Multiple sequence alignment - TraesCS6A01G409300

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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 TraesCS6A01G409300 chr6A 100.000 2288 0 0 1 2288 613337242 613339529 0.000000e+00 4226.0
1 TraesCS6A01G409300 chr6B 87.340 1722 102 46 1 1673 712245334 712246988 0.000000e+00 1866.0
2 TraesCS6A01G409300 chr6B 95.000 40 2 0 1608 1647 126137307 126137346 1.900000e-06 63.9
3 TraesCS6A01G409300 chr6D 88.609 1510 96 39 142 1611 467041599 467043072 0.000000e+00 1766.0
4 TraesCS6A01G409300 chr6D 93.388 121 8 0 1 121 467041490 467041610 1.810000e-41 180.0
5 TraesCS6A01G409300 chr6D 79.381 291 25 13 1821 2091 467043244 467043519 3.020000e-39 172.0
6 TraesCS6A01G409300 chr6D 97.222 36 0 1 1724 1758 34582554 34582589 2.450000e-05 60.2
7 TraesCS6A01G409300 chr1A 92.157 204 13 3 2082 2285 540023655 540023855 3.720000e-73 285.0
8 TraesCS6A01G409300 chr3A 92.424 198 13 2 2091 2288 480969123 480968928 4.810000e-72 281.0
9 TraesCS6A01G409300 chr3A 92.347 196 13 2 2091 2286 703433228 703433421 6.230000e-71 278.0
10 TraesCS6A01G409300 chr5A 91.919 198 14 2 2089 2286 105421369 105421564 2.240000e-70 276.0
11 TraesCS6A01G409300 chr5A 91.919 198 14 2 2091 2288 566643461 566643266 2.240000e-70 276.0
12 TraesCS6A01G409300 chr5A 91.414 198 15 2 2089 2286 343130266 343130071 1.040000e-68 270.0
13 TraesCS6A01G409300 chr7A 91.414 198 15 2 2089 2286 649492082 649491887 1.040000e-68 270.0
14 TraesCS6A01G409300 chr4A 91.414 198 15 2 2089 2286 684028132 684028327 1.040000e-68 270.0
15 TraesCS6A01G409300 chr4A 91.414 198 15 2 2089 2286 684054589 684054784 1.040000e-68 270.0
16 TraesCS6A01G409300 chr4A 96.970 33 1 0 1603 1635 200093503 200093535 3.180000e-04 56.5
17 TraesCS6A01G409300 chr4D 89.744 78 7 1 1608 1685 192735988 192735912 5.200000e-17 99.0
18 TraesCS6A01G409300 chr2B 87.500 80 7 3 1608 1685 643266170 643266092 3.130000e-14 89.8
19 TraesCS6A01G409300 chr2B 96.000 50 2 0 1707 1756 644545440 644545391 5.240000e-12 82.4
20 TraesCS6A01G409300 chr2B 92.500 40 3 0 1605 1644 629806325 629806286 8.830000e-05 58.4
21 TraesCS6A01G409300 chr1D 82.143 84 12 3 1602 1685 33549834 33549754 4.080000e-08 69.4
22 TraesCS6A01G409300 chr1D 90.698 43 4 0 1605 1647 49604550 49604592 8.830000e-05 58.4
23 TraesCS6A01G409300 chr2D 94.595 37 2 0 1608 1644 608200167 608200131 8.830000e-05 58.4
24 TraesCS6A01G409300 chr2D 92.308 39 3 0 1606 1644 529669669 529669631 3.180000e-04 56.5


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 TraesCS6A01G409300 chr6A 613337242 613339529 2287 False 4226 4226 100.000 1 2288 1 chr6A.!!$F1 2287
1 TraesCS6A01G409300 chr6B 712245334 712246988 1654 False 1866 1866 87.340 1 1673 1 chr6B.!!$F2 1672
2 TraesCS6A01G409300 chr6D 467041490 467043519 2029 False 706 1766 87.126 1 2091 3 chr6D.!!$F2 2090

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
319 324 0.187361 TATAACCAAGGGCATGGGGC 59.813 55.0 12.49 0.0 45.18 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1856 0.180406 ACAAAGGCGCCCCTACTATG 59.82 55.0 26.15 13.92 41.9 2.23 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
109 110 3.372440 AATGTGAGGGGACATTTCCTC 57.628 47.619 0.00 0.00 42.69 3.71
121 122 5.310857 GGGACATTTCCTCTCACCCTATTAT 59.689 44.000 0.00 0.00 42.38 1.28
185 186 8.768501 AGATAGATAACTTGTGTCTATGACCA 57.231 34.615 11.24 0.00 39.90 4.02
298 303 7.037873 TCCATTCACCCTATAGTTAACTTGTGT 60.038 37.037 14.49 2.10 0.00 3.72
303 308 9.925545 TCACCCTATAGTTAACTTGTGTCTATA 57.074 33.333 14.49 2.85 0.00 1.31
319 324 0.187361 TATAACCAAGGGCATGGGGC 59.813 55.000 12.49 0.00 45.18 5.80
358 363 1.134551 TGGTTTCCTTTGGTTGCTTGC 60.135 47.619 0.00 0.00 0.00 4.01
426 431 0.542702 CAAGGTTGTCAATGGCCCCT 60.543 55.000 0.00 0.00 0.00 4.79
427 432 0.542702 AAGGTTGTCAATGGCCCCTG 60.543 55.000 0.00 0.00 0.00 4.45
428 433 2.649129 GGTTGTCAATGGCCCCTGC 61.649 63.158 0.00 0.00 0.00 4.85
429 434 1.607467 GTTGTCAATGGCCCCTGCT 60.607 57.895 0.00 0.00 37.74 4.24
430 435 1.304381 TTGTCAATGGCCCCTGCTC 60.304 57.895 0.00 0.00 37.74 4.26
431 436 2.079088 TTGTCAATGGCCCCTGCTCA 62.079 55.000 0.00 0.00 37.74 4.26
432 437 1.751927 GTCAATGGCCCCTGCTCAG 60.752 63.158 0.00 0.00 37.74 3.35
433 438 3.145551 CAATGGCCCCTGCTCAGC 61.146 66.667 0.00 0.00 37.74 4.26
454 459 2.178580 CCAGCCCAGCCATTTTTCTAA 58.821 47.619 0.00 0.00 0.00 2.10
531 547 2.378038 AGTGCACTGCTTTTCCTCAAA 58.622 42.857 20.97 0.00 0.00 2.69
658 674 1.597989 TGCCCATGCATGCTTTTCC 59.402 52.632 21.69 5.32 44.23 3.13
670 686 1.713647 TGCTTTTCCCCTAACCATGGA 59.286 47.619 21.47 0.00 0.00 3.41
671 687 2.314549 TGCTTTTCCCCTAACCATGGAT 59.685 45.455 21.47 9.83 0.00 3.41
681 697 3.009275 CCATGGATGGCAGGTGGA 58.991 61.111 5.56 0.00 41.75 4.02
732 748 4.527816 TCCAAGAAATTCAGGAAACATGGG 59.472 41.667 4.98 0.00 0.00 4.00
819 839 4.402793 ACCATACCATGTAGTCAGAGTCAC 59.597 45.833 0.00 0.00 0.00 3.67
831 851 4.287585 AGTCAGAGTCACTGGAGTACTACT 59.712 45.833 6.66 0.00 45.76 2.57
832 852 4.393680 GTCAGAGTCACTGGAGTACTACTG 59.606 50.000 10.29 10.29 45.76 2.74
833 853 3.127895 CAGAGTCACTGGAGTACTACTGC 59.872 52.174 11.69 0.82 42.39 4.40
985 1005 1.477558 CCTGCTCCTCTCTCTCTCTCC 60.478 61.905 0.00 0.00 0.00 3.71
986 1006 0.550914 TGCTCCTCTCTCTCTCTCCC 59.449 60.000 0.00 0.00 0.00 4.30
987 1007 0.846693 GCTCCTCTCTCTCTCTCCCT 59.153 60.000 0.00 0.00 0.00 4.20
1042 1062 1.918467 CTCCTTGCTCCCCTGCATCA 61.918 60.000 0.00 0.00 42.96 3.07
1072 1095 3.087031 CTGCTCCTTGTTTCCATGTCAT 58.913 45.455 0.00 0.00 0.00 3.06
1073 1096 2.821378 TGCTCCTTGTTTCCATGTCATG 59.179 45.455 5.79 5.79 0.00 3.07
1075 1098 3.087031 CTCCTTGTTTCCATGTCATGCT 58.913 45.455 7.35 0.00 0.00 3.79
1183 1206 2.092914 CCAACCATCTCCCCTACTCAAC 60.093 54.545 0.00 0.00 0.00 3.18
1325 1368 2.507944 GCCGGTGGATCTCTGCAT 59.492 61.111 1.90 0.00 0.00 3.96
1338 1381 0.745486 TCTGCATCAGGTTCATGGCG 60.745 55.000 0.00 0.00 31.51 5.69
1366 1409 4.019411 CCATGGCCACCAGATACATATACA 60.019 45.833 8.16 0.00 36.75 2.29
1367 1410 4.890158 TGGCCACCAGATACATATACAG 57.110 45.455 0.00 0.00 0.00 2.74
1371 1414 5.480772 GGCCACCAGATACATATACAGTACT 59.519 44.000 0.00 0.00 0.00 2.73
1372 1415 6.662234 GGCCACCAGATACATATACAGTACTA 59.338 42.308 0.00 0.00 0.00 1.82
1374 1417 9.404848 GCCACCAGATACATATACAGTACTATA 57.595 37.037 0.00 0.00 0.00 1.31
1377 1420 9.917887 ACCAGATACATATACAGTACTATACCC 57.082 37.037 0.00 0.00 0.00 3.69
1502 1589 2.449322 CCCTCCCTCCCTCCATGG 60.449 72.222 4.97 4.97 0.00 3.66
1503 1590 3.174265 CCTCCCTCCCTCCATGGC 61.174 72.222 6.96 0.00 0.00 4.40
1504 1591 2.367377 CTCCCTCCCTCCATGGCA 60.367 66.667 6.96 0.00 0.00 4.92
1505 1592 1.773391 CTCCCTCCCTCCATGGCAT 60.773 63.158 6.96 0.00 0.00 4.40
1506 1593 2.065470 CTCCCTCCCTCCATGGCATG 62.065 65.000 20.56 20.56 0.00 4.06
1507 1594 2.203451 CCTCCCTCCATGGCATGC 60.203 66.667 22.02 9.90 0.00 4.06
1508 1595 2.764737 CCTCCCTCCATGGCATGCT 61.765 63.158 22.02 0.00 0.00 3.79
1509 1596 1.229359 CTCCCTCCATGGCATGCTT 59.771 57.895 22.02 2.40 0.00 3.91
1510 1597 0.822532 CTCCCTCCATGGCATGCTTC 60.823 60.000 22.02 1.78 0.00 3.86
1511 1598 1.831286 CCCTCCATGGCATGCTTCC 60.831 63.158 22.02 0.95 0.00 3.46
1512 1599 1.229359 CCTCCATGGCATGCTTCCT 59.771 57.895 22.02 0.00 0.00 3.36
1513 1600 0.396695 CCTCCATGGCATGCTTCCTT 60.397 55.000 22.02 0.00 0.00 3.36
1514 1601 1.030457 CTCCATGGCATGCTTCCTTC 58.970 55.000 22.02 0.00 0.00 3.46
1515 1602 0.396139 TCCATGGCATGCTTCCTTCC 60.396 55.000 22.02 0.00 0.00 3.46
1516 1603 1.397390 CCATGGCATGCTTCCTTCCC 61.397 60.000 22.02 0.00 0.00 3.97
1517 1604 0.396695 CATGGCATGCTTCCTTCCCT 60.397 55.000 18.92 0.00 0.00 4.20
1518 1605 0.396695 ATGGCATGCTTCCTTCCCTG 60.397 55.000 18.92 0.00 0.00 4.45
1519 1606 2.421399 GGCATGCTTCCTTCCCTGC 61.421 63.158 18.92 0.00 0.00 4.85
1520 1607 1.679977 GCATGCTTCCTTCCCTGCA 60.680 57.895 11.37 0.00 39.83 4.41
1521 1608 1.041447 GCATGCTTCCTTCCCTGCAT 61.041 55.000 11.37 0.00 45.57 3.96
1522 1609 3.202548 ATGCTTCCTTCCCTGCATG 57.797 52.632 0.00 0.00 43.41 4.06
1570 1657 6.822667 ATGCAGTGATTGATGTTACAAAGA 57.177 33.333 0.00 0.00 33.44 2.52
1572 1659 5.764686 TGCAGTGATTGATGTTACAAAGACT 59.235 36.000 0.00 0.00 33.44 3.24
1588 1676 4.616181 AAGACTTGAAAGTTGTTGGTCG 57.384 40.909 0.00 0.00 39.88 4.79
1598 1686 3.472652 AGTTGTTGGTCGAGCATTTACA 58.527 40.909 19.37 16.72 0.00 2.41
1600 1688 4.083324 AGTTGTTGGTCGAGCATTTACATG 60.083 41.667 19.37 0.00 0.00 3.21
1617 1721 0.539051 ATGCTGCTCCCTCTGTACAC 59.461 55.000 0.00 0.00 0.00 2.90
1627 1731 5.360144 GCTCCCTCTGTACACTAATGTAAGA 59.640 44.000 0.00 0.00 42.99 2.10
1628 1732 6.680872 GCTCCCTCTGTACACTAATGTAAGAC 60.681 46.154 0.00 0.00 42.99 3.01
1634 1738 8.876275 TCTGTACACTAATGTAAGACGTTTTT 57.124 30.769 0.00 0.00 42.99 1.94
1635 1739 8.971321 TCTGTACACTAATGTAAGACGTTTTTC 58.029 33.333 0.00 0.00 42.99 2.29
1637 1741 6.549912 ACACTAATGTAAGACGTTTTTCCC 57.450 37.500 0.00 0.00 37.26 3.97
1639 1743 5.178067 CACTAATGTAAGACGTTTTTCCCGT 59.822 40.000 0.00 0.00 42.06 5.28
1682 1786 9.545611 AAAACGTTTTATATTAGCGTACAAAGG 57.454 29.630 24.13 0.00 35.22 3.11
1683 1787 7.832503 ACGTTTTATATTAGCGTACAAAGGT 57.167 32.000 0.00 0.00 33.85 3.50
1684 1788 8.925161 ACGTTTTATATTAGCGTACAAAGGTA 57.075 30.769 0.00 0.00 33.85 3.08
1685 1789 9.533253 ACGTTTTATATTAGCGTACAAAGGTAT 57.467 29.630 0.00 0.00 33.85 2.73
1691 1795 8.983307 ATATTAGCGTACAAAGGTATAAGAGC 57.017 34.615 0.00 0.00 0.00 4.09
1692 1796 3.703420 AGCGTACAAAGGTATAAGAGCG 58.297 45.455 0.00 0.00 0.00 5.03
1693 1797 3.129988 AGCGTACAAAGGTATAAGAGCGT 59.870 43.478 0.00 0.00 0.00 5.07
1694 1798 3.861689 GCGTACAAAGGTATAAGAGCGTT 59.138 43.478 0.00 0.00 0.00 4.84
1695 1799 4.328169 GCGTACAAAGGTATAAGAGCGTTT 59.672 41.667 0.00 0.00 0.00 3.60
1696 1800 5.163923 GCGTACAAAGGTATAAGAGCGTTTT 60.164 40.000 0.00 0.00 0.00 2.43
1697 1801 6.619232 GCGTACAAAGGTATAAGAGCGTTTTT 60.619 38.462 0.00 0.00 0.00 1.94
1698 1802 6.952083 CGTACAAAGGTATAAGAGCGTTTTTC 59.048 38.462 0.00 0.00 0.00 2.29
1699 1803 6.870971 ACAAAGGTATAAGAGCGTTTTTCA 57.129 33.333 0.00 0.00 0.00 2.69
1700 1804 6.899114 ACAAAGGTATAAGAGCGTTTTTCAG 58.101 36.000 0.00 0.00 0.00 3.02
1701 1805 6.708949 ACAAAGGTATAAGAGCGTTTTTCAGA 59.291 34.615 0.00 0.00 0.00 3.27
1702 1806 6.723131 AAGGTATAAGAGCGTTTTTCAGAC 57.277 37.500 0.00 0.00 0.00 3.51
1703 1807 6.038997 AGGTATAAGAGCGTTTTTCAGACT 57.961 37.500 0.00 0.00 0.00 3.24
1704 1808 7.166691 AGGTATAAGAGCGTTTTTCAGACTA 57.833 36.000 0.00 0.00 0.00 2.59
1705 1809 7.259161 AGGTATAAGAGCGTTTTTCAGACTAG 58.741 38.462 0.00 0.00 0.00 2.57
1706 1810 7.034397 GGTATAAGAGCGTTTTTCAGACTAGT 58.966 38.462 0.00 0.00 0.00 2.57
1707 1811 8.186821 GGTATAAGAGCGTTTTTCAGACTAGTA 58.813 37.037 0.00 0.00 0.00 1.82
1708 1812 9.733219 GTATAAGAGCGTTTTTCAGACTAGTAT 57.267 33.333 0.00 0.00 0.00 2.12
1710 1814 9.953697 ATAAGAGCGTTTTTCAGACTAGTATAG 57.046 33.333 0.00 0.00 46.50 1.31
1757 1861 4.165758 AGAACGGAGGGAGTAGTACATAGT 59.834 45.833 2.52 0.00 0.00 2.12
1760 1864 4.041444 ACGGAGGGAGTAGTACATAGTAGG 59.959 50.000 2.52 0.00 0.00 3.18
1762 1866 4.263860 GGAGGGAGTAGTACATAGTAGGGG 60.264 54.167 2.52 0.00 0.00 4.79
1764 1868 3.080319 GGAGTAGTACATAGTAGGGGCG 58.920 54.545 2.52 0.00 0.00 6.13
1765 1869 2.487372 GAGTAGTACATAGTAGGGGCGC 59.513 54.545 0.00 0.00 0.00 6.53
1766 1870 1.543358 GTAGTACATAGTAGGGGCGCC 59.457 57.143 21.18 21.18 0.00 6.53
1767 1871 0.187851 AGTACATAGTAGGGGCGCCT 59.812 55.000 28.56 27.11 0.00 5.52
1768 1872 1.046204 GTACATAGTAGGGGCGCCTT 58.954 55.000 29.14 17.66 0.00 4.35
1769 1873 1.415289 GTACATAGTAGGGGCGCCTTT 59.585 52.381 29.14 18.48 0.00 3.11
1770 1874 0.180406 ACATAGTAGGGGCGCCTTTG 59.820 55.000 29.14 20.70 0.00 2.77
1772 1876 1.414919 CATAGTAGGGGCGCCTTTGTA 59.585 52.381 29.14 16.53 0.00 2.41
1773 1877 1.570803 TAGTAGGGGCGCCTTTGTAA 58.429 50.000 29.14 6.35 0.00 2.41
1775 1879 1.134189 AGTAGGGGCGCCTTTGTAATC 60.134 52.381 29.14 6.44 0.00 1.75
1776 1880 0.913205 TAGGGGCGCCTTTGTAATCA 59.087 50.000 29.14 3.79 0.00 2.57
1777 1881 0.679960 AGGGGCGCCTTTGTAATCAC 60.680 55.000 28.56 4.74 0.00 3.06
1778 1882 1.427819 GGGCGCCTTTGTAATCACG 59.572 57.895 28.56 0.00 0.00 4.35
1783 1887 1.727857 CGCCTTTGTAATCACGGTTGC 60.728 52.381 0.00 0.00 0.00 4.17
1784 1888 1.268352 GCCTTTGTAATCACGGTTGCA 59.732 47.619 0.00 0.00 0.00 4.08
1786 1890 3.500982 CCTTTGTAATCACGGTTGCATG 58.499 45.455 0.00 0.00 0.00 4.06
1793 1897 0.392863 TCACGGTTGCATGGGATCTG 60.393 55.000 0.00 0.00 0.00 2.90
1798 1902 2.428171 CGGTTGCATGGGATCTGAAATT 59.572 45.455 0.00 0.00 0.00 1.82
1803 1907 4.602107 TGCATGGGATCTGAAATTCTGAA 58.398 39.130 6.66 0.00 0.00 3.02
1807 1911 6.513180 CATGGGATCTGAAATTCTGAAATGG 58.487 40.000 6.66 0.00 0.00 3.16
1809 1913 6.730447 TGGGATCTGAAATTCTGAAATGGTA 58.270 36.000 6.66 0.00 0.00 3.25
1813 1917 8.689972 GGATCTGAAATTCTGAAATGGTATTGT 58.310 33.333 6.66 0.00 0.00 2.71
1818 1922 9.258826 TGAAATTCTGAAATGGTATTGTTGTTG 57.741 29.630 0.00 0.00 0.00 3.33
1819 1923 7.656707 AATTCTGAAATGGTATTGTTGTTGC 57.343 32.000 0.00 0.00 0.00 4.17
1824 1938 7.768120 TCTGAAATGGTATTGTTGTTGCTTTTT 59.232 29.630 0.00 0.00 0.00 1.94
1826 1940 6.523676 AATGGTATTGTTGTTGCTTTTTCG 57.476 33.333 0.00 0.00 0.00 3.46
1829 1943 5.289675 TGGTATTGTTGTTGCTTTTTCGTTG 59.710 36.000 0.00 0.00 0.00 4.10
1831 1945 4.637574 TTGTTGTTGCTTTTTCGTTGTG 57.362 36.364 0.00 0.00 0.00 3.33
1844 1958 8.539674 GCTTTTTCGTTGTGTGAAGAAATTAAT 58.460 29.630 0.00 0.00 33.37 1.40
1878 1992 8.635765 TTTTTGGGGCTGTGATATAATATCTC 57.364 34.615 0.00 0.00 0.00 2.75
1892 2006 4.819105 AATATCTCGTGGTTGTTGGAGA 57.181 40.909 0.00 0.00 39.62 3.71
1930 2055 9.456147 GTAGTATCTGCTGATCTATAAAGAGGA 57.544 37.037 9.62 0.00 34.49 3.71
1931 2056 8.579850 AGTATCTGCTGATCTATAAAGAGGAG 57.420 38.462 9.62 0.00 34.49 3.69
1932 2057 5.720371 TCTGCTGATCTATAAAGAGGAGC 57.280 43.478 0.00 0.00 39.08 4.70
1937 2062 5.243730 GCTGATCTATAAAGAGGAGCAGTCT 59.756 44.000 8.76 0.00 42.95 3.24
1938 2063 6.647334 TGATCTATAAAGAGGAGCAGTCTG 57.353 41.667 0.00 0.00 34.49 3.51
1953 2078 0.745845 GTCTGGAGGCGCATGTGAAT 60.746 55.000 10.83 0.00 0.00 2.57
1954 2079 0.745486 TCTGGAGGCGCATGTGAATG 60.745 55.000 10.83 0.00 0.00 2.67
1955 2080 2.332362 CTGGAGGCGCATGTGAATGC 62.332 60.000 10.83 3.03 43.72 3.56
1956 2081 2.117156 GGAGGCGCATGTGAATGCT 61.117 57.895 10.83 0.00 44.90 3.79
1976 2101 2.799126 TGCTTAATCAACCCCGTGAT 57.201 45.000 0.00 0.00 40.01 3.06
1983 2113 2.040544 CAACCCCGTGATCAGGTGC 61.041 63.158 13.98 0.00 33.05 5.01
1985 2115 2.124983 CCCCGTGATCAGGTGCTG 60.125 66.667 13.98 0.00 0.00 4.41
2002 2132 4.189231 GTGCTGATTAACTAATCACGGGT 58.811 43.478 7.86 0.00 45.03 5.28
2033 2163 1.815613 GCCTCCTCTCCTTTTTCTTGC 59.184 52.381 0.00 0.00 0.00 4.01
2041 2171 7.830739 TCCTCTCCTTTTTCTTGCAAATATTC 58.169 34.615 0.00 0.00 0.00 1.75
2046 2179 5.352293 CCTTTTTCTTGCAAATATTCTGGCC 59.648 40.000 0.00 0.00 0.00 5.36
2054 2187 5.663456 TGCAAATATTCTGGCCATCTTTTC 58.337 37.500 5.51 0.00 0.00 2.29
2055 2188 5.187381 TGCAAATATTCTGGCCATCTTTTCA 59.813 36.000 5.51 0.05 0.00 2.69
2060 2193 3.340814 TCTGGCCATCTTTTCAGAGAC 57.659 47.619 5.51 0.00 33.07 3.36
2061 2194 2.005451 CTGGCCATCTTTTCAGAGACG 58.995 52.381 5.51 0.00 30.36 4.18
2064 2197 2.003301 GCCATCTTTTCAGAGACGGAC 58.997 52.381 0.00 0.00 30.36 4.79
2069 2202 0.316204 TTTTCAGAGACGGACGGACC 59.684 55.000 0.00 0.00 0.00 4.46
2091 2224 3.122613 CGACTGAAGCAAAGCAGAGTAAG 59.877 47.826 0.00 0.00 36.07 2.34
2092 2225 3.406764 ACTGAAGCAAAGCAGAGTAAGG 58.593 45.455 0.00 0.00 36.07 2.69
2093 2226 2.746362 CTGAAGCAAAGCAGAGTAAGGG 59.254 50.000 0.00 0.00 34.06 3.95
2094 2227 1.470494 GAAGCAAAGCAGAGTAAGGGC 59.530 52.381 0.00 0.00 0.00 5.19
2095 2228 0.695347 AGCAAAGCAGAGTAAGGGCT 59.305 50.000 0.00 0.00 40.14 5.19
2096 2229 1.090728 GCAAAGCAGAGTAAGGGCTC 58.909 55.000 0.00 0.00 36.76 4.70
2097 2230 1.743996 CAAAGCAGAGTAAGGGCTCC 58.256 55.000 0.00 0.00 36.76 4.70
2098 2231 1.280421 CAAAGCAGAGTAAGGGCTCCT 59.720 52.381 0.00 0.00 36.76 3.69
2099 2232 1.662686 AAGCAGAGTAAGGGCTCCTT 58.337 50.000 10.76 10.76 46.63 3.36
2100 2233 1.662686 AGCAGAGTAAGGGCTCCTTT 58.337 50.000 11.15 0.00 41.69 3.11
2101 2234 1.280421 AGCAGAGTAAGGGCTCCTTTG 59.720 52.381 11.15 5.67 41.69 2.77
2102 2235 1.279271 GCAGAGTAAGGGCTCCTTTGA 59.721 52.381 11.15 0.00 41.69 2.69
2103 2236 2.092699 GCAGAGTAAGGGCTCCTTTGAT 60.093 50.000 11.15 0.00 41.69 2.57
2104 2237 3.623453 GCAGAGTAAGGGCTCCTTTGATT 60.623 47.826 11.15 0.00 41.69 2.57
2105 2238 4.195416 CAGAGTAAGGGCTCCTTTGATTC 58.805 47.826 11.15 2.62 41.69 2.52
2106 2239 3.846588 AGAGTAAGGGCTCCTTTGATTCA 59.153 43.478 11.15 0.00 41.69 2.57
2107 2240 4.289672 AGAGTAAGGGCTCCTTTGATTCAA 59.710 41.667 11.15 0.00 41.69 2.69
2108 2241 4.998051 AGTAAGGGCTCCTTTGATTCAAA 58.002 39.130 11.19 11.19 41.69 2.69
2122 2255 7.389803 TTTGATTCAAAGAAATCGCATAGGA 57.610 32.000 7.74 0.00 38.28 2.94
2123 2256 7.572523 TTGATTCAAAGAAATCGCATAGGAT 57.427 32.000 0.00 0.00 38.28 3.24
2124 2257 7.572523 TGATTCAAAGAAATCGCATAGGATT 57.427 32.000 0.00 0.00 38.28 3.01
2125 2258 7.999679 TGATTCAAAGAAATCGCATAGGATTT 58.000 30.769 0.52 0.52 46.40 2.17
2126 2259 8.469200 TGATTCAAAGAAATCGCATAGGATTTT 58.531 29.630 2.46 0.00 44.41 1.82
2127 2260 9.305925 GATTCAAAGAAATCGCATAGGATTTTT 57.694 29.630 2.46 0.00 44.41 1.94
2147 2280 6.709018 TTTTTGGAGGGTTTGAACTCTTAG 57.291 37.500 0.00 0.00 40.57 2.18
2148 2281 4.367039 TTGGAGGGTTTGAACTCTTAGG 57.633 45.455 0.00 0.00 40.57 2.69
2149 2282 3.593942 TGGAGGGTTTGAACTCTTAGGA 58.406 45.455 0.00 0.00 40.57 2.94
2150 2283 3.977999 TGGAGGGTTTGAACTCTTAGGAA 59.022 43.478 0.00 0.00 40.57 3.36
2151 2284 4.601857 TGGAGGGTTTGAACTCTTAGGAAT 59.398 41.667 0.00 0.00 40.57 3.01
2152 2285 5.074515 TGGAGGGTTTGAACTCTTAGGAATT 59.925 40.000 0.00 0.00 40.57 2.17
2153 2286 6.010850 GGAGGGTTTGAACTCTTAGGAATTT 58.989 40.000 0.00 0.00 40.57 1.82
2154 2287 6.493802 GGAGGGTTTGAACTCTTAGGAATTTT 59.506 38.462 0.00 0.00 40.57 1.82
2155 2288 7.015292 GGAGGGTTTGAACTCTTAGGAATTTTT 59.985 37.037 0.00 0.00 40.57 1.94
2177 2310 7.795431 TTTTCATGTTATGCTCGTTTGATTC 57.205 32.000 0.00 0.00 0.00 2.52
2178 2311 5.142635 TCATGTTATGCTCGTTTGATTCG 57.857 39.130 0.00 0.00 0.00 3.34
2179 2312 4.629634 TCATGTTATGCTCGTTTGATTCGT 59.370 37.500 0.00 0.00 0.00 3.85
2180 2313 5.808030 TCATGTTATGCTCGTTTGATTCGTA 59.192 36.000 0.00 0.00 0.00 3.43
2181 2314 5.696260 TGTTATGCTCGTTTGATTCGTAG 57.304 39.130 0.00 0.00 0.00 3.51
2182 2315 4.565166 TGTTATGCTCGTTTGATTCGTAGG 59.435 41.667 0.00 0.00 0.00 3.18
2183 2316 3.520290 ATGCTCGTTTGATTCGTAGGA 57.480 42.857 0.00 0.00 0.00 2.94
2184 2317 3.520290 TGCTCGTTTGATTCGTAGGAT 57.480 42.857 0.00 0.00 0.00 3.24
2185 2318 3.857052 TGCTCGTTTGATTCGTAGGATT 58.143 40.909 0.00 0.00 0.00 3.01
2186 2319 3.616821 TGCTCGTTTGATTCGTAGGATTG 59.383 43.478 0.00 0.00 0.00 2.67
2187 2320 3.001330 GCTCGTTTGATTCGTAGGATTGG 59.999 47.826 0.00 0.00 0.00 3.16
2188 2321 2.933906 TCGTTTGATTCGTAGGATTGGC 59.066 45.455 0.00 0.00 0.00 4.52
2189 2322 2.675844 CGTTTGATTCGTAGGATTGGCA 59.324 45.455 0.00 0.00 0.00 4.92
2190 2323 3.312421 CGTTTGATTCGTAGGATTGGCAT 59.688 43.478 0.00 0.00 0.00 4.40
2191 2324 4.552767 CGTTTGATTCGTAGGATTGGCATC 60.553 45.833 0.00 0.00 0.00 3.91
2192 2325 4.422073 TTGATTCGTAGGATTGGCATCT 57.578 40.909 0.00 0.00 0.00 2.90
2193 2326 4.422073 TGATTCGTAGGATTGGCATCTT 57.578 40.909 0.00 0.00 0.00 2.40
2194 2327 4.780815 TGATTCGTAGGATTGGCATCTTT 58.219 39.130 0.00 0.00 0.00 2.52
2195 2328 5.924356 TGATTCGTAGGATTGGCATCTTTA 58.076 37.500 0.00 0.00 0.00 1.85
2196 2329 5.991606 TGATTCGTAGGATTGGCATCTTTAG 59.008 40.000 0.00 0.00 0.00 1.85
2197 2330 4.336889 TCGTAGGATTGGCATCTTTAGG 57.663 45.455 0.00 0.00 0.00 2.69
2198 2331 3.964688 TCGTAGGATTGGCATCTTTAGGA 59.035 43.478 0.00 0.00 0.00 2.94
2199 2332 4.407621 TCGTAGGATTGGCATCTTTAGGAA 59.592 41.667 0.00 0.00 0.00 3.36
2200 2333 5.071788 TCGTAGGATTGGCATCTTTAGGAAT 59.928 40.000 0.00 0.00 0.00 3.01
2201 2334 5.765182 CGTAGGATTGGCATCTTTAGGAATT 59.235 40.000 0.00 0.00 0.00 2.17
2202 2335 6.263168 CGTAGGATTGGCATCTTTAGGAATTT 59.737 38.462 0.00 0.00 0.00 1.82
2203 2336 7.201821 CGTAGGATTGGCATCTTTAGGAATTTT 60.202 37.037 0.00 0.00 0.00 1.82
2204 2337 7.500629 AGGATTGGCATCTTTAGGAATTTTT 57.499 32.000 0.00 0.00 0.00 1.94
2205 2338 7.559486 AGGATTGGCATCTTTAGGAATTTTTC 58.441 34.615 0.00 0.00 0.00 2.29
2206 2339 7.401204 AGGATTGGCATCTTTAGGAATTTTTCT 59.599 33.333 0.00 0.00 0.00 2.52
2207 2340 8.695456 GGATTGGCATCTTTAGGAATTTTTCTA 58.305 33.333 0.00 0.00 0.00 2.10
2211 2344 9.354673 TGGCATCTTTAGGAATTTTTCTATAGG 57.645 33.333 0.00 0.00 0.00 2.57
2212 2345 9.574516 GGCATCTTTAGGAATTTTTCTATAGGA 57.425 33.333 0.00 0.00 0.00 2.94
2221 2354 9.942526 AGGAATTTTTCTATAGGATCCATTTGT 57.057 29.630 15.82 0.00 0.00 2.83
2235 2368 9.838339 AGGATCCATTTGTACTACATTTTAGAG 57.162 33.333 15.82 0.00 0.00 2.43
2236 2369 9.832445 GGATCCATTTGTACTACATTTTAGAGA 57.168 33.333 6.95 0.00 0.00 3.10
2258 2391 9.702494 AGAGAAAAATTTCCATTCACTCAAATC 57.298 29.630 2.37 0.00 37.92 2.17
2259 2392 9.702494 GAGAAAAATTTCCATTCACTCAAATCT 57.298 29.630 2.37 0.00 37.92 2.40
2260 2393 9.702494 AGAAAAATTTCCATTCACTCAAATCTC 57.298 29.630 2.37 0.00 37.92 2.75
2261 2394 9.702494 GAAAAATTTCCATTCACTCAAATCTCT 57.298 29.630 0.00 0.00 0.00 3.10
2264 2397 9.485206 AAATTTCCATTCACTCAAATCTCTTTG 57.515 29.630 0.00 0.00 42.60 2.77
2265 2398 7.587037 TTTCCATTCACTCAAATCTCTTTGT 57.413 32.000 0.00 0.00 42.02 2.83
2266 2399 8.690203 TTTCCATTCACTCAAATCTCTTTGTA 57.310 30.769 0.00 0.00 42.02 2.41
2267 2400 7.912056 TCCATTCACTCAAATCTCTTTGTAG 57.088 36.000 0.00 0.00 42.02 2.74
2268 2401 7.679783 TCCATTCACTCAAATCTCTTTGTAGA 58.320 34.615 0.00 0.00 42.02 2.59
2269 2402 8.156820 TCCATTCACTCAAATCTCTTTGTAGAA 58.843 33.333 0.00 0.00 42.02 2.10
2270 2403 8.954350 CCATTCACTCAAATCTCTTTGTAGAAT 58.046 33.333 0.00 0.00 42.02 2.40
2271 2404 9.770503 CATTCACTCAAATCTCTTTGTAGAATG 57.229 33.333 17.33 17.33 41.77 2.67
2272 2405 7.369803 TCACTCAAATCTCTTTGTAGAATGC 57.630 36.000 0.00 0.00 42.02 3.56
2273 2406 6.372659 TCACTCAAATCTCTTTGTAGAATGCC 59.627 38.462 0.00 0.00 42.02 4.40
2274 2407 6.373774 CACTCAAATCTCTTTGTAGAATGCCT 59.626 38.462 0.00 0.00 42.02 4.75
2275 2408 6.944862 ACTCAAATCTCTTTGTAGAATGCCTT 59.055 34.615 0.00 0.00 42.02 4.35
2276 2409 7.449704 ACTCAAATCTCTTTGTAGAATGCCTTT 59.550 33.333 0.00 0.00 42.02 3.11
2277 2410 7.596494 TCAAATCTCTTTGTAGAATGCCTTTG 58.404 34.615 0.00 0.00 42.02 2.77
2278 2411 7.231317 TCAAATCTCTTTGTAGAATGCCTTTGT 59.769 33.333 0.00 0.00 42.02 2.83
2279 2412 7.530426 AATCTCTTTGTAGAATGCCTTTGTT 57.470 32.000 0.00 0.00 0.00 2.83
2280 2413 6.959639 TCTCTTTGTAGAATGCCTTTGTTT 57.040 33.333 0.00 0.00 0.00 2.83
2281 2414 7.346751 TCTCTTTGTAGAATGCCTTTGTTTT 57.653 32.000 0.00 0.00 0.00 2.43
2282 2415 7.781056 TCTCTTTGTAGAATGCCTTTGTTTTT 58.219 30.769 0.00 0.00 0.00 1.94
2283 2416 7.920682 TCTCTTTGTAGAATGCCTTTGTTTTTC 59.079 33.333 0.00 0.00 0.00 2.29
2284 2417 6.983890 TCTTTGTAGAATGCCTTTGTTTTTCC 59.016 34.615 0.00 0.00 0.00 3.13
2285 2418 6.478512 TTGTAGAATGCCTTTGTTTTTCCT 57.521 33.333 0.00 0.00 0.00 3.36
2286 2419 5.841810 TGTAGAATGCCTTTGTTTTTCCTG 58.158 37.500 0.00 0.00 0.00 3.86
2287 2420 3.732212 AGAATGCCTTTGTTTTTCCTGC 58.268 40.909 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.760035 AGCAGCGTAGACCCCACG 61.760 66.667 0.00 0.00 42.24 4.94
94 95 1.210722 GGTGAGAGGAAATGTCCCCTC 59.789 57.143 6.50 6.50 46.56 4.30
185 186 2.361771 CAGGAGCCCCATGCCTTT 59.638 61.111 0.00 0.00 42.71 3.11
285 290 8.316214 CCCTTGGTTATAGACACAAGTTAACTA 58.684 37.037 8.92 0.00 36.04 2.24
298 303 1.780309 CCCCATGCCCTTGGTTATAGA 59.220 52.381 0.00 0.00 34.77 1.98
303 308 3.604133 AGCCCCATGCCCTTGGTT 61.604 61.111 0.00 0.00 42.71 3.67
430 435 4.772231 AATGGCTGGGCTGGGCTG 62.772 66.667 5.61 0.00 0.00 4.85
431 436 3.551081 AAAATGGCTGGGCTGGGCT 62.551 57.895 5.61 0.00 0.00 5.19
432 437 2.526450 GAAAAATGGCTGGGCTGGGC 62.526 60.000 0.00 0.00 0.00 5.36
433 438 0.906282 AGAAAAATGGCTGGGCTGGG 60.906 55.000 0.00 0.00 0.00 4.45
434 439 1.851304 TAGAAAAATGGCTGGGCTGG 58.149 50.000 0.00 0.00 0.00 4.85
435 440 2.417787 GCTTAGAAAAATGGCTGGGCTG 60.418 50.000 0.00 0.00 0.00 4.85
436 441 1.827344 GCTTAGAAAAATGGCTGGGCT 59.173 47.619 0.00 0.00 0.00 5.19
531 547 1.884067 GCAGGTGCTAGCAAGGTTTCT 60.884 52.381 21.29 7.48 38.21 2.52
670 686 4.111839 ATGGGATCCACCTGCCAT 57.888 55.556 15.23 3.47 41.98 4.40
671 687 3.009275 CATGGGATCCACCTGCCA 58.991 61.111 15.23 0.77 41.24 4.92
678 694 3.824425 GCCTGGGCATGGGATCCA 61.824 66.667 15.23 0.00 41.49 3.41
679 695 3.504204 GAGCCTGGGCATGGGATCC 62.504 68.421 14.39 1.92 44.88 3.36
680 696 2.114838 GAGCCTGGGCATGGGATC 59.885 66.667 14.39 0.00 44.88 3.36
681 697 2.369291 AGAGCCTGGGCATGGGAT 60.369 61.111 14.39 0.00 44.88 3.85
819 839 8.036575 CCTATAGTAGTAGCAGTAGTACTCCAG 58.963 44.444 0.00 0.00 42.27 3.86
831 851 9.179104 TCCTATATATGGCCTATAGTAGTAGCA 57.821 37.037 3.32 0.00 30.43 3.49
884 904 5.308825 AGGAGACACAGGTAACAAGAAATG 58.691 41.667 0.00 0.00 41.41 2.32
1042 1062 0.043940 ACAAGGAGCAGGAGGAGGAT 59.956 55.000 0.00 0.00 0.00 3.24
1075 1098 3.774528 ATGGCTCGAGCTCGGCAA 61.775 61.111 34.49 29.32 41.70 4.52
1096 1119 0.967887 TCCTCCCTCAGCGTTCTCAG 60.968 60.000 0.00 0.00 0.00 3.35
1183 1206 3.869272 GTCATCGCCGCCTGCTTG 61.869 66.667 0.00 0.00 38.05 4.01
1308 1351 1.596477 GATGCAGAGATCCACCGGC 60.596 63.158 0.00 0.00 0.00 6.13
1325 1368 1.375908 GTGAGCGCCATGAACCTGA 60.376 57.895 2.29 0.00 0.00 3.86
1338 1381 2.563013 ATCTGGTGGCCATGGTGAGC 62.563 60.000 9.72 10.30 30.82 4.26
1502 1589 1.041447 ATGCAGGGAAGGAAGCATGC 61.041 55.000 10.51 10.51 45.19 4.06
1503 1590 3.202548 ATGCAGGGAAGGAAGCATG 57.797 52.632 0.00 0.00 45.19 4.06
1505 1592 0.627451 ATCATGCAGGGAAGGAAGCA 59.373 50.000 0.00 0.00 41.73 3.91
1506 1593 1.772836 AATCATGCAGGGAAGGAAGC 58.227 50.000 0.00 0.00 0.00 3.86
1507 1594 2.883386 GCTAATCATGCAGGGAAGGAAG 59.117 50.000 0.00 0.00 0.00 3.46
1508 1595 2.511218 AGCTAATCATGCAGGGAAGGAA 59.489 45.455 0.00 0.00 0.00 3.36
1509 1596 2.130193 AGCTAATCATGCAGGGAAGGA 58.870 47.619 0.00 0.00 0.00 3.36
1510 1597 2.228059 CAGCTAATCATGCAGGGAAGG 58.772 52.381 0.00 0.00 0.00 3.46
1511 1598 2.928334 ACAGCTAATCATGCAGGGAAG 58.072 47.619 0.00 0.00 0.00 3.46
1512 1599 4.349048 AGATACAGCTAATCATGCAGGGAA 59.651 41.667 0.00 0.00 0.00 3.97
1513 1600 3.906218 AGATACAGCTAATCATGCAGGGA 59.094 43.478 0.00 0.00 0.00 4.20
1514 1601 4.020396 AGAGATACAGCTAATCATGCAGGG 60.020 45.833 0.00 0.00 0.00 4.45
1515 1602 5.149973 AGAGATACAGCTAATCATGCAGG 57.850 43.478 10.08 0.00 0.00 4.85
1516 1603 5.990386 ACAAGAGATACAGCTAATCATGCAG 59.010 40.000 10.08 0.00 0.00 4.41
1517 1604 5.756833 CACAAGAGATACAGCTAATCATGCA 59.243 40.000 10.08 0.00 0.00 3.96
1518 1605 5.757320 ACACAAGAGATACAGCTAATCATGC 59.243 40.000 10.08 0.00 0.00 4.06
1570 1657 2.354821 GCTCGACCAACAACTTTCAAGT 59.645 45.455 0.00 0.00 42.04 3.16
1572 1659 2.360844 TGCTCGACCAACAACTTTCAA 58.639 42.857 0.00 0.00 0.00 2.69
1598 1686 0.539051 GTGTACAGAGGGAGCAGCAT 59.461 55.000 0.00 0.00 0.00 3.79
1600 1688 1.475403 TAGTGTACAGAGGGAGCAGC 58.525 55.000 0.00 0.00 0.00 5.25
1603 1691 5.360144 TCTTACATTAGTGTACAGAGGGAGC 59.640 44.000 0.00 0.00 40.40 4.70
1605 1693 5.356190 CGTCTTACATTAGTGTACAGAGGGA 59.644 44.000 0.00 0.00 40.40 4.20
1606 1694 5.125097 ACGTCTTACATTAGTGTACAGAGGG 59.875 44.000 20.54 13.88 40.40 4.30
1608 1696 8.516811 AAAACGTCTTACATTAGTGTACAGAG 57.483 34.615 0.00 0.00 40.40 3.35
1609 1697 8.876275 AAAAACGTCTTACATTAGTGTACAGA 57.124 30.769 0.00 2.70 40.40 3.41
1610 1698 8.219105 GGAAAAACGTCTTACATTAGTGTACAG 58.781 37.037 0.00 0.54 40.40 2.74
1617 1721 5.851047 ACGGGAAAAACGTCTTACATTAG 57.149 39.130 0.00 0.00 41.25 1.73
1627 1731 4.563580 GTTCAATTTGAACGGGAAAAACGT 59.436 37.500 22.58 0.00 45.88 3.99
1628 1732 5.060884 GTTCAATTTGAACGGGAAAAACG 57.939 39.130 22.58 0.00 45.88 3.60
1673 1777 6.399204 AAAACGCTCTTATACCTTTGTACG 57.601 37.500 0.00 0.00 0.00 3.67
1674 1778 7.799784 TGAAAAACGCTCTTATACCTTTGTAC 58.200 34.615 0.00 0.00 0.00 2.90
1676 1780 6.708949 TCTGAAAAACGCTCTTATACCTTTGT 59.291 34.615 0.00 0.00 0.00 2.83
1677 1781 7.015877 GTCTGAAAAACGCTCTTATACCTTTG 58.984 38.462 0.00 0.00 0.00 2.77
1678 1782 6.935208 AGTCTGAAAAACGCTCTTATACCTTT 59.065 34.615 0.00 0.00 0.00 3.11
1679 1783 6.465084 AGTCTGAAAAACGCTCTTATACCTT 58.535 36.000 0.00 0.00 0.00 3.50
1680 1784 6.038997 AGTCTGAAAAACGCTCTTATACCT 57.961 37.500 0.00 0.00 0.00 3.08
1681 1785 7.034397 ACTAGTCTGAAAAACGCTCTTATACC 58.966 38.462 0.00 0.00 0.00 2.73
1682 1786 9.733219 ATACTAGTCTGAAAAACGCTCTTATAC 57.267 33.333 0.00 0.00 0.00 1.47
1684 1788 9.953697 CTATACTAGTCTGAAAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
1685 1789 8.954350 ACTATACTAGTCTGAAAAACGCTCTTA 58.046 33.333 0.00 0.00 32.47 2.10
1686 1790 7.755822 CACTATACTAGTCTGAAAAACGCTCTT 59.244 37.037 0.00 0.00 36.76 2.85
1687 1791 7.094291 ACACTATACTAGTCTGAAAAACGCTCT 60.094 37.037 0.00 0.00 36.76 4.09
1688 1792 7.028361 ACACTATACTAGTCTGAAAAACGCTC 58.972 38.462 0.00 0.00 36.76 5.03
1689 1793 6.921914 ACACTATACTAGTCTGAAAAACGCT 58.078 36.000 0.00 0.00 36.76 5.07
1690 1794 6.805271 TGACACTATACTAGTCTGAAAAACGC 59.195 38.462 0.00 0.00 36.76 4.84
1691 1795 8.738199 TTGACACTATACTAGTCTGAAAAACG 57.262 34.615 0.00 0.00 36.76 3.60
1695 1799 9.188588 CGTTTTTGACACTATACTAGTCTGAAA 57.811 33.333 0.00 0.00 36.76 2.69
1696 1800 8.355169 ACGTTTTTGACACTATACTAGTCTGAA 58.645 33.333 0.00 0.00 36.76 3.02
1697 1801 7.879070 ACGTTTTTGACACTATACTAGTCTGA 58.121 34.615 0.00 0.00 36.76 3.27
1698 1802 8.516811 AACGTTTTTGACACTATACTAGTCTG 57.483 34.615 0.00 0.00 36.76 3.51
1719 1823 9.466497 TCCCTCCGTTCTATAATATAATAACGT 57.534 33.333 18.17 0.00 38.34 3.99
1720 1824 9.947669 CTCCCTCCGTTCTATAATATAATAACG 57.052 37.037 15.15 15.15 39.38 3.18
1727 1831 8.609483 TGTACTACTCCCTCCGTTCTATAATAT 58.391 37.037 0.00 0.00 0.00 1.28
1728 1832 7.977818 TGTACTACTCCCTCCGTTCTATAATA 58.022 38.462 0.00 0.00 0.00 0.98
1729 1833 6.845908 TGTACTACTCCCTCCGTTCTATAAT 58.154 40.000 0.00 0.00 0.00 1.28
1730 1834 6.252599 TGTACTACTCCCTCCGTTCTATAA 57.747 41.667 0.00 0.00 0.00 0.98
1731 1835 5.894298 TGTACTACTCCCTCCGTTCTATA 57.106 43.478 0.00 0.00 0.00 1.31
1734 1838 3.666345 ATGTACTACTCCCTCCGTTCT 57.334 47.619 0.00 0.00 0.00 3.01
1738 1842 4.565236 CCCTACTATGTACTACTCCCTCCG 60.565 54.167 0.00 0.00 0.00 4.63
1742 1846 3.429492 GCCCCTACTATGTACTACTCCC 58.571 54.545 0.00 0.00 0.00 4.30
1749 1853 1.046204 AAGGCGCCCCTACTATGTAC 58.954 55.000 26.15 0.00 41.90 2.90
1752 1856 0.180406 ACAAAGGCGCCCCTACTATG 59.820 55.000 26.15 13.92 41.90 2.23
1757 1861 0.913205 TGATTACAAAGGCGCCCCTA 59.087 50.000 26.15 4.15 41.90 3.53
1760 1864 1.427819 CGTGATTACAAAGGCGCCC 59.572 57.895 26.15 5.30 0.00 6.13
1762 1866 0.519961 AACCGTGATTACAAAGGCGC 59.480 50.000 0.00 0.00 32.03 6.53
1764 1868 1.268352 TGCAACCGTGATTACAAAGGC 59.732 47.619 0.00 0.00 32.03 4.35
1765 1869 3.500982 CATGCAACCGTGATTACAAAGG 58.499 45.455 0.00 0.00 34.02 3.11
1766 1870 3.500982 CCATGCAACCGTGATTACAAAG 58.499 45.455 0.00 0.00 0.00 2.77
1767 1871 2.230025 CCCATGCAACCGTGATTACAAA 59.770 45.455 0.00 0.00 0.00 2.83
1768 1872 1.815613 CCCATGCAACCGTGATTACAA 59.184 47.619 0.00 0.00 0.00 2.41
1769 1873 1.003696 TCCCATGCAACCGTGATTACA 59.996 47.619 0.00 0.00 0.00 2.41
1770 1874 1.745232 TCCCATGCAACCGTGATTAC 58.255 50.000 0.00 0.00 0.00 1.89
1772 1876 1.064463 AGATCCCATGCAACCGTGATT 60.064 47.619 0.00 0.00 0.00 2.57
1773 1877 0.548031 AGATCCCATGCAACCGTGAT 59.452 50.000 0.00 0.00 0.00 3.06
1775 1879 0.392863 TCAGATCCCATGCAACCGTG 60.393 55.000 0.00 0.00 0.00 4.94
1776 1880 0.327924 TTCAGATCCCATGCAACCGT 59.672 50.000 0.00 0.00 0.00 4.83
1777 1881 1.462616 TTTCAGATCCCATGCAACCG 58.537 50.000 0.00 0.00 0.00 4.44
1778 1882 3.703052 AGAATTTCAGATCCCATGCAACC 59.297 43.478 0.00 0.00 0.00 3.77
1783 1887 6.097839 ACCATTTCAGAATTTCAGATCCCATG 59.902 38.462 0.00 0.00 0.00 3.66
1784 1888 6.200114 ACCATTTCAGAATTTCAGATCCCAT 58.800 36.000 0.00 0.00 0.00 4.00
1786 1890 7.830099 ATACCATTTCAGAATTTCAGATCCC 57.170 36.000 0.00 0.00 0.00 3.85
1793 1897 8.223100 GCAACAACAATACCATTTCAGAATTTC 58.777 33.333 0.00 0.00 0.00 2.17
1798 1902 6.403866 AAGCAACAACAATACCATTTCAGA 57.596 33.333 0.00 0.00 0.00 3.27
1803 1907 6.045955 ACGAAAAAGCAACAACAATACCATT 58.954 32.000 0.00 0.00 0.00 3.16
1807 1911 6.175087 CACAACGAAAAAGCAACAACAATAC 58.825 36.000 0.00 0.00 0.00 1.89
1809 1913 4.688413 ACACAACGAAAAAGCAACAACAAT 59.312 33.333 0.00 0.00 0.00 2.71
1813 1917 3.902150 TCACACAACGAAAAAGCAACAA 58.098 36.364 0.00 0.00 0.00 2.83
1818 1922 5.949233 ATTTCTTCACACAACGAAAAAGC 57.051 34.783 0.00 0.00 0.00 3.51
1824 1938 8.564574 AGCTTAATTAATTTCTTCACACAACGA 58.435 29.630 5.91 0.00 0.00 3.85
1826 1940 9.463443 ACAGCTTAATTAATTTCTTCACACAAC 57.537 29.630 5.91 0.00 0.00 3.32
1860 1974 5.967088 ACCACGAGATATTATATCACAGCC 58.033 41.667 13.87 0.00 0.00 4.85
1861 1975 6.868864 ACAACCACGAGATATTATATCACAGC 59.131 38.462 13.87 1.07 0.00 4.40
1862 1976 8.703336 CAACAACCACGAGATATTATATCACAG 58.297 37.037 13.87 7.32 0.00 3.66
1863 1977 7.655732 CCAACAACCACGAGATATTATATCACA 59.344 37.037 13.87 0.00 0.00 3.58
1864 1978 7.870954 TCCAACAACCACGAGATATTATATCAC 59.129 37.037 13.87 7.20 0.00 3.06
1865 1979 7.958088 TCCAACAACCACGAGATATTATATCA 58.042 34.615 13.87 0.00 0.00 2.15
1866 1980 8.304596 TCTCCAACAACCACGAGATATTATATC 58.695 37.037 4.15 4.15 0.00 1.63
1867 1981 8.190326 TCTCCAACAACCACGAGATATTATAT 57.810 34.615 0.00 0.00 0.00 0.86
1868 1982 7.591421 TCTCCAACAACCACGAGATATTATA 57.409 36.000 0.00 0.00 0.00 0.98
1869 1983 6.479972 TCTCCAACAACCACGAGATATTAT 57.520 37.500 0.00 0.00 0.00 1.28
1870 1984 5.681437 GCTCTCCAACAACCACGAGATATTA 60.681 44.000 0.00 0.00 31.25 0.98
1871 1985 4.759782 CTCTCCAACAACCACGAGATATT 58.240 43.478 0.00 0.00 31.25 1.28
1878 1992 2.533318 GAGCTCTCCAACAACCACG 58.467 57.895 6.43 0.00 0.00 4.94
1892 2006 4.044065 AGCAGATACTACTAGATGGGAGCT 59.956 45.833 0.00 0.00 0.00 4.09
1905 2019 9.679661 CTCCTCTTTATAGATCAGCAGATACTA 57.320 37.037 0.00 0.00 33.72 1.82
1927 2052 3.073735 CGCCTCCAGACTGCTCCT 61.074 66.667 0.00 0.00 0.00 3.69
1928 2053 4.828925 GCGCCTCCAGACTGCTCC 62.829 72.222 0.00 0.00 0.00 4.70
1930 2055 3.397439 ATGCGCCTCCAGACTGCT 61.397 61.111 4.18 0.00 0.00 4.24
1931 2056 3.200593 CATGCGCCTCCAGACTGC 61.201 66.667 4.18 0.00 0.00 4.40
1932 2057 2.104859 CACATGCGCCTCCAGACTG 61.105 63.158 4.18 0.00 0.00 3.51
1937 2062 2.409055 GCATTCACATGCGCCTCCA 61.409 57.895 4.18 0.00 46.45 3.86
1938 2063 2.410469 GCATTCACATGCGCCTCC 59.590 61.111 4.18 0.00 46.45 4.30
1953 2078 1.173043 CGGGGTTGATTAAGCAAGCA 58.827 50.000 29.99 0.00 45.41 3.91
1954 2079 1.135402 CACGGGGTTGATTAAGCAAGC 60.135 52.381 23.66 23.66 43.52 4.01
1955 2080 2.432444 TCACGGGGTTGATTAAGCAAG 58.568 47.619 6.36 0.00 36.03 4.01
1956 2081 2.570415 TCACGGGGTTGATTAAGCAA 57.430 45.000 1.13 1.13 36.03 3.91
2033 2163 7.067859 TCTCTGAAAAGATGGCCAGAATATTTG 59.932 37.037 13.05 0.00 35.52 2.32
2041 2171 2.005451 CGTCTCTGAAAAGATGGCCAG 58.995 52.381 13.05 0.00 0.00 4.85
2046 2179 2.094700 TCCGTCCGTCTCTGAAAAGATG 60.095 50.000 0.00 0.00 32.97 2.90
2061 2194 2.126031 GCTTCAGTCGGTCCGTCC 60.126 66.667 11.88 3.31 0.00 4.79
2064 2197 1.901650 GCTTTGCTTCAGTCGGTCCG 61.902 60.000 4.39 4.39 0.00 4.79
2069 2202 1.506493 ACTCTGCTTTGCTTCAGTCG 58.494 50.000 0.00 0.00 0.00 4.18
2071 2204 3.406764 CCTTACTCTGCTTTGCTTCAGT 58.593 45.455 0.00 0.00 0.00 3.41
2098 2231 7.389803 TCCTATGCGATTTCTTTGAATCAAA 57.610 32.000 8.25 8.25 36.12 2.69
2099 2232 7.572523 ATCCTATGCGATTTCTTTGAATCAA 57.427 32.000 0.00 0.00 36.12 2.57
2100 2233 7.572523 AATCCTATGCGATTTCTTTGAATCA 57.427 32.000 0.00 0.00 36.12 2.57
2101 2234 8.862550 AAAATCCTATGCGATTTCTTTGAATC 57.137 30.769 0.00 0.00 40.71 2.52
2124 2257 5.596772 CCTAAGAGTTCAAACCCTCCAAAAA 59.403 40.000 0.00 0.00 0.00 1.94
2125 2258 5.103855 TCCTAAGAGTTCAAACCCTCCAAAA 60.104 40.000 0.00 0.00 0.00 2.44
2126 2259 4.414182 TCCTAAGAGTTCAAACCCTCCAAA 59.586 41.667 0.00 0.00 0.00 3.28
2127 2260 3.977999 TCCTAAGAGTTCAAACCCTCCAA 59.022 43.478 0.00 0.00 0.00 3.53
2128 2261 3.593942 TCCTAAGAGTTCAAACCCTCCA 58.406 45.455 0.00 0.00 0.00 3.86
2129 2262 4.635699 TTCCTAAGAGTTCAAACCCTCC 57.364 45.455 0.00 0.00 0.00 4.30
2130 2263 7.526142 AAAATTCCTAAGAGTTCAAACCCTC 57.474 36.000 0.00 0.00 0.00 4.30
2131 2264 7.914427 AAAAATTCCTAAGAGTTCAAACCCT 57.086 32.000 0.00 0.00 0.00 4.34
2152 2285 7.060518 CGAATCAAACGAGCATAACATGAAAAA 59.939 33.333 0.00 0.00 0.00 1.94
2153 2286 6.522855 CGAATCAAACGAGCATAACATGAAAA 59.477 34.615 0.00 0.00 0.00 2.29
2154 2287 6.020984 CGAATCAAACGAGCATAACATGAAA 58.979 36.000 0.00 0.00 0.00 2.69
2155 2288 5.121611 ACGAATCAAACGAGCATAACATGAA 59.878 36.000 0.00 0.00 34.70 2.57
2156 2289 4.629634 ACGAATCAAACGAGCATAACATGA 59.370 37.500 0.00 0.00 34.70 3.07
2157 2290 4.897224 ACGAATCAAACGAGCATAACATG 58.103 39.130 0.00 0.00 34.70 3.21
2158 2291 5.234329 CCTACGAATCAAACGAGCATAACAT 59.766 40.000 0.00 0.00 34.70 2.71
2159 2292 4.565166 CCTACGAATCAAACGAGCATAACA 59.435 41.667 0.00 0.00 34.70 2.41
2160 2293 4.802039 TCCTACGAATCAAACGAGCATAAC 59.198 41.667 0.00 0.00 34.70 1.89
2161 2294 5.001237 TCCTACGAATCAAACGAGCATAA 57.999 39.130 0.00 0.00 34.70 1.90
2162 2295 4.642445 TCCTACGAATCAAACGAGCATA 57.358 40.909 0.00 0.00 34.70 3.14
2163 2296 3.520290 TCCTACGAATCAAACGAGCAT 57.480 42.857 0.00 0.00 34.70 3.79
2164 2297 3.520290 ATCCTACGAATCAAACGAGCA 57.480 42.857 0.00 0.00 34.70 4.26
2165 2298 3.001330 CCAATCCTACGAATCAAACGAGC 59.999 47.826 0.00 0.00 34.70 5.03
2166 2299 3.001330 GCCAATCCTACGAATCAAACGAG 59.999 47.826 0.00 0.00 34.70 4.18
2167 2300 2.933906 GCCAATCCTACGAATCAAACGA 59.066 45.455 0.00 0.00 34.70 3.85
2168 2301 2.675844 TGCCAATCCTACGAATCAAACG 59.324 45.455 0.00 0.00 0.00 3.60
2169 2302 4.576463 AGATGCCAATCCTACGAATCAAAC 59.424 41.667 0.00 0.00 32.77 2.93
2170 2303 4.780815 AGATGCCAATCCTACGAATCAAA 58.219 39.130 0.00 0.00 32.77 2.69
2171 2304 4.422073 AGATGCCAATCCTACGAATCAA 57.578 40.909 0.00 0.00 32.77 2.57
2172 2305 4.422073 AAGATGCCAATCCTACGAATCA 57.578 40.909 0.00 0.00 32.77 2.57
2173 2306 5.409826 CCTAAAGATGCCAATCCTACGAATC 59.590 44.000 0.00 0.00 32.77 2.52
2174 2307 5.071788 TCCTAAAGATGCCAATCCTACGAAT 59.928 40.000 0.00 0.00 32.77 3.34
2175 2308 4.407621 TCCTAAAGATGCCAATCCTACGAA 59.592 41.667 0.00 0.00 32.77 3.85
2176 2309 3.964688 TCCTAAAGATGCCAATCCTACGA 59.035 43.478 0.00 0.00 32.77 3.43
2177 2310 4.336889 TCCTAAAGATGCCAATCCTACG 57.663 45.455 0.00 0.00 32.77 3.51
2178 2311 7.588497 AAATTCCTAAAGATGCCAATCCTAC 57.412 36.000 0.00 0.00 32.77 3.18
2179 2312 8.608185 AAAAATTCCTAAAGATGCCAATCCTA 57.392 30.769 0.00 0.00 32.77 2.94
2180 2313 7.401204 AGAAAAATTCCTAAAGATGCCAATCCT 59.599 33.333 0.00 0.00 32.77 3.24
2181 2314 7.559486 AGAAAAATTCCTAAAGATGCCAATCC 58.441 34.615 0.00 0.00 32.77 3.01
2185 2318 9.354673 CCTATAGAAAAATTCCTAAAGATGCCA 57.645 33.333 0.00 0.00 0.00 4.92
2186 2319 9.574516 TCCTATAGAAAAATTCCTAAAGATGCC 57.425 33.333 0.00 0.00 0.00 4.40
2195 2328 9.942526 ACAAATGGATCCTATAGAAAAATTCCT 57.057 29.630 14.23 0.00 0.00 3.36
2209 2342 9.838339 CTCTAAAATGTAGTACAAATGGATCCT 57.162 33.333 14.23 0.00 0.00 3.24
2210 2343 9.832445 TCTCTAAAATGTAGTACAAATGGATCC 57.168 33.333 7.16 4.20 0.00 3.36
2232 2365 9.702494 GATTTGAGTGAATGGAAATTTTTCTCT 57.298 29.630 5.71 5.71 37.35 3.10
2233 2366 9.702494 AGATTTGAGTGAATGGAAATTTTTCTC 57.298 29.630 3.28 0.00 37.35 2.87
2234 2367 9.702494 GAGATTTGAGTGAATGGAAATTTTTCT 57.298 29.630 3.28 0.00 37.35 2.52
2235 2368 9.702494 AGAGATTTGAGTGAATGGAAATTTTTC 57.298 29.630 0.00 0.00 36.46 2.29
2238 2371 9.485206 CAAAGAGATTTGAGTGAATGGAAATTT 57.515 29.630 0.00 0.00 33.95 1.82
2239 2372 8.645110 ACAAAGAGATTTGAGTGAATGGAAATT 58.355 29.630 7.66 0.00 35.93 1.82
2240 2373 8.186709 ACAAAGAGATTTGAGTGAATGGAAAT 57.813 30.769 7.66 0.00 35.93 2.17
2241 2374 7.587037 ACAAAGAGATTTGAGTGAATGGAAA 57.413 32.000 7.66 0.00 35.93 3.13
2242 2375 8.156820 TCTACAAAGAGATTTGAGTGAATGGAA 58.843 33.333 7.66 0.00 35.93 3.53
2243 2376 7.679783 TCTACAAAGAGATTTGAGTGAATGGA 58.320 34.615 7.66 0.00 35.93 3.41
2244 2377 7.912056 TCTACAAAGAGATTTGAGTGAATGG 57.088 36.000 7.66 0.00 35.93 3.16
2245 2378 9.770503 CATTCTACAAAGAGATTTGAGTGAATG 57.229 33.333 19.50 19.50 38.36 2.67
2246 2379 8.457261 GCATTCTACAAAGAGATTTGAGTGAAT 58.543 33.333 7.66 9.80 35.93 2.57
2247 2380 7.094634 GGCATTCTACAAAGAGATTTGAGTGAA 60.095 37.037 7.66 8.32 35.93 3.18
2248 2381 6.372659 GGCATTCTACAAAGAGATTTGAGTGA 59.627 38.462 7.66 0.87 35.93 3.41
2249 2382 6.373774 AGGCATTCTACAAAGAGATTTGAGTG 59.626 38.462 7.66 0.00 35.93 3.51
2250 2383 6.479884 AGGCATTCTACAAAGAGATTTGAGT 58.520 36.000 7.66 0.00 35.93 3.41
2251 2384 6.998968 AGGCATTCTACAAAGAGATTTGAG 57.001 37.500 7.66 1.98 35.93 3.02
2252 2385 7.231317 ACAAAGGCATTCTACAAAGAGATTTGA 59.769 33.333 7.66 0.00 35.93 2.69
2253 2386 7.373493 ACAAAGGCATTCTACAAAGAGATTTG 58.627 34.615 0.00 0.00 37.89 2.32
2254 2387 7.530426 ACAAAGGCATTCTACAAAGAGATTT 57.470 32.000 0.00 0.00 31.96 2.17
2255 2388 7.530426 AACAAAGGCATTCTACAAAGAGATT 57.470 32.000 0.00 0.00 31.96 2.40
2256 2389 7.530426 AAACAAAGGCATTCTACAAAGAGAT 57.470 32.000 0.00 0.00 31.96 2.75
2257 2390 6.959639 AAACAAAGGCATTCTACAAAGAGA 57.040 33.333 0.00 0.00 31.96 3.10
2258 2391 7.169813 GGAAAAACAAAGGCATTCTACAAAGAG 59.830 37.037 0.00 0.00 31.96 2.85
2259 2392 6.983890 GGAAAAACAAAGGCATTCTACAAAGA 59.016 34.615 0.00 0.00 0.00 2.52
2260 2393 6.986231 AGGAAAAACAAAGGCATTCTACAAAG 59.014 34.615 0.00 0.00 0.00 2.77
2261 2394 6.760770 CAGGAAAAACAAAGGCATTCTACAAA 59.239 34.615 0.00 0.00 0.00 2.83
2262 2395 6.279882 CAGGAAAAACAAAGGCATTCTACAA 58.720 36.000 0.00 0.00 0.00 2.41
2263 2396 5.738783 GCAGGAAAAACAAAGGCATTCTACA 60.739 40.000 0.00 0.00 0.00 2.74
2264 2397 4.686091 GCAGGAAAAACAAAGGCATTCTAC 59.314 41.667 0.00 0.00 0.00 2.59
2265 2398 4.881920 GCAGGAAAAACAAAGGCATTCTA 58.118 39.130 0.00 0.00 0.00 2.10
2266 2399 3.732212 GCAGGAAAAACAAAGGCATTCT 58.268 40.909 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.