Multiple sequence alignment - TraesCS3A01G340200

Loading Multiple Alignment...

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 TraesCS3A01G340200 chr3A 100.000 3912 0 0 1 3912 587554224 587550313 0.000000e+00 7225.0
1 TraesCS3A01G340200 chr3B 92.185 3711 158 59 237 3912 584577833 584574220 0.000000e+00 5125.0
2 TraesCS3A01G340200 chr3D 94.310 3304 91 41 335 3606 445739449 445736211 0.000000e+00 4970.0
3 TraesCS3A01G340200 chr1A 79.987 1514 269 23 1399 2900 497498322 497496831 0.000000e+00 1086.0
4 TraesCS3A01G340200 chr1A 87.500 96 12 0 70 165 469201992 469202087 1.150000e-20 111.0
5 TraesCS3A01G340200 chr1D 79.868 1520 272 29 1399 2900 401565547 401564044 0.000000e+00 1081.0
6 TraesCS3A01G340200 chr1D 85.714 105 11 4 70 173 254638330 254638431 1.490000e-19 108.0
7 TraesCS3A01G340200 chr1B 79.982 1109 216 6 1399 2504 539482147 539481042 0.000000e+00 813.0
8 TraesCS3A01G340200 chr1B 86.577 298 38 2 2604 2900 539480960 539480664 1.050000e-85 327.0
9 TraesCS3A01G340200 chr2D 85.841 113 13 3 70 180 82093881 82093770 2.470000e-22 117.0
10 TraesCS3A01G340200 chr6D 88.000 100 9 3 72 171 446736294 446736198 8.880000e-22 115.0
11 TraesCS3A01G340200 chr6D 89.362 47 2 1 1143 1186 391563091 391563137 5.460000e-04 56.5
12 TraesCS3A01G340200 chr4D 88.542 96 10 1 70 165 82458439 82458345 8.880000e-22 115.0
13 TraesCS3A01G340200 chr4D 84.906 106 15 1 70 174 465599678 465599573 5.350000e-19 106.0
14 TraesCS3A01G340200 chr4A 88.542 96 10 1 70 165 660646900 660646806 8.880000e-22 115.0
15 TraesCS3A01G340200 chr7B 86.111 108 12 3 70 176 86845216 86845111 3.190000e-21 113.0
16 TraesCS3A01G340200 chr2B 85.714 105 11 4 70 172 160433425 160433323 1.490000e-19 108.0


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 TraesCS3A01G340200 chr3A 587550313 587554224 3911 True 7225 7225 100.0000 1 3912 1 chr3A.!!$R1 3911
1 TraesCS3A01G340200 chr3B 584574220 584577833 3613 True 5125 5125 92.1850 237 3912 1 chr3B.!!$R1 3675
2 TraesCS3A01G340200 chr3D 445736211 445739449 3238 True 4970 4970 94.3100 335 3606 1 chr3D.!!$R1 3271
3 TraesCS3A01G340200 chr1A 497496831 497498322 1491 True 1086 1086 79.9870 1399 2900 1 chr1A.!!$R1 1501
4 TraesCS3A01G340200 chr1D 401564044 401565547 1503 True 1081 1081 79.8680 1399 2900 1 chr1D.!!$R1 1501
5 TraesCS3A01G340200 chr1B 539480664 539482147 1483 True 570 813 83.2795 1399 2900 2 chr1B.!!$R1 1501

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
971 987 0.248907 AGCGAATCCATCCGTACACG 60.249 55.0 0.0 0.0 39.44 4.49 F
1231 1253 0.232303 CGTCAACGTCTTCAACCAGC 59.768 55.0 0.0 0.0 34.11 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2680 2728 0.976073 ACCTCGGGTACACCTGGATG 60.976 60.0 0.0 0.0 42.72 3.51 R
3154 3207 0.530744 CCTCCTCGTTCCGATGACAA 59.469 55.0 0.0 0.0 34.61 3.18 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
17 18 3.978164 GTGAGAGGGATGAGGGGG 58.022 66.667 0.00 0.00 0.00 5.40
51 52 3.061093 GCCTTCGGCCTTGTAGTAC 57.939 57.895 0.00 0.00 44.06 2.73
52 53 0.535797 GCCTTCGGCCTTGTAGTACT 59.464 55.000 0.00 0.00 44.06 2.73
53 54 1.471153 GCCTTCGGCCTTGTAGTACTC 60.471 57.143 0.00 0.00 44.06 2.59
54 55 2.100989 CCTTCGGCCTTGTAGTACTCT 58.899 52.381 0.00 0.00 0.00 3.24
55 56 2.099427 CCTTCGGCCTTGTAGTACTCTC 59.901 54.545 0.00 0.00 0.00 3.20
56 57 2.803030 TCGGCCTTGTAGTACTCTCT 57.197 50.000 0.00 0.00 0.00 3.10
57 58 2.641305 TCGGCCTTGTAGTACTCTCTC 58.359 52.381 0.00 0.00 0.00 3.20
58 59 1.677052 CGGCCTTGTAGTACTCTCTCC 59.323 57.143 0.00 0.00 0.00 3.71
59 60 1.677052 GGCCTTGTAGTACTCTCTCCG 59.323 57.143 0.00 0.00 0.00 4.63
60 61 2.367486 GCCTTGTAGTACTCTCTCCGT 58.633 52.381 0.00 0.00 0.00 4.69
61 62 2.355444 GCCTTGTAGTACTCTCTCCGTC 59.645 54.545 0.00 0.00 0.00 4.79
62 63 2.944349 CCTTGTAGTACTCTCTCCGTCC 59.056 54.545 0.00 0.00 0.00 4.79
63 64 2.706339 TGTAGTACTCTCTCCGTCCC 57.294 55.000 0.00 0.00 0.00 4.46
64 65 1.911357 TGTAGTACTCTCTCCGTCCCA 59.089 52.381 0.00 0.00 0.00 4.37
65 66 2.306805 TGTAGTACTCTCTCCGTCCCAA 59.693 50.000 0.00 0.00 0.00 4.12
66 67 2.599408 AGTACTCTCTCCGTCCCAAA 57.401 50.000 0.00 0.00 0.00 3.28
67 68 2.885616 AGTACTCTCTCCGTCCCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
68 69 3.442076 AGTACTCTCTCCGTCCCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
69 70 3.838903 AGTACTCTCTCCGTCCCAAAATT 59.161 43.478 0.00 0.00 0.00 1.82
70 71 3.059352 ACTCTCTCCGTCCCAAAATTG 57.941 47.619 0.00 0.00 0.00 2.32
86 87 7.636150 CCAAAATTGGTCTATGAATCTGAGT 57.364 36.000 3.95 0.00 43.43 3.41
87 88 7.478322 CCAAAATTGGTCTATGAATCTGAGTG 58.522 38.462 3.95 0.00 43.43 3.51
88 89 7.121759 CCAAAATTGGTCTATGAATCTGAGTGT 59.878 37.037 3.95 0.00 43.43 3.55
89 90 9.166173 CAAAATTGGTCTATGAATCTGAGTGTA 57.834 33.333 0.00 0.00 0.00 2.90
90 91 9.739276 AAAATTGGTCTATGAATCTGAGTGTAA 57.261 29.630 0.00 0.00 0.00 2.41
91 92 8.723942 AATTGGTCTATGAATCTGAGTGTAAC 57.276 34.615 0.00 0.00 0.00 2.50
115 116 9.537848 AACTTTTATTATTTCTAGCGTTCGTTG 57.462 29.630 0.00 0.00 0.00 4.10
116 117 8.715088 ACTTTTATTATTTCTAGCGTTCGTTGT 58.285 29.630 0.00 0.00 0.00 3.32
118 119 9.956797 TTTTATTATTTCTAGCGTTCGTTGTAC 57.043 29.630 0.00 0.00 0.00 2.90
119 120 8.915871 TTATTATTTCTAGCGTTCGTTGTACT 57.084 30.769 0.00 0.00 0.00 2.73
122 123 8.552469 TTATTTCTAGCGTTCGTTGTACTATC 57.448 34.615 0.00 0.00 0.00 2.08
123 124 5.550232 TTCTAGCGTTCGTTGTACTATCA 57.450 39.130 0.00 0.00 0.00 2.15
124 125 5.746307 TCTAGCGTTCGTTGTACTATCAT 57.254 39.130 0.00 0.00 0.00 2.45
125 126 5.507974 TCTAGCGTTCGTTGTACTATCATG 58.492 41.667 0.00 0.00 0.00 3.07
126 127 4.365899 AGCGTTCGTTGTACTATCATGA 57.634 40.909 0.00 0.00 0.00 3.07
127 128 4.933330 AGCGTTCGTTGTACTATCATGAT 58.067 39.130 13.81 13.81 0.00 2.45
128 129 5.348986 AGCGTTCGTTGTACTATCATGATT 58.651 37.500 14.65 0.00 0.00 2.57
129 130 5.232202 AGCGTTCGTTGTACTATCATGATTG 59.768 40.000 14.65 14.58 0.00 2.67
130 131 5.231357 GCGTTCGTTGTACTATCATGATTGA 59.769 40.000 21.64 1.13 36.00 2.57
131 132 6.237728 GCGTTCGTTGTACTATCATGATTGAA 60.238 38.462 21.64 5.14 34.96 2.69
132 133 7.330318 CGTTCGTTGTACTATCATGATTGAAG 58.670 38.462 21.64 12.40 34.96 3.02
133 134 7.220108 CGTTCGTTGTACTATCATGATTGAAGA 59.780 37.037 21.64 6.21 34.96 2.87
134 135 9.035607 GTTCGTTGTACTATCATGATTGAAGAT 57.964 33.333 21.64 4.07 34.96 2.40
135 136 8.579682 TCGTTGTACTATCATGATTGAAGATG 57.420 34.615 21.64 10.62 34.96 2.90
136 137 8.413229 TCGTTGTACTATCATGATTGAAGATGA 58.587 33.333 21.64 12.27 34.96 2.92
137 138 9.034544 CGTTGTACTATCATGATTGAAGATGAA 57.965 33.333 21.64 4.00 34.96 2.57
146 147 9.939802 ATCATGATTGAAGATGAATAGATCGAA 57.060 29.630 1.18 0.00 34.96 3.71
147 148 9.939802 TCATGATTGAAGATGAATAGATCGAAT 57.060 29.630 0.00 0.00 0.00 3.34
156 157 8.694975 AGATGAATAGATCGAATATTGTTCCG 57.305 34.615 10.11 0.00 0.00 4.30
157 158 8.307483 AGATGAATAGATCGAATATTGTTCCGT 58.693 33.333 10.11 0.03 0.00 4.69
158 159 9.569167 GATGAATAGATCGAATATTGTTCCGTA 57.431 33.333 10.11 0.00 0.00 4.02
159 160 9.923143 ATGAATAGATCGAATATTGTTCCGTAA 57.077 29.630 10.11 0.00 0.00 3.18
160 161 9.406828 TGAATAGATCGAATATTGTTCCGTAAG 57.593 33.333 10.11 0.00 0.00 2.34
161 162 9.622004 GAATAGATCGAATATTGTTCCGTAAGA 57.378 33.333 10.11 0.00 43.02 2.10
162 163 9.976511 AATAGATCGAATATTGTTCCGTAAGAA 57.023 29.630 0.00 0.00 43.02 2.52
163 164 9.976511 ATAGATCGAATATTGTTCCGTAAGAAA 57.023 29.630 0.00 0.00 43.02 2.52
164 165 8.712285 AGATCGAATATTGTTCCGTAAGAAAA 57.288 30.769 0.00 0.00 43.02 2.29
165 166 8.818057 AGATCGAATATTGTTCCGTAAGAAAAG 58.182 33.333 0.00 0.00 43.02 2.27
166 167 8.712285 ATCGAATATTGTTCCGTAAGAAAAGA 57.288 30.769 0.00 0.00 43.02 2.52
167 168 8.537049 TCGAATATTGTTCCGTAAGAAAAGAA 57.463 30.769 0.00 0.00 43.02 2.52
168 169 9.158233 TCGAATATTGTTCCGTAAGAAAAGAAT 57.842 29.630 0.00 0.00 43.02 2.40
174 175 7.972832 TGTTCCGTAAGAAAAGAATACATGT 57.027 32.000 2.69 2.69 43.02 3.21
175 176 9.491675 TTGTTCCGTAAGAAAAGAATACATGTA 57.508 29.630 8.27 8.27 43.02 2.29
176 177 9.491675 TGTTCCGTAAGAAAAGAATACATGTAA 57.508 29.630 10.14 0.00 43.02 2.41
197 198 9.844790 ATGTAAAAATACATGATATGATTGGCG 57.155 29.630 0.00 0.00 39.05 5.69
198 199 9.061435 TGTAAAAATACATGATATGATTGGCGA 57.939 29.630 0.00 0.00 0.00 5.54
199 200 9.546909 GTAAAAATACATGATATGATTGGCGAG 57.453 33.333 0.00 0.00 0.00 5.03
200 201 7.984422 AAAATACATGATATGATTGGCGAGA 57.016 32.000 0.00 0.00 0.00 4.04
201 202 7.984422 AAATACATGATATGATTGGCGAGAA 57.016 32.000 0.00 0.00 0.00 2.87
202 203 8.571461 AAATACATGATATGATTGGCGAGAAT 57.429 30.769 0.00 0.00 0.00 2.40
203 204 9.671279 AAATACATGATATGATTGGCGAGAATA 57.329 29.630 0.00 0.00 0.00 1.75
204 205 6.974932 ACATGATATGATTGGCGAGAATAC 57.025 37.500 0.00 0.00 0.00 1.89
205 206 5.578336 ACATGATATGATTGGCGAGAATACG 59.422 40.000 0.00 0.00 0.00 3.06
206 207 5.134202 TGATATGATTGGCGAGAATACGT 57.866 39.130 0.00 0.00 35.59 3.57
207 208 4.923281 TGATATGATTGGCGAGAATACGTG 59.077 41.667 0.00 0.00 35.59 4.49
208 209 2.951457 TGATTGGCGAGAATACGTGA 57.049 45.000 0.00 0.00 35.59 4.35
209 210 3.452755 TGATTGGCGAGAATACGTGAT 57.547 42.857 0.00 0.00 35.59 3.06
210 211 4.577834 TGATTGGCGAGAATACGTGATA 57.422 40.909 0.00 0.00 35.59 2.15
211 212 4.939271 TGATTGGCGAGAATACGTGATAA 58.061 39.130 0.00 0.00 35.59 1.75
212 213 5.353111 TGATTGGCGAGAATACGTGATAAA 58.647 37.500 0.00 0.00 35.59 1.40
213 214 5.813157 TGATTGGCGAGAATACGTGATAAAA 59.187 36.000 0.00 0.00 35.59 1.52
214 215 6.314152 TGATTGGCGAGAATACGTGATAAAAA 59.686 34.615 0.00 0.00 35.59 1.94
215 216 6.671614 TTGGCGAGAATACGTGATAAAAAT 57.328 33.333 0.00 0.00 35.59 1.82
216 217 6.281848 TGGCGAGAATACGTGATAAAAATC 57.718 37.500 0.00 0.00 35.59 2.17
217 218 5.813157 TGGCGAGAATACGTGATAAAAATCA 59.187 36.000 0.00 0.00 35.59 2.57
218 219 6.019075 TGGCGAGAATACGTGATAAAAATCAG 60.019 38.462 0.00 0.00 35.59 2.90
219 220 6.200286 GGCGAGAATACGTGATAAAAATCAGA 59.800 38.462 0.00 0.00 35.59 3.27
220 221 7.095607 GGCGAGAATACGTGATAAAAATCAGAT 60.096 37.037 0.00 0.00 35.59 2.90
221 222 8.912658 GCGAGAATACGTGATAAAAATCAGATA 58.087 33.333 0.00 0.00 35.59 1.98
240 241 8.470040 TCAGATAATAACACGTAGAAACAACC 57.530 34.615 0.00 0.00 0.00 3.77
241 242 8.308931 TCAGATAATAACACGTAGAAACAACCT 58.691 33.333 0.00 0.00 0.00 3.50
242 243 8.592998 CAGATAATAACACGTAGAAACAACCTC 58.407 37.037 0.00 0.00 0.00 3.85
243 244 7.763071 AGATAATAACACGTAGAAACAACCTCC 59.237 37.037 0.00 0.00 0.00 4.30
244 245 2.538512 ACACGTAGAAACAACCTCCC 57.461 50.000 0.00 0.00 0.00 4.30
245 246 1.764134 ACACGTAGAAACAACCTCCCA 59.236 47.619 0.00 0.00 0.00 4.37
246 247 2.370849 ACACGTAGAAACAACCTCCCAT 59.629 45.455 0.00 0.00 0.00 4.00
247 248 3.579586 ACACGTAGAAACAACCTCCCATA 59.420 43.478 0.00 0.00 0.00 2.74
248 249 4.224370 ACACGTAGAAACAACCTCCCATAT 59.776 41.667 0.00 0.00 0.00 1.78
249 250 5.183228 CACGTAGAAACAACCTCCCATATT 58.817 41.667 0.00 0.00 0.00 1.28
250 251 5.646360 CACGTAGAAACAACCTCCCATATTT 59.354 40.000 0.00 0.00 0.00 1.40
251 252 5.878669 ACGTAGAAACAACCTCCCATATTTC 59.121 40.000 0.00 0.00 0.00 2.17
252 253 5.296035 CGTAGAAACAACCTCCCATATTTCC 59.704 44.000 0.00 0.00 0.00 3.13
253 254 5.536497 AGAAACAACCTCCCATATTTCCT 57.464 39.130 0.00 0.00 0.00 3.36
254 255 5.903923 AGAAACAACCTCCCATATTTCCTT 58.096 37.500 0.00 0.00 0.00 3.36
298 299 1.960417 TGTCTGGCGACAACAAATGA 58.040 45.000 9.19 0.00 46.61 2.57
299 300 1.601903 TGTCTGGCGACAACAAATGAC 59.398 47.619 9.19 0.00 46.61 3.06
300 301 3.936623 TGTCTGGCGACAACAAATGACG 61.937 50.000 9.19 0.00 46.61 4.35
307 308 2.777845 CGACAACAAATGACGCATATGC 59.222 45.455 18.08 18.08 40.05 3.14
308 309 3.485711 CGACAACAAATGACGCATATGCT 60.486 43.478 24.56 12.20 40.05 3.79
329 331 2.961768 CGTCAATTGCCACCACCC 59.038 61.111 0.00 0.00 0.00 4.61
355 357 1.100510 GGTTCGGGGTAATCTTTGCC 58.899 55.000 0.00 0.00 34.30 4.52
361 363 2.495669 CGGGGTAATCTTTGCCAAATGT 59.504 45.455 0.00 0.00 37.12 2.71
362 364 3.056179 CGGGGTAATCTTTGCCAAATGTT 60.056 43.478 0.00 0.00 37.12 2.71
391 393 1.745087 CCAACTGATGATTTCGTGGGG 59.255 52.381 0.00 0.00 0.00 4.96
392 394 1.745087 CAACTGATGATTTCGTGGGGG 59.255 52.381 0.00 0.00 0.00 5.40
393 395 0.394352 ACTGATGATTTCGTGGGGGC 60.394 55.000 0.00 0.00 0.00 5.80
422 429 8.608844 AAAAATCAAGGTTGTGTTTTGTAACA 57.391 26.923 8.35 0.00 41.82 2.41
431 438 2.144730 TGTTTTGTAACACGATCCCCG 58.855 47.619 0.00 0.00 39.29 5.73
432 439 1.465777 GTTTTGTAACACGATCCCCGG 59.534 52.381 0.00 0.00 43.93 5.73
458 466 4.751767 ACAGCTGACAAAAATGGGAAAA 57.248 36.364 23.35 0.00 0.00 2.29
461 469 3.383185 AGCTGACAAAAATGGGAAAACGA 59.617 39.130 0.00 0.00 0.00 3.85
505 513 1.278238 GTTAAGATCACAGGGACGCG 58.722 55.000 3.53 3.53 0.00 6.01
512 520 1.447838 CACAGGGACGCGCAGTATT 60.448 57.895 5.73 0.00 0.00 1.89
631 645 1.169661 TGGCACCAACGGCAAAGTAG 61.170 55.000 0.00 0.00 38.71 2.57
632 646 0.887387 GGCACCAACGGCAAAGTAGA 60.887 55.000 0.00 0.00 0.00 2.59
633 647 0.517316 GCACCAACGGCAAAGTAGAG 59.483 55.000 0.00 0.00 0.00 2.43
634 648 1.878953 CACCAACGGCAAAGTAGAGT 58.121 50.000 0.00 0.00 0.00 3.24
635 649 2.868839 GCACCAACGGCAAAGTAGAGTA 60.869 50.000 0.00 0.00 0.00 2.59
647 661 4.522722 AAGTAGAGTACTTGGCTGTCAC 57.477 45.455 0.00 0.00 46.58 3.67
648 662 2.826725 AGTAGAGTACTTGGCTGTCACC 59.173 50.000 0.00 0.00 34.86 4.02
649 663 0.603569 AGAGTACTTGGCTGTCACCG 59.396 55.000 0.00 0.00 0.00 4.94
650 664 0.389948 GAGTACTTGGCTGTCACCGG 60.390 60.000 0.00 0.00 0.00 5.28
971 987 0.248907 AGCGAATCCATCCGTACACG 60.249 55.000 0.00 0.00 39.44 4.49
1203 1225 2.363306 TCAACTGCACCTCCAACAAT 57.637 45.000 0.00 0.00 0.00 2.71
1231 1253 0.232303 CGTCAACGTCTTCAACCAGC 59.768 55.000 0.00 0.00 34.11 4.85
1285 1307 4.926832 CCTTCCGTTTCTTCTTCTTCTCTC 59.073 45.833 0.00 0.00 0.00 3.20
1290 1312 5.861787 CCGTTTCTTCTTCTTCTCTCTTCTC 59.138 44.000 0.00 0.00 0.00 2.87
1293 1315 7.114811 CGTTTCTTCTTCTTCTCTCTTCTCTTG 59.885 40.741 0.00 0.00 0.00 3.02
1298 1320 7.825331 TCTTCTTCTCTCTTCTCTTGTGTTA 57.175 36.000 0.00 0.00 0.00 2.41
1299 1321 7.653647 TCTTCTTCTCTCTTCTCTTGTGTTAC 58.346 38.462 0.00 0.00 0.00 2.50
1302 1324 8.330466 TCTTCTCTCTTCTCTTGTGTTACTAG 57.670 38.462 0.00 0.00 0.00 2.57
1303 1325 8.158132 TCTTCTCTCTTCTCTTGTGTTACTAGA 58.842 37.037 0.00 0.00 0.00 2.43
1304 1326 7.675962 TCTCTCTTCTCTTGTGTTACTAGAC 57.324 40.000 0.00 0.00 0.00 2.59
1305 1327 7.455058 TCTCTCTTCTCTTGTGTTACTAGACT 58.545 38.462 0.00 0.00 0.00 3.24
1309 1331 8.550710 TCTTCTCTTGTGTTACTAGACTAGAC 57.449 38.462 16.55 5.52 29.19 2.59
1310 1332 8.377034 TCTTCTCTTGTGTTACTAGACTAGACT 58.623 37.037 16.55 0.00 29.19 3.24
1311 1333 9.656040 CTTCTCTTGTGTTACTAGACTAGACTA 57.344 37.037 16.55 0.00 29.19 2.59
1313 1335 9.033711 TCTCTTGTGTTACTAGACTAGACTAGA 57.966 37.037 28.46 12.83 41.42 2.43
1314 1336 9.090692 CTCTTGTGTTACTAGACTAGACTAGAC 57.909 40.741 28.46 19.54 41.42 2.59
1315 1337 8.814931 TCTTGTGTTACTAGACTAGACTAGACT 58.185 37.037 28.46 16.71 41.42 3.24
1318 1340 9.473007 TGTGTTACTAGACTAGACTAGACTAGA 57.527 37.037 35.34 23.68 46.78 2.43
1321 1343 9.918630 GTTACTAGACTAGACTAGACTAGATGG 57.081 40.741 35.34 21.11 46.78 3.51
1322 1344 9.880254 TTACTAGACTAGACTAGACTAGATGGA 57.120 37.037 35.34 22.39 46.78 3.41
1323 1345 8.786710 ACTAGACTAGACTAGACTAGATGGAA 57.213 38.462 35.34 13.76 46.78 3.53
1324 1346 8.867097 ACTAGACTAGACTAGACTAGATGGAAG 58.133 40.741 35.34 21.23 46.78 3.46
1325 1347 7.924358 AGACTAGACTAGACTAGATGGAAGA 57.076 40.000 28.46 0.00 41.42 2.87
1326 1348 7.963532 AGACTAGACTAGACTAGATGGAAGAG 58.036 42.308 28.46 8.35 41.42 2.85
1327 1349 7.787904 AGACTAGACTAGACTAGATGGAAGAGA 59.212 40.741 28.46 0.00 41.42 3.10
1328 1350 7.963532 ACTAGACTAGACTAGATGGAAGAGAG 58.036 42.308 28.46 7.29 41.42 3.20
1332 1354 4.178956 AGACTAGATGGAAGAGAGGGAC 57.821 50.000 0.00 0.00 0.00 4.46
1361 1383 3.725010 CGATCGATCATTCTGCATGCATG 60.725 47.826 22.97 22.70 32.13 4.06
1419 1441 0.758123 GGGATCCAGCAGAGGAAGAG 59.242 60.000 15.23 0.00 41.92 2.85
1767 1789 2.675242 CCTCCAACCCGCCCATGTA 61.675 63.158 0.00 0.00 0.00 2.29
1909 1931 0.520404 TGCAGAACGAGTACGACTCC 59.480 55.000 8.73 0.00 42.12 3.85
1947 1969 0.248843 CAGTGCCTCTCCTTCCTCAC 59.751 60.000 0.00 0.00 0.00 3.51
2405 2427 3.716195 CCCCCAGCGTCATCACCA 61.716 66.667 0.00 0.00 0.00 4.17
2510 2532 2.421399 GCCGCCGGGTAAGACTACT 61.421 63.158 4.77 0.00 34.97 2.57
2511 2533 1.103398 GCCGCCGGGTAAGACTACTA 61.103 60.000 4.77 0.00 34.97 1.82
2529 2565 9.877178 AGACTACTAACTAATTTCATGGAACTG 57.123 33.333 0.00 0.00 0.00 3.16
2575 2611 1.676529 TCATCGATCGGGTCTGTCTTC 59.323 52.381 16.41 0.00 0.00 2.87
2576 2612 1.678627 CATCGATCGGGTCTGTCTTCT 59.321 52.381 16.41 0.00 0.00 2.85
2585 2621 0.244178 GTCTGTCTTCTGACCGGACC 59.756 60.000 9.46 0.00 42.28 4.46
2627 2675 3.731886 ATGGGACCGGGGCTATGGT 62.732 63.158 6.32 0.00 42.42 3.55
2913 2961 1.602377 GCCCTACACCATCGCATAAAC 59.398 52.381 0.00 0.00 0.00 2.01
2914 2962 2.218603 CCCTACACCATCGCATAAACC 58.781 52.381 0.00 0.00 0.00 3.27
3112 3164 8.774586 CACTCTCTCTTTTCGAGGAAAATAAAA 58.225 33.333 4.20 0.00 40.14 1.52
3113 3165 8.775527 ACTCTCTCTTTTCGAGGAAAATAAAAC 58.224 33.333 4.20 0.00 40.14 2.43
3331 3385 4.141620 TGGGCAAATTGGTTATTGTGTGTT 60.142 37.500 0.00 0.00 0.00 3.32
3340 3394 9.796120 AATTGGTTATTGTGTGTTTATAATCCG 57.204 29.630 0.00 0.00 0.00 4.18
3350 3404 9.430623 TGTGTGTTTATAATCCGATACCATATG 57.569 33.333 0.00 0.00 0.00 1.78
3411 3465 6.525629 TCTTCTGTTTTCTCTAACTTCCCTG 58.474 40.000 0.00 0.00 0.00 4.45
3421 3478 5.480772 TCTCTAACTTCCCTGTGGAACTTAG 59.519 44.000 11.45 11.45 45.88 2.18
3534 3591 9.575783 AAAAGCGAAAGAAAACACTAACATAAA 57.424 25.926 0.00 0.00 0.00 1.40
3582 3649 6.905736 TCATAAACCTCAATAAGTATGGCCA 58.094 36.000 8.56 8.56 0.00 5.36
3617 3684 5.594317 ACTTGTAAGCCACAAACTTTCTGAT 59.406 36.000 3.37 0.00 46.37 2.90
3639 3706 3.112205 ATGGACTCCATGGCCTCGC 62.112 63.158 9.99 0.00 46.68 5.03
3652 3719 0.603975 GCCTCGCCTGACAAGACTTT 60.604 55.000 0.00 0.00 0.00 2.66
3673 3740 1.754226 GGCACAACAGGAAAAGAACCA 59.246 47.619 0.00 0.00 0.00 3.67
3679 3746 6.151144 GCACAACAGGAAAAGAACCATAGTAT 59.849 38.462 0.00 0.00 0.00 2.12
3680 3747 7.335924 GCACAACAGGAAAAGAACCATAGTATA 59.664 37.037 0.00 0.00 0.00 1.47
3681 3748 9.396022 CACAACAGGAAAAGAACCATAGTATAT 57.604 33.333 0.00 0.00 0.00 0.86
3682 3749 9.975218 ACAACAGGAAAAGAACCATAGTATATT 57.025 29.630 0.00 0.00 0.00 1.28
3706 3773 0.886490 CTTGCTGACACCACACCCTC 60.886 60.000 0.00 0.00 0.00 4.30
3707 3774 1.344953 TTGCTGACACCACACCCTCT 61.345 55.000 0.00 0.00 0.00 3.69
3715 3782 1.136329 ACCACACCCTCTGCCAGAAT 61.136 55.000 0.00 0.00 0.00 2.40
3721 3788 0.609957 CCCTCTGCCAGAATGTTGCA 60.610 55.000 0.00 0.00 32.44 4.08
3728 3795 2.490509 TGCCAGAATGTTGCAGATGAAG 59.509 45.455 0.00 0.00 29.90 3.02
3730 3797 3.427233 GCCAGAATGTTGCAGATGAAGAC 60.427 47.826 0.00 0.00 0.00 3.01
3731 3798 4.008330 CCAGAATGTTGCAGATGAAGACT 58.992 43.478 0.00 0.00 0.00 3.24
3741 3808 3.118482 GCAGATGAAGACTGAAGGGATCA 60.118 47.826 0.00 0.00 37.54 2.92
3745 3812 2.029020 TGAAGACTGAAGGGATCACACG 60.029 50.000 0.00 0.00 33.47 4.49
3746 3813 0.247736 AGACTGAAGGGATCACACGC 59.752 55.000 0.00 0.00 33.47 5.34
3760 3827 5.625311 GGATCACACGCTAAAAACTTTTGAG 59.375 40.000 0.00 0.00 0.00 3.02
3764 3831 5.797934 CACACGCTAAAAACTTTTGAGAACA 59.202 36.000 3.05 0.00 0.00 3.18
3769 3836 8.068380 ACGCTAAAAACTTTTGAGAACATCTAC 58.932 33.333 3.05 0.00 0.00 2.59
3820 3887 1.517832 GACGATGTGAGGTGAGGGG 59.482 63.158 0.00 0.00 0.00 4.79
3821 3888 0.970937 GACGATGTGAGGTGAGGGGA 60.971 60.000 0.00 0.00 0.00 4.81
3823 3890 0.108138 CGATGTGAGGTGAGGGGAAC 60.108 60.000 0.00 0.00 0.00 3.62
3826 3893 1.127567 TGTGAGGTGAGGGGAACTGG 61.128 60.000 0.00 0.00 0.00 4.00
3827 3894 2.224159 TGAGGTGAGGGGAACTGGC 61.224 63.158 0.00 0.00 0.00 4.85
3828 3895 3.316573 GAGGTGAGGGGAACTGGCG 62.317 68.421 0.00 0.00 0.00 5.69
3830 3897 2.747686 GTGAGGGGAACTGGCGAA 59.252 61.111 0.00 0.00 0.00 4.70
3831 3898 1.072505 GTGAGGGGAACTGGCGAAA 59.927 57.895 0.00 0.00 0.00 3.46
3833 3900 0.183971 TGAGGGGAACTGGCGAAAAA 59.816 50.000 0.00 0.00 0.00 1.94
3834 3901 0.596577 GAGGGGAACTGGCGAAAAAC 59.403 55.000 0.00 0.00 0.00 2.43
3835 3902 0.106419 AGGGGAACTGGCGAAAAACA 60.106 50.000 0.00 0.00 0.00 2.83
3836 3903 0.966179 GGGGAACTGGCGAAAAACAT 59.034 50.000 0.00 0.00 0.00 2.71
3837 3904 1.343142 GGGGAACTGGCGAAAAACATT 59.657 47.619 0.00 0.00 0.00 2.71
3838 3905 2.224185 GGGGAACTGGCGAAAAACATTT 60.224 45.455 0.00 0.00 0.00 2.32
3841 3908 4.260579 GGGAACTGGCGAAAAACATTTTTG 60.261 41.667 7.05 2.03 40.21 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.978164 CCCCCTCATCCCTCTCAC 58.022 66.667 0.00 0.00 0.00 3.51
35 36 3.018149 AGAGAGTACTACAAGGCCGAAG 58.982 50.000 0.00 0.00 0.00 3.79
36 37 3.015327 GAGAGAGTACTACAAGGCCGAA 58.985 50.000 0.00 0.00 0.00 4.30
37 38 2.641305 GAGAGAGTACTACAAGGCCGA 58.359 52.381 0.00 0.00 0.00 5.54
38 39 1.677052 GGAGAGAGTACTACAAGGCCG 59.323 57.143 0.00 0.00 0.00 6.13
39 40 1.677052 CGGAGAGAGTACTACAAGGCC 59.323 57.143 0.00 0.00 0.00 5.19
40 41 2.355444 GACGGAGAGAGTACTACAAGGC 59.645 54.545 0.00 0.00 0.00 4.35
41 42 2.944349 GGACGGAGAGAGTACTACAAGG 59.056 54.545 0.00 0.00 0.00 3.61
42 43 2.944349 GGGACGGAGAGAGTACTACAAG 59.056 54.545 0.00 0.00 0.00 3.16
43 44 2.306805 TGGGACGGAGAGAGTACTACAA 59.693 50.000 0.00 0.00 0.00 2.41
44 45 1.911357 TGGGACGGAGAGAGTACTACA 59.089 52.381 0.00 0.00 0.00 2.74
45 46 2.706339 TGGGACGGAGAGAGTACTAC 57.294 55.000 0.00 0.00 0.00 2.73
46 47 3.726557 TTTGGGACGGAGAGAGTACTA 57.273 47.619 0.00 0.00 0.00 1.82
47 48 2.599408 TTTGGGACGGAGAGAGTACT 57.401 50.000 0.00 0.00 0.00 2.73
48 49 3.889520 ATTTTGGGACGGAGAGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
49 50 3.055385 CCAATTTTGGGACGGAGAGAGTA 60.055 47.826 1.14 0.00 44.70 2.59
50 51 2.290323 CCAATTTTGGGACGGAGAGAGT 60.290 50.000 1.14 0.00 44.70 3.24
51 52 2.359900 CCAATTTTGGGACGGAGAGAG 58.640 52.381 1.14 0.00 44.70 3.20
52 53 2.489938 CCAATTTTGGGACGGAGAGA 57.510 50.000 1.14 0.00 44.70 3.10
63 64 8.048534 ACACTCAGATTCATAGACCAATTTTG 57.951 34.615 0.00 0.00 0.00 2.44
64 65 9.739276 TTACACTCAGATTCATAGACCAATTTT 57.261 29.630 0.00 0.00 0.00 1.82
65 66 9.167311 GTTACACTCAGATTCATAGACCAATTT 57.833 33.333 0.00 0.00 0.00 1.82
66 67 8.543774 AGTTACACTCAGATTCATAGACCAATT 58.456 33.333 0.00 0.00 0.00 2.32
67 68 8.083828 AGTTACACTCAGATTCATAGACCAAT 57.916 34.615 0.00 0.00 0.00 3.16
68 69 7.482169 AGTTACACTCAGATTCATAGACCAA 57.518 36.000 0.00 0.00 0.00 3.67
69 70 7.482169 AAGTTACACTCAGATTCATAGACCA 57.518 36.000 0.00 0.00 0.00 4.02
70 71 8.779354 AAAAGTTACACTCAGATTCATAGACC 57.221 34.615 0.00 0.00 0.00 3.85
89 90 9.537848 CAACGAACGCTAGAAATAATAAAAGTT 57.462 29.630 0.00 0.00 0.00 2.66
90 91 8.715088 ACAACGAACGCTAGAAATAATAAAAGT 58.285 29.630 0.00 0.00 0.00 2.66
92 93 9.956797 GTACAACGAACGCTAGAAATAATAAAA 57.043 29.630 0.00 0.00 0.00 1.52
93 94 9.357652 AGTACAACGAACGCTAGAAATAATAAA 57.642 29.630 0.00 0.00 0.00 1.40
94 95 8.915871 AGTACAACGAACGCTAGAAATAATAA 57.084 30.769 0.00 0.00 0.00 1.40
96 97 9.178427 GATAGTACAACGAACGCTAGAAATAAT 57.822 33.333 0.00 0.00 0.00 1.28
97 98 8.183536 TGATAGTACAACGAACGCTAGAAATAA 58.816 33.333 0.00 0.00 0.00 1.40
98 99 7.696755 TGATAGTACAACGAACGCTAGAAATA 58.303 34.615 0.00 0.00 0.00 1.40
99 100 6.558009 TGATAGTACAACGAACGCTAGAAAT 58.442 36.000 0.00 0.00 0.00 2.17
100 101 5.941733 TGATAGTACAACGAACGCTAGAAA 58.058 37.500 0.00 0.00 0.00 2.52
101 102 5.550232 TGATAGTACAACGAACGCTAGAA 57.450 39.130 0.00 0.00 0.00 2.10
102 103 5.295045 TCATGATAGTACAACGAACGCTAGA 59.705 40.000 0.00 0.00 0.00 2.43
103 104 5.507974 TCATGATAGTACAACGAACGCTAG 58.492 41.667 0.00 0.00 0.00 3.42
104 105 5.488645 TCATGATAGTACAACGAACGCTA 57.511 39.130 0.00 0.00 0.00 4.26
105 106 4.365899 TCATGATAGTACAACGAACGCT 57.634 40.909 0.00 0.00 0.00 5.07
106 107 5.231357 TCAATCATGATAGTACAACGAACGC 59.769 40.000 9.04 0.00 0.00 4.84
107 108 6.806120 TCAATCATGATAGTACAACGAACG 57.194 37.500 9.04 0.00 0.00 3.95
108 109 8.407457 TCTTCAATCATGATAGTACAACGAAC 57.593 34.615 9.04 0.00 34.96 3.95
109 110 9.034544 CATCTTCAATCATGATAGTACAACGAA 57.965 33.333 9.04 2.03 34.96 3.85
110 111 8.413229 TCATCTTCAATCATGATAGTACAACGA 58.587 33.333 9.04 0.00 34.96 3.85
111 112 8.579682 TCATCTTCAATCATGATAGTACAACG 57.420 34.615 9.04 0.00 34.96 4.10
120 121 9.939802 TTCGATCTATTCATCTTCAATCATGAT 57.060 29.630 1.18 1.18 34.96 2.45
121 122 9.939802 ATTCGATCTATTCATCTTCAATCATGA 57.060 29.630 0.00 0.00 0.00 3.07
130 131 9.144747 CGGAACAATATTCGATCTATTCATCTT 57.855 33.333 0.00 0.00 0.00 2.40
131 132 8.307483 ACGGAACAATATTCGATCTATTCATCT 58.693 33.333 1.72 0.00 0.00 2.90
132 133 8.467402 ACGGAACAATATTCGATCTATTCATC 57.533 34.615 1.72 0.00 0.00 2.92
133 134 9.923143 TTACGGAACAATATTCGATCTATTCAT 57.077 29.630 1.72 0.00 0.00 2.57
134 135 9.406828 CTTACGGAACAATATTCGATCTATTCA 57.593 33.333 1.72 0.00 0.00 2.57
135 136 9.622004 TCTTACGGAACAATATTCGATCTATTC 57.378 33.333 1.72 0.00 0.00 1.75
136 137 9.976511 TTCTTACGGAACAATATTCGATCTATT 57.023 29.630 1.72 0.00 0.00 1.73
137 138 9.976511 TTTCTTACGGAACAATATTCGATCTAT 57.023 29.630 1.72 0.00 33.13 1.98
138 139 9.806203 TTTTCTTACGGAACAATATTCGATCTA 57.194 29.630 1.72 0.00 33.13 1.98
139 140 8.712285 TTTTCTTACGGAACAATATTCGATCT 57.288 30.769 1.72 0.00 33.13 2.75
140 141 8.814235 TCTTTTCTTACGGAACAATATTCGATC 58.186 33.333 1.72 0.00 33.13 3.69
141 142 8.712285 TCTTTTCTTACGGAACAATATTCGAT 57.288 30.769 1.72 0.00 33.13 3.59
142 143 8.537049 TTCTTTTCTTACGGAACAATATTCGA 57.463 30.769 1.72 0.00 33.13 3.71
148 149 9.010029 ACATGTATTCTTTTCTTACGGAACAAT 57.990 29.630 0.00 0.00 33.13 2.71
149 150 8.385898 ACATGTATTCTTTTCTTACGGAACAA 57.614 30.769 0.00 0.00 33.13 2.83
150 151 7.972832 ACATGTATTCTTTTCTTACGGAACA 57.027 32.000 0.00 0.00 33.13 3.18
171 172 9.844790 CGCCAATCATATCATGTATTTTTACAT 57.155 29.630 0.00 0.00 40.99 2.29
172 173 9.061435 TCGCCAATCATATCATGTATTTTTACA 57.939 29.630 0.00 0.00 0.00 2.41
173 174 9.546909 CTCGCCAATCATATCATGTATTTTTAC 57.453 33.333 0.00 0.00 0.00 2.01
174 175 9.500785 TCTCGCCAATCATATCATGTATTTTTA 57.499 29.630 0.00 0.00 0.00 1.52
175 176 8.394971 TCTCGCCAATCATATCATGTATTTTT 57.605 30.769 0.00 0.00 0.00 1.94
176 177 7.984422 TCTCGCCAATCATATCATGTATTTT 57.016 32.000 0.00 0.00 0.00 1.82
177 178 7.984422 TTCTCGCCAATCATATCATGTATTT 57.016 32.000 0.00 0.00 0.00 1.40
178 179 9.102757 GTATTCTCGCCAATCATATCATGTATT 57.897 33.333 0.00 0.00 0.00 1.89
179 180 7.436376 CGTATTCTCGCCAATCATATCATGTAT 59.564 37.037 0.00 0.00 0.00 2.29
180 181 6.751888 CGTATTCTCGCCAATCATATCATGTA 59.248 38.462 0.00 0.00 0.00 2.29
181 182 5.578336 CGTATTCTCGCCAATCATATCATGT 59.422 40.000 0.00 0.00 0.00 3.21
182 183 5.578336 ACGTATTCTCGCCAATCATATCATG 59.422 40.000 0.00 0.00 0.00 3.07
183 184 5.578336 CACGTATTCTCGCCAATCATATCAT 59.422 40.000 0.00 0.00 0.00 2.45
184 185 4.923281 CACGTATTCTCGCCAATCATATCA 59.077 41.667 0.00 0.00 0.00 2.15
185 186 5.161358 TCACGTATTCTCGCCAATCATATC 58.839 41.667 0.00 0.00 0.00 1.63
186 187 5.134202 TCACGTATTCTCGCCAATCATAT 57.866 39.130 0.00 0.00 0.00 1.78
187 188 4.577834 TCACGTATTCTCGCCAATCATA 57.422 40.909 0.00 0.00 0.00 2.15
188 189 3.452755 TCACGTATTCTCGCCAATCAT 57.547 42.857 0.00 0.00 0.00 2.45
189 190 2.951457 TCACGTATTCTCGCCAATCA 57.049 45.000 0.00 0.00 0.00 2.57
190 191 5.900339 TTTATCACGTATTCTCGCCAATC 57.100 39.130 0.00 0.00 0.00 2.67
191 192 6.671614 TTTTTATCACGTATTCTCGCCAAT 57.328 33.333 0.00 0.00 0.00 3.16
192 193 6.314152 TGATTTTTATCACGTATTCTCGCCAA 59.686 34.615 0.00 0.00 0.00 4.52
193 194 5.813157 TGATTTTTATCACGTATTCTCGCCA 59.187 36.000 0.00 0.00 0.00 5.69
194 195 6.200286 TCTGATTTTTATCACGTATTCTCGCC 59.800 38.462 0.00 0.00 0.00 5.54
195 196 7.161829 TCTGATTTTTATCACGTATTCTCGC 57.838 36.000 0.00 0.00 0.00 5.03
214 215 9.095065 GGTTGTTTCTACGTGTTATTATCTGAT 57.905 33.333 0.00 0.00 0.00 2.90
215 216 8.308931 AGGTTGTTTCTACGTGTTATTATCTGA 58.691 33.333 0.00 0.00 0.00 3.27
216 217 8.475331 AGGTTGTTTCTACGTGTTATTATCTG 57.525 34.615 0.00 0.00 0.00 2.90
217 218 7.763071 GGAGGTTGTTTCTACGTGTTATTATCT 59.237 37.037 0.00 0.00 0.00 1.98
218 219 7.010830 GGGAGGTTGTTTCTACGTGTTATTATC 59.989 40.741 0.00 0.00 0.00 1.75
219 220 6.820152 GGGAGGTTGTTTCTACGTGTTATTAT 59.180 38.462 0.00 0.00 0.00 1.28
220 221 6.165577 GGGAGGTTGTTTCTACGTGTTATTA 58.834 40.000 0.00 0.00 0.00 0.98
221 222 4.999311 GGGAGGTTGTTTCTACGTGTTATT 59.001 41.667 0.00 0.00 0.00 1.40
222 223 4.040706 TGGGAGGTTGTTTCTACGTGTTAT 59.959 41.667 0.00 0.00 0.00 1.89
223 224 3.387374 TGGGAGGTTGTTTCTACGTGTTA 59.613 43.478 0.00 0.00 0.00 2.41
224 225 2.171027 TGGGAGGTTGTTTCTACGTGTT 59.829 45.455 0.00 0.00 0.00 3.32
225 226 1.764134 TGGGAGGTTGTTTCTACGTGT 59.236 47.619 0.00 0.00 0.00 4.49
226 227 2.536761 TGGGAGGTTGTTTCTACGTG 57.463 50.000 0.00 0.00 0.00 4.49
227 228 5.431179 AATATGGGAGGTTGTTTCTACGT 57.569 39.130 0.00 0.00 0.00 3.57
228 229 5.296035 GGAAATATGGGAGGTTGTTTCTACG 59.704 44.000 0.00 0.00 0.00 3.51
229 230 6.424032 AGGAAATATGGGAGGTTGTTTCTAC 58.576 40.000 0.00 0.00 0.00 2.59
230 231 6.652205 AGGAAATATGGGAGGTTGTTTCTA 57.348 37.500 0.00 0.00 0.00 2.10
231 232 5.536497 AGGAAATATGGGAGGTTGTTTCT 57.464 39.130 0.00 0.00 0.00 2.52
232 233 6.210584 TCAAAGGAAATATGGGAGGTTGTTTC 59.789 38.462 0.00 0.00 0.00 2.78
233 234 6.081356 TCAAAGGAAATATGGGAGGTTGTTT 58.919 36.000 0.00 0.00 0.00 2.83
234 235 5.650283 TCAAAGGAAATATGGGAGGTTGTT 58.350 37.500 0.00 0.00 0.00 2.83
235 236 5.269554 TCAAAGGAAATATGGGAGGTTGT 57.730 39.130 0.00 0.00 0.00 3.32
236 237 7.516198 CTATCAAAGGAAATATGGGAGGTTG 57.484 40.000 0.00 0.00 0.00 3.77
252 253 9.103861 GTTTTACTGGATCTTCTCCTATCAAAG 57.896 37.037 0.00 0.00 45.21 2.77
253 254 8.826765 AGTTTTACTGGATCTTCTCCTATCAAA 58.173 33.333 0.00 0.00 45.21 2.69
254 255 8.260818 CAGTTTTACTGGATCTTCTCCTATCAA 58.739 37.037 0.00 0.00 45.21 2.57
300 301 2.034339 GCAATTGACGCAAAGCATATGC 60.034 45.455 20.36 20.36 40.41 3.14
301 302 2.536803 GGCAATTGACGCAAAGCATATG 59.463 45.455 10.34 0.00 32.67 1.78
302 303 2.166050 TGGCAATTGACGCAAAGCATAT 59.834 40.909 10.34 0.00 32.67 1.78
303 304 1.543358 TGGCAATTGACGCAAAGCATA 59.457 42.857 10.34 0.00 32.67 3.14
304 305 0.317799 TGGCAATTGACGCAAAGCAT 59.682 45.000 10.34 0.00 32.67 3.79
305 306 0.597118 GTGGCAATTGACGCAAAGCA 60.597 50.000 20.05 0.00 32.67 3.91
306 307 1.284297 GGTGGCAATTGACGCAAAGC 61.284 55.000 25.54 4.97 34.61 3.51
307 308 0.031857 TGGTGGCAATTGACGCAAAG 59.968 50.000 25.54 0.00 34.61 2.77
308 309 0.249238 GTGGTGGCAATTGACGCAAA 60.249 50.000 25.54 11.02 34.61 3.68
317 318 1.002134 CTCTTCGGGTGGTGGCAAT 60.002 57.895 0.00 0.00 0.00 3.56
329 331 0.828677 ATTACCCCGAACCCTCTTCG 59.171 55.000 0.00 0.00 41.21 3.79
355 357 4.057432 CAGTTGGTTAAGGGCAACATTTG 58.943 43.478 0.00 0.00 37.19 2.32
361 363 3.517296 TCATCAGTTGGTTAAGGGCAA 57.483 42.857 0.00 0.00 0.00 4.52
362 364 3.737559 ATCATCAGTTGGTTAAGGGCA 57.262 42.857 0.00 0.00 0.00 5.36
413 420 1.810959 CCGGGGATCGTGTTACAAAA 58.189 50.000 0.00 0.00 37.11 2.44
414 421 0.674269 GCCGGGGATCGTGTTACAAA 60.674 55.000 2.18 0.00 37.11 2.83
429 436 3.583276 TTGTCAGCTGTACGGCCGG 62.583 63.158 31.76 15.55 0.00 6.13
430 437 1.225376 TTTTGTCAGCTGTACGGCCG 61.225 55.000 26.86 26.86 0.00 6.13
431 438 0.948678 TTTTTGTCAGCTGTACGGCC 59.051 50.000 23.09 8.71 0.00 6.13
432 439 2.584791 CATTTTTGTCAGCTGTACGGC 58.415 47.619 19.39 19.39 0.00 5.68
461 469 3.454447 TCAGGATCACATTGTACGGGAAT 59.546 43.478 0.00 0.00 0.00 3.01
505 513 2.024414 GGTCCATCCCAACAATACTGC 58.976 52.381 0.00 0.00 0.00 4.40
631 645 0.389948 CCGGTGACAGCCAAGTACTC 60.390 60.000 0.00 0.00 0.00 2.59
632 646 1.671742 CCGGTGACAGCCAAGTACT 59.328 57.895 0.00 0.00 0.00 2.73
633 647 2.033194 GCCGGTGACAGCCAAGTAC 61.033 63.158 1.90 0.00 0.00 2.73
634 648 2.345991 GCCGGTGACAGCCAAGTA 59.654 61.111 1.90 0.00 0.00 2.24
650 664 4.194720 ATCGCTCGGTGTCTCGGC 62.195 66.667 0.00 0.00 0.00 5.54
663 677 2.885676 CGTACTGCCATGCCATCGC 61.886 63.158 0.00 0.00 0.00 4.58
700 714 2.318966 TTCCTCCATGCATGCCCCT 61.319 57.895 21.69 0.00 0.00 4.79
702 716 1.380246 TGTTCCTCCATGCATGCCC 60.380 57.895 21.69 5.06 0.00 5.36
796 810 1.285950 GGTTGGTTTCTTCCAGCGC 59.714 57.895 0.00 0.00 39.14 5.92
834 848 0.949105 CCCGCGGCTTATATGTGTCC 60.949 60.000 22.85 0.00 0.00 4.02
960 974 1.226974 CCTCCTGCGTGTACGGATG 60.227 63.158 6.55 0.74 39.39 3.51
971 987 3.535962 CTCTCCGGCTCCTCCTGC 61.536 72.222 0.00 0.00 0.00 4.85
1203 1225 4.800784 TGAAGACGTTGACGATGATGTTA 58.199 39.130 10.87 0.00 43.02 2.41
1231 1253 4.200283 GAGGAGCGGCTGGTCGAG 62.200 72.222 18.07 0.00 43.60 4.04
1285 1307 8.556213 AGTCTAGTCTAGTAACACAAGAGAAG 57.444 38.462 6.77 0.00 0.00 2.85
1298 1320 8.786710 TTCCATCTAGTCTAGTCTAGTCTAGT 57.213 38.462 26.77 17.67 41.87 2.57
1299 1321 9.085645 TCTTCCATCTAGTCTAGTCTAGTCTAG 57.914 40.741 24.27 24.27 42.26 2.43
1302 1324 7.959175 TCTCTTCCATCTAGTCTAGTCTAGTC 58.041 42.308 19.35 1.51 38.66 2.59
1303 1325 7.016268 CCTCTCTTCCATCTAGTCTAGTCTAGT 59.984 44.444 19.35 8.06 38.66 2.57
1304 1326 7.386851 CCTCTCTTCCATCTAGTCTAGTCTAG 58.613 46.154 15.49 15.49 38.83 2.43
1305 1327 6.271391 CCCTCTCTTCCATCTAGTCTAGTCTA 59.729 46.154 6.77 0.00 0.00 2.59
1309 1331 5.313712 GTCCCTCTCTTCCATCTAGTCTAG 58.686 50.000 0.00 0.00 0.00 2.43
1310 1332 4.105057 GGTCCCTCTCTTCCATCTAGTCTA 59.895 50.000 0.00 0.00 0.00 2.59
1311 1333 3.117284 GGTCCCTCTCTTCCATCTAGTCT 60.117 52.174 0.00 0.00 0.00 3.24
1313 1335 2.423660 CGGTCCCTCTCTTCCATCTAGT 60.424 54.545 0.00 0.00 0.00 2.57
1314 1336 2.235016 CGGTCCCTCTCTTCCATCTAG 58.765 57.143 0.00 0.00 0.00 2.43
1315 1337 1.569548 ACGGTCCCTCTCTTCCATCTA 59.430 52.381 0.00 0.00 0.00 1.98
1316 1338 0.336737 ACGGTCCCTCTCTTCCATCT 59.663 55.000 0.00 0.00 0.00 2.90
1318 1340 2.599677 GATACGGTCCCTCTCTTCCAT 58.400 52.381 0.00 0.00 0.00 3.41
1319 1341 1.411216 GGATACGGTCCCTCTCTTCCA 60.411 57.143 0.00 0.00 41.50 3.53
1947 1969 3.365265 GCTTCTGGTTGGCGGTGG 61.365 66.667 0.00 0.00 0.00 4.61
2032 2054 1.122632 TGTTGGACCCCTTGTAGCGA 61.123 55.000 0.00 0.00 0.00 4.93
2405 2427 4.065281 GTAGGTGCGGTGCTCGGT 62.065 66.667 2.61 0.00 39.69 4.69
2510 2532 7.829211 AGCTTAGCAGTTCCATGAAATTAGTTA 59.171 33.333 7.07 0.00 0.00 2.24
2511 2533 6.660949 AGCTTAGCAGTTCCATGAAATTAGTT 59.339 34.615 7.07 0.00 0.00 2.24
2549 2585 1.547820 AGACCCGATCGATGATCCATG 59.452 52.381 18.66 0.00 35.83 3.66
2550 2586 1.547820 CAGACCCGATCGATGATCCAT 59.452 52.381 18.66 0.00 35.83 3.41
2575 2611 1.146930 CCATCCATGGTCCGGTCAG 59.853 63.158 12.58 0.00 43.05 3.51
2576 2612 3.319274 CCATCCATGGTCCGGTCA 58.681 61.111 12.58 1.41 43.05 4.02
2585 2621 2.100197 GCATCCATCCATCCATCCATG 58.900 52.381 0.00 0.00 0.00 3.66
2627 2675 1.076727 TCTTCCTGCTCTCCACCGA 59.923 57.895 0.00 0.00 0.00 4.69
2680 2728 0.976073 ACCTCGGGTACACCTGGATG 60.976 60.000 0.00 0.00 42.72 3.51
2782 2830 2.789813 GCTCACGTATAGCTGCTCG 58.210 57.895 4.91 6.55 37.01 5.03
2791 2839 1.139734 CGAGGTGCAGCTCACGTAT 59.860 57.895 37.01 8.97 46.56 3.06
2913 2961 3.086600 GGAGCTGGGGGAGAGTGG 61.087 72.222 0.00 0.00 0.00 4.00
2914 2962 1.277580 AATGGAGCTGGGGGAGAGTG 61.278 60.000 0.00 0.00 0.00 3.51
3066 3118 3.002759 GTGAACCTGACAAGAAGAACAGC 59.997 47.826 0.00 0.00 0.00 4.40
3154 3207 0.530744 CCTCCTCGTTCCGATGACAA 59.469 55.000 0.00 0.00 34.61 3.18
3167 3220 5.678583 TGTTCTGAAATCATCATCCTCCTC 58.321 41.667 0.00 0.00 37.44 3.71
3168 3221 5.705397 TGTTCTGAAATCATCATCCTCCT 57.295 39.130 0.00 0.00 37.44 3.69
3169 3222 6.118170 TCTTGTTCTGAAATCATCATCCTCC 58.882 40.000 0.00 0.00 37.44 4.30
3340 3394 6.199154 GCGCTCATGTACATACATATGGTATC 59.801 42.308 8.32 0.00 44.57 2.24
3345 3399 4.091945 GGTGCGCTCATGTACATACATATG 59.908 45.833 8.32 0.00 44.57 1.78
3350 3404 2.225068 AGGTGCGCTCATGTACATAC 57.775 50.000 8.32 1.71 0.00 2.39
3353 3407 1.155889 CAAAGGTGCGCTCATGTACA 58.844 50.000 9.73 0.00 0.00 2.90
3411 3465 8.074370 GTGAACCAGATTTTAACTAAGTTCCAC 58.926 37.037 0.00 0.00 33.14 4.02
3421 3478 7.506328 AAGGTACAGTGAACCAGATTTTAAC 57.494 36.000 0.00 0.00 39.64 2.01
3528 3585 9.113838 GTTCATATGGTTCTGATGAGTTTATGT 57.886 33.333 2.13 0.00 31.50 2.29
3534 3591 5.598416 TCGTTCATATGGTTCTGATGAGT 57.402 39.130 2.13 0.00 31.50 3.41
3544 3601 7.279615 TGAGGTTTATGATTCGTTCATATGGT 58.720 34.615 2.13 0.13 44.77 3.55
3572 3639 2.373335 TGGTGTGTTTGGCCATACTT 57.627 45.000 24.26 0.00 0.00 2.24
3573 3640 2.364002 GTTTGGTGTGTTTGGCCATACT 59.636 45.455 24.26 0.00 33.47 2.12
3582 3649 3.511934 TGGCTTACAAGTTTGGTGTGTTT 59.488 39.130 0.00 0.00 0.00 2.83
3635 3702 1.151668 CCAAAGTCTTGTCAGGCGAG 58.848 55.000 0.00 0.00 0.00 5.03
3637 3704 1.165907 TGCCAAAGTCTTGTCAGGCG 61.166 55.000 11.62 0.00 44.83 5.52
3639 3706 1.679139 TGTGCCAAAGTCTTGTCAGG 58.321 50.000 0.00 0.00 0.00 3.86
3652 3719 1.754226 GGTTCTTTTCCTGTTGTGCCA 59.246 47.619 0.00 0.00 0.00 4.92
3679 3746 5.414454 GGTGTGGTGTCAGCAAGAATAAATA 59.586 40.000 6.24 0.00 36.09 1.40
3680 3747 4.218417 GGTGTGGTGTCAGCAAGAATAAAT 59.782 41.667 6.24 0.00 36.09 1.40
3681 3748 3.568007 GGTGTGGTGTCAGCAAGAATAAA 59.432 43.478 6.24 0.00 36.09 1.40
3682 3749 3.146066 GGTGTGGTGTCAGCAAGAATAA 58.854 45.455 6.24 0.00 36.09 1.40
3683 3750 2.552155 GGGTGTGGTGTCAGCAAGAATA 60.552 50.000 6.24 0.00 37.53 1.75
3684 3751 1.609208 GGTGTGGTGTCAGCAAGAAT 58.391 50.000 6.24 0.00 36.09 2.40
3685 3752 0.465460 GGGTGTGGTGTCAGCAAGAA 60.465 55.000 6.24 0.00 37.53 2.52
3686 3753 1.148273 GGGTGTGGTGTCAGCAAGA 59.852 57.895 6.24 0.00 37.53 3.02
3698 3765 0.037303 ACATTCTGGCAGAGGGTGTG 59.963 55.000 22.87 17.23 0.00 3.82
3699 3766 0.773644 AACATTCTGGCAGAGGGTGT 59.226 50.000 17.91 19.10 0.00 4.16
3707 3774 2.203470 TCATCTGCAACATTCTGGCA 57.797 45.000 0.00 0.00 35.96 4.92
3715 3782 3.405831 CCTTCAGTCTTCATCTGCAACA 58.594 45.455 0.00 0.00 33.48 3.33
3721 3788 4.081198 GTGTGATCCCTTCAGTCTTCATCT 60.081 45.833 0.00 0.00 34.17 2.90
3728 3795 0.247736 AGCGTGTGATCCCTTCAGTC 59.752 55.000 0.00 0.00 34.17 3.51
3730 3797 2.672961 TTAGCGTGTGATCCCTTCAG 57.327 50.000 0.00 0.00 34.17 3.02
3731 3798 3.410631 TTTTAGCGTGTGATCCCTTCA 57.589 42.857 0.00 0.00 0.00 3.02
3741 3808 5.945155 TGTTCTCAAAAGTTTTTAGCGTGT 58.055 33.333 0.00 0.00 0.00 4.49
3745 3812 8.280497 TCGTAGATGTTCTCAAAAGTTTTTAGC 58.720 33.333 0.00 0.00 0.00 3.09
3764 3831 5.053145 GGAGAATGTTGCATCTTCGTAGAT 58.947 41.667 0.00 0.00 41.89 1.98
3769 3836 3.063180 GTGAGGAGAATGTTGCATCTTCG 59.937 47.826 0.00 0.00 0.00 3.79
3807 3874 1.127567 CCAGTTCCCCTCACCTCACA 61.128 60.000 0.00 0.00 0.00 3.58
3809 3876 2.224159 GCCAGTTCCCCTCACCTCA 61.224 63.158 0.00 0.00 0.00 3.86
3820 3887 5.463499 ACAAAAATGTTTTTCGCCAGTTC 57.537 34.783 0.71 0.00 38.23 3.01
3821 3888 5.871465 AACAAAAATGTTTTTCGCCAGTT 57.129 30.435 0.71 0.61 38.23 3.16
3873 3940 7.503566 CCATAGTTGTGTCATTCCTATTTGGAT 59.496 37.037 0.00 0.00 45.68 3.41
3875 3942 6.603201 ACCATAGTTGTGTCATTCCTATTTGG 59.397 38.462 0.00 0.00 37.10 3.28
3877 3944 9.342308 CATACCATAGTTGTGTCATTCCTATTT 57.658 33.333 0.00 0.00 0.00 1.40
3886 3953 8.661352 CATTATGTCATACCATAGTTGTGTCA 57.339 34.615 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.