Multiple sequence alignment - TraesCS6D01G221600

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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 TraesCS6D01G221600 chr6D 100.000 3635 0 0 1 3635 312557021 312560655 0.000000e+00 6713
1 TraesCS6D01G221600 chr6A 91.617 3197 156 55 512 3635 449180459 449183616 0.000000e+00 4316
2 TraesCS6D01G221600 chr6A 93.985 266 11 3 1 266 449180205 449180465 7.310000e-107 398
3 TraesCS6D01G221600 chr6A 90.421 261 18 2 262 515 471880993 471880733 1.620000e-88 337
4 TraesCS6D01G221600 chr6B 93.399 2621 89 26 674 3267 514479698 514477135 0.000000e+00 3805
5 TraesCS6D01G221600 chr6B 89.460 389 18 10 3263 3635 514476900 514476519 1.530000e-128 470
6 TraesCS6D01G221600 chr6B 98.990 99 1 0 1 99 514480092 514479994 1.040000e-40 178
7 TraesCS6D01G221600 chr6B 88.889 108 9 3 126 233 514479993 514479889 2.950000e-26 130
8 TraesCS6D01G221600 chr2A 78.626 655 81 36 1734 2352 635511719 635512350 2.650000e-101 379
9 TraesCS6D01G221600 chr2A 90.234 256 22 3 262 515 28141667 28141921 7.520000e-87 331
10 TraesCS6D01G221600 chr2D 78.374 652 81 36 1734 2349 491193870 491194497 5.730000e-98 368
11 TraesCS6D01G221600 chr2B 77.626 657 87 38 1734 2352 575836135 575836769 9.660000e-91 344
12 TraesCS6D01G221600 chr4D 90.299 268 16 8 259 517 48708921 48708655 3.480000e-90 342
13 TraesCS6D01G221600 chr7A 90.530 264 16 4 260 515 535468574 535468312 1.250000e-89 340
14 TraesCS6D01G221600 chr7A 89.925 268 16 9 259 517 711612112 711611847 5.820000e-88 335
15 TraesCS6D01G221600 chr4A 89.773 264 18 4 262 517 46310194 46310456 2.710000e-86 329
16 TraesCS6D01G221600 chr3D 89.773 264 18 7 262 517 416217590 416217328 2.710000e-86 329
17 TraesCS6D01G221600 chr3D 88.806 268 22 6 259 518 553423846 553424113 4.530000e-84 322
18 TraesCS6D01G221600 chr7D 89.394 264 19 7 262 517 426172195 426171933 1.260000e-84 324
19 TraesCS6D01G221600 chr3B 79.426 209 37 6 2088 2293 496615093 496615298 3.780000e-30 143


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 TraesCS6D01G221600 chr6D 312557021 312560655 3634 False 6713.00 6713 100.0000 1 3635 1 chr6D.!!$F1 3634
1 TraesCS6D01G221600 chr6A 449180205 449183616 3411 False 2357.00 4316 92.8010 1 3635 2 chr6A.!!$F1 3634
2 TraesCS6D01G221600 chr6B 514476519 514480092 3573 True 1145.75 3805 92.6845 1 3635 4 chr6B.!!$R1 3634
3 TraesCS6D01G221600 chr2A 635511719 635512350 631 False 379.00 379 78.6260 1734 2352 1 chr2A.!!$F2 618
4 TraesCS6D01G221600 chr2D 491193870 491194497 627 False 368.00 368 78.3740 1734 2349 1 chr2D.!!$F1 615
5 TraesCS6D01G221600 chr2B 575836135 575836769 634 False 344.00 344 77.6260 1734 2352 1 chr2B.!!$F1 618

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
250 251 0.603569 AGGCGACCTGTGTCTGTTAG 59.396 55.0 0.00 0.00 39.47 2.34 F
1224 1253 0.174389 GAGAGGATGTCTGCGCTGAA 59.826 55.0 19.14 9.72 34.71 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 1964 0.477597 TGAAGGTGGGGGAGTCCATT 60.478 55.0 12.3 0.0 39.26 3.16 R
2849 2970 1.477553 AGTAATGACGAAGGGCCGTA 58.522 50.0 0.0 0.0 43.49 4.02 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
113 114 8.207545 GTCAGATAAGAGGGTCAAATTATCACT 58.792 37.037 6.57 0.00 37.19 3.41
125 126 1.860641 TTATCACTCCTCTTCCCGCA 58.139 50.000 0.00 0.00 0.00 5.69
190 191 5.334879 GCAAATAAATAGTGGCAGTATCGGG 60.335 44.000 14.94 4.26 0.00 5.14
234 235 2.160022 TCGGCAACACGTTTATTAAGGC 59.840 45.455 0.00 0.00 34.94 4.35
250 251 0.603569 AGGCGACCTGTGTCTGTTAG 59.396 55.000 0.00 0.00 39.47 2.34
253 254 2.593257 GCGACCTGTGTCTGTTAGTAC 58.407 52.381 0.00 0.00 39.47 2.73
255 256 3.438087 GCGACCTGTGTCTGTTAGTACTA 59.562 47.826 0.00 0.00 39.47 1.82
256 257 4.437121 GCGACCTGTGTCTGTTAGTACTAG 60.437 50.000 2.23 0.00 39.47 2.57
258 259 4.664392 ACCTGTGTCTGTTAGTACTAGCT 58.336 43.478 16.50 0.00 0.00 3.32
259 260 5.813383 ACCTGTGTCTGTTAGTACTAGCTA 58.187 41.667 16.50 0.00 0.00 3.32
261 262 6.890814 ACCTGTGTCTGTTAGTACTAGCTAAT 59.109 38.462 16.50 0.00 34.03 1.73
262 263 8.051535 ACCTGTGTCTGTTAGTACTAGCTAATA 58.948 37.037 16.50 2.29 34.03 0.98
263 264 8.344098 CCTGTGTCTGTTAGTACTAGCTAATAC 58.656 40.741 16.50 4.16 34.03 1.89
265 266 9.107177 TGTGTCTGTTAGTACTAGCTAATACTC 57.893 37.037 17.64 6.18 34.03 2.59
266 267 8.558700 GTGTCTGTTAGTACTAGCTAATACTCC 58.441 40.741 17.64 10.67 34.03 3.85
267 268 7.718753 TGTCTGTTAGTACTAGCTAATACTCCC 59.281 40.741 17.64 10.36 34.03 4.30
268 269 7.938490 GTCTGTTAGTACTAGCTAATACTCCCT 59.062 40.741 17.64 0.00 34.03 4.20
269 270 8.156165 TCTGTTAGTACTAGCTAATACTCCCTC 58.844 40.741 17.64 8.14 34.03 4.30
270 271 7.230027 TGTTAGTACTAGCTAATACTCCCTCC 58.770 42.308 17.64 4.46 34.03 4.30
271 272 4.909001 AGTACTAGCTAATACTCCCTCCG 58.091 47.826 9.05 0.00 0.00 4.63
272 273 3.880168 ACTAGCTAATACTCCCTCCGT 57.120 47.619 0.00 0.00 0.00 4.69
273 274 4.181799 ACTAGCTAATACTCCCTCCGTT 57.818 45.455 0.00 0.00 0.00 4.44
274 275 4.544683 ACTAGCTAATACTCCCTCCGTTT 58.455 43.478 0.00 0.00 0.00 3.60
275 276 4.961099 ACTAGCTAATACTCCCTCCGTTTT 59.039 41.667 0.00 0.00 0.00 2.43
276 277 4.838904 AGCTAATACTCCCTCCGTTTTT 57.161 40.909 0.00 0.00 0.00 1.94
277 278 5.945144 AGCTAATACTCCCTCCGTTTTTA 57.055 39.130 0.00 0.00 0.00 1.52
278 279 6.496144 AGCTAATACTCCCTCCGTTTTTAT 57.504 37.500 0.00 0.00 0.00 1.40
279 280 6.896883 AGCTAATACTCCCTCCGTTTTTATT 58.103 36.000 0.00 0.00 0.00 1.40
280 281 7.344134 AGCTAATACTCCCTCCGTTTTTATTT 58.656 34.615 0.00 0.00 0.00 1.40
281 282 8.488668 AGCTAATACTCCCTCCGTTTTTATTTA 58.511 33.333 0.00 0.00 0.00 1.40
282 283 8.554528 GCTAATACTCCCTCCGTTTTTATTTAC 58.445 37.037 0.00 0.00 0.00 2.01
283 284 9.828039 CTAATACTCCCTCCGTTTTTATTTACT 57.172 33.333 0.00 0.00 0.00 2.24
284 285 8.728337 AATACTCCCTCCGTTTTTATTTACTC 57.272 34.615 0.00 0.00 0.00 2.59
285 286 5.494724 ACTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
286 287 4.506758 TCCCTCCGTTTTTATTTACTCCG 58.493 43.478 0.00 0.00 0.00 4.63
287 288 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
288 289 3.685756 CCTCCGTTTTTATTTACTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
289 290 4.334481 CCTCCGTTTTTATTTACTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
290 291 5.524646 CCTCCGTTTTTATTTACTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
291 292 6.204108 CCTCCGTTTTTATTTACTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
292 293 7.255001 CCTCCGTTTTTATTTACTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
293 294 8.659925 TCCGTTTTTATTTACTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
294 295 9.107177 TCCGTTTTTATTTACTCCGCATATTAA 57.893 29.630 0.00 0.00 0.00 1.40
295 296 9.161684 CCGTTTTTATTTACTCCGCATATTAAC 57.838 33.333 0.00 0.00 0.00 2.01
296 297 9.925268 CGTTTTTATTTACTCCGCATATTAACT 57.075 29.630 0.00 0.00 0.00 2.24
303 304 8.725405 TTTACTCCGCATATTAACTGAAATCA 57.275 30.769 0.00 0.00 0.00 2.57
304 305 8.725405 TTACTCCGCATATTAACTGAAATCAA 57.275 30.769 0.00 0.00 0.00 2.57
305 306 7.624360 ACTCCGCATATTAACTGAAATCAAA 57.376 32.000 0.00 0.00 0.00 2.69
306 307 8.225603 ACTCCGCATATTAACTGAAATCAAAT 57.774 30.769 0.00 0.00 0.00 2.32
307 308 8.686334 ACTCCGCATATTAACTGAAATCAAATT 58.314 29.630 0.00 0.00 0.00 1.82
308 309 9.520204 CTCCGCATATTAACTGAAATCAAATTT 57.480 29.630 0.00 0.00 34.64 1.82
309 310 9.868277 TCCGCATATTAACTGAAATCAAATTTT 57.132 25.926 0.00 0.00 31.47 1.82
310 311 9.904647 CCGCATATTAACTGAAATCAAATTTTG 57.095 29.630 2.59 2.59 31.47 2.44
320 321 9.883142 ACTGAAATCAAATTTTGTAAGGTTTGA 57.117 25.926 8.89 2.38 42.61 2.69
322 323 9.103861 TGAAATCAAATTTTGTAAGGTTTGACC 57.896 29.630 8.89 0.00 41.64 4.02
323 324 9.103861 GAAATCAAATTTTGTAAGGTTTGACCA 57.896 29.630 8.89 0.00 41.64 4.02
324 325 9.454859 AAATCAAATTTTGTAAGGTTTGACCAA 57.545 25.926 8.89 0.00 41.95 3.67
325 326 9.454859 AATCAAATTTTGTAAGGTTTGACCAAA 57.545 25.926 8.89 0.00 41.95 3.28
326 327 9.625747 ATCAAATTTTGTAAGGTTTGACCAAAT 57.374 25.926 8.89 0.00 41.95 2.32
327 328 9.454859 TCAAATTTTGTAAGGTTTGACCAAATT 57.545 25.926 8.89 0.62 41.95 1.82
391 392 7.715265 ATGATATGGAAGTACATTCGACAAC 57.285 36.000 0.00 0.00 38.95 3.32
392 393 5.746721 TGATATGGAAGTACATTCGACAACG 59.253 40.000 0.00 0.00 38.95 4.10
403 404 2.465860 TCGACAACGAATCCAATGGT 57.534 45.000 0.00 0.00 45.74 3.55
404 405 3.596310 TCGACAACGAATCCAATGGTA 57.404 42.857 0.00 0.00 45.74 3.25
405 406 4.131649 TCGACAACGAATCCAATGGTAT 57.868 40.909 0.00 0.00 45.74 2.73
406 407 4.509616 TCGACAACGAATCCAATGGTATT 58.490 39.130 0.00 0.00 45.74 1.89
407 408 4.331443 TCGACAACGAATCCAATGGTATTG 59.669 41.667 0.00 1.18 45.74 1.90
408 409 4.331443 CGACAACGAATCCAATGGTATTGA 59.669 41.667 0.00 0.00 42.66 2.57
409 410 5.007626 CGACAACGAATCCAATGGTATTGAT 59.992 40.000 0.00 0.00 42.66 2.57
410 411 6.458206 CGACAACGAATCCAATGGTATTGATT 60.458 38.462 0.00 0.00 42.66 2.57
411 412 7.169158 ACAACGAATCCAATGGTATTGATTT 57.831 32.000 0.00 0.00 0.00 2.17
412 413 7.035004 ACAACGAATCCAATGGTATTGATTTG 58.965 34.615 0.00 0.00 0.00 2.32
413 414 6.773976 ACGAATCCAATGGTATTGATTTGT 57.226 33.333 0.00 0.00 0.00 2.83
414 415 7.169158 ACGAATCCAATGGTATTGATTTGTT 57.831 32.000 0.00 0.00 0.00 2.83
415 416 8.287439 ACGAATCCAATGGTATTGATTTGTTA 57.713 30.769 0.00 0.00 0.00 2.41
416 417 8.912988 ACGAATCCAATGGTATTGATTTGTTAT 58.087 29.630 0.00 0.00 0.00 1.89
417 418 9.748708 CGAATCCAATGGTATTGATTTGTTATT 57.251 29.630 0.00 0.00 0.00 1.40
489 490 8.801913 GCTTGACTTTGATCAAAACTAATATGC 58.198 33.333 20.82 13.38 38.12 3.14
490 491 8.894409 TTGACTTTGATCAAAACTAATATGCG 57.106 30.769 20.82 8.44 35.65 4.73
492 493 8.726068 TGACTTTGATCAAAACTAATATGCGAA 58.274 29.630 20.82 0.00 0.00 4.70
493 494 9.214953 GACTTTGATCAAAACTAATATGCGAAG 57.785 33.333 20.82 7.30 0.00 3.79
494 495 8.730680 ACTTTGATCAAAACTAATATGCGAAGT 58.269 29.630 20.82 7.90 0.00 3.01
506 507 9.925268 ACTAATATGCGAAGTAAATAAAAACGG 57.075 29.630 0.00 0.00 0.00 4.44
521 522 2.599408 AACGGAGGAAGTACTCAGGA 57.401 50.000 0.00 0.00 39.27 3.86
525 526 2.561419 CGGAGGAAGTACTCAGGACAAA 59.439 50.000 0.00 0.00 39.27 2.83
551 552 6.262944 TGGTGAAATGGTATCATTACATCTGC 59.737 38.462 0.58 0.00 42.29 4.26
641 647 2.394545 TTGACAGTACACTCGTGTCG 57.605 50.000 5.89 0.00 42.98 4.35
642 648 1.585297 TGACAGTACACTCGTGTCGA 58.415 50.000 5.89 0.00 42.98 4.20
653 659 2.925563 ACTCGTGTCGAAAAACGTCTTT 59.074 40.909 14.00 0.00 43.13 2.52
660 667 6.460452 CGTGTCGAAAAACGTCTTTATTATGG 59.540 38.462 8.05 0.00 43.13 2.74
663 670 8.723311 TGTCGAAAAACGTCTTTATTATGGAAT 58.277 29.630 0.00 0.00 43.13 3.01
671 678 9.765795 AACGTCTTTATTATGGAATAGAGGAAG 57.234 33.333 0.00 0.00 32.85 3.46
772 782 9.871238 TGACTATTGACTGTAGTATTCTTTTCC 57.129 33.333 0.00 0.00 32.77 3.13
773 783 9.315525 GACTATTGACTGTAGTATTCTTTTCCC 57.684 37.037 0.00 0.00 32.77 3.97
837 851 0.958822 GCAAAGCGGGAGAAAAAGGA 59.041 50.000 0.00 0.00 0.00 3.36
899 913 2.417787 GGACTTTGGCAGCCATTCAATC 60.418 50.000 17.09 8.91 31.53 2.67
939 953 4.864334 CCGCCCCTGCTGCCTAAG 62.864 72.222 0.00 0.00 34.43 2.18
984 998 3.999285 ACCTCCTCCACGCCTCCT 61.999 66.667 0.00 0.00 0.00 3.69
985 999 3.151022 CCTCCTCCACGCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
997 1011 0.919780 GCCTCCTCCCCTACCCTTTT 60.920 60.000 0.00 0.00 0.00 2.27
1006 1020 1.682478 CCTACCCTTTTCCCCTCCTT 58.318 55.000 0.00 0.00 0.00 3.36
1024 1038 4.834453 CTCCTCTGCAGCCGCCTG 62.834 72.222 9.47 0.00 42.13 4.85
1080 1097 4.056740 CTCTCTGCAGGTAAGCATACATG 58.943 47.826 15.13 9.25 44.68 3.21
1110 1133 0.527600 GCTGAGACGTGTGTGTGTGA 60.528 55.000 0.00 0.00 0.00 3.58
1112 1135 1.065551 CTGAGACGTGTGTGTGTGAGA 59.934 52.381 0.00 0.00 0.00 3.27
1113 1136 1.065551 TGAGACGTGTGTGTGTGAGAG 59.934 52.381 0.00 0.00 0.00 3.20
1114 1137 1.333931 GAGACGTGTGTGTGTGAGAGA 59.666 52.381 0.00 0.00 0.00 3.10
1122 1145 0.523966 GTGTGTGAGAGAGAGACGGG 59.476 60.000 0.00 0.00 0.00 5.28
1124 1147 1.350019 TGTGTGAGAGAGAGACGGGTA 59.650 52.381 0.00 0.00 0.00 3.69
1134 1157 2.355444 GAGAGACGGGTACTAGCAAGAC 59.645 54.545 0.00 0.00 0.00 3.01
1139 1162 2.492484 ACGGGTACTAGCAAGACAGAAG 59.508 50.000 0.00 0.00 0.00 2.85
1143 1166 2.464157 ACTAGCAAGACAGAAGGTGC 57.536 50.000 0.00 0.00 37.26 5.01
1196 1225 4.043200 GCTTTCTGTGGGTGCGGC 62.043 66.667 0.00 0.00 0.00 6.53
1216 1245 2.465813 CTTCAGGTGGAGAGGATGTCT 58.534 52.381 0.00 0.00 38.71 3.41
1224 1253 0.174389 GAGAGGATGTCTGCGCTGAA 59.826 55.000 19.14 9.72 34.71 3.02
1477 1506 0.181114 AGCTCATGCCGCTTATTCCA 59.819 50.000 3.81 0.00 40.80 3.53
1479 1508 1.667236 CTCATGCCGCTTATTCCACA 58.333 50.000 0.00 0.00 0.00 4.17
1567 1597 4.932268 TTTAGGTTTCCAGCGTTATTCG 57.068 40.909 0.00 0.00 43.12 3.34
1778 1812 3.041940 CGCTTTCCACGGAAGCGT 61.042 61.111 23.08 0.00 41.72 5.07
1795 1829 4.308458 TTGGTGCCGGTGAGGTCG 62.308 66.667 1.90 0.00 43.70 4.79
1846 1880 3.681835 GTGTGGTCGCTCTCCGGT 61.682 66.667 0.00 0.00 37.59 5.28
1927 1964 1.356738 TCCCTGTCGTCCTTCTTCCTA 59.643 52.381 0.00 0.00 0.00 2.94
1963 2000 0.538977 TCAACCTCCTCGACGAACCT 60.539 55.000 0.00 0.00 0.00 3.50
1970 2007 3.966026 CTCGACGAACCTCCACGCC 62.966 68.421 0.00 0.00 0.00 5.68
1977 2014 2.406002 GAACCTCCACGCCCCAAGAA 62.406 60.000 0.00 0.00 0.00 2.52
2392 2482 0.800012 TACATCTTTTTCGGCCGTGC 59.200 50.000 27.15 0.00 0.00 5.34
2415 2505 4.433805 CCGTTGATTAGTCTGTTGTAACGC 60.434 45.833 0.00 0.00 38.52 4.84
2420 2510 1.767289 AGTCTGTTGTAACGCACTCG 58.233 50.000 0.00 0.00 42.43 4.18
2726 2825 4.827284 AGCTAGCTGCCTTGTTTTTCTTTA 59.173 37.500 18.57 0.00 44.23 1.85
2742 2841 3.561143 TCTTTAAAGGAAGCTGCCAACA 58.439 40.909 15.05 0.00 0.00 3.33
2848 2969 0.106015 ACCCAAGGAGTTGCAGCTTT 60.106 50.000 3.97 0.00 31.64 3.51
2849 2970 1.043022 CCCAAGGAGTTGCAGCTTTT 58.957 50.000 3.97 0.00 31.64 2.27
2922 3047 2.346803 CACATCGGGTACAAACAGGAG 58.653 52.381 0.00 0.00 0.00 3.69
2926 3051 0.899720 CGGGTACAAACAGGAGCCTA 59.100 55.000 0.00 0.00 0.00 3.93
2950 3075 0.173935 CTGCACCGTTACCGTCCATA 59.826 55.000 0.00 0.00 0.00 2.74
2969 3094 6.423001 GTCCATATACGACACCCAAATTACTC 59.577 42.308 0.00 0.00 0.00 2.59
3007 3132 0.395311 CAGTAGACTAGGCCACGGGA 60.395 60.000 5.01 0.00 0.00 5.14
3066 3191 7.979537 AGTGTATACGAGAAGAATGCAATTGTA 59.020 33.333 7.40 2.30 36.07 2.41
3232 3364 1.400494 GGTGCCTCGAATTTTGCGTAT 59.600 47.619 0.00 0.00 0.00 3.06
3278 3651 3.067833 GGACAGAGTAGTGCTTTGGTTC 58.932 50.000 3.85 0.00 33.98 3.62
3484 3869 4.637276 ACACCGTGATAAACATGAACTCA 58.363 39.130 5.28 0.00 37.69 3.41
3520 3906 9.214953 CTTCTTTGTTTCGCATGATTCTATAAC 57.785 33.333 0.00 0.00 0.00 1.89
3527 3913 4.857037 TCGCATGATTCTATAACGATTCGG 59.143 41.667 11.29 0.00 0.00 4.30
3530 3916 6.453003 CGCATGATTCTATAACGATTCGGAAG 60.453 42.308 11.29 2.40 0.00 3.46
3576 3962 3.689649 AGTTGCTTTCCTTTCGCGAATAT 59.310 39.130 24.05 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 8.503196 CGATACTGCCACTATTTATTTGCATTA 58.497 33.333 0.00 0.00 0.00 1.90
166 167 5.334879 CCCGATACTGCCACTATTTATTTGC 60.335 44.000 0.00 0.00 0.00 3.68
190 191 3.248125 GCATCTCTAAGCTTGACTCATGC 59.752 47.826 9.86 12.03 35.22 4.06
250 251 4.650734 ACGGAGGGAGTATTAGCTAGTAC 58.349 47.826 16.45 16.45 0.00 2.73
253 254 5.532664 AAAACGGAGGGAGTATTAGCTAG 57.467 43.478 0.00 0.00 0.00 3.42
255 256 4.838904 AAAAACGGAGGGAGTATTAGCT 57.161 40.909 0.00 0.00 0.00 3.32
256 257 7.563888 AAATAAAAACGGAGGGAGTATTAGC 57.436 36.000 0.00 0.00 0.00 3.09
258 259 9.822185 GAGTAAATAAAAACGGAGGGAGTATTA 57.178 33.333 0.00 0.00 0.00 0.98
259 260 7.772292 GGAGTAAATAAAAACGGAGGGAGTATT 59.228 37.037 0.00 0.00 0.00 1.89
261 262 6.627953 CGGAGTAAATAAAAACGGAGGGAGTA 60.628 42.308 0.00 0.00 0.00 2.59
262 263 5.494724 GGAGTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
263 264 4.569564 CGGAGTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
265 266 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
266 267 3.685756 TGCGGAGTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
267 268 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
268 269 7.556733 AATATGCGGAGTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
269 270 9.161684 GTTAATATGCGGAGTAAATAAAAACGG 57.838 33.333 0.00 0.00 0.00 4.44
270 271 9.925268 AGTTAATATGCGGAGTAAATAAAAACG 57.075 29.630 0.00 0.00 0.00 3.60
277 278 9.337396 TGATTTCAGTTAATATGCGGAGTAAAT 57.663 29.630 0.00 0.00 0.00 1.40
278 279 8.725405 TGATTTCAGTTAATATGCGGAGTAAA 57.275 30.769 0.00 0.00 0.00 2.01
279 280 8.725405 TTGATTTCAGTTAATATGCGGAGTAA 57.275 30.769 0.00 0.00 0.00 2.24
280 281 8.725405 TTTGATTTCAGTTAATATGCGGAGTA 57.275 30.769 0.00 0.00 0.00 2.59
281 282 7.624360 TTTGATTTCAGTTAATATGCGGAGT 57.376 32.000 0.00 0.00 0.00 3.85
282 283 9.520204 AAATTTGATTTCAGTTAATATGCGGAG 57.480 29.630 0.00 0.00 0.00 4.63
283 284 9.868277 AAAATTTGATTTCAGTTAATATGCGGA 57.132 25.926 0.00 0.00 0.00 5.54
284 285 9.904647 CAAAATTTGATTTCAGTTAATATGCGG 57.095 29.630 0.00 0.00 0.00 5.69
294 295 9.883142 TCAAACCTTACAAAATTTGATTTCAGT 57.117 25.926 13.19 0.00 36.42 3.41
296 297 9.103861 GGTCAAACCTTACAAAATTTGATTTCA 57.896 29.630 13.19 0.00 41.64 2.69
297 298 9.103861 TGGTCAAACCTTACAAAATTTGATTTC 57.896 29.630 13.19 0.00 41.64 2.17
298 299 9.454859 TTGGTCAAACCTTACAAAATTTGATTT 57.545 25.926 13.19 2.57 41.64 2.17
299 300 9.454859 TTTGGTCAAACCTTACAAAATTTGATT 57.545 25.926 13.19 0.00 41.64 2.57
300 301 9.625747 ATTTGGTCAAACCTTACAAAATTTGAT 57.374 25.926 13.19 0.00 41.64 2.57
301 302 9.454859 AATTTGGTCAAACCTTACAAAATTTGA 57.545 25.926 13.19 0.00 39.58 2.69
365 366 9.424319 GTTGTCGAATGTACTTCCATATCATAT 57.576 33.333 0.00 0.00 0.00 1.78
366 367 7.593644 CGTTGTCGAATGTACTTCCATATCATA 59.406 37.037 0.00 0.00 39.71 2.15
367 368 6.420903 CGTTGTCGAATGTACTTCCATATCAT 59.579 38.462 0.00 0.00 39.71 2.45
368 369 5.746721 CGTTGTCGAATGTACTTCCATATCA 59.253 40.000 0.00 0.00 39.71 2.15
369 370 5.975344 TCGTTGTCGAATGTACTTCCATATC 59.025 40.000 0.00 0.00 43.34 1.63
370 371 5.898174 TCGTTGTCGAATGTACTTCCATAT 58.102 37.500 0.00 0.00 43.34 1.78
371 372 5.313520 TCGTTGTCGAATGTACTTCCATA 57.686 39.130 0.00 0.00 43.34 2.74
372 373 4.182693 TCGTTGTCGAATGTACTTCCAT 57.817 40.909 0.00 0.00 43.34 3.41
373 374 3.646611 TCGTTGTCGAATGTACTTCCA 57.353 42.857 0.00 0.00 43.34 3.53
384 385 2.465860 ACCATTGGATTCGTTGTCGA 57.534 45.000 10.37 0.00 44.66 4.20
385 386 4.331443 TCAATACCATTGGATTCGTTGTCG 59.669 41.667 10.37 0.00 38.55 4.35
386 387 5.811399 TCAATACCATTGGATTCGTTGTC 57.189 39.130 10.37 0.00 0.00 3.18
387 388 6.773976 AATCAATACCATTGGATTCGTTGT 57.226 33.333 10.37 0.00 0.00 3.32
388 389 7.035004 ACAAATCAATACCATTGGATTCGTTG 58.965 34.615 10.37 7.12 0.00 4.10
389 390 7.169158 ACAAATCAATACCATTGGATTCGTT 57.831 32.000 10.37 0.50 0.00 3.85
390 391 6.773976 ACAAATCAATACCATTGGATTCGT 57.226 33.333 10.37 0.00 0.00 3.85
391 392 9.748708 AATAACAAATCAATACCATTGGATTCG 57.251 29.630 10.37 0.00 0.00 3.34
440 441 9.546428 AAGCTTTGCAAACTTTAACAGATTTAT 57.454 25.926 8.05 0.00 0.00 1.40
444 445 6.476706 GTCAAGCTTTGCAAACTTTAACAGAT 59.523 34.615 18.37 0.82 0.00 2.90
445 446 5.804979 GTCAAGCTTTGCAAACTTTAACAGA 59.195 36.000 18.37 12.33 0.00 3.41
446 447 5.807011 AGTCAAGCTTTGCAAACTTTAACAG 59.193 36.000 18.37 10.85 0.00 3.16
447 448 5.719173 AGTCAAGCTTTGCAAACTTTAACA 58.281 33.333 18.37 6.35 0.00 2.41
448 449 6.647212 AAGTCAAGCTTTGCAAACTTTAAC 57.353 33.333 18.37 17.95 32.57 2.01
463 464 8.801913 GCATATTAGTTTTGATCAAAGTCAAGC 58.198 33.333 19.64 13.61 39.13 4.01
464 465 9.003112 CGCATATTAGTTTTGATCAAAGTCAAG 57.997 33.333 19.64 8.64 39.13 3.02
465 466 8.726068 TCGCATATTAGTTTTGATCAAAGTCAA 58.274 29.630 19.64 14.55 36.38 3.18
467 468 9.214953 CTTCGCATATTAGTTTTGATCAAAGTC 57.785 33.333 19.64 16.31 30.16 3.01
468 469 8.730680 ACTTCGCATATTAGTTTTGATCAAAGT 58.269 29.630 19.64 14.00 32.41 2.66
480 481 9.925268 CCGTTTTTATTTACTTCGCATATTAGT 57.075 29.630 0.00 0.00 0.00 2.24
483 484 8.126700 CCTCCGTTTTTATTTACTTCGCATATT 58.873 33.333 0.00 0.00 0.00 1.28
484 485 7.496591 TCCTCCGTTTTTATTTACTTCGCATAT 59.503 33.333 0.00 0.00 0.00 1.78
487 488 4.996122 TCCTCCGTTTTTATTTACTTCGCA 59.004 37.500 0.00 0.00 0.00 5.10
488 489 5.535043 TCCTCCGTTTTTATTTACTTCGC 57.465 39.130 0.00 0.00 0.00 4.70
489 490 7.125536 ACTTCCTCCGTTTTTATTTACTTCG 57.874 36.000 0.00 0.00 0.00 3.79
490 491 9.212641 AGTACTTCCTCCGTTTTTATTTACTTC 57.787 33.333 0.00 0.00 0.00 3.01
492 493 8.370182 TGAGTACTTCCTCCGTTTTTATTTACT 58.630 33.333 0.00 0.00 0.00 2.24
493 494 8.538409 TGAGTACTTCCTCCGTTTTTATTTAC 57.462 34.615 0.00 0.00 0.00 2.01
494 495 7.820872 CCTGAGTACTTCCTCCGTTTTTATTTA 59.179 37.037 0.00 0.00 0.00 1.40
495 496 6.653740 CCTGAGTACTTCCTCCGTTTTTATTT 59.346 38.462 0.00 0.00 0.00 1.40
497 498 5.482878 TCCTGAGTACTTCCTCCGTTTTTAT 59.517 40.000 0.00 0.00 0.00 1.40
498 499 4.834496 TCCTGAGTACTTCCTCCGTTTTTA 59.166 41.667 0.00 0.00 0.00 1.52
499 500 3.644738 TCCTGAGTACTTCCTCCGTTTTT 59.355 43.478 0.00 0.00 0.00 1.94
501 502 2.561858 GTCCTGAGTACTTCCTCCGTTT 59.438 50.000 0.00 0.00 0.00 3.60
502 503 2.169330 GTCCTGAGTACTTCCTCCGTT 58.831 52.381 0.00 0.00 0.00 4.44
503 504 1.075050 TGTCCTGAGTACTTCCTCCGT 59.925 52.381 0.00 0.00 0.00 4.69
504 505 1.835494 TGTCCTGAGTACTTCCTCCG 58.165 55.000 0.00 0.00 0.00 4.63
505 506 4.508662 CATTTGTCCTGAGTACTTCCTCC 58.491 47.826 0.00 0.00 0.00 4.30
506 507 4.020128 ACCATTTGTCCTGAGTACTTCCTC 60.020 45.833 0.00 0.00 0.00 3.71
507 508 3.910627 ACCATTTGTCCTGAGTACTTCCT 59.089 43.478 0.00 0.00 0.00 3.36
508 509 4.003648 CACCATTTGTCCTGAGTACTTCC 58.996 47.826 0.00 0.00 0.00 3.46
521 522 8.359875 TGTAATGATACCATTTCACCATTTGT 57.640 30.769 0.00 0.00 42.56 2.83
525 526 7.040201 GCAGATGTAATGATACCATTTCACCAT 60.040 37.037 0.00 0.00 40.95 3.55
633 639 3.564408 AAAGACGTTTTTCGACACGAG 57.436 42.857 15.75 0.00 42.86 4.18
634 640 5.640218 AATAAAGACGTTTTTCGACACGA 57.360 34.783 15.75 0.00 42.86 4.35
635 641 6.460452 CCATAATAAAGACGTTTTTCGACACG 59.540 38.462 7.42 8.94 42.86 4.49
636 642 7.512297 TCCATAATAAAGACGTTTTTCGACAC 58.488 34.615 7.42 0.00 42.86 3.67
637 643 7.655236 TCCATAATAAAGACGTTTTTCGACA 57.345 32.000 7.42 0.00 42.86 4.35
676 683 9.284968 AGTTCCCGGATGAATATATGTAAAAAG 57.715 33.333 0.73 0.00 0.00 2.27
681 688 6.666113 TGCTAGTTCCCGGATGAATATATGTA 59.334 38.462 0.73 0.00 0.00 2.29
771 781 4.151883 TCCATTTCTTTTTCCTGTCAGGG 58.848 43.478 19.11 2.37 35.59 4.45
772 782 4.829492 ACTCCATTTCTTTTTCCTGTCAGG 59.171 41.667 13.21 13.21 36.46 3.86
773 783 5.278660 CCACTCCATTTCTTTTTCCTGTCAG 60.279 44.000 0.00 0.00 0.00 3.51
845 859 4.388469 ACAAATGCACTGTTGTGTTGTTTC 59.612 37.500 10.54 0.00 45.44 2.78
899 913 0.979665 AGATGAGTGTCTGGTGGGTG 59.020 55.000 0.00 0.00 0.00 4.61
939 953 0.388263 GAGGAAAAAGCAGCAGCAGC 60.388 55.000 3.17 0.46 45.49 5.25
940 954 1.068472 CAGAGGAAAAAGCAGCAGCAG 60.068 52.381 3.17 0.00 45.49 4.24
941 955 0.956633 CAGAGGAAAAAGCAGCAGCA 59.043 50.000 3.17 0.00 45.49 4.41
950 964 2.039084 GAGGTGAGGAGCAGAGGAAAAA 59.961 50.000 0.00 0.00 0.00 1.94
984 998 0.253488 GAGGGGAAAAGGGTAGGGGA 60.253 60.000 0.00 0.00 0.00 4.81
985 999 1.287038 GGAGGGGAAAAGGGTAGGGG 61.287 65.000 0.00 0.00 0.00 4.79
997 1011 1.002274 GCAGAGGAGAAGGAGGGGA 59.998 63.158 0.00 0.00 0.00 4.81
1061 1078 2.746142 GCCATGTATGCTTACCTGCAGA 60.746 50.000 17.39 0.00 46.71 4.26
1080 1097 1.217779 GTCTCAGCACAGAGAGGCC 59.782 63.158 0.00 0.00 44.76 5.19
1110 1133 1.838715 TGCTAGTACCCGTCTCTCTCT 59.161 52.381 0.00 0.00 0.00 3.10
1112 1135 2.239150 TCTTGCTAGTACCCGTCTCTCT 59.761 50.000 0.00 0.00 0.00 3.10
1113 1136 2.355444 GTCTTGCTAGTACCCGTCTCTC 59.645 54.545 0.00 0.00 0.00 3.20
1114 1137 2.290768 TGTCTTGCTAGTACCCGTCTCT 60.291 50.000 0.00 0.00 0.00 3.10
1122 1145 3.056465 AGCACCTTCTGTCTTGCTAGTAC 60.056 47.826 0.00 0.00 43.51 2.73
1124 1147 1.974236 AGCACCTTCTGTCTTGCTAGT 59.026 47.619 0.00 0.00 43.51 2.57
1139 1162 3.876589 TTCCCGCACGAGAAGCACC 62.877 63.158 0.00 0.00 0.00 5.01
1143 1166 1.009389 GTCAGTTCCCGCACGAGAAG 61.009 60.000 0.00 0.00 0.00 2.85
1196 1225 2.168106 CAGACATCCTCTCCACCTGAAG 59.832 54.545 0.00 0.00 0.00 3.02
1216 1245 1.250840 TGAGGCTACTCTTCAGCGCA 61.251 55.000 11.47 0.00 44.29 6.09
1479 1508 2.765807 CCGGCAGGTCCATCTCCT 60.766 66.667 0.00 0.00 35.45 3.69
1567 1597 3.975035 CCTAGAAAGCACGCAAAAGAAAC 59.025 43.478 0.00 0.00 0.00 2.78
1727 1761 3.467226 CCGCATAGGGTCCACGGT 61.467 66.667 0.00 0.00 39.05 4.83
1778 1812 4.308458 CGACCTCACCGGCACCAA 62.308 66.667 0.00 0.00 35.61 3.67
1846 1880 1.652563 CGAGTCGGATATGGACGCA 59.347 57.895 4.10 0.00 39.38 5.24
1927 1964 0.477597 TGAAGGTGGGGGAGTCCATT 60.478 55.000 12.30 0.00 39.26 3.16
1963 2000 1.228124 CTTGTTCTTGGGGCGTGGA 60.228 57.895 0.00 0.00 0.00 4.02
1970 2007 3.217626 ACTTCTTGCTCTTGTTCTTGGG 58.782 45.455 0.00 0.00 0.00 4.12
1977 2014 2.225467 GCTTGGACTTCTTGCTCTTGT 58.775 47.619 0.00 0.00 0.00 3.16
2367 2457 3.061697 CGGCCGAAAAAGATGTACACTAC 59.938 47.826 24.07 0.00 0.00 2.73
2392 2482 4.433805 GCGTTACAACAGACTAATCAACGG 60.434 45.833 0.00 0.00 38.28 4.44
2415 2505 2.665519 CGCCAAGAAAAATCCACGAGTG 60.666 50.000 0.00 0.00 0.00 3.51
2420 2510 1.886542 AGGACGCCAAGAAAAATCCAC 59.113 47.619 0.00 0.00 0.00 4.02
2726 2825 2.037641 GGAATTGTTGGCAGCTTCCTTT 59.962 45.455 13.01 0.00 36.31 3.11
2848 2969 1.826720 AGTAATGACGAAGGGCCGTAA 59.173 47.619 0.00 0.00 43.49 3.18
2849 2970 1.477553 AGTAATGACGAAGGGCCGTA 58.522 50.000 0.00 0.00 43.49 4.02
2922 3047 2.610833 GGTAACGGTGCAGTTATTAGGC 59.389 50.000 2.28 0.00 38.63 3.93
2950 3075 4.766375 CAGGAGTAATTTGGGTGTCGTAT 58.234 43.478 0.00 0.00 0.00 3.06
2969 3094 1.962807 TGGTTCCACTTTGAATGCAGG 59.037 47.619 0.00 0.00 0.00 4.85
3007 3132 3.071312 TGTGAAGATTTTTGGCTGGCAAT 59.929 39.130 17.75 2.63 0.00 3.56
3066 3191 6.099341 GTGAAAAGGGTCGAAATGCAAATAT 58.901 36.000 0.00 0.00 0.00 1.28
3078 3203 1.512926 CTGACTGGTGAAAAGGGTCG 58.487 55.000 0.00 0.00 0.00 4.79
3140 3265 6.898912 AGAAACGTTCTTTCGAAGTAACTT 57.101 33.333 17.40 9.36 36.36 2.66
3172 3304 1.879575 TAGCTCCAATGGCCAGTAGT 58.120 50.000 13.05 0.00 0.00 2.73
3232 3364 5.217978 ACGGAGTATATTAAAATGCGGGA 57.782 39.130 0.00 0.00 41.94 5.14
3400 3778 7.639113 TCCATTGTTCCAAAATGTATACTCC 57.361 36.000 4.17 0.00 33.93 3.85
3401 3779 9.520204 CAATCCATTGTTCCAAAATGTATACTC 57.480 33.333 4.17 0.00 33.93 2.59
3444 3822 9.304731 TCACGGTGTACTATTTCATGTAATTAC 57.695 33.333 8.75 8.75 0.00 1.89
3484 3869 4.445385 GCGAAACAAAGAAGCATGACATTT 59.555 37.500 0.00 0.00 0.00 2.32
3520 3906 6.149640 TCTCTATTCCACTATCTTCCGAATCG 59.850 42.308 0.00 0.00 0.00 3.34
3527 3913 8.668510 TGCATTTTCTCTATTCCACTATCTTC 57.331 34.615 0.00 0.00 0.00 2.87
3530 3916 7.930865 ACTCTGCATTTTCTCTATTCCACTATC 59.069 37.037 0.00 0.00 0.00 2.08
3576 3962 4.782019 AATGATAAGCGAACCTTTTGCA 57.218 36.364 1.10 0.00 42.69 4.08


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

AutoCloner maintained by Alex Coulton.