Multiple sequence alignment - TraesCS1D01G238700

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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 TraesCS1D01G238700 chr1D 100.000 3847 0 0 2851 6697 328113950 328110104 0.000000e+00 7105
1 TraesCS1D01G238700 chr1D 100.000 2661 0 0 1 2661 328116800 328114140 0.000000e+00 4915
2 TraesCS1D01G238700 chr1B 95.792 3256 111 15 2851 6083 442201556 442198304 0.000000e+00 5230
3 TraesCS1D01G238700 chr1B 93.478 2024 61 28 690 2659 442203994 442201988 0.000000e+00 2940
4 TraesCS1D01G238700 chr1B 93.860 570 31 4 1 566 442231797 442231228 0.000000e+00 856
5 TraesCS1D01G238700 chr1B 93.684 570 32 4 1 566 442217712 442217143 0.000000e+00 850
6 TraesCS1D01G238700 chr1B 93.509 570 33 4 1 566 442240153 442239584 0.000000e+00 845
7 TraesCS1D01G238700 chr1B 89.850 266 24 3 299 561 484926128 484926393 8.320000e-89 339
8 TraesCS1D01G238700 chr1A 95.031 3260 129 17 2851 6083 407334053 407330800 0.000000e+00 5092
9 TraesCS1D01G238700 chr1A 95.795 1760 58 12 902 2659 407335967 407334222 0.000000e+00 2826
10 TraesCS1D01G238700 chr2A 90.306 588 51 2 6113 6697 426752820 426752236 0.000000e+00 765
11 TraesCS1D01G238700 chr6D 89.590 586 57 3 6113 6696 90039348 90038765 0.000000e+00 741
12 TraesCS1D01G238700 chr2D 89.097 587 60 3 6113 6697 643348514 643349098 0.000000e+00 726
13 TraesCS1D01G238700 chr2D 98.333 120 2 0 564 683 158283408 158283289 1.890000e-50 211
14 TraesCS1D01G238700 chr2D 99.145 117 1 0 564 680 381869740 381869624 1.890000e-50 211
15 TraesCS1D01G238700 chr2D 99.145 117 1 0 564 680 572692734 572692618 1.890000e-50 211
16 TraesCS1D01G238700 chr4A 88.095 588 67 1 6113 6697 575953772 575953185 0.000000e+00 695
17 TraesCS1D01G238700 chr4A 95.968 124 5 0 564 687 744273084 744273207 1.140000e-47 202
18 TraesCS1D01G238700 chr4A 82.099 162 23 5 299 456 225340298 225340139 4.210000e-27 134
19 TraesCS1D01G238700 chr5B 81.772 587 93 11 6113 6697 620333096 620333670 4.700000e-131 479
20 TraesCS1D01G238700 chr5B 98.333 120 2 0 564 683 402870180 402870299 1.890000e-50 211
21 TraesCS1D01G238700 chr7A 80.369 596 103 8 6109 6697 214529890 214529302 2.220000e-119 440
22 TraesCS1D01G238700 chrUn 92.000 175 12 1 2389 2561 400145994 400146168 1.870000e-60 244
23 TraesCS1D01G238700 chrUn 99.145 117 1 0 564 680 100620763 100620879 1.890000e-50 211
24 TraesCS1D01G238700 chr3D 92.000 175 12 1 2389 2561 498471573 498471747 1.870000e-60 244
25 TraesCS1D01G238700 chr3D 80.000 160 27 4 302 457 469164551 469164393 5.490000e-21 113
26 TraesCS1D01G238700 chr3B 97.500 120 3 0 564 683 637086445 637086326 8.800000e-49 206
27 TraesCS1D01G238700 chr4B 94.074 135 7 1 564 697 141455924 141456058 3.170000e-48 204
28 TraesCS1D01G238700 chr6B 95.968 124 5 0 564 687 36133873 36133750 1.140000e-47 202


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 TraesCS1D01G238700 chr1D 328110104 328116800 6696 True 6010 7105 100.000 1 6697 2 chr1D.!!$R1 6696
1 TraesCS1D01G238700 chr1B 442198304 442203994 5690 True 4085 5230 94.635 690 6083 2 chr1B.!!$R4 5393
2 TraesCS1D01G238700 chr1B 442231228 442231797 569 True 856 856 93.860 1 566 1 chr1B.!!$R2 565
3 TraesCS1D01G238700 chr1B 442217143 442217712 569 True 850 850 93.684 1 566 1 chr1B.!!$R1 565
4 TraesCS1D01G238700 chr1B 442239584 442240153 569 True 845 845 93.509 1 566 1 chr1B.!!$R3 565
5 TraesCS1D01G238700 chr1A 407330800 407335967 5167 True 3959 5092 95.413 902 6083 2 chr1A.!!$R1 5181
6 TraesCS1D01G238700 chr2A 426752236 426752820 584 True 765 765 90.306 6113 6697 1 chr2A.!!$R1 584
7 TraesCS1D01G238700 chr6D 90038765 90039348 583 True 741 741 89.590 6113 6696 1 chr6D.!!$R1 583
8 TraesCS1D01G238700 chr2D 643348514 643349098 584 False 726 726 89.097 6113 6697 1 chr2D.!!$F1 584
9 TraesCS1D01G238700 chr4A 575953185 575953772 587 True 695 695 88.095 6113 6697 1 chr4A.!!$R2 584
10 TraesCS1D01G238700 chr5B 620333096 620333670 574 False 479 479 81.772 6113 6697 1 chr5B.!!$F2 584
11 TraesCS1D01G238700 chr7A 214529302 214529890 588 True 440 440 80.369 6109 6697 1 chr7A.!!$R1 588

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
676 680 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
678 682 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85 F
679 683 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 F
2571 2632 0.179936 GCAATCCTCTCCCCACTCAG 59.820 60.000 0.00 0.00 0.00 3.35 F
3873 4182 1.805943 CTTGGCACATGTGTCGATTGA 59.194 47.619 24.44 4.58 39.30 2.57 F
4016 4326 0.608640 AGTGTTGTCTCCTTAGGCGG 59.391 55.000 0.00 0.00 0.00 6.13 F
4543 4856 1.007118 CCAGGGAAGTAAAAGGGGCAT 59.993 52.381 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2150 0.455410 GCACCAAGTTCACTGCAACA 59.545 50.000 0.00 0.0 0.00 3.33 R
2561 2622 0.475632 ATTGGTGGACTGAGTGGGGA 60.476 55.000 0.00 0.0 0.00 4.81 R
2613 2674 1.869690 CTGTCTGCTCTCGACGACA 59.130 57.895 0.00 0.0 35.35 4.35 R
3959 4269 0.308684 CATGCGGACACCATGCATAC 59.691 55.000 0.00 0.0 46.91 2.39 R
4943 5259 1.427368 GCAACCCCATATATGACCCCA 59.573 52.381 14.54 0.0 0.00 4.96 R
5507 5823 2.024918 CAGCGGTGTCAGCTTGTTT 58.975 52.632 6.41 0.0 44.06 2.83 R
6206 6540 0.107831 TCAACAACCTGGTCCTTCCG 59.892 55.000 0.00 0.0 39.52 4.30 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
49 50 6.148480 GCCGATGTTGAAGCATTTATCTATCT 59.852 38.462 0.00 0.00 0.00 1.98
110 111 9.367160 TGTCACTATGTGGATATTTCTAGATGA 57.633 33.333 0.00 0.00 33.87 2.92
138 139 8.824756 AACAGAGAGTTGATGTACTCCTATAA 57.175 34.615 0.00 0.00 44.50 0.98
143 144 8.240267 AGAGTTGATGTACTCCTATAAGAACC 57.760 38.462 0.00 0.00 44.50 3.62
164 165 2.360475 AAGAAGCTTCAGCCGGGC 60.360 61.111 27.57 12.11 43.38 6.13
207 209 9.202273 GTTATCATCATGAGAGTCATCCTTTAC 57.798 37.037 0.09 0.00 34.28 2.01
220 222 4.407621 TCATCCTTTACTTCTCCGGCATAA 59.592 41.667 0.00 0.00 0.00 1.90
222 224 2.872858 CCTTTACTTCTCCGGCATAAGC 59.127 50.000 0.00 0.00 41.10 3.09
250 252 0.772384 ACCGTGGTTGTGGGGATTAA 59.228 50.000 0.00 0.00 0.00 1.40
258 260 3.404899 GTTGTGGGGATTAACTGAACGA 58.595 45.455 0.00 0.00 0.00 3.85
266 268 6.211184 TGGGGATTAACTGAACGACTAAGTAA 59.789 38.462 0.00 0.00 0.00 2.24
275 277 7.375834 ACTGAACGACTAAGTAATTGTGATGA 58.624 34.615 0.00 0.00 0.00 2.92
346 348 2.562738 GTGCTGCCCCATAGAAAAAGTT 59.437 45.455 0.00 0.00 0.00 2.66
409 412 0.319900 TGAACGACCTCTTGCAGAGC 60.320 55.000 7.44 0.00 40.98 4.09
414 417 0.319728 GACCTCTTGCAGAGCAGACA 59.680 55.000 7.44 0.00 40.98 3.41
415 418 0.982704 ACCTCTTGCAGAGCAGACAT 59.017 50.000 7.44 0.00 40.98 3.06
419 422 1.071228 TCTTGCAGAGCAGACATGTGT 59.929 47.619 1.15 0.00 40.61 3.72
460 463 6.427441 AGAAAGGAAGAGAAAAGAACCAGTT 58.573 36.000 0.00 0.00 0.00 3.16
482 485 2.436417 GCTGCATGTGTAGAGGGAAAA 58.564 47.619 2.14 0.00 0.00 2.29
484 487 2.421424 CTGCATGTGTAGAGGGAAAAGC 59.579 50.000 0.00 0.00 0.00 3.51
495 498 1.354705 AGGGAAAAGCAAGGGAGGTAC 59.645 52.381 0.00 0.00 0.00 3.34
499 502 1.053424 AAAGCAAGGGAGGTACGACA 58.947 50.000 0.00 0.00 0.00 4.35
503 506 2.007049 GCAAGGGAGGTACGACACATG 61.007 57.143 0.00 0.00 0.00 3.21
518 521 0.250295 ACATGTGTGGTCCGGTCAAG 60.250 55.000 0.00 0.00 0.00 3.02
525 528 0.687920 TGGTCCGGTCAAGTTATGCA 59.312 50.000 0.00 0.00 0.00 3.96
565 569 8.494016 AAAACTTATACAATGGTCTCAGCTAC 57.506 34.615 0.00 0.00 0.00 3.58
566 570 7.425224 AACTTATACAATGGTCTCAGCTACT 57.575 36.000 0.00 0.00 0.00 2.57
567 571 7.045126 ACTTATACAATGGTCTCAGCTACTC 57.955 40.000 0.00 0.00 0.00 2.59
568 572 4.946478 ATACAATGGTCTCAGCTACTCC 57.054 45.455 0.00 0.00 0.00 3.85
569 573 1.834263 ACAATGGTCTCAGCTACTCCC 59.166 52.381 0.00 0.00 0.00 4.30
570 574 1.139853 CAATGGTCTCAGCTACTCCCC 59.860 57.143 0.00 0.00 0.00 4.81
571 575 0.399233 ATGGTCTCAGCTACTCCCCC 60.399 60.000 0.00 0.00 0.00 5.40
585 589 3.638132 CCCCCGTCCGGAAATACT 58.362 61.111 5.23 0.00 37.50 2.12
586 590 1.909975 CCCCCGTCCGGAAATACTT 59.090 57.895 5.23 0.00 37.50 2.24
587 591 0.463116 CCCCCGTCCGGAAATACTTG 60.463 60.000 5.23 0.00 37.50 3.16
588 592 0.251073 CCCCGTCCGGAAATACTTGT 59.749 55.000 5.23 0.00 37.50 3.16
589 593 1.648504 CCCGTCCGGAAATACTTGTC 58.351 55.000 5.23 0.00 37.50 3.18
590 594 1.274596 CCGTCCGGAAATACTTGTCG 58.725 55.000 5.23 1.25 37.50 4.35
591 595 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
592 596 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
593 597 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
594 598 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
595 599 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
596 600 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
597 601 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
598 602 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
599 603 4.494199 CGGAAATACTTGTCGGAGAAATGC 60.494 45.833 0.00 0.00 39.69 3.56
600 604 4.394920 GGAAATACTTGTCGGAGAAATGCA 59.605 41.667 0.00 0.00 39.69 3.96
601 605 5.066505 GGAAATACTTGTCGGAGAAATGCAT 59.933 40.000 0.00 0.00 39.69 3.96
602 606 6.260050 GGAAATACTTGTCGGAGAAATGCATA 59.740 38.462 0.00 0.00 39.69 3.14
603 607 7.201696 GGAAATACTTGTCGGAGAAATGCATAA 60.202 37.037 0.00 0.00 39.69 1.90
604 608 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
605 609 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
606 610 6.325919 ACTTGTCGGAGAAATGCATAAAAA 57.674 33.333 0.00 0.00 39.69 1.94
607 611 6.924111 ACTTGTCGGAGAAATGCATAAAAAT 58.076 32.000 0.00 0.00 39.69 1.82
608 612 6.808212 ACTTGTCGGAGAAATGCATAAAAATG 59.192 34.615 0.00 0.00 39.69 2.32
609 613 5.649557 TGTCGGAGAAATGCATAAAAATGG 58.350 37.500 0.00 0.00 39.69 3.16
610 614 5.417266 TGTCGGAGAAATGCATAAAAATGGA 59.583 36.000 0.00 0.00 39.69 3.41
611 615 6.096705 TGTCGGAGAAATGCATAAAAATGGAT 59.903 34.615 0.00 0.00 39.69 3.41
612 616 6.418819 GTCGGAGAAATGCATAAAAATGGATG 59.581 38.462 0.00 0.00 39.69 3.51
613 617 6.096705 TCGGAGAAATGCATAAAAATGGATGT 59.903 34.615 0.00 0.00 32.82 3.06
614 618 7.284261 TCGGAGAAATGCATAAAAATGGATGTA 59.716 33.333 0.00 0.00 32.82 2.29
615 619 8.084073 CGGAGAAATGCATAAAAATGGATGTAT 58.916 33.333 0.00 0.00 32.82 2.29
616 620 9.415544 GGAGAAATGCATAAAAATGGATGTATC 57.584 33.333 0.00 0.00 32.82 2.24
623 627 9.851686 TGCATAAAAATGGATGTATCTAGAACT 57.148 29.630 0.00 0.00 0.00 3.01
650 654 8.423906 AAATACGTCTAGATACATCCATTCCT 57.576 34.615 0.00 0.00 0.00 3.36
651 655 8.423906 AATACGTCTAGATACATCCATTCCTT 57.576 34.615 0.00 0.00 0.00 3.36
652 656 6.334102 ACGTCTAGATACATCCATTCCTTC 57.666 41.667 0.00 0.00 0.00 3.46
653 657 5.048643 ACGTCTAGATACATCCATTCCTTCG 60.049 44.000 0.00 0.00 0.00 3.79
654 658 5.181433 CGTCTAGATACATCCATTCCTTCGA 59.819 44.000 0.00 0.00 0.00 3.71
655 659 6.383415 GTCTAGATACATCCATTCCTTCGAC 58.617 44.000 0.00 0.00 0.00 4.20
656 660 6.016192 GTCTAGATACATCCATTCCTTCGACA 60.016 42.308 0.00 0.00 0.00 4.35
657 661 5.614324 AGATACATCCATTCCTTCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
658 662 5.605534 AGATACATCCATTCCTTCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
659 663 3.703001 ACATCCATTCCTTCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
660 664 4.819105 ACATCCATTCCTTCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
661 665 5.359194 ACATCCATTCCTTCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
662 666 5.745227 ACATCCATTCCTTCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
663 667 6.180472 ACATCCATTCCTTCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
664 668 6.316390 ACATCCATTCCTTCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
665 669 5.183228 TCCATTCCTTCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
666 670 4.034048 CCATTCCTTCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
667 671 3.241067 TCCTTCGACAAGTATTTCCGG 57.759 47.619 0.00 0.00 0.00 5.14
668 672 2.827322 TCCTTCGACAAGTATTTCCGGA 59.173 45.455 0.00 0.00 0.00 5.14
669 673 2.928116 CCTTCGACAAGTATTTCCGGAC 59.072 50.000 1.83 0.00 0.00 4.79
670 674 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
671 675 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
672 676 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
673 677 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
674 678 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
675 679 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
676 680 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
677 681 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
678 682 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
679 683 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
680 684 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
681 685 2.044650 CCGGACGGAGGGAGTACA 60.045 66.667 4.40 0.00 37.50 2.90
682 686 1.455217 CCGGACGGAGGGAGTACAT 60.455 63.158 4.40 0.00 37.50 2.29
683 687 1.734137 CGGACGGAGGGAGTACATG 59.266 63.158 0.00 0.00 0.00 3.21
684 688 1.735376 CGGACGGAGGGAGTACATGG 61.735 65.000 0.00 0.00 0.00 3.66
685 689 1.442148 GACGGAGGGAGTACATGGC 59.558 63.158 0.00 0.00 0.00 4.40
686 690 1.305802 ACGGAGGGAGTACATGGCA 60.306 57.895 0.00 0.00 0.00 4.92
687 691 1.144057 CGGAGGGAGTACATGGCAC 59.856 63.158 0.00 0.00 0.00 5.01
715 719 6.936900 GCTACATGATGTTGTCCCTATTGTAT 59.063 38.462 2.29 0.00 0.00 2.29
726 730 7.582909 TGTCCCTATTGTATATGCCCTTATT 57.417 36.000 0.00 0.00 0.00 1.40
727 731 7.402054 TGTCCCTATTGTATATGCCCTTATTG 58.598 38.462 0.00 0.00 0.00 1.90
728 732 6.828785 GTCCCTATTGTATATGCCCTTATTGG 59.171 42.308 0.00 0.00 0.00 3.16
750 754 4.161001 GGACGGAGGGAGTAGTTGAATAAA 59.839 45.833 0.00 0.00 0.00 1.40
767 771 9.508567 GTTGAATAAAATCTACTTTCATCCTGC 57.491 33.333 0.00 0.00 0.00 4.85
809 816 5.241506 TCATGTGAAAAATGTTCCCTCTGTC 59.758 40.000 0.00 0.00 31.84 3.51
1800 1817 2.328099 GCTCGTGGGGAAGTGCAAG 61.328 63.158 0.00 0.00 0.00 4.01
2140 2157 9.630098 AAATGACAATTTAGAACTATGTTGCAG 57.370 29.630 0.00 0.00 34.14 4.41
2143 2160 7.443879 TGACAATTTAGAACTATGTTGCAGTGA 59.556 33.333 0.00 0.00 0.00 3.41
2144 2161 8.165239 ACAATTTAGAACTATGTTGCAGTGAA 57.835 30.769 0.00 0.00 0.00 3.18
2145 2162 8.076178 ACAATTTAGAACTATGTTGCAGTGAAC 58.924 33.333 0.00 0.00 0.00 3.18
2146 2163 7.986085 ATTTAGAACTATGTTGCAGTGAACT 57.014 32.000 0.00 0.00 0.00 3.01
2147 2164 7.801716 TTTAGAACTATGTTGCAGTGAACTT 57.198 32.000 0.00 0.00 0.00 2.66
2148 2165 5.679734 AGAACTATGTTGCAGTGAACTTG 57.320 39.130 0.00 0.00 0.00 3.16
2149 2166 4.516698 AGAACTATGTTGCAGTGAACTTGG 59.483 41.667 0.00 0.00 0.00 3.61
2150 2167 3.820557 ACTATGTTGCAGTGAACTTGGT 58.179 40.909 0.00 0.12 0.00 3.67
2151 2168 3.565482 ACTATGTTGCAGTGAACTTGGTG 59.435 43.478 0.00 0.00 0.00 4.17
2152 2169 0.455410 TGTTGCAGTGAACTTGGTGC 59.545 50.000 0.00 0.00 36.42 5.01
2153 2170 0.592247 GTTGCAGTGAACTTGGTGCG 60.592 55.000 0.00 0.00 38.84 5.34
2154 2171 0.746204 TTGCAGTGAACTTGGTGCGA 60.746 50.000 0.00 0.00 38.84 5.10
2155 2172 0.746204 TGCAGTGAACTTGGTGCGAA 60.746 50.000 0.00 0.00 38.84 4.70
2156 2173 0.380378 GCAGTGAACTTGGTGCGAAA 59.620 50.000 0.00 0.00 0.00 3.46
2162 2179 4.336993 AGTGAACTTGGTGCGAAAAACATA 59.663 37.500 0.00 0.00 0.00 2.29
2353 2404 5.428253 CTGGTGGGGATTTATGGTATATCG 58.572 45.833 0.00 0.00 0.00 2.92
2356 2407 6.113411 GGTGGGGATTTATGGTATATCGAAG 58.887 44.000 0.00 0.00 0.00 3.79
2431 2492 7.418483 GCCTCTGGTCTTTTGATTAGAGTAGAT 60.418 40.741 0.00 0.00 38.54 1.98
2442 2503 2.605837 AGAGTAGATGTCGCGAGAGA 57.394 50.000 10.24 0.00 43.49 3.10
2445 2506 0.658368 GTAGATGTCGCGAGAGAGCA 59.342 55.000 10.24 3.32 42.89 4.26
2450 2511 2.747855 TCGCGAGAGAGCAGAGCA 60.748 61.111 3.71 0.00 36.85 4.26
2485 2546 6.071840 GCCATAGTCGTGAGGATCTTAATAGT 60.072 42.308 0.00 0.00 34.92 2.12
2493 2554 3.488363 AGGATCTTAATAGTCGGTCGCT 58.512 45.455 0.00 0.00 0.00 4.93
2508 2569 3.436496 GGTCGCTACTGTTGTCATAGTC 58.564 50.000 0.00 0.00 0.00 2.59
2571 2632 0.179936 GCAATCCTCTCCCCACTCAG 59.820 60.000 0.00 0.00 0.00 3.35
2585 2646 3.517901 CCCACTCAGTCCACCAATAACTA 59.482 47.826 0.00 0.00 0.00 2.24
2586 2647 4.019681 CCCACTCAGTCCACCAATAACTAA 60.020 45.833 0.00 0.00 0.00 2.24
2596 2657 5.251932 TCCACCAATAACTAACATCTCCCAA 59.748 40.000 0.00 0.00 0.00 4.12
2613 2674 2.242196 CCCAACATCTCATTACCACCCT 59.758 50.000 0.00 0.00 0.00 4.34
2628 2689 2.041115 CCCTGTCGTCGAGAGCAGA 61.041 63.158 13.68 0.00 33.07 4.26
2659 2720 6.505044 TCTGTTGATGGAAACTGATGATTG 57.495 37.500 0.00 0.00 34.33 2.67
2660 2721 5.063180 TGTTGATGGAAACTGATGATTGC 57.937 39.130 0.00 0.00 0.00 3.56
2891 3192 5.993748 ATGTATAGCCTCTTCTAGCTTCC 57.006 43.478 0.00 0.00 40.56 3.46
2903 3204 5.365025 TCTTCTAGCTTCCATAATCACAGCT 59.635 40.000 0.00 0.00 43.33 4.24
2929 3230 6.884832 TCTGTTCTTCAGAGTTAAAAGTGGA 58.115 36.000 0.00 0.00 46.77 4.02
2993 3294 7.355101 TCTATGTCACTGTTCCTAGTTCCTAT 58.645 38.462 0.00 0.00 0.00 2.57
3005 3306 7.446106 TCCTAGTTCCTATATTGCCTCAAAA 57.554 36.000 0.00 0.00 0.00 2.44
3106 3407 2.026915 CACATCCTGTGTCTTGATCCCA 60.027 50.000 0.00 0.00 43.08 4.37
3109 3410 2.837947 TCCTGTGTCTTGATCCCATCT 58.162 47.619 0.00 0.00 0.00 2.90
3112 3413 4.782691 TCCTGTGTCTTGATCCCATCTTTA 59.217 41.667 0.00 0.00 0.00 1.85
3236 3537 2.524569 TTGTTAAGGCCTTTGCAAGC 57.475 45.000 26.08 8.19 40.13 4.01
3512 3813 4.223255 TCAAACCGTGGAAGTATACCATCA 59.777 41.667 0.00 0.00 39.69 3.07
3708 4009 8.135382 AGTCTGTAGGTATTTTCTGCTTTCTA 57.865 34.615 0.00 0.00 0.00 2.10
3710 4011 8.874816 GTCTGTAGGTATTTTCTGCTTTCTAAG 58.125 37.037 0.00 0.00 0.00 2.18
3750 4051 2.719739 CAAATGCTCCTCATGTCAGGT 58.280 47.619 0.65 0.00 35.13 4.00
3759 4060 2.821378 CCTCATGTCAGGTTGCATTGAA 59.179 45.455 0.00 0.00 0.00 2.69
3762 4063 5.449588 CCTCATGTCAGGTTGCATTGAATAC 60.450 44.000 0.00 0.00 0.00 1.89
3781 4082 6.429692 TGAATACAAGTTCCCAGTAATGTGTG 59.570 38.462 0.00 0.00 0.00 3.82
3809 4110 8.856490 AAACTTGTCTATACTTGTTTTTGCTG 57.144 30.769 0.00 0.00 32.19 4.41
3837 4146 6.707440 TTTAGCTCTTCCACATTGTTGAAA 57.293 33.333 5.01 0.00 0.00 2.69
3840 4149 6.165700 AGCTCTTCCACATTGTTGAAATTT 57.834 33.333 5.01 0.00 0.00 1.82
3841 4150 6.218746 AGCTCTTCCACATTGTTGAAATTTC 58.781 36.000 11.41 11.41 0.00 2.17
3842 4151 6.041296 AGCTCTTCCACATTGTTGAAATTTCT 59.959 34.615 18.64 0.00 0.00 2.52
3847 4156 6.514947 TCCACATTGTTGAAATTTCTCCAAG 58.485 36.000 18.64 14.67 0.00 3.61
3873 4182 1.805943 CTTGGCACATGTGTCGATTGA 59.194 47.619 24.44 4.58 39.30 2.57
3886 4195 3.059884 GTCGATTGACTTGAGCAGTTGA 58.940 45.455 5.79 0.00 42.08 3.18
3991 4301 3.207669 GCATGCCCGAGAAGCAGG 61.208 66.667 6.36 0.00 44.90 4.85
4016 4326 0.608640 AGTGTTGTCTCCTTAGGCGG 59.391 55.000 0.00 0.00 0.00 6.13
4017 4327 1.019805 GTGTTGTCTCCTTAGGCGGC 61.020 60.000 0.00 0.00 0.00 6.53
4031 4343 1.215655 GGCGGCTATAGTTGTCTGCG 61.216 60.000 0.00 0.00 0.00 5.18
4038 4350 3.735208 GCTATAGTTGTCTGCGAGCTCAA 60.735 47.826 15.40 0.00 0.00 3.02
4047 4359 2.071540 CTGCGAGCTCAATGTCTTGAA 58.928 47.619 15.40 0.00 40.78 2.69
4049 4361 1.129437 GCGAGCTCAATGTCTTGAACC 59.871 52.381 15.40 0.00 40.78 3.62
4104 4416 1.265454 AATCAGTCACCTCCCGTCCC 61.265 60.000 0.00 0.00 0.00 4.46
4187 4499 2.547211 CCTGCTCACACTTGTCAGAAAG 59.453 50.000 0.00 0.00 30.82 2.62
4192 4504 4.260538 GCTCACACTTGTCAGAAAGTCAAG 60.261 45.833 0.00 0.00 45.19 3.02
4251 4563 2.958355 CAGGTCTGTGATTGTTTGGGTT 59.042 45.455 0.00 0.00 0.00 4.11
4262 4574 1.501604 TGTTTGGGTTAGCTTTCCCCT 59.498 47.619 19.04 0.00 42.80 4.79
4263 4575 2.717515 TGTTTGGGTTAGCTTTCCCCTA 59.282 45.455 19.04 8.71 42.80 3.53
4298 4610 5.336372 GCTGTGGTTGCATCCATAAAAGTAA 60.336 40.000 19.23 0.00 39.81 2.24
4312 4624 8.637986 TCCATAAAAGTAATGCTTTCTTGTTGT 58.362 29.630 0.00 0.00 45.91 3.32
4317 4629 7.449934 AAGTAATGCTTTCTTGTTGTTTTCG 57.550 32.000 0.00 0.00 32.57 3.46
4321 4633 3.923461 TGCTTTCTTGTTGTTTTCGTTGG 59.077 39.130 0.00 0.00 0.00 3.77
4344 4656 7.254852 TGGCTAAACTTTTTGTTCTGTTACAG 58.745 34.615 5.94 5.94 38.03 2.74
4345 4657 6.198403 GGCTAAACTTTTTGTTCTGTTACAGC 59.802 38.462 7.61 0.00 38.03 4.40
4357 4669 4.827692 TCTGTTACAGCCGTATTGAATGT 58.172 39.130 7.61 0.00 0.00 2.71
4367 4679 5.125417 AGCCGTATTGAATGTTGCAAGTAAT 59.875 36.000 0.00 0.00 0.00 1.89
4466 4778 1.399440 CCTGTCTTCATGTGCATTCCG 59.601 52.381 0.00 0.00 0.00 4.30
4473 4785 1.672363 TCATGTGCATTCCGATTCAGC 59.328 47.619 0.00 0.00 0.00 4.26
4543 4856 1.007118 CCAGGGAAGTAAAAGGGGCAT 59.993 52.381 0.00 0.00 0.00 4.40
4593 4906 4.800554 ACCTGTTGGTGCTGCTAC 57.199 55.556 0.00 0.00 46.51 3.58
4612 4925 5.177511 TGCTACATGACAGTCTTCTTTTTCG 59.822 40.000 0.00 0.00 0.00 3.46
4745 5061 4.389890 TTGGCATCACTTCCATTATTGC 57.610 40.909 0.00 0.00 31.54 3.56
4943 5259 3.260205 TGAAGTCCTTTCCCCATCTCTT 58.740 45.455 0.00 0.00 34.77 2.85
5210 5526 4.990526 CCATAATGGTTAGAAGGATGGCT 58.009 43.478 0.00 0.00 31.35 4.75
5336 5652 2.632996 TGTCGGTCAGAATCTGTTTCCT 59.367 45.455 10.36 0.00 34.67 3.36
5399 5715 1.342672 GCCCCGTCCTATTCCTGGAA 61.343 60.000 12.26 12.26 35.10 3.53
5404 5720 3.206150 CCGTCCTATTCCTGGAAACATG 58.794 50.000 14.03 2.99 41.51 3.21
5438 5754 3.076182 AGTCTCCACTCCTTCAGGACTTA 59.924 47.826 0.00 0.00 39.78 2.24
5711 6027 1.136252 CCTTGACATGCGTTCAGTTCG 60.136 52.381 0.00 0.00 0.00 3.95
5870 6186 1.686052 TGTGTTTCTGGTGGGAATTGC 59.314 47.619 0.00 0.00 0.00 3.56
5932 6258 4.639310 GCTGGAGAATCATGTGAACTGAAT 59.361 41.667 0.00 0.00 36.25 2.57
6020 6348 2.299867 AGGCTTGGAACGAATTTGCATT 59.700 40.909 0.00 0.00 35.14 3.56
6092 6426 2.536761 TTTTGTGTGTACTCCCTCCG 57.463 50.000 0.00 0.00 0.00 4.63
6093 6427 1.416243 TTTGTGTGTACTCCCTCCGT 58.584 50.000 0.00 0.00 0.00 4.69
6094 6428 0.677288 TTGTGTGTACTCCCTCCGTG 59.323 55.000 0.00 0.00 0.00 4.94
6095 6429 0.178984 TGTGTGTACTCCCTCCGTGA 60.179 55.000 0.00 0.00 0.00 4.35
6096 6430 0.963962 GTGTGTACTCCCTCCGTGAA 59.036 55.000 0.00 0.00 0.00 3.18
6097 6431 1.067776 GTGTGTACTCCCTCCGTGAAG 60.068 57.143 0.00 0.00 0.00 3.02
6098 6432 1.202964 TGTGTACTCCCTCCGTGAAGA 60.203 52.381 0.00 0.00 0.00 2.87
6099 6433 1.891150 GTGTACTCCCTCCGTGAAGAA 59.109 52.381 0.00 0.00 0.00 2.52
6100 6434 2.298163 GTGTACTCCCTCCGTGAAGAAA 59.702 50.000 0.00 0.00 0.00 2.52
6101 6435 3.056035 GTGTACTCCCTCCGTGAAGAAAT 60.056 47.826 0.00 0.00 0.00 2.17
6102 6436 4.159135 GTGTACTCCCTCCGTGAAGAAATA 59.841 45.833 0.00 0.00 0.00 1.40
6103 6437 3.889520 ACTCCCTCCGTGAAGAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
6104 6438 3.170717 ACTCCCTCCGTGAAGAAATACA 58.829 45.455 0.00 0.00 0.00 2.29
6105 6439 3.581332 ACTCCCTCCGTGAAGAAATACAA 59.419 43.478 0.00 0.00 0.00 2.41
6106 6440 4.184629 CTCCCTCCGTGAAGAAATACAAG 58.815 47.826 0.00 0.00 0.00 3.16
6107 6441 3.835978 TCCCTCCGTGAAGAAATACAAGA 59.164 43.478 0.00 0.00 0.00 3.02
6108 6442 4.081642 TCCCTCCGTGAAGAAATACAAGAG 60.082 45.833 0.00 0.00 0.00 2.85
6109 6443 4.184629 CCTCCGTGAAGAAATACAAGAGG 58.815 47.826 0.00 0.00 34.70 3.69
6110 6444 4.184629 CTCCGTGAAGAAATACAAGAGGG 58.815 47.826 0.00 0.00 0.00 4.30
6111 6445 3.835978 TCCGTGAAGAAATACAAGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
6206 6540 1.778334 GAAAATTGTTGCGTGGGTCC 58.222 50.000 0.00 0.00 0.00 4.46
6211 6545 3.047877 GTTGCGTGGGTCCGGAAG 61.048 66.667 5.23 0.00 38.85 3.46
6257 6597 0.175989 GGCTCGGGTCTCAAGTAAGG 59.824 60.000 0.00 0.00 0.00 2.69
6340 6680 6.589907 AGCAAATTTGGATTATCAAACGGAAC 59.410 34.615 19.47 0.00 39.13 3.62
6373 6713 1.664151 GTACAATCTGTTGCCCGCTAC 59.336 52.381 0.00 0.00 38.96 3.58
6390 6730 1.746787 CTACACCAAAAATACCCCGGC 59.253 52.381 0.00 0.00 0.00 6.13
6424 6764 4.335416 CTCACCAACCTATCACCATTGTT 58.665 43.478 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 9.127277 GTTCTTATAGGAGTACATCAACTCTCT 57.873 37.037 0.00 3.08 44.42 3.10
136 137 4.067896 CTGAAGCTTCTTGCAGGTTCTTA 58.932 43.478 26.09 1.26 46.91 2.10
138 139 2.502295 CTGAAGCTTCTTGCAGGTTCT 58.498 47.619 26.09 0.66 46.91 3.01
143 144 1.500844 CGGCTGAAGCTTCTTGCAG 59.499 57.895 30.76 26.41 45.94 4.41
207 209 2.208431 CTTGAGCTTATGCCGGAGAAG 58.792 52.381 5.05 5.79 40.80 2.85
220 222 2.281070 CCACGGTGTGCTTGAGCT 60.281 61.111 7.45 0.00 42.66 4.09
222 224 1.095228 ACAACCACGGTGTGCTTGAG 61.095 55.000 7.45 0.00 34.08 3.02
250 252 7.328737 GTCATCACAATTACTTAGTCGTTCAGT 59.671 37.037 0.00 0.00 0.00 3.41
266 268 5.479306 AGCGTTAGTAGTTGTCATCACAAT 58.521 37.500 0.00 0.00 44.47 2.71
275 277 7.308229 CCCTAATATACGAGCGTTAGTAGTTGT 60.308 40.741 0.00 0.00 0.00 3.32
346 348 1.280133 CCTTCTTCCTCCACATCAGCA 59.720 52.381 0.00 0.00 0.00 4.41
384 387 2.094494 TGCAAGAGGTCGTTCATCTCTC 60.094 50.000 0.00 0.00 36.08 3.20
409 412 3.961477 TTTGGACGAAACACATGTCTG 57.039 42.857 0.00 0.00 33.21 3.51
414 417 4.974368 TTCACTTTTGGACGAAACACAT 57.026 36.364 0.00 0.00 0.00 3.21
415 418 4.456222 TCTTTCACTTTTGGACGAAACACA 59.544 37.500 0.00 0.00 0.00 3.72
419 422 5.416326 TCCTTTCTTTCACTTTTGGACGAAA 59.584 36.000 0.00 0.00 0.00 3.46
460 463 0.970427 TCCCTCTACACATGCAGCGA 60.970 55.000 0.00 0.00 0.00 4.93
482 485 0.830444 TGTGTCGTACCTCCCTTGCT 60.830 55.000 0.00 0.00 0.00 3.91
484 487 1.275291 ACATGTGTCGTACCTCCCTTG 59.725 52.381 0.00 0.00 0.00 3.61
495 498 2.027073 CCGGACCACACATGTGTCG 61.027 63.158 28.38 25.53 42.83 4.35
499 502 0.250295 CTTGACCGGACCACACATGT 60.250 55.000 9.46 0.00 0.00 3.21
503 506 2.073816 CATAACTTGACCGGACCACAC 58.926 52.381 9.46 0.00 0.00 3.82
518 521 4.374843 TTCTGTCCAATGCATGCATAAC 57.625 40.909 32.36 27.09 35.31 1.89
545 549 5.304614 GGGAGTAGCTGAGACCATTGTATAA 59.695 44.000 0.00 0.00 0.00 0.98
568 572 0.463116 CAAGTATTTCCGGACGGGGG 60.463 60.000 1.83 0.00 36.01 5.40
569 573 0.251073 ACAAGTATTTCCGGACGGGG 59.749 55.000 1.83 0.00 36.01 5.73
570 574 1.648504 GACAAGTATTTCCGGACGGG 58.351 55.000 1.83 1.55 35.59 5.28
571 575 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
572 576 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
573 577 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
574 578 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
575 579 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
576 580 4.494199 GCATTTCTCCGACAAGTATTTCCG 60.494 45.833 0.00 0.00 0.00 4.30
577 581 4.394920 TGCATTTCTCCGACAAGTATTTCC 59.605 41.667 0.00 0.00 0.00 3.13
578 582 5.545658 TGCATTTCTCCGACAAGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
579 583 7.624360 TTATGCATTTCTCCGACAAGTATTT 57.376 32.000 3.54 0.00 0.00 1.40
580 584 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
581 585 7.624360 TTTTATGCATTTCTCCGACAAGTAT 57.376 32.000 3.54 0.00 0.00 2.12
582 586 7.441890 TTTTTATGCATTTCTCCGACAAGTA 57.558 32.000 3.54 0.00 0.00 2.24
583 587 5.957842 TTTTATGCATTTCTCCGACAAGT 57.042 34.783 3.54 0.00 0.00 3.16
584 588 6.254157 CCATTTTTATGCATTTCTCCGACAAG 59.746 38.462 3.54 0.00 0.00 3.16
585 589 6.071672 TCCATTTTTATGCATTTCTCCGACAA 60.072 34.615 3.54 0.00 0.00 3.18
586 590 5.417266 TCCATTTTTATGCATTTCTCCGACA 59.583 36.000 3.54 0.00 0.00 4.35
587 591 5.890334 TCCATTTTTATGCATTTCTCCGAC 58.110 37.500 3.54 0.00 0.00 4.79
588 592 6.096705 ACATCCATTTTTATGCATTTCTCCGA 59.903 34.615 3.54 0.00 0.00 4.55
589 593 6.275335 ACATCCATTTTTATGCATTTCTCCG 58.725 36.000 3.54 0.00 0.00 4.63
590 594 9.415544 GATACATCCATTTTTATGCATTTCTCC 57.584 33.333 3.54 0.00 0.00 3.71
597 601 9.851686 AGTTCTAGATACATCCATTTTTATGCA 57.148 29.630 0.00 0.00 0.00 3.96
624 628 8.871125 AGGAATGGATGTATCTAGACGTATTTT 58.129 33.333 0.00 0.00 0.00 1.82
625 629 8.423906 AGGAATGGATGTATCTAGACGTATTT 57.576 34.615 0.00 0.00 0.00 1.40
626 630 8.423906 AAGGAATGGATGTATCTAGACGTATT 57.576 34.615 0.00 0.00 0.00 1.89
627 631 7.148222 CGAAGGAATGGATGTATCTAGACGTAT 60.148 40.741 0.00 0.00 0.00 3.06
628 632 6.148976 CGAAGGAATGGATGTATCTAGACGTA 59.851 42.308 0.00 0.00 0.00 3.57
629 633 5.048643 CGAAGGAATGGATGTATCTAGACGT 60.049 44.000 0.00 0.00 0.00 4.34
630 634 5.181433 TCGAAGGAATGGATGTATCTAGACG 59.819 44.000 0.00 0.00 0.00 4.18
631 635 6.016192 TGTCGAAGGAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 0.00 2.59
632 636 6.068670 TGTCGAAGGAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
633 637 6.332735 TGTCGAAGGAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
634 638 6.323996 ACTTGTCGAAGGAATGGATGTATCTA 59.676 38.462 0.00 0.00 32.95 1.98
635 639 5.129485 ACTTGTCGAAGGAATGGATGTATCT 59.871 40.000 0.00 0.00 32.95 1.98
636 640 5.360591 ACTTGTCGAAGGAATGGATGTATC 58.639 41.667 0.00 0.00 32.95 2.24
637 641 5.359194 ACTTGTCGAAGGAATGGATGTAT 57.641 39.130 0.00 0.00 32.95 2.29
638 642 4.819105 ACTTGTCGAAGGAATGGATGTA 57.181 40.909 0.00 0.00 32.95 2.29
639 643 3.703001 ACTTGTCGAAGGAATGGATGT 57.297 42.857 0.00 0.00 32.95 3.06
640 644 6.238484 GGAAATACTTGTCGAAGGAATGGATG 60.238 42.308 0.00 0.00 32.95 3.51
641 645 5.823045 GGAAATACTTGTCGAAGGAATGGAT 59.177 40.000 0.00 0.00 32.95 3.41
642 646 5.183228 GGAAATACTTGTCGAAGGAATGGA 58.817 41.667 0.00 0.00 32.95 3.41
643 647 4.034048 CGGAAATACTTGTCGAAGGAATGG 59.966 45.833 0.00 0.00 32.95 3.16
644 648 4.034048 CCGGAAATACTTGTCGAAGGAATG 59.966 45.833 0.00 0.00 32.95 2.67
645 649 4.081309 TCCGGAAATACTTGTCGAAGGAAT 60.081 41.667 0.00 0.00 32.95 3.01
646 650 3.258872 TCCGGAAATACTTGTCGAAGGAA 59.741 43.478 0.00 0.00 32.95 3.36
647 651 2.827322 TCCGGAAATACTTGTCGAAGGA 59.173 45.455 0.00 0.00 32.95 3.36
648 652 2.928116 GTCCGGAAATACTTGTCGAAGG 59.072 50.000 5.23 0.00 32.95 3.46
649 653 2.597305 CGTCCGGAAATACTTGTCGAAG 59.403 50.000 5.23 0.00 35.07 3.79
650 654 2.598589 CGTCCGGAAATACTTGTCGAA 58.401 47.619 5.23 0.00 0.00 3.71
651 655 1.135315 CCGTCCGGAAATACTTGTCGA 60.135 52.381 5.23 0.00 37.50 4.20
652 656 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
653 657 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
654 658 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
655 659 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
656 660 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
657 661 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
658 662 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
659 663 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
660 664 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
661 665 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
662 666 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
663 667 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
664 668 1.455217 ATGTACTCCCTCCGTCCGG 60.455 63.158 0.00 0.00 0.00 5.14
665 669 1.734137 CATGTACTCCCTCCGTCCG 59.266 63.158 0.00 0.00 0.00 4.79
666 670 2.029307 GCCATGTACTCCCTCCGTCC 62.029 65.000 0.00 0.00 0.00 4.79
667 671 1.327690 TGCCATGTACTCCCTCCGTC 61.328 60.000 0.00 0.00 0.00 4.79
668 672 1.305802 TGCCATGTACTCCCTCCGT 60.306 57.895 0.00 0.00 0.00 4.69
669 673 1.144057 GTGCCATGTACTCCCTCCG 59.856 63.158 0.00 0.00 0.00 4.63
670 674 0.839946 ATGTGCCATGTACTCCCTCC 59.160 55.000 0.00 0.00 0.00 4.30
671 675 1.959042 CATGTGCCATGTACTCCCTC 58.041 55.000 6.93 0.00 0.00 4.30
672 676 0.107017 GCATGTGCCATGTACTCCCT 60.107 55.000 14.21 0.00 34.31 4.20
673 677 0.107017 AGCATGTGCCATGTACTCCC 60.107 55.000 14.21 0.65 43.38 4.30
674 678 2.213499 GTAGCATGTGCCATGTACTCC 58.787 52.381 14.21 1.20 43.38 3.85
675 679 2.905075 TGTAGCATGTGCCATGTACTC 58.095 47.619 14.21 6.17 43.38 2.59
676 680 3.118298 TCATGTAGCATGTGCCATGTACT 60.118 43.478 17.68 8.12 43.38 2.73
677 681 3.205338 TCATGTAGCATGTGCCATGTAC 58.795 45.455 17.68 14.08 43.38 2.90
678 682 3.557228 TCATGTAGCATGTGCCATGTA 57.443 42.857 17.68 7.60 43.38 2.29
679 683 2.423446 TCATGTAGCATGTGCCATGT 57.577 45.000 17.68 6.37 43.38 3.21
680 684 2.621526 ACATCATGTAGCATGTGCCATG 59.378 45.455 14.28 14.28 43.38 3.66
681 685 2.940158 ACATCATGTAGCATGTGCCAT 58.060 42.857 8.68 0.00 43.38 4.40
682 686 2.423446 ACATCATGTAGCATGTGCCA 57.577 45.000 8.68 0.00 43.38 4.92
683 687 2.424601 ACAACATCATGTAGCATGTGCC 59.575 45.455 8.68 0.00 43.38 5.01
684 688 3.488047 GGACAACATCATGTAGCATGTGC 60.488 47.826 8.68 0.00 33.38 4.57
685 689 3.065786 GGGACAACATCATGTAGCATGTG 59.934 47.826 8.68 8.76 33.38 3.21
686 690 3.054139 AGGGACAACATCATGTAGCATGT 60.054 43.478 8.68 0.00 34.58 3.21
687 691 3.548770 AGGGACAACATCATGTAGCATG 58.451 45.455 0.00 2.93 32.57 4.06
688 692 3.939740 AGGGACAACATCATGTAGCAT 57.060 42.857 0.00 0.00 32.57 3.79
697 701 5.648092 GGGCATATACAATAGGGACAACATC 59.352 44.000 0.00 0.00 0.00 3.06
715 719 1.697432 CCTCCGTCCAATAAGGGCATA 59.303 52.381 0.00 0.00 44.49 3.14
726 730 0.406750 TCAACTACTCCCTCCGTCCA 59.593 55.000 0.00 0.00 0.00 4.02
727 731 1.553706 TTCAACTACTCCCTCCGTCC 58.446 55.000 0.00 0.00 0.00 4.79
728 732 4.996788 TTATTCAACTACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
780 784 5.055812 GGGAACATTTTTCACATGAAAGCA 58.944 37.500 0.00 0.04 43.90 3.91
809 816 5.778161 TTATTCACTGTCACGCTGTATTG 57.222 39.130 0.00 0.00 0.00 1.90
835 842 3.648339 AACATGAATGTCAGCGCTTTT 57.352 38.095 7.50 0.00 40.80 2.27
899 909 3.216187 TGGTCGGTTGAGAAAATTGGA 57.784 42.857 0.00 0.00 0.00 3.53
2131 2148 2.293122 GCACCAAGTTCACTGCAACATA 59.707 45.455 0.00 0.00 0.00 2.29
2133 2150 0.455410 GCACCAAGTTCACTGCAACA 59.545 50.000 0.00 0.00 0.00 3.33
2135 2152 0.746204 TCGCACCAAGTTCACTGCAA 60.746 50.000 0.00 0.00 0.00 4.08
2140 2157 2.869897 TGTTTTTCGCACCAAGTTCAC 58.130 42.857 0.00 0.00 0.00 3.18
2143 2160 4.578928 AGAGTATGTTTTTCGCACCAAGTT 59.421 37.500 0.00 0.00 0.00 2.66
2144 2161 4.134563 AGAGTATGTTTTTCGCACCAAGT 58.865 39.130 0.00 0.00 0.00 3.16
2145 2162 4.749245 AGAGTATGTTTTTCGCACCAAG 57.251 40.909 0.00 0.00 0.00 3.61
2146 2163 7.766738 TGATATAGAGTATGTTTTTCGCACCAA 59.233 33.333 0.00 0.00 0.00 3.67
2147 2164 7.269316 TGATATAGAGTATGTTTTTCGCACCA 58.731 34.615 0.00 0.00 0.00 4.17
2148 2165 7.709269 TGATATAGAGTATGTTTTTCGCACC 57.291 36.000 0.00 0.00 0.00 5.01
2149 2166 8.978539 TCATGATATAGAGTATGTTTTTCGCAC 58.021 33.333 0.00 0.00 0.00 5.34
2150 2167 9.710900 ATCATGATATAGAGTATGTTTTTCGCA 57.289 29.630 6.36 0.00 0.00 5.10
2218 2238 4.634184 TCGTATCTCTTTGACTGCCTAC 57.366 45.455 0.00 0.00 0.00 3.18
2270 2290 9.787435 AAACAGTGAAACCTAAACATATACTGA 57.213 29.630 0.00 0.00 37.80 3.41
2353 2404 9.624697 TTTGTGTAATCAATAACATTGCTCTTC 57.375 29.630 0.00 0.00 0.00 2.87
2411 2472 6.199342 GCGACATCTACTCTAATCAAAAGACC 59.801 42.308 0.00 0.00 0.00 3.85
2431 2492 3.045277 GCTCTGCTCTCTCGCGACA 62.045 63.158 3.71 0.00 0.00 4.35
2442 2503 3.842923 AGCGCGGTATGCTCTGCT 61.843 61.111 10.12 0.00 38.62 4.24
2445 2506 4.899239 GGCAGCGCGGTATGCTCT 62.899 66.667 11.92 0.00 41.72 4.09
2450 2511 1.006102 GACTATGGCAGCGCGGTAT 60.006 57.895 11.92 3.47 0.00 2.73
2485 2546 0.885879 ATGACAACAGTAGCGACCGA 59.114 50.000 0.00 0.00 0.00 4.69
2493 2554 5.047590 ACCATCGTTGACTATGACAACAGTA 60.048 40.000 0.00 0.00 45.09 2.74
2528 2589 3.496331 TCCCAATTCGAAGCTTTTTCCT 58.504 40.909 3.35 0.00 0.00 3.36
2561 2622 0.475632 ATTGGTGGACTGAGTGGGGA 60.476 55.000 0.00 0.00 0.00 4.81
2571 2632 5.123936 GGGAGATGTTAGTTATTGGTGGAC 58.876 45.833 0.00 0.00 0.00 4.02
2585 2646 5.044919 TGGTAATGAGATGTTGGGAGATGTT 60.045 40.000 0.00 0.00 0.00 2.71
2586 2647 4.474651 TGGTAATGAGATGTTGGGAGATGT 59.525 41.667 0.00 0.00 0.00 3.06
2596 2657 2.168521 CGACAGGGTGGTAATGAGATGT 59.831 50.000 0.00 0.00 0.00 3.06
2613 2674 1.869690 CTGTCTGCTCTCGACGACA 59.130 57.895 0.00 0.00 35.35 4.35
2872 3173 7.895962 TGATTATGGAAGCTAGAAGAGGCTATA 59.104 37.037 0.00 0.00 37.87 1.31
2929 3230 7.576287 CTGATTGCAGATAAAACATGGAACACT 60.576 37.037 0.00 0.00 43.69 3.55
2993 3294 8.502387 GCAAATGTAAACAATTTTGAGGCAATA 58.498 29.630 11.50 0.00 31.12 1.90
3005 3306 8.810652 AAACTATCGTTGCAAATGTAAACAAT 57.189 26.923 0.00 0.00 33.60 2.71
3015 3316 9.347934 CCAAACATATTAAACTATCGTTGCAAA 57.652 29.630 0.00 0.00 32.65 3.68
3036 3337 3.978855 GGAAACAAGCGAACATACCAAAC 59.021 43.478 0.00 0.00 0.00 2.93
3137 3438 8.478066 TCTGTCAGTATAAGTTCAAGCACATAT 58.522 33.333 0.00 0.00 0.00 1.78
3236 3537 4.142730 GCAGTAAAGACAGATTTCAGCTGG 60.143 45.833 15.13 0.00 37.69 4.85
3374 3675 4.530946 TGATCTTTTCCTTCGGGAGTAAGT 59.469 41.667 0.00 0.00 45.95 2.24
3680 3981 9.384764 GAAAGCAGAAAATACCTACAGACTTAT 57.615 33.333 0.00 0.00 0.00 1.73
3729 4030 1.404391 CCTGACATGAGGAGCATTTGC 59.596 52.381 0.00 0.00 42.49 3.68
3750 4051 4.832266 ACTGGGAACTTGTATTCAATGCAA 59.168 37.500 0.62 0.62 33.79 4.08
3759 4060 5.705441 CACACACATTACTGGGAACTTGTAT 59.295 40.000 0.00 0.00 0.00 2.29
3762 4063 4.133820 TCACACACATTACTGGGAACTTG 58.866 43.478 0.00 0.00 0.00 3.16
3781 4082 8.743099 GCAAAAACAAGTATAGACAAGTTTCAC 58.257 33.333 9.69 2.03 35.22 3.18
3809 4110 4.213482 ACAATGTGGAAGAGCTAAAACGAC 59.787 41.667 0.00 0.00 0.00 4.34
3847 4156 1.373748 CACATGTGCCAAGCCAAGC 60.374 57.895 13.94 0.00 0.00 4.01
3858 4167 3.424039 GCTCAAGTCAATCGACACATGTG 60.424 47.826 24.25 24.25 45.23 3.21
3890 4199 6.205101 AGATCAAAGCATCTTTAAAGCTGG 57.795 37.500 18.13 8.26 38.86 4.85
3959 4269 0.308684 CATGCGGACACCATGCATAC 59.691 55.000 0.00 0.00 46.91 2.39
3991 4301 4.393371 GCCTAAGGAGACAACACTGATTTC 59.607 45.833 0.00 0.00 0.00 2.17
4016 4326 2.223595 TGAGCTCGCAGACAACTATAGC 60.224 50.000 9.64 0.00 0.00 2.97
4017 4327 3.699779 TGAGCTCGCAGACAACTATAG 57.300 47.619 9.64 0.00 0.00 1.31
4031 4343 1.734465 CCGGTTCAAGACATTGAGCTC 59.266 52.381 6.82 6.82 45.89 4.09
4049 4361 3.317993 ACTCAGGAATGAAAAACCAACCG 59.682 43.478 0.00 0.00 0.00 4.44
4063 4375 1.420138 GGTTCCCACTCAACTCAGGAA 59.580 52.381 0.00 0.00 34.27 3.36
4104 4416 3.673809 GCGGCATCTAGTAATAAAGGTCG 59.326 47.826 0.00 0.00 0.00 4.79
4131 4443 5.871524 TCCAGAAGATGAGAAGAATCAAACG 59.128 40.000 0.00 0.00 31.76 3.60
4187 4499 3.010420 GGTCTCAATGGGTAAGCTTGAC 58.990 50.000 9.86 4.23 0.00 3.18
4192 4504 6.715347 ATTTATTGGTCTCAATGGGTAAGC 57.285 37.500 2.27 0.00 42.93 3.09
4251 4563 1.913419 CCACAACCTAGGGGAAAGCTA 59.087 52.381 14.81 0.00 36.25 3.32
4262 4574 1.724545 ACCACAGCTACCACAACCTA 58.275 50.000 0.00 0.00 0.00 3.08
4263 4575 0.843984 AACCACAGCTACCACAACCT 59.156 50.000 0.00 0.00 0.00 3.50
4298 4610 4.566360 CCAACGAAAACAACAAGAAAGCAT 59.434 37.500 0.00 0.00 0.00 3.79
4312 4624 6.869388 AGAACAAAAAGTTTAGCCAACGAAAA 59.131 30.769 0.00 0.00 41.51 2.29
4317 4629 6.961359 AACAGAACAAAAAGTTTAGCCAAC 57.039 33.333 0.00 0.00 41.51 3.77
4321 4633 6.198403 GGCTGTAACAGAACAAAAAGTTTAGC 59.802 38.462 0.00 0.00 41.51 3.09
4344 4656 3.216147 ACTTGCAACATTCAATACGGC 57.784 42.857 0.00 0.00 0.00 5.68
4345 4657 5.743398 CCATTACTTGCAACATTCAATACGG 59.257 40.000 0.00 0.00 0.00 4.02
4443 4755 2.119801 ATGCACATGAAGACAGGGAC 57.880 50.000 0.00 0.00 31.68 4.46
4473 4785 0.612229 ATGAGGGACAGCTGACACTG 59.388 55.000 25.60 0.00 43.59 3.66
4543 4856 4.801914 GCAGTTATAGGCTCAGATGATGCA 60.802 45.833 0.00 0.00 0.00 3.96
4593 4906 5.810525 ACAACGAAAAAGAAGACTGTCATG 58.189 37.500 10.88 0.00 0.00 3.07
4612 4925 7.982354 AGGCAGTGAGACTATAAATAAGACAAC 59.018 37.037 0.00 0.00 29.36 3.32
4671 4987 2.932614 CAGCACATACGAGGAAAGAAGG 59.067 50.000 0.00 0.00 0.00 3.46
4943 5259 1.427368 GCAACCCCATATATGACCCCA 59.573 52.381 14.54 0.00 0.00 4.96
5404 5720 4.104856 GAGTGGAGACTTGTCAAGCTGAC 61.105 52.174 12.66 8.75 39.15 3.51
5438 5754 2.607750 AGGATCACGCTGGGTGGT 60.608 61.111 22.42 17.23 46.96 4.16
5507 5823 2.024918 CAGCGGTGTCAGCTTGTTT 58.975 52.632 6.41 0.00 44.06 2.83
5711 6027 5.024133 ATACAAATGTACGCTGCACAGCC 62.024 47.826 16.59 3.93 40.60 4.85
5870 6186 8.680001 TCAAACATATCAGAATTCAGAACATGG 58.320 33.333 20.34 10.00 0.00 3.66
5932 6258 3.374988 CGCATCTTAATGAGGTTTGCAGA 59.625 43.478 0.00 0.00 34.61 4.26
6083 6417 3.170717 TGTATTTCTTCACGGAGGGAGT 58.829 45.455 0.00 0.00 0.00 3.85
6084 6418 3.887621 TGTATTTCTTCACGGAGGGAG 57.112 47.619 0.00 0.00 0.00 4.30
6085 6419 3.835978 TCTTGTATTTCTTCACGGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
6086 6420 4.184629 CTCTTGTATTTCTTCACGGAGGG 58.815 47.826 0.00 0.00 0.00 4.30
6087 6421 4.184629 CCTCTTGTATTTCTTCACGGAGG 58.815 47.826 0.00 0.00 32.26 4.30
6088 6422 4.081642 TCCCTCTTGTATTTCTTCACGGAG 60.082 45.833 0.00 0.00 0.00 4.63
6089 6423 3.835978 TCCCTCTTGTATTTCTTCACGGA 59.164 43.478 0.00 0.00 0.00 4.69
6090 6424 4.202245 TCCCTCTTGTATTTCTTCACGG 57.798 45.455 0.00 0.00 0.00 4.94
6091 6425 6.574350 ACTATCCCTCTTGTATTTCTTCACG 58.426 40.000 0.00 0.00 0.00 4.35
6092 6426 8.145122 CCTACTATCCCTCTTGTATTTCTTCAC 58.855 40.741 0.00 0.00 0.00 3.18
6093 6427 7.844779 ACCTACTATCCCTCTTGTATTTCTTCA 59.155 37.037 0.00 0.00 0.00 3.02
6094 6428 8.145122 CACCTACTATCCCTCTTGTATTTCTTC 58.855 40.741 0.00 0.00 0.00 2.87
6095 6429 7.419172 GCACCTACTATCCCTCTTGTATTTCTT 60.419 40.741 0.00 0.00 0.00 2.52
6096 6430 6.042208 GCACCTACTATCCCTCTTGTATTTCT 59.958 42.308 0.00 0.00 0.00 2.52
6097 6431 6.042208 AGCACCTACTATCCCTCTTGTATTTC 59.958 42.308 0.00 0.00 0.00 2.17
6098 6432 5.905913 AGCACCTACTATCCCTCTTGTATTT 59.094 40.000 0.00 0.00 0.00 1.40
6099 6433 5.305644 CAGCACCTACTATCCCTCTTGTATT 59.694 44.000 0.00 0.00 0.00 1.89
6100 6434 4.835615 CAGCACCTACTATCCCTCTTGTAT 59.164 45.833 0.00 0.00 0.00 2.29
6101 6435 4.215908 CAGCACCTACTATCCCTCTTGTA 58.784 47.826 0.00 0.00 0.00 2.41
6102 6436 3.034635 CAGCACCTACTATCCCTCTTGT 58.965 50.000 0.00 0.00 0.00 3.16
6103 6437 2.224161 GCAGCACCTACTATCCCTCTTG 60.224 54.545 0.00 0.00 0.00 3.02
6104 6438 2.043227 GCAGCACCTACTATCCCTCTT 58.957 52.381 0.00 0.00 0.00 2.85
6105 6439 1.062886 TGCAGCACCTACTATCCCTCT 60.063 52.381 0.00 0.00 0.00 3.69
6106 6440 1.414158 TGCAGCACCTACTATCCCTC 58.586 55.000 0.00 0.00 0.00 4.30
6107 6441 1.486726 GTTGCAGCACCTACTATCCCT 59.513 52.381 0.00 0.00 0.00 4.20
6108 6442 1.209504 TGTTGCAGCACCTACTATCCC 59.790 52.381 0.00 0.00 0.00 3.85
6109 6443 2.691409 TGTTGCAGCACCTACTATCC 57.309 50.000 0.00 0.00 0.00 2.59
6110 6444 4.396166 ACAAATGTTGCAGCACCTACTATC 59.604 41.667 5.00 0.00 0.00 2.08
6111 6445 4.156556 CACAAATGTTGCAGCACCTACTAT 59.843 41.667 5.00 0.00 0.00 2.12
6206 6540 0.107831 TCAACAACCTGGTCCTTCCG 59.892 55.000 0.00 0.00 39.52 4.30
6211 6545 0.464916 AACGGTCAACAACCTGGTCC 60.465 55.000 0.00 0.00 46.87 4.46
6257 6597 3.011949 TCTGCGCCAAATCTTTTGTTC 57.988 42.857 4.18 0.00 0.00 3.18
6313 6653 7.158021 TCCGTTTGATAATCCAAATTTGCTTT 58.842 30.769 12.92 10.21 38.18 3.51
6340 6680 1.119574 ATTGTACCGGATCCCTCCCG 61.120 60.000 9.46 0.00 46.10 5.14
6373 6713 1.894512 GGCCGGGGTATTTTTGGTG 59.105 57.895 2.18 0.00 0.00 4.17
6390 6730 2.434359 GGTGAGGAGGCGAAACGG 60.434 66.667 0.00 0.00 0.00 4.44
6424 6764 1.320344 CCGTGGTCTCGGGAATCTGA 61.320 60.000 0.00 0.00 45.88 3.27


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

AutoCloner maintained by Alex Coulton.