Multiple sequence alignment - TraesCS7D01G037500

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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 TraesCS7D01G037500 chr7D 100.000 3119 0 0 1 3119 18930655 18927537 0.000000e+00 5760
1 TraesCS7D01G037500 chr7D 86.124 1917 211 35 782 2674 18948530 18946645 0.000000e+00 2015
2 TraesCS7D01G037500 chr7D 82.162 185 16 9 168 338 11312898 11313079 3.240000e-30 143
3 TraesCS7D01G037500 chr7D 82.184 174 14 7 171 331 94123055 94122886 1.950000e-27 134
4 TraesCS7D01G037500 chr7D 80.822 146 28 0 1874 2019 15840985 15840840 7.070000e-22 115
5 TraesCS7D01G037500 chr7A 91.696 1963 114 28 673 2609 19422208 19420269 0.000000e+00 2676
6 TraesCS7D01G037500 chr7A 88.303 872 89 9 1370 2237 19387425 19386563 0.000000e+00 1033
7 TraesCS7D01G037500 chr7A 86.392 948 105 17 1028 1962 19505481 19504545 0.000000e+00 1014
8 TraesCS7D01G037500 chr7A 87.408 818 85 11 1159 1961 19447633 19446819 0.000000e+00 924
9 TraesCS7D01G037500 chr7A 86.531 735 69 18 1949 2674 19443354 19442641 0.000000e+00 782
10 TraesCS7D01G037500 chr7A 82.936 545 43 24 2594 3118 19419543 19419029 2.210000e-121 446
11 TraesCS7D01G037500 chr7A 82.711 509 45 23 2171 2676 19373978 19373510 2.240000e-111 412
12 TraesCS7D01G037500 chr7A 91.026 78 6 1 26 103 19422698 19422622 1.530000e-18 104
13 TraesCS7D01G037500 chr4A 89.526 2024 162 30 816 2820 713834960 713832968 0.000000e+00 2518
14 TraesCS7D01G037500 chr4A 90.824 534 49 0 1338 1871 713847540 713847007 0.000000e+00 715
15 TraesCS7D01G037500 chr4A 91.864 381 25 5 1868 2246 713838849 713838473 7.660000e-146 527
16 TraesCS7D01G037500 chr4A 83.974 156 13 3 195 338 714215272 714215117 4.190000e-29 139
17 TraesCS7D01G037500 chr4A 95.402 87 1 2 3023 3109 713832158 713832075 5.430000e-28 135
18 TraesCS7D01G037500 chr1A 80.917 1352 210 27 805 2118 516165067 516163726 0.000000e+00 1024
19 TraesCS7D01G037500 chr1A 87.582 153 13 4 180 332 409855022 409855168 4.140000e-39 172
20 TraesCS7D01G037500 chr1D 84.598 870 115 13 1248 2100 419071039 419070172 0.000000e+00 846
21 TraesCS7D01G037500 chr1D 82.486 177 14 9 177 339 160451492 160451665 4.190000e-29 139
22 TraesCS7D01G037500 chr2D 83.832 167 11 6 179 332 33734750 33734913 9.020000e-31 145
23 TraesCS7D01G037500 chr2D 82.941 170 13 6 176 332 399965314 399965148 4.190000e-29 139
24 TraesCS7D01G037500 chr6B 84.076 157 12 5 172 326 179705417 179705562 4.190000e-29 139
25 TraesCS7D01G037500 chr6B 83.673 147 20 4 195 339 15606523 15606667 5.430000e-28 135
26 TraesCS7D01G037500 chr6D 81.818 187 12 14 180 349 359354941 359354760 1.510000e-28 137
27 TraesCS7D01G037500 chr4D 82.659 173 12 9 177 335 484111760 484111928 1.510000e-28 137
28 TraesCS7D01G037500 chr4D 82.081 173 15 8 180 339 12704509 12704678 1.950000e-27 134
29 TraesCS7D01G037500 chr7B 82.036 167 15 7 178 332 311345656 311345819 9.080000e-26 128
30 TraesCS7D01G037500 chr7B 84.874 119 9 8 67 177 743564653 743564770 9.140000e-21 111
31 TraesCS7D01G037500 chr7B 79.235 183 17 13 180 347 159137917 159138093 1.180000e-19 108
32 TraesCS7D01G037500 chr2A 81.034 174 16 9 180 339 374517184 374517354 4.220000e-24 122
33 TraesCS7D01G037500 chr3D 90.323 93 6 2 178 270 66739112 66739201 5.460000e-23 119
34 TraesCS7D01G037500 chr3D 84.874 119 9 8 67 177 34337457 34337574 9.140000e-21 111
35 TraesCS7D01G037500 chr5B 84.874 119 9 8 67 177 506236384 506236501 9.140000e-21 111
36 TraesCS7D01G037500 chr1B 84.211 114 10 7 67 173 31378507 31378395 1.530000e-18 104


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 TraesCS7D01G037500 chr7D 18927537 18930655 3118 True 5760.000000 5760 100.000000 1 3119 1 chr7D.!!$R2 3118
1 TraesCS7D01G037500 chr7D 18946645 18948530 1885 True 2015.000000 2015 86.124000 782 2674 1 chr7D.!!$R3 1892
2 TraesCS7D01G037500 chr7A 19419029 19422698 3669 True 1075.333333 2676 88.552667 26 3118 3 chr7A.!!$R4 3092
3 TraesCS7D01G037500 chr7A 19386563 19387425 862 True 1033.000000 1033 88.303000 1370 2237 1 chr7A.!!$R2 867
4 TraesCS7D01G037500 chr7A 19504545 19505481 936 True 1014.000000 1014 86.392000 1028 1962 1 chr7A.!!$R3 934
5 TraesCS7D01G037500 chr7A 19442641 19447633 4992 True 853.000000 924 86.969500 1159 2674 2 chr7A.!!$R5 1515
6 TraesCS7D01G037500 chr4A 713832075 713838849 6774 True 1060.000000 2518 92.264000 816 3109 3 chr4A.!!$R3 2293
7 TraesCS7D01G037500 chr4A 713847007 713847540 533 True 715.000000 715 90.824000 1338 1871 1 chr4A.!!$R1 533
8 TraesCS7D01G037500 chr1A 516163726 516165067 1341 True 1024.000000 1024 80.917000 805 2118 1 chr1A.!!$R1 1313
9 TraesCS7D01G037500 chr1D 419070172 419071039 867 True 846.000000 846 84.598000 1248 2100 1 chr1D.!!$R1 852

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
197 198 0.033306 GTACTCCCTCCGTTCCTCCT 60.033 60.000 0.00 0.0 0.00 3.69 F
557 563 1.003812 TGTTGGGCCATACACTACACC 59.996 52.381 7.26 0.0 0.00 4.16 F
961 4056 1.117994 AGATCAGAAGCTGCGATCCA 58.882 50.000 17.65 0.0 36.95 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 4349 0.332293 TGGCTGGCTGGATCAATGAA 59.668 50.0 2.0 0.0 0.0 2.57 R
1386 4505 0.859232 ACGCATCAACAACGAGACAC 59.141 50.0 0.0 0.0 0.0 3.67 R
2865 10741 0.518636 CACCTTCAGCGAACACCATG 59.481 55.0 0.0 0.0 0.0 3.66 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 6.366315 CTAGTAGACTAGTAGCAACCAGTG 57.634 45.833 10.72 0.00 40.72 3.66
32 33 4.664392 AGTAGACTAGTAGCAACCAGTGT 58.336 43.478 0.00 0.00 26.81 3.55
48 49 4.528596 ACCAGTGTTGACTATAACTCTGCT 59.471 41.667 12.61 0.85 44.57 4.24
53 54 5.352569 GTGTTGACTATAACTCTGCTTGCAT 59.647 40.000 0.00 0.00 0.00 3.96
61 62 2.969990 ACTCTGCTTGCATAGTCAGTG 58.030 47.619 7.66 4.56 32.92 3.66
66 67 1.947678 GCTTGCATAGTCAGTGCCAGT 60.948 52.381 0.00 0.00 41.83 4.00
111 112 6.822442 TGTTGATATTAATAGCTCCCGAACA 58.178 36.000 11.74 9.98 0.00 3.18
114 115 9.431887 GTTGATATTAATAGCTCCCGAACAATA 57.568 33.333 11.74 0.00 0.00 1.90
116 117 8.590204 TGATATTAATAGCTCCCGAACAATACA 58.410 33.333 11.74 0.00 0.00 2.29
119 120 8.691661 ATTAATAGCTCCCGAACAATACATTT 57.308 30.769 0.00 0.00 0.00 2.32
121 122 2.423538 AGCTCCCGAACAATACATTTGC 59.576 45.455 0.00 0.00 0.00 3.68
122 123 2.423538 GCTCCCGAACAATACATTTGCT 59.576 45.455 0.00 0.00 0.00 3.91
124 125 3.013921 TCCCGAACAATACATTTGCTCC 58.986 45.455 0.00 0.00 0.00 4.70
125 126 3.016736 CCCGAACAATACATTTGCTCCT 58.983 45.455 0.00 0.00 0.00 3.69
126 127 4.080807 TCCCGAACAATACATTTGCTCCTA 60.081 41.667 0.00 0.00 0.00 2.94
129 130 5.116180 CGAACAATACATTTGCTCCTAGGA 58.884 41.667 11.98 11.98 0.00 2.94
130 131 5.760253 CGAACAATACATTTGCTCCTAGGAT 59.240 40.000 13.12 0.00 0.00 3.24
131 132 6.073548 CGAACAATACATTTGCTCCTAGGATC 60.074 42.308 13.12 9.09 0.00 3.36
132 133 6.252599 ACAATACATTTGCTCCTAGGATCA 57.747 37.500 13.12 12.15 0.00 2.92
133 134 6.845908 ACAATACATTTGCTCCTAGGATCAT 58.154 36.000 15.88 4.10 0.00 2.45
135 136 8.099537 ACAATACATTTGCTCCTAGGATCATAG 58.900 37.037 15.88 7.44 0.00 2.23
137 138 8.901472 ATACATTTGCTCCTAGGATCATAGTA 57.099 34.615 15.88 16.81 0.00 1.82
138 139 7.805083 ACATTTGCTCCTAGGATCATAGTAT 57.195 36.000 15.88 5.45 0.00 2.12
140 141 9.499369 ACATTTGCTCCTAGGATCATAGTATAT 57.501 33.333 15.88 0.41 0.00 0.86
191 192 5.021458 TCTTAAAGATGTACTCCCTCCGTT 58.979 41.667 0.00 0.00 0.00 4.44
192 193 3.889520 AAAGATGTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
193 194 1.777941 AGATGTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
195 196 1.682323 GATGTACTCCCTCCGTTCCTC 59.318 57.143 0.00 0.00 0.00 3.71
196 197 0.324091 TGTACTCCCTCCGTTCCTCC 60.324 60.000 0.00 0.00 0.00 4.30
197 198 0.033306 GTACTCCCTCCGTTCCTCCT 60.033 60.000 0.00 0.00 0.00 3.69
198 199 1.213926 GTACTCCCTCCGTTCCTCCTA 59.786 57.143 0.00 0.00 0.00 2.94
200 201 1.078324 ACTCCCTCCGTTCCTCCTAAA 59.922 52.381 0.00 0.00 0.00 1.85
201 202 2.292984 ACTCCCTCCGTTCCTCCTAAAT 60.293 50.000 0.00 0.00 0.00 1.40
203 204 4.161102 CTCCCTCCGTTCCTCCTAAATAT 58.839 47.826 0.00 0.00 0.00 1.28
205 206 5.719100 TCCCTCCGTTCCTCCTAAATATAA 58.281 41.667 0.00 0.00 0.00 0.98
206 207 5.778750 TCCCTCCGTTCCTCCTAAATATAAG 59.221 44.000 0.00 0.00 0.00 1.73
207 208 5.543020 CCCTCCGTTCCTCCTAAATATAAGT 59.457 44.000 0.00 0.00 0.00 2.24
208 209 6.723052 CCCTCCGTTCCTCCTAAATATAAGTA 59.277 42.308 0.00 0.00 0.00 2.24
211 212 8.773033 TCCGTTCCTCCTAAATATAAGTAGTT 57.227 34.615 0.00 0.00 0.00 2.24
213 214 8.419442 CCGTTCCTCCTAAATATAAGTAGTTGT 58.581 37.037 0.00 0.00 0.00 3.32
229 230 7.589958 AGTAGTTGTAGAGATTCCACTATGG 57.410 40.000 0.00 0.00 39.43 2.74
230 231 7.355101 AGTAGTTGTAGAGATTCCACTATGGA 58.645 38.462 0.00 0.00 46.61 3.41
240 241 2.036387 TCCACTATGGACCACATACGG 58.964 52.381 0.00 0.00 42.67 4.02
241 242 2.036387 CCACTATGGACCACATACGGA 58.964 52.381 0.00 0.00 40.96 4.69
245 246 3.964688 ACTATGGACCACATACGGATGAA 59.035 43.478 16.36 0.00 41.03 2.57
246 247 3.924114 ATGGACCACATACGGATGAAA 57.076 42.857 16.36 0.00 38.26 2.69
247 248 3.704800 TGGACCACATACGGATGAAAA 57.295 42.857 16.36 0.00 36.48 2.29
249 250 3.944650 TGGACCACATACGGATGAAAATG 59.055 43.478 16.36 1.29 36.48 2.32
250 251 4.196193 GGACCACATACGGATGAAAATGA 58.804 43.478 16.36 0.00 36.48 2.57
251 252 4.273480 GGACCACATACGGATGAAAATGAG 59.727 45.833 16.36 0.00 36.48 2.90
255 256 5.353956 CCACATACGGATGAAAATGAGTGAA 59.646 40.000 16.36 0.00 36.48 3.18
256 257 6.038603 CCACATACGGATGAAAATGAGTGAAT 59.961 38.462 16.36 0.00 36.48 2.57
257 258 7.128331 CACATACGGATGAAAATGAGTGAATC 58.872 38.462 16.36 0.00 36.48 2.52
260 261 6.910536 ACGGATGAAAATGAGTGAATCTAC 57.089 37.500 0.00 0.00 0.00 2.59
261 262 6.406370 ACGGATGAAAATGAGTGAATCTACA 58.594 36.000 0.00 0.00 0.00 2.74
262 263 6.313905 ACGGATGAAAATGAGTGAATCTACAC 59.686 38.462 0.00 0.00 40.60 2.90
288 289 5.890424 AAAAACCCGTATGTGGTTCATAG 57.110 39.130 7.92 0.00 45.23 2.23
289 290 4.563140 AAACCCGTATGTGGTTCATAGT 57.437 40.909 7.92 0.00 45.23 2.12
290 291 3.536956 ACCCGTATGTGGTTCATAGTG 57.463 47.619 0.00 0.00 39.36 2.74
291 292 2.169769 ACCCGTATGTGGTTCATAGTGG 59.830 50.000 0.00 0.00 39.36 4.00
292 293 2.432874 CCCGTATGTGGTTCATAGTGGA 59.567 50.000 0.00 0.00 39.36 4.02
293 294 3.118555 CCCGTATGTGGTTCATAGTGGAA 60.119 47.826 0.00 0.00 39.36 3.53
295 296 4.750098 CCGTATGTGGTTCATAGTGGAATC 59.250 45.833 0.00 0.00 39.36 2.52
296 297 5.453339 CCGTATGTGGTTCATAGTGGAATCT 60.453 44.000 0.00 0.00 39.36 2.40
299 300 7.255486 CGTATGTGGTTCATAGTGGAATCTCTA 60.255 40.741 0.00 0.00 39.36 2.43
300 301 6.222038 TGTGGTTCATAGTGGAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
302 303 6.212589 TGTGGTTCATAGTGGAATCTCTACAA 59.787 38.462 0.00 0.00 29.47 2.41
303 304 7.103641 GTGGTTCATAGTGGAATCTCTACAAA 58.896 38.462 0.00 0.00 29.47 2.83
304 305 7.278868 GTGGTTCATAGTGGAATCTCTACAAAG 59.721 40.741 0.00 0.00 29.47 2.77
326 327 6.705863 AGACTTATATTTACGAACGGAGGT 57.294 37.500 0.00 0.00 0.00 3.85
362 363 3.334691 ACAAGTCGTGGATGTAATGTGG 58.665 45.455 0.00 0.00 0.00 4.17
371 372 6.209788 TCGTGGATGTAATGTGGTATGCTATA 59.790 38.462 0.00 0.00 0.00 1.31
372 373 6.310467 CGTGGATGTAATGTGGTATGCTATAC 59.690 42.308 0.00 0.00 0.00 1.47
377 378 9.273016 GATGTAATGTGGTATGCTATACAAGTT 57.727 33.333 8.07 0.57 0.00 2.66
378 379 8.657074 TGTAATGTGGTATGCTATACAAGTTC 57.343 34.615 8.07 0.00 0.00 3.01
382 383 5.057149 GTGGTATGCTATACAAGTTCCAGG 58.943 45.833 8.07 0.00 0.00 4.45
383 384 4.966168 TGGTATGCTATACAAGTTCCAGGA 59.034 41.667 8.07 0.00 0.00 3.86
433 434 5.939296 CCTGCAAAATTTGACCCAAACATAT 59.061 36.000 10.26 0.00 36.13 1.78
440 441 5.559427 TTTGACCCAAACATATGTCGATG 57.441 39.130 9.23 8.79 0.00 3.84
441 442 4.214986 TGACCCAAACATATGTCGATGT 57.785 40.909 9.23 4.87 41.92 3.06
442 443 4.188462 TGACCCAAACATATGTCGATGTC 58.812 43.478 9.23 13.61 39.16 3.06
445 446 4.394920 ACCCAAACATATGTCGATGTCAAC 59.605 41.667 9.23 0.00 39.16 3.18
477 483 9.911138 AAAAAGAACAAACTTTGCATGATTTTT 57.089 22.222 0.00 6.11 39.57 1.94
496 502 2.727123 TTTTTCCAGAGCAGGACACA 57.273 45.000 0.00 0.00 37.42 3.72
497 503 2.727123 TTTTCCAGAGCAGGACACAA 57.273 45.000 0.00 0.00 37.42 3.33
498 504 2.727123 TTTCCAGAGCAGGACACAAA 57.273 45.000 0.00 0.00 37.42 2.83
499 505 2.957402 TTCCAGAGCAGGACACAAAT 57.043 45.000 0.00 0.00 37.42 2.32
500 506 2.957402 TCCAGAGCAGGACACAAATT 57.043 45.000 0.00 0.00 31.23 1.82
501 507 2.507484 TCCAGAGCAGGACACAAATTG 58.493 47.619 0.00 0.00 31.23 2.32
502 508 2.158623 TCCAGAGCAGGACACAAATTGT 60.159 45.455 0.00 0.00 43.10 2.71
503 509 2.624838 CCAGAGCAGGACACAAATTGTT 59.375 45.455 0.00 0.00 39.17 2.83
506 512 3.316308 AGAGCAGGACACAAATTGTTGTC 59.684 43.478 15.39 15.39 45.00 3.18
507 513 2.033299 AGCAGGACACAAATTGTTGTCG 59.967 45.455 16.43 9.24 45.00 4.35
508 514 2.223479 GCAGGACACAAATTGTTGTCGT 60.223 45.455 16.43 15.10 45.00 4.34
509 515 3.733684 GCAGGACACAAATTGTTGTCGTT 60.734 43.478 15.61 8.59 45.00 3.85
510 516 4.420168 CAGGACACAAATTGTTGTCGTTT 58.580 39.130 15.61 6.95 45.00 3.60
511 517 4.862018 CAGGACACAAATTGTTGTCGTTTT 59.138 37.500 15.61 5.33 45.00 2.43
512 518 5.347364 CAGGACACAAATTGTTGTCGTTTTT 59.653 36.000 15.61 3.72 45.00 1.94
535 541 8.810652 TTTTGTATGCAAGTTTTCAGGATTAC 57.189 30.769 0.00 0.00 35.82 1.89
537 543 7.701539 TGTATGCAAGTTTTCAGGATTACAT 57.298 32.000 0.00 0.00 0.00 2.29
538 544 7.537715 TGTATGCAAGTTTTCAGGATTACATG 58.462 34.615 0.00 0.00 0.00 3.21
539 545 6.594788 ATGCAAGTTTTCAGGATTACATGT 57.405 33.333 2.69 2.69 0.00 3.21
540 546 6.403866 TGCAAGTTTTCAGGATTACATGTT 57.596 33.333 2.30 0.00 0.00 2.71
541 547 6.215121 TGCAAGTTTTCAGGATTACATGTTG 58.785 36.000 2.30 0.00 0.00 3.33
542 548 5.634859 GCAAGTTTTCAGGATTACATGTTGG 59.365 40.000 2.30 0.00 0.00 3.77
543 549 5.982890 AGTTTTCAGGATTACATGTTGGG 57.017 39.130 2.30 0.00 0.00 4.12
544 550 4.220602 AGTTTTCAGGATTACATGTTGGGC 59.779 41.667 2.30 0.00 0.00 5.36
547 553 2.244510 TCAGGATTACATGTTGGGCCAT 59.755 45.455 7.26 0.00 0.00 4.40
549 555 3.569701 CAGGATTACATGTTGGGCCATAC 59.430 47.826 7.26 9.50 0.00 2.39
551 557 3.317993 GGATTACATGTTGGGCCATACAC 59.682 47.826 19.20 11.06 0.00 2.90
552 558 3.730215 TTACATGTTGGGCCATACACT 57.270 42.857 19.20 12.15 0.00 3.55
553 559 4.846168 TTACATGTTGGGCCATACACTA 57.154 40.909 19.20 11.42 0.00 2.74
554 560 2.999331 ACATGTTGGGCCATACACTAC 58.001 47.619 19.20 9.73 0.00 2.73
556 562 2.483014 TGTTGGGCCATACACTACAC 57.517 50.000 7.26 0.00 0.00 2.90
557 563 1.003812 TGTTGGGCCATACACTACACC 59.996 52.381 7.26 0.00 0.00 4.16
559 565 1.590591 TGGGCCATACACTACACCAT 58.409 50.000 0.00 0.00 0.00 3.55
561 567 1.211949 GGGCCATACACTACACCATGT 59.788 52.381 4.39 0.00 0.00 3.21
562 568 2.356741 GGGCCATACACTACACCATGTT 60.357 50.000 4.39 0.00 0.00 2.71
563 569 3.352648 GGCCATACACTACACCATGTTT 58.647 45.455 0.00 0.00 0.00 2.83
585 591 5.441709 TTTTTCAACAACTTCCCGATACC 57.558 39.130 0.00 0.00 0.00 2.73
587 593 3.604875 TCAACAACTTCCCGATACCTC 57.395 47.619 0.00 0.00 0.00 3.85
588 594 2.094390 TCAACAACTTCCCGATACCTCG 60.094 50.000 0.00 0.00 44.62 4.63
607 613 4.498345 CCTCGGAGTAAGATAAGAGCACAC 60.498 50.000 4.02 0.00 0.00 3.82
619 625 3.383620 AGAGCACACACTCTTCTCTTG 57.616 47.619 0.00 0.00 44.76 3.02
645 651 6.824305 AAAAATCAACTGTGTAGCTATGCT 57.176 33.333 0.00 0.00 43.41 3.79
700 738 1.127567 TTACTGCCTCTGCCAGTGGT 61.128 55.000 11.74 0.00 36.33 4.16
701 739 1.830587 TACTGCCTCTGCCAGTGGTG 61.831 60.000 11.74 9.76 36.33 4.17
705 743 2.044555 CCTCTGCCAGTGGTGCATG 61.045 63.158 11.74 0.00 38.22 4.06
708 746 2.986979 TGCCAGTGGTGCATGCAG 60.987 61.111 23.41 9.50 32.85 4.41
711 749 1.303074 CCAGTGGTGCATGCAGTCT 60.303 57.895 23.41 16.26 0.00 3.24
717 755 2.611292 GTGGTGCATGCAGTCTAATCTC 59.389 50.000 23.41 5.54 0.00 2.75
752 791 9.810231 GTTGATAATTTAGTTTTGCCAACAATG 57.190 29.630 0.00 0.00 35.21 2.82
753 792 9.553064 TTGATAATTTAGTTTTGCCAACAATGT 57.447 25.926 0.00 0.00 35.21 2.71
765 804 5.877031 TGCCAACAATGTTTTTGACAATTG 58.123 33.333 3.24 3.24 42.62 2.32
769 808 7.064674 CCAACAATGTTTTTGACAATTGATCG 58.935 34.615 13.59 0.00 42.62 3.69
770 809 7.042858 CCAACAATGTTTTTGACAATTGATCGA 60.043 33.333 13.59 3.30 42.62 3.59
775 815 8.728088 ATGTTTTTGACAATTGATCGAGTAAC 57.272 30.769 13.59 12.69 42.62 2.50
812 857 6.058833 TGTTGAAATGTAGCCTGTTTCTGTA 58.941 36.000 0.00 0.00 33.99 2.74
832 3907 2.704572 ACTTACAACCAGCATCTCAGC 58.295 47.619 0.00 0.00 0.00 4.26
851 3931 2.086869 GCAACCATATGTGCACTGTCT 58.913 47.619 19.41 2.80 0.00 3.41
876 3956 5.183713 TGTTTCTTAATCAGCACCCATTCTG 59.816 40.000 0.00 0.00 0.00 3.02
899 3984 8.522830 TCTGTTTCCTTTTTAATTAGCATCCAG 58.477 33.333 0.00 0.00 0.00 3.86
909 4004 9.859427 TTTTAATTAGCATCCAGTTCATTCTTG 57.141 29.630 0.00 0.00 0.00 3.02
918 4013 7.274250 GCATCCAGTTCATTCTTGTAATGTTTC 59.726 37.037 0.00 0.00 0.00 2.78
921 4016 7.719193 TCCAGTTCATTCTTGTAATGTTTCTCA 59.281 33.333 0.00 0.00 0.00 3.27
961 4056 1.117994 AGATCAGAAGCTGCGATCCA 58.882 50.000 17.65 0.00 36.95 3.41
1007 4106 3.002583 TGCCTCCGCCATGTCTGA 61.003 61.111 0.00 0.00 0.00 3.27
1033 4132 1.668826 AGGTTGGGCAGATCTACCAA 58.331 50.000 21.15 21.15 41.66 3.67
1051 4150 2.159338 CCAAATGTCCTGCTTCATTCCG 60.159 50.000 0.00 0.00 33.86 4.30
1060 4159 3.876914 CCTGCTTCATTCCGTTATTGCTA 59.123 43.478 0.00 0.00 0.00 3.49
1197 4300 2.438434 CAACCTGATGTCCCCGGC 60.438 66.667 0.00 0.00 0.00 6.13
1223 4326 1.535204 CCATGTCACCACCCCTTTGC 61.535 60.000 0.00 0.00 0.00 3.68
1234 4340 2.556622 CACCCCTTTGCTGATAAACGTT 59.443 45.455 0.00 0.00 0.00 3.99
1242 4348 5.681337 TTGCTGATAAACGTTCATGTCAA 57.319 34.783 0.00 0.00 0.00 3.18
1243 4349 5.878332 TGCTGATAAACGTTCATGTCAAT 57.122 34.783 0.00 0.00 0.00 2.57
1307 4413 7.236847 TCAGATTCCCCTAGTTAACTTTTCTCA 59.763 37.037 14.49 0.00 0.00 3.27
1386 4505 5.003692 TCATCTTCTCCAGAAACAGATCG 57.996 43.478 0.00 0.00 34.16 3.69
1546 4665 3.128349 TCTCACAGTTACTTTTGGCGTC 58.872 45.455 0.00 0.00 0.00 5.19
1646 4765 2.042831 GCATGGACTCTGGTGGCAC 61.043 63.158 9.70 9.70 0.00 5.01
1833 4958 1.469335 AAGTCTTCCGCCTCGACCAA 61.469 55.000 0.00 0.00 0.00 3.67
1881 5006 2.087646 GTGGAGGAGTTGGAGAATTGC 58.912 52.381 0.00 0.00 0.00 3.56
1930 5055 1.891150 GCCAGCCATTATCCTTCATGG 59.109 52.381 0.00 0.00 42.73 3.66
2149 8754 4.888326 TGCATTCCTTGTTTTAGGCATT 57.112 36.364 0.00 0.00 35.15 3.56
2177 8783 2.331132 GCTGGCTGGAGCAACTGAC 61.331 63.158 0.20 0.00 44.36 3.51
2272 8880 6.428159 GTCATTACTCTGCTGGTATAATTGGG 59.572 42.308 0.00 0.00 0.00 4.12
2470 9081 5.047872 TGTGCTACACATTGCTGATTTTGAT 60.048 36.000 0.00 0.00 39.62 2.57
2480 9091 8.286800 ACATTGCTGATTTTGATTGTTGATTTG 58.713 29.630 0.00 0.00 0.00 2.32
2483 9094 7.211573 TGCTGATTTTGATTGTTGATTTGAGT 58.788 30.769 0.00 0.00 0.00 3.41
2484 9095 7.170151 TGCTGATTTTGATTGTTGATTTGAGTG 59.830 33.333 0.00 0.00 0.00 3.51
2485 9096 7.410800 TGATTTTGATTGTTGATTTGAGTGC 57.589 32.000 0.00 0.00 0.00 4.40
2487 9098 3.557577 TGATTGTTGATTTGAGTGCCG 57.442 42.857 0.00 0.00 0.00 5.69
2488 9099 2.884012 TGATTGTTGATTTGAGTGCCGT 59.116 40.909 0.00 0.00 0.00 5.68
2489 9100 4.068599 TGATTGTTGATTTGAGTGCCGTA 58.931 39.130 0.00 0.00 0.00 4.02
2490 9101 3.889196 TTGTTGATTTGAGTGCCGTAC 57.111 42.857 0.00 0.00 0.00 3.67
2491 9102 3.120321 TGTTGATTTGAGTGCCGTACT 57.880 42.857 0.00 0.00 44.02 2.73
2493 9104 4.242475 TGTTGATTTGAGTGCCGTACTAG 58.758 43.478 0.00 0.00 40.53 2.57
2495 9106 2.829720 TGATTTGAGTGCCGTACTAGGT 59.170 45.455 0.00 0.00 40.53 3.08
2500 9111 2.629137 TGAGTGCCGTACTAGGTTTGAA 59.371 45.455 0.00 0.00 40.53 2.69
2517 9128 7.441836 AGGTTTGAATTTTAGTGTTCCATTCC 58.558 34.615 0.00 0.00 0.00 3.01
2518 9129 6.649141 GGTTTGAATTTTAGTGTTCCATTCCC 59.351 38.462 0.00 0.00 0.00 3.97
2530 9141 0.811281 CCATTCCCGTGCTTTCCTTC 59.189 55.000 0.00 0.00 0.00 3.46
2531 9142 0.447801 CATTCCCGTGCTTTCCTTCG 59.552 55.000 0.00 0.00 0.00 3.79
2532 9143 0.323629 ATTCCCGTGCTTTCCTTCGA 59.676 50.000 0.00 0.00 0.00 3.71
2534 9145 0.601841 TCCCGTGCTTTCCTTCGAAC 60.602 55.000 0.00 0.00 0.00 3.95
2536 9147 1.156736 CCGTGCTTTCCTTCGAACAT 58.843 50.000 0.00 0.00 0.00 2.71
2563 9201 7.879160 TCCAATCCTGATTTCTTCAAATTTTGG 59.121 33.333 9.18 0.00 31.94 3.28
2579 9217 8.366401 TCAAATTTTGGCAATTCTGAATGTCTA 58.634 29.630 0.00 0.00 0.00 2.59
2580 9218 9.158233 CAAATTTTGGCAATTCTGAATGTCTAT 57.842 29.630 0.00 0.00 0.00 1.98
2581 9219 8.937634 AATTTTGGCAATTCTGAATGTCTATC 57.062 30.769 0.00 0.00 0.00 2.08
2582 9220 7.707624 TTTTGGCAATTCTGAATGTCTATCT 57.292 32.000 0.00 0.00 0.00 1.98
2583 9221 6.932356 TTGGCAATTCTGAATGTCTATCTC 57.068 37.500 3.22 0.00 0.00 2.75
2585 9223 5.104402 TGGCAATTCTGAATGTCTATCTCCA 60.104 40.000 3.22 1.03 0.00 3.86
2719 10101 3.098636 GACACACAAAACGCTTCACTTC 58.901 45.455 0.00 0.00 0.00 3.01
2754 10136 8.704668 TCTATTGAAATCTAGCATAAGGTCACA 58.295 33.333 0.00 0.00 0.00 3.58
2828 10402 4.020218 AGCCTGTGACATACTGTACATTGT 60.020 41.667 0.00 0.69 0.00 2.71
2865 10741 0.388659 ACTGCAGAGCGATGATCCTC 59.611 55.000 23.35 3.62 0.00 3.71
2902 10778 2.947652 GGTGTTGATGCATATGACTGCT 59.052 45.455 6.97 0.00 42.75 4.24
2903 10779 3.242969 GGTGTTGATGCATATGACTGCTG 60.243 47.826 6.97 0.00 42.75 4.41
2916 10792 7.012327 GCATATGACTGCTGTTTAGTTAATGGA 59.988 37.037 6.97 0.00 39.12 3.41
2983 10884 8.512956 TCGAGTATTATGTTAGGATTGCTAGAC 58.487 37.037 0.00 0.00 0.00 2.59
2994 10895 6.567602 AGGATTGCTAGACCTGTTAATTCT 57.432 37.500 0.00 0.00 32.39 2.40
3034 11032 5.435686 TGGAATATGGCCGCTAATTCTAT 57.564 39.130 14.87 0.00 0.00 1.98
3118 11116 4.287067 GTGAATTGCCTCCTCTATCCCATA 59.713 45.833 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.881443 ACACTGGTTGCTACTAGTCTACTAG 59.119 44.000 13.96 14.26 43.38 2.57
9 10 5.813383 ACACTGGTTGCTACTAGTCTACTA 58.187 41.667 13.96 0.00 43.38 1.82
11 12 5.162075 CAACACTGGTTGCTACTAGTCTAC 58.838 45.833 13.96 0.00 46.98 2.59
13 14 4.258702 CAACACTGGTTGCTACTAGTCT 57.741 45.455 13.96 0.53 46.98 3.24
25 26 4.528596 AGCAGAGTTATAGTCAACACTGGT 59.471 41.667 10.80 10.80 46.14 4.00
27 28 5.163913 GCAAGCAGAGTTATAGTCAACACTG 60.164 44.000 8.47 8.47 44.81 3.66
28 29 4.932200 GCAAGCAGAGTTATAGTCAACACT 59.068 41.667 0.00 0.00 36.55 3.55
29 30 4.690748 TGCAAGCAGAGTTATAGTCAACAC 59.309 41.667 0.00 0.00 0.00 3.32
30 31 4.893608 TGCAAGCAGAGTTATAGTCAACA 58.106 39.130 0.00 0.00 0.00 3.33
31 32 6.758886 ACTATGCAAGCAGAGTTATAGTCAAC 59.241 38.462 15.86 0.00 44.87 3.18
32 33 6.878317 ACTATGCAAGCAGAGTTATAGTCAA 58.122 36.000 15.86 0.00 44.87 3.18
48 49 1.812235 CACTGGCACTGACTATGCAA 58.188 50.000 0.00 0.00 45.27 4.08
61 62 1.065102 CAGCAATCACTATGCACTGGC 59.935 52.381 0.00 0.00 46.22 4.85
66 67 7.498570 TCAACATAATACAGCAATCACTATGCA 59.501 33.333 0.00 0.00 46.22 3.96
103 104 3.013921 GGAGCAAATGTATTGTTCGGGA 58.986 45.455 0.00 0.00 31.58 5.14
105 106 4.273480 CCTAGGAGCAAATGTATTGTTCGG 59.727 45.833 1.05 0.00 31.58 4.30
107 108 6.767902 TGATCCTAGGAGCAAATGTATTGTTC 59.232 38.462 27.17 9.56 37.61 3.18
108 109 6.662755 TGATCCTAGGAGCAAATGTATTGTT 58.337 36.000 27.17 0.00 37.61 2.83
109 110 6.252599 TGATCCTAGGAGCAAATGTATTGT 57.747 37.500 27.17 0.00 37.61 2.71
111 112 8.212259 ACTATGATCCTAGGAGCAAATGTATT 57.788 34.615 32.06 16.90 43.95 1.89
114 115 7.805083 ATACTATGATCCTAGGAGCAAATGT 57.195 36.000 32.06 27.89 43.95 2.71
162 163 7.549842 GGAGGGAGTACATCTTTAAGAAGTTTC 59.450 40.741 8.14 6.98 34.41 2.78
203 204 9.132923 CCATAGTGGAATCTCTACAACTACTTA 57.867 37.037 0.00 0.00 40.96 2.24
205 206 7.355101 TCCATAGTGGAATCTCTACAACTACT 58.645 38.462 0.00 0.00 45.00 2.57
206 207 7.584122 TCCATAGTGGAATCTCTACAACTAC 57.416 40.000 0.00 0.00 45.00 2.73
221 222 2.036387 TCCGTATGTGGTCCATAGTGG 58.964 52.381 0.00 0.00 36.71 4.00
222 223 3.320826 TCATCCGTATGTGGTCCATAGTG 59.679 47.826 0.00 0.00 36.71 2.74
223 224 3.572642 TCATCCGTATGTGGTCCATAGT 58.427 45.455 0.00 0.00 36.71 2.12
224 225 4.600692 TTCATCCGTATGTGGTCCATAG 57.399 45.455 0.00 0.00 36.71 2.23
226 227 3.924114 TTTCATCCGTATGTGGTCCAT 57.076 42.857 0.00 0.00 37.58 3.41
229 230 4.876107 ACTCATTTTCATCCGTATGTGGTC 59.124 41.667 0.00 0.00 34.50 4.02
230 231 4.635765 CACTCATTTTCATCCGTATGTGGT 59.364 41.667 0.00 0.00 34.50 4.16
234 235 7.488187 AGATTCACTCATTTTCATCCGTATG 57.512 36.000 0.00 0.00 0.00 2.39
237 238 6.313905 GTGTAGATTCACTCATTTTCATCCGT 59.686 38.462 0.00 0.00 35.68 4.69
238 239 6.536582 AGTGTAGATTCACTCATTTTCATCCG 59.463 38.462 0.00 0.00 44.07 4.18
239 240 7.856145 AGTGTAGATTCACTCATTTTCATCC 57.144 36.000 0.00 0.00 44.07 3.51
270 271 2.169769 CCACTATGAACCACATACGGGT 59.830 50.000 0.00 0.00 41.41 5.28
271 272 2.432874 TCCACTATGAACCACATACGGG 59.567 50.000 0.00 0.00 40.07 5.28
272 273 3.812156 TCCACTATGAACCACATACGG 57.188 47.619 0.00 0.00 40.07 4.02
273 274 5.601662 AGATTCCACTATGAACCACATACG 58.398 41.667 0.00 0.00 40.07 3.06
274 275 6.821388 AGAGATTCCACTATGAACCACATAC 58.179 40.000 0.00 0.00 40.07 2.39
275 276 7.563556 TGTAGAGATTCCACTATGAACCACATA 59.436 37.037 0.00 0.00 40.07 2.29
276 277 5.965033 AGAGATTCCACTATGAACCACAT 57.035 39.130 0.00 0.00 42.39 3.21
277 278 5.719563 TGTAGAGATTCCACTATGAACCACA 59.280 40.000 0.00 0.00 0.00 4.17
278 279 6.222038 TGTAGAGATTCCACTATGAACCAC 57.778 41.667 0.00 0.00 0.00 4.16
279 280 6.867519 TTGTAGAGATTCCACTATGAACCA 57.132 37.500 0.00 0.00 0.00 3.67
280 281 7.492994 GTCTTTGTAGAGATTCCACTATGAACC 59.507 40.741 0.00 0.00 0.00 3.62
281 282 8.254508 AGTCTTTGTAGAGATTCCACTATGAAC 58.745 37.037 0.00 0.00 0.00 3.18
282 283 8.367660 AGTCTTTGTAGAGATTCCACTATGAA 57.632 34.615 0.00 0.00 0.00 2.57
283 284 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
296 297 9.507280 CCGTTCGTAAATATAAGTCTTTGTAGA 57.493 33.333 0.00 0.00 0.00 2.59
299 300 7.490402 CCTCCGTTCGTAAATATAAGTCTTTGT 59.510 37.037 0.00 0.00 0.00 2.83
300 301 7.490402 ACCTCCGTTCGTAAATATAAGTCTTTG 59.510 37.037 0.00 0.00 0.00 2.77
302 303 7.105241 ACCTCCGTTCGTAAATATAAGTCTT 57.895 36.000 0.00 0.00 0.00 3.01
303 304 6.705863 ACCTCCGTTCGTAAATATAAGTCT 57.294 37.500 0.00 0.00 0.00 3.24
304 305 7.643579 ACTACCTCCGTTCGTAAATATAAGTC 58.356 38.462 0.00 0.00 0.00 3.01
315 316 6.942532 TTATTACATACTACCTCCGTTCGT 57.057 37.500 0.00 0.00 0.00 3.85
316 317 9.334693 GTAATTATTACATACTACCTCCGTTCG 57.665 37.037 9.94 0.00 36.17 3.95
362 363 8.451908 AAAATCCTGGAACTTGTATAGCATAC 57.548 34.615 0.00 0.00 0.00 2.39
477 483 2.727123 TGTGTCCTGCTCTGGAAAAA 57.273 45.000 0.00 0.00 37.93 1.94
480 486 2.886523 CAATTTGTGTCCTGCTCTGGAA 59.113 45.455 0.00 0.00 37.93 3.53
481 487 2.158623 ACAATTTGTGTCCTGCTCTGGA 60.159 45.455 0.15 0.00 34.38 3.86
482 488 2.233271 ACAATTTGTGTCCTGCTCTGG 58.767 47.619 0.15 0.00 34.38 3.86
483 489 3.067180 ACAACAATTTGTGTCCTGCTCTG 59.933 43.478 2.13 0.00 44.66 3.35
484 490 3.290710 ACAACAATTTGTGTCCTGCTCT 58.709 40.909 2.13 0.00 44.66 4.09
490 496 5.771602 AAAAACGACAACAATTTGTGTCC 57.228 34.783 18.20 6.12 46.43 4.02
509 515 9.255304 GTAATCCTGAAAACTTGCATACAAAAA 57.745 29.630 0.00 0.00 34.74 1.94
510 516 8.417106 TGTAATCCTGAAAACTTGCATACAAAA 58.583 29.630 0.00 0.00 34.74 2.44
511 517 7.946207 TGTAATCCTGAAAACTTGCATACAAA 58.054 30.769 0.00 0.00 34.74 2.83
512 518 7.517614 TGTAATCCTGAAAACTTGCATACAA 57.482 32.000 0.00 0.00 0.00 2.41
513 519 7.176515 ACATGTAATCCTGAAAACTTGCATACA 59.823 33.333 0.00 0.00 0.00 2.29
514 520 7.538575 ACATGTAATCCTGAAAACTTGCATAC 58.461 34.615 0.00 0.00 0.00 2.39
515 521 7.701539 ACATGTAATCCTGAAAACTTGCATA 57.298 32.000 0.00 0.00 0.00 3.14
517 523 6.215121 CAACATGTAATCCTGAAAACTTGCA 58.785 36.000 0.00 0.00 0.00 4.08
519 525 6.158598 CCCAACATGTAATCCTGAAAACTTG 58.841 40.000 0.00 0.00 0.00 3.16
520 526 5.279456 GCCCAACATGTAATCCTGAAAACTT 60.279 40.000 0.00 0.00 0.00 2.66
521 527 4.220602 GCCCAACATGTAATCCTGAAAACT 59.779 41.667 0.00 0.00 0.00 2.66
522 528 4.494484 GCCCAACATGTAATCCTGAAAAC 58.506 43.478 0.00 0.00 0.00 2.43
524 530 3.096092 GGCCCAACATGTAATCCTGAAA 58.904 45.455 0.00 0.00 0.00 2.69
528 534 3.204158 TGTATGGCCCAACATGTAATCCT 59.796 43.478 0.00 0.00 32.39 3.24
529 535 3.317993 GTGTATGGCCCAACATGTAATCC 59.682 47.826 10.19 0.00 32.39 3.01
530 536 4.207165 AGTGTATGGCCCAACATGTAATC 58.793 43.478 10.19 0.00 32.39 1.75
531 537 4.249638 AGTGTATGGCCCAACATGTAAT 57.750 40.909 10.19 0.00 32.39 1.89
532 538 3.730215 AGTGTATGGCCCAACATGTAA 57.270 42.857 10.19 0.00 32.39 2.41
533 539 3.519913 TGTAGTGTATGGCCCAACATGTA 59.480 43.478 10.19 3.74 32.39 2.29
535 541 2.682856 GTGTAGTGTATGGCCCAACATG 59.317 50.000 10.19 0.00 32.39 3.21
537 543 1.003812 GGTGTAGTGTATGGCCCAACA 59.996 52.381 0.00 0.71 0.00 3.33
538 544 1.003812 TGGTGTAGTGTATGGCCCAAC 59.996 52.381 0.00 0.00 0.00 3.77
539 545 1.363246 TGGTGTAGTGTATGGCCCAA 58.637 50.000 0.00 0.00 0.00 4.12
540 546 1.211703 CATGGTGTAGTGTATGGCCCA 59.788 52.381 0.00 0.00 0.00 5.36
541 547 1.211949 ACATGGTGTAGTGTATGGCCC 59.788 52.381 0.00 0.00 0.00 5.80
542 548 2.710096 ACATGGTGTAGTGTATGGCC 57.290 50.000 0.00 0.00 0.00 5.36
543 549 5.385509 AAAAACATGGTGTAGTGTATGGC 57.614 39.130 0.00 0.00 0.00 4.40
563 569 5.134661 AGGTATCGGGAAGTTGTTGAAAAA 58.865 37.500 0.00 0.00 0.00 1.94
566 572 3.615592 CGAGGTATCGGGAAGTTGTTGAA 60.616 47.826 0.00 0.00 45.39 2.69
567 573 2.094390 CGAGGTATCGGGAAGTTGTTGA 60.094 50.000 0.00 0.00 45.39 3.18
568 574 2.268298 CGAGGTATCGGGAAGTTGTTG 58.732 52.381 0.00 0.00 45.39 3.33
569 575 2.667473 CGAGGTATCGGGAAGTTGTT 57.333 50.000 0.00 0.00 45.39 2.83
580 586 5.706369 TGCTCTTATCTTACTCCGAGGTATC 59.294 44.000 0.00 0.00 0.00 2.24
581 587 5.474189 GTGCTCTTATCTTACTCCGAGGTAT 59.526 44.000 0.00 0.00 0.00 2.73
582 588 4.820716 GTGCTCTTATCTTACTCCGAGGTA 59.179 45.833 0.00 0.00 0.00 3.08
584 590 3.632604 TGTGCTCTTATCTTACTCCGAGG 59.367 47.826 0.00 0.00 0.00 4.63
585 591 4.096532 TGTGTGCTCTTATCTTACTCCGAG 59.903 45.833 0.00 0.00 0.00 4.63
587 593 4.106197 GTGTGTGCTCTTATCTTACTCCG 58.894 47.826 0.00 0.00 0.00 4.63
588 594 5.126384 AGAGTGTGTGCTCTTATCTTACTCC 59.874 44.000 0.00 0.00 42.69 3.85
589 595 6.202516 AGAGTGTGTGCTCTTATCTTACTC 57.797 41.667 0.00 0.00 42.69 2.59
642 648 1.469940 GCTTCTCGCTGTTAGCTAGCA 60.470 52.381 18.83 10.09 41.18 3.49
644 650 2.568696 TGCTTCTCGCTGTTAGCTAG 57.431 50.000 0.00 0.00 39.60 3.42
645 651 2.231478 AGTTGCTTCTCGCTGTTAGCTA 59.769 45.455 0.00 0.00 39.60 3.32
651 657 1.202580 AGAACAGTTGCTTCTCGCTGT 60.203 47.619 0.00 0.00 43.13 4.40
653 659 3.060602 GTTAGAACAGTTGCTTCTCGCT 58.939 45.455 0.00 0.00 40.11 4.93
688 726 2.697761 GCATGCACCACTGGCAGAG 61.698 63.158 23.66 13.97 45.68 3.35
700 738 4.411256 TGATGAGATTAGACTGCATGCA 57.589 40.909 21.29 21.29 0.00 3.96
701 739 5.943706 ATTGATGAGATTAGACTGCATGC 57.056 39.130 11.82 11.82 0.00 4.06
705 743 8.599055 TCAACATATTGATGAGATTAGACTGC 57.401 34.615 0.00 0.00 40.01 4.40
742 781 5.645067 TCAATTGTCAAAAACATTGTTGGCA 59.355 32.000 5.13 0.00 37.56 4.92
752 791 8.067784 TCAGTTACTCGATCAATTGTCAAAAAC 58.932 33.333 5.13 3.62 0.00 2.43
753 792 8.148807 TCAGTTACTCGATCAATTGTCAAAAA 57.851 30.769 5.13 0.00 0.00 1.94
755 794 7.722795 TTCAGTTACTCGATCAATTGTCAAA 57.277 32.000 5.13 0.00 0.00 2.69
765 804 8.116624 ACATACGAAATTTCAGTTACTCGATC 57.883 34.615 17.99 0.00 0.00 3.69
769 808 9.872757 TTTCAACATACGAAATTTCAGTTACTC 57.127 29.630 17.99 0.00 0.00 2.59
775 815 8.788813 GCTACATTTCAACATACGAAATTTCAG 58.211 33.333 17.99 12.49 40.29 3.02
812 857 2.038952 TGCTGAGATGCTGGTTGTAAGT 59.961 45.455 0.00 0.00 0.00 2.24
832 3907 3.503363 ACAAGACAGTGCACATATGGTTG 59.497 43.478 21.04 17.07 0.00 3.77
851 3931 5.774690 AGAATGGGTGCTGATTAAGAAACAA 59.225 36.000 0.00 0.00 0.00 2.83
876 3956 9.140286 GAACTGGATGCTAATTAAAAAGGAAAC 57.860 33.333 0.00 0.00 0.00 2.78
899 3984 9.897744 TCAATGAGAAACATTACAAGAATGAAC 57.102 29.630 4.36 0.00 46.01 3.18
909 4004 9.455847 GGCTATGAATTCAATGAGAAACATTAC 57.544 33.333 13.09 0.00 46.01 1.89
918 4013 4.319333 GCGACAGGCTATGAATTCAATGAG 60.319 45.833 13.09 11.07 39.11 2.90
921 4016 3.544684 TGCGACAGGCTATGAATTCAAT 58.455 40.909 13.09 4.08 44.05 2.57
961 4056 4.709886 ACAACAGGCCTTTCTTAGTTTTGT 59.290 37.500 0.00 0.00 0.00 2.83
1007 4106 2.042162 AGATCTGCCCAACCTTGATGTT 59.958 45.455 0.00 0.00 0.00 2.71
1033 4132 2.496899 ACGGAATGAAGCAGGACATT 57.503 45.000 0.00 0.00 39.06 2.71
1060 4159 2.739996 CGGAGAAGGAGCCTGCCAT 61.740 63.158 0.00 0.00 0.00 4.40
1197 4300 1.448540 GTGGTGACATGGAGAGCGG 60.449 63.158 0.00 0.00 46.14 5.52
1223 4326 8.791605 CAATGAATTGACATGAACGTTTATCAG 58.208 33.333 0.46 0.00 40.14 2.90
1242 4348 1.063492 TGGCTGGCTGGATCAATGAAT 60.063 47.619 2.00 0.00 0.00 2.57
1243 4349 0.332293 TGGCTGGCTGGATCAATGAA 59.668 50.000 2.00 0.00 0.00 2.57
1386 4505 0.859232 ACGCATCAACAACGAGACAC 59.141 50.000 0.00 0.00 0.00 3.67
1493 4612 1.633432 CAAGGAGATGTGGGTTGGGTA 59.367 52.381 0.00 0.00 0.00 3.69
1546 4665 4.039245 TCTCAACCAAGAGTGACTACCAAG 59.961 45.833 0.00 0.00 36.97 3.61
1646 4765 1.469917 CAAGTGCACAACAAAGAGCG 58.530 50.000 21.04 0.00 0.00 5.03
1833 4958 2.485426 CCACTTTGCATGTTCAGTCGAT 59.515 45.455 0.00 0.00 0.00 3.59
1881 5006 1.556958 CGTGCTGATGAAGATCGCG 59.443 57.895 0.00 0.00 33.48 5.87
1971 8573 5.887598 CCAGTGTTCAGAATCATGGGAATAA 59.112 40.000 0.00 0.00 0.00 1.40
2149 8754 1.225426 CCAGCCAGCAGAATAGCCA 59.775 57.895 0.00 0.00 34.23 4.75
2272 8880 5.261209 TGAGTACAAAATATTGCCATGCC 57.739 39.130 0.00 0.00 40.34 4.40
2470 9081 3.472652 AGTACGGCACTCAAATCAACAA 58.527 40.909 0.00 0.00 28.33 2.83
2480 9091 3.308438 TTCAAACCTAGTACGGCACTC 57.692 47.619 0.00 0.00 38.80 3.51
2483 9094 6.148150 CACTAAAATTCAAACCTAGTACGGCA 59.852 38.462 0.00 0.00 0.00 5.69
2484 9095 6.148315 ACACTAAAATTCAAACCTAGTACGGC 59.852 38.462 0.00 0.00 0.00 5.68
2485 9096 7.662604 ACACTAAAATTCAAACCTAGTACGG 57.337 36.000 0.00 0.00 0.00 4.02
2487 9098 9.059260 TGGAACACTAAAATTCAAACCTAGTAC 57.941 33.333 0.00 0.00 0.00 2.73
2517 9128 1.156736 ATGTTCGAAGGAAAGCACGG 58.843 50.000 0.00 0.00 33.05 4.94
2518 9129 2.412847 GGAATGTTCGAAGGAAAGCACG 60.413 50.000 0.00 0.00 33.05 5.34
2530 9141 5.824904 AGAAATCAGGATTGGAATGTTCG 57.175 39.130 0.00 0.00 0.00 3.95
2531 9142 7.161773 TGAAGAAATCAGGATTGGAATGTTC 57.838 36.000 0.00 0.00 33.04 3.18
2532 9143 7.543359 TTGAAGAAATCAGGATTGGAATGTT 57.457 32.000 0.00 0.00 39.77 2.71
2534 9145 9.444600 AAATTTGAAGAAATCAGGATTGGAATG 57.555 29.630 0.00 0.00 39.77 2.67
2536 9147 9.275398 CAAAATTTGAAGAAATCAGGATTGGAA 57.725 29.630 0.00 0.00 39.77 3.53
2563 9201 6.932356 TTGGAGATAGACATTCAGAATTGC 57.068 37.500 0.00 0.00 0.00 3.56
2579 9217 2.234908 CAGACGGGACTCTTTTGGAGAT 59.765 50.000 0.00 0.00 44.45 2.75
2580 9218 1.618837 CAGACGGGACTCTTTTGGAGA 59.381 52.381 0.00 0.00 44.45 3.71
2581 9219 1.618837 TCAGACGGGACTCTTTTGGAG 59.381 52.381 0.00 0.00 46.87 3.86
2582 9220 1.712056 TCAGACGGGACTCTTTTGGA 58.288 50.000 0.00 0.00 0.00 3.53
2583 9221 2.770164 ATCAGACGGGACTCTTTTGG 57.230 50.000 0.00 0.00 0.00 3.28
2585 9223 5.677319 TCATTATCAGACGGGACTCTTTT 57.323 39.130 0.00 0.00 0.00 2.27
2621 10000 2.398588 TCTGTAATGCCTAGGACCCAG 58.601 52.381 14.75 10.15 0.00 4.45
2701 10083 3.181500 GGAAGAAGTGAAGCGTTTTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
2702 10084 3.181501 TGGAAGAAGTGAAGCGTTTTGTG 60.182 43.478 0.00 0.00 0.00 3.33
2719 10101 8.498054 TGCTAGATTTCAATAGAAGTTGGAAG 57.502 34.615 0.00 0.00 34.71 3.46
2828 10402 4.087892 GGCCTGCCGAGCTCTCAA 62.088 66.667 12.85 0.00 0.00 3.02
2848 10724 2.508361 TGAGGATCATCGCTCTGCA 58.492 52.632 2.49 0.00 42.56 4.41
2865 10741 0.518636 CACCTTCAGCGAACACCATG 59.481 55.000 0.00 0.00 0.00 3.66
2902 10778 3.267483 GCTCCGCTCCATTAACTAAACA 58.733 45.455 0.00 0.00 0.00 2.83
2903 10779 3.267483 TGCTCCGCTCCATTAACTAAAC 58.733 45.455 0.00 0.00 0.00 2.01
2999 10900 7.226523 GCGGCCATATTCCAAAAAGAAAATATT 59.773 33.333 2.24 0.00 0.00 1.28
3006 11002 2.733956 AGCGGCCATATTCCAAAAAGA 58.266 42.857 2.24 0.00 0.00 2.52
3007 11003 4.647424 TTAGCGGCCATATTCCAAAAAG 57.353 40.909 2.24 0.00 0.00 2.27
3017 11015 4.617253 ACACATAGAATTAGCGGCCATA 57.383 40.909 2.24 0.00 0.00 2.74
3049 11047 0.459489 TCAAAACTGCTGCAACACCC 59.541 50.000 3.02 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.