Multiple sequence alignment - TraesCS1B01G092600

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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 TraesCS1B01G092600 chr1B 100.000 3554 0 0 1 3554 94328298 94324745 0.000000e+00 6564.0
1 TraesCS1B01G092600 chr1B 82.099 2363 364 39 1089 3406 94233226 94230878 0.000000e+00 1965.0
2 TraesCS1B01G092600 chr1B 78.910 1394 255 24 1903 3263 57137999 57139386 0.000000e+00 909.0
3 TraesCS1B01G092600 chr1B 78.219 1460 283 20 1903 3333 56500849 56499396 0.000000e+00 902.0
4 TraesCS1B01G092600 chr1B 78.252 1476 271 32 1918 3356 70170777 70172239 0.000000e+00 902.0
5 TraesCS1B01G092600 chr1B 78.309 1443 264 35 1915 3319 70186452 70187883 0.000000e+00 885.0
6 TraesCS1B01G092600 chr1D 92.147 3247 179 28 353 3554 58870642 58867427 0.000000e+00 4514.0
7 TraesCS1B01G092600 chr1D 80.958 2547 419 49 1024 3526 58628687 58626163 0.000000e+00 1956.0
8 TraesCS1B01G092600 chr1D 82.269 2318 354 39 1133 3406 58764093 58761789 0.000000e+00 1951.0
9 TraesCS1B01G092600 chr1D 79.207 1462 266 23 1904 3333 36623655 36622200 0.000000e+00 981.0
10 TraesCS1B01G092600 chr1D 78.267 1454 272 28 1918 3334 50109575 50111021 0.000000e+00 894.0
11 TraesCS1B01G092600 chr1D 78.718 1264 242 24 1265 2516 38589144 38587896 0.000000e+00 819.0
12 TraesCS1B01G092600 chr1D 79.509 815 154 11 1083 1888 36618175 36617365 5.150000e-158 568.0
13 TraesCS1B01G092600 chr1A 80.887 2412 404 42 1148 3517 57405747 57403351 0.000000e+00 1847.0
14 TraesCS1B01G092600 chr1A 82.333 1449 238 15 1101 2538 57640146 57638705 0.000000e+00 1242.0
15 TraesCS1B01G092600 chr1A 79.645 1464 259 19 1903 3333 37504384 37502927 0.000000e+00 1016.0
16 TraesCS1B01G092600 chr1A 79.112 833 160 12 1066 1888 36188318 36187490 2.400000e-156 562.0
17 TraesCS1B01G092600 chr1A 97.436 39 0 1 10 48 529439566 529439603 8.240000e-07 65.8
18 TraesCS1B01G092600 chr5D 95.327 107 5 0 101 207 432404120 432404014 1.700000e-38 171.0
19 TraesCS1B01G092600 chr5D 97.368 38 1 0 11 48 5225344 5225381 8.240000e-07 65.8
20 TraesCS1B01G092600 chrUn 95.238 105 5 0 101 205 93410254 93410150 2.190000e-37 167.0
21 TraesCS1B01G092600 chrUn 95.238 105 5 0 101 205 216519225 216519121 2.190000e-37 167.0
22 TraesCS1B01G092600 chrUn 95.238 105 5 0 101 205 216521141 216521245 2.190000e-37 167.0
23 TraesCS1B01G092600 chrUn 95.238 105 5 0 101 205 216522613 216522509 2.190000e-37 167.0
24 TraesCS1B01G092600 chrUn 95.238 105 5 0 101 205 372772276 372772172 2.190000e-37 167.0
25 TraesCS1B01G092600 chrUn 93.023 43 3 0 5 47 79971620 79971662 2.960000e-06 63.9
26 TraesCS1B01G092600 chr6D 95.238 105 5 0 101 205 168250915 168251019 2.190000e-37 167.0
27 TraesCS1B01G092600 chr6D 95.238 105 5 0 101 205 168252387 168252283 2.190000e-37 167.0
28 TraesCS1B01G092600 chr6D 95.238 105 5 0 101 205 168254303 168254407 2.190000e-37 167.0
29 TraesCS1B01G092600 chr6D 88.710 62 6 1 1 61 386281813 386281874 1.370000e-09 75.0
30 TraesCS1B01G092600 chr5A 90.741 54 2 2 15 65 698621215 698621268 6.370000e-08 69.4
31 TraesCS1B01G092600 chr3A 95.238 42 2 0 10 51 32112779 32112738 2.290000e-07 67.6
32 TraesCS1B01G092600 chr3A 90.476 42 4 0 10 51 13833631 13833590 4.960000e-04 56.5
33 TraesCS1B01G092600 chr2B 80.220 91 16 2 14 103 16121206 16121117 2.290000e-07 67.6
34 TraesCS1B01G092600 chr3B 95.122 41 2 0 10 50 101389502 101389462 8.240000e-07 65.8


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 TraesCS1B01G092600 chr1B 94324745 94328298 3553 True 6564 6564 100.000 1 3554 1 chr1B.!!$R3 3553
1 TraesCS1B01G092600 chr1B 94230878 94233226 2348 True 1965 1965 82.099 1089 3406 1 chr1B.!!$R2 2317
2 TraesCS1B01G092600 chr1B 57137999 57139386 1387 False 909 909 78.910 1903 3263 1 chr1B.!!$F1 1360
3 TraesCS1B01G092600 chr1B 56499396 56500849 1453 True 902 902 78.219 1903 3333 1 chr1B.!!$R1 1430
4 TraesCS1B01G092600 chr1B 70170777 70172239 1462 False 902 902 78.252 1918 3356 1 chr1B.!!$F2 1438
5 TraesCS1B01G092600 chr1B 70186452 70187883 1431 False 885 885 78.309 1915 3319 1 chr1B.!!$F3 1404
6 TraesCS1B01G092600 chr1D 58867427 58870642 3215 True 4514 4514 92.147 353 3554 1 chr1D.!!$R6 3201
7 TraesCS1B01G092600 chr1D 58626163 58628687 2524 True 1956 1956 80.958 1024 3526 1 chr1D.!!$R4 2502
8 TraesCS1B01G092600 chr1D 58761789 58764093 2304 True 1951 1951 82.269 1133 3406 1 chr1D.!!$R5 2273
9 TraesCS1B01G092600 chr1D 36622200 36623655 1455 True 981 981 79.207 1904 3333 1 chr1D.!!$R2 1429
10 TraesCS1B01G092600 chr1D 50109575 50111021 1446 False 894 894 78.267 1918 3334 1 chr1D.!!$F1 1416
11 TraesCS1B01G092600 chr1D 38587896 38589144 1248 True 819 819 78.718 1265 2516 1 chr1D.!!$R3 1251
12 TraesCS1B01G092600 chr1D 36617365 36618175 810 True 568 568 79.509 1083 1888 1 chr1D.!!$R1 805
13 TraesCS1B01G092600 chr1A 57403351 57405747 2396 True 1847 1847 80.887 1148 3517 1 chr1A.!!$R3 2369
14 TraesCS1B01G092600 chr1A 57638705 57640146 1441 True 1242 1242 82.333 1101 2538 1 chr1A.!!$R4 1437
15 TraesCS1B01G092600 chr1A 37502927 37504384 1457 True 1016 1016 79.645 1903 3333 1 chr1A.!!$R2 1430
16 TraesCS1B01G092600 chr1A 36187490 36188318 828 True 562 562 79.112 1066 1888 1 chr1A.!!$R1 822

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
742 743 0.026285 GACAAATTCGATGACCGGCG 59.974 55.0 0.00 0.00 39.14 6.46 F
1252 1308 0.322456 CCCCAATCGCTTCCTGAACA 60.322 55.0 0.00 0.00 0.00 3.18 F
1876 1941 0.316204 CAAGGCAAAGCTGGTCCTTG 59.684 55.0 19.98 19.98 46.33 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1883 1.398041 CACAACGCACCAATCATCGAT 59.602 47.619 0.00 0.0 0.0 3.59 R
2518 2590 1.457346 GGCCTCTCACCAATGTTCAG 58.543 55.000 0.00 0.0 0.0 3.02 R
2811 2908 2.057922 ACTCACCATGGTTCCAGTTCT 58.942 47.619 16.84 0.0 0.0 3.01 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
95 96 9.513906 TCTTGGATGAACATTTTCTGTAATACA 57.486 29.630 0.00 0.00 36.98 2.29
98 99 9.460019 TGGATGAACATTTTCTGTAATACATGA 57.540 29.630 0.00 0.00 36.98 3.07
110 111 9.725019 TTCTGTAATACATGATCAATATCACCC 57.275 33.333 0.00 0.00 44.79 4.61
111 112 8.879227 TCTGTAATACATGATCAATATCACCCA 58.121 33.333 0.00 0.00 44.79 4.51
112 113 8.846943 TGTAATACATGATCAATATCACCCAC 57.153 34.615 0.00 0.00 44.79 4.61
113 114 8.659527 TGTAATACATGATCAATATCACCCACT 58.340 33.333 0.00 0.00 44.79 4.00
114 115 9.507329 GTAATACATGATCAATATCACCCACTT 57.493 33.333 0.00 0.00 44.79 3.16
115 116 7.991084 ATACATGATCAATATCACCCACTTG 57.009 36.000 0.00 0.00 44.79 3.16
116 117 5.759059 ACATGATCAATATCACCCACTTGT 58.241 37.500 0.00 0.00 44.79 3.16
117 118 5.824624 ACATGATCAATATCACCCACTTGTC 59.175 40.000 0.00 0.00 44.79 3.18
118 119 4.780815 TGATCAATATCACCCACTTGTCC 58.219 43.478 0.00 0.00 37.20 4.02
119 120 3.260475 TCAATATCACCCACTTGTCCG 57.740 47.619 0.00 0.00 0.00 4.79
120 121 2.835156 TCAATATCACCCACTTGTCCGA 59.165 45.455 0.00 0.00 0.00 4.55
121 122 2.936498 CAATATCACCCACTTGTCCGAC 59.064 50.000 0.00 0.00 0.00 4.79
122 123 1.933021 TATCACCCACTTGTCCGACT 58.067 50.000 0.00 0.00 0.00 4.18
123 124 0.321671 ATCACCCACTTGTCCGACTG 59.678 55.000 0.00 0.00 0.00 3.51
124 125 1.046472 TCACCCACTTGTCCGACTGT 61.046 55.000 0.00 0.00 0.00 3.55
125 126 0.179056 CACCCACTTGTCCGACTGTT 60.179 55.000 0.00 0.00 0.00 3.16
126 127 0.179056 ACCCACTTGTCCGACTGTTG 60.179 55.000 0.00 0.00 0.00 3.33
127 128 1.507141 CCCACTTGTCCGACTGTTGC 61.507 60.000 0.00 0.00 0.00 4.17
128 129 0.532862 CCACTTGTCCGACTGTTGCT 60.533 55.000 0.00 0.00 0.00 3.91
129 130 1.270094 CCACTTGTCCGACTGTTGCTA 60.270 52.381 0.00 0.00 0.00 3.49
130 131 2.479837 CACTTGTCCGACTGTTGCTAA 58.520 47.619 0.00 0.00 0.00 3.09
131 132 2.476619 CACTTGTCCGACTGTTGCTAAG 59.523 50.000 0.00 0.00 0.00 2.18
132 133 1.461127 CTTGTCCGACTGTTGCTAAGC 59.539 52.381 0.00 0.00 0.00 3.09
133 134 0.391228 TGTCCGACTGTTGCTAAGCA 59.609 50.000 0.00 0.00 36.47 3.91
134 135 1.071605 GTCCGACTGTTGCTAAGCAG 58.928 55.000 0.00 0.00 40.61 4.24
135 136 0.966179 TCCGACTGTTGCTAAGCAGA 59.034 50.000 0.00 0.00 40.61 4.26
136 137 1.550524 TCCGACTGTTGCTAAGCAGAT 59.449 47.619 0.00 0.00 40.61 2.90
137 138 2.028112 TCCGACTGTTGCTAAGCAGATT 60.028 45.455 0.00 0.00 40.61 2.40
138 139 2.744202 CCGACTGTTGCTAAGCAGATTT 59.256 45.455 0.00 0.00 40.61 2.17
139 140 3.425359 CCGACTGTTGCTAAGCAGATTTG 60.425 47.826 0.00 0.00 40.61 2.32
140 141 3.425359 CGACTGTTGCTAAGCAGATTTGG 60.425 47.826 0.00 0.00 40.61 3.28
141 142 2.821969 ACTGTTGCTAAGCAGATTTGGG 59.178 45.455 0.00 0.00 40.61 4.12
142 143 3.084039 CTGTTGCTAAGCAGATTTGGGA 58.916 45.455 0.00 0.00 40.61 4.37
143 144 3.698040 CTGTTGCTAAGCAGATTTGGGAT 59.302 43.478 0.00 0.00 40.61 3.85
144 145 4.854173 TGTTGCTAAGCAGATTTGGGATA 58.146 39.130 0.00 0.00 40.61 2.59
145 146 4.640201 TGTTGCTAAGCAGATTTGGGATAC 59.360 41.667 0.00 0.00 40.61 2.24
146 147 4.778213 TGCTAAGCAGATTTGGGATACT 57.222 40.909 0.00 0.00 33.32 2.12
147 148 5.887214 TGCTAAGCAGATTTGGGATACTA 57.113 39.130 0.00 0.00 33.32 1.82
148 149 6.247229 TGCTAAGCAGATTTGGGATACTAA 57.753 37.500 0.00 0.00 33.32 2.24
149 150 6.658849 TGCTAAGCAGATTTGGGATACTAAA 58.341 36.000 0.00 0.00 41.87 1.85
150 151 6.542370 TGCTAAGCAGATTTGGGATACTAAAC 59.458 38.462 0.00 0.00 41.08 2.01
151 152 8.588419 TGCTAAGCAGATTTGGGATACTAAACG 61.588 40.741 0.00 0.00 41.08 3.60
157 158 4.476628 TTTGGGATACTAAACGGACCTC 57.523 45.455 0.00 0.00 42.67 3.85
158 159 2.391678 TGGGATACTAAACGGACCTCC 58.608 52.381 0.00 0.00 0.00 4.30
159 160 1.690893 GGGATACTAAACGGACCTCCC 59.309 57.143 0.00 0.00 34.52 4.30
160 161 2.391678 GGATACTAAACGGACCTCCCA 58.608 52.381 0.00 0.00 34.14 4.37
161 162 2.767960 GGATACTAAACGGACCTCCCAA 59.232 50.000 0.00 0.00 34.14 4.12
162 163 3.181468 GGATACTAAACGGACCTCCCAAG 60.181 52.174 0.00 0.00 34.14 3.61
163 164 2.019807 ACTAAACGGACCTCCCAAGA 57.980 50.000 0.00 0.00 34.14 3.02
164 165 2.547990 ACTAAACGGACCTCCCAAGAT 58.452 47.619 0.00 0.00 34.14 2.40
165 166 2.236395 ACTAAACGGACCTCCCAAGATG 59.764 50.000 0.00 0.00 34.14 2.90
166 167 0.328258 AAACGGACCTCCCAAGATGG 59.672 55.000 0.00 0.00 37.25 3.51
167 168 0.840722 AACGGACCTCCCAAGATGGT 60.841 55.000 0.00 0.00 35.17 3.55
168 169 0.042131 ACGGACCTCCCAAGATGGTA 59.958 55.000 0.00 0.00 35.17 3.25
169 170 1.200519 CGGACCTCCCAAGATGGTAA 58.799 55.000 0.00 0.00 35.17 2.85
170 171 1.768870 CGGACCTCCCAAGATGGTAAT 59.231 52.381 0.00 0.00 35.17 1.89
171 172 2.224305 CGGACCTCCCAAGATGGTAATC 60.224 54.545 0.00 0.00 35.17 1.75
172 173 3.049344 GGACCTCCCAAGATGGTAATCT 58.951 50.000 0.00 0.00 45.48 2.40
183 184 4.451900 AGATGGTAATCTTAAAGTGGCCG 58.548 43.478 0.00 0.00 40.42 6.13
184 185 3.985019 TGGTAATCTTAAAGTGGCCGA 57.015 42.857 0.00 0.00 0.00 5.54
185 186 4.497291 TGGTAATCTTAAAGTGGCCGAT 57.503 40.909 0.00 0.00 0.00 4.18
186 187 4.850680 TGGTAATCTTAAAGTGGCCGATT 58.149 39.130 0.00 1.39 0.00 3.34
187 188 5.258051 TGGTAATCTTAAAGTGGCCGATTT 58.742 37.500 9.65 9.65 0.00 2.17
188 189 6.416415 TGGTAATCTTAAAGTGGCCGATTTA 58.584 36.000 7.85 7.85 0.00 1.40
189 190 6.316890 TGGTAATCTTAAAGTGGCCGATTTAC 59.683 38.462 10.79 0.00 0.00 2.01
190 191 5.830000 AATCTTAAAGTGGCCGATTTACC 57.170 39.130 10.79 0.00 0.00 2.85
191 192 3.613030 TCTTAAAGTGGCCGATTTACCC 58.387 45.455 10.79 0.00 0.00 3.69
192 193 3.264964 TCTTAAAGTGGCCGATTTACCCT 59.735 43.478 10.79 0.00 0.00 4.34
193 194 2.124277 AAAGTGGCCGATTTACCCTC 57.876 50.000 0.00 0.00 0.00 4.30
194 195 0.255033 AAGTGGCCGATTTACCCTCC 59.745 55.000 0.00 0.00 0.00 4.30
195 196 0.620700 AGTGGCCGATTTACCCTCCT 60.621 55.000 0.00 0.00 0.00 3.69
196 197 0.255033 GTGGCCGATTTACCCTCCTT 59.745 55.000 0.00 0.00 0.00 3.36
197 198 0.996583 TGGCCGATTTACCCTCCTTT 59.003 50.000 0.00 0.00 0.00 3.11
198 199 1.340600 TGGCCGATTTACCCTCCTTTG 60.341 52.381 0.00 0.00 0.00 2.77
199 200 0.738975 GCCGATTTACCCTCCTTTGC 59.261 55.000 0.00 0.00 0.00 3.68
200 201 1.953311 GCCGATTTACCCTCCTTTGCA 60.953 52.381 0.00 0.00 0.00 4.08
201 202 2.442413 CCGATTTACCCTCCTTTGCAA 58.558 47.619 0.00 0.00 0.00 4.08
202 203 3.023832 CCGATTTACCCTCCTTTGCAAT 58.976 45.455 0.00 0.00 0.00 3.56
203 204 3.181487 CCGATTTACCCTCCTTTGCAATG 60.181 47.826 0.00 1.92 0.00 2.82
204 205 3.694072 CGATTTACCCTCCTTTGCAATGA 59.306 43.478 13.58 6.47 0.00 2.57
205 206 4.157656 CGATTTACCCTCCTTTGCAATGAA 59.842 41.667 13.58 0.00 0.00 2.57
206 207 5.163519 CGATTTACCCTCCTTTGCAATGAAT 60.164 40.000 13.58 3.84 0.00 2.57
207 208 5.659440 TTTACCCTCCTTTGCAATGAATC 57.341 39.130 13.58 0.00 0.00 2.52
208 209 2.094675 ACCCTCCTTTGCAATGAATCG 58.905 47.619 13.58 1.84 0.00 3.34
209 210 2.094675 CCCTCCTTTGCAATGAATCGT 58.905 47.619 13.58 0.00 0.00 3.73
210 211 2.493278 CCCTCCTTTGCAATGAATCGTT 59.507 45.455 13.58 0.00 0.00 3.85
211 212 3.056607 CCCTCCTTTGCAATGAATCGTTT 60.057 43.478 13.58 0.00 0.00 3.60
212 213 4.168760 CCTCCTTTGCAATGAATCGTTTC 58.831 43.478 13.58 0.00 0.00 2.78
213 214 4.168760 CTCCTTTGCAATGAATCGTTTCC 58.831 43.478 13.58 0.00 0.00 3.13
214 215 3.571828 TCCTTTGCAATGAATCGTTTCCA 59.428 39.130 13.58 0.00 0.00 3.53
215 216 4.220382 TCCTTTGCAATGAATCGTTTCCAT 59.780 37.500 13.58 0.00 0.00 3.41
216 217 4.327898 CCTTTGCAATGAATCGTTTCCATG 59.672 41.667 13.58 4.36 0.00 3.66
217 218 2.878580 TGCAATGAATCGTTTCCATGC 58.121 42.857 18.84 18.84 40.28 4.06
218 219 2.230750 TGCAATGAATCGTTTCCATGCA 59.769 40.909 22.06 22.06 43.91 3.96
219 220 3.119065 TGCAATGAATCGTTTCCATGCAT 60.119 39.130 22.06 0.00 42.56 3.96
220 221 4.097589 TGCAATGAATCGTTTCCATGCATA 59.902 37.500 22.06 9.18 42.56 3.14
221 222 5.221283 TGCAATGAATCGTTTCCATGCATAT 60.221 36.000 22.06 1.28 42.56 1.78
222 223 5.693104 GCAATGAATCGTTTCCATGCATATT 59.307 36.000 19.94 0.00 39.93 1.28
223 224 6.862608 GCAATGAATCGTTTCCATGCATATTA 59.137 34.615 19.94 0.00 39.93 0.98
224 225 7.543172 GCAATGAATCGTTTCCATGCATATTAT 59.457 33.333 19.94 0.00 39.93 1.28
256 257 9.773328 ATTGTACACATTTTTCATATTCACGAG 57.227 29.630 0.00 0.00 0.00 4.18
257 258 8.541133 TGTACACATTTTTCATATTCACGAGA 57.459 30.769 0.00 0.00 0.00 4.04
258 259 8.994170 TGTACACATTTTTCATATTCACGAGAA 58.006 29.630 0.00 0.00 38.31 2.87
259 260 9.820229 GTACACATTTTTCATATTCACGAGAAA 57.180 29.630 0.00 0.00 37.29 2.52
260 261 8.728088 ACACATTTTTCATATTCACGAGAAAC 57.272 30.769 0.00 0.00 37.29 2.78
261 262 8.349245 ACACATTTTTCATATTCACGAGAAACA 58.651 29.630 0.00 0.00 37.29 2.83
262 263 9.345517 CACATTTTTCATATTCACGAGAAACAT 57.654 29.630 0.00 0.00 37.29 2.71
263 264 9.912634 ACATTTTTCATATTCACGAGAAACATT 57.087 25.926 0.00 0.00 37.29 2.71
379 380 7.941431 TCTGTAAGTACAAACAAAAGGGAAA 57.059 32.000 0.00 0.00 35.50 3.13
380 381 8.350852 TCTGTAAGTACAAACAAAAGGGAAAA 57.649 30.769 0.00 0.00 35.50 2.29
468 469 2.048127 GGGCGACTTCAGCGAGTT 60.048 61.111 0.00 0.00 35.00 3.01
475 476 0.603975 ACTTCAGCGAGTTGGAAGGC 60.604 55.000 0.00 0.00 41.73 4.35
482 483 1.743252 GAGTTGGAAGGCTGCCTCG 60.743 63.158 23.61 0.00 30.89 4.63
491 492 1.069765 GGCTGCCTCGCTATAAGCA 59.930 57.895 12.43 0.00 42.58 3.91
500 501 5.646577 CCTCGCTATAAGCAAGGTATAGT 57.353 43.478 0.00 0.00 40.52 2.12
501 502 6.026947 CCTCGCTATAAGCAAGGTATAGTT 57.973 41.667 0.00 0.00 40.52 2.24
502 503 5.864474 CCTCGCTATAAGCAAGGTATAGTTG 59.136 44.000 0.00 0.00 40.52 3.16
516 517 3.508845 ATAGTTGTGCCCCATGTATCC 57.491 47.619 0.00 0.00 0.00 2.59
525 526 2.420129 GCCCCATGTATCCCGCTATAAG 60.420 54.545 0.00 0.00 0.00 1.73
527 528 2.838202 CCCATGTATCCCGCTATAAGGT 59.162 50.000 0.00 0.00 0.00 3.50
544 545 6.754702 ATAAGGTAAATATAGCTCTCGCGA 57.245 37.500 9.26 9.26 38.89 5.87
545 546 4.688511 AGGTAAATATAGCTCTCGCGAG 57.311 45.455 30.03 30.03 42.32 5.03
569 570 2.361104 GATGGGCTTTGGCACGGA 60.361 61.111 0.00 0.00 46.54 4.69
570 571 1.976474 GATGGGCTTTGGCACGGAA 60.976 57.895 0.00 0.00 46.54 4.30
571 572 1.531739 GATGGGCTTTGGCACGGAAA 61.532 55.000 0.00 0.00 46.54 3.13
572 573 1.815817 ATGGGCTTTGGCACGGAAAC 61.816 55.000 0.00 0.00 46.54 2.78
573 574 2.494530 GGGCTTTGGCACGGAAACA 61.495 57.895 0.00 0.00 40.87 2.83
574 575 1.007387 GGCTTTGGCACGGAAACAG 60.007 57.895 0.00 0.00 40.87 3.16
575 576 1.733526 GCTTTGGCACGGAAACAGT 59.266 52.632 0.00 0.00 38.54 3.55
576 577 0.594796 GCTTTGGCACGGAAACAGTG 60.595 55.000 0.00 0.00 42.15 3.66
577 578 1.021202 CTTTGGCACGGAAACAGTGA 58.979 50.000 0.00 0.00 41.83 3.41
578 579 1.608590 CTTTGGCACGGAAACAGTGAT 59.391 47.619 0.00 0.00 41.83 3.06
579 580 0.950836 TTGGCACGGAAACAGTGATG 59.049 50.000 0.00 0.00 41.83 3.07
580 581 0.179032 TGGCACGGAAACAGTGATGT 60.179 50.000 0.00 0.00 41.83 3.06
581 582 0.238289 GGCACGGAAACAGTGATGTG 59.762 55.000 0.00 0.00 41.83 3.21
582 583 0.944386 GCACGGAAACAGTGATGTGT 59.056 50.000 0.00 0.00 41.83 3.72
609 610 4.722700 CACGGGCTTCAGGTGGGG 62.723 72.222 0.00 0.00 0.00 4.96
613 614 1.152333 GGGCTTCAGGTGGGGTTTT 60.152 57.895 0.00 0.00 0.00 2.43
617 618 2.032151 GCTTCAGGTGGGGTTTTTGGA 61.032 52.381 0.00 0.00 0.00 3.53
621 622 0.178906 AGGTGGGGTTTTTGGATGGG 60.179 55.000 0.00 0.00 0.00 4.00
623 624 1.537643 TGGGGTTTTTGGATGGGCC 60.538 57.895 0.00 0.00 37.10 5.80
625 626 1.608046 GGGTTTTTGGATGGGCCGA 60.608 57.895 0.00 0.00 40.66 5.54
626 627 1.604147 GGGTTTTTGGATGGGCCGAG 61.604 60.000 0.00 0.00 40.66 4.63
627 628 1.215382 GTTTTTGGATGGGCCGAGC 59.785 57.895 0.00 0.00 40.66 5.03
628 629 2.339556 TTTTTGGATGGGCCGAGCG 61.340 57.895 0.00 0.00 40.66 5.03
655 656 0.173708 GTCCGACATGACAGAGGTCC 59.826 60.000 0.00 0.00 43.65 4.46
659 660 1.732732 CGACATGACAGAGGTCCGAAC 60.733 57.143 0.00 0.00 43.65 3.95
662 663 1.251527 ATGACAGAGGTCCGAACGCT 61.252 55.000 0.00 0.00 43.65 5.07
664 665 1.863662 GACAGAGGTCCGAACGCTCA 61.864 60.000 0.00 0.00 38.12 4.26
676 677 0.182775 AACGCTCACAAACCTTCCCT 59.817 50.000 0.00 0.00 0.00 4.20
677 678 1.053424 ACGCTCACAAACCTTCCCTA 58.947 50.000 0.00 0.00 0.00 3.53
678 679 1.628846 ACGCTCACAAACCTTCCCTAT 59.371 47.619 0.00 0.00 0.00 2.57
679 680 2.009774 CGCTCACAAACCTTCCCTATG 58.990 52.381 0.00 0.00 0.00 2.23
680 681 2.615493 CGCTCACAAACCTTCCCTATGT 60.615 50.000 0.00 0.00 0.00 2.29
693 694 6.785466 ACCTTCCCTATGTTTTGTTTATGGTT 59.215 34.615 0.00 0.00 0.00 3.67
708 709 6.127054 TGTTTATGGTTTGTGGATTTTGGACA 60.127 34.615 0.00 0.00 0.00 4.02
709 710 6.678568 TTATGGTTTGTGGATTTTGGACAT 57.321 33.333 0.00 0.00 0.00 3.06
710 711 4.599047 TGGTTTGTGGATTTTGGACATC 57.401 40.909 0.00 0.00 0.00 3.06
714 715 5.710099 GGTTTGTGGATTTTGGACATCTAGA 59.290 40.000 0.00 0.00 0.00 2.43
722 723 2.031360 GGACATCTAGACCGGTCCG 58.969 63.158 30.82 21.57 40.29 4.79
738 739 1.664151 GTCCGGACAAATTCGATGACC 59.336 52.381 29.75 0.00 0.00 4.02
742 743 0.026285 GACAAATTCGATGACCGGCG 59.974 55.000 0.00 0.00 39.14 6.46
748 749 0.600518 TTCGATGACCGGCGTTGAAA 60.601 50.000 14.65 0.00 33.84 2.69
751 752 0.454452 GATGACCGGCGTTGAAAAGC 60.454 55.000 6.01 0.00 0.00 3.51
752 753 1.169661 ATGACCGGCGTTGAAAAGCA 61.170 50.000 6.01 0.00 34.54 3.91
756 757 0.852136 CCGGCGTTGAAAAGCAAAAG 59.148 50.000 6.01 0.00 38.44 2.27
761 762 4.517287 GGCGTTGAAAAGCAAAAGAAATG 58.483 39.130 3.46 0.00 38.44 2.32
768 769 6.420588 TGAAAAGCAAAAGAAATGAAATGCG 58.579 32.000 0.00 0.00 38.74 4.73
774 775 1.986698 AGAAATGAAATGCGCAGTGC 58.013 45.000 18.32 13.86 46.70 4.40
776 777 0.390209 AAATGAAATGCGCAGTGCCC 60.390 50.000 18.32 7.23 45.60 5.36
792 817 2.666098 CCCCCGGACATCGAGGTTT 61.666 63.158 3.38 0.00 42.43 3.27
793 818 1.298667 CCCCGGACATCGAGGTTTT 59.701 57.895 3.38 0.00 42.43 2.43
821 846 2.303175 GTGTTTGAGTTGCCCCAAGTA 58.697 47.619 0.00 0.00 0.00 2.24
823 848 2.303175 GTTTGAGTTGCCCCAAGTACA 58.697 47.619 0.00 0.00 0.00 2.90
838 863 1.985159 AGTACAAAGTCAGATGCCCCA 59.015 47.619 0.00 0.00 0.00 4.96
843 868 1.620822 AAGTCAGATGCCCCAAACAC 58.379 50.000 0.00 0.00 0.00 3.32
846 871 0.478072 TCAGATGCCCCAAACACTGT 59.522 50.000 0.00 0.00 0.00 3.55
847 872 0.883833 CAGATGCCCCAAACACTGTC 59.116 55.000 0.00 0.00 0.00 3.51
848 873 0.478072 AGATGCCCCAAACACTGTCA 59.522 50.000 0.00 0.00 0.00 3.58
849 874 1.133513 AGATGCCCCAAACACTGTCAA 60.134 47.619 0.00 0.00 0.00 3.18
850 875 1.686052 GATGCCCCAAACACTGTCAAA 59.314 47.619 0.00 0.00 0.00 2.69
851 876 1.561643 TGCCCCAAACACTGTCAAAA 58.438 45.000 0.00 0.00 0.00 2.44
852 877 1.902508 TGCCCCAAACACTGTCAAAAA 59.097 42.857 0.00 0.00 0.00 1.94
874 899 1.006639 AGAGAGAGGAGGGGAACACTC 59.993 57.143 0.00 0.00 0.00 3.51
912 954 2.997897 AGCCACTCGGTCCACTCC 60.998 66.667 0.00 0.00 33.28 3.85
916 958 0.611062 CCACTCGGTCCACTCCACTA 60.611 60.000 0.00 0.00 0.00 2.74
948 993 3.665675 GACACTCGGCCGCTCCATT 62.666 63.158 23.51 1.19 34.01 3.16
971 1016 1.670083 GGAACCACACGCCTACACC 60.670 63.158 0.00 0.00 0.00 4.16
1056 1101 4.803426 CCGCTGTCCGTGCTCCTC 62.803 72.222 0.00 0.00 34.38 3.71
1239 1295 2.533232 TCCAACCCGGTCCCCAAT 60.533 61.111 0.00 0.00 35.57 3.16
1252 1308 0.322456 CCCCAATCGCTTCCTGAACA 60.322 55.000 0.00 0.00 0.00 3.18
1350 1409 2.507992 CGCCTGTGCCGAGAAGAG 60.508 66.667 0.00 0.00 0.00 2.85
1444 1503 3.058160 CGGACCTTGGGCTTGCTG 61.058 66.667 0.00 0.00 0.00 4.41
1471 1530 2.711922 CGCCTACTCAAGTCGGGCT 61.712 63.158 18.45 0.00 41.57 5.19
1487 1546 0.676151 GGCTTCAAGGCAGACCAGAG 60.676 60.000 5.98 0.00 40.97 3.35
1491 1550 1.123861 TCAAGGCAGACCAGAGCACT 61.124 55.000 0.00 0.00 39.06 4.40
1523 1582 0.461516 CTCATGTGCCTCTGCGATGT 60.462 55.000 0.00 0.00 41.78 3.06
1635 1694 7.939784 TCTTAAGAGCTTATGTGACAGTAGA 57.060 36.000 0.00 0.00 0.00 2.59
1784 1849 7.480855 GTGCTCATTATTCTATGAAATGATGCG 59.519 37.037 0.00 0.00 38.55 4.73
1789 1854 4.979943 TTCTATGAAATGATGCGGCAAA 57.020 36.364 6.82 0.00 0.00 3.68
1818 1883 6.686484 ATGCCTAATGTGGTGACATATAGA 57.314 37.500 0.00 0.00 41.82 1.98
1853 1918 3.670377 GTGCAAGGTCGGGGCAAC 61.670 66.667 0.00 0.00 39.57 4.17
1876 1941 0.316204 CAAGGCAAAGCTGGTCCTTG 59.684 55.000 19.98 19.98 46.33 3.61
1878 1943 1.531602 GGCAAAGCTGGTCCTTGGT 60.532 57.895 0.00 0.00 0.00 3.67
1897 1962 5.199982 TGGTCATATGGTTGGTAATGGTT 57.800 39.130 2.13 0.00 0.00 3.67
1991 2060 5.911752 TGCACAACTTTTTGATTACATGGT 58.088 33.333 0.00 0.00 36.48 3.55
2293 2362 5.309020 AGGCTATCTGATGCTATGGAGAAAA 59.691 40.000 0.00 0.00 0.00 2.29
2518 2590 2.673368 CACGGTATCTTTGACTTGGCTC 59.327 50.000 0.00 0.00 0.00 4.70
2580 2662 2.565841 GCTATAGCTTGGTTGGTGAGG 58.434 52.381 17.75 0.00 38.21 3.86
2659 2741 9.563898 CGATGTTGTTACTTATACTACACTTCA 57.436 33.333 0.00 0.00 34.89 3.02
2811 2908 7.949690 AAGAAAATGTTCCATGAGATGATCA 57.050 32.000 0.00 0.00 37.05 2.92
2973 3070 8.143193 TCAATACCATGATTAATTCAATGCACC 58.857 33.333 0.00 0.00 38.03 5.01
3449 3559 3.385755 CCCTTTTGCTGGGATAGGAAATG 59.614 47.826 0.00 0.00 44.66 2.32
3450 3560 4.026052 CCTTTTGCTGGGATAGGAAATGT 58.974 43.478 0.00 0.00 44.66 2.71
3544 3654 4.082245 TGAATAGAGTTGCACAGTCATCGA 60.082 41.667 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 9.513906 TGTATTACAGAAAATGTTCATCCAAGA 57.486 29.630 0.00 0.00 39.96 3.02
72 73 9.460019 TCATGTATTACAGAAAATGTTCATCCA 57.540 29.630 2.53 0.00 39.96 3.41
84 85 9.725019 GGGTGATATTGATCATGTATTACAGAA 57.275 33.333 17.61 0.00 43.95 3.02
85 86 8.879227 TGGGTGATATTGATCATGTATTACAGA 58.121 33.333 17.61 1.37 43.95 3.41
86 87 8.939929 GTGGGTGATATTGATCATGTATTACAG 58.060 37.037 17.61 0.00 43.95 2.74
87 88 8.659527 AGTGGGTGATATTGATCATGTATTACA 58.340 33.333 17.61 0.00 43.95 2.41
88 89 9.507329 AAGTGGGTGATATTGATCATGTATTAC 57.493 33.333 0.00 5.73 43.95 1.89
89 90 9.506018 CAAGTGGGTGATATTGATCATGTATTA 57.494 33.333 0.00 0.00 43.95 0.98
90 91 8.000709 ACAAGTGGGTGATATTGATCATGTATT 58.999 33.333 0.00 0.00 43.95 1.89
91 92 7.520798 ACAAGTGGGTGATATTGATCATGTAT 58.479 34.615 0.00 0.00 43.95 2.29
92 93 6.899089 ACAAGTGGGTGATATTGATCATGTA 58.101 36.000 0.00 0.00 43.95 2.29
93 94 5.759059 ACAAGTGGGTGATATTGATCATGT 58.241 37.500 0.00 0.00 43.95 3.21
94 95 5.240183 GGACAAGTGGGTGATATTGATCATG 59.760 44.000 0.00 0.00 43.95 3.07
95 96 5.380043 GGACAAGTGGGTGATATTGATCAT 58.620 41.667 0.00 0.00 43.95 2.45
96 97 4.683129 CGGACAAGTGGGTGATATTGATCA 60.683 45.833 0.00 0.00 39.88 2.92
97 98 3.809832 CGGACAAGTGGGTGATATTGATC 59.190 47.826 0.00 0.00 0.00 2.92
98 99 3.454447 TCGGACAAGTGGGTGATATTGAT 59.546 43.478 0.00 0.00 0.00 2.57
99 100 2.835156 TCGGACAAGTGGGTGATATTGA 59.165 45.455 0.00 0.00 0.00 2.57
100 101 2.936498 GTCGGACAAGTGGGTGATATTG 59.064 50.000 2.62 0.00 0.00 1.90
101 102 2.838202 AGTCGGACAAGTGGGTGATATT 59.162 45.455 11.27 0.00 0.00 1.28
102 103 2.168521 CAGTCGGACAAGTGGGTGATAT 59.831 50.000 11.27 0.00 0.00 1.63
103 104 1.548719 CAGTCGGACAAGTGGGTGATA 59.451 52.381 11.27 0.00 0.00 2.15
104 105 0.321671 CAGTCGGACAAGTGGGTGAT 59.678 55.000 11.27 0.00 0.00 3.06
105 106 1.046472 ACAGTCGGACAAGTGGGTGA 61.046 55.000 11.27 0.00 0.00 4.02
106 107 0.179056 AACAGTCGGACAAGTGGGTG 60.179 55.000 11.27 0.37 0.00 4.61
107 108 0.179056 CAACAGTCGGACAAGTGGGT 60.179 55.000 11.27 0.00 0.00 4.51
108 109 1.507141 GCAACAGTCGGACAAGTGGG 61.507 60.000 11.27 6.20 0.00 4.61
109 110 0.532862 AGCAACAGTCGGACAAGTGG 60.533 55.000 11.27 7.28 0.00 4.00
110 111 2.148916 TAGCAACAGTCGGACAAGTG 57.851 50.000 11.27 5.83 0.00 3.16
111 112 2.755650 CTTAGCAACAGTCGGACAAGT 58.244 47.619 11.27 5.69 0.00 3.16
112 113 1.461127 GCTTAGCAACAGTCGGACAAG 59.539 52.381 11.27 5.03 0.00 3.16
113 114 1.202592 TGCTTAGCAACAGTCGGACAA 60.203 47.619 3.67 0.00 34.76 3.18
114 115 0.391228 TGCTTAGCAACAGTCGGACA 59.609 50.000 3.67 0.00 34.76 4.02
115 116 1.071605 CTGCTTAGCAACAGTCGGAC 58.928 55.000 8.68 0.00 38.41 4.79
116 117 0.966179 TCTGCTTAGCAACAGTCGGA 59.034 50.000 8.68 0.00 38.41 4.55
117 118 2.015736 ATCTGCTTAGCAACAGTCGG 57.984 50.000 8.68 0.00 38.41 4.79
118 119 3.425359 CCAAATCTGCTTAGCAACAGTCG 60.425 47.826 8.68 0.00 38.41 4.18
119 120 3.119708 CCCAAATCTGCTTAGCAACAGTC 60.120 47.826 8.68 0.00 38.41 3.51
120 121 2.821969 CCCAAATCTGCTTAGCAACAGT 59.178 45.455 8.68 0.00 38.41 3.55
121 122 3.084039 TCCCAAATCTGCTTAGCAACAG 58.916 45.455 8.68 0.00 38.41 3.16
122 123 3.153369 TCCCAAATCTGCTTAGCAACA 57.847 42.857 8.68 0.00 38.41 3.33
123 124 4.884164 AGTATCCCAAATCTGCTTAGCAAC 59.116 41.667 8.68 0.00 38.41 4.17
124 125 5.116084 AGTATCCCAAATCTGCTTAGCAA 57.884 39.130 8.68 0.00 38.41 3.91
125 126 4.778213 AGTATCCCAAATCTGCTTAGCA 57.222 40.909 6.76 6.76 36.92 3.49
126 127 6.292919 CGTTTAGTATCCCAAATCTGCTTAGC 60.293 42.308 0.00 0.00 0.00 3.09
127 128 6.202954 CCGTTTAGTATCCCAAATCTGCTTAG 59.797 42.308 0.00 0.00 0.00 2.18
128 129 6.053005 CCGTTTAGTATCCCAAATCTGCTTA 58.947 40.000 0.00 0.00 0.00 3.09
129 130 4.881850 CCGTTTAGTATCCCAAATCTGCTT 59.118 41.667 0.00 0.00 0.00 3.91
130 131 4.163458 TCCGTTTAGTATCCCAAATCTGCT 59.837 41.667 0.00 0.00 0.00 4.24
131 132 4.272748 GTCCGTTTAGTATCCCAAATCTGC 59.727 45.833 0.00 0.00 0.00 4.26
132 133 4.814771 GGTCCGTTTAGTATCCCAAATCTG 59.185 45.833 0.00 0.00 0.00 2.90
133 134 4.720273 AGGTCCGTTTAGTATCCCAAATCT 59.280 41.667 0.00 0.00 0.00 2.40
134 135 5.032327 AGGTCCGTTTAGTATCCCAAATC 57.968 43.478 0.00 0.00 0.00 2.17
135 136 4.141551 GGAGGTCCGTTTAGTATCCCAAAT 60.142 45.833 0.00 0.00 0.00 2.32
136 137 3.198417 GGAGGTCCGTTTAGTATCCCAAA 59.802 47.826 0.00 0.00 0.00 3.28
137 138 2.767960 GGAGGTCCGTTTAGTATCCCAA 59.232 50.000 0.00 0.00 0.00 4.12
138 139 2.391678 GGAGGTCCGTTTAGTATCCCA 58.608 52.381 0.00 0.00 0.00 4.37
139 140 1.690893 GGGAGGTCCGTTTAGTATCCC 59.309 57.143 0.00 0.00 38.29 3.85
140 141 2.391678 TGGGAGGTCCGTTTAGTATCC 58.608 52.381 0.00 0.00 38.76 2.59
141 142 3.703052 TCTTGGGAGGTCCGTTTAGTATC 59.297 47.826 0.00 0.00 38.76 2.24
142 143 3.716431 TCTTGGGAGGTCCGTTTAGTAT 58.284 45.455 0.00 0.00 38.76 2.12
143 144 3.173953 TCTTGGGAGGTCCGTTTAGTA 57.826 47.619 0.00 0.00 38.76 1.82
144 145 2.019807 TCTTGGGAGGTCCGTTTAGT 57.980 50.000 0.00 0.00 38.76 2.24
145 146 2.420129 CCATCTTGGGAGGTCCGTTTAG 60.420 54.545 0.00 0.00 38.76 1.85
146 147 1.557832 CCATCTTGGGAGGTCCGTTTA 59.442 52.381 0.00 0.00 38.76 2.01
147 148 0.328258 CCATCTTGGGAGGTCCGTTT 59.672 55.000 0.00 0.00 38.76 3.60
148 149 0.840722 ACCATCTTGGGAGGTCCGTT 60.841 55.000 0.00 0.00 43.37 4.44
149 150 0.042131 TACCATCTTGGGAGGTCCGT 59.958 55.000 0.00 0.00 43.37 4.69
150 151 1.200519 TTACCATCTTGGGAGGTCCG 58.799 55.000 0.00 0.00 43.37 4.79
151 152 3.049344 AGATTACCATCTTGGGAGGTCC 58.951 50.000 0.00 0.00 43.37 4.46
152 153 4.779993 AAGATTACCATCTTGGGAGGTC 57.220 45.455 0.00 0.00 46.38 3.85
161 162 4.163458 TCGGCCACTTTAAGATTACCATCT 59.837 41.667 2.24 0.00 42.05 2.90
162 163 4.448210 TCGGCCACTTTAAGATTACCATC 58.552 43.478 2.24 0.00 0.00 3.51
163 164 4.497291 TCGGCCACTTTAAGATTACCAT 57.503 40.909 2.24 0.00 0.00 3.55
164 165 3.985019 TCGGCCACTTTAAGATTACCA 57.015 42.857 2.24 0.00 0.00 3.25
165 166 5.830000 AAATCGGCCACTTTAAGATTACC 57.170 39.130 2.24 0.00 32.05 2.85
166 167 6.238566 GGGTAAATCGGCCACTTTAAGATTAC 60.239 42.308 2.24 1.91 32.05 1.89
167 168 5.824097 GGGTAAATCGGCCACTTTAAGATTA 59.176 40.000 2.24 0.00 32.05 1.75
168 169 4.643334 GGGTAAATCGGCCACTTTAAGATT 59.357 41.667 2.24 0.00 33.50 2.40
169 170 4.079958 AGGGTAAATCGGCCACTTTAAGAT 60.080 41.667 2.24 0.00 0.00 2.40
170 171 3.264964 AGGGTAAATCGGCCACTTTAAGA 59.735 43.478 2.24 0.00 0.00 2.10
171 172 3.617284 AGGGTAAATCGGCCACTTTAAG 58.383 45.455 2.24 0.00 0.00 1.85
172 173 3.613030 GAGGGTAAATCGGCCACTTTAA 58.387 45.455 2.24 0.00 0.00 1.52
173 174 2.092807 GGAGGGTAAATCGGCCACTTTA 60.093 50.000 2.24 2.87 0.00 1.85
174 175 1.340697 GGAGGGTAAATCGGCCACTTT 60.341 52.381 2.24 3.98 0.00 2.66
175 176 0.255033 GGAGGGTAAATCGGCCACTT 59.745 55.000 2.24 0.00 0.00 3.16
176 177 0.620700 AGGAGGGTAAATCGGCCACT 60.621 55.000 2.24 0.00 0.00 4.00
177 178 0.255033 AAGGAGGGTAAATCGGCCAC 59.745 55.000 2.24 0.00 0.00 5.01
178 179 0.996583 AAAGGAGGGTAAATCGGCCA 59.003 50.000 2.24 0.00 0.00 5.36
179 180 1.389555 CAAAGGAGGGTAAATCGGCC 58.610 55.000 0.00 0.00 0.00 6.13
180 181 0.738975 GCAAAGGAGGGTAAATCGGC 59.261 55.000 0.00 0.00 0.00 5.54
181 182 2.122783 TGCAAAGGAGGGTAAATCGG 57.877 50.000 0.00 0.00 0.00 4.18
182 183 3.694072 TCATTGCAAAGGAGGGTAAATCG 59.306 43.478 1.71 0.00 28.02 3.34
183 184 5.659440 TTCATTGCAAAGGAGGGTAAATC 57.341 39.130 1.71 0.00 38.16 2.17
184 185 5.163519 CGATTCATTGCAAAGGAGGGTAAAT 60.164 40.000 1.71 0.00 38.16 1.40
185 186 4.157656 CGATTCATTGCAAAGGAGGGTAAA 59.842 41.667 1.71 0.00 38.16 2.01
186 187 3.694072 CGATTCATTGCAAAGGAGGGTAA 59.306 43.478 1.71 0.00 38.16 2.85
187 188 3.278574 CGATTCATTGCAAAGGAGGGTA 58.721 45.455 1.71 0.00 38.16 3.69
188 189 2.094675 CGATTCATTGCAAAGGAGGGT 58.905 47.619 1.71 0.00 38.16 4.34
189 190 2.094675 ACGATTCATTGCAAAGGAGGG 58.905 47.619 1.71 0.76 38.16 4.30
190 191 3.855689 AACGATTCATTGCAAAGGAGG 57.144 42.857 1.71 1.10 38.16 4.30
191 192 4.168760 GGAAACGATTCATTGCAAAGGAG 58.831 43.478 1.71 0.00 38.16 3.69
192 193 3.571828 TGGAAACGATTCATTGCAAAGGA 59.428 39.130 1.71 0.94 37.29 3.36
193 194 3.911868 TGGAAACGATTCATTGCAAAGG 58.088 40.909 1.71 0.00 37.29 3.11
194 195 4.201647 GCATGGAAACGATTCATTGCAAAG 60.202 41.667 19.75 0.00 41.19 2.77
195 196 3.679025 GCATGGAAACGATTCATTGCAAA 59.321 39.130 19.75 0.00 41.19 3.68
196 197 3.252400 GCATGGAAACGATTCATTGCAA 58.748 40.909 19.75 0.00 41.19 4.08
197 198 2.230750 TGCATGGAAACGATTCATTGCA 59.769 40.909 21.99 21.99 45.13 4.08
198 199 2.878580 TGCATGGAAACGATTCATTGC 58.121 42.857 18.58 18.58 41.57 3.56
199 200 8.975410 ATAATATGCATGGAAACGATTCATTG 57.025 30.769 10.16 5.31 37.29 2.82
230 231 9.773328 CTCGTGAATATGAAAAATGTGTACAAT 57.227 29.630 0.00 0.00 0.00 2.71
231 232 8.994170 TCTCGTGAATATGAAAAATGTGTACAA 58.006 29.630 0.00 0.00 0.00 2.41
232 233 8.541133 TCTCGTGAATATGAAAAATGTGTACA 57.459 30.769 0.00 0.00 0.00 2.90
233 234 9.820229 TTTCTCGTGAATATGAAAAATGTGTAC 57.180 29.630 0.02 0.00 31.56 2.90
234 235 9.820229 GTTTCTCGTGAATATGAAAAATGTGTA 57.180 29.630 0.02 0.00 31.47 2.90
235 236 8.349245 TGTTTCTCGTGAATATGAAAAATGTGT 58.651 29.630 0.02 0.00 31.47 3.72
236 237 8.726650 TGTTTCTCGTGAATATGAAAAATGTG 57.273 30.769 0.02 0.00 31.47 3.21
237 238 9.912634 AATGTTTCTCGTGAATATGAAAAATGT 57.087 25.926 0.02 0.00 29.81 2.71
351 352 9.802039 TCCCTTTTGTTTGTACTTACAGATATT 57.198 29.630 0.00 0.00 37.52 1.28
352 353 9.802039 TTCCCTTTTGTTTGTACTTACAGATAT 57.198 29.630 0.00 0.00 37.52 1.63
353 354 9.629878 TTTCCCTTTTGTTTGTACTTACAGATA 57.370 29.630 0.00 0.00 37.52 1.98
354 355 8.528044 TTTCCCTTTTGTTTGTACTTACAGAT 57.472 30.769 0.00 0.00 37.52 2.90
355 356 7.941431 TTTCCCTTTTGTTTGTACTTACAGA 57.059 32.000 0.00 0.00 37.52 3.41
356 357 8.989653 TTTTTCCCTTTTGTTTGTACTTACAG 57.010 30.769 0.00 0.00 37.52 2.74
452 453 2.383527 CCAACTCGCTGAAGTCGCC 61.384 63.158 0.00 0.00 0.00 5.54
454 455 1.063806 CTTCCAACTCGCTGAAGTCG 58.936 55.000 0.00 0.00 32.68 4.18
468 469 0.759060 TATAGCGAGGCAGCCTTCCA 60.759 55.000 17.46 1.61 38.01 3.53
482 483 5.179555 GGCACAACTATACCTTGCTTATAGC 59.820 44.000 0.00 0.00 42.82 2.97
491 492 2.580783 ACATGGGGCACAACTATACCTT 59.419 45.455 0.00 0.00 0.00 3.50
500 501 1.225983 CGGGATACATGGGGCACAA 59.774 57.895 0.00 0.00 39.74 3.33
501 502 2.915079 CGGGATACATGGGGCACA 59.085 61.111 0.00 0.00 39.74 4.57
502 503 1.764571 TAGCGGGATACATGGGGCAC 61.765 60.000 0.00 0.00 39.74 5.01
544 545 2.174360 GCCAAAGCCCATCTTTTCTCT 58.826 47.619 0.00 0.00 42.82 3.10
545 546 1.895131 TGCCAAAGCCCATCTTTTCTC 59.105 47.619 0.00 0.00 42.82 2.87
569 570 3.761218 TGTTTGGACACACATCACTGTTT 59.239 39.130 0.00 0.00 31.62 2.83
570 571 3.351740 TGTTTGGACACACATCACTGTT 58.648 40.909 0.00 0.00 31.62 3.16
571 572 2.997980 TGTTTGGACACACATCACTGT 58.002 42.857 0.00 0.00 35.44 3.55
582 583 1.077357 AAGCCCGTGTGTTTGGACA 60.077 52.632 0.00 0.00 0.00 4.02
594 595 2.994643 AAAACCCCACCTGAAGCCCG 62.995 60.000 0.00 0.00 0.00 6.13
595 596 0.762842 AAAAACCCCACCTGAAGCCC 60.763 55.000 0.00 0.00 0.00 5.19
609 610 1.215382 GCTCGGCCCATCCAAAAAC 59.785 57.895 0.00 0.00 34.01 2.43
649 650 0.599204 TTTGTGAGCGTTCGGACCTC 60.599 55.000 5.62 5.62 0.00 3.85
655 656 0.234884 GGAAGGTTTGTGAGCGTTCG 59.765 55.000 0.00 0.00 33.41 3.95
659 660 2.009774 CATAGGGAAGGTTTGTGAGCG 58.990 52.381 0.00 0.00 0.00 5.03
662 663 5.205056 ACAAAACATAGGGAAGGTTTGTGA 58.795 37.500 7.68 0.00 35.14 3.58
664 665 6.553953 AAACAAAACATAGGGAAGGTTTGT 57.446 33.333 3.00 3.00 35.14 2.83
676 677 9.838339 AAATCCACAAACCATAAACAAAACATA 57.162 25.926 0.00 0.00 0.00 2.29
677 678 8.744568 AAATCCACAAACCATAAACAAAACAT 57.255 26.923 0.00 0.00 0.00 2.71
678 679 8.454106 CAAAATCCACAAACCATAAACAAAACA 58.546 29.630 0.00 0.00 0.00 2.83
679 680 7.912773 CCAAAATCCACAAACCATAAACAAAAC 59.087 33.333 0.00 0.00 0.00 2.43
680 681 7.829211 TCCAAAATCCACAAACCATAAACAAAA 59.171 29.630 0.00 0.00 0.00 2.44
693 694 5.253330 GGTCTAGATGTCCAAAATCCACAA 58.747 41.667 0.00 0.00 0.00 3.33
722 723 0.377203 GCCGGTCATCGAATTTGTCC 59.623 55.000 1.90 0.00 42.43 4.02
725 726 0.446222 AACGCCGGTCATCGAATTTG 59.554 50.000 1.90 0.00 42.43 2.32
738 739 1.833860 TCTTTTGCTTTTCAACGCCG 58.166 45.000 0.00 0.00 33.73 6.46
742 743 7.097329 CGCATTTCATTTCTTTTGCTTTTCAAC 60.097 33.333 0.00 0.00 33.73 3.18
748 749 3.808726 TGCGCATTTCATTTCTTTTGCTT 59.191 34.783 5.66 0.00 0.00 3.91
751 752 4.694177 CACTGCGCATTTCATTTCTTTTG 58.306 39.130 12.24 0.00 0.00 2.44
752 753 3.184986 GCACTGCGCATTTCATTTCTTTT 59.815 39.130 12.24 0.00 41.79 2.27
756 757 0.994263 GGCACTGCGCATTTCATTTC 59.006 50.000 12.24 0.00 45.17 2.17
761 762 4.133796 GGGGGCACTGCGCATTTC 62.134 66.667 12.24 0.00 45.17 2.17
776 777 0.321298 ACAAAACCTCGATGTCCGGG 60.321 55.000 0.00 0.00 39.14 5.73
785 810 1.011333 ACACGGTTCACAAAACCTCG 58.989 50.000 5.49 0.00 38.15 4.63
792 817 2.414824 GCAACTCAAACACGGTTCACAA 60.415 45.455 0.00 0.00 0.00 3.33
793 818 1.131504 GCAACTCAAACACGGTTCACA 59.868 47.619 0.00 0.00 0.00 3.58
821 846 1.963515 GTTTGGGGCATCTGACTTTGT 59.036 47.619 0.00 0.00 0.00 2.83
823 848 1.963515 GTGTTTGGGGCATCTGACTTT 59.036 47.619 0.00 0.00 0.00 2.66
850 875 3.073209 GTGTTCCCCTCCTCTCTCTTTTT 59.927 47.826 0.00 0.00 0.00 1.94
851 876 2.640332 GTGTTCCCCTCCTCTCTCTTTT 59.360 50.000 0.00 0.00 0.00 2.27
852 877 2.158081 AGTGTTCCCCTCCTCTCTCTTT 60.158 50.000 0.00 0.00 0.00 2.52
853 878 1.435168 AGTGTTCCCCTCCTCTCTCTT 59.565 52.381 0.00 0.00 0.00 2.85
854 879 1.006639 GAGTGTTCCCCTCCTCTCTCT 59.993 57.143 0.00 0.00 0.00 3.10
855 880 1.480789 GAGTGTTCCCCTCCTCTCTC 58.519 60.000 0.00 0.00 0.00 3.20
856 881 0.041982 GGAGTGTTCCCCTCCTCTCT 59.958 60.000 0.00 0.00 44.29 3.10
857 882 2.597995 GGAGTGTTCCCCTCCTCTC 58.402 63.158 0.00 0.00 44.29 3.20
858 883 4.899243 GGAGTGTTCCCCTCCTCT 57.101 61.111 0.00 0.00 44.29 3.69
864 889 2.352805 CCAGCTGGAGTGTTCCCC 59.647 66.667 29.88 0.00 43.33 4.81
870 895 1.220206 CTGTAGCCCAGCTGGAGTG 59.780 63.158 34.91 18.56 40.10 3.51
904 946 1.205893 CTTCCTGCTAGTGGAGTGGAC 59.794 57.143 6.69 0.00 34.76 4.02
912 954 2.447887 CGCGTGCTTCCTGCTAGTG 61.448 63.158 0.00 0.00 43.37 2.74
916 958 4.299547 TGTCGCGTGCTTCCTGCT 62.300 61.111 5.77 0.00 43.37 4.24
939 984 1.026718 GGTTCCTGTCAATGGAGCGG 61.027 60.000 0.00 0.00 35.95 5.52
948 993 1.116536 TAGGCGTGTGGTTCCTGTCA 61.117 55.000 0.00 0.00 0.00 3.58
971 1016 1.226746 GTTCCTGTTGGAGTGGTTCG 58.773 55.000 0.00 0.00 44.24 3.95
1056 1101 3.760035 CGGTGGAGGTGGTCGAGG 61.760 72.222 0.00 0.00 0.00 4.63
1239 1295 0.320771 GGAAGCTGTTCAGGAAGCGA 60.321 55.000 1.97 0.00 44.34 4.93
1252 1308 4.416738 GAGGGCGGCAAGGAAGCT 62.417 66.667 12.47 0.00 34.17 3.74
1444 1503 2.104530 GAGTAGGCGGCCGAAGAC 59.895 66.667 33.48 21.88 0.00 3.01
1471 1530 0.250467 GTGCTCTGGTCTGCCTTGAA 60.250 55.000 0.00 0.00 35.27 2.69
1491 1550 3.013327 ATGAGGAGGCTGCTGGCA 61.013 61.111 15.18 6.56 44.01 4.92
1523 1582 0.896940 AGCCTCGTTTGTCCGTCCTA 60.897 55.000 0.00 0.00 0.00 2.94
1762 1824 6.430616 TGCCGCATCATTTCATAGAATAATGA 59.569 34.615 0.00 0.00 41.12 2.57
1789 1854 2.849943 TCACCACATTAGGCATAACCCT 59.150 45.455 0.00 0.00 40.58 4.34
1818 1883 1.398041 CACAACGCACCAATCATCGAT 59.602 47.619 0.00 0.00 0.00 3.59
1853 1918 1.856265 GACCAGCTTTGCCTTGTCCG 61.856 60.000 0.00 0.00 0.00 4.79
1876 1941 6.538945 AAAACCATTACCAACCATATGACC 57.461 37.500 3.65 0.00 0.00 4.02
1878 1943 6.094325 GTCGAAAACCATTACCAACCATATGA 59.906 38.462 3.65 0.00 0.00 2.15
1897 1962 9.321562 GTTCCAAATATACTTATCTGGTCGAAA 57.678 33.333 0.00 0.00 0.00 3.46
1910 1975 7.062322 TGCCATGAATGAGTTCCAAATATACT 58.938 34.615 0.00 0.00 33.26 2.12
1916 1985 4.346730 AGATGCCATGAATGAGTTCCAAA 58.653 39.130 0.00 0.00 33.26 3.28
2122 2191 8.343366 TGCGTCAATTAGTATGTTAAAAACACA 58.657 29.630 0.00 0.00 45.50 3.72
2293 2362 7.902920 ATCCTGTAGCAACCATTTCATTTAT 57.097 32.000 0.00 0.00 0.00 1.40
2518 2590 1.457346 GGCCTCTCACCAATGTTCAG 58.543 55.000 0.00 0.00 0.00 3.02
2580 2662 1.737735 GCCCAAATGCTTTCGCCAC 60.738 57.895 0.00 0.00 34.43 5.01
2659 2741 9.110382 ACCTTCTATTTCTAGAATAGCCATGAT 57.890 33.333 5.89 0.00 41.87 2.45
2811 2908 2.057922 ACTCACCATGGTTCCAGTTCT 58.942 47.619 16.84 0.00 0.00 3.01
2973 3070 5.159273 AGCTTCTTTCTTCTCCTAACCAG 57.841 43.478 0.00 0.00 0.00 4.00
3449 3559 7.061094 CCGATTTTCTACAAGCAAGAAATTCAC 59.939 37.037 15.26 0.00 41.34 3.18
3450 3560 7.083858 CCGATTTTCTACAAGCAAGAAATTCA 58.916 34.615 15.26 0.00 41.34 2.57
3518 3628 6.074623 CGATGACTGTGCAACTCTATTCATAC 60.075 42.308 0.00 0.00 38.04 2.39


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

AutoCloner maintained by Alex Coulton.