Multiple sequence alignment - TraesCS5D01G152700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G152700 chr5D 100.000 4526 0 0 1 4526 241664134 241668659 0.000000e+00 8359.0
1 TraesCS5D01G152700 chr5A 96.953 4004 84 21 543 4525 311280202 311284188 0.000000e+00 6684.0
2 TraesCS5D01G152700 chr5A 90.270 185 16 2 364 546 29678149 29678333 1.630000e-59 241.0
3 TraesCS5D01G152700 chr5B 96.878 3139 53 9 546 3668 262057834 262054725 0.000000e+00 5212.0
4 TraesCS5D01G152700 chr5B 95.708 466 16 1 4060 4525 262052787 262052326 0.000000e+00 747.0
5 TraesCS5D01G152700 chr5B 97.512 402 10 0 3660 4061 262053512 262053111 0.000000e+00 688.0
6 TraesCS5D01G152700 chr5B 82.586 379 47 10 1 364 262058200 262057826 2.630000e-82 316.0
7 TraesCS5D01G152700 chr5B 75.090 277 52 10 4 266 492262184 492261911 3.700000e-21 113.0
8 TraesCS5D01G152700 chr5B 96.970 33 0 1 249 280 545153870 545153902 2.000000e-03 54.7
9 TraesCS5D01G152700 chr1B 90.860 186 15 2 362 545 493652198 493652383 9.720000e-62 248.0
10 TraesCS5D01G152700 chr2B 89.340 197 16 5 367 559 771215139 771215334 4.520000e-60 243.0
11 TraesCS5D01G152700 chr2B 77.366 243 47 5 13 253 364727560 364727324 2.200000e-28 137.0
12 TraesCS5D01G152700 chr2D 91.061 179 12 3 368 545 86563542 86563367 5.850000e-59 239.0
13 TraesCS5D01G152700 chr2D 89.785 186 15 3 362 545 109695972 109696155 7.570000e-58 235.0
14 TraesCS5D01G152700 chr2D 77.647 255 46 8 1 251 296855141 296855388 1.310000e-30 145.0
15 TraesCS5D01G152700 chr2A 89.785 186 18 1 362 546 604992201 604992016 2.100000e-58 237.0
16 TraesCS5D01G152700 chr6A 90.164 183 15 2 367 548 109973946 109973766 7.570000e-58 235.0
17 TraesCS5D01G152700 chr6A 87.879 198 21 3 358 553 494463091 494463287 3.520000e-56 230.0
18 TraesCS5D01G152700 chr3D 89.362 188 16 4 361 545 506177317 506177131 2.720000e-57 233.0
19 TraesCS5D01G152700 chr3B 77.211 294 42 16 1 276 98023836 98024122 1.010000e-31 148.0
20 TraesCS5D01G152700 chrUn 76.800 250 38 13 3 237 103138645 103138889 6.150000e-24 122.0
21 TraesCS5D01G152700 chr3A 74.074 297 55 13 1 282 124217739 124218028 8.010000e-18 102.0
22 TraesCS5D01G152700 chr3A 73.288 292 53 15 1 276 91482344 91482062 2.900000e-12 84.2
23 TraesCS5D01G152700 chr3A 81.111 90 14 3 17 106 20130701 20130787 8.120000e-08 69.4
24 TraesCS5D01G152700 chr6D 84.536 97 8 5 184 273 367877524 367877428 6.240000e-14 89.8
25 TraesCS5D01G152700 chr4B 80.870 115 20 2 163 276 105152925 105152812 6.240000e-14 89.8
26 TraesCS5D01G152700 chr6B 80.435 92 16 2 195 285 642369673 642369763 8.120000e-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 TraesCS5D01G152700 chr5D 241664134 241668659 4525 False 8359.00 8359 100.000 1 4526 1 chr5D.!!$F1 4525
1 TraesCS5D01G152700 chr5A 311280202 311284188 3986 False 6684.00 6684 96.953 543 4525 1 chr5A.!!$F2 3982
2 TraesCS5D01G152700 chr5B 262052326 262058200 5874 True 1740.75 5212 93.171 1 4525 4 chr5B.!!$R2 4524

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
150 153 0.036732 CAACCAGGTCAAGCTGGCTA 59.963 55.000 24.41 0.00 44.17 3.93 F
1217 1258 0.034059 AACTGCAGCGCTCTAGTGTT 59.966 50.000 20.23 12.62 0.00 3.32 F
1277 1318 1.134220 GTTCACTCACACAAGTCCCCA 60.134 52.381 0.00 0.00 0.00 4.96 F
1623 1664 1.248785 GCGTGTACCAGGAGGAGTCA 61.249 60.000 0.00 0.00 38.69 3.41 F
2841 2882 1.594331 GAATTGATGTACCCGAGCCC 58.406 55.000 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1364 0.385390 CCACAGAACCTGCCAAACAC 59.615 55.000 0.00 0.0 34.37 3.32 R
2115 2156 1.261480 TCAAGACCTCTGTCCTGCTC 58.739 55.000 0.00 0.0 42.81 4.26 R
2268 2309 1.618837 TCTCGCAGAACTGTAGCCTTT 59.381 47.619 3.77 0.0 34.09 3.11 R
3312 3353 3.561725 GCCACTGTTTATATGTCTCTGGC 59.438 47.826 0.00 0.0 35.26 4.85 R
3893 5155 1.484240 CCACTGCTCCTTTCCTCTAGG 59.516 57.143 0.00 0.0 0.00 3.02 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
87 90 2.807045 GACTGCGACTCCAGTGCG 60.807 66.667 0.00 0.00 45.55 5.34
88 91 3.559657 GACTGCGACTCCAGTGCGT 62.560 63.158 0.00 0.00 45.55 5.24
106 109 3.262448 TTGGTCCTTAGGGGCACGC 62.262 63.158 0.00 0.00 39.39 5.34
107 110 3.712907 GGTCCTTAGGGGCACGCA 61.713 66.667 0.00 0.00 46.88 5.24
116 119 1.675641 GGGGCACGCACAGAAAGAT 60.676 57.895 0.00 0.00 42.57 2.40
120 123 2.545742 GGGCACGCACAGAAAGATTTTT 60.546 45.455 0.00 0.00 0.00 1.94
135 138 5.382618 AGATTTTTCAGCTGTCATCAACC 57.617 39.130 14.67 0.00 0.00 3.77
150 153 0.036732 CAACCAGGTCAAGCTGGCTA 59.963 55.000 24.41 0.00 44.17 3.93
151 154 0.995024 AACCAGGTCAAGCTGGCTAT 59.005 50.000 24.41 11.04 44.17 2.97
158 161 1.762957 GTCAAGCTGGCTATGGTAGGA 59.237 52.381 0.00 0.00 0.00 2.94
159 162 1.762957 TCAAGCTGGCTATGGTAGGAC 59.237 52.381 0.00 0.00 0.00 3.85
160 163 1.486310 CAAGCTGGCTATGGTAGGACA 59.514 52.381 0.00 0.00 0.00 4.02
161 164 2.105477 CAAGCTGGCTATGGTAGGACAT 59.895 50.000 0.00 0.00 34.90 3.06
167 173 1.269621 GCTATGGTAGGACATCGCGTT 60.270 52.381 5.77 0.00 31.30 4.84
184 190 3.241364 CGCGTTGATGACTCTTTCTAACG 60.241 47.826 0.00 0.00 38.55 3.18
185 191 3.060895 GCGTTGATGACTCTTTCTAACGG 59.939 47.826 0.00 0.00 37.29 4.44
196 202 3.057033 TCTTTCTAACGGCAGTAGTGGTC 60.057 47.826 0.00 0.00 0.00 4.02
198 204 0.524862 CTAACGGCAGTAGTGGTCGT 59.475 55.000 0.00 0.00 35.48 4.34
209 215 1.068585 GTGGTCGTTCGGTGGTCTT 59.931 57.895 0.00 0.00 0.00 3.01
210 216 0.314935 GTGGTCGTTCGGTGGTCTTA 59.685 55.000 0.00 0.00 0.00 2.10
214 220 3.069289 GGTCGTTCGGTGGTCTTAAAAT 58.931 45.455 0.00 0.00 0.00 1.82
220 226 4.730949 TCGGTGGTCTTAAAATCTCGAT 57.269 40.909 0.00 0.00 0.00 3.59
222 228 4.081862 TCGGTGGTCTTAAAATCTCGATGT 60.082 41.667 0.00 0.00 0.00 3.06
223 229 5.125900 TCGGTGGTCTTAAAATCTCGATGTA 59.874 40.000 0.00 0.00 0.00 2.29
229 235 9.667107 TGGTCTTAAAATCTCGATGTAATTTCT 57.333 29.630 0.00 0.00 0.00 2.52
257 263 6.267496 TGTCTCAGATTGTCTGTATTTCGA 57.733 37.500 6.83 0.00 44.58 3.71
317 331 3.593096 TCAGATCACAGTGCAGATGAAC 58.407 45.455 5.87 0.59 0.00 3.18
329 343 0.172803 AGATGAACGACGGTGTAGGC 59.827 55.000 0.00 0.00 0.00 3.93
349 363 3.952508 TGCCCCATCAGCACACGT 61.953 61.111 0.00 0.00 34.69 4.49
364 378 4.884257 CACACGTGCCAAAAATGTATTC 57.116 40.909 17.22 0.00 0.00 1.75
365 379 3.360463 CACACGTGCCAAAAATGTATTCG 59.640 43.478 17.22 0.00 0.00 3.34
366 380 2.914214 CACGTGCCAAAAATGTATTCGG 59.086 45.455 0.82 0.00 0.00 4.30
367 381 2.554893 ACGTGCCAAAAATGTATTCGGT 59.445 40.909 0.00 0.00 0.00 4.69
368 382 3.004944 ACGTGCCAAAAATGTATTCGGTT 59.995 39.130 0.00 0.00 0.00 4.44
369 383 3.984633 CGTGCCAAAAATGTATTCGGTTT 59.015 39.130 0.00 0.00 0.00 3.27
370 384 4.143431 CGTGCCAAAAATGTATTCGGTTTG 60.143 41.667 0.00 0.00 0.00 2.93
372 386 4.919677 CCAAAAATGTATTCGGTTTGGC 57.080 40.909 0.88 0.00 41.14 4.52
373 387 4.565022 CCAAAAATGTATTCGGTTTGGCT 58.435 39.130 0.88 0.00 41.14 4.75
374 388 5.715070 CCAAAAATGTATTCGGTTTGGCTA 58.285 37.500 0.88 0.00 41.14 3.93
375 389 5.804979 CCAAAAATGTATTCGGTTTGGCTAG 59.195 40.000 0.88 0.00 41.14 3.42
376 390 6.386654 CAAAAATGTATTCGGTTTGGCTAGT 58.613 36.000 0.00 0.00 0.00 2.57
377 391 6.584185 AAAATGTATTCGGTTTGGCTAGTT 57.416 33.333 0.00 0.00 0.00 2.24
378 392 5.813080 AATGTATTCGGTTTGGCTAGTTC 57.187 39.130 0.00 0.00 0.00 3.01
379 393 4.274602 TGTATTCGGTTTGGCTAGTTCA 57.725 40.909 0.00 0.00 0.00 3.18
380 394 3.998341 TGTATTCGGTTTGGCTAGTTCAC 59.002 43.478 0.00 0.00 0.00 3.18
381 395 2.623878 TTCGGTTTGGCTAGTTCACA 57.376 45.000 0.00 0.00 0.00 3.58
382 396 2.851263 TCGGTTTGGCTAGTTCACAT 57.149 45.000 0.00 0.00 0.00 3.21
383 397 2.695359 TCGGTTTGGCTAGTTCACATC 58.305 47.619 0.00 0.00 0.00 3.06
384 398 2.301870 TCGGTTTGGCTAGTTCACATCT 59.698 45.455 0.00 0.00 0.00 2.90
385 399 3.512329 TCGGTTTGGCTAGTTCACATCTA 59.488 43.478 0.00 0.00 0.00 1.98
386 400 3.865745 CGGTTTGGCTAGTTCACATCTAG 59.134 47.826 0.00 0.00 38.22 2.43
387 401 4.381612 CGGTTTGGCTAGTTCACATCTAGA 60.382 45.833 0.00 0.00 37.62 2.43
388 402 5.675538 GGTTTGGCTAGTTCACATCTAGAT 58.324 41.667 0.00 0.00 37.62 1.98
389 403 6.461092 CGGTTTGGCTAGTTCACATCTAGATA 60.461 42.308 4.54 0.00 37.62 1.98
390 404 7.445945 GGTTTGGCTAGTTCACATCTAGATAT 58.554 38.462 4.54 0.00 37.62 1.63
391 405 7.934120 GGTTTGGCTAGTTCACATCTAGATATT 59.066 37.037 4.54 0.00 37.62 1.28
392 406 9.331282 GTTTGGCTAGTTCACATCTAGATATTT 57.669 33.333 4.54 0.00 37.62 1.40
393 407 9.905713 TTTGGCTAGTTCACATCTAGATATTTT 57.094 29.630 4.54 0.00 37.62 1.82
394 408 9.905713 TTGGCTAGTTCACATCTAGATATTTTT 57.094 29.630 4.54 0.00 37.62 1.94
417 431 8.561738 TTTTAAGGATGTCACATCTAAACTCC 57.438 34.615 17.46 0.18 0.00 3.85
418 432 4.762289 AGGATGTCACATCTAAACTCCC 57.238 45.455 17.46 0.00 0.00 4.30
419 433 4.104086 AGGATGTCACATCTAAACTCCCA 58.896 43.478 17.46 0.00 0.00 4.37
420 434 4.536090 AGGATGTCACATCTAAACTCCCAA 59.464 41.667 17.46 0.00 0.00 4.12
421 435 5.014123 AGGATGTCACATCTAAACTCCCAAA 59.986 40.000 17.46 0.00 0.00 3.28
422 436 5.710099 GGATGTCACATCTAAACTCCCAAAA 59.290 40.000 17.46 0.00 0.00 2.44
423 437 6.378280 GGATGTCACATCTAAACTCCCAAAAT 59.622 38.462 17.46 0.00 0.00 1.82
424 438 7.556275 GGATGTCACATCTAAACTCCCAAAATA 59.444 37.037 17.46 0.00 0.00 1.40
425 439 9.125026 GATGTCACATCTAAACTCCCAAAATAT 57.875 33.333 10.81 0.00 0.00 1.28
439 453 9.860650 ACTCCCAAAATATATAATGCAGTAACA 57.139 29.630 0.00 0.00 0.00 2.41
489 503 8.926715 AAAAATAGACCTCAAACAAAGTGAAC 57.073 30.769 0.00 0.00 0.00 3.18
490 504 7.639113 AAATAGACCTCAAACAAAGTGAACA 57.361 32.000 0.00 0.00 0.00 3.18
491 505 7.823745 AATAGACCTCAAACAAAGTGAACAT 57.176 32.000 0.00 0.00 0.00 2.71
492 506 7.823745 ATAGACCTCAAACAAAGTGAACATT 57.176 32.000 0.00 0.00 0.00 2.71
493 507 8.918202 ATAGACCTCAAACAAAGTGAACATTA 57.082 30.769 0.00 0.00 0.00 1.90
494 508 7.264373 AGACCTCAAACAAAGTGAACATTAG 57.736 36.000 0.00 0.00 0.00 1.73
495 509 5.831997 ACCTCAAACAAAGTGAACATTAGC 58.168 37.500 0.00 0.00 0.00 3.09
496 510 5.594317 ACCTCAAACAAAGTGAACATTAGCT 59.406 36.000 0.00 0.00 0.00 3.32
497 511 6.096846 ACCTCAAACAAAGTGAACATTAGCTT 59.903 34.615 0.00 0.00 0.00 3.74
498 512 7.284489 ACCTCAAACAAAGTGAACATTAGCTTA 59.716 33.333 0.00 0.00 0.00 3.09
499 513 8.134895 CCTCAAACAAAGTGAACATTAGCTTAA 58.865 33.333 0.00 0.00 0.00 1.85
500 514 9.515020 CTCAAACAAAGTGAACATTAGCTTAAA 57.485 29.630 0.00 0.00 0.00 1.52
504 518 8.801715 ACAAAGTGAACATTAGCTTAAATGTG 57.198 30.769 14.17 4.52 46.72 3.21
505 519 8.629158 ACAAAGTGAACATTAGCTTAAATGTGA 58.371 29.630 14.17 3.67 46.72 3.58
506 520 8.905702 CAAAGTGAACATTAGCTTAAATGTGAC 58.094 33.333 14.17 13.31 46.72 3.67
507 521 6.831769 AGTGAACATTAGCTTAAATGTGACG 58.168 36.000 14.17 0.00 46.72 4.35
508 522 6.426937 AGTGAACATTAGCTTAAATGTGACGT 59.573 34.615 14.17 0.00 46.72 4.34
509 523 7.601130 AGTGAACATTAGCTTAAATGTGACGTA 59.399 33.333 14.17 0.00 46.72 3.57
510 524 8.225107 GTGAACATTAGCTTAAATGTGACGTAA 58.775 33.333 14.17 0.00 46.72 3.18
511 525 8.225107 TGAACATTAGCTTAAATGTGACGTAAC 58.775 33.333 14.17 0.00 46.72 2.50
512 526 7.900782 ACATTAGCTTAAATGTGACGTAACT 57.099 32.000 12.96 0.00 45.90 2.24
513 527 8.991243 ACATTAGCTTAAATGTGACGTAACTA 57.009 30.769 12.96 0.00 45.90 2.24
514 528 9.595823 ACATTAGCTTAAATGTGACGTAACTAT 57.404 29.630 12.96 0.00 45.90 2.12
515 529 9.849607 CATTAGCTTAAATGTGACGTAACTATG 57.150 33.333 4.30 0.00 33.11 2.23
516 530 8.991243 TTAGCTTAAATGTGACGTAACTATGT 57.009 30.769 4.30 0.00 0.00 2.29
517 531 7.521509 AGCTTAAATGTGACGTAACTATGTC 57.478 36.000 4.30 2.66 41.45 3.06
518 532 7.094631 AGCTTAAATGTGACGTAACTATGTCA 58.905 34.615 4.30 7.54 46.66 3.58
527 541 7.803279 TGACGTAACTATGTCACATCTAGAT 57.197 36.000 7.54 0.00 44.70 1.98
528 542 7.639945 TGACGTAACTATGTCACATCTAGATG 58.360 38.462 27.63 27.63 44.70 2.90
544 558 3.983044 AGATGTGTCCTAAACAGACCC 57.017 47.619 0.00 0.00 38.97 4.46
556 570 8.027189 GTCCTAAACAGACCCAAATGTATTTTC 58.973 37.037 0.00 0.00 0.00 2.29
565 579 5.245977 ACCCAAATGTATTTTCCTCACAAGG 59.754 40.000 0.00 0.00 44.89 3.61
567 581 5.279406 CCAAATGTATTTTCCTCACAAGGCA 60.279 40.000 0.00 0.00 43.02 4.75
653 668 0.798776 ATTCGCGGTGCTGAAAAGAG 59.201 50.000 6.13 0.00 0.00 2.85
780 797 6.430308 GGGACGAGATTTCTTTTCCTTTTACT 59.570 38.462 0.00 0.00 31.42 2.24
797 814 1.258445 ACTAGCTCCGGGTCCAACTG 61.258 60.000 0.00 0.00 0.00 3.16
1165 1202 0.524392 CAGCGTCAGTCCGTGATCTC 60.524 60.000 0.00 0.00 37.56 2.75
1217 1258 0.034059 AACTGCAGCGCTCTAGTGTT 59.966 50.000 20.23 12.62 0.00 3.32
1244 1285 5.353678 CCTTCCTGTTATTTTCTGCTCAGAG 59.646 44.000 0.00 0.00 38.88 3.35
1245 1286 4.836825 TCCTGTTATTTTCTGCTCAGAGG 58.163 43.478 0.00 0.00 38.88 3.69
1263 1304 7.417342 GCTCAGAGGTCAAATAGATAGTTCACT 60.417 40.741 0.00 0.00 0.00 3.41
1265 1306 7.615757 TCAGAGGTCAAATAGATAGTTCACTCA 59.384 37.037 0.00 0.00 0.00 3.41
1266 1307 7.704472 CAGAGGTCAAATAGATAGTTCACTCAC 59.296 40.741 0.00 0.00 0.00 3.51
1267 1308 7.397476 AGAGGTCAAATAGATAGTTCACTCACA 59.603 37.037 0.00 0.00 0.00 3.58
1268 1309 7.324178 AGGTCAAATAGATAGTTCACTCACAC 58.676 38.462 0.00 0.00 0.00 3.82
1269 1310 7.039011 AGGTCAAATAGATAGTTCACTCACACA 60.039 37.037 0.00 0.00 0.00 3.72
1270 1311 7.602644 GGTCAAATAGATAGTTCACTCACACAA 59.397 37.037 0.00 0.00 0.00 3.33
1271 1312 8.651588 GTCAAATAGATAGTTCACTCACACAAG 58.348 37.037 0.00 0.00 0.00 3.16
1272 1313 8.367911 TCAAATAGATAGTTCACTCACACAAGT 58.632 33.333 0.00 0.00 0.00 3.16
1273 1314 8.651588 CAAATAGATAGTTCACTCACACAAGTC 58.348 37.037 0.00 0.00 0.00 3.01
1274 1315 5.140747 AGATAGTTCACTCACACAAGTCC 57.859 43.478 0.00 0.00 0.00 3.85
1275 1316 2.622064 AGTTCACTCACACAAGTCCC 57.378 50.000 0.00 0.00 0.00 4.46
1276 1317 1.141053 AGTTCACTCACACAAGTCCCC 59.859 52.381 0.00 0.00 0.00 4.81
1277 1318 1.134220 GTTCACTCACACAAGTCCCCA 60.134 52.381 0.00 0.00 0.00 4.96
1284 1325 1.333619 CACACAAGTCCCCAAAACTCG 59.666 52.381 0.00 0.00 0.00 4.18
1303 1344 4.460731 ACTCGATCACTTGACATCTTCTCA 59.539 41.667 0.00 0.00 0.00 3.27
1318 1359 7.222872 ACATCTTCTCACTGACTGAAGAATTT 58.777 34.615 12.41 0.00 45.87 1.82
1323 1364 5.936372 TCTCACTGACTGAAGAATTTCATGG 59.064 40.000 0.00 0.00 42.19 3.66
1623 1664 1.248785 GCGTGTACCAGGAGGAGTCA 61.249 60.000 0.00 0.00 38.69 3.41
1629 1670 1.611851 CCAGGAGGAGTCAGCCACT 60.612 63.158 3.67 0.00 38.45 4.00
1894 1935 4.603535 AGCCACTGGTTGCCCCAC 62.604 66.667 0.00 0.00 38.72 4.61
2184 2225 4.720649 TCTTGACTTGATAGAAGGACGG 57.279 45.455 0.00 0.00 0.00 4.79
2268 2309 7.875316 TGATTTGTTTCGTCAAACTGAAAAA 57.125 28.000 1.97 0.00 42.29 1.94
2736 2777 5.886960 AGAAGGTGCACATAATTGACTTC 57.113 39.130 20.43 17.68 34.77 3.01
2841 2882 1.594331 GAATTGATGTACCCGAGCCC 58.406 55.000 0.00 0.00 0.00 5.19
2889 2930 3.240134 GACGGGACAGAGGCTTGCA 62.240 63.158 0.00 0.00 0.00 4.08
3312 3353 0.732571 GCTCAGACAGAGTCGAGAGG 59.267 60.000 17.74 6.40 46.47 3.69
3373 3414 1.734465 CTGGATTTGTTCAGTCTCCGC 59.266 52.381 0.00 0.00 0.00 5.54
3609 3650 0.323725 CCAAGGTATGCACTGGGCTT 60.324 55.000 2.50 0.00 45.15 4.35
3813 5075 1.202580 GGACTCTTGTCACACTGCACT 60.203 52.381 0.00 0.00 44.61 4.40
3893 5155 5.302313 AGCCACTAGCCAGTACTAAGATAAC 59.698 44.000 0.00 0.00 45.47 1.89
4125 5712 6.093495 TGCTAATAAGAATGAGTTTGGGTTCG 59.907 38.462 0.00 0.00 0.00 3.95
4233 5820 6.040278 TGGTTCTTGTTGTTTGATGCTCATTA 59.960 34.615 0.00 0.00 0.00 1.90
4318 5905 4.153117 GCAAGACATGAGGTTACTTGTGAG 59.847 45.833 0.00 0.00 39.69 3.51
4433 6021 3.609373 CACAGTTTCATGCCGCTAATTTG 59.391 43.478 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.006888 ACCAAATCTCGCCACATTACG 58.993 47.619 0.00 0.00 0.00 3.18
11 12 1.909700 ACACCAAATCTCGCCACATT 58.090 45.000 0.00 0.00 0.00 2.71
56 59 1.398451 CGCAGTCGTCATTGTTGAACC 60.398 52.381 0.00 0.00 32.48 3.62
64 67 0.109086 CTGGAGTCGCAGTCGTCATT 60.109 55.000 1.61 0.00 36.96 2.57
66 69 1.897137 ACTGGAGTCGCAGTCGTCA 60.897 57.895 8.07 0.00 36.96 4.35
84 87 3.074281 CCCCTAAGGACCAACGCA 58.926 61.111 0.00 0.00 38.24 5.24
87 90 1.376812 CGTGCCCCTAAGGACCAAC 60.377 63.158 0.00 0.00 38.24 3.77
88 91 3.074281 CGTGCCCCTAAGGACCAA 58.926 61.111 0.00 0.00 38.24 3.67
106 109 5.824429 TGACAGCTGAAAAATCTTTCTGTG 58.176 37.500 23.35 1.62 41.41 3.66
107 110 6.263842 TGATGACAGCTGAAAAATCTTTCTGT 59.736 34.615 23.35 0.00 41.41 3.41
116 119 3.318839 CCTGGTTGATGACAGCTGAAAAA 59.681 43.478 23.35 4.39 33.43 1.94
120 123 1.002430 GACCTGGTTGATGACAGCTGA 59.998 52.381 23.35 0.00 33.43 4.26
135 138 0.254178 ACCATAGCCAGCTTGACCTG 59.746 55.000 0.00 0.00 0.00 4.00
150 153 0.821517 TCAACGCGATGTCCTACCAT 59.178 50.000 15.93 0.00 0.00 3.55
151 154 0.821517 ATCAACGCGATGTCCTACCA 59.178 50.000 15.93 0.00 31.20 3.25
160 163 3.238108 AGAAAGAGTCATCAACGCGAT 57.762 42.857 15.93 0.00 32.18 4.58
161 164 2.724977 AGAAAGAGTCATCAACGCGA 57.275 45.000 15.93 0.00 32.18 5.87
167 173 3.258372 ACTGCCGTTAGAAAGAGTCATCA 59.742 43.478 0.00 0.00 0.00 3.07
176 182 2.352030 CGACCACTACTGCCGTTAGAAA 60.352 50.000 0.00 0.00 0.00 2.52
184 190 1.445582 CCGAACGACCACTACTGCC 60.446 63.158 0.00 0.00 0.00 4.85
185 191 1.007336 CACCGAACGACCACTACTGC 61.007 60.000 0.00 0.00 0.00 4.40
196 202 3.060363 CGAGATTTTAAGACCACCGAACG 59.940 47.826 0.00 0.00 0.00 3.95
198 204 4.524316 TCGAGATTTTAAGACCACCGAA 57.476 40.909 0.00 0.00 0.00 4.30
295 301 3.967332 TCATCTGCACTGTGATCTGAA 57.033 42.857 12.86 0.00 0.00 3.02
296 302 3.593096 GTTCATCTGCACTGTGATCTGA 58.407 45.455 12.86 4.83 0.00 3.27
299 313 2.346847 GTCGTTCATCTGCACTGTGATC 59.653 50.000 12.86 0.00 0.00 2.92
305 319 0.667487 CACCGTCGTTCATCTGCACT 60.667 55.000 0.00 0.00 0.00 4.40
307 321 0.599060 TACACCGTCGTTCATCTGCA 59.401 50.000 0.00 0.00 0.00 4.41
349 363 4.310769 CCAAACCGAATACATTTTTGGCA 58.689 39.130 0.00 0.00 39.72 4.92
351 365 4.565022 AGCCAAACCGAATACATTTTTGG 58.435 39.130 6.98 6.98 46.05 3.28
352 366 6.386654 ACTAGCCAAACCGAATACATTTTTG 58.613 36.000 0.00 0.00 0.00 2.44
353 367 6.584185 ACTAGCCAAACCGAATACATTTTT 57.416 33.333 0.00 0.00 0.00 1.94
354 368 6.207810 TGAACTAGCCAAACCGAATACATTTT 59.792 34.615 0.00 0.00 0.00 1.82
355 369 5.708230 TGAACTAGCCAAACCGAATACATTT 59.292 36.000 0.00 0.00 0.00 2.32
356 370 5.123344 GTGAACTAGCCAAACCGAATACATT 59.877 40.000 0.00 0.00 0.00 2.71
357 371 4.634443 GTGAACTAGCCAAACCGAATACAT 59.366 41.667 0.00 0.00 0.00 2.29
358 372 3.998341 GTGAACTAGCCAAACCGAATACA 59.002 43.478 0.00 0.00 0.00 2.29
359 373 3.998341 TGTGAACTAGCCAAACCGAATAC 59.002 43.478 0.00 0.00 0.00 1.89
360 374 4.274602 TGTGAACTAGCCAAACCGAATA 57.725 40.909 0.00 0.00 0.00 1.75
361 375 3.134574 TGTGAACTAGCCAAACCGAAT 57.865 42.857 0.00 0.00 0.00 3.34
362 376 2.623878 TGTGAACTAGCCAAACCGAA 57.376 45.000 0.00 0.00 0.00 4.30
363 377 2.301870 AGATGTGAACTAGCCAAACCGA 59.698 45.455 0.00 0.00 0.00 4.69
364 378 2.699954 AGATGTGAACTAGCCAAACCG 58.300 47.619 0.00 0.00 0.00 4.44
365 379 5.086104 TCTAGATGTGAACTAGCCAAACC 57.914 43.478 0.00 0.00 37.73 3.27
366 380 8.894768 AATATCTAGATGTGAACTAGCCAAAC 57.105 34.615 15.79 0.00 37.73 2.93
367 381 9.905713 AAAATATCTAGATGTGAACTAGCCAAA 57.094 29.630 15.79 0.00 37.73 3.28
368 382 9.905713 AAAAATATCTAGATGTGAACTAGCCAA 57.094 29.630 15.79 0.00 37.73 4.52
391 405 9.010029 GGAGTTTAGATGTGACATCCTTAAAAA 57.990 33.333 21.05 11.39 0.00 1.94
392 406 7.610305 GGGAGTTTAGATGTGACATCCTTAAAA 59.390 37.037 21.05 13.52 0.00 1.52
393 407 7.110155 GGGAGTTTAGATGTGACATCCTTAAA 58.890 38.462 21.05 16.39 0.00 1.52
394 408 6.214615 TGGGAGTTTAGATGTGACATCCTTAA 59.785 38.462 21.05 11.73 0.00 1.85
395 409 5.724370 TGGGAGTTTAGATGTGACATCCTTA 59.276 40.000 21.05 6.22 0.00 2.69
396 410 4.536090 TGGGAGTTTAGATGTGACATCCTT 59.464 41.667 21.05 7.22 0.00 3.36
397 411 4.104086 TGGGAGTTTAGATGTGACATCCT 58.896 43.478 21.05 11.37 0.00 3.24
398 412 4.487714 TGGGAGTTTAGATGTGACATCC 57.512 45.455 21.05 6.28 0.00 3.51
399 413 6.817765 TTTTGGGAGTTTAGATGTGACATC 57.182 37.500 17.46 17.46 0.00 3.06
413 427 9.860650 TGTTACTGCATTATATATTTTGGGAGT 57.139 29.630 0.00 0.00 0.00 3.85
464 478 8.527810 TGTTCACTTTGTTTGAGGTCTATTTTT 58.472 29.630 0.00 0.00 0.00 1.94
465 479 8.062065 TGTTCACTTTGTTTGAGGTCTATTTT 57.938 30.769 0.00 0.00 0.00 1.82
466 480 7.639113 TGTTCACTTTGTTTGAGGTCTATTT 57.361 32.000 0.00 0.00 0.00 1.40
467 481 7.823745 ATGTTCACTTTGTTTGAGGTCTATT 57.176 32.000 0.00 0.00 0.00 1.73
468 482 7.823745 AATGTTCACTTTGTTTGAGGTCTAT 57.176 32.000 0.00 0.00 0.00 1.98
469 483 7.041372 GCTAATGTTCACTTTGTTTGAGGTCTA 60.041 37.037 0.00 0.00 0.00 2.59
470 484 6.238759 GCTAATGTTCACTTTGTTTGAGGTCT 60.239 38.462 0.00 0.00 0.00 3.85
471 485 5.915196 GCTAATGTTCACTTTGTTTGAGGTC 59.085 40.000 0.00 0.00 0.00 3.85
472 486 5.594317 AGCTAATGTTCACTTTGTTTGAGGT 59.406 36.000 0.00 0.00 0.00 3.85
473 487 6.076981 AGCTAATGTTCACTTTGTTTGAGG 57.923 37.500 0.00 0.00 0.00 3.86
474 488 9.515020 TTTAAGCTAATGTTCACTTTGTTTGAG 57.485 29.630 0.00 0.00 0.00 3.02
477 491 9.816354 ACATTTAAGCTAATGTTCACTTTGTTT 57.184 25.926 8.73 0.00 44.18 2.83
478 492 9.248291 CACATTTAAGCTAATGTTCACTTTGTT 57.752 29.630 11.39 0.00 44.18 2.83
479 493 8.629158 TCACATTTAAGCTAATGTTCACTTTGT 58.371 29.630 11.39 0.00 44.18 2.83
480 494 8.905702 GTCACATTTAAGCTAATGTTCACTTTG 58.094 33.333 11.39 1.12 44.18 2.77
481 495 7.803189 CGTCACATTTAAGCTAATGTTCACTTT 59.197 33.333 11.39 0.00 44.18 2.66
482 496 7.041372 ACGTCACATTTAAGCTAATGTTCACTT 60.041 33.333 11.39 4.09 44.18 3.16
483 497 6.426937 ACGTCACATTTAAGCTAATGTTCACT 59.573 34.615 11.39 1.87 44.18 3.41
484 498 6.599437 ACGTCACATTTAAGCTAATGTTCAC 58.401 36.000 11.39 10.23 44.18 3.18
485 499 6.795098 ACGTCACATTTAAGCTAATGTTCA 57.205 33.333 11.39 0.64 44.18 3.18
486 500 8.440833 AGTTACGTCACATTTAAGCTAATGTTC 58.559 33.333 11.39 7.75 44.18 3.18
487 501 8.319143 AGTTACGTCACATTTAAGCTAATGTT 57.681 30.769 11.39 1.86 44.18 2.71
488 502 7.900782 AGTTACGTCACATTTAAGCTAATGT 57.099 32.000 8.73 8.73 46.73 2.71
489 503 9.849607 CATAGTTACGTCACATTTAAGCTAATG 57.150 33.333 7.53 7.53 40.53 1.90
490 504 9.595823 ACATAGTTACGTCACATTTAAGCTAAT 57.404 29.630 2.23 0.00 0.00 1.73
491 505 8.991243 ACATAGTTACGTCACATTTAAGCTAA 57.009 30.769 2.23 0.00 0.00 3.09
492 506 8.245491 TGACATAGTTACGTCACATTTAAGCTA 58.755 33.333 2.23 0.00 37.23 3.32
493 507 7.094631 TGACATAGTTACGTCACATTTAAGCT 58.905 34.615 2.23 0.00 37.23 3.74
494 508 7.285783 TGACATAGTTACGTCACATTTAAGC 57.714 36.000 2.23 0.00 37.23 3.09
503 517 7.639945 CATCTAGATGTGACATAGTTACGTCA 58.360 38.462 22.42 0.00 39.49 4.35
519 533 6.276847 GGTCTGTTTAGGACACATCTAGATG 58.723 44.000 27.63 27.63 44.15 2.90
520 534 5.364157 GGGTCTGTTTAGGACACATCTAGAT 59.636 44.000 0.00 0.00 37.11 1.98
521 535 4.710375 GGGTCTGTTTAGGACACATCTAGA 59.290 45.833 0.00 0.00 37.11 2.43
522 536 4.466370 TGGGTCTGTTTAGGACACATCTAG 59.534 45.833 0.00 0.00 41.46 2.43
523 537 4.422057 TGGGTCTGTTTAGGACACATCTA 58.578 43.478 0.00 0.00 41.46 1.98
524 538 3.248024 TGGGTCTGTTTAGGACACATCT 58.752 45.455 0.00 0.00 41.46 2.90
525 539 3.695830 TGGGTCTGTTTAGGACACATC 57.304 47.619 0.00 0.00 41.46 3.06
526 540 4.447138 TTTGGGTCTGTTTAGGACACAT 57.553 40.909 0.00 0.00 44.98 3.21
527 541 3.935818 TTTGGGTCTGTTTAGGACACA 57.064 42.857 0.00 0.00 44.14 3.72
528 542 4.142038 ACATTTGGGTCTGTTTAGGACAC 58.858 43.478 0.00 0.00 37.60 3.67
529 543 4.447138 ACATTTGGGTCTGTTTAGGACA 57.553 40.909 0.00 0.00 35.61 4.02
530 544 7.462571 AAATACATTTGGGTCTGTTTAGGAC 57.537 36.000 0.00 0.00 0.00 3.85
531 545 7.177744 GGAAAATACATTTGGGTCTGTTTAGGA 59.822 37.037 0.00 0.00 0.00 2.94
532 546 7.178451 AGGAAAATACATTTGGGTCTGTTTAGG 59.822 37.037 0.00 0.00 0.00 2.69
533 547 8.122472 AGGAAAATACATTTGGGTCTGTTTAG 57.878 34.615 0.00 0.00 0.00 1.85
534 548 7.726291 TGAGGAAAATACATTTGGGTCTGTTTA 59.274 33.333 0.00 0.00 0.00 2.01
535 549 6.553100 TGAGGAAAATACATTTGGGTCTGTTT 59.447 34.615 0.00 0.00 0.00 2.83
536 550 6.015434 GTGAGGAAAATACATTTGGGTCTGTT 60.015 38.462 0.00 0.00 0.00 3.16
537 551 5.476945 GTGAGGAAAATACATTTGGGTCTGT 59.523 40.000 0.00 0.00 0.00 3.41
538 552 5.476599 TGTGAGGAAAATACATTTGGGTCTG 59.523 40.000 0.00 0.00 0.00 3.51
539 553 5.640147 TGTGAGGAAAATACATTTGGGTCT 58.360 37.500 0.00 0.00 0.00 3.85
540 554 5.975693 TGTGAGGAAAATACATTTGGGTC 57.024 39.130 0.00 0.00 0.00 4.46
541 555 5.245977 CCTTGTGAGGAAAATACATTTGGGT 59.754 40.000 0.00 0.00 46.74 4.51
544 558 5.782047 TGCCTTGTGAGGAAAATACATTTG 58.218 37.500 0.00 0.00 46.74 2.32
556 570 1.002868 CACCCTCTGCCTTGTGAGG 60.003 63.158 0.00 0.00 46.91 3.86
565 579 1.202818 AGTTGGAGAAACACCCTCTGC 60.203 52.381 0.00 0.00 41.61 4.26
567 581 2.695585 AGAGTTGGAGAAACACCCTCT 58.304 47.619 0.00 0.00 41.61 3.69
653 668 0.890683 CCTGCATGTGAGGGTTTTCC 59.109 55.000 5.26 0.00 39.75 3.13
780 797 2.656069 GCAGTTGGACCCGGAGCTA 61.656 63.158 0.73 0.00 0.00 3.32
899 918 0.033601 GGGGCAGACAGAGAGAGAGA 60.034 60.000 0.00 0.00 0.00 3.10
1119 1156 1.086634 GCTCACCTGAAGGCATCGAC 61.087 60.000 0.00 0.00 39.32 4.20
1165 1202 2.124983 CTGGTGGCGATGACAGGG 60.125 66.667 0.00 0.00 0.00 4.45
1217 1258 6.068010 TGAGCAGAAAATAACAGGAAGGAAA 58.932 36.000 0.00 0.00 0.00 3.13
1244 1285 7.097192 TGTGTGAGTGAACTATCTATTTGACC 58.903 38.462 0.00 0.00 0.00 4.02
1245 1286 8.534333 TTGTGTGAGTGAACTATCTATTTGAC 57.466 34.615 0.00 0.00 0.00 3.18
1263 1304 2.650322 GAGTTTTGGGGACTTGTGTGA 58.350 47.619 0.00 0.00 0.00 3.58
1265 1306 1.210967 TCGAGTTTTGGGGACTTGTGT 59.789 47.619 0.00 0.00 31.70 3.72
1266 1307 1.961793 TCGAGTTTTGGGGACTTGTG 58.038 50.000 0.00 0.00 31.70 3.33
1267 1308 2.105821 TGATCGAGTTTTGGGGACTTGT 59.894 45.455 0.00 0.00 31.70 3.16
1268 1309 2.484264 GTGATCGAGTTTTGGGGACTTG 59.516 50.000 0.00 0.00 0.00 3.16
1269 1310 2.372172 AGTGATCGAGTTTTGGGGACTT 59.628 45.455 0.00 0.00 0.00 3.01
1270 1311 1.978580 AGTGATCGAGTTTTGGGGACT 59.021 47.619 0.00 0.00 0.00 3.85
1271 1312 2.474410 AGTGATCGAGTTTTGGGGAC 57.526 50.000 0.00 0.00 0.00 4.46
1272 1313 2.370519 TCAAGTGATCGAGTTTTGGGGA 59.629 45.455 0.00 0.00 0.00 4.81
1273 1314 2.484264 GTCAAGTGATCGAGTTTTGGGG 59.516 50.000 0.00 0.00 0.00 4.96
1274 1315 3.138304 TGTCAAGTGATCGAGTTTTGGG 58.862 45.455 0.00 0.00 0.00 4.12
1275 1316 4.692625 AGATGTCAAGTGATCGAGTTTTGG 59.307 41.667 0.00 0.00 0.00 3.28
1276 1317 5.852738 AGATGTCAAGTGATCGAGTTTTG 57.147 39.130 0.00 0.00 0.00 2.44
1277 1318 6.226787 AGAAGATGTCAAGTGATCGAGTTTT 58.773 36.000 0.00 0.00 0.00 2.43
1284 1325 5.576384 GTCAGTGAGAAGATGTCAAGTGATC 59.424 44.000 0.00 0.00 31.13 2.92
1303 1344 5.380043 ACACCATGAAATTCTTCAGTCAGT 58.620 37.500 0.00 0.00 44.68 3.41
1318 1359 1.133513 AGAACCTGCCAAACACCATGA 60.134 47.619 0.00 0.00 0.00 3.07
1323 1364 0.385390 CCACAGAACCTGCCAAACAC 59.615 55.000 0.00 0.00 34.37 3.32
1894 1935 1.955778 TGCATCAGAAACACCACTTGG 59.044 47.619 0.00 0.00 42.17 3.61
2115 2156 1.261480 TCAAGACCTCTGTCCTGCTC 58.739 55.000 0.00 0.00 42.81 4.26
2184 2225 8.524870 AACAGAATGCAGATTGTTTAATGTTC 57.475 30.769 6.66 0.00 42.53 3.18
2268 2309 1.618837 TCTCGCAGAACTGTAGCCTTT 59.381 47.619 3.77 0.00 34.09 3.11
2376 2417 5.949354 CCTAAGGTCCACCACATCATTTTTA 59.051 40.000 0.00 0.00 38.89 1.52
2889 2930 4.042187 ACCTCAAACTTCTTGGCATACTCT 59.958 41.667 0.00 0.00 0.00 3.24
3312 3353 3.561725 GCCACTGTTTATATGTCTCTGGC 59.438 47.826 0.00 0.00 35.26 4.85
3373 3414 7.029563 GCTTTTATCACAATGTCCTGGTTTAG 58.970 38.462 0.00 0.00 0.00 1.85
3813 5075 3.168035 ACAAGCACCCACATTAATCCA 57.832 42.857 0.00 0.00 0.00 3.41
3893 5155 1.484240 CCACTGCTCCTTTCCTCTAGG 59.516 57.143 0.00 0.00 0.00 3.02
4035 5297 5.815581 TGATACTGGGCACTTGATTAACTT 58.184 37.500 0.00 0.00 0.00 2.66
4125 5712 2.967201 TCCCCATTGAATTGATGATGCC 59.033 45.455 1.00 0.00 0.00 4.40
4233 5820 9.376075 CAGTTAGTTGTCTGATCAGATTACAAT 57.624 33.333 27.51 17.38 39.97 2.71
4384 5971 1.508632 AAGTGTGTGAAACGGGATCG 58.491 50.000 0.00 0.00 42.39 3.69


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

AutoCloner maintained by Alex Coulton.