Multiple sequence alignment - TraesCS5B01G306300

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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 TraesCS5B01G306300 chr5B 100.000 3255 0 0 1 3255 490053423 490050169 0.000000e+00 6011.0
1 TraesCS5B01G306300 chr5B 96.753 154 5 0 2930 3083 567240455 567240302 1.160000e-64 257.0
2 TraesCS5B01G306300 chr5B 97.241 145 4 0 2939 3083 567295819 567295963 2.510000e-61 246.0
3 TraesCS5B01G306300 chr5D 91.071 3080 205 30 226 3254 408483976 408480916 0.000000e+00 4100.0
4 TraesCS5B01G306300 chr5D 76.042 288 49 12 1622 1907 408482758 408482489 7.330000e-27 132.0
5 TraesCS5B01G306300 chr5D 87.143 70 6 3 2839 2906 499444123 499444055 3.480000e-10 76.8
6 TraesCS5B01G306300 chr5A 91.871 2940 179 27 232 3130 514408987 514406067 0.000000e+00 4050.0
7 TraesCS5B01G306300 chr5A 81.919 271 39 8 2368 2633 381686388 381686653 1.520000e-53 220.0
8 TraesCS5B01G306300 chr5A 76.351 148 26 7 2768 2906 534815206 534815059 1.620000e-08 71.3
9 TraesCS5B01G306300 chrUn 95.294 170 7 1 3086 3255 86517426 86517258 5.350000e-68 268.0
10 TraesCS5B01G306300 chrUn 95.294 170 7 1 3086 3255 206784944 206784776 5.350000e-68 268.0
11 TraesCS5B01G306300 chrUn 95.294 170 7 1 3086 3255 345388354 345388522 5.350000e-68 268.0
12 TraesCS5B01G306300 chrUn 78.070 114 16 7 2759 2864 50947608 50947496 2.710000e-06 63.9
13 TraesCS5B01G306300 chr7D 95.294 170 7 1 3086 3255 203486285 203486117 5.350000e-68 268.0
14 TraesCS5B01G306300 chr7D 95.294 170 7 1 3086 3255 381906262 381906094 5.350000e-68 268.0
15 TraesCS5B01G306300 chr7D 77.931 145 23 6 2768 2903 375310249 375310393 7.490000e-12 82.4
16 TraesCS5B01G306300 chr6D 95.294 170 7 1 3086 3255 124503820 124503652 5.350000e-68 268.0
17 TraesCS5B01G306300 chr4D 95.294 170 7 1 3086 3255 123321771 123321603 5.350000e-68 268.0
18 TraesCS5B01G306300 chr4D 77.391 115 23 3 2758 2870 213419840 213419727 7.540000e-07 65.8
19 TraesCS5B01G306300 chr3D 95.294 170 7 1 3086 3255 523769635 523769467 5.350000e-68 268.0
20 TraesCS5B01G306300 chr3D 81.685 273 43 4 2368 2634 527520274 527520545 1.520000e-53 220.0
21 TraesCS5B01G306300 chr2B 96.273 161 6 0 2923 3083 391174738 391174578 6.920000e-67 265.0
22 TraesCS5B01G306300 chr2B 81.784 269 42 5 2370 2633 668684533 668684267 5.470000e-53 219.0
23 TraesCS5B01G306300 chr1D 82.051 273 43 3 2368 2634 14667395 14667667 9.090000e-56 228.0
24 TraesCS5B01G306300 chr2A 91.875 160 13 0 2923 3082 25257640 25257799 1.180000e-54 224.0
25 TraesCS5B01G306300 chr2A 91.875 160 13 0 2923 3082 25324101 25324260 1.180000e-54 224.0
26 TraesCS5B01G306300 chr2A 81.618 272 44 4 2368 2634 703337215 703336945 1.520000e-53 220.0
27 TraesCS5B01G306300 chr2A 91.250 160 14 0 2923 3082 25306908 25307067 5.470000e-53 219.0
28 TraesCS5B01G306300 chr2A 95.420 131 6 0 2952 3082 25275698 25275828 3.290000e-50 209.0
29 TraesCS5B01G306300 chr6A 81.685 273 44 5 2367 2633 46549127 46548855 4.230000e-54 222.0
30 TraesCS5B01G306300 chr3B 81.919 271 42 5 2368 2632 507303277 507303546 4.230000e-54 222.0
31 TraesCS5B01G306300 chr3B 80.451 133 20 6 64 192 820092790 820092660 2.670000e-16 97.1
32 TraesCS5B01G306300 chr3B 78.082 146 23 7 2768 2906 640705488 640705345 2.080000e-12 84.2
33 TraesCS5B01G306300 chr7A 89.041 73 8 0 2834 2906 725702417 725702489 1.240000e-14 91.6
34 TraesCS5B01G306300 chr7B 77.519 129 18 10 2757 2877 749291929 749292054 2.100000e-07 67.6


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 TraesCS5B01G306300 chr5B 490050169 490053423 3254 True 6011 6011 100.0000 1 3255 1 chr5B.!!$R1 3254
1 TraesCS5B01G306300 chr5D 408480916 408483976 3060 True 2116 4100 83.5565 226 3254 2 chr5D.!!$R2 3028
2 TraesCS5B01G306300 chr5A 514406067 514408987 2920 True 4050 4050 91.8710 232 3130 1 chr5A.!!$R1 2898

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
120 121 0.033366 CGACATGTGTGGTCTGGTCA 59.967 55.0 1.15 0.0 33.11 4.02 F
679 700 0.038166 TAGCTCTTGGCCCCAACAAG 59.962 55.0 0.00 0.0 45.08 3.16 F
1042 1083 0.322975 GCCTGACAGCCTGAGAGAAA 59.677 55.0 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1704 0.178950 AGCTCTGAGACTGGTGACCA 60.179 55.000 9.28 3.40 0.00 4.02 R
1655 1708 1.079266 GGCAGCTCTGAGACTGGTG 60.079 63.158 21.93 9.39 34.38 4.17 R
2755 2820 0.670239 CCACCCTTGCCGAAAAATGC 60.670 55.000 0.00 0.00 0.00 3.56 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
57 58 9.667107 TTTAGGAAAGTCATAAGGTGAACATAG 57.333 33.333 0.00 0.00 38.90 2.23
58 59 7.496346 AGGAAAGTCATAAGGTGAACATAGA 57.504 36.000 0.00 0.00 38.90 1.98
59 60 7.918076 AGGAAAGTCATAAGGTGAACATAGAA 58.082 34.615 0.00 0.00 38.90 2.10
60 61 8.043710 AGGAAAGTCATAAGGTGAACATAGAAG 58.956 37.037 0.00 0.00 38.90 2.85
61 62 7.824779 GGAAAGTCATAAGGTGAACATAGAAGT 59.175 37.037 0.00 0.00 38.90 3.01
62 63 9.220767 GAAAGTCATAAGGTGAACATAGAAGTT 57.779 33.333 0.00 0.00 38.90 2.66
63 64 8.779354 AAGTCATAAGGTGAACATAGAAGTTC 57.221 34.615 0.00 0.00 46.22 3.01
75 76 8.718102 GAACATAGAAGTTCATAAGTTAGCCA 57.282 34.615 5.50 0.00 45.53 4.75
76 77 9.162764 GAACATAGAAGTTCATAAGTTAGCCAA 57.837 33.333 5.50 0.00 45.53 4.52
77 78 8.723942 ACATAGAAGTTCATAAGTTAGCCAAG 57.276 34.615 5.50 0.00 0.00 3.61
78 79 8.322091 ACATAGAAGTTCATAAGTTAGCCAAGT 58.678 33.333 5.50 0.00 0.00 3.16
79 80 9.167311 CATAGAAGTTCATAAGTTAGCCAAGTT 57.833 33.333 5.50 0.00 0.00 2.66
80 81 9.740710 ATAGAAGTTCATAAGTTAGCCAAGTTT 57.259 29.630 5.50 0.00 0.00 2.66
81 82 8.465273 AGAAGTTCATAAGTTAGCCAAGTTTT 57.535 30.769 5.50 0.00 0.00 2.43
82 83 8.568794 AGAAGTTCATAAGTTAGCCAAGTTTTC 58.431 33.333 5.50 0.00 0.00 2.29
83 84 7.215719 AGTTCATAAGTTAGCCAAGTTTTCC 57.784 36.000 0.00 0.00 0.00 3.13
84 85 7.004691 AGTTCATAAGTTAGCCAAGTTTTCCT 58.995 34.615 0.00 0.00 0.00 3.36
85 86 7.175119 AGTTCATAAGTTAGCCAAGTTTTCCTC 59.825 37.037 0.00 0.00 0.00 3.71
86 87 6.779860 TCATAAGTTAGCCAAGTTTTCCTCT 58.220 36.000 0.00 0.00 0.00 3.69
87 88 6.879458 TCATAAGTTAGCCAAGTTTTCCTCTC 59.121 38.462 0.00 0.00 0.00 3.20
88 89 3.665190 AGTTAGCCAAGTTTTCCTCTCG 58.335 45.455 0.00 0.00 0.00 4.04
89 90 3.071167 AGTTAGCCAAGTTTTCCTCTCGT 59.929 43.478 0.00 0.00 0.00 4.18
90 91 2.171341 AGCCAAGTTTTCCTCTCGTC 57.829 50.000 0.00 0.00 0.00 4.20
91 92 1.416401 AGCCAAGTTTTCCTCTCGTCA 59.584 47.619 0.00 0.00 0.00 4.35
92 93 1.801178 GCCAAGTTTTCCTCTCGTCAG 59.199 52.381 0.00 0.00 0.00 3.51
93 94 2.417719 CCAAGTTTTCCTCTCGTCAGG 58.582 52.381 0.00 0.00 34.40 3.86
94 95 2.037251 CCAAGTTTTCCTCTCGTCAGGA 59.963 50.000 1.44 1.44 41.16 3.86
95 96 3.060602 CAAGTTTTCCTCTCGTCAGGAC 58.939 50.000 4.79 0.00 42.69 3.85
96 97 1.619332 AGTTTTCCTCTCGTCAGGACC 59.381 52.381 4.79 0.00 42.69 4.46
97 98 0.601558 TTTTCCTCTCGTCAGGACCG 59.398 55.000 4.79 0.00 42.69 4.79
98 99 1.248785 TTTCCTCTCGTCAGGACCGG 61.249 60.000 0.00 0.00 42.69 5.28
99 100 3.141488 CCTCTCGTCAGGACCGGG 61.141 72.222 6.32 0.00 35.20 5.73
100 101 2.045242 CTCTCGTCAGGACCGGGA 60.045 66.667 6.32 0.00 33.03 5.14
101 102 2.360852 TCTCGTCAGGACCGGGAC 60.361 66.667 6.32 1.89 27.94 4.46
117 118 2.827604 GACGACATGTGTGGTCTGG 58.172 57.895 17.52 0.00 46.06 3.86
118 119 0.033504 GACGACATGTGTGGTCTGGT 59.966 55.000 17.52 0.00 46.06 4.00
119 120 0.033504 ACGACATGTGTGGTCTGGTC 59.966 55.000 1.15 0.00 31.17 4.02
120 121 0.033366 CGACATGTGTGGTCTGGTCA 59.967 55.000 1.15 0.00 33.11 4.02
121 122 1.540146 CGACATGTGTGGTCTGGTCAA 60.540 52.381 1.15 0.00 33.11 3.18
122 123 2.783135 GACATGTGTGGTCTGGTCAAT 58.217 47.619 1.15 0.00 32.54 2.57
123 124 2.744202 GACATGTGTGGTCTGGTCAATC 59.256 50.000 1.15 0.00 32.54 2.67
124 125 2.086869 CATGTGTGGTCTGGTCAATCC 58.913 52.381 0.00 0.00 0.00 3.01
125 126 0.400213 TGTGTGGTCTGGTCAATCCC 59.600 55.000 0.00 0.00 34.77 3.85
126 127 0.400213 GTGTGGTCTGGTCAATCCCA 59.600 55.000 0.00 0.00 34.77 4.37
127 128 1.004745 GTGTGGTCTGGTCAATCCCAT 59.995 52.381 0.00 0.00 33.00 4.00
128 129 1.004628 TGTGGTCTGGTCAATCCCATG 59.995 52.381 0.00 0.00 33.00 3.66
129 130 1.281867 GTGGTCTGGTCAATCCCATGA 59.718 52.381 0.00 0.00 33.00 3.07
130 131 2.092212 GTGGTCTGGTCAATCCCATGAT 60.092 50.000 0.00 0.00 33.00 2.45
131 132 2.173356 TGGTCTGGTCAATCCCATGATC 59.827 50.000 0.00 0.00 33.00 2.92
132 133 2.487986 GGTCTGGTCAATCCCATGATCC 60.488 54.545 0.00 0.00 33.00 3.36
133 134 2.173356 GTCTGGTCAATCCCATGATCCA 59.827 50.000 0.00 0.00 33.00 3.41
134 135 2.851821 TCTGGTCAATCCCATGATCCAA 59.148 45.455 0.00 0.00 33.30 3.53
135 136 2.954318 CTGGTCAATCCCATGATCCAAC 59.046 50.000 0.00 0.00 33.30 3.77
136 137 2.582172 TGGTCAATCCCATGATCCAACT 59.418 45.455 0.00 0.00 31.80 3.16
137 138 3.011595 TGGTCAATCCCATGATCCAACTT 59.988 43.478 0.00 0.00 31.80 2.66
138 139 3.382546 GGTCAATCCCATGATCCAACTTG 59.617 47.826 0.00 0.00 0.00 3.16
139 140 4.019174 GTCAATCCCATGATCCAACTTGT 58.981 43.478 0.00 0.00 0.00 3.16
140 141 5.192927 GTCAATCCCATGATCCAACTTGTA 58.807 41.667 0.00 0.00 0.00 2.41
141 142 5.829924 GTCAATCCCATGATCCAACTTGTAT 59.170 40.000 0.00 0.00 0.00 2.29
142 143 6.016777 GTCAATCCCATGATCCAACTTGTATC 60.017 42.308 0.00 0.00 0.00 2.24
143 144 5.919348 ATCCCATGATCCAACTTGTATCT 57.081 39.130 0.00 0.00 0.00 1.98
144 145 5.296151 TCCCATGATCCAACTTGTATCTC 57.704 43.478 0.00 0.00 0.00 2.75
145 146 4.721274 TCCCATGATCCAACTTGTATCTCA 59.279 41.667 0.00 0.00 0.00 3.27
146 147 4.818546 CCCATGATCCAACTTGTATCTCAC 59.181 45.833 0.00 0.00 0.00 3.51
147 148 5.430886 CCATGATCCAACTTGTATCTCACA 58.569 41.667 0.00 0.00 34.51 3.58
148 149 5.526479 CCATGATCCAACTTGTATCTCACAG 59.474 44.000 0.00 0.00 38.72 3.66
149 150 4.507710 TGATCCAACTTGTATCTCACAGC 58.492 43.478 0.00 0.00 38.72 4.40
150 151 4.223700 TGATCCAACTTGTATCTCACAGCT 59.776 41.667 0.00 0.00 38.72 4.24
151 152 4.623932 TCCAACTTGTATCTCACAGCTT 57.376 40.909 0.00 0.00 38.72 3.74
152 153 4.318332 TCCAACTTGTATCTCACAGCTTG 58.682 43.478 0.00 0.00 38.72 4.01
153 154 4.067896 CCAACTTGTATCTCACAGCTTGT 58.932 43.478 0.00 0.00 38.72 3.16
165 166 4.044336 CACAGCTTGTGGTTTTTGATGA 57.956 40.909 8.03 0.00 44.27 2.92
166 167 4.431809 CACAGCTTGTGGTTTTTGATGAA 58.568 39.130 8.03 0.00 44.27 2.57
167 168 5.051816 CACAGCTTGTGGTTTTTGATGAAT 58.948 37.500 8.03 0.00 44.27 2.57
168 169 6.215121 CACAGCTTGTGGTTTTTGATGAATA 58.785 36.000 8.03 0.00 44.27 1.75
169 170 6.700960 CACAGCTTGTGGTTTTTGATGAATAA 59.299 34.615 8.03 0.00 44.27 1.40
170 171 7.224362 CACAGCTTGTGGTTTTTGATGAATAAA 59.776 33.333 8.03 0.00 44.27 1.40
171 172 7.768120 ACAGCTTGTGGTTTTTGATGAATAAAA 59.232 29.630 0.00 0.00 0.00 1.52
172 173 8.063630 CAGCTTGTGGTTTTTGATGAATAAAAC 58.936 33.333 0.00 0.00 41.31 2.43
173 174 7.986889 AGCTTGTGGTTTTTGATGAATAAAACT 59.013 29.630 0.00 0.00 41.60 2.66
174 175 8.611757 GCTTGTGGTTTTTGATGAATAAAACTT 58.388 29.630 0.00 0.00 41.60 2.66
175 176 9.919348 CTTGTGGTTTTTGATGAATAAAACTTG 57.081 29.630 0.00 0.00 41.60 3.16
176 177 9.658799 TTGTGGTTTTTGATGAATAAAACTTGA 57.341 25.926 0.00 0.00 41.60 3.02
177 178 9.829507 TGTGGTTTTTGATGAATAAAACTTGAT 57.170 25.926 0.00 0.00 41.60 2.57
183 184 9.500785 TTTTGATGAATAAAACTTGATTTCCCC 57.499 29.630 0.00 0.00 0.00 4.81
184 185 8.434589 TTGATGAATAAAACTTGATTTCCCCT 57.565 30.769 0.00 0.00 0.00 4.79
185 186 8.434589 TGATGAATAAAACTTGATTTCCCCTT 57.565 30.769 0.00 0.00 0.00 3.95
186 187 9.540538 TGATGAATAAAACTTGATTTCCCCTTA 57.459 29.630 0.00 0.00 0.00 2.69
209 210 4.637483 AAAATGTAGAATGGCATGACCG 57.363 40.909 0.00 0.00 43.94 4.79
210 211 3.281727 AATGTAGAATGGCATGACCGT 57.718 42.857 0.00 0.00 43.94 4.83
211 212 2.022764 TGTAGAATGGCATGACCGTG 57.977 50.000 0.00 0.00 43.94 4.94
212 213 1.277842 TGTAGAATGGCATGACCGTGT 59.722 47.619 0.00 0.00 43.94 4.49
213 214 2.290008 TGTAGAATGGCATGACCGTGTT 60.290 45.455 0.00 0.00 43.94 3.32
214 215 1.909700 AGAATGGCATGACCGTGTTT 58.090 45.000 0.00 0.00 43.94 2.83
215 216 2.238521 AGAATGGCATGACCGTGTTTT 58.761 42.857 0.00 0.00 43.94 2.43
216 217 2.627699 AGAATGGCATGACCGTGTTTTT 59.372 40.909 0.00 0.00 43.94 1.94
283 284 5.795939 CCGCTAGTAATAAGTATCTTGAGCG 59.204 44.000 0.00 0.00 46.30 5.03
298 299 2.036764 GAGCGGACCGTGCTAATTGC 62.037 60.000 16.73 0.00 44.18 3.56
309 310 2.124901 TAATTGCGCCCGGACCTG 60.125 61.111 0.73 0.00 0.00 4.00
444 445 0.393673 GGGCCTCTTCTTCTTGGCTC 60.394 60.000 0.84 0.00 44.36 4.70
464 465 1.852067 CTTCTCCCCGGCAAAACACG 61.852 60.000 0.00 0.00 0.00 4.49
496 509 2.865343 ACCGCTGGATAAGTAACGAG 57.135 50.000 1.50 0.00 0.00 4.18
509 522 4.650754 AGTAACGAGCGGTGAAATAGAT 57.349 40.909 0.00 0.00 0.00 1.98
534 547 2.420628 AACGAACATGCATGGTTGTG 57.579 45.000 33.27 21.25 41.15 3.33
540 553 2.580962 ACATGCATGGTTGTGTGTGTA 58.419 42.857 29.41 0.00 0.00 2.90
609 630 9.424319 CAGTATAATAAGTGTATGGTTAGGCTG 57.576 37.037 0.00 0.00 0.00 4.85
679 700 0.038166 TAGCTCTTGGCCCCAACAAG 59.962 55.000 0.00 0.00 45.08 3.16
695 716 4.570772 CCAACAAGTACCAATCGATCGATT 59.429 41.667 32.29 32.29 44.73 3.34
696 717 5.064707 CCAACAAGTACCAATCGATCGATTT 59.935 40.000 34.61 25.26 42.30 2.17
701 726 5.416083 AGTACCAATCGATCGATTTGTTCA 58.584 37.500 37.08 24.77 42.30 3.18
704 729 4.875536 ACCAATCGATCGATTTGTTCATCA 59.124 37.500 34.61 3.88 42.30 3.07
718 743 4.968626 TGTTCATCAATCCGACGAAAATG 58.031 39.130 0.00 0.00 25.30 2.32
719 744 4.454161 TGTTCATCAATCCGACGAAAATGT 59.546 37.500 0.00 0.00 25.30 2.71
722 747 5.656480 TCATCAATCCGACGAAAATGTCTA 58.344 37.500 0.00 0.00 36.71 2.59
732 757 6.682863 CCGACGAAAATGTCTAATTTTGCTAG 59.317 38.462 0.00 0.00 36.71 3.42
733 758 6.192863 CGACGAAAATGTCTAATTTTGCTAGC 59.807 38.462 8.10 8.10 36.71 3.42
734 759 6.908825 ACGAAAATGTCTAATTTTGCTAGCA 58.091 32.000 14.93 14.93 32.03 3.49
735 760 7.538575 ACGAAAATGTCTAATTTTGCTAGCAT 58.461 30.769 20.13 5.96 32.03 3.79
736 761 8.028938 ACGAAAATGTCTAATTTTGCTAGCATT 58.971 29.630 20.13 12.75 32.03 3.56
737 762 8.863049 CGAAAATGTCTAATTTTGCTAGCATTT 58.137 29.630 20.13 14.72 36.17 2.32
738 763 9.962759 GAAAATGTCTAATTTTGCTAGCATTTG 57.037 29.630 20.13 11.14 35.58 2.32
739 764 9.709495 AAAATGTCTAATTTTGCTAGCATTTGA 57.291 25.926 20.13 13.31 35.58 2.69
740 765 9.709495 AAATGTCTAATTTTGCTAGCATTTGAA 57.291 25.926 20.13 6.88 34.93 2.69
741 766 9.880157 AATGTCTAATTTTGCTAGCATTTGAAT 57.120 25.926 20.13 13.23 0.00 2.57
742 767 9.880157 ATGTCTAATTTTGCTAGCATTTGAATT 57.120 25.926 20.13 21.21 0.00 2.17
743 768 9.142515 TGTCTAATTTTGCTAGCATTTGAATTG 57.857 29.630 20.13 14.86 0.00 2.32
744 769 9.143631 GTCTAATTTTGCTAGCATTTGAATTGT 57.856 29.630 20.13 5.83 0.00 2.71
745 770 9.709495 TCTAATTTTGCTAGCATTTGAATTGTT 57.291 25.926 20.13 7.80 0.00 2.83
746 771 9.962759 CTAATTTTGCTAGCATTTGAATTGTTC 57.037 29.630 20.13 0.00 0.00 3.18
767 792 1.081094 CATGCATGCAGAGACGTTGA 58.919 50.000 26.69 0.00 0.00 3.18
768 793 1.081892 ATGCATGCAGAGACGTTGAC 58.918 50.000 26.69 0.00 0.00 3.18
769 794 1.284297 TGCATGCAGAGACGTTGACG 61.284 55.000 18.46 1.41 46.33 4.35
770 795 1.417592 CATGCAGAGACGTTGACGC 59.582 57.895 3.05 0.00 44.43 5.19
869 894 5.121298 CCATAGATTAGTGCATGTTGATCCG 59.879 44.000 0.00 0.00 0.00 4.18
870 895 2.874701 AGATTAGTGCATGTTGATCCGC 59.125 45.455 0.00 0.00 0.00 5.54
890 925 4.321601 CCGCCATAACCAGTTGAAAATTCA 60.322 41.667 0.00 0.00 34.92 2.57
974 1015 4.703093 CCTCTGGTAGGCTAGTATAAGAGC 59.297 50.000 0.00 0.00 38.97 4.09
981 1022 2.979240 GCTAGTATAAGAGCCATGGCC 58.021 52.381 33.14 23.29 43.17 5.36
986 1027 2.761786 ATAAGAGCCATGGCCATGTT 57.238 45.000 37.30 28.08 43.17 2.71
992 1033 0.757935 GCCATGGCCATGTTGATCCT 60.758 55.000 37.30 4.25 37.11 3.24
994 1035 1.684983 CCATGGCCATGTTGATCCTTC 59.315 52.381 37.30 0.00 37.11 3.46
997 1038 1.634973 TGGCCATGTTGATCCTTCTCA 59.365 47.619 0.00 0.00 0.00 3.27
1000 1041 3.548770 GCCATGTTGATCCTTCTCATCA 58.451 45.455 0.00 0.00 31.39 3.07
1042 1083 0.322975 GCCTGACAGCCTGAGAGAAA 59.677 55.000 0.00 0.00 0.00 2.52
1068 1109 2.592993 GCAGTAGGCACCACCCTCA 61.593 63.158 0.00 0.00 43.97 3.86
1294 1335 2.434428 CTGTCTCAGAGCTGCCATTTT 58.566 47.619 0.00 0.00 32.44 1.82
1296 1337 1.135460 GTCTCAGAGCTGCCATTTTGC 60.135 52.381 0.00 0.00 0.00 3.68
1617 1670 3.842923 CCTCGCCACAGCCGAGAT 61.843 66.667 11.87 0.00 40.08 2.75
1619 1672 4.819761 TCGCCACAGCCGAGATGC 62.820 66.667 0.00 0.00 34.57 3.91
1657 1710 4.430765 ATCGACGGCGGTGGTCAC 62.431 66.667 12.58 0.00 38.28 3.67
1675 1728 2.644212 CCAGTCTCAGAGCTGCCGT 61.644 63.158 13.54 0.00 0.00 5.68
1712 1765 1.645704 GCCTGTCGACGAGCTCAGTA 61.646 60.000 19.17 0.00 0.00 2.74
1991 2044 2.992114 AGGACCTCTCGCGCAAGT 60.992 61.111 8.75 0.00 41.68 3.16
1996 2049 2.734673 CCTCTCGCGCAAGTTGCTC 61.735 63.158 24.61 16.67 42.25 4.26
2111 2164 3.957260 TGCTTTCTGTCGAGCAGC 58.043 55.556 9.34 3.05 43.46 5.25
2203 2256 8.860128 TCTGAATATATTCGACGCATATTTCAC 58.140 33.333 18.35 0.00 39.62 3.18
2204 2257 8.757164 TGAATATATTCGACGCATATTTCACT 57.243 30.769 18.35 0.00 39.62 3.41
2305 2359 5.017294 TGGTCCACAAAAGAAAATGGTTC 57.983 39.130 0.00 0.00 33.67 3.62
2309 2363 5.006649 GTCCACAAAAGAAAATGGTTCAAGC 59.993 40.000 0.00 0.00 33.67 4.01
2314 2368 4.853924 AAGAAAATGGTTCAAGCGTGAT 57.146 36.364 2.36 0.00 32.48 3.06
2332 2386 3.002348 GTGATTAGGACGCCAACATAAGC 59.998 47.826 0.00 0.00 0.00 3.09
2403 2458 3.506067 GTCCATCAGGGTTTAAGTGTTGG 59.494 47.826 0.00 0.00 38.11 3.77
2408 2463 2.693074 CAGGGTTTAAGTGTTGGTGCTT 59.307 45.455 0.00 0.00 0.00 3.91
2458 2513 2.098298 GCGATGCGCGTTCAATGT 59.902 55.556 8.43 0.00 44.55 2.71
2469 2524 4.727734 GCGCGTTCAATGTGATAAGATGTT 60.728 41.667 8.43 0.00 0.00 2.71
2471 2526 5.794945 CGCGTTCAATGTGATAAGATGTTTT 59.205 36.000 0.00 0.00 0.00 2.43
2473 2528 6.251376 GCGTTCAATGTGATAAGATGTTTTCC 59.749 38.462 0.00 0.00 0.00 3.13
2511 2566 5.166398 CCTACGGTGACTTCGTAAAATCTT 58.834 41.667 0.00 0.00 41.62 2.40
2538 2593 1.195115 TATGCCGGCTCAGTCTTTCT 58.805 50.000 29.70 1.76 0.00 2.52
2567 2622 4.647853 GGTCATATGAGTAGGGTGTGTGTA 59.352 45.833 5.42 0.00 0.00 2.90
2569 2624 5.126545 GTCATATGAGTAGGGTGTGTGTACA 59.873 44.000 5.42 0.00 0.00 2.90
2577 2634 7.120923 AGTAGGGTGTGTGTACATTAATAGG 57.879 40.000 0.00 0.00 39.39 2.57
2601 2658 6.763135 GGGGTGAGTGTATGCATGTATATATG 59.237 42.308 10.16 5.16 0.00 1.78
2604 2661 9.605275 GGTGAGTGTATGCATGTATATATGAAT 57.395 33.333 10.16 10.47 31.28 2.57
2618 2675 9.705290 TGTATATATGAATGTTTGCGTCTGTAT 57.295 29.630 0.00 0.00 0.00 2.29
2719 2784 1.515631 CGCGAGCAAAATGATGAATGC 59.484 47.619 0.00 0.00 39.06 3.56
2788 2853 5.410924 GCAAGGGTGGATTTTATTGACTTC 58.589 41.667 0.00 0.00 0.00 3.01
2837 2902 9.546909 CAATGAGTACACATCTGATTTTTGTAC 57.453 33.333 17.99 17.99 41.83 2.90
2862 2927 1.286880 GATGCACACAGCCAACACC 59.713 57.895 0.00 0.00 44.83 4.16
2885 2950 6.148150 ACCAATACACGTAAAAACACATCGAT 59.852 34.615 0.00 0.00 0.00 3.59
2939 3004 3.372025 GCCTTTCTCTTGTGGATACCCAT 60.372 47.826 0.00 0.00 45.68 4.00
2963 3028 4.941873 CCATGGAAAAGTCAGTACCTTACC 59.058 45.833 5.56 0.00 0.00 2.85
3196 3261 7.955864 GTCAACAAGATTCTAAACGAATACCAC 59.044 37.037 0.00 0.00 42.31 4.16
3202 3267 7.383687 AGATTCTAAACGAATACCACAAGTGA 58.616 34.615 0.94 0.00 42.31 3.41
3206 3271 1.614903 ACGAATACCACAAGTGACGGA 59.385 47.619 0.94 0.00 0.00 4.69
3208 3273 3.259064 CGAATACCACAAGTGACGGAAT 58.741 45.455 0.94 0.00 0.00 3.01
3231 3296 4.216472 TCGACGATGATGAAGAGATAAGGG 59.784 45.833 0.00 0.00 0.00 3.95
3233 3298 4.227197 ACGATGATGAAGAGATAAGGGGT 58.773 43.478 0.00 0.00 0.00 4.95
3238 3303 5.032846 TGATGAAGAGATAAGGGGTGAAGT 58.967 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.667107 CTATGTTCACCTTATGACTTTCCTAAA 57.333 33.333 0.00 0.00 36.92 1.85
32 33 9.042450 TCTATGTTCACCTTATGACTTTCCTAA 57.958 33.333 0.00 0.00 36.92 2.69
33 34 8.603898 TCTATGTTCACCTTATGACTTTCCTA 57.396 34.615 0.00 0.00 36.92 2.94
34 35 7.496346 TCTATGTTCACCTTATGACTTTCCT 57.504 36.000 0.00 0.00 36.92 3.36
35 36 7.824779 ACTTCTATGTTCACCTTATGACTTTCC 59.175 37.037 0.00 0.00 36.92 3.13
36 37 8.779354 ACTTCTATGTTCACCTTATGACTTTC 57.221 34.615 0.00 0.00 36.92 2.62
37 38 9.220767 GAACTTCTATGTTCACCTTATGACTTT 57.779 33.333 0.00 0.00 44.00 2.66
38 39 8.779354 GAACTTCTATGTTCACCTTATGACTT 57.221 34.615 0.00 0.00 44.00 3.01
50 51 8.718102 TGGCTAACTTATGAACTTCTATGTTC 57.282 34.615 0.00 0.00 44.60 3.18
51 52 9.167311 CTTGGCTAACTTATGAACTTCTATGTT 57.833 33.333 0.00 0.00 0.00 2.71
52 53 8.322091 ACTTGGCTAACTTATGAACTTCTATGT 58.678 33.333 0.00 0.00 0.00 2.29
53 54 8.723942 ACTTGGCTAACTTATGAACTTCTATG 57.276 34.615 0.00 0.00 0.00 2.23
54 55 9.740710 AAACTTGGCTAACTTATGAACTTCTAT 57.259 29.630 0.00 0.00 0.00 1.98
55 56 9.569122 AAAACTTGGCTAACTTATGAACTTCTA 57.431 29.630 0.00 0.00 0.00 2.10
56 57 8.465273 AAAACTTGGCTAACTTATGAACTTCT 57.535 30.769 0.00 0.00 0.00 2.85
57 58 7.808381 GGAAAACTTGGCTAACTTATGAACTTC 59.192 37.037 0.00 0.00 0.00 3.01
58 59 7.505923 AGGAAAACTTGGCTAACTTATGAACTT 59.494 33.333 0.00 0.00 0.00 2.66
59 60 7.004691 AGGAAAACTTGGCTAACTTATGAACT 58.995 34.615 0.00 0.00 0.00 3.01
60 61 7.175119 AGAGGAAAACTTGGCTAACTTATGAAC 59.825 37.037 0.00 0.00 0.00 3.18
61 62 7.231467 AGAGGAAAACTTGGCTAACTTATGAA 58.769 34.615 0.00 0.00 0.00 2.57
62 63 6.779860 AGAGGAAAACTTGGCTAACTTATGA 58.220 36.000 0.00 0.00 0.00 2.15
63 64 6.183360 CGAGAGGAAAACTTGGCTAACTTATG 60.183 42.308 0.00 0.00 0.00 1.90
64 65 5.875359 CGAGAGGAAAACTTGGCTAACTTAT 59.125 40.000 0.00 0.00 0.00 1.73
65 66 5.221581 ACGAGAGGAAAACTTGGCTAACTTA 60.222 40.000 0.00 0.00 0.00 2.24
66 67 4.065789 CGAGAGGAAAACTTGGCTAACTT 58.934 43.478 0.00 0.00 0.00 2.66
67 68 3.071167 ACGAGAGGAAAACTTGGCTAACT 59.929 43.478 0.00 0.00 0.00 2.24
68 69 3.400255 ACGAGAGGAAAACTTGGCTAAC 58.600 45.455 0.00 0.00 0.00 2.34
69 70 3.070446 TGACGAGAGGAAAACTTGGCTAA 59.930 43.478 0.00 0.00 0.00 3.09
70 71 2.631062 TGACGAGAGGAAAACTTGGCTA 59.369 45.455 0.00 0.00 0.00 3.93
71 72 1.416401 TGACGAGAGGAAAACTTGGCT 59.584 47.619 0.00 0.00 0.00 4.75
72 73 1.801178 CTGACGAGAGGAAAACTTGGC 59.199 52.381 0.00 0.00 0.00 4.52
73 74 2.037251 TCCTGACGAGAGGAAAACTTGG 59.963 50.000 4.91 0.00 39.32 3.61
74 75 3.060602 GTCCTGACGAGAGGAAAACTTG 58.939 50.000 8.48 0.00 44.04 3.16
75 76 2.037381 GGTCCTGACGAGAGGAAAACTT 59.963 50.000 8.48 0.00 44.04 2.66
76 77 1.619332 GGTCCTGACGAGAGGAAAACT 59.381 52.381 8.48 0.00 44.04 2.66
77 78 1.669211 CGGTCCTGACGAGAGGAAAAC 60.669 57.143 8.48 3.06 44.04 2.43
78 79 0.601558 CGGTCCTGACGAGAGGAAAA 59.398 55.000 8.48 0.00 44.04 2.29
79 80 1.248785 CCGGTCCTGACGAGAGGAAA 61.249 60.000 8.48 0.00 44.04 3.13
80 81 1.677966 CCGGTCCTGACGAGAGGAA 60.678 63.158 8.48 0.00 44.04 3.36
81 82 2.045242 CCGGTCCTGACGAGAGGA 60.045 66.667 0.00 3.42 40.03 3.71
82 83 3.141488 CCCGGTCCTGACGAGAGG 61.141 72.222 0.00 0.00 0.00 3.69
83 84 2.045242 TCCCGGTCCTGACGAGAG 60.045 66.667 0.00 0.00 0.00 3.20
84 85 2.360852 GTCCCGGTCCTGACGAGA 60.361 66.667 0.00 0.00 0.00 4.04
88 89 2.348888 ATGTCGTCCCGGTCCTGAC 61.349 63.158 0.00 3.47 0.00 3.51
89 90 2.036731 ATGTCGTCCCGGTCCTGA 59.963 61.111 0.00 0.00 0.00 3.86
90 91 2.184322 CATGTCGTCCCGGTCCTG 59.816 66.667 0.00 0.00 0.00 3.86
91 92 2.283676 ACATGTCGTCCCGGTCCT 60.284 61.111 0.00 0.00 0.00 3.85
92 93 2.125673 CACATGTCGTCCCGGTCC 60.126 66.667 0.00 0.00 0.00 4.46
93 94 1.736645 CACACATGTCGTCCCGGTC 60.737 63.158 0.00 0.00 0.00 4.79
94 95 2.342279 CACACATGTCGTCCCGGT 59.658 61.111 0.00 0.00 0.00 5.28
95 96 2.434185 CCACACATGTCGTCCCGG 60.434 66.667 0.00 0.00 0.00 5.73
96 97 1.736645 GACCACACATGTCGTCCCG 60.737 63.158 0.00 0.00 31.34 5.14
97 98 0.670546 CAGACCACACATGTCGTCCC 60.671 60.000 6.20 0.00 36.94 4.46
98 99 0.670546 CCAGACCACACATGTCGTCC 60.671 60.000 6.20 0.00 36.94 4.79
99 100 0.033504 ACCAGACCACACATGTCGTC 59.966 55.000 0.00 2.08 36.59 4.20
100 101 0.033504 GACCAGACCACACATGTCGT 59.966 55.000 0.00 0.00 37.80 4.34
101 102 0.033366 TGACCAGACCACACATGTCG 59.967 55.000 0.00 0.00 37.80 4.35
102 103 2.254546 TTGACCAGACCACACATGTC 57.745 50.000 0.00 0.00 0.00 3.06
103 104 2.553028 GGATTGACCAGACCACACATGT 60.553 50.000 0.00 0.00 38.79 3.21
104 105 2.086869 GGATTGACCAGACCACACATG 58.913 52.381 0.00 0.00 38.79 3.21
105 106 1.004745 GGGATTGACCAGACCACACAT 59.995 52.381 0.00 0.00 41.20 3.21
106 107 0.400213 GGGATTGACCAGACCACACA 59.600 55.000 0.00 0.00 41.20 3.72
107 108 0.400213 TGGGATTGACCAGACCACAC 59.600 55.000 0.00 0.00 41.20 3.82
108 109 1.004628 CATGGGATTGACCAGACCACA 59.995 52.381 0.00 0.00 45.20 4.17
109 110 1.281867 TCATGGGATTGACCAGACCAC 59.718 52.381 0.00 0.00 45.20 4.16
110 111 1.667595 TCATGGGATTGACCAGACCA 58.332 50.000 0.00 0.00 45.20 4.02
111 112 2.487986 GGATCATGGGATTGACCAGACC 60.488 54.545 0.00 0.00 45.20 3.85
112 113 2.173356 TGGATCATGGGATTGACCAGAC 59.827 50.000 0.00 0.00 45.20 3.51
113 114 2.490961 TGGATCATGGGATTGACCAGA 58.509 47.619 0.00 0.00 45.20 3.86
114 115 2.954318 GTTGGATCATGGGATTGACCAG 59.046 50.000 0.00 0.00 45.20 4.00
115 116 2.582172 AGTTGGATCATGGGATTGACCA 59.418 45.455 0.00 0.00 46.24 4.02
116 117 3.303351 AGTTGGATCATGGGATTGACC 57.697 47.619 0.00 0.00 32.67 4.02
117 118 4.019174 ACAAGTTGGATCATGGGATTGAC 58.981 43.478 7.96 0.00 32.67 3.18
118 119 4.320546 ACAAGTTGGATCATGGGATTGA 57.679 40.909 7.96 0.00 32.67 2.57
119 120 6.066690 AGATACAAGTTGGATCATGGGATTG 58.933 40.000 26.45 0.00 40.21 2.67
120 121 6.126390 TGAGATACAAGTTGGATCATGGGATT 60.126 38.462 26.45 7.10 40.21 3.01
121 122 5.370584 TGAGATACAAGTTGGATCATGGGAT 59.629 40.000 26.45 7.78 40.21 3.85
122 123 4.721274 TGAGATACAAGTTGGATCATGGGA 59.279 41.667 26.45 5.81 40.21 4.37
123 124 4.818546 GTGAGATACAAGTTGGATCATGGG 59.181 45.833 26.45 0.00 40.21 4.00
124 125 5.430886 TGTGAGATACAAGTTGGATCATGG 58.569 41.667 26.45 0.00 40.21 3.66
125 126 5.007430 GCTGTGAGATACAAGTTGGATCATG 59.993 44.000 26.45 13.60 40.21 3.07
126 127 5.104610 AGCTGTGAGATACAAGTTGGATCAT 60.105 40.000 26.45 13.65 40.21 2.45
127 128 4.223700 AGCTGTGAGATACAAGTTGGATCA 59.776 41.667 26.45 8.90 40.21 2.92
128 129 4.764172 AGCTGTGAGATACAAGTTGGATC 58.236 43.478 18.96 18.96 38.00 3.36
129 130 4.833478 AGCTGTGAGATACAAGTTGGAT 57.167 40.909 0.00 0.00 39.20 3.41
130 131 4.202357 ACAAGCTGTGAGATACAAGTTGGA 60.202 41.667 7.96 0.00 39.20 3.53
131 132 4.067896 ACAAGCTGTGAGATACAAGTTGG 58.932 43.478 7.96 0.00 39.20 3.77
145 146 4.734398 TTCATCAAAAACCACAAGCTGT 57.266 36.364 0.00 0.00 0.00 4.40
146 147 7.712264 TTTATTCATCAAAAACCACAAGCTG 57.288 32.000 0.00 0.00 0.00 4.24
147 148 7.986889 AGTTTTATTCATCAAAAACCACAAGCT 59.013 29.630 6.97 0.00 43.43 3.74
148 149 8.141835 AGTTTTATTCATCAAAAACCACAAGC 57.858 30.769 6.97 0.00 43.43 4.01
149 150 9.919348 CAAGTTTTATTCATCAAAAACCACAAG 57.081 29.630 6.97 0.00 43.43 3.16
150 151 9.658799 TCAAGTTTTATTCATCAAAAACCACAA 57.341 25.926 6.97 0.00 43.43 3.33
151 152 9.829507 ATCAAGTTTTATTCATCAAAAACCACA 57.170 25.926 6.97 0.00 43.43 4.17
157 158 9.500785 GGGGAAATCAAGTTTTATTCATCAAAA 57.499 29.630 0.00 0.00 0.00 2.44
158 159 8.879227 AGGGGAAATCAAGTTTTATTCATCAAA 58.121 29.630 0.00 0.00 0.00 2.69
159 160 8.434589 AGGGGAAATCAAGTTTTATTCATCAA 57.565 30.769 0.00 0.00 0.00 2.57
160 161 8.434589 AAGGGGAAATCAAGTTTTATTCATCA 57.565 30.769 0.00 0.00 0.00 3.07
187 188 4.462483 ACGGTCATGCCATTCTACATTTTT 59.538 37.500 6.92 0.00 36.97 1.94
188 189 4.016444 ACGGTCATGCCATTCTACATTTT 58.984 39.130 6.92 0.00 36.97 1.82
189 190 3.378112 CACGGTCATGCCATTCTACATTT 59.622 43.478 6.92 0.00 36.97 2.32
190 191 2.945008 CACGGTCATGCCATTCTACATT 59.055 45.455 6.92 0.00 36.97 2.71
191 192 2.092968 ACACGGTCATGCCATTCTACAT 60.093 45.455 6.92 0.00 36.97 2.29
192 193 1.277842 ACACGGTCATGCCATTCTACA 59.722 47.619 6.92 0.00 36.97 2.74
193 194 2.024176 ACACGGTCATGCCATTCTAC 57.976 50.000 6.92 0.00 36.97 2.59
194 195 2.779755 AACACGGTCATGCCATTCTA 57.220 45.000 6.92 0.00 36.97 2.10
195 196 1.909700 AAACACGGTCATGCCATTCT 58.090 45.000 6.92 0.00 36.97 2.40
196 197 2.723124 AAAACACGGTCATGCCATTC 57.277 45.000 6.92 0.00 36.97 2.67
223 224 4.671880 TTTGAATTAACCACGGTCATCG 57.328 40.909 0.00 0.00 45.88 3.84
224 225 6.674066 TCTTTTTGAATTAACCACGGTCATC 58.326 36.000 0.00 0.00 0.00 2.92
283 284 2.403586 GCGCAATTAGCACGGTCC 59.596 61.111 0.30 0.00 46.13 4.46
298 299 3.291383 TTTTTGCAGGTCCGGGCG 61.291 61.111 0.00 0.00 0.00 6.13
444 445 1.228429 TGTTTTGCCGGGGAGAAGG 60.228 57.895 2.18 0.00 0.00 3.46
476 477 2.033801 GCTCGTTACTTATCCAGCGGTA 59.966 50.000 0.00 0.00 0.00 4.02
496 509 4.802039 TCGTTTGTCTATCTATTTCACCGC 59.198 41.667 0.00 0.00 0.00 5.68
509 522 3.407698 ACCATGCATGTTCGTTTGTCTA 58.592 40.909 24.58 0.00 0.00 2.59
534 547 7.278646 ACACAGACATACATCAATGATACACAC 59.721 37.037 0.00 0.00 0.00 3.82
540 553 7.609146 ACAGAAACACAGACATACATCAATGAT 59.391 33.333 0.00 0.00 0.00 2.45
609 630 2.678336 GCTCAACCATACACTAACAGGC 59.322 50.000 0.00 0.00 0.00 4.85
679 700 5.712217 TGAACAAATCGATCGATTGGTAC 57.288 39.130 38.18 28.52 45.18 3.34
701 726 7.553881 AATTAGACATTTTCGTCGGATTGAT 57.446 32.000 0.00 0.00 40.98 2.57
704 729 6.526674 GCAAAATTAGACATTTTCGTCGGATT 59.473 34.615 0.00 0.00 40.98 3.01
718 743 9.143631 ACAATTCAAATGCTAGCAAAATTAGAC 57.856 29.630 23.54 0.00 0.00 2.59
719 744 9.709495 AACAATTCAAATGCTAGCAAAATTAGA 57.291 25.926 23.54 11.08 0.00 2.10
722 747 7.512297 CGAACAATTCAAATGCTAGCAAAATT 58.488 30.769 23.54 19.80 0.00 1.82
732 757 2.412429 TGCATGCGAACAATTCAAATGC 59.588 40.909 14.09 14.19 43.25 3.56
733 758 4.573802 CATGCATGCGAACAATTCAAATG 58.426 39.130 14.93 2.53 0.00 2.32
734 759 3.062909 GCATGCATGCGAACAATTCAAAT 59.937 39.130 33.99 0.00 44.67 2.32
735 760 2.412429 GCATGCATGCGAACAATTCAAA 59.588 40.909 33.99 0.00 44.67 2.69
736 761 1.994074 GCATGCATGCGAACAATTCAA 59.006 42.857 33.99 0.00 44.67 2.69
737 762 1.631284 GCATGCATGCGAACAATTCA 58.369 45.000 33.99 0.00 44.67 2.57
757 782 2.088763 CGCATGCGTCAACGTCTCT 61.089 57.895 31.33 0.00 42.22 3.10
768 793 2.616776 CTTTACAGGCGACGCATGCG 62.617 60.000 36.79 36.79 44.57 4.73
769 794 1.060937 CTTTACAGGCGACGCATGC 59.939 57.895 31.87 7.91 44.57 4.06
770 795 0.095245 CACTTTACAGGCGACGCATG 59.905 55.000 30.57 30.57 46.22 4.06
869 894 4.627035 GCTGAATTTTCAACTGGTTATGGC 59.373 41.667 0.00 0.00 36.64 4.40
870 895 5.865552 CAGCTGAATTTTCAACTGGTTATGG 59.134 40.000 8.42 0.00 43.90 2.74
974 1015 1.684983 GAAGGATCAACATGGCCATGG 59.315 52.381 41.25 28.01 42.91 3.66
981 1022 4.186926 ACGTGATGAGAAGGATCAACATG 58.813 43.478 0.00 0.00 41.93 3.21
986 1027 3.763897 TCTTGACGTGATGAGAAGGATCA 59.236 43.478 0.00 0.00 0.00 2.92
992 1033 4.202212 TGAGGTTTCTTGACGTGATGAGAA 60.202 41.667 0.00 0.00 0.00 2.87
994 1035 3.653344 TGAGGTTTCTTGACGTGATGAG 58.347 45.455 0.00 0.00 0.00 2.90
997 1038 2.800544 CGTTGAGGTTTCTTGACGTGAT 59.199 45.455 0.00 0.00 31.53 3.06
1000 1041 1.931172 CACGTTGAGGTTTCTTGACGT 59.069 47.619 0.00 0.00 41.78 4.34
1042 1083 1.142870 TGGTGCCTACTGCTTTCTTGT 59.857 47.619 0.00 0.00 42.00 3.16
1267 1308 1.226435 GCTCTGAGACAGGTACGCG 60.226 63.158 9.28 3.53 31.51 6.01
1279 1320 1.588824 CGGCAAAATGGCAGCTCTGA 61.589 55.000 0.29 0.00 43.94 3.27
1294 1335 4.980805 GAAGGTGGACGCACGGCA 62.981 66.667 0.00 0.00 0.00 5.69
1357 1407 0.972883 GCAAGAGACTCTCTGGTGGT 59.027 55.000 9.44 0.00 40.28 4.16
1640 1693 4.430765 GTGACCACCGCCGTCGAT 62.431 66.667 0.00 0.00 38.10 3.59
1651 1704 0.178950 AGCTCTGAGACTGGTGACCA 60.179 55.000 9.28 3.40 0.00 4.02
1655 1708 1.079266 GGCAGCTCTGAGACTGGTG 60.079 63.158 21.93 9.39 34.38 4.17
1657 1710 2.164865 AACGGCAGCTCTGAGACTGG 62.165 60.000 21.93 13.37 34.38 4.00
1696 1749 2.475685 CGAAATACTGAGCTCGTCGACA 60.476 50.000 17.16 1.87 0.00 4.35
2031 2084 1.835927 GCTGCTGAACCTCAGGGACT 61.836 60.000 0.00 0.00 44.43 3.85
2145 2198 1.599071 TCAAAGCACTCAAAGCTCACG 59.401 47.619 0.00 0.00 42.53 4.35
2203 2256 9.037737 ACATTGATCAAACAATTGTTCTGAAAG 57.962 29.630 23.47 16.93 38.25 2.62
2204 2257 8.819015 CACATTGATCAAACAATTGTTCTGAAA 58.181 29.630 23.47 18.15 38.25 2.69
2207 2260 7.650504 AGACACATTGATCAAACAATTGTTCTG 59.349 33.333 23.47 20.82 38.25 3.02
2309 2363 1.651987 ATGTTGGCGTCCTAATCACG 58.348 50.000 0.00 0.00 40.35 4.35
2314 2368 2.772077 TGCTTATGTTGGCGTCCTAA 57.228 45.000 0.00 0.00 0.00 2.69
2325 2379 2.293677 CGTACTCCTCCGATGCTTATGT 59.706 50.000 0.00 0.00 0.00 2.29
2332 2386 3.770263 TGTTTACGTACTCCTCCGATG 57.230 47.619 0.00 0.00 0.00 3.84
2458 2513 6.094464 TCGTAGTCGAGGAAAACATCTTATCA 59.906 38.462 0.00 0.00 41.35 2.15
2511 2566 2.899900 ACTGAGCCGGCATATCATCTTA 59.100 45.455 31.54 0.00 0.00 2.10
2538 2593 4.835056 CACCCTACTCATATGACCATCTCA 59.165 45.833 0.00 0.00 0.00 3.27
2542 2597 4.101585 CACACACCCTACTCATATGACCAT 59.898 45.833 0.00 0.00 0.00 3.55
2567 2622 5.131977 TGCATACACTCACCCCTATTAATGT 59.868 40.000 0.00 0.00 0.00 2.71
2569 2624 5.904984 TGCATACACTCACCCCTATTAAT 57.095 39.130 0.00 0.00 0.00 1.40
2577 2634 7.555965 TCATATATACATGCATACACTCACCC 58.444 38.462 0.00 0.00 0.00 4.61
2601 2658 4.783242 ACACAATACAGACGCAAACATTC 58.217 39.130 0.00 0.00 0.00 2.67
2604 2661 5.736486 TTAACACAATACAGACGCAAACA 57.264 34.783 0.00 0.00 0.00 2.83
2606 2663 9.731819 TTTTATTTAACACAATACAGACGCAAA 57.268 25.926 0.00 0.00 0.00 3.68
2618 2675 9.528018 CTTTCTCAAGCCTTTTATTTAACACAA 57.472 29.630 0.00 0.00 0.00 3.33
2643 2700 6.463995 TTTAACTCAAAAATGGTCAGCACT 57.536 33.333 0.00 0.00 0.00 4.40
2698 2763 1.515631 CATTCATCATTTTGCTCGCGC 59.484 47.619 0.00 0.00 0.00 6.86
2719 2784 0.676184 TAGGGCTGCATCTCTAAGCG 59.324 55.000 0.50 0.00 37.83 4.68
2744 2809 2.097466 CCGAAAAATGCCGTATGCTCTT 59.903 45.455 0.00 0.00 42.00 2.85
2755 2820 0.670239 CCACCCTTGCCGAAAAATGC 60.670 55.000 0.00 0.00 0.00 3.56
2765 2830 5.047377 TGAAGTCAATAAAATCCACCCTTGC 60.047 40.000 0.00 0.00 0.00 4.01
2826 2891 6.488344 TGTGCATCCTAACTGTACAAAAATCA 59.512 34.615 0.00 0.00 36.49 2.57
2829 2894 5.590663 TGTGTGCATCCTAACTGTACAAAAA 59.409 36.000 0.00 0.00 40.20 1.94
2832 2897 4.314961 CTGTGTGCATCCTAACTGTACAA 58.685 43.478 0.00 0.00 40.20 2.41
2837 2902 1.089920 GGCTGTGTGCATCCTAACTG 58.910 55.000 0.00 0.00 45.15 3.16
2862 2927 9.531412 TTTATCGATGTGTTTTTACGTGTATTG 57.469 29.630 8.54 0.00 0.00 1.90
2906 2971 0.901124 GAGAAAGGCAGAGCAGGAGA 59.099 55.000 0.00 0.00 0.00 3.71
2939 3004 4.993705 AAGGTACTGACTTTTCCATGGA 57.006 40.909 11.44 11.44 40.86 3.41
2943 3008 4.657039 ACAGGTAAGGTACTGACTTTTCCA 59.343 41.667 0.00 0.00 40.48 3.53
2944 3009 5.224821 ACAGGTAAGGTACTGACTTTTCC 57.775 43.478 0.00 0.00 40.48 3.13
2963 3028 1.071385 AGTTGACCAGCTCAAGGACAG 59.929 52.381 0.00 0.00 39.69 3.51
3154 3219 3.762288 TGTTGACCATACTCGCTTACTCT 59.238 43.478 0.00 0.00 0.00 3.24
3168 3233 7.118680 GGTATTCGTTTAGAATCTTGTTGACCA 59.881 37.037 0.00 0.00 45.95 4.02
3196 3261 1.583856 CATCGTCGATTCCGTCACTTG 59.416 52.381 4.63 0.00 37.05 3.16
3202 3267 2.357952 TCTTCATCATCGTCGATTCCGT 59.642 45.455 4.63 0.00 37.05 4.69
3206 3271 6.385843 CCTTATCTCTTCATCATCGTCGATT 58.614 40.000 4.63 0.00 0.00 3.34
3208 3273 4.216472 CCCTTATCTCTTCATCATCGTCGA 59.784 45.833 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.