Multiple sequence alignment - TraesCS5B01G306400

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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 TraesCS5B01G306400 chr5B 100.000 3439 0 0 1268 4706 490080134 490083572 0.000000e+00 6351.0
1 TraesCS5B01G306400 chr5B 100.000 1030 0 0 1 1030 490078867 490079896 0.000000e+00 1903.0
2 TraesCS5B01G306400 chr5B 88.235 255 22 7 1624 1876 604448909 604449157 9.900000e-77 298.0
3 TraesCS5B01G306400 chr5B 89.565 230 23 1 1731 1960 702408986 702408758 1.660000e-74 291.0
4 TraesCS5B01G306400 chr5B 87.179 78 4 5 1624 1700 702409058 702408986 3.020000e-12 84.2
5 TraesCS5B01G306400 chr5B 100.000 33 0 0 2990 3022 294238378 294238346 1.410000e-05 62.1
6 TraesCS5B01G306400 chr5D 94.573 2414 91 17 1415 3808 408537016 408539409 0.000000e+00 3696.0
7 TraesCS5B01G306400 chr5D 93.151 584 34 4 3830 4411 408539728 408540307 0.000000e+00 852.0
8 TraesCS5B01G306400 chr5D 87.358 617 68 5 1 616 408535938 408536545 0.000000e+00 699.0
9 TraesCS5B01G306400 chr5D 92.278 259 10 6 4455 4706 408540652 408540907 4.480000e-95 359.0
10 TraesCS5B01G306400 chr5D 89.455 275 15 10 763 1030 408536562 408536829 7.550000e-88 335.0
11 TraesCS5B01G306400 chr5A 88.797 1330 118 17 1468 2781 514426550 514427864 0.000000e+00 1602.0
12 TraesCS5B01G306400 chr5A 86.756 1344 116 24 3031 4324 514427875 514429206 0.000000e+00 1439.0
13 TraesCS5B01G306400 chr5A 87.019 624 74 4 1 624 514425375 514425991 0.000000e+00 697.0
14 TraesCS5B01G306400 chr5A 91.732 254 12 5 4458 4706 514429543 514429792 1.250000e-90 344.0
15 TraesCS5B01G306400 chr5A 89.474 266 21 5 772 1030 514426044 514426309 3.510000e-86 329.0
16 TraesCS5B01G306400 chr5A 88.550 262 18 11 1624 1882 342330710 342330458 1.640000e-79 307.0
17 TraesCS5B01G306400 chr3D 91.395 337 25 3 1624 1960 8355457 8355125 4.290000e-125 459.0
18 TraesCS5B01G306400 chr7B 88.506 261 22 6 1624 1882 734400886 734400632 4.570000e-80 309.0
19 TraesCS5B01G306400 chr1D 88.506 261 22 7 1624 1882 11507254 11507000 4.570000e-80 309.0
20 TraesCS5B01G306400 chr6A 87.739 261 24 8 1624 1882 96083115 96082861 9.900000e-77 298.0


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 TraesCS5B01G306400 chr5B 490078867 490083572 4705 False 4127.0 6351 100.0000 1 4706 2 chr5B.!!$F2 4705
1 TraesCS5B01G306400 chr5D 408535938 408540907 4969 False 1188.2 3696 91.3630 1 4706 5 chr5D.!!$F1 4705
2 TraesCS5B01G306400 chr5A 514425375 514429792 4417 False 882.2 1602 88.7556 1 4706 5 chr5A.!!$F1 4705

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
696 704 0.029433 TAGAGCTGAGTGTATGCGCG 59.971 55.0 0.00 0.00 0.0 6.86 F
698 706 0.248498 GAGCTGAGTGTATGCGCGTA 60.248 55.0 8.43 4.92 0.0 4.42 F
1618 1690 0.242017 GAATCAGCCACACCAGTTGC 59.758 55.0 0.00 0.00 36.7 4.17 F
2701 2786 0.381801 AAGCTGTGCACAAAAGACGG 59.618 50.0 21.98 8.33 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 1690 0.096976 GCACAACGGAACATGGATCG 59.903 55.000 0.00 0.00 0.00 3.69 R
1752 1827 0.743688 ATCGCAGAGAAGCTCATCGT 59.256 50.000 0.00 0.00 43.63 3.73 R
3013 3104 2.084546 GATCTTAGCGCCTGTTTGGTT 58.915 47.619 2.29 0.00 38.35 3.67 R
4608 5390 0.042581 TGCTACTCCCAGGGTGATCA 59.957 55.000 14.95 5.91 0.00 2.92 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
45 46 4.735369 TGGTATTTTGTTCCCATGAGTGT 58.265 39.130 0.00 0.00 0.00 3.55
52 53 6.968263 TTTGTTCCCATGAGTGTGATTTTA 57.032 33.333 0.00 0.00 0.00 1.52
89 90 4.884961 TGAAGAATAGCCTAAGAGTCCCT 58.115 43.478 0.00 0.00 0.00 4.20
136 137 5.701224 AGAGGTTTTTACATCACCCTTTCA 58.299 37.500 0.00 0.00 0.00 2.69
138 139 6.782494 AGAGGTTTTTACATCACCCTTTCATT 59.218 34.615 0.00 0.00 0.00 2.57
140 141 5.408299 GGTTTTTACATCACCCTTTCATTGC 59.592 40.000 0.00 0.00 0.00 3.56
144 145 3.433343 ACATCACCCTTTCATTGCATCA 58.567 40.909 0.00 0.00 0.00 3.07
208 209 9.430838 CATTTCATTCATTATCTTGACGACTTC 57.569 33.333 0.00 0.00 0.00 3.01
217 218 3.165498 GACGACTTCGGCGCAAAT 58.835 55.556 10.83 0.00 44.95 2.32
234 235 4.142403 CGCAAATAGGGTTGAACATCACAT 60.142 41.667 0.00 0.00 0.00 3.21
280 282 9.257651 GCAAAGAATATACCGTGTCTATTAGTT 57.742 33.333 0.00 0.00 0.00 2.24
323 325 2.027460 GGTGCTTGTTTGCCGTGG 59.973 61.111 0.00 0.00 0.00 4.94
331 333 1.295357 TGTTTGCCGTGGCGATGTAG 61.295 55.000 6.37 0.00 45.51 2.74
358 360 2.325583 TGGTTTTCCAGGCTATAGCG 57.674 50.000 18.30 5.68 46.22 4.26
368 376 1.600636 GCTATAGCGCCCAATGCCA 60.601 57.895 9.40 0.00 36.24 4.92
371 379 0.608856 TATAGCGCCCAATGCCATGG 60.609 55.000 7.63 7.63 40.35 3.66
372 380 2.645394 ATAGCGCCCAATGCCATGGT 62.645 55.000 14.67 0.00 38.91 3.55
373 381 4.211502 GCGCCCAATGCCATGGTC 62.212 66.667 14.67 6.41 38.91 4.02
374 382 2.755064 CGCCCAATGCCATGGTCA 60.755 61.111 14.67 12.37 38.91 4.02
375 383 2.129146 CGCCCAATGCCATGGTCAT 61.129 57.895 14.67 14.17 38.91 3.06
376 384 1.444250 GCCCAATGCCATGGTCATG 59.556 57.895 18.52 12.39 38.91 3.07
377 385 1.332144 GCCCAATGCCATGGTCATGT 61.332 55.000 18.52 9.09 38.91 3.21
389 397 5.337491 GCCATGGTCATGTTATCAAGGTTTT 60.337 40.000 14.67 0.00 37.11 2.43
398 406 9.368674 TCATGTTATCAAGGTTTTAAATGCATG 57.631 29.630 0.00 0.00 0.00 4.06
419 427 2.218603 GACGTTCACCTTCACCATGTT 58.781 47.619 0.00 0.00 0.00 2.71
420 428 1.946768 ACGTTCACCTTCACCATGTTG 59.053 47.619 0.00 0.00 0.00 3.33
446 454 3.137176 GGTGGAAGATCCCATTCATCTCA 59.863 47.826 0.00 0.00 38.66 3.27
447 455 4.202545 GGTGGAAGATCCCATTCATCTCAT 60.203 45.833 0.00 0.00 38.66 2.90
486 494 2.265367 TGGGTGCCTTCTCATAGTTCA 58.735 47.619 0.00 0.00 0.00 3.18
489 497 3.370953 GGGTGCCTTCTCATAGTTCACAT 60.371 47.826 0.00 0.00 0.00 3.21
495 503 4.141756 CCTTCTCATAGTTCACATCAGGCT 60.142 45.833 0.00 0.00 0.00 4.58
505 513 3.635591 TCACATCAGGCTGATCTAGACA 58.364 45.455 26.62 5.62 36.64 3.41
507 515 3.384146 CACATCAGGCTGATCTAGACAGT 59.616 47.826 26.62 16.45 36.64 3.55
513 521 5.012046 TCAGGCTGATCTAGACAGTTTTCAA 59.988 40.000 14.43 0.00 36.64 2.69
541 549 2.647529 ACATCGACATGTTAGCGTCA 57.352 45.000 0.00 0.00 40.66 4.35
550 558 2.093306 TGTTAGCGTCATTCCCACTG 57.907 50.000 0.00 0.00 0.00 3.66
591 599 4.553323 GCTACCTGAAGTTTCGTAGACAA 58.447 43.478 9.63 0.00 34.32 3.18
624 632 9.152595 CAACCATCATATGATTATGACTCTCTG 57.847 37.037 15.74 1.82 45.29 3.35
625 633 7.329499 ACCATCATATGATTATGACTCTCTGC 58.671 38.462 15.74 0.00 45.29 4.26
626 634 6.476053 CCATCATATGATTATGACTCTCTGCG 59.524 42.308 15.74 0.00 45.29 5.18
627 635 5.958955 TCATATGATTATGACTCTCTGCGG 58.041 41.667 0.00 0.00 39.40 5.69
628 636 2.515926 TGATTATGACTCTCTGCGGC 57.484 50.000 0.00 0.00 0.00 6.53
629 637 2.034878 TGATTATGACTCTCTGCGGCT 58.965 47.619 0.00 0.00 0.00 5.52
630 638 2.035193 TGATTATGACTCTCTGCGGCTC 59.965 50.000 0.00 0.00 0.00 4.70
631 639 1.474330 TTATGACTCTCTGCGGCTCA 58.526 50.000 0.00 0.00 0.00 4.26
632 640 1.028130 TATGACTCTCTGCGGCTCAG 58.972 55.000 0.00 0.00 44.21 3.35
634 642 1.138671 GACTCTCTGCGGCTCAGTC 59.861 63.158 4.16 3.72 43.32 3.51
635 643 1.304052 ACTCTCTGCGGCTCAGTCT 60.304 57.895 4.16 0.00 43.32 3.24
636 644 1.312371 ACTCTCTGCGGCTCAGTCTC 61.312 60.000 4.16 0.00 43.32 3.36
637 645 1.001517 TCTCTGCGGCTCAGTCTCT 60.002 57.895 4.16 0.00 43.32 3.10
638 646 0.610509 TCTCTGCGGCTCAGTCTCTT 60.611 55.000 4.16 0.00 43.32 2.85
639 647 0.179140 CTCTGCGGCTCAGTCTCTTC 60.179 60.000 4.16 0.00 43.32 2.87
640 648 1.515952 CTGCGGCTCAGTCTCTTCG 60.516 63.158 0.00 0.00 38.02 3.79
641 649 1.927608 CTGCGGCTCAGTCTCTTCGA 61.928 60.000 0.00 0.00 38.02 3.71
642 650 1.226547 GCGGCTCAGTCTCTTCGAG 60.227 63.158 0.00 0.00 0.00 4.04
643 651 1.431440 CGGCTCAGTCTCTTCGAGG 59.569 63.158 0.00 0.00 0.00 4.63
644 652 1.309499 CGGCTCAGTCTCTTCGAGGT 61.309 60.000 0.00 0.00 0.00 3.85
645 653 0.172352 GGCTCAGTCTCTTCGAGGTG 59.828 60.000 0.00 0.00 0.00 4.00
646 654 0.885196 GCTCAGTCTCTTCGAGGTGT 59.115 55.000 0.00 0.00 0.00 4.16
647 655 1.271102 GCTCAGTCTCTTCGAGGTGTT 59.729 52.381 0.00 0.00 0.00 3.32
648 656 2.669950 GCTCAGTCTCTTCGAGGTGTTC 60.670 54.545 0.00 0.00 0.00 3.18
649 657 2.554462 CTCAGTCTCTTCGAGGTGTTCA 59.446 50.000 0.00 0.00 0.00 3.18
650 658 3.157881 TCAGTCTCTTCGAGGTGTTCAT 58.842 45.455 0.00 0.00 0.00 2.57
651 659 4.332828 TCAGTCTCTTCGAGGTGTTCATA 58.667 43.478 0.00 0.00 0.00 2.15
652 660 4.396478 TCAGTCTCTTCGAGGTGTTCATAG 59.604 45.833 0.00 0.00 0.00 2.23
653 661 3.697045 AGTCTCTTCGAGGTGTTCATAGG 59.303 47.826 0.00 0.00 0.00 2.57
654 662 3.024547 TCTCTTCGAGGTGTTCATAGGG 58.975 50.000 0.00 0.00 0.00 3.53
655 663 3.024547 CTCTTCGAGGTGTTCATAGGGA 58.975 50.000 0.00 0.00 0.00 4.20
656 664 3.639094 CTCTTCGAGGTGTTCATAGGGAT 59.361 47.826 0.00 0.00 0.00 3.85
657 665 4.800023 TCTTCGAGGTGTTCATAGGGATA 58.200 43.478 0.00 0.00 0.00 2.59
658 666 4.827835 TCTTCGAGGTGTTCATAGGGATAG 59.172 45.833 0.00 0.00 0.00 2.08
659 667 3.497332 TCGAGGTGTTCATAGGGATAGG 58.503 50.000 0.00 0.00 0.00 2.57
660 668 2.563179 CGAGGTGTTCATAGGGATAGGG 59.437 54.545 0.00 0.00 0.00 3.53
661 669 3.588569 GAGGTGTTCATAGGGATAGGGT 58.411 50.000 0.00 0.00 0.00 4.34
662 670 3.579151 GAGGTGTTCATAGGGATAGGGTC 59.421 52.174 0.00 0.00 0.00 4.46
663 671 3.210074 AGGTGTTCATAGGGATAGGGTCT 59.790 47.826 0.00 0.00 0.00 3.85
664 672 3.579151 GGTGTTCATAGGGATAGGGTCTC 59.421 52.174 0.00 0.00 0.00 3.36
665 673 3.579151 GTGTTCATAGGGATAGGGTCTCC 59.421 52.174 0.00 0.00 0.00 3.71
666 674 2.826725 GTTCATAGGGATAGGGTCTCCG 59.173 54.545 0.00 0.00 38.33 4.63
667 675 2.071372 TCATAGGGATAGGGTCTCCGT 58.929 52.381 0.00 0.00 38.33 4.69
668 676 2.171840 CATAGGGATAGGGTCTCCGTG 58.828 57.143 0.00 0.00 38.33 4.94
669 677 0.178970 TAGGGATAGGGTCTCCGTGC 60.179 60.000 0.00 0.00 38.33 5.34
670 678 2.728817 GGATAGGGTCTCCGTGCG 59.271 66.667 0.00 0.00 38.33 5.34
671 679 2.125961 GGATAGGGTCTCCGTGCGT 61.126 63.158 0.00 0.00 38.33 5.24
672 680 1.065928 GATAGGGTCTCCGTGCGTG 59.934 63.158 0.00 0.00 38.33 5.34
673 681 1.664321 GATAGGGTCTCCGTGCGTGT 61.664 60.000 0.00 0.00 38.33 4.49
674 682 1.255667 ATAGGGTCTCCGTGCGTGTT 61.256 55.000 0.00 0.00 38.33 3.32
675 683 1.870055 TAGGGTCTCCGTGCGTGTTC 61.870 60.000 0.00 0.00 38.33 3.18
676 684 2.028484 GGTCTCCGTGCGTGTTCA 59.972 61.111 0.00 0.00 0.00 3.18
677 685 1.374252 GGTCTCCGTGCGTGTTCAT 60.374 57.895 0.00 0.00 0.00 2.57
678 686 0.108992 GGTCTCCGTGCGTGTTCATA 60.109 55.000 0.00 0.00 0.00 2.15
679 687 1.269166 GTCTCCGTGCGTGTTCATAG 58.731 55.000 0.00 0.00 0.00 2.23
680 688 1.135489 GTCTCCGTGCGTGTTCATAGA 60.135 52.381 0.00 0.00 0.00 1.98
681 689 1.132453 TCTCCGTGCGTGTTCATAGAG 59.868 52.381 0.00 0.00 0.00 2.43
682 690 0.457853 TCCGTGCGTGTTCATAGAGC 60.458 55.000 0.00 0.00 0.00 4.09
683 691 0.458543 CCGTGCGTGTTCATAGAGCT 60.459 55.000 0.00 0.00 0.00 4.09
684 692 0.642291 CGTGCGTGTTCATAGAGCTG 59.358 55.000 0.00 0.00 0.00 4.24
685 693 1.732405 CGTGCGTGTTCATAGAGCTGA 60.732 52.381 0.00 0.00 0.00 4.26
686 694 1.923204 GTGCGTGTTCATAGAGCTGAG 59.077 52.381 0.00 0.00 0.00 3.35
687 695 1.546029 TGCGTGTTCATAGAGCTGAGT 59.454 47.619 0.00 0.00 0.00 3.41
688 696 1.923204 GCGTGTTCATAGAGCTGAGTG 59.077 52.381 0.00 0.00 0.00 3.51
689 697 2.672478 GCGTGTTCATAGAGCTGAGTGT 60.672 50.000 0.00 0.00 0.00 3.55
690 698 3.427638 GCGTGTTCATAGAGCTGAGTGTA 60.428 47.826 0.00 0.00 0.00 2.90
691 699 4.734989 GCGTGTTCATAGAGCTGAGTGTAT 60.735 45.833 0.00 0.00 0.00 2.29
692 700 4.737279 CGTGTTCATAGAGCTGAGTGTATG 59.263 45.833 0.00 0.00 0.00 2.39
693 701 4.505922 GTGTTCATAGAGCTGAGTGTATGC 59.494 45.833 0.00 0.00 0.00 3.14
694 702 3.632855 TCATAGAGCTGAGTGTATGCG 57.367 47.619 0.00 0.00 0.00 4.73
695 703 2.057316 CATAGAGCTGAGTGTATGCGC 58.943 52.381 0.00 0.00 0.00 6.09
696 704 0.029433 TAGAGCTGAGTGTATGCGCG 59.971 55.000 0.00 0.00 0.00 6.86
697 705 1.517257 GAGCTGAGTGTATGCGCGT 60.517 57.895 8.43 7.55 0.00 6.01
698 706 0.248498 GAGCTGAGTGTATGCGCGTA 60.248 55.000 8.43 4.92 0.00 4.42
699 707 0.385751 AGCTGAGTGTATGCGCGTAT 59.614 50.000 15.52 15.52 0.00 3.06
700 708 1.607148 AGCTGAGTGTATGCGCGTATA 59.393 47.619 13.13 13.13 0.00 1.47
701 709 2.229062 AGCTGAGTGTATGCGCGTATAT 59.771 45.455 19.79 4.31 0.00 0.86
702 710 3.439129 AGCTGAGTGTATGCGCGTATATA 59.561 43.478 19.79 14.59 0.00 0.86
703 711 4.096532 AGCTGAGTGTATGCGCGTATATAT 59.903 41.667 19.79 9.03 0.00 0.86
704 712 5.296035 AGCTGAGTGTATGCGCGTATATATA 59.704 40.000 19.79 7.33 0.00 0.86
705 713 5.969435 GCTGAGTGTATGCGCGTATATATAA 59.031 40.000 19.79 6.60 0.00 0.98
706 714 6.471198 GCTGAGTGTATGCGCGTATATATAAA 59.529 38.462 19.79 6.04 0.00 1.40
707 715 7.513196 GCTGAGTGTATGCGCGTATATATAAAC 60.513 40.741 19.79 9.19 0.00 2.01
708 716 6.466730 TGAGTGTATGCGCGTATATATAAACG 59.533 38.462 19.79 10.02 41.92 3.60
719 727 7.081526 CGTATATATAAACGCCTAGACCTGT 57.918 40.000 0.00 0.00 31.66 4.00
720 728 8.201554 CGTATATATAAACGCCTAGACCTGTA 57.798 38.462 0.00 0.00 31.66 2.74
721 729 8.119226 CGTATATATAAACGCCTAGACCTGTAC 58.881 40.741 0.00 0.00 31.66 2.90
722 730 5.718724 ATATAAACGCCTAGACCTGTACC 57.281 43.478 0.00 0.00 0.00 3.34
723 731 1.636148 AAACGCCTAGACCTGTACCA 58.364 50.000 0.00 0.00 0.00 3.25
724 732 1.861982 AACGCCTAGACCTGTACCAT 58.138 50.000 0.00 0.00 0.00 3.55
725 733 1.112113 ACGCCTAGACCTGTACCATG 58.888 55.000 0.00 0.00 0.00 3.66
726 734 1.112113 CGCCTAGACCTGTACCATGT 58.888 55.000 0.00 0.00 0.00 3.21
727 735 1.480954 CGCCTAGACCTGTACCATGTT 59.519 52.381 0.00 0.00 0.00 2.71
728 736 2.481449 CGCCTAGACCTGTACCATGTTC 60.481 54.545 0.00 0.00 0.00 3.18
729 737 2.766828 GCCTAGACCTGTACCATGTTCT 59.233 50.000 0.00 0.00 0.00 3.01
730 738 3.958798 GCCTAGACCTGTACCATGTTCTA 59.041 47.826 0.00 0.00 0.00 2.10
731 739 4.404715 GCCTAGACCTGTACCATGTTCTAA 59.595 45.833 0.00 0.00 0.00 2.10
732 740 5.105064 GCCTAGACCTGTACCATGTTCTAAA 60.105 44.000 0.00 0.00 0.00 1.85
733 741 6.575649 GCCTAGACCTGTACCATGTTCTAAAA 60.576 42.308 0.00 0.00 0.00 1.52
734 742 7.391620 CCTAGACCTGTACCATGTTCTAAAAA 58.608 38.462 0.00 0.00 0.00 1.94
830 872 1.825474 CTATGTGGACCGTGGAAGACT 59.175 52.381 0.00 0.00 0.00 3.24
836 878 2.821969 TGGACCGTGGAAGACTAGTTAC 59.178 50.000 0.00 0.00 0.00 2.50
954 997 2.052690 TCTCGCCTCTTTCCCCTCG 61.053 63.158 0.00 0.00 0.00 4.63
956 999 4.082523 CGCCTCTTTCCCCTCGCA 62.083 66.667 0.00 0.00 0.00 5.10
957 1000 2.351276 GCCTCTTTCCCCTCGCAA 59.649 61.111 0.00 0.00 0.00 4.85
959 1002 1.587043 GCCTCTTTCCCCTCGCAAAC 61.587 60.000 0.00 0.00 0.00 2.93
960 1003 0.960861 CCTCTTTCCCCTCGCAAACC 60.961 60.000 0.00 0.00 0.00 3.27
961 1004 0.250727 CTCTTTCCCCTCGCAAACCA 60.251 55.000 0.00 0.00 0.00 3.67
962 1005 0.404040 TCTTTCCCCTCGCAAACCAT 59.596 50.000 0.00 0.00 0.00 3.55
963 1006 1.631388 TCTTTCCCCTCGCAAACCATA 59.369 47.619 0.00 0.00 0.00 2.74
964 1007 2.017049 CTTTCCCCTCGCAAACCATAG 58.983 52.381 0.00 0.00 0.00 2.23
965 1008 0.393808 TTCCCCTCGCAAACCATAGC 60.394 55.000 0.00 0.00 0.00 2.97
968 1017 1.823899 CCTCGCAAACCATAGCCCC 60.824 63.158 0.00 0.00 0.00 5.80
976 1025 1.344953 AACCATAGCCCCAGCGATCA 61.345 55.000 0.00 0.00 46.67 2.92
992 1041 1.825474 GATCAAGAGTCGGAGGTGGAA 59.175 52.381 0.00 0.00 0.00 3.53
1335 1391 1.153429 CCGTCCCCTTGGTTCGATC 60.153 63.158 0.00 0.00 34.10 3.69
1345 1401 1.673009 GGTTCGATCCGGTTTGGCA 60.673 57.895 0.00 0.00 37.80 4.92
1352 1408 1.312371 ATCCGGTTTGGCATGGTTCG 61.312 55.000 0.00 0.00 37.80 3.95
1355 1411 1.288752 GGTTTGGCATGGTTCGGTG 59.711 57.895 0.00 0.00 0.00 4.94
1359 1415 1.458398 TTGGCATGGTTCGGTGTATG 58.542 50.000 0.00 0.00 0.00 2.39
1360 1416 0.615850 TGGCATGGTTCGGTGTATGA 59.384 50.000 0.00 0.00 0.00 2.15
1361 1417 1.003696 TGGCATGGTTCGGTGTATGAA 59.996 47.619 0.00 0.00 0.00 2.57
1362 1418 2.297701 GGCATGGTTCGGTGTATGAAT 58.702 47.619 0.00 0.00 0.00 2.57
1364 1420 3.250040 GGCATGGTTCGGTGTATGAATAC 59.750 47.826 0.00 0.00 0.00 1.89
1365 1421 4.127171 GCATGGTTCGGTGTATGAATACT 58.873 43.478 0.00 0.00 34.41 2.12
1366 1422 5.294356 GCATGGTTCGGTGTATGAATACTA 58.706 41.667 0.00 0.00 34.41 1.82
1367 1423 5.756347 GCATGGTTCGGTGTATGAATACTAA 59.244 40.000 0.00 0.00 34.41 2.24
1368 1424 6.073765 GCATGGTTCGGTGTATGAATACTAAG 60.074 42.308 0.00 0.00 34.41 2.18
1369 1425 5.909477 TGGTTCGGTGTATGAATACTAAGG 58.091 41.667 2.36 0.00 34.41 2.69
1370 1426 5.657745 TGGTTCGGTGTATGAATACTAAGGA 59.342 40.000 2.36 0.00 34.41 3.36
1377 1433 7.926555 CGGTGTATGAATACTAAGGAAATCAGT 59.073 37.037 2.36 0.00 34.41 3.41
1388 1444 4.822036 AGGAAATCAGTAGACGATCTCG 57.178 45.455 0.00 0.00 46.33 4.04
1389 1445 3.566322 AGGAAATCAGTAGACGATCTCGG 59.434 47.826 4.44 0.00 44.95 4.63
1390 1446 3.304794 GGAAATCAGTAGACGATCTCGGG 60.305 52.174 4.44 0.00 44.95 5.14
1391 1447 1.240256 ATCAGTAGACGATCTCGGGC 58.760 55.000 4.44 0.00 44.95 6.13
1392 1448 1.158484 TCAGTAGACGATCTCGGGCG 61.158 60.000 4.44 0.00 44.95 6.13
1410 1466 2.430244 CTGCGCCGTCGTTGTAGT 60.430 61.111 4.18 0.00 38.14 2.73
1412 1468 3.530104 GCGCCGTCGTTGTAGTCG 61.530 66.667 0.00 0.00 38.14 4.18
1413 1469 2.127118 CGCCGTCGTTGTAGTCGT 60.127 61.111 0.00 0.00 0.00 4.34
1437 1493 4.819761 TCTGTGCGAGATGGCGGC 62.820 66.667 0.00 0.00 35.06 6.53
1444 1500 2.894387 GAGATGGCGGCACTGCTC 60.894 66.667 16.34 17.48 34.52 4.26
1590 1662 1.684248 GGCCAGGCATGTCTTCAATCT 60.684 52.381 15.19 0.00 0.00 2.40
1618 1690 0.242017 GAATCAGCCACACCAGTTGC 59.758 55.000 0.00 0.00 36.70 4.17
1629 1702 1.131126 CACCAGTTGCGATCCATGTTC 59.869 52.381 0.00 0.00 0.00 3.18
1639 1712 1.539388 GATCCATGTTCCGTTGTGCAA 59.461 47.619 0.00 0.00 0.00 4.08
1640 1713 1.614996 TCCATGTTCCGTTGTGCAAT 58.385 45.000 0.00 0.00 0.00 3.56
1648 1721 5.364778 TGTTCCGTTGTGCAATAGCTATAT 58.635 37.500 6.68 0.00 42.74 0.86
1649 1722 6.517605 TGTTCCGTTGTGCAATAGCTATATA 58.482 36.000 6.68 0.00 42.74 0.86
1650 1723 6.422701 TGTTCCGTTGTGCAATAGCTATATAC 59.577 38.462 6.68 7.25 42.74 1.47
1651 1724 6.340962 TCCGTTGTGCAATAGCTATATACT 57.659 37.500 6.68 0.00 42.74 2.12
1652 1725 6.156519 TCCGTTGTGCAATAGCTATATACTG 58.843 40.000 6.68 2.62 42.74 2.74
1653 1726 5.348724 CCGTTGTGCAATAGCTATATACTGG 59.651 44.000 6.68 6.79 42.74 4.00
1679 1753 3.004862 CCCTTTGATGATTTTGCTTGCC 58.995 45.455 0.00 0.00 0.00 4.52
1689 1763 1.850377 TTTGCTTGCCATCGTTGTTG 58.150 45.000 0.00 0.00 0.00 3.33
1690 1764 0.743688 TTGCTTGCCATCGTTGTTGT 59.256 45.000 0.00 0.00 0.00 3.32
1691 1765 0.743688 TGCTTGCCATCGTTGTTGTT 59.256 45.000 0.00 0.00 0.00 2.83
1696 1770 1.601903 TGCCATCGTTGTTGTTCTGTC 59.398 47.619 0.00 0.00 0.00 3.51
1740 1815 2.289631 TGTGTGGATGTGAGTAGCTTGG 60.290 50.000 0.00 0.00 0.00 3.61
1752 1827 6.833933 TGTGAGTAGCTTGGTGAATCTATAGA 59.166 38.462 4.57 4.57 0.00 1.98
1778 1853 4.507710 TGAGCTTCTCTGCGATTTATTGT 58.492 39.130 0.00 0.00 38.13 2.71
1854 1929 4.499019 CCTTGTGGTCGCAACTTTGTTAAT 60.499 41.667 0.00 0.00 0.00 1.40
1864 1939 8.575454 GTCGCAACTTTGTTAATTGATGTATTC 58.425 33.333 0.00 0.00 0.00 1.75
1962 2037 4.586001 CCCAATGCCTGTATTAATGCTCTT 59.414 41.667 5.11 0.00 0.00 2.85
2033 2109 2.866156 ACAGATCGATACAACAATGCCG 59.134 45.455 0.00 0.00 0.00 5.69
2034 2110 3.123050 CAGATCGATACAACAATGCCGA 58.877 45.455 0.00 0.00 33.14 5.54
2035 2111 3.742882 CAGATCGATACAACAATGCCGAT 59.257 43.478 0.00 0.00 38.62 4.18
2038 2115 1.657260 CGATACAACAATGCCGATGCG 60.657 52.381 0.00 0.00 41.78 4.73
2046 2123 2.481568 ACAATGCCGATGCGAATATCTG 59.518 45.455 0.00 0.00 41.78 2.90
2050 2127 1.873903 GCCGATGCGAATATCTGTGGT 60.874 52.381 0.00 0.00 0.00 4.16
2055 2132 5.399013 CGATGCGAATATCTGTGGTGTATA 58.601 41.667 0.00 0.00 0.00 1.47
2218 2295 7.652105 TCGAGCAAGCTAATAATACCTACAAAG 59.348 37.037 0.00 0.00 0.00 2.77
2219 2296 7.438459 CGAGCAAGCTAATAATACCTACAAAGT 59.562 37.037 0.00 0.00 0.00 2.66
2287 2365 7.285172 GCATTTAAATAATGGGCCCTTTTCATT 59.715 33.333 26.63 18.02 35.57 2.57
2288 2366 8.623030 CATTTAAATAATGGGCCCTTTTCATTG 58.377 33.333 26.63 12.29 33.72 2.82
2386 2468 7.230510 TGTTCACAAAAGATAGTAGGCAATGTT 59.769 33.333 0.00 0.00 0.00 2.71
2701 2786 0.381801 AAGCTGTGCACAAAAGACGG 59.618 50.000 21.98 8.33 0.00 4.79
2867 2958 1.153353 GGTGAGCCGAACGAAATCAA 58.847 50.000 0.00 0.00 0.00 2.57
2868 2959 1.533731 GGTGAGCCGAACGAAATCAAA 59.466 47.619 0.00 0.00 0.00 2.69
2971 3062 3.412386 AGCAAACACCAGCTAAGGTTAG 58.588 45.455 0.00 0.00 40.77 2.34
3013 3104 1.231221 GTGGCATGTTGTGGTAACGA 58.769 50.000 0.00 0.00 42.51 3.85
3084 3175 3.688185 TCTGTAACTACTCCTGTACGCTG 59.312 47.826 0.00 0.00 0.00 5.18
3251 3344 9.426837 TGCTTTCTTTCAAATTCCATTTCTATG 57.573 29.630 0.00 0.00 0.00 2.23
3265 3358 9.679661 TTCCATTTCTATGTAGTGCTTCAAATA 57.320 29.630 0.00 0.00 0.00 1.40
3273 3366 9.803130 CTATGTAGTGCTTCAAATATTTCATCG 57.197 33.333 0.00 0.00 0.00 3.84
3314 3407 6.925610 TCTGTGTGAATTGTGGATAATAGC 57.074 37.500 0.00 0.00 0.00 2.97
3450 3543 8.181487 TGCGACATACAATCTACTTTAAGAAC 57.819 34.615 0.00 0.00 0.00 3.01
3528 3635 2.285602 CGGCTATCAATTCCGTTGTTCG 60.286 50.000 0.00 0.00 38.95 3.95
3539 3646 6.671614 ATTCCGTTGTTCGATATGCTTAAA 57.328 33.333 0.00 0.00 42.86 1.52
3552 3659 7.338196 TCGATATGCTTAAATTCCTTTGGTTGA 59.662 33.333 0.00 0.00 0.00 3.18
3623 3730 8.205131 TGTACTCCTTTTTGTTACTCAAGTTC 57.795 34.615 0.00 0.00 37.35 3.01
3744 3872 3.330701 TCCCTTATCCAGCTGAAACTTGT 59.669 43.478 17.39 0.00 0.00 3.16
3974 4399 2.283298 CAGAACTATCGCCAAGCATGT 58.717 47.619 0.00 0.00 0.00 3.21
4003 4428 2.531522 TCACTGTGATGTGAGGTGTG 57.468 50.000 6.36 0.00 41.43 3.82
4014 4439 4.257267 TGTGAGGTGTGTCTCTATGTTG 57.743 45.455 0.00 0.00 34.98 3.33
4037 4462 3.304659 CCGTCTGACCATTTTTGTTCTGG 60.305 47.826 1.55 0.00 36.09 3.86
4042 4467 6.262273 GTCTGACCATTTTTGTTCTGGAACTA 59.738 38.462 13.54 4.56 41.67 2.24
4058 4483 6.551601 TCTGGAACTACTCAGAAAGAAGAACT 59.448 38.462 0.00 0.00 37.11 3.01
4059 4484 7.724506 TCTGGAACTACTCAGAAAGAAGAACTA 59.275 37.037 0.00 0.00 37.11 2.24
4060 4485 8.423906 TGGAACTACTCAGAAAGAAGAACTAT 57.576 34.615 0.00 0.00 0.00 2.12
4061 4486 8.871125 TGGAACTACTCAGAAAGAAGAACTATT 58.129 33.333 0.00 0.00 0.00 1.73
4129 4554 4.399004 AGTTGGCTACTAGCTTGAGATG 57.601 45.455 7.99 0.00 41.99 2.90
4142 4567 6.022163 AGCTTGAGATGGAAATTTCACTTG 57.978 37.500 19.49 10.25 0.00 3.16
4215 4645 0.742281 CCACTCCATCGCTCTGTTGG 60.742 60.000 0.00 0.00 38.58 3.77
4252 4682 0.881118 GCAGGTTGCATTTTCCTCGA 59.119 50.000 0.00 0.00 44.26 4.04
4261 4691 5.022282 TGCATTTTCCTCGAGATGTATGA 57.978 39.130 15.71 0.00 0.00 2.15
4282 4712 3.190079 ACTCGCTGCATTGTACAGTATG 58.810 45.455 0.00 3.56 46.00 2.39
4382 4812 9.484806 AGGATTGAATCTGATAGGAATGTTTTT 57.515 29.630 5.03 0.00 0.00 1.94
4411 4841 6.621316 TTGGCAGAATTCGTTTGTAAGTAA 57.379 33.333 0.00 0.00 0.00 2.24
4412 4842 6.621316 TGGCAGAATTCGTTTGTAAGTAAA 57.379 33.333 0.00 0.00 0.00 2.01
4414 4844 7.136119 TGGCAGAATTCGTTTGTAAGTAAAAG 58.864 34.615 0.00 0.00 0.00 2.27
4415 4845 6.581166 GGCAGAATTCGTTTGTAAGTAAAAGG 59.419 38.462 0.00 0.00 0.00 3.11
4416 4846 6.581166 GCAGAATTCGTTTGTAAGTAAAAGGG 59.419 38.462 0.00 0.00 0.00 3.95
4421 4851 5.435291 TCGTTTGTAAGTAAAAGGGACCAA 58.565 37.500 0.00 0.00 0.00 3.67
4422 4852 5.884792 TCGTTTGTAAGTAAAAGGGACCAAA 59.115 36.000 0.00 0.00 0.00 3.28
4423 4853 6.376581 TCGTTTGTAAGTAAAAGGGACCAAAA 59.623 34.615 0.00 0.00 0.00 2.44
4424 4854 6.473131 CGTTTGTAAGTAAAAGGGACCAAAAC 59.527 38.462 0.00 0.00 0.00 2.43
4425 4855 5.754543 TGTAAGTAAAAGGGACCAAAACG 57.245 39.130 0.00 0.00 0.00 3.60
4427 4857 5.884792 TGTAAGTAAAAGGGACCAAAACGAA 59.115 36.000 0.00 0.00 0.00 3.85
4428 4858 6.546772 TGTAAGTAAAAGGGACCAAAACGAAT 59.453 34.615 0.00 0.00 0.00 3.34
4431 4861 6.880484 AGTAAAAGGGACCAAAACGAATTTT 58.120 32.000 0.00 0.00 38.61 1.82
4434 4864 6.474140 AAAGGGACCAAAACGAATTTTACT 57.526 33.333 0.00 0.00 35.79 2.24
4436 4866 7.585579 AAGGGACCAAAACGAATTTTACTTA 57.414 32.000 0.00 0.00 35.79 2.24
4438 4868 6.546772 AGGGACCAAAACGAATTTTACTTACA 59.453 34.615 0.00 0.00 35.79 2.41
4439 4869 7.068470 AGGGACCAAAACGAATTTTACTTACAA 59.932 33.333 0.00 0.00 35.79 2.41
4440 4870 7.705752 GGGACCAAAACGAATTTTACTTACAAA 59.294 33.333 0.00 0.00 35.79 2.83
4442 4872 8.106467 ACCAAAACGAATTTTACTTACAAACG 57.894 30.769 0.00 0.00 35.79 3.60
4592 5374 2.325661 AGGGGGTTCCTTTTCCATTG 57.674 50.000 0.00 0.00 45.47 2.82
4630 5415 0.708209 TCACCCTGGGAGTAGCACTA 59.292 55.000 22.23 0.00 0.00 2.74
4631 5416 1.115467 CACCCTGGGAGTAGCACTAG 58.885 60.000 22.23 0.00 0.00 2.57
4632 5417 0.711184 ACCCTGGGAGTAGCACTAGT 59.289 55.000 22.23 0.00 0.00 2.57
4633 5418 1.928077 ACCCTGGGAGTAGCACTAGTA 59.072 52.381 22.23 0.00 0.00 1.82
4657 5442 4.943705 TCTCATTTTTCCTCTTCCCGATTG 59.056 41.667 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 7.394359 ACTCTTAGGCTATTCTTCAATGCAAAA 59.606 33.333 0.00 0.00 0.00 2.44
68 69 4.502431 GCAGGGACTCTTAGGCTATTCTTC 60.502 50.000 0.00 0.00 34.60 2.87
72 73 2.764269 TGCAGGGACTCTTAGGCTATT 58.236 47.619 0.00 0.00 34.60 1.73
101 102 9.343539 GATGTAAAAACCTCTTAGGCTATGAAT 57.656 33.333 10.85 0.90 39.63 2.57
102 103 8.325787 TGATGTAAAAACCTCTTAGGCTATGAA 58.674 33.333 10.85 0.00 39.63 2.57
180 181 9.334947 AGTCGTCAAGATAATGAATGAAATGAT 57.665 29.630 0.00 0.00 0.00 2.45
181 182 8.722480 AGTCGTCAAGATAATGAATGAAATGA 57.278 30.769 0.00 0.00 0.00 2.57
208 209 0.179174 GTTCAACCCTATTTGCGCCG 60.179 55.000 4.18 0.00 0.00 6.46
217 218 4.380843 AACCATGTGATGTTCAACCCTA 57.619 40.909 0.00 0.00 0.00 3.53
323 325 2.094762 ACCAAGGTCAACTACATCGC 57.905 50.000 0.00 0.00 0.00 4.58
331 333 1.068588 GCCTGGAAAACCAAGGTCAAC 59.931 52.381 0.00 0.00 0.00 3.18
356 358 4.211502 GACCATGGCATTGGGCGC 62.212 66.667 13.04 0.00 46.16 6.53
358 360 1.332144 ACATGACCATGGCATTGGGC 61.332 55.000 13.04 15.00 45.85 5.36
368 376 9.874205 CATTTAAAACCTTGATAACATGACCAT 57.126 29.630 0.00 0.00 0.00 3.55
371 379 8.755696 TGCATTTAAAACCTTGATAACATGAC 57.244 30.769 0.00 0.00 0.00 3.06
372 380 9.368674 CATGCATTTAAAACCTTGATAACATGA 57.631 29.630 0.00 0.00 32.46 3.07
373 381 8.605746 CCATGCATTTAAAACCTTGATAACATG 58.394 33.333 0.00 0.00 0.00 3.21
374 382 8.538701 TCCATGCATTTAAAACCTTGATAACAT 58.461 29.630 0.00 0.00 0.00 2.71
375 383 7.816995 GTCCATGCATTTAAAACCTTGATAACA 59.183 33.333 0.00 0.00 0.00 2.41
376 384 7.009174 CGTCCATGCATTTAAAACCTTGATAAC 59.991 37.037 0.00 0.00 0.00 1.89
377 385 7.032580 CGTCCATGCATTTAAAACCTTGATAA 58.967 34.615 0.00 0.00 0.00 1.75
389 397 3.066291 AGGTGAACGTCCATGCATTTA 57.934 42.857 0.00 0.00 0.00 1.40
398 406 1.156736 CATGGTGAAGGTGAACGTCC 58.843 55.000 0.00 0.00 0.00 4.79
419 427 0.920763 ATGGGATCTTCCACCTGGCA 60.921 55.000 0.00 0.00 39.97 4.92
420 428 0.259938 AATGGGATCTTCCACCTGGC 59.740 55.000 0.00 0.00 39.97 4.85
446 454 3.941483 CCAACACCGCTCTAGATCAAAAT 59.059 43.478 0.00 0.00 0.00 1.82
447 455 3.334691 CCAACACCGCTCTAGATCAAAA 58.665 45.455 0.00 0.00 0.00 2.44
486 494 3.641046 ACTGTCTAGATCAGCCTGATGT 58.359 45.455 12.92 11.05 37.20 3.06
489 497 4.528206 TGAAAACTGTCTAGATCAGCCTGA 59.472 41.667 17.17 0.00 36.50 3.86
495 503 9.119418 TGAAATGTTTGAAAACTGTCTAGATCA 57.881 29.630 7.39 0.00 39.59 2.92
505 513 7.032580 TGTCGATGTTGAAATGTTTGAAAACT 58.967 30.769 7.39 0.00 39.59 2.66
507 515 7.490725 ACATGTCGATGTTGAAATGTTTGAAAA 59.509 29.630 0.00 0.00 42.81 2.29
550 558 6.599638 AGGTAGCCTTGATTTGTAGTTCATTC 59.400 38.462 0.00 0.00 0.00 2.67
557 565 5.491982 ACTTCAGGTAGCCTTGATTTGTAG 58.508 41.667 0.00 0.00 0.00 2.74
591 599 1.852309 TCATATGATGGTTGCAGGGGT 59.148 47.619 0.00 0.00 0.00 4.95
624 632 2.878429 TCGAAGAGACTGAGCCGC 59.122 61.111 0.00 0.00 0.00 6.53
635 643 3.095912 TCCCTATGAACACCTCGAAGA 57.904 47.619 0.00 0.00 0.00 2.87
636 644 4.021894 CCTATCCCTATGAACACCTCGAAG 60.022 50.000 0.00 0.00 0.00 3.79
637 645 3.895656 CCTATCCCTATGAACACCTCGAA 59.104 47.826 0.00 0.00 0.00 3.71
638 646 3.497332 CCTATCCCTATGAACACCTCGA 58.503 50.000 0.00 0.00 0.00 4.04
639 647 2.563179 CCCTATCCCTATGAACACCTCG 59.437 54.545 0.00 0.00 0.00 4.63
640 648 3.579151 GACCCTATCCCTATGAACACCTC 59.421 52.174 0.00 0.00 0.00 3.85
641 649 3.210074 AGACCCTATCCCTATGAACACCT 59.790 47.826 0.00 0.00 0.00 4.00
642 650 3.579151 GAGACCCTATCCCTATGAACACC 59.421 52.174 0.00 0.00 0.00 4.16
643 651 3.579151 GGAGACCCTATCCCTATGAACAC 59.421 52.174 0.00 0.00 0.00 3.32
644 652 3.754172 CGGAGACCCTATCCCTATGAACA 60.754 52.174 0.00 0.00 32.86 3.18
645 653 2.826725 CGGAGACCCTATCCCTATGAAC 59.173 54.545 0.00 0.00 32.86 3.18
646 654 2.449730 ACGGAGACCCTATCCCTATGAA 59.550 50.000 0.00 0.00 32.86 2.57
647 655 2.071372 ACGGAGACCCTATCCCTATGA 58.929 52.381 0.00 0.00 32.86 2.15
648 656 2.171840 CACGGAGACCCTATCCCTATG 58.828 57.143 0.00 0.00 32.86 2.23
649 657 1.550409 GCACGGAGACCCTATCCCTAT 60.550 57.143 0.00 0.00 32.86 2.57
650 658 0.178970 GCACGGAGACCCTATCCCTA 60.179 60.000 0.00 0.00 32.86 3.53
651 659 1.457831 GCACGGAGACCCTATCCCT 60.458 63.158 0.00 0.00 32.86 4.20
652 660 2.857744 CGCACGGAGACCCTATCCC 61.858 68.421 0.00 0.00 32.86 3.85
653 661 2.125961 ACGCACGGAGACCCTATCC 61.126 63.158 0.00 0.00 0.00 2.59
654 662 1.065928 CACGCACGGAGACCCTATC 59.934 63.158 0.00 0.00 0.00 2.08
655 663 1.255667 AACACGCACGGAGACCCTAT 61.256 55.000 0.00 0.00 0.00 2.57
656 664 1.870055 GAACACGCACGGAGACCCTA 61.870 60.000 0.00 0.00 0.00 3.53
657 665 3.222354 GAACACGCACGGAGACCCT 62.222 63.158 0.00 0.00 0.00 4.34
658 666 2.737376 GAACACGCACGGAGACCC 60.737 66.667 0.00 0.00 0.00 4.46
659 667 0.108992 TATGAACACGCACGGAGACC 60.109 55.000 0.00 0.00 0.00 3.85
660 668 1.135489 TCTATGAACACGCACGGAGAC 60.135 52.381 0.00 0.00 0.00 3.36
661 669 1.132453 CTCTATGAACACGCACGGAGA 59.868 52.381 0.00 0.00 0.00 3.71
662 670 1.550065 CTCTATGAACACGCACGGAG 58.450 55.000 0.00 0.00 0.00 4.63
663 671 0.457853 GCTCTATGAACACGCACGGA 60.458 55.000 0.00 0.00 0.00 4.69
664 672 0.458543 AGCTCTATGAACACGCACGG 60.459 55.000 0.00 0.00 0.00 4.94
665 673 0.642291 CAGCTCTATGAACACGCACG 59.358 55.000 0.00 0.00 0.00 5.34
666 674 1.923204 CTCAGCTCTATGAACACGCAC 59.077 52.381 0.00 0.00 0.00 5.34
667 675 1.546029 ACTCAGCTCTATGAACACGCA 59.454 47.619 0.00 0.00 0.00 5.24
668 676 1.923204 CACTCAGCTCTATGAACACGC 59.077 52.381 0.00 0.00 0.00 5.34
669 677 3.223423 ACACTCAGCTCTATGAACACG 57.777 47.619 0.00 0.00 0.00 4.49
670 678 4.505922 GCATACACTCAGCTCTATGAACAC 59.494 45.833 0.00 0.00 0.00 3.32
671 679 4.686972 GCATACACTCAGCTCTATGAACA 58.313 43.478 0.00 0.00 0.00 3.18
672 680 3.733224 CGCATACACTCAGCTCTATGAAC 59.267 47.826 0.00 0.00 0.00 3.18
673 681 3.796844 GCGCATACACTCAGCTCTATGAA 60.797 47.826 0.30 0.00 0.00 2.57
674 682 2.287849 GCGCATACACTCAGCTCTATGA 60.288 50.000 0.30 0.00 0.00 2.15
675 683 2.057316 GCGCATACACTCAGCTCTATG 58.943 52.381 0.30 0.00 0.00 2.23
676 684 1.335415 CGCGCATACACTCAGCTCTAT 60.335 52.381 8.75 0.00 0.00 1.98
677 685 0.029433 CGCGCATACACTCAGCTCTA 59.971 55.000 8.75 0.00 0.00 2.43
678 686 1.226802 CGCGCATACACTCAGCTCT 60.227 57.895 8.75 0.00 0.00 4.09
679 687 0.248498 TACGCGCATACACTCAGCTC 60.248 55.000 5.73 0.00 0.00 4.09
680 688 0.385751 ATACGCGCATACACTCAGCT 59.614 50.000 5.73 0.00 0.00 4.24
681 689 2.046283 TATACGCGCATACACTCAGC 57.954 50.000 5.73 0.00 0.00 4.26
682 690 7.304679 CGTTTATATATACGCGCATACACTCAG 60.305 40.741 5.73 0.00 0.00 3.35
683 691 6.466730 CGTTTATATATACGCGCATACACTCA 59.533 38.462 5.73 0.00 0.00 3.41
684 692 6.839649 CGTTTATATATACGCGCATACACTC 58.160 40.000 5.73 0.00 0.00 3.51
685 693 6.785633 CGTTTATATATACGCGCATACACT 57.214 37.500 5.73 0.00 0.00 3.55
695 703 7.081526 ACAGGTCTAGGCGTTTATATATACG 57.918 40.000 18.00 18.00 40.55 3.06
696 704 8.401709 GGTACAGGTCTAGGCGTTTATATATAC 58.598 40.741 0.00 0.00 0.00 1.47
697 705 8.108999 TGGTACAGGTCTAGGCGTTTATATATA 58.891 37.037 0.00 0.00 0.00 0.86
698 706 6.950041 TGGTACAGGTCTAGGCGTTTATATAT 59.050 38.462 0.00 0.00 0.00 0.86
699 707 6.306199 TGGTACAGGTCTAGGCGTTTATATA 58.694 40.000 0.00 0.00 0.00 0.86
700 708 5.142639 TGGTACAGGTCTAGGCGTTTATAT 58.857 41.667 0.00 0.00 0.00 0.86
701 709 4.535781 TGGTACAGGTCTAGGCGTTTATA 58.464 43.478 0.00 0.00 0.00 0.98
702 710 3.368248 TGGTACAGGTCTAGGCGTTTAT 58.632 45.455 0.00 0.00 0.00 1.40
703 711 2.806434 TGGTACAGGTCTAGGCGTTTA 58.194 47.619 0.00 0.00 0.00 2.01
704 712 1.636148 TGGTACAGGTCTAGGCGTTT 58.364 50.000 0.00 0.00 0.00 3.60
705 713 3.369042 TGGTACAGGTCTAGGCGTT 57.631 52.632 0.00 0.00 0.00 4.84
742 750 9.866655 GGGTCATAGAGAGATAGATAGAATCAT 57.133 37.037 0.00 0.00 0.00 2.45
743 751 9.067963 AGGGTCATAGAGAGATAGATAGAATCA 57.932 37.037 0.00 0.00 0.00 2.57
744 752 9.561069 GAGGGTCATAGAGAGATAGATAGAATC 57.439 40.741 0.00 0.00 0.00 2.52
745 753 9.296463 AGAGGGTCATAGAGAGATAGATAGAAT 57.704 37.037 0.00 0.00 0.00 2.40
746 754 8.694171 AGAGGGTCATAGAGAGATAGATAGAA 57.306 38.462 0.00 0.00 0.00 2.10
747 755 8.694171 AAGAGGGTCATAGAGAGATAGATAGA 57.306 38.462 0.00 0.00 0.00 1.98
748 756 8.772250 AGAAGAGGGTCATAGAGAGATAGATAG 58.228 40.741 0.00 0.00 0.00 2.08
749 757 8.694171 AGAAGAGGGTCATAGAGAGATAGATA 57.306 38.462 0.00 0.00 0.00 1.98
750 758 7.588866 AGAAGAGGGTCATAGAGAGATAGAT 57.411 40.000 0.00 0.00 0.00 1.98
751 759 7.311046 GCTAGAAGAGGGTCATAGAGAGATAGA 60.311 44.444 0.00 0.00 0.00 1.98
759 767 5.396057 AAGAGCTAGAAGAGGGTCATAGA 57.604 43.478 0.00 0.00 33.07 1.98
787 795 5.645497 AGCAGAGCTACAATTCTAACAAAGG 59.355 40.000 0.00 0.00 36.99 3.11
792 800 6.201806 CCACATAGCAGAGCTACAATTCTAAC 59.798 42.308 0.14 0.00 44.24 2.34
794 802 5.598417 TCCACATAGCAGAGCTACAATTCTA 59.402 40.000 0.14 0.00 44.24 2.10
795 803 4.406972 TCCACATAGCAGAGCTACAATTCT 59.593 41.667 0.14 0.00 44.24 2.40
801 843 1.269309 CGGTCCACATAGCAGAGCTAC 60.269 57.143 0.14 0.00 44.24 3.58
849 892 1.534729 GCTTTCGTGGACCATTTCCT 58.465 50.000 0.00 0.00 46.10 3.36
866 909 0.613012 GAGATGGCTTTGGTTGGGCT 60.613 55.000 0.00 0.00 0.00 5.19
954 997 2.774799 CGCTGGGGCTATGGTTTGC 61.775 63.158 0.00 0.00 36.09 3.68
956 999 0.179018 GATCGCTGGGGCTATGGTTT 60.179 55.000 0.00 0.00 36.09 3.27
957 1000 1.344953 TGATCGCTGGGGCTATGGTT 61.345 55.000 0.00 0.00 36.09 3.67
959 1002 0.604780 CTTGATCGCTGGGGCTATGG 60.605 60.000 0.00 0.00 36.09 2.74
960 1003 0.394192 TCTTGATCGCTGGGGCTATG 59.606 55.000 0.00 0.00 36.09 2.23
961 1004 0.683973 CTCTTGATCGCTGGGGCTAT 59.316 55.000 0.00 0.00 36.09 2.97
962 1005 0.687757 ACTCTTGATCGCTGGGGCTA 60.688 55.000 0.00 0.00 36.09 3.93
963 1006 1.965754 GACTCTTGATCGCTGGGGCT 61.966 60.000 0.00 0.00 36.09 5.19
964 1007 1.522580 GACTCTTGATCGCTGGGGC 60.523 63.158 0.00 0.00 0.00 5.80
965 1008 1.227089 CGACTCTTGATCGCTGGGG 60.227 63.158 0.00 0.00 31.96 4.96
968 1017 0.248825 CCTCCGACTCTTGATCGCTG 60.249 60.000 0.00 0.00 38.27 5.18
976 1025 1.551452 CTCTTCCACCTCCGACTCTT 58.449 55.000 0.00 0.00 0.00 2.85
992 1041 2.162608 CACGACTTCGACATCTTCCTCT 59.837 50.000 5.47 0.00 43.02 3.69
1316 1372 2.588856 GATCGAACCAAGGGGACGGG 62.589 65.000 0.00 0.00 37.78 5.28
1318 1374 1.153429 GGATCGAACCAAGGGGACG 60.153 63.158 6.88 0.00 38.05 4.79
1319 1375 1.153429 CGGATCGAACCAAGGGGAC 60.153 63.158 12.66 0.00 38.05 4.46
1320 1376 2.363975 CCGGATCGAACCAAGGGGA 61.364 63.158 12.66 0.00 38.05 4.81
1335 1391 2.566010 CGAACCATGCCAAACCGG 59.434 61.111 0.00 0.00 38.11 5.28
1345 1401 6.325545 TCCTTAGTATTCATACACCGAACCAT 59.674 38.462 0.00 0.00 35.74 3.55
1359 1415 9.615295 GATCGTCTACTGATTTCCTTAGTATTC 57.385 37.037 0.00 0.00 0.00 1.75
1360 1416 9.357161 AGATCGTCTACTGATTTCCTTAGTATT 57.643 33.333 0.00 0.00 0.00 1.89
1361 1417 8.927675 AGATCGTCTACTGATTTCCTTAGTAT 57.072 34.615 0.00 0.00 0.00 2.12
1362 1418 7.171167 CGAGATCGTCTACTGATTTCCTTAGTA 59.829 40.741 0.00 0.00 34.11 1.82
1364 1420 6.367421 CGAGATCGTCTACTGATTTCCTTAG 58.633 44.000 0.00 0.00 34.11 2.18
1365 1421 5.238868 CCGAGATCGTCTACTGATTTCCTTA 59.761 44.000 1.09 0.00 37.74 2.69
1366 1422 4.036971 CCGAGATCGTCTACTGATTTCCTT 59.963 45.833 1.09 0.00 37.74 3.36
1367 1423 3.566322 CCGAGATCGTCTACTGATTTCCT 59.434 47.826 1.09 0.00 37.74 3.36
1368 1424 3.304794 CCCGAGATCGTCTACTGATTTCC 60.305 52.174 1.09 0.00 37.74 3.13
1369 1425 3.854045 GCCCGAGATCGTCTACTGATTTC 60.854 52.174 1.09 0.00 37.74 2.17
1370 1426 2.034812 GCCCGAGATCGTCTACTGATTT 59.965 50.000 1.09 0.00 37.74 2.17
1377 1433 2.203167 AGCGCCCGAGATCGTCTA 60.203 61.111 2.29 0.00 37.74 2.59
1401 1457 0.885879 AGCATCCACGACTACAACGA 59.114 50.000 0.00 0.00 34.70 3.85
1402 1458 1.135373 AGAGCATCCACGACTACAACG 60.135 52.381 0.00 0.00 33.66 4.10
1410 1466 2.125952 CGCACAGAGCATCCACGA 60.126 61.111 0.00 0.00 46.13 4.35
1412 1468 0.179089 ATCTCGCACAGAGCATCCAC 60.179 55.000 0.00 0.00 46.44 4.02
1413 1469 0.179092 CATCTCGCACAGAGCATCCA 60.179 55.000 0.00 0.00 46.44 3.41
1437 1493 1.310933 GGCAGATGGGTTGAGCAGTG 61.311 60.000 0.00 0.00 0.00 3.66
1444 1500 1.380380 GGGAAGGGCAGATGGGTTG 60.380 63.158 0.00 0.00 0.00 3.77
1618 1690 0.096976 GCACAACGGAACATGGATCG 59.903 55.000 0.00 0.00 0.00 3.69
1629 1702 5.348724 CCAGTATATAGCTATTGCACAACGG 59.651 44.000 12.39 6.26 42.74 4.44
1653 1726 3.261643 AGCAAAATCATCAAAGGGGGAAC 59.738 43.478 0.00 0.00 0.00 3.62
1679 1753 1.718361 CGCGACAGAACAACAACGATG 60.718 52.381 0.00 0.00 0.00 3.84
1689 1763 1.630148 ATCTAACAGCGCGACAGAAC 58.370 50.000 12.10 0.00 0.00 3.01
1690 1764 3.710326 ATATCTAACAGCGCGACAGAA 57.290 42.857 12.10 0.00 0.00 3.02
1691 1765 3.710326 AATATCTAACAGCGCGACAGA 57.290 42.857 12.10 3.99 0.00 3.41
1696 1770 9.835315 CACATAATATTAATATCTAACAGCGCG 57.165 33.333 8.42 0.00 0.00 6.86
1740 1815 6.908825 AGAAGCTCATCGTCTATAGATTCAC 58.091 40.000 5.57 0.00 36.95 3.18
1752 1827 0.743688 ATCGCAGAGAAGCTCATCGT 59.256 50.000 0.00 0.00 43.63 3.73
1778 1853 3.700970 TGCTGGACGCCGGATTCA 61.701 61.111 5.05 0.00 38.05 2.57
1839 1914 8.511321 AGAATACATCAATTAACAAAGTTGCGA 58.489 29.630 0.00 0.00 0.00 5.10
1854 1929 8.049117 AGAAGCCAGTTCATAAGAATACATCAA 58.951 33.333 0.00 0.00 37.67 2.57
1864 1939 3.012518 CCACCAGAAGCCAGTTCATAAG 58.987 50.000 0.00 0.00 37.67 1.73
1940 2015 5.526115 CAAGAGCATTAATACAGGCATTGG 58.474 41.667 0.00 0.00 0.00 3.16
2033 2109 7.834068 ATTATACACCACAGATATTCGCATC 57.166 36.000 0.00 0.00 0.00 3.91
2034 2110 7.981789 CCTATTATACACCACAGATATTCGCAT 59.018 37.037 0.00 0.00 0.00 4.73
2035 2111 7.039293 ACCTATTATACACCACAGATATTCGCA 60.039 37.037 0.00 0.00 0.00 5.10
2064 2141 9.120538 ACATACAGAACAGACACAAATAAAACT 57.879 29.630 0.00 0.00 0.00 2.66
2218 2295 8.512966 AAGGAAGGAGCTTCTAATGAAATAAC 57.487 34.615 0.00 0.00 40.07 1.89
2219 2296 8.960591 CAAAGGAAGGAGCTTCTAATGAAATAA 58.039 33.333 0.00 0.00 40.07 1.40
2221 2298 7.177878 TCAAAGGAAGGAGCTTCTAATGAAAT 58.822 34.615 0.00 0.00 40.07 2.17
2222 2299 6.542821 TCAAAGGAAGGAGCTTCTAATGAAA 58.457 36.000 0.00 0.00 40.07 2.69
2223 2300 6.126863 TCAAAGGAAGGAGCTTCTAATGAA 57.873 37.500 0.00 0.00 40.07 2.57
2227 2305 5.163195 ACAGTTCAAAGGAAGGAGCTTCTAA 60.163 40.000 0.00 0.00 40.07 2.10
2269 2347 4.782156 TCAACAATGAAAAGGGCCCATTAT 59.218 37.500 27.56 6.90 30.99 1.28
2386 2468 8.567948 GCTGCTTATAGTTGCAATTATTTCCTA 58.432 33.333 18.25 6.48 38.81 2.94
2774 2865 3.459598 TGCCCCTGCTCTTCTTATTGTAT 59.540 43.478 0.00 0.00 38.71 2.29
2971 3062 4.660938 GCCACACCCCCTGACACC 62.661 72.222 0.00 0.00 0.00 4.16
3013 3104 2.084546 GATCTTAGCGCCTGTTTGGTT 58.915 47.619 2.29 0.00 38.35 3.67
3251 3344 8.175069 TCAACGATGAAATATTTGAAGCACTAC 58.825 33.333 5.17 0.00 30.99 2.73
3265 3358 6.648310 AGCTCGATATGAATCAACGATGAAAT 59.352 34.615 0.00 0.00 39.49 2.17
3273 3366 5.521735 ACACAGAAGCTCGATATGAATCAAC 59.478 40.000 0.00 0.00 31.93 3.18
3314 3407 2.731976 GAGCTGTTAACGAGAGGTGTTG 59.268 50.000 0.00 0.00 28.28 3.33
3521 3628 8.798153 CAAAGGAATTTAAGCATATCGAACAAC 58.202 33.333 0.00 0.00 0.00 3.32
3528 3635 9.822185 AATCAACCAAAGGAATTTAAGCATATC 57.178 29.630 0.00 0.00 0.00 1.63
3539 3646 6.652062 GCAAATCAAGAATCAACCAAAGGAAT 59.348 34.615 0.00 0.00 0.00 3.01
3577 3684 4.464597 ACAAAAGGCCTAAACAGAACAACA 59.535 37.500 5.16 0.00 0.00 3.33
3744 3872 4.927425 GTCTTGTAGTGACAATTCGGCTAA 59.073 41.667 0.00 0.00 44.53 3.09
3835 4260 3.495001 GTGTGCTGAGTTGGTTCTTCTAC 59.505 47.826 0.00 0.00 0.00 2.59
3955 4380 2.093500 TCACATGCTTGGCGATAGTTCT 60.093 45.455 4.44 0.00 39.35 3.01
3964 4389 3.253188 TGAAAACTACTCACATGCTTGGC 59.747 43.478 4.44 0.00 0.00 4.52
3974 4399 5.912892 TCACATCACAGTGAAAACTACTCA 58.087 37.500 7.50 0.00 44.92 3.41
4003 4428 2.531206 GTCAGACGGCAACATAGAGAC 58.469 52.381 0.00 0.00 0.00 3.36
4014 4439 2.293399 AGAACAAAAATGGTCAGACGGC 59.707 45.455 0.00 0.00 0.00 5.68
4058 4483 6.607198 AGCTTAGCTGCCCAAGATTTTAAATA 59.393 34.615 5.70 0.00 37.57 1.40
4059 4484 5.423290 AGCTTAGCTGCCCAAGATTTTAAAT 59.577 36.000 5.70 0.00 37.57 1.40
4060 4485 4.772100 AGCTTAGCTGCCCAAGATTTTAAA 59.228 37.500 5.70 0.00 37.57 1.52
4061 4486 4.344104 AGCTTAGCTGCCCAAGATTTTAA 58.656 39.130 5.70 0.00 37.57 1.52
4153 4578 4.392940 CATGGCCTATTCTAACAAGGGAG 58.607 47.826 3.32 0.00 0.00 4.30
4202 4630 1.667724 GGTCATTCCAACAGAGCGATG 59.332 52.381 0.00 0.00 35.97 3.84
4203 4631 1.556911 AGGTCATTCCAACAGAGCGAT 59.443 47.619 0.00 0.00 39.02 4.58
4252 4682 3.129109 CAATGCAGCGAGTCATACATCT 58.871 45.455 0.00 0.00 0.00 2.90
4261 4691 3.190079 CATACTGTACAATGCAGCGAGT 58.810 45.455 0.00 0.00 37.47 4.18
4282 4712 2.203266 GGCATCAGTAGGCTGGGC 60.203 66.667 0.00 0.00 42.78 5.36
4405 4835 7.585579 AATTCGTTTTGGTCCCTTTTACTTA 57.414 32.000 0.00 0.00 0.00 2.24
4411 4841 6.474140 AGTAAAATTCGTTTTGGTCCCTTT 57.526 33.333 0.00 0.00 0.00 3.11
4412 4842 6.474140 AAGTAAAATTCGTTTTGGTCCCTT 57.526 33.333 0.00 0.00 0.00 3.95
4414 4844 6.737118 TGTAAGTAAAATTCGTTTTGGTCCC 58.263 36.000 0.00 0.00 0.00 4.46
4415 4845 8.533965 GTTTGTAAGTAAAATTCGTTTTGGTCC 58.466 33.333 0.00 0.00 0.00 4.46
4416 4846 8.254470 CGTTTGTAAGTAAAATTCGTTTTGGTC 58.746 33.333 0.00 0.00 0.00 4.02
4423 4853 9.505995 ACAAATTCGTTTGTAAGTAAAATTCGT 57.494 25.926 4.85 0.00 42.74 3.85
4427 4857 9.088512 TGCAACAAATTCGTTTGTAAGTAAAAT 57.911 25.926 6.93 0.00 43.66 1.82
4428 4858 8.462143 TGCAACAAATTCGTTTGTAAGTAAAA 57.538 26.923 6.93 0.00 43.66 1.52
4431 4861 7.197017 ACATGCAACAAATTCGTTTGTAAGTA 58.803 30.769 6.93 4.05 43.66 2.24
4434 4864 8.581057 AATACATGCAACAAATTCGTTTGTAA 57.419 26.923 6.93 0.00 43.66 2.41
4436 4866 7.437862 AGAAATACATGCAACAAATTCGTTTGT 59.562 29.630 0.00 0.99 46.12 2.83
4438 4868 7.867403 AGAGAAATACATGCAACAAATTCGTTT 59.133 29.630 0.00 0.00 0.00 3.60
4439 4869 7.326789 CAGAGAAATACATGCAACAAATTCGTT 59.673 33.333 0.00 0.00 0.00 3.85
4440 4870 6.803320 CAGAGAAATACATGCAACAAATTCGT 59.197 34.615 0.00 0.00 0.00 3.85
4442 4872 7.274250 GGACAGAGAAATACATGCAACAAATTC 59.726 37.037 0.00 0.00 0.00 2.17
4445 4875 5.769662 AGGACAGAGAAATACATGCAACAAA 59.230 36.000 0.00 0.00 0.00 2.83
4446 4876 5.316167 AGGACAGAGAAATACATGCAACAA 58.684 37.500 0.00 0.00 0.00 2.83
4447 4877 4.910195 AGGACAGAGAAATACATGCAACA 58.090 39.130 0.00 0.00 0.00 3.33
4448 4878 5.886960 AAGGACAGAGAAATACATGCAAC 57.113 39.130 0.00 0.00 0.00 4.17
4608 5390 0.042581 TGCTACTCCCAGGGTGATCA 59.957 55.000 14.95 5.91 0.00 2.92
4630 5415 5.425539 TCGGGAAGAGGAAAAATGAGATACT 59.574 40.000 0.00 0.00 0.00 2.12
4631 5416 5.671493 TCGGGAAGAGGAAAAATGAGATAC 58.329 41.667 0.00 0.00 0.00 2.24
4632 5417 5.950544 TCGGGAAGAGGAAAAATGAGATA 57.049 39.130 0.00 0.00 0.00 1.98
4633 5418 4.844349 TCGGGAAGAGGAAAAATGAGAT 57.156 40.909 0.00 0.00 0.00 2.75
4657 5442 2.045926 ACAGGCTTCCATCACGGC 60.046 61.111 0.00 0.00 33.14 5.68


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

AutoCloner maintained by Alex Coulton.