGTATTGTATGTATTCTTAGC 57.288 33.333 0.00 0.00 0.00 3.09
296 297 7.496529 TGTATGTATTCTTAGCAAATCCAGC 57.503 36.000 0.00 0.00 0.00 4.85
297 298 7.053498 TGTATGTATTCTTAGCAAATCCAGCA 58.947 34.615 0.00 0.00 0.00 4.41
299 300 4.332543 TGTATTCTTAGCAAATCCAGCACG 59.667 41.667 0.00 0.00 0.00 5.34
300 301 1.086696 TCTTAGCAAATCCAGCACGC 58.913 50.000 0.00 0.00 0.00 5.34
302 303 0.521291 TTAGCAAATCCAGCACGCAC 59.479 50.000 0.00 0.00 0.00 5.34
304 305 1.730547 GCAAATCCAGCACGCACAC 60.731 57.895 0.00 0.00 0.00 3.82
305 306 1.081242 CAAATCCAGCACGCACACC 60.081 57.895 0.00 0.00 0.00 4.16
306 307 2.268076 AAATCCAGCACGCACACCC 61.268 57.895 0.00 0.00 0.00 4.61
308 309 3.907260 ATCCAGCACGCACACCCTG 62.907 63.158 0.00 0.00 0.00 4.45
319 320 3.927555 ACACCCTGTGAACCGTATG 57.072 52.632 0.49 0.00 36.96 2.39
320 321 1.344065 ACACCCTGTGAACCGTATGA 58.656 50.000 0.49 0.00 36.96 2.15
321 322 1.906574 ACACCCTGTGAACCGTATGAT 59.093 47.619 0.49 0.00 36.96 2.45
322 323 2.279741 CACCCTGTGAACCGTATGATG 58.720 52.381 0.00 0.00 35.23 3.07
323 324 2.093711 CACCCTGTGAACCGTATGATGA 60.094 50.000 0.00 0.00 35.23 2.92
325 326 3.008594 ACCCTGTGAACCGTATGATGAAA 59.991 43.478 0.00 0.00 0.00 2.69
332 333 7.081349 TGTGAACCGTATGATGAAAATGTTTC 58.919 34.615 0.00 0.00 0.00 2.78
333 334 7.081349 GTGAACCGTATGATGAAAATGTTTCA 58.919 34.615 5.92 5.92 0.00 2.69
335 336 8.138074 TGAACCGTATGATGAAAATGTTTCAAA 58.862 29.630 7.45 0.75 31.55 2.69
336 337 9.139174 GAACCGTATGATGAAAATGTTTCAAAT 57.861 29.630 7.45 7.29 31.55 2.32
354 355 9.076596 GTTTCAAATATCTGTGAACTAATTGGC 57.923 33.333 0.00 0.00 33.58 4.52
356 357 8.347004 TCAAATATCTGTGAACTAATTGGCAA 57.653 30.769 0.68 0.68 0.00 4.52
357 358 8.461222 TCAAATATCTGTGAACTAATTGGCAAG 58.539 33.333 5.96 0.00 0.00 4.01
358 359 7.944729 AATATCTGTGAACTAATTGGCAAGT 57.055 32.000 5.96 5.58 0.00 3.16
360 361 4.713553 TCTGTGAACTAATTGGCAAGTCA 58.286 39.130 2.32 0.00 0.00 3.41
363 364 5.587289 TGTGAACTAATTGGCAAGTCAAAC 58.413 37.500 2.32 0.00 0.00 2.93
364 365 4.982295 GTGAACTAATTGGCAAGTCAAACC 59.018 41.667 2.32 0.00 0.00 3.27
366 367 2.030274 ACTAATTGGCAAGTCAAACCGC 60.030 45.455 2.32 0.00 0.00 5.68
369 370 3.365535 GGCAAGTCAAACCGCCAT 58.634 55.556 0.00 0.00 44.25 4.40
371 372 1.080569 GCAAGTCAAACCGCCATGG 60.081 57.895 7.63 7.63 46.41 3.66
372 373 1.080569 CAAGTCAAACCGCCATGGC 60.081 57.895 27.67 27.67 43.94 4.40
373 374 2.275380 AAGTCAAACCGCCATGGCC 61.275 57.895 30.79 14.73 43.94 5.36
377 378 3.370231 AAACCGCCATGGCCGAAC 61.370 61.111 30.79 3.46 43.94 3.95
382 383 2.828549 GCCATGGCCGAACCGAAT 60.829 61.111 27.24 0.00 43.94 3.34
383 384 2.414785 GCCATGGCCGAACCGAATT 61.415 57.895 27.24 0.00 43.94 2.17
385 386 1.384525 CCATGGCCGAACCGAATTAA 58.615 50.000 0.00 0.00 43.94 1.40
387 388 2.031157 CCATGGCCGAACCGAATTAATC 60.031 50.000 0.00 0.00 43.94 1.75
390 391 1.332686 GGCCGAACCGAATTAATCCAC 59.667 52.381 0.00 0.00 0.00 4.02
391 392 2.011222 GCCGAACCGAATTAATCCACA 58.989 47.619 0.00 0.00 0.00 4.17
392 393 2.223180 GCCGAACCGAATTAATCCACAC 60.223 50.000 0.00 0.00 0.00 3.82
393 394 2.353579 CCGAACCGAATTAATCCACACC 59.646 50.000 0.00 0.00 0.00 4.16
395 396 3.308866 CGAACCGAATTAATCCACACCTC 59.691 47.826 0.00 0.00 0.00 3.85
396 397 2.901249 ACCGAATTAATCCACACCTCG 58.099 47.619 0.00 0.00 0.00 4.63
397 398 1.597663 CCGAATTAATCCACACCTCGC 59.402 52.381 0.00 0.00 0.00 5.03
399 400 1.597663 GAATTAATCCACACCTCGCCG 59.402 52.381 0.00 0.00 0.00 6.46
400 401 0.828022 ATTAATCCACACCTCGCCGA 59.172 50.000 0.00 0.00 0.00 5.54
402 403 2.292794 TAATCCACACCTCGCCGAGC 62.293 60.000 9.01 0.00 0.00 5.03
431 432 2.511373 CGGCCATTAGCTGCACGA 60.511 61.111 2.24 0.00 42.11 4.35
432 433 2.528743 CGGCCATTAGCTGCACGAG 61.529 63.158 2.24 0.00 42.11 4.18
444 445 4.386245 CACGAGGTCGAGCTTAGC 57.614 61.111 19.66 5.12 43.02 3.09
445 446 1.226717 CACGAGGTCGAGCTTAGCC 60.227 63.158 19.66 4.73 43.02 3.93
446 447 2.413765 CGAGGTCGAGCTTAGCCC 59.586 66.667 19.66 4.33 43.02 5.19
475 476 4.697756 CCGTCGAAGCAAGGGCCA 62.698 66.667 6.18 0.00 42.56 5.36
552 2629 1.762957 TCCAACCTATCAGTGCTAGCC 59.237 52.381 13.29 3.49 0.00 3.93
565 2642 2.126882 TGCTAGCCACTCCATTACCAT 58.873 47.619 13.29 0.00 0.00 3.55
566 2643 3.071023 GTGCTAGCCACTCCATTACCATA 59.929 47.826 13.29 0.00 41.35 2.74
567 2644 3.071023 TGCTAGCCACTCCATTACCATAC 59.929 47.826 13.29 0.00 0.00 2.39
568 2645 3.557264 GCTAGCCACTCCATTACCATACC 60.557 52.174 2.29 0.00 0.00 2.73
569 2646 2.487775 AGCCACTCCATTACCATACCA 58.512 47.619 0.00 0.00 0.00 3.25
575 2652 3.244215 ACTCCATTACCATACCAGCATCG 60.244 47.826 0.00 0.00 0.00 3.84
679 2772 2.860628 GCCGTCTTATCGCACGCTG 61.861 63.158 0.00 0.00 34.58 5.18
774 2875 5.416013 ACCGATCTGATATGCTTTATCTCGA 59.584 40.000 13.69 0.00 0.00 4.04
847 2986 3.067106 CACGCCTATATAAACCAGCCAG 58.933 50.000 0.00 0.00 0.00 4.85
866 3005 3.179284 TCCAGCTTGGAATGGGCA 58.821 55.556 2.78 0.00 45.00 5.36
867 3006 1.699137 TCCAGCTTGGAATGGGCAT 59.301 52.632 2.78 0.00 45.00 4.40
868 3007 0.396139 TCCAGCTTGGAATGGGCATC 60.396 55.000 2.78 0.00 45.00 3.91
870 3009 1.075748 AGCTTGGAATGGGCATCCC 60.076 57.895 0.00 0.00 45.71 3.85
885 3024 1.609072 CATCCCATGCATTCAGCTCAG 59.391 52.381 0.00 0.00 45.94 3.35
908 3068 3.431572 GCATTGAGATATCGAGCCTCAAC 59.568 47.826 21.37 11.43 45.92 3.18
913 3084 0.394565 ATATCGAGCCTCAACCTGCC 59.605 55.000 0.00 0.00 0.00 4.85
1066 3246 1.685355 GCTCCTGCTTCTCTCCTCCC 61.685 65.000 0.00 0.00 36.03 4.30
1067 3247 0.325110 CTCCTGCTTCTCTCCTCCCA 60.325 60.000 0.00 0.00 0.00 4.37
1115 3295 0.107456 CAATGGGATCACGGGAGAGG 59.893 60.000 0.00 0.00 0.00 3.69
1116 3299 1.700042 AATGGGATCACGGGAGAGGC 61.700 60.000 0.00 0.00 0.00 4.70
1262 3460 1.136529 CGATCCGCAGCATCATTAACG 60.137 52.381 0.00 0.00 0.00 3.18
1264 3462 0.813610 TCCGCAGCATCATTAACGGG 60.814 55.000 0.00 0.00 40.95 5.28
1265 3463 0.813610 CCGCAGCATCATTAACGGGA 60.814 55.000 0.00 0.00 37.04 5.14
1267 3465 1.806247 CGCAGCATCATTAACGGGAGA 60.806 52.381 0.00 0.00 0.00 3.71
1272 3471 2.760374 CATCATTAACGGGAGAGAGGC 58.240 52.381 0.00 0.00 0.00 4.70
1280 3479 3.775654 GGAGAGAGGCCACGGTGG 61.776 72.222 22.87 22.87 41.55 4.61
1299 3498 4.065088 GTGGATGCAGTTTCTCTACAACA 58.935 43.478 0.00 0.00 0.00 3.33
1300 3499 4.515191 GTGGATGCAGTTTCTCTACAACAA 59.485 41.667 0.00 0.00 0.00 2.83
1301 3500 5.182001 GTGGATGCAGTTTCTCTACAACAAT 59.818 40.000 0.00 0.00 0.00 2.71
1302 3501 6.371548 GTGGATGCAGTTTCTCTACAACAATA 59.628 38.462 0.00 0.00 0.00 1.90
1303 3502 7.066284 GTGGATGCAGTTTCTCTACAACAATAT 59.934 37.037 0.00 0.00 0.00 1.28
1304 3503 7.066163 TGGATGCAGTTTCTCTACAACAATATG 59.934 37.037 0.00 0.00 0.00 1.78
1305 3504 7.066284 GGATGCAGTTTCTCTACAACAATATGT 59.934 37.037 0.00 0.00 37.32 2.29
1306 3505 7.744087 TGCAGTTTCTCTACAACAATATGTT 57.256 32.000 0.00 0.00 42.08 2.71
1307 3506 8.165239 TGCAGTTTCTCTACAACAATATGTTT 57.835 30.769 0.00 0.00 38.77 2.83
1308 3507 9.278978 TGCAGTTTCTCTACAACAATATGTTTA 57.721 29.630 0.00 0.00 38.77 2.01
1323 3522 9.231297 ACAATATGTTTACCTGGCATCATATAC 57.769 33.333 11.65 0.00 31.24 1.47
1324 3523 9.453572 CAATATGTTTACCTGGCATCATATACT 57.546 33.333 11.65 0.72 31.24 2.12
1325 3524 9.672673 AATATGTTTACCTGGCATCATATACTC 57.327 33.333 11.65 0.00 31.24 2.59
1326 3525 5.865085 TGTTTACCTGGCATCATATACTCC 58.135 41.667 0.00 0.00 0.00 3.85
1344 3543 2.036475 CTCCTACATGGGACCTGAATCG 59.964 54.545 0.00 0.00 36.20 3.34
1353 3552 3.067833 GGGACCTGAATCGCTAAATAGC 58.932 50.000 2.27 2.27 45.62 2.97
1364 3604 2.989840 CGCTAAATAGCCGAAGAGATGG 59.010 50.000 6.84 0.00 46.34 3.51
1541 3814 2.909504 TAGCCACCCCTTTGCATAAA 57.090 45.000 0.00 0.00 0.00 1.40
1575 3853 3.258372 TGGGATTGTCTATCATAGTCGGC 59.742 47.826 0.00 0.00 34.77 5.54
1621 3899 5.163437 CCCTACCACACTCTAGTATTTGGAC 60.163 48.000 10.18 0.00 0.00 4.02
1754 4147 3.762823 CTCGGTTAAGGTCCTAGACTTGT 59.237 47.826 0.00 0.00 32.47 3.16
1757 4150 4.617762 CGGTTAAGGTCCTAGACTTGTCAC 60.618 50.000 3.49 0.00 32.47 3.67
1764 4157 1.798813 CCTAGACTTGTCACGGTTTGC 59.201 52.381 3.49 0.00 0.00 3.68
1766 4159 0.107410 AGACTTGTCACGGTTTGCCA 60.107 50.000 3.49 0.00 34.09 4.92
1767 4160 0.307760 GACTTGTCACGGTTTGCCAG 59.692 55.000 0.00 0.00 34.09 4.85
1794 4187 8.168058 ACTTTCCTAGGTTTATTTCAGGCTTTA 58.832 33.333 9.08 0.00 0.00 1.85
1844 4238 4.110482 GTCCATTAACTACGATGCGTCTT 58.890 43.478 4.05 0.00 41.54 3.01
1867 4261 5.152623 TGGTGACTTAGTCAATCTCAAGG 57.847 43.478 17.25 0.00 44.49 3.61
1868 4262 3.935828 GGTGACTTAGTCAATCTCAAGGC 59.064 47.826 17.25 1.12 44.49 4.35
1869 4263 3.614616 GTGACTTAGTCAATCTCAAGGCG 59.385 47.826 17.25 0.00 44.49 5.52
1892 4291 2.069465 CTCGGTCTCCCAGAGATGCG 62.069 65.000 0.00 0.00 40.98 4.73
1899 4298 3.508012 GTCTCCCAGAGATGCGTATACAT 59.492 47.826 3.32 0.00 40.98 2.29
1903 4302 4.217767 TCCCAGAGATGCGTATACATGTAC 59.782 45.833 7.96 0.00 0.00 2.90
1917 4316 7.274686 CGTATACATGTACAATGAGTGTGTGAA 59.725 37.037 7.96 0.00 41.89 3.18
1931 4330 3.073678 TGTGTGAACATGTATGTGAGCC 58.926 45.455 0.00 0.00 41.61 4.70
1949 4348 1.001158 GCCTCCGTGTCTATACTCTGC 60.001 57.143 0.00 0.00 0.00 4.26
1955 4354 3.628032 CCGTGTCTATACTCTGCTTCTCA 59.372 47.826 0.00 0.00 0.00 3.27
1958 4357 5.513495 CGTGTCTATACTCTGCTTCTCAAAC 59.487 44.000 0.00 0.00 0.00 2.93
1959 4358 6.390721 GTGTCTATACTCTGCTTCTCAAACA 58.609 40.000 0.00 0.00 0.00 2.83
1962 4361 7.385205 TGTCTATACTCTGCTTCTCAAACAAAC 59.615 37.037 0.00 0.00 0.00 2.93
1964 4363 6.942532 ATACTCTGCTTCTCAAACAAACAA 57.057 33.333 0.00 0.00 0.00 2.83
1990 4394 9.457436 AAAAACCATCGACTTAGGTAAATACAT 57.543 29.630 0.00 0.00 34.63 2.29
1995 4399 9.760077 CCATCGACTTAGGTAAATACATACTTT 57.240 33.333 0.00 0.00 0.00 2.66
1999 4403 9.245962 CGACTTAGGTAAATACATACTTTCAGG 57.754 37.037 0.00 0.00 0.00 3.86
2061 4466 5.731599 CAGATCACTGCCATTTTACTCTC 57.268 43.478 0.00 0.00 37.33 3.20
2065 4470 4.973168 TCACTGCCATTTTACTCTCTGTT 58.027 39.130 0.00 0.00 0.00 3.16
2072 4477 6.174049 GCCATTTTACTCTCTGTTAGTTCCT 58.826 40.000 0.00 0.00 0.00 3.36
2088 4494 1.034838 TCCTCTCGCCTTCAGCTCTC 61.035 60.000 0.00 0.00 40.39 3.20
2105 4511 1.833630 TCTCCACCTGACATCACCATC 59.166 52.381 0.00 0.00 0.00 3.51
2119 4525 3.472652 TCACCATCACTAAAAGTTGCGT 58.527 40.909 0.00 0.00 0.00 5.24
2121 4527 3.249799 CACCATCACTAAAAGTTGCGTCA 59.750 43.478 0.00 0.00 0.00 4.35
2122 4528 3.880490 ACCATCACTAAAAGTTGCGTCAA 59.120 39.130 0.00 0.00 0.00 3.18
2176 4582 2.866378 GGGGGTGATGGGGGTTTT 59.134 61.111 0.00 0.00 0.00 2.43
2182 4588 3.309994 GGGGTGATGGGGGTTTTTATACA 60.310 47.826 0.00 0.00 0.00 2.29
2186 4592 1.451067 TGGGGGTTTTTATACACGCG 58.549 50.000 3.53 3.53 37.20 6.01
2191 4597 2.743664 GGGTTTTTATACACGCGAAGGT 59.256 45.455 15.93 10.76 0.00 3.50
2196 4602 0.458889 TATACACGCGAAGGTGGCAC 60.459 55.000 15.93 9.70 42.23 5.01
2234 4640 0.179129 GGCTGATTTCCCGCATGTTG 60.179 55.000 0.00 0.00 0.00 3.33
2244 4650 1.468985 CCGCATGTTGGTGGGAAATA 58.531 50.000 0.00 0.00 34.75 1.40
2245 4651 2.031120 CCGCATGTTGGTGGGAAATAT 58.969 47.619 0.00 0.00 34.75 1.28
2255 4661 4.352009 TGGTGGGAAATATGTGCTGATTT 58.648 39.130 0.00 0.00 0.00 2.17
2259 4665 3.374745 GGAAATATGTGCTGATTTGCCG 58.625 45.455 0.00 0.00 29.82 5.69
2260 4666 2.497107 AATATGTGCTGATTTGCCGC 57.503 45.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.784550 CCCCATTTGAAGAAAATCTCCCTATAA 59.215 37.037 0.00 0.00 36.28 0.98
5 6 6.068260 TCCCCATTTGAAGAAAATCTCCCTAT 60.068 38.462 0.00 0.00 36.28 2.57
7 8 4.045846 TCCCCATTTGAAGAAAATCTCCCT 59.954 41.667 0.00 0.00 36.28 4.20
10 11 5.264395 TCCTCCCCATTTGAAGAAAATCTC 58.736 41.667 0.00 0.00 36.28 2.75
11 12 5.222421 ACTCCTCCCCATTTGAAGAAAATCT 60.222 40.000 0.00 0.00 36.28 2.40
12 13 5.019470 ACTCCTCCCCATTTGAAGAAAATC 58.981 41.667 0.00 0.00 36.28 2.17
14 15 4.469469 ACTCCTCCCCATTTGAAGAAAA 57.531 40.909 0.00 0.00 0.00 2.29
17 18 5.509498 CAATAACTCCTCCCCATTTGAAGA 58.491 41.667 0.00 0.00 0.00 2.87
18 19 4.646492 CCAATAACTCCTCCCCATTTGAAG 59.354 45.833 0.00 0.00 0.00 3.02
20 21 3.627237 GCCAATAACTCCTCCCCATTTGA 60.627 47.826 0.00 0.00 0.00 2.69
21 22 2.695147 GCCAATAACTCCTCCCCATTTG 59.305 50.000 0.00 0.00 0.00 2.32
24 25 1.607225 TGCCAATAACTCCTCCCCAT 58.393 50.000 0.00 0.00 0.00 4.00
26 27 2.525105 TTTGCCAATAACTCCTCCCC 57.475 50.000 0.00 0.00 0.00 4.81
29 30 4.738124 GCTCTTTTTGCCAATAACTCCTC 58.262 43.478 0.00 0.00 0.00 3.71
41 42 2.035449 ACCTTAAACGGGCTCTTTTTGC 59.965 45.455 0.00 0.00 0.00 3.68
46 47 0.683412 ACGACCTTAAACGGGCTCTT 59.317 50.000 0.00 0.00 0.00 2.85
48 49 1.516161 AAACGACCTTAAACGGGCTC 58.484 50.000 0.00 0.00 0.00 4.70
49 50 2.837532 TAAACGACCTTAAACGGGCT 57.162 45.000 0.00 0.00 0.00 5.19
50 51 2.029606 CGATAAACGACCTTAAACGGGC 59.970 50.000 0.00 0.00 45.77 6.13
51 52 3.061161 CACGATAAACGACCTTAAACGGG 59.939 47.826 0.00 0.00 45.77 5.28
52 53 3.919804 TCACGATAAACGACCTTAAACGG 59.080 43.478 0.00 0.00 45.77 4.44
53 54 5.300393 GTTCACGATAAACGACCTTAAACG 58.700 41.667 0.00 0.00 45.77 3.60
54 55 5.611919 GGTTCACGATAAACGACCTTAAAC 58.388 41.667 0.00 0.00 45.77 2.01
71 72 2.762745 AGACATGGTGTAACGGTTCAC 58.237 47.619 0.93 0.93 38.12 3.18
72 73 3.321396 TGTAGACATGGTGTAACGGTTCA 59.679 43.478 0.00 0.00 38.12 3.18
75 76 4.339872 TTTGTAGACATGGTGTAACGGT 57.660 40.909 0.00 0.00 38.12 4.83
78 79 6.183360 CCCATCATTTGTAGACATGGTGTAAC 60.183 42.308 0.00 0.00 30.58 2.50
79 80 5.885352 CCCATCATTTGTAGACATGGTGTAA 59.115 40.000 0.00 0.00 30.58 2.41
80 81 5.436175 CCCATCATTTGTAGACATGGTGTA 58.564 41.667 0.00 0.00 30.58 2.90
81 82 4.272489 CCCATCATTTGTAGACATGGTGT 58.728 43.478 0.00 0.00 30.58 4.16
83 84 3.053395 AGCCCATCATTTGTAGACATGGT 60.053 43.478 0.00 0.00 0.00 3.55
84 85 3.559069 AGCCCATCATTTGTAGACATGG 58.441 45.455 0.00 0.00 0.00 3.66
86 87 4.858850 TGAAGCCCATCATTTGTAGACAT 58.141 39.130 0.00 0.00 0.00 3.06
87 88 4.299586 TGAAGCCCATCATTTGTAGACA 57.700 40.909 0.00 0.00 0.00 3.41
101 102 3.733337 ACGATTATGACAGATGAAGCCC 58.267 45.455 0.00 0.00 0.00 5.19
102 103 4.371786 TGACGATTATGACAGATGAAGCC 58.628 43.478 0.00 0.00 0.00 4.35
104 105 7.704789 TTGATGACGATTATGACAGATGAAG 57.295 36.000 0.00 0.00 0.00 3.02
105 106 8.553696 CATTTGATGACGATTATGACAGATGAA 58.446 33.333 0.00 0.00 0.00 2.57
106 107 7.172019 CCATTTGATGACGATTATGACAGATGA 59.828 37.037 0.00 0.00 0.00 2.92
107 108 7.172019 TCCATTTGATGACGATTATGACAGATG 59.828 37.037 0.00 0.00 0.00 2.90
111 112 6.991531 TGATCCATTTGATGACGATTATGACA 59.008 34.615 0.00 0.00 32.41 3.58
113 114 8.449251 TTTGATCCATTTGATGACGATTATGA 57.551 30.769 0.00 0.00 32.41 2.15
114 115 8.347771 ACTTTGATCCATTTGATGACGATTATG 58.652 33.333 0.00 0.00 32.41 1.90
115 116 8.455903 ACTTTGATCCATTTGATGACGATTAT 57.544 30.769 0.00 0.00 32.41 1.28
117 118 6.764308 ACTTTGATCCATTTGATGACGATT 57.236 33.333 0.00 0.00 32.41 3.34
118 119 6.151648 ACAACTTTGATCCATTTGATGACGAT 59.848 34.615 0.00 0.00 32.41 3.73
119 120 5.473162 ACAACTTTGATCCATTTGATGACGA 59.527 36.000 0.00 0.00 32.41 4.20
121 122 6.680810 TGACAACTTTGATCCATTTGATGAC 58.319 36.000 0.00 0.00 32.41 3.06
122 123 6.897706 TGACAACTTTGATCCATTTGATGA 57.102 33.333 0.00 0.00 32.41 2.92
123 124 6.366877 GGTTGACAACTTTGATCCATTTGATG 59.633 38.462 17.52 0.00 32.41 3.07
124 125 6.458210 GGTTGACAACTTTGATCCATTTGAT 58.542 36.000 17.52 0.00 36.01 2.57
126 127 4.681025 CGGTTGACAACTTTGATCCATTTG 59.319 41.667 17.52 0.00 0.00 2.32
127 128 4.582656 TCGGTTGACAACTTTGATCCATTT 59.417 37.500 17.52 0.00 0.00 2.32
128 129 4.141287 TCGGTTGACAACTTTGATCCATT 58.859 39.130 17.52 0.00 0.00 3.16
129 130 3.750371 TCGGTTGACAACTTTGATCCAT 58.250 40.909 17.52 0.00 0.00 3.41
131 132 3.564225 ACTTCGGTTGACAACTTTGATCC 59.436 43.478 17.52 0.00 0.00 3.36
167 168 9.750125 GAAACCACAGATTTTTGACTTAATCTT 57.250 29.630 0.00 0.00 38.66 2.40
169 170 9.185192 CAGAAACCACAGATTTTTGACTTAATC 57.815 33.333 0.00 0.00 0.00 1.75
170 171 8.143835 CCAGAAACCACAGATTTTTGACTTAAT 58.856 33.333 0.00 0.00 0.00 1.40
171 172 7.488322 CCAGAAACCACAGATTTTTGACTTAA 58.512 34.615 0.00 0.00 0.00 1.85
172 173 6.460953 GCCAGAAACCACAGATTTTTGACTTA 60.461 38.462 0.00 0.00 0.00 2.24
174 175 4.202151 GCCAGAAACCACAGATTTTTGACT 60.202 41.667 0.00 0.00 0.00 3.41
176 177 3.703556 TGCCAGAAACCACAGATTTTTGA 59.296 39.130 0.00 0.00 0.00 2.69
180 181 4.751767 TTTTGCCAGAAACCACAGATTT 57.248 36.364 0.00 0.00 0.00 2.17
181 182 4.751767 TTTTTGCCAGAAACCACAGATT 57.248 36.364 0.00 0.00 0.00 2.40
199 200 4.776795 AAAACTCCGGTATGCGATTTTT 57.223 36.364 0.00 0.00 0.00 1.94
203 204 2.806244 GCATAAAACTCCGGTATGCGAT 59.194 45.455 15.68 0.00 40.36 4.58
222 223 3.056678 CCACATTGATGCCTAAGTTTGCA 60.057 43.478 2.68 2.68 42.52 4.08
223 224 3.056607 ACCACATTGATGCCTAAGTTTGC 60.057 43.478 0.00 0.00 0.00 3.68
224 225 4.487948 CACCACATTGATGCCTAAGTTTG 58.512 43.478 0.00 0.00 0.00 2.93
225 226 3.511146 CCACCACATTGATGCCTAAGTTT 59.489 43.478 0.00 0.00 0.00 2.66
226 227 3.091545 CCACCACATTGATGCCTAAGTT 58.908 45.455 0.00 0.00 0.00 2.66
227 228 2.041620 ACCACCACATTGATGCCTAAGT 59.958 45.455 0.00 0.00 0.00 2.24
228 229 2.726821 ACCACCACATTGATGCCTAAG 58.273 47.619 0.00 0.00 0.00 2.18
231 232 2.014010 AAACCACCACATTGATGCCT 57.986 45.000 0.00 0.00 0.00 4.75
233 234 3.618150 GCATAAAACCACCACATTGATGC 59.382 43.478 0.00 0.00 0.00 3.91
234 235 4.818642 TGCATAAAACCACCACATTGATG 58.181 39.130 0.00 0.00 0.00 3.07
239 240 5.011943 AGTGAATTGCATAAAACCACCACAT 59.988 36.000 0.00 0.00 0.00 3.21
240 241 4.343526 AGTGAATTGCATAAAACCACCACA 59.656 37.500 0.00 0.00 0.00 4.17
242 243 4.021544 GGAGTGAATTGCATAAAACCACCA 60.022 41.667 0.00 0.00 0.00 4.17
243 244 4.021544 TGGAGTGAATTGCATAAAACCACC 60.022 41.667 0.00 0.00 0.00 4.61
244 245 5.132897 TGGAGTGAATTGCATAAAACCAC 57.867 39.130 0.00 0.00 0.00 4.16
247 248 8.810427 CAATACATGGAGTGAATTGCATAAAAC 58.190 33.333 0.00 0.00 0.00 2.43
249 250 8.065473 ACAATACATGGAGTGAATTGCATAAA 57.935 30.769 13.34 0.00 32.02 1.40
250 251 7.643569 ACAATACATGGAGTGAATTGCATAA 57.356 32.000 13.34 0.00 32.02 1.90
251 252 8.785946 CATACAATACATGGAGTGAATTGCATA 58.214 33.333 13.34 0.00 32.02 3.14
252 253 7.286087 ACATACAATACATGGAGTGAATTGCAT 59.714 33.333 13.34 0.00 32.02 3.96
253 254 6.602803 ACATACAATACATGGAGTGAATTGCA 59.397 34.615 13.34 0.00 32.02 4.08
254 255 7.031226 ACATACAATACATGGAGTGAATTGC 57.969 36.000 13.34 0.00 32.02 3.56
261 262 9.712305 GCTAAGAATACATACAATACATGGAGT 57.288 33.333 0.00 0.00 0.00 3.85
262 263 9.710900 TGCTAAGAATACATACAATACATGGAG 57.289 33.333 0.00 0.00 0.00 3.86
270 271 8.571336 GCTGGATTTGCTAAGAATACATACAAT 58.429 33.333 0.00 0.00 27.53 2.71
273 274 7.355778 GTGCTGGATTTGCTAAGAATACATAC 58.644 38.462 0.00 0.00 27.53 2.39
275 276 5.008019 CGTGCTGGATTTGCTAAGAATACAT 59.992 40.000 0.00 0.00 27.53 2.29
276 277 4.332543 CGTGCTGGATTTGCTAAGAATACA 59.667 41.667 0.00 0.00 0.00 2.29
278 279 3.312421 GCGTGCTGGATTTGCTAAGAATA 59.688 43.478 0.00 0.00 0.00 1.75
279 280 2.098117 GCGTGCTGGATTTGCTAAGAAT 59.902 45.455 0.00 0.00 0.00 2.40
281 282 1.086696 GCGTGCTGGATTTGCTAAGA 58.913 50.000 0.00 0.00 0.00 2.10
282 283 0.804364 TGCGTGCTGGATTTGCTAAG 59.196 50.000 0.00 0.00 0.00 2.18
283 284 0.521291 GTGCGTGCTGGATTTGCTAA 59.479 50.000 0.00 0.00 0.00 3.09
287 288 1.081242 GGTGTGCGTGCTGGATTTG 60.081 57.895 0.00 0.00 0.00 2.32
289 290 2.672996 GGGTGTGCGTGCTGGATT 60.673 61.111 0.00 0.00 0.00 3.01
291 292 4.624364 CAGGGTGTGCGTGCTGGA 62.624 66.667 0.00 0.00 0.00 3.86
292 293 4.935495 ACAGGGTGTGCGTGCTGG 62.935 66.667 0.00 0.00 0.00 4.85
293 294 3.653009 CACAGGGTGTGCGTGCTG 61.653 66.667 0.00 0.00 41.89 4.41
302 303 2.093711 TCATCATACGGTTCACAGGGTG 60.094 50.000 0.00 0.00 34.45 4.61
304 305 2.979814 TCATCATACGGTTCACAGGG 57.020 50.000 0.00 0.00 0.00 4.45
305 306 5.123820 ACATTTTCATCATACGGTTCACAGG 59.876 40.000 0.00 0.00 0.00 4.00
306 307 6.182039 ACATTTTCATCATACGGTTCACAG 57.818 37.500 0.00 0.00 0.00 3.66
308 309 7.081349 TGAAACATTTTCATCATACGGTTCAC 58.919 34.615 0.00 0.00 0.00 3.18
332 333 8.246180 ACTTGCCAATTAGTTCACAGATATTTG 58.754 33.333 0.00 0.00 0.00 2.32
333 334 8.353423 ACTTGCCAATTAGTTCACAGATATTT 57.647 30.769 0.00 0.00 0.00 1.40
335 336 7.112122 TGACTTGCCAATTAGTTCACAGATAT 58.888 34.615 0.00 0.00 0.00 1.63
336 337 6.472016 TGACTTGCCAATTAGTTCACAGATA 58.528 36.000 0.00 0.00 0.00 1.98
337 338 5.316167 TGACTTGCCAATTAGTTCACAGAT 58.684 37.500 0.00 0.00 0.00 2.90
341 342 4.982295 GGTTTGACTTGCCAATTAGTTCAC 59.018 41.667 0.00 0.00 0.00 3.18
342 343 4.261405 CGGTTTGACTTGCCAATTAGTTCA 60.261 41.667 0.00 0.00 0.00 3.18
344 345 3.552068 GCGGTTTGACTTGCCAATTAGTT 60.552 43.478 0.00 0.00 0.00 2.24
346 347 2.595386 GCGGTTTGACTTGCCAATTAG 58.405 47.619 0.00 0.00 0.00 1.73
347 348 1.271102 GGCGGTTTGACTTGCCAATTA 59.729 47.619 9.07 0.00 46.76 1.40
349 350 1.665442 GGCGGTTTGACTTGCCAAT 59.335 52.632 9.07 0.00 46.76 3.16
350 351 3.124686 GGCGGTTTGACTTGCCAA 58.875 55.556 9.07 0.00 46.76 4.52
354 355 1.080569 GCCATGGCGGTTTGACTTG 60.081 57.895 23.48 0.00 36.97 3.16
356 357 2.676471 GGCCATGGCGGTTTGACT 60.676 61.111 29.90 0.00 43.06 3.41
366 367 1.384525 TTAATTCGGTTCGGCCATGG 58.615 50.000 7.63 7.63 36.97 3.66
368 369 2.227194 GGATTAATTCGGTTCGGCCAT 58.773 47.619 2.24 0.00 36.97 4.40
369 370 1.065345 TGGATTAATTCGGTTCGGCCA 60.065 47.619 2.24 0.00 36.97 5.36
371 372 2.011222 TGTGGATTAATTCGGTTCGGC 58.989 47.619 0.00 0.00 0.00 5.54
372 373 2.353579 GGTGTGGATTAATTCGGTTCGG 59.646 50.000 0.00 0.00 0.00 4.30
373 374 3.267483 AGGTGTGGATTAATTCGGTTCG 58.733 45.455 0.00 0.00 0.00 3.95
377 378 1.597663 GCGAGGTGTGGATTAATTCGG 59.402 52.381 5.80 0.00 0.00 4.30
378 379 1.597663 GGCGAGGTGTGGATTAATTCG 59.402 52.381 0.00 0.00 0.00 3.34
379 380 1.597663 CGGCGAGGTGTGGATTAATTC 59.402 52.381 0.00 0.00 0.00 2.17
382 383 0.174845 CTCGGCGAGGTGTGGATTAA 59.825 55.000 28.52 0.00 0.00 1.40
383 384 1.813859 CTCGGCGAGGTGTGGATTA 59.186 57.895 28.52 0.00 0.00 1.75
385 386 4.148825 GCTCGGCGAGGTGTGGAT 62.149 66.667 35.03 0.00 0.00 3.41
396 397 1.589196 GTGGATCTGTACGCTCGGC 60.589 63.158 0.00 0.00 0.00 5.54
397 398 1.298413 CGTGGATCTGTACGCTCGG 60.298 63.158 0.00 0.00 33.25 4.63
399 400 1.589196 GCCGTGGATCTGTACGCTC 60.589 63.158 10.69 3.68 38.87 5.03
400 401 2.494918 GCCGTGGATCTGTACGCT 59.505 61.111 10.69 0.00 38.87 5.07
402 403 0.179084 AATGGCCGTGGATCTGTACG 60.179 55.000 0.00 9.62 39.83 3.67
403 404 2.755650 CTAATGGCCGTGGATCTGTAC 58.244 52.381 0.00 0.00 0.00 2.90
404 405 1.070134 GCTAATGGCCGTGGATCTGTA 59.930 52.381 0.00 0.00 34.27 2.74
406 407 0.107456 AGCTAATGGCCGTGGATCTG 59.893 55.000 0.00 0.00 43.05 2.90
408 409 1.510480 GCAGCTAATGGCCGTGGATC 61.510 60.000 0.00 0.00 43.05 3.36
410 411 2.124736 GCAGCTAATGGCCGTGGA 60.125 61.111 0.00 0.00 43.05 4.02
412 413 2.793946 GTGCAGCTAATGGCCGTG 59.206 61.111 0.00 0.00 43.05 4.94
429 430 0.818445 TAGGGCTAAGCTCGACCTCG 60.818 60.000 13.33 0.00 41.45 4.63
431 432 0.551879 TCTAGGGCTAAGCTCGACCT 59.448 55.000 14.28 14.28 32.17 3.85
432 433 1.623163 ATCTAGGGCTAAGCTCGACC 58.377 55.000 0.00 0.00 32.17 4.79
444 445 2.228059 TCGACGGAAAGCTATCTAGGG 58.772 52.381 0.00 0.00 0.00 3.53
445 446 3.854045 GCTTCGACGGAAAGCTATCTAGG 60.854 52.174 12.58 0.00 0.00 3.02
446 447 3.243101 TGCTTCGACGGAAAGCTATCTAG 60.243 47.826 18.54 0.00 31.68 2.43
535 538 2.432510 GAGTGGCTAGCACTGATAGGTT 59.567 50.000 18.24 0.00 32.33 3.50
552 2629 3.558931 TGCTGGTATGGTAATGGAGTG 57.441 47.619 0.00 0.00 0.00 3.51
565 2642 3.384467 TGAAGATCATGTCGATGCTGGTA 59.616 43.478 0.00 0.00 33.17 3.25
566 2643 2.169144 TGAAGATCATGTCGATGCTGGT 59.831 45.455 0.00 0.00 33.17 4.00
567 2644 2.543012 GTGAAGATCATGTCGATGCTGG 59.457 50.000 0.00 0.00 33.17 4.85
568 2645 3.455327 AGTGAAGATCATGTCGATGCTG 58.545 45.455 0.00 0.00 33.17 4.41
569 2646 3.815856 AGTGAAGATCATGTCGATGCT 57.184 42.857 0.00 0.00 33.17 3.79
865 3004 1.609072 CTGAGCTGAATGCATGGGATG 59.391 52.381 0.00 0.00 45.94 3.51
866 3005 1.478837 CCTGAGCTGAATGCATGGGAT 60.479 52.381 0.00 0.00 45.94 3.85
867 3006 0.106868 CCTGAGCTGAATGCATGGGA 60.107 55.000 0.00 0.00 45.94 4.37
868 3007 1.735376 GCCTGAGCTGAATGCATGGG 61.735 60.000 0.00 0.00 45.94 4.00
870 3009 1.032794 ATGCCTGAGCTGAATGCATG 58.967 50.000 8.68 0.00 45.94 4.06
871 3010 1.409064 CAATGCCTGAGCTGAATGCAT 59.591 47.619 4.35 4.35 45.94 3.96
872 3011 0.815095 CAATGCCTGAGCTGAATGCA 59.185 50.000 0.00 0.00 45.94 3.96
882 3021 2.028658 GGCTCGATATCTCAATGCCTGA 60.029 50.000 0.34 0.00 36.32 3.86
885 3024 2.028658 TGAGGCTCGATATCTCAATGCC 60.029 50.000 10.42 7.09 34.97 4.40
908 3068 2.584418 CTGCGAGTGATCGGCAGG 60.584 66.667 15.86 3.06 35.37 4.85
913 3084 2.584418 CAGCCCTGCGAGTGATCG 60.584 66.667 0.00 0.00 0.00 3.69
944 3115 3.069079 ACAGCAAGTGATCTGCTCAAT 57.931 42.857 5.03 0.00 36.69 2.57
1005 3185 0.447801 CGCGGAGTATGCAAGCTTTT 59.552 50.000 0.00 0.00 0.00 2.27
1008 3188 2.202932 CCGCGGAGTATGCAAGCT 60.203 61.111 24.07 0.00 0.00 3.74
1015 3195 2.577059 CACCACACCGCGGAGTAT 59.423 61.111 35.90 18.93 0.00 2.12
1066 3246 2.768492 GCTCAGCCGCCAGGAAATG 61.768 63.158 0.00 0.00 41.02 2.32
1067 3247 2.439156 GCTCAGCCGCCAGGAAAT 60.439 61.111 0.00 0.00 41.02 2.17
1128 3311 4.794439 CTCGCCATGGTCGTCGCA 62.794 66.667 22.22 7.64 0.00 5.10
1149 3338 1.164041 ACACCTTCCTCGCAAAACGG 61.164 55.000 0.00 0.00 43.89 4.44
1245 3443 0.813610 CCCGTTAATGATGCTGCGGA 60.814 55.000 0.00 0.00 41.45 5.54
1262 3460 3.775654 CACCGTGGCCTCTCTCCC 61.776 72.222 3.32 0.00 0.00 4.30
1264 3462 2.060980 ATCCACCGTGGCCTCTCTC 61.061 63.158 13.19 0.00 37.47 3.20
1265 3463 2.039624 ATCCACCGTGGCCTCTCT 59.960 61.111 13.19 0.00 37.47 3.10
1267 3465 4.101448 GCATCCACCGTGGCCTCT 62.101 66.667 13.19 0.00 37.47 3.69
1272 3471 0.606401 AGAAACTGCATCCACCGTGG 60.606 55.000 11.73 11.73 39.43 4.94
1277 3476 4.065088 TGTTGTAGAGAAACTGCATCCAC 58.935 43.478 0.00 0.00 40.58 4.02
1280 3479 7.978982 ACATATTGTTGTAGAGAAACTGCATC 58.021 34.615 0.00 0.00 40.58 3.91
1299 3498 9.672673 GAGTATATGATGCCAGGTAAACATATT 57.327 33.333 18.41 8.09 34.36 1.28
1300 3499 8.267894 GGAGTATATGATGCCAGGTAAACATAT 58.732 37.037 17.76 17.76 35.84 1.78
1301 3500 7.457852 AGGAGTATATGATGCCAGGTAAACATA 59.542 37.037 9.14 9.14 0.00 2.29
1302 3501 6.273260 AGGAGTATATGATGCCAGGTAAACAT 59.727 38.462 6.03 6.03 0.00 2.71
1303 3502 5.606749 AGGAGTATATGATGCCAGGTAAACA 59.393 40.000 0.00 0.00 0.00 2.83
1304 3503 6.115448 AGGAGTATATGATGCCAGGTAAAC 57.885 41.667 0.00 0.00 0.00 2.01
1305 3504 6.785466 TGTAGGAGTATATGATGCCAGGTAAA 59.215 38.462 0.00 0.00 0.00 2.01
1306 3505 6.319715 TGTAGGAGTATATGATGCCAGGTAA 58.680 40.000 0.00 0.00 0.00 2.85
1307 3506 5.899278 TGTAGGAGTATATGATGCCAGGTA 58.101 41.667 0.00 0.00 0.00 3.08
1308 3507 4.752063 TGTAGGAGTATATGATGCCAGGT 58.248 43.478 0.00 0.00 0.00 4.00
1323 3522 2.036475 CGATTCAGGTCCCATGTAGGAG 59.964 54.545 0.00 0.00 41.22 3.69
1324 3523 2.039418 CGATTCAGGTCCCATGTAGGA 58.961 52.381 0.00 0.00 41.22 2.94
1325 3524 1.541233 GCGATTCAGGTCCCATGTAGG 60.541 57.143 0.00 0.00 37.03 3.18
1326 3525 1.414181 AGCGATTCAGGTCCCATGTAG 59.586 52.381 0.00 0.00 0.00 2.74
1353 3552 5.424757 TGGTATACAAAACCATCTCTTCGG 58.575 41.667 5.01 0.00 42.10 4.30
1470 3742 9.273016 TCCTTTTGAGAAAACTAGTCACAATAG 57.727 33.333 0.00 0.53 30.35 1.73
1507 3779 4.494484 GGTGGCTAAATGTGGATGAAAAC 58.506 43.478 0.00 0.00 0.00 2.43
1523 3796 2.252535 ATTTATGCAAAGGGGTGGCT 57.747 45.000 0.00 0.00 0.00 4.75
1541 3814 4.990526 AGACAATCCCACAGAACTGAAAT 58.009 39.130 8.87 0.00 0.00 2.17
1575 3853 8.051901 AGGGAGACTAAAATAAATTTTGGACG 57.948 34.615 15.72 3.89 39.63 4.79
1621 3899 7.545362 TGACCACAAAATGTAAAATTGTTGG 57.455 32.000 0.00 0.00 35.22 3.77
1680 3961 4.111375 AGTTATGCTCAGTCCGTAGTTG 57.889 45.455 0.00 0.00 0.00 3.16
1734 4016 3.508793 TGACAAGTCTAGGACCTTAACCG 59.491 47.826 0.00 0.00 32.18 4.44
1754 4147 1.305201 GAAAGTCTGGCAAACCGTGA 58.695 50.000 0.00 0.00 39.70 4.35
1757 4150 2.076863 CTAGGAAAGTCTGGCAAACCG 58.923 52.381 0.00 0.00 39.70 4.44
1764 4157 6.599638 CCTGAAATAAACCTAGGAAAGTCTGG 59.400 42.308 17.98 13.13 0.00 3.86
1766 4159 6.012421 AGCCTGAAATAAACCTAGGAAAGTCT 60.012 38.462 17.98 0.00 0.00 3.24
1767 4160 6.181190 AGCCTGAAATAAACCTAGGAAAGTC 58.819 40.000 17.98 5.46 0.00 3.01
1828 4222 3.057386 TCACCAAAGACGCATCGTAGTTA 60.057 43.478 0.00 0.00 41.37 2.24
1844 4238 5.551233 CCTTGAGATTGACTAAGTCACCAA 58.449 41.667 0.00 0.00 42.60 3.67
1882 4281 5.121221 TGTACATGTATACGCATCTCTGG 57.879 43.478 9.18 0.00 0.00 3.86
1883 4282 6.863126 TCATTGTACATGTATACGCATCTCTG 59.137 38.462 9.18 0.00 0.00 3.35
1892 4291 8.380644 GTTCACACACTCATTGTACATGTATAC 58.619 37.037 9.18 0.00 35.67 1.47
1899 4298 5.122519 ACATGTTCACACACTCATTGTACA 58.877 37.500 0.00 0.00 35.67 2.90
1903 4302 6.073112 TCACATACATGTTCACACACTCATTG 60.073 38.462 2.30 0.00 39.39 2.82
1917 4316 1.134699 CACGGAGGCTCACATACATGT 60.135 52.381 17.69 2.69 42.84 3.21
1931 4330 3.880490 AGAAGCAGAGTATAGACACGGAG 59.120 47.826 0.00 0.00 0.00 4.63
1964 4363 8.851541 TGTATTTACCTAAGTCGATGGTTTTT 57.148 30.769 7.47 0.00 35.48 1.94
1969 4368 9.760077 AAAGTATGTATTTACCTAAGTCGATGG 57.240 33.333 0.00 0.00 0.00 3.51
1973 4372 9.245962 CCTGAAAGTATGTATTTACCTAAGTCG 57.754 37.037 0.00 0.00 0.00 4.18
1974 4373 9.043079 GCCTGAAAGTATGTATTTACCTAAGTC 57.957 37.037 0.00 0.00 0.00 3.01
1980 4384 6.602009 ACTTGGCCTGAAAGTATGTATTTACC 59.398 38.462 3.32 0.00 36.11 2.85
1981 4385 7.625828 ACTTGGCCTGAAAGTATGTATTTAC 57.374 36.000 3.32 0.00 36.11 2.01
1986 4390 4.759693 CACAACTTGGCCTGAAAGTATGTA 59.240 41.667 3.32 0.00 36.87 2.29
1990 4394 3.135712 TCTCACAACTTGGCCTGAAAGTA 59.864 43.478 3.32 0.00 36.87 2.24
1995 4399 1.345741 CTCTCTCACAACTTGGCCTGA 59.654 52.381 3.32 0.00 0.00 3.86
1999 4403 3.063485 GACTTCTCTCTCACAACTTGGC 58.937 50.000 0.00 0.00 0.00 4.52
2061 4466 2.231478 TGAAGGCGAGAGGAACTAACAG 59.769 50.000 0.00 0.00 41.55 3.16
2065 4470 0.818296 GCTGAAGGCGAGAGGAACTA 59.182 55.000 0.00 0.00 41.55 2.24
2088 4494 1.280133 AGTGATGGTGATGTCAGGTGG 59.720 52.381 0.00 0.00 0.00 4.61
2105 4511 3.550030 CCCCTTTGACGCAACTTTTAGTG 60.550 47.826 0.00 0.00 0.00 2.74
2119 4525 2.785389 ACCCCCAAGCCCCTTTGA 60.785 61.111 0.00 0.00 0.00 2.69
2121 4527 2.785389 TCACCCCCAAGCCCCTTT 60.785 61.111 0.00 0.00 0.00 3.11
2122 4528 3.268032 CTCACCCCCAAGCCCCTT 61.268 66.667 0.00 0.00 0.00 3.95
2141 4547 1.153784 CCATCATTGTTGCCGCCAC 60.154 57.895 0.00 0.00 0.00 5.01
2163 4569 3.181494 GCGTGTATAAAAACCCCCATCAC 60.181 47.826 0.00 0.00 0.00 3.06
2164 4570 3.018149 GCGTGTATAAAAACCCCCATCA 58.982 45.455 0.00 0.00 0.00 3.07
2165 4571 2.032426 CGCGTGTATAAAAACCCCCATC 59.968 50.000 0.00 0.00 0.00 3.51
2166 4572 2.018515 CGCGTGTATAAAAACCCCCAT 58.981 47.619 0.00 0.00 0.00 4.00
2167 4573 1.002888 TCGCGTGTATAAAAACCCCCA 59.997 47.619 5.77 0.00 0.00 4.96
2169 4575 2.096335 CCTTCGCGTGTATAAAAACCCC 59.904 50.000 5.77 0.00 0.00 4.95
2170 4576 2.743664 ACCTTCGCGTGTATAAAAACCC 59.256 45.455 5.77 0.00 0.00 4.11
2176 4582 0.246910 TGCCACCTTCGCGTGTATAA 59.753 50.000 5.77 0.00 31.47 0.98
2186 4592 2.743928 CTGGAGCGTGCCACCTTC 60.744 66.667 7.10 0.00 33.52 3.46
2212 4618 2.693871 ATGCGGGAAATCAGCCCCT 61.694 57.895 0.00 0.00 42.92 4.79
2229 4635 3.448301 CAGCACATATTTCCCACCAACAT 59.552 43.478 0.00 0.00 0.00 2.71
2234 4640 4.685924 CAAATCAGCACATATTTCCCACC 58.314 43.478 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.