Multiple sequence alignment - TraesCS5D01G255500

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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 TraesCS5D01G255500 chr5D 100.000 2611 0 0 1 2611 361963946 361966556 0.000000e+00 4822.0
1 TraesCS5D01G255500 chr5D 88.119 202 22 2 1300 1500 362038135 362038335 3.360000e-59 239.0
2 TraesCS5D01G255500 chr5D 83.251 203 30 4 1299 1499 362007812 362008012 1.600000e-42 183.0
3 TraesCS5D01G255500 chr5B 90.395 1416 79 22 805 2172 427822752 427824158 0.000000e+00 1808.0
4 TraesCS5D01G255500 chr5B 82.353 238 35 6 1299 1531 427840174 427840409 1.580000e-47 200.0
5 TraesCS5D01G255500 chr5B 96.774 31 1 0 601 631 664884788 664884818 5.000000e-03 52.8
6 TraesCS5D01G255500 chr5A 90.828 676 57 5 1884 2556 462810817 462811490 0.000000e+00 900.0
7 TraesCS5D01G255500 chr5A 95.249 442 20 1 1 441 462806721 462807162 0.000000e+00 699.0
8 TraesCS5D01G255500 chr5A 93.062 418 11 3 1287 1686 462808111 462808528 1.730000e-166 595.0
9 TraesCS5D01G255500 chr5A 92.211 398 26 4 796 1188 462807658 462808055 2.270000e-155 558.0
10 TraesCS5D01G255500 chr7D 75.532 188 32 9 551 725 475470705 475470891 2.150000e-11 80.5
11 TraesCS5D01G255500 chr7D 96.774 31 1 0 601 631 575748759 575748789 5.000000e-03 52.8
12 TraesCS5D01G255500 chr2D 95.238 42 2 0 605 646 44481545 44481504 1.680000e-07 67.6
13 TraesCS5D01G255500 chr3B 90.698 43 4 0 604 646 94663324 94663282 1.010000e-04 58.4
14 TraesCS5D01G255500 chr7A 96.970 33 1 0 600 632 6528116 6528084 3.630000e-04 56.5
15 TraesCS5D01G255500 chr6B 100.000 28 0 0 604 631 619724436 619724409 5.000000e-03 52.8
16 TraesCS5D01G255500 chr3D 88.372 43 5 0 604 646 580990178 580990136 5.000000e-03 52.8


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 TraesCS5D01G255500 chr5D 361963946 361966556 2610 False 4822 4822 100.0000 1 2611 1 chr5D.!!$F1 2610
1 TraesCS5D01G255500 chr5B 427822752 427824158 1406 False 1808 1808 90.3950 805 2172 1 chr5B.!!$F1 1367
2 TraesCS5D01G255500 chr5A 462806721 462811490 4769 False 688 900 92.8375 1 2556 4 chr5A.!!$F1 2555

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
971 1429 0.034059 CAGTGCCAACCTCTCGTTCT 59.966 55.0 0.0 0.0 29.93 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 4909 0.179 ATCTCCTTCACCGACATGGC 59.821 55.0 0.0 0.0 43.94 4.4 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
35 36 5.300792 CAGGAAAACCAACTAAAACTAGCCA 59.699 40.000 0.00 0.00 0.00 4.75
54 55 2.562298 CCAATTGCCTTTGCTGTTCCTA 59.438 45.455 0.00 0.00 38.71 2.94
119 120 5.007724 GCACCCTACTACTCATAATGTTTGC 59.992 44.000 0.00 0.00 0.00 3.68
164 166 0.889186 GCCCTCCTTTTGCGTTCTCA 60.889 55.000 0.00 0.00 0.00 3.27
208 210 4.437930 CCTCGATCATTTGTCCAAAAGCTC 60.438 45.833 0.00 0.00 33.56 4.09
227 229 3.218398 CTCGCAGAAAATTCACACGTTC 58.782 45.455 0.00 0.00 34.09 3.95
229 231 2.307049 GCAGAAAATTCACACGTTCCG 58.693 47.619 0.00 0.00 0.00 4.30
238 240 0.170561 CACACGTTCCGGTCCTAGAG 59.829 60.000 0.00 0.00 0.00 2.43
269 271 1.566211 ACTGCTATGTGAGTGAGGCT 58.434 50.000 0.00 0.00 0.00 4.58
276 278 4.383861 TGAGTGAGGCTGCCAGCG 62.384 66.667 22.65 0.00 43.62 5.18
303 305 1.083401 GCGGAAATGATACTGCGCG 60.083 57.895 0.00 0.00 42.42 6.86
393 395 0.326927 TCCATTCCCTTCACGGTTCC 59.673 55.000 0.00 0.00 0.00 3.62
397 399 1.346479 TTCCCTTCACGGTTCCCACA 61.346 55.000 0.00 0.00 0.00 4.17
399 401 1.599797 CCTTCACGGTTCCCACACC 60.600 63.158 0.00 0.00 0.00 4.16
434 436 4.749245 AAGCATTTTGTCGACGAGAAAT 57.251 36.364 19.31 14.93 0.00 2.17
441 443 7.517417 GCATTTTGTCGACGAGAAATCATATCT 60.517 37.037 19.31 0.00 0.00 1.98
442 444 7.451281 TTTTGTCGACGAGAAATCATATCTC 57.549 36.000 19.31 0.00 39.94 2.75
443 445 6.378710 TTGTCGACGAGAAATCATATCTCT 57.621 37.500 11.62 0.00 40.93 3.10
444 446 7.492352 TTGTCGACGAGAAATCATATCTCTA 57.508 36.000 11.62 0.00 40.93 2.43
445 447 7.674471 TGTCGACGAGAAATCATATCTCTAT 57.326 36.000 11.62 0.00 40.93 1.98
446 448 7.744059 TGTCGACGAGAAATCATATCTCTATC 58.256 38.462 11.62 0.03 40.93 2.08
447 449 7.604545 TGTCGACGAGAAATCATATCTCTATCT 59.395 37.037 11.62 0.00 40.93 1.98
448 450 8.114290 GTCGACGAGAAATCATATCTCTATCTC 58.886 40.741 0.00 0.00 40.93 2.75
449 451 8.038351 TCGACGAGAAATCATATCTCTATCTCT 58.962 37.037 0.00 0.00 40.93 3.10
450 452 9.308318 CGACGAGAAATCATATCTCTATCTCTA 57.692 37.037 0.00 0.00 40.93 2.43
489 491 7.764695 AAAAATTGGGTTACTTTTTCTGTCG 57.235 32.000 0.00 0.00 28.63 4.35
490 492 5.447624 AATTGGGTTACTTTTTCTGTCGG 57.552 39.130 0.00 0.00 0.00 4.79
491 493 3.564053 TGGGTTACTTTTTCTGTCGGT 57.436 42.857 0.00 0.00 0.00 4.69
492 494 4.686191 TGGGTTACTTTTTCTGTCGGTA 57.314 40.909 0.00 0.00 0.00 4.02
493 495 5.033589 TGGGTTACTTTTTCTGTCGGTAA 57.966 39.130 0.00 0.00 0.00 2.85
494 496 5.058490 TGGGTTACTTTTTCTGTCGGTAAG 58.942 41.667 0.00 0.00 0.00 2.34
495 497 5.163322 TGGGTTACTTTTTCTGTCGGTAAGA 60.163 40.000 0.00 0.00 0.00 2.10
496 498 5.759763 GGGTTACTTTTTCTGTCGGTAAGAA 59.240 40.000 0.00 0.00 31.85 2.52
497 499 6.293081 GGGTTACTTTTTCTGTCGGTAAGAAC 60.293 42.308 0.00 0.00 33.46 3.01
498 500 6.258507 GGTTACTTTTTCTGTCGGTAAGAACA 59.741 38.462 0.00 0.00 33.46 3.18
499 501 5.729974 ACTTTTTCTGTCGGTAAGAACAC 57.270 39.130 0.00 0.00 33.46 3.32
500 502 5.425630 ACTTTTTCTGTCGGTAAGAACACT 58.574 37.500 0.00 0.00 33.46 3.55
501 503 5.878669 ACTTTTTCTGTCGGTAAGAACACTT 59.121 36.000 0.00 0.00 33.46 3.16
502 504 5.978934 TTTTCTGTCGGTAAGAACACTTC 57.021 39.130 0.00 0.00 33.46 3.01
503 505 3.278367 TCTGTCGGTAAGAACACTTCG 57.722 47.619 0.00 0.00 34.02 3.79
504 506 2.620115 TCTGTCGGTAAGAACACTTCGT 59.380 45.455 0.00 0.00 34.02 3.85
505 507 2.978489 CTGTCGGTAAGAACACTTCGTC 59.022 50.000 0.00 0.00 34.02 4.20
506 508 2.358582 TGTCGGTAAGAACACTTCGTCA 59.641 45.455 0.00 0.00 34.02 4.35
507 509 3.181488 TGTCGGTAAGAACACTTCGTCAA 60.181 43.478 0.00 0.00 34.02 3.18
508 510 3.181178 GTCGGTAAGAACACTTCGTCAAC 59.819 47.826 0.00 0.00 34.02 3.18
509 511 3.067180 TCGGTAAGAACACTTCGTCAACT 59.933 43.478 0.00 0.00 34.02 3.16
510 512 4.275689 TCGGTAAGAACACTTCGTCAACTA 59.724 41.667 0.00 0.00 34.02 2.24
511 513 4.977963 CGGTAAGAACACTTCGTCAACTAA 59.022 41.667 0.00 0.00 34.02 2.24
512 514 5.632347 CGGTAAGAACACTTCGTCAACTAAT 59.368 40.000 0.00 0.00 34.02 1.73
513 515 6.145048 CGGTAAGAACACTTCGTCAACTAATT 59.855 38.462 0.00 0.00 34.02 1.40
514 516 7.326789 CGGTAAGAACACTTCGTCAACTAATTA 59.673 37.037 0.00 0.00 34.02 1.40
515 517 9.148104 GGTAAGAACACTTCGTCAACTAATTAT 57.852 33.333 0.00 0.00 34.02 1.28
522 524 9.490379 ACACTTCGTCAACTAATTATTTTCTCT 57.510 29.630 0.00 0.00 0.00 3.10
523 525 9.959775 CACTTCGTCAACTAATTATTTTCTCTC 57.040 33.333 0.00 0.00 0.00 3.20
524 526 9.152595 ACTTCGTCAACTAATTATTTTCTCTCC 57.847 33.333 0.00 0.00 0.00 3.71
525 527 8.488651 TTCGTCAACTAATTATTTTCTCTCCC 57.511 34.615 0.00 0.00 0.00 4.30
526 528 7.617225 TCGTCAACTAATTATTTTCTCTCCCA 58.383 34.615 0.00 0.00 0.00 4.37
527 529 7.548075 TCGTCAACTAATTATTTTCTCTCCCAC 59.452 37.037 0.00 0.00 0.00 4.61
528 530 7.201617 CGTCAACTAATTATTTTCTCTCCCACC 60.202 40.741 0.00 0.00 0.00 4.61
529 531 7.610305 GTCAACTAATTATTTTCTCTCCCACCA 59.390 37.037 0.00 0.00 0.00 4.17
530 532 7.610305 TCAACTAATTATTTTCTCTCCCACCAC 59.390 37.037 0.00 0.00 0.00 4.16
531 533 7.027874 ACTAATTATTTTCTCTCCCACCACA 57.972 36.000 0.00 0.00 0.00 4.17
532 534 7.643123 ACTAATTATTTTCTCTCCCACCACAT 58.357 34.615 0.00 0.00 0.00 3.21
533 535 7.775561 ACTAATTATTTTCTCTCCCACCACATC 59.224 37.037 0.00 0.00 0.00 3.06
534 536 5.779241 TTATTTTCTCTCCCACCACATCT 57.221 39.130 0.00 0.00 0.00 2.90
535 537 3.703001 TTTTCTCTCCCACCACATCTC 57.297 47.619 0.00 0.00 0.00 2.75
536 538 2.630889 TTCTCTCCCACCACATCTCT 57.369 50.000 0.00 0.00 0.00 3.10
537 539 2.630889 TCTCTCCCACCACATCTCTT 57.369 50.000 0.00 0.00 0.00 2.85
538 540 2.182827 TCTCTCCCACCACATCTCTTG 58.817 52.381 0.00 0.00 0.00 3.02
539 541 2.182827 CTCTCCCACCACATCTCTTGA 58.817 52.381 0.00 0.00 0.00 3.02
540 542 2.770802 CTCTCCCACCACATCTCTTGAT 59.229 50.000 0.00 0.00 0.00 2.57
541 543 2.768527 TCTCCCACCACATCTCTTGATC 59.231 50.000 0.00 0.00 0.00 2.92
542 544 1.482182 TCCCACCACATCTCTTGATCG 59.518 52.381 0.00 0.00 0.00 3.69
543 545 1.208052 CCCACCACATCTCTTGATCGT 59.792 52.381 0.00 0.00 0.00 3.73
544 546 2.355108 CCCACCACATCTCTTGATCGTT 60.355 50.000 0.00 0.00 0.00 3.85
545 547 3.338249 CCACCACATCTCTTGATCGTTT 58.662 45.455 0.00 0.00 0.00 3.60
546 548 3.753272 CCACCACATCTCTTGATCGTTTT 59.247 43.478 0.00 0.00 0.00 2.43
547 549 4.216257 CCACCACATCTCTTGATCGTTTTT 59.784 41.667 0.00 0.00 0.00 1.94
572 574 9.949174 TTTTTCCGTCACTTAAATTTACTTACC 57.051 29.630 0.00 0.00 0.00 2.85
573 575 8.674263 TTTCCGTCACTTAAATTTACTTACCA 57.326 30.769 0.00 0.00 0.00 3.25
574 576 8.674263 TTCCGTCACTTAAATTTACTTACCAA 57.326 30.769 0.00 0.00 0.00 3.67
575 577 8.314143 TCCGTCACTTAAATTTACTTACCAAG 57.686 34.615 0.00 0.00 0.00 3.61
576 578 7.019418 CCGTCACTTAAATTTACTTACCAAGC 58.981 38.462 0.00 0.00 0.00 4.01
577 579 7.019418 CGTCACTTAAATTTACTTACCAAGCC 58.981 38.462 0.00 0.00 0.00 4.35
578 580 7.019418 GTCACTTAAATTTACTTACCAAGCCG 58.981 38.462 0.00 0.00 0.00 5.52
579 581 5.798434 CACTTAAATTTACTTACCAAGCCGC 59.202 40.000 0.00 0.00 0.00 6.53
580 582 5.474189 ACTTAAATTTACTTACCAAGCCGCA 59.526 36.000 0.00 0.00 0.00 5.69
581 583 3.842732 AATTTACTTACCAAGCCGCAC 57.157 42.857 0.00 0.00 0.00 5.34
582 584 1.525941 TTTACTTACCAAGCCGCACC 58.474 50.000 0.00 0.00 0.00 5.01
583 585 0.397187 TTACTTACCAAGCCGCACCA 59.603 50.000 0.00 0.00 0.00 4.17
584 586 0.320946 TACTTACCAAGCCGCACCAC 60.321 55.000 0.00 0.00 0.00 4.16
585 587 2.666862 TTACCAAGCCGCACCACG 60.667 61.111 0.00 0.00 43.15 4.94
596 598 1.278637 GCACCACGGTAATATGCGC 59.721 57.895 0.00 0.00 0.00 6.09
597 599 1.433053 GCACCACGGTAATATGCGCA 61.433 55.000 14.96 14.96 0.00 6.09
598 600 1.225855 CACCACGGTAATATGCGCAT 58.774 50.000 28.23 28.23 0.00 4.73
599 601 1.069973 CACCACGGTAATATGCGCATG 60.070 52.381 32.48 16.87 0.00 4.06
600 602 1.225855 CCACGGTAATATGCGCATGT 58.774 50.000 32.48 23.99 0.00 3.21
601 603 2.224090 ACCACGGTAATATGCGCATGTA 60.224 45.455 32.48 20.49 0.00 2.29
602 604 2.411748 CCACGGTAATATGCGCATGTAG 59.588 50.000 32.48 18.84 0.00 2.74
603 605 3.313690 CACGGTAATATGCGCATGTAGA 58.686 45.455 32.48 13.46 0.00 2.59
604 606 3.121279 CACGGTAATATGCGCATGTAGAC 59.879 47.826 32.48 24.12 0.00 2.59
605 607 3.243602 ACGGTAATATGCGCATGTAGACA 60.244 43.478 32.48 12.22 0.00 3.41
606 608 3.926527 CGGTAATATGCGCATGTAGACAT 59.073 43.478 32.48 14.15 36.96 3.06
607 609 4.388773 CGGTAATATGCGCATGTAGACATT 59.611 41.667 32.48 23.00 33.61 2.71
608 610 5.107104 CGGTAATATGCGCATGTAGACATTT 60.107 40.000 32.48 11.56 33.61 2.32
609 611 6.090223 CGGTAATATGCGCATGTAGACATTTA 59.910 38.462 32.48 10.52 33.61 1.40
610 612 7.201522 CGGTAATATGCGCATGTAGACATTTAT 60.202 37.037 32.48 11.06 33.61 1.40
611 613 8.450964 GGTAATATGCGCATGTAGACATTTATT 58.549 33.333 32.48 20.30 33.61 1.40
612 614 9.825972 GTAATATGCGCATGTAGACATTTATTT 57.174 29.630 32.48 8.83 33.61 1.40
614 616 9.825972 AATATGCGCATGTAGACATTTATTTAC 57.174 29.630 32.48 0.00 33.61 2.01
615 617 6.670077 TGCGCATGTAGACATTTATTTACA 57.330 33.333 5.66 0.00 33.61 2.41
616 618 6.482835 TGCGCATGTAGACATTTATTTACAC 58.517 36.000 5.66 0.00 33.61 2.90
617 619 6.092807 TGCGCATGTAGACATTTATTTACACA 59.907 34.615 5.66 0.00 33.61 3.72
618 620 6.964370 GCGCATGTAGACATTTATTTACACAA 59.036 34.615 0.30 0.00 33.61 3.33
619 621 7.643764 GCGCATGTAGACATTTATTTACACAAT 59.356 33.333 0.30 0.00 33.61 2.71
620 622 9.158364 CGCATGTAGACATTTATTTACACAATC 57.842 33.333 0.00 0.00 33.61 2.67
621 623 9.158364 GCATGTAGACATTTATTTACACAATCG 57.842 33.333 0.00 0.00 33.61 3.34
622 624 9.158364 CATGTAGACATTTATTTACACAATCGC 57.842 33.333 0.00 0.00 33.61 4.58
623 625 8.257830 TGTAGACATTTATTTACACAATCGCA 57.742 30.769 0.00 0.00 0.00 5.10
624 626 8.888716 TGTAGACATTTATTTACACAATCGCAT 58.111 29.630 0.00 0.00 0.00 4.73
625 627 9.716507 GTAGACATTTATTTACACAATCGCATT 57.283 29.630 0.00 0.00 0.00 3.56
707 709 9.674824 AATATAGAAGGTAATCACGAACTAACG 57.325 33.333 0.00 0.00 39.31 3.18
728 730 9.552114 CTAACGTGTTAGAATAGTTATATCCCG 57.448 37.037 13.28 0.00 43.90 5.14
729 731 7.516198 ACGTGTTAGAATAGTTATATCCCGT 57.484 36.000 0.00 0.00 0.00 5.28
730 732 7.365741 ACGTGTTAGAATAGTTATATCCCGTG 58.634 38.462 0.00 0.00 0.00 4.94
731 733 6.805271 CGTGTTAGAATAGTTATATCCCGTGG 59.195 42.308 0.00 0.00 0.00 4.94
732 734 7.522725 CGTGTTAGAATAGTTATATCCCGTGGT 60.523 40.741 0.00 0.00 0.00 4.16
733 735 8.796475 GTGTTAGAATAGTTATATCCCGTGGTA 58.204 37.037 0.00 0.00 0.00 3.25
734 736 9.017509 TGTTAGAATAGTTATATCCCGTGGTAG 57.982 37.037 0.00 0.00 0.00 3.18
735 737 6.527057 AGAATAGTTATATCCCGTGGTAGC 57.473 41.667 0.00 0.00 0.00 3.58
736 738 4.978083 ATAGTTATATCCCGTGGTAGCG 57.022 45.455 0.00 0.00 0.00 4.26
744 746 3.751246 CGTGGTAGCGGACGGGAA 61.751 66.667 0.00 0.00 31.84 3.97
745 747 2.897972 GTGGTAGCGGACGGGAAT 59.102 61.111 0.00 0.00 0.00 3.01
746 748 1.219935 GTGGTAGCGGACGGGAATT 59.780 57.895 0.00 0.00 0.00 2.17
747 749 1.087771 GTGGTAGCGGACGGGAATTG 61.088 60.000 0.00 0.00 0.00 2.32
748 750 1.219935 GGTAGCGGACGGGAATTGT 59.780 57.895 0.00 0.00 0.00 2.71
749 751 0.392060 GGTAGCGGACGGGAATTGTT 60.392 55.000 0.00 0.00 0.00 2.83
750 752 1.004595 GTAGCGGACGGGAATTGTTC 58.995 55.000 0.00 0.00 0.00 3.18
751 753 0.609151 TAGCGGACGGGAATTGTTCA 59.391 50.000 0.00 0.00 0.00 3.18
752 754 0.035439 AGCGGACGGGAATTGTTCAT 60.035 50.000 0.00 0.00 0.00 2.57
759 761 4.703093 GGACGGGAATTGTTCATAAAAGGA 59.297 41.667 0.00 0.00 0.00 3.36
761 763 6.020971 ACGGGAATTGTTCATAAAAGGAAC 57.979 37.500 0.00 0.00 43.78 3.62
768 770 7.781324 ATTGTTCATAAAAGGAACCTGTCAT 57.219 32.000 2.41 0.00 43.05 3.06
769 771 7.595819 TTGTTCATAAAAGGAACCTGTCATT 57.404 32.000 2.41 0.00 43.05 2.57
777 779 3.450904 AGGAACCTGTCATTGGCTACTA 58.549 45.455 0.00 0.00 0.00 1.82
782 784 3.197983 ACCTGTCATTGGCTACTAGTTCC 59.802 47.826 0.00 3.66 0.00 3.62
787 789 5.105310 TGTCATTGGCTACTAGTTCCTTCTC 60.105 44.000 0.00 0.00 0.00 2.87
811 1262 3.446310 ACTTTTTCGCACCGGAAATTT 57.554 38.095 9.46 0.00 34.19 1.82
814 1265 1.492720 TTTCGCACCGGAAATTTTGC 58.507 45.000 9.46 5.20 31.30 3.68
815 1266 0.385751 TTCGCACCGGAAATTTTGCA 59.614 45.000 9.46 0.00 34.49 4.08
822 1273 1.554617 CCGGAAATTTTGCAAGGGGAT 59.445 47.619 0.00 0.00 0.00 3.85
919 1372 2.039879 AGGGTTTGGTGACTGGTACATC 59.960 50.000 0.00 0.00 38.20 3.06
926 1382 2.420129 GGTGACTGGTACATCCATCCAC 60.420 54.545 0.00 0.00 46.12 4.02
951 1407 6.348786 CCGTCATATATCCTTTGCATCCTTTG 60.349 42.308 0.00 0.00 0.00 2.77
971 1429 0.034059 CAGTGCCAACCTCTCGTTCT 59.966 55.000 0.00 0.00 29.93 3.01
973 1431 0.670854 GTGCCAACCTCTCGTTCTCC 60.671 60.000 0.00 0.00 29.93 3.71
987 1445 2.092321 CGTTCTCCCTCTCCTTCCTCTA 60.092 54.545 0.00 0.00 0.00 2.43
1011 1469 1.542030 GTCGATCATATGGCGTCCTCT 59.458 52.381 15.21 0.00 0.00 3.69
1090 1548 4.388080 CGTACACCGTCGGCGACA 62.388 66.667 35.62 16.40 41.33 4.35
1092 1550 4.041917 TACACCGTCGGCGACACC 62.042 66.667 35.62 13.20 41.33 4.16
1190 1648 1.524482 GATCGAGCTCTTGGCCCTT 59.476 57.895 12.85 0.00 43.05 3.95
1209 1667 0.395586 TCTTGGCACCAACACTTGCT 60.396 50.000 0.00 0.00 38.85 3.91
1274 1739 6.191413 CGTACGTGTTGAAACTAAAACTGTTG 59.809 38.462 7.22 0.00 0.00 3.33
1277 1742 6.072893 ACGTGTTGAAACTAAAACTGTTGTCT 60.073 34.615 0.00 0.00 0.00 3.41
1282 1747 7.561021 TGAAACTAAAACTGTTGTCTATGCA 57.439 32.000 0.00 0.00 0.00 3.96
1285 1750 8.801715 AAACTAAAACTGTTGTCTATGCATTG 57.198 30.769 3.54 2.26 0.00 2.82
1297 1762 2.423446 ATGCATTGGGAATTTTGCCC 57.577 45.000 0.00 0.00 46.22 5.36
1315 1780 1.630244 CCTGCAGTGTTCAGCTACGC 61.630 60.000 13.81 0.00 0.00 4.42
1393 1858 3.964875 CAACGCGCTGGCCAACTT 61.965 61.111 7.01 0.00 35.02 2.66
1686 2242 6.846325 AGGATTTCGATCGTCTTAATTTCC 57.154 37.500 15.94 10.81 0.00 3.13
1687 2243 5.462398 AGGATTTCGATCGTCTTAATTTCCG 59.538 40.000 15.94 0.00 0.00 4.30
1688 2244 4.509915 TTTCGATCGTCTTAATTTCCGC 57.490 40.909 15.94 0.00 0.00 5.54
1689 2245 3.431922 TCGATCGTCTTAATTTCCGCT 57.568 42.857 15.94 0.00 0.00 5.52
1690 2246 4.556942 TCGATCGTCTTAATTTCCGCTA 57.443 40.909 15.94 0.00 0.00 4.26
1691 2247 4.923893 TCGATCGTCTTAATTTCCGCTAA 58.076 39.130 15.94 0.00 0.00 3.09
1692 2248 4.974275 TCGATCGTCTTAATTTCCGCTAAG 59.026 41.667 15.94 0.00 0.00 2.18
1693 2249 4.738740 CGATCGTCTTAATTTCCGCTAAGT 59.261 41.667 7.03 0.00 0.00 2.24
1694 2250 5.231568 CGATCGTCTTAATTTCCGCTAAGTT 59.768 40.000 7.03 0.00 0.00 2.66
1695 2251 6.237755 CGATCGTCTTAATTTCCGCTAAGTTT 60.238 38.462 7.03 0.00 0.00 2.66
1696 2252 6.790285 TCGTCTTAATTTCCGCTAAGTTTT 57.210 33.333 0.00 0.00 0.00 2.43
1697 2253 7.193377 TCGTCTTAATTTCCGCTAAGTTTTT 57.807 32.000 0.00 0.00 0.00 1.94
1718 2274 3.733960 GGGGCGCCGTTCTTTGAC 61.734 66.667 22.54 2.12 0.00 3.18
1719 2275 4.084888 GGGCGCCGTTCTTTGACG 62.085 66.667 22.54 0.00 42.43 4.35
1723 2279 4.007940 GCCGTTCTTTGACGCGCA 62.008 61.111 5.73 1.71 41.50 6.09
1724 2280 2.127758 CCGTTCTTTGACGCGCAC 60.128 61.111 5.73 0.41 41.50 5.34
1725 2281 2.594962 CCGTTCTTTGACGCGCACT 61.595 57.895 5.73 0.00 41.50 4.40
1726 2282 1.154836 CGTTCTTTGACGCGCACTC 60.155 57.895 5.73 0.87 36.12 3.51
1766 2324 1.826487 GTGTGTGCCTCCCGGTTTT 60.826 57.895 0.00 0.00 0.00 2.43
1811 2369 3.946308 TGTGCGTTTTGTGACGAAATA 57.054 38.095 0.70 0.00 45.47 1.40
1822 2380 9.142993 GTTTTGTGACGAAATATTTTCTTTTGC 57.857 29.630 1.43 0.00 0.00 3.68
1948 4638 3.311596 GTGCTTCAACCACTTCTTTACGT 59.688 43.478 0.00 0.00 0.00 3.57
1974 4665 4.024893 ACATGCGAACGATTATTTAGGCTG 60.025 41.667 0.00 0.00 0.00 4.85
1977 4668 4.201773 TGCGAACGATTATTTAGGCTGTTG 60.202 41.667 0.00 0.00 0.00 3.33
2040 4731 8.908172 TTTTTGAAAACAAATGGCAAAAGATC 57.092 26.923 0.00 0.00 38.95 2.75
2046 4737 3.069872 ACAAATGGCAAAAGATCTGCACA 59.930 39.130 7.62 4.07 41.78 4.57
2062 4753 6.839124 TCTGCACATTTCATTGATTAAGGT 57.161 33.333 0.00 0.00 0.00 3.50
2063 4754 7.936496 TCTGCACATTTCATTGATTAAGGTA 57.064 32.000 0.00 0.00 0.00 3.08
2099 4792 4.953940 ACAAACAAACAATGGCCATAGT 57.046 36.364 21.15 10.09 0.00 2.12
2165 4859 0.108041 TAGGATTTGGGACCGAACGC 60.108 55.000 0.00 0.00 0.00 4.84
2173 4867 2.674084 GGACCGAACGCCCTTTTCG 61.674 63.158 0.00 0.00 44.40 3.46
2183 4877 1.398692 GCCCTTTTCGCCATTGGATA 58.601 50.000 6.95 0.00 0.00 2.59
2203 4897 2.900122 TTGAGCACGCATCTTAAAGC 57.100 45.000 0.00 0.00 0.00 3.51
2215 4909 5.503031 CGCATCTTAAAGCATAAGACCACAG 60.503 44.000 12.53 4.62 36.51 3.66
2222 4916 1.672881 GCATAAGACCACAGCCATGTC 59.327 52.381 0.00 0.00 37.65 3.06
2223 4917 1.935873 CATAAGACCACAGCCATGTCG 59.064 52.381 0.00 0.00 37.65 4.35
2225 4919 1.768684 AAGACCACAGCCATGTCGGT 61.769 55.000 0.00 3.28 40.96 4.69
2227 4921 2.347114 CCACAGCCATGTCGGTGA 59.653 61.111 8.63 0.00 37.65 4.02
2244 4938 2.622436 GTGAAGGAGATTGTTCGGGAG 58.378 52.381 0.00 0.00 0.00 4.30
2256 4950 0.320421 TTCGGGAGAAGGCAAAGTCG 60.320 55.000 0.00 0.00 45.39 4.18
2261 4955 1.540363 GGAGAAGGCAAAGTCGTCACA 60.540 52.381 0.00 0.00 0.00 3.58
2264 4958 2.614057 AGAAGGCAAAGTCGTCACAAAG 59.386 45.455 0.00 0.00 0.00 2.77
2266 4960 0.317854 GGCAAAGTCGTCACAAAGGC 60.318 55.000 0.00 0.00 0.00 4.35
2291 4985 0.803117 TCCACTCTCTTCGCACTACG 59.197 55.000 0.00 0.00 45.62 3.51
2308 5003 0.616111 ACGCACCCCTTCTCTCTCAT 60.616 55.000 0.00 0.00 0.00 2.90
2319 5014 1.895798 TCTCTCTCATGTCGCCAACTT 59.104 47.619 0.00 0.00 0.00 2.66
2337 5032 5.825151 CCAACTTCTCCCTTATCATCTTTCC 59.175 44.000 0.00 0.00 0.00 3.13
2353 5048 2.923035 CCTCCCACCGACCACACT 60.923 66.667 0.00 0.00 0.00 3.55
2357 5052 2.355837 CCACCGACCACACTGACG 60.356 66.667 0.00 0.00 0.00 4.35
2364 5059 3.680786 CCACACTGACGGCCTCGA 61.681 66.667 0.00 0.00 40.11 4.04
2414 5109 4.208686 CGGGCTAGAGGTGGTCGC 62.209 72.222 0.00 0.00 0.00 5.19
2430 5125 4.459089 GCGGTGTGGAGGAGGAGC 62.459 72.222 0.00 0.00 0.00 4.70
2432 5127 2.997897 GGTGTGGAGGAGGAGCGT 60.998 66.667 0.00 0.00 0.00 5.07
2504 5199 6.759356 TGCATTTTTATTCAGATGGCAAGATG 59.241 34.615 0.00 0.00 0.00 2.90
2527 5222 4.501743 GGCCGTGATTTTTAGGGAACAAAA 60.502 41.667 0.00 0.00 0.00 2.44
2570 5265 3.042871 GCCATGGCAAATTTTGTCTCA 57.957 42.857 32.08 9.13 41.49 3.27
2571 5266 3.401182 GCCATGGCAAATTTTGTCTCAA 58.599 40.909 32.08 0.00 41.49 3.02
2572 5267 3.187022 GCCATGGCAAATTTTGTCTCAAC 59.813 43.478 32.08 0.00 41.49 3.18
2573 5268 4.634199 CCATGGCAAATTTTGTCTCAACT 58.366 39.130 14.34 0.00 35.94 3.16
2574 5269 5.058490 CCATGGCAAATTTTGTCTCAACTT 58.942 37.500 14.34 0.00 35.94 2.66
2575 5270 5.528320 CCATGGCAAATTTTGTCTCAACTTT 59.472 36.000 14.34 0.00 35.94 2.66
2576 5271 6.705381 CCATGGCAAATTTTGTCTCAACTTTA 59.295 34.615 14.34 0.00 35.94 1.85
2577 5272 7.307337 CCATGGCAAATTTTGTCTCAACTTTAC 60.307 37.037 14.34 0.00 35.94 2.01
2578 5273 6.634805 TGGCAAATTTTGTCTCAACTTTACA 58.365 32.000 14.34 0.00 35.94 2.41
2579 5274 7.271511 TGGCAAATTTTGTCTCAACTTTACAT 58.728 30.769 14.34 0.00 35.94 2.29
2580 5275 7.768120 TGGCAAATTTTGTCTCAACTTTACATT 59.232 29.630 14.34 0.00 35.94 2.71
2581 5276 8.611757 GGCAAATTTTGTCTCAACTTTACATTT 58.388 29.630 10.65 0.00 31.13 2.32
2582 5277 9.986833 GCAAATTTTGTCTCAACTTTACATTTT 57.013 25.926 10.65 0.00 0.00 1.82
2587 5282 9.810545 TTTTGTCTCAACTTTACATTTTTAGGG 57.189 29.630 0.00 0.00 0.00 3.53
2588 5283 7.519032 TGTCTCAACTTTACATTTTTAGGGG 57.481 36.000 0.00 0.00 0.00 4.79
2589 5284 7.291566 TGTCTCAACTTTACATTTTTAGGGGA 58.708 34.615 0.00 0.00 0.00 4.81
2590 5285 7.780745 TGTCTCAACTTTACATTTTTAGGGGAA 59.219 33.333 0.00 0.00 0.00 3.97
2591 5286 8.635328 GTCTCAACTTTACATTTTTAGGGGAAA 58.365 33.333 0.00 0.00 0.00 3.13
2592 5287 9.203163 TCTCAACTTTACATTTTTAGGGGAAAA 57.797 29.630 0.00 0.00 35.16 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.228822 CGTAGGAACAGCAAAGGCAATT 59.771 45.455 0.00 0.00 44.61 2.32
54 55 2.793946 GATGCGATGCCAAAGCGT 59.206 55.556 0.00 0.00 44.31 5.07
104 105 9.844790 CTTTTGAATGAGCAAACATTATGAGTA 57.155 29.630 0.00 0.00 40.03 2.59
108 109 6.369340 TGGCTTTTGAATGAGCAAACATTATG 59.631 34.615 0.00 0.00 40.03 1.90
119 120 3.735746 GGTTTCGTTGGCTTTTGAATGAG 59.264 43.478 0.00 0.00 0.00 2.90
164 166 2.215451 ATCAAGACCTGGGGCGCATT 62.215 55.000 10.83 0.00 0.00 3.56
198 200 3.317711 TGAATTTTCTGCGAGCTTTTGGA 59.682 39.130 0.00 0.00 0.00 3.53
208 210 2.307049 GGAACGTGTGAATTTTCTGCG 58.693 47.619 0.00 0.00 0.00 5.18
227 229 7.281324 CAGTATATATCACTTCTCTAGGACCGG 59.719 44.444 0.00 0.00 0.00 5.28
229 231 7.832187 AGCAGTATATATCACTTCTCTAGGACC 59.168 40.741 0.00 0.00 0.00 4.46
238 240 9.566530 CACTCACATAGCAGTATATATCACTTC 57.433 37.037 0.00 0.00 0.00 3.01
282 284 1.151777 CGCAGTATCATTTCCGCCGT 61.152 55.000 0.00 0.00 0.00 5.68
303 305 1.365633 CTAGCTGGTCGGCATCTCC 59.634 63.158 0.00 0.00 34.17 3.71
397 399 4.178169 TTTCGGTGTGGGTGCGGT 62.178 61.111 0.00 0.00 0.00 5.68
399 401 4.025401 GCTTTCGGTGTGGGTGCG 62.025 66.667 0.00 0.00 0.00 5.34
465 467 6.759356 CCGACAGAAAAAGTAACCCAATTTTT 59.241 34.615 0.00 0.00 38.47 1.94
466 468 6.127281 ACCGACAGAAAAAGTAACCCAATTTT 60.127 34.615 0.00 0.00 0.00 1.82
467 469 5.361571 ACCGACAGAAAAAGTAACCCAATTT 59.638 36.000 0.00 0.00 0.00 1.82
468 470 4.891168 ACCGACAGAAAAAGTAACCCAATT 59.109 37.500 0.00 0.00 0.00 2.32
469 471 4.466827 ACCGACAGAAAAAGTAACCCAAT 58.533 39.130 0.00 0.00 0.00 3.16
470 472 3.888583 ACCGACAGAAAAAGTAACCCAA 58.111 40.909 0.00 0.00 0.00 4.12
471 473 3.564053 ACCGACAGAAAAAGTAACCCA 57.436 42.857 0.00 0.00 0.00 4.51
472 474 5.299949 TCTTACCGACAGAAAAAGTAACCC 58.700 41.667 0.00 0.00 0.00 4.11
473 475 6.258507 TGTTCTTACCGACAGAAAAAGTAACC 59.741 38.462 0.00 0.00 31.98 2.85
474 476 7.010830 AGTGTTCTTACCGACAGAAAAAGTAAC 59.989 37.037 0.00 0.00 31.98 2.50
475 477 7.043565 AGTGTTCTTACCGACAGAAAAAGTAA 58.956 34.615 0.00 0.00 31.98 2.24
476 478 6.576185 AGTGTTCTTACCGACAGAAAAAGTA 58.424 36.000 0.00 0.00 31.98 2.24
477 479 5.425630 AGTGTTCTTACCGACAGAAAAAGT 58.574 37.500 0.00 0.00 31.98 2.66
478 480 5.986004 AGTGTTCTTACCGACAGAAAAAG 57.014 39.130 0.00 0.00 31.98 2.27
479 481 5.005971 CGAAGTGTTCTTACCGACAGAAAAA 59.994 40.000 0.00 0.00 31.98 1.94
480 482 4.505191 CGAAGTGTTCTTACCGACAGAAAA 59.495 41.667 0.00 0.00 31.98 2.29
481 483 4.046462 CGAAGTGTTCTTACCGACAGAAA 58.954 43.478 0.00 0.00 31.98 2.52
482 484 3.067180 ACGAAGTGTTCTTACCGACAGAA 59.933 43.478 0.00 0.00 42.51 3.02
483 485 2.620115 ACGAAGTGTTCTTACCGACAGA 59.380 45.455 0.00 0.00 42.51 3.41
484 486 3.009301 ACGAAGTGTTCTTACCGACAG 57.991 47.619 0.00 0.00 42.51 3.51
499 501 8.604890 GGGAGAGAAAATAATTAGTTGACGAAG 58.395 37.037 0.00 0.00 0.00 3.79
500 502 8.098286 TGGGAGAGAAAATAATTAGTTGACGAA 58.902 33.333 0.00 0.00 0.00 3.85
501 503 7.548075 GTGGGAGAGAAAATAATTAGTTGACGA 59.452 37.037 0.00 0.00 0.00 4.20
502 504 7.201617 GGTGGGAGAGAAAATAATTAGTTGACG 60.202 40.741 0.00 0.00 0.00 4.35
503 505 7.610305 TGGTGGGAGAGAAAATAATTAGTTGAC 59.390 37.037 0.00 0.00 0.00 3.18
504 506 7.610305 GTGGTGGGAGAGAAAATAATTAGTTGA 59.390 37.037 0.00 0.00 0.00 3.18
505 507 7.393234 TGTGGTGGGAGAGAAAATAATTAGTTG 59.607 37.037 0.00 0.00 0.00 3.16
506 508 7.466804 TGTGGTGGGAGAGAAAATAATTAGTT 58.533 34.615 0.00 0.00 0.00 2.24
507 509 7.027874 TGTGGTGGGAGAGAAAATAATTAGT 57.972 36.000 0.00 0.00 0.00 2.24
508 510 7.995488 AGATGTGGTGGGAGAGAAAATAATTAG 59.005 37.037 0.00 0.00 0.00 1.73
509 511 7.872138 AGATGTGGTGGGAGAGAAAATAATTA 58.128 34.615 0.00 0.00 0.00 1.40
510 512 6.735556 AGATGTGGTGGGAGAGAAAATAATT 58.264 36.000 0.00 0.00 0.00 1.40
511 513 6.159398 AGAGATGTGGTGGGAGAGAAAATAAT 59.841 38.462 0.00 0.00 0.00 1.28
512 514 5.488919 AGAGATGTGGTGGGAGAGAAAATAA 59.511 40.000 0.00 0.00 0.00 1.40
513 515 5.032846 AGAGATGTGGTGGGAGAGAAAATA 58.967 41.667 0.00 0.00 0.00 1.40
514 516 3.848975 AGAGATGTGGTGGGAGAGAAAAT 59.151 43.478 0.00 0.00 0.00 1.82
515 517 3.251484 AGAGATGTGGTGGGAGAGAAAA 58.749 45.455 0.00 0.00 0.00 2.29
516 518 2.907892 AGAGATGTGGTGGGAGAGAAA 58.092 47.619 0.00 0.00 0.00 2.52
517 519 2.568956 CAAGAGATGTGGTGGGAGAGAA 59.431 50.000 0.00 0.00 0.00 2.87
518 520 2.182827 CAAGAGATGTGGTGGGAGAGA 58.817 52.381 0.00 0.00 0.00 3.10
519 521 2.182827 TCAAGAGATGTGGTGGGAGAG 58.817 52.381 0.00 0.00 0.00 3.20
520 522 2.325661 TCAAGAGATGTGGTGGGAGA 57.674 50.000 0.00 0.00 0.00 3.71
521 523 2.482664 CGATCAAGAGATGTGGTGGGAG 60.483 54.545 0.00 0.00 33.72 4.30
522 524 1.482182 CGATCAAGAGATGTGGTGGGA 59.518 52.381 0.00 0.00 33.72 4.37
523 525 1.208052 ACGATCAAGAGATGTGGTGGG 59.792 52.381 0.00 0.00 33.72 4.61
524 526 2.680312 ACGATCAAGAGATGTGGTGG 57.320 50.000 0.00 0.00 33.72 4.61
525 527 5.362556 AAAAACGATCAAGAGATGTGGTG 57.637 39.130 0.00 0.00 33.72 4.17
546 548 9.949174 GGTAAGTAAATTTAAGTGACGGAAAAA 57.051 29.630 0.00 0.00 0.00 1.94
547 549 9.118300 TGGTAAGTAAATTTAAGTGACGGAAAA 57.882 29.630 0.00 0.00 0.00 2.29
548 550 8.674263 TGGTAAGTAAATTTAAGTGACGGAAA 57.326 30.769 0.00 0.00 0.00 3.13
549 551 8.674263 TTGGTAAGTAAATTTAAGTGACGGAA 57.326 30.769 0.00 0.00 0.00 4.30
550 552 7.095102 GCTTGGTAAGTAAATTTAAGTGACGGA 60.095 37.037 0.00 0.00 0.00 4.69
551 553 7.019418 GCTTGGTAAGTAAATTTAAGTGACGG 58.981 38.462 0.00 0.00 0.00 4.79
552 554 7.019418 GGCTTGGTAAGTAAATTTAAGTGACG 58.981 38.462 0.00 0.00 0.00 4.35
553 555 7.019418 CGGCTTGGTAAGTAAATTTAAGTGAC 58.981 38.462 0.00 0.00 0.00 3.67
554 556 6.348704 GCGGCTTGGTAAGTAAATTTAAGTGA 60.349 38.462 0.00 0.00 0.00 3.41
555 557 5.798434 GCGGCTTGGTAAGTAAATTTAAGTG 59.202 40.000 0.00 0.00 0.00 3.16
556 558 5.474189 TGCGGCTTGGTAAGTAAATTTAAGT 59.526 36.000 0.00 0.00 0.00 2.24
557 559 5.798434 GTGCGGCTTGGTAAGTAAATTTAAG 59.202 40.000 0.00 0.00 0.00 1.85
558 560 5.335819 GGTGCGGCTTGGTAAGTAAATTTAA 60.336 40.000 0.00 0.00 0.00 1.52
559 561 4.156373 GGTGCGGCTTGGTAAGTAAATTTA 59.844 41.667 0.00 0.00 0.00 1.40
560 562 3.057104 GGTGCGGCTTGGTAAGTAAATTT 60.057 43.478 0.00 0.00 0.00 1.82
561 563 2.490509 GGTGCGGCTTGGTAAGTAAATT 59.509 45.455 0.00 0.00 0.00 1.82
562 564 2.089201 GGTGCGGCTTGGTAAGTAAAT 58.911 47.619 0.00 0.00 0.00 1.40
563 565 1.202782 TGGTGCGGCTTGGTAAGTAAA 60.203 47.619 0.00 0.00 0.00 2.01
564 566 0.397187 TGGTGCGGCTTGGTAAGTAA 59.603 50.000 0.00 0.00 0.00 2.24
565 567 0.320946 GTGGTGCGGCTTGGTAAGTA 60.321 55.000 0.00 0.00 0.00 2.24
566 568 1.599797 GTGGTGCGGCTTGGTAAGT 60.600 57.895 0.00 0.00 0.00 2.24
567 569 2.677003 CGTGGTGCGGCTTGGTAAG 61.677 63.158 0.00 0.00 36.85 2.34
568 570 2.666862 CGTGGTGCGGCTTGGTAA 60.667 61.111 0.00 0.00 36.85 2.85
578 580 1.278637 GCGCATATTACCGTGGTGC 59.721 57.895 0.30 0.00 0.00 5.01
579 581 1.069973 CATGCGCATATTACCGTGGTG 60.070 52.381 24.84 3.36 0.00 4.17
580 582 1.225855 CATGCGCATATTACCGTGGT 58.774 50.000 24.84 0.00 0.00 4.16
581 583 1.225855 ACATGCGCATATTACCGTGG 58.774 50.000 24.84 9.86 0.00 4.94
582 584 3.121279 GTCTACATGCGCATATTACCGTG 59.879 47.826 24.84 12.43 0.00 4.94
583 585 3.243602 TGTCTACATGCGCATATTACCGT 60.244 43.478 24.84 17.69 0.00 4.83
584 586 3.313690 TGTCTACATGCGCATATTACCG 58.686 45.455 24.84 12.23 0.00 4.02
585 587 5.862924 AATGTCTACATGCGCATATTACC 57.137 39.130 24.84 11.74 36.56 2.85
586 588 9.825972 AAATAAATGTCTACATGCGCATATTAC 57.174 29.630 24.84 18.16 36.56 1.89
588 590 9.825972 GTAAATAAATGTCTACATGCGCATATT 57.174 29.630 24.84 15.04 36.56 1.28
589 591 8.998377 TGTAAATAAATGTCTACATGCGCATAT 58.002 29.630 24.84 15.96 36.56 1.78
590 592 8.279800 GTGTAAATAAATGTCTACATGCGCATA 58.720 33.333 24.84 7.75 36.56 3.14
591 593 7.132213 GTGTAAATAAATGTCTACATGCGCAT 58.868 34.615 19.28 19.28 36.56 4.73
592 594 6.092807 TGTGTAAATAAATGTCTACATGCGCA 59.907 34.615 14.96 14.96 36.56 6.09
593 595 6.482835 TGTGTAAATAAATGTCTACATGCGC 58.517 36.000 0.00 0.00 36.56 6.09
594 596 9.158364 GATTGTGTAAATAAATGTCTACATGCG 57.842 33.333 0.00 0.00 36.56 4.73
595 597 9.158364 CGATTGTGTAAATAAATGTCTACATGC 57.842 33.333 0.00 0.00 36.56 4.06
596 598 9.158364 GCGATTGTGTAAATAAATGTCTACATG 57.842 33.333 0.00 0.00 36.56 3.21
597 599 8.888716 TGCGATTGTGTAAATAAATGTCTACAT 58.111 29.630 0.00 0.00 38.41 2.29
598 600 8.257830 TGCGATTGTGTAAATAAATGTCTACA 57.742 30.769 0.00 0.00 0.00 2.74
599 601 9.716507 AATGCGATTGTGTAAATAAATGTCTAC 57.283 29.630 0.00 0.00 0.00 2.59
681 683 9.674824 CGTTAGTTCGTGATTACCTTCTATATT 57.325 33.333 0.00 0.00 0.00 1.28
682 684 8.844244 ACGTTAGTTCGTGATTACCTTCTATAT 58.156 33.333 0.00 0.00 42.56 0.86
683 685 8.213518 ACGTTAGTTCGTGATTACCTTCTATA 57.786 34.615 0.00 0.00 42.56 1.31
684 686 7.093322 ACGTTAGTTCGTGATTACCTTCTAT 57.907 36.000 0.00 0.00 42.56 1.98
685 687 6.500684 ACGTTAGTTCGTGATTACCTTCTA 57.499 37.500 0.00 0.00 42.56 2.10
686 688 5.382618 ACGTTAGTTCGTGATTACCTTCT 57.617 39.130 0.00 0.00 42.56 2.85
702 704 9.552114 CGGGATATAACTATTCTAACACGTTAG 57.448 37.037 10.15 10.15 42.86 2.34
703 705 9.066892 ACGGGATATAACTATTCTAACACGTTA 57.933 33.333 0.00 0.00 0.00 3.18
704 706 7.864379 CACGGGATATAACTATTCTAACACGTT 59.136 37.037 0.00 0.00 0.00 3.99
705 707 7.365741 CACGGGATATAACTATTCTAACACGT 58.634 38.462 0.00 0.00 0.00 4.49
706 708 6.805271 CCACGGGATATAACTATTCTAACACG 59.195 42.308 0.00 0.00 0.00 4.49
707 709 7.664758 ACCACGGGATATAACTATTCTAACAC 58.335 38.462 0.00 0.00 0.00 3.32
708 710 7.844493 ACCACGGGATATAACTATTCTAACA 57.156 36.000 0.00 0.00 0.00 2.41
709 711 7.972832 GCTACCACGGGATATAACTATTCTAAC 59.027 40.741 0.00 0.00 0.00 2.34
710 712 7.148188 CGCTACCACGGGATATAACTATTCTAA 60.148 40.741 0.00 0.00 0.00 2.10
711 713 6.317140 CGCTACCACGGGATATAACTATTCTA 59.683 42.308 0.00 0.00 0.00 2.10
712 714 5.125097 CGCTACCACGGGATATAACTATTCT 59.875 44.000 0.00 0.00 0.00 2.40
713 715 5.338365 CGCTACCACGGGATATAACTATTC 58.662 45.833 0.00 0.00 0.00 1.75
714 716 5.320549 CGCTACCACGGGATATAACTATT 57.679 43.478 0.00 0.00 0.00 1.73
715 717 4.978083 CGCTACCACGGGATATAACTAT 57.022 45.455 0.00 0.00 0.00 2.12
727 729 2.567564 AATTCCCGTCCGCTACCACG 62.568 60.000 0.00 0.00 35.72 4.94
728 730 1.087771 CAATTCCCGTCCGCTACCAC 61.088 60.000 0.00 0.00 0.00 4.16
729 731 1.219664 CAATTCCCGTCCGCTACCA 59.780 57.895 0.00 0.00 0.00 3.25
730 732 0.392060 AACAATTCCCGTCCGCTACC 60.392 55.000 0.00 0.00 0.00 3.18
731 733 1.004595 GAACAATTCCCGTCCGCTAC 58.995 55.000 0.00 0.00 0.00 3.58
732 734 0.609151 TGAACAATTCCCGTCCGCTA 59.391 50.000 0.00 0.00 0.00 4.26
733 735 0.035439 ATGAACAATTCCCGTCCGCT 60.035 50.000 0.00 0.00 0.00 5.52
734 736 1.658994 TATGAACAATTCCCGTCCGC 58.341 50.000 0.00 0.00 0.00 5.54
735 737 4.438200 CCTTTTATGAACAATTCCCGTCCG 60.438 45.833 0.00 0.00 0.00 4.79
736 738 4.703093 TCCTTTTATGAACAATTCCCGTCC 59.297 41.667 0.00 0.00 0.00 4.79
737 739 5.890424 TCCTTTTATGAACAATTCCCGTC 57.110 39.130 0.00 0.00 0.00 4.79
738 740 5.047590 GGTTCCTTTTATGAACAATTCCCGT 60.048 40.000 5.61 0.00 43.05 5.28
739 741 5.185056 AGGTTCCTTTTATGAACAATTCCCG 59.815 40.000 5.61 0.00 43.05 5.14
740 742 6.014584 ACAGGTTCCTTTTATGAACAATTCCC 60.015 38.462 5.61 0.00 43.05 3.97
741 743 6.993079 ACAGGTTCCTTTTATGAACAATTCC 58.007 36.000 5.61 0.00 43.05 3.01
742 744 7.657336 TGACAGGTTCCTTTTATGAACAATTC 58.343 34.615 5.61 0.00 43.05 2.17
743 745 7.595819 TGACAGGTTCCTTTTATGAACAATT 57.404 32.000 5.61 0.00 43.05 2.32
744 746 7.781324 ATGACAGGTTCCTTTTATGAACAAT 57.219 32.000 5.61 0.00 43.05 2.71
745 747 7.432869 CAATGACAGGTTCCTTTTATGAACAA 58.567 34.615 5.61 0.00 43.05 2.83
746 748 6.015519 CCAATGACAGGTTCCTTTTATGAACA 60.016 38.462 5.61 0.00 43.05 3.18
747 749 6.389906 CCAATGACAGGTTCCTTTTATGAAC 58.610 40.000 0.00 0.00 41.05 3.18
748 750 5.047377 GCCAATGACAGGTTCCTTTTATGAA 60.047 40.000 0.00 0.00 0.00 2.57
749 751 4.462483 GCCAATGACAGGTTCCTTTTATGA 59.538 41.667 0.00 0.00 0.00 2.15
750 752 4.463891 AGCCAATGACAGGTTCCTTTTATG 59.536 41.667 0.00 0.00 0.00 1.90
751 753 4.677182 AGCCAATGACAGGTTCCTTTTAT 58.323 39.130 0.00 0.00 0.00 1.40
752 754 4.112634 AGCCAATGACAGGTTCCTTTTA 57.887 40.909 0.00 0.00 0.00 1.52
759 761 4.323562 GGAACTAGTAGCCAATGACAGGTT 60.324 45.833 9.26 0.00 0.00 3.50
761 763 3.452627 AGGAACTAGTAGCCAATGACAGG 59.547 47.826 14.98 0.00 36.02 4.00
768 770 6.724905 AGTTTAGAGAAGGAACTAGTAGCCAA 59.275 38.462 14.98 0.00 38.49 4.52
769 771 6.254522 AGTTTAGAGAAGGAACTAGTAGCCA 58.745 40.000 14.98 0.00 38.49 4.75
782 784 4.455124 CGGTGCGAAAAAGTTTAGAGAAG 58.545 43.478 0.00 0.00 0.00 2.85
787 789 3.612472 TTCCGGTGCGAAAAAGTTTAG 57.388 42.857 0.00 0.00 0.00 1.85
811 1262 1.517538 ATCCCCACATCCCCTTGCAA 61.518 55.000 0.00 0.00 0.00 4.08
814 1265 0.184451 CAGATCCCCACATCCCCTTG 59.816 60.000 0.00 0.00 0.00 3.61
815 1266 0.046242 TCAGATCCCCACATCCCCTT 59.954 55.000 0.00 0.00 0.00 3.95
822 1273 5.966853 TTTATACACATCAGATCCCCACA 57.033 39.130 0.00 0.00 0.00 4.17
919 1372 4.826274 AAGGATATATGACGGTGGATGG 57.174 45.455 0.00 0.00 0.00 3.51
926 1382 4.836825 AGGATGCAAAGGATATATGACGG 58.163 43.478 0.00 0.00 0.00 4.79
951 1407 1.569479 GAACGAGAGGTTGGCACTGC 61.569 60.000 0.00 0.00 39.50 4.40
971 1429 2.514582 ACGATTAGAGGAAGGAGAGGGA 59.485 50.000 0.00 0.00 0.00 4.20
973 1431 2.550606 CGACGATTAGAGGAAGGAGAGG 59.449 54.545 0.00 0.00 0.00 3.69
987 1445 2.596452 GACGCCATATGATCGACGATT 58.404 47.619 12.40 0.00 0.00 3.34
1011 1469 4.135153 GCGAGGAGAGCGGCAGAA 62.135 66.667 1.45 0.00 0.00 3.02
1090 1548 3.580319 GGTCACCCAGCCCTTGGT 61.580 66.667 0.00 0.00 46.25 3.67
1092 1550 4.722700 CCGGTCACCCAGCCCTTG 62.723 72.222 0.00 0.00 0.00 3.61
1190 1648 0.395586 AGCAAGTGTTGGTGCCAAGA 60.396 50.000 3.57 0.00 41.88 3.02
1209 1667 0.808453 GGCGTTTGCGACTATGGCTA 60.808 55.000 0.00 0.00 44.12 3.93
1274 1739 4.122046 GGCAAAATTCCCAATGCATAGAC 58.878 43.478 0.00 0.00 40.51 2.59
1277 1742 3.113824 AGGGCAAAATTCCCAATGCATA 58.886 40.909 0.00 0.00 46.36 3.14
1282 1747 1.279846 CTGCAGGGCAAAATTCCCAAT 59.720 47.619 5.57 0.00 46.36 3.16
1285 1750 0.037046 CACTGCAGGGCAAAATTCCC 60.037 55.000 19.93 0.00 44.25 3.97
1315 1780 3.716006 CCGTGTGCACCTTGCTCG 61.716 66.667 15.69 9.15 45.31 5.03
1590 2091 0.957395 CAGAACAGCGCCACCTTGAT 60.957 55.000 2.29 0.00 0.00 2.57
1672 2186 6.980051 AAACTTAGCGGAAATTAAGACGAT 57.020 33.333 0.00 0.00 32.52 3.73
1701 2257 3.733960 GTCAAAGAACGGCGCCCC 61.734 66.667 23.46 10.66 0.00 5.80
1702 2258 4.084888 CGTCAAAGAACGGCGCCC 62.085 66.667 23.46 7.02 38.96 6.13
1703 2259 4.736631 GCGTCAAAGAACGGCGCC 62.737 66.667 19.07 19.07 42.81 6.53
1706 2262 4.007940 TGCGCGTCAAAGAACGGC 62.008 61.111 8.43 1.54 42.81 5.68
1707 2263 2.127758 GTGCGCGTCAAAGAACGG 60.128 61.111 8.43 0.00 42.81 4.44
1708 2264 1.154836 GAGTGCGCGTCAAAGAACG 60.155 57.895 8.43 0.00 45.31 3.95
1709 2265 1.154836 CGAGTGCGCGTCAAAGAAC 60.155 57.895 8.43 0.00 0.00 3.01
1710 2266 1.590525 ACGAGTGCGCGTCAAAGAA 60.591 52.632 8.43 0.00 41.22 2.52
1711 2267 2.027024 ACGAGTGCGCGTCAAAGA 59.973 55.556 8.43 0.00 41.22 2.52
1712 2268 2.168621 CACGAGTGCGCGTCAAAG 59.831 61.111 8.43 0.00 43.59 2.77
1713 2269 2.582265 GACACGAGTGCGCGTCAAA 61.582 57.895 8.43 0.00 45.95 2.69
1714 2270 3.028019 GACACGAGTGCGCGTCAA 61.028 61.111 8.43 0.00 45.95 3.18
1719 2275 1.800315 ATACACGACACGAGTGCGC 60.800 57.895 0.00 0.00 42.94 6.09
1720 2276 1.980924 CATACACGACACGAGTGCG 59.019 57.895 14.78 14.78 42.94 5.34
1721 2277 1.006825 TGCATACACGACACGAGTGC 61.007 55.000 2.76 0.00 42.94 4.40
1722 2278 0.708370 GTGCATACACGACACGAGTG 59.292 55.000 1.13 1.13 44.57 3.51
1723 2279 3.102515 GTGCATACACGACACGAGT 57.897 52.632 0.00 0.00 36.98 4.18
1811 2369 5.981915 GCAGAACTCTTCAGCAAAAGAAAAT 59.018 36.000 2.88 0.00 41.28 1.82
1822 2380 7.352719 ACTTTTATTACGCAGAACTCTTCAG 57.647 36.000 0.00 0.00 0.00 3.02
1882 2470 3.105937 TCGATAACGATTGCGACTCTTG 58.894 45.455 0.00 0.00 43.81 3.02
1948 4638 4.509970 CCTAAATAATCGTTCGCATGTGGA 59.490 41.667 6.39 0.00 0.00 4.02
1974 4665 2.949106 TCGGTCCTCGACGACAAC 59.051 61.111 15.07 0.00 43.74 3.32
2040 4731 8.984891 TTTACCTTAATCAATGAAATGTGCAG 57.015 30.769 0.00 0.00 0.00 4.41
2063 4754 9.503399 TTGTTTGTTTGTACTTAAAACCCATTT 57.497 25.926 5.20 0.00 36.82 2.32
2133 4827 4.637091 CCCAAATCCTAAAATACCGACGTT 59.363 41.667 0.00 0.00 0.00 3.99
2165 4859 3.636300 TCAATATCCAATGGCGAAAAGGG 59.364 43.478 0.00 0.00 0.00 3.95
2173 4867 1.335324 GCGTGCTCAATATCCAATGGC 60.335 52.381 0.00 0.00 0.00 4.40
2183 4877 2.749076 TGCTTTAAGATGCGTGCTCAAT 59.251 40.909 0.00 0.00 0.00 2.57
2203 4897 1.935873 CGACATGGCTGTGGTCTTATG 59.064 52.381 0.00 0.00 35.14 1.90
2215 4909 0.179000 ATCTCCTTCACCGACATGGC 59.821 55.000 0.00 0.00 43.94 4.40
2222 4916 1.359848 CCGAACAATCTCCTTCACCG 58.640 55.000 0.00 0.00 0.00 4.94
2223 4917 1.278127 TCCCGAACAATCTCCTTCACC 59.722 52.381 0.00 0.00 0.00 4.02
2225 4919 2.536066 TCTCCCGAACAATCTCCTTCA 58.464 47.619 0.00 0.00 0.00 3.02
2227 4921 2.237392 CCTTCTCCCGAACAATCTCCTT 59.763 50.000 0.00 0.00 0.00 3.36
2244 4938 2.287009 CCTTTGTGACGACTTTGCCTTC 60.287 50.000 0.00 0.00 0.00 3.46
2247 4941 0.317854 GCCTTTGTGACGACTTTGCC 60.318 55.000 0.00 0.00 0.00 4.52
2256 4950 1.537202 GTGGATCTGTGCCTTTGTGAC 59.463 52.381 0.00 0.00 0.00 3.67
2261 4955 2.264455 AGAGAGTGGATCTGTGCCTTT 58.736 47.619 0.00 0.00 38.84 3.11
2264 4958 1.470632 CGAAGAGAGTGGATCTGTGCC 60.471 57.143 0.00 0.00 38.84 5.01
2266 4960 1.203287 TGCGAAGAGAGTGGATCTGTG 59.797 52.381 0.00 0.00 38.84 3.66
2291 4985 0.908198 ACATGAGAGAGAAGGGGTGC 59.092 55.000 0.00 0.00 0.00 5.01
2308 5003 1.344065 TAAGGGAGAAGTTGGCGACA 58.656 50.000 7.78 0.00 39.83 4.35
2319 5014 4.235372 GGGAGGAAAGATGATAAGGGAGA 58.765 47.826 0.00 0.00 0.00 3.71
2337 5032 2.207229 TCAGTGTGGTCGGTGGGAG 61.207 63.158 0.00 0.00 0.00 4.30
2357 5052 4.467107 AGAGGGAGGGTCGAGGCC 62.467 72.222 0.00 0.00 0.00 5.19
2364 5059 4.390556 AGCGCAGAGAGGGAGGGT 62.391 66.667 11.47 0.00 0.00 4.34
2392 5087 2.499827 CCACCTCTAGCCCGCCTAC 61.500 68.421 0.00 0.00 0.00 3.18
2393 5088 2.123425 CCACCTCTAGCCCGCCTA 60.123 66.667 0.00 0.00 0.00 3.93
2403 5098 3.991051 CACACCGCGACCACCTCT 61.991 66.667 8.23 0.00 0.00 3.69
2414 5109 4.135153 CGCTCCTCCTCCACACCG 62.135 72.222 0.00 0.00 0.00 4.94
2474 5169 3.781079 TCTGAATAAAAATGCAGGCGG 57.219 42.857 0.00 0.00 0.00 6.13
2475 5170 4.046462 CCATCTGAATAAAAATGCAGGCG 58.954 43.478 0.00 0.00 0.00 5.52
2504 5199 2.164338 TGTTCCCTAAAAATCACGGCC 58.836 47.619 0.00 0.00 0.00 6.13
2550 5245 3.042871 TGAGACAAAATTTGCCATGGC 57.957 42.857 30.54 30.54 42.35 4.40
2552 5247 6.607735 AAAGTTGAGACAAAATTTGCCATG 57.392 33.333 5.52 0.00 0.00 3.66
2553 5248 7.271511 TGTAAAGTTGAGACAAAATTTGCCAT 58.728 30.769 5.52 0.00 31.49 4.40
2554 5249 6.634805 TGTAAAGTTGAGACAAAATTTGCCA 58.365 32.000 5.52 0.00 31.49 4.92
2555 5250 7.713764 ATGTAAAGTTGAGACAAAATTTGCC 57.286 32.000 5.52 0.00 31.49 4.52
2556 5251 9.986833 AAAATGTAAAGTTGAGACAAAATTTGC 57.013 25.926 5.52 0.00 32.62 3.68
2561 5256 9.810545 CCCTAAAAATGTAAAGTTGAGACAAAA 57.189 29.630 0.00 0.00 0.00 2.44
2562 5257 8.417884 CCCCTAAAAATGTAAAGTTGAGACAAA 58.582 33.333 0.00 0.00 0.00 2.83
2563 5258 7.780745 TCCCCTAAAAATGTAAAGTTGAGACAA 59.219 33.333 0.00 0.00 0.00 3.18
2564 5259 7.291566 TCCCCTAAAAATGTAAAGTTGAGACA 58.708 34.615 0.00 0.00 0.00 3.41
2565 5260 7.754851 TCCCCTAAAAATGTAAAGTTGAGAC 57.245 36.000 0.00 0.00 0.00 3.36
2566 5261 8.770010 TTTCCCCTAAAAATGTAAAGTTGAGA 57.230 30.769 0.00 0.00 0.00 3.27
2567 5262 9.825109 TTTTTCCCCTAAAAATGTAAAGTTGAG 57.175 29.630 0.00 0.00 41.13 3.02


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

AutoCloner maintained by Alex Coulton.