Multiple sequence alignment - TraesCS3A01G206300

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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 TraesCS3A01G206300 chr3A 100.000 4716 0 0 1 4716 362905623 362900908 0.000000e+00 8709.0
1 TraesCS3A01G206300 chr3A 87.698 252 26 4 1 249 685766743 685766494 5.970000e-74 289.0
2 TraesCS3A01G206300 chr3A 85.199 277 29 11 14 282 580810934 580810662 1.670000e-69 274.0
3 TraesCS3A01G206300 chr3A 86.454 251 26 8 2 249 685766845 685766600 7.780000e-68 268.0
4 TraesCS3A01G206300 chr3A 86.179 123 15 2 280 401 77405027 77404906 1.060000e-26 132.0
5 TraesCS3A01G206300 chr3D 92.711 3416 144 36 592 3953 276746913 276750277 0.000000e+00 4831.0
6 TraesCS3A01G206300 chr3D 95.882 777 22 4 3939 4715 276750294 276751060 0.000000e+00 1249.0
7 TraesCS3A01G206300 chr3D 77.778 468 66 28 1 452 603938569 603939014 2.180000e-63 254.0
8 TraesCS3A01G206300 chr3B 94.252 2105 94 15 1862 3952 373624544 373622453 0.000000e+00 3192.0
9 TraesCS3A01G206300 chr3B 88.595 1096 49 27 817 1876 373625649 373624594 0.000000e+00 1262.0
10 TraesCS3A01G206300 chr3B 93.724 733 36 5 3939 4670 373622426 373621703 0.000000e+00 1090.0
11 TraesCS3A01G206300 chr5D 89.388 245 24 2 5 249 429933437 429933195 1.650000e-79 307.0
12 TraesCS3A01G206300 chr5D 94.737 38 2 0 505 542 495913694 495913657 5.100000e-05 60.2
13 TraesCS3A01G206300 chr7D 87.649 251 28 3 4 253 72769553 72769305 5.970000e-74 289.0
14 TraesCS3A01G206300 chr7D 91.743 109 6 2 271 378 146998250 146998144 1.060000e-31 148.0
15 TraesCS3A01G206300 chr7D 92.381 105 6 1 274 378 607031886 607031988 1.060000e-31 148.0
16 TraesCS3A01G206300 chr5B 87.402 254 29 3 1 253 127708813 127708562 5.970000e-74 289.0
17 TraesCS3A01G206300 chr1B 87.600 250 27 4 2 248 363448239 363447991 2.150000e-73 287.0
18 TraesCS3A01G206300 chr6B 87.449 247 30 1 6 252 641416255 641416010 2.780000e-72 283.0
19 TraesCS3A01G206300 chr6B 93.939 99 6 0 279 377 693916545 693916447 2.940000e-32 150.0
20 TraesCS3A01G206300 chr4D 85.338 266 28 8 1 263 434101140 434100883 1.010000e-66 265.0
21 TraesCS3A01G206300 chr1A 94.898 98 5 0 281 378 204418826 204418923 2.270000e-33 154.0
22 TraesCS3A01G206300 chr1A 78.995 219 35 9 163 377 590991745 590991956 6.360000e-29 139.0
23 TraesCS3A01G206300 chr5A 93.069 101 7 0 281 381 229487923 229487823 1.060000e-31 148.0
24 TraesCS3A01G206300 chr5A 89.815 108 11 0 281 388 51677551 51677444 6.360000e-29 139.0
25 TraesCS3A01G206300 chr5A 88.182 110 10 3 280 387 1250587 1250479 1.380000e-25 128.0
26 TraesCS3A01G206300 chr7B 80.102 196 19 12 376 553 400135954 400135761 1.380000e-25 128.0
27 TraesCS3A01G206300 chr4A 92.405 79 4 1 375 451 57445593 57445515 1.390000e-20 111.0


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 TraesCS3A01G206300 chr3A 362900908 362905623 4715 True 8709 8709 100.000000 1 4716 1 chr3A.!!$R2 4715
1 TraesCS3A01G206300 chr3D 276746913 276751060 4147 False 3040 4831 94.296500 592 4715 2 chr3D.!!$F2 4123
2 TraesCS3A01G206300 chr3B 373621703 373625649 3946 True 1848 3192 92.190333 817 4670 3 chr3B.!!$R1 3853

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
510 511 0.175760 CGAACCATCATGGGAGACGT 59.824 55.000 9.04 0.0 43.37 4.34 F
1852 1926 0.392461 GCTGTGGCAATACGAGGGAA 60.392 55.000 0.00 0.0 38.54 3.97 F
2114 2256 1.349026 ACAGGACCTGTGGTTGATCTG 59.651 52.381 26.61 0.0 43.63 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2223 0.107654 GTCCTGTACCCACTGATGGC 60.108 60.000 0.0 0.0 45.76 4.40 R
2863 3010 2.225467 GCTATGGCCCAGATGAGTTTC 58.775 52.381 0.0 0.0 0.00 2.78 R
3769 3921 2.410262 CGACAACGCAGCTCAAAACTAG 60.410 50.000 0.0 0.0 0.00 2.57 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
289 290 9.708092 GAATAGTGTTTATTGTATACTCCCTCC 57.292 37.037 4.17 0.00 0.00 4.30
290 291 6.158023 AGTGTTTATTGTATACTCCCTCCG 57.842 41.667 4.17 0.00 0.00 4.63
291 292 5.659971 AGTGTTTATTGTATACTCCCTCCGT 59.340 40.000 4.17 0.00 0.00 4.69
292 293 5.981915 GTGTTTATTGTATACTCCCTCCGTC 59.018 44.000 4.17 0.00 0.00 4.79
293 294 5.069516 TGTTTATTGTATACTCCCTCCGTCC 59.930 44.000 4.17 0.00 0.00 4.79
294 295 2.077687 TTGTATACTCCCTCCGTCCC 57.922 55.000 4.17 0.00 0.00 4.46
295 296 0.928505 TGTATACTCCCTCCGTCCCA 59.071 55.000 4.17 0.00 0.00 4.37
296 297 1.288633 TGTATACTCCCTCCGTCCCAA 59.711 52.381 4.17 0.00 0.00 4.12
297 298 2.292389 TGTATACTCCCTCCGTCCCAAA 60.292 50.000 4.17 0.00 0.00 3.28
298 299 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
299 300 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
300 301 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
301 302 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
302 303 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
303 304 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
304 305 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
305 306 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
306 307 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
307 308 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
308 309 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
309 310 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
310 311 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
311 312 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
312 313 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
313 314 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
314 315 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
315 316 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
316 317 8.793592 GTCCCAAAATAAGTGACTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
348 349 6.281848 TGTCTTAAAGTTAGTGCAAAGTCG 57.718 37.500 0.00 0.00 0.00 4.18
349 350 6.044046 TGTCTTAAAGTTAGTGCAAAGTCGA 58.956 36.000 0.00 0.00 0.00 4.20
350 351 6.200286 TGTCTTAAAGTTAGTGCAAAGTCGAG 59.800 38.462 0.00 0.00 0.00 4.04
351 352 6.200475 GTCTTAAAGTTAGTGCAAAGTCGAGT 59.800 38.462 0.00 0.00 0.00 4.18
352 353 6.420008 TCTTAAAGTTAGTGCAAAGTCGAGTC 59.580 38.462 0.00 0.00 0.00 3.36
353 354 3.728076 AGTTAGTGCAAAGTCGAGTCA 57.272 42.857 0.00 0.00 0.00 3.41
354 355 3.381949 AGTTAGTGCAAAGTCGAGTCAC 58.618 45.455 0.00 0.00 0.00 3.67
355 356 3.068307 AGTTAGTGCAAAGTCGAGTCACT 59.932 43.478 15.12 15.12 40.60 3.41
356 357 2.604046 AGTGCAAAGTCGAGTCACTT 57.396 45.000 7.15 3.11 38.30 3.16
357 358 3.728076 AGTGCAAAGTCGAGTCACTTA 57.272 42.857 7.15 0.00 35.45 2.24
358 359 4.054780 AGTGCAAAGTCGAGTCACTTAA 57.945 40.909 7.15 0.00 35.45 1.85
359 360 4.632153 AGTGCAAAGTCGAGTCACTTAAT 58.368 39.130 7.15 0.00 35.45 1.40
360 361 5.057149 AGTGCAAAGTCGAGTCACTTAATT 58.943 37.500 7.15 0.00 35.45 1.40
361 362 5.527582 AGTGCAAAGTCGAGTCACTTAATTT 59.472 36.000 7.15 0.00 35.45 1.82
362 363 5.621228 GTGCAAAGTCGAGTCACTTAATTTG 59.379 40.000 8.78 8.78 35.45 2.32
363 364 5.525745 TGCAAAGTCGAGTCACTTAATTTGA 59.474 36.000 14.67 2.25 35.45 2.69
364 365 6.074005 GCAAAGTCGAGTCACTTAATTTGAG 58.926 40.000 14.67 0.00 35.45 3.02
365 366 6.073765 GCAAAGTCGAGTCACTTAATTTGAGA 60.074 38.462 14.67 0.00 35.45 3.27
366 367 7.284351 CAAAGTCGAGTCACTTAATTTGAGAC 58.716 38.462 7.80 0.00 35.45 3.36
367 368 5.154932 AGTCGAGTCACTTAATTTGAGACG 58.845 41.667 0.00 0.00 34.56 4.18
368 369 4.323868 GTCGAGTCACTTAATTTGAGACGG 59.676 45.833 0.00 0.00 34.56 4.79
369 370 4.216902 TCGAGTCACTTAATTTGAGACGGA 59.783 41.667 0.00 0.00 34.56 4.69
370 371 4.559251 CGAGTCACTTAATTTGAGACGGAG 59.441 45.833 0.00 0.00 34.56 4.63
371 372 4.822026 AGTCACTTAATTTGAGACGGAGG 58.178 43.478 0.00 0.00 34.56 4.30
372 373 3.933332 GTCACTTAATTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
373 374 3.835978 TCACTTAATTTGAGACGGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
374 375 4.081642 TCACTTAATTTGAGACGGAGGGAG 60.082 45.833 0.00 0.00 0.00 4.30
375 376 3.838903 ACTTAATTTGAGACGGAGGGAGT 59.161 43.478 0.00 0.00 0.00 3.85
376 377 5.021458 ACTTAATTTGAGACGGAGGGAGTA 58.979 41.667 0.00 0.00 0.00 2.59
377 378 5.661759 ACTTAATTTGAGACGGAGGGAGTAT 59.338 40.000 0.00 0.00 0.00 2.12
378 379 6.837568 ACTTAATTTGAGACGGAGGGAGTATA 59.162 38.462 0.00 0.00 0.00 1.47
379 380 7.509659 ACTTAATTTGAGACGGAGGGAGTATAT 59.490 37.037 0.00 0.00 0.00 0.86
380 381 8.945195 TTAATTTGAGACGGAGGGAGTATATA 57.055 34.615 0.00 0.00 0.00 0.86
381 382 9.543231 TTAATTTGAGACGGAGGGAGTATATAT 57.457 33.333 0.00 0.00 0.00 0.86
382 383 6.835819 TTTGAGACGGAGGGAGTATATATG 57.164 41.667 0.00 0.00 0.00 1.78
383 384 5.516059 TGAGACGGAGGGAGTATATATGT 57.484 43.478 0.00 0.00 0.00 2.29
384 385 6.631763 TGAGACGGAGGGAGTATATATGTA 57.368 41.667 0.00 0.00 0.00 2.29
385 386 6.651086 TGAGACGGAGGGAGTATATATGTAG 58.349 44.000 0.00 0.00 0.00 2.74
386 387 6.442885 TGAGACGGAGGGAGTATATATGTAGA 59.557 42.308 0.00 0.00 0.00 2.59
387 388 7.037802 TGAGACGGAGGGAGTATATATGTAGAA 60.038 40.741 0.00 0.00 0.00 2.10
388 389 7.874252 AGACGGAGGGAGTATATATGTAGAAT 58.126 38.462 0.00 0.00 0.00 2.40
389 390 9.000978 AGACGGAGGGAGTATATATGTAGAATA 57.999 37.037 0.00 0.00 0.00 1.75
390 391 9.796180 GACGGAGGGAGTATATATGTAGAATAT 57.204 37.037 0.00 0.00 0.00 1.28
469 470 4.455070 AAAAGACCTAGAAAACAGGCCT 57.545 40.909 0.00 0.00 36.57 5.19
470 471 4.455070 AAAGACCTAGAAAACAGGCCTT 57.545 40.909 0.00 0.00 37.46 4.35
471 472 4.455070 AAGACCTAGAAAACAGGCCTTT 57.545 40.909 0.00 0.00 32.53 3.11
472 473 3.756117 AGACCTAGAAAACAGGCCTTTG 58.244 45.455 0.00 0.00 36.57 2.77
473 474 2.229062 GACCTAGAAAACAGGCCTTTGC 59.771 50.000 0.00 0.00 36.57 3.68
486 487 4.408821 TTTGCCTCCCGCGCTGAT 62.409 61.111 5.56 0.00 42.08 2.90
497 498 4.776322 CGCTGATGGGCCGAACCA 62.776 66.667 0.00 0.45 46.24 3.67
503 504 2.275089 TGGGCCGAACCATCATGG 59.725 61.111 0.54 0.54 45.02 3.66
504 505 2.519302 GGGCCGAACCATCATGGG 60.519 66.667 9.04 0.00 43.37 4.00
505 506 2.595095 GGCCGAACCATCATGGGA 59.405 61.111 9.04 0.00 43.37 4.37
506 507 1.526917 GGCCGAACCATCATGGGAG 60.527 63.158 9.04 0.00 43.37 4.30
507 508 1.526887 GCCGAACCATCATGGGAGA 59.473 57.895 9.04 0.00 43.37 3.71
508 509 0.815615 GCCGAACCATCATGGGAGAC 60.816 60.000 9.04 0.00 43.37 3.36
509 510 0.530650 CCGAACCATCATGGGAGACG 60.531 60.000 9.04 7.75 43.37 4.18
510 511 0.175760 CGAACCATCATGGGAGACGT 59.824 55.000 9.04 0.00 43.37 4.34
511 512 1.405526 CGAACCATCATGGGAGACGTT 60.406 52.381 9.04 0.00 43.37 3.99
512 513 2.280628 GAACCATCATGGGAGACGTTC 58.719 52.381 9.04 0.00 43.37 3.95
513 514 0.541863 ACCATCATGGGAGACGTTCC 59.458 55.000 9.04 7.90 43.37 3.62
525 526 4.424430 CGTTCCCGTTTGCTCGCG 62.424 66.667 0.00 0.00 0.00 5.87
526 527 3.343421 GTTCCCGTTTGCTCGCGT 61.343 61.111 5.77 0.00 0.00 6.01
527 528 2.023223 GTTCCCGTTTGCTCGCGTA 61.023 57.895 5.77 0.00 0.00 4.42
528 529 1.300775 TTCCCGTTTGCTCGCGTAA 60.301 52.632 5.77 0.00 0.00 3.18
529 530 1.286354 TTCCCGTTTGCTCGCGTAAG 61.286 55.000 5.77 0.00 43.44 2.34
530 531 2.736682 CCCGTTTGCTCGCGTAAGG 61.737 63.158 5.77 1.29 38.28 2.69
531 532 2.095843 CGTTTGCTCGCGTAAGGC 59.904 61.111 5.77 7.57 38.69 4.35
543 544 2.344025 GCGTAAGGCGATAAATAGGGG 58.656 52.381 0.00 0.00 44.77 4.79
544 545 2.289257 GCGTAAGGCGATAAATAGGGGT 60.289 50.000 0.00 0.00 44.77 4.95
545 546 3.323243 CGTAAGGCGATAAATAGGGGTG 58.677 50.000 0.00 0.00 44.77 4.61
546 547 2.271944 AAGGCGATAAATAGGGGTGC 57.728 50.000 0.00 0.00 0.00 5.01
547 548 0.400594 AGGCGATAAATAGGGGTGCC 59.599 55.000 0.00 0.00 41.27 5.01
548 549 0.608308 GGCGATAAATAGGGGTGCCC 60.608 60.000 0.00 0.00 45.90 5.36
564 565 3.834799 CCCGACCGGACAGCCTAC 61.835 72.222 9.46 0.00 37.50 3.18
565 566 3.834799 CCGACCGGACAGCCTACC 61.835 72.222 9.46 0.00 37.50 3.18
566 567 3.834799 CGACCGGACAGCCTACCC 61.835 72.222 9.46 0.00 0.00 3.69
567 568 3.468140 GACCGGACAGCCTACCCC 61.468 72.222 9.46 0.00 0.00 4.95
568 569 3.978410 GACCGGACAGCCTACCCCT 62.978 68.421 9.46 0.00 0.00 4.79
569 570 3.155167 CCGGACAGCCTACCCCTC 61.155 72.222 0.00 0.00 0.00 4.30
570 571 2.363795 CGGACAGCCTACCCCTCA 60.364 66.667 0.00 0.00 0.00 3.86
571 572 1.762460 CGGACAGCCTACCCCTCAT 60.762 63.158 0.00 0.00 0.00 2.90
572 573 1.749334 CGGACAGCCTACCCCTCATC 61.749 65.000 0.00 0.00 0.00 2.92
573 574 0.691078 GGACAGCCTACCCCTCATCA 60.691 60.000 0.00 0.00 0.00 3.07
574 575 1.428869 GACAGCCTACCCCTCATCAT 58.571 55.000 0.00 0.00 0.00 2.45
575 576 1.346068 GACAGCCTACCCCTCATCATC 59.654 57.143 0.00 0.00 0.00 2.92
576 577 1.344393 ACAGCCTACCCCTCATCATCA 60.344 52.381 0.00 0.00 0.00 3.07
577 578 1.983691 CAGCCTACCCCTCATCATCAT 59.016 52.381 0.00 0.00 0.00 2.45
578 579 2.027377 CAGCCTACCCCTCATCATCATC 60.027 54.545 0.00 0.00 0.00 2.92
579 580 1.980765 GCCTACCCCTCATCATCATCA 59.019 52.381 0.00 0.00 0.00 3.07
580 581 2.373169 GCCTACCCCTCATCATCATCAA 59.627 50.000 0.00 0.00 0.00 2.57
581 582 3.181440 GCCTACCCCTCATCATCATCAAA 60.181 47.826 0.00 0.00 0.00 2.69
582 583 4.689705 GCCTACCCCTCATCATCATCAAAA 60.690 45.833 0.00 0.00 0.00 2.44
583 584 5.068636 CCTACCCCTCATCATCATCAAAAG 58.931 45.833 0.00 0.00 0.00 2.27
584 585 4.868172 ACCCCTCATCATCATCAAAAGA 57.132 40.909 0.00 0.00 0.00 2.52
585 586 5.197224 ACCCCTCATCATCATCAAAAGAA 57.803 39.130 0.00 0.00 0.00 2.52
586 587 5.582953 ACCCCTCATCATCATCAAAAGAAA 58.417 37.500 0.00 0.00 0.00 2.52
587 588 6.018469 ACCCCTCATCATCATCAAAAGAAAA 58.982 36.000 0.00 0.00 0.00 2.29
588 589 6.497954 ACCCCTCATCATCATCAAAAGAAAAA 59.502 34.615 0.00 0.00 0.00 1.94
589 590 7.181485 ACCCCTCATCATCATCAAAAGAAAAAT 59.819 33.333 0.00 0.00 0.00 1.82
590 591 7.494625 CCCCTCATCATCATCAAAAGAAAAATG 59.505 37.037 0.00 0.00 0.00 2.32
591 592 8.255206 CCCTCATCATCATCAAAAGAAAAATGA 58.745 33.333 0.00 0.00 33.04 2.57
592 593 9.647797 CCTCATCATCATCAAAAGAAAAATGAA 57.352 29.630 0.00 0.00 32.31 2.57
621 622 2.753043 GGACGACCGGACAGCCTA 60.753 66.667 9.46 0.00 0.00 3.93
664 665 2.875188 CACGTAGAGTGGAGCCTCT 58.125 57.895 0.00 0.00 46.77 3.69
727 728 3.365265 CCCACGCAAGGCACCTTC 61.365 66.667 0.00 0.00 46.39 3.46
728 729 2.281761 CCACGCAAGGCACCTTCT 60.282 61.111 0.00 0.00 46.39 2.85
729 730 1.898574 CCACGCAAGGCACCTTCTT 60.899 57.895 0.00 0.00 46.39 2.52
735 736 1.000938 GCAAGGCACCTTCTTCACTTG 60.001 52.381 0.00 0.00 38.57 3.16
736 737 2.575532 CAAGGCACCTTCTTCACTTGA 58.424 47.619 0.00 0.00 37.98 3.02
741 742 2.213499 CACCTTCTTCACTTGAGCGTT 58.787 47.619 0.00 0.00 0.00 4.84
742 743 2.221981 CACCTTCTTCACTTGAGCGTTC 59.778 50.000 0.00 0.00 0.00 3.95
747 748 1.532868 CTTCACTTGAGCGTTCCTTGG 59.467 52.381 0.00 0.00 0.00 3.61
754 755 2.159382 TGAGCGTTCCTTGGAATTTCC 58.841 47.619 8.59 8.59 36.96 3.13
767 768 3.277715 GGAATTTCCTGGAGAAGAGCTG 58.722 50.000 8.25 0.00 35.40 4.24
824 830 1.227438 TTTCGGCCGAATCGATCCC 60.227 57.895 38.89 0.35 36.49 3.85
1074 1089 1.341531 CGATCTGCCCGTATCCTCTTT 59.658 52.381 0.00 0.00 0.00 2.52
1083 1098 3.304794 CCCGTATCCTCTTTTCGCTCTAG 60.305 52.174 0.00 0.00 0.00 2.43
1108 1129 1.233019 CCTCAGCTGTGTTGTTGGAG 58.767 55.000 14.67 0.00 0.00 3.86
1114 1135 1.543429 GCTGTGTTGTTGGAGCCTAGT 60.543 52.381 0.00 0.00 0.00 2.57
1115 1136 2.146342 CTGTGTTGTTGGAGCCTAGTG 58.854 52.381 0.00 0.00 0.00 2.74
1116 1137 0.875059 GTGTTGTTGGAGCCTAGTGC 59.125 55.000 0.00 0.00 41.71 4.40
1135 1166 5.551233 AGTGCAGTATATCACAAGTGTTGT 58.449 37.500 0.00 0.00 46.75 3.32
1155 1186 7.599245 GTGTTGTCAATAGTTACTCTACAGCTT 59.401 37.037 0.00 0.00 0.00 3.74
1157 1188 6.864342 TGTCAATAGTTACTCTACAGCTTCC 58.136 40.000 0.00 0.00 0.00 3.46
1180 1211 3.726517 GCCACGCGAATGCTGTGT 61.727 61.111 15.93 0.00 41.10 3.72
1197 1248 1.413077 GTGTCCGGATCCCTCTTTAGG 59.587 57.143 7.81 0.00 43.25 2.69
1213 1267 9.908152 CCCTCTTTAGGTTGTTTATTTAACTTG 57.092 33.333 0.00 0.00 41.89 3.16
1220 1274 5.541101 GGTTGTTTATTTAACTTGGGAGGGT 59.459 40.000 0.00 0.00 37.64 4.34
1223 1277 8.301720 GTTGTTTATTTAACTTGGGAGGGTAAG 58.698 37.037 0.00 0.00 37.64 2.34
1270 1330 1.745827 CGGGCGATTGTTACCCAGATT 60.746 52.381 0.00 0.00 44.49 2.40
1309 1370 5.888161 CAGCTTCTTGTTTATCCTGGGTTAT 59.112 40.000 0.00 0.00 0.00 1.89
1312 1373 6.183360 GCTTCTTGTTTATCCTGGGTTATCAC 60.183 42.308 0.00 0.00 0.00 3.06
1316 1377 8.044908 TCTTGTTTATCCTGGGTTATCACTTAC 58.955 37.037 0.00 0.00 0.00 2.34
1340 1401 2.224137 TGAGTGCTGAGGAGACAAACTG 60.224 50.000 0.00 0.00 0.00 3.16
1344 1405 1.803555 GCTGAGGAGACAAACTGAAGC 59.196 52.381 0.00 0.00 0.00 3.86
1348 1409 3.879295 TGAGGAGACAAACTGAAGCTTTG 59.121 43.478 0.00 0.00 35.17 2.77
1375 1436 5.694995 TGTTCTTCCCATTTGGATATCCTC 58.305 41.667 22.35 0.00 44.66 3.71
1377 1438 6.619437 TGTTCTTCCCATTTGGATATCCTCTA 59.381 38.462 22.35 8.22 44.66 2.43
1413 1474 2.331132 GCAACACTCTGCTGCCCTC 61.331 63.158 0.00 0.00 39.34 4.30
1549 1622 3.367703 CCACATTTTCATCTGCCTCAACC 60.368 47.826 0.00 0.00 0.00 3.77
1683 1756 7.885399 GGTAAAGATCTTATTGCAGGTATGGAT 59.115 37.037 8.75 0.00 0.00 3.41
1693 1766 4.790937 TGCAGGTATGGATTGCTTAATCA 58.209 39.130 0.00 0.00 38.60 2.57
1708 1781 6.240894 TGCTTAATCATTCAGTTCCAGTTCT 58.759 36.000 0.00 0.00 0.00 3.01
1852 1926 0.392461 GCTGTGGCAATACGAGGGAA 60.392 55.000 0.00 0.00 38.54 3.97
1860 1998 2.483188 GCAATACGAGGGAATTCGAGGT 60.483 50.000 2.12 0.00 43.03 3.85
1895 2036 5.557866 AGTAAAGTGGAGAAAACGCCTTAT 58.442 37.500 0.00 0.00 0.00 1.73
1896 2037 4.766404 AAAGTGGAGAAAACGCCTTATG 57.234 40.909 0.00 0.00 0.00 1.90
1917 2058 2.810274 GCTCTGACTGTTGAATTCAGCA 59.190 45.455 21.73 21.73 35.93 4.41
1918 2059 3.364764 GCTCTGACTGTTGAATTCAGCAC 60.365 47.826 19.66 11.55 35.93 4.40
1925 2066 5.316167 ACTGTTGAATTCAGCACCTTGATA 58.684 37.500 19.66 0.00 36.50 2.15
1929 2070 7.092079 TGTTGAATTCAGCACCTTGATATTTG 58.908 34.615 19.66 0.00 32.11 2.32
1941 2083 7.542130 GCACCTTGATATTTGAGTTTTTACTGG 59.458 37.037 0.00 0.00 0.00 4.00
2081 2223 3.187227 GGTGCTGGATACTGAATAATGCG 59.813 47.826 0.00 0.00 37.83 4.73
2114 2256 1.349026 ACAGGACCTGTGGTTGATCTG 59.651 52.381 26.61 0.00 43.63 2.90
2117 2259 2.039084 AGGACCTGTGGTTGATCTGTTC 59.961 50.000 0.00 0.00 35.25 3.18
2280 2425 9.347240 CTTCAATGGAAGTGATATTGGACTAAT 57.653 33.333 1.20 0.00 42.30 1.73
2470 2615 2.464796 ACCGTGGGATAGGTATGTCA 57.535 50.000 0.00 0.00 39.30 3.58
2493 2638 4.202441 AGGCTATCAACTTGCGAAATCAT 58.798 39.130 0.00 0.00 0.00 2.45
2592 2737 7.410991 AGGGTGCTATAAATAAAGTTCAGGTT 58.589 34.615 0.00 0.00 0.00 3.50
2643 2790 9.859152 CTATCTCATCCATATCTGGTATCACTA 57.141 37.037 0.00 0.00 43.61 2.74
2685 2832 3.244457 GGCATAGTGGTATTAGGTGACCC 60.244 52.174 0.00 0.00 34.58 4.46
2792 2939 4.585879 ACATACATTACTGTGTCCAACCC 58.414 43.478 0.00 0.00 36.79 4.11
2795 2942 2.708861 ACATTACTGTGTCCAACCCTGA 59.291 45.455 0.00 0.00 33.22 3.86
2796 2943 3.330701 ACATTACTGTGTCCAACCCTGAT 59.669 43.478 0.00 0.00 33.22 2.90
2834 2981 9.339850 ACTATGTACCACTTAGTACTCTACATG 57.660 37.037 0.00 0.00 42.58 3.21
2841 2988 8.426489 ACCACTTAGTACTCTACATGTGAAAAA 58.574 33.333 9.11 0.00 30.79 1.94
2876 3023 6.764308 AATGTTATGTGAAACTCATCTGGG 57.236 37.500 0.00 0.00 38.04 4.45
2903 3050 3.064408 AGCATTACACTGCATGACAATCG 59.936 43.478 0.00 0.00 44.77 3.34
2910 3057 4.456911 ACACTGCATGACAATCGAATTTCT 59.543 37.500 0.00 0.00 0.00 2.52
2914 3061 8.337532 CACTGCATGACAATCGAATTTCTATTA 58.662 33.333 0.00 0.00 0.00 0.98
2948 3095 4.513442 CAACCTTGATCGGTATTCTTCCA 58.487 43.478 0.00 0.00 35.89 3.53
2954 3101 2.410785 TCGGTATTCTTCCATACGCG 57.589 50.000 3.53 3.53 31.24 6.01
2957 3104 1.069668 GGTATTCTTCCATACGCGGGT 59.930 52.381 12.47 10.91 31.24 5.28
2975 3122 6.708949 ACGCGGGTCTGAAATTTTACATATAT 59.291 34.615 12.47 0.00 0.00 0.86
2999 3146 3.055312 AGGACCTAAAATCTCGTGTTCCC 60.055 47.826 0.00 0.00 0.00 3.97
3077 3224 6.040504 GTCTTTTTGGACAAACCCTCACTTAT 59.959 38.462 0.00 0.00 38.00 1.73
3142 3289 9.933723 CACATTGTAGTCATGATAATCTATGGA 57.066 33.333 0.00 0.00 0.00 3.41
3169 3317 8.262715 TGTAAGTTCGATTGCAATTCTGATTA 57.737 30.769 14.33 8.08 0.00 1.75
3176 3324 6.018425 TCGATTGCAATTCTGATTAGCTTCTC 60.018 38.462 14.33 0.00 0.00 2.87
3177 3325 6.018098 CGATTGCAATTCTGATTAGCTTCTCT 60.018 38.462 14.33 0.00 0.00 3.10
3178 3326 6.432607 TTGCAATTCTGATTAGCTTCTCTG 57.567 37.500 0.00 0.00 0.00 3.35
3186 3334 5.595952 TCTGATTAGCTTCTCTGCTGTCATA 59.404 40.000 0.00 0.00 43.87 2.15
3354 3502 6.352016 TGAGGATTAGAAGTGGCAGATATC 57.648 41.667 0.00 0.00 0.00 1.63
3372 3520 8.907685 GCAGATATCGTATACTCTCACTTTTTC 58.092 37.037 0.56 0.00 0.00 2.29
3509 3659 1.517257 ACGCGAGAAAGCTCATCCG 60.517 57.895 15.93 0.00 41.36 4.18
3881 4033 3.279434 CCCTGGCTACCATCAAGTTTAC 58.721 50.000 0.00 0.00 30.82 2.01
3897 4049 7.391620 TCAAGTTTACGAATCAGTTCCCTATT 58.608 34.615 0.00 0.00 0.00 1.73
3935 4087 2.011947 TCTTCTCATTGGCATCGCAAG 58.988 47.619 0.00 0.00 0.00 4.01
3937 4089 0.035152 TCTCATTGGCATCGCAAGGT 60.035 50.000 0.00 0.00 38.47 3.50
3954 4146 5.397326 GCAAGGTTCACATGAAGATCTTTC 58.603 41.667 9.87 3.85 34.27 2.62
3958 4150 6.777782 AGGTTCACATGAAGATCTTTCTCTT 58.222 36.000 9.87 0.00 38.18 2.85
4229 4423 7.877612 ACATTAAGGACAATCCCAAAATGAAAC 59.122 33.333 15.78 0.00 37.19 2.78
4265 4459 4.291540 CACACAAGTGCAAACTGTACAT 57.708 40.909 0.00 0.00 39.21 2.29
4287 4481 2.361610 CATCCACAGCCACCCCAC 60.362 66.667 0.00 0.00 0.00 4.61
4668 4862 6.887002 GGGTTCTTTCTCTTTGGATTCTGTAT 59.113 38.462 0.00 0.00 0.00 2.29
4669 4863 8.047310 GGGTTCTTTCTCTTTGGATTCTGTATA 58.953 37.037 0.00 0.00 0.00 1.47
4670 4864 9.103861 GGTTCTTTCTCTTTGGATTCTGTATAG 57.896 37.037 0.00 0.00 0.00 1.31
4715 4909 8.173130 CCCAAATCGTCAAAACATTACTAGTAC 58.827 37.037 0.91 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 9.708092 GGAGGGAGTATACAATAAACACTATTC 57.292 37.037 5.50 0.00 0.00 1.75
264 265 8.365647 CGGAGGGAGTATACAATAAACACTATT 58.634 37.037 5.50 0.00 0.00 1.73
265 266 7.508296 ACGGAGGGAGTATACAATAAACACTAT 59.492 37.037 5.50 0.00 0.00 2.12
266 267 6.835488 ACGGAGGGAGTATACAATAAACACTA 59.165 38.462 5.50 0.00 0.00 2.74
267 268 5.659971 ACGGAGGGAGTATACAATAAACACT 59.340 40.000 5.50 0.00 0.00 3.55
268 269 5.910614 ACGGAGGGAGTATACAATAAACAC 58.089 41.667 5.50 0.00 0.00 3.32
269 270 5.069516 GGACGGAGGGAGTATACAATAAACA 59.930 44.000 5.50 0.00 0.00 2.83
270 271 5.510349 GGGACGGAGGGAGTATACAATAAAC 60.510 48.000 5.50 0.00 0.00 2.01
271 272 4.590222 GGGACGGAGGGAGTATACAATAAA 59.410 45.833 5.50 0.00 0.00 1.40
272 273 4.154942 GGGACGGAGGGAGTATACAATAA 58.845 47.826 5.50 0.00 0.00 1.40
273 274 3.140707 TGGGACGGAGGGAGTATACAATA 59.859 47.826 5.50 0.00 0.00 1.90
274 275 2.090943 TGGGACGGAGGGAGTATACAAT 60.091 50.000 5.50 0.00 0.00 2.71
275 276 1.288633 TGGGACGGAGGGAGTATACAA 59.711 52.381 5.50 0.00 0.00 2.41
276 277 0.928505 TGGGACGGAGGGAGTATACA 59.071 55.000 5.50 0.00 0.00 2.29
277 278 2.077687 TTGGGACGGAGGGAGTATAC 57.922 55.000 0.00 0.00 0.00 1.47
278 279 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
279 280 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
280 281 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
281 282 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
282 283 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
283 284 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
284 285 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
285 286 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
286 287 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
287 288 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
288 289 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
289 290 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
290 291 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
291 292 8.934023 ATAAAGTTGAGTCACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
322 323 8.492748 CGACTTTGCACTAACTTTAAGACAATA 58.507 33.333 0.00 0.00 0.00 1.90
323 324 7.225931 TCGACTTTGCACTAACTTTAAGACAAT 59.774 33.333 0.00 0.00 0.00 2.71
324 325 6.535865 TCGACTTTGCACTAACTTTAAGACAA 59.464 34.615 0.00 0.00 0.00 3.18
325 326 6.044046 TCGACTTTGCACTAACTTTAAGACA 58.956 36.000 0.00 0.00 0.00 3.41
326 327 6.200475 ACTCGACTTTGCACTAACTTTAAGAC 59.800 38.462 0.00 0.00 0.00 3.01
327 328 6.278363 ACTCGACTTTGCACTAACTTTAAGA 58.722 36.000 0.00 0.00 0.00 2.10
328 329 6.200286 TGACTCGACTTTGCACTAACTTTAAG 59.800 38.462 0.00 0.00 0.00 1.85
329 330 6.019318 GTGACTCGACTTTGCACTAACTTTAA 60.019 38.462 0.00 0.00 0.00 1.52
330 331 5.461078 GTGACTCGACTTTGCACTAACTTTA 59.539 40.000 0.00 0.00 0.00 1.85
331 332 4.270325 GTGACTCGACTTTGCACTAACTTT 59.730 41.667 0.00 0.00 0.00 2.66
332 333 3.802685 GTGACTCGACTTTGCACTAACTT 59.197 43.478 0.00 0.00 0.00 2.66
333 334 3.068307 AGTGACTCGACTTTGCACTAACT 59.932 43.478 0.00 0.00 37.98 2.24
334 335 3.381949 AGTGACTCGACTTTGCACTAAC 58.618 45.455 0.00 0.00 37.98 2.34
335 336 3.728076 AGTGACTCGACTTTGCACTAA 57.272 42.857 0.00 0.00 37.98 2.24
336 337 3.728076 AAGTGACTCGACTTTGCACTA 57.272 42.857 0.00 0.00 38.74 2.74
337 338 2.604046 AAGTGACTCGACTTTGCACT 57.396 45.000 0.00 0.00 41.19 4.40
338 339 4.992381 ATTAAGTGACTCGACTTTGCAC 57.008 40.909 0.00 0.00 37.38 4.57
339 340 5.525745 TCAAATTAAGTGACTCGACTTTGCA 59.474 36.000 0.00 0.00 37.38 4.08
340 341 5.985781 TCAAATTAAGTGACTCGACTTTGC 58.014 37.500 0.00 0.00 37.38 3.68
341 342 7.284351 GTCTCAAATTAAGTGACTCGACTTTG 58.716 38.462 0.00 0.00 37.38 2.77
342 343 6.144080 CGTCTCAAATTAAGTGACTCGACTTT 59.856 38.462 0.00 0.00 37.38 2.66
343 344 5.629849 CGTCTCAAATTAAGTGACTCGACTT 59.370 40.000 9.77 0.00 39.54 3.01
344 345 5.154932 CGTCTCAAATTAAGTGACTCGACT 58.845 41.667 9.77 0.00 0.00 4.18
345 346 4.323868 CCGTCTCAAATTAAGTGACTCGAC 59.676 45.833 9.77 6.33 0.00 4.20
346 347 4.216902 TCCGTCTCAAATTAAGTGACTCGA 59.783 41.667 9.77 0.00 0.00 4.04
347 348 4.482386 TCCGTCTCAAATTAAGTGACTCG 58.518 43.478 9.77 2.91 0.00 4.18
348 349 4.865365 CCTCCGTCTCAAATTAAGTGACTC 59.135 45.833 9.77 0.00 0.00 3.36
349 350 4.322801 CCCTCCGTCTCAAATTAAGTGACT 60.323 45.833 9.77 0.00 0.00 3.41
350 351 3.933332 CCCTCCGTCTCAAATTAAGTGAC 59.067 47.826 4.01 4.01 0.00 3.67
351 352 3.835978 TCCCTCCGTCTCAAATTAAGTGA 59.164 43.478 0.00 0.00 0.00 3.41
352 353 4.184629 CTCCCTCCGTCTCAAATTAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
353 354 3.838903 ACTCCCTCCGTCTCAAATTAAGT 59.161 43.478 0.00 0.00 0.00 2.24
354 355 4.473477 ACTCCCTCCGTCTCAAATTAAG 57.527 45.455 0.00 0.00 0.00 1.85
355 356 7.850935 ATATACTCCCTCCGTCTCAAATTAA 57.149 36.000 0.00 0.00 0.00 1.40
356 357 8.967918 CATATATACTCCCTCCGTCTCAAATTA 58.032 37.037 0.00 0.00 0.00 1.40
357 358 7.455008 ACATATATACTCCCTCCGTCTCAAATT 59.545 37.037 0.00 0.00 0.00 1.82
358 359 6.954684 ACATATATACTCCCTCCGTCTCAAAT 59.045 38.462 0.00 0.00 0.00 2.32
359 360 6.312529 ACATATATACTCCCTCCGTCTCAAA 58.687 40.000 0.00 0.00 0.00 2.69
360 361 5.888901 ACATATATACTCCCTCCGTCTCAA 58.111 41.667 0.00 0.00 0.00 3.02
361 362 5.516059 ACATATATACTCCCTCCGTCTCA 57.484 43.478 0.00 0.00 0.00 3.27
362 363 6.887013 TCTACATATATACTCCCTCCGTCTC 58.113 44.000 0.00 0.00 0.00 3.36
363 364 6.887886 TCTACATATATACTCCCTCCGTCT 57.112 41.667 0.00 0.00 0.00 4.18
364 365 9.796180 ATATTCTACATATATACTCCCTCCGTC 57.204 37.037 0.00 0.00 0.00 4.79
452 453 2.229062 GCAAAGGCCTGTTTTCTAGGTC 59.771 50.000 5.69 0.00 40.26 3.85
453 454 2.239400 GCAAAGGCCTGTTTTCTAGGT 58.761 47.619 5.69 0.00 37.64 3.08
469 470 4.408821 ATCAGCGCGGGAGGCAAA 62.409 61.111 8.83 0.00 43.84 3.68
480 481 4.776322 TGGTTCGGCCCATCAGCG 62.776 66.667 0.00 0.00 36.04 5.18
481 482 2.124151 ATGGTTCGGCCCATCAGC 60.124 61.111 0.00 0.00 41.47 4.26
486 487 2.275089 CCATGATGGTTCGGCCCA 59.725 61.111 2.54 0.00 39.27 5.36
487 488 2.519302 CCCATGATGGTTCGGCCC 60.519 66.667 11.09 0.00 35.17 5.80
488 489 1.526917 CTCCCATGATGGTTCGGCC 60.527 63.158 11.09 0.00 35.17 6.13
489 490 0.815615 GTCTCCCATGATGGTTCGGC 60.816 60.000 11.09 0.00 35.17 5.54
490 491 0.530650 CGTCTCCCATGATGGTTCGG 60.531 60.000 11.09 0.00 35.17 4.30
491 492 0.175760 ACGTCTCCCATGATGGTTCG 59.824 55.000 11.09 11.13 35.17 3.95
492 493 2.280628 GAACGTCTCCCATGATGGTTC 58.719 52.381 11.09 2.70 35.17 3.62
493 494 1.065418 GGAACGTCTCCCATGATGGTT 60.065 52.381 11.09 0.00 38.44 3.67
494 495 0.541863 GGAACGTCTCCCATGATGGT 59.458 55.000 11.09 0.00 38.44 3.55
495 496 3.386543 GGAACGTCTCCCATGATGG 57.613 57.895 3.98 3.98 38.44 3.51
509 510 1.559149 TTACGCGAGCAAACGGGAAC 61.559 55.000 15.93 0.00 46.30 3.62
510 511 1.286354 CTTACGCGAGCAAACGGGAA 61.286 55.000 15.93 9.36 46.30 3.97
511 512 1.735198 CTTACGCGAGCAAACGGGA 60.735 57.895 15.93 3.72 46.30 5.14
513 514 2.776072 CCTTACGCGAGCAAACGG 59.224 61.111 15.93 0.00 0.00 4.44
514 515 2.095843 GCCTTACGCGAGCAAACG 59.904 61.111 15.93 0.00 0.00 3.60
523 524 2.289257 ACCCCTATTTATCGCCTTACGC 60.289 50.000 0.00 0.00 43.23 4.42
524 525 3.323243 CACCCCTATTTATCGCCTTACG 58.677 50.000 0.00 0.00 45.62 3.18
525 526 3.072211 GCACCCCTATTTATCGCCTTAC 58.928 50.000 0.00 0.00 0.00 2.34
526 527 2.039348 GGCACCCCTATTTATCGCCTTA 59.961 50.000 0.00 0.00 35.17 2.69
527 528 1.202891 GGCACCCCTATTTATCGCCTT 60.203 52.381 0.00 0.00 35.17 4.35
528 529 0.400594 GGCACCCCTATTTATCGCCT 59.599 55.000 0.00 0.00 35.17 5.52
529 530 2.942641 GGCACCCCTATTTATCGCC 58.057 57.895 0.00 0.00 0.00 5.54
547 548 3.834799 GTAGGCTGTCCGGTCGGG 61.835 72.222 9.64 0.00 37.47 5.14
548 549 3.834799 GGTAGGCTGTCCGGTCGG 61.835 72.222 0.00 1.10 37.47 4.79
549 550 3.834799 GGGTAGGCTGTCCGGTCG 61.835 72.222 0.00 0.00 37.47 4.79
550 551 3.468140 GGGGTAGGCTGTCCGGTC 61.468 72.222 0.00 0.00 37.47 4.79
551 552 3.978410 GAGGGGTAGGCTGTCCGGT 62.978 68.421 0.00 0.00 37.47 5.28
552 553 3.155167 GAGGGGTAGGCTGTCCGG 61.155 72.222 0.00 0.00 37.47 5.14
553 554 1.749334 GATGAGGGGTAGGCTGTCCG 61.749 65.000 0.00 0.00 37.47 4.79
554 555 0.691078 TGATGAGGGGTAGGCTGTCC 60.691 60.000 0.00 0.00 0.00 4.02
555 556 1.346068 GATGATGAGGGGTAGGCTGTC 59.654 57.143 0.00 0.00 0.00 3.51
556 557 1.344393 TGATGATGAGGGGTAGGCTGT 60.344 52.381 0.00 0.00 0.00 4.40
557 558 1.427809 TGATGATGAGGGGTAGGCTG 58.572 55.000 0.00 0.00 0.00 4.85
558 559 2.264455 GATGATGATGAGGGGTAGGCT 58.736 52.381 0.00 0.00 0.00 4.58
559 560 1.980765 TGATGATGATGAGGGGTAGGC 59.019 52.381 0.00 0.00 0.00 3.93
560 561 4.712051 TTTGATGATGATGAGGGGTAGG 57.288 45.455 0.00 0.00 0.00 3.18
561 562 5.933617 TCTTTTGATGATGATGAGGGGTAG 58.066 41.667 0.00 0.00 0.00 3.18
562 563 5.974156 TCTTTTGATGATGATGAGGGGTA 57.026 39.130 0.00 0.00 0.00 3.69
563 564 4.868172 TCTTTTGATGATGATGAGGGGT 57.132 40.909 0.00 0.00 0.00 4.95
564 565 6.534475 TTTTCTTTTGATGATGATGAGGGG 57.466 37.500 0.00 0.00 0.00 4.79
565 566 8.255206 TCATTTTTCTTTTGATGATGATGAGGG 58.745 33.333 0.00 0.00 0.00 4.30
566 567 9.647797 TTCATTTTTCTTTTGATGATGATGAGG 57.352 29.630 0.00 0.00 0.00 3.86
621 622 0.756903 ACTACACCAACGGCAAGACT 59.243 50.000 0.00 0.00 0.00 3.24
721 722 1.871080 ACGCTCAAGTGAAGAAGGTG 58.129 50.000 0.00 0.00 0.00 4.00
722 723 2.484889 GAACGCTCAAGTGAAGAAGGT 58.515 47.619 0.00 0.00 0.00 3.50
723 724 1.801178 GGAACGCTCAAGTGAAGAAGG 59.199 52.381 0.00 0.00 0.00 3.46
724 725 2.760374 AGGAACGCTCAAGTGAAGAAG 58.240 47.619 0.00 0.00 0.00 2.85
725 726 2.872245 CAAGGAACGCTCAAGTGAAGAA 59.128 45.455 0.00 0.00 0.00 2.52
726 727 2.483876 CAAGGAACGCTCAAGTGAAGA 58.516 47.619 0.00 0.00 0.00 2.87
727 728 1.532868 CCAAGGAACGCTCAAGTGAAG 59.467 52.381 0.00 0.00 0.00 3.02
728 729 1.140052 TCCAAGGAACGCTCAAGTGAA 59.860 47.619 0.00 0.00 0.00 3.18
729 730 0.756294 TCCAAGGAACGCTCAAGTGA 59.244 50.000 0.00 0.00 0.00 3.41
735 736 2.162408 CAGGAAATTCCAAGGAACGCTC 59.838 50.000 15.21 1.45 39.61 5.03
736 737 2.162681 CAGGAAATTCCAAGGAACGCT 58.837 47.619 15.21 0.00 39.61 5.07
741 742 3.916349 TCTTCTCCAGGAAATTCCAAGGA 59.084 43.478 20.21 20.21 39.62 3.36
742 743 4.268359 CTCTTCTCCAGGAAATTCCAAGG 58.732 47.826 15.21 15.03 39.61 3.61
747 748 2.682352 GCAGCTCTTCTCCAGGAAATTC 59.318 50.000 0.00 0.00 33.07 2.17
802 808 3.560278 CGATTCGGCCGAAACCCG 61.560 66.667 41.31 35.22 46.88 5.28
805 811 1.496403 GGGATCGATTCGGCCGAAAC 61.496 60.000 41.31 36.16 39.62 2.78
806 812 1.227438 GGGATCGATTCGGCCGAAA 60.227 57.895 41.31 27.31 39.62 3.46
824 830 1.813513 AGGCAGTGATTCGTTTCCTG 58.186 50.000 0.00 0.00 0.00 3.86
1083 1098 1.073897 AACACAGCTGAGGGGCTTC 59.926 57.895 23.35 0.00 41.00 3.86
1108 1129 4.747108 CACTTGTGATATACTGCACTAGGC 59.253 45.833 13.81 0.00 40.52 3.93
1114 1135 5.546526 TGACAACACTTGTGATATACTGCA 58.453 37.500 7.83 0.00 45.52 4.41
1115 1136 6.480524 TTGACAACACTTGTGATATACTGC 57.519 37.500 7.83 0.00 45.52 4.40
1116 1137 9.371136 ACTATTGACAACACTTGTGATATACTG 57.629 33.333 7.83 0.00 45.52 2.74
1135 1166 5.884232 TCGGAAGCTGTAGAGTAACTATTGA 59.116 40.000 0.00 0.00 33.39 2.57
1155 1186 3.673956 ATTCGCGTGGCCAATCGGA 62.674 57.895 22.67 17.29 0.00 4.55
1157 1188 2.023181 CATTCGCGTGGCCAATCG 59.977 61.111 7.24 14.80 0.00 3.34
1197 1248 6.659745 ACCCTCCCAAGTTAAATAAACAAC 57.340 37.500 0.00 0.00 40.83 3.32
1213 1267 0.927029 AAGCCAATCCTTACCCTCCC 59.073 55.000 0.00 0.00 0.00 4.30
1220 1274 4.759693 CACACACAACTAAGCCAATCCTTA 59.240 41.667 0.00 0.00 0.00 2.69
1223 1277 2.884639 ACACACACAACTAAGCCAATCC 59.115 45.455 0.00 0.00 0.00 3.01
1312 1373 2.822561 TCTCCTCAGCACTCACAGTAAG 59.177 50.000 0.00 0.00 0.00 2.34
1316 1377 0.964700 TGTCTCCTCAGCACTCACAG 59.035 55.000 0.00 0.00 0.00 3.66
1326 1387 3.845781 AAGCTTCAGTTTGTCTCCTCA 57.154 42.857 0.00 0.00 0.00 3.86
1340 1401 5.200368 TGGGAAGAACAAATCAAAGCTTC 57.800 39.130 0.00 0.00 0.00 3.86
1344 1405 6.523840 TCCAAATGGGAAGAACAAATCAAAG 58.476 36.000 0.00 0.00 44.80 2.77
1375 1436 3.007940 TGCCAAGAATATGTCCCCGATAG 59.992 47.826 0.00 0.00 0.00 2.08
1377 1438 1.774254 TGCCAAGAATATGTCCCCGAT 59.226 47.619 0.00 0.00 0.00 4.18
1403 1464 5.619220 AGAATATCTTTTAGAGGGCAGCAG 58.381 41.667 0.00 0.00 0.00 4.24
1404 1465 5.636903 AGAATATCTTTTAGAGGGCAGCA 57.363 39.130 0.00 0.00 0.00 4.41
1405 1466 6.733145 CAAAGAATATCTTTTAGAGGGCAGC 58.267 40.000 2.70 0.00 43.62 5.25
1492 1565 1.331214 CCATGTTTCCAACTGGCTGT 58.669 50.000 0.00 0.00 34.44 4.40
1549 1622 2.462255 AAGCATTCACTTGTGCGGCG 62.462 55.000 0.51 0.51 45.69 6.46
1683 1756 6.716628 AGAACTGGAACTGAATGATTAAGCAA 59.283 34.615 0.00 0.00 0.00 3.91
1693 1766 3.825328 AGCAACAGAACTGGAACTGAAT 58.175 40.909 6.76 0.00 37.54 2.57
1708 1781 1.109609 TGCAATCACCACAAGCAACA 58.890 45.000 0.00 0.00 31.42 3.33
1768 1842 5.991568 GGTTCTTGTCTAGAAAGAAACAGC 58.008 41.667 24.94 15.96 46.23 4.40
1774 1848 4.041691 CCCTTGGGTTCTTGTCTAGAAAGA 59.958 45.833 11.16 11.16 44.25 2.52
1852 1926 9.420551 CTTTACTTACTTGTAGAAACCTCGAAT 57.579 33.333 0.00 0.00 0.00 3.34
1895 2036 2.810274 GCTGAATTCAACAGTCAGAGCA 59.190 45.455 9.88 0.00 41.08 4.26
1896 2037 2.810274 TGCTGAATTCAACAGTCAGAGC 59.190 45.455 9.88 6.59 41.08 4.09
1917 2058 8.706322 ACCAGTAAAAACTCAAATATCAAGGT 57.294 30.769 0.00 0.00 0.00 3.50
1925 2066 8.135529 GCTGAACTTACCAGTAAAAACTCAAAT 58.864 33.333 0.00 0.00 34.29 2.32
1929 2070 6.613755 TGCTGAACTTACCAGTAAAAACTC 57.386 37.500 0.00 0.00 34.29 3.01
1981 2123 1.209261 TCGCACCATTTCCTCTGCATA 59.791 47.619 0.00 0.00 0.00 3.14
2081 2223 0.107654 GTCCTGTACCCACTGATGGC 60.108 60.000 0.00 0.00 45.76 4.40
2208 2350 6.535274 AAAAAGAAAAGCAATGATCAGCAC 57.465 33.333 9.38 0.00 0.00 4.40
2268 2413 9.046296 GTGACGATCAAGAAATTAGTCCAATAT 57.954 33.333 0.00 0.00 0.00 1.28
2280 2425 3.411446 AGCCAATGTGACGATCAAGAAA 58.589 40.909 0.00 0.00 0.00 2.52
2470 2615 4.009675 TGATTTCGCAAGTTGATAGCCTT 58.990 39.130 7.16 0.00 39.48 4.35
2493 2638 5.473846 CCGATTGAGTAGGCTATAAGAGACA 59.526 44.000 0.00 0.00 34.40 3.41
2617 2762 8.765488 AGTGATACCAGATATGGATGAGATAG 57.235 38.462 14.70 0.00 0.00 2.08
2643 2790 2.682856 CCAGTGCGTGGCAGTATTAATT 59.317 45.455 0.00 0.00 40.54 1.40
2685 2832 3.436704 TGAGTCCTCGCAATTGCTTTTAG 59.563 43.478 26.86 17.47 39.32 1.85
2771 2918 4.635765 CAGGGTTGGACACAGTAATGTATG 59.364 45.833 0.00 0.00 31.24 2.39
2772 2919 4.534500 TCAGGGTTGGACACAGTAATGTAT 59.466 41.667 0.00 0.00 31.24 2.29
2785 2932 2.841266 TCAAATACCGATCAGGGTTGGA 59.159 45.455 8.20 3.83 46.96 3.53
2792 2939 7.709182 TGGTACATAGTTTCAAATACCGATCAG 59.291 37.037 0.00 0.00 35.79 2.90
2795 2942 7.562135 AGTGGTACATAGTTTCAAATACCGAT 58.438 34.615 0.00 0.00 44.52 4.18
2796 2943 6.938507 AGTGGTACATAGTTTCAAATACCGA 58.061 36.000 0.00 0.00 44.52 4.69
2853 3000 5.126061 GCCCAGATGAGTTTCACATAACATT 59.874 40.000 0.00 0.00 0.00 2.71
2863 3010 2.225467 GCTATGGCCCAGATGAGTTTC 58.775 52.381 0.00 0.00 0.00 2.78
2876 3023 2.880268 TCATGCAGTGTAATGCTATGGC 59.120 45.455 5.88 0.00 46.63 4.40
2903 3050 6.299141 TGGGCCTGACAGATAATAGAAATTC 58.701 40.000 4.53 0.00 0.00 2.17
2910 3057 3.857157 GGTTGGGCCTGACAGATAATA 57.143 47.619 4.53 0.00 0.00 0.98
2931 3078 4.304110 GCGTATGGAAGAATACCGATCAA 58.696 43.478 0.00 0.00 30.56 2.57
2948 3095 4.255301 TGTAAAATTTCAGACCCGCGTAT 58.745 39.130 4.92 0.00 0.00 3.06
2954 3101 9.793259 TCCTCATATATGTAAAATTTCAGACCC 57.207 33.333 12.42 0.00 0.00 4.46
2975 3122 4.322499 GGAACACGAGATTTTAGGTCCTCA 60.322 45.833 0.00 0.00 0.00 3.86
2984 3131 3.396260 TCTTCGGGAACACGAGATTTT 57.604 42.857 0.00 0.00 44.47 1.82
3142 3289 7.144722 TCAGAATTGCAATCGAACTTACAAT 57.855 32.000 13.38 0.00 0.00 2.71
3152 3300 6.018098 AGAGAAGCTAATCAGAATTGCAATCG 60.018 38.462 13.38 4.79 0.00 3.34
3176 3324 4.256110 TGAACCTGAACATATGACAGCAG 58.744 43.478 20.54 15.36 0.00 4.24
3177 3325 4.020307 TCTGAACCTGAACATATGACAGCA 60.020 41.667 20.54 15.03 0.00 4.41
3178 3326 4.507710 TCTGAACCTGAACATATGACAGC 58.492 43.478 20.54 12.53 0.00 4.40
3186 3334 3.554934 TGCTTGTTCTGAACCTGAACAT 58.445 40.909 17.26 0.00 46.12 2.71
3342 3490 5.413213 GTGAGAGTATACGATATCTGCCACT 59.587 44.000 0.34 0.00 0.00 4.00
3354 3502 9.746711 CAATTCAAGAAAAAGTGAGAGTATACG 57.253 33.333 0.00 0.00 0.00 3.06
3509 3659 4.364415 TTTGTTGCTGTTACCAGTCAAC 57.636 40.909 15.56 15.56 45.55 3.18
3767 3919 3.724374 ACAACGCAGCTCAAAACTAGTA 58.276 40.909 0.00 0.00 0.00 1.82
3768 3920 2.544267 GACAACGCAGCTCAAAACTAGT 59.456 45.455 0.00 0.00 0.00 2.57
3769 3921 2.410262 CGACAACGCAGCTCAAAACTAG 60.410 50.000 0.00 0.00 0.00 2.57
3881 4033 3.134458 GAGGCAATAGGGAACTGATTCG 58.866 50.000 0.00 0.00 43.88 3.34
3954 4146 3.971032 ACTTGCCAAAACGAAGAAGAG 57.029 42.857 0.00 0.00 0.00 2.85
3980 4172 3.766591 TGCACAAACAGAAAGAAAGGGAA 59.233 39.130 0.00 0.00 0.00 3.97
3981 4173 3.360867 TGCACAAACAGAAAGAAAGGGA 58.639 40.909 0.00 0.00 0.00 4.20
3983 4175 4.505191 CACATGCACAAACAGAAAGAAAGG 59.495 41.667 0.00 0.00 0.00 3.11
3984 4176 5.342433 TCACATGCACAAACAGAAAGAAAG 58.658 37.500 0.00 0.00 0.00 2.62
3985 4177 5.321959 TCACATGCACAAACAGAAAGAAA 57.678 34.783 0.00 0.00 0.00 2.52
3986 4178 4.979943 TCACATGCACAAACAGAAAGAA 57.020 36.364 0.00 0.00 0.00 2.52
3987 4179 4.979943 TTCACATGCACAAACAGAAAGA 57.020 36.364 0.00 0.00 0.00 2.52
3994 4186 5.910637 ACATGATTTTCACATGCACAAAC 57.089 34.783 0.00 0.00 45.95 2.93
4076 4268 6.959639 TTTCAAGGCTTCAGTGTAATTTCT 57.040 33.333 0.00 0.00 0.00 2.52
4121 4313 7.253422 GGATTTGATCCTATTTATGCGAATGG 58.747 38.462 0.00 0.00 46.19 3.16
4229 4423 6.237648 GCACTTGTGTGTTCTTTTGAGATTTG 60.238 38.462 2.61 0.00 45.44 2.32
4265 4459 1.609239 GGTGGCTGTGGATGGATGA 59.391 57.895 0.00 0.00 0.00 2.92
4287 4481 2.228582 TCAAAACTGAATGGTCCGCATG 59.771 45.455 0.00 0.00 0.00 4.06
4292 4486 5.241506 TGTCTTCATCAAAACTGAATGGTCC 59.758 40.000 0.00 0.00 32.50 4.46
4689 4883 7.141100 ACTAGTAATGTTTTGACGATTTGGG 57.859 36.000 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.