Multiple sequence alignment - TraesCS3D01G257800

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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 TraesCS3D01G257800 chr3D 100.000 2890 0 0 1 2890 360050065 360047176 0.000000e+00 5337.0
1 TraesCS3D01G257800 chr3D 83.230 161 24 3 1145 1303 492131525 492131684 8.350000e-31 145.0
2 TraesCS3D01G257800 chr3B 92.474 2126 101 29 632 2724 466107267 466105168 0.000000e+00 2985.0
3 TraesCS3D01G257800 chr3B 90.094 212 20 1 682 893 466189948 466189738 1.020000e-69 274.0
4 TraesCS3D01G257800 chr3B 81.879 298 34 5 296 592 466190568 466190290 1.730000e-57 233.0
5 TraesCS3D01G257800 chr3B 82.036 167 26 4 1139 1303 653152147 653152311 3.880000e-29 139.0
6 TraesCS3D01G257800 chr3B 97.260 73 2 0 2802 2874 466104647 466104575 1.090000e-24 124.0
7 TraesCS3D01G257800 chr3A 89.965 2302 100 50 654 2874 479482349 479480098 0.000000e+00 2850.0
8 TraesCS3D01G257800 chr3A 83.230 161 24 3 1145 1303 633922202 633922361 8.350000e-31 145.0
9 TraesCS3D01G257800 chr7A 80.000 225 34 8 1085 1303 285576567 285576348 3.860000e-34 156.0
10 TraesCS3D01G257800 chr7A 88.679 53 4 2 1065 1117 235473529 235473579 2.400000e-06 63.9
11 TraesCS3D01G257800 chr7D 79.646 226 33 10 1085 1303 262698915 262698696 1.790000e-32 150.0
12 TraesCS3D01G257800 chr7D 88.679 53 4 2 1065 1117 220989873 220989923 2.400000e-06 63.9
13 TraesCS3D01G257800 chr7B 79.646 226 33 10 1085 1303 241107722 241107941 1.790000e-32 150.0
14 TraesCS3D01G257800 chr7B 100.000 34 0 0 1084 1117 175992970 175992937 2.400000e-06 63.9
15 TraesCS3D01G257800 chr5D 88.333 120 12 2 1376 1494 200501539 200501657 3.000000e-30 143.0
16 TraesCS3D01G257800 chr5B 88.333 120 12 2 1376 1494 211146510 211146628 3.000000e-30 143.0
17 TraesCS3D01G257800 chr5B 84.426 122 17 2 1374 1494 514279244 514279124 5.060000e-23 119.0
18 TraesCS3D01G257800 chr5A 88.333 120 12 2 1376 1494 214166890 214167008 3.000000e-30 143.0
19 TraesCS3D01G257800 chr6D 81.169 154 27 2 1151 1303 298207172 298207020 3.910000e-24 122.0
20 TraesCS3D01G257800 chr4B 85.593 118 15 2 1370 1486 100576902 100577018 3.910000e-24 122.0
21 TraesCS3D01G257800 chr4A 85.593 118 15 2 1370 1486 517884840 517884956 3.910000e-24 122.0
22 TraesCS3D01G257800 chr1A 81.818 132 22 2 1378 1508 463461337 463461207 3.040000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G257800 chr3D 360047176 360050065 2889 True 5337.0 5337 100.0000 1 2890 1 chr3D.!!$R1 2889
1 TraesCS3D01G257800 chr3B 466104575 466107267 2692 True 1554.5 2985 94.8670 632 2874 2 chr3B.!!$R1 2242
2 TraesCS3D01G257800 chr3B 466189738 466190568 830 True 253.5 274 85.9865 296 893 2 chr3B.!!$R2 597
3 TraesCS3D01G257800 chr3A 479480098 479482349 2251 True 2850.0 2850 89.9650 654 2874 1 chr3A.!!$R1 2220

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
965 1282 0.035056 ACCGAGGAGCCAAAATCCAG 60.035 55.0 0.0 0.0 39.47 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2728 3164 0.031449 CTACGCTCCTCTTGCTAGCC 59.969 60.0 13.29 0.0 32.5 3.93 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 9.553064 AAACATTCAATGTGTATTAAAAAGGCA 57.447 25.926 3.07 0.00 44.07 4.75
32 33 9.723601 AACATTCAATGTGTATTAAAAAGGCAT 57.276 25.926 3.07 0.00 44.07 4.40
33 34 9.723601 ACATTCAATGTGTATTAAAAAGGCATT 57.276 25.926 0.98 0.00 43.01 3.56
35 36 9.941325 ATTCAATGTGTATTAAAAAGGCATTCA 57.059 25.926 0.00 0.00 0.00 2.57
36 37 9.941325 TTCAATGTGTATTAAAAAGGCATTCAT 57.059 25.926 0.00 0.00 0.00 2.57
37 38 9.368674 TCAATGTGTATTAAAAAGGCATTCATG 57.631 29.630 0.00 0.00 0.00 3.07
38 39 9.153721 CAATGTGTATTAAAAAGGCATTCATGT 57.846 29.630 0.00 0.00 0.00 3.21
50 51 9.603921 AAAAGGCATTCATGTATAAAAAGGATG 57.396 29.630 0.00 0.00 0.00 3.51
51 52 7.902920 AGGCATTCATGTATAAAAAGGATGT 57.097 32.000 0.00 0.00 0.00 3.06
52 53 8.310122 AGGCATTCATGTATAAAAAGGATGTT 57.690 30.769 0.00 0.00 0.00 2.71
53 54 8.416329 AGGCATTCATGTATAAAAAGGATGTTC 58.584 33.333 0.00 0.00 0.00 3.18
54 55 8.416329 GGCATTCATGTATAAAAAGGATGTTCT 58.584 33.333 0.00 0.00 0.00 3.01
55 56 9.807649 GCATTCATGTATAAAAAGGATGTTCTT 57.192 29.630 0.00 0.00 0.00 2.52
72 73 9.626045 GGATGTTCTTGTATAAAAAGAAACTGG 57.374 33.333 11.54 0.00 43.37 4.00
79 80 8.880878 TTGTATAAAAAGAAACTGGAAAAGGC 57.119 30.769 0.00 0.00 0.00 4.35
80 81 8.012957 TGTATAAAAAGAAACTGGAAAAGGCA 57.987 30.769 0.00 0.00 0.00 4.75
81 82 8.478877 TGTATAAAAAGAAACTGGAAAAGGCAA 58.521 29.630 0.00 0.00 0.00 4.52
82 83 9.320352 GTATAAAAAGAAACTGGAAAAGGCAAA 57.680 29.630 0.00 0.00 0.00 3.68
83 84 8.978874 ATAAAAAGAAACTGGAAAAGGCAAAT 57.021 26.923 0.00 0.00 0.00 2.32
84 85 6.682423 AAAAGAAACTGGAAAAGGCAAATG 57.318 33.333 0.00 0.00 0.00 2.32
85 86 5.612725 AAGAAACTGGAAAAGGCAAATGA 57.387 34.783 0.00 0.00 0.00 2.57
86 87 5.612725 AGAAACTGGAAAAGGCAAATGAA 57.387 34.783 0.00 0.00 0.00 2.57
87 88 5.359756 AGAAACTGGAAAAGGCAAATGAAC 58.640 37.500 0.00 0.00 0.00 3.18
88 89 5.129320 AGAAACTGGAAAAGGCAAATGAACT 59.871 36.000 0.00 0.00 0.00 3.01
89 90 6.323739 AGAAACTGGAAAAGGCAAATGAACTA 59.676 34.615 0.00 0.00 0.00 2.24
90 91 5.712152 ACTGGAAAAGGCAAATGAACTAG 57.288 39.130 0.00 0.00 0.00 2.57
91 92 5.385198 ACTGGAAAAGGCAAATGAACTAGA 58.615 37.500 0.00 0.00 0.00 2.43
92 93 5.833131 ACTGGAAAAGGCAAATGAACTAGAA 59.167 36.000 0.00 0.00 0.00 2.10
93 94 6.323739 ACTGGAAAAGGCAAATGAACTAGAAA 59.676 34.615 0.00 0.00 0.00 2.52
94 95 7.118496 TGGAAAAGGCAAATGAACTAGAAAA 57.882 32.000 0.00 0.00 0.00 2.29
95 96 7.734942 TGGAAAAGGCAAATGAACTAGAAAAT 58.265 30.769 0.00 0.00 0.00 1.82
96 97 8.865090 TGGAAAAGGCAAATGAACTAGAAAATA 58.135 29.630 0.00 0.00 0.00 1.40
97 98 9.705290 GGAAAAGGCAAATGAACTAGAAAATAA 57.295 29.630 0.00 0.00 0.00 1.40
145 146 9.701098 ACAATACGAAATAAGTACAAGAACAGA 57.299 29.630 0.00 0.00 0.00 3.41
149 150 8.827177 ACGAAATAAGTACAAGAACAGATGAA 57.173 30.769 0.00 0.00 0.00 2.57
150 151 9.268268 ACGAAATAAGTACAAGAACAGATGAAA 57.732 29.630 0.00 0.00 0.00 2.69
240 241 6.624710 TTAACACAATACAATCGCAATTGC 57.375 33.333 20.76 20.76 45.16 3.56
241 242 4.439305 ACACAATACAATCGCAATTGCT 57.561 36.364 26.86 11.33 45.16 3.91
242 243 4.808558 ACACAATACAATCGCAATTGCTT 58.191 34.783 26.86 13.53 45.16 3.91
243 244 5.948588 ACACAATACAATCGCAATTGCTTA 58.051 33.333 26.86 15.82 45.16 3.09
244 245 5.799936 ACACAATACAATCGCAATTGCTTAC 59.200 36.000 26.86 0.00 45.16 2.34
245 246 5.799435 CACAATACAATCGCAATTGCTTACA 59.201 36.000 26.86 9.47 45.16 2.41
246 247 6.473131 CACAATACAATCGCAATTGCTTACAT 59.527 34.615 26.86 12.69 45.16 2.29
247 248 7.643371 CACAATACAATCGCAATTGCTTACATA 59.357 33.333 26.86 14.32 45.16 2.29
248 249 7.643764 ACAATACAATCGCAATTGCTTACATAC 59.356 33.333 26.86 0.00 45.16 2.39
249 250 5.559427 ACAATCGCAATTGCTTACATACA 57.441 34.783 26.86 2.34 45.16 2.29
250 251 5.331902 ACAATCGCAATTGCTTACATACAC 58.668 37.500 26.86 0.00 45.16 2.90
251 252 3.649870 TCGCAATTGCTTACATACACG 57.350 42.857 26.86 8.41 39.32 4.49
252 253 2.997303 TCGCAATTGCTTACATACACGT 59.003 40.909 26.86 0.00 39.32 4.49
253 254 4.174762 TCGCAATTGCTTACATACACGTA 58.825 39.130 26.86 0.00 39.32 3.57
254 255 4.031991 TCGCAATTGCTTACATACACGTAC 59.968 41.667 26.86 0.00 39.32 3.67
255 256 4.201637 CGCAATTGCTTACATACACGTACA 60.202 41.667 26.86 0.00 39.32 2.90
256 257 5.501736 CGCAATTGCTTACATACACGTACAT 60.502 40.000 26.86 0.00 39.32 2.29
257 258 6.291902 CGCAATTGCTTACATACACGTACATA 60.292 38.462 26.86 0.00 39.32 2.29
258 259 6.844279 GCAATTGCTTACATACACGTACATAC 59.156 38.462 23.21 0.00 38.21 2.39
259 260 7.464844 GCAATTGCTTACATACACGTACATACA 60.465 37.037 23.21 0.00 38.21 2.29
260 261 7.694388 ATTGCTTACATACACGTACATACAG 57.306 36.000 0.00 0.00 0.00 2.74
261 262 6.439675 TGCTTACATACACGTACATACAGA 57.560 37.500 0.00 0.00 0.00 3.41
262 263 6.260377 TGCTTACATACACGTACATACAGAC 58.740 40.000 0.00 0.00 0.00 3.51
263 264 6.127952 TGCTTACATACACGTACATACAGACA 60.128 38.462 0.00 0.00 0.00 3.41
264 265 6.195983 GCTTACATACACGTACATACAGACAC 59.804 42.308 0.00 0.00 0.00 3.67
265 266 5.892160 ACATACACGTACATACAGACACT 57.108 39.130 0.00 0.00 0.00 3.55
266 267 5.877031 ACATACACGTACATACAGACACTC 58.123 41.667 0.00 0.00 0.00 3.51
267 268 5.646793 ACATACACGTACATACAGACACTCT 59.353 40.000 0.00 0.00 0.00 3.24
268 269 6.820152 ACATACACGTACATACAGACACTCTA 59.180 38.462 0.00 0.00 0.00 2.43
269 270 7.498239 ACATACACGTACATACAGACACTCTAT 59.502 37.037 0.00 0.00 0.00 1.98
270 271 6.120378 ACACGTACATACAGACACTCTATG 57.880 41.667 0.00 0.00 0.00 2.23
271 272 5.878669 ACACGTACATACAGACACTCTATGA 59.121 40.000 0.00 0.00 0.00 2.15
272 273 6.373495 ACACGTACATACAGACACTCTATGAA 59.627 38.462 0.00 0.00 0.00 2.57
273 274 6.687531 CACGTACATACAGACACTCTATGAAC 59.312 42.308 0.00 0.00 0.00 3.18
274 275 6.598457 ACGTACATACAGACACTCTATGAACT 59.402 38.462 0.00 0.00 0.00 3.01
275 276 7.127042 CGTACATACAGACACTCTATGAACTC 58.873 42.308 0.00 0.00 0.00 3.01
276 277 7.201617 CGTACATACAGACACTCTATGAACTCA 60.202 40.741 0.00 0.00 0.00 3.41
277 278 6.857956 ACATACAGACACTCTATGAACTCAC 58.142 40.000 0.00 0.00 0.00 3.51
278 279 6.434340 ACATACAGACACTCTATGAACTCACA 59.566 38.462 0.00 0.00 0.00 3.58
279 280 5.127693 ACAGACACTCTATGAACTCACAC 57.872 43.478 0.00 0.00 0.00 3.82
280 281 4.584743 ACAGACACTCTATGAACTCACACA 59.415 41.667 0.00 0.00 0.00 3.72
281 282 4.920340 CAGACACTCTATGAACTCACACAC 59.080 45.833 0.00 0.00 0.00 3.82
282 283 3.902150 ACACTCTATGAACTCACACACG 58.098 45.455 0.00 0.00 0.00 4.49
283 284 2.663602 CACTCTATGAACTCACACACGC 59.336 50.000 0.00 0.00 0.00 5.34
284 285 2.296190 ACTCTATGAACTCACACACGCA 59.704 45.455 0.00 0.00 0.00 5.24
285 286 2.663602 CTCTATGAACTCACACACGCAC 59.336 50.000 0.00 0.00 0.00 5.34
286 287 2.035321 TCTATGAACTCACACACGCACA 59.965 45.455 0.00 0.00 0.00 4.57
287 288 1.882912 ATGAACTCACACACGCACAT 58.117 45.000 0.00 0.00 0.00 3.21
288 289 1.217001 TGAACTCACACACGCACATC 58.783 50.000 0.00 0.00 0.00 3.06
289 290 1.202521 TGAACTCACACACGCACATCT 60.203 47.619 0.00 0.00 0.00 2.90
290 291 2.035321 TGAACTCACACACGCACATCTA 59.965 45.455 0.00 0.00 0.00 1.98
291 292 2.065993 ACTCACACACGCACATCTAC 57.934 50.000 0.00 0.00 0.00 2.59
292 293 1.613925 ACTCACACACGCACATCTACT 59.386 47.619 0.00 0.00 0.00 2.57
293 294 2.254459 CTCACACACGCACATCTACTC 58.746 52.381 0.00 0.00 0.00 2.59
294 295 1.886542 TCACACACGCACATCTACTCT 59.113 47.619 0.00 0.00 0.00 3.24
307 308 3.162147 TCTACTCTTGTGAGCACCTCT 57.838 47.619 0.00 0.00 43.85 3.69
308 309 2.822561 TCTACTCTTGTGAGCACCTCTG 59.177 50.000 0.00 0.00 43.85 3.35
325 326 3.428725 CCTCTGACATACTGAGCTGACAC 60.429 52.174 0.00 0.00 41.28 3.67
327 328 3.192212 TCTGACATACTGAGCTGACACAG 59.808 47.826 0.00 0.00 40.04 3.66
343 344 7.661437 AGCTGACACAGTATTTTAAGATTGACA 59.339 33.333 0.00 0.00 33.43 3.58
365 366 4.771590 AATTTACCACAGTCGTCTCGTA 57.228 40.909 0.00 0.00 0.00 3.43
369 370 1.154197 CCACAGTCGTCTCGTAGTCA 58.846 55.000 0.00 0.00 0.00 3.41
370 371 1.128878 CCACAGTCGTCTCGTAGTCAG 59.871 57.143 0.00 0.00 0.00 3.51
379 380 3.244764 TCGTAGTCAGCGAGAAGGT 57.755 52.632 0.00 0.00 34.11 3.50
395 396 5.202004 GAGAAGGTATCCTCCTACTGAACA 58.798 45.833 0.00 0.00 36.74 3.18
402 403 4.188247 TCCTCCTACTGAACAAACATCG 57.812 45.455 0.00 0.00 0.00 3.84
411 412 0.039527 AACAAACATCGCCGGAAAGC 60.040 50.000 5.05 0.00 0.00 3.51
460 461 5.164954 CAGTAGTGCCAAGTCTAGAACTTC 58.835 45.833 0.00 0.00 45.28 3.01
465 466 4.393371 GTGCCAAGTCTAGAACTTCAATCC 59.607 45.833 0.00 0.00 45.28 3.01
467 468 4.633565 GCCAAGTCTAGAACTTCAATCCTG 59.366 45.833 0.00 0.00 45.28 3.86
493 494 5.654497 GGATTGATTCCATCACAAAGAACC 58.346 41.667 0.70 0.00 44.74 3.62
494 495 5.420104 GGATTGATTCCATCACAAAGAACCT 59.580 40.000 0.70 0.00 44.74 3.50
495 496 6.603201 GGATTGATTCCATCACAAAGAACCTA 59.397 38.462 0.70 0.00 44.74 3.08
496 497 7.122650 GGATTGATTCCATCACAAAGAACCTAA 59.877 37.037 0.70 0.00 44.74 2.69
497 498 8.599624 ATTGATTCCATCACAAAGAACCTAAT 57.400 30.769 0.00 0.00 39.39 1.73
498 499 7.630242 TGATTCCATCACAAAGAACCTAATC 57.370 36.000 0.00 0.00 33.59 1.75
499 500 7.174413 TGATTCCATCACAAAGAACCTAATCA 58.826 34.615 0.00 0.00 33.59 2.57
500 501 7.835682 TGATTCCATCACAAAGAACCTAATCAT 59.164 33.333 0.00 0.00 33.59 2.45
501 502 9.342308 GATTCCATCACAAAGAACCTAATCATA 57.658 33.333 0.00 0.00 0.00 2.15
502 503 9.872684 ATTCCATCACAAAGAACCTAATCATAT 57.127 29.630 0.00 0.00 0.00 1.78
503 504 8.681486 TCCATCACAAAGAACCTAATCATATG 57.319 34.615 0.00 0.00 0.00 1.78
523 524 8.058235 TCATATGAGTTATTCCCATTTCACCAA 58.942 33.333 0.00 0.00 0.00 3.67
524 525 8.694540 CATATGAGTTATTCCCATTTCACCAAA 58.305 33.333 0.00 0.00 0.00 3.28
525 526 6.985653 TGAGTTATTCCCATTTCACCAAAA 57.014 33.333 0.00 0.00 0.00 2.44
526 527 7.366847 TGAGTTATTCCCATTTCACCAAAAA 57.633 32.000 0.00 0.00 0.00 1.94
576 577 8.918961 TTTTTAGAAATGAAAAACTGAAGCGA 57.081 26.923 0.00 0.00 32.29 4.93
577 578 8.918961 TTTTAGAAATGAAAAACTGAAGCGAA 57.081 26.923 0.00 0.00 0.00 4.70
578 579 7.908193 TTAGAAATGAAAAACTGAAGCGAAC 57.092 32.000 0.00 0.00 0.00 3.95
579 580 6.136541 AGAAATGAAAAACTGAAGCGAACT 57.863 33.333 0.00 0.00 0.00 3.01
580 581 7.259290 AGAAATGAAAAACTGAAGCGAACTA 57.741 32.000 0.00 0.00 0.00 2.24
581 582 7.875971 AGAAATGAAAAACTGAAGCGAACTAT 58.124 30.769 0.00 0.00 0.00 2.12
582 583 8.017946 AGAAATGAAAAACTGAAGCGAACTATC 58.982 33.333 0.00 0.00 0.00 2.08
583 584 5.607119 TGAAAAACTGAAGCGAACTATCC 57.393 39.130 0.00 0.00 0.00 2.59
584 585 4.151689 TGAAAAACTGAAGCGAACTATCCG 59.848 41.667 0.00 0.00 0.00 4.18
585 586 2.295253 AACTGAAGCGAACTATCCGG 57.705 50.000 0.00 0.00 0.00 5.14
586 587 1.183549 ACTGAAGCGAACTATCCGGT 58.816 50.000 0.00 0.00 39.59 5.28
587 588 1.135083 ACTGAAGCGAACTATCCGGTG 60.135 52.381 0.00 0.00 37.82 4.94
588 589 0.459585 TGAAGCGAACTATCCGGTGC 60.460 55.000 0.00 0.00 37.82 5.01
589 590 0.459585 GAAGCGAACTATCCGGTGCA 60.460 55.000 0.00 0.00 37.82 4.57
590 591 0.460284 AAGCGAACTATCCGGTGCAG 60.460 55.000 0.00 0.00 37.82 4.41
591 592 2.526120 GCGAACTATCCGGTGCAGC 61.526 63.158 5.64 5.64 0.00 5.25
592 593 1.141881 CGAACTATCCGGTGCAGCT 59.858 57.895 14.92 0.00 0.00 4.24
593 594 0.872021 CGAACTATCCGGTGCAGCTC 60.872 60.000 14.92 1.60 0.00 4.09
594 595 0.530870 GAACTATCCGGTGCAGCTCC 60.531 60.000 14.92 3.13 0.00 4.70
595 596 1.972660 AACTATCCGGTGCAGCTCCC 61.973 60.000 14.92 0.00 0.00 4.30
596 597 3.506059 CTATCCGGTGCAGCTCCCG 62.506 68.421 14.92 14.97 43.82 5.14
598 599 2.914756 TATCCGGTGCAGCTCCCGTA 62.915 60.000 14.92 7.41 42.67 4.02
599 600 4.077184 CCGGTGCAGCTCCCGTAA 62.077 66.667 14.92 0.00 42.67 3.18
600 601 2.047655 CGGTGCAGCTCCCGTAAA 60.048 61.111 14.92 0.00 39.38 2.01
601 602 1.669760 CGGTGCAGCTCCCGTAAAA 60.670 57.895 14.92 0.00 39.38 1.52
602 603 1.231958 CGGTGCAGCTCCCGTAAAAA 61.232 55.000 14.92 0.00 39.38 1.94
837 1154 4.619320 ACCACCCCACCGACCGTA 62.619 66.667 0.00 0.00 0.00 4.02
893 1210 1.170290 AAAAGCGACCAAACCCCTCG 61.170 55.000 0.00 0.00 0.00 4.63
965 1282 0.035056 ACCGAGGAGCCAAAATCCAG 60.035 55.000 0.00 0.00 39.47 3.86
1548 1884 0.603707 TCCTACCGACAAGACGACGT 60.604 55.000 0.00 0.00 35.09 4.34
1549 1885 0.453950 CCTACCGACAAGACGACGTG 60.454 60.000 4.58 0.00 35.09 4.49
1769 2105 1.335697 GCGGAGTCTTCAACGACGTC 61.336 60.000 5.18 5.18 38.90 4.34
1776 2112 0.037697 CTTCAACGACGTCATGGGGA 60.038 55.000 17.16 2.39 0.00 4.81
1804 2140 1.202268 GGTGGACGACGATACCTTCAG 60.202 57.143 0.00 0.00 0.00 3.02
1877 2213 1.009829 GTGTGATGAACGATCAGGGC 58.990 55.000 0.82 0.00 42.00 5.19
1916 2252 4.797471 TGCAGATTTACAAATGCACTGTC 58.203 39.130 6.54 0.00 0.00 3.51
1917 2253 4.277921 TGCAGATTTACAAATGCACTGTCA 59.722 37.500 6.54 0.00 0.00 3.58
1919 2255 5.514204 GCAGATTTACAAATGCACTGTCATC 59.486 40.000 6.54 9.61 0.00 2.92
1920 2256 6.032094 CAGATTTACAAATGCACTGTCATCC 58.968 40.000 6.54 0.00 0.00 3.51
1922 2258 5.375417 TTTACAAATGCACTGTCATCCTG 57.625 39.130 6.54 0.00 0.00 3.86
1923 2259 3.144657 ACAAATGCACTGTCATCCTGA 57.855 42.857 0.00 0.00 0.00 3.86
1924 2260 3.079578 ACAAATGCACTGTCATCCTGAG 58.920 45.455 0.00 0.00 0.00 3.35
1925 2261 1.747709 AATGCACTGTCATCCTGAGC 58.252 50.000 0.00 0.00 0.00 4.26
1927 2263 0.036671 TGCACTGTCATCCTGAGCAG 60.037 55.000 0.00 0.00 34.61 4.24
1928 2264 1.367599 GCACTGTCATCCTGAGCAGC 61.368 60.000 0.00 0.00 32.55 5.25
1929 2265 1.082679 CACTGTCATCCTGAGCAGCG 61.083 60.000 0.00 0.00 32.55 5.18
1949 2298 6.512253 GCAGCGAATAAGTTGATTGATGATGA 60.512 38.462 0.00 0.00 0.00 2.92
2078 2443 8.743085 ATTGCACAGACATAAGATTTGTAGAT 57.257 30.769 0.00 0.00 0.00 1.98
2182 2562 2.520069 CCTGCAGGTCTATCCGTCTAT 58.480 52.381 25.53 0.00 41.99 1.98
2220 2603 0.303796 CGAGACGCGTACAGCTCATA 59.696 55.000 13.97 0.00 45.59 2.15
2490 2922 1.489230 AGGGAACACCGACTGTTTTCT 59.511 47.619 0.66 0.20 43.60 2.52
2496 2928 4.516365 ACACCGACTGTTTTCTACCTAG 57.484 45.455 0.00 0.00 0.00 3.02
2497 2929 3.251571 CACCGACTGTTTTCTACCTAGC 58.748 50.000 0.00 0.00 0.00 3.42
2498 2930 3.056749 CACCGACTGTTTTCTACCTAGCT 60.057 47.826 0.00 0.00 0.00 3.32
2500 2932 4.954826 ACCGACTGTTTTCTACCTAGCTAT 59.045 41.667 0.00 0.00 0.00 2.97
2501 2933 6.039047 CACCGACTGTTTTCTACCTAGCTATA 59.961 42.308 0.00 0.00 0.00 1.31
2502 2934 6.039159 ACCGACTGTTTTCTACCTAGCTATAC 59.961 42.308 0.00 0.00 0.00 1.47
2503 2935 6.039047 CCGACTGTTTTCTACCTAGCTATACA 59.961 42.308 0.00 0.00 0.00 2.29
2504 2936 7.415989 CCGACTGTTTTCTACCTAGCTATACAA 60.416 40.741 0.00 0.00 0.00 2.41
2597 3029 9.953825 GTAAACATGAACAAAGAATCTACTACG 57.046 33.333 0.00 0.00 0.00 3.51
2598 3030 8.827177 AAACATGAACAAAGAATCTACTACGA 57.173 30.769 0.00 0.00 0.00 3.43
2599 3031 8.827177 AACATGAACAAAGAATCTACTACGAA 57.173 30.769 0.00 0.00 0.00 3.85
2635 3067 5.899696 CGCGCATCGTAACAAATAAATTACT 59.100 36.000 8.75 0.00 0.00 2.24
2702 3138 0.178998 CCATCCATGCTCCTGGGAAG 60.179 60.000 0.00 0.00 36.89 3.46
2705 3141 0.043183 TCCATGCTCCTGGGAAGAGA 59.957 55.000 0.00 0.00 36.89 3.10
2726 3162 2.431782 ACTTCAAGTTGCATGGCTGTTT 59.568 40.909 0.00 0.00 0.00 2.83
2727 3163 3.636300 ACTTCAAGTTGCATGGCTGTTTA 59.364 39.130 0.00 0.00 0.00 2.01
2728 3164 3.921119 TCAAGTTGCATGGCTGTTTAG 57.079 42.857 0.00 0.00 0.00 1.85
2729 3165 2.557924 TCAAGTTGCATGGCTGTTTAGG 59.442 45.455 0.00 0.00 0.00 2.69
2754 3213 0.749649 AAGAGGAGCGTAGAGGCATG 59.250 55.000 0.00 0.00 34.64 4.06
2814 3693 2.112815 GGCGCCTGCGAATTTACCT 61.113 57.895 22.15 0.00 44.10 3.08
2815 3694 1.062525 GCGCCTGCGAATTTACCTG 59.937 57.895 16.76 0.00 42.83 4.00
2879 3758 6.884280 TTGGAACCAACAAACAAACAAAAT 57.116 29.167 1.83 0.00 0.00 1.82
2880 3759 6.884280 TGGAACCAACAAACAAACAAAATT 57.116 29.167 0.00 0.00 0.00 1.82
2881 3760 6.672147 TGGAACCAACAAACAAACAAAATTG 58.328 32.000 0.00 0.00 36.37 2.32
2882 3761 6.089476 GGAACCAACAAACAAACAAAATTGG 58.911 36.000 0.00 0.00 40.76 3.16
2883 3762 5.635417 ACCAACAAACAAACAAAATTGGG 57.365 34.783 5.20 0.00 39.55 4.12
2884 3763 4.082517 ACCAACAAACAAACAAAATTGGGC 60.083 37.500 5.20 0.00 39.55 5.36
2885 3764 4.419280 CAACAAACAAACAAAATTGGGCC 58.581 39.130 0.00 0.00 34.56 5.80
2886 3765 3.961849 ACAAACAAACAAAATTGGGCCT 58.038 36.364 4.53 0.00 34.56 5.19
2887 3766 5.104259 ACAAACAAACAAAATTGGGCCTA 57.896 34.783 4.53 0.00 34.56 3.93
2888 3767 4.878971 ACAAACAAACAAAATTGGGCCTAC 59.121 37.500 4.53 0.00 34.56 3.18
2889 3768 5.122519 CAAACAAACAAAATTGGGCCTACT 58.877 37.500 4.53 0.00 34.56 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.553064 TGCCTTTTTAATACACATTGAATGTTT 57.447 25.926 8.30 5.05 42.70 2.83
6 7 9.723601 ATGCCTTTTTAATACACATTGAATGTT 57.276 25.926 8.30 3.46 42.70 2.71
7 8 9.723601 AATGCCTTTTTAATACACATTGAATGT 57.276 25.926 4.72 4.72 46.22 2.71
9 10 9.941325 TGAATGCCTTTTTAATACACATTGAAT 57.059 25.926 0.00 0.00 0.00 2.57
10 11 9.941325 ATGAATGCCTTTTTAATACACATTGAA 57.059 25.926 0.00 0.00 0.00 2.69
11 12 9.368674 CATGAATGCCTTTTTAATACACATTGA 57.631 29.630 0.00 0.00 0.00 2.57
12 13 9.153721 ACATGAATGCCTTTTTAATACACATTG 57.846 29.630 0.00 0.00 0.00 2.82
24 25 9.603921 CATCCTTTTTATACATGAATGCCTTTT 57.396 29.630 0.00 0.00 0.00 2.27
25 26 8.761689 ACATCCTTTTTATACATGAATGCCTTT 58.238 29.630 0.00 0.00 0.00 3.11
26 27 8.310122 ACATCCTTTTTATACATGAATGCCTT 57.690 30.769 0.00 0.00 0.00 4.35
27 28 7.902920 ACATCCTTTTTATACATGAATGCCT 57.097 32.000 0.00 0.00 0.00 4.75
28 29 8.416329 AGAACATCCTTTTTATACATGAATGCC 58.584 33.333 0.00 0.00 0.00 4.40
29 30 9.807649 AAGAACATCCTTTTTATACATGAATGC 57.192 29.630 0.00 0.00 0.00 3.56
46 47 9.626045 CCAGTTTCTTTTTATACAAGAACATCC 57.374 33.333 5.98 0.00 39.47 3.51
53 54 8.978539 GCCTTTTCCAGTTTCTTTTTATACAAG 58.021 33.333 0.00 0.00 0.00 3.16
54 55 8.478877 TGCCTTTTCCAGTTTCTTTTTATACAA 58.521 29.630 0.00 0.00 0.00 2.41
55 56 8.012957 TGCCTTTTCCAGTTTCTTTTTATACA 57.987 30.769 0.00 0.00 0.00 2.29
56 57 8.880878 TTGCCTTTTCCAGTTTCTTTTTATAC 57.119 30.769 0.00 0.00 0.00 1.47
58 59 8.839343 CATTTGCCTTTTCCAGTTTCTTTTTAT 58.161 29.630 0.00 0.00 0.00 1.40
59 60 8.043710 TCATTTGCCTTTTCCAGTTTCTTTTTA 58.956 29.630 0.00 0.00 0.00 1.52
60 61 6.883756 TCATTTGCCTTTTCCAGTTTCTTTTT 59.116 30.769 0.00 0.00 0.00 1.94
61 62 6.413892 TCATTTGCCTTTTCCAGTTTCTTTT 58.586 32.000 0.00 0.00 0.00 2.27
62 63 5.988287 TCATTTGCCTTTTCCAGTTTCTTT 58.012 33.333 0.00 0.00 0.00 2.52
63 64 5.612725 TCATTTGCCTTTTCCAGTTTCTT 57.387 34.783 0.00 0.00 0.00 2.52
64 65 5.129320 AGTTCATTTGCCTTTTCCAGTTTCT 59.871 36.000 0.00 0.00 0.00 2.52
65 66 5.359756 AGTTCATTTGCCTTTTCCAGTTTC 58.640 37.500 0.00 0.00 0.00 2.78
66 67 5.357742 AGTTCATTTGCCTTTTCCAGTTT 57.642 34.783 0.00 0.00 0.00 2.66
67 68 5.833131 TCTAGTTCATTTGCCTTTTCCAGTT 59.167 36.000 0.00 0.00 0.00 3.16
68 69 5.385198 TCTAGTTCATTTGCCTTTTCCAGT 58.615 37.500 0.00 0.00 0.00 4.00
69 70 5.964958 TCTAGTTCATTTGCCTTTTCCAG 57.035 39.130 0.00 0.00 0.00 3.86
70 71 6.723298 TTTCTAGTTCATTTGCCTTTTCCA 57.277 33.333 0.00 0.00 0.00 3.53
71 72 9.705290 TTATTTTCTAGTTCATTTGCCTTTTCC 57.295 29.630 0.00 0.00 0.00 3.13
119 120 9.701098 TCTGTTCTTGTACTTATTTCGTATTGT 57.299 29.630 0.00 0.00 0.00 2.71
123 124 9.917129 TTCATCTGTTCTTGTACTTATTTCGTA 57.083 29.630 0.00 0.00 0.00 3.43
124 125 8.827177 TTCATCTGTTCTTGTACTTATTTCGT 57.173 30.769 0.00 0.00 0.00 3.85
214 215 8.006590 GCAATTGCGATTGTATTGTGTTAAAAA 58.993 29.630 24.39 0.00 43.67 1.94
215 216 7.505646 GCAATTGCGATTGTATTGTGTTAAAA 58.494 30.769 24.39 0.00 43.67 1.52
216 217 7.043454 GCAATTGCGATTGTATTGTGTTAAA 57.957 32.000 24.39 0.00 43.67 1.52
217 218 6.624710 GCAATTGCGATTGTATTGTGTTAA 57.375 33.333 24.39 0.00 43.67 2.01
233 234 5.211266 TGTACGTGTATGTAAGCAATTGC 57.789 39.130 23.05 23.05 42.49 3.56
234 235 7.901002 TGTATGTACGTGTATGTAAGCAATTG 58.099 34.615 0.00 0.00 0.00 2.32
235 236 7.977293 TCTGTATGTACGTGTATGTAAGCAATT 59.023 33.333 0.00 0.00 0.00 2.32
236 237 7.434307 GTCTGTATGTACGTGTATGTAAGCAAT 59.566 37.037 0.00 0.00 0.00 3.56
237 238 6.748658 GTCTGTATGTACGTGTATGTAAGCAA 59.251 38.462 0.00 0.00 0.00 3.91
238 239 6.127952 TGTCTGTATGTACGTGTATGTAAGCA 60.128 38.462 0.00 0.00 0.00 3.91
239 240 6.195983 GTGTCTGTATGTACGTGTATGTAAGC 59.804 42.308 0.00 0.00 0.00 3.09
240 241 7.470079 AGTGTCTGTATGTACGTGTATGTAAG 58.530 38.462 0.00 0.00 0.00 2.34
241 242 7.335171 AGAGTGTCTGTATGTACGTGTATGTAA 59.665 37.037 0.00 0.00 0.00 2.41
242 243 6.820152 AGAGTGTCTGTATGTACGTGTATGTA 59.180 38.462 0.00 0.00 0.00 2.29
243 244 5.646793 AGAGTGTCTGTATGTACGTGTATGT 59.353 40.000 0.00 0.00 0.00 2.29
244 245 6.120378 AGAGTGTCTGTATGTACGTGTATG 57.880 41.667 0.00 0.00 0.00 2.39
245 246 7.713942 TCATAGAGTGTCTGTATGTACGTGTAT 59.286 37.037 0.00 0.00 38.40 2.29
246 247 7.043565 TCATAGAGTGTCTGTATGTACGTGTA 58.956 38.462 0.00 0.00 38.40 2.90
247 248 5.878669 TCATAGAGTGTCTGTATGTACGTGT 59.121 40.000 0.00 0.00 38.40 4.49
248 249 6.359480 TCATAGAGTGTCTGTATGTACGTG 57.641 41.667 0.00 0.00 38.40 4.49
249 250 6.598457 AGTTCATAGAGTGTCTGTATGTACGT 59.402 38.462 11.66 0.00 40.32 3.57
250 251 7.017498 AGTTCATAGAGTGTCTGTATGTACG 57.983 40.000 11.66 0.00 40.32 3.67
251 252 7.911205 GTGAGTTCATAGAGTGTCTGTATGTAC 59.089 40.741 12.24 12.24 38.40 2.90
252 253 7.610305 TGTGAGTTCATAGAGTGTCTGTATGTA 59.390 37.037 11.66 2.77 38.40 2.29
253 254 6.434340 TGTGAGTTCATAGAGTGTCTGTATGT 59.566 38.462 11.66 0.00 38.40 2.29
254 255 6.749578 GTGTGAGTTCATAGAGTGTCTGTATG 59.250 42.308 7.35 7.35 38.54 2.39
255 256 6.434340 TGTGTGAGTTCATAGAGTGTCTGTAT 59.566 38.462 0.00 0.00 0.00 2.29
256 257 5.768164 TGTGTGAGTTCATAGAGTGTCTGTA 59.232 40.000 0.00 0.00 0.00 2.74
257 258 4.584743 TGTGTGAGTTCATAGAGTGTCTGT 59.415 41.667 0.00 0.00 0.00 3.41
258 259 4.920340 GTGTGTGAGTTCATAGAGTGTCTG 59.080 45.833 0.00 0.00 0.00 3.51
259 260 4.320567 CGTGTGTGAGTTCATAGAGTGTCT 60.321 45.833 0.00 0.00 0.00 3.41
260 261 3.914966 CGTGTGTGAGTTCATAGAGTGTC 59.085 47.826 0.00 0.00 0.00 3.67
261 262 3.857383 GCGTGTGTGAGTTCATAGAGTGT 60.857 47.826 0.00 0.00 0.00 3.55
262 263 2.663602 GCGTGTGTGAGTTCATAGAGTG 59.336 50.000 0.00 0.00 0.00 3.51
263 264 2.296190 TGCGTGTGTGAGTTCATAGAGT 59.704 45.455 0.00 0.00 0.00 3.24
264 265 2.663602 GTGCGTGTGTGAGTTCATAGAG 59.336 50.000 0.00 0.00 0.00 2.43
265 266 2.035321 TGTGCGTGTGTGAGTTCATAGA 59.965 45.455 0.00 0.00 0.00 1.98
266 267 2.403259 TGTGCGTGTGTGAGTTCATAG 58.597 47.619 0.00 0.00 0.00 2.23
267 268 2.517650 TGTGCGTGTGTGAGTTCATA 57.482 45.000 0.00 0.00 0.00 2.15
268 269 1.800586 GATGTGCGTGTGTGAGTTCAT 59.199 47.619 0.00 0.00 0.00 2.57
269 270 1.202521 AGATGTGCGTGTGTGAGTTCA 60.203 47.619 0.00 0.00 0.00 3.18
270 271 1.502231 AGATGTGCGTGTGTGAGTTC 58.498 50.000 0.00 0.00 0.00 3.01
271 272 2.035961 AGTAGATGTGCGTGTGTGAGTT 59.964 45.455 0.00 0.00 0.00 3.01
272 273 1.613925 AGTAGATGTGCGTGTGTGAGT 59.386 47.619 0.00 0.00 0.00 3.41
273 274 2.095008 AGAGTAGATGTGCGTGTGTGAG 60.095 50.000 0.00 0.00 0.00 3.51
274 275 1.886542 AGAGTAGATGTGCGTGTGTGA 59.113 47.619 0.00 0.00 0.00 3.58
275 276 2.354109 AGAGTAGATGTGCGTGTGTG 57.646 50.000 0.00 0.00 0.00 3.82
276 277 2.035961 ACAAGAGTAGATGTGCGTGTGT 59.964 45.455 0.00 0.00 0.00 3.72
277 278 2.409715 CACAAGAGTAGATGTGCGTGTG 59.590 50.000 0.00 0.00 40.32 3.82
278 279 2.296190 TCACAAGAGTAGATGTGCGTGT 59.704 45.455 1.18 0.00 45.08 4.49
279 280 2.919859 CTCACAAGAGTAGATGTGCGTG 59.080 50.000 1.18 0.00 45.08 5.34
280 281 2.672478 GCTCACAAGAGTAGATGTGCGT 60.672 50.000 1.18 0.00 45.08 5.24
281 282 1.923204 GCTCACAAGAGTAGATGTGCG 59.077 52.381 1.18 0.00 45.08 5.34
282 283 2.670414 GTGCTCACAAGAGTAGATGTGC 59.330 50.000 1.18 0.00 45.08 4.57
283 284 3.056250 AGGTGCTCACAAGAGTAGATGTG 60.056 47.826 2.21 0.00 46.44 3.21
284 285 3.169099 AGGTGCTCACAAGAGTAGATGT 58.831 45.455 2.21 0.00 44.00 3.06
285 286 3.446873 AGAGGTGCTCACAAGAGTAGATG 59.553 47.826 2.21 0.00 44.00 2.90
286 287 3.446873 CAGAGGTGCTCACAAGAGTAGAT 59.553 47.826 2.21 0.00 44.00 1.98
287 288 2.822561 CAGAGGTGCTCACAAGAGTAGA 59.177 50.000 2.21 0.00 44.00 2.59
288 289 2.822561 TCAGAGGTGCTCACAAGAGTAG 59.177 50.000 2.21 0.00 44.00 2.57
289 290 2.558795 GTCAGAGGTGCTCACAAGAGTA 59.441 50.000 2.21 0.00 44.00 2.59
290 291 1.342819 GTCAGAGGTGCTCACAAGAGT 59.657 52.381 2.21 0.00 44.00 3.24
291 292 1.342496 TGTCAGAGGTGCTCACAAGAG 59.658 52.381 2.21 0.00 44.96 2.85
292 293 1.413118 TGTCAGAGGTGCTCACAAGA 58.587 50.000 2.21 0.00 32.06 3.02
293 294 2.469274 ATGTCAGAGGTGCTCACAAG 57.531 50.000 2.21 0.00 32.06 3.16
294 295 2.899900 AGTATGTCAGAGGTGCTCACAA 59.100 45.455 2.21 0.00 32.06 3.33
307 308 2.893489 ACTGTGTCAGCTCAGTATGTCA 59.107 45.455 4.07 0.00 44.59 3.58
308 309 3.584406 ACTGTGTCAGCTCAGTATGTC 57.416 47.619 4.07 0.00 44.59 3.06
331 332 9.959749 GACTGTGGTAAATTTGTCAATCTTAAA 57.040 29.630 0.00 0.00 0.00 1.52
343 344 3.986277 ACGAGACGACTGTGGTAAATTT 58.014 40.909 0.00 0.00 0.00 1.82
345 346 3.755378 ACTACGAGACGACTGTGGTAAAT 59.245 43.478 0.00 0.00 0.00 1.40
346 347 3.141398 ACTACGAGACGACTGTGGTAAA 58.859 45.455 0.00 0.00 0.00 2.01
356 357 4.584688 TCGCTGACTACGAGACGA 57.415 55.556 0.00 0.00 33.96 4.20
365 366 2.303175 GAGGATACCTTCTCGCTGACT 58.697 52.381 0.00 0.00 31.76 3.41
369 370 2.444010 AGTAGGAGGATACCTTCTCGCT 59.556 50.000 1.46 0.42 39.07 4.93
370 371 2.554893 CAGTAGGAGGATACCTTCTCGC 59.445 54.545 1.46 0.00 39.07 5.03
377 378 5.416271 TGTTTGTTCAGTAGGAGGATACC 57.584 43.478 0.00 0.00 37.17 2.73
379 380 5.681437 GCGATGTTTGTTCAGTAGGAGGATA 60.681 44.000 0.00 0.00 0.00 2.59
395 396 0.240945 CAAGCTTTCCGGCGATGTTT 59.759 50.000 9.30 0.00 37.29 2.83
402 403 4.998788 AGATTTATTTCAAGCTTTCCGGC 58.001 39.130 0.00 0.00 0.00 6.13
432 433 0.038159 GACTTGGCACTACTGCTCGT 60.038 55.000 0.00 0.00 43.66 4.18
476 477 9.872684 ATATGATTAGGTTCTTTGTGATGGAAT 57.127 29.630 0.00 0.00 0.00 3.01
495 496 9.082313 GGTGAAATGGGAATAACTCATATGATT 57.918 33.333 5.72 0.00 38.99 2.57
496 497 8.226810 TGGTGAAATGGGAATAACTCATATGAT 58.773 33.333 5.72 0.00 38.99 2.45
497 498 7.581814 TGGTGAAATGGGAATAACTCATATGA 58.418 34.615 5.07 5.07 38.99 2.15
498 499 7.822161 TGGTGAAATGGGAATAACTCATATG 57.178 36.000 0.00 0.00 38.99 1.78
499 500 8.837099 TTTGGTGAAATGGGAATAACTCATAT 57.163 30.769 0.00 0.00 38.99 1.78
500 501 8.657387 TTTTGGTGAAATGGGAATAACTCATA 57.343 30.769 0.00 0.00 38.99 2.15
501 502 7.552050 TTTTGGTGAAATGGGAATAACTCAT 57.448 32.000 0.00 0.00 42.14 2.90
502 503 6.985653 TTTTGGTGAAATGGGAATAACTCA 57.014 33.333 0.00 0.00 0.00 3.41
575 576 0.530870 GGAGCTGCACCGGATAGTTC 60.531 60.000 9.46 10.39 0.00 3.01
576 577 1.522569 GGAGCTGCACCGGATAGTT 59.477 57.895 9.46 0.17 0.00 2.24
577 578 2.435693 GGGAGCTGCACCGGATAGT 61.436 63.158 9.46 0.00 0.00 2.12
578 579 2.423446 GGGAGCTGCACCGGATAG 59.577 66.667 9.46 4.00 0.00 2.08
579 580 3.536917 CGGGAGCTGCACCGGATA 61.537 66.667 22.73 0.00 46.08 2.59
584 585 2.636299 TTTTTACGGGAGCTGCACC 58.364 52.632 7.79 7.65 0.00 5.01
625 626 8.466798 GCACTAGATAGTTCTCTTCTTCTTCTT 58.533 37.037 0.00 0.00 33.46 2.52
626 627 7.613801 TGCACTAGATAGTTCTCTTCTTCTTCT 59.386 37.037 0.00 0.00 33.46 2.85
627 628 7.767261 TGCACTAGATAGTTCTCTTCTTCTTC 58.233 38.462 0.00 0.00 33.46 2.87
628 629 7.630513 GCTGCACTAGATAGTTCTCTTCTTCTT 60.631 40.741 0.00 0.00 33.46 2.52
629 630 6.183360 GCTGCACTAGATAGTTCTCTTCTTCT 60.183 42.308 0.00 0.00 33.46 2.85
630 631 5.977129 GCTGCACTAGATAGTTCTCTTCTTC 59.023 44.000 0.00 0.00 33.46 2.87
631 632 5.449862 CGCTGCACTAGATAGTTCTCTTCTT 60.450 44.000 0.00 0.00 33.46 2.52
632 633 4.036262 CGCTGCACTAGATAGTTCTCTTCT 59.964 45.833 0.00 0.00 33.46 2.85
633 634 4.035792 TCGCTGCACTAGATAGTTCTCTTC 59.964 45.833 0.00 0.00 33.46 2.87
634 635 3.948473 TCGCTGCACTAGATAGTTCTCTT 59.052 43.478 0.00 0.00 33.46 2.85
635 636 3.546724 TCGCTGCACTAGATAGTTCTCT 58.453 45.455 0.00 0.00 33.46 3.10
636 637 3.972950 TCGCTGCACTAGATAGTTCTC 57.027 47.619 0.00 0.00 33.46 2.87
646 647 1.202521 CCACCATACATCGCTGCACTA 60.203 52.381 0.00 0.00 0.00 2.74
893 1210 1.195674 GGACGCTTTTTCTGAGACTGC 59.804 52.381 0.00 0.00 0.00 4.40
1654 1990 3.195698 GGTCGTCATTGCCTCCGC 61.196 66.667 0.00 0.00 0.00 5.54
1769 2105 3.196040 CACCATTGGACTCCCCATG 57.804 57.895 10.37 0.00 46.10 3.66
1796 2132 0.809385 CGAGGAACGAGCTGAAGGTA 59.191 55.000 0.00 0.00 45.77 3.08
1916 2252 2.831333 ACTTATTCGCTGCTCAGGATG 58.169 47.619 0.00 0.00 37.54 3.51
1917 2253 3.118629 TCAACTTATTCGCTGCTCAGGAT 60.119 43.478 0.00 0.00 0.00 3.24
1919 2255 2.621338 TCAACTTATTCGCTGCTCAGG 58.379 47.619 0.00 0.00 0.00 3.86
1920 2256 4.330894 TCAATCAACTTATTCGCTGCTCAG 59.669 41.667 0.00 0.00 0.00 3.35
1922 2258 4.864916 TCAATCAACTTATTCGCTGCTC 57.135 40.909 0.00 0.00 0.00 4.26
1923 2259 4.877823 TCATCAATCAACTTATTCGCTGCT 59.122 37.500 0.00 0.00 0.00 4.24
1924 2260 5.160699 TCATCAATCAACTTATTCGCTGC 57.839 39.130 0.00 0.00 0.00 5.25
1925 2261 6.951643 TCATCATCAATCAACTTATTCGCTG 58.048 36.000 0.00 0.00 0.00 5.18
1927 2263 5.850128 GCTCATCATCAATCAACTTATTCGC 59.150 40.000 0.00 0.00 0.00 4.70
1928 2264 6.951643 TGCTCATCATCAATCAACTTATTCG 58.048 36.000 0.00 0.00 0.00 3.34
1929 2265 8.151141 TCTGCTCATCATCAATCAACTTATTC 57.849 34.615 0.00 0.00 0.00 1.75
2078 2443 5.048434 TGAACACATTGATTAATTCGCACCA 60.048 36.000 0.00 0.00 0.00 4.17
2220 2603 1.008995 GGCACGCGTTGTCACAAAT 60.009 52.632 10.22 0.00 0.00 2.32
2315 2698 1.480954 CGAAGAAGAAAGATCCGGGGA 59.519 52.381 0.00 0.00 0.00 4.81
2490 2922 7.655732 TGAACGTACGTATTGTATAGCTAGGTA 59.344 37.037 23.12 3.73 35.02 3.08
2496 2928 5.164119 GGCATGAACGTACGTATTGTATAGC 60.164 44.000 23.12 16.19 35.02 2.97
2497 2929 5.058856 CGGCATGAACGTACGTATTGTATAG 59.941 44.000 23.12 6.57 35.02 1.31
2498 2930 4.911033 CGGCATGAACGTACGTATTGTATA 59.089 41.667 23.12 3.63 35.02 1.47
2500 2932 3.107407 CGGCATGAACGTACGTATTGTA 58.893 45.455 23.12 6.88 0.00 2.41
2501 2933 1.921887 CGGCATGAACGTACGTATTGT 59.078 47.619 23.12 5.53 0.00 2.71
2502 2934 1.256895 CCGGCATGAACGTACGTATTG 59.743 52.381 23.12 18.97 0.00 1.90
2503 2935 1.563111 CCGGCATGAACGTACGTATT 58.437 50.000 23.12 6.86 0.00 1.89
2504 2936 0.249155 CCCGGCATGAACGTACGTAT 60.249 55.000 23.12 9.79 0.00 3.06
2594 3026 1.124658 CGCGTTCCGATTTGTTTCGTA 59.875 47.619 0.00 0.00 40.02 3.43
2596 3028 1.385567 GCGCGTTCCGATTTGTTTCG 61.386 55.000 8.43 0.00 40.02 3.46
2597 3029 0.384974 TGCGCGTTCCGATTTGTTTC 60.385 50.000 8.43 0.00 40.02 2.78
2598 3030 0.239879 ATGCGCGTTCCGATTTGTTT 59.760 45.000 8.43 0.00 40.02 2.83
2599 3031 0.179200 GATGCGCGTTCCGATTTGTT 60.179 50.000 8.43 0.00 40.02 2.83
2702 3138 2.095364 CAGCCATGCAACTTGAAGTCTC 60.095 50.000 0.00 0.00 0.00 3.36
2705 3141 1.696063 ACAGCCATGCAACTTGAAGT 58.304 45.000 0.00 0.00 0.00 3.01
2726 3162 0.395862 ACGCTCCTCTTGCTAGCCTA 60.396 55.000 13.29 0.00 32.50 3.93
2727 3163 0.395862 TACGCTCCTCTTGCTAGCCT 60.396 55.000 13.29 0.00 32.50 4.58
2728 3164 0.031449 CTACGCTCCTCTTGCTAGCC 59.969 60.000 13.29 0.00 32.50 3.93
2729 3165 1.001815 CTCTACGCTCCTCTTGCTAGC 60.002 57.143 8.10 8.10 0.00 3.42
2800 3259 1.024579 ACGGCAGGTAAATTCGCAGG 61.025 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.