Multiple sequence alignment - TraesCS1D01G408300

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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 TraesCS1D01G408300 chr1D 100.000 4721 0 0 1 4721 470732957 470728237 0.000000e+00 8719.0
1 TraesCS1D01G408300 chr1B 91.390 2532 153 35 1339 3825 654029584 654027073 0.000000e+00 3408.0
2 TraesCS1D01G408300 chr1B 94.361 532 26 2 1 528 654030737 654030206 0.000000e+00 813.0
3 TraesCS1D01G408300 chr1B 89.773 528 34 8 744 1266 654030090 654029578 0.000000e+00 658.0
4 TraesCS1D01G408300 chr1B 89.871 464 39 4 4128 4589 654027074 654026617 1.460000e-164 590.0
5 TraesCS1D01G408300 chr1B 89.643 280 27 1 4310 4589 654021560 654021283 5.810000e-94 355.0
6 TraesCS1D01G408300 chr1B 92.381 210 13 2 4114 4323 654022955 654022749 3.570000e-76 296.0
7 TraesCS1D01G408300 chr1B 85.000 80 6 2 3093 3166 356207770 356207691 5.070000e-10 76.8
8 TraesCS1D01G408300 chr1B 91.667 48 4 0 4674 4721 654026403 654026356 3.050000e-07 67.6
9 TraesCS1D01G408300 chr1A 90.257 1283 90 18 1840 3094 564394486 564393211 0.000000e+00 1644.0
10 TraesCS1D01G408300 chr1A 90.208 817 43 11 776 1591 564395653 564394873 0.000000e+00 1031.0
11 TraesCS1D01G408300 chr1A 86.610 941 78 22 3183 4087 564393192 564392264 0.000000e+00 996.0
12 TraesCS1D01G408300 chr1A 89.513 677 52 10 1 661 564396316 564395643 0.000000e+00 839.0
13 TraesCS1D01G408300 chr1A 94.388 392 19 2 4112 4502 564392185 564391796 2.430000e-167 599.0
14 TraesCS1D01G408300 chr1A 94.500 200 11 0 1657 1856 564394721 564394522 4.590000e-80 309.0
15 TraesCS1D01G408300 chr1A 94.886 176 9 0 4546 4721 564391798 564391623 4.650000e-70 276.0
16 TraesCS1D01G408300 chr1A 83.908 87 7 3 3093 3172 330766856 330766942 5.070000e-10 76.8
17 TraesCS1D01G408300 chr3B 92.436 780 52 5 1319 2093 16303250 16302473 0.000000e+00 1107.0
18 TraesCS1D01G408300 chr3B 87.321 489 46 10 2200 2677 763523923 763523440 3.210000e-151 545.0
19 TraesCS1D01G408300 chr3B 88.776 392 30 11 1646 2028 763525158 763524772 7.150000e-128 468.0
20 TraesCS1D01G408300 chr3B 85.185 297 18 17 1802 2093 196142885 196143160 1.000000e-71 281.0
21 TraesCS1D01G408300 chr3B 87.919 149 18 0 1245 1393 763531062 763530914 4.860000e-40 176.0
22 TraesCS1D01G408300 chr3B 89.157 83 8 1 4588 4669 559321944 559322026 8.360000e-18 102.0
23 TraesCS1D01G408300 chr7B 92.011 701 49 5 1400 2095 176807247 176806549 0.000000e+00 977.0
24 TraesCS1D01G408300 chr2A 92.235 528 41 0 1319 1846 83249848 83250375 0.000000e+00 749.0
25 TraesCS1D01G408300 chr2A 92.857 42 3 0 4680 4721 496452659 496452700 1.420000e-05 62.1
26 TraesCS1D01G408300 chrUn 87.588 427 38 13 1622 2036 287140110 287139687 9.190000e-132 481.0
27 TraesCS1D01G408300 chrUn 87.588 427 38 13 1622 2036 287146278 287145855 9.190000e-132 481.0
28 TraesCS1D01G408300 chrUn 87.588 427 38 13 1622 2036 293606687 293607110 9.190000e-132 481.0
29 TraesCS1D01G408300 chrUn 92.593 54 4 0 1245 1298 287140620 287140567 1.410000e-10 78.7
30 TraesCS1D01G408300 chrUn 92.593 54 4 0 1245 1298 287146788 287146735 1.410000e-10 78.7
31 TraesCS1D01G408300 chrUn 94.118 51 3 0 1245 1295 293606177 293606227 1.410000e-10 78.7
32 TraesCS1D01G408300 chr5B 91.139 79 7 0 4586 4664 679802597 679802519 1.800000e-19 108.0
33 TraesCS1D01G408300 chr4B 91.026 78 7 0 4587 4664 575046335 575046258 6.460000e-19 106.0
34 TraesCS1D01G408300 chr2D 89.744 78 8 0 4587 4664 643817475 643817552 3.010000e-17 100.0
35 TraesCS1D01G408300 chr5D 89.744 78 5 1 4587 4664 285841514 285841440 3.890000e-16 97.1
36 TraesCS1D01G408300 chr5D 81.443 97 9 7 3093 3181 319689949 319690044 2.360000e-08 71.3
37 TraesCS1D01G408300 chr3D 90.411 73 7 0 4592 4664 3219217 3219145 3.890000e-16 97.1
38 TraesCS1D01G408300 chr3D 89.041 73 7 1 4592 4664 64766258 64766187 6.510000e-14 89.8
39 TraesCS1D01G408300 chr3A 87.342 79 9 1 4592 4669 7797164 7797086 6.510000e-14 89.8
40 TraesCS1D01G408300 chr3A 82.418 91 8 4 3089 3172 437863466 437863555 6.550000e-09 73.1
41 TraesCS1D01G408300 chr7A 84.270 89 8 2 3093 3175 632520644 632520556 1.090000e-11 82.4
42 TraesCS1D01G408300 chr4A 83.908 87 6 6 3093 3172 714207167 714207252 5.070000e-10 76.8
43 TraesCS1D01G408300 chr4A 100.000 29 0 0 4198 4226 164727687 164727659 2.000000e-03 54.7
44 TraesCS1D01G408300 chr6A 82.759 87 8 5 3092 3172 115022795 115022880 2.360000e-08 71.3
45 TraesCS1D01G408300 chr6A 91.667 48 4 0 4674 4721 572014404 572014357 3.050000e-07 67.6
46 TraesCS1D01G408300 chr6A 100.000 29 0 0 4198 4226 577698823 577698795 2.000000e-03 54.7
47 TraesCS1D01G408300 chr5A 82.022 89 10 4 3093 3175 465105953 465105865 2.360000e-08 71.3
48 TraesCS1D01G408300 chr2B 100.000 29 0 0 4198 4226 579959362 579959334 2.000000e-03 54.7


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 TraesCS1D01G408300 chr1D 470728237 470732957 4720 True 8719.000000 8719 100.000000 1 4721 1 chr1D.!!$R1 4720
1 TraesCS1D01G408300 chr1B 654021283 654030737 9454 True 883.942857 3408 91.298000 1 4721 7 chr1B.!!$R2 4720
2 TraesCS1D01G408300 chr1A 564391623 564396316 4693 True 813.428571 1644 91.480286 1 4721 7 chr1A.!!$R1 4720
3 TraesCS1D01G408300 chr3B 16302473 16303250 777 True 1107.000000 1107 92.436000 1319 2093 1 chr3B.!!$R1 774
4 TraesCS1D01G408300 chr3B 763523440 763525158 1718 True 506.500000 545 88.048500 1646 2677 2 chr3B.!!$R3 1031
5 TraesCS1D01G408300 chr7B 176806549 176807247 698 True 977.000000 977 92.011000 1400 2095 1 chr7B.!!$R1 695
6 TraesCS1D01G408300 chr2A 83249848 83250375 527 False 749.000000 749 92.235000 1319 1846 1 chr2A.!!$F1 527
7 TraesCS1D01G408300 chrUn 287139687 287140620 933 True 279.850000 481 90.090500 1245 2036 2 chrUn.!!$R1 791
8 TraesCS1D01G408300 chrUn 287145855 287146788 933 True 279.850000 481 90.090500 1245 2036 2 chrUn.!!$R2 791
9 TraesCS1D01G408300 chrUn 293606177 293607110 933 False 279.850000 481 90.853000 1245 2036 2 chrUn.!!$F1 791

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
868 888 0.038343 CTTTCGCCCAACCAACCATG 60.038 55.0 0.00 0.00 0.00 3.66 F
873 893 0.539438 GCCCAACCAACCATGTGAGA 60.539 55.0 0.00 0.00 0.00 3.27 F
2373 3310 0.174845 TCCGGTGAGCTAACCAATCG 59.825 55.0 20.85 5.86 40.53 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 3098 1.527034 TGCAGGACAGCAACAAGATC 58.473 50.0 0.00 0.00 42.46 2.75 R
2646 3592 2.192664 TGCCTGCATCGTAAAAGGAA 57.807 45.0 0.00 0.00 30.92 3.36 R
4054 5080 0.029834 GACGCTTGGCATGCTATTGG 59.970 55.0 18.92 7.32 0.00 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
288 289 2.444895 GACGGCCAGGAGGAGGAT 60.445 66.667 2.24 0.00 36.89 3.24
449 464 0.309612 GGTGTTCGTCAAAATGCGGT 59.690 50.000 0.00 0.00 0.00 5.68
494 510 8.723365 TGGTCATGTATTATTAGATTTCCTGGT 58.277 33.333 0.00 0.00 0.00 4.00
517 533 9.904198 TGGTCAAAATTCAATCTCTATGTCATA 57.096 29.630 0.00 0.00 0.00 2.15
538 554 8.643752 GTCATATTTTTAACCAACGATTTGTGG 58.356 33.333 0.00 0.00 0.00 4.17
540 556 9.364989 CATATTTTTAACCAACGATTTGTGGAT 57.635 29.630 0.00 0.00 0.00 3.41
541 557 7.650834 ATTTTTAACCAACGATTTGTGGATG 57.349 32.000 0.00 0.00 0.00 3.51
549 565 5.446709 CAACGATTTGTGGATGCTATCATC 58.553 41.667 0.00 0.00 46.46 2.92
565 581 8.055279 TGCTATCATCGATCATACTGTTATCA 57.945 34.615 0.00 0.00 0.00 2.15
596 612 3.561310 TCGCTGATTTGTGGATGCTATTC 59.439 43.478 0.00 0.00 0.00 1.75
600 616 5.163581 GCTGATTTGTGGATGCTATTCTTGT 60.164 40.000 0.00 0.00 0.00 3.16
602 618 7.230849 TGATTTGTGGATGCTATTCTTGTTT 57.769 32.000 0.00 0.00 0.00 2.83
603 619 8.347004 TGATTTGTGGATGCTATTCTTGTTTA 57.653 30.769 0.00 0.00 0.00 2.01
606 622 8.984891 TTTGTGGATGCTATTCTTGTTTATTG 57.015 30.769 0.00 0.00 0.00 1.90
607 623 7.701539 TGTGGATGCTATTCTTGTTTATTGT 57.298 32.000 0.00 0.00 0.00 2.71
609 625 8.028354 TGTGGATGCTATTCTTGTTTATTGTTG 58.972 33.333 0.00 0.00 0.00 3.33
610 626 8.243426 GTGGATGCTATTCTTGTTTATTGTTGA 58.757 33.333 0.00 0.00 0.00 3.18
612 628 9.241317 GGATGCTATTCTTGTTTATTGTTGATG 57.759 33.333 0.00 0.00 0.00 3.07
613 629 9.793252 GATGCTATTCTTGTTTATTGTTGATGT 57.207 29.630 0.00 0.00 0.00 3.06
615 631 9.624697 TGCTATTCTTGTTTATTGTTGATGTTC 57.375 29.630 0.00 0.00 0.00 3.18
616 632 9.624697 GCTATTCTTGTTTATTGTTGATGTTCA 57.375 29.630 0.00 0.00 0.00 3.18
619 635 8.627487 TTCTTGTTTATTGTTGATGTTCACAC 57.373 30.769 0.00 0.00 0.00 3.82
624 643 7.283354 TGTTTATTGTTGATGTTCACACCAGTA 59.717 33.333 0.00 0.00 0.00 2.74
625 644 7.809546 TTATTGTTGATGTTCACACCAGTAA 57.190 32.000 0.00 0.00 0.00 2.24
633 652 6.204688 TGATGTTCACACCAGTAATTCAGTTC 59.795 38.462 0.00 0.00 0.00 3.01
639 658 8.740123 TCACACCAGTAATTCAGTTCTTTTTA 57.260 30.769 0.00 0.00 0.00 1.52
647 666 9.403583 AGTAATTCAGTTCTTTTTACCAAGTGA 57.596 29.630 0.00 0.00 0.00 3.41
652 671 6.764560 TCAGTTCTTTTTACCAAGTGAGGTAC 59.235 38.462 0.00 0.00 43.57 3.34
670 689 5.990668 AGGTACTCTGATGAATTACCAACC 58.009 41.667 0.00 0.00 35.16 3.77
671 690 5.104485 AGGTACTCTGATGAATTACCAACCC 60.104 44.000 0.00 0.00 35.16 4.11
672 691 4.927267 ACTCTGATGAATTACCAACCCA 57.073 40.909 0.00 0.00 0.00 4.51
673 692 5.255397 ACTCTGATGAATTACCAACCCAA 57.745 39.130 0.00 0.00 0.00 4.12
674 693 5.256474 ACTCTGATGAATTACCAACCCAAG 58.744 41.667 0.00 0.00 0.00 3.61
675 694 5.014123 ACTCTGATGAATTACCAACCCAAGA 59.986 40.000 0.00 0.00 0.00 3.02
676 695 6.078456 TCTGATGAATTACCAACCCAAGAT 57.922 37.500 0.00 0.00 0.00 2.40
677 696 7.092444 ACTCTGATGAATTACCAACCCAAGATA 60.092 37.037 0.00 0.00 0.00 1.98
678 697 7.054124 TCTGATGAATTACCAACCCAAGATAC 58.946 38.462 0.00 0.00 0.00 2.24
679 698 6.726379 TGATGAATTACCAACCCAAGATACA 58.274 36.000 0.00 0.00 0.00 2.29
680 699 6.828273 TGATGAATTACCAACCCAAGATACAG 59.172 38.462 0.00 0.00 0.00 2.74
681 700 6.381498 TGAATTACCAACCCAAGATACAGA 57.619 37.500 0.00 0.00 0.00 3.41
682 701 6.969043 TGAATTACCAACCCAAGATACAGAT 58.031 36.000 0.00 0.00 0.00 2.90
683 702 7.410174 TGAATTACCAACCCAAGATACAGATT 58.590 34.615 0.00 0.00 0.00 2.40
684 703 7.556275 TGAATTACCAACCCAAGATACAGATTC 59.444 37.037 0.00 0.00 0.00 2.52
685 704 4.927267 ACCAACCCAAGATACAGATTCA 57.073 40.909 0.00 0.00 0.00 2.57
686 705 5.456921 ACCAACCCAAGATACAGATTCAT 57.543 39.130 0.00 0.00 0.00 2.57
687 706 6.575244 ACCAACCCAAGATACAGATTCATA 57.425 37.500 0.00 0.00 0.00 2.15
688 707 7.154191 ACCAACCCAAGATACAGATTCATAT 57.846 36.000 0.00 0.00 0.00 1.78
717 736 7.571798 GCCTTTTTACATTTGCATCTCCAAAAG 60.572 37.037 0.00 0.00 38.12 2.27
719 738 8.954950 TTTTTACATTTGCATCTCCAAAAGAA 57.045 26.923 0.00 0.00 38.12 2.52
720 739 8.954950 TTTTACATTTGCATCTCCAAAAGAAA 57.045 26.923 0.00 0.00 38.12 2.52
721 740 8.954950 TTTACATTTGCATCTCCAAAAGAAAA 57.045 26.923 0.00 0.00 38.12 2.29
722 741 6.849588 ACATTTGCATCTCCAAAAGAAAAC 57.150 33.333 0.00 0.00 38.12 2.43
725 744 5.350504 TTGCATCTCCAAAAGAAAACCAA 57.649 34.783 0.00 0.00 37.61 3.67
727 746 4.202243 TGCATCTCCAAAAGAAAACCAAGG 60.202 41.667 0.00 0.00 37.61 3.61
728 747 4.039124 GCATCTCCAAAAGAAAACCAAGGA 59.961 41.667 0.00 0.00 37.61 3.36
729 748 5.453198 GCATCTCCAAAAGAAAACCAAGGAA 60.453 40.000 0.00 0.00 37.61 3.36
730 749 5.852282 TCTCCAAAAGAAAACCAAGGAAG 57.148 39.130 0.00 0.00 0.00 3.46
731 750 5.269189 TCTCCAAAAGAAAACCAAGGAAGT 58.731 37.500 0.00 0.00 0.00 3.01
732 751 6.428295 TCTCCAAAAGAAAACCAAGGAAGTA 58.572 36.000 0.00 0.00 0.00 2.24
733 752 6.546034 TCTCCAAAAGAAAACCAAGGAAGTAG 59.454 38.462 0.00 0.00 0.00 2.57
734 753 5.068591 TCCAAAAGAAAACCAAGGAAGTAGC 59.931 40.000 0.00 0.00 0.00 3.58
735 754 5.163457 CCAAAAGAAAACCAAGGAAGTAGCA 60.163 40.000 0.00 0.00 0.00 3.49
736 755 5.774498 AAAGAAAACCAAGGAAGTAGCAG 57.226 39.130 0.00 0.00 0.00 4.24
737 756 4.439253 AGAAAACCAAGGAAGTAGCAGT 57.561 40.909 0.00 0.00 0.00 4.40
738 757 4.137543 AGAAAACCAAGGAAGTAGCAGTG 58.862 43.478 0.00 0.00 0.00 3.66
739 758 3.857157 AAACCAAGGAAGTAGCAGTGA 57.143 42.857 0.00 0.00 0.00 3.41
740 759 3.409026 AACCAAGGAAGTAGCAGTGAG 57.591 47.619 0.00 0.00 0.00 3.51
741 760 1.002544 ACCAAGGAAGTAGCAGTGAGC 59.997 52.381 0.00 0.00 46.19 4.26
758 777 3.605486 GTGAGCAAAAATTGAGACGATGC 59.395 43.478 0.00 0.00 0.00 3.91
795 815 6.556116 TCTTCTATTCAGATGATGGGATGTGA 59.444 38.462 0.00 0.00 31.78 3.58
851 871 4.890158 CTTGTAAAATTCCAAGGGCCTT 57.110 40.909 14.48 14.48 35.51 4.35
853 873 4.882842 TGTAAAATTCCAAGGGCCTTTC 57.117 40.909 18.16 0.00 0.00 2.62
864 884 2.338620 GCCTTTCGCCCAACCAAC 59.661 61.111 0.00 0.00 0.00 3.77
865 885 3.047735 CCTTTCGCCCAACCAACC 58.952 61.111 0.00 0.00 0.00 3.77
866 886 1.830408 CCTTTCGCCCAACCAACCA 60.830 57.895 0.00 0.00 0.00 3.67
867 887 1.184970 CCTTTCGCCCAACCAACCAT 61.185 55.000 0.00 0.00 0.00 3.55
868 888 0.038343 CTTTCGCCCAACCAACCATG 60.038 55.000 0.00 0.00 0.00 3.66
869 889 0.757188 TTTCGCCCAACCAACCATGT 60.757 50.000 0.00 0.00 0.00 3.21
870 890 1.459455 TTCGCCCAACCAACCATGTG 61.459 55.000 0.00 0.00 0.00 3.21
871 891 1.900981 CGCCCAACCAACCATGTGA 60.901 57.895 0.00 0.00 0.00 3.58
872 892 1.865788 CGCCCAACCAACCATGTGAG 61.866 60.000 0.00 0.00 0.00 3.51
873 893 0.539438 GCCCAACCAACCATGTGAGA 60.539 55.000 0.00 0.00 0.00 3.27
874 894 1.892329 GCCCAACCAACCATGTGAGAT 60.892 52.381 0.00 0.00 0.00 2.75
926 948 4.809673 TGCAAGATAGCATATCTACACCG 58.190 43.478 0.00 0.00 40.11 4.94
981 1003 4.712337 TCTCCTTATCTCTTTCACTCCCAC 59.288 45.833 0.00 0.00 0.00 4.61
1069 1093 4.308458 CCAAGTGCCGTCCGGTGA 62.308 66.667 7.66 0.00 37.65 4.02
1204 1228 3.381272 GGTCTCACTCTCTCCATCTTGAG 59.619 52.174 0.00 0.00 33.26 3.02
1575 1672 8.732746 TCTGTTTTCTTACACTTTAGCTCTTT 57.267 30.769 0.00 0.00 0.00 2.52
1616 1760 9.628500 GTTAACCTATGAACTTTATCTGGGATT 57.372 33.333 0.00 0.00 0.00 3.01
1636 1833 7.147759 TGGGATTGAATAACATAATGGTGTTGG 60.148 37.037 6.30 0.00 42.02 3.77
1852 2102 3.754850 TGGAGAAGTCATTGTCAATGCAG 59.245 43.478 19.02 0.00 38.77 4.41
1889 2139 4.691216 AGCGACAAAGTATCCTCTTCAAAC 59.309 41.667 0.00 0.00 0.00 2.93
2173 3076 9.391006 TCCACTTATCCAAACATAACAGTTATC 57.609 33.333 2.52 0.00 0.00 1.75
2195 3098 6.037786 TCCCACGAGGCTATTATCTTAATG 57.962 41.667 0.00 0.00 34.51 1.90
2373 3310 0.174845 TCCGGTGAGCTAACCAATCG 59.825 55.000 20.85 5.86 40.53 3.34
2389 3326 6.663944 ACCAATCGCAGAGTTATAAGAAAC 57.336 37.500 0.00 0.00 43.63 2.78
2390 3327 6.170506 ACCAATCGCAGAGTTATAAGAAACA 58.829 36.000 0.00 0.00 43.63 2.83
2415 3352 5.824097 GTCAACTGTAGTTCCTTTACCCAAA 59.176 40.000 0.00 0.00 35.83 3.28
2484 3422 5.174035 GCAGATATGTGTATCGTCTGTTGAC 59.826 44.000 1.37 0.00 41.32 3.18
2491 3429 3.513912 TGTATCGTCTGTTGACCCTTCAT 59.486 43.478 0.00 0.00 39.94 2.57
2545 3483 6.348050 GCAAATGGTCAGTCTCTAACTTTGAG 60.348 42.308 0.00 0.00 35.45 3.02
2573 3519 1.381165 GGGCAACGTGGTTCAACTGT 61.381 55.000 0.00 0.00 37.60 3.55
2579 3525 4.801516 GCAACGTGGTTCAACTGTATTTTT 59.198 37.500 0.00 0.00 0.00 1.94
2615 3561 1.756538 CCACTGGCCTTCACAAACTTT 59.243 47.619 3.32 0.00 0.00 2.66
2643 3589 5.295292 CGTGCAGATTGAGATTGGAAACTAT 59.705 40.000 0.00 0.00 0.00 2.12
2646 3592 7.013083 GTGCAGATTGAGATTGGAAACTATGAT 59.987 37.037 0.00 0.00 0.00 2.45
2698 3647 9.725019 TCTCTTCTGAGCAAGTAATTTTTATCA 57.275 29.630 0.00 0.00 40.03 2.15
2732 3705 7.482654 TTGTTTCATCTGTTTAGTGAGACAG 57.517 36.000 0.00 0.00 43.54 3.51
2753 3726 6.666678 ACAGACCATCATTTCTATGTGGAAT 58.333 36.000 11.21 0.00 36.88 3.01
2754 3727 7.121382 ACAGACCATCATTTCTATGTGGAATT 58.879 34.615 11.21 0.00 36.88 2.17
2755 3728 8.274322 ACAGACCATCATTTCTATGTGGAATTA 58.726 33.333 11.21 0.00 36.88 1.40
3020 3996 3.576118 CCGATATCATCCAGACTGAAGGT 59.424 47.826 3.32 0.00 0.00 3.50
3034 4010 3.714798 ACTGAAGGTGGGAAGTGTTCTAA 59.285 43.478 0.00 0.00 0.00 2.10
3110 4086 5.221581 GCTAAATACTCCCTCGGTTCCATAA 60.222 44.000 0.00 0.00 0.00 1.90
3111 4087 5.906772 AAATACTCCCTCGGTTCCATAAT 57.093 39.130 0.00 0.00 0.00 1.28
3112 4088 5.906772 AATACTCCCTCGGTTCCATAATT 57.093 39.130 0.00 0.00 0.00 1.40
3114 4090 3.385115 ACTCCCTCGGTTCCATAATTCT 58.615 45.455 0.00 0.00 0.00 2.40
3115 4091 3.780850 ACTCCCTCGGTTCCATAATTCTT 59.219 43.478 0.00 0.00 0.00 2.52
3116 4092 4.130118 CTCCCTCGGTTCCATAATTCTTG 58.870 47.826 0.00 0.00 0.00 3.02
3117 4093 2.618709 CCCTCGGTTCCATAATTCTTGC 59.381 50.000 0.00 0.00 0.00 4.01
3118 4094 2.618709 CCTCGGTTCCATAATTCTTGCC 59.381 50.000 0.00 0.00 0.00 4.52
3119 4095 3.278574 CTCGGTTCCATAATTCTTGCCA 58.721 45.455 0.00 0.00 0.00 4.92
3134 4110 5.287674 TCTTGCCATTGGTTCAAATTTGA 57.712 34.783 16.91 16.91 34.92 2.69
3161 4137 6.834168 AAAACCACGACAAGATTATGGAAT 57.166 33.333 0.00 0.00 34.38 3.01
3166 4142 5.118990 CACGACAAGATTATGGAATGGAGT 58.881 41.667 0.00 0.00 0.00 3.85
3180 4156 5.013079 TGGAATGGAGTGAGTAGAACACATT 59.987 40.000 0.00 0.00 40.25 2.71
3181 4157 5.940470 GGAATGGAGTGAGTAGAACACATTT 59.060 40.000 0.00 0.00 40.25 2.32
3236 4212 9.103048 CAAATTCATAACTAGTGTTCAACGAAC 57.897 33.333 0.00 0.00 42.26 3.95
3277 4253 0.320247 CAGCCGCATACTCCATCTCC 60.320 60.000 0.00 0.00 0.00 3.71
3280 4256 1.332195 CCGCATACTCCATCTCCAGA 58.668 55.000 0.00 0.00 0.00 3.86
3325 4301 0.037605 CGTCGGGGCTAAGTTCAGTT 60.038 55.000 0.00 0.00 0.00 3.16
3379 4357 2.034939 CGGCGTGGTATGTATCCTGTAA 59.965 50.000 0.00 0.00 0.00 2.41
3412 4390 4.702831 TGCGTAATGATGAGAAAGCCATA 58.297 39.130 0.00 0.00 0.00 2.74
3464 4447 3.679389 ACCAACACTGATCCAGAACATC 58.321 45.455 0.45 0.00 35.18 3.06
3466 4449 3.559811 CCAACACTGATCCAGAACATCCA 60.560 47.826 0.45 0.00 35.18 3.41
3498 4506 5.368145 TGACTTTTTGTGCTGTCTACTGAT 58.632 37.500 0.00 0.00 0.00 2.90
3499 4507 5.466728 TGACTTTTTGTGCTGTCTACTGATC 59.533 40.000 0.00 0.00 0.00 2.92
3500 4508 4.757149 ACTTTTTGTGCTGTCTACTGATCC 59.243 41.667 0.00 0.00 0.00 3.36
3502 4510 3.599730 TTGTGCTGTCTACTGATCCAG 57.400 47.619 0.00 0.00 37.52 3.86
3506 4514 4.223700 TGTGCTGTCTACTGATCCAGAAAT 59.776 41.667 0.45 0.00 35.18 2.17
3507 4515 4.808364 GTGCTGTCTACTGATCCAGAAATC 59.192 45.833 0.45 0.00 35.18 2.17
3508 4516 4.141846 TGCTGTCTACTGATCCAGAAATCC 60.142 45.833 0.45 0.00 35.18 3.01
3509 4517 4.615949 CTGTCTACTGATCCAGAAATCCG 58.384 47.826 0.45 0.00 35.18 4.18
3511 4519 4.895889 TGTCTACTGATCCAGAAATCCGAT 59.104 41.667 0.45 0.00 35.18 4.18
3512 4520 5.363868 TGTCTACTGATCCAGAAATCCGATT 59.636 40.000 0.45 0.00 35.18 3.34
3513 4521 6.127054 TGTCTACTGATCCAGAAATCCGATTT 60.127 38.462 6.04 6.04 35.18 2.17
3514 4522 6.763610 GTCTACTGATCCAGAAATCCGATTTT 59.236 38.462 7.78 0.00 35.18 1.82
3657 4671 2.895680 GAGGTGAGGAGCATCGCA 59.104 61.111 0.00 0.00 34.37 5.10
3906 4922 9.850628 GTTTACGCCTTCCTCTTTATTTATTTT 57.149 29.630 0.00 0.00 0.00 1.82
3907 4923 9.849166 TTTACGCCTTCCTCTTTATTTATTTTG 57.151 29.630 0.00 0.00 0.00 2.44
3956 4972 4.785346 ATTCTTGCTGGTGATATGACCT 57.215 40.909 12.86 0.00 36.88 3.85
3957 4973 3.548745 TCTTGCTGGTGATATGACCTG 57.451 47.619 12.86 12.88 36.88 4.00
3958 4974 3.106827 TCTTGCTGGTGATATGACCTGA 58.893 45.455 19.91 4.78 37.16 3.86
3959 4975 3.133542 TCTTGCTGGTGATATGACCTGAG 59.866 47.826 19.91 10.49 37.16 3.35
3960 4976 1.139654 TGCTGGTGATATGACCTGAGC 59.860 52.381 19.91 17.02 37.16 4.26
3961 4977 1.542108 GCTGGTGATATGACCTGAGCC 60.542 57.143 19.91 1.33 37.16 4.70
3962 4978 2.045524 CTGGTGATATGACCTGAGCCT 58.954 52.381 12.86 0.00 37.16 4.58
3963 4979 2.437281 CTGGTGATATGACCTGAGCCTT 59.563 50.000 12.86 0.00 37.16 4.35
3964 4980 2.846206 TGGTGATATGACCTGAGCCTTT 59.154 45.455 12.86 0.00 36.88 3.11
3965 4981 3.209410 GGTGATATGACCTGAGCCTTTG 58.791 50.000 3.79 0.00 32.69 2.77
3966 4982 3.118261 GGTGATATGACCTGAGCCTTTGA 60.118 47.826 3.79 0.00 32.69 2.69
3995 5011 9.035607 ACAGTGATAAAGCTACTTTGAATATCG 57.964 33.333 0.00 0.00 35.21 2.92
4015 5031 0.563173 AGCTAGCAGGGGTCCTATCA 59.437 55.000 18.83 0.00 29.64 2.15
4016 5032 1.150986 AGCTAGCAGGGGTCCTATCAT 59.849 52.381 18.83 0.00 29.64 2.45
4017 5033 1.552792 GCTAGCAGGGGTCCTATCATC 59.447 57.143 10.63 0.00 29.64 2.92
4018 5034 2.894731 CTAGCAGGGGTCCTATCATCA 58.105 52.381 0.00 0.00 29.64 3.07
4028 5054 3.118738 GGTCCTATCATCACAAGTTCGGT 60.119 47.826 0.00 0.00 0.00 4.69
4054 5080 7.482654 TGTTCTTATCGATCCATTTCATCAC 57.517 36.000 0.00 0.00 0.00 3.06
4060 5086 8.552083 TTATCGATCCATTTCATCACCAATAG 57.448 34.615 0.00 0.00 0.00 1.73
4079 5105 1.210931 CATGCCAAGCGTCCAACTG 59.789 57.895 0.00 0.00 0.00 3.16
4088 5175 3.444703 AGCGTCCAACTGATGTCTATC 57.555 47.619 0.00 0.00 32.20 2.08
4101 5188 6.106648 TGATGTCTATCATTTGCCTCTAGG 57.893 41.667 0.00 0.00 38.37 3.02
4105 5192 5.604231 TGTCTATCATTTGCCTCTAGGACAT 59.396 40.000 0.00 0.00 37.39 3.06
4106 5193 6.782494 TGTCTATCATTTGCCTCTAGGACATA 59.218 38.462 0.00 0.00 37.39 2.29
4107 5194 7.290014 TGTCTATCATTTGCCTCTAGGACATAA 59.710 37.037 0.00 0.00 37.39 1.90
4108 5195 8.150945 GTCTATCATTTGCCTCTAGGACATAAA 58.849 37.037 0.00 0.00 37.39 1.40
4109 5196 8.713971 TCTATCATTTGCCTCTAGGACATAAAA 58.286 33.333 0.00 0.00 37.39 1.52
4110 5197 7.814264 ATCATTTGCCTCTAGGACATAAAAG 57.186 36.000 0.00 0.00 37.39 2.27
4111 5198 6.957631 TCATTTGCCTCTAGGACATAAAAGA 58.042 36.000 0.00 0.00 37.39 2.52
4188 5275 4.801147 ATTACAGTTGCTGATACATGCG 57.199 40.909 2.91 0.00 35.18 4.73
4189 5276 0.729116 ACAGTTGCTGATACATGCGC 59.271 50.000 0.00 0.00 35.18 6.09
4227 5314 6.312141 TCATAGTTTCAATCACCTCCATGA 57.688 37.500 0.00 0.00 0.00 3.07
4270 5357 3.763897 CAGTTGCAATTTAGCCTAAGGGT 59.236 43.478 0.59 0.00 37.19 4.34
4350 5437 5.168569 TGATCAAGAAATTTACTCGACGCT 58.831 37.500 0.00 0.00 0.00 5.07
4354 5441 4.124851 AGAAATTTACTCGACGCTCCAT 57.875 40.909 0.00 0.00 0.00 3.41
4364 5451 1.135717 CGACGCTCCATTGAAATTGCA 60.136 47.619 0.00 0.00 0.00 4.08
4371 5458 4.439153 GCTCCATTGAAATTGCATCTCGAA 60.439 41.667 0.00 0.00 0.00 3.71
4422 5510 4.041567 ACATGGTATCCGCATCAAAGGATA 59.958 41.667 0.00 0.48 44.77 2.59
4504 5594 9.921637 ACTGTTGATTTTTCTTTTGTGAAACTA 57.078 25.926 0.00 0.00 38.04 2.24
4515 5605 9.932207 TTCTTTTGTGAAACTACCGATCTATTA 57.068 29.630 0.00 0.00 38.04 0.98
4522 5612 9.692749 GTGAAACTACCGATCTATTAATCATCA 57.307 33.333 0.00 0.00 0.00 3.07
4530 5620 7.281774 ACCGATCTATTAATCATCAATCATGGC 59.718 37.037 0.00 0.00 32.64 4.40
4531 5621 7.281549 CCGATCTATTAATCATCAATCATGGCA 59.718 37.037 0.00 0.00 32.64 4.92
4532 5622 8.336080 CGATCTATTAATCATCAATCATGGCAG 58.664 37.037 0.00 0.00 32.64 4.85
4533 5623 9.175312 GATCTATTAATCATCAATCATGGCAGT 57.825 33.333 0.00 0.00 32.64 4.40
4535 5625 9.440773 TCTATTAATCATCAATCATGGCAGTAC 57.559 33.333 0.00 0.00 32.64 2.73
4536 5626 9.223099 CTATTAATCATCAATCATGGCAGTACA 57.777 33.333 0.00 0.00 32.64 2.90
4539 5629 5.823209 TCATCAATCATGGCAGTACAAAG 57.177 39.130 0.00 0.00 32.64 2.77
4540 5630 4.641541 TCATCAATCATGGCAGTACAAAGG 59.358 41.667 0.00 0.00 32.64 3.11
4541 5631 4.299586 TCAATCATGGCAGTACAAAGGA 57.700 40.909 0.00 0.00 0.00 3.36
4542 5632 4.858850 TCAATCATGGCAGTACAAAGGAT 58.141 39.130 0.00 0.00 0.00 3.24
4544 5634 6.604171 TCAATCATGGCAGTACAAAGGATAT 58.396 36.000 0.00 0.00 0.00 1.63
4545 5635 7.744733 TCAATCATGGCAGTACAAAGGATATA 58.255 34.615 0.00 0.00 0.00 0.86
4546 5636 8.217111 TCAATCATGGCAGTACAAAGGATATAA 58.783 33.333 0.00 0.00 0.00 0.98
4547 5637 8.849168 CAATCATGGCAGTACAAAGGATATAAA 58.151 33.333 0.00 0.00 0.00 1.40
4645 5769 5.175673 GGCAAAACTTGTTGAAATAGACAGC 59.824 40.000 0.00 0.00 0.00 4.40
4647 5771 4.749245 AACTTGTTGAAATAGACAGCCG 57.251 40.909 0.00 0.00 0.00 5.52
4671 5865 0.889306 GTTGTCGTGCTAGGTCCTCT 59.111 55.000 0.00 0.00 0.00 3.69
4687 5907 1.480219 CTCTTGCCGCCGACGAATAC 61.480 60.000 0.00 0.00 43.93 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.523507 CGCGATCTTGCTGCTCTGG 61.524 63.158 0.00 0.00 0.00 3.86
117 118 3.991536 GAGGAACAGCCGCTCGTCC 62.992 68.421 9.95 9.95 43.43 4.79
288 289 2.280797 GGCAGCACGTTGACCTCA 60.281 61.111 0.00 0.00 0.00 3.86
414 418 2.360852 CCTGCCCTGCCTCACTTG 60.361 66.667 0.00 0.00 0.00 3.16
419 423 2.360475 GAACACCTGCCCTGCCTC 60.360 66.667 0.00 0.00 0.00 4.70
449 464 4.610333 ACCATGAGATACATATCCCGCTA 58.390 43.478 0.00 0.00 37.46 4.26
453 468 6.305272 ACATGACCATGAGATACATATCCC 57.695 41.667 16.07 0.00 41.20 3.85
485 500 7.787623 AGAGATTGAATTTTGACCAGGAAAT 57.212 32.000 0.00 0.00 0.00 2.17
517 533 6.147000 GCATCCACAAATCGTTGGTTAAAAAT 59.853 34.615 0.00 0.00 39.22 1.82
525 541 3.627123 TGATAGCATCCACAAATCGTTGG 59.373 43.478 0.00 0.00 39.22 3.77
530 546 5.640783 TGATCGATGATAGCATCCACAAATC 59.359 40.000 15.07 10.43 46.55 2.17
538 554 9.179552 GATAACAGTATGATCGATGATAGCATC 57.820 37.037 11.01 11.01 42.86 3.91
540 556 8.055279 TGATAACAGTATGATCGATGATAGCA 57.945 34.615 0.54 0.00 39.69 3.49
541 557 8.966194 CATGATAACAGTATGATCGATGATAGC 58.034 37.037 0.54 0.00 39.69 2.97
549 565 8.526218 AGTAAAGCATGATAACAGTATGATCG 57.474 34.615 0.00 0.00 39.69 3.69
553 569 6.422100 AGCGAGTAAAGCATGATAACAGTATG 59.578 38.462 0.00 0.00 38.75 2.39
557 573 4.805719 TCAGCGAGTAAAGCATGATAACAG 59.194 41.667 0.00 0.00 37.01 3.16
565 581 3.127548 CCACAAATCAGCGAGTAAAGCAT 59.872 43.478 0.00 0.00 37.01 3.79
596 612 6.977502 TGGTGTGAACATCAACAATAAACAAG 59.022 34.615 0.00 0.00 33.38 3.16
600 616 6.707440 ACTGGTGTGAACATCAACAATAAA 57.293 33.333 0.00 0.00 36.41 1.40
602 618 7.994425 ATTACTGGTGTGAACATCAACAATA 57.006 32.000 0.00 0.00 36.41 1.90
603 619 6.899393 ATTACTGGTGTGAACATCAACAAT 57.101 33.333 0.00 0.00 36.41 2.71
606 622 6.017109 ACTGAATTACTGGTGTGAACATCAAC 60.017 38.462 0.00 0.00 36.41 3.18
607 623 6.061441 ACTGAATTACTGGTGTGAACATCAA 58.939 36.000 0.00 0.00 36.41 2.57
609 625 6.428159 AGAACTGAATTACTGGTGTGAACATC 59.572 38.462 0.00 0.00 0.00 3.06
610 626 6.299141 AGAACTGAATTACTGGTGTGAACAT 58.701 36.000 0.00 0.00 0.00 2.71
612 628 6.619801 AAGAACTGAATTACTGGTGTGAAC 57.380 37.500 0.00 0.00 0.00 3.18
613 629 7.639113 AAAAGAACTGAATTACTGGTGTGAA 57.361 32.000 0.00 0.00 0.00 3.18
614 630 7.639113 AAAAAGAACTGAATTACTGGTGTGA 57.361 32.000 0.00 0.00 0.00 3.58
615 631 7.860872 GGTAAAAAGAACTGAATTACTGGTGTG 59.139 37.037 0.00 0.00 0.00 3.82
616 632 7.558444 TGGTAAAAAGAACTGAATTACTGGTGT 59.442 33.333 0.00 0.00 0.00 4.16
617 633 7.936584 TGGTAAAAAGAACTGAATTACTGGTG 58.063 34.615 0.00 0.00 0.00 4.17
619 635 8.630037 ACTTGGTAAAAAGAACTGAATTACTGG 58.370 33.333 0.00 0.00 0.00 4.00
624 643 7.342026 ACCTCACTTGGTAAAAAGAACTGAATT 59.658 33.333 0.00 0.00 38.79 2.17
625 644 6.833933 ACCTCACTTGGTAAAAAGAACTGAAT 59.166 34.615 0.00 0.00 38.79 2.57
633 652 6.522054 TCAGAGTACCTCACTTGGTAAAAAG 58.478 40.000 0.00 0.00 43.36 2.27
639 658 3.779444 TCATCAGAGTACCTCACTTGGT 58.221 45.455 0.00 0.00 43.66 3.67
647 666 5.104485 GGGTTGGTAATTCATCAGAGTACCT 60.104 44.000 2.97 0.00 37.25 3.08
652 671 5.500234 TCTTGGGTTGGTAATTCATCAGAG 58.500 41.667 0.00 0.00 0.00 3.35
655 674 6.726379 TGTATCTTGGGTTGGTAATTCATCA 58.274 36.000 0.00 0.00 0.00 3.07
661 680 6.969043 TGAATCTGTATCTTGGGTTGGTAAT 58.031 36.000 0.00 0.00 0.00 1.89
662 681 6.381498 TGAATCTGTATCTTGGGTTGGTAA 57.619 37.500 0.00 0.00 0.00 2.85
664 683 4.927267 TGAATCTGTATCTTGGGTTGGT 57.073 40.909 0.00 0.00 0.00 3.67
665 684 7.456725 AGATATGAATCTGTATCTTGGGTTGG 58.543 38.462 3.91 0.00 41.08 3.77
680 699 8.758715 GCAAATGTAAAAAGGCAGATATGAATC 58.241 33.333 0.00 0.00 0.00 2.52
681 700 8.259411 TGCAAATGTAAAAAGGCAGATATGAAT 58.741 29.630 0.00 0.00 0.00 2.57
682 701 7.609960 TGCAAATGTAAAAAGGCAGATATGAA 58.390 30.769 0.00 0.00 0.00 2.57
683 702 7.167924 TGCAAATGTAAAAAGGCAGATATGA 57.832 32.000 0.00 0.00 0.00 2.15
684 703 7.924412 AGATGCAAATGTAAAAAGGCAGATATG 59.076 33.333 0.00 0.00 34.43 1.78
685 704 8.015185 AGATGCAAATGTAAAAAGGCAGATAT 57.985 30.769 0.00 0.00 34.43 1.63
686 705 7.408756 AGATGCAAATGTAAAAAGGCAGATA 57.591 32.000 0.00 0.00 34.43 1.98
687 706 6.290294 AGATGCAAATGTAAAAAGGCAGAT 57.710 33.333 0.00 0.00 34.43 2.90
688 707 5.336690 GGAGATGCAAATGTAAAAAGGCAGA 60.337 40.000 0.00 0.00 34.43 4.26
694 713 8.954950 TTCTTTTGGAGATGCAAATGTAAAAA 57.045 26.923 10.86 0.00 33.49 1.94
717 736 4.134563 TCACTGCTACTTCCTTGGTTTTC 58.865 43.478 0.00 0.00 0.00 2.29
719 738 3.744660 CTCACTGCTACTTCCTTGGTTT 58.255 45.455 0.00 0.00 0.00 3.27
720 739 2.551071 GCTCACTGCTACTTCCTTGGTT 60.551 50.000 0.00 0.00 38.95 3.67
721 740 1.002544 GCTCACTGCTACTTCCTTGGT 59.997 52.381 0.00 0.00 38.95 3.67
722 741 1.002430 TGCTCACTGCTACTTCCTTGG 59.998 52.381 0.00 0.00 43.37 3.61
725 744 3.492102 TTTTGCTCACTGCTACTTCCT 57.508 42.857 0.00 0.00 43.37 3.36
727 746 5.762045 TCAATTTTTGCTCACTGCTACTTC 58.238 37.500 0.00 0.00 43.37 3.01
728 747 5.532406 TCTCAATTTTTGCTCACTGCTACTT 59.468 36.000 0.00 0.00 43.37 2.24
729 748 5.049129 GTCTCAATTTTTGCTCACTGCTACT 60.049 40.000 0.00 0.00 43.37 2.57
730 749 5.149977 GTCTCAATTTTTGCTCACTGCTAC 58.850 41.667 0.00 0.00 43.37 3.58
731 750 4.083855 CGTCTCAATTTTTGCTCACTGCTA 60.084 41.667 0.00 0.00 43.37 3.49
732 751 3.304257 CGTCTCAATTTTTGCTCACTGCT 60.304 43.478 0.00 0.00 43.37 4.24
733 752 2.975851 CGTCTCAATTTTTGCTCACTGC 59.024 45.455 0.00 0.00 43.25 4.40
734 753 4.472691 TCGTCTCAATTTTTGCTCACTG 57.527 40.909 0.00 0.00 0.00 3.66
735 754 4.614535 GCATCGTCTCAATTTTTGCTCACT 60.615 41.667 0.00 0.00 0.00 3.41
736 755 3.605486 GCATCGTCTCAATTTTTGCTCAC 59.395 43.478 0.00 0.00 0.00 3.51
737 756 3.503363 AGCATCGTCTCAATTTTTGCTCA 59.497 39.130 0.00 0.00 34.02 4.26
738 757 3.850273 CAGCATCGTCTCAATTTTTGCTC 59.150 43.478 0.00 0.00 36.87 4.26
739 758 3.829948 CAGCATCGTCTCAATTTTTGCT 58.170 40.909 0.00 0.00 39.38 3.91
740 759 2.343544 GCAGCATCGTCTCAATTTTTGC 59.656 45.455 0.00 0.00 0.00 3.68
741 760 3.362831 GTGCAGCATCGTCTCAATTTTTG 59.637 43.478 0.00 0.00 0.00 2.44
742 761 3.004629 TGTGCAGCATCGTCTCAATTTTT 59.995 39.130 0.00 0.00 0.00 1.94
758 777 7.463485 ATCTGAATAGAAGATGCCATGTGCAG 61.463 42.308 13.20 0.00 44.88 4.41
785 804 6.519721 GCTGTCAGATTAGTATCACATCCCAT 60.520 42.308 3.32 0.00 32.95 4.00
795 815 4.202305 GCTCCTTGGCTGTCAGATTAGTAT 60.202 45.833 3.32 0.00 0.00 2.12
834 854 2.232696 GCGAAAGGCCCTTGGAATTTTA 59.767 45.455 0.00 0.00 34.80 1.52
851 871 1.152652 ACATGGTTGGTTGGGCGAA 60.153 52.632 0.00 0.00 0.00 4.70
853 873 1.865788 CTCACATGGTTGGTTGGGCG 61.866 60.000 0.00 0.00 0.00 6.13
856 876 3.056607 GGAAATCTCACATGGTTGGTTGG 60.057 47.826 0.00 0.00 0.00 3.77
860 880 2.756760 CCTGGAAATCTCACATGGTTGG 59.243 50.000 0.00 0.00 0.00 3.77
861 881 3.192001 CACCTGGAAATCTCACATGGTTG 59.808 47.826 0.00 0.00 0.00 3.77
862 882 3.181429 ACACCTGGAAATCTCACATGGTT 60.181 43.478 0.00 0.00 0.00 3.67
863 883 2.376518 ACACCTGGAAATCTCACATGGT 59.623 45.455 0.00 0.00 0.00 3.55
864 884 3.012518 GACACCTGGAAATCTCACATGG 58.987 50.000 0.00 0.00 0.00 3.66
865 885 3.688185 CAGACACCTGGAAATCTCACATG 59.312 47.826 0.00 0.00 36.77 3.21
866 886 3.328931 ACAGACACCTGGAAATCTCACAT 59.671 43.478 0.00 0.00 44.60 3.21
867 887 2.705658 ACAGACACCTGGAAATCTCACA 59.294 45.455 0.00 0.00 44.60 3.58
868 888 3.244215 TGACAGACACCTGGAAATCTCAC 60.244 47.826 0.00 0.00 44.60 3.51
869 889 2.972021 TGACAGACACCTGGAAATCTCA 59.028 45.455 0.00 0.00 44.60 3.27
870 890 3.594134 CTGACAGACACCTGGAAATCTC 58.406 50.000 0.00 0.00 44.60 2.75
871 891 2.304180 CCTGACAGACACCTGGAAATCT 59.696 50.000 3.32 0.00 44.60 2.40
872 892 2.039084 ACCTGACAGACACCTGGAAATC 59.961 50.000 3.32 0.00 44.60 2.17
873 893 2.057922 ACCTGACAGACACCTGGAAAT 58.942 47.619 3.32 0.00 44.60 2.17
874 894 1.507140 ACCTGACAGACACCTGGAAA 58.493 50.000 3.32 0.00 44.60 3.13
925 947 2.747855 GCACAGGGAAAGGCTCCG 60.748 66.667 0.00 0.00 46.51 4.63
926 948 1.676967 CTGCACAGGGAAAGGCTCC 60.677 63.158 0.00 0.00 44.54 4.70
981 1003 3.314553 CATTCTTGCTGCTGAAGGTTTG 58.685 45.455 0.00 0.00 0.00 2.93
1017 1041 1.439644 CGCCTGGAGAAGTCCTAGC 59.560 63.158 0.00 0.00 44.30 3.42
1122 1146 4.269523 TTGGTGGCCGCAGAAGCT 62.270 61.111 19.98 0.00 39.10 3.74
1146 1170 1.536662 ACGGAAGGGCCTGAGAACT 60.537 57.895 6.92 0.00 0.00 3.01
1149 1173 1.984570 CTCACGGAAGGGCCTGAGA 60.985 63.158 6.92 0.00 40.99 3.27
1204 1228 5.813080 AATTTATTACTGCACGGAAGGTC 57.187 39.130 0.00 0.00 0.00 3.85
1242 1266 7.001073 ACACTACTACATCTATCATCAGAGCA 58.999 38.462 0.00 0.00 0.00 4.26
1575 1672 5.779241 AGGTTAACATTTCATCCCTCTGA 57.221 39.130 8.10 0.00 0.00 3.27
1616 1760 7.382110 CAAACCCAACACCATTATGTTATTCA 58.618 34.615 0.00 0.00 40.89 2.57
1630 1826 1.039856 ATCACCAGCAAACCCAACAC 58.960 50.000 0.00 0.00 0.00 3.32
1636 1833 0.242017 GAGCACATCACCAGCAAACC 59.758 55.000 0.00 0.00 0.00 3.27
1852 2102 2.006888 TGTCGCTGCAGCTAATTAACC 58.993 47.619 34.22 12.64 39.32 2.85
1889 2139 2.526304 TTCCTTTGACGTGGACTGAG 57.474 50.000 0.00 0.00 31.24 3.35
2049 2950 7.747799 CACTTGTACTGAATTCTGCTTGTTATG 59.252 37.037 11.86 0.74 0.00 1.90
2124 3025 8.423349 TGGATCATTTTTATATCCAAAGCAAGG 58.577 33.333 0.85 0.00 44.75 3.61
2161 3062 3.131396 GCCTCGTGGGATAACTGTTATG 58.869 50.000 17.21 3.52 37.23 1.90
2173 3076 6.037786 TCATTAAGATAATAGCCTCGTGGG 57.962 41.667 5.54 0.00 38.36 4.61
2195 3098 1.527034 TGCAGGACAGCAACAAGATC 58.473 50.000 0.00 0.00 42.46 2.75
2238 3175 8.201554 TGACAAGCTTGTGATAATGAGTTATC 57.798 34.615 35.67 16.16 44.20 1.75
2239 3176 8.743085 ATGACAAGCTTGTGATAATGAGTTAT 57.257 30.769 35.67 6.23 42.43 1.89
2241 3178 6.883217 AGATGACAAGCTTGTGATAATGAGTT 59.117 34.615 35.67 10.55 42.43 3.01
2373 3310 7.513968 CAGTTGACTGTTTCTTATAACTCTGC 58.486 38.462 2.98 0.00 39.09 4.26
2389 3326 4.995487 GGGTAAAGGAACTACAGTTGACTG 59.005 45.833 9.50 9.50 44.71 3.51
2390 3327 4.657039 TGGGTAAAGGAACTACAGTTGACT 59.343 41.667 0.00 0.00 38.49 3.41
2415 3352 3.580458 ACTTAGCAGACTCAACTCCACAT 59.420 43.478 0.00 0.00 0.00 3.21
2484 3422 2.292569 CGCAGATTGGAATGATGAAGGG 59.707 50.000 0.00 0.00 0.00 3.95
2491 3429 3.797039 CTTCTACCGCAGATTGGAATGA 58.203 45.455 0.00 0.00 31.77 2.57
2580 3526 3.674997 CCAGTGGCTAGCAGAGTAAAAA 58.325 45.455 18.24 0.00 0.00 1.94
2615 3561 3.055891 TCCAATCTCAATCTGCACGAGAA 60.056 43.478 0.00 0.00 39.15 2.87
2643 3589 2.682856 GCCTGCATCGTAAAAGGAATCA 59.317 45.455 0.00 0.00 30.92 2.57
2646 3592 2.192664 TGCCTGCATCGTAAAAGGAA 57.807 45.000 0.00 0.00 30.92 3.36
2705 3654 9.208022 TGTCTCACTAAACAGATGAAACAATAG 57.792 33.333 0.00 0.00 0.00 1.73
2706 3655 9.208022 CTGTCTCACTAAACAGATGAAACAATA 57.792 33.333 0.00 0.00 44.54 1.90
2707 3656 7.933577 TCTGTCTCACTAAACAGATGAAACAAT 59.066 33.333 1.26 0.00 45.18 2.71
2708 3657 7.272244 TCTGTCTCACTAAACAGATGAAACAA 58.728 34.615 1.26 0.00 45.18 2.83
2788 3763 3.045634 TCTTCCTTGTCTCCCTTGTCAA 58.954 45.455 0.00 0.00 0.00 3.18
3020 3996 2.901192 TGTCGGATTAGAACACTTCCCA 59.099 45.455 0.00 0.00 0.00 4.37
3034 4010 2.231380 ACCCCAGGCTTTGTCGGAT 61.231 57.895 0.00 0.00 0.00 4.18
3110 4086 6.297582 TCAAATTTGAACCAATGGCAAGAAT 58.702 32.000 18.45 0.00 33.55 2.40
3111 4087 5.678583 TCAAATTTGAACCAATGGCAAGAA 58.321 33.333 18.45 0.00 33.55 2.52
3112 4088 5.287674 TCAAATTTGAACCAATGGCAAGA 57.712 34.783 18.45 0.00 33.55 3.02
3134 4110 6.938030 TCCATAATCTTGTCGTGGTTTTAGTT 59.062 34.615 0.00 0.00 0.00 2.24
3147 4123 6.319048 ACTCACTCCATTCCATAATCTTGT 57.681 37.500 0.00 0.00 0.00 3.16
3161 4137 7.676004 TGATAAAATGTGTTCTACTCACTCCA 58.324 34.615 0.00 0.00 36.83 3.86
3166 4142 6.649141 ACGCTTGATAAAATGTGTTCTACTCA 59.351 34.615 0.00 0.00 0.00 3.41
3180 4156 9.522804 AACAAGAAAATAACAACGCTTGATAAA 57.477 25.926 0.00 0.00 36.96 1.40
3181 4157 8.963130 CAACAAGAAAATAACAACGCTTGATAA 58.037 29.630 0.00 0.00 36.96 1.75
3277 4253 1.589993 CGGTATGCTGACGGCTCTG 60.590 63.158 7.96 0.00 42.39 3.35
3379 4357 5.237815 TCATCATTACGCAGAAGTTTGAGT 58.762 37.500 0.00 1.61 35.28 3.41
3412 4390 2.811873 GCCACAGAGTTCACATGGTCTT 60.812 50.000 0.00 0.00 32.71 3.01
3464 4447 2.224113 ACAAAAAGTCATGGCAGCTTGG 60.224 45.455 0.00 0.00 0.00 3.61
3466 4449 2.804212 GCACAAAAAGTCATGGCAGCTT 60.804 45.455 0.00 0.00 0.00 3.74
3521 4529 0.607489 ACATGTTCCAGCAGACAGGC 60.607 55.000 0.00 0.00 31.25 4.85
3526 4534 2.936919 AACTCACATGTTCCAGCAGA 57.063 45.000 0.00 0.00 0.00 4.26
3557 4569 1.412937 GGGGAGGAGAAGATCAGCTCT 60.413 57.143 12.70 3.79 34.96 4.09
3657 4671 2.363147 GTCGTCCCCAGAGCCTCT 60.363 66.667 0.00 0.00 0.00 3.69
3956 4972 3.777106 ATCACTGTCTTCAAAGGCTCA 57.223 42.857 0.00 0.00 0.00 4.26
3957 4973 5.391416 GCTTTATCACTGTCTTCAAAGGCTC 60.391 44.000 0.00 0.00 0.00 4.70
3958 4974 4.457257 GCTTTATCACTGTCTTCAAAGGCT 59.543 41.667 0.00 0.00 0.00 4.58
3959 4975 4.457257 AGCTTTATCACTGTCTTCAAAGGC 59.543 41.667 0.00 0.00 0.00 4.35
3960 4976 6.876257 AGTAGCTTTATCACTGTCTTCAAAGG 59.124 38.462 0.00 0.00 0.00 3.11
3961 4977 7.897575 AGTAGCTTTATCACTGTCTTCAAAG 57.102 36.000 0.00 0.00 0.00 2.77
3962 4978 8.559536 CAAAGTAGCTTTATCACTGTCTTCAAA 58.440 33.333 0.00 0.00 31.96 2.69
3963 4979 7.931407 TCAAAGTAGCTTTATCACTGTCTTCAA 59.069 33.333 0.00 0.00 31.96 2.69
3964 4980 7.441836 TCAAAGTAGCTTTATCACTGTCTTCA 58.558 34.615 0.00 0.00 31.96 3.02
3965 4981 7.891183 TCAAAGTAGCTTTATCACTGTCTTC 57.109 36.000 0.00 0.00 31.96 2.87
3966 4982 8.854614 ATTCAAAGTAGCTTTATCACTGTCTT 57.145 30.769 0.00 0.00 31.96 3.01
3995 5011 1.262417 GATAGGACCCCTGCTAGCTC 58.738 60.000 17.23 4.20 34.61 4.09
4015 5031 6.347402 CGATAAGAACAAACCGAACTTGTGAT 60.347 38.462 0.00 0.00 37.10 3.06
4016 5032 5.050634 CGATAAGAACAAACCGAACTTGTGA 60.051 40.000 0.00 0.00 37.10 3.58
4017 5033 5.050634 TCGATAAGAACAAACCGAACTTGTG 60.051 40.000 0.00 0.00 37.10 3.33
4018 5034 5.051816 TCGATAAGAACAAACCGAACTTGT 58.948 37.500 0.00 0.00 38.65 3.16
4028 5054 8.397906 GTGATGAAATGGATCGATAAGAACAAA 58.602 33.333 0.00 0.00 0.00 2.83
4054 5080 0.029834 GACGCTTGGCATGCTATTGG 59.970 55.000 18.92 7.32 0.00 3.16
4060 5086 2.126346 GTTGGACGCTTGGCATGC 60.126 61.111 9.90 9.90 0.00 4.06
4079 5105 6.162777 GTCCTAGAGGCAAATGATAGACATC 58.837 44.000 0.00 0.00 34.94 3.06
4088 5175 7.814264 ATCTTTTATGTCCTAGAGGCAAATG 57.186 36.000 0.00 0.00 34.44 2.32
4101 5188 8.708742 GGCAACCTTTGTTTTATCTTTTATGTC 58.291 33.333 0.00 0.00 30.42 3.06
4105 5192 8.478877 TGAAGGCAACCTTTGTTTTATCTTTTA 58.521 29.630 0.00 0.00 44.82 1.52
4106 5193 7.279981 GTGAAGGCAACCTTTGTTTTATCTTTT 59.720 33.333 0.00 0.00 44.82 2.27
4107 5194 6.761242 GTGAAGGCAACCTTTGTTTTATCTTT 59.239 34.615 0.00 0.00 44.82 2.52
4108 5195 6.127196 TGTGAAGGCAACCTTTGTTTTATCTT 60.127 34.615 0.00 0.00 44.82 2.40
4109 5196 5.362430 TGTGAAGGCAACCTTTGTTTTATCT 59.638 36.000 0.00 0.00 44.82 1.98
4110 5197 5.596845 TGTGAAGGCAACCTTTGTTTTATC 58.403 37.500 0.00 0.00 44.82 1.75
4111 5198 5.606348 TGTGAAGGCAACCTTTGTTTTAT 57.394 34.783 0.00 0.00 44.82 1.40
4183 5270 0.661552 CAATGGAGGAAGAGCGCATG 59.338 55.000 11.47 0.00 0.00 4.06
4188 5275 4.775236 ACTATGAACAATGGAGGAAGAGC 58.225 43.478 0.00 0.00 0.00 4.09
4189 5276 6.881065 TGAAACTATGAACAATGGAGGAAGAG 59.119 38.462 0.00 0.00 0.00 2.85
4227 5314 4.655963 TGAGTTTGCTTCTAGGCAGATTT 58.344 39.130 0.00 0.00 43.39 2.17
4257 5344 8.905850 CGGAATTTATTTAACCCTTAGGCTAAA 58.094 33.333 8.54 0.00 37.92 1.85
4258 5345 8.054572 ACGGAATTTATTTAACCCTTAGGCTAA 58.945 33.333 6.80 6.80 36.11 3.09
4259 5346 7.499895 CACGGAATTTATTTAACCCTTAGGCTA 59.500 37.037 0.00 0.00 36.11 3.93
4263 5350 7.090953 TGCACGGAATTTATTTAACCCTTAG 57.909 36.000 0.00 0.00 0.00 2.18
4270 5357 7.653713 TGCTCTTTTTGCACGGAATTTATTTAA 59.346 29.630 0.00 0.00 35.31 1.52
4350 5437 5.591472 AGATTCGAGATGCAATTTCAATGGA 59.409 36.000 0.00 0.00 0.00 3.41
4354 5441 6.094719 CCAAAGATTCGAGATGCAATTTCAA 58.905 36.000 0.00 0.00 0.00 2.69
4364 5451 6.712547 GGGAATGATAACCAAAGATTCGAGAT 59.287 38.462 0.00 0.00 0.00 2.75
4371 5458 3.632145 GCGTGGGAATGATAACCAAAGAT 59.368 43.478 0.00 0.00 35.77 2.40
4422 5510 3.753294 AAGTGAAGGTCTCGTTGATGT 57.247 42.857 0.00 0.00 0.00 3.06
4504 5594 7.281774 GCCATGATTGATGATTAATAGATCGGT 59.718 37.037 0.00 0.00 33.31 4.69
4515 5605 6.183360 CCTTTGTACTGCCATGATTGATGATT 60.183 38.462 0.00 0.00 33.31 2.57
4520 5610 4.299586 TCCTTTGTACTGCCATGATTGA 57.700 40.909 0.00 0.00 0.00 2.57
4522 5612 8.995027 TTTATATCCTTTGTACTGCCATGATT 57.005 30.769 0.00 0.00 0.00 2.57
4569 5659 1.000496 GCGCTAGGTAATCTACGGCTT 60.000 52.381 0.00 0.00 0.00 4.35
4579 5669 1.672854 ATGACGGCAGCGCTAGGTAA 61.673 55.000 10.99 1.26 0.00 2.85
4645 5769 0.736325 CTAGCACGACAACTTCCCGG 60.736 60.000 0.00 0.00 0.00 5.73
4647 5771 0.320697 ACCTAGCACGACAACTTCCC 59.679 55.000 0.00 0.00 0.00 3.97
4671 5865 1.355796 CTTGTATTCGTCGGCGGCAA 61.356 55.000 13.62 9.32 38.89 4.52


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

AutoCloner maintained by Alex Coulton.