Multiple sequence alignment - TraesCS3B01G107400

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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 TraesCS3B01G107400 chr3B 100.000 2738 0 0 1 2738 72922314 72925051 0.000000e+00 5057
1 TraesCS3B01G107400 chr3B 90.578 1539 122 10 777 2305 72715952 72717477 0.000000e+00 2017
2 TraesCS3B01G107400 chr3B 92.369 629 23 11 2 606 72715317 72715944 0.000000e+00 872
3 TraesCS3B01G107400 chr3D 95.200 1729 64 12 775 2494 46525457 46527175 0.000000e+00 2715
4 TraesCS3B01G107400 chr3D 89.139 1556 121 28 775 2305 46486274 46487806 0.000000e+00 1893
5 TraesCS3B01G107400 chr3D 94.828 638 8 11 1 615 46524825 46525460 0.000000e+00 972
6 TraesCS3B01G107400 chr3D 90.966 642 30 13 2 615 46485636 46486277 0.000000e+00 839
7 TraesCS3B01G107400 chr3A 88.075 1543 125 27 775 2305 57905202 57906697 0.000000e+00 1775
8 TraesCS3B01G107400 chr3A 96.687 966 29 1 775 1737 57981069 57980104 0.000000e+00 1604
9 TraesCS3B01G107400 chr3A 91.888 641 26 11 1 615 57904565 57905205 0.000000e+00 872
10 TraesCS3B01G107400 chr3A 93.881 523 28 4 1933 2454 57968390 57967871 0.000000e+00 785
11 TraesCS3B01G107400 chr3A 94.737 133 3 4 1731 1863 57975410 57975282 1.290000e-48 204
12 TraesCS3B01G107400 chr3A 92.208 77 5 1 1861 1937 57974845 57974770 1.040000e-19 108
13 TraesCS3B01G107400 chr5A 81.188 606 103 8 1062 1660 143658944 143658343 6.860000e-131 477
14 TraesCS3B01G107400 chr5D 80.858 606 105 8 1062 1660 128642658 128642057 1.480000e-127 466
15 TraesCS3B01G107400 chr5B 80.890 607 103 10 1062 1660 141148174 141147573 1.480000e-127 466
16 TraesCS3B01G107400 chr5B 85.081 248 11 12 2491 2738 611935325 611935104 2.120000e-56 230
17 TraesCS3B01G107400 chr7A 80.816 490 89 5 126 612 631984736 631985223 1.990000e-101 379
18 TraesCS3B01G107400 chr7A 92.432 185 13 1 614 798 320981173 320981356 2.090000e-66 263
19 TraesCS3B01G107400 chr7A 85.062 241 10 6 2498 2738 544145950 544145736 3.550000e-54 222
20 TraesCS3B01G107400 chr6B 80.533 488 93 2 126 612 120317174 120316688 9.260000e-100 374
21 TraesCS3B01G107400 chr6B 80.705 482 91 2 126 606 120595122 120594642 9.260000e-100 374
22 TraesCS3B01G107400 chr6B 75.449 668 134 23 1070 1718 672461964 672461308 5.730000e-77 298
23 TraesCS3B01G107400 chr6B 96.364 165 6 0 614 778 96958654 96958818 3.470000e-69 272
24 TraesCS3B01G107400 chr7D 80.793 479 88 4 126 602 548231394 548231870 3.330000e-99 372
25 TraesCS3B01G107400 chr7D 95.322 171 8 0 608 778 69592830 69592660 3.470000e-69 272
26 TraesCS3B01G107400 chr7B 80.408 490 91 5 126 612 591461942 591462429 4.310000e-98 368
27 TraesCS3B01G107400 chr2B 94.350 177 8 2 604 779 174794996 174794821 1.250000e-68 270
28 TraesCS3B01G107400 chr2B 85.537 242 9 9 2497 2738 707730634 707730419 2.120000e-56 230
29 TraesCS3B01G107400 chr2D 95.758 165 7 0 614 778 426427801 426427965 1.620000e-67 267
30 TraesCS3B01G107400 chr2D 94.737 171 8 1 609 779 446317639 446317808 5.810000e-67 265
31 TraesCS3B01G107400 chr6D 94.186 172 10 0 607 778 392897146 392896975 2.090000e-66 263
32 TraesCS3B01G107400 chr4D 95.181 166 8 0 614 779 477898959 477898794 2.090000e-66 263
33 TraesCS3B01G107400 chr4D 85.000 240 9 7 2500 2738 313880871 313881084 4.590000e-53 219
34 TraesCS3B01G107400 chr1D 93.714 175 9 2 604 778 178466298 178466470 7.520000e-66 261
35 TraesCS3B01G107400 chr1B 74.845 644 129 23 1072 1690 4933876 4933241 7.520000e-66 261
36 TraesCS3B01G107400 chrUn 86.441 236 6 8 2503 2738 24587531 24587322 4.560000e-58 235
37 TraesCS3B01G107400 chrUn 86.441 236 6 8 2503 2738 24617393 24617184 4.560000e-58 235
38 TraesCS3B01G107400 chrUn 86.441 236 6 8 2503 2738 344622124 344621915 4.560000e-58 235
39 TraesCS3B01G107400 chrUn 86.441 236 6 8 2503 2738 344658487 344658278 4.560000e-58 235
40 TraesCS3B01G107400 chr4A 85.833 240 7 9 2500 2738 435445173 435444960 2.120000e-56 230
41 TraesCS3B01G107400 chr4B 83.544 237 13 9 2502 2738 462738600 462738390 5.980000e-47 198


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 TraesCS3B01G107400 chr3B 72922314 72925051 2737 False 5057.0 5057 100.0000 1 2738 1 chr3B.!!$F1 2737
1 TraesCS3B01G107400 chr3B 72715317 72717477 2160 False 1444.5 2017 91.4735 2 2305 2 chr3B.!!$F2 2303
2 TraesCS3B01G107400 chr3D 46524825 46527175 2350 False 1843.5 2715 95.0140 1 2494 2 chr3D.!!$F2 2493
3 TraesCS3B01G107400 chr3D 46485636 46487806 2170 False 1366.0 1893 90.0525 2 2305 2 chr3D.!!$F1 2303
4 TraesCS3B01G107400 chr3A 57980104 57981069 965 True 1604.0 1604 96.6870 775 1737 1 chr3A.!!$R2 962
5 TraesCS3B01G107400 chr3A 57904565 57906697 2132 False 1323.5 1775 89.9815 1 2305 2 chr3A.!!$F1 2304
6 TraesCS3B01G107400 chr3A 57967871 57968390 519 True 785.0 785 93.8810 1933 2454 1 chr3A.!!$R1 521
7 TraesCS3B01G107400 chr5A 143658343 143658944 601 True 477.0 477 81.1880 1062 1660 1 chr5A.!!$R1 598
8 TraesCS3B01G107400 chr5D 128642057 128642658 601 True 466.0 466 80.8580 1062 1660 1 chr5D.!!$R1 598
9 TraesCS3B01G107400 chr5B 141147573 141148174 601 True 466.0 466 80.8900 1062 1660 1 chr5B.!!$R1 598
10 TraesCS3B01G107400 chr6B 672461308 672461964 656 True 298.0 298 75.4490 1070 1718 1 chr6B.!!$R3 648
11 TraesCS3B01G107400 chr1B 4933241 4933876 635 True 261.0 261 74.8450 1072 1690 1 chr1B.!!$R1 618

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
623 652 1.270625 TGCAACAAAGTACTCCCTCCG 60.271 52.381 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2331 0.037697 TACTACGCACAGGCCAACAG 60.038 55.0 5.01 0.0 36.38 3.16 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
611 640 5.534278 TCTCCACATTATTGACTGCAACAAA 59.466 36.000 9.47 0.00 36.72 2.83
612 641 5.771469 TCCACATTATTGACTGCAACAAAG 58.229 37.500 9.47 4.41 36.72 2.77
613 642 5.301551 TCCACATTATTGACTGCAACAAAGT 59.698 36.000 9.47 0.00 36.72 2.66
614 643 6.488344 TCCACATTATTGACTGCAACAAAGTA 59.512 34.615 9.47 0.00 36.72 2.24
615 644 6.582295 CCACATTATTGACTGCAACAAAGTAC 59.418 38.462 9.47 0.00 36.72 2.73
616 645 7.362662 CACATTATTGACTGCAACAAAGTACT 58.637 34.615 9.47 0.00 36.72 2.73
617 646 7.535258 CACATTATTGACTGCAACAAAGTACTC 59.465 37.037 9.47 0.00 36.72 2.59
618 647 6.554334 TTATTGACTGCAACAAAGTACTCC 57.446 37.500 9.47 0.00 36.72 3.85
619 648 2.846193 TGACTGCAACAAAGTACTCCC 58.154 47.619 0.00 0.00 0.00 4.30
620 649 2.438021 TGACTGCAACAAAGTACTCCCT 59.562 45.455 0.00 0.00 0.00 4.20
621 650 3.067833 GACTGCAACAAAGTACTCCCTC 58.932 50.000 0.00 0.00 0.00 4.30
622 651 2.224548 ACTGCAACAAAGTACTCCCTCC 60.225 50.000 0.00 0.00 0.00 4.30
623 652 1.270625 TGCAACAAAGTACTCCCTCCG 60.271 52.381 0.00 0.00 0.00 4.63
624 653 1.270678 GCAACAAAGTACTCCCTCCGT 60.271 52.381 0.00 0.00 0.00 4.69
625 654 2.809299 GCAACAAAGTACTCCCTCCGTT 60.809 50.000 0.00 0.00 0.00 4.44
626 655 3.064931 CAACAAAGTACTCCCTCCGTTC 58.935 50.000 0.00 0.00 0.00 3.95
627 656 1.622312 ACAAAGTACTCCCTCCGTTCC 59.378 52.381 0.00 0.00 0.00 3.62
628 657 1.900486 CAAAGTACTCCCTCCGTTCCT 59.100 52.381 0.00 0.00 0.00 3.36
629 658 3.094572 CAAAGTACTCCCTCCGTTCCTA 58.905 50.000 0.00 0.00 0.00 2.94
630 659 3.463048 AAGTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
631 660 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
632 661 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
633 662 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
634 663 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
635 664 6.141790 AGTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
636 665 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
637 666 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
638 667 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
639 668 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
640 669 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
641 670 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
642 671 6.260271 CCCTCCGTTCCTAAATATTTGTCTTC 59.740 42.308 11.05 0.00 0.00 2.87
643 672 7.048512 CCTCCGTTCCTAAATATTTGTCTTCT 58.951 38.462 11.05 0.00 0.00 2.85
644 673 7.553044 CCTCCGTTCCTAAATATTTGTCTTCTT 59.447 37.037 11.05 0.00 0.00 2.52
645 674 9.595823 CTCCGTTCCTAAATATTTGTCTTCTTA 57.404 33.333 11.05 0.00 0.00 2.10
646 675 9.595823 TCCGTTCCTAAATATTTGTCTTCTTAG 57.404 33.333 11.05 0.00 0.00 2.18
647 676 9.595823 CCGTTCCTAAATATTTGTCTTCTTAGA 57.404 33.333 11.05 0.00 0.00 2.10
661 690 9.436957 TTGTCTTCTTAGAGATTGTAAATGGAC 57.563 33.333 0.00 0.00 0.00 4.02
662 691 8.816894 TGTCTTCTTAGAGATTGTAAATGGACT 58.183 33.333 0.00 0.00 0.00 3.85
667 696 8.198109 TCTTAGAGATTGTAAATGGACTACTGC 58.802 37.037 0.00 0.00 0.00 4.40
668 697 6.299805 AGAGATTGTAAATGGACTACTGCA 57.700 37.500 0.00 0.00 0.00 4.41
669 698 6.893583 AGAGATTGTAAATGGACTACTGCAT 58.106 36.000 0.00 0.00 0.00 3.96
670 699 8.023021 AGAGATTGTAAATGGACTACTGCATA 57.977 34.615 0.00 0.00 0.00 3.14
671 700 7.928706 AGAGATTGTAAATGGACTACTGCATAC 59.071 37.037 0.00 0.00 0.00 2.39
672 701 6.701841 AGATTGTAAATGGACTACTGCATACG 59.298 38.462 0.00 0.00 0.00 3.06
673 702 4.689071 TGTAAATGGACTACTGCATACGG 58.311 43.478 0.00 0.00 0.00 4.02
674 703 4.403113 TGTAAATGGACTACTGCATACGGA 59.597 41.667 0.00 0.00 0.00 4.69
675 704 4.689612 AAATGGACTACTGCATACGGAT 57.310 40.909 0.00 0.00 0.00 4.18
676 705 3.667497 ATGGACTACTGCATACGGATG 57.333 47.619 2.22 2.22 36.02 3.51
677 706 2.384828 TGGACTACTGCATACGGATGT 58.615 47.619 9.90 0.00 35.30 3.06
678 707 3.558033 TGGACTACTGCATACGGATGTA 58.442 45.455 9.90 3.37 35.30 2.29
679 708 4.149598 TGGACTACTGCATACGGATGTAT 58.850 43.478 9.90 0.00 42.03 2.29
680 709 5.318630 TGGACTACTGCATACGGATGTATA 58.681 41.667 9.90 0.00 39.28 1.47
681 710 5.949952 TGGACTACTGCATACGGATGTATAT 59.050 40.000 9.90 0.00 39.28 0.86
682 711 7.114095 TGGACTACTGCATACGGATGTATATA 58.886 38.462 9.90 0.00 39.28 0.86
683 712 7.282450 TGGACTACTGCATACGGATGTATATAG 59.718 40.741 9.90 11.67 39.28 1.31
684 713 7.498239 GGACTACTGCATACGGATGTATATAGA 59.502 40.741 18.28 0.00 39.28 1.98
685 714 8.211116 ACTACTGCATACGGATGTATATAGAC 57.789 38.462 18.28 0.00 39.28 2.59
686 715 7.827729 ACTACTGCATACGGATGTATATAGACA 59.172 37.037 18.28 2.07 39.28 3.41
687 716 7.646548 ACTGCATACGGATGTATATAGACAT 57.353 36.000 12.70 12.70 42.82 3.06
688 717 8.747538 ACTGCATACGGATGTATATAGACATA 57.252 34.615 12.82 0.00 40.18 2.29
689 718 9.355916 ACTGCATACGGATGTATATAGACATAT 57.644 33.333 12.82 5.08 40.18 1.78
707 736 8.430801 AGACATATTTTAGAGTGCAGATTCAC 57.569 34.615 0.00 0.00 37.24 3.18
716 745 4.170292 AGTGCAGATTCACTCATTTTGC 57.830 40.909 0.00 0.00 43.28 3.68
717 746 3.825014 AGTGCAGATTCACTCATTTTGCT 59.175 39.130 0.00 0.00 43.28 3.91
718 747 4.082895 AGTGCAGATTCACTCATTTTGCTC 60.083 41.667 0.00 0.00 43.28 4.26
719 748 3.192001 TGCAGATTCACTCATTTTGCTCC 59.808 43.478 0.00 0.00 0.00 4.70
720 749 3.730061 GCAGATTCACTCATTTTGCTCCG 60.730 47.826 0.00 0.00 0.00 4.63
721 750 3.438087 CAGATTCACTCATTTTGCTCCGT 59.562 43.478 0.00 0.00 0.00 4.69
722 751 4.631377 CAGATTCACTCATTTTGCTCCGTA 59.369 41.667 0.00 0.00 0.00 4.02
723 752 5.295292 CAGATTCACTCATTTTGCTCCGTAT 59.705 40.000 0.00 0.00 0.00 3.06
724 753 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
725 754 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
726 755 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
727 756 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
728 757 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
729 758 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
730 759 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
731 760 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
732 761 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
733 762 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
734 763 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
735 764 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
736 765 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
737 766 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
738 767 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
739 768 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
740 769 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
741 770 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
742 771 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
743 772 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
744 773 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
745 774 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
746 775 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
747 776 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
748 777 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
749 778 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
750 779 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
751 780 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
752 781 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
753 782 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
754 783 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
755 784 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
756 785 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
772 801 8.579863 AGAAAGACAAATATTTTGGAACAGAGG 58.420 33.333 0.00 0.00 42.39 3.69
773 802 6.840780 AGACAAATATTTTGGAACAGAGGG 57.159 37.500 0.00 0.00 42.39 4.30
1150 1180 6.883135 TTCGGGGTCTAAATGACAACGACC 62.883 50.000 11.41 0.00 46.68 4.79
1408 1453 0.388134 TCGTGTTCTCGTGCTAAGGC 60.388 55.000 0.00 0.00 39.26 4.35
1730 1782 5.736358 GCGAGCTAGAAAAATTGTTCATGAG 59.264 40.000 10.98 5.98 0.00 2.90
1744 1796 4.997395 TGTTCATGAGTTCTTAAGAGTGCC 59.003 41.667 5.12 0.00 0.00 5.01
1832 1885 0.815734 GTGCTGGCTCTGCATCAATT 59.184 50.000 9.30 0.00 40.15 2.32
1859 1912 1.728323 TGTCCCTGTCATCAACTCCA 58.272 50.000 0.00 0.00 0.00 3.86
1874 1941 6.288941 TCAACTCCATTATGTTTCTCCGTA 57.711 37.500 0.00 0.00 0.00 4.02
1891 1958 7.513371 TCTCCGTATTCTCCTTATCTTTCTC 57.487 40.000 0.00 0.00 0.00 2.87
1926 1994 2.582728 TTGACCTTTTGCTGCTGTTG 57.417 45.000 0.00 0.00 0.00 3.33
1930 1998 3.445450 TGACCTTTTGCTGCTGTTGTTTA 59.555 39.130 0.00 0.00 0.00 2.01
1939 2007 4.994852 TGCTGCTGTTGTTTACCTTAGTAG 59.005 41.667 0.00 0.00 0.00 2.57
1966 2036 1.452108 CTGCAGGGGATTTCGGACC 60.452 63.158 5.57 0.00 0.00 4.46
1974 2044 0.247185 GGATTTCGGACCGTGTACCA 59.753 55.000 14.79 0.00 0.00 3.25
2002 2072 6.633234 GCACTTTTCTTGCTCTTGTAGTTTAC 59.367 38.462 0.00 0.00 37.00 2.01
2007 2077 8.732746 TTTCTTGCTCTTGTAGTTTACTTTCT 57.267 30.769 0.00 0.00 0.00 2.52
2148 2218 2.668144 TAAGTGGTTTGGGGGACTTG 57.332 50.000 0.00 0.00 31.25 3.16
2250 2326 9.985730 AAAATCAACATTACATTGAGTTGTCAT 57.014 25.926 1.68 0.00 41.94 3.06
2255 2331 9.546909 CAACATTACATTGAGTTGTCATAGTTC 57.453 33.333 0.00 0.00 37.25 3.01
2316 2392 4.717991 TGTTTTGTTTCAGTTGAGACACG 58.282 39.130 5.12 0.00 38.63 4.49
2502 2579 9.908152 AATCGTTACAAAAGAAATTCTTTAGGG 57.092 29.630 19.83 14.68 45.19 3.53
2503 2580 8.454570 TCGTTACAAAAGAAATTCTTTAGGGT 57.545 30.769 19.83 18.65 45.19 4.34
2504 2581 8.347035 TCGTTACAAAAGAAATTCTTTAGGGTG 58.653 33.333 19.83 16.18 45.19 4.61
2505 2582 8.132995 CGTTACAAAAGAAATTCTTTAGGGTGT 58.867 33.333 19.83 20.17 45.19 4.16
2506 2583 9.244799 GTTACAAAAGAAATTCTTTAGGGTGTG 57.755 33.333 23.22 17.82 45.19 3.82
2507 2584 7.418337 ACAAAAGAAATTCTTTAGGGTGTGT 57.582 32.000 19.83 15.81 45.19 3.72
2508 2585 7.847096 ACAAAAGAAATTCTTTAGGGTGTGTT 58.153 30.769 19.83 0.15 45.19 3.32
2509 2586 8.318412 ACAAAAGAAATTCTTTAGGGTGTGTTT 58.682 29.630 19.83 0.00 45.19 2.83
2510 2587 8.603181 CAAAAGAAATTCTTTAGGGTGTGTTTG 58.397 33.333 19.83 7.94 45.19 2.93
2511 2588 7.654022 AAGAAATTCTTTAGGGTGTGTTTGA 57.346 32.000 1.80 0.00 31.57 2.69
2512 2589 7.039313 AGAAATTCTTTAGGGTGTGTTTGAC 57.961 36.000 0.00 0.00 0.00 3.18
2513 2590 6.605594 AGAAATTCTTTAGGGTGTGTTTGACA 59.394 34.615 0.00 0.00 0.00 3.58
2514 2591 6.391227 AATTCTTTAGGGTGTGTTTGACAG 57.609 37.500 0.00 0.00 34.28 3.51
2524 2601 5.871531 GTGTGTTTGACAGCAAAGTATTG 57.128 39.130 0.00 0.00 44.12 1.90
2549 2626 9.891828 TGCATAAACTGTAGTATTGAAAAACTG 57.108 29.630 0.00 0.00 0.00 3.16
2550 2627 8.850452 GCATAAACTGTAGTATTGAAAAACTGC 58.150 33.333 0.00 0.00 0.00 4.40
2551 2628 9.891828 CATAAACTGTAGTATTGAAAAACTGCA 57.108 29.630 2.85 2.85 36.21 4.41
2561 2638 9.816354 AGTATTGAAAAACTGCAGTATTTTTGT 57.184 25.926 26.23 19.61 37.96 2.83
2563 2640 8.947055 ATTGAAAAACTGCAGTATTTTTGTCT 57.053 26.923 26.23 9.13 37.96 3.41
2569 2646 8.863872 AAACTGCAGTATTTTTGTCTATAGGT 57.136 30.769 22.01 0.00 0.00 3.08
2570 2647 8.494016 AACTGCAGTATTTTTGTCTATAGGTC 57.506 34.615 22.01 0.00 0.00 3.85
2571 2648 7.048512 ACTGCAGTATTTTTGTCTATAGGTCC 58.951 38.462 20.16 0.00 0.00 4.46
2572 2649 7.092846 ACTGCAGTATTTTTGTCTATAGGTCCT 60.093 37.037 20.16 0.00 0.00 3.85
2573 2650 8.313944 TGCAGTATTTTTGTCTATAGGTCCTA 57.686 34.615 0.00 0.00 0.00 2.94
2574 2651 8.764558 TGCAGTATTTTTGTCTATAGGTCCTAA 58.235 33.333 1.78 0.00 0.00 2.69
2575 2652 9.609346 GCAGTATTTTTGTCTATAGGTCCTAAA 57.391 33.333 1.78 0.00 0.00 1.85
2580 2657 9.990868 ATTTTTGTCTATAGGTCCTAAAACCAT 57.009 29.630 1.78 0.00 42.12 3.55
2583 2660 8.849543 TTGTCTATAGGTCCTAAAACCATAGT 57.150 34.615 1.78 0.00 42.12 2.12
2584 2661 8.849543 TGTCTATAGGTCCTAAAACCATAGTT 57.150 34.615 1.78 0.00 42.12 2.24
2630 2707 4.568152 GCGGGTGCATATCAAAGTATTT 57.432 40.909 0.00 0.00 39.36 1.40
2631 2708 4.932146 GCGGGTGCATATCAAAGTATTTT 58.068 39.130 0.00 0.00 37.33 1.82
2632 2709 4.739716 GCGGGTGCATATCAAAGTATTTTG 59.260 41.667 4.40 4.40 42.01 2.44
2633 2710 5.678616 GCGGGTGCATATCAAAGTATTTTGT 60.679 40.000 10.15 1.91 41.69 2.83
2634 2711 6.459024 GCGGGTGCATATCAAAGTATTTTGTA 60.459 38.462 10.15 3.80 41.69 2.41
2635 2712 7.132213 CGGGTGCATATCAAAGTATTTTGTAG 58.868 38.462 10.15 1.75 43.33 2.74
2636 2713 7.201696 CGGGTGCATATCAAAGTATTTTGTAGT 60.202 37.037 10.15 2.13 43.33 2.73
2637 2714 9.116067 GGGTGCATATCAAAGTATTTTGTAGTA 57.884 33.333 10.15 3.96 43.33 1.82
2658 2735 4.640771 ATTGGGAATACTGTGACAGTGT 57.359 40.909 27.18 18.72 45.01 3.55
2659 2736 4.431416 TTGGGAATACTGTGACAGTGTT 57.569 40.909 27.18 25.80 45.71 3.32
2660 2737 4.431416 TGGGAATACTGTGACAGTGTTT 57.569 40.909 27.18 19.52 43.74 2.83
2661 2738 4.133820 TGGGAATACTGTGACAGTGTTTG 58.866 43.478 27.18 0.00 43.74 2.93
2662 2739 3.502211 GGGAATACTGTGACAGTGTTTGG 59.498 47.826 27.18 0.00 43.74 3.28
2663 2740 3.058224 GGAATACTGTGACAGTGTTTGGC 60.058 47.826 27.18 14.60 43.74 4.52
2664 2741 3.492102 ATACTGTGACAGTGTTTGGCT 57.508 42.857 27.18 0.77 45.01 4.75
2665 2742 1.382522 ACTGTGACAGTGTTTGGCTG 58.617 50.000 18.72 0.00 43.63 4.85
2666 2743 0.664761 CTGTGACAGTGTTTGGCTGG 59.335 55.000 4.01 0.00 38.22 4.85
2667 2744 0.034574 TGTGACAGTGTTTGGCTGGT 60.035 50.000 0.00 0.00 38.22 4.00
2668 2745 0.381801 GTGACAGTGTTTGGCTGGTG 59.618 55.000 0.00 0.00 38.22 4.17
2669 2746 1.360192 GACAGTGTTTGGCTGGTGC 59.640 57.895 0.00 0.00 38.22 5.01
2670 2747 1.379710 ACAGTGTTTGGCTGGTGCA 60.380 52.632 0.00 0.00 41.91 4.57
2671 2748 0.756442 ACAGTGTTTGGCTGGTGCAT 60.756 50.000 0.00 0.00 41.91 3.96
2672 2749 1.246649 CAGTGTTTGGCTGGTGCATA 58.753 50.000 0.00 0.00 41.91 3.14
2673 2750 1.820519 CAGTGTTTGGCTGGTGCATAT 59.179 47.619 0.00 0.00 41.91 1.78
2674 2751 2.231964 CAGTGTTTGGCTGGTGCATATT 59.768 45.455 0.00 0.00 41.91 1.28
2675 2752 2.899256 AGTGTTTGGCTGGTGCATATTT 59.101 40.909 0.00 0.00 41.91 1.40
2676 2753 4.082300 CAGTGTTTGGCTGGTGCATATTTA 60.082 41.667 0.00 0.00 41.91 1.40
2677 2754 4.158394 AGTGTTTGGCTGGTGCATATTTAG 59.842 41.667 0.00 0.00 41.91 1.85
2678 2755 3.446873 TGTTTGGCTGGTGCATATTTAGG 59.553 43.478 0.00 0.00 41.91 2.69
2679 2756 3.660970 TTGGCTGGTGCATATTTAGGA 57.339 42.857 0.00 0.00 41.91 2.94
2680 2757 2.930950 TGGCTGGTGCATATTTAGGAC 58.069 47.619 0.00 0.00 41.91 3.85
2681 2758 1.873591 GGCTGGTGCATATTTAGGACG 59.126 52.381 0.00 0.00 41.91 4.79
2682 2759 2.484770 GGCTGGTGCATATTTAGGACGA 60.485 50.000 0.00 0.00 41.91 4.20
2683 2760 3.403038 GCTGGTGCATATTTAGGACGAT 58.597 45.455 0.00 0.00 39.41 3.73
2684 2761 3.187227 GCTGGTGCATATTTAGGACGATG 59.813 47.826 0.00 0.00 39.41 3.84
2685 2762 4.380531 CTGGTGCATATTTAGGACGATGT 58.619 43.478 0.00 0.00 0.00 3.06
2686 2763 5.538118 CTGGTGCATATTTAGGACGATGTA 58.462 41.667 0.00 0.00 0.00 2.29
2687 2764 5.919755 TGGTGCATATTTAGGACGATGTAA 58.080 37.500 0.00 0.00 0.00 2.41
2688 2765 6.350103 TGGTGCATATTTAGGACGATGTAAA 58.650 36.000 0.00 0.00 0.00 2.01
2689 2766 6.995686 TGGTGCATATTTAGGACGATGTAAAT 59.004 34.615 0.00 0.00 34.13 1.40
2690 2767 7.500892 TGGTGCATATTTAGGACGATGTAAATT 59.499 33.333 0.00 0.00 32.39 1.82
2691 2768 8.995220 GGTGCATATTTAGGACGATGTAAATTA 58.005 33.333 0.00 0.00 32.39 1.40
2693 2770 8.717821 TGCATATTTAGGACGATGTAAATTAGC 58.282 33.333 0.00 4.06 32.39 3.09
2694 2771 8.936864 GCATATTTAGGACGATGTAAATTAGCT 58.063 33.333 0.00 0.00 32.39 3.32
2697 2774 7.941795 TTTAGGACGATGTAAATTAGCTAGC 57.058 36.000 6.62 6.62 0.00 3.42
2698 2775 5.793030 AGGACGATGTAAATTAGCTAGCT 57.207 39.130 23.12 23.12 0.00 3.32
2699 2776 6.896021 AGGACGATGTAAATTAGCTAGCTA 57.104 37.500 20.67 20.67 0.00 3.32
2700 2777 6.915349 AGGACGATGTAAATTAGCTAGCTAG 58.085 40.000 23.03 16.84 0.00 3.42
2712 2789 2.062519 GCTAGCTAGCCGTTTCATAGC 58.937 52.381 31.67 12.31 43.39 2.97
2713 2790 2.545952 GCTAGCTAGCCGTTTCATAGCA 60.546 50.000 31.67 0.00 43.49 3.49
2714 2791 2.231215 AGCTAGCCGTTTCATAGCAG 57.769 50.000 12.13 0.00 43.49 4.24
2715 2792 1.482593 AGCTAGCCGTTTCATAGCAGT 59.517 47.619 12.13 0.00 43.49 4.40
2716 2793 1.861575 GCTAGCCGTTTCATAGCAGTC 59.138 52.381 2.29 0.00 41.25 3.51
2717 2794 2.120232 CTAGCCGTTTCATAGCAGTCG 58.880 52.381 0.00 0.00 0.00 4.18
2718 2795 1.084370 AGCCGTTTCATAGCAGTCGC 61.084 55.000 0.00 0.00 38.99 5.19
2719 2796 1.358725 GCCGTTTCATAGCAGTCGCA 61.359 55.000 0.00 0.00 42.27 5.10
2720 2797 1.075542 CCGTTTCATAGCAGTCGCAA 58.924 50.000 0.00 0.00 42.27 4.85
2721 2798 1.061131 CCGTTTCATAGCAGTCGCAAG 59.939 52.381 0.00 0.00 42.27 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 39 8.973182 GGGCTATAAGATCACTTTAGCTATAGT 58.027 37.037 10.68 10.68 39.56 2.12
300 329 2.803155 AATCGGGTGCACAGCGATGT 62.803 55.000 20.43 0.00 0.00 3.06
611 640 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
612 641 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
613 642 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
614 643 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
615 644 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
616 645 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
617 646 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
618 647 7.048512 AGAAGACAAATATTTAGGAACGGAGG 58.951 38.462 0.00 0.00 0.00 4.30
619 648 8.494016 AAGAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
620 649 9.595823 CTAAGAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
621 650 9.595823 TCTAAGAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
635 664 9.436957 GTCCATTTACAATCTCTAAGAAGACAA 57.563 33.333 0.00 0.00 0.00 3.18
636 665 8.816894 AGTCCATTTACAATCTCTAAGAAGACA 58.183 33.333 0.00 0.00 0.00 3.41
641 670 8.198109 GCAGTAGTCCATTTACAATCTCTAAGA 58.802 37.037 0.00 0.00 0.00 2.10
642 671 7.981789 TGCAGTAGTCCATTTACAATCTCTAAG 59.018 37.037 0.00 0.00 0.00 2.18
643 672 7.847096 TGCAGTAGTCCATTTACAATCTCTAA 58.153 34.615 0.00 0.00 0.00 2.10
644 673 7.418337 TGCAGTAGTCCATTTACAATCTCTA 57.582 36.000 0.00 0.00 0.00 2.43
645 674 6.299805 TGCAGTAGTCCATTTACAATCTCT 57.700 37.500 0.00 0.00 0.00 3.10
646 675 7.096023 CGTATGCAGTAGTCCATTTACAATCTC 60.096 40.741 0.00 0.00 0.00 2.75
647 676 6.701841 CGTATGCAGTAGTCCATTTACAATCT 59.298 38.462 0.00 0.00 0.00 2.40
648 677 6.073765 CCGTATGCAGTAGTCCATTTACAATC 60.074 42.308 0.00 0.00 0.00 2.67
649 678 5.758296 CCGTATGCAGTAGTCCATTTACAAT 59.242 40.000 0.00 0.00 0.00 2.71
650 679 5.105269 TCCGTATGCAGTAGTCCATTTACAA 60.105 40.000 0.00 0.00 0.00 2.41
651 680 4.403113 TCCGTATGCAGTAGTCCATTTACA 59.597 41.667 0.00 0.00 0.00 2.41
652 681 4.940463 TCCGTATGCAGTAGTCCATTTAC 58.060 43.478 0.00 0.00 0.00 2.01
653 682 5.069914 ACATCCGTATGCAGTAGTCCATTTA 59.930 40.000 0.00 0.00 36.50 1.40
654 683 4.141711 ACATCCGTATGCAGTAGTCCATTT 60.142 41.667 0.00 0.00 36.50 2.32
655 684 3.388024 ACATCCGTATGCAGTAGTCCATT 59.612 43.478 0.00 0.00 36.50 3.16
656 685 2.965831 ACATCCGTATGCAGTAGTCCAT 59.034 45.455 0.00 0.00 36.50 3.41
657 686 2.384828 ACATCCGTATGCAGTAGTCCA 58.615 47.619 0.00 0.00 36.50 4.02
658 687 4.785511 ATACATCCGTATGCAGTAGTCC 57.214 45.455 0.00 0.00 36.94 3.85
659 688 8.336806 GTCTATATACATCCGTATGCAGTAGTC 58.663 40.741 0.00 0.00 38.79 2.59
660 689 7.827729 TGTCTATATACATCCGTATGCAGTAGT 59.172 37.037 0.00 0.00 38.79 2.73
661 690 8.209917 TGTCTATATACATCCGTATGCAGTAG 57.790 38.462 0.00 0.00 38.79 2.57
662 691 8.747538 ATGTCTATATACATCCGTATGCAGTA 57.252 34.615 0.00 0.00 38.79 2.74
663 692 7.646548 ATGTCTATATACATCCGTATGCAGT 57.353 36.000 0.00 0.00 38.79 4.40
681 710 9.534565 GTGAATCTGCACTCTAAAATATGTCTA 57.465 33.333 0.00 0.00 35.91 2.59
682 711 8.263640 AGTGAATCTGCACTCTAAAATATGTCT 58.736 33.333 0.00 0.00 45.54 3.41
683 712 8.430801 AGTGAATCTGCACTCTAAAATATGTC 57.569 34.615 0.00 0.00 45.54 3.06
696 725 4.164294 GAGCAAAATGAGTGAATCTGCAC 58.836 43.478 0.00 0.00 39.05 4.57
697 726 3.192001 GGAGCAAAATGAGTGAATCTGCA 59.808 43.478 0.00 0.00 0.00 4.41
698 727 3.730061 CGGAGCAAAATGAGTGAATCTGC 60.730 47.826 0.00 0.00 0.00 4.26
699 728 3.438087 ACGGAGCAAAATGAGTGAATCTG 59.562 43.478 0.00 0.00 0.00 2.90
700 729 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
701 730 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
702 731 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
703 732 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
704 733 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
705 734 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
706 735 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
707 736 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
708 737 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
709 738 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
710 739 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
711 740 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
712 741 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
713 742 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
714 743 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
715 744 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
716 745 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
717 746 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
718 747 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
719 748 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
720 749 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
722 751 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
723 752 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
724 753 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
725 754 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
726 755 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
727 756 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
728 757 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
729 758 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
730 759 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
746 775 8.579863 CCTCTGTTCCAAAATATTTGTCTTTCT 58.420 33.333 0.39 0.00 0.00 2.52
747 776 7.814587 CCCTCTGTTCCAAAATATTTGTCTTTC 59.185 37.037 0.39 0.00 0.00 2.62
748 777 7.508977 TCCCTCTGTTCCAAAATATTTGTCTTT 59.491 33.333 0.39 0.00 0.00 2.52
749 778 7.010160 TCCCTCTGTTCCAAAATATTTGTCTT 58.990 34.615 0.39 0.00 0.00 3.01
750 779 6.552008 TCCCTCTGTTCCAAAATATTTGTCT 58.448 36.000 0.39 0.00 0.00 3.41
751 780 6.434340 ACTCCCTCTGTTCCAAAATATTTGTC 59.566 38.462 0.39 0.00 0.00 3.18
752 781 6.314917 ACTCCCTCTGTTCCAAAATATTTGT 58.685 36.000 0.39 0.00 0.00 2.83
753 782 6.840780 ACTCCCTCTGTTCCAAAATATTTG 57.159 37.500 0.39 0.00 0.00 2.32
754 783 7.119387 CCTACTCCCTCTGTTCCAAAATATTT 58.881 38.462 0.00 0.00 0.00 1.40
755 784 6.217693 ACCTACTCCCTCTGTTCCAAAATATT 59.782 38.462 0.00 0.00 0.00 1.28
756 785 5.731678 ACCTACTCCCTCTGTTCCAAAATAT 59.268 40.000 0.00 0.00 0.00 1.28
757 786 5.098663 ACCTACTCCCTCTGTTCCAAAATA 58.901 41.667 0.00 0.00 0.00 1.40
758 787 3.916989 ACCTACTCCCTCTGTTCCAAAAT 59.083 43.478 0.00 0.00 0.00 1.82
759 788 3.323775 ACCTACTCCCTCTGTTCCAAAA 58.676 45.455 0.00 0.00 0.00 2.44
760 789 2.986050 ACCTACTCCCTCTGTTCCAAA 58.014 47.619 0.00 0.00 0.00 3.28
761 790 2.715763 ACCTACTCCCTCTGTTCCAA 57.284 50.000 0.00 0.00 0.00 3.53
762 791 2.623502 GCTACCTACTCCCTCTGTTCCA 60.624 54.545 0.00 0.00 0.00 3.53
763 792 2.033372 GCTACCTACTCCCTCTGTTCC 58.967 57.143 0.00 0.00 0.00 3.62
764 793 2.736347 TGCTACCTACTCCCTCTGTTC 58.264 52.381 0.00 0.00 0.00 3.18
765 794 2.921834 TGCTACCTACTCCCTCTGTT 57.078 50.000 0.00 0.00 0.00 3.16
766 795 2.921834 TTGCTACCTACTCCCTCTGT 57.078 50.000 0.00 0.00 0.00 3.41
767 796 3.366396 TCTTTGCTACCTACTCCCTCTG 58.634 50.000 0.00 0.00 0.00 3.35
768 797 3.759815 TCTTTGCTACCTACTCCCTCT 57.240 47.619 0.00 0.00 0.00 3.69
769 798 4.443598 CCAATCTTTGCTACCTACTCCCTC 60.444 50.000 0.00 0.00 0.00 4.30
770 799 3.456277 CCAATCTTTGCTACCTACTCCCT 59.544 47.826 0.00 0.00 0.00 4.20
771 800 3.200165 ACCAATCTTTGCTACCTACTCCC 59.800 47.826 0.00 0.00 0.00 4.30
772 801 4.489306 ACCAATCTTTGCTACCTACTCC 57.511 45.455 0.00 0.00 0.00 3.85
773 802 4.636206 CCAACCAATCTTTGCTACCTACTC 59.364 45.833 0.00 0.00 0.00 2.59
1150 1180 3.502595 CAGCTCTGGGATAATGCAATCAG 59.497 47.826 0.00 0.00 0.00 2.90
1408 1453 2.095969 TGTCATTAAAGAAGTTGGCGCG 60.096 45.455 0.00 0.00 0.00 6.86
1730 1782 3.994392 TCATCAACGGCACTCTTAAGAAC 59.006 43.478 6.63 0.00 0.00 3.01
1737 1789 1.609061 CCACTTCATCAACGGCACTCT 60.609 52.381 0.00 0.00 0.00 3.24
1738 1790 0.798776 CCACTTCATCAACGGCACTC 59.201 55.000 0.00 0.00 0.00 3.51
1739 1791 1.237285 GCCACTTCATCAACGGCACT 61.237 55.000 0.00 0.00 42.50 4.40
1744 1796 0.321564 TGGAGGCCACTTCATCAACG 60.322 55.000 5.01 0.00 0.00 4.10
1832 1885 3.449918 TGATGACAGGGACATCCAACTA 58.550 45.455 0.00 0.00 42.11 2.24
1859 1912 9.930693 GATAAGGAGAATACGGAGAAACATAAT 57.069 33.333 0.00 0.00 0.00 1.28
1926 1994 6.508777 CAGATGCTCTCCTACTAAGGTAAAC 58.491 44.000 0.00 0.00 44.09 2.01
1930 1998 2.962421 GCAGATGCTCTCCTACTAAGGT 59.038 50.000 0.00 0.00 40.02 3.50
1939 2007 1.417288 ATCCCCTGCAGATGCTCTCC 61.417 60.000 17.39 0.00 42.66 3.71
1966 2036 2.210116 AGAAAAGTGCACTGGTACACG 58.790 47.619 22.49 0.00 41.72 4.49
1974 2044 3.019564 ACAAGAGCAAGAAAAGTGCACT 58.980 40.909 15.25 15.25 43.53 4.40
2002 2072 4.214119 TCGGAAACATCAAGCTGAAGAAAG 59.786 41.667 0.00 0.00 0.00 2.62
2007 2077 5.009510 TGAATTTCGGAAACATCAAGCTGAA 59.990 36.000 14.79 0.00 0.00 3.02
2148 2218 9.390795 TCACGAGAAAAATATATAGAAGTACGC 57.609 33.333 0.00 0.00 0.00 4.42
2250 2326 0.602638 CGCACAGGCCAACAGAACTA 60.603 55.000 5.01 0.00 36.38 2.24
2255 2331 0.037697 TACTACGCACAGGCCAACAG 60.038 55.000 5.01 0.00 36.38 3.16
2490 2567 6.682861 GCTGTCAAACACACCCTAAAGAATTT 60.683 38.462 0.00 0.00 43.42 1.82
2493 2570 3.630312 GCTGTCAAACACACCCTAAAGAA 59.370 43.478 0.00 0.00 0.00 2.52
2495 2572 2.948979 TGCTGTCAAACACACCCTAAAG 59.051 45.455 0.00 0.00 0.00 1.85
2496 2573 3.006112 TGCTGTCAAACACACCCTAAA 57.994 42.857 0.00 0.00 0.00 1.85
2497 2574 2.719531 TGCTGTCAAACACACCCTAA 57.280 45.000 0.00 0.00 0.00 2.69
2498 2575 2.719531 TTGCTGTCAAACACACCCTA 57.280 45.000 0.00 0.00 0.00 3.53
2499 2576 1.750778 CTTTGCTGTCAAACACACCCT 59.249 47.619 0.00 0.00 37.28 4.34
2500 2577 1.476488 ACTTTGCTGTCAAACACACCC 59.524 47.619 0.00 0.00 37.28 4.61
2501 2578 2.939460 ACTTTGCTGTCAAACACACC 57.061 45.000 0.00 0.00 37.28 4.16
2502 2579 5.871531 CAATACTTTGCTGTCAAACACAC 57.128 39.130 0.00 0.00 37.28 3.82
2523 2600 9.891828 CAGTTTTTCAATACTACAGTTTATGCA 57.108 29.630 0.00 0.00 0.00 3.96
2524 2601 8.850452 GCAGTTTTTCAATACTACAGTTTATGC 58.150 33.333 0.00 0.00 0.00 3.14
2525 2602 9.891828 TGCAGTTTTTCAATACTACAGTTTATG 57.108 29.630 0.00 0.00 0.00 1.90
2527 2604 9.116067 ACTGCAGTTTTTCAATACTACAGTTTA 57.884 29.630 15.25 0.00 43.18 2.01
2528 2605 7.996385 ACTGCAGTTTTTCAATACTACAGTTT 58.004 30.769 15.25 0.00 43.18 2.66
2529 2606 7.568199 ACTGCAGTTTTTCAATACTACAGTT 57.432 32.000 15.25 0.00 43.18 3.16
2530 2607 8.848474 ATACTGCAGTTTTTCAATACTACAGT 57.152 30.769 27.06 15.87 45.91 3.55
2535 2612 9.816354 ACAAAAATACTGCAGTTTTTCAATACT 57.184 25.926 28.05 13.84 35.87 2.12
2538 2615 8.947055 AGACAAAAATACTGCAGTTTTTCAAT 57.053 26.923 28.05 18.67 35.87 2.57
2543 2620 9.297037 ACCTATAGACAAAAATACTGCAGTTTT 57.703 29.630 27.06 20.78 34.88 2.43
2544 2621 8.863872 ACCTATAGACAAAAATACTGCAGTTT 57.136 30.769 27.06 15.21 0.00 2.66
2545 2622 7.553044 GGACCTATAGACAAAAATACTGCAGTT 59.447 37.037 27.06 10.22 0.00 3.16
2546 2623 7.048512 GGACCTATAGACAAAAATACTGCAGT 58.951 38.462 25.12 25.12 0.00 4.40
2547 2624 7.275920 AGGACCTATAGACAAAAATACTGCAG 58.724 38.462 13.48 13.48 0.00 4.41
2548 2625 7.195374 AGGACCTATAGACAAAAATACTGCA 57.805 36.000 0.00 0.00 0.00 4.41
2549 2626 9.609346 TTTAGGACCTATAGACAAAAATACTGC 57.391 33.333 0.94 0.00 0.00 4.40
2554 2631 9.990868 ATGGTTTTAGGACCTATAGACAAAAAT 57.009 29.630 0.94 0.00 40.47 1.82
2557 2634 9.275572 ACTATGGTTTTAGGACCTATAGACAAA 57.724 33.333 11.95 3.23 40.47 2.83
2558 2635 8.849543 ACTATGGTTTTAGGACCTATAGACAA 57.150 34.615 11.95 2.50 40.47 3.18
2559 2636 8.849543 AACTATGGTTTTAGGACCTATAGACA 57.150 34.615 11.95 6.84 40.47 3.41
2609 2686 4.568152 AAATACTTTGATATGCACCCGC 57.432 40.909 0.00 0.00 39.24 6.13
2610 2687 5.890334 ACAAAATACTTTGATATGCACCCG 58.110 37.500 3.24 0.00 44.03 5.28
2611 2688 7.996385 ACTACAAAATACTTTGATATGCACCC 58.004 34.615 3.24 0.00 44.03 4.61
2635 2712 5.488341 ACACTGTCACAGTATTCCCAATAC 58.512 41.667 10.98 0.00 43.43 1.89
2636 2713 5.755409 ACACTGTCACAGTATTCCCAATA 57.245 39.130 10.98 0.00 43.43 1.90
2637 2714 4.640771 ACACTGTCACAGTATTCCCAAT 57.359 40.909 10.98 0.00 43.43 3.16
2638 2715 4.431416 AACACTGTCACAGTATTCCCAA 57.569 40.909 10.98 0.00 43.43 4.12
2639 2716 4.133820 CAAACACTGTCACAGTATTCCCA 58.866 43.478 10.98 0.00 43.43 4.37
2640 2717 3.502211 CCAAACACTGTCACAGTATTCCC 59.498 47.826 10.98 0.00 43.43 3.97
2641 2718 3.058224 GCCAAACACTGTCACAGTATTCC 60.058 47.826 10.98 0.00 43.43 3.01
2642 2719 3.815401 AGCCAAACACTGTCACAGTATTC 59.185 43.478 10.98 0.00 43.43 1.75
2643 2720 3.565482 CAGCCAAACACTGTCACAGTATT 59.435 43.478 10.98 1.86 43.43 1.89
2644 2721 3.141398 CAGCCAAACACTGTCACAGTAT 58.859 45.455 10.98 0.00 43.43 2.12
2645 2722 2.560504 CAGCCAAACACTGTCACAGTA 58.439 47.619 10.98 0.00 43.43 2.74
2646 2723 1.382522 CAGCCAAACACTGTCACAGT 58.617 50.000 3.98 3.98 46.51 3.55
2647 2724 0.664761 CCAGCCAAACACTGTCACAG 59.335 55.000 2.22 2.22 37.52 3.66
2648 2725 0.034574 ACCAGCCAAACACTGTCACA 60.035 50.000 0.00 0.00 33.09 3.58
2649 2726 0.381801 CACCAGCCAAACACTGTCAC 59.618 55.000 0.00 0.00 33.09 3.67
2650 2727 1.383456 GCACCAGCCAAACACTGTCA 61.383 55.000 0.00 0.00 33.09 3.58
2651 2728 1.360192 GCACCAGCCAAACACTGTC 59.640 57.895 0.00 0.00 33.09 3.51
2652 2729 0.756442 ATGCACCAGCCAAACACTGT 60.756 50.000 0.00 0.00 41.13 3.55
2653 2730 1.246649 TATGCACCAGCCAAACACTG 58.753 50.000 0.00 0.00 41.13 3.66
2654 2731 2.220653 ATATGCACCAGCCAAACACT 57.779 45.000 0.00 0.00 41.13 3.55
2655 2732 3.317603 AAATATGCACCAGCCAAACAC 57.682 42.857 0.00 0.00 41.13 3.32
2656 2733 3.446873 CCTAAATATGCACCAGCCAAACA 59.553 43.478 0.00 0.00 41.13 2.83
2657 2734 3.699038 TCCTAAATATGCACCAGCCAAAC 59.301 43.478 0.00 0.00 41.13 2.93
2658 2735 3.699038 GTCCTAAATATGCACCAGCCAAA 59.301 43.478 0.00 0.00 41.13 3.28
2659 2736 3.287222 GTCCTAAATATGCACCAGCCAA 58.713 45.455 0.00 0.00 41.13 4.52
2660 2737 2.744823 CGTCCTAAATATGCACCAGCCA 60.745 50.000 0.00 0.00 41.13 4.75
2661 2738 1.873591 CGTCCTAAATATGCACCAGCC 59.126 52.381 0.00 0.00 41.13 4.85
2662 2739 2.833794 TCGTCCTAAATATGCACCAGC 58.166 47.619 0.00 0.00 42.57 4.85
2663 2740 4.380531 ACATCGTCCTAAATATGCACCAG 58.619 43.478 0.00 0.00 0.00 4.00
2664 2741 4.415881 ACATCGTCCTAAATATGCACCA 57.584 40.909 0.00 0.00 0.00 4.17
2665 2742 6.854496 TTTACATCGTCCTAAATATGCACC 57.146 37.500 0.00 0.00 0.00 5.01
2667 2744 8.717821 GCTAATTTACATCGTCCTAAATATGCA 58.282 33.333 0.00 0.00 0.00 3.96
2668 2745 8.936864 AGCTAATTTACATCGTCCTAAATATGC 58.063 33.333 0.00 0.00 0.00 3.14
2671 2748 9.635520 GCTAGCTAATTTACATCGTCCTAAATA 57.364 33.333 7.70 0.00 0.00 1.40
2672 2749 8.368668 AGCTAGCTAATTTACATCGTCCTAAAT 58.631 33.333 17.69 0.00 0.00 1.40
2673 2750 7.723324 AGCTAGCTAATTTACATCGTCCTAAA 58.277 34.615 17.69 0.00 0.00 1.85
2674 2751 7.286215 AGCTAGCTAATTTACATCGTCCTAA 57.714 36.000 17.69 0.00 0.00 2.69
2675 2752 6.896021 AGCTAGCTAATTTACATCGTCCTA 57.104 37.500 17.69 0.00 0.00 2.94
2676 2753 5.793030 AGCTAGCTAATTTACATCGTCCT 57.207 39.130 17.69 0.00 0.00 3.85
2677 2754 5.573669 GCTAGCTAGCTAATTTACATCGTCC 59.426 44.000 33.71 3.16 45.62 4.79
2678 2755 6.620253 GCTAGCTAGCTAATTTACATCGTC 57.380 41.667 33.71 3.53 45.62 4.20
2693 2770 3.243569 ACTGCTATGAAACGGCTAGCTAG 60.244 47.826 16.84 16.84 38.89 3.42
2694 2771 2.693591 ACTGCTATGAAACGGCTAGCTA 59.306 45.455 15.72 0.00 38.89 3.32
2695 2772 1.482593 ACTGCTATGAAACGGCTAGCT 59.517 47.619 15.72 0.00 38.89 3.32
2696 2773 1.861575 GACTGCTATGAAACGGCTAGC 59.138 52.381 6.04 6.04 38.65 3.42
2697 2774 2.120232 CGACTGCTATGAAACGGCTAG 58.880 52.381 0.00 0.00 0.00 3.42
2698 2775 1.801395 GCGACTGCTATGAAACGGCTA 60.801 52.381 0.00 0.00 38.39 3.93
2699 2776 1.084370 GCGACTGCTATGAAACGGCT 61.084 55.000 0.00 0.00 38.39 5.52
2700 2777 1.348594 GCGACTGCTATGAAACGGC 59.651 57.895 0.00 0.00 38.39 5.68
2701 2778 1.061131 CTTGCGACTGCTATGAAACGG 59.939 52.381 0.00 0.00 43.34 4.44
2702 2779 1.992667 TCTTGCGACTGCTATGAAACG 59.007 47.619 0.00 0.00 43.34 3.60
2703 2780 2.736721 TGTCTTGCGACTGCTATGAAAC 59.263 45.455 0.00 0.00 43.34 2.78
2704 2781 3.038788 TGTCTTGCGACTGCTATGAAA 57.961 42.857 0.00 0.00 43.34 2.69
2705 2782 2.741759 TGTCTTGCGACTGCTATGAA 57.258 45.000 0.00 0.00 43.34 2.57
2706 2783 2.543641 CATGTCTTGCGACTGCTATGA 58.456 47.619 0.00 0.00 43.34 2.15
2707 2784 1.004185 GCATGTCTTGCGACTGCTATG 60.004 52.381 0.00 0.00 42.54 2.23
2708 2785 1.293924 GCATGTCTTGCGACTGCTAT 58.706 50.000 0.00 0.00 42.54 2.97
2709 2786 2.754648 GCATGTCTTGCGACTGCTA 58.245 52.632 0.00 0.00 42.54 3.49
2710 2787 3.571119 GCATGTCTTGCGACTGCT 58.429 55.556 0.00 0.00 42.54 4.24


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

AutoCloner maintained by Alex Coulton.