Multiple sequence alignment - TraesCS3A01G243300

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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 TraesCS3A01G243300 chr3A 100.000 3122 0 0 1 3122 456779579 456776458 0.000000e+00 5766
1 TraesCS3A01G243300 chr3B 92.928 2729 128 16 415 3122 436743372 436740688 0.000000e+00 3910
2 TraesCS3A01G243300 chr3D 93.592 1857 77 17 1291 3122 338492250 338490411 0.000000e+00 2732
3 TraesCS3A01G243300 chr3D 90.832 1178 76 12 138 1305 338493423 338492268 0.000000e+00 1548
4 TraesCS3A01G243300 chr4D 91.367 139 12 0 1 139 19640124 19640262 1.140000e-44 191
5 TraesCS3A01G243300 chr1A 88.321 137 16 0 1 137 515579384 515579248 6.930000e-37 165
6 TraesCS3A01G243300 chr5B 88.148 135 16 0 1 135 643534461 643534595 8.960000e-36 161
7 TraesCS3A01G243300 chr2B 88.060 134 16 0 1 134 19621043 19621176 3.220000e-35 159
8 TraesCS3A01G243300 chr2A 87.681 138 16 1 1 137 692950316 692950453 3.220000e-35 159
9 TraesCS3A01G243300 chr4B 87.500 136 15 2 5 139 641156295 641156429 4.170000e-34 156
10 TraesCS3A01G243300 chr7B 86.429 140 18 1 1 139 546380939 546380800 5.390000e-33 152
11 TraesCS3A01G243300 chr1B 86.429 140 18 1 1 139 396536040 396535901 5.390000e-33 152
12 TraesCS3A01G243300 chr6A 84.783 138 19 2 1 137 574382587 574382723 1.510000e-28 137


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 TraesCS3A01G243300 chr3A 456776458 456779579 3121 True 5766 5766 100.000 1 3122 1 chr3A.!!$R1 3121
1 TraesCS3A01G243300 chr3B 436740688 436743372 2684 True 3910 3910 92.928 415 3122 1 chr3B.!!$R1 2707
2 TraesCS3A01G243300 chr3D 338490411 338493423 3012 True 2140 2732 92.212 138 3122 2 chr3D.!!$R1 2984

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
77 78 0.251916 CGACTTCATTGCCCTACCCA 59.748 55.0 0.0 0.0 0.0 4.51 F
1387 1430 0.247460 TCGGTCTCTTGATGCCTGTG 59.753 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1437 0.247460 CTCGACATCCTGACCAGCAA 59.753 55.0 0.0 0.0 0.0 3.91 R
2916 3003 0.104934 AGACCCTCAACACCCTCACT 60.105 55.0 0.0 0.0 0.0 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
47 48 3.716195 CCACCGCATCCCAGGACA 61.716 66.667 0.00 0.00 0.00 4.02
48 49 2.124983 CACCGCATCCCAGGACAG 60.125 66.667 0.00 0.00 0.00 3.51
49 50 3.402681 ACCGCATCCCAGGACAGG 61.403 66.667 0.00 0.00 0.00 4.00
50 51 4.864334 CCGCATCCCAGGACAGGC 62.864 72.222 0.00 0.00 0.00 4.85
51 52 3.790437 CGCATCCCAGGACAGGCT 61.790 66.667 0.00 0.00 0.00 4.58
52 53 2.191641 GCATCCCAGGACAGGCTC 59.808 66.667 0.00 0.00 0.00 4.70
53 54 2.503061 CATCCCAGGACAGGCTCG 59.497 66.667 0.00 0.00 0.00 5.03
54 55 2.765807 ATCCCAGGACAGGCTCGG 60.766 66.667 0.00 0.00 0.00 4.63
55 56 3.317436 ATCCCAGGACAGGCTCGGA 62.317 63.158 0.00 0.00 0.00 4.55
56 57 3.775654 CCCAGGACAGGCTCGGAC 61.776 72.222 0.00 0.00 0.00 4.79
57 58 2.997315 CCAGGACAGGCTCGGACA 60.997 66.667 0.00 0.00 0.00 4.02
58 59 2.262915 CAGGACAGGCTCGGACAC 59.737 66.667 0.00 0.00 0.00 3.67
59 60 3.374402 AGGACAGGCTCGGACACG 61.374 66.667 0.00 0.00 42.74 4.49
61 62 2.126424 GACAGGCTCGGACACGAC 60.126 66.667 0.00 0.00 45.59 4.34
62 63 2.597805 ACAGGCTCGGACACGACT 60.598 61.111 0.00 0.00 45.59 4.18
63 64 2.143594 GACAGGCTCGGACACGACTT 62.144 60.000 0.00 0.00 45.59 3.01
64 65 1.444553 CAGGCTCGGACACGACTTC 60.445 63.158 0.00 0.00 45.59 3.01
65 66 1.901948 AGGCTCGGACACGACTTCA 60.902 57.895 0.00 0.00 45.59 3.02
66 67 1.215647 GGCTCGGACACGACTTCAT 59.784 57.895 0.00 0.00 45.59 2.57
67 68 0.389948 GGCTCGGACACGACTTCATT 60.390 55.000 0.00 0.00 45.59 2.57
68 69 0.716108 GCTCGGACACGACTTCATTG 59.284 55.000 0.00 0.00 45.59 2.82
69 70 0.716108 CTCGGACACGACTTCATTGC 59.284 55.000 0.00 0.00 45.59 3.56
70 71 0.669318 TCGGACACGACTTCATTGCC 60.669 55.000 0.00 0.00 45.59 4.52
71 72 1.635663 CGGACACGACTTCATTGCCC 61.636 60.000 0.00 0.00 44.60 5.36
72 73 0.321653 GGACACGACTTCATTGCCCT 60.322 55.000 0.00 0.00 0.00 5.19
73 74 1.066430 GGACACGACTTCATTGCCCTA 60.066 52.381 0.00 0.00 0.00 3.53
74 75 2.000447 GACACGACTTCATTGCCCTAC 59.000 52.381 0.00 0.00 0.00 3.18
75 76 1.338769 ACACGACTTCATTGCCCTACC 60.339 52.381 0.00 0.00 0.00 3.18
76 77 0.252197 ACGACTTCATTGCCCTACCC 59.748 55.000 0.00 0.00 0.00 3.69
77 78 0.251916 CGACTTCATTGCCCTACCCA 59.748 55.000 0.00 0.00 0.00 4.51
78 79 1.339631 CGACTTCATTGCCCTACCCAA 60.340 52.381 0.00 0.00 0.00 4.12
79 80 2.802719 GACTTCATTGCCCTACCCAAA 58.197 47.619 0.00 0.00 0.00 3.28
80 81 2.492088 GACTTCATTGCCCTACCCAAAC 59.508 50.000 0.00 0.00 0.00 2.93
81 82 1.472480 CTTCATTGCCCTACCCAAACG 59.528 52.381 0.00 0.00 0.00 3.60
82 83 0.322997 TCATTGCCCTACCCAAACGG 60.323 55.000 0.00 0.00 37.81 4.44
83 84 0.322997 CATTGCCCTACCCAAACGGA 60.323 55.000 0.00 0.00 34.64 4.69
84 85 0.323087 ATTGCCCTACCCAAACGGAC 60.323 55.000 0.00 0.00 34.64 4.79
85 86 1.706995 TTGCCCTACCCAAACGGACA 61.707 55.000 0.00 0.00 34.64 4.02
86 87 1.376812 GCCCTACCCAAACGGACAG 60.377 63.158 0.00 0.00 34.64 3.51
87 88 1.833787 GCCCTACCCAAACGGACAGA 61.834 60.000 0.00 0.00 34.64 3.41
88 89 0.909623 CCCTACCCAAACGGACAGAT 59.090 55.000 0.00 0.00 34.64 2.90
89 90 1.280998 CCCTACCCAAACGGACAGATT 59.719 52.381 0.00 0.00 34.64 2.40
90 91 2.629051 CCTACCCAAACGGACAGATTC 58.371 52.381 0.00 0.00 34.64 2.52
91 92 2.236395 CCTACCCAAACGGACAGATTCT 59.764 50.000 0.00 0.00 34.64 2.40
92 93 3.449737 CCTACCCAAACGGACAGATTCTA 59.550 47.826 0.00 0.00 34.64 2.10
93 94 3.611766 ACCCAAACGGACAGATTCTAG 57.388 47.619 0.00 0.00 34.64 2.43
94 95 2.236395 ACCCAAACGGACAGATTCTAGG 59.764 50.000 0.00 0.00 34.64 3.02
95 96 2.280628 CCAAACGGACAGATTCTAGGC 58.719 52.381 0.00 0.00 0.00 3.93
96 97 2.354704 CCAAACGGACAGATTCTAGGCA 60.355 50.000 0.00 0.00 0.00 4.75
97 98 2.932614 CAAACGGACAGATTCTAGGCAG 59.067 50.000 0.00 0.00 0.00 4.85
98 99 2.145397 ACGGACAGATTCTAGGCAGA 57.855 50.000 0.00 0.00 0.00 4.26
99 100 2.028130 ACGGACAGATTCTAGGCAGAG 58.972 52.381 0.00 0.00 30.73 3.35
100 101 1.269517 CGGACAGATTCTAGGCAGAGC 60.270 57.143 0.00 0.00 30.73 4.09
101 102 1.269517 GGACAGATTCTAGGCAGAGCG 60.270 57.143 0.00 0.00 30.73 5.03
102 103 0.749649 ACAGATTCTAGGCAGAGCGG 59.250 55.000 0.00 0.00 30.73 5.52
103 104 1.035923 CAGATTCTAGGCAGAGCGGA 58.964 55.000 0.00 0.00 30.73 5.54
104 105 1.036707 AGATTCTAGGCAGAGCGGAC 58.963 55.000 0.00 0.00 30.73 4.79
105 106 0.318275 GATTCTAGGCAGAGCGGACG 60.318 60.000 0.00 0.00 30.73 4.79
106 107 1.038130 ATTCTAGGCAGAGCGGACGT 61.038 55.000 0.00 0.00 30.73 4.34
107 108 1.654954 TTCTAGGCAGAGCGGACGTC 61.655 60.000 7.13 7.13 30.73 4.34
108 109 3.127352 CTAGGCAGAGCGGACGTCC 62.127 68.421 25.28 25.28 0.00 4.79
123 124 3.483665 TCCGTTTGGATTCGCGCG 61.484 61.111 26.76 26.76 40.17 6.86
124 125 4.514569 CCGTTTGGATTCGCGCGG 62.515 66.667 31.69 11.75 37.49 6.46
125 126 3.784412 CGTTTGGATTCGCGCGGT 61.784 61.111 31.69 19.49 0.00 5.68
126 127 2.202298 GTTTGGATTCGCGCGGTG 60.202 61.111 31.69 1.17 0.00 4.94
127 128 3.427425 TTTGGATTCGCGCGGTGG 61.427 61.111 31.69 0.71 0.00 4.61
128 129 3.885538 TTTGGATTCGCGCGGTGGA 62.886 57.895 31.69 14.11 0.00 4.02
129 130 4.812476 TGGATTCGCGCGGTGGAG 62.812 66.667 31.69 0.00 0.00 3.86
130 131 4.814294 GGATTCGCGCGGTGGAGT 62.814 66.667 31.69 7.00 0.00 3.85
131 132 2.813908 GATTCGCGCGGTGGAGTT 60.814 61.111 31.69 6.84 0.00 3.01
132 133 3.083600 GATTCGCGCGGTGGAGTTG 62.084 63.158 31.69 0.00 0.00 3.16
151 152 1.523938 GCCTAAACCCTAGCCGCTG 60.524 63.158 2.16 0.00 0.00 5.18
167 168 4.292145 TGCCGCCCCCAACAATCA 62.292 61.111 0.00 0.00 0.00 2.57
179 180 3.519510 CCCAACAATCACCTCTTCCTCTA 59.480 47.826 0.00 0.00 0.00 2.43
180 181 4.508662 CCAACAATCACCTCTTCCTCTAC 58.491 47.826 0.00 0.00 0.00 2.59
187 188 3.028130 CACCTCTTCCTCTACCCTTCTC 58.972 54.545 0.00 0.00 0.00 2.87
193 194 1.439644 CTCTACCCTTCTCGCTGCC 59.560 63.158 0.00 0.00 0.00 4.85
195 196 0.614979 TCTACCCTTCTCGCTGCCTT 60.615 55.000 0.00 0.00 0.00 4.35
204 205 0.596083 CTCGCTGCCTTAGGATGACG 60.596 60.000 0.69 0.00 0.00 4.35
209 210 1.889573 GCCTTAGGATGACGCTGGC 60.890 63.158 0.69 0.00 0.00 4.85
216 217 1.676678 GGATGACGCTGGCAGAGGTA 61.677 60.000 20.86 8.96 0.00 3.08
222 223 3.036429 GCTGGCAGAGGTAGGGTGG 62.036 68.421 20.86 0.00 0.00 4.61
226 227 2.990479 CAGAGGTAGGGTGGGTGC 59.010 66.667 0.00 0.00 0.00 5.01
230 231 0.540454 GAGGTAGGGTGGGTGCTTAC 59.460 60.000 0.00 0.00 0.00 2.34
231 232 0.912968 AGGTAGGGTGGGTGCTTACC 60.913 60.000 0.00 0.00 35.18 2.85
242 243 2.815503 GGGTGCTTACCGTGTTTGTAAT 59.184 45.455 0.00 0.00 0.00 1.89
247 248 4.817464 TGCTTACCGTGTTTGTAATCACTT 59.183 37.500 4.80 0.00 33.07 3.16
254 255 4.847757 CGTGTTTGTAATCACTTGATGCTG 59.152 41.667 0.00 0.00 34.49 4.41
261 262 6.731164 TGTAATCACTTGATGCTGCATTATG 58.269 36.000 17.36 16.34 34.49 1.90
262 263 4.848562 ATCACTTGATGCTGCATTATGG 57.151 40.909 17.36 10.73 32.68 2.74
263 264 2.953648 TCACTTGATGCTGCATTATGGG 59.046 45.455 17.36 15.44 0.00 4.00
264 265 2.691526 CACTTGATGCTGCATTATGGGT 59.308 45.455 17.36 9.03 0.00 4.51
268 269 5.599656 ACTTGATGCTGCATTATGGGTTAAT 59.400 36.000 17.36 0.00 0.00 1.40
274 281 8.891671 ATGCTGCATTATGGGTTAATAAAAAG 57.108 30.769 9.81 0.00 0.00 2.27
275 282 8.072321 TGCTGCATTATGGGTTAATAAAAAGA 57.928 30.769 0.00 0.00 0.00 2.52
326 333 6.992063 TTTGCTTTGTTTTGCTGGATTTTA 57.008 29.167 0.00 0.00 0.00 1.52
356 363 7.220890 AGGTGGGTAAAATATTAGGTCACAT 57.779 36.000 0.00 0.00 0.00 3.21
385 392 6.041423 CTGAAAGTTTAGGCCAAATCCATT 57.959 37.500 5.01 0.00 0.00 3.16
388 395 6.709846 TGAAAGTTTAGGCCAAATCCATTTTG 59.290 34.615 5.01 0.00 43.64 2.44
428 438 2.525105 AGAAATAAACATGGCCCCGT 57.475 45.000 0.00 0.00 0.00 5.28
538 549 1.647084 GAGACGCACCAACCAACAC 59.353 57.895 0.00 0.00 0.00 3.32
547 558 0.827507 CCAACCAACACCCAAGGAGG 60.828 60.000 0.00 0.00 37.03 4.30
598 609 4.404654 CGCACGGCAAAAGCCTCC 62.405 66.667 4.85 0.00 0.00 4.30
599 610 3.294493 GCACGGCAAAAGCCTCCA 61.294 61.111 4.85 0.00 0.00 3.86
645 656 1.456296 CCACACCATCATCACACCAG 58.544 55.000 0.00 0.00 0.00 4.00
722 733 2.519541 TCTCATCTCCTCCCGGCG 60.520 66.667 0.00 0.00 0.00 6.46
754 765 1.350071 TTGCAGGCCACCAATCAAAT 58.650 45.000 5.01 0.00 0.00 2.32
755 766 1.350071 TGCAGGCCACCAATCAAATT 58.650 45.000 5.01 0.00 0.00 1.82
756 767 1.275856 TGCAGGCCACCAATCAAATTC 59.724 47.619 5.01 0.00 0.00 2.17
757 768 1.275856 GCAGGCCACCAATCAAATTCA 59.724 47.619 5.01 0.00 0.00 2.57
758 769 2.093341 GCAGGCCACCAATCAAATTCAT 60.093 45.455 5.01 0.00 0.00 2.57
759 770 3.788937 CAGGCCACCAATCAAATTCATC 58.211 45.455 5.01 0.00 0.00 2.92
760 771 3.196039 CAGGCCACCAATCAAATTCATCA 59.804 43.478 5.01 0.00 0.00 3.07
761 772 3.839490 AGGCCACCAATCAAATTCATCAA 59.161 39.130 5.01 0.00 0.00 2.57
762 773 4.286549 AGGCCACCAATCAAATTCATCAAA 59.713 37.500 5.01 0.00 0.00 2.69
871 882 3.507622 CCAACCTCCACTTCAGAATTTCC 59.492 47.826 0.00 0.00 0.00 3.13
872 883 4.401925 CAACCTCCACTTCAGAATTTCCT 58.598 43.478 0.00 0.00 0.00 3.36
880 891 5.513788 CCACTTCAGAATTTCCTCTTCCAGA 60.514 44.000 0.00 0.00 0.00 3.86
909 920 4.384757 GGATTTTCTCCCTCCTCTTCTTCC 60.385 50.000 0.00 0.00 38.19 3.46
952 963 1.943340 GAATCTTGTCCCCATTCTCGC 59.057 52.381 0.00 0.00 0.00 5.03
959 970 1.222387 CCCCATTCTCGCCGGTTTA 59.778 57.895 1.90 0.00 0.00 2.01
968 979 1.997606 CTCGCCGGTTTATTTCTTCGT 59.002 47.619 1.90 0.00 0.00 3.85
1154 1165 2.074729 CCTCTCGAGGTAATCAGGGT 57.925 55.000 13.56 0.00 43.61 4.34
1184 1195 2.685388 TGCATCGAGTTTGTGGTTTTCA 59.315 40.909 0.00 0.00 0.00 2.69
1192 1203 5.277974 CGAGTTTGTGGTTTTCAGATCACAT 60.278 40.000 0.00 0.00 39.45 3.21
1387 1430 0.247460 TCGGTCTCTTGATGCCTGTG 59.753 55.000 0.00 0.00 0.00 3.66
1394 1437 2.374504 CTCTTGATGCCTGTGGGGATAT 59.625 50.000 0.00 0.00 43.86 1.63
1405 1448 0.846015 TGGGGATATTGCTGGTCAGG 59.154 55.000 0.00 0.00 0.00 3.86
1560 1630 3.339731 TTTTTCGTGCTCGGCTGG 58.660 55.556 8.49 0.00 37.69 4.85
1574 1644 1.010350 GCTGGATTTGCAGATCGCG 60.010 57.895 10.82 0.00 46.97 5.87
1586 1656 0.382515 AGATCGCGGCTGTACTTCTC 59.617 55.000 6.13 0.00 0.00 2.87
1740 1810 7.497925 AGGTGAGAAAAACTAGTTTCATGTC 57.502 36.000 20.78 18.76 39.52 3.06
1756 1835 0.955428 TGTCGCACCTTGCATCCTTC 60.955 55.000 0.00 0.00 45.36 3.46
1796 1878 3.459828 TCATACCTGAACCTGAATCCCA 58.540 45.455 0.00 0.00 0.00 4.37
1854 1940 1.072331 TGGTTCTTCTTCCACTGGCTC 59.928 52.381 0.00 0.00 0.00 4.70
1860 1946 3.003173 TTCCACTGGCTCCTCGGG 61.003 66.667 0.00 0.00 0.00 5.14
1918 2004 4.367023 GCCTCCGCACGTACCACA 62.367 66.667 0.00 0.00 34.03 4.17
1926 2012 1.602165 CGCACGTACCACAAGAGAACT 60.602 52.381 0.00 0.00 0.00 3.01
1929 2015 1.687123 ACGTACCACAAGAGAACTGCT 59.313 47.619 0.00 0.00 0.00 4.24
2033 2119 3.054875 AGCTACATGATCAAGCAAGGACA 60.055 43.478 17.82 0.00 38.75 4.02
2049 2135 1.945354 GACATCTCCCGGTCGAGCAA 61.945 60.000 15.89 0.00 0.00 3.91
2287 2373 8.292448 CAGCTTTTATACTTGTGTTGAGATTGT 58.708 33.333 0.00 0.00 0.00 2.71
2438 2524 9.784531 AGAAATTATCAGAAGTTTCAGAACTGA 57.215 29.630 0.00 0.00 45.18 3.41
2509 2595 4.154015 TCAGGTTGTCAATATCAAAGCGTG 59.846 41.667 0.00 0.00 0.00 5.34
2512 2598 1.202020 TGTCAATATCAAAGCGTGCGC 60.202 47.619 8.67 8.67 42.33 6.09
2513 2599 1.082690 TCAATATCAAAGCGTGCGCA 58.917 45.000 18.87 5.66 44.88 6.09
2514 2600 1.466558 TCAATATCAAAGCGTGCGCAA 59.533 42.857 14.00 0.00 44.88 4.85
2523 2609 3.425136 CGTGCGCAACATTTCACG 58.575 55.556 14.00 4.72 44.62 4.35
2537 2624 6.178239 ACATTTCACGGTGCTAATTCTTAC 57.822 37.500 2.51 0.00 0.00 2.34
2543 2630 5.180492 TCACGGTGCTAATTCTTACTTTTGG 59.820 40.000 2.51 0.00 0.00 3.28
2601 2688 5.417580 TCCTTGTGGCTAATGGATAAAACAC 59.582 40.000 0.00 0.00 0.00 3.32
2617 2704 8.850156 GGATAAAACACACTTATGCCATATCTT 58.150 33.333 0.00 0.00 0.00 2.40
2645 2732 6.923508 GCTTAATGGATAAAAACCTACATGCC 59.076 38.462 0.00 0.00 0.00 4.40
2714 2801 2.162408 GAGCCAAAGTACCTTCATGTGC 59.838 50.000 0.00 0.00 0.00 4.57
2752 2839 5.316987 AGATGACCACTAAAAACCTCTTGG 58.683 41.667 0.00 0.00 39.83 3.61
2847 2934 1.371389 ACCGACAGTCGCGAAGAAC 60.371 57.895 18.02 0.00 38.82 3.01
2850 2937 0.660595 CGACAGTCGCGAAGAACACT 60.661 55.000 12.06 0.00 31.14 3.55
2886 2973 0.323360 TAACCTTGGTGAGCATGGCC 60.323 55.000 15.43 0.00 0.00 5.36
2904 2991 2.016096 GCCTGCCTCTTGATGTTCCTC 61.016 57.143 0.00 0.00 0.00 3.71
2916 3003 2.381752 TGTTCCTCCTCTGTGAGACA 57.618 50.000 0.00 0.00 34.11 3.41
3021 3108 4.504916 AGCGCTACCAGCTGCTCG 62.505 66.667 8.99 9.30 43.64 5.03
3073 3160 2.223203 GCGGTTTCATTCTCTGAGCATG 60.223 50.000 10.52 10.52 34.68 4.06
3087 3174 2.779430 TGAGCATGAGGGGATGTAATGT 59.221 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.687321 CTGTCCTGGGATGCGGTGG 62.687 68.421 0.00 0.00 0.00 4.61
31 32 2.124983 CTGTCCTGGGATGCGGTG 60.125 66.667 0.00 0.00 0.00 4.94
32 33 3.402681 CCTGTCCTGGGATGCGGT 61.403 66.667 0.00 0.00 0.00 5.68
33 34 4.864334 GCCTGTCCTGGGATGCGG 62.864 72.222 0.00 0.00 0.00 5.69
34 35 3.746949 GAGCCTGTCCTGGGATGCG 62.747 68.421 0.00 0.00 0.00 4.73
35 36 2.191641 GAGCCTGTCCTGGGATGC 59.808 66.667 0.00 0.00 0.00 3.91
36 37 2.503061 CGAGCCTGTCCTGGGATG 59.497 66.667 0.00 0.00 0.00 3.51
37 38 2.765807 CCGAGCCTGTCCTGGGAT 60.766 66.667 0.00 0.00 33.00 3.85
38 39 3.992641 TCCGAGCCTGTCCTGGGA 61.993 66.667 0.00 0.00 37.39 4.37
39 40 3.775654 GTCCGAGCCTGTCCTGGG 61.776 72.222 0.00 0.00 32.55 4.45
40 41 2.997315 TGTCCGAGCCTGTCCTGG 60.997 66.667 0.00 0.00 0.00 4.45
41 42 2.262915 GTGTCCGAGCCTGTCCTG 59.737 66.667 0.00 0.00 0.00 3.86
42 43 3.374402 CGTGTCCGAGCCTGTCCT 61.374 66.667 0.00 0.00 35.63 3.85
43 44 3.371063 TCGTGTCCGAGCCTGTCC 61.371 66.667 0.00 0.00 38.40 4.02
44 45 2.126424 GTCGTGTCCGAGCCTGTC 60.126 66.667 0.00 0.00 45.26 3.51
45 46 2.143594 GAAGTCGTGTCCGAGCCTGT 62.144 60.000 0.00 0.00 45.26 4.00
46 47 1.444553 GAAGTCGTGTCCGAGCCTG 60.445 63.158 0.00 0.00 45.26 4.85
47 48 1.251527 ATGAAGTCGTGTCCGAGCCT 61.252 55.000 0.00 0.00 45.26 4.58
48 49 0.389948 AATGAAGTCGTGTCCGAGCC 60.390 55.000 0.00 0.00 45.26 4.70
49 50 0.716108 CAATGAAGTCGTGTCCGAGC 59.284 55.000 0.00 0.00 45.26 5.03
50 51 0.716108 GCAATGAAGTCGTGTCCGAG 59.284 55.000 0.00 0.00 45.26 4.63
51 52 0.669318 GGCAATGAAGTCGTGTCCGA 60.669 55.000 0.00 0.00 41.73 4.55
52 53 1.635663 GGGCAATGAAGTCGTGTCCG 61.636 60.000 0.00 0.00 0.00 4.79
53 54 0.321653 AGGGCAATGAAGTCGTGTCC 60.322 55.000 0.00 0.00 0.00 4.02
54 55 2.000447 GTAGGGCAATGAAGTCGTGTC 59.000 52.381 0.00 0.00 0.00 3.67
55 56 1.338769 GGTAGGGCAATGAAGTCGTGT 60.339 52.381 0.00 0.00 0.00 4.49
56 57 1.369625 GGTAGGGCAATGAAGTCGTG 58.630 55.000 0.00 0.00 0.00 4.35
57 58 0.252197 GGGTAGGGCAATGAAGTCGT 59.748 55.000 0.00 0.00 0.00 4.34
58 59 0.251916 TGGGTAGGGCAATGAAGTCG 59.748 55.000 0.00 0.00 0.00 4.18
59 60 2.492088 GTTTGGGTAGGGCAATGAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
60 61 2.525368 GTTTGGGTAGGGCAATGAAGT 58.475 47.619 0.00 0.00 0.00 3.01
61 62 1.472480 CGTTTGGGTAGGGCAATGAAG 59.528 52.381 0.00 0.00 0.00 3.02
62 63 1.540267 CGTTTGGGTAGGGCAATGAA 58.460 50.000 0.00 0.00 0.00 2.57
63 64 0.322997 CCGTTTGGGTAGGGCAATGA 60.323 55.000 0.00 0.00 0.00 2.57
64 65 0.322997 TCCGTTTGGGTAGGGCAATG 60.323 55.000 0.00 0.00 37.00 2.82
65 66 0.323087 GTCCGTTTGGGTAGGGCAAT 60.323 55.000 0.00 0.00 37.00 3.56
66 67 1.073548 GTCCGTTTGGGTAGGGCAA 59.926 57.895 0.00 0.00 37.00 4.52
67 68 2.119484 CTGTCCGTTTGGGTAGGGCA 62.119 60.000 0.00 0.00 37.30 5.36
68 69 1.376812 CTGTCCGTTTGGGTAGGGC 60.377 63.158 0.00 0.00 37.00 5.19
69 70 0.909623 ATCTGTCCGTTTGGGTAGGG 59.090 55.000 0.00 0.00 37.00 3.53
70 71 2.236395 AGAATCTGTCCGTTTGGGTAGG 59.764 50.000 0.00 0.00 37.00 3.18
71 72 3.611766 AGAATCTGTCCGTTTGGGTAG 57.388 47.619 0.00 0.00 37.00 3.18
72 73 3.449737 CCTAGAATCTGTCCGTTTGGGTA 59.550 47.826 0.00 0.00 37.00 3.69
73 74 2.236395 CCTAGAATCTGTCCGTTTGGGT 59.764 50.000 0.00 0.00 37.00 4.51
74 75 2.906354 CCTAGAATCTGTCCGTTTGGG 58.094 52.381 0.00 0.00 35.24 4.12
75 76 2.280628 GCCTAGAATCTGTCCGTTTGG 58.719 52.381 0.00 0.00 0.00 3.28
76 77 2.932614 CTGCCTAGAATCTGTCCGTTTG 59.067 50.000 0.00 0.00 0.00 2.93
77 78 2.832129 TCTGCCTAGAATCTGTCCGTTT 59.168 45.455 0.00 0.00 0.00 3.60
78 79 2.428890 CTCTGCCTAGAATCTGTCCGTT 59.571 50.000 0.00 0.00 31.21 4.44
79 80 2.028130 CTCTGCCTAGAATCTGTCCGT 58.972 52.381 0.00 0.00 31.21 4.69
80 81 1.269517 GCTCTGCCTAGAATCTGTCCG 60.270 57.143 0.00 0.00 31.21 4.79
81 82 1.269517 CGCTCTGCCTAGAATCTGTCC 60.270 57.143 0.00 0.00 31.21 4.02
82 83 1.269517 CCGCTCTGCCTAGAATCTGTC 60.270 57.143 0.00 0.00 31.21 3.51
83 84 0.749649 CCGCTCTGCCTAGAATCTGT 59.250 55.000 0.00 0.00 31.21 3.41
84 85 1.035923 TCCGCTCTGCCTAGAATCTG 58.964 55.000 0.00 0.00 31.21 2.90
85 86 1.036707 GTCCGCTCTGCCTAGAATCT 58.963 55.000 0.00 0.00 31.21 2.40
86 87 0.318275 CGTCCGCTCTGCCTAGAATC 60.318 60.000 0.00 0.00 31.21 2.52
87 88 1.038130 ACGTCCGCTCTGCCTAGAAT 61.038 55.000 0.00 0.00 31.21 2.40
88 89 1.654954 GACGTCCGCTCTGCCTAGAA 61.655 60.000 3.51 0.00 31.21 2.10
89 90 2.045242 ACGTCCGCTCTGCCTAGA 60.045 61.111 0.00 0.00 0.00 2.43
90 91 2.409651 GACGTCCGCTCTGCCTAG 59.590 66.667 3.51 0.00 0.00 3.02
91 92 3.138798 GGACGTCCGCTCTGCCTA 61.139 66.667 20.85 0.00 0.00 3.93
101 102 1.963190 GCGAATCCAAACGGACGTCC 61.963 60.000 25.28 25.28 34.62 4.79
102 103 1.418755 GCGAATCCAAACGGACGTC 59.581 57.895 7.13 7.13 34.62 4.34
103 104 2.377310 CGCGAATCCAAACGGACGT 61.377 57.895 0.00 0.00 34.62 4.34
104 105 2.394136 CGCGAATCCAAACGGACG 59.606 61.111 0.00 0.00 34.62 4.79
105 106 2.097728 GCGCGAATCCAAACGGAC 59.902 61.111 12.10 0.00 34.62 4.79
106 107 3.483665 CGCGCGAATCCAAACGGA 61.484 61.111 28.94 0.00 36.85 4.69
107 108 4.514569 CCGCGCGAATCCAAACGG 62.515 66.667 34.63 6.73 0.00 4.44
108 109 3.784412 ACCGCGCGAATCCAAACG 61.784 61.111 34.63 13.76 0.00 3.60
109 110 2.202298 CACCGCGCGAATCCAAAC 60.202 61.111 34.63 0.00 0.00 2.93
110 111 3.427425 CCACCGCGCGAATCCAAA 61.427 61.111 34.63 0.00 0.00 3.28
111 112 4.380781 TCCACCGCGCGAATCCAA 62.381 61.111 34.63 8.51 0.00 3.53
112 113 4.812476 CTCCACCGCGCGAATCCA 62.812 66.667 34.63 9.89 0.00 3.41
113 114 4.814294 ACTCCACCGCGCGAATCC 62.814 66.667 34.63 0.00 0.00 3.01
114 115 2.813908 AACTCCACCGCGCGAATC 60.814 61.111 34.63 0.00 0.00 2.52
115 116 3.118454 CAACTCCACCGCGCGAAT 61.118 61.111 34.63 16.98 0.00 3.34
120 121 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
121 122 1.302993 TTTAGGCCAACTCCACCGC 60.303 57.895 5.01 0.00 0.00 5.68
122 123 0.958876 GGTTTAGGCCAACTCCACCG 60.959 60.000 5.01 0.00 0.00 4.94
123 124 0.611062 GGGTTTAGGCCAACTCCACC 60.611 60.000 5.01 1.42 32.81 4.61
124 125 0.404426 AGGGTTTAGGCCAACTCCAC 59.596 55.000 5.01 0.00 0.00 4.02
125 126 1.913419 CTAGGGTTTAGGCCAACTCCA 59.087 52.381 5.01 0.00 0.00 3.86
126 127 1.408405 GCTAGGGTTTAGGCCAACTCC 60.408 57.143 5.01 5.49 0.00 3.85
127 128 1.408405 GGCTAGGGTTTAGGCCAACTC 60.408 57.143 5.01 0.47 43.59 3.01
128 129 0.624254 GGCTAGGGTTTAGGCCAACT 59.376 55.000 5.01 0.00 43.59 3.16
129 130 0.746923 CGGCTAGGGTTTAGGCCAAC 60.747 60.000 5.01 0.36 44.27 3.77
130 131 1.605453 CGGCTAGGGTTTAGGCCAA 59.395 57.895 5.01 0.00 44.27 4.52
131 132 3.038945 GCGGCTAGGGTTTAGGCCA 62.039 63.158 5.01 0.00 44.27 5.36
132 133 2.203167 GCGGCTAGGGTTTAGGCC 60.203 66.667 0.00 0.00 41.02 5.19
133 134 1.523938 CAGCGGCTAGGGTTTAGGC 60.524 63.158 0.26 0.00 36.84 3.93
134 135 1.523938 GCAGCGGCTAGGGTTTAGG 60.524 63.158 0.26 0.00 36.96 2.69
135 136 1.523938 GGCAGCGGCTAGGGTTTAG 60.524 63.158 9.17 0.00 40.87 1.85
136 137 2.587889 GGCAGCGGCTAGGGTTTA 59.412 61.111 9.17 0.00 40.87 2.01
151 152 3.758931 GTGATTGTTGGGGGCGGC 61.759 66.667 0.00 0.00 0.00 6.53
162 163 3.379452 AGGGTAGAGGAAGAGGTGATTG 58.621 50.000 0.00 0.00 0.00 2.67
167 168 2.357361 CGAGAAGGGTAGAGGAAGAGGT 60.357 54.545 0.00 0.00 0.00 3.85
179 180 1.617947 CCTAAGGCAGCGAGAAGGGT 61.618 60.000 0.00 0.00 0.00 4.34
180 181 1.144936 CCTAAGGCAGCGAGAAGGG 59.855 63.158 0.00 0.00 0.00 3.95
187 188 2.240500 GCGTCATCCTAAGGCAGCG 61.241 63.158 0.00 0.00 0.00 5.18
193 194 0.461548 TCTGCCAGCGTCATCCTAAG 59.538 55.000 0.00 0.00 0.00 2.18
195 196 1.395045 CCTCTGCCAGCGTCATCCTA 61.395 60.000 0.00 0.00 0.00 2.94
204 205 2.586792 CACCCTACCTCTGCCAGC 59.413 66.667 0.00 0.00 0.00 4.85
209 210 1.201429 AAGCACCCACCCTACCTCTG 61.201 60.000 0.00 0.00 0.00 3.35
216 217 2.528378 ACGGTAAGCACCCACCCT 60.528 61.111 0.00 0.00 42.43 4.34
222 223 3.499157 TGATTACAAACACGGTAAGCACC 59.501 43.478 0.00 0.00 40.84 5.01
226 227 6.533819 TCAAGTGATTACAAACACGGTAAG 57.466 37.500 0.00 0.00 41.22 2.34
230 231 4.083324 AGCATCAAGTGATTACAAACACGG 60.083 41.667 0.00 0.00 41.22 4.94
231 232 4.847757 CAGCATCAAGTGATTACAAACACG 59.152 41.667 0.00 0.00 41.22 4.49
242 243 2.953648 CCCATAATGCAGCATCAAGTGA 59.046 45.455 8.77 0.00 0.00 3.41
247 248 7.594351 TTTATTAACCCATAATGCAGCATCA 57.406 32.000 8.77 0.00 35.77 3.07
298 305 3.683822 CCAGCAAAACAAAGCAAAAGTGA 59.316 39.130 0.00 0.00 0.00 3.41
350 357 8.989980 GGCCTAAACTTTCAGTATATATGTGAC 58.010 37.037 0.00 0.00 0.00 3.67
352 359 8.902540 TGGCCTAAACTTTCAGTATATATGTG 57.097 34.615 3.32 0.00 0.00 3.21
356 363 9.569122 GGATTTGGCCTAAACTTTCAGTATATA 57.431 33.333 3.32 0.00 0.00 0.86
361 368 4.479158 TGGATTTGGCCTAAACTTTCAGT 58.521 39.130 3.32 0.00 0.00 3.41
428 438 7.013942 TGCAGTACAGTTTCTCTACTAAACTCA 59.986 37.037 0.00 0.00 43.52 3.41
598 609 0.323542 ACGGTAGGGAGAGTGGAGTG 60.324 60.000 0.00 0.00 0.00 3.51
599 610 0.034283 GACGGTAGGGAGAGTGGAGT 60.034 60.000 0.00 0.00 0.00 3.85
645 656 4.425520 AGCTTTTACATCTCTACTCGTGC 58.574 43.478 0.00 0.00 0.00 5.34
722 733 6.488683 TGGTGGCCTGCAAAATATATTAGTAC 59.511 38.462 3.32 0.00 0.00 2.73
754 765 2.025321 GGTAGGCTCCCCTTTTGATGAA 60.025 50.000 0.00 0.00 42.87 2.57
755 766 1.564348 GGTAGGCTCCCCTTTTGATGA 59.436 52.381 0.00 0.00 42.87 2.92
756 767 1.747206 CGGTAGGCTCCCCTTTTGATG 60.747 57.143 0.00 0.00 42.87 3.07
757 768 0.546598 CGGTAGGCTCCCCTTTTGAT 59.453 55.000 0.00 0.00 42.87 2.57
758 769 0.838987 ACGGTAGGCTCCCCTTTTGA 60.839 55.000 0.00 0.00 42.87 2.69
759 770 0.037734 AACGGTAGGCTCCCCTTTTG 59.962 55.000 0.00 0.00 42.87 2.44
760 771 0.037734 CAACGGTAGGCTCCCCTTTT 59.962 55.000 0.00 0.00 42.87 2.27
761 772 1.683441 CAACGGTAGGCTCCCCTTT 59.317 57.895 0.00 0.00 42.87 3.11
762 773 2.967946 GCAACGGTAGGCTCCCCTT 61.968 63.158 0.00 0.00 42.87 3.95
872 883 7.372312 GGAGAAAATCCCGTGATCTGGAAGA 62.372 48.000 6.18 0.00 45.70 2.87
909 920 1.991430 CCAGCGACGAAGAATGACG 59.009 57.895 0.00 0.00 0.00 4.35
952 963 4.117685 CCTCCTACGAAGAAATAAACCGG 58.882 47.826 0.00 0.00 0.00 5.28
959 970 5.693769 TTCAATCCCTCCTACGAAGAAAT 57.306 39.130 0.00 0.00 0.00 2.17
968 979 3.073062 GCTAGCCAATTCAATCCCTCCTA 59.927 47.826 2.29 0.00 0.00 2.94
1051 1062 1.728971 CAGCGTGAGAAGCGAAAGAAT 59.271 47.619 0.00 0.00 40.04 2.40
1108 1119 1.401539 GGTCTTGTTGCGGCTTTGATC 60.402 52.381 0.00 0.00 0.00 2.92
1154 1165 3.380004 ACAAACTCGATGCAAGAAAACCA 59.620 39.130 0.00 0.00 0.00 3.67
1184 1195 6.975196 AGTATCTTAGAGTGCATGTGATCT 57.025 37.500 0.00 0.00 0.00 2.75
1192 1203 5.337571 CCAGAACCAAGTATCTTAGAGTGCA 60.338 44.000 0.00 0.00 0.00 4.57
1387 1430 1.140312 TCCTGACCAGCAATATCCCC 58.860 55.000 0.00 0.00 0.00 4.81
1394 1437 0.247460 CTCGACATCCTGACCAGCAA 59.753 55.000 0.00 0.00 0.00 3.91
1405 1448 3.299020 CGCTTTTTGATTTGCTCGACATC 59.701 43.478 0.00 0.00 0.00 3.06
1513 1578 2.063156 TGCGCCATGAAACATGAAAC 57.937 45.000 4.18 3.10 0.00 2.78
1549 1614 2.262471 CTGCAAATCCAGCCGAGCAC 62.262 60.000 0.00 0.00 0.00 4.40
1556 1621 1.010350 CGCGATCTGCAAATCCAGC 60.010 57.895 0.00 0.00 46.97 4.85
1560 1630 1.010350 CAGCCGCGATCTGCAAATC 60.010 57.895 8.23 0.00 46.97 2.17
1574 1644 1.202313 CCAGTAGCGAGAAGTACAGCC 60.202 57.143 0.00 0.00 0.00 4.85
1731 1801 3.092081 GCAAGGTGCGACATGAAAC 57.908 52.632 0.00 0.00 31.71 2.78
1756 1835 8.950210 AGGTATGAACTTTGTATGAAACATGAG 58.050 33.333 0.00 0.00 38.10 2.90
1796 1878 5.026121 TGACACCTCTGTAGAGATGGAAAT 58.974 41.667 10.40 0.00 40.06 2.17
1854 1940 2.464459 GCAAACTGCGATCCCGAGG 61.464 63.158 0.00 0.00 38.22 4.63
1890 1976 2.052690 GCGGAGGCCAGAGTAGACA 61.053 63.158 5.01 0.00 0.00 3.41
1918 2004 2.558795 TCACGCTCTTAGCAGTTCTCTT 59.441 45.455 0.00 0.00 42.58 2.85
1926 2012 0.321671 AAAGGCTCACGCTCTTAGCA 59.678 50.000 0.00 0.00 42.58 3.49
1929 2015 0.973632 TCCAAAGGCTCACGCTCTTA 59.026 50.000 0.00 0.00 36.09 2.10
2033 2119 0.395311 TAGTTGCTCGACCGGGAGAT 60.395 55.000 6.32 0.00 36.08 2.75
2049 2135 6.070995 TCCTGTGATTATCGTTTGGTCTTAGT 60.071 38.462 0.00 0.00 0.00 2.24
2058 2144 5.855045 GGATAGGTCCTGTGATTATCGTTT 58.145 41.667 0.00 0.00 41.60 3.60
2438 2524 3.073062 AGACTACAGGTGCATTTCAACCT 59.927 43.478 0.00 0.00 30.95 3.50
2479 2565 9.918630 CTTTGATATTGACAACCTGAAGAAATT 57.081 29.630 0.00 0.00 0.00 1.82
2509 2595 2.364311 GCACCGTGAAATGTTGCGC 61.364 57.895 0.00 0.00 0.00 6.09
2512 2598 5.046910 AGAATTAGCACCGTGAAATGTTG 57.953 39.130 1.65 0.00 0.00 3.33
2513 2599 5.705609 AAGAATTAGCACCGTGAAATGTT 57.294 34.783 1.65 0.00 0.00 2.71
2514 2600 5.938125 AGTAAGAATTAGCACCGTGAAATGT 59.062 36.000 1.65 0.00 0.00 2.71
2523 2609 4.381612 GGGCCAAAAGTAAGAATTAGCACC 60.382 45.833 4.39 0.00 0.00 5.01
2537 2624 1.615392 CTCAACAAGGAGGGCCAAAAG 59.385 52.381 6.18 0.00 36.29 2.27
2543 2630 6.152831 ACAATATTAAACTCAACAAGGAGGGC 59.847 38.462 0.00 0.00 39.27 5.19
2601 2688 7.734924 TTAAGCAGAAGATATGGCATAAGTG 57.265 36.000 11.86 6.02 0.00 3.16
2617 2704 8.902806 CATGTAGGTTTTTATCCATTAAGCAGA 58.097 33.333 0.00 0.00 0.00 4.26
2714 2801 6.206243 AGTGGTCATCTTCAGACTTTTTCATG 59.794 38.462 0.00 0.00 36.29 3.07
2722 2809 5.998363 GGTTTTTAGTGGTCATCTTCAGACT 59.002 40.000 0.00 0.00 36.29 3.24
2752 2839 0.807496 GTCCAGCTCTTGCCATGAAC 59.193 55.000 0.00 0.00 40.80 3.18
2802 2889 4.569023 CTCGTGCCGCCTATCGCA 62.569 66.667 0.00 0.00 37.30 5.10
2847 2934 0.460987 GCGGGAGGAATGACTCAGTG 60.461 60.000 0.00 0.00 39.27 3.66
2850 2937 1.480954 GTTAGCGGGAGGAATGACTCA 59.519 52.381 0.00 0.00 39.27 3.41
2886 2973 1.558756 AGGAGGAACATCAAGAGGCAG 59.441 52.381 0.00 0.00 0.00 4.85
2916 3003 0.104934 AGACCCTCAACACCCTCACT 60.105 55.000 0.00 0.00 0.00 3.41
3021 3108 1.084370 GTGTGCTCACTACCATCCGC 61.084 60.000 11.58 0.00 40.98 5.54
3073 3160 7.990886 TGATAACTAACAACATTACATCCCCTC 59.009 37.037 0.00 0.00 0.00 4.30
3087 3174 6.126768 CCCCCTCTCTCATTGATAACTAACAA 60.127 42.308 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.