Multiple sequence alignment - TraesCS6D01G136500

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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 TraesCS6D01G136500 chr6D 100.000 2896 0 0 2072 4967 104965643 104962748 0.000000e+00 5349.0
1 TraesCS6D01G136500 chr6D 100.000 1759 0 0 1 1759 104967714 104965956 0.000000e+00 3249.0
2 TraesCS6D01G136500 chr6D 91.785 633 42 4 8 631 137122080 137121449 0.000000e+00 872.0
3 TraesCS6D01G136500 chr6D 100.000 38 0 0 3426 3463 104964167 104964130 2.480000e-08 71.3
4 TraesCS6D01G136500 chr6D 100.000 38 0 0 3548 3585 104964289 104964252 2.480000e-08 71.3
5 TraesCS6D01G136500 chr6A 94.574 2820 83 36 2087 4867 127095925 127093137 0.000000e+00 4296.0
6 TraesCS6D01G136500 chr6A 95.703 861 23 4 911 1759 127096855 127095997 0.000000e+00 1373.0
7 TraesCS6D01G136500 chr6A 82.692 312 18 11 631 918 127167193 127166894 1.380000e-60 244.0
8 TraesCS6D01G136500 chr6A 90.722 97 5 3 4868 4963 203647365 203647272 5.220000e-25 126.0
9 TraesCS6D01G136500 chr6A 97.368 38 1 0 3426 3463 127094453 127094416 1.150000e-06 65.8
10 TraesCS6D01G136500 chr6B 93.474 2942 95 42 2072 4967 191363584 191360694 0.000000e+00 4279.0
11 TraesCS6D01G136500 chr6B 95.587 997 30 4 768 1759 191364621 191363634 0.000000e+00 1585.0
12 TraesCS6D01G136500 chr2D 90.110 637 53 3 8 634 386839994 386840630 0.000000e+00 819.0
13 TraesCS6D01G136500 chr2D 90.032 632 52 5 8 630 168959936 168959307 0.000000e+00 808.0
14 TraesCS6D01G136500 chr2D 90.080 625 53 5 8 623 187619448 187620072 0.000000e+00 802.0
15 TraesCS6D01G136500 chr4D 89.580 643 56 4 8 641 431734214 431734854 0.000000e+00 806.0
16 TraesCS6D01G136500 chr4D 89.425 643 58 3 8 641 431555548 431556189 0.000000e+00 802.0
17 TraesCS6D01G136500 chr4D 89.425 643 58 3 8 641 431674675 431675316 0.000000e+00 802.0
18 TraesCS6D01G136500 chr4D 89.269 643 59 3 8 641 431621313 431621954 0.000000e+00 797.0
19 TraesCS6D01G136500 chr4D 90.000 100 7 3 4865 4963 118608246 118608343 5.220000e-25 126.0
20 TraesCS6D01G136500 chr4A 89.269 643 58 6 8 641 551396175 551396815 0.000000e+00 795.0
21 TraesCS6D01G136500 chr7D 85.841 565 46 18 2072 2621 436397806 436398351 2.010000e-158 569.0
22 TraesCS6D01G136500 chr7D 84.181 177 17 3 4647 4822 103635118 103635284 1.430000e-35 161.0
23 TraesCS6D01G136500 chr7D 87.156 109 10 3 4856 4963 174281358 174281463 2.430000e-23 121.0
24 TraesCS6D01G136500 chr4B 91.017 423 21 4 2207 2629 440440976 440441381 5.620000e-154 555.0
25 TraesCS6D01G136500 chr4B 89.835 423 27 3 2207 2629 422775376 422774970 3.410000e-146 529.0
26 TraesCS6D01G136500 chr4B 89.598 423 28 3 2207 2629 422774629 422774223 1.580000e-144 523.0
27 TraesCS6D01G136500 chr4B 91.753 97 5 3 4868 4963 13221374 13221280 1.120000e-26 132.0
28 TraesCS6D01G136500 chr4B 89.362 94 7 3 2795 2886 440442127 440442219 1.130000e-21 115.0
29 TraesCS6D01G136500 chr4B 92.405 79 6 0 2795 2873 440441380 440441458 4.060000e-21 113.0
30 TraesCS6D01G136500 chr4B 92.105 76 6 0 2798 2873 422774221 422774146 1.890000e-19 108.0
31 TraesCS6D01G136500 chr4B 92.105 76 6 0 2798 2873 422774968 422774893 1.890000e-19 108.0
32 TraesCS6D01G136500 chr1B 90.544 423 24 3 2207 2629 499394676 499394270 3.380000e-151 545.0
33 TraesCS6D01G136500 chr1B 89.835 423 27 3 2207 2629 499393495 499393089 3.410000e-146 529.0
34 TraesCS6D01G136500 chr1B 87.812 361 26 7 2077 2427 282853856 282853504 1.660000e-109 407.0
35 TraesCS6D01G136500 chr1B 91.000 100 5 3 4867 4965 52314367 52314271 1.120000e-26 132.0
36 TraesCS6D01G136500 chr1B 93.421 76 5 0 2798 2873 499393834 499393759 4.060000e-21 113.0
37 TraesCS6D01G136500 chr1B 91.139 79 7 0 2795 2873 368081504 368081582 1.890000e-19 108.0
38 TraesCS6D01G136500 chr5B 89.598 423 28 3 2207 2629 117937707 117938113 1.580000e-144 523.0
39 TraesCS6D01G136500 chr5B 87.258 361 32 4 2077 2427 360595194 360595550 2.790000e-107 399.0
40 TraesCS6D01G136500 chr5B 88.785 107 12 0 1647 1753 360595049 360595155 1.120000e-26 132.0
41 TraesCS6D01G136500 chr5B 91.139 79 7 0 2795 2873 117938112 117938190 1.890000e-19 108.0
42 TraesCS6D01G136500 chr3B 89.598 423 28 3 2207 2629 678843644 678843238 1.580000e-144 523.0
43 TraesCS6D01G136500 chr3B 86.034 179 14 3 4646 4822 768727430 768727599 1.100000e-41 182.0
44 TraesCS6D01G136500 chr5A 89.373 367 28 3 2072 2427 345359927 345359561 7.580000e-123 451.0
45 TraesCS6D01G136500 chr5A 88.430 121 12 2 4703 4822 255615800 255615919 1.440000e-30 145.0
46 TraesCS6D01G136500 chr5A 89.216 102 6 3 4865 4965 594007374 594007277 6.750000e-24 122.0
47 TraesCS6D01G136500 chr1A 87.293 362 27 7 2077 2427 186718974 186718621 3.600000e-106 396.0
48 TraesCS6D01G136500 chr1A 91.250 80 7 0 1680 1759 186719087 186719008 5.260000e-20 110.0
49 TraesCS6D01G136500 chr2B 85.393 178 14 4 4646 4822 59639059 59638893 1.840000e-39 174.0
50 TraesCS6D01G136500 chr2B 84.746 177 15 4 4647 4822 97385189 97385024 3.080000e-37 167.0
51 TraesCS6D01G136500 chr3D 84.358 179 17 3 4645 4822 335226181 335226013 1.110000e-36 165.0
52 TraesCS6D01G136500 chr7A 86.923 130 15 2 4703 4831 576105012 576104884 1.440000e-30 145.0
53 TraesCS6D01G136500 chr7A 90.816 98 5 3 4867 4963 84242923 84242829 1.450000e-25 128.0
54 TraesCS6D01G136500 chr7A 90.000 100 7 3 4867 4965 700772378 700772281 5.220000e-25 126.0
55 TraesCS6D01G136500 chr1D 91.837 98 5 3 4867 4963 273193628 273193723 3.120000e-27 134.0


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 TraesCS6D01G136500 chr6D 104962748 104967714 4966 True 2185.150000 5349 100.000000 1 4967 4 chr6D.!!$R2 4966
1 TraesCS6D01G136500 chr6D 137121449 137122080 631 True 872.000000 872 91.785000 8 631 1 chr6D.!!$R1 623
2 TraesCS6D01G136500 chr6A 127093137 127096855 3718 True 1911.600000 4296 95.881667 911 4867 3 chr6A.!!$R3 3956
3 TraesCS6D01G136500 chr6B 191360694 191364621 3927 True 2932.000000 4279 94.530500 768 4967 2 chr6B.!!$R1 4199
4 TraesCS6D01G136500 chr2D 386839994 386840630 636 False 819.000000 819 90.110000 8 634 1 chr2D.!!$F2 626
5 TraesCS6D01G136500 chr2D 168959307 168959936 629 True 808.000000 808 90.032000 8 630 1 chr2D.!!$R1 622
6 TraesCS6D01G136500 chr2D 187619448 187620072 624 False 802.000000 802 90.080000 8 623 1 chr2D.!!$F1 615
7 TraesCS6D01G136500 chr4D 431734214 431734854 640 False 806.000000 806 89.580000 8 641 1 chr4D.!!$F5 633
8 TraesCS6D01G136500 chr4D 431555548 431556189 641 False 802.000000 802 89.425000 8 641 1 chr4D.!!$F2 633
9 TraesCS6D01G136500 chr4D 431674675 431675316 641 False 802.000000 802 89.425000 8 641 1 chr4D.!!$F4 633
10 TraesCS6D01G136500 chr4D 431621313 431621954 641 False 797.000000 797 89.269000 8 641 1 chr4D.!!$F3 633
11 TraesCS6D01G136500 chr4A 551396175 551396815 640 False 795.000000 795 89.269000 8 641 1 chr4A.!!$F1 633
12 TraesCS6D01G136500 chr7D 436397806 436398351 545 False 569.000000 569 85.841000 2072 2621 1 chr7D.!!$F3 549
13 TraesCS6D01G136500 chr4B 422774146 422775376 1230 True 317.000000 529 90.910750 2207 2873 4 chr4B.!!$R2 666
14 TraesCS6D01G136500 chr4B 440440976 440442219 1243 False 261.000000 555 90.928000 2207 2886 3 chr4B.!!$F1 679
15 TraesCS6D01G136500 chr1B 499393089 499394676 1587 True 395.666667 545 91.266667 2207 2873 3 chr1B.!!$R3 666
16 TraesCS6D01G136500 chr5B 360595049 360595550 501 False 265.500000 399 88.021500 1647 2427 2 chr5B.!!$F2 780

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
593 604 0.672401 GATCCACGCGTTTGGGAGAA 60.672 55.000 19.87 0.70 37.24 2.87 F
913 924 1.067213 GCTTTGCCGGATTGCCTAAAA 60.067 47.619 5.05 0.00 0.00 1.52 F
1745 1768 1.830279 AACTGCACTGGATCCACATG 58.170 50.000 11.44 13.41 0.00 3.21 F
1753 1776 2.575279 ACTGGATCCACATGCTTTCTCT 59.425 45.455 11.44 0.00 0.00 3.10 F
3680 4194 2.992689 TGCACCGGACTCGCCTAA 60.993 61.111 9.46 0.00 34.56 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1480 1.865865 TCAAGGAGAAGCAACGTGTC 58.134 50.000 0.00 0.0 0.00 3.67 R
2621 3118 2.196595 TCCCCATTGGACGAAATCTCT 58.803 47.619 3.62 0.0 38.61 3.10 R
3680 4194 2.035632 CAGATTTACTCCCCGCTCTCT 58.964 52.381 0.00 0.0 0.00 3.10 R
3726 4240 7.325660 TGCATTTATTTTGTTTTGGAAAGCA 57.674 28.000 0.00 0.0 0.00 3.91 R
4660 5209 1.902765 ATCTCCTGTGGCATCGCACA 61.903 55.000 0.00 0.0 0.00 4.57 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
52 53 8.615878 ATGTAGTTGTAAAAGCATGTCAACTA 57.384 30.769 10.61 10.61 44.11 2.24
112 113 1.209127 GCAGTTGCCGCGTGTAATT 59.791 52.632 4.92 0.00 34.31 1.40
145 146 5.136816 TGCCGTGTGTGATTAACTACTTA 57.863 39.130 0.00 0.00 0.00 2.24
147 148 5.166398 GCCGTGTGTGATTAACTACTTACT 58.834 41.667 0.00 0.00 0.00 2.24
176 177 3.317993 GGTCAAACAGTAGTTGCCATGTT 59.682 43.478 0.00 0.00 38.17 2.71
242 243 6.804677 TGTATGGTTAATCACAATTGCCATC 58.195 36.000 12.88 7.61 39.96 3.51
257 258 3.346315 TGCCATCTGTGTTTATCTGGTG 58.654 45.455 0.00 0.00 0.00 4.17
339 344 1.135315 CCTAGTTGCCACGCGTAACTA 60.135 52.381 24.17 24.17 44.58 2.24
457 462 2.591429 CCCACACAACGCAGCTGA 60.591 61.111 20.43 0.00 0.00 4.26
466 472 3.349006 CGCAGCTGACAAACCGCT 61.349 61.111 20.43 0.00 39.54 5.52
553 564 2.542020 TTCTGCCGTGTCAAGATTCA 57.458 45.000 0.00 0.00 0.00 2.57
563 574 5.408299 CCGTGTCAAGATTCATGTAAACTCA 59.592 40.000 0.00 0.00 0.00 3.41
565 576 7.361201 CCGTGTCAAGATTCATGTAAACTCAAT 60.361 37.037 0.00 0.00 0.00 2.57
585 596 2.431942 GACGGTGATCCACGCGTT 60.432 61.111 10.22 0.00 39.72 4.84
590 601 1.669760 GTGATCCACGCGTTTGGGA 60.670 57.895 17.89 17.89 37.24 4.37
593 604 0.672401 GATCCACGCGTTTGGGAGAA 60.672 55.000 19.87 0.70 37.24 2.87
618 629 3.255642 GCAAAACTATCACACATGTGGGT 59.744 43.478 26.79 16.55 45.65 4.51
631 642 6.567687 CACATGTGGGTGTTAGTATTTTCA 57.432 37.500 18.51 0.00 34.09 2.69
683 694 4.513406 AAAAACTACCTCCCACTGTGAA 57.487 40.909 9.86 0.00 0.00 3.18
684 695 4.724279 AAAACTACCTCCCACTGTGAAT 57.276 40.909 9.86 0.00 0.00 2.57
685 696 5.836024 AAAACTACCTCCCACTGTGAATA 57.164 39.130 9.86 0.00 0.00 1.75
686 697 5.422214 AAACTACCTCCCACTGTGAATAG 57.578 43.478 9.86 3.42 0.00 1.73
687 698 2.766828 ACTACCTCCCACTGTGAATAGC 59.233 50.000 9.86 0.00 0.00 2.97
688 699 1.656587 ACCTCCCACTGTGAATAGCA 58.343 50.000 9.86 0.00 0.00 3.49
689 700 1.985159 ACCTCCCACTGTGAATAGCAA 59.015 47.619 9.86 0.00 0.00 3.91
690 701 2.026822 ACCTCCCACTGTGAATAGCAAG 60.027 50.000 9.86 0.00 0.00 4.01
691 702 2.026822 CCTCCCACTGTGAATAGCAAGT 60.027 50.000 9.86 0.00 0.00 3.16
692 703 3.005554 CTCCCACTGTGAATAGCAAGTG 58.994 50.000 9.86 0.00 36.37 3.16
693 704 2.371841 TCCCACTGTGAATAGCAAGTGT 59.628 45.455 9.86 0.00 35.61 3.55
694 705 3.580895 TCCCACTGTGAATAGCAAGTGTA 59.419 43.478 9.86 0.00 35.61 2.90
695 706 3.935203 CCCACTGTGAATAGCAAGTGTAG 59.065 47.826 9.86 0.00 35.61 2.74
696 707 3.372206 CCACTGTGAATAGCAAGTGTAGC 59.628 47.826 9.86 0.00 35.61 3.58
697 708 3.996363 CACTGTGAATAGCAAGTGTAGCA 59.004 43.478 0.32 0.00 34.15 3.49
698 709 3.997021 ACTGTGAATAGCAAGTGTAGCAC 59.003 43.478 0.00 0.00 34.10 4.40
699 710 3.996363 CTGTGAATAGCAAGTGTAGCACA 59.004 43.478 0.00 0.00 36.74 4.57
712 723 4.617253 TGTAGCACACACCTGACTAATT 57.383 40.909 0.00 0.00 30.04 1.40
713 724 4.566004 TGTAGCACACACCTGACTAATTC 58.434 43.478 0.00 0.00 30.04 2.17
714 725 2.688507 AGCACACACCTGACTAATTCG 58.311 47.619 0.00 0.00 0.00 3.34
715 726 2.299013 AGCACACACCTGACTAATTCGA 59.701 45.455 0.00 0.00 0.00 3.71
716 727 3.064207 GCACACACCTGACTAATTCGAA 58.936 45.455 0.00 0.00 0.00 3.71
717 728 3.123621 GCACACACCTGACTAATTCGAAG 59.876 47.826 3.35 0.00 0.00 3.79
718 729 4.556233 CACACACCTGACTAATTCGAAGA 58.444 43.478 3.35 0.00 0.00 2.87
719 730 5.171476 CACACACCTGACTAATTCGAAGAT 58.829 41.667 3.35 0.00 35.04 2.40
720 731 5.639506 CACACACCTGACTAATTCGAAGATT 59.360 40.000 3.35 0.00 35.04 2.40
721 732 5.639506 ACACACCTGACTAATTCGAAGATTG 59.360 40.000 3.35 0.00 35.04 2.67
722 733 5.639506 CACACCTGACTAATTCGAAGATTGT 59.360 40.000 3.35 2.27 35.04 2.71
723 734 5.869888 ACACCTGACTAATTCGAAGATTGTC 59.130 40.000 16.08 16.08 35.04 3.18
724 735 5.004821 CACCTGACTAATTCGAAGATTGTCG 59.995 44.000 17.07 13.33 42.48 4.35
734 745 3.367932 TCGAAGATTGTCGATGAGTTTGC 59.632 43.478 0.00 0.00 44.76 3.68
735 746 3.369147 CGAAGATTGTCGATGAGTTTGCT 59.631 43.478 0.00 0.00 43.86 3.91
736 747 4.143030 CGAAGATTGTCGATGAGTTTGCTT 60.143 41.667 0.00 0.00 43.86 3.91
737 748 5.062183 CGAAGATTGTCGATGAGTTTGCTTA 59.938 40.000 0.00 0.00 43.86 3.09
738 749 6.401047 CGAAGATTGTCGATGAGTTTGCTTAA 60.401 38.462 0.00 0.00 43.86 1.85
739 750 6.801539 AGATTGTCGATGAGTTTGCTTAAA 57.198 33.333 0.00 0.00 0.00 1.52
740 751 6.603095 AGATTGTCGATGAGTTTGCTTAAAC 58.397 36.000 0.00 0.00 0.00 2.01
741 752 5.743026 TTGTCGATGAGTTTGCTTAAACA 57.257 34.783 5.79 0.00 35.20 2.83
742 753 5.940192 TGTCGATGAGTTTGCTTAAACAT 57.060 34.783 5.79 0.00 35.20 2.71
743 754 5.688823 TGTCGATGAGTTTGCTTAAACATG 58.311 37.500 5.79 0.00 35.20 3.21
744 755 5.468409 TGTCGATGAGTTTGCTTAAACATGA 59.532 36.000 0.00 0.00 35.20 3.07
745 756 6.149308 TGTCGATGAGTTTGCTTAAACATGAT 59.851 34.615 0.00 0.00 35.20 2.45
746 757 7.023575 GTCGATGAGTTTGCTTAAACATGATT 58.976 34.615 0.00 0.00 35.20 2.57
747 758 7.007725 GTCGATGAGTTTGCTTAAACATGATTG 59.992 37.037 0.00 0.00 35.20 2.67
748 759 6.237384 CGATGAGTTTGCTTAAACATGATTGC 60.237 38.462 0.00 0.00 35.20 3.56
749 760 6.088016 TGAGTTTGCTTAAACATGATTGCT 57.912 33.333 0.00 0.00 35.20 3.91
750 761 7.213216 TGAGTTTGCTTAAACATGATTGCTA 57.787 32.000 0.00 0.00 35.20 3.49
751 762 7.829725 TGAGTTTGCTTAAACATGATTGCTAT 58.170 30.769 0.00 0.00 35.20 2.97
752 763 8.306038 TGAGTTTGCTTAAACATGATTGCTATT 58.694 29.630 0.00 0.00 35.20 1.73
753 764 8.470040 AGTTTGCTTAAACATGATTGCTATTG 57.530 30.769 0.00 0.00 35.20 1.90
754 765 8.306038 AGTTTGCTTAAACATGATTGCTATTGA 58.694 29.630 0.00 0.00 35.20 2.57
755 766 8.924691 GTTTGCTTAAACATGATTGCTATTGAA 58.075 29.630 0.00 0.00 33.08 2.69
756 767 9.656040 TTTGCTTAAACATGATTGCTATTGAAT 57.344 25.926 0.00 0.00 0.00 2.57
757 768 9.656040 TTGCTTAAACATGATTGCTATTGAATT 57.344 25.926 0.00 0.00 0.00 2.17
758 769 9.656040 TGCTTAAACATGATTGCTATTGAATTT 57.344 25.926 0.00 0.00 0.00 1.82
830 841 8.245491 TCATGTGGATGTTGTATTTGAATCAAG 58.755 33.333 0.00 0.00 0.00 3.02
837 848 6.437928 TGTTGTATTTGAATCAAGCACAGAC 58.562 36.000 10.26 11.30 0.00 3.51
853 864 6.166982 AGCACAGACATTTAACTAGTTCCTC 58.833 40.000 12.39 1.05 0.00 3.71
878 889 9.811995 TCTAAATATTGTTGCTGAATAGTACGT 57.188 29.630 0.00 0.00 0.00 3.57
881 892 9.595823 AAATATTGTTGCTGAATAGTACGTACT 57.404 29.630 29.62 29.62 40.24 2.73
882 893 6.887376 ATTGTTGCTGAATAGTACGTACTG 57.113 37.500 33.23 19.44 37.10 2.74
913 924 1.067213 GCTTTGCCGGATTGCCTAAAA 60.067 47.619 5.05 0.00 0.00 1.52
915 926 3.253230 CTTTGCCGGATTGCCTAAAAAG 58.747 45.455 5.05 0.00 0.00 2.27
1015 1038 3.411517 CCATGGCTTCCGGGTCCT 61.412 66.667 0.00 0.00 0.00 3.85
1363 1386 6.074142 GCTTTTCTTGTTATTTCTTGCACCAG 60.074 38.462 0.00 0.00 0.00 4.00
1436 1459 4.202111 CCTGAAAGTTCCGGTTTTCACATT 60.202 41.667 19.93 4.75 38.12 2.71
1457 1480 4.263139 TCGACAATTGAAATGATCTGCG 57.737 40.909 13.59 0.55 0.00 5.18
1677 1700 7.857456 TGAAAGAGAAGTAAATACCAGCCATA 58.143 34.615 0.00 0.00 0.00 2.74
1745 1768 1.830279 AACTGCACTGGATCCACATG 58.170 50.000 11.44 13.41 0.00 3.21
1753 1776 2.575279 ACTGGATCCACATGCTTTCTCT 59.425 45.455 11.44 0.00 0.00 3.10
2253 2302 3.711190 TGATAATGAGCTGTCTTGGGCTA 59.289 43.478 0.00 0.00 39.05 3.93
2621 3118 9.851686 AGCACAAGTATGATTCCTTTATAATCA 57.148 29.630 0.00 0.00 44.92 2.57
3202 3709 3.213206 TGCTCTCTTTCAAAGAAGCCA 57.787 42.857 21.60 9.33 39.12 4.75
3204 3711 4.147321 TGCTCTCTTTCAAAGAAGCCATT 58.853 39.130 21.60 0.00 39.12 3.16
3262 3769 8.062065 TGGCTTAGTCCCAATTAATTTAGTTG 57.938 34.615 0.00 5.03 0.00 3.16
3463 3977 4.718961 ACAGAGTAGAAACCATGCAGTTT 58.281 39.130 3.90 3.90 42.56 2.66
3680 4194 2.992689 TGCACCGGACTCGCCTAA 60.993 61.111 9.46 0.00 34.56 2.69
3710 4224 3.977326 GGGAGTAAATCTGAGAGGGGAAT 59.023 47.826 0.00 0.00 0.00 3.01
3990 4529 7.987458 TGAAGAACTTTATCAGCTATGGTAAGG 59.013 37.037 0.00 0.00 35.70 2.69
4076 4615 6.003950 TGCTTATCCTTTGTGCTCTTTTACT 58.996 36.000 0.00 0.00 0.00 2.24
4109 4650 3.196685 ACATCTCTCGAGGAAGGAAAAGG 59.803 47.826 13.56 0.00 0.00 3.11
4294 4835 0.911769 AAGCGGATCATGGAGTGGAA 59.088 50.000 0.00 0.00 0.00 3.53
4434 4977 5.487433 TCGCCAAATCTCATTGAAGTTCTA 58.513 37.500 4.17 0.00 31.84 2.10
4436 4979 6.024049 CGCCAAATCTCATTGAAGTTCTAAC 58.976 40.000 4.17 0.00 31.84 2.34
4482 5025 5.300792 TGTGAACTTATTTGGTTTGGAGACC 59.699 40.000 0.00 0.00 40.23 3.85
4523 5072 7.996066 GTGAGACATGCTATCCCTATCTATCTA 59.004 40.741 0.00 0.00 0.00 1.98
4524 5073 8.731901 TGAGACATGCTATCCCTATCTATCTAT 58.268 37.037 0.00 0.00 0.00 1.98
4525 5074 9.231297 GAGACATGCTATCCCTATCTATCTATC 57.769 40.741 0.00 0.00 0.00 2.08
4526 5075 8.958995 AGACATGCTATCCCTATCTATCTATCT 58.041 37.037 0.00 0.00 0.00 1.98
4660 5209 5.184479 TGTTTAGTGTACTAGTCGAATGCCT 59.816 40.000 0.00 0.00 0.00 4.75
4666 5215 0.179137 CTAGTCGAATGCCTGTGCGA 60.179 55.000 0.00 0.00 41.78 5.10
4681 5230 0.104855 TGCGATGCCACAGGAGATAC 59.895 55.000 0.00 0.00 0.00 2.24
4687 5236 3.517296 TGCCACAGGAGATACCAAAAA 57.483 42.857 0.00 0.00 42.04 1.94
4688 5237 3.153919 TGCCACAGGAGATACCAAAAAC 58.846 45.455 0.00 0.00 42.04 2.43
4689 5238 3.181434 TGCCACAGGAGATACCAAAAACT 60.181 43.478 0.00 0.00 42.04 2.66
4690 5239 4.042311 TGCCACAGGAGATACCAAAAACTA 59.958 41.667 0.00 0.00 42.04 2.24
4691 5240 5.007682 GCCACAGGAGATACCAAAAACTAA 58.992 41.667 0.00 0.00 42.04 2.24
4692 5241 5.652452 GCCACAGGAGATACCAAAAACTAAT 59.348 40.000 0.00 0.00 42.04 1.73
4693 5242 6.404734 GCCACAGGAGATACCAAAAACTAATG 60.405 42.308 0.00 0.00 42.04 1.90
4694 5243 6.884295 CCACAGGAGATACCAAAAACTAATGA 59.116 38.462 0.00 0.00 42.04 2.57
4695 5244 7.557719 CCACAGGAGATACCAAAAACTAATGAT 59.442 37.037 0.00 0.00 42.04 2.45
4727 5276 5.953183 TGTTACTGATCAAATCATTGCACC 58.047 37.500 0.00 0.00 38.85 5.01
4755 5304 4.582701 TGTTTGATGTGCTTACTTTGGG 57.417 40.909 0.00 0.00 0.00 4.12
4758 5509 3.237268 TGATGTGCTTACTTTGGGGTT 57.763 42.857 0.00 0.00 0.00 4.11
4870 5688 3.291383 CCGGTTGCCGCCTTTGAA 61.291 61.111 1.51 0.00 46.86 2.69
4893 5789 2.787473 TTGTGGATGTTGCCTAGAGG 57.213 50.000 0.00 0.00 38.53 3.69
4903 5799 2.844839 CCTAGAGGCGGGAAGGGG 60.845 72.222 0.00 0.00 0.00 4.79
4929 5825 9.239551 GGGGGATAGACGCTTTAAAATAATTAT 57.760 33.333 0.00 0.00 0.00 1.28
4951 5847 3.386078 TGGTTTAGGCTTGAACAAATGCA 59.614 39.130 5.84 0.00 0.00 3.96
4963 5859 7.809806 GCTTGAACAAATGCAGAATAAACTAGT 59.190 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.184431 TCCCGAATAACTACGTGCCA 58.816 50.000 0.00 0.00 0.00 4.92
2 3 2.132762 CATCCCGAATAACTACGTGCC 58.867 52.381 0.00 0.00 0.00 5.01
3 4 2.132762 CCATCCCGAATAACTACGTGC 58.867 52.381 0.00 0.00 0.00 5.34
4 5 2.132762 GCCATCCCGAATAACTACGTG 58.867 52.381 0.00 0.00 0.00 4.49
5 6 1.758280 TGCCATCCCGAATAACTACGT 59.242 47.619 0.00 0.00 0.00 3.57
6 7 2.519377 TGCCATCCCGAATAACTACG 57.481 50.000 0.00 0.00 0.00 3.51
95 96 2.884663 TTAATTACACGCGGCAACTG 57.115 45.000 12.47 0.56 0.00 3.16
112 113 2.809119 CACACACGGCAACTATGGTTTA 59.191 45.455 0.00 0.00 32.73 2.01
145 146 6.594159 GCAACTACTGTTTGACCATATGTAGT 59.406 38.462 1.24 0.00 40.19 2.73
147 148 5.878116 GGCAACTACTGTTTGACCATATGTA 59.122 40.000 1.24 0.00 33.52 2.29
176 177 2.873472 CACGTGGCAACTAGGTAAACAA 59.127 45.455 7.95 0.00 37.61 2.83
242 243 1.812571 GTGGCCACCAGATAAACACAG 59.187 52.381 26.31 0.00 32.34 3.66
295 296 6.317642 GGTAAACACACATGGCAACTATGATA 59.682 38.462 0.00 0.00 37.61 2.15
339 344 0.667993 CGTTGTTGGATGGCAACTGT 59.332 50.000 0.00 0.00 41.80 3.55
406 411 0.179004 CCCACACAGCCAACACCTAA 60.179 55.000 0.00 0.00 0.00 2.69
530 536 5.000591 TGAATCTTGACACGGCAGAATTTA 58.999 37.500 0.00 0.00 0.00 1.40
553 564 4.647611 TCACCGTCCAATTGAGTTTACAT 58.352 39.130 7.12 0.00 0.00 2.29
585 596 5.538053 TGTGATAGTTTTGCAATTCTCCCAA 59.462 36.000 0.00 0.00 0.00 4.12
590 601 6.985117 ACATGTGTGATAGTTTTGCAATTCT 58.015 32.000 0.00 4.53 0.00 2.40
662 673 4.513406 TTCACAGTGGGAGGTAGTTTTT 57.487 40.909 0.00 0.00 0.00 1.94
663 674 4.724279 ATTCACAGTGGGAGGTAGTTTT 57.276 40.909 0.00 0.00 0.00 2.43
664 675 4.323562 GCTATTCACAGTGGGAGGTAGTTT 60.324 45.833 14.68 0.00 0.00 2.66
665 676 3.197983 GCTATTCACAGTGGGAGGTAGTT 59.802 47.826 14.68 0.00 0.00 2.24
666 677 2.766828 GCTATTCACAGTGGGAGGTAGT 59.233 50.000 14.68 0.00 0.00 2.73
667 678 2.766263 TGCTATTCACAGTGGGAGGTAG 59.234 50.000 10.85 10.85 0.00 3.18
668 679 2.827755 TGCTATTCACAGTGGGAGGTA 58.172 47.619 0.00 0.00 0.00 3.08
669 680 1.656587 TGCTATTCACAGTGGGAGGT 58.343 50.000 0.00 0.00 0.00 3.85
670 681 2.026822 ACTTGCTATTCACAGTGGGAGG 60.027 50.000 0.00 0.00 0.00 4.30
671 682 3.005554 CACTTGCTATTCACAGTGGGAG 58.994 50.000 0.00 0.00 33.82 4.30
672 683 2.371841 ACACTTGCTATTCACAGTGGGA 59.628 45.455 0.00 0.00 37.74 4.37
673 684 2.783135 ACACTTGCTATTCACAGTGGG 58.217 47.619 0.00 0.00 37.74 4.61
674 685 3.372206 GCTACACTTGCTATTCACAGTGG 59.628 47.826 0.00 0.00 37.74 4.00
675 686 3.996363 TGCTACACTTGCTATTCACAGTG 59.004 43.478 0.00 0.00 38.54 3.66
676 687 3.997021 GTGCTACACTTGCTATTCACAGT 59.003 43.478 0.00 0.00 0.00 3.55
677 688 3.996363 TGTGCTACACTTGCTATTCACAG 59.004 43.478 0.00 0.00 35.11 3.66
678 689 3.745975 GTGTGCTACACTTGCTATTCACA 59.254 43.478 10.87 0.00 45.27 3.58
679 690 4.327854 GTGTGCTACACTTGCTATTCAC 57.672 45.455 10.87 0.00 45.27 3.18
691 702 4.566004 GAATTAGTCAGGTGTGTGCTACA 58.434 43.478 0.00 0.00 36.82 2.74
692 703 3.612860 CGAATTAGTCAGGTGTGTGCTAC 59.387 47.826 0.00 0.00 0.00 3.58
693 704 3.508402 TCGAATTAGTCAGGTGTGTGCTA 59.492 43.478 0.00 0.00 0.00 3.49
694 705 2.299013 TCGAATTAGTCAGGTGTGTGCT 59.701 45.455 0.00 0.00 0.00 4.40
695 706 2.683968 TCGAATTAGTCAGGTGTGTGC 58.316 47.619 0.00 0.00 0.00 4.57
696 707 4.556233 TCTTCGAATTAGTCAGGTGTGTG 58.444 43.478 0.00 0.00 0.00 3.82
697 708 4.866508 TCTTCGAATTAGTCAGGTGTGT 57.133 40.909 0.00 0.00 0.00 3.72
698 709 5.639506 ACAATCTTCGAATTAGTCAGGTGTG 59.360 40.000 0.00 0.00 0.00 3.82
699 710 5.794894 ACAATCTTCGAATTAGTCAGGTGT 58.205 37.500 0.00 0.00 0.00 4.16
700 711 5.004821 CGACAATCTTCGAATTAGTCAGGTG 59.995 44.000 15.61 2.73 41.78 4.00
701 712 5.103000 CGACAATCTTCGAATTAGTCAGGT 58.897 41.667 15.61 2.21 41.78 4.00
702 713 5.340803 TCGACAATCTTCGAATTAGTCAGG 58.659 41.667 15.61 5.49 44.86 3.86
713 724 3.369147 AGCAAACTCATCGACAATCTTCG 59.631 43.478 0.00 0.00 40.53 3.79
714 725 4.935885 AGCAAACTCATCGACAATCTTC 57.064 40.909 0.00 0.00 0.00 2.87
715 726 6.801539 TTAAGCAAACTCATCGACAATCTT 57.198 33.333 0.00 0.00 0.00 2.40
716 727 6.204688 TGTTTAAGCAAACTCATCGACAATCT 59.795 34.615 0.00 0.00 43.73 2.40
717 728 6.370593 TGTTTAAGCAAACTCATCGACAATC 58.629 36.000 0.00 0.00 43.73 2.67
718 729 6.312399 TGTTTAAGCAAACTCATCGACAAT 57.688 33.333 0.00 0.00 43.73 2.71
719 730 5.743026 TGTTTAAGCAAACTCATCGACAA 57.257 34.783 0.00 0.00 43.73 3.18
720 731 5.468409 TCATGTTTAAGCAAACTCATCGACA 59.532 36.000 0.00 0.00 43.73 4.35
721 732 5.927030 TCATGTTTAAGCAAACTCATCGAC 58.073 37.500 0.00 0.00 43.73 4.20
722 733 6.741992 ATCATGTTTAAGCAAACTCATCGA 57.258 33.333 0.00 0.00 43.73 3.59
723 734 6.237384 GCAATCATGTTTAAGCAAACTCATCG 60.237 38.462 0.00 0.00 43.73 3.84
724 735 6.810182 AGCAATCATGTTTAAGCAAACTCATC 59.190 34.615 0.00 0.00 43.73 2.92
725 736 6.694447 AGCAATCATGTTTAAGCAAACTCAT 58.306 32.000 0.00 0.00 43.73 2.90
726 737 6.088016 AGCAATCATGTTTAAGCAAACTCA 57.912 33.333 0.00 0.00 43.73 3.41
727 738 8.589629 CAATAGCAATCATGTTTAAGCAAACTC 58.410 33.333 0.00 0.00 43.73 3.01
728 739 8.306038 TCAATAGCAATCATGTTTAAGCAAACT 58.694 29.630 0.00 0.00 43.73 2.66
729 740 8.464770 TCAATAGCAATCATGTTTAAGCAAAC 57.535 30.769 0.00 0.00 43.67 2.93
730 741 9.656040 ATTCAATAGCAATCATGTTTAAGCAAA 57.344 25.926 0.00 0.00 0.00 3.68
731 742 9.656040 AATTCAATAGCAATCATGTTTAAGCAA 57.344 25.926 0.00 0.00 0.00 3.91
732 743 9.656040 AAATTCAATAGCAATCATGTTTAAGCA 57.344 25.926 0.00 0.00 0.00 3.91
830 841 6.166982 AGAGGAACTAGTTAAATGTCTGTGC 58.833 40.000 8.42 0.00 41.55 4.57
877 888 5.287992 CGGCAAAGCTTTACTAGTACAGTAC 59.712 44.000 12.25 2.05 39.52 2.73
878 889 5.404946 CGGCAAAGCTTTACTAGTACAGTA 58.595 41.667 12.25 0.00 38.80 2.74
879 890 4.243270 CGGCAAAGCTTTACTAGTACAGT 58.757 43.478 12.25 0.00 41.62 3.55
880 891 3.617263 CCGGCAAAGCTTTACTAGTACAG 59.383 47.826 12.25 11.09 0.00 2.74
881 892 3.258872 TCCGGCAAAGCTTTACTAGTACA 59.741 43.478 12.25 0.00 0.00 2.90
882 893 3.853475 TCCGGCAAAGCTTTACTAGTAC 58.147 45.455 12.25 0.00 0.00 2.73
913 924 6.547402 AGACCTCTTTTCTTAGAAATGGCTT 58.453 36.000 16.89 5.18 0.00 4.35
915 926 5.355630 GGAGACCTCTTTTCTTAGAAATGGC 59.644 44.000 16.89 11.49 0.00 4.40
1363 1386 7.383572 CAGTGATTAGTACACATGATAAGAGGC 59.616 40.741 0.00 0.00 40.25 4.70
1436 1459 3.932089 TCGCAGATCATTTCAATTGTCGA 59.068 39.130 5.13 0.00 0.00 4.20
1457 1480 1.865865 TCAAGGAGAAGCAACGTGTC 58.134 50.000 0.00 0.00 0.00 3.67
1677 1700 6.263617 ACCAACAAACACACCGAAAGTATAAT 59.736 34.615 0.00 0.00 0.00 1.28
1688 1711 3.535280 AATGGAACCAACAAACACACC 57.465 42.857 0.00 0.00 0.00 4.16
2088 2111 5.462729 CACTCAAGCATAAGATAGCAGACTG 59.537 44.000 0.00 0.00 0.00 3.51
2184 2233 5.401750 AGAGCCACATCAATAGAGGAGTAT 58.598 41.667 0.00 0.00 0.00 2.12
2253 2302 5.044919 TCCAGGTAGATCATTTGTCCAATGT 60.045 40.000 0.00 0.00 42.79 2.71
2321 2370 6.684555 CAGATGTTTTAGCGCTTGATAACTTC 59.315 38.462 18.68 19.48 0.00 3.01
2621 3118 2.196595 TCCCCATTGGACGAAATCTCT 58.803 47.619 3.62 0.00 38.61 3.10
2915 3412 8.295288 AGCAGTCAGAATAAAGAAAAGATGTTG 58.705 33.333 0.00 0.00 0.00 3.33
3236 3743 8.527810 CAACTAAATTAATTGGGACTAAGCCAA 58.472 33.333 0.39 0.00 0.00 4.52
3262 3769 7.826690 ACCAATGTAAATTCAGTTACCATGTC 58.173 34.615 0.00 0.00 33.76 3.06
3463 3977 8.706492 AAATACGTGGAATGTTTATAACGAGA 57.294 30.769 0.00 0.00 37.25 4.04
3680 4194 2.035632 CAGATTTACTCCCCGCTCTCT 58.964 52.381 0.00 0.00 0.00 3.10
3726 4240 7.325660 TGCATTTATTTTGTTTTGGAAAGCA 57.674 28.000 0.00 0.00 0.00 3.91
3990 4529 1.369091 AATGAACTCGGCGCCATCAC 61.369 55.000 28.98 13.58 0.00 3.06
4076 4615 8.521170 TTCCTCGAGAGATGTTTTCTATAGAA 57.479 34.615 15.71 11.24 40.84 2.10
4109 4650 3.572255 TGTTGTGAGCAAATAGGGGTTTC 59.428 43.478 0.00 0.00 36.22 2.78
4318 4859 1.153005 ACGTAGGCTAGGGTCGGAG 60.153 63.158 17.64 0.00 0.00 4.63
4434 4977 8.034804 ACAACTCAAAGCAAATAAGTTTCAGTT 58.965 29.630 0.00 0.00 0.00 3.16
4436 4979 7.701924 TCACAACTCAAAGCAAATAAGTTTCAG 59.298 33.333 0.00 0.00 0.00 3.02
4482 5025 8.239314 AGCATGTCTCACAATGTAACATAAAAG 58.761 33.333 7.57 0.01 0.00 2.27
4660 5209 1.902765 ATCTCCTGTGGCATCGCACA 61.903 55.000 0.00 0.00 0.00 4.57
4666 5215 3.737559 TTTTGGTATCTCCTGTGGCAT 57.262 42.857 0.00 0.00 37.07 4.40
4710 5259 5.662674 TGAATGGTGCAATGATTTGATCA 57.337 34.783 0.00 0.00 44.55 2.92
4727 5276 7.878477 AAGTAAGCACATCAAACATTGAATG 57.122 32.000 3.16 3.16 43.95 2.67
4870 5688 4.521146 CTCTAGGCAACATCCACAATCTT 58.479 43.478 0.00 0.00 41.41 2.40
4903 5799 7.520451 AATTATTTTAAAGCGTCTATCCCCC 57.480 36.000 0.00 0.00 0.00 5.40
4912 5808 9.524106 GCCTAAACCATAATTATTTTAAAGCGT 57.476 29.630 0.00 0.00 0.00 5.07
4929 5825 3.386078 TGCATTTGTTCAAGCCTAAACCA 59.614 39.130 0.00 0.00 0.00 3.67
4930 5826 3.988819 TGCATTTGTTCAAGCCTAAACC 58.011 40.909 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.