Multiple sequence alignment - TraesCS5D01G071300

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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 TraesCS5D01G071300 chr5D 100.000 4365 0 0 1 4365 69325556 69329920 0.000000e+00 8061.0
1 TraesCS5D01G071300 chr5A 96.289 1617 50 7 2059 3671 60109612 60111222 0.000000e+00 2645.0
2 TraesCS5D01G071300 chr5A 93.285 968 47 12 762 1717 60107478 60108439 0.000000e+00 1411.0
3 TraesCS5D01G071300 chr5A 92.049 327 22 4 1716 2041 60108468 60108791 1.430000e-124 457.0
4 TraesCS5D01G071300 chr5B 95.499 1622 62 6 2059 3674 75209281 75210897 0.000000e+00 2580.0
5 TraesCS5D01G071300 chr5B 92.140 916 43 16 805 1717 75206378 75207267 0.000000e+00 1266.0
6 TraesCS5D01G071300 chr5B 95.455 330 13 1 1716 2043 75207297 75207626 3.870000e-145 525.0
7 TraesCS5D01G071300 chr2D 92.142 789 58 3 2059 2843 49190691 49189903 0.000000e+00 1110.0
8 TraesCS5D01G071300 chr2D 90.635 299 20 4 1716 2010 49193077 49192783 1.470000e-104 390.0
9 TraesCS5D01G071300 chr2D 100.000 33 0 0 1685 1717 49193147 49193115 1.310000e-05 62.1
10 TraesCS5D01G071300 chr3B 92.388 670 48 3 1 668 3135927 3135259 0.000000e+00 952.0
11 TraesCS5D01G071300 chr3B 93.429 624 36 2 3742 4365 821047249 821047867 0.000000e+00 920.0
12 TraesCS5D01G071300 chr3B 87.975 632 57 15 3742 4365 379660363 379660983 0.000000e+00 728.0
13 TraesCS5D01G071300 chr3B 92.754 69 5 0 3673 3741 551496868 551496800 2.780000e-17 100.0
14 TraesCS5D01G071300 chr2A 91.876 677 50 5 1 674 549954344 549955018 0.000000e+00 941.0
15 TraesCS5D01G071300 chr2A 89.809 628 46 12 3741 4365 403607716 403608328 0.000000e+00 789.0
16 TraesCS5D01G071300 chr2A 89.507 629 47 14 3741 4365 401607753 401608366 0.000000e+00 778.0
17 TraesCS5D01G071300 chr1D 91.815 672 49 6 1 668 16204908 16205577 0.000000e+00 931.0
18 TraesCS5D01G071300 chr1D 91.892 629 39 4 3739 4365 310841235 310840617 0.000000e+00 869.0
19 TraesCS5D01G071300 chr1D 92.754 69 5 0 3673 3741 353568318 353568386 2.780000e-17 100.0
20 TraesCS5D01G071300 chr1D 90.909 44 4 0 766 809 467237971 467238014 4.710000e-05 60.2
21 TraesCS5D01G071300 chr3A 91.207 671 55 4 1 671 20910743 20911409 0.000000e+00 909.0
22 TraesCS5D01G071300 chr3A 91.054 626 45 6 3742 4365 9968839 9968223 0.000000e+00 835.0
23 TraesCS5D01G071300 chr6A 92.628 624 35 3 3742 4365 588055809 588055197 0.000000e+00 887.0
24 TraesCS5D01G071300 chr2B 90.611 671 59 4 3 672 477531253 477530586 0.000000e+00 887.0
25 TraesCS5D01G071300 chr2B 90.569 668 57 3 5 666 39974786 39975453 0.000000e+00 880.0
26 TraesCS5D01G071300 chr2B 94.231 52 3 0 758 809 58851660 58851609 3.620000e-11 80.5
27 TraesCS5D01G071300 chr6D 90.193 673 59 6 1 670 411995241 411994573 0.000000e+00 870.0
28 TraesCS5D01G071300 chr1B 90.193 673 56 8 1 671 530956181 530955517 0.000000e+00 869.0
29 TraesCS5D01G071300 chr1B 89.855 69 7 0 3673 3741 373317837 373317905 6.010000e-14 89.8
30 TraesCS5D01G071300 chr1B 92.000 50 2 2 757 806 606388269 606388222 7.830000e-08 69.4
31 TraesCS5D01G071300 chr1B 92.000 50 2 2 757 806 606393061 606393014 7.830000e-08 69.4
32 TraesCS5D01G071300 chr1B 92.000 50 2 2 757 806 606397861 606397814 7.830000e-08 69.4
33 TraesCS5D01G071300 chr7B 90.030 672 63 3 1 671 9000733 9000065 0.000000e+00 867.0
34 TraesCS5D01G071300 chr7B 90.196 51 5 0 761 811 199754569 199754619 2.820000e-07 67.6
35 TraesCS5D01G071300 chr4B 93.599 578 35 1 3740 4315 643287986 643288563 0.000000e+00 861.0
36 TraesCS5D01G071300 chr6B 90.000 630 46 11 3739 4365 720555787 720555172 0.000000e+00 798.0


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 TraesCS5D01G071300 chr5D 69325556 69329920 4364 False 8061.000000 8061 100.000000 1 4365 1 chr5D.!!$F1 4364
1 TraesCS5D01G071300 chr5A 60107478 60111222 3744 False 1504.333333 2645 93.874333 762 3671 3 chr5A.!!$F1 2909
2 TraesCS5D01G071300 chr5B 75206378 75210897 4519 False 1457.000000 2580 94.364667 805 3674 3 chr5B.!!$F1 2869
3 TraesCS5D01G071300 chr2D 49189903 49193147 3244 True 520.700000 1110 94.259000 1685 2843 3 chr2D.!!$R1 1158
4 TraesCS5D01G071300 chr3B 3135259 3135927 668 True 952.000000 952 92.388000 1 668 1 chr3B.!!$R1 667
5 TraesCS5D01G071300 chr3B 821047249 821047867 618 False 920.000000 920 93.429000 3742 4365 1 chr3B.!!$F2 623
6 TraesCS5D01G071300 chr3B 379660363 379660983 620 False 728.000000 728 87.975000 3742 4365 1 chr3B.!!$F1 623
7 TraesCS5D01G071300 chr2A 549954344 549955018 674 False 941.000000 941 91.876000 1 674 1 chr2A.!!$F3 673
8 TraesCS5D01G071300 chr2A 403607716 403608328 612 False 789.000000 789 89.809000 3741 4365 1 chr2A.!!$F2 624
9 TraesCS5D01G071300 chr2A 401607753 401608366 613 False 778.000000 778 89.507000 3741 4365 1 chr2A.!!$F1 624
10 TraesCS5D01G071300 chr1D 16204908 16205577 669 False 931.000000 931 91.815000 1 668 1 chr1D.!!$F1 667
11 TraesCS5D01G071300 chr1D 310840617 310841235 618 True 869.000000 869 91.892000 3739 4365 1 chr1D.!!$R1 626
12 TraesCS5D01G071300 chr3A 20910743 20911409 666 False 909.000000 909 91.207000 1 671 1 chr3A.!!$F1 670
13 TraesCS5D01G071300 chr3A 9968223 9968839 616 True 835.000000 835 91.054000 3742 4365 1 chr3A.!!$R1 623
14 TraesCS5D01G071300 chr6A 588055197 588055809 612 True 887.000000 887 92.628000 3742 4365 1 chr6A.!!$R1 623
15 TraesCS5D01G071300 chr2B 477530586 477531253 667 True 887.000000 887 90.611000 3 672 1 chr2B.!!$R2 669
16 TraesCS5D01G071300 chr2B 39974786 39975453 667 False 880.000000 880 90.569000 5 666 1 chr2B.!!$F1 661
17 TraesCS5D01G071300 chr6D 411994573 411995241 668 True 870.000000 870 90.193000 1 670 1 chr6D.!!$R1 669
18 TraesCS5D01G071300 chr1B 530955517 530956181 664 True 869.000000 869 90.193000 1 671 1 chr1B.!!$R1 670
19 TraesCS5D01G071300 chr7B 9000065 9000733 668 True 867.000000 867 90.030000 1 671 1 chr7B.!!$R1 670
20 TraesCS5D01G071300 chr4B 643287986 643288563 577 False 861.000000 861 93.599000 3740 4315 1 chr4B.!!$F1 575
21 TraesCS5D01G071300 chr6B 720555172 720555787 615 True 798.000000 798 90.000000 3739 4365 1 chr6B.!!$R1 626

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
161 163 0.597568 CAAGAATGAGCGTGGCCAAA 59.402 50.0 7.24 0.0 0.00 3.28 F
680 693 0.676736 ATGCTCTTAGCCTAGCGTCC 59.323 55.0 0.00 0.0 41.51 4.79 F
1343 1363 0.105194 TTCACCCTCACCCTCACTCA 60.105 55.0 0.00 0.0 0.00 3.41 F
1545 1570 0.683179 TGGTCGATGAGTGGGTCGAT 60.683 55.0 0.63 0.0 46.91 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1355 1.662438 GAGCGAGGGAGTGAGTGAGG 61.662 65.0 0.0 0.0 0.0 3.86 R
2195 5278 0.327924 TCGCACATTTCCCTGACCAT 59.672 50.0 0.0 0.0 0.0 3.55 R
2198 5281 0.521735 GGTTCGCACATTTCCCTGAC 59.478 55.0 0.0 0.0 0.0 3.51 R
3367 6457 0.813821 GCAGGATCAAGGCAAAGACC 59.186 55.0 0.0 0.0 0.0 3.85 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
81 83 5.023452 TGTGAGAGGACCAGCTAGATTTTA 58.977 41.667 0.00 0.00 0.00 1.52
161 163 0.597568 CAAGAATGAGCGTGGCCAAA 59.402 50.000 7.24 0.00 0.00 3.28
190 192 7.131907 AGACTACTCTCACTATGAGCTCTTA 57.868 40.000 16.19 12.12 43.95 2.10
288 290 3.734231 GCCGAAATGCATGATGATCTTTG 59.266 43.478 0.00 0.00 0.00 2.77
292 294 6.213677 CGAAATGCATGATGATCTTTGGAAT 58.786 36.000 0.00 0.00 0.00 3.01
315 319 1.680522 CTCATCGAGGAGTGGTGGGG 61.681 65.000 18.66 0.00 0.00 4.96
329 333 2.312640 TGGGGATGGAATGGCCGAA 61.313 57.895 0.00 0.00 40.66 4.30
480 484 8.134895 GTGTTTGATCTTCTTGGTTGTATTTGA 58.865 33.333 0.00 0.00 0.00 2.69
530 542 2.166007 GCGTAGTATTTTTGCAGCGTG 58.834 47.619 0.00 0.00 0.00 5.34
550 562 2.878429 CTGGAGCTACTCACGCGT 59.122 61.111 5.58 5.58 31.08 6.01
562 574 3.323243 ACTCACGCGTGCTAAAGTTTAT 58.677 40.909 33.63 7.47 0.00 1.40
563 575 3.367025 ACTCACGCGTGCTAAAGTTTATC 59.633 43.478 33.63 0.00 0.00 1.75
673 686 2.170187 CTGTTGGAGATGCTCTTAGCCT 59.830 50.000 0.00 0.00 41.51 4.58
674 687 3.374764 TGTTGGAGATGCTCTTAGCCTA 58.625 45.455 0.00 0.00 41.51 3.93
675 688 3.386078 TGTTGGAGATGCTCTTAGCCTAG 59.614 47.826 0.00 0.00 41.51 3.02
676 689 1.967066 TGGAGATGCTCTTAGCCTAGC 59.033 52.381 0.00 0.00 41.51 3.42
677 690 1.067915 GGAGATGCTCTTAGCCTAGCG 60.068 57.143 0.00 0.00 41.51 4.26
678 691 1.611491 GAGATGCTCTTAGCCTAGCGT 59.389 52.381 0.00 0.00 41.51 5.07
679 692 2.058913 GATGCTCTTAGCCTAGCGTC 57.941 55.000 0.00 0.00 44.83 5.19
680 693 0.676736 ATGCTCTTAGCCTAGCGTCC 59.323 55.000 0.00 0.00 41.51 4.79
681 694 1.364536 GCTCTTAGCCTAGCGTCCC 59.635 63.158 0.00 0.00 34.48 4.46
682 695 1.655329 CTCTTAGCCTAGCGTCCCG 59.345 63.158 0.00 0.00 0.00 5.14
694 707 2.806621 GTCCCGCGTTGGACGTAC 60.807 66.667 17.04 0.00 44.98 3.67
695 708 4.403137 TCCCGCGTTGGACGTACG 62.403 66.667 15.01 15.01 44.73 3.67
701 714 3.681705 CGTTGGACGTACGCTCTAA 57.318 52.632 16.72 13.00 36.74 2.10
702 715 1.531912 CGTTGGACGTACGCTCTAAG 58.468 55.000 16.72 3.52 36.74 2.18
703 716 1.129251 CGTTGGACGTACGCTCTAAGA 59.871 52.381 16.72 0.00 36.74 2.10
704 717 2.223203 CGTTGGACGTACGCTCTAAGAT 60.223 50.000 16.72 0.00 36.74 2.40
705 718 3.001634 CGTTGGACGTACGCTCTAAGATA 59.998 47.826 16.72 0.00 36.74 1.98
706 719 4.494690 CGTTGGACGTACGCTCTAAGATAA 60.495 45.833 16.72 0.00 36.74 1.75
707 720 5.335127 GTTGGACGTACGCTCTAAGATAAA 58.665 41.667 16.72 0.00 0.00 1.40
708 721 4.913376 TGGACGTACGCTCTAAGATAAAC 58.087 43.478 16.72 0.00 0.00 2.01
709 722 4.395854 TGGACGTACGCTCTAAGATAAACA 59.604 41.667 16.72 0.33 0.00 2.83
710 723 5.106197 TGGACGTACGCTCTAAGATAAACAA 60.106 40.000 16.72 0.00 0.00 2.83
711 724 5.975939 GGACGTACGCTCTAAGATAAACAAT 59.024 40.000 16.72 0.00 0.00 2.71
712 725 6.074994 GGACGTACGCTCTAAGATAAACAATG 60.075 42.308 16.72 0.00 0.00 2.82
713 726 6.327934 ACGTACGCTCTAAGATAAACAATGT 58.672 36.000 16.72 0.00 0.00 2.71
714 727 7.475015 ACGTACGCTCTAAGATAAACAATGTA 58.525 34.615 16.72 0.00 0.00 2.29
715 728 8.133627 ACGTACGCTCTAAGATAAACAATGTAT 58.866 33.333 16.72 0.00 0.00 2.29
716 729 8.628279 CGTACGCTCTAAGATAAACAATGTATC 58.372 37.037 0.52 0.00 0.00 2.24
717 730 9.459640 GTACGCTCTAAGATAAACAATGTATCA 57.540 33.333 0.00 0.00 31.49 2.15
719 732 9.547753 ACGCTCTAAGATAAACAATGTATCATT 57.452 29.630 0.00 0.00 31.49 2.57
754 767 9.495572 GGATAATAAGGTAGTCTTGATTCAAGG 57.504 37.037 22.86 7.77 41.33 3.61
758 771 9.807921 AATAAGGTAGTCTTGATTCAAGGAAAA 57.192 29.630 22.86 4.28 41.33 2.29
759 772 7.751768 AAGGTAGTCTTGATTCAAGGAAAAG 57.248 36.000 22.86 0.94 41.33 2.27
760 773 7.079451 AGGTAGTCTTGATTCAAGGAAAAGA 57.921 36.000 22.86 3.30 41.33 2.52
778 791 6.977502 GGAAAAGATAAGTACTTCCTCCGTAC 59.022 42.308 12.39 3.70 37.96 3.67
780 793 7.657023 AAAGATAAGTACTTCCTCCGTACAT 57.343 36.000 12.39 0.00 39.66 2.29
781 794 8.757982 AAAGATAAGTACTTCCTCCGTACATA 57.242 34.615 12.39 0.00 39.66 2.29
792 805 8.305317 ACTTCCTCCGTACATAAATATAAGAGC 58.695 37.037 0.00 0.00 0.00 4.09
795 808 7.040201 TCCTCCGTACATAAATATAAGAGCGTT 60.040 37.037 0.00 0.00 0.00 4.84
796 809 7.597743 CCTCCGTACATAAATATAAGAGCGTTT 59.402 37.037 0.00 0.00 0.00 3.60
798 811 9.616634 TCCGTACATAAATATAAGAGCGTTTAG 57.383 33.333 0.00 0.00 0.00 1.85
799 812 9.616634 CCGTACATAAATATAAGAGCGTTTAGA 57.383 33.333 0.00 0.00 0.00 2.10
815 832 5.644644 CGTTTAGATTACTACTCCCACGTT 58.355 41.667 0.00 0.00 0.00 3.99
824 841 5.027293 ACTACTCCCACGTTTAAGTTTGT 57.973 39.130 0.00 0.00 0.00 2.83
825 842 4.812626 ACTACTCCCACGTTTAAGTTTGTG 59.187 41.667 0.00 0.00 0.00 3.33
841 858 7.524717 AAGTTTGTGGCTAATACAGAACAAT 57.475 32.000 0.00 0.00 34.33 2.71
848 865 8.584157 TGTGGCTAATACAGAACAATCAATTTT 58.416 29.630 0.00 0.00 0.00 1.82
872 889 7.756395 TCCTAGAAAATACCATACTCTACCG 57.244 40.000 0.00 0.00 0.00 4.02
873 890 7.520798 TCCTAGAAAATACCATACTCTACCGA 58.479 38.462 0.00 0.00 0.00 4.69
874 891 8.000709 TCCTAGAAAATACCATACTCTACCGAA 58.999 37.037 0.00 0.00 0.00 4.30
906 923 4.442733 GTGAGAACGTCAGTTTTCTCTCTG 59.557 45.833 12.52 0.00 45.45 3.35
1335 1355 4.410400 CGCCCCTTCACCCTCACC 62.410 72.222 0.00 0.00 0.00 4.02
1341 1361 0.838122 CCTTCACCCTCACCCTCACT 60.838 60.000 0.00 0.00 0.00 3.41
1343 1363 0.105194 TTCACCCTCACCCTCACTCA 60.105 55.000 0.00 0.00 0.00 3.41
1370 1390 3.553437 CTCCGCGCCCGTATACCAG 62.553 68.421 0.00 0.00 0.00 4.00
1379 1404 2.729862 GTATACCAGCGCGCGAGG 60.730 66.667 37.18 33.87 0.00 4.63
1545 1570 0.683179 TGGTCGATGAGTGGGTCGAT 60.683 55.000 0.63 0.00 46.91 3.59
1569 1594 3.711814 TTGGCCCGCGAATGGAGA 61.712 61.111 8.23 0.00 0.00 3.71
1656 1681 2.125512 GGCGTGAGAGGAATGCGT 60.126 61.111 0.00 0.00 0.00 5.24
1772 1837 9.517609 CTGTAGAGCGTAGTGACTAAATTTTAT 57.482 33.333 0.00 0.00 0.00 1.40
1878 1955 1.473257 GCTGAGTCGCATATCAACCCA 60.473 52.381 2.68 0.00 0.00 4.51
2024 2101 3.737266 CACACAATGGTCAGTGCAATTTC 59.263 43.478 0.00 0.00 39.30 2.17
2054 2132 9.982291 TTCAATATTGTTTCTTCGTAATAGCAC 57.018 29.630 14.97 0.00 0.00 4.40
2055 2133 9.157104 TCAATATTGTTTCTTCGTAATAGCACA 57.843 29.630 14.97 0.00 0.00 4.57
2056 2134 9.210426 CAATATTGTTTCTTCGTAATAGCACAC 57.790 33.333 7.32 0.00 0.00 3.82
2057 2135 6.795098 ATTGTTTCTTCGTAATAGCACACA 57.205 33.333 0.00 0.00 0.00 3.72
2078 5159 7.701924 CACACAACGGATTCTTTTATGCAATAT 59.298 33.333 0.00 0.00 0.00 1.28
2129 5210 4.270325 AGTTTCTTCGTACAAGAAGCACAC 59.730 41.667 23.13 16.57 45.28 3.82
2147 5228 4.202050 GCACACCATGTTCTGACTTTTCTT 60.202 41.667 0.00 0.00 0.00 2.52
2177 5258 3.282021 CCATATATATGTGTGCCCTGGC 58.718 50.000 19.11 0.00 35.36 4.85
2195 5278 4.766891 CCTGGCTGATCCTTTTTAACTCAA 59.233 41.667 0.00 0.00 35.26 3.02
2198 5281 5.185635 TGGCTGATCCTTTTTAACTCAATGG 59.814 40.000 0.00 0.00 35.26 3.16
2428 5511 5.500234 CTCTTCCAATCCCACAAGATAACA 58.500 41.667 0.00 0.00 0.00 2.41
2658 5742 3.887621 TGCACTACTCCCTGTTATGAC 57.112 47.619 0.00 0.00 0.00 3.06
2671 5756 5.584649 CCCTGTTATGACGAATTAAGCAAGA 59.415 40.000 0.00 0.00 0.00 3.02
3052 6140 2.866762 GGGTTCAAGTATAGAAGCAGCG 59.133 50.000 7.32 0.00 43.33 5.18
3089 6177 5.970592 TGTCTCTTGGAGATCATGTAAGTG 58.029 41.667 0.00 0.00 40.98 3.16
3097 6185 3.881688 GAGATCATGTAAGTGCTGCCATT 59.118 43.478 0.00 0.00 0.00 3.16
3111 6199 3.305676 GCTGCCATTCTTCGCTCTATCTA 60.306 47.826 0.00 0.00 0.00 1.98
3128 6216 7.121907 GCTCTATCTACACTCCACATCATATCA 59.878 40.741 0.00 0.00 0.00 2.15
3129 6217 9.187996 CTCTATCTACACTCCACATCATATCAT 57.812 37.037 0.00 0.00 0.00 2.45
3130 6218 8.964772 TCTATCTACACTCCACATCATATCATG 58.035 37.037 0.00 0.00 0.00 3.07
3184 6274 1.067199 CGAGTCCGGTCGGTTTAACG 61.067 60.000 9.36 6.18 36.26 3.18
3253 6343 1.092345 GGCCTGAGGAGTTTGCGATC 61.092 60.000 0.65 0.00 0.00 3.69
3377 6467 2.017049 GCATATGAACGGTCTTTGCCT 58.983 47.619 6.97 0.00 0.00 4.75
3683 6773 4.146640 GGCACGAACCGAATTTGC 57.853 55.556 0.00 0.00 0.00 3.68
3684 6774 1.795962 GGCACGAACCGAATTTGCG 60.796 57.895 0.00 0.00 33.84 4.85
3715 6805 1.212616 GGCACGAAAGATCAGATCCG 58.787 55.000 6.80 6.41 0.00 4.18
3716 6806 1.212616 GCACGAAAGATCAGATCCGG 58.787 55.000 6.80 0.00 0.00 5.14
3717 6807 1.471676 GCACGAAAGATCAGATCCGGT 60.472 52.381 6.80 0.00 0.00 5.28
3718 6808 2.223735 GCACGAAAGATCAGATCCGGTA 60.224 50.000 6.80 0.00 0.00 4.02
3719 6809 3.737047 GCACGAAAGATCAGATCCGGTAA 60.737 47.826 6.80 0.00 0.00 2.85
3720 6810 4.430007 CACGAAAGATCAGATCCGGTAAA 58.570 43.478 6.80 0.00 0.00 2.01
3721 6811 4.267928 CACGAAAGATCAGATCCGGTAAAC 59.732 45.833 6.80 0.00 0.00 2.01
3722 6812 4.081862 ACGAAAGATCAGATCCGGTAAACA 60.082 41.667 6.80 0.00 0.00 2.83
3723 6813 4.267928 CGAAAGATCAGATCCGGTAAACAC 59.732 45.833 6.80 0.00 0.00 3.32
3724 6814 4.819105 AAGATCAGATCCGGTAAACACA 57.181 40.909 6.80 0.00 0.00 3.72
3725 6815 5.359194 AAGATCAGATCCGGTAAACACAT 57.641 39.130 6.80 0.00 0.00 3.21
3726 6816 6.479972 AAGATCAGATCCGGTAAACACATA 57.520 37.500 6.80 0.00 0.00 2.29
3727 6817 5.844004 AGATCAGATCCGGTAAACACATAC 58.156 41.667 6.80 0.00 0.00 2.39
3728 6818 4.395959 TCAGATCCGGTAAACACATACC 57.604 45.455 0.00 0.00 41.65 2.73
3822 6913 2.411628 AAAAACCCCACAAAACTGGC 57.588 45.000 0.00 0.00 0.00 4.85
3836 6927 1.352622 ACTGGCCCTCCAACTTGACA 61.353 55.000 0.00 0.00 42.91 3.58
3865 6957 2.437651 CAAAATCACCCAAAACCACCCT 59.562 45.455 0.00 0.00 0.00 4.34
3877 6969 1.152984 CCACCCTGAACTGCACACA 60.153 57.895 0.00 0.00 0.00 3.72
4058 7155 2.586425 CTGTCCTCTCCTCCTCATCTC 58.414 57.143 0.00 0.00 0.00 2.75
4059 7156 2.175499 CTGTCCTCTCCTCCTCATCTCT 59.825 54.545 0.00 0.00 0.00 3.10
4060 7157 2.091939 TGTCCTCTCCTCCTCATCTCTG 60.092 54.545 0.00 0.00 0.00 3.35
4061 7158 2.091885 GTCCTCTCCTCCTCATCTCTGT 60.092 54.545 0.00 0.00 0.00 3.41
4063 7160 2.586425 CTCTCCTCCTCATCTCTGTCC 58.414 57.143 0.00 0.00 0.00 4.02
4064 7161 2.175499 CTCTCCTCCTCATCTCTGTCCT 59.825 54.545 0.00 0.00 0.00 3.85
4334 7439 0.107800 GGGTTCGAAGGGGAAGTAGC 60.108 60.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 5.324409 TGTACCAAAGCATCTTTTGATCCT 58.676 37.500 0.37 0.00 39.79 3.24
190 192 1.079819 CACTCGCACGGGATGTCTT 60.080 57.895 0.00 0.00 0.00 3.01
288 290 3.305950 CCACTCCTCGATGAGATCATTCC 60.306 52.174 22.48 0.00 36.57 3.01
292 294 2.027385 CACCACTCCTCGATGAGATCA 58.973 52.381 22.48 0.00 36.22 2.92
315 319 2.480244 GCTCTTTTTCGGCCATTCCATC 60.480 50.000 2.24 0.00 34.01 3.51
329 333 4.171005 CGCACAAATCATGATGCTCTTTT 58.829 39.130 9.46 0.00 35.35 2.27
450 454 6.877236 ACAACCAAGAAGATCAAACACAAAT 58.123 32.000 0.00 0.00 0.00 2.32
480 484 3.307674 CGCACAAACAACATATGCACTT 58.692 40.909 1.58 0.00 36.02 3.16
513 524 3.196007 GCACACGCTGCAAAAATACTA 57.804 42.857 0.00 0.00 46.29 1.82
530 542 1.807573 GCGTGAGTAGCTCCAGCAC 60.808 63.158 0.48 0.00 45.16 4.40
550 562 1.011333 GGCCGCGATAAACTTTAGCA 58.989 50.000 8.23 0.00 0.00 3.49
646 659 2.270205 CATCTCCAACAGCCGCCT 59.730 61.111 0.00 0.00 0.00 5.52
684 697 2.907910 TCTTAGAGCGTACGTCCAAC 57.092 50.000 17.90 0.00 0.00 3.77
685 698 5.106197 TGTTTATCTTAGAGCGTACGTCCAA 60.106 40.000 17.90 7.67 0.00 3.53
686 699 4.395854 TGTTTATCTTAGAGCGTACGTCCA 59.604 41.667 17.90 0.00 0.00 4.02
687 700 4.913376 TGTTTATCTTAGAGCGTACGTCC 58.087 43.478 17.90 8.94 0.00 4.79
688 701 6.471519 ACATTGTTTATCTTAGAGCGTACGTC 59.528 38.462 17.90 12.77 0.00 4.34
689 702 6.327934 ACATTGTTTATCTTAGAGCGTACGT 58.672 36.000 17.90 3.43 0.00 3.57
690 703 6.807708 ACATTGTTTATCTTAGAGCGTACG 57.192 37.500 11.84 11.84 0.00 3.67
691 704 9.459640 TGATACATTGTTTATCTTAGAGCGTAC 57.540 33.333 0.00 0.00 0.00 3.67
693 706 9.547753 AATGATACATTGTTTATCTTAGAGCGT 57.452 29.630 0.00 0.00 0.00 5.07
728 741 9.495572 CCTTGAATCAAGACTACCTTATTATCC 57.504 37.037 23.32 0.00 43.42 2.59
732 745 9.807921 TTTTCCTTGAATCAAGACTACCTTATT 57.192 29.630 23.32 0.00 43.42 1.40
733 746 9.454859 CTTTTCCTTGAATCAAGACTACCTTAT 57.545 33.333 23.32 0.00 43.42 1.73
734 747 8.656806 TCTTTTCCTTGAATCAAGACTACCTTA 58.343 33.333 23.32 0.56 43.42 2.69
735 748 7.518188 TCTTTTCCTTGAATCAAGACTACCTT 58.482 34.615 23.32 0.00 43.42 3.50
736 749 7.079451 TCTTTTCCTTGAATCAAGACTACCT 57.921 36.000 23.32 0.00 43.42 3.08
737 750 7.929941 ATCTTTTCCTTGAATCAAGACTACC 57.070 36.000 23.32 0.00 43.42 3.18
745 758 9.449719 GGAAGTACTTATCTTTTCCTTGAATCA 57.550 33.333 8.42 0.00 35.53 2.57
746 759 9.674068 AGGAAGTACTTATCTTTTCCTTGAATC 57.326 33.333 8.42 0.00 43.80 2.52
747 760 9.674068 GAGGAAGTACTTATCTTTTCCTTGAAT 57.326 33.333 8.42 0.00 45.64 2.57
748 761 8.101419 GGAGGAAGTACTTATCTTTTCCTTGAA 58.899 37.037 8.42 0.00 45.64 2.69
749 762 7.578955 CGGAGGAAGTACTTATCTTTTCCTTGA 60.579 40.741 8.42 0.00 45.64 3.02
750 763 6.535508 CGGAGGAAGTACTTATCTTTTCCTTG 59.464 42.308 8.42 2.74 45.64 3.61
751 764 6.212993 ACGGAGGAAGTACTTATCTTTTCCTT 59.787 38.462 8.42 1.25 45.64 3.36
753 766 5.975282 ACGGAGGAAGTACTTATCTTTTCC 58.025 41.667 8.42 3.63 38.03 3.13
754 767 7.542025 TGTACGGAGGAAGTACTTATCTTTTC 58.458 38.462 8.42 0.00 43.41 2.29
755 768 7.472334 TGTACGGAGGAAGTACTTATCTTTT 57.528 36.000 8.42 2.13 43.41 2.27
756 769 7.657023 ATGTACGGAGGAAGTACTTATCTTT 57.343 36.000 8.42 4.28 43.41 2.52
757 770 8.757982 TTATGTACGGAGGAAGTACTTATCTT 57.242 34.615 8.42 0.00 43.41 2.40
758 771 8.757982 TTTATGTACGGAGGAAGTACTTATCT 57.242 34.615 8.42 9.27 43.41 1.98
769 782 6.432162 ACGCTCTTATATTTATGTACGGAGGA 59.568 38.462 0.00 0.00 0.00 3.71
787 800 5.655532 TGGGAGTAGTAATCTAAACGCTCTT 59.344 40.000 0.00 0.00 0.00 2.85
792 805 5.240713 ACGTGGGAGTAGTAATCTAAACG 57.759 43.478 14.21 14.21 0.00 3.60
795 808 8.353423 ACTTAAACGTGGGAGTAGTAATCTAA 57.647 34.615 0.00 0.00 0.00 2.10
796 809 7.944729 ACTTAAACGTGGGAGTAGTAATCTA 57.055 36.000 0.00 0.00 0.00 1.98
798 811 7.386025 ACAAACTTAAACGTGGGAGTAGTAATC 59.614 37.037 0.00 0.00 0.00 1.75
799 812 7.172019 CACAAACTTAAACGTGGGAGTAGTAAT 59.828 37.037 0.00 0.00 0.00 1.89
800 813 6.479660 CACAAACTTAAACGTGGGAGTAGTAA 59.520 38.462 0.00 0.00 0.00 2.24
801 814 5.984926 CACAAACTTAAACGTGGGAGTAGTA 59.015 40.000 0.00 0.00 0.00 1.82
802 815 4.812626 CACAAACTTAAACGTGGGAGTAGT 59.187 41.667 0.00 0.00 0.00 2.73
803 816 4.212636 CCACAAACTTAAACGTGGGAGTAG 59.787 45.833 0.00 0.00 44.26 2.57
815 832 8.453238 TTGTTCTGTATTAGCCACAAACTTAA 57.547 30.769 0.00 0.00 30.73 1.85
824 841 8.250332 GGAAAATTGATTGTTCTGTATTAGCCA 58.750 33.333 0.00 0.00 0.00 4.75
825 842 8.470002 AGGAAAATTGATTGTTCTGTATTAGCC 58.530 33.333 0.00 0.00 0.00 3.93
848 865 7.520798 TCGGTAGAGTATGGTATTTTCTAGGA 58.479 38.462 0.00 0.00 0.00 2.94
852 869 7.893124 TCTTCGGTAGAGTATGGTATTTTCT 57.107 36.000 0.00 0.00 0.00 2.52
866 883 0.242825 CACGGTTGCTCTTCGGTAGA 59.757 55.000 0.00 0.00 0.00 2.59
867 884 0.242825 TCACGGTTGCTCTTCGGTAG 59.757 55.000 0.00 0.00 0.00 3.18
869 886 1.006102 CTCACGGTTGCTCTTCGGT 60.006 57.895 0.00 0.00 0.00 4.69
870 887 0.319555 TTCTCACGGTTGCTCTTCGG 60.320 55.000 0.00 0.00 0.00 4.30
871 888 0.784778 GTTCTCACGGTTGCTCTTCG 59.215 55.000 0.00 0.00 0.00 3.79
872 889 0.784778 CGTTCTCACGGTTGCTCTTC 59.215 55.000 0.00 0.00 43.16 2.87
873 890 2.900528 CGTTCTCACGGTTGCTCTT 58.099 52.632 0.00 0.00 43.16 2.85
874 891 4.655527 CGTTCTCACGGTTGCTCT 57.344 55.556 0.00 0.00 43.16 4.09
906 923 9.930693 TTTTATCTTTACTTTGGAGAGAGAGAC 57.069 33.333 0.00 0.00 0.00 3.36
1143 1163 4.719369 GACTGCCGCGAGAACCGT 62.719 66.667 8.23 0.00 41.15 4.83
1305 1325 3.110178 GGGCGAACCGTGTCGAAG 61.110 66.667 8.97 0.00 43.86 3.79
1335 1355 1.662438 GAGCGAGGGAGTGAGTGAGG 61.662 65.000 0.00 0.00 0.00 3.86
1379 1404 2.436824 GCGAAAGGGGGAGTGAGC 60.437 66.667 0.00 0.00 0.00 4.26
1390 1415 4.383602 CACCAACGGCGGCGAAAG 62.384 66.667 38.93 25.26 0.00 2.62
1569 1594 1.810532 GAGCTCACCGATCGAACCT 59.189 57.895 18.66 5.08 0.00 3.50
1772 1837 5.413309 AAACTCCAACAACCAAATCACAA 57.587 34.783 0.00 0.00 0.00 3.33
1878 1955 6.435277 ACAACTTTAATCAGGTCATTCTGCAT 59.565 34.615 0.00 0.00 34.91 3.96
2044 2122 3.863424 AGAATCCGTTGTGTGCTATTACG 59.137 43.478 0.00 0.00 0.00 3.18
2045 2123 5.796350 AAGAATCCGTTGTGTGCTATTAC 57.204 39.130 0.00 0.00 0.00 1.89
2048 2126 6.677920 GCATAAAAGAATCCGTTGTGTGCTAT 60.678 38.462 0.00 0.00 0.00 2.97
2049 2127 5.391523 GCATAAAAGAATCCGTTGTGTGCTA 60.392 40.000 0.00 0.00 0.00 3.49
2050 2128 4.615912 GCATAAAAGAATCCGTTGTGTGCT 60.616 41.667 0.00 0.00 0.00 4.40
2051 2129 3.608073 GCATAAAAGAATCCGTTGTGTGC 59.392 43.478 0.00 0.00 0.00 4.57
2052 2130 4.793071 TGCATAAAAGAATCCGTTGTGTG 58.207 39.130 0.00 0.00 0.00 3.82
2053 2131 5.446143 TTGCATAAAAGAATCCGTTGTGT 57.554 34.783 0.00 0.00 0.00 3.72
2054 2132 7.379529 GGATATTGCATAAAAGAATCCGTTGTG 59.620 37.037 0.00 0.00 0.00 3.33
2055 2133 7.285401 AGGATATTGCATAAAAGAATCCGTTGT 59.715 33.333 0.00 0.00 0.00 3.32
2056 2134 7.651808 AGGATATTGCATAAAAGAATCCGTTG 58.348 34.615 0.00 0.00 0.00 4.10
2057 2135 7.040409 GGAGGATATTGCATAAAAGAATCCGTT 60.040 37.037 0.00 0.00 0.00 4.44
2078 5159 4.624913 AGATCCATGAACTGTAAGGAGGA 58.375 43.478 0.00 0.00 39.30 3.71
2129 5210 6.038603 TGTCTTGAAGAAAAGTCAGAACATGG 59.961 38.462 0.00 0.00 0.00 3.66
2147 5228 6.710295 GGCACACATATATATGGTTGTCTTGA 59.290 38.462 23.44 0.00 38.00 3.02
2177 5258 7.362401 CCTGACCATTGAGTTAAAAAGGATCAG 60.362 40.741 0.00 0.00 0.00 2.90
2195 5278 0.327924 TCGCACATTTCCCTGACCAT 59.672 50.000 0.00 0.00 0.00 3.55
2198 5281 0.521735 GGTTCGCACATTTCCCTGAC 59.478 55.000 0.00 0.00 0.00 3.51
2309 5392 4.753186 AGTAAGGACTTGGAAGAGAGGAA 58.247 43.478 0.00 0.00 28.61 3.36
2428 5511 3.445096 GCTCCTTCAAATGTGCCATAAGT 59.555 43.478 0.00 0.00 0.00 2.24
2658 5742 6.563422 TGGAAATTCCATCTTGCTTAATTCG 58.437 36.000 11.23 0.00 42.67 3.34
2702 5790 9.722317 ATGGTTAAATACATTAGGGAATTCCAA 57.278 29.630 25.67 12.90 38.24 3.53
2864 5952 3.430042 AGTCCAATGTGTGCATTCTCT 57.570 42.857 0.00 0.00 42.91 3.10
2931 6019 2.518349 CACCCCTGTGTTTGCCGT 60.518 61.111 0.00 0.00 37.72 5.68
3052 6140 3.460857 AGAGACATTCCGCTCAATACC 57.539 47.619 0.00 0.00 33.62 2.73
3089 6177 1.797635 GATAGAGCGAAGAATGGCAGC 59.202 52.381 0.00 0.00 31.86 5.25
3097 6185 3.878103 GTGGAGTGTAGATAGAGCGAAGA 59.122 47.826 0.00 0.00 0.00 2.87
3111 6199 7.414429 CGAAAAACATGATATGATGTGGAGTGT 60.414 37.037 8.66 0.00 36.66 3.55
3128 6216 7.651704 AGCTAGTTTGTTAAATGCGAAAAACAT 59.348 29.630 0.00 0.00 32.31 2.71
3129 6217 6.975772 AGCTAGTTTGTTAAATGCGAAAAACA 59.024 30.769 0.00 0.00 31.53 2.83
3130 6218 7.378728 AGAGCTAGTTTGTTAAATGCGAAAAAC 59.621 33.333 0.00 0.00 0.00 2.43
3184 6274 3.367630 CGACCTGCATTAACAAATTTGGC 59.632 43.478 21.74 14.77 0.00 4.52
3276 6366 3.889538 CCCGATGTCATGACCTTCTACTA 59.110 47.826 22.85 1.92 0.00 1.82
3367 6457 0.813821 GCAGGATCAAGGCAAAGACC 59.186 55.000 0.00 0.00 0.00 3.85
3484 6574 7.022055 TCAGCTTTCGACAAAATTTCTACAA 57.978 32.000 0.00 0.00 0.00 2.41
3689 6779 2.014093 GATCTTTCGTGCCGTCTGCG 62.014 60.000 0.00 0.00 45.60 5.18
3690 6780 1.014044 TGATCTTTCGTGCCGTCTGC 61.014 55.000 0.00 0.00 41.77 4.26
3691 6781 0.994995 CTGATCTTTCGTGCCGTCTG 59.005 55.000 0.00 0.00 0.00 3.51
3692 6782 0.888619 TCTGATCTTTCGTGCCGTCT 59.111 50.000 0.00 0.00 0.00 4.18
3693 6783 1.855360 GATCTGATCTTTCGTGCCGTC 59.145 52.381 10.37 0.00 0.00 4.79
3694 6784 1.471676 GGATCTGATCTTTCGTGCCGT 60.472 52.381 16.61 0.00 0.00 5.68
3695 6785 1.212616 GGATCTGATCTTTCGTGCCG 58.787 55.000 16.61 0.00 0.00 5.69
3696 6786 1.212616 CGGATCTGATCTTTCGTGCC 58.787 55.000 16.61 0.00 0.00 5.01
3697 6787 1.212616 CCGGATCTGATCTTTCGTGC 58.787 55.000 16.61 0.00 0.00 5.34
3698 6788 2.586258 ACCGGATCTGATCTTTCGTG 57.414 50.000 9.46 8.85 0.00 4.35
3699 6789 4.081862 TGTTTACCGGATCTGATCTTTCGT 60.082 41.667 9.46 10.06 0.00 3.85
3700 6790 4.267928 GTGTTTACCGGATCTGATCTTTCG 59.732 45.833 9.46 11.67 0.00 3.46
3701 6791 5.175859 TGTGTTTACCGGATCTGATCTTTC 58.824 41.667 9.46 0.49 0.00 2.62
3702 6792 5.160607 TGTGTTTACCGGATCTGATCTTT 57.839 39.130 9.46 4.86 0.00 2.52
3703 6793 4.819105 TGTGTTTACCGGATCTGATCTT 57.181 40.909 9.46 5.18 0.00 2.40
3704 6794 5.221461 GGTATGTGTTTACCGGATCTGATCT 60.221 44.000 9.46 0.73 32.78 2.75
3705 6795 4.989168 GGTATGTGTTTACCGGATCTGATC 59.011 45.833 9.46 9.18 32.78 2.92
3706 6796 4.957296 GGTATGTGTTTACCGGATCTGAT 58.043 43.478 9.46 0.00 32.78 2.90
3707 6797 4.395959 GGTATGTGTTTACCGGATCTGA 57.604 45.455 9.46 0.00 32.78 3.27
3715 6805 9.228636 CTTTAAATTATGCGGTATGTGTTTACC 57.771 33.333 0.00 0.00 38.63 2.85
3716 6806 9.991388 TCTTTAAATTATGCGGTATGTGTTTAC 57.009 29.630 0.00 0.00 0.00 2.01
3718 6808 8.736244 ACTCTTTAAATTATGCGGTATGTGTTT 58.264 29.630 0.00 0.00 0.00 2.83
3719 6809 8.276252 ACTCTTTAAATTATGCGGTATGTGTT 57.724 30.769 0.00 0.00 0.00 3.32
3720 6810 7.859325 ACTCTTTAAATTATGCGGTATGTGT 57.141 32.000 0.00 0.00 0.00 3.72
3822 6913 0.109342 ACAGCTGTCAAGTTGGAGGG 59.891 55.000 15.25 0.00 38.85 4.30
3836 6927 5.356426 GTTTTGGGTGATTTTGTTACAGCT 58.644 37.500 0.00 0.00 33.43 4.24
3865 6957 3.342909 CGCCATGTGTGCAGTTCA 58.657 55.556 0.00 0.00 0.00 3.18
3932 7025 1.130561 GAAATTGCTAAAGCGCGAGGT 59.869 47.619 12.10 0.00 45.83 3.85
4058 7155 2.183811 CGCAGGAGCAGAGGACAG 59.816 66.667 0.00 0.00 42.27 3.51
4059 7156 2.283173 TCGCAGGAGCAGAGGACA 60.283 61.111 0.00 0.00 42.27 4.02
4060 7157 2.493973 CTCGCAGGAGCAGAGGAC 59.506 66.667 0.00 0.00 42.27 3.85
4063 7160 4.869440 CGCCTCGCAGGAGCAGAG 62.869 72.222 6.40 0.00 42.27 3.35
4334 7439 2.441001 ACCCTGGATAAGCTCATGGAAG 59.559 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.