Multiple sequence alignment - TraesCS4A01G466100

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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 TraesCS4A01G466100 chr4A 100.000 2810 0 0 1 2810 729151542 729154351 0.000000e+00 5190.0
1 TraesCS4A01G466100 chr4A 91.105 1765 141 11 426 2182 729653924 729655680 0.000000e+00 2375.0
2 TraesCS4A01G466100 chr4A 90.734 1662 129 11 426 2080 729798282 729799925 0.000000e+00 2193.0
3 TraesCS4A01G466100 chr4A 90.118 1275 91 7 1281 2533 729120520 729119259 0.000000e+00 1624.0
4 TraesCS4A01G466100 chr4A 88.781 1337 116 22 587 1913 729213130 729214442 0.000000e+00 1607.0
5 TraesCS4A01G466100 chr4A 88.227 1342 98 16 1496 2810 729921293 729922601 0.000000e+00 1548.0
6 TraesCS4A01G466100 chr4A 83.136 931 84 27 1906 2810 729214771 729215654 0.000000e+00 782.0
7 TraesCS4A01G466100 chr4A 86.857 700 71 10 683 1367 729857232 729857925 0.000000e+00 763.0
8 TraesCS4A01G466100 chr4A 89.833 600 36 7 643 1217 729920322 729920921 0.000000e+00 747.0
9 TraesCS4A01G466100 chr4A 87.200 625 56 12 2196 2810 729657065 729657675 0.000000e+00 689.0
10 TraesCS4A01G466100 chr4A 85.835 593 65 7 699 1286 730007204 730006626 1.850000e-171 612.0
11 TraesCS4A01G466100 chr4A 96.889 225 7 0 427 651 729904299 729904523 7.350000e-101 377.0
12 TraesCS4A01G466100 chr4A 88.968 281 27 1 22 302 729904012 729904288 7.450000e-91 344.0
13 TraesCS4A01G466100 chr4A 89.320 206 15 6 1 201 729798025 729798228 4.650000e-63 252.0
14 TraesCS4A01G466100 chr4A 98.507 134 2 0 298 431 668166018 668166151 1.300000e-58 237.0
15 TraesCS4A01G466100 chr4A 87.562 201 21 3 1 197 729653667 729653867 2.180000e-56 230.0
16 TraesCS4A01G466100 chr4A 86.441 59 5 3 246 302 729798215 729798272 8.400000e-06 62.1
17 TraesCS4A01G466100 chr7A 90.991 1776 137 16 427 2182 9683956 9682184 0.000000e+00 2372.0
18 TraesCS4A01G466100 chr7A 87.895 1900 153 25 702 2562 9363814 9365675 0.000000e+00 2163.0
19 TraesCS4A01G466100 chr7A 88.732 639 52 6 2179 2810 9682141 9681516 0.000000e+00 763.0
20 TraesCS4A01G466100 chr7A 91.930 285 21 2 1 283 9507892 9508176 5.640000e-107 398.0
21 TraesCS4A01G466100 chr7A 89.908 218 18 1 2597 2810 9365678 9365895 7.670000e-71 278.0
22 TraesCS4A01G466100 chr7A 90.909 176 16 0 427 602 9362213 9362388 1.300000e-58 237.0
23 TraesCS4A01G466100 chr7A 82.069 290 39 7 25 302 9361914 9362202 4.680000e-58 235.0
24 TraesCS4A01G466100 chr7A 98.496 133 2 0 298 430 343843843 343843711 4.680000e-58 235.0
25 TraesCS4A01G466100 chr7A 92.742 124 9 0 427 550 9508206 9508329 2.220000e-41 180.0
26 TraesCS4A01G466100 chr7D 89.482 1873 152 23 426 2291 10056448 10058282 0.000000e+00 2326.0
27 TraesCS4A01G466100 chr7D 90.244 205 15 4 1 201 10056191 10056394 2.150000e-66 263.0
28 TraesCS4A01G466100 chr7D 97.143 140 4 0 298 437 161488861 161488722 1.300000e-58 237.0
29 TraesCS4A01G466100 chr7D 86.441 59 5 3 246 302 10056381 10056438 8.400000e-06 62.1
30 TraesCS4A01G466100 chr2D 80.259 1003 167 17 808 1796 564438222 564439207 0.000000e+00 726.0
31 TraesCS4A01G466100 chr2D 77.556 1203 212 40 610 1796 564475907 564477067 0.000000e+00 673.0
32 TraesCS4A01G466100 chr2D 75.473 1321 249 50 515 1803 564418201 564419478 2.430000e-160 575.0
33 TraesCS4A01G466100 chr2D 94.079 152 5 4 300 448 234328748 234328898 7.830000e-56 228.0
34 TraesCS4A01G466100 chr2D 100.000 33 0 0 2298 2330 313575441 313575473 8.400000e-06 62.1
35 TraesCS4A01G466100 chr5B 97.842 139 3 0 300 438 640272868 640272730 1.010000e-59 241.0
36 TraesCS4A01G466100 chr5B 97.761 134 3 0 297 430 243746812 243746945 6.050000e-57 231.0
37 TraesCS4A01G466100 chr3D 98.507 134 2 0 301 434 283321251 283321118 1.300000e-58 237.0
38 TraesCS4A01G466100 chr6A 96.503 143 3 2 287 427 32749046 32749188 4.680000e-58 235.0
39 TraesCS4A01G466100 chr4B 98.485 132 1 1 299 430 363315799 363315929 6.050000e-57 231.0
40 TraesCS4A01G466100 chr5D 100.000 28 0 0 2303 2330 219502564 219502591 5.000000e-03 52.8
41 TraesCS4A01G466100 chr4D 100.000 28 0 0 2303 2330 306454540 306454567 5.000000e-03 52.8
42 TraesCS4A01G466100 chr3B 100.000 28 0 0 2303 2330 670396900 670396927 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G466100 chr4A 729151542 729154351 2809 False 5190.00 5190 100.000000 1 2810 1 chr4A.!!$F2 2809
1 TraesCS4A01G466100 chr4A 729119259 729120520 1261 True 1624.00 1624 90.118000 1281 2533 1 chr4A.!!$R1 1252
2 TraesCS4A01G466100 chr4A 729213130 729215654 2524 False 1194.50 1607 85.958500 587 2810 2 chr4A.!!$F4 2223
3 TraesCS4A01G466100 chr4A 729920322 729922601 2279 False 1147.50 1548 89.030000 643 2810 2 chr4A.!!$F8 2167
4 TraesCS4A01G466100 chr4A 729653667 729657675 4008 False 1098.00 2375 88.622333 1 2810 3 chr4A.!!$F5 2809
5 TraesCS4A01G466100 chr4A 729798025 729799925 1900 False 835.70 2193 88.831667 1 2080 3 chr4A.!!$F6 2079
6 TraesCS4A01G466100 chr4A 729857232 729857925 693 False 763.00 763 86.857000 683 1367 1 chr4A.!!$F3 684
7 TraesCS4A01G466100 chr4A 730006626 730007204 578 True 612.00 612 85.835000 699 1286 1 chr4A.!!$R2 587
8 TraesCS4A01G466100 chr4A 729904012 729904523 511 False 360.50 377 92.928500 22 651 2 chr4A.!!$F7 629
9 TraesCS4A01G466100 chr7A 9681516 9683956 2440 True 1567.50 2372 89.861500 427 2810 2 chr7A.!!$R2 2383
10 TraesCS4A01G466100 chr7A 9361914 9365895 3981 False 728.25 2163 87.695250 25 2810 4 chr7A.!!$F1 2785
11 TraesCS4A01G466100 chr7D 10056191 10058282 2091 False 883.70 2326 88.722333 1 2291 3 chr7D.!!$F1 2290
12 TraesCS4A01G466100 chr2D 564438222 564439207 985 False 726.00 726 80.259000 808 1796 1 chr2D.!!$F4 988
13 TraesCS4A01G466100 chr2D 564475907 564477067 1160 False 673.00 673 77.556000 610 1796 1 chr2D.!!$F5 1186
14 TraesCS4A01G466100 chr2D 564418201 564419478 1277 False 575.00 575 75.473000 515 1803 1 chr2D.!!$F3 1288

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
316 333 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.0 0.0 0.0 0.0 4.12 F
317 334 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 2814 0.042581 TGCATAGACCACTCTCCCCA 59.957 55.000 0.0 0.0 0.0 4.96 R
1846 3447 1.065102 ACGTCCGACAACTCCATATCG 59.935 52.381 0.0 0.0 0.0 2.92 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
38 43 1.896220 ACGCACCATCAAGTTGTCAT 58.104 45.000 2.11 0.00 0.00 3.06
42 47 3.568538 GCACCATCAAGTTGTCATTGAC 58.431 45.455 9.93 9.93 39.36 3.18
49 54 5.913137 TCAAGTTGTCATTGACCAGTTTT 57.087 34.783 14.05 0.00 31.86 2.43
82 87 8.815141 TCTTAGCGTTTTTGTATGTTACACTA 57.185 30.769 0.00 0.00 38.63 2.74
171 188 6.097412 GGAAAAAGGGAGATGATTGCATAGTT 59.903 38.462 0.00 0.00 34.11 2.24
290 307 5.314718 TGATGATTCCCATTGACTATGCT 57.685 39.130 0.00 0.00 35.17 3.79
302 319 6.017605 CCATTGACTATGCTTCATCCAAGTAC 60.018 42.308 0.00 0.00 34.13 2.73
303 320 5.939764 TGACTATGCTTCATCCAAGTACT 57.060 39.130 0.00 0.00 34.13 2.73
304 321 5.907207 TGACTATGCTTCATCCAAGTACTC 58.093 41.667 0.00 0.00 34.13 2.59
306 323 3.567478 ATGCTTCATCCAAGTACTCCC 57.433 47.619 0.00 0.00 34.13 4.30
308 325 2.501723 TGCTTCATCCAAGTACTCCCTC 59.498 50.000 0.00 0.00 34.13 4.30
310 327 1.776662 TCATCCAAGTACTCCCTCCG 58.223 55.000 0.00 0.00 0.00 4.63
311 328 1.006758 TCATCCAAGTACTCCCTCCGT 59.993 52.381 0.00 0.00 0.00 4.69
312 329 1.409427 CATCCAAGTACTCCCTCCGTC 59.591 57.143 0.00 0.00 0.00 4.79
313 330 0.324091 TCCAAGTACTCCCTCCGTCC 60.324 60.000 0.00 0.00 0.00 4.79
314 331 1.328430 CCAAGTACTCCCTCCGTCCC 61.328 65.000 0.00 0.00 0.00 4.46
315 332 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
316 333 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
317 334 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
318 335 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
319 336 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
320 337 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
321 338 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
322 339 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
323 340 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
324 341 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
325 342 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
326 343 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
327 344 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
328 345 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
329 346 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
330 347 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
331 348 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
332 349 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
333 350 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
334 351 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
335 352 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
336 353 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
337 354 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
338 355 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
346 363 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
347 364 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
348 365 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
349 366 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
350 367 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
351 368 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
368 385 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
369 386 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
370 387 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
371 388 9.740239 GGATGTATCTAATACTAAAACGTGACA 57.260 33.333 0.00 0.00 36.70 3.58
381 398 6.903883 ACTAAAACGTGACATGATACATCC 57.096 37.500 0.00 0.00 0.00 3.51
382 399 4.857871 AAAACGTGACATGATACATCCG 57.142 40.909 0.00 0.86 0.00 4.18
383 400 3.520290 AACGTGACATGATACATCCGT 57.480 42.857 0.00 1.46 0.00 4.69
384 401 4.642445 AACGTGACATGATACATCCGTA 57.358 40.909 0.00 0.00 0.00 4.02
385 402 4.848562 ACGTGACATGATACATCCGTAT 57.151 40.909 0.00 0.00 41.16 3.06
386 403 5.196341 ACGTGACATGATACATCCGTATT 57.804 39.130 0.00 0.00 38.48 1.89
387 404 5.597806 ACGTGACATGATACATCCGTATTT 58.402 37.500 0.00 0.00 38.48 1.40
388 405 6.741109 ACGTGACATGATACATCCGTATTTA 58.259 36.000 0.00 0.00 38.48 1.40
389 406 6.861572 ACGTGACATGATACATCCGTATTTAG 59.138 38.462 0.00 0.00 38.48 1.85
390 407 7.081976 CGTGACATGATACATCCGTATTTAGA 58.918 38.462 0.00 0.00 38.48 2.10
391 408 7.060748 CGTGACATGATACATCCGTATTTAGAC 59.939 40.741 0.00 0.00 38.48 2.59
392 409 7.865889 GTGACATGATACATCCGTATTTAGACA 59.134 37.037 0.00 0.00 38.48 3.41
393 410 8.417884 TGACATGATACATCCGTATTTAGACAA 58.582 33.333 0.00 0.00 38.48 3.18
394 411 9.256477 GACATGATACATCCGTATTTAGACAAA 57.744 33.333 0.00 0.00 38.48 2.83
395 412 9.778741 ACATGATACATCCGTATTTAGACAAAT 57.221 29.630 0.00 0.00 38.48 2.32
402 419 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
403 420 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
405 422 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
406 423 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
414 431 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
415 432 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
416 433 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
417 434 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
418 435 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
419 436 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
420 437 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
421 438 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
422 439 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
423 440 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
424 441 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
479 496 7.800155 TGTTTTCTTTGACTACATCATGTGA 57.200 32.000 0.00 0.00 37.11 3.58
671 690 4.094294 TGTTAATGTCATTGTTCCGCTAGC 59.906 41.667 4.06 4.06 0.00 3.42
722 2091 2.238144 TGCCTCTTTTCATCCCTCTCTG 59.762 50.000 0.00 0.00 0.00 3.35
723 2092 2.238395 GCCTCTTTTCATCCCTCTCTGT 59.762 50.000 0.00 0.00 0.00 3.41
724 2093 3.871485 CCTCTTTTCATCCCTCTCTGTG 58.129 50.000 0.00 0.00 0.00 3.66
732 2101 5.157940 TCATCCCTCTCTGTGAAAAGAAG 57.842 43.478 0.00 0.00 0.00 2.85
734 2103 3.318313 TCCCTCTCTGTGAAAAGAAGGT 58.682 45.455 0.00 0.00 0.00 3.50
742 2111 4.006319 CTGTGAAAAGAAGGTGGGAGATC 58.994 47.826 0.00 0.00 0.00 2.75
744 2113 3.753797 GTGAAAAGAAGGTGGGAGATCAC 59.246 47.826 0.00 0.00 36.95 3.06
745 2114 3.394274 TGAAAAGAAGGTGGGAGATCACA 59.606 43.478 0.00 0.00 39.27 3.58
746 2115 4.043310 TGAAAAGAAGGTGGGAGATCACAT 59.957 41.667 0.00 0.00 39.27 3.21
757 2131 8.378565 AGGTGGGAGATCACATAATAAACATAG 58.621 37.037 0.00 0.00 39.27 2.23
789 2163 2.247358 AGCATCGGTCCCAACATTTTT 58.753 42.857 0.00 0.00 0.00 1.94
860 2255 9.178758 CACAAATATTATCCTAGGCTTTATCCC 57.821 37.037 2.96 0.00 0.00 3.85
896 2292 7.101652 TGACTATGTCTCTTCCATGTACTTC 57.898 40.000 0.00 0.00 33.15 3.01
906 2302 2.232941 TCCATGTACTTCGTCAACTCCC 59.767 50.000 0.00 0.00 0.00 4.30
948 2344 3.997021 AGCTTCAAAGTACAAGGATCGTG 59.003 43.478 0.00 0.00 0.00 4.35
961 2363 5.163437 ACAAGGATCGTGTAAATACTCCTCC 60.163 44.000 0.00 2.02 32.02 4.30
971 2377 4.495690 AAATACTCCTCCTTCCTGAAGC 57.504 45.455 1.25 0.00 37.11 3.86
1032 2446 4.279169 CCCAATACCAATAGCATGTTGAGG 59.721 45.833 0.00 0.00 0.00 3.86
1193 2620 1.907807 GTGCCCTGCAAATCACCCA 60.908 57.895 0.00 0.00 41.47 4.51
1218 2812 2.913765 CGGAAACATGCGCCACCAA 61.914 57.895 4.18 0.00 0.00 3.67
1220 2814 0.037419 GGAAACATGCGCCACCAATT 60.037 50.000 4.18 0.00 0.00 2.32
1315 2909 4.005650 GACAGATTTCCTGCTCAACATCA 58.994 43.478 0.00 0.00 46.81 3.07
1320 2914 1.588239 TCCTGCTCAACATCATCCCT 58.412 50.000 0.00 0.00 0.00 4.20
1439 3033 0.532573 ACGACAGATGGCACGAAGAT 59.467 50.000 1.25 0.00 0.00 2.40
1456 3050 3.116096 AGATGGACCCAGTAGTTGCTA 57.884 47.619 0.00 0.00 0.00 3.49
1655 3249 8.617809 GTTTCAAGTATTTCTAGTCCAACACAA 58.382 33.333 0.00 0.00 0.00 3.33
1731 3331 6.043012 AGCTTCTGCAGGACAAGATATATCTT 59.957 38.462 20.20 20.20 43.92 2.40
1812 3412 7.743749 ACTTCACCATGATAGATGAATAAGCT 58.256 34.615 0.00 0.00 31.00 3.74
1824 3424 5.874810 AGATGAATAAGCTTGCGTTTCACTA 59.125 36.000 9.86 0.00 0.00 2.74
1832 3433 0.315886 TGCGTTTCACTAGCCTTCGA 59.684 50.000 0.00 0.00 0.00 3.71
1881 3482 0.389948 GACGTCGGGTTGCTCTTCAT 60.390 55.000 0.00 0.00 0.00 2.57
1923 3860 2.906389 ACAGTTTCTGCTCCATGACCTA 59.094 45.455 0.00 0.00 34.37 3.08
2005 3946 5.102313 CGAGTGTTCACTATGATGTGCTTA 58.898 41.667 5.40 0.00 37.81 3.09
2016 3957 8.546244 CACTATGATGTGCTTATGAAGTTGTAG 58.454 37.037 0.00 0.00 0.00 2.74
2061 4002 9.838975 TTATGGCTGAATAATTTTATACATGCG 57.161 29.630 0.00 0.00 0.00 4.73
2082 4023 5.298276 TGCGTCAGTTCTTTTTAATCACCTT 59.702 36.000 0.00 0.00 0.00 3.50
2122 4063 5.587844 ACCAATGCTCAGATGTTGTCTTATC 59.412 40.000 0.00 0.00 34.00 1.75
2292 5646 1.466950 TCAATTGCGACGAAACATCCC 59.533 47.619 0.00 0.00 0.00 3.85
2353 5716 4.566545 ATTTGTTGTGCTCGATGTTTGA 57.433 36.364 0.00 0.00 0.00 2.69
2357 5720 0.107643 TGTGCTCGATGTTTGACCCA 59.892 50.000 0.00 0.00 0.00 4.51
2362 5725 1.800586 CTCGATGTTTGACCCACTGTG 59.199 52.381 0.00 0.00 0.00 3.66
2412 5775 7.458409 TCTGGAAGAAATGAAGGAAGAAATG 57.542 36.000 0.00 0.00 42.31 2.32
2413 5776 7.233632 TCTGGAAGAAATGAAGGAAGAAATGA 58.766 34.615 0.00 0.00 42.31 2.57
2441 5805 7.308408 GGGTTTGAGAAATAGTAAGTTGGTGAC 60.308 40.741 0.00 0.00 0.00 3.67
2468 5832 0.108329 CGCTTACCGACCTGTCCAAT 60.108 55.000 0.00 0.00 40.02 3.16
2482 5846 4.012374 CTGTCCAATTCTATGTGGCTGTT 58.988 43.478 0.00 0.00 34.68 3.16
2635 6004 6.595716 AGAAATACCAGCTGCTAGTTTGTAAG 59.404 38.462 8.66 0.00 0.00 2.34
2714 6083 1.004745 CTATTGACACCCAACCTGCCT 59.995 52.381 0.00 0.00 37.63 4.75
2744 6114 2.258591 CCACCACACCGTCTCGAG 59.741 66.667 5.93 5.93 0.00 4.04
2748 6118 1.210413 CCACACCGTCTCGAGACAG 59.790 63.158 37.14 30.88 44.99 3.51
2756 6126 1.001706 CGTCTCGAGACAGTTTCACCA 60.002 52.381 37.14 2.13 44.99 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 18 2.185004 ACTTGATGGTGCGTTAGCTT 57.815 45.000 0.00 0.00 45.42 3.74
16 21 2.805671 TGACAACTTGATGGTGCGTTAG 59.194 45.455 0.00 0.00 36.69 2.34
19 24 1.896220 ATGACAACTTGATGGTGCGT 58.104 45.000 0.00 0.00 36.69 5.24
20 25 2.226200 TCAATGACAACTTGATGGTGCG 59.774 45.455 0.00 0.00 36.69 5.34
49 54 7.658575 ACATACAAAAACGCTAAGAGGTAGAAA 59.341 33.333 0.00 0.00 30.50 2.52
82 87 3.432252 CGAGGCTGTTGAACGAGTAAAAT 59.568 43.478 0.00 0.00 0.00 1.82
290 307 2.108168 CGGAGGGAGTACTTGGATGAA 58.892 52.381 0.00 0.00 0.00 2.57
302 319 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
303 320 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
304 321 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
306 323 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
308 325 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
310 327 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
311 328 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
312 329 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
320 337 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
321 338 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
322 339 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
323 340 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
324 341 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
325 342 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
342 359 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
343 360 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
344 361 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
345 362 9.740239 TGTCACGTTTTAGTATTAGATACATCC 57.260 33.333 0.00 0.00 38.21 3.51
355 372 9.042008 GGATGTATCATGTCACGTTTTAGTATT 57.958 33.333 0.00 0.00 0.00 1.89
356 373 7.381408 CGGATGTATCATGTCACGTTTTAGTAT 59.619 37.037 0.00 0.00 0.00 2.12
357 374 6.693978 CGGATGTATCATGTCACGTTTTAGTA 59.306 38.462 0.00 0.00 0.00 1.82
358 375 5.518847 CGGATGTATCATGTCACGTTTTAGT 59.481 40.000 0.00 0.00 0.00 2.24
359 376 5.518847 ACGGATGTATCATGTCACGTTTTAG 59.481 40.000 0.00 0.00 0.00 1.85
360 377 5.412640 ACGGATGTATCATGTCACGTTTTA 58.587 37.500 0.00 0.00 0.00 1.52
361 378 4.250464 ACGGATGTATCATGTCACGTTTT 58.750 39.130 0.00 0.00 0.00 2.43
362 379 3.857052 ACGGATGTATCATGTCACGTTT 58.143 40.909 0.00 0.00 0.00 3.60
363 380 3.520290 ACGGATGTATCATGTCACGTT 57.480 42.857 0.00 0.00 0.00 3.99
364 381 4.848562 ATACGGATGTATCATGTCACGT 57.151 40.909 0.00 0.00 36.56 4.49
365 382 7.060748 GTCTAAATACGGATGTATCATGTCACG 59.939 40.741 0.00 0.00 40.42 4.35
366 383 7.865889 TGTCTAAATACGGATGTATCATGTCAC 59.134 37.037 0.00 0.00 40.42 3.67
367 384 7.947282 TGTCTAAATACGGATGTATCATGTCA 58.053 34.615 0.00 0.00 40.42 3.58
368 385 8.812147 TTGTCTAAATACGGATGTATCATGTC 57.188 34.615 0.00 0.00 40.42 3.06
369 386 9.778741 ATTTGTCTAAATACGGATGTATCATGT 57.221 29.630 0.00 0.00 40.42 3.21
376 393 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
377 394 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
379 396 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
380 397 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
388 405 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
389 406 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
390 407 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
391 408 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
392 409 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
393 410 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
394 411 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
395 412 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
396 413 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
397 414 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
398 415 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
399 416 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
400 417 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
401 418 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
402 419 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
403 420 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
404 421 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
405 422 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
406 423 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
407 424 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
408 425 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
409 426 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
410 427 4.687262 ATATATACTCCCTCCGTCCCAA 57.313 45.455 0.00 0.00 0.00 4.12
411 428 4.687262 AATATATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
412 429 6.096564 CACTTAATATATACTCCCTCCGTCCC 59.903 46.154 0.00 0.00 0.00 4.46
413 430 6.888632 TCACTTAATATATACTCCCTCCGTCC 59.111 42.308 0.00 0.00 0.00 4.79
414 431 7.611079 ACTCACTTAATATATACTCCCTCCGTC 59.389 40.741 0.00 0.00 0.00 4.79
415 432 7.468496 ACTCACTTAATATATACTCCCTCCGT 58.532 38.462 0.00 0.00 0.00 4.69
416 433 7.201626 CGACTCACTTAATATATACTCCCTCCG 60.202 44.444 0.00 0.00 0.00 4.63
417 434 7.828223 TCGACTCACTTAATATATACTCCCTCC 59.172 40.741 0.00 0.00 0.00 4.30
418 435 8.789825 TCGACTCACTTAATATATACTCCCTC 57.210 38.462 0.00 0.00 0.00 4.30
419 436 8.384718 ACTCGACTCACTTAATATATACTCCCT 58.615 37.037 0.00 0.00 0.00 4.20
420 437 8.452534 CACTCGACTCACTTAATATATACTCCC 58.547 40.741 0.00 0.00 0.00 4.30
421 438 9.217278 TCACTCGACTCACTTAATATATACTCC 57.783 37.037 0.00 0.00 0.00 3.85
423 440 8.710551 CGTCACTCGACTCACTTAATATATACT 58.289 37.037 0.00 0.00 42.86 2.12
424 441 8.706936 TCGTCACTCGACTCACTTAATATATAC 58.293 37.037 0.00 0.00 44.01 1.47
449 466 7.362662 TGATGTAGTCAAAGAAAACAAGCATC 58.637 34.615 0.00 0.00 32.78 3.91
671 690 5.799213 AGAGGATCAACAAGGTCTGTTTAG 58.201 41.667 0.00 0.00 46.49 1.85
722 2091 3.753797 GTGATCTCCCACCTTCTTTTCAC 59.246 47.826 0.00 0.00 0.00 3.18
723 2092 3.394274 TGTGATCTCCCACCTTCTTTTCA 59.606 43.478 0.00 0.00 36.26 2.69
724 2093 4.021102 TGTGATCTCCCACCTTCTTTTC 57.979 45.455 0.00 0.00 36.26 2.29
729 2098 7.054124 TGTTTATTATGTGATCTCCCACCTTC 58.946 38.462 0.00 0.00 36.26 3.46
732 2101 8.157476 ACTATGTTTATTATGTGATCTCCCACC 58.843 37.037 0.00 0.00 36.26 4.61
734 2103 7.661437 GCACTATGTTTATTATGTGATCTCCCA 59.339 37.037 0.00 0.00 0.00 4.37
742 2111 7.280876 ACTCACCAGCACTATGTTTATTATGTG 59.719 37.037 0.00 0.00 0.00 3.21
744 2113 7.792374 ACTCACCAGCACTATGTTTATTATG 57.208 36.000 0.00 0.00 0.00 1.90
745 2114 7.657761 GCTACTCACCAGCACTATGTTTATTAT 59.342 37.037 0.00 0.00 38.93 1.28
746 2115 6.984474 GCTACTCACCAGCACTATGTTTATTA 59.016 38.462 0.00 0.00 38.93 0.98
789 2163 3.516300 TGTTAGAATAAGAAGCGGTGGGA 59.484 43.478 0.00 0.00 0.00 4.37
848 2240 2.298163 GGAATCGTCGGGATAAAGCCTA 59.702 50.000 0.00 0.00 34.08 3.93
860 2255 4.611943 AGACATAGTCAATGGAATCGTCG 58.388 43.478 0.00 0.00 40.16 5.12
906 2302 1.455959 CTCAGTACGGAGGAGGGGG 60.456 68.421 14.53 0.00 0.00 5.40
948 2344 5.129650 AGCTTCAGGAAGGAGGAGTATTTAC 59.870 44.000 10.77 0.00 38.80 2.01
971 2377 3.118261 TGGTTCCTATAGCTTCCTGCAAG 60.118 47.826 0.00 0.00 45.94 4.01
1032 2446 4.814771 ACTGCATAAGCTATACGGGAAAAC 59.185 41.667 0.00 0.00 42.74 2.43
1193 2620 0.519961 GCGCATGTTTCCGGTACTTT 59.480 50.000 0.30 0.00 0.00 2.66
1218 2812 1.771255 GCATAGACCACTCTCCCCAAT 59.229 52.381 0.00 0.00 0.00 3.16
1220 2814 0.042581 TGCATAGACCACTCTCCCCA 59.957 55.000 0.00 0.00 0.00 4.96
1315 2909 1.649271 GCCCCATTCTGACCAGGGAT 61.649 60.000 8.82 0.00 44.30 3.85
1320 2914 1.541118 TCCAGCCCCATTCTGACCA 60.541 57.895 0.00 0.00 33.54 4.02
1439 3033 1.754803 CGATAGCAACTACTGGGTCCA 59.245 52.381 0.00 0.00 0.00 4.02
1456 3050 2.557056 TCTTCCTCGTGTCAAACTCGAT 59.443 45.455 4.93 0.00 42.15 3.59
1731 3331 2.513753 CCAGTGGAACCTGCAAATACA 58.486 47.619 1.68 0.00 37.80 2.29
1812 3412 1.144969 CGAAGGCTAGTGAAACGCAA 58.855 50.000 0.00 0.00 45.86 4.85
1824 3424 1.661341 CTAATTGCTGCTCGAAGGCT 58.339 50.000 0.00 0.00 0.00 4.58
1832 3433 1.462283 CATATCGCGCTAATTGCTGCT 59.538 47.619 5.56 0.00 40.11 4.24
1846 3447 1.065102 ACGTCCGACAACTCCATATCG 59.935 52.381 0.00 0.00 0.00 2.92
1923 3860 4.624913 TCACTTCCCCATGAGAGAAGTAT 58.375 43.478 18.54 2.36 46.41 2.12
2005 3946 5.648092 GCAGGAATGTAACCTACAACTTCAT 59.352 40.000 0.00 0.00 42.76 2.57
2016 3957 6.099341 CCATAAAACAAGCAGGAATGTAACC 58.901 40.000 0.00 0.00 0.00 2.85
2061 4002 9.665264 CTGTTAAGGTGATTAAAAAGAACTGAC 57.335 33.333 0.00 0.00 35.16 3.51
2082 4023 4.658063 CATTGGTTTGGTAGGTCCTGTTA 58.342 43.478 0.00 0.00 37.07 2.41
2145 4086 3.211865 AGTTATAGCGGGCTAAAAAGGC 58.788 45.455 4.26 0.00 31.73 4.35
2194 4192 9.453572 TGTAGATGAACAAGCAATCTCTTAAAT 57.546 29.630 0.00 0.00 0.00 1.40
2292 5646 6.432802 AACAATTTTTAGTTGAATCGCACG 57.567 33.333 0.00 0.00 0.00 5.34
2373 5736 1.494721 TCCAGAATAATGGTGGAGCCC 59.505 52.381 0.00 0.00 41.43 5.19
2380 5743 7.413446 TCCTTCATTTCTTCCAGAATAATGGT 58.587 34.615 12.00 0.00 41.43 3.55
2402 5765 5.324832 TCTCAAACCCTTCATTTCTTCCT 57.675 39.130 0.00 0.00 0.00 3.36
2403 5766 6.405278 TTTCTCAAACCCTTCATTTCTTCC 57.595 37.500 0.00 0.00 0.00 3.46
2404 5767 8.797438 ACTATTTCTCAAACCCTTCATTTCTTC 58.203 33.333 0.00 0.00 0.00 2.87
2405 5768 8.712228 ACTATTTCTCAAACCCTTCATTTCTT 57.288 30.769 0.00 0.00 0.00 2.52
2406 5769 9.807921 TTACTATTTCTCAAACCCTTCATTTCT 57.192 29.630 0.00 0.00 0.00 2.52
2408 5771 9.588096 ACTTACTATTTCTCAAACCCTTCATTT 57.412 29.630 0.00 0.00 0.00 2.32
2409 5772 9.588096 AACTTACTATTTCTCAAACCCTTCATT 57.412 29.630 0.00 0.00 0.00 2.57
2410 5773 9.014297 CAACTTACTATTTCTCAAACCCTTCAT 57.986 33.333 0.00 0.00 0.00 2.57
2411 5774 7.447238 CCAACTTACTATTTCTCAAACCCTTCA 59.553 37.037 0.00 0.00 0.00 3.02
2412 5775 7.447545 ACCAACTTACTATTTCTCAAACCCTTC 59.552 37.037 0.00 0.00 0.00 3.46
2413 5776 7.230712 CACCAACTTACTATTTCTCAAACCCTT 59.769 37.037 0.00 0.00 0.00 3.95
2441 5805 0.788391 GGTCGGTAAGCGACAAACTG 59.212 55.000 1.16 0.00 38.04 3.16
2449 5813 0.108329 ATTGGACAGGTCGGTAAGCG 60.108 55.000 0.00 0.00 0.00 4.68
2468 5832 1.621317 TCCGACAACAGCCACATAGAA 59.379 47.619 0.00 0.00 0.00 2.10
2482 5846 2.839486 AGCTTCACTCATTTCCGACA 57.161 45.000 0.00 0.00 0.00 4.35
2577 5942 2.799126 TGTTCAAGAACAGTGGTGGT 57.201 45.000 11.34 0.00 45.42 4.16
2635 6004 3.382048 AGGTTCGGACAAGTCAGTAAC 57.618 47.619 0.00 5.23 0.00 2.50
2744 6114 0.586802 GAAGCGGTGGTGAAACTGTC 59.413 55.000 0.00 0.00 36.74 3.51
2748 6118 1.652563 GGTGAAGCGGTGGTGAAAC 59.347 57.895 0.00 0.00 0.00 2.78
2756 6126 2.115266 CCAAAGGGGTGAAGCGGT 59.885 61.111 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.