Multiple sequence alignment - TraesCS1D01G300000

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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 TraesCS1D01G300000 chr1D 100.000 2597 0 0 1 2597 398378837 398381433 0.000000e+00 4796
1 TraesCS1D01G300000 chr1D 85.904 830 72 21 715 1531 398121296 398122093 0.000000e+00 843
2 TraesCS1D01G300000 chr1D 84.411 866 102 21 821 1683 398246149 398246984 0.000000e+00 821
3 TraesCS1D01G300000 chr1D 84.685 666 78 13 975 1632 398093760 398094409 0.000000e+00 643
4 TraesCS1D01G300000 chr1D 85.455 165 18 2 280 438 291789640 291789476 1.600000e-37 167
5 TraesCS1D01G300000 chr1D 80.203 197 38 1 274 470 482932668 482932473 2.080000e-31 147
6 TraesCS1D01G300000 chr1B 91.734 2347 123 28 270 2591 533814635 533816935 0.000000e+00 3193
7 TraesCS1D01G300000 chr1B 83.312 797 93 17 836 1630 533759781 533760539 0.000000e+00 699
8 TraesCS1D01G300000 chr1B 80.567 988 122 42 723 1683 533747577 533748521 0.000000e+00 697
9 TraesCS1D01G300000 chr1A 91.205 1876 113 27 739 2597 495332200 495334040 0.000000e+00 2503
10 TraesCS1D01G300000 chr1A 85.335 866 99 16 821 1683 495320043 495320883 0.000000e+00 870
11 TraesCS1D01G300000 chr1A 86.654 547 63 4 998 1543 495306560 495307097 4.780000e-167 597
12 TraesCS1D01G300000 chr1A 81.281 203 29 2 280 474 363692934 363692733 3.460000e-34 156
13 TraesCS1D01G300000 chr1A 79.661 177 34 2 294 469 511489994 511489819 2.710000e-25 126
14 TraesCS1D01G300000 chr5D 80.126 795 99 38 739 1525 409454294 409455037 2.940000e-149 538
15 TraesCS1D01G300000 chr3D 83.871 186 28 2 291 475 33382457 33382641 2.660000e-40 176
16 TraesCS1D01G300000 chr3A 84.211 190 20 9 291 475 46168223 46168407 2.660000e-40 176
17 TraesCS1D01G300000 chr3B 84.049 163 21 5 316 475 56343222 56343382 4.480000e-33 152
18 TraesCS1D01G300000 chr2D 79.167 192 35 5 280 469 420582981 420582793 7.540000e-26 128


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 TraesCS1D01G300000 chr1D 398378837 398381433 2596 False 4796 4796 100.000 1 2597 1 chr1D.!!$F4 2596
1 TraesCS1D01G300000 chr1D 398121296 398122093 797 False 843 843 85.904 715 1531 1 chr1D.!!$F2 816
2 TraesCS1D01G300000 chr1D 398246149 398246984 835 False 821 821 84.411 821 1683 1 chr1D.!!$F3 862
3 TraesCS1D01G300000 chr1D 398093760 398094409 649 False 643 643 84.685 975 1632 1 chr1D.!!$F1 657
4 TraesCS1D01G300000 chr1B 533814635 533816935 2300 False 3193 3193 91.734 270 2591 1 chr1B.!!$F3 2321
5 TraesCS1D01G300000 chr1B 533759781 533760539 758 False 699 699 83.312 836 1630 1 chr1B.!!$F2 794
6 TraesCS1D01G300000 chr1B 533747577 533748521 944 False 697 697 80.567 723 1683 1 chr1B.!!$F1 960
7 TraesCS1D01G300000 chr1A 495332200 495334040 1840 False 2503 2503 91.205 739 2597 1 chr1A.!!$F3 1858
8 TraesCS1D01G300000 chr1A 495320043 495320883 840 False 870 870 85.335 821 1683 1 chr1A.!!$F2 862
9 TraesCS1D01G300000 chr1A 495306560 495307097 537 False 597 597 86.654 998 1543 1 chr1A.!!$F1 545
10 TraesCS1D01G300000 chr5D 409454294 409455037 743 False 538 538 80.126 739 1525 1 chr5D.!!$F1 786

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
215 216 0.031857 CACCGCTAGGCTCTCTGATG 59.968 60.0 0.0 0.0 42.76 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1735 1.450848 GGCATGCAGAGCTGTGCTA 60.451 57.895 32.77 20.9 44.32 3.49 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
19 20 3.491652 GCGCTTGAACCGAGCCTC 61.492 66.667 0.00 0.00 37.58 4.70
20 21 2.815647 CGCTTGAACCGAGCCTCC 60.816 66.667 0.00 0.00 37.58 4.30
21 22 2.436824 GCTTGAACCGAGCCTCCC 60.437 66.667 0.00 0.00 35.00 4.30
22 23 2.269241 CTTGAACCGAGCCTCCCC 59.731 66.667 0.00 0.00 0.00 4.81
23 24 3.665675 CTTGAACCGAGCCTCCCCG 62.666 68.421 0.00 0.00 0.00 5.73
72 73 4.373116 GCCCTGACGACGGCAAGA 62.373 66.667 4.25 0.00 45.01 3.02
73 74 2.125912 CCCTGACGACGGCAAGAG 60.126 66.667 4.25 0.00 0.00 2.85
74 75 2.636412 CCCTGACGACGGCAAGAGA 61.636 63.158 4.25 0.00 0.00 3.10
75 76 1.289066 CCTGACGACGGCAAGAGAA 59.711 57.895 4.25 0.00 0.00 2.87
76 77 0.734253 CCTGACGACGGCAAGAGAAG 60.734 60.000 4.25 0.00 0.00 2.85
77 78 0.241213 CTGACGACGGCAAGAGAAGA 59.759 55.000 4.25 0.00 0.00 2.87
78 79 0.671796 TGACGACGGCAAGAGAAGAA 59.328 50.000 0.00 0.00 0.00 2.52
79 80 1.335964 TGACGACGGCAAGAGAAGAAG 60.336 52.381 0.00 0.00 0.00 2.85
80 81 0.038159 ACGACGGCAAGAGAAGAAGG 60.038 55.000 0.00 0.00 0.00 3.46
81 82 1.355066 CGACGGCAAGAGAAGAAGGC 61.355 60.000 0.00 0.00 0.00 4.35
82 83 3.479370 CGGCAAGAGAAGAAGGCG 58.521 61.111 0.00 0.00 43.34 5.52
83 84 2.103042 CGGCAAGAGAAGAAGGCGG 61.103 63.158 0.00 0.00 44.83 6.13
84 85 2.402572 GGCAAGAGAAGAAGGCGGC 61.403 63.158 0.00 0.00 0.00 6.53
85 86 1.376553 GCAAGAGAAGAAGGCGGCT 60.377 57.895 5.25 5.25 0.00 5.52
86 87 0.108138 GCAAGAGAAGAAGGCGGCTA 60.108 55.000 13.71 0.00 0.00 3.93
87 88 1.933247 CAAGAGAAGAAGGCGGCTAG 58.067 55.000 13.71 0.00 0.00 3.42
88 89 0.827368 AAGAGAAGAAGGCGGCTAGG 59.173 55.000 13.71 0.00 0.00 3.02
89 90 1.045911 AGAGAAGAAGGCGGCTAGGG 61.046 60.000 13.71 0.00 0.00 3.53
90 91 1.306226 AGAAGAAGGCGGCTAGGGT 60.306 57.895 13.71 0.00 0.00 4.34
91 92 0.032416 AGAAGAAGGCGGCTAGGGTA 60.032 55.000 13.71 0.00 0.00 3.69
92 93 0.104487 GAAGAAGGCGGCTAGGGTAC 59.896 60.000 13.71 0.00 0.00 3.34
93 94 1.673808 AAGAAGGCGGCTAGGGTACG 61.674 60.000 13.71 0.00 0.00 3.67
94 95 3.148031 GAAGGCGGCTAGGGTACGG 62.148 68.421 13.71 0.00 0.00 4.02
97 98 4.151582 GCGGCTAGGGTACGGCAA 62.152 66.667 0.00 0.00 32.85 4.52
98 99 2.202837 CGGCTAGGGTACGGCAAC 60.203 66.667 0.00 0.00 0.00 4.17
99 100 2.188731 GGCTAGGGTACGGCAACC 59.811 66.667 0.00 0.00 38.94 3.77
100 101 2.662070 GGCTAGGGTACGGCAACCA 61.662 63.158 8.16 0.00 41.67 3.67
101 102 1.449070 GCTAGGGTACGGCAACCAC 60.449 63.158 8.16 0.00 41.67 4.16
102 103 1.219935 CTAGGGTACGGCAACCACC 59.780 63.158 8.16 0.00 41.67 4.61
103 104 1.229272 TAGGGTACGGCAACCACCT 60.229 57.895 8.16 0.00 41.67 4.00
104 105 0.837260 TAGGGTACGGCAACCACCTT 60.837 55.000 8.16 0.00 41.67 3.50
105 106 1.969589 GGGTACGGCAACCACCTTG 60.970 63.158 8.16 0.00 41.67 3.61
106 107 1.969589 GGTACGGCAACCACCTTGG 60.970 63.158 1.29 0.00 45.02 3.61
111 112 4.621087 GCAACCACCTTGGCCCCT 62.621 66.667 0.00 0.00 42.67 4.79
112 113 2.201210 CAACCACCTTGGCCCCTT 59.799 61.111 0.00 0.00 42.67 3.95
113 114 2.201210 AACCACCTTGGCCCCTTG 59.799 61.111 0.00 0.00 42.67 3.61
114 115 4.621087 ACCACCTTGGCCCCTTGC 62.621 66.667 0.00 0.00 42.67 4.01
115 116 4.619320 CCACCTTGGCCCCTTGCA 62.619 66.667 0.00 0.00 43.89 4.08
116 117 2.523902 CACCTTGGCCCCTTGCAA 60.524 61.111 0.00 0.00 43.89 4.08
117 118 2.139484 CACCTTGGCCCCTTGCAAA 61.139 57.895 0.00 0.00 43.89 3.68
119 120 3.875390 CTTGGCCCCTTGCAAAGT 58.125 55.556 0.00 0.00 44.69 2.66
120 121 1.368579 CTTGGCCCCTTGCAAAGTG 59.631 57.895 0.00 0.00 44.69 3.16
121 122 1.382420 TTGGCCCCTTGCAAAGTGT 60.382 52.632 0.00 0.00 44.25 3.55
122 123 0.980231 TTGGCCCCTTGCAAAGTGTT 60.980 50.000 0.00 0.00 44.25 3.32
123 124 0.105964 TGGCCCCTTGCAAAGTGTTA 60.106 50.000 0.00 0.00 44.25 2.41
124 125 0.317160 GGCCCCTTGCAAAGTGTTAC 59.683 55.000 0.00 0.00 44.25 2.50
125 126 1.328279 GCCCCTTGCAAAGTGTTACT 58.672 50.000 0.00 0.00 44.25 2.24
126 127 1.686587 GCCCCTTGCAAAGTGTTACTT 59.313 47.619 0.00 0.00 44.25 2.24
127 128 2.288213 GCCCCTTGCAAAGTGTTACTTC 60.288 50.000 0.00 0.00 44.25 3.01
128 129 2.296190 CCCCTTGCAAAGTGTTACTTCC 59.704 50.000 0.00 0.00 44.25 3.46
129 130 3.222603 CCCTTGCAAAGTGTTACTTCCT 58.777 45.455 0.00 0.00 44.25 3.36
130 131 3.636764 CCCTTGCAAAGTGTTACTTCCTT 59.363 43.478 0.00 0.00 44.25 3.36
131 132 4.261614 CCCTTGCAAAGTGTTACTTCCTTC 60.262 45.833 0.00 0.00 44.25 3.46
132 133 4.580580 CCTTGCAAAGTGTTACTTCCTTCT 59.419 41.667 0.00 0.00 44.25 2.85
133 134 5.067805 CCTTGCAAAGTGTTACTTCCTTCTT 59.932 40.000 0.00 0.00 44.25 2.52
134 135 6.405842 CCTTGCAAAGTGTTACTTCCTTCTTT 60.406 38.462 0.00 0.00 44.25 2.52
135 136 6.524101 TGCAAAGTGTTACTTCCTTCTTTT 57.476 33.333 0.00 0.00 37.47 2.27
136 137 6.560711 TGCAAAGTGTTACTTCCTTCTTTTC 58.439 36.000 0.00 0.00 37.47 2.29
137 138 6.377146 TGCAAAGTGTTACTTCCTTCTTTTCT 59.623 34.615 0.00 0.00 37.47 2.52
138 139 6.693113 GCAAAGTGTTACTTCCTTCTTTTCTG 59.307 38.462 0.00 0.00 37.47 3.02
139 140 7.628580 GCAAAGTGTTACTTCCTTCTTTTCTGT 60.629 37.037 0.00 0.00 37.47 3.41
140 141 7.555306 AAGTGTTACTTCCTTCTTTTCTGTC 57.445 36.000 0.00 0.00 31.77 3.51
141 142 6.890293 AGTGTTACTTCCTTCTTTTCTGTCT 58.110 36.000 0.00 0.00 0.00 3.41
142 143 8.019656 AGTGTTACTTCCTTCTTTTCTGTCTA 57.980 34.615 0.00 0.00 0.00 2.59
143 144 8.145122 AGTGTTACTTCCTTCTTTTCTGTCTAG 58.855 37.037 0.00 0.00 0.00 2.43
144 145 6.929606 TGTTACTTCCTTCTTTTCTGTCTAGC 59.070 38.462 0.00 0.00 0.00 3.42
145 146 5.552870 ACTTCCTTCTTTTCTGTCTAGCA 57.447 39.130 0.00 0.00 0.00 3.49
146 147 5.930135 ACTTCCTTCTTTTCTGTCTAGCAA 58.070 37.500 0.00 0.00 0.00 3.91
147 148 5.994668 ACTTCCTTCTTTTCTGTCTAGCAAG 59.005 40.000 0.00 0.00 0.00 4.01
148 149 4.319177 TCCTTCTTTTCTGTCTAGCAAGC 58.681 43.478 0.00 0.00 0.00 4.01
149 150 4.067896 CCTTCTTTTCTGTCTAGCAAGCA 58.932 43.478 0.00 0.00 0.00 3.91
150 151 4.153835 CCTTCTTTTCTGTCTAGCAAGCAG 59.846 45.833 0.00 0.00 0.00 4.24
151 152 4.342862 TCTTTTCTGTCTAGCAAGCAGT 57.657 40.909 0.00 0.00 32.22 4.40
152 153 4.708177 TCTTTTCTGTCTAGCAAGCAGTT 58.292 39.130 0.00 0.00 32.22 3.16
153 154 4.752101 TCTTTTCTGTCTAGCAAGCAGTTC 59.248 41.667 0.00 0.00 32.22 3.01
154 155 3.751479 TTCTGTCTAGCAAGCAGTTCA 57.249 42.857 0.00 0.00 32.22 3.18
155 156 3.309961 TCTGTCTAGCAAGCAGTTCAG 57.690 47.619 0.00 0.00 32.22 3.02
156 157 2.630098 TCTGTCTAGCAAGCAGTTCAGT 59.370 45.455 0.00 0.00 32.22 3.41
157 158 3.826729 TCTGTCTAGCAAGCAGTTCAGTA 59.173 43.478 0.00 0.00 32.22 2.74
158 159 3.914312 TGTCTAGCAAGCAGTTCAGTAC 58.086 45.455 0.00 0.00 0.00 2.73
159 160 3.574396 TGTCTAGCAAGCAGTTCAGTACT 59.426 43.478 0.00 0.00 37.68 2.73
195 196 5.633996 ATTACATTGTTTTGTTGTGTGCG 57.366 34.783 0.00 0.00 0.00 5.34
196 197 1.658095 ACATTGTTTTGTTGTGTGCGC 59.342 42.857 0.00 0.00 0.00 6.09
197 198 1.657594 CATTGTTTTGTTGTGTGCGCA 59.342 42.857 5.66 5.66 0.00 6.09
198 199 1.063806 TTGTTTTGTTGTGTGCGCAC 58.936 45.000 33.11 33.11 45.44 5.34
199 200 0.734253 TGTTTTGTTGTGTGCGCACC 60.734 50.000 35.72 26.31 44.65 5.01
200 201 1.515088 TTTTGTTGTGTGCGCACCG 60.515 52.632 35.72 0.00 44.65 4.94
211 212 3.522731 CGCACCGCTAGGCTCTCT 61.523 66.667 0.00 0.00 42.76 3.10
212 213 2.105930 GCACCGCTAGGCTCTCTG 59.894 66.667 0.00 0.00 42.76 3.35
213 214 2.418910 GCACCGCTAGGCTCTCTGA 61.419 63.158 0.00 0.00 42.76 3.27
214 215 1.743321 GCACCGCTAGGCTCTCTGAT 61.743 60.000 0.00 0.00 42.76 2.90
215 216 0.031857 CACCGCTAGGCTCTCTGATG 59.968 60.000 0.00 0.00 42.76 3.07
216 217 0.106469 ACCGCTAGGCTCTCTGATGA 60.106 55.000 0.00 0.00 42.76 2.92
217 218 1.035923 CCGCTAGGCTCTCTGATGAA 58.964 55.000 0.00 0.00 0.00 2.57
218 219 1.000385 CCGCTAGGCTCTCTGATGAAG 60.000 57.143 0.00 0.00 0.00 3.02
219 220 1.602668 CGCTAGGCTCTCTGATGAAGC 60.603 57.143 0.00 0.00 0.00 3.86
220 221 1.602668 GCTAGGCTCTCTGATGAAGCG 60.603 57.143 0.00 0.00 0.00 4.68
221 222 1.952990 CTAGGCTCTCTGATGAAGCGA 59.047 52.381 0.00 0.00 0.00 4.93
222 223 1.412079 AGGCTCTCTGATGAAGCGAT 58.588 50.000 0.00 0.00 0.00 4.58
223 224 2.591923 AGGCTCTCTGATGAAGCGATA 58.408 47.619 0.00 0.00 0.00 2.92
224 225 2.557924 AGGCTCTCTGATGAAGCGATAG 59.442 50.000 0.00 0.00 0.00 2.08
236 237 2.050895 CGATAGCCGACCGAGCTG 60.051 66.667 13.05 0.00 41.71 4.24
237 238 2.355244 GATAGCCGACCGAGCTGC 60.355 66.667 13.05 0.00 41.71 5.25
238 239 3.138930 GATAGCCGACCGAGCTGCA 62.139 63.158 1.02 0.00 41.71 4.41
239 240 2.427540 GATAGCCGACCGAGCTGCAT 62.428 60.000 1.02 3.10 41.71 3.96
240 241 2.032860 ATAGCCGACCGAGCTGCATT 62.033 55.000 1.02 0.00 41.71 3.56
241 242 2.238847 TAGCCGACCGAGCTGCATTT 62.239 55.000 1.02 0.00 41.71 2.32
242 243 1.813753 GCCGACCGAGCTGCATTTA 60.814 57.895 1.02 0.00 0.00 1.40
243 244 2.006772 CCGACCGAGCTGCATTTAC 58.993 57.895 1.02 0.00 0.00 2.01
244 245 1.429148 CCGACCGAGCTGCATTTACC 61.429 60.000 1.02 0.00 0.00 2.85
245 246 0.739462 CGACCGAGCTGCATTTACCA 60.739 55.000 1.02 0.00 0.00 3.25
246 247 1.009829 GACCGAGCTGCATTTACCAG 58.990 55.000 1.02 0.00 0.00 4.00
247 248 0.324943 ACCGAGCTGCATTTACCAGT 59.675 50.000 1.02 0.00 32.93 4.00
248 249 1.271379 ACCGAGCTGCATTTACCAGTT 60.271 47.619 1.02 0.00 32.93 3.16
249 250 1.398390 CCGAGCTGCATTTACCAGTTC 59.602 52.381 1.02 0.00 37.24 3.01
250 251 2.076100 CGAGCTGCATTTACCAGTTCA 58.924 47.619 1.02 0.00 39.57 3.18
251 252 2.483877 CGAGCTGCATTTACCAGTTCAA 59.516 45.455 1.02 0.00 39.57 2.69
252 253 3.058293 CGAGCTGCATTTACCAGTTCAAA 60.058 43.478 1.02 0.00 39.57 2.69
253 254 4.479619 GAGCTGCATTTACCAGTTCAAAG 58.520 43.478 1.02 0.00 39.45 2.77
254 255 2.989166 GCTGCATTTACCAGTTCAAAGC 59.011 45.455 0.00 0.00 32.93 3.51
255 256 3.578688 CTGCATTTACCAGTTCAAAGCC 58.421 45.455 0.00 0.00 0.00 4.35
256 257 2.298729 TGCATTTACCAGTTCAAAGCCC 59.701 45.455 0.00 0.00 0.00 5.19
257 258 2.298729 GCATTTACCAGTTCAAAGCCCA 59.701 45.455 0.00 0.00 0.00 5.36
258 259 3.055891 GCATTTACCAGTTCAAAGCCCAT 60.056 43.478 0.00 0.00 0.00 4.00
259 260 4.563374 GCATTTACCAGTTCAAAGCCCATT 60.563 41.667 0.00 0.00 0.00 3.16
260 261 5.337169 GCATTTACCAGTTCAAAGCCCATTA 60.337 40.000 0.00 0.00 0.00 1.90
261 262 6.630188 GCATTTACCAGTTCAAAGCCCATTAT 60.630 38.462 0.00 0.00 0.00 1.28
262 263 6.926630 TTTACCAGTTCAAAGCCCATTATT 57.073 33.333 0.00 0.00 0.00 1.40
263 264 6.926630 TTACCAGTTCAAAGCCCATTATTT 57.073 33.333 0.00 0.00 0.00 1.40
264 265 8.423906 TTTACCAGTTCAAAGCCCATTATTTA 57.576 30.769 0.00 0.00 0.00 1.40
265 266 6.926630 ACCAGTTCAAAGCCCATTATTTAA 57.073 33.333 0.00 0.00 0.00 1.52
266 267 7.309770 ACCAGTTCAAAGCCCATTATTTAAA 57.690 32.000 0.00 0.00 0.00 1.52
267 268 7.740805 ACCAGTTCAAAGCCCATTATTTAAAA 58.259 30.769 0.00 0.00 0.00 1.52
268 269 7.659799 ACCAGTTCAAAGCCCATTATTTAAAAC 59.340 33.333 0.00 0.00 0.00 2.43
269 270 7.877612 CCAGTTCAAAGCCCATTATTTAAAACT 59.122 33.333 0.00 0.00 30.12 2.66
270 271 9.921637 CAGTTCAAAGCCCATTATTTAAAACTA 57.078 29.630 0.00 0.00 29.53 2.24
275 276 9.366216 CAAAGCCCATTATTTAAAACTAGAACC 57.634 33.333 0.00 0.00 0.00 3.62
276 277 8.895141 AAGCCCATTATTTAAAACTAGAACCT 57.105 30.769 0.00 0.00 0.00 3.50
277 278 9.984590 AAGCCCATTATTTAAAACTAGAACCTA 57.015 29.630 0.00 0.00 0.00 3.08
278 279 9.984590 AGCCCATTATTTAAAACTAGAACCTAA 57.015 29.630 0.00 0.00 0.00 2.69
325 326 3.661944 TGCATGGCAAATCGAATGTTTT 58.338 36.364 0.00 0.00 34.76 2.43
367 368 3.334691 CGAGGATGGCAAGTTTAGTTGA 58.665 45.455 0.00 0.00 0.00 3.18
376 377 3.186409 GCAAGTTTAGTTGACGAGCATGA 59.814 43.478 0.00 0.00 0.00 3.07
380 381 4.449068 AGTTTAGTTGACGAGCATGACAAG 59.551 41.667 0.00 0.00 0.00 3.16
384 385 1.418373 TGACGAGCATGACAAGTTCG 58.582 50.000 14.14 14.14 43.85 3.95
387 388 1.016130 CGAGCATGACAAGTTCGCCT 61.016 55.000 4.05 0.00 33.26 5.52
390 391 1.970917 GCATGACAAGTTCGCCTCGG 61.971 60.000 0.00 0.00 0.00 4.63
444 446 5.932021 CAAACTAAATTTGCTATCACGGC 57.068 39.130 0.00 0.00 41.30 5.68
448 450 1.724582 AATTTGCTATCACGGCGCCC 61.725 55.000 23.46 5.06 0.00 6.13
508 510 3.774702 GGTTGCGACGCCGTCTTC 61.775 66.667 18.69 7.50 38.24 2.87
600 602 1.300388 CCCAGGTTCGTTCGTTCGT 60.300 57.895 0.00 0.00 0.00 3.85
603 605 0.158096 CAGGTTCGTTCGTTCGTTCG 59.842 55.000 2.67 0.00 0.00 3.95
604 606 0.248621 AGGTTCGTTCGTTCGTTCGT 60.249 50.000 9.89 0.00 0.00 3.85
605 607 0.572125 GGTTCGTTCGTTCGTTCGTT 59.428 50.000 9.89 0.00 0.00 3.85
606 608 1.628985 GTTCGTTCGTTCGTTCGTTG 58.371 50.000 9.89 0.00 0.00 4.10
607 609 0.571661 TTCGTTCGTTCGTTCGTTGG 59.428 50.000 9.89 0.00 0.00 3.77
608 610 0.525242 TCGTTCGTTCGTTCGTTGGT 60.525 50.000 9.89 0.00 0.00 3.67
609 611 0.298411 CGTTCGTTCGTTCGTTGGTT 59.702 50.000 2.67 0.00 0.00 3.67
610 612 1.651773 CGTTCGTTCGTTCGTTGGTTC 60.652 52.381 2.67 0.00 0.00 3.62
611 613 0.929615 TTCGTTCGTTCGTTGGTTCC 59.070 50.000 2.67 0.00 0.00 3.62
711 713 3.036084 CGTGTGTGCGTGTCCCTC 61.036 66.667 0.00 0.00 0.00 4.30
712 714 2.665185 GTGTGTGCGTGTCCCTCC 60.665 66.667 0.00 0.00 0.00 4.30
713 715 3.936203 TGTGTGCGTGTCCCTCCC 61.936 66.667 0.00 0.00 0.00 4.30
752 760 3.608662 GCAGGCTGCAACTTGGCA 61.609 61.111 33.33 0.00 44.26 4.92
777 787 1.265905 AGCGCCCTTTTTCAAAGTACG 59.734 47.619 2.29 4.59 0.00 3.67
857 876 2.125753 CCACGACCAGAGCAGAGC 60.126 66.667 0.00 0.00 0.00 4.09
1473 1554 4.052518 GCCTGGCTGGTGTCCCAT 62.053 66.667 12.43 0.00 40.90 4.00
1654 1735 1.095228 CGGACACAGCACAACAAGGT 61.095 55.000 0.00 0.00 0.00 3.50
1683 1764 4.462280 GCATGCCCAAGCCCTTGC 62.462 66.667 6.36 0.00 39.16 4.01
1708 1789 1.269206 CCATTTTCCGGCATCGATTGG 60.269 52.381 0.00 0.00 39.00 3.16
1716 1797 3.174790 GCATCGATTGGCATGCTTC 57.825 52.632 18.92 11.24 41.93 3.86
1717 1798 0.382873 GCATCGATTGGCATGCTTCA 59.617 50.000 18.92 4.93 41.93 3.02
1741 1825 2.747460 CCAGGCGCTGCTTGCTAA 60.747 61.111 7.64 0.00 40.11 3.09
1746 1830 1.656818 GGCGCTGCTTGCTAATGGAA 61.657 55.000 7.64 0.00 40.11 3.53
1747 1831 0.171007 GCGCTGCTTGCTAATGGAAA 59.829 50.000 0.00 0.00 40.11 3.13
1811 1898 1.264288 GCAGAACACTGTACTGGCAAC 59.736 52.381 4.66 0.00 34.51 4.17
1822 1909 2.425592 TGGCAACCTGACAGACCG 59.574 61.111 3.32 0.00 28.05 4.79
2185 2275 4.778415 CCAGCTCCGTCCGTCGTG 62.778 72.222 0.00 0.00 37.94 4.35
2291 2384 1.947456 GTTCAGTTCAACCACCTGGAC 59.053 52.381 0.00 0.00 38.94 4.02
2379 2476 5.733937 GCCGACTAAAACTATCTCAGGAGTC 60.734 48.000 0.00 0.00 0.00 3.36
2380 2477 5.357314 CCGACTAAAACTATCTCAGGAGTCA 59.643 44.000 0.00 0.00 33.28 3.41
2381 2478 6.459024 CCGACTAAAACTATCTCAGGAGTCAG 60.459 46.154 0.00 0.00 33.28 3.51
2382 2479 6.459024 CGACTAAAACTATCTCAGGAGTCAGG 60.459 46.154 0.00 0.00 33.28 3.86
2383 2480 6.494952 ACTAAAACTATCTCAGGAGTCAGGA 58.505 40.000 0.00 0.00 0.00 3.86
2384 2481 5.930837 AAAACTATCTCAGGAGTCAGGAG 57.069 43.478 4.38 4.38 0.00 3.69
2385 2482 4.601406 AACTATCTCAGGAGTCAGGAGT 57.399 45.455 9.35 2.20 0.00 3.85
2408 2505 0.821711 CACTTCCGTGGCCAAAGGAA 60.822 55.000 30.76 30.76 41.28 3.36
2414 2511 1.000274 CCGTGGCCAAAGGAAGAAAAG 60.000 52.381 20.78 0.00 0.00 2.27
2416 2513 2.039418 GTGGCCAAAGGAAGAAAAGGT 58.961 47.619 7.24 0.00 0.00 3.50
2480 2578 3.570125 TGGTGGCTCGATTACTCTATCTG 59.430 47.826 0.00 0.00 0.00 2.90
2513 2611 5.409520 ACCATGAATCATCACGTATACATGC 59.590 40.000 3.32 0.00 38.69 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.491652 GAGGCTCGGTTCAAGCGC 61.492 66.667 3.51 0.00 40.77 5.92
3 4 2.815647 GGAGGCTCGGTTCAAGCG 60.816 66.667 8.69 1.56 40.77 4.68
4 5 2.436824 GGGAGGCTCGGTTCAAGC 60.437 66.667 8.69 0.00 39.09 4.01
6 7 3.702048 CGGGGAGGCTCGGTTCAA 61.702 66.667 8.69 0.00 0.00 2.69
56 57 2.125912 CTCTTGCCGTCGTCAGGG 60.126 66.667 0.00 0.00 0.00 4.45
57 58 0.734253 CTTCTCTTGCCGTCGTCAGG 60.734 60.000 0.00 0.00 0.00 3.86
58 59 0.241213 TCTTCTCTTGCCGTCGTCAG 59.759 55.000 0.00 0.00 0.00 3.51
59 60 0.671796 TTCTTCTCTTGCCGTCGTCA 59.328 50.000 0.00 0.00 0.00 4.35
60 61 1.341606 CTTCTTCTCTTGCCGTCGTC 58.658 55.000 0.00 0.00 0.00 4.20
61 62 0.038159 CCTTCTTCTCTTGCCGTCGT 60.038 55.000 0.00 0.00 0.00 4.34
62 63 1.355066 GCCTTCTTCTCTTGCCGTCG 61.355 60.000 0.00 0.00 0.00 5.12
63 64 1.355066 CGCCTTCTTCTCTTGCCGTC 61.355 60.000 0.00 0.00 0.00 4.79
64 65 1.374758 CGCCTTCTTCTCTTGCCGT 60.375 57.895 0.00 0.00 0.00 5.68
65 66 2.103042 CCGCCTTCTTCTCTTGCCG 61.103 63.158 0.00 0.00 0.00 5.69
66 67 2.402572 GCCGCCTTCTTCTCTTGCC 61.403 63.158 0.00 0.00 0.00 4.52
67 68 0.108138 TAGCCGCCTTCTTCTCTTGC 60.108 55.000 0.00 0.00 0.00 4.01
68 69 1.472376 CCTAGCCGCCTTCTTCTCTTG 60.472 57.143 0.00 0.00 0.00 3.02
69 70 0.827368 CCTAGCCGCCTTCTTCTCTT 59.173 55.000 0.00 0.00 0.00 2.85
70 71 1.045911 CCCTAGCCGCCTTCTTCTCT 61.046 60.000 0.00 0.00 0.00 3.10
71 72 1.331399 ACCCTAGCCGCCTTCTTCTC 61.331 60.000 0.00 0.00 0.00 2.87
72 73 0.032416 TACCCTAGCCGCCTTCTTCT 60.032 55.000 0.00 0.00 0.00 2.85
73 74 0.104487 GTACCCTAGCCGCCTTCTTC 59.896 60.000 0.00 0.00 0.00 2.87
74 75 1.673808 CGTACCCTAGCCGCCTTCTT 61.674 60.000 0.00 0.00 0.00 2.52
75 76 2.125961 CGTACCCTAGCCGCCTTCT 61.126 63.158 0.00 0.00 0.00 2.85
76 77 2.416260 CGTACCCTAGCCGCCTTC 59.584 66.667 0.00 0.00 0.00 3.46
77 78 3.152400 CCGTACCCTAGCCGCCTT 61.152 66.667 0.00 0.00 0.00 4.35
80 81 4.151582 TTGCCGTACCCTAGCCGC 62.152 66.667 0.00 0.00 0.00 6.53
81 82 2.202837 GTTGCCGTACCCTAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
82 83 2.188731 GGTTGCCGTACCCTAGCC 59.811 66.667 0.00 0.00 31.71 3.93
83 84 1.449070 GTGGTTGCCGTACCCTAGC 60.449 63.158 0.00 0.00 37.39 3.42
84 85 1.219935 GGTGGTTGCCGTACCCTAG 59.780 63.158 0.00 0.00 37.39 3.02
85 86 0.837260 AAGGTGGTTGCCGTACCCTA 60.837 55.000 0.00 0.00 37.39 3.53
86 87 2.151388 AAGGTGGTTGCCGTACCCT 61.151 57.895 0.00 0.00 37.39 4.34
87 88 1.969589 CAAGGTGGTTGCCGTACCC 60.970 63.158 0.00 0.00 37.39 3.69
88 89 1.969589 CCAAGGTGGTTGCCGTACC 60.970 63.158 0.00 0.00 38.73 3.34
89 90 2.622962 GCCAAGGTGGTTGCCGTAC 61.623 63.158 0.00 0.00 40.46 3.67
90 91 2.281900 GCCAAGGTGGTTGCCGTA 60.282 61.111 0.00 0.00 40.46 4.02
94 95 4.621087 AGGGGCCAAGGTGGTTGC 62.621 66.667 4.39 0.00 40.46 4.17
95 96 2.201210 AAGGGGCCAAGGTGGTTG 59.799 61.111 4.39 0.00 40.46 3.77
96 97 2.201210 CAAGGGGCCAAGGTGGTT 59.799 61.111 4.39 0.00 40.46 3.67
97 98 4.621087 GCAAGGGGCCAAGGTGGT 62.621 66.667 4.39 0.00 40.46 4.16
98 99 4.619320 TGCAAGGGGCCAAGGTGG 62.619 66.667 4.39 0.00 43.89 4.61
99 100 2.103339 CTTTGCAAGGGGCCAAGGTG 62.103 60.000 4.39 0.00 40.59 4.00
100 101 1.838396 CTTTGCAAGGGGCCAAGGT 60.838 57.895 4.39 0.00 40.59 3.50
101 102 1.838396 ACTTTGCAAGGGGCCAAGG 60.838 57.895 13.65 0.00 46.61 3.61
103 104 0.980231 AACACTTTGCAAGGGGCCAA 60.980 50.000 11.26 0.00 43.89 4.52
104 105 0.105964 TAACACTTTGCAAGGGGCCA 60.106 50.000 11.26 0.00 43.89 5.36
105 106 0.317160 GTAACACTTTGCAAGGGGCC 59.683 55.000 11.26 0.00 43.89 5.80
106 107 1.328279 AGTAACACTTTGCAAGGGGC 58.672 50.000 11.26 0.00 45.13 5.80
107 108 2.296190 GGAAGTAACACTTTGCAAGGGG 59.704 50.000 9.62 9.62 38.80 4.79
108 109 3.222603 AGGAAGTAACACTTTGCAAGGG 58.777 45.455 13.65 6.72 38.80 3.95
109 110 4.580580 AGAAGGAAGTAACACTTTGCAAGG 59.419 41.667 7.07 7.07 38.80 3.61
110 111 5.757850 AGAAGGAAGTAACACTTTGCAAG 57.242 39.130 0.00 0.00 38.80 4.01
111 112 6.524101 AAAGAAGGAAGTAACACTTTGCAA 57.476 33.333 0.00 0.00 38.80 4.08
112 113 6.377146 AGAAAAGAAGGAAGTAACACTTTGCA 59.623 34.615 0.00 0.00 38.80 4.08
113 114 6.693113 CAGAAAAGAAGGAAGTAACACTTTGC 59.307 38.462 0.00 0.00 38.80 3.68
114 115 7.762382 ACAGAAAAGAAGGAAGTAACACTTTG 58.238 34.615 0.00 0.00 38.80 2.77
115 116 7.829706 AGACAGAAAAGAAGGAAGTAACACTTT 59.170 33.333 0.00 0.00 38.80 2.66
116 117 7.339482 AGACAGAAAAGAAGGAAGTAACACTT 58.661 34.615 0.00 0.00 41.95 3.16
117 118 6.890293 AGACAGAAAAGAAGGAAGTAACACT 58.110 36.000 0.00 0.00 0.00 3.55
118 119 7.095565 GCTAGACAGAAAAGAAGGAAGTAACAC 60.096 40.741 0.00 0.00 0.00 3.32
119 120 6.929606 GCTAGACAGAAAAGAAGGAAGTAACA 59.070 38.462 0.00 0.00 0.00 2.41
120 121 6.929606 TGCTAGACAGAAAAGAAGGAAGTAAC 59.070 38.462 0.00 0.00 0.00 2.50
121 122 7.062749 TGCTAGACAGAAAAGAAGGAAGTAA 57.937 36.000 0.00 0.00 0.00 2.24
122 123 6.665992 TGCTAGACAGAAAAGAAGGAAGTA 57.334 37.500 0.00 0.00 0.00 2.24
123 124 5.552870 TGCTAGACAGAAAAGAAGGAAGT 57.447 39.130 0.00 0.00 0.00 3.01
124 125 5.106752 GCTTGCTAGACAGAAAAGAAGGAAG 60.107 44.000 0.00 0.00 36.04 3.46
125 126 4.757149 GCTTGCTAGACAGAAAAGAAGGAA 59.243 41.667 0.00 0.00 0.00 3.36
126 127 4.202357 TGCTTGCTAGACAGAAAAGAAGGA 60.202 41.667 0.00 0.00 0.00 3.36
127 128 4.067896 TGCTTGCTAGACAGAAAAGAAGG 58.932 43.478 0.00 0.00 0.00 3.46
128 129 4.754114 ACTGCTTGCTAGACAGAAAAGAAG 59.246 41.667 19.93 4.40 35.38 2.85
129 130 4.708177 ACTGCTTGCTAGACAGAAAAGAA 58.292 39.130 19.93 0.00 35.38 2.52
130 131 4.342862 ACTGCTTGCTAGACAGAAAAGA 57.657 40.909 19.93 0.00 35.38 2.52
131 132 4.512944 TGAACTGCTTGCTAGACAGAAAAG 59.487 41.667 19.93 0.00 35.38 2.27
132 133 4.450976 TGAACTGCTTGCTAGACAGAAAA 58.549 39.130 19.93 7.30 35.38 2.29
133 134 4.060900 CTGAACTGCTTGCTAGACAGAAA 58.939 43.478 19.93 8.72 35.38 2.52
134 135 3.070159 ACTGAACTGCTTGCTAGACAGAA 59.930 43.478 19.93 8.96 35.38 3.02
135 136 2.630098 ACTGAACTGCTTGCTAGACAGA 59.370 45.455 19.93 4.09 35.38 3.41
136 137 3.037431 ACTGAACTGCTTGCTAGACAG 57.963 47.619 14.41 14.41 37.45 3.51
137 138 3.574396 AGTACTGAACTGCTTGCTAGACA 59.426 43.478 0.00 0.00 36.93 3.41
138 139 4.181309 AGTACTGAACTGCTTGCTAGAC 57.819 45.455 0.00 0.00 36.93 2.59
169 170 8.906693 CGCACACAACAAAACAATGTAATAATA 58.093 29.630 0.00 0.00 32.02 0.98
170 171 7.568497 GCGCACACAACAAAACAATGTAATAAT 60.568 33.333 0.30 0.00 32.02 1.28
171 172 6.291849 GCGCACACAACAAAACAATGTAATAA 60.292 34.615 0.30 0.00 32.02 1.40
172 173 5.174035 GCGCACACAACAAAACAATGTAATA 59.826 36.000 0.30 0.00 32.02 0.98
173 174 4.026145 GCGCACACAACAAAACAATGTAAT 60.026 37.500 0.30 0.00 32.02 1.89
174 175 3.304559 GCGCACACAACAAAACAATGTAA 59.695 39.130 0.30 0.00 32.02 2.41
175 176 2.854777 GCGCACACAACAAAACAATGTA 59.145 40.909 0.30 0.00 32.02 2.29
176 177 1.658095 GCGCACACAACAAAACAATGT 59.342 42.857 0.30 0.00 34.24 2.71
177 178 1.657594 TGCGCACACAACAAAACAATG 59.342 42.857 5.66 0.00 0.00 2.82
178 179 1.658095 GTGCGCACACAACAAAACAAT 59.342 42.857 34.52 0.00 46.61 2.71
179 180 1.063806 GTGCGCACACAACAAAACAA 58.936 45.000 34.52 0.00 46.61 2.83
180 181 2.730626 GTGCGCACACAACAAAACA 58.269 47.368 34.52 0.00 46.61 2.83
194 195 3.522731 AGAGAGCCTAGCGGTGCG 61.523 66.667 0.00 0.00 0.00 5.34
195 196 1.743321 ATCAGAGAGCCTAGCGGTGC 61.743 60.000 0.00 0.00 0.00 5.01
196 197 0.031857 CATCAGAGAGCCTAGCGGTG 59.968 60.000 0.00 0.00 0.00 4.94
197 198 0.106469 TCATCAGAGAGCCTAGCGGT 60.106 55.000 0.00 0.00 0.00 5.68
198 199 1.000385 CTTCATCAGAGAGCCTAGCGG 60.000 57.143 0.00 0.00 0.00 5.52
199 200 1.602668 GCTTCATCAGAGAGCCTAGCG 60.603 57.143 0.00 0.00 0.00 4.26
200 201 1.602668 CGCTTCATCAGAGAGCCTAGC 60.603 57.143 0.00 0.00 0.00 3.42
201 202 1.952990 TCGCTTCATCAGAGAGCCTAG 59.047 52.381 0.00 0.00 0.00 3.02
202 203 2.058593 TCGCTTCATCAGAGAGCCTA 57.941 50.000 0.00 0.00 0.00 3.93
203 204 1.412079 ATCGCTTCATCAGAGAGCCT 58.588 50.000 0.00 0.00 34.38 4.58
204 205 2.926159 GCTATCGCTTCATCAGAGAGCC 60.926 54.545 0.43 0.00 41.69 4.70
205 206 2.327568 GCTATCGCTTCATCAGAGAGC 58.672 52.381 0.00 0.00 41.09 4.09
206 207 2.668001 CGGCTATCGCTTCATCAGAGAG 60.668 54.545 0.00 0.00 34.38 3.20
207 208 1.268079 CGGCTATCGCTTCATCAGAGA 59.732 52.381 0.00 0.00 35.53 3.10
208 209 1.268079 TCGGCTATCGCTTCATCAGAG 59.732 52.381 0.00 0.00 39.05 3.35
209 210 1.001268 GTCGGCTATCGCTTCATCAGA 60.001 52.381 0.00 0.00 39.05 3.27
210 211 1.413382 GTCGGCTATCGCTTCATCAG 58.587 55.000 0.00 0.00 39.05 2.90
211 212 0.032130 GGTCGGCTATCGCTTCATCA 59.968 55.000 0.00 0.00 39.05 3.07
212 213 1.004277 CGGTCGGCTATCGCTTCATC 61.004 60.000 0.00 0.00 39.05 2.92
213 214 1.007271 CGGTCGGCTATCGCTTCAT 60.007 57.895 0.00 0.00 39.05 2.57
214 215 2.060004 CTCGGTCGGCTATCGCTTCA 62.060 60.000 0.00 0.00 39.05 3.02
215 216 1.370657 CTCGGTCGGCTATCGCTTC 60.371 63.158 0.00 0.00 39.05 3.86
216 217 2.722487 CTCGGTCGGCTATCGCTT 59.278 61.111 0.00 0.00 39.05 4.68
217 218 3.967335 GCTCGGTCGGCTATCGCT 61.967 66.667 0.00 0.00 39.05 4.93
218 219 3.967335 AGCTCGGTCGGCTATCGC 61.967 66.667 4.94 0.00 38.36 4.58
219 220 2.050895 CAGCTCGGTCGGCTATCG 60.051 66.667 6.15 0.00 38.03 2.92
220 221 2.355244 GCAGCTCGGTCGGCTATC 60.355 66.667 6.15 0.34 38.03 2.08
221 222 2.032860 AATGCAGCTCGGTCGGCTAT 62.033 55.000 0.00 0.00 38.03 2.97
222 223 2.238847 AAATGCAGCTCGGTCGGCTA 62.239 55.000 0.00 0.00 38.03 3.93
223 224 2.238847 TAAATGCAGCTCGGTCGGCT 62.239 55.000 0.00 1.63 41.07 5.52
224 225 1.813753 TAAATGCAGCTCGGTCGGC 60.814 57.895 0.00 0.00 0.00 5.54
225 226 1.429148 GGTAAATGCAGCTCGGTCGG 61.429 60.000 0.00 0.00 0.00 4.79
226 227 0.739462 TGGTAAATGCAGCTCGGTCG 60.739 55.000 0.00 0.00 0.00 4.79
227 228 1.009829 CTGGTAAATGCAGCTCGGTC 58.990 55.000 0.00 0.00 0.00 4.79
228 229 0.324943 ACTGGTAAATGCAGCTCGGT 59.675 50.000 0.00 0.00 0.00 4.69
229 230 1.398390 GAACTGGTAAATGCAGCTCGG 59.602 52.381 0.00 0.00 0.00 4.63
230 231 2.076100 TGAACTGGTAAATGCAGCTCG 58.924 47.619 0.00 0.00 0.00 5.03
231 232 4.479619 CTTTGAACTGGTAAATGCAGCTC 58.520 43.478 0.00 0.00 0.00 4.09
232 233 3.305608 GCTTTGAACTGGTAAATGCAGCT 60.306 43.478 0.00 0.00 0.00 4.24
233 234 2.989166 GCTTTGAACTGGTAAATGCAGC 59.011 45.455 0.00 0.00 0.00 5.25
234 235 3.578688 GGCTTTGAACTGGTAAATGCAG 58.421 45.455 3.38 0.00 0.00 4.41
235 236 2.298729 GGGCTTTGAACTGGTAAATGCA 59.701 45.455 3.38 0.00 0.00 3.96
236 237 2.298729 TGGGCTTTGAACTGGTAAATGC 59.701 45.455 0.00 0.00 0.00 3.56
237 238 4.806640 ATGGGCTTTGAACTGGTAAATG 57.193 40.909 0.00 0.00 0.00 2.32
238 239 7.494922 AATAATGGGCTTTGAACTGGTAAAT 57.505 32.000 0.00 0.00 0.00 1.40
239 240 6.926630 AATAATGGGCTTTGAACTGGTAAA 57.073 33.333 0.00 0.00 0.00 2.01
240 241 6.926630 AAATAATGGGCTTTGAACTGGTAA 57.073 33.333 0.00 0.00 0.00 2.85
241 242 8.423906 TTTAAATAATGGGCTTTGAACTGGTA 57.576 30.769 0.00 0.00 0.00 3.25
242 243 6.926630 TTAAATAATGGGCTTTGAACTGGT 57.073 33.333 0.00 0.00 0.00 4.00
243 244 7.877612 AGTTTTAAATAATGGGCTTTGAACTGG 59.122 33.333 0.00 0.00 0.00 4.00
244 245 8.831715 AGTTTTAAATAATGGGCTTTGAACTG 57.168 30.769 0.00 0.00 0.00 3.16
249 250 9.366216 GGTTCTAGTTTTAAATAATGGGCTTTG 57.634 33.333 0.00 0.00 0.00 2.77
250 251 9.321532 AGGTTCTAGTTTTAAATAATGGGCTTT 57.678 29.630 0.00 0.00 0.00 3.51
251 252 8.895141 AGGTTCTAGTTTTAAATAATGGGCTT 57.105 30.769 0.00 0.00 0.00 4.35
252 253 9.984590 TTAGGTTCTAGTTTTAAATAATGGGCT 57.015 29.630 0.00 0.00 0.00 5.19
270 271 9.751542 CTGATGTTCGTTAGATATTTAGGTTCT 57.248 33.333 0.00 0.00 0.00 3.01
271 272 9.745880 TCTGATGTTCGTTAGATATTTAGGTTC 57.254 33.333 0.00 0.00 0.00 3.62
288 289 4.980434 GCCATGCATACAAATCTGATGTTC 59.020 41.667 0.00 0.00 32.27 3.18
325 326 7.032580 CCTCGGCAAACATAATTTGACATAAA 58.967 34.615 6.09 0.00 37.27 1.40
332 333 4.362279 CCATCCTCGGCAAACATAATTTG 58.638 43.478 0.00 0.00 0.00 2.32
345 346 2.403252 ACTAAACTTGCCATCCTCGG 57.597 50.000 0.00 0.00 0.00 4.63
367 368 1.291877 GGCGAACTTGTCATGCTCGT 61.292 55.000 11.67 0.00 32.23 4.18
376 377 0.034896 ATGAACCGAGGCGAACTTGT 59.965 50.000 0.00 0.00 0.00 3.16
380 381 2.699251 AAAAATGAACCGAGGCGAAC 57.301 45.000 0.00 0.00 0.00 3.95
405 407 4.866921 AGTTTGCAAGTACGGGAATTTTC 58.133 39.130 0.00 0.00 0.00 2.29
407 409 6.394025 TTTAGTTTGCAAGTACGGGAATTT 57.606 33.333 0.00 0.00 0.00 1.82
440 442 1.519408 GTGATTTATATGGGCGCCGT 58.481 50.000 22.54 14.61 0.00 5.68
441 443 0.802494 GGTGATTTATATGGGCGCCG 59.198 55.000 22.54 0.00 0.00 6.46
503 505 2.475685 GCGGTTTTAATGAGGCGAAGAC 60.476 50.000 0.00 0.00 0.00 3.01
508 510 0.802494 ACTGCGGTTTTAATGAGGCG 59.198 50.000 0.00 0.00 0.00 5.52
553 555 1.550327 ATCTCTGGACAGCGAACTCA 58.450 50.000 0.00 0.00 0.00 3.41
555 557 1.751924 GGTATCTCTGGACAGCGAACT 59.248 52.381 0.00 0.00 0.00 3.01
600 602 1.945522 CGTGCATGGAACCAACGAA 59.054 52.632 9.94 0.00 0.00 3.85
603 605 0.664166 CTTGCGTGCATGGAACCAAC 60.664 55.000 9.00 0.00 0.00 3.77
604 606 1.659233 CTTGCGTGCATGGAACCAA 59.341 52.632 9.00 2.82 0.00 3.67
605 607 2.267351 CCTTGCGTGCATGGAACCA 61.267 57.895 19.01 0.00 41.96 3.67
606 608 1.971167 TCCTTGCGTGCATGGAACC 60.971 57.895 22.72 0.00 44.08 3.62
607 609 3.667087 TCCTTGCGTGCATGGAAC 58.333 55.556 22.72 0.00 44.08 3.62
609 611 1.865788 GCTTTCCTTGCGTGCATGGA 61.866 55.000 21.54 21.54 44.94 3.41
610 612 1.444895 GCTTTCCTTGCGTGCATGG 60.445 57.895 18.00 18.00 41.10 3.66
611 613 1.444895 GGCTTTCCTTGCGTGCATG 60.445 57.895 0.09 0.09 0.00 4.06
674 676 0.033920 CCTTTTGGTGGCTTTGGAGC 59.966 55.000 0.00 0.00 40.60 4.70
710 712 2.446848 GCTGCTGCAGGGATAGGGA 61.447 63.158 29.05 0.00 39.41 4.20
711 713 2.112718 GCTGCTGCAGGGATAGGG 59.887 66.667 29.05 4.36 39.41 3.53
712 714 1.071128 GAGCTGCTGCAGGGATAGG 59.929 63.158 29.05 5.12 42.74 2.57
713 715 0.249953 CTGAGCTGCTGCAGGGATAG 60.250 60.000 29.05 5.87 42.74 2.08
742 744 3.376918 GCTCCCCTGCCAAGTTGC 61.377 66.667 0.00 0.00 0.00 4.17
743 745 3.058160 CGCTCCCCTGCCAAGTTG 61.058 66.667 0.00 0.00 0.00 3.16
785 795 2.335712 CCGTTCTTGGGGAGCTTGC 61.336 63.158 0.00 0.00 0.00 4.01
786 796 1.073199 ACCGTTCTTGGGGAGCTTG 59.927 57.895 0.00 0.00 0.00 4.01
787 797 1.073199 CACCGTTCTTGGGGAGCTT 59.927 57.895 0.00 0.00 32.57 3.74
789 799 2.359975 CCACCGTTCTTGGGGAGC 60.360 66.667 0.00 0.00 32.57 4.70
791 801 2.833227 CACCACCGTTCTTGGGGA 59.167 61.111 0.00 0.00 40.36 4.81
871 898 0.179000 ATGCCTGTGGTAGCTGCTAC 59.821 55.000 27.44 27.44 36.33 3.58
1284 1365 3.982316 CTTGATGCCGCTGCCTCCA 62.982 63.158 0.00 0.00 36.33 3.86
1562 1643 2.112198 GCGATCATTTCCGTGCCCA 61.112 57.895 0.00 0.00 0.00 5.36
1654 1735 1.450848 GGCATGCAGAGCTGTGCTA 60.451 57.895 32.77 20.90 44.32 3.49
1683 1764 2.612219 GATGCCGGAAAATGGTGCCG 62.612 60.000 5.05 0.00 44.42 5.69
1741 1825 5.028549 AGCACTTCGATCATACTTTCCAT 57.971 39.130 0.00 0.00 0.00 3.41
1746 1830 4.867047 CAGTTGAGCACTTCGATCATACTT 59.133 41.667 0.00 0.00 30.92 2.24
1747 1831 4.428209 CAGTTGAGCACTTCGATCATACT 58.572 43.478 0.00 0.00 30.92 2.12
1811 1898 3.380479 TTTTACTCACGGTCTGTCAGG 57.620 47.619 0.00 0.00 0.00 3.86
1822 1909 6.503524 TGATCCAGCAAAACTTTTTACTCAC 58.496 36.000 0.00 0.00 0.00 3.51
2401 2498 2.038659 TGGCCACCTTTTCTTCCTTTG 58.961 47.619 0.00 0.00 0.00 2.77
2408 2505 0.537371 CGGAAGTGGCCACCTTTTCT 60.537 55.000 32.29 10.03 0.00 2.52
2480 2578 2.214376 TGATTCATGGTTGGGTGGTC 57.786 50.000 0.00 0.00 0.00 4.02
2513 2611 2.093973 AGCTAGACCGTCCAATCAACAG 60.094 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.