Multiple sequence alignment - TraesCS7B01G123800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G123800 chr7B 100.000 3297 0 0 1 3297 144869140 144865844 0.000000e+00 6089
1 TraesCS7B01G123800 chr7B 95.086 2727 118 10 583 3297 398611055 398613777 0.000000e+00 4279
2 TraesCS7B01G123800 chr6A 96.076 2727 83 6 584 3297 557669503 557672218 0.000000e+00 4421
3 TraesCS7B01G123800 chr5A 96.367 2450 63 14 584 3019 646954812 646957249 0.000000e+00 4008
4 TraesCS7B01G123800 chr6B 94.719 2386 111 5 586 2958 363476811 363479194 0.000000e+00 3694
5 TraesCS7B01G123800 chr1D 94.968 2345 92 10 965 3297 38867046 38869376 0.000000e+00 3653
6 TraesCS7B01G123800 chr1D 90.792 1705 109 17 580 2281 425079401 425081060 0.000000e+00 2235
7 TraesCS7B01G123800 chr1D 96.055 583 23 0 1 583 379769779 379769197 0.000000e+00 950
8 TraesCS7B01G123800 chr1D 85.714 448 43 11 842 1287 24463355 24462927 1.390000e-123 453
9 TraesCS7B01G123800 chr1D 89.714 350 34 2 939 1287 24484358 24484010 2.330000e-121 446
10 TraesCS7B01G123800 chr1D 93.514 185 11 1 1302 1485 66629202 66629018 1.170000e-69 274
11 TraesCS7B01G123800 chrUn 94.831 1741 76 4 584 2311 155229181 155230920 0.000000e+00 2704
12 TraesCS7B01G123800 chrUn 97.213 933 26 0 2365 3297 155230931 155231863 0.000000e+00 1580
13 TraesCS7B01G123800 chr1B 94.435 1743 81 4 584 2311 36186158 36187899 0.000000e+00 2667
14 TraesCS7B01G123800 chr1B 93.726 1562 82 5 584 2133 595831219 595832776 0.000000e+00 2327
15 TraesCS7B01G123800 chr1B 93.534 1562 85 5 584 2133 595882633 595884190 0.000000e+00 2311
16 TraesCS7B01G123800 chr1B 96.228 1405 50 2 892 2295 284048246 284046844 0.000000e+00 2298
17 TraesCS7B01G123800 chr1B 96.147 1116 40 3 2181 3296 595832784 595833896 0.000000e+00 1820
18 TraesCS7B01G123800 chr1B 96.147 1116 39 4 2181 3296 595884198 595885309 0.000000e+00 1820
19 TraesCS7B01G123800 chr1B 97.532 1013 24 1 2286 3297 284046249 284045237 0.000000e+00 1731
20 TraesCS7B01G123800 chr1A 92.337 1566 100 9 584 2131 300543235 300541672 0.000000e+00 2209
21 TraesCS7B01G123800 chr5D 90.848 1497 92 25 584 2067 254079394 254080858 0.000000e+00 1964
22 TraesCS7B01G123800 chr5D 82.238 715 71 27 584 1287 542950251 542949582 1.720000e-157 566
23 TraesCS7B01G123800 chr5D 95.804 143 6 0 1238 1380 170712281 170712423 7.110000e-57 231
24 TraesCS7B01G123800 chr3D 88.357 919 67 22 584 1485 517387813 517388708 0.000000e+00 1068
25 TraesCS7B01G123800 chr3D 87.662 924 68 16 581 1485 603158014 603158910 0.000000e+00 1033
26 TraesCS7B01G123800 chr3D 85.515 932 66 22 584 1485 611640854 611641746 0.000000e+00 909
27 TraesCS7B01G123800 chr7D 96.558 581 20 0 1 581 477373785 477374365 0.000000e+00 963
28 TraesCS7B01G123800 chr7D 96.055 583 23 0 1 583 269656971 269657553 0.000000e+00 950
29 TraesCS7B01G123800 chr4D 96.226 583 22 0 1 583 314494381 314493799 0.000000e+00 955
30 TraesCS7B01G123800 chr4D 96.055 583 23 0 1 583 324244962 324244380 0.000000e+00 950
31 TraesCS7B01G123800 chr4D 95.883 583 24 0 1 583 211077665 211077083 0.000000e+00 944
32 TraesCS7B01G123800 chr2D 96.226 583 22 0 1 583 459805439 459804857 0.000000e+00 955
33 TraesCS7B01G123800 chr2D 90.442 565 36 4 939 1485 425601658 425602222 0.000000e+00 728
34 TraesCS7B01G123800 chr2D 89.558 565 28 6 939 1485 650897418 650896867 0.000000e+00 688
35 TraesCS7B01G123800 chr2D 88.649 370 39 3 434 801 20278860 20279228 6.490000e-122 448
36 TraesCS7B01G123800 chr4B 86.827 873 90 16 584 1433 30399498 30400368 0.000000e+00 952
37 TraesCS7B01G123800 chr6D 96.055 583 23 0 1 583 24729138 24728556 0.000000e+00 950
38 TraesCS7B01G123800 chr6D 96.055 583 23 0 1 583 275891656 275892238 0.000000e+00 950
39 TraesCS7B01G123800 chr6D 83.862 725 54 38 584 1287 154198813 154199495 1.670000e-177 632
40 TraesCS7B01G123800 chr6D 88.462 260 26 3 954 1213 343522010 343522265 8.880000e-81 311
41 TraesCS7B01G123800 chr6D 93.706 143 9 0 1238 1380 343523416 343523558 7.170000e-52 215


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 TraesCS7B01G123800 chr7B 144865844 144869140 3296 True 6089.0 6089 100.0000 1 3297 1 chr7B.!!$R1 3296
1 TraesCS7B01G123800 chr7B 398611055 398613777 2722 False 4279.0 4279 95.0860 583 3297 1 chr7B.!!$F1 2714
2 TraesCS7B01G123800 chr6A 557669503 557672218 2715 False 4421.0 4421 96.0760 584 3297 1 chr6A.!!$F1 2713
3 TraesCS7B01G123800 chr5A 646954812 646957249 2437 False 4008.0 4008 96.3670 584 3019 1 chr5A.!!$F1 2435
4 TraesCS7B01G123800 chr6B 363476811 363479194 2383 False 3694.0 3694 94.7190 586 2958 1 chr6B.!!$F1 2372
5 TraesCS7B01G123800 chr1D 38867046 38869376 2330 False 3653.0 3653 94.9680 965 3297 1 chr1D.!!$F1 2332
6 TraesCS7B01G123800 chr1D 425079401 425081060 1659 False 2235.0 2235 90.7920 580 2281 1 chr1D.!!$F2 1701
7 TraesCS7B01G123800 chr1D 379769197 379769779 582 True 950.0 950 96.0550 1 583 1 chr1D.!!$R4 582
8 TraesCS7B01G123800 chrUn 155229181 155231863 2682 False 2142.0 2704 96.0220 584 3297 2 chrUn.!!$F1 2713
9 TraesCS7B01G123800 chr1B 36186158 36187899 1741 False 2667.0 2667 94.4350 584 2311 1 chr1B.!!$F1 1727
10 TraesCS7B01G123800 chr1B 595831219 595833896 2677 False 2073.5 2327 94.9365 584 3296 2 chr1B.!!$F2 2712
11 TraesCS7B01G123800 chr1B 595882633 595885309 2676 False 2065.5 2311 94.8405 584 3296 2 chr1B.!!$F3 2712
12 TraesCS7B01G123800 chr1B 284045237 284048246 3009 True 2014.5 2298 96.8800 892 3297 2 chr1B.!!$R1 2405
13 TraesCS7B01G123800 chr1A 300541672 300543235 1563 True 2209.0 2209 92.3370 584 2131 1 chr1A.!!$R1 1547
14 TraesCS7B01G123800 chr5D 254079394 254080858 1464 False 1964.0 1964 90.8480 584 2067 1 chr5D.!!$F2 1483
15 TraesCS7B01G123800 chr5D 542949582 542950251 669 True 566.0 566 82.2380 584 1287 1 chr5D.!!$R1 703
16 TraesCS7B01G123800 chr3D 517387813 517388708 895 False 1068.0 1068 88.3570 584 1485 1 chr3D.!!$F1 901
17 TraesCS7B01G123800 chr3D 603158014 603158910 896 False 1033.0 1033 87.6620 581 1485 1 chr3D.!!$F2 904
18 TraesCS7B01G123800 chr3D 611640854 611641746 892 False 909.0 909 85.5150 584 1485 1 chr3D.!!$F3 901
19 TraesCS7B01G123800 chr7D 477373785 477374365 580 False 963.0 963 96.5580 1 581 1 chr7D.!!$F2 580
20 TraesCS7B01G123800 chr7D 269656971 269657553 582 False 950.0 950 96.0550 1 583 1 chr7D.!!$F1 582
21 TraesCS7B01G123800 chr4D 314493799 314494381 582 True 955.0 955 96.2260 1 583 1 chr4D.!!$R2 582
22 TraesCS7B01G123800 chr4D 324244380 324244962 582 True 950.0 950 96.0550 1 583 1 chr4D.!!$R3 582
23 TraesCS7B01G123800 chr4D 211077083 211077665 582 True 944.0 944 95.8830 1 583 1 chr4D.!!$R1 582
24 TraesCS7B01G123800 chr2D 459804857 459805439 582 True 955.0 955 96.2260 1 583 1 chr2D.!!$R1 582
25 TraesCS7B01G123800 chr2D 425601658 425602222 564 False 728.0 728 90.4420 939 1485 1 chr2D.!!$F2 546
26 TraesCS7B01G123800 chr2D 650896867 650897418 551 True 688.0 688 89.5580 939 1485 1 chr2D.!!$R2 546
27 TraesCS7B01G123800 chr4B 30399498 30400368 870 False 952.0 952 86.8270 584 1433 1 chr4B.!!$F1 849
28 TraesCS7B01G123800 chr6D 24728556 24729138 582 True 950.0 950 96.0550 1 583 1 chr6D.!!$R1 582
29 TraesCS7B01G123800 chr6D 275891656 275892238 582 False 950.0 950 96.0550 1 583 1 chr6D.!!$F2 582
30 TraesCS7B01G123800 chr6D 154198813 154199495 682 False 632.0 632 83.8620 584 1287 1 chr6D.!!$F1 703
31 TraesCS7B01G123800 chr6D 343522010 343523558 1548 False 263.0 311 91.0840 954 1380 2 chr6D.!!$F3 426

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
494 495 0.178987 GCCCAGAGATACCTCTCCGA 60.179 60.0 0.0 0.0 46.38 4.55 F
1525 2720 0.767998 TGGACAAGGTATGTGTGCCA 59.232 50.0 0.0 0.0 44.12 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 3218 1.329292 CTCAGAGACGAGGCTAACGAG 59.671 57.143 2.34 0.00 34.70 4.18 R
3219 5041 0.096976 CAACTTGATGGCGGCGTAAG 59.903 55.000 9.37 10.69 43.44 2.34 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
141 142 8.304596 ACATAAACTCATAATACCGATCGTCAT 58.695 33.333 15.09 3.54 0.00 3.06
331 332 3.196901 TGTCATCGGTATGTTACTTGCCT 59.803 43.478 4.16 0.00 34.50 4.75
377 378 9.482627 CTCAATACCTAGTTCAATCTCATTACC 57.517 37.037 0.00 0.00 0.00 2.85
378 379 8.988060 TCAATACCTAGTTCAATCTCATTACCA 58.012 33.333 0.00 0.00 0.00 3.25
379 380 9.265901 CAATACCTAGTTCAATCTCATTACCAG 57.734 37.037 0.00 0.00 0.00 4.00
380 381 5.675538 ACCTAGTTCAATCTCATTACCAGC 58.324 41.667 0.00 0.00 0.00 4.85
381 382 5.189736 ACCTAGTTCAATCTCATTACCAGCA 59.810 40.000 0.00 0.00 0.00 4.41
382 383 6.115446 CCTAGTTCAATCTCATTACCAGCAA 58.885 40.000 0.00 0.00 0.00 3.91
383 384 6.259608 CCTAGTTCAATCTCATTACCAGCAAG 59.740 42.308 0.00 0.00 0.00 4.01
384 385 5.564550 AGTTCAATCTCATTACCAGCAAGT 58.435 37.500 0.00 0.00 0.00 3.16
385 386 5.645497 AGTTCAATCTCATTACCAGCAAGTC 59.355 40.000 0.00 0.00 0.00 3.01
386 387 5.426689 TCAATCTCATTACCAGCAAGTCT 57.573 39.130 0.00 0.00 0.00 3.24
387 388 5.423015 TCAATCTCATTACCAGCAAGTCTC 58.577 41.667 0.00 0.00 0.00 3.36
388 389 5.188555 TCAATCTCATTACCAGCAAGTCTCT 59.811 40.000 0.00 0.00 0.00 3.10
389 390 5.690464 ATCTCATTACCAGCAAGTCTCTT 57.310 39.130 0.00 0.00 0.00 2.85
390 391 5.489792 TCTCATTACCAGCAAGTCTCTTT 57.510 39.130 0.00 0.00 0.00 2.52
391 392 6.605471 TCTCATTACCAGCAAGTCTCTTTA 57.395 37.500 0.00 0.00 0.00 1.85
392 393 6.398918 TCTCATTACCAGCAAGTCTCTTTAC 58.601 40.000 0.00 0.00 0.00 2.01
393 394 6.211584 TCTCATTACCAGCAAGTCTCTTTACT 59.788 38.462 0.00 0.00 0.00 2.24
394 395 6.398918 TCATTACCAGCAAGTCTCTTTACTC 58.601 40.000 0.00 0.00 0.00 2.59
395 396 3.305398 ACCAGCAAGTCTCTTTACTCG 57.695 47.619 0.00 0.00 0.00 4.18
396 397 2.628657 ACCAGCAAGTCTCTTTACTCGT 59.371 45.455 0.00 0.00 0.00 4.18
397 398 3.069729 ACCAGCAAGTCTCTTTACTCGTT 59.930 43.478 0.00 0.00 0.00 3.85
398 399 3.675698 CCAGCAAGTCTCTTTACTCGTTC 59.324 47.826 0.00 0.00 0.00 3.95
399 400 3.675698 CAGCAAGTCTCTTTACTCGTTCC 59.324 47.826 0.00 0.00 0.00 3.62
400 401 2.662156 GCAAGTCTCTTTACTCGTTCCG 59.338 50.000 0.00 0.00 0.00 4.30
401 402 3.856267 GCAAGTCTCTTTACTCGTTCCGT 60.856 47.826 0.00 0.00 0.00 4.69
402 403 4.614535 GCAAGTCTCTTTACTCGTTCCGTA 60.615 45.833 0.00 0.00 0.00 4.02
403 404 5.455392 CAAGTCTCTTTACTCGTTCCGTAA 58.545 41.667 0.00 0.00 0.00 3.18
404 405 5.893897 AGTCTCTTTACTCGTTCCGTAAT 57.106 39.130 0.00 0.00 0.00 1.89
405 406 5.638783 AGTCTCTTTACTCGTTCCGTAATG 58.361 41.667 0.00 0.00 0.00 1.90
406 407 4.264849 GTCTCTTTACTCGTTCCGTAATGC 59.735 45.833 0.00 0.00 0.00 3.56
407 408 4.082625 TCTCTTTACTCGTTCCGTAATGCA 60.083 41.667 0.00 0.00 0.00 3.96
408 409 4.751060 TCTTTACTCGTTCCGTAATGCAT 58.249 39.130 0.00 0.00 0.00 3.96
409 410 4.802039 TCTTTACTCGTTCCGTAATGCATC 59.198 41.667 0.00 0.00 0.00 3.91
410 411 2.665649 ACTCGTTCCGTAATGCATCA 57.334 45.000 0.00 0.00 0.00 3.07
411 412 3.179443 ACTCGTTCCGTAATGCATCAT 57.821 42.857 0.00 0.00 0.00 2.45
412 413 3.123804 ACTCGTTCCGTAATGCATCATC 58.876 45.455 0.00 0.00 0.00 2.92
413 414 2.476619 CTCGTTCCGTAATGCATCATCC 59.523 50.000 0.00 0.00 0.00 3.51
414 415 2.102420 TCGTTCCGTAATGCATCATCCT 59.898 45.455 0.00 0.00 0.00 3.24
415 416 2.221749 CGTTCCGTAATGCATCATCCTG 59.778 50.000 0.00 0.00 0.00 3.86
416 417 1.882912 TCCGTAATGCATCATCCTGC 58.117 50.000 0.00 0.00 42.62 4.85
425 426 3.959573 GCATCATCCTGCAACTAACTC 57.040 47.619 0.00 0.00 41.87 3.01
426 427 3.273434 GCATCATCCTGCAACTAACTCA 58.727 45.455 0.00 0.00 41.87 3.41
427 428 3.881688 GCATCATCCTGCAACTAACTCAT 59.118 43.478 0.00 0.00 41.87 2.90
428 429 4.337555 GCATCATCCTGCAACTAACTCATT 59.662 41.667 0.00 0.00 41.87 2.57
429 430 5.528690 GCATCATCCTGCAACTAACTCATTA 59.471 40.000 0.00 0.00 41.87 1.90
430 431 6.293298 GCATCATCCTGCAACTAACTCATTAG 60.293 42.308 0.00 0.00 41.40 1.73
431 432 8.593836 GCATCATCCTGCAACTAACTCATTAGT 61.594 40.741 0.00 0.00 42.47 2.24
444 445 6.573664 AACTCATTAGTTACATTGCTTGCA 57.426 33.333 0.00 0.00 44.26 4.08
445 446 6.573664 ACTCATTAGTTACATTGCTTGCAA 57.426 33.333 10.57 10.57 29.00 4.08
446 447 6.615088 ACTCATTAGTTACATTGCTTGCAAG 58.385 36.000 22.44 22.44 29.00 4.01
447 448 5.953183 TCATTAGTTACATTGCTTGCAAGG 58.047 37.500 27.10 16.77 0.00 3.61
448 449 2.730550 AGTTACATTGCTTGCAAGGC 57.269 45.000 27.10 18.97 0.00 4.35
449 450 2.242043 AGTTACATTGCTTGCAAGGCT 58.758 42.857 27.10 6.40 0.00 4.58
450 451 2.629617 AGTTACATTGCTTGCAAGGCTT 59.370 40.909 27.10 9.20 0.00 4.35
451 452 3.826157 AGTTACATTGCTTGCAAGGCTTA 59.174 39.130 27.10 12.08 0.00 3.09
452 453 4.463891 AGTTACATTGCTTGCAAGGCTTAT 59.536 37.500 27.10 13.52 0.00 1.73
453 454 5.652014 AGTTACATTGCTTGCAAGGCTTATA 59.348 36.000 27.10 8.83 0.00 0.98
454 455 4.644103 ACATTGCTTGCAAGGCTTATAG 57.356 40.909 27.10 0.54 0.00 1.31
455 456 4.019174 ACATTGCTTGCAAGGCTTATAGT 58.981 39.130 27.10 11.86 0.00 2.12
456 457 4.142315 ACATTGCTTGCAAGGCTTATAGTG 60.142 41.667 27.10 12.26 0.00 2.74
457 458 3.348647 TGCTTGCAAGGCTTATAGTGA 57.651 42.857 27.10 0.00 0.00 3.41
458 459 3.889815 TGCTTGCAAGGCTTATAGTGAT 58.110 40.909 27.10 0.00 0.00 3.06
459 460 3.628942 TGCTTGCAAGGCTTATAGTGATG 59.371 43.478 27.10 0.00 0.00 3.07
460 461 3.629398 GCTTGCAAGGCTTATAGTGATGT 59.371 43.478 27.10 0.00 0.00 3.06
461 462 4.497006 GCTTGCAAGGCTTATAGTGATGTG 60.497 45.833 27.10 0.00 0.00 3.21
462 463 2.945008 TGCAAGGCTTATAGTGATGTGC 59.055 45.455 0.00 0.00 0.00 4.57
463 464 2.945008 GCAAGGCTTATAGTGATGTGCA 59.055 45.455 0.00 0.00 0.00 4.57
464 465 3.567164 GCAAGGCTTATAGTGATGTGCAT 59.433 43.478 0.00 0.00 0.00 3.96
465 466 4.037208 GCAAGGCTTATAGTGATGTGCATT 59.963 41.667 0.00 0.00 0.00 3.56
466 467 5.239306 GCAAGGCTTATAGTGATGTGCATTA 59.761 40.000 0.00 0.00 0.00 1.90
467 468 6.662616 CAAGGCTTATAGTGATGTGCATTAC 58.337 40.000 0.00 0.00 0.00 1.89
468 469 5.308825 AGGCTTATAGTGATGTGCATTACC 58.691 41.667 0.00 0.00 0.00 2.85
469 470 4.152402 GGCTTATAGTGATGTGCATTACCG 59.848 45.833 0.00 0.00 0.00 4.02
470 471 4.988540 GCTTATAGTGATGTGCATTACCGA 59.011 41.667 0.00 0.00 0.00 4.69
471 472 5.119279 GCTTATAGTGATGTGCATTACCGAG 59.881 44.000 0.00 0.20 0.00 4.63
472 473 4.937201 ATAGTGATGTGCATTACCGAGA 57.063 40.909 0.00 0.00 0.00 4.04
473 474 3.170791 AGTGATGTGCATTACCGAGAG 57.829 47.619 0.00 0.00 0.00 3.20
485 486 4.932060 CGAGAGGGCCCAGAGATA 57.068 61.111 27.56 0.00 0.00 1.98
486 487 2.346597 CGAGAGGGCCCAGAGATAC 58.653 63.158 27.56 6.80 0.00 2.24
487 488 1.182385 CGAGAGGGCCCAGAGATACC 61.182 65.000 27.56 2.66 0.00 2.73
488 489 0.189822 GAGAGGGCCCAGAGATACCT 59.810 60.000 27.56 7.10 0.00 3.08
489 490 0.189822 AGAGGGCCCAGAGATACCTC 59.810 60.000 27.56 9.41 46.27 3.85
491 492 0.189822 AGGGCCCAGAGATACCTCTC 59.810 60.000 27.56 0.00 46.38 3.20
492 493 0.834261 GGGCCCAGAGATACCTCTCC 60.834 65.000 19.95 0.00 46.38 3.71
493 494 1.182385 GGCCCAGAGATACCTCTCCG 61.182 65.000 0.00 0.00 46.38 4.63
494 495 0.178987 GCCCAGAGATACCTCTCCGA 60.179 60.000 0.00 0.00 46.38 4.55
495 496 1.611519 CCCAGAGATACCTCTCCGAC 58.388 60.000 0.00 0.00 46.38 4.79
496 497 1.133761 CCCAGAGATACCTCTCCGACA 60.134 57.143 0.00 0.00 46.38 4.35
497 498 2.656002 CCAGAGATACCTCTCCGACAA 58.344 52.381 0.00 0.00 46.38 3.18
498 499 3.226777 CCAGAGATACCTCTCCGACAAT 58.773 50.000 0.00 0.00 46.38 2.71
499 500 3.254657 CCAGAGATACCTCTCCGACAATC 59.745 52.174 0.00 0.00 46.38 2.67
500 501 3.058570 CAGAGATACCTCTCCGACAATCG 60.059 52.174 0.00 0.00 46.38 3.34
501 502 4.057669 AGAGATACCTCTCCGACAATCGG 61.058 52.174 11.06 11.06 46.38 4.18
512 513 3.641439 CGACAATCGGAGTGACAAATC 57.359 47.619 12.93 0.00 36.00 2.17
513 514 2.348666 CGACAATCGGAGTGACAAATCC 59.651 50.000 12.93 0.00 36.00 3.01
514 515 3.600388 GACAATCGGAGTGACAAATCCT 58.400 45.455 12.93 0.00 33.12 3.24
515 516 4.676986 CGACAATCGGAGTGACAAATCCTA 60.677 45.833 12.93 0.00 36.00 2.94
516 517 5.160607 ACAATCGGAGTGACAAATCCTAA 57.839 39.130 12.93 0.00 33.12 2.69
517 518 5.745227 ACAATCGGAGTGACAAATCCTAAT 58.255 37.500 12.93 0.00 33.12 1.73
518 519 5.817816 ACAATCGGAGTGACAAATCCTAATC 59.182 40.000 12.93 0.00 33.12 1.75
519 520 5.878406 ATCGGAGTGACAAATCCTAATCT 57.122 39.130 6.43 0.00 33.12 2.40
520 521 5.263968 TCGGAGTGACAAATCCTAATCTC 57.736 43.478 6.43 0.00 33.12 2.75
521 522 4.045104 CGGAGTGACAAATCCTAATCTCG 58.955 47.826 6.43 0.00 33.12 4.04
522 523 4.202020 CGGAGTGACAAATCCTAATCTCGA 60.202 45.833 6.43 0.00 33.12 4.04
523 524 5.285651 GGAGTGACAAATCCTAATCTCGAG 58.714 45.833 5.93 5.93 32.51 4.04
524 525 4.688021 AGTGACAAATCCTAATCTCGAGC 58.312 43.478 7.81 0.00 0.00 5.03
525 526 4.404073 AGTGACAAATCCTAATCTCGAGCT 59.596 41.667 7.81 0.00 0.00 4.09
526 527 5.594725 AGTGACAAATCCTAATCTCGAGCTA 59.405 40.000 7.81 0.57 0.00 3.32
527 528 6.266558 AGTGACAAATCCTAATCTCGAGCTAT 59.733 38.462 7.81 0.00 0.00 2.97
528 529 6.364706 GTGACAAATCCTAATCTCGAGCTATG 59.635 42.308 7.81 0.00 0.00 2.23
529 530 5.233988 ACAAATCCTAATCTCGAGCTATGC 58.766 41.667 7.81 0.00 0.00 3.14
530 531 4.464069 AATCCTAATCTCGAGCTATGCC 57.536 45.455 7.81 0.00 0.00 4.40
531 532 2.876581 TCCTAATCTCGAGCTATGCCA 58.123 47.619 7.81 0.00 0.00 4.92
532 533 3.230976 TCCTAATCTCGAGCTATGCCAA 58.769 45.455 7.81 0.00 0.00 4.52
533 534 3.005897 TCCTAATCTCGAGCTATGCCAAC 59.994 47.826 7.81 0.00 0.00 3.77
534 535 3.006323 CCTAATCTCGAGCTATGCCAACT 59.994 47.826 7.81 0.00 0.00 3.16
535 536 2.810439 ATCTCGAGCTATGCCAACTC 57.190 50.000 7.81 0.00 0.00 3.01
536 537 1.474330 TCTCGAGCTATGCCAACTCA 58.526 50.000 7.81 0.00 0.00 3.41
537 538 1.824852 TCTCGAGCTATGCCAACTCAA 59.175 47.619 7.81 0.00 0.00 3.02
538 539 1.929836 CTCGAGCTATGCCAACTCAAC 59.070 52.381 0.00 0.00 0.00 3.18
539 540 1.275010 TCGAGCTATGCCAACTCAACA 59.725 47.619 0.00 0.00 0.00 3.33
540 541 2.076100 CGAGCTATGCCAACTCAACAA 58.924 47.619 0.00 0.00 0.00 2.83
541 542 2.094894 CGAGCTATGCCAACTCAACAAG 59.905 50.000 0.00 0.00 0.00 3.16
542 543 3.077359 GAGCTATGCCAACTCAACAAGT 58.923 45.455 0.00 0.00 41.10 3.16
543 544 4.253685 GAGCTATGCCAACTCAACAAGTA 58.746 43.478 0.00 0.00 37.17 2.24
544 545 4.003648 AGCTATGCCAACTCAACAAGTAC 58.996 43.478 0.00 0.00 37.17 2.73
545 546 3.127030 GCTATGCCAACTCAACAAGTACC 59.873 47.826 0.00 0.00 37.17 3.34
546 547 2.719531 TGCCAACTCAACAAGTACCA 57.280 45.000 0.00 0.00 37.17 3.25
547 548 3.222173 TGCCAACTCAACAAGTACCAT 57.778 42.857 0.00 0.00 37.17 3.55
548 549 3.146066 TGCCAACTCAACAAGTACCATC 58.854 45.455 0.00 0.00 37.17 3.51
549 550 2.159627 GCCAACTCAACAAGTACCATCG 59.840 50.000 0.00 0.00 37.17 3.84
550 551 3.659786 CCAACTCAACAAGTACCATCGA 58.340 45.455 0.00 0.00 37.17 3.59
551 552 4.062293 CCAACTCAACAAGTACCATCGAA 58.938 43.478 0.00 0.00 37.17 3.71
552 553 4.152402 CCAACTCAACAAGTACCATCGAAG 59.848 45.833 0.00 0.00 37.17 3.79
553 554 4.866508 ACTCAACAAGTACCATCGAAGA 57.133 40.909 0.00 0.00 37.44 2.87
554 555 4.557205 ACTCAACAAGTACCATCGAAGAC 58.443 43.478 0.00 0.00 36.00 3.01
555 556 4.038763 ACTCAACAAGTACCATCGAAGACA 59.961 41.667 0.00 0.00 36.00 3.41
556 557 4.304110 TCAACAAGTACCATCGAAGACAC 58.696 43.478 0.00 0.00 42.51 3.67
557 558 3.314541 ACAAGTACCATCGAAGACACC 57.685 47.619 0.00 0.00 42.51 4.16
558 559 2.897969 ACAAGTACCATCGAAGACACCT 59.102 45.455 0.00 0.00 42.51 4.00
559 560 4.084287 ACAAGTACCATCGAAGACACCTA 58.916 43.478 0.00 0.00 42.51 3.08
560 561 4.710375 ACAAGTACCATCGAAGACACCTAT 59.290 41.667 0.00 0.00 42.51 2.57
561 562 5.889853 ACAAGTACCATCGAAGACACCTATA 59.110 40.000 0.00 0.00 42.51 1.31
562 563 6.039493 ACAAGTACCATCGAAGACACCTATAG 59.961 42.308 0.00 0.00 42.51 1.31
563 564 5.938279 AGTACCATCGAAGACACCTATAGA 58.062 41.667 0.00 0.00 42.51 1.98
564 565 5.998981 AGTACCATCGAAGACACCTATAGAG 59.001 44.000 0.00 0.00 42.51 2.43
565 566 3.570550 ACCATCGAAGACACCTATAGAGC 59.429 47.826 0.00 0.00 42.51 4.09
566 567 3.570125 CCATCGAAGACACCTATAGAGCA 59.430 47.826 0.00 0.00 42.51 4.26
567 568 4.541779 CATCGAAGACACCTATAGAGCAC 58.458 47.826 0.00 0.00 42.51 4.40
568 569 2.950309 TCGAAGACACCTATAGAGCACC 59.050 50.000 0.00 0.00 0.00 5.01
569 570 2.952978 CGAAGACACCTATAGAGCACCT 59.047 50.000 0.00 0.00 0.00 4.00
570 571 3.381908 CGAAGACACCTATAGAGCACCTT 59.618 47.826 0.00 0.00 0.00 3.50
571 572 4.142138 CGAAGACACCTATAGAGCACCTTT 60.142 45.833 0.00 0.00 0.00 3.11
572 573 5.067413 CGAAGACACCTATAGAGCACCTTTA 59.933 44.000 0.00 0.00 0.00 1.85
573 574 6.239064 CGAAGACACCTATAGAGCACCTTTAT 60.239 42.308 0.00 0.00 0.00 1.40
574 575 7.040617 CGAAGACACCTATAGAGCACCTTTATA 60.041 40.741 0.00 0.00 0.00 0.98
575 576 8.548880 AAGACACCTATAGAGCACCTTTATAA 57.451 34.615 0.00 0.00 0.00 0.98
576 577 8.728596 AGACACCTATAGAGCACCTTTATAAT 57.271 34.615 0.00 0.00 0.00 1.28
577 578 8.808092 AGACACCTATAGAGCACCTTTATAATC 58.192 37.037 0.00 0.00 0.00 1.75
578 579 8.492415 ACACCTATAGAGCACCTTTATAATCA 57.508 34.615 0.00 0.00 0.00 2.57
579 580 8.368668 ACACCTATAGAGCACCTTTATAATCAC 58.631 37.037 0.00 0.00 0.00 3.06
580 581 7.819900 CACCTATAGAGCACCTTTATAATCACC 59.180 40.741 0.00 0.00 0.00 4.02
581 582 7.038231 ACCTATAGAGCACCTTTATAATCACCC 60.038 40.741 0.00 0.00 0.00 4.61
898 916 4.078516 GTGTCTAACGGCCGCCCT 62.079 66.667 28.58 13.10 0.00 5.19
930 950 2.747446 AGGCGACAAAGAATAAACGCAT 59.253 40.909 0.00 0.00 46.17 4.73
1036 1069 2.410687 CCAACCCACGCACACACAA 61.411 57.895 0.00 0.00 0.00 3.33
1058 1096 1.123928 ACGTTGGATCCCATCTCTCC 58.876 55.000 9.90 0.00 31.53 3.71
1490 2685 1.691689 AACCCCATCCGGTACCTCC 60.692 63.158 10.90 0.00 33.98 4.30
1525 2720 0.767998 TGGACAAGGTATGTGTGCCA 59.232 50.000 0.00 0.00 44.12 4.92
1639 2846 1.815421 GACGCGGTGCATTGGATCT 60.815 57.895 12.47 0.00 0.00 2.75
1651 2858 3.785859 GGATCTGGCAGGCGGTGA 61.786 66.667 15.73 0.00 0.00 4.02
1990 3198 3.709653 ACAGGAGGTGAAGTGAGTGTTAA 59.290 43.478 0.00 0.00 0.00 2.01
2010 3218 2.398554 TTCGCTGCGAATTGGAGGC 61.399 57.895 31.14 0.00 41.05 4.70
2083 3291 2.028112 AGTGGTTATGCGCTTTCTCTGA 60.028 45.455 9.73 0.00 0.00 3.27
3168 4990 4.502105 TCTTAAGCTGGCCATGTGATTA 57.498 40.909 5.51 0.56 0.00 1.75
3192 5014 1.146263 GCCTATAAGCTGGCCGTGT 59.854 57.895 0.00 0.00 43.11 4.49
3215 5037 1.080025 GGGCGTGTGGACTCTGTAC 60.080 63.158 0.00 0.00 0.00 2.90
3219 5041 1.080025 GTGTGGACTCTGTACGCCC 60.080 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
331 332 3.400255 AGATACCGACGATCGAATCTCA 58.600 45.455 24.34 2.26 43.74 3.27
372 373 5.047235 ACGAGTAAAGAGACTTGCTGGTAAT 60.047 40.000 0.00 0.00 34.59 1.89
373 374 4.280174 ACGAGTAAAGAGACTTGCTGGTAA 59.720 41.667 0.00 0.00 34.59 2.85
374 375 3.825014 ACGAGTAAAGAGACTTGCTGGTA 59.175 43.478 0.00 0.00 34.59 3.25
375 376 2.628657 ACGAGTAAAGAGACTTGCTGGT 59.371 45.455 0.00 0.00 34.59 4.00
376 377 3.305398 ACGAGTAAAGAGACTTGCTGG 57.695 47.619 0.00 0.00 34.59 4.85
377 378 3.675698 GGAACGAGTAAAGAGACTTGCTG 59.324 47.826 0.00 0.00 34.59 4.41
378 379 3.915536 GGAACGAGTAAAGAGACTTGCT 58.084 45.455 0.00 0.00 34.59 3.91
395 396 2.031682 GCAGGATGATGCATTACGGAAC 60.032 50.000 0.00 0.00 45.77 3.62
396 397 2.221169 GCAGGATGATGCATTACGGAA 58.779 47.619 0.00 0.00 45.77 4.30
397 398 1.882912 GCAGGATGATGCATTACGGA 58.117 50.000 0.00 0.00 45.77 4.69
405 406 3.273434 TGAGTTAGTTGCAGGATGATGC 58.727 45.455 0.00 0.00 46.68 3.91
406 407 6.765036 ACTAATGAGTTAGTTGCAGGATGATG 59.235 38.462 0.00 0.00 46.40 3.07
407 408 6.893583 ACTAATGAGTTAGTTGCAGGATGAT 58.106 36.000 0.00 0.00 46.40 2.45
408 409 6.299805 ACTAATGAGTTAGTTGCAGGATGA 57.700 37.500 0.00 0.00 46.40 2.92
419 420 7.751732 TGCAAGCAATGTAACTAATGAGTTAG 58.248 34.615 2.61 0.00 46.48 2.34
420 421 7.680442 TGCAAGCAATGTAACTAATGAGTTA 57.320 32.000 0.00 0.00 44.36 2.24
421 422 7.086376 CTTGCAAGCAATGTAACTAATGAGTT 58.914 34.615 14.65 0.00 40.93 3.01
422 423 6.349611 CCTTGCAAGCAATGTAACTAATGAGT 60.350 38.462 21.43 0.00 34.55 3.41
423 424 6.032094 CCTTGCAAGCAATGTAACTAATGAG 58.968 40.000 21.43 0.00 35.20 2.90
424 425 5.622007 GCCTTGCAAGCAATGTAACTAATGA 60.622 40.000 21.43 0.00 35.20 2.57
425 426 4.563976 GCCTTGCAAGCAATGTAACTAATG 59.436 41.667 21.43 3.20 35.20 1.90
426 427 4.463891 AGCCTTGCAAGCAATGTAACTAAT 59.536 37.500 21.43 0.00 35.20 1.73
427 428 3.826157 AGCCTTGCAAGCAATGTAACTAA 59.174 39.130 21.43 0.00 35.20 2.24
428 429 3.420893 AGCCTTGCAAGCAATGTAACTA 58.579 40.909 21.43 0.00 35.20 2.24
429 430 2.242043 AGCCTTGCAAGCAATGTAACT 58.758 42.857 21.43 4.59 35.20 2.24
430 431 2.730550 AGCCTTGCAAGCAATGTAAC 57.269 45.000 21.43 2.43 35.20 2.50
431 432 5.652014 ACTATAAGCCTTGCAAGCAATGTAA 59.348 36.000 21.43 2.51 35.20 2.41
432 433 5.066375 CACTATAAGCCTTGCAAGCAATGTA 59.934 40.000 21.43 9.73 35.20 2.29
433 434 4.019174 ACTATAAGCCTTGCAAGCAATGT 58.981 39.130 21.43 9.12 35.20 2.71
434 435 4.096833 TCACTATAAGCCTTGCAAGCAATG 59.903 41.667 21.43 8.47 35.20 2.82
435 436 4.272489 TCACTATAAGCCTTGCAAGCAAT 58.728 39.130 21.43 14.70 35.20 3.56
436 437 3.684908 TCACTATAAGCCTTGCAAGCAA 58.315 40.909 21.43 7.33 0.00 3.91
437 438 3.348647 TCACTATAAGCCTTGCAAGCA 57.651 42.857 21.43 5.88 0.00 3.91
438 439 3.629398 ACATCACTATAAGCCTTGCAAGC 59.371 43.478 21.43 15.79 0.00 4.01
439 440 4.497006 GCACATCACTATAAGCCTTGCAAG 60.497 45.833 19.93 19.93 0.00 4.01
440 441 3.378112 GCACATCACTATAAGCCTTGCAA 59.622 43.478 0.00 0.00 0.00 4.08
441 442 2.945008 GCACATCACTATAAGCCTTGCA 59.055 45.455 0.00 0.00 0.00 4.08
442 443 2.945008 TGCACATCACTATAAGCCTTGC 59.055 45.455 0.00 0.00 0.00 4.01
443 444 5.762825 AATGCACATCACTATAAGCCTTG 57.237 39.130 0.00 0.00 0.00 3.61
444 445 5.765182 GGTAATGCACATCACTATAAGCCTT 59.235 40.000 0.00 0.00 0.00 4.35
445 446 5.308825 GGTAATGCACATCACTATAAGCCT 58.691 41.667 0.00 0.00 0.00 4.58
446 447 4.152402 CGGTAATGCACATCACTATAAGCC 59.848 45.833 0.00 0.00 0.00 4.35
447 448 4.988540 TCGGTAATGCACATCACTATAAGC 59.011 41.667 0.00 0.00 0.00 3.09
448 449 6.447162 TCTCGGTAATGCACATCACTATAAG 58.553 40.000 0.00 0.00 0.00 1.73
449 450 6.399639 TCTCGGTAATGCACATCACTATAA 57.600 37.500 0.00 0.00 0.00 0.98
450 451 5.048013 CCTCTCGGTAATGCACATCACTATA 60.048 44.000 0.00 0.00 0.00 1.31
451 452 4.262207 CCTCTCGGTAATGCACATCACTAT 60.262 45.833 0.00 0.00 0.00 2.12
452 453 3.068165 CCTCTCGGTAATGCACATCACTA 59.932 47.826 0.00 0.00 0.00 2.74
453 454 2.159043 CCTCTCGGTAATGCACATCACT 60.159 50.000 0.00 0.00 0.00 3.41
454 455 2.205074 CCTCTCGGTAATGCACATCAC 58.795 52.381 0.00 0.00 0.00 3.06
455 456 1.138859 CCCTCTCGGTAATGCACATCA 59.861 52.381 0.00 0.00 0.00 3.07
456 457 1.871080 CCCTCTCGGTAATGCACATC 58.129 55.000 0.00 0.00 0.00 3.06
457 458 0.179045 GCCCTCTCGGTAATGCACAT 60.179 55.000 0.00 0.00 0.00 3.21
458 459 1.220749 GCCCTCTCGGTAATGCACA 59.779 57.895 0.00 0.00 0.00 4.57
459 460 1.523938 GGCCCTCTCGGTAATGCAC 60.524 63.158 0.00 0.00 0.00 4.57
460 461 2.742116 GGGCCCTCTCGGTAATGCA 61.742 63.158 17.04 0.00 0.00 3.96
461 462 2.111251 GGGCCCTCTCGGTAATGC 59.889 66.667 17.04 0.00 0.00 3.56
462 463 1.048724 TCTGGGCCCTCTCGGTAATG 61.049 60.000 25.70 0.29 0.00 1.90
463 464 0.760945 CTCTGGGCCCTCTCGGTAAT 60.761 60.000 25.70 0.00 0.00 1.89
464 465 1.381327 CTCTGGGCCCTCTCGGTAA 60.381 63.158 25.70 0.00 0.00 2.85
465 466 1.656092 ATCTCTGGGCCCTCTCGGTA 61.656 60.000 25.70 0.00 0.00 4.02
466 467 1.656092 TATCTCTGGGCCCTCTCGGT 61.656 60.000 25.70 7.65 0.00 4.69
467 468 1.153989 TATCTCTGGGCCCTCTCGG 59.846 63.158 25.70 8.84 0.00 4.63
468 469 1.182385 GGTATCTCTGGGCCCTCTCG 61.182 65.000 25.70 9.01 0.00 4.04
469 470 0.189822 AGGTATCTCTGGGCCCTCTC 59.810 60.000 25.70 6.25 0.00 3.20
470 471 0.189822 GAGGTATCTCTGGGCCCTCT 59.810 60.000 25.70 7.22 38.90 3.69
471 472 2.753319 GAGGTATCTCTGGGCCCTC 58.247 63.158 25.70 4.48 37.07 4.30
492 493 2.348666 GGATTTGTCACTCCGATTGTCG 59.651 50.000 0.00 0.00 40.07 4.35
493 494 3.600388 AGGATTTGTCACTCCGATTGTC 58.400 45.455 0.00 0.00 36.62 3.18
494 495 3.703001 AGGATTTGTCACTCCGATTGT 57.297 42.857 0.00 0.00 36.62 2.71
495 496 6.051717 AGATTAGGATTTGTCACTCCGATTG 58.948 40.000 0.00 0.00 36.62 2.67
496 497 6.240549 AGATTAGGATTTGTCACTCCGATT 57.759 37.500 0.00 0.00 36.62 3.34
497 498 5.508153 CGAGATTAGGATTTGTCACTCCGAT 60.508 44.000 0.00 0.00 36.62 4.18
498 499 4.202020 CGAGATTAGGATTTGTCACTCCGA 60.202 45.833 0.00 0.00 36.62 4.55
499 500 4.045104 CGAGATTAGGATTTGTCACTCCG 58.955 47.826 0.00 0.00 36.62 4.63
500 501 5.263968 TCGAGATTAGGATTTGTCACTCC 57.736 43.478 0.00 0.00 0.00 3.85
501 502 4.742659 GCTCGAGATTAGGATTTGTCACTC 59.257 45.833 18.75 0.00 0.00 3.51
502 503 4.404073 AGCTCGAGATTAGGATTTGTCACT 59.596 41.667 18.75 0.00 0.00 3.41
503 504 4.688021 AGCTCGAGATTAGGATTTGTCAC 58.312 43.478 18.75 0.00 0.00 3.67
504 505 6.450545 CATAGCTCGAGATTAGGATTTGTCA 58.549 40.000 18.75 0.00 0.00 3.58
505 506 5.347364 GCATAGCTCGAGATTAGGATTTGTC 59.653 44.000 18.75 0.00 0.00 3.18
506 507 5.233988 GCATAGCTCGAGATTAGGATTTGT 58.766 41.667 18.75 0.00 0.00 2.83
507 508 4.629200 GGCATAGCTCGAGATTAGGATTTG 59.371 45.833 18.75 3.93 0.00 2.32
508 509 4.284490 TGGCATAGCTCGAGATTAGGATTT 59.716 41.667 18.75 0.00 0.00 2.17
509 510 3.834813 TGGCATAGCTCGAGATTAGGATT 59.165 43.478 18.75 0.00 0.00 3.01
510 511 3.435275 TGGCATAGCTCGAGATTAGGAT 58.565 45.455 18.75 0.00 0.00 3.24
511 512 2.876581 TGGCATAGCTCGAGATTAGGA 58.123 47.619 18.75 0.00 0.00 2.94
512 513 3.006323 AGTTGGCATAGCTCGAGATTAGG 59.994 47.826 18.75 10.43 0.00 2.69
513 514 4.233789 GAGTTGGCATAGCTCGAGATTAG 58.766 47.826 18.75 7.18 0.00 1.73
514 515 3.636764 TGAGTTGGCATAGCTCGAGATTA 59.363 43.478 18.75 8.11 39.29 1.75
515 516 2.432146 TGAGTTGGCATAGCTCGAGATT 59.568 45.455 18.75 5.81 39.29 2.40
516 517 2.034878 TGAGTTGGCATAGCTCGAGAT 58.965 47.619 18.75 13.81 39.29 2.75
517 518 1.474330 TGAGTTGGCATAGCTCGAGA 58.526 50.000 18.75 0.00 39.29 4.04
518 519 1.929836 GTTGAGTTGGCATAGCTCGAG 59.070 52.381 8.45 8.45 39.29 4.04
519 520 1.275010 TGTTGAGTTGGCATAGCTCGA 59.725 47.619 0.00 0.00 39.29 4.04
520 521 1.725641 TGTTGAGTTGGCATAGCTCG 58.274 50.000 0.00 0.00 39.29 5.03
521 522 3.077359 ACTTGTTGAGTTGGCATAGCTC 58.923 45.455 0.00 0.00 33.92 4.09
522 523 3.146104 ACTTGTTGAGTTGGCATAGCT 57.854 42.857 0.00 0.00 33.92 3.32
523 524 3.127030 GGTACTTGTTGAGTTGGCATAGC 59.873 47.826 0.00 0.00 39.86 2.97
524 525 4.323417 TGGTACTTGTTGAGTTGGCATAG 58.677 43.478 0.00 0.00 39.86 2.23
525 526 4.359434 TGGTACTTGTTGAGTTGGCATA 57.641 40.909 0.00 0.00 39.86 3.14
526 527 3.222173 TGGTACTTGTTGAGTTGGCAT 57.778 42.857 0.00 0.00 39.86 4.40
527 528 2.719531 TGGTACTTGTTGAGTTGGCA 57.280 45.000 0.00 0.00 39.86 4.92
528 529 2.159627 CGATGGTACTTGTTGAGTTGGC 59.840 50.000 0.00 0.00 39.86 4.52
529 530 3.659786 TCGATGGTACTTGTTGAGTTGG 58.340 45.455 0.00 0.00 39.86 3.77
530 531 4.988540 TCTTCGATGGTACTTGTTGAGTTG 59.011 41.667 0.00 0.00 39.86 3.16
531 532 4.989168 GTCTTCGATGGTACTTGTTGAGTT 59.011 41.667 0.00 0.00 39.86 3.01
532 533 4.038763 TGTCTTCGATGGTACTTGTTGAGT 59.961 41.667 0.00 0.00 42.55 3.41
533 534 4.386049 GTGTCTTCGATGGTACTTGTTGAG 59.614 45.833 0.00 0.00 0.00 3.02
534 535 4.304110 GTGTCTTCGATGGTACTTGTTGA 58.696 43.478 0.00 0.00 0.00 3.18
535 536 3.432252 GGTGTCTTCGATGGTACTTGTTG 59.568 47.826 0.00 0.00 0.00 3.33
536 537 3.323979 AGGTGTCTTCGATGGTACTTGTT 59.676 43.478 0.00 0.00 0.00 2.83
537 538 2.897969 AGGTGTCTTCGATGGTACTTGT 59.102 45.455 0.00 0.00 0.00 3.16
538 539 3.594603 AGGTGTCTTCGATGGTACTTG 57.405 47.619 0.00 0.00 0.00 3.16
539 540 6.363065 TCTATAGGTGTCTTCGATGGTACTT 58.637 40.000 0.00 0.00 0.00 2.24
540 541 5.938279 TCTATAGGTGTCTTCGATGGTACT 58.062 41.667 0.00 0.00 0.00 2.73
541 542 5.335035 GCTCTATAGGTGTCTTCGATGGTAC 60.335 48.000 0.00 0.00 0.00 3.34
542 543 4.760715 GCTCTATAGGTGTCTTCGATGGTA 59.239 45.833 0.00 0.00 0.00 3.25
543 544 3.570550 GCTCTATAGGTGTCTTCGATGGT 59.429 47.826 0.00 0.00 0.00 3.55
544 545 3.570125 TGCTCTATAGGTGTCTTCGATGG 59.430 47.826 0.00 0.00 0.00 3.51
545 546 4.541779 GTGCTCTATAGGTGTCTTCGATG 58.458 47.826 0.00 0.00 0.00 3.84
546 547 3.570550 GGTGCTCTATAGGTGTCTTCGAT 59.429 47.826 0.00 0.00 0.00 3.59
547 548 2.950309 GGTGCTCTATAGGTGTCTTCGA 59.050 50.000 0.00 0.00 0.00 3.71
548 549 2.952978 AGGTGCTCTATAGGTGTCTTCG 59.047 50.000 0.00 0.00 0.00 3.79
549 550 5.346181 AAAGGTGCTCTATAGGTGTCTTC 57.654 43.478 0.00 0.00 0.00 2.87
550 551 8.548880 TTATAAAGGTGCTCTATAGGTGTCTT 57.451 34.615 0.00 0.00 0.00 3.01
551 552 8.728596 ATTATAAAGGTGCTCTATAGGTGTCT 57.271 34.615 0.00 0.00 0.00 3.41
552 553 8.585881 TGATTATAAAGGTGCTCTATAGGTGTC 58.414 37.037 0.00 0.00 0.00 3.67
553 554 8.368668 GTGATTATAAAGGTGCTCTATAGGTGT 58.631 37.037 0.00 0.00 0.00 4.16
554 555 7.819900 GGTGATTATAAAGGTGCTCTATAGGTG 59.180 40.741 0.00 0.00 0.00 4.00
555 556 7.038231 GGGTGATTATAAAGGTGCTCTATAGGT 60.038 40.741 0.00 0.00 0.00 3.08
556 557 7.038302 TGGGTGATTATAAAGGTGCTCTATAGG 60.038 40.741 0.00 0.00 0.00 2.57
557 558 7.819900 GTGGGTGATTATAAAGGTGCTCTATAG 59.180 40.741 0.00 0.00 0.00 1.31
558 559 7.291416 TGTGGGTGATTATAAAGGTGCTCTATA 59.709 37.037 0.00 0.00 0.00 1.31
559 560 6.101150 TGTGGGTGATTATAAAGGTGCTCTAT 59.899 38.462 0.00 0.00 0.00 1.98
560 561 5.427157 TGTGGGTGATTATAAAGGTGCTCTA 59.573 40.000 0.00 0.00 0.00 2.43
561 562 4.227300 TGTGGGTGATTATAAAGGTGCTCT 59.773 41.667 0.00 0.00 0.00 4.09
562 563 4.335594 GTGTGGGTGATTATAAAGGTGCTC 59.664 45.833 0.00 0.00 0.00 4.26
563 564 4.018415 AGTGTGGGTGATTATAAAGGTGCT 60.018 41.667 0.00 0.00 0.00 4.40
564 565 4.270008 AGTGTGGGTGATTATAAAGGTGC 58.730 43.478 0.00 0.00 0.00 5.01
565 566 6.538742 CAGTAGTGTGGGTGATTATAAAGGTG 59.461 42.308 0.00 0.00 0.00 4.00
566 567 6.352737 CCAGTAGTGTGGGTGATTATAAAGGT 60.353 42.308 0.00 0.00 33.46 3.50
567 568 6.055588 CCAGTAGTGTGGGTGATTATAAAGG 58.944 44.000 0.00 0.00 33.46 3.11
568 569 6.884832 TCCAGTAGTGTGGGTGATTATAAAG 58.115 40.000 0.00 0.00 38.26 1.85
569 570 6.877668 TCCAGTAGTGTGGGTGATTATAAA 57.122 37.500 0.00 0.00 38.26 1.40
570 571 6.877668 TTCCAGTAGTGTGGGTGATTATAA 57.122 37.500 0.00 0.00 38.26 0.98
571 572 6.613679 TGATTCCAGTAGTGTGGGTGATTATA 59.386 38.462 0.00 0.00 38.26 0.98
572 573 5.428457 TGATTCCAGTAGTGTGGGTGATTAT 59.572 40.000 0.00 0.00 38.26 1.28
573 574 4.780554 TGATTCCAGTAGTGTGGGTGATTA 59.219 41.667 0.00 0.00 38.26 1.75
574 575 3.587061 TGATTCCAGTAGTGTGGGTGATT 59.413 43.478 0.00 0.00 38.26 2.57
575 576 3.181329 TGATTCCAGTAGTGTGGGTGAT 58.819 45.455 0.00 0.00 38.26 3.06
576 577 2.567169 CTGATTCCAGTAGTGTGGGTGA 59.433 50.000 0.00 0.00 38.26 4.02
577 578 2.355108 CCTGATTCCAGTAGTGTGGGTG 60.355 54.545 0.00 0.00 38.74 4.61
578 579 1.909302 CCTGATTCCAGTAGTGTGGGT 59.091 52.381 0.00 0.00 38.74 4.51
579 580 2.187958 TCCTGATTCCAGTAGTGTGGG 58.812 52.381 0.00 0.00 38.74 4.61
580 581 3.708631 AGATCCTGATTCCAGTAGTGTGG 59.291 47.826 0.00 0.00 38.74 4.17
581 582 5.350504 AAGATCCTGATTCCAGTAGTGTG 57.649 43.478 0.00 0.00 38.74 3.82
663 665 1.070134 TGCCGTCAGCTTTCTGTAAGT 59.930 47.619 0.00 0.00 44.23 2.24
911 929 3.098636 GGATGCGTTTATTCTTTGTCGC 58.901 45.455 0.00 0.00 43.14 5.19
992 1019 1.674519 GGTGTGTGTGCATCGTGGATA 60.675 52.381 0.00 0.00 0.00 2.59
1036 1069 0.541863 GAGATGGGATCCAACGTGGT 59.458 55.000 15.23 0.00 39.03 4.16
1058 1096 1.043673 AAGGGGATCGAGGAAGACGG 61.044 60.000 0.00 0.00 0.00 4.79
1490 2685 2.807895 CAAGTACGCGTCGGGGTG 60.808 66.667 18.63 4.32 39.94 4.61
1686 2893 4.116328 CAGAAGGCGCCGACGAGA 62.116 66.667 23.20 0.00 43.93 4.04
2010 3218 1.329292 CTCAGAGACGAGGCTAACGAG 59.671 57.143 2.34 0.00 34.70 4.18
2083 3291 7.503549 TGAACAGCTCATGTCACATCTAATAT 58.496 34.615 0.00 0.00 43.00 1.28
3035 4857 3.493129 CACGGCACTACGCACATAATAAT 59.507 43.478 0.00 0.00 45.17 1.28
3042 4864 3.567478 CTCCACGGCACTACGCACA 62.567 63.158 0.00 0.00 45.17 4.57
3199 5021 4.148230 CGTACAGAGTCCACACGC 57.852 61.111 0.00 0.00 0.00 5.34
3219 5041 0.096976 CAACTTGATGGCGGCGTAAG 59.903 55.000 9.37 10.69 43.44 2.34


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

AutoCloner maintained by Alex Coulton.