Multiple sequence alignment - TraesCS6A01G185900

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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 TraesCS6A01G185900 chr6A 100.000 3323 0 0 1 3323 219563597 219560275 0.000000e+00 6137.0
1 TraesCS6A01G185900 chr6A 93.443 244 13 2 1 243 600807513 600807272 3.150000e-95 359.0
2 TraesCS6A01G185900 chr6A 90.909 66 5 1 3238 3303 189530813 189530749 1.640000e-13 87.9
3 TraesCS6A01G185900 chr6D 96.627 1749 44 10 716 2462 160430161 160428426 0.000000e+00 2889.0
4 TraesCS6A01G185900 chr6D 90.948 696 23 11 2509 3193 160428149 160427483 0.000000e+00 900.0
5 TraesCS6A01G185900 chr6D 93.915 493 15 2 254 733 160430672 160430182 0.000000e+00 730.0
6 TraesCS6A01G185900 chr6D 94.024 251 11 3 1 250 308585974 308586221 8.700000e-101 377.0
7 TraesCS6A01G185900 chr6B 94.622 1841 63 8 248 2070 290598312 290596490 0.000000e+00 2819.0
8 TraesCS6A01G185900 chr6B 95.545 1257 42 5 1221 2468 290628901 290627650 0.000000e+00 1999.0
9 TraesCS6A01G185900 chr6B 95.381 931 34 4 1542 2468 290657080 290656155 0.000000e+00 1472.0
10 TraesCS6A01G185900 chr6B 93.092 941 35 4 248 1175 290630084 290629161 0.000000e+00 1351.0
11 TraesCS6A01G185900 chr6B 92.627 746 34 7 2482 3216 290656102 290655367 0.000000e+00 1053.0
12 TraesCS6A01G185900 chr6B 92.916 734 31 8 2494 3216 290595740 290595017 0.000000e+00 1048.0
13 TraesCS6A01G185900 chr6B 92.605 622 27 9 2604 3216 290627206 290626595 0.000000e+00 876.0
14 TraesCS6A01G185900 chr6B 90.431 627 30 4 248 861 290658928 290658319 0.000000e+00 798.0
15 TraesCS6A01G185900 chr6B 95.062 81 4 0 3243 3323 204519158 204519238 9.680000e-26 128.0
16 TraesCS6A01G185900 chr6B 91.045 67 5 1 3238 3303 30084096 30084162 4.570000e-14 89.8
17 TraesCS6A01G185900 chr6B 91.045 67 5 1 3238 3303 30100346 30100412 4.570000e-14 89.8
18 TraesCS6A01G185900 chrUn 95.381 931 32 5 1542 2468 453960156 453961079 0.000000e+00 1471.0
19 TraesCS6A01G185900 chrUn 96.827 788 24 1 1283 2070 466322133 466322919 0.000000e+00 1315.0
20 TraesCS6A01G185900 chr7A 95.397 239 11 0 1 239 188858219 188857981 6.730000e-102 381.0
21 TraesCS6A01G185900 chr7A 94.239 243 12 1 1 243 645255892 645255652 1.460000e-98 370.0
22 TraesCS6A01G185900 chr7A 93.443 244 12 3 1 243 185196922 185196682 3.150000e-95 359.0
23 TraesCS6A01G185900 chr7A 89.873 79 8 0 1643 1721 537663146 537663224 5.870000e-18 102.0
24 TraesCS6A01G185900 chr5A 94.650 243 11 1 1 243 165365199 165364959 3.130000e-100 375.0
25 TraesCS6A01G185900 chr2A 94.672 244 10 2 1 243 144845892 144846133 3.130000e-100 375.0
26 TraesCS6A01G185900 chr4A 93.827 243 12 2 1 243 518118170 518118409 2.440000e-96 363.0
27 TraesCS6A01G185900 chr1A 94.468 235 13 0 1 235 254782198 254781964 2.440000e-96 363.0
28 TraesCS6A01G185900 chr3B 94.382 89 5 0 3235 3323 816244354 816244442 1.610000e-28 137.0
29 TraesCS6A01G185900 chr3D 94.118 85 5 0 3239 3323 609361157 609361073 2.690000e-26 130.0
30 TraesCS6A01G185900 chr4D 96.154 78 3 0 3240 3317 460580995 460581072 9.680000e-26 128.0
31 TraesCS6A01G185900 chr3A 93.976 83 5 0 3240 3322 747295804 747295886 3.480000e-25 126.0
32 TraesCS6A01G185900 chr7B 91.139 79 7 0 1643 1721 485430551 485430473 1.260000e-19 108.0
33 TraesCS6A01G185900 chr7D 96.774 62 2 0 1660 1721 462281558 462281497 1.630000e-18 104.0
34 TraesCS6A01G185900 chr5B 88.608 79 8 1 3239 3317 537537420 537537497 9.810000e-16 95.3


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 TraesCS6A01G185900 chr6A 219560275 219563597 3322 True 6137.000000 6137 100.000000 1 3323 1 chr6A.!!$R2 3322
1 TraesCS6A01G185900 chr6D 160427483 160430672 3189 True 1506.333333 2889 93.830000 254 3193 3 chr6D.!!$R1 2939
2 TraesCS6A01G185900 chr6B 290595017 290598312 3295 True 1933.500000 2819 93.769000 248 3216 2 chr6B.!!$R1 2968
3 TraesCS6A01G185900 chr6B 290626595 290630084 3489 True 1408.666667 1999 93.747333 248 3216 3 chr6B.!!$R2 2968
4 TraesCS6A01G185900 chr6B 290655367 290658928 3561 True 1107.666667 1472 92.813000 248 3216 3 chr6B.!!$R3 2968
5 TraesCS6A01G185900 chrUn 453960156 453961079 923 False 1471.000000 1471 95.381000 1542 2468 1 chrUn.!!$F1 926
6 TraesCS6A01G185900 chrUn 466322133 466322919 786 False 1315.000000 1315 96.827000 1283 2070 1 chrUn.!!$F2 787

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
574 575 0.545071 CTTGGGTTGGGCTTGGGAAT 60.545 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 3148 0.478507 CTCTCTCCCTCTCCCTCTCC 59.521 65.0 0.0 0.0 0.0 3.71 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
30 31 8.755696 GAGATGACATGTATCTCAATTCCTAC 57.244 38.462 24.95 3.52 46.22 3.18
31 32 8.255111 AGATGACATGTATCTCAATTCCTACA 57.745 34.615 0.00 0.00 29.05 2.74
32 33 8.366401 AGATGACATGTATCTCAATTCCTACAG 58.634 37.037 0.00 0.00 29.05 2.74
33 34 7.660030 TGACATGTATCTCAATTCCTACAGA 57.340 36.000 0.00 0.00 0.00 3.41
34 35 7.720442 TGACATGTATCTCAATTCCTACAGAG 58.280 38.462 0.00 0.00 0.00 3.35
35 36 7.561356 TGACATGTATCTCAATTCCTACAGAGA 59.439 37.037 0.00 0.00 40.96 3.10
36 37 8.311395 ACATGTATCTCAATTCCTACAGAGAA 57.689 34.615 0.00 0.00 40.19 2.87
37 38 8.762645 ACATGTATCTCAATTCCTACAGAGAAA 58.237 33.333 0.00 0.00 40.19 2.52
38 39 9.258826 CATGTATCTCAATTCCTACAGAGAAAG 57.741 37.037 0.00 0.00 40.19 2.62
39 40 8.595362 TGTATCTCAATTCCTACAGAGAAAGA 57.405 34.615 0.00 0.00 40.19 2.52
40 41 8.690884 TGTATCTCAATTCCTACAGAGAAAGAG 58.309 37.037 0.00 0.00 40.19 2.85
41 42 7.969690 ATCTCAATTCCTACAGAGAAAGAGA 57.030 36.000 9.81 9.81 40.19 3.10
42 43 7.969690 TCTCAATTCCTACAGAGAAAGAGAT 57.030 36.000 0.00 0.00 35.41 2.75
43 44 7.780064 TCTCAATTCCTACAGAGAAAGAGATG 58.220 38.462 0.00 0.00 35.41 2.90
44 45 7.398618 TCTCAATTCCTACAGAGAAAGAGATGT 59.601 37.037 0.00 0.00 35.41 3.06
45 46 7.551585 TCAATTCCTACAGAGAAAGAGATGTC 58.448 38.462 0.00 0.00 0.00 3.06
46 47 7.179160 TCAATTCCTACAGAGAAAGAGATGTCA 59.821 37.037 0.00 0.00 0.00 3.58
47 48 7.673641 ATTCCTACAGAGAAAGAGATGTCAT 57.326 36.000 0.00 0.00 0.00 3.06
48 49 7.487822 TTCCTACAGAGAAAGAGATGTCATT 57.512 36.000 0.00 0.00 0.00 2.57
49 50 7.487822 TCCTACAGAGAAAGAGATGTCATTT 57.512 36.000 0.00 0.00 0.00 2.32
50 51 7.326454 TCCTACAGAGAAAGAGATGTCATTTG 58.674 38.462 0.00 0.00 0.00 2.32
51 52 7.179160 TCCTACAGAGAAAGAGATGTCATTTGA 59.821 37.037 0.00 0.00 0.00 2.69
52 53 7.986320 CCTACAGAGAAAGAGATGTCATTTGAT 59.014 37.037 0.00 0.00 0.00 2.57
54 55 8.715191 ACAGAGAAAGAGATGTCATTTGATAC 57.285 34.615 0.00 0.00 0.00 2.24
55 56 8.316946 ACAGAGAAAGAGATGTCATTTGATACA 58.683 33.333 0.00 0.00 0.00 2.29
56 57 9.327628 CAGAGAAAGAGATGTCATTTGATACAT 57.672 33.333 0.00 0.00 39.00 2.29
59 60 9.775854 AGAAAGAGATGTCATTTGATACATAGG 57.224 33.333 0.00 0.00 36.48 2.57
60 61 9.770097 GAAAGAGATGTCATTTGATACATAGGA 57.230 33.333 0.00 0.00 36.48 2.94
64 65 9.814899 GAGATGTCATTTGATACATAGGATAGG 57.185 37.037 0.00 0.00 36.48 2.57
65 66 9.552695 AGATGTCATTTGATACATAGGATAGGA 57.447 33.333 0.00 0.00 36.48 2.94
92 93 8.635765 TTTTTCCATTGAGTCTTAGCTAATGT 57.364 30.769 6.64 0.00 0.00 2.71
93 94 8.635765 TTTTCCATTGAGTCTTAGCTAATGTT 57.364 30.769 6.64 0.00 0.00 2.71
94 95 8.635765 TTTCCATTGAGTCTTAGCTAATGTTT 57.364 30.769 6.64 0.00 0.00 2.83
95 96 8.635765 TTCCATTGAGTCTTAGCTAATGTTTT 57.364 30.769 6.64 0.00 0.00 2.43
96 97 8.635765 TCCATTGAGTCTTAGCTAATGTTTTT 57.364 30.769 6.64 0.00 0.00 1.94
115 116 4.953940 TTTTTCCTCCAAAATGTGAGGG 57.046 40.909 5.77 0.00 46.71 4.30
116 117 3.893753 TTTCCTCCAAAATGTGAGGGA 57.106 42.857 5.77 0.00 46.71 4.20
117 118 4.402616 TTTCCTCCAAAATGTGAGGGAT 57.597 40.909 5.77 0.00 46.71 3.85
118 119 4.402616 TTCCTCCAAAATGTGAGGGATT 57.597 40.909 5.77 0.00 46.71 3.01
119 120 3.700538 TCCTCCAAAATGTGAGGGATTG 58.299 45.455 5.77 0.00 46.71 2.67
120 121 3.333381 TCCTCCAAAATGTGAGGGATTGA 59.667 43.478 5.77 0.00 46.71 2.57
121 122 4.017222 TCCTCCAAAATGTGAGGGATTGAT 60.017 41.667 5.77 0.00 46.71 2.57
122 123 4.713321 CCTCCAAAATGTGAGGGATTGATT 59.287 41.667 0.00 0.00 43.69 2.57
123 124 5.163478 CCTCCAAAATGTGAGGGATTGATTC 60.163 44.000 0.00 0.00 43.69 2.52
124 125 4.711355 TCCAAAATGTGAGGGATTGATTCC 59.289 41.667 0.00 0.00 44.62 3.01
125 126 4.713321 CCAAAATGTGAGGGATTGATTCCT 59.287 41.667 0.00 0.00 44.75 3.36
126 127 5.893255 CCAAAATGTGAGGGATTGATTCCTA 59.107 40.000 0.00 0.00 44.75 2.94
127 128 6.552350 CCAAAATGTGAGGGATTGATTCCTAT 59.448 38.462 0.00 0.00 44.75 2.57
128 129 7.255730 CCAAAATGTGAGGGATTGATTCCTATC 60.256 40.741 0.00 0.00 44.75 2.08
129 130 4.982241 TGTGAGGGATTGATTCCTATCC 57.018 45.455 6.43 6.43 44.75 2.59
130 131 4.570926 TGTGAGGGATTGATTCCTATCCT 58.429 43.478 12.20 0.00 44.75 3.24
131 132 5.726560 TGTGAGGGATTGATTCCTATCCTA 58.273 41.667 12.20 1.55 44.75 2.94
132 133 5.544176 TGTGAGGGATTGATTCCTATCCTAC 59.456 44.000 12.20 10.18 44.75 3.18
133 134 5.544176 GTGAGGGATTGATTCCTATCCTACA 59.456 44.000 12.20 10.26 44.75 2.74
134 135 6.214412 GTGAGGGATTGATTCCTATCCTACAT 59.786 42.308 12.20 1.28 44.75 2.29
135 136 7.400339 GTGAGGGATTGATTCCTATCCTACATA 59.600 40.741 12.20 0.00 44.75 2.29
136 137 8.131627 TGAGGGATTGATTCCTATCCTACATAT 58.868 37.037 12.20 0.00 44.75 1.78
137 138 8.329346 AGGGATTGATTCCTATCCTACATATG 57.671 38.462 0.00 0.00 44.75 1.78
138 139 8.131627 AGGGATTGATTCCTATCCTACATATGA 58.868 37.037 10.38 0.00 44.75 2.15
139 140 8.772250 GGGATTGATTCCTATCCTACATATGAA 58.228 37.037 10.38 0.00 44.75 2.57
166 167 5.906073 GAATCCATTCCTACAAACCAATGG 58.094 41.667 0.00 0.00 44.64 3.16
167 168 3.707316 TCCATTCCTACAAACCAATGGG 58.293 45.455 3.55 0.00 43.80 4.00
168 169 2.168313 CCATTCCTACAAACCAATGGGC 59.832 50.000 3.55 0.00 41.11 5.36
169 170 2.990740 TTCCTACAAACCAATGGGCT 57.009 45.000 3.55 0.00 37.90 5.19
170 171 2.990740 TCCTACAAACCAATGGGCTT 57.009 45.000 3.55 0.00 37.90 4.35
171 172 2.802719 TCCTACAAACCAATGGGCTTC 58.197 47.619 3.55 0.00 37.90 3.86
172 173 2.109128 TCCTACAAACCAATGGGCTTCA 59.891 45.455 3.55 0.00 37.90 3.02
173 174 2.896685 CCTACAAACCAATGGGCTTCAA 59.103 45.455 3.55 0.00 37.90 2.69
174 175 3.323403 CCTACAAACCAATGGGCTTCAAA 59.677 43.478 3.55 0.00 37.90 2.69
175 176 3.473923 ACAAACCAATGGGCTTCAAAG 57.526 42.857 3.55 0.00 37.90 2.77
176 177 3.037549 ACAAACCAATGGGCTTCAAAGA 58.962 40.909 3.55 0.00 37.90 2.52
177 178 3.454082 ACAAACCAATGGGCTTCAAAGAA 59.546 39.130 3.55 0.00 37.90 2.52
178 179 4.080638 ACAAACCAATGGGCTTCAAAGAAA 60.081 37.500 3.55 0.00 37.90 2.52
179 180 4.769345 AACCAATGGGCTTCAAAGAAAA 57.231 36.364 3.55 0.00 37.90 2.29
180 181 4.769345 ACCAATGGGCTTCAAAGAAAAA 57.231 36.364 3.55 0.00 37.90 1.94
181 182 5.308976 ACCAATGGGCTTCAAAGAAAAAT 57.691 34.783 3.55 0.00 37.90 1.82
182 183 5.693961 ACCAATGGGCTTCAAAGAAAAATT 58.306 33.333 3.55 0.00 37.90 1.82
183 184 6.128486 ACCAATGGGCTTCAAAGAAAAATTT 58.872 32.000 3.55 0.00 37.90 1.82
184 185 6.606796 ACCAATGGGCTTCAAAGAAAAATTTT 59.393 30.769 3.55 0.00 37.90 1.82
185 186 7.140705 CCAATGGGCTTCAAAGAAAAATTTTC 58.859 34.615 10.26 10.26 0.00 2.29
186 187 7.013559 CCAATGGGCTTCAAAGAAAAATTTTCT 59.986 33.333 14.63 14.63 0.00 2.52
187 188 9.054922 CAATGGGCTTCAAAGAAAAATTTTCTA 57.945 29.630 19.83 3.60 0.00 2.10
188 189 9.797642 AATGGGCTTCAAAGAAAAATTTTCTAT 57.202 25.926 19.83 8.83 0.00 1.98
190 191 9.705290 TGGGCTTCAAAGAAAAATTTTCTATAC 57.295 29.630 19.83 7.94 0.00 1.47
191 192 9.705290 GGGCTTCAAAGAAAAATTTTCTATACA 57.295 29.630 19.83 5.95 0.00 2.29
231 232 8.753497 AAAATCCTATGAGATTCCTACAAACC 57.247 34.615 0.00 0.00 35.40 3.27
232 233 7.451731 AATCCTATGAGATTCCTACAAACCA 57.548 36.000 0.00 0.00 30.51 3.67
233 234 6.884472 TCCTATGAGATTCCTACAAACCAA 57.116 37.500 0.00 0.00 0.00 3.67
234 235 7.265599 TCCTATGAGATTCCTACAAACCAAA 57.734 36.000 0.00 0.00 0.00 3.28
235 236 7.695055 TCCTATGAGATTCCTACAAACCAAAA 58.305 34.615 0.00 0.00 0.00 2.44
236 237 8.167392 TCCTATGAGATTCCTACAAACCAAAAA 58.833 33.333 0.00 0.00 0.00 1.94
237 238 8.462016 CCTATGAGATTCCTACAAACCAAAAAG 58.538 37.037 0.00 0.00 0.00 2.27
238 239 6.648879 TGAGATTCCTACAAACCAAAAAGG 57.351 37.500 0.00 0.00 45.67 3.11
239 240 6.369629 TGAGATTCCTACAAACCAAAAAGGA 58.630 36.000 0.00 0.00 41.22 3.36
240 241 6.490040 TGAGATTCCTACAAACCAAAAAGGAG 59.510 38.462 0.00 0.00 41.22 3.69
241 242 5.775195 AGATTCCTACAAACCAAAAAGGAGG 59.225 40.000 0.00 0.00 41.22 4.30
242 243 3.227614 TCCTACAAACCAAAAAGGAGGC 58.772 45.455 0.00 0.00 41.22 4.70
243 244 2.962421 CCTACAAACCAAAAAGGAGGCA 59.038 45.455 0.00 0.00 41.22 4.75
244 245 3.578282 CCTACAAACCAAAAAGGAGGCAT 59.422 43.478 0.00 0.00 41.22 4.40
245 246 3.473923 ACAAACCAAAAAGGAGGCATG 57.526 42.857 0.00 0.00 41.22 4.06
246 247 3.037549 ACAAACCAAAAAGGAGGCATGA 58.962 40.909 0.00 0.00 41.22 3.07
264 265 5.346822 GGCATGAAGTATGTTTGCTTTGAAG 59.653 40.000 0.00 0.00 39.08 3.02
306 307 7.181485 ACATAGGGTAGTACAACACATTAACCT 59.819 37.037 2.06 0.00 0.00 3.50
308 309 4.939439 GGGTAGTACAACACATTAACCTGG 59.061 45.833 2.06 0.00 0.00 4.45
371 372 3.435169 GGAGAAGTTGTCCTTGAACCCTT 60.435 47.826 11.78 0.00 32.03 3.95
372 373 4.202430 GGAGAAGTTGTCCTTGAACCCTTA 60.202 45.833 11.78 0.00 32.03 2.69
381 382 5.903010 TGTCCTTGAACCCTTATATCTAGCA 59.097 40.000 0.00 0.00 0.00 3.49
383 384 6.931840 GTCCTTGAACCCTTATATCTAGCAAG 59.068 42.308 0.00 0.00 0.00 4.01
574 575 0.545071 CTTGGGTTGGGCTTGGGAAT 60.545 55.000 0.00 0.00 0.00 3.01
592 593 3.747010 GGAATGAATGTTTGCATGCACAA 59.253 39.130 22.58 14.94 43.03 3.33
680 694 4.890499 TCTCACTCTAGGAAAGGGATCT 57.110 45.455 0.00 0.00 0.00 2.75
733 749 3.900601 AGCTAGAGAGAGAGAGAGAGAGG 59.099 52.174 0.00 0.00 0.00 3.69
735 751 2.412591 AGAGAGAGAGAGAGAGAGGGG 58.587 57.143 0.00 0.00 0.00 4.79
761 817 3.190439 AGGGGGTGTTAGCTTGATAGTT 58.810 45.455 0.00 0.00 0.00 2.24
913 969 2.353208 GCTGCGTCTCCCTTATATCCAG 60.353 54.545 0.00 0.00 0.00 3.86
933 989 2.246067 AGCCTGATCTCTTCCACCTCTA 59.754 50.000 0.00 0.00 0.00 2.43
975 1031 7.768847 TAGCTTGAGGGCTAGAGATCTCTCG 62.769 52.000 28.38 22.63 43.84 4.04
997 1053 1.077334 TCTCGTTCCTCCTCTTCCCTT 59.923 52.381 0.00 0.00 0.00 3.95
1094 1150 3.372440 AGCCTTTCATCTACCCAAAGG 57.628 47.619 5.46 5.46 46.24 3.11
1151 1207 1.679977 TGGAGCATCAAGGGCAAGC 60.680 57.895 0.00 0.00 36.25 4.01
1271 1546 4.328712 TCAATATCGATGTGTTCCAACGTG 59.671 41.667 8.54 0.00 39.99 4.49
1289 1564 3.186409 ACGTGTTTAGTACATGCAAGCTG 59.814 43.478 0.00 0.00 45.83 4.24
1296 1571 6.721571 TTAGTACATGCAAGCTGTTCTTAC 57.278 37.500 3.79 0.00 32.74 2.34
1577 2191 3.636231 CACCAAGGAGGGACGGCA 61.636 66.667 0.00 0.00 43.89 5.69
1899 2513 1.265095 CAGTCTCTTTGCAACGCATGT 59.735 47.619 0.00 0.00 38.76 3.21
2066 2680 2.037385 AAGAAGGAGAAGAGGGCTGT 57.963 50.000 0.00 0.00 0.00 4.40
2070 2684 0.907230 AGGAGAAGAGGGCTGTGGAC 60.907 60.000 0.00 0.00 0.00 4.02
2131 2745 3.387050 GGTTGATCATCCTACCGTTACCT 59.613 47.826 14.55 0.00 0.00 3.08
2184 2798 3.679980 CGAAGGATCAAGATCACGTTGTT 59.320 43.478 11.78 0.00 39.54 2.83
2193 2807 0.036388 ATCACGTTGTTGCCGAGGAT 60.036 50.000 0.00 0.00 0.00 3.24
2229 2843 0.391661 GACTGAGCAAAGCCGATCCA 60.392 55.000 0.00 0.00 0.00 3.41
2231 2845 0.674581 CTGAGCAAAGCCGATCCACA 60.675 55.000 0.00 0.00 0.00 4.17
2316 2930 1.134367 CTATCCTGCGGTCTTGTTCGA 59.866 52.381 0.00 0.00 0.00 3.71
2468 3086 4.276146 GGTCGATCGGGGCGTACC 62.276 72.222 16.41 10.48 39.11 3.34
2477 3095 2.192187 GGGGCGTACCGGTAGAGAG 61.192 68.421 16.41 8.20 41.60 3.20
2479 3097 1.165284 GGGCGTACCGGTAGAGAGAG 61.165 65.000 16.41 3.81 36.48 3.20
2486 3143 4.680172 CGTACCGGTAGAGAGAGAAGAGAA 60.680 50.000 16.41 0.00 0.00 2.87
2491 3148 4.574828 CGGTAGAGAGAGAAGAGAAAGAGG 59.425 50.000 0.00 0.00 0.00 3.69
2497 3437 3.954258 GAGAGAAGAGAAAGAGGGAGAGG 59.046 52.174 0.00 0.00 0.00 3.69
2503 3443 1.290732 AGAAAGAGGGAGAGGGAGAGG 59.709 57.143 0.00 0.00 0.00 3.69
2679 3625 4.521639 TGTGTTCGTCCTCTGTAGTACAAT 59.478 41.667 4.21 0.00 0.00 2.71
2718 3664 6.847956 TTTCCGTAAGATCTTCGTTTTTCA 57.152 33.333 12.24 0.00 43.02 2.69
2736 3682 4.556942 TTCATTTGGAGCTGATAATGCG 57.443 40.909 0.00 0.00 35.28 4.73
2752 3701 0.527600 TGCGGAAAGGATCGATGACG 60.528 55.000 0.54 0.00 41.26 4.35
2766 3715 3.377485 TCGATGACGGGAGAAGAAACTAG 59.623 47.826 0.00 0.00 40.21 2.57
2811 3760 9.634163 TGGTTCATATATGTGACATATCGTTAC 57.366 33.333 20.38 14.14 34.74 2.50
2832 3785 7.169813 CGTTACTACTCACATGCATCATATTGT 59.830 37.037 0.00 0.00 0.00 2.71
2897 3850 4.142790 TGTTACTACTCCCTCATCGATCC 58.857 47.826 0.00 0.00 0.00 3.36
2955 3908 4.512944 AGAAACTACTGCGCATCATATTGG 59.487 41.667 12.24 0.00 0.00 3.16
2959 3912 1.232119 CTGCGCATCATATTGGCTGA 58.768 50.000 12.24 0.00 0.00 4.26
3137 4092 1.198637 GATCTGTGTCCTGCAACTTGC 59.801 52.381 6.82 6.82 45.29 4.01
3157 4113 3.192844 TGCTACAGAACTACTACAGGCAC 59.807 47.826 0.00 0.00 0.00 5.01
3158 4114 3.429135 GCTACAGAACTACTACAGGCACC 60.429 52.174 0.00 0.00 0.00 5.01
3159 4115 1.544691 ACAGAACTACTACAGGCACCG 59.455 52.381 0.00 0.00 0.00 4.94
3160 4116 1.816835 CAGAACTACTACAGGCACCGA 59.183 52.381 0.00 0.00 0.00 4.69
3161 4117 2.427453 CAGAACTACTACAGGCACCGAT 59.573 50.000 0.00 0.00 0.00 4.18
3188 4144 8.787884 CGGTATGTAAATTTTTAGCCGTTTTAC 58.212 33.333 0.00 0.00 34.76 2.01
3210 4166 8.624367 TTACTTTACTGCACCAAATTAGCTTA 57.376 30.769 0.00 0.00 0.00 3.09
3216 4172 7.461182 ACTGCACCAAATTAGCTTAAACATA 57.539 32.000 0.00 0.00 0.00 2.29
3217 4173 7.891561 ACTGCACCAAATTAGCTTAAACATAA 58.108 30.769 0.00 0.00 0.00 1.90
3218 4174 7.812669 ACTGCACCAAATTAGCTTAAACATAAC 59.187 33.333 0.00 0.00 0.00 1.89
3219 4175 7.093992 TGCACCAAATTAGCTTAAACATAACC 58.906 34.615 0.00 0.00 0.00 2.85
3220 4176 7.039363 TGCACCAAATTAGCTTAAACATAACCT 60.039 33.333 0.00 0.00 0.00 3.50
3221 4177 7.488150 GCACCAAATTAGCTTAAACATAACCTC 59.512 37.037 0.00 0.00 0.00 3.85
3222 4178 7.696453 CACCAAATTAGCTTAAACATAACCTCG 59.304 37.037 0.00 0.00 0.00 4.63
3223 4179 7.608761 ACCAAATTAGCTTAAACATAACCTCGA 59.391 33.333 0.00 0.00 0.00 4.04
3224 4180 8.621286 CCAAATTAGCTTAAACATAACCTCGAT 58.379 33.333 0.00 0.00 0.00 3.59
3225 4181 9.651718 CAAATTAGCTTAAACATAACCTCGATC 57.348 33.333 0.00 0.00 0.00 3.69
3226 4182 9.614792 AAATTAGCTTAAACATAACCTCGATCT 57.385 29.630 0.00 0.00 0.00 2.75
3227 4183 9.614792 AATTAGCTTAAACATAACCTCGATCTT 57.385 29.630 0.00 0.00 0.00 2.40
3230 4186 8.421673 AGCTTAAACATAACCTCGATCTTAAC 57.578 34.615 0.00 0.00 0.00 2.01
3231 4187 7.494952 AGCTTAAACATAACCTCGATCTTAACC 59.505 37.037 0.00 0.00 0.00 2.85
3232 4188 7.494952 GCTTAAACATAACCTCGATCTTAACCT 59.505 37.037 0.00 0.00 0.00 3.50
3233 4189 9.379791 CTTAAACATAACCTCGATCTTAACCTT 57.620 33.333 0.00 0.00 0.00 3.50
3234 4190 7.611213 AAACATAACCTCGATCTTAACCTTG 57.389 36.000 0.00 0.00 0.00 3.61
3235 4191 5.671493 ACATAACCTCGATCTTAACCTTGG 58.329 41.667 0.00 0.00 0.00 3.61
3236 4192 3.629142 AACCTCGATCTTAACCTTGGG 57.371 47.619 0.00 0.00 0.00 4.12
3237 4193 1.838077 ACCTCGATCTTAACCTTGGGG 59.162 52.381 0.00 0.00 38.88 4.96
3258 4214 5.473066 GGTTTTTCCCCTAAACCCTAAAC 57.527 43.478 6.28 0.00 45.63 2.01
3259 4215 4.284234 GGTTTTTCCCCTAAACCCTAAACC 59.716 45.833 6.28 0.00 45.63 3.27
3260 4216 3.831642 TTTCCCCTAAACCCTAAACCC 57.168 47.619 0.00 0.00 0.00 4.11
3261 4217 1.684982 TCCCCTAAACCCTAAACCCC 58.315 55.000 0.00 0.00 0.00 4.95
3262 4218 1.157066 TCCCCTAAACCCTAAACCCCT 59.843 52.381 0.00 0.00 0.00 4.79
3263 4219 2.005350 CCCCTAAACCCTAAACCCCTT 58.995 52.381 0.00 0.00 0.00 3.95
3264 4220 2.384375 CCCCTAAACCCTAAACCCCTTT 59.616 50.000 0.00 0.00 0.00 3.11
3265 4221 3.437213 CCCTAAACCCTAAACCCCTTTG 58.563 50.000 0.00 0.00 0.00 2.77
3266 4222 3.437213 CCTAAACCCTAAACCCCTTTGG 58.563 50.000 0.00 0.00 41.37 3.28
3267 4223 1.724545 AAACCCTAAACCCCTTTGGC 58.275 50.000 0.00 0.00 37.83 4.52
3268 4224 0.541063 AACCCTAAACCCCTTTGGCG 60.541 55.000 0.00 0.00 37.83 5.69
3269 4225 1.680989 CCCTAAACCCCTTTGGCGG 60.681 63.158 0.00 0.00 37.83 6.13
3270 4226 2.348104 CCTAAACCCCTTTGGCGGC 61.348 63.158 0.00 0.00 37.83 6.53
3271 4227 2.673687 TAAACCCCTTTGGCGGCG 60.674 61.111 0.51 0.51 37.83 6.46
3290 4246 3.857764 CCGAGGCGATCTAGGGTT 58.142 61.111 0.00 0.00 35.00 4.11
3291 4247 2.125178 CCGAGGCGATCTAGGGTTT 58.875 57.895 0.00 0.00 35.00 3.27
3292 4248 0.249489 CCGAGGCGATCTAGGGTTTG 60.249 60.000 0.00 0.00 35.00 2.93
3293 4249 0.249489 CGAGGCGATCTAGGGTTTGG 60.249 60.000 0.00 0.00 0.00 3.28
3294 4250 1.120530 GAGGCGATCTAGGGTTTGGA 58.879 55.000 0.00 0.00 0.00 3.53
3295 4251 0.831307 AGGCGATCTAGGGTTTGGAC 59.169 55.000 0.00 0.00 0.00 4.02
3296 4252 0.529992 GGCGATCTAGGGTTTGGACG 60.530 60.000 0.00 0.00 0.00 4.79
3297 4253 0.175073 GCGATCTAGGGTTTGGACGT 59.825 55.000 0.00 0.00 0.00 4.34
3298 4254 1.922570 CGATCTAGGGTTTGGACGTG 58.077 55.000 0.00 0.00 0.00 4.49
3299 4255 1.470979 CGATCTAGGGTTTGGACGTGG 60.471 57.143 0.00 0.00 0.00 4.94
3300 4256 1.829222 GATCTAGGGTTTGGACGTGGA 59.171 52.381 0.00 0.00 0.00 4.02
3301 4257 1.719529 TCTAGGGTTTGGACGTGGAA 58.280 50.000 0.00 0.00 0.00 3.53
3302 4258 1.345415 TCTAGGGTTTGGACGTGGAAC 59.655 52.381 0.00 0.00 0.00 3.62
3303 4259 1.071071 CTAGGGTTTGGACGTGGAACA 59.929 52.381 0.00 0.00 35.74 3.18
3304 4260 0.256464 AGGGTTTGGACGTGGAACAA 59.744 50.000 0.00 0.00 44.16 2.83
3305 4261 0.666374 GGGTTTGGACGTGGAACAAG 59.334 55.000 0.00 0.00 44.16 3.16
3306 4262 0.030235 GGTTTGGACGTGGAACAAGC 59.970 55.000 0.00 0.00 44.16 4.01
3307 4263 1.021968 GTTTGGACGTGGAACAAGCT 58.978 50.000 0.00 0.00 44.16 3.74
3308 4264 1.404035 GTTTGGACGTGGAACAAGCTT 59.596 47.619 0.00 0.00 44.16 3.74
3309 4265 1.305201 TTGGACGTGGAACAAGCTTC 58.695 50.000 0.00 0.00 44.16 3.86
3310 4266 0.468226 TGGACGTGGAACAAGCTTCT 59.532 50.000 0.00 0.00 44.16 2.85
3311 4267 1.149148 GGACGTGGAACAAGCTTCTC 58.851 55.000 0.00 0.00 44.16 2.87
3312 4268 1.270358 GGACGTGGAACAAGCTTCTCT 60.270 52.381 0.00 0.00 44.16 3.10
3313 4269 2.062519 GACGTGGAACAAGCTTCTCTC 58.937 52.381 0.00 0.00 44.16 3.20
3314 4270 1.270358 ACGTGGAACAAGCTTCTCTCC 60.270 52.381 0.00 3.40 44.16 3.71
3315 4271 1.001406 CGTGGAACAAGCTTCTCTCCT 59.999 52.381 15.59 0.00 44.16 3.69
3316 4272 2.421619 GTGGAACAAGCTTCTCTCCTG 58.578 52.381 15.59 0.00 44.16 3.86
3317 4273 1.271054 TGGAACAAGCTTCTCTCCTGC 60.271 52.381 15.59 0.00 31.92 4.85
3318 4274 1.271054 GGAACAAGCTTCTCTCCTGCA 60.271 52.381 0.00 0.00 0.00 4.41
3319 4275 2.075338 GAACAAGCTTCTCTCCTGCAG 58.925 52.381 6.78 6.78 0.00 4.41
3320 4276 1.346062 ACAAGCTTCTCTCCTGCAGA 58.654 50.000 17.39 0.00 0.00 4.26
3321 4277 1.907936 ACAAGCTTCTCTCCTGCAGAT 59.092 47.619 17.39 0.00 0.00 2.90
3322 4278 2.305343 ACAAGCTTCTCTCCTGCAGATT 59.695 45.455 17.39 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.363390 TGTAGGAATTGAGATACATGTCATCTC 58.637 37.037 24.04 24.04 45.76 2.75
6 7 8.255111 TGTAGGAATTGAGATACATGTCATCT 57.745 34.615 0.00 9.42 35.43 2.90
7 8 8.363390 TCTGTAGGAATTGAGATACATGTCATC 58.637 37.037 0.00 4.47 29.66 2.92
8 9 8.255111 TCTGTAGGAATTGAGATACATGTCAT 57.745 34.615 0.00 0.00 29.66 3.06
9 10 7.561356 TCTCTGTAGGAATTGAGATACATGTCA 59.439 37.037 0.00 0.00 31.53 3.58
10 11 7.946207 TCTCTGTAGGAATTGAGATACATGTC 58.054 38.462 0.00 0.00 31.53 3.06
11 12 7.904558 TCTCTGTAGGAATTGAGATACATGT 57.095 36.000 2.69 2.69 31.53 3.21
12 13 9.258826 CTTTCTCTGTAGGAATTGAGATACATG 57.741 37.037 0.00 0.00 35.78 3.21
13 14 9.206690 TCTTTCTCTGTAGGAATTGAGATACAT 57.793 33.333 0.00 0.00 35.78 2.29
14 15 8.595362 TCTTTCTCTGTAGGAATTGAGATACA 57.405 34.615 0.00 0.00 35.78 2.29
15 16 8.908903 TCTCTTTCTCTGTAGGAATTGAGATAC 58.091 37.037 0.00 0.00 35.78 2.24
16 17 9.653516 ATCTCTTTCTCTGTAGGAATTGAGATA 57.346 33.333 14.44 0.00 39.10 1.98
17 18 7.969690 TCTCTTTCTCTGTAGGAATTGAGAT 57.030 36.000 0.00 0.00 35.78 2.75
18 19 7.398618 ACATCTCTTTCTCTGTAGGAATTGAGA 59.601 37.037 0.00 0.00 37.23 3.27
19 20 7.555087 ACATCTCTTTCTCTGTAGGAATTGAG 58.445 38.462 0.00 0.00 0.00 3.02
20 21 7.179160 TGACATCTCTTTCTCTGTAGGAATTGA 59.821 37.037 0.00 0.00 0.00 2.57
21 22 7.326454 TGACATCTCTTTCTCTGTAGGAATTG 58.674 38.462 0.00 0.00 0.00 2.32
22 23 7.487822 TGACATCTCTTTCTCTGTAGGAATT 57.512 36.000 0.00 0.00 0.00 2.17
23 24 7.673641 ATGACATCTCTTTCTCTGTAGGAAT 57.326 36.000 0.00 0.00 0.00 3.01
24 25 7.487822 AATGACATCTCTTTCTCTGTAGGAA 57.512 36.000 0.00 0.00 0.00 3.36
25 26 7.179160 TCAAATGACATCTCTTTCTCTGTAGGA 59.821 37.037 0.00 0.00 0.00 2.94
26 27 7.326454 TCAAATGACATCTCTTTCTCTGTAGG 58.674 38.462 0.00 0.00 0.00 3.18
27 28 8.945481 ATCAAATGACATCTCTTTCTCTGTAG 57.055 34.615 0.00 0.00 0.00 2.74
28 29 9.809096 GTATCAAATGACATCTCTTTCTCTGTA 57.191 33.333 0.00 0.00 0.00 2.74
29 30 8.316946 TGTATCAAATGACATCTCTTTCTCTGT 58.683 33.333 0.00 0.00 0.00 3.41
30 31 8.713737 TGTATCAAATGACATCTCTTTCTCTG 57.286 34.615 0.00 0.00 0.00 3.35
33 34 9.775854 CCTATGTATCAAATGACATCTCTTTCT 57.224 33.333 0.00 0.00 37.47 2.52
34 35 9.770097 TCCTATGTATCAAATGACATCTCTTTC 57.230 33.333 0.00 0.00 37.47 2.62
38 39 9.814899 CCTATCCTATGTATCAAATGACATCTC 57.185 37.037 0.00 0.00 37.47 2.75
39 40 9.552695 TCCTATCCTATGTATCAAATGACATCT 57.447 33.333 0.00 0.00 37.47 2.90
66 67 9.247861 ACATTAGCTAAGACTCAATGGAAAAAT 57.752 29.630 12.54 0.00 32.20 1.82
67 68 8.635765 ACATTAGCTAAGACTCAATGGAAAAA 57.364 30.769 12.54 0.00 32.20 1.94
68 69 8.635765 AACATTAGCTAAGACTCAATGGAAAA 57.364 30.769 12.54 0.00 32.20 2.29
69 70 8.635765 AAACATTAGCTAAGACTCAATGGAAA 57.364 30.769 12.54 0.00 32.20 3.13
70 71 8.635765 AAAACATTAGCTAAGACTCAATGGAA 57.364 30.769 12.54 0.00 32.20 3.53
71 72 8.635765 AAAAACATTAGCTAAGACTCAATGGA 57.364 30.769 12.54 0.00 32.20 3.41
100 101 5.163478 GGAATCAATCCCTCACATTTTGGAG 60.163 44.000 0.00 0.00 43.00 3.86
101 102 4.711355 GGAATCAATCCCTCACATTTTGGA 59.289 41.667 0.00 0.00 43.00 3.53
102 103 5.014808 GGAATCAATCCCTCACATTTTGG 57.985 43.478 0.00 0.00 43.00 3.28
122 123 9.661954 GGATTCCTATTCATATGTAGGATAGGA 57.338 37.037 18.20 20.34 44.35 2.94
123 124 9.439461 TGGATTCCTATTCATATGTAGGATAGG 57.561 37.037 18.20 19.01 44.35 2.57
143 144 5.163416 CCCATTGGTTTGTAGGAATGGATTC 60.163 44.000 10.52 0.00 45.26 2.52
144 145 4.716287 CCCATTGGTTTGTAGGAATGGATT 59.284 41.667 10.52 0.00 45.26 3.01
145 146 4.289245 CCCATTGGTTTGTAGGAATGGAT 58.711 43.478 10.52 0.00 45.26 3.41
146 147 3.707316 CCCATTGGTTTGTAGGAATGGA 58.293 45.455 10.52 0.00 45.26 3.41
147 148 2.168313 GCCCATTGGTTTGTAGGAATGG 59.832 50.000 1.20 0.00 43.06 3.16
148 149 3.099141 AGCCCATTGGTTTGTAGGAATG 58.901 45.455 1.20 0.00 0.00 2.67
149 150 3.473113 AGCCCATTGGTTTGTAGGAAT 57.527 42.857 1.20 0.00 0.00 3.01
150 151 2.990740 AGCCCATTGGTTTGTAGGAA 57.009 45.000 1.20 0.00 0.00 3.36
151 152 2.109128 TGAAGCCCATTGGTTTGTAGGA 59.891 45.455 1.20 0.00 34.87 2.94
152 153 2.524306 TGAAGCCCATTGGTTTGTAGG 58.476 47.619 1.20 0.00 34.87 3.18
153 154 4.280677 TCTTTGAAGCCCATTGGTTTGTAG 59.719 41.667 1.20 0.00 34.87 2.74
154 155 4.219115 TCTTTGAAGCCCATTGGTTTGTA 58.781 39.130 1.20 0.00 34.87 2.41
155 156 3.037549 TCTTTGAAGCCCATTGGTTTGT 58.962 40.909 1.20 0.00 34.87 2.83
156 157 3.749665 TCTTTGAAGCCCATTGGTTTG 57.250 42.857 1.20 0.00 34.87 2.93
157 158 4.769345 TTTCTTTGAAGCCCATTGGTTT 57.231 36.364 1.20 0.00 37.85 3.27
158 159 4.769345 TTTTCTTTGAAGCCCATTGGTT 57.231 36.364 1.20 0.00 37.39 3.67
159 160 4.769345 TTTTTCTTTGAAGCCCATTGGT 57.231 36.364 1.20 0.00 0.00 3.67
160 161 6.638096 AAATTTTTCTTTGAAGCCCATTGG 57.362 33.333 0.00 0.00 0.00 3.16
161 162 7.933396 AGAAAATTTTTCTTTGAAGCCCATTG 58.067 30.769 16.82 0.00 0.00 2.82
162 163 9.797642 ATAGAAAATTTTTCTTTGAAGCCCATT 57.202 25.926 25.04 3.85 0.00 3.16
164 165 9.705290 GTATAGAAAATTTTTCTTTGAAGCCCA 57.295 29.630 25.04 8.28 0.00 5.36
165 166 9.705290 TGTATAGAAAATTTTTCTTTGAAGCCC 57.295 29.630 25.04 9.18 0.00 5.19
205 206 9.190317 GGTTTGTAGGAATCTCATAGGATTTTT 57.810 33.333 0.00 0.00 36.24 1.94
206 207 8.336235 TGGTTTGTAGGAATCTCATAGGATTTT 58.664 33.333 0.00 0.00 36.24 1.82
207 208 7.872138 TGGTTTGTAGGAATCTCATAGGATTT 58.128 34.615 0.00 0.00 36.24 2.17
208 209 7.451731 TGGTTTGTAGGAATCTCATAGGATT 57.548 36.000 0.00 0.00 38.47 3.01
209 210 7.451731 TTGGTTTGTAGGAATCTCATAGGAT 57.548 36.000 0.00 0.00 0.00 3.24
210 211 6.884472 TTGGTTTGTAGGAATCTCATAGGA 57.116 37.500 0.00 0.00 0.00 2.94
211 212 7.938140 TTTTGGTTTGTAGGAATCTCATAGG 57.062 36.000 0.00 0.00 0.00 2.57
212 213 8.462016 CCTTTTTGGTTTGTAGGAATCTCATAG 58.538 37.037 0.00 0.00 0.00 2.23
213 214 8.167392 TCCTTTTTGGTTTGTAGGAATCTCATA 58.833 33.333 0.00 0.00 37.07 2.15
214 215 7.010160 TCCTTTTTGGTTTGTAGGAATCTCAT 58.990 34.615 0.00 0.00 37.07 2.90
215 216 6.369629 TCCTTTTTGGTTTGTAGGAATCTCA 58.630 36.000 0.00 0.00 37.07 3.27
216 217 6.071896 CCTCCTTTTTGGTTTGTAGGAATCTC 60.072 42.308 0.00 0.00 34.77 2.75
217 218 5.775195 CCTCCTTTTTGGTTTGTAGGAATCT 59.225 40.000 0.00 0.00 34.77 2.40
218 219 5.566826 GCCTCCTTTTTGGTTTGTAGGAATC 60.567 44.000 0.00 0.00 34.77 2.52
219 220 4.283467 GCCTCCTTTTTGGTTTGTAGGAAT 59.717 41.667 0.00 0.00 34.77 3.01
220 221 3.639561 GCCTCCTTTTTGGTTTGTAGGAA 59.360 43.478 0.00 0.00 34.77 3.36
221 222 3.227614 GCCTCCTTTTTGGTTTGTAGGA 58.772 45.455 0.00 0.00 37.07 2.94
222 223 2.962421 TGCCTCCTTTTTGGTTTGTAGG 59.038 45.455 0.00 0.00 37.07 3.18
223 224 4.280677 TCATGCCTCCTTTTTGGTTTGTAG 59.719 41.667 0.00 0.00 37.07 2.74
224 225 4.219115 TCATGCCTCCTTTTTGGTTTGTA 58.781 39.130 0.00 0.00 37.07 2.41
225 226 3.037549 TCATGCCTCCTTTTTGGTTTGT 58.962 40.909 0.00 0.00 37.07 2.83
226 227 3.749665 TCATGCCTCCTTTTTGGTTTG 57.250 42.857 0.00 0.00 37.07 2.93
227 228 3.711190 ACTTCATGCCTCCTTTTTGGTTT 59.289 39.130 0.00 0.00 37.07 3.27
228 229 3.308401 ACTTCATGCCTCCTTTTTGGTT 58.692 40.909 0.00 0.00 37.07 3.67
229 230 2.962859 ACTTCATGCCTCCTTTTTGGT 58.037 42.857 0.00 0.00 37.07 3.67
230 231 4.463891 ACATACTTCATGCCTCCTTTTTGG 59.536 41.667 0.00 0.00 38.29 3.28
231 232 5.649782 ACATACTTCATGCCTCCTTTTTG 57.350 39.130 0.00 0.00 38.29 2.44
232 233 6.458210 CAAACATACTTCATGCCTCCTTTTT 58.542 36.000 0.00 0.00 38.29 1.94
233 234 5.567423 GCAAACATACTTCATGCCTCCTTTT 60.567 40.000 0.00 0.00 38.29 2.27
234 235 4.082026 GCAAACATACTTCATGCCTCCTTT 60.082 41.667 0.00 0.00 38.29 3.11
235 236 3.445096 GCAAACATACTTCATGCCTCCTT 59.555 43.478 0.00 0.00 38.29 3.36
236 237 3.019564 GCAAACATACTTCATGCCTCCT 58.980 45.455 0.00 0.00 38.29 3.69
237 238 3.019564 AGCAAACATACTTCATGCCTCC 58.980 45.455 0.00 0.00 38.29 4.30
238 239 4.708726 AAGCAAACATACTTCATGCCTC 57.291 40.909 0.00 0.00 38.29 4.70
239 240 4.523943 TCAAAGCAAACATACTTCATGCCT 59.476 37.500 0.00 0.00 38.29 4.75
240 241 4.808558 TCAAAGCAAACATACTTCATGCC 58.191 39.130 0.00 0.00 38.29 4.40
241 242 5.922544 ACTTCAAAGCAAACATACTTCATGC 59.077 36.000 0.00 0.00 38.29 4.06
242 243 7.140705 TCACTTCAAAGCAAACATACTTCATG 58.859 34.615 0.00 0.00 40.78 3.07
243 244 7.229306 TCTCACTTCAAAGCAAACATACTTCAT 59.771 33.333 0.00 0.00 0.00 2.57
244 245 6.542005 TCTCACTTCAAAGCAAACATACTTCA 59.458 34.615 0.00 0.00 0.00 3.02
245 246 6.959361 TCTCACTTCAAAGCAAACATACTTC 58.041 36.000 0.00 0.00 0.00 3.01
246 247 6.942532 TCTCACTTCAAAGCAAACATACTT 57.057 33.333 0.00 0.00 0.00 2.24
264 265 5.705905 ACCCTATGTTAAAAGTGCTTCTCAC 59.294 40.000 0.00 0.00 45.98 3.51
351 352 3.953542 AAGGGTTCAAGGACAACTTCT 57.046 42.857 0.00 0.00 37.29 2.85
371 372 4.458295 GTGGACGGCTACTTGCTAGATATA 59.542 45.833 0.00 0.00 42.39 0.86
372 373 3.256136 GTGGACGGCTACTTGCTAGATAT 59.744 47.826 0.00 0.00 42.39 1.63
381 382 2.254508 AGGTAAAGTGGACGGCTACTT 58.745 47.619 15.19 15.19 46.27 2.24
383 384 2.740447 CAAAGGTAAAGTGGACGGCTAC 59.260 50.000 0.00 0.00 0.00 3.58
393 394 5.049828 GCTGTTGAATTGCAAAGGTAAAGT 58.950 37.500 1.71 0.00 38.44 2.66
574 575 3.729966 ACATTGTGCATGCAAACATTCA 58.270 36.364 24.58 12.40 36.14 2.57
592 593 6.206634 AGTCGAACAAACACATTATTGGACAT 59.793 34.615 0.00 0.00 0.00 3.06
680 694 4.017037 AGAGGGACTTAGAAGGATGTCTGA 60.017 45.833 0.00 0.00 41.55 3.27
735 751 3.417779 GCTAACACCCCCTCCCCC 61.418 72.222 0.00 0.00 0.00 5.40
737 753 1.205460 TCAAGCTAACACCCCCTCCC 61.205 60.000 0.00 0.00 0.00 4.30
739 755 2.772515 ACTATCAAGCTAACACCCCCTC 59.227 50.000 0.00 0.00 0.00 4.30
740 756 2.846950 ACTATCAAGCTAACACCCCCT 58.153 47.619 0.00 0.00 0.00 4.79
741 757 3.279434 CAACTATCAAGCTAACACCCCC 58.721 50.000 0.00 0.00 0.00 5.40
743 759 3.610911 AGCAACTATCAAGCTAACACCC 58.389 45.455 0.00 0.00 36.73 4.61
761 817 1.604378 GCTAAGGGAGCCAAGAGCA 59.396 57.895 0.00 0.00 46.41 4.26
913 969 1.494960 AGAGGTGGAAGAGATCAGGC 58.505 55.000 0.00 0.00 0.00 4.85
975 1031 1.205179 GGGAAGAGGAGGAACGAGAAC 59.795 57.143 0.00 0.00 0.00 3.01
1094 1150 4.225267 TGAAAGGGAACAAGATAGGAGGAC 59.775 45.833 0.00 0.00 0.00 3.85
1151 1207 0.387202 CGAGTGCTGGTCTCCATAGG 59.613 60.000 0.00 0.00 30.82 2.57
1218 1274 5.462530 TTGTGTAGCTAGCTAGTTGTGAA 57.537 39.130 24.78 9.12 0.00 3.18
1271 1546 5.613358 AGAACAGCTTGCATGTACTAAAC 57.387 39.130 1.14 0.00 0.00 2.01
1289 1564 3.274288 CAGGGAGCAGGATTGTAAGAAC 58.726 50.000 0.00 0.00 0.00 3.01
1296 1571 1.035932 CAAGCCAGGGAGCAGGATTG 61.036 60.000 0.00 0.00 43.78 2.67
1577 2191 1.548809 GCCCTTCTCCTTGGCTTTCTT 60.549 52.381 0.00 0.00 42.01 2.52
2022 2636 2.667874 TTCACCGCTTGCGATGCA 60.668 55.556 16.99 0.00 36.47 3.96
2028 2642 2.050077 GTTGCCTTCACCGCTTGC 60.050 61.111 0.00 0.00 0.00 4.01
2088 2702 4.015084 CCATCTTGCACCTCTTCTTGAAT 58.985 43.478 0.00 0.00 0.00 2.57
2193 2807 4.100084 CTCTCCACCATGGCGCCA 62.100 66.667 34.80 34.80 37.47 5.69
2229 2843 0.952497 CGTGAGTGAATGCTGCCTGT 60.952 55.000 0.00 0.00 0.00 4.00
2231 2845 1.376424 CCGTGAGTGAATGCTGCCT 60.376 57.895 0.00 0.00 0.00 4.75
2468 3086 4.574828 CCTCTTTCTCTTCTCTCTCTACCG 59.425 50.000 0.00 0.00 0.00 4.02
2470 3088 5.751586 TCCCTCTTTCTCTTCTCTCTCTAC 58.248 45.833 0.00 0.00 0.00 2.59
2473 3091 4.855340 TCTCCCTCTTTCTCTTCTCTCTC 58.145 47.826 0.00 0.00 0.00 3.20
2475 3093 3.954258 CCTCTCCCTCTTTCTCTTCTCTC 59.046 52.174 0.00 0.00 0.00 3.20
2477 3095 3.031013 CCCTCTCCCTCTTTCTCTTCTC 58.969 54.545 0.00 0.00 0.00 2.87
2479 3097 3.031013 CTCCCTCTCCCTCTTTCTCTTC 58.969 54.545 0.00 0.00 0.00 2.87
2486 3143 0.556380 TCCCTCTCCCTCTCCCTCTT 60.556 60.000 0.00 0.00 0.00 2.85
2491 3148 0.478507 CTCTCTCCCTCTCCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
2497 3437 1.293683 ACCCTCCTCTCTCCCTCTCC 61.294 65.000 0.00 0.00 0.00 3.71
2503 3443 1.342474 TGTGATCACCCTCCTCTCTCC 60.342 57.143 22.85 0.00 0.00 3.71
2552 3492 8.771521 TCTGGGTTACTGCATATACTAACTAA 57.228 34.615 0.00 0.00 0.00 2.24
2718 3664 3.213206 TCCGCATTATCAGCTCCAAAT 57.787 42.857 0.00 0.00 0.00 2.32
2736 3682 0.750850 TCCCGTCATCGATCCTTTCC 59.249 55.000 0.00 0.00 39.71 3.13
2752 3701 1.628846 TGCACCCTAGTTTCTTCTCCC 59.371 52.381 0.00 0.00 0.00 4.30
2766 3715 2.559668 CCACATCCAATATGATGCACCC 59.440 50.000 0.00 0.00 44.84 4.61
2811 3760 6.704937 ACAGACAATATGATGCATGTGAGTAG 59.295 38.462 2.46 0.00 0.00 2.57
2817 3766 5.187687 TGTGACAGACAATATGATGCATGT 58.812 37.500 2.46 0.00 0.00 3.21
3042 3997 3.506398 TGAGGTAGAATGTCTGTGTCCA 58.494 45.455 0.00 0.00 0.00 4.02
3083 4038 1.066929 GGGTTCATTTGTCCCACATGC 60.067 52.381 0.00 0.00 40.79 4.06
3084 4039 1.550072 GGGGTTCATTTGTCCCACATG 59.450 52.381 12.72 0.00 42.71 3.21
3085 4040 1.432807 AGGGGTTCATTTGTCCCACAT 59.567 47.619 12.72 0.65 42.71 3.21
3086 4041 0.856982 AGGGGTTCATTTGTCCCACA 59.143 50.000 12.72 0.00 42.71 4.17
3137 4092 3.181499 CGGTGCCTGTAGTAGTTCTGTAG 60.181 52.174 0.00 0.00 0.00 2.74
3157 4113 6.368213 GGCTAAAAATTTACATACCGATCGG 58.632 40.000 32.20 32.20 42.03 4.18
3158 4114 6.068931 CGGCTAAAAATTTACATACCGATCG 58.931 40.000 8.51 8.51 40.49 3.69
3159 4115 6.951643 ACGGCTAAAAATTTACATACCGATC 58.048 36.000 19.89 0.00 40.49 3.69
3160 4116 6.930667 ACGGCTAAAAATTTACATACCGAT 57.069 33.333 19.89 7.33 40.49 4.18
3161 4117 6.740411 AACGGCTAAAAATTTACATACCGA 57.260 33.333 19.89 0.00 40.49 4.69
3188 4144 7.865385 TGTTTAAGCTAATTTGGTGCAGTAAAG 59.135 33.333 0.00 0.00 0.00 1.85
3191 4147 6.885952 TGTTTAAGCTAATTTGGTGCAGTA 57.114 33.333 0.00 0.00 0.00 2.74
3210 4166 6.598064 CCAAGGTTAAGATCGAGGTTATGTTT 59.402 38.462 0.00 0.00 0.00 2.83
3216 4172 2.238898 CCCCAAGGTTAAGATCGAGGTT 59.761 50.000 0.00 0.00 0.00 3.50
3217 4173 1.838077 CCCCAAGGTTAAGATCGAGGT 59.162 52.381 0.00 0.00 0.00 3.85
3218 4174 2.622064 CCCCAAGGTTAAGATCGAGG 57.378 55.000 0.00 0.00 0.00 4.63
3237 4193 4.284234 GGGTTTAGGGTTTAGGGGAAAAAC 59.716 45.833 0.00 0.00 36.34 2.43
3238 4194 4.491675 GGGTTTAGGGTTTAGGGGAAAAA 58.508 43.478 0.00 0.00 0.00 1.94
3239 4195 3.181408 GGGGTTTAGGGTTTAGGGGAAAA 60.181 47.826 0.00 0.00 0.00 2.29
3240 4196 2.382993 GGGGTTTAGGGTTTAGGGGAAA 59.617 50.000 0.00 0.00 0.00 3.13
3241 4197 2.002315 GGGGTTTAGGGTTTAGGGGAA 58.998 52.381 0.00 0.00 0.00 3.97
3242 4198 1.157066 AGGGGTTTAGGGTTTAGGGGA 59.843 52.381 0.00 0.00 0.00 4.81
3243 4199 1.690010 AGGGGTTTAGGGTTTAGGGG 58.310 55.000 0.00 0.00 0.00 4.79
3244 4200 3.437213 CAAAGGGGTTTAGGGTTTAGGG 58.563 50.000 0.00 0.00 0.00 3.53
3245 4201 3.437213 CCAAAGGGGTTTAGGGTTTAGG 58.563 50.000 0.00 0.00 0.00 2.69
3246 4202 2.829720 GCCAAAGGGGTTTAGGGTTTAG 59.170 50.000 0.00 0.00 39.65 1.85
3247 4203 2.818593 CGCCAAAGGGGTTTAGGGTTTA 60.819 50.000 0.00 0.00 39.65 2.01
3248 4204 1.724545 GCCAAAGGGGTTTAGGGTTT 58.275 50.000 0.00 0.00 39.65 3.27
3249 4205 0.541063 CGCCAAAGGGGTTTAGGGTT 60.541 55.000 0.00 0.00 39.65 4.11
3250 4206 1.076014 CGCCAAAGGGGTTTAGGGT 59.924 57.895 0.00 0.00 39.65 4.34
3251 4207 1.680989 CCGCCAAAGGGGTTTAGGG 60.681 63.158 0.00 0.00 41.20 3.53
3252 4208 4.012138 CCGCCAAAGGGGTTTAGG 57.988 61.111 0.00 0.00 41.20 2.69
3271 4227 3.686045 CCCTAGATCGCCTCGGGC 61.686 72.222 4.96 4.96 46.75 6.13
3273 4229 0.249489 CAAACCCTAGATCGCCTCGG 60.249 60.000 0.00 0.00 0.00 4.63
3274 4230 0.249489 CCAAACCCTAGATCGCCTCG 60.249 60.000 0.00 0.00 0.00 4.63
3275 4231 1.120530 TCCAAACCCTAGATCGCCTC 58.879 55.000 0.00 0.00 0.00 4.70
3276 4232 0.831307 GTCCAAACCCTAGATCGCCT 59.169 55.000 0.00 0.00 0.00 5.52
3277 4233 0.529992 CGTCCAAACCCTAGATCGCC 60.530 60.000 0.00 0.00 0.00 5.54
3278 4234 0.175073 ACGTCCAAACCCTAGATCGC 59.825 55.000 0.00 0.00 0.00 4.58
3279 4235 1.470979 CCACGTCCAAACCCTAGATCG 60.471 57.143 0.00 0.00 0.00 3.69
3280 4236 1.829222 TCCACGTCCAAACCCTAGATC 59.171 52.381 0.00 0.00 0.00 2.75
3281 4237 1.946984 TCCACGTCCAAACCCTAGAT 58.053 50.000 0.00 0.00 0.00 1.98
3282 4238 1.345415 GTTCCACGTCCAAACCCTAGA 59.655 52.381 0.00 0.00 0.00 2.43
3283 4239 1.071071 TGTTCCACGTCCAAACCCTAG 59.929 52.381 0.00 0.00 0.00 3.02
3284 4240 1.129917 TGTTCCACGTCCAAACCCTA 58.870 50.000 0.00 0.00 0.00 3.53
3285 4241 0.256464 TTGTTCCACGTCCAAACCCT 59.744 50.000 0.00 0.00 0.00 4.34
3286 4242 0.666374 CTTGTTCCACGTCCAAACCC 59.334 55.000 0.00 0.00 0.00 4.11
3287 4243 0.030235 GCTTGTTCCACGTCCAAACC 59.970 55.000 0.00 0.00 0.00 3.27
3288 4244 1.021968 AGCTTGTTCCACGTCCAAAC 58.978 50.000 0.00 0.00 0.00 2.93
3289 4245 1.673920 GAAGCTTGTTCCACGTCCAAA 59.326 47.619 2.10 0.00 0.00 3.28
3290 4246 1.134220 AGAAGCTTGTTCCACGTCCAA 60.134 47.619 2.10 0.00 0.00 3.53
3291 4247 0.468226 AGAAGCTTGTTCCACGTCCA 59.532 50.000 2.10 0.00 0.00 4.02
3292 4248 1.149148 GAGAAGCTTGTTCCACGTCC 58.851 55.000 2.10 0.00 0.00 4.79
3293 4249 2.062519 GAGAGAAGCTTGTTCCACGTC 58.937 52.381 2.10 0.00 0.00 4.34
3294 4250 1.270358 GGAGAGAAGCTTGTTCCACGT 60.270 52.381 2.10 0.00 0.00 4.49
3295 4251 1.001406 AGGAGAGAAGCTTGTTCCACG 59.999 52.381 19.63 0.00 0.00 4.94
3296 4252 2.421619 CAGGAGAGAAGCTTGTTCCAC 58.578 52.381 19.63 8.40 0.00 4.02
3297 4253 1.271054 GCAGGAGAGAAGCTTGTTCCA 60.271 52.381 19.63 0.00 0.00 3.53
3298 4254 1.271054 TGCAGGAGAGAAGCTTGTTCC 60.271 52.381 2.10 10.00 0.00 3.62
3299 4255 2.075338 CTGCAGGAGAGAAGCTTGTTC 58.925 52.381 2.10 0.96 0.00 3.18
3300 4256 1.696336 TCTGCAGGAGAGAAGCTTGTT 59.304 47.619 15.13 0.00 0.00 2.83
3301 4257 1.346062 TCTGCAGGAGAGAAGCTTGT 58.654 50.000 15.13 0.00 0.00 3.16
3302 4258 2.695127 ATCTGCAGGAGAGAAGCTTG 57.305 50.000 15.13 0.00 32.80 4.01


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

AutoCloner maintained by Alex Coulton.