Multiple sequence alignment - TraesCS5D01G448900

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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 TraesCS5D01G448900 chr5D 100.000 3098 0 0 1 3098 498184816 498187913 0.000000e+00 5722.0
1 TraesCS5D01G448900 chr5D 78.112 996 155 42 1019 1982 498352916 498353880 9.640000e-160 573.0
2 TraesCS5D01G448900 chr5D 90.909 110 10 0 1 110 557142327 557142436 6.920000e-32 148.0
3 TraesCS5D01G448900 chr5D 90.090 111 11 0 1 111 548292607 548292497 8.950000e-31 145.0
4 TraesCS5D01G448900 chr5A 92.571 1548 88 6 872 2404 622400658 622402193 0.000000e+00 2196.0
5 TraesCS5D01G448900 chr5A 78.247 970 150 40 1019 1957 622540782 622541721 1.610000e-157 566.0
6 TraesCS5D01G448900 chr5A 89.899 198 11 5 659 855 622400485 622400674 2.390000e-61 246.0
7 TraesCS5D01G448900 chr5A 92.857 112 8 0 1 112 618301867 618301978 2.470000e-36 163.0
8 TraesCS5D01G448900 chr5A 96.875 64 1 1 442 505 622400295 622400357 4.230000e-19 106.0
9 TraesCS5D01G448900 chr5A 85.577 104 8 5 2368 2468 622402235 622402334 5.470000e-18 102.0
10 TraesCS5D01G448900 chr5B 88.204 1509 121 33 872 2370 617589991 617591452 0.000000e+00 1748.0
11 TraesCS5D01G448900 chr5B 78.362 989 152 42 1025 1982 617663775 617664732 4.450000e-163 584.0
12 TraesCS5D01G448900 chr5B 89.487 390 21 5 273 661 617589400 617589770 2.800000e-130 475.0
13 TraesCS5D01G448900 chr5B 90.909 198 8 5 659 855 617589819 617590007 1.100000e-64 257.0
14 TraesCS5D01G448900 chr5B 92.199 141 8 2 145 284 617588383 617588521 2.440000e-46 196.0
15 TraesCS5D01G448900 chr7B 93.027 631 36 7 2469 3097 697282176 697282800 0.000000e+00 915.0
16 TraesCS5D01G448900 chr7B 88.235 68 6 2 2468 2535 691170894 691170959 2.560000e-11 80.5
17 TraesCS5D01G448900 chr2D 91.525 649 27 11 2470 3097 8461528 8460887 0.000000e+00 869.0
18 TraesCS5D01G448900 chr2D 96.970 33 0 1 2372 2404 119845587 119845618 2.000000e-03 54.7
19 TraesCS5D01G448900 chr6D 90.709 635 31 9 2466 3097 25348942 25349551 0.000000e+00 821.0
20 TraesCS5D01G448900 chr6D 94.393 107 5 1 2992 3098 121388091 121388196 2.470000e-36 163.0
21 TraesCS5D01G448900 chr2B 86.004 543 58 9 876 1413 90615822 90616351 1.610000e-157 566.0
22 TraesCS5D01G448900 chr2B 81.370 365 41 6 162 503 90588378 90588738 3.940000e-69 272.0
23 TraesCS5D01G448900 chr2B 90.826 109 9 1 1 109 109211149 109211256 8.950000e-31 145.0
24 TraesCS5D01G448900 chr2B 96.875 64 1 1 442 505 693091424 693091362 4.230000e-19 106.0
25 TraesCS5D01G448900 chr3A 89.252 214 20 2 2468 2680 586576009 586576220 6.590000e-67 265.0
26 TraesCS5D01G448900 chr3A 89.441 161 15 2 2830 2989 586576403 586576562 5.240000e-48 202.0
27 TraesCS5D01G448900 chr3D 93.750 112 7 0 1 112 21350556 21350445 5.310000e-38 169.0
28 TraesCS5D01G448900 chr3D 90.991 111 10 0 1 111 8291403 8291293 1.920000e-32 150.0
29 TraesCS5D01G448900 chr2A 92.105 114 9 0 1 114 72518689 72518576 8.890000e-36 161.0
30 TraesCS5D01G448900 chr2A 83.544 79 10 3 2480 2557 623101326 623101250 1.540000e-08 71.3
31 TraesCS5D01G448900 chr1A 92.793 111 7 1 1 111 8252383 8252274 3.200000e-35 159.0
32 TraesCS5D01G448900 chr7D 93.458 107 6 1 2992 3098 584301403 584301508 1.150000e-34 158.0
33 TraesCS5D01G448900 chr7D 96.970 33 0 1 2372 2404 96725703 96725734 2.000000e-03 54.7
34 TraesCS5D01G448900 chr7D 96.970 33 0 1 2372 2404 401113376 401113407 2.000000e-03 54.7
35 TraesCS5D01G448900 chr7D 96.875 32 0 1 2373 2404 196950052 196950082 6.000000e-03 52.8
36 TraesCS5D01G448900 chr3B 90.000 110 10 1 1 110 779624954 779624846 1.160000e-29 141.0
37 TraesCS5D01G448900 chr3B 85.185 81 9 3 2480 2559 66628003 66627925 2.560000e-11 80.5
38 TraesCS5D01G448900 chr3B 85.185 81 9 3 2480 2559 767302207 767302129 2.560000e-11 80.5
39 TraesCS5D01G448900 chr4A 82.716 81 11 3 2480 2559 547998466 547998388 5.540000e-08 69.4
40 TraesCS5D01G448900 chr7A 96.970 33 0 1 2372 2404 206009776 206009807 2.000000e-03 54.7
41 TraesCS5D01G448900 chr7A 96.970 33 0 1 2372 2404 292815049 292815018 2.000000e-03 54.7
42 TraesCS5D01G448900 chr6A 96.970 33 0 1 2372 2404 57047618 57047649 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G448900 chr5D 498184816 498187913 3097 False 5722.0 5722 100.00000 1 3098 1 chr5D.!!$F1 3097
1 TraesCS5D01G448900 chr5D 498352916 498353880 964 False 573.0 573 78.11200 1019 1982 1 chr5D.!!$F2 963
2 TraesCS5D01G448900 chr5A 622400295 622402334 2039 False 662.5 2196 91.23050 442 2468 4 chr5A.!!$F3 2026
3 TraesCS5D01G448900 chr5A 622540782 622541721 939 False 566.0 566 78.24700 1019 1957 1 chr5A.!!$F2 938
4 TraesCS5D01G448900 chr5B 617588383 617591452 3069 False 669.0 1748 90.19975 145 2370 4 chr5B.!!$F2 2225
5 TraesCS5D01G448900 chr5B 617663775 617664732 957 False 584.0 584 78.36200 1025 1982 1 chr5B.!!$F1 957
6 TraesCS5D01G448900 chr7B 697282176 697282800 624 False 915.0 915 93.02700 2469 3097 1 chr7B.!!$F2 628
7 TraesCS5D01G448900 chr2D 8460887 8461528 641 True 869.0 869 91.52500 2470 3097 1 chr2D.!!$R1 627
8 TraesCS5D01G448900 chr6D 25348942 25349551 609 False 821.0 821 90.70900 2466 3097 1 chr6D.!!$F1 631
9 TraesCS5D01G448900 chr2B 90615822 90616351 529 False 566.0 566 86.00400 876 1413 1 chr2B.!!$F2 537
10 TraesCS5D01G448900 chr3A 586576009 586576562 553 False 233.5 265 89.34650 2468 2989 2 chr3A.!!$F1 521

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
120 121 0.309612 AAAAACCTTGCGCCGTACAG 59.690 50.0 4.18 0.0 0.00 2.74 F
121 122 0.533308 AAAACCTTGCGCCGTACAGA 60.533 50.0 4.18 0.0 0.00 3.41 F
1557 2550 0.244994 CGTACTGGCTCTGCAAGTCT 59.755 55.0 2.54 0.0 38.65 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1023 1983 1.003118 CCGAGGATGTGTTTGGGAGAA 59.997 52.381 0.0 0.0 0.00 2.87 R
1870 2869 1.081092 CCCTGTCTCCCTTCTCCCA 59.919 63.158 0.0 0.0 0.00 4.37 R
2704 3843 0.038159 GAACACAGGAGACGAGGGTG 60.038 60.000 0.0 0.0 35.66 4.61 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
22 23 5.682943 AAACTTGAAATCGTGAAATCCGA 57.317 34.783 0.00 0.00 38.89 4.55
23 24 5.682943 AACTTGAAATCGTGAAATCCGAA 57.317 34.783 0.00 0.00 37.93 4.30
24 25 5.682943 ACTTGAAATCGTGAAATCCGAAA 57.317 34.783 0.00 0.00 37.93 3.46
25 26 6.254281 ACTTGAAATCGTGAAATCCGAAAT 57.746 33.333 0.00 0.00 37.93 2.17
26 27 7.372451 ACTTGAAATCGTGAAATCCGAAATA 57.628 32.000 0.00 0.00 37.93 1.40
27 28 7.812648 ACTTGAAATCGTGAAATCCGAAATAA 58.187 30.769 0.00 0.00 37.93 1.40
28 29 8.458843 ACTTGAAATCGTGAAATCCGAAATAAT 58.541 29.630 0.00 0.00 37.93 1.28
29 30 9.289303 CTTGAAATCGTGAAATCCGAAATAATT 57.711 29.630 0.00 0.00 37.93 1.40
30 31 9.632807 TTGAAATCGTGAAATCCGAAATAATTT 57.367 25.926 0.00 0.00 37.93 1.82
31 32 9.632807 TGAAATCGTGAAATCCGAAATAATTTT 57.367 25.926 0.00 0.00 37.93 1.82
55 56 8.909708 TTCGAAATATGCGAAATTTCTGAAAT 57.090 26.923 15.92 9.76 43.82 2.17
56 57 8.909708 TCGAAATATGCGAAATTTCTGAAATT 57.090 26.923 19.79 19.79 42.62 1.82
74 75 6.029607 TGAAATTTCGCATATTTCAGTGAGC 58.970 36.000 13.34 0.00 43.41 4.26
75 76 5.824904 AATTTCGCATATTTCAGTGAGCT 57.175 34.783 0.00 0.00 0.00 4.09
76 77 4.864916 TTTCGCATATTTCAGTGAGCTC 57.135 40.909 6.82 6.82 0.00 4.09
77 78 2.826428 TCGCATATTTCAGTGAGCTCC 58.174 47.619 12.15 2.40 0.00 4.70
78 79 1.524355 CGCATATTTCAGTGAGCTCCG 59.476 52.381 12.15 0.00 0.00 4.63
79 80 2.799562 CGCATATTTCAGTGAGCTCCGA 60.800 50.000 12.15 2.10 0.00 4.55
80 81 3.198068 GCATATTTCAGTGAGCTCCGAA 58.802 45.455 12.15 8.68 0.00 4.30
81 82 3.623060 GCATATTTCAGTGAGCTCCGAAA 59.377 43.478 19.34 19.34 0.00 3.46
82 83 4.274459 GCATATTTCAGTGAGCTCCGAAAT 59.726 41.667 26.10 26.10 40.30 2.17
83 84 5.466728 GCATATTTCAGTGAGCTCCGAAATA 59.533 40.000 27.64 27.64 41.82 1.40
84 85 6.017934 GCATATTTCAGTGAGCTCCGAAATAA 60.018 38.462 28.41 19.42 41.28 1.40
85 86 7.308229 GCATATTTCAGTGAGCTCCGAAATAAT 60.308 37.037 28.41 20.19 41.28 1.28
86 87 8.562892 CATATTTCAGTGAGCTCCGAAATAATT 58.437 33.333 28.41 18.95 41.28 1.40
87 88 6.817765 TTTCAGTGAGCTCCGAAATAATTT 57.182 33.333 12.15 0.00 0.00 1.82
88 89 5.801350 TCAGTGAGCTCCGAAATAATTTG 57.199 39.130 12.15 0.00 0.00 2.32
89 90 4.635765 TCAGTGAGCTCCGAAATAATTTGG 59.364 41.667 12.15 0.00 40.97 3.28
90 91 4.396166 CAGTGAGCTCCGAAATAATTTGGT 59.604 41.667 12.15 0.00 40.53 3.67
91 92 5.010282 AGTGAGCTCCGAAATAATTTGGTT 58.990 37.500 12.15 0.00 40.53 3.67
92 93 5.476945 AGTGAGCTCCGAAATAATTTGGTTT 59.523 36.000 12.15 0.00 40.53 3.27
93 94 5.800438 GTGAGCTCCGAAATAATTTGGTTTC 59.200 40.000 12.15 0.00 40.53 2.78
94 95 5.105917 TGAGCTCCGAAATAATTTGGTTTCC 60.106 40.000 12.15 0.00 40.53 3.13
95 96 4.102649 GCTCCGAAATAATTTGGTTTCCG 58.897 43.478 0.00 0.00 40.53 4.30
96 97 4.142556 GCTCCGAAATAATTTGGTTTCCGA 60.143 41.667 0.00 0.00 40.53 4.55
97 98 5.620429 GCTCCGAAATAATTTGGTTTCCGAA 60.620 40.000 0.00 0.00 40.53 4.30
98 99 6.328641 TCCGAAATAATTTGGTTTCCGAAA 57.671 33.333 0.00 0.00 40.53 3.46
99 100 6.926313 TCCGAAATAATTTGGTTTCCGAAAT 58.074 32.000 0.00 0.00 40.53 2.17
100 101 7.379750 TCCGAAATAATTTGGTTTCCGAAATT 58.620 30.769 0.00 0.00 40.53 1.82
101 102 8.521176 TCCGAAATAATTTGGTTTCCGAAATTA 58.479 29.630 0.00 0.00 40.53 1.40
102 103 9.141400 CCGAAATAATTTGGTTTCCGAAATTAA 57.859 29.630 0.00 0.00 37.49 1.40
108 109 8.740123 AATTTGGTTTCCGAAATTAAAAACCT 57.260 26.923 15.01 0.00 46.93 3.50
109 110 8.740123 ATTTGGTTTCCGAAATTAAAAACCTT 57.260 26.923 15.01 2.37 46.93 3.50
110 111 7.541122 TTGGTTTCCGAAATTAAAAACCTTG 57.459 32.000 15.01 0.00 46.93 3.61
111 112 5.524281 TGGTTTCCGAAATTAAAAACCTTGC 59.476 36.000 15.01 0.00 46.93 4.01
112 113 5.332732 GGTTTCCGAAATTAAAAACCTTGCG 60.333 40.000 9.13 0.00 44.62 4.85
113 114 3.310246 TCCGAAATTAAAAACCTTGCGC 58.690 40.909 0.00 0.00 0.00 6.09
114 115 2.410392 CCGAAATTAAAAACCTTGCGCC 59.590 45.455 4.18 0.00 0.00 6.53
115 116 2.089887 CGAAATTAAAAACCTTGCGCCG 59.910 45.455 4.18 0.00 0.00 6.46
116 117 2.804697 AATTAAAAACCTTGCGCCGT 57.195 40.000 4.18 0.00 0.00 5.68
117 118 3.919223 AATTAAAAACCTTGCGCCGTA 57.081 38.095 4.18 0.00 0.00 4.02
118 119 2.684754 TTAAAAACCTTGCGCCGTAC 57.315 45.000 4.18 0.00 0.00 3.67
119 120 1.590932 TAAAAACCTTGCGCCGTACA 58.409 45.000 4.18 0.00 0.00 2.90
120 121 0.309612 AAAAACCTTGCGCCGTACAG 59.690 50.000 4.18 0.00 0.00 2.74
121 122 0.533308 AAAACCTTGCGCCGTACAGA 60.533 50.000 4.18 0.00 0.00 3.41
122 123 1.226030 AAACCTTGCGCCGTACAGAC 61.226 55.000 4.18 0.00 0.00 3.51
123 124 2.095978 AACCTTGCGCCGTACAGACT 62.096 55.000 4.18 0.00 0.00 3.24
124 125 1.805945 CCTTGCGCCGTACAGACTC 60.806 63.158 4.18 0.00 0.00 3.36
125 126 1.805945 CTTGCGCCGTACAGACTCC 60.806 63.158 4.18 0.00 0.00 3.85
126 127 2.214181 CTTGCGCCGTACAGACTCCT 62.214 60.000 4.18 0.00 0.00 3.69
127 128 2.102553 GCGCCGTACAGACTCCTC 59.897 66.667 0.00 0.00 0.00 3.71
128 129 2.408241 GCGCCGTACAGACTCCTCT 61.408 63.158 0.00 0.00 0.00 3.69
129 130 1.722677 CGCCGTACAGACTCCTCTC 59.277 63.158 0.00 0.00 0.00 3.20
130 131 0.745128 CGCCGTACAGACTCCTCTCT 60.745 60.000 0.00 0.00 0.00 3.10
131 132 1.465794 GCCGTACAGACTCCTCTCTT 58.534 55.000 0.00 0.00 0.00 2.85
132 133 1.819903 GCCGTACAGACTCCTCTCTTT 59.180 52.381 0.00 0.00 0.00 2.52
133 134 2.231721 GCCGTACAGACTCCTCTCTTTT 59.768 50.000 0.00 0.00 0.00 2.27
134 135 3.306156 GCCGTACAGACTCCTCTCTTTTT 60.306 47.826 0.00 0.00 0.00 1.94
170 171 7.067981 GGATACCGACTCCTCTCTTAACTTTAA 59.932 40.741 0.00 0.00 0.00 1.52
212 213 7.735917 CAGTTTCCCTGTCACCATAATATCTA 58.264 38.462 0.00 0.00 36.37 1.98
243 244 8.888579 ACTCGAATACTTTATATCCAAACCAG 57.111 34.615 0.00 0.00 0.00 4.00
297 1189 3.916359 AATTGAATGCATGAATGGGCA 57.084 38.095 0.00 0.00 45.23 5.36
311 1203 1.324740 TGGGCAGCCATGAATGCTTC 61.325 55.000 15.19 12.53 42.19 3.86
324 1216 4.326826 TGAATGCTTCGGAGTCAAAAGAT 58.673 39.130 7.68 0.00 0.00 2.40
385 1278 2.126346 GTTGGCTTGGCGCATGTC 60.126 61.111 10.83 0.00 41.67 3.06
403 1296 1.547372 GTCAATGGATGGCTGCAAGTT 59.453 47.619 0.50 0.00 35.30 2.66
416 1309 3.192422 GCTGCAAGTTGTAGAGAGAGAGA 59.808 47.826 23.28 0.00 31.36 3.10
417 1310 4.675146 GCTGCAAGTTGTAGAGAGAGAGAG 60.675 50.000 23.28 0.00 31.36 3.20
418 1311 4.657013 TGCAAGTTGTAGAGAGAGAGAGA 58.343 43.478 4.48 0.00 0.00 3.10
419 1312 4.699735 TGCAAGTTGTAGAGAGAGAGAGAG 59.300 45.833 4.48 0.00 0.00 3.20
504 1397 7.050970 GGTAAGACCAAAAATCTTGGAAAGT 57.949 36.000 10.42 0.00 40.99 2.66
505 1398 7.497595 GGTAAGACCAAAAATCTTGGAAAGTT 58.502 34.615 10.42 1.44 40.99 2.66
506 1399 7.985184 GGTAAGACCAAAAATCTTGGAAAGTTT 59.015 33.333 10.42 0.00 40.99 2.66
507 1400 9.378551 GTAAGACCAAAAATCTTGGAAAGTTTT 57.621 29.630 10.42 0.00 45.08 2.43
568 1461 1.004745 GCAGGTTCCTCTGGATCCAAA 59.995 52.381 17.00 0.43 42.41 3.28
578 1471 4.457257 CCTCTGGATCCAAACAGTCTTTTC 59.543 45.833 17.00 0.00 36.17 2.29
621 1515 1.539929 CCGGATCCAAGCAGTCATCTC 60.540 57.143 13.41 0.00 0.00 2.75
622 1516 1.411977 CGGATCCAAGCAGTCATCTCT 59.588 52.381 13.41 0.00 0.00 3.10
623 1517 2.158986 CGGATCCAAGCAGTCATCTCTT 60.159 50.000 13.41 0.00 0.00 2.85
624 1518 3.681034 CGGATCCAAGCAGTCATCTCTTT 60.681 47.826 13.41 0.00 0.00 2.52
727 1672 3.197983 AGTTGGGCTGATAGGTACACTTC 59.802 47.826 0.00 0.00 0.00 3.01
742 1687 1.228124 CTTCAACACGGCCCCTCAA 60.228 57.895 0.00 0.00 0.00 3.02
743 1688 0.609131 CTTCAACACGGCCCCTCAAT 60.609 55.000 0.00 0.00 0.00 2.57
748 1693 3.074412 CAACACGGCCCCTCAATATATC 58.926 50.000 0.00 0.00 0.00 1.63
866 1813 2.919666 GCGATTAGCCAGCTCAAAAA 57.080 45.000 0.00 0.00 40.81 1.94
896 1843 1.618837 TCCTGCGATTAGGGCATAGAC 59.381 52.381 0.00 0.00 40.09 2.59
907 1855 1.600663 GGGCATAGACTGTGATCGACG 60.601 57.143 2.98 0.00 0.00 5.12
985 1945 3.241059 CGCGCGAGAGAAGAACGG 61.241 66.667 28.94 0.00 0.00 4.44
986 1946 2.178521 GCGCGAGAGAAGAACGGA 59.821 61.111 12.10 0.00 0.00 4.69
1023 1983 2.332654 GGCACAAGAATCGGGCGTT 61.333 57.895 0.00 0.00 0.00 4.84
1256 2228 3.764466 CTTGCCCGGTCTCTCGCT 61.764 66.667 0.00 0.00 0.00 4.93
1557 2550 0.244994 CGTACTGGCTCTGCAAGTCT 59.755 55.000 2.54 0.00 38.65 3.24
1588 2581 2.034532 TCGGCTACCACGTCCTCA 59.965 61.111 0.00 0.00 0.00 3.86
1779 2778 7.374649 CATATCTCTATGGACGCTGGACGAG 62.375 52.000 0.00 0.00 37.17 4.18
1983 2982 2.205307 GGATCGACCTACAAACCGAG 57.795 55.000 0.00 0.00 34.40 4.63
1984 2983 1.747355 GGATCGACCTACAAACCGAGA 59.253 52.381 0.00 0.00 34.40 4.04
1985 2984 2.165030 GGATCGACCTACAAACCGAGAA 59.835 50.000 0.00 0.00 34.40 2.87
1986 2985 3.367703 GGATCGACCTACAAACCGAGAAA 60.368 47.826 0.00 0.00 34.40 2.52
1987 2986 3.017265 TCGACCTACAAACCGAGAAAC 57.983 47.619 0.00 0.00 0.00 2.78
1988 2987 2.361757 TCGACCTACAAACCGAGAAACA 59.638 45.455 0.00 0.00 0.00 2.83
1989 2988 2.729882 CGACCTACAAACCGAGAAACAG 59.270 50.000 0.00 0.00 0.00 3.16
1990 2989 3.551454 CGACCTACAAACCGAGAAACAGA 60.551 47.826 0.00 0.00 0.00 3.41
1991 2990 3.725490 ACCTACAAACCGAGAAACAGAC 58.275 45.455 0.00 0.00 0.00 3.51
1992 2991 3.064931 CCTACAAACCGAGAAACAGACC 58.935 50.000 0.00 0.00 0.00 3.85
1996 2995 0.317479 AACCGAGAAACAGACCGAGG 59.683 55.000 0.00 0.00 0.00 4.63
2225 3246 4.023536 ACCGTGCACGAAGTAATTCAAATT 60.024 37.500 39.10 1.60 41.61 1.82
2232 3253 7.276658 TGCACGAAGTAATTCAAATTTTTGTGT 59.723 29.630 15.29 1.87 41.61 3.72
2323 3346 4.202020 TGTCTCGAGGTATGTGAAGTATGC 60.202 45.833 13.56 0.00 0.00 3.14
2332 3355 6.030228 GGTATGTGAAGTATGCTTTTTCTGC 58.970 40.000 0.00 0.00 34.61 4.26
2336 3359 3.436704 TGAAGTATGCTTTTTCTGCCTCG 59.563 43.478 0.00 0.00 34.61 4.63
2343 3366 2.426522 CTTTTTCTGCCTCGTGGATGA 58.573 47.619 7.92 1.22 34.57 2.92
2430 3527 9.314321 ACAGTACCAAGTAATTGAATTAGATCG 57.686 33.333 4.10 0.00 0.00 3.69
2576 3677 5.106752 CGATCTGCATCTTCTTCGATCTCTA 60.107 44.000 6.71 0.00 0.00 2.43
2729 3868 1.867919 CGTCTCCTGTGTTCCTCGCT 61.868 60.000 0.00 0.00 0.00 4.93
3025 4227 5.076182 TGGATGTAGCAAAATTTGTCTCCA 58.924 37.500 7.60 9.37 0.00 3.86
3026 4228 5.538053 TGGATGTAGCAAAATTTGTCTCCAA 59.462 36.000 7.60 0.00 0.00 3.53
3043 4245 5.406477 GTCTCCAATTCCAGCAAAATCAAAC 59.594 40.000 0.00 0.00 0.00 2.93
3097 4299 3.220507 ACATCACATTTGCACATTCCG 57.779 42.857 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.682943 TTCGGATTTCACGATTTCAAGTT 57.317 34.783 0.00 0.00 40.38 2.66
2 3 5.682943 TTTCGGATTTCACGATTTCAAGT 57.317 34.783 0.00 0.00 40.38 3.16
3 4 8.841444 ATTATTTCGGATTTCACGATTTCAAG 57.159 30.769 0.00 0.00 40.38 3.02
4 5 9.632807 AAATTATTTCGGATTTCACGATTTCAA 57.367 25.926 0.00 0.00 40.38 2.69
30 31 8.909708 ATTTCAGAAATTTCGCATATTTCGAA 57.090 26.923 12.42 0.00 43.46 3.71
31 32 8.909708 AATTTCAGAAATTTCGCATATTTCGA 57.090 26.923 14.43 0.00 43.46 3.71
50 51 6.029607 GCTCACTGAAATATGCGAAATTTCA 58.970 36.000 17.99 15.75 46.08 2.69
51 52 6.261118 AGCTCACTGAAATATGCGAAATTTC 58.739 36.000 8.20 8.20 41.60 2.17
52 53 6.199937 AGCTCACTGAAATATGCGAAATTT 57.800 33.333 0.00 0.00 0.00 1.82
53 54 5.220931 GGAGCTCACTGAAATATGCGAAATT 60.221 40.000 17.19 0.00 0.00 1.82
54 55 4.274459 GGAGCTCACTGAAATATGCGAAAT 59.726 41.667 17.19 0.00 0.00 2.17
55 56 3.623060 GGAGCTCACTGAAATATGCGAAA 59.377 43.478 17.19 0.00 0.00 3.46
56 57 3.198068 GGAGCTCACTGAAATATGCGAA 58.802 45.455 17.19 0.00 0.00 4.70
57 58 2.799562 CGGAGCTCACTGAAATATGCGA 60.800 50.000 17.19 0.00 0.00 5.10
58 59 1.524355 CGGAGCTCACTGAAATATGCG 59.476 52.381 17.19 0.89 0.00 4.73
59 60 2.826428 TCGGAGCTCACTGAAATATGC 58.174 47.619 17.19 0.00 0.00 3.14
60 61 5.998454 ATTTCGGAGCTCACTGAAATATG 57.002 39.130 26.30 3.81 46.98 1.78
62 63 8.397906 CAAATTATTTCGGAGCTCACTGAAATA 58.602 33.333 27.05 27.05 46.98 1.40
64 65 6.349280 CCAAATTATTTCGGAGCTCACTGAAA 60.349 38.462 22.25 22.25 45.21 2.69
65 66 5.123820 CCAAATTATTTCGGAGCTCACTGAA 59.876 40.000 17.19 13.10 33.98 3.02
66 67 4.635765 CCAAATTATTTCGGAGCTCACTGA 59.364 41.667 17.19 7.26 0.00 3.41
67 68 4.396166 ACCAAATTATTTCGGAGCTCACTG 59.604 41.667 17.19 4.71 0.00 3.66
68 69 4.589908 ACCAAATTATTTCGGAGCTCACT 58.410 39.130 17.19 0.00 0.00 3.41
69 70 4.965119 ACCAAATTATTTCGGAGCTCAC 57.035 40.909 17.19 4.01 0.00 3.51
70 71 5.105917 GGAAACCAAATTATTTCGGAGCTCA 60.106 40.000 17.19 0.00 35.97 4.26
71 72 5.340803 GGAAACCAAATTATTTCGGAGCTC 58.659 41.667 4.71 4.71 35.97 4.09
72 73 4.142469 CGGAAACCAAATTATTTCGGAGCT 60.142 41.667 11.23 0.00 37.34 4.09
73 74 4.102649 CGGAAACCAAATTATTTCGGAGC 58.897 43.478 11.23 0.00 37.34 4.70
74 75 5.554822 TCGGAAACCAAATTATTTCGGAG 57.445 39.130 11.23 5.06 38.49 4.63
75 76 5.961396 TTCGGAAACCAAATTATTTCGGA 57.039 34.783 11.23 12.26 40.38 4.55
76 77 7.589574 AATTTCGGAAACCAAATTATTTCGG 57.410 32.000 5.12 9.33 35.97 4.30
89 90 5.662324 CGCAAGGTTTTTAATTTCGGAAAC 58.338 37.500 5.12 0.00 0.00 2.78
90 91 4.209495 GCGCAAGGTTTTTAATTTCGGAAA 59.791 37.500 0.30 5.52 38.28 3.13
91 92 3.736759 GCGCAAGGTTTTTAATTTCGGAA 59.263 39.130 0.30 0.00 38.28 4.30
92 93 3.310246 GCGCAAGGTTTTTAATTTCGGA 58.690 40.909 0.30 0.00 38.28 4.55
93 94 2.410392 GGCGCAAGGTTTTTAATTTCGG 59.590 45.455 10.83 0.00 38.28 4.30
94 95 2.089887 CGGCGCAAGGTTTTTAATTTCG 59.910 45.455 10.83 0.00 38.28 3.46
95 96 3.054166 ACGGCGCAAGGTTTTTAATTTC 58.946 40.909 10.83 0.00 38.28 2.17
96 97 3.100658 ACGGCGCAAGGTTTTTAATTT 57.899 38.095 10.83 0.00 38.28 1.82
97 98 2.804697 ACGGCGCAAGGTTTTTAATT 57.195 40.000 10.83 0.00 38.28 1.40
98 99 2.553172 TGTACGGCGCAAGGTTTTTAAT 59.447 40.909 10.83 0.00 38.28 1.40
99 100 1.945394 TGTACGGCGCAAGGTTTTTAA 59.055 42.857 10.83 0.00 38.28 1.52
100 101 1.532007 CTGTACGGCGCAAGGTTTTTA 59.468 47.619 10.83 0.00 38.28 1.52
101 102 0.309612 CTGTACGGCGCAAGGTTTTT 59.690 50.000 10.83 0.00 38.28 1.94
102 103 0.533308 TCTGTACGGCGCAAGGTTTT 60.533 50.000 10.83 0.00 38.28 2.43
103 104 1.070105 TCTGTACGGCGCAAGGTTT 59.930 52.632 10.83 0.00 38.28 3.27
104 105 1.666872 GTCTGTACGGCGCAAGGTT 60.667 57.895 10.83 0.00 38.28 3.50
105 106 2.048503 GTCTGTACGGCGCAAGGT 60.049 61.111 10.83 6.47 38.28 3.50
106 107 1.805945 GAGTCTGTACGGCGCAAGG 60.806 63.158 10.83 0.00 38.28 3.61
107 108 1.805945 GGAGTCTGTACGGCGCAAG 60.806 63.158 10.83 4.90 43.44 4.01
108 109 2.209064 GAGGAGTCTGTACGGCGCAA 62.209 60.000 10.83 0.00 0.00 4.85
109 110 2.675423 AGGAGTCTGTACGGCGCA 60.675 61.111 10.83 0.00 0.00 6.09
110 111 2.102553 GAGGAGTCTGTACGGCGC 59.897 66.667 6.90 0.00 0.00 6.53
111 112 0.745128 AGAGAGGAGTCTGTACGGCG 60.745 60.000 4.80 4.80 30.97 6.46
112 113 1.465794 AAGAGAGGAGTCTGTACGGC 58.534 55.000 0.00 0.00 30.97 5.68
113 114 4.522722 AAAAAGAGAGGAGTCTGTACGG 57.477 45.455 0.00 0.00 30.97 4.02
141 142 0.540133 GAGAGGAGTCGGTATCCCCC 60.540 65.000 0.00 0.00 37.57 5.40
142 143 0.479378 AGAGAGGAGTCGGTATCCCC 59.521 60.000 0.00 0.00 37.57 4.81
143 144 2.368311 AAGAGAGGAGTCGGTATCCC 57.632 55.000 0.00 0.00 37.57 3.85
381 1274 1.754803 CTTGCAGCCATCCATTGACAT 59.245 47.619 0.00 0.00 0.00 3.06
385 1278 1.274167 ACAACTTGCAGCCATCCATTG 59.726 47.619 0.00 0.00 0.00 2.82
403 1296 4.707934 TCTTCGACTCTCTCTCTCTCTACA 59.292 45.833 0.00 0.00 0.00 2.74
416 1309 1.199558 GTGCTAACCGTCTTCGACTCT 59.800 52.381 0.00 0.00 39.71 3.24
417 1310 1.615502 GTGCTAACCGTCTTCGACTC 58.384 55.000 0.00 0.00 39.71 3.36
418 1311 0.109873 CGTGCTAACCGTCTTCGACT 60.110 55.000 0.00 0.00 39.71 4.18
419 1312 1.069378 CCGTGCTAACCGTCTTCGAC 61.069 60.000 0.00 0.00 39.71 4.20
432 1325 0.618968 ATTCTTCTCCTCCCCGTGCT 60.619 55.000 0.00 0.00 0.00 4.40
675 1620 2.102070 TACGTAGCCCAACCAACATG 57.898 50.000 0.00 0.00 0.00 3.21
727 1672 2.631160 TATATTGAGGGGCCGTGTTG 57.369 50.000 2.05 0.00 0.00 3.33
766 1711 0.387929 TCCGAATCCATACTGGCGTC 59.612 55.000 0.00 0.00 37.47 5.19
793 1739 1.843368 TCGGTAATCCAACTCGGTCT 58.157 50.000 0.00 0.00 35.57 3.85
832 1779 6.154534 TGGCTAATCGCAGGAGTTGTATATAT 59.845 38.462 0.00 0.00 41.67 0.86
833 1780 5.479027 TGGCTAATCGCAGGAGTTGTATATA 59.521 40.000 0.00 0.00 41.67 0.86
834 1781 4.283467 TGGCTAATCGCAGGAGTTGTATAT 59.717 41.667 0.00 0.00 41.67 0.86
835 1782 3.639561 TGGCTAATCGCAGGAGTTGTATA 59.360 43.478 0.00 0.00 41.67 1.47
836 1783 2.434336 TGGCTAATCGCAGGAGTTGTAT 59.566 45.455 0.00 0.00 41.67 2.29
837 1784 1.828595 TGGCTAATCGCAGGAGTTGTA 59.171 47.619 0.00 0.00 41.67 2.41
838 1785 0.613260 TGGCTAATCGCAGGAGTTGT 59.387 50.000 0.00 0.00 41.67 3.32
839 1786 1.293924 CTGGCTAATCGCAGGAGTTG 58.706 55.000 0.00 0.00 41.67 3.16
840 1787 0.462759 GCTGGCTAATCGCAGGAGTT 60.463 55.000 0.00 0.00 41.67 3.01
841 1788 1.144936 GCTGGCTAATCGCAGGAGT 59.855 57.895 0.00 0.00 41.67 3.85
842 1789 0.599728 GAGCTGGCTAATCGCAGGAG 60.600 60.000 0.00 0.00 41.67 3.69
843 1790 1.329913 TGAGCTGGCTAATCGCAGGA 61.330 55.000 0.00 0.00 41.67 3.86
844 1791 0.462581 TTGAGCTGGCTAATCGCAGG 60.463 55.000 0.00 0.00 41.67 4.85
845 1792 1.372582 TTTGAGCTGGCTAATCGCAG 58.627 50.000 0.00 0.00 41.67 5.18
846 1793 1.819928 TTTTGAGCTGGCTAATCGCA 58.180 45.000 0.00 0.00 41.67 5.10
847 1794 2.919666 TTTTTGAGCTGGCTAATCGC 57.080 45.000 0.00 0.00 38.13 4.58
867 1814 3.506067 CCCTAATCGCAGGAGTTGTTTTT 59.494 43.478 0.00 0.00 38.00 1.94
868 1815 3.081804 CCCTAATCGCAGGAGTTGTTTT 58.918 45.455 0.00 0.00 38.00 2.43
869 1816 2.711542 CCCTAATCGCAGGAGTTGTTT 58.288 47.619 0.00 0.00 38.00 2.83
870 1817 1.679032 GCCCTAATCGCAGGAGTTGTT 60.679 52.381 0.00 0.00 38.00 2.83
896 1843 3.119628 CACAACTTACACGTCGATCACAG 59.880 47.826 0.00 0.00 0.00 3.66
907 1855 2.683968 TGGCTCGATCACAACTTACAC 58.316 47.619 0.00 0.00 0.00 2.90
943 1896 3.400054 CCGGGTGTTCTCCCCTCC 61.400 72.222 0.00 0.00 44.32 4.30
949 1902 0.030235 GTTGTTTGCCGGGTGTTCTC 59.970 55.000 2.18 0.00 0.00 2.87
959 1912 3.911155 CTCTCGCGCGTTGTTTGCC 62.911 63.158 30.98 0.00 0.00 4.52
985 1945 2.100631 CCATGGTGACCGCGTCTTC 61.101 63.158 4.92 0.00 33.15 2.87
986 1946 2.047274 CCATGGTGACCGCGTCTT 60.047 61.111 4.92 0.00 33.15 3.01
1023 1983 1.003118 CCGAGGATGTGTTTGGGAGAA 59.997 52.381 0.00 0.00 0.00 2.87
1256 2228 4.069232 CGAGGTCTGAAGGCGGCA 62.069 66.667 13.08 0.00 0.00 5.69
1588 2581 4.405671 TCCGTCGAGAGGGAGCGT 62.406 66.667 10.15 0.00 40.13 5.07
1842 2841 2.438434 CGGCCCTTTCGCTCCAAT 60.438 61.111 0.00 0.00 0.00 3.16
1870 2869 1.081092 CCCTGTCTCCCTTCTCCCA 59.919 63.158 0.00 0.00 0.00 4.37
1982 2981 3.459386 ACCTCCTCGGTCTGTTTCT 57.541 52.632 0.00 0.00 44.93 2.52
2187 3208 4.927425 GTGCACGGTAAAATGAGAACTAGA 59.073 41.667 0.00 0.00 0.00 2.43
2225 3246 7.821652 TCTACTTCAATTTCACACACACAAAA 58.178 30.769 0.00 0.00 0.00 2.44
2232 3253 9.692749 CTACTAGTTCTACTTCAATTTCACACA 57.307 33.333 0.00 0.00 0.00 3.72
2323 3346 2.417933 CTCATCCACGAGGCAGAAAAAG 59.582 50.000 0.00 0.00 33.74 2.27
2332 3355 5.419542 TGAGAATTAAACTCATCCACGAGG 58.580 41.667 10.36 0.00 39.10 4.63
2336 3359 7.672983 TCACTTGAGAATTAAACTCATCCAC 57.327 36.000 13.75 0.00 42.68 4.02
2343 3366 6.959639 TGGCTTTCACTTGAGAATTAAACT 57.040 33.333 0.00 0.00 0.00 2.66
2451 3551 6.415573 CACTGCCCTAAAGTAAAGATACCTT 58.584 40.000 0.00 0.00 32.08 3.50
2458 3558 2.749621 CCAGCACTGCCCTAAAGTAAAG 59.250 50.000 0.00 0.00 0.00 1.85
2591 3692 3.414269 GAGGAAGGAGGTCTATACGAGG 58.586 54.545 0.00 0.00 0.00 4.63
2620 3721 1.202830 GCGAGGAGATCTAGGTGAGGA 60.203 57.143 0.00 0.00 0.00 3.71
2698 3837 4.131088 GAGACGAGGGTGGCGACC 62.131 72.222 9.83 9.83 42.27 4.79
2699 3838 4.131088 GGAGACGAGGGTGGCGAC 62.131 72.222 0.00 0.00 0.00 5.19
2700 3839 4.361971 AGGAGACGAGGGTGGCGA 62.362 66.667 0.00 0.00 0.00 5.54
2701 3840 4.135153 CAGGAGACGAGGGTGGCG 62.135 72.222 0.00 0.00 0.00 5.69
2702 3841 2.997897 ACAGGAGACGAGGGTGGC 60.998 66.667 0.00 0.00 0.00 5.01
2703 3842 1.472662 AACACAGGAGACGAGGGTGG 61.473 60.000 0.00 0.00 33.91 4.61
2704 3843 0.038159 GAACACAGGAGACGAGGGTG 60.038 60.000 0.00 0.00 35.66 4.61
2705 3844 1.186267 GGAACACAGGAGACGAGGGT 61.186 60.000 0.00 0.00 0.00 4.34
2706 3845 0.900647 AGGAACACAGGAGACGAGGG 60.901 60.000 0.00 0.00 0.00 4.30
2707 3846 0.528470 GAGGAACACAGGAGACGAGG 59.472 60.000 0.00 0.00 0.00 4.63
2708 3847 0.169230 CGAGGAACACAGGAGACGAG 59.831 60.000 0.00 0.00 0.00 4.18
2729 3868 4.657408 TTGCATGCCACGGAGCCA 62.657 61.111 16.68 0.00 0.00 4.75
2739 3878 0.109132 GGGTACAAGCTGTTGCATGC 60.109 55.000 11.82 11.82 41.09 4.06
3025 4227 5.005094 CCATGGTTTGATTTTGCTGGAATT 58.995 37.500 2.57 0.00 0.00 2.17
3026 4228 4.041938 ACCATGGTTTGATTTTGCTGGAAT 59.958 37.500 13.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.