Multiple sequence alignment - TraesCS4B01G342300

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 TraesCS4B01G342300 chr4B 100.000 2564 0 0 1 2564 635459570 635462133 0.000000e+00 4735.0
1 TraesCS4B01G342300 chr4D 92.413 1173 60 17 905 2064 495520277 495521433 0.000000e+00 1646.0
2 TraesCS4B01G342300 chr4D 90.590 797 45 13 1685 2466 495639355 495640136 0.000000e+00 1029.0
3 TraesCS4B01G342300 chr4D 90.469 640 42 10 669 1301 495638320 495638947 0.000000e+00 826.0
4 TraesCS4B01G342300 chr4D 90.462 346 24 6 1 342 495637816 495638156 5.030000e-122 448.0
5 TraesCS4B01G342300 chr4D 79.764 593 82 19 995 1565 495129587 495130163 1.850000e-106 396.0
6 TraesCS4B01G342300 chr4D 78.657 581 98 14 1045 1611 495074473 495075041 1.880000e-96 363.0
7 TraesCS4B01G342300 chr4D 89.041 292 12 5 137 410 495519402 495519691 6.790000e-91 344.0
8 TraesCS4B01G342300 chr4D 94.660 206 8 2 670 872 495519758 495519963 1.480000e-82 316.0
9 TraesCS4B01G342300 chr4D 89.167 240 17 4 1327 1566 495638943 495639173 8.970000e-75 291.0
10 TraesCS4B01G342300 chr4D 96.644 149 5 0 1 149 495473524 495473672 5.480000e-62 248.0
11 TraesCS4B01G342300 chr4D 86.740 181 20 2 2242 2422 495521556 495521732 5.600000e-47 198.0
12 TraesCS4B01G342300 chr5A 89.048 977 67 20 666 1640 675319948 675319010 0.000000e+00 1175.0
13 TraesCS4B01G342300 chr5A 87.735 799 56 24 1684 2466 675154534 675153762 0.000000e+00 894.0
14 TraesCS4B01G342300 chr5A 88.551 559 41 7 669 1223 675161034 675160495 0.000000e+00 656.0
15 TraesCS4B01G342300 chr5A 89.953 428 33 6 1215 1642 675155102 675154685 6.240000e-151 544.0
16 TraesCS4B01G342300 chr5A 90.351 342 11 4 1 342 675320415 675320096 1.820000e-116 429.0
17 TraesCS4B01G342300 chr5A 79.322 590 87 15 995 1565 674937364 674937937 5.180000e-102 381.0
18 TraesCS4B01G342300 chr5A 86.337 344 34 5 1 342 675189783 675189451 1.880000e-96 363.0
19 TraesCS4B01G342300 chr5A 89.347 291 20 8 391 678 281137458 281137740 3.140000e-94 355.0
20 TraesCS4B01G342300 chr5A 77.568 584 95 21 1045 1611 674852051 674852615 1.140000e-83 320.0
21 TraesCS4B01G342300 chr5A 82.251 231 25 6 2200 2422 675318340 675318118 4.360000e-43 185.0
22 TraesCS4B01G342300 chr3B 92.251 271 18 2 407 674 129501978 129501708 5.180000e-102 381.0
23 TraesCS4B01G342300 chr3B 91.882 271 19 2 407 674 129483593 129483323 2.410000e-100 375.0
24 TraesCS4B01G342300 chr6A 91.481 270 14 2 407 674 181909849 181910111 1.880000e-96 363.0
25 TraesCS4B01G342300 chr6A 89.716 282 19 3 407 686 107863445 107863172 4.060000e-93 351.0
26 TraesCS4B01G342300 chr2B 91.481 270 14 2 407 674 597223419 597223157 1.880000e-96 363.0
27 TraesCS4B01G342300 chr1D 90.809 272 17 2 403 674 38563084 38562821 8.720000e-95 357.0
28 TraesCS4B01G342300 chr3A 90.288 278 17 3 399 674 717620997 717621266 3.140000e-94 355.0
29 TraesCS4B01G342300 chr6B 89.753 283 17 7 407 686 673655630 673655357 4.060000e-93 351.0
30 TraesCS4B01G342300 chrUn 77.568 584 95 21 1045 1611 283623710 283624274 1.140000e-83 320.0
31 TraesCS4B01G342300 chr2D 81.174 409 52 18 1451 1850 334150539 334150147 3.210000e-79 305.0
32 TraesCS4B01G342300 chr5D 83.158 95 12 4 2465 2557 485275806 485275898 1.630000e-12 84.2
33 TraesCS4B01G342300 chr5D 82.979 94 13 3 2467 2558 421086922 421087014 5.880000e-12 82.4
34 TraesCS4B01G342300 chr2A 82.474 97 14 3 2464 2558 35537210 35537305 5.880000e-12 82.4
35 TraesCS4B01G342300 chr1B 85.294 68 8 2 2491 2556 94200145 94200212 4.580000e-08 69.4


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 TraesCS4B01G342300 chr4B 635459570 635462133 2563 False 4735.000000 4735 100.000000 1 2564 1 chr4B.!!$F1 2563
1 TraesCS4B01G342300 chr4D 495637816 495640136 2320 False 648.500000 1029 90.172000 1 2466 4 chr4D.!!$F5 2465
2 TraesCS4B01G342300 chr4D 495519402 495521732 2330 False 626.000000 1646 90.713500 137 2422 4 chr4D.!!$F4 2285
3 TraesCS4B01G342300 chr4D 495129587 495130163 576 False 396.000000 396 79.764000 995 1565 1 chr4D.!!$F2 570
4 TraesCS4B01G342300 chr4D 495074473 495075041 568 False 363.000000 363 78.657000 1045 1611 1 chr4D.!!$F1 566
5 TraesCS4B01G342300 chr5A 675153762 675155102 1340 True 719.000000 894 88.844000 1215 2466 2 chr5A.!!$R3 1251
6 TraesCS4B01G342300 chr5A 675160495 675161034 539 True 656.000000 656 88.551000 669 1223 1 chr5A.!!$R1 554
7 TraesCS4B01G342300 chr5A 675318118 675320415 2297 True 596.333333 1175 87.216667 1 2422 3 chr5A.!!$R4 2421
8 TraesCS4B01G342300 chr5A 674937364 674937937 573 False 381.000000 381 79.322000 995 1565 1 chr5A.!!$F3 570
9 TraesCS4B01G342300 chr5A 674852051 674852615 564 False 320.000000 320 77.568000 1045 1611 1 chr5A.!!$F2 566
10 TraesCS4B01G342300 chrUn 283623710 283624274 564 False 320.000000 320 77.568000 1045 1611 1 chrUn.!!$F1 566

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
518 565 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 3231 0.836606 TTCAGTGTCAGCTTGGGACA 59.163 50.0 1.42 1.42 42.62 4.02 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
78 81 2.865670 GCTGGAATATCTGGACGCAGAG 60.866 54.545 0.00 0.00 34.35 3.35
79 82 1.688735 TGGAATATCTGGACGCAGAGG 59.311 52.381 0.00 0.00 34.35 3.69
80 83 1.964223 GGAATATCTGGACGCAGAGGA 59.036 52.381 0.00 0.00 34.35 3.71
81 84 2.365617 GGAATATCTGGACGCAGAGGAA 59.634 50.000 0.00 0.00 34.35 3.36
82 85 3.385577 GAATATCTGGACGCAGAGGAAC 58.614 50.000 0.00 0.00 34.35 3.62
84 87 1.270907 ATCTGGACGCAGAGGAACTT 58.729 50.000 0.00 0.00 41.55 2.66
218 221 9.565090 TCCTTAACTGGATTGATCATTATCTTG 57.435 33.333 0.00 0.00 32.93 3.02
246 249 4.079787 AGCTCCCATGAACATTTTAGGCTA 60.080 41.667 0.00 0.00 0.00 3.93
273 278 8.050930 TCCTAGAACTGGTGTTTCTTAAGTTTT 58.949 33.333 1.63 0.00 36.39 2.43
433 480 3.917988 TGAGCATCAGTACAGACACAAG 58.082 45.455 0.00 0.00 42.56 3.16
434 481 2.670414 GAGCATCAGTACAGACACAAGC 59.330 50.000 0.00 0.00 33.17 4.01
435 482 1.391485 GCATCAGTACAGACACAAGCG 59.609 52.381 0.00 0.00 0.00 4.68
436 483 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
438 485 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
439 486 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
440 487 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
442 489 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
444 491 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
445 492 2.469147 CAGACACAAGCGCTCATATACG 59.531 50.000 12.06 0.00 0.00 3.06
453 500 1.613270 CGCTCATATACGCGCATACA 58.387 50.000 5.73 0.00 43.01 2.29
456 503 2.594654 GCTCATATACGCGCATACACTC 59.405 50.000 5.73 0.00 0.00 3.51
458 505 3.561503 TCATATACGCGCATACACTCAC 58.438 45.455 5.73 0.00 0.00 3.51
459 506 2.410785 TATACGCGCATACACTCACC 57.589 50.000 5.73 0.00 0.00 4.02
460 507 0.249322 ATACGCGCATACACTCACCC 60.249 55.000 5.73 0.00 0.00 4.61
461 508 2.287457 TACGCGCATACACTCACCCC 62.287 60.000 5.73 0.00 0.00 4.95
465 512 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
466 513 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
467 514 2.102420 CGCATACACTCACCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
468 515 3.244215 CGCATACACTCACCCCTATGAAT 60.244 47.826 0.00 0.00 0.00 2.57
470 517 2.717639 ACACTCACCCCTATGAATGC 57.282 50.000 0.00 0.00 28.78 3.56
471 518 1.915489 ACACTCACCCCTATGAATGCA 59.085 47.619 0.00 0.00 28.78 3.96
472 519 2.292267 CACTCACCCCTATGAATGCAC 58.708 52.381 0.00 0.00 0.00 4.57
476 523 1.745087 CACCCCTATGAATGCACACAC 59.255 52.381 0.00 0.00 0.00 3.82
477 524 1.016627 CCCCTATGAATGCACACACG 58.983 55.000 0.00 0.00 0.00 4.49
478 525 0.378257 CCCTATGAATGCACACACGC 59.622 55.000 0.00 0.00 0.00 5.34
480 527 1.202065 CCTATGAATGCACACACGCAC 60.202 52.381 0.00 0.00 46.56 5.34
482 529 0.040157 ATGAATGCACACACGCACAC 60.040 50.000 0.00 0.00 46.56 3.82
483 530 1.354858 GAATGCACACACGCACACA 59.645 52.632 0.00 0.00 46.56 3.72
484 531 0.929824 GAATGCACACACGCACACAC 60.930 55.000 0.00 0.00 46.56 3.82
485 532 2.645281 AATGCACACACGCACACACG 62.645 55.000 0.00 0.00 46.56 4.49
487 534 3.858989 CACACACGCACACACGCA 61.859 61.111 0.00 0.00 36.19 5.24
488 535 3.860125 ACACACGCACACACGCAC 61.860 61.111 0.00 0.00 36.19 5.34
489 536 3.858989 CACACGCACACACGCACA 61.859 61.111 0.00 0.00 36.19 4.57
490 537 3.860125 ACACGCACACACGCACAC 61.860 61.111 0.00 0.00 36.19 3.82
491 538 4.589700 CACGCACACACGCACACC 62.590 66.667 0.00 0.00 36.19 4.16
492 539 4.830765 ACGCACACACGCACACCT 62.831 61.111 0.00 0.00 36.19 4.00
493 540 2.660224 CGCACACACGCACACCTA 60.660 61.111 0.00 0.00 0.00 3.08
494 541 2.027073 CGCACACACGCACACCTAT 61.027 57.895 0.00 0.00 0.00 2.57
495 542 1.787847 GCACACACGCACACCTATC 59.212 57.895 0.00 0.00 0.00 2.08
496 543 1.635663 GCACACACGCACACCTATCC 61.636 60.000 0.00 0.00 0.00 2.59
497 544 1.019278 CACACACGCACACCTATCCC 61.019 60.000 0.00 0.00 0.00 3.85
498 545 1.192146 ACACACGCACACCTATCCCT 61.192 55.000 0.00 0.00 0.00 4.20
499 546 0.821517 CACACGCACACCTATCCCTA 59.178 55.000 0.00 0.00 0.00 3.53
500 547 1.412710 CACACGCACACCTATCCCTAT 59.587 52.381 0.00 0.00 0.00 2.57
501 548 1.412710 ACACGCACACCTATCCCTATG 59.587 52.381 0.00 0.00 0.00 2.23
502 549 1.686587 CACGCACACCTATCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
503 550 1.964223 ACGCACACCTATCCCTATGAG 59.036 52.381 0.00 0.00 0.00 2.90
504 551 1.337260 CGCACACCTATCCCTATGAGC 60.337 57.143 0.00 0.00 0.00 4.26
505 552 1.694150 GCACACCTATCCCTATGAGCA 59.306 52.381 0.00 0.00 0.00 4.26
506 553 2.548920 GCACACCTATCCCTATGAGCAC 60.549 54.545 0.00 0.00 0.00 4.40
507 554 2.037772 CACACCTATCCCTATGAGCACC 59.962 54.545 0.00 0.00 0.00 5.01
508 555 2.090494 ACACCTATCCCTATGAGCACCT 60.090 50.000 0.00 0.00 0.00 4.00
509 556 2.564947 CACCTATCCCTATGAGCACCTC 59.435 54.545 0.00 0.00 0.00 3.85
510 557 2.183679 CCTATCCCTATGAGCACCTCC 58.816 57.143 0.00 0.00 0.00 4.30
511 558 1.821753 CTATCCCTATGAGCACCTCCG 59.178 57.143 0.00 0.00 0.00 4.63
512 559 0.188587 ATCCCTATGAGCACCTCCGA 59.811 55.000 0.00 0.00 0.00 4.55
513 560 0.468214 TCCCTATGAGCACCTCCGAG 60.468 60.000 0.00 0.00 0.00 4.63
514 561 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
515 562 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
516 563 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
517 564 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
518 565 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
519 566 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
520 567 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
521 568 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
522 569 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
523 570 1.379309 ACCTCCGAGAGACTGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
524 571 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
525 572 2.438614 TCCGAGAGACTGAGCCGG 60.439 66.667 0.00 0.00 41.36 6.13
526 573 4.200283 CCGAGAGACTGAGCCGGC 62.200 72.222 21.89 21.89 33.47 6.13
527 574 3.443925 CGAGAGACTGAGCCGGCA 61.444 66.667 31.54 7.98 0.00 5.69
528 575 2.780094 CGAGAGACTGAGCCGGCAT 61.780 63.158 31.54 14.28 0.00 4.40
529 576 1.448119 CGAGAGACTGAGCCGGCATA 61.448 60.000 31.54 16.21 0.00 3.14
530 577 0.965439 GAGAGACTGAGCCGGCATAT 59.035 55.000 31.54 8.11 0.00 1.78
531 578 0.965439 AGAGACTGAGCCGGCATATC 59.035 55.000 31.54 18.63 0.00 1.63
532 579 0.676184 GAGACTGAGCCGGCATATCA 59.324 55.000 31.54 22.44 0.00 2.15
533 580 1.274728 GAGACTGAGCCGGCATATCAT 59.725 52.381 31.54 13.17 0.00 2.45
534 581 1.274728 AGACTGAGCCGGCATATCATC 59.725 52.381 31.54 19.98 0.00 2.92
535 582 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
536 583 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
537 584 2.899900 ACTGAGCCGGCATATCATCTTA 59.100 45.455 31.54 0.00 0.00 2.10
538 585 3.324846 ACTGAGCCGGCATATCATCTTAA 59.675 43.478 31.54 0.00 0.00 1.85
539 586 3.930336 TGAGCCGGCATATCATCTTAAG 58.070 45.455 31.54 0.00 0.00 1.85
540 587 3.578282 TGAGCCGGCATATCATCTTAAGA 59.422 43.478 31.54 7.82 0.00 2.10
541 588 4.223700 TGAGCCGGCATATCATCTTAAGAT 59.776 41.667 31.54 12.37 34.56 2.40
542 589 5.171339 AGCCGGCATATCATCTTAAGATT 57.829 39.130 31.54 5.12 31.21 2.40
543 590 5.564550 AGCCGGCATATCATCTTAAGATTT 58.435 37.500 31.54 8.78 31.21 2.17
544 591 6.711277 AGCCGGCATATCATCTTAAGATTTA 58.289 36.000 31.54 10.60 31.21 1.40
545 592 6.595716 AGCCGGCATATCATCTTAAGATTTAC 59.404 38.462 31.54 2.79 31.21 2.01
546 593 6.455646 GCCGGCATATCATCTTAAGATTTACG 60.456 42.308 24.80 12.15 31.21 3.18
547 594 6.811665 CCGGCATATCATCTTAAGATTTACGA 59.188 38.462 15.49 10.07 31.21 3.43
548 595 7.330946 CCGGCATATCATCTTAAGATTTACGAA 59.669 37.037 15.49 0.00 31.21 3.85
549 596 8.376203 CGGCATATCATCTTAAGATTTACGAAG 58.624 37.037 15.49 3.04 31.21 3.79
550 597 8.171840 GGCATATCATCTTAAGATTTACGAAGC 58.828 37.037 15.49 13.55 31.21 3.86
551 598 8.171840 GCATATCATCTTAAGATTTACGAAGCC 58.828 37.037 15.49 0.00 31.21 4.35
552 599 9.208022 CATATCATCTTAAGATTTACGAAGCCA 57.792 33.333 15.49 0.00 31.21 4.75
553 600 6.903883 TCATCTTAAGATTTACGAAGCCAC 57.096 37.500 15.49 0.00 31.21 5.01
554 601 5.815740 TCATCTTAAGATTTACGAAGCCACC 59.184 40.000 15.49 0.00 31.21 4.61
555 602 4.178540 TCTTAAGATTTACGAAGCCACCG 58.821 43.478 0.00 0.00 0.00 4.94
556 603 2.467566 AAGATTTACGAAGCCACCGT 57.532 45.000 0.00 0.00 43.26 4.83
557 604 3.598019 AAGATTTACGAAGCCACCGTA 57.402 42.857 0.00 0.00 40.95 4.02
558 605 3.160777 AGATTTACGAAGCCACCGTAG 57.839 47.619 0.00 0.00 42.42 3.51
571 618 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
572 619 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
593 640 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
594 641 3.277962 GGAACGTCTCCTCCCACTA 57.722 57.895 8.87 0.00 41.61 2.74
595 642 1.553706 GGAACGTCTCCTCCCACTAA 58.446 55.000 8.87 0.00 41.61 2.24
596 643 1.897802 GGAACGTCTCCTCCCACTAAA 59.102 52.381 8.87 0.00 41.61 1.85
597 644 2.301009 GGAACGTCTCCTCCCACTAAAA 59.699 50.000 8.87 0.00 41.61 1.52
598 645 3.586892 GAACGTCTCCTCCCACTAAAAG 58.413 50.000 0.00 0.00 0.00 2.27
599 646 1.275573 ACGTCTCCTCCCACTAAAAGC 59.724 52.381 0.00 0.00 0.00 3.51
600 647 1.736032 CGTCTCCTCCCACTAAAAGCG 60.736 57.143 0.00 0.00 0.00 4.68
601 648 0.249398 TCTCCTCCCACTAAAAGCGC 59.751 55.000 0.00 0.00 0.00 5.92
602 649 0.036388 CTCCTCCCACTAAAAGCGCA 60.036 55.000 11.47 0.00 0.00 6.09
603 650 0.618458 TCCTCCCACTAAAAGCGCAT 59.382 50.000 11.47 0.00 0.00 4.73
604 651 1.017387 CCTCCCACTAAAAGCGCATC 58.983 55.000 11.47 0.00 0.00 3.91
605 652 0.652592 CTCCCACTAAAAGCGCATCG 59.347 55.000 11.47 0.00 0.00 3.84
616 663 3.409856 CGCATCGCCGGAAATCTT 58.590 55.556 5.05 0.00 0.00 2.40
617 664 1.010797 CGCATCGCCGGAAATCTTG 60.011 57.895 5.05 0.00 0.00 3.02
618 665 1.428370 CGCATCGCCGGAAATCTTGA 61.428 55.000 5.05 0.00 0.00 3.02
619 666 0.732571 GCATCGCCGGAAATCTTGAA 59.267 50.000 5.05 0.00 0.00 2.69
620 667 1.132262 GCATCGCCGGAAATCTTGAAA 59.868 47.619 5.05 0.00 0.00 2.69
621 668 2.223572 GCATCGCCGGAAATCTTGAAAT 60.224 45.455 5.05 0.00 0.00 2.17
622 669 3.003275 GCATCGCCGGAAATCTTGAAATA 59.997 43.478 5.05 0.00 0.00 1.40
623 670 4.497340 GCATCGCCGGAAATCTTGAAATAA 60.497 41.667 5.05 0.00 0.00 1.40
624 671 5.577835 CATCGCCGGAAATCTTGAAATAAA 58.422 37.500 5.05 0.00 0.00 1.40
625 672 5.828299 TCGCCGGAAATCTTGAAATAAAT 57.172 34.783 5.05 0.00 0.00 1.40
626 673 6.202516 TCGCCGGAAATCTTGAAATAAATT 57.797 33.333 5.05 0.00 0.00 1.82
627 674 6.262601 TCGCCGGAAATCTTGAAATAAATTC 58.737 36.000 5.05 0.00 38.60 2.17
628 675 6.033341 CGCCGGAAATCTTGAAATAAATTCA 58.967 36.000 5.05 0.00 46.22 2.57
648 695 8.738199 AATTCAAATATAATGCGAGCATCAAG 57.262 30.769 11.26 0.00 35.31 3.02
649 696 7.495135 TTCAAATATAATGCGAGCATCAAGA 57.505 32.000 11.26 0.99 35.31 3.02
650 697 7.677454 TCAAATATAATGCGAGCATCAAGAT 57.323 32.000 11.26 3.27 35.31 2.40
651 698 8.102800 TCAAATATAATGCGAGCATCAAGATT 57.897 30.769 11.26 8.74 35.31 2.40
652 699 8.570488 TCAAATATAATGCGAGCATCAAGATTT 58.430 29.630 11.26 13.41 35.31 2.17
653 700 8.635983 CAAATATAATGCGAGCATCAAGATTTG 58.364 33.333 23.28 23.28 36.20 2.32
654 701 7.677454 ATATAATGCGAGCATCAAGATTTGA 57.323 32.000 11.26 0.00 45.01 2.69
655 702 4.707030 AATGCGAGCATCAAGATTTGAA 57.293 36.364 11.26 0.00 43.95 2.69
656 703 3.476295 TGCGAGCATCAAGATTTGAAC 57.524 42.857 0.00 0.00 43.95 3.18
657 704 2.162208 TGCGAGCATCAAGATTTGAACC 59.838 45.455 0.00 0.00 43.95 3.62
658 705 2.478539 GCGAGCATCAAGATTTGAACCC 60.479 50.000 0.00 0.00 43.95 4.11
659 706 3.012518 CGAGCATCAAGATTTGAACCCT 58.987 45.455 0.00 0.00 43.95 4.34
660 707 4.191544 CGAGCATCAAGATTTGAACCCTA 58.808 43.478 0.00 0.00 43.95 3.53
661 708 4.034510 CGAGCATCAAGATTTGAACCCTAC 59.965 45.833 0.00 0.00 43.95 3.18
662 709 5.184892 AGCATCAAGATTTGAACCCTACT 57.815 39.130 0.00 0.00 43.95 2.57
663 710 6.313519 AGCATCAAGATTTGAACCCTACTA 57.686 37.500 0.00 0.00 43.95 1.82
664 711 6.352516 AGCATCAAGATTTGAACCCTACTAG 58.647 40.000 0.00 0.00 43.95 2.57
665 712 5.529060 GCATCAAGATTTGAACCCTACTAGG 59.471 44.000 0.00 0.00 43.95 3.02
666 713 6.653989 CATCAAGATTTGAACCCTACTAGGT 58.346 40.000 1.25 0.00 43.95 3.08
676 723 2.047830 CCCTACTAGGTTGGGGATCAC 58.952 57.143 8.87 0.00 43.16 3.06
689 736 2.618709 GGGGATCACATTCGTCCAAATC 59.381 50.000 0.00 0.00 33.62 2.17
772 820 6.456315 CCGGTTGTTTGGAATTTTCTTTCAAC 60.456 38.462 0.00 0.00 34.08 3.18
783 831 2.543777 TCTTTCAACCACTTCCTCCG 57.456 50.000 0.00 0.00 0.00 4.63
790 838 0.620556 ACCACTTCCTCCGCAATGAT 59.379 50.000 0.00 0.00 0.00 2.45
805 853 1.158904 ATGATCTCCTCTCCGGGGTA 58.841 55.000 0.00 0.00 33.68 3.69
831 879 5.051641 GGTGACTCGCTTGACTTTAATATCG 60.052 44.000 0.00 0.00 0.00 2.92
882 931 5.310409 TCTCTGTTTTCTCACTTGGGAAT 57.690 39.130 0.00 0.00 0.00 3.01
887 1219 8.110860 TCTGTTTTCTCACTTGGGAATATTTC 57.889 34.615 0.00 0.00 0.00 2.17
896 1228 5.064707 CACTTGGGAATATTTCGTAGTGGTG 59.935 44.000 14.65 3.98 33.33 4.17
897 1229 4.829872 TGGGAATATTTCGTAGTGGTGT 57.170 40.909 0.00 0.00 0.00 4.16
903 1235 2.068837 TTTCGTAGTGGTGTTAGCCG 57.931 50.000 0.00 0.00 0.00 5.52
936 1268 7.288852 CCCATCGAGAAGTCCATATATAGGATT 59.711 40.741 0.00 1.82 37.52 3.01
946 1278 2.105006 ATATAGGATTGCCGCTGCTG 57.895 50.000 0.70 0.00 39.96 4.41
985 1323 5.013079 AGCAGCTACCTTGGCATACATATAA 59.987 40.000 0.00 0.00 0.00 0.98
988 1326 7.716998 GCAGCTACCTTGGCATACATATAATAT 59.283 37.037 0.00 0.00 0.00 1.28
1212 1559 2.740055 CTCAAGTCGCAGGCGCTT 60.740 61.111 7.64 12.38 36.95 4.68
1653 2212 4.927425 ACTACTCGCTCTTATCGATCTCTC 59.073 45.833 0.00 0.00 35.25 3.20
1662 2221 7.572168 CGCTCTTATCGATCTCTCTGTTGATTA 60.572 40.741 0.00 0.00 0.00 1.75
1707 2293 7.175990 TCCAACCTAGCTTAATTAACCAACTTG 59.824 37.037 0.00 0.00 0.00 3.16
1709 2295 5.417894 ACCTAGCTTAATTAACCAACTTGGC 59.582 40.000 7.81 0.00 42.67 4.52
1721 2307 3.941483 ACCAACTTGGCGATTAATCTCTG 59.059 43.478 13.45 0.00 42.67 3.35
1790 2377 3.616935 TCGCCGATCGAACTTGTAG 57.383 52.632 18.66 0.00 45.36 2.74
1981 2587 1.318576 CTGTTGCTTCCCCGTTCTTT 58.681 50.000 0.00 0.00 0.00 2.52
1982 2588 1.681264 CTGTTGCTTCCCCGTTCTTTT 59.319 47.619 0.00 0.00 0.00 2.27
2013 2620 4.082733 GGTTTTGCTATTCCTCTGACAACC 60.083 45.833 0.00 0.00 0.00 3.77
2053 2665 5.095145 TGACAGAGAGAGGAAATCCATTG 57.905 43.478 1.67 0.00 38.89 2.82
2057 2669 6.546484 ACAGAGAGAGGAAATCCATTGAAAA 58.454 36.000 1.67 0.00 38.89 2.29
2096 2790 8.303156 AGACGATTGATCTATAGGTGATTCTTG 58.697 37.037 0.00 0.00 0.00 3.02
2113 2807 6.995686 TGATTCTTGTTTTTACTGCTGTAGGA 59.004 34.615 3.54 0.00 0.00 2.94
2115 2809 9.162764 GATTCTTGTTTTTACTGCTGTAGGATA 57.837 33.333 3.54 0.00 0.00 2.59
2116 2810 9.686683 ATTCTTGTTTTTACTGCTGTAGGATAT 57.313 29.630 3.54 0.00 0.00 1.63
2117 2811 9.515226 TTCTTGTTTTTACTGCTGTAGGATATT 57.485 29.630 3.54 0.00 0.00 1.28
2180 2879 4.289934 TGGATGGACCAAACAAGTATACCA 59.710 41.667 0.00 0.00 46.75 3.25
2185 2884 5.013704 TGGACCAAACAAGTATACCATCTGT 59.986 40.000 0.00 0.00 0.00 3.41
2221 2953 3.153369 TGTTACTGCACCCATGTGATT 57.847 42.857 0.00 0.00 45.76 2.57
2222 2954 3.081061 TGTTACTGCACCCATGTGATTC 58.919 45.455 0.00 0.00 45.76 2.52
2223 2955 2.022764 TACTGCACCCATGTGATTCG 57.977 50.000 0.00 0.00 45.76 3.34
2224 2956 0.324614 ACTGCACCCATGTGATTCGA 59.675 50.000 0.00 0.00 45.76 3.71
2225 2957 1.012086 CTGCACCCATGTGATTCGAG 58.988 55.000 0.00 0.00 45.76 4.04
2226 2958 0.392863 TGCACCCATGTGATTCGAGG 60.393 55.000 0.00 0.00 45.76 4.63
2227 2959 0.107703 GCACCCATGTGATTCGAGGA 60.108 55.000 0.00 0.00 45.76 3.71
2228 2960 1.678728 GCACCCATGTGATTCGAGGAA 60.679 52.381 0.00 0.00 45.76 3.36
2344 3085 2.159099 GGCCGATCCATTATATGCTCGA 60.159 50.000 0.00 0.00 36.58 4.04
2396 3137 1.569479 GACCGACAGGCTGTTTGCTC 61.569 60.000 22.98 10.54 42.76 4.26
2448 3189 2.101082 TGCCCGCATACACTACGAAATA 59.899 45.455 0.00 0.00 0.00 1.40
2503 3244 3.801114 AAAAACTTGTCCCAAGCTGAC 57.199 42.857 3.96 0.00 0.00 3.51
2504 3245 2.435372 AAACTTGTCCCAAGCTGACA 57.565 45.000 1.42 1.42 40.80 3.58
2505 3246 1.680338 AACTTGTCCCAAGCTGACAC 58.320 50.000 4.94 0.00 42.13 3.67
2506 3247 0.839946 ACTTGTCCCAAGCTGACACT 59.160 50.000 4.94 0.00 42.13 3.55
2507 3248 1.233019 CTTGTCCCAAGCTGACACTG 58.767 55.000 4.94 0.00 42.13 3.66
2508 3249 0.836606 TTGTCCCAAGCTGACACTGA 59.163 50.000 4.94 0.00 42.13 3.41
2509 3250 0.836606 TGTCCCAAGCTGACACTGAA 59.163 50.000 1.42 0.00 37.80 3.02
2510 3251 1.211703 TGTCCCAAGCTGACACTGAAA 59.788 47.619 1.42 0.00 37.80 2.69
2511 3252 2.158623 TGTCCCAAGCTGACACTGAAAT 60.159 45.455 1.42 0.00 37.80 2.17
2512 3253 2.227388 GTCCCAAGCTGACACTGAAATG 59.773 50.000 0.00 0.00 32.91 2.32
2513 3254 2.106338 TCCCAAGCTGACACTGAAATGA 59.894 45.455 0.00 0.00 0.00 2.57
2514 3255 2.886523 CCCAAGCTGACACTGAAATGAA 59.113 45.455 0.00 0.00 0.00 2.57
2515 3256 3.508793 CCCAAGCTGACACTGAAATGAAT 59.491 43.478 0.00 0.00 0.00 2.57
2516 3257 4.482386 CCAAGCTGACACTGAAATGAATG 58.518 43.478 0.00 0.00 0.00 2.67
2517 3258 4.022589 CCAAGCTGACACTGAAATGAATGT 60.023 41.667 0.00 0.00 0.00 2.71
2518 3259 5.181811 CCAAGCTGACACTGAAATGAATGTA 59.818 40.000 0.00 0.00 0.00 2.29
2519 3260 6.127814 CCAAGCTGACACTGAAATGAATGTAT 60.128 38.462 0.00 0.00 0.00 2.29
2520 3261 6.674694 AGCTGACACTGAAATGAATGTATC 57.325 37.500 0.00 0.00 0.00 2.24
2521 3262 6.413052 AGCTGACACTGAAATGAATGTATCT 58.587 36.000 0.00 0.00 0.00 1.98
2522 3263 7.559486 AGCTGACACTGAAATGAATGTATCTA 58.441 34.615 0.00 0.00 0.00 1.98
2523 3264 7.710044 AGCTGACACTGAAATGAATGTATCTAG 59.290 37.037 0.00 0.00 0.00 2.43
2524 3265 7.518052 GCTGACACTGAAATGAATGTATCTAGC 60.518 40.741 0.00 0.00 0.00 3.42
2525 3266 7.330262 TGACACTGAAATGAATGTATCTAGCA 58.670 34.615 0.00 0.00 0.00 3.49
2526 3267 7.278646 TGACACTGAAATGAATGTATCTAGCAC 59.721 37.037 0.00 0.00 0.00 4.40
2527 3268 7.334090 ACACTGAAATGAATGTATCTAGCACT 58.666 34.615 0.00 0.00 0.00 4.40
2528 3269 8.478066 ACACTGAAATGAATGTATCTAGCACTA 58.522 33.333 0.00 0.00 0.00 2.74
2529 3270 9.317936 CACTGAAATGAATGTATCTAGCACTAA 57.682 33.333 0.00 0.00 0.00 2.24
2562 3303 7.552050 AGATACATCCATTTAAGGGAGAGAG 57.448 40.000 4.30 0.00 37.96 3.20
2563 3304 6.500049 AGATACATCCATTTAAGGGAGAGAGG 59.500 42.308 4.30 0.00 37.96 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 81 7.867909 CCTCAGGTTTGAAAATCTTAAAGTTCC 59.132 37.037 0.00 0.00 31.69 3.62
79 82 7.382488 GCCTCAGGTTTGAAAATCTTAAAGTTC 59.618 37.037 0.00 0.00 31.69 3.01
80 83 7.147742 TGCCTCAGGTTTGAAAATCTTAAAGTT 60.148 33.333 0.00 0.00 31.69 2.66
81 84 6.323739 TGCCTCAGGTTTGAAAATCTTAAAGT 59.676 34.615 0.00 0.00 31.69 2.66
82 85 6.642540 GTGCCTCAGGTTTGAAAATCTTAAAG 59.357 38.462 0.00 0.00 31.69 1.85
83 86 6.462347 GGTGCCTCAGGTTTGAAAATCTTAAA 60.462 38.462 0.00 0.00 31.69 1.52
84 87 5.010617 GGTGCCTCAGGTTTGAAAATCTTAA 59.989 40.000 0.00 0.00 31.69 1.85
218 221 4.725790 AAATGTTCATGGGAGCTTAAGC 57.274 40.909 20.09 20.09 42.49 3.09
246 249 7.317722 ACTTAAGAAACACCAGTTCTAGGAT 57.682 36.000 10.09 0.00 36.84 3.24
273 278 6.579666 AAGCATAGAAGCTCAAAATGAACA 57.420 33.333 0.00 0.00 45.89 3.18
408 455 5.122519 TGTGTCTGTACTGATGCTCAAAAA 58.877 37.500 5.69 0.00 0.00 1.94
413 460 2.670414 GCTTGTGTCTGTACTGATGCTC 59.330 50.000 5.69 0.00 0.00 4.26
415 462 1.391485 CGCTTGTGTCTGTACTGATGC 59.609 52.381 5.69 3.20 0.00 3.91
416 463 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
417 464 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
419 466 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
420 467 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
421 468 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
423 470 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
424 471 2.469147 CGTATATGAGCGCTTGTGTCTG 59.531 50.000 13.26 0.00 0.00 3.51
425 472 2.732366 CGTATATGAGCGCTTGTGTCT 58.268 47.619 13.26 0.00 0.00 3.41
435 482 2.594654 GAGTGTATGCGCGTATATGAGC 59.405 50.000 19.79 13.18 35.03 4.26
436 483 3.604198 GTGAGTGTATGCGCGTATATGAG 59.396 47.826 19.79 0.00 0.00 2.90
438 485 2.661675 GGTGAGTGTATGCGCGTATATG 59.338 50.000 19.79 0.00 0.00 1.78
439 486 2.352421 GGGTGAGTGTATGCGCGTATAT 60.352 50.000 19.79 4.31 0.00 0.86
440 487 1.001048 GGGTGAGTGTATGCGCGTATA 60.001 52.381 13.13 13.13 0.00 1.47
442 489 1.140161 GGGTGAGTGTATGCGCGTA 59.860 57.895 8.43 4.92 0.00 4.42
444 491 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
445 492 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
446 493 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
447 494 3.838244 TTCATAGGGGTGAGTGTATGC 57.162 47.619 0.00 0.00 0.00 3.14
453 500 1.915489 TGTGCATTCATAGGGGTGAGT 59.085 47.619 0.00 0.00 0.00 3.41
456 503 1.745087 GTGTGTGCATTCATAGGGGTG 59.255 52.381 0.00 0.00 0.00 4.61
458 505 1.016627 CGTGTGTGCATTCATAGGGG 58.983 55.000 0.00 0.00 0.00 4.79
459 506 0.378257 GCGTGTGTGCATTCATAGGG 59.622 55.000 0.00 0.00 34.15 3.53
460 507 1.085893 TGCGTGTGTGCATTCATAGG 58.914 50.000 0.00 0.00 40.62 2.57
468 515 3.858989 CGTGTGTGCGTGTGTGCA 61.859 61.111 0.00 0.00 43.95 4.57
470 517 3.858989 TGCGTGTGTGCGTGTGTG 61.859 61.111 0.00 0.00 37.81 3.82
471 518 3.860125 GTGCGTGTGTGCGTGTGT 61.860 61.111 0.00 0.00 37.81 3.72
472 519 3.858989 TGTGCGTGTGTGCGTGTG 61.859 61.111 0.00 0.00 37.81 3.82
476 523 1.955529 GATAGGTGTGCGTGTGTGCG 61.956 60.000 0.00 0.00 37.81 5.34
477 524 1.635663 GGATAGGTGTGCGTGTGTGC 61.636 60.000 0.00 0.00 0.00 4.57
478 525 1.019278 GGGATAGGTGTGCGTGTGTG 61.019 60.000 0.00 0.00 0.00 3.82
479 526 1.192146 AGGGATAGGTGTGCGTGTGT 61.192 55.000 0.00 0.00 0.00 3.72
480 527 0.821517 TAGGGATAGGTGTGCGTGTG 59.178 55.000 0.00 0.00 0.00 3.82
482 529 1.686587 TCATAGGGATAGGTGTGCGTG 59.313 52.381 0.00 0.00 0.00 5.34
483 530 1.964223 CTCATAGGGATAGGTGTGCGT 59.036 52.381 0.00 0.00 0.00 5.24
484 531 1.337260 GCTCATAGGGATAGGTGTGCG 60.337 57.143 0.00 0.00 0.00 5.34
485 532 1.694150 TGCTCATAGGGATAGGTGTGC 59.306 52.381 0.00 0.00 0.00 4.57
486 533 2.037772 GGTGCTCATAGGGATAGGTGTG 59.962 54.545 0.00 0.00 0.00 3.82
487 534 2.090494 AGGTGCTCATAGGGATAGGTGT 60.090 50.000 0.00 0.00 0.00 4.16
488 535 2.564947 GAGGTGCTCATAGGGATAGGTG 59.435 54.545 0.00 0.00 0.00 4.00
489 536 2.493687 GGAGGTGCTCATAGGGATAGGT 60.494 54.545 0.00 0.00 31.08 3.08
490 537 2.183679 GGAGGTGCTCATAGGGATAGG 58.816 57.143 0.00 0.00 31.08 2.57
491 538 1.821753 CGGAGGTGCTCATAGGGATAG 59.178 57.143 0.00 0.00 31.08 2.08
492 539 1.427753 TCGGAGGTGCTCATAGGGATA 59.572 52.381 0.00 0.00 31.08 2.59
493 540 0.188587 TCGGAGGTGCTCATAGGGAT 59.811 55.000 0.00 0.00 31.08 3.85
494 541 0.468214 CTCGGAGGTGCTCATAGGGA 60.468 60.000 0.00 0.00 31.08 4.20
495 542 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
496 543 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
497 544 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
498 545 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
499 546 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
500 547 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
501 548 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
502 549 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
503 550 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
504 551 1.662438 GGCTCAGTCTCTCGGAGGTG 61.662 65.000 4.96 0.00 38.48 4.00
505 552 1.379309 GGCTCAGTCTCTCGGAGGT 60.379 63.158 4.96 0.00 38.48 3.85
506 553 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
507 554 2.477176 CCGGCTCAGTCTCTCGGAG 61.477 68.421 0.00 0.00 42.94 4.63
508 555 2.438614 CCGGCTCAGTCTCTCGGA 60.439 66.667 0.00 0.00 42.94 4.55
509 556 4.200283 GCCGGCTCAGTCTCTCGG 62.200 72.222 22.15 0.00 43.13 4.63
510 557 1.448119 TATGCCGGCTCAGTCTCTCG 61.448 60.000 29.70 0.00 0.00 4.04
511 558 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
512 559 0.965439 GATATGCCGGCTCAGTCTCT 59.035 55.000 29.70 3.16 0.00 3.10
513 560 0.676184 TGATATGCCGGCTCAGTCTC 59.324 55.000 29.70 15.31 0.00 3.36
514 561 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
515 562 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
516 563 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
517 564 2.469274 AAGATGATATGCCGGCTCAG 57.531 50.000 29.70 0.00 0.00 3.35
518 565 3.578282 TCTTAAGATGATATGCCGGCTCA 59.422 43.478 29.70 23.34 0.00 4.26
519 566 4.193826 TCTTAAGATGATATGCCGGCTC 57.806 45.455 29.70 17.89 0.00 4.70
520 567 4.833478 ATCTTAAGATGATATGCCGGCT 57.167 40.909 29.70 15.76 32.68 5.52
521 568 5.886960 AAATCTTAAGATGATATGCCGGC 57.113 39.130 22.73 22.73 34.49 6.13
522 569 6.811665 TCGTAAATCTTAAGATGATATGCCGG 59.188 38.462 18.61 0.00 34.49 6.13
523 570 7.812309 TCGTAAATCTTAAGATGATATGCCG 57.188 36.000 18.61 13.49 34.49 5.69
524 571 8.171840 GCTTCGTAAATCTTAAGATGATATGCC 58.828 37.037 18.61 8.54 34.49 4.40
525 572 8.171840 GGCTTCGTAAATCTTAAGATGATATGC 58.828 37.037 18.61 15.19 34.49 3.14
526 573 9.208022 TGGCTTCGTAAATCTTAAGATGATATG 57.792 33.333 18.61 17.69 34.49 1.78
527 574 9.209175 GTGGCTTCGTAAATCTTAAGATGATAT 57.791 33.333 18.61 8.31 34.49 1.63
528 575 7.656137 GGTGGCTTCGTAAATCTTAAGATGATA 59.344 37.037 18.61 11.94 34.49 2.15
529 576 6.483640 GGTGGCTTCGTAAATCTTAAGATGAT 59.516 38.462 18.61 12.88 34.49 2.45
530 577 5.815740 GGTGGCTTCGTAAATCTTAAGATGA 59.184 40.000 18.61 8.72 34.49 2.92
531 578 5.276868 CGGTGGCTTCGTAAATCTTAAGATG 60.277 44.000 18.61 6.47 34.49 2.90
532 579 4.809426 CGGTGGCTTCGTAAATCTTAAGAT 59.191 41.667 12.37 12.37 36.07 2.40
533 580 4.178540 CGGTGGCTTCGTAAATCTTAAGA 58.821 43.478 7.82 7.82 0.00 2.10
534 581 3.930848 ACGGTGGCTTCGTAAATCTTAAG 59.069 43.478 0.00 0.00 39.22 1.85
535 582 3.929094 ACGGTGGCTTCGTAAATCTTAA 58.071 40.909 4.10 0.00 39.22 1.85
536 583 3.598019 ACGGTGGCTTCGTAAATCTTA 57.402 42.857 4.10 0.00 39.22 2.10
537 584 2.467566 ACGGTGGCTTCGTAAATCTT 57.532 45.000 4.10 0.00 39.22 2.40
538 585 2.159142 CCTACGGTGGCTTCGTAAATCT 60.159 50.000 12.25 0.00 41.62 2.40
539 586 2.199236 CCTACGGTGGCTTCGTAAATC 58.801 52.381 12.25 0.00 41.62 2.17
540 587 2.304751 CCTACGGTGGCTTCGTAAAT 57.695 50.000 12.25 0.00 41.62 1.40
541 588 3.818586 CCTACGGTGGCTTCGTAAA 57.181 52.632 12.25 0.00 41.62 2.01
551 598 4.849329 GACGAGGCGCCTACGGTG 62.849 72.222 34.97 23.88 40.57 4.94
554 601 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
577 624 3.586892 CTTTTAGTGGGAGGAGACGTTC 58.413 50.000 0.00 0.00 0.00 3.95
578 625 2.289506 GCTTTTAGTGGGAGGAGACGTT 60.290 50.000 0.00 0.00 0.00 3.99
579 626 1.275573 GCTTTTAGTGGGAGGAGACGT 59.724 52.381 0.00 0.00 0.00 4.34
580 627 1.736032 CGCTTTTAGTGGGAGGAGACG 60.736 57.143 0.00 0.00 0.00 4.18
581 628 2.007547 GCGCTTTTAGTGGGAGGAGAC 61.008 57.143 0.00 0.00 0.00 3.36
582 629 0.249398 GCGCTTTTAGTGGGAGGAGA 59.751 55.000 0.00 0.00 0.00 3.71
583 630 0.036388 TGCGCTTTTAGTGGGAGGAG 60.036 55.000 9.73 0.00 0.00 3.69
584 631 0.618458 ATGCGCTTTTAGTGGGAGGA 59.382 50.000 9.73 0.00 0.00 3.71
585 632 1.017387 GATGCGCTTTTAGTGGGAGG 58.983 55.000 9.73 0.00 0.00 4.30
586 633 0.652592 CGATGCGCTTTTAGTGGGAG 59.347 55.000 9.73 0.00 0.00 4.30
587 634 2.762360 CGATGCGCTTTTAGTGGGA 58.238 52.632 9.73 0.00 0.00 4.37
599 646 1.010797 CAAGATTTCCGGCGATGCG 60.011 57.895 9.30 0.00 0.00 4.73
600 647 0.732571 TTCAAGATTTCCGGCGATGC 59.267 50.000 9.30 0.00 0.00 3.91
601 648 3.698029 ATTTCAAGATTTCCGGCGATG 57.302 42.857 9.30 0.00 0.00 3.84
602 649 5.828299 TTTATTTCAAGATTTCCGGCGAT 57.172 34.783 9.30 0.00 0.00 4.58
603 650 5.828299 ATTTATTTCAAGATTTCCGGCGA 57.172 34.783 9.30 0.00 0.00 5.54
604 651 6.033341 TGAATTTATTTCAAGATTTCCGGCG 58.967 36.000 0.00 0.00 41.38 6.46
605 652 7.826260 TTGAATTTATTTCAAGATTTCCGGC 57.174 32.000 0.00 0.00 46.80 6.13
622 669 9.188588 CTTGATGCTCGCATTATATTTGAATTT 57.811 29.630 5.79 0.00 36.70 1.82
623 670 8.570488 TCTTGATGCTCGCATTATATTTGAATT 58.430 29.630 5.79 0.00 36.70 2.17
624 671 8.102800 TCTTGATGCTCGCATTATATTTGAAT 57.897 30.769 5.79 0.00 36.70 2.57
625 672 7.495135 TCTTGATGCTCGCATTATATTTGAA 57.505 32.000 5.79 0.00 36.70 2.69
626 673 7.677454 ATCTTGATGCTCGCATTATATTTGA 57.323 32.000 5.79 0.00 36.70 2.69
627 674 8.635983 CAAATCTTGATGCTCGCATTATATTTG 58.364 33.333 18.93 18.93 36.70 2.32
628 675 8.570488 TCAAATCTTGATGCTCGCATTATATTT 58.430 29.630 5.79 8.25 36.70 1.40
629 676 8.102800 TCAAATCTTGATGCTCGCATTATATT 57.897 30.769 5.79 3.13 36.70 1.28
630 677 7.677454 TCAAATCTTGATGCTCGCATTATAT 57.323 32.000 5.79 0.00 36.70 0.86
631 678 7.355017 GTTCAAATCTTGATGCTCGCATTATA 58.645 34.615 5.79 0.00 39.84 0.98
632 679 6.204359 GTTCAAATCTTGATGCTCGCATTAT 58.796 36.000 5.79 0.00 39.84 1.28
633 680 5.449041 GGTTCAAATCTTGATGCTCGCATTA 60.449 40.000 5.79 0.00 39.84 1.90
634 681 4.418392 GTTCAAATCTTGATGCTCGCATT 58.582 39.130 5.79 0.00 39.84 3.56
635 682 3.181493 GGTTCAAATCTTGATGCTCGCAT 60.181 43.478 3.70 3.70 39.84 4.73
636 683 2.162208 GGTTCAAATCTTGATGCTCGCA 59.838 45.455 0.00 0.00 39.84 5.10
637 684 2.478539 GGGTTCAAATCTTGATGCTCGC 60.479 50.000 0.00 0.00 39.84 5.03
638 685 3.012518 AGGGTTCAAATCTTGATGCTCG 58.987 45.455 0.00 0.00 39.84 5.03
639 686 5.189180 AGTAGGGTTCAAATCTTGATGCTC 58.811 41.667 0.00 0.00 39.84 4.26
640 687 5.184892 AGTAGGGTTCAAATCTTGATGCT 57.815 39.130 0.00 0.00 39.84 3.79
641 688 5.529060 CCTAGTAGGGTTCAAATCTTGATGC 59.471 44.000 8.50 0.00 39.84 3.91
642 689 6.653989 ACCTAGTAGGGTTCAAATCTTGATG 58.346 40.000 20.54 0.00 40.58 3.07
643 690 6.893020 ACCTAGTAGGGTTCAAATCTTGAT 57.107 37.500 20.54 0.00 40.58 2.57
644 691 6.472887 CAACCTAGTAGGGTTCAAATCTTGA 58.527 40.000 20.54 0.00 46.58 3.02
645 692 5.648092 CCAACCTAGTAGGGTTCAAATCTTG 59.352 44.000 20.54 11.33 46.58 3.02
646 693 5.281037 CCCAACCTAGTAGGGTTCAAATCTT 60.281 44.000 20.54 0.00 46.58 2.40
647 694 4.227527 CCCAACCTAGTAGGGTTCAAATCT 59.772 45.833 20.54 0.00 46.58 2.40
648 695 4.524053 CCCAACCTAGTAGGGTTCAAATC 58.476 47.826 20.54 0.00 46.58 2.17
649 696 3.268595 CCCCAACCTAGTAGGGTTCAAAT 59.731 47.826 20.54 0.00 46.58 2.32
650 697 2.645797 CCCCAACCTAGTAGGGTTCAAA 59.354 50.000 20.54 0.00 46.58 2.69
651 698 2.157973 TCCCCAACCTAGTAGGGTTCAA 60.158 50.000 20.54 0.00 46.58 2.69
652 699 1.437945 TCCCCAACCTAGTAGGGTTCA 59.562 52.381 20.54 0.00 46.58 3.18
653 700 2.259014 TCCCCAACCTAGTAGGGTTC 57.741 55.000 20.54 0.00 46.58 3.62
655 702 1.654997 TGATCCCCAACCTAGTAGGGT 59.345 52.381 20.54 11.57 40.58 4.34
656 703 2.047830 GTGATCCCCAACCTAGTAGGG 58.952 57.143 20.54 3.07 40.58 3.53
657 704 2.759355 TGTGATCCCCAACCTAGTAGG 58.241 52.381 15.09 15.09 42.49 3.18
658 705 4.501571 CGAATGTGATCCCCAACCTAGTAG 60.502 50.000 0.00 0.00 0.00 2.57
659 706 3.386726 CGAATGTGATCCCCAACCTAGTA 59.613 47.826 0.00 0.00 0.00 1.82
660 707 2.170607 CGAATGTGATCCCCAACCTAGT 59.829 50.000 0.00 0.00 0.00 2.57
661 708 2.170607 ACGAATGTGATCCCCAACCTAG 59.829 50.000 0.00 0.00 0.00 3.02
662 709 2.169769 GACGAATGTGATCCCCAACCTA 59.830 50.000 0.00 0.00 0.00 3.08
663 710 0.991920 ACGAATGTGATCCCCAACCT 59.008 50.000 0.00 0.00 0.00 3.50
664 711 1.379527 GACGAATGTGATCCCCAACC 58.620 55.000 0.00 0.00 0.00 3.77
665 712 1.339631 TGGACGAATGTGATCCCCAAC 60.340 52.381 0.00 0.00 0.00 3.77
666 713 0.988063 TGGACGAATGTGATCCCCAA 59.012 50.000 0.00 0.00 0.00 4.12
667 714 0.988063 TTGGACGAATGTGATCCCCA 59.012 50.000 0.00 0.00 0.00 4.96
676 723 3.603770 GCAACTTTCGATTTGGACGAATG 59.396 43.478 0.00 0.00 46.34 2.67
689 736 3.120199 ACATCTCGGATTTGCAACTTTCG 60.120 43.478 0.00 0.02 0.00 3.46
772 820 1.134280 AGATCATTGCGGAGGAAGTGG 60.134 52.381 0.00 0.00 44.16 4.00
783 831 0.034616 CCCGGAGAGGAGATCATTGC 59.965 60.000 0.73 0.00 45.00 3.56
790 838 2.593978 CGTACCCCGGAGAGGAGA 59.406 66.667 0.73 0.00 45.00 3.71
805 853 0.104304 AAAGTCAAGCGAGTCACCGT 59.896 50.000 0.00 0.00 0.00 4.83
882 931 3.193267 ACGGCTAACACCACTACGAAATA 59.807 43.478 0.00 0.00 0.00 1.40
887 1219 0.795735 CGACGGCTAACACCACTACG 60.796 60.000 0.00 0.00 0.00 3.51
896 1228 1.499049 GATGGGATTCGACGGCTAAC 58.501 55.000 0.00 0.00 0.00 2.34
897 1229 0.031585 CGATGGGATTCGACGGCTAA 59.968 55.000 0.00 0.00 41.62 3.09
903 1235 2.544069 GGACTTCTCGATGGGATTCGAC 60.544 54.545 0.00 0.00 42.81 4.20
919 1251 4.471386 AGCGGCAATCCTATATATGGACTT 59.529 41.667 1.45 0.00 36.30 3.01
946 1278 1.445716 CTGCTGCTGCTAGGATTGGC 61.446 60.000 17.00 0.00 40.48 4.52
1003 1341 4.052229 CGTCGACGTGGCCCTCTT 62.052 66.667 29.08 0.00 34.11 2.85
1058 1396 0.030908 CAATAGGTCGTCCTCCGCTC 59.969 60.000 3.91 0.00 43.94 5.03
1707 2293 4.051922 CACCTACACAGAGATTAATCGCC 58.948 47.826 14.69 8.77 0.00 5.54
1709 2295 4.970611 CGACACCTACACAGAGATTAATCG 59.029 45.833 9.78 0.00 0.00 3.34
1721 2307 1.862123 TCGTCGACGACACCTACAC 59.138 57.895 34.97 0.00 44.22 2.90
1981 2587 1.904287 ATAGCAAAACCGGACAGCAA 58.096 45.000 9.46 0.00 0.00 3.91
1982 2588 1.810151 GAATAGCAAAACCGGACAGCA 59.190 47.619 9.46 0.00 0.00 4.41
2069 2763 8.050778 AGAATCACCTATAGATCAATCGTCTC 57.949 38.462 0.00 0.00 0.00 3.36
2131 2830 1.391485 GTGCGTACATGAGCTTGTGAG 59.609 52.381 0.00 0.00 0.00 3.51
2180 2879 5.191426 ACATATGCAGAAGAAGCAACAGAT 58.809 37.500 1.58 0.00 46.27 2.90
2185 2884 5.163723 GCAGTAACATATGCAGAAGAAGCAA 60.164 40.000 1.58 0.00 46.27 3.91
2222 2954 1.332375 GAGTGTCTCCTCGATTCCTCG 59.668 57.143 0.00 0.00 46.41 4.63
2223 2955 1.679153 GGAGTGTCTCCTCGATTCCTC 59.321 57.143 8.38 0.00 46.41 3.71
2224 2956 1.770294 GGAGTGTCTCCTCGATTCCT 58.230 55.000 8.38 0.00 46.41 3.36
2344 3085 3.612681 CAGTGGGGGTCGACACGT 61.613 66.667 18.91 0.00 42.25 4.49
2358 3099 4.320023 GGTCCCAAAACAAAACAAACAGT 58.680 39.130 0.00 0.00 0.00 3.55
2396 3137 1.264288 GAGCTTGTCGGTCCAAAACTG 59.736 52.381 0.00 0.00 34.06 3.16
2490 3231 0.836606 TTCAGTGTCAGCTTGGGACA 59.163 50.000 1.42 1.42 42.62 4.02
2491 3232 1.967319 TTTCAGTGTCAGCTTGGGAC 58.033 50.000 0.00 0.00 35.83 4.46
2492 3233 2.106338 TCATTTCAGTGTCAGCTTGGGA 59.894 45.455 0.00 0.00 0.00 4.37
2493 3234 2.507484 TCATTTCAGTGTCAGCTTGGG 58.493 47.619 0.00 0.00 0.00 4.12
2494 3235 4.022589 ACATTCATTTCAGTGTCAGCTTGG 60.023 41.667 0.00 0.00 0.00 3.61
2495 3236 5.117355 ACATTCATTTCAGTGTCAGCTTG 57.883 39.130 0.00 0.00 0.00 4.01
2496 3237 6.883217 AGATACATTCATTTCAGTGTCAGCTT 59.117 34.615 0.00 0.00 0.00 3.74
2497 3238 6.413052 AGATACATTCATTTCAGTGTCAGCT 58.587 36.000 0.00 0.00 0.00 4.24
2498 3239 6.674694 AGATACATTCATTTCAGTGTCAGC 57.325 37.500 0.00 0.00 0.00 4.26
2499 3240 7.493645 TGCTAGATACATTCATTTCAGTGTCAG 59.506 37.037 0.00 0.00 0.00 3.51
2500 3241 7.278646 GTGCTAGATACATTCATTTCAGTGTCA 59.721 37.037 0.00 0.00 0.00 3.58
2501 3242 7.493971 AGTGCTAGATACATTCATTTCAGTGTC 59.506 37.037 0.00 0.00 0.00 3.67
2502 3243 7.334090 AGTGCTAGATACATTCATTTCAGTGT 58.666 34.615 0.00 0.00 0.00 3.55
2503 3244 7.783090 AGTGCTAGATACATTCATTTCAGTG 57.217 36.000 0.00 0.00 0.00 3.66
2536 3277 9.265862 CTCTCTCCCTTAAATGGATGTATCTAT 57.734 37.037 0.00 0.00 0.00 1.98
2537 3278 7.676043 CCTCTCTCCCTTAAATGGATGTATCTA 59.324 40.741 0.00 0.00 0.00 1.98
2538 3279 6.500049 CCTCTCTCCCTTAAATGGATGTATCT 59.500 42.308 0.00 0.00 0.00 1.98
2539 3280 6.706295 CCTCTCTCCCTTAAATGGATGTATC 58.294 44.000 0.00 0.00 0.00 2.24
2540 3281 6.694445 CCTCTCTCCCTTAAATGGATGTAT 57.306 41.667 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.