Multiple sequence alignment - TraesCS2D01G307700

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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 TraesCS2D01G307700 chr2D 100.000 4622 0 0 1 4622 394780243 394784864 0.000000e+00 8536.0
1 TraesCS2D01G307700 chr2A 95.429 4157 145 18 494 4622 532848609 532852748 0.000000e+00 6582.0
2 TraesCS2D01G307700 chr2A 93.750 224 12 2 41 264 532525827 532526048 7.410000e-88 335.0
3 TraesCS2D01G307700 chr2A 89.744 156 3 1 256 398 532848456 532848611 2.200000e-43 187.0
4 TraesCS2D01G307700 chr2B 93.608 3833 196 20 820 4622 467785277 467789090 0.000000e+00 5675.0
5 TraesCS2D01G307700 chr2B 77.698 278 38 16 551 807 467781254 467781528 1.040000e-31 148.0
6 TraesCS2D01G307700 chr7A 74.299 214 46 8 585 791 539538757 539538968 1.070000e-11 82.4
7 TraesCS2D01G307700 chr5D 80.435 92 15 3 562 650 111954767 111954858 2.980000e-07 67.6
8 TraesCS2D01G307700 chr1D 94.595 37 1 1 577 612 233902726 233902762 6.460000e-04 56.5


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 TraesCS2D01G307700 chr2D 394780243 394784864 4621 False 8536.0 8536 100.0000 1 4622 1 chr2D.!!$F1 4621
1 TraesCS2D01G307700 chr2A 532848456 532852748 4292 False 3384.5 6582 92.5865 256 4622 2 chr2A.!!$F2 4366
2 TraesCS2D01G307700 chr2B 467781254 467789090 7836 False 2911.5 5675 85.6530 551 4622 2 chr2B.!!$F1 4071

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
145 146 0.036306 ATCCTTGGGTCGGTGTTGAC 59.964 55.000 0.00 0.00 38.17 3.18 F
411 425 0.249398 AGTAAGCAGTTACCGGCCAG 59.751 55.000 0.00 0.00 39.65 4.85 F
472 486 0.527565 CCATGAGTTTCCGCCCTTTG 59.472 55.000 0.00 0.00 0.00 2.77 F
1445 5233 0.903942 TTTGATGAAATGGGCTGCCC 59.096 50.000 30.97 30.97 45.71 5.36 F
1480 5268 1.839994 GGAACATCCTGATCACTGGGA 59.160 52.381 4.76 4.76 36.08 4.37 F
1602 5390 2.160615 CGTCATTCCGGTATGTGCAAAA 59.839 45.455 19.20 0.00 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 5233 0.316689 GTTCCAACAAACCGCGTCAG 60.317 55.000 4.92 0.0 0.00 3.51 R
1569 5357 0.949105 GAATGACGACAGCCACCGTT 60.949 55.000 0.00 0.0 39.30 4.44 R
1602 5390 1.066573 CCAGCCGTCAAATCTCTCAGT 60.067 52.381 0.00 0.0 0.00 3.41 R
3350 7138 0.550914 GTGAGGGGGCATATCCAACA 59.449 55.000 0.00 0.0 36.21 3.33 R
3427 7215 1.068753 CGAGCTGGCCGATTCTGAT 59.931 57.895 0.00 0.0 0.00 2.90 R
3628 7416 8.963725 TCGTAGATAAAAGAACTATCTTGGTGA 58.036 33.333 0.00 0.0 45.19 4.02 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
34 35 8.882278 TTTTTAATTTTCCTTGCAACGTTTTC 57.118 26.923 0.00 0.00 0.00 2.29
35 36 6.591313 TTAATTTTCCTTGCAACGTTTTCC 57.409 33.333 0.00 0.00 0.00 3.13
36 37 3.594603 TTTTCCTTGCAACGTTTTCCA 57.405 38.095 0.00 0.00 0.00 3.53
37 38 3.594603 TTTCCTTGCAACGTTTTCCAA 57.405 38.095 0.00 1.80 0.00 3.53
38 39 2.570442 TCCTTGCAACGTTTTCCAAC 57.430 45.000 0.00 0.00 0.00 3.77
39 40 1.819288 TCCTTGCAACGTTTTCCAACA 59.181 42.857 0.00 0.00 32.54 3.33
40 41 2.159310 TCCTTGCAACGTTTTCCAACAG 60.159 45.455 0.00 0.00 32.54 3.16
41 42 2.159310 CCTTGCAACGTTTTCCAACAGA 60.159 45.455 0.00 0.00 32.54 3.41
42 43 2.553079 TGCAACGTTTTCCAACAGAC 57.447 45.000 0.00 0.00 32.54 3.51
43 44 1.202087 TGCAACGTTTTCCAACAGACG 60.202 47.619 0.00 0.00 41.00 4.18
44 45 1.062880 GCAACGTTTTCCAACAGACGA 59.937 47.619 0.00 0.00 38.74 4.20
45 46 2.286772 GCAACGTTTTCCAACAGACGAT 60.287 45.455 0.00 0.00 38.74 3.73
46 47 3.288242 CAACGTTTTCCAACAGACGATG 58.712 45.455 0.00 0.00 38.74 3.84
47 48 1.871039 ACGTTTTCCAACAGACGATGG 59.129 47.619 1.50 0.00 38.74 3.51
48 49 1.196808 CGTTTTCCAACAGACGATGGG 59.803 52.381 0.00 0.00 35.79 4.00
49 50 2.227194 GTTTTCCAACAGACGATGGGT 58.773 47.619 0.00 0.00 35.79 4.51
50 51 2.178912 TTTCCAACAGACGATGGGTC 57.821 50.000 0.00 0.00 46.45 4.46
61 62 2.649331 CGATGGGTCGTCAACTACTT 57.351 50.000 0.00 0.00 42.78 2.24
62 63 2.955614 CGATGGGTCGTCAACTACTTT 58.044 47.619 0.00 0.00 42.78 2.66
63 64 3.323243 CGATGGGTCGTCAACTACTTTT 58.677 45.455 0.00 0.00 42.78 2.27
64 65 3.122948 CGATGGGTCGTCAACTACTTTTG 59.877 47.826 0.00 0.00 42.78 2.44
65 66 3.823281 TGGGTCGTCAACTACTTTTGA 57.177 42.857 0.00 0.00 32.94 2.69
66 67 4.345859 TGGGTCGTCAACTACTTTTGAT 57.654 40.909 0.00 0.00 37.80 2.57
67 68 4.710324 TGGGTCGTCAACTACTTTTGATT 58.290 39.130 0.00 0.00 37.80 2.57
68 69 5.127491 TGGGTCGTCAACTACTTTTGATTT 58.873 37.500 0.00 0.00 37.80 2.17
69 70 5.591067 TGGGTCGTCAACTACTTTTGATTTT 59.409 36.000 0.00 0.00 37.80 1.82
70 71 5.912955 GGGTCGTCAACTACTTTTGATTTTG 59.087 40.000 0.00 0.00 37.80 2.44
71 72 6.238538 GGGTCGTCAACTACTTTTGATTTTGA 60.239 38.462 0.00 0.00 37.80 2.69
72 73 6.851330 GGTCGTCAACTACTTTTGATTTTGAG 59.149 38.462 0.00 0.00 37.80 3.02
73 74 7.254658 GGTCGTCAACTACTTTTGATTTTGAGA 60.255 37.037 0.00 0.00 37.80 3.27
74 75 7.794349 GTCGTCAACTACTTTTGATTTTGAGAG 59.206 37.037 0.00 0.00 37.80 3.20
75 76 7.042051 TCGTCAACTACTTTTGATTTTGAGAGG 60.042 37.037 0.00 0.00 37.80 3.69
76 77 6.858478 GTCAACTACTTTTGATTTTGAGAGGC 59.142 38.462 0.00 0.00 37.80 4.70
77 78 5.966742 ACTACTTTTGATTTTGAGAGGCC 57.033 39.130 0.00 0.00 0.00 5.19
78 79 4.767409 ACTACTTTTGATTTTGAGAGGCCC 59.233 41.667 0.00 0.00 0.00 5.80
79 80 2.558359 ACTTTTGATTTTGAGAGGCCCG 59.442 45.455 0.00 0.00 0.00 6.13
80 81 1.544724 TTTGATTTTGAGAGGCCCGG 58.455 50.000 0.00 0.00 0.00 5.73
81 82 0.695924 TTGATTTTGAGAGGCCCGGA 59.304 50.000 0.73 0.00 0.00 5.14
82 83 0.253044 TGATTTTGAGAGGCCCGGAG 59.747 55.000 0.73 0.00 0.00 4.63
83 84 0.253327 GATTTTGAGAGGCCCGGAGT 59.747 55.000 0.73 0.00 0.00 3.85
84 85 1.485066 GATTTTGAGAGGCCCGGAGTA 59.515 52.381 0.73 0.00 0.00 2.59
85 86 0.611714 TTTTGAGAGGCCCGGAGTAC 59.388 55.000 0.73 0.00 0.00 2.73
86 87 0.543410 TTTGAGAGGCCCGGAGTACA 60.543 55.000 0.73 0.00 0.00 2.90
87 88 1.255667 TTGAGAGGCCCGGAGTACAC 61.256 60.000 0.73 0.00 0.00 2.90
88 89 2.754658 AGAGGCCCGGAGTACACG 60.755 66.667 0.73 0.00 0.00 4.49
89 90 3.066814 GAGGCCCGGAGTACACGT 61.067 66.667 0.73 0.00 0.00 4.49
90 91 3.061260 GAGGCCCGGAGTACACGTC 62.061 68.421 0.73 0.00 0.00 4.34
91 92 4.139234 GGCCCGGAGTACACGTCC 62.139 72.222 0.73 6.15 0.00 4.79
98 99 1.799383 GAGTACACGTCCGACTCCC 59.201 63.158 9.03 0.00 34.72 4.30
99 100 1.975363 GAGTACACGTCCGACTCCCG 61.975 65.000 9.03 0.00 34.72 5.14
100 101 2.034879 GTACACGTCCGACTCCCGA 61.035 63.158 0.00 0.00 41.76 5.14
101 102 1.302431 TACACGTCCGACTCCCGAA 60.302 57.895 0.00 0.00 41.76 4.30
102 103 0.888736 TACACGTCCGACTCCCGAAA 60.889 55.000 0.00 0.00 41.76 3.46
103 104 1.731969 CACGTCCGACTCCCGAAAC 60.732 63.158 0.00 0.00 41.76 2.78
104 105 2.195567 ACGTCCGACTCCCGAAACA 61.196 57.895 0.00 0.00 41.76 2.83
105 106 1.007038 CGTCCGACTCCCGAAACAA 60.007 57.895 0.00 0.00 41.76 2.83
106 107 1.007336 CGTCCGACTCCCGAAACAAG 61.007 60.000 0.00 0.00 41.76 3.16
107 108 0.316204 GTCCGACTCCCGAAACAAGA 59.684 55.000 0.00 0.00 41.76 3.02
108 109 1.067071 GTCCGACTCCCGAAACAAGAT 60.067 52.381 0.00 0.00 41.76 2.40
109 110 1.067142 TCCGACTCCCGAAACAAGATG 60.067 52.381 0.00 0.00 41.76 2.90
110 111 0.721718 CGACTCCCGAAACAAGATGC 59.278 55.000 0.00 0.00 41.76 3.91
111 112 1.808411 GACTCCCGAAACAAGATGCA 58.192 50.000 0.00 0.00 0.00 3.96
112 113 2.359900 GACTCCCGAAACAAGATGCAT 58.640 47.619 0.00 0.00 0.00 3.96
113 114 2.352960 GACTCCCGAAACAAGATGCATC 59.647 50.000 19.37 19.37 0.00 3.91
114 115 1.328680 CTCCCGAAACAAGATGCATCG 59.671 52.381 20.67 10.34 0.00 3.84
115 116 0.248215 CCCGAAACAAGATGCATCGC 60.248 55.000 20.67 0.00 30.53 4.58
116 117 0.447406 CCGAAACAAGATGCATCGCA 59.553 50.000 20.67 0.00 44.86 5.10
128 129 2.866198 TGCATCGCATGTTGTCAAATC 58.134 42.857 0.00 0.00 31.71 2.17
129 130 2.187707 GCATCGCATGTTGTCAAATCC 58.812 47.619 0.00 0.00 0.00 3.01
130 131 2.159338 GCATCGCATGTTGTCAAATCCT 60.159 45.455 0.00 0.00 0.00 3.24
131 132 3.674138 GCATCGCATGTTGTCAAATCCTT 60.674 43.478 0.00 0.00 0.00 3.36
132 133 3.557577 TCGCATGTTGTCAAATCCTTG 57.442 42.857 0.00 0.00 0.00 3.61
133 134 2.228582 TCGCATGTTGTCAAATCCTTGG 59.771 45.455 0.00 0.00 33.01 3.61
134 135 2.671914 CGCATGTTGTCAAATCCTTGGG 60.672 50.000 0.00 0.00 33.01 4.12
135 136 2.299867 GCATGTTGTCAAATCCTTGGGT 59.700 45.455 0.00 0.00 33.01 4.51
136 137 3.614870 GCATGTTGTCAAATCCTTGGGTC 60.615 47.826 0.00 0.00 33.01 4.46
137 138 2.226330 TGTTGTCAAATCCTTGGGTCG 58.774 47.619 0.00 0.00 33.01 4.79
138 139 1.539827 GTTGTCAAATCCTTGGGTCGG 59.460 52.381 0.00 0.00 33.01 4.79
139 140 0.768622 TGTCAAATCCTTGGGTCGGT 59.231 50.000 0.00 0.00 33.01 4.69
140 141 1.165270 GTCAAATCCTTGGGTCGGTG 58.835 55.000 0.00 0.00 33.01 4.94
141 142 0.768622 TCAAATCCTTGGGTCGGTGT 59.231 50.000 0.00 0.00 33.01 4.16
142 143 1.144093 TCAAATCCTTGGGTCGGTGTT 59.856 47.619 0.00 0.00 33.01 3.32
143 144 1.269448 CAAATCCTTGGGTCGGTGTTG 59.731 52.381 0.00 0.00 0.00 3.33
144 145 0.768622 AATCCTTGGGTCGGTGTTGA 59.231 50.000 0.00 0.00 0.00 3.18
145 146 0.036306 ATCCTTGGGTCGGTGTTGAC 59.964 55.000 0.00 0.00 38.17 3.18
146 147 1.147376 CCTTGGGTCGGTGTTGACA 59.853 57.895 0.00 0.00 40.72 3.58
147 148 0.464735 CCTTGGGTCGGTGTTGACAA 60.465 55.000 0.00 0.00 40.72 3.18
148 149 0.661020 CTTGGGTCGGTGTTGACAAC 59.339 55.000 11.54 11.54 40.72 3.32
149 150 0.253610 TTGGGTCGGTGTTGACAACT 59.746 50.000 18.73 0.00 40.72 3.16
150 151 0.253610 TGGGTCGGTGTTGACAACTT 59.746 50.000 18.73 0.00 40.72 2.66
151 152 0.942252 GGGTCGGTGTTGACAACTTC 59.058 55.000 18.73 11.57 40.72 3.01
152 153 1.658994 GGTCGGTGTTGACAACTTCA 58.341 50.000 18.73 0.00 40.72 3.02
153 154 2.011222 GGTCGGTGTTGACAACTTCAA 58.989 47.619 18.73 0.00 42.26 2.69
154 155 2.031683 GGTCGGTGTTGACAACTTCAAG 59.968 50.000 18.73 9.90 45.23 3.02
155 156 2.933906 GTCGGTGTTGACAACTTCAAGA 59.066 45.455 18.73 11.60 45.23 3.02
156 157 3.560068 GTCGGTGTTGACAACTTCAAGAT 59.440 43.478 18.73 0.00 45.23 2.40
157 158 4.035208 GTCGGTGTTGACAACTTCAAGATT 59.965 41.667 18.73 0.00 45.23 2.40
158 159 5.235616 GTCGGTGTTGACAACTTCAAGATTA 59.764 40.000 18.73 0.00 45.23 1.75
159 160 5.995282 TCGGTGTTGACAACTTCAAGATTAT 59.005 36.000 18.73 0.00 45.23 1.28
160 161 7.117236 GTCGGTGTTGACAACTTCAAGATTATA 59.883 37.037 18.73 0.00 45.23 0.98
161 162 7.658167 TCGGTGTTGACAACTTCAAGATTATAA 59.342 33.333 18.73 0.00 45.23 0.98
162 163 8.450964 CGGTGTTGACAACTTCAAGATTATAAT 58.549 33.333 18.73 0.00 45.23 1.28
165 166 9.624697 TGTTGACAACTTCAAGATTATAATTGC 57.375 29.630 18.73 0.00 45.23 3.56
166 167 9.624697 GTTGACAACTTCAAGATTATAATTGCA 57.375 29.630 11.18 0.00 45.23 4.08
168 169 9.791820 TGACAACTTCAAGATTATAATTGCATG 57.208 29.630 0.00 0.00 0.00 4.06
169 170 9.793252 GACAACTTCAAGATTATAATTGCATGT 57.207 29.630 0.00 0.48 0.00 3.21
170 171 9.577110 ACAACTTCAAGATTATAATTGCATGTG 57.423 29.630 0.00 0.00 0.00 3.21
171 172 8.537223 CAACTTCAAGATTATAATTGCATGTGC 58.463 33.333 0.00 0.00 42.50 4.57
187 188 6.369059 GCATGTGCAACTACTATTTGATCT 57.631 37.500 0.00 0.00 41.59 2.75
188 189 6.789262 GCATGTGCAACTACTATTTGATCTT 58.211 36.000 0.00 0.00 41.59 2.40
189 190 6.690098 GCATGTGCAACTACTATTTGATCTTG 59.310 38.462 0.00 0.00 41.59 3.02
190 191 7.414429 GCATGTGCAACTACTATTTGATCTTGA 60.414 37.037 0.00 0.00 41.59 3.02
191 192 7.977789 TGTGCAACTACTATTTGATCTTGAA 57.022 32.000 0.00 0.00 38.04 2.69
192 193 8.389779 TGTGCAACTACTATTTGATCTTGAAA 57.610 30.769 0.00 0.00 38.04 2.69
193 194 8.845227 TGTGCAACTACTATTTGATCTTGAAAA 58.155 29.630 0.00 0.00 38.04 2.29
194 195 9.677567 GTGCAACTACTATTTGATCTTGAAAAA 57.322 29.630 0.00 0.00 0.00 1.94
195 196 9.677567 TGCAACTACTATTTGATCTTGAAAAAC 57.322 29.630 0.00 0.00 0.00 2.43
196 197 9.677567 GCAACTACTATTTGATCTTGAAAAACA 57.322 29.630 0.00 0.00 0.00 2.83
205 206 9.661563 ATTTGATCTTGAAAAACATATGTGCAT 57.338 25.926 9.63 0.00 0.00 3.96
206 207 9.491675 TTTGATCTTGAAAAACATATGTGCATT 57.508 25.926 9.63 4.98 0.00 3.56
207 208 9.491675 TTGATCTTGAAAAACATATGTGCATTT 57.508 25.926 9.63 11.11 0.00 2.32
210 211 9.926158 ATCTTGAAAAACATATGTGCATTTACA 57.074 25.926 9.63 8.79 34.63 2.41
211 212 9.190858 TCTTGAAAAACATATGTGCATTTACAC 57.809 29.630 9.63 3.52 41.10 2.90
212 213 7.881643 TGAAAAACATATGTGCATTTACACC 57.118 32.000 9.63 1.47 39.93 4.16
213 214 6.584184 TGAAAAACATATGTGCATTTACACCG 59.416 34.615 9.63 0.00 39.93 4.94
214 215 5.888691 AAACATATGTGCATTTACACCGA 57.111 34.783 9.63 0.00 39.93 4.69
215 216 5.484173 AACATATGTGCATTTACACCGAG 57.516 39.130 9.63 0.00 39.93 4.63
216 217 4.765273 ACATATGTGCATTTACACCGAGA 58.235 39.130 7.78 0.00 39.93 4.04
217 218 5.182487 ACATATGTGCATTTACACCGAGAA 58.818 37.500 7.78 0.00 39.93 2.87
218 219 5.645929 ACATATGTGCATTTACACCGAGAAA 59.354 36.000 7.78 0.00 39.93 2.52
219 220 3.889196 TGTGCATTTACACCGAGAAAC 57.111 42.857 0.00 0.00 39.93 2.78
220 221 3.472652 TGTGCATTTACACCGAGAAACT 58.527 40.909 0.00 0.00 39.93 2.66
221 222 4.633175 TGTGCATTTACACCGAGAAACTA 58.367 39.130 0.00 0.00 39.93 2.24
222 223 5.242434 TGTGCATTTACACCGAGAAACTAT 58.758 37.500 0.00 0.00 39.93 2.12
223 224 5.703592 TGTGCATTTACACCGAGAAACTATT 59.296 36.000 0.00 0.00 39.93 1.73
224 225 6.874664 TGTGCATTTACACCGAGAAACTATTA 59.125 34.615 0.00 0.00 39.93 0.98
225 226 7.388224 TGTGCATTTACACCGAGAAACTATTAA 59.612 33.333 0.00 0.00 39.93 1.40
226 227 8.231837 GTGCATTTACACCGAGAAACTATTAAA 58.768 33.333 0.00 0.00 34.35 1.52
227 228 8.952278 TGCATTTACACCGAGAAACTATTAAAT 58.048 29.630 0.00 0.00 0.00 1.40
228 229 9.783256 GCATTTACACCGAGAAACTATTAAATT 57.217 29.630 0.00 0.00 0.00 1.82
231 232 8.851541 TTACACCGAGAAACTATTAAATTGGT 57.148 30.769 0.00 0.00 0.00 3.67
232 233 7.141100 ACACCGAGAAACTATTAAATTGGTG 57.859 36.000 7.67 7.67 46.45 4.17
233 234 6.938030 ACACCGAGAAACTATTAAATTGGTGA 59.062 34.615 14.71 0.00 44.45 4.02
234 235 7.610305 ACACCGAGAAACTATTAAATTGGTGAT 59.390 33.333 14.71 0.00 44.45 3.06
235 236 7.910162 CACCGAGAAACTATTAAATTGGTGATG 59.090 37.037 3.75 0.00 44.45 3.07
236 237 7.610305 ACCGAGAAACTATTAAATTGGTGATGT 59.390 33.333 0.00 0.00 0.00 3.06
237 238 8.122952 CCGAGAAACTATTAAATTGGTGATGTC 58.877 37.037 0.00 0.00 0.00 3.06
238 239 8.664798 CGAGAAACTATTAAATTGGTGATGTCA 58.335 33.333 0.00 0.00 0.00 3.58
379 393 2.317040 TGCGTAAAAATGGGGGTTTGA 58.683 42.857 0.00 0.00 0.00 2.69
398 412 6.863645 GGTTTGAAAATGGAGAGAAAGTAAGC 59.136 38.462 0.00 0.00 0.00 3.09
399 413 7.425606 GTTTGAAAATGGAGAGAAAGTAAGCA 58.574 34.615 0.00 0.00 0.00 3.91
400 414 6.808008 TGAAAATGGAGAGAAAGTAAGCAG 57.192 37.500 0.00 0.00 0.00 4.24
401 415 6.299141 TGAAAATGGAGAGAAAGTAAGCAGT 58.701 36.000 0.00 0.00 0.00 4.40
402 416 6.772716 TGAAAATGGAGAGAAAGTAAGCAGTT 59.227 34.615 0.00 0.00 0.00 3.16
403 417 7.936847 TGAAAATGGAGAGAAAGTAAGCAGTTA 59.063 33.333 0.00 0.00 0.00 2.24
404 418 7.674471 AAATGGAGAGAAAGTAAGCAGTTAC 57.326 36.000 0.00 0.00 39.17 2.50
405 419 5.148651 TGGAGAGAAAGTAAGCAGTTACC 57.851 43.478 0.00 0.00 39.65 2.85
406 420 4.174762 GGAGAGAAAGTAAGCAGTTACCG 58.825 47.826 0.00 0.00 39.65 4.02
407 421 4.174762 GAGAGAAAGTAAGCAGTTACCGG 58.825 47.826 0.00 0.00 39.65 5.28
408 422 2.671888 GAGAAAGTAAGCAGTTACCGGC 59.328 50.000 0.00 0.00 39.65 6.13
409 423 1.736126 GAAAGTAAGCAGTTACCGGCC 59.264 52.381 0.00 0.00 39.65 6.13
410 424 0.688487 AAGTAAGCAGTTACCGGCCA 59.312 50.000 0.00 0.00 39.65 5.36
411 425 0.249398 AGTAAGCAGTTACCGGCCAG 59.751 55.000 0.00 0.00 39.65 4.85
425 439 4.993029 CCGGCCAGGTCAAAATTAATAA 57.007 40.909 2.24 0.00 34.51 1.40
426 440 5.529581 CCGGCCAGGTCAAAATTAATAAT 57.470 39.130 2.24 0.00 34.51 1.28
427 441 5.528870 CCGGCCAGGTCAAAATTAATAATC 58.471 41.667 2.24 0.00 34.51 1.75
428 442 5.301805 CCGGCCAGGTCAAAATTAATAATCT 59.698 40.000 2.24 0.00 34.51 2.40
429 443 6.488683 CCGGCCAGGTCAAAATTAATAATCTA 59.511 38.462 2.24 0.00 34.51 1.98
430 444 7.308589 CCGGCCAGGTCAAAATTAATAATCTAG 60.309 40.741 2.24 0.00 34.51 2.43
431 445 7.444183 CGGCCAGGTCAAAATTAATAATCTAGA 59.556 37.037 2.24 0.00 0.00 2.43
432 446 9.131791 GGCCAGGTCAAAATTAATAATCTAGAA 57.868 33.333 0.00 0.00 0.00 2.10
433 447 9.952188 GCCAGGTCAAAATTAATAATCTAGAAC 57.048 33.333 0.00 0.00 0.00 3.01
451 465 9.614792 ATCTAGAACTATGTAAAATGGGTTCAC 57.385 33.333 0.00 0.00 36.52 3.18
452 466 8.044908 TCTAGAACTATGTAAAATGGGTTCACC 58.955 37.037 0.00 0.00 36.52 4.02
464 478 1.545841 GGTTCACCCCATGAGTTTCC 58.454 55.000 0.00 0.00 38.99 3.13
465 479 1.165270 GTTCACCCCATGAGTTTCCG 58.835 55.000 0.00 0.00 38.99 4.30
466 480 0.608035 TTCACCCCATGAGTTTCCGC 60.608 55.000 0.00 0.00 38.99 5.54
467 481 2.046285 CACCCCATGAGTTTCCGCC 61.046 63.158 0.00 0.00 0.00 6.13
468 482 2.440247 CCCCATGAGTTTCCGCCC 60.440 66.667 0.00 0.00 0.00 6.13
469 483 2.677228 CCCATGAGTTTCCGCCCT 59.323 61.111 0.00 0.00 0.00 5.19
470 484 1.000896 CCCATGAGTTTCCGCCCTT 60.001 57.895 0.00 0.00 0.00 3.95
471 485 0.611896 CCCATGAGTTTCCGCCCTTT 60.612 55.000 0.00 0.00 0.00 3.11
472 486 0.527565 CCATGAGTTTCCGCCCTTTG 59.472 55.000 0.00 0.00 0.00 2.77
473 487 0.527565 CATGAGTTTCCGCCCTTTGG 59.472 55.000 0.00 0.00 0.00 3.28
500 514 3.790091 GGGGGATAGTCACGAAGTTTAC 58.210 50.000 0.00 0.00 41.61 2.01
501 515 3.442100 GGGGATAGTCACGAAGTTTACG 58.558 50.000 0.00 0.00 41.61 3.18
502 516 3.119352 GGGGATAGTCACGAAGTTTACGT 60.119 47.826 0.00 0.00 41.61 3.57
543 557 4.884744 CACGGGATTATTTTGACCACCATA 59.115 41.667 0.00 0.00 0.00 2.74
568 582 8.361592 AGATGCGGTAATTACTGTAATGTTAC 57.638 34.615 22.44 12.85 35.04 2.50
995 4777 1.132977 TCCACACTGGACCTTCCACTA 60.133 52.381 0.00 0.00 42.67 2.74
1445 5233 0.903942 TTTGATGAAATGGGCTGCCC 59.096 50.000 30.97 30.97 45.71 5.36
1480 5268 1.839994 GGAACATCCTGATCACTGGGA 59.160 52.381 4.76 4.76 36.08 4.37
1527 5315 2.433436 GTATTTGCCTTGTTCCGGTCT 58.567 47.619 0.00 0.00 0.00 3.85
1551 5339 2.412870 CTTGCGTGTGGTGTAGATGAA 58.587 47.619 0.00 0.00 0.00 2.57
1602 5390 2.160615 CGTCATTCCGGTATGTGCAAAA 59.839 45.455 19.20 0.00 0.00 2.44
1614 5402 6.088824 GGTATGTGCAAAACTGAGAGATTTG 58.911 40.000 0.00 0.00 39.88 2.32
1671 5459 3.133003 AGACTGGGTTGGAATCTGATACG 59.867 47.826 0.00 0.00 0.00 3.06
1695 5483 3.023119 GTGTGGGAATGCATTGGTATCA 58.977 45.455 18.59 6.73 0.00 2.15
1779 5567 5.534207 TTCATTGCAAGGATGTTGTTTCT 57.466 34.783 15.42 0.00 0.00 2.52
1791 5579 6.209391 AGGATGTTGTTTCTTGGAATTCGATT 59.791 34.615 0.00 0.00 0.00 3.34
1806 5594 5.906113 ATTCGATTATCGCAGGATACTCT 57.094 39.130 10.02 0.00 41.59 3.24
1884 5672 7.083875 GGAATGTCTTCCGAATTATTCAACA 57.916 36.000 5.76 2.12 41.60 3.33
1890 5678 5.815740 TCTTCCGAATTATTCAACAGTAGCC 59.184 40.000 5.76 0.00 0.00 3.93
1914 5702 6.260936 CCAATATTCTTCCTGTATGCTCGTTT 59.739 38.462 0.00 0.00 0.00 3.60
1986 5774 5.123820 CCGGTTTGGCTTATATATGGACATG 59.876 44.000 0.00 0.00 0.00 3.21
2361 6149 8.750298 AGATTTGATGATGCTCTTCATTCTTTT 58.250 29.630 0.71 0.00 36.48 2.27
2775 6563 5.892160 TCTTCAATCAAATGCCTGAGAAG 57.108 39.130 0.00 0.00 32.69 2.85
2802 6590 5.763355 AGGACAACATGGAATCTCATGATT 58.237 37.500 15.28 0.00 45.30 2.57
2898 6686 7.067494 ACTGTTGGCATTACAAATATTCTCCTC 59.933 37.037 0.00 0.00 31.17 3.71
3039 6827 6.350110 GCGGGAATATAACCAATGCATACAAT 60.350 38.462 0.00 0.00 0.00 2.71
3321 7109 4.699522 GACCTTCTTGCCCGCGGT 62.700 66.667 26.12 0.43 0.00 5.68
3350 7138 3.472652 TCCAAGACGCATACAGTTTTGT 58.527 40.909 0.00 0.00 41.39 2.83
3427 7215 1.211212 CATGCAAGGTCCATGGAGAGA 59.789 52.381 16.81 0.00 37.12 3.10
3628 7416 8.677300 CACTTGTTTATAGCCAGTGATGTTAAT 58.323 33.333 0.00 0.00 0.00 1.40
3720 7508 5.587289 TGGCAAAGAACATTCAGTTACAAC 58.413 37.500 0.00 0.00 41.51 3.32
3757 7545 2.566833 TTGATCTGGTCACAGGGTTG 57.433 50.000 0.00 0.00 44.99 3.77
3769 7557 2.033801 CACAGGGTTGCAGAAACTTGAG 59.966 50.000 0.00 0.00 38.92 3.02
3791 7579 6.432783 TGAGTTGGAGTTTTTCTTCTCAAACA 59.567 34.615 12.80 0.00 43.27 2.83
3798 7586 7.976175 GGAGTTTTTCTTCTCAAACATGTCTTT 59.024 33.333 0.00 0.00 35.66 2.52
3801 7589 8.382875 GTTTTTCTTCTCAAACATGTCTTTTGG 58.617 33.333 0.00 0.00 35.12 3.28
3812 7600 3.040147 TGTCTTTTGGTAGCTCTTCCG 57.960 47.619 0.00 0.00 0.00 4.30
3863 7651 6.745159 TGCAAATACGAAATTACCTAAGCA 57.255 33.333 0.00 0.00 0.00 3.91
3873 7661 7.700656 ACGAAATTACCTAAGCACATTAAATGC 59.299 33.333 6.92 6.92 43.74 3.56
3898 7686 2.604969 TTTTGGTCGTTTGCGCTATC 57.395 45.000 9.73 0.00 38.14 2.08
3934 7722 3.482156 AGATAACAGCATGCTACCAGG 57.518 47.619 22.19 10.36 42.53 4.45
3971 7759 6.503524 AGCGTTACTTGATTGAATTTTGTGT 58.496 32.000 0.00 0.00 0.00 3.72
3974 7762 8.365210 GCGTTACTTGATTGAATTTTGTGTATG 58.635 33.333 0.00 0.00 0.00 2.39
3976 7764 9.410556 GTTACTTGATTGAATTTTGTGTATGCT 57.589 29.630 0.00 0.00 0.00 3.79
4000 7788 1.893786 GTCTCCTGACATCCAGCGT 59.106 57.895 0.00 0.00 42.48 5.07
4006 7794 0.798776 CTGACATCCAGCGTTGGTTC 59.201 55.000 18.51 13.09 45.26 3.62
4074 7865 9.903682 CTTATGCTAACAAATTCATCCTATTGG 57.096 33.333 0.00 0.00 0.00 3.16
4079 7870 6.855763 AACAAATTCATCCTATTGGCAGAA 57.144 33.333 3.52 3.52 33.01 3.02
4106 7897 5.815581 AGACAAATAAGTAACATGGCTCCA 58.184 37.500 0.00 0.00 0.00 3.86
4123 7914 2.441532 AGGCCACAGCATGCATCC 60.442 61.111 21.98 12.45 42.53 3.51
4157 7949 5.526115 GCAAGCAGCAAATATATCATGTGT 58.474 37.500 0.00 0.00 44.79 3.72
4163 7955 7.119407 AGCAGCAAATATATCATGTGTCATCTC 59.881 37.037 0.00 0.00 0.00 2.75
4190 7982 3.193903 GGAACTCTCTTCGGCTTTCTACT 59.806 47.826 0.00 0.00 0.00 2.57
4211 8003 3.945640 AAGTACCAACCAAGGTTCAGT 57.054 42.857 0.51 5.56 43.08 3.41
4212 8004 3.208747 AGTACCAACCAAGGTTCAGTG 57.791 47.619 0.51 0.00 43.08 3.66
4217 8009 2.958355 CCAACCAAGGTTCAGTGACATT 59.042 45.455 0.51 0.00 36.00 2.71
4220 8012 2.878406 ACCAAGGTTCAGTGACATTTCG 59.122 45.455 0.00 0.00 0.00 3.46
4237 8029 5.584251 ACATTTCGTTTTTGTTCATGCCTTT 59.416 32.000 0.00 0.00 0.00 3.11
4251 8043 3.029320 TGCCTTTCATCACAACAATGC 57.971 42.857 0.00 0.00 0.00 3.56
4270 8062 5.779529 ATGCTGTTTGTTTCTGACATCTT 57.220 34.783 0.00 0.00 38.26 2.40
4272 8064 6.304356 TGCTGTTTGTTTCTGACATCTTAG 57.696 37.500 0.00 0.00 38.26 2.18
4274 8066 6.318648 TGCTGTTTGTTTCTGACATCTTAGTT 59.681 34.615 0.00 0.00 38.26 2.24
4275 8067 6.634436 GCTGTTTGTTTCTGACATCTTAGTTG 59.366 38.462 0.00 0.00 38.26 3.16
4282 8074 8.201464 TGTTTCTGACATCTTAGTTGTCTTGTA 58.799 33.333 19.97 7.98 43.12 2.41
4337 8129 3.196254 AGGGTGCCTGCTGATTAATTTTG 59.804 43.478 0.00 0.00 29.57 2.44
4367 8159 7.013846 CCAGAGGGAAACTTATTGTGTGTTTTA 59.986 37.037 0.00 0.00 34.55 1.52
4392 8184 1.001048 GCATGCTGACTTGCAAGAACA 60.001 47.619 32.50 26.08 46.61 3.18
4407 8203 1.318251 GAACACATTCTTGTTCGCGC 58.682 50.000 0.00 0.00 44.41 6.86
4468 8279 4.266714 TGCCTTAAGATTTACCTTTCCGG 58.733 43.478 3.36 0.00 39.35 5.14
4478 8289 1.220749 CCTTTCCGGCGATCCTTCA 59.779 57.895 9.30 0.00 0.00 3.02
4547 8358 8.364129 TGGAATTGTTTTCTTCATAAAGTTGC 57.636 30.769 0.00 0.00 33.95 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.963465 GGAAAACGTTGCAAGGAAAATTAAAAA 59.037 29.630 24.88 0.00 0.00 1.94
10 11 7.119262 TGGAAAACGTTGCAAGGAAAATTAAAA 59.881 29.630 24.88 0.54 31.30 1.52
11 12 6.594159 TGGAAAACGTTGCAAGGAAAATTAAA 59.406 30.769 24.88 1.85 31.30 1.52
12 13 6.106673 TGGAAAACGTTGCAAGGAAAATTAA 58.893 32.000 24.88 3.09 31.30 1.40
13 14 5.661458 TGGAAAACGTTGCAAGGAAAATTA 58.339 33.333 24.88 5.19 31.30 1.40
14 15 4.508662 TGGAAAACGTTGCAAGGAAAATT 58.491 34.783 24.88 13.03 31.30 1.82
15 16 4.130286 TGGAAAACGTTGCAAGGAAAAT 57.870 36.364 24.88 8.39 31.30 1.82
16 17 3.594603 TGGAAAACGTTGCAAGGAAAA 57.405 38.095 24.88 2.50 31.30 2.29
17 18 3.254892 GTTGGAAAACGTTGCAAGGAAA 58.745 40.909 24.88 6.99 44.59 3.13
18 19 2.231478 TGTTGGAAAACGTTGCAAGGAA 59.769 40.909 24.88 5.45 44.59 3.36
19 20 1.819288 TGTTGGAAAACGTTGCAAGGA 59.181 42.857 24.88 0.00 44.59 3.36
20 21 2.159310 TCTGTTGGAAAACGTTGCAAGG 60.159 45.455 17.21 17.21 44.59 3.61
21 22 2.851824 GTCTGTTGGAAAACGTTGCAAG 59.148 45.455 0.00 0.00 44.59 4.01
22 23 2.729467 CGTCTGTTGGAAAACGTTGCAA 60.729 45.455 0.00 0.00 42.14 4.08
23 24 1.202087 CGTCTGTTGGAAAACGTTGCA 60.202 47.619 0.00 0.00 32.56 4.08
24 25 1.062880 TCGTCTGTTGGAAAACGTTGC 59.937 47.619 0.00 0.00 36.55 4.17
25 26 3.288242 CATCGTCTGTTGGAAAACGTTG 58.712 45.455 0.00 0.00 36.55 4.10
26 27 2.289547 CCATCGTCTGTTGGAAAACGTT 59.710 45.455 0.00 0.00 37.16 3.99
27 28 1.871039 CCATCGTCTGTTGGAAAACGT 59.129 47.619 0.00 0.00 37.16 3.99
28 29 1.196808 CCCATCGTCTGTTGGAAAACG 59.803 52.381 0.00 0.00 37.16 3.60
29 30 2.225727 GACCCATCGTCTGTTGGAAAAC 59.774 50.000 0.00 0.00 37.16 2.43
30 31 2.500229 GACCCATCGTCTGTTGGAAAA 58.500 47.619 0.00 0.00 37.16 2.29
31 32 1.606994 CGACCCATCGTCTGTTGGAAA 60.607 52.381 0.00 0.00 43.66 3.13
32 33 0.037697 CGACCCATCGTCTGTTGGAA 60.038 55.000 0.00 0.00 43.66 3.53
33 34 1.589630 CGACCCATCGTCTGTTGGA 59.410 57.895 0.00 0.00 43.66 3.53
34 35 4.185413 CGACCCATCGTCTGTTGG 57.815 61.111 0.00 0.00 43.66 3.77
43 44 4.312443 TCAAAAGTAGTTGACGACCCATC 58.688 43.478 0.00 0.00 32.56 3.51
44 45 4.345859 TCAAAAGTAGTTGACGACCCAT 57.654 40.909 0.00 0.00 32.56 4.00
45 46 3.823281 TCAAAAGTAGTTGACGACCCA 57.177 42.857 0.00 0.00 32.56 4.51
46 47 5.684550 AAATCAAAAGTAGTTGACGACCC 57.315 39.130 0.00 0.00 40.22 4.46
47 48 6.721321 TCAAAATCAAAAGTAGTTGACGACC 58.279 36.000 0.00 0.00 40.22 4.79
48 49 7.627340 TCTCAAAATCAAAAGTAGTTGACGAC 58.373 34.615 0.00 0.00 40.22 4.34
49 50 7.042051 CCTCTCAAAATCAAAAGTAGTTGACGA 60.042 37.037 0.00 0.00 40.22 4.20
50 51 7.072030 CCTCTCAAAATCAAAAGTAGTTGACG 58.928 38.462 0.00 0.00 40.22 4.35
51 52 6.858478 GCCTCTCAAAATCAAAAGTAGTTGAC 59.142 38.462 0.00 0.00 40.22 3.18
52 53 6.016276 GGCCTCTCAAAATCAAAAGTAGTTGA 60.016 38.462 0.00 0.00 41.59 3.18
53 54 6.152379 GGCCTCTCAAAATCAAAAGTAGTTG 58.848 40.000 0.00 0.00 0.00 3.16
54 55 5.243954 GGGCCTCTCAAAATCAAAAGTAGTT 59.756 40.000 0.84 0.00 0.00 2.24
55 56 4.767409 GGGCCTCTCAAAATCAAAAGTAGT 59.233 41.667 0.84 0.00 0.00 2.73
56 57 4.142600 CGGGCCTCTCAAAATCAAAAGTAG 60.143 45.833 0.84 0.00 0.00 2.57
57 58 3.756434 CGGGCCTCTCAAAATCAAAAGTA 59.244 43.478 0.84 0.00 0.00 2.24
58 59 2.558359 CGGGCCTCTCAAAATCAAAAGT 59.442 45.455 0.84 0.00 0.00 2.66
59 60 2.094545 CCGGGCCTCTCAAAATCAAAAG 60.095 50.000 0.84 0.00 0.00 2.27
60 61 1.892474 CCGGGCCTCTCAAAATCAAAA 59.108 47.619 0.84 0.00 0.00 2.44
61 62 1.074727 TCCGGGCCTCTCAAAATCAAA 59.925 47.619 0.84 0.00 0.00 2.69
62 63 0.695924 TCCGGGCCTCTCAAAATCAA 59.304 50.000 0.84 0.00 0.00 2.57
63 64 0.253044 CTCCGGGCCTCTCAAAATCA 59.747 55.000 0.84 0.00 0.00 2.57
64 65 0.253327 ACTCCGGGCCTCTCAAAATC 59.747 55.000 0.84 0.00 0.00 2.17
65 66 1.209747 GTACTCCGGGCCTCTCAAAAT 59.790 52.381 0.84 0.00 0.00 1.82
66 67 0.611714 GTACTCCGGGCCTCTCAAAA 59.388 55.000 0.84 0.00 0.00 2.44
67 68 0.543410 TGTACTCCGGGCCTCTCAAA 60.543 55.000 0.84 0.00 0.00 2.69
68 69 1.077805 TGTACTCCGGGCCTCTCAA 59.922 57.895 0.84 0.00 0.00 3.02
69 70 1.681327 GTGTACTCCGGGCCTCTCA 60.681 63.158 0.84 0.00 0.00 3.27
70 71 2.772691 CGTGTACTCCGGGCCTCTC 61.773 68.421 0.84 0.00 0.00 3.20
71 72 2.754658 CGTGTACTCCGGGCCTCT 60.755 66.667 0.84 0.00 0.00 3.69
72 73 3.061260 GACGTGTACTCCGGGCCTC 62.061 68.421 0.84 0.00 0.00 4.70
73 74 3.066814 GACGTGTACTCCGGGCCT 61.067 66.667 0.84 0.00 0.00 5.19
74 75 4.139234 GGACGTGTACTCCGGGCC 62.139 72.222 0.00 0.00 0.00 5.80
75 76 4.487412 CGGACGTGTACTCCGGGC 62.487 72.222 12.90 3.92 45.90 6.13
80 81 1.799383 GGGAGTCGGACGTGTACTC 59.201 63.158 11.31 11.31 39.12 2.59
81 82 2.037136 CGGGAGTCGGACGTGTACT 61.037 63.158 0.00 0.00 34.75 2.73
82 83 1.577328 TTCGGGAGTCGGACGTGTAC 61.577 60.000 0.00 0.00 39.77 2.90
83 84 0.888736 TTTCGGGAGTCGGACGTGTA 60.889 55.000 0.00 0.00 39.77 2.90
84 85 2.195567 TTTCGGGAGTCGGACGTGT 61.196 57.895 0.00 0.00 39.77 4.49
85 86 1.731969 GTTTCGGGAGTCGGACGTG 60.732 63.158 0.00 0.00 39.77 4.49
86 87 1.737355 TTGTTTCGGGAGTCGGACGT 61.737 55.000 1.89 0.00 39.77 4.34
87 88 1.007038 TTGTTTCGGGAGTCGGACG 60.007 57.895 1.89 0.00 39.77 4.79
88 89 0.316204 TCTTGTTTCGGGAGTCGGAC 59.684 55.000 0.00 0.00 39.77 4.79
89 90 1.067142 CATCTTGTTTCGGGAGTCGGA 60.067 52.381 0.00 0.00 39.77 4.55
90 91 1.359848 CATCTTGTTTCGGGAGTCGG 58.640 55.000 0.00 0.00 39.77 4.79
91 92 0.721718 GCATCTTGTTTCGGGAGTCG 59.278 55.000 0.00 0.00 40.90 4.18
92 93 1.808411 TGCATCTTGTTTCGGGAGTC 58.192 50.000 0.00 0.00 0.00 3.36
93 94 2.359900 GATGCATCTTGTTTCGGGAGT 58.640 47.619 19.70 0.00 0.00 3.85
94 95 1.328680 CGATGCATCTTGTTTCGGGAG 59.671 52.381 23.73 0.47 0.00 4.30
95 96 1.368641 CGATGCATCTTGTTTCGGGA 58.631 50.000 23.73 0.00 0.00 5.14
96 97 0.248215 GCGATGCATCTTGTTTCGGG 60.248 55.000 23.73 6.60 0.00 5.14
97 98 0.447406 TGCGATGCATCTTGTTTCGG 59.553 50.000 23.73 7.30 31.71 4.30
98 99 3.973923 TGCGATGCATCTTGTTTCG 57.026 47.368 23.73 11.92 31.71 3.46
108 109 2.415759 GGATTTGACAACATGCGATGCA 60.416 45.455 0.00 0.00 44.86 3.96
109 110 2.159338 AGGATTTGACAACATGCGATGC 60.159 45.455 0.00 0.00 0.00 3.91
110 111 3.770263 AGGATTTGACAACATGCGATG 57.230 42.857 0.00 0.00 0.00 3.84
111 112 3.119388 CCAAGGATTTGACAACATGCGAT 60.119 43.478 0.00 0.00 36.36 4.58
112 113 2.228582 CCAAGGATTTGACAACATGCGA 59.771 45.455 0.00 0.00 36.36 5.10
113 114 2.598589 CCAAGGATTTGACAACATGCG 58.401 47.619 0.00 0.00 36.36 4.73
114 115 2.299867 ACCCAAGGATTTGACAACATGC 59.700 45.455 0.00 0.00 36.36 4.06
115 116 3.366273 CGACCCAAGGATTTGACAACATG 60.366 47.826 0.00 0.00 36.36 3.21
116 117 2.819608 CGACCCAAGGATTTGACAACAT 59.180 45.455 0.00 0.00 36.36 2.71
117 118 2.226330 CGACCCAAGGATTTGACAACA 58.774 47.619 0.00 0.00 36.36 3.33
118 119 1.539827 CCGACCCAAGGATTTGACAAC 59.460 52.381 0.00 0.00 36.36 3.32
119 120 1.144093 ACCGACCCAAGGATTTGACAA 59.856 47.619 0.00 0.00 36.36 3.18
120 121 0.768622 ACCGACCCAAGGATTTGACA 59.231 50.000 0.00 0.00 36.36 3.58
121 122 1.165270 CACCGACCCAAGGATTTGAC 58.835 55.000 0.00 0.00 36.36 3.18
122 123 0.768622 ACACCGACCCAAGGATTTGA 59.231 50.000 0.00 0.00 36.36 2.69
123 124 1.269448 CAACACCGACCCAAGGATTTG 59.731 52.381 0.00 0.00 0.00 2.32
124 125 1.144093 TCAACACCGACCCAAGGATTT 59.856 47.619 0.00 0.00 0.00 2.17
125 126 0.768622 TCAACACCGACCCAAGGATT 59.231 50.000 0.00 0.00 0.00 3.01
126 127 0.036306 GTCAACACCGACCCAAGGAT 59.964 55.000 0.00 0.00 0.00 3.24
127 128 1.338890 TGTCAACACCGACCCAAGGA 61.339 55.000 0.00 0.00 34.88 3.36
128 129 0.464735 TTGTCAACACCGACCCAAGG 60.465 55.000 0.00 0.00 34.88 3.61
129 130 0.661020 GTTGTCAACACCGACCCAAG 59.339 55.000 10.93 0.00 34.88 3.61
130 131 0.253610 AGTTGTCAACACCGACCCAA 59.746 50.000 17.78 0.00 34.88 4.12
131 132 0.253610 AAGTTGTCAACACCGACCCA 59.746 50.000 17.78 0.00 34.88 4.51
132 133 0.942252 GAAGTTGTCAACACCGACCC 59.058 55.000 17.78 0.00 34.88 4.46
133 134 1.658994 TGAAGTTGTCAACACCGACC 58.341 50.000 17.78 1.32 34.88 4.79
134 135 2.933906 TCTTGAAGTTGTCAACACCGAC 59.066 45.455 17.78 4.95 41.47 4.79
135 136 3.254470 TCTTGAAGTTGTCAACACCGA 57.746 42.857 17.78 7.60 41.47 4.69
136 137 4.552166 AATCTTGAAGTTGTCAACACCG 57.448 40.909 17.78 5.94 41.47 4.94
139 140 9.624697 GCAATTATAATCTTGAAGTTGTCAACA 57.375 29.630 17.78 0.00 41.47 3.33
140 141 9.624697 TGCAATTATAATCTTGAAGTTGTCAAC 57.375 29.630 7.68 7.68 41.47 3.18
142 143 9.791820 CATGCAATTATAATCTTGAAGTTGTCA 57.208 29.630 0.00 0.00 0.00 3.58
143 144 9.793252 ACATGCAATTATAATCTTGAAGTTGTC 57.207 29.630 0.00 0.00 0.00 3.18
144 145 9.577110 CACATGCAATTATAATCTTGAAGTTGT 57.423 29.630 0.00 0.00 0.00 3.32
145 146 8.537223 GCACATGCAATTATAATCTTGAAGTTG 58.463 33.333 0.00 0.00 41.59 3.16
146 147 8.638685 GCACATGCAATTATAATCTTGAAGTT 57.361 30.769 0.00 0.00 41.59 2.66
164 165 6.369059 AGATCAAATAGTAGTTGCACATGC 57.631 37.500 5.46 0.00 42.50 4.06
165 166 7.977904 TCAAGATCAAATAGTAGTTGCACATG 58.022 34.615 5.46 5.74 0.00 3.21
166 167 8.565896 TTCAAGATCAAATAGTAGTTGCACAT 57.434 30.769 5.46 0.00 0.00 3.21
167 168 7.977789 TTCAAGATCAAATAGTAGTTGCACA 57.022 32.000 5.46 0.00 0.00 4.57
168 169 9.677567 TTTTTCAAGATCAAATAGTAGTTGCAC 57.322 29.630 5.46 2.71 0.00 4.57
169 170 9.677567 GTTTTTCAAGATCAAATAGTAGTTGCA 57.322 29.630 5.46 0.00 0.00 4.08
170 171 9.677567 TGTTTTTCAAGATCAAATAGTAGTTGC 57.322 29.630 5.46 0.00 0.00 4.17
179 180 9.661563 ATGCACATATGTTTTTCAAGATCAAAT 57.338 25.926 5.37 0.00 0.00 2.32
180 181 9.491675 AATGCACATATGTTTTTCAAGATCAAA 57.508 25.926 5.37 0.00 0.00 2.69
181 182 9.491675 AAATGCACATATGTTTTTCAAGATCAA 57.508 25.926 5.37 0.00 0.00 2.57
184 185 9.926158 TGTAAATGCACATATGTTTTTCAAGAT 57.074 25.926 5.37 0.00 0.00 2.40
185 186 9.190858 GTGTAAATGCACATATGTTTTTCAAGA 57.809 29.630 5.37 0.00 39.07 3.02
186 187 8.434661 GGTGTAAATGCACATATGTTTTTCAAG 58.565 33.333 5.37 0.00 40.89 3.02
187 188 7.115520 CGGTGTAAATGCACATATGTTTTTCAA 59.884 33.333 5.37 0.00 40.89 2.69
188 189 6.584184 CGGTGTAAATGCACATATGTTTTTCA 59.416 34.615 5.37 6.21 40.89 2.69
189 190 6.804295 TCGGTGTAAATGCACATATGTTTTTC 59.196 34.615 5.37 3.69 40.89 2.29
190 191 6.682746 TCGGTGTAAATGCACATATGTTTTT 58.317 32.000 5.37 9.12 40.89 1.94
191 192 6.150307 TCTCGGTGTAAATGCACATATGTTTT 59.850 34.615 5.37 7.39 40.89 2.43
192 193 5.645929 TCTCGGTGTAAATGCACATATGTTT 59.354 36.000 5.37 0.43 40.89 2.83
193 194 5.182487 TCTCGGTGTAAATGCACATATGTT 58.818 37.500 5.37 0.00 40.89 2.71
194 195 4.765273 TCTCGGTGTAAATGCACATATGT 58.235 39.130 1.41 1.41 40.89 2.29
195 196 5.733226 TTCTCGGTGTAAATGCACATATG 57.267 39.130 0.00 0.00 40.89 1.78
196 197 5.880332 AGTTTCTCGGTGTAAATGCACATAT 59.120 36.000 4.09 0.00 40.89 1.78
197 198 5.242434 AGTTTCTCGGTGTAAATGCACATA 58.758 37.500 4.09 0.00 40.89 2.29
198 199 4.072131 AGTTTCTCGGTGTAAATGCACAT 58.928 39.130 4.09 0.00 40.89 3.21
199 200 3.472652 AGTTTCTCGGTGTAAATGCACA 58.527 40.909 4.09 0.00 40.89 4.57
200 201 5.796350 ATAGTTTCTCGGTGTAAATGCAC 57.204 39.130 0.00 0.00 38.56 4.57
201 202 7.908827 TTAATAGTTTCTCGGTGTAAATGCA 57.091 32.000 0.00 0.00 0.00 3.96
202 203 9.783256 AATTTAATAGTTTCTCGGTGTAAATGC 57.217 29.630 0.00 0.00 0.00 3.56
205 206 9.287373 ACCAATTTAATAGTTTCTCGGTGTAAA 57.713 29.630 0.00 0.00 0.00 2.01
206 207 8.723311 CACCAATTTAATAGTTTCTCGGTGTAA 58.277 33.333 0.00 0.00 36.33 2.41
207 208 8.095792 TCACCAATTTAATAGTTTCTCGGTGTA 58.904 33.333 0.00 0.00 40.76 2.90
208 209 6.938030 TCACCAATTTAATAGTTTCTCGGTGT 59.062 34.615 0.00 0.00 40.76 4.16
209 210 7.372451 TCACCAATTTAATAGTTTCTCGGTG 57.628 36.000 0.00 0.00 41.19 4.94
210 211 7.610305 ACATCACCAATTTAATAGTTTCTCGGT 59.390 33.333 0.00 0.00 0.00 4.69
211 212 7.985476 ACATCACCAATTTAATAGTTTCTCGG 58.015 34.615 0.00 0.00 0.00 4.63
212 213 8.664798 TGACATCACCAATTTAATAGTTTCTCG 58.335 33.333 0.00 0.00 0.00 4.04
369 383 2.448961 TCTCTCCATTTTCAAACCCCCA 59.551 45.455 0.00 0.00 0.00 4.96
379 393 7.175119 GGTAACTGCTTACTTTCTCTCCATTTT 59.825 37.037 0.00 0.00 33.83 1.82
404 418 4.993029 TTATTAATTTTGACCTGGCCGG 57.007 40.909 3.88 3.88 39.35 6.13
405 419 6.391227 AGATTATTAATTTTGACCTGGCCG 57.609 37.500 0.00 0.00 0.00 6.13
406 420 8.691661 TCTAGATTATTAATTTTGACCTGGCC 57.308 34.615 0.00 0.00 0.00 5.36
407 421 9.952188 GTTCTAGATTATTAATTTTGACCTGGC 57.048 33.333 0.00 0.00 0.00 4.85
425 439 9.614792 GTGAACCCATTTTACATAGTTCTAGAT 57.385 33.333 0.00 0.00 35.71 1.98
426 440 8.044908 GGTGAACCCATTTTACATAGTTCTAGA 58.955 37.037 0.00 0.00 35.71 2.43
427 441 8.209917 GGTGAACCCATTTTACATAGTTCTAG 57.790 38.462 0.00 0.00 35.71 2.43
445 459 1.545841 GGAAACTCATGGGGTGAACC 58.454 55.000 0.00 0.00 36.14 3.62
446 460 1.165270 CGGAAACTCATGGGGTGAAC 58.835 55.000 0.00 0.00 36.14 3.18
447 461 0.608035 GCGGAAACTCATGGGGTGAA 60.608 55.000 0.00 0.00 36.14 3.18
448 462 1.002624 GCGGAAACTCATGGGGTGA 60.003 57.895 0.00 0.00 35.05 4.02
449 463 2.046285 GGCGGAAACTCATGGGGTG 61.046 63.158 0.00 0.00 0.00 4.61
450 464 2.355115 GGCGGAAACTCATGGGGT 59.645 61.111 0.00 0.00 0.00 4.95
451 465 2.440247 GGGCGGAAACTCATGGGG 60.440 66.667 0.00 0.00 0.00 4.96
452 466 0.611896 AAAGGGCGGAAACTCATGGG 60.612 55.000 0.00 0.00 0.00 4.00
453 467 0.527565 CAAAGGGCGGAAACTCATGG 59.472 55.000 0.00 0.00 0.00 3.66
454 468 0.527565 CCAAAGGGCGGAAACTCATG 59.472 55.000 0.00 0.00 0.00 3.07
455 469 0.611896 CCCAAAGGGCGGAAACTCAT 60.612 55.000 0.00 0.00 35.35 2.90
456 470 1.228429 CCCAAAGGGCGGAAACTCA 60.228 57.895 0.00 0.00 35.35 3.41
457 471 3.681473 CCCAAAGGGCGGAAACTC 58.319 61.111 0.00 0.00 35.35 3.01
479 493 3.736126 CGTAAACTTCGTGACTATCCCCC 60.736 52.174 0.00 0.00 0.00 5.40
480 494 3.119352 ACGTAAACTTCGTGACTATCCCC 60.119 47.826 0.00 0.00 40.07 4.81
481 495 4.102035 ACGTAAACTTCGTGACTATCCC 57.898 45.455 0.00 0.00 40.07 3.85
490 504 5.096849 ACAAAAATTGCACGTAAACTTCGT 58.903 33.333 0.00 0.00 42.33 3.85
491 505 5.613964 ACAAAAATTGCACGTAAACTTCG 57.386 34.783 0.00 0.00 0.00 3.79
492 506 6.416750 AGCTACAAAAATTGCACGTAAACTTC 59.583 34.615 0.00 0.00 0.00 3.01
493 507 6.270064 AGCTACAAAAATTGCACGTAAACTT 58.730 32.000 0.00 0.00 0.00 2.66
494 508 5.827666 AGCTACAAAAATTGCACGTAAACT 58.172 33.333 0.00 0.00 0.00 2.66
495 509 6.344032 CAAGCTACAAAAATTGCACGTAAAC 58.656 36.000 0.00 0.00 0.00 2.01
496 510 5.051374 GCAAGCTACAAAAATTGCACGTAAA 60.051 36.000 4.02 0.00 45.66 2.01
497 511 4.442733 GCAAGCTACAAAAATTGCACGTAA 59.557 37.500 4.02 0.00 45.66 3.18
498 512 3.978217 GCAAGCTACAAAAATTGCACGTA 59.022 39.130 4.02 0.00 45.66 3.57
499 513 2.794350 GCAAGCTACAAAAATTGCACGT 59.206 40.909 4.02 0.00 45.66 4.49
500 514 3.422890 GCAAGCTACAAAAATTGCACG 57.577 42.857 4.02 0.00 45.66 5.34
503 517 2.155539 CCGTGCAAGCTACAAAAATTGC 59.844 45.455 0.00 1.96 46.36 3.56
504 518 2.730928 CCCGTGCAAGCTACAAAAATTG 59.269 45.455 0.00 0.00 0.00 2.32
521 535 3.443145 TGGTGGTCAAAATAATCCCGT 57.557 42.857 0.00 0.00 0.00 5.28
543 557 7.982919 TGTAACATTACAGTAATTACCGCATCT 59.017 33.333 12.05 0.00 38.64 2.90
568 582 7.383050 TGGTTAAAATTTGACGTCGAATTTG 57.617 32.000 38.58 0.00 44.76 2.32
693 709 9.546428 GCAATTTCCTAGCAATTATGGTAAATT 57.454 29.630 0.00 0.00 38.93 1.82
730 762 9.198837 ACCGGTTTTCATGTCAAATTTAATTAC 57.801 29.630 0.00 0.00 0.00 1.89
852 4621 0.107214 GAAATGATGGGGCCGAGACA 60.107 55.000 0.00 0.00 0.00 3.41
995 4777 1.203441 TGTGAGGAGGAGCATGGCTT 61.203 55.000 0.00 0.00 39.88 4.35
1362 5150 1.815003 CATGATCGCCTTCGCCACA 60.815 57.895 0.00 0.00 35.26 4.17
1422 5210 2.932187 GCAGCCCATTTCATCAAACACC 60.932 50.000 0.00 0.00 0.00 4.16
1445 5233 0.316689 GTTCCAACAAACCGCGTCAG 60.317 55.000 4.92 0.00 0.00 3.51
1455 5243 4.074259 CAGTGATCAGGATGTTCCAACAA 58.926 43.478 0.00 0.00 43.03 2.83
1495 5283 4.078363 AGGCAAATACGTCGTCAAAATG 57.922 40.909 0.00 0.00 0.00 2.32
1527 5315 1.273886 TCTACACCACACGCAAGCATA 59.726 47.619 0.00 0.00 45.62 3.14
1569 5357 0.949105 GAATGACGACAGCCACCGTT 60.949 55.000 0.00 0.00 39.30 4.44
1602 5390 1.066573 CCAGCCGTCAAATCTCTCAGT 60.067 52.381 0.00 0.00 0.00 3.41
1614 5402 2.997897 ACACTCCTCCCAGCCGTC 60.998 66.667 0.00 0.00 0.00 4.79
1671 5459 1.344114 ACCAATGCATTCCCACACAAC 59.656 47.619 9.53 0.00 0.00 3.32
1695 5483 4.268797 TGCACCACATTTTGCATACATT 57.731 36.364 0.00 0.00 43.79 2.71
1779 5567 4.066646 TCCTGCGATAATCGAATTCCAA 57.933 40.909 0.00 0.00 43.74 3.53
1791 5579 4.460731 CCATTCTCAGAGTATCCTGCGATA 59.539 45.833 0.00 0.00 33.66 2.92
1806 5594 3.762407 TCTTCGAACAACCCATTCTCA 57.238 42.857 0.00 0.00 0.00 3.27
1884 5672 6.043706 AGCATACAGGAAGAATATTGGCTACT 59.956 38.462 0.00 0.00 0.00 2.57
1890 5678 6.851222 AACGAGCATACAGGAAGAATATTG 57.149 37.500 0.00 0.00 0.00 1.90
1914 5702 5.342017 CCATAGTTCCTCCCATACTCCATA 58.658 45.833 0.00 0.00 0.00 2.74
1986 5774 3.125146 TCATCAGCGCATTACAAACAGAC 59.875 43.478 11.47 0.00 0.00 3.51
2176 5964 9.212641 CAGACTAATGAAAGAAACAGAATCAGA 57.787 33.333 0.00 0.00 0.00 3.27
2361 6149 5.951148 TGAATCCTTGTCCAAAATATCAGCA 59.049 36.000 0.00 0.00 0.00 4.41
2493 6281 7.821652 TGCGGATAAAATTTAAGATTGTGACA 58.178 30.769 0.00 0.00 0.00 3.58
2760 6548 4.040047 TCCTATCCTTCTCAGGCATTTGA 58.960 43.478 0.00 0.00 40.58 2.69
2775 6563 5.296151 TGAGATTCCATGTTGTCCTATCC 57.704 43.478 0.00 0.00 0.00 2.59
2802 6590 6.259829 ACATATTATTGCGTGCATACAACTGA 59.740 34.615 6.51 0.00 0.00 3.41
2898 6686 2.523015 GAACTCAAATGGATGCAAGCG 58.477 47.619 0.00 0.00 0.00 4.68
3039 6827 4.021229 TGTTAGGGCTGACTCGAAATAGA 58.979 43.478 0.00 0.00 0.00 1.98
3350 7138 0.550914 GTGAGGGGGCATATCCAACA 59.449 55.000 0.00 0.00 36.21 3.33
3427 7215 1.068753 CGAGCTGGCCGATTCTGAT 59.931 57.895 0.00 0.00 0.00 2.90
3628 7416 8.963725 TCGTAGATAAAAGAACTATCTTGGTGA 58.036 33.333 0.00 0.00 45.19 4.02
3720 7508 7.274904 CCAGATCAATTGCACTAATGTTGAAAG 59.725 37.037 0.00 0.00 0.00 2.62
3757 7545 4.639135 AAACTCCAACTCAAGTTTCTGC 57.361 40.909 0.00 0.00 40.74 4.26
3769 7557 7.035612 ACATGTTTGAGAAGAAAAACTCCAAC 58.964 34.615 0.00 0.00 38.44 3.77
3791 7579 3.260884 TCGGAAGAGCTACCAAAAGACAT 59.739 43.478 0.00 0.00 34.84 3.06
3870 7658 2.801679 CAAACGACCAAAATGCAAGCAT 59.198 40.909 0.86 0.86 38.46 3.79
3871 7659 2.200067 CAAACGACCAAAATGCAAGCA 58.800 42.857 0.00 0.00 0.00 3.91
3872 7660 1.070643 GCAAACGACCAAAATGCAAGC 60.071 47.619 0.00 0.00 37.00 4.01
3873 7661 1.189884 CGCAAACGACCAAAATGCAAG 59.810 47.619 0.00 0.00 43.93 4.01
3874 7662 1.203928 CGCAAACGACCAAAATGCAA 58.796 45.000 0.00 0.00 43.93 4.08
3875 7663 1.211818 GCGCAAACGACCAAAATGCA 61.212 50.000 0.30 0.00 43.93 3.96
3876 7664 0.939106 AGCGCAAACGACCAAAATGC 60.939 50.000 11.47 0.00 43.93 3.56
3898 7686 9.571810 TGCTGTTATCTTTACAAAAATGCTATG 57.428 29.630 0.00 0.00 0.00 2.23
3905 7693 8.026607 GGTAGCATGCTGTTATCTTTACAAAAA 58.973 33.333 30.42 0.04 0.00 1.94
3916 7704 1.811558 CGCCTGGTAGCATGCTGTTAT 60.812 52.381 30.42 5.99 0.00 1.89
3934 7722 1.005294 TAACGCTTTCTCGGACACGC 61.005 55.000 0.00 0.00 40.69 5.34
3936 7724 2.061740 AGTAACGCTTTCTCGGACAC 57.938 50.000 0.00 0.00 0.00 3.67
3971 7759 3.232213 GTCAGGAGACAAACGAGCATA 57.768 47.619 0.00 0.00 44.34 3.14
4000 7788 3.897239 AGTTCATCCACAGTTGAACCAA 58.103 40.909 11.46 0.00 46.86 3.67
4006 7794 6.808008 AGTTATCAAGTTCATCCACAGTTG 57.192 37.500 0.00 0.00 0.00 3.16
4041 7829 9.956720 GATGAATTTGTTAGCATAAGCATAACT 57.043 29.630 11.07 0.00 45.49 2.24
4042 7830 9.185192 GGATGAATTTGTTAGCATAAGCATAAC 57.815 33.333 0.00 0.00 45.49 1.89
4074 7865 9.282247 CATGTTACTTATTTGTCTCAATTCTGC 57.718 33.333 0.00 0.00 0.00 4.26
4079 7870 7.067494 GGAGCCATGTTACTTATTTGTCTCAAT 59.933 37.037 0.00 0.00 0.00 2.57
4106 7897 2.441532 GGATGCATGCTGTGGCCT 60.442 61.111 20.33 0.00 37.74 5.19
4123 7914 0.240411 GCTGCTTGCTTCAACTCCAG 59.760 55.000 0.00 0.00 38.95 3.86
4157 7949 4.142071 CGAAGAGAGTTCCAATGGAGATGA 60.142 45.833 0.86 0.00 31.21 2.92
4163 7955 1.065854 AGCCGAAGAGAGTTCCAATGG 60.066 52.381 0.00 0.00 0.00 3.16
4190 7982 4.409574 TCACTGAACCTTGGTTGGTACTTA 59.590 41.667 10.04 0.00 39.83 2.24
4211 8003 4.505922 GGCATGAACAAAAACGAAATGTCA 59.494 37.500 0.00 0.00 0.00 3.58
4212 8004 4.744631 AGGCATGAACAAAAACGAAATGTC 59.255 37.500 0.00 0.00 0.00 3.06
4217 8009 4.748892 TGAAAGGCATGAACAAAAACGAA 58.251 34.783 0.00 0.00 0.00 3.85
4220 8012 5.523188 TGTGATGAAAGGCATGAACAAAAAC 59.477 36.000 0.00 0.00 37.34 2.43
4237 8029 4.652421 ACAAACAGCATTGTTGTGATGA 57.348 36.364 19.50 0.00 46.54 2.92
4251 8043 7.697691 ACAACTAAGATGTCAGAAACAAACAG 58.302 34.615 0.00 0.00 42.37 3.16
4337 8129 4.938226 CACAATAAGTTTCCCTCTGGAGAC 59.062 45.833 0.00 0.00 44.29 3.36
4392 8184 2.032054 CCATATGCGCGAACAAGAATGT 59.968 45.455 12.10 0.00 43.14 2.71
4406 8202 1.605710 CAAGTACAGCAGCCCATATGC 59.394 52.381 0.00 0.00 44.18 3.14
4407 8203 2.923121 ACAAGTACAGCAGCCCATATG 58.077 47.619 0.00 0.00 0.00 1.78
4468 8279 3.462021 AGTTTAGCAGATGAAGGATCGC 58.538 45.455 0.00 0.00 36.04 4.58
4547 8358 0.744874 CCAGAAAGGCCATGCTGATG 59.255 55.000 18.02 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.