Multiple sequence alignment - TraesCS2D01G535000

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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 TraesCS2D01G535000 chr2D 100.000 3859 0 0 1 3859 618253489 618249631 0.000000e+00 7127.0
1 TraesCS2D01G535000 chr2D 82.094 363 36 11 478 815 598718528 598718886 2.270000e-72 283.0
2 TraesCS2D01G535000 chr2A 94.669 1932 96 5 1931 3859 749094114 749092187 0.000000e+00 2990.0
3 TraesCS2D01G535000 chr2A 92.553 752 52 3 1 750 749096619 749095870 0.000000e+00 1075.0
4 TraesCS2D01G535000 chr2A 84.455 1055 92 42 746 1750 749095716 749094684 0.000000e+00 974.0
5 TraesCS2D01G535000 chr2A 87.500 152 11 5 659 803 252089811 252089661 6.630000e-38 169.0
6 TraesCS2D01G535000 chr2B 87.949 1867 160 26 1798 3654 754867847 754866036 0.000000e+00 2141.0
7 TraesCS2D01G535000 chr2B 92.500 160 10 2 3639 3798 754865693 754865536 1.080000e-55 228.0
8 TraesCS2D01G535000 chr2B 100.000 30 0 0 3830 3859 754865536 754865507 5.390000e-04 56.5
9 TraesCS2D01G535000 chr3A 89.394 264 26 2 150 412 162081726 162081988 7.990000e-87 331.0
10 TraesCS2D01G535000 chr3A 87.970 266 28 4 149 412 664693110 664692847 1.040000e-80 311.0
11 TraesCS2D01G535000 chr5A 89.020 255 27 1 152 406 9609315 9609062 8.050000e-82 315.0
12 TraesCS2D01G535000 chr5A 87.023 262 31 3 152 412 440672994 440673253 3.770000e-75 292.0
13 TraesCS2D01G535000 chr5A 87.109 256 29 4 152 404 388577929 388578183 1.750000e-73 287.0
14 TraesCS2D01G535000 chr6D 87.121 264 32 2 150 412 423215653 423215391 8.110000e-77 298.0
15 TraesCS2D01G535000 chr5D 85.921 277 32 6 151 425 520654610 520654339 4.880000e-74 289.0
16 TraesCS2D01G535000 chr5D 84.146 164 22 4 483 645 559301609 559301449 5.160000e-34 156.0
17 TraesCS2D01G535000 chr3B 85.556 270 37 2 149 417 350130342 350130074 8.160000e-72 281.0
18 TraesCS2D01G535000 chr7D 82.647 340 36 13 476 796 638278500 638278835 2.940000e-71 279.0
19 TraesCS2D01G535000 chr7D 80.172 348 42 12 473 796 218598903 218598559 6.450000e-58 235.0
20 TraesCS2D01G535000 chr7D 80.321 249 24 13 573 798 101245161 101244915 8.580000e-37 165.0
21 TraesCS2D01G535000 chr7A 82.006 339 40 12 476 796 727790951 727790616 6.350000e-68 268.0
22 TraesCS2D01G535000 chr4A 79.501 361 43 16 474 808 729636232 729635877 1.080000e-55 228.0
23 TraesCS2D01G535000 chr1D 86.928 153 17 2 659 809 397166514 397166665 6.630000e-38 169.0


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 TraesCS2D01G535000 chr2D 618249631 618253489 3858 True 7127.000000 7127 100.000 1 3859 1 chr2D.!!$R1 3858
1 TraesCS2D01G535000 chr2A 749092187 749096619 4432 True 1679.666667 2990 90.559 1 3859 3 chr2A.!!$R2 3858
2 TraesCS2D01G535000 chr2B 754865507 754867847 2340 True 808.500000 2141 93.483 1798 3859 3 chr2B.!!$R1 2061

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
789 950 0.039346 TGCAACGCATGGTCACATTG 60.039 50.0 0.0 0.0 34.35 2.82 F
1461 1660 0.259356 TTTGTGGGACGGGGAAAGTT 59.741 50.0 0.0 0.0 0.00 2.66 F
1636 1850 0.464373 CCGGGATTGGACTGGATGTG 60.464 60.0 0.0 0.0 36.43 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2620 3238 0.033642 TTGTCCAATACACCGCGTGA 59.966 50.000 4.92 0.0 38.00 4.35 R
2632 3250 1.001487 CAACTGCGAGCAATTGTCCAA 60.001 47.619 10.63 0.0 29.78 3.53 R
3240 3862 1.358725 CGCATACTGTTCCACCCGTG 61.359 60.000 0.00 0.0 0.00 4.94 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
130 131 2.327325 TACTGGGAGCTCTCAAACCT 57.673 50.000 18.91 2.93 0.00 3.50
161 162 5.576563 TTGATTCTTTTGTACTCCCTCCA 57.423 39.130 0.00 0.00 0.00 3.86
175 176 4.018324 ACTCCCTCCAGTCCTTTTTATTCC 60.018 45.833 0.00 0.00 0.00 3.01
176 177 3.920197 TCCCTCCAGTCCTTTTTATTCCA 59.080 43.478 0.00 0.00 0.00 3.53
177 178 4.544152 TCCCTCCAGTCCTTTTTATTCCAT 59.456 41.667 0.00 0.00 0.00 3.41
226 227 7.440198 AGTACCTCTACTTTGACCAAACTTAC 58.560 38.462 0.00 0.00 27.62 2.34
329 330 8.997621 TTTGGTACTGTAGATGTTGATACTTC 57.002 34.615 0.00 0.00 0.00 3.01
396 397 9.448294 ACACAAATTTAATACGCGAAGTAAAAA 57.552 25.926 15.93 5.84 39.04 1.94
459 460 3.426560 GGTTAGCGTAATTTGGAAACCGG 60.427 47.826 0.00 0.00 0.00 5.28
462 463 0.179184 CGTAATTTGGAAACCGGCCG 60.179 55.000 21.04 21.04 0.00 6.13
471 472 3.860930 AAACCGGCCGAGCATTGGT 62.861 57.895 30.73 11.48 43.65 3.67
520 521 1.019673 AGTTGATGATGATGGTGCGC 58.980 50.000 0.00 0.00 0.00 6.09
524 525 0.816825 GATGATGATGGTGCGCCTGT 60.817 55.000 18.96 6.13 35.27 4.00
532 533 1.750399 GGTGCGCCTGTCATCCATT 60.750 57.895 9.68 0.00 0.00 3.16
538 539 2.880890 GCGCCTGTCATCCATTATTTCT 59.119 45.455 0.00 0.00 0.00 2.52
541 542 4.576053 CGCCTGTCATCCATTATTTCTGAA 59.424 41.667 0.00 0.00 0.00 3.02
570 571 7.043961 AGATTCGCATCTAACAACTATGAGA 57.956 36.000 0.00 0.00 38.06 3.27
577 578 8.483218 CGCATCTAACAACTATGAGATAAGTTG 58.517 37.037 12.36 12.36 44.86 3.16
614 615 6.737346 GCAACAATAACCCACTTTTCTGCTTA 60.737 38.462 0.00 0.00 0.00 3.09
678 681 8.632906 ATTCTCAGCCTGAGGAATATATTTTG 57.367 34.615 21.14 0.00 44.39 2.44
686 689 8.131731 GCCTGAGGAATATATTTTGAGTGAAAC 58.868 37.037 0.65 0.00 0.00 2.78
786 947 1.358402 GTTGCAACGCATGGTCACA 59.642 52.632 14.90 0.00 38.76 3.58
789 950 0.039346 TGCAACGCATGGTCACATTG 60.039 50.000 0.00 0.00 34.35 2.82
792 953 1.468127 CAACGCATGGTCACATTGCTA 59.532 47.619 0.00 0.00 34.35 3.49
793 954 1.372582 ACGCATGGTCACATTGCTAG 58.627 50.000 0.00 0.00 34.35 3.42
794 955 1.339055 ACGCATGGTCACATTGCTAGT 60.339 47.619 0.00 0.00 34.35 2.57
799 968 5.618863 CGCATGGTCACATTGCTAGTAAAAA 60.619 40.000 0.00 0.00 34.35 1.94
902 1071 4.317139 CGTGTTGACGTTGACTTTGACTAG 60.317 45.833 0.00 0.00 40.91 2.57
930 1099 3.441492 GCTTCTTGCGACTTACTTCAC 57.559 47.619 0.00 0.00 0.00 3.18
931 1100 2.800544 GCTTCTTGCGACTTACTTCACA 59.199 45.455 0.00 0.00 0.00 3.58
932 1101 3.433615 GCTTCTTGCGACTTACTTCACAT 59.566 43.478 0.00 0.00 0.00 3.21
933 1102 4.667668 GCTTCTTGCGACTTACTTCACATG 60.668 45.833 0.00 0.00 0.00 3.21
934 1103 3.325870 TCTTGCGACTTACTTCACATGG 58.674 45.455 0.00 0.00 0.00 3.66
1148 1320 1.153549 CCTACTCGGCTGGTCTTGC 60.154 63.158 0.00 0.00 0.00 4.01
1151 1323 4.379243 CTCGGCTGGTCTTGCGGT 62.379 66.667 0.00 0.00 33.41 5.68
1196 1368 2.759973 CTCAGGTGGCGGCCTCTA 60.760 66.667 21.46 5.94 36.58 2.43
1198 1370 4.514577 CAGGTGGCGGCCTCTACG 62.515 72.222 21.46 5.64 36.58 3.51
1251 1423 1.053424 TAACCGTCCAGCCTCACTTT 58.947 50.000 0.00 0.00 0.00 2.66
1256 1431 1.692411 GTCCAGCCTCACTTTTGGTT 58.308 50.000 0.00 0.00 32.51 3.67
1258 1433 1.214175 TCCAGCCTCACTTTTGGTTGA 59.786 47.619 0.00 0.00 36.81 3.18
1267 1442 6.239036 GCCTCACTTTTGGTTGAAGTAGATTT 60.239 38.462 0.00 0.00 35.68 2.17
1275 1450 8.836268 TTTGGTTGAAGTAGATTTATGTACGT 57.164 30.769 0.00 0.00 32.36 3.57
1276 1451 9.926158 TTTGGTTGAAGTAGATTTATGTACGTA 57.074 29.630 0.00 0.00 32.36 3.57
1278 1453 9.740239 TGGTTGAAGTAGATTTATGTACGTATC 57.260 33.333 0.00 0.00 32.36 2.24
1279 1454 9.740239 GGTTGAAGTAGATTTATGTACGTATCA 57.260 33.333 0.00 0.00 32.36 2.15
1294 1469 7.593825 TGTACGTATCATTATCAGACATCTGG 58.406 38.462 8.99 0.00 43.91 3.86
1295 1470 6.901081 ACGTATCATTATCAGACATCTGGA 57.099 37.500 8.99 0.00 43.91 3.86
1296 1471 7.290110 ACGTATCATTATCAGACATCTGGAA 57.710 36.000 8.99 4.66 43.91 3.53
1297 1472 7.148641 ACGTATCATTATCAGACATCTGGAAC 58.851 38.462 8.99 0.49 43.91 3.62
1302 1501 8.482852 TCATTATCAGACATCTGGAACATAGA 57.517 34.615 8.99 0.00 43.91 1.98
1311 1510 7.344093 AGACATCTGGAACATAGATTCTGAAGA 59.656 37.037 0.00 0.00 38.20 2.87
1312 1511 7.855375 ACATCTGGAACATAGATTCTGAAGAA 58.145 34.615 0.00 0.00 38.20 2.52
1313 1512 7.986320 ACATCTGGAACATAGATTCTGAAGAAG 59.014 37.037 0.00 0.00 38.20 2.85
1314 1513 7.724490 TCTGGAACATAGATTCTGAAGAAGA 57.276 36.000 0.00 0.00 38.20 2.87
1316 1515 8.256605 TCTGGAACATAGATTCTGAAGAAGAAG 58.743 37.037 0.00 0.00 43.32 2.85
1328 1527 7.721286 TCTGAAGAAGAAGAAAACATCTGAC 57.279 36.000 0.00 0.00 38.79 3.51
1329 1528 7.504403 TCTGAAGAAGAAGAAAACATCTGACT 58.496 34.615 0.00 0.00 38.79 3.41
1330 1529 7.655328 TCTGAAGAAGAAGAAAACATCTGACTC 59.345 37.037 0.00 0.00 38.79 3.36
1331 1530 6.708054 TGAAGAAGAAGAAAACATCTGACTCC 59.292 38.462 0.00 0.00 38.79 3.85
1332 1531 6.179906 AGAAGAAGAAAACATCTGACTCCA 57.820 37.500 0.00 0.00 38.79 3.86
1333 1532 6.777782 AGAAGAAGAAAACATCTGACTCCAT 58.222 36.000 0.00 0.00 38.79 3.41
1334 1533 7.911651 AGAAGAAGAAAACATCTGACTCCATA 58.088 34.615 0.00 0.00 38.79 2.74
1335 1534 8.378565 AGAAGAAGAAAACATCTGACTCCATAA 58.621 33.333 0.00 0.00 38.79 1.90
1336 1535 9.171877 GAAGAAGAAAACATCTGACTCCATAAT 57.828 33.333 0.00 0.00 38.79 1.28
1337 1536 9.525826 AAGAAGAAAACATCTGACTCCATAATT 57.474 29.630 0.00 0.00 38.79 1.40
1338 1537 8.954350 AGAAGAAAACATCTGACTCCATAATTG 58.046 33.333 0.00 0.00 38.79 2.32
1350 1549 4.646492 ACTCCATAATTGTCAGAATTGGGC 59.354 41.667 0.00 0.00 0.00 5.36
1362 1561 5.006746 GTCAGAATTGGGCGTAGTATTCTTG 59.993 44.000 0.00 0.00 35.70 3.02
1400 1599 8.349245 TGTTGTGTTGTATGAGAAAATTACAGG 58.651 33.333 0.00 0.00 0.00 4.00
1412 1611 7.020827 AGAAAATTACAGGAATGGAGAGACA 57.979 36.000 0.00 0.00 0.00 3.41
1460 1659 0.481128 ATTTGTGGGACGGGGAAAGT 59.519 50.000 0.00 0.00 0.00 2.66
1461 1660 0.259356 TTTGTGGGACGGGGAAAGTT 59.741 50.000 0.00 0.00 0.00 2.66
1470 1669 3.532542 GACGGGGAAAGTTAATCTGAGG 58.467 50.000 0.00 0.00 0.00 3.86
1472 1671 3.585732 ACGGGGAAAGTTAATCTGAGGAA 59.414 43.478 0.00 0.00 0.00 3.36
1475 1674 5.106277 CGGGGAAAGTTAATCTGAGGAAAAC 60.106 44.000 0.00 0.00 0.00 2.43
1477 1676 6.266786 GGGGAAAGTTAATCTGAGGAAAACAA 59.733 38.462 0.00 0.00 0.00 2.83
1484 1683 9.384764 AGTTAATCTGAGGAAAACAATACTAGC 57.615 33.333 0.00 0.00 0.00 3.42
1485 1684 9.162764 GTTAATCTGAGGAAAACAATACTAGCA 57.837 33.333 0.00 0.00 0.00 3.49
1486 1685 7.617041 AATCTGAGGAAAACAATACTAGCAC 57.383 36.000 0.00 0.00 0.00 4.40
1488 1687 6.711277 TCTGAGGAAAACAATACTAGCACAT 58.289 36.000 0.00 0.00 0.00 3.21
1490 1689 6.472016 TGAGGAAAACAATACTAGCACATGA 58.528 36.000 0.00 0.00 0.00 3.07
1491 1690 6.595326 TGAGGAAAACAATACTAGCACATGAG 59.405 38.462 0.00 0.00 0.00 2.90
1492 1691 5.355350 AGGAAAACAATACTAGCACATGAGC 59.645 40.000 7.07 7.07 0.00 4.26
1493 1692 5.123820 GGAAAACAATACTAGCACATGAGCA 59.876 40.000 17.61 2.84 36.85 4.26
1494 1693 5.551760 AAACAATACTAGCACATGAGCAC 57.448 39.130 17.61 0.00 36.85 4.40
1495 1694 4.206477 ACAATACTAGCACATGAGCACA 57.794 40.909 17.61 3.76 36.85 4.57
1497 1696 2.299993 TACTAGCACATGAGCACAGC 57.700 50.000 17.61 2.85 36.85 4.40
1499 1698 1.065636 ACTAGCACATGAGCACAGCAT 60.066 47.619 17.61 0.00 36.85 3.79
1500 1699 2.169144 ACTAGCACATGAGCACAGCATA 59.831 45.455 17.61 0.00 36.85 3.14
1501 1700 2.118313 AGCACATGAGCACAGCATAA 57.882 45.000 17.61 0.00 36.85 1.90
1503 1702 2.821378 AGCACATGAGCACAGCATAAAA 59.179 40.909 17.61 0.00 36.85 1.52
1510 1720 5.556355 TGAGCACAGCATAAAAGATTCAG 57.444 39.130 0.00 0.00 0.00 3.02
1591 1805 8.699130 CATCTATGCCATGTTATACTCCAGATA 58.301 37.037 0.00 0.00 0.00 1.98
1594 1808 9.896645 CTATGCCATGTTATACTCCAGATATTT 57.103 33.333 0.00 0.00 0.00 1.40
1606 1820 7.778470 ACTCCAGATATTTTAAGAGCTTTCG 57.222 36.000 0.00 0.00 0.00 3.46
1611 1825 9.050601 CCAGATATTTTAAGAGCTTTCGAAGAT 57.949 33.333 0.00 0.00 35.04 2.40
1624 1838 1.553248 TCGAAGATGTCAACCGGGATT 59.447 47.619 6.32 0.00 0.00 3.01
1625 1839 1.665679 CGAAGATGTCAACCGGGATTG 59.334 52.381 6.32 1.67 0.00 2.67
1628 1842 1.065418 AGATGTCAACCGGGATTGGAC 60.065 52.381 6.32 6.34 0.00 4.02
1631 1845 0.676782 GTCAACCGGGATTGGACTGG 60.677 60.000 6.32 0.00 40.32 4.00
1632 1846 0.838554 TCAACCGGGATTGGACTGGA 60.839 55.000 6.32 0.00 37.80 3.86
1635 1849 0.914417 ACCGGGATTGGACTGGATGT 60.914 55.000 6.32 0.00 37.80 3.06
1636 1850 0.464373 CCGGGATTGGACTGGATGTG 60.464 60.000 0.00 0.00 36.43 3.21
1644 1864 1.271001 TGGACTGGATGTGCACAAGAG 60.271 52.381 25.72 20.48 42.10 2.85
1649 1869 2.036256 ATGTGCACAAGAGGCCCC 59.964 61.111 25.72 0.00 0.00 5.80
1675 1895 4.331992 CACACTGAAGCATCTCCATAACTG 59.668 45.833 0.00 0.00 0.00 3.16
1722 1949 9.177608 TGTTCTTCAATCTATAGGGTTGATTTG 57.822 33.333 16.85 12.27 31.28 2.32
1761 1988 9.134734 GCTACTAGCAGATATTATGACTTGAAC 57.865 37.037 2.96 0.00 41.89 3.18
1775 2002 7.848223 ATGACTTGAACATATGACGAATTCA 57.152 32.000 10.38 5.68 39.11 2.57
1777 2004 7.687445 TGACTTGAACATATGACGAATTCATG 58.313 34.615 10.38 12.21 45.22 3.07
1778 2005 7.334171 TGACTTGAACATATGACGAATTCATGT 59.666 33.333 10.38 14.98 45.22 3.21
1779 2006 8.044060 ACTTGAACATATGACGAATTCATGTT 57.956 30.769 16.66 16.66 45.22 2.71
1780 2007 8.177663 ACTTGAACATATGACGAATTCATGTTC 58.822 33.333 26.42 26.42 46.06 3.18
1789 2016 7.848223 TGACGAATTCATGTTCATATTGACT 57.152 32.000 6.22 0.00 0.00 3.41
1790 2017 8.267620 TGACGAATTCATGTTCATATTGACTT 57.732 30.769 6.22 0.00 0.00 3.01
1791 2018 8.390354 TGACGAATTCATGTTCATATTGACTTC 58.610 33.333 6.22 0.00 0.00 3.01
1792 2019 8.498054 ACGAATTCATGTTCATATTGACTTCT 57.502 30.769 6.22 0.00 30.93 2.85
1793 2020 8.950210 ACGAATTCATGTTCATATTGACTTCTT 58.050 29.630 6.22 0.00 30.93 2.52
1794 2021 9.778993 CGAATTCATGTTCATATTGACTTCTTT 57.221 29.630 6.22 0.00 30.93 2.52
1837 2064 6.201044 CGGTCAGATAATTGGTCTAACACATC 59.799 42.308 0.00 0.00 0.00 3.06
1840 2067 9.988815 GTCAGATAATTGGTCTAACACATCTAT 57.011 33.333 0.00 0.00 0.00 1.98
1929 2499 4.336433 TCTTGCTGCTGATAAAACTATGCC 59.664 41.667 0.00 0.00 0.00 4.40
1943 2513 4.987963 ACTATGCCATGGAAGATCATCA 57.012 40.909 18.40 0.65 0.00 3.07
1987 2605 2.753055 TGTGCGAGTTATGCAGGTTA 57.247 45.000 0.00 0.00 44.21 2.85
1993 2611 5.981315 GTGCGAGTTATGCAGGTTATACTTA 59.019 40.000 0.00 0.00 44.21 2.24
2020 2638 1.899437 CGCTTAGTTCCCCTGCAGGA 61.899 60.000 34.91 13.12 38.24 3.86
2061 2679 0.512952 CGACTTCCGCCAAGTTCTTG 59.487 55.000 5.66 5.66 46.10 3.02
2102 2720 1.601171 CCCAGGCAGTCTCCAAGAG 59.399 63.158 0.00 0.00 0.00 2.85
2113 2731 0.668706 CTCCAAGAGTCACTGCACGG 60.669 60.000 0.00 0.00 0.00 4.94
2146 2764 4.020218 CCCCTTTATGCGATCCTTCTCATA 60.020 45.833 0.00 0.00 30.24 2.15
2199 2817 4.943705 GCATCTCCTCATTTTCCACAAGTA 59.056 41.667 0.00 0.00 0.00 2.24
2206 2824 6.269077 TCCTCATTTTCCACAAGTACTAGTGA 59.731 38.462 5.39 0.00 37.97 3.41
2218 2836 3.628487 AGTACTAGTGATGAGAGCCGAAC 59.372 47.826 5.39 0.00 0.00 3.95
2219 2837 2.447443 ACTAGTGATGAGAGCCGAACA 58.553 47.619 0.00 0.00 0.00 3.18
2242 2860 7.185565 ACATATGGTACTGGATATAGCAGAGT 58.814 38.462 7.80 0.00 33.80 3.24
2244 2862 8.535335 CATATGGTACTGGATATAGCAGAGTTT 58.465 37.037 0.00 0.00 33.80 2.66
2333 2951 1.530293 GCTGAGCTTATGATCCTTGCG 59.470 52.381 0.00 0.00 0.00 4.85
2359 2977 0.934436 GCACCAAACATGTGTCGTGC 60.934 55.000 20.79 20.79 37.87 5.34
2424 3042 1.338105 TGCTCGGTGTTCAGATTGAGG 60.338 52.381 0.00 0.00 0.00 3.86
2429 3047 4.065088 TCGGTGTTCAGATTGAGGAAAAG 58.935 43.478 0.00 0.00 0.00 2.27
2435 3053 4.371624 TCAGATTGAGGAAAAGAGCCAA 57.628 40.909 0.00 0.00 0.00 4.52
2438 3056 5.776716 TCAGATTGAGGAAAAGAGCCAAAAT 59.223 36.000 0.00 0.00 0.00 1.82
2556 3174 1.079057 GTCCTCCCTGAAGAACGCC 60.079 63.158 0.00 0.00 0.00 5.68
2558 3176 0.909610 TCCTCCCTGAAGAACGCCAT 60.910 55.000 0.00 0.00 0.00 4.40
2586 3204 2.749621 GCTCAGATTTTCGGGTGTGATT 59.250 45.455 0.00 0.00 0.00 2.57
2592 3210 3.907894 TTTTCGGGTGTGATTGTAAGC 57.092 42.857 0.00 0.00 0.00 3.09
2606 3224 1.210478 TGTAAGCTGGAGGAGGATTGC 59.790 52.381 0.00 0.00 0.00 3.56
2613 3231 1.379642 GGAGGAGGATTGCTTTGCCG 61.380 60.000 0.00 0.00 0.00 5.69
2620 3238 1.669999 GATTGCTTTGCCGGAGCCAT 61.670 55.000 5.05 2.07 39.38 4.40
2624 3242 2.745884 TTTGCCGGAGCCATCACG 60.746 61.111 5.05 0.00 38.69 4.35
2632 3250 1.227263 GAGCCATCACGCGGTGTAT 60.227 57.895 12.47 0.00 34.79 2.29
2924 3543 3.654321 TGGAGATATCCTGCCATTGACAT 59.346 43.478 8.09 0.00 31.46 3.06
2971 3590 6.817184 ACTACTTGTTGAGTACAATGACACT 58.183 36.000 0.00 0.00 45.31 3.55
3231 3853 0.464916 GGGAACGACAACCACCAACT 60.465 55.000 0.00 0.00 0.00 3.16
3240 3862 1.102978 AACCACCAACTGCTTGTCAC 58.897 50.000 0.00 0.00 0.00 3.67
3320 3942 1.412710 AGTTGAGTGATCACGGTGTGT 59.587 47.619 19.85 1.13 34.79 3.72
3321 3943 2.626266 AGTTGAGTGATCACGGTGTGTA 59.374 45.455 19.85 0.58 34.79 2.90
3351 3973 5.246981 TCTGTGAATTTCAGTCCAGGATT 57.753 39.130 12.82 0.00 34.86 3.01
3359 3981 3.969287 TCAGTCCAGGATTTGTCTCTG 57.031 47.619 0.00 0.00 0.00 3.35
3631 4253 2.159085 ACAAGGATCAGCGGTAAGTAGC 60.159 50.000 0.00 0.00 0.00 3.58
3651 4273 1.881973 CAGACACACAAATGGAGGTGG 59.118 52.381 0.00 0.00 39.31 4.61
3654 4276 2.489329 GACACACAAATGGAGGTGGATG 59.511 50.000 0.00 0.00 39.31 3.51
3656 4278 1.428912 ACACAAATGGAGGTGGATGGT 59.571 47.619 0.00 0.00 39.31 3.55
3657 4279 2.094675 CACAAATGGAGGTGGATGGTC 58.905 52.381 0.00 0.00 0.00 4.02
3665 4644 3.982730 TGGAGGTGGATGGTCAATCATAT 59.017 43.478 0.00 0.00 36.98 1.78
3687 4666 3.255888 TGTAGCAGAGTATGGCCTATTCG 59.744 47.826 3.32 0.00 0.00 3.34
3782 4761 4.524328 TCAGATTTCAGAGCACTAGACACA 59.476 41.667 0.00 0.00 0.00 3.72
3808 4787 0.251916 TGCCTATACTGGTGTGGTGC 59.748 55.000 0.00 0.00 0.00 5.01
3810 4789 0.180406 CCTATACTGGTGTGGTGCCC 59.820 60.000 0.00 0.00 0.00 5.36
3811 4790 0.908910 CTATACTGGTGTGGTGCCCA 59.091 55.000 0.00 0.00 0.00 5.36
3822 4801 1.266718 GTGGTGCCCATACATATTGCG 59.733 52.381 0.00 0.00 35.28 4.85
3824 4803 0.110238 GTGCCCATACATATTGCGCG 60.110 55.000 0.00 0.00 0.00 6.86
3827 4806 1.078709 CCCATACATATTGCGCGGAG 58.921 55.000 8.83 0.00 0.00 4.63
3828 4807 1.078709 CCATACATATTGCGCGGAGG 58.921 55.000 8.83 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 7.606456 GGAGTACAAAAGAATCAATGTAGGTGA 59.394 37.037 0.00 0.00 0.00 4.02
177 178 9.715121 ACTTTGACTTCGGACAAAACTTATATA 57.285 29.630 0.00 0.00 38.59 0.86
370 371 9.448294 TTTTTACTTCGCGTATTAAATTTGTGT 57.552 25.926 5.77 0.00 0.00 3.72
371 372 9.917139 CTTTTTACTTCGCGTATTAAATTTGTG 57.083 29.630 5.77 0.00 0.00 3.33
396 397 1.867363 ACATTACTCCCTTCGCTCCT 58.133 50.000 0.00 0.00 0.00 3.69
403 404 9.102453 AGAAGTTTTCTAGTACATTACTCCCTT 57.898 33.333 0.00 0.00 38.49 3.95
459 460 4.757149 AGAGATATTAAACCAATGCTCGGC 59.243 41.667 0.00 0.00 35.85 5.54
462 463 8.371699 AGGAGTAGAGATATTAAACCAATGCTC 58.628 37.037 0.00 0.00 33.18 4.26
495 496 4.157289 GCACCATCATCATCAACTGAGTTT 59.843 41.667 0.00 0.00 37.28 2.66
496 497 3.693085 GCACCATCATCATCAACTGAGTT 59.307 43.478 0.00 0.00 37.28 3.01
515 516 1.597742 ATAATGGATGACAGGCGCAC 58.402 50.000 10.83 0.00 0.00 5.34
520 521 7.578310 ATGTTCAGAAATAATGGATGACAGG 57.422 36.000 0.00 0.00 0.00 4.00
532 533 8.893219 AGATGCGAATCTAATGTTCAGAAATA 57.107 30.769 3.29 0.00 0.00 1.40
538 539 7.549134 AGTTGTTAGATGCGAATCTAATGTTCA 59.451 33.333 25.32 16.77 42.85 3.18
541 542 8.982685 CATAGTTGTTAGATGCGAATCTAATGT 58.017 33.333 25.32 14.16 42.85 2.71
551 552 8.483218 CAACTTATCTCATAGTTGTTAGATGCG 58.517 37.037 0.00 0.00 37.46 4.73
863 1032 4.180946 CGAGGAGAGACGTGGGCG 62.181 72.222 0.00 0.00 44.93 6.13
919 1088 2.924290 GAGACGCCATGTGAAGTAAGTC 59.076 50.000 0.00 0.00 0.00 3.01
928 1097 0.524392 GAGAGTCGAGACGCCATGTG 60.524 60.000 3.43 0.00 36.20 3.21
929 1098 0.960861 TGAGAGTCGAGACGCCATGT 60.961 55.000 3.43 0.00 36.20 3.21
930 1099 0.248417 CTGAGAGTCGAGACGCCATG 60.248 60.000 3.43 0.00 36.20 3.66
931 1100 1.380403 CCTGAGAGTCGAGACGCCAT 61.380 60.000 3.43 0.00 36.20 4.40
932 1101 2.041115 CCTGAGAGTCGAGACGCCA 61.041 63.158 3.43 1.72 36.20 5.69
933 1102 2.795297 CCTGAGAGTCGAGACGCC 59.205 66.667 3.43 0.00 36.20 5.68
934 1103 2.101380 GCCTGAGAGTCGAGACGC 59.899 66.667 0.00 0.00 36.20 5.19
1120 1289 2.403987 CGAGTAGGAGACGCCGTG 59.596 66.667 0.00 0.00 43.43 4.94
1230 1402 0.320697 AGTGAGGCTGGACGGTTAAC 59.679 55.000 0.00 0.00 0.00 2.01
1231 1403 1.053424 AAGTGAGGCTGGACGGTTAA 58.947 50.000 0.00 0.00 0.00 2.01
1236 1408 0.535102 ACCAAAAGTGAGGCTGGACG 60.535 55.000 0.00 0.00 32.97 4.79
1276 1451 9.097946 TCTATGTTCCAGATGTCTGATAATGAT 57.902 33.333 11.47 5.27 46.59 2.45
1278 1453 9.722184 AATCTATGTTCCAGATGTCTGATAATG 57.278 33.333 11.47 0.00 46.59 1.90
1279 1454 9.941325 GAATCTATGTTCCAGATGTCTGATAAT 57.059 33.333 11.47 3.04 46.59 1.28
1280 1455 9.152327 AGAATCTATGTTCCAGATGTCTGATAA 57.848 33.333 11.47 3.17 46.59 1.75
1281 1456 8.583296 CAGAATCTATGTTCCAGATGTCTGATA 58.417 37.037 11.47 1.25 46.59 2.15
1282 1457 7.289549 TCAGAATCTATGTTCCAGATGTCTGAT 59.710 37.037 11.47 0.13 46.59 2.90
1284 1459 6.814043 TCAGAATCTATGTTCCAGATGTCTG 58.186 40.000 3.01 3.01 43.40 3.51
1285 1460 7.344093 TCTTCAGAATCTATGTTCCAGATGTCT 59.656 37.037 0.00 0.00 33.03 3.41
1286 1461 7.495901 TCTTCAGAATCTATGTTCCAGATGTC 58.504 38.462 0.00 0.00 33.03 3.06
1287 1462 7.429374 TCTTCAGAATCTATGTTCCAGATGT 57.571 36.000 0.00 0.00 33.03 3.06
1288 1463 8.202811 TCTTCTTCAGAATCTATGTTCCAGATG 58.797 37.037 0.00 0.00 33.03 2.90
1289 1464 8.316497 TCTTCTTCAGAATCTATGTTCCAGAT 57.684 34.615 0.00 0.00 34.15 2.90
1291 1466 8.256605 TCTTCTTCTTCAGAATCTATGTTCCAG 58.743 37.037 0.00 0.00 40.95 3.86
1292 1467 8.138928 TCTTCTTCTTCAGAATCTATGTTCCA 57.861 34.615 0.00 0.00 40.95 3.53
1293 1468 9.442047 TTTCTTCTTCTTCAGAATCTATGTTCC 57.558 33.333 0.00 0.00 40.95 3.62
1296 1471 9.784531 TGTTTTCTTCTTCTTCAGAATCTATGT 57.215 29.630 0.00 0.00 40.95 2.29
1302 1501 8.782144 GTCAGATGTTTTCTTCTTCTTCAGAAT 58.218 33.333 0.00 0.00 40.95 2.40
1311 1510 9.525826 AATTATGGAGTCAGATGTTTTCTTCTT 57.474 29.630 0.00 0.00 32.98 2.52
1312 1511 8.954350 CAATTATGGAGTCAGATGTTTTCTTCT 58.046 33.333 0.00 0.00 35.16 2.85
1313 1512 8.734386 ACAATTATGGAGTCAGATGTTTTCTTC 58.266 33.333 0.00 0.00 29.93 2.87
1314 1513 8.641498 ACAATTATGGAGTCAGATGTTTTCTT 57.359 30.769 0.00 0.00 29.93 2.52
1316 1515 8.044060 TGACAATTATGGAGTCAGATGTTTTC 57.956 34.615 0.00 0.00 37.36 2.29
1325 1524 5.887598 CCCAATTCTGACAATTATGGAGTCA 59.112 40.000 0.00 0.00 39.74 3.41
1326 1525 5.221126 GCCCAATTCTGACAATTATGGAGTC 60.221 44.000 0.00 0.00 0.00 3.36
1327 1526 4.646492 GCCCAATTCTGACAATTATGGAGT 59.354 41.667 0.00 0.00 0.00 3.85
1328 1527 4.261322 CGCCCAATTCTGACAATTATGGAG 60.261 45.833 0.00 0.00 0.00 3.86
1329 1528 3.631686 CGCCCAATTCTGACAATTATGGA 59.368 43.478 0.00 0.00 0.00 3.41
1330 1529 3.381272 ACGCCCAATTCTGACAATTATGG 59.619 43.478 0.00 0.00 0.00 2.74
1331 1530 4.637483 ACGCCCAATTCTGACAATTATG 57.363 40.909 0.00 0.00 0.00 1.90
1332 1531 5.437060 ACTACGCCCAATTCTGACAATTAT 58.563 37.500 0.00 0.00 0.00 1.28
1333 1532 4.839121 ACTACGCCCAATTCTGACAATTA 58.161 39.130 0.00 0.00 0.00 1.40
1334 1533 3.686016 ACTACGCCCAATTCTGACAATT 58.314 40.909 0.00 0.00 0.00 2.32
1335 1534 3.350219 ACTACGCCCAATTCTGACAAT 57.650 42.857 0.00 0.00 0.00 2.71
1336 1535 2.851263 ACTACGCCCAATTCTGACAA 57.149 45.000 0.00 0.00 0.00 3.18
1337 1536 4.161565 AGAATACTACGCCCAATTCTGACA 59.838 41.667 3.66 0.00 37.31 3.58
1338 1537 4.694339 AGAATACTACGCCCAATTCTGAC 58.306 43.478 3.66 0.00 37.31 3.51
1350 1549 5.856126 TTGCTGAAACCAAGAATACTACG 57.144 39.130 0.00 0.00 0.00 3.51
1362 1561 3.932089 ACAACACAACATTTGCTGAAACC 59.068 39.130 0.00 0.00 0.00 3.27
1427 1626 6.363357 CGTCCCACAAATTCTTTTCAAGATTC 59.637 38.462 0.00 0.00 37.38 2.52
1440 1639 1.133294 ACTTTCCCCGTCCCACAAATT 60.133 47.619 0.00 0.00 0.00 1.82
1442 1641 0.259356 AACTTTCCCCGTCCCACAAA 59.741 50.000 0.00 0.00 0.00 2.83
1448 1647 3.532542 CTCAGATTAACTTTCCCCGTCC 58.467 50.000 0.00 0.00 0.00 4.79
1450 1649 3.178865 TCCTCAGATTAACTTTCCCCGT 58.821 45.455 0.00 0.00 0.00 5.28
1451 1650 3.906720 TCCTCAGATTAACTTTCCCCG 57.093 47.619 0.00 0.00 0.00 5.73
1460 1659 9.162764 GTGCTAGTATTGTTTTCCTCAGATTAA 57.837 33.333 0.00 0.00 0.00 1.40
1461 1660 8.318412 TGTGCTAGTATTGTTTTCCTCAGATTA 58.682 33.333 0.00 0.00 0.00 1.75
1470 1669 6.024049 GTGCTCATGTGCTAGTATTGTTTTC 58.976 40.000 19.60 0.00 0.00 2.29
1472 1671 5.003160 TGTGCTCATGTGCTAGTATTGTTT 58.997 37.500 19.60 0.00 0.00 2.83
1475 1674 3.002042 GCTGTGCTCATGTGCTAGTATTG 59.998 47.826 19.60 5.53 0.00 1.90
1477 1676 2.169144 TGCTGTGCTCATGTGCTAGTAT 59.831 45.455 19.60 0.00 0.00 2.12
1483 1682 2.925578 TTTATGCTGTGCTCATGTGC 57.074 45.000 12.78 12.78 0.00 4.57
1484 1683 4.690184 TCTTTTATGCTGTGCTCATGTG 57.310 40.909 0.00 0.00 0.00 3.21
1485 1684 5.416639 TGAATCTTTTATGCTGTGCTCATGT 59.583 36.000 0.00 0.00 0.00 3.21
1486 1685 5.886992 TGAATCTTTTATGCTGTGCTCATG 58.113 37.500 0.00 0.00 0.00 3.07
1488 1687 5.247862 TCTGAATCTTTTATGCTGTGCTCA 58.752 37.500 0.00 0.00 0.00 4.26
1490 1689 9.565090 TTATATCTGAATCTTTTATGCTGTGCT 57.435 29.630 0.00 0.00 0.00 4.40
1565 1775 6.939622 TCTGGAGTATAACATGGCATAGATG 58.060 40.000 0.00 0.00 0.00 2.90
1582 1792 7.556844 TCGAAAGCTCTTAAAATATCTGGAGT 58.443 34.615 0.00 0.00 0.00 3.85
1583 1793 8.425577 TTCGAAAGCTCTTAAAATATCTGGAG 57.574 34.615 0.00 0.00 0.00 3.86
1591 1805 7.672983 TGACATCTTCGAAAGCTCTTAAAAT 57.327 32.000 0.00 0.00 0.00 1.82
1594 1808 5.408604 GGTTGACATCTTCGAAAGCTCTTAA 59.591 40.000 0.00 0.00 0.00 1.85
1606 1820 2.017049 CCAATCCCGGTTGACATCTTC 58.983 52.381 6.38 0.00 0.00 2.87
1611 1825 0.036164 CAGTCCAATCCCGGTTGACA 59.964 55.000 6.38 0.00 0.00 3.58
1624 1838 0.764271 TCTTGTGCACATCCAGTCCA 59.236 50.000 22.39 1.35 0.00 4.02
1625 1839 1.446907 CTCTTGTGCACATCCAGTCC 58.553 55.000 22.39 0.00 0.00 3.85
1628 1842 1.310933 GGCCTCTTGTGCACATCCAG 61.311 60.000 22.39 15.54 0.00 3.86
1631 1845 2.048603 GGGGCCTCTTGTGCACATC 61.049 63.158 22.39 7.61 32.36 3.06
1632 1846 2.036256 GGGGCCTCTTGTGCACAT 59.964 61.111 22.39 0.00 32.36 3.21
1635 1849 4.666253 GCAGGGGCCTCTTGTGCA 62.666 66.667 0.00 0.00 34.18 4.57
1636 1850 4.666253 TGCAGGGGCCTCTTGTGC 62.666 66.667 0.00 5.07 40.13 4.57
1644 1864 2.674380 CTTCAGTGTGCAGGGGCC 60.674 66.667 0.00 0.00 40.13 5.80
1649 1869 1.085091 GGAGATGCTTCAGTGTGCAG 58.915 55.000 15.91 2.12 42.74 4.41
1750 1977 8.940768 TGAATTCGTCATATGTTCAAGTCATA 57.059 30.769 1.90 0.00 33.26 2.15
1751 1978 7.848223 TGAATTCGTCATATGTTCAAGTCAT 57.152 32.000 1.90 0.00 0.00 3.06
1752 1979 7.334171 ACATGAATTCGTCATATGTTCAAGTCA 59.666 33.333 0.00 10.93 45.69 3.41
1753 1980 7.688372 ACATGAATTCGTCATATGTTCAAGTC 58.312 34.615 0.00 6.73 45.69 3.01
1754 1981 7.615582 ACATGAATTCGTCATATGTTCAAGT 57.384 32.000 0.00 8.31 45.69 3.16
1755 1982 8.539062 GAACATGAATTCGTCATATGTTCAAG 57.461 34.615 27.33 7.80 46.44 3.02
1763 1990 9.546428 AGTCAATATGAACATGAATTCGTCATA 57.454 29.630 16.68 16.68 45.69 2.15
1765 1992 7.848223 AGTCAATATGAACATGAATTCGTCA 57.152 32.000 0.00 0.56 41.67 4.35
1766 1993 8.607459 AGAAGTCAATATGAACATGAATTCGTC 58.393 33.333 0.00 0.00 46.78 4.20
1767 1994 8.498054 AGAAGTCAATATGAACATGAATTCGT 57.502 30.769 0.00 0.00 46.78 3.85
1768 1995 9.778993 AAAGAAGTCAATATGAACATGAATTCG 57.221 29.630 0.00 0.00 46.78 3.34
1772 1999 9.065798 TGTCAAAGAAGTCAATATGAACATGAA 57.934 29.630 0.00 0.00 0.00 2.57
1773 2000 8.620116 TGTCAAAGAAGTCAATATGAACATGA 57.380 30.769 0.00 0.00 0.00 3.07
1774 2001 9.121517 GTTGTCAAAGAAGTCAATATGAACATG 57.878 33.333 0.00 0.00 0.00 3.21
1775 2002 8.849168 TGTTGTCAAAGAAGTCAATATGAACAT 58.151 29.630 0.00 0.00 0.00 2.71
1776 2003 8.219546 TGTTGTCAAAGAAGTCAATATGAACA 57.780 30.769 0.00 0.00 0.00 3.18
1813 2040 7.275920 AGATGTGTTAGACCAATTATCTGACC 58.724 38.462 9.85 4.53 33.01 4.02
1824 2051 9.567776 TTGAAAAGAAATAGATGTGTTAGACCA 57.432 29.630 0.00 0.00 0.00 4.02
1840 2067 8.463930 AGTGAGATTGTGGTATTGAAAAGAAA 57.536 30.769 0.00 0.00 0.00 2.52
1872 2442 7.598118 GCGGTAGAATAGTTTCTAGGGAAATAC 59.402 40.741 0.00 0.00 43.43 1.89
1890 2460 5.289595 CAGCAAGATATAAGTGCGGTAGAA 58.710 41.667 0.00 0.00 43.16 2.10
1929 2499 7.095144 GCTGAATTAGTCTGATGATCTTCCATG 60.095 40.741 6.17 0.00 0.00 3.66
1943 2513 7.288810 TGACCAAATTTTGCTGAATTAGTCT 57.711 32.000 18.20 0.00 35.52 3.24
1987 2605 6.541278 GGGAACTAAGCGGTCAATTTAAGTAT 59.459 38.462 0.00 0.00 0.00 2.12
1993 2611 2.041216 AGGGGAACTAAGCGGTCAATTT 59.959 45.455 0.00 0.00 0.00 1.82
2020 2638 1.064463 CCTCAAGGTGTACCATGGCAT 60.064 52.381 13.04 0.00 35.56 4.40
2061 2679 3.754850 GGGTATAAATATGTGCCCGAACC 59.245 47.826 0.00 0.00 0.00 3.62
2087 2705 0.972883 GTGACTCTTGGAGACTGCCT 59.027 55.000 1.31 0.00 33.32 4.75
2088 2706 0.972883 AGTGACTCTTGGAGACTGCC 59.027 55.000 1.31 0.00 33.32 4.85
2113 2731 0.105408 CATAAAGGGGGCAATGCAGC 59.895 55.000 7.79 0.00 0.00 5.25
2146 2764 4.335735 TCCAAGTTGGGGATTGATGAAT 57.664 40.909 21.85 0.00 38.32 2.57
2199 2817 2.447443 TGTTCGGCTCTCATCACTAGT 58.553 47.619 0.00 0.00 0.00 2.57
2206 2824 3.898123 AGTACCATATGTTCGGCTCTCAT 59.102 43.478 1.24 0.00 0.00 2.90
2218 2836 7.652524 ACTCTGCTATATCCAGTACCATATG 57.347 40.000 0.00 0.00 0.00 1.78
2219 2837 8.671987 AAACTCTGCTATATCCAGTACCATAT 57.328 34.615 0.00 0.00 0.00 1.78
2242 2860 3.554934 ACTTTCTCCATGCACACAGAAA 58.445 40.909 12.75 12.75 34.47 2.52
2244 2862 2.936919 ACTTTCTCCATGCACACAGA 57.063 45.000 0.00 0.00 0.00 3.41
2333 2951 1.078988 CATGTTTGGTGCATGGCCC 60.079 57.895 0.00 0.00 39.82 5.80
2359 2977 0.788391 GTGGCGTGTTTCTCCGTAAG 59.212 55.000 0.00 0.00 0.00 2.34
2424 3042 4.245660 GCTGGGTTATTTTGGCTCTTTTC 58.754 43.478 0.00 0.00 0.00 2.29
2429 3047 1.134995 GCTGCTGGGTTATTTTGGCTC 60.135 52.381 0.00 0.00 0.00 4.70
2435 3053 1.273327 GTTGCTGCTGCTGGGTTATTT 59.727 47.619 17.00 0.00 40.48 1.40
2438 3056 0.890542 CAGTTGCTGCTGCTGGGTTA 60.891 55.000 17.00 0.00 40.48 2.85
2483 3101 8.498054 TCCACATTTTCTGATTCTTCTCATAC 57.502 34.615 0.00 0.00 0.00 2.39
2586 3204 1.210478 GCAATCCTCCTCCAGCTTACA 59.790 52.381 0.00 0.00 0.00 2.41
2592 3210 1.101331 GCAAAGCAATCCTCCTCCAG 58.899 55.000 0.00 0.00 0.00 3.86
2606 3224 2.753966 CGTGATGGCTCCGGCAAAG 61.754 63.158 0.00 0.00 42.43 2.77
2613 3231 2.644555 ATACACCGCGTGATGGCTCC 62.645 60.000 4.92 0.00 36.96 4.70
2620 3238 0.033642 TTGTCCAATACACCGCGTGA 59.966 50.000 4.92 0.00 38.00 4.35
2624 3242 1.472480 AGCAATTGTCCAATACACCGC 59.528 47.619 7.40 0.00 38.00 5.68
2632 3250 1.001487 CAACTGCGAGCAATTGTCCAA 60.001 47.619 10.63 0.00 29.78 3.53
2924 3543 7.613585 AGTTCAATAAAAATGATGACATGGCA 58.386 30.769 2.18 2.18 36.79 4.92
2971 3590 7.400627 TCCACACGGGGTAATATATGATTGATA 59.599 37.037 0.00 0.00 37.22 2.15
3197 3816 2.093181 CGTTCCCCATGGACATACTCAA 60.093 50.000 15.22 0.00 41.57 3.02
3231 3853 2.203139 CCACCCGTGTGACAAGCA 60.203 61.111 0.00 0.00 45.76 3.91
3240 3862 1.358725 CGCATACTGTTCCACCCGTG 61.359 60.000 0.00 0.00 0.00 4.94
3341 3963 4.324099 CCATTCAGAGACAAATCCTGGACT 60.324 45.833 0.00 0.00 0.00 3.85
3351 3973 6.072286 GCTTTTTCTCATCCATTCAGAGACAA 60.072 38.462 0.00 0.00 38.07 3.18
3359 3981 6.860080 TCTTCATGCTTTTTCTCATCCATTC 58.140 36.000 0.00 0.00 0.00 2.67
3395 4017 5.513267 GGACCCTGCTTATTTCTCCGAATAT 60.513 44.000 0.00 0.00 0.00 1.28
3396 4018 4.202326 GGACCCTGCTTATTTCTCCGAATA 60.202 45.833 0.00 0.00 0.00 1.75
3631 4253 1.881973 CCACCTCCATTTGTGTGTCTG 59.118 52.381 0.00 0.00 0.00 3.51
3651 4273 6.462500 ACTCTGCTACATATGATTGACCATC 58.538 40.000 10.38 0.00 0.00 3.51
3654 4276 6.815641 CCATACTCTGCTACATATGATTGACC 59.184 42.308 10.38 0.00 0.00 4.02
3656 4278 6.401394 GCCATACTCTGCTACATATGATTGA 58.599 40.000 10.38 0.00 0.00 2.57
3657 4279 5.583854 GGCCATACTCTGCTACATATGATTG 59.416 44.000 10.38 0.01 0.00 2.67
3665 4644 3.255888 CGAATAGGCCATACTCTGCTACA 59.744 47.826 5.01 0.00 0.00 2.74
3687 4666 6.525629 ACACTAGTACATGATTAATGAGGCC 58.474 40.000 0.00 0.00 38.72 5.19
3782 4761 3.055819 CACACCAGTATAGGCAGTTGTCT 60.056 47.826 0.00 0.00 0.00 3.41
3808 4787 1.078709 CTCCGCGCAATATGTATGGG 58.921 55.000 8.75 0.00 0.00 4.00
3810 4789 0.443869 GCCTCCGCGCAATATGTATG 59.556 55.000 8.75 0.00 0.00 2.39
3811 4790 0.034756 TGCCTCCGCGCAATATGTAT 59.965 50.000 8.75 0.00 35.32 2.29
3822 4801 0.673022 GATCCTCATGATGCCTCCGC 60.673 60.000 0.00 0.00 32.41 5.54
3824 4803 1.003349 CCTGATCCTCATGATGCCTCC 59.997 57.143 0.00 0.00 32.41 4.30
3827 4806 3.436577 AATCCTGATCCTCATGATGCC 57.563 47.619 0.00 0.00 33.12 4.40
3828 4807 4.583489 ACAAAATCCTGATCCTCATGATGC 59.417 41.667 0.00 0.00 33.12 3.91


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

AutoCloner maintained by Alex Coulton.