Multiple sequence alignment - TraesCS7A01G537000

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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 TraesCS7A01G537000 chr7A 100.000 4570 0 0 1 4570 714598935 714594366 0.000000e+00 8440.0
1 TraesCS7A01G537000 chr7A 87.469 407 38 9 4139 4535 547434769 547435172 1.500000e-124 457.0
2 TraesCS7A01G537000 chr7D 92.553 2511 141 26 388 2866 620489434 620491930 0.000000e+00 3559.0
3 TraesCS7A01G537000 chr7D 92.120 1472 89 15 3099 4546 620492064 620493532 0.000000e+00 2050.0
4 TraesCS7A01G537000 chr7D 93.050 259 18 0 1 259 620489183 620489441 3.340000e-101 379.0
5 TraesCS7A01G537000 chr7D 83.791 401 53 9 4145 4541 30923642 30923250 2.010000e-98 370.0
6 TraesCS7A01G537000 chr7D 82.250 400 62 8 4145 4541 30949059 30948666 2.040000e-88 337.0
7 TraesCS7A01G537000 chr7D 87.288 118 12 3 231 345 620489318 620489435 1.030000e-26 132.0
8 TraesCS7A01G537000 chr7B 91.302 1874 95 22 2430 4277 716263437 716265268 0.000000e+00 2495.0
9 TraesCS7A01G537000 chr7B 91.982 1771 102 28 696 2441 716261627 716263382 0.000000e+00 2447.0
10 TraesCS7A01G537000 chr7B 90.735 313 25 4 1 310 716261106 716261417 9.150000e-112 414.0
11 TraesCS7A01G537000 chr7B 87.328 363 41 4 212 569 716261222 716261584 1.180000e-110 411.0
12 TraesCS7A01G537000 chr7B 88.755 249 26 1 4321 4567 716265259 716265507 2.070000e-78 303.0
13 TraesCS7A01G537000 chr7B 85.470 117 12 3 3954 4070 716265896 716266007 2.890000e-22 117.0
14 TraesCS7A01G537000 chr7B 97.778 45 1 0 637 681 716261585 716261629 1.360000e-10 78.7
15 TraesCS7A01G537000 chr6B 86.070 402 38 13 4147 4535 620577359 620576963 2.540000e-112 416.0
16 TraesCS7A01G537000 chr1A 85.000 400 43 13 4148 4537 569392569 569392177 1.540000e-104 390.0
17 TraesCS7A01G537000 chr6D 84.653 404 44 13 4145 4535 472371103 472370705 1.990000e-103 387.0
18 TraesCS7A01G537000 chr4B 84.694 392 48 11 4147 4533 23437512 23437128 9.280000e-102 381.0
19 TraesCS7A01G537000 chr2A 86.486 333 32 9 4214 4537 421212788 421212460 2.020000e-93 353.0
20 TraesCS7A01G537000 chr4A 97.297 37 1 0 2639 2675 323056878 323056914 3.820000e-06 63.9


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 TraesCS7A01G537000 chr7A 714594366 714598935 4569 True 8440.0 8440 100.000000 1 4570 1 chr7A.!!$R1 4569
1 TraesCS7A01G537000 chr7D 620489183 620493532 4349 False 1530.0 3559 91.252750 1 4546 4 chr7D.!!$F1 4545
2 TraesCS7A01G537000 chr7B 716261106 716266007 4901 False 895.1 2495 90.478571 1 4567 7 chr7B.!!$F1 4566

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
744 748 0.752009 AATGCATGCAGCTCTCCTGG 60.752 55.000 26.69 0.0 45.94 4.45 F
1470 1477 1.004918 AGGGTTCGCTTCGGAACAG 60.005 57.895 7.62 0.0 46.34 3.16 F
2203 2225 0.180171 TGCATTGCTAGTGCCCGTAT 59.820 50.000 10.49 0.0 41.83 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2206 0.180171 ATACGGGCACTAGCAATGCA 59.820 50.000 8.35 0.0 45.27 3.96 R
3130 3236 0.456653 GCCATGCCACGTCAACATTC 60.457 55.000 0.00 0.0 0.00 2.67 R
4153 4292 1.003233 GGAGCTCGGCCTTCTTTGT 60.003 57.895 7.83 0.0 0.00 2.83 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
162 164 9.528018 TGTTTTCAAGCAAAATCTTAGGTTTAG 57.472 29.630 0.00 0.00 36.35 1.85
208 210 1.480954 AGGTGTTCCGAGCGTATGATT 59.519 47.619 0.00 0.00 39.05 2.57
215 217 3.130633 TCCGAGCGTATGATTGGAAATG 58.869 45.455 6.71 0.00 41.15 2.32
216 218 2.872245 CCGAGCGTATGATTGGAAATGT 59.128 45.455 0.00 0.00 37.20 2.71
217 219 3.312421 CCGAGCGTATGATTGGAAATGTT 59.688 43.478 0.00 0.00 37.20 2.71
218 220 4.201910 CCGAGCGTATGATTGGAAATGTTT 60.202 41.667 0.00 0.00 37.20 2.83
219 221 5.331902 CGAGCGTATGATTGGAAATGTTTT 58.668 37.500 0.00 0.00 0.00 2.43
220 222 5.227805 CGAGCGTATGATTGGAAATGTTTTG 59.772 40.000 0.00 0.00 0.00 2.44
221 223 6.024552 AGCGTATGATTGGAAATGTTTTGT 57.975 33.333 0.00 0.00 0.00 2.83
222 224 6.454795 AGCGTATGATTGGAAATGTTTTGTT 58.545 32.000 0.00 0.00 0.00 2.83
223 225 6.365789 AGCGTATGATTGGAAATGTTTTGTTG 59.634 34.615 0.00 0.00 0.00 3.33
224 226 6.524490 CGTATGATTGGAAATGTTTTGTTGC 58.476 36.000 0.00 0.00 0.00 4.17
225 227 6.145209 CGTATGATTGGAAATGTTTTGTTGCA 59.855 34.615 0.00 0.00 0.00 4.08
226 228 5.987777 TGATTGGAAATGTTTTGTTGCAG 57.012 34.783 0.00 0.00 0.00 4.41
227 229 4.272991 TGATTGGAAATGTTTTGTTGCAGC 59.727 37.500 0.00 0.00 0.00 5.25
228 230 2.559440 TGGAAATGTTTTGTTGCAGCC 58.441 42.857 0.00 0.00 0.00 4.85
229 231 2.170187 TGGAAATGTTTTGTTGCAGCCT 59.830 40.909 0.00 0.00 0.00 4.58
230 232 3.386078 TGGAAATGTTTTGTTGCAGCCTA 59.614 39.130 0.00 0.00 0.00 3.93
231 233 4.040217 TGGAAATGTTTTGTTGCAGCCTAT 59.960 37.500 0.00 0.00 0.00 2.57
232 234 4.389687 GGAAATGTTTTGTTGCAGCCTATG 59.610 41.667 0.00 0.00 0.00 2.23
233 235 4.605640 AATGTTTTGTTGCAGCCTATGT 57.394 36.364 0.00 0.00 0.00 2.29
234 236 4.605640 ATGTTTTGTTGCAGCCTATGTT 57.394 36.364 0.00 0.00 0.00 2.71
235 237 4.399004 TGTTTTGTTGCAGCCTATGTTT 57.601 36.364 0.00 0.00 0.00 2.83
236 238 4.367450 TGTTTTGTTGCAGCCTATGTTTC 58.633 39.130 0.00 0.00 0.00 2.78
237 239 4.142071 TGTTTTGTTGCAGCCTATGTTTCA 60.142 37.500 0.00 0.00 0.00 2.69
238 240 4.870123 TTTGTTGCAGCCTATGTTTCAT 57.130 36.364 0.00 0.00 0.00 2.57
239 241 3.853831 TGTTGCAGCCTATGTTTCATG 57.146 42.857 0.00 0.00 0.00 3.07
240 242 3.156293 TGTTGCAGCCTATGTTTCATGT 58.844 40.909 0.00 0.00 0.00 3.21
241 243 4.331108 TGTTGCAGCCTATGTTTCATGTA 58.669 39.130 0.00 0.00 0.00 2.29
242 244 4.764308 TGTTGCAGCCTATGTTTCATGTAA 59.236 37.500 0.00 0.00 0.00 2.41
243 245 5.242615 TGTTGCAGCCTATGTTTCATGTAAA 59.757 36.000 0.00 0.00 0.00 2.01
244 246 5.973899 TGCAGCCTATGTTTCATGTAAAA 57.026 34.783 0.00 0.00 0.00 1.52
245 247 6.528537 TGCAGCCTATGTTTCATGTAAAAT 57.471 33.333 0.00 0.00 0.00 1.82
246 248 6.563422 TGCAGCCTATGTTTCATGTAAAATC 58.437 36.000 0.00 0.00 0.00 2.17
247 249 6.377996 TGCAGCCTATGTTTCATGTAAAATCT 59.622 34.615 0.00 0.00 0.00 2.40
248 250 7.093814 TGCAGCCTATGTTTCATGTAAAATCTT 60.094 33.333 0.00 0.00 0.00 2.40
249 251 8.405531 GCAGCCTATGTTTCATGTAAAATCTTA 58.594 33.333 0.00 0.00 0.00 2.10
250 252 9.941664 CAGCCTATGTTTCATGTAAAATCTTAG 57.058 33.333 0.00 0.00 0.00 2.18
251 253 9.125026 AGCCTATGTTTCATGTAAAATCTTAGG 57.875 33.333 0.00 2.75 0.00 2.69
252 254 8.903820 GCCTATGTTTCATGTAAAATCTTAGGT 58.096 33.333 12.46 0.00 30.47 3.08
261 263 9.739276 TCATGTAAAATCTTAGGTTTGATGAGT 57.261 29.630 0.00 0.00 0.00 3.41
264 266 8.296713 TGTAAAATCTTAGGTTTGATGAGTTGC 58.703 33.333 0.00 0.00 0.00 4.17
265 267 7.530426 AAAATCTTAGGTTTGATGAGTTGCT 57.470 32.000 0.00 0.00 0.00 3.91
266 268 8.635765 AAAATCTTAGGTTTGATGAGTTGCTA 57.364 30.769 0.00 0.00 0.00 3.49
267 269 8.814038 AAATCTTAGGTTTGATGAGTTGCTAT 57.186 30.769 0.00 0.00 0.00 2.97
268 270 9.905713 AAATCTTAGGTTTGATGAGTTGCTATA 57.094 29.630 0.00 0.00 0.00 1.31
269 271 9.905713 AATCTTAGGTTTGATGAGTTGCTATAA 57.094 29.630 0.00 0.00 0.00 0.98
270 272 8.948631 TCTTAGGTTTGATGAGTTGCTATAAG 57.051 34.615 0.00 0.00 0.00 1.73
271 273 8.540388 TCTTAGGTTTGATGAGTTGCTATAAGT 58.460 33.333 0.00 0.00 0.00 2.24
272 274 6.992063 AGGTTTGATGAGTTGCTATAAGTG 57.008 37.500 0.00 0.00 0.00 3.16
273 275 6.711277 AGGTTTGATGAGTTGCTATAAGTGA 58.289 36.000 0.00 0.00 0.00 3.41
274 276 6.820656 AGGTTTGATGAGTTGCTATAAGTGAG 59.179 38.462 0.00 0.00 0.00 3.51
275 277 6.595716 GGTTTGATGAGTTGCTATAAGTGAGT 59.404 38.462 0.00 0.00 0.00 3.41
276 278 7.119846 GGTTTGATGAGTTGCTATAAGTGAGTT 59.880 37.037 0.00 0.00 0.00 3.01
277 279 9.151471 GTTTGATGAGTTGCTATAAGTGAGTTA 57.849 33.333 0.00 0.00 0.00 2.24
278 280 8.703604 TTGATGAGTTGCTATAAGTGAGTTAC 57.296 34.615 0.00 0.00 0.00 2.50
279 281 7.265673 TGATGAGTTGCTATAAGTGAGTTACC 58.734 38.462 0.00 0.00 0.00 2.85
280 282 6.599356 TGAGTTGCTATAAGTGAGTTACCA 57.401 37.500 0.00 0.00 0.00 3.25
281 283 7.182817 TGAGTTGCTATAAGTGAGTTACCAT 57.817 36.000 0.00 0.00 0.00 3.55
282 284 8.301252 TGAGTTGCTATAAGTGAGTTACCATA 57.699 34.615 0.00 0.00 0.00 2.74
283 285 8.414003 TGAGTTGCTATAAGTGAGTTACCATAG 58.586 37.037 0.00 1.79 32.16 2.23
284 286 8.534954 AGTTGCTATAAGTGAGTTACCATAGA 57.465 34.615 7.91 0.00 31.29 1.98
285 287 9.148879 AGTTGCTATAAGTGAGTTACCATAGAT 57.851 33.333 7.91 0.00 31.29 1.98
286 288 9.197694 GTTGCTATAAGTGAGTTACCATAGATG 57.802 37.037 7.91 0.00 31.29 2.90
287 289 8.478775 TGCTATAAGTGAGTTACCATAGATGT 57.521 34.615 7.91 0.00 31.29 3.06
288 290 8.924303 TGCTATAAGTGAGTTACCATAGATGTT 58.076 33.333 7.91 0.00 31.29 2.71
289 291 9.765795 GCTATAAGTGAGTTACCATAGATGTTT 57.234 33.333 7.91 0.00 31.29 2.83
293 295 8.498054 AAGTGAGTTACCATAGATGTTTGATG 57.502 34.615 0.00 0.00 0.00 3.07
294 296 7.624549 AGTGAGTTACCATAGATGTTTGATGT 58.375 34.615 0.00 0.00 0.00 3.06
295 297 8.758829 AGTGAGTTACCATAGATGTTTGATGTA 58.241 33.333 0.00 0.00 0.00 2.29
296 298 9.547753 GTGAGTTACCATAGATGTTTGATGTAT 57.452 33.333 0.00 0.00 0.00 2.29
297 299 9.546428 TGAGTTACCATAGATGTTTGATGTATG 57.454 33.333 0.00 0.00 0.00 2.39
298 300 9.764363 GAGTTACCATAGATGTTTGATGTATGA 57.236 33.333 0.00 0.00 29.73 2.15
301 303 7.991084 ACCATAGATGTTTGATGTATGATGG 57.009 36.000 0.00 0.00 36.89 3.51
302 304 6.944290 ACCATAGATGTTTGATGTATGATGGG 59.056 38.462 0.00 0.00 35.48 4.00
303 305 7.170277 CCATAGATGTTTGATGTATGATGGGA 58.830 38.462 0.00 0.00 29.73 4.37
304 306 7.666804 CCATAGATGTTTGATGTATGATGGGAA 59.333 37.037 0.00 0.00 29.73 3.97
305 307 9.070179 CATAGATGTTTGATGTATGATGGGAAA 57.930 33.333 0.00 0.00 29.73 3.13
306 308 7.578310 AGATGTTTGATGTATGATGGGAAAG 57.422 36.000 0.00 0.00 0.00 2.62
329 331 1.643868 TTGCTGCGGCCTATGTTTCG 61.644 55.000 16.57 0.00 37.74 3.46
348 350 7.357303 TGTTTCGAGTAAAATCTTAGGTTTGC 58.643 34.615 0.00 0.00 0.00 3.68
355 357 8.465273 AGTAAAATCTTAGGTTTGCTGAGTTT 57.535 30.769 0.00 0.00 29.87 2.66
358 360 6.566197 AATCTTAGGTTTGCTGAGTTTCTG 57.434 37.500 0.00 0.00 0.00 3.02
362 364 6.706270 TCTTAGGTTTGCTGAGTTTCTGTAAG 59.294 38.462 0.00 0.00 0.00 2.34
372 374 4.127171 GAGTTTCTGTAAGTGAGTTGCCA 58.873 43.478 0.00 0.00 33.76 4.92
379 381 5.187772 TCTGTAAGTGAGTTGCCATAGATGT 59.812 40.000 0.00 0.00 33.76 3.06
382 384 6.714810 TGTAAGTGAGTTGCCATAGATGTTTT 59.285 34.615 0.00 0.00 0.00 2.43
385 387 5.413833 AGTGAGTTGCCATAGATGTTTTGAG 59.586 40.000 0.00 0.00 0.00 3.02
394 396 7.227314 TGCCATAGATGTTTTGAGTGTATGATC 59.773 37.037 0.00 0.00 0.00 2.92
591 595 6.063640 AGCAAGGCAATTTGATTTGTTTTC 57.936 33.333 0.00 0.00 0.00 2.29
615 619 7.723324 TCCCTACATCTGCTTGTACTATAAAC 58.277 38.462 0.00 0.00 0.00 2.01
647 651 3.521531 AGGAGATTCCTCAGACCCTTTTC 59.478 47.826 0.00 0.00 45.66 2.29
712 716 5.546621 ACATGGTAGACAAAGTGTGTACT 57.453 39.130 13.42 0.00 43.92 2.73
714 718 7.058023 ACATGGTAGACAAAGTGTGTACTTA 57.942 36.000 13.42 5.92 46.14 2.24
744 748 0.752009 AATGCATGCAGCTCTCCTGG 60.752 55.000 26.69 0.00 45.94 4.45
1227 1234 1.621992 TGAGCTTTCTCGACTCTGGT 58.378 50.000 0.00 0.00 42.26 4.00
1470 1477 1.004918 AGGGTTCGCTTCGGAACAG 60.005 57.895 7.62 0.00 46.34 3.16
1474 1481 1.128692 GGTTCGCTTCGGAACAGAATG 59.871 52.381 7.62 0.00 46.34 2.67
1629 1636 1.270971 GTGGCATGCTTTATGTTGCG 58.729 50.000 18.92 0.00 39.08 4.85
1710 1717 2.245159 CTGTCCAACTGTCAGCAGAA 57.755 50.000 0.00 0.00 45.28 3.02
1729 1736 5.163683 GCAGAACATAATGTCAGCATTGAGT 60.164 40.000 3.39 0.00 44.32 3.41
1793 1800 3.763097 TGTTGTTGTTCTCAAGCACAG 57.237 42.857 0.00 0.00 33.97 3.66
1858 1865 4.878397 CACTGGGGAGACATTTGTAGATTC 59.122 45.833 0.00 0.00 0.00 2.52
1872 1879 5.823209 TGTAGATTCGTGGAAGTTCGATA 57.177 39.130 0.00 0.00 36.01 2.92
1874 1881 7.500720 TGTAGATTCGTGGAAGTTCGATATA 57.499 36.000 0.00 0.00 36.01 0.86
1884 1891 7.042051 CGTGGAAGTTCGATATAATGGTCATTT 60.042 37.037 1.28 0.00 32.50 2.32
1898 1905 8.406730 TAATGGTCATTTCATATGCTTATGCA 57.593 30.769 13.42 5.68 41.59 3.96
1920 1927 6.098679 GCACATTCAGTTGGCAAAATATACA 58.901 36.000 0.00 0.00 0.00 2.29
1948 1955 8.581578 TCAATTTTACCACCTGGAAGTTTAATC 58.418 33.333 0.00 0.00 38.94 1.75
1958 1965 7.444183 CACCTGGAAGTTTAATCTTGTGTCTTA 59.556 37.037 0.00 0.00 0.00 2.10
1971 1992 7.482169 TCTTGTGTCTTACTCTGAATGGTAT 57.518 36.000 0.00 0.00 0.00 2.73
2063 2085 2.079158 GTAAGGGGGTAGAAACGCAAC 58.921 52.381 0.00 0.00 40.22 4.17
2079 2101 6.869421 AACGCAACAAACATATTCTTATGC 57.131 33.333 0.00 0.00 39.09 3.14
2090 2112 7.502120 ACATATTCTTATGCTTGTGGATGAC 57.498 36.000 0.00 0.00 39.09 3.06
2096 2118 7.558161 TCTTATGCTTGTGGATGACAATTAG 57.442 36.000 0.00 0.00 43.78 1.73
2112 2134 5.748402 ACAATTAGCCTCTTGATGTGATCA 58.252 37.500 0.00 0.00 37.55 2.92
2184 2206 7.973402 AGAGCTTAATAACAATTTGGGGTTTT 58.027 30.769 0.78 0.00 0.00 2.43
2185 2207 7.877612 AGAGCTTAATAACAATTTGGGGTTTTG 59.122 33.333 0.78 0.00 0.00 2.44
2186 2208 6.429692 AGCTTAATAACAATTTGGGGTTTTGC 59.570 34.615 0.78 0.00 0.00 3.68
2187 2209 6.205658 GCTTAATAACAATTTGGGGTTTTGCA 59.794 34.615 0.78 0.00 0.00 4.08
2188 2210 7.094420 GCTTAATAACAATTTGGGGTTTTGCAT 60.094 33.333 0.78 0.00 0.00 3.96
2189 2211 8.697507 TTAATAACAATTTGGGGTTTTGCATT 57.302 26.923 0.78 0.00 0.00 3.56
2190 2212 4.915158 AACAATTTGGGGTTTTGCATTG 57.085 36.364 0.78 0.00 0.00 2.82
2191 2213 2.622470 ACAATTTGGGGTTTTGCATTGC 59.378 40.909 0.46 0.46 0.00 3.56
2192 2214 2.885894 CAATTTGGGGTTTTGCATTGCT 59.114 40.909 10.49 0.00 0.00 3.91
2193 2215 4.070716 CAATTTGGGGTTTTGCATTGCTA 58.929 39.130 10.49 0.00 0.00 3.49
2194 2216 3.399440 TTTGGGGTTTTGCATTGCTAG 57.601 42.857 10.49 0.00 0.00 3.42
2195 2217 2.008242 TGGGGTTTTGCATTGCTAGT 57.992 45.000 10.49 0.00 0.00 2.57
2196 2218 1.617850 TGGGGTTTTGCATTGCTAGTG 59.382 47.619 10.49 0.00 0.00 2.74
2197 2219 1.672737 GGGGTTTTGCATTGCTAGTGC 60.673 52.381 10.49 0.00 42.81 4.40
2198 2220 1.672737 GGGTTTTGCATTGCTAGTGCC 60.673 52.381 10.49 5.86 41.83 5.01
2199 2221 1.672737 GGTTTTGCATTGCTAGTGCCC 60.673 52.381 10.49 0.00 41.83 5.36
2203 2225 0.180171 TGCATTGCTAGTGCCCGTAT 59.820 50.000 10.49 0.00 41.83 3.06
2204 2226 0.868406 GCATTGCTAGTGCCCGTATC 59.132 55.000 0.16 0.00 38.71 2.24
2205 2227 1.810031 GCATTGCTAGTGCCCGTATCA 60.810 52.381 0.16 0.00 38.71 2.15
2206 2228 2.771089 CATTGCTAGTGCCCGTATCAT 58.229 47.619 0.00 0.00 38.71 2.45
2207 2229 2.526304 TTGCTAGTGCCCGTATCATC 57.474 50.000 0.00 0.00 38.71 2.92
2208 2230 1.704641 TGCTAGTGCCCGTATCATCT 58.295 50.000 0.00 0.00 38.71 2.90
2209 2231 2.039418 TGCTAGTGCCCGTATCATCTT 58.961 47.619 0.00 0.00 38.71 2.40
2210 2232 2.434336 TGCTAGTGCCCGTATCATCTTT 59.566 45.455 0.00 0.00 38.71 2.52
2280 2308 8.553459 AGAAATATTATTATGGCTCAGTTCGG 57.447 34.615 0.00 0.00 0.00 4.30
2284 2312 9.436957 AATATTATTATGGCTCAGTTCGGTTAG 57.563 33.333 0.00 0.00 0.00 2.34
2289 2317 2.367567 TGGCTCAGTTCGGTTAGTTTCT 59.632 45.455 0.00 0.00 0.00 2.52
2293 2321 4.510340 GCTCAGTTCGGTTAGTTTCTTCAA 59.490 41.667 0.00 0.00 0.00 2.69
2296 2324 5.404366 TCAGTTCGGTTAGTTTCTTCAATCG 59.596 40.000 0.00 0.00 0.00 3.34
2308 2340 7.722363 AGTTTCTTCAATCGGTTTAACCATTT 58.278 30.769 14.97 3.96 38.47 2.32
2311 2343 7.045126 TCTTCAATCGGTTTAACCATTTGTT 57.955 32.000 14.97 0.00 38.47 2.83
2372 2404 4.877823 TGATAGGACATGCAGAAATGTGTC 59.122 41.667 7.23 7.23 40.87 3.67
2406 2438 8.575649 TGTCTTGTATGACTATGAGTAACAGA 57.424 34.615 0.00 0.00 37.79 3.41
2407 2439 9.190317 TGTCTTGTATGACTATGAGTAACAGAT 57.810 33.333 0.00 0.00 37.79 2.90
2425 2457 5.724328 ACAGATATATGATGGTACTTGCCG 58.276 41.667 3.93 0.00 0.00 5.69
2426 2458 5.480422 ACAGATATATGATGGTACTTGCCGA 59.520 40.000 3.93 0.00 0.00 5.54
2470 2576 5.409520 GGGACCAAATGAAGATTTTCTTTGC 59.590 40.000 11.83 0.00 36.73 3.68
2606 2712 5.396884 GCCCATACTAAGTTCAGAACCATCT 60.397 44.000 9.85 0.00 35.88 2.90
2615 2721 5.003804 AGTTCAGAACCATCTATTTGCGTT 58.996 37.500 9.85 0.00 33.50 4.84
2621 2727 3.686016 ACCATCTATTTGCGTTCAACCT 58.314 40.909 0.00 0.00 30.75 3.50
2643 2749 5.468072 CCTATACAGCCACATGATGAGTTTC 59.532 44.000 0.00 0.00 0.00 2.78
2794 2900 7.226720 ACTTCCATAATGTTTGGCGTATTCTAG 59.773 37.037 0.00 0.00 34.06 2.43
2821 2927 5.314923 ACTGTGCATGACATTATGGTTTC 57.685 39.130 0.00 0.00 32.74 2.78
2827 2933 8.136800 TGTGCATGACATTATGGTTTCATATTC 58.863 33.333 0.00 0.00 35.94 1.75
2871 2977 8.986477 ATTTACAAACTCAGAATTAACATGCC 57.014 30.769 0.00 0.00 0.00 4.40
2872 2978 7.517614 TTACAAACTCAGAATTAACATGCCA 57.482 32.000 0.00 0.00 0.00 4.92
2879 2985 8.438676 ACTCAGAATTAACATGCCACTATTAC 57.561 34.615 0.00 0.00 0.00 1.89
2917 3023 3.739703 CAGCATATGGAGCATGGGT 57.260 52.632 4.56 0.00 0.00 4.51
2980 3086 7.709613 GGCTTCTCTGAATGCAAAATTGATATT 59.290 33.333 0.00 0.00 0.00 1.28
2984 3090 9.797556 TCTCTGAATGCAAAATTGATATTTGAG 57.202 29.630 0.00 8.39 39.56 3.02
3033 3139 9.112725 TGATGTTGTAAAATAGAGACATGATGG 57.887 33.333 0.00 0.00 0.00 3.51
3034 3140 9.113838 GATGTTGTAAAATAGAGACATGATGGT 57.886 33.333 0.00 0.00 0.00 3.55
3035 3141 8.862325 TGTTGTAAAATAGAGACATGATGGTT 57.138 30.769 0.00 0.00 0.00 3.67
3036 3142 8.946085 TGTTGTAAAATAGAGACATGATGGTTC 58.054 33.333 0.00 0.00 0.00 3.62
3037 3143 9.167311 GTTGTAAAATAGAGACATGATGGTTCT 57.833 33.333 0.00 1.92 0.00 3.01
3038 3144 8.948631 TGTAAAATAGAGACATGATGGTTCTC 57.051 34.615 0.00 0.31 0.00 2.87
3039 3145 8.762645 TGTAAAATAGAGACATGATGGTTCTCT 58.237 33.333 16.62 16.62 40.43 3.10
3042 3148 8.546083 AAATAGAGACATGATGGTTCTCTACT 57.454 34.615 19.10 10.23 41.14 2.57
3043 3149 8.546083 AATAGAGACATGATGGTTCTCTACTT 57.454 34.615 19.10 13.60 41.14 2.24
3062 3168 8.840200 TCTACTTTATGGATGGTTCTCTACTT 57.160 34.615 0.00 0.00 0.00 2.24
3065 3171 8.794335 ACTTTATGGATGGTTCTCTACTTTTC 57.206 34.615 0.00 0.00 0.00 2.29
3066 3172 8.383175 ACTTTATGGATGGTTCTCTACTTTTCA 58.617 33.333 0.00 0.00 0.00 2.69
3067 3173 9.231297 CTTTATGGATGGTTCTCTACTTTTCAA 57.769 33.333 0.00 0.00 0.00 2.69
3094 3200 1.752498 ACTGCACATTACCATGGCATG 59.248 47.619 20.56 20.56 36.55 4.06
3096 3202 2.950975 CTGCACATTACCATGGCATGTA 59.049 45.455 23.52 14.52 36.55 2.29
3119 3225 8.190122 TGTATGCATTTAAAATCCAGTGATCAC 58.810 33.333 18.47 18.47 0.00 3.06
3130 3236 2.125952 TGATCACGCCGTCAGCTG 60.126 61.111 7.63 7.63 40.39 4.24
3134 3240 1.086067 ATCACGCCGTCAGCTGAATG 61.086 55.000 20.19 14.05 40.39 2.67
3149 3255 0.456653 GAATGTTGACGTGGCATGGC 60.457 55.000 13.29 13.29 0.00 4.40
3152 3258 1.081242 GTTGACGTGGCATGGCTTG 60.081 57.895 21.08 14.55 0.00 4.01
3167 3280 7.725397 TGGCATGGCTTGTATAGAAAATAGAAT 59.275 33.333 21.08 0.00 0.00 2.40
3207 3320 4.942852 TGTGAAGCAGTGGGTTAAAATTG 58.057 39.130 0.00 0.00 34.25 2.32
3213 3326 5.079643 AGCAGTGGGTTAAAATTGATCACT 58.920 37.500 0.00 0.00 34.78 3.41
3214 3327 6.245408 AGCAGTGGGTTAAAATTGATCACTA 58.755 36.000 0.00 0.00 33.39 2.74
3217 3330 7.335924 GCAGTGGGTTAAAATTGATCACTACTA 59.664 37.037 0.00 0.00 33.39 1.82
3222 3335 7.284489 GGGTTAAAATTGATCACTACTATGGCA 59.716 37.037 0.00 0.00 0.00 4.92
3244 3357 5.377358 CAGAAGCTTTGTGTCAGAATTACG 58.623 41.667 0.00 0.00 0.00 3.18
3428 3545 1.153369 CCGTCGCCACTTCCATGAT 60.153 57.895 0.00 0.00 0.00 2.45
3437 3554 3.002656 GCCACTTCCATGATGACATAACG 59.997 47.826 0.00 0.00 35.09 3.18
3682 3802 1.777272 AGGGCTTCTATCAATCCCCAC 59.223 52.381 0.00 0.00 37.70 4.61
3797 3919 3.406764 AGGCAGATGTCTCTTGTTGTTC 58.593 45.455 0.00 0.00 0.00 3.18
3798 3920 2.485814 GGCAGATGTCTCTTGTTGTTCC 59.514 50.000 0.00 0.00 0.00 3.62
3812 3937 4.608148 TTCCTCCCCTGCAGGAAT 57.392 55.556 34.91 0.00 43.84 3.01
3990 4121 2.127271 TGTTGGTATCCACTGGCATG 57.873 50.000 0.00 0.00 30.78 4.06
4007 4138 4.232221 GGCATGTGCTATTATGTGATTGC 58.768 43.478 4.84 0.00 41.70 3.56
4028 4159 3.734597 GCGTTTCCATGAATATGCAAGCA 60.735 43.478 0.00 0.00 32.79 3.91
4108 4243 2.047061 TCAGTCCACAAGCACCTAGTT 58.953 47.619 0.00 0.00 0.00 2.24
4130 4269 3.845860 TCCTAGGTTGTCTGAGAAGTGT 58.154 45.455 9.08 0.00 0.00 3.55
4153 4292 6.708502 TGTGGAATGAGTAACTCGAAAAATGA 59.291 34.615 0.00 0.00 32.35 2.57
4260 4399 7.806014 CACACGTGCACATGTATACTATGTATA 59.194 37.037 19.35 8.81 36.67 1.47
4297 4436 8.026026 CACAACATTATACTTTTACATGTGGCA 58.974 33.333 9.11 0.00 32.87 4.92
4386 4526 2.831685 TGTACAGCCGACAAATCACT 57.168 45.000 0.00 0.00 0.00 3.41
4436 4576 9.283768 TGATCTTGCGGAATACATATATGTTTT 57.716 29.630 22.90 20.21 41.97 2.43
4441 4581 8.389779 TGCGGAATACATATATGTTTTCATGT 57.610 30.769 32.13 12.86 44.88 3.21
4515 4657 6.267471 TCAAAATACCAAAATCACTGGAGCTT 59.733 34.615 0.00 0.00 37.40 3.74
4567 4709 1.670811 GACATGGAGTATTTGCACCCG 59.329 52.381 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 163 4.932200 GCAACTCACTTATAGCAACTCACT 59.068 41.667 0.00 0.00 0.00 3.41
162 164 4.093556 GGCAACTCACTTATAGCAACTCAC 59.906 45.833 0.00 0.00 0.00 3.51
190 192 1.593006 CCAATCATACGCTCGGAACAC 59.407 52.381 0.00 0.00 0.00 3.32
208 210 2.170187 AGGCTGCAACAAAACATTTCCA 59.830 40.909 0.50 0.00 0.00 3.53
215 217 4.367450 TGAAACATAGGCTGCAACAAAAC 58.633 39.130 0.50 0.00 0.00 2.43
216 218 4.662468 TGAAACATAGGCTGCAACAAAA 57.338 36.364 0.50 0.00 0.00 2.44
217 219 4.039004 ACATGAAACATAGGCTGCAACAAA 59.961 37.500 0.00 0.00 0.00 2.83
218 220 3.573538 ACATGAAACATAGGCTGCAACAA 59.426 39.130 0.00 0.00 0.00 2.83
219 221 3.156293 ACATGAAACATAGGCTGCAACA 58.844 40.909 0.00 0.00 0.00 3.33
220 222 3.855689 ACATGAAACATAGGCTGCAAC 57.144 42.857 0.00 0.00 0.00 4.17
221 223 5.973899 TTTACATGAAACATAGGCTGCAA 57.026 34.783 0.00 0.00 0.00 4.08
222 224 5.973899 TTTTACATGAAACATAGGCTGCA 57.026 34.783 0.00 0.00 0.00 4.41
223 225 6.799512 AGATTTTACATGAAACATAGGCTGC 58.200 36.000 0.00 0.00 0.00 5.25
224 226 9.941664 CTAAGATTTTACATGAAACATAGGCTG 57.058 33.333 0.00 0.00 0.00 4.85
225 227 9.125026 CCTAAGATTTTACATGAAACATAGGCT 57.875 33.333 0.00 0.00 0.00 4.58
226 228 8.903820 ACCTAAGATTTTACATGAAACATAGGC 58.096 33.333 0.00 0.00 31.36 3.93
235 237 9.739276 ACTCATCAAACCTAAGATTTTACATGA 57.261 29.630 0.00 0.00 0.00 3.07
238 240 8.296713 GCAACTCATCAAACCTAAGATTTTACA 58.703 33.333 0.00 0.00 0.00 2.41
239 241 8.515414 AGCAACTCATCAAACCTAAGATTTTAC 58.485 33.333 0.00 0.00 0.00 2.01
240 242 8.635765 AGCAACTCATCAAACCTAAGATTTTA 57.364 30.769 0.00 0.00 0.00 1.52
241 243 7.530426 AGCAACTCATCAAACCTAAGATTTT 57.470 32.000 0.00 0.00 0.00 1.82
242 244 8.814038 ATAGCAACTCATCAAACCTAAGATTT 57.186 30.769 0.00 0.00 0.00 2.17
243 245 9.905713 TTATAGCAACTCATCAAACCTAAGATT 57.094 29.630 0.00 0.00 0.00 2.40
244 246 9.553064 CTTATAGCAACTCATCAAACCTAAGAT 57.447 33.333 0.00 0.00 0.00 2.40
245 247 8.540388 ACTTATAGCAACTCATCAAACCTAAGA 58.460 33.333 0.00 0.00 0.00 2.10
246 248 8.607459 CACTTATAGCAACTCATCAAACCTAAG 58.393 37.037 0.00 0.00 0.00 2.18
247 249 8.318412 TCACTTATAGCAACTCATCAAACCTAA 58.682 33.333 0.00 0.00 0.00 2.69
248 250 7.847096 TCACTTATAGCAACTCATCAAACCTA 58.153 34.615 0.00 0.00 0.00 3.08
249 251 6.711277 TCACTTATAGCAACTCATCAAACCT 58.289 36.000 0.00 0.00 0.00 3.50
250 252 6.595716 ACTCACTTATAGCAACTCATCAAACC 59.404 38.462 0.00 0.00 0.00 3.27
251 253 7.602517 ACTCACTTATAGCAACTCATCAAAC 57.397 36.000 0.00 0.00 0.00 2.93
252 254 9.151471 GTAACTCACTTATAGCAACTCATCAAA 57.849 33.333 0.00 0.00 0.00 2.69
253 255 7.764443 GGTAACTCACTTATAGCAACTCATCAA 59.236 37.037 0.00 0.00 0.00 2.57
254 256 7.093509 TGGTAACTCACTTATAGCAACTCATCA 60.094 37.037 0.00 0.00 37.61 3.07
255 257 7.265673 TGGTAACTCACTTATAGCAACTCATC 58.734 38.462 0.00 0.00 37.61 2.92
256 258 7.182817 TGGTAACTCACTTATAGCAACTCAT 57.817 36.000 0.00 0.00 37.61 2.90
257 259 6.599356 TGGTAACTCACTTATAGCAACTCA 57.401 37.500 0.00 0.00 37.61 3.41
258 260 8.630917 TCTATGGTAACTCACTTATAGCAACTC 58.369 37.037 0.00 0.00 31.62 3.01
259 261 8.534954 TCTATGGTAACTCACTTATAGCAACT 57.465 34.615 0.00 0.00 31.62 3.16
260 262 9.197694 CATCTATGGTAACTCACTTATAGCAAC 57.802 37.037 0.00 0.00 31.62 4.17
261 263 8.924303 ACATCTATGGTAACTCACTTATAGCAA 58.076 33.333 0.00 0.00 31.62 3.91
262 264 8.478775 ACATCTATGGTAACTCACTTATAGCA 57.521 34.615 0.00 0.00 37.61 3.49
263 265 9.765795 AAACATCTATGGTAACTCACTTATAGC 57.234 33.333 0.00 0.00 37.61 2.97
267 269 9.599866 CATCAAACATCTATGGTAACTCACTTA 57.400 33.333 0.00 0.00 37.61 2.24
268 270 8.103305 ACATCAAACATCTATGGTAACTCACTT 58.897 33.333 0.00 0.00 37.61 3.16
269 271 7.624549 ACATCAAACATCTATGGTAACTCACT 58.375 34.615 0.00 0.00 37.61 3.41
270 272 7.849804 ACATCAAACATCTATGGTAACTCAC 57.150 36.000 0.00 0.00 37.61 3.51
271 273 9.546428 CATACATCAAACATCTATGGTAACTCA 57.454 33.333 0.00 0.00 37.61 3.41
272 274 9.764363 TCATACATCAAACATCTATGGTAACTC 57.236 33.333 0.00 0.00 37.61 3.01
275 277 9.506018 CCATCATACATCAAACATCTATGGTAA 57.494 33.333 0.00 0.00 0.00 2.85
276 278 8.102676 CCCATCATACATCAAACATCTATGGTA 58.897 37.037 0.00 0.00 0.00 3.25
277 279 6.944290 CCCATCATACATCAAACATCTATGGT 59.056 38.462 0.00 0.00 0.00 3.55
278 280 7.170277 TCCCATCATACATCAAACATCTATGG 58.830 38.462 0.00 0.00 0.00 2.74
279 281 8.625786 TTCCCATCATACATCAAACATCTATG 57.374 34.615 0.00 0.00 0.00 2.23
280 282 9.293404 CTTTCCCATCATACATCAAACATCTAT 57.707 33.333 0.00 0.00 0.00 1.98
281 283 7.720957 CCTTTCCCATCATACATCAAACATCTA 59.279 37.037 0.00 0.00 0.00 1.98
282 284 6.548622 CCTTTCCCATCATACATCAAACATCT 59.451 38.462 0.00 0.00 0.00 2.90
283 285 6.322201 ACCTTTCCCATCATACATCAAACATC 59.678 38.462 0.00 0.00 0.00 3.06
284 286 6.197168 ACCTTTCCCATCATACATCAAACAT 58.803 36.000 0.00 0.00 0.00 2.71
285 287 5.579047 ACCTTTCCCATCATACATCAAACA 58.421 37.500 0.00 0.00 0.00 2.83
286 288 6.530019 AACCTTTCCCATCATACATCAAAC 57.470 37.500 0.00 0.00 0.00 2.93
287 289 7.385267 CAAAACCTTTCCCATCATACATCAAA 58.615 34.615 0.00 0.00 0.00 2.69
288 290 6.574073 GCAAAACCTTTCCCATCATACATCAA 60.574 38.462 0.00 0.00 0.00 2.57
289 291 5.105392 GCAAAACCTTTCCCATCATACATCA 60.105 40.000 0.00 0.00 0.00 3.07
290 292 5.127682 AGCAAAACCTTTCCCATCATACATC 59.872 40.000 0.00 0.00 0.00 3.06
291 293 5.025453 AGCAAAACCTTTCCCATCATACAT 58.975 37.500 0.00 0.00 0.00 2.29
292 294 4.220382 CAGCAAAACCTTTCCCATCATACA 59.780 41.667 0.00 0.00 0.00 2.29
293 295 4.747810 CAGCAAAACCTTTCCCATCATAC 58.252 43.478 0.00 0.00 0.00 2.39
294 296 3.195396 GCAGCAAAACCTTTCCCATCATA 59.805 43.478 0.00 0.00 0.00 2.15
295 297 2.027837 GCAGCAAAACCTTTCCCATCAT 60.028 45.455 0.00 0.00 0.00 2.45
296 298 1.344114 GCAGCAAAACCTTTCCCATCA 59.656 47.619 0.00 0.00 0.00 3.07
297 299 1.669795 CGCAGCAAAACCTTTCCCATC 60.670 52.381 0.00 0.00 0.00 3.51
298 300 0.318120 CGCAGCAAAACCTTTCCCAT 59.682 50.000 0.00 0.00 0.00 4.00
299 301 1.739049 CGCAGCAAAACCTTTCCCA 59.261 52.632 0.00 0.00 0.00 4.37
300 302 1.006220 CCGCAGCAAAACCTTTCCC 60.006 57.895 0.00 0.00 0.00 3.97
301 303 1.664649 GCCGCAGCAAAACCTTTCC 60.665 57.895 0.00 0.00 39.53 3.13
302 304 1.664649 GGCCGCAGCAAAACCTTTC 60.665 57.895 0.00 0.00 42.56 2.62
303 305 0.825840 TAGGCCGCAGCAAAACCTTT 60.826 50.000 0.00 0.00 42.56 3.11
304 306 0.611896 ATAGGCCGCAGCAAAACCTT 60.612 50.000 0.00 0.00 42.56 3.50
305 307 1.000896 ATAGGCCGCAGCAAAACCT 60.001 52.632 0.00 0.00 42.56 3.50
306 308 1.139520 CATAGGCCGCAGCAAAACC 59.860 57.895 0.00 0.00 42.56 3.27
329 331 7.674471 ACTCAGCAAACCTAAGATTTTACTC 57.326 36.000 0.00 0.00 0.00 2.59
348 350 4.212214 GGCAACTCACTTACAGAAACTCAG 59.788 45.833 0.00 0.00 0.00 3.35
355 357 5.187772 ACATCTATGGCAACTCACTTACAGA 59.812 40.000 0.00 0.00 37.61 3.41
358 360 6.743575 AAACATCTATGGCAACTCACTTAC 57.256 37.500 0.00 0.00 37.61 2.34
362 364 5.182001 ACTCAAAACATCTATGGCAACTCAC 59.818 40.000 0.00 0.00 37.61 3.51
372 374 7.726216 TCCGATCATACACTCAAAACATCTAT 58.274 34.615 0.00 0.00 0.00 1.98
379 381 7.447374 AACATTTCCGATCATACACTCAAAA 57.553 32.000 0.00 0.00 0.00 2.44
382 384 4.803613 CGAACATTTCCGATCATACACTCA 59.196 41.667 0.00 0.00 0.00 3.41
385 387 3.303132 GGCGAACATTTCCGATCATACAC 60.303 47.826 0.00 0.00 0.00 2.90
394 396 1.447140 TCGAGGGCGAACATTTCCG 60.447 57.895 0.00 0.00 44.78 4.30
468 470 8.504812 TGCAAAAGAGACAAATGTATAGCATA 57.495 30.769 0.00 0.00 36.67 3.14
480 482 6.873076 ACTGTTTTTCATTGCAAAAGAGACAA 59.127 30.769 20.02 0.00 36.89 3.18
591 595 7.727181 AGTTTATAGTACAAGCAGATGTAGGG 58.273 38.462 0.00 0.00 36.51 3.53
679 683 9.733556 ACTTTGTCTACCATGTAACATTGAATA 57.266 29.630 0.00 0.00 0.00 1.75
684 688 6.770785 ACACACTTTGTCTACCATGTAACATT 59.229 34.615 0.00 0.00 29.79 2.71
685 689 6.296026 ACACACTTTGTCTACCATGTAACAT 58.704 36.000 0.00 0.00 29.79 2.71
712 716 6.095860 AGCTGCATGCATTTCTTCAGTAATAA 59.904 34.615 22.97 0.00 45.94 1.40
713 717 5.591472 AGCTGCATGCATTTCTTCAGTAATA 59.409 36.000 22.97 0.00 45.94 0.98
714 718 4.401519 AGCTGCATGCATTTCTTCAGTAAT 59.598 37.500 22.97 0.00 45.94 1.89
728 732 1.148723 ATCCAGGAGAGCTGCATGC 59.851 57.895 11.82 11.82 43.29 4.06
793 797 1.002134 CTCGGACAGGGGCACAATT 60.002 57.895 0.00 0.00 0.00 2.32
795 799 2.847234 ACTCGGACAGGGGCACAA 60.847 61.111 0.00 0.00 0.00 3.33
796 800 3.625897 CACTCGGACAGGGGCACA 61.626 66.667 0.00 0.00 0.00 4.57
800 804 2.046892 CTTGCACTCGGACAGGGG 60.047 66.667 0.00 0.00 0.00 4.79
804 811 2.930887 GCTTATCACTTGCACTCGGACA 60.931 50.000 0.00 0.00 0.00 4.02
1325 1332 3.653164 TGCATAGTGATCCCAGGTTAGA 58.347 45.455 0.00 0.00 0.00 2.10
1629 1636 1.401905 GCACGAGAATCCCCAACATTC 59.598 52.381 0.00 0.00 0.00 2.67
1692 1699 1.209261 TGTTCTGCTGACAGTTGGACA 59.791 47.619 3.99 5.68 44.77 4.02
1704 1711 4.945543 TCAATGCTGACATTATGTTCTGCT 59.054 37.500 18.63 8.78 44.83 4.24
1710 1717 5.353400 CACTGACTCAATGCTGACATTATGT 59.647 40.000 0.00 0.00 44.83 2.29
1729 1736 5.125356 TGACTGCAATTCTTTTCTCACTGA 58.875 37.500 0.00 0.00 0.00 3.41
1793 1800 1.483316 GCCTTTTACACGCCAAACAC 58.517 50.000 0.00 0.00 0.00 3.32
1829 1836 0.842030 ATGTCTCCCCAGTGGCAGAA 60.842 55.000 2.61 0.00 0.00 3.02
1858 1865 5.286438 TGACCATTATATCGAACTTCCACG 58.714 41.667 0.00 0.00 0.00 4.94
1898 1905 8.530311 TGAATGTATATTTTGCCAACTGAATGT 58.470 29.630 0.00 0.00 0.00 2.71
1920 1927 6.994421 AACTTCCAGGTGGTAAAATTGAAT 57.006 33.333 0.00 0.00 36.34 2.57
1929 1936 6.001460 CACAAGATTAAACTTCCAGGTGGTA 58.999 40.000 0.00 0.00 36.34 3.25
1948 1955 8.553459 AAATACCATTCAGAGTAAGACACAAG 57.447 34.615 0.00 0.00 0.00 3.16
1992 2013 7.397892 TTGTCTGTATCTTGGACAAAAACAA 57.602 32.000 5.45 0.00 43.84 2.83
2020 2041 1.343465 CCCTACGGCCTATACCACTTG 59.657 57.143 0.00 0.00 0.00 3.16
2033 2055 2.440817 CCCCCTTACAGCCCTACGG 61.441 68.421 0.00 0.00 0.00 4.02
2034 2056 0.397535 TACCCCCTTACAGCCCTACG 60.398 60.000 0.00 0.00 0.00 3.51
2090 2112 6.688637 TTGATCACATCAAGAGGCTAATTG 57.311 37.500 0.00 5.74 43.84 2.32
2125 2147 8.915036 AGCGCTACCTAATAAATATAGCAGTAT 58.085 33.333 8.99 0.00 38.53 2.12
2127 2149 7.036220 CAGCGCTACCTAATAAATATAGCAGT 58.964 38.462 10.99 0.00 38.53 4.40
2158 2180 6.775594 ACCCCAAATTGTTATTAAGCTCTC 57.224 37.500 0.00 0.00 0.00 3.20
2166 2188 6.516360 GCAATGCAAAACCCCAAATTGTTATT 60.516 34.615 0.00 0.00 0.00 1.40
2171 2193 2.885894 AGCAATGCAAAACCCCAAATTG 59.114 40.909 8.35 0.00 0.00 2.32
2172 2194 3.226682 AGCAATGCAAAACCCCAAATT 57.773 38.095 8.35 0.00 0.00 1.82
2184 2206 0.180171 ATACGGGCACTAGCAATGCA 59.820 50.000 8.35 0.00 45.27 3.96
2185 2207 0.868406 GATACGGGCACTAGCAATGC 59.132 55.000 0.00 0.00 44.61 3.56
2186 2208 2.238942 TGATACGGGCACTAGCAATG 57.761 50.000 0.00 0.00 44.61 2.82
2187 2209 2.634940 AGATGATACGGGCACTAGCAAT 59.365 45.455 0.00 0.00 44.61 3.56
2188 2210 2.039418 AGATGATACGGGCACTAGCAA 58.961 47.619 0.00 0.00 44.61 3.91
2189 2211 1.704641 AGATGATACGGGCACTAGCA 58.295 50.000 0.00 0.00 44.61 3.49
2190 2212 2.821991 AAGATGATACGGGCACTAGC 57.178 50.000 0.00 0.00 41.10 3.42
2191 2213 5.844004 AGTAAAAGATGATACGGGCACTAG 58.156 41.667 0.00 0.00 0.00 2.57
2192 2214 5.864418 AGTAAAAGATGATACGGGCACTA 57.136 39.130 0.00 0.00 0.00 2.74
2193 2215 4.755266 AGTAAAAGATGATACGGGCACT 57.245 40.909 0.00 0.00 0.00 4.40
2194 2216 6.047231 ACTAAGTAAAAGATGATACGGGCAC 58.953 40.000 0.00 0.00 0.00 5.01
2195 2217 6.229936 ACTAAGTAAAAGATGATACGGGCA 57.770 37.500 0.00 0.00 0.00 5.36
2196 2218 7.594386 GTCTACTAAGTAAAAGATGATACGGGC 59.406 40.741 0.00 0.00 0.00 6.13
2197 2219 8.848182 AGTCTACTAAGTAAAAGATGATACGGG 58.152 37.037 0.00 0.00 0.00 5.28
2264 2292 4.755266 ACTAACCGAACTGAGCCATAAT 57.245 40.909 0.00 0.00 0.00 1.28
2280 2308 7.641760 TGGTTAAACCGATTGAAGAAACTAAC 58.358 34.615 0.00 0.00 42.58 2.34
2284 2312 7.436970 ACAAATGGTTAAACCGATTGAAGAAAC 59.563 33.333 1.77 0.00 42.58 2.78
2315 2347 4.112634 TCAGTGGGGCTTAAGAACATTT 57.887 40.909 6.67 0.00 0.00 2.32
2322 2354 3.629398 GTGATGAATCAGTGGGGCTTAAG 59.371 47.826 0.00 0.00 37.51 1.85
2325 2357 1.637553 AGTGATGAATCAGTGGGGCTT 59.362 47.619 0.00 0.00 38.93 4.35
2372 2404 3.990469 AGTCATACAAGACAAACTCAGCG 59.010 43.478 0.00 0.00 40.98 5.18
2406 2438 8.486210 ACATAATCGGCAAGTACCATCATATAT 58.514 33.333 0.00 0.00 0.00 0.86
2407 2439 7.847096 ACATAATCGGCAAGTACCATCATATA 58.153 34.615 0.00 0.00 0.00 0.86
2425 2457 7.025365 GTCCCACGGTAAAAAGAAACATAATC 58.975 38.462 0.00 0.00 0.00 1.75
2426 2458 6.071784 GGTCCCACGGTAAAAAGAAACATAAT 60.072 38.462 0.00 0.00 0.00 1.28
2470 2576 4.151258 CAGACCTGCAACATACAACAAG 57.849 45.455 0.00 0.00 0.00 3.16
2534 2640 1.271856 TTGCATACAGAGGTTCCCGA 58.728 50.000 0.00 0.00 0.00 5.14
2606 2712 4.573201 GGCTGTATAGGTTGAACGCAAATA 59.427 41.667 0.00 0.00 35.42 1.40
2615 2721 4.408596 TCATCATGTGGCTGTATAGGTTGA 59.591 41.667 0.00 0.00 0.00 3.18
2621 2727 6.127083 TGAGAAACTCATCATGTGGCTGTATA 60.127 38.462 0.00 0.00 35.39 1.47
2643 2749 6.879276 AAGTCCATCAGATGCAAATATGAG 57.121 37.500 4.68 0.00 0.00 2.90
2751 2857 7.865706 ATGGAAGTATATTTGTCAGGTCAAC 57.134 36.000 0.00 0.00 0.00 3.18
2794 2900 5.123820 ACCATAATGTCATGCACAGTTGTAC 59.876 40.000 0.00 0.00 38.85 2.90
2848 2954 7.230510 AGTGGCATGTTAATTCTGAGTTTGTAA 59.769 33.333 0.00 0.00 0.00 2.41
2869 2975 6.563422 TGAATCAGCATTTTGTAATAGTGGC 58.437 36.000 0.00 0.00 0.00 5.01
2916 3022 8.250332 TCATAAATGAAAATCAGGGCAAGTAAC 58.750 33.333 0.00 0.00 33.08 2.50
2917 3023 8.359875 TCATAAATGAAAATCAGGGCAAGTAA 57.640 30.769 0.00 0.00 33.08 2.24
3022 3128 7.655328 CCATAAAGTAGAGAACCATCATGTCTC 59.345 40.741 2.77 2.77 0.00 3.36
3023 3129 7.345653 TCCATAAAGTAGAGAACCATCATGTCT 59.654 37.037 0.00 0.00 0.00 3.41
3024 3130 7.500992 TCCATAAAGTAGAGAACCATCATGTC 58.499 38.462 0.00 0.00 0.00 3.06
3025 3131 7.437713 TCCATAAAGTAGAGAACCATCATGT 57.562 36.000 0.00 0.00 0.00 3.21
3026 3132 7.389884 CCATCCATAAAGTAGAGAACCATCATG 59.610 40.741 0.00 0.00 0.00 3.07
3027 3133 7.072961 ACCATCCATAAAGTAGAGAACCATCAT 59.927 37.037 0.00 0.00 0.00 2.45
3028 3134 6.386927 ACCATCCATAAAGTAGAGAACCATCA 59.613 38.462 0.00 0.00 0.00 3.07
3029 3135 6.831976 ACCATCCATAAAGTAGAGAACCATC 58.168 40.000 0.00 0.00 0.00 3.51
3030 3136 6.831664 ACCATCCATAAAGTAGAGAACCAT 57.168 37.500 0.00 0.00 0.00 3.55
3031 3137 6.443849 AGAACCATCCATAAAGTAGAGAACCA 59.556 38.462 0.00 0.00 0.00 3.67
3032 3138 6.890293 AGAACCATCCATAAAGTAGAGAACC 58.110 40.000 0.00 0.00 0.00 3.62
3033 3139 7.787028 AGAGAACCATCCATAAAGTAGAGAAC 58.213 38.462 0.00 0.00 0.00 3.01
3034 3140 7.979786 AGAGAACCATCCATAAAGTAGAGAA 57.020 36.000 0.00 0.00 0.00 2.87
3035 3141 8.282982 AGTAGAGAACCATCCATAAAGTAGAGA 58.717 37.037 0.00 0.00 0.00 3.10
3036 3142 8.472007 AGTAGAGAACCATCCATAAAGTAGAG 57.528 38.462 0.00 0.00 0.00 2.43
3037 3143 8.840200 AAGTAGAGAACCATCCATAAAGTAGA 57.160 34.615 0.00 0.00 0.00 2.59
3038 3144 9.892130 AAAAGTAGAGAACCATCCATAAAGTAG 57.108 33.333 0.00 0.00 0.00 2.57
3039 3145 9.886132 GAAAAGTAGAGAACCATCCATAAAGTA 57.114 33.333 0.00 0.00 0.00 2.24
3040 3146 8.383175 TGAAAAGTAGAGAACCATCCATAAAGT 58.617 33.333 0.00 0.00 0.00 2.66
3041 3147 8.792830 TGAAAAGTAGAGAACCATCCATAAAG 57.207 34.615 0.00 0.00 0.00 1.85
3042 3148 9.010029 GTTGAAAAGTAGAGAACCATCCATAAA 57.990 33.333 0.00 0.00 0.00 1.40
3043 3149 8.383175 AGTTGAAAAGTAGAGAACCATCCATAA 58.617 33.333 0.00 0.00 0.00 1.90
3062 3168 6.095580 TGGTAATGTGCAGTTTGTAGTTGAAA 59.904 34.615 0.00 0.00 0.00 2.69
3065 3171 5.431420 TGGTAATGTGCAGTTTGTAGTTG 57.569 39.130 0.00 0.00 0.00 3.16
3066 3172 5.048083 CCATGGTAATGTGCAGTTTGTAGTT 60.048 40.000 2.57 0.00 31.27 2.24
3067 3173 4.458989 CCATGGTAATGTGCAGTTTGTAGT 59.541 41.667 2.57 0.00 31.27 2.73
3094 3200 7.376866 CGTGATCACTGGATTTTAAATGCATAC 59.623 37.037 22.95 5.11 32.67 2.39
3096 3202 6.267817 CGTGATCACTGGATTTTAAATGCAT 58.732 36.000 22.95 0.00 32.67 3.96
3102 3208 2.675844 CGGCGTGATCACTGGATTTTAA 59.324 45.455 22.95 0.00 32.67 1.52
3130 3236 0.456653 GCCATGCCACGTCAACATTC 60.457 55.000 0.00 0.00 0.00 2.67
3134 3240 1.081242 CAAGCCATGCCACGTCAAC 60.081 57.895 0.00 0.00 0.00 3.18
3167 3280 6.662865 TTCACAGCCAAAAATTATCAAGGA 57.337 33.333 0.00 0.00 0.00 3.36
3207 3320 4.599047 AGCTTCTGCCATAGTAGTGATC 57.401 45.455 0.00 0.00 40.80 2.92
3213 3326 4.253685 GACACAAAGCTTCTGCCATAGTA 58.746 43.478 0.00 0.00 40.80 1.82
3214 3327 3.077359 GACACAAAGCTTCTGCCATAGT 58.923 45.455 0.00 0.00 40.80 2.12
3217 3330 1.884579 CTGACACAAAGCTTCTGCCAT 59.115 47.619 0.00 0.00 40.80 4.40
3222 3335 5.057149 ACGTAATTCTGACACAAAGCTTCT 58.943 37.500 0.00 0.00 0.00 2.85
3244 3357 4.304110 GGCCTAGCAAAAACAAGGTAAAC 58.696 43.478 0.00 0.00 0.00 2.01
3437 3554 4.391155 AGTCGAGGTAGAGTATGATGACC 58.609 47.826 0.00 0.00 0.00 4.02
3583 3700 1.678123 GGATGATGATCCTGGCCGATG 60.678 57.143 3.60 0.00 44.58 3.84
3592 3709 5.655532 CCATTAATCAAGGGGATGATGATCC 59.344 44.000 1.95 1.95 46.99 3.36
3682 3802 9.334947 ACATTACTATGATCAAAGTCTTCATGG 57.665 33.333 0.00 0.00 35.29 3.66
3797 3919 1.942776 AAAAATTCCTGCAGGGGAGG 58.057 50.000 32.23 7.87 36.66 4.30
3798 3920 5.682234 AATTAAAAATTCCTGCAGGGGAG 57.318 39.130 32.23 7.17 36.66 4.30
3967 4098 2.824936 TGCCAGTGGATACCAACATTTG 59.175 45.455 15.20 0.00 34.18 2.32
3968 4099 3.168035 TGCCAGTGGATACCAACATTT 57.832 42.857 15.20 0.00 34.18 2.32
3990 4121 4.970003 GGAAACGCAATCACATAATAGCAC 59.030 41.667 0.00 0.00 0.00 4.40
4007 4138 4.031418 TGCTTGCATATTCATGGAAACG 57.969 40.909 0.00 0.00 41.33 3.60
4028 4159 5.122519 GCTAAGAAAGAGCTATTCTGGCTT 58.877 41.667 20.39 13.52 40.40 4.35
4108 4243 4.039245 CACACTTCTCAGACAACCTAGGAA 59.961 45.833 17.98 0.00 0.00 3.36
4130 4269 6.708502 TGTCATTTTTCGAGTTACTCATTCCA 59.291 34.615 13.14 0.00 0.00 3.53
4153 4292 1.003233 GGAGCTCGGCCTTCTTTGT 60.003 57.895 7.83 0.00 0.00 2.83
4225 4364 1.266989 TGTGCACGTGTGTTCACAAAA 59.733 42.857 19.94 2.36 44.02 2.44
4360 4500 6.200097 GTGATTTGTCGGCTGTACAAAATTTT 59.800 34.615 19.96 0.00 46.59 1.82
4361 4501 5.689961 GTGATTTGTCGGCTGTACAAAATTT 59.310 36.000 19.96 9.60 46.59 1.82
4362 4502 5.009610 AGTGATTTGTCGGCTGTACAAAATT 59.990 36.000 19.96 10.11 46.59 1.82
4363 4503 4.518970 AGTGATTTGTCGGCTGTACAAAAT 59.481 37.500 19.96 10.52 46.59 1.82
4386 4526 8.060679 TCACGTTAAATTTCGTCGAAAAATGTA 58.939 29.630 23.11 10.65 38.23 2.29
4500 4642 1.203100 AGGCCAAGCTCCAGTGATTTT 60.203 47.619 5.01 0.00 0.00 1.82
4502 4644 0.034670 GAGGCCAAGCTCCAGTGATT 60.035 55.000 5.01 0.00 0.00 2.57
4515 4657 2.272146 GCGGATTTCTGGAGGCCA 59.728 61.111 5.01 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.