Multiple sequence alignment - TraesCS3D01G005100

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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 TraesCS3D01G005100 chr3D 100.000 3909 0 0 1 3909 1994207 1990299 0.000000e+00 7219.0
1 TraesCS3D01G005100 chr3D 90.063 2053 128 19 840 2832 453985751 453983715 0.000000e+00 2591.0
2 TraesCS3D01G005100 chr3D 95.966 471 19 0 3362 3832 562965667 562965197 0.000000e+00 765.0
3 TraesCS3D01G005100 chr3D 93.182 484 30 3 3351 3832 45438192 45437710 0.000000e+00 708.0
4 TraesCS3D01G005100 chr3D 98.000 50 1 0 1 50 85843161 85843210 1.930000e-13 87.9
5 TraesCS3D01G005100 chr3D 85.507 69 8 2 653 721 574573209 574573143 1.950000e-08 71.3
6 TraesCS3D01G005100 chr3B 90.860 2057 112 27 840 2832 596412876 596410832 0.000000e+00 2687.0
7 TraesCS3D01G005100 chr3B 91.761 352 29 0 2481 2832 688159038 688159389 1.260000e-134 490.0
8 TraesCS3D01G005100 chr3B 91.329 346 30 0 2487 2832 737563524 737563179 1.270000e-129 473.0
9 TraesCS3D01G005100 chr3B 76.169 449 84 9 71 516 536266231 536265803 8.510000e-52 215.0
10 TraesCS3D01G005100 chr3B 96.000 50 2 0 1 50 136060937 136060986 9.000000e-12 82.4
11 TraesCS3D01G005100 chr7A 90.408 2012 103 37 763 2759 465819 463883 0.000000e+00 2564.0
12 TraesCS3D01G005100 chr7A 91.142 508 43 2 2833 3338 553032868 553032361 0.000000e+00 688.0
13 TraesCS3D01G005100 chr7A 76.215 391 56 17 70 458 470125491 470125846 5.190000e-39 172.0
14 TraesCS3D01G005100 chr3A 90.353 1047 71 11 840 1868 595934657 595933623 0.000000e+00 1347.0
15 TraesCS3D01G005100 chr3A 91.529 968 50 10 1878 2832 595933586 595932638 0.000000e+00 1304.0
16 TraesCS3D01G005100 chr7D 94.667 750 25 5 1 740 433731723 433732467 0.000000e+00 1149.0
17 TraesCS3D01G005100 chr7D 89.824 511 26 2 3348 3832 622270297 622269787 1.980000e-177 632.0
18 TraesCS3D01G005100 chr2B 91.771 559 38 2 3359 3909 63115456 63116014 0.000000e+00 771.0
19 TraesCS3D01G005100 chr6D 97.345 452 8 1 294 741 456568974 456568523 0.000000e+00 765.0
20 TraesCS3D01G005100 chr6D 97.664 214 4 1 1 214 456569413 456569201 2.220000e-97 366.0
21 TraesCS3D01G005100 chr2D 92.927 509 33 3 2833 3338 189847085 189846577 0.000000e+00 737.0
22 TraesCS3D01G005100 chr2D 91.731 520 31 9 3401 3909 92909738 92909220 0.000000e+00 712.0
23 TraesCS3D01G005100 chr2D 89.273 578 31 4 3362 3909 591394722 591395298 0.000000e+00 695.0
24 TraesCS3D01G005100 chr2D 89.529 573 27 12 3362 3909 631266112 631266676 0.000000e+00 695.0
25 TraesCS3D01G005100 chr2D 89.298 570 23 6 3361 3909 99560790 99560238 0.000000e+00 680.0
26 TraesCS3D01G005100 chr2D 89.276 373 26 6 995 1365 636085983 636085623 4.600000e-124 455.0
27 TraesCS3D01G005100 chr5D 92.871 505 30 4 3360 3863 510948509 510949008 0.000000e+00 728.0
28 TraesCS3D01G005100 chr5D 92.430 502 36 2 2833 3332 100937073 100937574 0.000000e+00 715.0
29 TraesCS3D01G005100 chr5D 85.666 593 25 13 3358 3909 26858938 26859511 1.580000e-158 569.0
30 TraesCS3D01G005100 chr2A 92.323 508 37 2 2833 3338 26837886 26837379 0.000000e+00 721.0
31 TraesCS3D01G005100 chr2A 91.228 513 37 5 2833 3338 775760861 775760350 0.000000e+00 691.0
32 TraesCS3D01G005100 chr2A 84.314 255 17 5 1015 1269 761070861 761071092 1.090000e-55 228.0
33 TraesCS3D01G005100 chr2A 83.673 147 20 4 364 509 558845431 558845574 6.810000e-28 135.0
34 TraesCS3D01G005100 chr1D 91.732 508 40 2 2833 3338 135891691 135891184 0.000000e+00 704.0
35 TraesCS3D01G005100 chr1D 79.800 802 144 15 1006 1801 391277855 391277066 5.670000e-158 568.0
36 TraesCS3D01G005100 chr1D 82.581 155 21 6 70 222 111858102 111857952 8.810000e-27 132.0
37 TraesCS3D01G005100 chrUn 91.159 509 42 3 2833 3338 154624071 154623563 0.000000e+00 688.0
38 TraesCS3D01G005100 chrUn 90.982 499 43 2 2833 3329 336391209 336391707 0.000000e+00 671.0
39 TraesCS3D01G005100 chrUn 90.551 508 46 2 2833 3338 350620146 350619639 0.000000e+00 671.0
40 TraesCS3D01G005100 chrUn 85.935 583 45 11 3360 3909 26489434 26490012 4.350000e-164 588.0
41 TraesCS3D01G005100 chrUn 88.949 371 25 5 995 1365 357706552 357706906 9.970000e-121 444.0
42 TraesCS3D01G005100 chrUn 80.819 537 49 31 3401 3909 30048802 30049312 4.770000e-99 372.0
43 TraesCS3D01G005100 chrUn 92.490 253 19 0 1113 1365 247902077 247902329 2.870000e-96 363.0
44 TraesCS3D01G005100 chr5A 90.056 533 34 9 224 740 535383360 535383889 0.000000e+00 673.0
45 TraesCS3D01G005100 chr5A 80.357 280 43 9 241 517 34845382 34845652 6.620000e-48 202.0
46 TraesCS3D01G005100 chr5B 88.351 558 54 6 3363 3909 535214017 535213460 0.000000e+00 660.0
47 TraesCS3D01G005100 chr5B 92.045 352 27 1 2481 2832 610348525 610348875 9.760000e-136 494.0
48 TraesCS3D01G005100 chr5B 90.909 44 4 0 678 721 684092725 684092682 4.220000e-05 60.2
49 TraesCS3D01G005100 chr4B 91.789 475 38 1 3358 3832 660202482 660202955 0.000000e+00 660.0
50 TraesCS3D01G005100 chr1A 80.573 803 141 13 1001 1798 494024271 494025063 4.320000e-169 604.0
51 TraesCS3D01G005100 chr1A 81.156 398 63 10 2351 2745 494025547 494025935 3.790000e-80 309.0
52 TraesCS3D01G005100 chr1A 80.357 280 43 9 241 517 2995470 2995740 6.620000e-48 202.0
53 TraesCS3D01G005100 chr1B 79.748 795 148 12 1008 1798 531535318 531536103 7.330000e-157 564.0
54 TraesCS3D01G005100 chr1B 75.661 378 52 18 71 443 188903686 188904028 6.760000e-33 152.0
55 TraesCS3D01G005100 chr1B 84.615 91 9 2 650 735 449249817 449249907 6.960000e-13 86.1
56 TraesCS3D01G005100 chr7B 78.971 447 75 7 73 517 226607486 226607057 1.780000e-73 287.0
57 TraesCS3D01G005100 chr6A 80.645 279 42 10 242 517 583677494 583677225 5.120000e-49 206.0


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 TraesCS3D01G005100 chr3D 1990299 1994207 3908 True 7219.0 7219 100.0000 1 3909 1 chr3D.!!$R1 3908
1 TraesCS3D01G005100 chr3D 453983715 453985751 2036 True 2591.0 2591 90.0630 840 2832 1 chr3D.!!$R3 1992
2 TraesCS3D01G005100 chr3B 596410832 596412876 2044 True 2687.0 2687 90.8600 840 2832 1 chr3B.!!$R2 1992
3 TraesCS3D01G005100 chr7A 463883 465819 1936 True 2564.0 2564 90.4080 763 2759 1 chr7A.!!$R1 1996
4 TraesCS3D01G005100 chr7A 553032361 553032868 507 True 688.0 688 91.1420 2833 3338 1 chr7A.!!$R2 505
5 TraesCS3D01G005100 chr3A 595932638 595934657 2019 True 1325.5 1347 90.9410 840 2832 2 chr3A.!!$R1 1992
6 TraesCS3D01G005100 chr7D 433731723 433732467 744 False 1149.0 1149 94.6670 1 740 1 chr7D.!!$F1 739
7 TraesCS3D01G005100 chr7D 622269787 622270297 510 True 632.0 632 89.8240 3348 3832 1 chr7D.!!$R1 484
8 TraesCS3D01G005100 chr2B 63115456 63116014 558 False 771.0 771 91.7710 3359 3909 1 chr2B.!!$F1 550
9 TraesCS3D01G005100 chr6D 456568523 456569413 890 True 565.5 765 97.5045 1 741 2 chr6D.!!$R1 740
10 TraesCS3D01G005100 chr2D 189846577 189847085 508 True 737.0 737 92.9270 2833 3338 1 chr2D.!!$R3 505
11 TraesCS3D01G005100 chr2D 92909220 92909738 518 True 712.0 712 91.7310 3401 3909 1 chr2D.!!$R1 508
12 TraesCS3D01G005100 chr2D 591394722 591395298 576 False 695.0 695 89.2730 3362 3909 1 chr2D.!!$F1 547
13 TraesCS3D01G005100 chr2D 631266112 631266676 564 False 695.0 695 89.5290 3362 3909 1 chr2D.!!$F2 547
14 TraesCS3D01G005100 chr2D 99560238 99560790 552 True 680.0 680 89.2980 3361 3909 1 chr2D.!!$R2 548
15 TraesCS3D01G005100 chr5D 100937073 100937574 501 False 715.0 715 92.4300 2833 3332 1 chr5D.!!$F2 499
16 TraesCS3D01G005100 chr5D 26858938 26859511 573 False 569.0 569 85.6660 3358 3909 1 chr5D.!!$F1 551
17 TraesCS3D01G005100 chr2A 26837379 26837886 507 True 721.0 721 92.3230 2833 3338 1 chr2A.!!$R1 505
18 TraesCS3D01G005100 chr2A 775760350 775760861 511 True 691.0 691 91.2280 2833 3338 1 chr2A.!!$R2 505
19 TraesCS3D01G005100 chr1D 135891184 135891691 507 True 704.0 704 91.7320 2833 3338 1 chr1D.!!$R2 505
20 TraesCS3D01G005100 chr1D 391277066 391277855 789 True 568.0 568 79.8000 1006 1801 1 chr1D.!!$R3 795
21 TraesCS3D01G005100 chrUn 154623563 154624071 508 True 688.0 688 91.1590 2833 3338 1 chrUn.!!$R1 505
22 TraesCS3D01G005100 chrUn 350619639 350620146 507 True 671.0 671 90.5510 2833 3338 1 chrUn.!!$R2 505
23 TraesCS3D01G005100 chrUn 26489434 26490012 578 False 588.0 588 85.9350 3360 3909 1 chrUn.!!$F1 549
24 TraesCS3D01G005100 chrUn 30048802 30049312 510 False 372.0 372 80.8190 3401 3909 1 chrUn.!!$F2 508
25 TraesCS3D01G005100 chr5A 535383360 535383889 529 False 673.0 673 90.0560 224 740 1 chr5A.!!$F2 516
26 TraesCS3D01G005100 chr5B 535213460 535214017 557 True 660.0 660 88.3510 3363 3909 1 chr5B.!!$R1 546
27 TraesCS3D01G005100 chr1A 494024271 494025935 1664 False 456.5 604 80.8645 1001 2745 2 chr1A.!!$F2 1744
28 TraesCS3D01G005100 chr1B 531535318 531536103 785 False 564.0 564 79.7480 1008 1798 1 chr1B.!!$F3 790

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
735 899 0.033504 CGTAGGCACGGGCATTCTAT 59.966 55.0 13.89 0.0 44.59 1.98 F
1282 1466 0.532862 CGGTGTGCAGTTCCTCTTGT 60.533 55.0 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1976 0.830648 TGGATCATGTTCTCCCCGAC 59.169 55.0 3.86 0.0 0.0 4.79 R
2955 3240 0.603439 GTTAGCCGGAAACCGTTGGA 60.603 55.0 5.05 0.0 46.8 3.53 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
320 468 1.511613 ACATGTGGGTAGGGGATCAG 58.488 55.000 0.00 0.00 0.00 2.90
571 719 4.042809 ACATGGAGGATAGTTTGGACAACA 59.957 41.667 0.00 0.00 0.00 3.33
674 834 4.944619 ATGAGCTTCGACATTGAGGATA 57.055 40.909 0.00 0.00 0.00 2.59
735 899 0.033504 CGTAGGCACGGGCATTCTAT 59.966 55.000 13.89 0.00 44.59 1.98
741 905 2.224305 GGCACGGGCATTCTATTAGTCT 60.224 50.000 13.89 0.00 43.71 3.24
742 906 3.006537 GGCACGGGCATTCTATTAGTCTA 59.993 47.826 13.89 0.00 43.71 2.59
743 907 4.238514 GCACGGGCATTCTATTAGTCTAG 58.761 47.826 3.77 0.00 40.72 2.43
744 908 4.022242 GCACGGGCATTCTATTAGTCTAGA 60.022 45.833 3.77 0.00 40.72 2.43
745 909 5.336849 GCACGGGCATTCTATTAGTCTAGAT 60.337 44.000 3.77 0.00 40.72 1.98
746 910 6.096036 CACGGGCATTCTATTAGTCTAGATG 58.904 44.000 0.00 0.00 0.00 2.90
747 911 6.010850 ACGGGCATTCTATTAGTCTAGATGA 58.989 40.000 0.00 0.00 0.00 2.92
748 912 6.151985 ACGGGCATTCTATTAGTCTAGATGAG 59.848 42.308 0.00 0.00 0.00 2.90
749 913 6.151985 CGGGCATTCTATTAGTCTAGATGAGT 59.848 42.308 0.00 0.00 0.00 3.41
750 914 7.309499 CGGGCATTCTATTAGTCTAGATGAGTT 60.309 40.741 0.00 0.00 0.00 3.01
751 915 9.026121 GGGCATTCTATTAGTCTAGATGAGTTA 57.974 37.037 0.00 0.00 0.00 2.24
752 916 9.849166 GGCATTCTATTAGTCTAGATGAGTTAC 57.151 37.037 0.00 0.00 0.00 2.50
759 923 8.596781 ATTAGTCTAGATGAGTTACAACTGGT 57.403 34.615 0.00 0.00 39.88 4.00
760 924 9.696572 ATTAGTCTAGATGAGTTACAACTGGTA 57.303 33.333 0.00 0.00 39.88 3.25
761 925 7.633193 AGTCTAGATGAGTTACAACTGGTAG 57.367 40.000 0.00 0.00 39.88 3.18
762 926 7.403671 AGTCTAGATGAGTTACAACTGGTAGA 58.596 38.462 0.00 0.00 39.88 2.59
763 927 7.889073 AGTCTAGATGAGTTACAACTGGTAGAA 59.111 37.037 0.00 0.00 39.88 2.10
764 928 7.969508 GTCTAGATGAGTTACAACTGGTAGAAC 59.030 40.741 0.00 0.00 39.88 3.01
765 929 6.665992 AGATGAGTTACAACTGGTAGAACA 57.334 37.500 0.00 0.00 39.88 3.18
766 930 7.062749 AGATGAGTTACAACTGGTAGAACAA 57.937 36.000 0.00 0.00 39.88 2.83
767 931 7.155328 AGATGAGTTACAACTGGTAGAACAAG 58.845 38.462 0.00 0.00 39.88 3.16
773 937 7.901135 AGTTACAACTGGTAGAACAAGGAGTTC 60.901 40.741 0.00 0.00 46.06 3.01
782 946 2.640316 ACAAGGAGTTCTCAACCACC 57.360 50.000 2.24 0.00 0.00 4.61
783 947 1.843851 ACAAGGAGTTCTCAACCACCA 59.156 47.619 2.24 0.00 32.95 4.17
786 950 0.602905 GGAGTTCTCAACCACCACGG 60.603 60.000 2.24 0.00 42.50 4.94
800 964 5.717302 ACCACCACGGGAGAGATTTATCTC 61.717 50.000 11.02 11.02 45.85 2.75
837 1001 5.646606 AGTACAACGCAATTCAAACAGTTT 58.353 33.333 0.00 0.00 0.00 2.66
838 1002 6.787225 AGTACAACGCAATTCAAACAGTTTA 58.213 32.000 0.00 0.00 0.00 2.01
847 1024 6.262601 CAATTCAAACAGTTTACGACTTGGT 58.737 36.000 0.00 0.00 36.10 3.67
872 1049 3.315949 TCGCCGGCTGGTTTACCT 61.316 61.111 26.68 0.00 37.67 3.08
879 1056 2.975536 CTGGTTTACCTCCGGCGA 59.024 61.111 9.30 0.00 36.82 5.54
891 1068 1.390123 CTCCGGCGATGCATAAATACG 59.610 52.381 9.30 0.00 0.00 3.06
918 1095 4.801330 GCCAGGGGCCATAATTAATTAC 57.199 45.455 10.07 0.00 44.06 1.89
926 1103 8.329502 AGGGGCCATAATTAATTACTATCAGAC 58.670 37.037 10.07 0.00 0.00 3.51
1056 1240 2.125326 CGTCGGGACCATCTGGCTA 61.125 63.158 0.00 0.00 39.32 3.93
1152 1336 1.669115 GCAGCTCAACTTCCTCGCA 60.669 57.895 0.00 0.00 0.00 5.10
1179 1363 3.050275 GACGCCGGCAAGCTCTTT 61.050 61.111 28.98 0.00 0.00 2.52
1282 1466 0.532862 CGGTGTGCAGTTCCTCTTGT 60.533 55.000 0.00 0.00 0.00 3.16
1377 1561 1.446792 CACCGTCTGCTACCTGCTG 60.447 63.158 0.00 0.00 43.37 4.41
1437 1621 2.185350 CTCGCCACCAGCTACCTG 59.815 66.667 0.00 0.00 40.39 4.00
1546 1730 2.994995 TGGTGCCGGTGATCGTCT 60.995 61.111 1.90 0.00 37.11 4.18
1752 1936 4.047125 CTGGCCGTCCCCATGGTT 62.047 66.667 11.73 0.00 33.64 3.67
1773 1957 3.197790 CCGGTGGCGCTCAAGATG 61.198 66.667 7.64 0.00 0.00 2.90
1792 1976 1.750399 CGGGAGGGCATGAACAAGG 60.750 63.158 0.00 0.00 0.00 3.61
1805 2007 1.003233 GAACAAGGTCGGGGAGAACAT 59.997 52.381 0.00 0.00 39.61 2.71
1820 2022 1.789464 GAACATGATCCACGATCTCGC 59.211 52.381 0.00 0.00 44.43 5.03
1945 2195 4.688413 GGCTATACTTCTTCAGCTACATGC 59.312 45.833 0.00 0.00 43.29 4.06
1970 2220 2.285368 CACCCTGGGCCTGGTCTA 60.285 66.667 25.76 0.00 30.70 2.59
1983 2233 3.307762 GCCTGGTCTACCTCAACAATCTT 60.308 47.826 0.02 0.00 36.82 2.40
2139 2391 3.435105 TTCCAAACACACTTGCATGAC 57.565 42.857 6.60 0.00 0.00 3.06
2143 2395 3.058016 CCAAACACACTTGCATGACTAGG 60.058 47.826 6.60 0.00 0.00 3.02
2164 2416 8.943002 ACTAGGTTAATGTTTATTTTCGTCTGG 58.057 33.333 0.00 0.00 0.00 3.86
2170 2422 7.513371 AATGTTTATTTTCGTCTGGTTGGTA 57.487 32.000 0.00 0.00 0.00 3.25
2216 2480 3.954258 CAGGATTCATGGGGTCCTTTTAC 59.046 47.826 10.53 0.00 40.31 2.01
2231 2495 6.072119 GGTCCTTTTACATGGGAAACTTGTAG 60.072 42.308 0.00 0.00 39.81 2.74
2317 2598 3.058639 CCAGAAGCAGAAGAAACGGAAAG 60.059 47.826 0.00 0.00 0.00 2.62
2318 2599 3.809832 CAGAAGCAGAAGAAACGGAAAGA 59.190 43.478 0.00 0.00 0.00 2.52
2349 2634 5.159273 ACTGAATTTGTTGGTTTGTGGTT 57.841 34.783 0.00 0.00 0.00 3.67
2371 2656 1.510480 GAAGCGGCCACAGCATATCC 61.510 60.000 2.24 0.00 42.56 2.59
2401 2686 4.166888 ATGGCGTCGCTGATGGCT 62.167 61.111 18.11 7.64 43.27 4.75
2404 2689 4.521062 GCGTCGCTGATGGCTCCT 62.521 66.667 10.68 0.00 39.13 3.69
2425 2710 3.491652 GCGTGCGCCTTCTTCCTC 61.492 66.667 4.18 0.00 34.56 3.71
2797 3082 0.685097 TGAGGTTACAGTGGCTGTCC 59.315 55.000 4.95 2.35 41.21 4.02
2838 3123 3.326747 GTGCTCGTCAGAAGGTAACATT 58.673 45.455 0.00 0.00 41.41 2.71
2849 3134 8.946085 GTCAGAAGGTAACATTCAAATACATGA 58.054 33.333 0.00 0.00 41.41 3.07
2892 3177 4.537135 TCCTAGTTAGCTTCCAACACAG 57.463 45.455 0.00 0.00 0.00 3.66
2955 3240 3.565307 TCACAAGATGGAGCCAAACTTT 58.435 40.909 8.77 1.72 0.00 2.66
2981 3266 0.389426 GTTTCCGGCTAACGCTCTCA 60.389 55.000 0.00 0.00 42.52 3.27
3030 3315 3.650139 GACATACTGTCTCAACGGTTGT 58.350 45.455 19.47 2.98 42.51 3.32
3038 3323 4.079970 TGTCTCAACGGTTGTATCTCTCT 58.920 43.478 19.47 0.00 0.00 3.10
3114 3401 3.840666 GCCATGTATCCTCCCAGAATCTA 59.159 47.826 0.00 0.00 0.00 1.98
3118 3405 6.900186 CCATGTATCCTCCCAGAATCTAGTAT 59.100 42.308 0.00 0.00 0.00 2.12
3130 3417 7.447853 CCCAGAATCTAGTATAAGTACCGTTCT 59.552 40.741 0.00 0.00 0.00 3.01
3186 3474 8.558973 CTGATTTAACTCTCATCAGTCCTTTT 57.441 34.615 6.09 0.00 39.34 2.27
3194 3482 6.042552 ACTCTCATCAGTCCTTTTCAGAAAGA 59.957 38.462 0.00 0.00 44.03 2.52
3229 3521 3.009033 CCTCACTGTCACCTGGGATAAAA 59.991 47.826 0.00 0.00 0.00 1.52
3297 3590 4.142556 GCCCGATCTCACTAGATAGCTTAC 60.143 50.000 0.00 0.00 42.73 2.34
3332 3625 7.939782 TGCTGAAAAGATATTTGTTCTTCACA 58.060 30.769 0.00 0.00 32.33 3.58
3335 3628 9.565213 CTGAAAAGATATTTGTTCTTCACATCC 57.435 33.333 0.00 0.00 34.43 3.51
3338 3631 8.641498 AAAGATATTTGTTCTTCACATCCAGT 57.359 30.769 0.00 0.00 34.43 4.00
3339 3632 9.739276 AAAGATATTTGTTCTTCACATCCAGTA 57.261 29.630 0.00 0.00 34.43 2.74
3340 3633 9.739276 AAGATATTTGTTCTTCACATCCAGTAA 57.261 29.630 0.00 0.00 34.43 2.24
3341 3634 9.911788 AGATATTTGTTCTTCACATCCAGTAAT 57.088 29.630 0.00 0.00 34.43 1.89
3342 3635 9.941664 GATATTTGTTCTTCACATCCAGTAATG 57.058 33.333 0.00 0.00 34.43 1.90
3343 3636 5.627499 TTGTTCTTCACATCCAGTAATGC 57.373 39.130 0.00 0.00 34.43 3.56
3344 3637 4.650734 TGTTCTTCACATCCAGTAATGCA 58.349 39.130 0.00 0.00 0.00 3.96
3345 3638 5.255687 TGTTCTTCACATCCAGTAATGCAT 58.744 37.500 0.00 0.00 0.00 3.96
3346 3639 5.124297 TGTTCTTCACATCCAGTAATGCATG 59.876 40.000 0.00 0.00 0.00 4.06
3347 3640 4.847198 TCTTCACATCCAGTAATGCATGT 58.153 39.130 0.00 0.00 0.00 3.21
3348 3641 5.255687 TCTTCACATCCAGTAATGCATGTT 58.744 37.500 0.00 0.00 0.00 2.71
3349 3642 6.413892 TCTTCACATCCAGTAATGCATGTTA 58.586 36.000 0.00 0.00 0.00 2.41
3350 3643 6.539826 TCTTCACATCCAGTAATGCATGTTAG 59.460 38.462 0.00 0.00 0.00 2.34
3351 3644 5.125356 TCACATCCAGTAATGCATGTTAGG 58.875 41.667 0.00 0.63 0.00 2.69
3352 3645 5.104569 TCACATCCAGTAATGCATGTTAGGA 60.105 40.000 0.00 6.82 0.00 2.94
3353 3646 5.237996 CACATCCAGTAATGCATGTTAGGAG 59.762 44.000 0.00 3.75 0.00 3.69
3354 3647 4.422073 TCCAGTAATGCATGTTAGGAGG 57.578 45.455 0.00 0.00 0.00 4.30
3494 3804 3.311596 CGTCGGCGTATATCCATCTATGA 59.688 47.826 6.85 0.00 0.00 2.15
3542 3852 1.584483 TCGGCGTCGCGAGAAATAC 60.584 57.895 10.24 0.00 45.01 1.89
3680 4064 1.152963 GCATAGCCCCCACGTCATT 60.153 57.895 0.00 0.00 0.00 2.57
3774 4158 1.473677 CATGGATGTTGCCACGTCATT 59.526 47.619 11.86 0.00 41.56 2.57
3805 4189 0.249120 TTTGCCACGTCATCGATCCT 59.751 50.000 0.00 0.00 40.62 3.24
3826 4210 1.881252 GCCGTGTGCGTAGGTATGG 60.881 63.158 0.00 0.00 36.15 2.74
3840 4255 0.031585 GTATGGCGACGCATACCTCA 59.968 55.000 23.09 9.48 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.460263 TGAAGCAACCACTGTGTCTATTT 58.540 39.130 7.08 0.00 0.00 1.40
183 184 4.703575 CCAATGTCTCCAAGTCATTGTCAT 59.296 41.667 18.71 0.00 44.51 3.06
320 468 1.617357 CAACTACCCTACTATCCGCCC 59.383 57.143 0.00 0.00 0.00 6.13
409 557 0.110678 CCAGATGATGCCCAGCTCAT 59.889 55.000 0.00 0.00 39.96 2.90
452 600 2.322161 ACGTCGTAGTGGAACATTTCG 58.678 47.619 0.00 0.00 44.52 3.46
584 737 8.007742 ACAGTCCTGTCAACCTTATATCTAGAT 58.992 37.037 10.73 10.73 40.24 1.98
735 899 9.175312 CTACCAGTTGTAACTCATCTAGACTAA 57.825 37.037 0.00 0.00 37.08 2.24
741 905 7.770366 TGTTCTACCAGTTGTAACTCATCTA 57.230 36.000 0.00 0.00 37.08 1.98
742 906 6.665992 TGTTCTACCAGTTGTAACTCATCT 57.334 37.500 0.00 0.00 37.08 2.90
743 907 6.369065 CCTTGTTCTACCAGTTGTAACTCATC 59.631 42.308 0.00 0.00 37.08 2.92
744 908 6.042781 TCCTTGTTCTACCAGTTGTAACTCAT 59.957 38.462 0.00 0.00 37.08 2.90
745 909 5.364446 TCCTTGTTCTACCAGTTGTAACTCA 59.636 40.000 0.00 0.00 37.08 3.41
746 910 5.850614 TCCTTGTTCTACCAGTTGTAACTC 58.149 41.667 0.00 0.00 37.08 3.01
747 911 5.365895 ACTCCTTGTTCTACCAGTTGTAACT 59.634 40.000 0.00 0.00 40.60 2.24
748 912 5.608449 ACTCCTTGTTCTACCAGTTGTAAC 58.392 41.667 0.00 0.00 0.00 2.50
749 913 5.881923 ACTCCTTGTTCTACCAGTTGTAA 57.118 39.130 0.00 0.00 0.00 2.41
750 914 5.881923 AACTCCTTGTTCTACCAGTTGTA 57.118 39.130 0.00 0.00 32.63 2.41
751 915 4.772886 AACTCCTTGTTCTACCAGTTGT 57.227 40.909 0.00 0.00 32.63 3.32
762 926 2.241176 TGGTGGTTGAGAACTCCTTGTT 59.759 45.455 0.00 0.00 42.38 2.83
763 927 1.843851 TGGTGGTTGAGAACTCCTTGT 59.156 47.619 0.00 0.00 0.00 3.16
764 928 2.222027 GTGGTGGTTGAGAACTCCTTG 58.778 52.381 0.00 0.00 0.00 3.61
765 929 1.202651 CGTGGTGGTTGAGAACTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
766 930 0.393077 CGTGGTGGTTGAGAACTCCT 59.607 55.000 0.00 0.00 0.00 3.69
767 931 0.602905 CCGTGGTGGTTGAGAACTCC 60.603 60.000 0.00 0.00 0.00 3.85
773 937 1.185618 TCTCTCCCGTGGTGGTTGAG 61.186 60.000 0.00 0.00 36.85 3.02
800 964 5.583854 TGCGTTGTACTCCTACTTAGTAGAG 59.416 44.000 19.89 16.05 38.29 2.43
807 971 4.890088 TGAATTGCGTTGTACTCCTACTT 58.110 39.130 0.00 0.00 0.00 2.24
808 972 4.530710 TGAATTGCGTTGTACTCCTACT 57.469 40.909 0.00 0.00 0.00 2.57
809 973 5.049954 TGTTTGAATTGCGTTGTACTCCTAC 60.050 40.000 0.00 0.00 0.00 3.18
810 974 5.057819 TGTTTGAATTGCGTTGTACTCCTA 58.942 37.500 0.00 0.00 0.00 2.94
811 975 3.880490 TGTTTGAATTGCGTTGTACTCCT 59.120 39.130 0.00 0.00 0.00 3.69
872 1049 1.424403 CGTATTTATGCATCGCCGGA 58.576 50.000 5.05 0.00 0.00 5.14
879 1056 0.238289 GCCGCTGCGTATTTATGCAT 59.762 50.000 21.59 3.79 46.08 3.96
918 1095 2.038295 GGAGGCAATGGAGGTCTGATAG 59.962 54.545 0.00 0.00 0.00 2.08
926 1103 0.967380 GGTGTTGGAGGCAATGGAGG 60.967 60.000 0.00 0.00 0.00 4.30
961 1138 3.200593 CTCCGTCGTCGATCGGGT 61.201 66.667 25.43 0.00 45.79 5.28
1036 1220 2.797278 GCCAGATGGTCCCGACGAT 61.797 63.158 0.00 0.00 37.57 3.73
1056 1240 2.351276 GGGCCGTTGATGGTCTGT 59.649 61.111 0.00 0.00 32.87 3.41
1266 1450 1.211703 TCCAACAAGAGGAACTGCACA 59.788 47.619 0.00 0.00 41.55 4.57
1377 1561 4.800166 GCGAAGTTGTTGACGCTC 57.200 55.556 0.00 0.00 46.06 5.03
1750 1934 2.588034 GAGCGCCACCGGGATAAC 60.588 66.667 6.32 0.00 35.59 1.89
1752 1936 3.078196 TTGAGCGCCACCGGGATA 61.078 61.111 6.32 0.00 35.59 2.59
1773 1957 2.361104 TTGTTCATGCCCTCCCGC 60.361 61.111 0.00 0.00 0.00 6.13
1780 1964 2.046285 CCCCGACCTTGTTCATGCC 61.046 63.158 0.00 0.00 0.00 4.40
1792 1976 0.830648 TGGATCATGTTCTCCCCGAC 59.169 55.000 3.86 0.00 0.00 4.79
1805 2007 1.437573 GTGGCGAGATCGTGGATCA 59.562 57.895 8.21 0.00 41.12 2.92
1970 2220 4.647564 ATCTGTCCAAGATTGTTGAGGT 57.352 40.909 0.00 0.00 43.52 3.85
1983 2233 1.215382 CGACTCGGCAATCTGTCCA 59.785 57.895 0.00 0.00 0.00 4.02
2124 2376 3.492102 ACCTAGTCATGCAAGTGTGTT 57.508 42.857 0.00 0.00 0.00 3.32
2139 2391 8.943002 ACCAGACGAAAATAAACATTAACCTAG 58.057 33.333 0.00 0.00 0.00 3.02
2143 2395 7.863877 ACCAACCAGACGAAAATAAACATTAAC 59.136 33.333 0.00 0.00 0.00 2.01
2216 2480 8.665685 GTTGATAGTTACTACAAGTTTCCCATG 58.334 37.037 0.00 0.00 0.00 3.66
2231 2495 8.521176 TCCACTCTAGAACTTGTTGATAGTTAC 58.479 37.037 0.00 0.00 36.04 2.50
2255 2530 4.074970 TGGACAAAAGCAGAGAAGATTCC 58.925 43.478 0.00 0.00 0.00 3.01
2317 2598 4.919754 CCAACAAATTCAGTTAGCTGCTTC 59.080 41.667 7.79 1.66 42.29 3.86
2318 2599 4.342092 ACCAACAAATTCAGTTAGCTGCTT 59.658 37.500 7.79 0.00 42.29 3.91
2349 2634 1.898330 TATGCTGTGGCCGCTTCTGA 61.898 55.000 18.96 0.00 37.74 3.27
2425 2710 2.633509 GCTGCCCTGGTTGAGCAAG 61.634 63.158 4.47 0.00 35.79 4.01
2683 2968 2.190578 CCCCAGATGGCGAAGGTC 59.809 66.667 0.00 0.00 0.00 3.85
2769 3054 2.172483 CTGTAACCTCACCGGCAGCT 62.172 60.000 0.00 0.00 35.61 4.24
2797 3082 2.694109 ACCTAGGAAGTTAGCTAAGCGG 59.306 50.000 17.98 2.73 0.00 5.52
2838 3123 8.788806 AGTTTACGGTCAAATTCATGTATTTGA 58.211 29.630 27.10 27.10 46.69 2.69
2849 3134 2.496111 TGGCGAGTTTACGGTCAAATT 58.504 42.857 0.00 0.00 0.00 1.82
2892 3177 2.301577 AGCTCAACGACCTGATAAGC 57.698 50.000 0.00 0.00 0.00 3.09
2955 3240 0.603439 GTTAGCCGGAAACCGTTGGA 60.603 55.000 5.05 0.00 46.80 3.53
2981 3266 7.920682 GTCCACGCCTTTTAATATTCAATTCAT 59.079 33.333 0.00 0.00 0.00 2.57
2997 3282 1.066858 CAGTATGTCAGTCCACGCCTT 60.067 52.381 0.00 0.00 0.00 4.35
3038 3323 7.882791 TCCTTCTCTTTATAGCATTGTTCAACA 59.117 33.333 0.00 0.00 0.00 3.33
3186 3474 2.738643 GCCGATGGATTCGTCTTTCTGA 60.739 50.000 0.00 0.00 46.65 3.27
3194 3482 1.144057 GTGAGGCCGATGGATTCGT 59.856 57.895 0.00 0.00 46.65 3.85
3229 3521 9.744468 GCGTAATAAATACCTTCATTCCAAAAT 57.256 29.630 0.00 0.00 0.00 1.82
3313 3606 8.641498 ACTGGATGTGAAGAACAAATATCTTT 57.359 30.769 0.00 0.00 43.61 2.52
3332 3625 4.747931 GCCTCCTAACATGCATTACTGGAT 60.748 45.833 0.00 0.00 33.05 3.41
3335 3628 3.544684 TGCCTCCTAACATGCATTACTG 58.455 45.455 0.00 0.00 0.00 2.74
3338 3631 3.961849 TGTTGCCTCCTAACATGCATTA 58.038 40.909 0.00 0.00 33.43 1.90
3339 3632 2.806434 TGTTGCCTCCTAACATGCATT 58.194 42.857 0.00 0.00 33.43 3.56
3340 3633 2.512692 TGTTGCCTCCTAACATGCAT 57.487 45.000 0.00 0.00 33.43 3.96
3341 3634 2.284754 TTGTTGCCTCCTAACATGCA 57.715 45.000 0.00 0.00 37.81 3.96
3342 3635 2.754552 TGATTGTTGCCTCCTAACATGC 59.245 45.455 0.00 0.00 37.81 4.06
3343 3636 4.012374 AGTGATTGTTGCCTCCTAACATG 58.988 43.478 0.00 0.00 37.81 3.21
3344 3637 4.307032 AGTGATTGTTGCCTCCTAACAT 57.693 40.909 0.00 0.00 37.81 2.71
3345 3638 3.788227 AGTGATTGTTGCCTCCTAACA 57.212 42.857 0.00 0.00 36.34 2.41
3346 3639 3.939592 GGTAGTGATTGTTGCCTCCTAAC 59.060 47.826 0.00 0.00 0.00 2.34
3347 3640 3.585289 TGGTAGTGATTGTTGCCTCCTAA 59.415 43.478 0.00 0.00 0.00 2.69
3348 3641 3.178046 TGGTAGTGATTGTTGCCTCCTA 58.822 45.455 0.00 0.00 0.00 2.94
3349 3642 1.985159 TGGTAGTGATTGTTGCCTCCT 59.015 47.619 0.00 0.00 0.00 3.69
3350 3643 2.027192 TCTGGTAGTGATTGTTGCCTCC 60.027 50.000 0.00 0.00 0.00 4.30
3351 3644 3.334583 TCTGGTAGTGATTGTTGCCTC 57.665 47.619 0.00 0.00 0.00 4.70
3352 3645 3.788227 TTCTGGTAGTGATTGTTGCCT 57.212 42.857 0.00 0.00 0.00 4.75
3353 3646 5.648092 AGTTATTCTGGTAGTGATTGTTGCC 59.352 40.000 0.00 0.00 0.00 4.52
3354 3647 6.546395 CAGTTATTCTGGTAGTGATTGTTGC 58.454 40.000 0.00 0.00 40.23 4.17
3511 3821 2.125673 GCCGACGGCTGAGCTTTA 60.126 61.111 31.30 0.00 46.69 1.85
3576 3886 2.270850 GGCCCACGTTCTATGCCA 59.729 61.111 0.00 0.00 41.76 4.92
3604 3914 4.383602 CAAAAGGCCGTGTCCGCG 62.384 66.667 0.00 0.00 0.00 6.46
3774 4158 4.440829 GGCAAAGGGCGGGGATCA 62.441 66.667 0.00 0.00 46.16 2.92
3805 4189 1.890625 ATACCTACGCACACGGCCAA 61.891 55.000 2.24 0.00 46.04 4.52
3826 4210 2.825086 AAAATTGAGGTATGCGTCGC 57.175 45.000 11.10 11.10 32.59 5.19


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

AutoCloner maintained by Alex Coulton.