Multiple sequence alignment - TraesCS2A01G038500

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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 TraesCS2A01G038500 chr2A 100.000 2779 0 0 1 2779 16128064 16125286 0.000000e+00 5132.0
1 TraesCS2A01G038500 chr2A 89.562 297 18 4 885 1181 16143603 16143320 5.660000e-97 364.0
2 TraesCS2A01G038500 chr2A 85.366 246 32 4 32 276 198598948 198599190 4.590000e-63 252.0
3 TraesCS2A01G038500 chr2A 89.011 91 5 3 1819 1907 16135873 16135786 1.050000e-19 108.0
4 TraesCS2A01G038500 chr2D 86.661 1237 59 43 849 2023 14087968 14089160 0.000000e+00 1273.0
5 TraesCS2A01G038500 chr2D 96.884 353 7 3 490 842 14087577 14087925 3.080000e-164 588.0
6 TraesCS2A01G038500 chr2D 94.558 294 14 2 1 293 14087036 14087328 1.170000e-123 453.0
7 TraesCS2A01G038500 chr2D 91.509 318 12 2 2420 2736 14089556 14089859 9.200000e-115 424.0
8 TraesCS2A01G038500 chr2D 94.652 187 9 1 2236 2422 14089196 14089381 3.500000e-74 289.0
9 TraesCS2A01G038500 chr2D 86.179 246 31 3 32 276 567416558 567416315 2.120000e-66 263.0
10 TraesCS2A01G038500 chr2D 84.774 243 34 3 33 274 7294956 7294716 9.950000e-60 241.0
11 TraesCS2A01G038500 chr2D 83.740 246 37 3 32 276 186199275 186199518 2.150000e-56 230.0
12 TraesCS2A01G038500 chr2D 76.846 298 42 16 1964 2256 14045493 14045768 2.890000e-30 143.0
13 TraesCS2A01G038500 chr2D 87.387 111 9 2 1453 1562 14043906 14044012 3.760000e-24 122.0
14 TraesCS2A01G038500 chr2D 100.000 34 0 0 2746 2779 14089941 14089974 2.310000e-06 63.9
15 TraesCS2A01G038500 chr2B 87.249 698 58 15 1373 2057 25589924 25590603 0.000000e+00 767.0
16 TraesCS2A01G038500 chr2B 81.197 468 40 22 381 844 25588655 25589078 1.600000e-87 333.0
17 TraesCS2A01G038500 chr2B 92.308 182 10 3 849 1026 25589119 25589300 3.550000e-64 255.0
18 TraesCS2A01G038500 chr2B 85.650 223 16 5 1128 1341 25589638 25589853 1.300000e-53 220.0
19 TraesCS2A01G038500 chr2B 90.826 109 8 2 265 372 250686558 250686451 8.020000e-31 145.0
20 TraesCS2A01G038500 chr2B 93.814 97 4 2 281 376 544770307 544770212 8.020000e-31 145.0
21 TraesCS2A01G038500 chr2B 86.076 79 11 0 395 473 547948941 547948863 4.930000e-13 86.1
22 TraesCS2A01G038500 chr5D 86.585 246 30 3 32 276 344791310 344791067 4.560000e-68 268.0
23 TraesCS2A01G038500 chr6D 86.179 246 31 3 32 276 324114771 324114528 2.120000e-66 263.0
24 TraesCS2A01G038500 chr3D 84.898 245 35 2 32 276 95109916 95110158 2.140000e-61 246.0
25 TraesCS2A01G038500 chr1A 84.034 238 35 3 34 270 104447523 104447758 2.780000e-55 226.0
26 TraesCS2A01G038500 chr7A 95.745 94 3 1 278 370 126943037 126943130 1.720000e-32 150.0
27 TraesCS2A01G038500 chr7A 91.743 109 5 4 268 373 238816396 238816503 6.200000e-32 148.0
28 TraesCS2A01G038500 chr4B 95.699 93 3 1 279 370 255382788 255382696 6.200000e-32 148.0
29 TraesCS2A01G038500 chr4B 89.908 109 8 3 283 389 40170069 40169962 1.340000e-28 137.0
30 TraesCS2A01G038500 chr3B 93.137 102 3 4 269 367 130628357 130628257 2.230000e-31 147.0
31 TraesCS2A01G038500 chr3B 93.878 98 4 2 272 367 249860874 249860971 2.230000e-31 147.0
32 TraesCS2A01G038500 chr3B 93.000 100 4 3 283 380 652291836 652291738 2.890000e-30 143.0


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 TraesCS2A01G038500 chr2A 16125286 16128064 2778 True 5132.00 5132 100.000 1 2779 1 chr2A.!!$R1 2778
1 TraesCS2A01G038500 chr2D 14087036 14089974 2938 False 515.15 1273 94.044 1 2779 6 chr2D.!!$F3 2778
2 TraesCS2A01G038500 chr2B 25588655 25590603 1948 False 393.75 767 86.601 381 2057 4 chr2B.!!$F1 1676

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
468 512 0.179076 TGACCTGGCGCTCATATGTG 60.179 55.0 7.64 1.02 0.0 3.21 F
1384 1762 0.762842 GGTGGTTCCCTTGGCCTTTT 60.763 55.0 3.32 0.00 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1839 0.105593 ATCATGGTCGATGCTCGCTT 59.894 50.0 0.0 0.0 40.21 4.68 R
2631 3260 0.106708 TCGGCCTAGCATCATCAACC 59.893 55.0 0.0 0.0 0.00 3.77 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
32 33 1.396301 GAGTGGACGTGACTACCTACG 59.604 57.143 0.00 0.00 45.19 3.51
41 42 3.799420 CGTGACTACCTACGTACTACCTC 59.201 52.174 0.00 0.00 35.70 3.85
61 62 4.832823 CCTCTGTCCTGGTTTATTGGTTTT 59.167 41.667 0.00 0.00 0.00 2.43
125 126 4.746115 ACAAAATGTCAATGCATGTCACAC 59.254 37.500 0.00 0.00 29.85 3.82
173 174 7.599171 TCTTCAAATACGAATCCAGCGATATA 58.401 34.615 0.00 0.00 0.00 0.86
273 275 7.499232 CCAATAAAACCAGGATGAAGGTAGTAG 59.501 40.741 0.00 0.00 39.69 2.57
276 278 6.541934 AAACCAGGATGAAGGTAGTAGTAC 57.458 41.667 0.00 0.00 39.69 2.73
293 295 2.237392 AGTACGTTACTACTCCCTCCGT 59.763 50.000 0.00 0.00 37.23 4.69
294 296 1.743996 ACGTTACTACTCCCTCCGTC 58.256 55.000 0.00 0.00 0.00 4.79
295 297 1.020437 CGTTACTACTCCCTCCGTCC 58.980 60.000 0.00 0.00 0.00 4.79
296 298 1.679944 CGTTACTACTCCCTCCGTCCA 60.680 57.143 0.00 0.00 0.00 4.02
297 299 2.450476 GTTACTACTCCCTCCGTCCAA 58.550 52.381 0.00 0.00 0.00 3.53
298 300 2.827921 GTTACTACTCCCTCCGTCCAAA 59.172 50.000 0.00 0.00 0.00 3.28
299 301 2.019807 ACTACTCCCTCCGTCCAAAA 57.980 50.000 0.00 0.00 0.00 2.44
301 303 3.716431 ACTACTCCCTCCGTCCAAAATA 58.284 45.455 0.00 0.00 0.00 1.40
302 304 3.705072 ACTACTCCCTCCGTCCAAAATAG 59.295 47.826 0.00 0.00 0.00 1.73
303 305 2.829023 ACTCCCTCCGTCCAAAATAGA 58.171 47.619 0.00 0.00 0.00 1.98
305 307 3.134804 ACTCCCTCCGTCCAAAATAGATG 59.865 47.826 0.00 0.00 0.00 2.90
306 308 3.380393 TCCCTCCGTCCAAAATAGATGA 58.620 45.455 0.00 0.00 0.00 2.92
307 309 3.134081 TCCCTCCGTCCAAAATAGATGAC 59.866 47.826 0.00 0.00 0.00 3.06
316 358 6.389906 GTCCAAAATAGATGACCCAACTTTG 58.610 40.000 0.00 0.00 0.00 2.77
319 361 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
320 362 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
324 366 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
325 367 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
327 369 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
328 370 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
330 372 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
353 395 9.965824 AGTACAAAGTTGAGTCATTTATTTTGG 57.034 29.630 12.94 0.78 0.00 3.28
356 398 9.883142 ACAAAGTTGAGTCATTTATTTTGGAAA 57.117 25.926 12.94 0.00 0.00 3.13
358 400 9.546428 AAAGTTGAGTCATTTATTTTGGAAAGG 57.454 29.630 0.00 0.00 0.00 3.11
360 402 8.579863 AGTTGAGTCATTTATTTTGGAAAGGAG 58.420 33.333 0.00 0.00 28.10 3.69
362 404 6.437162 TGAGTCATTTATTTTGGAAAGGAGGG 59.563 38.462 0.00 0.00 28.10 4.30
364 406 6.665248 AGTCATTTATTTTGGAAAGGAGGGAG 59.335 38.462 0.00 0.00 28.10 4.30
365 407 6.437477 GTCATTTATTTTGGAAAGGAGGGAGT 59.563 38.462 0.00 0.00 28.10 3.85
366 408 7.614192 GTCATTTATTTTGGAAAGGAGGGAGTA 59.386 37.037 0.00 0.00 28.10 2.59
367 409 7.614192 TCATTTATTTTGGAAAGGAGGGAGTAC 59.386 37.037 0.00 0.00 0.00 2.73
369 411 5.536497 ATTTTGGAAAGGAGGGAGTACAT 57.464 39.130 0.00 0.00 0.00 2.29
370 412 4.301072 TTTGGAAAGGAGGGAGTACATG 57.699 45.455 0.00 0.00 0.00 3.21
371 413 2.915869 TGGAAAGGAGGGAGTACATGT 58.084 47.619 2.69 2.69 0.00 3.21
372 414 3.256704 TGGAAAGGAGGGAGTACATGTT 58.743 45.455 2.30 0.00 0.00 2.71
373 415 3.655777 TGGAAAGGAGGGAGTACATGTTT 59.344 43.478 2.30 0.00 0.00 2.83
374 416 4.105697 TGGAAAGGAGGGAGTACATGTTTT 59.894 41.667 2.30 0.00 0.00 2.43
375 417 4.459337 GGAAAGGAGGGAGTACATGTTTTG 59.541 45.833 2.30 0.00 0.00 2.44
376 418 3.721087 AGGAGGGAGTACATGTTTTGG 57.279 47.619 2.30 0.00 0.00 3.28
377 419 2.092323 GGAGGGAGTACATGTTTTGGC 58.908 52.381 2.30 0.00 0.00 4.52
378 420 1.737793 GAGGGAGTACATGTTTTGGCG 59.262 52.381 2.30 0.00 0.00 5.69
379 421 1.349688 AGGGAGTACATGTTTTGGCGA 59.650 47.619 2.30 0.00 0.00 5.54
411 453 2.096417 GTGATGACTGTACCACGTTTGC 60.096 50.000 0.00 0.00 0.00 3.68
413 455 3.006003 TGATGACTGTACCACGTTTGCTA 59.994 43.478 0.00 0.00 0.00 3.49
455 497 9.695526 TTGACAATAAGAAATTCATTTGACCTG 57.304 29.630 8.74 0.00 0.00 4.00
468 512 0.179076 TGACCTGGCGCTCATATGTG 60.179 55.000 7.64 1.02 0.00 3.21
626 700 6.107901 TGGGGGTTTTGTTATTTGAGAATG 57.892 37.500 0.00 0.00 0.00 2.67
752 826 3.707102 GACCTCCTCCACTAGCAAAGTAT 59.293 47.826 0.00 0.00 35.76 2.12
753 827 4.880164 ACCTCCTCCACTAGCAAAGTATA 58.120 43.478 0.00 0.00 35.76 1.47
756 830 5.128827 CCTCCTCCACTAGCAAAGTATACAA 59.871 44.000 5.50 0.00 35.76 2.41
874 984 0.958822 ATCGTTCCCAACAGCCAAAC 59.041 50.000 0.00 0.00 0.00 2.93
882 992 3.073798 TCCCAACAGCCAAACTATTCTCA 59.926 43.478 0.00 0.00 0.00 3.27
932 1046 4.126437 CACCCATAATGCTCACGTCAATA 58.874 43.478 0.00 0.00 0.00 1.90
1007 1121 2.866156 CTCCAGCGTGTACCATGTTATG 59.134 50.000 0.00 0.00 0.00 1.90
1050 1164 1.207791 CCATACTGTCTCCTGCCCTT 58.792 55.000 0.00 0.00 0.00 3.95
1123 1237 1.531748 CTCGAGCTCCTCCTCTCCT 59.468 63.158 8.47 0.00 0.00 3.69
1169 1519 4.868356 GACGTACGTCGATCTCCG 57.132 61.111 30.48 0.00 42.86 4.63
1192 1542 2.004583 TGCAAACGGTTATCTCCTCG 57.995 50.000 0.00 0.00 0.00 4.63
1246 1596 7.561722 TCTCTGCTCTATGGATTGTTACTACTT 59.438 37.037 0.00 0.00 0.00 2.24
1247 1597 8.762481 TCTGCTCTATGGATTGTTACTACTTA 57.238 34.615 0.00 0.00 0.00 2.24
1248 1598 8.630917 TCTGCTCTATGGATTGTTACTACTTAC 58.369 37.037 0.00 0.00 0.00 2.34
1249 1599 8.534954 TGCTCTATGGATTGTTACTACTTACT 57.465 34.615 0.00 0.00 0.00 2.24
1250 1600 9.636789 TGCTCTATGGATTGTTACTACTTACTA 57.363 33.333 0.00 0.00 0.00 1.82
1251 1601 9.896263 GCTCTATGGATTGTTACTACTTACTAC 57.104 37.037 0.00 0.00 0.00 2.73
1259 1609 9.649024 GATTGTTACTACTTACTACTCATCGAC 57.351 37.037 0.00 0.00 0.00 4.20
1276 1626 4.814900 CGAGTGGTCGGATCCAAG 57.185 61.111 13.41 0.00 42.87 3.61
1341 1700 2.436109 GGTGAGGCCTTCCTGCAA 59.564 61.111 6.77 0.00 44.46 4.08
1375 1753 3.637273 GACGCCTGGTGGTTCCCT 61.637 66.667 12.58 0.00 35.27 4.20
1383 1761 1.152333 GGTGGTTCCCTTGGCCTTT 60.152 57.895 3.32 0.00 0.00 3.11
1384 1762 0.762842 GGTGGTTCCCTTGGCCTTTT 60.763 55.000 3.32 0.00 0.00 2.27
1409 1815 3.001406 GGTGCCTCCTACCGTGGT 61.001 66.667 0.00 0.00 0.00 4.16
1429 1839 1.522092 GGTCGCCATGGATGAGTGA 59.478 57.895 18.40 0.00 0.00 3.41
1455 1865 2.061773 GCATCGACCATGATTACCGAG 58.938 52.381 0.00 0.00 33.80 4.63
1576 1998 2.930562 GGTCCCTGGTGAGCTGGT 60.931 66.667 6.81 0.00 0.00 4.00
1590 2012 5.010213 GGTGAGCTGGTTGTTGGTTTAAATA 59.990 40.000 0.00 0.00 0.00 1.40
1620 2042 2.477245 ACTACATGCCACCAGGTGATA 58.523 47.619 22.37 9.65 36.53 2.15
1631 2053 3.025322 CCAGGTGATACTCTGGTCTCT 57.975 52.381 0.00 0.00 44.03 3.10
1664 2089 4.361253 GCAGAGACGCCAAAGACA 57.639 55.556 0.00 0.00 0.00 3.41
1721 2146 1.216175 CTCATGGGGTGGGATGAACAT 59.784 52.381 0.00 0.00 0.00 2.71
1732 2157 3.010472 TGGGATGAACATGATCCTGTTGT 59.990 43.478 19.44 9.05 39.40 3.32
1733 2158 4.019174 GGGATGAACATGATCCTGTTGTT 58.981 43.478 19.44 9.96 39.40 2.83
1737 2162 5.632244 TGAACATGATCCTGTTGTTGATG 57.368 39.130 19.44 2.10 39.40 3.07
1794 2219 0.320421 GTGAGCTCCACGGTGCTTAA 60.320 55.000 12.15 3.70 43.75 1.85
1795 2220 0.613260 TGAGCTCCACGGTGCTTAAT 59.387 50.000 12.15 0.00 43.75 1.40
1796 2221 1.003118 TGAGCTCCACGGTGCTTAATT 59.997 47.619 12.15 0.00 43.75 1.40
1797 2222 2.235155 TGAGCTCCACGGTGCTTAATTA 59.765 45.455 12.15 0.00 43.75 1.40
1834 2259 6.049790 GGTGGTATGAAGATGAAGTTCTACC 58.950 44.000 4.17 6.38 33.16 3.18
1843 2268 6.232581 AGATGAAGTTCTACCTCCAGATTG 57.767 41.667 4.17 0.00 0.00 2.67
1899 2345 3.536956 TTGAGATCCGGTGGTTATGTC 57.463 47.619 0.00 0.00 0.00 3.06
1911 2357 4.319984 GGTGGTTATGTCGGAAAGTTTCAC 60.320 45.833 17.16 8.32 0.00 3.18
1929 2380 1.065401 CACATTTGCACTGAACGGTGT 59.935 47.619 14.04 0.00 39.21 4.16
1981 2432 3.727726 TGATATGTGTTACTCCCATGCG 58.272 45.455 0.00 0.00 0.00 4.73
2032 2483 5.514500 TTTAGACTGAAATGCCCCTAGTT 57.486 39.130 0.00 0.00 0.00 2.24
2082 2534 8.779354 TTTTTGTGGGGCATAAACATAATTAC 57.221 30.769 0.00 0.00 0.00 1.89
2083 2535 6.472686 TTGTGGGGCATAAACATAATTACC 57.527 37.500 0.00 0.00 0.00 2.85
2084 2536 5.519808 TGTGGGGCATAAACATAATTACCA 58.480 37.500 0.00 0.00 0.00 3.25
2085 2537 6.139671 TGTGGGGCATAAACATAATTACCAT 58.860 36.000 0.00 0.00 0.00 3.55
2086 2538 7.298374 TGTGGGGCATAAACATAATTACCATA 58.702 34.615 0.00 0.00 0.00 2.74
2087 2539 7.450014 TGTGGGGCATAAACATAATTACCATAG 59.550 37.037 0.00 0.00 0.00 2.23
2088 2540 6.951198 TGGGGCATAAACATAATTACCATAGG 59.049 38.462 0.00 0.00 0.00 2.57
2089 2541 6.127451 GGGGCATAAACATAATTACCATAGGC 60.127 42.308 0.00 0.00 0.00 3.93
2090 2542 6.663523 GGGCATAAACATAATTACCATAGGCT 59.336 38.462 0.00 0.00 0.00 4.58
2091 2543 7.832187 GGGCATAAACATAATTACCATAGGCTA 59.168 37.037 0.00 0.00 0.00 3.93
2092 2544 9.238368 GGCATAAACATAATTACCATAGGCTAA 57.762 33.333 0.00 0.00 0.00 3.09
2106 2558 8.281529 ACCATAGGCTAATTAAGGATTCTTCT 57.718 34.615 0.00 0.00 34.59 2.85
2107 2559 9.393786 ACCATAGGCTAATTAAGGATTCTTCTA 57.606 33.333 0.00 0.00 34.59 2.10
2116 2568 8.470657 AATTAAGGATTCTTCTAATTCTGGGC 57.529 34.615 0.00 0.00 34.59 5.36
2117 2569 5.456921 AAGGATTCTTCTAATTCTGGGCA 57.543 39.130 0.00 0.00 0.00 5.36
2118 2570 5.659849 AGGATTCTTCTAATTCTGGGCAT 57.340 39.130 0.00 0.00 0.00 4.40
2119 2571 6.023334 AGGATTCTTCTAATTCTGGGCATT 57.977 37.500 0.00 0.00 0.00 3.56
2120 2572 5.832060 AGGATTCTTCTAATTCTGGGCATTG 59.168 40.000 0.00 0.00 0.00 2.82
2121 2573 5.829924 GGATTCTTCTAATTCTGGGCATTGA 59.170 40.000 0.00 0.00 0.00 2.57
2122 2574 6.492772 GGATTCTTCTAATTCTGGGCATTGAT 59.507 38.462 0.00 0.00 0.00 2.57
2123 2575 7.015001 GGATTCTTCTAATTCTGGGCATTGATT 59.985 37.037 0.00 0.00 0.00 2.57
2124 2576 7.722949 TTCTTCTAATTCTGGGCATTGATTT 57.277 32.000 0.00 0.00 0.00 2.17
2125 2577 7.104043 TCTTCTAATTCTGGGCATTGATTTG 57.896 36.000 0.00 0.00 0.00 2.32
2126 2578 6.891361 TCTTCTAATTCTGGGCATTGATTTGA 59.109 34.615 0.00 0.00 0.00 2.69
2127 2579 6.704289 TCTAATTCTGGGCATTGATTTGAG 57.296 37.500 0.00 0.00 0.00 3.02
2128 2580 6.189859 TCTAATTCTGGGCATTGATTTGAGT 58.810 36.000 0.00 0.00 0.00 3.41
2129 2581 7.345691 TCTAATTCTGGGCATTGATTTGAGTA 58.654 34.615 0.00 0.00 0.00 2.59
2130 2582 8.000709 TCTAATTCTGGGCATTGATTTGAGTAT 58.999 33.333 0.00 0.00 0.00 2.12
2131 2583 9.288576 CTAATTCTGGGCATTGATTTGAGTATA 57.711 33.333 0.00 0.00 0.00 1.47
2132 2584 8.537728 AATTCTGGGCATTGATTTGAGTATAA 57.462 30.769 0.00 0.00 0.00 0.98
2133 2585 8.716674 ATTCTGGGCATTGATTTGAGTATAAT 57.283 30.769 0.00 0.00 0.00 1.28
2134 2586 8.537728 TTCTGGGCATTGATTTGAGTATAATT 57.462 30.769 0.00 0.00 0.00 1.40
2135 2587 8.537728 TCTGGGCATTGATTTGAGTATAATTT 57.462 30.769 0.00 0.00 0.00 1.82
2136 2588 8.415553 TCTGGGCATTGATTTGAGTATAATTTG 58.584 33.333 0.00 0.00 0.00 2.32
2137 2589 7.499292 TGGGCATTGATTTGAGTATAATTTGG 58.501 34.615 0.00 0.00 0.00 3.28
2138 2590 6.930722 GGGCATTGATTTGAGTATAATTTGGG 59.069 38.462 0.00 0.00 0.00 4.12
2139 2591 7.201992 GGGCATTGATTTGAGTATAATTTGGGA 60.202 37.037 0.00 0.00 0.00 4.37
2140 2592 7.653311 GGCATTGATTTGAGTATAATTTGGGAC 59.347 37.037 0.00 0.00 0.00 4.46
2141 2593 8.416329 GCATTGATTTGAGTATAATTTGGGACT 58.584 33.333 0.00 0.00 0.00 3.85
2142 2594 9.740239 CATTGATTTGAGTATAATTTGGGACTG 57.260 33.333 0.00 0.00 0.00 3.51
2143 2595 9.699410 ATTGATTTGAGTATAATTTGGGACTGA 57.301 29.630 0.00 0.00 0.00 3.41
2144 2596 9.527157 TTGATTTGAGTATAATTTGGGACTGAA 57.473 29.630 0.00 0.00 0.00 3.02
2145 2597 9.527157 TGATTTGAGTATAATTTGGGACTGAAA 57.473 29.630 0.00 0.00 0.00 2.69
2148 2600 7.880160 TGAGTATAATTTGGGACTGAAATGG 57.120 36.000 0.00 0.00 0.00 3.16
2149 2601 6.321181 TGAGTATAATTTGGGACTGAAATGGC 59.679 38.462 0.00 0.00 0.00 4.40
2150 2602 5.598417 AGTATAATTTGGGACTGAAATGGCC 59.402 40.000 0.00 0.00 0.00 5.36
2151 2603 1.571955 ATTTGGGACTGAAATGGCCC 58.428 50.000 0.00 0.00 41.08 5.80
2152 2604 0.486879 TTTGGGACTGAAATGGCCCT 59.513 50.000 0.00 0.00 41.28 5.19
2153 2605 1.377690 TTGGGACTGAAATGGCCCTA 58.622 50.000 0.00 0.00 41.28 3.53
2154 2606 0.918983 TGGGACTGAAATGGCCCTAG 59.081 55.000 0.00 0.00 41.28 3.02
2155 2607 0.466372 GGGACTGAAATGGCCCTAGC 60.466 60.000 0.00 0.00 37.59 3.42
2156 2608 0.548510 GGACTGAAATGGCCCTAGCT 59.451 55.000 0.00 0.00 39.73 3.32
2157 2609 1.768870 GGACTGAAATGGCCCTAGCTA 59.231 52.381 0.00 0.00 39.73 3.32
2158 2610 2.172717 GGACTGAAATGGCCCTAGCTAA 59.827 50.000 0.00 0.00 39.73 3.09
2159 2611 3.371595 GGACTGAAATGGCCCTAGCTAAA 60.372 47.826 0.00 0.00 39.73 1.85
2160 2612 4.464947 GACTGAAATGGCCCTAGCTAAAT 58.535 43.478 0.00 0.00 39.73 1.40
2161 2613 5.456186 GGACTGAAATGGCCCTAGCTAAATA 60.456 44.000 0.00 0.00 39.73 1.40
2162 2614 5.377478 ACTGAAATGGCCCTAGCTAAATAC 58.623 41.667 0.00 0.00 39.73 1.89
2163 2615 5.132816 ACTGAAATGGCCCTAGCTAAATACT 59.867 40.000 0.00 0.00 39.73 2.12
2164 2616 6.329197 ACTGAAATGGCCCTAGCTAAATACTA 59.671 38.462 0.00 0.00 39.73 1.82
2165 2617 6.531021 TGAAATGGCCCTAGCTAAATACTAC 58.469 40.000 0.00 0.00 39.73 2.73
2166 2618 6.100569 TGAAATGGCCCTAGCTAAATACTACA 59.899 38.462 0.00 0.00 39.73 2.74
2167 2619 6.509523 AATGGCCCTAGCTAAATACTACAA 57.490 37.500 0.00 0.00 39.73 2.41
2168 2620 5.961398 TGGCCCTAGCTAAATACTACAAA 57.039 39.130 0.00 0.00 39.73 2.83
2169 2621 5.925509 TGGCCCTAGCTAAATACTACAAAG 58.074 41.667 0.00 0.00 39.73 2.77
2170 2622 5.427481 TGGCCCTAGCTAAATACTACAAAGT 59.573 40.000 0.00 0.00 39.73 2.66
2171 2623 6.069847 TGGCCCTAGCTAAATACTACAAAGTT 60.070 38.462 0.00 0.00 39.73 2.66
2172 2624 6.827251 GGCCCTAGCTAAATACTACAAAGTTT 59.173 38.462 0.00 0.00 39.73 2.66
2173 2625 7.201705 GGCCCTAGCTAAATACTACAAAGTTTG 60.202 40.741 14.13 14.13 39.73 2.93
2174 2626 7.551617 GCCCTAGCTAAATACTACAAAGTTTGA 59.448 37.037 22.23 5.24 34.89 2.69
2175 2627 9.614792 CCCTAGCTAAATACTACAAAGTTTGAT 57.385 33.333 22.23 8.93 37.15 2.57
2195 2647 9.886132 GTTTGATTAGAGGAGTAATTACCTTCA 57.114 33.333 12.05 1.85 36.57 3.02
2197 2649 7.727181 TGATTAGAGGAGTAATTACCTTCAGC 58.273 38.462 12.05 1.17 36.57 4.26
2198 2650 7.565398 TGATTAGAGGAGTAATTACCTTCAGCT 59.435 37.037 12.05 7.65 36.57 4.24
2199 2651 5.606348 AGAGGAGTAATTACCTTCAGCTG 57.394 43.478 7.63 7.63 36.57 4.24
2200 2652 5.273208 AGAGGAGTAATTACCTTCAGCTGA 58.727 41.667 13.74 13.74 36.57 4.26
2201 2653 5.128008 AGAGGAGTAATTACCTTCAGCTGAC 59.872 44.000 18.03 1.66 36.57 3.51
2202 2654 5.026790 AGGAGTAATTACCTTCAGCTGACT 58.973 41.667 18.03 7.31 31.95 3.41
2203 2655 6.195700 AGGAGTAATTACCTTCAGCTGACTA 58.804 40.000 18.03 1.07 31.95 2.59
2204 2656 6.668283 AGGAGTAATTACCTTCAGCTGACTAA 59.332 38.462 18.03 12.45 31.95 2.24
2205 2657 7.345914 AGGAGTAATTACCTTCAGCTGACTAAT 59.654 37.037 18.03 14.11 31.95 1.73
2206 2658 7.439655 GGAGTAATTACCTTCAGCTGACTAATG 59.560 40.741 18.03 5.77 0.00 1.90
2207 2659 8.079211 AGTAATTACCTTCAGCTGACTAATGA 57.921 34.615 18.03 8.22 0.00 2.57
2208 2660 8.709308 AGTAATTACCTTCAGCTGACTAATGAT 58.291 33.333 18.03 3.94 0.00 2.45
2209 2661 8.983724 GTAATTACCTTCAGCTGACTAATGATC 58.016 37.037 18.03 8.17 0.00 2.92
2210 2662 4.414337 ACCTTCAGCTGACTAATGATCC 57.586 45.455 18.03 0.00 0.00 3.36
2211 2663 4.036518 ACCTTCAGCTGACTAATGATCCT 58.963 43.478 18.03 0.00 0.00 3.24
2212 2664 4.472833 ACCTTCAGCTGACTAATGATCCTT 59.527 41.667 18.03 0.00 0.00 3.36
2213 2665 5.055812 CCTTCAGCTGACTAATGATCCTTC 58.944 45.833 18.03 0.00 0.00 3.46
2214 2666 4.679373 TCAGCTGACTAATGATCCTTCC 57.321 45.455 13.74 0.00 0.00 3.46
2215 2667 3.068732 TCAGCTGACTAATGATCCTTCCG 59.931 47.826 13.74 0.00 0.00 4.30
2216 2668 2.366916 AGCTGACTAATGATCCTTCCGG 59.633 50.000 0.00 0.00 0.00 5.14
2217 2669 2.103263 GCTGACTAATGATCCTTCCGGT 59.897 50.000 0.00 0.00 0.00 5.28
2218 2670 3.432326 GCTGACTAATGATCCTTCCGGTT 60.432 47.826 0.00 0.00 0.00 4.44
2219 2671 4.372656 CTGACTAATGATCCTTCCGGTTC 58.627 47.826 0.00 0.00 0.00 3.62
2220 2672 3.772572 TGACTAATGATCCTTCCGGTTCA 59.227 43.478 0.00 0.00 41.83 3.18
2221 2673 4.224147 TGACTAATGATCCTTCCGGTTCAA 59.776 41.667 0.00 0.00 41.17 2.69
2222 2674 4.770795 ACTAATGATCCTTCCGGTTCAAG 58.229 43.478 0.00 0.00 41.17 3.02
2223 2675 4.469945 ACTAATGATCCTTCCGGTTCAAGA 59.530 41.667 0.00 0.00 41.17 3.02
2224 2676 2.762535 TGATCCTTCCGGTTCAAGAC 57.237 50.000 0.00 0.00 36.36 3.01
2225 2677 1.974957 TGATCCTTCCGGTTCAAGACA 59.025 47.619 0.00 0.00 36.36 3.41
2226 2678 2.289444 TGATCCTTCCGGTTCAAGACAC 60.289 50.000 0.00 0.00 36.36 3.67
2227 2679 1.420430 TCCTTCCGGTTCAAGACACT 58.580 50.000 0.00 0.00 0.00 3.55
2228 2680 1.070134 TCCTTCCGGTTCAAGACACTG 59.930 52.381 0.00 0.00 0.00 3.66
2229 2681 1.202651 CCTTCCGGTTCAAGACACTGT 60.203 52.381 0.00 0.00 0.00 3.55
2230 2682 2.561569 CTTCCGGTTCAAGACACTGTT 58.438 47.619 0.00 0.00 0.00 3.16
2231 2683 2.702592 TCCGGTTCAAGACACTGTTT 57.297 45.000 0.00 0.00 0.00 2.83
2232 2684 2.285083 TCCGGTTCAAGACACTGTTTG 58.715 47.619 0.00 0.00 0.00 2.93
2233 2685 2.093394 TCCGGTTCAAGACACTGTTTGA 60.093 45.455 0.00 3.89 0.00 2.69
2234 2686 2.031683 CCGGTTCAAGACACTGTTTGAC 59.968 50.000 0.00 3.98 33.36 3.18
2235 2687 2.936498 CGGTTCAAGACACTGTTTGACT 59.064 45.455 6.39 0.00 33.36 3.41
2236 2688 4.116961 CGGTTCAAGACACTGTTTGACTA 58.883 43.478 6.39 0.00 33.36 2.59
2237 2689 4.209288 CGGTTCAAGACACTGTTTGACTAG 59.791 45.833 6.39 0.00 33.36 2.57
2238 2690 5.357257 GGTTCAAGACACTGTTTGACTAGA 58.643 41.667 0.00 0.00 33.36 2.43
2239 2691 5.815740 GGTTCAAGACACTGTTTGACTAGAA 59.184 40.000 0.00 0.00 33.36 2.10
2261 2713 1.548081 TGGGACTGAAATGCATGTGG 58.452 50.000 0.00 0.00 0.00 4.17
2323 2775 4.569719 ATTAGGGTTGAGGGTTACACAG 57.430 45.455 0.00 0.00 0.00 3.66
2369 2821 1.269569 ACGACGCAACTGAGAATGTGA 60.270 47.619 9.71 0.00 0.00 3.58
2373 2825 1.532437 CGCAACTGAGAATGTGAGCAA 59.468 47.619 0.00 0.00 0.00 3.91
2378 2830 2.105477 ACTGAGAATGTGAGCAACTGGT 59.895 45.455 0.00 0.00 0.00 4.00
2383 2835 3.324846 AGAATGTGAGCAACTGGTACTCA 59.675 43.478 0.00 0.00 38.09 3.41
2406 2858 1.378514 CGGGCAGGTTGGCAAGTAT 60.379 57.895 0.00 0.00 45.76 2.12
2408 2860 0.323360 GGGCAGGTTGGCAAGTATCA 60.323 55.000 0.00 0.00 45.76 2.15
2422 2874 5.105756 GGCAAGTATCAAACACCTGCTAATT 60.106 40.000 0.00 0.00 33.38 1.40
2423 2875 6.030228 GCAAGTATCAAACACCTGCTAATTC 58.970 40.000 0.00 0.00 31.38 2.17
2424 2876 6.349280 GCAAGTATCAAACACCTGCTAATTCA 60.349 38.462 0.00 0.00 31.38 2.57
2425 2877 6.743575 AGTATCAAACACCTGCTAATTCAC 57.256 37.500 0.00 0.00 0.00 3.18
2426 2878 6.237901 AGTATCAAACACCTGCTAATTCACA 58.762 36.000 0.00 0.00 0.00 3.58
2474 3103 1.509463 GTCGGGCATGAGTGACGTA 59.491 57.895 0.00 0.00 32.55 3.57
2536 3165 1.138859 CAGTCGATATTGTGGCCCAGA 59.861 52.381 0.00 0.00 0.00 3.86
2542 3171 0.616395 TATTGTGGCCCAGACGAGGA 60.616 55.000 0.00 0.00 0.00 3.71
2623 3252 3.132925 GCACTACAAACTAACCAACGGA 58.867 45.455 0.00 0.00 0.00 4.69
2625 3254 4.121317 CACTACAAACTAACCAACGGACA 58.879 43.478 0.00 0.00 0.00 4.02
2626 3255 4.753107 CACTACAAACTAACCAACGGACAT 59.247 41.667 0.00 0.00 0.00 3.06
2627 3256 4.753107 ACTACAAACTAACCAACGGACATG 59.247 41.667 0.00 0.00 0.00 3.21
2628 3257 2.292292 ACAAACTAACCAACGGACATGC 59.708 45.455 0.00 0.00 0.00 4.06
2629 3258 2.552315 CAAACTAACCAACGGACATGCT 59.448 45.455 0.00 0.00 0.00 3.79
2630 3259 3.688694 AACTAACCAACGGACATGCTA 57.311 42.857 0.00 0.00 0.00 3.49
2631 3260 3.247006 ACTAACCAACGGACATGCTAG 57.753 47.619 0.00 0.00 0.00 3.42
2632 3261 2.093658 ACTAACCAACGGACATGCTAGG 60.094 50.000 0.00 0.00 0.00 3.02
2633 3262 0.690762 AACCAACGGACATGCTAGGT 59.309 50.000 0.00 0.00 0.00 3.08
2634 3263 0.690762 ACCAACGGACATGCTAGGTT 59.309 50.000 0.00 0.00 0.00 3.50
2635 3264 1.086696 CCAACGGACATGCTAGGTTG 58.913 55.000 10.73 10.73 38.11 3.77
2636 3265 1.338674 CCAACGGACATGCTAGGTTGA 60.339 52.381 16.45 0.00 40.16 3.18
2637 3266 2.632377 CAACGGACATGCTAGGTTGAT 58.368 47.619 11.78 0.00 40.16 2.57
2638 3267 2.315925 ACGGACATGCTAGGTTGATG 57.684 50.000 0.00 0.00 0.00 3.07
2647 3276 2.224378 TGCTAGGTTGATGATGCTAGGC 60.224 50.000 0.00 0.00 0.00 3.93
2737 3367 5.064314 GGTAGGCTACCCTATATCCTAGG 57.936 52.174 29.75 0.82 45.22 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.786635 AGGTAGTACGTAGGTAGTCACG 58.213 50.000 6.21 0.00 43.63 4.35
32 33 6.338937 CAATAAACCAGGACAGAGGTAGTAC 58.661 44.000 0.00 0.00 37.07 2.73
41 42 6.405278 AAGAAAACCAATAAACCAGGACAG 57.595 37.500 0.00 0.00 0.00 3.51
149 150 6.712241 ATATCGCTGGATTCGTATTTGAAG 57.288 37.500 0.00 0.00 34.00 3.02
150 151 8.596271 TTTATATCGCTGGATTCGTATTTGAA 57.404 30.769 0.00 0.00 34.00 2.69
238 240 4.357399 TCCTGGTTTTATTGGTCCCCTTTA 59.643 41.667 0.00 0.00 0.00 1.85
242 244 2.911552 TCCTGGTTTTATTGGTCCCC 57.088 50.000 0.00 0.00 0.00 4.81
273 275 2.609916 GACGGAGGGAGTAGTAACGTAC 59.390 54.545 0.00 0.00 32.84 3.67
276 278 1.020437 GGACGGAGGGAGTAGTAACG 58.980 60.000 0.00 0.00 0.00 3.18
293 295 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
294 296 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
295 297 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
296 298 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
297 299 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
298 300 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
299 301 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
301 303 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
302 304 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
303 305 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
327 369 9.965824 CCAAAATAAATGACTCAACTTTGTACT 57.034 29.630 0.00 0.00 0.00 2.73
328 370 9.959749 TCCAAAATAAATGACTCAACTTTGTAC 57.040 29.630 0.00 0.00 0.00 2.90
330 372 9.883142 TTTCCAAAATAAATGACTCAACTTTGT 57.117 25.926 0.00 0.00 0.00 2.83
333 375 8.923270 TCCTTTCCAAAATAAATGACTCAACTT 58.077 29.630 0.00 0.00 0.00 2.66
335 377 7.814587 CCTCCTTTCCAAAATAAATGACTCAAC 59.185 37.037 0.00 0.00 0.00 3.18
336 378 7.039082 CCCTCCTTTCCAAAATAAATGACTCAA 60.039 37.037 0.00 0.00 0.00 3.02
338 380 6.663523 TCCCTCCTTTCCAAAATAAATGACTC 59.336 38.462 0.00 0.00 0.00 3.36
339 381 6.561294 TCCCTCCTTTCCAAAATAAATGACT 58.439 36.000 0.00 0.00 0.00 3.41
340 382 6.437477 ACTCCCTCCTTTCCAAAATAAATGAC 59.563 38.462 0.00 0.00 0.00 3.06
341 383 6.561294 ACTCCCTCCTTTCCAAAATAAATGA 58.439 36.000 0.00 0.00 0.00 2.57
342 384 6.857437 ACTCCCTCCTTTCCAAAATAAATG 57.143 37.500 0.00 0.00 0.00 2.32
344 386 6.854578 TGTACTCCCTCCTTTCCAAAATAAA 58.145 36.000 0.00 0.00 0.00 1.40
346 388 6.011981 ACATGTACTCCCTCCTTTCCAAAATA 60.012 38.462 0.00 0.00 0.00 1.40
348 390 4.105697 ACATGTACTCCCTCCTTTCCAAAA 59.894 41.667 0.00 0.00 0.00 2.44
349 391 3.655777 ACATGTACTCCCTCCTTTCCAAA 59.344 43.478 0.00 0.00 0.00 3.28
350 392 3.256704 ACATGTACTCCCTCCTTTCCAA 58.743 45.455 0.00 0.00 0.00 3.53
352 394 4.302559 AAACATGTACTCCCTCCTTTCC 57.697 45.455 0.00 0.00 0.00 3.13
353 395 4.459337 CCAAAACATGTACTCCCTCCTTTC 59.541 45.833 0.00 0.00 0.00 2.62
355 397 3.814316 GCCAAAACATGTACTCCCTCCTT 60.814 47.826 0.00 0.00 0.00 3.36
356 398 2.290960 GCCAAAACATGTACTCCCTCCT 60.291 50.000 0.00 0.00 0.00 3.69
357 399 2.092323 GCCAAAACATGTACTCCCTCC 58.908 52.381 0.00 0.00 0.00 4.30
358 400 1.737793 CGCCAAAACATGTACTCCCTC 59.262 52.381 0.00 0.00 0.00 4.30
360 402 1.816074 TCGCCAAAACATGTACTCCC 58.184 50.000 0.00 0.00 0.00 4.30
362 404 2.477863 GCCATCGCCAAAACATGTACTC 60.478 50.000 0.00 0.00 0.00 2.59
364 406 1.908065 GCCATCGCCAAAACATGTAC 58.092 50.000 0.00 0.00 0.00 2.90
390 432 2.096417 GCAAACGTGGTACAGTCATCAC 60.096 50.000 0.00 0.00 41.80 3.06
411 453 3.425193 GTCAAGCCGTTTGCAATTTGTAG 59.575 43.478 0.00 0.00 44.83 2.74
413 455 2.200899 GTCAAGCCGTTTGCAATTTGT 58.799 42.857 0.00 0.00 44.83 2.83
427 469 8.650714 GGTCAAATGAATTTCTTATTGTCAAGC 58.349 33.333 0.00 0.00 0.00 4.01
626 700 3.447944 ACCTACGAATGGTCTCTCTTTCC 59.552 47.826 0.00 0.00 31.03 3.13
752 826 4.624024 GTGCTAGCGTGTTTCTGTATTGTA 59.376 41.667 10.77 0.00 0.00 2.41
753 827 3.432252 GTGCTAGCGTGTTTCTGTATTGT 59.568 43.478 10.77 0.00 0.00 2.71
756 830 2.028476 TGGTGCTAGCGTGTTTCTGTAT 60.028 45.455 10.77 0.00 0.00 2.29
844 918 1.277842 TGGGAACGATCAAGCTGCTTA 59.722 47.619 15.51 4.41 0.00 3.09
845 919 0.036732 TGGGAACGATCAAGCTGCTT 59.963 50.000 9.53 9.53 0.00 3.91
846 920 0.036732 TTGGGAACGATCAAGCTGCT 59.963 50.000 0.00 0.00 0.00 4.24
847 921 0.169009 GTTGGGAACGATCAAGCTGC 59.831 55.000 0.00 0.00 0.00 5.25
855 965 0.958822 GTTTGGCTGTTGGGAACGAT 59.041 50.000 0.00 0.00 0.00 3.73
882 992 8.977267 AGTTAGGATGAGAATACGTACTACTT 57.023 34.615 0.00 0.00 0.00 2.24
932 1046 7.453393 TGTTGAGTTAGACCAAGAGATCAATT 58.547 34.615 0.00 0.00 0.00 2.32
1007 1121 8.786898 TGGTCGTATGGATACTAAGTACATAAC 58.213 37.037 0.00 0.00 37.61 1.89
1050 1164 2.175202 GAGCAAGTGAAGAGAGGGAGA 58.825 52.381 0.00 0.00 0.00 3.71
1162 1512 1.353103 CGTTTGCATGGCGGAGATC 59.647 57.895 0.00 0.00 0.00 2.75
1169 1519 1.065551 GGAGATAACCGTTTGCATGGC 59.934 52.381 0.00 0.00 31.07 4.40
1192 1542 3.181458 TGTGGGGTACAAAACAGAGAGAC 60.181 47.826 0.00 0.00 36.06 3.36
1259 1609 1.519455 GCTTGGATCCGACCACTCG 60.519 63.158 7.39 0.00 39.85 4.18
1312 1662 4.803426 CTCACCTCCGCCGTCTGC 62.803 72.222 0.00 0.00 0.00 4.26
1324 1674 1.973812 GTTGCAGGAAGGCCTCACC 60.974 63.158 17.97 17.97 44.80 4.02
1326 1676 0.609957 CATGTTGCAGGAAGGCCTCA 60.610 55.000 5.23 0.00 44.80 3.86
1341 1700 2.678934 CTGGCCCAAGCTGCATGT 60.679 61.111 0.00 0.00 39.73 3.21
1409 1815 2.058001 ACTCATCCATGGCGACCGA 61.058 57.895 6.96 0.00 0.00 4.69
1429 1839 0.105593 ATCATGGTCGATGCTCGCTT 59.894 50.000 0.00 0.00 40.21 4.68
1563 1985 1.174712 CCAACAACCAGCTCACCAGG 61.175 60.000 0.00 0.00 0.00 4.45
1576 1998 9.787435 AGTACATGTCTCTATTTAAACCAACAA 57.213 29.630 0.00 0.00 0.00 2.83
1607 2029 0.179000 CCAGAGTATCACCTGGTGGC 59.821 60.000 25.67 15.93 43.71 5.01
1620 2042 1.265236 CCTGAAGCAGAGACCAGAGT 58.735 55.000 0.00 0.00 32.44 3.24
1631 2053 2.747460 GCCATGACGCCTGAAGCA 60.747 61.111 0.00 0.00 44.04 3.91
1664 2089 0.557729 CCCCCAAGATGTAGCCCAAT 59.442 55.000 0.00 0.00 0.00 3.16
1721 2146 3.262660 AGAGAGCATCAACAACAGGATCA 59.737 43.478 0.00 0.00 37.82 2.92
1790 2215 4.634443 CACCTTCCGTTGGACCTAATTAAG 59.366 45.833 0.00 0.00 0.00 1.85
1794 2219 1.280998 CCACCTTCCGTTGGACCTAAT 59.719 52.381 0.00 0.00 0.00 1.73
1795 2220 0.688487 CCACCTTCCGTTGGACCTAA 59.312 55.000 0.00 0.00 0.00 2.69
1796 2221 0.472352 ACCACCTTCCGTTGGACCTA 60.472 55.000 0.00 0.00 0.00 3.08
1797 2222 0.472352 TACCACCTTCCGTTGGACCT 60.472 55.000 0.00 0.00 0.00 3.85
1817 2242 5.333581 TCTGGAGGTAGAACTTCATCTTCA 58.666 41.667 0.00 0.00 0.00 3.02
1834 2259 6.263168 GGTGGGATACATTTTACAATCTGGAG 59.737 42.308 0.00 0.00 39.74 3.86
1899 2345 3.486841 CAGTGCAAATGTGAAACTTTCCG 59.513 43.478 0.00 0.00 38.04 4.30
1902 2348 4.562394 CGTTCAGTGCAAATGTGAAACTTT 59.438 37.500 0.00 0.00 38.04 2.66
1911 2357 2.490328 AACACCGTTCAGTGCAAATG 57.510 45.000 0.00 0.00 41.67 2.32
1929 2380 3.892284 TGGTGACTTAGCAGGTGAAAAA 58.108 40.909 0.00 0.00 32.05 1.94
1981 2432 1.395635 AACCACCGTCAAAAAGGGAC 58.604 50.000 0.00 0.00 36.70 4.46
2080 2532 9.393786 AGAAGAATCCTTAATTAGCCTATGGTA 57.606 33.333 0.00 0.00 31.62 3.25
2081 2533 8.281529 AGAAGAATCCTTAATTAGCCTATGGT 57.718 34.615 0.00 0.00 31.62 3.55
2090 2542 9.574516 GCCCAGAATTAGAAGAATCCTTAATTA 57.425 33.333 0.00 0.00 31.62 1.40
2091 2543 8.061304 TGCCCAGAATTAGAAGAATCCTTAATT 58.939 33.333 0.00 0.00 31.62 1.40
2092 2544 7.586349 TGCCCAGAATTAGAAGAATCCTTAAT 58.414 34.615 0.00 0.00 31.62 1.40
2093 2545 6.969043 TGCCCAGAATTAGAAGAATCCTTAA 58.031 36.000 0.00 0.00 31.62 1.85
2094 2546 6.575244 TGCCCAGAATTAGAAGAATCCTTA 57.425 37.500 0.00 0.00 31.62 2.69
2095 2547 5.456921 TGCCCAGAATTAGAAGAATCCTT 57.543 39.130 0.00 0.00 34.81 3.36
2096 2548 5.659849 ATGCCCAGAATTAGAAGAATCCT 57.340 39.130 0.00 0.00 0.00 3.24
2097 2549 5.829924 TCAATGCCCAGAATTAGAAGAATCC 59.170 40.000 0.00 0.00 0.00 3.01
2098 2550 6.949352 TCAATGCCCAGAATTAGAAGAATC 57.051 37.500 0.00 0.00 0.00 2.52
2099 2551 7.909485 AATCAATGCCCAGAATTAGAAGAAT 57.091 32.000 0.00 0.00 0.00 2.40
2100 2552 7.396907 TCAAATCAATGCCCAGAATTAGAAGAA 59.603 33.333 0.00 0.00 0.00 2.52
2101 2553 6.891361 TCAAATCAATGCCCAGAATTAGAAGA 59.109 34.615 0.00 0.00 0.00 2.87
2102 2554 7.104043 TCAAATCAATGCCCAGAATTAGAAG 57.896 36.000 0.00 0.00 0.00 2.85
2103 2555 6.664816 ACTCAAATCAATGCCCAGAATTAGAA 59.335 34.615 0.00 0.00 0.00 2.10
2104 2556 6.189859 ACTCAAATCAATGCCCAGAATTAGA 58.810 36.000 0.00 0.00 0.00 2.10
2105 2557 6.461110 ACTCAAATCAATGCCCAGAATTAG 57.539 37.500 0.00 0.00 0.00 1.73
2106 2558 9.639563 TTATACTCAAATCAATGCCCAGAATTA 57.360 29.630 0.00 0.00 0.00 1.40
2107 2559 8.537728 TTATACTCAAATCAATGCCCAGAATT 57.462 30.769 0.00 0.00 0.00 2.17
2108 2560 8.716674 ATTATACTCAAATCAATGCCCAGAAT 57.283 30.769 0.00 0.00 0.00 2.40
2109 2561 8.537728 AATTATACTCAAATCAATGCCCAGAA 57.462 30.769 0.00 0.00 0.00 3.02
2110 2562 8.415553 CAAATTATACTCAAATCAATGCCCAGA 58.584 33.333 0.00 0.00 0.00 3.86
2111 2563 7.654520 CCAAATTATACTCAAATCAATGCCCAG 59.345 37.037 0.00 0.00 0.00 4.45
2112 2564 7.418827 CCCAAATTATACTCAAATCAATGCCCA 60.419 37.037 0.00 0.00 0.00 5.36
2113 2565 6.930722 CCCAAATTATACTCAAATCAATGCCC 59.069 38.462 0.00 0.00 0.00 5.36
2114 2566 7.653311 GTCCCAAATTATACTCAAATCAATGCC 59.347 37.037 0.00 0.00 0.00 4.40
2115 2567 8.416329 AGTCCCAAATTATACTCAAATCAATGC 58.584 33.333 0.00 0.00 0.00 3.56
2116 2568 9.740239 CAGTCCCAAATTATACTCAAATCAATG 57.260 33.333 0.00 0.00 0.00 2.82
2117 2569 9.699410 TCAGTCCCAAATTATACTCAAATCAAT 57.301 29.630 0.00 0.00 0.00 2.57
2118 2570 9.527157 TTCAGTCCCAAATTATACTCAAATCAA 57.473 29.630 0.00 0.00 0.00 2.57
2119 2571 9.527157 TTTCAGTCCCAAATTATACTCAAATCA 57.473 29.630 0.00 0.00 0.00 2.57
2122 2574 8.748412 CCATTTCAGTCCCAAATTATACTCAAA 58.252 33.333 0.00 0.00 0.00 2.69
2123 2575 7.147915 GCCATTTCAGTCCCAAATTATACTCAA 60.148 37.037 0.00 0.00 0.00 3.02
2124 2576 6.321181 GCCATTTCAGTCCCAAATTATACTCA 59.679 38.462 0.00 0.00 0.00 3.41
2125 2577 6.239036 GGCCATTTCAGTCCCAAATTATACTC 60.239 42.308 0.00 0.00 0.00 2.59
2126 2578 5.598417 GGCCATTTCAGTCCCAAATTATACT 59.402 40.000 0.00 0.00 0.00 2.12
2127 2579 5.221441 GGGCCATTTCAGTCCCAAATTATAC 60.221 44.000 4.39 0.00 38.62 1.47
2128 2580 4.898861 GGGCCATTTCAGTCCCAAATTATA 59.101 41.667 4.39 0.00 38.62 0.98
2129 2581 3.711190 GGGCCATTTCAGTCCCAAATTAT 59.289 43.478 4.39 0.00 38.62 1.28
2130 2582 3.103742 GGGCCATTTCAGTCCCAAATTA 58.896 45.455 4.39 0.00 38.62 1.40
2131 2583 1.908619 GGGCCATTTCAGTCCCAAATT 59.091 47.619 4.39 0.00 38.62 1.82
2132 2584 1.079323 AGGGCCATTTCAGTCCCAAAT 59.921 47.619 6.18 0.00 41.22 2.32
2133 2585 0.486879 AGGGCCATTTCAGTCCCAAA 59.513 50.000 6.18 0.00 41.22 3.28
2134 2586 1.284785 CTAGGGCCATTTCAGTCCCAA 59.715 52.381 6.18 0.00 41.22 4.12
2135 2587 0.918983 CTAGGGCCATTTCAGTCCCA 59.081 55.000 6.18 0.00 41.22 4.37
2136 2588 0.466372 GCTAGGGCCATTTCAGTCCC 60.466 60.000 6.18 0.00 39.05 4.46
2137 2589 0.548510 AGCTAGGGCCATTTCAGTCC 59.451 55.000 6.18 0.00 39.73 3.85
2138 2590 3.560636 TTAGCTAGGGCCATTTCAGTC 57.439 47.619 6.18 0.00 39.73 3.51
2139 2591 4.526438 ATTTAGCTAGGGCCATTTCAGT 57.474 40.909 6.18 0.00 39.73 3.41
2140 2592 5.625150 AGTATTTAGCTAGGGCCATTTCAG 58.375 41.667 6.18 0.00 39.73 3.02
2141 2593 5.646692 AGTATTTAGCTAGGGCCATTTCA 57.353 39.130 6.18 0.00 39.73 2.69
2142 2594 6.531021 TGTAGTATTTAGCTAGGGCCATTTC 58.469 40.000 6.18 0.00 39.73 2.17
2143 2595 6.509523 TGTAGTATTTAGCTAGGGCCATTT 57.490 37.500 6.18 0.00 39.73 2.32
2144 2596 6.509523 TTGTAGTATTTAGCTAGGGCCATT 57.490 37.500 6.18 0.00 39.73 3.16
2145 2597 6.101296 ACTTTGTAGTATTTAGCTAGGGCCAT 59.899 38.462 6.18 0.00 33.85 4.40
2146 2598 5.427481 ACTTTGTAGTATTTAGCTAGGGCCA 59.573 40.000 6.18 0.00 33.85 5.36
2147 2599 5.926663 ACTTTGTAGTATTTAGCTAGGGCC 58.073 41.667 0.00 0.00 33.85 5.80
2148 2600 7.551617 TCAAACTTTGTAGTATTTAGCTAGGGC 59.448 37.037 1.44 0.00 33.17 5.19
2149 2601 9.614792 ATCAAACTTTGTAGTATTTAGCTAGGG 57.385 33.333 1.44 0.00 33.17 3.53
2169 2621 9.886132 TGAAGGTAATTACTCCTCTAATCAAAC 57.114 33.333 15.05 0.00 33.09 2.93
2171 2623 8.204836 GCTGAAGGTAATTACTCCTCTAATCAA 58.795 37.037 15.05 0.00 33.09 2.57
2172 2624 7.565398 AGCTGAAGGTAATTACTCCTCTAATCA 59.435 37.037 15.05 5.18 33.09 2.57
2173 2625 7.870445 CAGCTGAAGGTAATTACTCCTCTAATC 59.130 40.741 8.42 1.12 33.09 1.75
2174 2626 7.565398 TCAGCTGAAGGTAATTACTCCTCTAAT 59.435 37.037 15.67 0.00 33.09 1.73
2175 2627 6.895756 TCAGCTGAAGGTAATTACTCCTCTAA 59.104 38.462 15.67 0.00 33.09 2.10
2176 2628 6.321690 GTCAGCTGAAGGTAATTACTCCTCTA 59.678 42.308 20.19 0.00 33.09 2.43
2177 2629 5.128008 GTCAGCTGAAGGTAATTACTCCTCT 59.872 44.000 20.19 1.25 33.09 3.69
2178 2630 5.128008 AGTCAGCTGAAGGTAATTACTCCTC 59.872 44.000 20.19 9.59 33.09 3.71
2179 2631 5.026790 AGTCAGCTGAAGGTAATTACTCCT 58.973 41.667 20.19 3.22 35.34 3.69
2180 2632 5.346181 AGTCAGCTGAAGGTAATTACTCC 57.654 43.478 20.19 0.55 0.00 3.85
2181 2633 8.198109 TCATTAGTCAGCTGAAGGTAATTACTC 58.802 37.037 20.19 6.73 0.00 2.59
2182 2634 8.079211 TCATTAGTCAGCTGAAGGTAATTACT 57.921 34.615 20.19 10.96 0.00 2.24
2183 2635 8.894768 ATCATTAGTCAGCTGAAGGTAATTAC 57.105 34.615 20.19 7.09 0.00 1.89
2184 2636 8.150945 GGATCATTAGTCAGCTGAAGGTAATTA 58.849 37.037 20.19 13.13 0.00 1.40
2185 2637 6.995091 GGATCATTAGTCAGCTGAAGGTAATT 59.005 38.462 20.19 8.05 0.00 1.40
2186 2638 6.328672 AGGATCATTAGTCAGCTGAAGGTAAT 59.671 38.462 20.19 17.65 0.00 1.89
2187 2639 5.663106 AGGATCATTAGTCAGCTGAAGGTAA 59.337 40.000 20.19 16.21 0.00 2.85
2188 2640 5.211973 AGGATCATTAGTCAGCTGAAGGTA 58.788 41.667 20.19 7.80 0.00 3.08
2189 2641 4.036518 AGGATCATTAGTCAGCTGAAGGT 58.963 43.478 20.19 8.87 0.00 3.50
2190 2642 4.686191 AGGATCATTAGTCAGCTGAAGG 57.314 45.455 20.19 4.94 0.00 3.46
2191 2643 5.055812 GGAAGGATCATTAGTCAGCTGAAG 58.944 45.833 20.19 6.51 0.00 3.02
2192 2644 4.442052 CGGAAGGATCATTAGTCAGCTGAA 60.442 45.833 20.19 2.92 0.00 3.02
2193 2645 3.068732 CGGAAGGATCATTAGTCAGCTGA 59.931 47.826 13.74 13.74 0.00 4.26
2194 2646 3.388308 CGGAAGGATCATTAGTCAGCTG 58.612 50.000 7.63 7.63 0.00 4.24
2195 2647 3.742433 CGGAAGGATCATTAGTCAGCT 57.258 47.619 0.00 0.00 0.00 4.24
2210 2662 2.240493 ACAGTGTCTTGAACCGGAAG 57.760 50.000 9.46 0.61 0.00 3.46
2211 2663 2.680841 CAAACAGTGTCTTGAACCGGAA 59.319 45.455 9.46 0.00 0.00 4.30
2212 2664 2.093394 TCAAACAGTGTCTTGAACCGGA 60.093 45.455 9.46 0.00 0.00 5.14
2213 2665 2.031683 GTCAAACAGTGTCTTGAACCGG 59.968 50.000 17.02 0.00 33.52 5.28
2214 2666 2.936498 AGTCAAACAGTGTCTTGAACCG 59.064 45.455 17.02 0.00 33.52 4.44
2215 2667 5.357257 TCTAGTCAAACAGTGTCTTGAACC 58.643 41.667 17.02 9.73 33.52 3.62
2216 2668 6.903883 TTCTAGTCAAACAGTGTCTTGAAC 57.096 37.500 17.02 12.95 34.29 3.18
2217 2669 8.397906 CAAATTCTAGTCAAACAGTGTCTTGAA 58.602 33.333 17.02 12.83 39.73 2.69
2218 2670 7.012327 CCAAATTCTAGTCAAACAGTGTCTTGA 59.988 37.037 13.46 13.46 0.00 3.02
2219 2671 7.134815 CCAAATTCTAGTCAAACAGTGTCTTG 58.865 38.462 0.00 4.16 0.00 3.02
2220 2672 6.263168 CCCAAATTCTAGTCAAACAGTGTCTT 59.737 38.462 0.00 0.00 0.00 3.01
2221 2673 5.765182 CCCAAATTCTAGTCAAACAGTGTCT 59.235 40.000 0.00 0.00 0.00 3.41
2222 2674 5.763204 TCCCAAATTCTAGTCAAACAGTGTC 59.237 40.000 0.00 0.00 0.00 3.67
2223 2675 5.531287 GTCCCAAATTCTAGTCAAACAGTGT 59.469 40.000 0.00 0.00 0.00 3.55
2224 2676 5.765182 AGTCCCAAATTCTAGTCAAACAGTG 59.235 40.000 0.00 0.00 0.00 3.66
2225 2677 5.765182 CAGTCCCAAATTCTAGTCAAACAGT 59.235 40.000 0.00 0.00 0.00 3.55
2226 2678 5.997746 TCAGTCCCAAATTCTAGTCAAACAG 59.002 40.000 0.00 0.00 0.00 3.16
2227 2679 5.935945 TCAGTCCCAAATTCTAGTCAAACA 58.064 37.500 0.00 0.00 0.00 2.83
2228 2680 6.877611 TTCAGTCCCAAATTCTAGTCAAAC 57.122 37.500 0.00 0.00 0.00 2.93
2229 2681 7.523709 GCATTTCAGTCCCAAATTCTAGTCAAA 60.524 37.037 0.00 0.00 0.00 2.69
2230 2682 6.071952 GCATTTCAGTCCCAAATTCTAGTCAA 60.072 38.462 0.00 0.00 0.00 3.18
2231 2683 5.415701 GCATTTCAGTCCCAAATTCTAGTCA 59.584 40.000 0.00 0.00 0.00 3.41
2232 2684 5.415701 TGCATTTCAGTCCCAAATTCTAGTC 59.584 40.000 0.00 0.00 0.00 2.59
2233 2685 5.324409 TGCATTTCAGTCCCAAATTCTAGT 58.676 37.500 0.00 0.00 0.00 2.57
2234 2686 5.902613 TGCATTTCAGTCCCAAATTCTAG 57.097 39.130 0.00 0.00 0.00 2.43
2235 2687 5.716228 ACATGCATTTCAGTCCCAAATTCTA 59.284 36.000 0.00 0.00 0.00 2.10
2236 2688 4.529377 ACATGCATTTCAGTCCCAAATTCT 59.471 37.500 0.00 0.00 0.00 2.40
2237 2689 4.628333 CACATGCATTTCAGTCCCAAATTC 59.372 41.667 0.00 0.00 0.00 2.17
2238 2690 4.563993 CCACATGCATTTCAGTCCCAAATT 60.564 41.667 0.00 0.00 0.00 1.82
2239 2691 3.055675 CCACATGCATTTCAGTCCCAAAT 60.056 43.478 0.00 0.00 0.00 2.32
2261 2713 5.708877 AGTCCTCTAGTCAACACTACAAC 57.291 43.478 0.00 0.00 33.62 3.32
2354 2806 2.551459 AGTTGCTCACATTCTCAGTTGC 59.449 45.455 0.00 0.00 0.00 4.17
2369 2821 2.548067 CCGAGTTTGAGTACCAGTTGCT 60.548 50.000 0.00 0.00 0.00 3.91
2373 2825 0.320697 GCCCGAGTTTGAGTACCAGT 59.679 55.000 0.00 0.00 0.00 4.00
2378 2830 1.053424 AACCTGCCCGAGTTTGAGTA 58.947 50.000 0.00 0.00 0.00 2.59
2383 2835 2.597510 GCCAACCTGCCCGAGTTT 60.598 61.111 0.00 0.00 0.00 2.66
2406 2858 4.887071 ACTTGTGAATTAGCAGGTGTTTGA 59.113 37.500 0.00 0.00 0.00 2.69
2408 2860 4.887071 TCACTTGTGAATTAGCAGGTGTTT 59.113 37.500 17.39 0.00 41.48 2.83
2422 2874 9.403583 TGACTATGTATACACTATCACTTGTGA 57.596 33.333 7.96 5.89 37.59 3.58
2423 2875 9.452065 GTGACTATGTATACACTATCACTTGTG 57.548 37.037 24.52 0.00 39.80 3.33
2424 2876 9.185680 TGTGACTATGTATACACTATCACTTGT 57.814 33.333 28.12 13.51 36.16 3.16
2455 3084 1.940883 TACGTCACTCATGCCCGACC 61.941 60.000 0.00 0.00 0.00 4.79
2491 3120 2.047274 ACCTGCGCGTGTTGCTAT 60.047 55.556 8.43 0.00 43.27 2.97
2511 3140 2.752903 GGCCACAATATCGACTGGTTTT 59.247 45.455 0.00 0.00 0.00 2.43
2536 3165 2.283388 TAACCACCGGCTCCTCGT 60.283 61.111 0.00 0.00 0.00 4.18
2560 3189 0.984109 CGTGAATTGCATGTTTCGCC 59.016 50.000 10.63 0.87 0.00 5.54
2623 3252 3.572632 AGCATCATCAACCTAGCATGT 57.427 42.857 0.00 0.00 0.00 3.21
2625 3254 3.558746 GCCTAGCATCATCAACCTAGCAT 60.559 47.826 0.00 0.00 0.00 3.79
2626 3255 2.224378 GCCTAGCATCATCAACCTAGCA 60.224 50.000 0.00 0.00 0.00 3.49
2627 3256 2.421619 GCCTAGCATCATCAACCTAGC 58.578 52.381 0.00 0.00 0.00 3.42
2628 3257 2.611473 CGGCCTAGCATCATCAACCTAG 60.611 54.545 0.00 0.00 0.00 3.02
2629 3258 1.344438 CGGCCTAGCATCATCAACCTA 59.656 52.381 0.00 0.00 0.00 3.08
2630 3259 0.107456 CGGCCTAGCATCATCAACCT 59.893 55.000 0.00 0.00 0.00 3.50
2631 3260 0.106708 TCGGCCTAGCATCATCAACC 59.893 55.000 0.00 0.00 0.00 3.77
2632 3261 2.072298 GATCGGCCTAGCATCATCAAC 58.928 52.381 0.00 0.00 0.00 3.18
2633 3262 1.693606 TGATCGGCCTAGCATCATCAA 59.306 47.619 0.00 0.00 0.00 2.57
2634 3263 1.341080 TGATCGGCCTAGCATCATCA 58.659 50.000 0.00 0.00 0.00 3.07
2635 3264 2.687700 ATGATCGGCCTAGCATCATC 57.312 50.000 1.48 0.00 32.81 2.92
2636 3265 3.681034 GCTTATGATCGGCCTAGCATCAT 60.681 47.826 11.78 14.59 39.89 2.45
2637 3266 2.354103 GCTTATGATCGGCCTAGCATCA 60.354 50.000 11.78 8.48 0.00 3.07
2638 3267 2.093764 AGCTTATGATCGGCCTAGCATC 60.094 50.000 11.78 2.77 0.00 3.91
2647 3276 1.342074 TCCAGGGAGCTTATGATCGG 58.658 55.000 0.00 0.00 0.00 4.18
2736 3366 8.591114 TGCCATCTAATCTACTAATACTACCC 57.409 38.462 0.00 0.00 0.00 3.69
2740 3370 9.442047 GCAATTGCCATCTAATCTACTAATACT 57.558 33.333 20.06 0.00 34.31 2.12
2741 3371 9.219603 TGCAATTGCCATCTAATCTACTAATAC 57.780 33.333 26.94 0.00 41.18 1.89
2742 3372 9.964354 ATGCAATTGCCATCTAATCTACTAATA 57.036 29.630 26.94 2.44 41.18 0.98
2743 3373 8.874744 ATGCAATTGCCATCTAATCTACTAAT 57.125 30.769 26.94 5.51 41.18 1.73
2744 3374 8.159447 AGATGCAATTGCCATCTAATCTACTAA 58.841 33.333 28.59 9.94 41.18 2.24


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

AutoCloner maintained by Alex Coulton.