Multiple sequence alignment - TraesCS5A01G125300

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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 TraesCS5A01G125300 chr5A 100.000 2495 0 0 1 2495 275261345 275258851 0.000000e+00 4608.0
1 TraesCS5A01G125300 chr5A 88.768 276 28 2 1707 1980 520224600 520224874 3.980000e-88 335.0
2 TraesCS5A01G125300 chr5A 87.500 296 30 5 1708 1998 671411958 671412251 3.980000e-88 335.0
3 TraesCS5A01G125300 chr5A 88.519 270 28 2 1713 1980 367334797 367334529 8.610000e-85 324.0
4 TraesCS5A01G125300 chr5A 96.970 33 1 0 1683 1715 307205028 307205060 3.470000e-04 56.5
5 TraesCS5A01G125300 chr5D 97.804 1548 31 3 134 1680 212253186 212251641 0.000000e+00 2667.0
6 TraesCS5A01G125300 chr5D 87.595 524 48 12 1981 2495 212251643 212251128 2.140000e-165 592.0
7 TraesCS5A01G125300 chr5D 96.667 60 2 0 1 60 212253262 212253203 1.580000e-17 100.0
8 TraesCS5A01G125300 chr6B 78.488 1111 199 21 404 1497 719386592 719387679 0.000000e+00 691.0
9 TraesCS5A01G125300 chr6B 94.545 55 1 2 61 114 46512043 46511990 1.590000e-12 84.2
10 TraesCS5A01G125300 chr7B 77.708 1108 217 20 404 1496 154144525 154145617 0.000000e+00 651.0
11 TraesCS5A01G125300 chr7B 100.000 45 0 0 69 113 709484046 709484090 1.590000e-12 84.2
12 TraesCS5A01G125300 chr7A 78.384 990 187 18 519 1496 191660726 191661700 3.530000e-173 617.0
13 TraesCS5A01G125300 chr7A 95.918 49 1 1 65 112 272586485 272586533 7.400000e-11 78.7
14 TraesCS5A01G125300 chr7A 94.231 52 1 2 61 111 724154920 724154970 7.400000e-11 78.7
15 TraesCS5A01G125300 chr4A 90.182 275 25 1 1708 1980 514989611 514989337 8.490000e-95 357.0
16 TraesCS5A01G125300 chr3A 88.809 277 28 2 1707 1981 216734958 216734683 1.110000e-88 337.0
17 TraesCS5A01G125300 chr3A 89.591 269 20 4 1713 1979 711114844 711114582 3.980000e-88 335.0
18 TraesCS5A01G125300 chr3A 88.727 275 28 2 1709 1980 11288468 11288194 1.430000e-87 333.0
19 TraesCS5A01G125300 chr6A 88.530 279 29 2 1705 1980 578692460 578692738 3.980000e-88 335.0
20 TraesCS5A01G125300 chr6A 84.585 253 25 7 1729 1979 457664908 457664668 3.210000e-59 239.0
21 TraesCS5A01G125300 chr6A 100.000 29 0 0 1689 1717 608339291 608339319 1.000000e-03 54.7
22 TraesCS5A01G125300 chr1A 88.971 272 28 1 1708 1977 388739353 388739082 3.980000e-88 335.0
23 TraesCS5A01G125300 chr1A 91.304 115 8 2 2382 2495 505557577 505557690 3.320000e-34 156.0
24 TraesCS5A01G125300 chr2B 82.490 257 29 8 2153 2400 404182496 404182247 6.990000e-51 211.0
25 TraesCS5A01G125300 chr2B 93.860 114 6 1 2382 2495 697769691 697769579 1.190000e-38 171.0
26 TraesCS5A01G125300 chr2B 92.035 113 9 0 2383 2495 397605807 397605695 2.570000e-35 159.0
27 TraesCS5A01G125300 chr2B 91.964 112 7 2 2384 2495 767467130 767467239 3.320000e-34 156.0
28 TraesCS5A01G125300 chr2B 100.000 46 0 0 69 114 494858609 494858654 4.420000e-13 86.1
29 TraesCS5A01G125300 chr5B 94.286 105 5 1 2391 2495 51865061 51864958 2.570000e-35 159.0
30 TraesCS5A01G125300 chr5B 92.035 113 8 1 1981 2093 226331444 226331333 9.240000e-35 158.0
31 TraesCS5A01G125300 chr5B 90.164 122 9 3 2375 2495 51626660 51626541 3.320000e-34 156.0
32 TraesCS5A01G125300 chr4B 93.458 107 7 0 2388 2494 421705515 421705409 2.570000e-35 159.0
33 TraesCS5A01G125300 chr4B 92.105 114 8 1 2382 2495 667421596 667421484 2.570000e-35 159.0
34 TraesCS5A01G125300 chrUn 100.000 45 0 0 69 113 325795872 325795828 1.590000e-12 84.2
35 TraesCS5A01G125300 chr2D 96.154 52 0 2 61 111 607606613 607606563 1.590000e-12 84.2
36 TraesCS5A01G125300 chr6D 97.872 47 1 0 69 115 405193857 405193811 5.720000e-12 82.4
37 TraesCS5A01G125300 chr7D 92.727 55 4 0 69 123 59107643 59107697 2.060000e-11 80.5
38 TraesCS5A01G125300 chr7D 100.000 29 0 0 1689 1717 70361688 70361660 1.000000e-03 54.7
39 TraesCS5A01G125300 chr3D 100.000 31 0 0 1689 1719 416135017 416134987 9.640000e-05 58.4
40 TraesCS5A01G125300 chr3B 100.000 29 0 0 1689 1717 16041266 16041238 1.000000e-03 54.7


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 TraesCS5A01G125300 chr5A 275258851 275261345 2494 True 4608.000000 4608 100.000 1 2495 1 chr5A.!!$R1 2494
1 TraesCS5A01G125300 chr5D 212251128 212253262 2134 True 1119.666667 2667 94.022 1 2495 3 chr5D.!!$R1 2494
2 TraesCS5A01G125300 chr6B 719386592 719387679 1087 False 691.000000 691 78.488 404 1497 1 chr6B.!!$F1 1093
3 TraesCS5A01G125300 chr7B 154144525 154145617 1092 False 651.000000 651 77.708 404 1496 1 chr7B.!!$F1 1092
4 TraesCS5A01G125300 chr7A 191660726 191661700 974 False 617.000000 617 78.384 519 1496 1 chr7A.!!$F1 977

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
26 27 0.104855 GCTGCTATGATCCCGACACA 59.895 55.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1813 0.106669 GCCGGGCCTCTTCCTTAAAT 60.107 55.0 8.12 0.0 0.0 1.4 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
26 27 0.104855 GCTGCTATGATCCCGACACA 59.895 55.000 0.00 0.00 0.00 3.72
87 88 9.277565 CACTTTAATACATTCATTTCTTGGACG 57.722 33.333 0.00 0.00 0.00 4.79
88 89 9.226606 ACTTTAATACATTCATTTCTTGGACGA 57.773 29.630 0.00 0.00 0.00 4.20
89 90 9.708222 CTTTAATACATTCATTTCTTGGACGAG 57.292 33.333 0.00 0.00 0.00 4.18
90 91 8.786826 TTAATACATTCATTTCTTGGACGAGT 57.213 30.769 0.00 0.00 0.00 4.18
91 92 9.878667 TTAATACATTCATTTCTTGGACGAGTA 57.121 29.630 0.00 0.00 0.00 2.59
92 93 8.786826 AATACATTCATTTCTTGGACGAGTAA 57.213 30.769 0.00 0.00 0.00 2.24
93 94 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
94 95 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
95 96 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
96 97 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
97 98 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
98 99 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
99 100 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
100 101 3.841643 TCTTGGACGAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
101 102 2.267188 TGGACGAGTAATTCCGAACG 57.733 50.000 0.00 0.00 0.00 3.95
102 103 1.811965 TGGACGAGTAATTCCGAACGA 59.188 47.619 0.00 0.00 0.00 3.85
103 104 2.228582 TGGACGAGTAATTCCGAACGAA 59.771 45.455 0.00 0.00 34.14 3.85
104 105 2.850647 GGACGAGTAATTCCGAACGAAG 59.149 50.000 0.00 0.00 32.78 3.79
105 106 2.850647 GACGAGTAATTCCGAACGAAGG 59.149 50.000 0.00 0.00 32.78 3.46
106 107 2.190981 CGAGTAATTCCGAACGAAGGG 58.809 52.381 0.00 0.00 32.78 3.95
107 108 2.159338 CGAGTAATTCCGAACGAAGGGA 60.159 50.000 0.00 0.00 32.78 4.20
108 109 3.445857 GAGTAATTCCGAACGAAGGGAG 58.554 50.000 0.00 0.00 32.78 4.30
109 110 2.830321 AGTAATTCCGAACGAAGGGAGT 59.170 45.455 0.00 0.00 32.78 3.85
110 111 4.019174 AGTAATTCCGAACGAAGGGAGTA 58.981 43.478 0.00 0.00 32.78 2.59
111 112 3.521947 AATTCCGAACGAAGGGAGTAG 57.478 47.619 0.00 0.00 32.78 2.57
112 113 2.205022 TTCCGAACGAAGGGAGTAGA 57.795 50.000 0.00 0.00 33.01 2.59
113 114 2.431954 TCCGAACGAAGGGAGTAGAT 57.568 50.000 0.00 0.00 0.00 1.98
114 115 2.295885 TCCGAACGAAGGGAGTAGATC 58.704 52.381 0.00 0.00 0.00 2.75
115 116 5.766960 ATTCCGAACGAAGGGAGTAGATCC 61.767 50.000 0.00 0.00 38.78 3.36
122 123 4.076244 GGAGTAGATCCCGCGCTA 57.924 61.111 5.56 0.00 43.01 4.26
123 124 1.580437 GGAGTAGATCCCGCGCTAC 59.420 63.158 5.56 12.08 43.01 3.58
124 125 1.580437 GAGTAGATCCCGCGCTACC 59.420 63.158 15.21 6.30 38.14 3.18
125 126 2.185103 GAGTAGATCCCGCGCTACCG 62.185 65.000 15.21 0.00 38.14 4.02
126 127 2.111669 TAGATCCCGCGCTACCGA 59.888 61.111 5.56 0.00 36.29 4.69
127 128 1.303074 TAGATCCCGCGCTACCGAT 60.303 57.895 5.56 0.00 36.29 4.18
128 129 1.583495 TAGATCCCGCGCTACCGATG 61.583 60.000 5.56 0.00 36.29 3.84
129 130 4.664677 ATCCCGCGCTACCGATGC 62.665 66.667 5.56 0.00 36.29 3.91
140 141 2.265467 TACCGATGCCCCTTTGAGCC 62.265 60.000 0.00 0.00 0.00 4.70
166 167 9.273016 CACAGTTATTTCCGGATACTGAATTAT 57.727 33.333 28.48 13.25 39.68 1.28
201 202 0.110238 CAAACGATCCACAGTTGCGG 60.110 55.000 0.00 0.00 0.00 5.69
219 220 1.578206 GGCCGTCTGGAAACAAGCTC 61.578 60.000 0.00 0.00 42.06 4.09
358 359 3.073678 TCTTCAAACGACATGGTCATGG 58.926 45.455 14.49 1.64 42.91 3.66
376 377 2.415010 CTCCAGCTCCCGACATCG 59.585 66.667 0.00 0.00 39.44 3.84
1072 1088 2.707849 AACATCGGCGGCTACGTCT 61.708 57.895 7.21 0.00 43.91 4.18
1508 1524 7.601073 TCAGTTGCTGATAGTTATGTTGAAG 57.399 36.000 0.00 0.00 35.39 3.02
1677 1694 3.493129 TGTGTTTACGCAAGAACTAGCTG 59.507 43.478 0.00 0.00 43.62 4.24
1678 1695 2.478894 TGTTTACGCAAGAACTAGCTGC 59.521 45.455 0.00 0.00 43.62 5.25
1679 1696 2.737252 GTTTACGCAAGAACTAGCTGCT 59.263 45.455 7.57 7.57 43.62 4.24
1680 1697 3.861276 TTACGCAAGAACTAGCTGCTA 57.139 42.857 9.34 9.34 43.62 3.49
1681 1698 1.997669 ACGCAAGAACTAGCTGCTAC 58.002 50.000 5.02 0.00 43.62 3.58
1682 1699 1.546476 ACGCAAGAACTAGCTGCTACT 59.454 47.619 5.02 0.00 43.62 2.57
1683 1700 1.923204 CGCAAGAACTAGCTGCTACTG 59.077 52.381 5.02 0.00 43.02 2.74
1684 1701 1.663135 GCAAGAACTAGCTGCTACTGC 59.337 52.381 5.02 6.29 40.20 4.40
1685 1702 1.923204 CAAGAACTAGCTGCTACTGCG 59.077 52.381 5.02 0.00 43.34 5.18
1686 1703 1.464734 AGAACTAGCTGCTACTGCGA 58.535 50.000 5.02 0.00 43.34 5.10
1687 1704 2.028130 AGAACTAGCTGCTACTGCGAT 58.972 47.619 5.02 0.00 43.34 4.58
1688 1705 2.428890 AGAACTAGCTGCTACTGCGATT 59.571 45.455 5.02 0.00 43.34 3.34
1689 1706 3.632604 AGAACTAGCTGCTACTGCGATTA 59.367 43.478 5.02 0.00 43.34 1.75
1690 1707 3.634568 ACTAGCTGCTACTGCGATTAG 57.365 47.619 5.02 0.00 43.34 1.73
1691 1708 2.952978 ACTAGCTGCTACTGCGATTAGT 59.047 45.455 5.02 0.00 43.34 2.24
1692 1709 2.500509 AGCTGCTACTGCGATTAGTC 57.499 50.000 0.00 0.00 43.34 2.59
1693 1710 1.067821 AGCTGCTACTGCGATTAGTCC 59.932 52.381 0.00 0.00 43.34 3.85
1694 1711 1.067821 GCTGCTACTGCGATTAGTCCT 59.932 52.381 0.00 0.00 43.34 3.85
1695 1712 2.736978 CTGCTACTGCGATTAGTCCTG 58.263 52.381 0.00 0.00 43.34 3.86
1696 1713 1.409064 TGCTACTGCGATTAGTCCTGG 59.591 52.381 0.00 0.00 43.34 4.45
1697 1714 1.870167 GCTACTGCGATTAGTCCTGGC 60.870 57.143 0.00 0.00 32.19 4.85
1698 1715 0.750850 TACTGCGATTAGTCCTGGCC 59.249 55.000 0.00 0.00 32.19 5.36
1699 1716 1.264749 ACTGCGATTAGTCCTGGCCA 61.265 55.000 4.71 4.71 0.00 5.36
1700 1717 0.107456 CTGCGATTAGTCCTGGCCAT 59.893 55.000 5.51 0.00 0.00 4.40
1701 1718 0.179048 TGCGATTAGTCCTGGCCATG 60.179 55.000 5.51 2.84 0.00 3.66
1702 1719 0.886490 GCGATTAGTCCTGGCCATGG 60.886 60.000 5.51 7.63 0.00 3.66
1703 1720 0.250467 CGATTAGTCCTGGCCATGGG 60.250 60.000 15.13 4.96 0.00 4.00
1721 1738 4.760047 CAGCCCGACCCGACCTTG 62.760 72.222 0.00 0.00 0.00 3.61
1723 1740 4.754667 GCCCGACCCGACCTTGTC 62.755 72.222 0.00 0.00 0.00 3.18
1724 1741 4.078516 CCCGACCCGACCTTGTCC 62.079 72.222 0.00 0.00 0.00 4.02
1725 1742 3.307906 CCGACCCGACCTTGTCCA 61.308 66.667 0.00 0.00 0.00 4.02
1726 1743 2.656069 CCGACCCGACCTTGTCCAT 61.656 63.158 0.00 0.00 0.00 3.41
1727 1744 1.153628 CGACCCGACCTTGTCCATC 60.154 63.158 0.00 0.00 0.00 3.51
1728 1745 1.221021 GACCCGACCTTGTCCATCC 59.779 63.158 0.00 0.00 0.00 3.51
1729 1746 2.253403 GACCCGACCTTGTCCATCCC 62.253 65.000 0.00 0.00 0.00 3.85
1730 1747 2.186903 CCGACCTTGTCCATCCCG 59.813 66.667 0.00 0.00 0.00 5.14
1731 1748 2.186903 CGACCTTGTCCATCCCGG 59.813 66.667 0.00 0.00 0.00 5.73
1732 1749 2.590092 GACCTTGTCCATCCCGGG 59.410 66.667 16.85 16.85 34.36 5.73
1733 1750 3.699134 GACCTTGTCCATCCCGGGC 62.699 68.421 18.49 0.73 41.21 6.13
1734 1751 3.411517 CCTTGTCCATCCCGGGCT 61.412 66.667 18.49 1.75 41.50 5.19
1735 1752 2.190578 CTTGTCCATCCCGGGCTC 59.809 66.667 18.49 4.40 41.50 4.70
1736 1753 3.740128 CTTGTCCATCCCGGGCTCG 62.740 68.421 18.49 0.00 41.50 5.03
1749 1766 3.905249 GCTCGGGCCTAGGTTTTG 58.095 61.111 11.31 0.00 0.00 2.44
1750 1767 1.298667 GCTCGGGCCTAGGTTTTGA 59.701 57.895 11.31 2.96 0.00 2.69
1751 1768 0.744771 GCTCGGGCCTAGGTTTTGAG 60.745 60.000 11.31 13.25 0.00 3.02
1752 1769 0.744771 CTCGGGCCTAGGTTTTGAGC 60.745 60.000 11.31 0.00 0.00 4.26
1753 1770 1.749258 CGGGCCTAGGTTTTGAGCC 60.749 63.158 11.31 2.81 43.09 4.70
1754 1771 4.338815 GGCCTAGGTTTTGAGCCC 57.661 61.111 11.31 0.00 37.66 5.19
1755 1772 1.382629 GGCCTAGGTTTTGAGCCCA 59.617 57.895 11.31 0.00 37.66 5.36
1756 1773 0.251608 GGCCTAGGTTTTGAGCCCAA 60.252 55.000 11.31 0.00 37.66 4.12
1757 1774 1.627864 GCCTAGGTTTTGAGCCCAAA 58.372 50.000 11.31 0.00 40.24 3.28
1758 1775 1.546029 GCCTAGGTTTTGAGCCCAAAG 59.454 52.381 11.31 0.00 42.55 2.77
1759 1776 1.546029 CCTAGGTTTTGAGCCCAAAGC 59.454 52.381 0.00 0.00 42.55 3.51
1762 1779 1.006220 GTTTTGAGCCCAAAGCCCG 60.006 57.895 0.00 0.00 45.47 6.13
1763 1780 2.206536 TTTTGAGCCCAAAGCCCGG 61.207 57.895 0.00 0.00 45.47 5.73
1790 1807 3.782443 GGTCTGGGCCCGTCGATT 61.782 66.667 19.37 0.00 0.00 3.34
1791 1808 2.267961 GTCTGGGCCCGTCGATTT 59.732 61.111 19.37 0.00 0.00 2.17
1792 1809 1.814169 GTCTGGGCCCGTCGATTTC 60.814 63.158 19.37 0.00 0.00 2.17
1793 1810 2.890474 CTGGGCCCGTCGATTTCG 60.890 66.667 19.37 0.00 41.45 3.46
1794 1811 3.659089 CTGGGCCCGTCGATTTCGT 62.659 63.158 19.37 0.00 40.80 3.85
1795 1812 2.889018 GGGCCCGTCGATTTCGTC 60.889 66.667 5.69 0.00 40.80 4.20
1796 1813 2.125832 GGCCCGTCGATTTCGTCA 60.126 61.111 0.00 0.00 40.80 4.35
1797 1814 1.520787 GGCCCGTCGATTTCGTCAT 60.521 57.895 0.00 0.00 40.80 3.06
1798 1815 1.087771 GGCCCGTCGATTTCGTCATT 61.088 55.000 0.00 0.00 40.80 2.57
1799 1816 0.725117 GCCCGTCGATTTCGTCATTT 59.275 50.000 0.00 0.00 40.80 2.32
1800 1817 1.928503 GCCCGTCGATTTCGTCATTTA 59.071 47.619 0.00 0.00 40.80 1.40
1801 1818 2.349275 GCCCGTCGATTTCGTCATTTAA 59.651 45.455 0.00 0.00 40.80 1.52
1802 1819 3.543460 GCCCGTCGATTTCGTCATTTAAG 60.543 47.826 0.00 0.00 40.80 1.85
1803 1820 3.000925 CCCGTCGATTTCGTCATTTAAGG 59.999 47.826 0.00 0.00 40.80 2.69
1804 1821 3.861113 CCGTCGATTTCGTCATTTAAGGA 59.139 43.478 0.00 0.00 40.80 3.36
1805 1822 4.327898 CCGTCGATTTCGTCATTTAAGGAA 59.672 41.667 0.00 0.00 40.80 3.36
1806 1823 5.481472 CGTCGATTTCGTCATTTAAGGAAG 58.519 41.667 0.00 0.00 40.80 3.46
1807 1824 5.287752 CGTCGATTTCGTCATTTAAGGAAGA 59.712 40.000 0.00 0.00 40.80 2.87
1808 1825 6.506513 CGTCGATTTCGTCATTTAAGGAAGAG 60.507 42.308 0.00 0.00 40.80 2.85
1809 1826 5.810587 TCGATTTCGTCATTTAAGGAAGAGG 59.189 40.000 0.00 0.00 40.80 3.69
1810 1827 5.502544 CGATTTCGTCATTTAAGGAAGAGGC 60.503 44.000 0.00 0.00 34.11 4.70
1811 1828 3.261981 TCGTCATTTAAGGAAGAGGCC 57.738 47.619 0.00 0.00 0.00 5.19
1812 1829 2.093128 TCGTCATTTAAGGAAGAGGCCC 60.093 50.000 0.00 0.00 0.00 5.80
1813 1830 2.289565 GTCATTTAAGGAAGAGGCCCG 58.710 52.381 0.00 0.00 0.00 6.13
1814 1831 1.211949 TCATTTAAGGAAGAGGCCCGG 59.788 52.381 0.00 0.00 0.00 5.73
1815 1832 0.106669 ATTTAAGGAAGAGGCCCGGC 60.107 55.000 0.00 0.00 0.00 6.13
1841 1858 4.692475 CGAGGCCCGACGGGTTTT 62.692 66.667 32.76 18.91 46.51 2.43
1842 1859 2.281970 GAGGCCCGACGGGTTTTT 60.282 61.111 32.76 16.41 46.51 1.94
1843 1860 1.003476 GAGGCCCGACGGGTTTTTA 60.003 57.895 32.76 0.00 46.51 1.52
1844 1861 1.002990 AGGCCCGACGGGTTTTTAG 60.003 57.895 32.76 7.25 46.51 1.85
1845 1862 1.302752 GGCCCGACGGGTTTTTAGT 60.303 57.895 32.76 0.00 46.51 2.24
1846 1863 1.579964 GGCCCGACGGGTTTTTAGTG 61.580 60.000 32.76 5.70 46.51 2.74
1847 1864 0.886043 GCCCGACGGGTTTTTAGTGT 60.886 55.000 32.76 0.00 46.51 3.55
1848 1865 0.869730 CCCGACGGGTTTTTAGTGTG 59.130 55.000 25.54 0.00 38.25 3.82
1849 1866 1.540797 CCCGACGGGTTTTTAGTGTGA 60.541 52.381 25.54 0.00 38.25 3.58
1850 1867 2.419667 CCGACGGGTTTTTAGTGTGAT 58.580 47.619 5.81 0.00 0.00 3.06
1851 1868 2.158841 CCGACGGGTTTTTAGTGTGATG 59.841 50.000 5.81 0.00 0.00 3.07
1852 1869 3.061322 CGACGGGTTTTTAGTGTGATGA 58.939 45.455 0.00 0.00 0.00 2.92
1853 1870 3.122948 CGACGGGTTTTTAGTGTGATGAG 59.877 47.826 0.00 0.00 0.00 2.90
1854 1871 2.812011 ACGGGTTTTTAGTGTGATGAGC 59.188 45.455 0.00 0.00 0.00 4.26
1855 1872 2.161609 CGGGTTTTTAGTGTGATGAGCC 59.838 50.000 0.00 0.00 0.00 4.70
1856 1873 2.161609 GGGTTTTTAGTGTGATGAGCCG 59.838 50.000 0.00 0.00 0.00 5.52
1857 1874 2.161609 GGTTTTTAGTGTGATGAGCCGG 59.838 50.000 0.00 0.00 0.00 6.13
1858 1875 2.107950 TTTTAGTGTGATGAGCCGGG 57.892 50.000 2.18 0.00 0.00 5.73
1859 1876 0.392461 TTTAGTGTGATGAGCCGGGC 60.392 55.000 12.11 12.11 0.00 6.13
1860 1877 1.264749 TTAGTGTGATGAGCCGGGCT 61.265 55.000 24.13 24.13 43.88 5.19
1877 1894 4.968370 TCGGGCCCGATTTTTAGG 57.032 55.556 42.66 12.44 44.01 2.69
1878 1895 1.452470 TCGGGCCCGATTTTTAGGC 60.452 57.895 42.66 0.00 44.01 3.93
1879 1896 1.453197 CGGGCCCGATTTTTAGGCT 60.453 57.895 41.82 0.00 46.31 4.58
1880 1897 1.035385 CGGGCCCGATTTTTAGGCTT 61.035 55.000 41.82 0.00 46.31 4.35
1881 1898 0.459899 GGGCCCGATTTTTAGGCTTG 59.540 55.000 5.69 0.00 46.31 4.01
1882 1899 1.470051 GGCCCGATTTTTAGGCTTGA 58.530 50.000 0.00 0.00 46.31 3.02
1883 1900 1.134367 GGCCCGATTTTTAGGCTTGAC 59.866 52.381 0.00 0.00 46.31 3.18
1884 1901 1.202143 GCCCGATTTTTAGGCTTGACG 60.202 52.381 0.00 0.00 43.62 4.35
1885 1902 1.202143 CCCGATTTTTAGGCTTGACGC 60.202 52.381 0.00 0.00 38.13 5.19
1914 1931 3.764466 CGAGCTCGAGCCTGGGTT 61.764 66.667 32.94 14.37 43.38 4.11
1915 1932 2.665603 GAGCTCGAGCCTGGGTTT 59.334 61.111 32.94 13.56 43.38 3.27
1916 1933 1.003233 GAGCTCGAGCCTGGGTTTT 60.003 57.895 32.94 12.74 43.38 2.43
1917 1934 0.606673 GAGCTCGAGCCTGGGTTTTT 60.607 55.000 32.94 11.94 43.38 1.94
1931 1948 4.719997 TTTTTGCGTCGGGCTTTG 57.280 50.000 0.00 0.00 44.05 2.77
1932 1949 1.066587 TTTTTGCGTCGGGCTTTGG 59.933 52.632 0.00 0.00 44.05 3.28
1933 1950 1.668101 TTTTTGCGTCGGGCTTTGGT 61.668 50.000 0.00 0.00 44.05 3.67
1934 1951 1.668101 TTTTGCGTCGGGCTTTGGTT 61.668 50.000 0.00 0.00 44.05 3.67
1935 1952 2.343163 TTTGCGTCGGGCTTTGGTTG 62.343 55.000 0.00 0.00 44.05 3.77
1936 1953 4.038080 GCGTCGGGCTTTGGTTGG 62.038 66.667 0.00 0.00 39.11 3.77
1937 1954 4.038080 CGTCGGGCTTTGGTTGGC 62.038 66.667 0.00 0.00 0.00 4.52
1938 1955 3.680786 GTCGGGCTTTGGTTGGCC 61.681 66.667 0.00 0.00 46.89 5.36
1969 1986 2.830370 GGCCCGGCCTGAGAAATG 60.830 66.667 22.31 0.00 46.69 2.32
1970 1987 2.830370 GCCCGGCCTGAGAAATGG 60.830 66.667 0.00 0.00 0.00 3.16
1976 1993 1.000396 GCCTGAGAAATGGCCAGGT 60.000 57.895 13.05 0.00 46.86 4.00
1977 1994 0.255890 GCCTGAGAAATGGCCAGGTA 59.744 55.000 13.05 0.00 46.86 3.08
1978 1995 1.133668 GCCTGAGAAATGGCCAGGTAT 60.134 52.381 13.05 0.00 46.86 2.73
1979 1996 2.106511 GCCTGAGAAATGGCCAGGTATA 59.893 50.000 13.05 0.00 46.86 1.47
1987 2004 1.128200 TGGCCAGGTATAACTGCGAT 58.872 50.000 12.62 0.00 37.16 4.58
2033 2050 8.212317 TGGTTGATGTTGAAGATATGTATGTG 57.788 34.615 0.00 0.00 0.00 3.21
2059 2076 8.611757 GTTCCTTTTGATTTGCAAACTTTATGT 58.388 29.630 15.41 0.00 45.64 2.29
2071 2088 7.721402 TGCAAACTTTATGTAAAATGTGAGGT 58.279 30.769 0.00 0.00 0.00 3.85
2113 2164 6.321690 TCTGTAGAGATACTAAGTTCCCTTGC 59.678 42.308 0.00 0.00 32.49 4.01
2125 2176 1.138247 CCCTTGCATTGAAGCGCTC 59.862 57.895 12.06 4.99 37.31 5.03
2126 2177 1.588824 CCCTTGCATTGAAGCGCTCA 61.589 55.000 12.06 8.04 37.31 4.26
2127 2178 0.454600 CCTTGCATTGAAGCGCTCAT 59.545 50.000 12.06 0.00 37.31 2.90
2128 2179 1.545759 CTTGCATTGAAGCGCTCATG 58.454 50.000 12.06 14.82 37.31 3.07
2129 2180 0.883153 TTGCATTGAAGCGCTCATGT 59.117 45.000 12.06 0.00 37.31 3.21
2130 2181 0.169451 TGCATTGAAGCGCTCATGTG 59.831 50.000 12.06 9.45 37.31 3.21
2137 2188 3.260483 GCGCTCATGTGCTCGAGG 61.260 66.667 15.58 3.09 45.43 4.63
2138 2189 2.584418 CGCTCATGTGCTCGAGGG 60.584 66.667 15.58 0.00 36.10 4.30
2139 2190 2.581354 GCTCATGTGCTCGAGGGT 59.419 61.111 15.58 0.00 0.00 4.34
2140 2191 1.078848 GCTCATGTGCTCGAGGGTT 60.079 57.895 15.58 0.00 0.00 4.11
2141 2192 1.364626 GCTCATGTGCTCGAGGGTTG 61.365 60.000 15.58 0.00 0.00 3.77
2142 2193 0.036952 CTCATGTGCTCGAGGGTTGT 60.037 55.000 15.58 0.00 0.00 3.32
2143 2194 0.320683 TCATGTGCTCGAGGGTTGTG 60.321 55.000 15.58 0.00 0.00 3.33
2144 2195 1.003355 ATGTGCTCGAGGGTTGTGG 60.003 57.895 15.58 0.00 0.00 4.17
2145 2196 1.768684 ATGTGCTCGAGGGTTGTGGT 61.769 55.000 15.58 0.00 0.00 4.16
2146 2197 1.668151 GTGCTCGAGGGTTGTGGTC 60.668 63.158 15.58 0.00 0.00 4.02
2147 2198 2.047179 GCTCGAGGGTTGTGGTCC 60.047 66.667 15.58 0.00 0.00 4.46
2148 2199 2.663196 CTCGAGGGTTGTGGTCCC 59.337 66.667 3.91 0.00 44.90 4.46
2154 2205 3.765968 GGGTTGTGGTCCCTTGAAT 57.234 52.632 0.00 0.00 41.58 2.57
2155 2206 2.009681 GGGTTGTGGTCCCTTGAATT 57.990 50.000 0.00 0.00 41.58 2.17
2156 2207 1.618343 GGGTTGTGGTCCCTTGAATTG 59.382 52.381 0.00 0.00 41.58 2.32
2157 2208 2.593026 GGTTGTGGTCCCTTGAATTGA 58.407 47.619 0.00 0.00 0.00 2.57
2158 2209 3.165071 GGTTGTGGTCCCTTGAATTGAT 58.835 45.455 0.00 0.00 0.00 2.57
2159 2210 3.056607 GGTTGTGGTCCCTTGAATTGATG 60.057 47.826 0.00 0.00 0.00 3.07
2160 2211 3.524095 TGTGGTCCCTTGAATTGATGT 57.476 42.857 0.00 0.00 0.00 3.06
2161 2212 3.156293 TGTGGTCCCTTGAATTGATGTG 58.844 45.455 0.00 0.00 0.00 3.21
2162 2213 2.094545 GTGGTCCCTTGAATTGATGTGC 60.095 50.000 0.00 0.00 0.00 4.57
2163 2214 2.225091 TGGTCCCTTGAATTGATGTGCT 60.225 45.455 0.00 0.00 0.00 4.40
2167 2218 2.426024 CCCTTGAATTGATGTGCTCCTG 59.574 50.000 0.00 0.00 0.00 3.86
2176 2227 0.251354 ATGTGCTCCTGTGCTTCGAT 59.749 50.000 0.00 0.00 0.00 3.59
2193 2244 1.002659 CGATGGTTGTGGGGTCACTAA 59.997 52.381 0.00 0.00 43.94 2.24
2225 2277 6.915349 TGCTAAGTGTGTGTTGTTTAGTTTT 58.085 32.000 0.00 0.00 0.00 2.43
2371 2429 7.739498 AGTGGATATTTGTAAAGTTCACGTT 57.261 32.000 0.00 0.00 0.00 3.99
2389 2447 8.803799 GTTCACGTTCATTTAAAGTTTGTGAAT 58.196 29.630 19.57 3.64 43.21 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.320826 CCTGTATGTGTGTCGGGATCATA 59.679 47.826 0.00 0.00 0.00 2.15
61 62 9.277565 CGTCCAAGAAATGAATGTATTAAAGTG 57.722 33.333 0.00 0.00 0.00 3.16
64 65 9.226606 ACTCGTCCAAGAAATGAATGTATTAAA 57.773 29.630 0.00 0.00 0.00 1.52
65 66 8.786826 ACTCGTCCAAGAAATGAATGTATTAA 57.213 30.769 0.00 0.00 0.00 1.40
66 67 9.878667 TTACTCGTCCAAGAAATGAATGTATTA 57.121 29.630 0.00 0.00 0.00 0.98
67 68 8.786826 TTACTCGTCCAAGAAATGAATGTATT 57.213 30.769 0.00 0.00 0.00 1.89
68 69 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
70 71 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
71 72 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
72 73 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
73 74 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
74 75 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
75 76 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
76 77 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
77 78 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
78 79 4.240096 GTTCGGAATTACTCGTCCAAGAA 58.760 43.478 0.00 0.00 33.10 2.52
79 80 3.671433 CGTTCGGAATTACTCGTCCAAGA 60.671 47.826 0.00 0.00 33.10 3.02
80 81 2.597305 CGTTCGGAATTACTCGTCCAAG 59.403 50.000 0.00 0.00 33.10 3.61
81 82 2.228582 TCGTTCGGAATTACTCGTCCAA 59.771 45.455 0.00 0.00 33.10 3.53
82 83 1.811965 TCGTTCGGAATTACTCGTCCA 59.188 47.619 0.00 0.00 33.10 4.02
83 84 2.549633 TCGTTCGGAATTACTCGTCC 57.450 50.000 0.00 0.00 0.00 4.79
84 85 2.850647 CCTTCGTTCGGAATTACTCGTC 59.149 50.000 0.00 0.00 33.26 4.20
85 86 2.416431 CCCTTCGTTCGGAATTACTCGT 60.416 50.000 0.00 0.00 33.26 4.18
86 87 2.159338 TCCCTTCGTTCGGAATTACTCG 60.159 50.000 0.00 0.00 33.26 4.18
87 88 3.119209 ACTCCCTTCGTTCGGAATTACTC 60.119 47.826 0.00 0.00 33.26 2.59
88 89 2.830321 ACTCCCTTCGTTCGGAATTACT 59.170 45.455 0.00 0.00 33.26 2.24
89 90 3.242549 ACTCCCTTCGTTCGGAATTAC 57.757 47.619 0.00 0.00 33.26 1.89
90 91 4.272489 TCTACTCCCTTCGTTCGGAATTA 58.728 43.478 0.00 0.00 33.26 1.40
91 92 3.094572 TCTACTCCCTTCGTTCGGAATT 58.905 45.455 0.00 0.00 33.26 2.17
92 93 2.731572 TCTACTCCCTTCGTTCGGAAT 58.268 47.619 0.00 0.00 33.26 3.01
93 94 2.205022 TCTACTCCCTTCGTTCGGAA 57.795 50.000 0.00 0.00 0.00 4.30
94 95 2.295885 GATCTACTCCCTTCGTTCGGA 58.704 52.381 0.00 0.00 0.00 4.55
95 96 1.337387 GGATCTACTCCCTTCGTTCGG 59.663 57.143 0.00 0.00 38.19 4.30
96 97 2.778187 GGATCTACTCCCTTCGTTCG 57.222 55.000 0.00 0.00 38.19 3.95
105 106 1.580437 GTAGCGCGGGATCTACTCC 59.420 63.158 8.83 0.00 44.11 3.85
106 107 1.580437 GGTAGCGCGGGATCTACTC 59.420 63.158 17.33 7.56 36.37 2.59
107 108 2.259439 CGGTAGCGCGGGATCTACT 61.259 63.158 17.33 3.91 36.37 2.57
108 109 1.584380 ATCGGTAGCGCGGGATCTAC 61.584 60.000 8.83 10.65 35.60 2.59
109 110 1.303074 ATCGGTAGCGCGGGATCTA 60.303 57.895 8.83 0.00 0.00 1.98
110 111 2.597805 ATCGGTAGCGCGGGATCT 60.598 61.111 8.83 0.00 0.00 2.75
111 112 2.430921 CATCGGTAGCGCGGGATC 60.431 66.667 8.83 0.00 0.00 3.36
112 113 4.664677 GCATCGGTAGCGCGGGAT 62.665 66.667 8.83 0.00 0.00 3.85
117 118 4.547367 AAGGGGCATCGGTAGCGC 62.547 66.667 9.99 0.00 43.37 5.92
118 119 2.180204 CAAAGGGGCATCGGTAGCG 61.180 63.158 8.29 8.29 0.00 4.26
119 120 0.815615 CTCAAAGGGGCATCGGTAGC 60.816 60.000 0.00 0.00 0.00 3.58
120 121 0.815615 GCTCAAAGGGGCATCGGTAG 60.816 60.000 0.00 0.00 0.00 3.18
121 122 1.223487 GCTCAAAGGGGCATCGGTA 59.777 57.895 0.00 0.00 0.00 4.02
122 123 2.044946 GCTCAAAGGGGCATCGGT 60.045 61.111 0.00 0.00 0.00 4.69
123 124 2.830370 GGCTCAAAGGGGCATCGG 60.830 66.667 0.00 0.00 0.00 4.18
124 125 2.045045 TGGCTCAAAGGGGCATCG 60.045 61.111 0.00 0.00 34.37 3.84
125 126 1.304381 TGTGGCTCAAAGGGGCATC 60.304 57.895 0.00 0.00 41.11 3.91
126 127 1.304713 CTGTGGCTCAAAGGGGCAT 60.305 57.895 0.00 0.00 41.11 4.40
127 128 2.115910 CTGTGGCTCAAAGGGGCA 59.884 61.111 0.00 0.00 36.92 5.36
128 129 0.251165 TAACTGTGGCTCAAAGGGGC 60.251 55.000 0.00 0.00 0.00 5.80
129 130 2.514458 ATAACTGTGGCTCAAAGGGG 57.486 50.000 0.00 0.00 0.00 4.79
132 133 3.119849 CCGGAAATAACTGTGGCTCAAAG 60.120 47.826 0.00 0.00 0.00 2.77
140 141 7.553881 AATTCAGTATCCGGAAATAACTGTG 57.446 36.000 25.93 12.60 0.00 3.66
166 167 2.541383 CGTTTGCAAGCAGTGTCATCAA 60.541 45.455 13.97 0.00 0.00 2.57
201 202 1.869690 GAGCTTGTTTCCAGACGGC 59.130 57.895 0.00 0.00 0.00 5.68
219 220 3.282157 CAAGCGGGATGGATGGCG 61.282 66.667 0.00 0.00 0.00 5.69
333 334 1.880027 ACCATGTCGTTTGAAGAAGCC 59.120 47.619 0.00 0.00 0.00 4.35
358 359 2.107953 GATGTCGGGAGCTGGAGC 59.892 66.667 0.00 0.00 42.49 4.70
380 381 0.804933 GACAGACGGCCACGGAATAC 60.805 60.000 2.24 0.00 46.48 1.89
426 427 2.186125 GTTCGGTCCGGGATGGTC 59.814 66.667 12.29 0.00 39.52 4.02
1508 1524 7.444487 ACTCTTCACTTATTTACCAACCAGAAC 59.556 37.037 0.00 0.00 0.00 3.01
1594 1611 6.382869 ACTCTTCACTTATTATTGCATGGC 57.617 37.500 0.00 0.00 0.00 4.40
1621 1638 2.877360 TACGCACGGCCTGAACGATC 62.877 60.000 0.00 0.00 34.93 3.69
1624 1641 3.475774 GTACGCACGGCCTGAACG 61.476 66.667 0.00 1.50 37.36 3.95
1650 1667 1.434555 TCTTGCGTAAACACATCCGG 58.565 50.000 0.00 0.00 0.00 5.14
1663 1680 1.923204 CAGTAGCAGCTAGTTCTTGCG 59.077 52.381 7.08 0.00 0.00 4.85
1677 1694 1.870167 GCCAGGACTAATCGCAGTAGC 60.870 57.143 0.00 0.00 37.42 3.58
1678 1695 1.269831 GGCCAGGACTAATCGCAGTAG 60.270 57.143 0.00 0.00 0.00 2.57
1679 1696 0.750850 GGCCAGGACTAATCGCAGTA 59.249 55.000 0.00 0.00 0.00 2.74
1680 1697 1.264749 TGGCCAGGACTAATCGCAGT 61.265 55.000 0.00 0.00 0.00 4.40
1681 1698 0.107456 ATGGCCAGGACTAATCGCAG 59.893 55.000 13.05 0.00 0.00 5.18
1682 1699 0.179048 CATGGCCAGGACTAATCGCA 60.179 55.000 13.35 0.00 0.00 5.10
1683 1700 0.886490 CCATGGCCAGGACTAATCGC 60.886 60.000 21.32 0.00 0.00 4.58
1684 1701 0.250467 CCCATGGCCAGGACTAATCG 60.250 60.000 21.32 0.00 0.00 3.34
1685 1702 0.538287 GCCCATGGCCAGGACTAATC 60.538 60.000 21.32 0.00 44.06 1.75
1686 1703 1.538666 GCCCATGGCCAGGACTAAT 59.461 57.895 21.32 0.00 44.06 1.73
1687 1704 3.006677 GCCCATGGCCAGGACTAA 58.993 61.111 21.32 0.00 44.06 2.24
1704 1721 4.760047 CAAGGTCGGGTCGGGCTG 62.760 72.222 0.00 0.00 0.00 4.85
1706 1723 4.754667 GACAAGGTCGGGTCGGGC 62.755 72.222 0.00 0.00 0.00 6.13
1707 1724 4.078516 GGACAAGGTCGGGTCGGG 62.079 72.222 0.00 0.00 34.87 5.14
1708 1725 2.573609 GATGGACAAGGTCGGGTCGG 62.574 65.000 0.00 0.00 34.87 4.79
1709 1726 1.153628 GATGGACAAGGTCGGGTCG 60.154 63.158 0.00 0.00 34.87 4.79
1710 1727 1.221021 GGATGGACAAGGTCGGGTC 59.779 63.158 0.00 0.00 32.65 4.46
1711 1728 2.298661 GGGATGGACAAGGTCGGGT 61.299 63.158 0.00 0.00 32.65 5.28
1712 1729 2.590092 GGGATGGACAAGGTCGGG 59.410 66.667 0.00 0.00 32.65 5.14
1713 1730 2.186903 CGGGATGGACAAGGTCGG 59.813 66.667 0.00 0.00 32.65 4.79
1714 1731 2.186903 CCGGGATGGACAAGGTCG 59.813 66.667 0.00 0.00 42.00 4.79
1715 1732 2.590092 CCCGGGATGGACAAGGTC 59.410 66.667 18.48 0.00 42.00 3.85
1716 1733 3.728373 GCCCGGGATGGACAAGGT 61.728 66.667 29.31 0.00 42.00 3.50
1717 1734 3.406595 GAGCCCGGGATGGACAAGG 62.407 68.421 29.31 0.00 42.00 3.61
1718 1735 2.190578 GAGCCCGGGATGGACAAG 59.809 66.667 29.31 0.00 42.00 3.16
1719 1736 3.781307 CGAGCCCGGGATGGACAA 61.781 66.667 29.31 0.00 42.00 3.18
1732 1749 0.744771 CTCAAAACCTAGGCCCGAGC 60.745 60.000 9.30 0.00 38.76 5.03
1733 1750 0.744771 GCTCAAAACCTAGGCCCGAG 60.745 60.000 9.30 10.89 0.00 4.63
1734 1751 1.298667 GCTCAAAACCTAGGCCCGA 59.701 57.895 9.30 0.00 0.00 5.14
1735 1752 1.749258 GGCTCAAAACCTAGGCCCG 60.749 63.158 9.30 0.00 37.12 6.13
1736 1753 4.338815 GGCTCAAAACCTAGGCCC 57.661 61.111 9.30 0.00 37.12 5.80
1738 1755 1.546029 CTTTGGGCTCAAAACCTAGGC 59.454 52.381 13.82 0.00 41.70 3.93
1739 1756 1.546029 GCTTTGGGCTCAAAACCTAGG 59.454 52.381 13.82 7.41 41.70 3.02
1740 1757 1.546029 GGCTTTGGGCTCAAAACCTAG 59.454 52.381 21.88 7.38 42.70 3.02
1741 1758 1.627864 GGCTTTGGGCTCAAAACCTA 58.372 50.000 21.88 0.00 42.70 3.08
1742 1759 1.121407 GGGCTTTGGGCTCAAAACCT 61.121 55.000 26.53 0.00 44.41 3.50
1743 1760 1.371183 GGGCTTTGGGCTCAAAACC 59.629 57.895 21.19 21.19 44.32 3.27
1744 1761 1.006220 CGGGCTTTGGGCTCAAAAC 60.006 57.895 13.82 8.70 42.70 2.43
1745 1762 2.206536 CCGGGCTTTGGGCTCAAAA 61.207 57.895 13.82 0.00 42.70 2.44
1746 1763 2.600173 CCGGGCTTTGGGCTCAAA 60.600 61.111 12.09 12.09 42.70 2.69
1747 1764 4.676951 CCCGGGCTTTGGGCTCAA 62.677 66.667 8.08 0.00 42.70 3.02
1773 1790 3.325201 AAATCGACGGGCCCAGACC 62.325 63.158 24.92 6.09 0.00 3.85
1774 1791 1.814169 GAAATCGACGGGCCCAGAC 60.814 63.158 24.92 13.86 0.00 3.51
1775 1792 2.582436 GAAATCGACGGGCCCAGA 59.418 61.111 24.92 18.29 0.00 3.86
1776 1793 2.890474 CGAAATCGACGGGCCCAG 60.890 66.667 24.92 17.36 43.02 4.45
1777 1794 3.652539 GACGAAATCGACGGGCCCA 62.653 63.158 24.92 1.02 43.02 5.36
1778 1795 2.889018 GACGAAATCGACGGGCCC 60.889 66.667 13.57 13.57 43.02 5.80
1779 1796 1.087771 AATGACGAAATCGACGGGCC 61.088 55.000 10.16 0.00 43.02 5.80
1780 1797 0.725117 AAATGACGAAATCGACGGGC 59.275 50.000 10.16 0.00 43.02 6.13
1781 1798 3.000925 CCTTAAATGACGAAATCGACGGG 59.999 47.826 10.16 0.00 43.02 5.28
1782 1799 3.861113 TCCTTAAATGACGAAATCGACGG 59.139 43.478 10.16 0.00 43.02 4.79
1783 1800 5.287752 TCTTCCTTAAATGACGAAATCGACG 59.712 40.000 10.16 0.00 43.02 5.12
1784 1801 6.237861 CCTCTTCCTTAAATGACGAAATCGAC 60.238 42.308 10.16 3.97 43.02 4.20
1785 1802 5.810587 CCTCTTCCTTAAATGACGAAATCGA 59.189 40.000 10.16 0.00 43.02 3.59
1786 1803 5.502544 GCCTCTTCCTTAAATGACGAAATCG 60.503 44.000 0.48 0.48 46.33 3.34
1787 1804 5.220873 GGCCTCTTCCTTAAATGACGAAATC 60.221 44.000 0.00 0.00 0.00 2.17
1788 1805 4.640647 GGCCTCTTCCTTAAATGACGAAAT 59.359 41.667 0.00 0.00 0.00 2.17
1789 1806 4.007659 GGCCTCTTCCTTAAATGACGAAA 58.992 43.478 0.00 0.00 0.00 3.46
1790 1807 3.606687 GGCCTCTTCCTTAAATGACGAA 58.393 45.455 0.00 0.00 0.00 3.85
1791 1808 2.093128 GGGCCTCTTCCTTAAATGACGA 60.093 50.000 0.84 0.00 0.00 4.20
1792 1809 2.289565 GGGCCTCTTCCTTAAATGACG 58.710 52.381 0.84 0.00 0.00 4.35
1793 1810 2.289565 CGGGCCTCTTCCTTAAATGAC 58.710 52.381 0.84 0.00 0.00 3.06
1794 1811 1.211949 CCGGGCCTCTTCCTTAAATGA 59.788 52.381 0.84 0.00 0.00 2.57
1795 1812 1.680338 CCGGGCCTCTTCCTTAAATG 58.320 55.000 0.84 0.00 0.00 2.32
1796 1813 0.106669 GCCGGGCCTCTTCCTTAAAT 60.107 55.000 8.12 0.00 0.00 1.40
1797 1814 1.301954 GCCGGGCCTCTTCCTTAAA 59.698 57.895 8.12 0.00 0.00 1.52
1798 1815 2.676265 GGCCGGGCCTCTTCCTTAA 61.676 63.158 30.86 0.00 46.69 1.85
1799 1816 3.087906 GGCCGGGCCTCTTCCTTA 61.088 66.667 30.86 0.00 46.69 2.69
1830 1847 1.868469 TCACACTAAAAACCCGTCGG 58.132 50.000 3.60 3.60 0.00 4.79
1831 1848 3.061322 TCATCACACTAAAAACCCGTCG 58.939 45.455 0.00 0.00 0.00 5.12
1832 1849 3.120304 GCTCATCACACTAAAAACCCGTC 60.120 47.826 0.00 0.00 0.00 4.79
1833 1850 2.812011 GCTCATCACACTAAAAACCCGT 59.188 45.455 0.00 0.00 0.00 5.28
1834 1851 2.161609 GGCTCATCACACTAAAAACCCG 59.838 50.000 0.00 0.00 0.00 5.28
1835 1852 2.161609 CGGCTCATCACACTAAAAACCC 59.838 50.000 0.00 0.00 0.00 4.11
1836 1853 2.161609 CCGGCTCATCACACTAAAAACC 59.838 50.000 0.00 0.00 0.00 3.27
1837 1854 2.161609 CCCGGCTCATCACACTAAAAAC 59.838 50.000 0.00 0.00 0.00 2.43
1838 1855 2.432444 CCCGGCTCATCACACTAAAAA 58.568 47.619 0.00 0.00 0.00 1.94
1839 1856 1.948611 GCCCGGCTCATCACACTAAAA 60.949 52.381 0.71 0.00 0.00 1.52
1840 1857 0.392461 GCCCGGCTCATCACACTAAA 60.392 55.000 0.71 0.00 0.00 1.85
1841 1858 1.220749 GCCCGGCTCATCACACTAA 59.779 57.895 0.71 0.00 0.00 2.24
1842 1859 1.685765 AGCCCGGCTCATCACACTA 60.686 57.895 5.94 0.00 30.62 2.74
1843 1860 3.005539 AGCCCGGCTCATCACACT 61.006 61.111 5.94 0.00 30.62 3.55
1861 1878 1.035385 AAGCCTAAAAATCGGGCCCG 61.035 55.000 39.13 39.13 46.31 6.13
1862 1879 0.459899 CAAGCCTAAAAATCGGGCCC 59.540 55.000 13.57 13.57 46.31 5.80
1863 1880 1.134367 GTCAAGCCTAAAAATCGGGCC 59.866 52.381 0.00 0.00 46.31 5.80
1864 1881 1.202143 CGTCAAGCCTAAAAATCGGGC 60.202 52.381 0.00 0.00 45.57 6.13
1865 1882 1.202143 GCGTCAAGCCTAAAAATCGGG 60.202 52.381 0.00 0.00 40.81 5.14
1866 1883 2.174060 GCGTCAAGCCTAAAAATCGG 57.826 50.000 0.00 0.00 40.81 4.18
1897 1914 2.788191 AAAACCCAGGCTCGAGCTCG 62.788 60.000 34.46 30.03 41.70 5.03
1898 1915 0.606673 AAAAACCCAGGCTCGAGCTC 60.607 55.000 34.46 24.39 41.70 4.09
1899 1916 1.456287 AAAAACCCAGGCTCGAGCT 59.544 52.632 34.46 19.07 41.70 4.09
1900 1917 4.081050 AAAAACCCAGGCTCGAGC 57.919 55.556 29.38 29.38 41.14 5.03
1914 1931 1.066587 CCAAAGCCCGACGCAAAAA 59.933 52.632 0.00 0.00 41.38 1.94
1915 1932 1.668101 AACCAAAGCCCGACGCAAAA 61.668 50.000 0.00 0.00 41.38 2.44
1916 1933 2.122167 AACCAAAGCCCGACGCAAA 61.122 52.632 0.00 0.00 41.38 3.68
1917 1934 2.517402 AACCAAAGCCCGACGCAA 60.517 55.556 0.00 0.00 41.38 4.85
1918 1935 3.283684 CAACCAAAGCCCGACGCA 61.284 61.111 0.00 0.00 41.38 5.24
1919 1936 4.038080 CCAACCAAAGCCCGACGC 62.038 66.667 0.00 0.00 37.98 5.19
1920 1937 4.038080 GCCAACCAAAGCCCGACG 62.038 66.667 0.00 0.00 0.00 5.12
1921 1938 3.680786 GGCCAACCAAAGCCCGAC 61.681 66.667 0.00 0.00 43.76 4.79
1953 1970 2.830370 CCATTTCTCAGGCCGGGC 60.830 66.667 22.67 22.67 0.00 6.13
1954 1971 2.830370 GCCATTTCTCAGGCCGGG 60.830 66.667 2.18 0.00 45.18 5.73
1960 1977 4.818546 CAGTTATACCTGGCCATTTCTCAG 59.181 45.833 5.51 0.00 0.00 3.35
1961 1978 4.780815 CAGTTATACCTGGCCATTTCTCA 58.219 43.478 5.51 0.00 0.00 3.27
1962 1979 3.565902 GCAGTTATACCTGGCCATTTCTC 59.434 47.826 5.51 0.00 32.92 2.87
1963 1980 3.555966 GCAGTTATACCTGGCCATTTCT 58.444 45.455 5.51 0.00 32.92 2.52
1964 1981 2.290641 CGCAGTTATACCTGGCCATTTC 59.709 50.000 5.51 0.00 32.92 2.17
1965 1982 2.092646 TCGCAGTTATACCTGGCCATTT 60.093 45.455 5.51 0.00 32.92 2.32
1966 1983 1.488812 TCGCAGTTATACCTGGCCATT 59.511 47.619 5.51 0.00 32.92 3.16
1967 1984 1.128200 TCGCAGTTATACCTGGCCAT 58.872 50.000 5.51 0.00 32.92 4.40
1968 1985 1.128200 ATCGCAGTTATACCTGGCCA 58.872 50.000 4.71 4.71 32.92 5.36
1969 1986 1.512926 CATCGCAGTTATACCTGGCC 58.487 55.000 0.00 0.00 32.92 5.36
1970 1987 1.512926 CCATCGCAGTTATACCTGGC 58.487 55.000 0.00 0.00 32.92 4.85
1971 1988 1.070758 AGCCATCGCAGTTATACCTGG 59.929 52.381 0.00 0.00 37.52 4.45
1972 1989 2.036475 AGAGCCATCGCAGTTATACCTG 59.964 50.000 0.00 0.00 37.52 4.00
1973 1990 2.320781 AGAGCCATCGCAGTTATACCT 58.679 47.619 0.00 0.00 37.52 3.08
1974 1991 2.821991 AGAGCCATCGCAGTTATACC 57.178 50.000 0.00 0.00 37.52 2.73
1975 1992 4.872664 ACTTAGAGCCATCGCAGTTATAC 58.127 43.478 0.00 0.00 37.52 1.47
1976 1993 5.289595 CAACTTAGAGCCATCGCAGTTATA 58.710 41.667 0.00 0.00 37.52 0.98
1977 1994 4.122776 CAACTTAGAGCCATCGCAGTTAT 58.877 43.478 0.00 0.00 37.52 1.89
1978 1995 3.521560 CAACTTAGAGCCATCGCAGTTA 58.478 45.455 0.00 0.00 37.52 2.24
1979 1996 2.350522 CAACTTAGAGCCATCGCAGTT 58.649 47.619 0.00 0.00 37.52 3.16
1987 2004 0.324943 GCCTCACCAACTTAGAGCCA 59.675 55.000 0.00 0.00 0.00 4.75
2033 2050 8.611757 ACATAAAGTTTGCAAATCAAAAGGAAC 58.388 29.630 16.21 0.00 45.35 3.62
2105 2156 0.895100 AGCGCTTCAATGCAAGGGAA 60.895 50.000 2.64 1.74 38.33 3.97
2113 2164 0.450583 AGCACATGAGCGCTTCAATG 59.549 50.000 13.26 18.20 39.77 2.82
2125 2176 1.300971 CCACAACCCTCGAGCACATG 61.301 60.000 6.99 5.60 0.00 3.21
2126 2177 1.003355 CCACAACCCTCGAGCACAT 60.003 57.895 6.99 0.00 0.00 3.21
2127 2178 2.377628 GACCACAACCCTCGAGCACA 62.378 60.000 6.99 0.00 0.00 4.57
2128 2179 1.668151 GACCACAACCCTCGAGCAC 60.668 63.158 6.99 0.00 0.00 4.40
2129 2180 2.741092 GACCACAACCCTCGAGCA 59.259 61.111 6.99 0.00 0.00 4.26
2130 2181 2.047179 GGACCACAACCCTCGAGC 60.047 66.667 6.99 0.00 0.00 5.03
2131 2182 2.663196 GGGACCACAACCCTCGAG 59.337 66.667 5.13 5.13 43.65 4.04
2137 2188 2.593026 TCAATTCAAGGGACCACAACC 58.407 47.619 0.00 0.00 0.00 3.77
2138 2189 3.573967 ACATCAATTCAAGGGACCACAAC 59.426 43.478 0.00 0.00 0.00 3.32
2139 2190 3.573538 CACATCAATTCAAGGGACCACAA 59.426 43.478 0.00 0.00 0.00 3.33
2140 2191 3.156293 CACATCAATTCAAGGGACCACA 58.844 45.455 0.00 0.00 0.00 4.17
2141 2192 2.094545 GCACATCAATTCAAGGGACCAC 60.095 50.000 0.00 0.00 0.00 4.16
2142 2193 2.170166 GCACATCAATTCAAGGGACCA 58.830 47.619 0.00 0.00 0.00 4.02
2143 2194 2.424956 GAGCACATCAATTCAAGGGACC 59.575 50.000 0.00 0.00 0.00 4.46
2144 2195 2.424956 GGAGCACATCAATTCAAGGGAC 59.575 50.000 0.00 0.00 0.00 4.46
2145 2196 2.309755 AGGAGCACATCAATTCAAGGGA 59.690 45.455 0.00 0.00 0.00 4.20
2146 2197 2.426024 CAGGAGCACATCAATTCAAGGG 59.574 50.000 0.00 0.00 0.00 3.95
2147 2198 3.087031 ACAGGAGCACATCAATTCAAGG 58.913 45.455 0.00 0.00 0.00 3.61
2148 2199 3.672511 GCACAGGAGCACATCAATTCAAG 60.673 47.826 0.00 0.00 0.00 3.02
2149 2200 2.229543 GCACAGGAGCACATCAATTCAA 59.770 45.455 0.00 0.00 0.00 2.69
2150 2201 1.814394 GCACAGGAGCACATCAATTCA 59.186 47.619 0.00 0.00 0.00 2.57
2151 2202 2.089980 AGCACAGGAGCACATCAATTC 58.910 47.619 0.00 0.00 36.85 2.17
2152 2203 2.211250 AGCACAGGAGCACATCAATT 57.789 45.000 0.00 0.00 36.85 2.32
2153 2204 2.089980 GAAGCACAGGAGCACATCAAT 58.910 47.619 0.00 0.00 36.85 2.57
2154 2205 1.527034 GAAGCACAGGAGCACATCAA 58.473 50.000 0.00 0.00 36.85 2.57
2155 2206 0.671472 CGAAGCACAGGAGCACATCA 60.671 55.000 0.00 0.00 36.85 3.07
2156 2207 0.390340 TCGAAGCACAGGAGCACATC 60.390 55.000 0.00 0.00 36.85 3.06
2157 2208 0.251354 ATCGAAGCACAGGAGCACAT 59.749 50.000 0.00 0.00 36.85 3.21
2158 2209 0.671472 CATCGAAGCACAGGAGCACA 60.671 55.000 0.00 0.00 36.85 4.57
2159 2210 1.364626 CCATCGAAGCACAGGAGCAC 61.365 60.000 0.00 0.00 36.85 4.40
2160 2211 1.078918 CCATCGAAGCACAGGAGCA 60.079 57.895 0.00 0.00 36.85 4.26
2161 2212 0.674895 AACCATCGAAGCACAGGAGC 60.675 55.000 0.00 0.00 0.00 4.70
2162 2213 1.081892 CAACCATCGAAGCACAGGAG 58.918 55.000 0.00 0.00 0.00 3.69
2163 2214 0.396435 ACAACCATCGAAGCACAGGA 59.604 50.000 0.00 0.00 0.00 3.86
2167 2218 1.586154 CCCCACAACCATCGAAGCAC 61.586 60.000 0.00 0.00 0.00 4.40
2176 2227 0.768622 CCTTAGTGACCCCACAACCA 59.231 55.000 0.00 0.00 45.54 3.67
2193 2244 1.304282 CACACTTAGCATGGGGCCT 59.696 57.895 0.84 0.00 46.50 5.19
2266 2320 9.033481 CACAAATTTTAAGAAGTGCTCATGAAA 57.967 29.630 0.00 0.00 0.00 2.69
2272 2326 9.516314 AAAGTACACAAATTTTAAGAAGTGCTC 57.484 29.630 0.00 0.00 0.00 4.26
2344 2399 9.275398 ACGTGAACTTTACAAATATCCACTTTA 57.725 29.630 0.00 0.00 0.00 1.85
2348 2403 7.577979 TGAACGTGAACTTTACAAATATCCAC 58.422 34.615 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.