Multiple sequence alignment - TraesCS2A01G540900

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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 TraesCS2A01G540900 chr2A 100.000 3050 0 0 1 3050 752747932 752750981 0.000000e+00 5633
1 TraesCS2A01G540900 chr2A 79.282 975 152 32 1700 2654 752758667 752759611 1.190000e-178 636
2 TraesCS2A01G540900 chr2A 75.465 1182 230 40 897 2051 752706762 752705614 3.480000e-144 521
3 TraesCS2A01G540900 chr2A 82.331 266 36 6 2394 2654 752779142 752779401 1.420000e-53 220
4 TraesCS2A01G540900 chr2A 93.182 88 4 1 319 404 676127947 676127860 8.880000e-26 128
5 TraesCS2A01G540900 chr2D 96.724 1740 37 3 403 2128 620883196 620884929 0.000000e+00 2880
6 TraesCS2A01G540900 chr2D 78.193 1096 207 21 1106 2179 620921569 620922654 0.000000e+00 671
7 TraesCS2A01G540900 chr2D 79.342 881 154 23 1688 2558 620910674 620911536 7.280000e-166 593
8 TraesCS2A01G540900 chr2D 89.367 395 23 3 2336 2729 620885110 620885486 2.130000e-131 479
9 TraesCS2A01G540900 chr2D 93.769 321 17 3 2733 3050 620885555 620885875 2.130000e-131 479
10 TraesCS2A01G540900 chr2D 93.443 244 12 2 1 243 620882945 620883185 2.890000e-95 359
11 TraesCS2A01G540900 chr2D 92.366 131 7 2 2127 2257 620884972 620885099 1.870000e-42 183
12 TraesCS2A01G540900 chr2D 84.810 158 17 5 2767 2918 620914532 620914688 5.270000e-33 152
13 TraesCS2A01G540900 chr2D 94.186 86 3 1 318 401 331376517 331376432 2.470000e-26 130
14 TraesCS2A01G540900 chr2B 78.132 1285 217 41 1382 2654 761888708 761889940 0.000000e+00 758
15 TraesCS2A01G540900 chr2B 75.819 1373 272 41 838 2179 761984322 761985665 2.560000e-180 641
16 TraesCS2A01G540900 chr2B 77.391 920 164 25 1279 2179 761960538 761961432 9.760000e-140 507
17 TraesCS2A01G540900 chr3A 96.512 86 1 1 318 401 406307406 406307321 1.140000e-29 141
18 TraesCS2A01G540900 chr1A 97.500 80 2 0 241 320 546321104 546321183 1.470000e-28 137
19 TraesCS2A01G540900 chr7A 98.684 76 1 0 245 320 651953094 651953169 5.300000e-28 135
20 TraesCS2A01G540900 chr4B 98.684 76 1 0 245 320 58974677 58974602 5.300000e-28 135
21 TraesCS2A01G540900 chr7D 96.296 81 3 0 240 320 133333225 133333145 1.910000e-27 134
22 TraesCS2A01G540900 chrUn 96.250 80 3 0 241 320 62199453 62199532 6.860000e-27 132
23 TraesCS2A01G540900 chrUn 96.250 80 3 0 241 320 252182059 252182138 6.860000e-27 132
24 TraesCS2A01G540900 chrUn 96.250 80 3 0 241 320 304197104 304197183 6.860000e-27 132
25 TraesCS2A01G540900 chrUn 93.103 87 5 1 318 403 314867460 314867374 3.190000e-25 126
26 TraesCS2A01G540900 chr6D 96.250 80 3 0 241 320 239253865 239253944 6.860000e-27 132
27 TraesCS2A01G540900 chr6D 94.118 85 4 1 318 401 37048860 37048944 8.880000e-26 128
28 TraesCS2A01G540900 chr3B 96.250 80 3 0 241 320 389662078 389661999 6.860000e-27 132
29 TraesCS2A01G540900 chr4D 94.186 86 3 1 318 401 68019406 68019491 2.470000e-26 130
30 TraesCS2A01G540900 chr4D 94.186 86 3 1 318 401 406881759 406881844 2.470000e-26 130
31 TraesCS2A01G540900 chr1D 94.186 86 3 1 318 401 376845805 376845890 2.470000e-26 130
32 TraesCS2A01G540900 chr1D 93.182 88 4 1 318 403 396411552 396411639 8.880000e-26 128


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 TraesCS2A01G540900 chr2A 752747932 752750981 3049 False 5633.0 5633 100.0000 1 3050 1 chr2A.!!$F1 3049
1 TraesCS2A01G540900 chr2A 752758667 752759611 944 False 636.0 636 79.2820 1700 2654 1 chr2A.!!$F2 954
2 TraesCS2A01G540900 chr2A 752705614 752706762 1148 True 521.0 521 75.4650 897 2051 1 chr2A.!!$R2 1154
3 TraesCS2A01G540900 chr2D 620882945 620885875 2930 False 876.0 2880 93.1338 1 3050 5 chr2D.!!$F2 3049
4 TraesCS2A01G540900 chr2D 620921569 620922654 1085 False 671.0 671 78.1930 1106 2179 1 chr2D.!!$F1 1073
5 TraesCS2A01G540900 chr2D 620910674 620914688 4014 False 372.5 593 82.0760 1688 2918 2 chr2D.!!$F3 1230
6 TraesCS2A01G540900 chr2B 761888708 761889940 1232 False 758.0 758 78.1320 1382 2654 1 chr2B.!!$F1 1272
7 TraesCS2A01G540900 chr2B 761984322 761985665 1343 False 641.0 641 75.8190 838 2179 1 chr2B.!!$F3 1341
8 TraesCS2A01G540900 chr2B 761960538 761961432 894 False 507.0 507 77.3910 1279 2179 1 chr2B.!!$F2 900

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
262 264 0.252696 TGCTGGTCATAGTGGGGAGT 60.253 55.000 0.0 0.00 0.00 3.85 F
263 265 1.007842 TGCTGGTCATAGTGGGGAGTA 59.992 52.381 0.0 0.00 0.00 2.59 F
1903 1952 1.039856 GGACCCTCAGCTCAGAGATC 58.960 60.000 0.0 0.89 37.87 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1932 0.636101 ATCTCTGAGCTGAGGGTCCT 59.364 55.000 0.00 0.0 39.02 3.85 R
1936 1985 1.447314 GGAAGTCGCGGTAACCTGG 60.447 63.158 6.13 0.0 0.00 4.45 R
2997 6191 0.398696 TTGGGCCTTCTTCGCTGTTA 59.601 50.000 4.53 0.0 0.00 2.41 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
30 31 3.824443 TGTGATTTCAGACGTCTAGACCA 59.176 43.478 19.57 9.95 0.00 4.02
65 66 9.671279 AAGTTTGATGTATGATGTTAGATGACA 57.329 29.630 0.00 0.00 0.00 3.58
88 89 2.859165 AGTGTCCGGACAACATGATT 57.141 45.000 37.75 14.75 43.77 2.57
89 90 3.973206 AGTGTCCGGACAACATGATTA 57.027 42.857 37.75 10.31 43.77 1.75
90 91 4.280436 AGTGTCCGGACAACATGATTAA 57.720 40.909 37.75 9.49 43.77 1.40
91 92 4.843728 AGTGTCCGGACAACATGATTAAT 58.156 39.130 37.75 9.47 43.77 1.40
95 96 5.820423 TGTCCGGACAACATGATTAATAAGG 59.180 40.000 34.60 0.00 38.56 2.69
108 109 5.588246 TGATTAATAAGGCATTTGCAGACGA 59.412 36.000 4.74 0.00 44.36 4.20
113 114 2.161855 AGGCATTTGCAGACGATTTGA 58.838 42.857 4.74 0.00 44.36 2.69
167 169 8.170553 GTGTCATTTACGACGGTTATGTTTTAT 58.829 33.333 0.00 0.00 38.84 1.40
172 174 7.649370 TTACGACGGTTATGTTTTATCAACA 57.351 32.000 0.00 0.00 34.31 3.33
222 224 6.631971 TTGCTCACTTATTCAACATGACAA 57.368 33.333 0.00 0.00 0.00 3.18
243 245 3.097614 ACTGTCCTAGTGGAGCGTTTAT 58.902 45.455 0.00 0.00 44.16 1.40
244 246 3.119101 ACTGTCCTAGTGGAGCGTTTATG 60.119 47.826 0.00 0.00 44.16 1.90
245 247 2.202566 GTCCTAGTGGAGCGTTTATGC 58.797 52.381 0.00 0.00 44.16 3.14
255 257 3.543680 AGCGTTTATGCTGGTCATAGT 57.456 42.857 0.00 0.00 45.28 2.12
256 258 3.198068 AGCGTTTATGCTGGTCATAGTG 58.802 45.455 0.00 0.00 45.28 2.74
257 259 2.287915 GCGTTTATGCTGGTCATAGTGG 59.712 50.000 0.00 0.00 38.75 4.00
258 260 2.872245 CGTTTATGCTGGTCATAGTGGG 59.128 50.000 0.00 0.00 38.75 4.61
259 261 3.214328 GTTTATGCTGGTCATAGTGGGG 58.786 50.000 0.00 0.00 38.75 4.96
260 262 2.487746 TATGCTGGTCATAGTGGGGA 57.512 50.000 0.00 0.00 36.63 4.81
261 263 1.135094 ATGCTGGTCATAGTGGGGAG 58.865 55.000 0.00 0.00 32.59 4.30
262 264 0.252696 TGCTGGTCATAGTGGGGAGT 60.253 55.000 0.00 0.00 0.00 3.85
263 265 1.007842 TGCTGGTCATAGTGGGGAGTA 59.992 52.381 0.00 0.00 0.00 2.59
264 266 2.116238 GCTGGTCATAGTGGGGAGTAA 58.884 52.381 0.00 0.00 0.00 2.24
265 267 2.158943 GCTGGTCATAGTGGGGAGTAAC 60.159 54.545 0.00 0.00 0.00 2.50
266 268 3.375699 CTGGTCATAGTGGGGAGTAACT 58.624 50.000 0.00 0.00 0.00 2.24
267 269 3.775316 CTGGTCATAGTGGGGAGTAACTT 59.225 47.826 0.00 0.00 0.00 2.66
268 270 4.950361 TGGTCATAGTGGGGAGTAACTTA 58.050 43.478 0.00 0.00 0.00 2.24
269 271 5.535029 TGGTCATAGTGGGGAGTAACTTAT 58.465 41.667 0.00 0.00 0.00 1.73
270 272 6.685541 TGGTCATAGTGGGGAGTAACTTATA 58.314 40.000 0.00 0.00 0.00 0.98
271 273 6.552350 TGGTCATAGTGGGGAGTAACTTATAC 59.448 42.308 0.00 0.00 0.00 1.47
272 274 6.781507 GGTCATAGTGGGGAGTAACTTATACT 59.218 42.308 0.00 0.00 0.00 2.12
273 275 7.946776 GGTCATAGTGGGGAGTAACTTATACTA 59.053 40.741 0.00 0.00 0.00 1.82
274 276 9.359653 GTCATAGTGGGGAGTAACTTATACTAA 57.640 37.037 0.00 0.00 0.00 2.24
277 279 9.893975 ATAGTGGGGAGTAACTTATACTAATGT 57.106 33.333 0.00 0.00 0.00 2.71
278 280 8.247666 AGTGGGGAGTAACTTATACTAATGTC 57.752 38.462 0.00 0.00 0.00 3.06
279 281 7.842743 AGTGGGGAGTAACTTATACTAATGTCA 59.157 37.037 0.00 0.00 0.00 3.58
280 282 8.648693 GTGGGGAGTAACTTATACTAATGTCAT 58.351 37.037 0.00 0.00 0.00 3.06
281 283 8.647796 TGGGGAGTAACTTATACTAATGTCATG 58.352 37.037 0.00 0.00 0.00 3.07
282 284 7.603024 GGGGAGTAACTTATACTAATGTCATGC 59.397 40.741 0.00 0.00 0.00 4.06
283 285 8.148351 GGGAGTAACTTATACTAATGTCATGCA 58.852 37.037 0.00 0.00 0.00 3.96
284 286 9.712305 GGAGTAACTTATACTAATGTCATGCAT 57.288 33.333 0.00 0.00 40.03 3.96
289 291 8.744008 ACTTATACTAATGTCATGCATACGAC 57.256 34.615 9.64 9.64 36.67 4.34
290 292 8.357402 ACTTATACTAATGTCATGCATACGACA 58.643 33.333 18.89 18.89 45.62 4.35
291 293 8.515473 TTATACTAATGTCATGCATACGACAC 57.485 34.615 18.95 4.05 44.45 3.67
292 294 5.011090 ACTAATGTCATGCATACGACACT 57.989 39.130 18.95 12.73 44.45 3.55
293 295 6.144078 ACTAATGTCATGCATACGACACTA 57.856 37.500 18.95 13.13 44.45 2.74
294 296 6.209361 ACTAATGTCATGCATACGACACTAG 58.791 40.000 23.47 23.47 43.88 2.57
295 297 4.655762 ATGTCATGCATACGACACTAGT 57.344 40.909 18.95 4.13 44.45 2.57
296 298 4.028852 TGTCATGCATACGACACTAGTC 57.971 45.455 14.14 0.00 37.23 2.59
297 299 3.694566 TGTCATGCATACGACACTAGTCT 59.305 43.478 14.14 0.00 42.73 3.24
298 300 4.879545 TGTCATGCATACGACACTAGTCTA 59.120 41.667 14.14 0.00 42.73 2.59
299 301 5.355910 TGTCATGCATACGACACTAGTCTAA 59.644 40.000 14.14 0.00 42.73 2.10
300 302 5.910166 GTCATGCATACGACACTAGTCTAAG 59.090 44.000 11.29 0.00 42.73 2.18
301 303 5.589050 TCATGCATACGACACTAGTCTAAGT 59.411 40.000 0.00 0.00 42.73 2.24
302 304 5.892160 TGCATACGACACTAGTCTAAGTT 57.108 39.130 0.00 0.00 42.73 2.66
303 305 6.990341 TGCATACGACACTAGTCTAAGTTA 57.010 37.500 0.00 0.00 42.73 2.24
304 306 6.779117 TGCATACGACACTAGTCTAAGTTAC 58.221 40.000 0.00 0.00 42.73 2.50
305 307 6.596888 TGCATACGACACTAGTCTAAGTTACT 59.403 38.462 0.00 0.00 42.73 2.24
306 308 7.765819 TGCATACGACACTAGTCTAAGTTACTA 59.234 37.037 0.00 0.00 42.73 1.82
307 309 8.061268 GCATACGACACTAGTCTAAGTTACTAC 58.939 40.741 0.00 0.00 42.73 2.73
308 310 6.976636 ACGACACTAGTCTAAGTTACTACC 57.023 41.667 0.00 0.00 42.73 3.18
309 311 6.706295 ACGACACTAGTCTAAGTTACTACCT 58.294 40.000 0.00 0.00 42.73 3.08
310 312 7.164803 ACGACACTAGTCTAAGTTACTACCTT 58.835 38.462 0.00 0.00 42.73 3.50
311 313 7.333174 ACGACACTAGTCTAAGTTACTACCTTC 59.667 40.741 0.00 0.00 42.73 3.46
312 314 7.332926 CGACACTAGTCTAAGTTACTACCTTCA 59.667 40.741 0.00 0.00 42.73 3.02
313 315 9.176460 GACACTAGTCTAAGTTACTACCTTCAT 57.824 37.037 0.00 0.00 41.64 2.57
318 320 7.998580 AGTCTAAGTTACTACCTTCATAGTGC 58.001 38.462 0.00 0.00 36.09 4.40
319 321 7.614583 AGTCTAAGTTACTACCTTCATAGTGCA 59.385 37.037 0.00 0.00 36.09 4.57
320 322 7.701501 GTCTAAGTTACTACCTTCATAGTGCAC 59.298 40.741 9.40 9.40 36.09 4.57
321 323 5.340439 AGTTACTACCTTCATAGTGCACC 57.660 43.478 14.63 0.00 36.09 5.01
322 324 5.024118 AGTTACTACCTTCATAGTGCACCT 58.976 41.667 14.63 3.48 36.09 4.00
323 325 5.127356 AGTTACTACCTTCATAGTGCACCTC 59.873 44.000 14.63 0.00 36.09 3.85
324 326 3.714144 ACTACCTTCATAGTGCACCTCT 58.286 45.455 14.63 0.00 34.02 3.69
325 327 4.097418 ACTACCTTCATAGTGCACCTCTT 58.903 43.478 14.63 0.00 34.02 2.85
326 328 4.532521 ACTACCTTCATAGTGCACCTCTTT 59.467 41.667 14.63 0.00 34.02 2.52
327 329 3.944087 ACCTTCATAGTGCACCTCTTTC 58.056 45.455 14.63 0.00 0.00 2.62
328 330 3.274288 CCTTCATAGTGCACCTCTTTCC 58.726 50.000 14.63 0.00 0.00 3.13
329 331 3.054802 CCTTCATAGTGCACCTCTTTCCT 60.055 47.826 14.63 0.00 0.00 3.36
330 332 3.895232 TCATAGTGCACCTCTTTCCTC 57.105 47.619 14.63 0.00 0.00 3.71
331 333 3.173151 TCATAGTGCACCTCTTTCCTCA 58.827 45.455 14.63 0.00 0.00 3.86
332 334 3.776969 TCATAGTGCACCTCTTTCCTCAT 59.223 43.478 14.63 0.00 0.00 2.90
333 335 4.225942 TCATAGTGCACCTCTTTCCTCATT 59.774 41.667 14.63 0.00 0.00 2.57
334 336 5.425217 TCATAGTGCACCTCTTTCCTCATTA 59.575 40.000 14.63 0.00 0.00 1.90
335 337 4.640771 AGTGCACCTCTTTCCTCATTAA 57.359 40.909 14.63 0.00 0.00 1.40
336 338 4.985538 AGTGCACCTCTTTCCTCATTAAA 58.014 39.130 14.63 0.00 0.00 1.52
337 339 5.574188 AGTGCACCTCTTTCCTCATTAAAT 58.426 37.500 14.63 0.00 0.00 1.40
338 340 6.721318 AGTGCACCTCTTTCCTCATTAAATA 58.279 36.000 14.63 0.00 0.00 1.40
339 341 6.599638 AGTGCACCTCTTTCCTCATTAAATAC 59.400 38.462 14.63 0.00 0.00 1.89
340 342 6.599638 GTGCACCTCTTTCCTCATTAAATACT 59.400 38.462 5.22 0.00 0.00 2.12
341 343 7.121315 GTGCACCTCTTTCCTCATTAAATACTT 59.879 37.037 5.22 0.00 0.00 2.24
342 344 7.121168 TGCACCTCTTTCCTCATTAAATACTTG 59.879 37.037 0.00 0.00 0.00 3.16
343 345 7.475840 CACCTCTTTCCTCATTAAATACTTGC 58.524 38.462 0.00 0.00 0.00 4.01
344 346 6.603599 ACCTCTTTCCTCATTAAATACTTGCC 59.396 38.462 0.00 0.00 0.00 4.52
345 347 6.603201 CCTCTTTCCTCATTAAATACTTGCCA 59.397 38.462 0.00 0.00 0.00 4.92
346 348 7.286316 CCTCTTTCCTCATTAAATACTTGCCAT 59.714 37.037 0.00 0.00 0.00 4.40
347 349 9.342308 CTCTTTCCTCATTAAATACTTGCCATA 57.658 33.333 0.00 0.00 0.00 2.74
348 350 9.866655 TCTTTCCTCATTAAATACTTGCCATAT 57.133 29.630 0.00 0.00 0.00 1.78
365 367 9.520204 CTTGCCATATAAGTAAAATTGTCTTGG 57.480 33.333 0.00 0.00 0.00 3.61
366 368 8.006298 TGCCATATAAGTAAAATTGTCTTGGG 57.994 34.615 0.00 0.00 0.00 4.12
367 369 7.836685 TGCCATATAAGTAAAATTGTCTTGGGA 59.163 33.333 0.00 0.00 0.00 4.37
368 370 8.860088 GCCATATAAGTAAAATTGTCTTGGGAT 58.140 33.333 0.00 0.00 0.00 3.85
372 374 6.976934 AAGTAAAATTGTCTTGGGATGTGT 57.023 33.333 0.00 0.00 0.00 3.72
373 375 6.976934 AGTAAAATTGTCTTGGGATGTGTT 57.023 33.333 0.00 0.00 0.00 3.32
374 376 8.472007 AAGTAAAATTGTCTTGGGATGTGTTA 57.528 30.769 0.00 0.00 0.00 2.41
375 377 8.472007 AGTAAAATTGTCTTGGGATGTGTTAA 57.528 30.769 0.00 0.00 0.00 2.01
376 378 8.919145 AGTAAAATTGTCTTGGGATGTGTTAAA 58.081 29.630 0.00 0.00 0.00 1.52
377 379 9.705290 GTAAAATTGTCTTGGGATGTGTTAAAT 57.295 29.630 0.00 0.00 0.00 1.40
380 382 9.705290 AAATTGTCTTGGGATGTGTTAAATTAC 57.295 29.630 0.00 0.00 0.00 1.89
381 383 8.650143 ATTGTCTTGGGATGTGTTAAATTACT 57.350 30.769 0.00 0.00 0.00 2.24
382 384 9.747898 ATTGTCTTGGGATGTGTTAAATTACTA 57.252 29.630 0.00 0.00 0.00 1.82
383 385 9.747898 TTGTCTTGGGATGTGTTAAATTACTAT 57.252 29.630 0.00 0.00 0.00 2.12
384 386 9.391006 TGTCTTGGGATGTGTTAAATTACTATC 57.609 33.333 0.00 0.00 0.00 2.08
385 387 9.614792 GTCTTGGGATGTGTTAAATTACTATCT 57.385 33.333 0.00 0.00 0.00 1.98
470 472 1.237285 GCCGTGCCACACTTCTCATT 61.237 55.000 0.00 0.00 31.34 2.57
496 498 1.751927 CCCTGCCTGCCAATCTCAC 60.752 63.158 0.00 0.00 0.00 3.51
644 646 1.476891 GTGACCGGAGCACAGATAAGA 59.523 52.381 21.54 0.00 36.31 2.10
645 647 2.101582 GTGACCGGAGCACAGATAAGAT 59.898 50.000 21.54 0.00 36.31 2.40
646 648 2.362397 TGACCGGAGCACAGATAAGATC 59.638 50.000 9.46 0.00 0.00 2.75
647 649 1.689273 ACCGGAGCACAGATAAGATCC 59.311 52.381 9.46 0.00 0.00 3.36
648 650 1.688735 CCGGAGCACAGATAAGATCCA 59.311 52.381 0.00 0.00 0.00 3.41
649 651 2.546795 CCGGAGCACAGATAAGATCCAC 60.547 54.545 0.00 0.00 0.00 4.02
1250 1278 7.338957 TGTCTCCAATGCATCATACATGTTTAA 59.661 33.333 2.30 0.00 0.00 1.52
1836 1885 5.538433 CACCTCTTCCCTAACCAAATTTGAA 59.462 40.000 19.86 3.14 0.00 2.69
1842 1891 3.447229 CCCTAACCAAATTTGAATCGGCT 59.553 43.478 19.86 0.00 0.00 5.52
1847 1896 3.987220 ACCAAATTTGAATCGGCTTTTCG 59.013 39.130 19.86 0.57 0.00 3.46
1881 1930 2.614229 GGCTCAGAAGTTCTGGAAGGTC 60.614 54.545 28.33 15.77 44.39 3.85
1883 1932 2.634940 CTCAGAAGTTCTGGAAGGTCCA 59.365 50.000 28.33 9.28 45.98 4.02
1903 1952 1.039856 GGACCCTCAGCTCAGAGATC 58.960 60.000 0.00 0.89 37.87 2.75
1936 1985 3.056304 GCTATTGCGGAGAGAGTCATTC 58.944 50.000 0.00 0.00 0.00 2.67
1952 2001 0.611714 ATTCCAGGTTACCGCGACTT 59.388 50.000 8.23 0.00 0.00 3.01
2206 4684 4.142249 TGGATACTACATCAACTGGTCACG 60.142 45.833 0.00 0.00 37.61 4.35
2249 4742 6.435430 TTTAATGTCCTGATTGAATGACGG 57.565 37.500 0.00 0.00 0.00 4.79
2258 4758 6.316140 TCCTGATTGAATGACGGATACTTTTG 59.684 38.462 0.00 0.00 0.00 2.44
2259 4759 6.094048 CCTGATTGAATGACGGATACTTTTGT 59.906 38.462 0.00 0.00 0.00 2.83
2270 4770 5.585047 ACGGATACTTTTGTATTCTGCTTCC 59.415 40.000 0.00 0.00 44.91 3.46
2271 4771 5.584649 CGGATACTTTTGTATTCTGCTTCCA 59.415 40.000 0.00 0.00 44.91 3.53
2272 4772 6.260936 CGGATACTTTTGTATTCTGCTTCCAT 59.739 38.462 0.00 0.00 44.91 3.41
2273 4773 7.519008 CGGATACTTTTGTATTCTGCTTCCATC 60.519 40.741 0.00 0.00 44.91 3.51
2274 4774 7.283127 GGATACTTTTGTATTCTGCTTCCATCA 59.717 37.037 0.00 0.00 44.91 3.07
2275 4775 8.757982 ATACTTTTGTATTCTGCTTCCATCAT 57.242 30.769 0.00 0.00 42.53 2.45
2276 4776 7.472334 ACTTTTGTATTCTGCTTCCATCATT 57.528 32.000 0.00 0.00 0.00 2.57
2277 4777 7.542025 ACTTTTGTATTCTGCTTCCATCATTC 58.458 34.615 0.00 0.00 0.00 2.67
2278 4778 6.455360 TTTGTATTCTGCTTCCATCATTCC 57.545 37.500 0.00 0.00 0.00 3.01
2279 4779 5.114764 TGTATTCTGCTTCCATCATTCCA 57.885 39.130 0.00 0.00 0.00 3.53
2280 4780 5.698104 TGTATTCTGCTTCCATCATTCCAT 58.302 37.500 0.00 0.00 0.00 3.41
2290 4790 5.503662 TCCATCATTCCATGTCAATTTCG 57.496 39.130 0.00 0.00 0.00 3.46
2292 4792 5.066375 TCCATCATTCCATGTCAATTTCGTC 59.934 40.000 0.00 0.00 0.00 4.20
2293 4793 4.963276 TCATTCCATGTCAATTTCGTCC 57.037 40.909 0.00 0.00 0.00 4.79
2294 4794 4.331108 TCATTCCATGTCAATTTCGTCCA 58.669 39.130 0.00 0.00 0.00 4.02
2306 4808 5.186992 TCAATTTCGTCCATAGACTTCCTCA 59.813 40.000 0.00 0.00 41.16 3.86
2307 4809 5.677319 ATTTCGTCCATAGACTTCCTCAA 57.323 39.130 0.00 0.00 41.16 3.02
2308 4810 5.477607 TTTCGTCCATAGACTTCCTCAAA 57.522 39.130 0.00 0.00 41.16 2.69
2309 4811 5.677319 TTCGTCCATAGACTTCCTCAAAT 57.323 39.130 0.00 0.00 41.16 2.32
2310 4812 6.785337 TTCGTCCATAGACTTCCTCAAATA 57.215 37.500 0.00 0.00 41.16 1.40
2311 4813 6.392625 TCGTCCATAGACTTCCTCAAATAG 57.607 41.667 0.00 0.00 41.16 1.73
2312 4814 6.127101 TCGTCCATAGACTTCCTCAAATAGA 58.873 40.000 0.00 0.00 41.16 1.98
2313 4815 6.605995 TCGTCCATAGACTTCCTCAAATAGAA 59.394 38.462 0.00 0.00 41.16 2.10
2314 4816 7.123697 TCGTCCATAGACTTCCTCAAATAGAAA 59.876 37.037 0.00 0.00 41.16 2.52
2315 4817 7.764443 CGTCCATAGACTTCCTCAAATAGAAAA 59.236 37.037 0.00 0.00 41.16 2.29
2316 4818 8.884726 GTCCATAGACTTCCTCAAATAGAAAAC 58.115 37.037 0.00 0.00 40.10 2.43
2317 4819 8.602424 TCCATAGACTTCCTCAAATAGAAAACA 58.398 33.333 0.00 0.00 0.00 2.83
2318 4820 8.669243 CCATAGACTTCCTCAAATAGAAAACAC 58.331 37.037 0.00 0.00 0.00 3.32
2319 4821 9.442047 CATAGACTTCCTCAAATAGAAAACACT 57.558 33.333 0.00 0.00 0.00 3.55
2320 4822 7.971183 AGACTTCCTCAAATAGAAAACACTC 57.029 36.000 0.00 0.00 0.00 3.51
2321 4823 7.509546 AGACTTCCTCAAATAGAAAACACTCA 58.490 34.615 0.00 0.00 0.00 3.41
2322 4824 8.160106 AGACTTCCTCAAATAGAAAACACTCAT 58.840 33.333 0.00 0.00 0.00 2.90
2323 4825 9.436957 GACTTCCTCAAATAGAAAACACTCATA 57.563 33.333 0.00 0.00 0.00 2.15
2326 4828 9.658799 TTCCTCAAATAGAAAACACTCATAGAG 57.341 33.333 0.00 0.00 35.52 2.43
2346 4848 5.858381 AGAGAACTGACATGCTTAGTTTCA 58.142 37.500 10.12 0.00 34.99 2.69
2352 4854 6.498304 ACTGACATGCTTAGTTTCAAGTTTG 58.502 36.000 0.00 0.00 0.00 2.93
2364 4866 5.807011 AGTTTCAAGTTTGCACAACATTCTC 59.193 36.000 12.28 2.08 0.00 2.87
2375 4878 5.465390 TGCACAACATTCTCTACACACTTAC 59.535 40.000 0.00 0.00 0.00 2.34
2424 4927 3.909430 TGTAGCAGTTAAACAGAGTCCG 58.091 45.455 0.00 0.00 0.00 4.79
2427 4930 3.805207 AGCAGTTAAACAGAGTCCGTTT 58.195 40.909 9.36 9.36 39.75 3.60
2513 5285 7.226325 GGTGATGGAAATCATTTGTGTTTTCAA 59.774 33.333 11.72 3.91 35.97 2.69
2520 5292 9.264782 GAAATCATTTGTGTTTTCAACAAAGTG 57.735 29.630 7.66 6.53 44.16 3.16
2593 5715 3.936453 GGTGAAGCACCGATATAAACACA 59.064 43.478 0.22 0.00 44.95 3.72
2620 5742 8.807667 ATCAACAATCAATCAGTCAAGAAAAC 57.192 30.769 0.00 0.00 0.00 2.43
2691 5813 2.223923 GCATGTAAGACGAGAGCCTCAT 60.224 50.000 0.00 0.00 0.00 2.90
2703 5825 2.427453 AGAGCCTCATCGAAATACGTGT 59.573 45.455 0.00 0.00 43.13 4.49
2709 5831 3.961182 TCATCGAAATACGTGTCCTAGC 58.039 45.455 0.00 0.00 43.13 3.42
2712 5834 2.107178 CGAAATACGTGTCCTAGCGAC 58.893 52.381 0.00 4.84 42.33 5.19
2714 5836 1.466856 AATACGTGTCCTAGCGACCA 58.533 50.000 0.00 0.00 41.18 4.02
2739 5926 9.318041 CATTTCGAGTATGAAGTAAAACAAGTG 57.682 33.333 4.13 0.00 0.00 3.16
2758 5945 1.609555 TGGTAAAACGGCCACATGTTC 59.390 47.619 2.24 0.00 0.00 3.18
2776 5963 0.756294 TCAGAACTTCGGACAGGCAA 59.244 50.000 0.00 0.00 0.00 4.52
2824 6017 1.153005 GGGAATCTGGAGCAGCTGG 60.153 63.158 17.12 0.00 0.00 4.85
2825 6018 1.823041 GGAATCTGGAGCAGCTGGC 60.823 63.158 17.12 7.98 45.30 4.85
2908 6101 1.997874 AGCCTAAGTGGGAGCCAGG 60.998 63.158 0.00 0.00 32.34 4.45
2961 6155 1.453155 CCAGCCGCTGTAACAAGATT 58.547 50.000 18.98 0.00 0.00 2.40
2997 6191 1.531423 CAGCAGCTCAAAGACCATGT 58.469 50.000 0.00 0.00 0.00 3.21
2999 6193 3.076621 CAGCAGCTCAAAGACCATGTAA 58.923 45.455 0.00 0.00 0.00 2.41
3004 6198 2.159653 GCTCAAAGACCATGTAACAGCG 60.160 50.000 0.00 0.00 0.00 5.18
3028 6222 3.321968 AGAAGGCCCAAGTTGAACAAATC 59.678 43.478 3.87 0.00 0.00 2.17
3035 6229 4.290155 CCAAGTTGAACAAATCCAGAACG 58.710 43.478 3.87 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.119699 ACATCATACATCAAACTTTCACGACAT 59.880 33.333 0.00 0.00 0.00 3.06
65 66 4.280436 TCATGTTGTCCGGACACTTTAT 57.720 40.909 36.40 22.95 41.67 1.40
81 82 7.205297 GTCTGCAAATGCCTTATTAATCATGT 58.795 34.615 2.46 0.00 41.18 3.21
88 89 6.094742 TCAAATCGTCTGCAAATGCCTTATTA 59.905 34.615 2.46 0.00 41.18 0.98
89 90 4.989279 AATCGTCTGCAAATGCCTTATT 57.011 36.364 2.46 0.00 41.18 1.40
90 91 4.398988 TCAAATCGTCTGCAAATGCCTTAT 59.601 37.500 2.46 0.00 41.18 1.73
91 92 3.755905 TCAAATCGTCTGCAAATGCCTTA 59.244 39.130 2.46 0.00 41.18 2.69
95 96 1.906966 CGTCAAATCGTCTGCAAATGC 59.093 47.619 0.00 0.00 42.50 3.56
108 109 4.050553 CAACCTCAATGTTTGCGTCAAAT 58.949 39.130 7.98 0.00 35.74 2.32
113 114 1.032014 AGCAACCTCAATGTTTGCGT 58.968 45.000 9.86 0.30 31.77 5.24
167 169 9.829507 ATTTATTTCAATCCACAAAAGTGTTGA 57.170 25.926 0.00 0.00 35.07 3.18
217 219 1.618837 GCTCCACTAGGACAGTTGTCA 59.381 52.381 13.73 0.00 46.47 3.58
222 224 1.339097 AAACGCTCCACTAGGACAGT 58.661 50.000 0.00 0.00 39.61 3.55
243 245 0.252696 ACTCCCCACTATGACCAGCA 60.253 55.000 0.00 0.00 0.00 4.41
244 246 1.789523 TACTCCCCACTATGACCAGC 58.210 55.000 0.00 0.00 0.00 4.85
245 247 3.375699 AGTTACTCCCCACTATGACCAG 58.624 50.000 0.00 0.00 0.00 4.00
246 248 3.484953 AGTTACTCCCCACTATGACCA 57.515 47.619 0.00 0.00 0.00 4.02
248 250 7.836479 AGTATAAGTTACTCCCCACTATGAC 57.164 40.000 0.00 0.00 0.00 3.06
251 253 9.893975 ACATTAGTATAAGTTACTCCCCACTAT 57.106 33.333 0.00 0.00 0.00 2.12
252 254 9.359653 GACATTAGTATAAGTTACTCCCCACTA 57.640 37.037 0.00 0.00 0.00 2.74
253 255 7.842743 TGACATTAGTATAAGTTACTCCCCACT 59.157 37.037 0.00 0.00 0.00 4.00
254 256 8.015185 TGACATTAGTATAAGTTACTCCCCAC 57.985 38.462 0.00 0.00 0.00 4.61
255 257 8.647796 CATGACATTAGTATAAGTTACTCCCCA 58.352 37.037 0.00 0.00 0.00 4.96
256 258 7.603024 GCATGACATTAGTATAAGTTACTCCCC 59.397 40.741 0.00 0.00 0.00 4.81
257 259 8.148351 TGCATGACATTAGTATAAGTTACTCCC 58.852 37.037 0.00 0.00 0.00 4.30
258 260 9.712305 ATGCATGACATTAGTATAAGTTACTCC 57.288 33.333 0.00 0.00 34.40 3.85
263 265 9.193133 GTCGTATGCATGACATTAGTATAAGTT 57.807 33.333 10.16 0.00 39.98 2.66
264 266 8.357402 TGTCGTATGCATGACATTAGTATAAGT 58.643 33.333 14.14 0.00 44.08 2.24
265 267 8.742554 TGTCGTATGCATGACATTAGTATAAG 57.257 34.615 14.14 0.00 44.08 1.73
275 277 3.694566 AGACTAGTGTCGTATGCATGACA 59.305 43.478 14.14 14.14 46.20 3.58
287 289 8.558973 TGAAGGTAGTAACTTAGACTAGTGTC 57.441 38.462 0.00 0.00 43.22 3.67
292 294 9.118300 GCACTATGAAGGTAGTAACTTAGACTA 57.882 37.037 0.00 0.00 33.29 2.59
293 295 7.614583 TGCACTATGAAGGTAGTAACTTAGACT 59.385 37.037 0.00 0.00 33.29 3.24
294 296 7.701501 GTGCACTATGAAGGTAGTAACTTAGAC 59.298 40.741 10.32 0.00 33.29 2.59
295 297 7.147949 GGTGCACTATGAAGGTAGTAACTTAGA 60.148 40.741 17.98 0.00 33.29 2.10
296 298 6.979238 GGTGCACTATGAAGGTAGTAACTTAG 59.021 42.308 17.98 0.00 33.29 2.18
297 299 6.666546 AGGTGCACTATGAAGGTAGTAACTTA 59.333 38.462 17.98 0.00 33.29 2.24
298 300 5.484290 AGGTGCACTATGAAGGTAGTAACTT 59.516 40.000 17.98 0.00 33.29 2.66
299 301 5.024118 AGGTGCACTATGAAGGTAGTAACT 58.976 41.667 17.98 0.00 33.29 2.24
300 302 5.127356 AGAGGTGCACTATGAAGGTAGTAAC 59.873 44.000 17.98 0.00 33.29 2.50
301 303 5.269991 AGAGGTGCACTATGAAGGTAGTAA 58.730 41.667 17.98 0.00 33.29 2.24
302 304 4.868268 AGAGGTGCACTATGAAGGTAGTA 58.132 43.478 17.98 0.00 33.29 1.82
303 305 3.714144 AGAGGTGCACTATGAAGGTAGT 58.286 45.455 17.98 0.00 35.34 2.73
304 306 4.744795 AAGAGGTGCACTATGAAGGTAG 57.255 45.455 17.98 0.00 0.00 3.18
305 307 4.081087 GGAAAGAGGTGCACTATGAAGGTA 60.081 45.833 17.98 0.00 0.00 3.08
306 308 3.307762 GGAAAGAGGTGCACTATGAAGGT 60.308 47.826 17.98 0.00 0.00 3.50
307 309 3.054802 AGGAAAGAGGTGCACTATGAAGG 60.055 47.826 17.98 0.00 0.00 3.46
308 310 4.187694 GAGGAAAGAGGTGCACTATGAAG 58.812 47.826 17.98 0.00 0.00 3.02
309 311 3.582647 TGAGGAAAGAGGTGCACTATGAA 59.417 43.478 17.98 0.00 0.00 2.57
310 312 3.173151 TGAGGAAAGAGGTGCACTATGA 58.827 45.455 17.98 0.00 0.00 2.15
311 313 3.616956 TGAGGAAAGAGGTGCACTATG 57.383 47.619 17.98 0.00 0.00 2.23
312 314 4.851639 AATGAGGAAAGAGGTGCACTAT 57.148 40.909 17.98 5.74 0.00 2.12
313 315 5.755409 TTAATGAGGAAAGAGGTGCACTA 57.245 39.130 17.98 0.00 0.00 2.74
314 316 4.640771 TTAATGAGGAAAGAGGTGCACT 57.359 40.909 17.98 2.27 0.00 4.40
315 317 5.904362 ATTTAATGAGGAAAGAGGTGCAC 57.096 39.130 8.80 8.80 0.00 4.57
316 318 6.721318 AGTATTTAATGAGGAAAGAGGTGCA 58.279 36.000 0.00 0.00 0.00 4.57
317 319 7.475840 CAAGTATTTAATGAGGAAAGAGGTGC 58.524 38.462 0.00 0.00 0.00 5.01
318 320 7.415653 GGCAAGTATTTAATGAGGAAAGAGGTG 60.416 40.741 0.00 0.00 0.00 4.00
319 321 6.603599 GGCAAGTATTTAATGAGGAAAGAGGT 59.396 38.462 0.00 0.00 0.00 3.85
320 322 6.603201 TGGCAAGTATTTAATGAGGAAAGAGG 59.397 38.462 0.00 0.00 0.00 3.69
321 323 7.630242 TGGCAAGTATTTAATGAGGAAAGAG 57.370 36.000 0.00 0.00 0.00 2.85
322 324 9.866655 ATATGGCAAGTATTTAATGAGGAAAGA 57.133 29.630 0.00 0.00 0.00 2.52
339 341 9.520204 CCAAGACAATTTTACTTATATGGCAAG 57.480 33.333 0.00 0.00 0.00 4.01
340 342 8.474025 CCCAAGACAATTTTACTTATATGGCAA 58.526 33.333 0.00 0.00 0.00 4.52
341 343 7.836685 TCCCAAGACAATTTTACTTATATGGCA 59.163 33.333 0.00 0.00 0.00 4.92
342 344 8.232913 TCCCAAGACAATTTTACTTATATGGC 57.767 34.615 0.00 0.00 0.00 4.40
346 348 9.747898 ACACATCCCAAGACAATTTTACTTATA 57.252 29.630 0.00 0.00 0.00 0.98
347 349 8.650143 ACACATCCCAAGACAATTTTACTTAT 57.350 30.769 0.00 0.00 0.00 1.73
348 350 8.472007 AACACATCCCAAGACAATTTTACTTA 57.528 30.769 0.00 0.00 0.00 2.24
349 351 6.976934 ACACATCCCAAGACAATTTTACTT 57.023 33.333 0.00 0.00 0.00 2.24
350 352 6.976934 AACACATCCCAAGACAATTTTACT 57.023 33.333 0.00 0.00 0.00 2.24
351 353 9.705290 ATTTAACACATCCCAAGACAATTTTAC 57.295 29.630 0.00 0.00 0.00 2.01
354 356 9.705290 GTAATTTAACACATCCCAAGACAATTT 57.295 29.630 0.00 0.00 0.00 1.82
355 357 9.088987 AGTAATTTAACACATCCCAAGACAATT 57.911 29.630 0.00 0.00 0.00 2.32
356 358 8.650143 AGTAATTTAACACATCCCAAGACAAT 57.350 30.769 0.00 0.00 0.00 2.71
357 359 9.747898 ATAGTAATTTAACACATCCCAAGACAA 57.252 29.630 0.00 0.00 0.00 3.18
358 360 9.391006 GATAGTAATTTAACACATCCCAAGACA 57.609 33.333 0.00 0.00 0.00 3.41
359 361 9.614792 AGATAGTAATTTAACACATCCCAAGAC 57.385 33.333 0.00 0.00 0.00 3.01
377 379 9.359653 GGTCATAGTGGGTAACTTAGATAGTAA 57.640 37.037 0.00 0.00 40.56 2.24
378 380 8.730948 AGGTCATAGTGGGTAACTTAGATAGTA 58.269 37.037 0.00 0.00 40.56 1.82
379 381 7.593653 AGGTCATAGTGGGTAACTTAGATAGT 58.406 38.462 0.00 0.00 40.56 2.12
380 382 7.724506 TGAGGTCATAGTGGGTAACTTAGATAG 59.275 40.741 0.00 0.00 40.56 2.08
381 383 7.589081 TGAGGTCATAGTGGGTAACTTAGATA 58.411 38.462 0.00 0.00 40.56 1.98
382 384 6.441222 TGAGGTCATAGTGGGTAACTTAGAT 58.559 40.000 0.00 0.00 40.56 1.98
383 385 5.834460 TGAGGTCATAGTGGGTAACTTAGA 58.166 41.667 0.00 0.00 40.56 2.10
384 386 5.452077 GCTGAGGTCATAGTGGGTAACTTAG 60.452 48.000 0.00 0.00 40.56 2.18
385 387 4.404715 GCTGAGGTCATAGTGGGTAACTTA 59.595 45.833 0.00 0.00 40.56 2.24
386 388 3.197983 GCTGAGGTCATAGTGGGTAACTT 59.802 47.826 0.00 0.00 40.56 2.66
387 389 2.766828 GCTGAGGTCATAGTGGGTAACT 59.233 50.000 0.00 0.00 43.40 2.24
388 390 2.766828 AGCTGAGGTCATAGTGGGTAAC 59.233 50.000 0.00 0.00 0.00 2.50
389 391 2.766263 CAGCTGAGGTCATAGTGGGTAA 59.234 50.000 8.42 0.00 0.00 2.85
390 392 2.388735 CAGCTGAGGTCATAGTGGGTA 58.611 52.381 8.42 0.00 0.00 3.69
391 393 1.198713 CAGCTGAGGTCATAGTGGGT 58.801 55.000 8.42 0.00 0.00 4.51
392 394 0.179062 GCAGCTGAGGTCATAGTGGG 60.179 60.000 20.43 0.00 0.00 4.61
393 395 0.829333 AGCAGCTGAGGTCATAGTGG 59.171 55.000 20.43 0.00 0.00 4.00
394 396 1.535649 CGAGCAGCTGAGGTCATAGTG 60.536 57.143 20.43 0.00 35.83 2.74
395 397 0.743688 CGAGCAGCTGAGGTCATAGT 59.256 55.000 20.43 0.00 35.83 2.12
396 398 0.743688 ACGAGCAGCTGAGGTCATAG 59.256 55.000 20.43 1.45 35.83 2.23
397 399 2.052782 TACGAGCAGCTGAGGTCATA 57.947 50.000 20.43 0.00 35.83 2.15
398 400 1.339610 GATACGAGCAGCTGAGGTCAT 59.660 52.381 20.43 3.94 35.83 3.06
399 401 0.741326 GATACGAGCAGCTGAGGTCA 59.259 55.000 20.43 0.00 35.83 4.02
400 402 0.317436 CGATACGAGCAGCTGAGGTC 60.317 60.000 20.43 9.48 0.00 3.85
401 403 1.032657 ACGATACGAGCAGCTGAGGT 61.033 55.000 20.43 13.63 0.00 3.85
470 472 3.005539 GCAGGCAGGGGAGTGAGA 61.006 66.667 0.00 0.00 0.00 3.27
496 498 4.821589 GCCCTTGGTCGAGCTCGG 62.822 72.222 33.98 18.24 40.29 4.63
644 646 2.676748 GAGGAGAGAGTGGATGTGGAT 58.323 52.381 0.00 0.00 0.00 3.41
645 647 1.342474 GGAGGAGAGAGTGGATGTGGA 60.342 57.143 0.00 0.00 0.00 4.02
646 648 1.118838 GGAGGAGAGAGTGGATGTGG 58.881 60.000 0.00 0.00 0.00 4.17
647 649 1.118838 GGGAGGAGAGAGTGGATGTG 58.881 60.000 0.00 0.00 0.00 3.21
648 650 0.712979 TGGGAGGAGAGAGTGGATGT 59.287 55.000 0.00 0.00 0.00 3.06
649 651 1.118838 GTGGGAGGAGAGAGTGGATG 58.881 60.000 0.00 0.00 0.00 3.51
1012 1036 1.078848 GTCTTGGAGCCATGACGCT 60.079 57.895 16.63 0.00 43.42 5.07
1250 1278 2.122167 GGAGAGATCACGACCGGCT 61.122 63.158 0.00 0.00 0.00 5.52
1722 1767 8.719648 CAAGAAACATCAAGATAGCTATCCATC 58.280 37.037 26.65 14.32 33.17 3.51
1821 1870 4.718940 AGCCGATTCAAATTTGGTTAGG 57.281 40.909 17.90 16.05 0.00 2.69
1836 1885 4.276431 TGGTAAGTTTTTCGAAAAGCCGAT 59.724 37.500 27.25 18.54 38.45 4.18
1842 1891 4.641094 TGAGCCTGGTAAGTTTTTCGAAAA 59.359 37.500 19.08 19.08 0.00 2.29
1847 1896 4.822350 ACTTCTGAGCCTGGTAAGTTTTTC 59.178 41.667 0.00 0.00 0.00 2.29
1881 1930 1.305633 TCTGAGCTGAGGGTCCTGG 60.306 63.158 0.00 0.00 39.02 4.45
1883 1932 0.636101 ATCTCTGAGCTGAGGGTCCT 59.364 55.000 0.00 0.00 39.02 3.85
1903 1952 1.497223 GCAATAGCTCTCCGCAGCAG 61.497 60.000 0.00 0.00 42.40 4.24
1923 1972 3.133183 GGTAACCTGGAATGACTCTCTCC 59.867 52.174 0.00 0.00 0.00 3.71
1936 1985 1.447314 GGAAGTCGCGGTAACCTGG 60.447 63.158 6.13 0.00 0.00 4.45
2143 4616 6.460781 ACGGAATTCAGTATACAACTTCACA 58.539 36.000 9.65 0.00 35.76 3.58
2229 4722 4.220693 TCCGTCATTCAATCAGGACATT 57.779 40.909 0.00 0.00 0.00 2.71
2242 4735 6.823689 AGCAGAATACAAAAGTATCCGTCATT 59.176 34.615 0.00 0.00 0.00 2.57
2249 4742 8.213518 TGATGGAAGCAGAATACAAAAGTATC 57.786 34.615 0.00 0.00 0.00 2.24
2273 4773 7.730226 GTCTATGGACGAAATTGACATGGAATG 60.730 40.741 0.00 0.00 40.62 2.67
2274 4774 6.260936 GTCTATGGACGAAATTGACATGGAAT 59.739 38.462 0.00 0.00 32.19 3.01
2275 4775 5.584649 GTCTATGGACGAAATTGACATGGAA 59.415 40.000 0.00 0.00 32.19 3.53
2276 4776 5.104941 AGTCTATGGACGAAATTGACATGGA 60.105 40.000 3.29 0.00 46.29 3.41
2277 4777 5.118990 AGTCTATGGACGAAATTGACATGG 58.881 41.667 3.29 0.00 46.29 3.66
2278 4778 6.238211 GGAAGTCTATGGACGAAATTGACATG 60.238 42.308 3.29 0.00 46.29 3.21
2279 4779 5.817816 GGAAGTCTATGGACGAAATTGACAT 59.182 40.000 3.29 0.00 46.29 3.06
2280 4780 5.046591 AGGAAGTCTATGGACGAAATTGACA 60.047 40.000 3.29 0.00 46.29 3.58
2290 4790 8.884726 GTTTTCTATTTGAGGAAGTCTATGGAC 58.115 37.037 0.00 0.00 42.41 4.02
2292 4792 8.669243 GTGTTTTCTATTTGAGGAAGTCTATGG 58.331 37.037 0.00 0.00 0.00 2.74
2293 4793 9.442047 AGTGTTTTCTATTTGAGGAAGTCTATG 57.558 33.333 0.00 0.00 0.00 2.23
2294 4794 9.660180 GAGTGTTTTCTATTTGAGGAAGTCTAT 57.340 33.333 0.00 0.00 0.00 1.98
2307 4809 9.646427 GTCAGTTCTCTATGAGTGTTTTCTATT 57.354 33.333 0.00 0.00 0.00 1.73
2308 4810 8.807118 TGTCAGTTCTCTATGAGTGTTTTCTAT 58.193 33.333 0.00 0.00 0.00 1.98
2309 4811 8.178313 TGTCAGTTCTCTATGAGTGTTTTCTA 57.822 34.615 0.00 0.00 0.00 2.10
2310 4812 7.055667 TGTCAGTTCTCTATGAGTGTTTTCT 57.944 36.000 0.00 0.00 0.00 2.52
2311 4813 7.623089 GCATGTCAGTTCTCTATGAGTGTTTTC 60.623 40.741 0.00 0.00 0.00 2.29
2312 4814 6.148480 GCATGTCAGTTCTCTATGAGTGTTTT 59.852 38.462 0.00 0.00 0.00 2.43
2313 4815 5.641209 GCATGTCAGTTCTCTATGAGTGTTT 59.359 40.000 0.00 0.00 0.00 2.83
2314 4816 5.046735 AGCATGTCAGTTCTCTATGAGTGTT 60.047 40.000 0.00 0.00 0.00 3.32
2315 4817 4.465660 AGCATGTCAGTTCTCTATGAGTGT 59.534 41.667 0.00 0.00 0.00 3.55
2316 4818 5.008619 AGCATGTCAGTTCTCTATGAGTG 57.991 43.478 0.00 0.00 0.00 3.51
2317 4819 5.674052 AAGCATGTCAGTTCTCTATGAGT 57.326 39.130 0.00 0.00 0.00 3.41
2318 4820 6.804677 ACTAAGCATGTCAGTTCTCTATGAG 58.195 40.000 0.00 0.00 0.00 2.90
2319 4821 6.782082 ACTAAGCATGTCAGTTCTCTATGA 57.218 37.500 0.00 0.00 0.00 2.15
2320 4822 7.547019 TGAAACTAAGCATGTCAGTTCTCTATG 59.453 37.037 8.52 0.00 31.43 2.23
2321 4823 7.615403 TGAAACTAAGCATGTCAGTTCTCTAT 58.385 34.615 8.52 0.00 31.43 1.98
2322 4824 6.993079 TGAAACTAAGCATGTCAGTTCTCTA 58.007 36.000 8.52 0.00 31.43 2.43
2323 4825 5.858381 TGAAACTAAGCATGTCAGTTCTCT 58.142 37.500 8.52 0.00 31.43 3.10
2326 4828 6.305693 ACTTGAAACTAAGCATGTCAGTTC 57.694 37.500 8.52 0.94 31.43 3.01
2329 4831 5.400485 GCAAACTTGAAACTAAGCATGTCAG 59.600 40.000 0.00 0.00 0.00 3.51
2346 4848 5.356751 TGTGTAGAGAATGTTGTGCAAACTT 59.643 36.000 11.34 4.59 0.00 2.66
2352 4854 5.696724 AGTAAGTGTGTAGAGAATGTTGTGC 59.303 40.000 0.00 0.00 0.00 4.57
2364 4866 9.347934 CTGAACTAGATGAAAGTAAGTGTGTAG 57.652 37.037 0.00 0.00 0.00 2.74
2424 4927 5.221224 TGTCCATCCATTGTTCTGTCAAAAC 60.221 40.000 0.00 0.00 0.00 2.43
2427 4930 4.074259 CTGTCCATCCATTGTTCTGTCAA 58.926 43.478 0.00 0.00 0.00 3.18
2528 5300 2.284190 GTGGAGAAGAGCTGGTTATGC 58.716 52.381 0.00 0.00 0.00 3.14
2529 5301 2.237143 TGGTGGAGAAGAGCTGGTTATG 59.763 50.000 0.00 0.00 0.00 1.90
2534 5306 1.078567 GCTGGTGGAGAAGAGCTGG 60.079 63.158 0.00 0.00 0.00 4.85
2560 5682 2.771089 GTGCTTCACCTGATGAGACAA 58.229 47.619 0.00 0.00 38.99 3.18
2593 5715 7.991084 TTCTTGACTGATTGATTGTTGATCT 57.009 32.000 0.00 0.00 35.69 2.75
2681 5803 3.046390 CACGTATTTCGATGAGGCTCTC 58.954 50.000 16.72 9.65 42.86 3.20
2691 5813 2.009051 TCGCTAGGACACGTATTTCGA 58.991 47.619 0.00 0.00 42.86 3.71
2712 5834 8.504005 ACTTGTTTTACTTCATACTCGAAATGG 58.496 33.333 7.39 0.00 0.00 3.16
2714 5836 8.504005 CCACTTGTTTTACTTCATACTCGAAAT 58.496 33.333 0.00 0.00 0.00 2.17
2722 5844 8.344098 CCGTTTTACCACTTGTTTTACTTCATA 58.656 33.333 0.00 0.00 0.00 2.15
2729 5851 3.698040 TGGCCGTTTTACCACTTGTTTTA 59.302 39.130 0.00 0.00 0.00 1.52
2731 5853 2.100989 TGGCCGTTTTACCACTTGTTT 58.899 42.857 0.00 0.00 0.00 2.83
2739 5926 1.609555 TGAACATGTGGCCGTTTTACC 59.390 47.619 0.00 0.00 0.00 2.85
2758 5945 1.593196 TTTGCCTGTCCGAAGTTCTG 58.407 50.000 0.56 0.00 0.00 3.02
2792 5979 7.160457 TCCAGATTCCCCATACATATTTTGA 57.840 36.000 0.00 0.00 0.00 2.69
2824 6017 0.460284 CAGTGAGTGACCCATACCGC 60.460 60.000 0.00 0.00 0.00 5.68
2825 6018 0.895530 ACAGTGAGTGACCCATACCG 59.104 55.000 0.00 0.00 0.00 4.02
2949 6143 6.304356 TCTTCAGTGCAAATCTTGTTACAG 57.696 37.500 0.00 0.00 0.00 2.74
2961 6155 1.066002 GCTGCAACTTCTTCAGTGCAA 59.934 47.619 0.00 0.00 38.36 4.08
2997 6191 0.398696 TTGGGCCTTCTTCGCTGTTA 59.601 50.000 4.53 0.00 0.00 2.41
2999 6193 1.302832 CTTGGGCCTTCTTCGCTGT 60.303 57.895 4.53 0.00 0.00 4.40
3004 6198 2.306847 TGTTCAACTTGGGCCTTCTTC 58.693 47.619 4.53 0.00 0.00 2.87
3028 6222 0.795085 CTTTGCTCTGCTCGTTCTGG 59.205 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.