Multiple sequence alignment - TraesCS6A01G183100

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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 TraesCS6A01G183100 chr6A 100.000 2654 0 0 1 2654 212358618 212355965 0.000000e+00 4902.0
1 TraesCS6A01G183100 chr6A 86.621 583 76 2 189 771 468467549 468468129 0.000000e+00 643.0
2 TraesCS6A01G183100 chr6A 98.438 192 2 1 2 192 451696275 451696084 1.180000e-88 337.0
3 TraesCS6A01G183100 chr6A 87.295 244 13 10 1002 1245 212583247 212583022 2.030000e-66 263.0
4 TraesCS6A01G183100 chr6A 89.535 86 6 1 2431 2513 12959625 12959710 3.610000e-19 106.0
5 TraesCS6A01G183100 chr6D 91.889 1048 69 9 848 1884 156730610 156731652 0.000000e+00 1450.0
6 TraesCS6A01G183100 chr6D 93.750 176 11 0 2254 2429 11710025 11710200 5.630000e-67 265.0
7 TraesCS6A01G183100 chr6D 96.250 80 3 0 998 1077 156699093 156699172 5.960000e-27 132.0
8 TraesCS6A01G183100 chr6D 89.535 86 6 2 2431 2513 11710253 11710338 3.610000e-19 106.0
9 TraesCS6A01G183100 chr6B 92.385 801 42 6 998 1788 279198813 279199604 0.000000e+00 1123.0
10 TraesCS6A01G183100 chr6B 85.542 581 81 3 192 771 257588506 257587928 2.920000e-169 604.0
11 TraesCS6A01G183100 chr6B 90.842 404 12 2 2275 2654 539277483 539277885 3.920000e-143 518.0
12 TraesCS6A01G183100 chr6B 92.045 176 14 0 2254 2429 21318259 21318434 5.670000e-62 248.0
13 TraesCS6A01G183100 chr6B 85.268 224 31 2 549 771 695915707 695915929 2.050000e-56 230.0
14 TraesCS6A01G183100 chr6B 91.346 104 9 0 2059 2162 539277372 539277475 2.750000e-30 143.0
15 TraesCS6A01G183100 chr6B 87.037 108 11 1 2431 2535 21318487 21318594 4.640000e-23 119.0
16 TraesCS6A01G183100 chr6B 94.737 76 3 1 1810 1884 279287051 279287126 1.670000e-22 117.0
17 TraesCS6A01G183100 chr5A 91.349 786 37 3 1885 2654 625752010 625752780 0.000000e+00 1046.0
18 TraesCS6A01G183100 chr5A 97.028 471 14 0 2184 2654 605801443 605801913 0.000000e+00 793.0
19 TraesCS6A01G183100 chr5A 84.283 579 59 14 192 770 599598550 599598004 1.080000e-148 536.0
20 TraesCS6A01G183100 chr5A 98.936 188 2 0 1 188 669053028 669053215 1.180000e-88 337.0
21 TraesCS6A01G183100 chr5A 96.985 199 4 2 1 197 373389226 373389028 1.520000e-87 333.0
22 TraesCS6A01G183100 chr5A 92.727 110 8 0 2077 2186 605801235 605801344 2.730000e-35 159.0
23 TraesCS6A01G183100 chr7A 89.581 787 50 5 1883 2654 645410961 645410192 0.000000e+00 970.0
24 TraesCS6A01G183100 chr7A 91.304 46 4 0 1882 1927 610196645 610196600 2.210000e-06 63.9
25 TraesCS6A01G183100 chr7D 92.110 583 46 0 189 771 108408016 108408598 0.000000e+00 822.0
26 TraesCS6A01G183100 chr1D 91.065 582 52 0 189 770 236520992 236521573 0.000000e+00 787.0
27 TraesCS6A01G183100 chr1D 85.185 297 41 3 1878 2173 167635621 167635915 4.290000e-78 302.0
28 TraesCS6A01G183100 chrUn 89.495 495 15 12 2184 2654 129541006 129540525 2.280000e-165 592.0
29 TraesCS6A01G183100 chrUn 91.367 139 12 0 2051 2189 129541240 129541102 9.700000e-45 191.0
30 TraesCS6A01G183100 chr5B 80.645 589 104 8 189 771 335741285 335741869 5.210000e-122 448.0
31 TraesCS6A01G183100 chr5B 98.551 69 1 0 2184 2252 541917117 541917049 3.590000e-24 122.0
32 TraesCS6A01G183100 chr2A 80.204 490 89 3 283 771 621375863 621376345 6.980000e-96 361.0
33 TraesCS6A01G183100 chr2A 95.122 205 10 0 1 205 445354692 445354896 9.160000e-85 324.0
34 TraesCS6A01G183100 chr3A 98.446 193 2 1 1 192 234027043 234026851 3.270000e-89 339.0
35 TraesCS6A01G183100 chr3A 98.942 189 2 0 1 189 571429218 571429030 3.270000e-89 339.0
36 TraesCS6A01G183100 chr3A 98.936 188 2 0 1 188 498790121 498789934 1.180000e-88 337.0
37 TraesCS6A01G183100 chr3A 96.985 199 4 2 1 197 11980908 11981106 1.520000e-87 333.0
38 TraesCS6A01G183100 chr1A 97.927 193 3 1 1 192 311862265 311862073 1.520000e-87 333.0
39 TraesCS6A01G183100 chr2D 84.175 297 36 5 1885 2173 154172540 154172833 7.240000e-71 278.0
40 TraesCS6A01G183100 chr2B 74.221 578 132 15 191 761 254050681 254050114 2.660000e-55 226.0
41 TraesCS6A01G183100 chr1B 90.625 128 12 0 2059 2186 453199419 453199546 1.260000e-38 171.0
42 TraesCS6A01G183100 chr5D 76.817 289 30 18 1885 2173 510218897 510219148 7.710000e-26 128.0


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 TraesCS6A01G183100 chr6A 212355965 212358618 2653 True 4902.0 4902 100.0000 1 2654 1 chr6A.!!$R1 2653
1 TraesCS6A01G183100 chr6A 468467549 468468129 580 False 643.0 643 86.6210 189 771 1 chr6A.!!$F2 582
2 TraesCS6A01G183100 chr6D 156730610 156731652 1042 False 1450.0 1450 91.8890 848 1884 1 chr6D.!!$F2 1036
3 TraesCS6A01G183100 chr6B 279198813 279199604 791 False 1123.0 1123 92.3850 998 1788 1 chr6B.!!$F1 790
4 TraesCS6A01G183100 chr6B 257587928 257588506 578 True 604.0 604 85.5420 192 771 1 chr6B.!!$R1 579
5 TraesCS6A01G183100 chr6B 539277372 539277885 513 False 330.5 518 91.0940 2059 2654 2 chr6B.!!$F5 595
6 TraesCS6A01G183100 chr5A 625752010 625752780 770 False 1046.0 1046 91.3490 1885 2654 1 chr5A.!!$F1 769
7 TraesCS6A01G183100 chr5A 599598004 599598550 546 True 536.0 536 84.2830 192 770 1 chr5A.!!$R2 578
8 TraesCS6A01G183100 chr5A 605801235 605801913 678 False 476.0 793 94.8775 2077 2654 2 chr5A.!!$F3 577
9 TraesCS6A01G183100 chr7A 645410192 645410961 769 True 970.0 970 89.5810 1883 2654 1 chr7A.!!$R2 771
10 TraesCS6A01G183100 chr7D 108408016 108408598 582 False 822.0 822 92.1100 189 771 1 chr7D.!!$F1 582
11 TraesCS6A01G183100 chr1D 236520992 236521573 581 False 787.0 787 91.0650 189 770 1 chr1D.!!$F2 581
12 TraesCS6A01G183100 chrUn 129540525 129541240 715 True 391.5 592 90.4310 2051 2654 2 chrUn.!!$R1 603
13 TraesCS6A01G183100 chr5B 335741285 335741869 584 False 448.0 448 80.6450 189 771 1 chr5B.!!$F1 582
14 TraesCS6A01G183100 chr2B 254050114 254050681 567 True 226.0 226 74.2210 191 761 1 chr2B.!!$R1 570

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
117 118 0.026803 GCAATCCGATCACTCGTTGC 59.973 55.0 7.32 7.32 44.33 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1739 0.179255 CGTCGTAGCGATAGTAGCCG 60.179 60.0 0.0 0.0 38.42 5.52 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
17 18 2.913060 GGCGCTAGGATCTCCGGT 60.913 66.667 7.64 0.00 42.08 5.28
18 19 2.336809 GCGCTAGGATCTCCGGTG 59.663 66.667 0.00 0.00 42.08 4.94
19 20 2.194212 GCGCTAGGATCTCCGGTGA 61.194 63.158 8.96 8.96 42.08 4.02
20 21 1.528292 GCGCTAGGATCTCCGGTGAT 61.528 60.000 18.63 18.63 42.08 3.06
21 22 0.962489 CGCTAGGATCTCCGGTGATT 59.038 55.000 19.47 8.05 42.08 2.57
22 23 1.341531 CGCTAGGATCTCCGGTGATTT 59.658 52.381 19.47 13.39 42.08 2.17
23 24 2.760374 GCTAGGATCTCCGGTGATTTG 58.240 52.381 19.47 11.15 42.08 2.32
24 25 2.548920 GCTAGGATCTCCGGTGATTTGG 60.549 54.545 19.47 13.63 42.08 3.28
25 26 1.879575 AGGATCTCCGGTGATTTGGA 58.120 50.000 19.47 0.40 42.08 3.53
26 27 2.412591 AGGATCTCCGGTGATTTGGAT 58.587 47.619 19.47 0.00 42.08 3.41
27 28 2.370189 AGGATCTCCGGTGATTTGGATC 59.630 50.000 19.47 7.17 42.08 3.36
28 29 2.104792 GGATCTCCGGTGATTTGGATCA 59.895 50.000 19.47 0.00 39.92 2.92
38 39 3.766151 TGATTTGGATCACGTCGAGTAC 58.234 45.455 0.00 0.00 37.37 2.73
54 55 2.295885 AGTACGACTTACTCATCCCCG 58.704 52.381 0.00 0.00 36.09 5.73
55 56 2.019984 GTACGACTTACTCATCCCCGT 58.980 52.381 0.00 0.00 0.00 5.28
56 57 1.553706 ACGACTTACTCATCCCCGTT 58.446 50.000 0.00 0.00 0.00 4.44
57 58 1.475682 ACGACTTACTCATCCCCGTTC 59.524 52.381 0.00 0.00 0.00 3.95
58 59 1.749634 CGACTTACTCATCCCCGTTCT 59.250 52.381 0.00 0.00 0.00 3.01
59 60 2.165845 CGACTTACTCATCCCCGTTCTT 59.834 50.000 0.00 0.00 0.00 2.52
60 61 3.368116 CGACTTACTCATCCCCGTTCTTT 60.368 47.826 0.00 0.00 0.00 2.52
61 62 3.933332 GACTTACTCATCCCCGTTCTTTG 59.067 47.826 0.00 0.00 0.00 2.77
62 63 3.581332 ACTTACTCATCCCCGTTCTTTGA 59.419 43.478 0.00 0.00 0.00 2.69
63 64 4.041198 ACTTACTCATCCCCGTTCTTTGAA 59.959 41.667 0.00 0.00 0.00 2.69
64 65 2.779506 ACTCATCCCCGTTCTTTGAAC 58.220 47.619 0.77 0.77 0.00 3.18
65 66 1.732259 CTCATCCCCGTTCTTTGAACG 59.268 52.381 21.32 21.32 42.74 3.95
66 67 0.168128 CATCCCCGTTCTTTGAACGC 59.832 55.000 22.42 0.00 41.85 4.84
67 68 0.036306 ATCCCCGTTCTTTGAACGCT 59.964 50.000 22.42 7.97 41.85 5.07
68 69 0.179040 TCCCCGTTCTTTGAACGCTT 60.179 50.000 22.42 0.00 41.85 4.68
69 70 0.237498 CCCCGTTCTTTGAACGCTTC 59.763 55.000 22.42 0.00 41.85 3.86
70 71 0.237498 CCCGTTCTTTGAACGCTTCC 59.763 55.000 22.42 0.00 41.85 3.46
71 72 0.110823 CCGTTCTTTGAACGCTTCCG 60.111 55.000 22.42 8.82 41.85 4.30
72 73 0.721483 CGTTCTTTGAACGCTTCCGC 60.721 55.000 17.66 0.00 36.82 5.54
82 83 2.278596 GCTTCCGCGCGTGATCTA 60.279 61.111 29.95 9.69 0.00 1.98
83 84 2.577785 GCTTCCGCGCGTGATCTAC 61.578 63.158 29.95 7.34 0.00 2.59
84 85 1.226575 CTTCCGCGCGTGATCTACA 60.227 57.895 29.95 8.99 0.00 2.74
85 86 0.800683 CTTCCGCGCGTGATCTACAA 60.801 55.000 29.95 8.30 0.00 2.41
86 87 0.388778 TTCCGCGCGTGATCTACAAA 60.389 50.000 29.95 5.81 0.00 2.83
87 88 0.800683 TCCGCGCGTGATCTACAAAG 60.801 55.000 29.95 8.57 0.00 2.77
88 89 1.631072 CGCGCGTGATCTACAAAGG 59.369 57.895 24.19 0.00 0.00 3.11
89 90 1.076533 CGCGCGTGATCTACAAAGGT 61.077 55.000 24.19 0.00 0.00 3.50
90 91 1.796253 CGCGCGTGATCTACAAAGGTA 60.796 52.381 24.19 0.00 0.00 3.08
91 92 2.470821 GCGCGTGATCTACAAAGGTAT 58.529 47.619 8.43 0.00 0.00 2.73
92 93 2.218759 GCGCGTGATCTACAAAGGTATG 59.781 50.000 8.43 0.00 0.00 2.39
93 94 3.444916 CGCGTGATCTACAAAGGTATGT 58.555 45.455 0.00 0.00 37.32 2.29
94 95 4.603985 CGCGTGATCTACAAAGGTATGTA 58.396 43.478 0.00 0.00 34.75 2.29
105 106 5.989168 TACAAAGGTATGTAGATGCAATCCG 59.011 40.000 0.00 0.00 38.24 4.18
106 107 6.183360 TACAAAGGTATGTAGATGCAATCCGA 60.183 38.462 0.00 0.00 38.24 4.55
107 108 7.472804 TACAAAGGTATGTAGATGCAATCCGAT 60.473 37.037 0.00 0.00 38.24 4.18
114 115 1.858091 GATGCAATCCGATCACTCGT 58.142 50.000 0.00 0.00 43.49 4.18
115 116 2.205074 GATGCAATCCGATCACTCGTT 58.795 47.619 0.00 0.00 43.49 3.85
116 117 1.358877 TGCAATCCGATCACTCGTTG 58.641 50.000 0.00 0.00 43.49 4.10
117 118 0.026803 GCAATCCGATCACTCGTTGC 59.973 55.000 7.32 7.32 44.33 4.17
118 119 1.645034 CAATCCGATCACTCGTTGCT 58.355 50.000 0.00 0.00 43.49 3.91
119 120 2.809446 CAATCCGATCACTCGTTGCTA 58.191 47.619 0.00 0.00 43.49 3.49
120 121 2.783828 ATCCGATCACTCGTTGCTAG 57.216 50.000 0.00 0.00 43.49 3.42
121 122 1.746470 TCCGATCACTCGTTGCTAGA 58.254 50.000 0.00 0.00 43.49 2.43
122 123 2.298610 TCCGATCACTCGTTGCTAGAT 58.701 47.619 0.00 0.00 43.49 1.98
123 124 2.033424 TCCGATCACTCGTTGCTAGATG 59.967 50.000 0.00 0.00 43.49 2.90
124 125 2.033424 CCGATCACTCGTTGCTAGATGA 59.967 50.000 0.00 0.00 43.49 2.92
125 126 3.489229 CCGATCACTCGTTGCTAGATGAA 60.489 47.826 0.00 0.00 43.49 2.57
126 127 3.483922 CGATCACTCGTTGCTAGATGAAC 59.516 47.826 0.00 0.00 40.07 3.18
127 128 4.677584 GATCACTCGTTGCTAGATGAACT 58.322 43.478 0.00 0.00 0.00 3.01
128 129 4.098055 TCACTCGTTGCTAGATGAACTC 57.902 45.455 0.00 0.00 0.00 3.01
129 130 3.506067 TCACTCGTTGCTAGATGAACTCA 59.494 43.478 0.00 0.00 0.00 3.41
130 131 4.158579 TCACTCGTTGCTAGATGAACTCAT 59.841 41.667 0.00 0.00 39.70 2.90
131 132 5.357032 TCACTCGTTGCTAGATGAACTCATA 59.643 40.000 0.00 0.00 36.57 2.15
132 133 5.685068 CACTCGTTGCTAGATGAACTCATAG 59.315 44.000 0.00 0.00 36.57 2.23
133 134 5.590663 ACTCGTTGCTAGATGAACTCATAGA 59.409 40.000 0.00 0.00 36.57 1.98
134 135 6.264292 ACTCGTTGCTAGATGAACTCATAGAT 59.736 38.462 0.00 0.00 36.57 1.98
135 136 6.442112 TCGTTGCTAGATGAACTCATAGATG 58.558 40.000 0.00 0.00 36.57 2.90
136 137 5.632764 CGTTGCTAGATGAACTCATAGATGG 59.367 44.000 0.00 0.00 36.57 3.51
137 138 6.515696 CGTTGCTAGATGAACTCATAGATGGA 60.516 42.308 0.00 0.00 36.57 3.41
138 139 7.385267 GTTGCTAGATGAACTCATAGATGGAT 58.615 38.462 0.00 0.00 36.57 3.41
139 140 7.167924 TGCTAGATGAACTCATAGATGGATC 57.832 40.000 0.00 0.00 36.57 3.36
140 141 6.952938 TGCTAGATGAACTCATAGATGGATCT 59.047 38.462 0.00 0.00 40.86 2.75
141 142 7.454066 TGCTAGATGAACTCATAGATGGATCTT 59.546 37.037 0.00 0.00 38.32 2.40
142 143 7.760794 GCTAGATGAACTCATAGATGGATCTTG 59.239 40.741 0.00 0.00 38.32 3.02
143 144 7.006865 AGATGAACTCATAGATGGATCTTGG 57.993 40.000 0.00 0.00 38.32 3.61
144 145 6.558014 AGATGAACTCATAGATGGATCTTGGT 59.442 38.462 0.00 0.00 38.32 3.67
145 146 5.922053 TGAACTCATAGATGGATCTTGGTG 58.078 41.667 0.00 0.00 38.32 4.17
146 147 5.662657 TGAACTCATAGATGGATCTTGGTGA 59.337 40.000 0.00 0.00 38.32 4.02
147 148 6.156775 TGAACTCATAGATGGATCTTGGTGAA 59.843 38.462 0.00 0.00 38.32 3.18
148 149 6.566079 ACTCATAGATGGATCTTGGTGAAA 57.434 37.500 0.00 0.00 38.32 2.69
149 150 6.352516 ACTCATAGATGGATCTTGGTGAAAC 58.647 40.000 0.00 0.00 38.32 2.78
173 174 8.153479 ACCATAGGAAAATTTTTGTTTTCTGC 57.847 30.769 4.63 0.00 43.94 4.26
174 175 7.772757 ACCATAGGAAAATTTTTGTTTTCTGCA 59.227 29.630 4.63 0.00 43.94 4.41
175 176 8.619546 CCATAGGAAAATTTTTGTTTTCTGCAA 58.380 29.630 4.63 0.00 43.94 4.08
178 179 8.054152 AGGAAAATTTTTGTTTTCTGCAATGT 57.946 26.923 4.63 0.00 43.94 2.71
179 180 8.522003 AGGAAAATTTTTGTTTTCTGCAATGTT 58.478 25.926 4.63 0.00 43.94 2.71
180 181 8.797215 GGAAAATTTTTGTTTTCTGCAATGTTC 58.203 29.630 4.63 0.00 43.94 3.18
181 182 8.686397 AAAATTTTTGTTTTCTGCAATGTTCC 57.314 26.923 0.00 0.00 0.00 3.62
182 183 5.809719 TTTTTGTTTTCTGCAATGTTCCC 57.190 34.783 0.00 0.00 0.00 3.97
183 184 3.467374 TTGTTTTCTGCAATGTTCCCC 57.533 42.857 0.00 0.00 0.00 4.81
184 185 2.392662 TGTTTTCTGCAATGTTCCCCA 58.607 42.857 0.00 0.00 0.00 4.96
185 186 2.768527 TGTTTTCTGCAATGTTCCCCAA 59.231 40.909 0.00 0.00 0.00 4.12
186 187 3.130633 GTTTTCTGCAATGTTCCCCAAC 58.869 45.455 0.00 0.00 0.00 3.77
187 188 2.079170 TTCTGCAATGTTCCCCAACA 57.921 45.000 0.00 0.00 46.71 3.33
270 271 3.716195 CCTGTCCATGGTGGCCGA 61.716 66.667 12.58 0.00 37.47 5.54
275 276 2.271821 CCATGGTGGCCGATGTCA 59.728 61.111 2.57 0.00 0.00 3.58
339 340 2.286523 CCAGCTCCTTGTCGACCCT 61.287 63.158 14.12 0.00 0.00 4.34
437 438 0.179073 CGGATTGGAAGAGGTCGCAT 60.179 55.000 0.00 0.00 0.00 4.73
462 463 3.680786 CGAGGAGGACACACCGCA 61.681 66.667 0.00 0.00 44.74 5.69
494 495 4.748798 CAGCCCCTCCCCCAGAGT 62.749 72.222 0.00 0.00 41.47 3.24
549 550 3.338250 GGAGGGGCCATGTCCACA 61.338 66.667 4.39 0.00 36.34 4.17
652 659 1.072331 AGCGTGTTCTTCCATGACCTT 59.928 47.619 0.00 0.00 0.00 3.50
657 664 2.565391 TGTTCTTCCATGACCTTCGCTA 59.435 45.455 0.00 0.00 0.00 4.26
773 780 4.162690 GCCCCAGGTCCTGCGTAG 62.163 72.222 13.99 0.00 0.00 3.51
793 800 0.166814 CGCAAAGCACACTAGGAAGC 59.833 55.000 0.00 0.00 0.00 3.86
794 801 1.238439 GCAAAGCACACTAGGAAGCA 58.762 50.000 0.00 0.00 0.00 3.91
795 802 1.815003 GCAAAGCACACTAGGAAGCAT 59.185 47.619 0.00 0.00 0.00 3.79
796 803 2.159462 GCAAAGCACACTAGGAAGCATC 60.159 50.000 0.00 0.00 0.00 3.91
797 804 3.076621 CAAAGCACACTAGGAAGCATCA 58.923 45.455 0.00 0.00 0.00 3.07
798 805 3.423539 AAGCACACTAGGAAGCATCAA 57.576 42.857 0.00 0.00 0.00 2.57
799 806 2.983229 AGCACACTAGGAAGCATCAAG 58.017 47.619 0.00 0.00 0.00 3.02
800 807 2.304180 AGCACACTAGGAAGCATCAAGT 59.696 45.455 0.00 0.00 0.00 3.16
801 808 3.515502 AGCACACTAGGAAGCATCAAGTA 59.484 43.478 0.00 0.00 0.00 2.24
802 809 4.020218 AGCACACTAGGAAGCATCAAGTAA 60.020 41.667 0.00 0.00 0.00 2.24
803 810 4.695455 GCACACTAGGAAGCATCAAGTAAA 59.305 41.667 0.00 0.00 0.00 2.01
804 811 5.355350 GCACACTAGGAAGCATCAAGTAAAT 59.645 40.000 0.00 0.00 0.00 1.40
805 812 6.127897 GCACACTAGGAAGCATCAAGTAAATT 60.128 38.462 0.00 0.00 0.00 1.82
806 813 7.575720 GCACACTAGGAAGCATCAAGTAAATTT 60.576 37.037 0.00 0.00 0.00 1.82
807 814 7.965107 CACACTAGGAAGCATCAAGTAAATTTC 59.035 37.037 0.00 0.00 0.00 2.17
808 815 7.885399 ACACTAGGAAGCATCAAGTAAATTTCT 59.115 33.333 0.00 0.00 0.00 2.52
809 816 8.734386 CACTAGGAAGCATCAAGTAAATTTCTT 58.266 33.333 0.00 0.00 0.00 2.52
810 817 8.951243 ACTAGGAAGCATCAAGTAAATTTCTTC 58.049 33.333 0.00 0.00 0.00 2.87
811 818 6.846350 AGGAAGCATCAAGTAAATTTCTTCG 58.154 36.000 0.00 0.00 31.99 3.79
812 819 6.030228 GGAAGCATCAAGTAAATTTCTTCGG 58.970 40.000 0.00 0.00 31.99 4.30
813 820 5.567138 AGCATCAAGTAAATTTCTTCGGG 57.433 39.130 0.00 0.00 0.00 5.14
814 821 5.253330 AGCATCAAGTAAATTTCTTCGGGA 58.747 37.500 0.00 0.00 0.00 5.14
815 822 5.123979 AGCATCAAGTAAATTTCTTCGGGAC 59.876 40.000 0.00 0.00 0.00 4.46
828 835 2.266055 GGGACGAAGGCACTCCTG 59.734 66.667 0.00 0.00 43.40 3.86
829 836 2.283529 GGGACGAAGGCACTCCTGA 61.284 63.158 0.00 0.00 43.40 3.86
830 837 1.216710 GGACGAAGGCACTCCTGAG 59.783 63.158 0.00 0.00 43.40 3.35
831 838 1.536943 GGACGAAGGCACTCCTGAGT 61.537 60.000 0.00 0.00 43.40 3.41
832 839 0.109039 GACGAAGGCACTCCTGAGTC 60.109 60.000 0.00 0.00 43.40 3.36
833 840 1.216710 CGAAGGCACTCCTGAGTCC 59.783 63.158 0.00 2.75 43.40 3.85
834 841 1.599576 GAAGGCACTCCTGAGTCCC 59.400 63.158 0.00 0.00 43.40 4.46
835 842 2.232298 GAAGGCACTCCTGAGTCCCG 62.232 65.000 1.66 0.00 44.05 5.14
836 843 2.680352 GGCACTCCTGAGTCCCGA 60.680 66.667 0.00 0.00 40.20 5.14
837 844 2.574399 GCACTCCTGAGTCCCGAC 59.426 66.667 0.00 0.00 40.20 4.79
838 845 1.979693 GCACTCCTGAGTCCCGACT 60.980 63.158 0.00 0.00 45.84 4.18
865 872 1.467920 CAAAGGCAATCCTGAGTCCC 58.532 55.000 0.00 0.00 43.40 4.46
902 909 5.473931 ACCTGAGCGCTGTCAATATATTAG 58.526 41.667 18.48 0.00 0.00 1.73
905 912 4.021104 TGAGCGCTGTCAATATATTAGGCT 60.021 41.667 18.48 4.08 0.00 4.58
913 920 5.759763 TGTCAATATATTAGGCTGTGCACAG 59.240 40.000 37.09 37.09 46.40 3.66
927 934 1.134128 TGCACAGTCCACACTTCACAT 60.134 47.619 0.00 0.00 0.00 3.21
934 941 2.476619 GTCCACACTTCACATCTTCACG 59.523 50.000 0.00 0.00 0.00 4.35
977 984 2.969238 GCCAGTGGATCATCGCGG 60.969 66.667 15.20 0.00 0.00 6.46
1137 1144 5.449304 TCGACGTTCATGTATGCTACTATG 58.551 41.667 0.00 0.00 0.00 2.23
1208 1215 2.219080 TGGCATGCAGATTCCTCAAA 57.781 45.000 21.36 0.00 0.00 2.69
1360 1367 4.096081 ACCGTCCAGTAGTATTCTCTTTCG 59.904 45.833 0.00 0.00 0.00 3.46
1442 1449 2.172293 AGGTGATGATGCTCCTCCTTTC 59.828 50.000 0.00 0.00 0.00 2.62
1581 1588 2.980233 GCGTGGGCTTTCACTGCT 60.980 61.111 0.00 0.00 35.74 4.24
1744 1763 1.362768 ACTATCGCTACGACGTCACA 58.637 50.000 17.16 0.75 39.18 3.58
1828 1854 5.789643 ATGTGATGCTTAAGTTTGGTTGT 57.210 34.783 4.02 0.00 0.00 3.32
1861 1887 0.445043 GATAACGTTTGCCGGTGGTC 59.555 55.000 5.91 0.00 42.24 4.02
1908 1934 4.335647 CTCCAGCCGTTGTGCCCT 62.336 66.667 0.00 0.00 0.00 5.19
1909 1935 3.850098 CTCCAGCCGTTGTGCCCTT 62.850 63.158 0.00 0.00 0.00 3.95
1912 1938 2.192861 CAGCCGTTGTGCCCTTCAA 61.193 57.895 0.00 0.00 0.00 2.69
1915 1941 0.179097 GCCGTTGTGCCCTTCAAAAA 60.179 50.000 0.00 0.00 0.00 1.94
1939 1966 0.752376 TTTTTCGCCGTTTGAGGGGT 60.752 50.000 0.16 0.00 43.76 4.95
1961 1988 0.528470 CCGGCGGAAATTTTGGCTTA 59.472 50.000 24.41 0.00 0.00 3.09
1993 2020 4.954118 TCCAGCCGTGTCCACCCT 62.954 66.667 0.00 0.00 0.00 4.34
2021 2048 3.240134 AATGACACAGCGAGCCCGT 62.240 57.895 0.00 0.00 38.24 5.28
2078 2120 2.590575 CGTCCAAGCCACGGTTGT 60.591 61.111 3.21 0.00 39.09 3.32
2208 2351 3.805307 CTCGCGACGTCCAGCTCT 61.805 66.667 3.71 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.913060 ACCGGAGATCCTAGCGCC 60.913 66.667 9.46 0.00 0.00 6.53
1 2 1.528292 ATCACCGGAGATCCTAGCGC 61.528 60.000 9.46 0.00 0.00 5.92
2 3 0.962489 AATCACCGGAGATCCTAGCG 59.038 55.000 15.13 0.00 0.00 4.26
3 4 2.548920 CCAAATCACCGGAGATCCTAGC 60.549 54.545 15.13 0.00 0.00 3.42
4 5 2.965831 TCCAAATCACCGGAGATCCTAG 59.034 50.000 15.13 5.05 0.00 3.02
5 6 3.040655 TCCAAATCACCGGAGATCCTA 57.959 47.619 15.13 0.00 0.00 2.94
6 7 1.879575 TCCAAATCACCGGAGATCCT 58.120 50.000 15.13 2.86 0.00 3.24
7 8 2.104792 TGATCCAAATCACCGGAGATCC 59.895 50.000 15.13 2.03 36.98 3.36
8 9 3.475566 TGATCCAAATCACCGGAGATC 57.524 47.619 15.13 10.62 36.98 2.75
16 17 5.760783 CGTACTCGACGTGATCCAAATCAC 61.761 50.000 3.58 8.20 46.68 3.06
17 18 3.729762 CGTACTCGACGTGATCCAAATCA 60.730 47.826 3.58 0.00 46.86 2.57
18 19 2.782192 CGTACTCGACGTGATCCAAATC 59.218 50.000 3.58 0.00 46.86 2.17
19 20 2.793933 CGTACTCGACGTGATCCAAAT 58.206 47.619 3.58 0.00 46.86 2.32
20 21 2.251869 CGTACTCGACGTGATCCAAA 57.748 50.000 3.58 0.00 46.86 3.28
21 22 3.982213 CGTACTCGACGTGATCCAA 57.018 52.632 3.58 0.00 46.86 3.53
34 35 2.295885 CGGGGATGAGTAAGTCGTACT 58.704 52.381 0.00 0.00 46.23 2.73
35 36 2.019984 ACGGGGATGAGTAAGTCGTAC 58.980 52.381 0.00 0.00 0.00 3.67
36 37 2.425143 ACGGGGATGAGTAAGTCGTA 57.575 50.000 0.00 0.00 0.00 3.43
37 38 1.475682 GAACGGGGATGAGTAAGTCGT 59.524 52.381 0.00 0.00 0.00 4.34
38 39 1.749634 AGAACGGGGATGAGTAAGTCG 59.250 52.381 0.00 0.00 0.00 4.18
39 40 3.889520 AAGAACGGGGATGAGTAAGTC 57.110 47.619 0.00 0.00 0.00 3.01
40 41 3.581332 TCAAAGAACGGGGATGAGTAAGT 59.419 43.478 0.00 0.00 0.00 2.24
41 42 4.202245 TCAAAGAACGGGGATGAGTAAG 57.798 45.455 0.00 0.00 0.00 2.34
42 43 4.320870 GTTCAAAGAACGGGGATGAGTAA 58.679 43.478 0.00 0.00 0.00 2.24
43 44 3.615592 CGTTCAAAGAACGGGGATGAGTA 60.616 47.826 20.89 0.00 39.73 2.59
44 45 2.779506 GTTCAAAGAACGGGGATGAGT 58.220 47.619 0.00 0.00 0.00 3.41
45 46 1.732259 CGTTCAAAGAACGGGGATGAG 59.268 52.381 20.89 0.00 39.73 2.90
46 47 1.803334 CGTTCAAAGAACGGGGATGA 58.197 50.000 20.89 0.00 39.73 2.92
47 48 0.168128 GCGTTCAAAGAACGGGGATG 59.832 55.000 27.01 5.43 43.25 3.51
48 49 0.036306 AGCGTTCAAAGAACGGGGAT 59.964 50.000 27.01 2.09 43.25 3.85
49 50 0.179040 AAGCGTTCAAAGAACGGGGA 60.179 50.000 27.01 0.00 43.25 4.81
50 51 0.237498 GAAGCGTTCAAAGAACGGGG 59.763 55.000 27.01 6.65 43.25 5.73
51 52 0.237498 GGAAGCGTTCAAAGAACGGG 59.763 55.000 27.01 7.26 43.25 5.28
52 53 0.110823 CGGAAGCGTTCAAAGAACGG 60.111 55.000 27.01 13.38 43.25 4.44
53 54 3.345087 CGGAAGCGTTCAAAGAACG 57.655 52.632 23.41 23.41 45.56 3.95
66 67 0.800683 TTGTAGATCACGCGCGGAAG 60.801 55.000 35.22 22.76 0.00 3.46
67 68 0.388778 TTTGTAGATCACGCGCGGAA 60.389 50.000 35.22 21.85 0.00 4.30
68 69 0.800683 CTTTGTAGATCACGCGCGGA 60.801 55.000 35.22 26.95 0.00 5.54
69 70 1.631072 CTTTGTAGATCACGCGCGG 59.369 57.895 35.22 22.52 0.00 6.46
70 71 1.076533 ACCTTTGTAGATCACGCGCG 61.077 55.000 30.96 30.96 0.00 6.86
71 72 1.917273 TACCTTTGTAGATCACGCGC 58.083 50.000 5.73 0.00 0.00 6.86
72 73 3.444916 ACATACCTTTGTAGATCACGCG 58.555 45.455 3.53 3.53 0.00 6.01
80 81 6.146184 CGGATTGCATCTACATACCTTTGTAG 59.854 42.308 5.47 5.47 46.85 2.74
81 82 5.989168 CGGATTGCATCTACATACCTTTGTA 59.011 40.000 0.00 0.00 0.00 2.41
82 83 4.816385 CGGATTGCATCTACATACCTTTGT 59.184 41.667 0.00 0.00 0.00 2.83
83 84 5.056480 TCGGATTGCATCTACATACCTTTG 58.944 41.667 0.00 0.00 0.00 2.77
84 85 5.290493 TCGGATTGCATCTACATACCTTT 57.710 39.130 0.00 0.00 0.00 3.11
85 86 4.955811 TCGGATTGCATCTACATACCTT 57.044 40.909 0.00 0.00 0.00 3.50
86 87 4.528206 TGATCGGATTGCATCTACATACCT 59.472 41.667 0.00 0.00 0.00 3.08
87 88 4.627467 GTGATCGGATTGCATCTACATACC 59.373 45.833 0.00 0.00 0.00 2.73
88 89 5.473931 AGTGATCGGATTGCATCTACATAC 58.526 41.667 0.00 0.00 0.00 2.39
89 90 5.619981 CGAGTGATCGGATTGCATCTACATA 60.620 44.000 0.00 0.00 0.00 2.29
90 91 4.564041 GAGTGATCGGATTGCATCTACAT 58.436 43.478 0.00 0.00 0.00 2.29
91 92 3.550842 CGAGTGATCGGATTGCATCTACA 60.551 47.826 0.00 0.00 0.00 2.74
92 93 2.983136 CGAGTGATCGGATTGCATCTAC 59.017 50.000 0.00 0.00 0.00 2.59
93 94 2.623416 ACGAGTGATCGGATTGCATCTA 59.377 45.455 2.46 0.00 37.45 1.98
94 95 1.410517 ACGAGTGATCGGATTGCATCT 59.589 47.619 2.46 0.00 37.45 2.90
95 96 1.858091 ACGAGTGATCGGATTGCATC 58.142 50.000 2.46 0.00 37.45 3.91
96 97 1.935873 CAACGAGTGATCGGATTGCAT 59.064 47.619 2.46 0.00 37.45 3.96
97 98 1.358877 CAACGAGTGATCGGATTGCA 58.641 50.000 2.46 0.00 37.45 4.08
98 99 0.026803 GCAACGAGTGATCGGATTGC 59.973 55.000 9.27 9.27 37.72 3.56
99 100 1.645034 AGCAACGAGTGATCGGATTG 58.355 50.000 2.46 0.33 37.45 2.67
100 101 2.688446 TCTAGCAACGAGTGATCGGATT 59.312 45.455 2.46 0.00 37.45 3.01
101 102 2.298610 TCTAGCAACGAGTGATCGGAT 58.701 47.619 2.46 0.00 37.45 4.18
102 103 1.746470 TCTAGCAACGAGTGATCGGA 58.254 50.000 2.46 0.00 37.45 4.55
103 104 2.033424 TCATCTAGCAACGAGTGATCGG 59.967 50.000 2.46 0.00 37.45 4.18
104 105 3.340337 TCATCTAGCAACGAGTGATCG 57.660 47.619 0.00 0.00 39.31 3.69
105 106 4.677584 AGTTCATCTAGCAACGAGTGATC 58.322 43.478 0.00 0.00 0.00 2.92
106 107 4.158579 TGAGTTCATCTAGCAACGAGTGAT 59.841 41.667 0.00 0.00 0.00 3.06
107 108 3.506067 TGAGTTCATCTAGCAACGAGTGA 59.494 43.478 0.00 0.00 0.00 3.41
108 109 3.838120 TGAGTTCATCTAGCAACGAGTG 58.162 45.455 0.00 0.00 0.00 3.51
109 110 4.727507 ATGAGTTCATCTAGCAACGAGT 57.272 40.909 0.00 0.00 28.78 4.18
110 111 6.066054 TCTATGAGTTCATCTAGCAACGAG 57.934 41.667 0.00 0.00 37.76 4.18
111 112 6.442112 CATCTATGAGTTCATCTAGCAACGA 58.558 40.000 0.00 0.00 37.76 3.85
112 113 5.632764 CCATCTATGAGTTCATCTAGCAACG 59.367 44.000 0.00 0.00 37.76 4.10
113 114 6.753180 TCCATCTATGAGTTCATCTAGCAAC 58.247 40.000 0.00 0.00 37.76 4.17
114 115 6.983906 TCCATCTATGAGTTCATCTAGCAA 57.016 37.500 0.00 0.00 37.76 3.91
115 116 6.952938 AGATCCATCTATGAGTTCATCTAGCA 59.047 38.462 0.00 0.00 37.76 3.49
116 117 7.408756 AGATCCATCTATGAGTTCATCTAGC 57.591 40.000 0.00 0.00 37.76 3.42
117 118 8.252417 CCAAGATCCATCTATGAGTTCATCTAG 58.748 40.741 0.00 0.00 35.76 2.43
118 119 7.732140 ACCAAGATCCATCTATGAGTTCATCTA 59.268 37.037 0.00 0.00 35.76 1.98
119 120 6.558014 ACCAAGATCCATCTATGAGTTCATCT 59.442 38.462 0.00 0.00 35.76 2.90
120 121 6.649973 CACCAAGATCCATCTATGAGTTCATC 59.350 42.308 0.00 0.00 35.76 2.92
121 122 6.328410 TCACCAAGATCCATCTATGAGTTCAT 59.672 38.462 0.00 0.00 35.76 2.57
122 123 5.662657 TCACCAAGATCCATCTATGAGTTCA 59.337 40.000 0.00 0.00 35.76 3.18
123 124 6.166984 TCACCAAGATCCATCTATGAGTTC 57.833 41.667 0.00 0.00 35.76 3.01
124 125 6.566079 TTCACCAAGATCCATCTATGAGTT 57.434 37.500 0.00 0.00 35.76 3.01
125 126 6.352516 GTTTCACCAAGATCCATCTATGAGT 58.647 40.000 0.00 0.00 35.76 3.41
126 127 5.762218 GGTTTCACCAAGATCCATCTATGAG 59.238 44.000 0.00 0.00 38.42 2.90
127 128 5.684704 GGTTTCACCAAGATCCATCTATGA 58.315 41.667 0.00 0.00 38.42 2.15
142 143 8.445275 AACAAAAATTTTCCTATGGTTTCACC 57.555 30.769 3.41 0.00 39.22 4.02
147 148 8.620416 GCAGAAAACAAAAATTTTCCTATGGTT 58.380 29.630 3.41 0.85 45.72 3.67
148 149 7.772757 TGCAGAAAACAAAAATTTTCCTATGGT 59.227 29.630 3.41 0.00 45.72 3.55
149 150 8.152309 TGCAGAAAACAAAAATTTTCCTATGG 57.848 30.769 3.41 0.00 45.72 2.74
152 153 9.171877 ACATTGCAGAAAACAAAAATTTTCCTA 57.828 25.926 3.41 0.00 45.72 2.94
153 154 8.054152 ACATTGCAGAAAACAAAAATTTTCCT 57.946 26.923 3.41 0.00 45.72 3.36
154 155 8.686397 AACATTGCAGAAAACAAAAATTTTCC 57.314 26.923 3.41 0.00 45.72 3.13
155 156 8.797215 GGAACATTGCAGAAAACAAAAATTTTC 58.203 29.630 3.41 3.34 45.18 2.29
156 157 7.758980 GGGAACATTGCAGAAAACAAAAATTTT 59.241 29.630 0.00 0.00 34.46 1.82
157 158 7.257003 GGGAACATTGCAGAAAACAAAAATTT 58.743 30.769 0.00 0.00 0.00 1.82
158 159 6.183360 GGGGAACATTGCAGAAAACAAAAATT 60.183 34.615 0.00 0.00 0.00 1.82
159 160 5.299028 GGGGAACATTGCAGAAAACAAAAAT 59.701 36.000 0.00 0.00 0.00 1.82
160 161 4.637977 GGGGAACATTGCAGAAAACAAAAA 59.362 37.500 0.00 0.00 0.00 1.94
161 162 4.195416 GGGGAACATTGCAGAAAACAAAA 58.805 39.130 0.00 0.00 0.00 2.44
162 163 3.198635 TGGGGAACATTGCAGAAAACAAA 59.801 39.130 0.00 0.00 0.00 2.83
163 164 2.768527 TGGGGAACATTGCAGAAAACAA 59.231 40.909 0.00 0.00 0.00 2.83
164 165 2.392662 TGGGGAACATTGCAGAAAACA 58.607 42.857 0.00 0.00 0.00 2.83
165 166 3.130633 GTTGGGGAACATTGCAGAAAAC 58.869 45.455 0.00 0.00 0.00 2.43
166 167 2.768527 TGTTGGGGAACATTGCAGAAAA 59.231 40.909 0.00 0.00 0.00 2.29
167 168 2.364970 CTGTTGGGGAACATTGCAGAAA 59.635 45.455 0.00 0.00 31.47 2.52
168 169 1.962807 CTGTTGGGGAACATTGCAGAA 59.037 47.619 0.00 0.00 31.47 3.02
169 170 1.619654 CTGTTGGGGAACATTGCAGA 58.380 50.000 0.00 0.00 31.47 4.26
170 171 0.604578 CCTGTTGGGGAACATTGCAG 59.395 55.000 0.00 0.00 31.47 4.41
171 172 2.744062 CCTGTTGGGGAACATTGCA 58.256 52.632 0.00 0.00 31.47 4.08
182 183 2.556840 ATCGACATGGGCCCTGTTGG 62.557 60.000 27.85 21.20 37.09 3.77
183 184 1.077501 ATCGACATGGGCCCTGTTG 60.078 57.895 25.70 25.24 0.00 3.33
184 185 1.077501 CATCGACATGGGCCCTGTT 60.078 57.895 25.70 6.28 0.00 3.16
185 186 2.257409 GACATCGACATGGGCCCTGT 62.257 60.000 25.70 23.68 33.82 4.00
186 187 1.524621 GACATCGACATGGGCCCTG 60.525 63.158 25.70 20.51 33.82 4.45
187 188 2.911143 GACATCGACATGGGCCCT 59.089 61.111 25.70 1.15 33.82 5.19
270 271 1.376466 GCAGTGGACAGGGTGACAT 59.624 57.895 0.00 0.00 0.00 3.06
321 322 2.266055 GGGTCGACAAGGAGCTGG 59.734 66.667 18.91 0.00 34.90 4.85
410 411 1.448540 CTTCCAATCCGCTGCTCGT 60.449 57.895 0.00 0.00 36.19 4.18
421 422 1.091771 CGCATGCGACCTCTTCCAAT 61.092 55.000 35.82 0.00 42.83 3.16
462 463 2.906458 CTGGATCAAGCCGCTCCT 59.094 61.111 0.00 0.00 30.67 3.69
639 646 1.137086 GCTAGCGAAGGTCATGGAAGA 59.863 52.381 0.00 0.00 40.68 2.87
771 778 0.606096 TCCTAGTGTGCTTTGCGCTA 59.394 50.000 9.73 0.00 40.03 4.26
772 779 0.250295 TTCCTAGTGTGCTTTGCGCT 60.250 50.000 9.73 0.00 40.03 5.92
773 780 0.166814 CTTCCTAGTGTGCTTTGCGC 59.833 55.000 0.00 0.00 39.75 6.09
774 781 0.166814 GCTTCCTAGTGTGCTTTGCG 59.833 55.000 0.00 0.00 0.00 4.85
775 782 1.238439 TGCTTCCTAGTGTGCTTTGC 58.762 50.000 0.00 0.00 0.00 3.68
776 783 3.076621 TGATGCTTCCTAGTGTGCTTTG 58.923 45.455 0.00 0.00 0.00 2.77
777 784 3.423539 TGATGCTTCCTAGTGTGCTTT 57.576 42.857 0.00 0.00 0.00 3.51
778 785 3.244700 ACTTGATGCTTCCTAGTGTGCTT 60.245 43.478 0.00 0.00 0.00 3.91
779 786 2.304180 ACTTGATGCTTCCTAGTGTGCT 59.696 45.455 0.00 0.00 0.00 4.40
780 787 2.704572 ACTTGATGCTTCCTAGTGTGC 58.295 47.619 0.00 0.00 0.00 4.57
781 788 6.992063 ATTTACTTGATGCTTCCTAGTGTG 57.008 37.500 12.12 0.00 0.00 3.82
782 789 7.885399 AGAAATTTACTTGATGCTTCCTAGTGT 59.115 33.333 12.12 1.98 0.00 3.55
783 790 8.273780 AGAAATTTACTTGATGCTTCCTAGTG 57.726 34.615 12.12 0.00 0.00 2.74
784 791 8.870075 AAGAAATTTACTTGATGCTTCCTAGT 57.130 30.769 0.00 8.76 0.00 2.57
785 792 8.119226 CGAAGAAATTTACTTGATGCTTCCTAG 58.881 37.037 7.37 0.00 0.00 3.02
786 793 7.065803 CCGAAGAAATTTACTTGATGCTTCCTA 59.934 37.037 7.37 0.00 0.00 2.94
787 794 6.127897 CCGAAGAAATTTACTTGATGCTTCCT 60.128 38.462 7.37 0.00 0.00 3.36
788 795 6.030228 CCGAAGAAATTTACTTGATGCTTCC 58.970 40.000 7.37 0.00 0.00 3.46
789 796 6.030228 CCCGAAGAAATTTACTTGATGCTTC 58.970 40.000 7.37 0.00 0.00 3.86
790 797 5.710099 TCCCGAAGAAATTTACTTGATGCTT 59.290 36.000 7.37 0.00 0.00 3.91
791 798 5.123979 GTCCCGAAGAAATTTACTTGATGCT 59.876 40.000 7.37 0.00 0.00 3.79
792 799 5.332707 GTCCCGAAGAAATTTACTTGATGC 58.667 41.667 7.37 0.00 0.00 3.91
793 800 5.350365 TCGTCCCGAAGAAATTTACTTGATG 59.650 40.000 7.37 5.49 31.06 3.07
794 801 5.484715 TCGTCCCGAAGAAATTTACTTGAT 58.515 37.500 7.37 0.00 31.06 2.57
795 802 4.885413 TCGTCCCGAAGAAATTTACTTGA 58.115 39.130 7.37 0.00 31.06 3.02
796 803 5.600908 TTCGTCCCGAAGAAATTTACTTG 57.399 39.130 7.37 0.00 41.05 3.16
808 815 2.654877 GAGTGCCTTCGTCCCGAA 59.345 61.111 0.00 0.00 43.75 4.30
809 816 3.379445 GGAGTGCCTTCGTCCCGA 61.379 66.667 0.00 0.00 0.00 5.14
810 817 3.382832 AGGAGTGCCTTCGTCCCG 61.383 66.667 0.00 0.00 43.90 5.14
811 818 2.232298 CTCAGGAGTGCCTTCGTCCC 62.232 65.000 0.00 0.00 43.90 4.46
812 819 1.216710 CTCAGGAGTGCCTTCGTCC 59.783 63.158 0.00 0.00 43.90 4.79
813 820 0.109039 GACTCAGGAGTGCCTTCGTC 60.109 60.000 6.68 0.00 43.90 4.20
814 821 1.536943 GGACTCAGGAGTGCCTTCGT 61.537 60.000 6.68 0.00 43.90 3.85
815 822 1.216710 GGACTCAGGAGTGCCTTCG 59.783 63.158 6.68 0.00 43.90 3.79
821 828 4.425099 AGTCGGGACTCAGGAGTG 57.575 61.111 6.68 0.00 42.66 3.51
834 841 4.778143 CCTTTGGCCGGGGAGTCG 62.778 72.222 2.18 0.00 0.00 4.18
845 852 1.467920 GGACTCAGGATTGCCTTTGG 58.532 55.000 0.00 0.00 43.90 3.28
846 853 1.467920 GGGACTCAGGATTGCCTTTG 58.532 55.000 0.00 0.00 43.90 2.77
902 909 2.203195 TGTGGACTGTGCACAGCC 60.203 61.111 39.95 36.83 43.78 4.85
905 912 0.251634 TGAAGTGTGGACTGTGCACA 59.748 50.000 27.82 27.82 46.44 4.57
913 920 2.476619 CGTGAAGATGTGAAGTGTGGAC 59.523 50.000 0.00 0.00 0.00 4.02
927 934 2.427453 GAGTAAGATGGAGCCGTGAAGA 59.573 50.000 0.00 0.00 0.00 2.87
934 941 2.034053 CGTGAGAGAGTAAGATGGAGCC 59.966 54.545 0.00 0.00 0.00 4.70
1342 1349 5.000012 AGCACGAAAGAGAATACTACTGG 58.000 43.478 0.00 0.00 0.00 4.00
1399 1406 1.317431 AATCCATGCATGCACGCACT 61.317 50.000 25.37 3.10 46.56 4.40
1483 1490 1.664016 GCAACGCCTCATGTTGTTCTG 60.664 52.381 7.57 0.00 46.48 3.02
1581 1588 1.153647 CATAACGCAGGCGACCAGA 60.154 57.895 21.62 0.70 42.83 3.86
1650 1657 0.321653 AGAAGTTGACCGCCCATCAC 60.322 55.000 0.00 0.00 0.00 3.06
1701 1716 6.046290 AGCCGAACTAAACTATTTACCAGT 57.954 37.500 0.00 0.00 0.00 4.00
1702 1717 7.263496 AGTAGCCGAACTAAACTATTTACCAG 58.737 38.462 0.00 0.00 30.90 4.00
1703 1718 7.174107 AGTAGCCGAACTAAACTATTTACCA 57.826 36.000 0.00 0.00 30.90 3.25
1704 1719 9.404348 GATAGTAGCCGAACTAAACTATTTACC 57.596 37.037 0.00 0.00 32.56 2.85
1720 1739 0.179255 CGTCGTAGCGATAGTAGCCG 60.179 60.000 0.00 0.00 38.42 5.52
1744 1763 3.736213 CGTCTACACGTACGTACACATT 58.264 45.455 22.34 8.63 41.42 2.71
1788 1808 7.931407 GCATCACATACGGGGAATAATATATCA 59.069 37.037 0.00 0.00 0.00 2.15
1789 1809 8.150945 AGCATCACATACGGGGAATAATATATC 58.849 37.037 0.00 0.00 0.00 1.63
1803 1829 5.545658 ACCAAACTTAAGCATCACATACG 57.454 39.130 1.29 0.00 0.00 3.06
1808 1834 4.298332 CCACAACCAAACTTAAGCATCAC 58.702 43.478 1.29 0.00 0.00 3.06
1828 1854 4.002906 ACGTTATCTTCAAAGTGAGCCA 57.997 40.909 0.00 0.00 0.00 4.75
1869 1895 1.244816 GCCCTTACCAACAGACAACC 58.755 55.000 0.00 0.00 0.00 3.77
1939 1966 1.005630 CCAAAATTTCCGCCGGCAA 60.006 52.632 28.98 14.33 0.00 4.52
1961 1988 3.445096 CGGCTGGAAAGAAATTCATCCTT 59.555 43.478 15.59 0.00 39.98 3.36
1993 2020 1.003580 GCTGTGTCATTCCTCCCTTGA 59.996 52.381 0.00 0.00 0.00 3.02
2005 2032 4.662961 CACGGGCTCGCTGTGTCA 62.663 66.667 5.51 0.00 40.63 3.58
2521 2712 3.528370 CCCCTCGCCGATCGACTT 61.528 66.667 18.66 0.00 43.16 3.01


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

AutoCloner maintained by Alex Coulton.