Multiple sequence alignment - TraesCS5A01G521000

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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 TraesCS5A01G521000 chr5A 100.000 3485 0 0 1 3485 681485636 681489120 0.000000e+00 6436.0
1 TraesCS5A01G521000 chr4B 92.472 1076 74 4 839 1911 644369030 644367959 0.000000e+00 1531.0
2 TraesCS5A01G521000 chr4B 92.090 1024 69 8 896 1911 644476157 644477176 0.000000e+00 1432.0
3 TraesCS5A01G521000 chr4B 89.552 871 51 18 1953 2822 644366840 644366009 0.000000e+00 1068.0
4 TraesCS5A01G521000 chr4B 91.399 686 47 5 1953 2637 644477606 644478280 0.000000e+00 929.0
5 TraesCS5A01G521000 chr4B 86.785 507 53 8 1 500 644475298 644475797 1.410000e-153 553.0
6 TraesCS5A01G521000 chr4B 78.462 780 165 3 1013 1792 577016181 577015405 1.120000e-139 507.0
7 TraesCS5A01G521000 chr4B 88.579 394 38 5 111 500 644370220 644369830 4.070000e-129 472.0
8 TraesCS5A01G521000 chr4B 87.288 236 12 9 618 836 644475802 644476036 1.610000e-63 254.0
9 TraesCS5A01G521000 chr4B 84.021 194 14 8 663 839 644369259 644369066 1.660000e-38 171.0
10 TraesCS5A01G521000 chr4B 89.231 130 8 5 497 620 625916186 625916315 1.290000e-34 158.0
11 TraesCS5A01G521000 chr4B 93.443 61 4 0 839 899 644476079 644476139 1.330000e-14 91.6
12 TraesCS5A01G521000 chr4D 91.674 1069 61 13 896 1956 500526851 500527899 0.000000e+00 1456.0
13 TraesCS5A01G521000 chr4D 89.955 896 54 10 1953 2822 500529017 500529902 0.000000e+00 1123.0
14 TraesCS5A01G521000 chr4D 87.081 418 40 6 96 509 500525822 500526229 8.810000e-126 460.0
15 TraesCS5A01G521000 chr4D 77.139 783 166 9 1013 1792 461510451 461509679 3.190000e-120 442.0
16 TraesCS5A01G521000 chr4D 76.854 782 170 7 1013 1792 461562117 461561345 6.910000e-117 431.0
17 TraesCS5A01G521000 chr4D 84.161 322 48 3 2114 2434 461561167 461560848 3.380000e-80 309.0
18 TraesCS5A01G521000 chr4D 85.648 216 12 10 636 834 500526513 500526726 3.520000e-50 209.0
19 TraesCS5A01G521000 chr4D 93.443 61 4 0 839 899 500526773 500526833 1.330000e-14 91.6
20 TraesCS5A01G521000 chrUn 91.055 872 57 9 1953 2822 10148881 10149733 0.000000e+00 1158.0
21 TraesCS5A01G521000 chrUn 81.006 358 55 10 2090 2443 37505380 37505728 4.430000e-69 272.0
22 TraesCS5A01G521000 chr2D 91.557 687 29 14 2822 3480 471992562 471993247 0.000000e+00 920.0
23 TraesCS5A01G521000 chr2D 90.593 691 37 4 2822 3484 471998305 471998995 0.000000e+00 891.0
24 TraesCS5A01G521000 chr2D 90.504 695 35 5 2822 3485 471996037 471996731 0.000000e+00 889.0
25 TraesCS5A01G521000 chr2D 81.856 970 127 26 850 1789 639460059 639461009 0.000000e+00 771.0
26 TraesCS5A01G521000 chr7B 86.199 884 70 14 1953 2822 477975768 477976613 0.000000e+00 909.0
27 TraesCS5A01G521000 chr7B 87.938 713 71 10 839 1546 477971818 477972520 0.000000e+00 826.0
28 TraesCS5A01G521000 chr7B 88.251 383 23 9 1532 1914 477974311 477974671 4.130000e-119 438.0
29 TraesCS5A01G521000 chr7B 88.000 150 5 9 699 836 477965276 477965424 7.740000e-37 165.0
30 TraesCS5A01G521000 chr4A 78.177 779 165 5 1012 1789 7154364 7155138 3.130000e-135 492.0
31 TraesCS5A01G521000 chr3D 76.806 789 143 23 1021 1789 507535380 507534612 1.160000e-109 407.0
32 TraesCS5A01G521000 chr3D 84.365 307 46 2 2125 2430 17777514 17777209 2.030000e-77 300.0
33 TraesCS5A01G521000 chr3D 89.231 130 8 5 497 620 208728204 208728333 1.290000e-34 158.0
34 TraesCS5A01G521000 chr3D 89.231 130 8 5 497 620 354450796 354450667 1.290000e-34 158.0
35 TraesCS5A01G521000 chr3A 83.230 322 50 3 2125 2443 18836295 18835975 3.400000e-75 292.0
36 TraesCS5A01G521000 chr6B 91.667 120 7 3 504 620 541391079 541391198 2.780000e-36 163.0
37 TraesCS5A01G521000 chr6D 89.231 130 8 5 497 620 373588878 373589007 1.290000e-34 158.0
38 TraesCS5A01G521000 chr1D 89.231 130 8 5 497 620 247418582 247418711 1.290000e-34 158.0
39 TraesCS5A01G521000 chr1D 89.231 130 8 5 497 620 449997784 449997655 1.290000e-34 158.0
40 TraesCS5A01G521000 chr1D 89.231 130 8 5 497 620 463745484 463745355 1.290000e-34 158.0
41 TraesCS5A01G521000 chr1A 89.231 130 8 5 497 620 538050433 538050304 1.290000e-34 158.0


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 TraesCS5A01G521000 chr5A 681485636 681489120 3484 False 6436.000000 6436 100.000000 1 3485 1 chr5A.!!$F1 3484
1 TraesCS5A01G521000 chr4B 644366009 644370220 4211 True 810.500000 1531 88.656000 111 2822 4 chr4B.!!$R2 2711
2 TraesCS5A01G521000 chr4B 644475298 644478280 2982 False 651.920000 1432 90.201000 1 2637 5 chr4B.!!$F2 2636
3 TraesCS5A01G521000 chr4B 577015405 577016181 776 True 507.000000 507 78.462000 1013 1792 1 chr4B.!!$R1 779
4 TraesCS5A01G521000 chr4D 500525822 500529902 4080 False 667.920000 1456 89.560200 96 2822 5 chr4D.!!$F1 2726
5 TraesCS5A01G521000 chr4D 461509679 461510451 772 True 442.000000 442 77.139000 1013 1792 1 chr4D.!!$R1 779
6 TraesCS5A01G521000 chr4D 461560848 461562117 1269 True 370.000000 431 80.507500 1013 2434 2 chr4D.!!$R2 1421
7 TraesCS5A01G521000 chrUn 10148881 10149733 852 False 1158.000000 1158 91.055000 1953 2822 1 chrUn.!!$F1 869
8 TraesCS5A01G521000 chr2D 471992562 471998995 6433 False 900.000000 920 90.884667 2822 3485 3 chr2D.!!$F2 663
9 TraesCS5A01G521000 chr2D 639460059 639461009 950 False 771.000000 771 81.856000 850 1789 1 chr2D.!!$F1 939
10 TraesCS5A01G521000 chr7B 477971818 477976613 4795 False 724.333333 909 87.462667 839 2822 3 chr7B.!!$F2 1983
11 TraesCS5A01G521000 chr4A 7154364 7155138 774 False 492.000000 492 78.177000 1012 1789 1 chr4A.!!$F1 777
12 TraesCS5A01G521000 chr3D 507534612 507535380 768 True 407.000000 407 76.806000 1021 1789 1 chr3D.!!$R3 768

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
20 21 0.248866 GGCACAAACAAACCCACTCG 60.249 55.0 0.00 0.0 0.0 4.18 F
406 412 0.250295 CGTTTGAGCTGTTCCCCTGA 60.250 55.0 0.00 0.0 0.0 3.86 F
777 1584 0.320247 GGCGTAGGAGGAGATGCATG 60.320 60.0 2.46 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 5102 0.811616 GGCTAGCAGTTGGATCACGG 60.812 60.000 18.24 0.0 0.0 4.94 R
1946 5140 6.127758 CCTTTGTGCTATGTGGCTATTAACAA 60.128 38.462 0.00 0.0 0.0 2.83 R
2549 6877 2.125269 CGACCGGCCCCTTAACAG 60.125 66.667 0.00 0.0 0.0 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
20 21 0.248866 GGCACAAACAAACCCACTCG 60.249 55.000 0.00 0.00 0.00 4.18
22 23 1.797348 GCACAAACAAACCCACTCGTG 60.797 52.381 0.00 0.00 0.00 4.35
30 31 0.763223 AACCCACTCGTGTCTCCCTT 60.763 55.000 0.00 0.00 0.00 3.95
55 56 3.007831 TGGGAAAGAATGCCACCAAAATC 59.992 43.478 0.00 0.00 45.86 2.17
56 57 3.253230 GGAAAGAATGCCACCAAAATCG 58.747 45.455 0.00 0.00 0.00 3.34
63 64 2.852449 TGCCACCAAAATCGTCAAGTA 58.148 42.857 0.00 0.00 0.00 2.24
64 65 2.811431 TGCCACCAAAATCGTCAAGTAG 59.189 45.455 0.00 0.00 0.00 2.57
70 74 3.181530 CCAAAATCGTCAAGTAGCGAGTG 60.182 47.826 0.00 0.00 40.56 3.51
82 86 0.532640 AGCGAGTGTCACACATGCAA 60.533 50.000 21.99 0.00 38.55 4.08
83 87 0.518636 GCGAGTGTCACACATGCAAT 59.481 50.000 16.93 0.00 36.96 3.56
101 105 4.202090 TGCAATGCAGTGTGTCATTTGTAA 60.202 37.500 16.47 0.00 33.32 2.41
157 161 1.553704 ACCCCTTAACAGACGATGTCC 59.446 52.381 0.00 0.00 43.00 4.02
208 213 8.608844 AAAATCACACGAAGTAAGATCTTTCT 57.391 30.769 14.36 11.23 41.61 2.52
209 214 9.706691 AAAATCACACGAAGTAAGATCTTTCTA 57.293 29.630 14.36 0.00 41.61 2.10
211 216 7.450124 TCACACGAAGTAAGATCTTTCTAGT 57.550 36.000 14.36 13.87 41.61 2.57
213 218 7.174426 TCACACGAAGTAAGATCTTTCTAGTGA 59.826 37.037 32.53 27.15 41.61 3.41
221 226 9.702253 AGTAAGATCTTTCTAGTGATAGAACCA 57.298 33.333 14.36 0.00 35.97 3.67
269 274 4.171234 TGGGCCCAAATTATTTTTCCTCA 58.829 39.130 26.33 0.00 0.00 3.86
275 280 5.422145 CCAAATTATTTTTCCTCAGGGCTG 58.578 41.667 0.00 0.00 0.00 4.85
293 298 3.758554 GGCTGGACACTCACATAAAACAT 59.241 43.478 0.00 0.00 0.00 2.71
375 381 8.161425 TCCTACAGCAAACTAGGTAATTTTTCT 58.839 33.333 0.00 0.00 32.59 2.52
397 403 2.743664 TGTGATGAATCCGTTTGAGCTG 59.256 45.455 0.00 0.00 0.00 4.24
398 404 2.744202 GTGATGAATCCGTTTGAGCTGT 59.256 45.455 0.00 0.00 0.00 4.40
404 410 1.073199 CCGTTTGAGCTGTTCCCCT 59.927 57.895 0.00 0.00 0.00 4.79
406 412 0.250295 CGTTTGAGCTGTTCCCCTGA 60.250 55.000 0.00 0.00 0.00 3.86
418 424 3.392285 TGTTCCCCTGATCCATACATCTG 59.608 47.826 0.00 0.00 0.00 2.90
444 450 7.041780 GGATACATTCAATTGAGCGACAAGTAT 60.042 37.037 8.41 6.47 42.02 2.12
450 456 5.007626 TCAATTGAGCGACAAGTATTATGGC 59.992 40.000 3.38 0.00 42.02 4.40
452 458 3.717707 TGAGCGACAAGTATTATGGCTC 58.282 45.455 3.35 3.35 40.64 4.70
453 459 3.060602 GAGCGACAAGTATTATGGCTCC 58.939 50.000 0.00 0.00 36.91 4.70
485 495 8.870116 AGTAGTAATGAATCCACATATGTGCTA 58.130 33.333 27.27 18.38 44.34 3.49
500 762 8.085296 ACATATGTGCTACTCTGAAGCTAATAC 58.915 37.037 7.78 0.00 40.73 1.89
502 764 6.137794 TGTGCTACTCTGAAGCTAATACTC 57.862 41.667 3.28 0.00 40.73 2.59
504 766 5.300792 GTGCTACTCTGAAGCTAATACTCCT 59.699 44.000 3.28 0.00 40.73 3.69
505 767 5.300539 TGCTACTCTGAAGCTAATACTCCTG 59.699 44.000 3.28 0.00 40.73 3.86
506 768 5.300792 GCTACTCTGAAGCTAATACTCCTGT 59.699 44.000 0.00 0.00 37.01 4.00
507 769 5.845391 ACTCTGAAGCTAATACTCCTGTC 57.155 43.478 0.00 0.00 0.00 3.51
508 770 4.647399 ACTCTGAAGCTAATACTCCTGTCC 59.353 45.833 0.00 0.00 0.00 4.02
509 771 3.632604 TCTGAAGCTAATACTCCTGTCCG 59.367 47.826 0.00 0.00 0.00 4.79
510 772 3.628008 TGAAGCTAATACTCCTGTCCGA 58.372 45.455 0.00 0.00 0.00 4.55
511 773 4.021229 TGAAGCTAATACTCCTGTCCGAA 58.979 43.478 0.00 0.00 0.00 4.30
512 774 4.464951 TGAAGCTAATACTCCTGTCCGAAA 59.535 41.667 0.00 0.00 0.00 3.46
513 775 5.046878 TGAAGCTAATACTCCTGTCCGAAAA 60.047 40.000 0.00 0.00 0.00 2.29
514 776 5.416271 AGCTAATACTCCTGTCCGAAAAA 57.584 39.130 0.00 0.00 0.00 1.94
515 777 5.176592 AGCTAATACTCCTGTCCGAAAAAC 58.823 41.667 0.00 0.00 0.00 2.43
516 778 5.046520 AGCTAATACTCCTGTCCGAAAAACT 60.047 40.000 0.00 0.00 0.00 2.66
517 779 5.063564 GCTAATACTCCTGTCCGAAAAACTG 59.936 44.000 0.00 0.00 0.00 3.16
518 780 4.618920 ATACTCCTGTCCGAAAAACTGT 57.381 40.909 0.00 0.00 0.00 3.55
519 781 2.835027 ACTCCTGTCCGAAAAACTGTC 58.165 47.619 0.00 0.00 0.00 3.51
520 782 2.169769 ACTCCTGTCCGAAAAACTGTCA 59.830 45.455 0.00 0.00 0.00 3.58
521 783 3.181454 ACTCCTGTCCGAAAAACTGTCAT 60.181 43.478 0.00 0.00 0.00 3.06
522 784 3.399330 TCCTGTCCGAAAAACTGTCATC 58.601 45.455 0.00 0.00 0.00 2.92
523 785 3.138304 CCTGTCCGAAAAACTGTCATCA 58.862 45.455 0.00 0.00 0.00 3.07
524 786 3.563808 CCTGTCCGAAAAACTGTCATCAA 59.436 43.478 0.00 0.00 0.00 2.57
525 787 4.036262 CCTGTCCGAAAAACTGTCATCAAA 59.964 41.667 0.00 0.00 0.00 2.69
526 788 5.449862 CCTGTCCGAAAAACTGTCATCAAAA 60.450 40.000 0.00 0.00 0.00 2.44
527 789 6.142818 TGTCCGAAAAACTGTCATCAAAAT 57.857 33.333 0.00 0.00 0.00 1.82
528 790 5.976534 TGTCCGAAAAACTGTCATCAAAATG 59.023 36.000 0.00 0.00 0.00 2.32
529 791 5.402270 GTCCGAAAAACTGTCATCAAAATGG 59.598 40.000 0.00 0.00 33.42 3.16
530 792 5.300539 TCCGAAAAACTGTCATCAAAATGGA 59.699 36.000 0.00 0.00 33.42 3.41
531 793 6.015519 TCCGAAAAACTGTCATCAAAATGGAT 60.016 34.615 0.00 0.00 33.42 3.41
532 794 7.175816 TCCGAAAAACTGTCATCAAAATGGATA 59.824 33.333 0.00 0.00 33.42 2.59
533 795 7.812191 CCGAAAAACTGTCATCAAAATGGATAA 59.188 33.333 0.00 0.00 33.42 1.75
534 796 9.190858 CGAAAAACTGTCATCAAAATGGATAAA 57.809 29.630 0.00 0.00 33.42 1.40
610 872 8.481974 TCTTAATGACAAATATTTTCGGACGA 57.518 30.769 0.00 0.00 0.00 4.20
611 873 8.937884 TCTTAATGACAAATATTTTCGGACGAA 58.062 29.630 2.62 2.62 0.00 3.85
612 874 9.210426 CTTAATGACAAATATTTTCGGACGAAG 57.790 33.333 7.25 0.00 35.38 3.79
613 875 5.539582 TGACAAATATTTTCGGACGAAGG 57.460 39.130 7.25 0.00 35.38 3.46
614 876 4.393680 TGACAAATATTTTCGGACGAAGGG 59.606 41.667 7.25 0.00 35.38 3.95
615 877 4.581868 ACAAATATTTTCGGACGAAGGGA 58.418 39.130 7.25 0.00 35.38 4.20
616 878 4.634443 ACAAATATTTTCGGACGAAGGGAG 59.366 41.667 7.25 0.00 35.38 4.30
630 892 3.314080 CGAAGGGAGTAGTTTGTTTGCAA 59.686 43.478 0.00 0.00 0.00 4.08
631 893 4.023193 CGAAGGGAGTAGTTTGTTTGCAAT 60.023 41.667 0.00 0.00 34.18 3.56
632 894 5.507315 CGAAGGGAGTAGTTTGTTTGCAATT 60.507 40.000 0.00 0.00 34.18 2.32
745 1552 7.504924 AGTTCCACGAGTGAAATTTAAATCA 57.495 32.000 4.59 0.00 0.00 2.57
769 1576 0.323999 TAGTTGCTGGCGTAGGAGGA 60.324 55.000 0.00 0.00 0.00 3.71
770 1577 1.153549 GTTGCTGGCGTAGGAGGAG 60.154 63.158 0.00 0.00 0.00 3.69
771 1578 1.304962 TTGCTGGCGTAGGAGGAGA 60.305 57.895 0.00 0.00 0.00 3.71
773 1580 1.365633 GCTGGCGTAGGAGGAGATG 59.634 63.158 0.00 0.00 0.00 2.90
774 1581 1.365633 CTGGCGTAGGAGGAGATGC 59.634 63.158 0.00 0.00 0.00 3.91
775 1582 1.381191 TGGCGTAGGAGGAGATGCA 60.381 57.895 0.00 0.00 0.00 3.96
776 1583 0.760567 TGGCGTAGGAGGAGATGCAT 60.761 55.000 0.00 0.00 0.00 3.96
777 1584 0.320247 GGCGTAGGAGGAGATGCATG 60.320 60.000 2.46 0.00 0.00 4.06
778 1585 0.948141 GCGTAGGAGGAGATGCATGC 60.948 60.000 11.82 11.82 0.00 4.06
795 1617 4.989797 TGCATGCTTTTAATTCCAACAGTG 59.010 37.500 20.33 0.00 0.00 3.66
836 1658 3.795688 TCATCTTCCCTGCAAGAAACT 57.204 42.857 0.95 0.00 35.99 2.66
908 1797 9.884636 TTTTAAATCATGTTAGTAGCTAGCAGA 57.115 29.630 18.83 0.56 31.30 4.26
952 1847 0.747283 CCCTTAAGCCAGCTGAGCAG 60.747 60.000 23.46 14.54 0.00 4.24
981 1876 1.203523 CACTACACAGCCCTGAGACTC 59.796 57.143 1.69 0.00 0.00 3.36
987 1882 1.752694 AGCCCTGAGACTCGAGAGC 60.753 63.158 21.68 10.70 0.00 4.09
1005 1903 0.510359 GCGATAGAGAAAGCATGGCG 59.490 55.000 0.00 0.00 39.76 5.69
1009 1907 0.462581 TAGAGAAAGCATGGCGGCTG 60.463 55.000 11.43 7.30 45.07 4.85
1221 2133 3.777925 CCGTTTCTCAGCCGCGTG 61.778 66.667 4.92 0.00 0.00 5.34
1341 2257 2.825264 GGCGAGGCTAGGCAGATT 59.175 61.111 19.70 0.00 0.00 2.40
1440 2374 1.700042 CCCTACCAGTGCCATCTCCC 61.700 65.000 0.00 0.00 0.00 4.30
1743 4483 4.465632 TGTTAACTATGTCGCTGGTGAT 57.534 40.909 7.22 0.00 0.00 3.06
1873 4619 8.189460 GGTATGGATATACGTACAGAGGAATTC 58.811 40.741 17.38 0.00 40.07 2.17
1912 5102 8.557029 CCAAACTAATATGGACCGTTAATTCTC 58.443 37.037 0.00 0.00 39.12 2.87
1936 5126 2.837591 TGATCCAACTGCTAGCCACTTA 59.162 45.455 13.29 0.00 0.00 2.24
1946 5140 5.305644 ACTGCTAGCCACTTATAGTATTGCT 59.694 40.000 13.29 0.00 33.35 3.91
1978 6299 4.526970 CCACATAGCACAAAGGGAACTAT 58.473 43.478 0.00 0.00 42.68 2.12
2474 6802 3.552699 TGTGTGTTCCGTATAAATAGCGC 59.447 43.478 0.00 0.00 0.00 5.92
2521 6849 0.904649 TGCCTCACTCGTCAATGGAT 59.095 50.000 0.00 0.00 0.00 3.41
2529 6857 5.125356 TCACTCGTCAATGGATAATGCAAT 58.875 37.500 0.00 0.00 0.00 3.56
2530 6858 5.007921 TCACTCGTCAATGGATAATGCAATG 59.992 40.000 0.00 0.00 0.00 2.82
2534 6862 7.445096 ACTCGTCAATGGATAATGCAATGAATA 59.555 33.333 0.00 0.00 29.52 1.75
2549 6877 8.181487 TGCAATGAATACTTAAGTAGACGAAC 57.819 34.615 19.58 7.99 33.52 3.95
2688 7051 9.418045 GCTTTGTTGTTTTGGTATGTGTATAAT 57.582 29.630 0.00 0.00 0.00 1.28
2714 7077 5.877031 TCTTCTCGAATAGTTTAGTGGACG 58.123 41.667 0.00 0.00 0.00 4.79
2739 7102 6.275335 AGCATTTGTGTATGTTTATCATGCC 58.725 36.000 0.00 0.00 38.16 4.40
2829 7194 2.566833 TCCATATGCCTCAAATCCCG 57.433 50.000 0.00 0.00 0.00 5.14
2832 7197 2.154462 CATATGCCTCAAATCCCGTCC 58.846 52.381 0.00 0.00 0.00 4.79
2838 7203 0.321564 CTCAAATCCCGTCCTGTGCA 60.322 55.000 0.00 0.00 0.00 4.57
2896 7261 4.436998 CGCACGTCCCCCTCTCAC 62.437 72.222 0.00 0.00 0.00 3.51
2902 7267 1.390926 GTCCCCCTCTCACCCACTA 59.609 63.158 0.00 0.00 0.00 2.74
2917 10757 0.658897 CACTACCGTGCGTGGTTTTT 59.341 50.000 4.88 0.00 43.56 1.94
2922 10762 1.061253 CGTGCGTGGTTTTTGTCGT 59.939 52.632 0.00 0.00 0.00 4.34
2958 10817 2.575993 CTCGGCTGGACTGGAGTG 59.424 66.667 0.00 0.00 0.00 3.51
2960 10819 4.767255 CGGCTGGACTGGAGTGGC 62.767 72.222 0.00 0.00 0.00 5.01
2976 10835 1.816835 GTGGCATACTATCCGATCCGA 59.183 52.381 0.00 0.00 0.00 4.55
2986 10845 1.210413 CCGATCCGATACGAGCCAG 59.790 63.158 0.00 0.00 0.00 4.85
2988 10847 1.660355 GATCCGATACGAGCCAGCA 59.340 57.895 0.00 0.00 0.00 4.41
2989 10848 0.244994 GATCCGATACGAGCCAGCAT 59.755 55.000 0.00 0.00 0.00 3.79
2990 10849 0.244994 ATCCGATACGAGCCAGCATC 59.755 55.000 0.00 0.00 0.00 3.91
2992 10851 0.665670 CCGATACGAGCCAGCATCTG 60.666 60.000 0.00 0.00 0.00 2.90
2993 10852 1.280886 CGATACGAGCCAGCATCTGC 61.281 60.000 0.00 0.00 42.49 4.26
3017 10887 1.227089 CAGTCGCCTCCATCTTCCG 60.227 63.158 0.00 0.00 0.00 4.30
3023 10893 2.498941 CCTCCATCTTCCGCCGCTA 61.499 63.158 0.00 0.00 0.00 4.26
3056 10926 1.537202 GGCATGGGATAAATCGAGTGC 59.463 52.381 0.00 0.00 0.00 4.40
3057 10927 2.221169 GCATGGGATAAATCGAGTGCA 58.779 47.619 0.00 0.00 32.13 4.57
3059 10929 1.953559 TGGGATAAATCGAGTGCAGC 58.046 50.000 0.00 0.00 0.00 5.25
3084 10954 1.809619 CCACACGACATAGGTGCGG 60.810 63.158 0.00 0.00 38.98 5.69
3138 11008 1.069765 CCTCGTCCCCCATTCATCG 59.930 63.158 0.00 0.00 0.00 3.84
3168 11038 8.571461 TCTGTTTCTGCATTCAATCTATTTCT 57.429 30.769 0.00 0.00 0.00 2.52
3202 11072 1.673920 TGTGACGCCTTTTGTTTCCTC 59.326 47.619 0.00 0.00 0.00 3.71
3210 11080 3.359654 CCTTTTGTTTCCTCGTTGTTCG 58.640 45.455 0.00 0.00 41.41 3.95
3425 13561 6.806751 TGTCTATATCACTTGGTGAAGTAGC 58.193 40.000 4.46 7.07 45.96 3.58
3438 13574 3.069289 TGAAGTAGCTGATTGTGTGCTG 58.931 45.455 0.00 0.00 37.62 4.41
3454 13590 4.275936 GTGTGCTGGACTTGTTCTTTGTAT 59.724 41.667 0.00 0.00 0.00 2.29
3484 13620 1.930908 GCTGATTGCAGTGGTCAGGC 61.931 60.000 16.85 9.25 44.17 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.213013 CCACGAAGGGAGACACGAG 59.787 63.158 0.00 0.00 0.00 4.18
30 31 2.941210 GTGGCATTCTTTCCCACGA 58.059 52.632 0.00 0.00 39.56 4.35
40 41 3.244976 CTTGACGATTTTGGTGGCATTC 58.755 45.455 0.00 0.00 0.00 2.67
41 42 2.627699 ACTTGACGATTTTGGTGGCATT 59.372 40.909 0.00 0.00 0.00 3.56
55 56 1.328439 GTGACACTCGCTACTTGACG 58.672 55.000 0.00 0.00 0.00 4.35
56 57 2.052157 GTGTGACACTCGCTACTTGAC 58.948 52.381 8.76 0.00 0.00 3.18
63 64 0.532640 TTGCATGTGTGACACTCGCT 60.533 50.000 23.29 3.87 34.84 4.93
64 65 0.518636 ATTGCATGTGTGACACTCGC 59.481 50.000 17.47 18.13 35.11 5.03
70 74 1.001048 ACACTGCATTGCATGTGTGAC 60.001 47.619 29.37 0.00 43.43 3.67
82 86 6.572519 AGTTTTTACAAATGACACACTGCAT 58.427 32.000 0.00 0.00 0.00 3.96
83 87 5.960113 AGTTTTTACAAATGACACACTGCA 58.040 33.333 0.00 0.00 0.00 4.41
84 88 6.265577 AGAGTTTTTACAAATGACACACTGC 58.734 36.000 0.00 0.00 0.00 4.40
85 89 7.471721 TGAGAGTTTTTACAAATGACACACTG 58.528 34.615 0.00 0.00 0.00 3.66
86 90 7.624360 TGAGAGTTTTTACAAATGACACACT 57.376 32.000 0.00 0.00 0.00 3.55
87 91 7.432252 CCTTGAGAGTTTTTACAAATGACACAC 59.568 37.037 0.00 0.00 0.00 3.82
88 92 7.122055 ACCTTGAGAGTTTTTACAAATGACACA 59.878 33.333 0.00 0.00 0.00 3.72
89 93 7.432252 CACCTTGAGAGTTTTTACAAATGACAC 59.568 37.037 0.00 0.00 0.00 3.67
191 195 9.616156 TCTATCACTAGAAAGATCTTACTTCGT 57.384 33.333 8.75 0.26 37.10 3.85
203 207 7.062371 CGTGAAACTGGTTCTATCACTAGAAAG 59.938 40.741 7.02 0.00 39.10 2.62
208 213 4.525487 ACCGTGAAACTGGTTCTATCACTA 59.475 41.667 7.02 0.00 39.97 2.74
209 214 3.323979 ACCGTGAAACTGGTTCTATCACT 59.676 43.478 7.02 0.00 39.97 3.41
211 216 3.556213 CCACCGTGAAACTGGTTCTATCA 60.556 47.826 7.02 0.00 40.73 2.15
213 218 2.370849 ACCACCGTGAAACTGGTTCTAT 59.629 45.455 7.02 0.00 42.08 1.98
218 223 1.822186 GCACCACCGTGAAACTGGT 60.822 57.895 0.00 0.00 45.22 4.00
221 226 0.667993 CATTGCACCACCGTGAAACT 59.332 50.000 0.00 0.00 40.48 2.66
269 274 1.656587 TTATGTGAGTGTCCAGCCCT 58.343 50.000 0.00 0.00 0.00 5.19
375 381 3.189080 CAGCTCAAACGGATTCATCACAA 59.811 43.478 0.00 0.00 0.00 3.33
386 392 1.073199 AGGGGAACAGCTCAAACGG 59.927 57.895 0.00 0.00 0.00 4.44
397 403 3.244700 CCAGATGTATGGATCAGGGGAAC 60.245 52.174 0.00 0.00 43.57 3.62
398 404 2.981784 CCAGATGTATGGATCAGGGGAA 59.018 50.000 0.00 0.00 43.57 3.97
418 424 5.065218 ACTTGTCGCTCAATTGAATGTATCC 59.935 40.000 9.88 0.00 35.35 2.59
428 434 5.126067 AGCCATAATACTTGTCGCTCAATT 58.874 37.500 0.00 0.00 35.35 2.32
452 458 5.221441 TGTGGATTCATTACTACTCCATCGG 60.221 44.000 0.00 0.00 38.23 4.18
453 459 5.842907 TGTGGATTCATTACTACTCCATCG 58.157 41.667 0.00 0.00 38.23 3.84
485 495 4.647399 GGACAGGAGTATTAGCTTCAGAGT 59.353 45.833 0.00 0.00 0.00 3.24
500 762 2.833794 TGACAGTTTTTCGGACAGGAG 58.166 47.619 0.00 0.00 0.00 3.69
502 764 3.138304 TGATGACAGTTTTTCGGACAGG 58.862 45.455 0.00 0.00 0.00 4.00
504 766 5.568685 TTTTGATGACAGTTTTTCGGACA 57.431 34.783 0.00 0.00 0.00 4.02
505 767 5.402270 CCATTTTGATGACAGTTTTTCGGAC 59.598 40.000 0.00 0.00 0.00 4.79
506 768 5.300539 TCCATTTTGATGACAGTTTTTCGGA 59.699 36.000 0.00 0.00 0.00 4.55
507 769 5.527951 TCCATTTTGATGACAGTTTTTCGG 58.472 37.500 0.00 0.00 0.00 4.30
508 770 8.741101 TTATCCATTTTGATGACAGTTTTTCG 57.259 30.769 0.00 0.00 0.00 3.46
584 846 9.104965 TCGTCCGAAAATATTTGTCATTAAGAT 57.895 29.630 0.39 0.00 0.00 2.40
585 847 8.481974 TCGTCCGAAAATATTTGTCATTAAGA 57.518 30.769 0.39 0.00 0.00 2.10
586 848 9.210426 CTTCGTCCGAAAATATTTGTCATTAAG 57.790 33.333 0.39 0.00 33.34 1.85
587 849 8.178964 CCTTCGTCCGAAAATATTTGTCATTAA 58.821 33.333 0.39 0.00 33.34 1.40
588 850 7.201661 CCCTTCGTCCGAAAATATTTGTCATTA 60.202 37.037 0.39 0.00 33.34 1.90
589 851 6.404293 CCCTTCGTCCGAAAATATTTGTCATT 60.404 38.462 0.39 0.00 33.34 2.57
590 852 5.065988 CCCTTCGTCCGAAAATATTTGTCAT 59.934 40.000 0.39 0.00 33.34 3.06
591 853 4.393680 CCCTTCGTCCGAAAATATTTGTCA 59.606 41.667 0.39 0.00 33.34 3.58
592 854 4.632688 TCCCTTCGTCCGAAAATATTTGTC 59.367 41.667 0.39 1.54 33.34 3.18
593 855 4.581868 TCCCTTCGTCCGAAAATATTTGT 58.418 39.130 0.39 0.00 33.34 2.83
594 856 4.634443 ACTCCCTTCGTCCGAAAATATTTG 59.366 41.667 0.39 0.00 33.34 2.32
595 857 4.840271 ACTCCCTTCGTCCGAAAATATTT 58.160 39.130 3.52 0.00 33.34 1.40
596 858 4.482952 ACTCCCTTCGTCCGAAAATATT 57.517 40.909 3.52 0.00 33.34 1.28
597 859 4.648307 ACTACTCCCTTCGTCCGAAAATAT 59.352 41.667 3.52 0.00 33.34 1.28
598 860 4.019174 ACTACTCCCTTCGTCCGAAAATA 58.981 43.478 3.52 0.00 33.34 1.40
599 861 2.830321 ACTACTCCCTTCGTCCGAAAAT 59.170 45.455 3.52 0.00 33.34 1.82
600 862 2.242043 ACTACTCCCTTCGTCCGAAAA 58.758 47.619 3.52 0.00 33.34 2.29
601 863 1.915141 ACTACTCCCTTCGTCCGAAA 58.085 50.000 3.52 0.00 33.34 3.46
602 864 1.915141 AACTACTCCCTTCGTCCGAA 58.085 50.000 1.81 1.81 0.00 4.30
603 865 1.542915 CAAACTACTCCCTTCGTCCGA 59.457 52.381 0.00 0.00 0.00 4.55
604 866 1.271656 ACAAACTACTCCCTTCGTCCG 59.728 52.381 0.00 0.00 0.00 4.79
605 867 3.397849 AACAAACTACTCCCTTCGTCC 57.602 47.619 0.00 0.00 0.00 4.79
606 868 3.059120 GCAAACAAACTACTCCCTTCGTC 60.059 47.826 0.00 0.00 0.00 4.20
607 869 2.876550 GCAAACAAACTACTCCCTTCGT 59.123 45.455 0.00 0.00 0.00 3.85
608 870 2.875933 TGCAAACAAACTACTCCCTTCG 59.124 45.455 0.00 0.00 0.00 3.79
609 871 4.911514 TTGCAAACAAACTACTCCCTTC 57.088 40.909 0.00 0.00 31.21 3.46
610 872 5.600696 CAATTGCAAACAAACTACTCCCTT 58.399 37.500 1.71 0.00 39.77 3.95
611 873 4.501400 GCAATTGCAAACAAACTACTCCCT 60.501 41.667 25.36 0.00 39.77 4.20
612 874 3.740832 GCAATTGCAAACAAACTACTCCC 59.259 43.478 25.36 0.00 39.77 4.30
613 875 4.972286 GCAATTGCAAACAAACTACTCC 57.028 40.909 25.36 0.00 39.77 3.85
736 1543 7.067008 ACGCCAGCAACTAATACTGATTTAAAT 59.933 33.333 0.00 0.00 33.10 1.40
745 1552 3.028850 TCCTACGCCAGCAACTAATACT 58.971 45.455 0.00 0.00 0.00 2.12
759 1566 0.948141 GCATGCATCTCCTCCTACGC 60.948 60.000 14.21 0.00 0.00 4.42
769 1576 6.040209 TGTTGGAATTAAAAGCATGCATCT 57.960 33.333 21.98 5.53 0.00 2.90
770 1577 5.870978 ACTGTTGGAATTAAAAGCATGCATC 59.129 36.000 21.98 5.93 0.00 3.91
771 1578 5.640357 CACTGTTGGAATTAAAAGCATGCAT 59.360 36.000 21.98 4.57 0.00 3.96
773 1580 5.229423 TCACTGTTGGAATTAAAAGCATGC 58.771 37.500 10.51 10.51 0.00 4.06
774 1581 5.865552 CCTCACTGTTGGAATTAAAAGCATG 59.134 40.000 0.00 0.00 0.00 4.06
775 1582 5.774690 TCCTCACTGTTGGAATTAAAAGCAT 59.225 36.000 0.00 0.00 0.00 3.79
776 1583 5.136828 TCCTCACTGTTGGAATTAAAAGCA 58.863 37.500 0.00 0.00 0.00 3.91
777 1584 5.703876 CTCCTCACTGTTGGAATTAAAAGC 58.296 41.667 1.70 0.00 31.23 3.51
778 1585 5.335976 GGCTCCTCACTGTTGGAATTAAAAG 60.336 44.000 1.70 0.00 31.23 2.27
795 1617 3.934962 GATCAGGCCGGGCTCCTC 61.935 72.222 30.43 22.72 0.00 3.71
810 1632 3.643320 TCTTGCAGGGAAGATGATACGAT 59.357 43.478 0.00 0.00 0.00 3.73
836 1658 1.001068 CCATGCTTTTGTGGACATGCA 59.999 47.619 0.00 0.00 38.83 3.96
908 1797 7.647715 GGATTTATATAGCATGCGTTTGTGTTT 59.352 33.333 13.01 0.00 0.00 2.83
952 1847 1.067071 GGCTGTGTAGTGGGTGTAGAC 60.067 57.143 0.00 0.00 0.00 2.59
981 1876 2.765108 TGCTTTCTCTATCGCTCTCG 57.235 50.000 0.00 0.00 0.00 4.04
987 1882 1.143305 CCGCCATGCTTTCTCTATCG 58.857 55.000 0.00 0.00 0.00 2.92
1005 1903 1.267574 TGGGGACTGTCATCTCAGCC 61.268 60.000 10.38 0.00 38.84 4.85
1009 1907 1.142748 CGCTGGGGACTGTCATCTC 59.857 63.158 10.38 0.00 0.00 2.75
1263 2175 1.682684 CAGGCTGTAGACCCCGTCT 60.683 63.158 6.28 0.00 45.54 4.18
1281 2193 1.442148 GATGTAGGACAGCGGGGTC 59.558 63.158 0.00 0.00 37.06 4.46
1440 2374 1.794785 CGCGTGCACATGCTCAAAG 60.795 57.895 18.64 0.00 41.02 2.77
1461 2395 3.816524 CTCTCGTCGAAGGGCGCT 61.817 66.667 7.64 0.00 40.61 5.92
1581 4320 1.798735 CGACTGCAGGCCATTGAAG 59.201 57.895 19.93 0.98 0.00 3.02
1692 4431 1.835494 TCGGGACTTTCTCGATCACT 58.165 50.000 0.00 0.00 45.56 3.41
1849 4595 8.957466 CAGAATTCCTCTGTACGTATATCCATA 58.043 37.037 0.65 0.00 45.76 2.74
1912 5102 0.811616 GGCTAGCAGTTGGATCACGG 60.812 60.000 18.24 0.00 0.00 4.94
1936 5126 8.924511 ATGTGGCTATTAACAAGCAATACTAT 57.075 30.769 12.37 4.38 41.93 2.12
1946 5140 6.127758 CCTTTGTGCTATGTGGCTATTAACAA 60.128 38.462 0.00 0.00 0.00 2.83
2035 6362 6.942532 ATTATGCATAGGTGTTGGTACTTG 57.057 37.500 6.50 0.00 0.00 3.16
2037 6364 7.570132 TGTAATTATGCATAGGTGTTGGTACT 58.430 34.615 6.50 0.00 0.00 2.73
2038 6365 7.795482 TGTAATTATGCATAGGTGTTGGTAC 57.205 36.000 6.50 3.29 0.00 3.34
2507 6835 4.880886 TTGCATTATCCATTGACGAGTG 57.119 40.909 0.00 0.00 0.00 3.51
2534 6862 6.294955 CCCCTTAACAGTTCGTCTACTTAAGT 60.295 42.308 13.68 13.68 30.97 2.24
2549 6877 2.125269 CGACCGGCCCCTTAACAG 60.125 66.667 0.00 0.00 0.00 3.16
2568 6896 3.367025 GGTTACGTGCATACAGTTCTGAC 59.633 47.826 6.83 0.00 0.00 3.51
2649 7012 7.755582 AAACAACAAAGCTTAACATCTCAAC 57.244 32.000 0.00 0.00 0.00 3.18
2688 7051 7.327761 CGTCCACTAAACTATTCGAGAAGAAAA 59.672 37.037 3.36 0.00 42.91 2.29
2692 7055 5.877031 TCGTCCACTAAACTATTCGAGAAG 58.123 41.667 0.00 0.00 0.00 2.85
2695 7058 4.036352 GCTCGTCCACTAAACTATTCGAG 58.964 47.826 0.00 0.00 43.78 4.04
2697 7060 3.766151 TGCTCGTCCACTAAACTATTCG 58.234 45.455 0.00 0.00 0.00 3.34
2714 7077 6.418819 GGCATGATAAACATACACAAATGCTC 59.581 38.462 0.00 0.00 38.31 4.26
2753 7116 7.432869 CAGCAGATCTGTAGCTATTCTTAAGT 58.567 38.462 23.38 0.00 38.02 2.24
2779 7142 4.159693 ACTTGTCTCCTTTCCCAAAACAAC 59.840 41.667 0.00 0.00 0.00 3.32
2829 7194 0.905357 ACAGAGGGTATGCACAGGAC 59.095 55.000 0.00 0.00 0.00 3.85
2832 7197 1.827344 TCTGACAGAGGGTATGCACAG 59.173 52.381 0.00 0.00 0.00 3.66
2838 7203 1.043816 CCGCATCTGACAGAGGGTAT 58.956 55.000 18.13 0.00 0.00 2.73
2902 7267 1.430228 GACAAAAACCACGCACGGT 59.570 52.632 0.00 0.00 42.71 4.83
2913 10753 1.705256 CGGGATCGAGACGACAAAAA 58.295 50.000 0.00 0.00 39.18 1.94
2917 10757 1.989966 GAAGCGGGATCGAGACGACA 61.990 60.000 9.89 0.00 39.18 4.35
2922 10762 3.422061 CGAGAAGCGGGATCGAGA 58.578 61.111 0.00 0.00 38.72 4.04
2958 10817 3.303857 CGTATCGGATCGGATAGTATGCC 60.304 52.174 19.98 8.96 29.89 4.40
2960 10819 4.318903 GCTCGTATCGGATCGGATAGTATG 60.319 50.000 19.98 9.48 29.89 2.39
2976 10835 4.766970 GCAGATGCTGGCTCGTAT 57.233 55.556 0.00 0.00 38.21 3.06
3017 10887 4.273257 GACGAGAGGGCTAGCGGC 62.273 72.222 9.00 0.00 40.90 6.53
3032 10902 1.156736 CGATTTATCCCATGCCGGAC 58.843 55.000 5.05 0.00 36.56 4.79
3084 10954 3.403968 GGAAGAGATAAGGAATTCGGCC 58.596 50.000 0.00 0.00 0.00 6.13
3138 11008 7.704789 AGATTGAATGCAGAAACAGAAAAAC 57.295 32.000 0.00 0.00 0.00 2.43
3168 11038 3.003275 GGCGTCACAACTTTCATCAGAAA 59.997 43.478 0.00 0.00 41.26 2.52
3202 11072 4.798574 ACTAGTAAAGGTACCGAACAACG 58.201 43.478 6.18 0.00 42.18 4.10
3210 11080 6.405619 CCTCACAGCTAACTAGTAAAGGTACC 60.406 46.154 2.73 2.73 0.00 3.34
3304 11174 5.234972 TGATACGCACTTTGCATATTCTGAG 59.765 40.000 0.00 0.00 45.36 3.35
3418 13554 2.417933 CCAGCACACAATCAGCTACTTC 59.582 50.000 0.00 0.00 36.73 3.01
3419 13555 2.038952 TCCAGCACACAATCAGCTACTT 59.961 45.455 0.00 0.00 36.73 2.24
3425 13561 2.224606 ACAAGTCCAGCACACAATCAG 58.775 47.619 0.00 0.00 0.00 2.90
3454 13590 7.282585 ACCACTGCAATCAGCTATTTAATCTA 58.717 34.615 0.00 0.00 44.10 1.98


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

AutoCloner maintained by Alex Coulton.