Multiple sequence alignment - TraesCS6A01G062600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G062600 chr6A 100.000 2849 0 0 1 2849 33536738 33533890 0.000000e+00 5262.0
1 TraesCS6A01G062600 chr6A 95.356 646 25 3 1047 1689 33010797 33011440 0.000000e+00 1022.0
2 TraesCS6A01G062600 chr6A 88.612 843 65 22 805 1642 16594041 16593225 0.000000e+00 996.0
3 TraesCS6A01G062600 chr6A 85.465 516 63 8 23 534 569430075 569430582 6.990000e-146 527.0
4 TraesCS6A01G062600 chr6A 84.791 526 72 3 1 523 493972938 493973458 3.250000e-144 521.0
5 TraesCS6A01G062600 chr6A 83.548 310 34 14 2357 2650 33390019 33389711 1.010000e-69 274.0
6 TraesCS6A01G062600 chr6D 88.235 1819 120 35 906 2677 29381439 29379668 0.000000e+00 2087.0
7 TraesCS6A01G062600 chr6D 91.910 1162 51 13 594 1743 29089232 29090362 0.000000e+00 1585.0
8 TraesCS6A01G062600 chr6D 88.235 850 70 15 809 1654 16307492 16306669 0.000000e+00 989.0
9 TraesCS6A01G062600 chr6D 90.511 685 45 12 943 1623 24001458 24002126 0.000000e+00 887.0
10 TraesCS6A01G062600 chr6D 86.490 718 57 23 972 1686 16390173 16389493 0.000000e+00 752.0
11 TraesCS6A01G062600 chr6D 83.810 630 67 9 1 601 350127258 350126635 1.480000e-157 566.0
12 TraesCS6A01G062600 chr6D 84.359 569 46 17 2312 2849 29090876 29091432 4.210000e-143 518.0
13 TraesCS6A01G062600 chr6D 85.581 430 55 4 1 427 35619056 35618631 7.240000e-121 444.0
14 TraesCS6A01G062600 chr6D 79.592 441 48 28 2445 2849 29096325 29096759 7.770000e-71 278.0
15 TraesCS6A01G062600 chr6D 76.978 139 14 10 463 597 79707733 79707609 2.370000e-06 63.9
16 TraesCS6A01G062600 chr6B 91.895 950 53 18 1047 1992 59723180 59724109 0.000000e+00 1306.0
17 TraesCS6A01G062600 chr6B 90.685 891 48 22 1043 1925 59100544 59101407 0.000000e+00 1153.0
18 TraesCS6A01G062600 chr6B 93.207 633 21 10 1043 1674 58812377 58812988 0.000000e+00 911.0
19 TraesCS6A01G062600 chr6B 86.700 812 37 26 2082 2849 60661856 60661072 0.000000e+00 835.0
20 TraesCS6A01G062600 chr6B 83.555 827 58 21 2006 2772 59724167 59724975 0.000000e+00 702.0
21 TraesCS6A01G062600 chr6B 81.096 529 58 28 2356 2849 60627378 60626857 4.450000e-103 385.0
22 TraesCS6A01G062600 chr6B 80.350 514 49 18 2373 2849 60636474 60635976 2.720000e-90 342.0
23 TraesCS6A01G062600 chr6B 80.384 469 50 28 2358 2791 60612604 60612143 4.580000e-83 318.0
24 TraesCS6A01G062600 chr6B 87.245 196 16 7 1734 1925 58816063 58816253 6.180000e-52 215.0
25 TraesCS6A01G062600 chr6B 76.308 325 37 19 2529 2844 59824455 59824748 1.380000e-28 137.0
26 TraesCS6A01G062600 chr6B 80.833 120 9 3 2617 2724 78289577 78289694 6.540000e-12 82.4
27 TraesCS6A01G062600 chr6B 89.062 64 6 1 2333 2395 59824288 59824351 8.460000e-11 78.7
28 TraesCS6A01G062600 chr3D 85.424 542 67 8 1 536 507765170 507764635 1.150000e-153 553.0
29 TraesCS6A01G062600 chr7D 83.307 629 71 19 1 600 159709543 159710166 1.490000e-152 549.0
30 TraesCS6A01G062600 chr3A 83.670 545 64 12 1 526 9048805 9049343 9.170000e-135 490.0
31 TraesCS6A01G062600 chr3A 93.478 46 3 0 555 600 261348302 261348347 5.090000e-08 69.4
32 TraesCS6A01G062600 chr5D 82.883 555 83 8 1 551 526830027 526829481 3.300000e-134 488.0
33 TraesCS6A01G062600 chr7B 82.662 571 69 17 1 545 673948966 673949532 1.990000e-131 479.0
34 TraesCS6A01G062600 chr7B 79.762 588 95 17 20 600 582652093 582652663 3.420000e-109 405.0
35 TraesCS6A01G062600 chr5B 80.827 532 72 16 87 601 655232776 655232258 9.570000e-105 390.0
36 TraesCS6A01G062600 chr2D 78.526 624 94 26 3 598 625193480 625194091 9.640000e-100 374.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G062600 chr6A 33533890 33536738 2848 True 5262.0 5262 100.0000 1 2849 1 chr6A.!!$R3 2848
1 TraesCS6A01G062600 chr6A 33010797 33011440 643 False 1022.0 1022 95.3560 1047 1689 1 chr6A.!!$F1 642
2 TraesCS6A01G062600 chr6A 16593225 16594041 816 True 996.0 996 88.6120 805 1642 1 chr6A.!!$R1 837
3 TraesCS6A01G062600 chr6A 569430075 569430582 507 False 527.0 527 85.4650 23 534 1 chr6A.!!$F3 511
4 TraesCS6A01G062600 chr6A 493972938 493973458 520 False 521.0 521 84.7910 1 523 1 chr6A.!!$F2 522
5 TraesCS6A01G062600 chr6D 29379668 29381439 1771 True 2087.0 2087 88.2350 906 2677 1 chr6D.!!$R3 1771
6 TraesCS6A01G062600 chr6D 29089232 29091432 2200 False 1051.5 1585 88.1345 594 2849 2 chr6D.!!$F3 2255
7 TraesCS6A01G062600 chr6D 16306669 16307492 823 True 989.0 989 88.2350 809 1654 1 chr6D.!!$R1 845
8 TraesCS6A01G062600 chr6D 24001458 24002126 668 False 887.0 887 90.5110 943 1623 1 chr6D.!!$F1 680
9 TraesCS6A01G062600 chr6D 16389493 16390173 680 True 752.0 752 86.4900 972 1686 1 chr6D.!!$R2 714
10 TraesCS6A01G062600 chr6D 350126635 350127258 623 True 566.0 566 83.8100 1 601 1 chr6D.!!$R6 600
11 TraesCS6A01G062600 chr6B 59100544 59101407 863 False 1153.0 1153 90.6850 1043 1925 1 chr6B.!!$F1 882
12 TraesCS6A01G062600 chr6B 59723180 59724975 1795 False 1004.0 1306 87.7250 1047 2772 2 chr6B.!!$F4 1725
13 TraesCS6A01G062600 chr6B 60661072 60661856 784 True 835.0 835 86.7000 2082 2849 1 chr6B.!!$R4 767
14 TraesCS6A01G062600 chr6B 58812377 58816253 3876 False 563.0 911 90.2260 1043 1925 2 chr6B.!!$F3 882
15 TraesCS6A01G062600 chr6B 60626857 60627378 521 True 385.0 385 81.0960 2356 2849 1 chr6B.!!$R2 493
16 TraesCS6A01G062600 chr3D 507764635 507765170 535 True 553.0 553 85.4240 1 536 1 chr3D.!!$R1 535
17 TraesCS6A01G062600 chr7D 159709543 159710166 623 False 549.0 549 83.3070 1 600 1 chr7D.!!$F1 599
18 TraesCS6A01G062600 chr3A 9048805 9049343 538 False 490.0 490 83.6700 1 526 1 chr3A.!!$F1 525
19 TraesCS6A01G062600 chr5D 526829481 526830027 546 True 488.0 488 82.8830 1 551 1 chr5D.!!$R1 550
20 TraesCS6A01G062600 chr7B 673948966 673949532 566 False 479.0 479 82.6620 1 545 1 chr7B.!!$F2 544
21 TraesCS6A01G062600 chr7B 582652093 582652663 570 False 405.0 405 79.7620 20 600 1 chr7B.!!$F1 580
22 TraesCS6A01G062600 chr5B 655232258 655232776 518 True 390.0 390 80.8270 87 601 1 chr5B.!!$R1 514
23 TraesCS6A01G062600 chr2D 625193480 625194091 611 False 374.0 374 78.5260 3 598 1 chr2D.!!$F1 595

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
552 592 0.107214 AATACCCACGGATGCACCAG 60.107 55.0 0.0 0.0 38.9 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 5265 1.00358 TCCCTGCATCTTGACTGGAAC 59.996 52.381 0.0 0.0 0.0 3.62 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
147 157 2.371259 GGGGAGTTGGAGGAGGAGC 61.371 68.421 0.00 0.00 0.00 4.70
148 158 2.726351 GGGAGTTGGAGGAGGAGCG 61.726 68.421 0.00 0.00 0.00 5.03
200 238 4.467084 GGCGACGGGGATCTGCAA 62.467 66.667 0.00 0.00 0.00 4.08
250 288 4.436998 GTCGGAGTCGGCTGTGGG 62.437 72.222 0.00 0.00 38.10 4.61
330 369 2.388735 AGTTCGCCTACATGGATGAGA 58.611 47.619 0.00 0.00 38.35 3.27
340 379 2.224233 ACATGGATGAGATCGAGCAAGG 60.224 50.000 2.38 0.00 0.00 3.61
379 419 4.832608 CTACCCGCCAGCCCGTTC 62.833 72.222 0.00 0.00 0.00 3.95
408 448 4.180496 GACCCCATCGTCGTGAAC 57.820 61.111 0.00 0.00 0.00 3.18
409 449 1.290955 GACCCCATCGTCGTGAACA 59.709 57.895 0.00 0.00 0.00 3.18
410 450 0.108329 GACCCCATCGTCGTGAACAT 60.108 55.000 0.00 0.00 0.00 2.71
411 451 0.108329 ACCCCATCGTCGTGAACATC 60.108 55.000 0.00 0.00 0.00 3.06
412 452 0.175760 CCCCATCGTCGTGAACATCT 59.824 55.000 0.00 0.00 0.00 2.90
413 453 1.560923 CCCATCGTCGTGAACATCTC 58.439 55.000 0.00 0.00 0.00 2.75
414 454 1.560923 CCATCGTCGTGAACATCTCC 58.439 55.000 0.00 0.00 0.00 3.71
415 455 1.191944 CATCGTCGTGAACATCTCCG 58.808 55.000 0.00 0.00 0.00 4.63
416 456 1.092348 ATCGTCGTGAACATCTCCGA 58.908 50.000 0.00 0.00 0.00 4.55
417 457 1.092348 TCGTCGTGAACATCTCCGAT 58.908 50.000 0.00 0.00 32.02 4.18
418 458 1.191944 CGTCGTGAACATCTCCGATG 58.808 55.000 2.49 2.49 32.02 3.84
419 459 1.202143 CGTCGTGAACATCTCCGATGA 60.202 52.381 10.54 0.00 36.58 2.92
420 460 2.186076 GTCGTGAACATCTCCGATGAC 58.814 52.381 10.54 5.24 32.02 3.06
421 461 1.191944 CGTGAACATCTCCGATGACG 58.808 55.000 10.54 6.53 39.43 4.35
422 462 1.202143 CGTGAACATCTCCGATGACGA 60.202 52.381 10.54 0.00 42.66 4.20
423 463 2.731027 CGTGAACATCTCCGATGACGAA 60.731 50.000 10.54 0.00 42.66 3.85
424 464 2.854777 GTGAACATCTCCGATGACGAAG 59.145 50.000 10.54 0.00 42.66 3.79
425 465 2.752903 TGAACATCTCCGATGACGAAGA 59.247 45.455 10.54 0.00 37.29 2.87
426 466 3.181496 TGAACATCTCCGATGACGAAGAG 60.181 47.826 10.54 0.00 36.19 2.85
427 467 2.370349 ACATCTCCGATGACGAAGAGT 58.630 47.619 10.54 0.00 36.19 3.24
428 468 3.542648 ACATCTCCGATGACGAAGAGTA 58.457 45.455 10.54 0.00 36.19 2.59
429 469 3.562141 ACATCTCCGATGACGAAGAGTAG 59.438 47.826 10.54 0.00 36.19 2.57
430 470 1.941294 TCTCCGATGACGAAGAGTAGC 59.059 52.381 0.00 0.00 42.66 3.58
431 471 1.944024 CTCCGATGACGAAGAGTAGCT 59.056 52.381 0.00 0.00 42.66 3.32
432 472 3.132160 CTCCGATGACGAAGAGTAGCTA 58.868 50.000 0.00 0.00 42.66 3.32
433 473 3.132160 TCCGATGACGAAGAGTAGCTAG 58.868 50.000 0.00 0.00 42.66 3.42
434 474 2.224549 CCGATGACGAAGAGTAGCTAGG 59.775 54.545 0.00 0.00 42.66 3.02
435 475 2.224549 CGATGACGAAGAGTAGCTAGGG 59.775 54.545 0.00 0.00 42.66 3.53
436 476 2.803030 TGACGAAGAGTAGCTAGGGT 57.197 50.000 0.00 0.00 0.00 4.34
437 477 3.920231 TGACGAAGAGTAGCTAGGGTA 57.080 47.619 0.00 0.00 0.00 3.69
438 478 4.434545 TGACGAAGAGTAGCTAGGGTAT 57.565 45.455 0.00 0.00 0.00 2.73
439 479 4.789807 TGACGAAGAGTAGCTAGGGTATT 58.210 43.478 0.00 0.00 0.00 1.89
440 480 5.933617 TGACGAAGAGTAGCTAGGGTATTA 58.066 41.667 0.00 0.00 0.00 0.98
441 481 5.762218 TGACGAAGAGTAGCTAGGGTATTAC 59.238 44.000 0.00 0.00 0.00 1.89
442 482 4.754114 ACGAAGAGTAGCTAGGGTATTACG 59.246 45.833 0.00 0.00 0.00 3.18
443 483 4.754114 CGAAGAGTAGCTAGGGTATTACGT 59.246 45.833 0.00 0.00 0.00 3.57
444 484 5.928839 CGAAGAGTAGCTAGGGTATTACGTA 59.071 44.000 0.00 0.00 0.00 3.57
445 485 6.593382 CGAAGAGTAGCTAGGGTATTACGTAT 59.407 42.308 0.00 0.00 0.00 3.06
446 486 7.412781 CGAAGAGTAGCTAGGGTATTACGTATG 60.413 44.444 0.00 0.00 0.00 2.39
447 487 7.013823 AGAGTAGCTAGGGTATTACGTATGA 57.986 40.000 0.00 0.00 0.00 2.15
448 488 7.631933 AGAGTAGCTAGGGTATTACGTATGAT 58.368 38.462 0.00 0.00 0.00 2.45
449 489 8.108364 AGAGTAGCTAGGGTATTACGTATGATT 58.892 37.037 0.00 0.00 0.00 2.57
450 490 8.278729 AGTAGCTAGGGTATTACGTATGATTC 57.721 38.462 0.00 0.00 0.00 2.52
451 491 6.527057 AGCTAGGGTATTACGTATGATTCC 57.473 41.667 0.00 0.00 0.00 3.01
452 492 6.254522 AGCTAGGGTATTACGTATGATTCCT 58.745 40.000 0.00 3.42 0.00 3.36
453 493 6.724905 AGCTAGGGTATTACGTATGATTCCTT 59.275 38.462 0.00 0.00 0.00 3.36
454 494 7.234988 AGCTAGGGTATTACGTATGATTCCTTT 59.765 37.037 0.00 0.00 0.00 3.11
455 495 7.876582 GCTAGGGTATTACGTATGATTCCTTTT 59.123 37.037 0.00 0.00 0.00 2.27
456 496 9.204570 CTAGGGTATTACGTATGATTCCTTTTG 57.795 37.037 0.00 0.00 0.00 2.44
457 497 6.485648 AGGGTATTACGTATGATTCCTTTTGC 59.514 38.462 0.00 0.00 0.00 3.68
458 498 6.261381 GGGTATTACGTATGATTCCTTTTGCA 59.739 38.462 0.00 0.00 0.00 4.08
459 499 7.040686 GGGTATTACGTATGATTCCTTTTGCAT 60.041 37.037 0.00 0.00 0.00 3.96
460 500 7.803189 GGTATTACGTATGATTCCTTTTGCATG 59.197 37.037 0.00 0.00 0.00 4.06
461 501 4.032703 ACGTATGATTCCTTTTGCATGC 57.967 40.909 11.82 11.82 0.00 4.06
462 502 3.696051 ACGTATGATTCCTTTTGCATGCT 59.304 39.130 20.33 0.00 0.00 3.79
463 503 4.158394 ACGTATGATTCCTTTTGCATGCTT 59.842 37.500 20.33 0.00 0.00 3.91
464 504 5.104374 CGTATGATTCCTTTTGCATGCTTT 58.896 37.500 20.33 0.00 0.00 3.51
465 505 5.005012 CGTATGATTCCTTTTGCATGCTTTG 59.995 40.000 20.33 6.42 0.00 2.77
466 506 4.339872 TGATTCCTTTTGCATGCTTTGT 57.660 36.364 20.33 0.00 0.00 2.83
467 507 5.465532 TGATTCCTTTTGCATGCTTTGTA 57.534 34.783 20.33 0.00 0.00 2.41
468 508 6.040209 TGATTCCTTTTGCATGCTTTGTAT 57.960 33.333 20.33 3.79 0.00 2.29
469 509 5.870433 TGATTCCTTTTGCATGCTTTGTATG 59.130 36.000 20.33 1.72 0.00 2.39
470 510 4.191033 TCCTTTTGCATGCTTTGTATGG 57.809 40.909 20.33 11.49 0.00 2.74
471 511 3.831333 TCCTTTTGCATGCTTTGTATGGA 59.169 39.130 20.33 13.49 0.00 3.41
472 512 4.467082 TCCTTTTGCATGCTTTGTATGGAT 59.533 37.500 20.33 0.00 0.00 3.41
473 513 5.046448 TCCTTTTGCATGCTTTGTATGGATT 60.046 36.000 20.33 0.00 0.00 3.01
474 514 5.644636 CCTTTTGCATGCTTTGTATGGATTT 59.355 36.000 20.33 0.00 0.00 2.17
475 515 6.817641 CCTTTTGCATGCTTTGTATGGATTTA 59.182 34.615 20.33 0.00 0.00 1.40
476 516 7.010738 CCTTTTGCATGCTTTGTATGGATTTAG 59.989 37.037 20.33 0.00 0.00 1.85
477 517 5.518848 TGCATGCTTTGTATGGATTTAGG 57.481 39.130 20.33 0.00 0.00 2.69
478 518 5.199723 TGCATGCTTTGTATGGATTTAGGA 58.800 37.500 20.33 0.00 0.00 2.94
479 519 5.655974 TGCATGCTTTGTATGGATTTAGGAA 59.344 36.000 20.33 0.00 0.00 3.36
480 520 6.154192 TGCATGCTTTGTATGGATTTAGGAAA 59.846 34.615 20.33 0.00 0.00 3.13
481 521 7.147689 TGCATGCTTTGTATGGATTTAGGAAAT 60.148 33.333 20.33 0.00 0.00 2.17
482 522 7.170320 GCATGCTTTGTATGGATTTAGGAAATG 59.830 37.037 11.37 0.00 0.00 2.32
483 523 7.953005 TGCTTTGTATGGATTTAGGAAATGA 57.047 32.000 0.00 0.00 0.00 2.57
484 524 8.359875 TGCTTTGTATGGATTTAGGAAATGAA 57.640 30.769 0.00 0.00 0.00 2.57
485 525 8.811017 TGCTTTGTATGGATTTAGGAAATGAAA 58.189 29.630 0.00 0.00 0.00 2.69
486 526 9.822185 GCTTTGTATGGATTTAGGAAATGAAAT 57.178 29.630 0.00 0.00 0.00 2.17
498 538 6.857777 AGGAAATGAAATATGAGAGAAGCG 57.142 37.500 0.00 0.00 0.00 4.68
499 539 5.762218 AGGAAATGAAATATGAGAGAAGCGG 59.238 40.000 0.00 0.00 0.00 5.52
500 540 5.760253 GGAAATGAAATATGAGAGAAGCGGA 59.240 40.000 0.00 0.00 0.00 5.54
501 541 6.429385 GGAAATGAAATATGAGAGAAGCGGAT 59.571 38.462 0.00 0.00 0.00 4.18
502 542 6.798315 AATGAAATATGAGAGAAGCGGATG 57.202 37.500 0.00 0.00 0.00 3.51
503 543 4.060900 TGAAATATGAGAGAAGCGGATGC 58.939 43.478 0.00 0.00 43.24 3.91
504 544 3.758755 AATATGAGAGAAGCGGATGCA 57.241 42.857 0.00 0.00 46.23 3.96
505 545 3.758755 ATATGAGAGAAGCGGATGCAA 57.241 42.857 0.00 0.00 46.23 4.08
506 546 2.408271 ATGAGAGAAGCGGATGCAAA 57.592 45.000 0.00 0.00 46.23 3.68
507 547 1.730501 TGAGAGAAGCGGATGCAAAG 58.269 50.000 0.00 0.00 46.23 2.77
508 548 1.002430 TGAGAGAAGCGGATGCAAAGT 59.998 47.619 0.00 0.00 46.23 2.66
509 549 1.396301 GAGAGAAGCGGATGCAAAGTG 59.604 52.381 0.00 0.00 46.23 3.16
510 550 1.002430 AGAGAAGCGGATGCAAAGTGA 59.998 47.619 0.00 0.00 46.23 3.41
511 551 1.129437 GAGAAGCGGATGCAAAGTGAC 59.871 52.381 0.00 0.00 46.23 3.67
512 552 1.160137 GAAGCGGATGCAAAGTGACT 58.840 50.000 0.00 0.00 46.23 3.41
513 553 2.028112 AGAAGCGGATGCAAAGTGACTA 60.028 45.455 0.00 0.00 46.23 2.59
514 554 2.472695 AGCGGATGCAAAGTGACTAA 57.527 45.000 0.00 0.00 46.23 2.24
515 555 2.991250 AGCGGATGCAAAGTGACTAAT 58.009 42.857 0.00 0.00 46.23 1.73
516 556 3.347216 AGCGGATGCAAAGTGACTAATT 58.653 40.909 0.00 0.00 46.23 1.40
517 557 3.758554 AGCGGATGCAAAGTGACTAATTT 59.241 39.130 0.00 0.00 46.23 1.82
518 558 4.941263 AGCGGATGCAAAGTGACTAATTTA 59.059 37.500 0.00 0.00 46.23 1.40
519 559 5.414454 AGCGGATGCAAAGTGACTAATTTAA 59.586 36.000 0.00 0.00 46.23 1.52
520 560 5.739161 GCGGATGCAAAGTGACTAATTTAAG 59.261 40.000 0.00 0.00 42.15 1.85
521 561 6.258160 CGGATGCAAAGTGACTAATTTAAGG 58.742 40.000 0.00 0.00 0.00 2.69
522 562 6.036470 GGATGCAAAGTGACTAATTTAAGGC 58.964 40.000 0.00 0.00 0.00 4.35
523 563 5.041951 TGCAAAGTGACTAATTTAAGGCG 57.958 39.130 0.00 0.00 0.00 5.52
524 564 4.517453 TGCAAAGTGACTAATTTAAGGCGT 59.483 37.500 0.00 0.00 0.00 5.68
525 565 4.851558 GCAAAGTGACTAATTTAAGGCGTG 59.148 41.667 0.00 0.00 0.00 5.34
526 566 5.562113 GCAAAGTGACTAATTTAAGGCGTGT 60.562 40.000 0.00 0.00 0.00 4.49
527 567 5.857822 AAGTGACTAATTTAAGGCGTGTC 57.142 39.130 0.00 0.00 0.00 3.67
528 568 4.890088 AGTGACTAATTTAAGGCGTGTCA 58.110 39.130 0.00 0.00 0.00 3.58
529 569 4.929808 AGTGACTAATTTAAGGCGTGTCAG 59.070 41.667 0.00 0.00 34.32 3.51
530 570 4.092968 GTGACTAATTTAAGGCGTGTCAGG 59.907 45.833 0.00 0.00 34.32 3.86
531 571 4.251268 GACTAATTTAAGGCGTGTCAGGT 58.749 43.478 0.00 0.00 0.00 4.00
532 572 4.251268 ACTAATTTAAGGCGTGTCAGGTC 58.749 43.478 0.00 0.00 0.00 3.85
533 573 2.851263 ATTTAAGGCGTGTCAGGTCA 57.149 45.000 0.00 0.00 0.00 4.02
534 574 2.623878 TTTAAGGCGTGTCAGGTCAA 57.376 45.000 0.00 0.00 0.00 3.18
535 575 2.851263 TTAAGGCGTGTCAGGTCAAT 57.149 45.000 0.00 0.00 0.00 2.57
536 576 3.965379 TTAAGGCGTGTCAGGTCAATA 57.035 42.857 0.00 0.00 0.00 1.90
537 577 2.094762 AAGGCGTGTCAGGTCAATAC 57.905 50.000 0.00 0.00 0.00 1.89
547 587 2.702847 GGTCAATACCCACGGATGC 58.297 57.895 0.00 0.00 40.21 3.91
548 588 0.107410 GGTCAATACCCACGGATGCA 60.107 55.000 0.00 0.00 40.21 3.96
549 589 1.014352 GTCAATACCCACGGATGCAC 58.986 55.000 0.00 0.00 0.00 4.57
550 590 0.107410 TCAATACCCACGGATGCACC 60.107 55.000 0.00 0.00 0.00 5.01
551 591 0.393673 CAATACCCACGGATGCACCA 60.394 55.000 0.00 0.00 38.90 4.17
552 592 0.107214 AATACCCACGGATGCACCAG 60.107 55.000 0.00 0.00 38.90 4.00
553 593 0.980754 ATACCCACGGATGCACCAGA 60.981 55.000 0.00 0.00 38.90 3.86
554 594 1.195442 TACCCACGGATGCACCAGAA 61.195 55.000 0.00 0.00 38.90 3.02
555 595 2.040544 CCCACGGATGCACCAGAAC 61.041 63.158 0.00 0.00 38.90 3.01
556 596 2.390599 CCACGGATGCACCAGAACG 61.391 63.158 0.00 0.00 38.90 3.95
557 597 1.667830 CACGGATGCACCAGAACGT 60.668 57.895 0.00 0.00 38.90 3.99
558 598 1.070786 ACGGATGCACCAGAACGTT 59.929 52.632 0.00 0.00 38.90 3.99
559 599 0.534203 ACGGATGCACCAGAACGTTT 60.534 50.000 0.46 0.00 38.90 3.60
560 600 0.110238 CGGATGCACCAGAACGTTTG 60.110 55.000 0.46 2.87 38.90 2.93
561 601 1.234821 GGATGCACCAGAACGTTTGA 58.765 50.000 0.46 0.00 38.79 2.69
562 602 1.197721 GGATGCACCAGAACGTTTGAG 59.802 52.381 0.46 0.00 38.79 3.02
563 603 1.197721 GATGCACCAGAACGTTTGAGG 59.802 52.381 0.46 7.65 0.00 3.86
564 604 0.817634 TGCACCAGAACGTTTGAGGG 60.818 55.000 0.46 4.61 0.00 4.30
565 605 1.515521 GCACCAGAACGTTTGAGGGG 61.516 60.000 0.46 7.38 0.00 4.79
566 606 0.179029 CACCAGAACGTTTGAGGGGT 60.179 55.000 0.46 3.40 0.00 4.95
567 607 0.108019 ACCAGAACGTTTGAGGGGTC 59.892 55.000 0.46 0.00 0.00 4.46
568 608 0.107831 CCAGAACGTTTGAGGGGTCA 59.892 55.000 0.46 0.00 0.00 4.02
569 609 1.512926 CAGAACGTTTGAGGGGTCAG 58.487 55.000 0.46 0.00 0.00 3.51
570 610 1.070134 CAGAACGTTTGAGGGGTCAGA 59.930 52.381 0.46 0.00 0.00 3.27
571 611 1.978580 AGAACGTTTGAGGGGTCAGAT 59.021 47.619 0.46 0.00 0.00 2.90
572 612 2.372172 AGAACGTTTGAGGGGTCAGATT 59.628 45.455 0.46 0.00 0.00 2.40
573 613 2.951229 ACGTTTGAGGGGTCAGATTT 57.049 45.000 0.00 0.00 0.00 2.17
574 614 2.504367 ACGTTTGAGGGGTCAGATTTG 58.496 47.619 0.00 0.00 0.00 2.32
575 615 1.200020 CGTTTGAGGGGTCAGATTTGC 59.800 52.381 0.00 0.00 0.00 3.68
576 616 2.238521 GTTTGAGGGGTCAGATTTGCA 58.761 47.619 0.00 0.00 0.00 4.08
577 617 2.627699 GTTTGAGGGGTCAGATTTGCAA 59.372 45.455 0.00 0.00 0.00 4.08
578 618 2.673775 TGAGGGGTCAGATTTGCAAA 57.326 45.000 15.44 15.44 0.00 3.68
579 619 2.517959 TGAGGGGTCAGATTTGCAAAG 58.482 47.619 18.19 4.27 0.00 2.77
580 620 2.158475 TGAGGGGTCAGATTTGCAAAGT 60.158 45.455 18.19 4.48 0.00 2.66
581 621 2.489722 GAGGGGTCAGATTTGCAAAGTC 59.510 50.000 18.19 14.17 31.98 3.01
582 622 1.546029 GGGGTCAGATTTGCAAAGTCC 59.454 52.381 18.19 10.71 32.26 3.85
583 623 1.546029 GGGTCAGATTTGCAAAGTCCC 59.454 52.381 18.19 15.54 32.26 4.46
584 624 1.200020 GGTCAGATTTGCAAAGTCCCG 59.800 52.381 18.19 9.31 32.26 5.14
585 625 0.881118 TCAGATTTGCAAAGTCCCGC 59.119 50.000 18.19 2.90 32.26 6.13
586 626 0.883833 CAGATTTGCAAAGTCCCGCT 59.116 50.000 18.19 0.00 32.26 5.52
587 627 0.883833 AGATTTGCAAAGTCCCGCTG 59.116 50.000 18.19 0.00 32.26 5.18
588 628 0.598065 GATTTGCAAAGTCCCGCTGT 59.402 50.000 18.19 0.00 0.00 4.40
589 629 1.810151 GATTTGCAAAGTCCCGCTGTA 59.190 47.619 18.19 0.00 0.00 2.74
590 630 1.234821 TTTGCAAAGTCCCGCTGTAG 58.765 50.000 8.05 0.00 0.00 2.74
591 631 0.394938 TTGCAAAGTCCCGCTGTAGA 59.605 50.000 0.00 0.00 0.00 2.59
592 632 0.613260 TGCAAAGTCCCGCTGTAGAT 59.387 50.000 0.00 0.00 0.00 1.98
596 636 0.461961 AAGTCCCGCTGTAGATGCTC 59.538 55.000 0.00 0.00 0.00 4.26
605 645 5.509840 CCCGCTGTAGATGCTCTAAGTTTAT 60.510 44.000 0.00 0.00 29.58 1.40
606 646 5.986135 CCGCTGTAGATGCTCTAAGTTTATT 59.014 40.000 0.00 0.00 29.58 1.40
608 648 7.815068 CCGCTGTAGATGCTCTAAGTTTATTAT 59.185 37.037 0.00 0.00 29.58 1.28
609 649 9.841880 CGCTGTAGATGCTCTAAGTTTATTATA 57.158 33.333 0.00 0.00 29.58 0.98
638 678 5.251764 AGCAGCACTCAGATAGAAAAATGT 58.748 37.500 0.00 0.00 0.00 2.71
641 681 8.206867 AGCAGCACTCAGATAGAAAAATGTATA 58.793 33.333 0.00 0.00 0.00 1.47
651 691 8.211629 AGATAGAAAAATGTATAGACACCCACC 58.788 37.037 0.00 0.00 38.76 4.61
662 702 1.073923 GACACCCACCTCATTCCAACT 59.926 52.381 0.00 0.00 0.00 3.16
672 712 6.115446 CACCTCATTCCAACTAGCAATTCTA 58.885 40.000 0.00 0.00 0.00 2.10
676 716 7.718753 CCTCATTCCAACTAGCAATTCTATCTT 59.281 37.037 0.00 0.00 0.00 2.40
684 724 7.527084 ACTAGCAATTCTATCTTCAACGAAC 57.473 36.000 0.00 0.00 0.00 3.95
687 727 5.352569 AGCAATTCTATCTTCAACGAACCAG 59.647 40.000 0.00 0.00 0.00 4.00
699 739 3.626028 ACGAACCAGCAAAATCAGAAC 57.374 42.857 0.00 0.00 0.00 3.01
712 752 8.078596 AGCAAAATCAGAACTCAAGTCATTTAC 58.921 33.333 0.00 0.00 0.00 2.01
713 753 7.327032 GCAAAATCAGAACTCAAGTCATTTACC 59.673 37.037 0.00 0.00 0.00 2.85
715 755 8.463930 AAATCAGAACTCAAGTCATTTACCAA 57.536 30.769 0.00 0.00 0.00 3.67
722 762 7.346751 ACTCAAGTCATTTACCAACAACAAT 57.653 32.000 0.00 0.00 0.00 2.71
759 802 7.387673 GCCACTTTTTAAAACATAGGCTGAATT 59.612 33.333 18.42 0.00 36.72 2.17
784 827 7.784633 TGGTTTTGAACTCATTTTGAATTCC 57.215 32.000 2.27 0.00 32.18 3.01
785 828 7.334090 TGGTTTTGAACTCATTTTGAATTCCA 58.666 30.769 2.27 0.00 32.18 3.53
786 829 7.826252 TGGTTTTGAACTCATTTTGAATTCCAA 59.174 29.630 2.27 0.00 32.18 3.53
787 830 8.337532 GGTTTTGAACTCATTTTGAATTCCAAG 58.662 33.333 2.27 0.00 32.18 3.61
788 831 8.882736 GTTTTGAACTCATTTTGAATTCCAAGT 58.117 29.630 2.27 0.00 32.18 3.16
1308 1363 0.604780 TGCTGCTCTGTTCCTCTTGC 60.605 55.000 0.00 0.00 0.00 4.01
1317 1372 1.202758 TGTTCCTCTTGCGTTGGACAT 60.203 47.619 0.00 0.00 0.00 3.06
1324 1379 4.188462 CTCTTGCGTTGGACATATAACCA 58.812 43.478 0.00 0.00 0.00 3.67
1534 1589 1.541368 CTCCCCAAGAAGTCCCCCA 60.541 63.158 0.00 0.00 0.00 4.96
1746 4932 3.700539 GGTAGTCTCTAGTGACCCTTTCC 59.299 52.174 18.86 11.52 37.66 3.13
1767 4956 2.337583 TCAGATTCGTCGAGCAAAAGG 58.662 47.619 0.00 0.00 0.00 3.11
1768 4957 1.394917 CAGATTCGTCGAGCAAAAGGG 59.605 52.381 0.00 0.00 0.00 3.95
1769 4958 1.002087 AGATTCGTCGAGCAAAAGGGT 59.998 47.619 0.00 0.00 0.00 4.34
1819 5014 8.934697 TGGGAAATACTAGTACTAAAGATGCAT 58.065 33.333 4.31 0.00 0.00 3.96
1820 5015 9.425577 GGGAAATACTAGTACTAAAGATGCATC 57.574 37.037 19.37 19.37 0.00 3.91
1822 5017 9.982651 GAAATACTAGTACTAAAGATGCATCCA 57.017 33.333 23.06 7.99 0.00 3.41
1893 5096 0.109597 GGTCTTGTGAATGCTTGCCG 60.110 55.000 0.00 0.00 0.00 5.69
1962 5167 9.912634 TTCCATTTGTATGAAATTTCTGTCTTC 57.087 29.630 18.64 5.02 33.37 2.87
1992 5197 5.829924 TCTGAAAATTCTCCTTGCTCTTTGT 59.170 36.000 0.00 0.00 0.00 2.83
1995 5200 6.322201 TGAAAATTCTCCTTGCTCTTTGTTCT 59.678 34.615 0.00 0.00 0.00 3.01
1997 5202 4.422073 TTCTCCTTGCTCTTTGTTCTCA 57.578 40.909 0.00 0.00 0.00 3.27
1998 5203 4.630644 TCTCCTTGCTCTTTGTTCTCAT 57.369 40.909 0.00 0.00 0.00 2.90
1999 5204 4.978099 TCTCCTTGCTCTTTGTTCTCATT 58.022 39.130 0.00 0.00 0.00 2.57
2003 5255 5.240183 TCCTTGCTCTTTGTTCTCATTTCAG 59.760 40.000 0.00 0.00 0.00 3.02
2004 5257 5.443185 TTGCTCTTTGTTCTCATTTCAGG 57.557 39.130 0.00 0.00 0.00 3.86
2012 5265 5.319140 TGTTCTCATTTCAGGCAATCATG 57.681 39.130 0.00 0.00 0.00 3.07
2015 5268 5.571784 TCTCATTTCAGGCAATCATGTTC 57.428 39.130 0.00 0.00 0.00 3.18
2018 5271 4.158949 TCATTTCAGGCAATCATGTTCCAG 59.841 41.667 0.00 0.00 0.00 3.86
2024 5277 3.084039 GGCAATCATGTTCCAGTCAAGA 58.916 45.455 0.00 0.00 0.00 3.02
2031 5284 1.271543 TGTTCCAGTCAAGATGCAGGG 60.272 52.381 0.00 0.00 0.00 4.45
2198 5459 5.835113 TGGCAAATTATAGCTTGACCTTC 57.165 39.130 0.00 0.00 28.73 3.46
2209 5470 2.413453 GCTTGACCTTCGTAGCTCAAAG 59.587 50.000 0.00 0.00 0.00 2.77
2218 5479 6.100004 CCTTCGTAGCTCAAAGTATTCTTGA 58.900 40.000 0.00 0.00 33.79 3.02
2221 5482 6.100004 TCGTAGCTCAAAGTATTCTTGAAGG 58.900 40.000 0.00 0.00 33.79 3.46
2240 5501 5.904802 GAAGGCAATTTAAGCTTTCAAACG 58.095 37.500 3.20 0.00 44.53 3.60
2296 5590 8.415950 ACACATGTTATTTTGGATTCACCTAA 57.584 30.769 0.00 0.00 39.86 2.69
2335 5632 3.459598 TGCTAGGAGGGCAGATTAAACAT 59.540 43.478 0.00 0.00 34.56 2.71
2379 5699 1.621107 GCATCACTGTTTGCATTCGG 58.379 50.000 7.42 0.00 38.72 4.30
2382 5702 3.641648 CATCACTGTTTGCATTCGGTTT 58.358 40.909 0.00 0.00 0.00 3.27
2491 5821 6.087456 TGAGGGATTATTTAGAGCTGGAGAT 58.913 40.000 0.00 0.00 0.00 2.75
2513 5864 9.255304 GAGATGTATCATTAGAACCTTCTGAAC 57.745 37.037 0.00 0.00 38.19 3.18
2599 5952 5.468072 AGACAGCAAATTCTACACAGTTCAG 59.532 40.000 0.00 0.00 0.00 3.02
2610 5963 0.326264 ACAGTTCAGATCCTGGGCAC 59.674 55.000 0.00 0.00 32.90 5.01
2612 5965 1.004044 CAGTTCAGATCCTGGGCACTT 59.996 52.381 0.00 0.00 31.51 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 134 2.726351 CGCTCCTCCTCCAACTCCC 61.726 68.421 0.00 0.00 0.00 4.30
148 158 3.237741 CCTCCTCCGGCTCATCCC 61.238 72.222 0.00 0.00 0.00 3.85
200 238 4.501285 ATGGCATGCTGCTCCGCT 62.501 61.111 18.92 0.00 44.28 5.52
299 338 2.261671 GCGAACTTCTCCGCCTCA 59.738 61.111 0.00 0.00 45.06 3.86
310 349 2.388735 TCTCATCCATGTAGGCGAACT 58.611 47.619 0.00 0.00 37.29 3.01
330 369 0.399091 TCATCCTCCCCTTGCTCGAT 60.399 55.000 0.00 0.00 0.00 3.59
340 379 1.454663 GGCTTTGGCTCATCCTCCC 60.455 63.158 0.00 0.00 38.73 4.30
391 431 0.108329 ATGTTCACGACGATGGGGTC 60.108 55.000 0.00 0.00 0.00 4.46
392 432 0.108329 GATGTTCACGACGATGGGGT 60.108 55.000 0.00 0.00 0.00 4.95
393 433 0.175760 AGATGTTCACGACGATGGGG 59.824 55.000 0.00 0.00 0.00 4.96
394 434 1.560923 GAGATGTTCACGACGATGGG 58.439 55.000 0.00 0.00 0.00 4.00
395 435 1.560923 GGAGATGTTCACGACGATGG 58.439 55.000 0.00 0.00 0.00 3.51
396 436 1.191944 CGGAGATGTTCACGACGATG 58.808 55.000 0.00 0.00 0.00 3.84
397 437 1.092348 TCGGAGATGTTCACGACGAT 58.908 50.000 0.00 0.00 0.00 3.73
398 438 1.092348 ATCGGAGATGTTCACGACGA 58.908 50.000 0.00 0.00 45.12 4.20
399 439 1.191944 CATCGGAGATGTTCACGACG 58.808 55.000 0.00 0.00 45.12 5.12
400 440 2.186076 GTCATCGGAGATGTTCACGAC 58.814 52.381 9.50 0.00 45.12 4.34
401 441 1.202143 CGTCATCGGAGATGTTCACGA 60.202 52.381 13.76 0.00 45.12 4.35
402 442 1.191944 CGTCATCGGAGATGTTCACG 58.808 55.000 9.50 8.59 45.12 4.35
403 443 2.561733 TCGTCATCGGAGATGTTCAC 57.438 50.000 9.50 1.21 45.12 3.18
404 444 2.752903 TCTTCGTCATCGGAGATGTTCA 59.247 45.455 9.50 0.00 45.42 3.18
405 445 3.422417 TCTTCGTCATCGGAGATGTTC 57.578 47.619 9.50 4.57 45.42 3.18
411 451 1.944024 AGCTACTCTTCGTCATCGGAG 59.056 52.381 0.00 0.00 43.44 4.63
412 452 2.039818 AGCTACTCTTCGTCATCGGA 57.960 50.000 0.00 0.00 37.69 4.55
413 453 2.224549 CCTAGCTACTCTTCGTCATCGG 59.775 54.545 0.00 0.00 37.69 4.18
414 454 2.224549 CCCTAGCTACTCTTCGTCATCG 59.775 54.545 0.00 0.00 38.55 3.84
415 455 3.215975 ACCCTAGCTACTCTTCGTCATC 58.784 50.000 0.00 0.00 0.00 2.92
416 456 3.300239 ACCCTAGCTACTCTTCGTCAT 57.700 47.619 0.00 0.00 0.00 3.06
417 457 2.803030 ACCCTAGCTACTCTTCGTCA 57.197 50.000 0.00 0.00 0.00 4.35
418 458 5.107143 CGTAATACCCTAGCTACTCTTCGTC 60.107 48.000 0.00 0.00 0.00 4.20
419 459 4.754114 CGTAATACCCTAGCTACTCTTCGT 59.246 45.833 0.00 0.00 0.00 3.85
420 460 4.754114 ACGTAATACCCTAGCTACTCTTCG 59.246 45.833 0.00 0.00 0.00 3.79
421 461 7.605691 TCATACGTAATACCCTAGCTACTCTTC 59.394 40.741 0.00 0.00 0.00 2.87
422 462 7.456725 TCATACGTAATACCCTAGCTACTCTT 58.543 38.462 0.00 0.00 0.00 2.85
423 463 7.013823 TCATACGTAATACCCTAGCTACTCT 57.986 40.000 0.00 0.00 0.00 3.24
424 464 7.862512 ATCATACGTAATACCCTAGCTACTC 57.137 40.000 0.00 0.00 0.00 2.59
425 465 7.338957 GGAATCATACGTAATACCCTAGCTACT 59.661 40.741 0.00 0.00 0.00 2.57
426 466 7.338957 AGGAATCATACGTAATACCCTAGCTAC 59.661 40.741 0.00 0.00 0.00 3.58
427 467 7.408543 AGGAATCATACGTAATACCCTAGCTA 58.591 38.462 0.00 0.00 0.00 3.32
428 468 6.254522 AGGAATCATACGTAATACCCTAGCT 58.745 40.000 0.00 0.00 0.00 3.32
429 469 6.527057 AGGAATCATACGTAATACCCTAGC 57.473 41.667 0.00 0.00 0.00 3.42
430 470 9.204570 CAAAAGGAATCATACGTAATACCCTAG 57.795 37.037 0.00 0.00 0.00 3.02
431 471 7.658575 GCAAAAGGAATCATACGTAATACCCTA 59.341 37.037 0.00 0.00 0.00 3.53
432 472 6.485648 GCAAAAGGAATCATACGTAATACCCT 59.514 38.462 0.00 0.22 0.00 4.34
433 473 6.261381 TGCAAAAGGAATCATACGTAATACCC 59.739 38.462 0.00 0.00 0.00 3.69
434 474 7.254227 TGCAAAAGGAATCATACGTAATACC 57.746 36.000 0.00 0.00 0.00 2.73
435 475 7.323656 GCATGCAAAAGGAATCATACGTAATAC 59.676 37.037 14.21 0.00 0.00 1.89
436 476 7.228507 AGCATGCAAAAGGAATCATACGTAATA 59.771 33.333 21.98 0.00 0.00 0.98
437 477 6.039717 AGCATGCAAAAGGAATCATACGTAAT 59.960 34.615 21.98 0.00 0.00 1.89
438 478 5.356751 AGCATGCAAAAGGAATCATACGTAA 59.643 36.000 21.98 0.00 0.00 3.18
439 479 4.881273 AGCATGCAAAAGGAATCATACGTA 59.119 37.500 21.98 0.00 0.00 3.57
440 480 3.696051 AGCATGCAAAAGGAATCATACGT 59.304 39.130 21.98 0.00 0.00 3.57
441 481 4.297299 AGCATGCAAAAGGAATCATACG 57.703 40.909 21.98 0.00 0.00 3.06
442 482 5.870978 ACAAAGCATGCAAAAGGAATCATAC 59.129 36.000 21.98 0.00 0.00 2.39
443 483 6.040209 ACAAAGCATGCAAAAGGAATCATA 57.960 33.333 21.98 0.00 0.00 2.15
444 484 4.901868 ACAAAGCATGCAAAAGGAATCAT 58.098 34.783 21.98 0.00 0.00 2.45
445 485 4.339872 ACAAAGCATGCAAAAGGAATCA 57.660 36.364 21.98 0.00 0.00 2.57
446 486 5.292589 CCATACAAAGCATGCAAAAGGAATC 59.707 40.000 21.98 0.00 0.00 2.52
447 487 5.046448 TCCATACAAAGCATGCAAAAGGAAT 60.046 36.000 21.98 1.32 0.00 3.01
448 488 4.282957 TCCATACAAAGCATGCAAAAGGAA 59.717 37.500 21.98 0.00 0.00 3.36
449 489 3.831333 TCCATACAAAGCATGCAAAAGGA 59.169 39.130 21.98 13.92 0.00 3.36
450 490 4.191033 TCCATACAAAGCATGCAAAAGG 57.809 40.909 21.98 11.81 0.00 3.11
451 491 6.730960 AAATCCATACAAAGCATGCAAAAG 57.269 33.333 21.98 9.13 0.00 2.27
452 492 6.817641 CCTAAATCCATACAAAGCATGCAAAA 59.182 34.615 21.98 0.20 0.00 2.44
453 493 6.154192 TCCTAAATCCATACAAAGCATGCAAA 59.846 34.615 21.98 0.00 0.00 3.68
454 494 5.655974 TCCTAAATCCATACAAAGCATGCAA 59.344 36.000 21.98 0.00 0.00 4.08
455 495 5.199723 TCCTAAATCCATACAAAGCATGCA 58.800 37.500 21.98 0.00 0.00 3.96
456 496 5.772825 TCCTAAATCCATACAAAGCATGC 57.227 39.130 10.51 10.51 0.00 4.06
457 497 8.415553 TCATTTCCTAAATCCATACAAAGCATG 58.584 33.333 0.00 0.00 0.00 4.06
458 498 8.537728 TCATTTCCTAAATCCATACAAAGCAT 57.462 30.769 0.00 0.00 0.00 3.79
459 499 7.953005 TCATTTCCTAAATCCATACAAAGCA 57.047 32.000 0.00 0.00 0.00 3.91
460 500 9.822185 ATTTCATTTCCTAAATCCATACAAAGC 57.178 29.630 0.00 0.00 0.00 3.51
472 512 8.830580 CGCTTCTCTCATATTTCATTTCCTAAA 58.169 33.333 0.00 0.00 0.00 1.85
473 513 7.442364 CCGCTTCTCTCATATTTCATTTCCTAA 59.558 37.037 0.00 0.00 0.00 2.69
474 514 6.931281 CCGCTTCTCTCATATTTCATTTCCTA 59.069 38.462 0.00 0.00 0.00 2.94
475 515 5.762218 CCGCTTCTCTCATATTTCATTTCCT 59.238 40.000 0.00 0.00 0.00 3.36
476 516 5.760253 TCCGCTTCTCTCATATTTCATTTCC 59.240 40.000 0.00 0.00 0.00 3.13
477 517 6.851222 TCCGCTTCTCTCATATTTCATTTC 57.149 37.500 0.00 0.00 0.00 2.17
478 518 6.293845 GCATCCGCTTCTCTCATATTTCATTT 60.294 38.462 0.00 0.00 34.30 2.32
479 519 5.180868 GCATCCGCTTCTCTCATATTTCATT 59.819 40.000 0.00 0.00 34.30 2.57
480 520 4.694509 GCATCCGCTTCTCTCATATTTCAT 59.305 41.667 0.00 0.00 34.30 2.57
481 521 4.060900 GCATCCGCTTCTCTCATATTTCA 58.939 43.478 0.00 0.00 34.30 2.69
482 522 4.060900 TGCATCCGCTTCTCTCATATTTC 58.939 43.478 0.00 0.00 39.64 2.17
483 523 4.077300 TGCATCCGCTTCTCTCATATTT 57.923 40.909 0.00 0.00 39.64 1.40
484 524 3.758755 TGCATCCGCTTCTCTCATATT 57.241 42.857 0.00 0.00 39.64 1.28
485 525 3.758755 TTGCATCCGCTTCTCTCATAT 57.241 42.857 0.00 0.00 39.64 1.78
486 526 3.118629 ACTTTGCATCCGCTTCTCTCATA 60.119 43.478 0.00 0.00 39.64 2.15
487 527 2.286872 CTTTGCATCCGCTTCTCTCAT 58.713 47.619 0.00 0.00 39.64 2.90
488 528 1.002430 ACTTTGCATCCGCTTCTCTCA 59.998 47.619 0.00 0.00 39.64 3.27
489 529 1.396301 CACTTTGCATCCGCTTCTCTC 59.604 52.381 0.00 0.00 39.64 3.20
490 530 1.002430 TCACTTTGCATCCGCTTCTCT 59.998 47.619 0.00 0.00 39.64 3.10
491 531 1.129437 GTCACTTTGCATCCGCTTCTC 59.871 52.381 0.00 0.00 39.64 2.87
492 532 1.160137 GTCACTTTGCATCCGCTTCT 58.840 50.000 0.00 0.00 39.64 2.85
493 533 1.160137 AGTCACTTTGCATCCGCTTC 58.840 50.000 0.00 0.00 39.64 3.86
494 534 2.472695 TAGTCACTTTGCATCCGCTT 57.527 45.000 0.00 0.00 39.64 4.68
495 535 2.472695 TTAGTCACTTTGCATCCGCT 57.527 45.000 0.00 0.00 39.64 5.52
496 536 3.764885 AATTAGTCACTTTGCATCCGC 57.235 42.857 0.00 0.00 39.24 5.54
497 537 6.258160 CCTTAAATTAGTCACTTTGCATCCG 58.742 40.000 0.00 0.00 0.00 4.18
498 538 6.036470 GCCTTAAATTAGTCACTTTGCATCC 58.964 40.000 0.00 0.00 0.00 3.51
499 539 5.739161 CGCCTTAAATTAGTCACTTTGCATC 59.261 40.000 0.00 0.00 0.00 3.91
500 540 5.183140 ACGCCTTAAATTAGTCACTTTGCAT 59.817 36.000 0.00 0.00 0.00 3.96
501 541 4.517453 ACGCCTTAAATTAGTCACTTTGCA 59.483 37.500 0.00 0.00 0.00 4.08
502 542 4.851558 CACGCCTTAAATTAGTCACTTTGC 59.148 41.667 0.00 0.00 0.00 3.68
503 543 5.997385 ACACGCCTTAAATTAGTCACTTTG 58.003 37.500 0.00 0.00 0.00 2.77
504 544 5.761234 TGACACGCCTTAAATTAGTCACTTT 59.239 36.000 0.00 0.00 30.43 2.66
505 545 5.302360 TGACACGCCTTAAATTAGTCACTT 58.698 37.500 0.00 0.00 30.43 3.16
506 546 4.890088 TGACACGCCTTAAATTAGTCACT 58.110 39.130 0.00 0.00 30.43 3.41
507 547 4.092968 CCTGACACGCCTTAAATTAGTCAC 59.907 45.833 0.00 0.00 31.93 3.67
508 548 4.250464 CCTGACACGCCTTAAATTAGTCA 58.750 43.478 0.00 0.00 33.92 3.41
509 549 4.251268 ACCTGACACGCCTTAAATTAGTC 58.749 43.478 0.00 0.00 0.00 2.59
510 550 4.251268 GACCTGACACGCCTTAAATTAGT 58.749 43.478 0.00 0.00 0.00 2.24
511 551 4.250464 TGACCTGACACGCCTTAAATTAG 58.750 43.478 0.00 0.00 0.00 1.73
512 552 4.274602 TGACCTGACACGCCTTAAATTA 57.725 40.909 0.00 0.00 0.00 1.40
513 553 3.134574 TGACCTGACACGCCTTAAATT 57.865 42.857 0.00 0.00 0.00 1.82
514 554 2.851263 TGACCTGACACGCCTTAAAT 57.149 45.000 0.00 0.00 0.00 1.40
515 555 2.623878 TTGACCTGACACGCCTTAAA 57.376 45.000 0.00 0.00 0.00 1.52
516 556 2.851263 ATTGACCTGACACGCCTTAA 57.149 45.000 0.00 0.00 0.00 1.85
517 557 2.093869 GGTATTGACCTGACACGCCTTA 60.094 50.000 0.00 0.00 43.16 2.69
518 558 1.338769 GGTATTGACCTGACACGCCTT 60.339 52.381 0.00 0.00 43.16 4.35
519 559 0.249398 GGTATTGACCTGACACGCCT 59.751 55.000 0.00 0.00 43.16 5.52
520 560 0.743345 GGGTATTGACCTGACACGCC 60.743 60.000 0.00 0.00 46.09 5.68
521 561 0.036765 TGGGTATTGACCTGACACGC 60.037 55.000 0.00 0.00 46.09 5.34
522 562 1.722011 GTGGGTATTGACCTGACACG 58.278 55.000 0.00 0.00 46.09 4.49
523 563 1.674817 CCGTGGGTATTGACCTGACAC 60.675 57.143 0.00 0.00 46.09 3.67
524 564 0.611200 CCGTGGGTATTGACCTGACA 59.389 55.000 0.00 0.00 46.09 3.58
525 565 0.899720 TCCGTGGGTATTGACCTGAC 59.100 55.000 0.00 0.00 46.09 3.51
526 566 1.484653 CATCCGTGGGTATTGACCTGA 59.515 52.381 0.00 0.00 46.09 3.86
527 567 1.953559 CATCCGTGGGTATTGACCTG 58.046 55.000 0.00 0.00 46.09 4.00
528 568 0.180406 GCATCCGTGGGTATTGACCT 59.820 55.000 0.00 0.00 46.09 3.85
529 569 0.107410 TGCATCCGTGGGTATTGACC 60.107 55.000 0.00 0.00 46.13 4.02
530 570 1.014352 GTGCATCCGTGGGTATTGAC 58.986 55.000 0.00 0.00 0.00 3.18
531 571 0.107410 GGTGCATCCGTGGGTATTGA 60.107 55.000 0.00 0.00 0.00 2.57
532 572 0.393673 TGGTGCATCCGTGGGTATTG 60.394 55.000 0.00 0.00 39.52 1.90
533 573 0.107214 CTGGTGCATCCGTGGGTATT 60.107 55.000 0.00 0.00 39.52 1.89
534 574 0.980754 TCTGGTGCATCCGTGGGTAT 60.981 55.000 0.00 0.00 39.52 2.73
535 575 1.195442 TTCTGGTGCATCCGTGGGTA 61.195 55.000 0.00 0.00 39.52 3.69
536 576 2.525124 TTCTGGTGCATCCGTGGGT 61.525 57.895 0.00 0.00 39.52 4.51
537 577 2.040544 GTTCTGGTGCATCCGTGGG 61.041 63.158 0.00 0.00 39.52 4.61
538 578 2.390599 CGTTCTGGTGCATCCGTGG 61.391 63.158 0.00 0.00 39.52 4.94
539 579 1.227999 AACGTTCTGGTGCATCCGTG 61.228 55.000 0.00 0.00 39.52 4.94
540 580 0.534203 AAACGTTCTGGTGCATCCGT 60.534 50.000 0.00 0.00 39.52 4.69
541 581 0.110238 CAAACGTTCTGGTGCATCCG 60.110 55.000 0.00 0.00 39.52 4.18
542 582 1.197721 CTCAAACGTTCTGGTGCATCC 59.802 52.381 0.00 0.00 0.00 3.51
543 583 1.197721 CCTCAAACGTTCTGGTGCATC 59.802 52.381 0.00 0.00 0.00 3.91
544 584 1.238439 CCTCAAACGTTCTGGTGCAT 58.762 50.000 0.00 0.00 0.00 3.96
545 585 0.817634 CCCTCAAACGTTCTGGTGCA 60.818 55.000 0.00 0.00 0.00 4.57
546 586 1.515521 CCCCTCAAACGTTCTGGTGC 61.516 60.000 0.00 0.00 0.00 5.01
547 587 0.179029 ACCCCTCAAACGTTCTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
548 588 0.108019 GACCCCTCAAACGTTCTGGT 59.892 55.000 0.00 4.03 0.00 4.00
549 589 0.107831 TGACCCCTCAAACGTTCTGG 59.892 55.000 0.00 4.20 0.00 3.86
550 590 1.070134 TCTGACCCCTCAAACGTTCTG 59.930 52.381 0.00 2.62 0.00 3.02
551 591 1.420430 TCTGACCCCTCAAACGTTCT 58.580 50.000 0.00 0.00 0.00 3.01
552 592 2.474410 ATCTGACCCCTCAAACGTTC 57.526 50.000 0.00 0.00 0.00 3.95
553 593 2.884639 CAAATCTGACCCCTCAAACGTT 59.115 45.455 0.00 0.00 0.00 3.99
554 594 2.504367 CAAATCTGACCCCTCAAACGT 58.496 47.619 0.00 0.00 0.00 3.99
555 595 1.200020 GCAAATCTGACCCCTCAAACG 59.800 52.381 0.00 0.00 0.00 3.60
556 596 2.238521 TGCAAATCTGACCCCTCAAAC 58.761 47.619 0.00 0.00 0.00 2.93
557 597 2.673775 TGCAAATCTGACCCCTCAAA 57.326 45.000 0.00 0.00 0.00 2.69
558 598 2.673775 TTGCAAATCTGACCCCTCAA 57.326 45.000 0.00 0.00 0.00 3.02
559 599 2.158475 ACTTTGCAAATCTGACCCCTCA 60.158 45.455 13.23 0.00 0.00 3.86
560 600 2.489722 GACTTTGCAAATCTGACCCCTC 59.510 50.000 13.23 0.00 0.00 4.30
561 601 2.519013 GACTTTGCAAATCTGACCCCT 58.481 47.619 13.23 0.00 0.00 4.79
562 602 1.546029 GGACTTTGCAAATCTGACCCC 59.454 52.381 13.23 3.04 0.00 4.95
563 603 1.546029 GGGACTTTGCAAATCTGACCC 59.454 52.381 13.23 15.72 0.00 4.46
564 604 1.200020 CGGGACTTTGCAAATCTGACC 59.800 52.381 13.23 10.69 0.00 4.02
565 605 1.401539 GCGGGACTTTGCAAATCTGAC 60.402 52.381 13.23 1.65 0.00 3.51
566 606 0.881118 GCGGGACTTTGCAAATCTGA 59.119 50.000 13.23 0.00 0.00 3.27
567 607 0.883833 AGCGGGACTTTGCAAATCTG 59.116 50.000 13.23 11.28 0.00 2.90
568 608 0.883833 CAGCGGGACTTTGCAAATCT 59.116 50.000 13.23 0.29 0.00 2.40
569 609 0.598065 ACAGCGGGACTTTGCAAATC 59.402 50.000 13.23 11.89 0.00 2.17
570 610 1.812571 CTACAGCGGGACTTTGCAAAT 59.187 47.619 13.23 3.03 0.00 2.32
571 611 1.202710 TCTACAGCGGGACTTTGCAAA 60.203 47.619 12.14 12.14 0.00 3.68
572 612 0.394938 TCTACAGCGGGACTTTGCAA 59.605 50.000 0.00 0.00 0.00 4.08
573 613 0.613260 ATCTACAGCGGGACTTTGCA 59.387 50.000 0.00 0.00 0.00 4.08
574 614 1.009829 CATCTACAGCGGGACTTTGC 58.990 55.000 0.00 0.00 0.00 3.68
575 615 1.009829 GCATCTACAGCGGGACTTTG 58.990 55.000 0.00 0.00 0.00 2.77
576 616 0.905357 AGCATCTACAGCGGGACTTT 59.095 50.000 0.00 0.00 37.01 2.66
577 617 0.461961 GAGCATCTACAGCGGGACTT 59.538 55.000 0.00 0.00 37.01 3.01
578 618 2.119886 GAGCATCTACAGCGGGACT 58.880 57.895 0.00 0.00 37.01 3.85
579 619 4.740235 GAGCATCTACAGCGGGAC 57.260 61.111 0.00 0.00 37.01 4.46
609 649 9.618890 TTTTTCTATCTGAGTGCTGCTATAAAT 57.381 29.630 0.00 0.00 0.00 1.40
611 651 9.049523 CATTTTTCTATCTGAGTGCTGCTATAA 57.950 33.333 0.00 0.00 0.00 0.98
626 666 8.211629 AGGTGGGTGTCTATACATTTTTCTATC 58.788 37.037 0.00 0.00 38.08 2.08
631 671 6.134535 TGAGGTGGGTGTCTATACATTTTT 57.865 37.500 0.00 0.00 38.08 1.94
638 678 4.002256 TGGAATGAGGTGGGTGTCTATA 57.998 45.455 0.00 0.00 0.00 1.31
641 681 1.073923 GTTGGAATGAGGTGGGTGTCT 59.926 52.381 0.00 0.00 0.00 3.41
651 691 8.674263 AAGATAGAATTGCTAGTTGGAATGAG 57.326 34.615 0.00 0.00 36.81 2.90
662 702 6.403049 TGGTTCGTTGAAGATAGAATTGCTA 58.597 36.000 0.00 0.00 0.00 3.49
672 712 4.278170 TGATTTTGCTGGTTCGTTGAAGAT 59.722 37.500 0.00 0.00 0.00 2.40
676 716 3.210227 TCTGATTTTGCTGGTTCGTTGA 58.790 40.909 0.00 0.00 0.00 3.18
684 724 4.276678 TGACTTGAGTTCTGATTTTGCTGG 59.723 41.667 0.00 0.00 0.00 4.85
687 727 7.327032 GGTAAATGACTTGAGTTCTGATTTTGC 59.673 37.037 0.00 0.00 0.00 3.68
699 739 9.912634 ATTATTGTTGTTGGTAAATGACTTGAG 57.087 29.630 0.00 0.00 0.00 3.02
712 752 7.818930 AGTGGCTTGAATTATTATTGTTGTTGG 59.181 33.333 0.00 0.00 0.00 3.77
713 753 8.761575 AGTGGCTTGAATTATTATTGTTGTTG 57.238 30.769 0.00 0.00 0.00 3.33
715 755 9.777297 AAAAGTGGCTTGAATTATTATTGTTGT 57.223 25.926 0.00 0.00 0.00 3.32
754 797 8.783833 TCAAAATGAGTTCAAAACCAAATTCA 57.216 26.923 0.00 0.00 0.00 2.57
759 802 7.826252 TGGAATTCAAAATGAGTTCAAAACCAA 59.174 29.630 14.78 0.00 42.62 3.67
785 828 9.044290 AGATTTGCATCGTCCAGGATACTACTT 62.044 40.741 0.00 0.00 38.87 2.24
786 829 7.646583 AGATTTGCATCGTCCAGGATACTACT 61.647 42.308 0.00 0.00 38.87 2.57
787 830 5.509840 AGATTTGCATCGTCCAGGATACTAC 60.510 44.000 0.00 0.00 38.87 2.73
788 831 4.588951 AGATTTGCATCGTCCAGGATACTA 59.411 41.667 0.00 0.00 38.87 1.82
789 832 3.389329 AGATTTGCATCGTCCAGGATACT 59.611 43.478 0.00 0.00 40.83 2.12
865 909 1.342819 CGTTGGATCTGAGGGGAGATC 59.657 57.143 0.00 0.00 45.35 2.75
1308 1363 4.573201 ACGGAATTGGTTATATGTCCAACG 59.427 41.667 13.20 13.90 44.80 4.10
1324 1379 5.782893 TCATTTCAACCAAGAACGGAATT 57.217 34.783 0.00 0.00 0.00 2.17
1554 1707 1.338769 GCCTTCTTCTTGGGCGACTTA 60.339 52.381 0.00 0.00 36.37 2.24
1746 4932 2.346847 CCTTTTGCTCGACGAATCTGAG 59.653 50.000 0.00 0.00 0.00 3.35
1767 4956 3.498774 ATCAGAGATACAATGCCCACC 57.501 47.619 0.00 0.00 0.00 4.61
1768 4957 5.008415 CAGAAATCAGAGATACAATGCCCAC 59.992 44.000 0.00 0.00 0.00 4.61
1769 4958 5.128205 CAGAAATCAGAGATACAATGCCCA 58.872 41.667 0.00 0.00 0.00 5.36
1842 5043 6.780031 AGACAGCCATAGACATATAGAACAGT 59.220 38.462 0.00 0.00 0.00 3.55
1843 5044 7.089538 CAGACAGCCATAGACATATAGAACAG 58.910 42.308 0.00 0.00 0.00 3.16
1854 5055 2.357009 CCAATTGCAGACAGCCATAGAC 59.643 50.000 0.00 0.00 44.83 2.59
1954 5159 9.814899 GAGAATTTTCAGATGATAGAAGACAGA 57.185 33.333 0.00 0.00 0.00 3.41
1957 5162 9.612066 AAGGAGAATTTTCAGATGATAGAAGAC 57.388 33.333 0.00 0.00 0.00 3.01
1962 5167 7.716123 AGAGCAAGGAGAATTTTCAGATGATAG 59.284 37.037 0.00 0.00 0.00 2.08
1979 5184 5.132502 TGAAATGAGAACAAAGAGCAAGGA 58.867 37.500 0.00 0.00 0.00 3.36
1992 5197 5.105635 GGAACATGATTGCCTGAAATGAGAA 60.106 40.000 0.00 0.00 0.00 2.87
1995 5200 4.087907 TGGAACATGATTGCCTGAAATGA 58.912 39.130 0.00 0.00 0.00 2.57
1997 5202 4.091549 ACTGGAACATGATTGCCTGAAAT 58.908 39.130 0.00 0.00 38.20 2.17
1998 5203 3.499338 ACTGGAACATGATTGCCTGAAA 58.501 40.909 0.00 0.00 38.20 2.69
1999 5204 3.084039 GACTGGAACATGATTGCCTGAA 58.916 45.455 0.00 0.00 38.20 3.02
2003 5255 3.084039 TCTTGACTGGAACATGATTGCC 58.916 45.455 0.00 0.00 38.20 4.52
2004 5257 4.669318 CATCTTGACTGGAACATGATTGC 58.331 43.478 0.00 0.00 38.20 3.56
2012 5265 1.003580 TCCCTGCATCTTGACTGGAAC 59.996 52.381 0.00 0.00 0.00 3.62
2015 5268 1.004044 AGTTCCCTGCATCTTGACTGG 59.996 52.381 0.00 0.00 0.00 4.00
2018 5271 2.479566 TCAGTTCCCTGCATCTTGAC 57.520 50.000 0.00 0.00 38.66 3.18
2024 5277 4.038271 TCAAAGAATCAGTTCCCTGCAT 57.962 40.909 0.00 0.00 38.66 3.96
2031 5284 6.304208 GCGTGATTTCTTCAAAGAATCAGTTC 59.696 38.462 6.05 1.30 43.92 3.01
2055 5309 4.382147 GGAGGATTATAGGAATCGTCAGGC 60.382 50.000 17.12 2.42 41.04 4.85
2198 5459 5.220491 GCCTTCAAGAATACTTTGAGCTACG 60.220 44.000 0.00 0.00 33.70 3.51
2209 5470 8.763049 AAAGCTTAAATTGCCTTCAAGAATAC 57.237 30.769 0.00 0.00 35.37 1.89
2218 5479 5.356426 ACGTTTGAAAGCTTAAATTGCCTT 58.644 33.333 0.00 0.00 0.00 4.35
2221 5482 5.397240 ACGTACGTTTGAAAGCTTAAATTGC 59.603 36.000 16.72 0.00 0.00 3.56
2240 5501 7.389479 GCTTAGTTTAGTTTGCATCTACGTAC 58.611 38.462 0.00 0.00 0.00 3.67
2296 5590 7.246171 TCCTAGCATCTGTTTCTACTTTCTT 57.754 36.000 0.00 0.00 0.00 2.52
2335 5632 7.466725 GCCTGTTATTGCACGTTTAATCATCTA 60.467 37.037 0.00 0.00 0.00 1.98
2369 5689 4.130286 AGAAAACCAAACCGAATGCAAA 57.870 36.364 0.00 0.00 0.00 3.68
2370 5690 3.810310 AGAAAACCAAACCGAATGCAA 57.190 38.095 0.00 0.00 0.00 4.08
2371 5691 3.810310 AAGAAAACCAAACCGAATGCA 57.190 38.095 0.00 0.00 0.00 3.96
2379 5699 8.547967 AAAAAGAGGAAGAAAGAAAACCAAAC 57.452 30.769 0.00 0.00 0.00 2.93
2491 5821 6.931838 ACGTTCAGAAGGTTCTAATGATACA 58.068 36.000 2.49 0.00 35.34 2.29
2513 5864 5.712217 TGAGTTATTTCGCTGGAATTACG 57.288 39.130 0.00 0.00 30.88 3.18
2551 5902 3.696051 TGGCTCAGGATGCATAAAGTTTC 59.304 43.478 0.00 0.00 34.76 2.78
2599 5952 2.092323 GTTACCAAAGTGCCCAGGATC 58.908 52.381 0.00 0.00 0.00 3.36
2610 5963 3.386402 ACCCCATTGTGTTGTTACCAAAG 59.614 43.478 0.00 0.00 30.94 2.77
2612 5965 2.695666 CACCCCATTGTGTTGTTACCAA 59.304 45.455 0.00 0.00 0.00 3.67
2751 6125 1.887242 GTGCGTGCTCACAGGTTCA 60.887 57.895 0.69 0.00 36.97 3.18


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

AutoCloner maintained by Alex Coulton.