Multiple sequence alignment - TraesCS1D01G159900

Loading Multiple Alignment...

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 TraesCS1D01G159900 chr1D 100.000 2957 0 0 1 2957 225861628 225858672 0.000000e+00 5461
1 TraesCS1D01G159900 chr1A 92.644 2284 112 31 115 2360 291973669 291975934 0.000000e+00 3236
2 TraesCS1D01G159900 chr1A 91.015 601 48 5 2357 2957 292017833 292018427 0.000000e+00 806
3 TraesCS1D01G159900 chr1A 92.763 304 18 3 2060 2360 291979113 291979415 1.260000e-118 436
4 TraesCS1D01G159900 chr1B 93.573 1867 77 19 439 2272 326004991 326003135 0.000000e+00 2743
5 TraesCS1D01G159900 chr1B 88.112 143 11 3 2357 2495 325980840 325980700 6.560000e-37 165
6 TraesCS1D01G159900 chr1B 93.407 91 5 1 2271 2360 325989803 325989713 1.850000e-27 134


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 TraesCS1D01G159900 chr1D 225858672 225861628 2956 True 5461 5461 100.0000 1 2957 1 chr1D.!!$R1 2956
1 TraesCS1D01G159900 chr1A 291973669 291979415 5746 False 1836 3236 92.7035 115 2360 2 chr1A.!!$F2 2245
2 TraesCS1D01G159900 chr1A 292017833 292018427 594 False 806 806 91.0150 2357 2957 1 chr1A.!!$F1 600
3 TraesCS1D01G159900 chr1B 326003135 326004991 1856 True 2743 2743 93.5730 439 2272 1 chr1B.!!$R3 1833

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
207 209 0.998928 ATGGTAGTGACCCATTGGCA 59.001 50.000 0.0 0.0 46.32 4.92 F
487 490 1.202817 GTTCCAAACCAACCAACGTGT 59.797 47.619 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 1164 0.689623 ACAGCAGTTGGGAGAAGAGG 59.310 55.0 0.00 0.00 0.0 3.69 R
2248 5784 0.523072 CCAGACGGCCTTCAACATTG 59.477 55.0 12.41 0.17 0.0 2.82 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
25 26 6.956299 ACTCAAAATGCTTGTCATTATTGC 57.044 33.333 0.00 0.00 44.23 3.56
26 27 5.870978 ACTCAAAATGCTTGTCATTATTGCC 59.129 36.000 0.00 0.00 44.23 4.52
27 28 5.791666 TCAAAATGCTTGTCATTATTGCCA 58.208 33.333 0.00 0.00 44.23 4.92
28 29 6.408035 TCAAAATGCTTGTCATTATTGCCAT 58.592 32.000 0.00 0.00 44.23 4.40
29 30 6.879993 TCAAAATGCTTGTCATTATTGCCATT 59.120 30.769 0.00 0.00 44.23 3.16
30 31 8.039538 TCAAAATGCTTGTCATTATTGCCATTA 58.960 29.630 0.00 0.00 44.23 1.90
31 32 7.775397 AAATGCTTGTCATTATTGCCATTAC 57.225 32.000 0.00 0.00 44.23 1.89
32 33 4.919206 TGCTTGTCATTATTGCCATTACG 58.081 39.130 0.00 0.00 0.00 3.18
33 34 4.637977 TGCTTGTCATTATTGCCATTACGA 59.362 37.500 0.00 0.00 0.00 3.43
34 35 5.124617 TGCTTGTCATTATTGCCATTACGAA 59.875 36.000 0.00 0.00 0.00 3.85
35 36 5.455525 GCTTGTCATTATTGCCATTACGAAC 59.544 40.000 0.00 0.00 0.00 3.95
36 37 6.677920 GCTTGTCATTATTGCCATTACGAACT 60.678 38.462 0.00 0.00 0.00 3.01
37 38 7.466725 GCTTGTCATTATTGCCATTACGAACTA 60.467 37.037 0.00 0.00 0.00 2.24
38 39 7.477144 TGTCATTATTGCCATTACGAACTAG 57.523 36.000 0.00 0.00 0.00 2.57
39 40 6.018262 TGTCATTATTGCCATTACGAACTAGC 60.018 38.462 0.00 0.00 0.00 3.42
40 41 5.468746 TCATTATTGCCATTACGAACTAGCC 59.531 40.000 0.00 0.00 0.00 3.93
41 42 2.772077 TTGCCATTACGAACTAGCCA 57.228 45.000 0.00 0.00 0.00 4.75
42 43 2.772077 TGCCATTACGAACTAGCCAA 57.228 45.000 0.00 0.00 0.00 4.52
43 44 2.352388 TGCCATTACGAACTAGCCAAC 58.648 47.619 0.00 0.00 0.00 3.77
44 45 2.289756 TGCCATTACGAACTAGCCAACA 60.290 45.455 0.00 0.00 0.00 3.33
45 46 2.943033 GCCATTACGAACTAGCCAACAT 59.057 45.455 0.00 0.00 0.00 2.71
46 47 3.242739 GCCATTACGAACTAGCCAACATG 60.243 47.826 0.00 0.00 0.00 3.21
47 48 3.312421 CCATTACGAACTAGCCAACATGG 59.688 47.826 0.00 0.00 41.55 3.66
66 67 4.320608 TGGCAAAATTTGTCAACTCCTC 57.679 40.909 10.88 0.00 43.24 3.71
67 68 3.243367 TGGCAAAATTTGTCAACTCCTCG 60.243 43.478 10.88 0.00 43.24 4.63
68 69 3.243401 GGCAAAATTTGTCAACTCCTCGT 60.243 43.478 5.33 0.00 34.79 4.18
69 70 4.023536 GGCAAAATTTGTCAACTCCTCGTA 60.024 41.667 5.33 0.00 34.79 3.43
70 71 5.335661 GGCAAAATTTGTCAACTCCTCGTAT 60.336 40.000 5.33 0.00 34.79 3.06
71 72 6.128117 GGCAAAATTTGTCAACTCCTCGTATA 60.128 38.462 5.33 0.00 34.79 1.47
72 73 7.415206 GGCAAAATTTGTCAACTCCTCGTATAT 60.415 37.037 5.33 0.00 34.79 0.86
73 74 8.609176 GCAAAATTTGTCAACTCCTCGTATATA 58.391 33.333 7.60 0.00 0.00 0.86
78 79 9.645059 ATTTGTCAACTCCTCGTATATATCATG 57.355 33.333 0.00 0.00 0.00 3.07
79 80 7.158099 TGTCAACTCCTCGTATATATCATGG 57.842 40.000 0.00 0.00 0.00 3.66
80 81 6.946009 TGTCAACTCCTCGTATATATCATGGA 59.054 38.462 0.00 0.00 0.00 3.41
81 82 7.615757 TGTCAACTCCTCGTATATATCATGGAT 59.384 37.037 0.00 0.00 0.00 3.41
82 83 9.121658 GTCAACTCCTCGTATATATCATGGATA 57.878 37.037 0.00 0.00 0.00 2.59
83 84 9.695155 TCAACTCCTCGTATATATCATGGATAA 57.305 33.333 0.00 0.00 0.00 1.75
86 87 9.475620 ACTCCTCGTATATATCATGGATAAACA 57.524 33.333 0.00 0.00 0.00 2.83
91 92 9.830975 TCGTATATATCATGGATAAACAATGGG 57.169 33.333 0.00 0.00 0.00 4.00
92 93 9.056005 CGTATATATCATGGATAAACAATGGGG 57.944 37.037 0.00 0.00 0.00 4.96
93 94 9.920946 GTATATATCATGGATAAACAATGGGGT 57.079 33.333 0.00 0.00 0.00 4.95
96 97 5.985175 TCATGGATAAACAATGGGGTAGA 57.015 39.130 0.00 0.00 0.00 2.59
97 98 5.940617 TCATGGATAAACAATGGGGTAGAG 58.059 41.667 0.00 0.00 0.00 2.43
98 99 5.669904 TCATGGATAAACAATGGGGTAGAGA 59.330 40.000 0.00 0.00 0.00 3.10
99 100 6.159575 TCATGGATAAACAATGGGGTAGAGAA 59.840 38.462 0.00 0.00 0.00 2.87
100 101 6.395780 TGGATAAACAATGGGGTAGAGAAA 57.604 37.500 0.00 0.00 0.00 2.52
101 102 6.795590 TGGATAAACAATGGGGTAGAGAAAA 58.204 36.000 0.00 0.00 0.00 2.29
102 103 6.889722 TGGATAAACAATGGGGTAGAGAAAAG 59.110 38.462 0.00 0.00 0.00 2.27
103 104 6.890268 GGATAAACAATGGGGTAGAGAAAAGT 59.110 38.462 0.00 0.00 0.00 2.66
104 105 7.148069 GGATAAACAATGGGGTAGAGAAAAGTG 60.148 40.741 0.00 0.00 0.00 3.16
105 106 4.034285 ACAATGGGGTAGAGAAAAGTGG 57.966 45.455 0.00 0.00 0.00 4.00
106 107 3.655777 ACAATGGGGTAGAGAAAAGTGGA 59.344 43.478 0.00 0.00 0.00 4.02
107 108 4.105697 ACAATGGGGTAGAGAAAAGTGGAA 59.894 41.667 0.00 0.00 0.00 3.53
108 109 5.076873 CAATGGGGTAGAGAAAAGTGGAAA 58.923 41.667 0.00 0.00 0.00 3.13
109 110 4.799715 TGGGGTAGAGAAAAGTGGAAAA 57.200 40.909 0.00 0.00 0.00 2.29
110 111 5.333566 TGGGGTAGAGAAAAGTGGAAAAT 57.666 39.130 0.00 0.00 0.00 1.82
111 112 6.457159 TGGGGTAGAGAAAAGTGGAAAATA 57.543 37.500 0.00 0.00 0.00 1.40
112 113 6.854578 TGGGGTAGAGAAAAGTGGAAAATAA 58.145 36.000 0.00 0.00 0.00 1.40
113 114 7.475299 TGGGGTAGAGAAAAGTGGAAAATAAT 58.525 34.615 0.00 0.00 0.00 1.28
145 147 9.490663 CTTTGTACGATTTTGAATATCCTTGTC 57.509 33.333 0.00 0.00 0.00 3.18
175 177 3.827302 TCTAGGGAGCATAGTTCGATTCC 59.173 47.826 0.00 0.00 0.00 3.01
202 204 2.169769 CGGTTACATGGTAGTGACCCAT 59.830 50.000 0.00 0.00 46.32 4.00
207 209 0.998928 ATGGTAGTGACCCATTGGCA 59.001 50.000 0.00 0.00 46.32 4.92
211 213 3.713951 GGTAGTGACCCATTGGCACAAC 61.714 54.545 13.75 5.42 41.75 3.32
224 226 2.880268 TGGCACAACACATCTTCTCTTG 59.120 45.455 0.00 0.00 31.92 3.02
235 237 8.450578 ACACATCTTCTCTTGTTTCATTTGTA 57.549 30.769 0.00 0.00 0.00 2.41
236 238 8.902806 ACACATCTTCTCTTGTTTCATTTGTAA 58.097 29.630 0.00 0.00 0.00 2.41
237 239 9.173939 CACATCTTCTCTTGTTTCATTTGTAAC 57.826 33.333 0.00 0.00 0.00 2.50
238 240 9.125026 ACATCTTCTCTTGTTTCATTTGTAACT 57.875 29.630 2.47 0.00 0.00 2.24
241 243 9.832445 TCTTCTCTTGTTTCATTTGTAACTAGT 57.168 29.630 9.81 0.00 32.98 2.57
267 269 1.531149 CACACTGTTCACGTGGGATTC 59.469 52.381 17.00 2.85 38.02 2.52
270 272 3.254060 CACTGTTCACGTGGGATTCTAG 58.746 50.000 17.00 7.40 0.00 2.43
271 273 2.271800 CTGTTCACGTGGGATTCTAGC 58.728 52.381 17.00 0.00 0.00 3.42
273 275 2.236146 TGTTCACGTGGGATTCTAGCAT 59.764 45.455 17.00 0.00 0.00 3.79
284 287 8.197439 CGTGGGATTCTAGCATACATATATCAA 58.803 37.037 0.00 0.00 0.00 2.57
292 295 9.875691 TCTAGCATACATATATCAACATTCACC 57.124 33.333 0.00 0.00 0.00 4.02
300 303 8.698210 ACATATATCAACATTCACCAGCATTTT 58.302 29.630 0.00 0.00 0.00 1.82
307 310 5.815581 ACATTCACCAGCATTTTCCTAGTA 58.184 37.500 0.00 0.00 0.00 1.82
308 311 5.882557 ACATTCACCAGCATTTTCCTAGTAG 59.117 40.000 0.00 0.00 0.00 2.57
309 312 5.499004 TTCACCAGCATTTTCCTAGTAGT 57.501 39.130 0.00 0.00 0.00 2.73
316 319 5.355071 CAGCATTTTCCTAGTAGTTGCATCA 59.645 40.000 0.00 0.00 0.00 3.07
329 332 4.450976 AGTTGCATCACATATAAAGGCGA 58.549 39.130 0.00 0.00 0.00 5.54
352 355 7.361286 GCGATTTTTCTAGTTTGGTCAAGATCT 60.361 37.037 0.00 0.00 0.00 2.75
356 359 6.918067 TTCTAGTTTGGTCAAGATCTCTGA 57.082 37.500 0.00 0.00 0.00 3.27
362 365 3.653344 TGGTCAAGATCTCTGAACAACG 58.347 45.455 17.76 0.00 0.00 4.10
369 372 3.511540 AGATCTCTGAACAACGTCCATCA 59.488 43.478 0.00 0.00 0.00 3.07
379 382 4.196193 ACAACGTCCATCAGAAAGAACAA 58.804 39.130 0.00 0.00 0.00 2.83
404 407 1.269206 ACGTGAGGCAAATGCAAAGTG 60.269 47.619 7.80 0.00 44.36 3.16
419 422 3.612479 GCAAAGTGTAAAGGAGGCATGTG 60.612 47.826 0.00 0.00 0.00 3.21
436 439 1.763655 TGCCATGCCAAACCAACCA 60.764 52.632 0.00 0.00 0.00 3.67
487 490 1.202817 GTTCCAAACCAACCAACGTGT 59.797 47.619 0.00 0.00 0.00 4.49
496 499 2.159226 CCAACCAACGTGTTTGCCTTAA 60.159 45.455 0.00 0.00 33.34 1.85
501 504 3.066203 CCAACGTGTTTGCCTTAACTTCT 59.934 43.478 0.00 0.00 33.34 2.85
542 545 4.507710 CACTAGCTAGCACATTTCCTTCA 58.492 43.478 20.91 0.00 0.00 3.02
655 676 1.656652 AGCTAACTGTAAGCATGCCG 58.343 50.000 15.66 0.36 42.62 5.69
826 848 2.583593 GATGAGGCGACGGTGAGC 60.584 66.667 0.00 0.00 0.00 4.26
1062 1085 2.626743 GCCTTCCTTTGCATATGCTGAT 59.373 45.455 27.13 0.00 42.66 2.90
1068 1091 4.820173 TCCTTTGCATATGCTGATGAGAAG 59.180 41.667 27.13 17.02 42.66 2.85
1086 1109 4.145052 AGAAGACACAAGGAAAACCATCC 58.855 43.478 0.00 0.00 39.96 3.51
1131 1160 3.782523 AGGGTAATGATCTCTTCTTGCCA 59.217 43.478 0.00 0.00 0.00 4.92
1135 1164 6.238869 GGGTAATGATCTCTTCTTGCCAAATC 60.239 42.308 0.00 0.00 0.00 2.17
1203 1232 4.634703 TTCCTTGGCGCCGCAGAA 62.635 61.111 23.90 20.31 0.00 3.02
1311 1346 7.400439 AGCATGCCATCTAATATCTGTGTATT 58.600 34.615 15.66 0.00 0.00 1.89
1325 1360 6.558771 TCTGTGTATTCCAACAAGTTGATG 57.441 37.500 10.54 8.11 42.93 3.07
1327 1362 7.220740 TCTGTGTATTCCAACAAGTTGATGTA 58.779 34.615 10.54 0.00 42.93 2.29
1364 1402 4.334759 CCAGGCAACAATTCTCATCACTAG 59.665 45.833 0.00 0.00 41.41 2.57
1366 1404 5.413833 CAGGCAACAATTCTCATCACTAGTT 59.586 40.000 0.00 0.00 41.41 2.24
1368 1406 7.281774 CAGGCAACAATTCTCATCACTAGTTAT 59.718 37.037 0.00 0.00 41.41 1.89
1489 1527 4.729868 ACAAGGTCTTCAGGCAATACTTT 58.270 39.130 0.00 0.00 0.00 2.66
1609 1647 3.776969 AGATTGCCTTCCATAGTGACAGA 59.223 43.478 0.00 0.00 0.00 3.41
1727 1766 8.688151 TGGATTAAAACCCGGTTAAGAAATATG 58.312 33.333 2.39 0.00 0.00 1.78
1732 1771 3.524380 ACCCGGTTAAGAAATATGTGGGA 59.476 43.478 0.00 0.00 37.56 4.37
1759 1799 5.335113 CCATTTGAACTCGAAGCTGATGAAA 60.335 40.000 0.00 0.00 0.00 2.69
1783 1823 1.522668 TTGCATCTTTCCACAGGTCG 58.477 50.000 0.00 0.00 0.00 4.79
1906 1946 5.975693 TTGGTTTATGGGTTTCATCAGTC 57.024 39.130 0.00 0.00 37.30 3.51
2128 2180 4.453136 TGTTTTCCACGGTTATGAGCTTAC 59.547 41.667 0.00 0.00 0.00 2.34
2217 5750 4.843728 AGGCTCGATTGTGGAAAGATTTA 58.156 39.130 0.00 0.00 0.00 1.40
2248 5784 5.767816 AACCAAATGTAACAGGAAGTGAC 57.232 39.130 0.00 0.00 31.61 3.67
2267 5803 0.523072 CAATGTTGAAGGCCGTCTGG 59.477 55.000 19.81 0.00 38.77 3.86
2274 5810 0.591659 GAAGGCCGTCTGGTGTTTTC 59.408 55.000 11.87 0.00 37.67 2.29
2283 5819 4.069304 CGTCTGGTGTTTTCCCATAAAGA 58.931 43.478 0.00 0.00 0.00 2.52
2292 5828 6.366061 GTGTTTTCCCATAAAGAAGAATGCAC 59.634 38.462 0.00 0.00 0.00 4.57
2298 5834 5.327091 CCATAAAGAAGAATGCACGTTCAG 58.673 41.667 5.46 0.00 0.00 3.02
2324 5860 7.010460 GCAGATAAATACCAGCACAAATTTTCC 59.990 37.037 0.00 0.00 0.00 3.13
2333 5869 7.322664 ACCAGCACAAATTTTCCACATTATAG 58.677 34.615 0.00 0.00 0.00 1.31
2352 5888 3.932545 AGCCGACATTGTTGCAAAATA 57.067 38.095 0.00 0.00 0.00 1.40
2378 5914 1.516892 CTCTCTCTGCTGCCACCTC 59.483 63.158 0.00 0.00 0.00 3.85
2384 5920 1.376942 CTGCTGCCACCTCCTTCTG 60.377 63.158 0.00 0.00 0.00 3.02
2399 5935 3.730761 CTGCTGCGCCACCTTCAC 61.731 66.667 4.18 0.00 0.00 3.18
2412 5948 1.205893 ACCTTCACTGATTCCTCGAGC 59.794 52.381 6.99 0.00 0.00 5.03
2425 5961 3.796443 CGAGCGTCCGACGGAGAA 61.796 66.667 18.98 0.00 42.82 2.87
2497 6033 4.015406 CGGGTGCTGGTGGTGCTA 62.015 66.667 0.00 0.00 0.00 3.49
2500 6036 2.750350 GTGCTGGTGGTGCTAGGT 59.250 61.111 0.00 0.00 0.00 3.08
2501 6037 1.376037 GTGCTGGTGGTGCTAGGTC 60.376 63.158 0.00 0.00 0.00 3.85
2503 6039 1.219393 GCTGGTGGTGCTAGGTCTC 59.781 63.158 0.00 0.00 0.00 3.36
2505 6041 2.184579 GGTGGTGCTAGGTCTCGC 59.815 66.667 0.00 0.00 0.00 5.03
2513 6049 0.243907 GCTAGGTCTCGCTGTTCACA 59.756 55.000 0.00 0.00 0.00 3.58
2514 6050 1.983972 CTAGGTCTCGCTGTTCACAC 58.016 55.000 0.00 0.00 0.00 3.82
2524 6060 1.723542 GCTGTTCACACTGTCATCTCG 59.276 52.381 0.00 0.00 0.00 4.04
2526 6062 1.341209 TGTTCACACTGTCATCTCGCT 59.659 47.619 0.00 0.00 0.00 4.93
2537 6073 1.145598 ATCTCGCTGTGGATGGCAG 59.854 57.895 0.00 0.00 37.06 4.85
2542 6078 1.818785 GCTGTGGATGGCAGAGAGC 60.819 63.158 0.00 0.00 44.65 4.09
2548 6084 4.172512 ATGGCAGAGAGCGGGCAG 62.173 66.667 0.00 0.00 46.67 4.85
2562 6098 3.971702 GCAGGGCAGGGTTGGACT 61.972 66.667 0.00 0.00 0.00 3.85
2574 6110 1.918293 TTGGACTGCCACGGAGGAT 60.918 57.895 0.00 0.00 45.94 3.24
2575 6111 2.184020 TTGGACTGCCACGGAGGATG 62.184 60.000 0.00 0.00 45.94 3.51
2603 6139 2.359975 CCAGGAAGTTGGGGACGC 60.360 66.667 0.00 0.00 34.46 5.19
2647 6183 3.625897 CCATCCCCGAGCGCCATA 61.626 66.667 2.29 0.00 0.00 2.74
2678 6214 2.567049 CGCGACCTCCTTCTCGTT 59.433 61.111 0.00 0.00 32.30 3.85
2684 6220 1.249469 ACCTCCTTCTCGTTCGGGTC 61.249 60.000 0.00 0.00 0.00 4.46
2794 6330 0.921256 ATTGGGTGGAAGGGGAGGAG 60.921 60.000 0.00 0.00 0.00 3.69
2795 6331 2.692741 GGGTGGAAGGGGAGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
2796 6332 2.454941 GGTGGAAGGGGAGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
2799 6335 0.978667 GTGGAAGGGGAGGAGGAGAC 60.979 65.000 0.00 0.00 0.00 3.36
2808 6344 2.123640 GGAGGAGACGGAGGGGAG 60.124 72.222 0.00 0.00 0.00 4.30
2846 6382 1.971695 GAAGCGGAGTGGGGTTTGG 60.972 63.158 0.00 0.00 0.00 3.28
2847 6383 2.406002 GAAGCGGAGTGGGGTTTGGA 62.406 60.000 0.00 0.00 0.00 3.53
2848 6384 2.671963 GCGGAGTGGGGTTTGGAC 60.672 66.667 0.00 0.00 0.00 4.02
2849 6385 3.157680 CGGAGTGGGGTTTGGACT 58.842 61.111 0.00 0.00 0.00 3.85
2850 6386 1.833787 GCGGAGTGGGGTTTGGACTA 61.834 60.000 0.00 0.00 0.00 2.59
2853 6389 1.652947 GAGTGGGGTTTGGACTAGGA 58.347 55.000 0.00 0.00 0.00 2.94
2890 6426 1.535226 GCTTTTTGTGGGAACGGTGAC 60.535 52.381 0.00 0.00 0.00 3.67
2914 6450 4.910585 GGCGTGGGACATAGCGGG 62.911 72.222 0.00 0.00 44.52 6.13
2916 6452 4.910585 CGTGGGACATAGCGGGCC 62.911 72.222 0.00 0.00 44.52 5.80
2917 6453 4.910585 GTGGGACATAGCGGGCCG 62.911 72.222 24.35 24.35 44.52 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.095102 GGCAATAATGACAAGCATTTTGAGTTT 60.095 33.333 0.48 0.00 44.68 2.66
1 2 6.369615 GGCAATAATGACAAGCATTTTGAGTT 59.630 34.615 0.48 0.00 44.68 3.01
2 3 5.870978 GGCAATAATGACAAGCATTTTGAGT 59.129 36.000 0.48 0.00 44.68 3.41
3 4 5.870433 TGGCAATAATGACAAGCATTTTGAG 59.130 36.000 0.48 0.00 43.21 3.02
4 5 5.791666 TGGCAATAATGACAAGCATTTTGA 58.208 33.333 0.48 0.00 43.21 2.69
15 16 6.363473 GCTAGTTCGTAATGGCAATAATGAC 58.637 40.000 0.00 0.00 34.00 3.06
16 17 5.468746 GGCTAGTTCGTAATGGCAATAATGA 59.531 40.000 0.00 0.00 0.00 2.57
17 18 5.238432 TGGCTAGTTCGTAATGGCAATAATG 59.762 40.000 0.00 0.00 0.00 1.90
18 19 5.373222 TGGCTAGTTCGTAATGGCAATAAT 58.627 37.500 0.00 0.00 0.00 1.28
19 20 4.771903 TGGCTAGTTCGTAATGGCAATAA 58.228 39.130 0.00 0.00 0.00 1.40
20 21 4.409718 TGGCTAGTTCGTAATGGCAATA 57.590 40.909 0.00 0.00 0.00 1.90
21 22 3.275617 TGGCTAGTTCGTAATGGCAAT 57.724 42.857 0.00 0.00 0.00 3.56
22 23 2.745281 GTTGGCTAGTTCGTAATGGCAA 59.255 45.455 0.00 0.00 40.07 4.52
23 24 2.289756 TGTTGGCTAGTTCGTAATGGCA 60.290 45.455 0.00 0.00 0.00 4.92
24 25 2.352388 TGTTGGCTAGTTCGTAATGGC 58.648 47.619 0.00 0.00 0.00 4.40
25 26 3.312421 CCATGTTGGCTAGTTCGTAATGG 59.688 47.826 0.00 0.00 0.00 3.16
26 27 4.536364 CCATGTTGGCTAGTTCGTAATG 57.464 45.455 0.00 0.00 0.00 1.90
39 40 4.575645 AGTTGACAAATTTTGCCATGTTGG 59.424 37.500 9.04 0.00 41.55 3.77
40 41 5.277442 GGAGTTGACAAATTTTGCCATGTTG 60.277 40.000 9.04 0.00 0.00 3.33
41 42 4.815846 GGAGTTGACAAATTTTGCCATGTT 59.184 37.500 9.04 0.00 0.00 2.71
42 43 4.101430 AGGAGTTGACAAATTTTGCCATGT 59.899 37.500 9.04 0.00 0.00 3.21
43 44 4.634199 AGGAGTTGACAAATTTTGCCATG 58.366 39.130 9.04 0.00 0.00 3.66
44 45 4.559300 CGAGGAGTTGACAAATTTTGCCAT 60.559 41.667 9.04 0.00 0.00 4.40
45 46 3.243367 CGAGGAGTTGACAAATTTTGCCA 60.243 43.478 9.04 1.32 0.00 4.92
46 47 3.243401 ACGAGGAGTTGACAAATTTTGCC 60.243 43.478 9.04 0.00 0.00 4.52
47 48 3.964909 ACGAGGAGTTGACAAATTTTGC 58.035 40.909 9.04 3.32 0.00 3.68
52 53 9.645059 CATGATATATACGAGGAGTTGACAAAT 57.355 33.333 0.00 0.00 0.00 2.32
53 54 8.088365 CCATGATATATACGAGGAGTTGACAAA 58.912 37.037 0.00 0.00 0.00 2.83
54 55 7.450323 TCCATGATATATACGAGGAGTTGACAA 59.550 37.037 0.00 0.00 0.00 3.18
55 56 6.946009 TCCATGATATATACGAGGAGTTGACA 59.054 38.462 0.00 0.00 0.00 3.58
56 57 7.392494 TCCATGATATATACGAGGAGTTGAC 57.608 40.000 0.00 0.00 0.00 3.18
57 58 9.695155 TTATCCATGATATATACGAGGAGTTGA 57.305 33.333 0.00 0.00 0.00 3.18
60 61 9.475620 TGTTTATCCATGATATATACGAGGAGT 57.524 33.333 0.00 0.00 0.00 3.85
65 66 9.830975 CCCATTGTTTATCCATGATATATACGA 57.169 33.333 0.00 0.00 0.00 3.43
66 67 9.056005 CCCCATTGTTTATCCATGATATATACG 57.944 37.037 0.00 0.00 0.00 3.06
67 68 9.920946 ACCCCATTGTTTATCCATGATATATAC 57.079 33.333 0.00 0.00 0.00 1.47
70 71 9.345254 TCTACCCCATTGTTTATCCATGATATA 57.655 33.333 0.00 0.00 0.00 0.86
71 72 8.230848 TCTACCCCATTGTTTATCCATGATAT 57.769 34.615 0.00 0.00 0.00 1.63
72 73 7.515861 TCTCTACCCCATTGTTTATCCATGATA 59.484 37.037 0.00 0.00 0.00 2.15
73 74 6.332635 TCTCTACCCCATTGTTTATCCATGAT 59.667 38.462 0.00 0.00 0.00 2.45
74 75 5.669904 TCTCTACCCCATTGTTTATCCATGA 59.330 40.000 0.00 0.00 0.00 3.07
75 76 5.940617 TCTCTACCCCATTGTTTATCCATG 58.059 41.667 0.00 0.00 0.00 3.66
76 77 6.590656 TTCTCTACCCCATTGTTTATCCAT 57.409 37.500 0.00 0.00 0.00 3.41
77 78 6.395780 TTTCTCTACCCCATTGTTTATCCA 57.604 37.500 0.00 0.00 0.00 3.41
78 79 6.890268 ACTTTTCTCTACCCCATTGTTTATCC 59.110 38.462 0.00 0.00 0.00 2.59
79 80 7.148069 CCACTTTTCTCTACCCCATTGTTTATC 60.148 40.741 0.00 0.00 0.00 1.75
80 81 6.663523 CCACTTTTCTCTACCCCATTGTTTAT 59.336 38.462 0.00 0.00 0.00 1.40
81 82 6.007703 CCACTTTTCTCTACCCCATTGTTTA 58.992 40.000 0.00 0.00 0.00 2.01
82 83 4.832823 CCACTTTTCTCTACCCCATTGTTT 59.167 41.667 0.00 0.00 0.00 2.83
83 84 4.105697 TCCACTTTTCTCTACCCCATTGTT 59.894 41.667 0.00 0.00 0.00 2.83
84 85 3.655777 TCCACTTTTCTCTACCCCATTGT 59.344 43.478 0.00 0.00 0.00 2.71
85 86 4.301072 TCCACTTTTCTCTACCCCATTG 57.699 45.455 0.00 0.00 0.00 2.82
86 87 5.333566 TTTCCACTTTTCTCTACCCCATT 57.666 39.130 0.00 0.00 0.00 3.16
87 88 5.333566 TTTTCCACTTTTCTCTACCCCAT 57.666 39.130 0.00 0.00 0.00 4.00
88 89 4.799715 TTTTCCACTTTTCTCTACCCCA 57.200 40.909 0.00 0.00 0.00 4.96
89 90 7.956328 ATTATTTTCCACTTTTCTCTACCCC 57.044 36.000 0.00 0.00 0.00 4.95
101 102 8.943002 CGTACAAAGAGGTAATTATTTTCCACT 58.057 33.333 0.00 0.00 0.00 4.00
102 103 8.938906 TCGTACAAAGAGGTAATTATTTTCCAC 58.061 33.333 0.00 0.00 0.00 4.02
103 104 9.675464 ATCGTACAAAGAGGTAATTATTTTCCA 57.325 29.630 0.00 0.00 0.00 3.53
126 127 5.006649 TGAGCGACAAGGATATTCAAAATCG 59.993 40.000 0.00 0.00 0.00 3.34
175 177 1.205417 ACTACCATGTAACCGGGTTCG 59.795 52.381 17.19 3.75 36.14 3.95
202 204 3.213206 AGAGAAGATGTGTTGTGCCAA 57.787 42.857 0.00 0.00 0.00 4.52
207 209 6.949352 ATGAAACAAGAGAAGATGTGTTGT 57.051 33.333 0.00 0.00 34.54 3.32
211 213 9.173939 GTTACAAATGAAACAAGAGAAGATGTG 57.826 33.333 0.00 0.00 0.00 3.21
224 226 9.997482 TGTGAAGAAACTAGTTACAAATGAAAC 57.003 29.630 8.92 0.49 0.00 2.78
235 237 5.291128 CGTGAACAGTGTGAAGAAACTAGTT 59.709 40.000 1.12 1.12 0.00 2.24
236 238 4.804139 CGTGAACAGTGTGAAGAAACTAGT 59.196 41.667 0.00 0.00 0.00 2.57
237 239 4.804139 ACGTGAACAGTGTGAAGAAACTAG 59.196 41.667 0.00 0.00 0.00 2.57
238 240 4.565166 CACGTGAACAGTGTGAAGAAACTA 59.435 41.667 10.90 0.00 35.66 2.24
239 241 3.370978 CACGTGAACAGTGTGAAGAAACT 59.629 43.478 10.90 0.00 35.66 2.66
240 242 3.485216 CCACGTGAACAGTGTGAAGAAAC 60.485 47.826 19.30 0.00 37.88 2.78
241 243 2.675844 CCACGTGAACAGTGTGAAGAAA 59.324 45.455 19.30 0.00 37.88 2.52
242 244 2.276201 CCACGTGAACAGTGTGAAGAA 58.724 47.619 19.30 0.00 37.88 2.52
243 245 1.472552 CCCACGTGAACAGTGTGAAGA 60.473 52.381 19.30 0.00 37.88 2.87
244 246 0.937304 CCCACGTGAACAGTGTGAAG 59.063 55.000 19.30 0.00 37.88 3.02
245 247 0.537653 TCCCACGTGAACAGTGTGAA 59.462 50.000 19.30 0.00 37.88 3.18
246 248 0.756294 ATCCCACGTGAACAGTGTGA 59.244 50.000 19.30 0.59 37.88 3.58
247 249 1.531149 GAATCCCACGTGAACAGTGTG 59.469 52.381 19.30 0.00 37.88 3.82
248 250 1.416401 AGAATCCCACGTGAACAGTGT 59.584 47.619 19.30 0.00 37.88 3.55
267 269 9.657419 TGGTGAATGTTGATATATGTATGCTAG 57.343 33.333 0.00 0.00 0.00 3.42
270 272 7.094677 TGCTGGTGAATGTTGATATATGTATGC 60.095 37.037 0.00 0.00 0.00 3.14
271 273 8.326680 TGCTGGTGAATGTTGATATATGTATG 57.673 34.615 0.00 0.00 0.00 2.39
273 275 8.922931 AATGCTGGTGAATGTTGATATATGTA 57.077 30.769 0.00 0.00 0.00 2.29
284 287 4.666512 ACTAGGAAAATGCTGGTGAATGT 58.333 39.130 0.00 0.00 26.66 2.71
292 295 5.355071 TGATGCAACTACTAGGAAAATGCTG 59.645 40.000 0.00 0.00 33.66 4.41
300 303 8.367911 CCTTTATATGTGATGCAACTACTAGGA 58.632 37.037 0.00 0.00 0.00 2.94
307 310 4.450976 TCGCCTTTATATGTGATGCAACT 58.549 39.130 0.00 0.00 0.00 3.16
308 311 4.811555 TCGCCTTTATATGTGATGCAAC 57.188 40.909 0.00 0.00 0.00 4.17
309 312 6.389830 AAATCGCCTTTATATGTGATGCAA 57.610 33.333 0.00 0.00 32.37 4.08
329 332 9.007901 CAGAGATCTTGACCAAACTAGAAAAAT 57.992 33.333 0.00 0.00 0.00 1.82
352 355 3.744238 TTCTGATGGACGTTGTTCAGA 57.256 42.857 16.55 16.55 42.01 3.27
356 359 4.196193 TGTTCTTTCTGATGGACGTTGTT 58.804 39.130 0.00 0.00 0.00 2.83
419 422 0.036590 ATTGGTTGGTTTGGCATGGC 59.963 50.000 13.29 13.29 0.00 4.40
455 458 3.458857 TGGTTTGGAACAGGTTACTGGTA 59.541 43.478 0.00 0.00 46.90 3.25
487 490 5.531287 GGAGTGAAGAAGAAGTTAAGGCAAA 59.469 40.000 0.00 0.00 0.00 3.68
496 499 2.695585 ACTGGGGAGTGAAGAAGAAGT 58.304 47.619 0.00 0.00 0.00 3.01
501 504 1.064825 GGGAACTGGGGAGTGAAGAA 58.935 55.000 0.00 0.00 0.00 2.52
542 545 3.377172 CGGTTGTTCTTTCACCTTTCAGT 59.623 43.478 0.00 0.00 0.00 3.41
655 676 5.059833 AGAGAAGTTGATGAGTTGGTTGAC 58.940 41.667 0.00 0.00 0.00 3.18
768 789 5.736207 GCACACTTTTCTTGGGTAAAGGAAG 60.736 44.000 0.00 0.00 34.72 3.46
1029 1052 1.453928 GGAAGGCAGGGGAATTCCG 60.454 63.158 18.30 5.97 36.71 4.30
1062 1085 4.229304 TGGTTTTCCTTGTGTCTTCTCA 57.771 40.909 0.00 0.00 41.38 3.27
1068 1091 3.222603 ACAGGATGGTTTTCCTTGTGTC 58.777 45.455 0.00 0.00 43.88 3.67
1086 1109 3.181501 TGTTGCGAACCAAAGAAGAACAG 60.182 43.478 0.00 0.00 34.68 3.16
1131 1160 2.646798 AGCAGTTGGGAGAAGAGGATTT 59.353 45.455 0.00 0.00 0.00 2.17
1135 1164 0.689623 ACAGCAGTTGGGAGAAGAGG 59.310 55.000 0.00 0.00 0.00 3.69
1337 1375 5.048083 GTGATGAGAATTGTTGCCTGGTTAA 60.048 40.000 0.00 0.00 0.00 2.01
1489 1527 3.120130 GCTTCTCTTCTTTCTCGACTCGA 60.120 47.826 0.29 0.29 0.00 4.04
1609 1647 3.835395 TGGGCGATTTTAAATCCAAAGGT 59.165 39.130 11.53 0.00 0.00 3.50
1710 1749 3.524380 TCCCACATATTTCTTAACCGGGT 59.476 43.478 6.32 0.00 32.73 5.28
1732 1771 1.168714 GCTTCGAGTTCAAATGGGCT 58.831 50.000 0.00 0.00 0.00 5.19
1783 1823 5.882557 TCTTTATCCTCTTTGCAGGAATCAC 59.117 40.000 0.00 0.00 46.10 3.06
1906 1946 9.338291 CTGAAGATATTTCAGTGATTTTGTGTG 57.662 33.333 14.50 0.00 40.63 3.82
2052 2102 9.674068 TTTTGAGGGTAAAGTAAAAATGCTTTT 57.326 25.926 0.00 0.00 38.34 2.27
2095 2146 3.315191 ACCGTGGAAAACATCTTGAACAG 59.685 43.478 0.00 0.00 0.00 3.16
2097 2148 3.982576 ACCGTGGAAAACATCTTGAAC 57.017 42.857 0.00 0.00 0.00 3.18
2128 2180 1.003545 CGTTGGCCTTTCAGCATATCG 60.004 52.381 3.32 0.00 0.00 2.92
2248 5784 0.523072 CCAGACGGCCTTCAACATTG 59.477 55.000 12.41 0.17 0.00 2.82
2267 5803 6.366061 GTGCATTCTTCTTTATGGGAAAACAC 59.634 38.462 0.00 0.00 0.00 3.32
2274 5810 4.155826 TGAACGTGCATTCTTCTTTATGGG 59.844 41.667 0.00 0.00 0.00 4.00
2283 5819 1.882912 TCTGCTGAACGTGCATTCTT 58.117 45.000 0.00 0.00 39.86 2.52
2292 5828 3.871006 TGCTGGTATTTATCTGCTGAACG 59.129 43.478 0.00 0.00 33.13 3.95
2298 5834 7.010460 GGAAAATTTGTGCTGGTATTTATCTGC 59.990 37.037 0.00 0.00 32.63 4.26
2324 5860 4.201901 TGCAACAATGTCGGCTATAATGTG 60.202 41.667 10.54 0.00 0.00 3.21
2333 5869 2.345341 GCTATTTTGCAACAATGTCGGC 59.655 45.455 0.00 3.45 0.00 5.54
2399 5935 1.298713 CGGACGCTCGAGGAATCAG 60.299 63.158 15.58 0.00 0.00 2.90
2497 6033 0.032678 CAGTGTGAACAGCGAGACCT 59.967 55.000 0.00 0.00 0.00 3.85
2500 6036 0.744281 TGACAGTGTGAACAGCGAGA 59.256 50.000 0.00 0.00 0.00 4.04
2501 6037 1.723542 GATGACAGTGTGAACAGCGAG 59.276 52.381 0.00 0.00 0.00 5.03
2503 6039 1.723542 GAGATGACAGTGTGAACAGCG 59.276 52.381 0.00 0.00 0.00 5.18
2505 6041 1.723542 GCGAGATGACAGTGTGAACAG 59.276 52.381 0.00 0.00 0.00 3.16
2513 6049 1.134877 CATCCACAGCGAGATGACAGT 60.135 52.381 0.00 0.00 42.04 3.55
2514 6050 1.568606 CATCCACAGCGAGATGACAG 58.431 55.000 0.00 0.00 42.04 3.51
2524 6060 1.818785 GCTCTCTGCCATCCACAGC 60.819 63.158 0.00 0.00 35.04 4.40
2526 6062 2.580815 CGCTCTCTGCCATCCACA 59.419 61.111 0.00 0.00 38.78 4.17
2562 6098 2.685017 AGCTCATCCTCCGTGGCA 60.685 61.111 0.00 0.00 35.26 4.92
2566 6102 3.842923 CGGCAGCTCATCCTCCGT 61.843 66.667 0.00 0.00 35.75 4.69
2575 6111 3.672295 CTTCCTGGGTCGGCAGCTC 62.672 68.421 0.00 0.00 0.00 4.09
2603 6139 3.151022 GGAGCTCCTCCTGGACGG 61.151 72.222 26.25 0.00 46.41 4.79
2645 6181 3.723172 CGCTCCGCATTGTGCTAT 58.277 55.556 0.10 0.00 42.25 2.97
2657 6193 3.418744 GAGAAGGAGGTCGCGCTCC 62.419 68.421 21.16 21.16 39.93 4.70
2663 6199 1.136984 CCGAACGAGAAGGAGGTCG 59.863 63.158 0.00 0.00 42.04 4.79
2672 6208 3.425713 CGTCCGACCCGAACGAGA 61.426 66.667 0.00 0.00 38.65 4.04
2684 6220 3.423077 GACTCGTCGAGCTCGTCCG 62.423 68.421 33.33 31.83 40.80 4.79
2767 6303 0.548510 CTTCCACCCAATCTCCCCTC 59.451 60.000 0.00 0.00 0.00 4.30
2795 6331 4.816984 TCCGCTCCCCTCCGTCTC 62.817 72.222 0.00 0.00 0.00 3.36
2796 6332 4.824515 CTCCGCTCCCCTCCGTCT 62.825 72.222 0.00 0.00 0.00 4.18
2846 6382 5.292101 CACATCCGAACAAGAAATCCTAGTC 59.708 44.000 0.00 0.00 0.00 2.59
2847 6383 5.178797 CACATCCGAACAAGAAATCCTAGT 58.821 41.667 0.00 0.00 0.00 2.57
2848 6384 4.034510 GCACATCCGAACAAGAAATCCTAG 59.965 45.833 0.00 0.00 0.00 3.02
2849 6385 3.938963 GCACATCCGAACAAGAAATCCTA 59.061 43.478 0.00 0.00 0.00 2.94
2850 6386 2.749621 GCACATCCGAACAAGAAATCCT 59.250 45.455 0.00 0.00 0.00 3.24
2853 6389 4.853924 AAAGCACATCCGAACAAGAAAT 57.146 36.364 0.00 0.00 0.00 2.17
2903 6439 4.603946 GACCGGCCCGCTATGTCC 62.604 72.222 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.