Multiple sequence alignment - TraesCS7D01G186500

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 TraesCS7D01G186500 chr7D 100.000 3794 0 0 1 3794 139095071 139091278 0.000000e+00 7007.0
1 TraesCS7D01G186500 chr7B 96.213 2878 84 7 920 3794 104476962 104474107 0.000000e+00 4687.0
2 TraesCS7D01G186500 chr7B 93.884 2011 97 14 1789 3794 104308128 104306139 0.000000e+00 3009.0
3 TraesCS7D01G186500 chr7B 92.490 719 41 3 1038 1749 104308849 104308137 0.000000e+00 1016.0
4 TraesCS7D01G186500 chr7B 90.112 445 34 10 9 449 104477828 104477390 1.530000e-158 569.0
5 TraesCS7D01G186500 chr7B 91.606 274 20 3 1 272 104309156 104308884 3.580000e-100 375.0
6 TraesCS7D01G186500 chr7A 95.806 2456 74 7 907 3358 139128325 139125895 0.000000e+00 3938.0
7 TraesCS7D01G186500 chr7A 85.463 454 37 12 1 449 139132016 139131587 2.690000e-121 446.0
8 TraesCS7D01G186500 chr7A 87.432 366 26 12 3430 3794 139125899 139125553 1.640000e-108 403.0
9 TraesCS7D01G186500 chr1B 90.970 299 18 7 450 741 357414599 357414895 9.880000e-106 394.0
10 TraesCS7D01G186500 chr1B 97.826 46 1 0 810 855 622608700 622608745 3.140000e-11 80.5
11 TraesCS7D01G186500 chr3A 89.474 304 20 7 450 741 12743835 12743532 1.290000e-99 374.0
12 TraesCS7D01G186500 chr3A 89.597 298 21 7 450 741 222038255 222037962 1.660000e-98 370.0
13 TraesCS7D01G186500 chr3A 88.742 302 24 6 450 741 515860337 515860638 1.000000e-95 361.0
14 TraesCS7D01G186500 chr6D 88.387 310 24 8 452 750 285810090 285809782 2.790000e-96 363.0
15 TraesCS7D01G186500 chr6D 95.745 47 0 2 811 856 392512755 392512710 1.460000e-09 75.0
16 TraesCS7D01G186500 chr5B 88.816 304 22 8 450 741 360403133 360403436 2.790000e-96 363.0
17 TraesCS7D01G186500 chr1D 88.742 302 22 6 450 747 7178429 7178136 3.600000e-95 359.0
18 TraesCS7D01G186500 chr1D 97.674 43 1 0 808 850 219735120 219735078 1.460000e-09 75.0
19 TraesCS7D01G186500 chr1D 95.652 46 2 0 810 855 452589070 452589115 1.460000e-09 75.0
20 TraesCS7D01G186500 chr5A 87.948 307 23 8 447 741 624677395 624677699 2.170000e-92 350.0
21 TraesCS7D01G186500 chr2A 87.138 311 32 6 446 750 486466485 486466177 2.810000e-91 346.0
22 TraesCS7D01G186500 chr1A 97.826 46 1 0 810 855 547344852 547344897 3.140000e-11 80.5
23 TraesCS7D01G186500 chr4B 100.000 42 0 0 812 853 665982637 665982596 1.130000e-10 78.7
24 TraesCS7D01G186500 chr3D 94.231 52 2 1 814 864 572461824 572461773 1.130000e-10 78.7
25 TraesCS7D01G186500 chr3D 95.652 46 1 1 814 858 569545607 569545652 5.260000e-09 73.1
26 TraesCS7D01G186500 chr6B 97.727 44 1 0 812 855 462034246 462034289 4.060000e-10 76.8


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 TraesCS7D01G186500 chr7D 139091278 139095071 3793 True 7007.000000 7007 100.0000 1 3794 1 chr7D.!!$R1 3793
1 TraesCS7D01G186500 chr7B 104474107 104477828 3721 True 2628.000000 4687 93.1625 9 3794 2 chr7B.!!$R2 3785
2 TraesCS7D01G186500 chr7B 104306139 104309156 3017 True 1466.666667 3009 92.6600 1 3794 3 chr7B.!!$R1 3793
3 TraesCS7D01G186500 chr7A 139125553 139132016 6463 True 1595.666667 3938 89.5670 1 3794 3 chr7A.!!$R1 3793

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
690 698 0.036765 GTGTGCGTTCATAGGGGTGA 60.037 55.0 0.00 0.0 0.00 4.02 F
717 725 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.0 13.26 0.0 46.56 4.01 F
1733 4860 0.370273 GCACAGATTGGCTCGTTACG 59.630 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 4906 0.457443 TGCAAACACGAACATTGCCA 59.543 45.000 14.00 4.06 46.74 4.92 R
2596 5723 0.769873 AACCCAAATGCAATGGCCAA 59.230 45.000 10.96 0.00 40.13 4.52 R
3487 6619 1.227527 CAACCGTGACTGTGCAGGA 60.228 57.895 4.11 0.00 0.00 3.86 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
33 34 6.408206 CGTAAATCTATCTCCTGTTTCCCCTT 60.408 42.308 0.00 0.00 0.00 3.95
231 236 6.651755 ATTCATGATTTTTGAATTCACGGC 57.348 33.333 7.89 0.00 40.08 5.68
269 275 7.244166 TGCAAACATTTTCAAATTCGTGAAT 57.756 28.000 0.00 0.00 37.36 2.57
449 457 2.425668 ACCACTGAAAACAAGAAACCGG 59.574 45.455 0.00 0.00 0.00 5.28
450 458 2.459934 CACTGAAAACAAGAAACCGGC 58.540 47.619 0.00 0.00 0.00 6.13
451 459 1.064952 ACTGAAAACAAGAAACCGGCG 59.935 47.619 0.00 0.00 0.00 6.46
452 460 1.332375 CTGAAAACAAGAAACCGGCGA 59.668 47.619 9.30 0.00 0.00 5.54
453 461 1.743958 TGAAAACAAGAAACCGGCGAA 59.256 42.857 9.30 0.00 0.00 4.70
454 462 2.114056 GAAAACAAGAAACCGGCGAAC 58.886 47.619 9.30 0.00 0.00 3.95
455 463 0.382873 AAACAAGAAACCGGCGAACC 59.617 50.000 9.30 0.00 0.00 3.62
456 464 0.748729 AACAAGAAACCGGCGAACCA 60.749 50.000 9.30 0.00 34.57 3.67
457 465 0.748729 ACAAGAAACCGGCGAACCAA 60.749 50.000 9.30 0.00 34.57 3.67
458 466 0.317519 CAAGAAACCGGCGAACCAAC 60.318 55.000 9.30 0.00 34.57 3.77
459 467 1.449726 AAGAAACCGGCGAACCAACC 61.450 55.000 9.30 0.00 34.57 3.77
460 468 1.895231 GAAACCGGCGAACCAACCT 60.895 57.895 9.30 0.00 34.57 3.50
461 469 2.125202 GAAACCGGCGAACCAACCTG 62.125 60.000 9.30 0.00 34.57 4.00
462 470 2.897172 AAACCGGCGAACCAACCTGT 62.897 55.000 9.30 0.00 34.57 4.00
463 471 3.353836 CCGGCGAACCAACCTGTG 61.354 66.667 9.30 0.00 34.57 3.66
476 484 2.879103 ACCTGTGGTTGGATGGTTAG 57.121 50.000 0.00 0.00 27.29 2.34
477 485 2.344592 ACCTGTGGTTGGATGGTTAGA 58.655 47.619 0.00 0.00 27.29 2.10
478 486 2.305927 ACCTGTGGTTGGATGGTTAGAG 59.694 50.000 0.00 0.00 27.29 2.43
479 487 2.356125 CCTGTGGTTGGATGGTTAGAGG 60.356 54.545 0.00 0.00 0.00 3.69
480 488 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
481 489 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
482 490 1.913419 TGGTTGGATGGTTAGAGGGAC 59.087 52.381 0.00 0.00 0.00 4.46
484 492 2.092914 GGTTGGATGGTTAGAGGGACTG 60.093 54.545 0.00 0.00 41.55 3.51
485 493 2.572104 GTTGGATGGTTAGAGGGACTGT 59.428 50.000 0.00 0.00 41.55 3.55
486 494 2.187958 TGGATGGTTAGAGGGACTGTG 58.812 52.381 0.00 0.00 41.55 3.66
487 495 1.486726 GGATGGTTAGAGGGACTGTGG 59.513 57.143 0.00 0.00 41.55 4.17
488 496 2.188817 GATGGTTAGAGGGACTGTGGT 58.811 52.381 0.00 0.00 41.55 4.16
489 497 3.371965 GATGGTTAGAGGGACTGTGGTA 58.628 50.000 0.00 0.00 41.55 3.25
490 498 3.484953 TGGTTAGAGGGACTGTGGTAT 57.515 47.619 0.00 0.00 41.55 2.73
491 499 3.371965 TGGTTAGAGGGACTGTGGTATC 58.628 50.000 0.00 0.00 41.55 2.24
492 500 2.699321 GGTTAGAGGGACTGTGGTATCC 59.301 54.545 0.00 0.00 41.55 2.59
502 510 3.844063 TGGTATCCCCAACCCACC 58.156 61.111 0.00 0.00 41.50 4.61
503 511 1.151565 TGGTATCCCCAACCCACCA 60.152 57.895 0.00 0.00 41.50 4.17
504 512 1.211567 TGGTATCCCCAACCCACCAG 61.212 60.000 0.00 0.00 41.50 4.00
505 513 0.917333 GGTATCCCCAACCCACCAGA 60.917 60.000 0.00 0.00 0.00 3.86
506 514 0.546598 GTATCCCCAACCCACCAGAG 59.453 60.000 0.00 0.00 0.00 3.35
507 515 0.120377 TATCCCCAACCCACCAGAGT 59.880 55.000 0.00 0.00 0.00 3.24
508 516 0.776080 ATCCCCAACCCACCAGAGTT 60.776 55.000 0.00 0.00 0.00 3.01
509 517 1.074951 CCCCAACCCACCAGAGTTC 59.925 63.158 0.00 0.00 0.00 3.01
510 518 1.715019 CCCCAACCCACCAGAGTTCA 61.715 60.000 0.00 0.00 0.00 3.18
511 519 0.184933 CCCAACCCACCAGAGTTCAA 59.815 55.000 0.00 0.00 0.00 2.69
512 520 1.410932 CCCAACCCACCAGAGTTCAAA 60.411 52.381 0.00 0.00 0.00 2.69
513 521 2.597455 CCAACCCACCAGAGTTCAAAT 58.403 47.619 0.00 0.00 0.00 2.32
514 522 2.558359 CCAACCCACCAGAGTTCAAATC 59.442 50.000 0.00 0.00 0.00 2.17
515 523 3.490348 CAACCCACCAGAGTTCAAATCT 58.510 45.455 0.00 0.00 0.00 2.40
516 524 3.425162 ACCCACCAGAGTTCAAATCTC 57.575 47.619 0.00 0.00 0.00 2.75
517 525 2.289694 ACCCACCAGAGTTCAAATCTCG 60.290 50.000 0.00 0.00 37.07 4.04
518 526 1.734465 CCACCAGAGTTCAAATCTCGC 59.266 52.381 0.00 0.00 37.07 5.03
519 527 2.416747 CACCAGAGTTCAAATCTCGCA 58.583 47.619 0.00 0.00 37.07 5.10
520 528 3.005554 CACCAGAGTTCAAATCTCGCAT 58.994 45.455 0.00 0.00 37.07 4.73
521 529 3.438087 CACCAGAGTTCAAATCTCGCATT 59.562 43.478 0.00 0.00 37.07 3.56
522 530 4.074970 ACCAGAGTTCAAATCTCGCATTT 58.925 39.130 0.00 0.00 37.07 2.32
523 531 5.122239 CACCAGAGTTCAAATCTCGCATTTA 59.878 40.000 0.00 0.00 37.07 1.40
524 532 5.882557 ACCAGAGTTCAAATCTCGCATTTAT 59.117 36.000 0.00 0.00 37.07 1.40
525 533 6.375455 ACCAGAGTTCAAATCTCGCATTTATT 59.625 34.615 0.00 0.00 37.07 1.40
526 534 6.909357 CCAGAGTTCAAATCTCGCATTTATTC 59.091 38.462 0.00 0.00 37.07 1.75
527 535 7.414429 CCAGAGTTCAAATCTCGCATTTATTCA 60.414 37.037 0.00 0.00 37.07 2.57
528 536 8.127327 CAGAGTTCAAATCTCGCATTTATTCAT 58.873 33.333 0.00 0.00 37.07 2.57
529 537 8.127327 AGAGTTCAAATCTCGCATTTATTCATG 58.873 33.333 0.00 0.00 37.07 3.07
530 538 7.198390 AGTTCAAATCTCGCATTTATTCATGG 58.802 34.615 0.00 0.00 0.00 3.66
531 539 6.940831 TCAAATCTCGCATTTATTCATGGA 57.059 33.333 0.00 0.00 0.00 3.41
532 540 7.514784 TCAAATCTCGCATTTATTCATGGAT 57.485 32.000 0.00 0.00 0.00 3.41
533 541 7.944061 TCAAATCTCGCATTTATTCATGGATT 58.056 30.769 0.00 0.00 0.00 3.01
534 542 8.415553 TCAAATCTCGCATTTATTCATGGATTT 58.584 29.630 0.00 0.00 33.15 2.17
535 543 9.681692 CAAATCTCGCATTTATTCATGGATTTA 57.318 29.630 0.00 0.00 32.17 1.40
539 547 9.897744 TCTCGCATTTATTCATGGATTTATTTC 57.102 29.630 0.00 0.00 0.00 2.17
540 548 9.681692 CTCGCATTTATTCATGGATTTATTTCA 57.318 29.630 0.00 0.00 0.00 2.69
541 549 9.681692 TCGCATTTATTCATGGATTTATTTCAG 57.318 29.630 0.00 0.00 0.00 3.02
542 550 8.918658 CGCATTTATTCATGGATTTATTTCAGG 58.081 33.333 0.00 0.00 0.00 3.86
543 551 9.985730 GCATTTATTCATGGATTTATTTCAGGA 57.014 29.630 0.00 0.00 0.00 3.86
549 557 7.275888 TCATGGATTTATTTCAGGATTTCGG 57.724 36.000 0.00 0.00 0.00 4.30
550 558 5.514274 TGGATTTATTTCAGGATTTCGGC 57.486 39.130 0.00 0.00 0.00 5.54
551 559 4.036262 TGGATTTATTTCAGGATTTCGGCG 59.964 41.667 0.00 0.00 0.00 6.46
552 560 4.274950 GGATTTATTTCAGGATTTCGGCGA 59.725 41.667 4.99 4.99 0.00 5.54
553 561 5.048713 GGATTTATTTCAGGATTTCGGCGAT 60.049 40.000 11.76 0.00 0.00 4.58
554 562 4.811555 TTATTTCAGGATTTCGGCGATG 57.188 40.909 11.76 5.65 0.00 3.84
555 563 0.732571 TTTCAGGATTTCGGCGATGC 59.267 50.000 11.76 1.21 0.00 3.91
556 564 1.428370 TTCAGGATTTCGGCGATGCG 61.428 55.000 11.76 0.00 0.00 4.73
567 575 2.711311 CGATGCGCATTCAGTGGG 59.289 61.111 26.12 4.47 43.21 4.61
568 576 1.815003 CGATGCGCATTCAGTGGGA 60.815 57.895 26.12 0.00 43.02 4.37
569 577 1.769098 CGATGCGCATTCAGTGGGAG 61.769 60.000 26.12 4.12 43.02 4.30
570 578 1.442526 GATGCGCATTCAGTGGGAGG 61.443 60.000 26.12 0.00 43.02 4.30
571 579 1.913951 ATGCGCATTCAGTGGGAGGA 61.914 55.000 19.28 0.00 43.02 3.71
572 580 1.817099 GCGCATTCAGTGGGAGGAG 60.817 63.158 0.30 0.00 43.02 3.69
573 581 1.900351 CGCATTCAGTGGGAGGAGA 59.100 57.895 0.00 0.00 43.02 3.71
574 582 0.460987 CGCATTCAGTGGGAGGAGAC 60.461 60.000 0.00 0.00 43.02 3.36
575 583 0.460987 GCATTCAGTGGGAGGAGACG 60.461 60.000 0.00 0.00 0.00 4.18
576 584 0.898320 CATTCAGTGGGAGGAGACGT 59.102 55.000 0.00 0.00 0.00 4.34
577 585 1.276421 CATTCAGTGGGAGGAGACGTT 59.724 52.381 0.00 0.00 0.00 3.99
578 586 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
598 606 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
601 609 4.849329 GACGAGGCGCCTACGGTG 62.849 72.222 34.97 23.88 40.57 4.94
603 611 4.849329 CGAGGCGCCTACGGTGAC 62.849 72.222 32.97 14.51 42.50 3.67
606 614 2.508663 GGCGCCTACGGTGACTTC 60.509 66.667 22.15 0.00 38.38 3.01
607 615 2.879462 GCGCCTACGGTGACTTCG 60.879 66.667 0.00 0.00 40.57 3.79
608 616 2.564975 CGCCTACGGTGACTTCGT 59.435 61.111 0.00 0.00 43.64 3.85
609 617 1.796151 CGCCTACGGTGACTTCGTA 59.204 57.895 0.00 0.00 41.38 3.43
610 618 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
611 619 1.401409 CGCCTACGGTGACTTCGTAAA 60.401 52.381 0.00 0.00 41.62 2.01
612 620 2.733227 CGCCTACGGTGACTTCGTAAAT 60.733 50.000 0.00 0.00 41.62 1.40
613 621 3.487376 CGCCTACGGTGACTTCGTAAATA 60.487 47.826 0.00 0.00 41.62 1.40
614 622 4.614946 GCCTACGGTGACTTCGTAAATAT 58.385 43.478 0.00 0.00 41.62 1.28
615 623 4.678742 GCCTACGGTGACTTCGTAAATATC 59.321 45.833 0.00 0.00 41.62 1.63
616 624 5.734220 GCCTACGGTGACTTCGTAAATATCA 60.734 44.000 0.00 0.00 41.62 2.15
617 625 6.267817 CCTACGGTGACTTCGTAAATATCAA 58.732 40.000 0.00 0.00 41.62 2.57
618 626 6.417044 CCTACGGTGACTTCGTAAATATCAAG 59.583 42.308 0.00 0.00 41.62 3.02
619 627 5.957798 ACGGTGACTTCGTAAATATCAAGA 58.042 37.500 0.00 0.00 39.22 3.02
620 628 6.570692 ACGGTGACTTCGTAAATATCAAGAT 58.429 36.000 0.00 0.00 39.22 2.40
621 629 6.475727 ACGGTGACTTCGTAAATATCAAGATG 59.524 38.462 0.00 0.00 39.22 2.90
622 630 6.695713 CGGTGACTTCGTAAATATCAAGATGA 59.304 38.462 0.00 0.00 0.00 2.92
623 631 7.382488 CGGTGACTTCGTAAATATCAAGATGAT 59.618 37.037 0.00 0.00 40.72 2.45
624 632 9.692749 GGTGACTTCGTAAATATCAAGATGATA 57.307 33.333 2.79 2.79 42.83 2.15
630 638 8.911247 TCGTAAATATCAAGATGATATGTCGG 57.089 34.615 12.30 4.73 46.26 4.79
631 639 7.488150 TCGTAAATATCAAGATGATATGTCGGC 59.512 37.037 12.30 3.10 46.26 5.54
632 640 7.489435 CGTAAATATCAAGATGATATGTCGGCT 59.511 37.037 12.30 0.00 46.26 5.52
633 641 7.840342 AAATATCAAGATGATATGTCGGCTC 57.160 36.000 12.30 0.00 46.26 4.70
634 642 4.879197 ATCAAGATGATATGTCGGCTCA 57.121 40.909 0.00 0.00 34.88 4.26
635 643 4.248691 TCAAGATGATATGTCGGCTCAG 57.751 45.455 0.00 0.00 0.00 3.35
636 644 3.638627 TCAAGATGATATGTCGGCTCAGT 59.361 43.478 0.00 0.00 0.00 3.41
637 645 3.932545 AGATGATATGTCGGCTCAGTC 57.067 47.619 0.00 0.00 0.00 3.51
638 646 3.495331 AGATGATATGTCGGCTCAGTCT 58.505 45.455 0.00 0.00 0.00 3.24
639 647 3.894427 AGATGATATGTCGGCTCAGTCTT 59.106 43.478 0.00 0.00 0.00 3.01
640 648 4.343526 AGATGATATGTCGGCTCAGTCTTT 59.656 41.667 0.00 0.00 0.00 2.52
641 649 4.046938 TGATATGTCGGCTCAGTCTTTC 57.953 45.455 0.00 0.00 0.00 2.62
642 650 2.561733 TATGTCGGCTCAGTCTTTCG 57.438 50.000 0.00 0.00 0.00 3.46
643 651 0.108615 ATGTCGGCTCAGTCTTTCGG 60.109 55.000 0.00 0.00 0.00 4.30
644 652 1.176619 TGTCGGCTCAGTCTTTCGGA 61.177 55.000 0.00 0.00 0.00 4.55
645 653 0.456995 GTCGGCTCAGTCTTTCGGAG 60.457 60.000 0.00 0.00 40.44 4.63
646 654 1.153745 CGGCTCAGTCTTTCGGAGG 60.154 63.158 0.00 0.00 38.48 4.30
647 655 1.878656 CGGCTCAGTCTTTCGGAGGT 61.879 60.000 0.00 0.00 38.48 3.85
648 656 0.390472 GGCTCAGTCTTTCGGAGGTG 60.390 60.000 0.00 0.00 38.48 4.00
649 657 1.016653 GCTCAGTCTTTCGGAGGTGC 61.017 60.000 0.00 0.00 38.48 5.01
650 658 0.605589 CTCAGTCTTTCGGAGGTGCT 59.394 55.000 0.00 0.00 35.32 4.40
651 659 1.001406 CTCAGTCTTTCGGAGGTGCTT 59.999 52.381 0.00 0.00 35.32 3.91
652 660 2.231478 CTCAGTCTTTCGGAGGTGCTTA 59.769 50.000 0.00 0.00 35.32 3.09
653 661 2.832129 TCAGTCTTTCGGAGGTGCTTAT 59.168 45.455 0.00 0.00 0.00 1.73
654 662 4.021229 TCAGTCTTTCGGAGGTGCTTATA 58.979 43.478 0.00 0.00 0.00 0.98
655 663 4.098044 TCAGTCTTTCGGAGGTGCTTATAG 59.902 45.833 0.00 0.00 0.00 1.31
656 664 3.385111 AGTCTTTCGGAGGTGCTTATAGG 59.615 47.826 0.00 0.00 0.00 2.57
657 665 2.698797 TCTTTCGGAGGTGCTTATAGGG 59.301 50.000 0.00 0.00 0.00 3.53
658 666 1.420430 TTCGGAGGTGCTTATAGGGG 58.580 55.000 0.00 0.00 0.00 4.79
659 667 0.263765 TCGGAGGTGCTTATAGGGGT 59.736 55.000 0.00 0.00 0.00 4.95
660 668 1.500303 TCGGAGGTGCTTATAGGGGTA 59.500 52.381 0.00 0.00 0.00 3.69
661 669 1.893801 CGGAGGTGCTTATAGGGGTAG 59.106 57.143 0.00 0.00 0.00 3.18
662 670 2.258109 GGAGGTGCTTATAGGGGTAGG 58.742 57.143 0.00 0.00 0.00 3.18
663 671 2.158204 GGAGGTGCTTATAGGGGTAGGA 60.158 54.545 0.00 0.00 0.00 2.94
664 672 3.504343 GGAGGTGCTTATAGGGGTAGGAT 60.504 52.174 0.00 0.00 0.00 3.24
665 673 3.515901 GAGGTGCTTATAGGGGTAGGATG 59.484 52.174 0.00 0.00 0.00 3.51
666 674 3.116317 AGGTGCTTATAGGGGTAGGATGT 60.116 47.826 0.00 0.00 0.00 3.06
667 675 3.008049 GGTGCTTATAGGGGTAGGATGTG 59.992 52.174 0.00 0.00 0.00 3.21
668 676 2.637872 TGCTTATAGGGGTAGGATGTGC 59.362 50.000 0.00 0.00 0.00 4.57
669 677 2.353803 GCTTATAGGGGTAGGATGTGCG 60.354 54.545 0.00 0.00 0.00 5.34
670 678 2.688902 TATAGGGGTAGGATGTGCGT 57.311 50.000 0.00 0.00 0.00 5.24
671 679 1.048601 ATAGGGGTAGGATGTGCGTG 58.951 55.000 0.00 0.00 0.00 5.34
672 680 0.324923 TAGGGGTAGGATGTGCGTGT 60.325 55.000 0.00 0.00 0.00 4.49
673 681 1.449601 GGGGTAGGATGTGCGTGTG 60.450 63.158 0.00 0.00 0.00 3.82
674 682 1.295423 GGGTAGGATGTGCGTGTGT 59.705 57.895 0.00 0.00 0.00 3.72
675 683 1.019278 GGGTAGGATGTGCGTGTGTG 61.019 60.000 0.00 0.00 0.00 3.82
676 684 1.635663 GGTAGGATGTGCGTGTGTGC 61.636 60.000 0.00 0.00 0.00 4.57
677 685 1.736282 TAGGATGTGCGTGTGTGCG 60.736 57.895 0.00 0.00 37.81 5.34
678 686 2.428960 TAGGATGTGCGTGTGTGCGT 62.429 55.000 0.00 0.00 37.81 5.24
679 687 2.631428 GATGTGCGTGTGTGCGTT 59.369 55.556 0.00 0.00 37.81 4.84
680 688 1.438710 GATGTGCGTGTGTGCGTTC 60.439 57.895 0.00 0.00 37.81 3.95
681 689 2.100024 GATGTGCGTGTGTGCGTTCA 62.100 55.000 0.00 0.00 37.81 3.18
682 690 1.506309 ATGTGCGTGTGTGCGTTCAT 61.506 50.000 0.00 0.00 37.81 2.57
683 691 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
684 692 0.179250 GTGCGTGTGTGCGTTCATAG 60.179 55.000 0.00 0.00 37.81 2.23
685 693 1.288419 TGCGTGTGTGCGTTCATAGG 61.288 55.000 0.00 0.00 37.81 2.57
686 694 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
687 695 1.358725 CGTGTGTGCGTTCATAGGGG 61.359 60.000 0.00 0.00 0.00 4.79
688 696 0.321298 GTGTGTGCGTTCATAGGGGT 60.321 55.000 0.00 0.00 0.00 4.95
689 697 0.321210 TGTGTGCGTTCATAGGGGTG 60.321 55.000 0.00 0.00 0.00 4.61
690 698 0.036765 GTGTGCGTTCATAGGGGTGA 60.037 55.000 0.00 0.00 0.00 4.02
691 699 0.249120 TGTGCGTTCATAGGGGTGAG 59.751 55.000 0.00 0.00 0.00 3.51
692 700 0.249398 GTGCGTTCATAGGGGTGAGT 59.751 55.000 0.00 0.00 0.00 3.41
693 701 0.249120 TGCGTTCATAGGGGTGAGTG 59.751 55.000 0.00 0.00 0.00 3.51
694 702 0.249398 GCGTTCATAGGGGTGAGTGT 59.751 55.000 0.00 0.00 0.00 3.55
695 703 1.479323 GCGTTCATAGGGGTGAGTGTA 59.521 52.381 0.00 0.00 0.00 2.90
696 704 2.102588 GCGTTCATAGGGGTGAGTGTAT 59.897 50.000 0.00 0.00 0.00 2.29
697 705 3.717707 CGTTCATAGGGGTGAGTGTATG 58.282 50.000 0.00 0.00 0.00 2.39
698 706 3.467803 GTTCATAGGGGTGAGTGTATGC 58.532 50.000 0.00 0.00 0.00 3.14
699 707 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
700 708 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
701 709 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
702 710 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
703 711 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
704 712 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
705 713 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
706 714 1.556564 GTGAGTGTATGCGCGTGTAT 58.443 50.000 13.61 4.63 0.00 2.29
707 715 2.542205 GGTGAGTGTATGCGCGTGTATA 60.542 50.000 13.61 2.40 0.00 1.47
708 716 3.305964 GTGAGTGTATGCGCGTGTATAT 58.694 45.455 13.61 0.00 0.00 0.86
709 717 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
710 718 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
711 719 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
712 720 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
715 723 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
716 724 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
717 725 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
718 726 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
719 727 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
720 728 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
721 729 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
722 730 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
723 731 4.607955 GTGTATATGAGCGCTTGTGTCTA 58.392 43.478 13.26 0.00 0.00 2.59
724 732 5.223382 GTGTATATGAGCGCTTGTGTCTAT 58.777 41.667 13.26 5.57 0.00 1.98
725 733 6.379386 GTGTATATGAGCGCTTGTGTCTATA 58.621 40.000 13.26 4.61 0.00 1.31
726 734 6.305877 GTGTATATGAGCGCTTGTGTCTATAC 59.694 42.308 13.26 15.61 0.00 1.47
727 735 5.713792 ATATGAGCGCTTGTGTCTATACT 57.286 39.130 13.26 0.00 0.00 2.12
728 736 3.150848 TGAGCGCTTGTGTCTATACTG 57.849 47.619 13.26 0.00 0.00 2.74
729 737 2.752903 TGAGCGCTTGTGTCTATACTGA 59.247 45.455 13.26 0.00 0.00 3.41
730 738 3.381590 TGAGCGCTTGTGTCTATACTGAT 59.618 43.478 13.26 0.00 0.00 2.90
731 739 3.711086 AGCGCTTGTGTCTATACTGATG 58.289 45.455 2.64 0.00 0.00 3.07
732 740 3.131223 AGCGCTTGTGTCTATACTGATGT 59.869 43.478 2.64 0.00 0.00 3.06
733 741 3.865745 GCGCTTGTGTCTATACTGATGTT 59.134 43.478 0.00 0.00 0.00 2.71
734 742 5.041287 GCGCTTGTGTCTATACTGATGTTA 58.959 41.667 0.00 0.00 0.00 2.41
735 743 5.518847 GCGCTTGTGTCTATACTGATGTTAA 59.481 40.000 0.00 0.00 0.00 2.01
736 744 6.035650 GCGCTTGTGTCTATACTGATGTTAAA 59.964 38.462 0.00 0.00 0.00 1.52
737 745 7.412563 GCGCTTGTGTCTATACTGATGTTAAAA 60.413 37.037 0.00 0.00 0.00 1.52
738 746 8.440059 CGCTTGTGTCTATACTGATGTTAAAAA 58.560 33.333 0.00 0.00 0.00 1.94
785 793 8.631480 AAGACCAACTAAAAAGACCGAAATAT 57.369 30.769 0.00 0.00 0.00 1.28
787 1375 9.901172 AGACCAACTAAAAAGACCGAAATATAT 57.099 29.630 0.00 0.00 0.00 0.86
823 1760 9.965824 ATTAAATAAAACTCACCACTTGACAAG 57.034 29.630 13.77 13.77 0.00 3.16
834 1771 3.733337 CACTTGACAAGAGTGGTAAGCT 58.267 45.455 21.95 0.00 40.58 3.74
837 1774 6.631016 CACTTGACAAGAGTGGTAAGCTATA 58.369 40.000 21.95 0.00 40.58 1.31
846 1783 8.946085 CAAGAGTGGTAAGCTATATCAAAAACA 58.054 33.333 0.00 0.00 0.00 2.83
848 1785 9.686683 AGAGTGGTAAGCTATATCAAAAACATT 57.313 29.630 0.00 0.00 0.00 2.71
849 1786 9.722056 GAGTGGTAAGCTATATCAAAAACATTG 57.278 33.333 0.00 0.00 0.00 2.82
850 1787 9.461312 AGTGGTAAGCTATATCAAAAACATTGA 57.539 29.630 0.00 0.00 0.00 2.57
1733 4860 0.370273 GCACAGATTGGCTCGTTACG 59.630 55.000 0.00 0.00 0.00 3.18
2199 5326 5.604231 AGATATTGTCCTCTGGCAGACATTA 59.396 40.000 14.43 11.87 42.32 1.90
2596 5723 6.262944 TGCATTGTCCTATCATAGCGAAAAAT 59.737 34.615 0.00 0.00 0.00 1.82
2848 5977 5.366477 TGATGGAGTTGATAATGAGCCACTA 59.634 40.000 0.00 0.00 0.00 2.74
2905 6035 2.284754 TCATACAAACCCAGCTTGCA 57.715 45.000 0.00 0.00 0.00 4.08
2911 6041 0.746659 AAACCCAGCTTGCAAGTGTC 59.253 50.000 26.55 11.11 0.00 3.67
2917 6047 1.439365 GCTTGCAAGTGTCGCTTCG 60.439 57.895 26.55 0.00 34.69 3.79
2969 6099 0.944386 CAAGTGAACTCAACCCCACG 59.056 55.000 0.00 0.00 34.93 4.94
3016 6146 5.983118 TGTGTTACTACATGAGTGTTCACAG 59.017 40.000 0.00 0.00 39.39 3.66
3022 6152 4.090761 ACATGAGTGTTCACAGTCCATT 57.909 40.909 11.48 0.00 43.80 3.16
3105 6235 3.372206 AGCTTTGCACTAGCGTTATTCTG 59.628 43.478 12.85 0.00 46.23 3.02
3188 6319 1.005924 TGGGAGCCCAGAGAAATTTCC 59.994 52.381 14.61 6.57 41.89 3.13
3235 6366 4.917906 ACATTGCTTTCTAGTTCCTCCT 57.082 40.909 0.00 0.00 0.00 3.69
3487 6619 5.453762 CCTTTTGCTCCTTTCTCCATTTTGT 60.454 40.000 0.00 0.00 0.00 2.83
3499 6631 1.955778 CCATTTTGTCCTGCACAGTCA 59.044 47.619 0.00 0.00 35.97 3.41
3588 6722 8.477984 TTTAAAGCAAATTTATTAGCAGCAGG 57.522 30.769 0.00 0.00 33.40 4.85
3615 6749 7.230849 TGAGTTTTCACTATGCAAAATGGAT 57.769 32.000 0.00 0.00 31.22 3.41
3616 6750 7.669427 TGAGTTTTCACTATGCAAAATGGATT 58.331 30.769 0.00 0.00 31.22 3.01
3617 6751 8.149647 TGAGTTTTCACTATGCAAAATGGATTT 58.850 29.630 0.00 0.00 31.22 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.022451 GGCGTGGCGATTTAGGTCAA 61.022 55.000 0.00 0.00 0.00 3.18
372 379 5.814188 TGCATTACAGAAATGTGCACAAAAA 59.186 32.000 25.72 10.45 45.78 1.94
457 465 2.305927 CTCTAACCATCCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
458 466 2.356125 CCTCTAACCATCCAACCACAGG 60.356 54.545 0.00 0.00 0.00 4.00
459 467 2.356125 CCCTCTAACCATCCAACCACAG 60.356 54.545 0.00 0.00 0.00 3.66
460 468 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
461 469 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
462 470 1.913419 GTCCCTCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
463 471 2.092914 CAGTCCCTCTAACCATCCAACC 60.093 54.545 0.00 0.00 0.00 3.77
464 472 2.572104 ACAGTCCCTCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
465 473 2.571653 CACAGTCCCTCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
466 474 2.187958 CACAGTCCCTCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
467 475 1.486726 CCACAGTCCCTCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
468 476 2.188817 ACCACAGTCCCTCTAACCATC 58.811 52.381 0.00 0.00 0.00 3.51
469 477 2.344093 ACCACAGTCCCTCTAACCAT 57.656 50.000 0.00 0.00 0.00 3.55
470 478 3.371965 GATACCACAGTCCCTCTAACCA 58.628 50.000 0.00 0.00 0.00 3.67
471 479 2.699321 GGATACCACAGTCCCTCTAACC 59.301 54.545 0.00 0.00 0.00 2.85
487 495 0.546598 CTCTGGTGGGTTGGGGATAC 59.453 60.000 0.00 0.00 0.00 2.24
488 496 0.120377 ACTCTGGTGGGTTGGGGATA 59.880 55.000 0.00 0.00 0.00 2.59
489 497 0.776080 AACTCTGGTGGGTTGGGGAT 60.776 55.000 0.00 0.00 0.00 3.85
490 498 1.386772 AACTCTGGTGGGTTGGGGA 60.387 57.895 0.00 0.00 0.00 4.81
491 499 1.074951 GAACTCTGGTGGGTTGGGG 59.925 63.158 0.00 0.00 0.00 4.96
492 500 0.184933 TTGAACTCTGGTGGGTTGGG 59.815 55.000 0.00 0.00 0.00 4.12
493 501 2.065899 TTTGAACTCTGGTGGGTTGG 57.934 50.000 0.00 0.00 0.00 3.77
494 502 3.490348 AGATTTGAACTCTGGTGGGTTG 58.510 45.455 0.00 0.00 0.00 3.77
495 503 3.756117 GAGATTTGAACTCTGGTGGGTT 58.244 45.455 0.00 0.00 0.00 4.11
496 504 2.289694 CGAGATTTGAACTCTGGTGGGT 60.290 50.000 0.00 0.00 32.87 4.51
497 505 2.350522 CGAGATTTGAACTCTGGTGGG 58.649 52.381 0.00 0.00 32.87 4.61
498 506 1.734465 GCGAGATTTGAACTCTGGTGG 59.266 52.381 0.00 0.00 32.87 4.61
499 507 2.416747 TGCGAGATTTGAACTCTGGTG 58.583 47.619 0.00 0.00 32.87 4.17
500 508 2.839486 TGCGAGATTTGAACTCTGGT 57.161 45.000 0.00 0.00 32.87 4.00
501 509 4.691860 AAATGCGAGATTTGAACTCTGG 57.308 40.909 0.00 0.00 32.87 3.86
502 510 7.466805 TGAATAAATGCGAGATTTGAACTCTG 58.533 34.615 0.00 0.00 32.87 3.35
503 511 7.615582 TGAATAAATGCGAGATTTGAACTCT 57.384 32.000 0.00 0.00 32.87 3.24
504 512 7.377928 CCATGAATAAATGCGAGATTTGAACTC 59.622 37.037 0.00 0.00 0.00 3.01
505 513 7.067372 TCCATGAATAAATGCGAGATTTGAACT 59.933 33.333 0.00 0.00 0.00 3.01
506 514 7.195646 TCCATGAATAAATGCGAGATTTGAAC 58.804 34.615 0.00 0.00 0.00 3.18
507 515 7.332213 TCCATGAATAAATGCGAGATTTGAA 57.668 32.000 0.00 0.00 0.00 2.69
508 516 6.940831 TCCATGAATAAATGCGAGATTTGA 57.059 33.333 0.00 0.00 0.00 2.69
509 517 8.583810 AAATCCATGAATAAATGCGAGATTTG 57.416 30.769 0.00 0.00 30.96 2.32
513 521 9.897744 GAAATAAATCCATGAATAAATGCGAGA 57.102 29.630 0.00 0.00 0.00 4.04
514 522 9.681692 TGAAATAAATCCATGAATAAATGCGAG 57.318 29.630 0.00 0.00 0.00 5.03
515 523 9.681692 CTGAAATAAATCCATGAATAAATGCGA 57.318 29.630 0.00 0.00 0.00 5.10
516 524 8.918658 CCTGAAATAAATCCATGAATAAATGCG 58.081 33.333 0.00 0.00 0.00 4.73
517 525 9.985730 TCCTGAAATAAATCCATGAATAAATGC 57.014 29.630 0.00 0.00 0.00 3.56
523 531 8.362639 CCGAAATCCTGAAATAAATCCATGAAT 58.637 33.333 0.00 0.00 0.00 2.57
524 532 7.684187 GCCGAAATCCTGAAATAAATCCATGAA 60.684 37.037 0.00 0.00 0.00 2.57
525 533 6.239008 GCCGAAATCCTGAAATAAATCCATGA 60.239 38.462 0.00 0.00 0.00 3.07
526 534 5.922544 GCCGAAATCCTGAAATAAATCCATG 59.077 40.000 0.00 0.00 0.00 3.66
527 535 5.278463 CGCCGAAATCCTGAAATAAATCCAT 60.278 40.000 0.00 0.00 0.00 3.41
528 536 4.036262 CGCCGAAATCCTGAAATAAATCCA 59.964 41.667 0.00 0.00 0.00 3.41
529 537 4.274950 TCGCCGAAATCCTGAAATAAATCC 59.725 41.667 0.00 0.00 0.00 3.01
530 538 5.418310 TCGCCGAAATCCTGAAATAAATC 57.582 39.130 0.00 0.00 0.00 2.17
531 539 5.762045 CATCGCCGAAATCCTGAAATAAAT 58.238 37.500 0.00 0.00 0.00 1.40
532 540 4.497340 GCATCGCCGAAATCCTGAAATAAA 60.497 41.667 0.00 0.00 0.00 1.40
533 541 3.003275 GCATCGCCGAAATCCTGAAATAA 59.997 43.478 0.00 0.00 0.00 1.40
534 542 2.548057 GCATCGCCGAAATCCTGAAATA 59.452 45.455 0.00 0.00 0.00 1.40
535 543 1.334869 GCATCGCCGAAATCCTGAAAT 59.665 47.619 0.00 0.00 0.00 2.17
536 544 0.732571 GCATCGCCGAAATCCTGAAA 59.267 50.000 0.00 0.00 0.00 2.69
537 545 1.428370 CGCATCGCCGAAATCCTGAA 61.428 55.000 0.00 0.00 0.00 3.02
538 546 1.882625 CGCATCGCCGAAATCCTGA 60.883 57.895 0.00 0.00 0.00 3.86
539 547 2.628106 CGCATCGCCGAAATCCTG 59.372 61.111 0.00 0.00 0.00 3.86
550 558 1.769098 CTCCCACTGAATGCGCATCG 61.769 60.000 25.53 17.09 0.00 3.84
551 559 1.442526 CCTCCCACTGAATGCGCATC 61.443 60.000 25.53 17.12 0.00 3.91
552 560 1.452651 CCTCCCACTGAATGCGCAT 60.453 57.895 19.28 19.28 0.00 4.73
553 561 2.046023 CCTCCCACTGAATGCGCA 60.046 61.111 14.96 14.96 0.00 6.09
554 562 1.817099 CTCCTCCCACTGAATGCGC 60.817 63.158 0.00 0.00 0.00 6.09
555 563 0.460987 GTCTCCTCCCACTGAATGCG 60.461 60.000 0.00 0.00 0.00 4.73
556 564 0.460987 CGTCTCCTCCCACTGAATGC 60.461 60.000 0.00 0.00 0.00 3.56
557 565 0.898320 ACGTCTCCTCCCACTGAATG 59.102 55.000 0.00 0.00 0.00 2.67
558 566 1.550976 GAACGTCTCCTCCCACTGAAT 59.449 52.381 0.00 0.00 0.00 2.57
559 567 0.966920 GAACGTCTCCTCCCACTGAA 59.033 55.000 0.00 0.00 0.00 3.02
560 568 0.898789 GGAACGTCTCCTCCCACTGA 60.899 60.000 8.87 0.00 41.61 3.41
561 569 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
562 570 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
580 588 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
581 589 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
594 602 7.191551 TCTTGATATTTACGAAGTCACCGTAG 58.808 38.462 0.00 0.00 43.93 3.51
595 603 7.087409 TCTTGATATTTACGAAGTCACCGTA 57.913 36.000 0.00 0.00 43.93 4.02
596 604 5.957798 TCTTGATATTTACGAAGTCACCGT 58.042 37.500 0.00 0.00 43.93 4.83
597 605 6.695713 TCATCTTGATATTTACGAAGTCACCG 59.304 38.462 0.00 0.00 43.93 4.94
598 606 8.594881 ATCATCTTGATATTTACGAAGTCACC 57.405 34.615 0.00 0.00 37.35 4.02
604 612 9.353999 CCGACATATCATCTTGATATTTACGAA 57.646 33.333 18.37 0.00 45.10 3.85
605 613 7.488150 GCCGACATATCATCTTGATATTTACGA 59.512 37.037 18.37 0.00 45.10 3.43
606 614 7.489435 AGCCGACATATCATCTTGATATTTACG 59.511 37.037 7.17 11.42 45.10 3.18
607 615 8.709386 AGCCGACATATCATCTTGATATTTAC 57.291 34.615 7.17 2.85 45.10 2.01
608 616 8.531146 TGAGCCGACATATCATCTTGATATTTA 58.469 33.333 7.17 0.00 45.10 1.40
609 617 7.389232 TGAGCCGACATATCATCTTGATATTT 58.611 34.615 7.17 2.35 45.10 1.40
610 618 6.939622 TGAGCCGACATATCATCTTGATATT 58.060 36.000 7.17 1.35 45.10 1.28
612 620 5.478332 ACTGAGCCGACATATCATCTTGATA 59.522 40.000 0.05 0.05 42.83 2.15
613 621 4.282957 ACTGAGCCGACATATCATCTTGAT 59.717 41.667 0.00 0.00 40.72 2.57
614 622 3.638627 ACTGAGCCGACATATCATCTTGA 59.361 43.478 0.00 0.00 0.00 3.02
615 623 3.986572 GACTGAGCCGACATATCATCTTG 59.013 47.826 0.00 0.00 0.00 3.02
616 624 3.894427 AGACTGAGCCGACATATCATCTT 59.106 43.478 0.00 0.00 0.00 2.40
617 625 3.495331 AGACTGAGCCGACATATCATCT 58.505 45.455 0.00 0.00 0.00 2.90
618 626 3.932545 AGACTGAGCCGACATATCATC 57.067 47.619 0.00 0.00 0.00 2.92
619 627 4.626042 GAAAGACTGAGCCGACATATCAT 58.374 43.478 0.00 0.00 0.00 2.45
620 628 3.489229 CGAAAGACTGAGCCGACATATCA 60.489 47.826 0.00 0.00 0.00 2.15
621 629 3.046390 CGAAAGACTGAGCCGACATATC 58.954 50.000 0.00 0.00 0.00 1.63
622 630 2.223829 CCGAAAGACTGAGCCGACATAT 60.224 50.000 0.00 0.00 0.00 1.78
623 631 1.134367 CCGAAAGACTGAGCCGACATA 59.866 52.381 0.00 0.00 0.00 2.29
624 632 0.108615 CCGAAAGACTGAGCCGACAT 60.109 55.000 0.00 0.00 0.00 3.06
625 633 1.176619 TCCGAAAGACTGAGCCGACA 61.177 55.000 0.00 0.00 0.00 4.35
626 634 0.456995 CTCCGAAAGACTGAGCCGAC 60.457 60.000 0.00 0.00 0.00 4.79
627 635 1.595993 CCTCCGAAAGACTGAGCCGA 61.596 60.000 0.00 0.00 0.00 5.54
628 636 1.153745 CCTCCGAAAGACTGAGCCG 60.154 63.158 0.00 0.00 0.00 5.52
629 637 0.390472 CACCTCCGAAAGACTGAGCC 60.390 60.000 0.00 0.00 0.00 4.70
630 638 1.016653 GCACCTCCGAAAGACTGAGC 61.017 60.000 0.00 0.00 0.00 4.26
631 639 0.605589 AGCACCTCCGAAAGACTGAG 59.394 55.000 0.00 0.00 0.00 3.35
632 640 1.048601 AAGCACCTCCGAAAGACTGA 58.951 50.000 0.00 0.00 0.00 3.41
633 641 2.743636 TAAGCACCTCCGAAAGACTG 57.256 50.000 0.00 0.00 0.00 3.51
634 642 3.385111 CCTATAAGCACCTCCGAAAGACT 59.615 47.826 0.00 0.00 0.00 3.24
635 643 3.492829 CCCTATAAGCACCTCCGAAAGAC 60.493 52.174 0.00 0.00 0.00 3.01
636 644 2.698797 CCCTATAAGCACCTCCGAAAGA 59.301 50.000 0.00 0.00 0.00 2.52
637 645 2.224305 CCCCTATAAGCACCTCCGAAAG 60.224 54.545 0.00 0.00 0.00 2.62
638 646 1.766496 CCCCTATAAGCACCTCCGAAA 59.234 52.381 0.00 0.00 0.00 3.46
639 647 1.343681 ACCCCTATAAGCACCTCCGAA 60.344 52.381 0.00 0.00 0.00 4.30
640 648 0.263765 ACCCCTATAAGCACCTCCGA 59.736 55.000 0.00 0.00 0.00 4.55
641 649 1.893801 CTACCCCTATAAGCACCTCCG 59.106 57.143 0.00 0.00 0.00 4.63
642 650 2.158204 TCCTACCCCTATAAGCACCTCC 60.158 54.545 0.00 0.00 0.00 4.30
643 651 3.255634 TCCTACCCCTATAAGCACCTC 57.744 52.381 0.00 0.00 0.00 3.85
644 652 3.116317 ACATCCTACCCCTATAAGCACCT 60.116 47.826 0.00 0.00 0.00 4.00
645 653 3.008049 CACATCCTACCCCTATAAGCACC 59.992 52.174 0.00 0.00 0.00 5.01
646 654 3.557264 GCACATCCTACCCCTATAAGCAC 60.557 52.174 0.00 0.00 0.00 4.40
647 655 2.637872 GCACATCCTACCCCTATAAGCA 59.362 50.000 0.00 0.00 0.00 3.91
648 656 2.353803 CGCACATCCTACCCCTATAAGC 60.354 54.545 0.00 0.00 0.00 3.09
649 657 2.897969 ACGCACATCCTACCCCTATAAG 59.102 50.000 0.00 0.00 0.00 1.73
650 658 2.631062 CACGCACATCCTACCCCTATAA 59.369 50.000 0.00 0.00 0.00 0.98
651 659 2.244695 CACGCACATCCTACCCCTATA 58.755 52.381 0.00 0.00 0.00 1.31
652 660 1.048601 CACGCACATCCTACCCCTAT 58.951 55.000 0.00 0.00 0.00 2.57
653 661 0.324923 ACACGCACATCCTACCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
654 662 1.612442 ACACGCACATCCTACCCCT 60.612 57.895 0.00 0.00 0.00 4.79
655 663 1.449601 CACACGCACATCCTACCCC 60.450 63.158 0.00 0.00 0.00 4.95
656 664 1.019278 CACACACGCACATCCTACCC 61.019 60.000 0.00 0.00 0.00 3.69
657 665 1.635663 GCACACACGCACATCCTACC 61.636 60.000 0.00 0.00 0.00 3.18
658 666 1.787847 GCACACACGCACATCCTAC 59.212 57.895 0.00 0.00 0.00 3.18
659 667 1.736282 CGCACACACGCACATCCTA 60.736 57.895 0.00 0.00 0.00 2.94
660 668 3.043713 CGCACACACGCACATCCT 61.044 61.111 0.00 0.00 0.00 3.24
661 669 2.764251 GAACGCACACACGCACATCC 62.764 60.000 0.00 0.00 36.19 3.51
662 670 1.438710 GAACGCACACACGCACATC 60.439 57.895 0.00 0.00 36.19 3.06
663 671 1.506309 ATGAACGCACACACGCACAT 61.506 50.000 0.00 0.00 36.19 3.21
664 672 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
665 673 0.179250 CTATGAACGCACACACGCAC 60.179 55.000 0.00 0.00 36.19 5.34
666 674 1.288419 CCTATGAACGCACACACGCA 61.288 55.000 0.00 0.00 36.19 5.24
667 675 1.419922 CCTATGAACGCACACACGC 59.580 57.895 0.00 0.00 36.19 5.34
668 676 1.358725 CCCCTATGAACGCACACACG 61.359 60.000 0.00 0.00 39.50 4.49
669 677 0.321298 ACCCCTATGAACGCACACAC 60.321 55.000 0.00 0.00 0.00 3.82
670 678 0.321210 CACCCCTATGAACGCACACA 60.321 55.000 0.00 0.00 0.00 3.72
671 679 0.036765 TCACCCCTATGAACGCACAC 60.037 55.000 0.00 0.00 0.00 3.82
672 680 0.249120 CTCACCCCTATGAACGCACA 59.751 55.000 0.00 0.00 0.00 4.57
673 681 0.249398 ACTCACCCCTATGAACGCAC 59.751 55.000 0.00 0.00 0.00 5.34
674 682 0.249120 CACTCACCCCTATGAACGCA 59.751 55.000 0.00 0.00 0.00 5.24
675 683 0.249398 ACACTCACCCCTATGAACGC 59.751 55.000 0.00 0.00 0.00 4.84
676 684 3.717707 CATACACTCACCCCTATGAACG 58.282 50.000 0.00 0.00 0.00 3.95
677 685 3.467803 GCATACACTCACCCCTATGAAC 58.532 50.000 0.00 0.00 0.00 3.18
678 686 2.102420 CGCATACACTCACCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
679 687 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
680 688 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
681 689 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
682 690 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
683 691 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
684 692 2.890474 CGCGCATACACTCACCCC 60.890 66.667 8.75 0.00 0.00 4.95
685 693 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
686 694 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
687 695 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
688 696 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
689 697 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
690 698 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
691 699 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
692 700 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
693 701 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
694 702 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
695 703 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
696 704 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
700 708 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
701 709 3.448686 AGACACAAGCGCTCATATACAC 58.551 45.455 12.06 0.00 0.00 2.90
702 710 3.801114 AGACACAAGCGCTCATATACA 57.199 42.857 12.06 0.00 0.00 2.29
703 711 6.524933 CAGTATAGACACAAGCGCTCATATAC 59.475 42.308 12.06 15.71 0.00 1.47
704 712 6.430000 TCAGTATAGACACAAGCGCTCATATA 59.570 38.462 12.06 4.88 0.00 0.86
705 713 5.241728 TCAGTATAGACACAAGCGCTCATAT 59.758 40.000 12.06 5.85 0.00 1.78
706 714 4.578928 TCAGTATAGACACAAGCGCTCATA 59.421 41.667 12.06 0.00 0.00 2.15
707 715 3.381590 TCAGTATAGACACAAGCGCTCAT 59.618 43.478 12.06 0.00 0.00 2.90
708 716 2.752903 TCAGTATAGACACAAGCGCTCA 59.247 45.455 12.06 0.00 0.00 4.26
709 717 3.422417 TCAGTATAGACACAAGCGCTC 57.578 47.619 12.06 0.00 0.00 5.03
710 718 3.131223 ACATCAGTATAGACACAAGCGCT 59.869 43.478 2.64 2.64 0.00 5.92
711 719 3.448686 ACATCAGTATAGACACAAGCGC 58.551 45.455 0.00 0.00 0.00 5.92
712 720 7.520119 TTTAACATCAGTATAGACACAAGCG 57.480 36.000 0.00 0.00 0.00 4.68
799 1387 8.740123 TCTTGTCAAGTGGTGAGTTTTATTTA 57.260 30.769 12.30 0.00 36.74 1.40
803 1391 5.584649 CACTCTTGTCAAGTGGTGAGTTTTA 59.415 40.000 23.74 0.70 40.36 1.52
813 1401 3.733337 AGCTTACCACTCTTGTCAAGTG 58.267 45.455 12.30 12.20 43.04 3.16
815 1403 7.492524 TGATATAGCTTACCACTCTTGTCAAG 58.507 38.462 6.21 6.21 0.00 3.02
817 1405 7.418337 TTGATATAGCTTACCACTCTTGTCA 57.582 36.000 0.00 0.00 0.00 3.58
818 1406 8.718102 TTTTGATATAGCTTACCACTCTTGTC 57.282 34.615 0.00 0.00 0.00 3.18
819 1407 8.947115 GTTTTTGATATAGCTTACCACTCTTGT 58.053 33.333 0.00 0.00 0.00 3.16
823 1760 9.722056 CAATGTTTTTGATATAGCTTACCACTC 57.278 33.333 0.00 0.00 0.00 3.51
851 1788 8.544597 GCACGGTGAGTTTTATTTAATTTTTGT 58.455 29.630 13.29 0.00 0.00 2.83
852 1789 7.733868 CGCACGGTGAGTTTTATTTAATTTTTG 59.266 33.333 13.29 0.00 0.00 2.44
859 2117 2.159814 CGCGCACGGTGAGTTTTATTTA 60.160 45.455 13.29 0.00 34.97 1.40
863 2121 2.945615 GCGCGCACGGTGAGTTTTA 61.946 57.895 29.10 0.00 40.57 1.52
893 2153 3.740128 ATAGGCTTGACCCAGCGCG 62.740 63.158 0.00 0.00 41.12 6.86
903 2163 1.200483 CACGCGACTACATAGGCTTG 58.800 55.000 15.93 0.00 0.00 4.01
905 2165 1.065928 GCACGCGACTACATAGGCT 59.934 57.895 15.93 0.00 0.00 4.58
1043 4157 2.997897 GGACGGACTCCAGGTGCT 60.998 66.667 0.00 0.00 39.21 4.40
1057 4171 2.224159 TGGTCAGGCAAGGGAGGAC 61.224 63.158 0.00 0.00 0.00 3.85
1242 4363 2.431260 GCGGCGTTGAGGTCGTTA 60.431 61.111 9.37 0.00 37.35 3.18
1461 4588 2.432456 GTGATCAGCCGCACGTCA 60.432 61.111 0.00 0.00 0.00 4.35
1733 4860 1.603802 CATGCACATACAATCCGTCCC 59.396 52.381 0.00 0.00 0.00 4.46
1779 4906 0.457443 TGCAAACACGAACATTGCCA 59.543 45.000 14.00 4.06 46.74 4.92
2151 5278 4.196193 CAGGAAACGGCATGGACTTAATA 58.804 43.478 0.00 0.00 0.00 0.98
2199 5326 2.426023 GTCTTGGACGCACCCAGT 59.574 61.111 0.00 0.00 37.53 4.00
2263 5390 4.101430 ACCATCAACATTTGAACCAAGCTT 59.899 37.500 0.00 0.00 43.95 3.74
2505 5632 1.190833 CCGGCTCATATCCCAGCTCT 61.191 60.000 0.00 0.00 35.82 4.09
2596 5723 0.769873 AACCCAAATGCAATGGCCAA 59.230 45.000 10.96 0.00 40.13 4.52
2848 5977 6.161855 TGTAGTCTGTTGATCTGTGAAGTT 57.838 37.500 0.00 0.00 0.00 2.66
2905 6035 3.845178 TGAATCATACGAAGCGACACTT 58.155 40.909 0.00 0.00 42.98 3.16
2911 6041 5.203358 TGAAAGTTGAATCATACGAAGCG 57.797 39.130 0.00 0.00 0.00 4.68
2969 6099 5.993106 AACACAGAGTAAAGTTCAAGCTC 57.007 39.130 0.00 0.00 0.00 4.09
3105 6235 4.116238 GTTGCTCTCTCTAATAGCACACC 58.884 47.826 0.00 0.00 45.41 4.16
3398 6530 2.338577 ATGGTCTTATGGCAGACAGC 57.661 50.000 7.54 0.00 44.53 4.40
3487 6619 1.227527 CAACCGTGACTGTGCAGGA 60.228 57.895 4.11 0.00 0.00 3.86
3499 6631 5.000012 TGTTTTTAAATCTGTGCAACCGT 58.000 34.783 0.00 0.00 34.36 4.83
3588 6722 8.243426 TCCATTTTGCATAGTGAAAACTCATAC 58.757 33.333 1.21 0.00 0.00 2.39
3615 6749 9.757227 CAAAGAAAACAATATCTTGTGGGTAAA 57.243 29.630 0.00 0.00 44.83 2.01
3616 6750 9.137459 TCAAAGAAAACAATATCTTGTGGGTAA 57.863 29.630 0.00 0.00 44.83 2.85
3617 6751 8.698973 TCAAAGAAAACAATATCTTGTGGGTA 57.301 30.769 0.00 0.00 44.83 3.69


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

AutoCloner maintained by Alex Coulton.