Multiple sequence alignment - TraesCS2B01G492000

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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 TraesCS2B01G492000 chr2B 100.000 4889 0 0 825 5713 690221402 690216514 0.000000e+00 9029.0
1 TraesCS2B01G492000 chr2B 100.000 513 0 0 1 513 690222226 690221714 0.000000e+00 948.0
2 TraesCS2B01G492000 chr2D 95.321 3740 116 32 1767 5472 574354101 574350387 0.000000e+00 5882.0
3 TraesCS2B01G492000 chr2D 84.758 971 75 40 826 1772 574354946 574354025 0.000000e+00 905.0
4 TraesCS2B01G492000 chr2D 87.052 502 10 18 34 513 574355433 574354965 3.050000e-142 516.0
5 TraesCS2B01G492000 chr2D 90.610 213 13 5 5503 5713 574350291 574350084 5.640000e-70 276.0
6 TraesCS2B01G492000 chr2A 93.876 3756 149 44 1884 5571 712723990 712720248 0.000000e+00 5587.0
7 TraesCS2B01G492000 chr2A 85.513 994 63 41 911 1838 712724968 712723990 0.000000e+00 963.0
8 TraesCS2B01G492000 chr2A 90.345 145 13 1 5570 5713 712720124 712719980 7.560000e-44 189.0
9 TraesCS2B01G492000 chr2A 88.966 145 2 5 380 513 712725172 712725031 3.540000e-37 167.0
10 TraesCS2B01G492000 chr2A 90.141 71 5 2 825 894 712725020 712724951 2.190000e-14 91.6


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 TraesCS2B01G492000 chr2B 690216514 690222226 5712 True 4988.50 9029 100.00000 1 5713 2 chr2B.!!$R1 5712
1 TraesCS2B01G492000 chr2D 574350084 574355433 5349 True 1894.75 5882 89.43525 34 5713 4 chr2D.!!$R1 5679
2 TraesCS2B01G492000 chr2A 712719980 712725172 5192 True 1399.52 5587 89.76820 380 5713 5 chr2A.!!$R1 5333

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
21 22 0.392193 CAACGGCTGGAGATGCTCTT 60.392 55.0 0.00 0.0 0.00 2.85 F
874 899 0.402504 ACGTCTCTCTGACCTGACCT 59.597 55.0 0.00 0.0 42.49 3.85 F
2147 2297 0.029163 TAGGATCCTTCCCATGCCCA 60.029 55.0 22.03 0.0 43.76 5.36 F
2778 2936 0.614697 GTTCTTGGGTGGATTGGGGG 60.615 60.0 0.00 0.0 0.00 5.40 F
3995 4154 0.586319 TTTTTGAAGAGCTGCGTCCG 59.414 50.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1456 0.104304 CATCACCGCCTACCACCTAC 59.896 60.0 0.00 0.0 0.00 3.18 R
2640 2798 0.247736 AACTGCTCGAGGGACATCAC 59.752 55.0 15.58 0.0 0.00 3.06 R
3389 3548 0.322366 GCCAAGCTGCTTTCTCCTCT 60.322 55.0 13.10 0.0 0.00 3.69 R
4295 4454 0.033109 TCAGCTTCTCGATCTCCCCA 60.033 55.0 0.00 0.0 0.00 4.96 R
5255 5467 0.673985 TGGACACTTCAGTCTCCACG 59.326 55.0 0.05 0.0 38.04 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
19 20 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
20 21 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
21 22 0.392193 CAACGGCTGGAGATGCTCTT 60.392 55.000 0.00 0.00 0.00 2.85
22 23 1.134699 CAACGGCTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
23 24 1.195115 ACGGCTGGAGATGCTCTTAA 58.805 50.000 0.00 0.00 0.00 1.85
24 25 1.765314 ACGGCTGGAGATGCTCTTAAT 59.235 47.619 0.00 0.00 0.00 1.40
25 26 2.171448 ACGGCTGGAGATGCTCTTAATT 59.829 45.455 0.00 0.00 0.00 1.40
26 27 3.209410 CGGCTGGAGATGCTCTTAATTT 58.791 45.455 0.00 0.00 0.00 1.82
27 28 3.003068 CGGCTGGAGATGCTCTTAATTTG 59.997 47.826 0.00 0.00 0.00 2.32
28 29 3.243334 GGCTGGAGATGCTCTTAATTTGC 60.243 47.826 0.00 0.00 0.00 3.68
29 30 3.631227 GCTGGAGATGCTCTTAATTTGCT 59.369 43.478 0.00 0.00 0.00 3.91
30 31 4.497674 GCTGGAGATGCTCTTAATTTGCTG 60.498 45.833 0.00 0.00 0.00 4.41
31 32 4.847198 TGGAGATGCTCTTAATTTGCTGA 58.153 39.130 0.00 0.00 0.00 4.26
32 33 4.880120 TGGAGATGCTCTTAATTTGCTGAG 59.120 41.667 0.00 0.00 0.00 3.35
99 100 3.211045 GGGCAATGTACCATGTACGAAT 58.789 45.455 0.00 0.00 0.00 3.34
100 101 3.630312 GGGCAATGTACCATGTACGAATT 59.370 43.478 0.00 0.00 0.00 2.17
101 102 4.817464 GGGCAATGTACCATGTACGAATTA 59.183 41.667 0.00 0.00 0.00 1.40
106 107 5.918426 TGTACCATGTACGAATTACTGGA 57.082 39.130 0.00 0.00 35.01 3.86
150 155 1.070615 CACACATCCCCACGACACA 59.929 57.895 0.00 0.00 0.00 3.72
173 178 1.546548 GGGCCCCTTCAGATGATAAGC 60.547 57.143 12.23 0.00 0.00 3.09
182 187 5.417266 CCTTCAGATGATAAGCCTATCTCGA 59.583 44.000 4.03 0.00 35.79 4.04
188 193 3.690139 TGATAAGCCTATCTCGACGATCC 59.310 47.826 0.00 0.00 35.79 3.36
316 324 2.523168 CCAACAAAACCCGGCCCT 60.523 61.111 0.00 0.00 0.00 5.19
318 326 2.596338 AACAAAACCCGGCCCTCG 60.596 61.111 0.00 0.00 38.88 4.63
319 327 3.424780 AACAAAACCCGGCCCTCGT 62.425 57.895 0.00 0.00 37.11 4.18
320 328 2.054473 AACAAAACCCGGCCCTCGTA 62.054 55.000 0.00 0.00 37.11 3.43
321 329 1.743995 CAAAACCCGGCCCTCGTAG 60.744 63.158 0.00 0.00 37.11 3.51
344 352 2.279784 CAGCCGAGCCGAGGAATC 60.280 66.667 0.00 0.00 0.00 2.52
345 353 3.541713 AGCCGAGCCGAGGAATCC 61.542 66.667 0.00 0.00 0.00 3.01
346 354 3.849951 GCCGAGCCGAGGAATCCA 61.850 66.667 0.61 0.00 0.00 3.41
347 355 3.142393 CCGAGCCGAGGAATCCAT 58.858 61.111 0.61 0.00 0.00 3.41
485 508 3.385111 CGAATCCTGCCTAGTTTACTCCT 59.615 47.826 0.00 0.00 0.00 3.69
874 899 0.402504 ACGTCTCTCTGACCTGACCT 59.597 55.000 0.00 0.00 42.49 3.85
875 900 1.091537 CGTCTCTCTGACCTGACCTC 58.908 60.000 0.00 0.00 42.49 3.85
876 901 1.611936 CGTCTCTCTGACCTGACCTCA 60.612 57.143 0.00 0.00 42.49 3.86
877 902 1.816224 GTCTCTCTGACCTGACCTCAC 59.184 57.143 0.00 0.00 39.69 3.51
894 919 4.787280 CTCACCCTCCCCGCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
895 920 4.779733 TCACCCTCCCCGCCTCTC 62.780 72.222 0.00 0.00 0.00 3.20
907 933 1.754745 GCCTCTCCCACTGTTCACA 59.245 57.895 0.00 0.00 0.00 3.58
916 942 2.587753 CTGTTCACACCCGCACGT 60.588 61.111 0.00 0.00 0.00 4.49
942 968 1.728778 CATCCATCTCGCTCGCTCG 60.729 63.158 0.00 0.00 0.00 5.03
948 974 3.870422 CTCGCTCGCTCGCTCTCA 61.870 66.667 0.00 0.00 0.00 3.27
949 975 3.788586 CTCGCTCGCTCGCTCTCAG 62.789 68.421 0.00 0.00 0.00 3.35
950 976 4.172772 CGCTCGCTCGCTCTCAGT 62.173 66.667 0.00 0.00 0.00 3.41
953 979 1.351707 CTCGCTCGCTCTCAGTCTC 59.648 63.158 0.00 0.00 0.00 3.36
954 980 2.047151 CTCGCTCGCTCTCAGTCTCC 62.047 65.000 0.00 0.00 0.00 3.71
955 981 2.407210 GCTCGCTCTCAGTCTCCG 59.593 66.667 0.00 0.00 0.00 4.63
956 982 2.407210 CTCGCTCTCAGTCTCCGC 59.593 66.667 0.00 0.00 0.00 5.54
1332 1397 2.358737 GAGGGCAGGGTTCACGTG 60.359 66.667 9.94 9.94 37.99 4.49
1385 1450 6.520792 TTTTTCGTTTTTGGTTTCGTTTCA 57.479 29.167 0.00 0.00 0.00 2.69
1387 1452 5.688348 TTCGTTTTTGGTTTCGTTTCATG 57.312 34.783 0.00 0.00 0.00 3.07
1388 1453 3.548268 TCGTTTTTGGTTTCGTTTCATGC 59.452 39.130 0.00 0.00 0.00 4.06
1389 1454 3.549873 CGTTTTTGGTTTCGTTTCATGCT 59.450 39.130 0.00 0.00 0.00 3.79
1390 1455 4.032331 CGTTTTTGGTTTCGTTTCATGCTT 59.968 37.500 0.00 0.00 0.00 3.91
1391 1456 5.254842 GTTTTTGGTTTCGTTTCATGCTTG 58.745 37.500 0.00 0.00 0.00 4.01
1392 1457 3.791973 TTGGTTTCGTTTCATGCTTGT 57.208 38.095 0.00 0.00 0.00 3.16
1393 1458 4.902443 TTGGTTTCGTTTCATGCTTGTA 57.098 36.364 0.00 0.00 0.00 2.41
1394 1459 4.481930 TGGTTTCGTTTCATGCTTGTAG 57.518 40.909 0.00 0.00 0.00 2.74
1395 1460 3.252215 TGGTTTCGTTTCATGCTTGTAGG 59.748 43.478 0.00 0.00 0.00 3.18
1396 1461 3.252458 GGTTTCGTTTCATGCTTGTAGGT 59.748 43.478 0.00 0.00 0.00 3.08
1414 1483 4.530857 GGTAGGCGGTGATGCGCT 62.531 66.667 9.73 0.00 35.06 5.92
1488 1557 1.559682 ACCATCTGTTTCCCGCACTAT 59.440 47.619 0.00 0.00 0.00 2.12
1527 1596 2.736721 GCTGCGTGTTTAGTGAATCTGA 59.263 45.455 0.00 0.00 0.00 3.27
1552 1624 6.434028 ACTTAGTCAAATCATGCTAAAAGGCA 59.566 34.615 0.00 0.00 46.63 4.75
1596 1672 7.036996 TGTTCTGATTTGATGTGTTTTAGCA 57.963 32.000 0.00 0.00 0.00 3.49
1612 1688 1.084289 AGCATAAACCGAGCGAAACC 58.916 50.000 0.00 0.00 0.00 3.27
1618 1694 0.872388 AACCGAGCGAAACCAATGTC 59.128 50.000 0.00 0.00 0.00 3.06
1620 1696 0.165944 CCGAGCGAAACCAATGTCAC 59.834 55.000 0.00 0.00 0.00 3.67
1621 1697 0.865111 CGAGCGAAACCAATGTCACA 59.135 50.000 0.00 0.00 0.00 3.58
1623 1699 0.586319 AGCGAAACCAATGTCACACG 59.414 50.000 0.00 0.00 0.00 4.49
1624 1700 0.306533 GCGAAACCAATGTCACACGT 59.693 50.000 0.00 0.00 0.00 4.49
1625 1701 1.659211 GCGAAACCAATGTCACACGTC 60.659 52.381 0.00 0.00 0.00 4.34
1628 1704 0.944386 AACCAATGTCACACGTCTGC 59.056 50.000 0.00 0.00 0.00 4.26
1630 1706 1.577328 CCAATGTCACACGTCTGCCC 61.577 60.000 0.00 0.00 0.00 5.36
1631 1707 0.884259 CAATGTCACACGTCTGCCCA 60.884 55.000 0.00 0.00 0.00 5.36
1632 1708 0.179032 AATGTCACACGTCTGCCCAA 60.179 50.000 0.00 0.00 0.00 4.12
1633 1709 0.036732 ATGTCACACGTCTGCCCAAT 59.963 50.000 0.00 0.00 0.00 3.16
1634 1710 0.884259 TGTCACACGTCTGCCCAATG 60.884 55.000 0.00 0.00 0.00 2.82
1635 1711 0.884704 GTCACACGTCTGCCCAATGT 60.885 55.000 0.00 0.00 0.00 2.71
1638 1714 0.603707 ACACGTCTGCCCAATGTCTG 60.604 55.000 0.00 0.00 0.00 3.51
1652 1728 5.163447 CCCAATGTCTGGTAAATCTCGTAGA 60.163 44.000 0.00 0.00 44.76 2.59
1654 1730 7.255836 CCCAATGTCTGGTAAATCTCGTAGATA 60.256 40.741 0.00 0.00 44.76 1.98
1655 1731 7.810282 CCAATGTCTGGTAAATCTCGTAGATAG 59.190 40.741 0.00 0.00 40.78 2.08
1659 1735 7.140048 GTCTGGTAAATCTCGTAGATAGTTGG 58.860 42.308 0.00 0.00 32.89 3.77
1701 1777 5.862323 CCAGAGATCTCTTGCAAACATTTTG 59.138 40.000 22.95 7.56 37.98 2.44
1702 1778 5.862323 CAGAGATCTCTTGCAAACATTTTGG 59.138 40.000 22.95 2.66 37.98 3.28
1703 1779 5.047519 AGAGATCTCTTGCAAACATTTTGGG 60.048 40.000 19.92 0.00 36.31 4.12
1704 1780 3.110447 TCTCTTGCAAACATTTTGGGC 57.890 42.857 0.00 0.00 0.00 5.36
1705 1781 2.433604 TCTCTTGCAAACATTTTGGGCA 59.566 40.909 0.00 0.00 0.00 5.36
1706 1782 3.071312 TCTCTTGCAAACATTTTGGGCAT 59.929 39.130 0.00 0.00 34.03 4.40
1708 1784 3.814283 TCTTGCAAACATTTTGGGCATTC 59.186 39.130 0.00 0.00 34.03 2.67
1709 1785 3.488778 TGCAAACATTTTGGGCATTCT 57.511 38.095 1.07 0.00 0.00 2.40
1710 1786 3.401182 TGCAAACATTTTGGGCATTCTC 58.599 40.909 1.07 0.00 0.00 2.87
1712 1788 3.434299 GCAAACATTTTGGGCATTCTCTG 59.566 43.478 1.07 0.00 0.00 3.35
1714 1790 4.796038 AACATTTTGGGCATTCTCTGAG 57.204 40.909 0.00 0.00 0.00 3.35
1717 1793 3.507162 TTTTGGGCATTCTCTGAGTGA 57.493 42.857 4.32 0.00 0.00 3.41
1719 1795 3.726557 TTGGGCATTCTCTGAGTGATT 57.273 42.857 4.32 0.00 0.00 2.57
1720 1796 3.726557 TGGGCATTCTCTGAGTGATTT 57.273 42.857 4.32 0.00 0.00 2.17
1721 1797 3.614092 TGGGCATTCTCTGAGTGATTTC 58.386 45.455 4.32 0.00 0.00 2.17
1722 1798 3.265221 TGGGCATTCTCTGAGTGATTTCT 59.735 43.478 4.32 0.00 0.00 2.52
1724 1800 4.383989 GGGCATTCTCTGAGTGATTTCTCT 60.384 45.833 4.32 0.00 35.68 3.10
1725 1801 4.810491 GGCATTCTCTGAGTGATTTCTCTC 59.190 45.833 4.32 3.30 37.10 3.20
1727 1803 5.291614 GCATTCTCTGAGTGATTTCTCTCAC 59.708 44.000 4.32 0.00 44.78 3.51
1737 1813 5.462405 GTGATTTCTCTCACTCAACTACGT 58.538 41.667 0.00 0.00 41.87 3.57
1738 1814 6.609533 GTGATTTCTCTCACTCAACTACGTA 58.390 40.000 0.00 0.00 41.87 3.57
1739 1815 6.523893 GTGATTTCTCTCACTCAACTACGTAC 59.476 42.308 0.00 0.00 41.87 3.67
1740 1816 6.206048 TGATTTCTCTCACTCAACTACGTACA 59.794 38.462 0.00 0.00 0.00 2.90
1741 1817 6.570672 TTTCTCTCACTCAACTACGTACAT 57.429 37.500 0.00 0.00 0.00 2.29
1742 1818 6.570672 TTCTCTCACTCAACTACGTACATT 57.429 37.500 0.00 0.00 0.00 2.71
1743 1819 6.570672 TCTCTCACTCAACTACGTACATTT 57.429 37.500 0.00 0.00 0.00 2.32
1744 1820 6.978338 TCTCTCACTCAACTACGTACATTTT 58.022 36.000 0.00 0.00 0.00 1.82
1745 1821 7.431249 TCTCTCACTCAACTACGTACATTTTT 58.569 34.615 0.00 0.00 0.00 1.94
1746 1822 7.381408 TCTCTCACTCAACTACGTACATTTTTG 59.619 37.037 0.00 0.00 0.00 2.44
1747 1823 6.982141 TCTCACTCAACTACGTACATTTTTGT 59.018 34.615 0.00 0.00 0.00 2.83
1748 1824 7.493320 TCTCACTCAACTACGTACATTTTTGTT 59.507 33.333 0.00 0.00 0.00 2.83
1749 1825 7.623770 TCACTCAACTACGTACATTTTTGTTC 58.376 34.615 0.00 0.00 0.00 3.18
1750 1826 6.849305 CACTCAACTACGTACATTTTTGTTCC 59.151 38.462 0.00 0.00 0.00 3.62
1751 1827 6.764560 ACTCAACTACGTACATTTTTGTTCCT 59.235 34.615 0.00 0.00 0.00 3.36
1752 1828 7.042254 ACTCAACTACGTACATTTTTGTTCCTC 60.042 37.037 0.00 0.00 0.00 3.71
1753 1829 6.987992 TCAACTACGTACATTTTTGTTCCTCT 59.012 34.615 0.00 0.00 0.00 3.69
1754 1830 8.143193 TCAACTACGTACATTTTTGTTCCTCTA 58.857 33.333 0.00 0.00 0.00 2.43
1755 1831 8.932791 CAACTACGTACATTTTTGTTCCTCTAT 58.067 33.333 0.00 0.00 0.00 1.98
1757 1833 9.578439 ACTACGTACATTTTTGTTCCTCTATAC 57.422 33.333 0.00 0.00 0.00 1.47
1758 1834 9.798994 CTACGTACATTTTTGTTCCTCTATACT 57.201 33.333 0.00 0.00 0.00 2.12
1760 1836 9.798994 ACGTACATTTTTGTTCCTCTATACTAG 57.201 33.333 0.00 0.00 0.00 2.57
1761 1837 8.753175 CGTACATTTTTGTTCCTCTATACTAGC 58.247 37.037 0.00 0.00 0.00 3.42
1762 1838 9.819267 GTACATTTTTGTTCCTCTATACTAGCT 57.181 33.333 0.00 0.00 0.00 3.32
1763 1839 8.723942 ACATTTTTGTTCCTCTATACTAGCTG 57.276 34.615 0.00 0.00 0.00 4.24
1764 1840 7.281100 ACATTTTTGTTCCTCTATACTAGCTGC 59.719 37.037 0.00 0.00 0.00 5.25
1765 1841 6.546428 TTTTGTTCCTCTATACTAGCTGCT 57.454 37.500 7.57 7.57 0.00 4.24
1766 1842 5.776173 TTGTTCCTCTATACTAGCTGCTC 57.224 43.478 4.91 0.00 0.00 4.26
1767 1843 4.793201 TGTTCCTCTATACTAGCTGCTCA 58.207 43.478 4.91 0.00 0.00 4.26
1768 1844 5.389520 TGTTCCTCTATACTAGCTGCTCAT 58.610 41.667 4.91 0.75 0.00 2.90
1769 1845 5.835819 TGTTCCTCTATACTAGCTGCTCATT 59.164 40.000 4.91 0.00 0.00 2.57
1770 1846 6.325028 TGTTCCTCTATACTAGCTGCTCATTT 59.675 38.462 4.91 0.00 0.00 2.32
1784 1860 3.004862 GCTCATTTTGGGCATTTTCTGG 58.995 45.455 0.00 0.00 45.01 3.86
1786 1862 2.978278 TCATTTTGGGCATTTTCTGGGT 59.022 40.909 0.00 0.00 0.00 4.51
1803 1879 2.711009 TGGGTGATTTCTCCACTGAACT 59.289 45.455 1.49 0.00 35.05 3.01
1804 1880 3.907474 TGGGTGATTTCTCCACTGAACTA 59.093 43.478 1.49 0.00 35.05 2.24
1838 1985 6.441093 TGTTCCTCTATTTTTAGCTGCATG 57.559 37.500 1.02 0.00 0.00 4.06
1843 1990 7.315142 TCCTCTATTTTTAGCTGCATGTTTTG 58.685 34.615 1.02 0.00 0.00 2.44
1875 2022 7.775561 ACTAGTCAAATCTATGAACCCATTTCC 59.224 37.037 0.00 0.00 34.31 3.13
1879 2026 7.505585 GTCAAATCTATGAACCCATTTCCCATA 59.494 37.037 0.00 0.00 34.31 2.74
1942 2092 2.733127 CGTCGACGCATTTAGTGGT 58.267 52.632 26.59 0.00 0.00 4.16
2111 2261 2.398498 CTCGTCATGTGATCCCGAATC 58.602 52.381 0.00 0.00 34.72 2.52
2147 2297 0.029163 TAGGATCCTTCCCATGCCCA 60.029 55.000 22.03 0.00 43.76 5.36
2331 2483 1.045407 TTAGGCAGTATAGGCACCCG 58.955 55.000 0.00 0.00 36.37 5.28
2333 2485 1.069258 GGCAGTATAGGCACCCGAC 59.931 63.158 0.00 0.00 0.00 4.79
2467 2622 2.576615 GGACTATTCTTGCCCCATCAC 58.423 52.381 0.00 0.00 0.00 3.06
2471 2626 2.077687 ATTCTTGCCCCATCACCATC 57.922 50.000 0.00 0.00 0.00 3.51
2578 2736 3.128764 CACTGTGCATGCTCTCATTTGAT 59.871 43.478 20.33 0.00 0.00 2.57
2640 2798 6.541641 CCCTTCAGATTCTCTATGTCTTTTGG 59.458 42.308 0.00 0.00 0.00 3.28
2642 2800 7.065563 CCTTCAGATTCTCTATGTCTTTTGGTG 59.934 40.741 0.00 0.00 0.00 4.17
2778 2936 0.614697 GTTCTTGGGTGGATTGGGGG 60.615 60.000 0.00 0.00 0.00 5.40
2784 2942 2.553330 GGTGGATTGGGGGTTGGGA 61.553 63.158 0.00 0.00 0.00 4.37
2788 2946 0.636647 GGATTGGGGGTTGGGAAGAT 59.363 55.000 0.00 0.00 0.00 2.40
2792 2950 2.319025 TGGGGGTTGGGAAGATTTTC 57.681 50.000 0.00 0.00 0.00 2.29
2793 2951 1.792651 TGGGGGTTGGGAAGATTTTCT 59.207 47.619 0.00 0.00 33.68 2.52
2794 2952 2.179427 GGGGGTTGGGAAGATTTTCTG 58.821 52.381 0.00 0.00 33.68 3.02
2795 2953 2.225267 GGGGGTTGGGAAGATTTTCTGA 60.225 50.000 0.00 0.00 33.68 3.27
2796 2954 3.566553 GGGGGTTGGGAAGATTTTCTGAT 60.567 47.826 0.00 0.00 33.68 2.90
2799 2957 5.482006 GGGTTGGGAAGATTTTCTGATTTG 58.518 41.667 0.00 0.00 33.68 2.32
2800 2958 4.931601 GGTTGGGAAGATTTTCTGATTTGC 59.068 41.667 0.00 0.00 33.68 3.68
2809 2967 9.148104 GAAGATTTTCTGATTTGCTGCTTAATT 57.852 29.630 0.00 0.00 0.00 1.40
2842 3000 4.201851 GGAGTGCACATGTAGCAATAGTTG 60.202 45.833 21.04 0.00 44.64 3.16
2875 3033 6.734104 AACTGATGAATTTTCTTCTCCTCG 57.266 37.500 7.46 0.00 33.80 4.63
3368 3527 6.205658 GCAGGTCAACTAAGAAGAAACTTGAT 59.794 38.462 0.00 0.00 0.00 2.57
3389 3548 3.016031 TCACTTGTTCAAGAAGCTTGCA 58.984 40.909 17.75 0.00 0.00 4.08
3901 4060 5.428253 ACAAGCGGAGAACATTATACATGT 58.572 37.500 2.69 2.69 0.00 3.21
3995 4154 0.586319 TTTTTGAAGAGCTGCGTCCG 59.414 50.000 0.00 0.00 0.00 4.79
4009 4168 1.446966 GTCCGAGTGAAGAGCCTGC 60.447 63.158 0.00 0.00 0.00 4.85
4223 4382 1.544759 GGTTCAAGTGGTTCACCCGAT 60.545 52.381 0.00 0.00 34.49 4.18
4283 4442 1.561643 TCTCCTGGACGAGCAGAAAT 58.438 50.000 0.00 0.00 0.00 2.17
4295 4454 5.352284 ACGAGCAGAAATGATTTCGAGTAT 58.648 37.500 11.83 3.49 44.29 2.12
4526 4685 0.249911 GCGTTCAGGATATCGGCCTT 60.250 55.000 0.00 0.00 32.12 4.35
4718 4877 5.728471 CTCAAGCAGAAGATCTAGGTGAAA 58.272 41.667 0.00 0.00 0.00 2.69
4767 4946 2.673368 AGAAATTACTTCGCCGCTTCAG 59.327 45.455 0.00 0.00 39.22 3.02
4994 5190 2.285977 ACAAAGTTCACGTCCAGGAAC 58.714 47.619 8.10 8.10 42.82 3.62
5021 5225 6.385649 TGTTTTTAGGCTTTTCACTGTAGG 57.614 37.500 0.00 0.00 0.00 3.18
5024 5228 7.227910 TGTTTTTAGGCTTTTCACTGTAGGTAG 59.772 37.037 0.00 0.00 0.00 3.18
5081 5285 5.685954 GGTGTTCCTGATTCGTTTCTTTTTC 59.314 40.000 0.00 0.00 0.00 2.29
5111 5318 3.326981 GGTTGCGCACGTTTTGGC 61.327 61.111 11.12 0.00 0.00 4.52
5148 5355 0.251341 ATGCTGTGACCAAGGAACCC 60.251 55.000 0.00 0.00 0.00 4.11
5193 5400 0.099968 TATGCGTCGTTCTTCTCCCG 59.900 55.000 0.00 0.00 0.00 5.14
5230 5437 2.662791 CGTTCATTCTGAAAGTGGCACG 60.663 50.000 12.71 0.00 38.22 5.34
5278 5490 1.789506 GAGACTGAAGTGTCCACTGC 58.210 55.000 0.00 0.00 41.58 4.40
5330 5543 2.740055 GACCTGACTGCCGTGCTG 60.740 66.667 0.00 2.15 0.00 4.41
5429 5642 4.605183 AGCAGTTAGGACTAGTCTCACAT 58.395 43.478 21.88 3.99 33.90 3.21
5472 5685 1.408422 GTTGCCATTTTGTCTCACGC 58.592 50.000 0.00 0.00 0.00 5.34
5473 5686 1.001378 GTTGCCATTTTGTCTCACGCT 60.001 47.619 0.00 0.00 0.00 5.07
5514 5793 6.672657 ACAAAGATGTACCTACTATCCCTTGT 59.327 38.462 0.00 0.00 38.24 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
10 11 8.590099 GCACTCAGCAAATTAAGAGCATCTCC 62.590 46.154 0.00 0.00 45.39 3.71
11 12 5.730010 GCACTCAGCAAATTAAGAGCATCTC 60.730 44.000 0.00 0.00 45.39 2.75
13 14 4.349501 GCACTCAGCAAATTAAGAGCATC 58.650 43.478 0.00 0.00 44.79 3.91
14 15 4.367386 GCACTCAGCAAATTAAGAGCAT 57.633 40.909 0.00 0.00 44.79 3.79
15 16 3.837213 GCACTCAGCAAATTAAGAGCA 57.163 42.857 0.00 0.00 44.79 4.26
32 33 1.266404 CGACGAAAATAGTGCGAGCAC 60.266 52.381 19.45 19.45 46.50 4.40
70 71 3.074675 TGGTACATTGCCCGTTTATGT 57.925 42.857 0.00 0.00 36.53 2.29
99 100 5.079643 TGATCCGATGATCTGATCCAGTAA 58.920 41.667 19.66 3.00 46.34 2.24
100 101 4.666512 TGATCCGATGATCTGATCCAGTA 58.333 43.478 19.66 3.31 46.34 2.74
101 102 3.504375 TGATCCGATGATCTGATCCAGT 58.496 45.455 19.66 1.51 46.34 4.00
106 107 3.006644 CACCACTGATCCGATGATCTGAT 59.993 47.826 14.00 0.00 46.34 2.90
150 155 1.281925 ATCATCTGAAGGGGCCCGTT 61.282 55.000 29.50 29.50 0.00 4.44
229 234 4.374702 GACTTGCGCAGTGTGCCG 62.375 66.667 25.10 17.92 41.12 5.69
261 269 1.391485 CGACTCTTTTGACGATGCCTG 59.609 52.381 0.00 0.00 0.00 4.85
344 352 0.407139 GGGAGGGGATTGATGGATGG 59.593 60.000 0.00 0.00 0.00 3.51
345 353 1.453633 AGGGAGGGGATTGATGGATG 58.546 55.000 0.00 0.00 0.00 3.51
346 354 2.068977 GAAGGGAGGGGATTGATGGAT 58.931 52.381 0.00 0.00 0.00 3.41
347 355 1.522900 GAAGGGAGGGGATTGATGGA 58.477 55.000 0.00 0.00 0.00 3.41
485 508 1.855451 GGGAAAAGGGAGGTGGGGA 60.855 63.158 0.00 0.00 0.00 4.81
824 849 0.537371 GGGGTGACAAGTTGGGTCTG 60.537 60.000 7.96 0.00 36.26 3.51
877 902 4.787280 AGAGGCGGGGAGGGTGAG 62.787 72.222 0.00 0.00 0.00 3.51
894 919 2.825982 CGGGTGTGAACAGTGGGA 59.174 61.111 0.00 0.00 0.00 4.37
895 920 2.978010 GCGGGTGTGAACAGTGGG 60.978 66.667 0.00 0.00 0.00 4.61
916 942 4.950062 GAGATGGATGCGCGGCGA 62.950 66.667 28.54 11.83 0.00 5.54
925 951 2.642129 CGAGCGAGCGAGATGGAT 59.358 61.111 0.00 0.00 0.00 3.41
949 975 2.413765 GACATCGGAGGCGGAGAC 59.586 66.667 0.00 0.00 0.00 3.36
950 976 3.209812 CGACATCGGAGGCGGAGA 61.210 66.667 0.00 0.00 35.37 3.71
1373 1438 3.252215 CCTACAAGCATGAAACGAAACCA 59.748 43.478 0.00 0.00 0.00 3.67
1375 1440 4.219033 CACCTACAAGCATGAAACGAAAC 58.781 43.478 0.00 0.00 0.00 2.78
1385 1450 0.178068 CGCCTACCACCTACAAGCAT 59.822 55.000 0.00 0.00 0.00 3.79
1387 1452 1.153429 CCGCCTACCACCTACAAGC 60.153 63.158 0.00 0.00 0.00 4.01
1388 1453 0.108329 CACCGCCTACCACCTACAAG 60.108 60.000 0.00 0.00 0.00 3.16
1389 1454 0.542467 TCACCGCCTACCACCTACAA 60.542 55.000 0.00 0.00 0.00 2.41
1390 1455 0.324923 ATCACCGCCTACCACCTACA 60.325 55.000 0.00 0.00 0.00 2.74
1391 1456 0.104304 CATCACCGCCTACCACCTAC 59.896 60.000 0.00 0.00 0.00 3.18
1392 1457 1.682451 GCATCACCGCCTACCACCTA 61.682 60.000 0.00 0.00 0.00 3.08
1393 1458 3.031417 GCATCACCGCCTACCACCT 62.031 63.158 0.00 0.00 0.00 4.00
1394 1459 2.513897 GCATCACCGCCTACCACC 60.514 66.667 0.00 0.00 0.00 4.61
1395 1460 2.890474 CGCATCACCGCCTACCAC 60.890 66.667 0.00 0.00 0.00 4.16
1414 1483 2.013563 GCACGAGCCTCCAATGAATGA 61.014 52.381 0.00 0.00 33.58 2.57
1516 1585 9.591792 CATGATTTGACTAAGTCAGATTCACTA 57.408 33.333 0.00 0.00 43.69 2.74
1527 1596 6.434028 TGCCTTTTAGCATGATTTGACTAAGT 59.566 34.615 0.00 0.00 38.00 2.24
1552 1624 5.376854 ACAAAATCTAAGAAACAGCGCAT 57.623 34.783 11.47 0.00 0.00 4.73
1596 1672 3.078837 ACATTGGTTTCGCTCGGTTTAT 58.921 40.909 0.00 0.00 0.00 1.40
1612 1688 0.884259 TGGGCAGACGTGTGACATTG 60.884 55.000 21.42 0.00 0.00 2.82
1618 1694 0.603707 AGACATTGGGCAGACGTGTG 60.604 55.000 8.61 8.61 0.00 3.82
1620 1696 1.300971 CCAGACATTGGGCAGACGTG 61.301 60.000 0.00 0.00 43.75 4.49
1621 1697 1.003355 CCAGACATTGGGCAGACGT 60.003 57.895 0.00 0.00 43.75 4.34
1628 1704 6.463049 ATCTACGAGATTTACCAGACATTGGG 60.463 42.308 0.00 0.00 40.88 4.12
1630 1706 8.353684 ACTATCTACGAGATTTACCAGACATTG 58.646 37.037 0.00 0.00 36.20 2.82
1631 1707 8.466617 ACTATCTACGAGATTTACCAGACATT 57.533 34.615 0.00 0.00 36.20 2.71
1632 1708 8.353684 CAACTATCTACGAGATTTACCAGACAT 58.646 37.037 0.00 0.00 36.20 3.06
1633 1709 7.201794 CCAACTATCTACGAGATTTACCAGACA 60.202 40.741 0.00 0.00 36.20 3.41
1634 1710 7.140048 CCAACTATCTACGAGATTTACCAGAC 58.860 42.308 0.00 0.00 36.20 3.51
1635 1711 6.832384 ACCAACTATCTACGAGATTTACCAGA 59.168 38.462 0.00 0.00 36.20 3.86
1638 1714 7.035840 TGACCAACTATCTACGAGATTTACC 57.964 40.000 0.00 0.00 36.20 2.85
1652 1728 6.710597 TTAGAGCTACGAATGACCAACTAT 57.289 37.500 0.00 0.00 0.00 2.12
1654 1730 4.678309 GCTTAGAGCTACGAATGACCAACT 60.678 45.833 0.00 0.00 38.45 3.16
1655 1731 3.552294 GCTTAGAGCTACGAATGACCAAC 59.448 47.826 0.00 0.00 38.45 3.77
1659 1735 3.066900 TCTGGCTTAGAGCTACGAATGAC 59.933 47.826 0.00 0.00 41.99 3.06
1701 1777 3.876320 GAGAAATCACTCAGAGAATGCCC 59.124 47.826 3.79 0.00 36.95 5.36
1702 1778 4.768583 AGAGAAATCACTCAGAGAATGCC 58.231 43.478 3.79 0.00 39.14 4.40
1703 1779 5.291614 GTGAGAGAAATCACTCAGAGAATGC 59.708 44.000 10.26 0.00 45.03 3.56
1704 1780 6.890663 GTGAGAGAAATCACTCAGAGAATG 57.109 41.667 10.26 0.00 45.03 2.67
1714 1790 5.462405 ACGTAGTTGAGTGAGAGAAATCAC 58.538 41.667 0.00 0.00 44.74 3.06
1717 1793 6.570672 TGTACGTAGTTGAGTGAGAGAAAT 57.429 37.500 0.00 0.00 37.78 2.17
1719 1795 6.570672 AATGTACGTAGTTGAGTGAGAGAA 57.429 37.500 0.00 0.00 37.78 2.87
1720 1796 6.570672 AAATGTACGTAGTTGAGTGAGAGA 57.429 37.500 0.00 0.00 37.78 3.10
1721 1797 7.169308 ACAAAAATGTACGTAGTTGAGTGAGAG 59.831 37.037 14.47 0.00 37.78 3.20
1722 1798 6.982141 ACAAAAATGTACGTAGTTGAGTGAGA 59.018 34.615 14.47 0.00 37.78 3.27
1724 1800 7.254522 GGAACAAAAATGTACGTAGTTGAGTGA 60.255 37.037 14.47 0.00 37.78 3.41
1725 1801 6.849305 GGAACAAAAATGTACGTAGTTGAGTG 59.151 38.462 14.47 0.00 37.78 3.51
1727 1803 7.170998 AGAGGAACAAAAATGTACGTAGTTGAG 59.829 37.037 14.47 2.01 37.78 3.02
1728 1804 6.987992 AGAGGAACAAAAATGTACGTAGTTGA 59.012 34.615 14.47 0.00 37.78 3.18
1729 1805 7.186021 AGAGGAACAAAAATGTACGTAGTTG 57.814 36.000 0.00 8.43 37.78 3.16
1732 1808 9.798994 AGTATAGAGGAACAAAAATGTACGTAG 57.201 33.333 0.00 0.00 0.00 3.51
1734 1810 9.798994 CTAGTATAGAGGAACAAAAATGTACGT 57.201 33.333 0.00 0.00 42.77 3.57
1735 1811 8.753175 GCTAGTATAGAGGAACAAAAATGTACG 58.247 37.037 0.00 0.00 42.77 3.67
1736 1812 9.819267 AGCTAGTATAGAGGAACAAAAATGTAC 57.181 33.333 0.00 0.00 42.77 2.90
1737 1813 9.817809 CAGCTAGTATAGAGGAACAAAAATGTA 57.182 33.333 0.00 0.00 42.77 2.29
1738 1814 7.281100 GCAGCTAGTATAGAGGAACAAAAATGT 59.719 37.037 0.00 0.00 42.77 2.71
1739 1815 7.497249 AGCAGCTAGTATAGAGGAACAAAAATG 59.503 37.037 0.00 0.00 42.77 2.32
1740 1816 7.569240 AGCAGCTAGTATAGAGGAACAAAAAT 58.431 34.615 0.00 0.00 42.77 1.82
1741 1817 6.947464 AGCAGCTAGTATAGAGGAACAAAAA 58.053 36.000 0.00 0.00 42.77 1.94
1742 1818 6.154534 TGAGCAGCTAGTATAGAGGAACAAAA 59.845 38.462 0.00 0.00 42.77 2.44
1743 1819 5.656859 TGAGCAGCTAGTATAGAGGAACAAA 59.343 40.000 0.00 0.00 42.77 2.83
1744 1820 5.201243 TGAGCAGCTAGTATAGAGGAACAA 58.799 41.667 0.00 0.00 42.77 2.83
1745 1821 4.793201 TGAGCAGCTAGTATAGAGGAACA 58.207 43.478 0.00 0.00 42.77 3.18
1746 1822 5.975693 ATGAGCAGCTAGTATAGAGGAAC 57.024 43.478 0.00 0.00 42.77 3.62
1747 1823 6.985653 AAATGAGCAGCTAGTATAGAGGAA 57.014 37.500 0.00 0.00 42.77 3.36
1748 1824 6.239430 CCAAAATGAGCAGCTAGTATAGAGGA 60.239 42.308 0.00 0.00 42.77 3.71
1749 1825 5.931146 CCAAAATGAGCAGCTAGTATAGAGG 59.069 44.000 0.00 0.00 42.77 3.69
1750 1826 5.931146 CCCAAAATGAGCAGCTAGTATAGAG 59.069 44.000 0.00 0.00 42.77 2.43
1751 1827 5.743130 GCCCAAAATGAGCAGCTAGTATAGA 60.743 44.000 0.00 0.00 42.77 1.98
1752 1828 4.453819 GCCCAAAATGAGCAGCTAGTATAG 59.546 45.833 0.00 0.00 43.09 1.31
1753 1829 4.141505 TGCCCAAAATGAGCAGCTAGTATA 60.142 41.667 0.00 0.00 31.65 1.47
1754 1830 3.217626 GCCCAAAATGAGCAGCTAGTAT 58.782 45.455 0.00 0.00 0.00 2.12
1755 1831 2.026356 TGCCCAAAATGAGCAGCTAGTA 60.026 45.455 0.00 0.00 31.65 1.82
1756 1832 1.272092 TGCCCAAAATGAGCAGCTAGT 60.272 47.619 0.00 0.00 31.65 2.57
1757 1833 1.466856 TGCCCAAAATGAGCAGCTAG 58.533 50.000 0.00 0.00 31.65 3.42
1758 1834 2.148446 ATGCCCAAAATGAGCAGCTA 57.852 45.000 0.00 0.00 40.40 3.32
1759 1835 1.272807 AATGCCCAAAATGAGCAGCT 58.727 45.000 0.00 0.00 40.40 4.24
1760 1836 2.103537 AAATGCCCAAAATGAGCAGC 57.896 45.000 0.00 0.00 40.40 5.25
1761 1837 3.682858 CAGAAAATGCCCAAAATGAGCAG 59.317 43.478 0.00 0.00 40.40 4.24
1762 1838 3.557475 CCAGAAAATGCCCAAAATGAGCA 60.557 43.478 0.00 0.00 41.50 4.26
1763 1839 3.004862 CCAGAAAATGCCCAAAATGAGC 58.995 45.455 0.00 0.00 0.00 4.26
1764 1840 3.008266 ACCCAGAAAATGCCCAAAATGAG 59.992 43.478 0.00 0.00 0.00 2.90
1765 1841 2.978278 ACCCAGAAAATGCCCAAAATGA 59.022 40.909 0.00 0.00 0.00 2.57
1766 1842 3.075884 CACCCAGAAAATGCCCAAAATG 58.924 45.455 0.00 0.00 0.00 2.32
1767 1843 2.978278 TCACCCAGAAAATGCCCAAAAT 59.022 40.909 0.00 0.00 0.00 1.82
1768 1844 2.402564 TCACCCAGAAAATGCCCAAAA 58.597 42.857 0.00 0.00 0.00 2.44
1769 1845 2.094100 TCACCCAGAAAATGCCCAAA 57.906 45.000 0.00 0.00 0.00 3.28
1770 1846 2.323999 ATCACCCAGAAAATGCCCAA 57.676 45.000 0.00 0.00 0.00 4.12
1779 1855 2.978978 TCAGTGGAGAAATCACCCAGAA 59.021 45.455 0.00 0.00 35.87 3.02
1784 1860 3.927142 CGTAGTTCAGTGGAGAAATCACC 59.073 47.826 0.00 0.00 35.87 4.02
1786 1862 4.866508 ACGTAGTTCAGTGGAGAAATCA 57.133 40.909 0.00 0.00 37.78 2.57
1863 2010 6.159575 TCAGTAAGATATGGGAAATGGGTTCA 59.840 38.462 0.00 0.00 38.06 3.18
1875 2022 7.197017 GCCGATACTACATCAGTAAGATATGG 58.803 42.308 0.00 0.00 43.00 2.74
1879 2026 4.156190 CCGCCGATACTACATCAGTAAGAT 59.844 45.833 0.00 0.00 43.00 2.40
2090 2240 0.459899 TTCGGGATCACATGACGAGG 59.540 55.000 0.00 0.00 34.85 4.63
2111 2261 0.321671 CTATGTATGCCTGGGTCCCG 59.678 60.000 2.65 0.00 0.00 5.14
2115 2265 2.157942 AGGATCCTATGTATGCCTGGGT 60.158 50.000 14.27 0.00 0.00 4.51
2331 2483 2.103263 AGTCCAATCATTCCGGCTAGTC 59.897 50.000 0.00 0.00 0.00 2.59
2333 2485 2.103094 TCAGTCCAATCATTCCGGCTAG 59.897 50.000 0.00 0.00 0.00 3.42
2607 2765 1.432807 AGAATCTGAAGGGGGCCAAAA 59.567 47.619 4.39 0.00 0.00 2.44
2640 2798 0.247736 AACTGCTCGAGGGACATCAC 59.752 55.000 15.58 0.00 0.00 3.06
2642 2800 0.532573 TGAACTGCTCGAGGGACATC 59.467 55.000 15.58 0.27 0.00 3.06
2778 2936 5.636543 CAGCAAATCAGAAAATCTTCCCAAC 59.363 40.000 0.00 0.00 31.28 3.77
2788 2946 8.530311 TCCATAATTAAGCAGCAAATCAGAAAA 58.470 29.630 0.00 0.00 0.00 2.29
2792 2950 7.259882 TGTTCCATAATTAAGCAGCAAATCAG 58.740 34.615 0.00 0.00 0.00 2.90
2793 2951 7.167924 TGTTCCATAATTAAGCAGCAAATCA 57.832 32.000 0.00 0.00 0.00 2.57
2794 2952 6.698766 CCTGTTCCATAATTAAGCAGCAAATC 59.301 38.462 0.00 0.00 0.00 2.17
2795 2953 6.407299 CCCTGTTCCATAATTAAGCAGCAAAT 60.407 38.462 0.00 0.00 0.00 2.32
2796 2954 5.105392 CCCTGTTCCATAATTAAGCAGCAAA 60.105 40.000 0.00 0.00 0.00 3.68
2799 2957 4.207165 TCCCTGTTCCATAATTAAGCAGC 58.793 43.478 0.00 0.00 0.00 5.25
2800 2958 5.297776 CACTCCCTGTTCCATAATTAAGCAG 59.702 44.000 0.00 0.00 0.00 4.24
2809 2967 1.357137 TGTGCACTCCCTGTTCCATA 58.643 50.000 19.41 0.00 0.00 2.74
2822 2980 4.685169 ACAACTATTGCTACATGTGCAC 57.315 40.909 18.50 10.75 40.40 4.57
3059 3218 7.109501 ACATACCAGTACATGCAAAATAGTCA 58.890 34.615 0.00 0.00 0.00 3.41
3275 3434 4.042311 TCCAACTGGAGGTTAGCAACATAA 59.958 41.667 0.00 0.00 39.78 1.90
3345 3504 7.442666 GTGATCAAGTTTCTTCTTAGTTGACCT 59.557 37.037 0.00 0.00 36.75 3.85
3368 3527 3.016031 TGCAAGCTTCTTGAACAAGTGA 58.984 40.909 13.15 4.48 39.38 3.41
3389 3548 0.322366 GCCAAGCTGCTTTCTCCTCT 60.322 55.000 13.10 0.00 0.00 3.69
3901 4060 1.547820 GTGCTCTGACTGACCTGATCA 59.452 52.381 0.00 0.00 35.45 2.92
3974 4133 2.726066 CGGACGCAGCTCTTCAAAAATC 60.726 50.000 0.00 0.00 0.00 2.17
3995 4154 2.698855 TAATGGCAGGCTCTTCACTC 57.301 50.000 0.00 0.00 0.00 3.51
4009 4168 3.388308 CACTGCTCGATCTCCTTAATGG 58.612 50.000 0.00 0.00 37.10 3.16
4052 4211 4.440880 CCTCTTGGATCTCTGATTCACAC 58.559 47.826 0.00 0.00 34.57 3.82
4223 4382 1.248101 TGATCGACGACTGGCTTCCA 61.248 55.000 0.00 0.00 0.00 3.53
4283 4442 3.255888 CGATCTCCCCATACTCGAAATCA 59.744 47.826 0.00 0.00 0.00 2.57
4295 4454 0.033109 TCAGCTTCTCGATCTCCCCA 60.033 55.000 0.00 0.00 0.00 4.96
4439 4598 2.164865 CTCTGCCGTTCAGTGCCTCT 62.165 60.000 2.48 0.00 43.32 3.69
4458 4617 4.505217 CAGCCGCACGTTCGATGC 62.505 66.667 9.73 4.85 39.81 3.91
4628 4787 0.036022 GCTTCTCCTTCAGGCTGTGT 59.964 55.000 15.27 0.00 34.44 3.72
4718 4877 0.685097 TTCTTCTAGGCTTGCACCGT 59.315 50.000 0.00 0.00 33.69 4.83
4830 5011 4.299155 GCCGACTCGATTGATCTATTTCA 58.701 43.478 0.00 0.00 0.00 2.69
4994 5190 4.917415 CAGTGAAAAGCCTAAAAACATCGG 59.083 41.667 0.00 0.00 0.00 4.18
5021 5225 5.303333 GCATATATAGGGAGAAGGGAGCTAC 59.697 48.000 0.00 0.00 0.00 3.58
5024 5228 4.100808 CAGCATATATAGGGAGAAGGGAGC 59.899 50.000 0.00 0.00 0.00 4.70
5111 5318 2.097925 GCATTTTGCGTCTTTTCACACG 60.098 45.455 0.00 0.00 39.09 4.49
5148 5355 3.191371 ACGCTTTCCAAAGGCAAAGATAG 59.809 43.478 1.32 0.00 36.53 2.08
5193 5400 0.896226 AACGAGGCCTACACCTTCTC 59.104 55.000 4.42 0.00 41.32 2.87
5230 5437 4.699522 GCCAGTCGGGTGTGGGAC 62.700 72.222 0.00 0.00 39.65 4.46
5255 5467 0.673985 TGGACACTTCAGTCTCCACG 59.326 55.000 0.05 0.00 38.04 4.94
5278 5490 4.154347 GCCTGGCTCTCCACTCCG 62.154 72.222 12.43 0.00 37.47 4.63
5310 5522 2.047844 CACGGCAGTCAGGTCAGG 60.048 66.667 0.00 0.00 0.00 3.86
5314 5527 3.233980 TCAGCACGGCAGTCAGGT 61.234 61.111 0.00 0.00 0.00 4.00
5330 5543 3.343941 TGGTAATGTGGTTGGCTAGTC 57.656 47.619 0.00 0.00 0.00 2.59
5413 5626 7.999545 AGTTGCTAATATGTGAGACTAGTCCTA 59.000 37.037 19.38 5.92 0.00 2.94
5452 5665 1.930371 GCGTGAGACAAAATGGCAACC 60.930 52.381 0.00 0.00 0.00 3.77
5472 5685 8.517878 ACATCTTTGTGAGATAAAATCCAACAG 58.482 33.333 0.00 0.00 43.32 3.16
5473 5686 8.408043 ACATCTTTGTGAGATAAAATCCAACA 57.592 30.769 0.00 0.00 43.32 3.33
5599 6003 5.060940 GTGTGAGAAACTGTGAACAAAAAGC 59.939 40.000 0.00 0.00 0.00 3.51
5602 6006 5.240623 ACTGTGTGAGAAACTGTGAACAAAA 59.759 36.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.