Multiple sequence alignment - TraesCS3A01G169300

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 TraesCS3A01G169300 chr3A 100.000 2587 0 0 1 2587 177645984 177648570 0.000000e+00 4778.0
1 TraesCS3A01G169300 chr3A 89.130 506 38 10 1142 1631 177671314 177671818 4.730000e-172 614.0
2 TraesCS3A01G169300 chr3A 92.000 325 26 0 1307 1631 177888055 177888379 8.440000e-125 457.0
3 TraesCS3A01G169300 chr3A 96.970 33 0 1 34 66 738131533 738131502 1.000000e-03 54.7
4 TraesCS3A01G169300 chr7D 94.473 959 49 3 1632 2587 139853317 139854274 0.000000e+00 1474.0
5 TraesCS3A01G169300 chr7D 93.562 963 55 2 1632 2587 29754624 29753662 0.000000e+00 1428.0
6 TraesCS3A01G169300 chr7D 93.528 958 54 4 1632 2587 180969529 180968578 0.000000e+00 1419.0
7 TraesCS3A01G169300 chr2A 94.387 962 51 2 1628 2587 670662396 670663356 0.000000e+00 1474.0
8 TraesCS3A01G169300 chr1D 94.283 962 48 4 1628 2587 188325576 188324620 0.000000e+00 1465.0
9 TraesCS3A01G169300 chr1D 94.179 962 49 3 1633 2587 188336812 188335851 0.000000e+00 1459.0
10 TraesCS3A01G169300 chr1D 93.763 962 58 1 1628 2587 410645479 410644518 0.000000e+00 1443.0
11 TraesCS3A01G169300 chr5D 94.069 961 52 2 1628 2587 506105557 506106513 0.000000e+00 1454.0
12 TraesCS3A01G169300 chr2D 93.347 962 62 1 1628 2587 476737574 476738535 0.000000e+00 1421.0
13 TraesCS3A01G169300 chr3D 88.346 635 46 10 1022 1631 152852328 152851697 0.000000e+00 737.0
14 TraesCS3A01G169300 chr3D 87.671 584 47 9 1073 1631 152702671 152702088 0.000000e+00 656.0
15 TraesCS3A01G169300 chr3D 80.142 423 56 17 1 406 152854324 152853913 9.060000e-75 291.0
16 TraesCS3A01G169300 chr3B 88.214 560 51 10 1081 1631 224287112 224286559 0.000000e+00 654.0
17 TraesCS3A01G169300 chr3B 87.544 562 53 10 1081 1631 224164630 224164075 3.630000e-178 634.0
18 TraesCS3A01G169300 chr3B 88.117 547 45 6 1099 1631 223558923 223558383 1.310000e-177 632.0
19 TraesCS3A01G169300 chr3B 84.722 576 60 15 1080 1631 223678145 223677574 3.760000e-153 551.0
20 TraesCS3A01G169300 chr3B 87.143 420 36 8 1109 1511 223690763 223690345 6.520000e-126 460.0
21 TraesCS3A01G169300 chr3B 89.053 338 33 3 1295 1630 215104797 215105132 1.430000e-112 416.0
22 TraesCS3A01G169300 chr3B 90.411 146 13 1 1145 1289 224253608 224253463 9.450000e-45 191.0
23 TraesCS3A01G169300 chr3B 84.507 71 9 2 1211 1281 203345604 203345672 4.620000e-08 69.4
24 TraesCS3A01G169300 chr6D 85.333 75 8 3 16 87 363382431 363382357 9.930000e-10 75.0
25 TraesCS3A01G169300 chr4A 100.000 33 0 0 39 71 425960275 425960243 7.730000e-06 62.1
26 TraesCS3A01G169300 chr6A 89.362 47 5 0 38 84 3320522 3320568 2.780000e-05 60.2
27 TraesCS3A01G169300 chr5B 97.059 34 1 0 38 71 657713591 657713558 1.000000e-04 58.4


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 TraesCS3A01G169300 chr3A 177645984 177648570 2586 False 4778 4778 100.000 1 2587 1 chr3A.!!$F1 2586
1 TraesCS3A01G169300 chr3A 177671314 177671818 504 False 614 614 89.130 1142 1631 1 chr3A.!!$F2 489
2 TraesCS3A01G169300 chr7D 139853317 139854274 957 False 1474 1474 94.473 1632 2587 1 chr7D.!!$F1 955
3 TraesCS3A01G169300 chr7D 29753662 29754624 962 True 1428 1428 93.562 1632 2587 1 chr7D.!!$R1 955
4 TraesCS3A01G169300 chr7D 180968578 180969529 951 True 1419 1419 93.528 1632 2587 1 chr7D.!!$R2 955
5 TraesCS3A01G169300 chr2A 670662396 670663356 960 False 1474 1474 94.387 1628 2587 1 chr2A.!!$F1 959
6 TraesCS3A01G169300 chr1D 188324620 188325576 956 True 1465 1465 94.283 1628 2587 1 chr1D.!!$R1 959
7 TraesCS3A01G169300 chr1D 188335851 188336812 961 True 1459 1459 94.179 1633 2587 1 chr1D.!!$R2 954
8 TraesCS3A01G169300 chr1D 410644518 410645479 961 True 1443 1443 93.763 1628 2587 1 chr1D.!!$R3 959
9 TraesCS3A01G169300 chr5D 506105557 506106513 956 False 1454 1454 94.069 1628 2587 1 chr5D.!!$F1 959
10 TraesCS3A01G169300 chr2D 476737574 476738535 961 False 1421 1421 93.347 1628 2587 1 chr2D.!!$F1 959
11 TraesCS3A01G169300 chr3D 152702088 152702671 583 True 656 656 87.671 1073 1631 1 chr3D.!!$R1 558
12 TraesCS3A01G169300 chr3D 152851697 152854324 2627 True 514 737 84.244 1 1631 2 chr3D.!!$R2 1630
13 TraesCS3A01G169300 chr3B 224286559 224287112 553 True 654 654 88.214 1081 1631 1 chr3B.!!$R6 550
14 TraesCS3A01G169300 chr3B 224164075 224164630 555 True 634 634 87.544 1081 1631 1 chr3B.!!$R4 550
15 TraesCS3A01G169300 chr3B 223558383 223558923 540 True 632 632 88.117 1099 1631 1 chr3B.!!$R1 532
16 TraesCS3A01G169300 chr3B 223677574 223678145 571 True 551 551 84.722 1080 1631 1 chr3B.!!$R2 551

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
409 427 0.036765 AACGCTACTGCCAATTCGGA 60.037 50.0 0.0 0.0 36.56 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 3014 0.395862 ACGTCCATGACCTCCTCGAT 60.396 55.0 0.0 0.0 0.0 3.59 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
48 49 5.105756 CCTCCATCCCATAAGTGTCAAAAAC 60.106 44.000 0.00 0.00 0.00 2.43
49 50 4.457603 TCCATCCCATAAGTGTCAAAAACG 59.542 41.667 0.00 0.00 0.00 3.60
66 67 7.012421 GTCAAAAACGCTCTTATATTCTGGGAT 59.988 37.037 0.00 0.00 0.00 3.85
67 68 6.867662 AAAACGCTCTTATATTCTGGGATG 57.132 37.500 0.00 0.00 0.00 3.51
68 69 4.543590 ACGCTCTTATATTCTGGGATGG 57.456 45.455 0.00 0.00 0.00 3.51
71 72 4.464244 CGCTCTTATATTCTGGGATGGAGA 59.536 45.833 0.00 0.00 0.00 3.71
74 75 7.227156 GCTCTTATATTCTGGGATGGAGAAAA 58.773 38.462 0.00 0.00 33.22 2.29
135 136 3.872771 AGAAAAGAAAAGTTACACGCGGA 59.127 39.130 12.47 0.00 0.00 5.54
157 158 4.898829 TCGTTGGATCTTTAATGCATGG 57.101 40.909 0.00 0.00 0.00 3.66
174 175 2.685106 TGGCCCAAATTGACCAAGTA 57.315 45.000 0.00 0.00 0.00 2.24
183 184 5.455392 CAAATTGACCAAGTAACAGCTCAG 58.545 41.667 0.00 0.00 0.00 3.35
229 240 0.693049 CAGGCTAACCAGGGTCAGTT 59.307 55.000 0.00 0.00 39.06 3.16
233 244 3.591977 AGGCTAACCAGGGTCAGTTAAAT 59.408 43.478 0.00 0.00 39.06 1.40
234 245 3.694566 GGCTAACCAGGGTCAGTTAAATG 59.305 47.826 0.00 0.00 35.26 2.32
243 254 7.037873 ACCAGGGTCAGTTAAATGTAACTATCA 60.038 37.037 8.01 0.00 46.71 2.15
258 276 2.952978 ACTATCACTAGACGCCTTCCAG 59.047 50.000 0.00 0.00 0.00 3.86
259 277 1.853963 ATCACTAGACGCCTTCCAGT 58.146 50.000 0.00 0.00 0.00 4.00
265 283 1.598130 GACGCCTTCCAGTGTTGCT 60.598 57.895 0.00 0.00 0.00 3.91
266 284 0.320421 GACGCCTTCCAGTGTTGCTA 60.320 55.000 0.00 0.00 0.00 3.49
267 285 0.324943 ACGCCTTCCAGTGTTGCTAT 59.675 50.000 0.00 0.00 0.00 2.97
269 287 1.826385 GCCTTCCAGTGTTGCTATGT 58.174 50.000 0.00 0.00 0.00 2.29
290 308 3.745723 GGAACCCAACTGTGATGGT 57.254 52.632 0.00 0.00 36.14 3.55
300 318 4.082787 CCAACTGTGATGGTGAAACATACC 60.083 45.833 0.00 0.00 39.98 2.73
306 324 1.803334 TGGTGAAACATACCTGTCGC 58.197 50.000 0.00 0.00 39.98 5.19
308 326 1.609580 GGTGAAACATACCTGTCGCCA 60.610 52.381 0.00 0.00 39.98 5.69
314 332 1.004277 ACATACCTGTCGCCACCAATT 59.996 47.619 0.00 0.00 0.00 2.32
315 333 2.091541 CATACCTGTCGCCACCAATTT 58.908 47.619 0.00 0.00 0.00 1.82
324 342 2.340427 CCACCAATTTGGCGACTGT 58.660 52.632 15.49 0.00 42.67 3.55
336 354 4.035102 GACTGTCCCCAGCCCCAC 62.035 72.222 0.00 0.00 42.81 4.61
345 363 2.282462 CAGCCCCACCAACACTCC 60.282 66.667 0.00 0.00 0.00 3.85
346 364 2.776526 AGCCCCACCAACACTCCA 60.777 61.111 0.00 0.00 0.00 3.86
347 365 2.597510 GCCCCACCAACACTCCAC 60.598 66.667 0.00 0.00 0.00 4.02
348 366 2.115266 CCCCACCAACACTCCACC 59.885 66.667 0.00 0.00 0.00 4.61
357 375 1.177256 AACACTCCACCGCTCGTACT 61.177 55.000 0.00 0.00 0.00 2.73
363 381 4.157958 ACCGCTCGTACTCGTCGC 62.158 66.667 0.00 0.00 38.33 5.19
365 383 3.862402 CGCTCGTACTCGTCGCCT 61.862 66.667 0.00 0.00 38.33 5.52
374 392 2.075979 ACTCGTCGCCTAAGAAAACC 57.924 50.000 0.00 0.00 0.00 3.27
398 416 0.456312 CGGAAGCTCGAAACGCTACT 60.456 55.000 0.00 0.00 36.56 2.57
399 417 0.992802 GGAAGCTCGAAACGCTACTG 59.007 55.000 0.00 0.00 36.56 2.74
406 424 1.730064 TCGAAACGCTACTGCCAATTC 59.270 47.619 0.00 0.00 35.36 2.17
407 425 1.526986 CGAAACGCTACTGCCAATTCG 60.527 52.381 0.00 0.00 38.05 3.34
408 426 0.802494 AAACGCTACTGCCAATTCGG 59.198 50.000 0.00 0.00 35.36 4.30
409 427 0.036765 AACGCTACTGCCAATTCGGA 60.037 50.000 0.00 0.00 36.56 4.55
410 428 0.178068 ACGCTACTGCCAATTCGGAT 59.822 50.000 0.00 0.00 36.56 4.18
411 429 1.411246 ACGCTACTGCCAATTCGGATA 59.589 47.619 0.00 0.00 36.56 2.59
412 430 2.061773 CGCTACTGCCAATTCGGATAG 58.938 52.381 0.00 0.00 36.56 2.08
413 431 2.545952 CGCTACTGCCAATTCGGATAGT 60.546 50.000 0.00 4.61 37.46 2.12
414 432 3.305131 CGCTACTGCCAATTCGGATAGTA 60.305 47.826 0.00 5.32 35.85 1.82
415 433 4.618460 CGCTACTGCCAATTCGGATAGTAT 60.618 45.833 0.00 0.00 36.18 2.12
416 434 4.865365 GCTACTGCCAATTCGGATAGTATC 59.135 45.833 1.11 1.11 36.18 2.24
417 435 4.273148 ACTGCCAATTCGGATAGTATCC 57.727 45.455 18.04 18.04 46.22 2.59
424 442 3.295800 GGATAGTATCCCCGCCCG 58.704 66.667 17.32 0.00 43.88 6.13
425 443 1.304713 GGATAGTATCCCCGCCCGA 60.305 63.158 17.32 0.00 43.88 5.14
426 444 1.321074 GGATAGTATCCCCGCCCGAG 61.321 65.000 17.32 0.00 43.88 4.63
427 445 0.323178 GATAGTATCCCCGCCCGAGA 60.323 60.000 0.00 0.00 0.00 4.04
428 446 0.335361 ATAGTATCCCCGCCCGAGAT 59.665 55.000 0.00 0.00 0.00 2.75
429 447 0.611062 TAGTATCCCCGCCCGAGATG 60.611 60.000 0.00 0.00 0.00 2.90
430 448 2.603473 TATCCCCGCCCGAGATGG 60.603 66.667 0.00 0.00 37.55 3.51
431 449 3.462056 TATCCCCGCCCGAGATGGT 62.462 63.158 0.00 0.00 35.15 3.55
442 460 2.333389 CGAGATGGTCGCACTATACC 57.667 55.000 0.00 0.00 43.03 2.73
448 466 3.660501 TGGTCGCACTATACCATCATC 57.339 47.619 0.00 0.00 40.84 2.92
449 467 2.962421 TGGTCGCACTATACCATCATCA 59.038 45.455 0.00 0.00 40.84 3.07
450 468 3.005791 TGGTCGCACTATACCATCATCAG 59.994 47.826 0.00 0.00 40.84 2.90
451 469 2.989840 GTCGCACTATACCATCATCAGC 59.010 50.000 0.00 0.00 0.00 4.26
452 470 2.029020 TCGCACTATACCATCATCAGCC 60.029 50.000 0.00 0.00 0.00 4.85
453 471 2.289010 CGCACTATACCATCATCAGCCA 60.289 50.000 0.00 0.00 0.00 4.75
454 472 3.618263 CGCACTATACCATCATCAGCCAT 60.618 47.826 0.00 0.00 0.00 4.40
455 473 3.937706 GCACTATACCATCATCAGCCATC 59.062 47.826 0.00 0.00 0.00 3.51
456 474 4.511527 CACTATACCATCATCAGCCATCC 58.488 47.826 0.00 0.00 0.00 3.51
457 475 4.019950 CACTATACCATCATCAGCCATCCA 60.020 45.833 0.00 0.00 0.00 3.41
458 476 3.715638 ATACCATCATCAGCCATCCAG 57.284 47.619 0.00 0.00 0.00 3.86
459 477 0.477204 ACCATCATCAGCCATCCAGG 59.523 55.000 0.00 0.00 41.84 4.45
460 478 0.477204 CCATCATCAGCCATCCAGGT 59.523 55.000 0.00 0.00 40.61 4.00
461 479 1.133575 CCATCATCAGCCATCCAGGTT 60.134 52.381 0.00 0.00 40.61 3.50
462 480 2.662866 CATCATCAGCCATCCAGGTTT 58.337 47.619 0.00 0.00 40.61 3.27
463 481 3.435457 CCATCATCAGCCATCCAGGTTTA 60.435 47.826 0.00 0.00 40.61 2.01
464 482 4.404640 CATCATCAGCCATCCAGGTTTAT 58.595 43.478 0.00 0.00 40.61 1.40
465 483 4.524802 TCATCAGCCATCCAGGTTTATT 57.475 40.909 0.00 0.00 40.61 1.40
466 484 5.645056 TCATCAGCCATCCAGGTTTATTA 57.355 39.130 0.00 0.00 40.61 0.98
467 485 5.624159 TCATCAGCCATCCAGGTTTATTAG 58.376 41.667 0.00 0.00 40.61 1.73
468 486 5.369404 TCATCAGCCATCCAGGTTTATTAGA 59.631 40.000 0.00 0.00 40.61 2.10
469 487 5.708736 TCAGCCATCCAGGTTTATTAGAA 57.291 39.130 0.00 0.00 40.61 2.10
476 743 4.098894 TCCAGGTTTATTAGAAGTCGGGT 58.901 43.478 0.00 0.00 0.00 5.28
477 744 5.271598 TCCAGGTTTATTAGAAGTCGGGTA 58.728 41.667 0.00 0.00 0.00 3.69
480 747 6.221659 CAGGTTTATTAGAAGTCGGGTATCC 58.778 44.000 0.00 0.00 0.00 2.59
495 762 3.498334 GGTATCCTCCAATCTACCGACT 58.502 50.000 0.00 0.00 0.00 4.18
496 763 3.506844 GGTATCCTCCAATCTACCGACTC 59.493 52.174 0.00 0.00 0.00 3.36
503 770 1.402259 CAATCTACCGACTCGAGCACT 59.598 52.381 13.61 0.00 0.00 4.40
505 772 0.321387 TCTACCGACTCGAGCACTGT 60.321 55.000 13.61 11.79 0.00 3.55
506 773 1.066645 TCTACCGACTCGAGCACTGTA 60.067 52.381 13.61 12.28 0.00 2.74
509 776 0.375454 CCGACTCGAGCACTGTAGAG 59.625 60.000 13.61 0.00 36.83 2.43
513 780 1.080298 CTCGAGCACTGTAGAGTCGT 58.920 55.000 0.00 0.00 0.00 4.34
515 782 1.197036 TCGAGCACTGTAGAGTCGTTG 59.803 52.381 0.00 0.00 0.00 4.10
519 786 0.603569 CACTGTAGAGTCGTTGGCCT 59.396 55.000 3.32 0.00 0.00 5.19
521 788 0.179161 CTGTAGAGTCGTTGGCCTCG 60.179 60.000 3.32 9.57 32.88 4.63
524 791 0.524862 TAGAGTCGTTGGCCTCGTTC 59.475 55.000 17.35 15.61 32.88 3.95
531 798 2.879233 TTGGCCTCGTTCGGAGCTT 61.879 57.895 3.32 0.00 41.71 3.74
533 800 2.509561 GCCTCGTTCGGAGCTTCC 60.510 66.667 0.00 0.00 41.71 3.46
544 811 2.581354 AGCTTCCGCGCTCTCAAT 59.419 55.556 5.56 0.00 42.32 2.57
557 824 3.484229 CGCTCTCAATCGTTGGATTTCAC 60.484 47.826 0.00 0.00 40.90 3.18
561 828 4.513692 TCTCAATCGTTGGATTTCACGTTT 59.486 37.500 0.00 0.00 40.90 3.60
564 831 6.726230 TCAATCGTTGGATTTCACGTTTAAA 58.274 32.000 0.00 0.00 40.90 1.52
566 833 7.863375 TCAATCGTTGGATTTCACGTTTAAATT 59.137 29.630 6.99 0.00 40.90 1.82
567 834 6.978024 TCGTTGGATTTCACGTTTAAATTG 57.022 33.333 6.99 0.00 0.00 2.32
572 839 7.401484 TGGATTTCACGTTTAAATTGCTTTC 57.599 32.000 6.99 0.00 0.00 2.62
576 843 7.778470 TTTCACGTTTAAATTGCTTTCCAAT 57.222 28.000 0.00 0.00 45.90 3.16
609 876 4.186159 CCAGCTTTTGGGCATATGAAAAG 58.814 43.478 17.58 17.58 43.75 2.27
613 880 5.535043 CTTTTGGGCATATGAAAAGCAAC 57.465 39.130 6.97 0.00 31.79 4.17
614 881 2.937469 TGGGCATATGAAAAGCAACG 57.063 45.000 6.97 0.00 0.00 4.10
615 882 1.476085 TGGGCATATGAAAAGCAACGG 59.524 47.619 6.97 0.00 0.00 4.44
616 883 1.202405 GGGCATATGAAAAGCAACGGG 60.202 52.381 6.97 0.00 0.00 5.28
638 905 1.318576 GGCACGGGGGAAAATATCAG 58.681 55.000 0.00 0.00 0.00 2.90
645 912 3.487372 GGGGGAAAATATCAGGTGCTAC 58.513 50.000 0.00 0.00 0.00 3.58
646 913 3.138468 GGGGGAAAATATCAGGTGCTACT 59.862 47.826 0.00 0.00 0.00 2.57
647 914 4.349930 GGGGGAAAATATCAGGTGCTACTA 59.650 45.833 0.00 0.00 0.00 1.82
664 931 7.652507 GGTGCTACTAACTCTTTATGTGATACC 59.347 40.741 0.00 0.00 0.00 2.73
665 932 8.195436 GTGCTACTAACTCTTTATGTGATACCA 58.805 37.037 0.00 0.00 0.00 3.25
683 950 7.971168 GTGATACCATGATATAGACTTTCGAGG 59.029 40.741 0.00 0.00 0.00 4.63
684 951 5.140747 ACCATGATATAGACTTTCGAGGC 57.859 43.478 0.00 0.00 0.00 4.70
685 952 4.588951 ACCATGATATAGACTTTCGAGGCA 59.411 41.667 0.00 0.00 0.00 4.75
686 953 5.247110 ACCATGATATAGACTTTCGAGGCAT 59.753 40.000 0.00 0.00 0.00 4.40
699 966 2.036862 TCGAGGCATTGGATCTCAGATG 59.963 50.000 0.00 0.00 0.00 2.90
705 972 3.502595 GCATTGGATCTCAGATGTGATGG 59.497 47.826 0.00 0.00 30.18 3.51
706 973 2.924757 TGGATCTCAGATGTGATGGC 57.075 50.000 0.00 0.00 30.18 4.40
709 976 2.633967 GGATCTCAGATGTGATGGCTCT 59.366 50.000 0.00 0.00 30.18 4.09
712 980 0.835276 TCAGATGTGATGGCTCTGGG 59.165 55.000 0.00 0.00 37.57 4.45
729 997 4.144297 TCTGGGAGGTCTTGAACATTTTG 58.856 43.478 0.00 0.00 0.00 2.44
736 1004 6.238184 GGAGGTCTTGAACATTTTGCAAAAAG 60.238 38.462 27.10 24.37 0.00 2.27
737 1005 6.405538 AGGTCTTGAACATTTTGCAAAAAGA 58.594 32.000 28.34 21.26 0.00 2.52
738 1006 6.878389 AGGTCTTGAACATTTTGCAAAAAGAA 59.122 30.769 28.34 14.40 0.00 2.52
739 1007 7.390162 AGGTCTTGAACATTTTGCAAAAAGAAA 59.610 29.630 28.34 18.57 0.00 2.52
740 1008 8.020244 GGTCTTGAACATTTTGCAAAAAGAAAA 58.980 29.630 28.34 18.30 0.00 2.29
741 1009 9.392021 GTCTTGAACATTTTGCAAAAAGAAAAA 57.608 25.926 28.34 18.43 39.06 1.94
742 1010 9.609950 TCTTGAACATTTTGCAAAAAGAAAAAG 57.390 25.926 28.34 24.49 38.14 2.27
745 1013 9.392021 TGAACATTTTGCAAAAAGAAAAAGAAC 57.608 25.926 28.34 12.86 38.14 3.01
750 1018 7.920160 TTTGCAAAAAGAAAAAGAACCATCT 57.080 28.000 10.02 0.00 37.57 2.90
764 1032 7.971183 AAGAACCATCTAAGAGTCTCAAAAC 57.029 36.000 1.94 0.00 33.77 2.43
768 1036 5.221722 ACCATCTAAGAGTCTCAAAACTGCA 60.222 40.000 1.94 0.00 0.00 4.41
769 1037 5.879223 CCATCTAAGAGTCTCAAAACTGCAT 59.121 40.000 1.94 0.00 0.00 3.96
771 1039 3.911661 AAGAGTCTCAAAACTGCATGC 57.088 42.857 11.82 11.82 0.00 4.06
783 1051 3.321682 AAACTGCATGCAGGTACAACAAT 59.678 39.130 42.07 22.99 44.18 2.71
790 1058 5.771469 CATGCAGGTACAACAATTTCTCAA 58.229 37.500 0.00 0.00 0.00 3.02
803 1071 4.864916 ATTTCTCAAATGTCGTCGGATG 57.135 40.909 0.00 0.00 0.00 3.51
810 1078 5.416083 TCAAATGTCGTCGGATGTAAGATT 58.584 37.500 0.00 0.00 0.00 2.40
819 1087 2.285220 CGGATGTAAGATTCAACGGCTG 59.715 50.000 0.00 0.00 0.00 4.85
823 1091 1.398390 GTAAGATTCAACGGCTGCCAG 59.602 52.381 20.29 13.76 0.00 4.85
826 1094 1.098050 GATTCAACGGCTGCCAGAAT 58.902 50.000 22.86 22.86 0.00 2.40
832 1100 1.264749 ACGGCTGCCAGAATCCTGTA 61.265 55.000 20.29 0.00 38.74 2.74
839 1107 1.139058 GCCAGAATCCTGTATCACGGT 59.861 52.381 0.00 0.00 38.74 4.83
848 1116 4.795469 TCCTGTATCACGGTATCACCTAA 58.205 43.478 0.00 0.00 35.66 2.69
853 1121 1.120530 CACGGTATCACCTAAGGGCT 58.879 55.000 0.00 0.00 35.66 5.19
873 1141 5.470437 GGGCTAGTAGCACCTGATATTTTTC 59.530 44.000 23.24 1.00 44.75 2.29
874 1142 5.470437 GGCTAGTAGCACCTGATATTTTTCC 59.530 44.000 23.24 0.00 44.75 3.13
882 1150 2.624838 CCTGATATTTTTCCGCAGCCAT 59.375 45.455 0.00 0.00 0.00 4.40
884 1152 2.361757 TGATATTTTTCCGCAGCCATGG 59.638 45.455 7.63 7.63 0.00 3.66
925 1193 7.913789 TCTCTTCTGGCCTATAACTGTTTTTA 58.086 34.615 3.32 0.00 0.00 1.52
927 1195 7.455058 TCTTCTGGCCTATAACTGTTTTTACA 58.545 34.615 3.32 0.00 0.00 2.41
931 1199 8.052748 TCTGGCCTATAACTGTTTTTACATCAT 58.947 33.333 3.32 0.00 0.00 2.45
932 1200 8.220755 TGGCCTATAACTGTTTTTACATCATC 57.779 34.615 3.32 0.00 0.00 2.92
952 1229 6.902341 TCATCAAGTTTAACACAAGATGCTC 58.098 36.000 0.00 0.00 38.16 4.26
961 1238 5.474578 AACACAAGATGCTCTAAGACTCA 57.525 39.130 0.00 0.00 0.00 3.41
962 1239 4.815269 ACACAAGATGCTCTAAGACTCAC 58.185 43.478 0.00 0.00 0.00 3.51
963 1240 4.281941 ACACAAGATGCTCTAAGACTCACA 59.718 41.667 0.00 0.00 0.00 3.58
964 1241 4.624882 CACAAGATGCTCTAAGACTCACAC 59.375 45.833 0.00 0.00 0.00 3.82
965 1242 4.281941 ACAAGATGCTCTAAGACTCACACA 59.718 41.667 0.00 0.00 0.00 3.72
966 1243 4.448537 AGATGCTCTAAGACTCACACAC 57.551 45.455 0.00 0.00 0.00 3.82
968 1245 3.371102 TGCTCTAAGACTCACACACAC 57.629 47.619 0.00 0.00 0.00 3.82
971 1248 4.202253 TGCTCTAAGACTCACACACACAAT 60.202 41.667 0.00 0.00 0.00 2.71
1001 1975 6.538945 ACTCCAACAAAACCAACTAAACAT 57.461 33.333 0.00 0.00 0.00 2.71
1003 1977 7.712797 ACTCCAACAAAACCAACTAAACATAG 58.287 34.615 0.00 0.00 0.00 2.23
1071 2068 4.873817 TCACAGCCTTTGATTTGTTGATG 58.126 39.130 0.00 0.00 0.00 3.07
1075 2072 5.479375 ACAGCCTTTGATTTGTTGATGAGAT 59.521 36.000 0.00 0.00 0.00 2.75
1094 2093 4.718961 AGATTAGAAATAGCGCCAACCAT 58.281 39.130 2.29 0.00 0.00 3.55
1164 2180 4.373116 GCCTCCCGAAGCGTGACA 62.373 66.667 0.00 0.00 0.00 3.58
1195 2211 6.127897 ACAAATCAGATTTCGATCCCAACTTC 60.128 38.462 5.32 0.00 0.00 3.01
1202 2218 1.527370 GATCCCAACTTCCCCCGAG 59.473 63.158 0.00 0.00 0.00 4.63
1207 2223 1.374947 CAACTTCCCCCGAGCTTCA 59.625 57.895 0.00 0.00 0.00 3.02
1222 2255 1.276421 GCTTCACTGCCCTAGTTCTCA 59.724 52.381 0.00 0.00 37.60 3.27
1225 2258 3.895232 TCACTGCCCTAGTTCTCAATC 57.105 47.619 0.00 0.00 37.60 2.67
1275 2322 3.844804 AGTTTTCGATCCCTAGTTTCCCT 59.155 43.478 0.00 0.00 0.00 4.20
1291 2338 1.169661 CCCTGATCTCGACTCTCGGG 61.170 65.000 0.00 5.40 42.83 5.14
1302 2364 1.676529 GACTCTCGGGATCGAACATGA 59.323 52.381 0.00 0.00 45.47 3.07
1393 2455 1.416049 CGACGTGCATGAAAGACGG 59.584 57.895 14.17 0.00 37.42 4.79
1395 2457 0.669318 GACGTGCATGAAAGACGGGA 60.669 55.000 14.17 0.00 37.42 5.14
1482 2544 2.048597 CGGTGCTTCGCAGGTACA 60.049 61.111 0.00 0.00 40.08 2.90
1486 2548 1.676014 GGTGCTTCGCAGGTACATTCT 60.676 52.381 0.00 0.00 40.08 2.40
1499 2561 6.516527 GCAGGTACATTCTTCCAAAACATCAA 60.517 38.462 0.00 0.00 0.00 2.57
1501 2563 6.549364 AGGTACATTCTTCCAAAACATCAACA 59.451 34.615 0.00 0.00 0.00 3.33
1532 2594 3.565307 TCAATTTTGCAGGGAACTCACT 58.435 40.909 0.00 0.00 40.21 3.41
1533 2595 3.960102 TCAATTTTGCAGGGAACTCACTT 59.040 39.130 0.00 0.00 40.21 3.16
1609 2671 1.534235 ACGACTCCTGGCTGAAGGT 60.534 57.895 0.00 0.00 38.58 3.50
1616 2678 3.535629 CTGGCTGAAGGTGGCGACA 62.536 63.158 0.00 0.00 38.70 4.35
1703 2765 8.580720 ACTAGATAAAGCATGACCAGTATAGTG 58.419 37.037 0.00 0.09 0.00 2.74
1751 2813 8.740123 TTGACAAAGAGAAGGTAAACAACATA 57.260 30.769 0.00 0.00 0.00 2.29
1845 2907 8.589338 AGTCTAACATATCTAGGGCAAATACTG 58.411 37.037 0.00 0.00 0.00 2.74
1952 3014 3.002583 TCCTCGCCTGCCATGTCA 61.003 61.111 0.00 0.00 0.00 3.58
1964 3026 1.114627 CCATGTCATCGAGGAGGTCA 58.885 55.000 0.00 0.00 0.00 4.02
2003 3065 1.100510 CGTCATCGGGGAAGTAGTCA 58.899 55.000 0.00 0.00 0.00 3.41
2022 3084 3.606662 CGGCGACCGGATCATCCT 61.607 66.667 9.46 0.00 44.15 3.24
2046 3108 2.543687 GAAGCAGCCAGTAGTCGCGA 62.544 60.000 3.71 3.71 0.00 5.87
2102 3164 2.805295 CGTACAGGACTCAAAAGGTGCA 60.805 50.000 0.00 0.00 0.00 4.57
2125 3187 1.977544 CGGAGGCCTACTATCCCGG 60.978 68.421 14.69 0.00 32.19 5.73
2214 3277 1.623811 GGAAGGAGTAGTTCTGGTGCA 59.376 52.381 0.00 0.00 0.00 4.57
2215 3278 2.613223 GGAAGGAGTAGTTCTGGTGCAC 60.613 54.545 8.80 8.80 0.00 4.57
2248 3311 2.699321 GAGCGACCTCCCTTTTATAGGT 59.301 50.000 0.00 0.00 46.33 3.08
2290 3353 0.249868 CAGCGACAGGAGGTGAAACA 60.250 55.000 0.00 0.00 39.98 2.83
2297 3360 4.646572 GACAGGAGGTGAAACAAAGAGAT 58.353 43.478 0.00 0.00 39.98 2.75
2305 3368 4.397417 GGTGAAACAAAGAGATGGAGATGG 59.603 45.833 0.00 0.00 39.98 3.51
2380 3444 5.186996 TCGCAAAAATCTTTTCAGCTTCT 57.813 34.783 9.58 0.00 32.40 2.85
2381 3445 6.312399 TCGCAAAAATCTTTTCAGCTTCTA 57.688 33.333 9.58 0.00 32.40 2.10
2450 3516 1.754234 GCTCATTCCCGCAACCCAT 60.754 57.895 0.00 0.00 0.00 4.00
2454 3520 3.598747 ATTCCCGCAACCCATGGCA 62.599 57.895 6.09 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.129262 TGACACTTATGGGATGGAGGA 57.871 47.619 0.00 0.00 0.00 3.71
27 28 4.732784 CGTTTTTGACACTTATGGGATGG 58.267 43.478 0.00 0.00 0.00 3.51
48 49 4.464244 TCTCCATCCCAGAATATAAGAGCG 59.536 45.833 0.00 0.00 0.00 5.03
49 50 6.365970 TTCTCCATCCCAGAATATAAGAGC 57.634 41.667 0.00 0.00 0.00 4.09
114 115 4.199840 TCCGCGTGTAACTTTTCTTTTC 57.800 40.909 4.92 0.00 31.75 2.29
116 117 3.120786 CGATCCGCGTGTAACTTTTCTTT 60.121 43.478 4.92 0.00 34.64 2.52
117 118 2.410730 CGATCCGCGTGTAACTTTTCTT 59.589 45.455 4.92 0.00 34.64 2.52
118 119 1.990563 CGATCCGCGTGTAACTTTTCT 59.009 47.619 4.92 0.00 34.64 2.52
119 120 2.414768 CGATCCGCGTGTAACTTTTC 57.585 50.000 4.92 0.00 34.64 2.29
132 133 3.559655 TGCATTAAAGATCCAACGATCCG 59.440 43.478 0.00 0.00 45.32 4.18
135 136 4.261741 GCCATGCATTAAAGATCCAACGAT 60.262 41.667 0.00 0.00 0.00 3.73
157 158 3.860754 GCTGTTACTTGGTCAATTTGGGC 60.861 47.826 0.00 0.00 0.00 5.36
229 240 7.578310 AGGCGTCTAGTGATAGTTACATTTA 57.422 36.000 0.00 0.00 0.00 1.40
233 244 4.337555 GGAAGGCGTCTAGTGATAGTTACA 59.662 45.833 0.00 0.00 0.00 2.41
234 245 4.337555 TGGAAGGCGTCTAGTGATAGTTAC 59.662 45.833 0.00 0.00 0.00 2.50
249 267 0.729116 CATAGCAACACTGGAAGGCG 59.271 55.000 0.00 0.00 39.30 5.52
258 276 1.084289 GGTTCCCGACATAGCAACAC 58.916 55.000 0.00 0.00 0.00 3.32
259 277 0.035820 GGGTTCCCGACATAGCAACA 60.036 55.000 0.00 0.00 0.00 3.33
265 283 1.002659 CACAGTTGGGTTCCCGACATA 59.997 52.381 25.01 0.00 41.74 2.29
266 284 0.250727 CACAGTTGGGTTCCCGACAT 60.251 55.000 25.01 13.17 41.74 3.06
267 285 1.147376 CACAGTTGGGTTCCCGACA 59.853 57.895 25.01 1.21 41.74 4.35
269 287 0.036164 CATCACAGTTGGGTTCCCGA 59.964 55.000 3.27 0.00 0.00 5.14
278 296 4.761739 AGGTATGTTTCACCATCACAGTTG 59.238 41.667 0.00 0.00 38.62 3.16
282 300 4.323417 GACAGGTATGTTTCACCATCACA 58.677 43.478 0.00 0.00 40.68 3.58
284 302 3.595173 CGACAGGTATGTTTCACCATCA 58.405 45.455 0.00 0.00 40.68 3.07
285 303 2.351726 GCGACAGGTATGTTTCACCATC 59.648 50.000 0.00 0.00 40.68 3.51
290 308 1.609580 GGTGGCGACAGGTATGTTTCA 60.610 52.381 0.00 0.00 44.46 2.69
308 326 0.893727 GGGACAGTCGCCAAATTGGT 60.894 55.000 14.17 0.00 40.46 3.67
335 353 2.426023 GAGCGGTGGAGTGTTGGT 59.574 61.111 0.00 0.00 0.00 3.67
336 354 2.149803 TACGAGCGGTGGAGTGTTGG 62.150 60.000 2.87 0.00 0.00 3.77
338 356 1.177256 AGTACGAGCGGTGGAGTGTT 61.177 55.000 2.87 0.00 0.00 3.32
339 357 1.584380 GAGTACGAGCGGTGGAGTGT 61.584 60.000 2.87 0.00 0.00 3.55
345 363 2.276493 CGACGAGTACGAGCGGTG 60.276 66.667 0.00 0.00 42.66 4.94
346 364 4.157958 GCGACGAGTACGAGCGGT 62.158 66.667 0.00 0.00 42.66 5.68
347 365 4.883300 GGCGACGAGTACGAGCGG 62.883 72.222 0.00 0.00 42.95 5.52
348 366 2.028766 TTAGGCGACGAGTACGAGCG 62.029 60.000 0.00 4.66 42.95 5.03
357 375 0.314935 ACGGTTTTCTTAGGCGACGA 59.685 50.000 0.00 0.00 0.00 4.20
374 392 1.154654 GTTTCGAGCTTCCGCAACG 60.155 57.895 0.00 0.00 39.10 4.10
395 413 5.401531 GGATACTATCCGAATTGGCAGTA 57.598 43.478 0.00 4.10 40.13 2.74
408 426 0.323178 TCTCGGGCGGGGATACTATC 60.323 60.000 0.00 0.00 0.00 2.08
409 427 0.335361 ATCTCGGGCGGGGATACTAT 59.665 55.000 5.51 0.00 0.00 2.12
410 428 0.611062 CATCTCGGGCGGGGATACTA 60.611 60.000 7.15 0.00 0.00 1.82
411 429 1.908793 CATCTCGGGCGGGGATACT 60.909 63.158 7.15 0.00 0.00 2.12
412 430 2.657237 CATCTCGGGCGGGGATAC 59.343 66.667 7.15 0.00 0.00 2.24
413 431 2.603473 CCATCTCGGGCGGGGATA 60.603 66.667 7.15 0.00 0.00 2.59
414 432 4.880426 ACCATCTCGGGCGGGGAT 62.880 66.667 0.91 0.91 40.22 3.85
420 438 2.088674 ATAGTGCGACCATCTCGGGC 62.089 60.000 0.00 0.00 43.18 6.13
421 439 1.068472 GTATAGTGCGACCATCTCGGG 60.068 57.143 0.00 0.00 43.18 5.14
422 440 1.068472 GGTATAGTGCGACCATCTCGG 60.068 57.143 0.00 0.00 43.18 4.63
423 441 1.607148 TGGTATAGTGCGACCATCTCG 59.393 52.381 0.00 0.00 40.87 4.04
429 447 3.579709 CTGATGATGGTATAGTGCGACC 58.420 50.000 0.00 0.00 36.17 4.79
430 448 2.989840 GCTGATGATGGTATAGTGCGAC 59.010 50.000 0.00 0.00 0.00 5.19
431 449 2.029020 GGCTGATGATGGTATAGTGCGA 60.029 50.000 0.00 0.00 0.00 5.10
432 450 2.289010 TGGCTGATGATGGTATAGTGCG 60.289 50.000 0.00 0.00 0.00 5.34
433 451 3.407424 TGGCTGATGATGGTATAGTGC 57.593 47.619 0.00 0.00 0.00 4.40
434 452 4.019950 TGGATGGCTGATGATGGTATAGTG 60.020 45.833 0.00 0.00 0.00 2.74
435 453 4.170449 TGGATGGCTGATGATGGTATAGT 58.830 43.478 0.00 0.00 0.00 2.12
436 454 4.383880 CCTGGATGGCTGATGATGGTATAG 60.384 50.000 0.00 0.00 0.00 1.31
437 455 3.520721 CCTGGATGGCTGATGATGGTATA 59.479 47.826 0.00 0.00 0.00 1.47
438 456 2.307980 CCTGGATGGCTGATGATGGTAT 59.692 50.000 0.00 0.00 0.00 2.73
439 457 1.701292 CCTGGATGGCTGATGATGGTA 59.299 52.381 0.00 0.00 0.00 3.25
440 458 0.477204 CCTGGATGGCTGATGATGGT 59.523 55.000 0.00 0.00 0.00 3.55
441 459 0.477204 ACCTGGATGGCTGATGATGG 59.523 55.000 0.00 0.00 40.22 3.51
442 460 2.359981 AACCTGGATGGCTGATGATG 57.640 50.000 0.00 0.00 40.22 3.07
443 461 4.736611 ATAAACCTGGATGGCTGATGAT 57.263 40.909 0.00 0.00 40.22 2.45
444 462 4.524802 AATAAACCTGGATGGCTGATGA 57.475 40.909 0.00 0.00 40.22 2.92
445 463 5.624159 TCTAATAAACCTGGATGGCTGATG 58.376 41.667 0.00 0.00 40.22 3.07
446 464 5.912149 TCTAATAAACCTGGATGGCTGAT 57.088 39.130 0.00 0.00 40.22 2.90
447 465 5.191722 ACTTCTAATAAACCTGGATGGCTGA 59.808 40.000 0.00 0.00 40.22 4.26
448 466 5.440610 ACTTCTAATAAACCTGGATGGCTG 58.559 41.667 0.00 0.00 40.22 4.85
449 467 5.685075 CGACTTCTAATAAACCTGGATGGCT 60.685 44.000 0.00 0.00 40.22 4.75
450 468 4.511826 CGACTTCTAATAAACCTGGATGGC 59.488 45.833 0.00 0.00 40.22 4.40
451 469 5.057149 CCGACTTCTAATAAACCTGGATGG 58.943 45.833 0.00 0.00 42.93 3.51
452 470 5.057149 CCCGACTTCTAATAAACCTGGATG 58.943 45.833 0.00 0.00 0.00 3.51
453 471 4.720273 ACCCGACTTCTAATAAACCTGGAT 59.280 41.667 0.00 0.00 0.00 3.41
454 472 4.098894 ACCCGACTTCTAATAAACCTGGA 58.901 43.478 0.00 0.00 0.00 3.86
455 473 4.482952 ACCCGACTTCTAATAAACCTGG 57.517 45.455 0.00 0.00 0.00 4.45
456 474 6.041751 AGGATACCCGACTTCTAATAAACCTG 59.958 42.308 0.00 0.00 37.58 4.00
457 475 6.141790 AGGATACCCGACTTCTAATAAACCT 58.858 40.000 0.00 0.00 37.58 3.50
458 476 6.416631 AGGATACCCGACTTCTAATAAACC 57.583 41.667 0.00 0.00 37.58 3.27
459 477 6.041296 TGGAGGATACCCGACTTCTAATAAAC 59.959 42.308 0.00 0.00 37.58 2.01
460 478 6.138263 TGGAGGATACCCGACTTCTAATAAA 58.862 40.000 0.00 0.00 37.58 1.40
461 479 5.708544 TGGAGGATACCCGACTTCTAATAA 58.291 41.667 0.00 0.00 37.58 1.40
462 480 5.329191 TGGAGGATACCCGACTTCTAATA 57.671 43.478 0.00 0.00 37.58 0.98
463 481 4.194678 TGGAGGATACCCGACTTCTAAT 57.805 45.455 0.00 0.00 37.58 1.73
464 482 3.675348 TGGAGGATACCCGACTTCTAA 57.325 47.619 0.00 0.00 37.58 2.10
465 483 3.675348 TTGGAGGATACCCGACTTCTA 57.325 47.619 0.00 0.00 37.58 2.10
466 484 2.544844 TTGGAGGATACCCGACTTCT 57.455 50.000 0.00 0.00 37.58 2.85
467 485 2.966516 AGATTGGAGGATACCCGACTTC 59.033 50.000 0.00 0.00 37.58 3.01
468 486 3.047695 AGATTGGAGGATACCCGACTT 57.952 47.619 0.00 0.00 37.58 3.01
469 487 2.777459 AGATTGGAGGATACCCGACT 57.223 50.000 0.00 0.00 37.58 4.18
476 743 3.072038 TCGAGTCGGTAGATTGGAGGATA 59.928 47.826 13.54 0.00 0.00 2.59
477 744 2.158652 TCGAGTCGGTAGATTGGAGGAT 60.159 50.000 13.54 0.00 0.00 3.24
480 747 1.002251 GCTCGAGTCGGTAGATTGGAG 60.002 57.143 15.13 0.00 40.27 3.86
495 762 1.197036 CAACGACTCTACAGTGCTCGA 59.803 52.381 0.00 0.00 30.63 4.04
496 763 1.607713 CAACGACTCTACAGTGCTCG 58.392 55.000 0.00 0.00 30.63 5.03
503 770 0.892358 ACGAGGCCAACGACTCTACA 60.892 55.000 24.75 0.00 34.70 2.74
505 772 0.524862 GAACGAGGCCAACGACTCTA 59.475 55.000 24.75 0.00 34.70 2.43
506 773 1.289380 GAACGAGGCCAACGACTCT 59.711 57.895 24.75 9.20 34.70 3.24
509 776 3.110178 CCGAACGAGGCCAACGAC 61.110 66.667 24.75 17.03 34.70 4.34
513 780 2.781595 GAAGCTCCGAACGAGGCCAA 62.782 60.000 5.01 0.00 39.22 4.52
515 782 2.509561 GAAGCTCCGAACGAGGCC 60.510 66.667 0.00 0.00 39.22 5.19
531 798 1.805539 CAACGATTGAGAGCGCGGA 60.806 57.895 8.83 0.00 38.46 5.54
533 800 1.148157 ATCCAACGATTGAGAGCGCG 61.148 55.000 0.00 0.00 38.46 6.86
535 802 2.672874 TGAAATCCAACGATTGAGAGCG 59.327 45.455 0.00 0.00 38.75 5.03
536 803 3.484229 CGTGAAATCCAACGATTGAGAGC 60.484 47.826 0.00 0.00 38.75 4.09
544 811 5.399892 GCAATTTAAACGTGAAATCCAACGA 59.600 36.000 8.65 0.00 0.00 3.85
591 858 4.091800 CGTTGCTTTTCATATGCCCAAAAG 59.908 41.667 17.58 17.58 39.25 2.27
597 864 1.802508 GCCCGTTGCTTTTCATATGCC 60.803 52.381 0.00 0.00 36.87 4.40
616 883 3.999297 TATTTTCCCCCGTGCCCGC 62.999 63.158 0.00 0.00 0.00 6.13
618 885 0.106419 TGATATTTTCCCCCGTGCCC 60.106 55.000 0.00 0.00 0.00 5.36
620 887 1.318576 CCTGATATTTTCCCCCGTGC 58.681 55.000 0.00 0.00 0.00 5.34
624 891 2.755952 AGCACCTGATATTTTCCCCC 57.244 50.000 0.00 0.00 0.00 5.40
625 892 4.439253 AGTAGCACCTGATATTTTCCCC 57.561 45.455 0.00 0.00 0.00 4.81
638 905 7.652507 GGTATCACATAAAGAGTTAGTAGCACC 59.347 40.741 0.00 0.00 0.00 5.01
656 923 8.404107 TCGAAAGTCTATATCATGGTATCACA 57.596 34.615 0.56 0.00 0.00 3.58
664 931 6.091849 CCAATGCCTCGAAAGTCTATATCATG 59.908 42.308 0.00 0.00 0.00 3.07
665 932 6.014242 TCCAATGCCTCGAAAGTCTATATCAT 60.014 38.462 0.00 0.00 0.00 2.45
677 944 2.110578 TCTGAGATCCAATGCCTCGAA 58.889 47.619 0.00 0.00 0.00 3.71
678 945 1.780503 TCTGAGATCCAATGCCTCGA 58.219 50.000 0.00 0.00 0.00 4.04
679 946 2.224233 ACATCTGAGATCCAATGCCTCG 60.224 50.000 0.00 0.00 0.00 4.63
680 947 3.139850 CACATCTGAGATCCAATGCCTC 58.860 50.000 0.00 0.00 0.00 4.70
683 950 3.502595 CCATCACATCTGAGATCCAATGC 59.497 47.826 0.00 0.00 0.00 3.56
684 951 3.502595 GCCATCACATCTGAGATCCAATG 59.497 47.826 0.00 0.00 0.00 2.82
685 952 3.394940 AGCCATCACATCTGAGATCCAAT 59.605 43.478 0.00 0.00 0.00 3.16
686 953 2.775960 AGCCATCACATCTGAGATCCAA 59.224 45.455 0.00 0.00 0.00 3.53
699 966 0.980231 AGACCTCCCAGAGCCATCAC 60.980 60.000 0.00 0.00 0.00 3.06
705 972 0.687354 TGTTCAAGACCTCCCAGAGC 59.313 55.000 0.00 0.00 0.00 4.09
706 973 3.710209 AATGTTCAAGACCTCCCAGAG 57.290 47.619 0.00 0.00 0.00 3.35
709 976 2.627699 GCAAAATGTTCAAGACCTCCCA 59.372 45.455 0.00 0.00 0.00 4.37
712 980 6.534793 TCTTTTTGCAAAATGTTCAAGACCTC 59.465 34.615 27.37 0.00 0.00 3.85
729 997 8.871686 TCTTAGATGGTTCTTTTTCTTTTTGC 57.128 30.769 0.00 0.00 33.17 3.68
736 1004 8.608844 TTGAGACTCTTAGATGGTTCTTTTTC 57.391 34.615 3.68 0.00 33.17 2.29
737 1005 8.980481 TTTGAGACTCTTAGATGGTTCTTTTT 57.020 30.769 3.68 0.00 33.17 1.94
738 1006 8.841300 GTTTTGAGACTCTTAGATGGTTCTTTT 58.159 33.333 3.68 0.00 33.17 2.27
739 1007 8.214364 AGTTTTGAGACTCTTAGATGGTTCTTT 58.786 33.333 3.68 0.00 33.17 2.52
740 1008 7.659390 CAGTTTTGAGACTCTTAGATGGTTCTT 59.341 37.037 3.68 0.00 33.17 2.52
741 1009 7.158021 CAGTTTTGAGACTCTTAGATGGTTCT 58.842 38.462 3.68 0.00 35.90 3.01
742 1010 6.128418 GCAGTTTTGAGACTCTTAGATGGTTC 60.128 42.308 3.68 0.00 0.00 3.62
745 1013 5.240891 TGCAGTTTTGAGACTCTTAGATGG 58.759 41.667 3.68 0.00 0.00 3.51
750 1018 4.388485 TGCATGCAGTTTTGAGACTCTTA 58.612 39.130 18.46 0.00 0.00 2.10
764 1032 3.581024 AATTGTTGTACCTGCATGCAG 57.419 42.857 35.88 35.88 43.26 4.41
768 1036 6.403866 TTTGAGAAATTGTTGTACCTGCAT 57.596 33.333 0.00 0.00 0.00 3.96
769 1037 5.843673 TTTGAGAAATTGTTGTACCTGCA 57.156 34.783 0.00 0.00 0.00 4.41
771 1039 6.578545 CGACATTTGAGAAATTGTTGTACCTG 59.421 38.462 0.00 0.00 0.00 4.00
774 1042 6.299966 CGACGACATTTGAGAAATTGTTGTAC 59.700 38.462 0.00 0.00 32.09 2.90
783 1051 3.659786 ACATCCGACGACATTTGAGAAA 58.340 40.909 0.00 0.00 0.00 2.52
790 1058 5.006153 TGAATCTTACATCCGACGACATT 57.994 39.130 0.00 0.00 0.00 2.71
803 1071 1.398390 CTGGCAGCCGTTGAATCTTAC 59.602 52.381 7.03 0.00 0.00 2.34
810 1078 1.377202 GGATTCTGGCAGCCGTTGA 60.377 57.895 10.34 1.96 0.00 3.18
819 1087 1.139058 ACCGTGATACAGGATTCTGGC 59.861 52.381 5.84 0.00 44.99 4.85
823 1091 4.281182 AGGTGATACCGTGATACAGGATTC 59.719 45.833 0.00 0.00 44.90 2.52
826 1094 3.308035 AGGTGATACCGTGATACAGGA 57.692 47.619 0.00 0.00 44.90 3.86
832 1100 1.692519 GCCCTTAGGTGATACCGTGAT 59.307 52.381 0.00 0.00 44.90 3.06
839 1107 4.150359 GTGCTACTAGCCCTTAGGTGATA 58.850 47.826 5.58 0.00 41.51 2.15
848 1116 3.551635 ATATCAGGTGCTACTAGCCCT 57.448 47.619 5.58 8.58 41.51 5.19
853 1121 5.054477 GCGGAAAAATATCAGGTGCTACTA 58.946 41.667 0.00 0.00 0.00 1.82
884 1152 3.073274 AGAGATAAGGTGTTTGGGCAC 57.927 47.619 0.00 0.00 38.56 5.01
888 1156 3.691609 GCCAGAAGAGATAAGGTGTTTGG 59.308 47.826 0.00 0.00 0.00 3.28
898 1166 7.676683 AAACAGTTATAGGCCAGAAGAGATA 57.323 36.000 5.01 0.00 0.00 1.98
899 1167 6.567602 AAACAGTTATAGGCCAGAAGAGAT 57.432 37.500 5.01 0.00 0.00 2.75
925 1193 7.040201 AGCATCTTGTGTTAAACTTGATGATGT 60.040 33.333 10.65 0.00 39.41 3.06
927 1195 7.458409 AGCATCTTGTGTTAAACTTGATGAT 57.542 32.000 10.65 3.91 39.41 2.45
1001 1975 6.590234 TGTGCTAGAAGACTCATTTGACTA 57.410 37.500 0.00 0.00 0.00 2.59
1003 1977 4.092675 GCTGTGCTAGAAGACTCATTTGAC 59.907 45.833 0.00 0.00 0.00 3.18
1009 1983 1.632589 TGGCTGTGCTAGAAGACTCA 58.367 50.000 0.00 0.00 0.00 3.41
1043 2040 4.523943 ACAAATCAAAGGCTGTGATTAGCA 59.476 37.500 28.54 0.00 43.32 3.49
1071 2068 4.127171 TGGTTGGCGCTATTTCTAATCTC 58.873 43.478 7.64 0.00 0.00 2.75
1075 2072 3.616219 ACATGGTTGGCGCTATTTCTAA 58.384 40.909 7.64 0.00 0.00 2.10
1115 2130 4.918810 ATCCAATCCGATACTTTTTGGC 57.081 40.909 0.00 0.00 37.37 4.52
1164 2180 7.039784 TGGGATCGAAATCTGATTTGTTTTCTT 60.040 33.333 19.59 0.00 31.47 2.52
1195 2211 4.785453 GGCAGTGAAGCTCGGGGG 62.785 72.222 0.00 0.00 34.17 5.40
1202 2218 1.276421 TGAGAACTAGGGCAGTGAAGC 59.724 52.381 0.00 0.00 37.63 3.86
1207 2223 1.840635 GGGATTGAGAACTAGGGCAGT 59.159 52.381 0.00 0.00 40.05 4.40
1222 2255 1.141185 GATCGGGGAAAGAGGGGATT 58.859 55.000 0.00 0.00 0.00 3.01
1225 2258 0.470341 GAAGATCGGGGAAAGAGGGG 59.530 60.000 0.00 0.00 0.00 4.79
1292 2339 2.584492 TGATCGCTGTCATGTTCGAT 57.416 45.000 11.56 11.56 43.33 3.59
1302 2364 2.893895 CGCTGCCATGATCGCTGT 60.894 61.111 0.00 0.00 0.00 4.40
1393 2455 1.584724 TTCCTGTGGGAAGATCCTCC 58.415 55.000 1.23 1.23 45.72 4.30
1406 2468 2.092914 GGGGAACTCGATGATTTCCTGT 60.093 50.000 13.49 0.00 40.02 4.00
1470 2532 2.972625 TGGAAGAATGTACCTGCGAAG 58.027 47.619 0.00 0.00 0.00 3.79
1482 2544 5.697633 GCACATGTTGATGTTTTGGAAGAAT 59.302 36.000 0.00 0.00 41.12 2.40
1486 2548 4.099113 TCAGCACATGTTGATGTTTTGGAA 59.901 37.500 0.00 0.00 42.63 3.53
1499 2561 3.068448 TGCAAAATTGAGTCAGCACATGT 59.932 39.130 0.00 0.00 0.00 3.21
1501 2563 3.305813 CCTGCAAAATTGAGTCAGCACAT 60.306 43.478 0.17 0.00 0.00 3.21
1585 2647 1.986757 AGCCAGGAGTCGTGCATCT 60.987 57.895 7.33 1.71 0.00 2.90
1616 2678 4.990910 ACACTCCCTGCCCCTGCT 62.991 66.667 0.00 0.00 38.71 4.24
1619 2681 3.260100 CCAACACTCCCTGCCCCT 61.260 66.667 0.00 0.00 0.00 4.79
1703 2765 2.163412 TCGCATGGCTTGTTTTATCACC 59.837 45.455 2.12 0.00 0.00 4.02
1845 2907 2.038557 TCCTGCTACAGTTCCTTGTTCC 59.961 50.000 0.00 0.00 32.56 3.62
1912 2974 3.959991 GACCCCAAGTCCAGCGCTC 62.960 68.421 7.13 0.00 39.84 5.03
1952 3014 0.395862 ACGTCCATGACCTCCTCGAT 60.396 55.000 0.00 0.00 0.00 3.59
1964 3026 1.550976 GACTTCTTCCCTGACGTCCAT 59.449 52.381 14.12 0.00 31.60 3.41
2022 3084 2.675032 CGACTACTGGCTGCTTCATCAA 60.675 50.000 0.00 0.00 0.00 2.57
2046 3108 1.250840 GGTTTTTGGGGAGCGCTCAT 61.251 55.000 36.27 2.81 0.00 2.90
2102 3164 2.317973 GGATAGTAGGCCTCCGAAACT 58.682 52.381 9.68 9.88 0.00 2.66
2248 3311 0.900182 TCTCGCCTCCTTCTCTTGCA 60.900 55.000 0.00 0.00 0.00 4.08
2278 3341 3.652869 TCCATCTCTTTGTTTCACCTCCT 59.347 43.478 0.00 0.00 0.00 3.69
2290 3353 2.392662 TCGCTCCATCTCCATCTCTTT 58.607 47.619 0.00 0.00 0.00 2.52
2297 3360 1.219124 GCTGTTCGCTCCATCTCCA 59.781 57.895 0.00 0.00 35.14 3.86
2305 3368 3.797546 GCTGCTGGCTGTTCGCTC 61.798 66.667 0.00 0.00 39.13 5.03
2329 3393 2.202349 GAATGCGAACGGTGCAGC 60.202 61.111 5.64 5.64 46.98 5.25
2380 3444 6.779049 ACTACGGGTATATGAAAGGTCACATA 59.221 38.462 0.00 0.00 36.31 2.29
2381 3445 5.601313 ACTACGGGTATATGAAAGGTCACAT 59.399 40.000 0.00 0.00 36.31 3.21
2450 3516 2.261361 CCTCGTCACGATGTGCCA 59.739 61.111 0.00 0.00 34.61 4.92
2454 3520 2.126463 CACGCCTCGTCACGATGT 60.126 61.111 0.00 0.00 38.32 3.06
2456 3522 4.796231 GCCACGCCTCGTCACGAT 62.796 66.667 0.00 0.00 38.32 3.73


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

AutoCloner maintained by Alex Coulton.