Multiple sequence alignment - TraesCS3B01G336600

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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 TraesCS3B01G336600 chr3B 100.000 2498 0 0 1 2498 542731196 542728699 0.000000e+00 4614.0
1 TraesCS3B01G336600 chr3B 88.290 965 74 17 574 1507 542723017 542722061 0.000000e+00 1120.0
2 TraesCS3B01G336600 chr3B 87.258 620 72 7 1882 2498 126915807 126915192 0.000000e+00 701.0
3 TraesCS3B01G336600 chr3B 84.579 629 95 2 1871 2498 566196210 566196837 7.590000e-175 623.0
4 TraesCS3B01G336600 chr3B 84.420 629 86 9 1879 2498 55367991 55368616 2.120000e-170 608.0
5 TraesCS3B01G336600 chr3B 95.667 300 12 1 246 545 584454864 584454566 4.830000e-132 481.0
6 TraesCS3B01G336600 chr3B 94.949 297 15 0 245 541 503860003 503859707 1.350000e-127 466.0
7 TraesCS3B01G336600 chr3B 94.949 297 15 0 245 541 788594406 788594110 1.350000e-127 466.0
8 TraesCS3B01G336600 chr3D 87.396 1317 82 34 540 1820 416199553 416198285 0.000000e+00 1435.0
9 TraesCS3B01G336600 chr3D 87.373 982 60 26 574 1514 416193677 416192719 0.000000e+00 1068.0
10 TraesCS3B01G336600 chr3D 86.508 630 84 1 1867 2496 464321063 464321691 0.000000e+00 691.0
11 TraesCS3B01G336600 chr3D 83.750 640 93 11 1865 2496 86365574 86366210 1.650000e-166 595.0
12 TraesCS3B01G336600 chr3D 94.054 185 6 5 52 232 416210626 416210443 2.450000e-70 276.0
13 TraesCS3B01G336600 chr3D 80.426 235 33 5 1829 2050 154009923 154009689 1.540000e-37 167.0
14 TraesCS3B01G336600 chr3D 78.488 172 23 6 1829 1987 349646252 349646422 1.580000e-17 100.0
15 TraesCS3B01G336600 chr3D 93.939 66 4 0 3 68 416210752 416210687 1.580000e-17 100.0
16 TraesCS3B01G336600 chr3D 76.536 179 27 7 1829 1993 434891043 434891220 1.590000e-12 84.2
17 TraesCS3B01G336600 chr3A 89.030 948 77 17 574 1504 534199900 534200837 0.000000e+00 1149.0
18 TraesCS3B01G336600 chr3A 87.227 963 68 22 574 1533 534185658 534186568 0.000000e+00 1046.0
19 TraesCS3B01G336600 chr3A 85.992 257 14 16 2 239 534185373 534185626 3.190000e-64 255.0
20 TraesCS3B01G336600 chr3A 92.647 136 10 0 1685 1820 534196549 534196684 1.960000e-46 196.0
21 TraesCS3B01G336600 chr7D 86.230 1024 52 30 536 1514 6438674 6437695 0.000000e+00 1027.0
22 TraesCS3B01G336600 chr7D 87.903 248 12 12 5 239 6438939 6438697 2.450000e-70 276.0
23 TraesCS3B01G336600 chr1D 88.328 634 72 1 1865 2498 95443986 95444617 0.000000e+00 760.0
24 TraesCS3B01G336600 chr1D 85.179 641 84 9 1865 2498 287468658 287469294 0.000000e+00 647.0
25 TraesCS3B01G336600 chr5D 84.638 690 83 8 1829 2498 443306627 443305941 0.000000e+00 665.0
26 TraesCS3B01G336600 chr5D 84.735 642 87 11 1865 2498 394834322 394834960 1.260000e-177 632.0
27 TraesCS3B01G336600 chr5D 81.974 233 28 5 1829 2048 532757421 532757652 4.240000e-43 185.0
28 TraesCS3B01G336600 chr2B 86.926 566 70 4 1865 2429 17831546 17832108 1.260000e-177 632.0
29 TraesCS3B01G336600 chr2B 96.284 296 11 0 246 541 139803688 139803983 1.040000e-133 486.0
30 TraesCS3B01G336600 chr2B 95.946 296 11 1 246 541 147052055 147051761 1.740000e-131 479.0
31 TraesCS3B01G336600 chr6B 84.102 629 94 6 1865 2492 574427908 574428531 9.880000e-169 603.0
32 TraesCS3B01G336600 chr6B 95.623 297 13 0 245 541 166642423 166642719 6.250000e-131 477.0
33 TraesCS3B01G336600 chr4B 96.622 296 10 0 246 541 27117962 27117667 2.230000e-135 492.0
34 TraesCS3B01G336600 chr5B 95.333 300 14 0 246 545 488193233 488192934 6.250000e-131 477.0
35 TraesCS3B01G336600 chr5B 81.952 543 72 9 1829 2357 271098763 271098233 1.060000e-118 436.0
36 TraesCS3B01G336600 chr1B 95.302 298 13 1 245 541 398900829 398900532 2.910000e-129 472.0
37 TraesCS3B01G336600 chr6D 78.978 685 120 17 1829 2498 298210517 298211192 1.760000e-121 446.0
38 TraesCS3B01G336600 chr2D 81.702 235 28 4 1829 2049 470381948 470381715 5.490000e-42 182.0
39 TraesCS3B01G336600 chr7B 76.549 226 36 9 1827 2048 367490310 367490522 9.450000e-20 108.0


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 TraesCS3B01G336600 chr3B 542728699 542731196 2497 True 4614.0 4614 100.0000 1 2498 1 chr3B.!!$R4 2497
1 TraesCS3B01G336600 chr3B 542722061 542723017 956 True 1120.0 1120 88.2900 574 1507 1 chr3B.!!$R3 933
2 TraesCS3B01G336600 chr3B 126915192 126915807 615 True 701.0 701 87.2580 1882 2498 1 chr3B.!!$R1 616
3 TraesCS3B01G336600 chr3B 566196210 566196837 627 False 623.0 623 84.5790 1871 2498 1 chr3B.!!$F2 627
4 TraesCS3B01G336600 chr3B 55367991 55368616 625 False 608.0 608 84.4200 1879 2498 1 chr3B.!!$F1 619
5 TraesCS3B01G336600 chr3D 416198285 416199553 1268 True 1435.0 1435 87.3960 540 1820 1 chr3D.!!$R3 1280
6 TraesCS3B01G336600 chr3D 416192719 416193677 958 True 1068.0 1068 87.3730 574 1514 1 chr3D.!!$R2 940
7 TraesCS3B01G336600 chr3D 464321063 464321691 628 False 691.0 691 86.5080 1867 2496 1 chr3D.!!$F4 629
8 TraesCS3B01G336600 chr3D 86365574 86366210 636 False 595.0 595 83.7500 1865 2496 1 chr3D.!!$F1 631
9 TraesCS3B01G336600 chr3A 534196549 534200837 4288 False 672.5 1149 90.8385 574 1820 2 chr3A.!!$F2 1246
10 TraesCS3B01G336600 chr3A 534185373 534186568 1195 False 650.5 1046 86.6095 2 1533 2 chr3A.!!$F1 1531
11 TraesCS3B01G336600 chr7D 6437695 6438939 1244 True 651.5 1027 87.0665 5 1514 2 chr7D.!!$R1 1509
12 TraesCS3B01G336600 chr1D 95443986 95444617 631 False 760.0 760 88.3280 1865 2498 1 chr1D.!!$F1 633
13 TraesCS3B01G336600 chr1D 287468658 287469294 636 False 647.0 647 85.1790 1865 2498 1 chr1D.!!$F2 633
14 TraesCS3B01G336600 chr5D 443305941 443306627 686 True 665.0 665 84.6380 1829 2498 1 chr5D.!!$R1 669
15 TraesCS3B01G336600 chr5D 394834322 394834960 638 False 632.0 632 84.7350 1865 2498 1 chr5D.!!$F1 633
16 TraesCS3B01G336600 chr2B 17831546 17832108 562 False 632.0 632 86.9260 1865 2429 1 chr2B.!!$F1 564
17 TraesCS3B01G336600 chr6B 574427908 574428531 623 False 603.0 603 84.1020 1865 2492 1 chr6B.!!$F2 627
18 TraesCS3B01G336600 chr5B 271098233 271098763 530 True 436.0 436 81.9520 1829 2357 1 chr5B.!!$R1 528
19 TraesCS3B01G336600 chr6D 298210517 298211192 675 False 446.0 446 78.9780 1829 2498 1 chr6D.!!$F1 669

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
486 508 0.320421 AATGCACCGCGTCTAAGTGT 60.32 50.0 4.92 0.0 33.96 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 4942 0.037734 GGTCTTCGGGGTGGATTTGT 59.962 55.0 0.0 0.0 0.0 2.83 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
106 109 4.819769 GCAAGTGGCCAATCAGAAATTTA 58.180 39.130 7.24 0.00 36.11 1.40
162 181 3.515502 TCCTCAGGAGACATGGTTTACTG 59.484 47.826 0.00 0.00 0.00 2.74
176 198 4.882427 TGGTTTACTGGACAATCGAAACAA 59.118 37.500 0.00 0.00 0.00 2.83
193 215 3.402628 ACAATAGAGGTCGCTGTGTTT 57.597 42.857 0.00 0.00 0.00 2.83
239 261 8.683550 AACAAGCAACAGTAGAAAAGTTTTAC 57.316 30.769 0.00 0.00 0.00 2.01
241 263 9.169592 ACAAGCAACAGTAGAAAAGTTTTACTA 57.830 29.630 0.00 2.68 0.00 1.82
255 277 8.543862 AAAGTTTTACTATTGTACTTCCTCCG 57.456 34.615 0.00 0.00 0.00 4.63
256 278 7.237209 AGTTTTACTATTGTACTTCCTCCGT 57.763 36.000 0.00 0.00 0.00 4.69
257 279 7.318893 AGTTTTACTATTGTACTTCCTCCGTC 58.681 38.462 0.00 0.00 0.00 4.79
258 280 7.178097 AGTTTTACTATTGTACTTCCTCCGTCT 59.822 37.037 0.00 0.00 0.00 4.18
260 282 7.798596 TTACTATTGTACTTCCTCCGTCTAG 57.201 40.000 0.00 0.00 0.00 2.43
261 283 5.131784 ACTATTGTACTTCCTCCGTCTAGG 58.868 45.833 0.00 0.00 42.97 3.02
262 284 3.446442 TTGTACTTCCTCCGTCTAGGT 57.554 47.619 0.00 0.00 41.99 3.08
263 285 2.719739 TGTACTTCCTCCGTCTAGGTG 58.280 52.381 0.00 0.00 41.99 4.00
264 286 2.306805 TGTACTTCCTCCGTCTAGGTGA 59.693 50.000 0.00 0.00 41.99 4.02
267 289 2.575279 ACTTCCTCCGTCTAGGTGAGTA 59.425 50.000 0.00 0.00 41.99 2.59
268 290 3.009916 ACTTCCTCCGTCTAGGTGAGTAA 59.990 47.826 0.00 0.00 41.99 2.24
270 292 2.575279 TCCTCCGTCTAGGTGAGTAAGT 59.425 50.000 0.00 0.00 41.99 2.24
271 293 2.944349 CCTCCGTCTAGGTGAGTAAGTC 59.056 54.545 0.00 0.00 41.99 3.01
272 294 3.607741 CTCCGTCTAGGTGAGTAAGTCA 58.392 50.000 0.00 0.00 41.99 3.41
273 295 4.200874 CTCCGTCTAGGTGAGTAAGTCAT 58.799 47.826 0.00 0.00 41.99 3.06
274 296 4.597004 TCCGTCTAGGTGAGTAAGTCATT 58.403 43.478 0.00 0.00 41.99 2.57
275 297 5.014858 TCCGTCTAGGTGAGTAAGTCATTT 58.985 41.667 0.00 0.00 41.99 2.32
276 298 5.479375 TCCGTCTAGGTGAGTAAGTCATTTT 59.521 40.000 0.00 0.00 41.99 1.82
278 300 6.973474 CCGTCTAGGTGAGTAAGTCATTTTAG 59.027 42.308 0.00 0.00 37.56 1.85
279 301 6.973474 CGTCTAGGTGAGTAAGTCATTTTAGG 59.027 42.308 0.00 0.00 37.56 2.69
280 302 7.362747 CGTCTAGGTGAGTAAGTCATTTTAGGT 60.363 40.741 0.00 0.00 37.56 3.08
281 303 8.312564 GTCTAGGTGAGTAAGTCATTTTAGGTT 58.687 37.037 0.00 0.00 37.56 3.50
282 304 8.311836 TCTAGGTGAGTAAGTCATTTTAGGTTG 58.688 37.037 0.00 0.00 37.56 3.77
284 306 6.710744 AGGTGAGTAAGTCATTTTAGGTTGTG 59.289 38.462 0.00 0.00 37.56 3.33
285 307 6.371389 GTGAGTAAGTCATTTTAGGTTGTGC 58.629 40.000 0.00 0.00 37.56 4.57
286 308 6.017440 GTGAGTAAGTCATTTTAGGTTGTGCA 60.017 38.462 0.00 0.00 37.56 4.57
287 309 6.017440 TGAGTAAGTCATTTTAGGTTGTGCAC 60.017 38.462 10.75 10.75 0.00 4.57
295 317 2.515057 GGTTGTGCACCGTGACCA 60.515 61.111 15.69 0.00 35.12 4.02
297 319 1.355210 GTTGTGCACCGTGACCAAG 59.645 57.895 15.69 0.00 0.00 3.61
299 321 2.110213 GTGCACCGTGACCAAGGA 59.890 61.111 5.22 0.00 33.97 3.36
301 323 2.358737 GCACCGTGACCAAGGAGG 60.359 66.667 8.91 2.33 45.67 4.30
305 327 1.609501 CCGTGACCAAGGAGGAGGA 60.610 63.158 0.00 0.00 41.22 3.71
306 328 1.192146 CCGTGACCAAGGAGGAGGAA 61.192 60.000 0.00 0.00 41.22 3.36
307 329 0.685097 CGTGACCAAGGAGGAGGAAA 59.315 55.000 0.00 0.00 41.22 3.13
308 330 1.071699 CGTGACCAAGGAGGAGGAAAA 59.928 52.381 0.00 0.00 41.22 2.29
309 331 2.486548 CGTGACCAAGGAGGAGGAAAAA 60.487 50.000 0.00 0.00 41.22 1.94
371 393 3.855689 ATGCAATGAACTAACCACTGC 57.144 42.857 0.00 0.00 0.00 4.40
372 394 2.580962 TGCAATGAACTAACCACTGCA 58.419 42.857 0.00 0.00 36.06 4.41
373 395 3.156293 TGCAATGAACTAACCACTGCAT 58.844 40.909 0.00 0.00 33.65 3.96
374 396 3.057386 TGCAATGAACTAACCACTGCATG 60.057 43.478 0.00 0.00 33.65 4.06
375 397 3.057315 GCAATGAACTAACCACTGCATGT 60.057 43.478 0.00 0.00 0.00 3.21
376 398 4.726416 CAATGAACTAACCACTGCATGTC 58.274 43.478 0.00 0.00 0.00 3.06
377 399 2.412870 TGAACTAACCACTGCATGTCG 58.587 47.619 0.00 0.00 0.00 4.35
378 400 2.224185 TGAACTAACCACTGCATGTCGT 60.224 45.455 0.00 0.00 0.00 4.34
379 401 1.795768 ACTAACCACTGCATGTCGTG 58.204 50.000 8.87 8.87 0.00 4.35
381 403 2.143122 CTAACCACTGCATGTCGTGTT 58.857 47.619 13.12 10.39 0.00 3.32
382 404 1.388547 AACCACTGCATGTCGTGTTT 58.611 45.000 13.12 5.09 0.00 2.83
383 405 0.662619 ACCACTGCATGTCGTGTTTG 59.337 50.000 13.12 3.87 0.00 2.93
384 406 0.943673 CCACTGCATGTCGTGTTTGA 59.056 50.000 13.12 0.00 0.00 2.69
385 407 1.536766 CCACTGCATGTCGTGTTTGAT 59.463 47.619 13.12 0.00 0.00 2.57
387 409 3.181517 CCACTGCATGTCGTGTTTGATAG 60.182 47.826 13.12 0.00 0.00 2.08
392 414 3.926527 GCATGTCGTGTTTGATAGTCTCA 59.073 43.478 0.00 0.00 0.00 3.27
393 415 4.388773 GCATGTCGTGTTTGATAGTCTCAA 59.611 41.667 0.00 0.00 42.15 3.02
394 416 5.445142 GCATGTCGTGTTTGATAGTCTCAAG 60.445 44.000 0.00 0.00 44.48 3.02
395 417 5.196341 TGTCGTGTTTGATAGTCTCAAGT 57.804 39.130 0.00 0.00 44.48 3.16
396 418 5.597806 TGTCGTGTTTGATAGTCTCAAGTT 58.402 37.500 0.00 0.00 44.48 2.66
397 419 6.741109 TGTCGTGTTTGATAGTCTCAAGTTA 58.259 36.000 0.00 0.00 44.48 2.24
398 420 7.375834 TGTCGTGTTTGATAGTCTCAAGTTAT 58.624 34.615 0.00 0.00 44.48 1.89
400 422 9.350357 GTCGTGTTTGATAGTCTCAAGTTATTA 57.650 33.333 0.00 0.00 44.48 0.98
401 423 9.917129 TCGTGTTTGATAGTCTCAAGTTATTAA 57.083 29.630 0.00 0.00 44.48 1.40
409 431 9.657121 GATAGTCTCAAGTTATTAAAAGCATGC 57.343 33.333 10.51 10.51 0.00 4.06
410 432 7.452880 AGTCTCAAGTTATTAAAAGCATGCA 57.547 32.000 21.98 0.00 0.00 3.96
412 434 7.040478 AGTCTCAAGTTATTAAAAGCATGCACA 60.040 33.333 21.98 0.00 0.00 4.57
414 436 6.155827 TCAAGTTATTAAAAGCATGCACACC 58.844 36.000 21.98 0.00 0.00 4.16
415 437 5.982890 AGTTATTAAAAGCATGCACACCT 57.017 34.783 21.98 2.16 0.00 4.00
416 438 6.345096 AGTTATTAAAAGCATGCACACCTT 57.655 33.333 21.98 1.21 0.00 3.50
417 439 7.461182 AGTTATTAAAAGCATGCACACCTTA 57.539 32.000 21.98 6.66 0.00 2.69
418 440 7.312899 AGTTATTAAAAGCATGCACACCTTAC 58.687 34.615 21.98 8.66 0.00 2.34
419 441 5.982890 ATTAAAAGCATGCACACCTTACT 57.017 34.783 21.98 1.49 0.00 2.24
420 442 5.782893 TTAAAAGCATGCACACCTTACTT 57.217 34.783 21.98 0.00 0.00 2.24
422 444 2.867109 AGCATGCACACCTTACTTCT 57.133 45.000 21.98 0.00 0.00 2.85
423 445 2.704572 AGCATGCACACCTTACTTCTC 58.295 47.619 21.98 0.00 0.00 2.87
424 446 2.304180 AGCATGCACACCTTACTTCTCT 59.696 45.455 21.98 0.00 0.00 3.10
425 447 3.077359 GCATGCACACCTTACTTCTCTT 58.923 45.455 14.21 0.00 0.00 2.85
426 448 4.020218 AGCATGCACACCTTACTTCTCTTA 60.020 41.667 21.98 0.00 0.00 2.10
428 450 5.355350 GCATGCACACCTTACTTCTCTTATT 59.645 40.000 14.21 0.00 0.00 1.40
429 451 6.676456 GCATGCACACCTTACTTCTCTTATTG 60.676 42.308 14.21 0.00 0.00 1.90
430 452 5.245531 TGCACACCTTACTTCTCTTATTGG 58.754 41.667 0.00 0.00 0.00 3.16
431 453 5.221843 TGCACACCTTACTTCTCTTATTGGT 60.222 40.000 0.00 0.00 0.00 3.67
432 454 5.705905 GCACACCTTACTTCTCTTATTGGTT 59.294 40.000 0.00 0.00 0.00 3.67
433 455 6.348540 GCACACCTTACTTCTCTTATTGGTTG 60.349 42.308 0.00 0.00 0.00 3.77
434 456 6.934645 CACACCTTACTTCTCTTATTGGTTGA 59.065 38.462 0.00 0.00 0.00 3.18
436 458 8.822805 ACACCTTACTTCTCTTATTGGTTGATA 58.177 33.333 0.00 0.00 0.00 2.15
437 459 9.838339 CACCTTACTTCTCTTATTGGTTGATAT 57.162 33.333 0.00 0.00 0.00 1.63
438 460 9.838339 ACCTTACTTCTCTTATTGGTTGATATG 57.162 33.333 0.00 0.00 0.00 1.78
439 461 9.838339 CCTTACTTCTCTTATTGGTTGATATGT 57.162 33.333 0.00 0.00 0.00 2.29
443 465 9.388506 ACTTCTCTTATTGGTTGATATGTCAAG 57.611 33.333 4.98 0.00 44.58 3.02
445 467 9.958180 TTCTCTTATTGGTTGATATGTCAAGAA 57.042 29.630 4.98 2.47 44.58 2.52
446 468 9.958180 TCTCTTATTGGTTGATATGTCAAGAAA 57.042 29.630 4.98 3.84 44.58 2.52
448 470 9.513906 TCTTATTGGTTGATATGTCAAGAAACA 57.486 29.630 4.98 0.63 44.58 2.83
452 474 9.829507 ATTGGTTGATATGTCAAGAAACAAAAA 57.170 25.926 4.98 0.00 44.58 1.94
475 497 9.520204 AAAAATGAGATAGAATTTAATGCACCG 57.480 29.630 0.00 0.00 0.00 4.94
479 501 2.825086 AGAATTTAATGCACCGCGTC 57.175 45.000 4.92 0.00 0.00 5.19
480 502 2.356135 AGAATTTAATGCACCGCGTCT 58.644 42.857 4.92 0.00 0.00 4.18
481 503 3.527533 AGAATTTAATGCACCGCGTCTA 58.472 40.909 4.92 0.00 0.00 2.59
482 504 3.936453 AGAATTTAATGCACCGCGTCTAA 59.064 39.130 4.92 0.00 0.00 2.10
484 506 2.373540 TTAATGCACCGCGTCTAAGT 57.626 45.000 4.92 0.00 0.00 2.24
486 508 0.320421 AATGCACCGCGTCTAAGTGT 60.320 50.000 4.92 0.00 33.96 3.55
488 510 0.531090 TGCACCGCGTCTAAGTGTTT 60.531 50.000 4.92 0.00 33.96 2.83
489 511 0.584876 GCACCGCGTCTAAGTGTTTT 59.415 50.000 4.92 0.00 33.96 2.43
490 512 1.659211 GCACCGCGTCTAAGTGTTTTG 60.659 52.381 4.92 0.00 33.96 2.44
494 516 2.073816 CGCGTCTAAGTGTTTTGGGAT 58.926 47.619 0.00 0.00 0.00 3.85
497 519 4.331717 CGCGTCTAAGTGTTTTGGGATTAT 59.668 41.667 0.00 0.00 0.00 1.28
498 520 5.163794 CGCGTCTAAGTGTTTTGGGATTATT 60.164 40.000 0.00 0.00 0.00 1.40
499 521 6.617879 GCGTCTAAGTGTTTTGGGATTATTT 58.382 36.000 0.00 0.00 0.00 1.40
500 522 6.526674 GCGTCTAAGTGTTTTGGGATTATTTG 59.473 38.462 0.00 0.00 0.00 2.32
501 523 7.027161 CGTCTAAGTGTTTTGGGATTATTTGG 58.973 38.462 0.00 0.00 0.00 3.28
502 524 7.308951 CGTCTAAGTGTTTTGGGATTATTTGGT 60.309 37.037 0.00 0.00 0.00 3.67
503 525 8.364894 GTCTAAGTGTTTTGGGATTATTTGGTT 58.635 33.333 0.00 0.00 0.00 3.67
505 527 9.554395 CTAAGTGTTTTGGGATTATTTGGTTTT 57.446 29.630 0.00 0.00 0.00 2.43
506 528 8.445275 AAGTGTTTTGGGATTATTTGGTTTTC 57.555 30.769 0.00 0.00 0.00 2.29
507 529 6.704050 AGTGTTTTGGGATTATTTGGTTTTCG 59.296 34.615 0.00 0.00 0.00 3.46
508 530 6.480651 GTGTTTTGGGATTATTTGGTTTTCGT 59.519 34.615 0.00 0.00 0.00 3.85
509 531 7.652507 GTGTTTTGGGATTATTTGGTTTTCGTA 59.347 33.333 0.00 0.00 0.00 3.43
531 553 4.966965 AGATGACTTACACACCTAGACG 57.033 45.455 0.00 0.00 0.00 4.18
532 554 3.695060 AGATGACTTACACACCTAGACGG 59.305 47.826 0.00 0.00 39.35 4.79
533 555 3.144657 TGACTTACACACCTAGACGGA 57.855 47.619 0.00 0.00 36.31 4.69
534 556 3.079578 TGACTTACACACCTAGACGGAG 58.920 50.000 0.00 0.00 36.31 4.63
535 557 2.422832 GACTTACACACCTAGACGGAGG 59.577 54.545 0.00 0.00 42.89 4.30
536 558 1.749634 CTTACACACCTAGACGGAGGG 59.250 57.143 5.42 0.00 41.36 4.30
537 559 0.994247 TACACACCTAGACGGAGGGA 59.006 55.000 5.42 0.00 41.36 4.20
554 598 3.577415 GAGGGAGTATATTTGCCGGTAGT 59.423 47.826 1.90 0.00 0.00 2.73
556 600 4.525874 AGGGAGTATATTTGCCGGTAGTAC 59.474 45.833 1.90 0.99 0.00 2.73
557 601 4.281688 GGGAGTATATTTGCCGGTAGTACA 59.718 45.833 1.90 0.00 0.00 2.90
558 602 5.467705 GGAGTATATTTGCCGGTAGTACAG 58.532 45.833 1.90 0.00 0.00 2.74
559 603 5.010415 GGAGTATATTTGCCGGTAGTACAGT 59.990 44.000 1.90 0.00 0.00 3.55
560 604 6.207417 GGAGTATATTTGCCGGTAGTACAGTA 59.793 42.308 1.90 0.00 0.00 2.74
562 606 6.774656 AGTATATTTGCCGGTAGTACAGTACT 59.225 38.462 17.51 17.51 42.68 2.73
563 607 3.855689 TTTGCCGGTAGTACAGTACTC 57.144 47.619 16.91 8.72 40.14 2.59
564 608 1.755179 TGCCGGTAGTACAGTACTCC 58.245 55.000 16.91 15.52 40.14 3.85
667 3466 2.436646 CGAGTTGGCCAGCCGATT 60.437 61.111 16.95 0.00 39.42 3.34
685 3484 3.560068 CGATTTATACCACCTGTTGCTCC 59.440 47.826 0.00 0.00 0.00 4.70
883 3722 6.307318 GTCGACGAAATGGAAGCGTATATATT 59.693 38.462 0.00 0.00 38.51 1.28
1027 3894 1.896660 GGTGGCAGGAAAACGAGCA 60.897 57.895 0.00 0.00 0.00 4.26
1104 3971 3.503363 GTGAGCTGCATGTCCGGC 61.503 66.667 1.02 0.00 37.37 6.13
1325 4202 4.821589 CCTGTCGCGGAGGAAGCC 62.822 72.222 17.42 0.00 31.48 4.35
1549 4426 9.952030 ATAAAACTTAGCTTCTTTCTTCTAGCT 57.048 29.630 0.00 0.00 45.32 3.32
1551 4428 8.996024 AAACTTAGCTTCTTTCTTCTAGCTAG 57.004 34.615 15.01 15.01 44.39 3.42
1552 4429 7.948034 ACTTAGCTTCTTTCTTCTAGCTAGA 57.052 36.000 19.72 19.72 44.39 2.43
1561 4438 7.721402 TCTTTCTTCTAGCTAGATGTCCATTC 58.279 38.462 27.04 0.00 31.40 2.67
1571 4448 5.182760 GCTAGATGTCCATTCATTGATTCCC 59.817 44.000 0.00 0.00 0.00 3.97
1573 4450 3.754219 TGTCCATTCATTGATTCCCCA 57.246 42.857 0.00 0.00 0.00 4.96
1582 4459 4.848357 TCATTGATTCCCCAAGTTCTCTC 58.152 43.478 0.00 0.00 0.00 3.20
1594 4471 4.382901 CCAAGTTCTCTCTCCCTCTTGATG 60.383 50.000 0.00 0.00 35.69 3.07
1596 4473 4.882559 AGTTCTCTCTCCCTCTTGATGAT 58.117 43.478 0.00 0.00 0.00 2.45
1602 4479 7.128751 TCTCTCTCCCTCTTGATGATTTCTTA 58.871 38.462 0.00 0.00 0.00 2.10
1668 4546 7.977789 ATTACATTGAAATTTCCAAACCACC 57.022 32.000 15.48 0.00 0.00 4.61
1669 4547 5.365021 ACATTGAAATTTCCAAACCACCA 57.635 34.783 15.48 0.00 0.00 4.17
1677 4555 0.752376 TCCAAACCACCAAACGACCC 60.752 55.000 0.00 0.00 0.00 4.46
1685 4563 1.071071 CACCAAACGACCCCTTACTGA 59.929 52.381 0.00 0.00 0.00 3.41
1686 4564 1.071228 ACCAAACGACCCCTTACTGAC 59.929 52.381 0.00 0.00 0.00 3.51
1699 4586 4.330074 CCCTTACTGACGCAAATAGAACTG 59.670 45.833 0.00 0.00 0.00 3.16
1706 4593 3.589988 ACGCAAATAGAACTGTCTCCAG 58.410 45.455 0.00 0.00 44.68 3.86
1747 4634 2.309528 TAAATGCTAGCTGGTCACGG 57.690 50.000 17.23 0.00 0.00 4.94
1791 4678 5.009210 CGGTTTGAAACTGGAAATGACCTTA 59.991 40.000 8.99 0.00 34.07 2.69
1793 4680 6.183360 GGTTTGAAACTGGAAATGACCTTACA 60.183 38.462 8.09 0.00 0.00 2.41
1796 4683 5.411361 TGAAACTGGAAATGACCTTACATCG 59.589 40.000 0.00 0.00 0.00 3.84
1802 4689 4.457949 GGAAATGACCTTACATCGTTGGTT 59.542 41.667 0.00 0.00 32.30 3.67
1820 4707 4.697514 TGGTTGAAGAGAACTGAACTCTG 58.302 43.478 0.00 0.00 42.85 3.35
1821 4708 4.061596 GGTTGAAGAGAACTGAACTCTGG 58.938 47.826 0.00 0.00 42.85 3.86
1822 4709 4.202264 GGTTGAAGAGAACTGAACTCTGGA 60.202 45.833 0.00 0.00 42.85 3.86
1823 4710 5.360591 GTTGAAGAGAACTGAACTCTGGAA 58.639 41.667 0.00 0.00 42.85 3.53
1824 4711 5.207110 TGAAGAGAACTGAACTCTGGAAG 57.793 43.478 0.00 0.00 42.85 3.46
1825 4712 3.676291 AGAGAACTGAACTCTGGAAGC 57.324 47.619 0.00 0.00 42.20 3.86
1826 4713 2.968574 AGAGAACTGAACTCTGGAAGCA 59.031 45.455 0.00 0.00 42.20 3.91
1827 4714 3.389329 AGAGAACTGAACTCTGGAAGCAA 59.611 43.478 0.00 0.00 42.20 3.91
1836 4723 3.871485 ACTCTGGAAGCAAAGCATCTAG 58.129 45.455 1.87 1.87 36.48 2.43
1839 4726 3.771479 TCTGGAAGCAAAGCATCTAGAGA 59.229 43.478 6.26 0.00 38.52 3.10
1876 4776 1.070134 GCCTCATACGCCTGGTCATTA 59.930 52.381 0.00 0.00 0.00 1.90
1946 4848 4.742201 CTGGACTGACCGGCACCG 62.742 72.222 0.00 1.02 42.61 4.94
1968 4871 5.767665 CCGTTCATATCCAACCCAAATATGA 59.232 40.000 0.00 0.00 39.44 2.15
2018 4921 2.035312 ACGTCCTACCCGACAGCT 59.965 61.111 0.00 0.00 32.74 4.24
2039 4942 1.755959 CGATCCCATCCCAAATTGCAA 59.244 47.619 0.00 0.00 0.00 4.08
2102 5006 1.354705 TCTCTTCTTCCTCCTCCACGA 59.645 52.381 0.00 0.00 0.00 4.35
2114 5018 1.645704 CTCCACGACGTCCATCTCGT 61.646 60.000 10.58 0.15 43.83 4.18
2260 5198 0.540830 ACTCTCTGTCTCCGCCTTGT 60.541 55.000 0.00 0.00 0.00 3.16
2381 5320 4.660168 ACAGAGCTTGACCAAATGATTCT 58.340 39.130 0.00 0.00 0.00 2.40
2397 5336 8.538856 CAAATGATTCTAGATGAGTTCTTCGAC 58.461 37.037 0.00 0.00 35.79 4.20
2425 5365 3.256136 AGATTCGAACGAAGAAGTGGACT 59.744 43.478 14.52 0.00 37.56 3.85
2429 5369 2.726760 CGAACGAAGAAGTGGACTTGAG 59.273 50.000 0.00 0.00 36.11 3.02
2461 5401 5.072055 TGAGCATGAAAGAGGAAATGAACA 58.928 37.500 0.00 0.00 0.00 3.18
2463 5403 5.075493 AGCATGAAAGAGGAAATGAACAGT 58.925 37.500 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.759959 ACACGGACACACCACCATTA 59.240 50.000 0.00 0.00 38.90 1.90
24 25 1.070786 GACACGGACACACCACCAT 59.929 57.895 0.00 0.00 38.90 3.55
116 122 5.385198 AGCTACCATCACTTTTCCTTTTCA 58.615 37.500 0.00 0.00 0.00 2.69
162 181 4.267928 CGACCTCTATTGTTTCGATTGTCC 59.732 45.833 0.00 0.00 0.00 4.02
176 198 3.678056 TTGAAACACAGCGACCTCTAT 57.322 42.857 0.00 0.00 0.00 1.98
193 215 1.375396 AGCGCACGTAAGCCATTGA 60.375 52.632 11.47 0.00 45.62 2.57
239 261 5.008811 CACCTAGACGGAGGAAGTACAATAG 59.991 48.000 7.23 0.00 39.15 1.73
241 263 3.700038 CACCTAGACGGAGGAAGTACAAT 59.300 47.826 7.23 0.00 39.15 2.71
242 264 3.087031 CACCTAGACGGAGGAAGTACAA 58.913 50.000 7.23 0.00 39.15 2.41
243 265 2.306805 TCACCTAGACGGAGGAAGTACA 59.693 50.000 7.23 0.00 39.15 2.90
246 268 1.355043 ACTCACCTAGACGGAGGAAGT 59.645 52.381 7.23 7.11 39.15 3.01
247 269 2.131776 ACTCACCTAGACGGAGGAAG 57.868 55.000 7.23 6.60 39.15 3.46
248 270 3.009916 ACTTACTCACCTAGACGGAGGAA 59.990 47.826 7.23 0.00 39.15 3.36
249 271 2.575279 ACTTACTCACCTAGACGGAGGA 59.425 50.000 7.23 0.00 39.15 3.71
252 274 3.708403 TGACTTACTCACCTAGACGGA 57.292 47.619 0.00 0.00 36.31 4.69
253 275 4.985538 AATGACTTACTCACCTAGACGG 57.014 45.455 0.00 0.00 39.35 4.79
254 276 6.973474 CCTAAAATGACTTACTCACCTAGACG 59.027 42.308 0.00 0.00 0.00 4.18
255 277 7.838884 ACCTAAAATGACTTACTCACCTAGAC 58.161 38.462 0.00 0.00 0.00 2.59
256 278 8.311836 CAACCTAAAATGACTTACTCACCTAGA 58.688 37.037 0.00 0.00 0.00 2.43
257 279 8.095169 ACAACCTAAAATGACTTACTCACCTAG 58.905 37.037 0.00 0.00 0.00 3.02
258 280 7.876068 CACAACCTAAAATGACTTACTCACCTA 59.124 37.037 0.00 0.00 0.00 3.08
260 282 6.567891 GCACAACCTAAAATGACTTACTCACC 60.568 42.308 0.00 0.00 0.00 4.02
261 283 6.017440 TGCACAACCTAAAATGACTTACTCAC 60.017 38.462 0.00 0.00 0.00 3.51
262 284 6.017440 GTGCACAACCTAAAATGACTTACTCA 60.017 38.462 13.17 0.00 0.00 3.41
263 285 6.371389 GTGCACAACCTAAAATGACTTACTC 58.629 40.000 13.17 0.00 0.00 2.59
264 286 5.240844 GGTGCACAACCTAAAATGACTTACT 59.759 40.000 20.43 0.00 46.55 2.24
267 289 4.584327 GGTGCACAACCTAAAATGACTT 57.416 40.909 20.43 0.00 46.55 3.01
278 300 2.058829 CTTGGTCACGGTGCACAACC 62.059 60.000 20.43 18.91 46.60 3.77
279 301 1.355210 CTTGGTCACGGTGCACAAC 59.645 57.895 20.43 10.47 0.00 3.32
280 302 1.821759 CCTTGGTCACGGTGCACAA 60.822 57.895 20.43 9.76 0.00 3.33
281 303 2.203139 CCTTGGTCACGGTGCACA 60.203 61.111 20.43 1.81 0.00 4.57
282 304 1.961277 CTCCTTGGTCACGGTGCAC 60.961 63.158 8.80 8.80 0.00 4.57
284 306 2.358737 CCTCCTTGGTCACGGTGC 60.359 66.667 2.51 0.00 0.00 5.01
285 307 1.293498 CTCCTCCTTGGTCACGGTG 59.707 63.158 0.56 0.56 37.07 4.94
286 308 1.913762 CCTCCTCCTTGGTCACGGT 60.914 63.158 0.00 0.00 37.07 4.83
287 309 1.192146 TTCCTCCTCCTTGGTCACGG 61.192 60.000 0.00 0.00 37.07 4.94
288 310 0.685097 TTTCCTCCTCCTTGGTCACG 59.315 55.000 0.00 0.00 37.07 4.35
289 311 2.951229 TTTTCCTCCTCCTTGGTCAC 57.049 50.000 0.00 0.00 37.07 3.67
346 368 4.221262 AGTGGTTAGTTCATTGCATGCAAT 59.779 37.500 34.78 34.78 46.35 3.56
348 370 3.057386 CAGTGGTTAGTTCATTGCATGCA 60.057 43.478 18.46 18.46 0.00 3.96
350 372 3.504863 GCAGTGGTTAGTTCATTGCATG 58.495 45.455 6.68 0.00 44.01 4.06
351 373 3.855689 GCAGTGGTTAGTTCATTGCAT 57.144 42.857 6.68 0.00 44.01 3.96
353 375 3.057315 ACATGCAGTGGTTAGTTCATTGC 60.057 43.478 0.00 4.92 44.56 3.56
354 376 4.669965 CGACATGCAGTGGTTAGTTCATTG 60.670 45.833 0.00 0.00 0.00 2.82
355 377 3.436704 CGACATGCAGTGGTTAGTTCATT 59.563 43.478 0.00 0.00 0.00 2.57
356 378 3.002791 CGACATGCAGTGGTTAGTTCAT 58.997 45.455 0.00 0.00 0.00 2.57
358 380 2.157668 CACGACATGCAGTGGTTAGTTC 59.842 50.000 11.93 0.00 37.03 3.01
361 383 1.795768 ACACGACATGCAGTGGTTAG 58.204 50.000 20.60 1.38 42.25 2.34
362 384 2.248280 AACACGACATGCAGTGGTTA 57.752 45.000 20.60 0.00 42.25 2.85
363 385 1.388547 AAACACGACATGCAGTGGTT 58.611 45.000 20.60 18.36 42.73 3.67
364 386 0.662619 CAAACACGACATGCAGTGGT 59.337 50.000 20.60 14.15 42.25 4.16
366 388 2.975410 ATCAAACACGACATGCAGTG 57.025 45.000 16.62 16.62 43.46 3.66
367 389 3.664107 ACTATCAAACACGACATGCAGT 58.336 40.909 0.00 0.00 0.00 4.40
368 390 3.928992 AGACTATCAAACACGACATGCAG 59.071 43.478 0.00 0.00 0.00 4.41
369 391 3.925379 AGACTATCAAACACGACATGCA 58.075 40.909 0.00 0.00 0.00 3.96
383 405 9.657121 GCATGCTTTTAATAACTTGAGACTATC 57.343 33.333 11.37 0.00 0.00 2.08
384 406 9.177608 TGCATGCTTTTAATAACTTGAGACTAT 57.822 29.630 20.33 0.00 0.00 2.12
385 407 8.450964 GTGCATGCTTTTAATAACTTGAGACTA 58.549 33.333 20.33 0.00 0.00 2.59
387 409 7.061094 GTGTGCATGCTTTTAATAACTTGAGAC 59.939 37.037 20.33 2.56 0.00 3.36
392 414 6.345096 AGGTGTGCATGCTTTTAATAACTT 57.655 33.333 20.33 0.00 0.00 2.66
393 415 5.982890 AGGTGTGCATGCTTTTAATAACT 57.017 34.783 20.33 0.92 0.00 2.24
394 416 7.312899 AGTAAGGTGTGCATGCTTTTAATAAC 58.687 34.615 20.33 6.41 0.00 1.89
395 417 7.461182 AGTAAGGTGTGCATGCTTTTAATAA 57.539 32.000 20.33 0.00 0.00 1.40
396 418 7.393234 AGAAGTAAGGTGTGCATGCTTTTAATA 59.607 33.333 20.33 3.11 0.00 0.98
397 419 5.982890 AGTAAGGTGTGCATGCTTTTAAT 57.017 34.783 20.33 6.78 0.00 1.40
398 420 5.534654 AGAAGTAAGGTGTGCATGCTTTTAA 59.465 36.000 20.33 0.00 0.00 1.52
400 422 3.891366 AGAAGTAAGGTGTGCATGCTTTT 59.109 39.130 20.33 8.36 0.00 2.27
401 423 3.490348 AGAAGTAAGGTGTGCATGCTTT 58.510 40.909 20.33 8.03 0.00 3.51
402 424 3.077359 GAGAAGTAAGGTGTGCATGCTT 58.923 45.455 20.33 6.81 0.00 3.91
404 426 2.704572 AGAGAAGTAAGGTGTGCATGC 58.295 47.619 11.82 11.82 0.00 4.06
405 427 6.183360 CCAATAAGAGAAGTAAGGTGTGCATG 60.183 42.308 0.00 0.00 0.00 4.06
406 428 5.882557 CCAATAAGAGAAGTAAGGTGTGCAT 59.117 40.000 0.00 0.00 0.00 3.96
407 429 5.221843 ACCAATAAGAGAAGTAAGGTGTGCA 60.222 40.000 0.00 0.00 0.00 4.57
408 430 5.246307 ACCAATAAGAGAAGTAAGGTGTGC 58.754 41.667 0.00 0.00 0.00 4.57
409 431 6.934645 TCAACCAATAAGAGAAGTAAGGTGTG 59.065 38.462 0.00 0.00 0.00 3.82
410 432 7.074653 TCAACCAATAAGAGAAGTAAGGTGT 57.925 36.000 0.00 0.00 0.00 4.16
412 434 9.838339 CATATCAACCAATAAGAGAAGTAAGGT 57.162 33.333 0.00 0.00 0.00 3.50
417 439 9.388506 CTTGACATATCAACCAATAAGAGAAGT 57.611 33.333 0.00 0.00 40.01 3.01
418 440 9.605275 TCTTGACATATCAACCAATAAGAGAAG 57.395 33.333 0.00 0.00 40.01 2.85
419 441 9.958180 TTCTTGACATATCAACCAATAAGAGAA 57.042 29.630 0.00 0.00 40.01 2.87
420 442 9.958180 TTTCTTGACATATCAACCAATAAGAGA 57.042 29.630 0.00 0.00 40.01 3.10
422 444 9.513906 TGTTTCTTGACATATCAACCAATAAGA 57.486 29.630 0.00 0.00 40.01 2.10
426 448 9.829507 TTTTTGTTTCTTGACATATCAACCAAT 57.170 25.926 0.00 0.00 40.01 3.16
449 471 9.520204 CGGTGCATTAAATTCTATCTCATTTTT 57.480 29.630 0.00 0.00 0.00 1.94
450 472 7.649306 GCGGTGCATTAAATTCTATCTCATTTT 59.351 33.333 0.00 0.00 0.00 1.82
451 473 7.141363 GCGGTGCATTAAATTCTATCTCATTT 58.859 34.615 0.00 0.00 0.00 2.32
452 474 6.566564 CGCGGTGCATTAAATTCTATCTCATT 60.567 38.462 0.00 0.00 0.00 2.57
453 475 5.106948 CGCGGTGCATTAAATTCTATCTCAT 60.107 40.000 0.00 0.00 0.00 2.90
458 480 4.127171 AGACGCGGTGCATTAAATTCTAT 58.873 39.130 12.47 0.00 0.00 1.98
459 481 3.527533 AGACGCGGTGCATTAAATTCTA 58.472 40.909 12.47 0.00 0.00 2.10
460 482 2.356135 AGACGCGGTGCATTAAATTCT 58.644 42.857 12.47 0.00 0.00 2.40
462 484 3.687698 ACTTAGACGCGGTGCATTAAATT 59.312 39.130 12.47 0.00 0.00 1.82
463 485 3.063452 CACTTAGACGCGGTGCATTAAAT 59.937 43.478 12.47 0.00 0.00 1.40
464 486 2.413796 CACTTAGACGCGGTGCATTAAA 59.586 45.455 12.47 0.00 0.00 1.52
465 487 1.996898 CACTTAGACGCGGTGCATTAA 59.003 47.619 12.47 0.00 0.00 1.40
466 488 1.067425 ACACTTAGACGCGGTGCATTA 60.067 47.619 12.47 0.00 34.70 1.90
469 491 0.531090 AAACACTTAGACGCGGTGCA 60.531 50.000 12.47 0.00 34.70 4.57
470 492 0.584876 AAAACACTTAGACGCGGTGC 59.415 50.000 12.47 0.00 34.70 5.01
471 493 1.070175 CCAAAACACTTAGACGCGGTG 60.070 52.381 12.47 11.18 37.05 4.94
473 495 0.515564 CCCAAAACACTTAGACGCGG 59.484 55.000 12.47 0.00 0.00 6.46
475 497 5.813080 ATAATCCCAAAACACTTAGACGC 57.187 39.130 0.00 0.00 0.00 5.19
479 501 9.554395 AAAACCAAATAATCCCAAAACACTTAG 57.446 29.630 0.00 0.00 0.00 2.18
480 502 9.549078 GAAAACCAAATAATCCCAAAACACTTA 57.451 29.630 0.00 0.00 0.00 2.24
481 503 7.225734 CGAAAACCAAATAATCCCAAAACACTT 59.774 33.333 0.00 0.00 0.00 3.16
482 504 6.704050 CGAAAACCAAATAATCCCAAAACACT 59.296 34.615 0.00 0.00 0.00 3.55
484 506 6.583562 ACGAAAACCAAATAATCCCAAAACA 58.416 32.000 0.00 0.00 0.00 2.83
486 508 8.639761 TCTTACGAAAACCAAATAATCCCAAAA 58.360 29.630 0.00 0.00 0.00 2.44
488 510 7.762588 TCTTACGAAAACCAAATAATCCCAA 57.237 32.000 0.00 0.00 0.00 4.12
489 511 7.612244 TCATCTTACGAAAACCAAATAATCCCA 59.388 33.333 0.00 0.00 0.00 4.37
490 512 7.913821 GTCATCTTACGAAAACCAAATAATCCC 59.086 37.037 0.00 0.00 0.00 3.85
506 528 9.720809 CCGTCTAGGTGTGTAAGTCATCTTACG 62.721 48.148 11.67 0.00 44.84 3.18
507 529 6.677431 CCGTCTAGGTGTGTAAGTCATCTTAC 60.677 46.154 10.12 10.12 43.75 2.34
508 530 5.356190 CCGTCTAGGTGTGTAAGTCATCTTA 59.644 44.000 0.00 0.00 33.66 2.10
509 531 4.158025 CCGTCTAGGTGTGTAAGTCATCTT 59.842 45.833 0.00 0.00 35.02 2.40
513 535 3.079578 CTCCGTCTAGGTGTGTAAGTCA 58.920 50.000 0.00 0.00 41.99 3.41
514 536 2.422832 CCTCCGTCTAGGTGTGTAAGTC 59.577 54.545 0.00 0.00 41.99 3.01
516 538 1.749634 CCCTCCGTCTAGGTGTGTAAG 59.250 57.143 0.00 0.00 41.99 2.34
517 539 1.355381 TCCCTCCGTCTAGGTGTGTAA 59.645 52.381 0.00 0.00 41.99 2.41
518 540 0.994247 TCCCTCCGTCTAGGTGTGTA 59.006 55.000 0.00 0.00 41.99 2.90
520 542 0.323542 ACTCCCTCCGTCTAGGTGTG 60.324 60.000 0.00 0.00 41.99 3.82
521 543 1.293062 TACTCCCTCCGTCTAGGTGT 58.707 55.000 0.00 0.00 41.99 4.16
522 544 2.660670 ATACTCCCTCCGTCTAGGTG 57.339 55.000 0.00 0.00 41.99 4.00
523 545 5.078256 CAAATATACTCCCTCCGTCTAGGT 58.922 45.833 0.00 0.00 41.99 3.08
524 546 4.082136 GCAAATATACTCCCTCCGTCTAGG 60.082 50.000 0.00 0.00 42.97 3.02
526 548 3.830755 GGCAAATATACTCCCTCCGTCTA 59.169 47.826 0.00 0.00 0.00 2.59
527 549 2.633481 GGCAAATATACTCCCTCCGTCT 59.367 50.000 0.00 0.00 0.00 4.18
529 551 1.343465 CGGCAAATATACTCCCTCCGT 59.657 52.381 0.00 0.00 0.00 4.69
530 552 1.337823 CCGGCAAATATACTCCCTCCG 60.338 57.143 0.00 0.00 35.80 4.63
531 553 1.697982 ACCGGCAAATATACTCCCTCC 59.302 52.381 0.00 0.00 0.00 4.30
532 554 3.577415 ACTACCGGCAAATATACTCCCTC 59.423 47.826 0.00 0.00 0.00 4.30
533 555 3.584294 ACTACCGGCAAATATACTCCCT 58.416 45.455 0.00 0.00 0.00 4.20
534 556 4.281688 TGTACTACCGGCAAATATACTCCC 59.718 45.833 0.00 0.00 0.00 4.30
535 557 5.010415 ACTGTACTACCGGCAAATATACTCC 59.990 44.000 0.00 0.00 0.00 3.85
536 558 6.081872 ACTGTACTACCGGCAAATATACTC 57.918 41.667 0.00 0.00 0.00 2.59
537 559 6.774656 AGTACTGTACTACCGGCAAATATACT 59.225 38.462 18.42 0.00 37.23 2.12
554 598 3.433274 CGTGTCTGTTACGGAGTACTGTA 59.567 47.826 0.00 0.00 45.76 2.74
556 600 2.847901 CGTGTCTGTTACGGAGTACTG 58.152 52.381 0.00 0.00 45.76 2.74
557 601 1.198637 GCGTGTCTGTTACGGAGTACT 59.801 52.381 0.00 0.00 45.76 2.73
558 602 1.069022 TGCGTGTCTGTTACGGAGTAC 60.069 52.381 0.00 0.00 45.76 2.73
559 603 1.237533 TGCGTGTCTGTTACGGAGTA 58.762 50.000 0.00 0.00 45.11 2.59
560 604 0.386476 TTGCGTGTCTGTTACGGAGT 59.614 50.000 0.00 0.00 42.57 3.85
562 606 1.937278 TTTTGCGTGTCTGTTACGGA 58.063 45.000 0.00 0.00 41.56 4.69
563 607 2.741122 TTTTTGCGTGTCTGTTACGG 57.259 45.000 0.00 0.00 41.56 4.02
667 3466 2.684001 CGGAGCAACAGGTGGTATAA 57.316 50.000 0.00 0.00 38.34 0.98
685 3484 1.148498 GGGTTTGGAGGATAGGGCG 59.852 63.158 0.00 0.00 0.00 6.13
865 3690 7.117812 CCTCGTGAAATATATACGCTTCCATTT 59.882 37.037 2.29 0.00 37.70 2.32
883 3722 1.668919 GCAACTCGATCACCTCGTGAA 60.669 52.381 0.00 0.00 45.96 3.18
900 3741 4.629634 CGTTATGAGAGTGTACAATGGCAA 59.370 41.667 0.00 0.00 0.00 4.52
1027 3894 1.294780 CGAGGCAGAAGAAGCACCT 59.705 57.895 0.00 0.00 0.00 4.00
1548 4425 5.709164 GGGGAATCAATGAATGGACATCTAG 59.291 44.000 0.00 0.00 0.00 2.43
1549 4426 5.134169 TGGGGAATCAATGAATGGACATCTA 59.866 40.000 0.00 0.00 0.00 1.98
1550 4427 4.079038 TGGGGAATCAATGAATGGACATCT 60.079 41.667 0.00 0.00 0.00 2.90
1551 4428 4.217510 TGGGGAATCAATGAATGGACATC 58.782 43.478 0.00 0.00 0.00 3.06
1552 4429 4.268828 TGGGGAATCAATGAATGGACAT 57.731 40.909 0.00 0.00 0.00 3.06
1561 4438 4.853007 AGAGAGAACTTGGGGAATCAATG 58.147 43.478 0.00 0.00 0.00 2.82
1571 4448 3.169099 TCAAGAGGGAGAGAGAACTTGG 58.831 50.000 0.00 0.00 36.45 3.61
1573 4450 4.682563 TCATCAAGAGGGAGAGAGAACTT 58.317 43.478 0.00 0.00 0.00 2.66
1582 4459 7.772292 TGTCAATAAGAAATCATCAAGAGGGAG 59.228 37.037 0.00 0.00 0.00 4.30
1651 4528 4.081642 TCGTTTGGTGGTTTGGAAATTTCA 60.082 37.500 19.49 3.64 0.00 2.69
1652 4529 4.269123 GTCGTTTGGTGGTTTGGAAATTTC 59.731 41.667 9.83 9.83 0.00 2.17
1658 4535 0.752376 GGGTCGTTTGGTGGTTTGGA 60.752 55.000 0.00 0.00 0.00 3.53
1660 4537 0.753848 AGGGGTCGTTTGGTGGTTTG 60.754 55.000 0.00 0.00 0.00 2.93
1668 4546 1.425412 CGTCAGTAAGGGGTCGTTTG 58.575 55.000 0.00 0.00 0.00 2.93
1669 4547 0.320160 GCGTCAGTAAGGGGTCGTTT 60.320 55.000 0.00 0.00 0.00 3.60
1677 4555 4.929808 ACAGTTCTATTTGCGTCAGTAAGG 59.070 41.667 0.00 0.00 0.00 2.69
1685 4563 3.678056 TGGAGACAGTTCTATTTGCGT 57.322 42.857 0.00 0.00 35.01 5.24
1699 4586 0.678366 TCCTGCGAGAGACTGGAGAC 60.678 60.000 0.00 0.00 33.74 3.36
1747 4634 4.166011 GCTCCATCACCGCAACGC 62.166 66.667 0.00 0.00 0.00 4.84
1753 4640 1.234615 AAACCGTTGCTCCATCACCG 61.235 55.000 0.00 0.00 0.00 4.94
1791 4678 3.809832 CAGTTCTCTTCAACCAACGATGT 59.190 43.478 0.00 0.00 0.00 3.06
1793 4680 4.336889 TCAGTTCTCTTCAACCAACGAT 57.663 40.909 0.00 0.00 0.00 3.73
1796 4683 5.007136 CAGAGTTCAGTTCTCTTCAACCAAC 59.993 44.000 0.00 0.00 39.84 3.77
1802 4689 4.502259 GCTTCCAGAGTTCAGTTCTCTTCA 60.502 45.833 0.00 0.00 39.84 3.02
1820 4707 2.863137 CGTCTCTAGATGCTTTGCTTCC 59.137 50.000 0.00 0.00 33.95 3.46
1821 4708 2.863137 CCGTCTCTAGATGCTTTGCTTC 59.137 50.000 0.00 0.00 33.70 3.86
1822 4709 2.419297 CCCGTCTCTAGATGCTTTGCTT 60.419 50.000 0.00 0.00 0.00 3.91
1823 4710 1.137872 CCCGTCTCTAGATGCTTTGCT 59.862 52.381 0.00 0.00 0.00 3.91
1824 4711 1.576356 CCCGTCTCTAGATGCTTTGC 58.424 55.000 0.00 0.00 0.00 3.68
1825 4712 1.576356 GCCCGTCTCTAGATGCTTTG 58.424 55.000 0.00 0.00 0.00 2.77
1826 4713 0.103208 CGCCCGTCTCTAGATGCTTT 59.897 55.000 0.00 0.00 0.00 3.51
1827 4714 1.736586 CGCCCGTCTCTAGATGCTT 59.263 57.895 0.00 0.00 0.00 3.91
1836 4723 3.119096 GTTTGAGGCGCCCGTCTC 61.119 66.667 26.15 15.26 46.19 3.36
1897 4798 0.245539 CGTTTAAGAGGCCCGTCTGA 59.754 55.000 0.00 0.00 0.00 3.27
1946 4848 6.294731 GCCTCATATTTGGGTTGGATATGAAC 60.295 42.308 6.70 0.00 40.37 3.18
1947 4849 5.774690 GCCTCATATTTGGGTTGGATATGAA 59.225 40.000 6.70 0.00 40.37 2.57
1968 4871 2.520536 GGCACCTCCATATCCGCCT 61.521 63.158 0.00 0.00 36.58 5.52
2006 4909 1.655329 GGATCGAGCTGTCGGGTAG 59.345 63.158 0.00 0.00 46.80 3.18
2007 4910 1.826921 GGGATCGAGCTGTCGGGTA 60.827 63.158 0.00 0.00 46.80 3.69
2018 4921 1.064091 TGCAATTTGGGATGGGATCGA 60.064 47.619 0.00 0.00 0.00 3.59
2039 4942 0.037734 GGTCTTCGGGGTGGATTTGT 59.962 55.000 0.00 0.00 0.00 2.83
2102 5006 2.885861 GGAGCACGAGATGGACGT 59.114 61.111 0.00 0.00 44.83 4.34
2381 5320 4.251268 TGACGAGTCGAAGAACTCATCTA 58.749 43.478 21.50 0.00 39.69 1.98
2397 5336 3.118807 TCTTCGTTCGAATCTGACGAG 57.881 47.619 0.00 0.94 40.72 4.18
2403 5342 3.256136 AGTCCACTTCTTCGTTCGAATCT 59.744 43.478 0.00 0.00 0.00 2.40
2446 5386 5.300286 CCACTTGACTGTTCATTTCCTCTTT 59.700 40.000 0.00 0.00 0.00 2.52
2461 5401 5.046014 AGTTGAGAATATGCTCCACTTGACT 60.046 40.000 11.02 2.52 37.55 3.41
2463 5403 5.426689 AGTTGAGAATATGCTCCACTTGA 57.573 39.130 11.02 0.00 37.55 3.02


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

AutoCloner maintained by Alex Coulton.