Multiple sequence alignment - TraesCS7A01G050500

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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 TraesCS7A01G050500 chr7A 100.000 2621 0 0 1 2621 23693098 23690478 0.000000e+00 4841.0
1 TraesCS7A01G050500 chr7A 96.154 78 3 0 487 564 635016481 635016558 7.610000e-26 128.0
2 TraesCS7A01G050500 chr7D 94.938 1778 66 15 555 2321 23095546 23093782 0.000000e+00 2763.0
3 TraesCS7A01G050500 chr7D 92.434 304 23 0 2318 2621 23093741 23093438 4.010000e-118 435.0
4 TraesCS7A01G050500 chr7D 96.203 79 2 1 487 565 101006070 101005993 7.610000e-26 128.0
5 TraesCS7A01G050500 chr7D 91.667 48 3 1 453 499 84895321 84895368 6.050000e-07 65.8
6 TraesCS7A01G050500 chr4A 93.304 1359 75 11 559 1905 706537037 706538391 0.000000e+00 1991.0
7 TraesCS7A01G050500 chr4A 84.010 419 55 7 1903 2321 706545413 706545819 2.450000e-105 392.0
8 TraesCS7A01G050500 chr4A 89.145 304 33 0 2318 2621 706545860 706546163 1.900000e-101 379.0
9 TraesCS7A01G050500 chr3A 97.741 487 11 0 1 487 738349756 738350242 0.000000e+00 839.0
10 TraesCS7A01G050500 chr5D 89.775 489 44 5 1 488 541173023 541173506 2.870000e-174 621.0
11 TraesCS7A01G050500 chr5D 98.571 70 1 0 487 556 360780978 360781047 9.850000e-25 124.0
12 TraesCS7A01G050500 chr5B 95.455 88 2 2 487 572 510453124 510453211 3.520000e-29 139.0
13 TraesCS7A01G050500 chr6B 94.048 84 2 3 478 560 11989949 11990030 9.850000e-25 124.0
14 TraesCS7A01G050500 chr6B 83.077 65 7 4 434 497 542817549 542817610 3.640000e-04 56.5
15 TraesCS7A01G050500 chr4D 95.000 80 2 2 487 565 488740790 488740868 9.850000e-25 124.0
16 TraesCS7A01G050500 chr2B 94.048 84 2 3 487 568 66032506 66032588 9.850000e-25 124.0
17 TraesCS7A01G050500 chr1B 95.062 81 1 3 487 567 187202565 187202642 9.850000e-25 124.0
18 TraesCS7A01G050500 chr2D 91.209 91 5 3 482 570 580418364 580418453 1.270000e-23 121.0
19 TraesCS7A01G050500 chr1D 91.667 48 3 1 453 499 336448898 336448851 6.050000e-07 65.8


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 TraesCS7A01G050500 chr7A 23690478 23693098 2620 True 4841.0 4841 100.0000 1 2621 1 chr7A.!!$R1 2620
1 TraesCS7A01G050500 chr7D 23093438 23095546 2108 True 1599.0 2763 93.6860 555 2621 2 chr7D.!!$R2 2066
2 TraesCS7A01G050500 chr4A 706537037 706538391 1354 False 1991.0 1991 93.3040 559 1905 1 chr4A.!!$F1 1346
3 TraesCS7A01G050500 chr4A 706545413 706546163 750 False 385.5 392 86.5775 1903 2621 2 chr4A.!!$F2 718

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
120 121 0.110486 AACGCACCTCCCAATCTGTT 59.890 50.0 0.0 0.0 0.0 3.16 F
486 487 0.249398 GGCACGGGTTGATGACTAGT 59.751 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1016 0.378257 ATGTCGTGCAATCGAATGCC 59.622 50.0 22.13 12.5 45.83 4.40 R
2334 2405 0.186873 GGGAAGCCACCATGATGGAT 59.813 55.0 20.11 0.0 43.02 3.41 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
105 106 9.856803 ATTTTGTAAATTGTGTATTTTCAACGC 57.143 25.926 0.00 0.00 40.77 4.84
106 107 7.987268 TTGTAAATTGTGTATTTTCAACGCA 57.013 28.000 0.00 0.00 38.08 5.24
107 108 7.383050 TGTAAATTGTGTATTTTCAACGCAC 57.617 32.000 0.00 0.00 37.10 5.34
108 109 5.898630 AAATTGTGTATTTTCAACGCACC 57.101 34.783 0.00 0.00 37.10 5.01
109 110 4.846779 ATTGTGTATTTTCAACGCACCT 57.153 36.364 0.00 0.00 37.10 4.00
110 111 3.889196 TGTGTATTTTCAACGCACCTC 57.111 42.857 0.00 0.00 32.67 3.85
111 112 2.550606 TGTGTATTTTCAACGCACCTCC 59.449 45.455 0.00 0.00 32.67 4.30
112 113 2.095415 GTGTATTTTCAACGCACCTCCC 60.095 50.000 0.00 0.00 0.00 4.30
113 114 2.156098 GTATTTTCAACGCACCTCCCA 58.844 47.619 0.00 0.00 0.00 4.37
114 115 1.698506 ATTTTCAACGCACCTCCCAA 58.301 45.000 0.00 0.00 0.00 4.12
115 116 1.698506 TTTTCAACGCACCTCCCAAT 58.301 45.000 0.00 0.00 0.00 3.16
116 117 1.243902 TTTCAACGCACCTCCCAATC 58.756 50.000 0.00 0.00 0.00 2.67
117 118 0.400213 TTCAACGCACCTCCCAATCT 59.600 50.000 0.00 0.00 0.00 2.40
118 119 0.321564 TCAACGCACCTCCCAATCTG 60.322 55.000 0.00 0.00 0.00 2.90
119 120 0.606401 CAACGCACCTCCCAATCTGT 60.606 55.000 0.00 0.00 0.00 3.41
120 121 0.110486 AACGCACCTCCCAATCTGTT 59.890 50.000 0.00 0.00 0.00 3.16
121 122 0.981183 ACGCACCTCCCAATCTGTTA 59.019 50.000 0.00 0.00 0.00 2.41
122 123 1.338769 ACGCACCTCCCAATCTGTTAC 60.339 52.381 0.00 0.00 0.00 2.50
123 124 1.338674 CGCACCTCCCAATCTGTTACA 60.339 52.381 0.00 0.00 0.00 2.41
124 125 2.790433 GCACCTCCCAATCTGTTACAA 58.210 47.619 0.00 0.00 0.00 2.41
125 126 2.749621 GCACCTCCCAATCTGTTACAAG 59.250 50.000 0.00 0.00 0.00 3.16
126 127 3.810743 GCACCTCCCAATCTGTTACAAGT 60.811 47.826 0.00 0.00 0.00 3.16
127 128 4.564821 GCACCTCCCAATCTGTTACAAGTA 60.565 45.833 0.00 0.00 0.00 2.24
128 129 5.556915 CACCTCCCAATCTGTTACAAGTAA 58.443 41.667 0.00 0.00 0.00 2.24
129 130 6.001460 CACCTCCCAATCTGTTACAAGTAAA 58.999 40.000 0.00 0.00 0.00 2.01
130 131 6.002082 ACCTCCCAATCTGTTACAAGTAAAC 58.998 40.000 0.00 0.00 0.00 2.01
131 132 6.001460 CCTCCCAATCTGTTACAAGTAAACA 58.999 40.000 0.00 0.00 0.00 2.83
132 133 6.659242 CCTCCCAATCTGTTACAAGTAAACAT 59.341 38.462 0.00 0.00 0.00 2.71
133 134 7.827236 CCTCCCAATCTGTTACAAGTAAACATA 59.173 37.037 0.00 0.00 0.00 2.29
134 135 8.786826 TCCCAATCTGTTACAAGTAAACATAG 57.213 34.615 0.00 0.00 0.00 2.23
135 136 8.598916 TCCCAATCTGTTACAAGTAAACATAGA 58.401 33.333 0.00 0.00 0.00 1.98
136 137 9.396022 CCCAATCTGTTACAAGTAAACATAGAT 57.604 33.333 0.00 0.88 0.00 1.98
140 141 9.614792 ATCTGTTACAAGTAAACATAGATTCCC 57.385 33.333 0.00 0.00 0.00 3.97
141 142 8.598916 TCTGTTACAAGTAAACATAGATTCCCA 58.401 33.333 0.00 0.00 0.00 4.37
142 143 8.786826 TGTTACAAGTAAACATAGATTCCCAG 57.213 34.615 0.00 0.00 0.00 4.45
143 144 8.598916 TGTTACAAGTAAACATAGATTCCCAGA 58.401 33.333 0.00 0.00 0.00 3.86
144 145 9.444600 GTTACAAGTAAACATAGATTCCCAGAA 57.555 33.333 0.00 0.00 0.00 3.02
147 148 9.533831 ACAAGTAAACATAGATTCCCAGAAATT 57.466 29.630 0.00 0.00 0.00 1.82
209 210 9.549509 TGTATATAAAACGAACTTCACATTTGC 57.450 29.630 0.00 0.00 0.00 3.68
210 211 9.549509 GTATATAAAACGAACTTCACATTTGCA 57.450 29.630 0.00 0.00 0.00 4.08
212 213 5.448926 AAAACGAACTTCACATTTGCAAC 57.551 34.783 0.00 0.00 0.00 4.17
213 214 4.370364 AACGAACTTCACATTTGCAACT 57.630 36.364 0.00 0.00 0.00 3.16
214 215 5.493133 AACGAACTTCACATTTGCAACTA 57.507 34.783 0.00 0.00 0.00 2.24
215 216 5.689383 ACGAACTTCACATTTGCAACTAT 57.311 34.783 0.00 0.00 0.00 2.12
216 217 5.451908 ACGAACTTCACATTTGCAACTATG 58.548 37.500 0.00 3.82 0.00 2.23
217 218 5.008613 ACGAACTTCACATTTGCAACTATGT 59.991 36.000 10.35 10.35 35.45 2.29
222 223 3.836949 CACATTTGCAACTATGTGGACC 58.163 45.455 26.33 0.00 44.90 4.46
223 224 3.255395 CACATTTGCAACTATGTGGACCA 59.745 43.478 26.33 0.00 44.90 4.02
224 225 3.507233 ACATTTGCAACTATGTGGACCAG 59.493 43.478 14.49 0.00 33.90 4.00
225 226 1.533625 TTGCAACTATGTGGACCAGC 58.466 50.000 0.00 0.00 0.00 4.85
226 227 0.399833 TGCAACTATGTGGACCAGCA 59.600 50.000 0.00 0.00 0.00 4.41
227 228 1.202867 TGCAACTATGTGGACCAGCAA 60.203 47.619 0.00 0.00 0.00 3.91
228 229 2.094675 GCAACTATGTGGACCAGCAAT 58.905 47.619 0.00 0.00 0.00 3.56
229 230 3.278574 GCAACTATGTGGACCAGCAATA 58.721 45.455 0.00 0.00 0.00 1.90
230 231 3.065371 GCAACTATGTGGACCAGCAATAC 59.935 47.826 0.00 0.00 0.00 1.89
231 232 3.560636 ACTATGTGGACCAGCAATACC 57.439 47.619 0.00 0.00 0.00 2.73
232 233 2.158957 ACTATGTGGACCAGCAATACCG 60.159 50.000 0.00 0.00 0.00 4.02
233 234 0.748005 ATGTGGACCAGCAATACCGC 60.748 55.000 0.00 0.00 0.00 5.68
234 235 2.112815 GTGGACCAGCAATACCGCC 61.113 63.158 0.00 0.00 0.00 6.13
235 236 2.297895 TGGACCAGCAATACCGCCT 61.298 57.895 0.00 0.00 0.00 5.52
236 237 1.077716 GGACCAGCAATACCGCCTT 60.078 57.895 0.00 0.00 0.00 4.35
237 238 1.095807 GGACCAGCAATACCGCCTTC 61.096 60.000 0.00 0.00 0.00 3.46
238 239 0.392461 GACCAGCAATACCGCCTTCA 60.392 55.000 0.00 0.00 0.00 3.02
239 240 0.255890 ACCAGCAATACCGCCTTCAT 59.744 50.000 0.00 0.00 0.00 2.57
240 241 1.488812 ACCAGCAATACCGCCTTCATA 59.511 47.619 0.00 0.00 0.00 2.15
241 242 2.106511 ACCAGCAATACCGCCTTCATAT 59.893 45.455 0.00 0.00 0.00 1.78
242 243 3.149196 CCAGCAATACCGCCTTCATATT 58.851 45.455 0.00 0.00 0.00 1.28
243 244 3.189287 CCAGCAATACCGCCTTCATATTC 59.811 47.826 0.00 0.00 0.00 1.75
244 245 3.814842 CAGCAATACCGCCTTCATATTCA 59.185 43.478 0.00 0.00 0.00 2.57
245 246 4.456911 CAGCAATACCGCCTTCATATTCAT 59.543 41.667 0.00 0.00 0.00 2.57
246 247 4.456911 AGCAATACCGCCTTCATATTCATG 59.543 41.667 0.00 0.00 0.00 3.07
247 248 4.216257 GCAATACCGCCTTCATATTCATGT 59.784 41.667 0.00 0.00 33.57 3.21
248 249 5.617751 GCAATACCGCCTTCATATTCATGTC 60.618 44.000 0.00 0.00 33.57 3.06
249 250 3.558931 ACCGCCTTCATATTCATGTCA 57.441 42.857 0.00 0.00 33.57 3.58
250 251 3.884895 ACCGCCTTCATATTCATGTCAA 58.115 40.909 0.00 0.00 33.57 3.18
251 252 4.269183 ACCGCCTTCATATTCATGTCAAA 58.731 39.130 0.00 0.00 33.57 2.69
252 253 4.889409 ACCGCCTTCATATTCATGTCAAAT 59.111 37.500 0.00 0.00 33.57 2.32
253 254 6.061441 ACCGCCTTCATATTCATGTCAAATA 58.939 36.000 0.00 0.00 33.57 1.40
254 255 6.545666 ACCGCCTTCATATTCATGTCAAATAA 59.454 34.615 0.00 0.00 33.57 1.40
255 256 7.068103 ACCGCCTTCATATTCATGTCAAATAAA 59.932 33.333 0.00 0.00 33.57 1.40
256 257 8.084073 CCGCCTTCATATTCATGTCAAATAAAT 58.916 33.333 0.00 0.00 33.57 1.40
287 288 7.538575 AGTTGAAAATTATGAGAAATGGGACG 58.461 34.615 0.00 0.00 0.00 4.79
288 289 7.393234 AGTTGAAAATTATGAGAAATGGGACGA 59.607 33.333 0.00 0.00 0.00 4.20
289 290 7.083875 TGAAAATTATGAGAAATGGGACGAC 57.916 36.000 0.00 0.00 0.00 4.34
290 291 6.094881 TGAAAATTATGAGAAATGGGACGACC 59.905 38.462 0.00 0.00 40.81 4.79
300 301 3.425122 GGGACGACCAAAAGGGAAA 57.575 52.632 6.20 0.00 41.15 3.13
301 302 1.694844 GGGACGACCAAAAGGGAAAA 58.305 50.000 6.20 0.00 41.15 2.29
302 303 2.033372 GGGACGACCAAAAGGGAAAAA 58.967 47.619 6.20 0.00 41.15 1.94
303 304 2.631062 GGGACGACCAAAAGGGAAAAAT 59.369 45.455 6.20 0.00 41.15 1.82
304 305 3.070446 GGGACGACCAAAAGGGAAAAATT 59.930 43.478 6.20 0.00 41.15 1.82
305 306 4.304110 GGACGACCAAAAGGGAAAAATTC 58.696 43.478 0.00 0.00 41.15 2.17
306 307 4.202172 GGACGACCAAAAGGGAAAAATTCA 60.202 41.667 0.00 0.00 41.15 2.57
307 308 5.510690 GGACGACCAAAAGGGAAAAATTCAT 60.511 40.000 0.00 0.00 41.15 2.57
308 309 5.296748 ACGACCAAAAGGGAAAAATTCATG 58.703 37.500 0.00 0.00 41.15 3.07
309 310 4.152223 CGACCAAAAGGGAAAAATTCATGC 59.848 41.667 0.00 0.00 41.15 4.06
310 311 5.046288 ACCAAAAGGGAAAAATTCATGCA 57.954 34.783 0.00 0.00 41.15 3.96
311 312 5.444176 ACCAAAAGGGAAAAATTCATGCAA 58.556 33.333 0.00 0.00 41.15 4.08
312 313 5.890419 ACCAAAAGGGAAAAATTCATGCAAA 59.110 32.000 0.00 0.00 41.15 3.68
313 314 6.183360 ACCAAAAGGGAAAAATTCATGCAAAC 60.183 34.615 0.00 0.00 41.15 2.93
314 315 6.207928 CAAAAGGGAAAAATTCATGCAAACC 58.792 36.000 0.00 0.00 0.00 3.27
315 316 4.703379 AGGGAAAAATTCATGCAAACCA 57.297 36.364 0.00 0.00 0.00 3.67
316 317 5.245584 AGGGAAAAATTCATGCAAACCAT 57.754 34.783 0.00 0.00 33.39 3.55
317 318 5.247862 AGGGAAAAATTCATGCAAACCATC 58.752 37.500 0.00 0.00 29.71 3.51
318 319 5.013391 AGGGAAAAATTCATGCAAACCATCT 59.987 36.000 0.00 0.00 29.71 2.90
319 320 6.213195 AGGGAAAAATTCATGCAAACCATCTA 59.787 34.615 0.00 0.00 29.71 1.98
320 321 6.878389 GGGAAAAATTCATGCAAACCATCTAA 59.122 34.615 0.00 0.00 29.71 2.10
321 322 7.553760 GGGAAAAATTCATGCAAACCATCTAAT 59.446 33.333 0.00 0.00 29.71 1.73
322 323 8.606602 GGAAAAATTCATGCAAACCATCTAATC 58.393 33.333 0.00 0.00 29.71 1.75
323 324 9.153721 GAAAAATTCATGCAAACCATCTAATCA 57.846 29.630 0.00 0.00 29.71 2.57
324 325 8.483307 AAAATTCATGCAAACCATCTAATCAC 57.517 30.769 0.00 0.00 29.71 3.06
325 326 6.778834 ATTCATGCAAACCATCTAATCACA 57.221 33.333 0.00 0.00 29.71 3.58
326 327 6.587206 TTCATGCAAACCATCTAATCACAA 57.413 33.333 0.00 0.00 29.71 3.33
327 328 5.953183 TCATGCAAACCATCTAATCACAAC 58.047 37.500 0.00 0.00 29.71 3.32
328 329 5.711506 TCATGCAAACCATCTAATCACAACT 59.288 36.000 0.00 0.00 29.71 3.16
329 330 6.209192 TCATGCAAACCATCTAATCACAACTT 59.791 34.615 0.00 0.00 29.71 2.66
330 331 6.012658 TGCAAACCATCTAATCACAACTTC 57.987 37.500 0.00 0.00 0.00 3.01
331 332 5.534278 TGCAAACCATCTAATCACAACTTCA 59.466 36.000 0.00 0.00 0.00 3.02
332 333 6.209192 TGCAAACCATCTAATCACAACTTCAT 59.791 34.615 0.00 0.00 0.00 2.57
333 334 6.749118 GCAAACCATCTAATCACAACTTCATC 59.251 38.462 0.00 0.00 0.00 2.92
334 335 7.575532 GCAAACCATCTAATCACAACTTCATCA 60.576 37.037 0.00 0.00 0.00 3.07
335 336 8.298854 CAAACCATCTAATCACAACTTCATCAA 58.701 33.333 0.00 0.00 0.00 2.57
336 337 8.408043 AACCATCTAATCACAACTTCATCAAA 57.592 30.769 0.00 0.00 0.00 2.69
337 338 7.820648 ACCATCTAATCACAACTTCATCAAAC 58.179 34.615 0.00 0.00 0.00 2.93
338 339 7.448161 ACCATCTAATCACAACTTCATCAAACA 59.552 33.333 0.00 0.00 0.00 2.83
339 340 8.298854 CCATCTAATCACAACTTCATCAAACAA 58.701 33.333 0.00 0.00 0.00 2.83
340 341 9.850628 CATCTAATCACAACTTCATCAAACAAT 57.149 29.630 0.00 0.00 0.00 2.71
342 343 9.681692 TCTAATCACAACTTCATCAAACAATTG 57.318 29.630 3.24 3.24 37.92 2.32
343 344 9.467258 CTAATCACAACTTCATCAAACAATTGT 57.533 29.630 4.92 4.92 37.79 2.71
345 346 9.814899 AATCACAACTTCATCAAACAATTGTAA 57.185 25.926 12.39 0.06 37.79 2.41
346 347 9.985730 ATCACAACTTCATCAAACAATTGTAAT 57.014 25.926 12.39 3.45 37.79 1.89
347 348 9.462174 TCACAACTTCATCAAACAATTGTAATC 57.538 29.630 12.39 0.00 37.79 1.75
348 349 8.702438 CACAACTTCATCAAACAATTGTAATCC 58.298 33.333 12.39 0.00 37.79 3.01
349 350 8.641541 ACAACTTCATCAAACAATTGTAATCCT 58.358 29.630 12.39 0.00 37.79 3.24
358 359 8.247562 TCAAACAATTGTAATCCTATTTTCCCG 58.752 33.333 12.39 0.00 37.79 5.14
359 360 6.709018 ACAATTGTAATCCTATTTTCCCGG 57.291 37.500 9.97 0.00 0.00 5.73
360 361 5.596772 ACAATTGTAATCCTATTTTCCCGGG 59.403 40.000 16.85 16.85 0.00 5.73
361 362 5.656549 ATTGTAATCCTATTTTCCCGGGA 57.343 39.130 22.63 22.63 0.00 5.14
362 363 5.656549 TTGTAATCCTATTTTCCCGGGAT 57.343 39.130 27.48 12.94 39.91 3.85
363 364 5.237236 TGTAATCCTATTTTCCCGGGATC 57.763 43.478 27.48 0.99 37.57 3.36
364 365 4.661240 TGTAATCCTATTTTCCCGGGATCA 59.339 41.667 27.48 14.94 37.57 2.92
365 366 5.312178 TGTAATCCTATTTTCCCGGGATCAT 59.688 40.000 27.48 21.14 37.57 2.45
366 367 5.339423 AATCCTATTTTCCCGGGATCATT 57.661 39.130 27.48 12.98 37.57 2.57
367 368 4.098914 TCCTATTTTCCCGGGATCATTG 57.901 45.455 27.48 18.76 0.00 2.82
368 369 3.719479 TCCTATTTTCCCGGGATCATTGA 59.281 43.478 27.48 14.22 0.00 2.57
369 370 4.167113 TCCTATTTTCCCGGGATCATTGAA 59.833 41.667 27.48 12.05 0.00 2.69
370 371 4.278419 CCTATTTTCCCGGGATCATTGAAC 59.722 45.833 27.48 0.00 0.00 3.18
371 372 2.889170 TTTCCCGGGATCATTGAACA 57.111 45.000 27.48 1.92 0.00 3.18
372 373 2.889170 TTCCCGGGATCATTGAACAA 57.111 45.000 27.48 0.98 0.00 2.83
373 374 2.889170 TCCCGGGATCATTGAACAAA 57.111 45.000 22.63 0.00 0.00 2.83
374 375 3.162147 TCCCGGGATCATTGAACAAAA 57.838 42.857 22.63 0.00 0.00 2.44
375 376 3.707316 TCCCGGGATCATTGAACAAAAT 58.293 40.909 22.63 0.00 0.00 1.82
376 377 4.093011 TCCCGGGATCATTGAACAAAATT 58.907 39.130 22.63 0.00 0.00 1.82
377 378 5.265191 TCCCGGGATCATTGAACAAAATTA 58.735 37.500 22.63 0.00 0.00 1.40
378 379 5.126384 TCCCGGGATCATTGAACAAAATTAC 59.874 40.000 22.63 0.00 0.00 1.89
379 380 5.105554 CCCGGGATCATTGAACAAAATTACA 60.106 40.000 18.48 0.00 0.00 2.41
380 381 6.406849 CCCGGGATCATTGAACAAAATTACAT 60.407 38.462 18.48 0.00 0.00 2.29
381 382 6.476380 CCGGGATCATTGAACAAAATTACATG 59.524 38.462 0.00 0.00 0.00 3.21
382 383 7.035004 CGGGATCATTGAACAAAATTACATGT 58.965 34.615 2.69 2.69 0.00 3.21
383 384 7.545265 CGGGATCATTGAACAAAATTACATGTT 59.455 33.333 2.30 4.43 42.18 2.71
384 385 9.218440 GGGATCATTGAACAAAATTACATGTTT 57.782 29.630 2.30 0.00 39.73 2.83
422 423 9.862149 ATTCTTCCCTTAAACTTTACTTCTTCA 57.138 29.630 0.00 0.00 0.00 3.02
423 424 8.904099 TCTTCCCTTAAACTTTACTTCTTCAG 57.096 34.615 0.00 0.00 0.00 3.02
424 425 8.491958 TCTTCCCTTAAACTTTACTTCTTCAGT 58.508 33.333 0.00 0.00 39.87 3.41
425 426 9.121658 CTTCCCTTAAACTTTACTTCTTCAGTT 57.878 33.333 0.00 0.00 36.88 3.16
426 427 9.470399 TTCCCTTAAACTTTACTTCTTCAGTTT 57.530 29.630 0.00 0.00 41.33 2.66
427 428 9.117183 TCCCTTAAACTTTACTTCTTCAGTTTC 57.883 33.333 0.00 0.00 39.58 2.78
428 429 8.899771 CCCTTAAACTTTACTTCTTCAGTTTCA 58.100 33.333 0.00 0.00 39.58 2.69
435 436 9.832445 ACTTTACTTCTTCAGTTTCATAAGTCA 57.168 29.630 0.00 0.00 36.88 3.41
459 460 9.720769 TCATAAATAGTAAACATTAGCTAGCCC 57.279 33.333 12.13 0.00 0.00 5.19
460 461 8.656849 CATAAATAGTAAACATTAGCTAGCCCG 58.343 37.037 12.13 0.00 0.00 6.13
461 462 5.803237 ATAGTAAACATTAGCTAGCCCGT 57.197 39.130 12.13 0.15 0.00 5.28
462 463 3.793559 AGTAAACATTAGCTAGCCCGTG 58.206 45.455 12.13 10.06 0.00 4.94
463 464 1.379527 AAACATTAGCTAGCCCGTGC 58.620 50.000 12.13 0.00 37.95 5.34
479 480 4.740822 GCTGGGGCACGGGTTGAT 62.741 66.667 0.00 0.00 38.54 2.57
480 481 2.751436 CTGGGGCACGGGTTGATG 60.751 66.667 0.00 0.00 0.00 3.07
481 482 3.253061 TGGGGCACGGGTTGATGA 61.253 61.111 0.00 0.00 0.00 2.92
482 483 2.750237 GGGGCACGGGTTGATGAC 60.750 66.667 0.00 0.00 0.00 3.06
483 484 2.351276 GGGCACGGGTTGATGACT 59.649 61.111 0.00 0.00 0.00 3.41
484 485 1.600107 GGGCACGGGTTGATGACTA 59.400 57.895 0.00 0.00 0.00 2.59
485 486 0.462047 GGGCACGGGTTGATGACTAG 60.462 60.000 0.00 0.00 0.00 2.57
486 487 0.249398 GGCACGGGTTGATGACTAGT 59.751 55.000 0.00 0.00 0.00 2.57
487 488 1.338769 GGCACGGGTTGATGACTAGTT 60.339 52.381 0.00 0.00 0.00 2.24
488 489 2.093869 GGCACGGGTTGATGACTAGTTA 60.094 50.000 0.00 0.00 0.00 2.24
489 490 3.592059 GCACGGGTTGATGACTAGTTAA 58.408 45.455 0.00 0.00 0.00 2.01
490 491 3.370061 GCACGGGTTGATGACTAGTTAAC 59.630 47.826 0.00 0.00 0.00 2.01
491 492 4.562082 CACGGGTTGATGACTAGTTAACA 58.438 43.478 8.61 0.00 0.00 2.41
492 493 5.175859 CACGGGTTGATGACTAGTTAACAT 58.824 41.667 8.61 0.00 0.00 2.71
493 494 6.334989 CACGGGTTGATGACTAGTTAACATA 58.665 40.000 8.61 0.00 0.00 2.29
494 495 6.814644 CACGGGTTGATGACTAGTTAACATAA 59.185 38.462 8.61 0.00 0.00 1.90
495 496 7.494625 CACGGGTTGATGACTAGTTAACATAAT 59.505 37.037 8.61 0.00 0.00 1.28
496 497 8.044908 ACGGGTTGATGACTAGTTAACATAATT 58.955 33.333 8.61 0.00 0.00 1.40
497 498 8.335356 CGGGTTGATGACTAGTTAACATAATTG 58.665 37.037 8.61 0.00 0.00 2.32
498 499 9.391006 GGGTTGATGACTAGTTAACATAATTGA 57.609 33.333 8.61 0.00 0.00 2.57
528 529 6.096673 ACTTTTAAAGTTAATGTGGCCCTG 57.903 37.500 4.30 0.00 39.04 4.45
529 530 5.600898 ACTTTTAAAGTTAATGTGGCCCTGT 59.399 36.000 4.30 0.00 39.04 4.00
530 531 6.099125 ACTTTTAAAGTTAATGTGGCCCTGTT 59.901 34.615 4.30 0.00 39.04 3.16
531 532 5.461032 TTAAAGTTAATGTGGCCCTGTTG 57.539 39.130 0.00 0.00 0.00 3.33
532 533 1.256812 AGTTAATGTGGCCCTGTTGC 58.743 50.000 0.00 0.00 0.00 4.17
533 534 0.965439 GTTAATGTGGCCCTGTTGCA 59.035 50.000 0.00 0.00 0.00 4.08
534 535 1.342819 GTTAATGTGGCCCTGTTGCAA 59.657 47.619 0.00 0.00 0.00 4.08
535 536 0.965439 TAATGTGGCCCTGTTGCAAC 59.035 50.000 22.83 22.83 35.65 4.17
536 537 2.086251 AATGTGGCCCTGTTGCAACG 62.086 55.000 23.79 17.58 38.05 4.10
537 538 4.645921 GTGGCCCTGTTGCAACGC 62.646 66.667 23.79 19.96 0.00 4.84
539 540 4.645921 GGCCCTGTTGCAACGCAC 62.646 66.667 23.79 13.10 38.71 5.34
540 541 4.980903 GCCCTGTTGCAACGCACG 62.981 66.667 23.79 12.32 38.71 5.34
541 542 4.326766 CCCTGTTGCAACGCACGG 62.327 66.667 23.79 19.21 38.71 4.94
542 543 4.326766 CCTGTTGCAACGCACGGG 62.327 66.667 23.79 12.20 38.71 5.28
543 544 4.980903 CTGTTGCAACGCACGGGC 62.981 66.667 23.79 0.00 38.71 6.13
553 554 3.782042 GCACGGGCGTTCTTCTAG 58.218 61.111 0.00 0.00 0.00 2.43
752 760 2.929903 GCAAGGCACGGGCATTCAA 61.930 57.895 13.89 0.00 43.08 2.69
773 781 7.598759 TCAACTAGTTTTGAGGTAAGAGACT 57.401 36.000 5.07 0.00 31.68 3.24
830 838 7.147976 AGAAATAGACAAAAAGGTGTGCATTC 58.852 34.615 0.00 0.00 0.00 2.67
845 853 5.124457 GTGTGCATTCAATGTCCAGAATAGT 59.876 40.000 0.00 0.00 33.41 2.12
993 1001 1.088340 TTCGCCAACGTCGTTTCCAA 61.088 50.000 8.15 0.00 41.18 3.53
1007 1016 3.367910 CGTTTCCAACATTAACCCCATGG 60.368 47.826 4.14 4.14 37.80 3.66
1203 1215 2.483745 GACGACGAGATGGACGCA 59.516 61.111 0.00 0.00 0.00 5.24
1348 1360 1.066587 GAGATGAGGGAGGCGTTCG 59.933 63.158 0.00 0.00 0.00 3.95
1588 1600 6.183360 GGGAATGGTTCATTGTGGTACTATTG 60.183 42.308 0.00 0.00 33.90 1.90
1680 1697 8.397906 CAAATACATGAGTATGAAACGACCAAT 58.602 33.333 0.00 0.00 40.00 3.16
1683 1700 5.354234 ACATGAGTATGAAACGACCAATTCC 59.646 40.000 0.00 0.00 37.73 3.01
1700 1717 7.649057 ACCAATTCCTCTCTTTTAAAAAGACG 58.351 34.615 1.66 3.45 0.00 4.18
1759 1776 4.142600 GGCTGGATTGGATTCATTATACGC 60.143 45.833 0.00 0.00 0.00 4.42
1787 1804 8.964150 GTAAATGGTATTTATCATGGAAAACGC 58.036 33.333 0.00 0.00 0.00 4.84
1834 1851 3.384789 CCTATCCACTCCTTTGACGATCA 59.615 47.826 0.00 0.00 0.00 2.92
1994 2021 4.210093 TGGTTGTCGCGACGGTGT 62.210 61.111 31.88 0.00 0.00 4.16
2071 2098 1.475169 CGGCTCTCCAGATATGGGCA 61.475 60.000 6.52 0.00 0.00 5.36
2088 2115 2.107343 AACGTGTGGTGCGTGCTA 59.893 55.556 0.00 0.00 42.10 3.49
2146 2173 2.995547 GGGTAGTGGCCCGATGTT 59.004 61.111 0.00 0.00 39.17 2.71
2162 2189 1.598962 GTTGCTGCTGCTCCTGTCA 60.599 57.895 17.00 0.00 40.48 3.58
2213 2240 4.308458 TGGGTGCGGTGTCCTTCG 62.308 66.667 0.00 0.00 0.00 3.79
2225 2252 2.048877 CCTTCGTACGGCGTGGTT 60.049 61.111 24.86 0.00 42.13 3.67
2227 2254 1.372004 CTTCGTACGGCGTGGTTGA 60.372 57.895 24.86 11.82 42.13 3.18
2309 2336 0.536233 TTTGCAAGCGGCCTAGTTCA 60.536 50.000 0.00 0.00 43.89 3.18
2334 2405 1.923395 GGTCCACTCCCCATCACCA 60.923 63.158 0.00 0.00 0.00 4.17
2395 2466 2.697425 CGCTCATCACTTTCGCCG 59.303 61.111 0.00 0.00 0.00 6.46
2397 2468 3.093278 CTCATCACTTTCGCCGGC 58.907 61.111 19.07 19.07 0.00 6.13
2442 2513 1.341383 GGTGTTGGGATCTTGGATGCT 60.341 52.381 0.00 0.00 0.00 3.79
2513 2584 1.454104 CACAGGTGTGGGCTGGTTA 59.546 57.895 1.90 0.00 42.10 2.85
2529 2600 2.430694 TGGTTATCATGGTCGTGAGAGG 59.569 50.000 0.00 0.00 43.49 3.69
2572 2643 1.031571 TTCAATGAGGATGGTGCGGC 61.032 55.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 9.856803 GCGTTGAAAATACACAATTTACAAAAT 57.143 25.926 0.00 0.00 36.76 1.82
80 81 8.869897 TGCGTTGAAAATACACAATTTACAAAA 58.130 25.926 0.00 0.00 36.76 2.44
81 82 8.321716 GTGCGTTGAAAATACACAATTTACAAA 58.678 29.630 0.00 0.00 36.76 2.83
82 83 7.043325 GGTGCGTTGAAAATACACAATTTACAA 60.043 33.333 0.00 0.00 36.76 2.41
83 84 6.418226 GGTGCGTTGAAAATACACAATTTACA 59.582 34.615 0.00 0.00 36.76 2.41
84 85 6.639279 AGGTGCGTTGAAAATACACAATTTAC 59.361 34.615 0.00 0.00 36.76 2.01
85 86 6.740110 AGGTGCGTTGAAAATACACAATTTA 58.260 32.000 0.00 0.00 36.76 1.40
86 87 5.596845 AGGTGCGTTGAAAATACACAATTT 58.403 33.333 0.00 0.00 39.56 1.82
87 88 5.195001 AGGTGCGTTGAAAATACACAATT 57.805 34.783 0.00 0.00 36.55 2.32
88 89 4.320935 GGAGGTGCGTTGAAAATACACAAT 60.321 41.667 0.00 0.00 36.55 2.71
89 90 3.003897 GGAGGTGCGTTGAAAATACACAA 59.996 43.478 0.00 0.00 36.55 3.33
90 91 2.550606 GGAGGTGCGTTGAAAATACACA 59.449 45.455 0.00 0.00 36.55 3.72
91 92 2.095415 GGGAGGTGCGTTGAAAATACAC 60.095 50.000 0.00 0.00 34.81 2.90
92 93 2.156098 GGGAGGTGCGTTGAAAATACA 58.844 47.619 0.00 0.00 0.00 2.29
93 94 2.156098 TGGGAGGTGCGTTGAAAATAC 58.844 47.619 0.00 0.00 0.00 1.89
94 95 2.570415 TGGGAGGTGCGTTGAAAATA 57.430 45.000 0.00 0.00 0.00 1.40
95 96 1.698506 TTGGGAGGTGCGTTGAAAAT 58.301 45.000 0.00 0.00 0.00 1.82
96 97 1.611491 GATTGGGAGGTGCGTTGAAAA 59.389 47.619 0.00 0.00 0.00 2.29
97 98 1.202879 AGATTGGGAGGTGCGTTGAAA 60.203 47.619 0.00 0.00 0.00 2.69
98 99 0.400213 AGATTGGGAGGTGCGTTGAA 59.600 50.000 0.00 0.00 0.00 2.69
99 100 0.321564 CAGATTGGGAGGTGCGTTGA 60.322 55.000 0.00 0.00 0.00 3.18
100 101 0.606401 ACAGATTGGGAGGTGCGTTG 60.606 55.000 0.00 0.00 0.00 4.10
101 102 0.110486 AACAGATTGGGAGGTGCGTT 59.890 50.000 0.00 0.00 0.00 4.84
102 103 0.981183 TAACAGATTGGGAGGTGCGT 59.019 50.000 0.00 0.00 0.00 5.24
103 104 1.338674 TGTAACAGATTGGGAGGTGCG 60.339 52.381 0.00 0.00 0.00 5.34
104 105 2.489938 TGTAACAGATTGGGAGGTGC 57.510 50.000 0.00 0.00 0.00 5.01
105 106 4.021102 ACTTGTAACAGATTGGGAGGTG 57.979 45.455 0.00 0.00 0.00 4.00
106 107 5.836024 TTACTTGTAACAGATTGGGAGGT 57.164 39.130 0.00 0.00 0.00 3.85
107 108 6.001460 TGTTTACTTGTAACAGATTGGGAGG 58.999 40.000 0.00 0.00 32.15 4.30
108 109 7.687941 ATGTTTACTTGTAACAGATTGGGAG 57.312 36.000 0.00 0.00 38.74 4.30
109 110 8.598916 TCTATGTTTACTTGTAACAGATTGGGA 58.401 33.333 0.00 0.00 38.74 4.37
110 111 8.786826 TCTATGTTTACTTGTAACAGATTGGG 57.213 34.615 0.00 0.00 38.74 4.12
114 115 9.614792 GGGAATCTATGTTTACTTGTAACAGAT 57.385 33.333 0.00 0.00 38.74 2.90
115 116 8.598916 TGGGAATCTATGTTTACTTGTAACAGA 58.401 33.333 0.00 0.00 38.74 3.41
116 117 8.786826 TGGGAATCTATGTTTACTTGTAACAG 57.213 34.615 0.00 0.00 38.74 3.16
117 118 8.598916 TCTGGGAATCTATGTTTACTTGTAACA 58.401 33.333 0.00 0.00 39.58 2.41
118 119 9.444600 TTCTGGGAATCTATGTTTACTTGTAAC 57.555 33.333 0.00 0.00 0.00 2.50
121 122 9.533831 AATTTCTGGGAATCTATGTTTACTTGT 57.466 29.630 0.00 0.00 0.00 3.16
183 184 9.549509 GCAAATGTGAAGTTCGTTTTATATACA 57.450 29.630 0.00 0.00 0.00 2.29
184 185 9.549509 TGCAAATGTGAAGTTCGTTTTATATAC 57.450 29.630 0.00 0.00 0.00 1.47
186 187 8.911662 GTTGCAAATGTGAAGTTCGTTTTATAT 58.088 29.630 0.00 0.00 0.00 0.86
187 188 8.132362 AGTTGCAAATGTGAAGTTCGTTTTATA 58.868 29.630 0.00 0.00 0.00 0.98
188 189 6.978080 AGTTGCAAATGTGAAGTTCGTTTTAT 59.022 30.769 0.00 0.00 0.00 1.40
189 190 6.326375 AGTTGCAAATGTGAAGTTCGTTTTA 58.674 32.000 0.00 0.00 0.00 1.52
190 191 5.167845 AGTTGCAAATGTGAAGTTCGTTTT 58.832 33.333 0.00 0.00 0.00 2.43
191 192 4.743493 AGTTGCAAATGTGAAGTTCGTTT 58.257 34.783 0.00 0.00 0.00 3.60
192 193 4.370364 AGTTGCAAATGTGAAGTTCGTT 57.630 36.364 0.00 0.00 0.00 3.85
193 194 5.008613 ACATAGTTGCAAATGTGAAGTTCGT 59.991 36.000 26.87 3.07 35.06 3.85
194 195 5.451908 ACATAGTTGCAAATGTGAAGTTCG 58.548 37.500 26.87 2.39 35.06 3.95
202 203 3.495331 TGGTCCACATAGTTGCAAATGT 58.505 40.909 10.14 10.26 36.78 2.71
203 204 3.674138 GCTGGTCCACATAGTTGCAAATG 60.674 47.826 10.14 9.57 0.00 2.32
204 205 2.493278 GCTGGTCCACATAGTTGCAAAT 59.507 45.455 4.23 4.23 0.00 2.32
205 206 1.885887 GCTGGTCCACATAGTTGCAAA 59.114 47.619 0.00 0.00 0.00 3.68
206 207 1.202867 TGCTGGTCCACATAGTTGCAA 60.203 47.619 0.00 0.00 0.00 4.08
207 208 0.399833 TGCTGGTCCACATAGTTGCA 59.600 50.000 0.00 0.00 0.00 4.08
208 209 1.533625 TTGCTGGTCCACATAGTTGC 58.466 50.000 0.00 0.00 0.00 4.17
209 210 3.627577 GGTATTGCTGGTCCACATAGTTG 59.372 47.826 0.00 0.00 0.00 3.16
210 211 3.681594 CGGTATTGCTGGTCCACATAGTT 60.682 47.826 0.00 0.00 0.00 2.24
211 212 2.158957 CGGTATTGCTGGTCCACATAGT 60.159 50.000 0.00 0.00 0.00 2.12
212 213 2.483876 CGGTATTGCTGGTCCACATAG 58.516 52.381 0.00 0.00 0.00 2.23
213 214 1.474320 GCGGTATTGCTGGTCCACATA 60.474 52.381 0.00 0.00 0.00 2.29
214 215 0.748005 GCGGTATTGCTGGTCCACAT 60.748 55.000 0.00 0.00 0.00 3.21
215 216 1.376683 GCGGTATTGCTGGTCCACA 60.377 57.895 0.00 0.00 0.00 4.17
216 217 2.112815 GGCGGTATTGCTGGTCCAC 61.113 63.158 0.00 0.00 34.52 4.02
217 218 1.847798 AAGGCGGTATTGCTGGTCCA 61.848 55.000 0.00 0.00 34.52 4.02
218 219 1.077716 AAGGCGGTATTGCTGGTCC 60.078 57.895 0.00 0.00 34.52 4.46
219 220 0.392461 TGAAGGCGGTATTGCTGGTC 60.392 55.000 0.00 0.00 34.52 4.02
220 221 0.255890 ATGAAGGCGGTATTGCTGGT 59.744 50.000 0.00 0.00 34.52 4.00
221 222 2.254546 TATGAAGGCGGTATTGCTGG 57.745 50.000 0.00 0.00 34.52 4.85
222 223 3.814842 TGAATATGAAGGCGGTATTGCTG 59.185 43.478 0.00 0.00 34.52 4.41
223 224 4.085357 TGAATATGAAGGCGGTATTGCT 57.915 40.909 0.00 0.00 34.52 3.91
224 225 4.216257 ACATGAATATGAAGGCGGTATTGC 59.784 41.667 0.00 0.00 37.73 3.56
225 226 5.469760 TGACATGAATATGAAGGCGGTATTG 59.530 40.000 0.00 0.00 37.73 1.90
226 227 5.620206 TGACATGAATATGAAGGCGGTATT 58.380 37.500 0.00 0.00 37.73 1.89
227 228 5.227569 TGACATGAATATGAAGGCGGTAT 57.772 39.130 0.00 0.00 37.73 2.73
228 229 4.681074 TGACATGAATATGAAGGCGGTA 57.319 40.909 0.00 0.00 37.73 4.02
229 230 3.558931 TGACATGAATATGAAGGCGGT 57.441 42.857 0.00 0.00 37.73 5.68
230 231 4.898829 TTTGACATGAATATGAAGGCGG 57.101 40.909 0.00 0.00 37.73 6.13
261 262 8.673711 CGTCCCATTTCTCATAATTTTCAACTA 58.326 33.333 0.00 0.00 0.00 2.24
262 263 7.393234 TCGTCCCATTTCTCATAATTTTCAACT 59.607 33.333 0.00 0.00 0.00 3.16
263 264 7.484959 GTCGTCCCATTTCTCATAATTTTCAAC 59.515 37.037 0.00 0.00 0.00 3.18
264 265 7.362574 GGTCGTCCCATTTCTCATAATTTTCAA 60.363 37.037 0.00 0.00 0.00 2.69
265 266 6.094881 GGTCGTCCCATTTCTCATAATTTTCA 59.905 38.462 0.00 0.00 0.00 2.69
266 267 6.094881 TGGTCGTCCCATTTCTCATAATTTTC 59.905 38.462 0.00 0.00 38.72 2.29
267 268 5.949354 TGGTCGTCCCATTTCTCATAATTTT 59.051 36.000 0.00 0.00 38.72 1.82
268 269 5.505780 TGGTCGTCCCATTTCTCATAATTT 58.494 37.500 0.00 0.00 38.72 1.82
269 270 5.110814 TGGTCGTCCCATTTCTCATAATT 57.889 39.130 0.00 0.00 38.72 1.40
270 271 4.771114 TGGTCGTCCCATTTCTCATAAT 57.229 40.909 0.00 0.00 38.72 1.28
271 272 4.561500 TTGGTCGTCCCATTTCTCATAA 57.438 40.909 0.00 0.00 44.74 1.90
272 273 4.561500 TTTGGTCGTCCCATTTCTCATA 57.438 40.909 0.00 0.00 44.74 2.15
273 274 3.433306 TTTGGTCGTCCCATTTCTCAT 57.567 42.857 0.00 0.00 44.74 2.90
274 275 2.940994 TTTGGTCGTCCCATTTCTCA 57.059 45.000 0.00 0.00 44.74 3.27
275 276 2.488153 CCTTTTGGTCGTCCCATTTCTC 59.512 50.000 0.00 0.00 44.74 2.87
276 277 2.514803 CCTTTTGGTCGTCCCATTTCT 58.485 47.619 0.00 0.00 44.74 2.52
277 278 1.544246 CCCTTTTGGTCGTCCCATTTC 59.456 52.381 0.00 0.00 44.74 2.17
278 279 1.146152 TCCCTTTTGGTCGTCCCATTT 59.854 47.619 0.00 0.00 44.74 2.32
279 280 0.774908 TCCCTTTTGGTCGTCCCATT 59.225 50.000 0.00 0.00 44.74 3.16
280 281 0.774908 TTCCCTTTTGGTCGTCCCAT 59.225 50.000 0.00 0.00 44.74 4.00
281 282 0.551879 TTTCCCTTTTGGTCGTCCCA 59.448 50.000 0.00 0.00 43.27 4.37
282 283 1.694844 TTTTCCCTTTTGGTCGTCCC 58.305 50.000 0.00 0.00 38.10 4.46
283 284 4.202172 TGAATTTTTCCCTTTTGGTCGTCC 60.202 41.667 0.00 0.00 38.10 4.79
284 285 4.939271 TGAATTTTTCCCTTTTGGTCGTC 58.061 39.130 0.00 0.00 38.10 4.20
285 286 5.296748 CATGAATTTTTCCCTTTTGGTCGT 58.703 37.500 0.00 0.00 38.10 4.34
286 287 4.152223 GCATGAATTTTTCCCTTTTGGTCG 59.848 41.667 0.00 0.00 38.10 4.79
287 288 5.062528 TGCATGAATTTTTCCCTTTTGGTC 58.937 37.500 0.00 0.00 38.10 4.02
288 289 5.046288 TGCATGAATTTTTCCCTTTTGGT 57.954 34.783 0.00 0.00 38.10 3.67
289 290 6.207928 GTTTGCATGAATTTTTCCCTTTTGG 58.792 36.000 0.00 0.00 39.97 3.28
290 291 6.183360 TGGTTTGCATGAATTTTTCCCTTTTG 60.183 34.615 0.00 0.00 0.00 2.44
291 292 5.890419 TGGTTTGCATGAATTTTTCCCTTTT 59.110 32.000 0.00 0.00 0.00 2.27
292 293 5.444176 TGGTTTGCATGAATTTTTCCCTTT 58.556 33.333 0.00 0.00 0.00 3.11
293 294 5.046288 TGGTTTGCATGAATTTTTCCCTT 57.954 34.783 0.00 0.00 0.00 3.95
294 295 4.703379 TGGTTTGCATGAATTTTTCCCT 57.297 36.364 0.00 0.00 0.00 4.20
295 296 5.247862 AGATGGTTTGCATGAATTTTTCCC 58.752 37.500 0.00 0.00 0.00 3.97
296 297 7.903995 TTAGATGGTTTGCATGAATTTTTCC 57.096 32.000 0.00 0.00 0.00 3.13
297 298 9.153721 TGATTAGATGGTTTGCATGAATTTTTC 57.846 29.630 0.00 0.00 0.00 2.29
298 299 8.938906 GTGATTAGATGGTTTGCATGAATTTTT 58.061 29.630 0.00 0.00 0.00 1.94
299 300 8.095792 TGTGATTAGATGGTTTGCATGAATTTT 58.904 29.630 0.00 0.00 0.00 1.82
300 301 7.613585 TGTGATTAGATGGTTTGCATGAATTT 58.386 30.769 0.00 0.00 0.00 1.82
301 302 7.172868 TGTGATTAGATGGTTTGCATGAATT 57.827 32.000 0.00 0.00 0.00 2.17
302 303 6.778834 TGTGATTAGATGGTTTGCATGAAT 57.221 33.333 0.00 0.00 0.00 2.57
303 304 6.209192 AGTTGTGATTAGATGGTTTGCATGAA 59.791 34.615 0.00 0.00 0.00 2.57
304 305 5.711506 AGTTGTGATTAGATGGTTTGCATGA 59.288 36.000 0.00 0.00 0.00 3.07
305 306 5.957798 AGTTGTGATTAGATGGTTTGCATG 58.042 37.500 0.00 0.00 0.00 4.06
306 307 6.209192 TGAAGTTGTGATTAGATGGTTTGCAT 59.791 34.615 0.00 0.00 0.00 3.96
307 308 5.534278 TGAAGTTGTGATTAGATGGTTTGCA 59.466 36.000 0.00 0.00 0.00 4.08
308 309 6.012658 TGAAGTTGTGATTAGATGGTTTGC 57.987 37.500 0.00 0.00 0.00 3.68
309 310 7.819644 TGATGAAGTTGTGATTAGATGGTTTG 58.180 34.615 0.00 0.00 0.00 2.93
310 311 8.408043 TTGATGAAGTTGTGATTAGATGGTTT 57.592 30.769 0.00 0.00 0.00 3.27
311 312 8.299570 GTTTGATGAAGTTGTGATTAGATGGTT 58.700 33.333 0.00 0.00 0.00 3.67
312 313 7.448161 TGTTTGATGAAGTTGTGATTAGATGGT 59.552 33.333 0.00 0.00 0.00 3.55
313 314 7.819644 TGTTTGATGAAGTTGTGATTAGATGG 58.180 34.615 0.00 0.00 0.00 3.51
314 315 9.850628 ATTGTTTGATGAAGTTGTGATTAGATG 57.149 29.630 0.00 0.00 0.00 2.90
316 317 9.681692 CAATTGTTTGATGAAGTTGTGATTAGA 57.318 29.630 0.00 0.00 34.60 2.10
317 318 9.467258 ACAATTGTTTGATGAAGTTGTGATTAG 57.533 29.630 4.92 0.00 36.64 1.73
319 320 9.814899 TTACAATTGTTTGATGAAGTTGTGATT 57.185 25.926 17.78 0.00 36.64 2.57
320 321 9.985730 ATTACAATTGTTTGATGAAGTTGTGAT 57.014 25.926 17.78 0.00 36.64 3.06
321 322 9.462174 GATTACAATTGTTTGATGAAGTTGTGA 57.538 29.630 17.78 0.00 36.64 3.58
322 323 8.702438 GGATTACAATTGTTTGATGAAGTTGTG 58.298 33.333 17.78 0.00 36.64 3.33
323 324 8.641541 AGGATTACAATTGTTTGATGAAGTTGT 58.358 29.630 17.78 0.00 36.64 3.32
332 333 8.247562 CGGGAAAATAGGATTACAATTGTTTGA 58.752 33.333 17.78 3.95 36.64 2.69
333 334 7.491048 CCGGGAAAATAGGATTACAATTGTTTG 59.509 37.037 17.78 0.00 38.86 2.93
334 335 7.364320 CCCGGGAAAATAGGATTACAATTGTTT 60.364 37.037 18.48 4.84 0.00 2.83
335 336 6.097696 CCCGGGAAAATAGGATTACAATTGTT 59.902 38.462 18.48 0.00 0.00 2.83
336 337 5.596772 CCCGGGAAAATAGGATTACAATTGT 59.403 40.000 18.48 16.68 0.00 2.71
337 338 5.830991 TCCCGGGAAAATAGGATTACAATTG 59.169 40.000 24.50 3.24 0.00 2.32
338 339 6.020881 TCCCGGGAAAATAGGATTACAATT 57.979 37.500 24.50 0.00 0.00 2.32
339 340 5.656549 TCCCGGGAAAATAGGATTACAAT 57.343 39.130 24.50 0.00 0.00 2.71
340 341 5.132985 TGATCCCGGGAAAATAGGATTACAA 59.867 40.000 30.84 0.00 39.24 2.41
341 342 4.661240 TGATCCCGGGAAAATAGGATTACA 59.339 41.667 30.84 9.97 39.24 2.41
342 343 5.237236 TGATCCCGGGAAAATAGGATTAC 57.763 43.478 30.84 7.58 39.24 1.89
343 344 6.044989 TCAATGATCCCGGGAAAATAGGATTA 59.955 38.462 30.84 5.16 39.24 1.75
344 345 5.079643 CAATGATCCCGGGAAAATAGGATT 58.920 41.667 30.84 14.17 39.24 3.01
345 346 4.353788 TCAATGATCCCGGGAAAATAGGAT 59.646 41.667 30.84 8.27 41.86 3.24
346 347 3.719479 TCAATGATCCCGGGAAAATAGGA 59.281 43.478 30.84 20.03 0.00 2.94
347 348 4.098914 TCAATGATCCCGGGAAAATAGG 57.901 45.455 30.84 18.23 0.00 2.57
348 349 4.887071 TGTTCAATGATCCCGGGAAAATAG 59.113 41.667 30.84 17.83 0.00 1.73
349 350 4.861196 TGTTCAATGATCCCGGGAAAATA 58.139 39.130 30.84 14.57 0.00 1.40
350 351 3.707316 TGTTCAATGATCCCGGGAAAAT 58.293 40.909 30.84 21.15 0.00 1.82
351 352 3.162147 TGTTCAATGATCCCGGGAAAA 57.838 42.857 30.84 19.66 0.00 2.29
352 353 2.889170 TGTTCAATGATCCCGGGAAA 57.111 45.000 30.84 20.08 0.00 3.13
353 354 2.889170 TTGTTCAATGATCCCGGGAA 57.111 45.000 30.84 13.46 0.00 3.97
354 355 2.889170 TTTGTTCAATGATCCCGGGA 57.111 45.000 29.18 29.18 0.00 5.14
355 356 4.470334 AATTTTGTTCAATGATCCCGGG 57.530 40.909 16.85 16.85 0.00 5.73
356 357 5.960113 TGTAATTTTGTTCAATGATCCCGG 58.040 37.500 0.00 0.00 0.00 5.73
357 358 7.035004 ACATGTAATTTTGTTCAATGATCCCG 58.965 34.615 0.00 0.00 0.00 5.14
358 359 8.776376 AACATGTAATTTTGTTCAATGATCCC 57.224 30.769 0.00 0.00 30.43 3.85
396 397 9.862149 TGAAGAAGTAAAGTTTAAGGGAAGAAT 57.138 29.630 0.00 0.00 0.00 2.40
397 398 9.338622 CTGAAGAAGTAAAGTTTAAGGGAAGAA 57.661 33.333 0.00 0.00 0.00 2.52
398 399 8.491958 ACTGAAGAAGTAAAGTTTAAGGGAAGA 58.508 33.333 0.00 0.00 37.36 2.87
399 400 8.678593 ACTGAAGAAGTAAAGTTTAAGGGAAG 57.321 34.615 0.00 0.00 37.36 3.46
400 401 9.470399 AAACTGAAGAAGTAAAGTTTAAGGGAA 57.530 29.630 0.00 0.00 40.21 3.97
401 402 9.117183 GAAACTGAAGAAGTAAAGTTTAAGGGA 57.883 33.333 0.00 0.00 41.62 4.20
402 403 8.899771 TGAAACTGAAGAAGTAAAGTTTAAGGG 58.100 33.333 0.00 0.00 41.62 3.95
409 410 9.832445 TGACTTATGAAACTGAAGAAGTAAAGT 57.168 29.630 0.00 0.00 38.56 2.66
433 434 9.720769 GGGCTAGCTAATGTTTACTATTTATGA 57.279 33.333 15.72 0.00 0.00 2.15
434 435 8.656849 CGGGCTAGCTAATGTTTACTATTTATG 58.343 37.037 15.72 0.00 0.00 1.90
435 436 8.373220 ACGGGCTAGCTAATGTTTACTATTTAT 58.627 33.333 15.72 0.00 0.00 1.40
436 437 7.654520 CACGGGCTAGCTAATGTTTACTATTTA 59.345 37.037 15.72 0.00 0.00 1.40
437 438 6.482308 CACGGGCTAGCTAATGTTTACTATTT 59.518 38.462 15.72 0.00 0.00 1.40
438 439 5.989777 CACGGGCTAGCTAATGTTTACTATT 59.010 40.000 15.72 0.00 0.00 1.73
439 440 5.539048 CACGGGCTAGCTAATGTTTACTAT 58.461 41.667 15.72 0.00 0.00 2.12
440 441 4.738541 GCACGGGCTAGCTAATGTTTACTA 60.739 45.833 15.72 0.00 36.96 1.82
441 442 3.793559 CACGGGCTAGCTAATGTTTACT 58.206 45.455 15.72 0.00 0.00 2.24
442 443 2.287103 GCACGGGCTAGCTAATGTTTAC 59.713 50.000 15.72 0.00 36.96 2.01
443 444 2.557317 GCACGGGCTAGCTAATGTTTA 58.443 47.619 15.72 0.00 36.96 2.01
444 445 1.379527 GCACGGGCTAGCTAATGTTT 58.620 50.000 15.72 0.00 36.96 2.83
445 446 3.080647 GCACGGGCTAGCTAATGTT 57.919 52.632 15.72 0.00 36.96 2.71
446 447 4.857251 GCACGGGCTAGCTAATGT 57.143 55.556 15.72 5.32 36.96 2.71
462 463 4.740822 ATCAACCCGTGCCCCAGC 62.741 66.667 0.00 0.00 40.48 4.85
463 464 2.751436 CATCAACCCGTGCCCCAG 60.751 66.667 0.00 0.00 0.00 4.45
464 465 3.253061 TCATCAACCCGTGCCCCA 61.253 61.111 0.00 0.00 0.00 4.96
465 466 1.906105 TAGTCATCAACCCGTGCCCC 61.906 60.000 0.00 0.00 0.00 5.80
466 467 0.462047 CTAGTCATCAACCCGTGCCC 60.462 60.000 0.00 0.00 0.00 5.36
467 468 0.249398 ACTAGTCATCAACCCGTGCC 59.751 55.000 0.00 0.00 0.00 5.01
468 469 2.094762 AACTAGTCATCAACCCGTGC 57.905 50.000 0.00 0.00 0.00 5.34
469 470 4.562082 TGTTAACTAGTCATCAACCCGTG 58.438 43.478 7.22 0.00 0.00 4.94
470 471 4.877378 TGTTAACTAGTCATCAACCCGT 57.123 40.909 7.22 0.00 0.00 5.28
471 472 8.335356 CAATTATGTTAACTAGTCATCAACCCG 58.665 37.037 7.22 0.00 0.00 5.28
472 473 9.391006 TCAATTATGTTAACTAGTCATCAACCC 57.609 33.333 7.22 0.00 0.00 4.11
505 506 5.600898 ACAGGGCCACATTAACTTTAAAAGT 59.399 36.000 6.18 0.00 45.46 2.66
506 507 6.096673 ACAGGGCCACATTAACTTTAAAAG 57.903 37.500 6.18 0.00 0.00 2.27
507 508 6.284459 CAACAGGGCCACATTAACTTTAAAA 58.716 36.000 6.18 0.00 0.00 1.52
508 509 5.740513 GCAACAGGGCCACATTAACTTTAAA 60.741 40.000 6.18 0.00 0.00 1.52
509 510 4.262249 GCAACAGGGCCACATTAACTTTAA 60.262 41.667 6.18 0.00 0.00 1.52
510 511 3.257127 GCAACAGGGCCACATTAACTTTA 59.743 43.478 6.18 0.00 0.00 1.85
511 512 2.037121 GCAACAGGGCCACATTAACTTT 59.963 45.455 6.18 0.00 0.00 2.66
512 513 1.618343 GCAACAGGGCCACATTAACTT 59.382 47.619 6.18 0.00 0.00 2.66
513 514 1.256812 GCAACAGGGCCACATTAACT 58.743 50.000 6.18 0.00 0.00 2.24
514 515 0.965439 TGCAACAGGGCCACATTAAC 59.035 50.000 6.18 0.00 0.00 2.01
515 516 1.342819 GTTGCAACAGGGCCACATTAA 59.657 47.619 24.52 0.00 30.39 1.40
516 517 0.965439 GTTGCAACAGGGCCACATTA 59.035 50.000 24.52 0.00 30.39 1.90
517 518 1.747774 GTTGCAACAGGGCCACATT 59.252 52.632 24.52 0.00 30.39 2.71
518 519 2.563798 CGTTGCAACAGGGCCACAT 61.564 57.895 28.01 0.00 30.39 3.21
519 520 3.215568 CGTTGCAACAGGGCCACA 61.216 61.111 28.01 0.00 30.39 4.17
520 521 4.645921 GCGTTGCAACAGGGCCAC 62.646 66.667 28.01 0.24 0.00 5.01
522 523 4.645921 GTGCGTTGCAACAGGGCC 62.646 66.667 28.01 13.56 41.47 5.80
523 524 4.980903 CGTGCGTTGCAACAGGGC 62.981 66.667 28.01 22.50 41.47 5.19
524 525 4.326766 CCGTGCGTTGCAACAGGG 62.327 66.667 28.01 19.75 41.47 4.45
525 526 4.326766 CCCGTGCGTTGCAACAGG 62.327 66.667 28.01 22.31 41.47 4.00
526 527 4.980903 GCCCGTGCGTTGCAACAG 62.981 66.667 28.01 20.60 41.47 3.16
536 537 0.171903 TACTAGAAGAACGCCCGTGC 59.828 55.000 0.00 0.00 0.00 5.34
537 538 2.159282 ACATACTAGAAGAACGCCCGTG 60.159 50.000 0.00 0.00 0.00 4.94
538 539 2.097825 ACATACTAGAAGAACGCCCGT 58.902 47.619 0.00 0.00 0.00 5.28
539 540 2.865343 ACATACTAGAAGAACGCCCG 57.135 50.000 0.00 0.00 0.00 6.13
540 541 8.684520 ACATATATACATACTAGAAGAACGCCC 58.315 37.037 0.00 0.00 0.00 6.13
541 542 9.504710 CACATATATACATACTAGAAGAACGCC 57.495 37.037 0.00 0.00 0.00 5.68
542 543 9.011407 GCACATATATACATACTAGAAGAACGC 57.989 37.037 0.00 0.00 0.00 4.84
638 639 3.999663 TGTATGATGATTGTGTTGCGACA 59.000 39.130 1.50 1.50 0.00 4.35
732 740 4.684134 AATGCCCGTGCCTTGCCT 62.684 61.111 0.00 0.00 36.33 4.75
752 760 8.366401 GGTTTAGTCTCTTACCTCAAAACTAGT 58.634 37.037 0.00 0.00 0.00 2.57
830 838 6.428159 GGCCATACTAACTATTCTGGACATTG 59.572 42.308 0.00 0.00 31.83 2.82
993 1001 2.397597 GAATGCCCATGGGGTTAATGT 58.602 47.619 32.23 0.00 46.51 2.71
1007 1016 0.378257 ATGTCGTGCAATCGAATGCC 59.622 50.000 22.13 12.50 45.83 4.40
1203 1215 3.299503 GGTATCAATCTTGGCCATGGTT 58.700 45.455 17.95 14.71 0.00 3.67
1680 1697 5.529800 CACCCGTCTTTTTAAAAGAGAGGAA 59.470 40.000 28.13 6.47 31.04 3.36
1683 1700 5.179555 CCTCACCCGTCTTTTTAAAAGAGAG 59.820 44.000 19.01 18.76 0.00 3.20
1700 1717 3.959991 GACGAAGGCAGCCTCACCC 62.960 68.421 16.53 3.71 30.89 4.61
1735 1752 5.003160 CGTATAATGAATCCAATCCAGCCA 58.997 41.667 0.00 0.00 0.00 4.75
1787 1804 5.119694 GGAATACTTGCTTCTTCACCCTAG 58.880 45.833 0.00 0.00 0.00 3.02
1834 1851 2.074948 CCTCCCCTGCTGCCTACAT 61.075 63.158 0.00 0.00 0.00 2.29
1994 2021 4.129737 GCGAGCAGCCTACCACGA 62.130 66.667 0.00 0.00 40.81 4.35
2022 2049 3.349006 CGCAGGTCACAGCACCAC 61.349 66.667 0.00 0.00 39.16 4.16
2048 2075 2.279069 ATATCTGGAGAGCCGGGCG 61.279 63.158 14.39 0.00 41.20 6.13
2071 2098 1.954146 CTAGCACGCACCACACGTT 60.954 57.895 0.00 0.00 42.96 3.99
2088 2115 1.037579 TCCATGCGTCGGATCTGTCT 61.038 55.000 0.42 0.00 0.00 3.41
2146 2173 1.376812 CATGACAGGAGCAGCAGCA 60.377 57.895 3.17 0.00 45.49 4.41
2213 2240 1.079681 TGGATCAACCACGCCGTAC 60.080 57.895 0.00 0.00 44.64 3.67
2225 2252 1.775385 TGCTGATCTACCGTGGATCA 58.225 50.000 22.12 22.12 44.69 2.92
2227 2254 2.042464 ACATGCTGATCTACCGTGGAT 58.958 47.619 0.00 0.00 0.00 3.41
2281 2308 1.226211 CGCTTGCAAATGAGCCGAG 60.226 57.895 0.00 0.00 35.49 4.63
2291 2318 0.955428 CTGAACTAGGCCGCTTGCAA 60.955 55.000 0.00 0.00 43.89 4.08
2334 2405 0.186873 GGGAAGCCACCATGATGGAT 59.813 55.000 20.11 0.00 43.02 3.41
2364 2435 1.745264 GAGCGGAAGATCCCTCCTG 59.255 63.158 9.24 4.99 41.55 3.86
2491 2562 3.161450 AGCCCACACCTGTGTCGT 61.161 61.111 0.00 0.00 42.83 4.34
2494 2565 1.349542 TAACCAGCCCACACCTGTGT 61.350 55.000 4.76 0.00 46.17 3.72
2513 2584 1.690219 GCCCCTCTCACGACCATGAT 61.690 60.000 0.00 0.00 0.00 2.45
2572 2643 1.447838 CCAATCACGAGGACACCCG 60.448 63.158 0.00 0.00 37.58 5.28


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

AutoCloner maintained by Alex Coulton.