Multiple sequence alignment - TraesCS2D01G431600

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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 TraesCS2D01G431600 chr2D 100.000 3148 0 0 1 3148 543848651 543845504 0.000000e+00 5814
1 TraesCS2D01G431600 chr2D 84.714 1243 126 38 939 2151 544171647 544170439 0.000000e+00 1184
2 TraesCS2D01G431600 chr2D 94.118 136 8 0 3 138 543848805 543848940 1.140000e-49 207
3 TraesCS2D01G431600 chr2D 94.161 137 7 1 3 139 619857806 619857941 1.140000e-49 207
4 TraesCS2D01G431600 chr2D 85.475 179 26 0 1755 1933 544260178 544260356 1.490000e-43 187
5 TraesCS2D01G431600 chr2D 85.393 178 26 0 1434 1611 544259872 544260049 5.360000e-43 185
6 TraesCS2D01G431600 chr2A 91.258 2734 119 50 446 3143 686705275 686702626 0.000000e+00 3615
7 TraesCS2D01G431600 chr2A 84.181 1258 120 43 902 2146 686778270 686777079 0.000000e+00 1147
8 TraesCS2D01G431600 chr2A 91.803 305 19 2 144 448 686705666 686705368 1.350000e-113 420
9 TraesCS2D01G431600 chr2A 78.935 413 36 32 288 672 686778866 686778477 1.890000e-57 233
10 TraesCS2D01G431600 chr2A 86.111 180 23 2 1755 1933 686797862 686798040 3.200000e-45 193
11 TraesCS2D01G431600 chr2A 85.955 178 25 0 1434 1611 686797549 686797726 1.150000e-44 191
12 TraesCS2D01G431600 chr2B 91.272 2452 127 35 146 2570 649481436 649479045 0.000000e+00 3262
13 TraesCS2D01G431600 chr2B 92.662 586 26 7 2570 3148 649478212 649477637 0.000000e+00 828
14 TraesCS2D01G431600 chr2B 85.955 178 25 0 1434 1611 649670188 649670365 1.150000e-44 191
15 TraesCS2D01G431600 chr6D 82.677 254 42 2 1746 1998 426984491 426984743 1.140000e-54 224
16 TraesCS2D01G431600 chr6D 95.556 135 6 0 3 137 62138328 62138194 1.900000e-52 217
17 TraesCS2D01G431600 chr6D 94.891 137 7 0 3 139 62145377 62145513 6.840000e-52 215
18 TraesCS2D01G431600 chr6B 82.283 254 43 2 1746 1998 642724705 642724957 5.290000e-53 219
19 TraesCS2D01G431600 chr4D 95.556 135 6 0 3 137 470199404 470199538 1.900000e-52 217
20 TraesCS2D01G431600 chr4D 93.478 138 9 0 3 140 470192338 470192201 4.120000e-49 206
21 TraesCS2D01G431600 chr5D 94.891 137 7 0 3 139 108146474 108146610 6.840000e-52 215
22 TraesCS2D01G431600 chr6A 81.890 254 44 2 1746 1998 571683601 571683853 2.460000e-51 213
23 TraesCS2D01G431600 chr3D 94.815 135 7 0 3 137 446920370 446920236 8.850000e-51 211
24 TraesCS2D01G431600 chr7D 93.525 139 9 0 3 141 528565516 528565654 1.140000e-49 207


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 TraesCS2D01G431600 chr2D 543845504 543848651 3147 True 5814.0 5814 100.0000 1 3148 1 chr2D.!!$R1 3147
1 TraesCS2D01G431600 chr2D 544170439 544171647 1208 True 1184.0 1184 84.7140 939 2151 1 chr2D.!!$R2 1212
2 TraesCS2D01G431600 chr2A 686702626 686705666 3040 True 2017.5 3615 91.5305 144 3143 2 chr2A.!!$R1 2999
3 TraesCS2D01G431600 chr2A 686777079 686778866 1787 True 690.0 1147 81.5580 288 2146 2 chr2A.!!$R2 1858
4 TraesCS2D01G431600 chr2B 649477637 649481436 3799 True 2045.0 3262 91.9670 146 3148 2 chr2B.!!$R1 3002

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
871 1009 0.038159 CACCACCTTCGTCTCCACTC 60.038 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2617 3721 0.179184 ACGTGCGGTGTTTTGTGTTC 60.179 50.0 0.0 0.0 0.0 3.18 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
22 23 4.728102 CGGCGGTAGGACGTGCAA 62.728 66.667 10.52 0.00 44.12 4.08
23 24 2.357760 GGCGGTAGGACGTGCAAA 60.358 61.111 10.52 0.00 35.98 3.68
24 25 2.674084 GGCGGTAGGACGTGCAAAC 61.674 63.158 10.52 6.94 35.98 2.93
25 26 2.674084 GCGGTAGGACGTGCAAACC 61.674 63.158 17.96 17.96 35.98 3.27
26 27 1.005394 CGGTAGGACGTGCAAACCT 60.005 57.895 22.85 12.68 37.76 3.50
27 28 0.244450 CGGTAGGACGTGCAAACCTA 59.756 55.000 22.85 11.77 35.52 3.08
29 30 1.718396 GTAGGACGTGCAAACCTACC 58.282 55.000 23.35 12.55 45.85 3.18
30 31 0.244450 TAGGACGTGCAAACCTACCG 59.756 55.000 10.52 0.58 35.52 4.02
31 32 2.674084 GGACGTGCAAACCTACCGC 61.674 63.158 0.63 0.00 0.00 5.68
32 33 2.667199 ACGTGCAAACCTACCGCC 60.667 61.111 0.00 0.00 0.00 6.13
33 34 2.666862 CGTGCAAACCTACCGCCA 60.667 61.111 0.00 0.00 0.00 5.69
34 35 2.677003 CGTGCAAACCTACCGCCAG 61.677 63.158 0.00 0.00 0.00 4.85
35 36 1.302192 GTGCAAACCTACCGCCAGA 60.302 57.895 0.00 0.00 0.00 3.86
36 37 1.302192 TGCAAACCTACCGCCAGAC 60.302 57.895 0.00 0.00 0.00 3.51
37 38 2.038837 GCAAACCTACCGCCAGACC 61.039 63.158 0.00 0.00 0.00 3.85
38 39 1.376812 CAAACCTACCGCCAGACCC 60.377 63.158 0.00 0.00 0.00 4.46
39 40 2.599757 AAACCTACCGCCAGACCCC 61.600 63.158 0.00 0.00 0.00 4.95
41 42 4.798682 CCTACCGCCAGACCCCCT 62.799 72.222 0.00 0.00 0.00 4.79
42 43 3.470888 CTACCGCCAGACCCCCTG 61.471 72.222 0.00 0.00 42.55 4.45
49 50 3.470888 CAGACCCCCTGGCGGTAG 61.471 72.222 2.29 0.00 39.23 3.18
50 51 4.798682 AGACCCCCTGGCGGTAGG 62.799 72.222 2.29 0.00 37.59 3.18
59 60 2.035155 GGCGGTAGGCAAAAGGGT 59.965 61.111 0.00 0.00 46.16 4.34
60 61 2.044555 GGCGGTAGGCAAAAGGGTC 61.045 63.158 0.00 0.00 46.16 4.46
61 62 1.302993 GCGGTAGGCAAAAGGGTCA 60.303 57.895 0.00 0.00 42.87 4.02
62 63 1.305930 GCGGTAGGCAAAAGGGTCAG 61.306 60.000 0.00 0.00 42.87 3.51
63 64 0.323629 CGGTAGGCAAAAGGGTCAGA 59.676 55.000 0.00 0.00 0.00 3.27
64 65 1.065418 CGGTAGGCAAAAGGGTCAGAT 60.065 52.381 0.00 0.00 0.00 2.90
65 66 2.618045 CGGTAGGCAAAAGGGTCAGATT 60.618 50.000 0.00 0.00 0.00 2.40
66 67 3.017442 GGTAGGCAAAAGGGTCAGATTC 58.983 50.000 0.00 0.00 0.00 2.52
67 68 2.222227 AGGCAAAAGGGTCAGATTCC 57.778 50.000 0.00 0.00 0.00 3.01
68 69 0.811281 GGCAAAAGGGTCAGATTCCG 59.189 55.000 0.00 0.00 0.00 4.30
69 70 1.613255 GGCAAAAGGGTCAGATTCCGA 60.613 52.381 0.00 0.00 0.00 4.55
70 71 2.159382 GCAAAAGGGTCAGATTCCGAA 58.841 47.619 0.00 0.00 0.00 4.30
71 72 2.556622 GCAAAAGGGTCAGATTCCGAAA 59.443 45.455 0.00 0.00 0.00 3.46
72 73 3.193479 GCAAAAGGGTCAGATTCCGAAAT 59.807 43.478 0.00 0.00 0.00 2.17
73 74 4.398044 GCAAAAGGGTCAGATTCCGAAATA 59.602 41.667 0.00 0.00 0.00 1.40
74 75 5.067805 GCAAAAGGGTCAGATTCCGAAATAT 59.932 40.000 0.00 0.00 0.00 1.28
75 76 6.405842 GCAAAAGGGTCAGATTCCGAAATATT 60.406 38.462 0.00 0.00 0.00 1.28
76 77 7.547227 CAAAAGGGTCAGATTCCGAAATATTT 58.453 34.615 0.00 0.00 0.00 1.40
77 78 7.718334 AAAGGGTCAGATTCCGAAATATTTT 57.282 32.000 1.43 0.00 0.00 1.82
78 79 6.944234 AGGGTCAGATTCCGAAATATTTTC 57.056 37.500 1.43 0.00 0.00 2.29
79 80 5.527582 AGGGTCAGATTCCGAAATATTTTCG 59.472 40.000 13.82 13.82 41.21 3.46
80 81 5.526111 GGGTCAGATTCCGAAATATTTTCGA 59.474 40.000 20.46 5.35 43.97 3.71
81 82 6.037830 GGGTCAGATTCCGAAATATTTTCGAA 59.962 38.462 20.46 13.74 43.97 3.71
82 83 6.905609 GGTCAGATTCCGAAATATTTTCGAAC 59.094 38.462 20.46 10.30 43.97 3.95
83 84 6.623743 GTCAGATTCCGAAATATTTTCGAACG 59.376 38.462 20.46 9.41 43.97 3.95
84 85 5.901884 CAGATTCCGAAATATTTTCGAACGG 59.098 40.000 20.46 15.56 43.97 4.44
85 86 4.603231 TTCCGAAATATTTTCGAACGGG 57.397 40.909 20.46 6.60 43.97 5.28
86 87 3.598299 TCCGAAATATTTTCGAACGGGT 58.402 40.909 20.46 0.00 43.97 5.28
87 88 4.753233 TCCGAAATATTTTCGAACGGGTA 58.247 39.130 20.46 4.69 43.97 3.69
88 89 5.358922 TCCGAAATATTTTCGAACGGGTAT 58.641 37.500 20.46 3.87 43.97 2.73
89 90 5.463061 TCCGAAATATTTTCGAACGGGTATC 59.537 40.000 20.46 4.68 43.97 2.24
90 91 5.234757 CCGAAATATTTTCGAACGGGTATCA 59.765 40.000 20.46 0.00 43.97 2.15
91 92 6.352526 CGAAATATTTTCGAACGGGTATCAG 58.647 40.000 15.28 0.00 43.97 2.90
92 93 6.199531 CGAAATATTTTCGAACGGGTATCAGA 59.800 38.462 15.28 0.00 43.97 3.27
93 94 7.095774 CGAAATATTTTCGAACGGGTATCAGAT 60.096 37.037 15.28 0.00 43.97 2.90
94 95 7.653767 AATATTTTCGAACGGGTATCAGATC 57.346 36.000 0.00 0.00 0.00 2.75
95 96 3.447918 TTTCGAACGGGTATCAGATCC 57.552 47.619 0.00 0.00 0.00 3.36
96 97 2.359981 TCGAACGGGTATCAGATCCT 57.640 50.000 0.00 0.00 0.00 3.24
97 98 1.954382 TCGAACGGGTATCAGATCCTG 59.046 52.381 6.29 6.29 36.29 3.86
98 99 1.954382 CGAACGGGTATCAGATCCTGA 59.046 52.381 12.34 0.00 44.99 3.86
109 110 3.673902 TCAGATCCTGATTTCGTTTGCA 58.326 40.909 0.00 0.00 35.39 4.08
110 111 4.264253 TCAGATCCTGATTTCGTTTGCAT 58.736 39.130 0.00 0.00 35.39 3.96
111 112 5.427378 TCAGATCCTGATTTCGTTTGCATA 58.573 37.500 0.00 0.00 35.39 3.14
112 113 5.879777 TCAGATCCTGATTTCGTTTGCATAA 59.120 36.000 0.00 0.00 35.39 1.90
113 114 6.374053 TCAGATCCTGATTTCGTTTGCATAAA 59.626 34.615 0.00 0.00 35.39 1.40
114 115 6.690098 CAGATCCTGATTTCGTTTGCATAAAG 59.310 38.462 0.00 0.00 32.44 1.85
115 116 5.309323 TCCTGATTTCGTTTGCATAAAGG 57.691 39.130 0.00 0.00 33.99 3.11
116 117 4.157656 TCCTGATTTCGTTTGCATAAAGGG 59.842 41.667 0.00 0.00 33.62 3.95
117 118 4.082245 CCTGATTTCGTTTGCATAAAGGGT 60.082 41.667 0.00 0.00 33.62 4.34
118 119 5.054390 TGATTTCGTTTGCATAAAGGGTC 57.946 39.130 0.00 0.00 33.62 4.46
119 120 4.520874 TGATTTCGTTTGCATAAAGGGTCA 59.479 37.500 0.00 0.00 33.62 4.02
120 121 4.920640 TTTCGTTTGCATAAAGGGTCAA 57.079 36.364 0.00 0.00 33.62 3.18
121 122 4.920640 TTCGTTTGCATAAAGGGTCAAA 57.079 36.364 0.00 0.00 33.62 2.69
122 123 4.920640 TCGTTTGCATAAAGGGTCAAAA 57.079 36.364 0.00 0.00 33.62 2.44
123 124 4.612943 TCGTTTGCATAAAGGGTCAAAAC 58.387 39.130 0.00 0.00 33.62 2.43
124 125 4.098044 TCGTTTGCATAAAGGGTCAAAACA 59.902 37.500 0.00 0.00 33.62 2.83
125 126 4.208253 CGTTTGCATAAAGGGTCAAAACAC 59.792 41.667 0.00 0.00 31.29 3.32
126 127 3.634568 TGCATAAAGGGTCAAAACACG 57.365 42.857 0.00 0.00 32.44 4.49
127 128 3.215151 TGCATAAAGGGTCAAAACACGA 58.785 40.909 0.00 0.00 32.44 4.35
128 129 3.632604 TGCATAAAGGGTCAAAACACGAA 59.367 39.130 0.00 0.00 32.44 3.85
129 130 4.098044 TGCATAAAGGGTCAAAACACGAAA 59.902 37.500 0.00 0.00 32.44 3.46
130 131 5.221342 TGCATAAAGGGTCAAAACACGAAAT 60.221 36.000 0.00 0.00 32.44 2.17
131 132 5.694458 GCATAAAGGGTCAAAACACGAAATT 59.306 36.000 0.00 0.00 32.44 1.82
132 133 6.201997 GCATAAAGGGTCAAAACACGAAATTT 59.798 34.615 0.00 0.00 32.44 1.82
133 134 7.254624 GCATAAAGGGTCAAAACACGAAATTTT 60.255 33.333 0.00 0.00 32.44 1.82
134 135 6.415798 AAAGGGTCAAAACACGAAATTTTG 57.584 33.333 3.73 3.73 44.74 2.44
135 136 3.868661 AGGGTCAAAACACGAAATTTTGC 59.131 39.130 5.27 11.02 43.62 3.68
136 137 3.001838 GGGTCAAAACACGAAATTTTGCC 59.998 43.478 5.27 16.17 43.62 4.52
137 138 3.868661 GGTCAAAACACGAAATTTTGCCT 59.131 39.130 5.27 0.00 43.62 4.75
138 139 4.026062 GGTCAAAACACGAAATTTTGCCTC 60.026 41.667 5.27 9.52 43.62 4.70
139 140 4.564769 GTCAAAACACGAAATTTTGCCTCA 59.435 37.500 5.27 1.15 43.62 3.86
140 141 5.062809 GTCAAAACACGAAATTTTGCCTCAA 59.937 36.000 5.27 0.89 43.62 3.02
141 142 5.062809 TCAAAACACGAAATTTTGCCTCAAC 59.937 36.000 5.27 0.00 43.62 3.18
142 143 2.726633 ACACGAAATTTTGCCTCAACG 58.273 42.857 5.27 0.00 0.00 4.10
179 180 4.705507 TCTCACTAAGCGAAGTGTCCTTAT 59.294 41.667 17.53 0.00 45.78 1.73
186 187 6.481954 AAGCGAAGTGTCCTTATTAAACTG 57.518 37.500 0.00 0.00 0.00 3.16
233 234 2.292292 GCAAGTTTCTACCGCCTCAAAA 59.708 45.455 0.00 0.00 0.00 2.44
241 242 1.159098 ACCGCCTCAAAACGCGTTTA 61.159 50.000 34.89 20.78 46.83 2.01
376 377 0.179073 CAAATCTGTCTCCCGCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
377 378 0.105039 AAATCTGTCTCCCGCCGATC 59.895 55.000 0.00 0.00 0.00 3.69
453 550 3.066342 TCACGGCTTAGCATGTAGAGTAC 59.934 47.826 6.53 0.00 0.00 2.73
512 609 2.881074 TGACAACTAGCGAATCTGAGC 58.119 47.619 0.00 0.00 0.00 4.26
541 661 1.068250 GGTGAGGATAGGTCAGCGC 59.932 63.158 0.00 0.00 33.10 5.92
613 733 3.113745 CTCCCATGCGTTGATGCC 58.886 61.111 0.00 0.00 0.00 4.40
749 876 2.354259 CTAGCAAGCTTGTCTTCCCAG 58.646 52.381 26.55 13.92 31.27 4.45
774 901 0.325671 CAGCAGGTTCTCCCTCCCTA 60.326 60.000 0.00 0.00 43.86 3.53
798 932 0.257039 AAGGCTGGCATTCGATTCCT 59.743 50.000 3.38 0.00 0.00 3.36
837 975 0.972471 CCCAGCAAATTCCTCCACCC 60.972 60.000 0.00 0.00 0.00 4.61
871 1009 0.038159 CACCACCTTCGTCTCCACTC 60.038 60.000 0.00 0.00 0.00 3.51
872 1010 1.186267 ACCACCTTCGTCTCCACTCC 61.186 60.000 0.00 0.00 0.00 3.85
873 1011 1.185618 CCACCTTCGTCTCCACTCCA 61.186 60.000 0.00 0.00 0.00 3.86
874 1012 0.244994 CACCTTCGTCTCCACTCCAG 59.755 60.000 0.00 0.00 0.00 3.86
875 1013 1.216710 CCTTCGTCTCCACTCCAGC 59.783 63.158 0.00 0.00 0.00 4.85
879 1020 1.103803 TCGTCTCCACTCCAGCATAC 58.896 55.000 0.00 0.00 0.00 2.39
891 1032 6.407412 CCACTCCAGCATACATATATACAGGG 60.407 46.154 0.00 0.00 0.00 4.45
908 1098 4.200283 GGCCGCTGACCTCTCTCG 62.200 72.222 0.00 0.00 0.00 4.04
926 1116 4.389576 CCGCGTTGGAAGCAGCAC 62.390 66.667 4.92 0.00 42.00 4.40
941 1131 1.226831 GCACGACAGAGGCTAGCTC 60.227 63.158 15.72 10.16 0.00 4.09
1079 1269 4.101448 CTTCCTCCTGGCCGTGGG 62.101 72.222 13.76 8.60 0.00 4.61
1312 1502 4.090354 CCGTCTACGTAAGATCTCGATCTC 59.910 50.000 10.50 0.00 41.45 2.75
1314 1504 6.085573 CGTCTACGTAAGATCTCGATCTCTA 58.914 44.000 10.50 3.26 39.70 2.43
1359 1566 1.165907 TAGCTTGCCAGTGTGTGTGC 61.166 55.000 0.00 0.00 0.00 4.57
1396 1603 6.513806 TGACTTTTGACATGGGTGAATATG 57.486 37.500 0.00 0.00 0.00 1.78
1522 1739 1.891919 CACCCTCCACACCAACGTG 60.892 63.158 0.00 0.00 46.11 4.49
1702 1938 5.873712 AGAGTATATATGTAGGTCGACCGTG 59.126 44.000 28.26 0.00 42.08 4.94
1713 1950 0.745486 TCGACCGTGCCGATCTTCTA 60.745 55.000 0.00 0.00 0.00 2.10
1718 1955 1.659098 CCGTGCCGATCTTCTAAACAC 59.341 52.381 0.00 0.00 0.00 3.32
1721 1958 3.000322 CGTGCCGATCTTCTAAACACATC 60.000 47.826 0.00 0.00 0.00 3.06
1740 1983 2.315386 GGCCGACGTGAACTGAACC 61.315 63.158 0.00 0.00 0.00 3.62
2224 2481 7.094805 CCGATTCATTGTTTGGGTTCGATATAT 60.095 37.037 0.00 0.00 0.00 0.86
2230 2487 7.780008 TTGTTTGGGTTCGATATATACAGTG 57.220 36.000 0.00 0.00 0.00 3.66
2239 2496 4.937620 TCGATATATACAGTGTCGTACCCC 59.062 45.833 0.00 0.00 34.24 4.95
2264 2521 9.708222 CCGATTATTTTTGTACATCTGAAGAAG 57.292 33.333 0.00 0.00 0.00 2.85
2311 2568 6.570692 CCTGATTCTTTCATTGGATTTCTGG 58.429 40.000 0.00 0.00 32.72 3.86
2349 2606 6.573664 TTCCTCCACTTGTATCAACATTTG 57.426 37.500 0.00 0.00 34.97 2.32
2361 2618 7.805700 TGTATCAACATTTGTATGACACACAG 58.194 34.615 0.00 0.00 36.69 3.66
2412 2671 0.532573 TCCAGGCTCAAGATGTCGAC 59.467 55.000 9.11 9.11 0.00 4.20
2426 2685 7.819415 TCAAGATGTCGACAAATGAGTTAATCT 59.181 33.333 24.13 13.39 0.00 2.40
2427 2686 8.446273 CAAGATGTCGACAAATGAGTTAATCTT 58.554 33.333 24.13 18.36 32.39 2.40
2428 2687 9.653287 AAGATGTCGACAAATGAGTTAATCTTA 57.347 29.630 24.13 0.00 30.91 2.10
2429 2688 9.653287 AGATGTCGACAAATGAGTTAATCTTAA 57.347 29.630 24.13 0.00 0.00 1.85
2492 2755 2.137177 TACAGCAGGGGCAGGTTTCC 62.137 60.000 0.00 0.00 44.61 3.13
2534 2797 3.884091 TGATCCGCTAGAGAAACTCCTAC 59.116 47.826 0.00 0.00 0.00 3.18
2535 2798 3.361281 TCCGCTAGAGAAACTCCTACA 57.639 47.619 0.00 0.00 0.00 2.74
2617 3721 0.867753 CAGGCTACGCTAGAAGCACG 60.868 60.000 12.45 0.66 42.58 5.34
2623 3727 0.031585 ACGCTAGAAGCACGAACACA 59.968 50.000 0.00 0.00 42.58 3.72
2632 3736 1.468340 GCACGAACACAAAACACCGC 61.468 55.000 0.00 0.00 0.00 5.68
2676 3782 0.791983 CGACACGTGTGCGGTAGTAG 60.792 60.000 28.82 1.89 43.45 2.57
2677 3783 0.239347 GACACGTGTGCGGTAGTAGT 59.761 55.000 28.82 0.00 43.45 2.73
2678 3784 1.464608 GACACGTGTGCGGTAGTAGTA 59.535 52.381 28.82 0.00 43.45 1.82
2706 3812 2.139917 CGGAACCAAACAATCAGACGA 58.860 47.619 0.00 0.00 0.00 4.20
2708 3814 2.225727 GGAACCAAACAATCAGACGACC 59.774 50.000 0.00 0.00 0.00 4.79
2714 3820 1.874019 CAATCAGACGACCGAGGCG 60.874 63.158 0.00 0.00 0.00 5.52
2715 3821 2.044555 AATCAGACGACCGAGGCGA 61.045 57.895 6.14 0.00 0.00 5.54
2716 3822 1.994507 AATCAGACGACCGAGGCGAG 61.995 60.000 6.14 0.00 0.00 5.03
2717 3823 4.838486 CAGACGACCGAGGCGAGC 62.838 72.222 6.14 0.00 0.00 5.03
2719 3825 4.838486 GACGACCGAGGCGAGCTG 62.838 72.222 6.14 0.00 0.00 4.24
2792 3898 3.430236 CGCAGTAGTCCATCACCATGTAA 60.430 47.826 0.00 0.00 0.00 2.41
2903 4009 2.903357 GGCGCTCCTTCCTGATCA 59.097 61.111 7.64 0.00 0.00 2.92
2904 4010 1.449353 GGCGCTCCTTCCTGATCAT 59.551 57.895 7.64 0.00 0.00 2.45
3035 4141 3.716195 CCGTCCCAGATGGTGGCA 61.716 66.667 0.00 0.00 46.45 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.487412 CACGTCCTACCGCCGTCC 62.487 72.222 0.00 0.00 31.46 4.79
5 6 4.728102 TTGCACGTCCTACCGCCG 62.728 66.667 0.00 0.00 0.00 6.46
6 7 2.357760 TTTGCACGTCCTACCGCC 60.358 61.111 0.00 0.00 0.00 6.13
7 8 2.674084 GGTTTGCACGTCCTACCGC 61.674 63.158 0.00 0.00 0.00 5.68
8 9 0.244450 TAGGTTTGCACGTCCTACCG 59.756 55.000 6.63 0.00 34.09 4.02
9 10 1.718396 GTAGGTTTGCACGTCCTACC 58.282 55.000 21.16 6.26 44.43 3.18
11 12 0.244450 CGGTAGGTTTGCACGTCCTA 59.756 55.000 6.63 6.63 33.34 2.94
12 13 1.005394 CGGTAGGTTTGCACGTCCT 60.005 57.895 8.30 8.30 35.60 3.85
13 14 2.674084 GCGGTAGGTTTGCACGTCC 61.674 63.158 0.00 0.00 0.00 4.79
14 15 2.674084 GGCGGTAGGTTTGCACGTC 61.674 63.158 0.00 0.00 0.00 4.34
15 16 2.667199 GGCGGTAGGTTTGCACGT 60.667 61.111 0.00 0.00 0.00 4.49
16 17 2.666862 TGGCGGTAGGTTTGCACG 60.667 61.111 0.00 0.00 0.00 5.34
17 18 1.302192 TCTGGCGGTAGGTTTGCAC 60.302 57.895 0.00 0.00 0.00 4.57
18 19 1.302192 GTCTGGCGGTAGGTTTGCA 60.302 57.895 0.00 0.00 0.00 4.08
19 20 2.038837 GGTCTGGCGGTAGGTTTGC 61.039 63.158 0.00 0.00 0.00 3.68
20 21 1.376812 GGGTCTGGCGGTAGGTTTG 60.377 63.158 0.00 0.00 0.00 2.93
21 22 2.599757 GGGGTCTGGCGGTAGGTTT 61.600 63.158 0.00 0.00 0.00 3.27
22 23 3.007323 GGGGTCTGGCGGTAGGTT 61.007 66.667 0.00 0.00 0.00 3.50
24 25 4.798682 AGGGGGTCTGGCGGTAGG 62.799 72.222 0.00 0.00 0.00 3.18
25 26 3.470888 CAGGGGGTCTGGCGGTAG 61.471 72.222 0.00 0.00 39.76 3.18
32 33 3.470888 CTACCGCCAGGGGGTCTG 61.471 72.222 31.13 20.48 45.92 3.51
33 34 4.798682 CCTACCGCCAGGGGGTCT 62.799 72.222 31.13 11.22 45.92 3.85
37 38 3.577334 TTTTGCCTACCGCCAGGGG 62.577 63.158 0.00 0.00 43.47 4.79
38 39 2.034999 TTTTGCCTACCGCCAGGG 59.965 61.111 3.06 0.00 43.47 4.45
39 40 2.046285 CCTTTTGCCTACCGCCAGG 61.046 63.158 0.00 0.00 45.13 4.45
40 41 2.046285 CCCTTTTGCCTACCGCCAG 61.046 63.158 0.00 0.00 36.24 4.85
41 42 2.034999 CCCTTTTGCCTACCGCCA 59.965 61.111 0.00 0.00 36.24 5.69
42 43 2.035155 ACCCTTTTGCCTACCGCC 59.965 61.111 0.00 0.00 36.24 6.13
43 44 1.302993 TGACCCTTTTGCCTACCGC 60.303 57.895 0.00 0.00 38.31 5.68
44 45 0.323629 TCTGACCCTTTTGCCTACCG 59.676 55.000 0.00 0.00 0.00 4.02
45 46 2.808906 ATCTGACCCTTTTGCCTACC 57.191 50.000 0.00 0.00 0.00 3.18
46 47 3.017442 GGAATCTGACCCTTTTGCCTAC 58.983 50.000 0.00 0.00 0.00 3.18
47 48 2.355716 CGGAATCTGACCCTTTTGCCTA 60.356 50.000 0.00 0.00 0.00 3.93
48 49 1.614317 CGGAATCTGACCCTTTTGCCT 60.614 52.381 0.00 0.00 0.00 4.75
49 50 0.811281 CGGAATCTGACCCTTTTGCC 59.189 55.000 0.00 0.00 0.00 4.52
50 51 1.821216 TCGGAATCTGACCCTTTTGC 58.179 50.000 0.00 0.00 0.00 3.68
51 52 6.699575 ATATTTCGGAATCTGACCCTTTTG 57.300 37.500 0.00 0.00 0.00 2.44
52 53 7.718334 AAATATTTCGGAATCTGACCCTTTT 57.282 32.000 0.00 0.00 0.00 2.27
53 54 7.415206 CGAAAATATTTCGGAATCTGACCCTTT 60.415 37.037 15.41 0.00 38.19 3.11
54 55 6.038271 CGAAAATATTTCGGAATCTGACCCTT 59.962 38.462 15.41 0.00 38.19 3.95
55 56 5.527582 CGAAAATATTTCGGAATCTGACCCT 59.472 40.000 15.41 0.00 38.19 4.34
56 57 5.526111 TCGAAAATATTTCGGAATCTGACCC 59.474 40.000 20.94 0.00 41.78 4.46
57 58 6.598753 TCGAAAATATTTCGGAATCTGACC 57.401 37.500 20.94 0.00 41.78 4.02
58 59 6.623743 CGTTCGAAAATATTTCGGAATCTGAC 59.376 38.462 20.94 10.14 41.78 3.51
59 60 6.237996 CCGTTCGAAAATATTTCGGAATCTGA 60.238 38.462 20.94 0.00 41.78 3.27
60 61 5.901884 CCGTTCGAAAATATTTCGGAATCTG 59.098 40.000 20.94 9.85 41.78 2.90
61 62 5.007332 CCCGTTCGAAAATATTTCGGAATCT 59.993 40.000 20.81 0.00 41.78 2.40
62 63 5.202640 CCCGTTCGAAAATATTTCGGAATC 58.797 41.667 20.81 6.75 41.78 2.52
63 64 4.637091 ACCCGTTCGAAAATATTTCGGAAT 59.363 37.500 20.81 9.99 41.78 3.01
64 65 4.002316 ACCCGTTCGAAAATATTTCGGAA 58.998 39.130 20.81 14.87 41.78 4.30
65 66 3.598299 ACCCGTTCGAAAATATTTCGGA 58.402 40.909 20.81 12.72 41.78 4.55
66 67 5.234757 TGATACCCGTTCGAAAATATTTCGG 59.765 40.000 20.94 15.00 41.78 4.30
67 68 6.199531 TCTGATACCCGTTCGAAAATATTTCG 59.800 38.462 16.71 16.71 42.74 3.46
68 69 7.473027 TCTGATACCCGTTCGAAAATATTTC 57.527 36.000 0.00 0.00 0.00 2.17
69 70 7.172703 GGATCTGATACCCGTTCGAAAATATTT 59.827 37.037 0.00 0.00 0.00 1.40
70 71 6.649557 GGATCTGATACCCGTTCGAAAATATT 59.350 38.462 0.00 0.00 0.00 1.28
71 72 6.014499 AGGATCTGATACCCGTTCGAAAATAT 60.014 38.462 0.00 0.00 0.00 1.28
72 73 5.303589 AGGATCTGATACCCGTTCGAAAATA 59.696 40.000 0.00 0.00 0.00 1.40
73 74 4.101119 AGGATCTGATACCCGTTCGAAAAT 59.899 41.667 0.00 0.00 0.00 1.82
74 75 3.449737 AGGATCTGATACCCGTTCGAAAA 59.550 43.478 0.00 0.00 0.00 2.29
75 76 3.028850 AGGATCTGATACCCGTTCGAAA 58.971 45.455 0.00 0.00 0.00 3.46
76 77 2.361119 CAGGATCTGATACCCGTTCGAA 59.639 50.000 0.00 0.00 32.44 3.71
77 78 1.954382 CAGGATCTGATACCCGTTCGA 59.046 52.381 0.00 0.00 32.44 3.71
78 79 1.954382 TCAGGATCTGATACCCGTTCG 59.046 52.381 0.00 0.00 35.39 3.95
88 89 3.673902 TGCAAACGAAATCAGGATCTGA 58.326 40.909 0.00 0.00 44.99 3.27
89 90 4.627611 ATGCAAACGAAATCAGGATCTG 57.372 40.909 0.00 0.00 0.00 2.90
90 91 6.183360 CCTTTATGCAAACGAAATCAGGATCT 60.183 38.462 0.00 0.00 0.00 2.75
91 92 5.973565 CCTTTATGCAAACGAAATCAGGATC 59.026 40.000 0.00 0.00 0.00 3.36
92 93 5.163519 CCCTTTATGCAAACGAAATCAGGAT 60.164 40.000 0.00 0.00 0.00 3.24
93 94 4.157656 CCCTTTATGCAAACGAAATCAGGA 59.842 41.667 0.00 0.00 0.00 3.86
94 95 4.082245 ACCCTTTATGCAAACGAAATCAGG 60.082 41.667 0.00 0.00 0.00 3.86
95 96 5.059404 ACCCTTTATGCAAACGAAATCAG 57.941 39.130 0.00 0.00 0.00 2.90
96 97 4.520874 TGACCCTTTATGCAAACGAAATCA 59.479 37.500 0.00 0.00 0.00 2.57
97 98 5.054390 TGACCCTTTATGCAAACGAAATC 57.946 39.130 0.00 0.00 0.00 2.17
98 99 5.461032 TTGACCCTTTATGCAAACGAAAT 57.539 34.783 0.00 0.00 0.00 2.17
99 100 4.920640 TTGACCCTTTATGCAAACGAAA 57.079 36.364 0.00 0.00 0.00 3.46
100 101 4.920640 TTTGACCCTTTATGCAAACGAA 57.079 36.364 0.00 0.00 0.00 3.85
101 102 4.098044 TGTTTTGACCCTTTATGCAAACGA 59.902 37.500 0.00 0.00 30.77 3.85
102 103 4.208253 GTGTTTTGACCCTTTATGCAAACG 59.792 41.667 0.00 0.00 30.77 3.60
103 104 4.208253 CGTGTTTTGACCCTTTATGCAAAC 59.792 41.667 0.00 0.00 30.77 2.93
104 105 4.098044 TCGTGTTTTGACCCTTTATGCAAA 59.902 37.500 0.00 0.00 0.00 3.68
105 106 3.632604 TCGTGTTTTGACCCTTTATGCAA 59.367 39.130 0.00 0.00 0.00 4.08
106 107 3.215151 TCGTGTTTTGACCCTTTATGCA 58.785 40.909 0.00 0.00 0.00 3.96
107 108 3.907894 TCGTGTTTTGACCCTTTATGC 57.092 42.857 0.00 0.00 0.00 3.14
108 109 7.707774 AAATTTCGTGTTTTGACCCTTTATG 57.292 32.000 0.00 0.00 0.00 1.90
109 110 7.254624 GCAAAATTTCGTGTTTTGACCCTTTAT 60.255 33.333 19.19 0.00 45.02 1.40
110 111 6.036191 GCAAAATTTCGTGTTTTGACCCTTTA 59.964 34.615 19.19 0.00 45.02 1.85
111 112 5.163804 GCAAAATTTCGTGTTTTGACCCTTT 60.164 36.000 19.19 0.00 45.02 3.11
112 113 4.331443 GCAAAATTTCGTGTTTTGACCCTT 59.669 37.500 19.19 0.00 45.02 3.95
113 114 3.868661 GCAAAATTTCGTGTTTTGACCCT 59.131 39.130 19.19 0.00 45.02 4.34
114 115 3.001838 GGCAAAATTTCGTGTTTTGACCC 59.998 43.478 19.19 11.78 44.81 4.46
115 116 4.190304 GGCAAAATTTCGTGTTTTGACC 57.810 40.909 19.19 16.15 44.81 4.02
117 118 4.748892 TGAGGCAAAATTTCGTGTTTTGA 58.251 34.783 19.19 3.75 45.02 2.69
118 119 5.254842 GTTGAGGCAAAATTTCGTGTTTTG 58.745 37.500 14.02 14.02 45.01 2.44
119 120 4.032331 CGTTGAGGCAAAATTTCGTGTTTT 59.968 37.500 0.00 0.00 0.00 2.43
120 121 3.549873 CGTTGAGGCAAAATTTCGTGTTT 59.450 39.130 0.00 0.00 0.00 2.83
121 122 3.112580 CGTTGAGGCAAAATTTCGTGTT 58.887 40.909 0.00 0.00 0.00 3.32
122 123 2.542824 CCGTTGAGGCAAAATTTCGTGT 60.543 45.455 0.00 0.00 0.00 4.49
123 124 2.050691 CCGTTGAGGCAAAATTTCGTG 58.949 47.619 0.00 0.00 0.00 4.35
124 125 1.679153 ACCGTTGAGGCAAAATTTCGT 59.321 42.857 0.00 0.00 46.52 3.85
125 126 2.415697 ACCGTTGAGGCAAAATTTCG 57.584 45.000 0.00 0.00 46.52 3.46
126 127 3.978855 GTGTACCGTTGAGGCAAAATTTC 59.021 43.478 0.00 0.00 46.52 2.17
127 128 3.634910 AGTGTACCGTTGAGGCAAAATTT 59.365 39.130 0.00 0.00 46.52 1.82
128 129 3.219281 AGTGTACCGTTGAGGCAAAATT 58.781 40.909 0.00 0.00 46.52 1.82
129 130 2.858745 AGTGTACCGTTGAGGCAAAAT 58.141 42.857 0.00 0.00 46.52 1.82
130 131 2.335316 AGTGTACCGTTGAGGCAAAA 57.665 45.000 0.00 0.00 46.52 2.44
131 132 2.366266 ACTAGTGTACCGTTGAGGCAAA 59.634 45.455 0.00 0.00 46.52 3.68
132 133 1.965643 ACTAGTGTACCGTTGAGGCAA 59.034 47.619 0.00 0.00 46.52 4.52
133 134 1.271379 CACTAGTGTACCGTTGAGGCA 59.729 52.381 15.06 0.00 46.52 4.75
134 135 1.992170 CACTAGTGTACCGTTGAGGC 58.008 55.000 15.06 0.00 46.52 4.70
136 137 3.057456 AGAAGCACTAGTGTACCGTTGAG 60.057 47.826 23.44 0.00 0.00 3.02
137 138 2.889045 AGAAGCACTAGTGTACCGTTGA 59.111 45.455 23.44 0.00 0.00 3.18
138 139 3.243336 GAGAAGCACTAGTGTACCGTTG 58.757 50.000 23.44 0.00 0.00 4.10
139 140 2.889045 TGAGAAGCACTAGTGTACCGTT 59.111 45.455 23.44 9.87 0.00 4.44
140 141 2.228343 GTGAGAAGCACTAGTGTACCGT 59.772 50.000 23.44 5.96 44.27 4.83
141 142 2.864968 GTGAGAAGCACTAGTGTACCG 58.135 52.381 23.44 0.00 44.27 4.02
179 180 2.695359 GGAGATCACACCGCAGTTTAA 58.305 47.619 0.00 0.00 0.00 1.52
233 234 2.075761 GCGACTTCCATAAACGCGT 58.924 52.632 5.58 5.58 39.90 6.01
283 284 4.252878 GCCAGGTTAATTTCCAATTGGTG 58.747 43.478 23.76 11.14 36.34 4.17
284 285 3.056179 CGCCAGGTTAATTTCCAATTGGT 60.056 43.478 23.76 7.46 36.34 3.67
321 322 0.813184 AGATGTTCAAGCAATGCCCG 59.187 50.000 0.00 0.00 0.00 6.13
376 377 0.538746 TACTGGTGTGTGGAGAGCGA 60.539 55.000 0.00 0.00 0.00 4.93
377 378 0.317160 TTACTGGTGTGTGGAGAGCG 59.683 55.000 0.00 0.00 0.00 5.03
453 550 4.002982 TGCTCATAGTTTAGTGTTGGCAG 58.997 43.478 0.00 0.00 0.00 4.85
541 661 3.932545 ACTGCTATCTTATCAGAGGCG 57.067 47.619 0.00 0.00 35.58 5.52
613 733 2.433604 TCTTTGCTAGATGGAGAGCTGG 59.566 50.000 0.00 0.00 39.54 4.85
749 876 1.376553 GGAGAACCTGCTGCTGGTC 60.377 63.158 28.02 20.72 34.63 4.02
774 901 3.064324 GAATGCCAGCCTTGCCGT 61.064 61.111 0.00 0.00 0.00 5.68
837 975 1.452108 GGTGAGGAAATGGGCGAGG 60.452 63.158 0.00 0.00 0.00 4.63
871 1009 4.444876 GGCCCCTGTATATATGTATGCTGG 60.445 50.000 13.67 13.67 39.82 4.85
872 1010 4.708177 GGCCCCTGTATATATGTATGCTG 58.292 47.826 0.00 0.00 0.00 4.41
873 1011 3.388024 CGGCCCCTGTATATATGTATGCT 59.612 47.826 0.00 0.00 0.00 3.79
874 1012 3.728845 CGGCCCCTGTATATATGTATGC 58.271 50.000 0.00 0.00 0.00 3.14
875 1013 3.388024 AGCGGCCCCTGTATATATGTATG 59.612 47.826 0.00 0.00 0.00 2.39
879 1020 1.831106 TCAGCGGCCCCTGTATATATG 59.169 52.381 16.95 0.00 34.47 1.78
891 1032 4.200283 CGAGAGAGGTCAGCGGCC 62.200 72.222 0.00 0.00 0.00 6.13
926 1116 2.025441 GCGAGCTAGCCTCTGTCG 59.975 66.667 12.13 14.76 38.49 4.35
983 1173 2.159310 GCCATGACTAGCTAGCTATCCG 60.159 54.545 24.36 15.36 0.00 4.18
1337 1544 0.239347 CACACACTGGCAAGCTAAGC 59.761 55.000 2.60 2.60 0.00 3.09
1339 1546 1.308047 CACACACACTGGCAAGCTAA 58.692 50.000 0.00 0.00 0.00 3.09
1344 1551 3.886694 GCGCACACACACTGGCAA 61.887 61.111 0.30 0.00 0.00 4.52
1359 1566 3.164011 GTCAACTCGACCGACGCG 61.164 66.667 3.53 3.53 42.26 6.01
1702 1938 2.540101 CCGATGTGTTTAGAAGATCGGC 59.460 50.000 8.75 0.00 46.44 5.54
1713 1950 2.029964 ACGTCGGCCGATGTGTTT 59.970 55.556 43.67 24.84 42.16 2.83
1718 1955 2.126071 AGTTCACGTCGGCCGATG 60.126 61.111 39.07 39.07 40.70 3.84
1721 1958 2.355363 TTCAGTTCACGTCGGCCG 60.355 61.111 22.12 22.12 44.03 6.13
1723 1960 1.300697 AGGTTCAGTTCACGTCGGC 60.301 57.895 0.00 0.00 0.00 5.54
1740 1983 1.153489 CCACCTCGATCCTGCACAG 60.153 63.158 0.00 0.00 0.00 3.66
1997 2240 1.448717 GGAGAGGTTGAAGAGCGGC 60.449 63.158 0.00 0.00 0.00 6.53
2239 2496 9.214953 GCTTCTTCAGATGTACAAAAATAATCG 57.785 33.333 0.00 0.00 0.00 3.34
2288 2545 7.166691 ACCAGAAATCCAATGAAAGAATCAG 57.833 36.000 0.00 0.00 42.53 2.90
2311 2568 2.045242 GAAAGGGGAGGCCGGAAC 60.045 66.667 5.05 0.00 0.00 3.62
2349 2606 5.869753 AAATTGCTCTCTGTGTGTCATAC 57.130 39.130 0.00 0.00 0.00 2.39
2381 2640 0.321122 AGCCTGGACGAAGAGCAAAG 60.321 55.000 0.00 0.00 0.00 2.77
2426 2685 8.303876 TGCATATACAGACGCTGAGATAATTAA 58.696 33.333 12.77 0.00 35.18 1.40
2427 2686 7.826690 TGCATATACAGACGCTGAGATAATTA 58.173 34.615 12.77 0.00 35.18 1.40
2428 2687 6.691508 TGCATATACAGACGCTGAGATAATT 58.308 36.000 12.77 0.00 35.18 1.40
2429 2688 6.272822 TGCATATACAGACGCTGAGATAAT 57.727 37.500 12.77 2.87 35.18 1.28
2504 2767 3.756117 TCTCTAGCGGATCATAGCAAGA 58.244 45.455 9.23 6.38 35.48 3.02
2617 3721 0.179184 ACGTGCGGTGTTTTGTGTTC 60.179 50.000 0.00 0.00 0.00 3.18
2623 3727 0.461339 AGACAGACGTGCGGTGTTTT 60.461 50.000 0.00 0.00 0.00 2.43
2632 3736 3.914966 GTGTTATCAGACAGACAGACGTG 59.085 47.826 0.00 0.00 0.00 4.49
2676 3782 0.674269 TTTGGTTCCGTCGGCCATAC 60.674 55.000 6.34 0.00 31.71 2.39
2677 3783 0.674269 GTTTGGTTCCGTCGGCCATA 60.674 55.000 6.34 1.55 31.71 2.74
2678 3784 1.969589 GTTTGGTTCCGTCGGCCAT 60.970 57.895 6.34 0.00 31.71 4.40
2719 3825 2.512515 GCGACATGGACCAGCTCC 60.513 66.667 0.00 0.00 39.97 4.70
3035 4141 2.117156 GCAGGCGATGAAGGTGCAT 61.117 57.895 0.00 0.00 34.18 3.96


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

AutoCloner maintained by Alex Coulton.