Multiple sequence alignment - TraesCS2D01G397800

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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 TraesCS2D01G397800 chr2D 100.000 5625 0 0 1 5625 509756927 509751303 0.000000e+00 10388.0
1 TraesCS2D01G397800 chr2D 89.247 93 9 1 1 92 89220427 89220519 1.280000e-21 115.0
2 TraesCS2D01G397800 chr2B 93.845 4728 193 56 149 4830 598975250 598970575 0.000000e+00 7029.0
3 TraesCS2D01G397800 chr2B 85.181 830 61 33 4815 5625 598970556 598969770 0.000000e+00 795.0
4 TraesCS2D01G397800 chr2B 87.500 56 4 3 2844 2896 8943796 8943741 1.690000e-05 62.1
5 TraesCS2D01G397800 chr2A 92.532 4861 270 49 303 5093 653396512 653391675 0.000000e+00 6879.0
6 TraesCS2D01G397800 chr2A 91.456 515 40 4 5111 5625 653391366 653390856 0.000000e+00 704.0
7 TraesCS2D01G397800 chr2A 92.857 126 6 2 140 263 653396634 653396510 4.480000e-41 180.0
8 TraesCS2D01G397800 chr3A 83.913 230 26 7 5359 5578 574865702 574865474 5.710000e-50 209.0
9 TraesCS2D01G397800 chr3A 84.211 209 28 4 5372 5575 501028567 501028775 1.240000e-46 198.0
10 TraesCS2D01G397800 chr3A 80.408 245 40 4 5360 5596 515827391 515827635 4.480000e-41 180.0
11 TraesCS2D01G397800 chr3D 82.969 229 29 6 5359 5578 436163173 436162946 1.240000e-46 198.0
12 TraesCS2D01G397800 chr3D 79.518 249 39 8 5366 5604 526990410 526990656 3.490000e-37 167.0
13 TraesCS2D01G397800 chr6A 79.817 218 30 8 5363 5571 6585207 6585419 4.540000e-31 147.0
14 TraesCS2D01G397800 chr6A 94.444 90 5 0 3 92 539613606 539613695 7.600000e-29 139.0
15 TraesCS2D01G397800 chr5D 80.105 191 30 4 5389 5571 370360269 370360079 9.830000e-28 135.0
16 TraesCS2D01G397800 chr7D 91.398 93 8 0 1 93 147991684 147991776 1.640000e-25 128.0
17 TraesCS2D01G397800 chr7D 91.765 85 7 0 1 85 549364900 549364984 9.900000e-23 119.0
18 TraesCS2D01G397800 chr5B 91.304 92 8 0 1 92 487911187 487911278 5.920000e-25 126.0
19 TraesCS2D01G397800 chr1D 82.051 156 20 5 5358 5506 65905018 65905172 5.920000e-25 126.0
20 TraesCS2D01G397800 chr6B 91.765 85 7 0 1 85 309272332 309272416 9.900000e-23 119.0
21 TraesCS2D01G397800 chr1B 91.765 85 7 0 1 85 688981479 688981395 9.900000e-23 119.0
22 TraesCS2D01G397800 chr3B 89.888 89 9 0 5 93 779966461 779966549 1.280000e-21 115.0
23 TraesCS2D01G397800 chr3B 100.000 28 0 0 2863 2890 715732654 715732681 1.000000e-02 52.8
24 TraesCS2D01G397800 chr5A 89.011 91 9 1 1 90 650621336 650621426 1.660000e-20 111.0
25 TraesCS2D01G397800 chr7A 82.192 73 8 4 2822 2890 719747022 719747093 2.190000e-04 58.4
26 TraesCS2D01G397800 chrUn 85.455 55 6 2 2844 2896 27600990 27600936 7.870000e-04 56.5


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 TraesCS2D01G397800 chr2D 509751303 509756927 5624 True 10388.000000 10388 100.000000 1 5625 1 chr2D.!!$R1 5624
1 TraesCS2D01G397800 chr2B 598969770 598975250 5480 True 3912.000000 7029 89.513000 149 5625 2 chr2B.!!$R2 5476
2 TraesCS2D01G397800 chr2A 653390856 653396634 5778 True 2587.666667 6879 92.281667 140 5625 3 chr2A.!!$R1 5485

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
95 96 0.179067 CCGAATAGGGTTTGCCGCTA 60.179 55.000 0.00 0.00 42.18 4.26 F
100 101 0.179067 TAGGGTTTGCCGCTAATCCG 60.179 55.000 10.66 0.00 35.81 4.18 F
115 116 0.327576 ATCCGATCCCTTCAACCCCT 60.328 55.000 0.00 0.00 0.00 4.79 F
1579 1657 0.331278 TCGCCAGATCCAAATGGGTT 59.669 50.000 0.00 0.00 37.05 4.11 F
2343 2421 2.301870 TGTCCGACTTGGCAAGAAGTAT 59.698 45.455 32.50 10.73 36.27 2.12 F
2699 2786 2.542597 ACACGCTTCGTTCTTACACAA 58.457 42.857 0.00 0.00 38.32 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1273 0.371989 CAACGACAACAACACGCAGA 59.628 50.000 0.00 0.00 0.00 4.26 R
1796 1874 1.004277 TGGATGGCCACAACTAGAACC 59.996 52.381 8.16 1.21 39.92 3.62 R
1818 1896 2.178912 TCTTCGCCCACTCGATTTTT 57.821 45.000 0.00 0.00 38.37 1.94 R
2661 2739 0.248565 GTTGAGGGTCGTAGGTTCCC 59.751 60.000 9.31 9.31 41.36 3.97 R
3183 3274 2.032030 CCCCAAATATTTGCGTCGCTAG 60.032 50.000 20.67 6.31 36.86 3.42 R
4678 4771 1.016130 CCTGCCTGCGTAAGTGACAG 61.016 60.000 0.00 0.00 41.68 3.51 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
37 38 2.887568 CTAACGCGGCTGCAGGAG 60.888 66.667 19.50 6.75 42.97 3.69
45 46 4.215349 GCTGCAGGAGCTGGTTAG 57.785 61.111 17.12 0.00 45.21 2.34
46 47 1.451028 GCTGCAGGAGCTGGTTAGG 60.451 63.158 17.12 0.00 45.21 2.69
47 48 1.903877 GCTGCAGGAGCTGGTTAGGA 61.904 60.000 17.12 0.00 45.21 2.94
48 49 0.615331 CTGCAGGAGCTGGTTAGGAA 59.385 55.000 5.57 0.00 42.74 3.36
49 50 1.003580 CTGCAGGAGCTGGTTAGGAAA 59.996 52.381 5.57 0.00 42.74 3.13
50 51 1.423541 TGCAGGAGCTGGTTAGGAAAA 59.576 47.619 0.00 0.00 42.74 2.29
51 52 2.041620 TGCAGGAGCTGGTTAGGAAAAT 59.958 45.455 0.00 0.00 42.74 1.82
52 53 3.092301 GCAGGAGCTGGTTAGGAAAATT 58.908 45.455 0.00 0.00 37.91 1.82
53 54 3.511540 GCAGGAGCTGGTTAGGAAAATTT 59.488 43.478 0.00 0.00 37.91 1.82
54 55 4.380973 GCAGGAGCTGGTTAGGAAAATTTC 60.381 45.833 0.00 0.00 37.91 2.17
55 56 7.349645 GCAGGAGCTGGTTAGGAAAATTTCC 62.350 48.000 16.59 16.59 43.43 3.13
65 66 3.241067 GGAAAATTTCCCTTAACCGGC 57.759 47.619 13.61 0.00 44.30 6.13
66 67 2.416296 GGAAAATTTCCCTTAACCGGCG 60.416 50.000 13.61 0.00 44.30 6.46
67 68 0.528924 AAATTTCCCTTAACCGGCGC 59.471 50.000 0.00 0.00 0.00 6.53
68 69 1.317431 AATTTCCCTTAACCGGCGCC 61.317 55.000 19.07 19.07 0.00 6.53
69 70 2.206182 ATTTCCCTTAACCGGCGCCT 62.206 55.000 26.68 8.66 0.00 5.52
70 71 3.615509 TTCCCTTAACCGGCGCCTG 62.616 63.158 26.68 21.87 0.00 4.85
73 74 3.499737 CTTAACCGGCGCCTGCAG 61.500 66.667 26.68 6.78 45.35 4.41
83 84 3.643978 GCCTGCAGCGCCGAATAG 61.644 66.667 8.66 0.00 0.00 1.73
84 85 2.969238 CCTGCAGCGCCGAATAGG 60.969 66.667 8.66 1.07 44.97 2.57
85 86 2.969238 CTGCAGCGCCGAATAGGG 60.969 66.667 2.29 0.00 41.48 3.53
86 87 3.740128 CTGCAGCGCCGAATAGGGT 62.740 63.158 2.29 0.00 41.48 4.34
87 88 2.513897 GCAGCGCCGAATAGGGTT 60.514 61.111 2.29 0.00 41.48 4.11
88 89 2.112815 GCAGCGCCGAATAGGGTTT 61.113 57.895 2.29 0.00 41.48 3.27
89 90 1.721487 CAGCGCCGAATAGGGTTTG 59.279 57.895 2.29 0.00 41.48 2.93
90 91 2.112815 AGCGCCGAATAGGGTTTGC 61.113 57.895 2.29 0.00 41.48 3.68
91 92 3.107447 CGCCGAATAGGGTTTGCC 58.893 61.111 0.00 0.00 41.48 4.52
92 93 2.819552 CGCCGAATAGGGTTTGCCG 61.820 63.158 0.00 0.00 41.48 5.69
93 94 3.107447 CCGAATAGGGTTTGCCGC 58.893 61.111 0.00 0.00 35.97 6.53
94 95 1.451387 CCGAATAGGGTTTGCCGCT 60.451 57.895 0.00 0.00 40.00 5.52
95 96 0.179067 CCGAATAGGGTTTGCCGCTA 60.179 55.000 0.00 0.00 42.18 4.26
96 97 1.658994 CGAATAGGGTTTGCCGCTAA 58.341 50.000 0.00 0.00 41.41 3.09
97 98 2.218603 CGAATAGGGTTTGCCGCTAAT 58.781 47.619 0.00 0.00 41.41 1.73
98 99 2.223377 CGAATAGGGTTTGCCGCTAATC 59.777 50.000 0.00 0.00 41.41 1.75
99 100 2.271944 ATAGGGTTTGCCGCTAATCC 57.728 50.000 8.65 8.65 41.41 3.01
100 101 0.179067 TAGGGTTTGCCGCTAATCCG 60.179 55.000 10.66 0.00 35.81 4.18
101 102 1.450669 GGGTTTGCCGCTAATCCGA 60.451 57.895 0.88 0.00 34.97 4.55
102 103 0.818040 GGGTTTGCCGCTAATCCGAT 60.818 55.000 0.88 0.00 34.97 4.18
103 104 0.586802 GGTTTGCCGCTAATCCGATC 59.413 55.000 0.00 0.00 0.00 3.69
104 105 0.586802 GTTTGCCGCTAATCCGATCC 59.413 55.000 0.00 0.00 0.00 3.36
105 106 0.534203 TTTGCCGCTAATCCGATCCC 60.534 55.000 0.00 0.00 0.00 3.85
106 107 1.407656 TTGCCGCTAATCCGATCCCT 61.408 55.000 0.00 0.00 0.00 4.20
107 108 1.371558 GCCGCTAATCCGATCCCTT 59.628 57.895 0.00 0.00 0.00 3.95
108 109 0.670854 GCCGCTAATCCGATCCCTTC 60.671 60.000 0.00 0.00 0.00 3.46
109 110 0.679505 CCGCTAATCCGATCCCTTCA 59.320 55.000 0.00 0.00 0.00 3.02
110 111 1.070134 CCGCTAATCCGATCCCTTCAA 59.930 52.381 0.00 0.00 0.00 2.69
111 112 2.135933 CGCTAATCCGATCCCTTCAAC 58.864 52.381 0.00 0.00 0.00 3.18
112 113 2.495084 GCTAATCCGATCCCTTCAACC 58.505 52.381 0.00 0.00 0.00 3.77
113 114 2.810767 GCTAATCCGATCCCTTCAACCC 60.811 54.545 0.00 0.00 0.00 4.11
114 115 0.551396 AATCCGATCCCTTCAACCCC 59.449 55.000 0.00 0.00 0.00 4.95
115 116 0.327576 ATCCGATCCCTTCAACCCCT 60.328 55.000 0.00 0.00 0.00 4.79
116 117 0.981277 TCCGATCCCTTCAACCCCTC 60.981 60.000 0.00 0.00 0.00 4.30
117 118 1.144057 CGATCCCTTCAACCCCTCG 59.856 63.158 0.00 0.00 0.00 4.63
118 119 1.327690 CGATCCCTTCAACCCCTCGA 61.328 60.000 0.00 0.00 0.00 4.04
119 120 0.909623 GATCCCTTCAACCCCTCGAA 59.090 55.000 0.00 0.00 0.00 3.71
120 121 1.280998 GATCCCTTCAACCCCTCGAAA 59.719 52.381 0.00 0.00 0.00 3.46
121 122 0.690762 TCCCTTCAACCCCTCGAAAG 59.309 55.000 0.00 0.00 0.00 2.62
122 123 0.690762 CCCTTCAACCCCTCGAAAGA 59.309 55.000 0.00 0.00 39.12 2.52
123 124 1.073284 CCCTTCAACCCCTCGAAAGAA 59.927 52.381 0.00 0.00 41.32 2.52
124 125 2.488347 CCCTTCAACCCCTCGAAAGAAA 60.488 50.000 0.00 0.00 41.32 2.52
125 126 3.219281 CCTTCAACCCCTCGAAAGAAAA 58.781 45.455 0.00 0.00 41.32 2.29
126 127 3.634910 CCTTCAACCCCTCGAAAGAAAAA 59.365 43.478 0.00 0.00 41.32 1.94
178 179 4.681978 GTCACGCCTGCTTCCGGT 62.682 66.667 0.00 0.00 0.00 5.28
300 303 4.396522 CATGATTTGATTCTCTCTCCCCC 58.603 47.826 0.00 0.00 0.00 5.40
316 319 2.043115 TCCCCCGACTATGATATCAGCT 59.957 50.000 11.78 0.00 0.00 4.24
317 320 2.167281 CCCCCGACTATGATATCAGCTG 59.833 54.545 7.63 7.63 0.00 4.24
401 404 0.538516 CGTCGATCCTCCCCTCTCAT 60.539 60.000 0.00 0.00 0.00 2.90
465 473 2.217510 TCGTTCCTAGGTGAGCTTCT 57.782 50.000 9.08 0.00 0.00 2.85
566 587 2.437359 GGCGCTTGATCTGTGGCT 60.437 61.111 7.64 0.00 37.48 4.75
567 588 2.758089 GGCGCTTGATCTGTGGCTG 61.758 63.158 7.64 4.37 37.48 4.85
578 600 3.721706 GTGGCTGGTGGGGGAGAG 61.722 72.222 0.00 0.00 0.00 3.20
588 610 2.321719 GTGGGGGAGAGATCCTAGTTC 58.678 57.143 0.00 0.00 0.00 3.01
618 665 3.482722 GAGGCATTATGGCATCGATTG 57.517 47.619 20.59 0.00 46.46 2.67
664 724 3.365472 TGTCTCTCGAGGATGGATTCAA 58.635 45.455 13.56 0.00 0.00 2.69
667 729 4.026744 TCTCTCGAGGATGGATTCAAACT 58.973 43.478 13.56 0.00 0.00 2.66
671 733 3.118629 TCGAGGATGGATTCAAACTCAGG 60.119 47.826 8.52 0.00 32.64 3.86
711 779 7.928103 AGTTTAGTATACTAGTGTCGGTGATG 58.072 38.462 12.28 0.00 0.00 3.07
968 1036 2.498167 GCAAATCTAGCATGATCCGGT 58.502 47.619 0.00 0.00 0.00 5.28
1155 1224 6.038603 CACAAGTTCTTCAAGATCAGGTTTCA 59.961 38.462 0.00 0.00 0.00 2.69
1202 1271 0.530744 GCTGTGTCCATCGTGTCCTA 59.469 55.000 0.00 0.00 0.00 2.94
1204 1273 1.819288 CTGTGTCCATCGTGTCCTAGT 59.181 52.381 0.00 0.00 0.00 2.57
1579 1657 0.331278 TCGCCAGATCCAAATGGGTT 59.669 50.000 0.00 0.00 37.05 4.11
1634 1712 6.870971 TCTTCATTTAAAGTGTTTAGGCGT 57.129 33.333 0.00 0.00 0.00 5.68
1645 1723 6.300354 AGTGTTTAGGCGTAATTGATATGC 57.700 37.500 0.00 0.00 44.37 3.14
1719 1797 7.333528 TCTCATTAATTTGCCTATTGTCACC 57.666 36.000 0.00 0.00 0.00 4.02
1773 1851 4.284234 CCAAGGAAATGATGGAAGTGGTTT 59.716 41.667 0.00 0.00 36.27 3.27
1777 1855 5.893824 AGGAAATGATGGAAGTGGTTTATCC 59.106 40.000 0.00 0.00 0.00 2.59
2030 2108 9.887406 ATGGTACGACTTTTAAATGTTGTTAAG 57.113 29.630 24.39 5.35 33.96 1.85
2202 2280 6.252995 AGATAAAGCCACCTTGTTATTCCAA 58.747 36.000 0.00 0.00 0.00 3.53
2335 2413 2.851263 AGTTAATGTCCGACTTGGCA 57.149 45.000 0.00 0.00 37.80 4.92
2343 2421 2.301870 TGTCCGACTTGGCAAGAAGTAT 59.698 45.455 32.50 10.73 36.27 2.12
2359 2437 6.015027 AGAAGTATTTCAGATCGTATCGGG 57.985 41.667 0.44 0.00 35.70 5.14
2394 2472 8.139350 GGCTGATGTCATGAAATAATCAAATGA 58.861 33.333 0.00 0.00 42.54 2.57
2480 2558 3.392228 TGGCTCGGCAAGACAGAT 58.608 55.556 0.00 0.00 38.45 2.90
2498 2576 3.742369 CAGATGTGGTGGCAATTTTCAAC 59.258 43.478 0.00 0.00 0.00 3.18
2699 2786 2.542597 ACACGCTTCGTTCTTACACAA 58.457 42.857 0.00 0.00 38.32 3.33
2851 2939 7.703328 TCAAATCAGACCTGTTTAAGTTTGAC 58.297 34.615 0.00 0.00 30.84 3.18
2857 2945 7.175990 TCAGACCTGTTTAAGTTTGACAAGTTT 59.824 33.333 0.00 0.00 0.00 2.66
2966 3054 7.740346 GTGTTGTAGATGCGGATATATTTTTCG 59.260 37.037 0.00 0.00 0.00 3.46
3058 3148 2.729360 CGAGTATCATTTTGCGCGGATA 59.271 45.455 8.83 0.00 33.17 2.59
3059 3149 3.367932 CGAGTATCATTTTGCGCGGATAT 59.632 43.478 8.83 0.00 33.17 1.63
3137 3227 3.253921 TCATCAATGTTGTGTGCTGAAGG 59.746 43.478 0.00 0.00 0.00 3.46
3175 3266 8.207350 AGGCATGTAAGAGTATAACACCATAT 57.793 34.615 0.00 0.00 0.00 1.78
3257 3349 2.698855 TTCCTCTATCTTGCCACTGC 57.301 50.000 0.00 0.00 38.26 4.40
3269 3361 1.276705 TGCCACTGCAGGTATTAACGA 59.723 47.619 19.93 0.00 44.23 3.85
3276 3368 4.161565 ACTGCAGGTATTAACGAAGGATGA 59.838 41.667 19.93 0.00 0.00 2.92
3369 3461 0.482446 TTCCATCAAGGGTTGTGCCT 59.518 50.000 0.00 0.00 38.24 4.75
3383 3475 4.324267 GTTGTGCCTCACTACCAGTTAAT 58.676 43.478 1.14 0.00 34.93 1.40
3426 3519 3.636153 ATCTGAAAGGACCCTTGTAGC 57.364 47.619 1.50 0.00 36.26 3.58
3532 3625 5.295787 AGTTTGTTTCGACATCTGTTAAGCA 59.704 36.000 0.00 0.00 0.00 3.91
3567 3660 8.938801 ATACATAAAAATGGGATGCTACATGA 57.061 30.769 0.00 0.00 0.00 3.07
3700 3793 8.833231 TCTCCTTAAGTCTTCAACATACAAAG 57.167 34.615 0.97 0.00 0.00 2.77
3921 4014 2.684374 GACATTGTGCCAGCATGTGATA 59.316 45.455 2.28 0.00 0.00 2.15
3928 4021 4.202493 TGTGCCAGCATGTGATATTCCTAT 60.202 41.667 0.00 0.00 0.00 2.57
4207 4300 1.952621 TCCACAGGAACTTCTAGGGG 58.047 55.000 0.00 0.00 34.60 4.79
4227 4320 4.399934 GGGGTTGTTGTAGTTTTCTGTGAA 59.600 41.667 0.00 0.00 0.00 3.18
4229 4322 5.106078 GGGTTGTTGTAGTTTTCTGTGAACA 60.106 40.000 0.00 0.00 0.00 3.18
4240 4333 5.947228 TTTCTGTGAACATGACCAGATTC 57.053 39.130 0.00 0.00 34.19 2.52
4397 4490 6.779539 AGGAAGGGATTTTATGGCTAGAAATG 59.220 38.462 0.00 0.00 0.00 2.32
4469 4562 7.349859 TCACCTAATTGTTAATGATAGGGGAGT 59.650 37.037 7.18 0.00 40.39 3.85
4524 4617 2.223409 ACCGTTTTCCTTCGCTGTTTTC 60.223 45.455 0.00 0.00 0.00 2.29
4629 4722 0.316689 GTTTTTGGGTCGTGACAGCG 60.317 55.000 2.00 0.00 0.00 5.18
4652 4745 0.962356 ACCGTAGATTCACCCGACGT 60.962 55.000 0.00 0.00 0.00 4.34
4678 4771 2.286950 TGTCAACATGCTTCAGAAACGC 60.287 45.455 0.00 0.00 0.00 4.84
4683 4776 1.532437 CATGCTTCAGAAACGCTGTCA 59.468 47.619 0.00 0.00 45.14 3.58
4689 4782 2.390938 TCAGAAACGCTGTCACTTACG 58.609 47.619 0.00 0.00 45.14 3.18
4690 4783 1.136611 CAGAAACGCTGTCACTTACGC 60.137 52.381 0.00 0.00 39.85 4.42
4691 4784 0.856641 GAAACGCTGTCACTTACGCA 59.143 50.000 0.00 0.00 0.00 5.24
4716 4809 1.207593 CCGCGAAAGAGGCAAACTG 59.792 57.895 8.23 0.00 46.21 3.16
4786 4879 2.094752 TCGCCAGCAAAATAAAGAAGGC 60.095 45.455 0.00 0.00 37.54 4.35
4869 5002 1.363807 GTTTCAAGCTTGGCGCCTT 59.636 52.632 29.70 10.89 40.39 4.35
4870 5003 0.249447 GTTTCAAGCTTGGCGCCTTT 60.249 50.000 29.70 13.76 40.39 3.11
4898 5036 4.551702 TGCACCATACTGTAGATTGTGT 57.448 40.909 0.00 0.00 0.00 3.72
5022 5165 1.144936 GAGCTCTGATGGAACCGGG 59.855 63.158 6.32 0.00 0.00 5.73
5045 5193 5.254115 GCCTGGGTAGTTAAGATTTTCTGT 58.746 41.667 0.00 0.00 0.00 3.41
5102 5250 5.591067 TCTTCTTAGCTACTCAAGGCTACTC 59.409 44.000 0.00 0.00 40.21 2.59
5103 5251 4.208746 TCTTAGCTACTCAAGGCTACTCC 58.791 47.826 0.00 0.00 40.21 3.85
5105 5253 3.955524 AGCTACTCAAGGCTACTCCTA 57.044 47.619 0.00 0.00 46.94 2.94
5106 5254 3.558033 AGCTACTCAAGGCTACTCCTAC 58.442 50.000 0.00 0.00 46.94 3.18
5107 5255 3.053544 AGCTACTCAAGGCTACTCCTACA 60.054 47.826 0.00 0.00 46.94 2.74
5108 5256 3.700038 GCTACTCAAGGCTACTCCTACAA 59.300 47.826 0.00 0.00 46.94 2.41
5109 5257 4.202070 GCTACTCAAGGCTACTCCTACAAG 60.202 50.000 0.00 0.00 46.94 3.16
5171 5610 0.821711 TGGACAAAAGGGGACAAGCG 60.822 55.000 0.00 0.00 0.00 4.68
5211 5650 0.960861 TTCCACACACGCAACAACCA 60.961 50.000 0.00 0.00 0.00 3.67
5233 5672 5.351465 CCATAGTAGGCAGTAAAATATGGCG 59.649 44.000 0.00 0.00 45.91 5.69
5313 5752 9.031537 TCGGACTAGATATTTTTGCTGGATATA 57.968 33.333 0.00 0.00 0.00 0.86
5364 5803 4.708726 TGCGGAGTAGTTAACTTACCTC 57.291 45.455 14.49 15.34 39.07 3.85
5410 5849 1.532078 TGGCACTCCGGTACTGACA 60.532 57.895 2.31 0.04 34.14 3.58
5515 5954 8.443953 AAAATTGTTATGCTTGCCAACTAAAA 57.556 26.923 8.09 0.00 0.00 1.52
5519 5958 5.407995 TGTTATGCTTGCCAACTAAAATTGC 59.592 36.000 8.09 0.00 0.00 3.56
5579 6020 2.401583 TGCCATGTGCTTGTACCTAG 57.598 50.000 7.54 0.00 42.00 3.02
5581 6022 1.678728 GCCATGTGCTTGTACCTAGCA 60.679 52.381 13.89 13.89 45.78 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.887568 CTCCTGCAGCCGCGTTAG 60.888 66.667 8.66 0.00 42.97 2.34
29 30 0.615331 TTCCTAACCAGCTCCTGCAG 59.385 55.000 6.78 6.78 42.74 4.41
30 31 1.064003 TTTCCTAACCAGCTCCTGCA 58.936 50.000 0.00 0.00 42.74 4.41
31 32 2.200373 TTTTCCTAACCAGCTCCTGC 57.800 50.000 0.00 0.00 40.05 4.85
32 33 4.158579 GGAAATTTTCCTAACCAGCTCCTG 59.841 45.833 19.01 0.00 46.57 3.86
33 34 4.344978 GGAAATTTTCCTAACCAGCTCCT 58.655 43.478 19.01 0.00 46.57 3.69
34 35 4.720649 GGAAATTTTCCTAACCAGCTCC 57.279 45.455 19.01 0.00 46.57 4.70
40 41 5.105635 CCGGTTAAGGGAAATTTTCCTAACC 60.106 44.000 29.02 29.02 46.72 2.85
46 47 2.871133 CGCCGGTTAAGGGAAATTTTC 58.129 47.619 1.90 0.24 0.00 2.29
47 48 1.067425 GCGCCGGTTAAGGGAAATTTT 60.067 47.619 1.90 0.00 0.00 1.82
48 49 0.528924 GCGCCGGTTAAGGGAAATTT 59.471 50.000 1.90 0.00 0.00 1.82
49 50 1.317431 GGCGCCGGTTAAGGGAAATT 61.317 55.000 12.58 0.00 0.00 1.82
50 51 1.751544 GGCGCCGGTTAAGGGAAAT 60.752 57.895 12.58 0.00 0.00 2.17
51 52 2.360225 GGCGCCGGTTAAGGGAAA 60.360 61.111 12.58 0.00 0.00 3.13
52 53 3.324108 AGGCGCCGGTTAAGGGAA 61.324 61.111 23.20 0.00 0.00 3.97
53 54 4.090588 CAGGCGCCGGTTAAGGGA 62.091 66.667 23.20 0.00 0.00 4.20
56 57 3.499737 CTGCAGGCGCCGGTTAAG 61.500 66.667 27.43 18.02 37.32 1.85
66 67 3.643978 CTATTCGGCGCTGCAGGC 61.644 66.667 17.12 16.58 37.64 4.85
67 68 2.969238 CCTATTCGGCGCTGCAGG 60.969 66.667 17.12 13.74 0.00 4.85
68 69 2.969238 CCCTATTCGGCGCTGCAG 60.969 66.667 12.58 10.11 0.00 4.41
69 70 2.813226 AAACCCTATTCGGCGCTGCA 62.813 55.000 12.58 0.00 0.00 4.41
70 71 2.112815 AAACCCTATTCGGCGCTGC 61.113 57.895 12.58 0.00 0.00 5.25
71 72 1.721487 CAAACCCTATTCGGCGCTG 59.279 57.895 10.86 10.86 0.00 5.18
72 73 2.112815 GCAAACCCTATTCGGCGCT 61.113 57.895 7.64 0.00 0.00 5.92
73 74 2.407616 GCAAACCCTATTCGGCGC 59.592 61.111 0.00 0.00 0.00 6.53
74 75 2.819552 CGGCAAACCCTATTCGGCG 61.820 63.158 0.00 0.00 39.29 6.46
75 76 3.107447 CGGCAAACCCTATTCGGC 58.893 61.111 0.00 0.00 0.00 5.54
76 77 0.179067 TAGCGGCAAACCCTATTCGG 60.179 55.000 1.45 0.00 0.00 4.30
77 78 1.658994 TTAGCGGCAAACCCTATTCG 58.341 50.000 1.45 0.00 0.00 3.34
78 79 2.552743 GGATTAGCGGCAAACCCTATTC 59.447 50.000 1.45 0.00 0.00 1.75
79 80 2.583143 GGATTAGCGGCAAACCCTATT 58.417 47.619 1.45 0.00 0.00 1.73
80 81 1.542547 CGGATTAGCGGCAAACCCTAT 60.543 52.381 1.45 0.00 0.00 2.57
81 82 0.179067 CGGATTAGCGGCAAACCCTA 60.179 55.000 1.45 0.00 0.00 3.53
82 83 1.451387 CGGATTAGCGGCAAACCCT 60.451 57.895 1.45 0.00 0.00 4.34
83 84 0.818040 ATCGGATTAGCGGCAAACCC 60.818 55.000 1.45 0.00 0.00 4.11
84 85 0.586802 GATCGGATTAGCGGCAAACC 59.413 55.000 1.45 2.33 0.00 3.27
85 86 0.586802 GGATCGGATTAGCGGCAAAC 59.413 55.000 1.45 0.00 0.00 2.93
86 87 0.534203 GGGATCGGATTAGCGGCAAA 60.534 55.000 1.45 0.00 0.00 3.68
87 88 1.070786 GGGATCGGATTAGCGGCAA 59.929 57.895 1.45 0.00 0.00 4.52
88 89 1.407656 AAGGGATCGGATTAGCGGCA 61.408 55.000 1.45 0.00 0.00 5.69
89 90 0.670854 GAAGGGATCGGATTAGCGGC 60.671 60.000 0.00 0.00 0.00 6.53
90 91 0.679505 TGAAGGGATCGGATTAGCGG 59.320 55.000 0.00 0.00 0.00 5.52
91 92 2.135933 GTTGAAGGGATCGGATTAGCG 58.864 52.381 0.00 0.00 0.00 4.26
92 93 2.495084 GGTTGAAGGGATCGGATTAGC 58.505 52.381 0.00 0.00 0.00 3.09
93 94 2.224548 GGGGTTGAAGGGATCGGATTAG 60.225 54.545 0.00 0.00 0.00 1.73
94 95 1.772453 GGGGTTGAAGGGATCGGATTA 59.228 52.381 0.00 0.00 0.00 1.75
95 96 0.551396 GGGGTTGAAGGGATCGGATT 59.449 55.000 0.00 0.00 0.00 3.01
96 97 0.327576 AGGGGTTGAAGGGATCGGAT 60.328 55.000 0.00 0.00 0.00 4.18
97 98 0.981277 GAGGGGTTGAAGGGATCGGA 60.981 60.000 0.00 0.00 0.00 4.55
98 99 1.527370 GAGGGGTTGAAGGGATCGG 59.473 63.158 0.00 0.00 0.00 4.18
99 100 1.144057 CGAGGGGTTGAAGGGATCG 59.856 63.158 0.00 0.00 0.00 3.69
100 101 0.909623 TTCGAGGGGTTGAAGGGATC 59.090 55.000 0.00 0.00 0.00 3.36
101 102 1.282157 CTTTCGAGGGGTTGAAGGGAT 59.718 52.381 0.00 0.00 0.00 3.85
102 103 0.690762 CTTTCGAGGGGTTGAAGGGA 59.309 55.000 0.00 0.00 0.00 4.20
103 104 0.690762 TCTTTCGAGGGGTTGAAGGG 59.309 55.000 0.00 0.00 0.00 3.95
104 105 2.561478 TTCTTTCGAGGGGTTGAAGG 57.439 50.000 0.00 0.00 0.00 3.46
105 106 4.911514 TTTTTCTTTCGAGGGGTTGAAG 57.088 40.909 0.00 0.00 0.00 3.02
123 124 4.261614 GCACCTTTGAAGAGTCGGATTTTT 60.262 41.667 0.00 0.00 0.00 1.94
124 125 3.253432 GCACCTTTGAAGAGTCGGATTTT 59.747 43.478 0.00 0.00 0.00 1.82
125 126 2.814336 GCACCTTTGAAGAGTCGGATTT 59.186 45.455 0.00 0.00 0.00 2.17
126 127 2.039084 AGCACCTTTGAAGAGTCGGATT 59.961 45.455 0.00 0.00 0.00 3.01
127 128 1.625818 AGCACCTTTGAAGAGTCGGAT 59.374 47.619 0.00 0.00 0.00 4.18
128 129 1.048601 AGCACCTTTGAAGAGTCGGA 58.951 50.000 0.00 0.00 0.00 4.55
129 130 1.151668 CAGCACCTTTGAAGAGTCGG 58.848 55.000 0.00 0.00 0.00 4.79
130 131 1.151668 CCAGCACCTTTGAAGAGTCG 58.848 55.000 0.00 0.00 0.00 4.18
131 132 0.877743 GCCAGCACCTTTGAAGAGTC 59.122 55.000 0.00 0.00 0.00 3.36
132 133 0.183492 TGCCAGCACCTTTGAAGAGT 59.817 50.000 0.00 0.00 0.00 3.24
133 134 0.879765 CTGCCAGCACCTTTGAAGAG 59.120 55.000 0.00 0.00 0.00 2.85
134 135 1.174712 GCTGCCAGCACCTTTGAAGA 61.175 55.000 12.82 0.00 41.89 2.87
135 136 1.288127 GCTGCCAGCACCTTTGAAG 59.712 57.895 12.82 0.00 41.89 3.02
136 137 2.202395 GGCTGCCAGCACCTTTGAA 61.202 57.895 19.95 0.00 44.75 2.69
137 138 2.598394 GGCTGCCAGCACCTTTGA 60.598 61.111 19.95 0.00 44.75 2.69
138 139 4.047059 CGGCTGCCAGCACCTTTG 62.047 66.667 19.95 0.00 44.75 2.77
263 266 1.763968 TCATGGTGGTCTCTCGGTAG 58.236 55.000 0.00 0.00 0.00 3.18
264 267 2.454336 ATCATGGTGGTCTCTCGGTA 57.546 50.000 0.00 0.00 0.00 4.02
300 303 2.913590 CGCACAGCTGATATCATAGTCG 59.086 50.000 23.35 7.52 0.00 4.18
465 473 2.166459 CGAATCTGCAGGAGTGGAAGTA 59.834 50.000 15.13 0.00 0.00 2.24
532 553 2.664916 CGCCTGACAACCATTTCTTTG 58.335 47.619 0.00 0.00 0.00 2.77
566 587 0.563173 CTAGGATCTCTCCCCCACCA 59.437 60.000 0.00 0.00 43.21 4.17
567 588 0.563672 ACTAGGATCTCTCCCCCACC 59.436 60.000 0.00 0.00 43.21 4.61
578 600 5.336134 GCCTCGGATCTAAAGAACTAGGATC 60.336 48.000 10.95 0.00 34.00 3.36
588 610 3.686726 GCCATAATGCCTCGGATCTAAAG 59.313 47.826 0.00 0.00 0.00 1.85
664 724 0.475906 AGGAAAGCAGTGCCTGAGTT 59.524 50.000 12.58 0.00 32.44 3.01
671 733 4.065789 ACTAAACTACAGGAAAGCAGTGC 58.934 43.478 7.13 7.13 0.00 4.40
813 881 5.541953 TCAGACATCACATTATCTCAGGG 57.458 43.478 0.00 0.00 0.00 4.45
872 940 3.820467 TGTCAGACCCACAATCATTGTTC 59.180 43.478 0.00 0.00 43.23 3.18
916 984 8.642885 CAGAAAACGCTGCTAATCATACTATAG 58.357 37.037 0.00 0.00 0.00 1.31
968 1036 5.308497 TGACAAGGGAACAGGTAGAACATTA 59.692 40.000 0.00 0.00 0.00 1.90
1155 1224 4.778143 GCGGACAGGGAACGGCAT 62.778 66.667 0.00 0.00 33.65 4.40
1202 1271 0.459585 ACGACAACAACACGCAGACT 60.460 50.000 0.00 0.00 0.00 3.24
1204 1273 0.371989 CAACGACAACAACACGCAGA 59.628 50.000 0.00 0.00 0.00 4.26
1556 1634 1.818060 CCATTTGGATCTGGCGACAAA 59.182 47.619 0.00 0.00 37.33 2.83
1670 1748 9.901724 GAATGTTCTGTCATATTTTGTACTACG 57.098 33.333 0.00 0.00 0.00 3.51
1719 1797 6.878317 TGATACACTATTTCCTGAACAGAGG 58.122 40.000 3.19 0.00 0.00 3.69
1773 1851 5.085275 AGGATCTGAATGAGTCCTGGATA 57.915 43.478 0.00 0.00 39.54 2.59
1796 1874 1.004277 TGGATGGCCACAACTAGAACC 59.996 52.381 8.16 1.21 39.92 3.62
1818 1896 2.178912 TCTTCGCCCACTCGATTTTT 57.821 45.000 0.00 0.00 38.37 1.94
1969 2047 7.309744 GCAAGATATAGAAGAGTACCAGCAGAT 60.310 40.741 0.00 0.00 0.00 2.90
2030 2108 3.502595 GGCTTTCTTCCTAAACAGGTGTC 59.497 47.826 0.00 0.00 0.00 3.67
2235 2313 5.218179 TCCTCCGTTATAATTAGGACCCAA 58.782 41.667 8.55 0.00 31.41 4.12
2290 2368 3.455327 TGTTTGGATGCAAACACATGTG 58.545 40.909 33.47 24.25 46.32 3.21
2318 2396 3.410631 TCTTGCCAAGTCGGACATTAA 57.589 42.857 11.27 0.00 36.56 1.40
2335 2413 6.448006 CCCGATACGATCTGAAATACTTCTT 58.552 40.000 0.00 0.00 32.33 2.52
2343 2421 2.498481 ACAACCCCGATACGATCTGAAA 59.502 45.455 0.00 0.00 0.00 2.69
2359 2437 3.947196 TCATGACATCAGCCAATACAACC 59.053 43.478 0.00 0.00 0.00 3.77
2394 2472 9.933723 AAGCATATACAAAGCAAAAAGATTTCT 57.066 25.926 0.00 0.00 32.59 2.52
2480 2558 3.902881 AAGTTGAAAATTGCCACCACA 57.097 38.095 0.00 0.00 0.00 4.17
2498 2576 9.543018 GTACAGCTAAAGTAAACTAATGCAAAG 57.457 33.333 0.00 0.00 0.00 2.77
2610 2688 8.949953 CGTTTTAGTTTTACGTTGAATTCACAT 58.050 29.630 7.89 0.00 0.00 3.21
2661 2739 0.248565 GTTGAGGGTCGTAGGTTCCC 59.751 60.000 9.31 9.31 41.36 3.97
2699 2786 6.835174 ACTGCATGTATTCTAGGATGTCATT 58.165 36.000 0.00 0.00 0.00 2.57
2784 2872 8.789767 CATGTATATATGGAAGGAGGAGGTAT 57.210 38.462 1.64 0.00 0.00 2.73
2801 2889 6.327626 AGACAAGACTAGTTGGCCATGTATAT 59.672 38.462 6.09 0.00 35.89 0.86
3037 3127 0.927537 TCCGCGCAAAATGATACTCG 59.072 50.000 8.75 0.00 0.00 4.18
3109 3199 6.374894 TCAGCACACAACATTGATGATCATAA 59.625 34.615 8.54 0.00 33.33 1.90
3137 3227 3.230743 ACATGCCTTAATTTTCACGGC 57.769 42.857 0.00 0.00 41.06 5.68
3175 3266 4.678509 ATTTGCGTCGCTAGATTTTCAA 57.321 36.364 19.50 0.00 0.00 2.69
3183 3274 2.032030 CCCCAAATATTTGCGTCGCTAG 60.032 50.000 20.67 6.31 36.86 3.42
3203 3295 6.451064 AATTAAATACAACTAGCAGGTGCC 57.549 37.500 0.00 0.00 36.04 5.01
3236 3328 3.347216 GCAGTGGCAAGATAGAGGAAAA 58.653 45.455 0.00 0.00 40.72 2.29
3257 3349 6.816640 TCAACTTCATCCTTCGTTAATACCTG 59.183 38.462 0.00 0.00 0.00 4.00
3369 3461 7.279750 GGAACCAAAAATTAACTGGTAGTGA 57.720 36.000 6.48 0.00 42.72 3.41
3406 3499 2.239907 GGCTACAAGGGTCCTTTCAGAT 59.760 50.000 0.00 0.00 33.42 2.90
3418 3511 4.201851 CGATTCACATCAAAGGCTACAAGG 60.202 45.833 0.00 0.00 0.00 3.61
3426 3519 5.353956 TGTTATCCACGATTCACATCAAAGG 59.646 40.000 0.00 0.00 0.00 3.11
3500 3593 4.271590 TGTCGAAACAAACTGATGTGTG 57.728 40.909 0.00 0.00 37.43 3.82
3508 3601 5.295787 TGCTTAACAGATGTCGAAACAAACT 59.704 36.000 0.00 0.00 39.30 2.66
3700 3793 7.703058 TTTCCTTTCTTGAGAATATCCCAAC 57.297 36.000 0.00 0.00 33.54 3.77
3921 4014 8.568617 AGAAAATAGTACTCCACCATAGGAAT 57.431 34.615 0.00 0.00 37.20 3.01
3928 4021 8.148351 GCATACATAGAAAATAGTACTCCACCA 58.852 37.037 0.00 0.00 0.00 4.17
4207 4300 7.218204 GTCATGTTCACAGAAAACTACAACAAC 59.782 37.037 0.00 0.00 0.00 3.32
4227 4320 3.370953 GGCAAGTAGGAATCTGGTCATGT 60.371 47.826 0.00 0.00 0.00 3.21
4229 4322 2.846206 TGGCAAGTAGGAATCTGGTCAT 59.154 45.455 0.00 0.00 0.00 3.06
4240 4333 8.137437 CCAAGAAACAATTATATGGCAAGTAGG 58.863 37.037 0.00 0.00 0.00 3.18
4344 4437 4.147219 ACGAAGAATAAACTGCACTTGC 57.853 40.909 0.00 0.00 42.50 4.01
4469 4562 2.025981 AGCAAGCATTACAGGACATCCA 60.026 45.455 0.00 0.00 38.89 3.41
4524 4617 7.440556 TCAGAAGTCAAACATCTCAAGAGAAAG 59.559 37.037 3.59 2.98 41.36 2.62
4629 4722 1.747355 TCGGGTGAATCTACGGTCTTC 59.253 52.381 0.00 0.00 0.00 2.87
4652 4745 3.753815 TCTGAAGCATGTTGACATTGGA 58.246 40.909 0.00 0.00 33.61 3.53
4678 4771 1.016130 CCTGCCTGCGTAAGTGACAG 61.016 60.000 0.00 0.00 41.68 3.51
4683 4776 4.760047 CGGCCTGCCTGCGTAAGT 62.760 66.667 6.60 0.00 41.68 2.24
4691 4784 4.767255 CTCTTTCGCGGCCTGCCT 62.767 66.667 6.13 0.00 42.08 4.75
4706 4799 3.618690 AGAGTACATCCAGTTTGCCTC 57.381 47.619 0.00 0.00 0.00 4.70
4713 4806 7.642082 ACGATAACTAAAGAGTACATCCAGT 57.358 36.000 0.00 0.00 33.58 4.00
4786 4879 3.181526 GCTAAACTCAACACGAGCATCTG 60.182 47.826 0.00 0.00 46.63 2.90
4869 5002 6.538945 TCTACAGTATGGTGCAATACAGAA 57.461 37.500 10.42 0.00 43.62 3.02
4870 5003 6.731292 ATCTACAGTATGGTGCAATACAGA 57.269 37.500 10.42 5.72 43.62 3.41
4898 5036 3.285484 GAGGGAATAGGTCACGACTACA 58.715 50.000 0.00 0.00 33.41 2.74
4933 5071 1.670083 GCCAACGGTCACCACTACC 60.670 63.158 0.00 0.00 0.00 3.18
5022 5165 5.254115 ACAGAAAATCTTAACTACCCAGGC 58.746 41.667 0.00 0.00 0.00 4.85
5045 5193 6.361433 TCAGGTTGGTTCAGAAGTCAAAATA 58.639 36.000 1.58 0.00 0.00 1.40
5109 5257 9.901172 ATTTAATATACGGATGGAAGGATTACC 57.099 33.333 0.00 0.00 0.00 2.85
5156 5595 0.310854 GTCACGCTTGTCCCCTTTTG 59.689 55.000 0.00 0.00 0.00 2.44
5171 5610 4.673534 ATTTTATTCCGGTGAACGTCAC 57.326 40.909 0.00 8.94 46.23 3.67
5211 5650 6.014499 ACTCGCCATATTTTACTGCCTACTAT 60.014 38.462 0.00 0.00 0.00 2.12
5233 5672 3.088532 TGTGGCCACCAATTATGAACTC 58.911 45.455 32.62 3.13 34.18 3.01
5333 5772 2.394632 ACTACTCCGCATATCAACCCA 58.605 47.619 0.00 0.00 0.00 4.51
5493 5932 7.361116 GCAATTTTAGTTGGCAAGCATAACAAT 60.361 33.333 0.00 2.04 0.00 2.71
5506 5945 3.181487 CCGAGGATGGCAATTTTAGTTGG 60.181 47.826 0.00 0.00 0.00 3.77
5515 5954 4.974645 TTAGTTATCCGAGGATGGCAAT 57.025 40.909 14.50 1.31 36.17 3.56
5519 5958 4.511826 GCAAGTTTAGTTATCCGAGGATGG 59.488 45.833 14.50 0.00 36.17 3.51
5579 6020 4.702131 AGGACCTTGATAAGTGTCAAATGC 59.298 41.667 0.00 0.00 37.63 3.56
5581 6022 8.164070 AGTTAAGGACCTTGATAAGTGTCAAAT 58.836 33.333 17.47 0.00 37.63 2.32


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

AutoCloner maintained by Alex Coulton.