Multiple sequence alignment - TraesCS1D01G165700

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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 TraesCS1D01G165700 chr1D 100.000 2554 0 0 1 2554 236807745 236810298 0.000000e+00 4717.0
1 TraesCS1D01G165700 chr1D 93.846 65 4 0 772 836 38554126 38554190 5.820000e-17 99.0
2 TraesCS1D01G165700 chr1A 88.333 1380 63 45 625 1971 308811878 308810564 0.000000e+00 1567.0
3 TraesCS1D01G165700 chr1A 89.605 481 24 13 1 473 308812353 308811891 2.830000e-164 588.0
4 TraesCS1D01G165700 chr1A 92.857 84 4 2 755 836 37499538 37499621 1.240000e-23 121.0
5 TraesCS1D01G165700 chr1A 98.529 68 1 0 1981 2048 308810340 308810273 1.240000e-23 121.0
6 TraesCS1D01G165700 chr1A 84.615 91 9 4 2046 2133 26195673 26195761 4.530000e-13 86.1
7 TraesCS1D01G165700 chr1B 92.462 597 26 9 909 1504 342122249 342122827 0.000000e+00 835.0
8 TraesCS1D01G165700 chr1B 92.437 476 26 8 3 471 342118103 342118575 0.000000e+00 671.0
9 TraesCS1D01G165700 chr1B 92.157 408 15 4 1498 1889 342122953 342123359 6.170000e-156 560.0
10 TraesCS1D01G165700 chr1B 81.073 317 21 13 614 924 342118575 342118858 1.540000e-52 217.0
11 TraesCS1D01G165700 chr1B 94.203 69 3 1 1981 2049 342202039 342202106 1.250000e-18 104.0
12 TraesCS1D01G165700 chr3A 91.732 508 34 5 2049 2554 435805002 435804501 0.000000e+00 699.0
13 TraesCS1D01G165700 chr3A 89.370 508 38 8 2049 2554 691371744 691372237 2.160000e-175 625.0
14 TraesCS1D01G165700 chr6D 91.212 330 20 5 2049 2372 372816732 372816406 8.390000e-120 440.0
15 TraesCS1D01G165700 chr6D 94.022 184 9 2 2372 2554 372816277 372816095 6.960000e-71 278.0
16 TraesCS1D01G165700 chr2D 100.000 30 0 0 2059 2088 6452973 6453002 3.550000e-04 56.5


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 TraesCS1D01G165700 chr1D 236807745 236810298 2553 False 4717.000000 4717 100.000000 1 2554 1 chr1D.!!$F2 2553
1 TraesCS1D01G165700 chr1A 308810273 308812353 2080 True 758.666667 1567 92.155667 1 2048 3 chr1A.!!$R1 2047
2 TraesCS1D01G165700 chr1B 342118103 342123359 5256 False 570.750000 835 89.532250 3 1889 4 chr1B.!!$F2 1886
3 TraesCS1D01G165700 chr3A 435804501 435805002 501 True 699.000000 699 91.732000 2049 2554 1 chr3A.!!$R1 505
4 TraesCS1D01G165700 chr6D 372816095 372816732 637 True 359.000000 440 92.617000 2049 2554 2 chr6D.!!$R1 505

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
685 697 0.109458 TTTCACCGTCCTCGTCATCG 60.109 55.0 0.0 0.0 38.55 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 5562 0.543749 GCAGTCTACATGAAGGGGCT 59.456 55.0 0.0 0.0 0.0 5.19 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
80 81 1.405105 TGGCGAATTTGCATCTTAGGC 59.595 47.619 19.31 7.96 36.28 3.93
83 84 2.542411 GCGAATTTGCATCTTAGGCCTG 60.542 50.000 17.99 0.00 34.15 4.85
98 99 2.031012 CTGGTTCTCTGTGCGGCA 59.969 61.111 0.00 0.00 0.00 5.69
195 196 3.002759 GGTGCTAGCTTTACTAATGCTGC 59.997 47.826 17.23 16.03 41.39 5.25
196 197 3.873952 GTGCTAGCTTTACTAATGCTGCT 59.126 43.478 17.23 0.00 41.39 4.24
197 198 3.873361 TGCTAGCTTTACTAATGCTGCTG 59.127 43.478 17.23 9.23 41.39 4.41
206 207 3.204526 ACTAATGCTGCTGATTGAGAGC 58.795 45.455 0.00 0.00 36.95 4.09
233 234 1.005340 GGAATCAAGAGTGCAGCGAG 58.995 55.000 0.00 0.00 0.00 5.03
251 252 0.252479 AGGCCAGTTCATCTGCTGAG 59.748 55.000 5.01 0.00 42.38 3.35
254 255 0.747283 CCAGTTCATCTGCTGAGGGC 60.747 60.000 5.39 0.00 42.38 5.19
397 409 2.154854 AACTGTCACACATCACGAGG 57.845 50.000 0.00 0.00 0.00 4.63
412 424 1.204146 CGAGGGATTCAGGGAGGAAA 58.796 55.000 0.00 0.00 0.00 3.13
435 447 2.288025 GGGTTCAGGTAGTCGGCCA 61.288 63.158 2.24 0.00 0.00 5.36
452 464 1.583054 CCAGACTTTATACCGCTGCC 58.417 55.000 0.00 0.00 0.00 4.85
458 470 1.593006 CTTTATACCGCTGCCGAGTTG 59.407 52.381 0.00 0.00 36.29 3.16
473 485 3.961651 TTGGGTAGGGGCTGGGGA 61.962 66.667 0.00 0.00 0.00 4.81
474 486 3.525348 TTGGGTAGGGGCTGGGGAA 62.525 63.158 0.00 0.00 0.00 3.97
475 487 2.369706 GGGTAGGGGCTGGGGAAT 60.370 66.667 0.00 0.00 0.00 3.01
476 488 1.073242 GGGTAGGGGCTGGGGAATA 60.073 63.158 0.00 0.00 0.00 1.75
477 489 1.134438 GGGTAGGGGCTGGGGAATAG 61.134 65.000 0.00 0.00 0.00 1.73
479 491 0.401541 GTAGGGGCTGGGGAATAGGT 60.402 60.000 0.00 0.00 0.00 3.08
480 492 0.401395 TAGGGGCTGGGGAATAGGTG 60.401 60.000 0.00 0.00 0.00 4.00
481 493 2.768022 GGGGCTGGGGAATAGGTGG 61.768 68.421 0.00 0.00 0.00 4.61
482 494 1.696314 GGGCTGGGGAATAGGTGGA 60.696 63.158 0.00 0.00 0.00 4.02
485 497 1.439543 GCTGGGGAATAGGTGGATCT 58.560 55.000 0.00 0.00 0.00 2.75
486 498 1.072965 GCTGGGGAATAGGTGGATCTG 59.927 57.143 0.00 0.00 0.00 2.90
487 499 2.694397 CTGGGGAATAGGTGGATCTGA 58.306 52.381 0.00 0.00 0.00 3.27
488 500 3.048600 CTGGGGAATAGGTGGATCTGAA 58.951 50.000 0.00 0.00 0.00 3.02
489 501 3.048600 TGGGGAATAGGTGGATCTGAAG 58.951 50.000 0.00 0.00 0.00 3.02
490 502 2.224646 GGGGAATAGGTGGATCTGAAGC 60.225 54.545 0.00 0.00 0.00 3.86
491 503 2.708325 GGGAATAGGTGGATCTGAAGCT 59.292 50.000 0.00 0.00 0.00 3.74
492 504 3.244387 GGGAATAGGTGGATCTGAAGCTC 60.244 52.174 0.00 0.00 0.00 4.09
493 505 3.645687 GGAATAGGTGGATCTGAAGCTCT 59.354 47.826 0.00 0.00 0.00 4.09
494 506 4.502950 GGAATAGGTGGATCTGAAGCTCTG 60.503 50.000 0.00 0.00 0.00 3.35
495 507 2.244486 AGGTGGATCTGAAGCTCTGA 57.756 50.000 0.00 0.00 0.00 3.27
496 508 2.544721 AGGTGGATCTGAAGCTCTGAA 58.455 47.619 0.00 0.00 0.00 3.02
497 509 2.235898 AGGTGGATCTGAAGCTCTGAAC 59.764 50.000 0.00 0.00 0.00 3.18
498 510 2.626840 GTGGATCTGAAGCTCTGAACC 58.373 52.381 0.00 0.00 37.64 3.62
499 511 2.027745 GTGGATCTGAAGCTCTGAACCA 60.028 50.000 13.59 13.59 42.12 3.67
500 512 2.639347 TGGATCTGAAGCTCTGAACCAA 59.361 45.455 14.54 4.76 41.69 3.67
501 513 3.265221 TGGATCTGAAGCTCTGAACCAAT 59.735 43.478 14.54 0.00 41.69 3.16
502 514 4.471025 TGGATCTGAAGCTCTGAACCAATA 59.529 41.667 14.54 0.19 41.69 1.90
503 515 4.813697 GGATCTGAAGCTCTGAACCAATAC 59.186 45.833 11.45 0.00 37.28 1.89
504 516 4.207891 TCTGAAGCTCTGAACCAATACC 57.792 45.455 0.00 0.00 0.00 2.73
505 517 3.055094 TCTGAAGCTCTGAACCAATACCC 60.055 47.826 0.00 0.00 0.00 3.69
506 518 2.642311 TGAAGCTCTGAACCAATACCCA 59.358 45.455 0.00 0.00 0.00 4.51
507 519 3.073798 TGAAGCTCTGAACCAATACCCAA 59.926 43.478 0.00 0.00 0.00 4.12
508 520 3.806949 AGCTCTGAACCAATACCCAAA 57.193 42.857 0.00 0.00 0.00 3.28
509 521 3.421844 AGCTCTGAACCAATACCCAAAC 58.578 45.455 0.00 0.00 0.00 2.93
510 522 3.153919 GCTCTGAACCAATACCCAAACA 58.846 45.455 0.00 0.00 0.00 2.83
511 523 3.572255 GCTCTGAACCAATACCCAAACAA 59.428 43.478 0.00 0.00 0.00 2.83
512 524 4.558697 GCTCTGAACCAATACCCAAACAAC 60.559 45.833 0.00 0.00 0.00 3.32
513 525 3.892588 TCTGAACCAATACCCAAACAACC 59.107 43.478 0.00 0.00 0.00 3.77
514 526 2.966516 TGAACCAATACCCAAACAACCC 59.033 45.455 0.00 0.00 0.00 4.11
515 527 2.777459 ACCAATACCCAAACAACCCA 57.223 45.000 0.00 0.00 0.00 4.51
516 528 3.268034 ACCAATACCCAAACAACCCAT 57.732 42.857 0.00 0.00 0.00 4.00
517 529 2.903135 ACCAATACCCAAACAACCCATG 59.097 45.455 0.00 0.00 0.00 3.66
518 530 2.354604 CCAATACCCAAACAACCCATGC 60.355 50.000 0.00 0.00 0.00 4.06
519 531 2.301296 CAATACCCAAACAACCCATGCA 59.699 45.455 0.00 0.00 0.00 3.96
520 532 2.088104 TACCCAAACAACCCATGCAA 57.912 45.000 0.00 0.00 0.00 4.08
521 533 1.207791 ACCCAAACAACCCATGCAAA 58.792 45.000 0.00 0.00 0.00 3.68
522 534 1.773653 ACCCAAACAACCCATGCAAAT 59.226 42.857 0.00 0.00 0.00 2.32
523 535 2.174424 ACCCAAACAACCCATGCAAATT 59.826 40.909 0.00 0.00 0.00 1.82
524 536 2.813172 CCCAAACAACCCATGCAAATTC 59.187 45.455 0.00 0.00 0.00 2.17
525 537 3.496515 CCCAAACAACCCATGCAAATTCT 60.497 43.478 0.00 0.00 0.00 2.40
526 538 4.136051 CCAAACAACCCATGCAAATTCTT 58.864 39.130 0.00 0.00 0.00 2.52
527 539 4.023878 CCAAACAACCCATGCAAATTCTTG 60.024 41.667 0.00 0.00 35.49 3.02
528 540 4.686191 AACAACCCATGCAAATTCTTGA 57.314 36.364 0.00 0.00 34.14 3.02
529 541 3.993920 ACAACCCATGCAAATTCTTGAC 58.006 40.909 0.00 0.00 34.14 3.18
530 542 3.642848 ACAACCCATGCAAATTCTTGACT 59.357 39.130 0.00 0.00 34.14 3.41
531 543 4.240096 CAACCCATGCAAATTCTTGACTC 58.760 43.478 0.00 0.00 34.14 3.36
532 544 2.827921 ACCCATGCAAATTCTTGACTCC 59.172 45.455 0.00 0.00 34.14 3.85
533 545 2.159338 CCCATGCAAATTCTTGACTCCG 60.159 50.000 0.00 0.00 34.14 4.63
534 546 2.489329 CCATGCAAATTCTTGACTCCGT 59.511 45.455 0.00 0.00 34.14 4.69
535 547 3.689161 CCATGCAAATTCTTGACTCCGTA 59.311 43.478 0.00 0.00 34.14 4.02
536 548 4.201851 CCATGCAAATTCTTGACTCCGTAG 60.202 45.833 0.00 0.00 34.14 3.51
537 549 4.002906 TGCAAATTCTTGACTCCGTAGT 57.997 40.909 0.00 0.00 39.21 2.73
538 550 3.745975 TGCAAATTCTTGACTCCGTAGTG 59.254 43.478 0.00 0.00 35.56 2.74
539 551 3.746492 GCAAATTCTTGACTCCGTAGTGT 59.254 43.478 0.00 0.00 35.56 3.55
540 552 4.927425 GCAAATTCTTGACTCCGTAGTGTA 59.073 41.667 0.00 0.00 35.56 2.90
541 553 5.163982 GCAAATTCTTGACTCCGTAGTGTAC 60.164 44.000 0.00 0.00 35.56 2.90
542 554 5.717078 AATTCTTGACTCCGTAGTGTACA 57.283 39.130 0.00 0.00 35.56 2.90
543 555 5.916661 ATTCTTGACTCCGTAGTGTACAT 57.083 39.130 0.00 0.00 35.56 2.29
544 556 4.959596 TCTTGACTCCGTAGTGTACATC 57.040 45.455 0.00 0.00 35.56 3.06
545 557 3.693085 TCTTGACTCCGTAGTGTACATCC 59.307 47.826 0.00 0.00 35.56 3.51
546 558 3.361281 TGACTCCGTAGTGTACATCCT 57.639 47.619 0.00 0.00 35.56 3.24
547 559 4.492494 TGACTCCGTAGTGTACATCCTA 57.508 45.455 0.00 0.00 35.56 2.94
548 560 4.449131 TGACTCCGTAGTGTACATCCTAG 58.551 47.826 0.00 0.00 35.56 3.02
549 561 4.080695 TGACTCCGTAGTGTACATCCTAGT 60.081 45.833 0.00 0.00 35.56 2.57
550 562 5.129320 TGACTCCGTAGTGTACATCCTAGTA 59.871 44.000 0.00 0.00 35.56 1.82
551 563 5.363939 ACTCCGTAGTGTACATCCTAGTAC 58.636 45.833 0.00 0.00 43.58 2.73
552 564 4.371786 TCCGTAGTGTACATCCTAGTACG 58.628 47.826 0.00 4.77 45.66 3.67
553 565 4.122776 CCGTAGTGTACATCCTAGTACGT 58.877 47.826 13.37 0.00 45.66 3.57
554 566 5.068591 TCCGTAGTGTACATCCTAGTACGTA 59.931 44.000 13.37 0.00 45.66 3.57
555 567 5.928839 CCGTAGTGTACATCCTAGTACGTAT 59.071 44.000 13.37 0.00 45.66 3.06
556 568 7.039993 TCCGTAGTGTACATCCTAGTACGTATA 60.040 40.741 13.37 0.00 45.66 1.47
557 569 7.761704 CCGTAGTGTACATCCTAGTACGTATAT 59.238 40.741 13.37 0.00 45.66 0.86
558 570 9.144747 CGTAGTGTACATCCTAGTACGTATATT 57.855 37.037 0.00 0.00 45.66 1.28
561 573 9.007901 AGTGTACATCCTAGTACGTATATTTCC 57.992 37.037 0.00 0.00 45.66 3.13
562 574 8.786898 GTGTACATCCTAGTACGTATATTTCCA 58.213 37.037 0.00 0.00 45.66 3.53
563 575 9.006839 TGTACATCCTAGTACGTATATTTCCAG 57.993 37.037 0.00 0.00 45.66 3.86
564 576 9.224267 GTACATCCTAGTACGTATATTTCCAGA 57.776 37.037 0.00 0.00 35.51 3.86
565 577 8.701908 ACATCCTAGTACGTATATTTCCAGAA 57.298 34.615 0.00 0.00 0.00 3.02
566 578 8.794553 ACATCCTAGTACGTATATTTCCAGAAG 58.205 37.037 0.00 0.00 0.00 2.85
567 579 9.011095 CATCCTAGTACGTATATTTCCAGAAGA 57.989 37.037 0.00 0.00 0.00 2.87
568 580 8.985315 TCCTAGTACGTATATTTCCAGAAGAA 57.015 34.615 0.00 0.00 0.00 2.52
569 581 9.584008 TCCTAGTACGTATATTTCCAGAAGAAT 57.416 33.333 0.00 0.00 33.44 2.40
573 585 8.827677 AGTACGTATATTTCCAGAAGAATTTGC 58.172 33.333 0.00 0.00 33.44 3.68
574 586 7.624360 ACGTATATTTCCAGAAGAATTTGCA 57.376 32.000 0.00 0.00 33.44 4.08
575 587 7.697691 ACGTATATTTCCAGAAGAATTTGCAG 58.302 34.615 0.00 0.00 33.44 4.41
576 588 7.134815 CGTATATTTCCAGAAGAATTTGCAGG 58.865 38.462 0.00 0.00 33.44 4.85
577 589 7.201732 CGTATATTTCCAGAAGAATTTGCAGGT 60.202 37.037 0.00 0.00 33.44 4.00
578 590 5.813513 ATTTCCAGAAGAATTTGCAGGTT 57.186 34.783 0.00 0.00 33.44 3.50
579 591 4.589216 TTCCAGAAGAATTTGCAGGTTG 57.411 40.909 0.00 0.00 0.00 3.77
580 592 3.565307 TCCAGAAGAATTTGCAGGTTGT 58.435 40.909 0.00 0.00 0.00 3.32
581 593 3.960102 TCCAGAAGAATTTGCAGGTTGTT 59.040 39.130 0.00 0.00 0.00 2.83
582 594 4.405358 TCCAGAAGAATTTGCAGGTTGTTT 59.595 37.500 0.00 0.00 0.00 2.83
583 595 4.508861 CCAGAAGAATTTGCAGGTTGTTTG 59.491 41.667 0.00 0.00 0.00 2.93
584 596 5.111293 CAGAAGAATTTGCAGGTTGTTTGT 58.889 37.500 0.00 0.00 0.00 2.83
585 597 6.272318 CAGAAGAATTTGCAGGTTGTTTGTA 58.728 36.000 0.00 0.00 0.00 2.41
586 598 6.198966 CAGAAGAATTTGCAGGTTGTTTGTAC 59.801 38.462 0.00 0.00 0.00 2.90
587 599 5.852282 AGAATTTGCAGGTTGTTTGTACT 57.148 34.783 0.00 0.00 0.00 2.73
588 600 6.952773 AGAATTTGCAGGTTGTTTGTACTA 57.047 33.333 0.00 0.00 0.00 1.82
589 601 6.735130 AGAATTTGCAGGTTGTTTGTACTAC 58.265 36.000 0.00 0.00 0.00 2.73
590 602 6.546034 AGAATTTGCAGGTTGTTTGTACTACT 59.454 34.615 0.00 0.00 31.77 2.57
591 603 6.709018 ATTTGCAGGTTGTTTGTACTACTT 57.291 33.333 0.00 0.00 31.77 2.24
592 604 5.744666 TTGCAGGTTGTTTGTACTACTTC 57.255 39.130 0.00 0.00 31.77 3.01
593 605 4.771903 TGCAGGTTGTTTGTACTACTTCA 58.228 39.130 0.00 0.00 31.77 3.02
594 606 4.573201 TGCAGGTTGTTTGTACTACTTCAC 59.427 41.667 0.00 0.00 31.77 3.18
595 607 4.573201 GCAGGTTGTTTGTACTACTTCACA 59.427 41.667 0.00 0.00 31.77 3.58
596 608 5.238650 GCAGGTTGTTTGTACTACTTCACAT 59.761 40.000 0.00 0.00 31.77 3.21
597 609 6.565999 GCAGGTTGTTTGTACTACTTCACATC 60.566 42.308 0.00 0.00 31.77 3.06
598 610 5.694910 AGGTTGTTTGTACTACTTCACATCG 59.305 40.000 0.00 0.00 31.77 3.84
599 611 5.371629 GTTGTTTGTACTACTTCACATCGC 58.628 41.667 0.00 0.00 0.00 4.58
600 612 4.623002 TGTTTGTACTACTTCACATCGCA 58.377 39.130 0.00 0.00 0.00 5.10
601 613 5.051153 TGTTTGTACTACTTCACATCGCAA 58.949 37.500 0.00 0.00 0.00 4.85
602 614 5.699001 TGTTTGTACTACTTCACATCGCAAT 59.301 36.000 0.00 0.00 0.00 3.56
603 615 5.778161 TTGTACTACTTCACATCGCAATG 57.222 39.130 0.00 0.00 38.93 2.82
605 617 5.956642 TGTACTACTTCACATCGCAATGTA 58.043 37.500 0.00 0.00 44.41 2.29
606 618 5.803461 TGTACTACTTCACATCGCAATGTAC 59.197 40.000 0.00 0.00 44.41 2.90
607 619 4.816392 ACTACTTCACATCGCAATGTACA 58.184 39.130 0.00 0.00 44.41 2.90
608 620 5.419542 ACTACTTCACATCGCAATGTACAT 58.580 37.500 1.41 1.41 44.41 2.29
609 621 4.604843 ACTTCACATCGCAATGTACATG 57.395 40.909 9.63 5.10 44.41 3.21
610 622 4.002982 ACTTCACATCGCAATGTACATGT 58.997 39.130 9.63 2.69 44.41 3.21
611 623 5.175127 ACTTCACATCGCAATGTACATGTA 58.825 37.500 9.63 0.08 44.41 2.29
612 624 5.063438 ACTTCACATCGCAATGTACATGTAC 59.937 40.000 25.99 25.99 44.41 2.90
613 625 3.549873 TCACATCGCAATGTACATGTACG 59.450 43.478 26.59 16.69 44.41 3.67
614 626 3.549873 CACATCGCAATGTACATGTACGA 59.450 43.478 26.59 22.48 44.41 3.43
615 627 3.796717 ACATCGCAATGTACATGTACGAG 59.203 43.478 26.59 19.99 44.38 4.18
616 628 3.497297 TCGCAATGTACATGTACGAGT 57.503 42.857 26.59 14.93 38.85 4.18
617 629 3.840468 TCGCAATGTACATGTACGAGTT 58.160 40.909 26.59 19.05 38.85 3.01
618 630 4.984205 TCGCAATGTACATGTACGAGTTA 58.016 39.130 26.59 12.50 38.85 2.24
619 631 5.032220 TCGCAATGTACATGTACGAGTTAG 58.968 41.667 26.59 17.25 38.85 2.34
620 632 5.032220 CGCAATGTACATGTACGAGTTAGA 58.968 41.667 26.59 11.18 38.85 2.10
621 633 5.171516 CGCAATGTACATGTACGAGTTAGAG 59.828 44.000 26.59 13.29 38.85 2.43
622 634 6.263344 GCAATGTACATGTACGAGTTAGAGA 58.737 40.000 26.59 9.86 38.85 3.10
623 635 6.918569 GCAATGTACATGTACGAGTTAGAGAT 59.081 38.462 26.59 11.54 38.85 2.75
646 658 8.994170 AGATTTCTTCTTTGAAGCTTGTACTAC 58.006 33.333 2.10 0.00 0.00 2.73
670 682 1.002251 GTTTCGTGCCACGGAATTTCA 60.002 47.619 14.97 0.00 41.63 2.69
685 697 0.109458 TTTCACCGTCCTCGTCATCG 60.109 55.000 0.00 0.00 38.55 3.84
687 699 1.226323 CACCGTCCTCGTCATCGTC 60.226 63.158 0.00 0.00 38.33 4.20
693 706 2.944557 CTCGTCATCGTCGCACCG 60.945 66.667 0.00 0.00 38.33 4.94
727 741 2.829720 TGAAGCCTAACCACGTGATACT 59.170 45.455 19.30 2.36 0.00 2.12
767 781 3.270027 TCGGAATGACATGCTAAACAGG 58.730 45.455 0.00 0.00 35.74 4.00
782 796 3.731728 AGGGGCCATGCGTGTCAT 61.732 61.111 4.39 0.00 35.31 3.06
786 800 1.160329 GGGCCATGCGTGTCATCTAC 61.160 60.000 4.39 0.00 31.79 2.59
789 803 1.858091 CCATGCGTGTCATCTACCTC 58.142 55.000 4.96 0.00 31.79 3.85
790 804 1.136891 CCATGCGTGTCATCTACCTCA 59.863 52.381 4.96 0.00 31.79 3.86
791 805 2.418609 CCATGCGTGTCATCTACCTCAA 60.419 50.000 4.96 0.00 31.79 3.02
792 806 2.363788 TGCGTGTCATCTACCTCAAC 57.636 50.000 0.00 0.00 0.00 3.18
793 807 1.269166 GCGTGTCATCTACCTCAACG 58.731 55.000 0.00 0.00 0.00 4.10
794 808 1.269166 CGTGTCATCTACCTCAACGC 58.731 55.000 0.00 0.00 0.00 4.84
795 809 1.641577 GTGTCATCTACCTCAACGCC 58.358 55.000 0.00 0.00 0.00 5.68
796 810 0.535335 TGTCATCTACCTCAACGCCC 59.465 55.000 0.00 0.00 0.00 6.13
804 818 1.373435 CCTCAACGCCCCAGTGTAA 59.627 57.895 0.00 0.00 35.03 2.41
830 844 1.001406 AGCTGGGCTGCTCGAATATAC 59.999 52.381 0.00 0.00 39.34 1.47
833 847 3.668447 CTGGGCTGCTCGAATATACAAT 58.332 45.455 0.00 0.00 0.00 2.71
837 851 5.221641 TGGGCTGCTCGAATATACAATTACT 60.222 40.000 0.00 0.00 0.00 2.24
838 852 5.348997 GGGCTGCTCGAATATACAATTACTC 59.651 44.000 0.00 0.00 0.00 2.59
839 853 5.348997 GGCTGCTCGAATATACAATTACTCC 59.651 44.000 0.00 0.00 0.00 3.85
840 854 6.159988 GCTGCTCGAATATACAATTACTCCT 58.840 40.000 0.00 0.00 0.00 3.69
841 855 7.313646 GCTGCTCGAATATACAATTACTCCTA 58.686 38.462 0.00 0.00 0.00 2.94
842 856 7.273815 GCTGCTCGAATATACAATTACTCCTAC 59.726 40.741 0.00 0.00 0.00 3.18
884 898 4.976731 CACGCTACTACTAGCTGTTAATGG 59.023 45.833 0.00 0.00 43.07 3.16
936 4356 2.496470 CAAGAGTTCCTAGGCCGTAAGT 59.504 50.000 2.96 0.00 0.00 2.24
965 4385 2.603473 CCACTCGGTGTCTCCCCA 60.603 66.667 3.82 0.00 0.00 4.96
1025 4445 0.900647 CTTGAGGTCGTCCCAGTCCT 60.901 60.000 0.00 0.00 34.66 3.85
1060 4480 2.364317 CCTTCTCCCTCCGCCTCA 60.364 66.667 0.00 0.00 0.00 3.86
1095 4515 2.029623 TCGACGCTATAGCTTTTCCCT 58.970 47.619 21.98 0.00 39.32 4.20
1096 4516 2.034305 TCGACGCTATAGCTTTTCCCTC 59.966 50.000 21.98 0.00 39.32 4.30
1100 4520 2.545946 CGCTATAGCTTTTCCCTCAAGC 59.454 50.000 21.98 0.00 46.05 4.01
1175 4601 0.532573 TCGCCCTTCTTCTGCTAGTG 59.467 55.000 0.00 0.00 0.00 2.74
1285 4711 2.262915 CTCCGAGCAGGCGTCTTT 59.737 61.111 0.00 0.00 40.77 2.52
1292 4718 2.668280 GCAGGCGTCTTTGTCGACC 61.668 63.158 14.12 0.00 36.97 4.79
1333 4759 0.861450 GTTTATCGGCGCATGCACAC 60.861 55.000 19.57 6.14 45.35 3.82
1385 4811 2.263741 CCCACTGCACAACTGAGCC 61.264 63.158 0.00 0.00 0.00 4.70
1386 4812 1.228063 CCACTGCACAACTGAGCCT 60.228 57.895 0.00 0.00 0.00 4.58
1387 4813 1.512996 CCACTGCACAACTGAGCCTG 61.513 60.000 0.00 0.00 0.00 4.85
1388 4814 0.533531 CACTGCACAACTGAGCCTGA 60.534 55.000 0.00 0.00 0.00 3.86
1389 4815 0.250209 ACTGCACAACTGAGCCTGAG 60.250 55.000 0.00 0.00 0.00 3.35
1390 4816 1.575576 CTGCACAACTGAGCCTGAGC 61.576 60.000 0.00 0.00 40.32 4.26
1439 4865 5.115480 CCTGCAAAGAGGAGAATTAGAGAC 58.885 45.833 0.00 0.00 38.04 3.36
1499 5064 7.093354 TCTGAGTGATGTGAAATAGAACACTC 58.907 38.462 1.27 1.27 46.91 3.51
1519 5084 6.130569 CACTCAGGGGTATAGAAGTACTCTT 58.869 44.000 0.00 0.00 35.41 2.85
1520 5085 6.039941 CACTCAGGGGTATAGAAGTACTCTTG 59.960 46.154 0.00 0.00 34.46 3.02
1521 5086 6.088541 TCAGGGGTATAGAAGTACTCTTGT 57.911 41.667 0.00 0.00 34.69 3.16
1522 5087 7.092083 ACTCAGGGGTATAGAAGTACTCTTGTA 60.092 40.741 0.00 0.00 34.69 2.41
1523 5088 7.823635 TCAGGGGTATAGAAGTACTCTTGTAT 58.176 38.462 0.00 0.00 41.14 2.29
1524 5089 7.724506 TCAGGGGTATAGAAGTACTCTTGTATG 59.275 40.741 0.00 0.00 39.43 2.39
1525 5090 7.506261 CAGGGGTATAGAAGTACTCTTGTATGT 59.494 40.741 0.00 0.00 39.43 2.29
1527 5092 9.359653 GGGGTATAGAAGTACTCTTGTATGTAA 57.640 37.037 0.00 0.00 39.43 2.41
1563 5130 6.639279 CAGTTAAACAAGTAAAATGGGAACGG 59.361 38.462 0.00 0.00 0.00 4.44
1633 5217 4.764679 TGTGTTTATTGGAGTGATGCAC 57.235 40.909 0.00 0.00 34.10 4.57
1875 5462 8.481641 CGTCCAAATGCATATGATTGTTTATTG 58.518 33.333 6.97 0.00 0.00 1.90
1971 5558 5.999044 ACCAGAGAGATCACAAGCATATTT 58.001 37.500 0.00 0.00 0.00 1.40
1972 5559 6.421485 ACCAGAGAGATCACAAGCATATTTT 58.579 36.000 0.00 0.00 0.00 1.82
1973 5560 6.888632 ACCAGAGAGATCACAAGCATATTTTT 59.111 34.615 0.00 0.00 0.00 1.94
1974 5561 7.066766 ACCAGAGAGATCACAAGCATATTTTTC 59.933 37.037 0.00 0.00 0.00 2.29
1975 5562 7.066645 CCAGAGAGATCACAAGCATATTTTTCA 59.933 37.037 0.00 0.00 0.00 2.69
1979 5566 4.454728 TCACAAGCATATTTTTCAGCCC 57.545 40.909 0.00 0.00 0.00 5.19
1985 5786 4.292643 AGCATATTTTTCAGCCCCTTCAT 58.707 39.130 0.00 0.00 0.00 2.57
2057 5858 4.956700 TCAAAGGACAAACATACCCACAAA 59.043 37.500 0.00 0.00 0.00 2.83
2091 5892 7.393216 AGCCATCCATTTACTCTAATCTGATC 58.607 38.462 0.00 0.00 0.00 2.92
2136 5939 2.965671 TAGATACCTGGGAGTACCGG 57.034 55.000 0.00 0.00 44.64 5.28
2160 5963 3.052642 ACCAATAGTCCGGGAGTACCTTA 60.053 47.826 13.71 0.00 36.97 2.69
2182 5985 7.763985 CCTTAATTGCAAGGGTAAATTGGTAAG 59.236 37.037 4.94 0.00 41.30 2.34
2291 6096 1.423845 GCCAGGATTTGCACGTACG 59.576 57.895 15.01 15.01 0.00 3.67
2336 6141 7.278868 AGGATTTGTTAGCATCTTCGAACTAAG 59.721 37.037 6.28 0.00 0.00 2.18
2337 6142 7.277981 GGATTTGTTAGCATCTTCGAACTAAGA 59.722 37.037 6.28 3.43 39.71 2.10
2339 6144 8.547967 TTTGTTAGCATCTTCGAACTAAGAAT 57.452 30.769 13.20 0.00 38.90 2.40
2340 6145 7.757097 TGTTAGCATCTTCGAACTAAGAATC 57.243 36.000 6.28 0.00 38.90 2.52
2342 6147 7.489435 TGTTAGCATCTTCGAACTAAGAATCAG 59.511 37.037 6.28 0.00 38.90 2.90
2343 6148 6.214191 AGCATCTTCGAACTAAGAATCAGA 57.786 37.500 0.00 0.00 38.90 3.27
2344 6149 6.272318 AGCATCTTCGAACTAAGAATCAGAG 58.728 40.000 0.00 0.00 38.90 3.35
2346 6151 6.922957 GCATCTTCGAACTAAGAATCAGAGAT 59.077 38.462 0.00 0.00 38.90 2.75
2347 6152 7.114811 GCATCTTCGAACTAAGAATCAGAGATC 59.885 40.741 0.00 0.00 38.90 2.75
2435 6370 2.588620 AGCCGAGTACTCAGATAAGGG 58.411 52.381 22.37 13.84 0.00 3.95
2440 6375 3.031736 GAGTACTCAGATAAGGGGCACA 58.968 50.000 18.20 0.00 0.00 4.57
2445 6380 0.758734 CAGATAAGGGGCACATCCGA 59.241 55.000 0.00 0.00 34.94 4.55
2484 6420 6.262193 ACCATGGTTGTAATTAAGTTTCCG 57.738 37.500 13.00 0.00 0.00 4.30
2511 6447 2.580326 GCCGGCGACAAATGCATG 60.580 61.111 12.58 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.743928 GCCGCACAGAGAACCAGG 60.744 66.667 0.00 0.00 0.00 4.45
83 84 2.946762 GTTGCCGCACAGAGAACC 59.053 61.111 0.00 0.00 0.00 3.62
98 99 5.639506 CACAAGATACCAAGATGTCTTCGTT 59.360 40.000 0.00 0.00 33.11 3.85
148 149 1.372087 GCAGCAATCGTCCAAGGGAG 61.372 60.000 0.00 0.00 29.39 4.30
195 196 1.202394 CCGTCTCAGGCTCTCAATCAG 60.202 57.143 0.00 0.00 0.00 2.90
196 197 0.820226 CCGTCTCAGGCTCTCAATCA 59.180 55.000 0.00 0.00 0.00 2.57
197 198 1.107114 TCCGTCTCAGGCTCTCAATC 58.893 55.000 0.00 0.00 0.00 2.67
206 207 2.886081 CACTCTTGATTCCGTCTCAGG 58.114 52.381 0.00 0.00 0.00 3.86
233 234 0.747283 CCTCAGCAGATGAACTGGCC 60.747 60.000 0.00 0.00 45.82 5.36
251 252 2.677848 GAAAGGAGAGGGGTGCCC 59.322 66.667 0.00 0.00 45.90 5.36
254 255 1.597461 GGACGAAAGGAGAGGGGTG 59.403 63.158 0.00 0.00 0.00 4.61
255 256 1.612739 GGGACGAAAGGAGAGGGGT 60.613 63.158 0.00 0.00 0.00 4.95
358 363 7.103641 ACAGTTTAAGAGTCTTCACACTTGAA 58.896 34.615 9.12 0.00 39.55 2.69
379 391 0.318441 CCCTCGTGATGTGTGACAGT 59.682 55.000 0.00 0.00 0.00 3.55
397 409 2.576615 CCGATTTTCCTCCCTGAATCC 58.423 52.381 0.00 0.00 0.00 3.01
412 424 0.822164 CGACTACCTGAACCCCGATT 59.178 55.000 0.00 0.00 0.00 3.34
435 447 1.067212 CTCGGCAGCGGTATAAAGTCT 59.933 52.381 0.00 0.00 0.00 3.24
452 464 2.584608 CAGCCCCTACCCAACTCG 59.415 66.667 0.00 0.00 0.00 4.18
458 470 1.073242 TATTCCCCAGCCCCTACCC 60.073 63.158 0.00 0.00 0.00 3.69
473 485 4.293494 TCAGAGCTTCAGATCCACCTATT 58.707 43.478 0.00 0.00 0.00 1.73
474 486 3.921104 TCAGAGCTTCAGATCCACCTAT 58.079 45.455 0.00 0.00 0.00 2.57
475 487 3.388552 TCAGAGCTTCAGATCCACCTA 57.611 47.619 0.00 0.00 0.00 3.08
476 488 2.235898 GTTCAGAGCTTCAGATCCACCT 59.764 50.000 0.00 0.00 0.00 4.00
477 489 2.626840 GTTCAGAGCTTCAGATCCACC 58.373 52.381 0.00 0.00 0.00 4.61
479 491 2.259917 TGGTTCAGAGCTTCAGATCCA 58.740 47.619 8.76 8.76 31.85 3.41
480 492 3.340814 TTGGTTCAGAGCTTCAGATCC 57.659 47.619 0.00 0.00 0.00 3.36
481 493 4.813697 GGTATTGGTTCAGAGCTTCAGATC 59.186 45.833 0.00 0.00 0.00 2.75
482 494 4.384647 GGGTATTGGTTCAGAGCTTCAGAT 60.385 45.833 0.00 0.00 0.00 2.90
485 497 2.642311 TGGGTATTGGTTCAGAGCTTCA 59.358 45.455 0.00 0.00 0.00 3.02
486 498 3.350219 TGGGTATTGGTTCAGAGCTTC 57.650 47.619 0.00 0.00 0.00 3.86
487 499 3.806949 TTGGGTATTGGTTCAGAGCTT 57.193 42.857 0.00 0.00 0.00 3.74
488 500 3.181434 TGTTTGGGTATTGGTTCAGAGCT 60.181 43.478 0.00 0.00 0.00 4.09
489 501 3.153919 TGTTTGGGTATTGGTTCAGAGC 58.846 45.455 0.00 0.00 0.00 4.09
490 502 4.022329 GGTTGTTTGGGTATTGGTTCAGAG 60.022 45.833 0.00 0.00 0.00 3.35
491 503 3.892588 GGTTGTTTGGGTATTGGTTCAGA 59.107 43.478 0.00 0.00 0.00 3.27
492 504 3.006430 GGGTTGTTTGGGTATTGGTTCAG 59.994 47.826 0.00 0.00 0.00 3.02
493 505 2.966516 GGGTTGTTTGGGTATTGGTTCA 59.033 45.455 0.00 0.00 0.00 3.18
494 506 2.966516 TGGGTTGTTTGGGTATTGGTTC 59.033 45.455 0.00 0.00 0.00 3.62
495 507 3.047695 TGGGTTGTTTGGGTATTGGTT 57.952 42.857 0.00 0.00 0.00 3.67
496 508 2.777459 TGGGTTGTTTGGGTATTGGT 57.223 45.000 0.00 0.00 0.00 3.67
497 509 2.354604 GCATGGGTTGTTTGGGTATTGG 60.355 50.000 0.00 0.00 0.00 3.16
498 510 2.301296 TGCATGGGTTGTTTGGGTATTG 59.699 45.455 0.00 0.00 0.00 1.90
499 511 2.614259 TGCATGGGTTGTTTGGGTATT 58.386 42.857 0.00 0.00 0.00 1.89
500 512 2.317371 TGCATGGGTTGTTTGGGTAT 57.683 45.000 0.00 0.00 0.00 2.73
501 513 2.088104 TTGCATGGGTTGTTTGGGTA 57.912 45.000 0.00 0.00 0.00 3.69
502 514 1.207791 TTTGCATGGGTTGTTTGGGT 58.792 45.000 0.00 0.00 0.00 4.51
503 515 2.565046 ATTTGCATGGGTTGTTTGGG 57.435 45.000 0.00 0.00 0.00 4.12
504 516 3.742385 AGAATTTGCATGGGTTGTTTGG 58.258 40.909 0.00 0.00 0.00 3.28
505 517 4.815308 TCAAGAATTTGCATGGGTTGTTTG 59.185 37.500 0.00 0.00 34.21 2.93
506 518 4.815846 GTCAAGAATTTGCATGGGTTGTTT 59.184 37.500 0.00 0.00 34.21 2.83
507 519 4.101430 AGTCAAGAATTTGCATGGGTTGTT 59.899 37.500 0.00 0.00 34.21 2.83
508 520 3.642848 AGTCAAGAATTTGCATGGGTTGT 59.357 39.130 0.00 0.00 34.21 3.32
509 521 4.240096 GAGTCAAGAATTTGCATGGGTTG 58.760 43.478 0.00 0.00 34.21 3.77
510 522 3.259123 GGAGTCAAGAATTTGCATGGGTT 59.741 43.478 0.00 0.00 34.21 4.11
511 523 2.827921 GGAGTCAAGAATTTGCATGGGT 59.172 45.455 0.00 0.00 34.21 4.51
512 524 2.159338 CGGAGTCAAGAATTTGCATGGG 60.159 50.000 0.00 0.00 34.21 4.00
513 525 2.489329 ACGGAGTCAAGAATTTGCATGG 59.511 45.455 0.00 0.00 29.74 3.66
514 526 3.837213 ACGGAGTCAAGAATTTGCATG 57.163 42.857 0.00 0.00 29.74 4.06
515 527 4.393062 CACTACGGAGTCAAGAATTTGCAT 59.607 41.667 0.00 0.00 43.93 3.96
516 528 3.745975 CACTACGGAGTCAAGAATTTGCA 59.254 43.478 0.00 0.00 43.93 4.08
517 529 3.746492 ACACTACGGAGTCAAGAATTTGC 59.254 43.478 0.00 0.00 43.93 3.68
518 530 5.924254 TGTACACTACGGAGTCAAGAATTTG 59.076 40.000 0.00 0.00 43.93 2.32
519 531 6.092955 TGTACACTACGGAGTCAAGAATTT 57.907 37.500 0.00 0.00 43.93 1.82
520 532 5.717078 TGTACACTACGGAGTCAAGAATT 57.283 39.130 0.00 0.00 43.93 2.17
521 533 5.163540 GGATGTACACTACGGAGTCAAGAAT 60.164 44.000 0.00 0.00 43.93 2.40
522 534 4.157289 GGATGTACACTACGGAGTCAAGAA 59.843 45.833 0.00 0.00 43.93 2.52
523 535 3.693085 GGATGTACACTACGGAGTCAAGA 59.307 47.826 0.00 0.00 43.93 3.02
524 536 3.695060 AGGATGTACACTACGGAGTCAAG 59.305 47.826 0.00 0.00 43.93 3.02
525 537 3.693807 AGGATGTACACTACGGAGTCAA 58.306 45.455 0.00 0.00 43.93 3.18
526 538 3.361281 AGGATGTACACTACGGAGTCA 57.639 47.619 0.00 0.00 43.93 3.41
527 539 4.450053 ACTAGGATGTACACTACGGAGTC 58.550 47.826 0.00 0.00 43.93 3.36
528 540 5.363939 GTACTAGGATGTACACTACGGAGT 58.636 45.833 0.00 0.00 42.61 3.85
529 541 4.447054 CGTACTAGGATGTACACTACGGAG 59.553 50.000 0.00 0.00 41.92 4.63
530 542 4.141937 ACGTACTAGGATGTACACTACGGA 60.142 45.833 0.00 0.00 41.92 4.69
531 543 4.122776 ACGTACTAGGATGTACACTACGG 58.877 47.826 0.00 0.00 41.92 4.02
532 544 8.694975 ATATACGTACTAGGATGTACACTACG 57.305 38.462 9.30 5.79 41.92 3.51
535 547 9.007901 GGAAATATACGTACTAGGATGTACACT 57.992 37.037 9.30 0.00 41.92 3.55
536 548 8.786898 TGGAAATATACGTACTAGGATGTACAC 58.213 37.037 9.30 0.58 41.92 2.90
537 549 8.922931 TGGAAATATACGTACTAGGATGTACA 57.077 34.615 9.30 0.00 41.92 2.90
538 550 9.224267 TCTGGAAATATACGTACTAGGATGTAC 57.776 37.037 9.30 0.00 39.35 2.90
539 551 9.797642 TTCTGGAAATATACGTACTAGGATGTA 57.202 33.333 9.52 9.52 0.00 2.29
540 552 8.701908 TTCTGGAAATATACGTACTAGGATGT 57.298 34.615 4.90 4.90 0.00 3.06
541 553 9.011095 TCTTCTGGAAATATACGTACTAGGATG 57.989 37.037 0.00 0.00 0.00 3.51
542 554 9.584008 TTCTTCTGGAAATATACGTACTAGGAT 57.416 33.333 0.00 0.00 0.00 3.24
543 555 8.985315 TTCTTCTGGAAATATACGTACTAGGA 57.015 34.615 0.00 0.00 0.00 2.94
547 559 8.827677 GCAAATTCTTCTGGAAATATACGTACT 58.172 33.333 0.00 0.00 37.49 2.73
548 560 8.609176 TGCAAATTCTTCTGGAAATATACGTAC 58.391 33.333 0.00 0.00 37.49 3.67
549 561 8.725405 TGCAAATTCTTCTGGAAATATACGTA 57.275 30.769 0.00 0.00 37.49 3.57
550 562 7.201732 CCTGCAAATTCTTCTGGAAATATACGT 60.202 37.037 0.00 0.00 37.49 3.57
551 563 7.134815 CCTGCAAATTCTTCTGGAAATATACG 58.865 38.462 0.00 0.00 37.49 3.06
552 564 8.000780 ACCTGCAAATTCTTCTGGAAATATAC 57.999 34.615 0.00 0.00 37.49 1.47
553 565 8.469200 CAACCTGCAAATTCTTCTGGAAATATA 58.531 33.333 0.00 0.00 37.49 0.86
554 566 7.038799 ACAACCTGCAAATTCTTCTGGAAATAT 60.039 33.333 0.00 0.00 37.49 1.28
555 567 6.267471 ACAACCTGCAAATTCTTCTGGAAATA 59.733 34.615 0.00 0.00 37.49 1.40
556 568 5.070847 ACAACCTGCAAATTCTTCTGGAAAT 59.929 36.000 0.00 0.00 37.49 2.17
557 569 4.405358 ACAACCTGCAAATTCTTCTGGAAA 59.595 37.500 0.00 0.00 37.49 3.13
558 570 3.960102 ACAACCTGCAAATTCTTCTGGAA 59.040 39.130 0.00 0.00 38.41 3.53
559 571 3.565307 ACAACCTGCAAATTCTTCTGGA 58.435 40.909 0.00 0.00 0.00 3.86
560 572 4.326504 AACAACCTGCAAATTCTTCTGG 57.673 40.909 0.00 0.00 0.00 3.86
561 573 5.111293 ACAAACAACCTGCAAATTCTTCTG 58.889 37.500 0.00 0.00 0.00 3.02
562 574 5.343307 ACAAACAACCTGCAAATTCTTCT 57.657 34.783 0.00 0.00 0.00 2.85
563 575 6.273071 AGTACAAACAACCTGCAAATTCTTC 58.727 36.000 0.00 0.00 0.00 2.87
564 576 6.220726 AGTACAAACAACCTGCAAATTCTT 57.779 33.333 0.00 0.00 0.00 2.52
565 577 5.852282 AGTACAAACAACCTGCAAATTCT 57.148 34.783 0.00 0.00 0.00 2.40
566 578 6.735130 AGTAGTACAAACAACCTGCAAATTC 58.265 36.000 2.52 0.00 0.00 2.17
567 579 6.709018 AGTAGTACAAACAACCTGCAAATT 57.291 33.333 2.52 0.00 0.00 1.82
568 580 6.320164 TGAAGTAGTACAAACAACCTGCAAAT 59.680 34.615 2.52 0.00 0.00 2.32
569 581 5.648526 TGAAGTAGTACAAACAACCTGCAAA 59.351 36.000 2.52 0.00 0.00 3.68
570 582 5.065474 GTGAAGTAGTACAAACAACCTGCAA 59.935 40.000 2.52 0.00 0.00 4.08
571 583 4.573201 GTGAAGTAGTACAAACAACCTGCA 59.427 41.667 2.52 0.00 0.00 4.41
572 584 4.573201 TGTGAAGTAGTACAAACAACCTGC 59.427 41.667 2.52 0.00 0.00 4.85
573 585 6.346598 CGATGTGAAGTAGTACAAACAACCTG 60.347 42.308 2.52 0.00 0.00 4.00
574 586 5.694910 CGATGTGAAGTAGTACAAACAACCT 59.305 40.000 2.52 0.00 0.00 3.50
575 587 5.614013 GCGATGTGAAGTAGTACAAACAACC 60.614 44.000 2.52 0.95 0.00 3.77
576 588 5.050634 TGCGATGTGAAGTAGTACAAACAAC 60.051 40.000 2.52 2.36 0.00 3.32
577 589 5.051153 TGCGATGTGAAGTAGTACAAACAA 58.949 37.500 2.52 0.00 0.00 2.83
578 590 4.623002 TGCGATGTGAAGTAGTACAAACA 58.377 39.130 2.52 4.32 0.00 2.83
579 591 5.585500 TTGCGATGTGAAGTAGTACAAAC 57.415 39.130 2.52 0.00 0.00 2.93
580 592 5.699001 ACATTGCGATGTGAAGTAGTACAAA 59.301 36.000 19.06 0.00 44.64 2.83
581 593 5.234752 ACATTGCGATGTGAAGTAGTACAA 58.765 37.500 19.06 0.00 44.64 2.41
582 594 4.816392 ACATTGCGATGTGAAGTAGTACA 58.184 39.130 19.06 0.00 44.64 2.90
583 595 5.803461 TGTACATTGCGATGTGAAGTAGTAC 59.197 40.000 26.87 15.56 45.80 2.73
584 596 5.956642 TGTACATTGCGATGTGAAGTAGTA 58.043 37.500 26.87 3.94 45.80 1.82
585 597 4.816392 TGTACATTGCGATGTGAAGTAGT 58.184 39.130 26.87 2.49 45.80 2.73
586 598 5.291858 ACATGTACATTGCGATGTGAAGTAG 59.708 40.000 26.87 14.64 45.80 2.57
587 599 5.175127 ACATGTACATTGCGATGTGAAGTA 58.825 37.500 26.87 6.13 45.80 2.24
588 600 4.002982 ACATGTACATTGCGATGTGAAGT 58.997 39.130 26.87 16.99 45.80 3.01
589 601 4.604843 ACATGTACATTGCGATGTGAAG 57.395 40.909 26.87 16.44 45.80 3.02
590 602 4.032331 CGTACATGTACATTGCGATGTGAA 59.968 41.667 30.17 16.03 45.80 3.18
591 603 3.549873 CGTACATGTACATTGCGATGTGA 59.450 43.478 30.17 14.92 45.80 3.58
592 604 3.549873 TCGTACATGTACATTGCGATGTG 59.450 43.478 30.17 14.04 45.80 3.21
594 606 3.796717 ACTCGTACATGTACATTGCGATG 59.203 43.478 30.17 12.66 39.25 3.84
595 607 4.041740 ACTCGTACATGTACATTGCGAT 57.958 40.909 30.17 12.11 35.87 4.58
596 608 3.497297 ACTCGTACATGTACATTGCGA 57.503 42.857 30.17 21.32 35.87 5.10
597 609 5.032220 TCTAACTCGTACATGTACATTGCG 58.968 41.667 30.17 18.67 35.87 4.85
598 610 6.263344 TCTCTAACTCGTACATGTACATTGC 58.737 40.000 30.17 8.35 35.87 3.56
599 611 8.858003 AATCTCTAACTCGTACATGTACATTG 57.142 34.615 30.17 21.67 35.87 2.82
600 612 9.517609 GAAATCTCTAACTCGTACATGTACATT 57.482 33.333 30.17 22.85 35.87 2.71
601 613 8.904834 AGAAATCTCTAACTCGTACATGTACAT 58.095 33.333 30.17 17.55 35.87 2.29
602 614 8.277490 AGAAATCTCTAACTCGTACATGTACA 57.723 34.615 30.17 18.38 35.87 2.90
603 615 9.224058 GAAGAAATCTCTAACTCGTACATGTAC 57.776 37.037 23.53 23.53 0.00 2.90
604 616 9.175312 AGAAGAAATCTCTAACTCGTACATGTA 57.825 33.333 0.08 0.08 30.46 2.29
605 617 8.057536 AGAAGAAATCTCTAACTCGTACATGT 57.942 34.615 2.69 2.69 30.46 3.21
606 618 8.918961 AAGAAGAAATCTCTAACTCGTACATG 57.081 34.615 0.00 0.00 37.42 3.21
607 619 9.360093 CAAAGAAGAAATCTCTAACTCGTACAT 57.640 33.333 0.00 0.00 37.42 2.29
608 620 8.573885 TCAAAGAAGAAATCTCTAACTCGTACA 58.426 33.333 0.00 0.00 37.42 2.90
609 621 8.967552 TCAAAGAAGAAATCTCTAACTCGTAC 57.032 34.615 0.00 0.00 37.42 3.67
610 622 9.627395 CTTCAAAGAAGAAATCTCTAACTCGTA 57.373 33.333 0.52 0.00 37.42 3.43
611 623 7.117092 GCTTCAAAGAAGAAATCTCTAACTCGT 59.883 37.037 10.72 0.00 37.42 4.18
612 624 7.330700 AGCTTCAAAGAAGAAATCTCTAACTCG 59.669 37.037 10.72 0.00 37.42 4.18
613 625 8.546597 AGCTTCAAAGAAGAAATCTCTAACTC 57.453 34.615 10.72 0.00 37.42 3.01
614 626 8.782144 CAAGCTTCAAAGAAGAAATCTCTAACT 58.218 33.333 10.72 0.00 37.42 2.24
615 627 8.563732 ACAAGCTTCAAAGAAGAAATCTCTAAC 58.436 33.333 10.72 0.00 37.42 2.34
616 628 8.682936 ACAAGCTTCAAAGAAGAAATCTCTAA 57.317 30.769 10.72 0.00 37.42 2.10
617 629 9.209175 GTACAAGCTTCAAAGAAGAAATCTCTA 57.791 33.333 10.72 0.00 37.42 2.43
618 630 7.936301 AGTACAAGCTTCAAAGAAGAAATCTCT 59.064 33.333 10.72 0.00 37.42 3.10
619 631 8.093659 AGTACAAGCTTCAAAGAAGAAATCTC 57.906 34.615 10.72 0.00 37.42 2.75
620 632 8.994170 GTAGTACAAGCTTCAAAGAAGAAATCT 58.006 33.333 10.72 3.84 41.32 2.40
621 633 8.231161 GGTAGTACAAGCTTCAAAGAAGAAATC 58.769 37.037 10.72 0.00 0.00 2.17
622 634 7.719633 TGGTAGTACAAGCTTCAAAGAAGAAAT 59.280 33.333 10.72 0.00 0.00 2.17
623 635 7.051623 TGGTAGTACAAGCTTCAAAGAAGAAA 58.948 34.615 10.72 0.00 0.00 2.52
646 658 1.511318 TTCCGTGGCACGAAACATGG 61.511 55.000 38.91 21.09 46.05 3.66
670 682 2.747822 CGACGATGACGAGGACGGT 61.748 63.158 0.00 0.00 44.46 4.83
767 781 1.146041 TAGATGACACGCATGGCCC 59.854 57.895 0.00 0.00 37.34 5.80
782 796 1.229082 ACTGGGGCGTTGAGGTAGA 60.229 57.895 0.00 0.00 0.00 2.59
786 800 0.250553 TTTACACTGGGGCGTTGAGG 60.251 55.000 0.00 0.00 0.00 3.86
789 803 0.309612 GTGTTTACACTGGGGCGTTG 59.690 55.000 5.78 0.00 43.25 4.10
790 804 0.820482 GGTGTTTACACTGGGGCGTT 60.820 55.000 12.32 0.00 45.73 4.84
791 805 1.228033 GGTGTTTACACTGGGGCGT 60.228 57.895 12.32 0.00 45.73 5.68
792 806 1.228003 TGGTGTTTACACTGGGGCG 60.228 57.895 12.32 0.00 45.73 6.13
793 807 1.524008 GCTGGTGTTTACACTGGGGC 61.524 60.000 12.32 8.12 45.73 5.80
794 808 0.110486 AGCTGGTGTTTACACTGGGG 59.890 55.000 12.32 2.91 45.73 4.96
795 809 1.238439 CAGCTGGTGTTTACACTGGG 58.762 55.000 5.57 4.97 45.73 4.45
796 810 1.238439 CCAGCTGGTGTTTACACTGG 58.762 55.000 25.53 8.42 45.73 4.00
833 847 7.664731 CGGATTGACCTAATCTAGTAGGAGTAA 59.335 40.741 12.28 5.70 43.06 2.24
837 851 5.950023 ACGGATTGACCTAATCTAGTAGGA 58.050 41.667 12.28 0.00 43.06 2.94
838 852 5.768662 TGACGGATTGACCTAATCTAGTAGG 59.231 44.000 5.13 5.13 45.47 3.18
839 853 6.566187 CGTGACGGATTGACCTAATCTAGTAG 60.566 46.154 0.00 0.00 43.81 2.57
840 854 5.237996 CGTGACGGATTGACCTAATCTAGTA 59.762 44.000 0.00 0.00 43.81 1.82
841 855 4.036498 CGTGACGGATTGACCTAATCTAGT 59.964 45.833 0.00 0.00 43.81 2.57
842 856 4.537965 CGTGACGGATTGACCTAATCTAG 58.462 47.826 0.00 0.00 43.81 2.43
884 898 3.112709 GCACCGACTTGGACTCGC 61.113 66.667 0.00 0.00 42.00 5.03
908 922 3.361786 GCCTAGGAACTCTTGAGACTCT 58.638 50.000 14.75 1.67 41.75 3.24
936 4356 0.899720 CCGAGTGGCCAACTACCTTA 59.100 55.000 7.24 0.00 40.07 2.69
965 4385 6.084277 GCGTTGCTTTGCTACTTTTTATAGT 58.916 36.000 3.16 0.00 32.61 2.12
1025 4445 1.432023 GGTGGGGAGGGGAGTTGAAA 61.432 60.000 0.00 0.00 0.00 2.69
1175 4601 3.044059 GCTGACGCTTGCCATGTCC 62.044 63.158 0.00 0.00 0.00 4.02
1211 4637 3.576356 GCCATGGCATCCACGTCG 61.576 66.667 32.08 0.00 41.49 5.12
1292 4718 4.241999 GCCGTATGCTGCCTTGCG 62.242 66.667 0.00 0.00 36.87 4.85
1390 4816 1.958902 GAGAGTCTCAGCTGGGGCAG 61.959 65.000 22.62 7.44 41.70 4.85
1391 4817 1.986757 GAGAGTCTCAGCTGGGGCA 60.987 63.158 22.62 0.00 41.70 5.36
1392 4818 1.264045 AAGAGAGTCTCAGCTGGGGC 61.264 60.000 22.05 11.20 39.06 5.80
1393 4819 0.823460 GAAGAGAGTCTCAGCTGGGG 59.177 60.000 22.05 7.52 32.06 4.96
1394 4820 1.851304 AGAAGAGAGTCTCAGCTGGG 58.149 55.000 22.05 11.57 32.06 4.45
1450 4876 4.717629 TGACCGCGAGCAACCGAG 62.718 66.667 8.23 0.00 0.00 4.63
1453 4879 4.681978 AGGTGACCGCGAGCAACC 62.682 66.667 8.23 10.00 0.00 3.77
1454 4880 2.665185 AAGGTGACCGCGAGCAAC 60.665 61.111 8.23 8.05 0.00 4.17
1455 4881 2.357034 GAAGGTGACCGCGAGCAA 60.357 61.111 8.23 0.00 0.00 3.91
1499 5064 7.506261 ACATACAAGAGTACTTCTATACCCCTG 59.494 40.741 0.00 0.00 34.14 4.45
1563 5130 0.896479 GGAGAGTCGGAGGCCCTATC 60.896 65.000 0.00 0.00 0.00 2.08
1633 5217 3.431572 GCTGAAGACTTTGACTAGCACAG 59.568 47.826 0.00 0.00 0.00 3.66
1634 5218 3.393800 GCTGAAGACTTTGACTAGCACA 58.606 45.455 0.00 0.00 0.00 4.57
1875 5462 3.031736 TCCATCAGCTACCACCTAACTC 58.968 50.000 0.00 0.00 0.00 3.01
1930 5517 1.276622 GTTGACTAGGAGGGGCTGAA 58.723 55.000 0.00 0.00 0.00 3.02
1971 5558 2.912956 AGTCTACATGAAGGGGCTGAAA 59.087 45.455 0.00 0.00 0.00 2.69
1972 5559 2.237143 CAGTCTACATGAAGGGGCTGAA 59.763 50.000 0.00 0.00 0.00 3.02
1973 5560 1.833630 CAGTCTACATGAAGGGGCTGA 59.166 52.381 0.00 0.00 0.00 4.26
1974 5561 1.745141 GCAGTCTACATGAAGGGGCTG 60.745 57.143 0.00 4.59 0.00 4.85
1975 5562 0.543749 GCAGTCTACATGAAGGGGCT 59.456 55.000 0.00 0.00 0.00 5.19
1979 5566 4.471904 TTACCAGCAGTCTACATGAAGG 57.528 45.455 0.00 0.00 0.00 3.46
1985 5786 6.995686 TCAATTTTCTTTACCAGCAGTCTACA 59.004 34.615 0.00 0.00 0.00 2.74
2136 5939 2.102084 GGTACTCCCGGACTATTGGTTC 59.898 54.545 0.73 0.00 0.00 3.62
2160 5963 5.487433 GCTTACCAATTTACCCTTGCAATT 58.513 37.500 0.00 0.00 0.00 2.32
2336 6141 7.725818 TTATTGTGCATCTGATCTCTGATTC 57.274 36.000 0.00 0.00 33.14 2.52
2337 6142 8.693120 AATTATTGTGCATCTGATCTCTGATT 57.307 30.769 0.00 0.00 33.14 2.57
2339 6144 9.788889 ATTAATTATTGTGCATCTGATCTCTGA 57.211 29.630 0.00 0.00 0.00 3.27
2370 6305 4.394300 CCAGAGTTCTGATCTTGCGATTTT 59.606 41.667 10.64 0.00 46.59 1.82
2391 6326 1.375908 GTCGGCAGTTGCATCTCCA 60.376 57.895 6.43 0.00 44.36 3.86
2421 6356 3.244249 GGATGTGCCCCTTATCTGAGTAC 60.244 52.174 0.00 0.00 0.00 2.73
2435 6370 3.453070 GAGGCCTCTCGGATGTGCC 62.453 68.421 26.25 0.00 42.48 5.01
2504 6440 3.305314 CAGGCCCTTGCATGCATT 58.695 55.556 23.37 0.33 42.96 3.56
2525 6461 1.293963 CGGCCATGGCTACATCATCG 61.294 60.000 34.70 22.83 41.60 3.84


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

AutoCloner maintained by Alex Coulton.