Multiple sequence alignment - TraesCS5A01G077400

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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 TraesCS5A01G077400 chr5A 100.000 1507 0 0 974 2480 94310774 94312280 0.000000e+00 2784.0
1 TraesCS5A01G077400 chr5A 100.000 557 0 0 1 557 94309801 94310357 0.000000e+00 1029.0
2 TraesCS5A01G077400 chr5A 88.571 595 54 9 974 1561 94092368 94092955 0.000000e+00 710.0
3 TraesCS5A01G077400 chr5A 78.102 137 18 4 423 557 94092227 94092353 2.640000e-10 76.8
4 TraesCS5A01G077400 chr5A 100.000 39 0 0 2334 2372 94312096 94312134 3.420000e-09 73.1
5 TraesCS5A01G077400 chr5A 100.000 39 0 0 2296 2334 94312134 94312172 3.420000e-09 73.1
6 TraesCS5A01G077400 chr5B 87.855 1375 94 23 974 2332 113328000 113326683 0.000000e+00 1546.0
7 TraesCS5A01G077400 chr5B 91.489 517 43 1 988 1504 113456867 113456352 0.000000e+00 710.0
8 TraesCS5A01G077400 chr5B 89.326 534 37 11 36 557 113328539 113328014 0.000000e+00 652.0
9 TraesCS5A01G077400 chr5D 85.962 1382 112 29 974 2331 104113170 104111847 0.000000e+00 1402.0
10 TraesCS5A01G077400 chr5D 89.545 593 54 7 975 1561 104142980 104142390 0.000000e+00 745.0
11 TraesCS5A01G077400 chr5D 88.909 541 22 10 36 557 104113705 104113184 1.250000e-177 632.0
12 TraesCS5A01G077400 chr6A 88.934 497 49 2 1001 1491 10138117 10137621 2.110000e-170 608.0
13 TraesCS5A01G077400 chr6D 88.600 500 48 2 1001 1491 9195541 9195042 1.270000e-167 599.0
14 TraesCS5A01G077400 chr6B 87.500 520 59 4 1001 1516 16970593 16971110 1.640000e-166 595.0
15 TraesCS5A01G077400 chr6B 86.998 523 57 6 1001 1514 17091656 17091136 1.650000e-161 579.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G077400 chr5A 94309801 94312280 2479 False 989.8 2784 100.0000 1 2480 4 chr5A.!!$F2 2479
1 TraesCS5A01G077400 chr5A 94092227 94092955 728 False 393.4 710 83.3365 423 1561 2 chr5A.!!$F1 1138
2 TraesCS5A01G077400 chr5B 113326683 113328539 1856 True 1099.0 1546 88.5905 36 2332 2 chr5B.!!$R2 2296
3 TraesCS5A01G077400 chr5B 113456352 113456867 515 True 710.0 710 91.4890 988 1504 1 chr5B.!!$R1 516
4 TraesCS5A01G077400 chr5D 104111847 104113705 1858 True 1017.0 1402 87.4355 36 2331 2 chr5D.!!$R2 2295
5 TraesCS5A01G077400 chr5D 104142390 104142980 590 True 745.0 745 89.5450 975 1561 1 chr5D.!!$R1 586
6 TraesCS5A01G077400 chr6B 16970593 16971110 517 False 595.0 595 87.5000 1001 1516 1 chr6B.!!$F1 515
7 TraesCS5A01G077400 chr6B 17091136 17091656 520 True 579.0 579 86.9980 1001 1514 1 chr6B.!!$R1 513

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
539 564 0.400213 CCTCACCCCAAAGCAGTGTA 59.6 55.0 0.0 0.0 33.21 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2463 0.100325 TCTGTTTGCAACAAGTGGCG 59.9 50.0 0.0 0.0 41.61 5.69 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
56 57 7.697691 AGGAGATTTGTGCGATATGTTTAAAG 58.302 34.615 0.00 0.00 0.00 1.85
58 59 7.201696 GGAGATTTGTGCGATATGTTTAAAGGA 60.202 37.037 0.00 0.00 0.00 3.36
74 75 7.173735 TGTTTAAAGGAACGGGAGAATAAGAAC 59.826 37.037 0.00 0.00 32.18 3.01
82 83 4.809426 ACGGGAGAATAAGAACAATAAGCG 59.191 41.667 0.00 0.00 0.00 4.68
115 132 1.273327 AGTGCCAAATTTACTGCCAGC 59.727 47.619 0.00 0.00 0.00 4.85
120 137 2.353011 CCAAATTTACTGCCAGCCACTG 60.353 50.000 0.00 0.00 0.00 3.66
138 155 4.082523 CCGACTGGATGGCCACGT 62.083 66.667 8.16 2.42 39.92 4.49
139 156 2.717044 CCGACTGGATGGCCACGTA 61.717 63.158 8.16 0.00 39.92 3.57
140 157 1.518572 CGACTGGATGGCCACGTAC 60.519 63.158 8.16 0.00 39.92 3.67
141 158 1.898154 GACTGGATGGCCACGTACT 59.102 57.895 8.16 0.00 39.92 2.73
159 176 4.387862 CGTACTGTACTACCCAAAGCAAAG 59.612 45.833 15.35 0.00 0.00 2.77
160 177 4.432980 ACTGTACTACCCAAAGCAAAGT 57.567 40.909 0.00 0.00 0.00 2.66
161 178 5.556006 ACTGTACTACCCAAAGCAAAGTA 57.444 39.130 0.00 0.00 0.00 2.24
162 179 5.303165 ACTGTACTACCCAAAGCAAAGTAC 58.697 41.667 0.00 0.00 41.74 2.73
163 180 5.071384 ACTGTACTACCCAAAGCAAAGTACT 59.929 40.000 11.07 0.00 41.85 2.73
164 181 6.268387 ACTGTACTACCCAAAGCAAAGTACTA 59.732 38.462 0.00 0.15 41.85 1.82
165 182 7.065120 TGTACTACCCAAAGCAAAGTACTAA 57.935 36.000 0.00 0.00 41.85 2.24
182 202 8.591114 AAGTACTAACATGTGATACCAGTACT 57.409 34.615 18.29 18.29 45.49 2.73
186 206 6.893554 ACTAACATGTGATACCAGTACTACCA 59.106 38.462 0.00 0.00 0.00 3.25
187 207 5.593679 ACATGTGATACCAGTACTACCAC 57.406 43.478 0.00 0.57 0.00 4.16
188 208 4.404715 ACATGTGATACCAGTACTACCACC 59.595 45.833 0.00 0.00 0.00 4.61
189 209 3.368248 TGTGATACCAGTACTACCACCC 58.632 50.000 0.00 0.00 0.00 4.61
190 210 3.245694 TGTGATACCAGTACTACCACCCA 60.246 47.826 0.00 0.00 0.00 4.51
191 211 3.770933 GTGATACCAGTACTACCACCCAA 59.229 47.826 0.00 0.00 0.00 4.12
193 213 4.468510 TGATACCAGTACTACCACCCAAAG 59.531 45.833 0.00 0.00 0.00 2.77
194 214 1.350019 ACCAGTACTACCACCCAAAGC 59.650 52.381 0.00 0.00 0.00 3.51
538 563 1.151450 CCTCACCCCAAAGCAGTGT 59.849 57.895 0.00 0.00 33.21 3.55
539 564 0.400213 CCTCACCCCAAAGCAGTGTA 59.600 55.000 0.00 0.00 33.21 2.90
546 573 1.545428 CCCAAAGCAGTGTAAGCCTCA 60.545 52.381 0.00 0.00 0.00 3.86
1476 1515 3.376234 TCAAGATCGTCTACTACAACCCG 59.624 47.826 0.00 0.00 0.00 5.28
1489 1528 1.332997 ACAACCCGTAGATCGATCGAC 59.667 52.381 22.06 23.93 42.86 4.20
1492 1531 1.496393 CCGTAGATCGATCGACCCG 59.504 63.158 26.48 21.19 42.86 5.28
1517 1559 1.221840 GCCTAGGTAGCTGCTGCAA 59.778 57.895 19.24 6.02 42.74 4.08
1544 1587 5.283717 GCTTGTAGTGTTGAATAATGTTGCG 59.716 40.000 0.00 0.00 0.00 4.85
1549 1592 4.094887 AGTGTTGAATAATGTTGCGGCTAG 59.905 41.667 0.00 0.00 0.00 3.42
1553 1596 1.865865 ATAATGTTGCGGCTAGGTCG 58.134 50.000 0.00 0.00 0.00 4.79
1554 1597 0.818938 TAATGTTGCGGCTAGGTCGA 59.181 50.000 0.00 0.00 29.41 4.20
1555 1598 0.178068 AATGTTGCGGCTAGGTCGAT 59.822 50.000 0.00 0.00 29.41 3.59
1556 1599 0.249489 ATGTTGCGGCTAGGTCGATC 60.249 55.000 0.00 0.00 29.41 3.69
1557 1600 1.320344 TGTTGCGGCTAGGTCGATCT 61.320 55.000 2.49 2.49 29.41 2.75
1558 1601 0.595310 GTTGCGGCTAGGTCGATCTC 60.595 60.000 0.00 0.00 29.41 2.75
1559 1602 1.035385 TTGCGGCTAGGTCGATCTCA 61.035 55.000 0.00 0.00 29.41 3.27
1560 1603 1.284408 GCGGCTAGGTCGATCTCAG 59.716 63.158 0.00 0.00 29.41 3.35
1561 1604 1.284408 CGGCTAGGTCGATCTCAGC 59.716 63.158 0.00 9.89 29.41 4.26
1562 1605 1.169661 CGGCTAGGTCGATCTCAGCT 61.170 60.000 19.65 3.26 29.41 4.24
1563 1606 0.596082 GGCTAGGTCGATCTCAGCTC 59.404 60.000 19.65 10.90 32.78 4.09
1564 1607 1.604604 GCTAGGTCGATCTCAGCTCT 58.395 55.000 0.00 0.00 0.00 4.09
1565 1608 1.266718 GCTAGGTCGATCTCAGCTCTG 59.733 57.143 0.00 0.00 0.00 3.35
1566 1609 2.571212 CTAGGTCGATCTCAGCTCTGT 58.429 52.381 0.00 0.00 0.00 3.41
1567 1610 1.846007 AGGTCGATCTCAGCTCTGTT 58.154 50.000 0.00 0.00 0.00 3.16
1568 1611 1.476085 AGGTCGATCTCAGCTCTGTTG 59.524 52.381 0.00 0.00 0.00 3.33
1569 1612 1.203523 GGTCGATCTCAGCTCTGTTGT 59.796 52.381 0.00 0.00 0.00 3.32
1570 1613 2.525055 GTCGATCTCAGCTCTGTTGTC 58.475 52.381 0.00 0.00 0.00 3.18
1590 1637 4.636648 TGTCGGTTAATCTGTTGTGTGTTT 59.363 37.500 0.00 0.00 0.00 2.83
1591 1638 5.202640 GTCGGTTAATCTGTTGTGTGTTTC 58.797 41.667 0.00 0.00 0.00 2.78
1592 1639 4.876679 TCGGTTAATCTGTTGTGTGTTTCA 59.123 37.500 0.00 0.00 0.00 2.69
1593 1640 5.354513 TCGGTTAATCTGTTGTGTGTTTCAA 59.645 36.000 0.00 0.00 0.00 2.69
1594 1641 5.681105 CGGTTAATCTGTTGTGTGTTTCAAG 59.319 40.000 0.00 0.00 0.00 3.02
1595 1642 6.560711 GGTTAATCTGTTGTGTGTTTCAAGT 58.439 36.000 0.00 0.00 0.00 3.16
1596 1643 7.033185 GGTTAATCTGTTGTGTGTTTCAAGTT 58.967 34.615 0.00 0.00 0.00 2.66
1597 1644 7.544217 GGTTAATCTGTTGTGTGTTTCAAGTTT 59.456 33.333 0.00 0.00 0.00 2.66
1608 1655 5.064198 TGTGTTTCAAGTTTCAACGAGGTAG 59.936 40.000 0.00 0.00 0.00 3.18
1609 1656 5.064325 GTGTTTCAAGTTTCAACGAGGTAGT 59.936 40.000 0.00 0.00 0.00 2.73
1639 1686 1.724929 CCGTCGTCAGTCGTGTGTC 60.725 63.158 0.00 0.00 40.80 3.67
1640 1687 2.067598 CGTCGTCAGTCGTGTGTCG 61.068 63.158 1.47 1.47 40.80 4.35
1654 1701 3.667695 CGTGTGTCGTAGTGTCGGATTTA 60.668 47.826 0.00 0.00 34.52 1.40
1664 1711 6.363088 CGTAGTGTCGGATTTACAGTTTAACA 59.637 38.462 0.00 0.00 32.80 2.41
1671 1718 6.930164 TCGGATTTACAGTTTAACAAGCTGTA 59.070 34.615 10.41 10.41 42.60 2.74
1678 1725 5.977129 ACAGTTTAACAAGCTGTATTTGCAC 59.023 36.000 6.61 0.00 41.12 4.57
1716 1763 5.390145 GCTTAGCTCAAATGCAAATGTTTGG 60.390 40.000 9.90 3.64 38.57 3.28
1717 1764 4.075963 AGCTCAAATGCAAATGTTTGGT 57.924 36.364 9.90 2.55 38.57 3.67
1718 1765 3.810941 AGCTCAAATGCAAATGTTTGGTG 59.189 39.130 9.90 5.71 38.57 4.17
1719 1766 3.560896 GCTCAAATGCAAATGTTTGGTGT 59.439 39.130 9.90 0.00 38.57 4.16
1721 1768 5.481200 TCAAATGCAAATGTTTGGTGTTG 57.519 34.783 9.90 0.00 38.57 3.33
1722 1769 4.940046 TCAAATGCAAATGTTTGGTGTTGT 59.060 33.333 9.90 0.00 38.57 3.32
1723 1770 5.064452 TCAAATGCAAATGTTTGGTGTTGTC 59.936 36.000 9.90 0.00 38.57 3.18
1724 1771 3.599730 TGCAAATGTTTGGTGTTGTCA 57.400 38.095 7.51 0.00 38.57 3.58
1725 1772 3.257393 TGCAAATGTTTGGTGTTGTCAC 58.743 40.909 7.51 0.00 43.19 3.67
1729 1776 5.445806 GCAAATGTTTGGTGTTGTCACTTTC 60.446 40.000 7.51 0.00 43.41 2.62
1732 1779 5.461032 TGTTTGGTGTTGTCACTTTCTTT 57.539 34.783 0.00 0.00 43.41 2.52
1733 1780 5.848406 TGTTTGGTGTTGTCACTTTCTTTT 58.152 33.333 0.00 0.00 43.41 2.27
1770 1817 5.762825 AGTACCGATCTTATTTCTACGCA 57.237 39.130 0.00 0.00 0.00 5.24
1782 1829 9.880157 TCTTATTTCTACGCACCTAAATTAAGT 57.120 29.630 0.00 0.00 0.00 2.24
1787 1834 9.573133 TTTCTACGCACCTAAATTAAGTACTAC 57.427 33.333 0.00 0.00 0.00 2.73
1788 1835 8.511604 TCTACGCACCTAAATTAAGTACTACT 57.488 34.615 0.00 0.00 0.00 2.57
1789 1836 8.400947 TCTACGCACCTAAATTAAGTACTACTG 58.599 37.037 0.00 0.00 0.00 2.74
1790 1837 6.928520 ACGCACCTAAATTAAGTACTACTGT 58.071 36.000 0.00 0.00 0.00 3.55
1791 1838 8.055279 ACGCACCTAAATTAAGTACTACTGTA 57.945 34.615 0.00 0.00 0.00 2.74
1792 1839 7.970614 ACGCACCTAAATTAAGTACTACTGTAC 59.029 37.037 0.00 0.00 46.89 2.90
1833 1880 3.255888 TGCTTTGTTGGTTGTGTTGTGTA 59.744 39.130 0.00 0.00 0.00 2.90
1834 1881 4.081972 TGCTTTGTTGGTTGTGTTGTGTAT 60.082 37.500 0.00 0.00 0.00 2.29
1866 1913 0.322456 TGGATTTGGGAGAAGGCACG 60.322 55.000 0.00 0.00 0.00 5.34
1868 1915 1.065709 GGATTTGGGAGAAGGCACGTA 60.066 52.381 0.00 0.00 0.00 3.57
1882 1929 3.451178 AGGCACGTACTGAATATGAACCT 59.549 43.478 0.00 0.00 0.00 3.50
1895 1942 8.810652 TGAATATGAACCTGCTTGTTAAAAAC 57.189 30.769 0.00 0.00 0.00 2.43
1896 1943 8.417106 TGAATATGAACCTGCTTGTTAAAAACA 58.583 29.630 0.00 0.00 40.21 2.83
1897 1944 8.816640 AATATGAACCTGCTTGTTAAAAACAG 57.183 30.769 0.00 0.00 43.27 3.16
1900 1947 7.575414 TGAACCTGCTTGTTAAAAACAGATA 57.425 32.000 8.63 0.00 43.27 1.98
1973 2022 6.676237 ATTTCACATGTATATGTTCGCACA 57.324 33.333 1.82 0.00 45.01 4.57
1998 2047 0.444651 TGCGCGGCACAAAGTATTAC 59.555 50.000 8.83 0.00 31.71 1.89
2000 2049 0.717224 CGCGGCACAAAGTATTACGT 59.283 50.000 0.00 0.00 0.00 3.57
2001 2050 1.526184 CGCGGCACAAAGTATTACGTG 60.526 52.381 0.00 0.00 35.43 4.49
2002 2051 1.461897 GCGGCACAAAGTATTACGTGT 59.538 47.619 0.00 1.65 34.96 4.49
2003 2052 2.096119 GCGGCACAAAGTATTACGTGTT 60.096 45.455 0.00 0.00 34.96 3.32
2004 2053 3.607542 GCGGCACAAAGTATTACGTGTTT 60.608 43.478 0.00 0.00 34.96 2.83
2005 2054 4.145997 CGGCACAAAGTATTACGTGTTTC 58.854 43.478 0.00 0.00 34.96 2.78
2006 2055 4.318903 CGGCACAAAGTATTACGTGTTTCA 60.319 41.667 0.00 0.00 34.96 2.69
2007 2056 5.615984 CGGCACAAAGTATTACGTGTTTCAT 60.616 40.000 0.00 0.00 34.96 2.57
2008 2057 5.567534 GGCACAAAGTATTACGTGTTTCATG 59.432 40.000 0.00 0.00 34.96 3.07
2009 2058 6.367421 GCACAAAGTATTACGTGTTTCATGA 58.633 36.000 0.00 0.00 34.96 3.07
2010 2059 6.302313 GCACAAAGTATTACGTGTTTCATGAC 59.698 38.462 0.00 0.00 34.96 3.06
2011 2060 7.348956 CACAAAGTATTACGTGTTTCATGACA 58.651 34.615 0.00 0.00 29.77 3.58
2013 2062 6.476243 AAGTATTACGTGTTTCATGACACC 57.524 37.500 9.45 0.76 45.49 4.16
2015 2064 5.867716 AGTATTACGTGTTTCATGACACCTC 59.132 40.000 9.45 2.55 45.49 3.85
2016 2065 2.910688 ACGTGTTTCATGACACCTCT 57.089 45.000 9.45 0.00 45.49 3.69
2017 2066 2.483876 ACGTGTTTCATGACACCTCTG 58.516 47.619 9.45 0.25 45.49 3.35
2018 2067 1.195448 CGTGTTTCATGACACCTCTGC 59.805 52.381 9.45 0.00 45.49 4.26
2099 2167 6.647895 CACATGCCAAAGAAGAAGCTATTTTT 59.352 34.615 0.00 0.00 0.00 1.94
2100 2168 6.647895 ACATGCCAAAGAAGAAGCTATTTTTG 59.352 34.615 0.00 0.00 0.00 2.44
2101 2169 5.540911 TGCCAAAGAAGAAGCTATTTTTGG 58.459 37.500 17.76 17.76 44.49 3.28
2109 2177 5.551305 AGAAGCTATTTTTGGGCAAAACT 57.449 34.783 0.00 0.00 39.70 2.66
2127 2195 7.354257 GCAAAACTTTTTGTGCATACATGAAT 58.646 30.769 14.35 0.00 44.47 2.57
2142 2210 3.811497 ACATGAATGTGGAGATGTATGCG 59.189 43.478 0.00 0.00 40.03 4.73
2188 2256 9.565213 TTTTTGGCATTTAGAAATGTGTTTTTG 57.435 25.926 14.72 0.00 45.77 2.44
2203 2271 6.744112 TGTGTTTTTGAAGTGGGTTCATATC 58.256 36.000 0.00 0.00 44.89 1.63
2215 2283 5.046591 GTGGGTTCATATCTATCCGGATTCA 60.047 44.000 24.71 10.04 0.00 2.57
2249 2318 5.576563 TCTTAGATTTGACCCAAGGACAA 57.423 39.130 0.00 0.00 35.80 3.18
2259 2328 5.202765 TGACCCAAGGACAATACGTAGATA 58.797 41.667 0.08 0.00 0.00 1.98
2260 2329 5.301045 TGACCCAAGGACAATACGTAGATAG 59.699 44.000 0.08 0.00 0.00 2.08
2261 2330 4.587684 ACCCAAGGACAATACGTAGATAGG 59.412 45.833 0.08 0.00 0.00 2.57
2266 2335 6.576662 AGGACAATACGTAGATAGGATGTG 57.423 41.667 0.08 0.00 0.00 3.21
2276 2345 6.150318 CGTAGATAGGATGTGTTGGACATAC 58.850 44.000 0.00 0.00 45.90 2.39
2281 2352 3.596214 GGATGTGTTGGACATACTTCGT 58.404 45.455 0.00 0.00 45.90 3.85
2297 2368 0.596577 TCGTGAGGCCTATATGTCGC 59.403 55.000 4.42 0.00 0.00 5.19
2303 2374 3.508402 TGAGGCCTATATGTCGCGAAATA 59.492 43.478 20.80 20.80 0.00 1.40
2305 2376 4.495422 AGGCCTATATGTCGCGAAATAAG 58.505 43.478 22.21 18.28 0.00 1.73
2308 2379 5.287992 GGCCTATATGTCGCGAAATAAGTAC 59.712 44.000 22.21 12.35 0.00 2.73
2310 2381 7.246311 GCCTATATGTCGCGAAATAAGTACTA 58.754 38.462 22.21 9.31 0.00 1.82
2338 2409 3.975246 CCTTACAAAGGCCGCGAA 58.025 55.556 8.23 0.00 42.78 4.70
2339 2410 2.249692 CCTTACAAAGGCCGCGAAA 58.750 52.632 8.23 0.00 42.78 3.46
2340 2411 0.808755 CCTTACAAAGGCCGCGAAAT 59.191 50.000 8.23 0.00 42.78 2.17
2341 2412 2.011222 CCTTACAAAGGCCGCGAAATA 58.989 47.619 8.23 0.00 42.78 1.40
2342 2413 2.420722 CCTTACAAAGGCCGCGAAATAA 59.579 45.455 8.23 0.00 42.78 1.40
2343 2414 3.486875 CCTTACAAAGGCCGCGAAATAAG 60.487 47.826 8.23 5.56 42.78 1.73
2344 2415 1.530323 ACAAAGGCCGCGAAATAAGT 58.470 45.000 8.23 0.00 0.00 2.24
2345 2416 2.702261 ACAAAGGCCGCGAAATAAGTA 58.298 42.857 8.23 0.00 0.00 2.24
2346 2417 2.417586 ACAAAGGCCGCGAAATAAGTAC 59.582 45.455 8.23 0.00 0.00 2.73
2347 2418 2.676342 CAAAGGCCGCGAAATAAGTACT 59.324 45.455 8.23 0.00 0.00 2.73
2348 2419 3.806625 AAGGCCGCGAAATAAGTACTA 57.193 42.857 8.23 0.00 0.00 1.82
2349 2420 3.806625 AGGCCGCGAAATAAGTACTAA 57.193 42.857 8.23 0.00 0.00 2.24
2350 2421 4.127566 AGGCCGCGAAATAAGTACTAAA 57.872 40.909 8.23 0.00 0.00 1.85
2351 2422 4.117685 AGGCCGCGAAATAAGTACTAAAG 58.882 43.478 8.23 0.00 0.00 1.85
2352 2423 4.114794 GGCCGCGAAATAAGTACTAAAGA 58.885 43.478 8.23 0.00 0.00 2.52
2353 2424 4.208666 GGCCGCGAAATAAGTACTAAAGAG 59.791 45.833 8.23 0.00 0.00 2.85
2354 2425 4.208666 GCCGCGAAATAAGTACTAAAGAGG 59.791 45.833 8.23 0.00 0.00 3.69
2355 2426 5.346522 CCGCGAAATAAGTACTAAAGAGGT 58.653 41.667 8.23 0.00 0.00 3.85
2356 2427 6.498304 CCGCGAAATAAGTACTAAAGAGGTA 58.502 40.000 8.23 0.00 0.00 3.08
2357 2428 6.416161 CCGCGAAATAAGTACTAAAGAGGTAC 59.584 42.308 8.23 0.00 39.60 3.34
2358 2429 6.416161 CGCGAAATAAGTACTAAAGAGGTACC 59.584 42.308 2.73 2.73 40.01 3.34
2359 2430 6.699204 GCGAAATAAGTACTAAAGAGGTACCC 59.301 42.308 8.74 0.00 40.01 3.69
2360 2431 7.205992 CGAAATAAGTACTAAAGAGGTACCCC 58.794 42.308 8.74 0.00 40.01 4.95
2361 2432 7.069208 CGAAATAAGTACTAAAGAGGTACCCCT 59.931 40.741 8.74 0.00 46.66 4.79
2362 2433 8.691194 AAATAAGTACTAAAGAGGTACCCCTT 57.309 34.615 8.74 5.34 42.86 3.95
2363 2434 9.788815 AAATAAGTACTAAAGAGGTACCCCTTA 57.211 33.333 9.37 3.70 42.86 2.69
2364 2435 8.774546 ATAAGTACTAAAGAGGTACCCCTTAC 57.225 38.462 9.37 3.98 42.86 2.34
2365 2436 6.157862 AGTACTAAAGAGGTACCCCTTACA 57.842 41.667 9.37 0.00 42.86 2.41
2366 2437 6.565036 AGTACTAAAGAGGTACCCCTTACAA 58.435 40.000 9.37 0.00 42.86 2.41
2367 2438 7.018769 AGTACTAAAGAGGTACCCCTTACAAA 58.981 38.462 9.37 0.00 42.86 2.83
2368 2439 6.370186 ACTAAAGAGGTACCCCTTACAAAG 57.630 41.667 9.37 7.48 42.86 2.77
2369 2440 7.580302 GTACTAAAGAGGTACCCCTTACAAAGG 60.580 44.444 9.37 0.00 42.86 3.11
2379 2450 2.807676 CCTTACAAAGGCCATCCAACT 58.192 47.619 5.01 0.00 42.78 3.16
2380 2451 3.165071 CCTTACAAAGGCCATCCAACTT 58.835 45.455 5.01 0.00 42.78 2.66
2381 2452 3.578282 CCTTACAAAGGCCATCCAACTTT 59.422 43.478 5.01 0.00 42.78 2.66
2382 2453 4.321974 CCTTACAAAGGCCATCCAACTTTC 60.322 45.833 5.01 0.00 42.78 2.62
2383 2454 2.962859 ACAAAGGCCATCCAACTTTCT 58.037 42.857 5.01 0.00 32.52 2.52
2384 2455 2.629617 ACAAAGGCCATCCAACTTTCTG 59.370 45.455 5.01 0.00 32.52 3.02
2385 2456 2.629617 CAAAGGCCATCCAACTTTCTGT 59.370 45.455 5.01 0.00 32.52 3.41
2386 2457 1.915141 AGGCCATCCAACTTTCTGTG 58.085 50.000 5.01 0.00 33.74 3.66
2387 2458 1.425066 AGGCCATCCAACTTTCTGTGA 59.575 47.619 5.01 0.00 33.74 3.58
2388 2459 2.042162 AGGCCATCCAACTTTCTGTGAT 59.958 45.455 5.01 0.00 33.74 3.06
2389 2460 2.165030 GGCCATCCAACTTTCTGTGATG 59.835 50.000 0.00 0.00 0.00 3.07
2390 2461 2.821969 GCCATCCAACTTTCTGTGATGT 59.178 45.455 0.00 0.00 0.00 3.06
2391 2462 3.366679 GCCATCCAACTTTCTGTGATGTG 60.367 47.826 0.00 0.00 0.00 3.21
2392 2463 3.366679 CCATCCAACTTTCTGTGATGTGC 60.367 47.826 0.00 0.00 0.00 4.57
2393 2464 1.872952 TCCAACTTTCTGTGATGTGCG 59.127 47.619 0.00 0.00 0.00 5.34
2394 2465 1.664016 CCAACTTTCTGTGATGTGCGC 60.664 52.381 0.00 0.00 0.00 6.09
2395 2466 0.593128 AACTTTCTGTGATGTGCGCC 59.407 50.000 4.18 0.00 0.00 6.53
2396 2467 0.534877 ACTTTCTGTGATGTGCGCCA 60.535 50.000 4.18 2.31 0.00 5.69
2397 2468 0.110056 CTTTCTGTGATGTGCGCCAC 60.110 55.000 4.18 6.22 34.56 5.01
2398 2469 0.534877 TTTCTGTGATGTGCGCCACT 60.535 50.000 4.18 0.00 35.11 4.00
2399 2470 0.534877 TTCTGTGATGTGCGCCACTT 60.535 50.000 4.18 1.20 35.11 3.16
2400 2471 1.208358 CTGTGATGTGCGCCACTTG 59.792 57.895 4.18 0.00 35.11 3.16
2401 2472 1.509644 CTGTGATGTGCGCCACTTGT 61.510 55.000 4.18 0.00 35.11 3.16
2402 2473 1.100463 TGTGATGTGCGCCACTTGTT 61.100 50.000 4.18 0.00 35.11 2.83
2403 2474 0.661187 GTGATGTGCGCCACTTGTTG 60.661 55.000 4.18 0.00 35.11 3.33
2404 2475 1.730547 GATGTGCGCCACTTGTTGC 60.731 57.895 4.18 0.00 35.11 4.17
2405 2476 2.405061 GATGTGCGCCACTTGTTGCA 62.405 55.000 4.18 0.00 35.11 4.08
2406 2477 2.014064 ATGTGCGCCACTTGTTGCAA 62.014 50.000 4.18 0.00 39.34 4.08
2407 2478 1.518133 GTGCGCCACTTGTTGCAAA 60.518 52.632 4.18 0.00 39.34 3.68
2472 2543 9.221775 CAAAACATTTTATCTATAGAACCGTGC 57.778 33.333 6.52 0.00 0.00 5.34
2473 2544 6.764877 ACATTTTATCTATAGAACCGTGCG 57.235 37.500 6.52 0.00 0.00 5.34
2474 2545 5.694910 ACATTTTATCTATAGAACCGTGCGG 59.305 40.000 6.52 9.29 42.03 5.69
2475 2546 3.293311 TTATCTATAGAACCGTGCGGC 57.707 47.619 6.52 0.00 39.32 6.53
2476 2547 0.317479 ATCTATAGAACCGTGCGGCC 59.683 55.000 6.52 0.00 39.32 6.13
2477 2548 1.660575 CTATAGAACCGTGCGGCCG 60.661 63.158 24.05 24.05 39.32 6.13
2478 2549 2.067091 CTATAGAACCGTGCGGCCGA 62.067 60.000 33.48 11.82 39.32 5.54
2479 2550 1.665264 TATAGAACCGTGCGGCCGAA 61.665 55.000 33.48 19.06 39.32 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.135225 TCGCACAAATCTCCTCGAAAAA 58.865 40.909 0.00 0.00 0.00 1.94
25 26 2.761559 TCGCACAAATCTCCTCGAAAA 58.238 42.857 0.00 0.00 0.00 2.29
26 27 2.448926 TCGCACAAATCTCCTCGAAA 57.551 45.000 0.00 0.00 0.00 3.46
27 28 2.672961 ATCGCACAAATCTCCTCGAA 57.327 45.000 0.00 0.00 0.00 3.71
28 29 3.068165 ACATATCGCACAAATCTCCTCGA 59.932 43.478 0.00 0.00 0.00 4.04
29 30 3.384668 ACATATCGCACAAATCTCCTCG 58.615 45.455 0.00 0.00 0.00 4.63
30 31 5.741388 AAACATATCGCACAAATCTCCTC 57.259 39.130 0.00 0.00 0.00 3.71
31 32 7.201732 CCTTTAAACATATCGCACAAATCTCCT 60.202 37.037 0.00 0.00 0.00 3.69
32 33 6.912591 CCTTTAAACATATCGCACAAATCTCC 59.087 38.462 0.00 0.00 0.00 3.71
33 34 7.693952 TCCTTTAAACATATCGCACAAATCTC 58.306 34.615 0.00 0.00 0.00 2.75
34 35 7.624360 TCCTTTAAACATATCGCACAAATCT 57.376 32.000 0.00 0.00 0.00 2.40
40 41 4.495184 CCCGTTCCTTTAAACATATCGCAC 60.495 45.833 0.00 0.00 0.00 5.34
56 57 6.238402 GCTTATTGTTCTTATTCTCCCGTTCC 60.238 42.308 0.00 0.00 0.00 3.62
58 59 5.293569 CGCTTATTGTTCTTATTCTCCCGTT 59.706 40.000 0.00 0.00 0.00 4.44
91 92 2.610232 GGCAGTAAATTTGGCACTGGTG 60.610 50.000 17.26 0.00 40.03 4.17
92 93 1.618343 GGCAGTAAATTTGGCACTGGT 59.382 47.619 17.26 0.00 40.03 4.00
93 94 1.617850 TGGCAGTAAATTTGGCACTGG 59.382 47.619 17.26 4.21 44.86 4.00
94 95 2.927871 GCTGGCAGTAAATTTGGCACTG 60.928 50.000 17.16 13.12 44.86 3.66
95 96 1.273327 GCTGGCAGTAAATTTGGCACT 59.727 47.619 17.16 0.00 44.86 4.40
96 97 1.672737 GGCTGGCAGTAAATTTGGCAC 60.673 52.381 17.16 0.00 44.86 5.01
98 99 0.607620 TGGCTGGCAGTAAATTTGGC 59.392 50.000 17.16 0.69 41.12 4.52
99 100 1.895131 AGTGGCTGGCAGTAAATTTGG 59.105 47.619 17.16 0.00 0.00 3.28
100 101 2.927871 GCAGTGGCTGGCAGTAAATTTG 60.928 50.000 17.16 8.63 36.96 2.32
101 102 1.273327 GCAGTGGCTGGCAGTAAATTT 59.727 47.619 17.16 0.00 36.96 1.82
102 103 0.890683 GCAGTGGCTGGCAGTAAATT 59.109 50.000 17.16 0.00 36.96 1.82
104 105 4.079446 GCAGTGGCTGGCAGTAAA 57.921 55.556 17.16 0.00 36.96 2.01
115 132 2.124983 CCATCCAGTCGGCAGTGG 60.125 66.667 0.00 4.90 43.94 4.00
137 154 5.303165 ACTTTGCTTTGGGTAGTACAGTAC 58.697 41.667 2.05 2.05 0.00 2.73
138 155 5.556006 ACTTTGCTTTGGGTAGTACAGTA 57.444 39.130 2.06 0.00 0.00 2.74
139 156 4.432980 ACTTTGCTTTGGGTAGTACAGT 57.567 40.909 2.06 0.00 0.00 3.55
140 157 5.548406 AGTACTTTGCTTTGGGTAGTACAG 58.452 41.667 11.80 0.00 42.13 2.74
141 158 5.556006 AGTACTTTGCTTTGGGTAGTACA 57.444 39.130 11.80 0.00 42.13 2.90
159 176 8.348507 GGTAGTACTGGTATCACATGTTAGTAC 58.651 40.741 5.39 8.53 39.31 2.73
160 177 8.054572 TGGTAGTACTGGTATCACATGTTAGTA 58.945 37.037 5.39 0.00 0.00 1.82
161 178 6.893554 TGGTAGTACTGGTATCACATGTTAGT 59.106 38.462 5.39 0.00 0.00 2.24
162 179 7.201145 GTGGTAGTACTGGTATCACATGTTAG 58.799 42.308 5.39 0.00 0.00 2.34
163 180 6.097270 GGTGGTAGTACTGGTATCACATGTTA 59.903 42.308 5.39 0.00 0.00 2.41
164 181 5.105064 GGTGGTAGTACTGGTATCACATGTT 60.105 44.000 5.39 0.00 0.00 2.71
165 182 4.404715 GGTGGTAGTACTGGTATCACATGT 59.595 45.833 5.39 0.00 0.00 3.21
182 202 4.279145 TGTTACTTTTGCTTTGGGTGGTA 58.721 39.130 0.00 0.00 0.00 3.25
186 206 5.800296 ACTTTTGTTACTTTTGCTTTGGGT 58.200 33.333 0.00 0.00 0.00 4.51
187 207 7.332182 TGTTACTTTTGTTACTTTTGCTTTGGG 59.668 33.333 0.00 0.00 33.56 4.12
188 208 8.245701 TGTTACTTTTGTTACTTTTGCTTTGG 57.754 30.769 0.00 0.00 33.56 3.28
189 209 9.900264 GATGTTACTTTTGTTACTTTTGCTTTG 57.100 29.630 0.00 0.00 33.56 2.77
190 210 9.646427 TGATGTTACTTTTGTTACTTTTGCTTT 57.354 25.926 0.00 0.00 33.56 3.51
191 211 9.083080 GTGATGTTACTTTTGTTACTTTTGCTT 57.917 29.630 0.00 0.00 33.56 3.91
193 213 8.401046 TGTGATGTTACTTTTGTTACTTTTGC 57.599 30.769 0.00 0.00 33.56 3.68
262 282 0.109873 CGTTCGTTGTCTCGTAGCCT 60.110 55.000 0.00 0.00 0.00 4.58
407 429 7.501559 TGATATTCGCTACCTAGTCACTTAGTT 59.498 37.037 0.00 0.00 0.00 2.24
1083 1122 3.484806 ACCGTCACCTTGTGGGCA 61.485 61.111 0.00 0.00 39.10 5.36
1085 1124 2.978010 GCACCGTCACCTTGTGGG 60.978 66.667 0.00 0.00 41.89 4.61
1492 1531 4.281947 GCTACCTAGGCGGGCGAC 62.282 72.222 9.30 0.00 36.97 5.19
1517 1559 7.362662 CAACATTATTCAACACTACAAGCAGT 58.637 34.615 0.00 0.00 0.00 4.40
1544 1587 0.596082 GAGCTGAGATCGACCTAGCC 59.404 60.000 0.00 0.00 35.05 3.93
1549 1592 1.203523 ACAACAGAGCTGAGATCGACC 59.796 52.381 4.21 0.00 0.00 4.79
1553 1596 1.203523 ACCGACAACAGAGCTGAGATC 59.796 52.381 4.21 0.00 0.00 2.75
1554 1597 1.261480 ACCGACAACAGAGCTGAGAT 58.739 50.000 4.21 0.00 0.00 2.75
1555 1598 1.040646 AACCGACAACAGAGCTGAGA 58.959 50.000 4.21 0.00 0.00 3.27
1556 1599 2.724977 TAACCGACAACAGAGCTGAG 57.275 50.000 4.21 0.00 0.00 3.35
1557 1600 3.258372 AGATTAACCGACAACAGAGCTGA 59.742 43.478 4.21 0.00 0.00 4.26
1558 1601 3.369147 CAGATTAACCGACAACAGAGCTG 59.631 47.826 0.00 0.00 0.00 4.24
1559 1602 3.006967 ACAGATTAACCGACAACAGAGCT 59.993 43.478 0.00 0.00 0.00 4.09
1560 1603 3.326747 ACAGATTAACCGACAACAGAGC 58.673 45.455 0.00 0.00 0.00 4.09
1561 1604 4.750098 ACAACAGATTAACCGACAACAGAG 59.250 41.667 0.00 0.00 0.00 3.35
1562 1605 4.509970 CACAACAGATTAACCGACAACAGA 59.490 41.667 0.00 0.00 0.00 3.41
1563 1606 4.272504 ACACAACAGATTAACCGACAACAG 59.727 41.667 0.00 0.00 0.00 3.16
1564 1607 4.034626 CACACAACAGATTAACCGACAACA 59.965 41.667 0.00 0.00 0.00 3.33
1565 1608 4.034742 ACACACAACAGATTAACCGACAAC 59.965 41.667 0.00 0.00 0.00 3.32
1566 1609 4.193090 ACACACAACAGATTAACCGACAA 58.807 39.130 0.00 0.00 0.00 3.18
1567 1610 3.799366 ACACACAACAGATTAACCGACA 58.201 40.909 0.00 0.00 0.00 4.35
1568 1611 4.806342 AACACACAACAGATTAACCGAC 57.194 40.909 0.00 0.00 0.00 4.79
1569 1612 4.876679 TGAAACACACAACAGATTAACCGA 59.123 37.500 0.00 0.00 0.00 4.69
1570 1613 5.163302 TGAAACACACAACAGATTAACCG 57.837 39.130 0.00 0.00 0.00 4.44
1590 1637 5.779529 ACTACTACCTCGTTGAAACTTGA 57.220 39.130 0.00 0.00 0.00 3.02
1591 1638 6.906659 TCTACTACTACCTCGTTGAAACTTG 58.093 40.000 0.00 0.00 0.00 3.16
1592 1639 7.700022 ATCTACTACTACCTCGTTGAAACTT 57.300 36.000 0.00 0.00 0.00 2.66
1593 1640 7.176340 ACAATCTACTACTACCTCGTTGAAACT 59.824 37.037 0.00 0.00 0.00 2.66
1594 1641 7.311408 ACAATCTACTACTACCTCGTTGAAAC 58.689 38.462 0.00 0.00 0.00 2.78
1595 1642 7.458409 ACAATCTACTACTACCTCGTTGAAA 57.542 36.000 0.00 0.00 0.00 2.69
1596 1643 7.066284 GGTACAATCTACTACTACCTCGTTGAA 59.934 40.741 0.00 0.00 0.00 2.69
1597 1644 6.540189 GGTACAATCTACTACTACCTCGTTGA 59.460 42.308 0.00 0.00 0.00 3.18
1608 1655 4.331168 ACTGACGACGGTACAATCTACTAC 59.669 45.833 0.00 0.00 33.41 2.73
1609 1656 4.507710 ACTGACGACGGTACAATCTACTA 58.492 43.478 0.00 0.00 33.41 1.82
1639 1686 6.363088 TGTTAAACTGTAAATCCGACACTACG 59.637 38.462 0.00 0.00 0.00 3.51
1640 1687 7.642071 TGTTAAACTGTAAATCCGACACTAC 57.358 36.000 0.00 0.00 0.00 2.73
1654 1701 5.977129 GTGCAAATACAGCTTGTTAAACTGT 59.023 36.000 0.00 0.00 46.05 3.55
1664 1711 2.436417 ACATCCGTGCAAATACAGCTT 58.564 42.857 0.00 0.00 0.00 3.74
1671 1718 3.809832 GCTCATACTACATCCGTGCAAAT 59.190 43.478 0.00 0.00 0.00 2.32
1678 1725 4.775058 AGCTAAGCTCATACTACATCCG 57.225 45.455 0.00 0.00 30.62 4.18
1732 1779 5.417811 TCGGTACTTATATGCCGTTCAAAA 58.582 37.500 2.28 0.00 46.69 2.44
1733 1780 5.008619 TCGGTACTTATATGCCGTTCAAA 57.991 39.130 2.28 0.00 46.69 2.69
1735 1782 4.521639 AGATCGGTACTTATATGCCGTTCA 59.478 41.667 13.39 0.00 46.69 3.18
1736 1783 5.056894 AGATCGGTACTTATATGCCGTTC 57.943 43.478 2.28 4.08 46.69 3.95
1737 1784 5.464030 AAGATCGGTACTTATATGCCGTT 57.536 39.130 2.28 0.00 46.69 4.44
1782 1829 6.239543 CCAGCTAGTAGCCTAGTACAGTAGTA 60.240 46.154 18.65 0.00 43.77 1.82
1783 1830 5.455040 CCAGCTAGTAGCCTAGTACAGTAGT 60.455 48.000 18.65 0.00 43.77 2.73
1784 1831 4.998672 CCAGCTAGTAGCCTAGTACAGTAG 59.001 50.000 18.65 0.00 43.77 2.57
1785 1832 4.657504 TCCAGCTAGTAGCCTAGTACAGTA 59.342 45.833 18.65 0.00 43.77 2.74
1786 1833 3.458857 TCCAGCTAGTAGCCTAGTACAGT 59.541 47.826 18.65 0.00 43.77 3.55
1787 1834 4.088056 TCCAGCTAGTAGCCTAGTACAG 57.912 50.000 18.65 0.00 43.77 2.74
1788 1835 4.726035 ATCCAGCTAGTAGCCTAGTACA 57.274 45.455 18.65 0.00 43.77 2.90
1789 1836 5.774630 CAAATCCAGCTAGTAGCCTAGTAC 58.225 45.833 18.65 0.00 43.77 2.73
1790 1837 4.281182 GCAAATCCAGCTAGTAGCCTAGTA 59.719 45.833 18.65 0.91 43.77 1.82
1791 1838 3.070302 GCAAATCCAGCTAGTAGCCTAGT 59.930 47.826 18.65 0.96 43.77 2.57
1792 1839 3.323403 AGCAAATCCAGCTAGTAGCCTAG 59.677 47.826 18.65 8.97 43.77 3.02
1793 1840 3.309296 AGCAAATCCAGCTAGTAGCCTA 58.691 45.455 18.65 4.90 43.77 3.93
1794 1841 2.122768 AGCAAATCCAGCTAGTAGCCT 58.877 47.619 18.65 3.12 43.77 4.58
1795 1842 2.629336 AGCAAATCCAGCTAGTAGCC 57.371 50.000 18.65 0.69 43.77 3.93
1796 1843 3.691609 ACAAAGCAAATCCAGCTAGTAGC 59.308 43.478 14.62 14.62 42.53 3.58
1797 1844 5.392380 CCAACAAAGCAAATCCAGCTAGTAG 60.392 44.000 0.00 0.00 42.53 2.57
1833 1880 2.226962 AATCCAGCTCAAACTGCCAT 57.773 45.000 0.00 0.00 36.29 4.40
1834 1881 1.614903 CAAATCCAGCTCAAACTGCCA 59.385 47.619 0.00 0.00 36.29 4.92
1866 1913 6.743575 AACAAGCAGGTTCATATTCAGTAC 57.256 37.500 0.00 0.00 0.00 2.73
1868 1915 7.759489 TTTAACAAGCAGGTTCATATTCAGT 57.241 32.000 0.00 0.00 32.29 3.41
1956 2005 7.998081 CACATATTGTGCGAACATATACATG 57.002 36.000 0.00 0.00 41.89 3.21
2000 2049 2.636647 TGCAGAGGTGTCATGAAACA 57.363 45.000 17.81 0.35 0.00 2.83
2001 2050 3.988379 TTTGCAGAGGTGTCATGAAAC 57.012 42.857 7.56 7.56 0.00 2.78
2002 2051 4.998671 TTTTTGCAGAGGTGTCATGAAA 57.001 36.364 0.00 0.00 0.00 2.69
2027 2086 9.862371 AACACTATGTAGAAGTACTGAGATTTG 57.138 33.333 0.00 0.00 0.00 2.32
2031 2090 8.631480 TGAAACACTATGTAGAAGTACTGAGA 57.369 34.615 0.00 0.00 0.00 3.27
2038 2097 7.891183 GTGTCATGAAACACTATGTAGAAGT 57.109 36.000 11.36 0.00 44.90 3.01
2064 2123 2.299993 TTGGCATGTGCGAAACAAAA 57.700 40.000 0.00 0.00 43.61 2.44
2072 2131 1.973138 CTTCTTCTTTGGCATGTGCG 58.027 50.000 0.00 0.00 43.26 5.34
2109 2177 6.015603 TCTCCACATTCATGTATGCACAAAAA 60.016 34.615 11.83 0.00 39.39 1.94
2127 2195 0.248843 TGCACGCATACATCTCCACA 59.751 50.000 0.00 0.00 0.00 4.17
2187 2255 4.283467 CCGGATAGATATGAACCCACTTCA 59.717 45.833 0.00 0.00 43.28 3.02
2188 2256 4.527038 TCCGGATAGATATGAACCCACTTC 59.473 45.833 0.00 0.00 0.00 3.01
2215 2283 8.314021 GGGTCAAATCTAAGAAAACAAATGGAT 58.686 33.333 0.00 0.00 0.00 3.41
2221 2289 6.836527 TCCTTGGGTCAAATCTAAGAAAACAA 59.163 34.615 0.00 0.00 0.00 2.83
2223 2291 6.264518 TGTCCTTGGGTCAAATCTAAGAAAAC 59.735 38.462 0.00 0.00 0.00 2.43
2229 2297 5.878116 CGTATTGTCCTTGGGTCAAATCTAA 59.122 40.000 1.05 0.00 34.81 2.10
2231 2299 4.261801 CGTATTGTCCTTGGGTCAAATCT 58.738 43.478 1.05 0.00 34.81 2.40
2249 2318 5.831525 TGTCCAACACATCCTATCTACGTAT 59.168 40.000 0.00 0.00 0.00 3.06
2259 2328 3.260884 ACGAAGTATGTCCAACACATCCT 59.739 43.478 0.00 0.00 42.62 3.24
2260 2329 3.370978 CACGAAGTATGTCCAACACATCC 59.629 47.826 0.00 0.00 45.23 3.51
2261 2330 4.242475 TCACGAAGTATGTCCAACACATC 58.758 43.478 0.00 0.00 45.23 3.06
2266 2335 2.000447 GCCTCACGAAGTATGTCCAAC 59.000 52.381 0.00 0.00 41.61 3.77
2276 2345 2.922758 GCGACATATAGGCCTCACGAAG 60.923 54.545 9.68 0.00 0.00 3.79
2281 2352 1.324383 TTCGCGACATATAGGCCTCA 58.676 50.000 9.68 0.00 0.00 3.86
2332 2403 5.346522 ACCTCTTTAGTACTTATTTCGCGG 58.653 41.667 6.13 0.00 0.00 6.46
2333 2404 6.416161 GGTACCTCTTTAGTACTTATTTCGCG 59.584 42.308 4.06 0.00 40.01 5.87
2334 2405 7.691430 GGTACCTCTTTAGTACTTATTTCGC 57.309 40.000 4.06 0.00 40.01 4.70
2360 2431 4.524328 AGAAAGTTGGATGGCCTTTGTAAG 59.476 41.667 3.32 0.00 34.31 2.34
2361 2432 4.280677 CAGAAAGTTGGATGGCCTTTGTAA 59.719 41.667 3.32 0.00 34.31 2.41
2362 2433 3.826157 CAGAAAGTTGGATGGCCTTTGTA 59.174 43.478 3.32 0.00 34.31 2.41
2363 2434 2.629617 CAGAAAGTTGGATGGCCTTTGT 59.370 45.455 3.32 0.00 34.31 2.83
2364 2435 2.629617 ACAGAAAGTTGGATGGCCTTTG 59.370 45.455 3.32 0.00 34.31 2.77
2365 2436 2.629617 CACAGAAAGTTGGATGGCCTTT 59.370 45.455 3.32 0.00 34.31 3.11
2366 2437 2.158475 TCACAGAAAGTTGGATGGCCTT 60.158 45.455 3.32 0.00 34.31 4.35
2367 2438 1.425066 TCACAGAAAGTTGGATGGCCT 59.575 47.619 3.32 0.00 34.31 5.19
2368 2439 1.909700 TCACAGAAAGTTGGATGGCC 58.090 50.000 0.00 0.00 0.00 5.36
2369 2440 2.821969 ACATCACAGAAAGTTGGATGGC 59.178 45.455 0.00 0.00 39.63 4.40
2370 2441 3.366679 GCACATCACAGAAAGTTGGATGG 60.367 47.826 0.00 0.00 39.63 3.51
2371 2442 3.668757 CGCACATCACAGAAAGTTGGATG 60.669 47.826 0.00 0.00 40.78 3.51
2372 2443 2.485426 CGCACATCACAGAAAGTTGGAT 59.515 45.455 0.00 0.00 0.00 3.41
2373 2444 1.872952 CGCACATCACAGAAAGTTGGA 59.127 47.619 0.00 0.00 0.00 3.53
2374 2445 1.664016 GCGCACATCACAGAAAGTTGG 60.664 52.381 0.30 0.00 0.00 3.77
2375 2446 1.664016 GGCGCACATCACAGAAAGTTG 60.664 52.381 10.83 0.00 0.00 3.16
2376 2447 0.593128 GGCGCACATCACAGAAAGTT 59.407 50.000 10.83 0.00 0.00 2.66
2377 2448 0.534877 TGGCGCACATCACAGAAAGT 60.535 50.000 10.83 0.00 0.00 2.66
2378 2449 0.110056 GTGGCGCACATCACAGAAAG 60.110 55.000 10.83 0.00 34.08 2.62
2379 2450 0.534877 AGTGGCGCACATCACAGAAA 60.535 50.000 10.83 0.00 36.74 2.52
2380 2451 0.534877 AAGTGGCGCACATCACAGAA 60.535 50.000 10.83 0.00 36.74 3.02
2381 2452 1.071299 AAGTGGCGCACATCACAGA 59.929 52.632 10.83 0.00 36.74 3.41
2382 2453 1.208358 CAAGTGGCGCACATCACAG 59.792 57.895 10.83 1.21 36.74 3.66
2383 2454 1.100463 AACAAGTGGCGCACATCACA 61.100 50.000 10.83 0.00 36.74 3.58
2384 2455 0.661187 CAACAAGTGGCGCACATCAC 60.661 55.000 10.83 8.22 36.74 3.06
2385 2456 1.653667 CAACAAGTGGCGCACATCA 59.346 52.632 10.83 0.00 36.74 3.07
2386 2457 1.730547 GCAACAAGTGGCGCACATC 60.731 57.895 10.83 0.00 36.74 3.06
2387 2458 2.014064 TTGCAACAAGTGGCGCACAT 62.014 50.000 10.83 0.00 36.74 3.21
2388 2459 2.218037 TTTGCAACAAGTGGCGCACA 62.218 50.000 10.83 1.22 36.74 4.57
2389 2460 1.518133 TTTGCAACAAGTGGCGCAC 60.518 52.632 10.83 5.73 33.29 5.34
2390 2461 1.518133 GTTTGCAACAAGTGGCGCA 60.518 52.632 10.83 0.00 0.00 6.09
2391 2462 1.481819 CTGTTTGCAACAAGTGGCGC 61.482 55.000 0.00 0.00 41.61 6.53
2392 2463 0.100325 TCTGTTTGCAACAAGTGGCG 59.900 50.000 0.00 0.00 41.61 5.69
2393 2464 1.134946 ACTCTGTTTGCAACAAGTGGC 59.865 47.619 0.00 0.00 41.61 5.01
2394 2465 2.164219 ACACTCTGTTTGCAACAAGTGG 59.836 45.455 25.19 16.29 44.89 4.00
2395 2466 3.492421 ACACTCTGTTTGCAACAAGTG 57.508 42.857 23.04 23.04 45.41 3.16
2446 2517 9.221775 GCACGGTTCTATAGATAAAATGTTTTG 57.778 33.333 2.58 0.00 0.00 2.44
2447 2518 8.120465 CGCACGGTTCTATAGATAAAATGTTTT 58.880 33.333 2.58 0.00 0.00 2.43
2448 2519 7.254658 CCGCACGGTTCTATAGATAAAATGTTT 60.255 37.037 2.58 0.00 0.00 2.83
2449 2520 6.202188 CCGCACGGTTCTATAGATAAAATGTT 59.798 38.462 2.58 0.00 0.00 2.71
2450 2521 5.694910 CCGCACGGTTCTATAGATAAAATGT 59.305 40.000 2.58 0.00 0.00 2.71
2451 2522 5.389516 GCCGCACGGTTCTATAGATAAAATG 60.390 44.000 11.27 0.82 37.65 2.32
2452 2523 4.689345 GCCGCACGGTTCTATAGATAAAAT 59.311 41.667 11.27 0.00 37.65 1.82
2453 2524 4.053295 GCCGCACGGTTCTATAGATAAAA 58.947 43.478 11.27 0.00 37.65 1.52
2454 2525 3.553508 GGCCGCACGGTTCTATAGATAAA 60.554 47.826 11.27 0.00 37.65 1.40
2455 2526 2.029649 GGCCGCACGGTTCTATAGATAA 60.030 50.000 11.27 0.00 37.65 1.75
2456 2527 1.542915 GGCCGCACGGTTCTATAGATA 59.457 52.381 11.27 0.00 37.65 1.98
2457 2528 0.317479 GGCCGCACGGTTCTATAGAT 59.683 55.000 11.27 0.00 37.65 1.98
2458 2529 1.737816 GGCCGCACGGTTCTATAGA 59.262 57.895 11.27 0.00 37.65 1.98
2459 2530 1.660575 CGGCCGCACGGTTCTATAG 60.661 63.158 14.67 0.00 37.65 1.31
2460 2531 1.665264 TTCGGCCGCACGGTTCTATA 61.665 55.000 23.51 0.00 37.65 1.31
2461 2532 3.009192 TTCGGCCGCACGGTTCTAT 62.009 57.895 23.51 0.00 37.65 1.98
2462 2533 3.682885 TTCGGCCGCACGGTTCTA 61.683 61.111 23.51 0.00 37.65 2.10


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

AutoCloner maintained by Alex Coulton.