Multiple sequence alignment - TraesCS3D01G475500

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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 TraesCS3D01G475500 chr3D 100.000 2532 0 0 1 2532 575855235 575852704 0.000 4676.0
1 TraesCS3D01G475500 chr3A 89.146 1944 105 54 672 2532 711408737 711406817 0.000 2324.0
2 TraesCS3D01G475500 chr3B 89.761 1045 65 23 742 1757 768249110 768250141 0.000 1299.0
3 TraesCS3D01G475500 chr3B 91.197 727 49 12 1812 2532 768250439 768251156 0.000 974.0
4 TraesCS3D01G475500 chr7B 100.000 28 0 0 220 247 750447398 750447425 0.005 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 TraesCS3D01G475500 chr3D 575852704 575855235 2531 True 4676.0 4676 100.000 1 2532 1 chr3D.!!$R1 2531
1 TraesCS3D01G475500 chr3A 711406817 711408737 1920 True 2324.0 2324 89.146 672 2532 1 chr3A.!!$R1 1860
2 TraesCS3D01G475500 chr3B 768249110 768251156 2046 False 1136.5 1299 90.479 742 2532 2 chr3B.!!$F1 1790

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
667 668 0.040425 GCTAGAGTAGAGCTGCTCGC 60.04 60.0 22.77 18.92 45.24 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 2901 1.198759 ACACGGTAAGGCAGGATGGT 61.199 55.0 0.0 0.0 35.86 3.55 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
112 113 9.995003 TTTGAAGTTTTCATAATATTGCCAAGT 57.005 25.926 0.00 0.00 39.84 3.16
113 114 9.995003 TTGAAGTTTTCATAATATTGCCAAGTT 57.005 25.926 0.00 0.00 39.84 2.66
114 115 9.995003 TGAAGTTTTCATAATATTGCCAAGTTT 57.005 25.926 0.00 0.00 34.08 2.66
124 125 9.884636 ATAATATTGCCAAGTTTAAAAGTTCCC 57.115 29.630 0.00 0.00 0.00 3.97
125 126 5.622346 ATTGCCAAGTTTAAAAGTTCCCA 57.378 34.783 0.00 0.00 0.00 4.37
126 127 4.664150 TGCCAAGTTTAAAAGTTCCCAG 57.336 40.909 0.00 0.00 0.00 4.45
127 128 4.282496 TGCCAAGTTTAAAAGTTCCCAGA 58.718 39.130 0.00 0.00 0.00 3.86
128 129 4.712337 TGCCAAGTTTAAAAGTTCCCAGAA 59.288 37.500 0.00 0.00 0.00 3.02
129 130 5.365314 TGCCAAGTTTAAAAGTTCCCAGAAT 59.635 36.000 0.00 0.00 0.00 2.40
130 131 6.551601 TGCCAAGTTTAAAAGTTCCCAGAATA 59.448 34.615 0.00 0.00 0.00 1.75
131 132 7.234577 TGCCAAGTTTAAAAGTTCCCAGAATAT 59.765 33.333 0.00 0.00 0.00 1.28
132 133 8.094548 GCCAAGTTTAAAAGTTCCCAGAATATT 58.905 33.333 0.00 0.00 0.00 1.28
160 161 8.801882 AAATAGGGAAAACGTGAGATTATCAA 57.198 30.769 0.00 0.00 40.43 2.57
161 162 8.801882 AATAGGGAAAACGTGAGATTATCAAA 57.198 30.769 0.00 0.00 40.43 2.69
162 163 8.801882 ATAGGGAAAACGTGAGATTATCAAAA 57.198 30.769 0.00 0.00 40.43 2.44
163 164 7.519032 AGGGAAAACGTGAGATTATCAAAAA 57.481 32.000 0.00 0.00 40.43 1.94
186 187 8.962884 AAAATGAAGCCAATTCTAAAGTTTGT 57.037 26.923 0.00 0.00 38.83 2.83
187 188 8.962884 AAATGAAGCCAATTCTAAAGTTTGTT 57.037 26.923 0.00 0.00 38.83 2.83
188 189 8.593492 AATGAAGCCAATTCTAAAGTTTGTTC 57.407 30.769 0.00 0.00 38.83 3.18
189 190 7.106439 TGAAGCCAATTCTAAAGTTTGTTCA 57.894 32.000 0.00 0.00 38.83 3.18
190 191 7.202526 TGAAGCCAATTCTAAAGTTTGTTCAG 58.797 34.615 0.00 0.00 38.83 3.02
191 192 6.959639 AGCCAATTCTAAAGTTTGTTCAGA 57.040 33.333 0.00 0.00 0.00 3.27
192 193 7.346751 AGCCAATTCTAAAGTTTGTTCAGAA 57.653 32.000 0.00 0.00 0.00 3.02
193 194 7.781056 AGCCAATTCTAAAGTTTGTTCAGAAA 58.219 30.769 0.00 0.00 0.00 2.52
194 195 8.257306 AGCCAATTCTAAAGTTTGTTCAGAAAA 58.743 29.630 0.00 0.00 0.00 2.29
195 196 8.328146 GCCAATTCTAAAGTTTGTTCAGAAAAC 58.672 33.333 0.00 0.00 37.71 2.43
206 207 9.705290 AGTTTGTTCAGAAAACTTGTAAACATT 57.295 25.926 0.00 0.00 43.60 2.71
209 210 9.482627 TTGTTCAGAAAACTTGTAAACATTTGT 57.517 25.926 0.00 0.00 0.00 2.83
267 268 8.846943 TGTTCTGAATTTCTAGTAAATGAGCA 57.153 30.769 0.00 0.00 0.00 4.26
268 269 8.721478 TGTTCTGAATTTCTAGTAAATGAGCAC 58.279 33.333 0.00 0.00 0.00 4.40
269 270 8.721478 GTTCTGAATTTCTAGTAAATGAGCACA 58.279 33.333 0.00 0.00 0.00 4.57
270 271 9.453572 TTCTGAATTTCTAGTAAATGAGCACAT 57.546 29.630 0.00 0.00 38.50 3.21
271 272 9.453572 TCTGAATTTCTAGTAAATGAGCACATT 57.546 29.630 3.28 3.28 46.99 2.71
307 308 9.932207 TTCATATTTTCAGAAAATGCTCATGTT 57.068 25.926 25.51 4.95 41.01 2.71
308 309 9.932207 TCATATTTTCAGAAAATGCTCATGTTT 57.068 25.926 25.51 4.31 41.01 2.83
310 311 9.932207 ATATTTTCAGAAAATGCTCATGTTTCA 57.068 25.926 25.51 6.58 41.01 2.69
311 312 7.703298 TTTTCAGAAAATGCTCATGTTTCAG 57.297 32.000 4.06 1.57 34.40 3.02
312 313 6.638096 TTCAGAAAATGCTCATGTTTCAGA 57.362 33.333 8.06 3.55 34.40 3.27
313 314 6.250344 TCAGAAAATGCTCATGTTTCAGAG 57.750 37.500 8.06 0.00 34.40 3.35
314 315 5.999600 TCAGAAAATGCTCATGTTTCAGAGA 59.000 36.000 8.06 1.92 34.40 3.10
315 316 6.072838 TCAGAAAATGCTCATGTTTCAGAGAC 60.073 38.462 8.06 0.00 34.40 3.36
316 317 6.002704 AGAAAATGCTCATGTTTCAGAGACT 58.997 36.000 8.06 0.00 34.40 3.24
317 318 5.624344 AAATGCTCATGTTTCAGAGACTG 57.376 39.130 0.00 0.00 33.74 3.51
318 319 3.758755 TGCTCATGTTTCAGAGACTGT 57.241 42.857 0.00 0.00 33.74 3.55
319 320 4.077300 TGCTCATGTTTCAGAGACTGTT 57.923 40.909 0.00 0.00 33.74 3.16
320 321 4.060900 TGCTCATGTTTCAGAGACTGTTC 58.939 43.478 0.00 0.00 33.74 3.18
321 322 4.060900 GCTCATGTTTCAGAGACTGTTCA 58.939 43.478 0.00 0.00 33.74 3.18
322 323 4.084118 GCTCATGTTTCAGAGACTGTTCAC 60.084 45.833 0.00 0.00 33.74 3.18
323 324 5.022282 TCATGTTTCAGAGACTGTTCACA 57.978 39.130 0.00 0.00 32.61 3.58
324 325 5.427378 TCATGTTTCAGAGACTGTTCACAA 58.573 37.500 0.00 0.00 32.61 3.33
325 326 5.879777 TCATGTTTCAGAGACTGTTCACAAA 59.120 36.000 0.00 0.00 32.61 2.83
326 327 6.543465 TCATGTTTCAGAGACTGTTCACAAAT 59.457 34.615 0.00 0.00 32.61 2.32
327 328 6.757897 TGTTTCAGAGACTGTTCACAAATT 57.242 33.333 0.00 0.00 32.61 1.82
328 329 7.156876 TGTTTCAGAGACTGTTCACAAATTT 57.843 32.000 0.00 0.00 32.61 1.82
329 330 7.601856 TGTTTCAGAGACTGTTCACAAATTTT 58.398 30.769 0.00 0.00 32.61 1.82
330 331 8.735315 TGTTTCAGAGACTGTTCACAAATTTTA 58.265 29.630 0.00 0.00 32.61 1.52
331 332 9.567848 GTTTCAGAGACTGTTCACAAATTTTAA 57.432 29.630 0.00 0.00 32.61 1.52
357 358 9.768662 AAAATAGTCTCAATTTGAAAGCAATGT 57.231 25.926 0.01 0.00 33.25 2.71
358 359 9.768662 AAATAGTCTCAATTTGAAAGCAATGTT 57.231 25.926 0.01 0.00 33.25 2.71
359 360 8.976986 ATAGTCTCAATTTGAAAGCAATGTTC 57.023 30.769 0.01 0.00 33.25 3.18
360 361 6.808829 AGTCTCAATTTGAAAGCAATGTTCA 58.191 32.000 0.01 0.00 33.25 3.18
361 362 7.439381 AGTCTCAATTTGAAAGCAATGTTCAT 58.561 30.769 0.01 0.00 35.03 2.57
362 363 7.384115 AGTCTCAATTTGAAAGCAATGTTCATG 59.616 33.333 0.01 0.00 35.03 3.07
363 364 7.170320 GTCTCAATTTGAAAGCAATGTTCATGT 59.830 33.333 0.01 0.00 35.03 3.21
364 365 7.711772 TCTCAATTTGAAAGCAATGTTCATGTT 59.288 29.630 0.01 0.00 35.03 2.71
365 366 8.211116 TCAATTTGAAAGCAATGTTCATGTTT 57.789 26.923 0.00 0.00 35.03 2.83
366 367 8.675504 TCAATTTGAAAGCAATGTTCATGTTTT 58.324 25.926 0.00 0.00 35.03 2.43
367 368 9.291664 CAATTTGAAAGCAATGTTCATGTTTTT 57.708 25.926 0.00 0.00 35.03 1.94
380 381 9.881529 ATGTTCATGTTTTTAAAATCAATGCAC 57.118 25.926 14.05 12.16 0.00 4.57
381 382 8.060679 TGTTCATGTTTTTAAAATCAATGCACG 58.939 29.630 14.05 0.00 0.00 5.34
382 383 7.706281 TCATGTTTTTAAAATCAATGCACGT 57.294 28.000 14.05 1.64 0.00 4.49
383 384 8.136057 TCATGTTTTTAAAATCAATGCACGTT 57.864 26.923 14.05 0.00 0.00 3.99
384 385 8.607459 TCATGTTTTTAAAATCAATGCACGTTT 58.393 25.926 14.05 0.00 0.00 3.60
385 386 9.855361 CATGTTTTTAAAATCAATGCACGTTTA 57.145 25.926 14.05 0.00 0.00 2.01
387 388 9.302345 TGTTTTTAAAATCAATGCACGTTTAGA 57.698 25.926 8.85 0.00 0.00 2.10
416 417 7.894376 AAAACACAATATCAAAGAATGCTGG 57.106 32.000 0.00 0.00 0.00 4.85
417 418 6.839124 AACACAATATCAAAGAATGCTGGA 57.161 33.333 0.00 0.00 0.00 3.86
418 419 6.446781 ACACAATATCAAAGAATGCTGGAG 57.553 37.500 0.00 0.00 0.00 3.86
419 420 5.948162 ACACAATATCAAAGAATGCTGGAGT 59.052 36.000 0.00 0.00 0.00 3.85
420 421 6.435277 ACACAATATCAAAGAATGCTGGAGTT 59.565 34.615 0.00 0.00 0.00 3.01
421 422 7.039504 ACACAATATCAAAGAATGCTGGAGTTT 60.040 33.333 0.00 0.00 0.00 2.66
422 423 7.816031 CACAATATCAAAGAATGCTGGAGTTTT 59.184 33.333 0.00 0.00 0.00 2.43
423 424 8.370182 ACAATATCAAAGAATGCTGGAGTTTTT 58.630 29.630 0.00 0.00 0.00 1.94
532 533 7.826260 AAAACATGTTATCCTAAAAATGCGG 57.174 32.000 12.39 0.00 0.00 5.69
533 534 6.767524 AACATGTTATCCTAAAAATGCGGA 57.232 33.333 9.97 0.00 0.00 5.54
534 535 6.959639 ACATGTTATCCTAAAAATGCGGAT 57.040 33.333 0.00 0.00 40.48 4.18
535 536 7.346751 ACATGTTATCCTAAAAATGCGGATT 57.653 32.000 0.00 0.00 38.45 3.01
536 537 7.781056 ACATGTTATCCTAAAAATGCGGATTT 58.219 30.769 9.31 9.31 38.45 2.17
537 538 8.908903 ACATGTTATCCTAAAAATGCGGATTTA 58.091 29.630 15.63 0.00 38.45 1.40
538 539 9.398170 CATGTTATCCTAAAAATGCGGATTTAG 57.602 33.333 15.63 9.93 38.45 1.85
539 540 8.514330 TGTTATCCTAAAAATGCGGATTTAGT 57.486 30.769 15.63 9.22 38.45 2.24
540 541 9.616156 TGTTATCCTAAAAATGCGGATTTAGTA 57.384 29.630 15.63 9.84 38.45 1.82
545 546 9.796120 TCCTAAAAATGCGGATTTAGTAAATTG 57.204 29.630 15.63 6.94 37.40 2.32
546 547 8.539674 CCTAAAAATGCGGATTTAGTAAATTGC 58.460 33.333 15.63 19.23 37.40 3.56
547 548 6.902224 AAAATGCGGATTTAGTAAATTGCC 57.098 33.333 15.63 13.79 33.95 4.52
548 549 5.852282 AATGCGGATTTAGTAAATTGCCT 57.148 34.783 21.45 14.09 33.95 4.75
549 550 6.952773 AATGCGGATTTAGTAAATTGCCTA 57.047 33.333 21.45 11.13 33.95 3.93
550 551 5.744666 TGCGGATTTAGTAAATTGCCTAC 57.255 39.130 21.45 11.05 33.95 3.18
551 552 5.433526 TGCGGATTTAGTAAATTGCCTACT 58.566 37.500 21.45 0.00 33.95 2.57
552 553 6.584488 TGCGGATTTAGTAAATTGCCTACTA 58.416 36.000 21.45 8.14 33.95 1.82
553 554 7.221450 TGCGGATTTAGTAAATTGCCTACTAT 58.779 34.615 21.45 0.00 33.08 2.12
554 555 7.717875 TGCGGATTTAGTAAATTGCCTACTATT 59.282 33.333 21.45 0.00 33.08 1.73
555 556 8.565416 GCGGATTTAGTAAATTGCCTACTATTT 58.435 33.333 16.89 0.00 35.74 1.40
570 571 9.891828 TGCCTACTATTTTTGCATAATTATTCG 57.108 29.630 0.00 0.00 0.00 3.34
571 572 8.850452 GCCTACTATTTTTGCATAATTATTCGC 58.150 33.333 0.00 0.00 0.00 4.70
572 573 9.341899 CCTACTATTTTTGCATAATTATTCGCC 57.658 33.333 0.00 0.00 0.00 5.54
575 576 9.816354 ACTATTTTTGCATAATTATTCGCCTTT 57.184 25.926 0.00 0.00 0.00 3.11
578 579 8.539770 TTTTTGCATAATTATTCGCCTTTTGA 57.460 26.923 0.00 0.00 0.00 2.69
579 580 8.715191 TTTTGCATAATTATTCGCCTTTTGAT 57.285 26.923 0.00 0.00 0.00 2.57
580 581 9.809096 TTTTGCATAATTATTCGCCTTTTGATA 57.191 25.926 0.00 0.00 0.00 2.15
581 582 9.979578 TTTGCATAATTATTCGCCTTTTGATAT 57.020 25.926 0.00 0.00 0.00 1.63
592 593 7.548196 TCGCCTTTTGATATAAAAATCGAGT 57.452 32.000 14.12 0.00 33.25 4.18
593 594 7.406553 TCGCCTTTTGATATAAAAATCGAGTG 58.593 34.615 14.12 5.79 33.25 3.51
594 595 7.279090 TCGCCTTTTGATATAAAAATCGAGTGA 59.721 33.333 14.12 7.36 33.25 3.41
595 596 7.908082 CGCCTTTTGATATAAAAATCGAGTGAA 59.092 33.333 11.68 0.00 31.90 3.18
596 597 9.567848 GCCTTTTGATATAAAAATCGAGTGAAA 57.432 29.630 0.00 0.00 0.00 2.69
630 631 2.821307 ACGTAACGCTAGAGTACAGC 57.179 50.000 0.00 0.00 35.61 4.40
631 632 2.354259 ACGTAACGCTAGAGTACAGCT 58.646 47.619 0.00 0.00 36.86 4.24
632 633 2.746362 ACGTAACGCTAGAGTACAGCTT 59.254 45.455 0.00 0.00 36.86 3.74
633 634 3.190118 ACGTAACGCTAGAGTACAGCTTT 59.810 43.478 0.00 0.00 36.86 3.51
634 635 4.164294 CGTAACGCTAGAGTACAGCTTTT 58.836 43.478 0.00 0.00 36.86 2.27
635 636 4.620184 CGTAACGCTAGAGTACAGCTTTTT 59.380 41.667 0.00 0.00 36.86 1.94
660 661 3.768468 AGACAAACGCTAGAGTAGAGC 57.232 47.619 0.00 0.00 36.54 4.09
661 662 3.349022 AGACAAACGCTAGAGTAGAGCT 58.651 45.455 0.00 0.00 37.81 4.09
662 663 3.127895 AGACAAACGCTAGAGTAGAGCTG 59.872 47.826 0.00 0.00 37.81 4.24
663 664 2.189342 CAAACGCTAGAGTAGAGCTGC 58.811 52.381 0.00 0.00 37.81 5.25
664 665 1.757682 AACGCTAGAGTAGAGCTGCT 58.242 50.000 0.00 0.00 37.81 4.24
665 666 1.305201 ACGCTAGAGTAGAGCTGCTC 58.695 55.000 21.72 21.72 41.72 4.26
666 667 0.234625 CGCTAGAGTAGAGCTGCTCG 59.765 60.000 22.77 8.82 45.24 5.03
667 668 0.040425 GCTAGAGTAGAGCTGCTCGC 60.040 60.000 22.77 18.92 45.24 5.03
694 695 1.016130 GTGCTGCTTGCTAGAGCGAA 61.016 55.000 0.00 0.00 45.64 4.70
695 696 1.016130 TGCTGCTTGCTAGAGCGAAC 61.016 55.000 0.00 0.00 45.64 3.95
703 704 1.068588 TGCTAGAGCGAACTGTTGTGT 59.931 47.619 0.00 0.00 45.83 3.72
704 705 1.457303 GCTAGAGCGAACTGTTGTGTG 59.543 52.381 0.00 0.00 0.00 3.82
705 706 2.862530 GCTAGAGCGAACTGTTGTGTGA 60.863 50.000 0.00 0.00 0.00 3.58
706 707 2.309528 AGAGCGAACTGTTGTGTGAA 57.690 45.000 0.00 0.00 0.00 3.18
707 708 2.627945 AGAGCGAACTGTTGTGTGAAA 58.372 42.857 0.00 0.00 0.00 2.69
708 709 2.609459 AGAGCGAACTGTTGTGTGAAAG 59.391 45.455 0.00 0.00 0.00 2.62
709 710 2.351726 GAGCGAACTGTTGTGTGAAAGT 59.648 45.455 0.00 0.00 0.00 2.66
710 711 2.351726 AGCGAACTGTTGTGTGAAAGTC 59.648 45.455 0.00 0.00 0.00 3.01
711 712 2.845764 GCGAACTGTTGTGTGAAAGTCG 60.846 50.000 0.00 0.00 0.00 4.18
712 713 2.601314 CGAACTGTTGTGTGAAAGTCGA 59.399 45.455 0.00 0.00 0.00 4.20
719 720 1.591158 TGTGTGAAAGTCGAGCGTTTC 59.409 47.619 7.56 7.56 33.94 2.78
758 759 5.357257 CAATAGGCGCTCCTTCTTTACTAA 58.643 41.667 7.64 0.00 40.66 2.24
767 773 2.669924 CCTTCTTTACTAACCCGTTCGC 59.330 50.000 0.00 0.00 0.00 4.70
815 821 1.682005 CCATTGGCCGATGGGTTGT 60.682 57.895 36.54 0.00 42.36 3.32
816 822 1.666209 CCATTGGCCGATGGGTTGTC 61.666 60.000 36.54 0.00 42.36 3.18
817 823 1.748879 ATTGGCCGATGGGTTGTCG 60.749 57.895 4.07 0.00 38.75 4.35
818 824 2.478335 ATTGGCCGATGGGTTGTCGT 62.478 55.000 4.07 0.00 37.39 4.34
819 825 1.828461 TTGGCCGATGGGTTGTCGTA 61.828 55.000 0.00 0.00 37.39 3.43
820 826 1.520787 GGCCGATGGGTTGTCGTAG 60.521 63.158 0.00 0.00 37.39 3.51
821 827 2.171725 GCCGATGGGTTGTCGTAGC 61.172 63.158 0.00 0.00 37.39 3.58
822 828 1.520787 CCGATGGGTTGTCGTAGCC 60.521 63.158 0.00 0.00 37.39 3.93
1301 1364 3.197549 TCTGCTGATTGGCATGTACTGTA 59.802 43.478 0.00 0.00 41.63 2.74
1302 1365 3.534554 TGCTGATTGGCATGTACTGTAG 58.465 45.455 0.00 0.00 37.29 2.74
1303 1366 3.055167 TGCTGATTGGCATGTACTGTAGT 60.055 43.478 0.00 0.00 37.29 2.73
1304 1367 4.161377 TGCTGATTGGCATGTACTGTAGTA 59.839 41.667 0.00 0.00 37.29 1.82
1594 1660 1.009829 GATGTGTCCGTCAATCAGCC 58.990 55.000 0.00 0.00 0.00 4.85
1621 1688 9.809096 TGTAAATCTTTTGCAAATGTTTCAGTA 57.191 25.926 20.69 8.84 0.00 2.74
1655 1722 6.198687 GCATATACAAGTTAATGCGCTTTCA 58.801 36.000 12.27 0.00 35.81 2.69
1658 1725 9.071221 CATATACAAGTTAATGCGCTTTCAAAA 57.929 29.630 12.27 0.00 0.00 2.44
1693 1760 2.818274 GGCGGCCGAAGAACGAAT 60.818 61.111 33.48 0.00 45.77 3.34
1694 1761 1.519898 GGCGGCCGAAGAACGAATA 60.520 57.895 33.48 0.00 45.77 1.75
1696 1763 1.603678 GGCGGCCGAAGAACGAATATA 60.604 52.381 33.48 0.00 45.77 0.86
1697 1764 2.334838 GCGGCCGAAGAACGAATATAT 58.665 47.619 33.48 0.00 45.77 0.86
1698 1765 2.092211 GCGGCCGAAGAACGAATATATG 59.908 50.000 33.48 0.00 45.77 1.78
1702 1769 5.004440 CGGCCGAAGAACGAATATATGTATG 59.996 44.000 24.07 0.00 45.77 2.39
1746 1817 3.686622 TGAAGCGCTTCAGAACTGT 57.313 47.368 41.19 10.73 43.90 3.55
1782 2099 3.555586 CCATACATCCATGCTGTCGATCA 60.556 47.826 2.76 0.00 0.00 2.92
1783 2100 2.924757 ACATCCATGCTGTCGATCAT 57.075 45.000 0.00 0.00 0.00 2.45
1784 2101 5.413499 CATACATCCATGCTGTCGATCATA 58.587 41.667 2.76 0.00 0.00 2.15
1785 2102 4.548451 ACATCCATGCTGTCGATCATAT 57.452 40.909 0.00 0.00 0.00 1.78
1786 2103 4.502016 ACATCCATGCTGTCGATCATATC 58.498 43.478 0.00 0.00 0.00 1.63
1787 2104 4.020839 ACATCCATGCTGTCGATCATATCA 60.021 41.667 0.00 0.00 0.00 2.15
1789 2106 3.321682 TCCATGCTGTCGATCATATCACA 59.678 43.478 0.00 0.00 0.00 3.58
1791 2108 4.092968 CCATGCTGTCGATCATATCACATG 59.907 45.833 0.00 0.00 0.00 3.21
1792 2109 3.062042 TGCTGTCGATCATATCACATGC 58.938 45.455 0.00 0.00 0.00 4.06
1793 2110 3.062042 GCTGTCGATCATATCACATGCA 58.938 45.455 0.00 0.00 0.00 3.96
1804 2148 6.458210 TCATATCACATGCATAGTGGTGTAG 58.542 40.000 21.35 12.86 37.58 2.74
1842 2186 2.094494 TGTGCAACGGTGAAATTTGTGT 60.094 40.909 3.55 0.00 42.39 3.72
1880 2224 5.511571 TCGTAAAGAGATACTGATGAAGCG 58.488 41.667 0.00 0.00 0.00 4.68
1884 2228 3.561143 AGAGATACTGATGAAGCGAGGT 58.439 45.455 0.00 0.00 0.00 3.85
1893 2274 5.105310 ACTGATGAAGCGAGGTACTACATTT 60.105 40.000 0.00 0.00 41.55 2.32
1897 2278 5.168569 TGAAGCGAGGTACTACATTTTCAG 58.831 41.667 0.00 0.00 41.55 3.02
1901 2282 4.694037 GCGAGGTACTACATTTTCAGGTTT 59.306 41.667 0.00 0.00 41.55 3.27
1907 2288 9.582648 AGGTACTACATTTTCAGGTTTTACAAT 57.417 29.630 0.00 0.00 36.02 2.71
1914 2295 9.665719 ACATTTTCAGGTTTTACAATTCAACTT 57.334 25.926 0.00 0.00 0.00 2.66
1917 2298 9.712305 TTTTCAGGTTTTACAATTCAACTTTCA 57.288 25.926 0.00 0.00 0.00 2.69
1918 2299 8.696410 TTCAGGTTTTACAATTCAACTTTCAC 57.304 30.769 0.00 0.00 0.00 3.18
1919 2300 7.262048 TCAGGTTTTACAATTCAACTTTCACC 58.738 34.615 0.00 0.00 0.00 4.02
1920 2301 7.038659 CAGGTTTTACAATTCAACTTTCACCA 58.961 34.615 0.00 0.00 0.00 4.17
1921 2302 7.010091 CAGGTTTTACAATTCAACTTTCACCAC 59.990 37.037 0.00 0.00 0.00 4.16
1922 2303 6.020201 GGTTTTACAATTCAACTTTCACCACG 60.020 38.462 0.00 0.00 0.00 4.94
1923 2304 6.438259 TTTACAATTCAACTTTCACCACGA 57.562 33.333 0.00 0.00 0.00 4.35
1924 2305 4.287238 ACAATTCAACTTTCACCACGAC 57.713 40.909 0.00 0.00 0.00 4.34
1925 2306 3.692101 ACAATTCAACTTTCACCACGACA 59.308 39.130 0.00 0.00 0.00 4.35
1926 2307 4.156922 ACAATTCAACTTTCACCACGACAA 59.843 37.500 0.00 0.00 0.00 3.18
2052 2433 4.274705 CACATGCTTGTACCAGTTTGTGTA 59.725 41.667 16.48 0.00 33.76 2.90
2104 2491 7.597369 TGTGTAAACAGTGATACATACAGTGTC 59.403 37.037 0.00 0.00 46.71 3.67
2108 2495 4.457949 ACAGTGATACATACAGTGTCGTCA 59.542 41.667 0.00 0.00 45.07 4.35
2135 2522 6.544197 TCTTTGTAACATCTGGTGCAGTTTTA 59.456 34.615 0.00 0.00 32.61 1.52
2136 2523 6.892658 TTGTAACATCTGGTGCAGTTTTAT 57.107 33.333 0.00 0.00 32.61 1.40
2139 2526 7.812648 TGTAACATCTGGTGCAGTTTTATAAC 58.187 34.615 0.00 0.00 32.61 1.89
2143 2530 7.593825 ACATCTGGTGCAGTTTTATAACTTTC 58.406 34.615 0.00 0.00 41.85 2.62
2167 2555 5.721876 AAACGACGAAAACATCTTACACA 57.278 34.783 0.00 0.00 0.00 3.72
2323 2711 3.276846 GGCCACGACGCAAACTGT 61.277 61.111 0.00 0.00 0.00 3.55
2444 2832 2.289882 TGTCAACCATTCAGCTCTCAGG 60.290 50.000 0.00 0.00 0.00 3.86
2507 2901 5.116180 CAAGACCTCATAAATGCCGTAGAA 58.884 41.667 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 9.995003 ACTTGGCAATATTATGAAAACTTCAAA 57.005 25.926 0.00 0.00 43.95 2.69
87 88 9.995003 AACTTGGCAATATTATGAAAACTTCAA 57.005 25.926 0.00 0.00 43.95 2.69
88 89 9.995003 AAACTTGGCAATATTATGAAAACTTCA 57.005 25.926 0.00 0.00 45.01 3.02
98 99 9.884636 GGGAACTTTTAAACTTGGCAATATTAT 57.115 29.630 0.00 0.00 0.00 1.28
99 100 8.871125 TGGGAACTTTTAAACTTGGCAATATTA 58.129 29.630 0.00 0.42 0.00 0.98
100 101 7.740805 TGGGAACTTTTAAACTTGGCAATATT 58.259 30.769 0.00 1.46 0.00 1.28
101 102 7.234577 TCTGGGAACTTTTAAACTTGGCAATAT 59.765 33.333 0.00 0.00 0.00 1.28
102 103 6.551601 TCTGGGAACTTTTAAACTTGGCAATA 59.448 34.615 0.00 0.00 0.00 1.90
103 104 5.365314 TCTGGGAACTTTTAAACTTGGCAAT 59.635 36.000 0.00 0.00 0.00 3.56
104 105 4.712337 TCTGGGAACTTTTAAACTTGGCAA 59.288 37.500 0.00 0.00 0.00 4.52
105 106 4.282496 TCTGGGAACTTTTAAACTTGGCA 58.718 39.130 0.00 0.00 0.00 4.92
106 107 4.929819 TCTGGGAACTTTTAAACTTGGC 57.070 40.909 0.00 0.00 0.00 4.52
134 135 9.893634 TTGATAATCTCACGTTTTCCCTATTTA 57.106 29.630 0.00 0.00 32.17 1.40
135 136 8.801882 TTGATAATCTCACGTTTTCCCTATTT 57.198 30.769 0.00 0.00 32.17 1.40
136 137 8.801882 TTTGATAATCTCACGTTTTCCCTATT 57.198 30.769 0.00 0.00 32.17 1.73
137 138 8.801882 TTTTGATAATCTCACGTTTTCCCTAT 57.198 30.769 0.00 0.00 32.17 2.57
138 139 8.624367 TTTTTGATAATCTCACGTTTTCCCTA 57.376 30.769 0.00 0.00 32.17 3.53
139 140 7.519032 TTTTTGATAATCTCACGTTTTCCCT 57.481 32.000 0.00 0.00 32.17 4.20
160 161 9.394767 ACAAACTTTAGAATTGGCTTCATTTTT 57.605 25.926 0.00 0.00 36.24 1.94
161 162 8.962884 ACAAACTTTAGAATTGGCTTCATTTT 57.037 26.923 0.00 0.00 36.24 1.82
162 163 8.962884 AACAAACTTTAGAATTGGCTTCATTT 57.037 26.923 0.00 0.00 36.24 2.32
163 164 8.203485 TGAACAAACTTTAGAATTGGCTTCATT 58.797 29.630 0.00 0.00 36.24 2.57
164 165 7.725251 TGAACAAACTTTAGAATTGGCTTCAT 58.275 30.769 0.00 0.00 36.24 2.57
165 166 7.068103 TCTGAACAAACTTTAGAATTGGCTTCA 59.932 33.333 0.00 0.00 36.24 3.02
166 167 7.425606 TCTGAACAAACTTTAGAATTGGCTTC 58.574 34.615 0.00 0.00 0.00 3.86
167 168 7.346751 TCTGAACAAACTTTAGAATTGGCTT 57.653 32.000 0.00 0.00 0.00 4.35
168 169 6.959639 TCTGAACAAACTTTAGAATTGGCT 57.040 33.333 0.00 0.00 0.00 4.75
169 170 8.328146 GTTTTCTGAACAAACTTTAGAATTGGC 58.672 33.333 0.00 0.00 32.32 4.52
170 171 9.586435 AGTTTTCTGAACAAACTTTAGAATTGG 57.414 29.630 2.43 0.00 40.83 3.16
180 181 9.705290 AATGTTTACAAGTTTTCTGAACAAACT 57.295 25.926 2.43 2.43 44.67 2.66
183 184 9.482627 ACAAATGTTTACAAGTTTTCTGAACAA 57.517 25.926 0.00 0.00 0.00 2.83
241 242 9.453572 TGCTCATTTACTAGAAATTCAGAACAT 57.546 29.630 0.00 0.00 0.00 2.71
242 243 8.721478 GTGCTCATTTACTAGAAATTCAGAACA 58.279 33.333 0.00 0.00 0.00 3.18
243 244 8.721478 TGTGCTCATTTACTAGAAATTCAGAAC 58.279 33.333 0.00 3.07 0.00 3.01
244 245 8.846943 TGTGCTCATTTACTAGAAATTCAGAA 57.153 30.769 0.00 0.00 0.00 3.02
245 246 9.453572 AATGTGCTCATTTACTAGAAATTCAGA 57.546 29.630 8.17 0.00 40.88 3.27
281 282 9.932207 AACATGAGCATTTTCTGAAAATATGAA 57.068 25.926 27.04 16.61 38.97 2.57
282 283 9.932207 AAACATGAGCATTTTCTGAAAATATGA 57.068 25.926 27.04 16.55 38.97 2.15
284 285 9.932207 TGAAACATGAGCATTTTCTGAAAATAT 57.068 25.926 23.64 16.78 38.97 1.28
285 286 9.414295 CTGAAACATGAGCATTTTCTGAAAATA 57.586 29.630 23.64 11.93 38.97 1.40
286 287 8.145767 TCTGAAACATGAGCATTTTCTGAAAAT 58.854 29.630 19.79 19.79 41.57 1.82
287 288 7.490840 TCTGAAACATGAGCATTTTCTGAAAA 58.509 30.769 17.04 17.04 35.51 2.29
288 289 7.013559 TCTCTGAAACATGAGCATTTTCTGAAA 59.986 33.333 0.00 0.00 37.00 2.69
289 290 6.487668 TCTCTGAAACATGAGCATTTTCTGAA 59.512 34.615 0.00 0.00 37.00 3.02
290 291 5.999600 TCTCTGAAACATGAGCATTTTCTGA 59.000 36.000 0.00 7.34 36.42 3.27
291 292 6.072618 AGTCTCTGAAACATGAGCATTTTCTG 60.073 38.462 0.00 3.16 31.68 3.02
292 293 6.002704 AGTCTCTGAAACATGAGCATTTTCT 58.997 36.000 0.00 0.00 31.68 2.52
293 294 6.084925 CAGTCTCTGAAACATGAGCATTTTC 58.915 40.000 0.00 0.00 32.44 2.29
294 295 5.533903 ACAGTCTCTGAAACATGAGCATTTT 59.466 36.000 0.00 0.00 35.18 1.82
295 296 5.068636 ACAGTCTCTGAAACATGAGCATTT 58.931 37.500 0.00 0.00 35.18 2.32
296 297 4.649692 ACAGTCTCTGAAACATGAGCATT 58.350 39.130 0.00 0.00 35.18 3.56
297 298 4.283363 ACAGTCTCTGAAACATGAGCAT 57.717 40.909 0.00 0.00 35.18 3.79
298 299 3.758755 ACAGTCTCTGAAACATGAGCA 57.241 42.857 0.00 0.00 35.18 4.26
299 300 4.060900 TGAACAGTCTCTGAAACATGAGC 58.939 43.478 0.00 0.00 35.18 4.26
300 301 5.052481 TGTGAACAGTCTCTGAAACATGAG 58.948 41.667 0.00 0.00 35.18 2.90
301 302 5.022282 TGTGAACAGTCTCTGAAACATGA 57.978 39.130 0.00 0.00 35.18 3.07
302 303 5.739752 TTGTGAACAGTCTCTGAAACATG 57.260 39.130 3.70 0.00 35.18 3.21
303 304 6.949352 ATTTGTGAACAGTCTCTGAAACAT 57.051 33.333 3.70 0.00 35.18 2.71
304 305 6.757897 AATTTGTGAACAGTCTCTGAAACA 57.242 33.333 3.70 2.72 35.18 2.83
305 306 9.567848 TTAAAATTTGTGAACAGTCTCTGAAAC 57.432 29.630 3.70 0.43 35.18 2.78
331 332 9.768662 ACATTGCTTTCAAATTGAGACTATTTT 57.231 25.926 0.00 0.00 35.56 1.82
332 333 9.768662 AACATTGCTTTCAAATTGAGACTATTT 57.231 25.926 0.00 0.00 35.56 1.40
333 334 9.415544 GAACATTGCTTTCAAATTGAGACTATT 57.584 29.630 0.00 0.00 35.56 1.73
334 335 8.579006 TGAACATTGCTTTCAAATTGAGACTAT 58.421 29.630 0.00 0.00 35.56 2.12
335 336 7.939782 TGAACATTGCTTTCAAATTGAGACTA 58.060 30.769 0.00 0.00 35.56 2.59
336 337 6.808829 TGAACATTGCTTTCAAATTGAGACT 58.191 32.000 0.00 0.00 35.56 3.24
337 338 7.170320 ACATGAACATTGCTTTCAAATTGAGAC 59.830 33.333 0.00 0.00 36.57 3.36
338 339 7.211573 ACATGAACATTGCTTTCAAATTGAGA 58.788 30.769 0.00 0.00 36.57 3.27
339 340 7.416154 ACATGAACATTGCTTTCAAATTGAG 57.584 32.000 0.00 0.00 36.57 3.02
340 341 7.789273 AACATGAACATTGCTTTCAAATTGA 57.211 28.000 0.00 0.00 36.57 2.57
341 342 8.844441 AAAACATGAACATTGCTTTCAAATTG 57.156 26.923 0.00 0.00 36.57 2.32
354 355 9.881529 GTGCATTGATTTTAAAAACATGAACAT 57.118 25.926 11.18 0.21 0.00 2.71
355 356 8.060679 CGTGCATTGATTTTAAAAACATGAACA 58.939 29.630 19.11 11.32 0.00 3.18
356 357 8.061268 ACGTGCATTGATTTTAAAAACATGAAC 58.939 29.630 11.18 12.66 0.00 3.18
357 358 8.136057 ACGTGCATTGATTTTAAAAACATGAA 57.864 26.923 11.18 3.52 0.00 2.57
358 359 7.706281 ACGTGCATTGATTTTAAAAACATGA 57.294 28.000 11.18 0.00 0.00 3.07
359 360 8.765044 AAACGTGCATTGATTTTAAAAACATG 57.235 26.923 11.18 10.92 0.00 3.21
361 362 9.302345 TCTAAACGTGCATTGATTTTAAAAACA 57.698 25.926 4.44 5.73 0.00 2.83
391 392 8.149647 TCCAGCATTCTTTGATATTGTGTTTTT 58.850 29.630 0.00 0.00 0.00 1.94
392 393 7.669427 TCCAGCATTCTTTGATATTGTGTTTT 58.331 30.769 0.00 0.00 0.00 2.43
393 394 7.039504 ACTCCAGCATTCTTTGATATTGTGTTT 60.040 33.333 0.00 0.00 0.00 2.83
394 395 6.435277 ACTCCAGCATTCTTTGATATTGTGTT 59.565 34.615 0.00 0.00 0.00 3.32
395 396 5.948162 ACTCCAGCATTCTTTGATATTGTGT 59.052 36.000 0.00 0.00 0.00 3.72
396 397 6.446781 ACTCCAGCATTCTTTGATATTGTG 57.553 37.500 0.00 0.00 0.00 3.33
397 398 7.472334 AAACTCCAGCATTCTTTGATATTGT 57.528 32.000 0.00 0.00 0.00 2.71
398 399 8.767478 AAAAACTCCAGCATTCTTTGATATTG 57.233 30.769 0.00 0.00 0.00 1.90
507 508 8.091449 TCCGCATTTTTAGGATAACATGTTTTT 58.909 29.630 17.78 4.84 0.00 1.94
508 509 7.607250 TCCGCATTTTTAGGATAACATGTTTT 58.393 30.769 17.78 9.08 0.00 2.43
509 510 7.164230 TCCGCATTTTTAGGATAACATGTTT 57.836 32.000 17.78 4.68 0.00 2.83
510 511 6.767524 TCCGCATTTTTAGGATAACATGTT 57.232 33.333 16.68 16.68 0.00 2.71
511 512 6.959639 ATCCGCATTTTTAGGATAACATGT 57.040 33.333 0.00 0.00 42.47 3.21
512 513 9.398170 CTAAATCCGCATTTTTAGGATAACATG 57.602 33.333 0.00 0.00 43.39 3.21
513 514 9.131791 ACTAAATCCGCATTTTTAGGATAACAT 57.868 29.630 11.65 0.00 43.39 2.71
514 515 8.514330 ACTAAATCCGCATTTTTAGGATAACA 57.486 30.769 11.65 0.00 43.39 2.41
519 520 9.796120 CAATTTACTAAATCCGCATTTTTAGGA 57.204 29.630 11.65 3.31 38.93 2.94
520 521 8.539674 GCAATTTACTAAATCCGCATTTTTAGG 58.460 33.333 11.65 0.00 38.93 2.69
521 522 8.539674 GGCAATTTACTAAATCCGCATTTTTAG 58.460 33.333 13.76 7.40 39.95 1.85
522 523 8.254508 AGGCAATTTACTAAATCCGCATTTTTA 58.745 29.630 13.76 0.00 33.95 1.52
523 524 7.102993 AGGCAATTTACTAAATCCGCATTTTT 58.897 30.769 13.76 0.00 33.95 1.94
524 525 6.639563 AGGCAATTTACTAAATCCGCATTTT 58.360 32.000 13.76 0.00 33.95 1.82
525 526 6.220726 AGGCAATTTACTAAATCCGCATTT 57.779 33.333 13.76 0.00 36.18 2.32
526 527 5.852282 AGGCAATTTACTAAATCCGCATT 57.148 34.783 13.76 3.91 33.32 3.56
527 528 6.062095 AGTAGGCAATTTACTAAATCCGCAT 58.938 36.000 13.76 10.80 33.32 4.73
528 529 5.433526 AGTAGGCAATTTACTAAATCCGCA 58.566 37.500 13.76 0.00 33.32 5.69
529 530 7.668525 ATAGTAGGCAATTTACTAAATCCGC 57.331 36.000 0.77 7.10 37.22 5.54
544 545 9.891828 CGAATAATTATGCAAAAATAGTAGGCA 57.108 29.630 4.29 0.00 39.03 4.75
545 546 8.850452 GCGAATAATTATGCAAAAATAGTAGGC 58.150 33.333 4.29 0.00 0.00 3.93
546 547 9.341899 GGCGAATAATTATGCAAAAATAGTAGG 57.658 33.333 4.29 0.00 0.00 3.18
549 550 9.816354 AAAGGCGAATAATTATGCAAAAATAGT 57.184 25.926 4.29 0.00 0.00 2.12
552 553 9.160496 TCAAAAGGCGAATAATTATGCAAAAAT 57.840 25.926 4.29 0.00 0.00 1.82
553 554 8.539770 TCAAAAGGCGAATAATTATGCAAAAA 57.460 26.923 4.29 0.00 0.00 1.94
554 555 8.715191 ATCAAAAGGCGAATAATTATGCAAAA 57.285 26.923 4.29 0.00 0.00 2.44
555 556 9.979578 ATATCAAAAGGCGAATAATTATGCAAA 57.020 25.926 4.29 0.00 0.00 3.68
566 567 8.621286 ACTCGATTTTTATATCAAAAGGCGAAT 58.379 29.630 16.67 9.51 36.64 3.34
567 568 7.908082 CACTCGATTTTTATATCAAAAGGCGAA 59.092 33.333 16.67 7.50 36.64 4.70
568 569 7.279090 TCACTCGATTTTTATATCAAAAGGCGA 59.721 33.333 15.79 15.79 35.64 5.54
569 570 7.406553 TCACTCGATTTTTATATCAAAAGGCG 58.593 34.615 11.12 11.12 32.73 5.52
570 571 9.567848 TTTCACTCGATTTTTATATCAAAAGGC 57.432 29.630 1.65 0.00 0.00 4.35
607 608 4.383948 GCTGTACTCTAGCGTTACGTTTTT 59.616 41.667 6.63 0.00 0.00 1.94
608 609 3.916776 GCTGTACTCTAGCGTTACGTTTT 59.083 43.478 6.63 0.00 0.00 2.43
609 610 3.190118 AGCTGTACTCTAGCGTTACGTTT 59.810 43.478 6.63 0.00 45.61 3.60
610 611 2.746362 AGCTGTACTCTAGCGTTACGTT 59.254 45.455 6.63 2.32 45.61 3.99
611 612 2.354259 AGCTGTACTCTAGCGTTACGT 58.646 47.619 6.63 0.00 45.61 3.57
612 613 3.402058 AAGCTGTACTCTAGCGTTACG 57.598 47.619 0.00 0.00 45.61 3.18
635 636 6.585322 GCTCTACTCTAGCGTTTGTCTAAAAA 59.415 38.462 0.00 0.00 0.00 1.94
636 637 6.072064 AGCTCTACTCTAGCGTTTGTCTAAAA 60.072 38.462 0.00 0.00 44.87 1.52
637 638 5.415077 AGCTCTACTCTAGCGTTTGTCTAAA 59.585 40.000 0.00 0.00 44.87 1.85
638 639 4.942483 AGCTCTACTCTAGCGTTTGTCTAA 59.058 41.667 0.00 0.00 44.87 2.10
639 640 4.333095 CAGCTCTACTCTAGCGTTTGTCTA 59.667 45.833 0.00 0.00 44.87 2.59
640 641 3.127895 CAGCTCTACTCTAGCGTTTGTCT 59.872 47.826 0.00 0.00 44.87 3.41
641 642 3.430931 CAGCTCTACTCTAGCGTTTGTC 58.569 50.000 0.00 0.00 44.87 3.18
642 643 2.416162 GCAGCTCTACTCTAGCGTTTGT 60.416 50.000 0.00 0.00 44.87 2.83
643 644 2.159310 AGCAGCTCTACTCTAGCGTTTG 60.159 50.000 0.00 0.00 44.87 2.93
644 645 2.096248 AGCAGCTCTACTCTAGCGTTT 58.904 47.619 0.00 0.00 44.87 3.60
645 646 1.673920 GAGCAGCTCTACTCTAGCGTT 59.326 52.381 15.78 0.00 44.87 4.84
646 647 1.305201 GAGCAGCTCTACTCTAGCGT 58.695 55.000 15.78 0.00 44.87 5.07
647 648 0.234625 CGAGCAGCTCTACTCTAGCG 59.765 60.000 20.39 0.22 44.87 4.26
648 649 0.040425 GCGAGCAGCTCTACTCTAGC 60.040 60.000 20.39 10.35 44.04 3.42
660 661 0.453793 AGCACTACTGTAGCGAGCAG 59.546 55.000 21.52 4.16 39.67 4.24
661 662 0.171231 CAGCACTACTGTAGCGAGCA 59.829 55.000 21.52 0.00 41.86 4.26
662 663 2.950877 CAGCACTACTGTAGCGAGC 58.049 57.895 14.55 15.07 41.86 5.03
682 683 2.135139 CACAACAGTTCGCTCTAGCAA 58.865 47.619 2.44 0.00 42.21 3.91
694 695 1.933853 GCTCGACTTTCACACAACAGT 59.066 47.619 0.00 0.00 0.00 3.55
695 696 1.071239 CGCTCGACTTTCACACAACAG 60.071 52.381 0.00 0.00 0.00 3.16
730 731 1.614241 AAGGAGCGCCTATTGGACGT 61.614 55.000 10.31 0.00 46.28 4.34
732 733 0.466124 AGAAGGAGCGCCTATTGGAC 59.534 55.000 10.31 0.00 46.28 4.02
799 805 1.748879 CGACAACCCATCGGCCAAT 60.749 57.895 2.24 0.00 35.92 3.16
812 818 2.485677 CCCTACGAGGCTACGACAA 58.514 57.895 12.16 0.00 32.73 3.18
821 827 1.325476 AACCGTTAGGCCCTACGAGG 61.325 60.000 24.24 13.34 42.76 4.63
822 828 1.392589 TAACCGTTAGGCCCTACGAG 58.607 55.000 24.24 17.21 42.76 4.18
903 937 3.312697 GGCGTTTGTCTTATCCATTCTCC 59.687 47.826 0.00 0.00 0.00 3.71
966 1000 0.969917 GACTGGAGAGGCTCAGCTCA 60.970 60.000 18.26 7.95 32.83 4.26
967 1001 0.684153 AGACTGGAGAGGCTCAGCTC 60.684 60.000 18.26 5.44 27.05 4.09
968 1002 1.387737 AGACTGGAGAGGCTCAGCT 59.612 57.895 18.26 5.24 27.05 4.24
969 1003 4.032653 AGACTGGAGAGGCTCAGC 57.967 61.111 18.26 8.07 27.05 4.26
1594 1660 8.819974 ACTGAAACATTTGCAAAAGATTTACAG 58.180 29.630 20.40 22.07 0.00 2.74
1680 1747 6.946229 ACATACATATATTCGTTCTTCGGC 57.054 37.500 0.00 0.00 40.32 5.54
1782 2099 6.041979 TCACTACACCACTATGCATGTGATAT 59.958 38.462 22.76 13.38 37.60 1.63
1783 2100 5.362430 TCACTACACCACTATGCATGTGATA 59.638 40.000 22.76 14.12 37.60 2.15
1784 2101 4.162131 TCACTACACCACTATGCATGTGAT 59.838 41.667 22.76 9.70 37.60 3.06
1785 2102 3.513515 TCACTACACCACTATGCATGTGA 59.486 43.478 22.76 15.43 37.60 3.58
1786 2103 3.618594 GTCACTACACCACTATGCATGTG 59.381 47.826 10.16 14.78 35.39 3.21
1787 2104 3.515502 AGTCACTACACCACTATGCATGT 59.484 43.478 10.16 0.88 0.00 3.21
1789 2106 5.932619 TTAGTCACTACACCACTATGCAT 57.067 39.130 3.79 3.79 0.00 3.96
1791 2108 5.902681 TCATTAGTCACTACACCACTATGC 58.097 41.667 0.00 0.00 0.00 3.14
1792 2109 7.334844 TCTCATTAGTCACTACACCACTATG 57.665 40.000 0.00 0.00 0.00 2.23
1793 2110 7.956328 TTCTCATTAGTCACTACACCACTAT 57.044 36.000 0.00 0.00 0.00 2.12
1804 2148 5.673337 TGCACAACTTTCTCATTAGTCAC 57.327 39.130 0.00 0.00 0.00 3.67
1858 2202 5.511571 TCGCTTCATCAGTATCTCTTTACG 58.488 41.667 0.00 0.00 0.00 3.18
1880 2224 8.611654 TGTAAAACCTGAAAATGTAGTACCTC 57.388 34.615 0.00 0.00 0.00 3.85
1893 2274 7.762159 GGTGAAAGTTGAATTGTAAAACCTGAA 59.238 33.333 0.00 0.00 0.00 3.02
1897 2278 6.020201 CGTGGTGAAAGTTGAATTGTAAAACC 60.020 38.462 0.00 0.00 0.00 3.27
1901 2282 5.354513 TGTCGTGGTGAAAGTTGAATTGTAA 59.645 36.000 0.00 0.00 0.00 2.41
1907 2288 3.340034 AGTTGTCGTGGTGAAAGTTGAA 58.660 40.909 0.00 0.00 0.00 2.69
1908 2289 2.980568 AGTTGTCGTGGTGAAAGTTGA 58.019 42.857 0.00 0.00 0.00 3.18
1909 2290 3.247648 CCTAGTTGTCGTGGTGAAAGTTG 59.752 47.826 0.00 0.00 0.00 3.16
1910 2291 3.463944 CCTAGTTGTCGTGGTGAAAGTT 58.536 45.455 0.00 0.00 0.00 2.66
1911 2292 2.224209 CCCTAGTTGTCGTGGTGAAAGT 60.224 50.000 0.00 0.00 0.00 2.66
1912 2293 2.036733 TCCCTAGTTGTCGTGGTGAAAG 59.963 50.000 0.00 0.00 0.00 2.62
1913 2294 2.036733 CTCCCTAGTTGTCGTGGTGAAA 59.963 50.000 0.00 0.00 0.00 2.69
1914 2295 1.616865 CTCCCTAGTTGTCGTGGTGAA 59.383 52.381 0.00 0.00 0.00 3.18
1915 2296 1.202964 TCTCCCTAGTTGTCGTGGTGA 60.203 52.381 0.00 0.00 0.00 4.02
1916 2297 1.254026 TCTCCCTAGTTGTCGTGGTG 58.746 55.000 0.00 0.00 0.00 4.17
1917 2298 1.893801 CTTCTCCCTAGTTGTCGTGGT 59.106 52.381 0.00 0.00 0.00 4.16
1918 2299 1.404315 GCTTCTCCCTAGTTGTCGTGG 60.404 57.143 0.00 0.00 0.00 4.94
1919 2300 1.272490 TGCTTCTCCCTAGTTGTCGTG 59.728 52.381 0.00 0.00 0.00 4.35
1920 2301 1.629043 TGCTTCTCCCTAGTTGTCGT 58.371 50.000 0.00 0.00 0.00 4.34
1921 2302 2.743636 TTGCTTCTCCCTAGTTGTCG 57.256 50.000 0.00 0.00 0.00 4.35
1922 2303 7.040686 TGTTTATTTTGCTTCTCCCTAGTTGTC 60.041 37.037 0.00 0.00 0.00 3.18
1923 2304 6.775629 TGTTTATTTTGCTTCTCCCTAGTTGT 59.224 34.615 0.00 0.00 0.00 3.32
1924 2305 7.174946 TCTGTTTATTTTGCTTCTCCCTAGTTG 59.825 37.037 0.00 0.00 0.00 3.16
1925 2306 7.175119 GTCTGTTTATTTTGCTTCTCCCTAGTT 59.825 37.037 0.00 0.00 0.00 2.24
1926 2307 6.655425 GTCTGTTTATTTTGCTTCTCCCTAGT 59.345 38.462 0.00 0.00 0.00 2.57
1977 2358 8.752005 TGTAATAAGCTGGAATAAATGCTTCT 57.248 30.769 2.24 0.00 43.55 2.85
2052 2433 3.067180 CACAAACACCTCTTGCTTGACAT 59.933 43.478 0.00 0.00 35.23 3.06
2104 2491 5.621422 CACCAGATGTTACAAAGAATGACG 58.379 41.667 0.00 0.00 0.00 4.35
2108 2495 5.072741 ACTGCACCAGATGTTACAAAGAAT 58.927 37.500 0.00 0.00 35.18 2.40
2135 2522 8.126700 AGATGTTTTCGTCGTTTTGAAAGTTAT 58.873 29.630 0.00 0.00 40.47 1.89
2136 2523 7.465989 AGATGTTTTCGTCGTTTTGAAAGTTA 58.534 30.769 0.00 0.00 40.47 2.24
2139 2526 6.790336 AAGATGTTTTCGTCGTTTTGAAAG 57.210 33.333 0.00 0.00 40.47 2.62
2143 2530 5.960683 TGTGTAAGATGTTTTCGTCGTTTTG 59.039 36.000 0.00 0.00 40.47 2.44
2167 2555 1.465794 GCTAGACGGAGACAGGTCTT 58.534 55.000 3.07 0.00 43.02 3.01
2323 2711 2.681064 GCCATTTGCCAGCCAGGA 60.681 61.111 0.00 0.00 41.22 3.86
2444 2832 4.351192 TCTTTCTTTGCTTTGCGTTTCTC 58.649 39.130 0.00 0.00 0.00 2.87
2507 2901 1.198759 ACACGGTAAGGCAGGATGGT 61.199 55.000 0.00 0.00 35.86 3.55


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

AutoCloner maintained by Alex Coulton.