Multiple sequence alignment - TraesCS7D01G361200

Loading Multiple Alignment...

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 TraesCS7D01G361200 chr7D 100.000 4302 0 0 1 4302 463896096 463891795 0.000000e+00 7945.0
1 TraesCS7D01G361200 chr7D 83.614 415 61 6 91 501 206847407 206846996 2.430000e-102 383.0
2 TraesCS7D01G361200 chr7D 74.865 923 159 48 2266 3165 463962441 463961569 6.840000e-93 351.0
3 TraesCS7D01G361200 chr7D 80.815 417 66 6 89 502 579966692 579967097 8.980000e-82 315.0
4 TraesCS7D01G361200 chr7D 79.675 246 48 2 4045 4289 355562409 355562653 4.420000e-40 176.0
5 TraesCS7D01G361200 chr7A 92.413 2346 110 30 1083 3385 536506921 536509241 0.000000e+00 3284.0
6 TraesCS7D01G361200 chr7A 90.935 706 27 19 3604 4302 536509372 536510047 0.000000e+00 915.0
7 TraesCS7D01G361200 chr7A 88.596 456 44 6 646 1094 536506287 536506741 8.130000e-152 547.0
8 TraesCS7D01G361200 chr7A 74.674 920 162 47 2268 3165 536124249 536125119 4.120000e-90 342.0
9 TraesCS7D01G361200 chr7A 80.488 246 46 2 4051 4295 377980890 377980646 2.040000e-43 187.0
10 TraesCS7D01G361200 chr7B 96.047 1366 36 7 827 2189 487800132 487801482 0.000000e+00 2207.0
11 TraesCS7D01G361200 chr7B 94.837 1317 52 7 2256 3562 487801573 487802883 0.000000e+00 2041.0
12 TraesCS7D01G361200 chr7B 96.453 733 24 1 3570 4302 487802998 487803728 0.000000e+00 1208.0
13 TraesCS7D01G361200 chr7B 94.673 657 34 1 180 836 487798024 487798679 0.000000e+00 1018.0
14 TraesCS7D01G361200 chr7B 74.295 922 162 50 2268 3165 487220991 487221861 1.930000e-83 320.0
15 TraesCS7D01G361200 chr7B 80.488 246 46 2 4045 4289 307363421 307363665 2.040000e-43 187.0
16 TraesCS7D01G361200 chr7B 82.243 107 14 5 652 757 164158912 164159014 2.130000e-13 87.9
17 TraesCS7D01G361200 chr7B 88.732 71 8 0 703 773 226444341 226444271 2.130000e-13 87.9
18 TraesCS7D01G361200 chr5D 86.321 424 46 8 89 501 404474546 404474968 6.560000e-123 451.0
19 TraesCS7D01G361200 chr2B 83.924 423 62 5 89 507 148249701 148250121 2.410000e-107 399.0
20 TraesCS7D01G361200 chr2B 94.915 59 3 0 3852 3910 30133312 30133370 4.580000e-15 93.5
21 TraesCS7D01G361200 chr2D 82.464 422 67 5 89 507 97231246 97231663 3.160000e-96 363.0
22 TraesCS7D01G361200 chr2D 84.857 350 49 2 89 436 71257021 71256674 2.460000e-92 350.0
23 TraesCS7D01G361200 chr2D 85.065 308 37 5 119 423 83826448 83826749 5.400000e-79 305.0
24 TraesCS7D01G361200 chr2D 85.200 250 36 1 256 505 491956535 491956287 5.520000e-64 255.0
25 TraesCS7D01G361200 chr2D 85.294 68 9 1 700 766 558161404 558161337 7.720000e-08 69.4
26 TraesCS7D01G361200 chr1B 81.146 419 68 5 89 505 645086117 645085708 4.150000e-85 326.0
27 TraesCS7D01G361200 chr3B 80.193 414 55 14 89 502 574721214 574721600 7.040000e-73 285.0
28 TraesCS7D01G361200 chr1D 82.462 325 51 3 176 494 11252968 11252644 3.280000e-71 279.0
29 TraesCS7D01G361200 chr5A 86.420 81 11 0 561 641 353156963 353157043 5.930000e-14 89.8
30 TraesCS7D01G361200 chr5A 80.882 68 11 2 664 730 92218781 92218847 8.000000e-03 52.8
31 TraesCS7D01G361200 chr3A 84.416 77 10 2 696 771 66909028 66908953 1.660000e-09 75.0
32 TraesCS7D01G361200 chr1A 80.000 105 18 2 659 762 577888623 577888725 1.660000e-09 75.0
33 TraesCS7D01G361200 chr4A 95.238 42 2 0 602 643 610038950 610038909 2.780000e-07 67.6
34 TraesCS7D01G361200 chr2A 82.667 75 13 0 700 774 168978009 168977935 2.780000e-07 67.6
35 TraesCS7D01G361200 chr4D 83.333 72 10 2 659 729 401634007 401634077 9.990000e-07 65.8
36 TraesCS7D01G361200 chr5B 82.857 70 11 1 700 768 572341190 572341121 1.290000e-05 62.1


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 TraesCS7D01G361200 chr7D 463891795 463896096 4301 True 7945.0 7945 100.0000 1 4302 1 chr7D.!!$R2 4301
1 TraesCS7D01G361200 chr7D 463961569 463962441 872 True 351.0 351 74.8650 2266 3165 1 chr7D.!!$R3 899
2 TraesCS7D01G361200 chr7A 536506287 536510047 3760 False 1582.0 3284 90.6480 646 4302 3 chr7A.!!$F2 3656
3 TraesCS7D01G361200 chr7A 536124249 536125119 870 False 342.0 342 74.6740 2268 3165 1 chr7A.!!$F1 897
4 TraesCS7D01G361200 chr7B 487798024 487803728 5704 False 1618.5 2207 95.5025 180 4302 4 chr7B.!!$F4 4122
5 TraesCS7D01G361200 chr7B 487220991 487221861 870 False 320.0 320 74.2950 2268 3165 1 chr7B.!!$F3 897

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
151 152 0.297525 CCGTACGCGTTGACATGATG 59.702 55.0 20.78 1.98 36.15 3.07 F
764 765 0.625849 AAGGTGCTCATAGGGGTTGG 59.374 55.0 0.00 0.00 0.00 3.77 F
2189 3865 0.035343 GCAGGTCCAAGGGGTAAGAC 60.035 60.0 0.00 0.00 34.93 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 3305 0.034896 TTCAGTTCAGTTCCTCGGGC 59.965 55.0 0.00 0.0 0.00 6.13 R
2237 3952 0.263172 ACAAAACCCCCACCATGTCA 59.737 50.0 0.00 0.0 0.00 3.58 R
3356 5101 0.103937 TGGAAGGCCTTTGTTTTGCG 59.896 50.0 21.54 0.0 34.31 4.85 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
73 74 2.201210 GGGGGCATATTGGGGGTG 59.799 66.667 0.00 0.00 0.00 4.61
74 75 2.524148 GGGGCATATTGGGGGTGC 60.524 66.667 0.00 0.00 38.12 5.01
75 76 2.912025 GGGCATATTGGGGGTGCG 60.912 66.667 0.00 0.00 39.69 5.34
76 77 2.912025 GGCATATTGGGGGTGCGG 60.912 66.667 0.00 0.00 39.69 5.69
77 78 3.605664 GCATATTGGGGGTGCGGC 61.606 66.667 0.00 0.00 0.00 6.53
78 79 2.195683 CATATTGGGGGTGCGGCT 59.804 61.111 0.00 0.00 0.00 5.52
79 80 2.195567 CATATTGGGGGTGCGGCTG 61.196 63.158 0.00 0.00 0.00 4.85
80 81 2.382770 ATATTGGGGGTGCGGCTGA 61.383 57.895 0.00 0.00 0.00 4.26
81 82 1.932156 ATATTGGGGGTGCGGCTGAA 61.932 55.000 0.00 0.00 0.00 3.02
82 83 2.550699 TATTGGGGGTGCGGCTGAAG 62.551 60.000 0.00 0.00 0.00 3.02
84 85 4.115199 GGGGGTGCGGCTGAAGAT 62.115 66.667 0.00 0.00 0.00 2.40
85 86 2.825836 GGGGTGCGGCTGAAGATG 60.826 66.667 0.00 0.00 0.00 2.90
86 87 3.512516 GGGTGCGGCTGAAGATGC 61.513 66.667 0.00 0.00 0.00 3.91
87 88 2.437359 GGTGCGGCTGAAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
88 89 2.042831 GGTGCGGCTGAAGATGCTT 61.043 57.895 0.00 0.00 0.00 3.91
89 90 1.589716 GGTGCGGCTGAAGATGCTTT 61.590 55.000 0.00 0.00 0.00 3.51
90 91 0.455633 GTGCGGCTGAAGATGCTTTG 60.456 55.000 0.00 0.00 0.00 2.77
91 92 0.606130 TGCGGCTGAAGATGCTTTGA 60.606 50.000 0.00 0.00 0.00 2.69
92 93 0.523072 GCGGCTGAAGATGCTTTGAA 59.477 50.000 0.00 0.00 0.00 2.69
93 94 1.133790 GCGGCTGAAGATGCTTTGAAT 59.866 47.619 0.00 0.00 0.00 2.57
94 95 2.793933 GCGGCTGAAGATGCTTTGAATC 60.794 50.000 0.00 0.00 0.00 2.52
95 96 2.421073 CGGCTGAAGATGCTTTGAATCA 59.579 45.455 0.00 0.00 0.00 2.57
96 97 3.066342 CGGCTGAAGATGCTTTGAATCAT 59.934 43.478 0.00 0.00 0.00 2.45
97 98 4.439700 CGGCTGAAGATGCTTTGAATCATT 60.440 41.667 0.00 0.00 0.00 2.57
98 99 5.041940 GGCTGAAGATGCTTTGAATCATTC 58.958 41.667 0.00 0.00 0.00 2.67
99 100 5.393787 GGCTGAAGATGCTTTGAATCATTCA 60.394 40.000 0.00 0.00 38.04 2.57
100 101 6.273825 GCTGAAGATGCTTTGAATCATTCAT 58.726 36.000 0.00 0.00 39.84 2.57
101 102 6.757010 GCTGAAGATGCTTTGAATCATTCATT 59.243 34.615 0.00 0.00 39.84 2.57
102 103 7.043325 GCTGAAGATGCTTTGAATCATTCATTC 60.043 37.037 0.00 1.08 41.42 2.67
112 113 6.990341 TGAATCATTCATTCACTCGATGTT 57.010 33.333 0.00 0.00 45.12 2.71
113 114 6.778108 TGAATCATTCATTCACTCGATGTTG 58.222 36.000 0.00 0.00 45.12 3.33
114 115 4.604843 TCATTCATTCACTCGATGTTGC 57.395 40.909 0.00 0.00 0.00 4.17
115 116 4.256110 TCATTCATTCACTCGATGTTGCT 58.744 39.130 0.00 0.00 0.00 3.91
116 117 4.330894 TCATTCATTCACTCGATGTTGCTC 59.669 41.667 0.00 0.00 0.00 4.26
117 118 3.599730 TCATTCACTCGATGTTGCTCT 57.400 42.857 0.00 0.00 0.00 4.09
118 119 4.718940 TCATTCACTCGATGTTGCTCTA 57.281 40.909 0.00 0.00 0.00 2.43
119 120 4.424626 TCATTCACTCGATGTTGCTCTAC 58.575 43.478 0.00 0.00 0.00 2.59
120 121 3.934457 TTCACTCGATGTTGCTCTACA 57.066 42.857 0.00 0.00 0.00 2.74
121 122 3.217599 TCACTCGATGTTGCTCTACAC 57.782 47.619 0.00 0.00 0.00 2.90
122 123 2.556622 TCACTCGATGTTGCTCTACACA 59.443 45.455 0.00 0.00 0.00 3.72
123 124 3.193479 TCACTCGATGTTGCTCTACACAT 59.807 43.478 0.00 0.00 0.00 3.21
124 125 3.928992 CACTCGATGTTGCTCTACACATT 59.071 43.478 0.00 0.00 0.00 2.71
125 126 3.928992 ACTCGATGTTGCTCTACACATTG 59.071 43.478 0.00 0.00 0.00 2.82
126 127 3.925379 TCGATGTTGCTCTACACATTGT 58.075 40.909 0.00 0.00 0.00 2.71
127 128 3.679502 TCGATGTTGCTCTACACATTGTG 59.320 43.478 15.18 15.18 39.75 3.33
129 130 4.625311 CGATGTTGCTCTACACATTGTGTA 59.375 41.667 24.25 24.25 45.56 2.90
137 138 2.088950 ACACATTGTGTAGCCCGTAC 57.911 50.000 20.56 0.00 45.56 3.67
138 139 0.996462 CACATTGTGTAGCCCGTACG 59.004 55.000 8.69 8.69 33.87 3.67
139 140 0.738412 ACATTGTGTAGCCCGTACGC 60.738 55.000 10.49 0.00 41.80 4.42
140 141 1.517694 ATTGTGTAGCCCGTACGCG 60.518 57.895 10.49 3.53 44.01 6.01
141 142 2.216750 ATTGTGTAGCCCGTACGCGT 62.217 55.000 19.17 19.17 44.01 6.01
142 143 2.126346 GTGTAGCCCGTACGCGTT 60.126 61.111 20.78 0.00 32.54 4.84
143 144 2.126385 TGTAGCCCGTACGCGTTG 60.126 61.111 20.78 11.05 33.87 4.10
144 145 2.179018 GTAGCCCGTACGCGTTGA 59.821 61.111 20.78 0.00 36.15 3.18
145 146 2.154569 GTAGCCCGTACGCGTTGAC 61.155 63.158 20.78 10.07 36.15 3.18
146 147 2.624868 TAGCCCGTACGCGTTGACA 61.625 57.895 20.78 0.00 36.15 3.58
147 148 1.936436 TAGCCCGTACGCGTTGACAT 61.936 55.000 20.78 2.07 36.15 3.06
148 149 3.077705 CCCGTACGCGTTGACATG 58.922 61.111 20.78 4.17 36.15 3.21
149 150 1.444724 CCCGTACGCGTTGACATGA 60.445 57.895 20.78 0.00 36.15 3.07
150 151 0.804544 CCCGTACGCGTTGACATGAT 60.805 55.000 20.78 0.00 36.15 2.45
151 152 0.297525 CCGTACGCGTTGACATGATG 59.702 55.000 20.78 1.98 36.15 3.07
152 153 0.989164 CGTACGCGTTGACATGATGT 59.011 50.000 20.78 0.00 0.00 3.06
153 154 2.178783 CGTACGCGTTGACATGATGTA 58.821 47.619 20.78 0.00 0.00 2.29
154 155 2.036004 CGTACGCGTTGACATGATGTAC 60.036 50.000 20.78 3.29 0.00 2.90
155 156 1.355971 ACGCGTTGACATGATGTACC 58.644 50.000 5.58 0.00 0.00 3.34
156 157 1.337354 ACGCGTTGACATGATGTACCA 60.337 47.619 5.58 0.00 0.00 3.25
157 158 1.933181 CGCGTTGACATGATGTACCAT 59.067 47.619 0.00 0.00 0.00 3.55
158 159 3.120041 CGCGTTGACATGATGTACCATA 58.880 45.455 0.00 0.00 0.00 2.74
159 160 3.182372 CGCGTTGACATGATGTACCATAG 59.818 47.826 0.00 0.00 0.00 2.23
160 161 3.494626 GCGTTGACATGATGTACCATAGG 59.505 47.826 0.00 0.00 0.00 2.57
161 162 4.739436 GCGTTGACATGATGTACCATAGGA 60.739 45.833 0.00 0.00 0.00 2.94
162 163 5.356426 CGTTGACATGATGTACCATAGGAA 58.644 41.667 0.00 0.00 0.00 3.36
163 164 5.815222 CGTTGACATGATGTACCATAGGAAA 59.185 40.000 0.00 0.00 0.00 3.13
164 165 6.018751 CGTTGACATGATGTACCATAGGAAAG 60.019 42.308 0.00 0.00 0.00 2.62
165 166 6.806668 TGACATGATGTACCATAGGAAAGA 57.193 37.500 0.00 0.00 0.00 2.52
166 167 6.820335 TGACATGATGTACCATAGGAAAGAG 58.180 40.000 0.00 0.00 0.00 2.85
167 168 6.179906 ACATGATGTACCATAGGAAAGAGG 57.820 41.667 0.00 0.00 0.00 3.69
168 169 5.072329 ACATGATGTACCATAGGAAAGAGGG 59.928 44.000 0.00 0.00 0.00 4.30
169 170 4.890988 TGATGTACCATAGGAAAGAGGGA 58.109 43.478 0.00 0.00 0.00 4.20
170 171 5.476983 TGATGTACCATAGGAAAGAGGGAT 58.523 41.667 0.00 0.00 0.00 3.85
171 172 5.307976 TGATGTACCATAGGAAAGAGGGATG 59.692 44.000 0.00 0.00 0.00 3.51
172 173 4.631234 TGTACCATAGGAAAGAGGGATGT 58.369 43.478 0.00 0.00 0.00 3.06
173 174 5.036916 TGTACCATAGGAAAGAGGGATGTT 58.963 41.667 0.00 0.00 0.00 2.71
174 175 4.779993 ACCATAGGAAAGAGGGATGTTC 57.220 45.455 0.00 0.00 0.00 3.18
175 176 4.111577 ACCATAGGAAAGAGGGATGTTCA 58.888 43.478 0.00 0.00 0.00 3.18
176 177 4.728860 ACCATAGGAAAGAGGGATGTTCAT 59.271 41.667 0.00 0.00 0.00 2.57
177 178 5.194537 ACCATAGGAAAGAGGGATGTTCATT 59.805 40.000 0.00 0.00 0.00 2.57
178 179 6.131961 CCATAGGAAAGAGGGATGTTCATTT 58.868 40.000 0.00 0.00 0.00 2.32
179 180 7.091993 ACCATAGGAAAGAGGGATGTTCATTTA 60.092 37.037 0.00 0.00 0.00 1.40
180 181 7.229506 CCATAGGAAAGAGGGATGTTCATTTAC 59.770 40.741 0.00 0.00 0.00 2.01
181 182 5.186198 AGGAAAGAGGGATGTTCATTTACG 58.814 41.667 0.00 0.00 0.00 3.18
182 183 4.941873 GGAAAGAGGGATGTTCATTTACGT 59.058 41.667 0.00 0.00 0.00 3.57
183 184 6.070424 AGGAAAGAGGGATGTTCATTTACGTA 60.070 38.462 0.00 0.00 0.00 3.57
184 185 6.036844 GGAAAGAGGGATGTTCATTTACGTAC 59.963 42.308 0.00 0.00 0.00 3.67
185 186 5.670792 AGAGGGATGTTCATTTACGTACA 57.329 39.130 0.00 0.00 0.00 2.90
186 187 5.416947 AGAGGGATGTTCATTTACGTACAC 58.583 41.667 0.00 0.00 0.00 2.90
191 192 5.407387 GGATGTTCATTTACGTACACACACT 59.593 40.000 0.00 0.00 0.00 3.55
192 193 6.587226 GGATGTTCATTTACGTACACACACTA 59.413 38.462 0.00 0.00 0.00 2.74
208 209 6.311445 ACACACACTATCGAATAAAGCTGAAG 59.689 38.462 0.00 0.00 0.00 3.02
223 224 1.278985 CTGAAGGGGCAGTATGTGTGA 59.721 52.381 0.00 0.00 39.31 3.58
256 257 3.314080 TCCGTTGAAACTTGTTGGACATC 59.686 43.478 0.00 0.00 0.00 3.06
347 348 5.123227 TCCGAACTTTGATGAATATCCACC 58.877 41.667 0.00 0.00 32.09 4.61
348 349 4.881273 CCGAACTTTGATGAATATCCACCA 59.119 41.667 0.00 0.00 32.09 4.17
362 363 3.940209 TCCACCAGTTTGCATGAATTC 57.060 42.857 0.00 0.00 0.00 2.17
384 385 1.808390 CCGCTAAGTCGAAACCCGG 60.808 63.158 0.00 0.00 39.14 5.73
482 483 2.450160 CGAATACCGGAGCAAATTTGC 58.550 47.619 31.36 31.36 43.79 3.68
491 492 2.088178 GCAAATTTGCGGGTCAGCG 61.088 57.895 26.15 0.00 45.11 5.18
516 517 8.031864 CGTTGGAGATGCTCTAATCTATAACAT 58.968 37.037 0.00 0.00 37.03 2.71
736 737 7.828717 TCAATCTCAAAATATTGTGCTACCTCA 59.171 33.333 0.22 0.00 37.79 3.86
764 765 0.625849 AAGGTGCTCATAGGGGTTGG 59.374 55.000 0.00 0.00 0.00 3.77
790 791 1.386748 CATCTGCGTTGTACTGTGTCG 59.613 52.381 0.00 0.00 0.00 4.35
981 2452 9.677567 TGTTGTTTGCAAAGATTTATAACTCTC 57.322 29.630 13.26 0.00 36.22 3.20
982 2453 9.677567 GTTGTTTGCAAAGATTTATAACTCTCA 57.322 29.630 13.26 0.00 36.22 3.27
1165 2833 1.195115 GATGACCAGGCCTCACACTA 58.805 55.000 0.00 0.00 0.00 2.74
1169 2837 1.220206 CCAGGCCTCACACTAGCAG 59.780 63.158 0.00 0.00 0.00 4.24
1170 2838 1.548357 CCAGGCCTCACACTAGCAGT 61.548 60.000 0.00 0.00 0.00 4.40
1171 2839 1.186200 CAGGCCTCACACTAGCAGTA 58.814 55.000 0.00 0.00 0.00 2.74
1227 2895 1.856265 GCACGTTTCTCCTGGCCTTG 61.856 60.000 3.32 0.00 0.00 3.61
1315 2983 3.475899 CGTGGGACGTGGAGTACATCC 62.476 61.905 0.00 0.00 39.83 3.51
1622 3298 4.652131 AATGGCCGGGCACGTGAA 62.652 61.111 35.30 9.87 38.78 3.18
1629 3305 1.574428 CGGGCACGTGAAGAAAAGG 59.426 57.895 22.23 0.00 34.81 3.11
1641 3317 0.036875 AGAAAAGGCCCGAGGAACTG 59.963 55.000 0.00 0.00 41.55 3.16
1656 3332 2.544267 GGAACTGAACTGAACTGAACCG 59.456 50.000 0.00 0.00 0.00 4.44
1660 3336 4.058817 ACTGAACTGAACTGAACCGAATC 58.941 43.478 0.00 0.00 0.00 2.52
1930 3606 4.028490 ATCAACGGGCGAGGGCAA 62.028 61.111 0.00 0.00 42.47 4.52
2189 3865 0.035343 GCAGGTCCAAGGGGTAAGAC 60.035 60.000 0.00 0.00 34.93 3.01
2190 3866 1.657804 CAGGTCCAAGGGGTAAGACT 58.342 55.000 0.00 0.00 34.93 3.24
2191 3867 2.829023 CAGGTCCAAGGGGTAAGACTA 58.171 52.381 0.00 0.00 34.93 2.59
2192 3868 3.385115 CAGGTCCAAGGGGTAAGACTAT 58.615 50.000 0.00 0.00 34.93 2.12
2194 3870 4.589374 CAGGTCCAAGGGGTAAGACTATAG 59.411 50.000 0.00 0.00 34.93 1.31
2195 3871 4.485021 AGGTCCAAGGGGTAAGACTATAGA 59.515 45.833 6.78 0.00 34.93 1.98
2196 3872 5.138123 AGGTCCAAGGGGTAAGACTATAGAT 59.862 44.000 6.78 0.00 34.93 1.98
2197 3873 5.845065 GGTCCAAGGGGTAAGACTATAGATT 59.155 44.000 6.78 3.62 34.93 2.40
2198 3874 6.329460 GGTCCAAGGGGTAAGACTATAGATTT 59.671 42.308 6.78 2.96 34.93 2.17
2199 3875 7.147355 GGTCCAAGGGGTAAGACTATAGATTTT 60.147 40.741 6.78 0.50 34.93 1.82
2201 3877 7.626084 TCCAAGGGGTAAGACTATAGATTTTCA 59.374 37.037 6.78 0.00 34.93 2.69
2202 3878 8.440771 CCAAGGGGTAAGACTATAGATTTTCAT 58.559 37.037 6.78 0.00 0.00 2.57
2205 3881 9.670442 AGGGGTAAGACTATAGATTTTCATACA 57.330 33.333 6.78 0.00 0.00 2.29
2230 3945 4.571919 TCACGGTGAGAAATTATTCGGTT 58.428 39.130 6.76 0.00 40.63 4.44
2231 3946 4.390603 TCACGGTGAGAAATTATTCGGTTG 59.609 41.667 6.76 0.00 40.63 3.77
2232 3947 4.390603 CACGGTGAGAAATTATTCGGTTGA 59.609 41.667 0.74 0.00 40.63 3.18
2233 3948 4.390909 ACGGTGAGAAATTATTCGGTTGAC 59.609 41.667 0.00 0.00 40.63 3.18
2234 3949 4.630069 CGGTGAGAAATTATTCGGTTGACT 59.370 41.667 0.00 0.00 40.63 3.41
2235 3950 5.808540 CGGTGAGAAATTATTCGGTTGACTA 59.191 40.000 0.00 0.00 40.63 2.59
2236 3951 6.479001 CGGTGAGAAATTATTCGGTTGACTAT 59.521 38.462 0.00 0.00 40.63 2.12
2237 3952 7.011109 CGGTGAGAAATTATTCGGTTGACTATT 59.989 37.037 0.00 0.00 40.63 1.73
2239 3954 8.879759 GTGAGAAATTATTCGGTTGACTATTGA 58.120 33.333 0.00 0.00 40.63 2.57
2240 3955 8.879759 TGAGAAATTATTCGGTTGACTATTGAC 58.120 33.333 0.00 0.00 40.63 3.18
2241 3956 8.786826 AGAAATTATTCGGTTGACTATTGACA 57.213 30.769 0.00 0.00 40.63 3.58
2242 3957 9.396022 AGAAATTATTCGGTTGACTATTGACAT 57.604 29.630 0.00 0.00 40.63 3.06
2243 3958 9.438291 GAAATTATTCGGTTGACTATTGACATG 57.562 33.333 0.00 0.00 0.00 3.21
2244 3959 6.918892 TTATTCGGTTGACTATTGACATGG 57.081 37.500 0.00 0.00 0.00 3.66
2245 3960 3.973206 TCGGTTGACTATTGACATGGT 57.027 42.857 0.00 0.00 0.00 3.55
2246 3961 3.595173 TCGGTTGACTATTGACATGGTG 58.405 45.455 0.00 0.00 0.00 4.17
2247 3962 2.677836 CGGTTGACTATTGACATGGTGG 59.322 50.000 0.00 0.00 0.00 4.61
2248 3963 3.016736 GGTTGACTATTGACATGGTGGG 58.983 50.000 0.00 0.00 0.00 4.61
2249 3964 3.016736 GTTGACTATTGACATGGTGGGG 58.983 50.000 0.00 0.00 0.00 4.96
2250 3965 1.563879 TGACTATTGACATGGTGGGGG 59.436 52.381 0.00 0.00 0.00 5.40
2251 3966 1.564348 GACTATTGACATGGTGGGGGT 59.436 52.381 0.00 0.00 0.00 4.95
2252 3967 2.000048 ACTATTGACATGGTGGGGGTT 59.000 47.619 0.00 0.00 0.00 4.11
2253 3968 2.381961 ACTATTGACATGGTGGGGGTTT 59.618 45.455 0.00 0.00 0.00 3.27
2254 3969 2.414250 ATTGACATGGTGGGGGTTTT 57.586 45.000 0.00 0.00 0.00 2.43
2264 3979 2.217750 GTGGGGGTTTTGTGATTTTGC 58.782 47.619 0.00 0.00 0.00 3.68
2323 4038 3.998672 GAGCCGTTCACCGTCCCA 61.999 66.667 0.00 0.00 33.66 4.37
2398 4113 1.881602 GCCGACGTTCTACAGGTCT 59.118 57.895 0.00 0.00 38.03 3.85
2411 4126 0.545309 CAGGTCTGGGTCCTTCTGGA 60.545 60.000 0.00 0.00 40.69 3.86
2569 4287 2.025887 GGACTTCACCCACAGGATCAAT 60.026 50.000 0.00 0.00 36.73 2.57
3166 4896 4.388499 ATGGGCGCCGTCTTCGTT 62.388 61.111 22.54 0.00 35.01 3.85
3178 4908 1.000896 CTTCGTTGAAGGGGCCCAT 60.001 57.895 27.72 16.07 36.16 4.00
3180 4910 0.699399 TTCGTTGAAGGGGCCCATAA 59.301 50.000 27.72 13.75 0.00 1.90
3272 5002 4.148825 CCGCTAAGCCAGGCTCGT 62.149 66.667 16.53 1.81 38.25 4.18
3273 5003 2.583593 CGCTAAGCCAGGCTCGTC 60.584 66.667 16.53 5.55 38.25 4.20
3274 5004 2.583593 GCTAAGCCAGGCTCGTCG 60.584 66.667 16.53 4.63 38.25 5.12
3275 5005 2.105128 CTAAGCCAGGCTCGTCGG 59.895 66.667 16.53 0.00 38.25 4.79
3276 5006 4.143333 TAAGCCAGGCTCGTCGGC 62.143 66.667 16.53 5.48 46.62 5.54
3351 5096 1.414550 TCCGTGGTCATTTGTCAGTGA 59.585 47.619 0.00 0.00 0.00 3.41
3356 5101 1.198637 GGTCATTTGTCAGTGAGCAGC 59.801 52.381 12.12 0.00 41.26 5.25
3385 5130 1.439543 AGGCCTTCCAGTCAGAACTT 58.560 50.000 0.00 0.00 31.71 2.66
3402 5147 9.209175 GTCAGAACTTCAAATATCAGTAGTTGT 57.791 33.333 0.00 0.00 37.23 3.32
3417 5162 8.645730 TCAGTAGTTGTCAAACGTAAAATGTA 57.354 30.769 0.00 0.00 41.45 2.29
3448 5193 8.993121 ACTACACATTCTCACTGAATAAAGTTG 58.007 33.333 0.00 0.00 43.00 3.16
3482 5229 2.602257 AAAGTTTGCTTTCTGGTGGC 57.398 45.000 0.00 0.00 40.65 5.01
3483 5230 0.385390 AAGTTTGCTTTCTGGTGGCG 59.615 50.000 0.00 0.00 0.00 5.69
3484 5231 0.751643 AGTTTGCTTTCTGGTGGCGT 60.752 50.000 0.00 0.00 0.00 5.68
3485 5232 0.317854 GTTTGCTTTCTGGTGGCGTC 60.318 55.000 0.00 0.00 0.00 5.19
3486 5233 0.465460 TTTGCTTTCTGGTGGCGTCT 60.465 50.000 0.00 0.00 0.00 4.18
3487 5234 0.465460 TTGCTTTCTGGTGGCGTCTT 60.465 50.000 0.00 0.00 0.00 3.01
3488 5235 0.884704 TGCTTTCTGGTGGCGTCTTC 60.885 55.000 0.00 0.00 0.00 2.87
3529 5284 6.990939 TGTTCTGAAATTTTCATTGATTGGCA 59.009 30.769 12.04 0.00 39.30 4.92
3532 5287 8.447924 TCTGAAATTTTCATTGATTGGCAAAA 57.552 26.923 12.04 0.00 40.48 2.44
3534 5289 9.123709 CTGAAATTTTCATTGATTGGCAAAATG 57.876 29.630 15.36 15.36 40.48 2.32
3563 5390 9.918630 TTTAAGATTCAGGTACACAGTTACTAC 57.081 33.333 0.00 0.00 0.00 2.73
3564 5391 6.527057 AGATTCAGGTACACAGTTACTACC 57.473 41.667 0.00 0.00 0.00 3.18
3565 5392 6.014647 AGATTCAGGTACACAGTTACTACCA 58.985 40.000 5.04 0.00 33.54 3.25
3568 5395 7.400599 TTCAGGTACACAGTTACTACCATAG 57.599 40.000 5.04 0.00 33.54 2.23
3592 5454 2.748532 AGAGAGTAACAGACAGTACGCC 59.251 50.000 0.00 0.00 0.00 5.68
3593 5455 2.748532 GAGAGTAACAGACAGTACGCCT 59.251 50.000 0.00 0.00 0.00 5.52
3599 5461 1.067071 ACAGACAGTACGCCTTTAGCC 60.067 52.381 0.00 0.00 38.78 3.93
3677 5539 2.025981 AGAAATAGTGCCATGTCCAGCA 60.026 45.455 0.00 0.00 36.44 4.41
3724 5587 5.305128 ACAAATGGAACAGACATGGTCAATT 59.695 36.000 0.00 0.00 46.86 2.32
3821 5686 4.808414 TCTCTCTTCAACATCCGTGAAT 57.192 40.909 0.00 0.00 0.00 2.57
3837 5702 5.069383 TCCGTGAATATCCGGTGATTCTTAA 59.931 40.000 22.85 8.28 44.51 1.85
3904 5771 8.101309 TCTCAAATCCCAGTTTCCTTCATATA 57.899 34.615 0.00 0.00 0.00 0.86
3905 5772 8.727149 TCTCAAATCCCAGTTTCCTTCATATAT 58.273 33.333 0.00 0.00 0.00 0.86
3921 5788 7.254692 CCTTCATATATGTCACTTGAACAGCAG 60.255 40.741 12.42 0.00 0.00 4.24
3958 5825 1.348036 AGAAAACCTTGTCCGGGAGAG 59.652 52.381 0.00 0.00 0.00 3.20
3959 5826 1.071857 GAAAACCTTGTCCGGGAGAGT 59.928 52.381 0.00 0.00 0.00 3.24
3989 5856 4.583871 AGCAGACAGGAAACTTATCTTGG 58.416 43.478 0.00 0.00 40.21 3.61
4079 5946 0.250858 CAATGGTGCCAGTCAGGACA 60.251 55.000 1.84 0.00 41.22 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.201210 CACCCCCAATATGCCCCC 59.799 66.667 0.00 0.00 0.00 5.40
57 58 2.524148 GCACCCCCAATATGCCCC 60.524 66.667 0.00 0.00 33.06 5.80
58 59 2.912025 CGCACCCCCAATATGCCC 60.912 66.667 0.00 0.00 35.91 5.36
59 60 2.912025 CCGCACCCCCAATATGCC 60.912 66.667 0.00 0.00 35.91 4.40
60 61 3.605664 GCCGCACCCCCAATATGC 61.606 66.667 0.00 0.00 35.96 3.14
61 62 2.195567 CAGCCGCACCCCCAATATG 61.196 63.158 0.00 0.00 0.00 1.78
62 63 1.932156 TTCAGCCGCACCCCCAATAT 61.932 55.000 0.00 0.00 0.00 1.28
63 64 2.550699 CTTCAGCCGCACCCCCAATA 62.551 60.000 0.00 0.00 0.00 1.90
64 65 3.944250 CTTCAGCCGCACCCCCAAT 62.944 63.158 0.00 0.00 0.00 3.16
65 66 4.659172 CTTCAGCCGCACCCCCAA 62.659 66.667 0.00 0.00 0.00 4.12
67 68 4.115199 ATCTTCAGCCGCACCCCC 62.115 66.667 0.00 0.00 0.00 5.40
68 69 2.825836 CATCTTCAGCCGCACCCC 60.826 66.667 0.00 0.00 0.00 4.95
69 70 3.512516 GCATCTTCAGCCGCACCC 61.513 66.667 0.00 0.00 0.00 4.61
70 71 1.589716 AAAGCATCTTCAGCCGCACC 61.590 55.000 0.00 0.00 0.00 5.01
71 72 0.455633 CAAAGCATCTTCAGCCGCAC 60.456 55.000 0.00 0.00 0.00 5.34
72 73 0.606130 TCAAAGCATCTTCAGCCGCA 60.606 50.000 0.00 0.00 0.00 5.69
73 74 0.523072 TTCAAAGCATCTTCAGCCGC 59.477 50.000 0.00 0.00 0.00 6.53
74 75 2.421073 TGATTCAAAGCATCTTCAGCCG 59.579 45.455 0.00 0.00 0.00 5.52
75 76 4.650754 ATGATTCAAAGCATCTTCAGCC 57.349 40.909 0.00 0.00 26.60 4.85
76 77 5.647589 TGAATGATTCAAAGCATCTTCAGC 58.352 37.500 5.21 0.00 36.59 4.26
77 78 7.973944 TGAATGAATGATTCAAAGCATCTTCAG 59.026 33.333 12.36 0.00 46.19 3.02
78 79 7.832769 TGAATGAATGATTCAAAGCATCTTCA 58.167 30.769 12.36 12.01 46.19 3.02
89 90 6.676213 GCAACATCGAGTGAATGAATGATTCA 60.676 38.462 10.65 10.65 46.85 2.57
90 91 5.680229 GCAACATCGAGTGAATGAATGATTC 59.320 40.000 0.00 0.00 40.99 2.52
91 92 5.356190 AGCAACATCGAGTGAATGAATGATT 59.644 36.000 0.00 0.00 0.00 2.57
92 93 4.880120 AGCAACATCGAGTGAATGAATGAT 59.120 37.500 0.00 0.00 0.00 2.45
93 94 4.256110 AGCAACATCGAGTGAATGAATGA 58.744 39.130 0.00 0.00 0.00 2.57
94 95 4.331992 AGAGCAACATCGAGTGAATGAATG 59.668 41.667 0.00 0.00 0.00 2.67
95 96 4.511527 AGAGCAACATCGAGTGAATGAAT 58.488 39.130 0.00 0.00 0.00 2.57
96 97 3.930336 AGAGCAACATCGAGTGAATGAA 58.070 40.909 0.00 0.00 0.00 2.57
97 98 3.599730 AGAGCAACATCGAGTGAATGA 57.400 42.857 0.00 0.00 0.00 2.57
98 99 4.032217 GTGTAGAGCAACATCGAGTGAATG 59.968 45.833 0.00 0.00 0.00 2.67
99 100 4.177026 GTGTAGAGCAACATCGAGTGAAT 58.823 43.478 0.00 0.00 0.00 2.57
100 101 3.005367 TGTGTAGAGCAACATCGAGTGAA 59.995 43.478 0.00 0.00 0.00 3.18
101 102 2.556622 TGTGTAGAGCAACATCGAGTGA 59.443 45.455 0.00 0.00 0.00 3.41
102 103 2.946564 TGTGTAGAGCAACATCGAGTG 58.053 47.619 0.00 0.00 0.00 3.51
103 104 3.876274 ATGTGTAGAGCAACATCGAGT 57.124 42.857 0.00 0.00 0.00 4.18
104 105 3.928992 ACAATGTGTAGAGCAACATCGAG 59.071 43.478 0.00 0.00 0.00 4.04
105 106 3.679502 CACAATGTGTAGAGCAACATCGA 59.320 43.478 5.00 0.00 0.00 3.59
106 107 3.433274 ACACAATGTGTAGAGCAACATCG 59.567 43.478 18.40 0.00 45.56 3.84
117 118 2.415759 CGTACGGGCTACACAATGTGTA 60.416 50.000 22.95 22.95 45.56 2.90
119 120 0.996462 CGTACGGGCTACACAATGTG 59.004 55.000 12.40 12.40 39.75 3.21
120 121 0.738412 GCGTACGGGCTACACAATGT 60.738 55.000 18.39 0.00 0.00 2.71
121 122 1.748647 CGCGTACGGGCTACACAATG 61.749 60.000 19.76 0.00 34.97 2.82
122 123 1.517694 CGCGTACGGGCTACACAAT 60.518 57.895 19.76 0.00 34.97 2.71
123 124 2.126385 CGCGTACGGGCTACACAA 60.126 61.111 19.76 0.00 34.97 3.33
124 125 2.918345 AACGCGTACGGGCTACACA 61.918 57.895 29.56 0.00 46.04 3.72
125 126 2.126346 AACGCGTACGGGCTACAC 60.126 61.111 29.56 4.51 46.04 2.90
126 127 2.126385 CAACGCGTACGGGCTACA 60.126 61.111 29.56 0.00 46.04 2.74
127 128 2.154569 GTCAACGCGTACGGGCTAC 61.155 63.158 29.56 20.72 46.04 3.58
128 129 1.936436 ATGTCAACGCGTACGGGCTA 61.936 55.000 29.56 14.01 46.04 3.93
129 130 3.291101 ATGTCAACGCGTACGGGCT 62.291 57.895 29.56 17.17 46.04 5.19
130 131 2.812178 ATGTCAACGCGTACGGGC 60.812 61.111 29.56 15.20 46.04 6.13
131 132 0.804544 ATCATGTCAACGCGTACGGG 60.805 55.000 28.27 28.27 46.04 5.28
132 133 0.297525 CATCATGTCAACGCGTACGG 59.702 55.000 14.46 5.54 46.04 4.02
134 135 2.280708 GGTACATCATGTCAACGCGTAC 59.719 50.000 14.46 9.06 0.00 3.67
135 136 2.094649 TGGTACATCATGTCAACGCGTA 60.095 45.455 14.46 0.00 0.00 4.42
136 137 1.337354 TGGTACATCATGTCAACGCGT 60.337 47.619 5.58 5.58 0.00 6.01
137 138 1.355005 TGGTACATCATGTCAACGCG 58.645 50.000 3.53 3.53 0.00 6.01
151 152 5.130477 TGAACATCCCTCTTTCCTATGGTAC 59.870 44.000 0.00 0.00 0.00 3.34
152 153 5.285401 TGAACATCCCTCTTTCCTATGGTA 58.715 41.667 0.00 0.00 0.00 3.25
153 154 4.111577 TGAACATCCCTCTTTCCTATGGT 58.888 43.478 0.00 0.00 0.00 3.55
154 155 4.778213 TGAACATCCCTCTTTCCTATGG 57.222 45.455 0.00 0.00 0.00 2.74
155 156 7.041780 CGTAAATGAACATCCCTCTTTCCTATG 60.042 40.741 0.00 0.00 0.00 2.23
156 157 6.992715 CGTAAATGAACATCCCTCTTTCCTAT 59.007 38.462 0.00 0.00 0.00 2.57
157 158 6.070424 ACGTAAATGAACATCCCTCTTTCCTA 60.070 38.462 0.00 0.00 0.00 2.94
158 159 5.186198 CGTAAATGAACATCCCTCTTTCCT 58.814 41.667 0.00 0.00 0.00 3.36
159 160 4.941873 ACGTAAATGAACATCCCTCTTTCC 59.058 41.667 0.00 0.00 0.00 3.13
160 161 6.592607 TGTACGTAAATGAACATCCCTCTTTC 59.407 38.462 0.00 0.00 0.00 2.62
161 162 6.370718 GTGTACGTAAATGAACATCCCTCTTT 59.629 38.462 0.00 0.00 0.00 2.52
162 163 5.873164 GTGTACGTAAATGAACATCCCTCTT 59.127 40.000 0.00 0.00 0.00 2.85
163 164 5.046878 TGTGTACGTAAATGAACATCCCTCT 60.047 40.000 0.00 0.00 0.00 3.69
164 165 5.063060 GTGTGTACGTAAATGAACATCCCTC 59.937 44.000 0.00 0.00 0.00 4.30
165 166 4.933400 GTGTGTACGTAAATGAACATCCCT 59.067 41.667 0.00 0.00 0.00 4.20
166 167 4.691685 TGTGTGTACGTAAATGAACATCCC 59.308 41.667 0.00 0.00 0.00 3.85
167 168 5.407387 AGTGTGTGTACGTAAATGAACATCC 59.593 40.000 0.00 0.00 0.00 3.51
168 169 6.462073 AGTGTGTGTACGTAAATGAACATC 57.538 37.500 0.00 0.00 0.00 3.06
169 170 7.008901 CGATAGTGTGTGTACGTAAATGAACAT 59.991 37.037 0.00 0.00 0.00 2.71
170 171 6.306117 CGATAGTGTGTGTACGTAAATGAACA 59.694 38.462 0.00 0.00 0.00 3.18
171 172 6.524239 TCGATAGTGTGTGTACGTAAATGAAC 59.476 38.462 0.00 0.00 37.40 3.18
172 173 6.610456 TCGATAGTGTGTGTACGTAAATGAA 58.390 36.000 0.00 0.00 37.40 2.57
173 174 6.180771 TCGATAGTGTGTGTACGTAAATGA 57.819 37.500 0.00 0.00 37.40 2.57
174 175 6.858104 TTCGATAGTGTGTGTACGTAAATG 57.142 37.500 0.00 0.00 37.40 2.32
175 176 9.571810 TTTATTCGATAGTGTGTGTACGTAAAT 57.428 29.630 0.00 0.00 37.40 1.40
176 177 8.962857 TTTATTCGATAGTGTGTGTACGTAAA 57.037 30.769 0.00 0.00 37.40 2.01
177 178 7.218773 GCTTTATTCGATAGTGTGTGTACGTAA 59.781 37.037 0.00 0.00 37.40 3.18
178 179 6.688385 GCTTTATTCGATAGTGTGTGTACGTA 59.312 38.462 0.00 0.00 37.40 3.57
179 180 5.514204 GCTTTATTCGATAGTGTGTGTACGT 59.486 40.000 0.00 0.00 37.40 3.57
180 181 5.742453 AGCTTTATTCGATAGTGTGTGTACG 59.258 40.000 0.00 0.00 37.40 3.67
181 182 6.750501 TCAGCTTTATTCGATAGTGTGTGTAC 59.249 38.462 0.00 0.00 37.40 2.90
182 183 6.859017 TCAGCTTTATTCGATAGTGTGTGTA 58.141 36.000 0.00 0.00 37.40 2.90
183 184 5.720202 TCAGCTTTATTCGATAGTGTGTGT 58.280 37.500 0.00 0.00 37.40 3.72
184 185 6.237942 CCTTCAGCTTTATTCGATAGTGTGTG 60.238 42.308 0.00 0.00 37.40 3.82
185 186 5.812642 CCTTCAGCTTTATTCGATAGTGTGT 59.187 40.000 0.00 0.00 37.40 3.72
186 187 5.235186 CCCTTCAGCTTTATTCGATAGTGTG 59.765 44.000 0.00 0.00 37.40 3.82
191 192 3.135712 TGCCCCTTCAGCTTTATTCGATA 59.864 43.478 0.00 0.00 0.00 2.92
192 193 2.092429 TGCCCCTTCAGCTTTATTCGAT 60.092 45.455 0.00 0.00 0.00 3.59
208 209 1.475751 CCATCTCACACATACTGCCCC 60.476 57.143 0.00 0.00 0.00 5.80
223 224 2.684881 GTTTCAACGGATCATGCCATCT 59.315 45.455 0.00 0.00 0.00 2.90
256 257 5.862924 AGTACACCAATGTCTCAAATTCG 57.137 39.130 0.00 0.00 40.48 3.34
327 328 7.396540 AACTGGTGGATATTCATCAAAGTTC 57.603 36.000 0.00 0.00 32.32 3.01
347 348 2.728846 CGGACGGAATTCATGCAAACTG 60.729 50.000 7.93 0.00 0.00 3.16
348 349 1.468520 CGGACGGAATTCATGCAAACT 59.531 47.619 7.93 0.00 0.00 2.66
362 363 1.074872 GGTTTCGACTTAGCGGACGG 61.075 60.000 0.00 0.00 0.00 4.79
384 385 2.669391 GCTGCCCGCATATATTTCAAGC 60.669 50.000 0.00 0.00 38.92 4.01
416 417 1.890979 GACATGGATGCTGGAGCCG 60.891 63.158 0.00 0.00 41.18 5.52
459 460 1.949465 ATTTGCTCCGGTATTCGTCC 58.051 50.000 0.00 0.00 37.11 4.79
482 483 1.811266 CATCTCCAACGCTGACCCG 60.811 63.158 0.00 0.00 0.00 5.28
579 580 4.022849 GGTTGGTTTCATCAGAAGGAACAG 60.023 45.833 0.00 0.00 34.71 3.16
580 581 3.888930 GGTTGGTTTCATCAGAAGGAACA 59.111 43.478 0.00 0.00 34.71 3.18
588 589 1.993956 TGGTGGGTTGGTTTCATCAG 58.006 50.000 0.00 0.00 0.00 2.90
613 614 4.764823 CACCAATGCCAAGTTTAGGACTTA 59.235 41.667 0.00 0.00 46.75 2.24
736 737 1.261480 ATGAGCACCTTCGAGTGACT 58.739 50.000 8.85 5.47 40.34 3.41
764 765 1.376683 TACAACGCAGATGCCCACC 60.377 57.895 0.00 0.00 37.91 4.61
939 2406 7.230510 TGCAAACAACAAGTAACTCTATCCAAT 59.769 33.333 0.00 0.00 0.00 3.16
1169 2837 3.238108 CCATCAGTGGTGACTCACTAC 57.762 52.381 15.96 15.96 45.24 2.73
1622 3298 0.036875 CAGTTCCTCGGGCCTTTTCT 59.963 55.000 0.84 0.00 0.00 2.52
1629 3305 0.034896 TTCAGTTCAGTTCCTCGGGC 59.965 55.000 0.00 0.00 0.00 6.13
1641 3317 4.058817 ACAGATTCGGTTCAGTTCAGTTC 58.941 43.478 0.00 0.00 0.00 3.01
1656 3332 2.543578 TGCACAAGCGGACAGATTC 58.456 52.632 0.00 0.00 46.23 2.52
1930 3606 1.524621 GCCCAGCATGCAGTCGTAT 60.525 57.895 21.98 0.00 31.97 3.06
2189 3865 9.133627 CACCGTGAGATGTATGAAAATCTATAG 57.866 37.037 0.00 0.00 33.26 1.31
2190 3866 8.856103 TCACCGTGAGATGTATGAAAATCTATA 58.144 33.333 0.00 0.00 33.26 1.31
2191 3867 7.726216 TCACCGTGAGATGTATGAAAATCTAT 58.274 34.615 0.00 0.00 33.26 1.98
2192 3868 7.107639 TCACCGTGAGATGTATGAAAATCTA 57.892 36.000 0.00 0.00 33.26 1.98
2209 3885 4.390603 TCAACCGAATAATTTCTCACCGTG 59.609 41.667 0.00 0.00 0.00 4.94
2210 3886 4.390909 GTCAACCGAATAATTTCTCACCGT 59.609 41.667 0.00 0.00 0.00 4.83
2211 3887 4.630069 AGTCAACCGAATAATTTCTCACCG 59.370 41.667 0.00 0.00 0.00 4.94
2212 3888 7.787725 ATAGTCAACCGAATAATTTCTCACC 57.212 36.000 0.00 0.00 0.00 4.02
2224 3939 4.000325 CACCATGTCAATAGTCAACCGAA 59.000 43.478 0.00 0.00 0.00 4.30
2226 3941 2.677836 CCACCATGTCAATAGTCAACCG 59.322 50.000 0.00 0.00 0.00 4.44
2227 3942 3.016736 CCCACCATGTCAATAGTCAACC 58.983 50.000 0.00 0.00 0.00 3.77
2228 3943 3.016736 CCCCACCATGTCAATAGTCAAC 58.983 50.000 0.00 0.00 0.00 3.18
2230 3945 1.563879 CCCCCACCATGTCAATAGTCA 59.436 52.381 0.00 0.00 0.00 3.41
2231 3946 1.564348 ACCCCCACCATGTCAATAGTC 59.436 52.381 0.00 0.00 0.00 2.59
2232 3947 1.681229 ACCCCCACCATGTCAATAGT 58.319 50.000 0.00 0.00 0.00 2.12
2233 3948 2.826674 AACCCCCACCATGTCAATAG 57.173 50.000 0.00 0.00 0.00 1.73
2234 3949 3.169099 CAAAACCCCCACCATGTCAATA 58.831 45.455 0.00 0.00 0.00 1.90
2235 3950 1.977129 CAAAACCCCCACCATGTCAAT 59.023 47.619 0.00 0.00 0.00 2.57
2236 3951 1.343478 ACAAAACCCCCACCATGTCAA 60.343 47.619 0.00 0.00 0.00 3.18
2237 3952 0.263172 ACAAAACCCCCACCATGTCA 59.737 50.000 0.00 0.00 0.00 3.58
2239 3954 0.263172 TCACAAAACCCCCACCATGT 59.737 50.000 0.00 0.00 0.00 3.21
2240 3955 1.643310 ATCACAAAACCCCCACCATG 58.357 50.000 0.00 0.00 0.00 3.66
2241 3956 2.414250 AATCACAAAACCCCCACCAT 57.586 45.000 0.00 0.00 0.00 3.55
2242 3957 2.171448 CAAAATCACAAAACCCCCACCA 59.829 45.455 0.00 0.00 0.00 4.17
2243 3958 2.844946 CAAAATCACAAAACCCCCACC 58.155 47.619 0.00 0.00 0.00 4.61
2244 3959 2.217750 GCAAAATCACAAAACCCCCAC 58.782 47.619 0.00 0.00 0.00 4.61
2245 3960 1.839994 TGCAAAATCACAAAACCCCCA 59.160 42.857 0.00 0.00 0.00 4.96
2246 3961 2.493035 CTGCAAAATCACAAAACCCCC 58.507 47.619 0.00 0.00 0.00 5.40
2247 3962 1.872952 GCTGCAAAATCACAAAACCCC 59.127 47.619 0.00 0.00 0.00 4.95
2248 3963 2.287644 GTGCTGCAAAATCACAAAACCC 59.712 45.455 2.77 0.00 0.00 4.11
2249 3964 2.033832 CGTGCTGCAAAATCACAAAACC 60.034 45.455 2.77 0.00 0.00 3.27
2250 3965 2.857152 TCGTGCTGCAAAATCACAAAAC 59.143 40.909 2.77 0.00 0.00 2.43
2251 3966 2.857152 GTCGTGCTGCAAAATCACAAAA 59.143 40.909 2.77 0.00 0.00 2.44
2252 3967 2.458951 GTCGTGCTGCAAAATCACAAA 58.541 42.857 2.77 0.00 0.00 2.83
2253 3968 1.268999 GGTCGTGCTGCAAAATCACAA 60.269 47.619 2.77 0.00 0.00 3.33
2254 3969 0.310543 GGTCGTGCTGCAAAATCACA 59.689 50.000 2.77 0.00 0.00 3.58
2323 4038 2.222886 CCGGAGTAGATGTCGATGTCT 58.777 52.381 0.00 7.54 0.00 3.41
2411 4126 2.437895 TCTCACGCCGACGGAGAT 60.438 61.111 25.04 5.77 46.04 2.75
2462 4177 2.910319 TGCTGTTGGTGTACCTTAGGAT 59.090 45.455 4.77 0.00 36.82 3.24
3166 4896 1.697432 CGTATCTTATGGGCCCCTTCA 59.303 52.381 22.27 0.00 0.00 3.02
3178 4908 0.231534 CGTCGAGCTCGCGTATCTTA 59.768 55.000 30.99 13.67 39.60 2.10
3180 4910 2.172372 ACGTCGAGCTCGCGTATCT 61.172 57.895 38.01 23.63 44.89 1.98
3296 5041 0.600557 ATGCGAGGAGGAGCTTATCG 59.399 55.000 0.00 0.00 36.51 2.92
3351 5096 1.592400 GCCTTTGTTTTGCGCTGCT 60.592 52.632 9.73 0.00 0.00 4.24
3356 5101 0.103937 TGGAAGGCCTTTGTTTTGCG 59.896 50.000 21.54 0.00 34.31 4.85
3385 5130 7.956420 ACGTTTGACAACTACTGATATTTGA 57.044 32.000 0.00 0.00 0.00 2.69
3402 5147 9.866936 GTGTAGTGAAATACATTTTACGTTTGA 57.133 29.630 0.00 0.00 40.09 2.69
3417 5162 9.725019 TTATTCAGTGAGAATGTGTAGTGAAAT 57.275 29.630 0.00 0.00 46.24 2.17
3425 5170 7.807977 ACAACTTTATTCAGTGAGAATGTGT 57.192 32.000 0.00 0.87 46.24 3.72
3468 5215 0.465460 AAGACGCCACCAGAAAGCAA 60.465 50.000 0.00 0.00 0.00 3.91
3478 5225 5.803020 ATCTTTTCATTAGAAGACGCCAC 57.197 39.130 0.00 0.00 34.96 5.01
3480 5227 8.398665 ACAATTATCTTTTCATTAGAAGACGCC 58.601 33.333 0.00 0.00 34.96 5.68
3481 5228 9.774742 AACAATTATCTTTTCATTAGAAGACGC 57.225 29.630 0.00 0.00 34.96 5.19
3532 5287 9.520515 AACTGTGTACCTGAATCTTAAAATCAT 57.479 29.630 0.00 0.00 0.00 2.45
3562 5389 7.176490 ACTGTCTGTTACTCTCTTACTATGGT 58.824 38.462 0.00 0.00 0.00 3.55
3563 5390 7.633193 ACTGTCTGTTACTCTCTTACTATGG 57.367 40.000 0.00 0.00 0.00 2.74
3564 5391 8.329583 CGTACTGTCTGTTACTCTCTTACTATG 58.670 40.741 0.00 0.00 0.00 2.23
3565 5392 7.011295 GCGTACTGTCTGTTACTCTCTTACTAT 59.989 40.741 0.00 0.00 0.00 2.12
3568 5395 5.323105 GCGTACTGTCTGTTACTCTCTTAC 58.677 45.833 0.00 0.00 0.00 2.34
3582 5444 0.248289 TGGGCTAAAGGCGTACTGTC 59.752 55.000 0.00 0.00 42.94 3.51
3592 5454 0.257039 ACCCTGATGCTGGGCTAAAG 59.743 55.000 9.05 0.00 45.01 1.85
3593 5455 1.211949 GTACCCTGATGCTGGGCTAAA 59.788 52.381 9.05 0.00 45.01 1.85
3599 5461 2.239400 TCGATAGTACCCTGATGCTGG 58.761 52.381 0.00 0.00 37.40 4.85
3677 5539 6.647481 TGTGTTTTATGTCTTACACGCAGTAT 59.353 34.615 0.00 0.00 41.61 2.12
3724 5587 3.427573 TCCTGTACTGTTTCGGATCTCA 58.572 45.455 0.00 0.00 0.00 3.27
3821 5686 6.079336 TGGTAGGATTAAGAATCACCGGATA 58.921 40.000 9.46 0.00 36.98 2.59
3837 5702 5.958987 GGTAGAATATGTAGCCTGGTAGGAT 59.041 44.000 0.00 0.00 37.67 3.24
3904 5771 1.971481 TGCTGCTGTTCAAGTGACAT 58.029 45.000 0.00 0.00 0.00 3.06
3905 5772 1.605232 CATGCTGCTGTTCAAGTGACA 59.395 47.619 0.00 0.00 0.00 3.58
3921 5788 7.205297 AGGTTTTCTTGCAATATCATACATGC 58.795 34.615 0.00 0.00 39.22 4.06
3958 5825 4.219725 AGTTTCCTGTCTGCTTCTAGAGAC 59.780 45.833 3.49 3.49 39.31 3.36
3959 5826 4.411927 AGTTTCCTGTCTGCTTCTAGAGA 58.588 43.478 0.00 0.00 0.00 3.10
3989 5856 4.677584 AGATCGACTGATGTAGCAACTTC 58.322 43.478 0.00 0.00 34.09 3.01
4079 5946 6.379133 TGCTGATCATTTCTTATGCCTTCTTT 59.621 34.615 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.