Multiple sequence alignment - TraesCS7B01G289400

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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 TraesCS7B01G289400 chr7B 100.000 3185 0 0 1 3185 524918301 524921485 0.000000e+00 5882.0
1 TraesCS7B01G289400 chr7A 91.751 2873 190 25 336 3185 562215030 562217878 0.000000e+00 3949.0
2 TraesCS7B01G289400 chr7D 91.582 2851 177 23 344 3185 496784890 496787686 0.000000e+00 3877.0
3 TraesCS7B01G289400 chr1D 88.235 1530 138 15 981 2483 436654294 436652780 0.000000e+00 1790.0
4 TraesCS7B01G289400 chr1D 85.581 215 29 2 126 338 411276692 411276906 1.150000e-54 224.0
5 TraesCS7B01G289400 chr1A 88.611 1440 139 13 981 2396 533733787 533732349 0.000000e+00 1727.0
6 TraesCS7B01G289400 chr1B 88.475 1397 130 15 969 2334 591451883 591450487 0.000000e+00 1659.0
7 TraesCS7B01G289400 chr1B 85.577 208 29 1 134 340 58253266 58253059 1.920000e-52 217.0
8 TraesCS7B01G289400 chr1B 74.709 344 52 22 2493 2820 591452546 591452222 1.550000e-23 121.0
9 TraesCS7B01G289400 chr5A 86.408 206 27 1 134 338 654405663 654405868 1.150000e-54 224.0
10 TraesCS7B01G289400 chr5A 85.990 207 28 1 134 339 606255606 606255400 1.490000e-53 220.0
11 TraesCS7B01G289400 chr2B 86.473 207 22 4 134 339 502955320 502955119 4.140000e-54 222.0
12 TraesCS7B01G289400 chr6A 85.922 206 28 1 134 338 613891928 613892133 5.350000e-53 219.0
13 TraesCS7B01G289400 chr2A 85.577 208 28 2 134 339 738347220 738347427 1.920000e-52 217.0
14 TraesCS7B01G289400 chr4A 85.507 207 29 1 134 339 45376089 45375883 6.920000e-52 215.0
15 TraesCS7B01G289400 chr6D 85.167 209 30 1 134 341 466013040 466012832 2.490000e-51 213.0
16 TraesCS7B01G289400 chr6D 92.453 53 3 1 2518 2569 401172308 401172256 1.230000e-09 75.0
17 TraesCS7B01G289400 chrUn 90.323 62 5 1 2509 2569 69454503 69454564 2.630000e-11 80.5


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 TraesCS7B01G289400 chr7B 524918301 524921485 3184 False 5882 5882 100.000 1 3185 1 chr7B.!!$F1 3184
1 TraesCS7B01G289400 chr7A 562215030 562217878 2848 False 3949 3949 91.751 336 3185 1 chr7A.!!$F1 2849
2 TraesCS7B01G289400 chr7D 496784890 496787686 2796 False 3877 3877 91.582 344 3185 1 chr7D.!!$F1 2841
3 TraesCS7B01G289400 chr1D 436652780 436654294 1514 True 1790 1790 88.235 981 2483 1 chr1D.!!$R1 1502
4 TraesCS7B01G289400 chr1A 533732349 533733787 1438 True 1727 1727 88.611 981 2396 1 chr1A.!!$R1 1415
5 TraesCS7B01G289400 chr1B 591450487 591452546 2059 True 890 1659 81.592 969 2820 2 chr1B.!!$R2 1851

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
21 22 0.048117 AGGAGGAGGAGAGTAGGGGA 59.952 60.0 0.00 0.00 0.00 4.81 F
1544 1565 0.037975 GTTGCAGACAATTGCCCTGG 60.038 55.0 22.25 10.14 43.43 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1803 0.321671 CCGTGAAGGTGACAGATGGT 59.678 55.0 0.00 0.00 34.51 3.55 R
2619 2667 0.331616 GTACAAAGGGGGCCATCTGT 59.668 55.0 4.39 5.43 0.00 3.41 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
20 21 0.481128 GAGGAGGAGGAGAGTAGGGG 59.519 65.000 0.00 0.00 0.00 4.79
21 22 0.048117 AGGAGGAGGAGAGTAGGGGA 59.952 60.000 0.00 0.00 0.00 4.81
22 23 0.935194 GGAGGAGGAGAGTAGGGGAA 59.065 60.000 0.00 0.00 0.00 3.97
23 24 1.411930 GGAGGAGGAGAGTAGGGGAAC 60.412 61.905 0.00 0.00 0.00 3.62
24 25 0.259356 AGGAGGAGAGTAGGGGAACG 59.741 60.000 0.00 0.00 0.00 3.95
25 26 1.393487 GGAGGAGAGTAGGGGAACGC 61.393 65.000 0.00 0.00 43.76 4.84
85 86 2.774687 GTCGAGACCTATCCTCTCCTC 58.225 57.143 0.00 0.00 31.92 3.71
86 87 2.370849 GTCGAGACCTATCCTCTCCTCT 59.629 54.545 0.00 0.00 31.92 3.69
87 88 3.579586 GTCGAGACCTATCCTCTCCTCTA 59.420 52.174 0.00 0.00 31.92 2.43
88 89 4.040706 GTCGAGACCTATCCTCTCCTCTAA 59.959 50.000 0.00 0.00 31.92 2.10
89 90 4.847512 TCGAGACCTATCCTCTCCTCTAAT 59.152 45.833 0.00 0.00 31.92 1.73
90 91 5.046159 TCGAGACCTATCCTCTCCTCTAATC 60.046 48.000 0.00 0.00 31.92 1.75
91 92 5.174037 AGACCTATCCTCTCCTCTAATCG 57.826 47.826 0.00 0.00 0.00 3.34
92 93 4.847512 AGACCTATCCTCTCCTCTAATCGA 59.152 45.833 0.00 0.00 0.00 3.59
94 95 5.318630 ACCTATCCTCTCCTCTAATCGAAC 58.681 45.833 0.00 0.00 0.00 3.95
95 96 5.163077 ACCTATCCTCTCCTCTAATCGAACA 60.163 44.000 0.00 0.00 0.00 3.18
96 97 5.770663 CCTATCCTCTCCTCTAATCGAACAA 59.229 44.000 0.00 0.00 0.00 2.83
97 98 5.782893 ATCCTCTCCTCTAATCGAACAAG 57.217 43.478 0.00 0.00 0.00 3.16
98 99 4.601084 TCCTCTCCTCTAATCGAACAAGT 58.399 43.478 0.00 0.00 0.00 3.16
99 100 4.641094 TCCTCTCCTCTAATCGAACAAGTC 59.359 45.833 0.00 0.00 0.00 3.01
100 101 4.202070 CCTCTCCTCTAATCGAACAAGTCC 60.202 50.000 0.00 0.00 0.00 3.85
101 102 4.601084 TCTCCTCTAATCGAACAAGTCCT 58.399 43.478 0.00 0.00 0.00 3.85
102 103 4.399618 TCTCCTCTAATCGAACAAGTCCTG 59.600 45.833 0.00 0.00 0.00 3.86
103 104 4.087182 TCCTCTAATCGAACAAGTCCTGT 58.913 43.478 0.00 0.00 41.27 4.00
111 112 1.589803 AACAAGTCCTGTTACCACGC 58.410 50.000 0.00 0.00 46.75 5.34
113 114 0.865769 CAAGTCCTGTTACCACGCAC 59.134 55.000 0.00 0.00 0.00 5.34
114 115 0.756903 AAGTCCTGTTACCACGCACT 59.243 50.000 0.00 0.00 0.00 4.40
115 116 0.756903 AGTCCTGTTACCACGCACTT 59.243 50.000 0.00 0.00 0.00 3.16
116 117 1.140252 AGTCCTGTTACCACGCACTTT 59.860 47.619 0.00 0.00 0.00 2.66
117 118 1.944709 GTCCTGTTACCACGCACTTTT 59.055 47.619 0.00 0.00 0.00 2.27
118 119 1.944024 TCCTGTTACCACGCACTTTTG 59.056 47.619 0.00 0.00 0.00 2.44
119 120 1.673920 CCTGTTACCACGCACTTTTGT 59.326 47.619 0.00 0.00 0.00 2.83
120 121 2.873472 CCTGTTACCACGCACTTTTGTA 59.127 45.455 0.00 0.00 0.00 2.41
121 122 3.500680 CCTGTTACCACGCACTTTTGTAT 59.499 43.478 0.00 0.00 0.00 2.29
122 123 4.023536 CCTGTTACCACGCACTTTTGTATT 60.024 41.667 0.00 0.00 0.00 1.89
125 126 5.066117 TGTTACCACGCACTTTTGTATTTCA 59.934 36.000 0.00 0.00 0.00 2.69
127 128 3.630312 ACCACGCACTTTTGTATTTCACT 59.370 39.130 0.00 0.00 0.00 3.41
129 130 4.675114 CCACGCACTTTTGTATTTCACTTC 59.325 41.667 0.00 0.00 0.00 3.01
130 131 4.675114 CACGCACTTTTGTATTTCACTTCC 59.325 41.667 0.00 0.00 0.00 3.46
131 132 4.336993 ACGCACTTTTGTATTTCACTTCCA 59.663 37.500 0.00 0.00 0.00 3.53
133 134 5.920273 CGCACTTTTGTATTTCACTTCCAAT 59.080 36.000 0.00 0.00 0.00 3.16
135 136 7.754924 CGCACTTTTGTATTTCACTTCCAATAT 59.245 33.333 0.00 0.00 0.00 1.28
136 137 9.076596 GCACTTTTGTATTTCACTTCCAATATC 57.923 33.333 0.00 0.00 0.00 1.63
144 145 9.869844 GTATTTCACTTCCAATATCTTTGATCG 57.130 33.333 0.00 0.00 0.00 3.69
146 147 9.613428 ATTTCACTTCCAATATCTTTGATCGTA 57.387 29.630 0.00 0.00 0.00 3.43
148 149 9.613428 TTCACTTCCAATATCTTTGATCGTATT 57.387 29.630 0.00 0.00 0.00 1.89
149 150 9.613428 TCACTTCCAATATCTTTGATCGTATTT 57.387 29.630 0.00 0.00 0.00 1.40
238 239 8.627487 TTTTCATCATATGCGTATTTGGTTTC 57.373 30.769 0.00 0.00 0.00 2.78
239 240 6.934048 TCATCATATGCGTATTTGGTTTCA 57.066 33.333 0.00 0.00 0.00 2.69
240 241 7.326968 TCATCATATGCGTATTTGGTTTCAA 57.673 32.000 0.00 0.00 0.00 2.69
241 242 7.766283 TCATCATATGCGTATTTGGTTTCAAA 58.234 30.769 0.00 0.00 45.61 2.69
242 243 8.246871 TCATCATATGCGTATTTGGTTTCAAAA 58.753 29.630 0.00 0.00 44.83 2.44
243 244 9.033481 CATCATATGCGTATTTGGTTTCAAAAT 57.967 29.630 0.00 0.00 44.83 1.82
244 245 8.994429 TCATATGCGTATTTGGTTTCAAAATT 57.006 26.923 0.00 0.00 44.83 1.82
245 246 9.429359 TCATATGCGTATTTGGTTTCAAAATTT 57.571 25.926 0.00 0.00 44.83 1.82
251 252 9.923786 GCGTATTTGGTTTCAAAATTTTTACTT 57.076 25.926 0.00 0.00 44.83 2.24
270 271 9.522804 TTTTACTTATTTTTGCACAAACTCGAT 57.477 25.926 0.00 0.00 0.00 3.59
271 272 8.722342 TTACTTATTTTTGCACAAACTCGATC 57.278 30.769 0.00 0.00 0.00 3.69
272 273 6.734137 ACTTATTTTTGCACAAACTCGATCA 58.266 32.000 0.00 0.00 0.00 2.92
273 274 7.199766 ACTTATTTTTGCACAAACTCGATCAA 58.800 30.769 0.00 0.00 0.00 2.57
274 275 7.704472 ACTTATTTTTGCACAAACTCGATCAAA 59.296 29.630 0.00 0.00 0.00 2.69
275 276 8.586570 TTATTTTTGCACAAACTCGATCAAAT 57.413 26.923 0.00 0.00 0.00 2.32
277 278 6.900568 TTTTGCACAAACTCGATCAAATTT 57.099 29.167 0.00 0.00 0.00 1.82
279 280 7.993821 TTTGCACAAACTCGATCAAATTTTA 57.006 28.000 0.00 0.00 0.00 1.52
280 281 8.586570 TTTGCACAAACTCGATCAAATTTTAT 57.413 26.923 0.00 0.00 0.00 1.40
281 282 7.565450 TGCACAAACTCGATCAAATTTTATG 57.435 32.000 0.00 0.00 0.00 1.90
282 283 7.366513 TGCACAAACTCGATCAAATTTTATGA 58.633 30.769 0.00 0.00 0.00 2.15
283 284 8.028354 TGCACAAACTCGATCAAATTTTATGAT 58.972 29.630 0.00 0.00 40.14 2.45
284 285 9.502145 GCACAAACTCGATCAAATTTTATGATA 57.498 29.630 0.00 0.00 37.64 2.15
293 294 9.450807 CGATCAAATTTTATGATAGTTTGACCC 57.549 33.333 10.04 6.57 40.36 4.46
296 297 8.966868 TCAAATTTTATGATAGTTTGACCCTCC 58.033 33.333 0.00 0.00 34.82 4.30
297 298 8.748412 CAAATTTTATGATAGTTTGACCCTCCA 58.252 33.333 0.00 0.00 32.93 3.86
300 301 7.743116 TTTATGATAGTTTGACCCTCCAGTA 57.257 36.000 0.00 0.00 0.00 2.74
301 302 7.743116 TTATGATAGTTTGACCCTCCAGTAA 57.257 36.000 0.00 0.00 0.00 2.24
306 307 7.393234 TGATAGTTTGACCCTCCAGTAAAATTG 59.607 37.037 0.00 0.00 0.00 2.32
308 309 4.733077 TTGACCCTCCAGTAAAATTGGA 57.267 40.909 0.00 0.00 42.30 3.53
310 311 5.068215 TGACCCTCCAGTAAAATTGGAAA 57.932 39.130 0.00 0.00 43.79 3.13
312 313 6.795590 TGACCCTCCAGTAAAATTGGAAATA 58.204 36.000 0.00 0.00 43.79 1.40
313 314 6.661805 TGACCCTCCAGTAAAATTGGAAATAC 59.338 38.462 0.00 0.00 43.79 1.89
314 315 6.557568 ACCCTCCAGTAAAATTGGAAATACA 58.442 36.000 0.00 0.00 43.79 2.29
315 316 7.189087 ACCCTCCAGTAAAATTGGAAATACAT 58.811 34.615 0.00 0.00 43.79 2.29
316 317 7.678171 ACCCTCCAGTAAAATTGGAAATACATT 59.322 33.333 0.00 0.00 43.79 2.71
317 318 8.197439 CCCTCCAGTAAAATTGGAAATACATTC 58.803 37.037 0.00 0.00 43.79 2.67
318 319 8.971073 CCTCCAGTAAAATTGGAAATACATTCT 58.029 33.333 0.00 0.00 43.79 2.40
329 330 9.855021 ATTGGAAATACATTCTTTAAAGAACGG 57.145 29.630 28.38 24.34 46.80 4.44
332 333 8.182227 GGAAATACATTCTTTAAAGAACGGAGG 58.818 37.037 28.38 18.34 46.80 4.30
334 335 5.237236 ACATTCTTTAAAGAACGGAGGGA 57.763 39.130 28.38 8.40 46.80 4.20
341 342 5.859205 TTAAAGAACGGAGGGAGTATACC 57.141 43.478 0.00 0.00 0.00 2.73
394 398 7.989741 AGAAATGTTCATTATTCGGACTCTGAT 59.010 33.333 0.00 0.00 0.00 2.90
486 491 2.247358 TGGTGGCCCATTCTTTTCTTC 58.753 47.619 0.00 0.00 35.17 2.87
540 545 2.588877 CCGCCTTGCCATACCTCG 60.589 66.667 0.00 0.00 0.00 4.63
671 679 4.031129 CTGCTGCTGCCTCCACCT 62.031 66.667 13.47 0.00 38.71 4.00
684 692 0.471211 TCCACCTCGTCCCAGTCTTT 60.471 55.000 0.00 0.00 0.00 2.52
707 715 2.294078 ACTGGGCCTCCTTCCTTCG 61.294 63.158 4.53 0.00 0.00 3.79
746 754 4.521146 CAGCTAGGTTGATTTCATCCAGT 58.479 43.478 9.69 0.00 38.01 4.00
759 767 1.132453 CATCCAGTGCAGCATCACTTG 59.868 52.381 0.00 5.80 44.26 3.16
779 787 9.554395 TCACTTGTCTTAGTTGTTGAATCAATA 57.446 29.630 0.00 0.00 0.00 1.90
784 792 9.166173 TGTCTTAGTTGTTGAATCAATAGATGG 57.834 33.333 0.00 0.00 33.90 3.51
877 885 3.243771 CCCCTGGATCACGTATTAGTGTC 60.244 52.174 0.00 0.00 42.40 3.67
913 921 0.821517 TGTATGCTCCCGTAGTGTGG 59.178 55.000 0.00 0.00 0.00 4.17
919 927 0.179100 CTCCCGTAGTGTGGCATCAG 60.179 60.000 0.00 0.00 0.00 2.90
945 953 1.550524 TCTACCGATGCTTGCAAGAGT 59.449 47.619 30.39 16.67 0.00 3.24
948 956 2.778299 ACCGATGCTTGCAAGAGTTTA 58.222 42.857 30.39 10.07 0.00 2.01
953 961 6.095440 ACCGATGCTTGCAAGAGTTTATTATT 59.905 34.615 30.39 0.63 0.00 1.40
954 962 7.282224 ACCGATGCTTGCAAGAGTTTATTATTA 59.718 33.333 30.39 1.27 0.00 0.98
1071 1080 3.173953 TCAAAGCCAAGGAATCATGGT 57.826 42.857 6.25 0.00 39.00 3.55
1338 1359 1.084370 CGAATGTCAAGGGAGTCGCC 61.084 60.000 3.13 0.00 0.00 5.54
1365 1386 2.519302 AGCCACTGCAACACACCC 60.519 61.111 0.00 0.00 41.13 4.61
1374 1395 0.179018 GCAACACACCCTCTCAGGTT 60.179 55.000 0.00 0.00 38.39 3.50
1476 1497 1.153549 GCCAGGGATGACTCGTGAC 60.154 63.158 0.00 0.00 0.00 3.67
1544 1565 0.037975 GTTGCAGACAATTGCCCTGG 60.038 55.000 22.25 10.14 43.43 4.45
1612 1633 4.142752 CGATTGCTGCTGAGATTCTGAAAA 60.143 41.667 0.00 0.00 0.00 2.29
1935 1956 2.577378 GTCGAGTCTTCGCTCCGC 60.577 66.667 0.00 0.00 46.28 5.54
2023 2044 2.413837 TCTTTGCGTCCAGAGTTAAGC 58.586 47.619 0.00 0.00 0.00 3.09
2058 2079 5.006386 GGTGTTGAGTCCATCATTTCTTCT 58.994 41.667 0.00 0.00 37.89 2.85
2090 2111 3.555168 GGAATAACCGAGTATGAGGCCAG 60.555 52.174 5.01 0.00 0.00 4.85
2097 2118 0.987294 AGTATGAGGCCAGTGCACTT 59.013 50.000 18.94 1.55 40.13 3.16
2142 2163 1.481871 CCAGCATTGAGAAGGGCATT 58.518 50.000 0.00 0.00 0.00 3.56
2172 2193 0.106519 ACAAACAACAGGGAGCTGCT 60.107 50.000 0.00 0.00 0.00 4.24
2175 2196 3.060615 CAACAGGGAGCTGCTGCC 61.061 66.667 30.25 30.25 42.52 4.85
2186 2207 0.888285 GCTGCTGCCTCTGTTTGAGT 60.888 55.000 3.85 0.00 41.11 3.41
2187 2208 0.873054 CTGCTGCCTCTGTTTGAGTG 59.127 55.000 0.00 0.00 41.11 3.51
2208 2234 9.109246 TGAGTGAGGAGAATGATAATTCCATAT 57.891 33.333 0.00 0.00 32.02 1.78
2215 2244 9.393512 GGAGAATGATAATTCCATATGAAGAGG 57.606 37.037 3.65 0.00 36.14 3.69
2217 2246 9.956640 AGAATGATAATTCCATATGAAGAGGAC 57.043 33.333 3.65 0.00 36.14 3.85
2227 2256 5.393461 CCATATGAAGAGGACAAAGGCAAAC 60.393 44.000 3.65 0.00 0.00 2.93
2263 2295 2.498167 AGTTTTGCAGCCTAGAGTGTG 58.502 47.619 0.00 0.00 0.00 3.82
2275 2317 2.751166 AGAGTGTGGACATGTAGCAC 57.249 50.000 15.09 15.09 0.00 4.40
2301 2345 3.672808 CCCTGGAGCAGCTATATTTCTG 58.327 50.000 0.00 0.92 0.00 3.02
2436 2483 2.289945 CCTGCTGTTCTTGTAGCTTCCT 60.290 50.000 0.00 0.00 40.52 3.36
2445 2492 4.806330 TCTTGTAGCTTCCTAAGTTGACG 58.194 43.478 0.00 0.00 0.00 4.35
2449 2496 4.280174 TGTAGCTTCCTAAGTTGACGAACT 59.720 41.667 0.00 0.00 44.79 3.01
2498 2546 0.521291 CGTTACCAAGGCACACCATG 59.479 55.000 0.00 0.00 39.06 3.66
2505 2553 2.292267 CAAGGCACACCATGTAGATCC 58.708 52.381 0.00 0.00 39.06 3.36
2509 2557 0.532862 CACACCATGTAGATCCGCCC 60.533 60.000 0.00 0.00 0.00 6.13
2512 2560 1.372683 CCATGTAGATCCGCCCCTG 59.627 63.158 0.00 0.00 0.00 4.45
2542 2590 6.880529 TGGCATCATATTGTATGGTGTCATAG 59.119 38.462 12.14 0.00 39.53 2.23
2547 2595 9.944376 ATCATATTGTATGGTGTCATAGGTTAC 57.056 33.333 0.00 0.00 36.62 2.50
2591 2639 6.064717 AGCCAGTGGGATGAATAATACTTTC 58.935 40.000 12.15 0.00 35.59 2.62
2592 2640 5.241728 GCCAGTGGGATGAATAATACTTTCC 59.758 44.000 12.15 0.00 35.59 3.13
2610 2658 2.468831 TCCGCAAGATTTTTGTGCAAC 58.531 42.857 0.00 0.00 38.19 4.17
2612 2660 2.801679 CCGCAAGATTTTTGTGCAACAT 59.198 40.909 0.00 0.00 46.09 2.71
2626 2674 3.001634 GTGCAACATCATCGTACAGATGG 59.998 47.826 20.15 11.97 46.44 3.51
2640 2688 0.625849 AGATGGCCCCCTTTGTACAG 59.374 55.000 0.00 0.00 0.00 2.74
2686 2743 5.762825 ATCATACAACTGCCATCATGTTC 57.237 39.130 0.00 0.00 0.00 3.18
2695 2752 2.359848 TGCCATCATGTTCTGCATAAGC 59.640 45.455 0.00 0.00 42.57 3.09
2796 2853 5.863397 CCTGATACGTTTCATTTGTTTGCAT 59.137 36.000 9.19 0.00 0.00 3.96
2798 2856 7.095691 CCTGATACGTTTCATTTGTTTGCATTT 60.096 33.333 9.19 0.00 0.00 2.32
2800 2858 7.436376 TGATACGTTTCATTTGTTTGCATTTCA 59.564 29.630 4.46 0.00 0.00 2.69
2803 2861 7.786114 ACGTTTCATTTGTTTGCATTTCATAG 58.214 30.769 0.00 0.00 0.00 2.23
2809 2867 5.940192 TTGTTTGCATTTCATAGTCTCGT 57.060 34.783 0.00 0.00 0.00 4.18
2821 2879 8.786826 TTTCATAGTCTCGTGGAATAAATGTT 57.213 30.769 0.00 0.00 0.00 2.71
2825 2883 8.664798 CATAGTCTCGTGGAATAAATGTTTTGA 58.335 33.333 0.00 0.00 0.00 2.69
2826 2884 7.133891 AGTCTCGTGGAATAAATGTTTTGAG 57.866 36.000 0.00 0.00 0.00 3.02
2827 2885 6.710744 AGTCTCGTGGAATAAATGTTTTGAGT 59.289 34.615 0.00 0.00 0.00 3.41
2828 2886 7.876068 AGTCTCGTGGAATAAATGTTTTGAGTA 59.124 33.333 0.00 0.00 0.00 2.59
2839 2897 7.851822 AAATGTTTTGAGTATTTGTGCGTAG 57.148 32.000 0.00 0.00 0.00 3.51
2869 2927 2.081955 AGCCCTGGTGCTTTCAGAT 58.918 52.632 4.13 0.00 38.85 2.90
2898 2956 4.462483 GGACAGGCATGGTAAAATTCTCAA 59.538 41.667 2.31 0.00 0.00 3.02
2910 2969 9.685828 TGGTAAAATTCTCAACTTTTTATTCGG 57.314 29.630 0.00 0.00 30.19 4.30
2911 2970 8.644619 GGTAAAATTCTCAACTTTTTATTCGGC 58.355 33.333 0.00 0.00 30.19 5.54
2930 2989 1.070914 GCTCTTCCCTATGCACCCTAC 59.929 57.143 0.00 0.00 0.00 3.18
3031 3090 2.423185 TGTTGTCTTGTTCCTGCTGTTG 59.577 45.455 0.00 0.00 0.00 3.33
3033 3092 2.722094 TGTCTTGTTCCTGCTGTTGTT 58.278 42.857 0.00 0.00 0.00 2.83
3070 3129 2.509964 TGGAAGGATTAGGGGAGAAAGC 59.490 50.000 0.00 0.00 0.00 3.51
3112 3171 4.159506 TGTTCTTGGGTTTCTGGTCAAAAG 59.840 41.667 0.00 0.00 0.00 2.27
3126 3185 4.340950 TGGTCAAAAGATTGGGTGAAGTTC 59.659 41.667 0.00 0.00 37.15 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.481128 CCCTACTCTCCTCCTCCTCC 59.519 65.000 0.00 0.00 0.00 4.30
1 2 0.481128 CCCCTACTCTCCTCCTCCTC 59.519 65.000 0.00 0.00 0.00 3.71
2 3 0.048117 TCCCCTACTCTCCTCCTCCT 59.952 60.000 0.00 0.00 0.00 3.69
3 4 0.935194 TTCCCCTACTCTCCTCCTCC 59.065 60.000 0.00 0.00 0.00 4.30
4 5 1.751382 CGTTCCCCTACTCTCCTCCTC 60.751 61.905 0.00 0.00 0.00 3.71
5 6 0.259356 CGTTCCCCTACTCTCCTCCT 59.741 60.000 0.00 0.00 0.00 3.69
6 7 1.393487 GCGTTCCCCTACTCTCCTCC 61.393 65.000 0.00 0.00 0.00 4.30
7 8 0.396001 AGCGTTCCCCTACTCTCCTC 60.396 60.000 0.00 0.00 0.00 3.71
10 11 1.728672 CGAGCGTTCCCCTACTCTC 59.271 63.158 0.00 0.00 0.00 3.20
11 12 2.416432 GCGAGCGTTCCCCTACTCT 61.416 63.158 0.00 0.00 0.00 3.24
12 13 2.104530 GCGAGCGTTCCCCTACTC 59.895 66.667 0.00 0.00 0.00 2.59
13 14 3.823330 CGCGAGCGTTCCCCTACT 61.823 66.667 0.00 0.00 34.35 2.57
65 66 2.370849 AGAGGAGAGGATAGGTCTCGAC 59.629 54.545 0.00 0.00 41.32 4.20
66 67 2.696775 AGAGGAGAGGATAGGTCTCGA 58.303 52.381 0.00 0.00 41.32 4.04
67 68 4.627284 TTAGAGGAGAGGATAGGTCTCG 57.373 50.000 0.00 0.00 41.32 4.04
72 73 5.317808 TGTTCGATTAGAGGAGAGGATAGG 58.682 45.833 0.00 0.00 0.00 2.57
73 74 6.488683 ACTTGTTCGATTAGAGGAGAGGATAG 59.511 42.308 0.00 0.00 0.00 2.08
74 75 6.366340 ACTTGTTCGATTAGAGGAGAGGATA 58.634 40.000 0.00 0.00 0.00 2.59
75 76 5.205056 ACTTGTTCGATTAGAGGAGAGGAT 58.795 41.667 0.00 0.00 0.00 3.24
76 77 4.601084 ACTTGTTCGATTAGAGGAGAGGA 58.399 43.478 0.00 0.00 0.00 3.71
77 78 4.202070 GGACTTGTTCGATTAGAGGAGAGG 60.202 50.000 0.00 0.00 0.00 3.69
78 79 4.642885 AGGACTTGTTCGATTAGAGGAGAG 59.357 45.833 0.00 0.00 0.00 3.20
79 80 4.399618 CAGGACTTGTTCGATTAGAGGAGA 59.600 45.833 0.00 0.00 0.00 3.71
80 81 4.158764 ACAGGACTTGTTCGATTAGAGGAG 59.841 45.833 0.00 0.00 36.31 3.69
81 82 4.087182 ACAGGACTTGTTCGATTAGAGGA 58.913 43.478 0.00 0.00 36.31 3.71
102 103 5.397240 GTGAAATACAAAAGTGCGTGGTAAC 59.603 40.000 0.00 0.00 0.00 2.50
103 104 5.297278 AGTGAAATACAAAAGTGCGTGGTAA 59.703 36.000 0.00 0.00 0.00 2.85
104 105 4.817464 AGTGAAATACAAAAGTGCGTGGTA 59.183 37.500 0.00 0.00 0.00 3.25
105 106 3.630312 AGTGAAATACAAAAGTGCGTGGT 59.370 39.130 0.00 0.00 0.00 4.16
106 107 4.223320 AGTGAAATACAAAAGTGCGTGG 57.777 40.909 0.00 0.00 0.00 4.94
108 109 4.336993 TGGAAGTGAAATACAAAAGTGCGT 59.663 37.500 0.00 0.00 0.00 5.24
109 110 4.854399 TGGAAGTGAAATACAAAAGTGCG 58.146 39.130 0.00 0.00 0.00 5.34
110 111 8.986477 ATATTGGAAGTGAAATACAAAAGTGC 57.014 30.769 0.00 0.00 0.00 4.40
118 119 9.869844 CGATCAAAGATATTGGAAGTGAAATAC 57.130 33.333 0.00 0.00 0.00 1.89
119 120 9.613428 ACGATCAAAGATATTGGAAGTGAAATA 57.387 29.630 0.00 0.00 0.00 1.40
120 121 8.511604 ACGATCAAAGATATTGGAAGTGAAAT 57.488 30.769 0.00 0.00 0.00 2.17
121 122 7.921786 ACGATCAAAGATATTGGAAGTGAAA 57.078 32.000 0.00 0.00 0.00 2.69
122 123 9.613428 AATACGATCAAAGATATTGGAAGTGAA 57.387 29.630 0.00 0.00 0.00 3.18
212 213 9.248291 GAAACCAAATACGCATATGATGAAAAT 57.752 29.630 6.97 0.00 0.00 1.82
213 214 8.246871 TGAAACCAAATACGCATATGATGAAAA 58.753 29.630 6.97 0.00 0.00 2.29
214 215 7.766283 TGAAACCAAATACGCATATGATGAAA 58.234 30.769 6.97 0.00 0.00 2.69
215 216 7.326968 TGAAACCAAATACGCATATGATGAA 57.673 32.000 6.97 0.00 0.00 2.57
216 217 6.934048 TGAAACCAAATACGCATATGATGA 57.066 33.333 6.97 0.00 0.00 2.92
217 218 7.984002 TTTGAAACCAAATACGCATATGATG 57.016 32.000 6.97 0.00 0.00 3.07
225 226 9.923786 AAGTAAAAATTTTGAAACCAAATACGC 57.076 25.926 3.73 0.00 33.96 4.42
243 244 9.355215 TCGAGTTTGTGCAAAAATAAGTAAAAA 57.645 25.926 5.11 0.00 31.33 1.94
244 245 8.912787 TCGAGTTTGTGCAAAAATAAGTAAAA 57.087 26.923 5.11 0.00 31.33 1.52
245 246 9.176181 GATCGAGTTTGTGCAAAAATAAGTAAA 57.824 29.630 5.11 0.00 31.33 2.01
246 247 8.346300 TGATCGAGTTTGTGCAAAAATAAGTAA 58.654 29.630 5.11 0.00 31.33 2.24
248 249 6.734137 TGATCGAGTTTGTGCAAAAATAAGT 58.266 32.000 5.11 0.00 31.33 2.24
251 252 8.586570 AATTTGATCGAGTTTGTGCAAAAATA 57.413 26.923 5.11 0.00 31.33 1.40
252 253 7.481275 AATTTGATCGAGTTTGTGCAAAAAT 57.519 28.000 5.11 0.00 31.33 1.82
253 254 6.900568 AATTTGATCGAGTTTGTGCAAAAA 57.099 29.167 0.00 0.00 31.33 1.94
255 256 6.900568 AAAATTTGATCGAGTTTGTGCAAA 57.099 29.167 4.33 0.00 0.00 3.68
256 257 7.864882 TCATAAAATTTGATCGAGTTTGTGCAA 59.135 29.630 4.33 0.00 0.00 4.08
267 268 9.450807 GGGTCAAACTATCATAAAATTTGATCG 57.549 33.333 0.00 0.00 39.98 3.69
270 271 8.966868 GGAGGGTCAAACTATCATAAAATTTGA 58.033 33.333 0.00 0.00 37.03 2.69
271 272 8.748412 TGGAGGGTCAAACTATCATAAAATTTG 58.252 33.333 0.00 0.00 0.00 2.32
272 273 8.893563 TGGAGGGTCAAACTATCATAAAATTT 57.106 30.769 0.00 0.00 0.00 1.82
273 274 8.116026 ACTGGAGGGTCAAACTATCATAAAATT 58.884 33.333 0.00 0.00 0.00 1.82
274 275 7.643123 ACTGGAGGGTCAAACTATCATAAAAT 58.357 34.615 0.00 0.00 0.00 1.82
275 276 7.027874 ACTGGAGGGTCAAACTATCATAAAA 57.972 36.000 0.00 0.00 0.00 1.52
277 278 7.743116 TTACTGGAGGGTCAAACTATCATAA 57.257 36.000 0.00 0.00 0.00 1.90
279 280 6.636454 TTTACTGGAGGGTCAAACTATCAT 57.364 37.500 0.00 0.00 0.00 2.45
280 281 6.442541 TTTTACTGGAGGGTCAAACTATCA 57.557 37.500 0.00 0.00 0.00 2.15
281 282 7.148069 CCAATTTTACTGGAGGGTCAAACTATC 60.148 40.741 0.00 0.00 35.85 2.08
282 283 6.663523 CCAATTTTACTGGAGGGTCAAACTAT 59.336 38.462 0.00 0.00 35.85 2.12
283 284 6.007703 CCAATTTTACTGGAGGGTCAAACTA 58.992 40.000 0.00 0.00 35.85 2.24
284 285 4.832823 CCAATTTTACTGGAGGGTCAAACT 59.167 41.667 0.00 0.00 35.85 2.66
285 286 4.830600 TCCAATTTTACTGGAGGGTCAAAC 59.169 41.667 0.00 0.00 38.07 2.93
286 287 5.068215 TCCAATTTTACTGGAGGGTCAAA 57.932 39.130 0.00 0.00 38.07 2.69
287 288 4.733077 TCCAATTTTACTGGAGGGTCAA 57.267 40.909 0.00 0.00 38.07 3.18
289 290 6.661805 TGTATTTCCAATTTTACTGGAGGGTC 59.338 38.462 0.00 0.00 43.79 4.46
290 291 6.557568 TGTATTTCCAATTTTACTGGAGGGT 58.442 36.000 0.00 0.00 43.79 4.34
292 293 8.971073 AGAATGTATTTCCAATTTTACTGGAGG 58.029 33.333 0.00 0.00 43.79 4.30
306 307 8.182227 CCTCCGTTCTTTAAAGAATGTATTTCC 58.818 37.037 33.00 18.94 45.97 3.13
308 309 7.886446 TCCCTCCGTTCTTTAAAGAATGTATTT 59.114 33.333 33.00 0.00 45.97 1.40
310 311 6.954232 TCCCTCCGTTCTTTAAAGAATGTAT 58.046 36.000 33.00 0.00 45.97 2.29
312 313 5.221864 ACTCCCTCCGTTCTTTAAAGAATGT 60.222 40.000 33.00 19.07 45.97 2.71
313 314 5.246307 ACTCCCTCCGTTCTTTAAAGAATG 58.754 41.667 30.82 30.82 45.83 2.67
314 315 5.500546 ACTCCCTCCGTTCTTTAAAGAAT 57.499 39.130 28.46 10.65 45.83 2.40
315 316 4.968971 ACTCCCTCCGTTCTTTAAAGAA 57.031 40.909 23.65 23.65 42.41 2.52
316 317 6.097412 GGTATACTCCCTCCGTTCTTTAAAGA 59.903 42.308 13.99 13.99 0.00 2.52
317 318 6.127253 TGGTATACTCCCTCCGTTCTTTAAAG 60.127 42.308 9.04 9.04 0.00 1.85
318 319 5.721000 TGGTATACTCCCTCCGTTCTTTAAA 59.279 40.000 2.25 0.00 0.00 1.52
320 321 4.870636 TGGTATACTCCCTCCGTTCTTTA 58.129 43.478 2.25 0.00 0.00 1.85
323 324 3.614568 ATGGTATACTCCCTCCGTTCT 57.385 47.619 2.25 0.00 0.00 3.01
394 398 1.407299 CGATGGGAGTCATTTCCAGCA 60.407 52.381 2.93 0.00 39.09 4.41
671 679 2.144078 TGGCCAAAGACTGGGACGA 61.144 57.895 0.61 0.00 46.54 4.20
695 703 0.173708 CCTCGAACGAAGGAAGGAGG 59.826 60.000 0.00 0.00 35.56 4.30
746 754 3.407424 ACTAAGACAAGTGATGCTGCA 57.593 42.857 4.13 4.13 0.00 4.41
759 767 9.383519 TCCATCTATTGATTCAACAACTAAGAC 57.616 33.333 0.15 0.00 32.50 3.01
779 787 2.877866 CTACCGTAGTGGGATCCATCT 58.122 52.381 15.23 13.10 44.64 2.90
840 848 1.049289 AGGGGCGGATCTAGTTGGTC 61.049 60.000 0.00 0.00 0.00 4.02
913 921 1.883084 CGGTAGAACGGCCTGATGC 60.883 63.158 0.00 0.00 40.16 3.91
919 927 1.153429 AAGCATCGGTAGAACGGCC 60.153 57.895 0.00 0.00 0.00 6.13
929 937 4.361451 AATAAACTCTTGCAAGCATCGG 57.639 40.909 21.99 10.77 0.00 4.18
964 973 8.579850 AGGAACAGAATTGCATTAGATTTGTA 57.420 30.769 0.00 0.00 0.00 2.41
965 974 7.472334 AGGAACAGAATTGCATTAGATTTGT 57.528 32.000 0.00 0.00 0.00 2.83
967 976 8.579850 TGTAGGAACAGAATTGCATTAGATTT 57.420 30.769 0.00 0.00 0.00 2.17
1071 1080 3.459598 AGGATGCCTTTAAGCCACTGATA 59.540 43.478 0.00 0.00 0.00 2.15
1267 1288 3.588842 AGAGGGGACATCTTGATCAACAA 59.411 43.478 3.38 0.00 36.97 2.83
1365 1386 4.382470 CCAGTGAAGTCCATAACCTGAGAG 60.382 50.000 0.00 0.00 0.00 3.20
1374 1395 0.911769 CAGGGCCAGTGAAGTCCATA 59.088 55.000 6.18 0.00 0.00 2.74
1476 1497 2.910482 CGCATTGATGTTGAAAAGGTCG 59.090 45.455 0.00 0.00 0.00 4.79
1544 1565 5.509498 TGCTGATAATATGGATAAAGGCCC 58.491 41.667 0.00 0.00 0.00 5.80
1612 1633 3.256704 TGGGATTGTAGACACCCTTCTT 58.743 45.455 9.18 0.00 42.49 2.52
1782 1803 0.321671 CCGTGAAGGTGACAGATGGT 59.678 55.000 0.00 0.00 34.51 3.55
1935 1956 2.821366 GGATCACCAGCCAGTGCG 60.821 66.667 0.00 0.00 44.33 5.34
2023 2044 3.490348 ACTCAACACCATTCTTCCCAAG 58.510 45.455 0.00 0.00 0.00 3.61
2058 2079 1.200519 CGGTTATTCCCTCCAGGTCA 58.799 55.000 0.00 0.00 36.75 4.02
2090 2111 1.668047 GCTTCAATGCCTCAAGTGCAC 60.668 52.381 9.40 9.40 42.38 4.57
2160 2181 3.715097 GAGGCAGCAGCTCCCTGT 61.715 66.667 10.64 0.00 41.26 4.00
2186 2207 9.955102 CTTCATATGGAATTATCATTCTCCTCA 57.045 33.333 2.13 0.00 39.17 3.86
2195 2218 9.565090 CTTTGTCCTCTTCATATGGAATTATCA 57.435 33.333 2.13 0.00 34.32 2.15
2208 2234 2.951642 CAGTTTGCCTTTGTCCTCTTCA 59.048 45.455 0.00 0.00 0.00 3.02
2215 2244 3.319122 AGGACAATCAGTTTGCCTTTGTC 59.681 43.478 5.72 5.72 43.31 3.18
2217 2246 4.326504 AAGGACAATCAGTTTGCCTTTG 57.673 40.909 11.33 0.00 43.37 2.77
2227 2256 6.738114 TGCAAAACTAGAAAAGGACAATCAG 58.262 36.000 0.00 0.00 0.00 2.90
2263 2295 1.417890 AGGGCATAGTGCTACATGTCC 59.582 52.381 0.00 7.33 45.50 4.02
2275 2317 0.982704 ATAGCTGCTCCAGGGCATAG 59.017 55.000 4.91 0.00 41.63 2.23
2375 2422 9.442047 AAATTTATGTGTCAAACAAAACAAGGA 57.558 25.926 0.00 0.00 43.61 3.36
2436 2483 9.661563 ATTATTATTCCACAGTTCGTCAACTTA 57.338 29.630 0.00 0.00 41.24 2.24
2445 2492 8.232913 TGGGCTTTATTATTATTCCACAGTTC 57.767 34.615 0.00 0.00 0.00 3.01
2449 2496 9.432982 AAAGATGGGCTTTATTATTATTCCACA 57.567 29.630 0.00 0.00 44.78 4.17
2512 2560 3.125829 CCATACAATATGATGCCACGAGC 59.874 47.826 0.00 0.00 44.14 5.03
2520 2568 8.853077 AACCTATGACACCATACAATATGATG 57.147 34.615 0.00 0.00 34.31 3.07
2522 2570 9.154632 AGTAACCTATGACACCATACAATATGA 57.845 33.333 0.00 0.00 34.31 2.15
2542 2590 8.263940 TCATCTTACAACAGCAATTAGTAACC 57.736 34.615 0.00 0.00 0.00 2.85
2547 2595 5.355071 TGGCTCATCTTACAACAGCAATTAG 59.645 40.000 0.00 0.00 0.00 1.73
2591 2639 2.200067 TGTTGCACAAAAATCTTGCGG 58.800 42.857 0.00 0.00 39.22 5.69
2592 2640 3.490155 TGATGTTGCACAAAAATCTTGCG 59.510 39.130 0.00 0.00 39.22 4.85
2603 2651 3.311486 TCTGTACGATGATGTTGCACA 57.689 42.857 0.00 0.00 0.00 4.57
2619 2667 0.331616 GTACAAAGGGGGCCATCTGT 59.668 55.000 4.39 5.43 0.00 3.41
2626 2674 0.623723 TGGATCTGTACAAAGGGGGC 59.376 55.000 0.00 0.00 0.00 5.80
2640 2688 4.344679 ACTCAGACAATCAGATCCTGGATC 59.655 45.833 25.90 25.90 39.17 3.36
2672 2729 2.139323 ATGCAGAACATGATGGCAGT 57.861 45.000 0.00 0.00 37.70 4.40
2675 2732 2.359848 TGCTTATGCAGAACATGATGGC 59.640 45.455 0.00 0.00 45.31 4.40
2703 2760 5.531753 ATTGCCTCCTGATATGGATGAAT 57.468 39.130 0.00 0.00 35.30 2.57
2779 2836 7.786114 ACTATGAAATGCAAACAAATGAAACG 58.214 30.769 0.00 0.00 0.00 3.60
2796 2853 8.786826 AACATTTATTCCACGAGACTATGAAA 57.213 30.769 0.00 0.00 0.00 2.69
2798 2856 8.664798 CAAAACATTTATTCCACGAGACTATGA 58.335 33.333 0.00 0.00 0.00 2.15
2800 2858 8.786826 TCAAAACATTTATTCCACGAGACTAT 57.213 30.769 0.00 0.00 0.00 2.12
2803 2861 6.899114 ACTCAAAACATTTATTCCACGAGAC 58.101 36.000 0.00 0.00 0.00 3.36
2809 2867 9.202273 GCACAAATACTCAAAACATTTATTCCA 57.798 29.630 0.00 0.00 0.00 3.53
2821 2879 4.688879 CCAGACTACGCACAAATACTCAAA 59.311 41.667 0.00 0.00 0.00 2.69
2825 2883 2.829720 TCCCAGACTACGCACAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
2826 2884 3.241067 TCCCAGACTACGCACAAATAC 57.759 47.619 0.00 0.00 0.00 1.89
2827 2885 3.449377 TGATCCCAGACTACGCACAAATA 59.551 43.478 0.00 0.00 0.00 1.40
2828 2886 2.236146 TGATCCCAGACTACGCACAAAT 59.764 45.455 0.00 0.00 0.00 2.32
2839 2897 0.394899 CCAGGGCTTTGATCCCAGAC 60.395 60.000 0.48 0.00 46.36 3.51
2869 2927 4.051167 CCATGCCTGTCCCTGCCA 62.051 66.667 0.00 0.00 0.00 4.92
2898 2956 4.302559 AGGGAAGAGCCGAATAAAAAGT 57.697 40.909 0.00 0.00 37.63 2.66
2910 2969 1.070914 GTAGGGTGCATAGGGAAGAGC 59.929 57.143 0.00 0.00 0.00 4.09
2911 2970 1.694696 GGTAGGGTGCATAGGGAAGAG 59.305 57.143 0.00 0.00 0.00 2.85
2962 3021 1.341531 GGGAGCGAGCATGTATACTGT 59.658 52.381 4.17 0.00 0.00 3.55
2964 3023 2.002505 AGGGAGCGAGCATGTATACT 57.997 50.000 4.17 0.00 0.00 2.12
3070 3129 4.559862 ACATCAACTAACTCTTCCCCTG 57.440 45.455 0.00 0.00 0.00 4.45
3112 3171 2.519013 AGGCTTGAACTTCACCCAATC 58.481 47.619 9.32 0.00 0.00 2.67
3126 3185 5.841810 TCCTTTTAACACATTCAAGGCTTG 58.158 37.500 21.17 21.17 34.99 4.01


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

AutoCloner maintained by Alex Coulton.