Multiple sequence alignment - TraesCS4D01G303500

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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 TraesCS4D01G303500 chr4D 100.000 3414 0 0 1 3414 471960107 471963520 0.000000e+00 6305.0
1 TraesCS4D01G303500 chr4D 86.538 208 24 3 2 206 401538422 401538216 3.430000e-55 226.0
2 TraesCS4D01G303500 chr4D 87.000 200 20 4 11 206 464370594 464370791 1.590000e-53 220.0
3 TraesCS4D01G303500 chr4D 82.828 198 16 3 11 206 12300573 12300392 9.800000e-36 161.0
4 TraesCS4D01G303500 chr4D 96.739 92 3 0 2918 3009 383781285 383781376 1.640000e-33 154.0
5 TraesCS4D01G303500 chr4B 92.526 2395 77 33 514 2841 593421791 593424150 0.000000e+00 3338.0
6 TraesCS4D01G303500 chr4B 90.137 365 23 5 3044 3408 593424547 593424898 2.400000e-126 462.0
7 TraesCS4D01G303500 chr4B 91.223 319 18 4 204 516 593421219 593421533 3.150000e-115 425.0
8 TraesCS4D01G303500 chr4B 91.837 49 3 1 2878 2926 593424269 593424316 2.200000e-07 67.6
9 TraesCS4D01G303500 chr4A 93.592 1623 50 23 1286 2881 678872139 678873734 0.000000e+00 2372.0
10 TraesCS4D01G303500 chr4A 93.812 808 33 5 458 1255 678871342 678872142 0.000000e+00 1199.0
11 TraesCS4D01G303500 chr4A 93.985 266 16 0 3006 3271 678873873 678874138 1.480000e-108 403.0
12 TraesCS4D01G303500 chr4A 89.116 147 16 0 3268 3414 678875612 678875758 2.090000e-42 183.0
13 TraesCS4D01G303500 chr4A 80.784 255 27 8 204 450 678870854 678871094 2.710000e-41 180.0
14 TraesCS4D01G303500 chr4A 94.318 88 5 0 2923 3010 732285686 732285599 5.940000e-28 135.0
15 TraesCS4D01G303500 chr4A 95.349 43 2 0 2882 2924 678873832 678873874 6.110000e-08 69.4
16 TraesCS4D01G303500 chr5A 88.849 278 25 5 1550 1824 463452312 463452586 1.520000e-88 337.0
17 TraesCS4D01G303500 chr5A 85.784 204 27 1 4 207 706928684 706928483 7.420000e-52 215.0
18 TraesCS4D01G303500 chr5B 88.087 277 29 4 1550 1824 428461851 428462125 3.290000e-85 326.0
19 TraesCS4D01G303500 chr5B 87.692 65 3 2 308 371 373687184 373687244 1.700000e-08 71.3
20 TraesCS4D01G303500 chr5D 87.726 277 30 4 1550 1824 362548004 362548278 1.530000e-83 320.0
21 TraesCS4D01G303500 chr5D 90.769 65 1 2 308 371 322386672 322386732 7.850000e-12 82.4
22 TraesCS4D01G303500 chr5D 85.714 70 5 4 303 371 496955454 496955519 6.110000e-08 69.4
23 TraesCS4D01G303500 chr1A 87.793 213 18 5 4 208 325030858 325030646 3.400000e-60 243.0
24 TraesCS4D01G303500 chr1A 88.325 197 16 3 17 207 61034794 61034599 2.650000e-56 230.0
25 TraesCS4D01G303500 chr1A 85.238 210 21 6 6 207 26597716 26597923 1.240000e-49 207.0
26 TraesCS4D01G303500 chr3A 89.000 200 14 4 11 204 399502954 399503151 1.220000e-59 241.0
27 TraesCS4D01G303500 chr2A 86.047 172 19 2 40 206 682015863 682015692 2.710000e-41 180.0
28 TraesCS4D01G303500 chr6B 80.556 216 36 5 1585 1797 568258599 568258387 9.800000e-36 161.0
29 TraesCS4D01G303500 chr6B 95.294 85 3 1 2923 3007 706325495 706325412 2.140000e-27 134.0
30 TraesCS4D01G303500 chr6B 97.297 37 0 1 308 343 367659101 367659065 1.020000e-05 62.1
31 TraesCS4D01G303500 chr6A 80.093 216 37 5 1585 1797 522227015 522226803 4.560000e-34 156.0
32 TraesCS4D01G303500 chr6A 97.297 37 0 1 308 343 266102722 266102758 1.020000e-05 62.1
33 TraesCS4D01G303500 chr6D 79.167 216 39 5 1585 1797 380800280 380800068 9.870000e-31 145.0
34 TraesCS4D01G303500 chr6D 97.297 37 0 1 308 343 202459687 202459651 1.020000e-05 62.1
35 TraesCS4D01G303500 chr7B 94.253 87 5 0 2921 3007 74735528 74735614 2.140000e-27 134.0
36 TraesCS4D01G303500 chr7B 87.273 110 10 3 2920 3025 733715451 733715342 4.630000e-24 122.0
37 TraesCS4D01G303500 chr7B 100.000 32 0 0 308 339 709523908 709523877 3.680000e-05 60.2
38 TraesCS4D01G303500 chr1D 90.909 99 7 2 2912 3010 229606086 229605990 7.690000e-27 132.0
39 TraesCS4D01G303500 chr7A 91.579 95 7 1 2919 3013 16368613 16368520 2.760000e-26 130.0
40 TraesCS4D01G303500 chr2B 91.304 92 8 0 2923 3014 245822389 245822298 3.580000e-25 126.0
41 TraesCS4D01G303500 chr2D 89.796 98 9 1 2916 3013 472231215 472231119 1.290000e-24 124.0


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 TraesCS4D01G303500 chr4D 471960107 471963520 3413 False 6305.00 6305 100.000000 1 3414 1 chr4D.!!$F3 3413
1 TraesCS4D01G303500 chr4B 593421219 593424898 3679 False 1073.15 3338 91.430750 204 3408 4 chr4B.!!$F1 3204
2 TraesCS4D01G303500 chr4A 678870854 678875758 4904 False 734.40 2372 91.106333 204 3414 6 chr4A.!!$F1 3210

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
253 254 0.037326 TTGCTTGAGACGGATCGCTT 60.037 50.0 0.00 0.00 0.00 4.68 F
489 738 0.107643 GAGGCCTGTAGAGGATTGCC 59.892 60.0 12.00 3.29 42.93 4.52 F
1834 2417 0.249398 GGTACGTGCTCCACTCCATT 59.751 55.0 3.01 0.00 31.34 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 2418 0.110192 GACAAACAGCTAGCGGCAAC 60.110 55.0 15.21 0.0 44.79 4.17 R
1836 2419 0.533978 TGACAAACAGCTAGCGGCAA 60.534 50.0 15.21 0.0 44.79 4.52 R
3356 5731 0.234884 CGAGTTCCAAAGGTCGTTGC 59.765 55.0 0.00 0.0 0.00 4.17 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
25 26 2.748461 GCGAGCGCCACAATTTATAA 57.252 45.000 2.29 0.00 34.56 0.98
26 27 2.639751 GCGAGCGCCACAATTTATAAG 58.360 47.619 2.29 0.00 34.56 1.73
27 28 2.639751 CGAGCGCCACAATTTATAAGC 58.360 47.619 2.29 0.00 0.00 3.09
28 29 2.639751 GAGCGCCACAATTTATAAGCG 58.360 47.619 2.29 9.44 45.91 4.68
30 31 1.385038 CGCCACAATTTATAAGCGCG 58.615 50.000 0.00 0.00 36.89 6.86
31 32 1.120437 GCCACAATTTATAAGCGCGC 58.880 50.000 26.66 26.66 0.00 6.86
32 33 1.753956 CCACAATTTATAAGCGCGCC 58.246 50.000 30.33 10.31 0.00 6.53
33 34 1.385038 CACAATTTATAAGCGCGCCG 58.615 50.000 30.33 7.48 0.00 6.46
34 35 0.306533 ACAATTTATAAGCGCGCCGG 59.693 50.000 30.33 9.10 0.00 6.13
35 36 0.584396 CAATTTATAAGCGCGCCGGA 59.416 50.000 30.33 14.20 0.00 5.14
36 37 0.584876 AATTTATAAGCGCGCCGGAC 59.415 50.000 30.33 0.00 0.00 4.79
55 56 4.886925 CGGCGCGCCAAATGTAGC 62.887 66.667 45.26 18.93 35.37 3.58
61 62 3.860125 GCCAAATGTAGCGCGCGA 61.860 61.111 37.18 19.65 0.00 5.87
62 63 2.321060 CCAAATGTAGCGCGCGAG 59.679 61.111 37.18 8.39 0.00 5.03
76 77 3.804193 CGAGCTGCCGCCTTTTCC 61.804 66.667 0.00 0.00 36.60 3.13
77 78 3.443925 GAGCTGCCGCCTTTTCCC 61.444 66.667 0.00 0.00 36.60 3.97
95 96 4.776647 GCCCGCGCGCAATCTTTT 62.777 61.111 32.61 0.00 0.00 2.27
96 97 2.576847 CCCGCGCGCAATCTTTTC 60.577 61.111 32.61 0.00 0.00 2.29
97 98 2.939003 CCGCGCGCAATCTTTTCG 60.939 61.111 32.61 11.04 0.00 3.46
98 99 3.588337 CGCGCGCAATCTTTTCGC 61.588 61.111 32.61 0.00 44.76 4.70
102 103 3.588337 CGCAATCTTTTCGCGCGC 61.588 61.111 27.95 23.91 42.79 6.86
103 104 3.588337 GCAATCTTTTCGCGCGCG 61.588 61.111 44.84 44.84 41.35 6.86
104 105 3.588337 CAATCTTTTCGCGCGCGC 61.588 61.111 45.41 42.65 39.59 6.86
118 119 4.700365 GCGCAAGTTTCCCGCCAC 62.700 66.667 0.30 0.00 41.72 5.01
119 120 4.038080 CGCAAGTTTCCCGCCACC 62.038 66.667 0.00 0.00 0.00 4.61
120 121 4.038080 GCAAGTTTCCCGCCACCG 62.038 66.667 0.00 0.00 0.00 4.94
121 122 4.038080 CAAGTTTCCCGCCACCGC 62.038 66.667 0.00 0.00 0.00 5.68
122 123 4.265056 AAGTTTCCCGCCACCGCT 62.265 61.111 0.00 0.00 0.00 5.52
137 138 4.166011 GCTGGAGCGCGCGAAAAT 62.166 61.111 37.18 16.05 0.00 1.82
138 139 2.276868 CTGGAGCGCGCGAAAATG 60.277 61.111 37.18 15.99 0.00 2.32
139 140 3.027170 CTGGAGCGCGCGAAAATGT 62.027 57.895 37.18 5.81 0.00 2.71
140 141 2.276680 GGAGCGCGCGAAAATGTC 60.277 61.111 37.18 15.71 0.00 3.06
141 142 2.276680 GAGCGCGCGAAAATGTCC 60.277 61.111 37.18 13.39 0.00 4.02
142 143 3.718480 GAGCGCGCGAAAATGTCCC 62.718 63.158 37.18 12.54 0.00 4.46
143 144 4.829518 GCGCGCGAAAATGTCCCC 62.830 66.667 37.18 7.60 0.00 4.81
144 145 4.174129 CGCGCGAAAATGTCCCCC 62.174 66.667 28.94 0.00 0.00 5.40
145 146 4.174129 GCGCGAAAATGTCCCCCG 62.174 66.667 12.10 0.00 0.00 5.73
146 147 4.174129 CGCGAAAATGTCCCCCGC 62.174 66.667 0.00 0.00 42.11 6.13
147 148 4.174129 GCGAAAATGTCCCCCGCG 62.174 66.667 0.00 0.00 36.53 6.46
148 149 4.174129 CGAAAATGTCCCCCGCGC 62.174 66.667 0.00 0.00 0.00 6.86
149 150 4.174129 GAAAATGTCCCCCGCGCG 62.174 66.667 25.67 25.67 0.00 6.86
156 157 4.701290 TCCCCCGCGCGCTAAAAA 62.701 61.111 30.48 8.98 0.00 1.94
157 158 4.174129 CCCCCGCGCGCTAAAAAG 62.174 66.667 30.48 12.26 0.00 2.27
158 159 4.829518 CCCCGCGCGCTAAAAAGC 62.830 66.667 30.48 0.00 0.00 3.51
159 160 4.829518 CCCGCGCGCTAAAAAGCC 62.830 66.667 30.48 0.00 0.00 4.35
160 161 4.096558 CCGCGCGCTAAAAAGCCA 62.097 61.111 30.48 0.00 0.00 4.75
161 162 2.574212 CGCGCGCTAAAAAGCCAG 60.574 61.111 30.48 5.07 0.00 4.85
162 163 2.561373 GCGCGCTAAAAAGCCAGT 59.439 55.556 26.67 0.00 0.00 4.00
163 164 1.081442 GCGCGCTAAAAAGCCAGTT 60.081 52.632 26.67 0.00 0.00 3.16
164 165 0.663269 GCGCGCTAAAAAGCCAGTTT 60.663 50.000 26.67 0.00 0.00 2.66
165 166 1.400500 GCGCGCTAAAAAGCCAGTTTA 60.400 47.619 26.67 0.00 0.00 2.01
166 167 2.239201 CGCGCTAAAAAGCCAGTTTAC 58.761 47.619 5.56 0.00 0.00 2.01
167 168 2.095919 CGCGCTAAAAAGCCAGTTTACT 60.096 45.455 5.56 0.00 0.00 2.24
168 169 3.234386 GCGCTAAAAAGCCAGTTTACTG 58.766 45.455 0.00 2.86 43.40 2.74
169 170 3.234386 CGCTAAAAAGCCAGTTTACTGC 58.766 45.455 4.34 1.05 42.47 4.40
170 171 3.234386 GCTAAAAAGCCAGTTTACTGCG 58.766 45.455 4.34 0.07 42.47 5.18
171 172 2.134201 AAAAAGCCAGTTTACTGCGC 57.866 45.000 0.00 0.00 42.47 6.09
172 173 0.040425 AAAAGCCAGTTTACTGCGCG 60.040 50.000 0.00 0.00 42.47 6.86
173 174 1.164041 AAAGCCAGTTTACTGCGCGT 61.164 50.000 8.43 6.51 42.47 6.01
174 175 1.841663 AAGCCAGTTTACTGCGCGTG 61.842 55.000 8.43 3.52 42.47 5.34
175 176 2.604174 GCCAGTTTACTGCGCGTGT 61.604 57.895 8.43 10.13 42.47 4.49
176 177 1.491563 CCAGTTTACTGCGCGTGTC 59.508 57.895 8.43 0.00 42.47 3.67
177 178 0.944311 CCAGTTTACTGCGCGTGTCT 60.944 55.000 8.43 0.00 42.47 3.41
178 179 0.859232 CAGTTTACTGCGCGTGTCTT 59.141 50.000 8.43 0.00 37.15 3.01
179 180 1.260561 CAGTTTACTGCGCGTGTCTTT 59.739 47.619 8.43 0.00 37.15 2.52
180 181 1.937899 AGTTTACTGCGCGTGTCTTTT 59.062 42.857 8.43 0.00 0.00 2.27
181 182 2.034076 GTTTACTGCGCGTGTCTTTTG 58.966 47.619 8.43 0.00 0.00 2.44
182 183 0.584396 TTACTGCGCGTGTCTTTTGG 59.416 50.000 8.43 0.00 0.00 3.28
183 184 1.837538 TACTGCGCGTGTCTTTTGGC 61.838 55.000 8.43 0.00 0.00 4.52
189 190 3.660111 GTGTCTTTTGGCGCGGCT 61.660 61.111 33.23 0.00 0.00 5.52
190 191 3.659092 TGTCTTTTGGCGCGGCTG 61.659 61.111 33.23 19.47 0.00 4.85
191 192 3.660111 GTCTTTTGGCGCGGCTGT 61.660 61.111 33.23 0.00 0.00 4.40
192 193 2.904866 TCTTTTGGCGCGGCTGTT 60.905 55.556 33.23 0.00 0.00 3.16
193 194 2.730604 CTTTTGGCGCGGCTGTTG 60.731 61.111 33.23 16.78 0.00 3.33
194 195 3.192954 CTTTTGGCGCGGCTGTTGA 62.193 57.895 33.23 10.23 0.00 3.18
195 196 2.676016 CTTTTGGCGCGGCTGTTGAA 62.676 55.000 33.23 16.24 0.00 2.69
196 197 2.676016 TTTTGGCGCGGCTGTTGAAG 62.676 55.000 33.23 0.00 0.00 3.02
197 198 4.617520 TGGCGCGGCTGTTGAAGA 62.618 61.111 33.23 7.69 0.00 2.87
198 199 3.127533 GGCGCGGCTGTTGAAGAT 61.128 61.111 27.05 0.00 0.00 2.40
199 200 2.099062 GCGCGGCTGTTGAAGATG 59.901 61.111 8.83 0.00 0.00 2.90
200 201 2.099062 CGCGGCTGTTGAAGATGC 59.901 61.111 0.00 0.00 0.00 3.91
201 202 2.393768 CGCGGCTGTTGAAGATGCT 61.394 57.895 0.00 0.00 0.00 3.79
202 203 1.427020 GCGGCTGTTGAAGATGCTC 59.573 57.895 0.00 0.00 0.00 4.26
217 218 3.135530 AGATGCTCTTAGGGATTGTCACC 59.864 47.826 0.00 0.00 0.00 4.02
227 228 1.804748 GGATTGTCACCGTGGAAGTTC 59.195 52.381 0.00 0.00 0.00 3.01
253 254 0.037326 TTGCTTGAGACGGATCGCTT 60.037 50.000 0.00 0.00 0.00 4.68
266 267 3.535561 GGATCGCTTGGATTTCTCTTCA 58.464 45.455 0.00 0.00 34.82 3.02
330 331 7.494952 TGAATTTGAGTTTGTTTGATTGCATCA 59.505 29.630 0.00 0.00 37.55 3.07
347 348 5.916318 TGCATCACAGGAAAACAAAGAATT 58.084 33.333 0.00 0.00 0.00 2.17
348 349 6.347696 TGCATCACAGGAAAACAAAGAATTT 58.652 32.000 0.00 0.00 40.26 1.82
349 350 6.822676 TGCATCACAGGAAAACAAAGAATTTT 59.177 30.769 0.00 0.00 35.03 1.82
381 382 7.563888 CAAGATGTTGGAGTCAATGTATCAT 57.436 36.000 0.00 0.00 35.10 2.45
443 453 4.577687 TTACGAATCAAGCGATCAACAC 57.422 40.909 0.00 0.00 0.00 3.32
489 738 0.107643 GAGGCCTGTAGAGGATTGCC 59.892 60.000 12.00 3.29 42.93 4.52
589 1100 5.102313 GGTAAATGTAAATGCTGCAAGGAC 58.898 41.667 6.36 5.33 36.81 3.85
744 1255 3.304190 CCCCGCTTTTATTTATACGCCAC 60.304 47.826 0.00 0.00 0.00 5.01
1109 1656 6.708502 TGTACTTGTTGCTAGCTTGATGTTTA 59.291 34.615 17.23 0.00 0.00 2.01
1151 1720 6.489127 TTGAGCTTAAATTTTAGTAGCGCA 57.511 33.333 11.47 12.42 39.33 6.09
1152 1721 6.677781 TGAGCTTAAATTTTAGTAGCGCAT 57.322 33.333 11.47 0.00 36.87 4.73
1153 1722 6.715464 TGAGCTTAAATTTTAGTAGCGCATC 58.285 36.000 11.47 1.13 36.87 3.91
1154 1723 6.061231 AGCTTAAATTTTAGTAGCGCATCC 57.939 37.500 11.47 0.00 36.96 3.51
1155 1724 4.904154 GCTTAAATTTTAGTAGCGCATCCG 59.096 41.667 11.47 0.00 37.57 4.18
1265 1834 1.117994 CCTGCTCACTCTATGCTCCA 58.882 55.000 0.00 0.00 0.00 3.86
1272 1849 4.677584 CTCACTCTATGCTCCAACAGTAC 58.322 47.826 0.00 0.00 0.00 2.73
1277 1854 5.008811 ACTCTATGCTCCAACAGTACGTATC 59.991 44.000 0.00 0.00 0.00 2.24
1317 1894 6.591062 GCATTTGGAAGCATTTTGTGATCTAA 59.409 34.615 0.00 0.00 0.00 2.10
1339 1916 4.406456 AGGCAATTATGGAACACAAGTGA 58.594 39.130 7.28 0.00 43.99 3.41
1345 1922 8.243426 GCAATTATGGAACACAAGTGATTCTTA 58.757 33.333 7.28 0.00 43.99 2.10
1373 1952 2.375014 TGTGTGTGTGAGGACTAGGA 57.625 50.000 0.00 0.00 0.00 2.94
1406 1986 2.575532 GAAGCTAACCATGCTGGCATA 58.424 47.619 7.79 0.00 42.67 3.14
1407 1987 2.965671 AGCTAACCATGCTGGCATAT 57.034 45.000 7.79 1.13 42.67 1.78
1408 1988 3.234234 AGCTAACCATGCTGGCATATT 57.766 42.857 7.79 8.26 42.67 1.28
1409 1989 2.889045 AGCTAACCATGCTGGCATATTG 59.111 45.455 7.79 3.13 42.67 1.90
1410 1990 2.608752 GCTAACCATGCTGGCATATTGC 60.609 50.000 7.79 6.76 42.67 3.56
1828 2411 2.181021 CCGAGGTACGTGCTCCAC 59.819 66.667 3.01 0.00 40.78 4.02
1830 2413 1.136984 CGAGGTACGTGCTCCACTC 59.863 63.158 3.01 0.65 37.22 3.51
1832 2415 1.228769 AGGTACGTGCTCCACTCCA 60.229 57.895 3.01 0.00 31.34 3.86
1833 2416 0.614979 AGGTACGTGCTCCACTCCAT 60.615 55.000 3.01 0.00 31.34 3.41
1834 2417 0.249398 GGTACGTGCTCCACTCCATT 59.751 55.000 3.01 0.00 31.34 3.16
1835 2418 1.359848 GTACGTGCTCCACTCCATTG 58.640 55.000 0.00 0.00 31.34 2.82
1836 2419 0.973632 TACGTGCTCCACTCCATTGT 59.026 50.000 0.00 0.00 31.34 2.71
1837 2420 0.108585 ACGTGCTCCACTCCATTGTT 59.891 50.000 0.00 0.00 31.34 2.83
1838 2421 0.518636 CGTGCTCCACTCCATTGTTG 59.481 55.000 0.00 0.00 31.34 3.33
1839 2422 0.242017 GTGCTCCACTCCATTGTTGC 59.758 55.000 0.00 0.00 0.00 4.17
1840 2423 0.895100 TGCTCCACTCCATTGTTGCC 60.895 55.000 0.00 0.00 0.00 4.52
1853 2437 0.817634 TGTTGCCGCTAGCTGTTTGT 60.818 50.000 13.93 0.00 44.23 2.83
1856 2440 0.950555 TGCCGCTAGCTGTTTGTCAG 60.951 55.000 13.93 0.00 46.12 3.51
1877 2461 2.961669 GCGGCCACGTCGTTTGATT 61.962 57.895 2.24 0.00 43.45 2.57
1880 2464 0.309612 GGCCACGTCGTTTGATTGTT 59.690 50.000 0.00 0.00 0.00 2.83
1881 2465 1.394697 GCCACGTCGTTTGATTGTTG 58.605 50.000 0.00 0.00 0.00 3.33
1899 2483 4.245660 TGTTGTACTTATCTGTGCTCTGC 58.754 43.478 0.00 0.00 0.00 4.26
2125 2709 2.125350 GTCTTCGAGCAGCAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
2494 3088 0.460311 GCCTAGCTAGCGGACAAGAA 59.540 55.000 15.74 0.00 0.00 2.52
2501 3095 1.899437 TAGCGGACAAGAAGGGCAGG 61.899 60.000 0.00 0.00 0.00 4.85
2502 3096 2.045926 CGGACAAGAAGGGCAGGG 60.046 66.667 0.00 0.00 0.00 4.45
2504 3098 1.301293 GGACAAGAAGGGCAGGGAG 59.699 63.158 0.00 0.00 0.00 4.30
2507 3101 1.925455 CAAGAAGGGCAGGGAGGGA 60.925 63.158 0.00 0.00 0.00 4.20
2508 3102 1.617839 AAGAAGGGCAGGGAGGGAG 60.618 63.158 0.00 0.00 0.00 4.30
2509 3103 3.093172 GAAGGGCAGGGAGGGAGG 61.093 72.222 0.00 0.00 0.00 4.30
2510 3104 3.952799 GAAGGGCAGGGAGGGAGGT 62.953 68.421 0.00 0.00 0.00 3.85
2511 3105 3.952799 AAGGGCAGGGAGGGAGGTC 62.953 68.421 0.00 0.00 0.00 3.85
2512 3106 4.741239 GGGCAGGGAGGGAGGTCA 62.741 72.222 0.00 0.00 0.00 4.02
2513 3107 3.086600 GGCAGGGAGGGAGGTCAG 61.087 72.222 0.00 0.00 0.00 3.51
2514 3108 3.791586 GCAGGGAGGGAGGTCAGC 61.792 72.222 0.00 0.00 0.00 4.26
2515 3109 2.284921 CAGGGAGGGAGGTCAGCA 60.285 66.667 0.00 0.00 0.00 4.41
2516 3110 1.920325 CAGGGAGGGAGGTCAGCAA 60.920 63.158 0.00 0.00 0.00 3.91
2517 3111 1.083706 AGGGAGGGAGGTCAGCAAT 59.916 57.895 0.00 0.00 0.00 3.56
2518 3112 1.225704 GGGAGGGAGGTCAGCAATG 59.774 63.158 0.00 0.00 0.00 2.82
2519 3113 1.225704 GGAGGGAGGTCAGCAATGG 59.774 63.158 0.00 0.00 0.00 3.16
2520 3114 1.452833 GAGGGAGGTCAGCAATGGC 60.453 63.158 0.00 0.00 41.61 4.40
2763 3367 1.522668 TGCGACAAAATGGTCAGAGG 58.477 50.000 0.00 0.00 37.66 3.69
2776 3380 4.431131 AGAGGGCACGCCAATGGG 62.431 66.667 10.83 0.00 37.98 4.00
2812 3416 1.524355 CAGACTGAAACACACTGCTCG 59.476 52.381 0.00 0.00 0.00 5.03
2847 3451 4.269123 TCATTGTACCGATGAAATACGCAC 59.731 41.667 6.57 0.00 32.02 5.34
2935 3637 7.362802 ACAAATTATACTACTCCCTCTGTCC 57.637 40.000 0.00 0.00 0.00 4.02
2936 3638 6.326843 ACAAATTATACTACTCCCTCTGTCCC 59.673 42.308 0.00 0.00 0.00 4.46
2937 3639 5.681494 ATTATACTACTCCCTCTGTCCCA 57.319 43.478 0.00 0.00 0.00 4.37
2938 3640 2.822707 TACTACTCCCTCTGTCCCAC 57.177 55.000 0.00 0.00 0.00 4.61
2939 3641 0.784495 ACTACTCCCTCTGTCCCACA 59.216 55.000 0.00 0.00 0.00 4.17
2940 3642 1.149288 ACTACTCCCTCTGTCCCACAA 59.851 52.381 0.00 0.00 0.00 3.33
2941 3643 2.225650 ACTACTCCCTCTGTCCCACAAT 60.226 50.000 0.00 0.00 0.00 2.71
2942 3644 2.642171 ACTCCCTCTGTCCCACAATA 57.358 50.000 0.00 0.00 0.00 1.90
2943 3645 3.136641 ACTCCCTCTGTCCCACAATAT 57.863 47.619 0.00 0.00 0.00 1.28
2944 3646 4.280789 ACTCCCTCTGTCCCACAATATA 57.719 45.455 0.00 0.00 0.00 0.86
2945 3647 4.631234 ACTCCCTCTGTCCCACAATATAA 58.369 43.478 0.00 0.00 0.00 0.98
2946 3648 4.656112 ACTCCCTCTGTCCCACAATATAAG 59.344 45.833 0.00 0.00 0.00 1.73
2947 3649 4.890988 TCCCTCTGTCCCACAATATAAGA 58.109 43.478 0.00 0.00 0.00 2.10
2948 3650 5.285401 TCCCTCTGTCCCACAATATAAGAA 58.715 41.667 0.00 0.00 0.00 2.52
2949 3651 5.130477 TCCCTCTGTCCCACAATATAAGAAC 59.870 44.000 0.00 0.00 0.00 3.01
2950 3652 5.050490 CCTCTGTCCCACAATATAAGAACG 58.950 45.833 0.00 0.00 0.00 3.95
2951 3653 5.395324 CCTCTGTCCCACAATATAAGAACGT 60.395 44.000 0.00 0.00 0.00 3.99
2952 3654 6.045072 TCTGTCCCACAATATAAGAACGTT 57.955 37.500 0.00 0.00 0.00 3.99
2953 3655 6.469410 TCTGTCCCACAATATAAGAACGTTT 58.531 36.000 0.46 0.00 0.00 3.60
2954 3656 6.938030 TCTGTCCCACAATATAAGAACGTTTT 59.062 34.615 0.46 0.00 0.00 2.43
2955 3657 7.446013 TCTGTCCCACAATATAAGAACGTTTTT 59.554 33.333 9.22 9.22 0.00 1.94
2956 3658 8.618702 TGTCCCACAATATAAGAACGTTTTTA 57.381 30.769 13.02 13.02 0.00 1.52
2957 3659 9.064706 TGTCCCACAATATAAGAACGTTTTTAA 57.935 29.630 14.41 5.85 0.00 1.52
2958 3660 9.333497 GTCCCACAATATAAGAACGTTTTTAAC 57.667 33.333 14.41 2.76 0.00 2.01
2959 3661 9.064706 TCCCACAATATAAGAACGTTTTTAACA 57.935 29.630 14.41 6.96 0.00 2.41
2960 3662 9.849166 CCCACAATATAAGAACGTTTTTAACAT 57.151 29.630 14.41 8.70 0.00 2.71
2970 3672 9.925268 AAGAACGTTTTTAACATTACACTAGTG 57.075 29.630 21.44 21.44 0.00 2.74
2971 3673 9.101655 AGAACGTTTTTAACATTACACTAGTGT 57.898 29.630 30.13 30.13 46.87 3.55
2972 3674 9.361712 GAACGTTTTTAACATTACACTAGTGTC 57.638 33.333 31.11 11.71 43.74 3.67
2973 3675 8.422973 ACGTTTTTAACATTACACTAGTGTCA 57.577 30.769 31.11 21.55 43.74 3.58
2974 3676 8.881743 ACGTTTTTAACATTACACTAGTGTCAA 58.118 29.630 31.11 21.79 43.74 3.18
2975 3677 9.705471 CGTTTTTAACATTACACTAGTGTCAAA 57.295 29.630 31.11 21.02 43.74 2.69
2979 3681 9.705471 TTTAACATTACACTAGTGTCAAAAACG 57.295 29.630 31.11 15.26 43.74 3.60
2980 3682 6.913873 ACATTACACTAGTGTCAAAAACGT 57.086 33.333 31.11 15.91 43.74 3.99
2981 3683 7.311364 ACATTACACTAGTGTCAAAAACGTT 57.689 32.000 31.11 6.17 43.74 3.99
2982 3684 7.754625 ACATTACACTAGTGTCAAAAACGTTT 58.245 30.769 31.11 7.96 43.74 3.60
2983 3685 8.238631 ACATTACACTAGTGTCAAAAACGTTTT 58.761 29.630 31.11 20.26 43.74 2.43
2984 3686 9.068008 CATTACACTAGTGTCAAAAACGTTTTT 57.932 29.630 31.11 28.62 43.74 1.94
3001 3703 9.893305 AAACGTTTTTATATTTTGAGACAGAGG 57.107 29.630 7.96 0.00 0.00 3.69
3002 3704 8.040716 ACGTTTTTATATTTTGAGACAGAGGG 57.959 34.615 0.00 0.00 0.00 4.30
3003 3705 7.881232 ACGTTTTTATATTTTGAGACAGAGGGA 59.119 33.333 0.00 0.00 0.00 4.20
3065 3963 9.177304 GTAAATACACTTGGTAAAACTGAAAGC 57.823 33.333 0.00 0.00 33.90 3.51
3077 3975 1.203994 ACTGAAAGCTGCATCAATGGC 59.796 47.619 1.02 0.00 37.60 4.40
3103 4001 3.788227 AAAGGCCGCATGATAGGAATA 57.212 42.857 0.00 0.00 0.00 1.75
3158 4056 0.324943 TGGCTACTCTTCAAGGGCAC 59.675 55.000 0.00 0.00 31.98 5.01
3223 4121 1.003839 CCTGCTTGCCCTCGTTGTA 60.004 57.895 0.00 0.00 0.00 2.41
3261 4159 3.466836 TGCCGTGCATATTTTCCTCTAG 58.533 45.455 0.00 0.00 31.71 2.43
3285 5660 2.432444 CATTAGGCCGTTCAGGTTTGA 58.568 47.619 0.00 0.00 43.70 2.69
3295 5670 0.322456 TCAGGTTTGAATGGCCCTCG 60.322 55.000 0.00 0.00 0.00 4.63
3356 5731 1.722677 GCACTCTAGACGACCTCGG 59.277 63.158 0.00 0.00 44.95 4.63
3410 5785 5.221501 CCATCTTGTGAACAATTTGGGACTT 60.222 40.000 13.10 0.00 35.68 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.639751 CTTATAAATTGTGGCGCTCGC 58.360 47.619 7.64 5.60 41.06 5.03
7 8 2.639751 GCTTATAAATTGTGGCGCTCG 58.360 47.619 7.64 0.00 0.00 5.03
8 9 2.639751 CGCTTATAAATTGTGGCGCTC 58.360 47.619 7.64 1.21 36.46 5.03
9 10 2.755836 CGCTTATAAATTGTGGCGCT 57.244 45.000 7.64 0.00 36.46 5.92
11 12 1.385038 CGCGCTTATAAATTGTGGCG 58.615 50.000 5.56 9.44 44.40 5.69
12 13 1.120437 GCGCGCTTATAAATTGTGGC 58.880 50.000 26.67 0.00 0.00 5.01
13 14 1.753956 GGCGCGCTTATAAATTGTGG 58.246 50.000 32.29 0.00 0.00 4.17
14 15 1.385038 CGGCGCGCTTATAAATTGTG 58.615 50.000 32.29 2.60 0.00 3.33
15 16 0.306533 CCGGCGCGCTTATAAATTGT 59.693 50.000 32.29 0.00 0.00 2.71
16 17 0.584396 TCCGGCGCGCTTATAAATTG 59.416 50.000 32.29 9.16 0.00 2.32
17 18 0.584876 GTCCGGCGCGCTTATAAATT 59.415 50.000 32.29 0.00 0.00 1.82
18 19 1.554042 CGTCCGGCGCGCTTATAAAT 61.554 55.000 32.29 0.00 0.00 1.40
19 20 2.232296 CGTCCGGCGCGCTTATAAA 61.232 57.895 32.29 8.04 0.00 1.40
20 21 2.656007 CGTCCGGCGCGCTTATAA 60.656 61.111 32.29 9.58 0.00 0.98
38 39 4.886925 GCTACATTTGGCGCGCCG 62.887 66.667 41.73 30.38 39.42 6.46
39 40 4.886925 CGCTACATTTGGCGCGCC 62.887 66.667 42.35 42.35 44.64 6.53
44 45 3.773649 CTCGCGCGCTACATTTGGC 62.774 63.158 30.48 0.00 0.00 4.52
45 46 2.321060 CTCGCGCGCTACATTTGG 59.679 61.111 30.48 11.00 0.00 3.28
46 47 2.350091 GCTCGCGCGCTACATTTG 60.350 61.111 30.48 11.83 0.00 2.32
47 48 2.509336 AGCTCGCGCGCTACATTT 60.509 55.556 30.48 6.70 42.32 2.32
48 49 3.257561 CAGCTCGCGCGCTACATT 61.258 61.111 30.48 7.88 42.32 2.71
59 60 3.804193 GGAAAAGGCGGCAGCTCG 61.804 66.667 13.08 0.00 44.37 5.03
60 61 3.443925 GGGAAAAGGCGGCAGCTC 61.444 66.667 13.08 3.55 44.37 4.09
78 79 4.776647 AAAAGATTGCGCGCGGGC 62.777 61.111 37.55 37.55 0.00 6.13
79 80 2.576847 GAAAAGATTGCGCGCGGG 60.577 61.111 33.06 20.05 0.00 6.13
80 81 2.939003 CGAAAAGATTGCGCGCGG 60.939 61.111 33.06 13.66 0.00 6.46
81 82 3.588337 GCGAAAAGATTGCGCGCG 61.588 61.111 28.44 28.44 41.37 6.86
101 102 4.700365 GTGGCGGGAAACTTGCGC 62.700 66.667 0.00 0.00 37.73 6.09
102 103 4.038080 GGTGGCGGGAAACTTGCG 62.038 66.667 0.00 0.00 33.39 4.85
103 104 4.038080 CGGTGGCGGGAAACTTGC 62.038 66.667 0.00 0.00 0.00 4.01
104 105 4.038080 GCGGTGGCGGGAAACTTG 62.038 66.667 0.00 0.00 0.00 3.16
105 106 4.265056 AGCGGTGGCGGGAAACTT 62.265 61.111 0.00 0.00 46.35 2.66
120 121 4.166011 ATTTTCGCGCGCTCCAGC 62.166 61.111 30.48 0.00 37.78 4.85
121 122 2.276868 CATTTTCGCGCGCTCCAG 60.277 61.111 30.48 13.90 0.00 3.86
122 123 3.022401 GACATTTTCGCGCGCTCCA 62.022 57.895 30.48 10.10 0.00 3.86
123 124 2.276680 GACATTTTCGCGCGCTCC 60.277 61.111 30.48 5.67 0.00 4.70
124 125 2.276680 GGACATTTTCGCGCGCTC 60.277 61.111 30.48 17.47 0.00 5.03
125 126 3.799755 GGGACATTTTCGCGCGCT 61.800 61.111 30.48 8.24 0.00 5.92
126 127 4.829518 GGGGACATTTTCGCGCGC 62.830 66.667 27.95 23.91 38.08 6.86
127 128 4.174129 GGGGGACATTTTCGCGCG 62.174 66.667 26.76 26.76 39.80 6.86
128 129 4.174129 CGGGGGACATTTTCGCGC 62.174 66.667 0.00 0.00 44.21 6.86
129 130 4.174129 GCGGGGGACATTTTCGCG 62.174 66.667 0.00 0.00 38.08 5.87
130 131 4.174129 CGCGGGGGACATTTTCGC 62.174 66.667 0.00 0.00 42.51 4.70
131 132 4.174129 GCGCGGGGGACATTTTCG 62.174 66.667 8.83 0.00 0.00 3.46
132 133 4.174129 CGCGCGGGGGACATTTTC 62.174 66.667 24.84 0.00 0.00 2.29
139 140 4.701290 TTTTTAGCGCGCGGGGGA 62.701 61.111 33.06 10.56 0.00 4.81
140 141 4.174129 CTTTTTAGCGCGCGGGGG 62.174 66.667 33.06 12.45 0.00 5.40
141 142 4.829518 GCTTTTTAGCGCGCGGGG 62.830 66.667 33.06 14.48 0.00 5.73
142 143 4.829518 GGCTTTTTAGCGCGCGGG 62.830 66.667 33.06 20.05 35.24 6.13
143 144 4.096558 TGGCTTTTTAGCGCGCGG 62.097 61.111 33.06 14.04 35.24 6.46
144 145 2.574212 CTGGCTTTTTAGCGCGCG 60.574 61.111 28.44 28.44 35.24 6.86
145 146 0.663269 AAACTGGCTTTTTAGCGCGC 60.663 50.000 26.66 26.66 35.24 6.86
146 147 2.095919 AGTAAACTGGCTTTTTAGCGCG 60.096 45.455 0.00 0.00 35.24 6.86
147 148 3.234386 CAGTAAACTGGCTTTTTAGCGC 58.766 45.455 0.00 0.00 40.20 5.92
148 149 3.234386 GCAGTAAACTGGCTTTTTAGCG 58.766 45.455 11.86 0.00 43.94 4.26
149 150 3.234386 CGCAGTAAACTGGCTTTTTAGC 58.766 45.455 11.86 0.00 43.94 3.09
150 151 3.234386 GCGCAGTAAACTGGCTTTTTAG 58.766 45.455 11.86 0.00 43.94 1.85
151 152 2.350007 CGCGCAGTAAACTGGCTTTTTA 60.350 45.455 8.75 0.00 43.94 1.52
152 153 1.599419 CGCGCAGTAAACTGGCTTTTT 60.599 47.619 8.75 0.00 43.94 1.94
153 154 0.040425 CGCGCAGTAAACTGGCTTTT 60.040 50.000 8.75 0.00 43.94 2.27
154 155 1.164041 ACGCGCAGTAAACTGGCTTT 61.164 50.000 5.73 1.86 43.94 3.51
155 156 1.597027 ACGCGCAGTAAACTGGCTT 60.597 52.632 5.73 4.87 43.94 4.35
156 157 2.030562 ACGCGCAGTAAACTGGCT 59.969 55.556 5.73 2.38 43.94 4.75
157 158 2.173382 CACGCGCAGTAAACTGGC 59.827 61.111 5.73 11.57 43.94 4.85
158 159 0.944311 AGACACGCGCAGTAAACTGG 60.944 55.000 5.73 3.72 43.94 4.00
159 160 0.859232 AAGACACGCGCAGTAAACTG 59.141 50.000 5.73 5.73 46.40 3.16
160 161 1.578583 AAAGACACGCGCAGTAAACT 58.421 45.000 5.73 4.12 0.00 2.66
161 162 2.034076 CAAAAGACACGCGCAGTAAAC 58.966 47.619 5.73 1.94 0.00 2.01
162 163 1.003331 CCAAAAGACACGCGCAGTAAA 60.003 47.619 5.73 0.00 0.00 2.01
163 164 0.584396 CCAAAAGACACGCGCAGTAA 59.416 50.000 5.73 0.00 0.00 2.24
164 165 1.837538 GCCAAAAGACACGCGCAGTA 61.838 55.000 5.73 0.00 0.00 2.74
165 166 3.022287 CCAAAAGACACGCGCAGT 58.978 55.556 5.73 4.91 0.00 4.40
166 167 2.427410 GCCAAAAGACACGCGCAG 60.427 61.111 5.73 0.55 0.00 5.18
167 168 4.306471 CGCCAAAAGACACGCGCA 62.306 61.111 5.73 0.00 37.97 6.09
172 173 3.660111 AGCCGCGCCAAAAGACAC 61.660 61.111 0.00 0.00 0.00 3.67
173 174 3.659092 CAGCCGCGCCAAAAGACA 61.659 61.111 0.00 0.00 0.00 3.41
174 175 3.194272 AACAGCCGCGCCAAAAGAC 62.194 57.895 0.00 0.00 0.00 3.01
175 176 2.904866 AACAGCCGCGCCAAAAGA 60.905 55.556 0.00 0.00 0.00 2.52
176 177 2.676016 TTCAACAGCCGCGCCAAAAG 62.676 55.000 0.00 0.00 0.00 2.27
177 178 2.676016 CTTCAACAGCCGCGCCAAAA 62.676 55.000 0.00 0.00 0.00 2.44
178 179 3.192954 CTTCAACAGCCGCGCCAAA 62.193 57.895 0.00 0.00 0.00 3.28
179 180 3.659092 CTTCAACAGCCGCGCCAA 61.659 61.111 0.00 0.00 0.00 4.52
180 181 3.899981 ATCTTCAACAGCCGCGCCA 62.900 57.895 0.00 0.00 0.00 5.69
181 182 3.127533 ATCTTCAACAGCCGCGCC 61.128 61.111 0.00 0.00 0.00 6.53
182 183 2.099062 CATCTTCAACAGCCGCGC 59.901 61.111 0.00 0.00 0.00 6.86
183 184 2.099062 GCATCTTCAACAGCCGCG 59.901 61.111 0.00 0.00 0.00 6.46
184 185 1.427020 GAGCATCTTCAACAGCCGC 59.573 57.895 0.00 0.00 0.00 6.53
196 197 3.471680 GGTGACAATCCCTAAGAGCATC 58.528 50.000 0.00 0.00 0.00 3.91
197 198 2.158900 CGGTGACAATCCCTAAGAGCAT 60.159 50.000 0.00 0.00 0.00 3.79
198 199 1.207089 CGGTGACAATCCCTAAGAGCA 59.793 52.381 0.00 0.00 0.00 4.26
199 200 1.207329 ACGGTGACAATCCCTAAGAGC 59.793 52.381 0.00 0.00 0.00 4.09
200 201 2.418746 CCACGGTGACAATCCCTAAGAG 60.419 54.545 10.28 0.00 0.00 2.85
201 202 1.553248 CCACGGTGACAATCCCTAAGA 59.447 52.381 10.28 0.00 0.00 2.10
202 203 1.553248 TCCACGGTGACAATCCCTAAG 59.447 52.381 10.28 0.00 0.00 2.18
227 228 4.201628 CGATCCGTCTCAAGCAAGTTAAAG 60.202 45.833 0.00 0.00 0.00 1.85
253 254 8.576442 GTTTTTACAATCCTGAAGAGAAATCCA 58.424 33.333 0.00 0.00 0.00 3.41
266 267 6.433093 ACTTATTCCAGCGTTTTTACAATCCT 59.567 34.615 0.00 0.00 0.00 3.24
412 413 5.240844 TCGCTTGATTCGTAATCCTATGAGA 59.759 40.000 5.51 0.00 37.09 3.27
413 414 5.461526 TCGCTTGATTCGTAATCCTATGAG 58.538 41.667 5.51 0.00 37.09 2.90
416 417 6.025749 TGATCGCTTGATTCGTAATCCTAT 57.974 37.500 5.51 0.00 37.09 2.57
419 420 4.270084 TGTTGATCGCTTGATTCGTAATCC 59.730 41.667 5.51 0.00 37.09 3.01
420 421 5.191059 GTGTTGATCGCTTGATTCGTAATC 58.809 41.667 0.00 0.00 38.40 1.75
421 422 4.629634 TGTGTTGATCGCTTGATTCGTAAT 59.370 37.500 0.00 0.00 30.70 1.89
422 423 3.991121 TGTGTTGATCGCTTGATTCGTAA 59.009 39.130 0.00 0.00 30.70 3.18
489 738 1.380771 GCACAACGAAATAAAACCGCG 59.619 47.619 0.00 0.00 0.00 6.46
589 1100 0.460109 TGCGTCGGGATCAGTTCATG 60.460 55.000 0.00 0.00 0.00 3.07
802 1316 4.467107 ACGGAGGAGAGGGGAGGC 62.467 72.222 0.00 0.00 0.00 4.70
1109 1656 5.180117 GCTCAAAAGCGATGATGGTACATAT 59.820 40.000 0.00 0.00 40.80 1.78
1151 1720 3.366052 AAAGGGCACATACTTTCGGAT 57.634 42.857 0.00 0.00 31.69 4.18
1152 1721 2.817258 CAAAAGGGCACATACTTTCGGA 59.183 45.455 0.00 0.00 35.99 4.55
1153 1722 2.817258 TCAAAAGGGCACATACTTTCGG 59.183 45.455 0.00 0.00 35.99 4.30
1154 1723 3.252215 TGTCAAAAGGGCACATACTTTCG 59.748 43.478 0.00 0.00 35.99 3.46
1155 1724 4.846779 TGTCAAAAGGGCACATACTTTC 57.153 40.909 0.00 0.00 35.99 2.62
1265 1834 5.450137 GGTGACTGCATAGATACGTACTGTT 60.450 44.000 0.00 0.00 0.00 3.16
1272 1849 2.797156 GCAAGGTGACTGCATAGATACG 59.203 50.000 0.00 0.00 42.68 3.06
1277 1854 3.428452 CCAAATGCAAGGTGACTGCATAG 60.428 47.826 11.92 8.38 46.94 2.23
1317 1894 4.406456 TCACTTGTGTTCCATAATTGCCT 58.594 39.130 0.46 0.00 0.00 4.75
1339 1916 6.942005 TCACACACACATGATCCTTTAAGAAT 59.058 34.615 0.00 0.00 0.00 2.40
1345 1922 3.072915 TCCTCACACACACATGATCCTTT 59.927 43.478 0.00 0.00 0.00 3.11
1373 1952 1.531423 TAGCTTCGTGTCCGTCTCTT 58.469 50.000 0.00 0.00 35.01 2.85
1406 1986 0.962356 CTTCTCCCCTGCAACGCAAT 60.962 55.000 0.00 0.00 38.41 3.56
1407 1987 1.600636 CTTCTCCCCTGCAACGCAA 60.601 57.895 0.00 0.00 38.41 4.85
1408 1988 2.032528 CTTCTCCCCTGCAACGCA 59.967 61.111 0.00 0.00 36.92 5.24
1409 1989 3.435186 GCTTCTCCCCTGCAACGC 61.435 66.667 0.00 0.00 0.00 4.84
1410 1990 2.037136 CAGCTTCTCCCCTGCAACG 61.037 63.158 0.00 0.00 0.00 4.10
1828 2411 0.745845 AGCTAGCGGCAACAATGGAG 60.746 55.000 9.55 0.00 44.79 3.86
1830 2413 1.308069 ACAGCTAGCGGCAACAATGG 61.308 55.000 15.21 0.00 44.79 3.16
1832 2415 1.068333 CAAACAGCTAGCGGCAACAAT 60.068 47.619 15.21 0.00 44.79 2.71
1833 2416 0.310543 CAAACAGCTAGCGGCAACAA 59.689 50.000 15.21 0.00 44.79 2.83
1834 2417 0.817634 ACAAACAGCTAGCGGCAACA 60.818 50.000 15.21 0.00 44.79 3.33
1835 2418 0.110192 GACAAACAGCTAGCGGCAAC 60.110 55.000 15.21 0.00 44.79 4.17
1836 2419 0.533978 TGACAAACAGCTAGCGGCAA 60.534 50.000 15.21 0.00 44.79 4.52
1837 2420 0.950555 CTGACAAACAGCTAGCGGCA 60.951 55.000 15.21 4.81 44.79 5.69
1838 2421 1.639298 CCTGACAAACAGCTAGCGGC 61.639 60.000 15.21 0.00 44.52 6.53
1839 2422 1.639298 GCCTGACAAACAGCTAGCGG 61.639 60.000 13.69 13.69 44.52 5.52
1840 2423 1.790387 GCCTGACAAACAGCTAGCG 59.210 57.895 9.55 7.05 44.52 4.26
1871 2455 7.661437 AGAGCACAGATAAGTACAACAATCAAA 59.339 33.333 0.00 0.00 0.00 2.69
1877 2461 4.245660 GCAGAGCACAGATAAGTACAACA 58.754 43.478 0.00 0.00 0.00 3.33
1880 2464 2.492088 ACGCAGAGCACAGATAAGTACA 59.508 45.455 0.00 0.00 0.00 2.90
1881 2465 3.109619 GACGCAGAGCACAGATAAGTAC 58.890 50.000 0.00 0.00 0.00 2.73
2125 2709 3.810896 GCGCCGAACCCCATGAAC 61.811 66.667 0.00 0.00 0.00 3.18
2494 3088 4.423209 GACCTCCCTCCCTGCCCT 62.423 72.222 0.00 0.00 0.00 5.19
2501 3095 1.225704 CCATTGCTGACCTCCCTCC 59.774 63.158 0.00 0.00 0.00 4.30
2502 3096 1.452833 GCCATTGCTGACCTCCCTC 60.453 63.158 0.00 0.00 33.53 4.30
2504 3098 2.825836 CGCCATTGCTGACCTCCC 60.826 66.667 0.00 0.00 34.43 4.30
2507 3101 0.323725 AATTCCGCCATTGCTGACCT 60.324 50.000 0.00 0.00 29.81 3.85
2508 3102 0.532115 AAATTCCGCCATTGCTGACC 59.468 50.000 0.00 0.00 29.81 4.02
2509 3103 1.202114 TCAAATTCCGCCATTGCTGAC 59.798 47.619 0.00 0.00 29.81 3.51
2510 3104 1.543607 TCAAATTCCGCCATTGCTGA 58.456 45.000 0.00 0.00 34.43 4.26
2511 3105 2.159212 TCATCAAATTCCGCCATTGCTG 60.159 45.455 0.00 0.00 34.43 4.41
2512 3106 2.100252 CTCATCAAATTCCGCCATTGCT 59.900 45.455 0.00 0.00 34.43 3.91
2513 3107 2.099592 TCTCATCAAATTCCGCCATTGC 59.900 45.455 0.00 0.00 0.00 3.56
2514 3108 4.357142 CTTCTCATCAAATTCCGCCATTG 58.643 43.478 0.00 0.00 0.00 2.82
2515 3109 3.382546 CCTTCTCATCAAATTCCGCCATT 59.617 43.478 0.00 0.00 0.00 3.16
2516 3110 2.954318 CCTTCTCATCAAATTCCGCCAT 59.046 45.455 0.00 0.00 0.00 4.40
2517 3111 2.368439 CCTTCTCATCAAATTCCGCCA 58.632 47.619 0.00 0.00 0.00 5.69
2518 3112 1.678101 CCCTTCTCATCAAATTCCGCC 59.322 52.381 0.00 0.00 0.00 6.13
2519 3113 2.098117 CACCCTTCTCATCAAATTCCGC 59.902 50.000 0.00 0.00 0.00 5.54
2520 3114 3.609853 TCACCCTTCTCATCAAATTCCG 58.390 45.455 0.00 0.00 0.00 4.30
2776 3380 0.971386 TCTGAAACCTGTACGTCCCC 59.029 55.000 0.00 0.00 0.00 4.81
2812 3416 3.307480 CGGTACAATGAATCCCTATCCCC 60.307 52.174 0.00 0.00 0.00 4.81
2912 3614 6.326583 TGGGACAGAGGGAGTAGTATAATTTG 59.673 42.308 0.00 0.00 0.00 2.32
2922 3624 2.642171 ATTGTGGGACAGAGGGAGTA 57.358 50.000 0.00 0.00 41.80 2.59
2923 3625 2.642171 TATTGTGGGACAGAGGGAGT 57.358 50.000 0.00 0.00 41.80 3.85
2924 3626 4.901849 TCTTATATTGTGGGACAGAGGGAG 59.098 45.833 0.00 0.00 41.80 4.30
2925 3627 4.890988 TCTTATATTGTGGGACAGAGGGA 58.109 43.478 0.00 0.00 41.80 4.20
2926 3628 5.368989 GTTCTTATATTGTGGGACAGAGGG 58.631 45.833 0.00 0.00 41.80 4.30
2927 3629 5.050490 CGTTCTTATATTGTGGGACAGAGG 58.950 45.833 0.00 0.00 41.80 3.69
2928 3630 5.661458 ACGTTCTTATATTGTGGGACAGAG 58.339 41.667 0.00 0.00 41.80 3.35
2929 3631 5.670792 ACGTTCTTATATTGTGGGACAGA 57.329 39.130 0.00 0.00 41.80 3.41
2930 3632 6.737254 AAACGTTCTTATATTGTGGGACAG 57.263 37.500 0.00 0.00 41.80 3.51
2931 3633 7.513371 AAAAACGTTCTTATATTGTGGGACA 57.487 32.000 0.00 0.00 0.00 4.02
2932 3634 9.333497 GTTAAAAACGTTCTTATATTGTGGGAC 57.667 33.333 0.00 0.00 0.00 4.46
2933 3635 9.064706 TGTTAAAAACGTTCTTATATTGTGGGA 57.935 29.630 0.00 0.00 0.00 4.37
2934 3636 9.849166 ATGTTAAAAACGTTCTTATATTGTGGG 57.151 29.630 0.00 0.00 0.00 4.61
2944 3646 9.925268 CACTAGTGTAATGTTAAAAACGTTCTT 57.075 29.630 15.06 0.00 40.80 2.52
2945 3647 9.101655 ACACTAGTGTAATGTTAAAAACGTTCT 57.898 29.630 26.91 0.00 42.90 3.01
2946 3648 9.361712 GACACTAGTGTAATGTTAAAAACGTTC 57.638 33.333 27.98 6.11 45.05 3.95
2947 3649 8.881743 TGACACTAGTGTAATGTTAAAAACGTT 58.118 29.630 27.98 0.00 45.05 3.99
2948 3650 8.422973 TGACACTAGTGTAATGTTAAAAACGT 57.577 30.769 27.98 0.00 45.05 3.99
2949 3651 9.705471 TTTGACACTAGTGTAATGTTAAAAACG 57.295 29.630 27.98 0.00 45.05 3.60
2953 3655 9.705471 CGTTTTTGACACTAGTGTAATGTTAAA 57.295 29.630 27.98 14.90 45.05 1.52
2954 3656 8.881743 ACGTTTTTGACACTAGTGTAATGTTAA 58.118 29.630 27.98 9.63 45.05 2.01
2955 3657 8.422973 ACGTTTTTGACACTAGTGTAATGTTA 57.577 30.769 27.98 9.86 45.05 2.41
2956 3658 7.311364 ACGTTTTTGACACTAGTGTAATGTT 57.689 32.000 27.98 4.69 45.05 2.71
2957 3659 6.913873 ACGTTTTTGACACTAGTGTAATGT 57.086 33.333 27.98 23.70 45.05 2.71
2958 3660 8.609478 AAAACGTTTTTGACACTAGTGTAATG 57.391 30.769 27.98 23.11 45.05 1.90
2975 3677 9.893305 CCTCTGTCTCAAAATATAAAAACGTTT 57.107 29.630 7.96 7.96 0.00 3.60
2976 3678 8.512138 CCCTCTGTCTCAAAATATAAAAACGTT 58.488 33.333 0.00 0.00 0.00 3.99
2977 3679 7.881232 TCCCTCTGTCTCAAAATATAAAAACGT 59.119 33.333 0.00 0.00 0.00 3.99
2978 3680 8.263940 TCCCTCTGTCTCAAAATATAAAAACG 57.736 34.615 0.00 0.00 0.00 3.60
2979 3681 9.232473 ACTCCCTCTGTCTCAAAATATAAAAAC 57.768 33.333 0.00 0.00 0.00 2.43
2982 3684 9.268282 ACTACTCCCTCTGTCTCAAAATATAAA 57.732 33.333 0.00 0.00 0.00 1.40
2983 3685 8.840200 ACTACTCCCTCTGTCTCAAAATATAA 57.160 34.615 0.00 0.00 0.00 0.98
2984 3686 9.575868 CTACTACTCCCTCTGTCTCAAAATATA 57.424 37.037 0.00 0.00 0.00 0.86
2985 3687 8.282982 TCTACTACTCCCTCTGTCTCAAAATAT 58.717 37.037 0.00 0.00 0.00 1.28
2986 3688 7.640313 TCTACTACTCCCTCTGTCTCAAAATA 58.360 38.462 0.00 0.00 0.00 1.40
2987 3689 6.494952 TCTACTACTCCCTCTGTCTCAAAAT 58.505 40.000 0.00 0.00 0.00 1.82
2988 3690 5.888901 TCTACTACTCCCTCTGTCTCAAAA 58.111 41.667 0.00 0.00 0.00 2.44
2989 3691 5.516059 TCTACTACTCCCTCTGTCTCAAA 57.484 43.478 0.00 0.00 0.00 2.69
2990 3692 5.718801 ATCTACTACTCCCTCTGTCTCAA 57.281 43.478 0.00 0.00 0.00 3.02
2991 3693 5.191921 TCAATCTACTACTCCCTCTGTCTCA 59.808 44.000 0.00 0.00 0.00 3.27
2992 3694 5.686753 TCAATCTACTACTCCCTCTGTCTC 58.313 45.833 0.00 0.00 0.00 3.36
2993 3695 5.718801 TCAATCTACTACTCCCTCTGTCT 57.281 43.478 0.00 0.00 0.00 3.41
2994 3696 6.777213 TTTCAATCTACTACTCCCTCTGTC 57.223 41.667 0.00 0.00 0.00 3.51
2995 3697 7.554959 TTTTTCAATCTACTACTCCCTCTGT 57.445 36.000 0.00 0.00 0.00 3.41
3048 3946 4.305989 TGCAGCTTTCAGTTTTACCAAG 57.694 40.909 0.00 0.00 0.00 3.61
3077 3975 2.660189 ATCATGCGGCCTTTTCAAAG 57.340 45.000 0.00 0.00 35.79 2.77
3103 4001 2.430694 GCCGCTTATTTGGGGATCTTTT 59.569 45.455 1.74 0.00 41.89 2.27
3158 4056 4.528206 AGAGGTTGCTTTTGGAATTAAGGG 59.472 41.667 0.00 0.00 31.02 3.95
3205 4103 0.605319 TTACAACGAGGGCAAGCAGG 60.605 55.000 0.00 0.00 0.00 4.85
3223 4121 2.029623 GGCATCTTCACATGGAGCATT 58.970 47.619 0.00 0.00 0.00 3.56
3273 5648 0.243636 GGGCCATTCAAACCTGAACG 59.756 55.000 4.39 0.00 44.28 3.95
3285 5660 2.680370 GGGAAGACCGAGGGCCATT 61.680 63.158 6.18 0.00 36.97 3.16
3295 5670 2.125766 GAGTGGGGTGTGGGAAGACC 62.126 65.000 0.00 0.00 40.81 3.85
3356 5731 0.234884 CGAGTTCCAAAGGTCGTTGC 59.765 55.000 0.00 0.00 0.00 4.17
3361 5736 1.594331 ACAAGCGAGTTCCAAAGGTC 58.406 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.