Multiple sequence alignment - TraesCS3D01G221000

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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 TraesCS3D01G221000 chr3D 100.000 2390 0 0 1 2390 301579132 301576743 0.000000e+00 4414.0
1 TraesCS3D01G221000 chr3B 94.109 2139 74 20 264 2390 419565473 419567571 0.000000e+00 3205.0
2 TraesCS3D01G221000 chr3B 100.000 33 0 0 1 33 419565392 419565424 7.130000e-06 62.1
3 TraesCS3D01G221000 chr3A 91.506 1966 105 27 159 2082 433885966 433887911 0.000000e+00 2649.0
4 TraesCS3D01G221000 chr3A 91.800 500 33 8 1587 2082 433963235 433963730 0.000000e+00 689.0
5 TraesCS3D01G221000 chr3A 93.091 275 19 0 2116 2390 433887974 433888248 1.030000e-108 403.0
6 TraesCS3D01G221000 chr3A 92.364 275 21 0 2116 2390 433963792 433964066 2.230000e-105 392.0
7 TraesCS3D01G221000 chr5A 90.909 143 11 1 35 175 644443768 644443910 8.720000e-45 191.0
8 TraesCS3D01G221000 chr6A 90.210 143 12 1 35 175 528356436 528356294 4.060000e-43 185.0
9 TraesCS3D01G221000 chr6A 88.811 143 9 5 35 175 528578943 528578806 4.090000e-38 169.0
10 TraesCS3D01G221000 chr1B 91.045 134 10 2 35 166 631775957 631776090 1.890000e-41 180.0
11 TraesCS3D01G221000 chr5B 87.500 144 14 4 35 175 591197172 591197030 1.900000e-36 163.0
12 TraesCS3D01G221000 chr5B 94.737 76 3 1 101 175 641818562 641818487 1.500000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G221000 chr3D 301576743 301579132 2389 True 4414.00 4414 100.0000 1 2390 1 chr3D.!!$R1 2389
1 TraesCS3D01G221000 chr3B 419565392 419567571 2179 False 1633.55 3205 97.0545 1 2390 2 chr3B.!!$F1 2389
2 TraesCS3D01G221000 chr3A 433885966 433888248 2282 False 1526.00 2649 92.2985 159 2390 2 chr3A.!!$F1 2231
3 TraesCS3D01G221000 chr3A 433963235 433964066 831 False 540.50 689 92.0820 1587 2390 2 chr3A.!!$F2 803

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
62 63 0.03601 AGATTTGGTCAGCACGAGGG 60.036 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2067 0.037512 CCCATTTTGCATGCACGGAA 60.038 50.0 22.58 15.77 0.0 4.3 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
33 34 5.189934 ACCCAACTAGTATTAAGCTTGCTCT 59.810 40.000 9.86 5.00 0.00 4.09
34 35 6.383147 ACCCAACTAGTATTAAGCTTGCTCTA 59.617 38.462 9.86 5.88 0.00 2.43
35 36 7.071321 ACCCAACTAGTATTAAGCTTGCTCTAT 59.929 37.037 9.86 0.00 0.00 1.98
36 37 7.600752 CCCAACTAGTATTAAGCTTGCTCTATC 59.399 40.741 9.86 0.00 0.00 2.08
37 38 8.364142 CCAACTAGTATTAAGCTTGCTCTATCT 58.636 37.037 9.86 1.38 0.00 1.98
38 39 9.757227 CAACTAGTATTAAGCTTGCTCTATCTT 57.243 33.333 9.86 0.00 0.00 2.40
39 40 9.974980 AACTAGTATTAAGCTTGCTCTATCTTC 57.025 33.333 9.86 0.00 0.00 2.87
40 41 9.362151 ACTAGTATTAAGCTTGCTCTATCTTCT 57.638 33.333 9.86 0.00 0.00 2.85
41 42 9.840427 CTAGTATTAAGCTTGCTCTATCTTCTC 57.160 37.037 9.86 0.00 0.00 2.87
42 43 8.477419 AGTATTAAGCTTGCTCTATCTTCTCT 57.523 34.615 9.86 0.00 0.00 3.10
43 44 9.581289 AGTATTAAGCTTGCTCTATCTTCTCTA 57.419 33.333 9.86 0.00 0.00 2.43
44 45 9.840427 GTATTAAGCTTGCTCTATCTTCTCTAG 57.160 37.037 9.86 0.00 0.00 2.43
45 46 8.704849 ATTAAGCTTGCTCTATCTTCTCTAGA 57.295 34.615 9.86 0.00 37.28 2.43
46 47 8.704849 TTAAGCTTGCTCTATCTTCTCTAGAT 57.295 34.615 9.86 0.00 45.59 1.98
47 48 7.601705 AAGCTTGCTCTATCTTCTCTAGATT 57.398 36.000 0.00 0.00 40.84 2.40
48 49 7.601705 AGCTTGCTCTATCTTCTCTAGATTT 57.398 36.000 0.00 0.00 40.84 2.17
49 50 7.436118 AGCTTGCTCTATCTTCTCTAGATTTG 58.564 38.462 0.00 0.00 40.84 2.32
50 51 6.646240 GCTTGCTCTATCTTCTCTAGATTTGG 59.354 42.308 0.00 0.00 40.84 3.28
51 52 7.667575 TTGCTCTATCTTCTCTAGATTTGGT 57.332 36.000 0.00 0.00 40.84 3.67
52 53 7.283625 TGCTCTATCTTCTCTAGATTTGGTC 57.716 40.000 0.00 0.00 40.84 4.02
53 54 6.836007 TGCTCTATCTTCTCTAGATTTGGTCA 59.164 38.462 0.00 0.00 40.84 4.02
54 55 7.014134 TGCTCTATCTTCTCTAGATTTGGTCAG 59.986 40.741 0.00 0.00 40.84 3.51
55 56 7.283625 TCTATCTTCTCTAGATTTGGTCAGC 57.716 40.000 0.00 0.00 40.84 4.26
56 57 5.946942 ATCTTCTCTAGATTTGGTCAGCA 57.053 39.130 0.00 0.00 40.84 4.41
57 58 5.078411 TCTTCTCTAGATTTGGTCAGCAC 57.922 43.478 0.00 0.00 0.00 4.40
58 59 3.510388 TCTCTAGATTTGGTCAGCACG 57.490 47.619 0.00 0.00 0.00 5.34
59 60 3.089284 TCTCTAGATTTGGTCAGCACGA 58.911 45.455 0.00 0.00 0.00 4.35
60 61 3.129462 TCTCTAGATTTGGTCAGCACGAG 59.871 47.826 0.00 0.00 0.00 4.18
61 62 2.166459 TCTAGATTTGGTCAGCACGAGG 59.834 50.000 0.00 0.00 0.00 4.63
62 63 0.036010 AGATTTGGTCAGCACGAGGG 60.036 55.000 0.00 0.00 0.00 4.30
63 64 0.321653 GATTTGGTCAGCACGAGGGT 60.322 55.000 0.00 0.00 0.00 4.34
64 65 0.321653 ATTTGGTCAGCACGAGGGTC 60.322 55.000 0.00 0.00 0.00 4.46
65 66 2.709125 TTTGGTCAGCACGAGGGTCG 62.709 60.000 0.00 0.00 46.93 4.79
66 67 3.371063 GGTCAGCACGAGGGTCGA 61.371 66.667 2.82 0.00 43.74 4.20
67 68 2.649034 GTCAGCACGAGGGTCGAA 59.351 61.111 2.82 0.00 43.74 3.71
68 69 1.733399 GTCAGCACGAGGGTCGAAC 60.733 63.158 2.82 0.00 43.74 3.95
69 70 1.901948 TCAGCACGAGGGTCGAACT 60.902 57.895 0.00 0.00 43.74 3.01
70 71 1.734477 CAGCACGAGGGTCGAACTG 60.734 63.158 0.00 6.20 43.74 3.16
71 72 3.112709 GCACGAGGGTCGAACTGC 61.113 66.667 0.00 0.00 43.74 4.40
72 73 2.338620 CACGAGGGTCGAACTGCA 59.661 61.111 0.00 0.00 43.74 4.41
73 74 1.734477 CACGAGGGTCGAACTGCAG 60.734 63.158 13.48 13.48 43.74 4.41
74 75 2.201022 ACGAGGGTCGAACTGCAGT 61.201 57.895 15.25 15.25 43.74 4.40
75 76 0.892358 ACGAGGGTCGAACTGCAGTA 60.892 55.000 22.01 0.65 43.74 2.74
76 77 0.456221 CGAGGGTCGAACTGCAGTAT 59.544 55.000 22.01 10.57 43.74 2.12
77 78 1.799181 CGAGGGTCGAACTGCAGTATG 60.799 57.143 22.01 15.66 43.74 2.39
78 79 0.537188 AGGGTCGAACTGCAGTATGG 59.463 55.000 22.01 12.39 35.86 2.74
79 80 0.249398 GGGTCGAACTGCAGTATGGT 59.751 55.000 22.01 3.60 35.86 3.55
80 81 1.338769 GGGTCGAACTGCAGTATGGTT 60.339 52.381 22.01 3.13 35.86 3.67
81 82 2.093869 GGGTCGAACTGCAGTATGGTTA 60.094 50.000 22.01 0.00 35.86 2.85
82 83 3.187700 GGTCGAACTGCAGTATGGTTAG 58.812 50.000 22.01 4.41 35.86 2.34
83 84 3.187700 GTCGAACTGCAGTATGGTTAGG 58.812 50.000 22.01 3.61 35.86 2.69
84 85 2.167693 TCGAACTGCAGTATGGTTAGGG 59.832 50.000 22.01 2.04 35.86 3.53
85 86 2.093658 CGAACTGCAGTATGGTTAGGGT 60.094 50.000 22.01 0.00 35.86 4.34
86 87 3.532542 GAACTGCAGTATGGTTAGGGTC 58.467 50.000 22.01 5.91 35.86 4.46
87 88 2.546899 ACTGCAGTATGGTTAGGGTCA 58.453 47.619 20.16 0.00 35.86 4.02
88 89 2.501723 ACTGCAGTATGGTTAGGGTCAG 59.498 50.000 20.16 0.00 35.86 3.51
89 90 1.837439 TGCAGTATGGTTAGGGTCAGG 59.163 52.381 0.00 0.00 35.86 3.86
90 91 1.475213 GCAGTATGGTTAGGGTCAGGC 60.475 57.143 0.00 0.00 35.86 4.85
91 92 1.141053 CAGTATGGTTAGGGTCAGGCC 59.859 57.143 0.00 0.00 0.00 5.19
101 102 3.987594 GGTCAGGCCCTGAAGAAAT 57.012 52.632 16.70 0.00 42.46 2.17
102 103 2.222227 GGTCAGGCCCTGAAGAAATT 57.778 50.000 16.70 0.00 42.46 1.82
103 104 2.529632 GGTCAGGCCCTGAAGAAATTT 58.470 47.619 16.70 0.00 42.46 1.82
104 105 2.899900 GGTCAGGCCCTGAAGAAATTTT 59.100 45.455 16.70 0.00 42.46 1.82
105 106 4.086457 GGTCAGGCCCTGAAGAAATTTTA 58.914 43.478 16.70 0.00 42.46 1.52
106 107 4.158579 GGTCAGGCCCTGAAGAAATTTTAG 59.841 45.833 16.70 0.00 42.46 1.85
107 108 4.158579 GTCAGGCCCTGAAGAAATTTTAGG 59.841 45.833 16.70 0.00 42.46 2.69
108 109 3.099905 AGGCCCTGAAGAAATTTTAGGC 58.900 45.455 0.00 0.00 38.45 3.93
109 110 3.526931 GCCCTGAAGAAATTTTAGGCC 57.473 47.619 0.00 0.00 32.93 5.19
110 111 3.099905 GCCCTGAAGAAATTTTAGGCCT 58.900 45.455 11.78 11.78 32.93 5.19
111 112 3.515502 GCCCTGAAGAAATTTTAGGCCTT 59.484 43.478 12.58 0.00 32.93 4.35
112 113 4.382040 GCCCTGAAGAAATTTTAGGCCTTC 60.382 45.833 12.58 0.00 35.18 3.46
113 114 5.019470 CCCTGAAGAAATTTTAGGCCTTCT 58.981 41.667 12.58 2.83 35.53 2.85
114 115 5.126222 CCCTGAAGAAATTTTAGGCCTTCTC 59.874 44.000 12.58 1.69 35.53 2.87
115 116 5.126222 CCTGAAGAAATTTTAGGCCTTCTCC 59.874 44.000 12.58 0.00 35.53 3.71
116 117 5.892348 TGAAGAAATTTTAGGCCTTCTCCT 58.108 37.500 12.58 0.00 40.21 3.69
117 118 6.314917 TGAAGAAATTTTAGGCCTTCTCCTT 58.685 36.000 12.58 5.84 37.66 3.36
118 119 6.434340 TGAAGAAATTTTAGGCCTTCTCCTTC 59.566 38.462 12.58 14.81 37.66 3.46
119 120 4.944317 AGAAATTTTAGGCCTTCTCCTTCG 59.056 41.667 12.58 0.00 37.66 3.79
120 121 2.781681 TTTTAGGCCTTCTCCTTCGG 57.218 50.000 12.58 0.00 37.66 4.30
121 122 0.909623 TTTAGGCCTTCTCCTTCGGG 59.090 55.000 12.58 0.00 37.66 5.14
122 123 0.042131 TTAGGCCTTCTCCTTCGGGA 59.958 55.000 12.58 0.00 42.74 5.14
123 124 0.264955 TAGGCCTTCTCCTTCGGGAT 59.735 55.000 12.58 0.00 44.11 3.85
124 125 0.621862 AGGCCTTCTCCTTCGGGATT 60.622 55.000 0.00 0.00 44.11 3.01
125 126 0.464554 GGCCTTCTCCTTCGGGATTG 60.465 60.000 0.00 0.00 44.11 2.67
126 127 0.253327 GCCTTCTCCTTCGGGATTGT 59.747 55.000 0.00 0.00 44.11 2.71
127 128 1.485066 GCCTTCTCCTTCGGGATTGTA 59.515 52.381 0.00 0.00 44.11 2.41
128 129 2.093128 GCCTTCTCCTTCGGGATTGTAA 60.093 50.000 0.00 0.00 44.11 2.41
129 130 3.433740 GCCTTCTCCTTCGGGATTGTAAT 60.434 47.826 0.00 0.00 44.11 1.89
130 131 4.130118 CCTTCTCCTTCGGGATTGTAATG 58.870 47.826 0.00 0.00 44.11 1.90
131 132 4.384208 CCTTCTCCTTCGGGATTGTAATGT 60.384 45.833 0.00 0.00 44.11 2.71
132 133 4.137116 TCTCCTTCGGGATTGTAATGTG 57.863 45.455 0.00 0.00 44.11 3.21
133 134 3.772572 TCTCCTTCGGGATTGTAATGTGA 59.227 43.478 0.00 0.00 44.11 3.58
134 135 3.869065 TCCTTCGGGATTGTAATGTGAC 58.131 45.455 0.00 0.00 39.58 3.67
135 136 3.517901 TCCTTCGGGATTGTAATGTGACT 59.482 43.478 0.00 0.00 39.58 3.41
136 137 3.871594 CCTTCGGGATTGTAATGTGACTC 59.128 47.826 0.00 0.00 37.25 3.36
137 138 4.383118 CCTTCGGGATTGTAATGTGACTCT 60.383 45.833 0.00 0.00 37.25 3.24
138 139 4.819105 TCGGGATTGTAATGTGACTCTT 57.181 40.909 0.00 0.00 0.00 2.85
139 140 5.925506 TCGGGATTGTAATGTGACTCTTA 57.074 39.130 0.00 0.00 0.00 2.10
140 141 5.657474 TCGGGATTGTAATGTGACTCTTAC 58.343 41.667 2.92 2.92 0.00 2.34
141 142 5.421056 TCGGGATTGTAATGTGACTCTTACT 59.579 40.000 9.06 0.00 0.00 2.24
142 143 6.070995 TCGGGATTGTAATGTGACTCTTACTT 60.071 38.462 9.06 0.25 0.00 2.24
143 144 7.123098 TCGGGATTGTAATGTGACTCTTACTTA 59.877 37.037 9.06 1.10 0.00 2.24
144 145 7.762615 CGGGATTGTAATGTGACTCTTACTTAA 59.237 37.037 9.06 0.01 0.00 1.85
145 146 9.614792 GGGATTGTAATGTGACTCTTACTTAAT 57.385 33.333 9.06 3.60 0.00 1.40
155 156 9.856488 TGTGACTCTTACTTAATCAGTACAATC 57.144 33.333 0.00 0.00 37.74 2.67
156 157 9.303537 GTGACTCTTACTTAATCAGTACAATCC 57.696 37.037 0.00 0.00 37.74 3.01
157 158 8.475639 TGACTCTTACTTAATCAGTACAATCCC 58.524 37.037 0.00 0.00 37.74 3.85
158 159 7.793036 ACTCTTACTTAATCAGTACAATCCCC 58.207 38.462 0.00 0.00 37.74 4.81
159 160 7.624077 ACTCTTACTTAATCAGTACAATCCCCT 59.376 37.037 0.00 0.00 37.74 4.79
160 161 8.388656 TCTTACTTAATCAGTACAATCCCCTT 57.611 34.615 0.00 0.00 37.74 3.95
161 162 8.832735 TCTTACTTAATCAGTACAATCCCCTTT 58.167 33.333 0.00 0.00 37.74 3.11
163 164 9.895138 TTACTTAATCAGTACAATCCCCTTTAC 57.105 33.333 0.00 0.00 37.74 2.01
164 165 7.344134 ACTTAATCAGTACAATCCCCTTTACC 58.656 38.462 0.00 0.00 31.97 2.85
165 166 4.790718 ATCAGTACAATCCCCTTTACCC 57.209 45.455 0.00 0.00 0.00 3.69
166 167 3.810623 TCAGTACAATCCCCTTTACCCT 58.189 45.455 0.00 0.00 0.00 4.34
167 168 3.521937 TCAGTACAATCCCCTTTACCCTG 59.478 47.826 0.00 0.00 0.00 4.45
169 170 2.068831 ACAATCCCCTTTACCCTGGA 57.931 50.000 0.00 0.00 0.00 3.86
195 196 2.621998 ACTATTAAGCTAGCTCCGCGAA 59.378 45.455 19.65 7.96 0.00 4.70
245 251 4.377841 GCAAGCATGTGTAGAGTGAGTTTC 60.378 45.833 0.00 0.00 0.00 2.78
246 252 3.931578 AGCATGTGTAGAGTGAGTTTCC 58.068 45.455 0.00 0.00 0.00 3.13
247 253 3.324846 AGCATGTGTAGAGTGAGTTTCCA 59.675 43.478 0.00 0.00 0.00 3.53
249 255 3.364889 TGTGTAGAGTGAGTTTCCACG 57.635 47.619 0.00 0.00 41.67 4.94
252 258 1.000506 GTAGAGTGAGTTTCCACGGCA 59.999 52.381 0.00 0.00 41.67 5.69
314 320 1.854939 AGGCCAGGATCAATGGATGAA 59.145 47.619 17.93 0.00 42.54 2.57
315 321 2.449730 AGGCCAGGATCAATGGATGAAT 59.550 45.455 17.93 0.00 42.54 2.57
474 486 2.102357 GCACGACGCTAGCAGCTA 59.898 61.111 16.45 1.13 39.60 3.32
475 487 1.941734 GCACGACGCTAGCAGCTAG 60.942 63.158 23.40 23.40 39.60 3.42
476 488 1.429825 CACGACGCTAGCAGCTAGT 59.570 57.895 27.00 12.16 39.60 2.57
477 489 0.656259 CACGACGCTAGCAGCTAGTA 59.344 55.000 27.00 0.00 39.60 1.82
737 755 1.990060 GCCAGCTCAGGAGGTACCA 60.990 63.158 15.94 0.00 42.04 3.25
743 761 1.745141 GCTCAGGAGGTACCAATGCTG 60.745 57.143 15.94 15.02 42.04 4.41
789 807 0.249398 TTACGCCTTCCTCTGCTTCC 59.751 55.000 0.00 0.00 0.00 3.46
886 912 0.590195 GCATCATAAGAAGGCTGGCG 59.410 55.000 0.00 0.00 0.00 5.69
946 972 0.037232 GCTTCTTACCGAGCCACACT 60.037 55.000 0.00 0.00 0.00 3.55
1008 1034 2.734591 GTGGATAGGATGCGGCGA 59.265 61.111 12.98 0.00 0.00 5.54
1179 1205 2.345124 ACTACTACTACAGCCCTCCG 57.655 55.000 0.00 0.00 0.00 4.63
1399 1425 1.328680 CCTTTTGGTGATCGATCTGCG 59.671 52.381 25.02 7.49 36.61 5.18
1404 1430 1.638467 GTGATCGATCTGCGGCAAC 59.362 57.895 25.02 10.13 41.33 4.17
1531 1557 7.719633 ACTGGTCATATGTTTTGTAGTTCTTGT 59.280 33.333 1.90 0.00 0.00 3.16
1545 1578 8.703604 TGTAGTTCTTGTAATACATCAAGCTC 57.296 34.615 0.00 0.00 40.27 4.09
1546 1579 7.764443 TGTAGTTCTTGTAATACATCAAGCTCC 59.236 37.037 0.00 0.00 40.27 4.70
1552 1585 8.730680 TCTTGTAATACATCAAGCTCCTTTTTC 58.269 33.333 0.00 0.00 40.27 2.29
1555 1588 7.882791 TGTAATACATCAAGCTCCTTTTTCTCA 59.117 33.333 0.00 0.00 0.00 3.27
1556 1589 7.765695 AATACATCAAGCTCCTTTTTCTCAA 57.234 32.000 0.00 0.00 0.00 3.02
1559 1592 7.059202 ACATCAAGCTCCTTTTTCTCAATTT 57.941 32.000 0.00 0.00 0.00 1.82
1561 1594 7.440255 ACATCAAGCTCCTTTTTCTCAATTTTG 59.560 33.333 0.00 0.00 0.00 2.44
1565 1598 7.776933 AGCTCCTTTTTCTCAATTTTGTTTC 57.223 32.000 0.00 0.00 0.00 2.78
1672 1706 4.058124 GTGGGTGATCTTTTTGGCTTTTC 58.942 43.478 0.00 0.00 0.00 2.29
1837 1885 3.438434 ACAACAACAAACAACAAATGGGC 59.562 39.130 0.00 0.00 0.00 5.36
1860 1908 5.333416 GCAAAATGGCTAAGCTATACGACTC 60.333 44.000 0.00 0.00 0.00 3.36
1866 1914 5.469421 TGGCTAAGCTATACGACTCTTACTC 59.531 44.000 0.00 0.00 0.00 2.59
1886 1934 2.552315 TCACAATTCTGCTTCCGTTTCC 59.448 45.455 0.00 0.00 0.00 3.13
1902 1950 2.552743 GTTTCCGGAGAAGGGAAAGTTG 59.447 50.000 3.34 0.00 38.87 3.16
1932 1980 1.791555 GCGATCATGCCAGTTTGTTCG 60.792 52.381 0.00 0.00 37.84 3.95
1970 2018 5.817816 AGTAGCTTTTTCCGGATCAACTATG 59.182 40.000 4.15 0.00 0.00 2.23
2000 2048 1.128200 TGGTGGATCTATGGGGAACG 58.872 55.000 0.00 0.00 0.00 3.95
2019 2067 2.037772 ACGCAGTTCTTCTCACAAGGAT 59.962 45.455 0.00 0.00 37.78 3.24
2022 2070 3.438434 GCAGTTCTTCTCACAAGGATTCC 59.562 47.826 0.00 0.00 0.00 3.01
2094 2142 6.229733 CACATTCTTTCTCACTCCTCTTTCT 58.770 40.000 0.00 0.00 0.00 2.52
2100 2148 4.000331 TCTCACTCCTCTTTCTTTGCAG 58.000 45.455 0.00 0.00 0.00 4.41
2158 2248 1.778334 CCCCTTTTTGCTTTGCGTAC 58.222 50.000 0.00 0.00 0.00 3.67
2168 2258 7.527084 TTTTGCTTTGCGTACAAGTTAAAAT 57.473 28.000 0.00 0.00 37.04 1.82
2169 2259 7.527084 TTTGCTTTGCGTACAAGTTAAAATT 57.473 28.000 0.00 0.00 37.04 1.82
2182 2272 7.973601 ACAAGTTAAAATTTTCAGCAACAAGG 58.026 30.769 6.72 3.31 0.00 3.61
2196 2286 5.007430 CAGCAACAAGGCTAACTATCATCAG 59.993 44.000 0.00 0.00 43.68 2.90
2245 2335 3.379688 GGCTTGGAATGAAAGATCAGACC 59.620 47.826 0.00 0.00 39.39 3.85
2281 2371 3.192212 CCAAATCCTCTTCCACAAGCTTC 59.808 47.826 0.00 0.00 0.00 3.86
2299 2389 2.080286 TCTGCGAACTAGTCAAAGGC 57.920 50.000 0.00 0.00 0.00 4.35
2329 2419 4.735822 CCTAGCGTAAAACGATCTTCTCTG 59.264 45.833 3.22 0.00 46.05 3.35
2336 2426 3.584406 AACGATCTTCTCTGACCACAG 57.416 47.619 0.00 0.00 44.66 3.66
2356 2446 0.953471 GGTGCAACTACACATGGCGA 60.953 55.000 0.00 0.00 42.55 5.54
2377 2467 1.616865 TCGGTTGTGTCTTAGTCCCTG 59.383 52.381 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.460261 CGTGCTGACCAAATCTAGAGAAGATA 60.460 42.308 0.00 0.00 44.56 1.98
35 36 4.380973 CGTGCTGACCAAATCTAGAGAAGA 60.381 45.833 0.00 0.00 39.02 2.87
36 37 3.862267 CGTGCTGACCAAATCTAGAGAAG 59.138 47.826 0.00 0.00 0.00 2.85
37 38 3.509967 TCGTGCTGACCAAATCTAGAGAA 59.490 43.478 0.00 0.00 0.00 2.87
38 39 3.089284 TCGTGCTGACCAAATCTAGAGA 58.911 45.455 0.00 0.00 0.00 3.10
39 40 3.443037 CTCGTGCTGACCAAATCTAGAG 58.557 50.000 0.00 0.00 0.00 2.43
40 41 2.166459 CCTCGTGCTGACCAAATCTAGA 59.834 50.000 0.00 0.00 0.00 2.43
41 42 2.544685 CCTCGTGCTGACCAAATCTAG 58.455 52.381 0.00 0.00 0.00 2.43
42 43 1.207089 CCCTCGTGCTGACCAAATCTA 59.793 52.381 0.00 0.00 0.00 1.98
43 44 0.036010 CCCTCGTGCTGACCAAATCT 60.036 55.000 0.00 0.00 0.00 2.40
44 45 0.321653 ACCCTCGTGCTGACCAAATC 60.322 55.000 0.00 0.00 0.00 2.17
45 46 0.321653 GACCCTCGTGCTGACCAAAT 60.322 55.000 0.00 0.00 0.00 2.32
46 47 1.070786 GACCCTCGTGCTGACCAAA 59.929 57.895 0.00 0.00 0.00 3.28
47 48 2.741092 GACCCTCGTGCTGACCAA 59.259 61.111 0.00 0.00 0.00 3.67
48 49 3.680786 CGACCCTCGTGCTGACCA 61.681 66.667 0.00 0.00 34.72 4.02
49 50 2.927580 TTCGACCCTCGTGCTGACC 61.928 63.158 0.00 0.00 41.35 4.02
50 51 1.733399 GTTCGACCCTCGTGCTGAC 60.733 63.158 0.00 0.00 41.35 3.51
51 52 1.901948 AGTTCGACCCTCGTGCTGA 60.902 57.895 0.00 0.00 41.35 4.26
52 53 1.734477 CAGTTCGACCCTCGTGCTG 60.734 63.158 0.00 0.00 41.35 4.41
53 54 2.651361 CAGTTCGACCCTCGTGCT 59.349 61.111 0.00 0.00 41.35 4.40
54 55 3.112709 GCAGTTCGACCCTCGTGC 61.113 66.667 0.00 0.00 41.35 5.34
55 56 1.734477 CTGCAGTTCGACCCTCGTG 60.734 63.158 5.25 0.00 41.35 4.35
56 57 0.892358 TACTGCAGTTCGACCCTCGT 60.892 55.000 27.06 0.00 41.35 4.18
57 58 0.456221 ATACTGCAGTTCGACCCTCG 59.544 55.000 27.06 0.00 42.10 4.63
58 59 1.471676 CCATACTGCAGTTCGACCCTC 60.472 57.143 27.06 0.00 0.00 4.30
59 60 0.537188 CCATACTGCAGTTCGACCCT 59.463 55.000 27.06 0.00 0.00 4.34
60 61 0.249398 ACCATACTGCAGTTCGACCC 59.751 55.000 27.06 0.00 0.00 4.46
61 62 2.094762 AACCATACTGCAGTTCGACC 57.905 50.000 27.06 0.00 0.00 4.79
62 63 3.187700 CCTAACCATACTGCAGTTCGAC 58.812 50.000 27.06 0.00 0.00 4.20
63 64 2.167693 CCCTAACCATACTGCAGTTCGA 59.832 50.000 27.06 7.61 0.00 3.71
64 65 2.093658 ACCCTAACCATACTGCAGTTCG 60.094 50.000 27.06 16.07 0.00 3.95
65 66 3.055385 TGACCCTAACCATACTGCAGTTC 60.055 47.826 27.06 12.61 0.00 3.01
66 67 2.910319 TGACCCTAACCATACTGCAGTT 59.090 45.455 27.06 9.16 0.00 3.16
67 68 2.501723 CTGACCCTAACCATACTGCAGT 59.498 50.000 25.12 25.12 0.00 4.40
68 69 2.158900 CCTGACCCTAACCATACTGCAG 60.159 54.545 13.48 13.48 0.00 4.41
69 70 1.837439 CCTGACCCTAACCATACTGCA 59.163 52.381 0.00 0.00 0.00 4.41
70 71 1.475213 GCCTGACCCTAACCATACTGC 60.475 57.143 0.00 0.00 0.00 4.40
71 72 1.141053 GGCCTGACCCTAACCATACTG 59.859 57.143 0.00 0.00 0.00 2.74
72 73 1.508256 GGCCTGACCCTAACCATACT 58.492 55.000 0.00 0.00 0.00 2.12
83 84 2.222227 AATTTCTTCAGGGCCTGACC 57.778 50.000 35.18 0.00 40.46 4.02
84 85 4.158579 CCTAAAATTTCTTCAGGGCCTGAC 59.841 45.833 35.18 0.00 40.46 3.51
85 86 4.344104 CCTAAAATTTCTTCAGGGCCTGA 58.656 43.478 32.01 32.01 38.87 3.86
86 87 3.118992 GCCTAAAATTTCTTCAGGGCCTG 60.119 47.826 28.01 28.01 33.07 4.85
87 88 3.099905 GCCTAAAATTTCTTCAGGGCCT 58.900 45.455 0.00 0.00 33.07 5.19
88 89 3.526931 GCCTAAAATTTCTTCAGGGCC 57.473 47.619 0.00 0.00 33.07 5.80
89 90 3.526931 GGCCTAAAATTTCTTCAGGGC 57.473 47.619 14.62 14.62 43.62 5.19
90 91 5.019470 AGAAGGCCTAAAATTTCTTCAGGG 58.981 41.667 5.16 4.06 37.04 4.45
91 92 5.126222 GGAGAAGGCCTAAAATTTCTTCAGG 59.874 44.000 5.16 10.05 37.04 3.86
92 93 5.948758 AGGAGAAGGCCTAAAATTTCTTCAG 59.051 40.000 5.16 2.21 36.22 3.02
93 94 5.892348 AGGAGAAGGCCTAAAATTTCTTCA 58.108 37.500 5.16 0.00 36.22 3.02
94 95 6.403746 CGAAGGAGAAGGCCTAAAATTTCTTC 60.404 42.308 5.16 12.02 37.26 2.87
95 96 5.416013 CGAAGGAGAAGGCCTAAAATTTCTT 59.584 40.000 5.16 3.95 37.26 2.52
96 97 4.944317 CGAAGGAGAAGGCCTAAAATTTCT 59.056 41.667 5.16 3.20 37.26 2.52
97 98 5.236655 CGAAGGAGAAGGCCTAAAATTTC 57.763 43.478 5.16 7.41 37.26 2.17
114 115 8.582375 GTAAGAGTCACATTACAATCCCGAAGG 61.582 44.444 0.00 0.00 38.42 3.46
115 116 4.759782 AGAGTCACATTACAATCCCGAAG 58.240 43.478 0.00 0.00 0.00 3.79
116 117 4.819105 AGAGTCACATTACAATCCCGAA 57.181 40.909 0.00 0.00 0.00 4.30
117 118 4.819105 AAGAGTCACATTACAATCCCGA 57.181 40.909 0.00 0.00 0.00 5.14
118 119 5.661458 AGTAAGAGTCACATTACAATCCCG 58.339 41.667 5.90 0.00 34.91 5.14
119 120 9.614792 ATTAAGTAAGAGTCACATTACAATCCC 57.385 33.333 5.90 0.00 34.91 3.85
129 130 9.856488 GATTGTACTGATTAAGTAAGAGTCACA 57.144 33.333 0.00 0.00 43.08 3.58
130 131 9.303537 GGATTGTACTGATTAAGTAAGAGTCAC 57.696 37.037 0.00 0.00 43.08 3.67
131 132 8.475639 GGGATTGTACTGATTAAGTAAGAGTCA 58.524 37.037 0.00 0.00 43.08 3.41
132 133 7.927092 GGGGATTGTACTGATTAAGTAAGAGTC 59.073 40.741 0.00 0.00 43.08 3.36
133 134 7.624077 AGGGGATTGTACTGATTAAGTAAGAGT 59.376 37.037 0.00 0.00 43.08 3.24
134 135 8.024145 AGGGGATTGTACTGATTAAGTAAGAG 57.976 38.462 0.00 0.00 43.08 2.85
135 136 7.989947 AGGGGATTGTACTGATTAAGTAAGA 57.010 36.000 0.00 0.00 43.08 2.10
137 138 9.895138 GTAAAGGGGATTGTACTGATTAAGTAA 57.105 33.333 0.00 0.00 43.08 2.24
138 139 8.488668 GGTAAAGGGGATTGTACTGATTAAGTA 58.511 37.037 0.00 0.00 40.56 2.24
139 140 7.344134 GGTAAAGGGGATTGTACTGATTAAGT 58.656 38.462 0.00 0.00 43.40 2.24
140 141 6.771267 GGGTAAAGGGGATTGTACTGATTAAG 59.229 42.308 0.00 0.00 0.00 1.85
141 142 6.449041 AGGGTAAAGGGGATTGTACTGATTAA 59.551 38.462 0.00 0.00 0.00 1.40
142 143 5.974370 AGGGTAAAGGGGATTGTACTGATTA 59.026 40.000 0.00 0.00 0.00 1.75
143 144 4.794067 AGGGTAAAGGGGATTGTACTGATT 59.206 41.667 0.00 0.00 0.00 2.57
144 145 4.166144 CAGGGTAAAGGGGATTGTACTGAT 59.834 45.833 0.00 0.00 0.00 2.90
145 146 3.521937 CAGGGTAAAGGGGATTGTACTGA 59.478 47.826 0.00 0.00 0.00 3.41
146 147 3.371595 CCAGGGTAAAGGGGATTGTACTG 60.372 52.174 0.00 0.00 0.00 2.74
147 148 2.850568 CCAGGGTAAAGGGGATTGTACT 59.149 50.000 0.00 0.00 0.00 2.73
148 149 2.848071 TCCAGGGTAAAGGGGATTGTAC 59.152 50.000 0.00 0.00 0.00 2.90
149 150 3.223940 TCCAGGGTAAAGGGGATTGTA 57.776 47.619 0.00 0.00 0.00 2.41
150 151 2.068831 TCCAGGGTAAAGGGGATTGT 57.931 50.000 0.00 0.00 0.00 2.71
151 152 3.466395 TTTCCAGGGTAAAGGGGATTG 57.534 47.619 0.00 0.00 0.00 2.67
152 153 4.495459 TTTTTCCAGGGTAAAGGGGATT 57.505 40.909 0.00 0.00 0.00 3.01
178 179 9.340996 AGAATATTCTTCGCGGAGCTAGCTTAA 62.341 40.741 20.42 7.81 44.05 1.85
179 180 7.959954 AGAATATTCTTCGCGGAGCTAGCTTA 61.960 42.308 20.42 3.17 44.05 3.09
183 184 4.167554 AGAATATTCTTCGCGGAGCTAG 57.832 45.455 10.36 0.00 44.05 3.42
185 186 3.612955 GCTAGAATATTCTTCGCGGAGCT 60.613 47.826 22.60 2.00 45.26 4.09
189 190 1.387084 GCGCTAGAATATTCTTCGCGG 59.613 52.381 36.05 26.47 46.50 6.46
195 196 5.847304 TCATCAAGTGCGCTAGAATATTCT 58.153 37.500 21.28 21.28 41.24 2.40
245 251 0.791422 CATTTTGCATGTTGCCGTGG 59.209 50.000 0.00 0.00 44.23 4.94
246 252 0.164217 GCATTTTGCATGTTGCCGTG 59.836 50.000 0.00 0.00 44.23 4.94
247 253 2.531055 GCATTTTGCATGTTGCCGT 58.469 47.368 0.00 0.00 44.23 5.68
314 320 1.077212 GGCTGCCATGTGACTGGAT 60.077 57.895 15.17 0.00 38.69 3.41
315 321 2.352422 GGCTGCCATGTGACTGGA 59.648 61.111 15.17 0.00 38.69 3.86
341 353 1.754226 AGAAGCTTCCGATCTGTCCTC 59.246 52.381 22.81 0.00 0.00 3.71
407 419 4.617875 CCAACTACGGGGAGCTTG 57.382 61.111 0.00 0.00 0.00 4.01
435 447 2.048503 GTGGGGAACGTGGAGTCG 60.049 66.667 0.00 0.00 0.00 4.18
743 761 2.044650 TGCATCAAGGAGGCAGGC 60.045 61.111 0.97 0.00 44.36 4.85
789 807 0.958876 GAACGGGGGCAGTAGGTTTG 60.959 60.000 0.00 0.00 0.00 2.93
1531 1557 8.862325 TTGAGAAAAAGGAGCTTGATGTATTA 57.138 30.769 0.00 0.00 0.00 0.98
1535 1561 6.661304 AATTGAGAAAAAGGAGCTTGATGT 57.339 33.333 0.00 0.00 0.00 3.06
1552 1585 9.573133 AGTTCTGTAACAAGAAACAAAATTGAG 57.427 29.630 0.00 0.00 37.90 3.02
1561 1594 9.836076 ACAAGTAAAAGTTCTGTAACAAGAAAC 57.164 29.630 0.00 0.00 37.90 2.78
1672 1706 9.631452 AGAAGAAAGTTGTTTCAAGAAAGAAAG 57.369 29.630 6.69 0.00 44.08 2.62
1798 1834 8.417780 TGTTGTTGTTGATAAACCATTTGAAG 57.582 30.769 0.00 0.00 0.00 3.02
1837 1885 5.986135 AGAGTCGTATAGCTTAGCCATTTTG 59.014 40.000 0.00 0.00 0.00 2.44
1860 1908 3.997021 ACGGAAGCAGAATTGTGAGTAAG 59.003 43.478 6.80 0.00 0.00 2.34
1866 1914 2.933769 GGAAACGGAAGCAGAATTGTG 58.066 47.619 0.00 0.00 0.00 3.33
1886 1934 2.143925 GTCACAACTTTCCCTTCTCCG 58.856 52.381 0.00 0.00 0.00 4.63
1958 2006 6.293626 CCAATTTCTAAGCCATAGTTGATCCG 60.294 42.308 0.00 0.00 33.08 4.18
1970 2018 5.474876 CCATAGATCCACCAATTTCTAAGCC 59.525 44.000 0.00 0.00 0.00 4.35
2000 2048 3.438434 GGAATCCTTGTGAGAAGAACTGC 59.562 47.826 0.00 0.00 0.00 4.40
2019 2067 0.037512 CCCATTTTGCATGCACGGAA 60.038 50.000 22.58 15.77 0.00 4.30
2022 2070 2.101835 GGCCCATTTTGCATGCACG 61.102 57.895 22.58 9.23 0.00 5.34
2114 2162 5.961843 CACGCATTTGATCATTGTCTAGTTC 59.038 40.000 0.00 0.00 0.00 3.01
2158 2248 6.906678 GCCTTGTTGCTGAAAATTTTAACTTG 59.093 34.615 2.75 2.80 0.00 3.16
2168 2258 5.767665 TGATAGTTAGCCTTGTTGCTGAAAA 59.232 36.000 0.00 0.00 42.77 2.29
2169 2259 5.312895 TGATAGTTAGCCTTGTTGCTGAAA 58.687 37.500 0.00 0.00 42.77 2.69
2182 2272 8.331742 GCTGAAGTTAAACTGATGATAGTTAGC 58.668 37.037 0.00 0.00 39.86 3.09
2196 2286 6.037062 AGGCATTTTTGTTGCTGAAGTTAAAC 59.963 34.615 0.00 0.00 40.03 2.01
2245 2335 0.899720 ATTTGGCAAGGCTCCACATG 59.100 50.000 0.00 0.00 32.45 3.21
2281 2371 1.728971 CAGCCTTTGACTAGTTCGCAG 59.271 52.381 0.00 0.00 0.00 5.18
2299 2389 0.997196 GTTTTACGCTAGGACCGCAG 59.003 55.000 0.00 0.00 0.00 5.18
2329 2419 0.107831 TGTAGTTGCACCCTGTGGTC 59.892 55.000 0.00 0.00 45.57 4.02
2336 2426 1.883021 GCCATGTGTAGTTGCACCC 59.117 57.895 0.00 0.00 38.52 4.61
2356 2446 2.233922 CAGGGACTAAGACACAACCGAT 59.766 50.000 0.00 0.00 36.02 4.18


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

AutoCloner maintained by Alex Coulton.