Multiple sequence alignment - TraesCS5B01G513700

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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 TraesCS5B01G513700 chr5B 100.000 2684 0 0 982 3665 678622534 678619851 0.000000e+00 4957
1 TraesCS5B01G513700 chr5B 100.000 339 0 0 1 339 678623515 678623177 8.640000e-176 627
2 TraesCS5B01G513700 chr5B 94.964 278 10 2 3 279 7012052 7012326 2.020000e-117 433
3 TraesCS5B01G513700 chr5D 94.672 2740 72 16 982 3665 537969681 537966960 0.000000e+00 4183
4 TraesCS5B01G513700 chr4A 94.975 2229 64 9 982 3179 632155325 632153114 0.000000e+00 3452
5 TraesCS5B01G513700 chr4A 94.301 386 8 2 3280 3665 632151809 632151438 2.450000e-161 579
6 TraesCS5B01G513700 chr4A 97.333 75 2 0 3225 3299 632152044 632151970 1.070000e-25 128
7 TraesCS5B01G513700 chr4A 100.000 53 0 0 3180 3232 632153088 632153036 8.380000e-17 99
8 TraesCS5B01G513700 chr5A 93.214 280 12 3 1 279 90781729 90782002 4.410000e-109 405
9 TraesCS5B01G513700 chr5A 85.663 279 35 3 2 279 490675751 490676025 4.630000e-74 289
10 TraesCS5B01G513700 chr2D 86.786 280 32 3 1 279 516986084 516986359 1.280000e-79 307
11 TraesCS5B01G513700 chr7B 86.022 279 34 3 2 279 657558852 657558578 9.950000e-76 294
12 TraesCS5B01G513700 chr7B 84.342 281 36 6 1 279 695282425 695282151 6.030000e-68 268
13 TraesCS5B01G513700 chr3D 85.714 280 34 3 1 279 47132185 47131911 1.290000e-74 291
14 TraesCS5B01G513700 chr3B 83.929 280 38 5 1 279 766719115 766718842 1.010000e-65 261
15 TraesCS5B01G513700 chr6B 83.401 247 35 4 34 279 261511937 261511696 1.320000e-54 224


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 TraesCS5B01G513700 chr5B 678619851 678623515 3664 True 2792.0 4957 100.00000 1 3665 2 chr5B.!!$R1 3664
1 TraesCS5B01G513700 chr5D 537966960 537969681 2721 True 4183.0 4183 94.67200 982 3665 1 chr5D.!!$R1 2683
2 TraesCS5B01G513700 chr4A 632151438 632155325 3887 True 1064.5 3452 96.65225 982 3665 4 chr4A.!!$R1 2683

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
75 76 0.108019 GGTGGTCAAACCGTTCTCCT 59.892 55.0 0.0 0.0 42.58 3.69 F
1302 1303 0.179000 AAGGCATCATCGTCCTCACC 59.821 55.0 0.0 0.0 0.00 4.02 F
1933 1934 0.103026 CATCGATCTCAAGGACCGCA 59.897 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1454 0.178068 AATAGGGCCAGCGTGTAGTG 59.822 55.00 6.18 0.0 0.00 2.74 R
2433 2434 0.829990 GAGGAAGAGGAAGAGGCCTG 59.170 60.00 12.00 0.0 38.73 4.85 R
2911 2920 4.881920 GCAAGGAAGTTTGCCATTTCTAA 58.118 39.13 0.00 0.0 45.93 2.10 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
46 47 8.866970 ATCCAAGAAAATATTTGCAAAATGGT 57.133 26.923 17.19 1.72 0.00 3.55
47 48 8.097078 TCCAAGAAAATATTTGCAAAATGGTG 57.903 30.769 17.19 6.54 0.00 4.17
48 49 7.718753 TCCAAGAAAATATTTGCAAAATGGTGT 59.281 29.630 17.19 0.49 0.00 4.16
49 50 7.804129 CCAAGAAAATATTTGCAAAATGGTGTG 59.196 33.333 17.19 7.84 0.00 3.82
50 51 6.901265 AGAAAATATTTGCAAAATGGTGTGC 58.099 32.000 17.19 2.42 41.29 4.57
51 52 5.625921 AAATATTTGCAAAATGGTGTGCC 57.374 34.783 17.19 0.00 40.14 5.01
68 69 2.029743 CCAAGTGGTGGTCAAACCG 58.970 57.895 0.00 0.00 42.58 4.44
69 70 0.750182 CCAAGTGGTGGTCAAACCGT 60.750 55.000 0.00 0.00 42.58 4.83
70 71 1.099689 CAAGTGGTGGTCAAACCGTT 58.900 50.000 0.00 0.00 42.58 4.44
71 72 1.064952 CAAGTGGTGGTCAAACCGTTC 59.935 52.381 0.00 0.00 42.58 3.95
72 73 0.544697 AGTGGTGGTCAAACCGTTCT 59.455 50.000 0.00 0.00 42.58 3.01
73 74 0.942252 GTGGTGGTCAAACCGTTCTC 59.058 55.000 0.00 0.00 42.58 2.87
74 75 0.179040 TGGTGGTCAAACCGTTCTCC 60.179 55.000 0.00 0.00 42.58 3.71
75 76 0.108019 GGTGGTCAAACCGTTCTCCT 59.892 55.000 0.00 0.00 42.58 3.69
76 77 1.476291 GGTGGTCAAACCGTTCTCCTT 60.476 52.381 0.00 0.00 42.58 3.36
77 78 2.224354 GGTGGTCAAACCGTTCTCCTTA 60.224 50.000 0.00 0.00 42.58 2.69
78 79 3.064931 GTGGTCAAACCGTTCTCCTTAG 58.935 50.000 0.00 0.00 42.58 2.18
79 80 2.701951 TGGTCAAACCGTTCTCCTTAGT 59.298 45.455 0.00 0.00 42.58 2.24
80 81 3.243975 TGGTCAAACCGTTCTCCTTAGTC 60.244 47.826 0.00 0.00 42.58 2.59
81 82 3.324117 GTCAAACCGTTCTCCTTAGTCC 58.676 50.000 0.00 0.00 0.00 3.85
82 83 2.967201 TCAAACCGTTCTCCTTAGTCCA 59.033 45.455 0.00 0.00 0.00 4.02
83 84 3.581332 TCAAACCGTTCTCCTTAGTCCAT 59.419 43.478 0.00 0.00 0.00 3.41
84 85 3.611766 AACCGTTCTCCTTAGTCCATG 57.388 47.619 0.00 0.00 0.00 3.66
85 86 2.816411 ACCGTTCTCCTTAGTCCATGA 58.184 47.619 0.00 0.00 0.00 3.07
86 87 3.170717 ACCGTTCTCCTTAGTCCATGAA 58.829 45.455 0.00 0.00 0.00 2.57
87 88 3.056035 ACCGTTCTCCTTAGTCCATGAAC 60.056 47.826 0.00 0.00 0.00 3.18
88 89 3.179830 CGTTCTCCTTAGTCCATGAACG 58.820 50.000 10.74 10.74 46.19 3.95
89 90 2.930682 GTTCTCCTTAGTCCATGAACGC 59.069 50.000 0.00 0.00 0.00 4.84
90 91 2.457598 TCTCCTTAGTCCATGAACGCT 58.542 47.619 0.00 0.00 0.00 5.07
91 92 3.628008 TCTCCTTAGTCCATGAACGCTA 58.372 45.455 0.00 0.00 0.00 4.26
92 93 4.021229 TCTCCTTAGTCCATGAACGCTAA 58.979 43.478 0.00 0.00 0.00 3.09
93 94 4.649674 TCTCCTTAGTCCATGAACGCTAAT 59.350 41.667 0.00 0.00 0.00 1.73
94 95 4.693283 TCCTTAGTCCATGAACGCTAATG 58.307 43.478 0.00 0.00 0.00 1.90
95 96 3.809832 CCTTAGTCCATGAACGCTAATGG 59.190 47.826 0.00 0.00 44.06 3.16
98 99 2.325583 TCCATGAACGCTAATGGACC 57.674 50.000 0.27 0.00 45.86 4.46
99 100 1.557371 TCCATGAACGCTAATGGACCA 59.443 47.619 0.27 0.00 45.86 4.02
100 101 2.026729 TCCATGAACGCTAATGGACCAA 60.027 45.455 0.27 0.00 45.86 3.67
101 102 2.951642 CCATGAACGCTAATGGACCAAT 59.048 45.455 0.00 0.00 45.29 3.16
102 103 4.133820 CCATGAACGCTAATGGACCAATA 58.866 43.478 0.00 0.00 45.29 1.90
103 104 4.578516 CCATGAACGCTAATGGACCAATAA 59.421 41.667 0.00 0.00 45.29 1.40
104 105 5.505654 CCATGAACGCTAATGGACCAATAAC 60.506 44.000 0.00 0.00 45.29 1.89
105 106 3.942748 TGAACGCTAATGGACCAATAACC 59.057 43.478 0.00 0.00 0.00 2.85
106 107 3.637911 ACGCTAATGGACCAATAACCA 57.362 42.857 0.00 0.00 40.57 3.67
107 108 3.958018 ACGCTAATGGACCAATAACCAA 58.042 40.909 0.00 0.00 39.69 3.67
108 109 3.692593 ACGCTAATGGACCAATAACCAAC 59.307 43.478 0.00 0.00 39.69 3.77
109 110 3.945285 CGCTAATGGACCAATAACCAACT 59.055 43.478 0.00 0.00 39.69 3.16
110 111 5.120399 CGCTAATGGACCAATAACCAACTA 58.880 41.667 0.00 0.00 39.69 2.24
111 112 5.236478 CGCTAATGGACCAATAACCAACTAG 59.764 44.000 0.00 0.00 39.69 2.57
112 113 5.531287 GCTAATGGACCAATAACCAACTAGG 59.469 44.000 0.00 0.00 45.67 3.02
113 114 3.359695 TGGACCAATAACCAACTAGGC 57.640 47.619 0.00 0.00 43.14 3.93
114 115 2.025699 TGGACCAATAACCAACTAGGCC 60.026 50.000 0.00 0.00 43.14 5.19
115 116 2.025699 GGACCAATAACCAACTAGGCCA 60.026 50.000 5.01 0.00 43.14 5.36
116 117 3.372675 GGACCAATAACCAACTAGGCCAT 60.373 47.826 5.01 0.00 43.14 4.40
117 118 4.141344 GGACCAATAACCAACTAGGCCATA 60.141 45.833 5.01 0.00 43.14 2.74
118 119 5.442391 GACCAATAACCAACTAGGCCATAA 58.558 41.667 5.01 0.00 43.14 1.90
119 120 5.833340 ACCAATAACCAACTAGGCCATAAA 58.167 37.500 5.01 0.00 43.14 1.40
120 121 5.655090 ACCAATAACCAACTAGGCCATAAAC 59.345 40.000 5.01 0.00 43.14 2.01
121 122 5.654650 CCAATAACCAACTAGGCCATAAACA 59.345 40.000 5.01 0.00 43.14 2.83
122 123 6.405397 CCAATAACCAACTAGGCCATAAACAC 60.405 42.308 5.01 0.00 43.14 3.32
123 124 4.382386 AACCAACTAGGCCATAAACACT 57.618 40.909 5.01 0.00 43.14 3.55
124 125 4.382386 ACCAACTAGGCCATAAACACTT 57.618 40.909 5.01 0.00 43.14 3.16
125 126 4.736473 ACCAACTAGGCCATAAACACTTT 58.264 39.130 5.01 0.00 43.14 2.66
126 127 4.522789 ACCAACTAGGCCATAAACACTTTG 59.477 41.667 5.01 0.00 43.14 2.77
127 128 4.522789 CCAACTAGGCCATAAACACTTTGT 59.477 41.667 5.01 0.00 0.00 2.83
128 129 5.335661 CCAACTAGGCCATAAACACTTTGTC 60.336 44.000 5.01 0.00 0.00 3.18
129 130 4.980573 ACTAGGCCATAAACACTTTGTCA 58.019 39.130 5.01 0.00 0.00 3.58
130 131 5.570320 ACTAGGCCATAAACACTTTGTCAT 58.430 37.500 5.01 0.00 0.00 3.06
131 132 6.717289 ACTAGGCCATAAACACTTTGTCATA 58.283 36.000 5.01 0.00 0.00 2.15
132 133 6.823689 ACTAGGCCATAAACACTTTGTCATAG 59.176 38.462 5.01 0.00 0.00 2.23
133 134 5.570320 AGGCCATAAACACTTTGTCATAGT 58.430 37.500 5.01 0.00 0.00 2.12
134 135 6.010219 AGGCCATAAACACTTTGTCATAGTT 58.990 36.000 5.01 0.00 0.00 2.24
135 136 6.493458 AGGCCATAAACACTTTGTCATAGTTT 59.507 34.615 5.01 0.00 36.49 2.66
136 137 7.668052 AGGCCATAAACACTTTGTCATAGTTTA 59.332 33.333 5.01 0.00 38.53 2.01
137 138 8.301002 GGCCATAAACACTTTGTCATAGTTTAA 58.699 33.333 0.00 0.00 37.94 1.52
138 139 9.855021 GCCATAAACACTTTGTCATAGTTTAAT 57.145 29.630 0.00 0.00 37.94 1.40
166 167 9.366216 GATTACATCCAATATTACGCATACTCA 57.634 33.333 0.00 0.00 0.00 3.41
167 168 9.890629 ATTACATCCAATATTACGCATACTCAT 57.109 29.630 0.00 0.00 0.00 2.90
168 169 9.719355 TTACATCCAATATTACGCATACTCATT 57.281 29.630 0.00 0.00 0.00 2.57
169 170 8.256611 ACATCCAATATTACGCATACTCATTC 57.743 34.615 0.00 0.00 0.00 2.67
170 171 7.877612 ACATCCAATATTACGCATACTCATTCA 59.122 33.333 0.00 0.00 0.00 2.57
171 172 8.720562 CATCCAATATTACGCATACTCATTCAA 58.279 33.333 0.00 0.00 0.00 2.69
172 173 8.846943 TCCAATATTACGCATACTCATTCAAT 57.153 30.769 0.00 0.00 0.00 2.57
173 174 8.935844 TCCAATATTACGCATACTCATTCAATC 58.064 33.333 0.00 0.00 0.00 2.67
174 175 8.939929 CCAATATTACGCATACTCATTCAATCT 58.060 33.333 0.00 0.00 0.00 2.40
178 179 7.889589 TTACGCATACTCATTCAATCTATGG 57.110 36.000 0.00 0.00 0.00 2.74
179 180 5.858381 ACGCATACTCATTCAATCTATGGT 58.142 37.500 0.00 0.00 0.00 3.55
180 181 6.291377 ACGCATACTCATTCAATCTATGGTT 58.709 36.000 0.00 0.00 0.00 3.67
181 182 6.203530 ACGCATACTCATTCAATCTATGGTTG 59.796 38.462 0.00 0.00 0.00 3.77
182 183 6.203530 CGCATACTCATTCAATCTATGGTTGT 59.796 38.462 0.00 0.00 0.00 3.32
183 184 7.254898 CGCATACTCATTCAATCTATGGTTGTT 60.255 37.037 0.00 0.00 0.00 2.83
184 185 8.408601 GCATACTCATTCAATCTATGGTTGTTT 58.591 33.333 0.00 0.00 0.00 2.83
230 231 4.822036 TTTTTGTCGTGAATGAACCGAT 57.178 36.364 0.00 0.00 32.68 4.18
231 232 3.804518 TTTGTCGTGAATGAACCGATG 57.195 42.857 0.00 0.00 32.68 3.84
232 233 2.734276 TGTCGTGAATGAACCGATGA 57.266 45.000 0.00 0.00 32.68 2.92
233 234 2.606108 TGTCGTGAATGAACCGATGAG 58.394 47.619 0.00 0.00 32.68 2.90
234 235 1.324736 GTCGTGAATGAACCGATGAGC 59.675 52.381 0.00 0.00 32.68 4.26
235 236 0.652592 CGTGAATGAACCGATGAGCC 59.347 55.000 0.00 0.00 0.00 4.70
236 237 0.652592 GTGAATGAACCGATGAGCCG 59.347 55.000 0.00 0.00 0.00 5.52
245 246 4.467084 GATGAGCCGGCGGTCCAA 62.467 66.667 28.82 11.48 35.55 3.53
246 247 4.778143 ATGAGCCGGCGGTCCAAC 62.778 66.667 28.82 10.36 35.55 3.77
272 273 3.826637 CCGCTCCTTCGGTTTTAGA 57.173 52.632 0.00 0.00 44.18 2.10
273 274 2.088950 CCGCTCCTTCGGTTTTAGAA 57.911 50.000 0.00 0.00 44.18 2.10
274 275 2.419667 CCGCTCCTTCGGTTTTAGAAA 58.580 47.619 0.00 0.00 44.18 2.52
275 276 2.159037 CCGCTCCTTCGGTTTTAGAAAC 59.841 50.000 0.00 0.00 44.18 2.78
276 277 3.064931 CGCTCCTTCGGTTTTAGAAACT 58.935 45.455 3.85 0.00 0.00 2.66
277 278 4.240096 CGCTCCTTCGGTTTTAGAAACTA 58.760 43.478 3.85 0.00 0.00 2.24
278 279 4.868734 CGCTCCTTCGGTTTTAGAAACTAT 59.131 41.667 3.85 0.00 0.00 2.12
279 280 5.350640 CGCTCCTTCGGTTTTAGAAACTATT 59.649 40.000 3.85 0.00 0.00 1.73
280 281 6.543736 GCTCCTTCGGTTTTAGAAACTATTG 58.456 40.000 3.85 0.00 0.00 1.90
281 282 6.148976 GCTCCTTCGGTTTTAGAAACTATTGT 59.851 38.462 3.85 0.00 0.00 2.71
282 283 7.332678 GCTCCTTCGGTTTTAGAAACTATTGTA 59.667 37.037 3.85 0.00 0.00 2.41
283 284 9.211485 CTCCTTCGGTTTTAGAAACTATTGTAA 57.789 33.333 3.85 0.00 0.00 2.41
284 285 9.558396 TCCTTCGGTTTTAGAAACTATTGTAAA 57.442 29.630 3.85 0.00 33.79 2.01
327 328 8.309163 TGACACAAAATTGAAATAAATCCAGC 57.691 30.769 0.00 0.00 0.00 4.85
328 329 8.149647 TGACACAAAATTGAAATAAATCCAGCT 58.850 29.630 0.00 0.00 0.00 4.24
329 330 9.638239 GACACAAAATTGAAATAAATCCAGCTA 57.362 29.630 0.00 0.00 0.00 3.32
336 337 8.773033 ATTGAAATAAATCCAGCTATGAAGGT 57.227 30.769 0.00 0.00 0.00 3.50
337 338 8.593945 TTGAAATAAATCCAGCTATGAAGGTT 57.406 30.769 0.00 0.00 0.00 3.50
338 339 8.593945 TGAAATAAATCCAGCTATGAAGGTTT 57.406 30.769 0.00 0.00 0.00 3.27
1091 1092 4.265792 CGATGATGAGAATGATCTGATCGC 59.734 45.833 12.65 5.25 35.54 4.58
1092 1093 3.572584 TGATGAGAATGATCTGATCGCG 58.427 45.455 12.65 0.00 35.54 5.87
1198 1199 2.808543 GTTCAGAGCTTACACCTTGGTG 59.191 50.000 17.34 17.34 0.00 4.17
1302 1303 0.179000 AAGGCATCATCGTCCTCACC 59.821 55.000 0.00 0.00 0.00 4.02
1305 1306 1.148157 GCATCATCGTCCTCACCACG 61.148 60.000 0.00 0.00 38.67 4.94
1409 1410 2.711174 AGACCCCTCATGGCTATTCAT 58.289 47.619 0.00 0.00 0.00 2.57
1445 1446 1.651240 CTTCTCATTGTGCGCCCCAG 61.651 60.000 4.18 0.00 0.00 4.45
1452 1453 3.518068 GTGCGCCCCAGTTATGGC 61.518 66.667 4.18 0.00 46.19 4.40
1453 1454 4.813235 TGCGCCCCAGTTATGGCC 62.813 66.667 4.18 0.00 46.19 5.36
1493 1494 1.148048 GGAAGCTGGATGGAGAGGC 59.852 63.158 0.00 0.00 0.00 4.70
1494 1495 1.630126 GGAAGCTGGATGGAGAGGCA 61.630 60.000 0.00 0.00 0.00 4.75
1496 1497 0.619832 AAGCTGGATGGAGAGGCAGA 60.620 55.000 0.00 0.00 0.00 4.26
1497 1498 1.049855 AGCTGGATGGAGAGGCAGAG 61.050 60.000 0.00 0.00 0.00 3.35
1498 1499 2.042404 GCTGGATGGAGAGGCAGAGG 62.042 65.000 0.00 0.00 0.00 3.69
1499 1500 1.383664 TGGATGGAGAGGCAGAGGG 60.384 63.158 0.00 0.00 0.00 4.30
1500 1501 2.146061 GGATGGAGAGGCAGAGGGG 61.146 68.421 0.00 0.00 0.00 4.79
1501 1502 2.040043 ATGGAGAGGCAGAGGGGG 60.040 66.667 0.00 0.00 0.00 5.40
1502 1503 2.611964 GATGGAGAGGCAGAGGGGGA 62.612 65.000 0.00 0.00 0.00 4.81
1503 1504 1.983035 ATGGAGAGGCAGAGGGGGAT 61.983 60.000 0.00 0.00 0.00 3.85
1504 1505 2.146061 GGAGAGGCAGAGGGGGATG 61.146 68.421 0.00 0.00 0.00 3.51
1505 1506 2.771762 AGAGGCAGAGGGGGATGC 60.772 66.667 0.00 0.00 41.80 3.91
1527 1528 3.369921 GCCCTCTTGGTTTGGCAG 58.630 61.111 0.00 0.00 43.46 4.85
1531 1532 2.597217 TCTTGGTTTGGCAGCCCG 60.597 61.111 9.64 0.57 0.00 6.13
1586 1587 1.268352 GGCAGTTGGCGTTAAATCACA 59.732 47.619 0.00 0.00 46.16 3.58
1610 1611 4.834828 CAAGAGCTCGTTGCAAGC 57.165 55.556 8.37 0.00 45.94 4.01
1681 1682 1.598130 GGCGTCACCTTCTGCAACT 60.598 57.895 0.00 0.00 34.51 3.16
1683 1684 1.569479 GCGTCACCTTCTGCAACTCC 61.569 60.000 0.00 0.00 0.00 3.85
1684 1685 1.284982 CGTCACCTTCTGCAACTCCG 61.285 60.000 0.00 0.00 0.00 4.63
1685 1686 0.951040 GTCACCTTCTGCAACTCCGG 60.951 60.000 0.00 0.00 0.00 5.14
1717 1718 3.689649 CACTACAGGGCTCCACAATAAAC 59.310 47.826 0.00 0.00 0.00 2.01
1720 1721 2.890945 ACAGGGCTCCACAATAAACAAC 59.109 45.455 0.00 0.00 0.00 3.32
1933 1934 0.103026 CATCGATCTCAAGGACCGCA 59.897 55.000 0.00 0.00 0.00 5.69
1941 1942 1.005394 CAAGGACCGCACCGTAACT 60.005 57.895 0.00 0.00 34.73 2.24
2072 2073 3.155167 GTACCCCCTCCTCAGCCG 61.155 72.222 0.00 0.00 0.00 5.52
2433 2434 5.516696 GCAAGAAAAACTGAAGGAACAAGAC 59.483 40.000 0.00 0.00 0.00 3.01
2552 2553 7.222031 TCAAAATCTACGAATACTGAACATCCG 59.778 37.037 0.00 0.00 0.00 4.18
2585 2586 8.059502 CCATGAATATTCAATTGAAAATGTGCG 58.940 33.333 23.91 11.12 41.13 5.34
2624 2625 5.011227 GTCCTGAGGTTGTTTACTCTCTCTT 59.989 44.000 0.00 0.00 34.84 2.85
2751 2752 3.055819 AGTCTGTGTACATAGGCCACTTG 60.056 47.826 19.25 1.10 0.00 3.16
2967 2976 3.058224 GTCACAGTACAGGAATTTGGTGC 60.058 47.826 0.00 0.00 0.00 5.01
3001 3010 5.072741 ACAATTCACATTCAGTACTTGGCT 58.927 37.500 0.00 0.00 0.00 4.75
3002 3011 5.048504 ACAATTCACATTCAGTACTTGGCTG 60.049 40.000 0.00 0.00 35.43 4.85
3026 3035 4.220382 CCTTATGAGGTTTGAACAATGGCA 59.780 41.667 0.00 0.00 38.32 4.92
3462 4705 6.499106 TTCCAGCTGATCCATTACTCAATA 57.501 37.500 17.39 0.00 0.00 1.90
3467 4710 8.316946 CCAGCTGATCCATTACTCAATAGATAA 58.683 37.037 17.39 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.299465 ACCATTTTGCAAATATTTTCTTGGATT 57.701 25.926 13.65 0.00 0.00 3.01
21 22 8.732531 CACCATTTTGCAAATATTTTCTTGGAT 58.267 29.630 13.65 0.00 0.00 3.41
22 23 7.718753 ACACCATTTTGCAAATATTTTCTTGGA 59.281 29.630 13.65 0.00 0.00 3.53
23 24 7.804129 CACACCATTTTGCAAATATTTTCTTGG 59.196 33.333 13.65 11.64 0.00 3.61
24 25 7.324135 GCACACCATTTTGCAAATATTTTCTTG 59.676 33.333 13.65 5.43 38.68 3.02
25 26 7.361894 GCACACCATTTTGCAAATATTTTCTT 58.638 30.769 13.65 0.00 38.68 2.52
26 27 6.072563 GGCACACCATTTTGCAAATATTTTCT 60.073 34.615 13.65 0.00 40.75 2.52
27 28 6.085573 GGCACACCATTTTGCAAATATTTTC 58.914 36.000 13.65 0.00 40.75 2.29
28 29 5.533903 TGGCACACCATTTTGCAAATATTTT 59.466 32.000 13.65 0.00 42.67 1.82
29 30 5.068636 TGGCACACCATTTTGCAAATATTT 58.931 33.333 13.65 0.00 42.67 1.40
30 31 4.649692 TGGCACACCATTTTGCAAATATT 58.350 34.783 13.65 0.00 42.67 1.28
31 32 4.283363 TGGCACACCATTTTGCAAATAT 57.717 36.364 13.65 6.85 42.67 1.28
32 33 3.758755 TGGCACACCATTTTGCAAATA 57.241 38.095 13.65 4.65 42.67 1.40
33 34 2.634815 TGGCACACCATTTTGCAAAT 57.365 40.000 13.65 0.39 42.67 2.32
51 52 1.064952 GAACGGTTTGACCACCACTTG 59.935 52.381 0.00 0.00 38.47 3.16
52 53 1.064979 AGAACGGTTTGACCACCACTT 60.065 47.619 0.00 0.00 38.47 3.16
53 54 0.544697 AGAACGGTTTGACCACCACT 59.455 50.000 0.00 0.00 38.47 4.00
54 55 0.942252 GAGAACGGTTTGACCACCAC 59.058 55.000 0.00 0.00 38.47 4.16
55 56 0.179040 GGAGAACGGTTTGACCACCA 60.179 55.000 0.00 0.00 38.47 4.17
56 57 0.108019 AGGAGAACGGTTTGACCACC 59.892 55.000 0.00 0.00 38.47 4.61
57 58 1.963172 AAGGAGAACGGTTTGACCAC 58.037 50.000 0.00 0.00 38.47 4.16
58 59 2.701951 ACTAAGGAGAACGGTTTGACCA 59.298 45.455 0.00 0.00 38.47 4.02
59 60 3.324117 GACTAAGGAGAACGGTTTGACC 58.676 50.000 0.00 0.00 34.05 4.02
60 61 3.243975 TGGACTAAGGAGAACGGTTTGAC 60.244 47.826 0.00 0.00 0.00 3.18
61 62 2.967201 TGGACTAAGGAGAACGGTTTGA 59.033 45.455 0.00 0.00 0.00 2.69
62 63 3.396260 TGGACTAAGGAGAACGGTTTG 57.604 47.619 0.00 0.00 0.00 2.93
63 64 3.581332 TCATGGACTAAGGAGAACGGTTT 59.419 43.478 0.00 0.00 0.00 3.27
64 65 3.170717 TCATGGACTAAGGAGAACGGTT 58.829 45.455 0.00 0.00 0.00 4.44
65 66 2.816411 TCATGGACTAAGGAGAACGGT 58.184 47.619 0.00 0.00 0.00 4.83
66 67 3.522553 GTTCATGGACTAAGGAGAACGG 58.477 50.000 0.00 0.00 0.00 4.44
68 69 2.930682 GCGTTCATGGACTAAGGAGAAC 59.069 50.000 1.86 0.00 33.82 3.01
69 70 2.832129 AGCGTTCATGGACTAAGGAGAA 59.168 45.455 1.86 0.00 0.00 2.87
70 71 2.457598 AGCGTTCATGGACTAAGGAGA 58.542 47.619 1.86 0.00 0.00 3.71
71 72 2.969628 AGCGTTCATGGACTAAGGAG 57.030 50.000 1.86 0.00 0.00 3.69
72 73 4.442893 CCATTAGCGTTCATGGACTAAGGA 60.443 45.833 6.63 0.00 42.49 3.36
73 74 3.809832 CCATTAGCGTTCATGGACTAAGG 59.190 47.826 6.63 0.00 42.49 2.69
74 75 4.693283 TCCATTAGCGTTCATGGACTAAG 58.307 43.478 10.75 0.00 43.44 2.18
75 76 4.746535 TCCATTAGCGTTCATGGACTAA 57.253 40.909 10.75 0.00 43.44 2.24
79 80 1.557371 TGGTCCATTAGCGTTCATGGA 59.443 47.619 10.75 10.75 45.65 3.41
80 81 2.036958 TGGTCCATTAGCGTTCATGG 57.963 50.000 6.15 6.15 41.39 3.66
81 82 5.505654 GGTTATTGGTCCATTAGCGTTCATG 60.506 44.000 0.00 0.00 0.00 3.07
82 83 4.578928 GGTTATTGGTCCATTAGCGTTCAT 59.421 41.667 0.00 0.00 0.00 2.57
83 84 3.942748 GGTTATTGGTCCATTAGCGTTCA 59.057 43.478 0.00 0.00 0.00 3.18
84 85 3.942748 TGGTTATTGGTCCATTAGCGTTC 59.057 43.478 0.00 0.00 0.00 3.95
85 86 3.958018 TGGTTATTGGTCCATTAGCGTT 58.042 40.909 0.00 0.00 0.00 4.84
86 87 3.637911 TGGTTATTGGTCCATTAGCGT 57.362 42.857 0.00 0.00 0.00 5.07
87 88 3.945285 AGTTGGTTATTGGTCCATTAGCG 59.055 43.478 0.00 0.00 33.50 4.26
88 89 5.531287 CCTAGTTGGTTATTGGTCCATTAGC 59.469 44.000 0.00 0.00 33.50 3.09
89 90 5.531287 GCCTAGTTGGTTATTGGTCCATTAG 59.469 44.000 0.00 0.00 38.35 1.73
90 91 5.442391 GCCTAGTTGGTTATTGGTCCATTA 58.558 41.667 0.00 0.00 38.35 1.90
91 92 4.278310 GCCTAGTTGGTTATTGGTCCATT 58.722 43.478 0.00 0.00 38.35 3.16
92 93 3.372675 GGCCTAGTTGGTTATTGGTCCAT 60.373 47.826 0.00 0.00 38.35 3.41
93 94 2.025699 GGCCTAGTTGGTTATTGGTCCA 60.026 50.000 0.00 0.00 38.35 4.02
94 95 2.025699 TGGCCTAGTTGGTTATTGGTCC 60.026 50.000 3.32 0.00 38.35 4.46
95 96 3.359695 TGGCCTAGTTGGTTATTGGTC 57.640 47.619 3.32 0.00 38.35 4.02
96 97 5.459982 TTATGGCCTAGTTGGTTATTGGT 57.540 39.130 3.32 0.00 38.35 3.67
97 98 5.654650 TGTTTATGGCCTAGTTGGTTATTGG 59.345 40.000 3.32 0.00 38.35 3.16
98 99 6.377146 AGTGTTTATGGCCTAGTTGGTTATTG 59.623 38.462 3.32 0.00 38.35 1.90
99 100 6.490492 AGTGTTTATGGCCTAGTTGGTTATT 58.510 36.000 3.32 0.00 38.35 1.40
100 101 6.074698 AGTGTTTATGGCCTAGTTGGTTAT 57.925 37.500 3.32 0.00 38.35 1.89
101 102 5.508280 AGTGTTTATGGCCTAGTTGGTTA 57.492 39.130 3.32 0.00 38.35 2.85
102 103 4.382386 AGTGTTTATGGCCTAGTTGGTT 57.618 40.909 3.32 0.00 38.35 3.67
103 104 4.382386 AAGTGTTTATGGCCTAGTTGGT 57.618 40.909 3.32 0.00 38.35 3.67
104 105 4.522789 ACAAAGTGTTTATGGCCTAGTTGG 59.477 41.667 3.32 0.00 39.35 3.77
105 106 5.240623 TGACAAAGTGTTTATGGCCTAGTTG 59.759 40.000 3.32 0.00 0.00 3.16
106 107 5.381757 TGACAAAGTGTTTATGGCCTAGTT 58.618 37.500 3.32 0.00 0.00 2.24
107 108 4.980573 TGACAAAGTGTTTATGGCCTAGT 58.019 39.130 3.32 0.00 0.00 2.57
108 109 6.823689 ACTATGACAAAGTGTTTATGGCCTAG 59.176 38.462 3.32 0.00 0.00 3.02
109 110 6.717289 ACTATGACAAAGTGTTTATGGCCTA 58.283 36.000 3.32 0.00 0.00 3.93
110 111 5.570320 ACTATGACAAAGTGTTTATGGCCT 58.430 37.500 3.32 0.00 0.00 5.19
111 112 5.897377 ACTATGACAAAGTGTTTATGGCC 57.103 39.130 0.00 0.00 0.00 5.36
112 113 9.855021 ATTAAACTATGACAAAGTGTTTATGGC 57.145 29.630 0.00 0.00 34.47 4.40
140 141 9.366216 TGAGTATGCGTAATATTGGATGTAATC 57.634 33.333 0.00 0.00 44.55 1.75
141 142 9.890629 ATGAGTATGCGTAATATTGGATGTAAT 57.109 29.630 0.00 0.00 0.00 1.89
142 143 9.719355 AATGAGTATGCGTAATATTGGATGTAA 57.281 29.630 0.00 0.00 0.00 2.41
143 144 9.366216 GAATGAGTATGCGTAATATTGGATGTA 57.634 33.333 0.00 0.00 0.00 2.29
144 145 7.877612 TGAATGAGTATGCGTAATATTGGATGT 59.122 33.333 0.00 0.00 0.00 3.06
145 146 8.255394 TGAATGAGTATGCGTAATATTGGATG 57.745 34.615 0.00 0.00 0.00 3.51
146 147 8.846943 TTGAATGAGTATGCGTAATATTGGAT 57.153 30.769 0.00 0.00 0.00 3.41
147 148 8.846943 ATTGAATGAGTATGCGTAATATTGGA 57.153 30.769 0.00 0.00 0.00 3.53
148 149 8.939929 AGATTGAATGAGTATGCGTAATATTGG 58.060 33.333 0.00 0.00 0.00 3.16
152 153 9.586435 CCATAGATTGAATGAGTATGCGTAATA 57.414 33.333 0.00 0.00 0.00 0.98
153 154 8.097038 ACCATAGATTGAATGAGTATGCGTAAT 58.903 33.333 0.00 0.00 0.00 1.89
154 155 7.441836 ACCATAGATTGAATGAGTATGCGTAA 58.558 34.615 0.00 0.00 0.00 3.18
155 156 6.993079 ACCATAGATTGAATGAGTATGCGTA 58.007 36.000 0.00 0.00 0.00 4.42
156 157 5.858381 ACCATAGATTGAATGAGTATGCGT 58.142 37.500 0.00 0.00 0.00 5.24
157 158 6.203530 ACAACCATAGATTGAATGAGTATGCG 59.796 38.462 0.00 0.00 0.00 4.73
158 159 7.502120 ACAACCATAGATTGAATGAGTATGC 57.498 36.000 0.00 0.00 0.00 3.14
209 210 4.273724 TCATCGGTTCATTCACGACAAAAA 59.726 37.500 0.00 0.00 39.64 1.94
210 211 3.810386 TCATCGGTTCATTCACGACAAAA 59.190 39.130 0.00 0.00 39.64 2.44
211 212 3.394719 TCATCGGTTCATTCACGACAAA 58.605 40.909 0.00 0.00 39.64 2.83
212 213 2.993220 CTCATCGGTTCATTCACGACAA 59.007 45.455 0.00 0.00 39.64 3.18
213 214 2.606108 CTCATCGGTTCATTCACGACA 58.394 47.619 0.00 0.00 39.64 4.35
214 215 1.324736 GCTCATCGGTTCATTCACGAC 59.675 52.381 0.00 0.00 39.64 4.34
215 216 1.640428 GCTCATCGGTTCATTCACGA 58.360 50.000 0.00 0.00 41.20 4.35
216 217 0.652592 GGCTCATCGGTTCATTCACG 59.347 55.000 0.00 0.00 0.00 4.35
217 218 0.652592 CGGCTCATCGGTTCATTCAC 59.347 55.000 0.00 0.00 0.00 3.18
218 219 0.461870 CCGGCTCATCGGTTCATTCA 60.462 55.000 0.00 0.00 44.60 2.57
219 220 2.311294 CCGGCTCATCGGTTCATTC 58.689 57.895 0.00 0.00 44.60 2.67
220 221 4.540153 CCGGCTCATCGGTTCATT 57.460 55.556 0.00 0.00 44.60 2.57
228 229 4.467084 TTGGACCGCCGGCTCATC 62.467 66.667 26.68 18.18 36.79 2.92
229 230 4.778143 GTTGGACCGCCGGCTCAT 62.778 66.667 26.68 9.57 36.79 2.90
301 302 8.772705 GCTGGATTTATTTCAATTTTGTGTCAA 58.227 29.630 0.00 0.00 0.00 3.18
302 303 8.149647 AGCTGGATTTATTTCAATTTTGTGTCA 58.850 29.630 0.00 0.00 0.00 3.58
303 304 8.538409 AGCTGGATTTATTTCAATTTTGTGTC 57.462 30.769 0.00 0.00 0.00 3.67
310 311 9.205513 ACCTTCATAGCTGGATTTATTTCAATT 57.794 29.630 0.00 0.00 0.00 2.32
311 312 8.773033 ACCTTCATAGCTGGATTTATTTCAAT 57.227 30.769 0.00 0.00 0.00 2.57
312 313 8.593945 AACCTTCATAGCTGGATTTATTTCAA 57.406 30.769 0.00 0.00 0.00 2.69
313 314 8.593945 AAACCTTCATAGCTGGATTTATTTCA 57.406 30.769 0.00 0.00 0.00 2.69
1063 1064 4.981054 CAGATCATTCTCATCATCGTCGTT 59.019 41.667 0.00 0.00 0.00 3.85
1091 1092 0.598419 TATCTCGAATGGCTGCAGCG 60.598 55.000 31.19 17.72 43.26 5.18
1092 1093 0.864455 GTATCTCGAATGGCTGCAGC 59.136 55.000 30.88 30.88 41.14 5.25
1105 1106 1.066303 CTCCACGCACCTGAGTATCTC 59.934 57.143 0.00 0.00 34.92 2.75
1224 1225 1.693627 GGAGGCCGAGACAAGATAGA 58.306 55.000 0.00 0.00 0.00 1.98
1302 1303 3.818961 AAGTCATGCAGAAATGTCGTG 57.181 42.857 0.00 0.00 0.00 4.35
1305 1306 4.666237 GGCTAAAGTCATGCAGAAATGTC 58.334 43.478 0.00 0.00 0.00 3.06
1409 1410 1.407656 AAGGCGAACAGTGAGACCCA 61.408 55.000 0.00 0.00 0.00 4.51
1445 1446 1.006832 CAGCGTGTAGTGGCCATAAC 58.993 55.000 9.72 11.38 0.00 1.89
1452 1453 1.686325 ATAGGGCCAGCGTGTAGTGG 61.686 60.000 6.18 0.00 36.85 4.00
1453 1454 0.178068 AATAGGGCCAGCGTGTAGTG 59.822 55.000 6.18 0.00 0.00 2.74
1499 1500 3.078843 AAGAGGGCATGGGCATCCC 62.079 63.158 0.71 0.00 45.71 3.85
1500 1501 1.831286 CAAGAGGGCATGGGCATCC 60.831 63.158 0.71 0.00 39.68 3.51
1501 1502 1.831286 CCAAGAGGGCATGGGCATC 60.831 63.158 0.00 0.00 43.71 3.91
1502 1503 2.172229 AACCAAGAGGGCATGGGCAT 62.172 55.000 0.00 0.00 43.71 4.40
1503 1504 2.384933 AAACCAAGAGGGCATGGGCA 62.385 55.000 0.00 0.00 43.71 5.36
1504 1505 1.610379 AAACCAAGAGGGCATGGGC 60.610 57.895 0.00 0.00 41.17 5.36
1505 1506 1.259840 CCAAACCAAGAGGGCATGGG 61.260 60.000 0.00 0.00 40.41 4.00
1506 1507 1.891722 GCCAAACCAAGAGGGCATGG 61.892 60.000 0.00 0.00 45.70 3.66
1507 1508 1.593265 GCCAAACCAAGAGGGCATG 59.407 57.895 0.00 0.00 45.70 4.06
1512 1513 2.278330 GGGCTGCCAAACCAAGAGG 61.278 63.158 22.05 0.00 42.21 3.69
1531 1532 3.706373 TGGCAAGGACGAGGAGCC 61.706 66.667 0.00 0.00 45.41 4.70
1543 1544 2.063015 ATCTTGGACCACGGTGGCAA 62.063 55.000 26.62 20.57 42.67 4.52
1579 1580 1.470098 GCTCTTGCCGATGTGTGATTT 59.530 47.619 0.00 0.00 0.00 2.17
1586 1587 1.016130 CAACGAGCTCTTGCCGATGT 61.016 55.000 12.85 0.00 40.80 3.06
1610 1611 0.595095 GGCTGAAAAGGTGCAGTCAG 59.405 55.000 0.00 0.00 40.40 3.51
1681 1682 3.949885 TAGTGAAGAGGCCGCCGGA 62.950 63.158 7.68 0.00 0.00 5.14
1683 1684 2.202756 GTAGTGAAGAGGCCGCCG 60.203 66.667 1.49 0.00 0.00 6.46
1684 1685 1.153549 CTGTAGTGAAGAGGCCGCC 60.154 63.158 1.49 0.00 0.00 6.13
1685 1686 1.153549 CCTGTAGTGAAGAGGCCGC 60.154 63.158 0.00 0.00 30.63 6.53
1717 1718 4.311816 AGCCAAACTTGAGAATGTGTTG 57.688 40.909 0.00 0.00 0.00 3.33
1720 1721 4.843220 AGAAGCCAAACTTGAGAATGTG 57.157 40.909 0.00 0.00 39.29 3.21
1933 1934 1.227734 GCCACCACACAGTTACGGT 60.228 57.895 0.00 0.00 0.00 4.83
2433 2434 0.829990 GAGGAAGAGGAAGAGGCCTG 59.170 60.000 12.00 0.00 38.73 4.85
2488 2489 8.499406 AGACAAGTTAGAGATACCTATGAGTCT 58.501 37.037 0.00 0.00 0.00 3.24
2590 2591 3.581332 ACAACCTCAGGACCGAGAATAAA 59.419 43.478 0.00 0.00 34.79 1.40
2598 2599 2.299297 AGAGTAAACAACCTCAGGACCG 59.701 50.000 0.00 0.00 0.00 4.79
2624 2625 4.645863 ATGGTATCTGCATTGCCTATGA 57.354 40.909 6.12 0.00 36.26 2.15
2751 2752 5.283457 AGTAAGATAGTTGGTGCTCCATC 57.717 43.478 8.61 8.06 43.91 3.51
2911 2920 4.881920 GCAAGGAAGTTTGCCATTTCTAA 58.118 39.130 0.00 0.00 45.93 2.10
2928 2937 5.047802 ACTGTGACCTTCAAAATATGCAAGG 60.048 40.000 0.00 0.00 39.88 3.61
2940 2949 4.974645 AATTCCTGTACTGTGACCTTCA 57.025 40.909 0.00 0.00 0.00 3.02
2967 2976 9.897744 ACTGAATGTGAATTGTAATGTAAGTTG 57.102 29.630 0.00 0.00 0.00 3.16
3266 4329 9.631452 ATTCTAAATGTTTAGCAGAGAAAAAGC 57.369 29.630 7.49 0.00 39.90 3.51
3435 4678 6.528321 TGAGTAATGGATCAGCTGGAAATAG 58.472 40.000 15.13 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.