Multiple sequence alignment - TraesCS5B01G159000

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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 TraesCS5B01G159000 chr5B 100.000 4789 0 0 1 4789 293211745 293206957 0.000000e+00 8844.0
1 TraesCS5B01G159000 chr5A 92.774 3543 164 52 378 3856 343961885 343958371 0.000000e+00 5040.0
2 TraesCS5B01G159000 chr5A 90.608 937 63 15 3861 4789 343958323 343957404 0.000000e+00 1219.0
3 TraesCS5B01G159000 chr5A 86.243 189 23 3 3894 4081 478267303 478267489 8.130000e-48 202.0
4 TraesCS5B01G159000 chr5A 95.413 109 5 0 269 377 343962914 343962806 1.770000e-39 174.0
5 TraesCS5B01G159000 chr5D 94.991 2935 105 12 955 3856 259236535 259233610 0.000000e+00 4567.0
6 TraesCS5B01G159000 chr5D 91.933 719 43 11 4078 4789 259233541 259232831 0.000000e+00 992.0
7 TraesCS5B01G159000 chr5D 88.364 593 43 13 334 907 259237505 259236920 0.000000e+00 689.0
8 TraesCS5B01G159000 chr7B 86.772 189 21 4 3894 4081 283043094 283042909 1.750000e-49 207.0
9 TraesCS5B01G159000 chr3D 86.772 189 21 4 3894 4081 450608446 450608261 1.750000e-49 207.0
10 TraesCS5B01G159000 chr3D 86.243 189 23 3 3894 4081 374860748 374860934 8.130000e-48 202.0
11 TraesCS5B01G159000 chr2A 86.772 189 21 4 3894 4081 480782742 480782557 1.750000e-49 207.0
12 TraesCS5B01G159000 chr7A 86.772 189 20 4 3894 4081 490325326 490325142 6.280000e-49 206.0
13 TraesCS5B01G159000 chr2D 86.772 189 20 5 3894 4081 515324672 515324856 6.280000e-49 206.0
14 TraesCS5B01G159000 chr4D 86.243 189 22 4 3894 4081 386613764 386613579 8.130000e-48 202.0
15 TraesCS5B01G159000 chr4D 86.243 189 22 4 3894 4081 471379480 471379665 8.130000e-48 202.0
16 TraesCS5B01G159000 chr4D 84.416 77 8 4 2808 2882 81908777 81908851 6.650000e-09 73.1
17 TraesCS5B01G159000 chr4D 83.582 67 9 2 2975 3041 38304759 38304823 1.440000e-05 62.1
18 TraesCS5B01G159000 chr4A 85.714 77 7 4 2808 2882 491689078 491689152 1.430000e-10 78.7
19 TraesCS5B01G159000 chr4A 85.246 61 8 1 2981 3041 562483509 562483450 1.440000e-05 62.1
20 TraesCS5B01G159000 chr4B 83.582 67 9 2 2975 3041 55704977 55705041 1.440000e-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 TraesCS5B01G159000 chr5B 293206957 293211745 4788 True 8844.000000 8844 100.000000 1 4789 1 chr5B.!!$R1 4788
1 TraesCS5B01G159000 chr5A 343957404 343962914 5510 True 2144.333333 5040 92.931667 269 4789 3 chr5A.!!$R1 4520
2 TraesCS5B01G159000 chr5D 259232831 259237505 4674 True 2082.666667 4567 91.762667 334 4789 3 chr5D.!!$R1 4455

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
199 200 0.038159 ACTGTAGCCACGCTCTTCAC 60.038 55.0 0.00 0.0 40.44 3.18 F
1805 3117 0.108329 ATTCCGAGTACAACGCCAGG 60.108 55.0 0.00 0.0 0.00 4.45 F
2162 3474 0.320374 TGTCCGACGATGGAAAGCTT 59.680 50.0 0.00 0.0 40.44 3.74 F
2192 3504 0.459585 GTGATCGTAAGCTGCCGGAA 60.460 55.0 5.05 0.0 37.18 4.30 F
3611 4923 0.034670 GGAGATTGCAGGCTCTTGGT 60.035 55.0 14.94 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 3363 0.038744 CCACCTCCAGGAGCACAATT 59.961 55.0 11.57 0.0 38.94 2.32 R
3483 4795 0.179100 CCGTCCAGAATGCTGACGAT 60.179 55.0 20.62 0.0 45.17 3.73 R
3590 4902 1.094073 CAAGAGCCTGCAATCTCCGG 61.094 60.0 10.30 0.0 0.00 5.14 R
3665 4977 2.244486 TGACAGCCTCTTCTCAGGAT 57.756 50.0 0.00 0.0 35.20 3.24 R
4524 5922 0.173481 CTCGACGGACATGACACCAT 59.827 55.0 0.00 0.0 0.00 3.55 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
26 27 8.015185 ACAAATGATAAAGAAAGATGGATGGG 57.985 34.615 0.00 0.00 0.00 4.00
27 28 7.070322 ACAAATGATAAAGAAAGATGGATGGGG 59.930 37.037 0.00 0.00 0.00 4.96
28 29 4.473444 TGATAAAGAAAGATGGATGGGGC 58.527 43.478 0.00 0.00 0.00 5.80
29 30 2.165357 AAAGAAAGATGGATGGGGCC 57.835 50.000 0.00 0.00 0.00 5.80
30 31 1.312884 AAGAAAGATGGATGGGGCCT 58.687 50.000 0.84 0.00 0.00 5.19
31 32 1.312884 AGAAAGATGGATGGGGCCTT 58.687 50.000 0.84 0.00 0.00 4.35
32 33 1.063417 AGAAAGATGGATGGGGCCTTG 60.063 52.381 0.84 0.00 0.00 3.61
33 34 0.712380 AAAGATGGATGGGGCCTTGT 59.288 50.000 0.84 0.00 0.00 3.16
34 35 0.259938 AAGATGGATGGGGCCTTGTC 59.740 55.000 0.84 0.00 0.00 3.18
35 36 1.526917 GATGGATGGGGCCTTGTCG 60.527 63.158 0.84 0.00 0.00 4.35
36 37 3.721370 ATGGATGGGGCCTTGTCGC 62.721 63.158 0.84 0.00 0.00 5.19
37 38 4.115199 GGATGGGGCCTTGTCGCT 62.115 66.667 0.84 0.00 0.00 4.93
38 39 2.742116 GGATGGGGCCTTGTCGCTA 61.742 63.158 0.84 0.00 0.00 4.26
39 40 1.227674 GATGGGGCCTTGTCGCTAG 60.228 63.158 0.84 0.00 0.00 3.42
40 41 3.406595 ATGGGGCCTTGTCGCTAGC 62.407 63.158 4.06 4.06 0.00 3.42
42 43 4.452733 GGGCCTTGTCGCTAGCGT 62.453 66.667 34.10 0.00 40.74 5.07
43 44 2.886124 GGCCTTGTCGCTAGCGTC 60.886 66.667 34.10 29.14 40.74 5.19
44 45 2.182030 GCCTTGTCGCTAGCGTCT 59.818 61.111 34.10 0.00 40.74 4.18
45 46 1.874466 GCCTTGTCGCTAGCGTCTC 60.874 63.158 34.10 24.49 40.74 3.36
46 47 1.803943 CCTTGTCGCTAGCGTCTCT 59.196 57.895 34.10 0.00 40.74 3.10
47 48 0.524392 CCTTGTCGCTAGCGTCTCTG 60.524 60.000 34.10 21.07 40.74 3.35
48 49 0.524392 CTTGTCGCTAGCGTCTCTGG 60.524 60.000 34.10 17.39 40.74 3.86
49 50 2.278271 GTCGCTAGCGTCTCTGGC 60.278 66.667 34.10 14.10 44.79 4.85
50 51 3.518998 TCGCTAGCGTCTCTGGCC 61.519 66.667 34.10 0.00 45.37 5.36
51 52 3.522731 CGCTAGCGTCTCTGGCCT 61.523 66.667 28.66 0.00 45.37 5.19
52 53 2.896443 GCTAGCGTCTCTGGCCTT 59.104 61.111 3.32 0.00 42.75 4.35
53 54 1.227118 GCTAGCGTCTCTGGCCTTC 60.227 63.158 3.32 0.00 42.75 3.46
54 55 1.064946 CTAGCGTCTCTGGCCTTCG 59.935 63.158 3.32 2.76 0.00 3.79
55 56 1.377366 CTAGCGTCTCTGGCCTTCGA 61.377 60.000 3.32 0.00 0.00 3.71
56 57 0.752009 TAGCGTCTCTGGCCTTCGAT 60.752 55.000 3.32 2.99 0.00 3.59
57 58 1.880340 GCGTCTCTGGCCTTCGATG 60.880 63.158 3.32 3.95 0.00 3.84
58 59 1.809869 CGTCTCTGGCCTTCGATGA 59.190 57.895 3.32 0.00 0.00 2.92
59 60 0.248825 CGTCTCTGGCCTTCGATGAG 60.249 60.000 3.32 2.39 0.00 2.90
60 61 0.103937 GTCTCTGGCCTTCGATGAGG 59.896 60.000 3.32 0.00 39.93 3.86
66 67 4.844420 CCTTCGATGAGGCCTGAC 57.156 61.111 12.00 0.00 0.00 3.51
67 68 1.227089 CCTTCGATGAGGCCTGACG 60.227 63.158 12.00 13.47 0.00 4.35
68 69 1.227089 CTTCGATGAGGCCTGACGG 60.227 63.158 12.00 0.00 0.00 4.79
86 87 4.496670 CTACACGCCACTGTAGCC 57.503 61.111 0.00 0.00 37.80 3.93
87 88 1.589630 CTACACGCCACTGTAGCCA 59.410 57.895 0.00 0.00 37.80 4.75
88 89 0.458543 CTACACGCCACTGTAGCCAG 60.459 60.000 0.00 0.00 44.68 4.85
98 99 0.456221 CTGTAGCCAGTAGGTCGTGG 59.544 60.000 0.00 0.00 37.19 4.94
99 100 0.251474 TGTAGCCAGTAGGTCGTGGT 60.251 55.000 0.00 0.00 36.10 4.16
100 101 0.172803 GTAGCCAGTAGGTCGTGGTG 59.827 60.000 0.00 0.00 36.10 4.17
101 102 0.251474 TAGCCAGTAGGTCGTGGTGT 60.251 55.000 0.00 0.00 36.10 4.16
102 103 1.080025 GCCAGTAGGTCGTGGTGTC 60.080 63.158 0.00 0.00 36.10 3.67
103 104 1.812686 GCCAGTAGGTCGTGGTGTCA 61.813 60.000 0.00 0.00 36.10 3.58
104 105 0.038526 CCAGTAGGTCGTGGTGTCAC 60.039 60.000 0.00 0.00 40.36 3.67
120 121 2.743718 ACGGAGTGGTTGGCTCTG 59.256 61.111 0.00 0.00 42.51 3.35
121 122 2.140792 ACGGAGTGGTTGGCTCTGT 61.141 57.895 1.37 1.37 44.92 3.41
122 123 1.669115 CGGAGTGGTTGGCTCTGTG 60.669 63.158 0.00 0.00 35.29 3.66
123 124 1.968540 GGAGTGGTTGGCTCTGTGC 60.969 63.158 0.00 0.00 41.94 4.57
124 125 1.072159 GAGTGGTTGGCTCTGTGCT 59.928 57.895 1.44 0.00 42.39 4.40
125 126 0.536006 GAGTGGTTGGCTCTGTGCTT 60.536 55.000 1.44 0.00 42.39 3.91
126 127 0.536006 AGTGGTTGGCTCTGTGCTTC 60.536 55.000 1.44 0.00 42.39 3.86
127 128 1.228245 TGGTTGGCTCTGTGCTTCC 60.228 57.895 1.44 3.28 42.39 3.46
128 129 1.228245 GGTTGGCTCTGTGCTTCCA 60.228 57.895 1.44 0.00 42.39 3.53
129 130 1.518903 GGTTGGCTCTGTGCTTCCAC 61.519 60.000 1.44 0.00 42.39 4.02
136 137 4.436515 TGTGCTTCCACAGTGTCG 57.563 55.556 0.00 0.00 46.51 4.35
137 138 1.227527 TGTGCTTCCACAGTGTCGG 60.228 57.895 0.00 0.00 46.51 4.79
138 139 1.961277 GTGCTTCCACAGTGTCGGG 60.961 63.158 10.61 3.08 41.67 5.14
139 140 3.050275 GCTTCCACAGTGTCGGGC 61.050 66.667 10.61 5.13 0.00 6.13
140 141 2.358737 CTTCCACAGTGTCGGGCC 60.359 66.667 0.00 0.00 0.00 5.80
141 142 4.308458 TTCCACAGTGTCGGGCCG 62.308 66.667 22.51 22.51 0.00 6.13
177 178 2.584143 CGATCAACGGTACCGGCC 60.584 66.667 35.86 18.64 44.69 6.13
184 185 3.443045 CGGTACCGGCCGTACTGT 61.443 66.667 27.00 17.17 45.68 3.55
185 186 2.112198 CGGTACCGGCCGTACTGTA 61.112 63.158 27.00 16.04 45.68 2.74
186 187 1.729881 GGTACCGGCCGTACTGTAG 59.270 63.158 26.12 9.27 45.76 2.74
187 188 1.064783 GTACCGGCCGTACTGTAGC 59.935 63.158 26.12 9.67 43.53 3.58
188 189 2.120909 TACCGGCCGTACTGTAGCC 61.121 63.158 26.12 7.78 43.53 3.93
191 192 2.202703 GGCCGTACTGTAGCCACG 60.203 66.667 11.90 3.90 46.34 4.94
192 193 2.884207 GCCGTACTGTAGCCACGC 60.884 66.667 0.00 0.00 34.42 5.34
193 194 2.882876 CCGTACTGTAGCCACGCT 59.117 61.111 0.00 0.00 43.41 5.07
194 195 1.226603 CCGTACTGTAGCCACGCTC 60.227 63.158 0.00 0.00 40.44 5.03
195 196 1.654954 CCGTACTGTAGCCACGCTCT 61.655 60.000 0.00 0.00 40.44 4.09
196 197 0.170561 CGTACTGTAGCCACGCTCTT 59.829 55.000 0.00 0.00 40.44 2.85
197 198 1.794437 CGTACTGTAGCCACGCTCTTC 60.794 57.143 0.00 0.00 40.44 2.87
198 199 1.201647 GTACTGTAGCCACGCTCTTCA 59.798 52.381 0.00 0.00 40.44 3.02
199 200 0.038159 ACTGTAGCCACGCTCTTCAC 60.038 55.000 0.00 0.00 40.44 3.18
200 201 1.073216 CTGTAGCCACGCTCTTCACG 61.073 60.000 0.00 0.00 40.44 4.35
201 202 1.211969 GTAGCCACGCTCTTCACGA 59.788 57.895 0.00 0.00 40.44 4.35
202 203 1.071567 GTAGCCACGCTCTTCACGAC 61.072 60.000 0.00 0.00 40.44 4.34
203 204 2.523184 TAGCCACGCTCTTCACGACG 62.523 60.000 0.00 0.00 40.44 5.12
204 205 2.050351 CCACGCTCTTCACGACGT 60.050 61.111 0.00 0.00 39.78 4.34
206 207 2.050351 ACGCTCTTCACGACGTGG 60.050 61.111 26.55 12.58 37.37 4.94
207 208 2.805353 CGCTCTTCACGACGTGGG 60.805 66.667 26.55 19.00 33.87 4.61
208 209 2.649034 GCTCTTCACGACGTGGGA 59.351 61.111 26.55 21.66 33.87 4.37
209 210 1.444553 GCTCTTCACGACGTGGGAG 60.445 63.158 29.56 29.56 37.11 4.30
210 211 1.863662 GCTCTTCACGACGTGGGAGA 61.864 60.000 33.85 29.08 36.64 3.71
211 212 0.169230 CTCTTCACGACGTGGGAGAG 59.831 60.000 29.91 29.91 37.63 3.20
212 213 1.213013 CTTCACGACGTGGGAGAGG 59.787 63.158 26.55 5.19 33.87 3.69
213 214 1.524863 CTTCACGACGTGGGAGAGGT 61.525 60.000 26.55 0.00 33.87 3.85
214 215 1.521450 TTCACGACGTGGGAGAGGTC 61.521 60.000 26.55 0.00 36.32 3.85
215 216 1.972223 CACGACGTGGGAGAGGTCT 60.972 63.158 20.26 0.00 37.33 3.85
216 217 1.228490 ACGACGTGGGAGAGGTCTT 60.228 57.895 0.00 0.00 37.33 3.01
217 218 1.213013 CGACGTGGGAGAGGTCTTG 59.787 63.158 0.00 0.00 37.33 3.02
218 219 1.524863 CGACGTGGGAGAGGTCTTGT 61.525 60.000 0.00 0.00 37.33 3.16
219 220 0.244178 GACGTGGGAGAGGTCTTGTC 59.756 60.000 0.00 0.00 36.66 3.18
220 221 1.213013 CGTGGGAGAGGTCTTGTCG 59.787 63.158 0.00 0.00 0.00 4.35
221 222 1.524863 CGTGGGAGAGGTCTTGTCGT 61.525 60.000 0.00 0.00 0.00 4.34
222 223 1.542492 GTGGGAGAGGTCTTGTCGTA 58.458 55.000 0.00 0.00 0.00 3.43
223 224 1.201880 GTGGGAGAGGTCTTGTCGTAC 59.798 57.143 0.00 0.00 0.00 3.67
224 225 0.450983 GGGAGAGGTCTTGTCGTACG 59.549 60.000 9.53 9.53 0.00 3.67
225 226 0.450983 GGAGAGGTCTTGTCGTACGG 59.549 60.000 16.52 0.00 0.00 4.02
226 227 0.179169 GAGAGGTCTTGTCGTACGGC 60.179 60.000 14.12 14.12 0.00 5.68
227 228 1.513586 GAGGTCTTGTCGTACGGCG 60.514 63.158 16.05 4.80 43.01 6.46
235 236 3.908189 TCGTACGGCGAGATTGGA 58.092 55.556 16.62 0.00 45.68 3.53
236 237 2.411535 TCGTACGGCGAGATTGGAT 58.588 52.632 16.62 0.00 45.68 3.41
237 238 1.596603 TCGTACGGCGAGATTGGATA 58.403 50.000 16.62 0.00 45.68 2.59
238 239 1.534163 TCGTACGGCGAGATTGGATAG 59.466 52.381 16.62 0.00 45.68 2.08
239 240 1.401148 CGTACGGCGAGATTGGATAGG 60.401 57.143 16.62 0.00 44.77 2.57
240 241 0.601558 TACGGCGAGATTGGATAGGC 59.398 55.000 16.62 0.00 0.00 3.93
241 242 1.734477 CGGCGAGATTGGATAGGCG 60.734 63.158 0.00 0.00 43.73 5.52
242 243 2.029844 GGCGAGATTGGATAGGCGC 61.030 63.158 0.00 0.00 43.27 6.53
243 244 1.005630 GCGAGATTGGATAGGCGCT 60.006 57.895 7.64 0.00 41.09 5.92
244 245 1.287730 GCGAGATTGGATAGGCGCTG 61.288 60.000 7.64 0.00 41.09 5.18
245 246 0.315251 CGAGATTGGATAGGCGCTGA 59.685 55.000 7.64 0.00 0.00 4.26
246 247 1.789506 GAGATTGGATAGGCGCTGAC 58.210 55.000 7.64 0.00 0.00 3.51
247 248 0.394565 AGATTGGATAGGCGCTGACC 59.605 55.000 7.64 6.93 0.00 4.02
248 249 0.603975 GATTGGATAGGCGCTGACCC 60.604 60.000 7.64 4.87 0.00 4.46
249 250 1.056700 ATTGGATAGGCGCTGACCCT 61.057 55.000 7.64 0.00 36.47 4.34
250 251 1.971505 TTGGATAGGCGCTGACCCTG 61.972 60.000 7.64 0.00 33.88 4.45
251 252 2.280457 GATAGGCGCTGACCCTGC 60.280 66.667 7.64 0.00 33.88 4.85
356 357 6.478344 CCCGATGTTTTGAAAAATTGACTTGA 59.522 34.615 0.00 0.00 0.00 3.02
403 1325 4.037446 CCCCGACATTGACTGAAAGAAAAA 59.963 41.667 0.00 0.00 37.43 1.94
516 1448 2.610374 GCTAACGTTGAGACAAACACCA 59.390 45.455 11.99 0.00 0.00 4.17
548 1480 4.083643 CCGGCTTGACACAATCATATCATC 60.084 45.833 0.00 0.00 37.11 2.92
632 1564 4.987912 CACCACCAAACCATGTGAAAATAC 59.012 41.667 0.00 0.00 34.37 1.89
634 1566 4.233789 CACCAAACCATGTGAAAATACGG 58.766 43.478 0.00 0.00 34.37 4.02
673 1605 2.096496 CCGATCTGGACAAGACAATTGC 59.904 50.000 5.05 0.00 42.00 3.56
675 1607 3.425359 CGATCTGGACAAGACAATTGCAC 60.425 47.826 5.05 0.00 37.88 4.57
678 1610 0.603065 GGACAAGACAATTGCACCCC 59.397 55.000 5.05 0.00 0.00 4.95
704 1636 3.479370 CGCCCTCTCGCTTTCAAG 58.521 61.111 0.00 0.00 0.00 3.02
791 1733 2.291043 CCACCACCCGAGCTACCTT 61.291 63.158 0.00 0.00 0.00 3.50
792 1734 1.218316 CACCACCCGAGCTACCTTC 59.782 63.158 0.00 0.00 0.00 3.46
797 1759 2.571757 CCGAGCTACCTTCGCACA 59.428 61.111 0.00 0.00 36.76 4.57
823 1785 3.214123 ACACTATCGCCGCGCCTA 61.214 61.111 8.21 1.31 0.00 3.93
824 1786 2.027024 CACTATCGCCGCGCCTAA 59.973 61.111 8.21 0.00 0.00 2.69
825 1787 1.590525 CACTATCGCCGCGCCTAAA 60.591 57.895 8.21 0.00 0.00 1.85
826 1788 1.142314 ACTATCGCCGCGCCTAAAA 59.858 52.632 8.21 0.00 0.00 1.52
827 1789 1.149964 ACTATCGCCGCGCCTAAAAC 61.150 55.000 8.21 0.00 0.00 2.43
828 1790 1.828331 CTATCGCCGCGCCTAAAACC 61.828 60.000 8.21 0.00 0.00 3.27
829 1791 2.575125 TATCGCCGCGCCTAAAACCA 62.575 55.000 8.21 0.00 0.00 3.67
830 1792 3.728636 CGCCGCGCCTAAAACCAA 61.729 61.111 0.00 0.00 0.00 3.67
831 1793 2.646143 GCCGCGCCTAAAACCAAA 59.354 55.556 0.00 0.00 0.00 3.28
832 1794 1.443702 GCCGCGCCTAAAACCAAAG 60.444 57.895 0.00 0.00 0.00 2.77
833 1795 1.953772 CCGCGCCTAAAACCAAAGT 59.046 52.632 0.00 0.00 0.00 2.66
834 1796 0.109919 CCGCGCCTAAAACCAAAGTC 60.110 55.000 0.00 0.00 0.00 3.01
835 1797 0.109919 CGCGCCTAAAACCAAAGTCC 60.110 55.000 0.00 0.00 0.00 3.85
836 1798 1.244816 GCGCCTAAAACCAAAGTCCT 58.755 50.000 0.00 0.00 0.00 3.85
841 1803 3.889538 GCCTAAAACCAAAGTCCTCTTGT 59.110 43.478 0.00 0.00 33.79 3.16
865 1831 3.791320 TCTTGTGTCACCTTCCTATCCT 58.209 45.455 0.00 0.00 0.00 3.24
1022 2325 2.884012 CGAGCACCATTAATTATGCCCA 59.116 45.455 14.38 0.00 38.92 5.36
1026 2329 3.553508 GCACCATTAATTATGCCCAGCTG 60.554 47.826 6.78 6.78 32.60 4.24
1028 2331 3.891366 ACCATTAATTATGCCCAGCTGAC 59.109 43.478 17.39 7.59 32.60 3.51
1029 2332 3.890756 CCATTAATTATGCCCAGCTGACA 59.109 43.478 17.39 13.74 32.60 3.58
1030 2333 4.525487 CCATTAATTATGCCCAGCTGACAT 59.475 41.667 17.39 19.80 32.60 3.06
1035 2338 3.415087 GCCCAGCTGACATCCCCT 61.415 66.667 17.39 0.00 0.00 4.79
1067 2370 2.436646 CATCTTCCGCCCAACGCT 60.437 61.111 0.00 0.00 41.76 5.07
1133 2436 2.363147 GAGGTCCTCGTGGCCTCT 60.363 66.667 26.32 13.34 45.20 3.69
1146 2449 4.813526 CCTCTGCCGACGACGACG 62.814 72.222 12.66 12.66 42.66 5.12
1226 2538 3.699894 CTGTCCTGCCTCCGCTGT 61.700 66.667 0.00 0.00 35.36 4.40
1376 2688 1.361668 GCGGCTTCAGCGATCAAGAA 61.362 55.000 0.00 0.00 43.26 2.52
1379 2691 1.663135 GGCTTCAGCGATCAAGAAGTC 59.337 52.381 15.82 11.91 43.26 3.01
1385 2697 0.173708 GCGATCAAGAAGTCCTCGGT 59.826 55.000 0.00 0.00 0.00 4.69
1394 2706 4.828296 GTCCTCGGTAGCGGGGGA 62.828 72.222 31.56 24.99 0.00 4.81
1457 2769 3.276846 GTGGCCGTCAAGTGCGTT 61.277 61.111 0.00 0.00 0.00 4.84
1803 3115 0.604073 TGATTCCGAGTACAACGCCA 59.396 50.000 0.00 0.00 0.00 5.69
1805 3117 0.108329 ATTCCGAGTACAACGCCAGG 60.108 55.000 0.00 0.00 0.00 4.45
1853 3165 4.148825 GAGCACGCCGTGGAGGAT 62.149 66.667 20.07 0.00 45.00 3.24
2051 3363 1.371267 CGACGTGTTCAGCTTCGGA 60.371 57.895 0.00 0.00 0.00 4.55
2126 3438 2.029728 CGACGACCAAATCTTCATGCTC 59.970 50.000 0.00 0.00 0.00 4.26
2162 3474 0.320374 TGTCCGACGATGGAAAGCTT 59.680 50.000 0.00 0.00 40.44 3.74
2192 3504 0.459585 GTGATCGTAAGCTGCCGGAA 60.460 55.000 5.05 0.00 37.18 4.30
2382 3694 2.213310 TCTCTCTCACCTCATCCTCCT 58.787 52.381 0.00 0.00 0.00 3.69
2383 3695 2.174639 TCTCTCTCACCTCATCCTCCTC 59.825 54.545 0.00 0.00 0.00 3.71
2432 3744 2.179547 CACGAACAGCACAGCCACA 61.180 57.895 0.00 0.00 0.00 4.17
2441 3753 4.334118 ACAGCCACATCTGCCGCA 62.334 61.111 0.00 0.00 37.59 5.69
2444 3756 2.515523 GCCACATCTGCCGCATCT 60.516 61.111 0.00 0.00 0.00 2.90
2492 3804 1.271926 GGCACCACCATTTACCTCACT 60.272 52.381 0.00 0.00 38.86 3.41
2633 3945 3.066900 CGTACAAGGAGATCGTGGAGATT 59.933 47.826 0.00 0.00 40.26 2.40
2889 4201 3.880591 TCGTCTACGACCACTCCG 58.119 61.111 0.14 0.00 44.22 4.63
3134 4446 5.106555 CCTGTCAAGAAACGAGCACAATAAT 60.107 40.000 0.00 0.00 0.00 1.28
3143 4455 2.482316 CGAGCACAATAATCCCCACGTA 60.482 50.000 0.00 0.00 0.00 3.57
3146 4458 3.054655 AGCACAATAATCCCCACGTAGTT 60.055 43.478 0.00 0.00 41.61 2.24
3211 4523 1.065928 CGCCGGAGTACATGGAGAC 59.934 63.158 5.05 0.00 0.00 3.36
3483 4795 1.745115 CGGCCGAGCATGAGGAAAA 60.745 57.895 24.07 0.00 0.00 2.29
3590 4902 2.435059 GCGGCTCTGTCCTTGGTC 60.435 66.667 0.00 0.00 0.00 4.02
3591 4903 2.266055 CGGCTCTGTCCTTGGTCC 59.734 66.667 0.00 0.00 0.00 4.46
3597 4909 0.041238 TCTGTCCTTGGTCCGGAGAT 59.959 55.000 3.06 0.00 0.00 2.75
3611 4923 0.034670 GGAGATTGCAGGCTCTTGGT 60.035 55.000 14.94 0.00 0.00 3.67
3663 4975 7.748683 CGCAGTTAATGTAAGCTGACAATTTAA 59.251 33.333 8.32 6.94 31.83 1.52
3699 5011 6.017400 AGGCTGTCATATGTTTCTTTGTTG 57.983 37.500 1.90 0.00 0.00 3.33
3779 5128 8.584063 TGTAGTGACTATATTGGTAAGTGTCA 57.416 34.615 0.00 0.00 0.00 3.58
3790 5139 9.733556 ATATTGGTAAGTGTCACATTGAGTTAA 57.266 29.630 5.62 0.00 0.00 2.01
3797 5146 7.750229 AGTGTCACATTGAGTTAAACATGAT 57.250 32.000 5.62 0.00 0.00 2.45
3798 5147 8.169977 AGTGTCACATTGAGTTAAACATGATT 57.830 30.769 5.62 0.00 0.00 2.57
3799 5148 8.632679 AGTGTCACATTGAGTTAAACATGATTT 58.367 29.630 5.62 0.00 0.00 2.17
3800 5149 9.248291 GTGTCACATTGAGTTAAACATGATTTT 57.752 29.630 0.00 0.00 0.00 1.82
3891 5284 5.873179 TTGAAGCAAAGTAAAGGATACGG 57.127 39.130 0.00 0.00 46.39 4.02
3907 5300 6.165700 GGATACGGAAATCCTAAACCTACA 57.834 41.667 6.49 0.00 41.99 2.74
3911 5304 4.692155 ACGGAAATCCTAAACCTACAAACG 59.308 41.667 0.00 0.00 0.00 3.60
3917 5310 3.834231 TCCTAAACCTACAAACGGCTACT 59.166 43.478 0.00 0.00 0.00 2.57
3936 5329 6.669278 GCTACTTAGCTGCTACAAAAACTTT 58.331 36.000 9.27 0.00 45.62 2.66
3958 5351 4.532834 TCAACTAATCTAAACATGCCCCC 58.467 43.478 0.00 0.00 0.00 5.40
3959 5352 3.208747 ACTAATCTAAACATGCCCCCG 57.791 47.619 0.00 0.00 0.00 5.73
3960 5353 1.880027 CTAATCTAAACATGCCCCCGC 59.120 52.381 0.00 0.00 0.00 6.13
3961 5354 0.755327 AATCTAAACATGCCCCCGCC 60.755 55.000 0.00 0.00 0.00 6.13
3962 5355 2.640581 ATCTAAACATGCCCCCGCCC 62.641 60.000 0.00 0.00 0.00 6.13
3963 5356 4.450612 TAAACATGCCCCCGCCCC 62.451 66.667 0.00 0.00 0.00 5.80
3972 5365 3.420482 CCCCGCCCCCTCTGATTT 61.420 66.667 0.00 0.00 0.00 2.17
3973 5366 2.683475 CCCGCCCCCTCTGATTTT 59.317 61.111 0.00 0.00 0.00 1.82
3974 5367 1.453928 CCCGCCCCCTCTGATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
3975 5368 1.302949 CCGCCCCCTCTGATTTTCA 59.697 57.895 0.00 0.00 0.00 2.69
3991 5384 7.681259 TGATTTTCAGATGGAGAGATCCTAA 57.319 36.000 0.00 0.00 0.00 2.69
3992 5385 7.504403 TGATTTTCAGATGGAGAGATCCTAAC 58.496 38.462 0.00 0.00 0.00 2.34
3993 5386 5.878406 TTTCAGATGGAGAGATCCTAACC 57.122 43.478 0.00 0.00 0.00 2.85
3994 5387 3.850752 TCAGATGGAGAGATCCTAACCC 58.149 50.000 0.00 0.00 0.00 4.11
4005 5398 6.698670 AGAGATCCTAACCCTCTCCTTTAAT 58.301 40.000 0.00 0.00 36.84 1.40
4026 5419 6.910536 AATCCAATCAAATAGTCTCACGTC 57.089 37.500 0.00 0.00 0.00 4.34
4036 5429 3.840890 AGTCTCACGTCAGATCAGTTC 57.159 47.619 0.00 0.00 0.00 3.01
4046 5439 4.792189 CGTCAGATCAGTTCGTAACCTTAC 59.208 45.833 0.00 0.00 0.00 2.34
4089 5482 6.538742 TGTAGCATTGCTCTAAAGGTTATGAC 59.461 38.462 15.81 3.48 40.44 3.06
4108 5501 5.505181 TGACTAGAAAAATCAGCCCTTCT 57.495 39.130 0.00 0.00 32.95 2.85
4114 5507 9.314133 ACTAGAAAAATCAGCCCTTCTTTTAAT 57.686 29.630 0.00 0.00 30.90 1.40
4198 5592 6.759827 GGACAGTACTAATTTCCGAATGCTAA 59.240 38.462 0.00 0.00 0.00 3.09
4222 5616 2.286654 GGATCTATTGCGAAACTGCTGC 60.287 50.000 0.00 0.00 35.36 5.25
4223 5617 2.099141 TCTATTGCGAAACTGCTGCT 57.901 45.000 0.00 0.00 35.36 4.24
4492 5888 2.235155 TGGATAGTCAAACTGCGCCTTA 59.765 45.455 4.18 0.00 0.00 2.69
4499 5896 1.029947 AAACTGCGCCTTATTCCCCG 61.030 55.000 4.18 0.00 0.00 5.73
4500 5897 3.279875 CTGCGCCTTATTCCCCGC 61.280 66.667 4.18 0.00 45.99 6.13
4562 5960 1.066143 AGGTCCAAACTCACTATGGCG 60.066 52.381 0.00 0.00 34.13 5.69
4604 6002 0.584785 CGATCGTGATGCTTGCAACG 60.585 55.000 7.03 12.01 0.00 4.10
4616 6014 3.589579 GCAACGATGCCACCATCA 58.410 55.556 6.36 0.00 46.59 3.07
4709 6109 1.014564 GGTCTTCCCAAAGCTCGTCG 61.015 60.000 0.00 0.00 32.18 5.12
4712 6112 0.319555 CTTCCCAAAGCTCGTCGTCA 60.320 55.000 0.00 0.00 0.00 4.35
4713 6113 0.320374 TTCCCAAAGCTCGTCGTCAT 59.680 50.000 0.00 0.00 0.00 3.06
4723 6124 3.380637 AGCTCGTCGTCATAATGGTAACT 59.619 43.478 0.00 0.00 37.61 2.24
4725 6126 4.026804 GCTCGTCGTCATAATGGTAACTTG 60.027 45.833 0.00 0.00 37.61 3.16
4778 6179 6.874134 GTGAGATCACCAACTAACAACTATGT 59.126 38.462 1.33 0.00 40.25 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.135189 CCCATCCATCTTTCTTTATCATTTGTA 57.865 33.333 0.00 0.00 0.00 2.41
1 2 7.070322 CCCCATCCATCTTTCTTTATCATTTGT 59.930 37.037 0.00 0.00 0.00 2.83
2 3 7.439381 CCCCATCCATCTTTCTTTATCATTTG 58.561 38.462 0.00 0.00 0.00 2.32
3 4 6.042437 GCCCCATCCATCTTTCTTTATCATTT 59.958 38.462 0.00 0.00 0.00 2.32
4 5 5.541484 GCCCCATCCATCTTTCTTTATCATT 59.459 40.000 0.00 0.00 0.00 2.57
5 6 5.082425 GCCCCATCCATCTTTCTTTATCAT 58.918 41.667 0.00 0.00 0.00 2.45
6 7 4.473444 GCCCCATCCATCTTTCTTTATCA 58.527 43.478 0.00 0.00 0.00 2.15
7 8 3.829026 GGCCCCATCCATCTTTCTTTATC 59.171 47.826 0.00 0.00 0.00 1.75
8 9 3.468625 AGGCCCCATCCATCTTTCTTTAT 59.531 43.478 0.00 0.00 0.00 1.40
9 10 2.858768 AGGCCCCATCCATCTTTCTTTA 59.141 45.455 0.00 0.00 0.00 1.85
10 11 1.648037 AGGCCCCATCCATCTTTCTTT 59.352 47.619 0.00 0.00 0.00 2.52
11 12 1.312884 AGGCCCCATCCATCTTTCTT 58.687 50.000 0.00 0.00 0.00 2.52
12 13 1.063417 CAAGGCCCCATCCATCTTTCT 60.063 52.381 0.00 0.00 0.00 2.52
13 14 1.342374 ACAAGGCCCCATCCATCTTTC 60.342 52.381 0.00 0.00 0.00 2.62
14 15 0.712380 ACAAGGCCCCATCCATCTTT 59.288 50.000 0.00 0.00 0.00 2.52
15 16 0.259938 GACAAGGCCCCATCCATCTT 59.740 55.000 0.00 0.00 0.00 2.40
16 17 1.925888 GACAAGGCCCCATCCATCT 59.074 57.895 0.00 0.00 0.00 2.90
17 18 1.526917 CGACAAGGCCCCATCCATC 60.527 63.158 0.00 0.00 0.00 3.51
18 19 2.597340 CGACAAGGCCCCATCCAT 59.403 61.111 0.00 0.00 0.00 3.41
19 20 4.424711 GCGACAAGGCCCCATCCA 62.425 66.667 0.00 0.00 0.00 3.41
20 21 2.666596 CTAGCGACAAGGCCCCATCC 62.667 65.000 0.00 0.00 0.00 3.51
21 22 1.227674 CTAGCGACAAGGCCCCATC 60.228 63.158 0.00 0.00 0.00 3.51
22 23 2.911143 CTAGCGACAAGGCCCCAT 59.089 61.111 0.00 0.00 0.00 4.00
23 24 4.096003 GCTAGCGACAAGGCCCCA 62.096 66.667 0.00 0.00 0.00 4.96
25 26 4.452733 ACGCTAGCGACAAGGCCC 62.453 66.667 41.33 0.00 42.83 5.80
26 27 2.886124 GACGCTAGCGACAAGGCC 60.886 66.667 41.33 17.00 42.83 5.19
27 28 1.874466 GAGACGCTAGCGACAAGGC 60.874 63.158 41.33 21.51 42.83 4.35
28 29 0.524392 CAGAGACGCTAGCGACAAGG 60.524 60.000 41.33 23.29 42.83 3.61
29 30 0.524392 CCAGAGACGCTAGCGACAAG 60.524 60.000 41.33 26.05 42.83 3.16
30 31 1.506718 CCAGAGACGCTAGCGACAA 59.493 57.895 41.33 0.00 42.83 3.18
31 32 3.052620 GCCAGAGACGCTAGCGACA 62.053 63.158 41.33 0.00 42.83 4.35
32 33 2.278271 GCCAGAGACGCTAGCGAC 60.278 66.667 41.33 34.47 42.83 5.19
33 34 3.518998 GGCCAGAGACGCTAGCGA 61.519 66.667 41.33 0.00 42.83 4.93
34 35 2.945398 GAAGGCCAGAGACGCTAGCG 62.945 65.000 34.27 34.27 46.03 4.26
35 36 1.227118 GAAGGCCAGAGACGCTAGC 60.227 63.158 5.01 4.06 0.00 3.42
36 37 1.064946 CGAAGGCCAGAGACGCTAG 59.935 63.158 5.01 0.00 0.00 3.42
37 38 0.752009 ATCGAAGGCCAGAGACGCTA 60.752 55.000 5.01 0.00 0.00 4.26
38 39 2.055042 ATCGAAGGCCAGAGACGCT 61.055 57.895 5.01 0.00 0.00 5.07
39 40 1.880340 CATCGAAGGCCAGAGACGC 60.880 63.158 5.01 0.00 0.00 5.19
40 41 0.248825 CTCATCGAAGGCCAGAGACG 60.249 60.000 5.01 2.95 0.00 4.18
41 42 0.103937 CCTCATCGAAGGCCAGAGAC 59.896 60.000 5.01 0.00 0.00 3.36
42 43 2.509512 CCTCATCGAAGGCCAGAGA 58.490 57.895 5.01 0.00 0.00 3.10
49 50 1.227089 CGTCAGGCCTCATCGAAGG 60.227 63.158 0.00 0.00 39.62 3.46
50 51 1.227089 CCGTCAGGCCTCATCGAAG 60.227 63.158 18.41 9.01 0.00 3.79
51 52 2.892640 CCGTCAGGCCTCATCGAA 59.107 61.111 18.41 0.00 0.00 3.71
70 71 1.589630 CTGGCTACAGTGGCGTGTA 59.410 57.895 2.36 0.24 39.92 2.90
71 72 2.343758 CTGGCTACAGTGGCGTGT 59.656 61.111 2.36 0.00 39.92 4.49
80 81 0.251474 ACCACGACCTACTGGCTACA 60.251 55.000 0.00 0.00 36.63 2.74
81 82 0.172803 CACCACGACCTACTGGCTAC 59.827 60.000 0.00 0.00 36.63 3.58
82 83 0.251474 ACACCACGACCTACTGGCTA 60.251 55.000 0.00 0.00 36.63 3.93
83 84 1.533273 ACACCACGACCTACTGGCT 60.533 57.895 0.00 0.00 36.63 4.75
84 85 1.080025 GACACCACGACCTACTGGC 60.080 63.158 0.00 0.00 36.63 4.85
85 86 0.038526 GTGACACCACGACCTACTGG 60.039 60.000 0.00 0.00 34.81 4.00
86 87 3.491581 GTGACACCACGACCTACTG 57.508 57.895 0.00 0.00 33.10 2.74
95 96 1.145377 AACCACTCCGTGACACCAC 59.855 57.895 0.00 0.00 39.86 4.16
96 97 1.145156 CAACCACTCCGTGACACCA 59.855 57.895 0.00 0.00 35.23 4.17
97 98 1.597027 CCAACCACTCCGTGACACC 60.597 63.158 0.00 0.00 35.23 4.16
98 99 2.251642 GCCAACCACTCCGTGACAC 61.252 63.158 0.00 0.00 35.23 3.67
99 100 2.110213 GCCAACCACTCCGTGACA 59.890 61.111 0.00 0.00 35.23 3.58
100 101 1.668151 GAGCCAACCACTCCGTGAC 60.668 63.158 0.00 0.00 35.23 3.67
101 102 1.837051 AGAGCCAACCACTCCGTGA 60.837 57.895 0.00 0.00 35.23 4.35
102 103 1.669115 CAGAGCCAACCACTCCGTG 60.669 63.158 0.00 0.00 34.56 4.94
103 104 2.140792 ACAGAGCCAACCACTCCGT 61.141 57.895 0.00 0.00 34.56 4.69
104 105 1.669115 CACAGAGCCAACCACTCCG 60.669 63.158 0.00 0.00 34.56 4.63
105 106 1.968540 GCACAGAGCCAACCACTCC 60.969 63.158 0.00 0.00 37.23 3.85
106 107 3.660621 GCACAGAGCCAACCACTC 58.339 61.111 0.00 0.00 37.23 3.51
119 120 1.227527 CCGACACTGTGGAAGCACA 60.228 57.895 13.09 0.00 0.00 4.57
120 121 1.961277 CCCGACACTGTGGAAGCAC 60.961 63.158 13.09 0.00 0.00 4.40
121 122 2.425592 CCCGACACTGTGGAAGCA 59.574 61.111 13.09 0.00 0.00 3.91
122 123 3.050275 GCCCGACACTGTGGAAGC 61.050 66.667 13.09 5.74 0.00 3.86
123 124 2.358737 GGCCCGACACTGTGGAAG 60.359 66.667 13.09 2.81 0.00 3.46
124 125 4.308458 CGGCCCGACACTGTGGAA 62.308 66.667 13.09 0.00 0.00 3.53
142 143 3.545481 GTGCGACCGATGTCAGCG 61.545 66.667 2.86 2.86 41.85 5.18
143 144 3.188786 GGTGCGACCGATGTCAGC 61.189 66.667 0.00 0.00 41.85 4.26
160 161 2.584143 GGCCGGTACCGTTGATCG 60.584 66.667 31.24 16.64 37.81 3.69
170 171 2.120909 GGCTACAGTACGGCCGGTA 61.121 63.158 31.76 19.93 36.37 4.02
171 172 3.455469 GGCTACAGTACGGCCGGT 61.455 66.667 31.76 19.87 36.37 5.28
174 175 2.202703 CGTGGCTACAGTACGGCC 60.203 66.667 0.00 12.79 45.45 6.13
175 176 2.884207 GCGTGGCTACAGTACGGC 60.884 66.667 0.00 0.00 38.20 5.68
176 177 1.226603 GAGCGTGGCTACAGTACGG 60.227 63.158 0.00 0.00 39.88 4.02
177 178 0.170561 AAGAGCGTGGCTACAGTACG 59.829 55.000 0.00 0.00 39.88 3.67
178 179 1.201647 TGAAGAGCGTGGCTACAGTAC 59.798 52.381 0.00 0.00 39.88 2.73
179 180 1.201647 GTGAAGAGCGTGGCTACAGTA 59.798 52.381 0.00 0.00 39.88 2.74
180 181 0.038159 GTGAAGAGCGTGGCTACAGT 60.038 55.000 0.00 0.00 39.88 3.55
181 182 1.073216 CGTGAAGAGCGTGGCTACAG 61.073 60.000 0.00 0.00 39.88 2.74
182 183 1.080772 CGTGAAGAGCGTGGCTACA 60.081 57.895 0.00 0.00 39.88 2.74
183 184 1.071567 GTCGTGAAGAGCGTGGCTAC 61.072 60.000 0.00 0.00 39.88 3.58
184 185 1.211969 GTCGTGAAGAGCGTGGCTA 59.788 57.895 0.00 0.00 39.88 3.93
185 186 2.049063 GTCGTGAAGAGCGTGGCT 60.049 61.111 0.00 0.00 43.88 4.75
186 187 3.470567 CGTCGTGAAGAGCGTGGC 61.471 66.667 0.00 0.00 0.00 5.01
187 188 2.050351 ACGTCGTGAAGAGCGTGG 60.050 61.111 0.00 0.00 36.07 4.94
188 189 2.365068 CCACGTCGTGAAGAGCGTG 61.365 63.158 26.53 13.12 45.20 5.34
189 190 2.050351 CCACGTCGTGAAGAGCGT 60.050 61.111 26.53 0.00 37.18 5.07
190 191 2.805353 CCCACGTCGTGAAGAGCG 60.805 66.667 26.53 8.41 35.23 5.03
191 192 1.444553 CTCCCACGTCGTGAAGAGC 60.445 63.158 26.53 0.00 35.23 4.09
192 193 0.169230 CTCTCCCACGTCGTGAAGAG 59.831 60.000 27.98 27.98 35.23 2.85
193 194 1.241990 CCTCTCCCACGTCGTGAAGA 61.242 60.000 26.53 23.48 35.23 2.87
194 195 1.213013 CCTCTCCCACGTCGTGAAG 59.787 63.158 26.53 20.92 35.23 3.02
195 196 1.521450 GACCTCTCCCACGTCGTGAA 61.521 60.000 26.53 12.87 35.23 3.18
196 197 1.970114 GACCTCTCCCACGTCGTGA 60.970 63.158 26.53 6.77 35.23 4.35
197 198 1.524863 AAGACCTCTCCCACGTCGTG 61.525 60.000 18.54 18.54 0.00 4.35
198 199 1.228490 AAGACCTCTCCCACGTCGT 60.228 57.895 0.00 0.00 0.00 4.34
199 200 1.213013 CAAGACCTCTCCCACGTCG 59.787 63.158 0.00 0.00 0.00 5.12
200 201 0.244178 GACAAGACCTCTCCCACGTC 59.756 60.000 0.00 0.00 0.00 4.34
201 202 1.524863 CGACAAGACCTCTCCCACGT 61.525 60.000 0.00 0.00 0.00 4.49
202 203 1.213013 CGACAAGACCTCTCCCACG 59.787 63.158 0.00 0.00 0.00 4.94
203 204 1.201880 GTACGACAAGACCTCTCCCAC 59.798 57.143 0.00 0.00 0.00 4.61
204 205 1.542492 GTACGACAAGACCTCTCCCA 58.458 55.000 0.00 0.00 0.00 4.37
205 206 0.450983 CGTACGACAAGACCTCTCCC 59.549 60.000 10.44 0.00 0.00 4.30
206 207 0.450983 CCGTACGACAAGACCTCTCC 59.549 60.000 18.76 0.00 0.00 3.71
207 208 0.179169 GCCGTACGACAAGACCTCTC 60.179 60.000 18.76 0.00 0.00 3.20
208 209 1.881602 GCCGTACGACAAGACCTCT 59.118 57.895 18.76 0.00 0.00 3.69
209 210 4.472702 GCCGTACGACAAGACCTC 57.527 61.111 18.76 0.00 0.00 3.85
219 220 1.401148 CCTATCCAATCTCGCCGTACG 60.401 57.143 8.69 8.69 45.62 3.67
220 221 1.669211 GCCTATCCAATCTCGCCGTAC 60.669 57.143 0.00 0.00 0.00 3.67
221 222 0.601558 GCCTATCCAATCTCGCCGTA 59.398 55.000 0.00 0.00 0.00 4.02
222 223 1.367840 GCCTATCCAATCTCGCCGT 59.632 57.895 0.00 0.00 0.00 5.68
223 224 1.734477 CGCCTATCCAATCTCGCCG 60.734 63.158 0.00 0.00 0.00 6.46
224 225 2.029844 GCGCCTATCCAATCTCGCC 61.030 63.158 0.00 0.00 37.02 5.54
225 226 1.005630 AGCGCCTATCCAATCTCGC 60.006 57.895 2.29 0.00 42.46 5.03
226 227 0.315251 TCAGCGCCTATCCAATCTCG 59.685 55.000 2.29 0.00 0.00 4.04
227 228 1.606737 GGTCAGCGCCTATCCAATCTC 60.607 57.143 2.29 0.00 0.00 2.75
228 229 0.394565 GGTCAGCGCCTATCCAATCT 59.605 55.000 2.29 0.00 0.00 2.40
229 230 0.603975 GGGTCAGCGCCTATCCAATC 60.604 60.000 2.29 0.00 0.00 2.67
230 231 1.056700 AGGGTCAGCGCCTATCCAAT 61.057 55.000 2.29 0.00 0.00 3.16
231 232 1.689233 AGGGTCAGCGCCTATCCAA 60.689 57.895 2.29 0.00 0.00 3.53
232 233 2.041922 AGGGTCAGCGCCTATCCA 60.042 61.111 2.29 0.00 0.00 3.41
233 234 2.423446 CAGGGTCAGCGCCTATCC 59.577 66.667 2.29 1.26 0.00 2.59
234 235 2.280457 GCAGGGTCAGCGCCTATC 60.280 66.667 2.29 0.00 0.00 2.08
235 236 3.866582 GGCAGGGTCAGCGCCTAT 61.867 66.667 2.29 0.00 42.78 2.57
332 333 7.462109 TCAAGTCAATTTTTCAAAACATCGG 57.538 32.000 0.00 0.00 0.00 4.18
356 357 1.691689 CCCGGTAGGCTTAGGGGTT 60.692 63.158 12.21 0.00 40.18 4.11
493 1425 2.610374 GTGTTTGTCTCAACGTTAGCCA 59.390 45.455 0.00 0.00 0.00 4.75
506 1438 0.317020 GTGCTCGCTTGGTGTTTGTC 60.317 55.000 0.00 0.00 0.00 3.18
548 1480 0.733729 CACTTCTCCTACCGTCTCCG 59.266 60.000 0.00 0.00 0.00 4.63
632 1564 2.678580 AATGGTTTTCCGGCCCCG 60.679 61.111 0.00 0.00 44.36 5.73
634 1566 1.320344 GGAGAATGGTTTTCCGGCCC 61.320 60.000 0.00 0.00 44.36 5.80
719 1661 0.770499 TTGACTTGGATGGCAGGTGA 59.230 50.000 0.00 0.00 0.00 4.02
791 1733 1.520564 GTGTGAGTGTGGTGTGCGA 60.521 57.895 0.00 0.00 0.00 5.10
792 1734 0.249280 TAGTGTGAGTGTGGTGTGCG 60.249 55.000 0.00 0.00 0.00 5.34
797 1759 0.246635 GGCGATAGTGTGAGTGTGGT 59.753 55.000 0.00 0.00 39.35 4.16
823 1785 5.449553 AGATGACAAGAGGACTTTGGTTTT 58.550 37.500 0.00 0.00 33.70 2.43
824 1786 5.053978 AGATGACAAGAGGACTTTGGTTT 57.946 39.130 0.00 0.00 33.70 3.27
825 1787 4.713792 AGATGACAAGAGGACTTTGGTT 57.286 40.909 0.00 0.00 33.70 3.67
826 1788 4.141390 ACAAGATGACAAGAGGACTTTGGT 60.141 41.667 0.00 0.00 33.70 3.67
827 1789 4.214971 CACAAGATGACAAGAGGACTTTGG 59.785 45.833 0.00 0.00 33.70 3.28
828 1790 4.818546 ACACAAGATGACAAGAGGACTTTG 59.181 41.667 0.00 0.00 33.70 2.77
829 1791 5.041191 ACACAAGATGACAAGAGGACTTT 57.959 39.130 0.00 0.00 33.70 2.66
830 1792 4.101585 TGACACAAGATGACAAGAGGACTT 59.898 41.667 0.00 0.00 36.73 3.01
831 1793 3.643320 TGACACAAGATGACAAGAGGACT 59.357 43.478 0.00 0.00 29.61 3.85
832 1794 3.743396 GTGACACAAGATGACAAGAGGAC 59.257 47.826 0.00 0.00 34.69 3.85
833 1795 3.244215 GGTGACACAAGATGACAAGAGGA 60.244 47.826 8.08 0.00 34.69 3.71
834 1796 3.070018 GGTGACACAAGATGACAAGAGG 58.930 50.000 8.08 0.00 34.69 3.69
835 1797 4.000331 AGGTGACACAAGATGACAAGAG 58.000 45.455 8.08 0.00 34.69 2.85
836 1798 4.380531 GAAGGTGACACAAGATGACAAGA 58.619 43.478 8.08 0.00 34.69 3.02
841 1803 4.162320 GGATAGGAAGGTGACACAAGATGA 59.838 45.833 8.08 0.00 0.00 2.92
967 2270 0.386352 GCGTTTAAAGTTGCGGGGAC 60.386 55.000 0.00 0.00 0.00 4.46
968 2271 1.517210 GGCGTTTAAAGTTGCGGGGA 61.517 55.000 0.00 0.00 0.00 4.81
1003 2306 2.629617 GCTGGGCATAATTAATGGTGCT 59.370 45.455 19.01 0.00 37.70 4.40
1022 2325 0.326264 GTGTCAAGGGGATGTCAGCT 59.674 55.000 0.00 0.00 0.00 4.24
1026 2329 1.003839 TGCGTGTCAAGGGGATGTC 60.004 57.895 0.00 0.00 0.00 3.06
1028 2331 2.390599 CGTGCGTGTCAAGGGGATG 61.391 63.158 0.00 0.00 0.00 3.51
1029 2332 1.537814 TACGTGCGTGTCAAGGGGAT 61.538 55.000 7.55 0.00 0.00 3.85
1030 2333 1.746322 TTACGTGCGTGTCAAGGGGA 61.746 55.000 7.55 0.00 0.00 4.81
1035 2338 2.143008 AGATGTTACGTGCGTGTCAA 57.857 45.000 7.55 0.00 0.00 3.18
1164 2476 2.978298 TACGAGCCCATCCTCTCCCG 62.978 65.000 0.00 0.00 0.00 5.14
1173 2485 4.203076 GCGGACGTACGAGCCCAT 62.203 66.667 27.46 0.00 35.47 4.00
1313 2625 4.722700 CTGAACACCCTGGGCCCG 62.723 72.222 19.37 12.19 0.00 6.13
1376 2688 4.835891 CCCCCGCTACCGAGGACT 62.836 72.222 0.00 0.00 33.65 3.85
1379 2691 2.842936 AATCCCCCGCTACCGAGG 60.843 66.667 0.00 0.00 36.29 4.63
1424 2736 1.600636 CACCGTGGTGCCATCACTT 60.601 57.895 6.52 0.00 42.72 3.16
1742 3054 2.212327 GTCCCGGTGGATGATCTGT 58.788 57.895 0.00 0.00 44.28 3.41
1853 3165 3.279974 CTTTTTCATGGGCGGCGCA 62.280 57.895 34.36 22.27 0.00 6.09
2051 3363 0.038744 CCACCTCCAGGAGCACAATT 59.961 55.000 11.57 0.00 38.94 2.32
2086 3398 2.420568 GGGTACGCCAGATCGACCA 61.421 63.158 0.00 0.00 34.02 4.02
2126 3438 4.524318 AGCCGGCGTACCCAATCG 62.524 66.667 23.20 0.00 0.00 3.34
2162 3474 3.849911 CTTACGATCACAGGCTTTGAGA 58.150 45.455 9.49 0.00 0.00 3.27
2172 3484 1.153647 CCGGCAGCTTACGATCACA 60.154 57.895 8.29 0.00 0.00 3.58
2177 3489 2.577059 CCTTCCGGCAGCTTACGA 59.423 61.111 8.29 0.00 0.00 3.43
2432 3744 3.577231 CTTCGTAGATGCGGCAGAT 57.423 52.632 9.25 1.57 35.04 2.90
2441 3753 2.460918 GCGTACATGTGCTTCGTAGAT 58.539 47.619 9.11 0.00 35.04 1.98
2444 3756 0.244178 TGGCGTACATGTGCTTCGTA 59.756 50.000 9.11 0.27 0.00 3.43
2474 3786 1.812571 GCAGTGAGGTAAATGGTGGTG 59.187 52.381 0.00 0.00 0.00 4.17
2492 3804 2.343758 GACCTGCCGTCTTCTGCA 59.656 61.111 0.00 0.00 38.57 4.41
2594 3906 1.875009 ACGATATCTCACGCGGAGTA 58.125 50.000 12.47 9.57 44.40 2.59
2633 3945 2.222886 CGACTCGGAGAAATCGTTCGTA 60.223 50.000 12.86 0.00 39.46 3.43
2889 4201 2.436824 GCTCAAGAGGTTCCCCGC 60.437 66.667 0.00 0.00 35.12 6.13
3134 4446 1.073548 GGGCAAAACTACGTGGGGA 59.926 57.895 3.26 0.00 0.00 4.81
3290 4602 2.362503 TCCGGCGACCTCATGTCT 60.363 61.111 9.30 0.00 42.13 3.41
3320 4632 1.600916 GCCGACCTGCACCTTCTTT 60.601 57.895 0.00 0.00 0.00 2.52
3322 4634 4.021925 GGCCGACCTGCACCTTCT 62.022 66.667 0.00 0.00 0.00 2.85
3483 4795 0.179100 CCGTCCAGAATGCTGACGAT 60.179 55.000 20.62 0.00 45.17 3.73
3590 4902 1.094073 CAAGAGCCTGCAATCTCCGG 61.094 60.000 10.30 0.00 0.00 5.14
3591 4903 1.094073 CCAAGAGCCTGCAATCTCCG 61.094 60.000 10.30 3.98 0.00 4.63
3597 4909 2.571653 AGTGTATACCAAGAGCCTGCAA 59.428 45.455 0.00 0.00 0.00 4.08
3611 4923 7.446001 TGCATGTTTGATGTTTCAGTGTATA 57.554 32.000 0.00 0.00 32.27 1.47
3663 4975 2.909006 TGACAGCCTCTTCTCAGGATTT 59.091 45.455 0.00 0.00 35.20 2.17
3665 4977 2.244486 TGACAGCCTCTTCTCAGGAT 57.756 50.000 0.00 0.00 35.20 3.24
3699 5011 6.833342 AATGCGCCAGAAAATTTTCATATC 57.167 33.333 28.00 15.16 39.61 1.63
3856 5205 3.811722 TGCTTCAAAGTTCGTGCTATG 57.188 42.857 0.00 0.00 0.00 2.23
3857 5206 4.787598 CTTTGCTTCAAAGTTCGTGCTAT 58.212 39.130 10.28 0.00 43.85 2.97
3858 5207 4.209452 CTTTGCTTCAAAGTTCGTGCTA 57.791 40.909 10.28 0.00 43.85 3.49
3886 5279 6.536224 CGTTTGTAGGTTTAGGATTTCCGTAT 59.464 38.462 0.00 0.00 42.08 3.06
3890 5283 4.142534 GCCGTTTGTAGGTTTAGGATTTCC 60.143 45.833 0.00 0.00 0.00 3.13
3891 5284 4.698780 AGCCGTTTGTAGGTTTAGGATTTC 59.301 41.667 0.00 0.00 0.00 2.17
3917 5310 7.095695 AGTTGAAAGTTTTTGTAGCAGCTAA 57.904 32.000 2.87 0.00 0.00 3.09
3936 5329 4.532834 GGGGGCATGTTTAGATTAGTTGA 58.467 43.478 0.00 0.00 0.00 3.18
3964 5357 6.042322 AGGATCTCTCCATCTGAAAATCAGAG 59.958 42.308 14.66 7.67 46.47 3.35
3967 5360 7.419518 GGTTAGGATCTCTCCATCTGAAAATCA 60.420 40.741 0.00 0.00 44.79 2.57
3969 5362 6.183361 GGGTTAGGATCTCTCCATCTGAAAAT 60.183 42.308 0.00 0.00 44.79 1.82
3971 5364 4.656112 GGGTTAGGATCTCTCCATCTGAAA 59.344 45.833 0.00 0.00 44.79 2.69
3972 5365 4.078336 AGGGTTAGGATCTCTCCATCTGAA 60.078 45.833 0.00 0.00 44.79 3.02
3973 5366 3.469006 AGGGTTAGGATCTCTCCATCTGA 59.531 47.826 0.00 0.00 44.79 3.27
3974 5367 3.831911 GAGGGTTAGGATCTCTCCATCTG 59.168 52.174 0.00 0.00 44.79 2.90
3975 5368 3.732204 AGAGGGTTAGGATCTCTCCATCT 59.268 47.826 7.63 7.63 44.79 2.90
3977 5370 4.126520 GAGAGGGTTAGGATCTCTCCAT 57.873 50.000 8.02 0.00 44.52 3.41
3978 5371 3.603965 GAGAGGGTTAGGATCTCTCCA 57.396 52.381 8.02 0.00 44.52 3.86
3981 5374 4.635558 AAAGGAGAGGGTTAGGATCTCT 57.364 45.455 0.00 0.00 39.53 3.10
3982 5375 6.014070 GGATTAAAGGAGAGGGTTAGGATCTC 60.014 46.154 0.00 0.00 39.00 2.75
3983 5376 5.847265 GGATTAAAGGAGAGGGTTAGGATCT 59.153 44.000 0.00 0.00 0.00 2.75
3984 5377 5.607171 TGGATTAAAGGAGAGGGTTAGGATC 59.393 44.000 0.00 0.00 0.00 3.36
3985 5378 5.548573 TGGATTAAAGGAGAGGGTTAGGAT 58.451 41.667 0.00 0.00 0.00 3.24
3986 5379 4.967871 TGGATTAAAGGAGAGGGTTAGGA 58.032 43.478 0.00 0.00 0.00 2.94
3987 5380 5.710409 TTGGATTAAAGGAGAGGGTTAGG 57.290 43.478 0.00 0.00 0.00 2.69
3988 5381 6.900194 TGATTGGATTAAAGGAGAGGGTTAG 58.100 40.000 0.00 0.00 0.00 2.34
3989 5382 6.901615 TGATTGGATTAAAGGAGAGGGTTA 57.098 37.500 0.00 0.00 0.00 2.85
3990 5383 5.796502 TGATTGGATTAAAGGAGAGGGTT 57.203 39.130 0.00 0.00 0.00 4.11
3991 5384 5.796502 TTGATTGGATTAAAGGAGAGGGT 57.203 39.130 0.00 0.00 0.00 4.34
3992 5385 8.001292 ACTATTTGATTGGATTAAAGGAGAGGG 58.999 37.037 0.00 0.00 0.00 4.30
3993 5386 8.986929 ACTATTTGATTGGATTAAAGGAGAGG 57.013 34.615 0.00 0.00 0.00 3.69
3994 5387 9.844257 AGACTATTTGATTGGATTAAAGGAGAG 57.156 33.333 0.00 0.00 0.00 3.20
4005 5398 5.185056 TCTGACGTGAGACTATTTGATTGGA 59.815 40.000 0.00 0.00 0.00 3.53
4062 5455 7.442364 TCATAACCTTTAGAGCAATGCTACATC 59.558 37.037 8.12 0.00 39.88 3.06
4069 5462 8.948631 TTCTAGTCATAACCTTTAGAGCAATG 57.051 34.615 0.00 0.00 0.00 2.82
4089 5482 9.578439 CATTAAAAGAAGGGCTGATTTTTCTAG 57.422 33.333 0.00 0.00 30.19 2.43
4108 5501 3.694072 CGAGCTGATTGTCCCCATTAAAA 59.306 43.478 0.00 0.00 0.00 1.52
4114 5507 2.268920 GCGAGCTGATTGTCCCCA 59.731 61.111 0.00 0.00 0.00 4.96
4198 5592 3.133721 AGCAGTTTCGCAATAGATCCTCT 59.866 43.478 0.00 0.00 0.00 3.69
4222 5616 6.002062 ACAAGAAAGCTAAATTCCGAACAG 57.998 37.500 0.00 0.00 0.00 3.16
4223 5617 6.385649 AACAAGAAAGCTAAATTCCGAACA 57.614 33.333 0.00 0.00 0.00 3.18
4524 5922 0.173481 CTCGACGGACATGACACCAT 59.827 55.000 0.00 0.00 0.00 3.55
4534 5932 0.388263 GAGTTTGGACCTCGACGGAC 60.388 60.000 7.76 2.16 36.31 4.79
4562 5960 5.048991 CGATATACTTTGTTGGTAATGGCCC 60.049 44.000 0.00 0.00 0.00 5.80
4604 6002 2.653234 AGAAGGATGATGGTGGCATC 57.347 50.000 0.00 0.00 41.03 3.91
4616 6014 6.114187 TGTGTTGACAATCACTAGAAGGAT 57.886 37.500 16.53 0.00 35.82 3.24
4703 6103 5.100259 ACAAGTTACCATTATGACGACGAG 58.900 41.667 0.00 0.00 0.00 4.18
4709 6109 7.145932 AGAAGCAACAAGTTACCATTATGAC 57.854 36.000 0.00 0.00 0.00 3.06
4712 6112 7.883311 AGTGTAGAAGCAACAAGTTACCATTAT 59.117 33.333 0.00 0.00 0.00 1.28
4713 6113 7.221450 AGTGTAGAAGCAACAAGTTACCATTA 58.779 34.615 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.