Multiple sequence alignment - TraesCS7D01G257800

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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 TraesCS7D01G257800 chr7D 100.000 3473 0 0 1 3473 233215406 233211934 0.000000e+00 6414.0
1 TraesCS7D01G257800 chr7A 93.985 2893 101 23 550 3432 245594540 245597369 0.000000e+00 4311.0
2 TraesCS7D01G257800 chr7A 94.161 274 14 2 1 273 245593304 245593576 1.930000e-112 416.0
3 TraesCS7D01G257800 chr7A 94.286 70 4 0 457 526 245594472 245594541 1.320000e-19 108.0
4 TraesCS7D01G257800 chr7B 95.641 2684 84 11 594 3258 204687741 204685072 0.000000e+00 4277.0
5 TraesCS7D01G257800 chr7B 88.321 137 6 1 3337 3473 204684753 204684627 4.640000e-34 156.0
6 TraesCS7D01G257800 chr7B 78.065 155 28 5 172 323 154365470 154365621 3.690000e-15 93.5
7 TraesCS7D01G257800 chr5A 84.329 1372 170 27 1042 2389 490816647 490815297 0.000000e+00 1301.0
8 TraesCS7D01G257800 chr5A 79.545 220 36 7 99 317 19490423 19490212 7.770000e-32 148.0
9 TraesCS7D01G257800 chr5D 83.942 1370 177 26 1043 2389 387729260 387727911 0.000000e+00 1271.0
10 TraesCS7D01G257800 chr5D 95.455 44 2 0 33 76 28727192 28727149 1.730000e-08 71.3
11 TraesCS7D01G257800 chr5B 83.796 1370 176 24 1043 2389 466334002 466332656 0.000000e+00 1258.0
12 TraesCS7D01G257800 chr1A 78.891 469 52 19 4 457 497266730 497267166 1.230000e-69 274.0
13 TraesCS7D01G257800 chr1A 98.000 50 1 0 33 82 497268087 497268136 1.720000e-13 87.9
14 TraesCS7D01G257800 chr1B 78.733 221 37 8 99 317 498062979 498063191 4.670000e-29 139.0
15 TraesCS7D01G257800 chr2D 82.781 151 19 7 85 233 629736432 629736577 1.010000e-25 128.0
16 TraesCS7D01G257800 chr2D 80.292 137 20 7 227 357 118896007 118895872 2.850000e-16 97.1
17 TraesCS7D01G257800 chr3A 89.583 96 7 3 169 263 493800283 493800190 6.090000e-23 119.0
18 TraesCS7D01G257800 chr4A 77.320 194 32 8 98 290 137181904 137181722 1.710000e-18 104.0
19 TraesCS7D01G257800 chr6A 95.455 44 2 0 33 76 515555179 515555136 1.730000e-08 71.3
20 TraesCS7D01G257800 chr3B 93.478 46 3 0 31 76 158239099 158239054 6.220000e-08 69.4


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 TraesCS7D01G257800 chr7D 233211934 233215406 3472 True 6414.000000 6414 100.000 1 3473 1 chr7D.!!$R1 3472
1 TraesCS7D01G257800 chr7A 245593304 245597369 4065 False 1611.666667 4311 94.144 1 3432 3 chr7A.!!$F1 3431
2 TraesCS7D01G257800 chr7B 204684627 204687741 3114 True 2216.500000 4277 91.981 594 3473 2 chr7B.!!$R1 2879
3 TraesCS7D01G257800 chr5A 490815297 490816647 1350 True 1301.000000 1301 84.329 1042 2389 1 chr5A.!!$R2 1347
4 TraesCS7D01G257800 chr5D 387727911 387729260 1349 True 1271.000000 1271 83.942 1043 2389 1 chr5D.!!$R2 1346
5 TraesCS7D01G257800 chr5B 466332656 466334002 1346 True 1258.000000 1258 83.796 1043 2389 1 chr5B.!!$R1 1346

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
379 381 0.03213 GCGCGATCTATCTTGGACCA 59.968 55.0 12.1 0.0 0.00 4.02 F
529 1405 0.24746 GTTGGCCCAGAAGGAAATGC 59.753 55.0 0.0 0.0 38.24 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 2298 0.802222 CCGTGACTAGCACCGACATG 60.802 60.0 10.44 0.0 44.85 3.21 R
2508 3432 0.947244 CACACTTGGTGGACTGAAGC 59.053 55.0 2.75 0.0 44.04 3.86 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
45 46 1.549170 TCCCGTTGGAGAAGAACTAGC 59.451 52.381 0.00 0.00 35.03 3.42
66 67 3.054802 GCCCCACCATCTATCTTAGGATG 60.055 52.174 0.00 0.00 39.04 3.51
69 70 5.046014 CCCCACCATCTATCTTAGGATGAAG 60.046 48.000 0.00 0.00 41.05 3.02
80 81 1.673767 AGGATGAAGTCATGGGTGGT 58.326 50.000 0.00 0.00 36.57 4.16
84 85 3.535561 GATGAAGTCATGGGTGGTGTAG 58.464 50.000 0.00 0.00 36.57 2.74
107 108 1.880027 GATCGCCACAACCCCATTATC 59.120 52.381 0.00 0.00 0.00 1.75
115 116 6.303839 GCCACAACCCCATTATCTATCTTAA 58.696 40.000 0.00 0.00 0.00 1.85
122 123 5.044846 CCCCATTATCTATCTTAAGGGTGGG 60.045 48.000 1.85 8.52 41.68 4.61
124 125 6.069963 CCCATTATCTATCTTAAGGGTGGGAG 60.070 46.154 1.85 0.00 44.10 4.30
144 145 0.691078 TGGGGTAGAGCAGATCACCC 60.691 60.000 14.66 14.66 43.32 4.61
153 154 1.087501 GCAGATCACCCGAGGTTTTC 58.912 55.000 0.00 0.00 31.02 2.29
184 185 2.392662 CTGAGCTTAGAGGGATGGTCA 58.607 52.381 0.00 0.00 35.92 4.02
198 199 4.767255 GTCAGAGCGGGTGGCCAG 62.767 72.222 5.11 0.00 45.17 4.85
224 225 3.339093 GTGGGGGAGGTTGAGGGG 61.339 72.222 0.00 0.00 0.00 4.79
225 226 3.882670 TGGGGGAGGTTGAGGGGT 61.883 66.667 0.00 0.00 0.00 4.95
292 294 3.793888 GGGGACCGGCTGTTAGGG 61.794 72.222 0.00 0.00 40.86 3.53
293 295 2.686106 GGGACCGGCTGTTAGGGA 60.686 66.667 0.00 0.00 0.00 4.20
294 296 2.732619 GGGACCGGCTGTTAGGGAG 61.733 68.421 0.00 0.00 0.00 4.30
295 297 2.732619 GGACCGGCTGTTAGGGAGG 61.733 68.421 0.00 0.00 0.00 4.30
296 298 2.687566 ACCGGCTGTTAGGGAGGG 60.688 66.667 0.00 0.00 0.00 4.30
297 299 2.365105 CCGGCTGTTAGGGAGGGA 60.365 66.667 0.00 0.00 0.00 4.20
298 300 1.766461 CCGGCTGTTAGGGAGGGAT 60.766 63.158 0.00 0.00 0.00 3.85
299 301 0.471211 CCGGCTGTTAGGGAGGGATA 60.471 60.000 0.00 0.00 0.00 2.59
300 302 0.969894 CGGCTGTTAGGGAGGGATAG 59.030 60.000 0.00 0.00 0.00 2.08
301 303 1.353091 GGCTGTTAGGGAGGGATAGG 58.647 60.000 0.00 0.00 0.00 2.57
302 304 1.353091 GCTGTTAGGGAGGGATAGGG 58.647 60.000 0.00 0.00 0.00 3.53
303 305 1.414685 GCTGTTAGGGAGGGATAGGGT 60.415 57.143 0.00 0.00 0.00 4.34
304 306 2.330216 CTGTTAGGGAGGGATAGGGTG 58.670 57.143 0.00 0.00 0.00 4.61
305 307 1.061657 TGTTAGGGAGGGATAGGGTGG 60.062 57.143 0.00 0.00 0.00 4.61
306 308 0.571236 TTAGGGAGGGATAGGGTGGG 59.429 60.000 0.00 0.00 0.00 4.61
307 309 1.385153 TAGGGAGGGATAGGGTGGGG 61.385 65.000 0.00 0.00 0.00 4.96
308 310 2.121918 GGAGGGATAGGGTGGGGG 60.122 72.222 0.00 0.00 0.00 5.40
309 311 2.733666 GGAGGGATAGGGTGGGGGA 61.734 68.421 0.00 0.00 0.00 4.81
310 312 1.152008 GAGGGATAGGGTGGGGGAG 60.152 68.421 0.00 0.00 0.00 4.30
311 313 1.952766 AGGGATAGGGTGGGGGAGT 60.953 63.158 0.00 0.00 0.00 3.85
312 314 1.005690 GGGATAGGGTGGGGGAGTT 59.994 63.158 0.00 0.00 0.00 3.01
313 315 1.060743 GGGATAGGGTGGGGGAGTTC 61.061 65.000 0.00 0.00 0.00 3.01
314 316 1.408453 GGATAGGGTGGGGGAGTTCG 61.408 65.000 0.00 0.00 0.00 3.95
315 317 1.384082 ATAGGGTGGGGGAGTTCGG 60.384 63.158 0.00 0.00 0.00 4.30
316 318 2.909292 ATAGGGTGGGGGAGTTCGGG 62.909 65.000 0.00 0.00 0.00 5.14
318 320 4.029809 GGTGGGGGAGTTCGGGTG 62.030 72.222 0.00 0.00 0.00 4.61
319 321 4.029809 GTGGGGGAGTTCGGGTGG 62.030 72.222 0.00 0.00 0.00 4.61
320 322 4.257810 TGGGGGAGTTCGGGTGGA 62.258 66.667 0.00 0.00 0.00 4.02
321 323 3.400054 GGGGGAGTTCGGGTGGAG 61.400 72.222 0.00 0.00 0.00 3.86
322 324 3.400054 GGGGAGTTCGGGTGGAGG 61.400 72.222 0.00 0.00 0.00 4.30
323 325 2.606826 GGGAGTTCGGGTGGAGGT 60.607 66.667 0.00 0.00 0.00 3.85
324 326 2.663196 GGAGTTCGGGTGGAGGTG 59.337 66.667 0.00 0.00 0.00 4.00
325 327 2.663196 GAGTTCGGGTGGAGGTGG 59.337 66.667 0.00 0.00 0.00 4.61
326 328 1.911766 GAGTTCGGGTGGAGGTGGA 60.912 63.158 0.00 0.00 0.00 4.02
327 329 1.889530 GAGTTCGGGTGGAGGTGGAG 61.890 65.000 0.00 0.00 0.00 3.86
328 330 2.606519 TTCGGGTGGAGGTGGAGG 60.607 66.667 0.00 0.00 0.00 4.30
329 331 3.168759 TTCGGGTGGAGGTGGAGGA 62.169 63.158 0.00 0.00 0.00 3.71
330 332 2.606519 CGGGTGGAGGTGGAGGAA 60.607 66.667 0.00 0.00 0.00 3.36
331 333 2.660064 CGGGTGGAGGTGGAGGAAG 61.660 68.421 0.00 0.00 0.00 3.46
332 334 1.229529 GGGTGGAGGTGGAGGAAGA 60.230 63.158 0.00 0.00 0.00 2.87
333 335 0.840722 GGGTGGAGGTGGAGGAAGAA 60.841 60.000 0.00 0.00 0.00 2.52
334 336 0.615850 GGTGGAGGTGGAGGAAGAAG 59.384 60.000 0.00 0.00 0.00 2.85
335 337 0.615850 GTGGAGGTGGAGGAAGAAGG 59.384 60.000 0.00 0.00 0.00 3.46
336 338 0.491823 TGGAGGTGGAGGAAGAAGGA 59.508 55.000 0.00 0.00 0.00 3.36
337 339 1.132527 TGGAGGTGGAGGAAGAAGGAA 60.133 52.381 0.00 0.00 0.00 3.36
338 340 1.557371 GGAGGTGGAGGAAGAAGGAAG 59.443 57.143 0.00 0.00 0.00 3.46
339 341 2.541466 GAGGTGGAGGAAGAAGGAAGA 58.459 52.381 0.00 0.00 0.00 2.87
340 342 2.499693 GAGGTGGAGGAAGAAGGAAGAG 59.500 54.545 0.00 0.00 0.00 2.85
341 343 2.112691 AGGTGGAGGAAGAAGGAAGAGA 59.887 50.000 0.00 0.00 0.00 3.10
342 344 2.499693 GGTGGAGGAAGAAGGAAGAGAG 59.500 54.545 0.00 0.00 0.00 3.20
343 345 2.499693 GTGGAGGAAGAAGGAAGAGAGG 59.500 54.545 0.00 0.00 0.00 3.69
344 346 2.383683 TGGAGGAAGAAGGAAGAGAGGA 59.616 50.000 0.00 0.00 0.00 3.71
345 347 3.181406 TGGAGGAAGAAGGAAGAGAGGAA 60.181 47.826 0.00 0.00 0.00 3.36
346 348 3.450817 GGAGGAAGAAGGAAGAGAGGAAG 59.549 52.174 0.00 0.00 0.00 3.46
347 349 4.349365 GAGGAAGAAGGAAGAGAGGAAGA 58.651 47.826 0.00 0.00 0.00 2.87
348 350 4.757692 AGGAAGAAGGAAGAGAGGAAGAA 58.242 43.478 0.00 0.00 0.00 2.52
349 351 4.530553 AGGAAGAAGGAAGAGAGGAAGAAC 59.469 45.833 0.00 0.00 0.00 3.01
350 352 4.284746 GGAAGAAGGAAGAGAGGAAGAACA 59.715 45.833 0.00 0.00 0.00 3.18
351 353 5.045942 GGAAGAAGGAAGAGAGGAAGAACAT 60.046 44.000 0.00 0.00 0.00 2.71
352 354 5.419239 AGAAGGAAGAGAGGAAGAACATG 57.581 43.478 0.00 0.00 0.00 3.21
353 355 5.090139 AGAAGGAAGAGAGGAAGAACATGA 58.910 41.667 0.00 0.00 0.00 3.07
354 356 5.545723 AGAAGGAAGAGAGGAAGAACATGAA 59.454 40.000 0.00 0.00 0.00 2.57
355 357 5.159273 AGGAAGAGAGGAAGAACATGAAC 57.841 43.478 0.00 0.00 0.00 3.18
356 358 4.594920 AGGAAGAGAGGAAGAACATGAACA 59.405 41.667 0.00 0.00 0.00 3.18
357 359 4.934602 GGAAGAGAGGAAGAACATGAACAG 59.065 45.833 0.00 0.00 0.00 3.16
358 360 5.512232 GGAAGAGAGGAAGAACATGAACAGT 60.512 44.000 0.00 0.00 0.00 3.55
359 361 6.295349 GGAAGAGAGGAAGAACATGAACAGTA 60.295 42.308 0.00 0.00 0.00 2.74
360 362 6.279513 AGAGAGGAAGAACATGAACAGTAG 57.720 41.667 0.00 0.00 0.00 2.57
361 363 4.826556 AGAGGAAGAACATGAACAGTAGC 58.173 43.478 0.00 0.00 0.00 3.58
362 364 3.589988 AGGAAGAACATGAACAGTAGCG 58.410 45.455 0.00 0.00 0.00 4.26
363 365 2.094417 GGAAGAACATGAACAGTAGCGC 59.906 50.000 0.00 0.00 0.00 5.92
364 366 1.350193 AGAACATGAACAGTAGCGCG 58.650 50.000 0.00 0.00 0.00 6.86
365 367 1.067846 AGAACATGAACAGTAGCGCGA 60.068 47.619 12.10 0.00 0.00 5.87
366 368 1.927174 GAACATGAACAGTAGCGCGAT 59.073 47.619 12.10 5.99 0.00 4.58
367 369 1.560923 ACATGAACAGTAGCGCGATC 58.439 50.000 12.10 0.00 0.00 3.69
368 370 1.135139 ACATGAACAGTAGCGCGATCT 59.865 47.619 12.10 0.00 0.00 2.75
369 371 2.357952 ACATGAACAGTAGCGCGATCTA 59.642 45.455 12.10 0.00 0.00 1.98
370 372 3.004839 ACATGAACAGTAGCGCGATCTAT 59.995 43.478 12.10 0.00 0.00 1.98
371 373 3.269486 TGAACAGTAGCGCGATCTATC 57.731 47.619 12.10 6.13 0.00 2.08
372 374 2.879026 TGAACAGTAGCGCGATCTATCT 59.121 45.455 12.10 0.00 0.00 1.98
373 375 3.315470 TGAACAGTAGCGCGATCTATCTT 59.685 43.478 12.10 0.00 0.00 2.40
374 376 3.275400 ACAGTAGCGCGATCTATCTTG 57.725 47.619 12.10 5.91 0.00 3.02
375 377 2.030717 ACAGTAGCGCGATCTATCTTGG 60.031 50.000 12.10 0.00 0.00 3.61
376 378 2.226674 CAGTAGCGCGATCTATCTTGGA 59.773 50.000 12.10 0.00 0.00 3.53
377 379 2.226912 AGTAGCGCGATCTATCTTGGAC 59.773 50.000 12.10 0.00 0.00 4.02
378 380 0.315568 AGCGCGATCTATCTTGGACC 59.684 55.000 12.10 0.00 0.00 4.46
379 381 0.032130 GCGCGATCTATCTTGGACCA 59.968 55.000 12.10 0.00 0.00 4.02
380 382 1.337260 GCGCGATCTATCTTGGACCAT 60.337 52.381 12.10 0.00 0.00 3.55
381 383 2.868044 GCGCGATCTATCTTGGACCATT 60.868 50.000 12.10 0.00 0.00 3.16
382 384 2.733552 CGCGATCTATCTTGGACCATTG 59.266 50.000 0.00 0.00 0.00 2.82
383 385 3.070018 GCGATCTATCTTGGACCATTGG 58.930 50.000 0.00 0.00 0.00 3.16
384 386 3.244215 GCGATCTATCTTGGACCATTGGA 60.244 47.826 10.37 0.00 0.00 3.53
385 387 4.564406 GCGATCTATCTTGGACCATTGGAT 60.564 45.833 10.37 2.84 0.00 3.41
386 388 5.174395 CGATCTATCTTGGACCATTGGATC 58.826 45.833 10.37 5.58 0.00 3.36
387 389 5.279657 CGATCTATCTTGGACCATTGGATCA 60.280 44.000 10.37 4.21 0.00 2.92
388 390 5.974156 TCTATCTTGGACCATTGGATCAA 57.026 39.130 10.37 11.65 0.00 2.57
389 391 5.933617 TCTATCTTGGACCATTGGATCAAG 58.066 41.667 23.75 23.75 37.48 3.02
390 392 4.868172 ATCTTGGACCATTGGATCAAGA 57.132 40.909 28.97 28.97 43.05 3.02
391 393 4.868172 TCTTGGACCATTGGATCAAGAT 57.132 40.909 26.10 1.51 38.80 2.40
392 394 4.529897 TCTTGGACCATTGGATCAAGATG 58.470 43.478 26.10 13.23 38.80 2.90
393 395 3.301794 TGGACCATTGGATCAAGATGG 57.698 47.619 10.37 15.67 44.64 3.51
394 396 1.959282 GGACCATTGGATCAAGATGGC 59.041 52.381 10.37 11.37 43.25 4.40
395 397 2.423947 GGACCATTGGATCAAGATGGCT 60.424 50.000 10.37 7.92 43.25 4.75
396 398 2.621998 GACCATTGGATCAAGATGGCTG 59.378 50.000 10.37 0.66 43.25 4.85
397 399 1.340248 CCATTGGATCAAGATGGCTGC 59.660 52.381 0.00 0.00 34.47 5.25
398 400 2.307768 CATTGGATCAAGATGGCTGCT 58.692 47.619 0.00 0.00 0.00 4.24
399 401 3.483421 CATTGGATCAAGATGGCTGCTA 58.517 45.455 0.00 0.00 0.00 3.49
400 402 3.650281 TTGGATCAAGATGGCTGCTAA 57.350 42.857 0.00 0.00 0.00 3.09
401 403 3.870538 TGGATCAAGATGGCTGCTAAT 57.129 42.857 0.00 0.00 0.00 1.73
402 404 4.980339 TGGATCAAGATGGCTGCTAATA 57.020 40.909 0.00 0.00 0.00 0.98
403 405 5.308976 TGGATCAAGATGGCTGCTAATAA 57.691 39.130 0.00 0.00 0.00 1.40
404 406 5.693961 TGGATCAAGATGGCTGCTAATAAA 58.306 37.500 0.00 0.00 0.00 1.40
405 407 6.128486 TGGATCAAGATGGCTGCTAATAAAA 58.872 36.000 0.00 0.00 0.00 1.52
406 408 6.779049 TGGATCAAGATGGCTGCTAATAAAAT 59.221 34.615 0.00 0.00 0.00 1.82
407 409 7.288389 TGGATCAAGATGGCTGCTAATAAAATT 59.712 33.333 0.00 0.00 0.00 1.82
408 410 7.597743 GGATCAAGATGGCTGCTAATAAAATTG 59.402 37.037 0.00 0.00 0.00 2.32
409 411 7.643569 TCAAGATGGCTGCTAATAAAATTGA 57.356 32.000 0.00 0.00 0.00 2.57
410 412 7.483307 TCAAGATGGCTGCTAATAAAATTGAC 58.517 34.615 0.00 0.00 0.00 3.18
411 413 7.340232 TCAAGATGGCTGCTAATAAAATTGACT 59.660 33.333 0.00 0.00 0.00 3.41
412 414 7.035840 AGATGGCTGCTAATAAAATTGACTG 57.964 36.000 0.00 0.00 0.00 3.51
413 415 6.830324 AGATGGCTGCTAATAAAATTGACTGA 59.170 34.615 0.00 0.00 0.00 3.41
414 416 7.504911 AGATGGCTGCTAATAAAATTGACTGAT 59.495 33.333 0.00 0.00 0.00 2.90
415 417 6.798482 TGGCTGCTAATAAAATTGACTGATG 58.202 36.000 0.00 0.00 0.00 3.07
416 418 6.183360 TGGCTGCTAATAAAATTGACTGATGG 60.183 38.462 0.00 0.00 0.00 3.51
417 419 5.689068 GCTGCTAATAAAATTGACTGATGGC 59.311 40.000 0.00 0.00 0.00 4.40
418 420 6.681120 GCTGCTAATAAAATTGACTGATGGCA 60.681 38.462 0.00 0.00 0.00 4.92
419 421 7.167924 TGCTAATAAAATTGACTGATGGCAA 57.832 32.000 0.00 0.00 0.00 4.52
420 422 7.609960 TGCTAATAAAATTGACTGATGGCAAA 58.390 30.769 0.00 0.00 0.00 3.68
421 423 8.093307 TGCTAATAAAATTGACTGATGGCAAAA 58.907 29.630 0.00 0.00 0.00 2.44
422 424 8.598075 GCTAATAAAATTGACTGATGGCAAAAG 58.402 33.333 0.00 0.00 0.00 2.27
423 425 9.859427 CTAATAAAATTGACTGATGGCAAAAGA 57.141 29.630 6.78 0.00 0.00 2.52
425 427 9.558396 AATAAAATTGACTGATGGCAAAAGAAA 57.442 25.926 6.78 2.18 0.00 2.52
426 428 9.729281 ATAAAATTGACTGATGGCAAAAGAAAT 57.271 25.926 6.78 4.07 0.00 2.17
427 429 8.454570 AAAATTGACTGATGGCAAAAGAAATT 57.545 26.923 6.78 8.70 0.00 1.82
428 430 8.454570 AAATTGACTGATGGCAAAAGAAATTT 57.545 26.923 16.07 16.07 0.00 1.82
429 431 7.662604 ATTGACTGATGGCAAAAGAAATTTC 57.337 32.000 10.33 10.33 0.00 2.17
430 432 6.159299 TGACTGATGGCAAAAGAAATTTCA 57.841 33.333 19.99 0.00 0.00 2.69
434 436 6.267471 ACTGATGGCAAAAGAAATTTCAGGTA 59.733 34.615 19.99 0.75 0.00 3.08
438 440 6.454795 TGGCAAAAGAAATTTCAGGTACATC 58.545 36.000 19.99 3.82 0.00 3.06
448 450 8.915057 AAATTTCAGGTACATCATGGATAGAG 57.085 34.615 0.00 0.00 0.00 2.43
460 462 3.717507 TGGATAGAGGGTCCCAATACA 57.282 47.619 11.55 4.69 34.76 2.29
473 1349 5.180271 GTCCCAATACAAAATAGGTCGTCA 58.820 41.667 0.00 0.00 0.00 4.35
474 1350 5.820947 GTCCCAATACAAAATAGGTCGTCAT 59.179 40.000 0.00 0.00 0.00 3.06
526 1402 0.260230 TGTGTTGGCCCAGAAGGAAA 59.740 50.000 0.00 0.00 38.24 3.13
527 1403 1.133199 TGTGTTGGCCCAGAAGGAAAT 60.133 47.619 0.00 0.00 38.24 2.17
528 1404 1.273327 GTGTTGGCCCAGAAGGAAATG 59.727 52.381 0.00 0.00 38.24 2.32
529 1405 0.247460 GTTGGCCCAGAAGGAAATGC 59.753 55.000 0.00 0.00 38.24 3.56
530 1406 0.904394 TTGGCCCAGAAGGAAATGCC 60.904 55.000 0.00 0.00 38.55 4.40
531 1407 2.418083 GGCCCAGAAGGAAATGCCG 61.418 63.158 0.00 0.00 43.43 5.69
532 1408 1.678970 GCCCAGAAGGAAATGCCGT 60.679 57.895 0.00 0.00 43.43 5.68
533 1409 1.937546 GCCCAGAAGGAAATGCCGTG 61.938 60.000 0.00 0.00 43.43 4.94
534 1410 0.322456 CCCAGAAGGAAATGCCGTGA 60.322 55.000 0.00 0.00 43.43 4.35
535 1411 1.089920 CCAGAAGGAAATGCCGTGAG 58.910 55.000 0.00 0.00 43.43 3.51
536 1412 1.611673 CCAGAAGGAAATGCCGTGAGT 60.612 52.381 0.00 0.00 43.43 3.41
537 1413 2.154462 CAGAAGGAAATGCCGTGAGTT 58.846 47.619 0.00 0.00 43.43 3.01
538 1414 2.095567 CAGAAGGAAATGCCGTGAGTTG 60.096 50.000 0.00 0.00 43.43 3.16
539 1415 2.151202 GAAGGAAATGCCGTGAGTTGA 58.849 47.619 0.00 0.00 43.43 3.18
540 1416 2.496899 AGGAAATGCCGTGAGTTGAT 57.503 45.000 0.00 0.00 43.43 2.57
541 1417 2.795329 AGGAAATGCCGTGAGTTGATT 58.205 42.857 0.00 0.00 43.43 2.57
542 1418 2.489329 AGGAAATGCCGTGAGTTGATTG 59.511 45.455 0.00 0.00 43.43 2.67
543 1419 2.415893 GGAAATGCCGTGAGTTGATTGG 60.416 50.000 0.00 0.00 0.00 3.16
544 1420 2.198827 AATGCCGTGAGTTGATTGGA 57.801 45.000 0.00 0.00 0.00 3.53
545 1421 1.742761 ATGCCGTGAGTTGATTGGAG 58.257 50.000 0.00 0.00 0.00 3.86
546 1422 0.955428 TGCCGTGAGTTGATTGGAGC 60.955 55.000 0.00 0.00 0.00 4.70
547 1423 0.674895 GCCGTGAGTTGATTGGAGCT 60.675 55.000 0.00 0.00 0.00 4.09
548 1424 1.405526 GCCGTGAGTTGATTGGAGCTA 60.406 52.381 0.00 0.00 0.00 3.32
549 1425 2.935238 GCCGTGAGTTGATTGGAGCTAA 60.935 50.000 0.00 0.00 0.00 3.09
550 1426 3.334691 CCGTGAGTTGATTGGAGCTAAA 58.665 45.455 0.00 0.00 0.00 1.85
551 1427 3.125316 CCGTGAGTTGATTGGAGCTAAAC 59.875 47.826 0.00 0.00 0.00 2.01
554 1430 3.007506 TGAGTTGATTGGAGCTAAACGGA 59.992 43.478 0.00 0.00 0.00 4.69
563 1439 2.590092 CTAAACGGAGCCCCCTGG 59.410 66.667 0.00 0.00 0.00 4.45
583 1459 1.153667 GCGTCCAAGGCAGAGAGAG 60.154 63.158 0.00 0.00 0.00 3.20
608 1486 3.793888 GGGAGGGAACGCGGGAAT 61.794 66.667 12.47 0.00 0.00 3.01
643 1521 5.897377 AGTTGTAGCAACAAACTTCTGTT 57.103 34.783 13.48 0.00 46.84 3.16
697 1575 2.735259 TAAACCACCTCCCCTCTTCT 57.265 50.000 0.00 0.00 0.00 2.85
1025 1913 4.374702 CCCGTCGTCGTCGTCGTT 62.375 66.667 17.80 0.00 44.09 3.85
1389 2310 3.792736 GGGGGCATGTCGGTGCTA 61.793 66.667 7.96 0.00 44.45 3.49
1479 2400 0.320374 TCGGCCTCGACAACTTCAAT 59.680 50.000 0.00 0.00 40.88 2.57
1494 2415 1.100510 TCAATGCGTACTACGAGCCT 58.899 50.000 12.87 0.00 46.05 4.58
1851 2772 1.962306 GTACGCGGCCACCAAGAAA 60.962 57.895 12.47 0.00 0.00 2.52
2334 3258 2.858974 CACCCCACCACCTCCCTT 60.859 66.667 0.00 0.00 0.00 3.95
2340 3264 2.526873 ACCACCTCCCTTGACGCT 60.527 61.111 0.00 0.00 0.00 5.07
2456 3380 0.614415 AAGAAATCCATGGGCGCCAA 60.614 50.000 30.85 20.37 36.95 4.52
2511 3435 4.410400 CTTCCCGGCCCGAAGCTT 62.410 66.667 3.71 0.00 43.05 3.74
2535 3459 0.038892 CCACCAAGTGTGCATTCTGC 60.039 55.000 0.00 0.00 44.01 4.26
2542 3466 1.350351 AGTGTGCATTCTGCTCTCCTT 59.650 47.619 0.00 0.00 45.31 3.36
2553 3477 2.203983 TCTCCTTGGAGGCTGGCA 60.204 61.111 15.81 0.00 34.61 4.92
2714 3639 8.340618 TCTTTCTTCATAGCATAAGCAAAACT 57.659 30.769 0.00 0.00 45.49 2.66
2725 3650 8.986477 AGCATAAGCAAAACTAAACTATTTGG 57.014 30.769 0.00 0.00 45.49 3.28
2791 3716 2.766400 GGAGCGAGGAGGACACGAG 61.766 68.421 0.00 0.00 0.00 4.18
2937 3862 8.412456 TGAAAATGTCAACAATTGTGTACTCAT 58.588 29.630 12.82 9.87 36.80 2.90
2939 3864 7.509141 AATGTCAACAATTGTGTACTCATGA 57.491 32.000 12.82 7.31 36.80 3.07
2940 3865 6.544038 TGTCAACAATTGTGTACTCATGAG 57.456 37.500 21.37 21.37 36.80 2.90
2941 3866 6.054941 TGTCAACAATTGTGTACTCATGAGT 58.945 36.000 30.11 30.11 45.02 3.41
2942 3867 6.202762 TGTCAACAATTGTGTACTCATGAGTC 59.797 38.462 31.09 21.44 42.54 3.36
3147 4074 1.227556 GTCCCTGACTTGTGCGTGT 60.228 57.895 0.00 0.00 0.00 4.49
3149 4076 2.633657 CCTGACTTGTGCGTGTGC 59.366 61.111 0.00 0.00 43.20 4.57
3218 4145 1.152567 TTTGGTGGCAAGTGAGGGG 60.153 57.895 0.00 0.00 0.00 4.79
3250 4181 0.391263 GAGCCTTGGACTTGGTACCG 60.391 60.000 7.57 0.00 0.00 4.02
3267 4198 1.079503 CCGCTTCTTTCCAGTAGCAC 58.920 55.000 0.00 0.00 42.23 4.40
3273 4204 2.047061 TCTTTCCAGTAGCACCACACT 58.953 47.619 0.00 0.00 0.00 3.55
3307 4428 4.990543 TTGATGTTTCTTGCTGTCTACG 57.009 40.909 0.00 0.00 0.00 3.51
3332 4504 1.728971 GGCGTGATGACTGAAGTTGAG 59.271 52.381 0.00 0.00 0.00 3.02
3335 4507 2.411069 CGTGATGACTGAAGTTGAGCTG 59.589 50.000 0.00 0.00 0.00 4.24
3392 4564 1.159713 TGTGGAACTGTGAAGCTGCG 61.160 55.000 0.00 0.00 38.04 5.18
3432 4604 6.431234 GGATTCCTACTAAACATAATGGCCAG 59.569 42.308 13.05 0.00 0.00 4.85
3433 4605 5.968676 TCCTACTAAACATAATGGCCAGT 57.031 39.130 13.05 12.48 0.00 4.00
3434 4606 7.440505 TTCCTACTAAACATAATGGCCAGTA 57.559 36.000 16.43 16.43 0.00 2.74
3435 4607 7.062749 TCCTACTAAACATAATGGCCAGTAG 57.937 40.000 19.01 15.76 35.74 2.57
3436 4608 6.614087 TCCTACTAAACATAATGGCCAGTAGT 59.386 38.462 19.01 13.55 34.70 2.73
3437 4609 6.706270 CCTACTAAACATAATGGCCAGTAGTG 59.294 42.308 19.01 17.30 34.70 2.74
3438 4610 6.062258 ACTAAACATAATGGCCAGTAGTGT 57.938 37.500 19.01 17.87 0.00 3.55
3439 4611 6.113411 ACTAAACATAATGGCCAGTAGTGTC 58.887 40.000 19.01 0.00 0.00 3.67
3440 4612 3.560636 ACATAATGGCCAGTAGTGTCC 57.439 47.619 19.01 0.00 0.00 4.02
3441 4613 2.843730 ACATAATGGCCAGTAGTGTCCA 59.156 45.455 19.01 2.15 0.00 4.02
3451 4623 3.291584 CAGTAGTGTCCATCTGCCTAGA 58.708 50.000 0.00 0.00 37.35 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 4.429505 TCATCCTAAGATAGATGGTGGGG 58.570 47.826 0.00 0.00 0.00 4.96
66 67 1.065418 CCCTACACCACCCATGACTTC 60.065 57.143 0.00 0.00 0.00 3.01
69 70 0.912487 TCCCCTACACCACCCATGAC 60.912 60.000 0.00 0.00 0.00 3.06
80 81 1.600107 GTTGTGGCGATCCCCTACA 59.400 57.895 0.00 0.00 0.00 2.74
107 108 2.706190 CCCACTCCCACCCTTAAGATAG 59.294 54.545 3.36 0.00 0.00 2.08
115 116 2.181773 TCTACCCCACTCCCACCCT 61.182 63.158 0.00 0.00 0.00 4.34
122 123 1.410882 GTGATCTGCTCTACCCCACTC 59.589 57.143 0.00 0.00 0.00 3.51
124 125 0.466124 GGTGATCTGCTCTACCCCAC 59.534 60.000 0.00 0.00 0.00 4.61
144 145 0.881118 CACCACCCATGAAAACCTCG 59.119 55.000 0.00 0.00 0.00 4.63
153 154 0.035152 TAAGCTCAGCACCACCCATG 60.035 55.000 0.00 0.00 0.00 3.66
272 274 3.324108 TAACAGCCGGTCCCCACC 61.324 66.667 1.90 0.00 39.69 4.61
273 275 2.267961 CTAACAGCCGGTCCCCAC 59.732 66.667 1.90 0.00 0.00 4.61
274 276 3.006728 CCTAACAGCCGGTCCCCA 61.007 66.667 1.90 0.00 0.00 4.96
275 277 3.793888 CCCTAACAGCCGGTCCCC 61.794 72.222 1.90 0.00 0.00 4.81
276 278 2.686106 TCCCTAACAGCCGGTCCC 60.686 66.667 1.90 0.00 0.00 4.46
277 279 2.732619 CCTCCCTAACAGCCGGTCC 61.733 68.421 1.90 0.00 0.00 4.46
278 280 2.732619 CCCTCCCTAACAGCCGGTC 61.733 68.421 1.90 0.00 0.00 4.79
279 281 2.547123 ATCCCTCCCTAACAGCCGGT 62.547 60.000 1.90 0.00 0.00 5.28
280 282 0.471211 TATCCCTCCCTAACAGCCGG 60.471 60.000 0.00 0.00 0.00 6.13
281 283 0.969894 CTATCCCTCCCTAACAGCCG 59.030 60.000 0.00 0.00 0.00 5.52
282 284 1.353091 CCTATCCCTCCCTAACAGCC 58.647 60.000 0.00 0.00 0.00 4.85
283 285 1.353091 CCCTATCCCTCCCTAACAGC 58.647 60.000 0.00 0.00 0.00 4.40
284 286 2.330216 CACCCTATCCCTCCCTAACAG 58.670 57.143 0.00 0.00 0.00 3.16
285 287 1.061657 CCACCCTATCCCTCCCTAACA 60.062 57.143 0.00 0.00 0.00 2.41
286 288 1.730851 CCACCCTATCCCTCCCTAAC 58.269 60.000 0.00 0.00 0.00 2.34
287 289 0.571236 CCCACCCTATCCCTCCCTAA 59.429 60.000 0.00 0.00 0.00 2.69
288 290 1.385153 CCCCACCCTATCCCTCCCTA 61.385 65.000 0.00 0.00 0.00 3.53
289 291 2.738094 CCCCACCCTATCCCTCCCT 61.738 68.421 0.00 0.00 0.00 4.20
290 292 2.121918 CCCCACCCTATCCCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
291 293 2.121918 CCCCCACCCTATCCCTCC 60.122 72.222 0.00 0.00 0.00 4.30
292 294 1.152008 CTCCCCCACCCTATCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
293 295 1.546740 AACTCCCCCACCCTATCCCT 61.547 60.000 0.00 0.00 0.00 4.20
294 296 1.005690 AACTCCCCCACCCTATCCC 59.994 63.158 0.00 0.00 0.00 3.85
295 297 1.408453 CGAACTCCCCCACCCTATCC 61.408 65.000 0.00 0.00 0.00 2.59
296 298 1.408453 CCGAACTCCCCCACCCTATC 61.408 65.000 0.00 0.00 0.00 2.08
297 299 1.384082 CCGAACTCCCCCACCCTAT 60.384 63.158 0.00 0.00 0.00 2.57
298 300 2.039951 CCGAACTCCCCCACCCTA 59.960 66.667 0.00 0.00 0.00 3.53
301 303 4.029809 CACCCGAACTCCCCCACC 62.030 72.222 0.00 0.00 0.00 4.61
302 304 4.029809 CCACCCGAACTCCCCCAC 62.030 72.222 0.00 0.00 0.00 4.61
303 305 4.257810 TCCACCCGAACTCCCCCA 62.258 66.667 0.00 0.00 0.00 4.96
304 306 3.400054 CTCCACCCGAACTCCCCC 61.400 72.222 0.00 0.00 0.00 5.40
305 307 3.400054 CCTCCACCCGAACTCCCC 61.400 72.222 0.00 0.00 0.00 4.81
306 308 2.606826 ACCTCCACCCGAACTCCC 60.607 66.667 0.00 0.00 0.00 4.30
307 309 2.663196 CACCTCCACCCGAACTCC 59.337 66.667 0.00 0.00 0.00 3.85
308 310 1.889530 CTCCACCTCCACCCGAACTC 61.890 65.000 0.00 0.00 0.00 3.01
309 311 1.913762 CTCCACCTCCACCCGAACT 60.914 63.158 0.00 0.00 0.00 3.01
310 312 2.663196 CTCCACCTCCACCCGAAC 59.337 66.667 0.00 0.00 0.00 3.95
311 313 2.606519 CCTCCACCTCCACCCGAA 60.607 66.667 0.00 0.00 0.00 4.30
312 314 3.168759 TTCCTCCACCTCCACCCGA 62.169 63.158 0.00 0.00 0.00 5.14
313 315 2.606519 TTCCTCCACCTCCACCCG 60.607 66.667 0.00 0.00 0.00 5.28
314 316 0.840722 TTCTTCCTCCACCTCCACCC 60.841 60.000 0.00 0.00 0.00 4.61
315 317 0.615850 CTTCTTCCTCCACCTCCACC 59.384 60.000 0.00 0.00 0.00 4.61
316 318 0.615850 CCTTCTTCCTCCACCTCCAC 59.384 60.000 0.00 0.00 0.00 4.02
317 319 0.491823 TCCTTCTTCCTCCACCTCCA 59.508 55.000 0.00 0.00 0.00 3.86
318 320 1.557371 CTTCCTTCTTCCTCCACCTCC 59.443 57.143 0.00 0.00 0.00 4.30
319 321 2.499693 CTCTTCCTTCTTCCTCCACCTC 59.500 54.545 0.00 0.00 0.00 3.85
320 322 2.112691 TCTCTTCCTTCTTCCTCCACCT 59.887 50.000 0.00 0.00 0.00 4.00
321 323 2.499693 CTCTCTTCCTTCTTCCTCCACC 59.500 54.545 0.00 0.00 0.00 4.61
322 324 2.499693 CCTCTCTTCCTTCTTCCTCCAC 59.500 54.545 0.00 0.00 0.00 4.02
323 325 2.383683 TCCTCTCTTCCTTCTTCCTCCA 59.616 50.000 0.00 0.00 0.00 3.86
324 326 3.108847 TCCTCTCTTCCTTCTTCCTCC 57.891 52.381 0.00 0.00 0.00 4.30
325 327 4.349365 TCTTCCTCTCTTCCTTCTTCCTC 58.651 47.826 0.00 0.00 0.00 3.71
326 328 4.412060 TCTTCCTCTCTTCCTTCTTCCT 57.588 45.455 0.00 0.00 0.00 3.36
327 329 4.284746 TGTTCTTCCTCTCTTCCTTCTTCC 59.715 45.833 0.00 0.00 0.00 3.46
328 330 5.476091 TGTTCTTCCTCTCTTCCTTCTTC 57.524 43.478 0.00 0.00 0.00 2.87
329 331 5.545723 TCATGTTCTTCCTCTCTTCCTTCTT 59.454 40.000 0.00 0.00 0.00 2.52
330 332 5.090139 TCATGTTCTTCCTCTCTTCCTTCT 58.910 41.667 0.00 0.00 0.00 2.85
331 333 5.413309 TCATGTTCTTCCTCTCTTCCTTC 57.587 43.478 0.00 0.00 0.00 3.46
332 334 5.072329 TGTTCATGTTCTTCCTCTCTTCCTT 59.928 40.000 0.00 0.00 0.00 3.36
333 335 4.594920 TGTTCATGTTCTTCCTCTCTTCCT 59.405 41.667 0.00 0.00 0.00 3.36
334 336 4.899502 TGTTCATGTTCTTCCTCTCTTCC 58.100 43.478 0.00 0.00 0.00 3.46
335 337 5.546526 ACTGTTCATGTTCTTCCTCTCTTC 58.453 41.667 0.00 0.00 0.00 2.87
336 338 5.559148 ACTGTTCATGTTCTTCCTCTCTT 57.441 39.130 0.00 0.00 0.00 2.85
337 339 5.337169 GCTACTGTTCATGTTCTTCCTCTCT 60.337 44.000 0.00 0.00 0.00 3.10
338 340 4.867608 GCTACTGTTCATGTTCTTCCTCTC 59.132 45.833 0.00 0.00 0.00 3.20
339 341 4.619394 CGCTACTGTTCATGTTCTTCCTCT 60.619 45.833 0.00 0.00 0.00 3.69
340 342 3.614616 CGCTACTGTTCATGTTCTTCCTC 59.385 47.826 0.00 0.00 0.00 3.71
341 343 3.589988 CGCTACTGTTCATGTTCTTCCT 58.410 45.455 0.00 0.00 0.00 3.36
342 344 2.094417 GCGCTACTGTTCATGTTCTTCC 59.906 50.000 0.00 0.00 0.00 3.46
343 345 2.222596 CGCGCTACTGTTCATGTTCTTC 60.223 50.000 5.56 0.00 0.00 2.87
344 346 1.726791 CGCGCTACTGTTCATGTTCTT 59.273 47.619 5.56 0.00 0.00 2.52
345 347 1.067846 TCGCGCTACTGTTCATGTTCT 60.068 47.619 5.56 0.00 0.00 3.01
346 348 1.346365 TCGCGCTACTGTTCATGTTC 58.654 50.000 5.56 0.00 0.00 3.18
347 349 1.927174 GATCGCGCTACTGTTCATGTT 59.073 47.619 5.56 0.00 0.00 2.71
348 350 1.135139 AGATCGCGCTACTGTTCATGT 59.865 47.619 5.56 0.00 0.00 3.21
349 351 1.845266 AGATCGCGCTACTGTTCATG 58.155 50.000 5.56 0.00 0.00 3.07
350 352 3.504134 AGATAGATCGCGCTACTGTTCAT 59.496 43.478 5.56 0.00 0.00 2.57
351 353 2.879026 AGATAGATCGCGCTACTGTTCA 59.121 45.455 5.56 0.00 0.00 3.18
352 354 3.546002 AGATAGATCGCGCTACTGTTC 57.454 47.619 5.56 4.33 0.00 3.18
353 355 3.551046 CCAAGATAGATCGCGCTACTGTT 60.551 47.826 5.56 0.00 0.00 3.16
354 356 2.030717 CCAAGATAGATCGCGCTACTGT 60.031 50.000 5.56 0.00 0.00 3.55
355 357 2.226674 TCCAAGATAGATCGCGCTACTG 59.773 50.000 5.56 0.00 0.00 2.74
356 358 2.226912 GTCCAAGATAGATCGCGCTACT 59.773 50.000 5.56 4.40 0.00 2.57
357 359 2.586900 GTCCAAGATAGATCGCGCTAC 58.413 52.381 5.56 0.00 0.00 3.58
358 360 1.540267 GGTCCAAGATAGATCGCGCTA 59.460 52.381 5.56 0.00 0.00 4.26
359 361 0.315568 GGTCCAAGATAGATCGCGCT 59.684 55.000 5.56 0.00 0.00 5.92
360 362 0.032130 TGGTCCAAGATAGATCGCGC 59.968 55.000 0.00 0.00 0.00 6.86
361 363 2.732412 ATGGTCCAAGATAGATCGCG 57.268 50.000 0.00 0.00 0.00 5.87
362 364 3.070018 CCAATGGTCCAAGATAGATCGC 58.930 50.000 0.00 0.00 0.00 4.58
363 365 4.607293 TCCAATGGTCCAAGATAGATCG 57.393 45.455 0.00 0.00 0.00 3.69
364 366 6.119240 TGATCCAATGGTCCAAGATAGATC 57.881 41.667 0.00 4.91 0.00 2.75
365 367 6.331042 TCTTGATCCAATGGTCCAAGATAGAT 59.669 38.462 23.83 0.00 37.33 1.98
366 368 5.667172 TCTTGATCCAATGGTCCAAGATAGA 59.333 40.000 23.83 10.99 37.33 1.98
367 369 5.933617 TCTTGATCCAATGGTCCAAGATAG 58.066 41.667 23.83 9.42 37.33 2.08
368 370 5.974156 TCTTGATCCAATGGTCCAAGATA 57.026 39.130 23.83 11.56 37.33 1.98
369 371 4.868172 TCTTGATCCAATGGTCCAAGAT 57.132 40.909 23.83 0.00 37.33 2.40
370 372 4.529897 CATCTTGATCCAATGGTCCAAGA 58.470 43.478 27.01 27.01 41.73 3.02
371 373 3.635373 CCATCTTGATCCAATGGTCCAAG 59.365 47.826 21.22 21.22 36.10 3.61
372 374 3.634504 CCATCTTGATCCAATGGTCCAA 58.365 45.455 0.00 4.20 36.10 3.53
373 375 2.687614 GCCATCTTGATCCAATGGTCCA 60.688 50.000 15.57 0.00 41.67 4.02
374 376 1.959282 GCCATCTTGATCCAATGGTCC 59.041 52.381 15.57 0.00 41.67 4.46
375 377 2.621998 CAGCCATCTTGATCCAATGGTC 59.378 50.000 15.57 10.15 41.67 4.02
376 378 2.662866 CAGCCATCTTGATCCAATGGT 58.337 47.619 15.57 4.65 41.67 3.55
377 379 1.340248 GCAGCCATCTTGATCCAATGG 59.660 52.381 11.78 11.78 42.38 3.16
378 380 2.307768 AGCAGCCATCTTGATCCAATG 58.692 47.619 0.00 0.00 0.00 2.82
379 381 2.750141 AGCAGCCATCTTGATCCAAT 57.250 45.000 0.00 0.00 0.00 3.16
380 382 3.650281 TTAGCAGCCATCTTGATCCAA 57.350 42.857 0.00 0.00 0.00 3.53
381 383 3.870538 ATTAGCAGCCATCTTGATCCA 57.129 42.857 0.00 0.00 0.00 3.41
382 384 6.639632 TTTTATTAGCAGCCATCTTGATCC 57.360 37.500 0.00 0.00 0.00 3.36
383 385 8.355169 TCAATTTTATTAGCAGCCATCTTGATC 58.645 33.333 0.00 0.00 0.00 2.92
384 386 8.139989 GTCAATTTTATTAGCAGCCATCTTGAT 58.860 33.333 0.00 0.00 0.00 2.57
385 387 7.340232 AGTCAATTTTATTAGCAGCCATCTTGA 59.660 33.333 0.00 0.00 0.00 3.02
386 388 7.434307 CAGTCAATTTTATTAGCAGCCATCTTG 59.566 37.037 0.00 0.00 0.00 3.02
387 389 7.340232 TCAGTCAATTTTATTAGCAGCCATCTT 59.660 33.333 0.00 0.00 0.00 2.40
388 390 6.830324 TCAGTCAATTTTATTAGCAGCCATCT 59.170 34.615 0.00 0.00 0.00 2.90
389 391 7.031226 TCAGTCAATTTTATTAGCAGCCATC 57.969 36.000 0.00 0.00 0.00 3.51
390 392 7.431249 CATCAGTCAATTTTATTAGCAGCCAT 58.569 34.615 0.00 0.00 0.00 4.40
391 393 6.183360 CCATCAGTCAATTTTATTAGCAGCCA 60.183 38.462 0.00 0.00 0.00 4.75
392 394 6.211515 CCATCAGTCAATTTTATTAGCAGCC 58.788 40.000 0.00 0.00 0.00 4.85
393 395 5.689068 GCCATCAGTCAATTTTATTAGCAGC 59.311 40.000 0.00 0.00 0.00 5.25
394 396 6.798482 TGCCATCAGTCAATTTTATTAGCAG 58.202 36.000 0.00 0.00 0.00 4.24
395 397 6.772360 TGCCATCAGTCAATTTTATTAGCA 57.228 33.333 0.00 0.00 0.00 3.49
396 398 8.477984 TTTTGCCATCAGTCAATTTTATTAGC 57.522 30.769 0.00 0.00 0.00 3.09
397 399 9.859427 TCTTTTGCCATCAGTCAATTTTATTAG 57.141 29.630 0.00 0.00 0.00 1.73
399 401 9.558396 TTTCTTTTGCCATCAGTCAATTTTATT 57.442 25.926 0.00 0.00 0.00 1.40
400 402 9.729281 ATTTCTTTTGCCATCAGTCAATTTTAT 57.271 25.926 0.00 0.00 0.00 1.40
401 403 9.558396 AATTTCTTTTGCCATCAGTCAATTTTA 57.442 25.926 0.00 0.00 0.00 1.52
402 404 8.454570 AATTTCTTTTGCCATCAGTCAATTTT 57.545 26.923 0.00 0.00 0.00 1.82
403 405 8.454570 AAATTTCTTTTGCCATCAGTCAATTT 57.545 26.923 0.00 0.00 0.00 1.82
404 406 7.716123 TGAAATTTCTTTTGCCATCAGTCAATT 59.284 29.630 18.64 0.00 0.00 2.32
405 407 7.218614 TGAAATTTCTTTTGCCATCAGTCAAT 58.781 30.769 18.64 0.00 0.00 2.57
406 408 6.580788 TGAAATTTCTTTTGCCATCAGTCAA 58.419 32.000 18.64 0.00 0.00 3.18
407 409 6.159299 TGAAATTTCTTTTGCCATCAGTCA 57.841 33.333 18.64 0.00 0.00 3.41
408 410 5.636543 CCTGAAATTTCTTTTGCCATCAGTC 59.363 40.000 18.64 0.00 0.00 3.51
409 411 5.070847 ACCTGAAATTTCTTTTGCCATCAGT 59.929 36.000 18.64 0.00 0.00 3.41
410 412 5.544650 ACCTGAAATTTCTTTTGCCATCAG 58.455 37.500 18.64 4.82 0.00 2.90
411 413 5.549742 ACCTGAAATTTCTTTTGCCATCA 57.450 34.783 18.64 0.00 0.00 3.07
412 414 6.454795 TGTACCTGAAATTTCTTTTGCCATC 58.545 36.000 18.64 2.64 0.00 3.51
413 415 6.418057 TGTACCTGAAATTTCTTTTGCCAT 57.582 33.333 18.64 0.00 0.00 4.40
414 416 5.860941 TGTACCTGAAATTTCTTTTGCCA 57.139 34.783 18.64 6.38 0.00 4.92
415 417 6.454795 TGATGTACCTGAAATTTCTTTTGCC 58.545 36.000 18.64 4.09 0.00 4.52
416 418 7.063780 CCATGATGTACCTGAAATTTCTTTTGC 59.936 37.037 18.64 7.08 0.00 3.68
417 419 8.306038 TCCATGATGTACCTGAAATTTCTTTTG 58.694 33.333 18.64 7.35 0.00 2.44
418 420 8.421249 TCCATGATGTACCTGAAATTTCTTTT 57.579 30.769 18.64 5.65 0.00 2.27
419 421 8.599624 ATCCATGATGTACCTGAAATTTCTTT 57.400 30.769 18.64 5.98 0.00 2.52
420 422 9.347240 CTATCCATGATGTACCTGAAATTTCTT 57.653 33.333 18.64 6.30 0.00 2.52
421 423 8.717717 TCTATCCATGATGTACCTGAAATTTCT 58.282 33.333 18.64 1.90 0.00 2.52
422 424 8.908786 TCTATCCATGATGTACCTGAAATTTC 57.091 34.615 11.41 11.41 0.00 2.17
423 425 7.941238 CCTCTATCCATGATGTACCTGAAATTT 59.059 37.037 0.00 0.00 0.00 1.82
424 426 7.456725 CCTCTATCCATGATGTACCTGAAATT 58.543 38.462 0.00 0.00 0.00 1.82
425 427 6.013032 CCCTCTATCCATGATGTACCTGAAAT 60.013 42.308 0.00 0.00 0.00 2.17
426 428 5.307976 CCCTCTATCCATGATGTACCTGAAA 59.692 44.000 0.00 0.00 0.00 2.69
427 429 4.840680 CCCTCTATCCATGATGTACCTGAA 59.159 45.833 0.00 0.00 0.00 3.02
428 430 4.140686 ACCCTCTATCCATGATGTACCTGA 60.141 45.833 0.00 0.00 0.00 3.86
429 431 4.163427 ACCCTCTATCCATGATGTACCTG 58.837 47.826 0.00 0.00 0.00 4.00
430 432 4.421131 GACCCTCTATCCATGATGTACCT 58.579 47.826 0.00 0.00 0.00 3.08
434 436 2.089982 TGGGACCCTCTATCCATGATGT 60.090 50.000 13.00 0.00 38.06 3.06
438 440 3.909995 TGTATTGGGACCCTCTATCCATG 59.090 47.826 13.00 0.00 38.06 3.66
448 450 3.881089 CGACCTATTTTGTATTGGGACCC 59.119 47.826 2.45 2.45 0.00 4.46
460 462 6.095440 CCCTGATTTTCATGACGACCTATTTT 59.905 38.462 0.00 0.00 0.00 1.82
497 1373 1.454847 GCCAACACACCCAGGACAA 60.455 57.895 0.00 0.00 0.00 3.18
526 1402 1.742761 CTCCAATCAACTCACGGCAT 58.257 50.000 0.00 0.00 0.00 4.40
527 1403 0.955428 GCTCCAATCAACTCACGGCA 60.955 55.000 0.00 0.00 0.00 5.69
528 1404 0.674895 AGCTCCAATCAACTCACGGC 60.675 55.000 0.00 0.00 0.00 5.68
529 1405 2.672961 TAGCTCCAATCAACTCACGG 57.327 50.000 0.00 0.00 0.00 4.94
530 1406 3.181530 CGTTTAGCTCCAATCAACTCACG 60.182 47.826 0.00 0.00 0.00 4.35
531 1407 3.125316 CCGTTTAGCTCCAATCAACTCAC 59.875 47.826 0.00 0.00 0.00 3.51
532 1408 3.007506 TCCGTTTAGCTCCAATCAACTCA 59.992 43.478 0.00 0.00 0.00 3.41
533 1409 3.596214 TCCGTTTAGCTCCAATCAACTC 58.404 45.455 0.00 0.00 0.00 3.01
534 1410 3.600388 CTCCGTTTAGCTCCAATCAACT 58.400 45.455 0.00 0.00 0.00 3.16
535 1411 2.096013 GCTCCGTTTAGCTCCAATCAAC 59.904 50.000 0.00 0.00 39.50 3.18
536 1412 2.356135 GCTCCGTTTAGCTCCAATCAA 58.644 47.619 0.00 0.00 39.50 2.57
537 1413 1.406887 GGCTCCGTTTAGCTCCAATCA 60.407 52.381 0.00 0.00 42.37 2.57
538 1414 1.300481 GGCTCCGTTTAGCTCCAATC 58.700 55.000 0.00 0.00 42.37 2.67
539 1415 0.107165 GGGCTCCGTTTAGCTCCAAT 60.107 55.000 0.00 0.00 42.37 3.16
540 1416 1.298667 GGGCTCCGTTTAGCTCCAA 59.701 57.895 0.00 0.00 42.37 3.53
541 1417 2.987125 GGGCTCCGTTTAGCTCCA 59.013 61.111 0.00 0.00 42.37 3.86
543 1419 2.189784 GGGGGCTCCGTTTAGCTC 59.810 66.667 0.00 0.00 42.62 4.09
544 1420 2.285442 AGGGGGCTCCGTTTAGCT 60.285 61.111 0.00 0.00 42.37 3.32
545 1421 2.124695 CAGGGGGCTCCGTTTAGC 60.125 66.667 0.00 0.00 41.52 3.09
546 1422 2.590092 CCAGGGGGCTCCGTTTAG 59.410 66.667 0.00 0.00 41.52 1.85
563 1439 4.742201 TCTCTGCCTTGGACGCGC 62.742 66.667 5.73 0.00 0.00 6.86
583 1459 1.004918 CGTTCCCTCCCACTGTGTC 60.005 63.158 7.08 0.00 0.00 3.67
643 1521 4.337177 TGGCCGCCCAATCAACGA 62.337 61.111 7.03 0.00 38.46 3.85
697 1575 2.110213 GCTGTGGTGTGTCGGGAA 59.890 61.111 0.00 0.00 0.00 3.97
962 1850 1.651240 GCTCACGGGCTCACGTACTA 61.651 60.000 0.00 0.00 46.75 1.82
988 1876 0.533491 TGCGGCATTTAGTCCGTACT 59.467 50.000 0.00 0.00 46.79 2.73
1025 1913 2.144078 TCCACACTGGCCGAGGAAA 61.144 57.895 0.00 0.00 37.47 3.13
1377 2298 0.802222 CCGTGACTAGCACCGACATG 60.802 60.000 10.44 0.00 44.85 3.21
1479 2400 2.488355 GCAGGCTCGTAGTACGCA 59.512 61.111 17.90 6.28 42.21 5.24
2196 3120 1.299773 GAGCTTCTCGAGGATGGCG 60.300 63.158 13.56 0.00 0.00 5.69
2456 3380 4.498520 CTCACGATGCCGCGGACT 62.499 66.667 33.48 15.61 39.95 3.85
2506 3430 1.212935 ACACTTGGTGGACTGAAGCTT 59.787 47.619 0.00 0.00 37.94 3.74
2508 3432 0.947244 CACACTTGGTGGACTGAAGC 59.053 55.000 2.75 0.00 44.04 3.86
2535 3459 2.254737 CTGCCAGCCTCCAAGGAGAG 62.255 65.000 17.57 8.67 44.53 3.20
2542 3466 1.708993 AAGACAACTGCCAGCCTCCA 61.709 55.000 0.00 0.00 0.00 3.86
2714 3639 5.618616 TCCCTTTTCCCCCAAATAGTTTA 57.381 39.130 0.00 0.00 0.00 2.01
2724 3649 2.696244 CCCCATCCCTTTTCCCCC 59.304 66.667 0.00 0.00 0.00 5.40
2725 3650 2.696244 CCCCCATCCCTTTTCCCC 59.304 66.667 0.00 0.00 0.00 4.81
2791 3716 2.797177 AGCCCAGGACTTCATCTTTC 57.203 50.000 0.00 0.00 0.00 2.62
2863 3788 5.474578 TGAGCAAGAACAAGATAGTGACT 57.525 39.130 0.00 0.00 0.00 3.41
2937 3862 2.951457 TGTGTTCTTGTCGTGACTCA 57.049 45.000 1.23 0.00 0.00 3.41
2939 3864 3.520290 TCTTGTGTTCTTGTCGTGACT 57.480 42.857 1.23 0.00 0.00 3.41
2940 3865 3.604772 GCATCTTGTGTTCTTGTCGTGAC 60.605 47.826 0.00 0.00 0.00 3.67
2941 3866 2.543848 GCATCTTGTGTTCTTGTCGTGA 59.456 45.455 0.00 0.00 0.00 4.35
2942 3867 2.545526 AGCATCTTGTGTTCTTGTCGTG 59.454 45.455 0.00 0.00 0.00 4.35
3147 4074 4.158394 GCCCACATAAATCAGAAGAAAGCA 59.842 41.667 0.00 0.00 0.00 3.91
3149 4076 5.902613 TGCCCACATAAATCAGAAGAAAG 57.097 39.130 0.00 0.00 0.00 2.62
3218 4145 4.988540 GTCCAAGGCTCAAACAAATTAACC 59.011 41.667 0.00 0.00 0.00 2.85
3250 4181 1.807142 GTGGTGCTACTGGAAAGAAGC 59.193 52.381 0.00 0.00 35.51 3.86
3267 4198 4.323417 TCAATGTACAAAGGCTAGTGTGG 58.677 43.478 12.66 0.43 0.00 4.17
3273 4204 7.592938 CAAGAAACATCAATGTACAAAGGCTA 58.407 34.615 0.00 0.00 40.80 3.93
3307 4428 2.835701 TTCAGTCATCACGCCGCCTC 62.836 60.000 0.00 0.00 0.00 4.70
3332 4504 4.154737 TGACAAACTAGAATGTGCATCAGC 59.845 41.667 9.37 0.00 42.57 4.26
3335 4507 5.091431 GCTTGACAAACTAGAATGTGCATC 58.909 41.667 9.37 0.00 0.00 3.91
3392 4564 8.240267 AGTAGGAATCCTTAGTTCATACTGAC 57.760 38.462 7.30 0.00 45.78 3.51
3405 4577 7.004691 GGCCATTATGTTTAGTAGGAATCCTT 58.995 38.462 7.30 0.00 34.61 3.36
3432 4604 3.181474 GGTTCTAGGCAGATGGACACTAC 60.181 52.174 0.00 0.00 0.00 2.73
3433 4605 3.031736 GGTTCTAGGCAGATGGACACTA 58.968 50.000 0.00 0.00 0.00 2.74
3434 4606 1.834263 GGTTCTAGGCAGATGGACACT 59.166 52.381 0.00 0.00 0.00 3.55
3435 4607 1.555075 TGGTTCTAGGCAGATGGACAC 59.445 52.381 0.00 0.00 0.00 3.67
3436 4608 1.951209 TGGTTCTAGGCAGATGGACA 58.049 50.000 0.00 0.00 0.00 4.02
3437 4609 4.573900 CATATGGTTCTAGGCAGATGGAC 58.426 47.826 0.00 0.00 0.00 4.02
3438 4610 3.008375 GCATATGGTTCTAGGCAGATGGA 59.992 47.826 4.56 0.00 0.00 3.41
3439 4611 3.008813 AGCATATGGTTCTAGGCAGATGG 59.991 47.826 0.40 0.00 31.03 3.51
3440 4612 4.283363 AGCATATGGTTCTAGGCAGATG 57.717 45.455 0.40 0.00 31.03 2.90
3441 4613 4.904241 GAAGCATATGGTTCTAGGCAGAT 58.096 43.478 31.07 4.48 45.93 2.90
3451 4623 1.064758 TCGCCCTTGAAGCATATGGTT 60.065 47.619 19.65 19.65 38.61 3.67


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

AutoCloner maintained by Alex Coulton.