Multiple sequence alignment - TraesCS4A01G036400

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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 TraesCS4A01G036400 chr4A 100.000 2940 0 0 996 3935 29063322 29060383 0.000000e+00 5430
1 TraesCS4A01G036400 chr4A 100.000 655 0 0 1 655 29064317 29063663 0.000000e+00 1210
2 TraesCS4A01G036400 chr4D 92.151 2497 121 34 996 3473 439752952 439750512 0.000000e+00 3456
3 TraesCS4A01G036400 chr4D 79.464 672 100 24 1 655 439753733 439753083 3.610000e-120 442
4 TraesCS4A01G036400 chr4B 89.017 2786 198 51 996 3709 544297415 544294666 0.000000e+00 3350
5 TraesCS4A01G036400 chr4B 88.591 298 25 8 360 655 544297832 544297542 1.740000e-93 353
6 TraesCS4A01G036400 chr4B 94.845 97 3 2 3782 3878 544294387 544294293 2.450000e-32 150


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 TraesCS4A01G036400 chr4A 29060383 29064317 3934 True 3320.000000 5430 100.000000 1 3935 2 chr4A.!!$R1 3934
1 TraesCS4A01G036400 chr4D 439750512 439753733 3221 True 1949.000000 3456 85.807500 1 3473 2 chr4D.!!$R1 3472
2 TraesCS4A01G036400 chr4B 544294293 544297832 3539 True 1284.333333 3350 90.817667 360 3878 3 chr4B.!!$R1 3518

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
275 291 0.178944 TCAGGTTTCGGTCCTCTCCA 60.179 55.0 0.00 0.0 32.37 3.86 F
399 415 0.179215 CAAACGAGCGCAGAATCCAC 60.179 55.0 11.47 0.0 0.00 4.02 F
1426 1459 0.107848 CGTATGGGGGTTGTCTGTCC 60.108 60.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1441 0.255033 GGGACAGACAACCCCCATAC 59.745 60.000 0.0 0.0 40.19 2.39 R
1961 2026 1.202348 GCCCTGAATGCAGTAACCAAC 59.798 52.381 0.0 0.0 40.63 3.77 R
3292 3360 0.106519 ACCAAGCACTTCCACAAGCT 60.107 50.000 0.0 0.0 39.37 3.74 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.795085 GAGTCGGCTCATGCATATGC 59.205 55.000 21.09 21.09 41.29 3.14
58 59 0.321919 CATGCATATGCGGCTAGGGT 60.322 55.000 22.21 0.00 45.83 4.34
70 71 2.036089 CGGCTAGGGTGAAGTTATCCTC 59.964 54.545 0.00 0.00 32.21 3.71
71 72 2.369203 GGCTAGGGTGAAGTTATCCTCC 59.631 54.545 0.00 0.00 32.21 4.30
72 73 2.369203 GCTAGGGTGAAGTTATCCTCCC 59.631 54.545 0.00 0.00 39.83 4.30
75 76 1.769465 GGGTGAAGTTATCCTCCCCTC 59.231 57.143 0.00 0.00 36.06 4.30
86 87 2.610859 TCCCCTCCAAGCTCCACC 60.611 66.667 0.00 0.00 0.00 4.61
88 89 4.785453 CCCTCCAAGCTCCACCGC 62.785 72.222 0.00 0.00 0.00 5.68
90 91 2.125350 CTCCAAGCTCCACCGCTC 60.125 66.667 0.00 0.00 39.86 5.03
91 92 3.672295 CTCCAAGCTCCACCGCTCC 62.672 68.421 0.00 0.00 39.86 4.70
92 93 3.710722 CCAAGCTCCACCGCTCCT 61.711 66.667 0.00 0.00 39.86 3.69
94 95 3.394836 AAGCTCCACCGCTCCTCC 61.395 66.667 0.00 0.00 39.86 4.30
97 98 3.003173 CTCCACCGCTCCTCCCAA 61.003 66.667 0.00 0.00 0.00 4.12
115 116 2.648059 CAAGGATTTGCTACCCCTCTG 58.352 52.381 0.00 0.00 0.00 3.35
118 119 1.840635 GGATTTGCTACCCCTCTGTCT 59.159 52.381 0.00 0.00 0.00 3.41
125 126 4.154347 CCCCTCTGTCTGCCGCTC 62.154 72.222 0.00 0.00 0.00 5.03
130 131 4.056125 CTGTCTGCCGCTCCGACA 62.056 66.667 9.34 9.34 36.37 4.35
131 132 3.978723 CTGTCTGCCGCTCCGACAG 62.979 68.421 17.41 17.41 45.75 3.51
132 133 4.057428 GTCTGCCGCTCCGACAGT 62.057 66.667 1.20 0.00 38.43 3.55
135 136 4.680237 TGCCGCTCCGACAGTTGG 62.680 66.667 0.00 0.00 0.00 3.77
140 141 2.425592 CTCCGACAGTTGGTGGCA 59.574 61.111 6.73 0.00 30.77 4.92
143 144 2.334946 CCGACAGTTGGTGGCATGG 61.335 63.158 0.00 0.00 30.77 3.66
150 151 2.166346 TTGGTGGCATGGAGGGGAA 61.166 57.895 0.00 0.00 0.00 3.97
153 154 1.152673 GTGGCATGGAGGGGAATCC 60.153 63.158 0.00 0.00 40.03 3.01
162 163 3.739613 GGGGAATCCCGGTGCCTT 61.740 66.667 12.94 0.00 46.66 4.35
164 165 3.140814 GGAATCCCGGTGCCTTGC 61.141 66.667 0.00 0.00 0.00 4.01
177 178 1.144913 TGCCTTGCCTCCAGTTAGTTT 59.855 47.619 0.00 0.00 0.00 2.66
178 179 1.813178 GCCTTGCCTCCAGTTAGTTTC 59.187 52.381 0.00 0.00 0.00 2.78
183 185 2.835764 TGCCTCCAGTTAGTTTCGGTAT 59.164 45.455 0.00 0.00 0.00 2.73
222 224 1.967535 CAGAGAGAGGCGGTGTTCA 59.032 57.895 0.00 0.00 0.00 3.18
226 228 0.251653 AGAGAGGCGGTGTTCAGGTA 60.252 55.000 0.00 0.00 0.00 3.08
231 233 0.462047 GGCGGTGTTCAGGTAGATGG 60.462 60.000 0.00 0.00 0.00 3.51
232 234 1.090052 GCGGTGTTCAGGTAGATGGC 61.090 60.000 0.00 0.00 0.00 4.40
233 235 0.806102 CGGTGTTCAGGTAGATGGCG 60.806 60.000 0.00 0.00 0.00 5.69
234 236 1.090052 GGTGTTCAGGTAGATGGCGC 61.090 60.000 0.00 0.00 0.00 6.53
245 261 0.813184 AGATGGCGCCACTTCATTTG 59.187 50.000 35.50 0.00 0.00 2.32
247 263 1.202114 GATGGCGCCACTTCATTTGAA 59.798 47.619 35.50 3.63 0.00 2.69
248 264 0.313672 TGGCGCCACTTCATTTGAAC 59.686 50.000 29.03 0.00 0.00 3.18
258 274 5.067674 CCACTTCATTTGAACTGGTCTTTCA 59.932 40.000 9.54 0.00 35.00 2.69
264 280 5.576447 TTTGAACTGGTCTTTCAGGTTTC 57.424 39.130 0.00 0.00 38.98 2.78
266 282 2.256117 ACTGGTCTTTCAGGTTTCGG 57.744 50.000 0.00 0.00 38.98 4.30
271 287 2.414806 GTCTTTCAGGTTTCGGTCCTC 58.585 52.381 0.00 0.00 32.37 3.71
273 289 2.299297 TCTTTCAGGTTTCGGTCCTCTC 59.701 50.000 0.00 0.00 32.37 3.20
274 290 0.974383 TTCAGGTTTCGGTCCTCTCC 59.026 55.000 0.00 0.00 32.37 3.71
275 291 0.178944 TCAGGTTTCGGTCCTCTCCA 60.179 55.000 0.00 0.00 32.37 3.86
286 302 2.092914 GGTCCTCTCCAAATTCGTCCAT 60.093 50.000 0.00 0.00 0.00 3.41
287 303 2.939103 GTCCTCTCCAAATTCGTCCATG 59.061 50.000 0.00 0.00 0.00 3.66
295 311 7.735917 TCTCCAAATTCGTCCATGACTTATAT 58.264 34.615 0.00 0.00 0.00 0.86
297 313 7.505258 TCCAAATTCGTCCATGACTTATATGA 58.495 34.615 0.00 0.00 0.00 2.15
301 317 8.908786 AATTCGTCCATGACTTATATGACAAT 57.091 30.769 0.00 0.00 0.00 2.71
305 321 6.146184 CGTCCATGACTTATATGACAATGGTC 59.854 42.308 0.00 0.00 44.57 4.02
332 348 9.986833 AACATTTTCATAAAACTTTTGAAGTGC 57.013 25.926 0.00 0.00 41.91 4.40
342 358 7.552458 AAACTTTTGAAGTGCTTATTTTGGG 57.448 32.000 0.00 0.00 41.91 4.12
343 359 6.478512 ACTTTTGAAGTGCTTATTTTGGGA 57.521 33.333 0.00 0.00 41.01 4.37
344 360 6.883744 ACTTTTGAAGTGCTTATTTTGGGAA 58.116 32.000 0.00 0.00 41.01 3.97
345 361 7.334858 ACTTTTGAAGTGCTTATTTTGGGAAA 58.665 30.769 0.00 0.00 41.01 3.13
347 363 9.487790 CTTTTGAAGTGCTTATTTTGGGAAATA 57.512 29.630 0.00 0.00 36.82 1.40
348 364 9.838339 TTTTGAAGTGCTTATTTTGGGAAATAA 57.162 25.926 4.76 4.76 42.49 1.40
349 365 9.838339 TTTGAAGTGCTTATTTTGGGAAATAAA 57.162 25.926 5.99 0.00 43.47 1.40
389 405 2.425773 GTGCAGTGCAAACGAGCG 60.426 61.111 21.67 0.00 41.47 5.03
399 415 0.179215 CAAACGAGCGCAGAATCCAC 60.179 55.000 11.47 0.00 0.00 4.02
400 416 0.320771 AAACGAGCGCAGAATCCACT 60.321 50.000 11.47 0.00 0.00 4.00
411 427 3.768406 CAGAATCCACTCTCTCTCGTTG 58.232 50.000 0.00 0.00 0.00 4.10
435 451 4.470664 TGCAAGCAATCCCTTATCCATTTT 59.529 37.500 0.00 0.00 0.00 1.82
436 452 4.812626 GCAAGCAATCCCTTATCCATTTTG 59.187 41.667 0.00 0.00 0.00 2.44
510 527 1.676006 CAGCCGAACCTTGTTTTGTCT 59.324 47.619 0.00 0.00 0.00 3.41
515 532 3.303791 CCGAACCTTGTTTTGTCTGTAGC 60.304 47.826 0.00 0.00 0.00 3.58
516 533 3.311322 CGAACCTTGTTTTGTCTGTAGCA 59.689 43.478 0.00 0.00 0.00 3.49
573 590 1.591594 CAATCCGGACCGTCCATCG 60.592 63.158 17.87 3.69 35.91 3.84
579 596 2.509336 GACCGTCCATCGCCACAG 60.509 66.667 0.00 0.00 38.35 3.66
584 601 2.100631 GTCCATCGCCACAGAACCG 61.101 63.158 0.00 0.00 0.00 4.44
614 631 4.222847 GCCACGATCCGTCCTCCC 62.223 72.222 0.00 0.00 38.32 4.30
636 653 1.228124 CCTGTGGCCACGGAAAAGA 60.228 57.895 40.70 17.35 40.06 2.52
1201 1224 1.765657 GAGCAGCCCCTGGATCTCT 60.766 63.158 0.00 0.00 31.21 3.10
1206 1229 2.447714 GCCCCTGGATCTCTCCACC 61.448 68.421 0.00 0.00 46.95 4.61
1261 1286 2.672996 ATGTTGCCCGAGCGCTTT 60.673 55.556 13.26 0.00 44.31 3.51
1274 1299 2.486966 GCTTTGACCAGCGATGCC 59.513 61.111 0.00 0.00 0.00 4.40
1319 1344 5.791666 TGAGAGATGAGTGATATTGATGCC 58.208 41.667 0.00 0.00 0.00 4.40
1325 1350 0.944386 GTGATATTGATGCCGCGGTT 59.056 50.000 28.70 15.31 0.00 4.44
1332 1357 3.267597 GATGCCGCGGTTGCTGTTT 62.268 57.895 28.70 2.40 39.65 2.83
1339 1364 1.082756 CGGTTGCTGTTTCGTGCTC 60.083 57.895 0.00 0.00 0.00 4.26
1365 1398 3.458487 GAGATGGTAGTTGGTAATGGGGT 59.542 47.826 0.00 0.00 0.00 4.95
1408 1441 3.163594 GGCAGAATGTCGATTTGTTTCG 58.836 45.455 0.00 0.00 39.31 3.46
1411 1444 5.447279 GGCAGAATGTCGATTTGTTTCGTAT 60.447 40.000 0.00 0.00 39.31 3.06
1416 1449 2.353579 GTCGATTTGTTTCGTATGGGGG 59.646 50.000 0.00 0.00 40.03 5.40
1418 1451 2.750712 CGATTTGTTTCGTATGGGGGTT 59.249 45.455 0.00 0.00 34.46 4.11
1419 1452 3.426963 CGATTTGTTTCGTATGGGGGTTG 60.427 47.826 0.00 0.00 34.46 3.77
1420 1453 2.660670 TTGTTTCGTATGGGGGTTGT 57.339 45.000 0.00 0.00 0.00 3.32
1421 1454 2.188062 TGTTTCGTATGGGGGTTGTC 57.812 50.000 0.00 0.00 0.00 3.18
1422 1455 1.700739 TGTTTCGTATGGGGGTTGTCT 59.299 47.619 0.00 0.00 0.00 3.41
1423 1456 2.081462 GTTTCGTATGGGGGTTGTCTG 58.919 52.381 0.00 0.00 0.00 3.51
1424 1457 1.354101 TTCGTATGGGGGTTGTCTGT 58.646 50.000 0.00 0.00 0.00 3.41
1425 1458 0.899720 TCGTATGGGGGTTGTCTGTC 59.100 55.000 0.00 0.00 0.00 3.51
1426 1459 0.107848 CGTATGGGGGTTGTCTGTCC 60.108 60.000 0.00 0.00 0.00 4.02
1443 1476 2.562738 TGTCCCTGTACTGATCTGTGTG 59.437 50.000 14.91 5.29 0.00 3.82
1444 1477 2.563179 GTCCCTGTACTGATCTGTGTGT 59.437 50.000 14.91 0.00 0.00 3.72
1484 1518 2.444624 CGGGTTCGATCTGCGTGTG 61.445 63.158 0.00 0.00 41.80 3.82
1485 1519 2.740714 GGGTTCGATCTGCGTGTGC 61.741 63.158 0.00 0.00 41.80 4.57
1580 1614 1.079405 CGGTAACATGGTGCCTCGT 60.079 57.895 16.42 0.00 0.00 4.18
1592 1626 4.477975 CCTCGTCGAGTCACCGCC 62.478 72.222 20.37 0.00 0.00 6.13
1666 1716 6.086222 GTCATACTAAACAGCAACATGTTGG 58.914 40.000 33.56 22.62 42.49 3.77
1676 1732 3.957497 AGCAACATGTTGGTCCTTGTTAA 59.043 39.130 32.03 0.00 47.00 2.01
1692 1748 9.626045 GTCCTTGTTAATAAAACTGAAATGGAG 57.374 33.333 0.00 0.00 0.00 3.86
1713 1769 2.611292 GCTTCATTTCGGGACTGAGATG 59.389 50.000 5.54 5.54 33.11 2.90
1714 1770 3.866651 CTTCATTTCGGGACTGAGATGT 58.133 45.455 10.37 0.00 33.47 3.06
1715 1771 3.981071 TCATTTCGGGACTGAGATGTT 57.019 42.857 10.37 0.00 33.47 2.71
1756 1812 3.677601 CTGTTATTCAGTGCGCATGAAG 58.322 45.455 27.13 16.56 39.86 3.02
1782 1839 7.004555 TGTTAATGATATATGCCGTCCTTCT 57.995 36.000 0.00 0.00 0.00 2.85
1783 1840 8.129496 TGTTAATGATATATGCCGTCCTTCTA 57.871 34.615 0.00 0.00 0.00 2.10
1812 1869 7.771183 TCCATGGAAATAACTTTGTGCTATTC 58.229 34.615 13.46 0.00 0.00 1.75
1884 1941 3.003394 TGAATGGGTAGCTGGAATGTG 57.997 47.619 0.00 0.00 0.00 3.21
1960 2025 9.884636 TGTATATTAAACAGTCATGCTTACACT 57.115 29.630 0.00 0.00 0.00 3.55
1977 2042 3.550820 ACACTGTTGGTTACTGCATTCA 58.449 40.909 0.00 0.00 0.00 2.57
2002 2067 8.868916 CAGGGCAATAACAATTTTATTGTGTAC 58.131 33.333 21.21 14.48 41.80 2.90
2125 2190 6.571731 GCACCGTATAGGAGTATATTTGAGCA 60.572 42.308 0.00 0.00 45.00 4.26
2131 2196 9.804758 GTATAGGAGTATATTTGAGCACCATAC 57.195 37.037 0.00 0.00 0.00 2.39
2138 2203 9.060347 AGTATATTTGAGCACCATACTCATTTG 57.940 33.333 0.00 0.00 43.40 2.32
2154 2219 4.890088 TCATTTGTACCACTGTACTCACC 58.110 43.478 4.68 0.00 46.19 4.02
2155 2220 4.345547 TCATTTGTACCACTGTACTCACCA 59.654 41.667 4.68 0.00 46.19 4.17
2163 2228 3.997021 CCACTGTACTCACCAAAAGCTAG 59.003 47.826 0.00 0.00 0.00 3.42
2210 2275 4.884668 TTGTATCCTGGGAATATCGACC 57.115 45.455 0.00 0.00 0.00 4.79
2260 2325 9.283768 TGCGGATTCAAGTTTATTCATGTATAT 57.716 29.630 0.00 0.00 0.00 0.86
2300 2365 3.066621 TCCTGGCGTCATCAATATTTTGC 59.933 43.478 0.00 0.00 32.61 3.68
2304 2369 3.182972 GGCGTCATCAATATTTTGCATGC 59.817 43.478 11.82 11.82 32.61 4.06
2329 2394 6.071447 CCATCCTCATGTGTGTTAAATTTGGA 60.071 38.462 0.00 0.00 0.00 3.53
2347 2412 2.951642 TGGACAGAAGAGGCAACAAAAG 59.048 45.455 0.00 0.00 41.41 2.27
2361 2426 3.275617 ACAAAAGGGAAAAGGCAAACC 57.724 42.857 0.00 0.00 0.00 3.27
2458 2523 9.573133 GCAGCTACAAATGTAAATGTTTCTTAT 57.427 29.630 0.00 0.00 0.00 1.73
2526 2591 3.430929 GCGGTATTATCTATCAGGGCCTG 60.431 52.174 28.01 28.01 0.00 4.85
2844 2909 2.203294 GTTCCGTTGCTGTGGGGT 60.203 61.111 0.00 0.00 0.00 4.95
2947 3012 1.199615 GTTCTAAGAGCCCAGAGCCT 58.800 55.000 0.00 0.00 45.47 4.58
2948 3013 1.134551 GTTCTAAGAGCCCAGAGCCTG 60.135 57.143 0.00 0.00 45.47 4.85
2955 3020 2.996395 CCCAGAGCCTGCAGACAT 59.004 61.111 17.39 0.00 0.00 3.06
3019 3084 3.899981 TAACTGGCCTGGCTGCACG 62.900 63.158 19.68 5.27 0.00 5.34
3066 3131 3.286751 TCCTTGTGCGCAACCAGC 61.287 61.111 14.00 0.00 40.87 4.85
3067 3132 3.594775 CCTTGTGCGCAACCAGCA 61.595 61.111 14.00 1.50 46.13 4.41
3068 3133 2.412525 CTTGTGCGCAACCAGCAA 59.587 55.556 14.00 11.23 46.97 3.91
3207 3275 2.165167 CATTGGCATCTGGAGTTGTGT 58.835 47.619 0.00 0.00 0.00 3.72
3282 3350 3.256704 ACCTGGAGATTTGAGGTAACCA 58.743 45.455 0.00 0.00 38.38 3.67
3292 3360 4.835284 TTGAGGTAACCATGAGCACATA 57.165 40.909 0.00 0.00 35.09 2.29
3308 3376 3.146104 ACATAGCTTGTGGAAGTGCTT 57.854 42.857 0.00 0.00 37.11 3.91
3309 3377 2.816087 ACATAGCTTGTGGAAGTGCTTG 59.184 45.455 0.00 0.00 37.11 4.01
3310 3378 1.896220 TAGCTTGTGGAAGTGCTTGG 58.104 50.000 0.00 0.00 37.02 3.61
3311 3379 0.106519 AGCTTGTGGAAGTGCTTGGT 60.107 50.000 0.00 0.00 30.96 3.67
3312 3380 0.312102 GCTTGTGGAAGTGCTTGGTC 59.688 55.000 0.00 0.00 0.00 4.02
3313 3381 1.679139 CTTGTGGAAGTGCTTGGTCA 58.321 50.000 0.00 0.00 0.00 4.02
3314 3382 1.605710 CTTGTGGAAGTGCTTGGTCAG 59.394 52.381 0.00 0.00 0.00 3.51
3315 3383 0.546122 TGTGGAAGTGCTTGGTCAGT 59.454 50.000 0.00 0.00 0.00 3.41
3326 3394 2.291741 GCTTGGTCAGTTGGTCTTGAAG 59.708 50.000 0.00 0.00 0.00 3.02
3328 3396 3.194005 TGGTCAGTTGGTCTTGAAGAC 57.806 47.619 16.70 16.70 44.32 3.01
3356 3424 6.051717 GGTGACAACTCAGATGCAGTATTAT 58.948 40.000 0.00 0.00 0.00 1.28
3416 3485 4.081087 TGGGAAACTAGGCACTACTCATTC 60.081 45.833 0.00 0.00 41.75 2.67
3464 3533 0.319297 CTTTTGCCAGCCTGACAAGC 60.319 55.000 0.00 0.00 0.00 4.01
3487 3581 7.114095 AGCAGATGATTAAAATGGGCATTTTT 58.886 30.769 0.39 7.21 45.67 1.94
3510 3604 1.834263 AGTGGGCATCTGACCTAGTTC 59.166 52.381 3.24 0.00 45.91 3.01
3518 3612 5.510520 GGCATCTGACCTAGTTCCATTAGAG 60.511 48.000 0.00 0.00 0.00 2.43
3520 3614 6.737346 GCATCTGACCTAGTTCCATTAGAGTC 60.737 46.154 0.00 0.00 0.00 3.36
3533 3627 9.941664 GTTCCATTAGAGTCATCAAAATACATG 57.058 33.333 0.00 0.00 0.00 3.21
3659 3760 5.941948 AGTAATTTGGAACGGAAGAAGTG 57.058 39.130 0.00 0.00 0.00 3.16
3664 3765 3.116079 TGGAACGGAAGAAGTGGTAAC 57.884 47.619 0.00 0.00 0.00 2.50
3670 3771 3.125316 CGGAAGAAGTGGTAACGTTTGA 58.875 45.455 5.91 0.00 42.51 2.69
3673 3774 4.514066 GGAAGAAGTGGTAACGTTTGATGT 59.486 41.667 5.91 0.00 42.51 3.06
3674 3775 5.418310 AAGAAGTGGTAACGTTTGATGTG 57.582 39.130 5.91 0.00 42.51 3.21
3695 3800 0.168788 CGGCTGCGACAATCAAACAT 59.831 50.000 0.00 0.00 0.00 2.71
3702 3807 4.793071 TGCGACAATCAAACATAAAGTGG 58.207 39.130 0.00 0.00 0.00 4.00
3703 3808 4.517075 TGCGACAATCAAACATAAAGTGGA 59.483 37.500 0.00 0.00 0.00 4.02
3713 3992 9.965824 ATCAAACATAAAGTGGAAGTAAAACTG 57.034 29.630 0.00 0.00 0.00 3.16
3725 4004 3.690460 AGTAAAACTGGCAAGAGGATGG 58.310 45.455 0.00 0.00 0.00 3.51
3734 4013 0.109132 CAAGAGGATGGCGTTTTGGC 60.109 55.000 0.00 0.00 45.12 4.52
3762 4041 2.433604 ACTCATCTACACCTGCCATGAG 59.566 50.000 0.00 5.82 44.10 2.90
3808 4119 0.598562 CGAGTGTGCTAGGAGTGTGT 59.401 55.000 0.00 0.00 0.00 3.72
3813 4124 5.221067 CGAGTGTGCTAGGAGTGTGTATAAT 60.221 44.000 0.00 0.00 0.00 1.28
3819 4130 8.046708 TGTGCTAGGAGTGTGTATAATTTGAAT 58.953 33.333 0.00 0.00 0.00 2.57
3885 4196 3.599412 TTCGAAAGAAGGGACGTGG 57.401 52.632 0.00 0.00 46.92 4.94
3886 4197 1.042229 TTCGAAAGAAGGGACGTGGA 58.958 50.000 0.00 0.00 46.92 4.02
3887 4198 0.601558 TCGAAAGAAGGGACGTGGAG 59.398 55.000 0.00 0.00 37.03 3.86
3888 4199 0.317479 CGAAAGAAGGGACGTGGAGT 59.683 55.000 0.00 0.00 0.00 3.85
3889 4200 1.542915 CGAAAGAAGGGACGTGGAGTA 59.457 52.381 0.00 0.00 0.00 2.59
3890 4201 2.165845 CGAAAGAAGGGACGTGGAGTAT 59.834 50.000 0.00 0.00 0.00 2.12
3891 4202 3.734293 CGAAAGAAGGGACGTGGAGTATC 60.734 52.174 0.00 0.00 0.00 2.24
3892 4203 2.830651 AGAAGGGACGTGGAGTATCT 57.169 50.000 0.00 0.00 33.73 1.98
3893 4204 2.379972 AGAAGGGACGTGGAGTATCTG 58.620 52.381 0.00 0.00 33.73 2.90
3894 4205 0.824759 AAGGGACGTGGAGTATCTGC 59.175 55.000 0.00 0.00 33.73 4.26
3895 4206 0.033011 AGGGACGTGGAGTATCTGCT 60.033 55.000 0.00 0.00 33.73 4.24
3896 4207 0.386113 GGGACGTGGAGTATCTGCTC 59.614 60.000 0.00 0.00 33.73 4.26
3906 4217 3.988819 GAGTATCTGCTCCCTCATGAAC 58.011 50.000 0.00 0.00 0.00 3.18
3907 4218 3.378512 AGTATCTGCTCCCTCATGAACA 58.621 45.455 0.00 0.00 0.00 3.18
3908 4219 3.387374 AGTATCTGCTCCCTCATGAACAG 59.613 47.826 0.00 0.27 31.24 3.16
3909 4220 1.649321 TCTGCTCCCTCATGAACAGT 58.351 50.000 0.00 0.00 31.80 3.55
3910 4221 2.820178 TCTGCTCCCTCATGAACAGTA 58.180 47.619 0.00 0.00 31.80 2.74
3911 4222 3.173151 TCTGCTCCCTCATGAACAGTAA 58.827 45.455 0.00 0.00 31.80 2.24
3912 4223 3.582647 TCTGCTCCCTCATGAACAGTAAA 59.417 43.478 0.00 0.00 31.80 2.01
3913 4224 4.041567 TCTGCTCCCTCATGAACAGTAAAA 59.958 41.667 0.00 0.00 31.80 1.52
3914 4225 4.724399 TGCTCCCTCATGAACAGTAAAAA 58.276 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.152023 ACTCAACTAGAAGAAATAACTGGGAT 57.848 34.615 0.00 0.00 0.00 3.85
11 12 6.531948 CCGACTCAACTAGAAGAAATAACTGG 59.468 42.308 0.00 0.00 0.00 4.00
41 42 1.071299 CACCCTAGCCGCATATGCA 59.929 57.895 26.52 6.89 42.21 3.96
47 48 1.138266 GATAACTTCACCCTAGCCGCA 59.862 52.381 0.00 0.00 0.00 5.69
49 50 2.036089 GAGGATAACTTCACCCTAGCCG 59.964 54.545 0.00 0.00 0.00 5.52
58 59 2.961536 TGGAGGGGAGGATAACTTCA 57.038 50.000 0.00 0.00 0.00 3.02
70 71 4.101448 CGGTGGAGCTTGGAGGGG 62.101 72.222 0.00 0.00 0.00 4.79
71 72 4.785453 GCGGTGGAGCTTGGAGGG 62.785 72.222 0.00 0.00 0.00 4.30
72 73 3.710722 AGCGGTGGAGCTTGGAGG 61.711 66.667 0.00 0.00 46.80 4.30
90 91 1.410224 GGGTAGCAAATCCTTGGGAGG 60.410 57.143 0.00 0.00 45.02 4.30
91 92 1.410224 GGGGTAGCAAATCCTTGGGAG 60.410 57.143 0.00 0.00 34.05 4.30
92 93 0.629058 GGGGTAGCAAATCCTTGGGA 59.371 55.000 0.00 0.00 35.55 4.37
94 95 1.566231 AGAGGGGTAGCAAATCCTTGG 59.434 52.381 0.00 0.00 32.76 3.61
95 96 2.025887 ACAGAGGGGTAGCAAATCCTTG 60.026 50.000 0.00 0.00 35.49 3.61
96 97 2.239907 GACAGAGGGGTAGCAAATCCTT 59.760 50.000 0.00 0.00 0.00 3.36
97 98 1.840635 GACAGAGGGGTAGCAAATCCT 59.159 52.381 0.00 0.00 0.00 3.24
103 104 1.990060 GGCAGACAGAGGGGTAGCA 60.990 63.158 0.00 0.00 0.00 3.49
105 106 3.082579 GCGGCAGACAGAGGGGTAG 62.083 68.421 0.00 0.00 0.00 3.18
106 107 3.075005 GCGGCAGACAGAGGGGTA 61.075 66.667 0.00 0.00 0.00 3.69
118 119 4.680237 CCAACTGTCGGAGCGGCA 62.680 66.667 1.45 0.00 39.83 5.69
125 126 2.334946 CCATGCCACCAACTGTCGG 61.335 63.158 0.00 0.00 0.00 4.79
130 131 2.765969 CCCTCCATGCCACCAACT 59.234 61.111 0.00 0.00 0.00 3.16
131 132 2.362889 CCCCTCCATGCCACCAAC 60.363 66.667 0.00 0.00 0.00 3.77
132 133 1.517538 ATTCCCCTCCATGCCACCAA 61.518 55.000 0.00 0.00 0.00 3.67
135 136 1.152673 GGATTCCCCTCCATGCCAC 60.153 63.158 0.00 0.00 35.24 5.01
150 151 4.115199 GAGGCAAGGCACCGGGAT 62.115 66.667 6.32 0.00 0.00 3.85
154 155 2.463589 TAACTGGAGGCAAGGCACCG 62.464 60.000 5.70 3.70 31.52 4.94
159 160 2.076863 CGAAACTAACTGGAGGCAAGG 58.923 52.381 0.00 0.00 0.00 3.61
162 163 1.053424 ACCGAAACTAACTGGAGGCA 58.947 50.000 0.00 0.00 0.00 4.75
164 165 4.467198 ACATACCGAAACTAACTGGAGG 57.533 45.455 0.00 0.00 0.00 4.30
190 192 4.322080 TCTCTCTGCGAGAACTGAAAAA 57.678 40.909 9.08 0.00 45.55 1.94
206 208 1.216710 CCTGAACACCGCCTCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
207 209 0.251653 TACCTGAACACCGCCTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
208 210 0.173708 CTACCTGAACACCGCCTCTC 59.826 60.000 0.00 0.00 0.00 3.20
209 211 0.251653 TCTACCTGAACACCGCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
210 212 0.824759 ATCTACCTGAACACCGCCTC 59.175 55.000 0.00 0.00 0.00 4.70
211 213 0.537188 CATCTACCTGAACACCGCCT 59.463 55.000 0.00 0.00 0.00 5.52
215 217 1.090052 GCGCCATCTACCTGAACACC 61.090 60.000 0.00 0.00 0.00 4.16
216 218 1.090052 GGCGCCATCTACCTGAACAC 61.090 60.000 24.80 0.00 0.00 3.32
217 219 1.220749 GGCGCCATCTACCTGAACA 59.779 57.895 24.80 0.00 0.00 3.18
222 224 1.264749 TGAAGTGGCGCCATCTACCT 61.265 55.000 35.23 21.98 0.00 3.08
226 228 0.813184 CAAATGAAGTGGCGCCATCT 59.187 50.000 35.23 26.92 0.00 2.90
231 233 1.689959 CAGTTCAAATGAAGTGGCGC 58.310 50.000 18.90 0.00 46.46 6.53
245 261 2.548480 CCGAAACCTGAAAGACCAGTTC 59.452 50.000 0.00 0.00 34.07 3.01
247 263 1.489230 ACCGAAACCTGAAAGACCAGT 59.511 47.619 0.00 0.00 34.07 4.00
248 264 2.143925 GACCGAAACCTGAAAGACCAG 58.856 52.381 0.00 0.00 34.07 4.00
258 274 1.430992 TTTGGAGAGGACCGAAACCT 58.569 50.000 0.00 0.00 40.80 3.50
264 280 1.641577 GACGAATTTGGAGAGGACCG 58.358 55.000 0.00 0.00 0.00 4.79
266 282 2.762535 TGGACGAATTTGGAGAGGAC 57.237 50.000 0.00 0.00 0.00 3.85
271 287 7.657354 TCATATAAGTCATGGACGAATTTGGAG 59.343 37.037 0.00 0.00 37.67 3.86
273 289 7.226523 TGTCATATAAGTCATGGACGAATTTGG 59.773 37.037 0.00 0.00 37.67 3.28
274 290 8.141835 TGTCATATAAGTCATGGACGAATTTG 57.858 34.615 0.00 0.00 37.67 2.32
275 291 8.731275 TTGTCATATAAGTCATGGACGAATTT 57.269 30.769 0.00 0.00 37.67 1.82
297 313 9.612066 AAGTTTTATGAAAATGTTGACCATTGT 57.388 25.926 0.00 0.00 43.04 2.71
301 317 9.658799 TCAAAAGTTTTATGAAAATGTTGACCA 57.341 25.926 10.85 0.00 40.31 4.02
307 323 9.382275 AGCACTTCAAAAGTTTTATGAAAATGT 57.618 25.926 0.00 0.00 40.46 2.71
317 333 7.826744 TCCCAAAATAAGCACTTCAAAAGTTTT 59.173 29.630 0.00 0.00 40.46 2.43
351 367 9.705290 CTGCACCCTTTATTTGTTTATTTACTT 57.295 29.630 0.00 0.00 0.00 2.24
352 368 8.866093 ACTGCACCCTTTATTTGTTTATTTACT 58.134 29.630 0.00 0.00 0.00 2.24
353 369 8.921670 CACTGCACCCTTTATTTGTTTATTTAC 58.078 33.333 0.00 0.00 0.00 2.01
354 370 7.600752 GCACTGCACCCTTTATTTGTTTATTTA 59.399 33.333 0.00 0.00 0.00 1.40
355 371 6.426633 GCACTGCACCCTTTATTTGTTTATTT 59.573 34.615 0.00 0.00 0.00 1.40
356 372 5.931724 GCACTGCACCCTTTATTTGTTTATT 59.068 36.000 0.00 0.00 0.00 1.40
357 373 5.011533 TGCACTGCACCCTTTATTTGTTTAT 59.988 36.000 0.00 0.00 31.71 1.40
358 374 4.342378 TGCACTGCACCCTTTATTTGTTTA 59.658 37.500 0.00 0.00 31.71 2.01
363 379 3.727726 GTTTGCACTGCACCCTTTATTT 58.272 40.909 2.26 0.00 38.71 1.40
389 405 1.748493 ACGAGAGAGAGTGGATTCTGC 59.252 52.381 0.00 0.00 0.00 4.26
399 415 1.066914 GCTTGCACAACGAGAGAGAG 58.933 55.000 0.00 0.00 30.27 3.20
400 416 0.389025 TGCTTGCACAACGAGAGAGA 59.611 50.000 0.00 0.00 30.27 3.10
411 427 2.378038 TGGATAAGGGATTGCTTGCAC 58.622 47.619 0.00 0.00 0.00 4.57
436 452 0.864455 GGATATTCAGTGCTGCTCGC 59.136 55.000 0.00 0.00 39.77 5.03
510 527 1.448365 CCGCTGCTGATGTGCTACA 60.448 57.895 0.00 0.00 0.00 2.74
515 532 1.331756 GGTTTATCCGCTGCTGATGTG 59.668 52.381 15.60 0.00 0.00 3.21
516 533 1.065491 TGGTTTATCCGCTGCTGATGT 60.065 47.619 15.60 0.00 39.52 3.06
566 583 2.100631 CGGTTCTGTGGCGATGGAC 61.101 63.158 0.00 0.00 0.00 4.02
607 624 2.689034 CCACAGGAGGGGGAGGAC 60.689 72.222 0.00 0.00 0.00 3.85
608 625 4.741239 GCCACAGGAGGGGGAGGA 62.741 72.222 0.00 0.00 0.00 3.71
636 653 2.985847 GTGCCTTTCTTGCGGGCT 60.986 61.111 0.00 0.00 45.45 5.19
1173 1196 4.162690 GGCTGCTCCCACGGGTAG 62.163 72.222 1.07 0.00 36.47 3.18
1206 1229 4.604114 GGGAGTTTACCGAACCCG 57.396 61.111 0.00 0.00 39.13 5.28
1242 1265 3.899981 AAGCGCTCGGGCAACATCA 62.900 57.895 12.06 0.00 38.60 3.07
1243 1266 2.690778 AAAGCGCTCGGGCAACATC 61.691 57.895 12.06 0.00 38.60 3.06
1244 1267 2.672996 AAAGCGCTCGGGCAACAT 60.673 55.556 12.06 0.00 38.60 2.71
1261 1286 3.034924 AAAAAGGCATCGCTGGTCA 57.965 47.368 0.00 0.00 0.00 4.02
1293 1318 6.704937 GCATCAATATCACTCATCTCTCAACA 59.295 38.462 0.00 0.00 0.00 3.33
1304 1329 0.792640 CCGCGGCATCAATATCACTC 59.207 55.000 14.67 0.00 0.00 3.51
1314 1339 3.267597 AAACAGCAACCGCGGCATC 62.268 57.895 28.58 14.35 45.49 3.91
1319 1344 2.425124 CACGAAACAGCAACCGCG 60.425 61.111 0.00 0.00 45.49 6.46
1339 1364 3.880047 TTACCAACTACCATCTCACGG 57.120 47.619 0.00 0.00 0.00 4.94
1365 1398 1.142531 CGATGAGCACAGCAGCCTA 59.857 57.895 0.00 0.00 34.23 3.93
1408 1441 0.255033 GGGACAGACAACCCCCATAC 59.745 60.000 0.00 0.00 40.19 2.39
1411 1444 2.153401 CAGGGACAGACAACCCCCA 61.153 63.158 0.00 0.00 46.64 4.96
1416 1449 3.511934 AGATCAGTACAGGGACAGACAAC 59.488 47.826 0.00 0.00 0.00 3.32
1418 1451 3.092301 CAGATCAGTACAGGGACAGACA 58.908 50.000 0.00 0.00 0.00 3.41
1419 1452 3.093057 ACAGATCAGTACAGGGACAGAC 58.907 50.000 0.00 0.00 0.00 3.51
1420 1453 3.092301 CACAGATCAGTACAGGGACAGA 58.908 50.000 0.00 0.00 0.00 3.41
1421 1454 2.828520 ACACAGATCAGTACAGGGACAG 59.171 50.000 0.00 0.00 0.00 3.51
1422 1455 2.562738 CACACAGATCAGTACAGGGACA 59.437 50.000 0.00 0.00 0.00 4.02
1423 1456 2.563179 ACACACAGATCAGTACAGGGAC 59.437 50.000 0.00 0.00 0.00 4.46
1424 1457 2.562738 CACACACAGATCAGTACAGGGA 59.437 50.000 0.00 0.00 0.00 4.20
1425 1458 2.300152 ACACACACAGATCAGTACAGGG 59.700 50.000 0.00 0.00 0.00 4.45
1426 1459 3.667497 ACACACACAGATCAGTACAGG 57.333 47.619 0.00 0.00 0.00 4.00
1461 1495 2.167861 GCAGATCGAACCCGTCAGC 61.168 63.158 0.00 0.00 37.05 4.26
1484 1518 1.615883 TCGATATCTGCCAGGAGAAGC 59.384 52.381 0.34 0.00 0.00 3.86
1485 1519 2.890311 ACTCGATATCTGCCAGGAGAAG 59.110 50.000 9.26 0.00 0.00 2.85
1580 1614 4.710167 TCGGAGGCGGTGACTCGA 62.710 66.667 0.00 0.00 38.87 4.04
1592 1626 4.082190 TCAACAAGATTCAGTACCTCGGAG 60.082 45.833 0.00 0.00 0.00 4.63
1666 1716 9.626045 CTCCATTTCAGTTTTATTAACAAGGAC 57.374 33.333 0.00 0.00 0.00 3.85
1692 1748 2.386661 TCTCAGTCCCGAAATGAAGC 57.613 50.000 0.00 0.00 0.00 3.86
1713 1769 7.083858 ACAGTGTTCACAATATGCATAACAAC 58.916 34.615 11.13 9.45 0.00 3.32
1714 1770 7.213216 ACAGTGTTCACAATATGCATAACAA 57.787 32.000 11.13 0.00 0.00 2.83
1715 1771 6.816134 ACAGTGTTCACAATATGCATAACA 57.184 33.333 11.13 8.40 0.00 2.41
1756 1812 7.766278 AGAAGGACGGCATATATCATTAACATC 59.234 37.037 0.00 0.00 0.00 3.06
1782 1839 7.232534 AGCACAAAGTTATTTCCATGGAAACTA 59.767 33.333 36.31 25.74 45.34 2.24
1783 1840 6.041979 AGCACAAAGTTATTTCCATGGAAACT 59.958 34.615 36.31 27.82 45.34 2.66
1812 1869 6.627395 TTTGTGGTACAGTGAACAAATAGG 57.373 37.500 0.00 0.00 41.80 2.57
1869 1926 5.031066 TGTTATACACATTCCAGCTACCC 57.969 43.478 0.00 0.00 0.00 3.69
1884 1941 9.933723 AGTTACATATATTTCCCGGTGTTATAC 57.066 33.333 0.00 0.00 0.00 1.47
1904 1961 9.537192 CTCGGTGTTATATAATTTCCAGTTACA 57.463 33.333 0.00 0.00 0.00 2.41
1960 2025 2.513753 CCCTGAATGCAGTAACCAACA 58.486 47.619 0.00 0.00 40.63 3.33
1961 2026 1.202348 GCCCTGAATGCAGTAACCAAC 59.798 52.381 0.00 0.00 40.63 3.77
1977 2042 7.757624 CGTACACAATAAAATTGTTATTGCCCT 59.242 33.333 16.10 4.91 42.89 5.19
2076 2141 7.663905 TGCTGCTTTTCAAGGTTTTATAGTCTA 59.336 33.333 0.00 0.00 0.00 2.59
2125 2190 5.499004 ACAGTGGTACAAATGAGTATGGT 57.501 39.130 4.36 0.00 44.16 3.55
2163 2228 7.889589 AAATAATTGTAAGCTTTCAGGCAAC 57.110 32.000 3.20 0.00 34.17 4.17
2260 2325 4.022068 CCAGGATAAAGCAACTTCAGCAAA 60.022 41.667 0.00 0.00 0.00 3.68
2300 2365 1.758936 ACACACATGAGGATGGCATG 58.241 50.000 3.81 0.00 46.49 4.06
2304 2369 6.071447 TCCAAATTTAACACACATGAGGATGG 60.071 38.462 0.00 0.00 33.39 3.51
2329 2394 2.091885 TCCCTTTTGTTGCCTCTTCTGT 60.092 45.455 0.00 0.00 0.00 3.41
2347 2412 3.056458 CGGGGTTTGCCTTTTCCC 58.944 61.111 0.00 0.00 39.22 3.97
2361 2426 3.665675 CTCTCCTGAAACCGGCGGG 62.666 68.421 31.78 11.80 40.11 6.13
2511 2576 3.176411 CATGTCCAGGCCCTGATAGATA 58.824 50.000 13.74 0.00 32.44 1.98
2526 2591 4.973168 TGCATAATCTTCTACCCATGTCC 58.027 43.478 0.00 0.00 0.00 4.02
2559 2624 5.064707 GCTTAGCATTTCAATAGACCGACAA 59.935 40.000 0.00 0.00 0.00 3.18
2655 2720 7.974675 TGACTGCACTTTGTTAAGATTATAGC 58.025 34.615 0.00 0.00 35.30 2.97
2826 2891 2.203280 CCCCACAGCAACGGAACA 60.203 61.111 0.00 0.00 0.00 3.18
2947 3012 5.781210 TTATTTGTCAACCAATGTCTGCA 57.219 34.783 0.00 0.00 31.81 4.41
2948 3013 5.807011 GGATTATTTGTCAACCAATGTCTGC 59.193 40.000 0.00 0.00 31.81 4.26
2955 3020 3.835395 GGGGTGGATTATTTGTCAACCAA 59.165 43.478 2.40 0.00 40.79 3.67
3019 3084 1.134226 GTTGCAAGCTGACACAATGC 58.866 50.000 0.00 0.00 37.52 3.56
3032 3097 0.730265 GGACACGAACACAGTTGCAA 59.270 50.000 0.00 0.00 0.00 4.08
3207 3275 1.032014 GTGCAAGTGCTTTCCTCCAA 58.968 50.000 4.69 0.00 42.66 3.53
3292 3360 0.106519 ACCAAGCACTTCCACAAGCT 60.107 50.000 0.00 0.00 39.37 3.74
3308 3376 2.771943 AGTCTTCAAGACCAACTGACCA 59.228 45.455 14.27 0.00 46.18 4.02
3309 3377 3.477210 AGTCTTCAAGACCAACTGACC 57.523 47.619 14.27 0.00 46.18 4.02
3310 3378 4.932200 CCATAGTCTTCAAGACCAACTGAC 59.068 45.833 14.27 0.00 46.18 3.51
3311 3379 4.593206 ACCATAGTCTTCAAGACCAACTGA 59.407 41.667 14.27 0.00 46.18 3.41
3312 3380 4.692625 CACCATAGTCTTCAAGACCAACTG 59.307 45.833 14.27 6.60 46.18 3.16
3313 3381 4.593206 TCACCATAGTCTTCAAGACCAACT 59.407 41.667 14.27 0.00 46.18 3.16
3314 3382 4.691216 GTCACCATAGTCTTCAAGACCAAC 59.309 45.833 14.27 0.00 46.18 3.77
3315 3383 4.346709 TGTCACCATAGTCTTCAAGACCAA 59.653 41.667 14.27 3.25 46.18 3.67
3326 3394 3.868077 GCATCTGAGTTGTCACCATAGTC 59.132 47.826 0.00 0.00 0.00 2.59
3328 3396 3.865446 TGCATCTGAGTTGTCACCATAG 58.135 45.455 0.00 0.00 0.00 2.23
3377 3445 9.231297 CTAGTTTCCCAATCATGAAAACTTCTA 57.769 33.333 21.45 8.47 32.68 2.10
3379 3447 7.315890 CCTAGTTTCCCAATCATGAAAACTTC 58.684 38.462 21.45 2.20 32.68 3.01
3416 3485 7.117454 CGCCGAACAGTTTATACAAAGATAAG 58.883 38.462 0.00 0.00 0.00 1.73
3487 3581 3.450904 ACTAGGTCAGATGCCCACTAAA 58.549 45.455 0.00 0.00 0.00 1.85
3489 3583 2.848678 ACTAGGTCAGATGCCCACTA 57.151 50.000 0.00 0.00 0.00 2.74
3490 3584 1.834263 GAACTAGGTCAGATGCCCACT 59.166 52.381 1.90 0.00 0.00 4.00
3540 3634 8.642908 AATGTTCATGCAATCTCAAATATGTG 57.357 30.769 0.00 0.00 0.00 3.21
3542 3636 8.912658 GCTAATGTTCATGCAATCTCAAATATG 58.087 33.333 0.00 0.00 0.00 1.78
3549 3650 5.239359 TGTGCTAATGTTCATGCAATCTC 57.761 39.130 0.00 0.00 37.17 2.75
3552 3653 7.675962 AAAAATGTGCTAATGTTCATGCAAT 57.324 28.000 0.00 0.00 37.17 3.56
3577 3678 6.522625 TTTGAGATTTGACCAAGTTTGTGA 57.477 33.333 0.00 0.00 0.00 3.58
3626 3727 6.293735 CCGTTCCAAATTACTTGCAGTTCTTA 60.294 38.462 0.00 0.00 33.27 2.10
3627 3728 5.507315 CCGTTCCAAATTACTTGCAGTTCTT 60.507 40.000 0.00 0.00 33.27 2.52
3631 3732 3.482436 TCCGTTCCAAATTACTTGCAGT 58.518 40.909 0.00 0.00 33.27 4.40
3637 3738 4.760204 CCACTTCTTCCGTTCCAAATTACT 59.240 41.667 0.00 0.00 0.00 2.24
3646 3747 2.747436 ACGTTACCACTTCTTCCGTTC 58.253 47.619 0.00 0.00 0.00 3.95
3650 3751 4.514066 ACATCAAACGTTACCACTTCTTCC 59.486 41.667 0.00 0.00 0.00 3.46
3652 3753 4.274950 CCACATCAAACGTTACCACTTCTT 59.725 41.667 0.00 0.00 0.00 2.52
3659 3760 0.167251 CCGCCACATCAAACGTTACC 59.833 55.000 0.00 0.00 0.00 2.85
3664 3765 2.176546 CAGCCGCCACATCAAACG 59.823 61.111 0.00 0.00 0.00 3.60
3673 3774 4.695993 TGATTGTCGCAGCCGCCA 62.696 61.111 0.00 0.00 33.11 5.69
3674 3775 2.976840 TTTGATTGTCGCAGCCGCC 61.977 57.895 0.00 0.00 33.11 6.13
3689 3794 7.169140 GCCAGTTTTACTTCCACTTTATGTTTG 59.831 37.037 0.00 0.00 0.00 2.93
3695 3800 6.123651 TCTTGCCAGTTTTACTTCCACTTTA 58.876 36.000 0.00 0.00 0.00 1.85
3702 3807 4.156739 CCATCCTCTTGCCAGTTTTACTTC 59.843 45.833 0.00 0.00 0.00 3.01
3703 3808 4.082125 CCATCCTCTTGCCAGTTTTACTT 58.918 43.478 0.00 0.00 0.00 2.24
3713 3992 0.109132 CAAAACGCCATCCTCTTGCC 60.109 55.000 0.00 0.00 0.00 4.52
3734 4013 3.338249 CAGGTGTAGATGAGTTTGGGTG 58.662 50.000 0.00 0.00 0.00 4.61
3735 4014 2.290323 GCAGGTGTAGATGAGTTTGGGT 60.290 50.000 0.00 0.00 0.00 4.51
3737 4016 2.290260 TGGCAGGTGTAGATGAGTTTGG 60.290 50.000 0.00 0.00 0.00 3.28
3740 4019 2.840038 TCATGGCAGGTGTAGATGAGTT 59.160 45.455 0.00 0.00 0.00 3.01
3778 4057 1.160137 GCACACTCGAGCATCCTTTT 58.840 50.000 13.61 0.00 0.00 2.27
3780 4059 1.135915 CTAGCACACTCGAGCATCCTT 59.864 52.381 13.61 0.00 0.00 3.36
3795 4106 8.046708 ACATTCAAATTATACACACTCCTAGCA 58.953 33.333 0.00 0.00 0.00 3.49
3813 4124 8.985315 AGCTCCTCAAATATCATACATTCAAA 57.015 30.769 0.00 0.00 0.00 2.69
3847 4158 5.754406 TCGAAGTTTCTTTGACAACCGATTA 59.246 36.000 0.00 0.00 0.00 1.75
3878 4189 3.949031 GAGCAGATACTCCACGTCC 57.051 57.895 0.00 0.00 0.00 4.79
3885 4196 3.386078 TGTTCATGAGGGAGCAGATACTC 59.614 47.826 0.00 0.00 35.86 2.59
3886 4197 3.378512 TGTTCATGAGGGAGCAGATACT 58.621 45.455 0.00 0.00 0.00 2.12
3887 4198 3.133721 ACTGTTCATGAGGGAGCAGATAC 59.866 47.826 12.86 1.54 45.60 2.24
3888 4199 3.378512 ACTGTTCATGAGGGAGCAGATA 58.621 45.455 12.86 0.00 45.60 1.98
3889 4200 2.194859 ACTGTTCATGAGGGAGCAGAT 58.805 47.619 12.86 0.00 45.60 2.90
3890 4201 1.649321 ACTGTTCATGAGGGAGCAGA 58.351 50.000 12.86 0.00 45.60 4.26
3892 4203 4.365514 TTTTACTGTTCATGAGGGAGCA 57.634 40.909 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.