Multiple sequence alignment - TraesCS5D01G074200

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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 TraesCS5D01G074200 chr5D 100.000 2641 0 0 1 2641 73401010 73398370 0.000000e+00 4878.0
1 TraesCS5D01G074200 chr5D 98.689 534 7 0 1 534 73406469 73405936 0.000000e+00 948.0
2 TraesCS5D01G074200 chr5D 98.315 534 9 0 1 534 326411290 326411823 0.000000e+00 937.0
3 TraesCS5D01G074200 chr5D 98.138 537 10 0 1 537 457556399 457555863 0.000000e+00 937.0
4 TraesCS5D01G074200 chr5D 98.127 534 10 0 1 534 457561865 457561332 0.000000e+00 931.0
5 TraesCS5D01G074200 chr5D 83.879 794 75 30 849 1595 73464750 73463963 0.000000e+00 708.0
6 TraesCS5D01G074200 chr5A 89.590 1854 96 51 845 2641 68551468 68549655 0.000000e+00 2265.0
7 TraesCS5D01G074200 chr5A 91.589 321 24 2 534 851 675532828 675532508 8.680000e-120 440.0
8 TraesCS5D01G074200 chr5B 91.130 947 50 20 921 1856 81194750 81193827 0.000000e+00 1253.0
9 TraesCS5D01G074200 chr5B 89.820 668 52 8 1985 2641 81193805 81193143 0.000000e+00 843.0
10 TraesCS5D01G074200 chr5B 85.222 406 42 13 1416 1813 711573392 711572997 4.090000e-108 401.0
11 TraesCS5D01G074200 chr5B 93.671 79 2 3 845 922 81195062 81194986 5.970000e-22 115.0
12 TraesCS5D01G074200 chr2D 98.131 535 10 0 1 535 284514578 284515112 0.000000e+00 933.0
13 TraesCS5D01G074200 chr2D 98.127 534 10 0 1 534 234348836 234349369 0.000000e+00 931.0
14 TraesCS5D01G074200 chr2D 90.741 324 27 3 534 856 47987674 47987353 1.880000e-116 429.0
15 TraesCS5D01G074200 chr2D 82.373 295 39 9 1434 1721 94489681 94489393 7.300000e-61 244.0
16 TraesCS5D01G074200 chr7D 97.441 547 13 1 1 547 351660373 351659828 0.000000e+00 931.0
17 TraesCS5D01G074200 chr7D 91.718 326 25 2 534 858 14571165 14571489 4.010000e-123 451.0
18 TraesCS5D01G074200 chr7D 87.889 289 20 7 1556 1833 60613746 60613462 2.540000e-85 326.0
19 TraesCS5D01G074200 chr7D 87.209 86 9 1 1416 1501 60613827 60613744 2.160000e-16 97.1
20 TraesCS5D01G074200 chr1D 98.127 534 10 0 1 534 115026114 115025581 0.000000e+00 931.0
21 TraesCS5D01G074200 chr4D 97.422 543 14 0 1 543 437717448 437716906 0.000000e+00 926.0
22 TraesCS5D01G074200 chr4D 92.523 321 20 3 534 851 7071451 7071132 8.620000e-125 457.0
23 TraesCS5D01G074200 chr4A 93.125 320 20 1 534 851 516341741 516342060 3.980000e-128 468.0
24 TraesCS5D01G074200 chr7A 86.816 402 36 14 1416 1809 12398580 12398972 1.450000e-117 433.0
25 TraesCS5D01G074200 chr7A 89.669 242 22 1 2400 2641 522495208 522495446 3.300000e-79 305.0
26 TraesCS5D01G074200 chr2A 90.769 325 27 3 534 856 734616219 734616542 5.220000e-117 431.0
27 TraesCS5D01G074200 chr2A 90.625 320 28 2 534 852 706515490 706515172 8.740000e-115 424.0
28 TraesCS5D01G074200 chr6D 90.966 321 25 4 534 851 461524094 461524413 1.880000e-116 429.0
29 TraesCS5D01G074200 chr3D 89.053 338 33 3 534 869 59922870 59922535 1.460000e-112 416.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G074200 chr5D 73398370 73401010 2640 True 4878 4878 100.000000 1 2641 1 chr5D.!!$R1 2640
1 TraesCS5D01G074200 chr5D 73405936 73406469 533 True 948 948 98.689000 1 534 1 chr5D.!!$R2 533
2 TraesCS5D01G074200 chr5D 326411290 326411823 533 False 937 937 98.315000 1 534 1 chr5D.!!$F1 533
3 TraesCS5D01G074200 chr5D 457555863 457556399 536 True 937 937 98.138000 1 537 1 chr5D.!!$R4 536
4 TraesCS5D01G074200 chr5D 457561332 457561865 533 True 931 931 98.127000 1 534 1 chr5D.!!$R5 533
5 TraesCS5D01G074200 chr5D 73463963 73464750 787 True 708 708 83.879000 849 1595 1 chr5D.!!$R3 746
6 TraesCS5D01G074200 chr5A 68549655 68551468 1813 True 2265 2265 89.590000 845 2641 1 chr5A.!!$R1 1796
7 TraesCS5D01G074200 chr5B 81193143 81195062 1919 True 737 1253 91.540333 845 2641 3 chr5B.!!$R2 1796
8 TraesCS5D01G074200 chr2D 284514578 284515112 534 False 933 933 98.131000 1 535 1 chr2D.!!$F2 534
9 TraesCS5D01G074200 chr2D 234348836 234349369 533 False 931 931 98.127000 1 534 1 chr2D.!!$F1 533
10 TraesCS5D01G074200 chr7D 351659828 351660373 545 True 931 931 97.441000 1 547 1 chr7D.!!$R1 546
11 TraesCS5D01G074200 chr1D 115025581 115026114 533 True 931 931 98.127000 1 534 1 chr1D.!!$R1 533
12 TraesCS5D01G074200 chr4D 437716906 437717448 542 True 926 926 97.422000 1 543 1 chr4D.!!$R2 542

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
681 682 0.027194 CAATCAATCAGCGCGACCTG 59.973 55.0 12.1 9.17 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 2193 0.391927 TGGGCCCGAATGAAGTAACG 60.392 55.0 19.37 0.0 0.0 3.18 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
71 72 3.382227 CCGAAAAACACCTAGGGTTTTGT 59.618 43.478 27.61 20.86 45.02 2.83
215 216 3.057806 CGAATTAGGTTTTTGGGAAGCGT 60.058 43.478 0.00 0.00 32.52 5.07
322 323 1.005037 AGCAGATCGTCGCCAACAA 60.005 52.632 1.78 0.00 0.00 2.83
351 352 1.841277 ACCCTGTCGCACCCATAATAA 59.159 47.619 0.00 0.00 0.00 1.40
367 368 6.307318 CCCATAATAACTAACGATCAGTACGC 59.693 42.308 0.00 0.00 0.00 4.42
380 381 1.754803 CAGTACGCCCAACATCCTCTA 59.245 52.381 0.00 0.00 0.00 2.43
540 541 6.698008 TGCCTAATATTCCAACATCAAGTG 57.302 37.500 0.00 0.00 0.00 3.16
543 544 6.498304 CCTAATATTCCAACATCAAGTGTGC 58.502 40.000 0.00 0.00 41.14 4.57
545 546 5.981088 ATATTCCAACATCAAGTGTGCAA 57.019 34.783 0.00 0.00 41.14 4.08
546 547 3.713858 TTCCAACATCAAGTGTGCAAG 57.286 42.857 0.00 0.00 41.14 4.01
547 548 2.929641 TCCAACATCAAGTGTGCAAGA 58.070 42.857 0.00 0.00 41.14 3.02
548 549 2.880268 TCCAACATCAAGTGTGCAAGAG 59.120 45.455 0.00 0.00 41.14 2.85
549 550 2.030540 CCAACATCAAGTGTGCAAGAGG 60.031 50.000 0.00 0.00 41.14 3.69
550 551 1.242076 ACATCAAGTGTGCAAGAGGC 58.758 50.000 0.00 0.00 40.28 4.70
559 560 3.343972 GCAAGAGGCGCAGTGAAA 58.656 55.556 10.83 0.00 0.00 2.69
560 561 1.208614 GCAAGAGGCGCAGTGAAAG 59.791 57.895 10.83 0.00 0.00 2.62
561 562 1.230635 GCAAGAGGCGCAGTGAAAGA 61.231 55.000 10.83 0.00 0.00 2.52
562 563 1.229428 CAAGAGGCGCAGTGAAAGAA 58.771 50.000 10.83 0.00 0.00 2.52
563 564 1.808945 CAAGAGGCGCAGTGAAAGAAT 59.191 47.619 10.83 0.00 0.00 2.40
564 565 1.731720 AGAGGCGCAGTGAAAGAATC 58.268 50.000 10.83 0.00 0.00 2.52
565 566 1.002430 AGAGGCGCAGTGAAAGAATCA 59.998 47.619 10.83 0.00 35.05 2.57
566 567 2.012673 GAGGCGCAGTGAAAGAATCAT 58.987 47.619 10.83 0.00 40.97 2.45
567 568 2.012673 AGGCGCAGTGAAAGAATCATC 58.987 47.619 10.83 0.00 40.97 2.92
568 569 2.012673 GGCGCAGTGAAAGAATCATCT 58.987 47.619 10.83 0.00 40.97 2.90
569 570 3.118629 AGGCGCAGTGAAAGAATCATCTA 60.119 43.478 10.83 0.00 40.97 1.98
570 571 3.001736 GGCGCAGTGAAAGAATCATCTAC 59.998 47.826 10.83 0.00 40.97 2.59
571 572 3.618594 GCGCAGTGAAAGAATCATCTACA 59.381 43.478 0.30 0.00 40.97 2.74
572 573 4.493220 GCGCAGTGAAAGAATCATCTACAC 60.493 45.833 0.30 0.00 40.97 2.90
573 574 4.259570 CGCAGTGAAAGAATCATCTACACG 60.260 45.833 0.00 0.00 42.57 4.49
574 575 4.864806 GCAGTGAAAGAATCATCTACACGA 59.135 41.667 0.00 0.00 42.57 4.35
575 576 5.521735 GCAGTGAAAGAATCATCTACACGAT 59.478 40.000 0.00 0.00 42.57 3.73
576 577 6.697455 GCAGTGAAAGAATCATCTACACGATA 59.303 38.462 0.00 0.00 42.57 2.92
577 578 7.383572 GCAGTGAAAGAATCATCTACACGATAT 59.616 37.037 0.00 0.00 42.57 1.63
578 579 8.697960 CAGTGAAAGAATCATCTACACGATATG 58.302 37.037 0.00 0.00 42.57 1.78
579 580 7.869937 AGTGAAAGAATCATCTACACGATATGG 59.130 37.037 0.00 0.00 42.57 2.74
580 581 7.653713 GTGAAAGAATCATCTACACGATATGGT 59.346 37.037 0.00 0.00 40.97 3.55
581 582 7.867909 TGAAAGAATCATCTACACGATATGGTC 59.132 37.037 0.00 0.00 33.77 4.02
582 583 6.274157 AGAATCATCTACACGATATGGTCC 57.726 41.667 0.00 0.00 32.88 4.46
583 584 5.775195 AGAATCATCTACACGATATGGTCCA 59.225 40.000 0.00 0.00 32.88 4.02
584 585 6.438741 AGAATCATCTACACGATATGGTCCAT 59.561 38.462 9.88 9.88 32.88 3.41
585 586 7.615757 AGAATCATCTACACGATATGGTCCATA 59.384 37.037 14.08 14.08 32.88 2.74
586 587 7.904558 ATCATCTACACGATATGGTCCATAT 57.095 36.000 22.18 22.18 39.43 1.78
587 588 7.100458 TCATCTACACGATATGGTCCATATG 57.900 40.000 26.13 19.47 37.20 1.78
588 589 5.914898 TCTACACGATATGGTCCATATGG 57.085 43.478 26.13 25.38 37.20 2.74
589 590 5.576128 TCTACACGATATGGTCCATATGGA 58.424 41.667 30.26 20.98 43.08 3.41
602 603 5.152623 TCCATATGGAAGGAGCGAAATAG 57.847 43.478 22.52 0.00 42.18 1.73
603 604 4.020218 TCCATATGGAAGGAGCGAAATAGG 60.020 45.833 22.52 0.00 42.18 2.57
604 605 2.262423 ATGGAAGGAGCGAAATAGGC 57.738 50.000 0.00 0.00 0.00 3.93
605 606 0.179084 TGGAAGGAGCGAAATAGGCG 60.179 55.000 0.00 0.00 35.00 5.52
606 607 0.880718 GGAAGGAGCGAAATAGGCGG 60.881 60.000 0.00 0.00 35.00 6.13
607 608 0.880718 GAAGGAGCGAAATAGGCGGG 60.881 60.000 0.00 0.00 35.00 6.13
608 609 1.623542 AAGGAGCGAAATAGGCGGGT 61.624 55.000 0.00 0.00 35.00 5.28
609 610 1.887707 GGAGCGAAATAGGCGGGTG 60.888 63.158 0.00 0.00 35.00 4.61
610 611 1.153429 GAGCGAAATAGGCGGGTGT 60.153 57.895 0.00 0.00 35.00 4.16
611 612 0.743345 GAGCGAAATAGGCGGGTGTT 60.743 55.000 0.00 0.00 35.00 3.32
612 613 0.743345 AGCGAAATAGGCGGGTGTTC 60.743 55.000 0.00 0.00 35.00 3.18
613 614 1.022451 GCGAAATAGGCGGGTGTTCA 61.022 55.000 0.00 0.00 0.00 3.18
614 615 0.725117 CGAAATAGGCGGGTGTTCAC 59.275 55.000 0.00 0.00 0.00 3.18
615 616 0.725117 GAAATAGGCGGGTGTTCACG 59.275 55.000 0.00 0.00 44.09 4.35
616 617 0.675522 AAATAGGCGGGTGTTCACGG 60.676 55.000 0.00 0.00 41.24 4.94
617 618 2.530958 AATAGGCGGGTGTTCACGGG 62.531 60.000 0.00 0.00 41.24 5.28
620 621 4.309950 GCGGGTGTTCACGGGACT 62.310 66.667 0.00 0.00 41.24 3.85
621 622 2.934570 GCGGGTGTTCACGGGACTA 61.935 63.158 0.00 0.00 41.24 2.59
622 623 1.667151 CGGGTGTTCACGGGACTAA 59.333 57.895 0.00 0.00 36.76 2.24
623 624 0.389426 CGGGTGTTCACGGGACTAAG 60.389 60.000 0.00 0.00 36.76 2.18
624 625 0.036671 GGGTGTTCACGGGACTAAGG 60.037 60.000 0.00 0.00 0.00 2.69
625 626 0.683412 GGTGTTCACGGGACTAAGGT 59.317 55.000 0.00 0.00 0.00 3.50
626 627 1.071228 GGTGTTCACGGGACTAAGGTT 59.929 52.381 0.00 0.00 0.00 3.50
627 628 2.140717 GTGTTCACGGGACTAAGGTTG 58.859 52.381 0.00 0.00 0.00 3.77
628 629 2.040939 TGTTCACGGGACTAAGGTTGA 58.959 47.619 0.00 0.00 0.00 3.18
629 630 2.635915 TGTTCACGGGACTAAGGTTGAT 59.364 45.455 0.00 0.00 0.00 2.57
630 631 3.000727 GTTCACGGGACTAAGGTTGATG 58.999 50.000 0.00 0.00 0.00 3.07
631 632 1.066430 TCACGGGACTAAGGTTGATGC 60.066 52.381 0.00 0.00 0.00 3.91
632 633 0.981183 ACGGGACTAAGGTTGATGCA 59.019 50.000 0.00 0.00 0.00 3.96
633 634 1.559682 ACGGGACTAAGGTTGATGCAT 59.440 47.619 0.00 0.00 0.00 3.96
634 635 2.213499 CGGGACTAAGGTTGATGCATC 58.787 52.381 20.14 20.14 0.00 3.91
635 636 2.419990 CGGGACTAAGGTTGATGCATCA 60.420 50.000 25.42 25.42 34.44 3.07
636 637 2.945668 GGGACTAAGGTTGATGCATCAC 59.054 50.000 28.72 21.43 36.36 3.06
637 638 2.609459 GGACTAAGGTTGATGCATCACG 59.391 50.000 28.72 14.43 36.36 4.35
638 639 2.609459 GACTAAGGTTGATGCATCACGG 59.391 50.000 28.72 15.98 36.36 4.94
639 640 1.942657 CTAAGGTTGATGCATCACGGG 59.057 52.381 28.72 11.85 36.36 5.28
640 641 0.680921 AAGGTTGATGCATCACGGGG 60.681 55.000 28.72 0.00 36.36 5.73
641 642 1.378514 GGTTGATGCATCACGGGGT 60.379 57.895 28.72 0.00 36.36 4.95
642 643 1.656818 GGTTGATGCATCACGGGGTG 61.657 60.000 28.72 0.00 36.36 4.61
643 644 1.378382 TTGATGCATCACGGGGTGG 60.378 57.895 28.72 0.00 36.36 4.61
644 645 3.211963 GATGCATCACGGGGTGGC 61.212 66.667 21.92 0.00 33.87 5.01
663 664 3.843304 GCTCTAGCCCTAGACGCA 58.157 61.111 15.54 0.00 37.28 5.24
664 665 2.116383 GCTCTAGCCCTAGACGCAA 58.884 57.895 15.54 0.00 37.28 4.85
665 666 0.676736 GCTCTAGCCCTAGACGCAAT 59.323 55.000 15.54 0.00 37.28 3.56
666 667 1.336424 GCTCTAGCCCTAGACGCAATC 60.336 57.143 15.54 0.00 37.28 2.67
667 668 1.957177 CTCTAGCCCTAGACGCAATCA 59.043 52.381 0.97 0.00 37.28 2.57
668 669 2.362397 CTCTAGCCCTAGACGCAATCAA 59.638 50.000 0.97 0.00 37.28 2.57
669 670 2.965831 TCTAGCCCTAGACGCAATCAAT 59.034 45.455 0.97 0.00 37.28 2.57
670 671 2.246719 AGCCCTAGACGCAATCAATC 57.753 50.000 0.00 0.00 0.00 2.67
671 672 1.486310 AGCCCTAGACGCAATCAATCA 59.514 47.619 0.00 0.00 0.00 2.57
672 673 1.869767 GCCCTAGACGCAATCAATCAG 59.130 52.381 0.00 0.00 0.00 2.90
673 674 1.869767 CCCTAGACGCAATCAATCAGC 59.130 52.381 0.00 0.00 0.00 4.26
678 679 4.275282 GCAATCAATCAGCGCGAC 57.725 55.556 12.10 0.04 0.00 5.19
679 680 1.297893 GCAATCAATCAGCGCGACC 60.298 57.895 12.10 0.00 0.00 4.79
680 681 1.709147 GCAATCAATCAGCGCGACCT 61.709 55.000 12.10 0.00 0.00 3.85
681 682 0.027194 CAATCAATCAGCGCGACCTG 59.973 55.000 12.10 9.17 0.00 4.00
682 683 1.091771 AATCAATCAGCGCGACCTGG 61.092 55.000 12.10 0.00 33.64 4.45
683 684 3.869272 CAATCAGCGCGACCTGGC 61.869 66.667 12.10 0.00 33.64 4.85
691 692 4.389576 GCGACCTGGCGTTTGCTG 62.390 66.667 11.14 0.00 42.25 4.41
692 693 3.726517 CGACCTGGCGTTTGCTGG 61.727 66.667 0.00 0.00 42.25 4.85
693 694 4.043200 GACCTGGCGTTTGCTGGC 62.043 66.667 0.00 0.00 42.25 4.85
694 695 4.892965 ACCTGGCGTTTGCTGGCA 62.893 61.111 0.00 0.00 42.25 4.92
699 700 4.712425 GCGTTTGCTGGCAGCCTG 62.712 66.667 34.58 21.94 41.51 4.85
700 701 4.712425 CGTTTGCTGGCAGCCTGC 62.712 66.667 34.58 31.29 46.46 4.85
722 723 3.944871 CCGCAGGCATTGGTTAATC 57.055 52.632 0.00 0.00 46.14 1.75
723 724 1.392589 CCGCAGGCATTGGTTAATCT 58.607 50.000 0.00 0.00 46.14 2.40
724 725 2.571212 CCGCAGGCATTGGTTAATCTA 58.429 47.619 0.00 0.00 46.14 1.98
725 726 2.549754 CCGCAGGCATTGGTTAATCTAG 59.450 50.000 0.00 0.00 46.14 2.43
726 727 3.206150 CGCAGGCATTGGTTAATCTAGT 58.794 45.455 0.00 0.00 0.00 2.57
727 728 3.627577 CGCAGGCATTGGTTAATCTAGTT 59.372 43.478 0.00 0.00 0.00 2.24
728 729 4.260784 CGCAGGCATTGGTTAATCTAGTTC 60.261 45.833 0.00 0.00 0.00 3.01
729 730 4.884164 GCAGGCATTGGTTAATCTAGTTCT 59.116 41.667 0.00 0.00 0.00 3.01
730 731 6.055588 GCAGGCATTGGTTAATCTAGTTCTA 58.944 40.000 0.00 0.00 0.00 2.10
731 732 6.203723 GCAGGCATTGGTTAATCTAGTTCTAG 59.796 42.308 0.83 0.83 0.00 2.43
732 733 6.708054 CAGGCATTGGTTAATCTAGTTCTAGG 59.292 42.308 6.96 0.00 0.00 3.02
733 734 6.387220 AGGCATTGGTTAATCTAGTTCTAGGT 59.613 38.462 6.96 0.00 0.00 3.08
734 735 7.054751 GGCATTGGTTAATCTAGTTCTAGGTT 58.945 38.462 9.78 9.78 0.00 3.50
735 736 7.012421 GGCATTGGTTAATCTAGTTCTAGGTTG 59.988 40.741 13.61 0.21 0.00 3.77
736 737 7.553044 GCATTGGTTAATCTAGTTCTAGGTTGT 59.447 37.037 13.61 0.00 0.00 3.32
737 738 9.449719 CATTGGTTAATCTAGTTCTAGGTTGTT 57.550 33.333 13.61 5.00 0.00 2.83
739 740 9.856162 TTGGTTAATCTAGTTCTAGGTTGTTTT 57.144 29.630 13.61 0.00 0.00 2.43
740 741 9.856162 TGGTTAATCTAGTTCTAGGTTGTTTTT 57.144 29.630 13.61 0.00 0.00 1.94
767 768 2.712057 GTTTCTACGACGTTCCCTGA 57.288 50.000 5.50 0.00 0.00 3.86
768 769 3.017265 GTTTCTACGACGTTCCCTGAA 57.983 47.619 5.50 1.21 0.00 3.02
769 770 3.383761 GTTTCTACGACGTTCCCTGAAA 58.616 45.455 5.50 7.17 0.00 2.69
770 771 3.731652 TTCTACGACGTTCCCTGAAAA 57.268 42.857 5.50 0.00 0.00 2.29
771 772 3.017265 TCTACGACGTTCCCTGAAAAC 57.983 47.619 5.50 0.00 0.00 2.43
776 777 2.612200 CGTTCCCTGAAAACGCTCA 58.388 52.632 0.00 0.00 42.40 4.26
777 778 0.234884 CGTTCCCTGAAAACGCTCAC 59.765 55.000 0.00 0.00 42.40 3.51
778 779 0.591659 GTTCCCTGAAAACGCTCACC 59.408 55.000 0.00 0.00 0.00 4.02
779 780 0.536460 TTCCCTGAAAACGCTCACCC 60.536 55.000 0.00 0.00 0.00 4.61
780 781 1.971695 CCCTGAAAACGCTCACCCC 60.972 63.158 0.00 0.00 0.00 4.95
781 782 1.073199 CCTGAAAACGCTCACCCCT 59.927 57.895 0.00 0.00 0.00 4.79
782 783 0.955919 CCTGAAAACGCTCACCCCTC 60.956 60.000 0.00 0.00 0.00 4.30
783 784 0.035458 CTGAAAACGCTCACCCCTCT 59.965 55.000 0.00 0.00 0.00 3.69
784 785 0.250295 TGAAAACGCTCACCCCTCTG 60.250 55.000 0.00 0.00 0.00 3.35
785 786 0.250338 GAAAACGCTCACCCCTCTGT 60.250 55.000 0.00 0.00 0.00 3.41
786 787 1.001633 GAAAACGCTCACCCCTCTGTA 59.998 52.381 0.00 0.00 0.00 2.74
787 788 1.276622 AAACGCTCACCCCTCTGTAT 58.723 50.000 0.00 0.00 0.00 2.29
788 789 2.154567 AACGCTCACCCCTCTGTATA 57.845 50.000 0.00 0.00 0.00 1.47
789 790 2.383442 ACGCTCACCCCTCTGTATAT 57.617 50.000 0.00 0.00 0.00 0.86
790 791 2.679082 ACGCTCACCCCTCTGTATATT 58.321 47.619 0.00 0.00 0.00 1.28
791 792 2.365617 ACGCTCACCCCTCTGTATATTG 59.634 50.000 0.00 0.00 0.00 1.90
792 793 2.365617 CGCTCACCCCTCTGTATATTGT 59.634 50.000 0.00 0.00 0.00 2.71
793 794 3.733337 GCTCACCCCTCTGTATATTGTG 58.267 50.000 0.00 0.00 0.00 3.33
794 795 3.134804 GCTCACCCCTCTGTATATTGTGT 59.865 47.826 0.00 0.00 0.00 3.72
795 796 4.740934 GCTCACCCCTCTGTATATTGTGTC 60.741 50.000 0.00 0.00 0.00 3.67
796 797 3.709653 TCACCCCTCTGTATATTGTGTCC 59.290 47.826 0.00 0.00 0.00 4.02
797 798 3.711704 CACCCCTCTGTATATTGTGTCCT 59.288 47.826 0.00 0.00 0.00 3.85
798 799 4.164221 CACCCCTCTGTATATTGTGTCCTT 59.836 45.833 0.00 0.00 0.00 3.36
799 800 4.788617 ACCCCTCTGTATATTGTGTCCTTT 59.211 41.667 0.00 0.00 0.00 3.11
800 801 5.104485 ACCCCTCTGTATATTGTGTCCTTTC 60.104 44.000 0.00 0.00 0.00 2.62
801 802 5.050490 CCCTCTGTATATTGTGTCCTTTCG 58.950 45.833 0.00 0.00 0.00 3.46
802 803 4.508124 CCTCTGTATATTGTGTCCTTTCGC 59.492 45.833 0.00 0.00 0.00 4.70
803 804 4.439057 TCTGTATATTGTGTCCTTTCGCC 58.561 43.478 0.00 0.00 0.00 5.54
804 805 4.081365 TCTGTATATTGTGTCCTTTCGCCA 60.081 41.667 0.00 0.00 0.00 5.69
805 806 4.776349 TGTATATTGTGTCCTTTCGCCAT 58.224 39.130 0.00 0.00 0.00 4.40
806 807 4.814234 TGTATATTGTGTCCTTTCGCCATC 59.186 41.667 0.00 0.00 0.00 3.51
807 808 2.496899 ATTGTGTCCTTTCGCCATCT 57.503 45.000 0.00 0.00 0.00 2.90
808 809 2.270352 TTGTGTCCTTTCGCCATCTT 57.730 45.000 0.00 0.00 0.00 2.40
809 810 2.270352 TGTGTCCTTTCGCCATCTTT 57.730 45.000 0.00 0.00 0.00 2.52
810 811 2.582052 TGTGTCCTTTCGCCATCTTTT 58.418 42.857 0.00 0.00 0.00 2.27
811 812 2.552315 TGTGTCCTTTCGCCATCTTTTC 59.448 45.455 0.00 0.00 0.00 2.29
812 813 2.814336 GTGTCCTTTCGCCATCTTTTCT 59.186 45.455 0.00 0.00 0.00 2.52
813 814 4.000988 GTGTCCTTTCGCCATCTTTTCTA 58.999 43.478 0.00 0.00 0.00 2.10
814 815 4.636206 GTGTCCTTTCGCCATCTTTTCTAT 59.364 41.667 0.00 0.00 0.00 1.98
815 816 5.815740 GTGTCCTTTCGCCATCTTTTCTATA 59.184 40.000 0.00 0.00 0.00 1.31
816 817 6.315393 GTGTCCTTTCGCCATCTTTTCTATAA 59.685 38.462 0.00 0.00 0.00 0.98
817 818 6.538742 TGTCCTTTCGCCATCTTTTCTATAAG 59.461 38.462 0.00 0.00 0.00 1.73
818 819 6.761714 GTCCTTTCGCCATCTTTTCTATAAGA 59.238 38.462 0.00 0.00 38.43 2.10
819 820 7.280205 GTCCTTTCGCCATCTTTTCTATAAGAA 59.720 37.037 0.00 0.00 37.66 2.52
820 821 7.827236 TCCTTTCGCCATCTTTTCTATAAGAAA 59.173 33.333 0.00 0.00 42.00 2.52
832 833 6.743575 TTCTATAAGAAAAAGGCAGTGCTC 57.256 37.500 16.11 3.97 29.99 4.26
833 834 5.186198 TCTATAAGAAAAAGGCAGTGCTCC 58.814 41.667 16.11 0.00 0.00 4.70
834 835 1.332195 AAGAAAAAGGCAGTGCTCCC 58.668 50.000 16.11 0.00 0.00 4.30
835 836 0.890996 AGAAAAAGGCAGTGCTCCCG 60.891 55.000 16.11 0.00 0.00 5.14
836 837 2.477972 GAAAAAGGCAGTGCTCCCGC 62.478 60.000 16.11 0.00 0.00 6.13
847 848 2.281900 CTCCCGCCGGTTCCAAAA 60.282 61.111 1.90 0.00 0.00 2.44
954 1193 6.485648 ACCCGGAGTACTAAAATCATAATTGC 59.514 38.462 0.73 0.00 0.00 3.56
1019 1258 1.680651 CACTCCCCTCACTCGCTCT 60.681 63.158 0.00 0.00 0.00 4.09
1020 1259 1.379309 ACTCCCCTCACTCGCTCTC 60.379 63.158 0.00 0.00 0.00 3.20
1063 1302 1.599071 CGCACACAAAGCTCTCAAGAA 59.401 47.619 0.00 0.00 0.00 2.52
1121 1386 2.358737 GTGTCCAAGAGCCCACCG 60.359 66.667 0.00 0.00 0.00 4.94
1409 1709 1.419381 GACCTTCTGGATCTCCCTCC 58.581 60.000 0.00 0.00 37.04 4.30
1422 1722 4.263572 CCTCCCCGTGGTGCACAA 62.264 66.667 20.43 3.78 33.40 3.33
1424 1724 2.282110 TCCCCGTGGTGCACAATG 60.282 61.111 20.43 13.40 33.40 2.82
1523 1823 4.344679 TGATGTGTCCCATGCTTTTCTTTT 59.655 37.500 0.00 0.00 32.56 2.27
1530 1830 8.034804 GTGTCCCATGCTTTTCTTTTTATGTAT 58.965 33.333 0.00 0.00 0.00 2.29
1532 1839 8.872845 GTCCCATGCTTTTCTTTTTATGTATTG 58.127 33.333 0.00 0.00 0.00 1.90
1533 1840 8.811017 TCCCATGCTTTTCTTTTTATGTATTGA 58.189 29.630 0.00 0.00 0.00 2.57
1591 1900 8.508883 AGTAGGAGTACTAATTCAGTGTGTAG 57.491 38.462 0.00 0.00 37.76 2.74
1608 1917 6.312918 AGTGTGTAGGTCACTTAATTATTGCG 59.687 38.462 0.00 0.00 46.27 4.85
1629 1938 2.099098 GTGGATGCAAAGGAATAACCGG 59.901 50.000 0.00 0.00 44.74 5.28
1676 1992 9.661563 TTTACCTAATAACAATGTCAGGTGTAG 57.338 33.333 14.98 1.42 37.02 2.74
1708 2024 7.554118 AGAATAAAAATCAGCTCATTTCTCGGA 59.446 33.333 0.00 0.00 0.00 4.55
1889 2214 1.065709 GTTACTTCATTCGGGCCCAGA 60.066 52.381 24.92 17.49 0.00 3.86
1893 2218 0.107214 TTCATTCGGGCCCAGACATC 60.107 55.000 24.92 0.00 0.00 3.06
2031 2369 7.326063 GTGCAACTTACCAAACATTAAGATGAC 59.674 37.037 0.00 0.00 36.73 3.06
2055 2393 2.911819 ACAAATACATTTCGCACCCG 57.088 45.000 0.00 0.00 0.00 5.28
2068 2406 4.569180 ACCCGCTGCACTTGTGCT 62.569 61.111 23.53 2.57 35.49 4.40
2088 2426 3.727970 GCTTGAGCGCTAATTGTTGTACC 60.728 47.826 11.50 0.00 0.00 3.34
2112 2450 5.575957 GTTGCACAAGATGATTACAGATGG 58.424 41.667 0.00 0.00 0.00 3.51
2151 2489 7.168135 GCAAGTTGAACAGAAACAAAAGGATAG 59.832 37.037 7.16 0.00 0.00 2.08
2157 2495 7.231317 TGAACAGAAACAAAAGGATAGAGCATT 59.769 33.333 0.00 0.00 0.00 3.56
2171 2509 6.648725 GGATAGAGCATTAACCTCAGATTGTC 59.351 42.308 7.49 0.00 0.00 3.18
2200 2538 5.011840 TGCAGATCAGCTAAGCAGATAATCT 59.988 40.000 11.68 0.00 35.03 2.40
2297 2641 5.064962 CACATGTGCCAACAACTTCATTTTT 59.935 36.000 13.94 0.00 40.46 1.94
2345 2689 3.758554 GGCCTTCTGAGCTCTAGAGATAG 59.241 52.174 24.24 16.09 0.00 2.08
2359 2703 7.225145 GCTCTAGAGATAGTACGAGAAAGAACA 59.775 40.741 24.24 0.00 0.00 3.18
2459 2803 1.293924 CCGAAGGCATCACATCAGAC 58.706 55.000 0.00 0.00 46.14 3.51
2542 2886 2.358737 CTGGAACCGCCTCACCAC 60.359 66.667 0.00 0.00 37.63 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.432514 GCGCAAGTTGTGAGATGAGA 58.567 50.000 20.42 0.00 41.68 3.27
322 323 1.374252 GCGACAGGGTTGATGACGT 60.374 57.895 0.00 0.00 37.96 4.34
351 352 1.466856 TGGGCGTACTGATCGTTAGT 58.533 50.000 0.00 0.00 0.00 2.24
367 368 5.061853 CAGACATGAATAGAGGATGTTGGG 58.938 45.833 0.00 0.00 30.39 4.12
540 541 1.785041 TTTCACTGCGCCTCTTGCAC 61.785 55.000 4.18 0.00 41.33 4.57
543 544 1.229428 TTCTTTCACTGCGCCTCTTG 58.771 50.000 4.18 0.00 0.00 3.02
545 546 1.002430 TGATTCTTTCACTGCGCCTCT 59.998 47.619 4.18 0.00 0.00 3.69
546 547 1.442769 TGATTCTTTCACTGCGCCTC 58.557 50.000 4.18 0.00 0.00 4.70
547 548 2.012673 GATGATTCTTTCACTGCGCCT 58.987 47.619 4.18 0.00 37.11 5.52
548 549 2.012673 AGATGATTCTTTCACTGCGCC 58.987 47.619 4.18 0.00 37.11 6.53
549 550 3.618594 TGTAGATGATTCTTTCACTGCGC 59.381 43.478 0.00 0.00 37.11 6.09
550 551 4.259570 CGTGTAGATGATTCTTTCACTGCG 60.260 45.833 0.00 0.00 37.11 5.18
551 552 4.864806 TCGTGTAGATGATTCTTTCACTGC 59.135 41.667 0.00 0.00 37.11 4.40
552 553 8.697960 CATATCGTGTAGATGATTCTTTCACTG 58.302 37.037 0.00 0.00 40.40 3.66
553 554 7.869937 CCATATCGTGTAGATGATTCTTTCACT 59.130 37.037 0.00 0.00 40.40 3.41
554 555 7.653713 ACCATATCGTGTAGATGATTCTTTCAC 59.346 37.037 0.00 0.00 40.40 3.18
555 556 7.726216 ACCATATCGTGTAGATGATTCTTTCA 58.274 34.615 0.00 0.00 40.40 2.69
556 557 7.329717 GGACCATATCGTGTAGATGATTCTTTC 59.670 40.741 0.00 0.00 40.40 2.62
557 558 7.155328 GGACCATATCGTGTAGATGATTCTTT 58.845 38.462 0.00 0.00 40.40 2.52
558 559 6.267699 TGGACCATATCGTGTAGATGATTCTT 59.732 38.462 0.00 0.00 40.40 2.52
559 560 5.775195 TGGACCATATCGTGTAGATGATTCT 59.225 40.000 0.00 0.00 40.40 2.40
560 561 6.025749 TGGACCATATCGTGTAGATGATTC 57.974 41.667 0.00 0.00 40.40 2.52
561 562 6.611613 ATGGACCATATCGTGTAGATGATT 57.388 37.500 4.75 0.00 40.40 2.57
562 563 7.201947 CCATATGGACCATATCGTGTAGATGAT 60.202 40.741 22.00 0.00 35.18 2.45
563 564 6.096846 CCATATGGACCATATCGTGTAGATGA 59.903 42.308 22.00 0.00 35.18 2.92
564 565 6.096846 TCCATATGGACCATATCGTGTAGATG 59.903 42.308 22.00 11.51 39.78 2.90
565 566 6.194967 TCCATATGGACCATATCGTGTAGAT 58.805 40.000 22.00 0.00 39.78 1.98
566 567 5.576128 TCCATATGGACCATATCGTGTAGA 58.424 41.667 22.00 10.55 39.78 2.59
567 568 5.914898 TCCATATGGACCATATCGTGTAG 57.085 43.478 22.00 11.11 39.78 2.74
568 569 5.186992 CCTTCCATATGGACCATATCGTGTA 59.813 44.000 24.47 4.12 45.39 2.90
569 570 4.020218 CCTTCCATATGGACCATATCGTGT 60.020 45.833 24.47 1.50 45.39 4.49
570 571 4.222810 TCCTTCCATATGGACCATATCGTG 59.777 45.833 24.47 13.83 45.39 4.35
571 572 4.425772 TCCTTCCATATGGACCATATCGT 58.574 43.478 24.47 2.24 45.39 3.73
572 573 4.681781 GCTCCTTCCATATGGACCATATCG 60.682 50.000 24.47 16.72 45.39 2.92
573 574 4.681781 CGCTCCTTCCATATGGACCATATC 60.682 50.000 24.47 10.73 45.39 1.63
574 575 3.198635 CGCTCCTTCCATATGGACCATAT 59.801 47.826 24.47 19.61 45.39 1.78
575 576 2.567169 CGCTCCTTCCATATGGACCATA 59.433 50.000 24.47 16.59 45.39 2.74
576 577 1.349026 CGCTCCTTCCATATGGACCAT 59.651 52.381 24.47 12.67 45.39 3.55
577 578 0.758734 CGCTCCTTCCATATGGACCA 59.241 55.000 24.47 9.95 45.39 4.02
578 579 1.048601 TCGCTCCTTCCATATGGACC 58.951 55.000 24.47 9.25 45.39 4.46
579 580 2.910688 TTCGCTCCTTCCATATGGAC 57.089 50.000 24.47 11.30 45.39 4.02
580 581 4.020218 CCTATTTCGCTCCTTCCATATGGA 60.020 45.833 20.98 20.98 43.73 3.41
581 582 4.256920 CCTATTTCGCTCCTTCCATATGG 58.743 47.826 16.25 16.25 0.00 2.74
582 583 3.686726 GCCTATTTCGCTCCTTCCATATG 59.313 47.826 0.00 0.00 0.00 1.78
583 584 3.617531 CGCCTATTTCGCTCCTTCCATAT 60.618 47.826 0.00 0.00 0.00 1.78
584 585 2.288825 CGCCTATTTCGCTCCTTCCATA 60.289 50.000 0.00 0.00 0.00 2.74
585 586 1.541233 CGCCTATTTCGCTCCTTCCAT 60.541 52.381 0.00 0.00 0.00 3.41
586 587 0.179084 CGCCTATTTCGCTCCTTCCA 60.179 55.000 0.00 0.00 0.00 3.53
587 588 0.880718 CCGCCTATTTCGCTCCTTCC 60.881 60.000 0.00 0.00 0.00 3.46
588 589 0.880718 CCCGCCTATTTCGCTCCTTC 60.881 60.000 0.00 0.00 0.00 3.46
589 590 1.146263 CCCGCCTATTTCGCTCCTT 59.854 57.895 0.00 0.00 0.00 3.36
590 591 2.064581 ACCCGCCTATTTCGCTCCT 61.065 57.895 0.00 0.00 0.00 3.69
591 592 1.887707 CACCCGCCTATTTCGCTCC 60.888 63.158 0.00 0.00 0.00 4.70
592 593 0.743345 AACACCCGCCTATTTCGCTC 60.743 55.000 0.00 0.00 0.00 5.03
593 594 0.743345 GAACACCCGCCTATTTCGCT 60.743 55.000 0.00 0.00 0.00 4.93
594 595 1.022451 TGAACACCCGCCTATTTCGC 61.022 55.000 0.00 0.00 0.00 4.70
595 596 0.725117 GTGAACACCCGCCTATTTCG 59.275 55.000 0.00 0.00 0.00 3.46
596 597 0.725117 CGTGAACACCCGCCTATTTC 59.275 55.000 0.00 0.00 0.00 2.17
597 598 0.675522 CCGTGAACACCCGCCTATTT 60.676 55.000 0.00 0.00 0.00 1.40
598 599 1.078708 CCGTGAACACCCGCCTATT 60.079 57.895 0.00 0.00 0.00 1.73
599 600 2.582436 CCGTGAACACCCGCCTAT 59.418 61.111 0.00 0.00 0.00 2.57
600 601 3.697747 CCCGTGAACACCCGCCTA 61.698 66.667 0.00 0.00 0.00 3.93
603 604 2.438951 TTAGTCCCGTGAACACCCGC 62.439 60.000 0.00 0.00 0.00 6.13
604 605 0.389426 CTTAGTCCCGTGAACACCCG 60.389 60.000 0.00 0.00 0.00 5.28
605 606 0.036671 CCTTAGTCCCGTGAACACCC 60.037 60.000 0.00 0.00 0.00 4.61
606 607 0.683412 ACCTTAGTCCCGTGAACACC 59.317 55.000 0.00 0.00 0.00 4.16
607 608 2.140717 CAACCTTAGTCCCGTGAACAC 58.859 52.381 0.00 0.00 0.00 3.32
608 609 2.040939 TCAACCTTAGTCCCGTGAACA 58.959 47.619 0.00 0.00 0.00 3.18
609 610 2.825861 TCAACCTTAGTCCCGTGAAC 57.174 50.000 0.00 0.00 0.00 3.18
610 611 2.614481 GCATCAACCTTAGTCCCGTGAA 60.614 50.000 0.00 0.00 0.00 3.18
611 612 1.066430 GCATCAACCTTAGTCCCGTGA 60.066 52.381 0.00 0.00 0.00 4.35
612 613 1.338674 TGCATCAACCTTAGTCCCGTG 60.339 52.381 0.00 0.00 0.00 4.94
613 614 0.981183 TGCATCAACCTTAGTCCCGT 59.019 50.000 0.00 0.00 0.00 5.28
614 615 2.213499 GATGCATCAACCTTAGTCCCG 58.787 52.381 21.92 0.00 0.00 5.14
615 616 2.945668 GTGATGCATCAACCTTAGTCCC 59.054 50.000 30.24 10.61 38.75 4.46
616 617 2.609459 CGTGATGCATCAACCTTAGTCC 59.391 50.000 30.24 13.67 38.75 3.85
617 618 2.609459 CCGTGATGCATCAACCTTAGTC 59.391 50.000 30.24 14.36 38.75 2.59
618 619 2.632377 CCGTGATGCATCAACCTTAGT 58.368 47.619 30.24 0.00 38.75 2.24
619 620 1.942657 CCCGTGATGCATCAACCTTAG 59.057 52.381 30.24 16.21 38.75 2.18
620 621 1.408127 CCCCGTGATGCATCAACCTTA 60.408 52.381 30.24 4.36 38.75 2.69
621 622 0.680921 CCCCGTGATGCATCAACCTT 60.681 55.000 30.24 0.00 38.75 3.50
622 623 1.077501 CCCCGTGATGCATCAACCT 60.078 57.895 30.24 0.00 38.75 3.50
623 624 1.378514 ACCCCGTGATGCATCAACC 60.379 57.895 30.24 17.91 38.75 3.77
624 625 1.656818 CCACCCCGTGATGCATCAAC 61.657 60.000 30.24 21.46 38.75 3.18
625 626 1.378382 CCACCCCGTGATGCATCAA 60.378 57.895 30.24 12.46 38.75 2.57
626 627 2.271821 CCACCCCGTGATGCATCA 59.728 61.111 25.42 25.42 35.23 3.07
627 628 3.211963 GCCACCCCGTGATGCATC 61.212 66.667 20.14 20.14 35.23 3.91
646 647 0.676736 ATTGCGTCTAGGGCTAGAGC 59.323 55.000 0.00 0.00 42.31 4.09
647 648 1.957177 TGATTGCGTCTAGGGCTAGAG 59.043 52.381 0.00 0.00 42.31 2.43
648 649 2.067365 TGATTGCGTCTAGGGCTAGA 57.933 50.000 0.00 0.00 39.67 2.43
649 650 2.890808 TTGATTGCGTCTAGGGCTAG 57.109 50.000 7.95 0.00 34.56 3.42
650 651 2.698274 TGATTGATTGCGTCTAGGGCTA 59.302 45.455 7.95 1.68 0.00 3.93
651 652 1.486310 TGATTGATTGCGTCTAGGGCT 59.514 47.619 7.95 0.00 0.00 5.19
652 653 1.869767 CTGATTGATTGCGTCTAGGGC 59.130 52.381 0.00 0.00 0.00 5.19
653 654 1.869767 GCTGATTGATTGCGTCTAGGG 59.130 52.381 0.00 0.00 0.00 3.53
654 655 1.524355 CGCTGATTGATTGCGTCTAGG 59.476 52.381 0.00 0.00 44.00 3.02
655 656 2.918656 CGCTGATTGATTGCGTCTAG 57.081 50.000 0.00 0.00 44.00 2.43
661 662 1.297893 GGTCGCGCTGATTGATTGC 60.298 57.895 5.56 0.00 0.00 3.56
662 663 0.027194 CAGGTCGCGCTGATTGATTG 59.973 55.000 5.56 0.00 0.00 2.67
663 664 1.091771 CCAGGTCGCGCTGATTGATT 61.092 55.000 14.33 0.00 0.00 2.57
664 665 1.522355 CCAGGTCGCGCTGATTGAT 60.522 57.895 14.33 0.00 0.00 2.57
665 666 2.125552 CCAGGTCGCGCTGATTGA 60.126 61.111 14.33 0.00 0.00 2.57
666 667 3.869272 GCCAGGTCGCGCTGATTG 61.869 66.667 14.33 7.61 0.00 2.67
674 675 4.389576 CAGCAAACGCCAGGTCGC 62.390 66.667 3.49 0.00 0.00 5.19
675 676 3.726517 CCAGCAAACGCCAGGTCG 61.727 66.667 2.15 2.15 0.00 4.79
676 677 4.043200 GCCAGCAAACGCCAGGTC 62.043 66.667 0.00 0.00 0.00 3.85
677 678 4.892965 TGCCAGCAAACGCCAGGT 62.893 61.111 0.00 0.00 0.00 4.00
678 679 4.047059 CTGCCAGCAAACGCCAGG 62.047 66.667 0.00 0.00 0.00 4.45
679 680 4.712425 GCTGCCAGCAAACGCCAG 62.712 66.667 12.82 0.00 41.89 4.85
682 683 4.712425 CAGGCTGCCAGCAAACGC 62.712 66.667 22.65 0.00 44.75 4.84
683 684 4.712425 GCAGGCTGCCAGCAAACG 62.712 66.667 28.87 4.30 44.75 3.60
700 701 1.247419 TAACCAATGCCTGCGGTTGG 61.247 55.000 18.76 18.76 46.08 3.77
701 702 0.600557 TTAACCAATGCCTGCGGTTG 59.399 50.000 9.35 5.46 42.88 3.77
702 703 1.476488 GATTAACCAATGCCTGCGGTT 59.524 47.619 0.00 0.00 44.98 4.44
703 704 1.102978 GATTAACCAATGCCTGCGGT 58.897 50.000 0.00 0.00 33.32 5.68
704 705 1.392589 AGATTAACCAATGCCTGCGG 58.607 50.000 0.00 0.00 0.00 5.69
705 706 3.206150 ACTAGATTAACCAATGCCTGCG 58.794 45.455 0.00 0.00 0.00 5.18
706 707 4.884164 AGAACTAGATTAACCAATGCCTGC 59.116 41.667 0.00 0.00 0.00 4.85
707 708 6.708054 CCTAGAACTAGATTAACCAATGCCTG 59.292 42.308 10.04 0.00 35.21 4.85
708 709 6.387220 ACCTAGAACTAGATTAACCAATGCCT 59.613 38.462 10.04 0.00 35.21 4.75
709 710 6.592870 ACCTAGAACTAGATTAACCAATGCC 58.407 40.000 10.04 0.00 35.21 4.40
710 711 7.553044 ACAACCTAGAACTAGATTAACCAATGC 59.447 37.037 10.04 0.00 35.21 3.56
711 712 9.449719 AACAACCTAGAACTAGATTAACCAATG 57.550 33.333 10.04 0.00 35.21 2.82
713 714 9.856162 AAAACAACCTAGAACTAGATTAACCAA 57.144 29.630 10.04 0.00 35.21 3.67
714 715 9.856162 AAAAACAACCTAGAACTAGATTAACCA 57.144 29.630 10.04 0.00 35.21 3.67
748 749 2.712057 TCAGGGAACGTCGTAGAAAC 57.288 50.000 0.00 0.00 39.69 2.78
749 750 3.731652 TTTCAGGGAACGTCGTAGAAA 57.268 42.857 0.00 2.43 39.69 2.52
750 751 3.383761 GTTTTCAGGGAACGTCGTAGAA 58.616 45.455 0.00 0.00 39.69 2.10
751 752 2.605338 CGTTTTCAGGGAACGTCGTAGA 60.605 50.000 0.00 0.00 43.44 2.59
752 753 1.717645 CGTTTTCAGGGAACGTCGTAG 59.282 52.381 0.00 0.00 43.44 3.51
753 754 1.769733 CGTTTTCAGGGAACGTCGTA 58.230 50.000 0.00 0.00 43.44 3.43
754 755 2.596875 CGTTTTCAGGGAACGTCGT 58.403 52.632 0.00 0.00 43.44 4.34
759 760 0.591659 GGTGAGCGTTTTCAGGGAAC 59.408 55.000 0.00 0.00 0.00 3.62
760 761 0.536460 GGGTGAGCGTTTTCAGGGAA 60.536 55.000 0.00 0.00 0.00 3.97
761 762 1.072505 GGGTGAGCGTTTTCAGGGA 59.927 57.895 0.00 0.00 0.00 4.20
762 763 1.971695 GGGGTGAGCGTTTTCAGGG 60.972 63.158 0.00 0.00 0.00 4.45
763 764 0.955919 GAGGGGTGAGCGTTTTCAGG 60.956 60.000 0.00 0.00 0.00 3.86
764 765 0.035458 AGAGGGGTGAGCGTTTTCAG 59.965 55.000 0.00 0.00 0.00 3.02
765 766 0.250295 CAGAGGGGTGAGCGTTTTCA 60.250 55.000 0.00 0.00 0.00 2.69
766 767 0.250338 ACAGAGGGGTGAGCGTTTTC 60.250 55.000 0.00 0.00 0.00 2.29
767 768 1.053424 TACAGAGGGGTGAGCGTTTT 58.947 50.000 0.00 0.00 0.00 2.43
768 769 1.276622 ATACAGAGGGGTGAGCGTTT 58.723 50.000 0.00 0.00 0.00 3.60
769 770 2.154567 TATACAGAGGGGTGAGCGTT 57.845 50.000 0.00 0.00 0.00 4.84
770 771 2.365617 CAATATACAGAGGGGTGAGCGT 59.634 50.000 0.00 0.00 0.00 5.07
771 772 2.365617 ACAATATACAGAGGGGTGAGCG 59.634 50.000 0.00 0.00 0.00 5.03
772 773 3.134804 ACACAATATACAGAGGGGTGAGC 59.865 47.826 0.00 0.00 0.00 4.26
773 774 4.202264 GGACACAATATACAGAGGGGTGAG 60.202 50.000 0.00 0.00 0.00 3.51
774 775 3.709653 GGACACAATATACAGAGGGGTGA 59.290 47.826 0.00 0.00 0.00 4.02
775 776 3.711704 AGGACACAATATACAGAGGGGTG 59.288 47.826 0.00 0.00 0.00 4.61
776 777 4.008916 AGGACACAATATACAGAGGGGT 57.991 45.455 0.00 0.00 0.00 4.95
777 778 5.368989 GAAAGGACACAATATACAGAGGGG 58.631 45.833 0.00 0.00 0.00 4.79
778 779 5.050490 CGAAAGGACACAATATACAGAGGG 58.950 45.833 0.00 0.00 0.00 4.30
779 780 4.508124 GCGAAAGGACACAATATACAGAGG 59.492 45.833 0.00 0.00 0.00 3.69
780 781 4.508124 GGCGAAAGGACACAATATACAGAG 59.492 45.833 0.00 0.00 0.00 3.35
781 782 4.081365 TGGCGAAAGGACACAATATACAGA 60.081 41.667 0.00 0.00 0.00 3.41
782 783 4.188462 TGGCGAAAGGACACAATATACAG 58.812 43.478 0.00 0.00 0.00 2.74
783 784 4.209307 TGGCGAAAGGACACAATATACA 57.791 40.909 0.00 0.00 0.00 2.29
784 785 5.057149 AGATGGCGAAAGGACACAATATAC 58.943 41.667 0.00 0.00 35.56 1.47
785 786 5.290493 AGATGGCGAAAGGACACAATATA 57.710 39.130 0.00 0.00 35.56 0.86
786 787 4.156455 AGATGGCGAAAGGACACAATAT 57.844 40.909 0.00 0.00 35.56 1.28
787 788 3.627395 AGATGGCGAAAGGACACAATA 57.373 42.857 0.00 0.00 35.56 1.90
788 789 2.496899 AGATGGCGAAAGGACACAAT 57.503 45.000 0.00 0.00 35.56 2.71
789 790 2.270352 AAGATGGCGAAAGGACACAA 57.730 45.000 0.00 0.00 35.56 3.33
790 791 2.270352 AAAGATGGCGAAAGGACACA 57.730 45.000 0.00 0.00 35.56 3.72
791 792 2.814336 AGAAAAGATGGCGAAAGGACAC 59.186 45.455 0.00 0.00 35.56 3.67
792 793 3.140325 AGAAAAGATGGCGAAAGGACA 57.860 42.857 0.00 0.00 38.71 4.02
793 794 6.761714 TCTTATAGAAAAGATGGCGAAAGGAC 59.238 38.462 0.00 0.00 30.54 3.85
794 795 6.884832 TCTTATAGAAAAGATGGCGAAAGGA 58.115 36.000 0.00 0.00 30.54 3.36
795 796 7.553881 TTCTTATAGAAAAGATGGCGAAAGG 57.446 36.000 0.00 0.00 35.48 3.11
808 809 6.151144 GGAGCACTGCCTTTTTCTTATAGAAA 59.849 38.462 0.00 0.00 42.00 2.52
809 810 5.648092 GGAGCACTGCCTTTTTCTTATAGAA 59.352 40.000 0.00 0.00 31.28 2.10
810 811 5.186198 GGAGCACTGCCTTTTTCTTATAGA 58.814 41.667 0.00 0.00 0.00 1.98
811 812 4.336713 GGGAGCACTGCCTTTTTCTTATAG 59.663 45.833 0.20 0.00 38.15 1.31
812 813 4.270008 GGGAGCACTGCCTTTTTCTTATA 58.730 43.478 0.20 0.00 38.15 0.98
813 814 3.092301 GGGAGCACTGCCTTTTTCTTAT 58.908 45.455 0.20 0.00 38.15 1.73
814 815 2.514803 GGGAGCACTGCCTTTTTCTTA 58.485 47.619 0.20 0.00 38.15 2.10
815 816 1.332195 GGGAGCACTGCCTTTTTCTT 58.668 50.000 0.20 0.00 38.15 2.52
816 817 0.890996 CGGGAGCACTGCCTTTTTCT 60.891 55.000 6.63 0.00 39.13 2.52
817 818 1.581447 CGGGAGCACTGCCTTTTTC 59.419 57.895 6.63 0.00 39.13 2.29
818 819 3.763671 CGGGAGCACTGCCTTTTT 58.236 55.556 6.63 0.00 39.13 1.94
830 831 1.899534 TTTTTGGAACCGGCGGGAG 60.900 57.895 31.78 5.33 36.97 4.30
831 832 2.195139 TTTTTGGAACCGGCGGGA 59.805 55.556 31.78 8.08 36.97 5.14
1019 1258 2.491298 GCTGAGTGAGTGAGTGATGAGA 59.509 50.000 0.00 0.00 0.00 3.27
1020 1259 2.492881 AGCTGAGTGAGTGAGTGATGAG 59.507 50.000 0.00 0.00 0.00 2.90
1063 1302 1.666700 CGATCGGACTTCTTCTCGTCT 59.333 52.381 7.38 0.00 0.00 4.18
1409 1709 2.644418 CACATTGTGCACCACGGG 59.356 61.111 15.69 0.00 37.14 5.28
1541 1848 9.647797 CTCTACCACAAATACTACACAAATACA 57.352 33.333 0.00 0.00 0.00 2.29
1542 1849 9.649167 ACTCTACCACAAATACTACACAAATAC 57.351 33.333 0.00 0.00 0.00 1.89
1544 1851 9.871238 CTACTCTACCACAAATACTACACAAAT 57.129 33.333 0.00 0.00 0.00 2.32
1547 1854 7.177184 TCCTACTCTACCACAAATACTACACA 58.823 38.462 0.00 0.00 0.00 3.72
1548 1855 7.338957 ACTCCTACTCTACCACAAATACTACAC 59.661 40.741 0.00 0.00 0.00 2.90
1550 1857 7.878547 ACTCCTACTCTACCACAAATACTAC 57.121 40.000 0.00 0.00 0.00 2.73
1551 1858 8.776119 AGTACTCCTACTCTACCACAAATACTA 58.224 37.037 0.00 0.00 0.00 1.82
1552 1859 7.641249 AGTACTCCTACTCTACCACAAATACT 58.359 38.462 0.00 0.00 0.00 2.12
1591 1900 5.510671 CATCCACGCAATAATTAAGTGACC 58.489 41.667 12.35 0.00 35.03 4.02
1608 1917 2.099098 CCGGTTATTCCTTTGCATCCAC 59.901 50.000 0.00 0.00 0.00 4.02
1662 1978 2.183478 TGCCACTACACCTGACATTG 57.817 50.000 0.00 0.00 0.00 2.82
1676 1992 5.713025 TGAGCTGATTTTTATTCTTGCCAC 58.287 37.500 0.00 0.00 0.00 5.01
1708 2024 5.843019 TTGGGACACTAGGAAGATTTCTT 57.157 39.130 0.00 0.00 39.29 2.52
1727 2043 1.483415 CCAAAATGGAGCCCTCATTGG 59.517 52.381 0.00 3.14 40.96 3.16
1769 2089 4.021981 ACAGGATTTCTTAAGCAAGTTGCC 60.022 41.667 24.02 6.71 46.52 4.52
1868 2193 0.391927 TGGGCCCGAATGAAGTAACG 60.392 55.000 19.37 0.00 0.00 3.18
1879 2204 1.383109 AGATGATGTCTGGGCCCGA 60.383 57.895 19.37 14.97 35.31 5.14
1889 2214 7.566879 AGAGTATTTCCTTCTACCAGATGATGT 59.433 37.037 0.00 0.00 0.00 3.06
1893 2218 5.988561 GCAGAGTATTTCCTTCTACCAGATG 59.011 44.000 0.00 0.00 0.00 2.90
1899 2224 6.311690 GTCACAAGCAGAGTATTTCCTTCTAC 59.688 42.308 0.00 0.00 0.00 2.59
1903 2228 4.973168 TGTCACAAGCAGAGTATTTCCTT 58.027 39.130 0.00 0.00 0.00 3.36
2024 2362 7.060633 GCGAAATGTATTTGTTTTCGTCATCTT 59.939 33.333 15.63 0.00 44.18 2.40
2031 2369 4.089351 GGGTGCGAAATGTATTTGTTTTCG 59.911 41.667 11.45 11.45 44.86 3.46
2068 2406 2.413796 CGGTACAACAATTAGCGCTCAA 59.586 45.455 16.34 7.54 34.08 3.02
2088 2426 4.926860 TCTGTAATCATCTTGTGCAACG 57.073 40.909 0.00 0.00 42.39 4.10
2112 2450 4.818534 TCAACTTGCAACTGTTCAGATC 57.181 40.909 6.83 0.00 0.00 2.75
2151 2489 4.433615 TCGACAATCTGAGGTTAATGCTC 58.566 43.478 0.00 0.00 0.00 4.26
2157 2495 5.301805 TCTGCATATCGACAATCTGAGGTTA 59.698 40.000 0.00 0.00 0.00 2.85
2171 2509 3.582780 TGCTTAGCTGATCTGCATATCG 58.417 45.455 24.33 10.17 34.99 2.92
2200 2538 9.566432 AAATTATGATTTGGCACCTTTACAAAA 57.434 25.926 0.00 0.00 37.60 2.44
2345 2689 6.476053 GGTCCTTATGATGTTCTTTCTCGTAC 59.524 42.308 0.00 0.00 0.00 3.67
2359 2703 3.762288 TCTTATAGCGCGGTCCTTATGAT 59.238 43.478 16.92 2.92 0.00 2.45
2449 2793 6.558771 ATTTTGAAATGTCGTCTGATGTGA 57.441 33.333 0.00 0.00 0.00 3.58
2452 2796 7.005380 GCAAAATTTTGAAATGTCGTCTGATG 58.995 34.615 30.40 2.99 40.55 3.07
2459 2803 4.905295 GCCAAGCAAAATTTTGAAATGTCG 59.095 37.500 30.40 15.08 40.55 4.35
2542 2886 3.829886 TTGCGATAACAGCTTTGGAAG 57.170 42.857 0.00 0.00 35.28 3.46


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

AutoCloner maintained by Alex Coulton.