Multiple sequence alignment - TraesCS1D01G276500

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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 TraesCS1D01G276500 chr1D 100.000 4727 0 0 1 4727 372873634 372878360 0.000000e+00 8730.0
1 TraesCS1D01G276500 chr1D 78.133 814 122 42 990 1784 372860223 372860999 2.580000e-127 466.0
2 TraesCS1D01G276500 chr1D 79.538 606 80 23 1238 1806 372835147 372835745 4.430000e-105 392.0
3 TraesCS1D01G276500 chr1D 80.769 494 68 16 3216 3705 372862219 372862689 1.250000e-95 361.0
4 TraesCS1D01G276500 chr1D 82.609 299 34 6 2686 2967 372861805 372862102 1.020000e-61 248.0
5 TraesCS1D01G276500 chr1D 100.000 44 0 0 3014 3057 372876603 372876646 1.090000e-11 82.4
6 TraesCS1D01G276500 chr1D 100.000 44 0 0 2970 3013 372876647 372876690 1.090000e-11 82.4
7 TraesCS1D01G276500 chr1B 93.521 1852 76 15 337 2172 497798685 497800508 0.000000e+00 2715.0
8 TraesCS1D01G276500 chr1B 92.963 810 37 10 2170 2969 497820534 497821333 0.000000e+00 1162.0
9 TraesCS1D01G276500 chr1B 84.372 1043 93 27 3741 4727 497822038 497823066 0.000000e+00 959.0
10 TraesCS1D01G276500 chr1B 93.045 647 43 2 3083 3729 497821351 497821995 0.000000e+00 944.0
11 TraesCS1D01G276500 chr1B 83.377 385 48 10 1428 1806 497471224 497471598 4.530000e-90 342.0
12 TraesCS1D01G276500 chr1B 93.607 219 11 2 1 217 497798484 497798701 1.640000e-84 324.0
13 TraesCS1D01G276500 chr1B 81.699 306 44 12 1243 1541 497779341 497779641 1.310000e-60 244.0
14 TraesCS1D01G276500 chr1B 80.282 213 30 9 986 1189 497779108 497779317 2.950000e-32 150.0
15 TraesCS1D01G276500 chr1B 82.390 159 19 6 1034 1191 497470744 497470894 3.840000e-26 130.0
16 TraesCS1D01G276500 chr1B 86.813 91 9 1 1586 1676 67503023 67502936 1.080000e-16 99.0
17 TraesCS1D01G276500 chr1A 91.322 1256 72 11 642 1873 472164167 472165409 0.000000e+00 1681.0
18 TraesCS1D01G276500 chr1A 90.990 1010 54 9 3741 4727 472169036 472170031 0.000000e+00 1327.0
19 TraesCS1D01G276500 chr1A 94.923 847 32 8 2170 3013 472167500 472168338 0.000000e+00 1315.0
20 TraesCS1D01G276500 chr1A 93.629 722 28 2 3014 3735 472168295 472168998 0.000000e+00 1062.0
21 TraesCS1D01G276500 chr1A 83.594 384 51 7 1428 1806 472080307 472080683 2.710000e-92 350.0
22 TraesCS1D01G276500 chr1A 80.080 502 70 18 3216 3705 472142825 472143308 3.500000e-91 346.0
23 TraesCS1D01G276500 chr1A 82.986 288 35 5 2686 2959 472142416 472142703 1.020000e-61 248.0
24 TraesCS1D01G276500 chr1A 88.060 201 12 8 1915 2113 472166232 472166422 1.320000e-55 228.0
25 TraesCS1D01G276500 chr1A 75.087 574 75 40 990 1541 472140895 472141422 6.200000e-49 206.0
26 TraesCS1D01G276500 chr1A 95.876 97 3 1 254 350 27397105 27397200 6.330000e-34 156.0
27 TraesCS1D01G276500 chr1A 80.423 189 25 9 999 1186 472079808 472079985 2.970000e-27 134.0
28 TraesCS1D01G276500 chr5B 96.040 101 2 2 254 353 264932456 264932555 3.780000e-36 163.0
29 TraesCS1D01G276500 chr5B 94.059 101 5 1 254 353 163273267 163273167 8.190000e-33 152.0
30 TraesCS1D01G276500 chr2A 96.939 98 2 1 254 351 1218188 1218284 3.780000e-36 163.0
31 TraesCS1D01G276500 chr2A 94.118 102 4 2 254 355 569281748 569281649 2.280000e-33 154.0
32 TraesCS1D01G276500 chr3B 95.960 99 4 0 254 352 299129019 299129117 1.360000e-35 161.0
33 TraesCS1D01G276500 chr5A 95.833 96 4 0 254 349 219371706 219371801 6.330000e-34 156.0
34 TraesCS1D01G276500 chr7A 94.898 98 3 2 254 351 700109770 700109865 8.190000e-33 152.0
35 TraesCS1D01G276500 chr6B 97.701 87 2 0 254 340 1160028 1160114 2.950000e-32 150.0
36 TraesCS1D01G276500 chr4B 100.000 28 0 0 3043 3070 43225782 43225809 9.000000e-03 52.8


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 TraesCS1D01G276500 chr1D 372873634 372878360 4726 False 2964.933333 8730 100.000000 1 4727 3 chr1D.!!$F3 4726
1 TraesCS1D01G276500 chr1D 372835147 372835745 598 False 392.000000 392 79.538000 1238 1806 1 chr1D.!!$F1 568
2 TraesCS1D01G276500 chr1D 372860223 372862689 2466 False 358.333333 466 80.503667 990 3705 3 chr1D.!!$F2 2715
3 TraesCS1D01G276500 chr1B 497798484 497800508 2024 False 1519.500000 2715 93.564000 1 2172 2 chr1B.!!$F3 2171
4 TraesCS1D01G276500 chr1B 497820534 497823066 2532 False 1021.666667 1162 90.126667 2170 4727 3 chr1B.!!$F4 2557
5 TraesCS1D01G276500 chr1B 497470744 497471598 854 False 236.000000 342 82.883500 1034 1806 2 chr1B.!!$F1 772
6 TraesCS1D01G276500 chr1A 472164167 472170031 5864 False 1122.600000 1681 91.784800 642 4727 5 chr1A.!!$F4 4085
7 TraesCS1D01G276500 chr1A 472140895 472143308 2413 False 266.666667 346 79.384333 990 3705 3 chr1A.!!$F3 2715
8 TraesCS1D01G276500 chr1A 472079808 472080683 875 False 242.000000 350 82.008500 999 1806 2 chr1A.!!$F2 807

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
305 308 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.0 0.00 44.78 4.85 F
1643 1819 0.107993 ACTCATCCATCACCAGCGTG 60.108 55.000 0.0 0.00 41.72 5.34 F
2009 2974 1.594276 GCAATTTGGCAAACAACGTGC 60.594 47.619 16.0 15.01 40.09 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1891 0.897621 CCCCCAGAAATTGCCAGAAC 59.102 55.0 0.00 0.00 0.0 3.01 R
2992 5170 2.167075 CCCTAAATGTAAGACGGTCCGT 59.833 50.0 18.94 18.94 45.1 4.69 R
3736 5944 0.036952 CACAGGCTCAATCAGACCGT 60.037 55.0 0.00 0.00 0.0 4.83 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
123 126 5.643664 TGTGAATCAAACTGCTAATCATGC 58.356 37.500 0.00 0.00 0.00 4.06
130 133 5.010922 TCAAACTGCTAATCATGCCTGTTTT 59.989 36.000 0.00 0.00 35.57 2.43
200 203 6.751888 GCCTAGTGCAAAATAAGTTTATGTGG 59.248 38.462 0.00 0.00 40.77 4.17
235 238 4.233558 AAAAAGGGGCAGCCCGGT 62.234 61.111 25.18 11.58 46.66 5.28
236 239 4.994756 AAAAGGGGCAGCCCGGTG 62.995 66.667 25.18 0.00 46.66 4.94
242 245 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
243 246 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
244 247 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
245 248 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
246 249 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
251 254 3.093278 GTGCATGTAGCTCCACGC 58.907 61.111 0.00 0.00 45.94 5.34
261 264 2.755929 GCTCCACGCTTGTAAGAGG 58.244 57.895 0.00 0.00 35.14 3.69
262 265 1.362406 GCTCCACGCTTGTAAGAGGC 61.362 60.000 0.00 0.00 35.14 4.70
263 266 0.247736 CTCCACGCTTGTAAGAGGCT 59.752 55.000 0.00 0.00 0.00 4.58
264 267 0.037326 TCCACGCTTGTAAGAGGCTG 60.037 55.000 0.00 0.00 0.00 4.85
265 268 0.320771 CCACGCTTGTAAGAGGCTGT 60.321 55.000 0.00 0.00 0.00 4.40
266 269 1.512926 CACGCTTGTAAGAGGCTGTT 58.487 50.000 1.39 1.39 0.00 3.16
267 270 1.873591 CACGCTTGTAAGAGGCTGTTT 59.126 47.619 0.90 0.00 0.00 2.83
268 271 2.096218 CACGCTTGTAAGAGGCTGTTTC 60.096 50.000 0.90 0.00 0.00 2.78
269 272 1.464997 CGCTTGTAAGAGGCTGTTTCC 59.535 52.381 0.90 0.00 0.00 3.13
270 273 2.504367 GCTTGTAAGAGGCTGTTTCCA 58.496 47.619 0.90 0.00 0.00 3.53
271 274 2.485814 GCTTGTAAGAGGCTGTTTCCAG 59.514 50.000 0.90 0.00 41.91 3.86
272 275 2.859165 TGTAAGAGGCTGTTTCCAGG 57.141 50.000 0.90 0.00 39.22 4.45
273 276 2.334977 TGTAAGAGGCTGTTTCCAGGA 58.665 47.619 0.90 0.00 39.22 3.86
274 277 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
275 278 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
276 279 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
277 280 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
278 281 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
279 282 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
280 283 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
281 284 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
282 285 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
283 286 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
284 287 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
285 288 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
286 289 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
287 290 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
288 291 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
289 292 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
290 293 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
291 294 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
292 295 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
293 296 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
304 307 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
305 308 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
306 309 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
307 310 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
308 311 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
309 312 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
310 313 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
311 314 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
312 315 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
313 316 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
314 317 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
315 318 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
316 319 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
317 320 1.180029 CAAGGCAGCAGCTTTACCAT 58.820 50.000 0.00 0.00 38.07 3.55
318 321 1.547372 CAAGGCAGCAGCTTTACCATT 59.453 47.619 0.00 0.00 38.07 3.16
319 322 1.180029 AGGCAGCAGCTTTACCATTG 58.820 50.000 0.00 0.00 41.70 2.82
320 323 0.459063 GGCAGCAGCTTTACCATTGC 60.459 55.000 0.00 0.00 41.70 3.56
321 324 0.799534 GCAGCAGCTTTACCATTGCG 60.800 55.000 0.00 0.00 41.27 4.85
322 325 0.799534 CAGCAGCTTTACCATTGCGC 60.800 55.000 0.00 0.00 41.27 6.09
323 326 1.517039 GCAGCTTTACCATTGCGCC 60.517 57.895 4.18 0.00 0.00 6.53
324 327 1.882311 CAGCTTTACCATTGCGCCA 59.118 52.632 4.18 0.00 0.00 5.69
325 328 0.243365 CAGCTTTACCATTGCGCCAA 59.757 50.000 4.18 0.00 0.00 4.52
326 329 0.527565 AGCTTTACCATTGCGCCAAG 59.472 50.000 4.18 0.00 0.00 3.61
327 330 0.458370 GCTTTACCATTGCGCCAAGG 60.458 55.000 4.18 2.13 0.00 3.61
328 331 0.458370 CTTTACCATTGCGCCAAGGC 60.458 55.000 4.18 0.00 37.85 4.35
329 332 0.897863 TTTACCATTGCGCCAAGGCT 60.898 50.000 4.18 0.00 39.32 4.58
330 333 1.312371 TTACCATTGCGCCAAGGCTC 61.312 55.000 4.18 1.20 39.32 4.70
331 334 3.830192 CCATTGCGCCAAGGCTCC 61.830 66.667 4.18 0.71 39.32 4.70
332 335 3.830192 CATTGCGCCAAGGCTCCC 61.830 66.667 4.18 0.00 39.32 4.30
345 348 2.279173 AGGCTCCCCTTCAAATACTGT 58.721 47.619 0.00 0.00 38.74 3.55
346 349 3.460825 AGGCTCCCCTTCAAATACTGTA 58.539 45.455 0.00 0.00 38.74 2.74
467 470 9.132521 GGAGTGAATATTTTGTCATGTTTTGAG 57.867 33.333 0.00 0.00 34.17 3.02
493 496 0.969917 CCATGGTGCCGAAAATCCCA 60.970 55.000 2.57 0.00 0.00 4.37
581 584 3.515630 ACTCATCTGACGTACTTGCATG 58.484 45.455 0.00 0.00 0.00 4.06
618 621 5.163893 GGATATTTCGTTTCGTCTGCTCAAA 60.164 40.000 0.00 0.00 0.00 2.69
628 631 1.876156 GTCTGCTCAAAACTGTCCCAG 59.124 52.381 0.00 0.00 37.52 4.45
668 671 3.051496 TCCATCAGATCCTCTCCCTTTCT 60.051 47.826 0.00 0.00 0.00 2.52
697 700 2.827800 ATCTGACATGGGCGTATCAG 57.172 50.000 0.00 0.00 39.99 2.90
745 755 1.321474 CTCCTTTCAGGCAGTTGCAA 58.679 50.000 6.43 0.00 44.36 4.08
775 785 0.978667 AAAACCAAAACAGGCCCGGT 60.979 50.000 0.00 0.00 0.00 5.28
949 959 3.149196 GGAGACTCTCCTCTGCATCTAG 58.851 54.545 16.91 0.00 46.41 2.43
967 977 4.759782 TCTAGTACAAATCTGAGGCTTGC 58.240 43.478 0.00 0.00 0.00 4.01
1098 1108 4.774503 GCCTGCAGCTTCGCCTCT 62.775 66.667 8.66 0.00 38.99 3.69
1121 1131 4.780815 TCTTTCATTGCCAATCTCGGTAT 58.219 39.130 0.00 0.00 0.00 2.73
1133 1144 5.221521 CCAATCTCGGTATCATCCTTCTCAA 60.222 44.000 0.00 0.00 0.00 3.02
1247 1334 5.989168 TCGGTAAAGCATATACTTCCATGTG 59.011 40.000 0.00 0.00 0.00 3.21
1291 1378 0.443478 TCGCACAATCATTCTGCACG 59.557 50.000 0.00 0.00 0.00 5.34
1425 1569 1.165907 TCTCACTGTTTTGGCCGCTG 61.166 55.000 0.00 0.00 0.00 5.18
1505 1656 4.224370 GGGAACTATCTGGGTGAGTACAAA 59.776 45.833 0.00 0.00 0.00 2.83
1561 1734 5.885230 CATTCCTTGCTACTGATGACAAA 57.115 39.130 0.00 0.00 0.00 2.83
1562 1735 5.634896 CATTCCTTGCTACTGATGACAAAC 58.365 41.667 0.00 0.00 0.00 2.93
1563 1736 4.350368 TCCTTGCTACTGATGACAAACA 57.650 40.909 0.00 0.00 0.00 2.83
1567 1740 5.877012 CCTTGCTACTGATGACAAACATACT 59.123 40.000 0.00 0.00 39.56 2.12
1643 1819 0.107993 ACTCATCCATCACCAGCGTG 60.108 55.000 0.00 0.00 41.72 5.34
1784 1960 3.159472 TGTGCTCCTTTCAGATGCAAAT 58.841 40.909 0.00 0.00 35.34 2.32
1870 2046 3.189606 TGGGTATTGGACAGTGGATTCT 58.810 45.455 0.00 0.00 0.00 2.40
1871 2047 4.367166 TGGGTATTGGACAGTGGATTCTA 58.633 43.478 0.00 0.00 0.00 2.10
1872 2048 4.785914 TGGGTATTGGACAGTGGATTCTAA 59.214 41.667 0.00 0.00 0.00 2.10
1873 2049 5.251932 TGGGTATTGGACAGTGGATTCTAAA 59.748 40.000 0.00 0.00 0.00 1.85
1874 2050 6.069088 TGGGTATTGGACAGTGGATTCTAAAT 60.069 38.462 0.00 0.00 0.00 1.40
1875 2051 6.833933 GGGTATTGGACAGTGGATTCTAAATT 59.166 38.462 0.00 0.00 0.00 1.82
1876 2052 7.342026 GGGTATTGGACAGTGGATTCTAAATTT 59.658 37.037 0.00 0.00 0.00 1.82
1877 2053 8.406297 GGTATTGGACAGTGGATTCTAAATTTC 58.594 37.037 0.00 0.00 0.00 2.17
1902 2078 3.089284 CCCATCCCCACAACTTAGTTTC 58.911 50.000 0.00 0.00 0.00 2.78
1903 2079 3.499563 CCCATCCCCACAACTTAGTTTCA 60.500 47.826 0.00 0.00 0.00 2.69
1907 2083 6.407525 CCATCCCCACAACTTAGTTTCAAAAA 60.408 38.462 0.00 0.00 0.00 1.94
1942 2907 7.041712 TGTGCGTTGAATAAAATCTCTACAACA 60.042 33.333 0.00 0.00 36.84 3.33
1971 2936 6.121590 TGAGCCATCAGATATTTGCTAACAA 58.878 36.000 0.00 0.00 0.00 2.83
1974 2939 7.431249 AGCCATCAGATATTTGCTAACAATTG 58.569 34.615 3.24 3.24 35.21 2.32
1993 2958 4.804868 TTGTAGCAAACATGATGGCAAT 57.195 36.364 5.01 0.00 38.10 3.56
1994 2959 4.804868 TGTAGCAAACATGATGGCAATT 57.195 36.364 5.01 0.00 31.43 2.32
1995 2960 5.149973 TGTAGCAAACATGATGGCAATTT 57.850 34.783 5.01 0.00 31.43 1.82
1996 2961 4.930405 TGTAGCAAACATGATGGCAATTTG 59.070 37.500 5.01 2.07 37.29 2.32
1997 2962 3.340034 AGCAAACATGATGGCAATTTGG 58.660 40.909 5.01 0.00 35.93 3.28
1998 2963 2.159490 GCAAACATGATGGCAATTTGGC 60.159 45.455 15.53 15.53 44.03 4.52
2009 2974 1.594276 GCAATTTGGCAAACAACGTGC 60.594 47.619 16.00 15.01 40.09 5.34
2097 3062 4.788075 TCCCATCATCCTCCTTTCTTGTTA 59.212 41.667 0.00 0.00 0.00 2.41
2126 3091 3.228188 ACTTTTCAGCCTCACAATCCA 57.772 42.857 0.00 0.00 0.00 3.41
2216 4320 6.403866 AGAATAGGTAGAGATGTGCTCAAG 57.596 41.667 0.00 0.00 46.45 3.02
2253 4358 2.376518 AGAAACCTCCAGGCTGAAATCA 59.623 45.455 17.94 0.00 39.32 2.57
2355 4461 2.124411 TCTAGGGGATGCCCTTGTTAC 58.876 52.381 31.88 0.00 44.66 2.50
2410 4516 1.913419 GGGGAGGTTGGTGATGTCTTA 59.087 52.381 0.00 0.00 0.00 2.10
2411 4517 2.509964 GGGGAGGTTGGTGATGTCTTAT 59.490 50.000 0.00 0.00 0.00 1.73
2412 4518 3.714798 GGGGAGGTTGGTGATGTCTTATA 59.285 47.826 0.00 0.00 0.00 0.98
2490 4605 4.576463 CCCTTGATTATGTAGGAACACTGC 59.424 45.833 0.00 0.00 38.78 4.40
2563 4678 3.189287 GGTGCTTGTCAGTACAATTCAGG 59.811 47.826 0.00 0.00 44.43 3.86
2934 5112 3.684788 CACCATTACTCCTTTTGTCCTCG 59.315 47.826 0.00 0.00 0.00 4.63
2979 5157 7.496346 TGTTTAATCAGATAGACCCTCTGTT 57.504 36.000 0.71 0.00 40.79 3.16
2980 5158 7.556844 TGTTTAATCAGATAGACCCTCTGTTC 58.443 38.462 0.71 0.00 40.79 3.18
2981 5159 6.732896 TTAATCAGATAGACCCTCTGTTCC 57.267 41.667 0.71 0.00 40.79 3.62
2982 5160 4.551215 ATCAGATAGACCCTCTGTTCCT 57.449 45.455 0.71 0.00 40.79 3.36
2983 5161 5.671463 ATCAGATAGACCCTCTGTTCCTA 57.329 43.478 0.71 0.00 40.79 2.94
2984 5162 5.467668 TCAGATAGACCCTCTGTTCCTAA 57.532 43.478 0.71 0.00 40.79 2.69
2985 5163 5.838955 TCAGATAGACCCTCTGTTCCTAAA 58.161 41.667 0.71 0.00 40.79 1.85
2986 5164 6.444704 TCAGATAGACCCTCTGTTCCTAAAT 58.555 40.000 0.71 0.00 40.79 1.40
2987 5165 6.325028 TCAGATAGACCCTCTGTTCCTAAATG 59.675 42.308 0.71 0.00 40.79 2.32
2988 5166 6.098982 CAGATAGACCCTCTGTTCCTAAATGT 59.901 42.308 0.00 0.00 36.26 2.71
2989 5167 7.287927 CAGATAGACCCTCTGTTCCTAAATGTA 59.712 40.741 0.00 0.00 36.26 2.29
2990 5168 7.844779 AGATAGACCCTCTGTTCCTAAATGTAA 59.155 37.037 0.00 0.00 0.00 2.41
2991 5169 6.301169 AGACCCTCTGTTCCTAAATGTAAG 57.699 41.667 0.00 0.00 0.00 2.34
2992 5170 6.023603 AGACCCTCTGTTCCTAAATGTAAGA 58.976 40.000 0.00 0.00 0.00 2.10
2993 5171 6.051179 ACCCTCTGTTCCTAAATGTAAGAC 57.949 41.667 0.00 0.00 0.00 3.01
2994 5172 5.109903 CCCTCTGTTCCTAAATGTAAGACG 58.890 45.833 0.00 0.00 0.00 4.18
2995 5173 5.109903 CCTCTGTTCCTAAATGTAAGACGG 58.890 45.833 0.00 0.00 0.00 4.79
2996 5174 5.105473 CCTCTGTTCCTAAATGTAAGACGGA 60.105 44.000 0.00 0.00 0.00 4.69
2997 5175 5.717119 TCTGTTCCTAAATGTAAGACGGAC 58.283 41.667 0.00 0.00 0.00 4.79
2998 5176 4.824289 TGTTCCTAAATGTAAGACGGACC 58.176 43.478 0.00 0.00 0.00 4.46
2999 5177 3.788333 TCCTAAATGTAAGACGGACCG 57.212 47.619 13.61 13.61 0.00 4.79
3000 5178 3.091545 TCCTAAATGTAAGACGGACCGT 58.908 45.455 21.93 21.93 45.10 4.83
3012 5190 3.515330 ACGGACCGTCTTACATTTAGG 57.485 47.619 15.37 0.00 33.69 2.69
3013 5191 2.167075 ACGGACCGTCTTACATTTAGGG 59.833 50.000 15.37 0.00 33.69 3.53
3014 5192 2.428171 CGGACCGTCTTACATTTAGGGA 59.572 50.000 5.48 0.00 0.00 4.20
3015 5193 3.736126 CGGACCGTCTTACATTTAGGGAC 60.736 52.174 5.48 0.00 0.00 4.46
3016 5194 3.431346 GGACCGTCTTACATTTAGGGACC 60.431 52.174 0.00 0.00 0.00 4.46
3017 5195 2.502947 ACCGTCTTACATTTAGGGACCC 59.497 50.000 0.59 0.59 0.00 4.46
3018 5196 2.770232 CCGTCTTACATTTAGGGACCCT 59.230 50.000 19.48 19.48 37.71 4.34
3019 5197 3.181468 CCGTCTTACATTTAGGGACCCTC 60.181 52.174 19.05 0.00 34.61 4.30
3020 5198 3.705072 CGTCTTACATTTAGGGACCCTCT 59.295 47.826 19.05 0.00 34.61 3.69
3021 5199 4.441634 CGTCTTACATTTAGGGACCCTCTG 60.442 50.000 19.05 15.57 34.61 3.35
3022 5200 4.470304 GTCTTACATTTAGGGACCCTCTGT 59.530 45.833 19.05 20.33 34.61 3.41
3103 5286 6.650807 CACAAGTAGGCAACAAAGAGAATCTA 59.349 38.462 0.00 0.00 44.11 1.98
3129 5312 7.629157 TCCAGTCAAGTGGTTATGAATTATCA 58.371 34.615 3.85 0.00 38.88 2.15
3339 5530 6.420903 TCGCCATTCGAGTATTTTTCTATCAG 59.579 38.462 0.00 0.00 43.16 2.90
3543 5748 1.718178 GCAGATATGTGACTCATCGCG 59.282 52.381 3.61 0.00 38.25 5.87
3567 5772 4.680171 AACCTAACACGCTTAATTGCTC 57.320 40.909 0.00 0.00 0.00 4.26
3649 5854 4.391216 CAGCTCACTATGAACAACTTCCAG 59.609 45.833 0.00 0.00 0.00 3.86
3680 5888 5.568620 AACTCAACAGGAAGTGGTTCTAT 57.431 39.130 0.00 0.00 32.72 1.98
3705 5913 3.885297 TGGACAGAAAAGAAAGGAAGCAG 59.115 43.478 0.00 0.00 0.00 4.24
3735 5943 2.846206 TCACATCTGTTAAGGGAGCCAT 59.154 45.455 0.00 0.00 0.00 4.40
3736 5944 4.037222 TCACATCTGTTAAGGGAGCCATA 58.963 43.478 0.00 0.00 0.00 2.74
3737 5945 4.130118 CACATCTGTTAAGGGAGCCATAC 58.870 47.826 0.00 0.00 0.00 2.39
3738 5946 3.181465 ACATCTGTTAAGGGAGCCATACG 60.181 47.826 0.00 0.00 0.00 3.06
3739 5947 1.760613 TCTGTTAAGGGAGCCATACGG 59.239 52.381 0.00 0.00 0.00 4.02
3838 6080 3.986572 TGCCATTTGCGTGTTCATAAAAG 59.013 39.130 0.00 0.00 45.60 2.27
4006 6258 4.880120 TGAAATCTTGCATGGATCTCAGTC 59.120 41.667 0.00 0.00 0.00 3.51
4008 6260 4.774660 ATCTTGCATGGATCTCAGTCTT 57.225 40.909 0.00 0.00 0.00 3.01
4009 6261 3.870274 TCTTGCATGGATCTCAGTCTTG 58.130 45.455 0.00 0.00 0.00 3.02
4016 6268 4.478206 TGGATCTCAGTCTTGGATCAAC 57.522 45.455 11.61 0.00 37.99 3.18
4017 6269 3.840078 TGGATCTCAGTCTTGGATCAACA 59.160 43.478 11.61 2.48 37.99 3.33
4154 6409 0.039165 GCAGGTTGCAGCAGTTTACC 60.039 55.000 5.91 5.91 44.26 2.85
4231 6493 5.375417 TGCATCACTTTTAGGTGTGAATG 57.625 39.130 0.00 0.00 44.81 2.67
4276 6548 5.944013 TCTGTTCTCTTCATCGTAAGTCTG 58.056 41.667 0.00 0.00 39.48 3.51
4288 6560 7.573627 TCATCGTAAGTCTGTCATAAGATACG 58.426 38.462 0.00 0.00 36.88 3.06
4296 6568 2.424246 TGTCATAAGATACGTCGCACCA 59.576 45.455 0.00 0.00 0.00 4.17
4329 6601 5.048224 TCTCTTACCTTACTGAAACTCGGTG 60.048 44.000 0.00 0.00 36.50 4.94
4373 6652 7.979444 AAAATCTTCCTCGTTTTCATCTGTA 57.021 32.000 0.00 0.00 0.00 2.74
4380 6659 6.464222 TCCTCGTTTTCATCTGTAATGTTCT 58.536 36.000 0.00 0.00 0.00 3.01
4498 6788 4.520492 AGCAACAATCTCACCAGTTTTAGG 59.480 41.667 0.00 0.00 0.00 2.69
4549 6839 8.710835 TTTTTCACCTTCAGGATTTGTTTAAC 57.289 30.769 0.00 0.00 38.94 2.01
4550 6840 6.399639 TTCACCTTCAGGATTTGTTTAACC 57.600 37.500 0.00 0.00 38.94 2.85
4551 6841 5.701224 TCACCTTCAGGATTTGTTTAACCT 58.299 37.500 0.00 0.00 38.94 3.50
4552 6842 6.133356 TCACCTTCAGGATTTGTTTAACCTT 58.867 36.000 0.00 0.00 38.94 3.50
4553 6843 6.040391 TCACCTTCAGGATTTGTTTAACCTTG 59.960 38.462 0.00 0.00 38.94 3.61
4596 6901 3.811497 TCGACACGTCATCTATAATCGGT 59.189 43.478 0.00 0.00 0.00 4.69
4637 6943 1.150827 AAACTTGGTTACGCCTACGC 58.849 50.000 0.00 0.00 45.53 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.479837 TGTAGCTGTTGAAGGAACGTG 58.520 47.619 0.00 0.00 37.38 4.49
87 90 0.035439 ATTCACAGCAGGGGTTACGG 60.035 55.000 0.00 0.00 0.00 4.02
92 95 1.145738 AGTTTGATTCACAGCAGGGGT 59.854 47.619 0.00 0.00 0.00 4.95
123 126 3.077359 CTGCTCAGGGAGTAAAAACAGG 58.923 50.000 0.00 0.00 31.39 4.00
147 150 2.276116 ACACATGGAGCTCGTCGGT 61.276 57.895 7.83 0.19 0.00 4.69
225 228 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
226 229 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
227 230 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
228 231 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
229 232 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
230 233 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
244 247 0.247736 AGCCTCTTACAAGCGTGGAG 59.752 55.000 4.26 1.85 0.00 3.86
245 248 0.037326 CAGCCTCTTACAAGCGTGGA 60.037 55.000 4.26 0.00 0.00 4.02
246 249 0.320771 ACAGCCTCTTACAAGCGTGG 60.321 55.000 4.26 0.00 0.00 4.94
247 250 1.512926 AACAGCCTCTTACAAGCGTG 58.487 50.000 0.00 0.00 0.00 5.34
248 251 2.143925 GAAACAGCCTCTTACAAGCGT 58.856 47.619 0.00 0.00 0.00 5.07
249 252 1.464997 GGAAACAGCCTCTTACAAGCG 59.535 52.381 0.00 0.00 0.00 4.68
250 253 2.504367 TGGAAACAGCCTCTTACAAGC 58.496 47.619 0.00 0.00 35.01 4.01
263 266 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
264 267 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
265 268 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
266 269 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
267 270 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
268 271 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
269 272 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
270 273 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
271 274 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
272 275 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
273 276 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
274 277 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
275 278 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
276 279 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
277 280 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
287 290 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
288 291 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
289 292 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
290 293 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
291 294 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
292 295 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
293 296 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
294 297 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
295 298 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
296 299 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
297 300 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
298 301 1.180029 ATGGTAAAGCTGCTGCCTTG 58.820 50.000 12.44 0.00 40.80 3.61
299 302 1.547372 CAATGGTAAAGCTGCTGCCTT 59.453 47.619 12.44 8.34 40.80 4.35
300 303 1.180029 CAATGGTAAAGCTGCTGCCT 58.820 50.000 12.44 2.45 40.80 4.75
301 304 0.459063 GCAATGGTAAAGCTGCTGCC 60.459 55.000 12.44 7.07 40.80 4.85
302 305 0.799534 CGCAATGGTAAAGCTGCTGC 60.800 55.000 1.35 7.62 40.05 5.25
303 306 0.799534 GCGCAATGGTAAAGCTGCTG 60.800 55.000 1.35 0.00 32.52 4.41
304 307 1.508088 GCGCAATGGTAAAGCTGCT 59.492 52.632 0.30 0.00 32.52 4.24
305 308 1.517039 GGCGCAATGGTAAAGCTGC 60.517 57.895 10.83 0.00 0.00 5.25
306 309 0.243365 TTGGCGCAATGGTAAAGCTG 59.757 50.000 10.83 0.00 0.00 4.24
307 310 0.527565 CTTGGCGCAATGGTAAAGCT 59.472 50.000 10.83 0.00 0.00 3.74
308 311 0.458370 CCTTGGCGCAATGGTAAAGC 60.458 55.000 10.83 0.00 0.00 3.51
309 312 0.458370 GCCTTGGCGCAATGGTAAAG 60.458 55.000 17.44 5.26 0.00 1.85
310 313 0.897863 AGCCTTGGCGCAATGGTAAA 60.898 50.000 17.44 0.00 0.00 2.01
311 314 1.304052 AGCCTTGGCGCAATGGTAA 60.304 52.632 17.44 0.00 0.00 2.85
312 315 1.748879 GAGCCTTGGCGCAATGGTA 60.749 57.895 17.44 0.00 0.00 3.25
313 316 3.064324 GAGCCTTGGCGCAATGGT 61.064 61.111 17.44 8.55 0.00 3.55
314 317 3.830192 GGAGCCTTGGCGCAATGG 61.830 66.667 12.38 12.38 0.00 3.16
315 318 3.830192 GGGAGCCTTGGCGCAATG 61.830 66.667 16.55 0.00 0.00 2.82
320 323 3.567579 TTGAAGGGGAGCCTTGGCG 62.568 63.158 5.95 0.00 0.00 5.69
321 324 0.615827 ATTTGAAGGGGAGCCTTGGC 60.616 55.000 2.97 2.97 0.00 4.52
322 325 2.024941 AGTATTTGAAGGGGAGCCTTGG 60.025 50.000 0.00 0.00 0.00 3.61
323 326 3.019564 CAGTATTTGAAGGGGAGCCTTG 58.980 50.000 0.00 0.00 0.00 3.61
324 327 2.649816 ACAGTATTTGAAGGGGAGCCTT 59.350 45.455 0.00 0.00 0.00 4.35
325 328 2.279173 ACAGTATTTGAAGGGGAGCCT 58.721 47.619 0.00 0.00 0.00 4.58
326 329 2.808906 ACAGTATTTGAAGGGGAGCC 57.191 50.000 0.00 0.00 0.00 4.70
327 330 7.224297 TGAATATACAGTATTTGAAGGGGAGC 58.776 38.462 0.00 0.00 0.00 4.70
328 331 8.651389 TCTGAATATACAGTATTTGAAGGGGAG 58.349 37.037 0.00 0.00 38.79 4.30
329 332 8.561536 TCTGAATATACAGTATTTGAAGGGGA 57.438 34.615 0.00 0.00 38.79 4.81
330 333 9.799106 AATCTGAATATACAGTATTTGAAGGGG 57.201 33.333 0.00 0.00 38.79 4.79
364 367 6.183361 GGAACTAGTAATCTCCACCATGACAT 60.183 42.308 6.47 0.00 0.00 3.06
370 373 4.081087 GCTTGGAACTAGTAATCTCCACCA 60.081 45.833 12.63 0.60 37.69 4.17
434 437 6.414732 TGACAAAATATTCACTCCCCTGTAG 58.585 40.000 0.00 0.00 0.00 2.74
484 487 2.562298 TGATGCTTGTGGTGGGATTTTC 59.438 45.455 0.00 0.00 0.00 2.29
493 496 1.340889 ACGCAATTTGATGCTTGTGGT 59.659 42.857 0.00 0.00 44.21 4.16
581 584 5.103000 ACGAAATATCCGCTGCATATAGAC 58.897 41.667 0.00 0.00 0.00 2.59
628 631 0.813210 GAGTCTGCTGGTAGGCATGC 60.813 60.000 9.90 9.90 41.63 4.06
668 671 1.542472 CCATGTCAGATTTGCTGCACA 59.458 47.619 0.00 0.00 44.52 4.57
745 755 6.705825 GCCTGTTTTGGTTTTTGATTCACTAT 59.294 34.615 0.00 0.00 0.00 2.12
775 785 3.147595 CCTGTCGAGGCATCCCGA 61.148 66.667 0.00 0.00 35.76 5.14
949 959 2.076863 ACGCAAGCCTCAGATTTGTAC 58.923 47.619 0.00 0.00 45.62 2.90
967 977 0.929824 CAAGGTGCACGCTGAAAACG 60.930 55.000 11.45 0.00 0.00 3.60
1098 1108 3.420893 ACCGAGATTGGCAATGAAAGAA 58.579 40.909 19.07 0.00 0.00 2.52
1121 1131 3.365472 TGGAGATCGTTGAGAAGGATGA 58.635 45.455 0.00 0.00 36.24 2.92
1247 1334 1.804151 TGCGTCAACTCCTGCATAAAC 59.196 47.619 0.00 0.00 31.31 2.01
1291 1378 3.618690 ACTAAGGTCAACAGGAGATGC 57.381 47.619 0.00 0.00 0.00 3.91
1370 1464 2.007608 GGTAAGCTCCACGGTTGATTC 58.992 52.381 0.00 0.00 34.65 2.52
1505 1656 3.501828 TGACTGAAATGCGTATTGCTTGT 59.498 39.130 5.76 4.71 46.63 3.16
1643 1819 4.037923 ACAGTCCAACAATCCAACAATGTC 59.962 41.667 0.00 0.00 0.00 3.06
1715 1891 0.897621 CCCCCAGAAATTGCCAGAAC 59.102 55.000 0.00 0.00 0.00 3.01
1784 1960 2.543037 TACCCTGTGCATCTGGAGTA 57.457 50.000 11.83 9.72 37.33 2.59
1870 2046 5.538082 TGTGGGGATGGGTTAGAAATTTA 57.462 39.130 0.00 0.00 0.00 1.40
1871 2047 4.412060 TGTGGGGATGGGTTAGAAATTT 57.588 40.909 0.00 0.00 0.00 1.82
1872 2048 4.093743 GTTGTGGGGATGGGTTAGAAATT 58.906 43.478 0.00 0.00 0.00 1.82
1873 2049 3.336694 AGTTGTGGGGATGGGTTAGAAAT 59.663 43.478 0.00 0.00 0.00 2.17
1874 2050 2.719705 AGTTGTGGGGATGGGTTAGAAA 59.280 45.455 0.00 0.00 0.00 2.52
1875 2051 2.354328 AGTTGTGGGGATGGGTTAGAA 58.646 47.619 0.00 0.00 0.00 2.10
1876 2052 2.053747 AGTTGTGGGGATGGGTTAGA 57.946 50.000 0.00 0.00 0.00 2.10
1877 2053 2.899303 AAGTTGTGGGGATGGGTTAG 57.101 50.000 0.00 0.00 0.00 2.34
1912 2088 9.982291 GTAGAGATTTTATTCAACGCACAAATA 57.018 29.630 0.00 0.00 0.00 1.40
1913 2089 8.511321 TGTAGAGATTTTATTCAACGCACAAAT 58.489 29.630 0.00 0.00 0.00 2.32
1942 2907 6.482524 AGCAAATATCTGATGGCTCATGTAT 58.517 36.000 0.00 0.00 0.00 2.29
1971 2936 4.804868 TTGCCATCATGTTTGCTACAAT 57.195 36.364 1.98 0.00 40.89 2.71
1974 2939 4.330620 CCAAATTGCCATCATGTTTGCTAC 59.669 41.667 1.98 0.00 31.95 3.58
1993 2958 2.015736 ATTGCACGTTGTTTGCCAAA 57.984 40.000 0.00 0.00 39.39 3.28
1994 2959 2.871182 TATTGCACGTTGTTTGCCAA 57.129 40.000 0.00 0.00 39.39 4.52
1995 2960 4.505313 TTATATTGCACGTTGTTTGCCA 57.495 36.364 0.00 0.00 39.39 4.92
1996 2961 7.513190 TTTATTATATTGCACGTTGTTTGCC 57.487 32.000 0.00 0.00 39.39 4.52
1997 2962 7.110511 GCTTTATTATATTGCACGTTGTTTGC 58.889 34.615 0.00 0.00 40.63 3.68
1998 2963 8.101510 GTGCTTTATTATATTGCACGTTGTTTG 58.898 33.333 11.89 0.00 43.19 2.93
1999 2964 8.168681 GTGCTTTATTATATTGCACGTTGTTT 57.831 30.769 11.89 0.00 43.19 2.83
2000 2965 7.734538 GTGCTTTATTATATTGCACGTTGTT 57.265 32.000 11.89 0.00 43.19 2.83
2009 2974 8.891671 ATTGCCTTTGGTGCTTTATTATATTG 57.108 30.769 0.00 0.00 0.00 1.90
2097 3062 4.021981 GTGAGGCTGAAAAGTTTAGGCAAT 60.022 41.667 12.86 0.00 39.24 3.56
2126 3091 7.251321 AGAACAACAACCTAGAGAGAATCAT 57.749 36.000 0.00 0.00 37.82 2.45
2216 4320 8.635328 TGGAGGTTTCTAAAATTAGGTTTTGAC 58.365 33.333 0.62 0.00 40.17 3.18
2297 4403 4.456911 TGGATCTGCAGACAAATGAAGTTC 59.543 41.667 20.97 8.34 0.00 3.01
2308 4414 7.067494 AGTGGTATTTTATTTGGATCTGCAGAC 59.933 37.037 20.97 12.88 0.00 3.51
2355 4461 1.468520 CATAACAAACTGTCCCGGCAG 59.531 52.381 7.47 7.47 41.92 4.85
2448 4561 9.902684 ATCAAGGGAATGATATCATTATCAGAC 57.097 33.333 26.97 15.15 45.59 3.51
2490 4605 3.001395 ACTCTGTCGTTCTTCTTGACG 57.999 47.619 0.00 0.00 35.40 4.35
2563 4678 4.160439 TGATGAACTGTGGAGAGGATACAC 59.840 45.833 0.00 0.00 41.41 2.90
2659 4798 4.274602 TGCTCCGGAAAACAATGTAGTA 57.725 40.909 5.23 0.00 0.00 1.82
2979 5157 3.091545 ACGGTCCGTCTTACATTTAGGA 58.908 45.455 12.23 0.00 33.69 2.94
2980 5158 3.515330 ACGGTCCGTCTTACATTTAGG 57.485 47.619 12.23 0.00 33.69 2.69
2992 5170 2.167075 CCCTAAATGTAAGACGGTCCGT 59.833 50.000 18.94 18.94 45.10 4.69
2993 5171 2.428171 TCCCTAAATGTAAGACGGTCCG 59.572 50.000 10.48 10.48 0.00 4.79
2994 5172 3.431346 GGTCCCTAAATGTAAGACGGTCC 60.431 52.174 4.14 0.00 0.00 4.46
2995 5173 3.431346 GGGTCCCTAAATGTAAGACGGTC 60.431 52.174 0.00 0.00 0.00 4.79
2996 5174 2.502947 GGGTCCCTAAATGTAAGACGGT 59.497 50.000 0.00 0.00 0.00 4.83
2997 5175 2.770232 AGGGTCCCTAAATGTAAGACGG 59.230 50.000 9.39 0.00 28.47 4.79
2998 5176 3.705072 AGAGGGTCCCTAAATGTAAGACG 59.295 47.826 11.58 0.00 31.76 4.18
2999 5177 4.470304 ACAGAGGGTCCCTAAATGTAAGAC 59.530 45.833 11.58 0.00 31.76 3.01
3000 5178 4.695606 ACAGAGGGTCCCTAAATGTAAGA 58.304 43.478 11.58 0.00 31.76 2.10
3001 5179 5.429130 GAACAGAGGGTCCCTAAATGTAAG 58.571 45.833 11.58 0.00 31.76 2.34
3002 5180 4.226620 GGAACAGAGGGTCCCTAAATGTAA 59.773 45.833 11.58 0.00 31.76 2.41
3003 5181 3.778629 GGAACAGAGGGTCCCTAAATGTA 59.221 47.826 11.58 0.00 31.76 2.29
3004 5182 2.576648 GGAACAGAGGGTCCCTAAATGT 59.423 50.000 11.58 13.43 31.76 2.71
3005 5183 2.846827 AGGAACAGAGGGTCCCTAAATG 59.153 50.000 11.58 12.75 31.76 2.32
3006 5184 3.222394 AGGAACAGAGGGTCCCTAAAT 57.778 47.619 11.58 0.00 31.76 1.40
3007 5185 2.735259 AGGAACAGAGGGTCCCTAAA 57.265 50.000 11.58 0.00 31.76 1.85
3008 5186 3.858696 TTAGGAACAGAGGGTCCCTAA 57.141 47.619 11.58 0.00 37.20 2.69
3009 5187 3.858696 TTTAGGAACAGAGGGTCCCTA 57.141 47.619 11.58 0.00 31.76 3.53
3010 5188 2.735259 TTTAGGAACAGAGGGTCCCT 57.265 50.000 11.38 11.38 36.03 4.20
3011 5189 2.576648 ACATTTAGGAACAGAGGGTCCC 59.423 50.000 0.00 0.00 0.00 4.46
3012 5190 5.189145 TCTTACATTTAGGAACAGAGGGTCC 59.811 44.000 0.00 0.00 0.00 4.46
3013 5191 6.107343 GTCTTACATTTAGGAACAGAGGGTC 58.893 44.000 0.00 0.00 0.00 4.46
3014 5192 5.337330 CGTCTTACATTTAGGAACAGAGGGT 60.337 44.000 0.00 0.00 0.00 4.34
3015 5193 5.109903 CGTCTTACATTTAGGAACAGAGGG 58.890 45.833 0.00 0.00 0.00 4.30
3016 5194 5.105473 TCCGTCTTACATTTAGGAACAGAGG 60.105 44.000 0.00 0.00 0.00 3.69
3017 5195 5.805994 GTCCGTCTTACATTTAGGAACAGAG 59.194 44.000 0.00 0.00 0.00 3.35
3018 5196 5.337009 GGTCCGTCTTACATTTAGGAACAGA 60.337 44.000 0.00 0.00 35.66 3.41
3019 5197 4.868734 GGTCCGTCTTACATTTAGGAACAG 59.131 45.833 0.00 0.00 35.66 3.16
3020 5198 4.618927 CGGTCCGTCTTACATTTAGGAACA 60.619 45.833 2.08 0.00 35.34 3.18
3021 5199 3.861689 CGGTCCGTCTTACATTTAGGAAC 59.138 47.826 2.08 0.00 32.48 3.62
3022 5200 3.511146 ACGGTCCGTCTTACATTTAGGAA 59.489 43.478 12.23 0.00 33.69 3.36
3103 5286 8.274322 TGATAATTCATAACCACTTGACTGGAT 58.726 33.333 0.00 0.00 35.04 3.41
3339 5530 3.715628 ACAGAAATTGTCACCTGTTGC 57.284 42.857 0.00 0.00 36.57 4.17
3543 5748 4.082949 AGCAATTAAGCGTGTTAGGTTTCC 60.083 41.667 0.00 0.00 40.15 3.13
3567 5772 5.128499 AGAACTCTCACTTCATACATCAGGG 59.872 44.000 0.00 0.00 0.00 4.45
3637 5842 2.930826 TCCTCACCTGGAAGTTGTTC 57.069 50.000 0.00 0.00 32.39 3.18
3680 5888 5.186797 TGCTTCCTTTCTTTTCTGTCCAAAA 59.813 36.000 0.00 0.00 0.00 2.44
3705 5913 4.142730 CCTTAACAGATGTGAGCTTCTTGC 60.143 45.833 0.00 0.00 43.29 4.01
3735 5943 1.204704 CACAGGCTCAATCAGACCGTA 59.795 52.381 0.00 0.00 0.00 4.02
3736 5944 0.036952 CACAGGCTCAATCAGACCGT 60.037 55.000 0.00 0.00 0.00 4.83
3737 5945 1.364626 GCACAGGCTCAATCAGACCG 61.365 60.000 0.00 0.00 36.96 4.79
3738 5946 2.475666 GCACAGGCTCAATCAGACC 58.524 57.895 0.00 0.00 36.96 3.85
3791 6031 6.132791 AGCATGAAATCTATGTTGCTTCTG 57.867 37.500 0.00 0.00 37.12 3.02
3838 6080 4.082679 AGTCGACCAAGACATAGACACTTC 60.083 45.833 13.01 0.00 43.24 3.01
4006 6258 3.045601 ACGAAGGACTGTTGATCCAAG 57.954 47.619 0.00 0.00 38.86 3.61
4008 6260 3.181490 CGATACGAAGGACTGTTGATCCA 60.181 47.826 0.00 0.00 38.86 3.41
4009 6261 3.066342 TCGATACGAAGGACTGTTGATCC 59.934 47.826 0.00 0.00 36.38 3.36
4016 6268 5.676532 ATCTAAGTCGATACGAAGGACTG 57.323 43.478 0.00 0.00 40.67 3.51
4017 6269 8.934825 GTTATATCTAAGTCGATACGAAGGACT 58.065 37.037 0.00 0.00 42.52 3.85
4056 6309 2.359900 CGGGTTTGCTAATTCTCAGCT 58.640 47.619 0.69 0.00 39.83 4.24
4154 6409 1.925185 CTGATGTCAGATGTGCGAGTG 59.075 52.381 3.96 0.00 46.59 3.51
4231 6493 7.746929 CAGATTTCTCTGTCATGTTAAGGAAC 58.253 38.462 0.00 0.00 43.35 3.62
4248 6520 7.607250 ACTTACGATGAAGAGAACAGATTTCT 58.393 34.615 0.00 0.00 0.00 2.52
4276 6548 3.043586 CTGGTGCGACGTATCTTATGAC 58.956 50.000 0.00 0.00 0.00 3.06
4288 6560 1.862806 GAAGTGCTTCTGGTGCGAC 59.137 57.895 4.80 0.00 36.69 5.19
4329 6601 6.737254 TTTTAAAGAATGGTGATCCGAGAC 57.263 37.500 0.00 0.00 36.30 3.36
4373 6652 6.094881 TGAGTCGGAGAAAACAAAAGAACATT 59.905 34.615 0.00 0.00 39.69 2.71
4380 6659 4.024048 GCTGATGAGTCGGAGAAAACAAAA 60.024 41.667 0.00 0.00 39.69 2.44
4552 6842 9.731819 GTCGATTCATCTACAATAGAAGTTACA 57.268 33.333 0.00 0.00 38.50 2.41
4553 6843 9.731819 TGTCGATTCATCTACAATAGAAGTTAC 57.268 33.333 0.00 0.00 38.50 2.50
4576 6881 6.823678 AAAACCGATTATAGATGACGTGTC 57.176 37.500 0.00 0.00 0.00 3.67
4603 6908 4.202367 ACCAAGTTTACCTGTTGGAGAGAG 60.202 45.833 7.32 0.00 43.01 3.20
4609 6915 3.304190 GCGTAACCAAGTTTACCTGTTGG 60.304 47.826 0.00 0.00 45.39 3.77
4613 6919 2.774687 AGGCGTAACCAAGTTTACCTG 58.225 47.619 0.00 0.00 43.14 4.00


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

AutoCloner maintained by Alex Coulton.