Multiple sequence alignment - TraesCS5B01G248800

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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 TraesCS5B01G248800 chr5B 100.000 2156 0 0 1 2156 431059311 431061466 0.000000e+00 3982
1 TraesCS5B01G248800 chr5D 86.667 1350 82 40 737 2006 365081406 365082737 0.000000e+00 1406
2 TraesCS5B01G248800 chr5D 83.146 445 49 13 303 739 365079929 365080355 1.210000e-102 383
3 TraesCS5B01G248800 chr5D 86.869 297 30 2 1 288 394856372 394856668 7.420000e-85 324
4 TraesCS5B01G248800 chr5D 87.838 222 27 0 2 223 107476248 107476469 5.900000e-66 261
5 TraesCS5B01G248800 chr5D 85.143 175 24 2 360 533 150835738 150835565 6.110000e-41 178
6 TraesCS5B01G248800 chr5D 86.916 107 7 4 2043 2142 365082740 365082846 1.750000e-21 113
7 TraesCS5B01G248800 chr5A 87.084 1231 66 41 704 1866 466571278 466572483 0.000000e+00 1306
8 TraesCS5B01G248800 chr5A 83.429 175 27 2 360 533 206730807 206730634 6.160000e-36 161
9 TraesCS5B01G248800 chr5A 91.589 107 8 1 1900 2006 466572482 466572587 1.720000e-31 147
10 TraesCS5B01G248800 chr3B 87.629 291 26 2 1 281 763282706 763282416 1.600000e-86 329
11 TraesCS5B01G248800 chrUn 86.301 292 28 4 1 283 126689044 126689332 7.470000e-80 307
12 TraesCS5B01G248800 chr7A 84.068 295 22 3 1 287 720958671 720958948 5.900000e-66 261
13 TraesCS5B01G248800 chr4B 87.582 153 18 1 369 520 182666190 182666342 2.200000e-40 176
14 TraesCS5B01G248800 chr7D 85.366 164 21 3 370 531 549315203 549315041 1.320000e-37 167
15 TraesCS5B01G248800 chr6A 84.663 163 23 2 369 530 371331260 371331099 6.160000e-36 161
16 TraesCS5B01G248800 chr4D 84.242 165 25 1 367 530 465125307 465125471 2.210000e-35 159
17 TraesCS5B01G248800 chr4D 83.750 160 22 4 370 526 29317169 29317011 4.790000e-32 148
18 TraesCS5B01G248800 chr4A 84.568 162 24 1 371 531 597183856 597184017 2.210000e-35 159


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 TraesCS5B01G248800 chr5B 431059311 431061466 2155 False 3982.0 3982 100.000000 1 2156 1 chr5B.!!$F1 2155
1 TraesCS5B01G248800 chr5D 365079929 365082846 2917 False 634.0 1406 85.576333 303 2142 3 chr5D.!!$F3 1839
2 TraesCS5B01G248800 chr5A 466571278 466572587 1309 False 726.5 1306 89.336500 704 2006 2 chr5A.!!$F1 1302

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
292 293 0.033699 GGGGGACGAGTGGTAGTACT 60.034 60.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1397 2514 0.033366 CCATCGTGGCATCGTCCATA 59.967 55.0 8.8 0.0 38.57 2.74 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
67 68 4.711949 AGCTCAAGCCACCGCCAG 62.712 66.667 0.00 0.00 43.38 4.85
95 96 2.126228 CGTCGCACGGGCTCTAAA 60.126 61.111 8.62 0.00 38.08 1.85
96 97 1.518572 CGTCGCACGGGCTCTAAAT 60.519 57.895 8.62 0.00 38.08 1.40
97 98 1.480219 CGTCGCACGGGCTCTAAATC 61.480 60.000 8.62 0.00 38.08 2.17
98 99 1.143183 TCGCACGGGCTCTAAATCC 59.857 57.895 8.62 0.00 38.10 3.01
100 101 2.534903 GCACGGGCTCTAAATCCGC 61.535 63.158 0.00 0.00 46.87 5.54
101 102 1.887707 CACGGGCTCTAAATCCGCC 60.888 63.158 0.00 0.00 46.87 6.13
102 103 2.363975 ACGGGCTCTAAATCCGCCA 61.364 57.895 0.00 0.00 46.87 5.69
103 104 1.887707 CGGGCTCTAAATCCGCCAC 60.888 63.158 0.00 0.00 45.53 5.01
104 105 1.526225 GGGCTCTAAATCCGCCACC 60.526 63.158 0.00 0.00 45.53 4.61
105 106 1.887707 GGCTCTAAATCCGCCACCG 60.888 63.158 0.00 0.00 43.25 4.94
106 107 2.534903 GCTCTAAATCCGCCACCGC 61.535 63.158 0.00 0.00 0.00 5.68
107 108 1.887707 CTCTAAATCCGCCACCGCC 60.888 63.158 0.00 0.00 0.00 6.13
108 109 2.189521 CTAAATCCGCCACCGCCT 59.810 61.111 0.00 0.00 0.00 5.52
109 110 1.887707 CTAAATCCGCCACCGCCTC 60.888 63.158 0.00 0.00 0.00 4.70
110 111 3.394635 TAAATCCGCCACCGCCTCC 62.395 63.158 0.00 0.00 0.00 4.30
117 118 4.436998 CCACCGCCTCCTGTCGTC 62.437 72.222 0.00 0.00 0.00 4.20
118 119 4.778415 CACCGCCTCCTGTCGTCG 62.778 72.222 0.00 0.00 0.00 5.12
120 121 4.477975 CCGCCTCCTGTCGTCGTC 62.478 72.222 0.00 0.00 0.00 4.20
121 122 4.813526 CGCCTCCTGTCGTCGTCG 62.814 72.222 0.00 0.00 38.55 5.12
122 123 4.477975 GCCTCCTGTCGTCGTCGG 62.478 72.222 1.55 0.00 37.69 4.79
123 124 2.745100 CCTCCTGTCGTCGTCGGA 60.745 66.667 1.55 2.16 37.69 4.55
124 125 2.751913 CCTCCTGTCGTCGTCGGAG 61.752 68.421 16.85 16.85 42.09 4.63
125 126 2.745100 TCCTGTCGTCGTCGGAGG 60.745 66.667 12.44 12.44 37.97 4.30
126 127 2.745100 CCTGTCGTCGTCGGAGGA 60.745 66.667 13.08 0.00 38.48 3.71
127 128 2.751913 CCTGTCGTCGTCGGAGGAG 61.752 68.421 13.08 0.00 37.71 3.69
128 129 1.740664 CTGTCGTCGTCGGAGGAGA 60.741 63.158 1.55 0.00 37.71 3.71
129 130 1.697772 CTGTCGTCGTCGGAGGAGAG 61.698 65.000 1.55 0.00 40.55 3.20
130 131 2.125229 TCGTCGTCGGAGGAGAGG 60.125 66.667 1.55 0.00 37.69 3.69
131 132 2.125229 CGTCGTCGGAGGAGAGGA 60.125 66.667 0.00 0.00 33.30 3.71
132 133 1.744368 CGTCGTCGGAGGAGAGGAA 60.744 63.158 0.00 0.00 36.88 3.36
133 134 1.707239 CGTCGTCGGAGGAGAGGAAG 61.707 65.000 0.00 0.00 36.88 3.46
134 135 0.392729 GTCGTCGGAGGAGAGGAAGA 60.393 60.000 0.00 0.00 36.88 2.87
135 136 0.107606 TCGTCGGAGGAGAGGAAGAG 60.108 60.000 0.00 0.00 32.86 2.85
136 137 1.098712 CGTCGGAGGAGAGGAAGAGG 61.099 65.000 0.00 0.00 0.00 3.69
137 138 0.256464 GTCGGAGGAGAGGAAGAGGA 59.744 60.000 0.00 0.00 0.00 3.71
138 139 1.000496 TCGGAGGAGAGGAAGAGGAA 59.000 55.000 0.00 0.00 0.00 3.36
139 140 1.064314 TCGGAGGAGAGGAAGAGGAAG 60.064 57.143 0.00 0.00 0.00 3.46
140 141 1.788229 GGAGGAGAGGAAGAGGAAGG 58.212 60.000 0.00 0.00 0.00 3.46
141 142 1.691163 GGAGGAGAGGAAGAGGAAGGG 60.691 61.905 0.00 0.00 0.00 3.95
142 143 0.341609 AGGAGAGGAAGAGGAAGGGG 59.658 60.000 0.00 0.00 0.00 4.79
143 144 0.340208 GGAGAGGAAGAGGAAGGGGA 59.660 60.000 0.00 0.00 0.00 4.81
144 145 1.273896 GGAGAGGAAGAGGAAGGGGAA 60.274 57.143 0.00 0.00 0.00 3.97
145 146 2.115427 GAGAGGAAGAGGAAGGGGAAG 58.885 57.143 0.00 0.00 0.00 3.46
146 147 1.725182 AGAGGAAGAGGAAGGGGAAGA 59.275 52.381 0.00 0.00 0.00 2.87
147 148 1.834896 GAGGAAGAGGAAGGGGAAGAC 59.165 57.143 0.00 0.00 0.00 3.01
148 149 0.913205 GGAAGAGGAAGGGGAAGACC 59.087 60.000 0.00 0.00 39.11 3.85
158 159 3.363351 GGAAGACCCAGTCGTCGT 58.637 61.111 4.91 0.00 40.82 4.34
159 160 1.212229 GGAAGACCCAGTCGTCGTC 59.788 63.158 4.91 0.00 40.82 4.20
160 161 1.154263 GAAGACCCAGTCGTCGTCG 60.154 63.158 0.00 0.00 37.67 5.12
161 162 1.849976 GAAGACCCAGTCGTCGTCGT 61.850 60.000 1.33 0.00 37.67 4.34
162 163 1.849976 AAGACCCAGTCGTCGTCGTC 61.850 60.000 1.33 0.00 37.67 4.20
163 164 3.319926 GACCCAGTCGTCGTCGTCC 62.320 68.421 1.33 0.00 38.33 4.79
164 165 4.456253 CCCAGTCGTCGTCGTCCG 62.456 72.222 1.33 0.00 38.33 4.79
168 169 4.808238 GTCGTCGTCGTCCGCCTC 62.808 72.222 1.33 0.00 38.33 4.70
190 191 4.893601 GCTTAGCCCGGCGGACTC 62.894 72.222 30.79 15.98 0.00 3.36
191 192 3.148279 CTTAGCCCGGCGGACTCT 61.148 66.667 30.79 22.20 0.00 3.24
192 193 2.682494 TTAGCCCGGCGGACTCTT 60.682 61.111 30.79 10.09 0.00 2.85
193 194 2.240162 CTTAGCCCGGCGGACTCTTT 62.240 60.000 30.79 1.31 0.00 2.52
194 195 2.234913 TTAGCCCGGCGGACTCTTTC 62.235 60.000 30.79 6.91 0.00 2.62
196 197 4.814294 CCCGGCGGACTCTTTCGG 62.814 72.222 30.79 2.47 40.32 4.30
200 201 3.179939 GCGGACTCTTTCGGCGAC 61.180 66.667 10.16 0.00 40.38 5.19
260 261 3.518998 GCTCTGCCCGAGTCGCTA 61.519 66.667 7.12 0.00 41.98 4.26
261 262 2.718731 CTCTGCCCGAGTCGCTAG 59.281 66.667 7.12 4.86 34.95 3.42
262 263 1.820056 CTCTGCCCGAGTCGCTAGA 60.820 63.158 7.12 8.97 34.95 2.43
263 264 1.781025 CTCTGCCCGAGTCGCTAGAG 61.781 65.000 18.15 18.15 34.95 2.43
264 265 1.820056 CTGCCCGAGTCGCTAGAGA 60.820 63.158 7.12 0.00 0.00 3.10
265 266 1.781025 CTGCCCGAGTCGCTAGAGAG 61.781 65.000 7.12 0.00 0.00 3.20
266 267 2.548295 GCCCGAGTCGCTAGAGAGG 61.548 68.421 7.12 1.93 0.00 3.69
267 268 2.548295 CCCGAGTCGCTAGAGAGGC 61.548 68.421 7.12 0.00 0.00 4.70
274 275 4.615834 GCTAGAGAGGCGACGCGG 62.616 72.222 14.61 0.00 34.13 6.46
275 276 3.955101 CTAGAGAGGCGACGCGGG 61.955 72.222 14.61 2.38 34.13 6.13
291 292 2.498077 GGGGGACGAGTGGTAGTAC 58.502 63.158 0.00 0.00 0.00 2.73
292 293 0.033699 GGGGGACGAGTGGTAGTACT 60.034 60.000 0.00 0.00 0.00 2.73
293 294 1.387539 GGGGACGAGTGGTAGTACTC 58.612 60.000 0.00 0.00 42.83 2.59
294 295 1.387539 GGGACGAGTGGTAGTACTCC 58.612 60.000 0.00 1.20 43.23 3.85
295 296 1.064832 GGGACGAGTGGTAGTACTCCT 60.065 57.143 0.00 0.00 43.23 3.69
296 297 2.287769 GGACGAGTGGTAGTACTCCTC 58.712 57.143 0.00 2.11 43.23 3.71
297 298 2.355513 GGACGAGTGGTAGTACTCCTCA 60.356 54.545 0.00 0.00 43.23 3.86
298 299 3.543665 GACGAGTGGTAGTACTCCTCAT 58.456 50.000 0.00 4.93 43.23 2.90
299 300 3.946558 GACGAGTGGTAGTACTCCTCATT 59.053 47.826 0.00 0.00 43.23 2.57
300 301 4.342359 ACGAGTGGTAGTACTCCTCATTT 58.658 43.478 0.00 0.00 43.23 2.32
301 302 4.771054 ACGAGTGGTAGTACTCCTCATTTT 59.229 41.667 0.00 0.00 43.23 1.82
354 355 8.592155 GTGCTTGAATTTTACCGGATTTATTTC 58.408 33.333 9.46 4.67 0.00 2.17
541 543 4.285863 AGAGAGGAGTATTTCTCTGGTGG 58.714 47.826 0.00 0.00 46.27 4.61
546 548 5.529289 AGGAGTATTTCTCTGGTGGTATGA 58.471 41.667 0.00 0.00 42.40 2.15
547 549 5.364157 AGGAGTATTTCTCTGGTGGTATGAC 59.636 44.000 0.00 0.00 42.40 3.06
561 563 4.331168 GTGGTATGACATGCTTCTCAACTC 59.669 45.833 3.43 0.00 0.00 3.01
575 577 0.962489 CAACTCCAGGTGTCTCTCGT 59.038 55.000 0.00 0.00 0.00 4.18
576 578 2.160205 CAACTCCAGGTGTCTCTCGTA 58.840 52.381 0.00 0.00 0.00 3.43
581 583 4.283722 ACTCCAGGTGTCTCTCGTAATTTT 59.716 41.667 0.00 0.00 0.00 1.82
582 584 5.479375 ACTCCAGGTGTCTCTCGTAATTTTA 59.521 40.000 0.00 0.00 0.00 1.52
616 618 9.798885 CAAGTTTACTAGTCAATCTTTCGAAAG 57.201 33.333 28.26 28.26 37.36 2.62
630 632 5.578336 TCTTTCGAAAGTGCTCATAGTGATG 59.422 40.000 31.29 6.99 37.31 3.07
631 633 4.456280 TCGAAAGTGCTCATAGTGATGT 57.544 40.909 0.00 0.00 34.41 3.06
632 634 4.176271 TCGAAAGTGCTCATAGTGATGTG 58.824 43.478 0.00 0.00 34.41 3.21
637 639 5.604758 AGTGCTCATAGTGATGTGTGTAT 57.395 39.130 0.00 0.00 34.41 2.29
640 642 5.233050 GTGCTCATAGTGATGTGTGTATGTC 59.767 44.000 0.00 0.00 34.41 3.06
643 645 6.237942 GCTCATAGTGATGTGTGTATGTCAAC 60.238 42.308 0.00 0.00 34.41 3.18
644 646 6.935167 TCATAGTGATGTGTGTATGTCAACT 58.065 36.000 0.00 0.00 34.41 3.16
649 651 4.996758 TGATGTGTGTATGTCAACTTCTGG 59.003 41.667 0.00 0.00 0.00 3.86
655 657 6.649141 GTGTGTATGTCAACTTCTGGTCAATA 59.351 38.462 0.00 0.00 0.00 1.90
664 666 6.260050 TCAACTTCTGGTCAATACTGTGTTTC 59.740 38.462 0.00 0.00 0.00 2.78
665 667 5.063880 ACTTCTGGTCAATACTGTGTTTCC 58.936 41.667 0.00 0.00 0.00 3.13
666 668 4.015872 TCTGGTCAATACTGTGTTTCCC 57.984 45.455 0.00 0.00 0.00 3.97
671 673 5.068460 TGGTCAATACTGTGTTTCCCAAAAG 59.932 40.000 3.22 0.00 0.00 2.27
672 674 5.508994 GGTCAATACTGTGTTTCCCAAAAGG 60.509 44.000 0.00 0.00 0.00 3.11
673 675 5.300792 GTCAATACTGTGTTTCCCAAAAGGA 59.699 40.000 0.00 0.00 45.68 3.36
782 1847 2.987413 TTTCCATGTGATCGTTGTGC 57.013 45.000 0.00 0.00 0.00 4.57
783 1848 1.164411 TTCCATGTGATCGTTGTGCC 58.836 50.000 0.00 0.00 0.00 5.01
784 1849 0.036022 TCCATGTGATCGTTGTGCCA 59.964 50.000 0.00 0.00 0.00 4.92
785 1850 0.168788 CCATGTGATCGTTGTGCCAC 59.831 55.000 0.00 0.00 0.00 5.01
786 1851 1.159285 CATGTGATCGTTGTGCCACT 58.841 50.000 0.00 0.00 0.00 4.00
787 1852 1.135888 CATGTGATCGTTGTGCCACTG 60.136 52.381 0.00 0.00 0.00 3.66
788 1853 0.105778 TGTGATCGTTGTGCCACTGA 59.894 50.000 0.00 0.00 0.00 3.41
789 1854 0.512952 GTGATCGTTGTGCCACTGAC 59.487 55.000 0.00 0.00 0.00 3.51
883 1969 4.070552 GTGTCCCGCCGCTTCTCT 62.071 66.667 0.00 0.00 0.00 3.10
1117 2216 4.007644 CCACCGTGCTCTGCTCCA 62.008 66.667 0.00 0.00 0.00 3.86
1144 2243 2.449518 TCCACCACTCCAAGCCCA 60.450 61.111 0.00 0.00 0.00 5.36
1178 2277 4.660938 GGCCGCCTCCCACAAAGT 62.661 66.667 0.71 0.00 0.00 2.66
1185 2284 0.107831 CCTCCCACAAAGTCCACGAA 59.892 55.000 0.00 0.00 0.00 3.85
1213 2312 2.224305 GGCACATCCTAATCGTAAGCCT 60.224 50.000 0.00 0.00 36.72 4.58
1217 2316 5.300752 CACATCCTAATCGTAAGCCTGATT 58.699 41.667 0.00 0.00 38.34 2.57
1218 2317 5.760253 CACATCCTAATCGTAAGCCTGATTT 59.240 40.000 0.00 0.00 36.32 2.17
1219 2318 5.992217 ACATCCTAATCGTAAGCCTGATTTC 59.008 40.000 0.00 0.00 36.32 2.17
1220 2319 5.871396 TCCTAATCGTAAGCCTGATTTCT 57.129 39.130 0.00 0.00 36.32 2.52
1221 2320 6.971726 TCCTAATCGTAAGCCTGATTTCTA 57.028 37.500 0.00 0.00 36.32 2.10
1224 2323 6.814146 CCTAATCGTAAGCCTGATTTCTATCC 59.186 42.308 0.00 0.00 36.32 2.59
1236 2335 7.572724 GCCTGATTTCTATCCAGAATTTCATCG 60.573 40.741 0.00 0.00 40.47 3.84
1252 2351 8.830201 AATTTCATCGGTTCATTTCAATTCAA 57.170 26.923 0.00 0.00 0.00 2.69
1253 2352 8.830201 ATTTCATCGGTTCATTTCAATTCAAA 57.170 26.923 0.00 0.00 0.00 2.69
1268 2367 0.958091 TCAAATCCAAGGTTGTGCCG 59.042 50.000 0.00 0.00 43.70 5.69
1273 2389 3.343972 CAAGGTTGTGCCGTGGAG 58.656 61.111 0.00 0.00 42.04 3.86
1278 2394 0.533308 GGTTGTGCCGTGGAGTGTAA 60.533 55.000 0.00 0.00 0.00 2.41
1279 2395 1.519408 GTTGTGCCGTGGAGTGTAAT 58.481 50.000 0.00 0.00 0.00 1.89
1290 2406 2.290641 TGGAGTGTAATGCGGTGGAATT 60.291 45.455 0.00 0.00 0.00 2.17
1310 2427 6.701400 GGAATTGATTTGTTTGCACTGTAGTT 59.299 34.615 0.00 0.00 0.00 2.24
1311 2428 7.224557 GGAATTGATTTGTTTGCACTGTAGTTT 59.775 33.333 0.00 0.00 0.00 2.66
1331 2448 6.158598 AGTTTGTGAATTTTGGATGGAATCG 58.841 36.000 0.00 0.00 46.86 3.34
1352 2469 0.792640 AGAAACAATGTGCTCGCTCG 59.207 50.000 0.00 0.00 0.00 5.03
1387 2504 3.234353 TCCTGACTGGCTATGTGGATAG 58.766 50.000 0.00 0.00 35.51 2.08
1389 2506 2.968574 CTGACTGGCTATGTGGATAGGT 59.031 50.000 0.00 0.00 33.29 3.08
1390 2507 4.152647 CTGACTGGCTATGTGGATAGGTA 58.847 47.826 0.00 0.00 33.29 3.08
1391 2508 4.752063 TGACTGGCTATGTGGATAGGTAT 58.248 43.478 0.00 0.00 33.29 2.73
1392 2509 4.528206 TGACTGGCTATGTGGATAGGTATG 59.472 45.833 0.00 0.00 33.29 2.39
1393 2510 3.840666 ACTGGCTATGTGGATAGGTATGG 59.159 47.826 0.00 0.00 33.29 2.74
1394 2511 2.571653 TGGCTATGTGGATAGGTATGGC 59.428 50.000 0.00 0.00 33.29 4.40
1395 2512 2.092914 GGCTATGTGGATAGGTATGGCC 60.093 54.545 0.00 0.00 39.45 5.36
1396 2513 2.418746 GCTATGTGGATAGGTATGGCCG 60.419 54.545 0.00 0.00 43.70 6.13
1397 2514 1.729586 ATGTGGATAGGTATGGCCGT 58.270 50.000 1.35 1.35 43.70 5.68
1423 2540 1.453155 GATGCCACGATGGTTTGAGT 58.547 50.000 0.00 0.00 40.46 3.41
1434 2551 1.000506 TGGTTTGAGTAGGAGCACGTC 59.999 52.381 0.00 0.00 0.00 4.34
1438 2555 1.303799 TGAGTAGGAGCACGTCGTCC 61.304 60.000 0.00 4.74 0.00 4.79
1465 2582 6.214005 ACTTGGAATCCATGGAATTGACATTT 59.786 34.615 20.67 5.50 33.63 2.32
1470 2587 5.840243 TCCATGGAATTGACATTTAGCAG 57.160 39.130 13.46 0.00 0.00 4.24
1488 2605 2.687914 GCAGGATTCCCCTAGCATTGTT 60.688 50.000 0.00 0.00 45.60 2.83
1490 2607 4.026052 CAGGATTCCCCTAGCATTGTTTT 58.974 43.478 0.00 0.00 45.60 2.43
1516 2659 0.696143 TTCCCTGACCCTTGTCACCA 60.696 55.000 0.00 0.00 46.40 4.17
1517 2660 1.073199 CCCTGACCCTTGTCACCAC 59.927 63.158 0.00 0.00 46.40 4.16
1522 2669 2.958355 CTGACCCTTGTCACCACATTTT 59.042 45.455 0.00 0.00 46.40 1.82
1527 2674 3.511146 CCCTTGTCACCACATTTTAGCAT 59.489 43.478 0.00 0.00 30.55 3.79
1530 2677 6.295011 CCCTTGTCACCACATTTTAGCATTTA 60.295 38.462 0.00 0.00 30.55 1.40
1532 2679 8.465999 CCTTGTCACCACATTTTAGCATTTATA 58.534 33.333 0.00 0.00 30.55 0.98
1566 2713 5.163632 TGTGCCATGTGAAGTATATTTGCTG 60.164 40.000 0.00 0.00 0.00 4.41
1570 2717 6.057533 CCATGTGAAGTATATTTGCTGAGGA 58.942 40.000 0.00 0.00 0.00 3.71
1647 2794 4.702131 GTCCTAGCCTTGTTGTGATTGATT 59.298 41.667 0.00 0.00 0.00 2.57
1648 2795 5.880332 GTCCTAGCCTTGTTGTGATTGATTA 59.120 40.000 0.00 0.00 0.00 1.75
1653 2800 5.536161 AGCCTTGTTGTGATTGATTACTTGT 59.464 36.000 0.00 0.00 0.00 3.16
1654 2801 6.714810 AGCCTTGTTGTGATTGATTACTTGTA 59.285 34.615 0.00 0.00 0.00 2.41
1655 2802 7.023575 GCCTTGTTGTGATTGATTACTTGTAG 58.976 38.462 0.00 0.00 0.00 2.74
1656 2803 7.094805 GCCTTGTTGTGATTGATTACTTGTAGA 60.095 37.037 0.00 0.00 0.00 2.59
1657 2804 8.446273 CCTTGTTGTGATTGATTACTTGTAGAG 58.554 37.037 0.00 0.00 0.00 2.43
1660 2807 5.428253 TGTGATTGATTACTTGTAGAGGGC 58.572 41.667 0.00 0.00 0.00 5.19
1680 2837 1.604593 CCAAGCTGGAACACCCTGG 60.605 63.158 0.00 0.00 40.96 4.45
1683 2840 1.062488 AAGCTGGAACACCCTGGACT 61.062 55.000 0.00 0.00 34.72 3.85
1684 2841 1.302832 GCTGGAACACCCTGGACTG 60.303 63.158 0.00 0.00 34.72 3.51
1685 2842 1.768684 GCTGGAACACCCTGGACTGA 61.769 60.000 0.00 0.00 34.72 3.41
1686 2843 0.987294 CTGGAACACCCTGGACTGAT 59.013 55.000 0.00 0.00 35.38 2.90
1757 2915 5.838521 TGGTGTGAGATTAGGCATGATAGTA 59.161 40.000 0.00 0.00 0.00 1.82
1773 2931 7.310671 GCATGATAGTAATCTGGGTGATTAGGA 60.311 40.741 0.00 0.00 45.23 2.94
1776 2934 8.816894 TGATAGTAATCTGGGTGATTAGGAATC 58.183 37.037 0.00 0.00 45.23 2.52
1785 2943 7.394359 TCTGGGTGATTAGGAATCTTTCTTTTG 59.606 37.037 1.24 0.00 38.72 2.44
1787 2945 6.127338 GGGTGATTAGGAATCTTTCTTTTGGG 60.127 42.308 1.24 0.00 38.72 4.12
1789 2947 5.957774 TGATTAGGAATCTTTCTTTTGGGGG 59.042 40.000 1.24 0.00 38.72 5.40
1810 2968 1.474677 CCTTGAGCTGGCTACTGATGG 60.475 57.143 0.00 0.00 0.00 3.51
1825 2983 6.072508 GCTACTGATGGTTTTGAATGAAGTGA 60.073 38.462 0.00 0.00 0.00 3.41
1898 3057 0.111639 TAGGTCTTGTTTGGCCACCC 59.888 55.000 3.88 0.00 0.00 4.61
1909 3068 1.384191 GGCCACCCCTGAGTGAAAT 59.616 57.895 0.00 0.00 40.34 2.17
1921 3080 6.940298 CCCCTGAGTGAAATGACTTAAAGTTA 59.060 38.462 0.00 0.00 0.00 2.24
1924 3083 7.119846 CCTGAGTGAAATGACTTAAAGTTAGGG 59.880 40.741 0.00 0.00 0.00 3.53
1993 3152 4.084589 TCACAATGAAACATCAACTCGACG 60.085 41.667 0.00 0.00 0.00 5.12
2006 3165 1.922135 CTCGACGGCCAAAACCATGG 61.922 60.000 11.19 11.19 43.70 3.66
2007 3166 2.265182 CGACGGCCAAAACCATGGT 61.265 57.895 13.00 13.00 42.75 3.55
2008 3167 1.801309 CGACGGCCAAAACCATGGTT 61.801 55.000 24.86 24.86 42.75 3.67
2023 3182 8.491331 AAACCATGGTTTTTAACATGCATATC 57.509 30.769 32.77 0.00 44.84 1.63
2024 3183 7.422465 ACCATGGTTTTTAACATGCATATCT 57.578 32.000 13.00 0.00 42.31 1.98
2025 3184 7.267128 ACCATGGTTTTTAACATGCATATCTG 58.733 34.615 13.00 0.00 42.31 2.90
2036 3195 2.557920 GCATATCTGCTGTAAGGCCT 57.442 50.000 0.00 0.00 45.32 5.19
2037 3196 3.685139 GCATATCTGCTGTAAGGCCTA 57.315 47.619 5.16 0.00 45.32 3.93
2038 3197 4.213564 GCATATCTGCTGTAAGGCCTAT 57.786 45.455 5.16 0.00 45.32 2.57
2039 3198 4.187694 GCATATCTGCTGTAAGGCCTATC 58.812 47.826 5.16 2.35 45.32 2.08
2040 3199 4.428209 CATATCTGCTGTAAGGCCTATCG 58.572 47.826 5.16 0.00 0.00 2.92
2041 3200 2.067365 TCTGCTGTAAGGCCTATCGA 57.933 50.000 5.16 0.00 0.00 3.59
2045 3204 4.130118 CTGCTGTAAGGCCTATCGAAATT 58.870 43.478 5.16 0.00 0.00 1.82
2054 3213 3.066621 GGCCTATCGAAATTGATTGTGCA 59.933 43.478 0.00 0.00 0.00 4.57
2066 3225 0.179009 ATTGTGCACAGTGCTCACCT 60.179 50.000 26.15 15.56 45.08 4.00
2086 3252 8.498054 TCACCTTCATCTGAAATAACTCAATC 57.502 34.615 0.00 0.00 33.07 2.67
2088 3254 8.180267 CACCTTCATCTGAAATAACTCAATCAC 58.820 37.037 0.00 0.00 33.07 3.06
2095 3261 8.553459 TCTGAAATAACTCAATCACCTCTTTC 57.447 34.615 0.00 0.00 0.00 2.62
2129 3295 3.857157 ACCCTGTCTTTGCTAGTTCAA 57.143 42.857 0.00 0.00 0.00 2.69
2131 3297 4.327680 ACCCTGTCTTTGCTAGTTCAATC 58.672 43.478 0.00 0.00 0.00 2.67
2149 3315 7.910304 GTTCAATCGAACTCTTTAGCATATGT 58.090 34.615 4.29 0.00 46.72 2.29
2150 3316 9.031360 GTTCAATCGAACTCTTTAGCATATGTA 57.969 33.333 4.29 0.00 46.72 2.29
2151 3317 8.575565 TCAATCGAACTCTTTAGCATATGTAC 57.424 34.615 4.29 0.00 0.00 2.90
2152 3318 7.652105 TCAATCGAACTCTTTAGCATATGTACC 59.348 37.037 4.29 0.00 0.00 3.34
2153 3319 6.459670 TCGAACTCTTTAGCATATGTACCA 57.540 37.500 4.29 0.00 0.00 3.25
2154 3320 6.869695 TCGAACTCTTTAGCATATGTACCAA 58.130 36.000 4.29 0.00 0.00 3.67
2155 3321 6.755141 TCGAACTCTTTAGCATATGTACCAAC 59.245 38.462 4.29 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 4.711949 CTGGCGGTGGCTTGAGCT 62.712 66.667 2.66 0.00 41.70 4.09
78 79 1.480219 GATTTAGAGCCCGTGCGACG 61.480 60.000 0.00 0.00 44.33 5.12
79 80 1.152383 GGATTTAGAGCCCGTGCGAC 61.152 60.000 0.00 0.00 44.33 5.19
80 81 1.143183 GGATTTAGAGCCCGTGCGA 59.857 57.895 0.00 0.00 44.33 5.10
81 82 2.237751 CGGATTTAGAGCCCGTGCG 61.238 63.158 0.00 0.00 44.33 5.34
82 83 2.534903 GCGGATTTAGAGCCCGTGC 61.535 63.158 0.00 0.00 44.63 5.34
83 84 1.887707 GGCGGATTTAGAGCCCGTG 60.888 63.158 0.00 0.00 44.80 4.94
84 85 2.504519 GGCGGATTTAGAGCCCGT 59.495 61.111 0.00 0.00 44.80 5.28
88 89 2.534903 GCGGTGGCGGATTTAGAGC 61.535 63.158 0.00 0.00 0.00 4.09
89 90 1.887707 GGCGGTGGCGGATTTAGAG 60.888 63.158 0.00 0.00 41.24 2.43
90 91 2.188469 GGCGGTGGCGGATTTAGA 59.812 61.111 0.00 0.00 41.24 2.10
91 92 1.887707 GAGGCGGTGGCGGATTTAG 60.888 63.158 0.00 0.00 41.24 1.85
92 93 2.188469 GAGGCGGTGGCGGATTTA 59.812 61.111 0.00 0.00 41.24 1.40
93 94 4.796495 GGAGGCGGTGGCGGATTT 62.796 66.667 0.00 0.00 41.24 2.17
100 101 4.436998 GACGACAGGAGGCGGTGG 62.437 72.222 0.00 0.00 0.00 4.61
101 102 4.778415 CGACGACAGGAGGCGGTG 62.778 72.222 0.00 0.00 0.00 4.94
103 104 4.477975 GACGACGACAGGAGGCGG 62.478 72.222 0.00 0.00 0.00 6.13
104 105 4.813526 CGACGACGACAGGAGGCG 62.814 72.222 0.00 0.00 42.66 5.52
105 106 4.477975 CCGACGACGACAGGAGGC 62.478 72.222 9.28 0.00 42.66 4.70
106 107 2.745100 TCCGACGACGACAGGAGG 60.745 66.667 9.28 0.00 42.66 4.30
107 108 2.785921 CTCCGACGACGACAGGAG 59.214 66.667 17.99 17.99 43.43 3.69
108 109 2.745100 CCTCCGACGACGACAGGA 60.745 66.667 16.28 6.20 39.86 3.86
109 110 2.745100 TCCTCCGACGACGACAGG 60.745 66.667 9.28 13.15 42.66 4.00
110 111 1.697772 CTCTCCTCCGACGACGACAG 61.698 65.000 9.28 4.13 42.66 3.51
111 112 1.740664 CTCTCCTCCGACGACGACA 60.741 63.158 9.28 0.00 42.66 4.35
112 113 2.462782 CCTCTCCTCCGACGACGAC 61.463 68.421 9.28 0.00 42.66 4.34
113 114 2.125229 CCTCTCCTCCGACGACGA 60.125 66.667 9.28 0.00 42.66 4.20
114 115 1.707239 CTTCCTCTCCTCCGACGACG 61.707 65.000 0.00 0.00 39.43 5.12
115 116 0.392729 TCTTCCTCTCCTCCGACGAC 60.393 60.000 0.00 0.00 0.00 4.34
116 117 0.107606 CTCTTCCTCTCCTCCGACGA 60.108 60.000 0.00 0.00 0.00 4.20
117 118 1.098712 CCTCTTCCTCTCCTCCGACG 61.099 65.000 0.00 0.00 0.00 5.12
118 119 0.256464 TCCTCTTCCTCTCCTCCGAC 59.744 60.000 0.00 0.00 0.00 4.79
119 120 1.000496 TTCCTCTTCCTCTCCTCCGA 59.000 55.000 0.00 0.00 0.00 4.55
120 121 1.398692 CTTCCTCTTCCTCTCCTCCG 58.601 60.000 0.00 0.00 0.00 4.63
121 122 1.691163 CCCTTCCTCTTCCTCTCCTCC 60.691 61.905 0.00 0.00 0.00 4.30
122 123 1.691163 CCCCTTCCTCTTCCTCTCCTC 60.691 61.905 0.00 0.00 0.00 3.71
123 124 0.341609 CCCCTTCCTCTTCCTCTCCT 59.658 60.000 0.00 0.00 0.00 3.69
124 125 0.340208 TCCCCTTCCTCTTCCTCTCC 59.660 60.000 0.00 0.00 0.00 3.71
125 126 2.115427 CTTCCCCTTCCTCTTCCTCTC 58.885 57.143 0.00 0.00 0.00 3.20
126 127 1.725182 TCTTCCCCTTCCTCTTCCTCT 59.275 52.381 0.00 0.00 0.00 3.69
127 128 1.834896 GTCTTCCCCTTCCTCTTCCTC 59.165 57.143 0.00 0.00 0.00 3.71
128 129 1.556002 GGTCTTCCCCTTCCTCTTCCT 60.556 57.143 0.00 0.00 0.00 3.36
129 130 0.913205 GGTCTTCCCCTTCCTCTTCC 59.087 60.000 0.00 0.00 0.00 3.46
141 142 1.212229 GACGACGACTGGGTCTTCC 59.788 63.158 0.00 0.00 34.75 3.46
142 143 1.154263 CGACGACGACTGGGTCTTC 60.154 63.158 0.00 0.00 42.66 2.87
143 144 1.849976 GACGACGACGACTGGGTCTT 61.850 60.000 15.32 0.00 42.66 3.01
144 145 2.281345 ACGACGACGACTGGGTCT 60.281 61.111 15.32 0.00 42.66 3.85
145 146 2.175322 GACGACGACGACTGGGTC 59.825 66.667 15.32 0.00 42.66 4.46
146 147 3.360340 GGACGACGACGACTGGGT 61.360 66.667 15.32 0.00 42.66 4.51
173 174 4.893601 GAGTCCGCCGGGCTAAGC 62.894 72.222 11.78 0.00 0.00 3.09
174 175 2.240162 AAAGAGTCCGCCGGGCTAAG 62.240 60.000 11.78 5.83 0.00 2.18
175 176 2.234913 GAAAGAGTCCGCCGGGCTAA 62.235 60.000 11.78 1.29 0.00 3.09
176 177 2.682494 AAAGAGTCCGCCGGGCTA 60.682 61.111 11.78 1.67 0.00 3.93
177 178 4.083862 GAAAGAGTCCGCCGGGCT 62.084 66.667 11.57 11.57 0.00 5.19
179 180 4.814294 CCGAAAGAGTCCGCCGGG 62.814 72.222 1.90 0.00 36.81 5.73
182 183 4.430765 TCGCCGAAAGAGTCCGCC 62.431 66.667 0.00 0.00 0.00 6.13
183 184 3.179939 GTCGCCGAAAGAGTCCGC 61.180 66.667 0.00 0.00 0.00 5.54
184 185 2.874780 CGTCGCCGAAAGAGTCCG 60.875 66.667 0.00 0.00 35.63 4.79
185 186 2.506438 CCGTCGCCGAAAGAGTCC 60.506 66.667 0.00 0.00 35.63 3.85
186 187 3.179939 GCCGTCGCCGAAAGAGTC 61.180 66.667 0.00 0.00 35.63 3.36
188 189 4.771356 TCGCCGTCGCCGAAAGAG 62.771 66.667 0.00 0.00 35.63 2.85
189 190 4.771356 CTCGCCGTCGCCGAAAGA 62.771 66.667 0.00 0.00 35.63 2.52
245 246 1.820056 CTCTAGCGACTCGGGCAGA 60.820 63.158 0.00 0.00 0.00 4.26
246 247 1.781025 CTCTCTAGCGACTCGGGCAG 61.781 65.000 0.00 0.00 0.00 4.85
247 248 1.820056 CTCTCTAGCGACTCGGGCA 60.820 63.158 0.00 0.00 0.00 5.36
248 249 2.548295 CCTCTCTAGCGACTCGGGC 61.548 68.421 0.00 0.00 0.00 6.13
249 250 2.548295 GCCTCTCTAGCGACTCGGG 61.548 68.421 0.00 0.00 0.00 5.14
250 251 3.027292 GCCTCTCTAGCGACTCGG 58.973 66.667 0.00 0.00 0.00 4.63
257 258 4.615834 CCGCGTCGCCTCTCTAGC 62.616 72.222 12.44 0.00 0.00 3.42
258 259 3.955101 CCCGCGTCGCCTCTCTAG 61.955 72.222 12.44 0.00 0.00 2.43
271 272 3.834799 CTACCACTCGTCCCCCGC 61.835 72.222 0.00 0.00 36.19 6.13
272 273 1.077501 TACTACCACTCGTCCCCCG 60.078 63.158 0.00 0.00 38.13 5.73
273 274 0.033699 AGTACTACCACTCGTCCCCC 60.034 60.000 0.00 0.00 0.00 5.40
274 275 1.387539 GAGTACTACCACTCGTCCCC 58.612 60.000 0.00 0.00 35.92 4.81
275 276 1.064832 AGGAGTACTACCACTCGTCCC 60.065 57.143 0.00 0.00 44.93 4.46
276 277 2.416680 AGGAGTACTACCACTCGTCC 57.583 55.000 0.00 0.00 44.93 4.79
278 279 3.648507 ATGAGGAGTACTACCACTCGT 57.351 47.619 0.00 3.65 44.93 4.18
279 280 4.985538 AAATGAGGAGTACTACCACTCG 57.014 45.455 0.00 0.00 44.93 4.18
280 281 8.312564 ACTTAAAAATGAGGAGTACTACCACTC 58.687 37.037 0.00 5.55 43.55 3.51
281 282 8.203681 ACTTAAAAATGAGGAGTACTACCACT 57.796 34.615 0.00 0.00 0.00 4.00
282 283 8.312564 AGACTTAAAAATGAGGAGTACTACCAC 58.687 37.037 0.00 1.98 0.00 4.16
283 284 8.431910 AGACTTAAAAATGAGGAGTACTACCA 57.568 34.615 0.00 0.00 0.00 3.25
284 285 9.722184 AAAGACTTAAAAATGAGGAGTACTACC 57.278 33.333 0.00 2.33 0.00 3.18
287 288 9.274206 GTCAAAGACTTAAAAATGAGGAGTACT 57.726 33.333 0.00 0.00 0.00 2.73
288 289 9.274206 AGTCAAAGACTTAAAAATGAGGAGTAC 57.726 33.333 0.00 0.00 40.28 2.73
318 319 2.086054 ATTCAAGCACTCGTGTCCTC 57.914 50.000 0.00 0.00 0.00 3.71
320 321 3.626028 AAAATTCAAGCACTCGTGTCC 57.374 42.857 0.00 0.00 0.00 4.02
321 322 4.464112 GGTAAAATTCAAGCACTCGTGTC 58.536 43.478 0.00 0.00 0.00 3.67
354 355 6.531948 CGAAGGGAGTAGTATCAAAAAGACTG 59.468 42.308 0.00 0.00 0.00 3.51
520 521 4.027437 ACCACCAGAGAAATACTCCTCTC 58.973 47.826 0.00 0.00 45.96 3.20
522 523 5.598830 TCATACCACCAGAGAAATACTCCTC 59.401 44.000 0.00 0.00 45.96 3.71
538 540 4.256920 AGTTGAGAAGCATGTCATACCAC 58.743 43.478 0.00 0.00 0.00 4.16
541 543 4.507710 TGGAGTTGAGAAGCATGTCATAC 58.492 43.478 0.00 0.00 0.00 2.39
546 548 1.701847 ACCTGGAGTTGAGAAGCATGT 59.298 47.619 0.00 0.00 0.00 3.21
547 549 2.082231 CACCTGGAGTTGAGAAGCATG 58.918 52.381 0.00 0.00 0.00 4.06
561 563 8.712285 TTAATAAAATTACGAGAGACACCTGG 57.288 34.615 0.00 0.00 0.00 4.45
595 597 7.152645 AGCACTTTCGAAAGATTGACTAGTAA 58.847 34.615 37.54 0.53 41.60 2.24
600 602 4.380531 TGAGCACTTTCGAAAGATTGACT 58.619 39.130 37.54 25.67 41.60 3.41
602 604 6.091305 CACTATGAGCACTTTCGAAAGATTGA 59.909 38.462 37.54 19.64 41.60 2.57
603 605 6.091305 TCACTATGAGCACTTTCGAAAGATTG 59.909 38.462 37.54 27.75 41.60 2.67
606 608 5.134202 TCACTATGAGCACTTTCGAAAGA 57.866 39.130 37.54 19.59 39.31 2.52
616 618 5.111989 ACATACACACATCACTATGAGCAC 58.888 41.667 0.00 0.00 36.54 4.40
630 632 4.377021 TGACCAGAAGTTGACATACACAC 58.623 43.478 0.00 0.00 0.00 3.82
631 633 4.681074 TGACCAGAAGTTGACATACACA 57.319 40.909 0.00 0.00 0.00 3.72
632 634 6.874134 AGTATTGACCAGAAGTTGACATACAC 59.126 38.462 0.00 0.00 0.00 2.90
637 639 5.056480 CACAGTATTGACCAGAAGTTGACA 58.944 41.667 0.00 0.00 0.00 3.58
640 642 6.377327 AAACACAGTATTGACCAGAAGTTG 57.623 37.500 0.00 0.00 0.00 3.16
643 645 4.455877 GGGAAACACAGTATTGACCAGAAG 59.544 45.833 0.00 0.00 0.00 2.85
644 646 4.141367 TGGGAAACACAGTATTGACCAGAA 60.141 41.667 0.00 0.00 0.00 3.02
649 651 5.300792 TCCTTTTGGGAAACACAGTATTGAC 59.699 40.000 0.00 0.00 41.91 3.18
664 666 8.956533 TTTCTCTTAAAAATGTTCCTTTTGGG 57.043 30.769 0.00 0.00 40.87 4.12
694 696 9.268268 AGAAGTTTCGAAAATATAAGACACACA 57.732 29.630 13.10 0.00 0.00 3.72
697 699 9.882856 CGTAGAAGTTTCGAAAATATAAGACAC 57.117 33.333 13.10 0.00 0.00 3.67
698 700 9.079833 CCGTAGAAGTTTCGAAAATATAAGACA 57.920 33.333 13.10 0.00 0.00 3.41
699 701 9.294030 TCCGTAGAAGTTTCGAAAATATAAGAC 57.706 33.333 13.10 5.60 0.00 3.01
746 1807 9.070179 CACATGGAAATCAGGAAATGTGATATA 57.930 33.333 7.63 0.00 44.81 0.86
758 1823 3.691118 ACAACGATCACATGGAAATCAGG 59.309 43.478 0.00 0.00 0.00 3.86
782 1847 0.104120 TGTGAACCGTGAGTCAGTGG 59.896 55.000 9.34 9.34 0.00 4.00
783 1848 1.067060 TCTGTGAACCGTGAGTCAGTG 59.933 52.381 0.00 0.00 0.00 3.66
784 1849 1.399714 TCTGTGAACCGTGAGTCAGT 58.600 50.000 0.00 0.00 0.00 3.41
785 1850 2.332104 CATCTGTGAACCGTGAGTCAG 58.668 52.381 0.00 0.00 0.00 3.51
786 1851 1.000843 CCATCTGTGAACCGTGAGTCA 59.999 52.381 0.00 0.00 0.00 3.41
787 1852 1.714794 CCATCTGTGAACCGTGAGTC 58.285 55.000 0.00 0.00 0.00 3.36
788 1853 0.320771 GCCATCTGTGAACCGTGAGT 60.321 55.000 0.00 0.00 0.00 3.41
789 1854 0.320683 TGCCATCTGTGAACCGTGAG 60.321 55.000 0.00 0.00 0.00 3.51
883 1969 1.002274 GCCAGAGGAGGAGGAGGAA 59.998 63.158 0.00 0.00 0.00 3.36
942 2031 2.746671 ACGCGCTCTTCTCGGAGA 60.747 61.111 5.73 2.97 35.52 3.71
1117 2216 3.637273 GTGGTGGAGGAAGGCGGT 61.637 66.667 0.00 0.00 0.00 5.68
1161 2260 4.660938 ACTTTGTGGGAGGCGGCC 62.661 66.667 12.11 12.11 0.00 6.13
1164 2263 1.966451 GTGGACTTTGTGGGAGGCG 60.966 63.158 0.00 0.00 0.00 5.52
1174 2273 1.370064 CGAGGGGTTCGTGGACTTT 59.630 57.895 0.00 0.00 44.27 2.66
1185 2284 0.694444 ATTAGGATGTGCCGAGGGGT 60.694 55.000 0.00 0.00 43.43 4.95
1195 2294 5.552870 AATCAGGCTTACGATTAGGATGT 57.447 39.130 0.00 0.00 30.12 3.06
1213 2312 7.282585 ACCGATGAAATTCTGGATAGAAATCA 58.717 34.615 6.52 9.70 45.47 2.57
1217 2316 6.649155 TGAACCGATGAAATTCTGGATAGAA 58.351 36.000 6.52 0.00 46.32 2.10
1218 2317 6.233905 TGAACCGATGAAATTCTGGATAGA 57.766 37.500 6.52 0.00 0.00 1.98
1219 2318 7.502120 AATGAACCGATGAAATTCTGGATAG 57.498 36.000 6.52 0.00 0.00 2.08
1220 2319 7.555914 TGAAATGAACCGATGAAATTCTGGATA 59.444 33.333 6.52 0.00 0.00 2.59
1221 2320 6.377996 TGAAATGAACCGATGAAATTCTGGAT 59.622 34.615 6.52 0.00 0.00 3.41
1224 2323 8.470040 AATTGAAATGAACCGATGAAATTCTG 57.530 30.769 0.00 0.00 0.00 3.02
1236 2335 6.936335 ACCTTGGATTTGAATTGAAATGAACC 59.064 34.615 7.65 3.95 0.00 3.62
1252 2351 2.340427 CACGGCACAACCTTGGATT 58.660 52.632 0.00 0.00 34.01 3.01
1253 2352 4.079446 CACGGCACAACCTTGGAT 57.921 55.556 0.00 0.00 34.01 3.41
1268 2367 0.036765 TCCACCGCATTACACTCCAC 60.037 55.000 0.00 0.00 0.00 4.02
1273 2389 4.370364 AATCAATTCCACCGCATTACAC 57.630 40.909 0.00 0.00 0.00 2.90
1278 2394 3.959535 AACAAATCAATTCCACCGCAT 57.040 38.095 0.00 0.00 0.00 4.73
1279 2395 3.388308 CAAACAAATCAATTCCACCGCA 58.612 40.909 0.00 0.00 0.00 5.69
1290 2406 5.804473 CACAAACTACAGTGCAAACAAATCA 59.196 36.000 0.00 0.00 0.00 2.57
1310 2427 5.973899 TCGATTCCATCCAAAATTCACAA 57.026 34.783 0.00 0.00 0.00 3.33
1311 2428 5.709631 TCTTCGATTCCATCCAAAATTCACA 59.290 36.000 0.00 0.00 0.00 3.58
1331 2448 2.723010 CGAGCGAGCACATTGTTTCTTC 60.723 50.000 0.00 0.00 0.00 2.87
1352 2469 3.126514 CAGTCAGGAAGCATGAACATGTC 59.873 47.826 14.82 6.73 40.80 3.06
1387 2504 4.667420 CGTCCATACGGCCATACC 57.333 61.111 2.24 0.00 45.50 2.73
1396 2513 1.139989 CATCGTGGCATCGTCCATAC 58.860 55.000 8.80 0.00 38.57 2.39
1397 2514 0.033366 CCATCGTGGCATCGTCCATA 59.967 55.000 8.80 0.00 38.57 2.74
1406 2523 1.338674 CCTACTCAAACCATCGTGGCA 60.339 52.381 4.23 0.00 42.67 4.92
1423 2540 0.251354 AGTAGGACGACGTGCTCCTA 59.749 55.000 25.82 16.64 38.01 2.94
1438 2555 5.887598 TGTCAATTCCATGGATTCCAAGTAG 59.112 40.000 17.06 0.45 36.95 2.57
1454 2571 5.221322 GGGGAATCCTGCTAAATGTCAATTC 60.221 44.000 0.00 0.00 0.00 2.17
1493 2610 2.951229 GACAAGGGTCAGGGAAGAAA 57.049 50.000 0.00 0.00 43.73 2.52
1508 2651 9.632807 GTTATAAATGCTAAAATGTGGTGACAA 57.367 29.630 0.00 0.00 46.06 3.18
1553 2700 7.592885 AAATGCATCCTCAGCAAATATACTT 57.407 32.000 0.00 0.00 46.27 2.24
1558 2705 5.047164 ACACAAAATGCATCCTCAGCAAATA 60.047 36.000 0.00 0.00 46.27 1.40
1566 2713 6.072508 TGAGACTAAACACAAAATGCATCCTC 60.073 38.462 0.00 0.00 0.00 3.71
1570 2717 6.389830 TGTGAGACTAAACACAAAATGCAT 57.610 33.333 0.00 0.00 42.72 3.96
1653 2800 1.392131 TCCAGCTTGGAGCCCTCTA 59.608 57.895 1.25 0.00 42.67 2.43
1654 2801 2.123632 TCCAGCTTGGAGCCCTCT 59.876 61.111 1.25 0.00 42.67 3.69
1680 2837 5.238214 GCACAATCTTCAGGGAATATCAGTC 59.762 44.000 0.00 0.00 0.00 3.51
1683 2840 4.166725 AGGCACAATCTTCAGGGAATATCA 59.833 41.667 0.00 0.00 0.00 2.15
1684 2841 4.518211 CAGGCACAATCTTCAGGGAATATC 59.482 45.833 0.00 0.00 0.00 1.63
1685 2842 4.467769 CAGGCACAATCTTCAGGGAATAT 58.532 43.478 0.00 0.00 0.00 1.28
1686 2843 3.889815 CAGGCACAATCTTCAGGGAATA 58.110 45.455 0.00 0.00 0.00 1.75
1773 2931 2.639347 CAAGGCCCCCAAAAGAAAGATT 59.361 45.455 0.00 0.00 0.00 2.40
1776 2934 1.620323 CTCAAGGCCCCCAAAAGAAAG 59.380 52.381 0.00 0.00 0.00 2.62
1810 2968 9.301153 ACACATAAAAGTCACTTCATTCAAAAC 57.699 29.630 0.00 0.00 0.00 2.43
1866 3024 4.161102 ACAAGACCTAAGACCTTAGCTGT 58.839 43.478 10.49 5.21 40.79 4.40
1869 3027 4.695928 CCAAACAAGACCTAAGACCTTAGC 59.304 45.833 10.49 0.26 40.79 3.09
1882 3041 1.152546 AGGGGTGGCCAAACAAGAC 60.153 57.895 7.24 0.00 0.00 3.01
1898 3057 7.119846 CCCTAACTTTAAGTCATTTCACTCAGG 59.880 40.741 0.00 0.00 0.00 3.86
1909 3068 8.754991 TTTGTGAAATCCCTAACTTTAAGTCA 57.245 30.769 0.00 0.00 0.00 3.41
1921 3080 4.026052 GGATGGTGATTTGTGAAATCCCT 58.974 43.478 6.59 0.33 45.23 4.20
1924 3083 4.731773 GCGAGGATGGTGATTTGTGAAATC 60.732 45.833 0.00 0.00 45.86 2.17
1944 3103 5.186409 AGTTACAGTTATCCAAAGTAGGCGA 59.814 40.000 0.00 0.00 0.00 5.54
1945 3104 5.416947 AGTTACAGTTATCCAAAGTAGGCG 58.583 41.667 0.00 0.00 0.00 5.52
2006 3165 8.909708 TTACAGCAGATATGCATGTTAAAAAC 57.090 30.769 15.82 0.00 37.25 2.43
2007 3166 8.190122 CCTTACAGCAGATATGCATGTTAAAAA 58.810 33.333 15.82 6.43 37.25 1.94
2008 3167 7.681782 GCCTTACAGCAGATATGCATGTTAAAA 60.682 37.037 15.82 6.73 37.25 1.52
2009 3168 6.238731 GCCTTACAGCAGATATGCATGTTAAA 60.239 38.462 15.82 7.33 37.25 1.52
2010 3169 5.239306 GCCTTACAGCAGATATGCATGTTAA 59.761 40.000 15.82 5.15 37.25 2.01
2011 3170 4.756642 GCCTTACAGCAGATATGCATGTTA 59.243 41.667 15.82 8.84 37.25 2.41
2012 3171 3.567164 GCCTTACAGCAGATATGCATGTT 59.433 43.478 15.82 0.00 37.25 2.71
2013 3172 3.144506 GCCTTACAGCAGATATGCATGT 58.855 45.455 15.82 16.77 37.25 3.21
2014 3173 2.486982 GGCCTTACAGCAGATATGCATG 59.513 50.000 15.82 11.98 37.25 4.06
2015 3174 2.374504 AGGCCTTACAGCAGATATGCAT 59.625 45.455 15.82 3.79 37.25 3.96
2016 3175 1.770658 AGGCCTTACAGCAGATATGCA 59.229 47.619 15.82 0.00 37.25 3.96
2017 3176 2.557920 AGGCCTTACAGCAGATATGC 57.442 50.000 3.54 3.54 0.00 3.14
2018 3177 4.158579 TCGATAGGCCTTACAGCAGATATG 59.841 45.833 12.58 0.00 0.00 1.78
2019 3178 4.344978 TCGATAGGCCTTACAGCAGATAT 58.655 43.478 12.58 0.00 0.00 1.63
2020 3179 3.763057 TCGATAGGCCTTACAGCAGATA 58.237 45.455 12.58 0.00 0.00 1.98
2021 3180 2.598565 TCGATAGGCCTTACAGCAGAT 58.401 47.619 12.58 0.00 0.00 2.90
2022 3181 2.067365 TCGATAGGCCTTACAGCAGA 57.933 50.000 12.58 0.00 0.00 4.26
2023 3182 2.890808 TTCGATAGGCCTTACAGCAG 57.109 50.000 12.58 0.00 0.00 4.24
2024 3183 3.838244 ATTTCGATAGGCCTTACAGCA 57.162 42.857 12.58 0.00 0.00 4.41
2025 3184 4.127171 TCAATTTCGATAGGCCTTACAGC 58.873 43.478 12.58 0.00 0.00 4.40
2026 3185 6.260936 ACAATCAATTTCGATAGGCCTTACAG 59.739 38.462 12.58 0.00 0.00 2.74
2027 3186 6.038161 CACAATCAATTTCGATAGGCCTTACA 59.962 38.462 12.58 0.00 0.00 2.41
2028 3187 6.430451 CACAATCAATTTCGATAGGCCTTAC 58.570 40.000 12.58 4.45 0.00 2.34
2029 3188 5.008613 GCACAATCAATTTCGATAGGCCTTA 59.991 40.000 12.58 0.00 0.00 2.69
2030 3189 4.202050 GCACAATCAATTTCGATAGGCCTT 60.202 41.667 12.58 0.00 0.00 4.35
2031 3190 3.316308 GCACAATCAATTTCGATAGGCCT 59.684 43.478 11.78 11.78 0.00 5.19
2032 3191 3.066621 TGCACAATCAATTTCGATAGGCC 59.933 43.478 0.00 0.00 0.00 5.19
2033 3192 4.037690 GTGCACAATCAATTTCGATAGGC 58.962 43.478 13.17 0.00 0.00 3.93
2034 3193 5.163723 ACTGTGCACAATCAATTTCGATAGG 60.164 40.000 21.98 5.53 0.00 2.57
2035 3194 5.735892 CACTGTGCACAATCAATTTCGATAG 59.264 40.000 21.98 6.21 0.00 2.08
2036 3195 5.630061 CACTGTGCACAATCAATTTCGATA 58.370 37.500 21.98 0.00 0.00 2.92
2037 3196 4.478699 CACTGTGCACAATCAATTTCGAT 58.521 39.130 21.98 0.00 0.00 3.59
2038 3197 3.852939 GCACTGTGCACAATCAATTTCGA 60.853 43.478 26.70 0.00 44.26 3.71
2039 3198 2.406024 GCACTGTGCACAATCAATTTCG 59.594 45.455 26.70 8.18 44.26 3.46
2054 3213 1.973515 TCAGATGAAGGTGAGCACTGT 59.026 47.619 0.16 0.00 0.00 3.55
2066 3225 8.324306 AGAGGTGATTGAGTTATTTCAGATGAA 58.676 33.333 0.00 0.00 0.00 2.57
2086 3252 1.334869 AGCAAAACTGCGAAAGAGGTG 59.665 47.619 0.00 0.00 40.27 4.00
2088 3254 2.781945 AAGCAAAACTGCGAAAGAGG 57.218 45.000 0.00 0.00 40.27 3.69
2095 3261 1.336755 ACAGGGTAAAGCAAAACTGCG 59.663 47.619 0.00 0.00 40.27 5.18
2129 3295 7.050970 TGGTACATATGCTAAAGAGTTCGAT 57.949 36.000 1.58 0.00 0.00 3.59
2131 3297 6.934210 GTTGGTACATATGCTAAAGAGTTCG 58.066 40.000 1.58 0.00 39.30 3.95


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

AutoCloner maintained by Alex Coulton.