Multiple sequence alignment - TraesCS1A01G307800

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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 TraesCS1A01G307800 chr1A 100.000 3071 0 0 1 3071 499196695 499193625 0.000000e+00 5672.0
1 TraesCS1A01G307800 chr1A 95.973 149 6 0 1 149 416544259 416544111 3.060000e-60 243.0
2 TraesCS1A01G307800 chr1D 96.891 2091 56 7 986 3071 403708038 403705952 0.000000e+00 3493.0
3 TraesCS1A01G307800 chr1D 84.368 902 49 38 149 986 403708968 403708095 0.000000e+00 800.0
4 TraesCS1A01G307800 chr1D 84.354 294 37 8 2767 3059 403704843 403704558 2.330000e-71 279.0
5 TraesCS1A01G307800 chr1D 88.000 150 18 0 1 150 446734677 446734826 8.750000e-41 178.0
6 TraesCS1A01G307800 chr1B 95.120 2090 76 8 986 3071 543021563 543019496 0.000000e+00 3271.0
7 TraesCS1A01G307800 chr1B 82.556 900 50 44 161 986 543022486 543021620 0.000000e+00 693.0
8 TraesCS1A01G307800 chr1B 92.308 78 5 1 2767 2843 543018468 543018391 3.240000e-20 110.0
9 TraesCS1A01G307800 chr3D 86.651 1266 143 12 1001 2253 601618545 601617293 0.000000e+00 1378.0
10 TraesCS1A01G307800 chr3B 80.741 1080 184 18 1001 2071 580205750 580206814 0.000000e+00 821.0
11 TraesCS1A01G307800 chr2A 94.771 153 8 0 1 153 4796143 4795991 3.960000e-59 239.0
12 TraesCS1A01G307800 chr3A 94.595 148 8 0 1 148 367762732 367762879 2.380000e-56 230.0
13 TraesCS1A01G307800 chr3A 94.595 148 8 0 1 148 367770597 367770744 2.380000e-56 230.0
14 TraesCS1A01G307800 chr3A 89.189 148 16 0 1 148 434067981 434068128 5.230000e-43 185.0
15 TraesCS1A01G307800 chr3A 77.536 138 24 5 2546 2681 715142029 715142161 3.280000e-10 76.8
16 TraesCS1A01G307800 chr6B 85.333 225 28 4 2636 2856 539534721 539534944 8.570000e-56 228.0
17 TraesCS1A01G307800 chr5A 90.667 150 14 0 1 150 419409218 419409069 1.870000e-47 200.0
18 TraesCS1A01G307800 chr7B 88.050 159 18 1 2 159 538871919 538872077 1.450000e-43 187.0
19 TraesCS1A01G307800 chr2D 87.919 149 18 0 1 149 305908335 305908483 3.150000e-40 176.0


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 TraesCS1A01G307800 chr1A 499193625 499196695 3070 True 5672 5672 100.000000 1 3071 1 chr1A.!!$R2 3070
1 TraesCS1A01G307800 chr1D 403704558 403708968 4410 True 1524 3493 88.537667 149 3071 3 chr1D.!!$R1 2922
2 TraesCS1A01G307800 chr1B 543018391 543022486 4095 True 1358 3271 89.994667 161 3071 3 chr1B.!!$R1 2910
3 TraesCS1A01G307800 chr3D 601617293 601618545 1252 True 1378 1378 86.651000 1001 2253 1 chr3D.!!$R1 1252
4 TraesCS1A01G307800 chr3B 580205750 580206814 1064 False 821 821 80.741000 1001 2071 1 chr3B.!!$F1 1070

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
136 137 0.109153 AAACTTTTAGGACCGCCCGT 59.891 50.0 0.0 0.0 40.87 5.28 F
782 831 0.178301 GATTCCACTCTCCCGGTTCC 59.822 60.0 0.0 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2155 0.107993 CCTCTTCATCAGCGCCTTCA 60.108 55.000 2.29 0.0 0.0 3.02 R
2423 2577 1.891150 GGTTTCTCAGTCGGACAGGTA 59.109 52.381 11.27 0.0 0.0 3.08 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
17 18 2.256158 CACACGTGCAGGGCAATG 59.744 61.111 17.22 0.00 41.47 2.82
18 19 2.112928 ACACGTGCAGGGCAATGA 59.887 55.556 17.22 0.00 41.47 2.57
19 20 1.968017 ACACGTGCAGGGCAATGAG 60.968 57.895 17.22 0.64 41.47 2.90
20 21 3.058160 ACGTGCAGGGCAATGAGC 61.058 61.111 11.67 0.00 41.47 4.26
35 36 2.183478 TGAGCGCTCATGGAAAAAGA 57.817 45.000 35.30 9.45 34.14 2.52
36 37 2.503331 TGAGCGCTCATGGAAAAAGAA 58.497 42.857 35.30 8.88 34.14 2.52
37 38 2.226437 TGAGCGCTCATGGAAAAAGAAC 59.774 45.455 35.30 5.99 34.14 3.01
38 39 1.541588 AGCGCTCATGGAAAAAGAACC 59.458 47.619 2.64 0.00 0.00 3.62
39 40 1.541588 GCGCTCATGGAAAAAGAACCT 59.458 47.619 0.00 0.00 0.00 3.50
40 41 2.414691 GCGCTCATGGAAAAAGAACCTC 60.415 50.000 0.00 0.00 0.00 3.85
41 42 2.159653 CGCTCATGGAAAAAGAACCTCG 60.160 50.000 0.00 0.00 0.00 4.63
42 43 2.414691 GCTCATGGAAAAAGAACCTCGC 60.415 50.000 0.00 0.00 0.00 5.03
43 44 2.813754 CTCATGGAAAAAGAACCTCGCA 59.186 45.455 0.00 0.00 0.00 5.10
44 45 3.420893 TCATGGAAAAAGAACCTCGCAT 58.579 40.909 0.00 0.00 0.00 4.73
45 46 3.191162 TCATGGAAAAAGAACCTCGCATG 59.809 43.478 0.00 0.00 0.00 4.06
46 47 2.857483 TGGAAAAAGAACCTCGCATGA 58.143 42.857 0.00 0.00 0.00 3.07
47 48 3.218453 TGGAAAAAGAACCTCGCATGAA 58.782 40.909 0.00 0.00 0.00 2.57
48 49 3.004315 TGGAAAAAGAACCTCGCATGAAC 59.996 43.478 0.00 0.00 0.00 3.18
49 50 3.565516 GAAAAAGAACCTCGCATGAACC 58.434 45.455 0.00 0.00 0.00 3.62
50 51 2.270352 AAAGAACCTCGCATGAACCA 57.730 45.000 0.00 0.00 0.00 3.67
51 52 1.523758 AAGAACCTCGCATGAACCAC 58.476 50.000 0.00 0.00 0.00 4.16
52 53 0.687354 AGAACCTCGCATGAACCACT 59.313 50.000 0.00 0.00 0.00 4.00
53 54 1.072331 AGAACCTCGCATGAACCACTT 59.928 47.619 0.00 0.00 0.00 3.16
54 55 2.301870 AGAACCTCGCATGAACCACTTA 59.698 45.455 0.00 0.00 0.00 2.24
55 56 2.094762 ACCTCGCATGAACCACTTAC 57.905 50.000 0.00 0.00 0.00 2.34
56 57 1.623811 ACCTCGCATGAACCACTTACT 59.376 47.619 0.00 0.00 0.00 2.24
57 58 2.829720 ACCTCGCATGAACCACTTACTA 59.170 45.455 0.00 0.00 0.00 1.82
58 59 3.259876 ACCTCGCATGAACCACTTACTAA 59.740 43.478 0.00 0.00 0.00 2.24
59 60 4.250464 CCTCGCATGAACCACTTACTAAA 58.750 43.478 0.00 0.00 0.00 1.85
60 61 4.330074 CCTCGCATGAACCACTTACTAAAG 59.670 45.833 0.00 0.00 38.77 1.85
61 62 5.142061 TCGCATGAACCACTTACTAAAGA 57.858 39.130 0.00 0.00 36.50 2.52
62 63 5.543714 TCGCATGAACCACTTACTAAAGAA 58.456 37.500 0.00 0.00 36.50 2.52
63 64 6.170506 TCGCATGAACCACTTACTAAAGAAT 58.829 36.000 0.00 0.00 36.50 2.40
64 65 6.092122 TCGCATGAACCACTTACTAAAGAATG 59.908 38.462 0.00 0.00 36.50 2.67
65 66 6.092122 CGCATGAACCACTTACTAAAGAATGA 59.908 38.462 0.00 0.00 36.50 2.57
66 67 7.467623 GCATGAACCACTTACTAAAGAATGAG 58.532 38.462 0.00 0.00 36.50 2.90
67 68 7.414540 GCATGAACCACTTACTAAAGAATGAGG 60.415 40.741 0.00 0.00 36.50 3.86
68 69 7.311092 TGAACCACTTACTAAAGAATGAGGA 57.689 36.000 0.00 0.00 36.50 3.71
69 70 7.159372 TGAACCACTTACTAAAGAATGAGGAC 58.841 38.462 0.00 0.00 36.50 3.85
70 71 6.051179 ACCACTTACTAAAGAATGAGGACC 57.949 41.667 0.00 0.00 36.50 4.46
71 72 5.785940 ACCACTTACTAAAGAATGAGGACCT 59.214 40.000 0.00 0.00 36.50 3.85
72 73 6.958192 ACCACTTACTAAAGAATGAGGACCTA 59.042 38.462 0.00 0.00 36.50 3.08
73 74 7.456902 ACCACTTACTAAAGAATGAGGACCTAA 59.543 37.037 0.00 0.00 36.50 2.69
74 75 8.319146 CCACTTACTAAAGAATGAGGACCTAAA 58.681 37.037 0.00 0.00 36.50 1.85
75 76 9.372369 CACTTACTAAAGAATGAGGACCTAAAG 57.628 37.037 0.00 0.00 36.50 1.85
76 77 9.322769 ACTTACTAAAGAATGAGGACCTAAAGA 57.677 33.333 0.00 0.00 36.50 2.52
79 80 7.051000 ACTAAAGAATGAGGACCTAAAGATGC 58.949 38.462 0.00 0.00 0.00 3.91
80 81 5.441718 AAGAATGAGGACCTAAAGATGCA 57.558 39.130 0.00 0.00 0.00 3.96
81 82 5.643421 AGAATGAGGACCTAAAGATGCAT 57.357 39.130 0.00 0.00 0.00 3.96
82 83 6.011122 AGAATGAGGACCTAAAGATGCATT 57.989 37.500 0.00 0.00 0.00 3.56
83 84 6.430007 AGAATGAGGACCTAAAGATGCATTT 58.570 36.000 0.00 0.00 0.00 2.32
84 85 6.894103 AGAATGAGGACCTAAAGATGCATTTT 59.106 34.615 0.00 0.00 0.00 1.82
85 86 5.902613 TGAGGACCTAAAGATGCATTTTG 57.097 39.130 0.00 0.00 0.00 2.44
86 87 5.569355 TGAGGACCTAAAGATGCATTTTGA 58.431 37.500 0.00 0.00 0.00 2.69
87 88 6.009589 TGAGGACCTAAAGATGCATTTTGAA 58.990 36.000 0.00 0.00 0.00 2.69
88 89 6.493115 TGAGGACCTAAAGATGCATTTTGAAA 59.507 34.615 0.00 0.00 0.00 2.69
89 90 6.928520 AGGACCTAAAGATGCATTTTGAAAG 58.071 36.000 0.00 0.73 0.00 2.62
90 91 6.721208 AGGACCTAAAGATGCATTTTGAAAGA 59.279 34.615 0.00 0.00 0.00 2.52
91 92 7.233348 AGGACCTAAAGATGCATTTTGAAAGAA 59.767 33.333 0.00 0.00 0.00 2.52
92 93 8.037166 GGACCTAAAGATGCATTTTGAAAGAAT 58.963 33.333 0.00 0.00 0.00 2.40
93 94 9.428097 GACCTAAAGATGCATTTTGAAAGAATT 57.572 29.630 0.00 0.00 0.00 2.17
110 111 9.010029 TGAAAGAATTAGGATTAAAGTGACACC 57.990 33.333 0.84 0.00 0.00 4.16
111 112 7.939784 AAGAATTAGGATTAAAGTGACACCC 57.060 36.000 0.84 0.00 0.00 4.61
112 113 6.424032 AGAATTAGGATTAAAGTGACACCCC 58.576 40.000 0.84 0.00 0.00 4.95
113 114 2.781681 AGGATTAAAGTGACACCCCG 57.218 50.000 0.84 0.00 0.00 5.73
114 115 2.262637 AGGATTAAAGTGACACCCCGA 58.737 47.619 0.84 0.00 0.00 5.14
115 116 2.844348 AGGATTAAAGTGACACCCCGAT 59.156 45.455 0.84 0.00 0.00 4.18
116 117 2.943033 GGATTAAAGTGACACCCCGATG 59.057 50.000 0.84 0.00 0.00 3.84
117 118 3.370103 GGATTAAAGTGACACCCCGATGA 60.370 47.826 0.84 0.00 0.00 2.92
118 119 3.773418 TTAAAGTGACACCCCGATGAA 57.227 42.857 0.84 0.00 0.00 2.57
119 120 2.649531 AAAGTGACACCCCGATGAAA 57.350 45.000 0.84 0.00 0.00 2.69
120 121 1.892209 AAGTGACACCCCGATGAAAC 58.108 50.000 0.84 0.00 0.00 2.78
121 122 1.056660 AGTGACACCCCGATGAAACT 58.943 50.000 0.84 0.00 0.00 2.66
122 123 1.420138 AGTGACACCCCGATGAAACTT 59.580 47.619 0.84 0.00 0.00 2.66
123 124 2.158667 AGTGACACCCCGATGAAACTTT 60.159 45.455 0.84 0.00 0.00 2.66
124 125 2.621526 GTGACACCCCGATGAAACTTTT 59.378 45.455 0.00 0.00 0.00 2.27
125 126 3.816523 GTGACACCCCGATGAAACTTTTA 59.183 43.478 0.00 0.00 0.00 1.52
126 127 4.069304 TGACACCCCGATGAAACTTTTAG 58.931 43.478 0.00 0.00 0.00 1.85
127 128 3.418047 ACACCCCGATGAAACTTTTAGG 58.582 45.455 0.00 0.00 0.00 2.69
128 129 3.073356 ACACCCCGATGAAACTTTTAGGA 59.927 43.478 0.00 0.00 0.00 2.94
129 130 3.439129 CACCCCGATGAAACTTTTAGGAC 59.561 47.826 0.00 0.00 0.00 3.85
130 131 3.014623 CCCCGATGAAACTTTTAGGACC 58.985 50.000 0.00 0.00 0.00 4.46
131 132 2.676342 CCCGATGAAACTTTTAGGACCG 59.324 50.000 0.00 0.00 0.00 4.79
132 133 2.095372 CCGATGAAACTTTTAGGACCGC 59.905 50.000 0.00 0.00 0.00 5.68
133 134 2.095372 CGATGAAACTTTTAGGACCGCC 59.905 50.000 0.00 0.00 0.00 6.13
134 135 1.900245 TGAAACTTTTAGGACCGCCC 58.100 50.000 0.00 0.00 33.31 6.13
135 136 0.800631 GAAACTTTTAGGACCGCCCG 59.199 55.000 0.00 0.00 40.87 6.13
136 137 0.109153 AAACTTTTAGGACCGCCCGT 59.891 50.000 0.00 0.00 40.87 5.28
137 138 0.604511 AACTTTTAGGACCGCCCGTG 60.605 55.000 0.00 0.00 40.87 4.94
138 139 2.358984 TTTTAGGACCGCCCGTGC 60.359 61.111 0.00 0.00 40.87 5.34
139 140 3.179888 TTTTAGGACCGCCCGTGCA 62.180 57.895 0.00 0.00 40.87 4.57
140 141 2.472414 TTTTAGGACCGCCCGTGCAT 62.472 55.000 0.00 0.00 40.87 3.96
141 142 2.472414 TTTAGGACCGCCCGTGCATT 62.472 55.000 0.00 0.00 40.87 3.56
142 143 2.472414 TTAGGACCGCCCGTGCATTT 62.472 55.000 0.00 0.00 40.87 2.32
143 144 1.615165 TAGGACCGCCCGTGCATTTA 61.615 55.000 0.00 0.00 40.87 1.40
144 145 2.041686 GGACCGCCCGTGCATTTAA 61.042 57.895 0.00 0.00 37.32 1.52
145 146 1.135939 GACCGCCCGTGCATTTAAC 59.864 57.895 0.00 0.00 37.32 2.01
146 147 1.302993 ACCGCCCGTGCATTTAACT 60.303 52.632 0.00 0.00 37.32 2.24
147 148 1.303091 ACCGCCCGTGCATTTAACTC 61.303 55.000 0.00 0.00 37.32 3.01
154 155 5.049680 CGCCCGTGCATTTAACTCTTTATAT 60.050 40.000 0.00 0.00 37.32 0.86
454 476 6.608922 CAGAGGAGAAAAATATCCCCAATCT 58.391 40.000 0.00 0.00 36.14 2.40
455 477 6.714356 CAGAGGAGAAAAATATCCCCAATCTC 59.286 42.308 0.00 0.00 36.14 2.75
456 478 6.623183 AGAGGAGAAAAATATCCCCAATCTCT 59.377 38.462 0.00 0.00 36.14 3.10
457 479 6.846988 AGGAGAAAAATATCCCCAATCTCTC 58.153 40.000 0.00 0.00 36.14 3.20
458 480 6.623183 AGGAGAAAAATATCCCCAATCTCTCT 59.377 38.462 0.00 0.00 36.14 3.10
459 481 6.939730 GGAGAAAAATATCCCCAATCTCTCTC 59.060 42.308 0.00 0.00 33.92 3.20
460 482 6.529220 AGAAAAATATCCCCAATCTCTCTCG 58.471 40.000 0.00 0.00 0.00 4.04
478 500 1.949631 GCCTCGCCTCCGATAAACG 60.950 63.158 0.00 0.00 43.47 3.60
600 639 4.612412 TGCGGCGAGTTTTCGGGT 62.612 61.111 12.98 0.00 46.76 5.28
603 642 2.254350 GGCGAGTTTTCGGGTTGC 59.746 61.111 0.00 0.00 46.76 4.17
679 718 4.493747 CGGGTCTCGGTTCGGCTC 62.494 72.222 0.00 0.00 34.75 4.70
680 719 4.144703 GGGTCTCGGTTCGGCTCC 62.145 72.222 0.00 0.00 0.00 4.70
710 749 4.020617 CTCGCCTGGGCTGGTTGA 62.021 66.667 10.04 0.00 39.32 3.18
782 831 0.178301 GATTCCACTCTCCCGGTTCC 59.822 60.000 0.00 0.00 0.00 3.62
818 867 7.587037 TCCCTTTGATTATTGATGGTGATTC 57.413 36.000 0.00 0.00 0.00 2.52
837 913 5.364735 TGATTCTGCTTCATCCATGTCTCTA 59.635 40.000 0.00 0.00 0.00 2.43
849 925 3.623060 CCATGTCTCTAATGTTTCCCGTG 59.377 47.826 0.00 0.00 0.00 4.94
854 930 1.153353 CTAATGTTTCCCGTGCGTGT 58.847 50.000 0.00 0.00 0.00 4.49
868 944 1.569479 GCGTGTTCTGAGCTGTTCCC 61.569 60.000 0.00 0.00 0.00 3.97
878 954 1.352687 GAGCTGTTCCCCTTCTCCTTT 59.647 52.381 0.00 0.00 0.00 3.11
890 966 1.746991 CTCCTTTCCTTCAGGCGGC 60.747 63.158 0.00 0.00 34.44 6.53
1101 1235 2.783135 GTCCTGCTCATCCTCAACAAA 58.217 47.619 0.00 0.00 0.00 2.83
1244 1378 1.613630 AGGACGCCCTCAACCTGAT 60.614 57.895 0.00 0.00 38.86 2.90
1512 1649 0.233332 GCACGCTTCAGAACTGTGTC 59.767 55.000 10.35 2.27 33.23 3.67
1659 1796 1.804396 CGATCAGCTCCCTCATCGCT 61.804 60.000 0.00 0.00 32.44 4.93
1881 2018 1.670590 GCCATATCTCGAGCTGCCT 59.329 57.895 7.81 0.00 0.00 4.75
2017 2154 4.833811 GGCCATTCAAATTCGCCC 57.166 55.556 0.00 0.00 33.30 6.13
2018 2155 2.201927 GGCCATTCAAATTCGCCCT 58.798 52.632 0.00 0.00 33.30 5.19
2163 2312 5.926542 TGTAATAGTCTGTGCTTGTTGTCTC 59.073 40.000 0.00 0.00 0.00 3.36
2196 2345 5.560953 GCTCTTTGTACAGTGGTGACATTTC 60.561 44.000 0.00 0.00 46.14 2.17
2297 2451 3.256631 ACCCTCATACAAGCTGCTTTTTG 59.743 43.478 13.10 10.44 0.00 2.44
2304 2458 7.432869 TCATACAAGCTGCTTTTTGTTGTTAT 58.567 30.769 13.10 0.00 38.41 1.89
2331 2485 3.152341 AGCTGATTTTTCACTCCCACAG 58.848 45.455 0.00 0.00 0.00 3.66
2370 2524 6.983906 TGAGATATCTGAAGAGGCAATGTA 57.016 37.500 10.74 0.00 0.00 2.29
2371 2525 6.990798 TGAGATATCTGAAGAGGCAATGTAG 58.009 40.000 10.74 0.00 0.00 2.74
2384 2538 7.318141 AGAGGCAATGTAGATTTTGACATTTG 58.682 34.615 0.00 0.00 42.27 2.32
2385 2539 7.177216 AGAGGCAATGTAGATTTTGACATTTGA 59.823 33.333 0.00 0.00 42.27 2.69
2564 2718 5.462729 TGAGCTGCATGTGTAAAAACAAATG 59.537 36.000 1.02 4.61 32.81 2.32
2621 2778 2.286418 CCGAACTTCACAGCAGTTTCAC 60.286 50.000 0.00 0.00 34.49 3.18
2738 2895 3.133721 GGACTAATCTGATGCTGACTGGT 59.866 47.826 0.00 0.00 0.00 4.00
2797 2954 8.066668 TGGTTTGCGTATTTATTTTGAAACTG 57.933 30.769 0.00 0.00 0.00 3.16
2850 3007 5.476945 AGGTTGACTTTGCTAATAAGTTGGG 59.523 40.000 0.00 0.00 36.04 4.12
2851 3008 5.243060 GGTTGACTTTGCTAATAAGTTGGGT 59.757 40.000 0.00 0.00 36.04 4.51
2852 3009 6.431852 GGTTGACTTTGCTAATAAGTTGGGTA 59.568 38.462 0.00 0.00 36.04 3.69
2853 3010 7.122204 GGTTGACTTTGCTAATAAGTTGGGTAT 59.878 37.037 0.00 0.00 36.04 2.73
2854 3011 9.169592 GTTGACTTTGCTAATAAGTTGGGTATA 57.830 33.333 0.00 0.00 36.04 1.47
2855 3012 8.726870 TGACTTTGCTAATAAGTTGGGTATAC 57.273 34.615 0.00 0.00 36.04 1.47
2856 3013 8.545472 TGACTTTGCTAATAAGTTGGGTATACT 58.455 33.333 2.25 0.00 36.04 2.12
2858 3015 9.828039 ACTTTGCTAATAAGTTGGGTATACTAC 57.172 33.333 2.25 0.00 32.06 2.73
2860 3017 9.826574 TTTGCTAATAAGTTGGGTATACTACTG 57.173 33.333 2.25 0.00 0.00 2.74
2869 3026 6.439692 AGTTGGGTATACTACTGCTACTTGTT 59.560 38.462 2.25 0.00 0.00 2.83
2946 3103 7.046033 ACCTTATGGAGTATCGTTGGTAAAAG 58.954 38.462 0.81 0.00 34.37 2.27
2959 3116 6.037610 TCGTTGGTAAAAGCAATTGCAATTTT 59.962 30.769 30.89 27.32 45.16 1.82
3022 3179 8.461222 CCATTAATGACAAGATGCAGACTTAAA 58.539 33.333 17.23 0.02 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.191354 CTCATTGCCCTGCACGTGTG 62.191 60.000 18.38 10.39 38.71 3.82
1 2 1.968017 CTCATTGCCCTGCACGTGT 60.968 57.895 18.38 0.00 38.71 4.49
2 3 2.872557 CTCATTGCCCTGCACGTG 59.127 61.111 12.28 12.28 38.71 4.49
3 4 3.058160 GCTCATTGCCCTGCACGT 61.058 61.111 0.00 0.00 38.71 4.49
4 5 4.170062 CGCTCATTGCCCTGCACG 62.170 66.667 0.00 0.00 38.71 5.34
5 6 4.487412 GCGCTCATTGCCCTGCAC 62.487 66.667 0.00 0.00 38.71 4.57
6 7 4.728110 AGCGCTCATTGCCCTGCA 62.728 61.111 2.64 0.00 38.78 4.41
7 8 3.885521 GAGCGCTCATTGCCCTGC 61.886 66.667 31.91 0.42 38.78 4.85
8 9 2.437180 TGAGCGCTCATTGCCCTG 60.437 61.111 35.30 0.00 38.78 4.45
16 17 2.183478 TCTTTTTCCATGAGCGCTCA 57.817 45.000 39.63 39.63 44.59 4.26
17 18 2.414691 GGTTCTTTTTCCATGAGCGCTC 60.415 50.000 30.42 30.42 0.00 5.03
18 19 1.541588 GGTTCTTTTTCCATGAGCGCT 59.458 47.619 11.27 11.27 0.00 5.92
19 20 1.541588 AGGTTCTTTTTCCATGAGCGC 59.458 47.619 0.00 0.00 0.00 5.92
20 21 2.159653 CGAGGTTCTTTTTCCATGAGCG 60.160 50.000 0.00 0.00 0.00 5.03
21 22 2.414691 GCGAGGTTCTTTTTCCATGAGC 60.415 50.000 0.00 0.00 0.00 4.26
22 23 2.813754 TGCGAGGTTCTTTTTCCATGAG 59.186 45.455 0.00 0.00 0.00 2.90
23 24 2.857483 TGCGAGGTTCTTTTTCCATGA 58.143 42.857 0.00 0.00 0.00 3.07
24 25 3.191162 TCATGCGAGGTTCTTTTTCCATG 59.809 43.478 0.00 0.00 0.00 3.66
25 26 3.420893 TCATGCGAGGTTCTTTTTCCAT 58.579 40.909 0.00 0.00 0.00 3.41
26 27 2.857483 TCATGCGAGGTTCTTTTTCCA 58.143 42.857 0.00 0.00 0.00 3.53
27 28 3.565516 GTTCATGCGAGGTTCTTTTTCC 58.434 45.455 0.00 0.00 0.00 3.13
28 29 3.004315 TGGTTCATGCGAGGTTCTTTTTC 59.996 43.478 0.00 0.00 0.00 2.29
29 30 2.955660 TGGTTCATGCGAGGTTCTTTTT 59.044 40.909 0.00 0.00 0.00 1.94
30 31 2.293399 GTGGTTCATGCGAGGTTCTTTT 59.707 45.455 0.00 0.00 0.00 2.27
31 32 1.880027 GTGGTTCATGCGAGGTTCTTT 59.120 47.619 0.00 0.00 0.00 2.52
32 33 1.072331 AGTGGTTCATGCGAGGTTCTT 59.928 47.619 0.00 0.00 0.00 2.52
33 34 0.687354 AGTGGTTCATGCGAGGTTCT 59.313 50.000 0.00 0.00 0.00 3.01
34 35 1.523758 AAGTGGTTCATGCGAGGTTC 58.476 50.000 0.00 0.00 0.00 3.62
35 36 2.038557 AGTAAGTGGTTCATGCGAGGTT 59.961 45.455 0.00 0.00 0.00 3.50
36 37 1.623811 AGTAAGTGGTTCATGCGAGGT 59.376 47.619 0.00 0.00 0.00 3.85
37 38 2.386661 AGTAAGTGGTTCATGCGAGG 57.613 50.000 0.00 0.00 0.00 4.63
38 39 5.168569 TCTTTAGTAAGTGGTTCATGCGAG 58.831 41.667 0.00 0.00 32.98 5.03
39 40 5.142061 TCTTTAGTAAGTGGTTCATGCGA 57.858 39.130 0.00 0.00 32.98 5.10
40 41 5.856126 TTCTTTAGTAAGTGGTTCATGCG 57.144 39.130 0.00 0.00 32.98 4.73
41 42 7.377766 TCATTCTTTAGTAAGTGGTTCATGC 57.622 36.000 0.00 0.00 32.98 4.06
42 43 7.824289 TCCTCATTCTTTAGTAAGTGGTTCATG 59.176 37.037 0.00 0.00 32.98 3.07
43 44 7.824779 GTCCTCATTCTTTAGTAAGTGGTTCAT 59.175 37.037 0.00 0.00 32.98 2.57
44 45 7.159372 GTCCTCATTCTTTAGTAAGTGGTTCA 58.841 38.462 0.00 0.00 32.98 3.18
45 46 6.594547 GGTCCTCATTCTTTAGTAAGTGGTTC 59.405 42.308 0.00 0.00 32.98 3.62
46 47 6.272558 AGGTCCTCATTCTTTAGTAAGTGGTT 59.727 38.462 0.00 0.00 32.98 3.67
47 48 5.785940 AGGTCCTCATTCTTTAGTAAGTGGT 59.214 40.000 0.00 0.00 32.98 4.16
48 49 6.301169 AGGTCCTCATTCTTTAGTAAGTGG 57.699 41.667 0.00 0.00 32.98 4.00
49 50 9.372369 CTTTAGGTCCTCATTCTTTAGTAAGTG 57.628 37.037 0.00 0.00 32.98 3.16
50 51 9.322769 TCTTTAGGTCCTCATTCTTTAGTAAGT 57.677 33.333 0.00 0.00 32.98 2.24
53 54 8.204836 GCATCTTTAGGTCCTCATTCTTTAGTA 58.795 37.037 0.00 0.00 0.00 1.82
54 55 7.051000 GCATCTTTAGGTCCTCATTCTTTAGT 58.949 38.462 0.00 0.00 0.00 2.24
55 56 7.050377 TGCATCTTTAGGTCCTCATTCTTTAG 58.950 38.462 0.00 0.00 0.00 1.85
56 57 6.957631 TGCATCTTTAGGTCCTCATTCTTTA 58.042 36.000 0.00 0.00 0.00 1.85
57 58 5.819991 TGCATCTTTAGGTCCTCATTCTTT 58.180 37.500 0.00 0.00 0.00 2.52
58 59 5.441718 TGCATCTTTAGGTCCTCATTCTT 57.558 39.130 0.00 0.00 0.00 2.52
59 60 5.643421 ATGCATCTTTAGGTCCTCATTCT 57.357 39.130 0.00 0.00 0.00 2.40
60 61 6.705863 AAATGCATCTTTAGGTCCTCATTC 57.294 37.500 0.00 0.00 0.00 2.67
61 62 6.664816 TCAAAATGCATCTTTAGGTCCTCATT 59.335 34.615 0.00 0.00 0.00 2.57
62 63 6.189859 TCAAAATGCATCTTTAGGTCCTCAT 58.810 36.000 0.00 0.00 0.00 2.90
63 64 5.569355 TCAAAATGCATCTTTAGGTCCTCA 58.431 37.500 0.00 0.00 0.00 3.86
64 65 6.515272 TTCAAAATGCATCTTTAGGTCCTC 57.485 37.500 0.00 0.00 0.00 3.71
65 66 6.721208 TCTTTCAAAATGCATCTTTAGGTCCT 59.279 34.615 0.00 0.00 0.00 3.85
66 67 6.924111 TCTTTCAAAATGCATCTTTAGGTCC 58.076 36.000 0.00 0.00 0.00 4.46
67 68 8.992835 ATTCTTTCAAAATGCATCTTTAGGTC 57.007 30.769 0.00 0.00 0.00 3.85
84 85 9.010029 GGTGTCACTTTAATCCTAATTCTTTCA 57.990 33.333 2.35 0.00 0.00 2.69
85 86 8.459635 GGGTGTCACTTTAATCCTAATTCTTTC 58.540 37.037 2.35 0.00 0.00 2.62
86 87 7.396339 GGGGTGTCACTTTAATCCTAATTCTTT 59.604 37.037 2.35 0.00 0.00 2.52
87 88 6.890268 GGGGTGTCACTTTAATCCTAATTCTT 59.110 38.462 2.35 0.00 0.00 2.52
88 89 6.424032 GGGGTGTCACTTTAATCCTAATTCT 58.576 40.000 2.35 0.00 0.00 2.40
89 90 5.296035 CGGGGTGTCACTTTAATCCTAATTC 59.704 44.000 2.35 0.00 0.00 2.17
90 91 5.045432 TCGGGGTGTCACTTTAATCCTAATT 60.045 40.000 2.35 0.00 0.00 1.40
91 92 4.472108 TCGGGGTGTCACTTTAATCCTAAT 59.528 41.667 2.35 0.00 0.00 1.73
92 93 3.839490 TCGGGGTGTCACTTTAATCCTAA 59.161 43.478 2.35 0.00 0.00 2.69
93 94 3.443052 TCGGGGTGTCACTTTAATCCTA 58.557 45.455 2.35 0.00 0.00 2.94
94 95 2.262637 TCGGGGTGTCACTTTAATCCT 58.737 47.619 2.35 0.00 0.00 3.24
95 96 2.773993 TCGGGGTGTCACTTTAATCC 57.226 50.000 2.35 0.00 0.00 3.01
96 97 3.869065 TCATCGGGGTGTCACTTTAATC 58.131 45.455 2.35 0.00 0.00 1.75
97 98 3.992943 TCATCGGGGTGTCACTTTAAT 57.007 42.857 2.35 0.00 0.00 1.40
98 99 3.773418 TTCATCGGGGTGTCACTTTAA 57.227 42.857 2.35 0.00 0.00 1.52
99 100 3.071892 AGTTTCATCGGGGTGTCACTTTA 59.928 43.478 2.35 0.00 0.00 1.85
100 101 2.158667 AGTTTCATCGGGGTGTCACTTT 60.159 45.455 2.35 0.00 0.00 2.66
101 102 1.420138 AGTTTCATCGGGGTGTCACTT 59.580 47.619 2.35 0.00 0.00 3.16
102 103 1.056660 AGTTTCATCGGGGTGTCACT 58.943 50.000 2.35 0.00 0.00 3.41
103 104 1.892209 AAGTTTCATCGGGGTGTCAC 58.108 50.000 0.00 0.00 0.00 3.67
104 105 2.649531 AAAGTTTCATCGGGGTGTCA 57.350 45.000 0.00 0.00 0.00 3.58
105 106 3.439129 CCTAAAAGTTTCATCGGGGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
106 107 3.073356 TCCTAAAAGTTTCATCGGGGTGT 59.927 43.478 0.00 0.00 0.00 4.16
107 108 3.439129 GTCCTAAAAGTTTCATCGGGGTG 59.561 47.826 0.00 0.00 0.00 4.61
108 109 3.560668 GGTCCTAAAAGTTTCATCGGGGT 60.561 47.826 0.00 0.00 0.00 4.95
109 110 3.014623 GGTCCTAAAAGTTTCATCGGGG 58.985 50.000 0.00 0.00 0.00 5.73
110 111 2.676342 CGGTCCTAAAAGTTTCATCGGG 59.324 50.000 0.00 0.00 0.00 5.14
111 112 2.095372 GCGGTCCTAAAAGTTTCATCGG 59.905 50.000 0.00 0.00 0.00 4.18
112 113 2.095372 GGCGGTCCTAAAAGTTTCATCG 59.905 50.000 0.00 0.00 0.00 3.84
113 114 2.422479 GGGCGGTCCTAAAAGTTTCATC 59.578 50.000 0.00 0.00 0.00 2.92
114 115 2.443416 GGGCGGTCCTAAAAGTTTCAT 58.557 47.619 0.00 0.00 0.00 2.57
115 116 1.878948 CGGGCGGTCCTAAAAGTTTCA 60.879 52.381 0.00 0.00 0.00 2.69
116 117 0.800631 CGGGCGGTCCTAAAAGTTTC 59.199 55.000 0.00 0.00 0.00 2.78
117 118 0.109153 ACGGGCGGTCCTAAAAGTTT 59.891 50.000 0.00 0.00 0.00 2.66
118 119 0.604511 CACGGGCGGTCCTAAAAGTT 60.605 55.000 0.00 0.00 0.00 2.66
119 120 1.004200 CACGGGCGGTCCTAAAAGT 60.004 57.895 0.00 0.00 0.00 2.66
120 121 2.396157 GCACGGGCGGTCCTAAAAG 61.396 63.158 0.00 0.00 0.00 2.27
121 122 2.358984 GCACGGGCGGTCCTAAAA 60.359 61.111 0.00 0.00 0.00 1.52
122 123 2.472414 AATGCACGGGCGGTCCTAAA 62.472 55.000 4.58 0.00 45.35 1.85
123 124 2.472414 AAATGCACGGGCGGTCCTAA 62.472 55.000 4.58 0.00 45.35 2.69
124 125 1.615165 TAAATGCACGGGCGGTCCTA 61.615 55.000 4.58 0.00 45.35 2.94
125 126 2.472414 TTAAATGCACGGGCGGTCCT 62.472 55.000 4.58 0.00 45.35 3.85
126 127 2.041686 TTAAATGCACGGGCGGTCC 61.042 57.895 4.58 0.00 45.35 4.46
127 128 1.135939 GTTAAATGCACGGGCGGTC 59.864 57.895 4.58 0.00 45.35 4.79
128 129 1.302993 AGTTAAATGCACGGGCGGT 60.303 52.632 4.58 0.00 45.35 5.68
129 130 1.024579 AGAGTTAAATGCACGGGCGG 61.025 55.000 4.58 0.00 45.35 6.13
130 131 0.802494 AAGAGTTAAATGCACGGGCG 59.198 50.000 4.58 0.00 45.35 6.13
131 132 4.632538 ATAAAGAGTTAAATGCACGGGC 57.367 40.909 0.34 0.34 41.68 6.13
132 133 8.621286 AGAAATATAAAGAGTTAAATGCACGGG 58.379 33.333 0.00 0.00 0.00 5.28
133 134 9.651718 GAGAAATATAAAGAGTTAAATGCACGG 57.348 33.333 0.00 0.00 0.00 4.94
154 155 4.199310 CACCCACAGTTTTCTCAGAGAAA 58.801 43.478 19.96 19.96 42.00 2.52
163 164 2.794631 CGACAAAGCACCCACAGTTTTC 60.795 50.000 0.00 0.00 0.00 2.29
168 169 2.186160 TGCGACAAAGCACCCACAG 61.186 57.895 0.00 0.00 42.92 3.66
208 210 4.436998 CTCCCGGTCCACGTCAGC 62.437 72.222 0.00 0.00 42.24 4.26
209 211 1.246056 TTACTCCCGGTCCACGTCAG 61.246 60.000 0.00 0.00 42.24 3.51
333 336 0.240145 GGGCGGCTTTTAATATCGGC 59.760 55.000 9.56 0.00 43.92 5.54
430 452 6.608922 AGATTGGGGATATTTTTCTCCTCTG 58.391 40.000 0.00 0.00 37.16 3.35
433 455 6.623183 AGAGAGATTGGGGATATTTTTCTCCT 59.377 38.462 0.00 0.00 37.16 3.69
456 478 2.953247 TTATCGGAGGCGAGGCGAGA 62.953 60.000 0.00 0.00 0.00 4.04
457 479 2.071844 TTTATCGGAGGCGAGGCGAG 62.072 60.000 0.00 0.00 0.00 5.03
458 480 2.122797 TTTATCGGAGGCGAGGCGA 61.123 57.895 0.00 0.00 0.00 5.54
459 481 1.949631 GTTTATCGGAGGCGAGGCG 60.950 63.158 0.00 0.00 0.00 5.52
460 482 1.949631 CGTTTATCGGAGGCGAGGC 60.950 63.158 0.00 0.00 35.71 4.70
555 584 4.180946 CGACCGACAGCTCCTCCG 62.181 72.222 0.00 0.00 0.00 4.63
557 586 3.827898 CCCGACCGACAGCTCCTC 61.828 72.222 0.00 0.00 0.00 3.71
677 716 4.489771 AGCAAATCGGGGGCGGAG 62.490 66.667 0.00 0.00 0.00 4.63
678 717 4.483243 GAGCAAATCGGGGGCGGA 62.483 66.667 0.00 0.00 0.00 5.54
740 788 7.016153 TCACCAATCTTTTACATACCTCAGT 57.984 36.000 0.00 0.00 0.00 3.41
805 854 4.583489 GGATGAAGCAGAATCACCATCAAT 59.417 41.667 0.00 0.00 33.92 2.57
818 867 5.366460 ACATTAGAGACATGGATGAAGCAG 58.634 41.667 0.00 0.00 0.00 4.24
837 913 0.309612 GAACACGCACGGGAAACATT 59.690 50.000 0.00 0.00 0.00 2.71
849 925 1.569479 GGGAACAGCTCAGAACACGC 61.569 60.000 0.00 0.00 0.00 5.34
854 930 1.625818 GAGAAGGGGAACAGCTCAGAA 59.374 52.381 0.00 0.00 0.00 3.02
868 944 1.677217 CGCCTGAAGGAAAGGAGAAGG 60.677 57.143 0.00 0.00 36.79 3.46
967 1043 2.824041 CCGGGAATGGCAGGAACG 60.824 66.667 0.00 0.00 0.00 3.95
1053 1187 2.973899 GGCAGGCAGTCGAAGAGA 59.026 61.111 0.00 0.00 36.95 3.10
1101 1235 2.338984 GAACGCACGTCCTCCACT 59.661 61.111 0.00 0.00 0.00 4.00
1512 1649 2.043652 CTGGTGCCCCCAAGGATG 60.044 66.667 0.00 0.00 44.65 3.51
1659 1796 0.594028 GATAATGCCTCGTCGACGCA 60.594 55.000 32.19 24.10 39.60 5.24
1881 2018 2.033911 TGCAGCGCAATTCCTCCA 59.966 55.556 11.47 0.00 34.76 3.86
1971 2108 1.485397 CTCCAGAGATGAATGCGTCG 58.515 55.000 0.00 0.00 35.16 5.12
2017 2154 1.288350 CTCTTCATCAGCGCCTTCAG 58.712 55.000 2.29 0.00 0.00 3.02
2018 2155 0.107993 CCTCTTCATCAGCGCCTTCA 60.108 55.000 2.29 0.00 0.00 3.02
2163 2312 4.049186 ACTGTACAAAGAGCTAACACACG 58.951 43.478 0.00 0.00 0.00 4.49
2297 2451 7.583762 GTGAAAAATCAGCTTTGCAATAACAAC 59.416 33.333 0.00 0.00 0.00 3.32
2304 2458 4.370917 GGAGTGAAAAATCAGCTTTGCAA 58.629 39.130 0.00 0.00 0.00 4.08
2331 2485 3.340814 TCTCAACTGGCAGAATCCTTC 57.659 47.619 23.66 0.00 0.00 3.46
2370 2524 6.888632 AGTAGAGGCATCAAATGTCAAAATCT 59.111 34.615 0.00 0.00 37.34 2.40
2371 2525 7.093322 AGTAGAGGCATCAAATGTCAAAATC 57.907 36.000 0.00 0.00 37.34 2.17
2423 2577 1.891150 GGTTTCTCAGTCGGACAGGTA 59.109 52.381 11.27 0.00 0.00 3.08
2564 2718 5.470098 TGGAAGCATAAGAGAAGTTGTGAAC 59.530 40.000 0.00 0.00 0.00 3.18
2602 2759 3.623060 TCTGTGAAACTGCTGTGAAGTTC 59.377 43.478 0.00 0.00 36.87 3.01
2621 2778 2.544685 CCTCGTGTATGCTTCCTTCTG 58.455 52.381 0.00 0.00 0.00 3.02
2704 2861 8.127954 GCATCAGATTAGTCCTTTTCATTTCTC 58.872 37.037 0.00 0.00 0.00 2.87
2738 2895 2.432444 CTGTTCCCCTGCACGAATTTA 58.568 47.619 0.00 0.00 0.00 1.40
2797 2954 2.277084 CATCCTGGCAACCGTAACTAC 58.723 52.381 0.00 0.00 0.00 2.73
2827 2984 5.243060 ACCCAACTTATTAGCAAAGTCAACC 59.757 40.000 0.00 0.00 36.17 3.77
2854 3011 9.245481 AGATAAGAGTAAACAAGTAGCAGTAGT 57.755 33.333 0.00 0.00 0.00 2.73
2855 3012 9.724839 GAGATAAGAGTAAACAAGTAGCAGTAG 57.275 37.037 0.00 0.00 0.00 2.57
2856 3013 8.684520 GGAGATAAGAGTAAACAAGTAGCAGTA 58.315 37.037 0.00 0.00 0.00 2.74
2857 3014 7.397761 AGGAGATAAGAGTAAACAAGTAGCAGT 59.602 37.037 0.00 0.00 0.00 4.40
2858 3015 7.777095 AGGAGATAAGAGTAAACAAGTAGCAG 58.223 38.462 0.00 0.00 0.00 4.24
2859 3016 7.719871 AGGAGATAAGAGTAAACAAGTAGCA 57.280 36.000 0.00 0.00 0.00 3.49
2860 3017 8.874816 CAAAGGAGATAAGAGTAAACAAGTAGC 58.125 37.037 0.00 0.00 0.00 3.58
2869 3026 5.013704 TGCAACCCAAAGGAGATAAGAGTAA 59.986 40.000 0.00 0.00 36.73 2.24
3022 3179 3.168773 CCGAATCAAACGGGATGGT 57.831 52.632 0.00 0.00 45.65 3.55


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

AutoCloner maintained by Alex Coulton.