Multiple sequence alignment - TraesCS3D01G280400

Loading Multiple Alignment...

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 TraesCS3D01G280400 chr3D 100.000 4090 0 0 1 4090 388453021 388448932 0.000000e+00 7553
1 TraesCS3D01G280400 chr3D 80.995 563 71 7 1731 2275 388451222 388450678 8.180000e-112 414
2 TraesCS3D01G280400 chr3D 80.995 563 71 7 1800 2344 388451291 388450747 8.180000e-112 414
3 TraesCS3D01G280400 chr3D 91.279 172 13 2 170 340 329681755 329681925 2.460000e-57 233
4 TraesCS3D01G280400 chr3D 85.135 148 21 1 1737 1884 388450820 388450674 2.550000e-32 150
5 TraesCS3D01G280400 chr3D 85.135 148 21 1 2202 2348 388451285 388451138 2.550000e-32 150
6 TraesCS3D01G280400 chr3A 95.997 1449 45 6 2067 3502 509549219 509547771 0.000000e+00 2342
7 TraesCS3D01G280400 chr3A 93.884 654 25 9 1365 2005 509550252 509549601 0.000000e+00 972
8 TraesCS3D01G280400 chr3A 91.603 524 25 12 798 1318 509551005 509550498 0.000000e+00 706
9 TraesCS3D01G280400 chr3A 92.025 489 35 2 3606 4090 509544292 509543804 0.000000e+00 684
10 TraesCS3D01G280400 chr3A 88.288 222 15 5 410 623 509551395 509551177 5.250000e-64 255
11 TraesCS3D01G280400 chr3A 82.877 292 26 6 2002 2275 509549227 509548942 1.470000e-59 241
12 TraesCS3D01G280400 chr3A 97.170 106 3 0 3498 3603 509544747 509544642 3.250000e-41 180
13 TraesCS3D01G280400 chr3A 85.135 148 21 1 2202 2348 509549869 509549722 2.550000e-32 150
14 TraesCS3D01G280400 chr3B 92.737 1611 96 10 1800 3392 505288435 505286828 0.000000e+00 2307
15 TraesCS3D01G280400 chr3B 90.618 874 34 21 427 1272 505289854 505289001 0.000000e+00 1116
16 TraesCS3D01G280400 chr3B 88.972 934 52 17 1365 2275 505288784 505287879 0.000000e+00 1107
17 TraesCS3D01G280400 chr3B 90.395 354 20 5 3751 4090 505268901 505268548 1.730000e-123 453
18 TraesCS3D01G280400 chr3B 78.557 499 73 15 1869 2344 505288435 505287948 8.590000e-77 298
19 TraesCS3D01G280400 chr3B 86.420 162 17 3 16 174 505291164 505291005 5.440000e-39 172
20 TraesCS3D01G280400 chr3B 85.135 148 21 1 1737 1884 505288021 505287875 2.550000e-32 150
21 TraesCS3D01G280400 chr3B 85.135 148 21 1 2202 2348 505288429 505288282 2.550000e-32 150
22 TraesCS3D01G280400 chr7D 88.000 600 67 4 2486 3084 629599272 629598677 0.000000e+00 704
23 TraesCS3D01G280400 chr7D 94.012 167 8 2 173 338 519969064 519968899 6.790000e-63 252
24 TraesCS3D01G280400 chr7D 81.818 209 26 9 802 1008 577378405 577378207 9.100000e-37 165
25 TraesCS3D01G280400 chr7D 81.340 209 27 9 802 1008 548341992 548341794 4.230000e-35 159
26 TraesCS3D01G280400 chr6B 83.086 674 99 7 2417 3078 9478306 9478976 2.100000e-167 599
27 TraesCS3D01G280400 chr6B 80.882 680 93 12 2417 3084 11111494 11110840 6.100000e-138 501
28 TraesCS3D01G280400 chr7A 85.470 585 65 11 2421 2989 725613781 725613201 3.520000e-165 592
29 TraesCS3D01G280400 chr7A 90.476 105 10 0 2980 3084 725612520 725612416 5.510000e-29 139
30 TraesCS3D01G280400 chrUn 94.643 168 7 2 171 337 70231882 70231716 4.060000e-65 259
31 TraesCS3D01G280400 chr6D 93.452 168 9 2 171 337 412111114 412111280 8.780000e-62 248
32 TraesCS3D01G280400 chr1D 93.452 168 9 2 171 337 414467620 414467454 8.780000e-62 248
33 TraesCS3D01G280400 chr1D 90.698 172 14 2 170 340 9218205 9218375 1.140000e-55 228
34 TraesCS3D01G280400 chr2D 92.308 169 11 2 173 340 609886955 609886788 5.280000e-59 239
35 TraesCS3D01G280400 chr2D 81.340 209 27 9 802 1008 27630181 27630379 4.230000e-35 159
36 TraesCS3D01G280400 chr5D 91.228 171 13 2 168 337 42949555 42949724 8.840000e-57 231
37 TraesCS3D01G280400 chr5D 81.818 209 26 9 802 1008 505024635 505024437 9.100000e-37 165
38 TraesCS3D01G280400 chr5D 81.313 198 25 9 802 997 505010015 505009828 2.550000e-32 150
39 TraesCS3D01G280400 chr4A 91.176 170 13 2 169 337 141122663 141122831 3.180000e-56 230
40 TraesCS3D01G280400 chr4D 81.340 209 27 9 802 1008 509211439 509211241 4.230000e-35 159


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 TraesCS3D01G280400 chr3D 388448932 388453021 4089 True 1736.200000 7553 86.452000 1 4090 5 chr3D.!!$R1 4089
1 TraesCS3D01G280400 chr3A 509543804 509551395 7591 True 691.250000 2342 90.872375 410 4090 8 chr3A.!!$R1 3680
2 TraesCS3D01G280400 chr3B 505286828 505291164 4336 True 757.142857 2307 86.796286 16 3392 7 chr3B.!!$R2 3376
3 TraesCS3D01G280400 chr7D 629598677 629599272 595 True 704.000000 704 88.000000 2486 3084 1 chr7D.!!$R4 598
4 TraesCS3D01G280400 chr6B 9478306 9478976 670 False 599.000000 599 83.086000 2417 3078 1 chr6B.!!$F1 661
5 TraesCS3D01G280400 chr6B 11110840 11111494 654 True 501.000000 501 80.882000 2417 3084 1 chr6B.!!$R1 667
6 TraesCS3D01G280400 chr7A 725612416 725613781 1365 True 365.500000 592 87.973000 2421 3084 2 chr7A.!!$R1 663

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
21 22 0.099082 TTTTGCGGGTGACGTTCAAC 59.901 50.0 0.0 0.0 46.52 3.18 F
1080 2220 0.039798 GCCCTTCGTTTTTCGTTCCC 60.040 55.0 0.0 0.0 40.80 3.97 F
1649 3012 0.035056 AAGCATTGACCCTTCTCCGG 60.035 55.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 2289 0.324943 TGCCTCCCACAAGAAGTAGC 59.675 55.0 0.0 0.00 0.0 3.58 R
2078 3818 0.756070 CTCCCTTCCCTACTCCGACC 60.756 65.0 0.0 0.00 0.0 4.79 R
3487 5947 0.802607 CGAGTCTTAGTTGGCGCCTC 60.803 60.0 29.7 20.25 0.0 4.70 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
19 20 2.478989 TTTTTGCGGGTGACGTTCA 58.521 47.368 0.00 0.00 46.52 3.18
21 22 0.099082 TTTTGCGGGTGACGTTCAAC 59.901 50.000 0.00 0.00 46.52 3.18
39 40 0.732880 ACGTTCAAGACTCGGCATCG 60.733 55.000 0.00 0.00 37.82 3.84
72 73 1.068281 CTCGATCCTGGAGTGGTCATG 59.932 57.143 1.52 0.00 0.00 3.07
77 78 2.457598 TCCTGGAGTGGTCATGTACTC 58.542 52.381 14.75 14.75 41.95 2.59
79 80 1.819288 CTGGAGTGGTCATGTACTCGT 59.181 52.381 15.84 0.00 43.24 4.18
83 84 1.202582 AGTGGTCATGTACTCGTGCTC 59.797 52.381 0.00 0.00 0.00 4.26
86 87 2.263077 GGTCATGTACTCGTGCTCTTG 58.737 52.381 0.00 0.00 0.00 3.02
89 90 1.995484 CATGTACTCGTGCTCTTGTGG 59.005 52.381 0.00 0.00 0.00 4.17
93 94 2.325583 ACTCGTGCTCTTGTGGAAAA 57.674 45.000 0.00 0.00 0.00 2.29
95 96 1.532868 CTCGTGCTCTTGTGGAAAAGG 59.467 52.381 0.00 0.00 0.00 3.11
100 101 3.381590 GTGCTCTTGTGGAAAAGGAAGTT 59.618 43.478 0.00 0.00 0.00 2.66
111 112 9.416284 TGTGGAAAAGGAAGTTAAGTTTATTCT 57.584 29.630 0.00 0.00 0.00 2.40
179 183 9.886132 AAAAATGTCGTATAAGATGTACTTCCT 57.114 29.630 5.19 0.00 39.72 3.36
182 186 5.237996 TGTCGTATAAGATGTACTTCCTCCG 59.762 44.000 5.19 2.45 39.72 4.63
183 187 5.238214 GTCGTATAAGATGTACTTCCTCCGT 59.762 44.000 5.19 0.00 39.72 4.69
184 188 5.824624 TCGTATAAGATGTACTTCCTCCGTT 59.175 40.000 5.19 0.00 39.72 4.44
185 189 6.017605 TCGTATAAGATGTACTTCCTCCGTTC 60.018 42.308 5.19 0.00 39.72 3.95
186 190 3.889520 AAGATGTACTTCCTCCGTTCC 57.110 47.619 5.19 0.00 32.91 3.62
187 191 3.103080 AGATGTACTTCCTCCGTTCCT 57.897 47.619 5.19 0.00 0.00 3.36
188 192 4.246712 AGATGTACTTCCTCCGTTCCTA 57.753 45.455 5.19 0.00 0.00 2.94
189 193 4.607239 AGATGTACTTCCTCCGTTCCTAA 58.393 43.478 5.19 0.00 0.00 2.69
190 194 5.021458 AGATGTACTTCCTCCGTTCCTAAA 58.979 41.667 5.19 0.00 0.00 1.85
191 195 5.661759 AGATGTACTTCCTCCGTTCCTAAAT 59.338 40.000 5.19 0.00 0.00 1.40
192 196 6.837568 AGATGTACTTCCTCCGTTCCTAAATA 59.162 38.462 5.19 0.00 0.00 1.40
193 197 7.509659 AGATGTACTTCCTCCGTTCCTAAATAT 59.490 37.037 5.19 0.00 0.00 1.28
194 198 8.716674 ATGTACTTCCTCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
195 199 8.537728 TGTACTTCCTCCGTTCCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
196 200 8.636213 TGTACTTCCTCCGTTCCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
197 201 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
198 202 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
199 203 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
200 204 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
201 205 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
202 206 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
203 207 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
220 224 9.598517 AAGTCTTTTTAGACATTTCAAATGCAA 57.401 25.926 10.21 0.00 41.02 4.08
221 225 9.768662 AGTCTTTTTAGACATTTCAAATGCAAT 57.231 25.926 10.21 0.00 41.02 3.56
224 228 9.941991 CTTTTTAGACATTTCAAATGCAATACG 57.058 29.630 10.21 0.00 0.00 3.06
225 229 9.684448 TTTTTAGACATTTCAAATGCAATACGA 57.316 25.926 10.21 0.00 0.00 3.43
226 230 8.667987 TTTAGACATTTCAAATGCAATACGAC 57.332 30.769 10.21 0.00 0.00 4.34
227 231 6.252967 AGACATTTCAAATGCAATACGACA 57.747 33.333 10.21 0.00 0.00 4.35
228 232 6.855836 AGACATTTCAAATGCAATACGACAT 58.144 32.000 10.21 0.00 0.00 3.06
229 233 7.984391 AGACATTTCAAATGCAATACGACATA 58.016 30.769 10.21 0.00 0.00 2.29
230 234 7.910162 AGACATTTCAAATGCAATACGACATAC 59.090 33.333 10.21 0.00 0.00 2.39
235 239 4.990543 AATGCAATACGACATACGGATG 57.009 40.909 5.94 5.94 45.65 3.51
236 240 3.446310 TGCAATACGACATACGGATGT 57.554 42.857 14.62 14.62 45.65 3.06
237 241 4.571372 TGCAATACGACATACGGATGTA 57.429 40.909 14.70 0.00 45.65 2.29
238 242 5.128992 TGCAATACGACATACGGATGTAT 57.871 39.130 14.70 7.78 45.65 2.29
263 267 9.988815 ATGTAGACATTATTTTAGAGCGAAGAT 57.011 29.630 0.00 0.00 31.37 2.40
264 268 9.817809 TGTAGACATTATTTTAGAGCGAAGATT 57.182 29.630 0.00 0.00 0.00 2.40
277 281 9.871238 TTAGAGCGAAGATTTACTCATTTTACT 57.129 29.630 0.00 0.00 0.00 2.24
278 282 8.413899 AGAGCGAAGATTTACTCATTTTACTC 57.586 34.615 0.00 0.00 0.00 2.59
279 283 7.492994 AGAGCGAAGATTTACTCATTTTACTCC 59.507 37.037 0.00 0.00 0.00 3.85
280 284 6.255887 AGCGAAGATTTACTCATTTTACTCCG 59.744 38.462 0.00 0.00 0.00 4.63
281 285 6.035758 GCGAAGATTTACTCATTTTACTCCGT 59.964 38.462 0.00 0.00 0.00 4.69
282 286 7.221452 GCGAAGATTTACTCATTTTACTCCGTA 59.779 37.037 0.00 0.00 0.00 4.02
283 287 9.245962 CGAAGATTTACTCATTTTACTCCGTAT 57.754 33.333 0.00 0.00 0.00 3.06
285 289 9.886132 AAGATTTACTCATTTTACTCCGTATGT 57.114 29.630 0.00 0.00 0.00 2.29
289 293 9.793252 TTTACTCATTTTACTCCGTATGTACTC 57.207 33.333 0.00 0.00 0.00 2.59
290 294 7.400599 ACTCATTTTACTCCGTATGTACTCA 57.599 36.000 0.00 0.00 0.00 3.41
291 295 7.256286 ACTCATTTTACTCCGTATGTACTCAC 58.744 38.462 0.00 0.00 0.00 3.51
292 296 7.122353 ACTCATTTTACTCCGTATGTACTCACT 59.878 37.037 0.00 0.00 0.00 3.41
293 297 7.833786 TCATTTTACTCCGTATGTACTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
294 298 7.758076 TCATTTTACTCCGTATGTACTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
295 299 6.579666 TTTACTCCGTATGTACTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
296 300 6.579666 TTACTCCGTATGTACTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
297 301 7.686438 TTACTCCGTATGTACTCACTTGTTA 57.314 36.000 0.00 0.00 0.00 2.41
298 302 6.579666 ACTCCGTATGTACTCACTTGTTAA 57.420 37.500 0.00 0.00 0.00 2.01
299 303 6.985117 ACTCCGTATGTACTCACTTGTTAAA 58.015 36.000 0.00 0.00 0.00 1.52
300 304 7.436118 ACTCCGTATGTACTCACTTGTTAAAA 58.564 34.615 0.00 0.00 0.00 1.52
301 305 8.092687 ACTCCGTATGTACTCACTTGTTAAAAT 58.907 33.333 0.00 0.00 0.00 1.82
302 306 9.577110 CTCCGTATGTACTCACTTGTTAAAATA 57.423 33.333 0.00 0.00 0.00 1.40
328 332 7.723324 TCTAGAAAGACTTATATTTGGGACGG 58.277 38.462 0.00 0.00 0.00 4.79
329 333 6.555463 AGAAAGACTTATATTTGGGACGGA 57.445 37.500 0.00 0.00 0.00 4.69
330 334 6.583562 AGAAAGACTTATATTTGGGACGGAG 58.416 40.000 0.00 0.00 0.00 4.63
331 335 4.957684 AGACTTATATTTGGGACGGAGG 57.042 45.455 0.00 0.00 0.00 4.30
332 336 4.553678 AGACTTATATTTGGGACGGAGGA 58.446 43.478 0.00 0.00 0.00 3.71
333 337 4.966805 AGACTTATATTTGGGACGGAGGAA 59.033 41.667 0.00 0.00 0.00 3.36
334 338 5.070580 AGACTTATATTTGGGACGGAGGAAG 59.929 44.000 0.00 0.00 0.00 3.46
335 339 4.720273 ACTTATATTTGGGACGGAGGAAGT 59.280 41.667 0.00 0.00 0.00 3.01
336 340 5.901276 ACTTATATTTGGGACGGAGGAAGTA 59.099 40.000 0.00 0.00 0.00 2.24
337 341 6.557633 ACTTATATTTGGGACGGAGGAAGTAT 59.442 38.462 0.00 0.00 0.00 2.12
338 342 7.731688 ACTTATATTTGGGACGGAGGAAGTATA 59.268 37.037 0.00 0.00 0.00 1.47
339 343 8.674925 TTATATTTGGGACGGAGGAAGTATAT 57.325 34.615 0.00 0.00 0.00 0.86
340 344 9.772605 TTATATTTGGGACGGAGGAAGTATATA 57.227 33.333 0.00 0.00 0.00 0.86
341 345 5.796424 TTTGGGACGGAGGAAGTATATAC 57.204 43.478 4.60 4.60 0.00 1.47
342 346 4.458256 TGGGACGGAGGAAGTATATACA 57.542 45.455 15.18 0.00 0.00 2.29
343 347 4.147321 TGGGACGGAGGAAGTATATACAC 58.853 47.826 15.18 8.29 0.00 2.90
344 348 3.509184 GGGACGGAGGAAGTATATACACC 59.491 52.174 15.18 15.89 0.00 4.16
345 349 3.509184 GGACGGAGGAAGTATATACACCC 59.491 52.174 15.18 13.89 0.00 4.61
346 350 4.147321 GACGGAGGAAGTATATACACCCA 58.853 47.826 15.18 0.00 0.00 4.51
347 351 4.150359 ACGGAGGAAGTATATACACCCAG 58.850 47.826 15.18 12.48 0.00 4.45
348 352 4.141088 ACGGAGGAAGTATATACACCCAGA 60.141 45.833 15.18 0.00 0.00 3.86
349 353 5.017490 CGGAGGAAGTATATACACCCAGAT 58.983 45.833 15.18 2.80 0.00 2.90
356 360 6.115448 AGTATATACACCCAGATCCAAAGC 57.885 41.667 15.18 0.00 0.00 3.51
360 364 1.338769 ACACCCAGATCCAAAGCGTAC 60.339 52.381 0.00 0.00 0.00 3.67
366 370 1.906574 AGATCCAAAGCGTACTTCCCA 59.093 47.619 0.00 0.00 34.05 4.37
367 371 2.007608 GATCCAAAGCGTACTTCCCAC 58.992 52.381 0.00 0.00 34.05 4.61
368 372 1.053424 TCCAAAGCGTACTTCCCACT 58.947 50.000 0.00 0.00 34.05 4.00
369 373 1.001633 TCCAAAGCGTACTTCCCACTC 59.998 52.381 0.00 0.00 34.05 3.51
370 374 1.068474 CAAAGCGTACTTCCCACTCG 58.932 55.000 0.00 0.00 34.05 4.18
371 375 0.963962 AAAGCGTACTTCCCACTCGA 59.036 50.000 0.00 0.00 34.05 4.04
372 376 1.183549 AAGCGTACTTCCCACTCGAT 58.816 50.000 0.00 0.00 0.00 3.59
373 377 0.739561 AGCGTACTTCCCACTCGATC 59.260 55.000 0.00 0.00 0.00 3.69
374 378 0.248949 GCGTACTTCCCACTCGATCC 60.249 60.000 0.00 0.00 0.00 3.36
375 379 1.390565 CGTACTTCCCACTCGATCCT 58.609 55.000 0.00 0.00 0.00 3.24
376 380 2.569059 CGTACTTCCCACTCGATCCTA 58.431 52.381 0.00 0.00 0.00 2.94
377 381 2.290093 CGTACTTCCCACTCGATCCTAC 59.710 54.545 0.00 0.00 0.00 3.18
378 382 1.777941 ACTTCCCACTCGATCCTACC 58.222 55.000 0.00 0.00 0.00 3.18
379 383 1.288335 ACTTCCCACTCGATCCTACCT 59.712 52.381 0.00 0.00 0.00 3.08
380 384 2.292323 ACTTCCCACTCGATCCTACCTT 60.292 50.000 0.00 0.00 0.00 3.50
381 385 3.053095 ACTTCCCACTCGATCCTACCTTA 60.053 47.826 0.00 0.00 0.00 2.69
382 386 2.941480 TCCCACTCGATCCTACCTTAC 58.059 52.381 0.00 0.00 0.00 2.34
392 803 7.071069 TCGATCCTACCTTACTCTGTATACA 57.929 40.000 5.25 5.25 0.00 2.29
422 1493 0.186386 AGGACTATGCGTAGGAGGCT 59.814 55.000 17.19 0.00 31.96 4.58
508 1587 2.507992 CGTCAGCTGCCGGAGAAG 60.508 66.667 9.76 0.00 0.00 2.85
509 1588 2.973899 GTCAGCTGCCGGAGAAGA 59.026 61.111 9.47 0.00 0.00 2.87
589 1676 1.935933 GGCGACCGACATTCAATACT 58.064 50.000 0.00 0.00 0.00 2.12
624 1711 0.388134 CACGGACGGTTGAGTCGATT 60.388 55.000 0.00 0.00 41.81 3.34
709 1796 0.976641 CCTGGACAGGTGCAACTCTA 59.023 55.000 0.00 0.00 43.61 2.43
710 1797 1.066573 CCTGGACAGGTGCAACTCTAG 60.067 57.143 0.00 0.00 43.61 2.43
711 1798 0.321671 TGGACAGGTGCAACTCTAGC 59.678 55.000 0.00 0.00 36.74 3.42
712 1799 0.610687 GGACAGGTGCAACTCTAGCT 59.389 55.000 0.00 0.00 36.74 3.32
716 1803 0.827368 AGGTGCAACTCTAGCTAGCC 59.173 55.000 16.35 9.33 36.74 3.93
738 1833 4.092821 CCACGTATGGTGTACAATCAGTTG 59.907 45.833 0.00 0.00 45.52 3.16
791 1903 0.960861 ACTCGGCGACTCAGTGATGA 60.961 55.000 4.99 0.00 0.00 2.92
792 1904 0.383590 CTCGGCGACTCAGTGATGAT 59.616 55.000 4.99 0.00 0.00 2.45
793 1905 0.101219 TCGGCGACTCAGTGATGATG 59.899 55.000 4.99 0.00 0.00 3.07
794 1906 1.485838 CGGCGACTCAGTGATGATGC 61.486 60.000 0.00 0.00 0.00 3.91
906 2045 4.948864 ATAAATATCGACGTTCGTGCTG 57.051 40.909 1.74 0.00 41.35 4.41
908 2047 0.454600 ATATCGACGTTCGTGCTGGT 59.545 50.000 1.74 0.00 41.35 4.00
997 2137 0.609131 AGTTTCCTCATTGGTGCCCG 60.609 55.000 0.00 0.00 37.07 6.13
1073 2213 2.556622 CACTACCATGCCCTTCGTTTTT 59.443 45.455 0.00 0.00 0.00 1.94
1077 2217 1.000717 CCATGCCCTTCGTTTTTCGTT 60.001 47.619 0.00 0.00 40.80 3.85
1080 2220 0.039798 GCCCTTCGTTTTTCGTTCCC 60.040 55.000 0.00 0.00 40.80 3.97
1109 2252 2.026915 TCATCATCTCCAACACACCTGG 60.027 50.000 0.00 0.00 35.05 4.45
1110 2253 1.728323 TCATCTCCAACACACCTGGA 58.272 50.000 0.00 0.00 40.77 3.86
1111 2254 2.269023 TCATCTCCAACACACCTGGAT 58.731 47.619 0.00 0.00 42.12 3.41
1146 2289 6.016943 TGGTTGTGTTCTTAATTTTCCCTACG 60.017 38.462 0.00 0.00 0.00 3.51
1149 2295 6.465948 TGTGTTCTTAATTTTCCCTACGCTA 58.534 36.000 0.00 0.00 0.00 4.26
1150 2296 6.369615 TGTGTTCTTAATTTTCCCTACGCTAC 59.630 38.462 0.00 0.00 0.00 3.58
1151 2297 6.592994 GTGTTCTTAATTTTCCCTACGCTACT 59.407 38.462 0.00 0.00 0.00 2.57
1175 2321 1.141657 TGTGGGAGGCATATTGCTCTC 59.858 52.381 0.00 4.79 44.28 3.20
1217 2365 4.100189 AGTTCCATGCTTATTCGAGTAGCT 59.900 41.667 14.06 0.00 35.93 3.32
1236 2384 8.074613 AGTAGCTGTACTAAAACATATGGTGA 57.925 34.615 7.80 0.00 37.76 4.02
1249 2397 8.899427 AAACATATGGTGATCTACATCTGAAG 57.101 34.615 7.80 5.09 0.00 3.02
1253 2403 8.583296 CATATGGTGATCTACATCTGAAGAAGA 58.417 37.037 6.07 0.00 39.94 2.87
1258 2408 8.663911 GGTGATCTACATCTGAAGAAGAAAAAG 58.336 37.037 0.00 0.00 38.79 2.27
1271 2421 8.421002 TGAAGAAGAAAAAGGAAAAACATAGGG 58.579 33.333 0.00 0.00 0.00 3.53
1272 2422 7.914427 AGAAGAAAAAGGAAAAACATAGGGT 57.086 32.000 0.00 0.00 0.00 4.34
1273 2423 7.726216 AGAAGAAAAAGGAAAAACATAGGGTG 58.274 34.615 0.00 0.00 0.00 4.61
1274 2424 7.563556 AGAAGAAAAAGGAAAAACATAGGGTGA 59.436 33.333 0.00 0.00 0.00 4.02
1275 2425 7.855784 AGAAAAAGGAAAAACATAGGGTGAT 57.144 32.000 0.00 0.00 0.00 3.06
1276 2426 7.896811 AGAAAAAGGAAAAACATAGGGTGATC 58.103 34.615 0.00 0.00 0.00 2.92
1277 2427 7.730332 AGAAAAAGGAAAAACATAGGGTGATCT 59.270 33.333 0.00 0.00 0.00 2.75
1278 2428 8.950007 AAAAAGGAAAAACATAGGGTGATCTA 57.050 30.769 0.00 0.00 0.00 1.98
1279 2429 9.547279 AAAAAGGAAAAACATAGGGTGATCTAT 57.453 29.630 0.00 0.00 0.00 1.98
1283 2433 9.398921 AGGAAAAACATAGGGTGATCTATATCT 57.601 33.333 0.00 0.00 32.93 1.98
1321 2471 7.987750 TTACAGAGTATAAAATGGTGTGCAA 57.012 32.000 0.00 0.00 0.00 4.08
1323 2473 6.913170 ACAGAGTATAAAATGGTGTGCAAAG 58.087 36.000 0.00 0.00 0.00 2.77
1327 2477 7.397192 AGAGTATAAAATGGTGTGCAAAGGAAT 59.603 33.333 0.00 0.00 0.00 3.01
1338 2549 8.682710 TGGTGTGCAAAGGAATATTTCTATTAC 58.317 33.333 0.00 0.00 0.00 1.89
1359 2570 8.798748 ATTACGCTAGTACTATGTGCTAAAAG 57.201 34.615 14.86 0.00 31.05 2.27
1373 2723 3.259876 TGCTAAAAGGTCGGTGACAGTAT 59.740 43.478 0.00 0.00 33.68 2.12
1375 2725 5.041940 GCTAAAAGGTCGGTGACAGTATAG 58.958 45.833 0.00 0.00 33.68 1.31
1383 2733 5.154932 GTCGGTGACAGTATAGTATCATGC 58.845 45.833 0.00 0.00 32.09 4.06
1384 2734 4.825085 TCGGTGACAGTATAGTATCATGCA 59.175 41.667 0.00 0.00 0.00 3.96
1387 2737 5.349817 GGTGACAGTATAGTATCATGCATGC 59.650 44.000 22.25 11.82 0.00 4.06
1460 2815 6.750501 TGATCTAAAATCGTAGAAACTGACCG 59.249 38.462 0.00 0.00 43.58 4.79
1462 2817 4.985044 AAAATCGTAGAAACTGACCGTG 57.015 40.909 0.00 0.00 43.58 4.94
1497 2858 2.202756 GCGTCGGTAGGAAGCCAG 60.203 66.667 0.00 0.00 43.32 4.85
1557 2918 0.039618 CCAACACCCCTATGCCAAGT 59.960 55.000 0.00 0.00 0.00 3.16
1575 2936 2.534990 AGTTCCCTCTCTCAACTCCTG 58.465 52.381 0.00 0.00 0.00 3.86
1580 2941 2.233431 CCCTCTCTCAACTCCTGAACAG 59.767 54.545 0.00 0.00 32.17 3.16
1601 2964 9.339850 GAACAGTCAAGGTATACTACTCTATCA 57.660 37.037 2.25 0.00 0.00 2.15
1649 3012 0.035056 AAGCATTGACCCTTCTCCGG 60.035 55.000 0.00 0.00 0.00 5.14
1650 3013 1.201429 AGCATTGACCCTTCTCCGGT 61.201 55.000 0.00 0.00 35.88 5.28
1653 3016 0.249398 ATTGACCCTTCTCCGGTTCG 59.751 55.000 0.00 0.00 32.27 3.95
1700 3063 4.353437 GTGAACGTCGGCTCGGGT 62.353 66.667 0.00 0.00 34.94 5.28
1928 3291 2.980562 CGTCAACGTCAAACCTGGA 58.019 52.632 0.00 0.00 34.11 3.86
2087 3827 3.376078 GGCACCACGGTCGGAGTA 61.376 66.667 4.04 0.00 0.00 2.59
2088 3828 2.181021 GCACCACGGTCGGAGTAG 59.819 66.667 4.04 0.00 0.00 2.57
2089 3829 2.882876 CACCACGGTCGGAGTAGG 59.117 66.667 4.04 0.00 0.00 3.18
2090 3830 2.362120 ACCACGGTCGGAGTAGGG 60.362 66.667 4.04 0.00 0.00 3.53
2091 3831 2.044650 CCACGGTCGGAGTAGGGA 60.045 66.667 0.00 0.00 0.00 4.20
2092 3832 1.679977 CCACGGTCGGAGTAGGGAA 60.680 63.158 0.00 0.00 0.00 3.97
2093 3833 1.664321 CCACGGTCGGAGTAGGGAAG 61.664 65.000 0.00 0.00 0.00 3.46
2094 3834 1.379576 ACGGTCGGAGTAGGGAAGG 60.380 63.158 0.00 0.00 0.00 3.46
2095 3835 2.125961 CGGTCGGAGTAGGGAAGGG 61.126 68.421 0.00 0.00 0.00 3.95
2096 3836 1.309006 GGTCGGAGTAGGGAAGGGA 59.691 63.158 0.00 0.00 0.00 4.20
2097 3837 0.756070 GGTCGGAGTAGGGAAGGGAG 60.756 65.000 0.00 0.00 0.00 4.30
2098 3838 0.756070 GTCGGAGTAGGGAAGGGAGG 60.756 65.000 0.00 0.00 0.00 4.30
2099 3839 2.134933 CGGAGTAGGGAAGGGAGGC 61.135 68.421 0.00 0.00 0.00 4.70
2100 3840 2.134933 GGAGTAGGGAAGGGAGGCG 61.135 68.421 0.00 0.00 0.00 5.52
2101 3841 1.381463 GAGTAGGGAAGGGAGGCGT 60.381 63.158 0.00 0.00 0.00 5.68
2102 3842 1.381463 AGTAGGGAAGGGAGGCGTC 60.381 63.158 0.00 0.00 0.00 5.19
2103 3843 2.441532 TAGGGAAGGGAGGCGTCG 60.442 66.667 0.00 0.00 0.00 5.12
2116 3856 3.025743 CGTCGGCGTGAACGTGAA 61.026 61.111 6.85 0.00 42.22 3.18
2117 3857 2.844146 GTCGGCGTGAACGTGAAG 59.156 61.111 6.85 0.00 42.22 3.02
2118 3858 3.033764 TCGGCGTGAACGTGAAGC 61.034 61.111 6.85 0.00 42.22 3.86
2119 3859 4.072088 CGGCGTGAACGTGAAGCC 62.072 66.667 12.90 12.90 44.00 4.35
2120 3860 2.665185 GGCGTGAACGTGAAGCCT 60.665 61.111 14.92 0.00 44.06 4.58
2121 3861 2.551270 GCGTGAACGTGAAGCCTG 59.449 61.111 4.59 0.00 42.22 4.85
2122 3862 2.954753 GCGTGAACGTGAAGCCTGG 61.955 63.158 4.59 0.00 42.22 4.45
2123 3863 2.946762 GTGAACGTGAAGCCTGGC 59.053 61.111 11.65 11.65 0.00 4.85
2124 3864 2.664851 TGAACGTGAAGCCTGGCG 60.665 61.111 13.96 0.43 0.00 5.69
2125 3865 2.357034 GAACGTGAAGCCTGGCGA 60.357 61.111 13.96 0.00 0.00 5.54
2126 3866 2.665185 AACGTGAAGCCTGGCGAC 60.665 61.111 13.96 11.81 0.00 5.19
2330 4070 2.663196 GTCAAGCCTGGCTACGGT 59.337 61.111 23.69 2.56 38.25 4.83
2385 4125 1.615107 CGTCAACGTCTCGCCTTTCC 61.615 60.000 0.00 0.00 34.11 3.13
2918 4673 3.637926 GAGGGCGTACACGGTGTCC 62.638 68.421 18.43 12.75 40.23 4.02
3190 5637 3.568538 GTTCGTTTACGTTCTAGCCTCA 58.431 45.455 0.00 0.00 40.80 3.86
3240 5695 8.844865 ATGAGTATATGGTATCTTGCATCCTA 57.155 34.615 0.00 0.00 0.00 2.94
3297 5752 3.925238 GCGTTGCCAGTATCGCCG 61.925 66.667 0.44 0.00 42.33 6.46
3454 5914 6.538742 AGAAAAACTTCTCTTGATCGTCAACA 59.461 34.615 0.00 0.00 32.21 3.33
3458 5918 7.588143 AACTTCTCTTGATCGTCAACATAAG 57.412 36.000 0.00 0.00 32.21 1.73
3463 5923 5.478407 TCTTGATCGTCAACATAAGCAGAA 58.522 37.500 0.00 0.00 32.21 3.02
3474 5934 2.425143 TAAGCAGAAAGAGCATGGGG 57.575 50.000 0.00 0.00 0.00 4.96
3487 5947 3.512724 GAGCATGGGGATTCAAATATGGG 59.487 47.826 0.00 0.00 0.00 4.00
3507 8995 1.214589 GGCGCCAACTAAGACTCGA 59.785 57.895 24.80 0.00 0.00 4.04
3581 9069 6.037172 CACCGGTTTATTCAAGGTTATCTCAG 59.963 42.308 2.97 0.00 32.04 3.35
3584 9072 5.299531 GGTTTATTCAAGGTTATCTCAGCCC 59.700 44.000 0.00 0.00 0.00 5.19
3622 9457 6.015434 CAGCCAAGTTAATACCAAGGAAAACT 60.015 38.462 0.00 0.00 0.00 2.66
3626 9462 9.292195 CCAAGTTAATACCAAGGAAAACTAGAA 57.708 33.333 0.00 0.00 0.00 2.10
3662 9498 5.939883 GGACAAACATATATGCAGATGGCTA 59.060 40.000 12.79 0.00 45.15 3.93
3690 9526 2.370281 TTCAGCCTGTCTCGAATGAC 57.630 50.000 0.00 0.00 37.47 3.06
3697 9533 1.991264 CTGTCTCGAATGACACTGCAG 59.009 52.381 13.48 13.48 41.43 4.41
3706 9542 4.611355 CGAATGACACTGCAGGTTTAACTG 60.611 45.833 19.93 7.70 41.41 3.16
3721 9557 5.397240 GGTTTAACTGTTCAAACGGAAATCG 59.603 40.000 8.65 0.00 45.88 3.34
3765 9601 7.715249 TCATAGTAAATATTCAAGACTGGCCAC 59.285 37.037 0.00 0.00 0.00 5.01
3812 9648 8.877864 TCCTACATCATAAGGTCAACAAATTT 57.122 30.769 0.00 0.00 34.30 1.82
3820 9656 8.296713 TCATAAGGTCAACAAATTTAACAGAGC 58.703 33.333 0.00 0.00 0.00 4.09
3821 9657 6.463995 AAGGTCAACAAATTTAACAGAGCA 57.536 33.333 11.35 0.00 0.00 4.26
3824 9660 5.569059 GGTCAACAAATTTAACAGAGCATCG 59.431 40.000 0.00 0.00 42.67 3.84
3827 9663 4.726416 ACAAATTTAACAGAGCATCGCAG 58.274 39.130 0.00 0.00 42.67 5.18
3839 9675 3.081061 AGCATCGCAGATTAAAACCACA 58.919 40.909 0.00 0.00 45.12 4.17
3855 9691 4.771590 ACCACATCAAATACAGCAACTG 57.228 40.909 0.00 0.00 37.52 3.16
3867 9703 4.785767 CAACTGCTGCTCTCACCA 57.214 55.556 0.00 0.00 0.00 4.17
3868 9704 2.242113 CAACTGCTGCTCTCACCAC 58.758 57.895 0.00 0.00 0.00 4.16
3871 9707 0.321387 ACTGCTGCTCTCACCACATG 60.321 55.000 0.00 0.00 0.00 3.21
3883 9719 4.704540 TCTCACCACATGTCACTTGTTTTT 59.295 37.500 0.00 0.00 0.00 1.94
3892 9728 7.001674 ACATGTCACTTGTTTTTATCCCACTA 58.998 34.615 0.00 0.00 0.00 2.74
3894 9730 5.467399 TGTCACTTGTTTTTATCCCACTACG 59.533 40.000 0.00 0.00 0.00 3.51
3901 9737 9.550811 CTTGTTTTTATCCCACTACGTAAAATC 57.449 33.333 0.00 0.00 0.00 2.17
3905 9741 6.913873 TTATCCCACTACGTAAAATCAAGC 57.086 37.500 0.00 0.00 0.00 4.01
3907 9743 2.350498 CCCACTACGTAAAATCAAGCCG 59.650 50.000 0.00 0.00 0.00 5.52
3914 9753 2.084546 GTAAAATCAAGCCGCCACTCT 58.915 47.619 0.00 0.00 0.00 3.24
3925 9764 0.512952 CGCCACTCTTCTTTGAACCG 59.487 55.000 0.00 0.00 0.00 4.44
3936 9775 3.581755 TCTTTGAACCGAACCTACATCG 58.418 45.455 0.00 0.00 39.92 3.84
3968 9807 4.102524 ACAGATACAACAGTGAAACAGGGA 59.897 41.667 0.00 0.00 41.43 4.20
3989 9828 6.339587 GGAATGTGTTTGATTTCCCTTGTA 57.660 37.500 0.00 0.00 33.08 2.41
3990 9829 6.935167 GGAATGTGTTTGATTTCCCTTGTAT 58.065 36.000 0.00 0.00 33.08 2.29
4017 9856 6.642683 TTTCCGTCGAAGAATAAATGACTC 57.357 37.500 0.00 0.00 39.69 3.36
4019 9858 5.340803 TCCGTCGAAGAATAAATGACTCTG 58.659 41.667 0.00 0.00 39.69 3.35
4055 9894 9.929180 TTATGTGCAGATATACATCTACTTTCC 57.071 33.333 4.14 0.00 39.62 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.809385 TTGAACGTCACCCGCAAAAA 59.191 45.000 0.00 0.00 41.42 1.94
2 3 0.099082 GTTGAACGTCACCCGCAAAA 59.901 50.000 0.00 0.00 41.42 2.44
3 4 1.722677 GTTGAACGTCACCCGCAAA 59.277 52.632 0.00 0.00 41.42 3.68
4 5 2.526993 CGTTGAACGTCACCCGCAA 61.527 57.895 9.94 0.00 41.42 4.85
5 6 2.962786 CGTTGAACGTCACCCGCA 60.963 61.111 9.94 0.00 41.42 5.69
19 20 1.429463 GATGCCGAGTCTTGAACGTT 58.571 50.000 0.00 0.00 0.00 3.99
21 22 1.413767 CCGATGCCGAGTCTTGAACG 61.414 60.000 0.00 0.00 38.22 3.95
72 73 2.433868 TTCCACAAGAGCACGAGTAC 57.566 50.000 0.00 0.00 0.00 2.73
77 78 1.593196 TCCTTTTCCACAAGAGCACG 58.407 50.000 0.00 0.00 0.00 5.34
79 80 3.297134 ACTTCCTTTTCCACAAGAGCA 57.703 42.857 0.00 0.00 0.00 4.26
159 163 5.238214 ACGGAGGAAGTACATCTTATACGAC 59.762 44.000 9.12 0.00 36.40 4.34
167 171 3.103080 AGGAACGGAGGAAGTACATCT 57.897 47.619 0.00 0.00 0.00 2.90
174 178 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
175 179 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
177 181 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
194 198 9.598517 TTGCATTTGAAATGTCTAAAAAGACTT 57.401 25.926 18.12 0.00 39.41 3.01
195 199 9.768662 ATTGCATTTGAAATGTCTAAAAAGACT 57.231 25.926 18.12 0.00 39.41 3.24
198 202 9.941991 CGTATTGCATTTGAAATGTCTAAAAAG 57.058 29.630 18.12 2.02 0.00 2.27
199 203 9.684448 TCGTATTGCATTTGAAATGTCTAAAAA 57.316 25.926 18.12 5.57 0.00 1.94
200 204 9.123709 GTCGTATTGCATTTGAAATGTCTAAAA 57.876 29.630 18.12 7.04 0.00 1.52
201 205 8.293157 TGTCGTATTGCATTTGAAATGTCTAAA 58.707 29.630 18.12 9.12 0.00 1.85
202 206 7.811653 TGTCGTATTGCATTTGAAATGTCTAA 58.188 30.769 18.12 11.76 0.00 2.10
203 207 7.371126 TGTCGTATTGCATTTGAAATGTCTA 57.629 32.000 18.12 8.77 0.00 2.59
204 208 6.252967 TGTCGTATTGCATTTGAAATGTCT 57.747 33.333 18.12 6.93 0.00 3.41
205 209 7.097449 CGTATGTCGTATTGCATTTGAAATGTC 60.097 37.037 18.12 11.39 34.52 3.06
206 210 6.686679 CGTATGTCGTATTGCATTTGAAATGT 59.313 34.615 18.12 2.65 34.52 2.71
207 211 6.140580 CCGTATGTCGTATTGCATTTGAAATG 59.859 38.462 13.32 13.32 37.94 2.32
208 212 6.037720 TCCGTATGTCGTATTGCATTTGAAAT 59.962 34.615 0.00 0.00 37.94 2.17
209 213 5.351740 TCCGTATGTCGTATTGCATTTGAAA 59.648 36.000 0.00 0.00 37.94 2.69
210 214 4.870991 TCCGTATGTCGTATTGCATTTGAA 59.129 37.500 0.00 0.00 37.94 2.69
211 215 4.434520 TCCGTATGTCGTATTGCATTTGA 58.565 39.130 0.00 0.00 37.94 2.69
212 216 4.787381 TCCGTATGTCGTATTGCATTTG 57.213 40.909 0.00 0.00 37.94 2.32
213 217 4.814234 ACATCCGTATGTCGTATTGCATTT 59.186 37.500 0.00 0.00 42.92 2.32
214 218 4.377021 ACATCCGTATGTCGTATTGCATT 58.623 39.130 0.00 0.00 42.92 3.56
215 219 3.990092 ACATCCGTATGTCGTATTGCAT 58.010 40.909 0.00 0.00 42.92 3.96
216 220 3.446310 ACATCCGTATGTCGTATTGCA 57.554 42.857 0.00 0.00 42.92 4.08
217 221 5.435948 CATACATCCGTATGTCGTATTGC 57.564 43.478 0.00 0.00 46.70 3.56
237 241 9.988815 ATCTTCGCTCTAAAATAATGTCTACAT 57.011 29.630 0.00 0.00 38.41 2.29
238 242 9.817809 AATCTTCGCTCTAAAATAATGTCTACA 57.182 29.630 0.00 0.00 0.00 2.74
251 255 9.871238 AGTAAAATGAGTAAATCTTCGCTCTAA 57.129 29.630 0.00 0.00 0.00 2.10
252 256 9.517609 GAGTAAAATGAGTAAATCTTCGCTCTA 57.482 33.333 0.00 0.00 0.00 2.43
253 257 7.492994 GGAGTAAAATGAGTAAATCTTCGCTCT 59.507 37.037 0.00 0.00 0.00 4.09
254 258 7.515371 CGGAGTAAAATGAGTAAATCTTCGCTC 60.515 40.741 0.00 0.00 0.00 5.03
255 259 6.255887 CGGAGTAAAATGAGTAAATCTTCGCT 59.744 38.462 0.00 0.00 0.00 4.93
256 260 6.035758 ACGGAGTAAAATGAGTAAATCTTCGC 59.964 38.462 0.00 0.00 41.94 4.70
257 261 7.521509 ACGGAGTAAAATGAGTAAATCTTCG 57.478 36.000 0.00 0.00 41.94 3.79
276 280 7.878477 TTTTAACAAGTGAGTACATACGGAG 57.122 36.000 0.00 0.00 0.00 4.63
302 306 8.368668 CCGTCCCAAATATAAGTCTTTCTAGAT 58.631 37.037 0.00 0.00 31.86 1.98
303 307 7.562454 TCCGTCCCAAATATAAGTCTTTCTAGA 59.438 37.037 0.00 0.00 0.00 2.43
304 308 7.723324 TCCGTCCCAAATATAAGTCTTTCTAG 58.277 38.462 0.00 0.00 0.00 2.43
305 309 7.201974 CCTCCGTCCCAAATATAAGTCTTTCTA 60.202 40.741 0.00 0.00 0.00 2.10
306 310 6.408206 CCTCCGTCCCAAATATAAGTCTTTCT 60.408 42.308 0.00 0.00 0.00 2.52
307 311 5.758784 CCTCCGTCCCAAATATAAGTCTTTC 59.241 44.000 0.00 0.00 0.00 2.62
308 312 5.427481 TCCTCCGTCCCAAATATAAGTCTTT 59.573 40.000 0.00 0.00 0.00 2.52
309 313 4.966805 TCCTCCGTCCCAAATATAAGTCTT 59.033 41.667 0.00 0.00 0.00 3.01
310 314 4.553678 TCCTCCGTCCCAAATATAAGTCT 58.446 43.478 0.00 0.00 0.00 3.24
311 315 4.950205 TCCTCCGTCCCAAATATAAGTC 57.050 45.455 0.00 0.00 0.00 3.01
312 316 4.720273 ACTTCCTCCGTCCCAAATATAAGT 59.280 41.667 0.00 0.00 0.00 2.24
313 317 5.291905 ACTTCCTCCGTCCCAAATATAAG 57.708 43.478 0.00 0.00 0.00 1.73
314 318 8.674925 ATATACTTCCTCCGTCCCAAATATAA 57.325 34.615 0.00 0.00 0.00 0.98
315 319 9.193806 GTATATACTTCCTCCGTCCCAAATATA 57.806 37.037 5.58 0.00 0.00 0.86
316 320 7.676893 TGTATATACTTCCTCCGTCCCAAATAT 59.323 37.037 13.89 0.00 0.00 1.28
317 321 7.011994 TGTATATACTTCCTCCGTCCCAAATA 58.988 38.462 13.89 0.00 0.00 1.40
318 322 5.842328 TGTATATACTTCCTCCGTCCCAAAT 59.158 40.000 13.89 0.00 0.00 2.32
319 323 5.069516 GTGTATATACTTCCTCCGTCCCAAA 59.930 44.000 13.89 0.00 0.00 3.28
320 324 4.586001 GTGTATATACTTCCTCCGTCCCAA 59.414 45.833 13.89 0.00 0.00 4.12
321 325 4.147321 GTGTATATACTTCCTCCGTCCCA 58.853 47.826 13.89 0.00 0.00 4.37
322 326 3.509184 GGTGTATATACTTCCTCCGTCCC 59.491 52.174 13.89 0.00 0.00 4.46
323 327 3.509184 GGGTGTATATACTTCCTCCGTCC 59.491 52.174 13.89 3.39 0.00 4.79
324 328 4.147321 TGGGTGTATATACTTCCTCCGTC 58.853 47.826 13.89 4.82 0.00 4.79
325 329 4.141088 TCTGGGTGTATATACTTCCTCCGT 60.141 45.833 13.89 0.00 0.00 4.69
326 330 4.404640 TCTGGGTGTATATACTTCCTCCG 58.595 47.826 13.89 8.15 0.00 4.63
327 331 5.422650 GGATCTGGGTGTATATACTTCCTCC 59.577 48.000 13.89 13.20 0.00 4.30
328 332 6.017192 TGGATCTGGGTGTATATACTTCCTC 58.983 44.000 13.89 9.20 0.00 3.71
329 333 5.977533 TGGATCTGGGTGTATATACTTCCT 58.022 41.667 13.89 1.83 0.00 3.36
330 334 6.681729 TTGGATCTGGGTGTATATACTTCC 57.318 41.667 13.89 14.45 0.00 3.46
331 335 6.651225 GCTTTGGATCTGGGTGTATATACTTC 59.349 42.308 13.89 7.15 0.00 3.01
332 336 6.534634 GCTTTGGATCTGGGTGTATATACTT 58.465 40.000 13.89 0.00 0.00 2.24
333 337 5.279506 CGCTTTGGATCTGGGTGTATATACT 60.280 44.000 13.89 0.00 0.00 2.12
334 338 4.929808 CGCTTTGGATCTGGGTGTATATAC 59.070 45.833 5.89 5.89 0.00 1.47
335 339 4.591498 ACGCTTTGGATCTGGGTGTATATA 59.409 41.667 0.00 0.00 0.00 0.86
336 340 3.391296 ACGCTTTGGATCTGGGTGTATAT 59.609 43.478 0.00 0.00 0.00 0.86
337 341 2.769663 ACGCTTTGGATCTGGGTGTATA 59.230 45.455 0.00 0.00 0.00 1.47
338 342 1.559682 ACGCTTTGGATCTGGGTGTAT 59.440 47.619 0.00 0.00 0.00 2.29
339 343 0.981183 ACGCTTTGGATCTGGGTGTA 59.019 50.000 0.00 0.00 0.00 2.90
340 344 0.981183 TACGCTTTGGATCTGGGTGT 59.019 50.000 0.00 0.00 0.00 4.16
341 345 1.066143 AGTACGCTTTGGATCTGGGTG 60.066 52.381 0.00 0.00 0.00 4.61
342 346 1.276622 AGTACGCTTTGGATCTGGGT 58.723 50.000 0.00 0.00 0.00 4.51
343 347 2.280628 GAAGTACGCTTTGGATCTGGG 58.719 52.381 0.00 0.00 34.61 4.45
344 348 2.280628 GGAAGTACGCTTTGGATCTGG 58.719 52.381 0.00 0.00 34.61 3.86
345 349 2.280628 GGGAAGTACGCTTTGGATCTG 58.719 52.381 0.00 0.00 34.61 2.90
346 350 1.906574 TGGGAAGTACGCTTTGGATCT 59.093 47.619 0.00 0.00 34.61 2.75
347 351 2.007608 GTGGGAAGTACGCTTTGGATC 58.992 52.381 0.00 0.00 34.61 3.36
348 352 1.628846 AGTGGGAAGTACGCTTTGGAT 59.371 47.619 0.00 0.00 34.61 3.41
349 353 1.001633 GAGTGGGAAGTACGCTTTGGA 59.998 52.381 0.00 0.00 34.61 3.53
356 360 1.390565 AGGATCGAGTGGGAAGTACG 58.609 55.000 0.00 0.00 0.00 3.67
360 364 2.074729 AGGTAGGATCGAGTGGGAAG 57.925 55.000 0.00 0.00 0.00 3.46
366 370 4.506937 ACAGAGTAAGGTAGGATCGAGT 57.493 45.455 0.00 0.00 0.00 4.18
367 371 7.160049 TGTATACAGAGTAAGGTAGGATCGAG 58.840 42.308 0.08 0.00 0.00 4.04
368 372 7.071069 TGTATACAGAGTAAGGTAGGATCGA 57.929 40.000 0.08 0.00 0.00 3.59
369 373 7.367159 CTGTATACAGAGTAAGGTAGGATCG 57.633 44.000 25.83 0.00 46.59 3.69
392 803 3.391955 ACGCATAGTCCTAGGAGTACTCT 59.608 47.826 25.65 15.01 33.45 3.24
407 1478 1.546476 CCCTAAGCCTCCTACGCATAG 59.454 57.143 0.00 0.00 0.00 2.23
422 1493 2.571653 ACTTCACACATGCTAGCCCTAA 59.428 45.455 13.29 0.00 0.00 2.69
507 1586 4.421479 CGCGCCTCCACGTCTTCT 62.421 66.667 0.00 0.00 34.88 2.85
550 1632 3.337889 CGTGCCATGCCGATACCG 61.338 66.667 0.00 0.00 0.00 4.02
551 1633 2.108157 TCGTGCCATGCCGATACC 59.892 61.111 0.00 0.00 0.00 2.73
552 1634 2.585869 CGTCGTGCCATGCCGATAC 61.586 63.158 4.11 0.00 34.90 2.24
553 1635 2.279186 CGTCGTGCCATGCCGATA 60.279 61.111 4.11 0.00 34.90 2.92
607 1694 0.109458 TCAATCGACTCAACCGTCCG 60.109 55.000 0.00 0.00 0.00 4.79
624 1711 2.616256 GGTGCATCCACTGTTCTGATCA 60.616 50.000 0.00 0.00 41.75 2.92
738 1833 8.506437 TGCAGGTAATACGTACAGTATATACAC 58.494 37.037 15.18 3.99 44.78 2.90
743 1838 6.513884 GCTGTGCAGGTAATACGTACAGTATA 60.514 42.308 13.94 0.00 44.78 1.47
745 1840 4.439153 GCTGTGCAGGTAATACGTACAGTA 60.439 45.833 13.94 0.00 40.03 2.74
746 1841 3.675228 GCTGTGCAGGTAATACGTACAGT 60.675 47.826 13.94 0.00 37.11 3.55
747 1842 2.858344 GCTGTGCAGGTAATACGTACAG 59.142 50.000 0.00 10.15 37.65 2.74
748 1843 2.417651 GGCTGTGCAGGTAATACGTACA 60.418 50.000 0.00 0.00 34.01 2.90
906 2045 3.983044 AGGAGATGTGTCCTTGTAACC 57.017 47.619 0.00 0.00 45.39 2.85
1073 2213 6.486657 GGAGATGATGAATAAATTGGGAACGA 59.513 38.462 0.00 0.00 0.00 3.85
1077 2217 7.068593 GTGTTGGAGATGATGAATAAATTGGGA 59.931 37.037 0.00 0.00 0.00 4.37
1080 2220 7.703621 GGTGTGTTGGAGATGATGAATAAATTG 59.296 37.037 0.00 0.00 0.00 2.32
1109 2252 7.849804 AAGAACACAACCACATCTACATATC 57.150 36.000 0.00 0.00 0.00 1.63
1110 2253 9.905713 ATTAAGAACACAACCACATCTACATAT 57.094 29.630 0.00 0.00 0.00 1.78
1111 2254 9.733556 AATTAAGAACACAACCACATCTACATA 57.266 29.630 0.00 0.00 0.00 2.29
1146 2289 0.324943 TGCCTCCCACAAGAAGTAGC 59.675 55.000 0.00 0.00 0.00 3.58
1149 2295 3.624777 CAATATGCCTCCCACAAGAAGT 58.375 45.455 0.00 0.00 0.00 3.01
1150 2296 2.360165 GCAATATGCCTCCCACAAGAAG 59.640 50.000 0.00 0.00 37.42 2.85
1151 2297 2.025037 AGCAATATGCCTCCCACAAGAA 60.025 45.455 0.00 0.00 46.52 2.52
1175 2321 7.556844 TGGAACTAGCTAGGAAGAACAATAAG 58.443 38.462 24.35 0.00 0.00 1.73
1236 2384 9.799106 TTTCCTTTTTCTTCTTCAGATGTAGAT 57.201 29.630 0.00 0.00 0.00 1.98
1249 2397 7.722363 TCACCCTATGTTTTTCCTTTTTCTTC 58.278 34.615 0.00 0.00 0.00 2.87
1253 2403 7.855784 AGATCACCCTATGTTTTTCCTTTTT 57.144 32.000 0.00 0.00 0.00 1.94
1258 2408 9.442047 CAGATATAGATCACCCTATGTTTTTCC 57.558 37.037 0.00 0.00 34.17 3.13
1318 2468 8.989980 ACTAGCGTAATAGAAATATTCCTTTGC 58.010 33.333 0.00 0.00 0.00 3.68
1331 2542 8.837788 TTAGCACATAGTACTAGCGTAATAGA 57.162 34.615 8.85 0.00 30.69 1.98
1338 2549 5.589192 ACCTTTTAGCACATAGTACTAGCG 58.411 41.667 8.85 4.78 0.00 4.26
1359 2570 5.700846 CATGATACTATACTGTCACCGACC 58.299 45.833 0.00 0.00 0.00 4.79
1373 2723 7.332557 TCATGATGTATGCATGCATGATACTA 58.667 34.615 37.43 21.33 40.44 1.82
1375 2725 6.315393 TCTCATGATGTATGCATGCATGATAC 59.685 38.462 37.43 28.45 42.09 2.24
1383 2733 3.685272 GCTCCTCTCATGATGTATGCATG 59.315 47.826 10.16 0.00 43.39 4.06
1384 2734 3.326880 TGCTCCTCTCATGATGTATGCAT 59.673 43.478 3.79 3.79 36.70 3.96
1387 2737 6.879276 AAATTGCTCCTCTCATGATGTATG 57.121 37.500 0.00 0.00 38.17 2.39
1429 2780 8.200792 AGTTTCTACGATTTTAGATCATCAGCT 58.799 33.333 0.00 0.00 0.00 4.24
1441 2792 4.374399 ACACGGTCAGTTTCTACGATTTT 58.626 39.130 0.00 0.00 0.00 1.82
1460 2815 3.000476 CGCAATCTGCATGCAAATTACAC 60.000 43.478 22.88 11.86 45.36 2.90
1462 2817 3.181397 ACGCAATCTGCATGCAAATTAC 58.819 40.909 22.88 14.18 45.36 1.89
1557 2918 2.900546 GTTCAGGAGTTGAGAGAGGGAA 59.099 50.000 0.00 0.00 37.07 3.97
1575 2936 9.339850 TGATAGAGTAGTATACCTTGACTGTTC 57.660 37.037 0.00 0.45 44.47 3.18
1611 2974 1.180456 TTCCCGTGTACCGAAGCTGA 61.180 55.000 5.46 0.00 39.56 4.26
1649 3012 1.856265 CTGTGGAAAGCAGGGCGAAC 61.856 60.000 0.00 0.00 0.00 3.95
1650 3013 1.600636 CTGTGGAAAGCAGGGCGAA 60.601 57.895 0.00 0.00 0.00 4.70
1653 3016 3.376918 GGCTGTGGAAAGCAGGGC 61.377 66.667 0.00 0.00 45.43 5.19
1679 3042 2.504244 GAGCCGACGTTCACCGAG 60.504 66.667 0.00 0.00 40.70 4.63
1700 3063 2.048597 GCGTCGACATGGACACCA 60.049 61.111 17.16 0.00 36.73 4.17
2077 3817 2.125961 CCCTTCCCTACTCCGACCG 61.126 68.421 0.00 0.00 0.00 4.79
2078 3818 0.756070 CTCCCTTCCCTACTCCGACC 60.756 65.000 0.00 0.00 0.00 4.79
2079 3819 0.756070 CCTCCCTTCCCTACTCCGAC 60.756 65.000 0.00 0.00 0.00 4.79
2080 3820 1.619143 CCTCCCTTCCCTACTCCGA 59.381 63.158 0.00 0.00 0.00 4.55
2081 3821 2.134933 GCCTCCCTTCCCTACTCCG 61.135 68.421 0.00 0.00 0.00 4.63
2082 3822 2.134933 CGCCTCCCTTCCCTACTCC 61.135 68.421 0.00 0.00 0.00 3.85
2083 3823 1.381463 ACGCCTCCCTTCCCTACTC 60.381 63.158 0.00 0.00 0.00 2.59
2084 3824 1.381463 GACGCCTCCCTTCCCTACT 60.381 63.158 0.00 0.00 0.00 2.57
2085 3825 2.783288 CGACGCCTCCCTTCCCTAC 61.783 68.421 0.00 0.00 0.00 3.18
2086 3826 2.441532 CGACGCCTCCCTTCCCTA 60.442 66.667 0.00 0.00 0.00 3.53
2099 3839 2.983977 CTTCACGTTCACGCCGACG 61.984 63.158 0.00 0.00 44.43 5.12
2100 3840 2.844146 CTTCACGTTCACGCCGAC 59.156 61.111 0.00 0.00 44.43 4.79
2101 3841 3.033764 GCTTCACGTTCACGCCGA 61.034 61.111 0.00 0.00 44.43 5.54
2102 3842 4.072088 GGCTTCACGTTCACGCCG 62.072 66.667 0.00 0.00 44.43 6.46
2103 3843 2.665185 AGGCTTCACGTTCACGCC 60.665 61.111 0.00 4.03 44.43 5.68
2104 3844 2.551270 CAGGCTTCACGTTCACGC 59.449 61.111 0.00 0.00 44.43 5.34
2105 3845 2.954753 GCCAGGCTTCACGTTCACG 61.955 63.158 3.29 0.00 46.33 4.35
2106 3846 2.946762 GCCAGGCTTCACGTTCAC 59.053 61.111 3.29 0.00 0.00 3.18
2107 3847 2.664851 CGCCAGGCTTCACGTTCA 60.665 61.111 10.54 0.00 0.00 3.18
2108 3848 2.357034 TCGCCAGGCTTCACGTTC 60.357 61.111 10.54 0.00 0.00 3.95
2109 3849 2.665185 GTCGCCAGGCTTCACGTT 60.665 61.111 10.54 0.00 0.00 3.99
2237 3977 3.411351 CCGGGCTTGACGTTGACG 61.411 66.667 1.41 1.41 46.33 4.35
2385 4125 1.392756 GTCGCGGCGTAGTTGTATAG 58.607 55.000 22.90 0.00 0.00 1.31
2569 4324 3.237741 GGCTGAGGATCTCGGGGG 61.238 72.222 5.97 0.00 37.35 5.40
2618 4373 2.226896 CGTCTGCTTCATCTCCGCG 61.227 63.158 0.00 0.00 0.00 6.46
2918 4673 2.819595 CCGTCCTTGCCGACCATG 60.820 66.667 0.00 0.00 0.00 3.66
3240 5695 4.545610 CAACAACAACGGAAATGTATGCT 58.454 39.130 0.00 0.00 0.00 3.79
3297 5752 1.375523 CCCACACTCCGTACAAGCC 60.376 63.158 0.00 0.00 0.00 4.35
3454 5914 2.511218 TCCCCATGCTCTTTCTGCTTAT 59.489 45.455 0.00 0.00 0.00 1.73
3458 5918 1.680207 GAATCCCCATGCTCTTTCTGC 59.320 52.381 0.00 0.00 0.00 4.26
3463 5923 4.836736 CCATATTTGAATCCCCATGCTCTT 59.163 41.667 0.00 0.00 0.00 2.85
3474 5934 1.541588 GGCGCCTCCCATATTTGAATC 59.458 52.381 22.15 0.00 0.00 2.52
3487 5947 0.802607 CGAGTCTTAGTTGGCGCCTC 60.803 60.000 29.70 20.25 0.00 4.70
3507 8995 5.278266 GCGAGATCTATTTCAGCTCTACAGT 60.278 44.000 0.00 0.00 29.75 3.55
3622 9457 6.419791 TGTTTGTCCTTGGTTCTTCTTTCTA 58.580 36.000 0.00 0.00 0.00 2.10
3626 9462 8.960591 CATATATGTTTGTCCTTGGTTCTTCTT 58.039 33.333 4.43 0.00 0.00 2.52
3690 9526 4.630894 TTGAACAGTTAAACCTGCAGTG 57.369 40.909 13.81 6.81 35.83 3.66
3697 9533 5.397240 CGATTTCCGTTTGAACAGTTAAACC 59.603 40.000 10.36 0.00 34.21 3.27
3721 9557 3.111853 TGACGCCCTATGATCATTCAC 57.888 47.619 14.65 0.78 33.85 3.18
3812 9648 5.064707 GGTTTTAATCTGCGATGCTCTGTTA 59.935 40.000 0.00 0.00 0.00 2.41
3820 9656 5.233957 TGATGTGGTTTTAATCTGCGATG 57.766 39.130 0.00 0.00 0.00 3.84
3821 9657 5.895636 TTGATGTGGTTTTAATCTGCGAT 57.104 34.783 0.00 0.00 0.00 4.58
3824 9660 7.009540 GCTGTATTTGATGTGGTTTTAATCTGC 59.990 37.037 0.00 0.00 0.00 4.26
3827 9663 8.647226 GTTGCTGTATTTGATGTGGTTTTAATC 58.353 33.333 0.00 0.00 0.00 1.75
3855 9691 0.321034 TGACATGTGGTGAGAGCAGC 60.321 55.000 1.15 0.00 42.72 5.25
3867 9703 5.833131 AGTGGGATAAAAACAAGTGACATGT 59.167 36.000 0.00 0.00 0.00 3.21
3868 9704 6.331369 AGTGGGATAAAAACAAGTGACATG 57.669 37.500 0.00 0.00 0.00 3.21
3871 9707 5.467735 ACGTAGTGGGATAAAAACAAGTGAC 59.532 40.000 0.00 0.00 42.51 3.67
3883 9719 5.362263 GGCTTGATTTTACGTAGTGGGATA 58.638 41.667 0.00 0.00 45.73 2.59
3892 9728 0.519961 GTGGCGGCTTGATTTTACGT 59.480 50.000 11.43 0.00 0.00 3.57
3894 9730 2.084546 AGAGTGGCGGCTTGATTTTAC 58.915 47.619 11.43 0.00 0.00 2.01
3901 9737 0.239347 CAAAGAAGAGTGGCGGCTTG 59.761 55.000 11.43 0.00 0.00 4.01
3905 9741 0.875059 GGTTCAAAGAAGAGTGGCGG 59.125 55.000 0.00 0.00 0.00 6.13
3907 9743 1.878953 TCGGTTCAAAGAAGAGTGGC 58.121 50.000 0.00 0.00 0.00 5.01
3914 9753 3.991773 CGATGTAGGTTCGGTTCAAAGAA 59.008 43.478 0.00 0.00 33.05 2.52
3936 9775 4.804139 CACTGTTGTATCTGTATTCGGGAC 59.196 45.833 0.00 0.00 0.00 4.46
3968 9807 9.625747 AAAAATACAAGGGAAATCAAACACATT 57.374 25.926 0.00 0.00 0.00 2.71
3996 9835 5.105877 ACAGAGTCATTTATTCTTCGACGGA 60.106 40.000 0.00 0.00 0.00 4.69
3998 9837 7.858382 AGATACAGAGTCATTTATTCTTCGACG 59.142 37.037 0.00 0.00 0.00 5.12
4055 9894 6.653273 TTCAGCGTAGATCAAAGATTTCAG 57.347 37.500 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.