Multiple sequence alignment - TraesCS6A01G209300

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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 TraesCS6A01G209300 chr6A 100.000 2426 0 0 1 2426 378262131 378259706 0.000000e+00 4481.0
1 TraesCS6A01G209300 chr6A 95.547 539 23 1 1889 2426 596718706 596719244 0.000000e+00 861.0
2 TraesCS6A01G209300 chr6A 92.073 328 22 4 253 579 108087804 108087480 2.200000e-125 459.0
3 TraesCS6A01G209300 chr6A 97.487 199 5 0 1 199 378279707 378279509 8.310000e-90 340.0
4 TraesCS6A01G209300 chr6A 93.396 106 7 0 1 106 508616862 508616757 8.980000e-35 158.0
5 TraesCS6A01G209300 chr6A 89.655 87 8 1 1184 1269 596718095 596718181 2.550000e-20 110.0
6 TraesCS6A01G209300 chr6A 95.918 49 2 0 209 257 349889649 349889601 2.000000e-11 80.5
7 TraesCS6A01G209300 chr7A 97.089 1477 39 1 260 1732 23114481 23115957 0.000000e+00 2486.0
8 TraesCS6A01G209300 chr7A 99.077 650 5 1 1778 2426 23115950 23116599 0.000000e+00 1166.0
9 TraesCS6A01G209300 chr7A 95.362 539 24 1 1889 2426 280088648 280088110 0.000000e+00 856.0
10 TraesCS6A01G209300 chr7A 87.910 579 38 16 258 824 41256910 41256352 0.000000e+00 652.0
11 TraesCS6A01G209300 chr7A 89.674 184 7 5 25 199 89026657 89026837 8.730000e-55 224.0
12 TraesCS6A01G209300 chr7A 94.340 106 6 0 1 106 307981343 307981448 1.930000e-36 163.0
13 TraesCS6A01G209300 chr7A 83.060 183 16 2 1084 1253 65476517 65476697 4.180000e-33 152.0
14 TraesCS6A01G209300 chr7A 91.111 90 6 2 110 199 266810257 266810344 1.180000e-23 121.0
15 TraesCS6A01G209300 chr5A 85.204 1203 139 28 1259 2425 328014907 328013708 0.000000e+00 1199.0
16 TraesCS6A01G209300 chr5A 85.929 732 74 16 1719 2426 593097383 593096657 0.000000e+00 754.0
17 TraesCS6A01G209300 chr5A 92.000 100 6 2 90 189 362570689 362570786 3.250000e-29 139.0
18 TraesCS6A01G209300 chr3D 85.215 1001 106 28 1463 2426 416395679 416396674 0.000000e+00 990.0
19 TraesCS6A01G209300 chr3D 96.610 59 2 0 199 257 551083548 551083606 5.520000e-17 99.0
20 TraesCS6A01G209300 chr7D 95.176 539 25 1 1889 2426 45850567 45850029 0.000000e+00 850.0
21 TraesCS6A01G209300 chr2B 91.405 605 42 7 1828 2426 747759619 747760219 0.000000e+00 821.0
22 TraesCS6A01G209300 chr1D 94.063 539 28 2 1889 2426 292572631 292572096 0.000000e+00 815.0
23 TraesCS6A01G209300 chr6B 93.346 541 30 5 1889 2426 658977748 658977211 0.000000e+00 795.0
24 TraesCS6A01G209300 chr6B 89.362 188 16 3 640 824 678290029 678289843 1.450000e-57 233.0
25 TraesCS6A01G209300 chr1A 88.732 639 55 11 1797 2425 487614647 487614016 0.000000e+00 765.0
26 TraesCS6A01G209300 chr1A 83.607 183 15 2 1084 1253 118288719 118288539 8.980000e-35 158.0
27 TraesCS6A01G209300 chr3A 87.979 574 49 12 257 824 611173345 611173904 0.000000e+00 660.0
28 TraesCS6A01G209300 chr3A 93.871 310 18 1 258 566 742905568 742905877 1.310000e-127 466.0
29 TraesCS6A01G209300 chr3A 96.739 92 3 0 2 93 238768296 238768387 1.160000e-33 154.0
30 TraesCS6A01G209300 chr3A 96.739 92 3 0 5 96 494612589 494612498 1.160000e-33 154.0
31 TraesCS6A01G209300 chr3A 100.000 41 0 0 212 252 702415150 702415190 2.590000e-10 76.8
32 TraesCS6A01G209300 chr1B 88.091 571 45 11 257 824 554137993 554138543 0.000000e+00 656.0
33 TraesCS6A01G209300 chr7B 87.346 569 48 12 260 824 7260511 7261059 4.400000e-177 630.0
34 TraesCS6A01G209300 chr2A 87.086 573 54 12 258 824 720444599 720444041 4.400000e-177 630.0
35 TraesCS6A01G209300 chr2A 92.260 323 21 4 258 579 706640631 706640312 2.840000e-124 455.0
36 TraesCS6A01G209300 chr3B 86.733 505 43 15 280 780 770050872 770051356 7.630000e-150 540.0
37 TraesCS6A01G209300 chr3B 97.872 47 1 0 778 824 770063202 770063248 5.560000e-12 82.4
38 TraesCS6A01G209300 chr2D 85.175 371 30 13 459 824 634785979 634786329 8.250000e-95 357.0
39 TraesCS6A01G209300 chr4A 95.500 200 8 1 1 199 259639063 259638864 3.890000e-83 318.0
40 TraesCS6A01G209300 chr4A 95.000 200 9 1 1 199 259673241 259673042 1.810000e-81 313.0
41 TraesCS6A01G209300 chr4A 94.500 200 10 1 1 199 259615639 259615440 8.430000e-80 307.0
42 TraesCS6A01G209300 chr4A 90.000 140 8 6 64 199 491982319 491982456 2.480000e-40 176.0
43 TraesCS6A01G209300 chr4A 90.000 140 8 6 64 199 492025875 492026012 2.480000e-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 TraesCS6A01G209300 chr6A 378259706 378262131 2425 True 4481.0 4481 100.000 1 2426 1 chr6A.!!$R3 2425
1 TraesCS6A01G209300 chr6A 596718095 596719244 1149 False 485.5 861 92.601 1184 2426 2 chr6A.!!$F1 1242
2 TraesCS6A01G209300 chr7A 23114481 23116599 2118 False 1826.0 2486 98.083 260 2426 2 chr7A.!!$F5 2166
3 TraesCS6A01G209300 chr7A 280088110 280088648 538 True 856.0 856 95.362 1889 2426 1 chr7A.!!$R2 537
4 TraesCS6A01G209300 chr7A 41256352 41256910 558 True 652.0 652 87.910 258 824 1 chr7A.!!$R1 566
5 TraesCS6A01G209300 chr5A 328013708 328014907 1199 True 1199.0 1199 85.204 1259 2425 1 chr5A.!!$R1 1166
6 TraesCS6A01G209300 chr5A 593096657 593097383 726 True 754.0 754 85.929 1719 2426 1 chr5A.!!$R2 707
7 TraesCS6A01G209300 chr3D 416395679 416396674 995 False 990.0 990 85.215 1463 2426 1 chr3D.!!$F1 963
8 TraesCS6A01G209300 chr7D 45850029 45850567 538 True 850.0 850 95.176 1889 2426 1 chr7D.!!$R1 537
9 TraesCS6A01G209300 chr2B 747759619 747760219 600 False 821.0 821 91.405 1828 2426 1 chr2B.!!$F1 598
10 TraesCS6A01G209300 chr1D 292572096 292572631 535 True 815.0 815 94.063 1889 2426 1 chr1D.!!$R1 537
11 TraesCS6A01G209300 chr6B 658977211 658977748 537 True 795.0 795 93.346 1889 2426 1 chr6B.!!$R1 537
12 TraesCS6A01G209300 chr1A 487614016 487614647 631 True 765.0 765 88.732 1797 2425 1 chr1A.!!$R2 628
13 TraesCS6A01G209300 chr3A 611173345 611173904 559 False 660.0 660 87.979 257 824 1 chr3A.!!$F2 567
14 TraesCS6A01G209300 chr1B 554137993 554138543 550 False 656.0 656 88.091 257 824 1 chr1B.!!$F1 567
15 TraesCS6A01G209300 chr7B 7260511 7261059 548 False 630.0 630 87.346 260 824 1 chr7B.!!$F1 564
16 TraesCS6A01G209300 chr2A 720444041 720444599 558 True 630.0 630 87.086 258 824 1 chr2A.!!$R2 566

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
189 190 0.033894 AGGAACGAGAGGGAGAGGTC 60.034 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1791 0.03601 ACCCGAAGACATGAGGCTTG 60.036 55.0 0.0 0.0 0.0 4.01 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
27 28 3.869272 CGGCGCATCTGTTGGCTC 61.869 66.667 10.83 0.00 0.00 4.70
28 29 3.512516 GGCGCATCTGTTGGCTCC 61.513 66.667 10.83 0.00 0.00 4.70
29 30 2.437359 GCGCATCTGTTGGCTCCT 60.437 61.111 0.30 0.00 0.00 3.69
30 31 2.758089 GCGCATCTGTTGGCTCCTG 61.758 63.158 0.30 0.00 0.00 3.86
31 32 2.110967 CGCATCTGTTGGCTCCTGG 61.111 63.158 0.00 0.00 0.00 4.45
32 33 1.300963 GCATCTGTTGGCTCCTGGA 59.699 57.895 0.00 0.00 0.00 3.86
33 34 0.747283 GCATCTGTTGGCTCCTGGAG 60.747 60.000 19.55 19.55 0.00 3.86
56 57 4.821589 GCTTGACCGCGGAGGGAG 62.822 72.222 35.90 22.89 46.37 4.30
57 58 4.148825 CTTGACCGCGGAGGGAGG 62.149 72.222 35.90 12.47 46.37 4.30
81 82 4.200283 GCGCGAGGTGGAGGAGAG 62.200 72.222 12.10 0.00 0.00 3.20
82 83 3.522731 CGCGAGGTGGAGGAGAGG 61.523 72.222 0.00 0.00 0.00 3.69
83 84 2.043852 GCGAGGTGGAGGAGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
84 85 2.124693 GCGAGGTGGAGGAGAGGAG 61.125 68.421 0.00 0.00 0.00 3.69
85 86 2.124693 CGAGGTGGAGGAGAGGAGC 61.125 68.421 0.00 0.00 0.00 4.70
86 87 2.043450 AGGTGGAGGAGAGGAGCG 60.043 66.667 0.00 0.00 0.00 5.03
87 88 3.844090 GGTGGAGGAGAGGAGCGC 61.844 72.222 0.00 0.00 0.00 5.92
88 89 4.200283 GTGGAGGAGAGGAGCGCG 62.200 72.222 0.00 0.00 0.00 6.86
110 111 4.504916 CTCCTCCTGGCGCGTGAG 62.505 72.222 8.43 6.90 0.00 3.51
113 114 4.069232 CTCCTGGCGCGTGAGGAA 62.069 66.667 23.16 11.46 37.93 3.36
114 115 3.997064 CTCCTGGCGCGTGAGGAAG 62.997 68.421 23.16 15.58 37.93 3.46
115 116 4.069232 CCTGGCGCGTGAGGAAGA 62.069 66.667 17.77 0.00 0.00 2.87
116 117 2.507992 CTGGCGCGTGAGGAAGAG 60.508 66.667 8.43 0.00 0.00 2.85
117 118 2.989253 TGGCGCGTGAGGAAGAGA 60.989 61.111 8.43 0.00 0.00 3.10
118 119 2.202676 GGCGCGTGAGGAAGAGAG 60.203 66.667 8.43 0.00 0.00 3.20
119 120 2.883253 GCGCGTGAGGAAGAGAGC 60.883 66.667 8.43 0.00 0.00 4.09
120 121 2.578178 CGCGTGAGGAAGAGAGCG 60.578 66.667 0.00 0.00 41.56 5.03
121 122 2.878429 GCGTGAGGAAGAGAGCGA 59.122 61.111 0.00 0.00 0.00 4.93
122 123 1.226547 GCGTGAGGAAGAGAGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
123 124 1.649390 GCGTGAGGAAGAGAGCGAGA 61.649 60.000 0.00 0.00 0.00 4.04
124 125 0.376852 CGTGAGGAAGAGAGCGAGAG 59.623 60.000 0.00 0.00 0.00 3.20
125 126 0.738389 GTGAGGAAGAGAGCGAGAGG 59.262 60.000 0.00 0.00 0.00 3.69
126 127 0.621082 TGAGGAAGAGAGCGAGAGGA 59.379 55.000 0.00 0.00 0.00 3.71
127 128 1.308998 GAGGAAGAGAGCGAGAGGAG 58.691 60.000 0.00 0.00 0.00 3.69
128 129 0.106719 AGGAAGAGAGCGAGAGGAGG 60.107 60.000 0.00 0.00 0.00 4.30
129 130 0.106918 GGAAGAGAGCGAGAGGAGGA 60.107 60.000 0.00 0.00 0.00 3.71
130 131 1.683629 GGAAGAGAGCGAGAGGAGGAA 60.684 57.143 0.00 0.00 0.00 3.36
131 132 1.676006 GAAGAGAGCGAGAGGAGGAAG 59.324 57.143 0.00 0.00 0.00 3.46
132 133 0.916086 AGAGAGCGAGAGGAGGAAGA 59.084 55.000 0.00 0.00 0.00 2.87
133 134 1.134098 AGAGAGCGAGAGGAGGAAGAG 60.134 57.143 0.00 0.00 0.00 2.85
134 135 0.916086 AGAGCGAGAGGAGGAAGAGA 59.084 55.000 0.00 0.00 0.00 3.10
135 136 1.494721 AGAGCGAGAGGAGGAAGAGAT 59.505 52.381 0.00 0.00 0.00 2.75
136 137 1.608590 GAGCGAGAGGAGGAAGAGATG 59.391 57.143 0.00 0.00 0.00 2.90
137 138 0.673437 GCGAGAGGAGGAAGAGATGG 59.327 60.000 0.00 0.00 0.00 3.51
138 139 1.327303 CGAGAGGAGGAAGAGATGGG 58.673 60.000 0.00 0.00 0.00 4.00
139 140 1.715785 GAGAGGAGGAAGAGATGGGG 58.284 60.000 0.00 0.00 0.00 4.96
140 141 1.219213 GAGAGGAGGAAGAGATGGGGA 59.781 57.143 0.00 0.00 0.00 4.81
141 142 1.872367 AGAGGAGGAAGAGATGGGGAT 59.128 52.381 0.00 0.00 0.00 3.85
142 143 2.158173 AGAGGAGGAAGAGATGGGGATC 60.158 54.545 0.00 0.00 0.00 3.36
143 144 0.972883 GGAGGAAGAGATGGGGATCG 59.027 60.000 0.00 0.00 0.00 3.69
144 145 1.481428 GGAGGAAGAGATGGGGATCGA 60.481 57.143 0.00 0.00 0.00 3.59
145 146 1.892474 GAGGAAGAGATGGGGATCGAG 59.108 57.143 0.00 0.00 0.00 4.04
146 147 0.320050 GGAAGAGATGGGGATCGAGC 59.680 60.000 0.00 0.00 0.00 5.03
147 148 0.038709 GAAGAGATGGGGATCGAGCG 60.039 60.000 0.00 0.00 0.00 5.03
148 149 0.468214 AAGAGATGGGGATCGAGCGA 60.468 55.000 0.00 0.00 0.00 4.93
149 150 0.251564 AGAGATGGGGATCGAGCGAT 60.252 55.000 4.89 4.89 37.59 4.58
150 151 0.108898 GAGATGGGGATCGAGCGATG 60.109 60.000 10.42 0.00 34.60 3.84
151 152 1.739562 GATGGGGATCGAGCGATGC 60.740 63.158 14.75 14.75 41.36 3.91
152 153 3.580100 ATGGGGATCGAGCGATGCG 62.580 63.158 16.18 0.00 42.71 4.73
155 156 4.286320 GGATCGAGCGATGCGGGT 62.286 66.667 10.42 0.00 33.57 5.28
156 157 3.032609 GATCGAGCGATGCGGGTG 61.033 66.667 10.42 0.00 34.60 4.61
157 158 3.774959 GATCGAGCGATGCGGGTGT 62.775 63.158 10.42 0.00 34.60 4.16
158 159 4.794439 TCGAGCGATGCGGGTGTG 62.794 66.667 0.00 0.00 0.00 3.82
179 180 4.373116 GCGGGCACAGGAACGAGA 62.373 66.667 0.00 0.00 0.00 4.04
180 181 2.125912 CGGGCACAGGAACGAGAG 60.126 66.667 0.00 0.00 0.00 3.20
181 182 2.266055 GGGCACAGGAACGAGAGG 59.734 66.667 0.00 0.00 0.00 3.69
182 183 2.266055 GGCACAGGAACGAGAGGG 59.734 66.667 0.00 0.00 0.00 4.30
183 184 2.283529 GGCACAGGAACGAGAGGGA 61.284 63.158 0.00 0.00 0.00 4.20
184 185 1.216710 GCACAGGAACGAGAGGGAG 59.783 63.158 0.00 0.00 0.00 4.30
185 186 1.251527 GCACAGGAACGAGAGGGAGA 61.252 60.000 0.00 0.00 0.00 3.71
186 187 0.814457 CACAGGAACGAGAGGGAGAG 59.186 60.000 0.00 0.00 0.00 3.20
187 188 0.323908 ACAGGAACGAGAGGGAGAGG 60.324 60.000 0.00 0.00 0.00 3.69
188 189 0.323908 CAGGAACGAGAGGGAGAGGT 60.324 60.000 0.00 0.00 0.00 3.85
189 190 0.033894 AGGAACGAGAGGGAGAGGTC 60.034 60.000 0.00 0.00 0.00 3.85
190 191 1.378124 GGAACGAGAGGGAGAGGTCG 61.378 65.000 0.00 0.00 38.40 4.79
191 192 1.378124 GAACGAGAGGGAGAGGTCGG 61.378 65.000 0.00 0.00 36.74 4.79
192 193 2.517402 CGAGAGGGAGAGGTCGGG 60.517 72.222 0.00 0.00 0.00 5.14
193 194 2.123640 GAGAGGGAGAGGTCGGGG 60.124 72.222 0.00 0.00 0.00 5.73
194 195 4.467107 AGAGGGAGAGGTCGGGGC 62.467 72.222 0.00 0.00 0.00 5.80
197 198 4.153330 GGGAGAGGTCGGGGCCTA 62.153 72.222 0.84 0.00 39.34 3.93
198 199 2.522193 GGAGAGGTCGGGGCCTAG 60.522 72.222 0.84 0.00 39.34 3.02
199 200 2.279408 GAGAGGTCGGGGCCTAGT 59.721 66.667 0.84 0.00 39.34 2.57
200 201 1.829096 GAGAGGTCGGGGCCTAGTC 60.829 68.421 0.84 0.00 39.34 2.59
201 202 2.043248 GAGGTCGGGGCCTAGTCA 60.043 66.667 0.84 0.00 39.34 3.41
202 203 2.363925 AGGTCGGGGCCTAGTCAC 60.364 66.667 0.84 0.00 37.04 3.67
203 204 3.834799 GGTCGGGGCCTAGTCACG 61.835 72.222 0.84 0.00 0.00 4.35
204 205 4.509737 GTCGGGGCCTAGTCACGC 62.510 72.222 0.84 0.00 0.00 5.34
205 206 4.753662 TCGGGGCCTAGTCACGCT 62.754 66.667 0.84 0.00 0.00 5.07
206 207 4.514577 CGGGGCCTAGTCACGCTG 62.515 72.222 0.84 0.00 0.00 5.18
207 208 4.840005 GGGGCCTAGTCACGCTGC 62.840 72.222 0.84 0.00 0.00 5.25
208 209 4.082523 GGGCCTAGTCACGCTGCA 62.083 66.667 0.84 0.00 0.00 4.41
209 210 2.510238 GGCCTAGTCACGCTGCAG 60.510 66.667 10.11 10.11 0.00 4.41
210 211 2.510238 GCCTAGTCACGCTGCAGG 60.510 66.667 17.12 8.27 0.00 4.85
211 212 2.973899 CCTAGTCACGCTGCAGGT 59.026 61.111 17.12 8.98 0.00 4.00
212 213 1.446792 CCTAGTCACGCTGCAGGTG 60.447 63.158 22.21 22.21 36.74 4.00
213 214 1.446792 CTAGTCACGCTGCAGGTGG 60.447 63.158 25.49 12.41 36.09 4.61
214 215 1.877576 CTAGTCACGCTGCAGGTGGA 61.878 60.000 25.49 14.84 36.09 4.02
215 216 1.877576 TAGTCACGCTGCAGGTGGAG 61.878 60.000 25.49 9.14 36.09 3.86
216 217 4.007644 TCACGCTGCAGGTGGAGG 62.008 66.667 25.49 8.87 36.09 4.30
217 218 4.320456 CACGCTGCAGGTGGAGGT 62.320 66.667 17.12 0.00 33.79 3.85
218 219 4.320456 ACGCTGCAGGTGGAGGTG 62.320 66.667 17.12 0.00 33.79 4.00
220 221 4.729918 GCTGCAGGTGGAGGTGGG 62.730 72.222 17.12 0.00 33.79 4.61
221 222 2.930019 CTGCAGGTGGAGGTGGGA 60.930 66.667 5.57 0.00 0.00 4.37
222 223 2.449518 TGCAGGTGGAGGTGGGAA 60.450 61.111 0.00 0.00 0.00 3.97
223 224 1.852157 TGCAGGTGGAGGTGGGAAT 60.852 57.895 0.00 0.00 0.00 3.01
224 225 0.548926 TGCAGGTGGAGGTGGGAATA 60.549 55.000 0.00 0.00 0.00 1.75
225 226 0.623723 GCAGGTGGAGGTGGGAATAA 59.376 55.000 0.00 0.00 0.00 1.40
226 227 1.408822 GCAGGTGGAGGTGGGAATAAG 60.409 57.143 0.00 0.00 0.00 1.73
227 228 1.916181 CAGGTGGAGGTGGGAATAAGT 59.084 52.381 0.00 0.00 0.00 2.24
228 229 1.916181 AGGTGGAGGTGGGAATAAGTG 59.084 52.381 0.00 0.00 0.00 3.16
229 230 1.064685 GGTGGAGGTGGGAATAAGTGG 60.065 57.143 0.00 0.00 0.00 4.00
230 231 1.064685 GTGGAGGTGGGAATAAGTGGG 60.065 57.143 0.00 0.00 0.00 4.61
231 232 1.203505 TGGAGGTGGGAATAAGTGGGA 60.204 52.381 0.00 0.00 0.00 4.37
232 233 1.212195 GGAGGTGGGAATAAGTGGGAC 59.788 57.143 0.00 0.00 0.00 4.46
233 234 2.197465 GAGGTGGGAATAAGTGGGACT 58.803 52.381 0.00 0.00 0.00 3.85
234 235 3.381335 GAGGTGGGAATAAGTGGGACTA 58.619 50.000 0.00 0.00 0.00 2.59
235 236 3.385115 AGGTGGGAATAAGTGGGACTAG 58.615 50.000 0.00 0.00 0.00 2.57
236 237 3.013648 AGGTGGGAATAAGTGGGACTAGA 59.986 47.826 0.00 0.00 0.00 2.43
237 238 3.778629 GGTGGGAATAAGTGGGACTAGAA 59.221 47.826 0.00 0.00 0.00 2.10
238 239 4.412528 GGTGGGAATAAGTGGGACTAGAAT 59.587 45.833 0.00 0.00 0.00 2.40
239 240 5.104067 GGTGGGAATAAGTGGGACTAGAATT 60.104 44.000 0.00 0.00 0.00 2.17
240 241 6.056236 GTGGGAATAAGTGGGACTAGAATTC 58.944 44.000 0.00 0.00 0.00 2.17
241 242 5.132144 TGGGAATAAGTGGGACTAGAATTCC 59.868 44.000 0.65 12.64 39.23 3.01
249 250 3.493767 GGACTAGAATTCCCATCCCAC 57.506 52.381 0.65 0.00 0.00 4.61
250 251 3.049344 GGACTAGAATTCCCATCCCACT 58.951 50.000 0.65 0.00 0.00 4.00
251 252 3.459969 GGACTAGAATTCCCATCCCACTT 59.540 47.826 0.65 0.00 0.00 3.16
252 253 4.658901 GGACTAGAATTCCCATCCCACTTA 59.341 45.833 0.65 0.00 0.00 2.24
253 254 5.132144 GGACTAGAATTCCCATCCCACTTAA 59.868 44.000 0.65 0.00 0.00 1.85
254 255 6.353602 GGACTAGAATTCCCATCCCACTTAAA 60.354 42.308 0.65 0.00 0.00 1.52
255 256 7.039722 ACTAGAATTCCCATCCCACTTAAAA 57.960 36.000 0.65 0.00 0.00 1.52
520 521 9.875675 CAAACTCTCTCATTCTTTACTTTTCAG 57.124 33.333 0.00 0.00 0.00 3.02
541 543 5.061684 TCAGTCAAAATACGTTATCAGCACG 59.938 40.000 0.00 0.00 43.52 5.34
542 544 5.061684 CAGTCAAAATACGTTATCAGCACGA 59.938 40.000 0.00 0.00 40.20 4.35
605 624 3.139029 CCTAACAGACGAGGCCAAC 57.861 57.895 5.01 0.00 0.00 3.77
606 625 0.736325 CCTAACAGACGAGGCCAACG 60.736 60.000 18.24 18.24 0.00 4.10
607 626 0.242825 CTAACAGACGAGGCCAACGA 59.757 55.000 24.75 4.61 34.70 3.85
608 627 0.675083 TAACAGACGAGGCCAACGAA 59.325 50.000 24.75 4.50 34.70 3.85
609 628 0.600255 AACAGACGAGGCCAACGAAG 60.600 55.000 24.75 16.35 34.70 3.79
610 629 1.289066 CAGACGAGGCCAACGAAGA 59.711 57.895 24.75 0.00 34.70 2.87
611 630 0.319555 CAGACGAGGCCAACGAAGAA 60.320 55.000 24.75 0.00 34.70 2.52
612 631 0.319641 AGACGAGGCCAACGAAGAAC 60.320 55.000 24.75 12.12 34.70 3.01
613 632 0.599204 GACGAGGCCAACGAAGAACA 60.599 55.000 24.75 0.00 34.70 3.18
614 633 0.878961 ACGAGGCCAACGAAGAACAC 60.879 55.000 24.75 0.00 34.70 3.32
615 634 1.860078 GAGGCCAACGAAGAACACG 59.140 57.895 5.01 0.00 0.00 4.49
616 635 2.171489 GAGGCCAACGAAGAACACGC 62.171 60.000 5.01 0.00 0.00 5.34
617 636 2.127758 GCCAACGAAGAACACGCG 60.128 61.111 3.53 3.53 0.00 6.01
971 1008 2.747460 GCCTTCGCCATGACAGCA 60.747 61.111 0.00 0.00 0.00 4.41
982 1019 1.855441 ATGACAGCATGGAGGCCACA 61.855 55.000 5.01 3.49 43.62 4.17
1094 1131 4.722700 CCCCACACCGGCTCAAGG 62.723 72.222 0.00 0.00 0.00 3.61
1472 1532 1.326548 CGGCGTCTAGAAAAATTCCCG 59.673 52.381 0.00 0.00 0.00 5.14
1697 1808 3.181503 CCATTTCAAGCCTCATGTCTTCG 60.182 47.826 0.00 0.00 0.00 3.79
1748 1874 6.867662 ATTGCCTCAGTAATACTATTGCAC 57.132 37.500 8.70 0.00 0.00 4.57
2346 2507 7.931948 GTCTACACATATGGTTATAAAGCACCT 59.068 37.037 7.80 0.00 42.32 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.869272 GAGCCAACAGATGCGCCG 61.869 66.667 4.18 0.00 0.00 6.46
11 12 3.512516 GGAGCCAACAGATGCGCC 61.513 66.667 4.18 0.00 40.22 6.53
12 13 2.437359 AGGAGCCAACAGATGCGC 60.437 61.111 0.00 0.00 0.00 6.09
13 14 2.110967 CCAGGAGCCAACAGATGCG 61.111 63.158 0.00 0.00 0.00 4.73
14 15 0.747283 CTCCAGGAGCCAACAGATGC 60.747 60.000 2.60 0.00 0.00 3.91
15 16 3.473147 CTCCAGGAGCCAACAGATG 57.527 57.895 2.60 0.00 0.00 2.90
39 40 4.821589 CTCCCTCCGCGGTCAAGC 62.822 72.222 27.15 0.00 0.00 4.01
40 41 4.148825 CCTCCCTCCGCGGTCAAG 62.149 72.222 27.15 15.59 0.00 3.02
64 65 4.200283 CTCTCCTCCACCTCGCGC 62.200 72.222 0.00 0.00 0.00 6.86
65 66 3.522731 CCTCTCCTCCACCTCGCG 61.523 72.222 0.00 0.00 0.00 5.87
66 67 2.043852 TCCTCTCCTCCACCTCGC 60.044 66.667 0.00 0.00 0.00 5.03
67 68 2.124693 GCTCCTCTCCTCCACCTCG 61.125 68.421 0.00 0.00 0.00 4.63
68 69 2.124693 CGCTCCTCTCCTCCACCTC 61.125 68.421 0.00 0.00 0.00 3.85
69 70 2.043450 CGCTCCTCTCCTCCACCT 60.043 66.667 0.00 0.00 0.00 4.00
70 71 3.844090 GCGCTCCTCTCCTCCACC 61.844 72.222 0.00 0.00 0.00 4.61
71 72 4.200283 CGCGCTCCTCTCCTCCAC 62.200 72.222 5.56 0.00 0.00 4.02
93 94 4.504916 CTCACGCGCCAGGAGGAG 62.505 72.222 5.73 0.00 36.89 3.69
96 97 3.997064 CTTCCTCACGCGCCAGGAG 62.997 68.421 22.05 15.97 40.05 3.69
97 98 4.069232 CTTCCTCACGCGCCAGGA 62.069 66.667 20.02 20.02 37.00 3.86
98 99 3.997064 CTCTTCCTCACGCGCCAGG 62.997 68.421 16.21 16.21 0.00 4.45
99 100 2.507992 CTCTTCCTCACGCGCCAG 60.508 66.667 5.73 0.99 0.00 4.85
100 101 2.989253 TCTCTTCCTCACGCGCCA 60.989 61.111 5.73 0.00 0.00 5.69
101 102 2.202676 CTCTCTTCCTCACGCGCC 60.203 66.667 5.73 0.00 0.00 6.53
102 103 2.883253 GCTCTCTTCCTCACGCGC 60.883 66.667 5.73 0.00 0.00 6.86
103 104 2.578178 CGCTCTCTTCCTCACGCG 60.578 66.667 3.53 3.53 34.50 6.01
104 105 1.226547 CTCGCTCTCTTCCTCACGC 60.227 63.158 0.00 0.00 0.00 5.34
105 106 0.376852 CTCTCGCTCTCTTCCTCACG 59.623 60.000 0.00 0.00 0.00 4.35
106 107 0.738389 CCTCTCGCTCTCTTCCTCAC 59.262 60.000 0.00 0.00 0.00 3.51
107 108 0.621082 TCCTCTCGCTCTCTTCCTCA 59.379 55.000 0.00 0.00 0.00 3.86
108 109 1.308998 CTCCTCTCGCTCTCTTCCTC 58.691 60.000 0.00 0.00 0.00 3.71
109 110 0.106719 CCTCCTCTCGCTCTCTTCCT 60.107 60.000 0.00 0.00 0.00 3.36
110 111 0.106918 TCCTCCTCTCGCTCTCTTCC 60.107 60.000 0.00 0.00 0.00 3.46
111 112 1.676006 CTTCCTCCTCTCGCTCTCTTC 59.324 57.143 0.00 0.00 0.00 2.87
112 113 1.283613 TCTTCCTCCTCTCGCTCTCTT 59.716 52.381 0.00 0.00 0.00 2.85
113 114 0.916086 TCTTCCTCCTCTCGCTCTCT 59.084 55.000 0.00 0.00 0.00 3.10
114 115 1.134220 TCTCTTCCTCCTCTCGCTCTC 60.134 57.143 0.00 0.00 0.00 3.20
115 116 0.916086 TCTCTTCCTCCTCTCGCTCT 59.084 55.000 0.00 0.00 0.00 4.09
116 117 1.608590 CATCTCTTCCTCCTCTCGCTC 59.391 57.143 0.00 0.00 0.00 5.03
117 118 1.691196 CATCTCTTCCTCCTCTCGCT 58.309 55.000 0.00 0.00 0.00 4.93
118 119 0.673437 CCATCTCTTCCTCCTCTCGC 59.327 60.000 0.00 0.00 0.00 5.03
119 120 1.327303 CCCATCTCTTCCTCCTCTCG 58.673 60.000 0.00 0.00 0.00 4.04
120 121 1.219213 TCCCCATCTCTTCCTCCTCTC 59.781 57.143 0.00 0.00 0.00 3.20
121 122 1.324014 TCCCCATCTCTTCCTCCTCT 58.676 55.000 0.00 0.00 0.00 3.69
122 123 2.256306 GATCCCCATCTCTTCCTCCTC 58.744 57.143 0.00 0.00 0.00 3.71
123 124 1.482177 CGATCCCCATCTCTTCCTCCT 60.482 57.143 0.00 0.00 0.00 3.69
124 125 0.972883 CGATCCCCATCTCTTCCTCC 59.027 60.000 0.00 0.00 0.00 4.30
125 126 1.892474 CTCGATCCCCATCTCTTCCTC 59.108 57.143 0.00 0.00 0.00 3.71
126 127 2.008242 CTCGATCCCCATCTCTTCCT 57.992 55.000 0.00 0.00 0.00 3.36
127 128 0.320050 GCTCGATCCCCATCTCTTCC 59.680 60.000 0.00 0.00 0.00 3.46
128 129 0.038709 CGCTCGATCCCCATCTCTTC 60.039 60.000 0.00 0.00 0.00 2.87
129 130 0.468214 TCGCTCGATCCCCATCTCTT 60.468 55.000 0.00 0.00 0.00 2.85
130 131 0.251564 ATCGCTCGATCCCCATCTCT 60.252 55.000 0.00 0.00 0.00 3.10
131 132 0.108898 CATCGCTCGATCCCCATCTC 60.109 60.000 1.30 0.00 31.62 2.75
132 133 1.970639 CATCGCTCGATCCCCATCT 59.029 57.895 1.30 0.00 31.62 2.90
133 134 1.739562 GCATCGCTCGATCCCCATC 60.740 63.158 1.30 0.00 31.62 3.51
134 135 2.345244 GCATCGCTCGATCCCCAT 59.655 61.111 1.30 0.00 31.62 4.00
135 136 4.284860 CGCATCGCTCGATCCCCA 62.285 66.667 1.30 0.00 31.62 4.96
138 139 4.286320 ACCCGCATCGCTCGATCC 62.286 66.667 1.30 0.00 31.62 3.36
139 140 3.032609 CACCCGCATCGCTCGATC 61.033 66.667 1.30 0.00 31.62 3.69
140 141 3.838271 ACACCCGCATCGCTCGAT 61.838 61.111 0.00 0.00 34.81 3.59
141 142 4.794439 CACACCCGCATCGCTCGA 62.794 66.667 0.00 0.00 0.00 4.04
162 163 4.373116 TCTCGTTCCTGTGCCCGC 62.373 66.667 0.00 0.00 0.00 6.13
163 164 2.125912 CTCTCGTTCCTGTGCCCG 60.126 66.667 0.00 0.00 0.00 6.13
164 165 2.266055 CCTCTCGTTCCTGTGCCC 59.734 66.667 0.00 0.00 0.00 5.36
165 166 2.232298 CTCCCTCTCGTTCCTGTGCC 62.232 65.000 0.00 0.00 0.00 5.01
166 167 1.216710 CTCCCTCTCGTTCCTGTGC 59.783 63.158 0.00 0.00 0.00 4.57
167 168 0.814457 CTCTCCCTCTCGTTCCTGTG 59.186 60.000 0.00 0.00 0.00 3.66
168 169 0.323908 CCTCTCCCTCTCGTTCCTGT 60.324 60.000 0.00 0.00 0.00 4.00
169 170 0.323908 ACCTCTCCCTCTCGTTCCTG 60.324 60.000 0.00 0.00 0.00 3.86
170 171 0.033894 GACCTCTCCCTCTCGTTCCT 60.034 60.000 0.00 0.00 0.00 3.36
171 172 1.378124 CGACCTCTCCCTCTCGTTCC 61.378 65.000 0.00 0.00 0.00 3.62
172 173 1.378124 CCGACCTCTCCCTCTCGTTC 61.378 65.000 0.00 0.00 0.00 3.95
173 174 1.378778 CCGACCTCTCCCTCTCGTT 60.379 63.158 0.00 0.00 0.00 3.85
174 175 2.272797 CCGACCTCTCCCTCTCGT 59.727 66.667 0.00 0.00 0.00 4.18
175 176 2.517402 CCCGACCTCTCCCTCTCG 60.517 72.222 0.00 0.00 0.00 4.04
176 177 2.123640 CCCCGACCTCTCCCTCTC 60.124 72.222 0.00 0.00 0.00 3.20
177 178 4.467107 GCCCCGACCTCTCCCTCT 62.467 72.222 0.00 0.00 0.00 3.69
180 181 4.153330 TAGGCCCCGACCTCTCCC 62.153 72.222 0.00 0.00 41.50 4.30
181 182 2.522193 CTAGGCCCCGACCTCTCC 60.522 72.222 0.00 0.00 41.50 3.71
182 183 1.829096 GACTAGGCCCCGACCTCTC 60.829 68.421 0.00 0.00 41.50 3.20
183 184 2.279408 GACTAGGCCCCGACCTCT 59.721 66.667 0.00 0.00 41.50 3.69
184 185 2.043248 TGACTAGGCCCCGACCTC 60.043 66.667 0.00 0.00 41.50 3.85
185 186 2.363925 GTGACTAGGCCCCGACCT 60.364 66.667 0.00 0.00 44.31 3.85
186 187 3.834799 CGTGACTAGGCCCCGACC 61.835 72.222 0.00 0.00 0.00 4.79
187 188 4.509737 GCGTGACTAGGCCCCGAC 62.510 72.222 8.80 0.00 0.00 4.79
188 189 4.753662 AGCGTGACTAGGCCCCGA 62.754 66.667 8.80 0.00 38.43 5.14
189 190 4.514577 CAGCGTGACTAGGCCCCG 62.515 72.222 0.00 0.00 38.43 5.73
190 191 4.840005 GCAGCGTGACTAGGCCCC 62.840 72.222 0.00 0.00 38.43 5.80
191 192 4.082523 TGCAGCGTGACTAGGCCC 62.083 66.667 0.00 0.00 38.43 5.80
192 193 2.510238 CTGCAGCGTGACTAGGCC 60.510 66.667 0.00 0.00 38.43 5.19
193 194 2.510238 CCTGCAGCGTGACTAGGC 60.510 66.667 8.66 0.00 37.95 3.93
194 195 1.446792 CACCTGCAGCGTGACTAGG 60.447 63.158 23.25 5.52 32.77 3.02
195 196 1.446792 CCACCTGCAGCGTGACTAG 60.447 63.158 27.05 12.99 32.77 2.57
196 197 1.877576 CTCCACCTGCAGCGTGACTA 61.878 60.000 27.05 15.61 32.77 2.59
197 198 3.231889 CTCCACCTGCAGCGTGACT 62.232 63.158 27.05 0.00 32.77 3.41
198 199 2.740055 CTCCACCTGCAGCGTGAC 60.740 66.667 27.05 0.00 32.77 3.67
199 200 4.007644 CCTCCACCTGCAGCGTGA 62.008 66.667 27.05 14.38 32.77 4.35
200 201 4.320456 ACCTCCACCTGCAGCGTG 62.320 66.667 21.62 21.62 0.00 5.34
201 202 4.320456 CACCTCCACCTGCAGCGT 62.320 66.667 8.66 4.99 0.00 5.07
203 204 4.729918 CCCACCTCCACCTGCAGC 62.730 72.222 8.66 0.00 0.00 5.25
204 205 1.856539 ATTCCCACCTCCACCTGCAG 61.857 60.000 6.78 6.78 0.00 4.41
205 206 0.548926 TATTCCCACCTCCACCTGCA 60.549 55.000 0.00 0.00 0.00 4.41
206 207 0.623723 TTATTCCCACCTCCACCTGC 59.376 55.000 0.00 0.00 0.00 4.85
207 208 1.916181 ACTTATTCCCACCTCCACCTG 59.084 52.381 0.00 0.00 0.00 4.00
208 209 1.916181 CACTTATTCCCACCTCCACCT 59.084 52.381 0.00 0.00 0.00 4.00
209 210 1.064685 CCACTTATTCCCACCTCCACC 60.065 57.143 0.00 0.00 0.00 4.61
210 211 1.064685 CCCACTTATTCCCACCTCCAC 60.065 57.143 0.00 0.00 0.00 4.02
211 212 1.203505 TCCCACTTATTCCCACCTCCA 60.204 52.381 0.00 0.00 0.00 3.86
212 213 1.212195 GTCCCACTTATTCCCACCTCC 59.788 57.143 0.00 0.00 0.00 4.30
213 214 2.197465 AGTCCCACTTATTCCCACCTC 58.803 52.381 0.00 0.00 0.00 3.85
214 215 2.361085 AGTCCCACTTATTCCCACCT 57.639 50.000 0.00 0.00 0.00 4.00
215 216 3.381335 TCTAGTCCCACTTATTCCCACC 58.619 50.000 0.00 0.00 0.00 4.61
216 217 5.632034 ATTCTAGTCCCACTTATTCCCAC 57.368 43.478 0.00 0.00 0.00 4.61
217 218 5.132144 GGAATTCTAGTCCCACTTATTCCCA 59.868 44.000 5.23 0.00 35.59 4.37
218 219 5.622180 GGAATTCTAGTCCCACTTATTCCC 58.378 45.833 5.23 0.00 35.59 3.97
229 230 3.049344 AGTGGGATGGGAATTCTAGTCC 58.951 50.000 5.23 9.66 0.00 3.85
230 231 4.779993 AAGTGGGATGGGAATTCTAGTC 57.220 45.455 5.23 1.17 0.00 2.59
231 232 6.652205 TTTAAGTGGGATGGGAATTCTAGT 57.348 37.500 5.23 0.00 0.00 2.57
232 233 7.067494 CAGTTTTAAGTGGGATGGGAATTCTAG 59.933 40.741 5.23 0.00 0.00 2.43
233 234 6.889722 CAGTTTTAAGTGGGATGGGAATTCTA 59.110 38.462 5.23 0.00 0.00 2.10
234 235 5.716703 CAGTTTTAAGTGGGATGGGAATTCT 59.283 40.000 5.23 0.00 0.00 2.40
235 236 5.480422 ACAGTTTTAAGTGGGATGGGAATTC 59.520 40.000 0.00 0.00 33.62 2.17
236 237 5.402630 ACAGTTTTAAGTGGGATGGGAATT 58.597 37.500 2.66 0.00 33.62 2.17
237 238 5.010708 ACAGTTTTAAGTGGGATGGGAAT 57.989 39.130 2.66 0.00 33.62 3.01
238 239 4.463050 ACAGTTTTAAGTGGGATGGGAA 57.537 40.909 2.66 0.00 33.62 3.97
239 240 4.463050 AACAGTTTTAAGTGGGATGGGA 57.537 40.909 2.66 0.00 33.62 4.37
240 241 6.007703 TCTTAACAGTTTTAAGTGGGATGGG 58.992 40.000 8.31 0.00 34.51 4.00
241 242 7.519032 TTCTTAACAGTTTTAAGTGGGATGG 57.481 36.000 8.31 0.00 34.51 3.51
520 521 5.245850 GTCGTGCTGATAACGTATTTTGAC 58.754 41.667 0.00 0.00 41.70 3.18
601 620 0.382636 GTTCGCGTGTTCTTCGTTGG 60.383 55.000 5.77 0.00 0.00 3.77
602 621 0.713718 CGTTCGCGTGTTCTTCGTTG 60.714 55.000 5.77 0.00 35.57 4.10
603 622 1.556484 CGTTCGCGTGTTCTTCGTT 59.444 52.632 5.77 0.00 35.57 3.85
604 623 2.297912 CCGTTCGCGTGTTCTTCGT 61.298 57.895 5.77 0.00 39.32 3.85
605 624 2.464189 CCGTTCGCGTGTTCTTCG 59.536 61.111 5.77 1.95 39.32 3.79
606 625 2.170273 GCCGTTCGCGTGTTCTTC 59.830 61.111 5.77 0.00 39.32 2.87
607 626 2.586635 TGCCGTTCGCGTGTTCTT 60.587 55.556 5.77 0.00 42.08 2.52
608 627 3.335534 GTGCCGTTCGCGTGTTCT 61.336 61.111 5.77 0.00 42.08 3.01
609 628 4.364409 GGTGCCGTTCGCGTGTTC 62.364 66.667 5.77 0.00 42.08 3.18
923 960 7.223971 GGTACTCAATCGATAGTATTTGTTGCA 59.776 37.037 10.47 0.00 31.25 4.08
971 1008 2.034687 GTGCACTGTGGCCTCCAT 59.965 61.111 10.32 0.00 35.28 3.41
1111 1148 3.374402 CCGCTCCAGTCTCCACGT 61.374 66.667 0.00 0.00 0.00 4.49
1200 1237 4.030452 GTGTCTGCAAGCGGCCAC 62.030 66.667 2.24 0.00 43.89 5.01
1472 1532 7.144000 CGTTGGTATAGTTACTATTCCCTGTC 58.856 42.308 20.36 10.24 34.39 3.51
1681 1791 0.036010 ACCCGAAGACATGAGGCTTG 60.036 55.000 0.00 0.00 0.00 4.01
1697 1808 8.677300 CATATGGATGCAGTTTATGTAATACCC 58.323 37.037 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.