Multiple sequence alignment - TraesCS2A01G061500

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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 TraesCS2A01G061500 chr2A 100.000 5263 0 0 1 5263 27548793 27543531 0.000000e+00 9720.0
1 TraesCS2A01G061500 chr2A 83.277 2063 228 65 1470 3460 27550822 27552839 0.000000e+00 1790.0
2 TraesCS2A01G061500 chr2B 93.814 3039 107 23 1793 4774 40512538 40509524 0.000000e+00 4495.0
3 TraesCS2A01G061500 chr2B 88.875 791 40 20 657 1444 40513514 40512769 0.000000e+00 929.0
4 TraesCS2A01G061500 chr2B 90.000 70 5 2 406 474 40525743 40525675 7.260000e-14 89.8
5 TraesCS2A01G061500 chr2B 85.000 60 8 1 820 878 176181107 176181166 5.690000e-05 60.2
6 TraesCS2A01G061500 chr2D 94.575 1272 44 8 1002 2264 25048117 25046862 0.000000e+00 1943.0
7 TraesCS2A01G061500 chr2D 88.996 1245 85 14 2260 3460 25046723 25045487 0.000000e+00 1493.0
8 TraesCS2A01G061500 chr2D 84.988 806 87 24 1470 2268 25285877 25285099 0.000000e+00 787.0
9 TraesCS2A01G061500 chr2D 84.988 806 87 24 1470 2268 25292612 25291834 0.000000e+00 787.0
10 TraesCS2A01G061500 chr2D 84.882 807 88 23 1470 2268 25299499 25298719 0.000000e+00 784.0
11 TraesCS2A01G061500 chr2D 91.439 549 47 0 3835 4383 25044617 25044069 0.000000e+00 754.0
12 TraesCS2A01G061500 chr2D 85.793 725 68 21 1553 2268 25181084 25181782 0.000000e+00 736.0
13 TraesCS2A01G061500 chr2D 91.101 427 32 5 239 660 25049149 25048724 1.640000e-159 573.0
14 TraesCS2A01G061500 chr2D 93.333 195 10 1 4845 5036 25040238 25040044 8.630000e-73 285.0
15 TraesCS2A01G061500 chr2D 88.785 214 8 3 5050 5263 25039457 25039260 1.130000e-61 248.0
16 TraesCS2A01G061500 chr2D 91.791 134 6 5 657 788 25048541 25048411 1.160000e-41 182.0
17 TraesCS2A01G061500 chr2D 93.617 47 3 0 1470 1516 25181042 25181088 2.630000e-08 71.3
18 TraesCS2A01G061500 chrUn 85.025 808 86 22 1470 2268 24854335 24853554 0.000000e+00 789.0
19 TraesCS2A01G061500 chrUn 83.251 806 77 37 1470 2268 24847381 24846627 0.000000e+00 688.0
20 TraesCS2A01G061500 chr5B 83.784 111 10 4 849 959 511060594 511060696 1.210000e-16 99.0
21 TraesCS2A01G061500 chr1B 82.927 82 7 3 849 929 444177888 444177963 3.400000e-07 67.6


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 TraesCS2A01G061500 chr2A 27543531 27548793 5262 True 9720.000000 9720 100.000000 1 5263 1 chr2A.!!$R1 5262
1 TraesCS2A01G061500 chr2A 27550822 27552839 2017 False 1790.000000 1790 83.277000 1470 3460 1 chr2A.!!$F1 1990
2 TraesCS2A01G061500 chr2B 40509524 40513514 3990 True 2712.000000 4495 91.344500 657 4774 2 chr2B.!!$R2 4117
3 TraesCS2A01G061500 chr2D 25285099 25285877 778 True 787.000000 787 84.988000 1470 2268 1 chr2D.!!$R1 798
4 TraesCS2A01G061500 chr2D 25291834 25292612 778 True 787.000000 787 84.988000 1470 2268 1 chr2D.!!$R2 798
5 TraesCS2A01G061500 chr2D 25298719 25299499 780 True 784.000000 784 84.882000 1470 2268 1 chr2D.!!$R3 798
6 TraesCS2A01G061500 chr2D 25039260 25049149 9889 True 782.571429 1943 91.431429 239 5263 7 chr2D.!!$R4 5024
7 TraesCS2A01G061500 chr2D 25181042 25181782 740 False 403.650000 736 89.705000 1470 2268 2 chr2D.!!$F1 798
8 TraesCS2A01G061500 chrUn 24853554 24854335 781 True 789.000000 789 85.025000 1470 2268 1 chrUn.!!$R2 798
9 TraesCS2A01G061500 chrUn 24846627 24847381 754 True 688.000000 688 83.251000 1470 2268 1 chrUn.!!$R1 798

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
181 182 0.105039 CTAGGCGCCTGAAACCCTAG 59.895 60.0 38.98 21.33 40.52 3.02 F
1368 1650 0.034476 TTCTGACAGCCACTGCAGAG 59.966 55.0 23.35 13.32 41.55 3.35 F
2115 2414 0.389166 GAGGTGTGGAGCGTTCTCTG 60.389 60.0 0.00 0.00 39.31 3.35 F
3029 3498 0.179000 GCACCATCCTCGACCTTGAT 59.821 55.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1676 0.320858 TTGCCAATCTAACCGCGACA 60.321 50.000 8.23 0.0 0.00 4.35 R
3029 3498 1.202915 TGCTTCCCATCAGCACTGAAA 60.203 47.619 4.14 0.0 42.49 2.69 R
3799 4847 1.681264 CTTGTTCCCTGAAACACCCAC 59.319 52.381 0.00 0.0 38.80 4.61 R
4833 5902 0.175760 CGTCGATGGATGGGACTGTT 59.824 55.000 0.00 0.0 0.00 3.16 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
31 32 8.518430 ACATATTAATAAAGTGTGCATGACCA 57.482 30.769 0.00 0.00 0.00 4.02
32 33 8.405531 ACATATTAATAAAGTGTGCATGACCAC 58.594 33.333 0.00 1.53 36.28 4.16
33 34 5.637006 TTAATAAAGTGTGCATGACCACC 57.363 39.130 10.51 0.00 34.85 4.61
34 35 2.949177 TAAAGTGTGCATGACCACCT 57.051 45.000 10.51 3.25 34.85 4.00
35 36 1.609208 AAAGTGTGCATGACCACCTC 58.391 50.000 10.51 1.31 34.85 3.85
36 37 0.767375 AAGTGTGCATGACCACCTCT 59.233 50.000 10.51 3.18 34.85 3.69
37 38 0.767375 AGTGTGCATGACCACCTCTT 59.233 50.000 10.51 0.00 34.85 2.85
38 39 0.877071 GTGTGCATGACCACCTCTTG 59.123 55.000 0.00 0.00 34.85 3.02
39 40 0.473755 TGTGCATGACCACCTCTTGT 59.526 50.000 0.00 0.00 34.85 3.16
40 41 1.133823 TGTGCATGACCACCTCTTGTT 60.134 47.619 0.00 0.00 34.85 2.83
41 42 1.956477 GTGCATGACCACCTCTTGTTT 59.044 47.619 0.00 0.00 0.00 2.83
42 43 2.362077 GTGCATGACCACCTCTTGTTTT 59.638 45.455 0.00 0.00 0.00 2.43
43 44 3.030291 TGCATGACCACCTCTTGTTTTT 58.970 40.909 0.00 0.00 0.00 1.94
96 97 9.903682 GGTAGTTTTAACTTACAGGAAAAATCC 57.096 33.333 0.00 0.00 40.37 3.01
97 98 9.603298 GTAGTTTTAACTTACAGGAAAAATCCG 57.397 33.333 0.00 0.00 40.37 4.18
98 99 8.454570 AGTTTTAACTTACAGGAAAAATCCGA 57.545 30.769 0.00 0.00 35.21 4.55
99 100 8.905850 AGTTTTAACTTACAGGAAAAATCCGAA 58.094 29.630 0.00 0.00 35.21 4.30
100 101 9.687210 GTTTTAACTTACAGGAAAAATCCGAAT 57.313 29.630 0.00 0.00 34.28 3.34
125 126 7.895975 ATTATTTTTGAAGCAAAAGAGAGCC 57.104 32.000 5.60 0.00 42.91 4.70
126 127 4.734398 TTTTTGAAGCAAAAGAGAGCCA 57.266 36.364 5.60 0.00 42.91 4.75
127 128 4.942761 TTTTGAAGCAAAAGAGAGCCAT 57.057 36.364 1.51 0.00 38.24 4.40
128 129 4.942761 TTTGAAGCAAAAGAGAGCCATT 57.057 36.364 0.00 0.00 29.89 3.16
129 130 6.403866 TTTTGAAGCAAAAGAGAGCCATTA 57.596 33.333 1.51 0.00 38.24 1.90
130 131 5.633830 TTGAAGCAAAAGAGAGCCATTAG 57.366 39.130 0.00 0.00 0.00 1.73
131 132 4.012374 TGAAGCAAAAGAGAGCCATTAGG 58.988 43.478 0.00 0.00 38.23 2.69
132 133 8.456214 TTTGAAGCAAAAGAGAGCCATTAGGC 62.456 42.308 0.00 0.00 44.88 3.93
145 146 3.897239 CCATTAGGCAAGTCCCATAACA 58.103 45.455 0.00 0.00 34.51 2.41
146 147 4.277476 CCATTAGGCAAGTCCCATAACAA 58.723 43.478 0.00 0.00 34.51 2.83
147 148 4.709397 CCATTAGGCAAGTCCCATAACAAA 59.291 41.667 0.00 0.00 34.51 2.83
148 149 5.163519 CCATTAGGCAAGTCCCATAACAAAG 60.164 44.000 0.00 0.00 34.51 2.77
149 150 2.807676 AGGCAAGTCCCATAACAAAGG 58.192 47.619 0.00 0.00 34.51 3.11
150 151 2.378547 AGGCAAGTCCCATAACAAAGGA 59.621 45.455 0.00 0.00 34.51 3.36
151 152 2.755103 GGCAAGTCCCATAACAAAGGAG 59.245 50.000 0.00 0.00 0.00 3.69
152 153 3.561313 GGCAAGTCCCATAACAAAGGAGA 60.561 47.826 0.00 0.00 0.00 3.71
153 154 3.440522 GCAAGTCCCATAACAAAGGAGAC 59.559 47.826 0.00 0.00 0.00 3.36
154 155 4.010349 CAAGTCCCATAACAAAGGAGACC 58.990 47.826 0.00 0.00 0.00 3.85
155 156 3.532102 AGTCCCATAACAAAGGAGACCT 58.468 45.455 0.00 0.00 33.87 3.85
156 157 3.264450 AGTCCCATAACAAAGGAGACCTG 59.736 47.826 0.00 0.00 32.13 4.00
157 158 2.576191 TCCCATAACAAAGGAGACCTGG 59.424 50.000 0.00 0.00 32.13 4.45
158 159 2.357154 CCCATAACAAAGGAGACCTGGG 60.357 54.545 0.00 0.00 32.13 4.45
159 160 2.357154 CCATAACAAAGGAGACCTGGGG 60.357 54.545 0.00 0.00 32.13 4.96
160 161 1.368374 TAACAAAGGAGACCTGGGGG 58.632 55.000 0.00 0.00 32.13 5.40
174 175 3.081409 GGGGTCTAGGCGCCTGAA 61.081 66.667 38.98 23.30 38.31 3.02
175 176 2.666098 GGGGTCTAGGCGCCTGAAA 61.666 63.158 38.98 20.58 38.31 2.69
176 177 1.449778 GGGTCTAGGCGCCTGAAAC 60.450 63.158 38.98 29.28 0.00 2.78
177 178 1.449778 GGTCTAGGCGCCTGAAACC 60.450 63.158 38.98 33.24 0.00 3.27
178 179 1.449778 GTCTAGGCGCCTGAAACCC 60.450 63.158 38.98 16.77 0.00 4.11
179 180 1.612442 TCTAGGCGCCTGAAACCCT 60.612 57.895 38.98 12.97 0.00 4.34
180 181 0.324923 TCTAGGCGCCTGAAACCCTA 60.325 55.000 38.98 15.52 0.00 3.53
181 182 0.105039 CTAGGCGCCTGAAACCCTAG 59.895 60.000 38.98 21.33 40.52 3.02
182 183 1.335132 TAGGCGCCTGAAACCCTAGG 61.335 60.000 38.98 0.06 37.14 3.02
183 184 2.124695 GCGCCTGAAACCCTAGGG 60.125 66.667 27.36 27.36 42.03 3.53
184 185 2.666098 GCGCCTGAAACCCTAGGGA 61.666 63.158 35.38 11.08 38.96 4.20
185 186 1.988015 CGCCTGAAACCCTAGGGAA 59.012 57.895 35.38 15.05 38.96 3.97
186 187 0.326927 CGCCTGAAACCCTAGGGAAA 59.673 55.000 35.38 14.69 38.96 3.13
187 188 1.064685 CGCCTGAAACCCTAGGGAAAT 60.065 52.381 35.38 18.91 38.96 2.17
188 189 2.656002 GCCTGAAACCCTAGGGAAATC 58.344 52.381 35.38 25.57 38.96 2.17
189 190 2.919228 CCTGAAACCCTAGGGAAATCG 58.081 52.381 35.38 20.39 38.96 3.34
190 191 2.504175 CCTGAAACCCTAGGGAAATCGA 59.496 50.000 35.38 16.12 38.96 3.59
191 192 3.432326 CCTGAAACCCTAGGGAAATCGAG 60.432 52.174 35.38 22.29 38.96 4.04
192 193 3.446968 TGAAACCCTAGGGAAATCGAGA 58.553 45.455 35.38 10.16 38.96 4.04
193 194 3.451178 TGAAACCCTAGGGAAATCGAGAG 59.549 47.826 35.38 3.62 38.96 3.20
194 195 3.399952 AACCCTAGGGAAATCGAGAGA 57.600 47.619 35.38 0.00 41.38 3.10
195 196 2.952116 ACCCTAGGGAAATCGAGAGAG 58.048 52.381 35.38 2.82 40.74 3.20
196 197 2.243810 CCCTAGGGAAATCGAGAGAGG 58.756 57.143 24.99 0.00 40.20 3.69
197 198 2.425102 CCCTAGGGAAATCGAGAGAGGT 60.425 54.545 24.99 0.00 40.20 3.85
198 199 4.564319 CCCTAGGGAAATCGAGAGAGGTG 61.564 56.522 24.99 0.00 40.20 4.00
205 206 3.432262 TCGAGAGAGGTGGTTGTGA 57.568 52.632 0.00 0.00 34.84 3.58
206 207 1.699730 TCGAGAGAGGTGGTTGTGAA 58.300 50.000 0.00 0.00 34.84 3.18
207 208 1.340248 TCGAGAGAGGTGGTTGTGAAC 59.660 52.381 0.00 0.00 34.84 3.18
208 209 1.068588 CGAGAGAGGTGGTTGTGAACA 59.931 52.381 0.00 0.00 0.00 3.18
209 210 2.484889 GAGAGAGGTGGTTGTGAACAC 58.515 52.381 0.00 0.00 36.89 3.32
210 211 2.103263 GAGAGAGGTGGTTGTGAACACT 59.897 50.000 6.51 0.00 37.72 3.55
211 212 2.505819 AGAGAGGTGGTTGTGAACACTT 59.494 45.455 6.51 0.00 37.72 3.16
212 213 3.054361 AGAGAGGTGGTTGTGAACACTTT 60.054 43.478 6.51 0.00 37.72 2.66
213 214 3.016736 AGAGGTGGTTGTGAACACTTTG 58.983 45.455 6.51 0.00 37.72 2.77
214 215 1.476488 AGGTGGTTGTGAACACTTTGC 59.524 47.619 6.51 0.00 37.72 3.68
215 216 1.203523 GGTGGTTGTGAACACTTTGCA 59.796 47.619 6.51 0.00 37.72 4.08
216 217 2.258755 GTGGTTGTGAACACTTTGCAC 58.741 47.619 6.51 0.00 34.84 4.57
217 218 2.094752 GTGGTTGTGAACACTTTGCACT 60.095 45.455 6.51 0.00 34.84 4.40
218 219 2.163412 TGGTTGTGAACACTTTGCACTC 59.837 45.455 6.51 0.00 33.83 3.51
219 220 2.163412 GGTTGTGAACACTTTGCACTCA 59.837 45.455 6.51 0.00 33.83 3.41
220 221 3.366883 GGTTGTGAACACTTTGCACTCAA 60.367 43.478 6.51 0.00 33.83 3.02
221 222 4.233789 GTTGTGAACACTTTGCACTCAAA 58.766 39.130 6.51 0.00 39.67 2.69
222 223 3.832276 TGTGAACACTTTGCACTCAAAC 58.168 40.909 6.51 0.00 37.28 2.93
223 224 3.254411 TGTGAACACTTTGCACTCAAACA 59.746 39.130 6.51 0.00 37.28 2.83
224 225 4.233789 GTGAACACTTTGCACTCAAACAA 58.766 39.130 0.00 0.00 37.28 2.83
225 226 4.089923 GTGAACACTTTGCACTCAAACAAC 59.910 41.667 0.00 0.00 37.28 3.32
226 227 4.022416 TGAACACTTTGCACTCAAACAACT 60.022 37.500 0.00 0.00 37.28 3.16
227 228 4.519540 ACACTTTGCACTCAAACAACTT 57.480 36.364 0.00 0.00 37.28 2.66
228 229 5.637006 ACACTTTGCACTCAAACAACTTA 57.363 34.783 0.00 0.00 37.28 2.24
229 230 6.207691 ACACTTTGCACTCAAACAACTTAT 57.792 33.333 0.00 0.00 37.28 1.73
230 231 7.328277 ACACTTTGCACTCAAACAACTTATA 57.672 32.000 0.00 0.00 37.28 0.98
231 232 7.940850 ACACTTTGCACTCAAACAACTTATAT 58.059 30.769 0.00 0.00 37.28 0.86
232 233 9.062524 ACACTTTGCACTCAAACAACTTATATA 57.937 29.630 0.00 0.00 37.28 0.86
302 303 6.906157 ATCCAAAATCTCGATAATTGCCAT 57.094 33.333 0.00 0.00 0.00 4.40
306 307 6.418819 CCAAAATCTCGATAATTGCCATTGTC 59.581 38.462 0.00 0.00 0.00 3.18
308 309 8.344831 CAAAATCTCGATAATTGCCATTGTCTA 58.655 33.333 5.85 0.00 30.20 2.59
309 310 8.627208 AAATCTCGATAATTGCCATTGTCTAT 57.373 30.769 5.85 0.00 30.20 1.98
310 311 8.627208 AATCTCGATAATTGCCATTGTCTATT 57.373 30.769 5.85 1.55 30.20 1.73
311 312 9.725019 AATCTCGATAATTGCCATTGTCTATTA 57.275 29.630 5.85 0.00 30.20 0.98
312 313 8.763049 TCTCGATAATTGCCATTGTCTATTAG 57.237 34.615 5.85 0.02 30.20 1.73
314 315 7.676004 TCGATAATTGCCATTGTCTATTAGGA 58.324 34.615 5.85 0.00 30.20 2.94
363 365 7.938490 AGGTGATTGTTTTTCTAAATTTGGCAT 59.062 29.630 0.00 0.00 0.00 4.40
383 385 9.610705 TTGGCATGTGCATTTTTATTATATGTT 57.389 25.926 7.36 0.00 44.36 2.71
389 391 9.813446 TGTGCATTTTTATTATATGTTGCATGA 57.187 25.926 0.00 0.00 40.52 3.07
585 590 7.014134 TGACATTTTTCTGACTAAGCATGGAAA 59.986 33.333 0.00 0.00 0.00 3.13
628 633 7.653311 GTGGCAGTTTTATTTTTGAGAGAATGT 59.347 33.333 0.00 0.00 0.00 2.71
710 901 8.592105 TTTCTTATCAAAGATGGCAGTTTTTG 57.408 30.769 12.31 12.31 41.36 2.44
776 967 5.859205 AAAAAGGCAGATCACTCAAAACT 57.141 34.783 0.00 0.00 0.00 2.66
777 968 6.959639 AAAAAGGCAGATCACTCAAAACTA 57.040 33.333 0.00 0.00 0.00 2.24
778 969 7.530426 AAAAAGGCAGATCACTCAAAACTAT 57.470 32.000 0.00 0.00 0.00 2.12
925 1118 1.131771 GCTGGCGAAAGAGCAAAAAC 58.868 50.000 0.00 0.00 39.27 2.43
938 1131 1.599797 AAAAACGGTCGCTGGGAGG 60.600 57.895 0.00 0.00 0.00 4.30
939 1132 4.699522 AAACGGTCGCTGGGAGGC 62.700 66.667 0.00 0.00 0.00 4.70
961 1154 4.891727 CCCCCTGGCGATCGAACG 62.892 72.222 21.57 11.09 0.00 3.95
972 1165 2.661594 CGATCGAACGCCAGATATTGA 58.338 47.619 10.26 0.00 0.00 2.57
978 1171 0.736636 ACGCCAGATATTGACGTCGA 59.263 50.000 8.21 8.21 42.46 4.20
1171 1444 4.354943 CACCACCTCCCCTCCCCT 62.355 72.222 0.00 0.00 0.00 4.79
1336 1618 2.283966 ACTCCCCAGGTGAGGACG 60.284 66.667 3.71 0.00 34.06 4.79
1366 1648 0.954449 CCTTCTGACAGCCACTGCAG 60.954 60.000 13.48 13.48 41.13 4.41
1368 1650 0.034476 TTCTGACAGCCACTGCAGAG 59.966 55.000 23.35 13.32 41.55 3.35
1394 1676 4.469945 TGGATAAGACATTCCGAGTTCCTT 59.530 41.667 0.00 0.00 34.58 3.36
1513 1802 7.988737 TGTGTCATCCATGTCAAGATAAAATC 58.011 34.615 0.00 0.00 0.00 2.17
1519 1808 6.115446 TCCATGTCAAGATAAAATCGAGCTT 58.885 36.000 0.00 0.00 0.00 3.74
1608 1897 9.118236 GTAGTTAATGATTGAACTTGAAACTGC 57.882 33.333 5.71 0.00 37.16 4.40
1713 2002 5.411669 CCTGTTTTGTCCCTTGTAGTGATAC 59.588 44.000 0.00 0.00 0.00 2.24
1728 2017 9.665719 TTGTAGTGATACTTTGCTCATATGAAA 57.334 29.630 6.90 0.00 0.00 2.69
1741 2030 6.548251 TGCTCATATGAAACATTGGTGATGAT 59.452 34.615 6.90 0.00 39.15 2.45
1742 2031 6.861572 GCTCATATGAAACATTGGTGATGATG 59.138 38.462 6.90 0.00 39.15 3.07
1743 2032 7.255346 GCTCATATGAAACATTGGTGATGATGA 60.255 37.037 6.90 0.00 39.15 2.92
1811 2102 8.865590 TTTCTTGCTTCTTAAACACCATTTAC 57.134 30.769 0.00 0.00 0.00 2.01
1886 2177 6.078479 GCTGATTCAAATATTCGAGCTGATG 58.922 40.000 0.00 0.00 0.00 3.07
2021 2312 2.231478 CCGAGCCATGGTATGTAGGTAG 59.769 54.545 14.67 0.00 0.00 3.18
2027 2318 5.074652 AGCCATGGTATGTAGGTAGTCTCTA 59.925 44.000 14.67 0.00 0.00 2.43
2105 2404 6.830912 CCTCTTATAAATGATGAGGTGTGGA 58.169 40.000 8.79 0.00 39.39 4.02
2115 2414 0.389166 GAGGTGTGGAGCGTTCTCTG 60.389 60.000 0.00 0.00 39.31 3.35
2141 2440 7.755822 GGGATTATGCGTTACATGTTTAAAACA 59.244 33.333 2.30 0.00 46.94 2.83
2277 2718 3.058085 TGCAATACATGTCAGCAGTTGTG 60.058 43.478 13.70 0.00 0.00 3.33
2361 2821 5.109903 CCCACAAGTAAGAAGTCGGATAAG 58.890 45.833 0.00 0.00 0.00 1.73
2449 2909 4.241590 TGATGTTGTGTTGCTCAATTCC 57.758 40.909 0.00 0.00 0.00 3.01
2543 3012 4.700700 TGCATGAGATGACTTGATGGTAG 58.299 43.478 0.00 0.00 0.00 3.18
2939 3408 2.334006 ATCTCTTCCTGTCTGGTGGT 57.666 50.000 0.00 0.00 37.07 4.16
3029 3498 0.179000 GCACCATCCTCGACCTTGAT 59.821 55.000 0.00 0.00 0.00 2.57
3065 3534 4.396478 GGGAAGCAGTTTATCTCTTCAACC 59.604 45.833 0.00 0.00 34.80 3.77
3252 3732 8.752187 ACACATTCAAGTTAGGCATATTTTGAT 58.248 29.630 6.08 0.00 0.00 2.57
3254 3734 8.199449 ACATTCAAGTTAGGCATATTTTGATGG 58.801 33.333 6.08 4.95 0.00 3.51
3368 3851 6.127897 ACCTGTATAGCTCATTTTTGTCAAGC 60.128 38.462 0.00 0.00 0.00 4.01
3494 3993 8.225107 TGAAGTTACGTGATGTGCTTTTATAAC 58.775 33.333 0.00 0.00 30.64 1.89
3536 4542 7.621428 ATGAACTGAACTCAATGTCCTAATG 57.379 36.000 0.00 0.00 0.00 1.90
3568 4574 6.294397 GGACTACCTAACCCAATCTATGTACG 60.294 46.154 0.00 0.00 0.00 3.67
3604 4644 5.505780 TCCCTATATTTCACTGTGTTTGGG 58.494 41.667 7.79 10.48 0.00 4.12
3655 4695 1.269309 CCTAATGCCTTCCGACTCTCG 60.269 57.143 0.00 0.00 40.07 4.04
3682 4722 1.762957 TGCAAGCTAGTCCTATCCACC 59.237 52.381 0.00 0.00 0.00 4.61
3777 4825 6.713762 AAAGTTCCTGTTTCATGTTGATGA 57.286 33.333 0.00 0.00 36.78 2.92
3829 4877 4.543590 TCAGGGAACAAGTTTTGCAAAA 57.456 36.364 20.46 20.46 0.00 2.44
3841 4889 8.778358 ACAAGTTTTGCAAAAATTTGAACTGTA 58.222 25.926 34.15 10.91 40.55 2.74
4088 5136 0.972983 TCTCTTTGAGCGGGAGGGAG 60.973 60.000 0.00 0.00 0.00 4.30
4121 5169 0.941463 CGTCCGATGGCTGCATCTAC 60.941 60.000 0.50 3.86 0.00 2.59
4124 5172 1.486310 TCCGATGGCTGCATCTACTTT 59.514 47.619 0.50 0.00 0.00 2.66
4154 5202 2.588464 AGTCCTCGAGGTTTCTGAGA 57.412 50.000 30.17 6.22 36.34 3.27
4264 5312 8.572185 TGGTGAAATATCTGTTTTCGAATGAAA 58.428 29.630 0.00 0.00 42.21 2.69
4424 5472 3.183793 TGGTCATCATCCGATCACAAG 57.816 47.619 0.00 0.00 0.00 3.16
4454 5502 6.878923 CACTTGGGAATTGACTACTGAATGTA 59.121 38.462 0.00 0.00 0.00 2.29
4677 5745 3.260100 CAAGGTGCCCCTGTCCCT 61.260 66.667 0.00 0.00 41.56 4.20
4751 5819 2.166664 CCTCTTCAGGTAGGGTCTTTCG 59.833 54.545 0.00 0.00 34.60 3.46
4757 5826 2.238898 CAGGTAGGGTCTTTCGGGATTT 59.761 50.000 0.00 0.00 0.00 2.17
4789 5858 6.029607 GCATCTTTGTGCTAAATCAATCGAA 58.970 36.000 0.00 0.00 41.82 3.71
4790 5859 6.694411 GCATCTTTGTGCTAAATCAATCGAAT 59.306 34.615 0.00 0.00 41.82 3.34
4791 5860 7.305820 GCATCTTTGTGCTAAATCAATCGAATG 60.306 37.037 0.00 0.00 41.82 2.67
4792 5861 7.376435 TCTTTGTGCTAAATCAATCGAATGA 57.624 32.000 5.48 5.48 0.00 2.57
4808 5877 8.980481 AATCGAATGATTGGACCTTAGTTATT 57.020 30.769 0.00 0.00 43.17 1.40
4810 5879 8.882415 TCGAATGATTGGACCTTAGTTATTAC 57.118 34.615 0.00 0.00 0.00 1.89
4811 5880 8.479689 TCGAATGATTGGACCTTAGTTATTACA 58.520 33.333 0.00 0.00 0.00 2.41
4812 5881 8.548721 CGAATGATTGGACCTTAGTTATTACAC 58.451 37.037 0.00 0.00 0.00 2.90
4813 5882 9.391006 GAATGATTGGACCTTAGTTATTACACA 57.609 33.333 0.00 0.00 0.00 3.72
4814 5883 9.747898 AATGATTGGACCTTAGTTATTACACAA 57.252 29.630 0.00 0.00 0.00 3.33
4815 5884 9.920946 ATGATTGGACCTTAGTTATTACACAAT 57.079 29.630 0.00 0.00 0.00 2.71
4816 5885 9.173021 TGATTGGACCTTAGTTATTACACAATG 57.827 33.333 0.00 0.00 0.00 2.82
4818 5887 6.477253 TGGACCTTAGTTATTACACAATGCA 58.523 36.000 0.00 0.00 0.00 3.96
4820 5889 7.120579 TGGACCTTAGTTATTACACAATGCAAG 59.879 37.037 0.00 0.00 0.00 4.01
4821 5890 7.335924 GGACCTTAGTTATTACACAATGCAAGA 59.664 37.037 0.00 0.00 0.00 3.02
4823 5892 8.730680 ACCTTAGTTATTACACAATGCAAGAAG 58.269 33.333 0.00 0.00 0.00 2.85
4824 5893 8.184192 CCTTAGTTATTACACAATGCAAGAAGG 58.816 37.037 0.00 0.00 0.00 3.46
4825 5894 8.856153 TTAGTTATTACACAATGCAAGAAGGA 57.144 30.769 0.00 0.00 0.00 3.36
4826 5895 7.759489 AGTTATTACACAATGCAAGAAGGAA 57.241 32.000 0.00 0.00 0.00 3.36
4827 5896 8.353423 AGTTATTACACAATGCAAGAAGGAAT 57.647 30.769 0.00 0.00 0.00 3.01
4828 5897 9.461312 AGTTATTACACAATGCAAGAAGGAATA 57.539 29.630 0.00 0.00 0.00 1.75
4831 5900 5.391312 ACACAATGCAAGAAGGAATAACC 57.609 39.130 0.00 0.00 39.35 2.85
4832 5901 4.832266 ACACAATGCAAGAAGGAATAACCA 59.168 37.500 0.00 0.00 42.04 3.67
4833 5902 5.304101 ACACAATGCAAGAAGGAATAACCAA 59.696 36.000 0.00 0.00 42.04 3.67
4834 5903 6.183360 ACACAATGCAAGAAGGAATAACCAAA 60.183 34.615 0.00 0.00 42.04 3.28
4835 5904 6.146021 CACAATGCAAGAAGGAATAACCAAAC 59.854 38.462 0.00 0.00 42.04 2.93
4838 5907 4.892934 TGCAAGAAGGAATAACCAAACAGT 59.107 37.500 0.00 0.00 42.04 3.55
4842 9322 4.105697 AGAAGGAATAACCAAACAGTCCCA 59.894 41.667 0.00 0.00 42.04 4.37
4843 9323 4.675063 AGGAATAACCAAACAGTCCCAT 57.325 40.909 0.00 0.00 42.04 4.00
4850 9330 1.065491 CCAAACAGTCCCATCCATCGA 60.065 52.381 0.00 0.00 0.00 3.59
4852 9332 0.175760 AACAGTCCCATCCATCGACG 59.824 55.000 0.00 0.00 0.00 5.12
4854 9334 0.249073 CAGTCCCATCCATCGACGAC 60.249 60.000 0.00 0.00 0.00 4.34
4870 9350 2.990967 ACCACCCGCAATGGCTTG 60.991 61.111 0.00 0.00 41.31 4.01
4914 9397 1.202806 CGCCATGGGGATCTTGTACAT 60.203 52.381 23.98 0.00 35.59 2.29
4929 9412 1.580704 GTACATCGCGAACCACTTACG 59.419 52.381 15.24 0.00 0.00 3.18
4941 9424 2.259618 CCACTTACGATTCTCCACGTG 58.740 52.381 9.08 9.08 42.61 4.49
5010 9493 4.162690 GGCCGCGACCAGGAAGAT 62.163 66.667 8.23 0.00 0.00 2.40
5022 9505 0.250513 AGGAAGATGTTGACCTCCGC 59.749 55.000 0.00 0.00 0.00 5.54
5039 9522 4.007644 CCAGGCTCCTGTCGCACA 62.008 66.667 14.27 0.00 42.15 4.57
5040 9523 2.740055 CAGGCTCCTGTCGCACAC 60.740 66.667 7.75 0.00 39.10 3.82
5044 9527 4.662961 CTCCTGTCGCACACGCCA 62.663 66.667 0.00 0.00 39.84 5.69
5045 9528 4.662961 TCCTGTCGCACACGCCAG 62.663 66.667 0.00 0.00 39.84 4.85
5070 10126 2.203832 TCCTCCTGGAGCTGCACA 60.204 61.111 18.51 0.00 37.46 4.57
5089 10145 1.306970 CCCTCGAGGTACAGGAGGT 59.693 63.158 29.25 0.00 44.92 3.85
5135 10191 3.823330 GGGCGACGTCGTGGAGAT 61.823 66.667 35.48 0.00 42.22 2.75
5161 10217 2.028567 GGTAGAGCTATCTGGCATGTCC 60.029 54.545 0.00 0.00 36.96 4.02
5178 10234 3.460857 GTCCAGGGACATGACACTATC 57.539 52.381 13.49 0.00 44.02 2.08
5179 10235 2.031870 TCCAGGGACATGACACTATCG 58.968 52.381 0.00 0.00 0.00 2.92
5180 10236 1.757118 CCAGGGACATGACACTATCGT 59.243 52.381 0.00 0.00 0.00 3.73
5181 10237 2.223829 CCAGGGACATGACACTATCGTC 60.224 54.545 0.00 0.00 36.40 4.20
5221 10277 1.005394 CCGCTACGGTGACTTTGGT 60.005 57.895 0.00 0.00 42.73 3.67
5227 10283 1.366366 CGGTGACTTTGGTCTCGGT 59.634 57.895 0.00 0.00 42.54 4.69
5228 10284 0.599558 CGGTGACTTTGGTCTCGGTA 59.400 55.000 0.00 0.00 42.54 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.965819 TGGTCATGCACACTTTATTAATATGTT 58.034 29.630 0.00 0.00 0.00 2.71
6 7 8.405531 GTGGTCATGCACACTTTATTAATATGT 58.594 33.333 11.03 0.00 34.84 2.29
7 8 7.862372 GGTGGTCATGCACACTTTATTAATATG 59.138 37.037 15.91 0.00 37.72 1.78
8 9 7.779798 AGGTGGTCATGCACACTTTATTAATAT 59.220 33.333 15.91 0.00 37.72 1.28
9 10 7.116075 AGGTGGTCATGCACACTTTATTAATA 58.884 34.615 15.91 0.00 37.72 0.98
10 11 5.951747 AGGTGGTCATGCACACTTTATTAAT 59.048 36.000 15.91 0.00 37.72 1.40
11 12 5.321102 AGGTGGTCATGCACACTTTATTAA 58.679 37.500 15.91 0.00 37.72 1.40
12 13 4.917385 AGGTGGTCATGCACACTTTATTA 58.083 39.130 15.91 0.00 37.72 0.98
13 14 3.758554 GAGGTGGTCATGCACACTTTATT 59.241 43.478 15.91 2.20 37.72 1.40
14 15 3.009473 AGAGGTGGTCATGCACACTTTAT 59.991 43.478 15.91 3.37 37.72 1.40
15 16 2.371841 AGAGGTGGTCATGCACACTTTA 59.628 45.455 15.91 0.00 37.72 1.85
16 17 1.143684 AGAGGTGGTCATGCACACTTT 59.856 47.619 15.91 7.73 37.72 2.66
17 18 0.767375 AGAGGTGGTCATGCACACTT 59.233 50.000 15.91 10.58 37.72 3.16
18 19 0.767375 AAGAGGTGGTCATGCACACT 59.233 50.000 15.91 7.64 37.72 3.55
19 20 0.877071 CAAGAGGTGGTCATGCACAC 59.123 55.000 10.12 10.12 36.89 3.82
20 21 0.473755 ACAAGAGGTGGTCATGCACA 59.526 50.000 5.92 0.00 0.00 4.57
21 22 1.609208 AACAAGAGGTGGTCATGCAC 58.391 50.000 0.00 0.00 0.00 4.57
22 23 2.363306 AAACAAGAGGTGGTCATGCA 57.637 45.000 0.00 0.00 0.00 3.96
23 24 3.733443 AAAAACAAGAGGTGGTCATGC 57.267 42.857 0.00 0.00 0.00 4.06
70 71 9.903682 GGATTTTTCCTGTAAGTTAAAACTACC 57.096 33.333 0.00 0.00 38.57 3.18
71 72 9.603298 CGGATTTTTCCTGTAAGTTAAAACTAC 57.397 33.333 0.00 0.00 38.57 2.73
72 73 9.558396 TCGGATTTTTCCTGTAAGTTAAAACTA 57.442 29.630 0.00 0.00 38.57 2.24
73 74 8.454570 TCGGATTTTTCCTGTAAGTTAAAACT 57.545 30.769 0.00 0.00 42.04 2.66
74 75 9.687210 ATTCGGATTTTTCCTGTAAGTTAAAAC 57.313 29.630 0.00 0.00 30.56 2.43
99 100 9.591792 GGCTCTCTTTTGCTTCAAAAATAATAT 57.408 29.630 6.25 0.00 41.77 1.28
100 101 8.584157 TGGCTCTCTTTTGCTTCAAAAATAATA 58.416 29.630 6.25 0.00 41.77 0.98
101 102 7.444299 TGGCTCTCTTTTGCTTCAAAAATAAT 58.556 30.769 6.25 0.00 41.77 1.28
102 103 6.815089 TGGCTCTCTTTTGCTTCAAAAATAA 58.185 32.000 6.25 0.00 41.77 1.40
103 104 6.403866 TGGCTCTCTTTTGCTTCAAAAATA 57.596 33.333 6.25 0.00 41.77 1.40
104 105 5.280654 TGGCTCTCTTTTGCTTCAAAAAT 57.719 34.783 6.25 0.00 41.77 1.82
105 106 4.734398 TGGCTCTCTTTTGCTTCAAAAA 57.266 36.364 6.25 0.00 41.77 1.94
106 107 4.942761 ATGGCTCTCTTTTGCTTCAAAA 57.057 36.364 4.87 4.87 40.41 2.44
107 108 4.942761 AATGGCTCTCTTTTGCTTCAAA 57.057 36.364 0.00 0.00 0.00 2.69
108 109 4.460382 CCTAATGGCTCTCTTTTGCTTCAA 59.540 41.667 0.00 0.00 0.00 2.69
109 110 4.012374 CCTAATGGCTCTCTTTTGCTTCA 58.988 43.478 0.00 0.00 0.00 3.02
110 111 4.629251 CCTAATGGCTCTCTTTTGCTTC 57.371 45.455 0.00 0.00 0.00 3.86
124 125 3.897239 TGTTATGGGACTTGCCTAATGG 58.103 45.455 0.00 0.00 36.66 3.16
125 126 5.163519 CCTTTGTTATGGGACTTGCCTAATG 60.164 44.000 0.00 0.00 36.66 1.90
126 127 4.956075 CCTTTGTTATGGGACTTGCCTAAT 59.044 41.667 0.00 0.00 36.66 1.73
127 128 4.043561 TCCTTTGTTATGGGACTTGCCTAA 59.956 41.667 0.00 0.00 36.66 2.69
128 129 3.589735 TCCTTTGTTATGGGACTTGCCTA 59.410 43.478 0.00 0.00 36.66 3.93
129 130 2.378547 TCCTTTGTTATGGGACTTGCCT 59.621 45.455 0.00 0.00 36.66 4.75
130 131 2.755103 CTCCTTTGTTATGGGACTTGCC 59.245 50.000 0.00 0.00 0.00 4.52
131 132 3.440522 GTCTCCTTTGTTATGGGACTTGC 59.559 47.826 0.00 0.00 0.00 4.01
132 133 4.010349 GGTCTCCTTTGTTATGGGACTTG 58.990 47.826 0.00 0.00 0.00 3.16
133 134 3.916989 AGGTCTCCTTTGTTATGGGACTT 59.083 43.478 0.00 0.00 0.00 3.01
134 135 3.264450 CAGGTCTCCTTTGTTATGGGACT 59.736 47.826 0.00 0.00 0.00 3.85
135 136 3.610911 CAGGTCTCCTTTGTTATGGGAC 58.389 50.000 0.00 0.00 0.00 4.46
136 137 2.576191 CCAGGTCTCCTTTGTTATGGGA 59.424 50.000 0.00 0.00 0.00 4.37
137 138 2.357154 CCCAGGTCTCCTTTGTTATGGG 60.357 54.545 0.00 0.00 40.18 4.00
138 139 2.357154 CCCCAGGTCTCCTTTGTTATGG 60.357 54.545 0.00 0.00 0.00 2.74
139 140 2.357154 CCCCCAGGTCTCCTTTGTTATG 60.357 54.545 0.00 0.00 0.00 1.90
140 141 1.923148 CCCCCAGGTCTCCTTTGTTAT 59.077 52.381 0.00 0.00 0.00 1.89
141 142 1.368374 CCCCCAGGTCTCCTTTGTTA 58.632 55.000 0.00 0.00 0.00 2.41
142 143 0.701310 ACCCCCAGGTCTCCTTTGTT 60.701 55.000 0.00 0.00 46.45 2.83
143 144 1.072930 ACCCCCAGGTCTCCTTTGT 60.073 57.895 0.00 0.00 46.45 2.83
144 145 3.922366 ACCCCCAGGTCTCCTTTG 58.078 61.111 0.00 0.00 46.45 2.77
157 158 2.666098 TTTCAGGCGCCTAGACCCC 61.666 63.158 32.30 0.00 0.00 4.95
158 159 1.449778 GTTTCAGGCGCCTAGACCC 60.450 63.158 32.30 16.43 0.00 4.46
159 160 1.449778 GGTTTCAGGCGCCTAGACC 60.450 63.158 32.30 29.91 0.00 3.85
160 161 1.449778 GGGTTTCAGGCGCCTAGAC 60.450 63.158 32.30 25.53 0.00 2.59
161 162 0.324923 TAGGGTTTCAGGCGCCTAGA 60.325 55.000 32.30 25.04 0.00 2.43
162 163 0.105039 CTAGGGTTTCAGGCGCCTAG 59.895 60.000 32.30 23.08 0.00 3.02
163 164 1.335132 CCTAGGGTTTCAGGCGCCTA 61.335 60.000 32.30 12.88 0.00 3.93
164 165 2.670148 CCTAGGGTTTCAGGCGCCT 61.670 63.158 27.08 27.08 0.00 5.52
165 166 2.124695 CCTAGGGTTTCAGGCGCC 60.125 66.667 21.89 21.89 0.00 6.53
166 167 2.124695 CCCTAGGGTTTCAGGCGC 60.125 66.667 20.88 0.00 0.00 6.53
167 168 0.326927 TTTCCCTAGGGTTTCAGGCG 59.673 55.000 27.58 0.00 36.47 5.52
168 169 2.656002 GATTTCCCTAGGGTTTCAGGC 58.344 52.381 27.58 8.15 36.47 4.85
169 170 2.504175 TCGATTTCCCTAGGGTTTCAGG 59.496 50.000 27.58 13.39 36.47 3.86
170 171 3.451178 TCTCGATTTCCCTAGGGTTTCAG 59.549 47.826 27.58 16.60 36.47 3.02
171 172 3.446968 TCTCGATTTCCCTAGGGTTTCA 58.553 45.455 27.58 5.11 36.47 2.69
172 173 3.705072 TCTCTCGATTTCCCTAGGGTTTC 59.295 47.826 27.58 19.54 36.47 2.78
173 174 3.707102 CTCTCTCGATTTCCCTAGGGTTT 59.293 47.826 27.58 13.26 36.47 3.27
174 175 3.301274 CTCTCTCGATTTCCCTAGGGTT 58.699 50.000 27.58 13.62 36.47 4.11
175 176 2.425102 CCTCTCTCGATTTCCCTAGGGT 60.425 54.545 27.58 8.62 36.47 4.34
176 177 2.243810 CCTCTCTCGATTTCCCTAGGG 58.756 57.143 23.22 23.22 0.00 3.53
177 178 2.625790 CACCTCTCTCGATTTCCCTAGG 59.374 54.545 0.06 0.06 0.00 3.02
178 179 2.625790 CCACCTCTCTCGATTTCCCTAG 59.374 54.545 0.00 0.00 0.00 3.02
179 180 2.024273 ACCACCTCTCTCGATTTCCCTA 60.024 50.000 0.00 0.00 0.00 3.53
180 181 1.273324 ACCACCTCTCTCGATTTCCCT 60.273 52.381 0.00 0.00 0.00 4.20
181 182 1.196012 ACCACCTCTCTCGATTTCCC 58.804 55.000 0.00 0.00 0.00 3.97
182 183 2.028020 ACAACCACCTCTCTCGATTTCC 60.028 50.000 0.00 0.00 0.00 3.13
183 184 2.996621 CACAACCACCTCTCTCGATTTC 59.003 50.000 0.00 0.00 0.00 2.17
184 185 2.632996 TCACAACCACCTCTCTCGATTT 59.367 45.455 0.00 0.00 0.00 2.17
185 186 2.248248 TCACAACCACCTCTCTCGATT 58.752 47.619 0.00 0.00 0.00 3.34
186 187 1.924731 TCACAACCACCTCTCTCGAT 58.075 50.000 0.00 0.00 0.00 3.59
187 188 1.340248 GTTCACAACCACCTCTCTCGA 59.660 52.381 0.00 0.00 0.00 4.04
188 189 1.068588 TGTTCACAACCACCTCTCTCG 59.931 52.381 0.00 0.00 0.00 4.04
189 190 2.103263 AGTGTTCACAACCACCTCTCTC 59.897 50.000 5.74 0.00 0.00 3.20
190 191 2.119495 AGTGTTCACAACCACCTCTCT 58.881 47.619 5.74 0.00 0.00 3.10
191 192 2.622064 AGTGTTCACAACCACCTCTC 57.378 50.000 5.74 0.00 0.00 3.20
192 193 3.016736 CAAAGTGTTCACAACCACCTCT 58.983 45.455 5.74 0.00 0.00 3.69
193 194 2.479560 GCAAAGTGTTCACAACCACCTC 60.480 50.000 5.74 0.00 0.00 3.85
194 195 1.476488 GCAAAGTGTTCACAACCACCT 59.524 47.619 5.74 0.00 0.00 4.00
195 196 1.203523 TGCAAAGTGTTCACAACCACC 59.796 47.619 5.74 0.00 0.00 4.61
196 197 2.094752 AGTGCAAAGTGTTCACAACCAC 60.095 45.455 5.74 6.77 33.44 4.16
197 198 2.163412 GAGTGCAAAGTGTTCACAACCA 59.837 45.455 5.74 0.00 33.44 3.67
198 199 2.163412 TGAGTGCAAAGTGTTCACAACC 59.837 45.455 5.74 0.00 33.44 3.77
199 200 3.485947 TGAGTGCAAAGTGTTCACAAC 57.514 42.857 5.74 0.00 33.44 3.32
200 201 4.233789 GTTTGAGTGCAAAGTGTTCACAA 58.766 39.130 5.74 0.00 44.12 3.33
201 202 3.254411 TGTTTGAGTGCAAAGTGTTCACA 59.746 39.130 5.74 0.00 44.12 3.58
202 203 3.832276 TGTTTGAGTGCAAAGTGTTCAC 58.168 40.909 0.00 0.00 44.12 3.18
203 204 4.022416 AGTTGTTTGAGTGCAAAGTGTTCA 60.022 37.500 0.00 0.00 44.12 3.18
204 205 4.485163 AGTTGTTTGAGTGCAAAGTGTTC 58.515 39.130 0.00 0.00 44.12 3.18
205 206 4.519540 AGTTGTTTGAGTGCAAAGTGTT 57.480 36.364 0.00 0.00 44.12 3.32
206 207 4.519540 AAGTTGTTTGAGTGCAAAGTGT 57.480 36.364 0.00 0.00 44.12 3.55
279 280 6.906157 ATGGCAATTATCGAGATTTTGGAT 57.094 33.333 0.00 0.00 0.00 3.41
280 281 6.096705 ACAATGGCAATTATCGAGATTTTGGA 59.903 34.615 0.00 0.00 0.00 3.53
289 290 7.602644 GTCCTAATAGACAATGGCAATTATCGA 59.397 37.037 0.00 0.00 36.73 3.59
290 291 7.387673 TGTCCTAATAGACAATGGCAATTATCG 59.612 37.037 0.00 0.00 43.65 2.92
358 360 9.043079 CAACATATAATAAAAATGCACATGCCA 57.957 29.630 0.49 0.00 41.18 4.92
363 365 9.813446 TCATGCAACATATAATAAAAATGCACA 57.187 25.926 0.00 0.00 44.27 4.57
383 385 4.620589 AACATGGGAAAATTGTCATGCA 57.379 36.364 0.00 0.00 40.22 3.96
389 391 6.223120 GCACTCTAAAACATGGGAAAATTGT 58.777 36.000 0.00 0.00 0.00 2.71
397 399 1.474330 GGGGCACTCTAAAACATGGG 58.526 55.000 0.00 0.00 0.00 4.00
552 555 8.730680 GCTTAGTCAGAAAAATGTCATCCTTTA 58.269 33.333 0.00 0.00 0.00 1.85
556 559 6.500684 TGCTTAGTCAGAAAAATGTCATCC 57.499 37.500 0.00 0.00 0.00 3.51
628 633 9.887629 ATGCCATGTCAACAATAATAAAAATGA 57.112 25.926 0.00 0.00 0.00 2.57
636 641 6.402334 CGCAAAAATGCCATGTCAACAATAAT 60.402 34.615 0.00 0.00 0.00 1.28
688 879 7.951530 AACAAAAACTGCCATCTTTGATAAG 57.048 32.000 0.73 0.00 33.84 1.73
691 882 7.628769 AAAAACAAAAACTGCCATCTTTGAT 57.371 28.000 0.73 0.00 33.84 2.57
692 883 8.729805 ATAAAAACAAAAACTGCCATCTTTGA 57.270 26.923 0.73 0.00 33.84 2.69
693 884 8.829612 AGATAAAAACAAAAACTGCCATCTTTG 58.170 29.630 0.00 0.00 35.39 2.77
694 885 8.829612 CAGATAAAAACAAAAACTGCCATCTTT 58.170 29.630 0.00 0.00 0.00 2.52
697 888 6.928492 TCCAGATAAAAACAAAAACTGCCATC 59.072 34.615 0.00 0.00 0.00 3.51
710 901 4.273318 ACTGCCATCCTCCAGATAAAAAC 58.727 43.478 0.00 0.00 32.37 2.43
814 1005 7.722795 AATTGCCACATTACAACTTTAAACC 57.277 32.000 0.00 0.00 0.00 3.27
944 1137 4.891727 CGTTCGATCGCCAGGGGG 62.892 72.222 11.09 0.00 37.18 5.40
952 1145 2.405357 GTCAATATCTGGCGTTCGATCG 59.595 50.000 9.36 9.36 0.00 3.69
961 1154 4.593597 TTTTTCGACGTCAATATCTGGC 57.406 40.909 17.16 0.00 0.00 4.85
990 1183 1.005630 GAGATCCATCGGCCGGAAG 60.006 63.158 27.83 15.23 35.77 3.46
993 1186 2.919856 AGGAGATCCATCGGCCGG 60.920 66.667 27.83 10.29 38.89 6.13
1209 1482 1.679898 GTACCTTCTGCCAGCCAGT 59.320 57.895 0.00 0.00 42.38 4.00
1336 1618 2.231380 TCAGAAGGGGGTCAAGGGC 61.231 63.158 0.00 0.00 0.00 5.19
1366 1648 4.141914 ACTCGGAATGTCTTATCCAACCTC 60.142 45.833 0.00 0.00 35.34 3.85
1368 1650 4.138487 ACTCGGAATGTCTTATCCAACC 57.862 45.455 0.00 0.00 35.34 3.77
1394 1676 0.320858 TTGCCAATCTAACCGCGACA 60.321 50.000 8.23 0.00 0.00 4.35
1513 1802 3.306973 TGCTATTGACGAATGAAAGCTCG 59.693 43.478 0.00 0.00 40.87 5.03
1519 1808 6.616774 TGCATTATGCTATTGACGAATGAA 57.383 33.333 18.44 0.00 45.31 2.57
1592 1881 3.003689 CCTCACGCAGTTTCAAGTTCAAT 59.996 43.478 0.00 0.00 41.61 2.57
1608 1897 6.094048 ACAATAATTCTCCACAATTCCTCACG 59.906 38.462 0.00 0.00 0.00 4.35
1713 2002 6.623486 TCACCAATGTTTCATATGAGCAAAG 58.377 36.000 5.39 6.50 0.00 2.77
1728 2017 4.019950 TCACTGAGTCATCATCACCAATGT 60.020 41.667 0.00 0.00 36.68 2.71
1741 2030 2.035832 TCACTCGCAATTCACTGAGTCA 59.964 45.455 0.00 0.00 39.55 3.41
1742 2031 2.677199 TCACTCGCAATTCACTGAGTC 58.323 47.619 0.00 0.00 39.55 3.36
1743 2032 2.820059 TCACTCGCAATTCACTGAGT 57.180 45.000 0.00 0.00 42.14 3.41
1811 2102 0.445436 GAGCACATGAGCAAGGAACG 59.555 55.000 17.61 0.00 36.85 3.95
1886 2177 2.729360 GGCACCGTAAAGAATGCAAAAC 59.271 45.455 0.00 0.00 39.92 2.43
1929 2220 2.225255 GAGAGCTTCAAAGGTGAACTGC 59.775 50.000 0.00 0.00 38.88 4.40
2105 2404 1.539065 CGCATAATCCCAGAGAACGCT 60.539 52.381 0.00 0.00 0.00 5.07
2115 2414 7.755822 TGTTTTAAACATGTAACGCATAATCCC 59.244 33.333 6.41 0.00 36.25 3.85
2141 2440 6.954102 ACCAAAAGGCTAGAATCCTACATTTT 59.046 34.615 0.00 0.00 32.65 1.82
2201 2500 6.270000 TCCTCTTTTCATGTTAGAAGACCAGA 59.730 38.462 0.00 0.00 0.00 3.86
2277 2718 6.205658 GCCAGGTTCATCATATCCTTAACTTC 59.794 42.308 0.00 0.00 0.00 3.01
2361 2821 8.293699 ACTTTGTTCCCATGAATAATAGAACC 57.706 34.615 0.00 0.00 32.53 3.62
2372 2832 4.285863 ACTTTCCAACTTTGTTCCCATGA 58.714 39.130 0.00 0.00 0.00 3.07
2482 2950 7.928706 GCAGTAGTTAAGAGTGGAACATGATAT 59.071 37.037 0.00 0.00 44.52 1.63
2939 3408 2.572104 GAGCCTAAGAGAACCCTTGGAA 59.428 50.000 0.00 0.00 0.00 3.53
3029 3498 1.202915 TGCTTCCCATCAGCACTGAAA 60.203 47.619 4.14 0.00 42.49 2.69
3065 3534 5.694910 ACTAACATTACTTCTGGTTGTGTCG 59.305 40.000 0.00 0.00 0.00 4.35
3170 3650 6.494952 ACTGGAAGGAAGAGAGATACTAACA 58.505 40.000 0.00 0.00 39.30 2.41
3172 3652 8.103660 TCTACTGGAAGGAAGAGAGATACTAA 57.896 38.462 0.00 0.00 39.30 2.24
3181 3661 6.041865 ACATCATGATCTACTGGAAGGAAGAG 59.958 42.308 4.86 0.00 39.30 2.85
3252 3732 6.209391 GGATCATTTCTCCTTTCTTTCAACCA 59.791 38.462 0.00 0.00 0.00 3.67
3254 3734 7.459795 AGGATCATTTCTCCTTTCTTTCAAC 57.540 36.000 0.00 0.00 40.29 3.18
3304 3787 6.817140 CGGGTAAGATAGAGGCAAATATAACC 59.183 42.308 0.00 0.00 0.00 2.85
3368 3851 7.776933 TCTAGACACTAAATTTGCAGCTATG 57.223 36.000 0.00 0.00 0.00 2.23
3494 3993 9.538508 TCAGTTCATATCAGATCAGTTGTTATG 57.461 33.333 0.00 0.90 32.97 1.90
3536 4542 3.692690 TGGGTTAGGTAGTCCATTTTGC 58.307 45.455 0.00 0.00 35.89 3.68
3682 4722 2.478134 CTCCAAACTGCAAAGAGAGTCG 59.522 50.000 0.00 0.00 0.00 4.18
3799 4847 1.681264 CTTGTTCCCTGAAACACCCAC 59.319 52.381 0.00 0.00 38.80 4.61
4088 5136 1.796796 GGACGAACCAGATGCAAGC 59.203 57.895 0.00 0.00 38.79 4.01
4121 5169 7.942990 ACCTCGAGGACTTATAGTCATAAAAG 58.057 38.462 37.69 4.42 46.79 2.27
4124 5172 7.778853 AGAAACCTCGAGGACTTATAGTCATAA 59.221 37.037 37.69 0.00 46.79 1.90
4154 5202 4.083057 GCTTCTTTGAAGGCTTCGATCTTT 60.083 41.667 21.42 0.00 0.00 2.52
4264 5312 1.238439 CACTGCAAGGATCGGTGTTT 58.762 50.000 0.00 0.00 39.30 2.83
4270 5318 1.363744 GGAGAACACTGCAAGGATCG 58.636 55.000 0.00 0.00 39.30 3.69
4424 5472 1.880027 AGTCAATTCCCAAGTGCGTTC 59.120 47.619 0.00 0.00 0.00 3.95
4454 5502 7.725844 AGAAGTTTTCAAGATTTCACCTGGTAT 59.274 33.333 0.00 0.00 0.00 2.73
4574 5641 3.963428 TTGAGAGGAGTAAAGTGAGCC 57.037 47.619 0.00 0.00 0.00 4.70
4677 5745 5.547666 TCCCAGCATTAAGGAGCAGAATATA 59.452 40.000 0.00 0.00 0.00 0.86
4751 5819 5.636543 CACAAAGATGCAAGAGAAAAATCCC 59.363 40.000 0.00 0.00 0.00 3.85
4789 5858 9.920946 ATTGTGTAATAACTAAGGTCCAATCAT 57.079 29.630 0.00 0.00 0.00 2.45
4790 5859 9.173021 CATTGTGTAATAACTAAGGTCCAATCA 57.827 33.333 0.00 0.00 0.00 2.57
4791 5860 8.129211 GCATTGTGTAATAACTAAGGTCCAATC 58.871 37.037 0.00 0.00 0.00 2.67
4792 5861 7.613801 TGCATTGTGTAATAACTAAGGTCCAAT 59.386 33.333 0.00 0.00 0.00 3.16
4799 5868 8.946085 TCCTTCTTGCATTGTGTAATAACTAAG 58.054 33.333 0.00 0.00 0.00 2.18
4801 5870 8.856153 TTCCTTCTTGCATTGTGTAATAACTA 57.144 30.769 0.00 0.00 0.00 2.24
4805 5874 8.682710 GGTTATTCCTTCTTGCATTGTGTAATA 58.317 33.333 0.00 0.00 0.00 0.98
4807 5876 6.491745 TGGTTATTCCTTCTTGCATTGTGTAA 59.508 34.615 0.00 0.00 37.07 2.41
4808 5877 6.007076 TGGTTATTCCTTCTTGCATTGTGTA 58.993 36.000 0.00 0.00 37.07 2.90
4810 5879 5.389859 TGGTTATTCCTTCTTGCATTGTG 57.610 39.130 0.00 0.00 37.07 3.33
4811 5880 6.183360 TGTTTGGTTATTCCTTCTTGCATTGT 60.183 34.615 0.00 0.00 37.07 2.71
4812 5881 6.222389 TGTTTGGTTATTCCTTCTTGCATTG 58.778 36.000 0.00 0.00 37.07 2.82
4813 5882 6.041979 ACTGTTTGGTTATTCCTTCTTGCATT 59.958 34.615 0.00 0.00 37.07 3.56
4814 5883 5.539955 ACTGTTTGGTTATTCCTTCTTGCAT 59.460 36.000 0.00 0.00 37.07 3.96
4815 5884 4.892934 ACTGTTTGGTTATTCCTTCTTGCA 59.107 37.500 0.00 0.00 37.07 4.08
4816 5885 5.453567 ACTGTTTGGTTATTCCTTCTTGC 57.546 39.130 0.00 0.00 37.07 4.01
4818 5887 5.077564 GGGACTGTTTGGTTATTCCTTCTT 58.922 41.667 0.00 0.00 37.07 2.52
4820 5889 4.403734 TGGGACTGTTTGGTTATTCCTTC 58.596 43.478 0.00 0.00 37.07 3.46
4821 5890 4.463050 TGGGACTGTTTGGTTATTCCTT 57.537 40.909 0.00 0.00 37.07 3.36
4823 5892 3.699538 GGATGGGACTGTTTGGTTATTCC 59.300 47.826 0.00 0.00 0.00 3.01
4824 5893 4.340617 TGGATGGGACTGTTTGGTTATTC 58.659 43.478 0.00 0.00 0.00 1.75
4825 5894 4.396357 TGGATGGGACTGTTTGGTTATT 57.604 40.909 0.00 0.00 0.00 1.40
4826 5895 4.536765 GATGGATGGGACTGTTTGGTTAT 58.463 43.478 0.00 0.00 0.00 1.89
4827 5896 3.621214 CGATGGATGGGACTGTTTGGTTA 60.621 47.826 0.00 0.00 0.00 2.85
4828 5897 2.807676 GATGGATGGGACTGTTTGGTT 58.192 47.619 0.00 0.00 0.00 3.67
4829 5898 1.340017 CGATGGATGGGACTGTTTGGT 60.340 52.381 0.00 0.00 0.00 3.67
4830 5899 1.065491 TCGATGGATGGGACTGTTTGG 60.065 52.381 0.00 0.00 0.00 3.28
4831 5900 2.009774 GTCGATGGATGGGACTGTTTG 58.990 52.381 0.00 0.00 0.00 2.93
4832 5901 1.405526 CGTCGATGGATGGGACTGTTT 60.406 52.381 0.00 0.00 0.00 2.83
4833 5902 0.175760 CGTCGATGGATGGGACTGTT 59.824 55.000 0.00 0.00 0.00 3.16
4834 5903 0.683179 TCGTCGATGGATGGGACTGT 60.683 55.000 4.48 0.00 0.00 3.55
4835 5904 0.249073 GTCGTCGATGGATGGGACTG 60.249 60.000 4.48 0.00 0.00 3.51
4838 5907 1.380650 TGGTCGTCGATGGATGGGA 60.381 57.895 4.48 0.00 0.00 4.37
4842 9322 2.782222 CGGGTGGTCGTCGATGGAT 61.782 63.158 4.48 0.00 0.00 3.41
4843 9323 3.445687 CGGGTGGTCGTCGATGGA 61.446 66.667 4.48 0.00 0.00 3.41
4870 9350 1.137825 CGAGGGAGTCAGCTTCGAC 59.862 63.158 0.00 0.00 36.08 4.20
4914 9397 1.200716 AGAATCGTAAGTGGTTCGCGA 59.799 47.619 3.71 3.71 39.48 5.87
5009 9492 2.671070 CCTGGCGGAGGTCAACAT 59.329 61.111 0.00 0.00 37.02 2.71
5010 9493 4.329545 GCCTGGCGGAGGTCAACA 62.330 66.667 1.35 0.00 44.97 3.33
5036 9519 3.521308 GACGTTTGCCTGGCGTGTG 62.521 63.158 14.98 6.72 39.06 3.82
5037 9520 3.276846 GACGTTTGCCTGGCGTGT 61.277 61.111 14.98 9.34 39.06 4.49
5038 9521 4.025401 GGACGTTTGCCTGGCGTG 62.025 66.667 14.98 5.97 39.06 5.34
5039 9522 4.250305 AGGACGTTTGCCTGGCGT 62.250 61.111 14.98 5.33 41.81 5.68
5040 9523 3.423154 GAGGACGTTTGCCTGGCG 61.423 66.667 14.98 1.58 35.44 5.69
5042 9525 1.672356 CAGGAGGACGTTTGCCTGG 60.672 63.158 18.39 0.00 43.22 4.45
5044 9527 1.831652 CTCCAGGAGGACGTTTGCCT 61.832 60.000 8.88 0.00 39.61 4.75
5045 9528 1.376037 CTCCAGGAGGACGTTTGCC 60.376 63.158 8.88 0.00 39.61 4.52
5046 9529 2.035442 GCTCCAGGAGGACGTTTGC 61.035 63.158 18.83 0.00 39.61 3.68
5047 9530 0.671781 CAGCTCCAGGAGGACGTTTG 60.672 60.000 18.83 0.00 39.61 2.93
5048 9531 1.674057 CAGCTCCAGGAGGACGTTT 59.326 57.895 18.83 0.00 39.61 3.60
5089 10145 2.427905 CGAAGCCGACGACGACAA 60.428 61.111 9.28 0.00 42.66 3.18
5135 10191 1.982660 CCAGATAGCTCTACCGGACA 58.017 55.000 9.46 0.00 0.00 4.02
5174 10230 2.960129 GGCGGCCGTTGACGATAG 60.960 66.667 28.70 0.00 43.02 2.08
5175 10231 4.858433 CGGCGGCCGTTGACGATA 62.858 66.667 32.14 0.00 42.73 2.92
5216 10272 0.974010 ATCCCGCTACCGAGACCAAA 60.974 55.000 0.00 0.00 36.29 3.28
5221 10277 2.593725 CCGATCCCGCTACCGAGA 60.594 66.667 0.00 0.00 36.29 4.04
5227 10283 0.036448 CCTACTCTCCGATCCCGCTA 59.964 60.000 0.00 0.00 0.00 4.26
5228 10284 1.228306 CCTACTCTCCGATCCCGCT 60.228 63.158 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.