Multiple sequence alignment - TraesCS2A01G098600

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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 TraesCS2A01G098600 chr2A 100.000 5544 0 0 1 5544 51935945 51941488 0.000000e+00 10238.0
1 TraesCS2A01G098600 chr2A 75.143 350 69 8 29 377 112598848 112598516 1.240000e-31 148.0
2 TraesCS2A01G098600 chr2A 97.403 77 2 0 1721 1797 51937590 51937666 1.250000e-26 132.0
3 TraesCS2A01G098600 chr2A 97.403 77 2 0 1646 1722 51937665 51937741 1.250000e-26 132.0
4 TraesCS2A01G098600 chr2B 92.440 3783 189 51 1721 5463 78063518 78067243 0.000000e+00 5312.0
5 TraesCS2A01G098600 chr2B 91.725 713 32 17 866 1557 78062750 78063456 0.000000e+00 965.0
6 TraesCS2A01G098600 chr2B 91.529 425 29 3 330 748 78062146 78062569 3.720000e-161 579.0
7 TraesCS2A01G098600 chr2B 87.662 154 13 3 1575 1722 78063443 78063596 2.050000e-39 174.0
8 TraesCS2A01G098600 chr2B 74.545 330 63 13 29 357 161937685 161937376 2.100000e-24 124.0
9 TraesCS2A01G098600 chr2D 93.341 3289 138 31 1721 4965 50230821 50234072 0.000000e+00 4785.0
10 TraesCS2A01G098600 chr2D 90.574 732 37 13 844 1559 50230047 50230762 0.000000e+00 941.0
11 TraesCS2A01G098600 chr2D 89.672 610 60 3 5 613 50229277 50229884 0.000000e+00 774.0
12 TraesCS2A01G098600 chr2D 89.960 498 23 9 4996 5475 50234073 50234561 7.890000e-173 617.0
13 TraesCS2A01G098600 chr2D 95.722 187 3 5 643 828 50229884 50230066 4.200000e-76 296.0
14 TraesCS2A01G098600 chr2D 91.333 150 10 2 1576 1722 50230748 50230897 9.420000e-48 202.0
15 TraesCS2A01G098600 chr2D 95.833 72 1 1 5473 5544 50234589 50234658 1.260000e-21 115.0
16 TraesCS2A01G098600 chr3A 78.882 322 57 4 37 357 595756170 595755859 2.020000e-49 207.0
17 TraesCS2A01G098600 chr6B 77.370 327 74 0 46 372 125344996 125345322 1.580000e-45 195.0
18 TraesCS2A01G098600 chr4D 75.915 328 62 16 38 357 126898996 126899314 9.620000e-33 152.0
19 TraesCS2A01G098600 chr3D 78.448 232 44 6 38 267 2247315 2247088 4.480000e-31 147.0
20 TraesCS2A01G098600 chr3D 81.739 115 17 4 74 187 56587059 56587170 5.910000e-15 93.5
21 TraesCS2A01G098600 chr5D 81.507 146 27 0 45 190 432170920 432171065 2.710000e-23 121.0
22 TraesCS2A01G098600 chr4B 72.783 327 77 11 56 378 190690460 190690778 3.530000e-17 100.0
23 TraesCS2A01G098600 chr7D 83.495 103 17 0 29 131 74411719 74411821 4.570000e-16 97.1
24 TraesCS2A01G098600 chr7A 82.432 74 9 1 284 357 68193192 68193123 1.670000e-05 62.1
25 TraesCS2A01G098600 chr7A 100.000 28 0 0 590 617 52142531 52142504 1.000000e-02 52.8
26 TraesCS2A01G098600 chr7A 100.000 28 0 0 590 617 52144795 52144768 1.000000e-02 52.8
27 TraesCS2A01G098600 chr7A 100.000 28 0 0 590 617 52189670 52189643 1.000000e-02 52.8
28 TraesCS2A01G098600 chr7A 100.000 28 0 0 590 617 52191933 52191906 1.000000e-02 52.8


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 TraesCS2A01G098600 chr2A 51935945 51941488 5543 False 3500.666667 10238 98.268667 1 5544 3 chr2A.!!$F1 5543
1 TraesCS2A01G098600 chr2B 78062146 78067243 5097 False 1757.500000 5312 90.839000 330 5463 4 chr2B.!!$F1 5133
2 TraesCS2A01G098600 chr2D 50229277 50234658 5381 False 1104.285714 4785 92.347857 5 5544 7 chr2D.!!$F1 5539

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
908 1028 0.108567 AACCGTTTTGCTTTTGCCGT 60.109 45.000 0.00 0.00 46.87 5.68 F
1952 2105 0.035056 GACCATGTGAACTGAGGGGG 60.035 60.000 0.00 0.00 0.00 5.40 F
2394 2555 0.107410 TACTTCGCCGGGCATCAAAT 60.107 50.000 20.71 0.57 0.00 2.32 F
3537 3704 1.239347 GAGCTTGGTCACCAGGAAAC 58.761 55.000 10.88 0.00 31.89 2.78 F
3546 3713 1.347707 TCACCAGGAAACCACTGCTAG 59.652 52.381 0.00 0.00 34.65 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 2574 0.605589 AACGGCGAAAGGAGAAAGGG 60.606 55.0 16.62 0.00 0.00 3.95 R
2935 3102 0.025001 CGAGGCACGCAGTTTTATCG 59.975 55.0 0.00 0.00 41.61 2.92 R
4297 4464 0.389757 GGGCCTTGGTATCGACTCTC 59.610 60.0 0.84 0.00 0.00 3.20 R
4423 4590 0.036952 CCTTCTTGAGCGCTTCCAGA 60.037 55.0 13.26 10.83 0.00 3.86 R
5291 5514 0.389166 GAGGCGATCCGATGATGGAC 60.389 60.0 0.00 0.00 41.85 4.02 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
29 30 2.548480 GTGTCTACCCTTTGCACTTCAC 59.452 50.000 0.00 0.00 0.00 3.18
33 34 0.751643 ACCCTTTGCACTTCACGCTT 60.752 50.000 0.00 0.00 0.00 4.68
38 39 1.723608 TTGCACTTCACGCTTGTGGG 61.724 55.000 0.00 0.00 44.00 4.61
54 55 1.743252 GGGCGCCACTCTCTTCTTG 60.743 63.158 30.85 0.00 0.00 3.02
59 60 2.676463 GCGCCACTCTCTTCTTGAAGAT 60.676 50.000 12.72 0.00 0.00 2.40
64 65 4.321601 CCACTCTCTTCTTGAAGATGTCGT 60.322 45.833 12.72 6.05 0.00 4.34
65 66 4.856487 CACTCTCTTCTTGAAGATGTCGTC 59.144 45.833 12.72 0.00 0.00 4.20
66 67 4.520874 ACTCTCTTCTTGAAGATGTCGTCA 59.479 41.667 12.72 0.00 32.73 4.35
77 78 2.047179 GTCGTCAAGGTGCCCCTC 60.047 66.667 0.00 0.00 41.56 4.30
79 80 2.266055 CGTCAAGGTGCCCCTCTC 59.734 66.667 0.00 0.00 41.56 3.20
93 94 0.900647 CCTCTCCGTGTCAGGGTTCT 60.901 60.000 11.26 0.00 0.00 3.01
129 130 0.734889 CCATTTTGGACTAGGCAGCG 59.265 55.000 0.00 0.00 40.96 5.18
135 136 2.125673 GACTAGGCAGCGGCGAAA 60.126 61.111 12.98 0.00 42.47 3.46
148 149 3.220276 GCGAAACTTAGCGCCATTC 57.780 52.632 2.29 0.75 46.93 2.67
156 157 1.139853 CTTAGCGCCATTCTCCCTTCT 59.860 52.381 2.29 0.00 0.00 2.85
196 197 4.223953 CCTTAGGTGTTCTAGGGCATAGA 58.776 47.826 4.50 4.50 38.20 1.98
197 198 4.282195 CCTTAGGTGTTCTAGGGCATAGAG 59.718 50.000 9.04 0.00 41.57 2.43
198 199 2.043227 AGGTGTTCTAGGGCATAGAGC 58.957 52.381 14.91 14.91 41.57 4.09
212 213 4.112634 GCATAGAGCGACATTGTACTCAA 58.887 43.478 17.15 0.00 37.98 3.02
219 220 5.237815 AGCGACATTGTACTCAAATCTTCA 58.762 37.500 0.00 0.00 37.11 3.02
220 221 5.120830 AGCGACATTGTACTCAAATCTTCAC 59.879 40.000 0.00 0.00 37.11 3.18
221 222 5.541910 CGACATTGTACTCAAATCTTCACG 58.458 41.667 0.00 0.00 37.11 4.35
232 233 6.018669 ACTCAAATCTTCACGTGTTCTCTTTC 60.019 38.462 16.51 0.00 0.00 2.62
291 293 7.362574 CGTTATCCTGGGAACAATTTTGTATGT 60.363 37.037 11.34 0.00 41.31 2.29
303 305 7.473177 ACAATTTTGTATGTGGACTACCCCAC 61.473 42.308 6.15 6.15 46.67 4.61
310 312 0.492730 TGGACTACCCCACCACCTTA 59.507 55.000 0.00 0.00 34.81 2.69
320 322 2.547218 CCCACCACCTTATATCGTTCGG 60.547 54.545 0.00 0.00 0.00 4.30
322 324 1.069668 ACCACCTTATATCGTTCGGCC 59.930 52.381 0.00 0.00 0.00 6.13
333 335 0.940519 CGTTCGGCCGTGTACTTTGA 60.941 55.000 27.15 0.00 0.00 2.69
342 344 2.803956 CCGTGTACTTTGATCGGTTGTT 59.196 45.455 0.00 0.00 36.99 2.83
347 349 4.336993 TGTACTTTGATCGGTTGTTGCTTT 59.663 37.500 0.00 0.00 0.00 3.51
382 384 3.609103 GCGAACGCCTATTTCATGAAT 57.391 42.857 9.40 2.50 34.56 2.57
632 635 6.367422 TGTCATTTTGGTTTTGTCTTTGACAC 59.633 34.615 0.00 0.00 42.60 3.67
639 642 7.581213 TGGTTTTGTCTTTGACACTATTCAT 57.419 32.000 0.00 0.00 42.60 2.57
823 942 3.718434 AGCACCTGATGATATTTCTCCCA 59.282 43.478 0.00 0.00 0.00 4.37
824 943 4.353191 AGCACCTGATGATATTTCTCCCAT 59.647 41.667 0.00 0.00 0.00 4.00
825 944 4.458295 GCACCTGATGATATTTCTCCCATG 59.542 45.833 0.00 0.00 0.00 3.66
826 945 5.628130 CACCTGATGATATTTCTCCCATGT 58.372 41.667 0.00 0.00 0.00 3.21
827 946 5.472478 CACCTGATGATATTTCTCCCATGTG 59.528 44.000 0.00 0.00 0.00 3.21
828 947 5.370584 ACCTGATGATATTTCTCCCATGTGA 59.629 40.000 0.00 0.00 0.00 3.58
829 948 6.045224 ACCTGATGATATTTCTCCCATGTGAT 59.955 38.462 0.00 0.00 0.00 3.06
830 949 6.946583 CCTGATGATATTTCTCCCATGTGATT 59.053 38.462 0.00 0.00 0.00 2.57
831 950 7.450634 CCTGATGATATTTCTCCCATGTGATTT 59.549 37.037 0.00 0.00 0.00 2.17
832 951 8.400184 TGATGATATTTCTCCCATGTGATTTC 57.600 34.615 0.00 0.00 0.00 2.17
833 952 8.222637 TGATGATATTTCTCCCATGTGATTTCT 58.777 33.333 0.00 0.00 0.00 2.52
834 953 8.632906 ATGATATTTCTCCCATGTGATTTCTC 57.367 34.615 0.00 0.00 0.00 2.87
835 954 7.576403 TGATATTTCTCCCATGTGATTTCTCA 58.424 34.615 0.00 0.00 0.00 3.27
836 955 8.054572 TGATATTTCTCCCATGTGATTTCTCAA 58.945 33.333 0.00 0.00 31.85 3.02
837 956 8.827832 ATATTTCTCCCATGTGATTTCTCAAA 57.172 30.769 0.00 0.00 31.85 2.69
838 957 6.975196 TTTCTCCCATGTGATTTCTCAAAA 57.025 33.333 0.00 0.00 31.85 2.44
839 958 6.975196 TTCTCCCATGTGATTTCTCAAAAA 57.025 33.333 0.00 0.00 31.85 1.94
908 1028 0.108567 AACCGTTTTGCTTTTGCCGT 60.109 45.000 0.00 0.00 46.87 5.68
912 1032 0.878523 GTTTTGCTTTTGCCGTCCCC 60.879 55.000 0.00 0.00 46.87 4.81
1286 1407 1.701031 TTTGCCCCTGTTCCGACTCA 61.701 55.000 0.00 0.00 0.00 3.41
1334 1469 1.214992 GGGTCTCAATGGGGGTTCCT 61.215 60.000 0.00 0.00 36.20 3.36
1340 1475 1.786441 TCAATGGGGGTTCCTTGTTCT 59.214 47.619 0.00 0.00 36.20 3.01
1341 1476 1.895131 CAATGGGGGTTCCTTGTTCTG 59.105 52.381 0.00 0.00 36.20 3.02
1342 1477 1.158007 ATGGGGGTTCCTTGTTCTGT 58.842 50.000 0.00 0.00 36.20 3.41
1343 1478 0.930726 TGGGGGTTCCTTGTTCTGTT 59.069 50.000 0.00 0.00 36.20 3.16
1344 1479 1.133606 TGGGGGTTCCTTGTTCTGTTC 60.134 52.381 0.00 0.00 36.20 3.18
1345 1480 1.235724 GGGGTTCCTTGTTCTGTTCG 58.764 55.000 0.00 0.00 0.00 3.95
1346 1481 1.476291 GGGGTTCCTTGTTCTGTTCGT 60.476 52.381 0.00 0.00 0.00 3.85
1500 1638 3.257393 GTGTCATGCTCTCCTAACTGTG 58.743 50.000 0.00 0.00 0.00 3.66
1544 1684 3.127425 GGGATCCTACATTTCCCGAAG 57.873 52.381 12.58 0.00 39.80 3.79
1620 1761 7.542534 TCGTTTAGCTTTTCAGAAAACAGTA 57.457 32.000 4.06 0.00 31.51 2.74
1622 1763 6.357240 CGTTTAGCTTTTCAGAAAACAGTAGC 59.643 38.462 4.06 6.34 31.51 3.58
1633 1774 4.953579 AGAAAACAGTAGCTGTGGGAAAAA 59.046 37.500 0.00 0.00 44.62 1.94
1699 1843 4.708177 CTGGTATGTTAGCCAGTTATGCT 58.292 43.478 2.66 0.00 45.28 3.79
1703 1847 5.765182 GGTATGTTAGCCAGTTATGCTTGAT 59.235 40.000 0.00 0.00 40.23 2.57
1722 1866 4.717877 TGATTGGATCACAACTCACAAGT 58.282 39.130 0.00 0.00 42.94 3.16
1725 1869 2.172505 TGGATCACAACTCACAAGTGGT 59.827 45.455 0.00 0.00 40.51 4.16
1726 1870 3.214328 GGATCACAACTCACAAGTGGTT 58.786 45.455 0.00 1.40 37.59 3.67
1727 1871 3.632145 GGATCACAACTCACAAGTGGTTT 59.368 43.478 0.00 0.00 37.59 3.27
1728 1872 4.097892 GGATCACAACTCACAAGTGGTTTT 59.902 41.667 0.00 0.00 37.59 2.43
1729 1873 5.298276 GGATCACAACTCACAAGTGGTTTTA 59.702 40.000 0.00 0.00 37.59 1.52
1730 1874 5.554822 TCACAACTCACAAGTGGTTTTAC 57.445 39.130 0.00 0.00 37.59 2.01
1731 1875 4.396790 TCACAACTCACAAGTGGTTTTACC 59.603 41.667 0.00 0.00 37.59 2.85
1732 1876 4.398044 CACAACTCACAAGTGGTTTTACCT 59.602 41.667 0.00 0.00 37.59 3.08
1733 1877 4.398044 ACAACTCACAAGTGGTTTTACCTG 59.602 41.667 0.00 0.00 36.13 4.00
1734 1878 4.230745 ACTCACAAGTGGTTTTACCTGT 57.769 40.909 0.00 0.00 39.58 4.00
1735 1879 4.196971 ACTCACAAGTGGTTTTACCTGTC 58.803 43.478 0.00 0.00 39.58 3.51
1736 1880 4.196193 CTCACAAGTGGTTTTACCTGTCA 58.804 43.478 0.00 0.00 39.58 3.58
1737 1881 4.590918 TCACAAGTGGTTTTACCTGTCAA 58.409 39.130 0.00 0.00 39.58 3.18
1738 1882 5.010933 TCACAAGTGGTTTTACCTGTCAAA 58.989 37.500 0.00 0.00 39.58 2.69
1739 1883 5.654650 TCACAAGTGGTTTTACCTGTCAAAT 59.345 36.000 0.00 0.00 39.58 2.32
1740 1884 6.153680 TCACAAGTGGTTTTACCTGTCAAATT 59.846 34.615 0.00 0.00 39.58 1.82
1741 1885 6.816140 CACAAGTGGTTTTACCTGTCAAATTT 59.184 34.615 0.00 0.00 39.58 1.82
1742 1886 7.010091 CACAAGTGGTTTTACCTGTCAAATTTC 59.990 37.037 0.00 0.00 39.58 2.17
1743 1887 5.827666 AGTGGTTTTACCTGTCAAATTTCG 58.172 37.500 0.00 0.00 39.58 3.46
1744 1888 4.443063 GTGGTTTTACCTGTCAAATTTCGC 59.557 41.667 0.00 0.00 39.58 4.70
1745 1889 4.339814 TGGTTTTACCTGTCAAATTTCGCT 59.660 37.500 0.00 0.00 39.58 4.93
1746 1890 4.915667 GGTTTTACCTGTCAAATTTCGCTC 59.084 41.667 0.00 0.00 34.73 5.03
1747 1891 5.278315 GGTTTTACCTGTCAAATTTCGCTCT 60.278 40.000 0.00 0.00 34.73 4.09
1748 1892 5.356882 TTTACCTGTCAAATTTCGCTCTG 57.643 39.130 0.00 0.00 0.00 3.35
1749 1893 3.126001 ACCTGTCAAATTTCGCTCTGA 57.874 42.857 0.00 0.00 0.00 3.27
1750 1894 3.476552 ACCTGTCAAATTTCGCTCTGAA 58.523 40.909 0.00 0.00 33.85 3.02
1751 1895 4.074970 ACCTGTCAAATTTCGCTCTGAAT 58.925 39.130 0.00 0.00 36.22 2.57
1752 1896 4.154918 ACCTGTCAAATTTCGCTCTGAATC 59.845 41.667 0.00 0.00 36.22 2.52
1753 1897 4.394300 CCTGTCAAATTTCGCTCTGAATCT 59.606 41.667 0.00 0.00 36.22 2.40
1754 1898 5.106396 CCTGTCAAATTTCGCTCTGAATCTT 60.106 40.000 0.00 0.00 36.22 2.40
1755 1899 5.692814 TGTCAAATTTCGCTCTGAATCTTG 58.307 37.500 0.00 0.00 36.22 3.02
1756 1900 5.239306 TGTCAAATTTCGCTCTGAATCTTGT 59.761 36.000 0.00 0.00 36.22 3.16
1757 1901 6.426633 TGTCAAATTTCGCTCTGAATCTTGTA 59.573 34.615 0.00 0.00 36.22 2.41
1758 1902 7.119699 TGTCAAATTTCGCTCTGAATCTTGTAT 59.880 33.333 0.00 0.00 36.22 2.29
1759 1903 7.427606 GTCAAATTTCGCTCTGAATCTTGTATG 59.572 37.037 0.00 0.00 36.22 2.39
1760 1904 6.992063 AATTTCGCTCTGAATCTTGTATGT 57.008 33.333 0.00 0.00 36.22 2.29
1761 1905 6.992063 ATTTCGCTCTGAATCTTGTATGTT 57.008 33.333 0.00 0.00 36.22 2.71
1762 1906 8.492673 AATTTCGCTCTGAATCTTGTATGTTA 57.507 30.769 0.00 0.00 36.22 2.41
1763 1907 7.525688 TTTCGCTCTGAATCTTGTATGTTAG 57.474 36.000 0.00 0.00 36.22 2.34
1764 1908 5.043903 TCGCTCTGAATCTTGTATGTTAGC 58.956 41.667 0.00 0.00 0.00 3.09
1765 1909 4.805719 CGCTCTGAATCTTGTATGTTAGCA 59.194 41.667 0.00 0.00 0.00 3.49
1766 1910 5.291858 CGCTCTGAATCTTGTATGTTAGCAA 59.708 40.000 0.00 0.00 0.00 3.91
1767 1911 6.509199 CGCTCTGAATCTTGTATGTTAGCAAG 60.509 42.308 0.00 0.00 42.32 4.01
1768 1912 6.314896 GCTCTGAATCTTGTATGTTAGCAAGT 59.685 38.462 0.00 0.00 41.83 3.16
1874 2019 6.631016 TCATACCTCACACTACTTTGATGAC 58.369 40.000 0.00 0.00 0.00 3.06
1913 2058 3.716601 GGAATGCATTAATTCCCAACCG 58.283 45.455 12.97 0.00 46.81 4.44
1915 2060 4.142049 GGAATGCATTAATTCCCAACCGAA 60.142 41.667 12.97 0.00 46.81 4.30
1916 2061 3.859411 TGCATTAATTCCCAACCGAAC 57.141 42.857 0.00 0.00 0.00 3.95
1952 2105 0.035056 GACCATGTGAACTGAGGGGG 60.035 60.000 0.00 0.00 0.00 5.40
1969 2122 1.683385 GGGGCAATCCATGTAAAGCTC 59.317 52.381 0.00 0.00 37.22 4.09
2008 2162 6.104665 AGTTCCTCGCCAAATAAACTAGTAC 58.895 40.000 0.00 0.00 0.00 2.73
2171 2329 5.067805 TCCTTTTCTGCAAAAAGAGAACCTC 59.932 40.000 23.82 0.00 39.04 3.85
2239 2400 5.924769 TGTCCTCCTAGTATGATGTAGGA 57.075 43.478 5.56 5.56 42.18 2.94
2240 2401 6.470456 TGTCCTCCTAGTATGATGTAGGAT 57.530 41.667 6.01 0.00 43.19 3.24
2337 2498 4.904241 ACCTAGAAGATGCAGCATATTCC 58.096 43.478 30.55 17.46 41.32 3.01
2382 2543 2.656560 ACCTGTCATCAGTACTTCGC 57.343 50.000 0.00 0.00 39.82 4.70
2394 2555 0.107410 TACTTCGCCGGGCATCAAAT 60.107 50.000 20.71 0.57 0.00 2.32
2413 2574 9.185192 CATCAAATGTAAGAACCTTTTGTCTTC 57.815 33.333 0.00 0.00 33.10 2.87
2428 2589 2.077627 GTCTTCCCTTTCTCCTTTCGC 58.922 52.381 0.00 0.00 0.00 4.70
2483 2649 5.336945 TCATATAGGCCTCTCAGCAGTAAT 58.663 41.667 9.68 0.00 0.00 1.89
2487 2653 1.488393 GGCCTCTCAGCAGTAATCCTT 59.512 52.381 0.00 0.00 0.00 3.36
2583 2750 3.089573 TGCTGTGAGAGATATTGAGCG 57.910 47.619 0.00 0.00 0.00 5.03
2935 3102 3.860536 GCCTGTCAGATTCGAAGTACTTC 59.139 47.826 23.25 23.25 36.29 3.01
2953 3120 1.355971 TCGATAAAACTGCGTGCCTC 58.644 50.000 0.00 0.00 0.00 4.70
3058 3225 7.112452 ACAACCAGAGTTTATTTTTGCTCTT 57.888 32.000 0.00 0.00 36.31 2.85
3101 3268 3.782656 TCATGGATGGAGTGGATGATG 57.217 47.619 0.00 0.00 0.00 3.07
3475 3642 8.400947 GCACAGAATAAGCTCAAATCTGAATTA 58.599 33.333 19.51 0.00 39.85 1.40
3484 3651 7.218614 AGCTCAAATCTGAATTAGAGGATGAG 58.781 38.462 8.90 8.90 41.48 2.90
3537 3704 1.239347 GAGCTTGGTCACCAGGAAAC 58.761 55.000 10.88 0.00 31.89 2.78
3546 3713 1.347707 TCACCAGGAAACCACTGCTAG 59.652 52.381 0.00 0.00 34.65 3.42
3562 3729 5.741510 CACTGCTAGATTTCTTCTGTCTACG 59.258 44.000 0.00 0.00 35.79 3.51
3616 3783 4.566545 ATTTGTCGTCAAAACTGCATCA 57.433 36.364 11.69 0.00 44.97 3.07
3725 3892 5.111293 ACTTCTTTGTTTTGTTGCATGAGG 58.889 37.500 0.00 0.00 0.00 3.86
3766 3933 6.209391 AGTTGCCAAATACAGCTTTACAAGAT 59.791 34.615 0.00 0.00 0.00 2.40
3796 3963 5.477984 TCTGTTGAAAGCTTCCTATGCAATT 59.522 36.000 0.00 0.00 0.00 2.32
3837 4004 2.428544 TATGTTGTTCGGGAATGGGG 57.571 50.000 0.00 0.00 0.00 4.96
4027 4194 4.645535 TCCTGATTGAGTTTGAAGACCTG 58.354 43.478 0.00 0.00 0.00 4.00
4071 4238 7.162761 AGCATTGGATCATCAAATGAACAAAA 58.837 30.769 17.84 2.60 43.50 2.44
4291 4458 3.633094 CTCTGACCCCGCAGTCGTG 62.633 68.421 0.00 0.00 39.77 4.35
4423 4590 1.272769 GAGACAGACGCCCAGTACTTT 59.727 52.381 0.00 0.00 0.00 2.66
4441 4608 1.800805 TTCTGGAAGCGCTCAAGAAG 58.199 50.000 12.06 4.72 38.92 2.85
4451 4618 0.693049 GCTCAAGAAGGGGAAGGACA 59.307 55.000 0.00 0.00 0.00 4.02
4497 4664 1.216178 GGTTGCACCATGTGGATGC 59.784 57.895 5.96 11.87 38.42 3.91
4526 4693 1.270305 CCGTGAAAGTCCTGAGAAGCA 60.270 52.381 0.00 0.00 0.00 3.91
4555 4722 8.554490 AGTCTGGTGGATAATCTTGTTAGTAT 57.446 34.615 0.00 0.00 0.00 2.12
4650 4824 0.915364 GTCCTCCTTCCAGGAAGCAT 59.085 55.000 22.58 0.00 45.28 3.79
4692 4870 1.206132 ACCGACTTGACTGACAACACA 59.794 47.619 0.00 0.00 34.56 3.72
4695 4873 2.670905 CGACTTGACTGACAACACAACA 59.329 45.455 0.00 0.00 34.56 3.33
4696 4874 3.483574 CGACTTGACTGACAACACAACAC 60.484 47.826 0.00 0.00 34.56 3.32
4697 4875 2.747446 ACTTGACTGACAACACAACACC 59.253 45.455 0.00 0.00 34.56 4.16
4698 4876 2.481289 TGACTGACAACACAACACCA 57.519 45.000 0.00 0.00 0.00 4.17
4699 4877 2.080693 TGACTGACAACACAACACCAC 58.919 47.619 0.00 0.00 0.00 4.16
4700 4878 1.400494 GACTGACAACACAACACCACC 59.600 52.381 0.00 0.00 0.00 4.61
4701 4879 1.271652 ACTGACAACACAACACCACCA 60.272 47.619 0.00 0.00 0.00 4.17
4702 4880 2.023673 CTGACAACACAACACCACCAT 58.976 47.619 0.00 0.00 0.00 3.55
4703 4881 2.020720 TGACAACACAACACCACCATC 58.979 47.619 0.00 0.00 0.00 3.51
4704 4882 2.297701 GACAACACAACACCACCATCT 58.702 47.619 0.00 0.00 0.00 2.90
4730 4908 5.929697 TCTGCAGAAAAAGATGTACACAG 57.070 39.130 15.67 0.00 0.00 3.66
4734 4912 6.521162 TGCAGAAAAAGATGTACACAGACTA 58.479 36.000 0.00 0.00 0.00 2.59
4799 5000 4.428294 TCCAGGAAGCTGATGATAAAGG 57.572 45.455 0.00 0.00 0.00 3.11
4801 5002 4.102210 TCCAGGAAGCTGATGATAAAGGAG 59.898 45.833 0.00 0.00 0.00 3.69
4826 5027 3.488553 GGCAAACAACTTTCTTACGTGCT 60.489 43.478 0.00 0.00 0.00 4.40
4850 5051 1.655597 CACTGGATTGACATGACGACG 59.344 52.381 0.00 0.00 0.00 5.12
4868 5069 2.480419 GACGTCTGTGACAAATTGGAGG 59.520 50.000 8.70 0.00 32.09 4.30
4887 5089 1.073177 GTAATGACAACACGACCGGG 58.927 55.000 6.32 0.00 0.00 5.73
4912 5114 1.776034 GATTTCCGCCATCTGTCGGC 61.776 60.000 0.00 0.00 44.91 5.54
4965 5167 1.990799 TCACGGTCAATCTAAGCACG 58.009 50.000 0.00 0.00 0.00 5.34
4981 5183 2.095282 CGTCGTCGTCGTCGTCAT 59.905 61.111 12.51 0.00 41.73 3.06
4982 5184 1.922220 CGTCGTCGTCGTCGTCATC 60.922 63.158 12.51 1.74 41.73 2.92
4983 5185 1.922220 GTCGTCGTCGTCGTCATCG 60.922 63.158 11.41 4.14 38.33 3.84
4984 5186 2.095282 CGTCGTCGTCGTCATCGT 59.905 61.111 3.67 0.00 38.33 3.73
4985 5187 2.200073 CGTCGTCGTCGTCATCGTG 61.200 63.158 3.67 0.00 38.33 4.35
4986 5188 1.131218 GTCGTCGTCGTCATCGTGA 59.869 57.895 1.33 0.00 38.33 4.35
4987 5189 0.247576 GTCGTCGTCGTCATCGTGAT 60.248 55.000 1.33 0.00 38.33 3.06
5014 5216 2.159585 CGCACCGCAAACATAGATTGAA 60.160 45.455 0.00 0.00 0.00 2.69
5153 5359 6.201044 GTGTATTCATCAGATCCGACGAAATT 59.799 38.462 0.00 0.00 0.00 1.82
5186 5392 6.935741 TCTAATCGGTGGATTGTTTTATGG 57.064 37.500 0.00 0.00 42.72 2.74
5187 5393 6.419791 TCTAATCGGTGGATTGTTTTATGGT 58.580 36.000 0.00 0.00 42.72 3.55
5188 5394 7.566569 TCTAATCGGTGGATTGTTTTATGGTA 58.433 34.615 0.00 0.00 42.72 3.25
5189 5395 8.215050 TCTAATCGGTGGATTGTTTTATGGTAT 58.785 33.333 0.00 0.00 42.72 2.73
5190 5396 7.654022 AATCGGTGGATTGTTTTATGGTATT 57.346 32.000 0.00 0.00 41.29 1.89
5197 5403 9.019764 GTGGATTGTTTTATGGTATTTGATTCG 57.980 33.333 0.00 0.00 0.00 3.34
5212 5418 2.301583 TGATTCGTTGTCCTGTCATCCA 59.698 45.455 0.00 0.00 0.00 3.41
5281 5504 7.352739 AGAATTCACGAATCGGCATATAAAAC 58.647 34.615 7.80 0.00 0.00 2.43
5340 5564 4.797471 TGACTTCCATTCAATTTTCGCTG 58.203 39.130 0.00 0.00 0.00 5.18
5341 5565 4.278170 TGACTTCCATTCAATTTTCGCTGT 59.722 37.500 0.00 0.00 0.00 4.40
5393 5617 3.016736 GAGGTCAATGTGTGTAATGGGG 58.983 50.000 0.00 0.00 0.00 4.96
5411 5635 3.720193 GTGAGCTGTGCACAGGCG 61.720 66.667 39.92 22.27 45.35 5.52
5443 5667 2.365582 GGTATCCAAATGGCGACTGTT 58.634 47.619 0.00 0.00 34.44 3.16
5475 5699 2.159707 GCCGTAGAACGTACGAAGTGTA 60.160 50.000 24.41 6.70 42.94 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.036306 AAGGGTAGACACAAAGGGCG 59.964 55.000 0.00 0.00 0.00 6.13
1 2 1.886542 CAAAGGGTAGACACAAAGGGC 59.113 52.381 0.00 0.00 0.00 5.19
2 3 1.886542 GCAAAGGGTAGACACAAAGGG 59.113 52.381 0.00 0.00 0.00 3.95
3 4 2.293399 GTGCAAAGGGTAGACACAAAGG 59.707 50.000 0.00 0.00 0.00 3.11
38 39 1.074752 CTTCAAGAAGAGAGTGGCGC 58.925 55.000 0.00 0.00 40.79 6.53
54 55 1.079503 GGCACCTTGACGACATCTTC 58.920 55.000 0.00 0.00 0.00 2.87
71 72 3.775654 CCTGACACGGAGAGGGGC 61.776 72.222 0.00 0.00 0.00 5.80
77 78 1.293498 CCAGAACCCTGACACGGAG 59.707 63.158 0.00 0.00 43.02 4.63
79 80 2.347490 CCCAGAACCCTGACACGG 59.653 66.667 0.00 0.00 43.02 4.94
125 126 2.395690 CGCTAAGTTTCGCCGCTG 59.604 61.111 0.00 0.00 0.00 5.18
135 136 0.912486 AAGGGAGAATGGCGCTAAGT 59.088 50.000 7.64 0.00 0.00 2.24
156 157 1.444250 GTCCACGACAACACCCTCA 59.556 57.895 0.00 0.00 32.09 3.86
162 163 1.069513 CACCTAAGGTCCACGACAACA 59.930 52.381 0.00 0.00 31.02 3.33
196 197 5.120830 GTGAAGATTTGAGTACAATGTCGCT 59.879 40.000 0.00 0.00 35.85 4.93
197 198 5.316770 GTGAAGATTTGAGTACAATGTCGC 58.683 41.667 0.00 0.00 35.85 5.19
198 199 5.118664 ACGTGAAGATTTGAGTACAATGTCG 59.881 40.000 0.00 0.00 35.85 4.35
212 213 3.741344 CCGAAAGAGAACACGTGAAGATT 59.259 43.478 25.01 5.56 0.00 2.40
219 220 1.665161 CGCTACCGAAAGAGAACACGT 60.665 52.381 0.00 0.00 36.29 4.49
220 221 0.982673 CGCTACCGAAAGAGAACACG 59.017 55.000 0.00 0.00 36.29 4.49
221 222 2.061740 ACGCTACCGAAAGAGAACAC 57.938 50.000 0.00 0.00 38.29 3.32
251 252 0.104304 ATAACGGGATCACGCAGGAC 59.896 55.000 19.30 0.00 37.37 3.85
254 255 0.389391 AGGATAACGGGATCACGCAG 59.611 55.000 19.30 0.00 37.37 5.18
258 259 1.420430 TCCCAGGATAACGGGATCAC 58.580 55.000 0.00 0.00 46.93 3.06
265 266 5.385509 ACAAAATTGTTCCCAGGATAACG 57.614 39.130 0.00 0.00 38.47 3.18
266 267 7.759433 CACATACAAAATTGTTCCCAGGATAAC 59.241 37.037 3.85 0.00 42.35 1.89
278 279 5.014202 GGGGTAGTCCACATACAAAATTGT 58.986 41.667 4.01 4.01 39.95 2.71
281 282 4.938575 TGGGGTAGTCCACATACAAAAT 57.061 40.909 0.00 0.00 42.97 1.82
291 293 0.492730 TAAGGTGGTGGGGTAGTCCA 59.507 55.000 0.00 0.00 37.22 4.02
303 305 1.792006 GGCCGAACGATATAAGGTGG 58.208 55.000 0.00 0.00 0.00 4.61
310 312 1.027357 AGTACACGGCCGAACGATAT 58.973 50.000 35.90 3.57 37.61 1.63
320 322 1.127951 CAACCGATCAAAGTACACGGC 59.872 52.381 0.00 0.00 46.18 5.68
322 324 3.794536 CAACAACCGATCAAAGTACACG 58.205 45.455 0.00 0.00 0.00 4.49
342 344 8.875803 CGTTCGCCCTATTTTATATATAAAGCA 58.124 33.333 15.65 5.32 34.13 3.91
362 364 3.609103 ATTCATGAAATAGGCGTTCGC 57.391 42.857 13.09 8.75 0.00 4.70
363 365 4.908736 ACAATTCATGAAATAGGCGTTCG 58.091 39.130 13.09 0.00 0.00 3.95
367 369 8.131100 ACTCATAAACAATTCATGAAATAGGCG 58.869 33.333 13.09 0.37 0.00 5.52
382 384 7.138081 CGCCATATATTGCAACTCATAAACAA 58.862 34.615 0.00 0.00 0.00 2.83
501 504 5.122239 CACATGTGTTATGAACCTTCACGAT 59.878 40.000 18.03 0.00 40.49 3.73
503 506 4.213270 ACACATGTGTTATGAACCTTCACG 59.787 41.667 25.76 0.00 41.83 4.35
586 589 6.942005 TGACACTATTCACATCTGGATTTGTT 59.058 34.615 0.00 0.00 0.00 2.83
838 957 7.253422 CCACATGCGAGAAATATCTTCTTTTT 58.747 34.615 0.00 0.00 35.54 1.94
839 958 6.678900 GCCACATGCGAGAAATATCTTCTTTT 60.679 38.462 0.00 0.00 35.54 2.27
840 959 5.220931 GCCACATGCGAGAAATATCTTCTTT 60.221 40.000 0.00 0.00 35.54 2.52
841 960 4.274459 GCCACATGCGAGAAATATCTTCTT 59.726 41.667 0.00 0.00 35.54 2.52
842 961 3.812053 GCCACATGCGAGAAATATCTTCT 59.188 43.478 0.00 1.33 35.54 2.85
843 962 4.139183 GCCACATGCGAGAAATATCTTC 57.861 45.455 0.00 0.00 35.54 2.87
877 996 1.029681 AAACGGTTTTGCCTCTCACC 58.970 50.000 0.00 0.00 34.25 4.02
932 1052 5.386447 GCCAGAGAAAAGAAATCGAAGTTC 58.614 41.667 4.46 4.46 0.00 3.01
1334 1469 3.255149 GTCTCCTCCTACGAACAGAACAA 59.745 47.826 0.00 0.00 0.00 2.83
1340 1475 2.376109 GGATGTCTCCTCCTACGAACA 58.624 52.381 0.00 0.00 38.65 3.18
1341 1476 1.682323 GGGATGTCTCCTCCTACGAAC 59.318 57.143 0.00 0.00 41.74 3.95
1342 1477 1.569548 AGGGATGTCTCCTCCTACGAA 59.430 52.381 0.00 0.00 41.74 3.85
1343 1478 1.133761 CAGGGATGTCTCCTCCTACGA 60.134 57.143 0.00 0.00 41.74 3.43
1344 1479 1.323412 CAGGGATGTCTCCTCCTACG 58.677 60.000 0.00 0.00 41.74 3.51
1345 1480 1.044611 GCAGGGATGTCTCCTCCTAC 58.955 60.000 0.00 0.00 41.74 3.18
1346 1481 0.105453 GGCAGGGATGTCTCCTCCTA 60.105 60.000 0.00 0.00 41.74 2.94
1426 1561 1.209275 CGAATGGTGTCGATCCGCTC 61.209 60.000 0.00 0.00 43.86 5.03
1500 1638 5.446473 CCAATTAGTCAGATCGTGCAACTTC 60.446 44.000 0.00 0.00 31.75 3.01
1573 1713 9.613428 ACGATTAATCATCTAAAACATTCCTCA 57.387 29.630 15.57 0.00 0.00 3.86
1633 1774 7.724061 ACAGGTAAAACCACTCACAATCTAATT 59.276 33.333 0.00 0.00 41.95 1.40
1634 1775 7.231467 ACAGGTAAAACCACTCACAATCTAAT 58.769 34.615 0.00 0.00 41.95 1.73
1635 1776 6.597562 ACAGGTAAAACCACTCACAATCTAA 58.402 36.000 0.00 0.00 41.95 2.10
1653 1797 4.265904 TCAGAGCGAAATTTGACAGGTA 57.734 40.909 0.00 0.00 0.00 3.08
1699 1843 5.008911 CACTTGTGAGTTGTGATCCAATCAA 59.991 40.000 0.00 0.37 35.91 2.57
1703 1847 3.213506 CCACTTGTGAGTTGTGATCCAA 58.786 45.455 1.89 0.00 32.54 3.53
1722 1866 4.339814 AGCGAAATTTGACAGGTAAAACCA 59.660 37.500 0.00 0.00 41.95 3.67
1725 1869 5.529430 TCAGAGCGAAATTTGACAGGTAAAA 59.471 36.000 0.00 0.00 0.00 1.52
1726 1870 5.060506 TCAGAGCGAAATTTGACAGGTAAA 58.939 37.500 0.00 0.00 0.00 2.01
1727 1871 4.637276 TCAGAGCGAAATTTGACAGGTAA 58.363 39.130 0.00 0.00 0.00 2.85
1728 1872 4.265904 TCAGAGCGAAATTTGACAGGTA 57.734 40.909 0.00 0.00 0.00 3.08
1729 1873 3.126001 TCAGAGCGAAATTTGACAGGT 57.874 42.857 0.00 0.00 0.00 4.00
1730 1874 4.394300 AGATTCAGAGCGAAATTTGACAGG 59.606 41.667 0.00 0.00 37.12 4.00
1731 1875 5.542616 AGATTCAGAGCGAAATTTGACAG 57.457 39.130 0.00 0.00 37.12 3.51
1732 1876 5.239306 ACAAGATTCAGAGCGAAATTTGACA 59.761 36.000 0.00 0.00 37.12 3.58
1733 1877 5.693814 ACAAGATTCAGAGCGAAATTTGAC 58.306 37.500 0.00 0.00 37.12 3.18
1734 1878 5.947228 ACAAGATTCAGAGCGAAATTTGA 57.053 34.783 0.00 0.00 37.12 2.69
1735 1879 7.246311 ACATACAAGATTCAGAGCGAAATTTG 58.754 34.615 0.00 0.00 37.12 2.32
1736 1880 7.383102 ACATACAAGATTCAGAGCGAAATTT 57.617 32.000 0.00 0.00 37.12 1.82
1737 1881 6.992063 ACATACAAGATTCAGAGCGAAATT 57.008 33.333 0.00 0.00 37.12 1.82
1738 1882 6.992063 AACATACAAGATTCAGAGCGAAAT 57.008 33.333 0.00 0.00 37.12 2.17
1739 1883 6.036083 GCTAACATACAAGATTCAGAGCGAAA 59.964 38.462 0.00 0.00 37.12 3.46
1740 1884 5.520288 GCTAACATACAAGATTCAGAGCGAA 59.480 40.000 0.00 0.00 38.22 4.70
1741 1885 5.043903 GCTAACATACAAGATTCAGAGCGA 58.956 41.667 0.00 0.00 0.00 4.93
1742 1886 4.805719 TGCTAACATACAAGATTCAGAGCG 59.194 41.667 0.00 0.00 0.00 5.03
1743 1887 6.314896 ACTTGCTAACATACAAGATTCAGAGC 59.685 38.462 9.54 0.00 44.89 4.09
1744 1888 7.840342 ACTTGCTAACATACAAGATTCAGAG 57.160 36.000 9.54 0.00 44.89 3.35
1745 1889 9.890629 ATAACTTGCTAACATACAAGATTCAGA 57.109 29.630 9.54 0.00 44.89 3.27
1746 1890 9.926751 CATAACTTGCTAACATACAAGATTCAG 57.073 33.333 9.54 0.00 44.89 3.02
1765 1909 6.435277 AGTTGTGATCCAATCAAGCATAACTT 59.565 34.615 0.00 0.00 41.69 2.66
1766 1910 5.948162 AGTTGTGATCCAATCAAGCATAACT 59.052 36.000 0.00 0.00 41.69 2.24
1767 1911 6.127925 TGAGTTGTGATCCAATCAAGCATAAC 60.128 38.462 0.00 0.00 41.69 1.89
1768 1912 5.945191 TGAGTTGTGATCCAATCAAGCATAA 59.055 36.000 0.00 0.00 41.69 1.90
1874 2019 6.095377 GCATTCCTTTTGGTGTTAGATCAAG 58.905 40.000 0.00 0.00 41.38 3.02
1908 2053 0.859232 CTCAGTTGGACGTTCGGTTG 59.141 55.000 0.00 0.00 0.00 3.77
1910 2055 1.366366 CCTCAGTTGGACGTTCGGT 59.634 57.895 0.00 0.00 0.00 4.69
1912 2057 0.666577 GTCCCTCAGTTGGACGTTCG 60.667 60.000 0.00 0.00 42.63 3.95
1913 2058 3.212450 GTCCCTCAGTTGGACGTTC 57.788 57.895 0.00 0.00 42.63 3.95
1952 2105 5.586243 TGAGTAAGAGCTTTACATGGATTGC 59.414 40.000 16.14 0.00 0.00 3.56
1969 2122 5.157781 CGAGGAACTTCTCAACTGAGTAAG 58.842 45.833 6.61 10.59 41.55 2.34
2081 2236 8.417106 TGATCACACCAAATTTAAGCAGTTAAA 58.583 29.630 0.00 0.00 41.34 1.52
2171 2329 2.305927 AGGGACATCTACCACACCAAAG 59.694 50.000 0.00 0.00 0.00 2.77
2204 2363 3.468850 AGGAGGACATGGAAGGAGAAAT 58.531 45.455 0.00 0.00 0.00 2.17
2206 2365 2.649742 AGGAGGACATGGAAGGAGAA 57.350 50.000 0.00 0.00 0.00 2.87
2215 2374 6.249192 TCCTACATCATACTAGGAGGACATG 58.751 44.000 0.00 0.00 34.71 3.21
2216 2375 6.470456 TCCTACATCATACTAGGAGGACAT 57.530 41.667 0.00 0.00 34.71 3.06
2248 2409 4.761739 AGCACAGCAAAGTTATAGAAAGCA 59.238 37.500 0.00 0.00 0.00 3.91
2267 2428 1.818642 AGCTTCTGGAATGTCAGCAC 58.181 50.000 0.00 0.00 34.91 4.40
2337 2498 4.074970 ACTTTGAGGCCTGTCTAACAATG 58.925 43.478 12.00 11.77 0.00 2.82
2382 2543 2.099098 GGTTCTTACATTTGATGCCCGG 59.901 50.000 0.00 0.00 0.00 5.73
2394 2555 5.382664 AGGGAAGACAAAAGGTTCTTACA 57.617 39.130 0.00 0.00 0.00 2.41
2413 2574 0.605589 AACGGCGAAAGGAGAAAGGG 60.606 55.000 16.62 0.00 0.00 3.95
2428 2589 9.712305 ATCTATTATTAGTTTCATCCAGAACGG 57.288 33.333 0.00 0.00 35.56 4.44
2483 2649 9.847224 AAAGAAAGAGTAACACTTAATGAAGGA 57.153 29.630 0.00 0.00 36.95 3.36
2583 2750 4.517285 TGTGCTGATCCTTACCAATTCTC 58.483 43.478 0.00 0.00 0.00 2.87
2935 3102 0.025001 CGAGGCACGCAGTTTTATCG 59.975 55.000 0.00 0.00 41.61 2.92
2953 3120 4.097741 TCAATTGCCCAAAGTCCATTATCG 59.902 41.667 0.00 0.00 0.00 2.92
3101 3268 2.813754 TGTCAATCAAAGGCTGCAGTAC 59.186 45.455 16.64 9.04 0.00 2.73
3398 3565 3.426695 CGAAGCCAATCAGAATGTCCAAC 60.427 47.826 0.00 0.00 37.40 3.77
3475 3642 1.366319 ACCAACTTGCCTCATCCTCT 58.634 50.000 0.00 0.00 0.00 3.69
3484 3651 6.995511 TCAATACTACATAACCAACTTGCC 57.004 37.500 0.00 0.00 0.00 4.52
3537 3704 5.083533 AGACAGAAGAAATCTAGCAGTGG 57.916 43.478 0.00 0.00 36.32 4.00
3562 3729 4.873259 GGTGGAGCTTTGTAATCTTCTCTC 59.127 45.833 0.00 0.00 0.00 3.20
3616 3783 5.413833 AGCATGACTTCTTTCAATCATCGTT 59.586 36.000 0.00 0.00 29.25 3.85
3725 3892 1.135199 CAACTGCAATGCCTCACATCC 60.135 52.381 1.53 0.00 38.34 3.51
3766 3933 3.389329 AGGAAGCTTTCAACAGAGACTCA 59.611 43.478 7.68 0.00 0.00 3.41
3773 3940 4.771590 TTGCATAGGAAGCTTTCAACAG 57.228 40.909 7.68 0.00 0.00 3.16
3796 3963 9.948964 ACATATTCACAATATCTAGCTGCATTA 57.051 29.630 1.02 0.00 31.83 1.90
3802 3969 8.982685 CGAACAACATATTCACAATATCTAGCT 58.017 33.333 0.00 0.00 31.83 3.32
3811 3978 5.105957 CCATTCCCGAACAACATATTCACAA 60.106 40.000 0.00 0.00 0.00 3.33
4116 4283 3.664025 CTGGCGACGAATCCAGGCA 62.664 63.158 11.04 4.04 44.64 4.75
4240 4407 0.810031 CCCACCGTATGCTGCTGTAC 60.810 60.000 0.00 3.61 0.00 2.90
4291 4458 0.741326 TGGTATCGACTCTCAGCTGC 59.259 55.000 9.47 0.00 0.00 5.25
4297 4464 0.389757 GGGCCTTGGTATCGACTCTC 59.610 60.000 0.84 0.00 0.00 3.20
4423 4590 0.036952 CCTTCTTGAGCGCTTCCAGA 60.037 55.000 13.26 10.83 0.00 3.86
4441 4608 1.971695 CTTGCCGTTGTCCTTCCCC 60.972 63.158 0.00 0.00 0.00 4.81
4497 4664 0.741221 GACTTTCACGGCCTGGCTAG 60.741 60.000 19.68 15.22 0.00 3.42
4526 4693 4.785376 ACAAGATTATCCACCAGACTTCCT 59.215 41.667 0.00 0.00 0.00 3.36
4555 4722 1.411246 ACAGGTCTCAGCAACGTGTTA 59.589 47.619 0.00 0.00 41.51 2.41
4650 4824 2.974285 TCAGGGTAGGGTTCCCATTA 57.026 50.000 10.73 0.00 46.82 1.90
4662 4836 1.822990 GTCAAGTCGGTCATCAGGGTA 59.177 52.381 0.00 0.00 0.00 3.69
4692 4870 2.158623 TGCAGAAGAAGATGGTGGTGTT 60.159 45.455 0.00 0.00 0.00 3.32
4695 4873 1.980765 TCTGCAGAAGAAGATGGTGGT 59.019 47.619 15.67 0.00 29.54 4.16
4696 4874 2.775911 TCTGCAGAAGAAGATGGTGG 57.224 50.000 15.67 0.00 29.54 4.61
4697 4875 5.240183 TCTTTTTCTGCAGAAGAAGATGGTG 59.760 40.000 38.78 24.15 44.86 4.17
4698 4876 5.380043 TCTTTTTCTGCAGAAGAAGATGGT 58.620 37.500 38.78 0.00 44.86 3.55
4699 4877 5.954296 TCTTTTTCTGCAGAAGAAGATGG 57.046 39.130 38.78 24.95 44.86 3.51
4703 4881 7.074502 GTGTACATCTTTTTCTGCAGAAGAAG 58.925 38.462 36.50 36.50 45.64 2.85
4704 4882 6.542005 TGTGTACATCTTTTTCTGCAGAAGAA 59.458 34.615 27.02 26.31 43.37 2.52
4730 4908 2.095768 TGAAATGCAGCACGCTTTAGTC 60.096 45.455 0.00 0.00 43.06 2.59
4734 4912 1.337703 TCTTGAAATGCAGCACGCTTT 59.662 42.857 0.00 0.00 43.06 3.51
4787 4988 4.428294 TTGCCTCCTCCTTTATCATCAG 57.572 45.455 0.00 0.00 0.00 2.90
4790 4991 4.591321 TGTTTGCCTCCTCCTTTATCAT 57.409 40.909 0.00 0.00 0.00 2.45
4799 5000 4.319549 CGTAAGAAAGTTGTTTGCCTCCTC 60.320 45.833 0.00 0.00 43.02 3.71
4801 5002 3.314357 ACGTAAGAAAGTTGTTTGCCTCC 59.686 43.478 0.00 0.00 43.62 4.30
4826 5027 3.761752 TCGTCATGTCAATCCAGTGAGTA 59.238 43.478 0.00 0.00 0.00 2.59
4850 5051 5.705441 TCATTACCTCCAATTTGTCACAGAC 59.295 40.000 0.00 0.00 0.00 3.51
4868 5069 1.073177 CCCGGTCGTGTTGTCATTAC 58.927 55.000 0.00 0.00 0.00 1.89
4887 5089 1.667724 CAGATGGCGGAAATCTGTCAC 59.332 52.381 0.00 0.00 43.98 3.67
4912 5114 2.141535 GCAGGAAGCAGGATAGTACG 57.858 55.000 0.00 0.00 44.79 3.67
4965 5167 1.922220 CGATGACGACGACGACGAC 60.922 63.158 25.15 19.21 41.06 4.34
4975 5177 1.226575 GCCACGATCACGATGACGA 60.227 57.895 0.00 0.00 42.66 4.20
4976 5178 2.568031 CGCCACGATCACGATGACG 61.568 63.158 0.00 0.00 42.66 4.35
4977 5179 2.860628 GCGCCACGATCACGATGAC 61.861 63.158 0.00 0.00 42.66 3.06
4978 5180 2.582226 GCGCCACGATCACGATGA 60.582 61.111 0.00 0.00 42.66 2.92
4979 5181 2.885164 TGCGCCACGATCACGATG 60.885 61.111 4.18 0.00 42.66 3.84
4980 5182 2.885644 GTGCGCCACGATCACGAT 60.886 61.111 4.18 0.00 42.66 3.73
5153 5359 5.265290 TCCACCGATTAGATATGGTCCTA 57.735 43.478 0.00 0.00 30.72 2.94
5185 5391 4.693566 TGACAGGACAACGAATCAAATACC 59.306 41.667 0.00 0.00 0.00 2.73
5186 5392 5.856126 TGACAGGACAACGAATCAAATAC 57.144 39.130 0.00 0.00 0.00 1.89
5187 5393 5.584649 GGATGACAGGACAACGAATCAAATA 59.415 40.000 0.00 0.00 0.00 1.40
5188 5394 4.396166 GGATGACAGGACAACGAATCAAAT 59.604 41.667 0.00 0.00 0.00 2.32
5189 5395 3.751175 GGATGACAGGACAACGAATCAAA 59.249 43.478 0.00 0.00 0.00 2.69
5190 5396 3.244387 TGGATGACAGGACAACGAATCAA 60.244 43.478 0.00 0.00 0.00 2.57
5212 5418 1.697982 GGTTGAACTGGTCTACCCACT 59.302 52.381 14.36 0.00 43.96 4.00
5231 5437 2.579787 CGGAGCAGACGTAAGCGG 60.580 66.667 6.11 0.00 43.45 5.52
5281 5504 0.952280 GATGATGGACCTGCATGCAG 59.048 55.000 35.88 35.88 43.26 4.41
5291 5514 0.389166 GAGGCGATCCGATGATGGAC 60.389 60.000 0.00 0.00 41.85 4.02
5366 5590 7.415541 CCCATTACACACATTGACCTCTATTTG 60.416 40.741 0.00 0.00 0.00 2.32
5393 5617 3.360340 GCCTGTGCACAGCTCACC 61.360 66.667 36.38 19.11 42.47 4.02
5411 5635 0.468226 TGGATACCGTCAATGGCTCC 59.532 55.000 4.29 4.29 35.62 4.70
5443 5667 1.529152 TTCTACGGCGTCTGCTCCAA 61.529 55.000 19.21 0.00 42.25 3.53
5475 5699 7.735326 AGGATTGACTACCACTAGTATTTGT 57.265 36.000 0.00 0.00 32.96 2.83
5476 5700 9.751542 CTTAGGATTGACTACCACTAGTATTTG 57.248 37.037 0.00 0.00 32.96 2.32
5477 5701 9.710818 TCTTAGGATTGACTACCACTAGTATTT 57.289 33.333 0.00 0.00 32.96 1.40
5478 5702 9.357161 CTCTTAGGATTGACTACCACTAGTATT 57.643 37.037 0.00 0.00 32.96 1.89
5479 5703 8.725256 TCTCTTAGGATTGACTACCACTAGTAT 58.275 37.037 0.00 0.00 32.96 2.12
5480 5704 8.098963 TCTCTTAGGATTGACTACCACTAGTA 57.901 38.462 0.00 0.00 32.96 1.82
5482 5706 7.504238 ACATCTCTTAGGATTGACTACCACTAG 59.496 40.741 0.00 0.00 0.00 2.57
5483 5707 7.355101 ACATCTCTTAGGATTGACTACCACTA 58.645 38.462 0.00 0.00 0.00 2.74
5484 5708 6.198639 ACATCTCTTAGGATTGACTACCACT 58.801 40.000 0.00 0.00 0.00 4.00
5487 5711 6.322712 AGTGACATCTCTTAGGATTGACTACC 59.677 42.308 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.