Multiple sequence alignment - TraesCS5A01G163400

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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 TraesCS5A01G163400 chr5A 100.000 3996 0 0 1 3996 350239142 350235147 0.000000e+00 7380.0
1 TraesCS5A01G163400 chr5A 96.970 33 1 0 2874 2906 440265579 440265611 5.580000e-04 56.5
2 TraesCS5A01G163400 chr5B 93.095 2100 88 26 1872 3938 296378150 296376075 0.000000e+00 3022.0
3 TraesCS5A01G163400 chr5B 93.432 1690 78 19 71 1737 296379893 296378214 0.000000e+00 2475.0
4 TraesCS5A01G163400 chr5B 76.395 466 75 25 3371 3818 148642699 148642251 6.720000e-53 219.0
5 TraesCS5A01G163400 chr5B 96.970 33 1 0 2874 2906 398349949 398349981 5.580000e-04 56.5
6 TraesCS5A01G163400 chr5D 96.544 1389 36 5 1874 3257 264018284 264016903 0.000000e+00 2289.0
7 TraesCS5A01G163400 chr5D 91.582 1580 64 28 124 1669 264020095 264018551 0.000000e+00 2117.0
8 TraesCS5A01G163400 chr5D 91.717 495 24 7 3243 3732 263995706 263995224 0.000000e+00 671.0
9 TraesCS5A01G163400 chr5D 91.200 125 4 1 3821 3938 263994791 263994667 3.200000e-36 163.0
10 TraesCS5A01G163400 chr5D 91.509 106 8 1 3732 3836 263994917 263994812 1.160000e-30 145.0
11 TraesCS5A01G163400 chr5D 92.857 56 4 0 71 126 264020189 264020134 9.200000e-12 82.4
12 TraesCS5A01G163400 chr5D 96.970 33 1 0 2874 2906 339356061 339356093 5.580000e-04 56.5
13 TraesCS5A01G163400 chr6D 75.464 485 78 33 3401 3867 3371706 3372167 8.760000e-47 198.0
14 TraesCS5A01G163400 chr6D 95.604 91 3 1 1757 1846 413410035 413410125 1.160000e-30 145.0
15 TraesCS5A01G163400 chr6D 86.301 73 7 2 1043 1113 104988303 104988232 4.280000e-10 76.8
16 TraesCS5A01G163400 chr7A 75.269 465 82 24 3371 3818 32955109 32955557 1.470000e-44 191.0
17 TraesCS5A01G163400 chr2A 96.591 88 3 0 1760 1847 602770028 602770115 3.220000e-31 147.0
18 TraesCS5A01G163400 chr2A 91.089 101 7 2 1748 1848 661154287 661154385 6.970000e-28 135.0
19 TraesCS5A01G163400 chr2A 96.875 32 1 0 38 69 587952706 587952737 2.000000e-03 54.7
20 TraesCS5A01G163400 chr4A 94.565 92 5 0 1760 1851 613419991 613419900 4.160000e-30 143.0
21 TraesCS5A01G163400 chr7B 92.079 101 6 2 1761 1859 458165638 458165738 1.500000e-29 141.0
22 TraesCS5A01G163400 chr7B 92.079 101 6 2 1761 1859 510387545 510387645 1.500000e-29 141.0
23 TraesCS5A01G163400 chr7B 92.079 101 6 2 1761 1859 510433681 510433781 1.500000e-29 141.0
24 TraesCS5A01G163400 chr7B 91.176 102 8 1 1761 1862 54323436 54323336 1.940000e-28 137.0
25 TraesCS5A01G163400 chr2D 73.412 425 88 18 3386 3799 603659137 603658727 6.970000e-28 135.0
26 TraesCS5A01G163400 chr2B 89.189 111 8 4 1761 1867 227276361 227276251 6.970000e-28 135.0
27 TraesCS5A01G163400 chr2B 88.732 71 7 1 5 75 503984553 503984484 7.120000e-13 86.1
28 TraesCS5A01G163400 chr1D 93.103 87 6 0 3 89 143452099 143452185 1.170000e-25 128.0
29 TraesCS5A01G163400 chr3B 77.056 231 25 16 3482 3700 495277049 495277263 1.520000e-19 108.0
30 TraesCS5A01G163400 chr7D 88.312 77 9 0 3 79 574886557 574886481 4.250000e-15 93.5
31 TraesCS5A01G163400 chr3D 86.076 79 9 2 3 79 557269511 557269433 2.560000e-12 84.2
32 TraesCS5A01G163400 chr1A 83.117 77 12 1 4 79 272602879 272602803 7.170000e-08 69.4
33 TraesCS5A01G163400 chr6A 86.154 65 6 2 1043 1105 127192076 127192013 2.580000e-07 67.6
34 TraesCS5A01G163400 chr3A 91.489 47 4 0 43 89 92301489 92301535 9.270000e-07 65.8
35 TraesCS5A01G163400 chr1B 97.143 35 1 0 45 79 626107156 626107122 4.310000e-05 60.2
36 TraesCS5A01G163400 chr1B 94.595 37 2 0 43 79 177679590 177679554 1.550000e-04 58.4


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 TraesCS5A01G163400 chr5A 350235147 350239142 3995 True 7380.000000 7380 100.000000 1 3996 1 chr5A.!!$R1 3995
1 TraesCS5A01G163400 chr5B 296376075 296379893 3818 True 2748.500000 3022 93.263500 71 3938 2 chr5B.!!$R2 3867
2 TraesCS5A01G163400 chr5D 264016903 264020189 3286 True 1496.133333 2289 93.661000 71 3257 3 chr5D.!!$R2 3186
3 TraesCS5A01G163400 chr5D 263994667 263995706 1039 True 326.333333 671 91.475333 3243 3938 3 chr5D.!!$R1 695

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
936 1001 0.464036 CGATACCTTGCTAGGCACCA 59.536 55.0 14.6 0.0 46.22 4.17 F
1590 1673 0.035598 CACGGTGTACATGAACCCCA 59.964 55.0 0.0 0.0 32.44 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2633 2941 0.902984 TACTCGGGGAAGAGCTTGCA 60.903 55.0 4.17 0.0 41.77 4.08 R
3054 3368 0.459899 TGACCGATCGAATGGACAGG 59.540 55.0 18.66 0.0 0.00 4.00 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
73 74 2.278531 GCAACGCACGTGCCTTTT 60.279 55.556 33.23 20.92 37.91 2.27
76 77 1.117234 CAACGCACGTGCCTTTTTAC 58.883 50.000 33.23 5.19 37.91 2.01
80 81 2.809696 ACGCACGTGCCTTTTTACTATT 59.190 40.909 33.23 1.73 37.91 1.73
236 282 1.439353 TACGGAGTATGGCGTCGTCC 61.439 60.000 0.00 0.00 45.11 4.79
237 283 2.767445 CGGAGTATGGCGTCGTCCA 61.767 63.158 10.19 10.19 40.97 4.02
239 285 0.597637 GGAGTATGGCGTCGTCCATG 60.598 60.000 23.16 0.00 45.84 3.66
360 417 3.266636 CCCACATAAAGCACATGTACGA 58.733 45.455 0.00 0.00 34.88 3.43
387 446 9.459640 AATACGTACATATGACAACATACAGAC 57.540 33.333 10.38 0.00 41.03 3.51
397 456 3.089267 CAACATACAGACGACGAGTACG 58.911 50.000 0.00 0.00 45.75 3.67
404 469 3.388134 CGACGAGTACGCCGTAGA 58.612 61.111 14.53 0.00 43.96 2.59
458 523 5.998553 TCACGAATCACGATTCCTATAGTC 58.001 41.667 12.91 0.00 43.14 2.59
611 676 6.074088 GCATGTAGTACTACTGTGAATCATGC 60.074 42.308 28.56 25.74 44.15 4.06
675 740 2.945456 AGAAAGTTTCCCACCAACTCC 58.055 47.619 12.05 0.00 33.12 3.85
776 841 5.770663 TCTCTTTCGCTGCCTCTATAAGTAT 59.229 40.000 0.00 0.00 0.00 2.12
936 1001 0.464036 CGATACCTTGCTAGGCACCA 59.536 55.000 14.60 0.00 46.22 4.17
1026 1091 3.414700 GAGGCGGCAGACAACGTG 61.415 66.667 13.08 0.00 0.00 4.49
1113 1178 3.064987 GCTCGTCAAGCGCCTCCTA 62.065 63.158 2.29 0.00 42.21 2.94
1122 1187 2.501610 CGCCTCCTACAGAAGGGC 59.498 66.667 0.00 0.00 46.55 5.19
1127 1192 2.467880 CCTCCTACAGAAGGGCTACAA 58.532 52.381 0.00 0.00 46.55 2.41
1163 1228 1.070105 GCAACCCTGGTACGTGTGA 59.930 57.895 0.00 0.00 0.00 3.58
1164 1229 0.321298 GCAACCCTGGTACGTGTGAT 60.321 55.000 0.00 0.00 0.00 3.06
1167 1232 3.181473 GCAACCCTGGTACGTGTGATATA 60.181 47.826 0.00 0.00 0.00 0.86
1169 1234 3.907221 ACCCTGGTACGTGTGATATAGT 58.093 45.455 0.00 0.00 0.00 2.12
1171 1236 5.068636 ACCCTGGTACGTGTGATATAGTAG 58.931 45.833 0.00 0.00 0.00 2.57
1172 1237 4.082895 CCCTGGTACGTGTGATATAGTAGC 60.083 50.000 0.00 0.00 37.87 3.58
1173 1238 4.517832 CCTGGTACGTGTGATATAGTAGCA 59.482 45.833 0.00 6.26 42.75 3.49
1174 1239 5.428496 TGGTACGTGTGATATAGTAGCAC 57.572 43.478 0.00 0.00 44.83 4.40
1188 1261 3.085533 AGTAGCACACTCGAGTTCATCT 58.914 45.455 17.26 12.73 28.33 2.90
1357 1437 4.681978 GAGGCGTTCACGGGCTGT 62.682 66.667 0.81 0.00 40.78 4.40
1425 1505 1.097232 ACCATTGATGCCACACGATG 58.903 50.000 0.00 0.00 0.00 3.84
1440 1520 2.679837 CACGATGAATTGCTAACCTGCT 59.320 45.455 0.00 0.00 0.00 4.24
1454 1534 5.009710 GCTAACCTGCTTGGAAACTAAACTT 59.990 40.000 3.40 0.00 39.71 2.66
1456 1536 4.793201 ACCTGCTTGGAAACTAAACTTCT 58.207 39.130 3.40 0.00 39.71 2.85
1459 1539 5.278022 CCTGCTTGGAAACTAAACTTCTGAC 60.278 44.000 0.00 0.00 38.35 3.51
1520 1603 3.914426 GGGACCAAGTATGTGATCACT 57.086 47.619 25.55 13.92 0.00 3.41
1590 1673 0.035598 CACGGTGTACATGAACCCCA 59.964 55.000 0.00 0.00 32.44 4.96
1686 1957 6.089685 ACGTGGTAATTGTTTGTTTTGTTCAC 59.910 34.615 0.00 0.00 0.00 3.18
1693 1964 8.770438 AATTGTTTGTTTTGTTCACATACAGT 57.230 26.923 0.00 0.00 37.39 3.55
1716 1987 6.886459 AGTGACACAATAATCCATTGCTACTT 59.114 34.615 8.59 0.00 46.85 2.24
1717 1988 8.046708 AGTGACACAATAATCCATTGCTACTTA 58.953 33.333 8.59 0.00 46.85 2.24
1718 1989 8.840321 GTGACACAATAATCCATTGCTACTTAT 58.160 33.333 0.00 0.00 46.85 1.73
1730 2001 7.064609 TCCATTGCTACTTATCTTTGAAACTCG 59.935 37.037 0.00 0.00 0.00 4.18
1737 2008 5.472478 ACTTATCTTTGAAACTCGGAAACCC 59.528 40.000 0.00 0.00 0.00 4.11
1739 2010 1.265905 CTTTGAAACTCGGAAACCCGG 59.734 52.381 0.00 0.00 46.72 5.73
1740 2011 0.180878 TTGAAACTCGGAAACCCGGT 59.819 50.000 0.00 0.00 46.72 5.28
1741 2012 1.047002 TGAAACTCGGAAACCCGGTA 58.953 50.000 0.00 0.00 46.72 4.02
1742 2013 1.415659 TGAAACTCGGAAACCCGGTAA 59.584 47.619 0.00 0.00 46.72 2.85
1743 2014 2.038820 TGAAACTCGGAAACCCGGTAAT 59.961 45.455 0.00 0.00 46.72 1.89
1744 2015 3.260380 TGAAACTCGGAAACCCGGTAATA 59.740 43.478 0.00 0.00 46.72 0.98
1745 2016 4.080975 TGAAACTCGGAAACCCGGTAATAT 60.081 41.667 0.00 0.00 46.72 1.28
1746 2017 5.128499 TGAAACTCGGAAACCCGGTAATATA 59.872 40.000 0.00 0.00 46.72 0.86
1747 2018 5.813513 AACTCGGAAACCCGGTAATATAT 57.186 39.130 0.00 0.00 46.72 0.86
1748 2019 5.143376 ACTCGGAAACCCGGTAATATATG 57.857 43.478 0.00 0.00 46.72 1.78
1749 2020 4.590222 ACTCGGAAACCCGGTAATATATGT 59.410 41.667 0.00 0.00 46.72 2.29
1750 2021 5.070847 ACTCGGAAACCCGGTAATATATGTT 59.929 40.000 0.00 0.00 46.72 2.71
1751 2022 5.927819 TCGGAAACCCGGTAATATATGTTT 58.072 37.500 0.00 0.18 46.72 2.83
1752 2023 7.060383 TCGGAAACCCGGTAATATATGTTTA 57.940 36.000 0.00 0.00 46.72 2.01
1753 2024 6.928492 TCGGAAACCCGGTAATATATGTTTAC 59.072 38.462 0.00 0.55 46.72 2.01
1754 2025 6.930722 CGGAAACCCGGTAATATATGTTTACT 59.069 38.462 0.00 0.00 43.22 2.24
1755 2026 7.095523 CGGAAACCCGGTAATATATGTTTACTG 60.096 40.741 0.00 10.24 43.22 2.74
1756 2027 7.716560 GGAAACCCGGTAATATATGTTTACTGT 59.283 37.037 0.00 0.00 35.20 3.55
1757 2028 8.441312 AAACCCGGTAATATATGTTTACTGTG 57.559 34.615 0.00 8.31 35.20 3.66
1758 2029 7.364149 ACCCGGTAATATATGTTTACTGTGA 57.636 36.000 0.00 0.00 35.20 3.58
1759 2030 7.794041 ACCCGGTAATATATGTTTACTGTGAA 58.206 34.615 0.00 0.00 35.20 3.18
1760 2031 8.434392 ACCCGGTAATATATGTTTACTGTGAAT 58.566 33.333 0.00 0.00 35.20 2.57
1761 2032 9.932207 CCCGGTAATATATGTTTACTGTGAATA 57.068 33.333 0.00 0.00 35.20 1.75
1769 2040 5.416271 TGTTTACTGTGAATACTCCCTCC 57.584 43.478 0.00 0.00 0.00 4.30
1770 2041 4.081862 TGTTTACTGTGAATACTCCCTCCG 60.082 45.833 0.00 0.00 0.00 4.63
1771 2042 2.233305 ACTGTGAATACTCCCTCCGT 57.767 50.000 0.00 0.00 0.00 4.69
1772 2043 2.537143 ACTGTGAATACTCCCTCCGTT 58.463 47.619 0.00 0.00 0.00 4.44
1773 2044 2.904434 ACTGTGAATACTCCCTCCGTTT 59.096 45.455 0.00 0.00 0.00 3.60
1774 2045 3.056035 ACTGTGAATACTCCCTCCGTTTC 60.056 47.826 0.00 0.00 0.00 2.78
1775 2046 2.901192 TGTGAATACTCCCTCCGTTTCA 59.099 45.455 0.00 0.00 0.00 2.69
1776 2047 3.325425 TGTGAATACTCCCTCCGTTTCAA 59.675 43.478 0.00 0.00 0.00 2.69
1777 2048 4.202377 TGTGAATACTCCCTCCGTTTCAAA 60.202 41.667 0.00 0.00 0.00 2.69
1778 2049 4.941873 GTGAATACTCCCTCCGTTTCAAAT 59.058 41.667 0.00 0.00 0.00 2.32
1779 2050 5.414765 GTGAATACTCCCTCCGTTTCAAATT 59.585 40.000 0.00 0.00 0.00 1.82
1780 2051 6.596497 GTGAATACTCCCTCCGTTTCAAATTA 59.404 38.462 0.00 0.00 0.00 1.40
1781 2052 6.596497 TGAATACTCCCTCCGTTTCAAATTAC 59.404 38.462 0.00 0.00 0.00 1.89
1782 2053 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1783 2054 4.981812 ACTCCCTCCGTTTCAAATTACTT 58.018 39.130 0.00 0.00 0.00 2.24
1784 2055 4.760204 ACTCCCTCCGTTTCAAATTACTTG 59.240 41.667 0.00 0.00 36.25 3.16
1785 2056 4.721132 TCCCTCCGTTTCAAATTACTTGT 58.279 39.130 0.00 0.00 36.34 3.16
1786 2057 4.758165 TCCCTCCGTTTCAAATTACTTGTC 59.242 41.667 0.00 0.00 36.34 3.18
1787 2058 4.378046 CCCTCCGTTTCAAATTACTTGTCG 60.378 45.833 0.00 0.00 36.34 4.35
1788 2059 4.212636 CCTCCGTTTCAAATTACTTGTCGT 59.787 41.667 0.00 0.00 36.34 4.34
1789 2060 5.085636 TCCGTTTCAAATTACTTGTCGTG 57.914 39.130 0.00 0.00 36.34 4.35
1790 2061 4.024725 TCCGTTTCAAATTACTTGTCGTGG 60.025 41.667 0.00 0.00 36.34 4.94
1791 2062 4.260866 CCGTTTCAAATTACTTGTCGTGGT 60.261 41.667 0.00 0.00 36.34 4.16
1792 2063 5.267776 CGTTTCAAATTACTTGTCGTGGTT 58.732 37.500 0.00 0.00 36.34 3.67
1793 2064 5.740099 CGTTTCAAATTACTTGTCGTGGTTT 59.260 36.000 0.00 0.00 36.34 3.27
1794 2065 6.251801 CGTTTCAAATTACTTGTCGTGGTTTT 59.748 34.615 0.00 0.00 36.34 2.43
1795 2066 7.428761 CGTTTCAAATTACTTGTCGTGGTTTTA 59.571 33.333 0.00 0.00 36.34 1.52
1796 2067 9.074443 GTTTCAAATTACTTGTCGTGGTTTTAA 57.926 29.630 0.00 0.00 36.34 1.52
1797 2068 9.804758 TTTCAAATTACTTGTCGTGGTTTTAAT 57.195 25.926 0.00 0.00 36.34 1.40
1798 2069 9.804758 TTCAAATTACTTGTCGTGGTTTTAATT 57.195 25.926 0.00 0.00 36.34 1.40
1799 2070 9.453325 TCAAATTACTTGTCGTGGTTTTAATTC 57.547 29.630 0.00 0.00 36.34 2.17
1800 2071 9.239002 CAAATTACTTGTCGTGGTTTTAATTCA 57.761 29.630 0.00 0.00 0.00 2.57
1801 2072 9.804758 AAATTACTTGTCGTGGTTTTAATTCAA 57.195 25.926 0.00 0.00 0.00 2.69
1802 2073 9.804758 AATTACTTGTCGTGGTTTTAATTCAAA 57.195 25.926 0.00 0.00 0.00 2.69
1803 2074 9.974980 ATTACTTGTCGTGGTTTTAATTCAAAT 57.025 25.926 0.00 0.00 0.00 2.32
1804 2075 9.804758 TTACTTGTCGTGGTTTTAATTCAAATT 57.195 25.926 0.00 0.00 0.00 1.82
1805 2076 8.710835 ACTTGTCGTGGTTTTAATTCAAATTT 57.289 26.923 0.00 0.00 0.00 1.82
1806 2077 8.599774 ACTTGTCGTGGTTTTAATTCAAATTTG 58.400 29.630 12.15 12.15 0.00 2.32
1807 2078 8.703604 TTGTCGTGGTTTTAATTCAAATTTGA 57.296 26.923 16.91 16.91 34.92 2.69
1821 2092 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
1822 2093 6.853720 TCAAATTTGAACTAAAACCACGACA 58.146 32.000 18.45 0.00 33.55 4.35
1823 2094 7.313646 TCAAATTTGAACTAAAACCACGACAA 58.686 30.769 18.45 0.00 33.55 3.18
1824 2095 7.486551 TCAAATTTGAACTAAAACCACGACAAG 59.513 33.333 18.45 0.00 33.55 3.16
1825 2096 5.883503 TTTGAACTAAAACCACGACAAGT 57.116 34.783 0.00 0.00 0.00 3.16
1826 2097 6.981762 TTTGAACTAAAACCACGACAAGTA 57.018 33.333 0.00 0.00 0.00 2.24
1827 2098 6.981762 TTGAACTAAAACCACGACAAGTAA 57.018 33.333 0.00 0.00 0.00 2.24
1828 2099 7.556733 TTGAACTAAAACCACGACAAGTAAT 57.443 32.000 0.00 0.00 0.00 1.89
1829 2100 7.556733 TGAACTAAAACCACGACAAGTAATT 57.443 32.000 0.00 0.00 0.00 1.40
1830 2101 7.987649 TGAACTAAAACCACGACAAGTAATTT 58.012 30.769 0.00 0.00 0.00 1.82
1831 2102 7.911205 TGAACTAAAACCACGACAAGTAATTTG 59.089 33.333 0.00 0.00 42.68 2.32
1832 2103 6.731164 ACTAAAACCACGACAAGTAATTTGG 58.269 36.000 0.00 0.00 41.25 3.28
1833 2104 5.838531 AAAACCACGACAAGTAATTTGGA 57.161 34.783 0.00 0.00 41.25 3.53
1834 2105 5.838531 AAACCACGACAAGTAATTTGGAA 57.161 34.783 0.00 0.00 41.25 3.53
1835 2106 5.838531 AACCACGACAAGTAATTTGGAAA 57.161 34.783 0.00 0.00 41.25 3.13
1836 2107 5.432885 ACCACGACAAGTAATTTGGAAAG 57.567 39.130 0.00 0.00 41.25 2.62
1837 2108 4.277423 ACCACGACAAGTAATTTGGAAAGG 59.723 41.667 0.00 0.00 41.25 3.11
1838 2109 4.517453 CCACGACAAGTAATTTGGAAAGGA 59.483 41.667 0.00 0.00 41.25 3.36
1839 2110 5.334879 CCACGACAAGTAATTTGGAAAGGAG 60.335 44.000 0.00 0.00 41.25 3.69
1840 2111 4.760204 ACGACAAGTAATTTGGAAAGGAGG 59.240 41.667 0.00 0.00 41.25 4.30
1841 2112 4.156008 CGACAAGTAATTTGGAAAGGAGGG 59.844 45.833 0.00 0.00 41.25 4.30
1842 2113 5.321927 GACAAGTAATTTGGAAAGGAGGGA 58.678 41.667 0.00 0.00 41.25 4.20
1843 2114 5.325239 ACAAGTAATTTGGAAAGGAGGGAG 58.675 41.667 0.00 0.00 41.25 4.30
1844 2115 5.162980 ACAAGTAATTTGGAAAGGAGGGAGT 60.163 40.000 0.00 0.00 41.25 3.85
1845 2116 6.045106 ACAAGTAATTTGGAAAGGAGGGAGTA 59.955 38.462 0.00 0.00 41.25 2.59
1847 2118 5.791141 AGTAATTTGGAAAGGAGGGAGTAGT 59.209 40.000 0.00 0.00 0.00 2.73
1849 2120 5.695424 ATTTGGAAAGGAGGGAGTAGTAC 57.305 43.478 0.00 0.00 0.00 2.73
1854 2125 6.608922 TGGAAAGGAGGGAGTAGTACTATAC 58.391 44.000 5.75 3.55 0.00 1.47
1856 2127 5.903198 AAGGAGGGAGTAGTACTATACGT 57.097 43.478 5.75 0.00 0.00 3.57
1860 2131 6.728164 AGGAGGGAGTAGTACTATACGTATGA 59.272 42.308 18.37 0.57 0.00 2.15
1957 2261 3.305361 GCGACGTTGATTTCTTACCTACC 59.695 47.826 7.08 0.00 0.00 3.18
2041 2345 2.682856 TCTAGCTTGCGGCCATTTTTAG 59.317 45.455 2.24 0.00 43.05 1.85
2182 2490 2.358737 CTCGGCAGTTGGGGACAC 60.359 66.667 0.00 0.00 42.67 3.67
2183 2491 4.308458 TCGGCAGTTGGGGACACG 62.308 66.667 0.00 0.00 42.67 4.49
2185 2493 4.265056 GGCAGTTGGGGACACGGT 62.265 66.667 0.00 0.00 42.67 4.83
2530 2838 1.781555 CGTGCACGTCAAGGATGTC 59.218 57.895 30.50 0.00 28.28 3.06
2732 3041 3.869832 GCTGGTTCTACCGAGGTATTTTC 59.130 47.826 2.04 0.00 42.58 2.29
2743 3052 5.539582 CGAGGTATTTTCGGTTGATTTGA 57.460 39.130 0.00 0.00 34.56 2.69
2747 3056 7.467267 CGAGGTATTTTCGGTTGATTTGATCAT 60.467 37.037 0.00 0.00 35.42 2.45
2757 3067 6.020440 CGGTTGATTTGATCATTAACACATGC 60.020 38.462 0.00 0.00 39.39 4.06
3073 3387 0.459899 CCTGTCCATTCGATCGGTCA 59.540 55.000 16.41 2.22 0.00 4.02
3083 3397 5.635280 CCATTCGATCGGTCATATATATGCC 59.365 44.000 16.41 17.86 33.76 4.40
3107 3429 4.481463 ACACGTATGCACTTTTAATTGGC 58.519 39.130 0.00 0.00 0.00 4.52
3152 3474 1.608590 GGGTTGGTTGGCGATCATATG 59.391 52.381 0.00 0.00 0.00 1.78
3294 3618 3.916172 GCAAATATATCCGTGCATTGCAG 59.084 43.478 12.53 6.36 40.08 4.41
3295 3619 4.557296 GCAAATATATCCGTGCATTGCAGT 60.557 41.667 12.53 1.46 40.08 4.40
3298 3623 0.747644 TATCCGTGCATTGCAGTGGG 60.748 55.000 22.89 18.66 40.08 4.61
3324 3649 3.706802 ACACAATGCGTTCAAATGTGA 57.293 38.095 13.30 0.00 42.14 3.58
3329 3654 6.085573 CACAATGCGTTCAAATGTGATCTAA 58.914 36.000 2.12 0.00 42.14 2.10
3359 3684 2.158856 TGATGATCTCAGCCATCACACC 60.159 50.000 5.71 0.00 42.76 4.16
3412 3738 9.476202 AAGTGAATGTCCAATAGTTTTAAAAGC 57.524 29.630 0.00 0.00 0.00 3.51
3421 3747 8.573035 TCCAATAGTTTTAAAAGCAATCTCGTT 58.427 29.630 0.00 0.00 0.00 3.85
3476 3802 1.413077 GCCTACACCTAGTCCATCACC 59.587 57.143 0.00 0.00 0.00 4.02
3477 3803 2.747177 CCTACACCTAGTCCATCACCA 58.253 52.381 0.00 0.00 0.00 4.17
3581 3909 9.778993 CACTTTCTAAATCACATGGACTATTTG 57.221 33.333 0.00 0.00 0.00 2.32
3751 4390 9.191995 CACATATAGTCTAAAATGCACATACGA 57.808 33.333 0.00 0.00 0.00 3.43
3884 4560 9.851686 TGATCAGGTGCTAACAAATATTATTCT 57.148 29.630 0.00 0.00 0.00 2.40
3922 4605 4.864704 TCCTTCTTTTTAATGGGCACAC 57.135 40.909 0.00 0.00 0.00 3.82
3938 4621 3.192633 GGCACACCGGAGTTTATCATTTT 59.807 43.478 9.46 0.00 0.00 1.82
3939 4622 4.321675 GGCACACCGGAGTTTATCATTTTT 60.322 41.667 9.46 0.00 0.00 1.94
3940 4623 4.621034 GCACACCGGAGTTTATCATTTTTG 59.379 41.667 9.46 0.00 0.00 2.44
3941 4624 4.621034 CACACCGGAGTTTATCATTTTTGC 59.379 41.667 9.46 0.00 0.00 3.68
3942 4625 4.173256 CACCGGAGTTTATCATTTTTGCC 58.827 43.478 9.46 0.00 0.00 4.52
3943 4626 3.119637 ACCGGAGTTTATCATTTTTGCCG 60.120 43.478 9.46 0.00 36.25 5.69
3944 4627 2.851824 CGGAGTTTATCATTTTTGCCGC 59.148 45.455 0.00 0.00 0.00 6.53
3945 4628 3.671971 CGGAGTTTATCATTTTTGCCGCA 60.672 43.478 0.00 0.00 0.00 5.69
3946 4629 4.241681 GGAGTTTATCATTTTTGCCGCAA 58.758 39.130 0.38 0.38 0.00 4.85
3947 4630 4.688413 GGAGTTTATCATTTTTGCCGCAAA 59.312 37.500 14.60 14.60 0.00 3.68
3948 4631 5.178438 GGAGTTTATCATTTTTGCCGCAAAA 59.822 36.000 24.13 24.13 40.85 2.44
3993 4676 7.745620 TTTTAGTTCATTTCCTTCCTGAGAC 57.254 36.000 0.00 0.00 0.00 3.36
3994 4677 4.982241 AGTTCATTTCCTTCCTGAGACA 57.018 40.909 0.00 0.00 0.00 3.41
3995 4678 5.511386 AGTTCATTTCCTTCCTGAGACAT 57.489 39.130 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.749735 AAGGCACGTGCGTTGCAAC 62.750 57.895 38.62 22.21 45.90 4.17
54 55 2.549611 AAAAGGCACGTGCGTTGCAA 62.550 50.000 39.37 0.00 46.80 4.08
55 56 2.549611 AAAAAGGCACGTGCGTTGCA 62.550 50.000 39.37 0.00 46.80 4.08
56 57 0.592754 TAAAAAGGCACGTGCGTTGC 60.593 50.000 39.37 24.43 46.80 4.17
57 58 1.117234 GTAAAAAGGCACGTGCGTTG 58.883 50.000 39.37 7.44 46.80 4.10
59 60 1.868469 TAGTAAAAAGGCACGTGCGT 58.132 45.000 32.35 30.51 43.26 5.24
60 61 3.124636 AGAATAGTAAAAAGGCACGTGCG 59.875 43.478 32.35 0.65 43.26 5.34
61 62 4.680171 AGAATAGTAAAAAGGCACGTGC 57.320 40.909 32.15 32.15 41.14 5.34
80 81 9.020731 GGGACAAACCTCTTTTCATTATAAAGA 57.979 33.333 0.00 0.00 39.20 2.52
137 179 5.076182 TCACATTTTAGCCCACTTCAATGA 58.924 37.500 0.00 0.00 32.35 2.57
145 187 4.381932 CCCTGATTTCACATTTTAGCCCAC 60.382 45.833 0.00 0.00 0.00 4.61
199 245 8.658499 ACTCCGTATTTTCCACAAGATAATAC 57.342 34.615 6.16 6.16 41.91 1.89
239 285 1.890489 TCAAGCCCATCATGCATATGC 59.110 47.619 21.09 21.09 42.50 3.14
278 324 2.024590 GCCGCCCTAGGTAACGTCAT 62.025 60.000 8.29 0.00 46.39 3.06
381 440 2.081526 GGCGTACTCGTCGTCTGTA 58.918 57.895 0.00 0.00 39.49 2.74
397 456 4.503370 CCGAAGAAAAGTATTCTCTACGGC 59.497 45.833 13.75 0.00 35.15 5.68
404 469 5.172205 GTGAGAGCCGAAGAAAAGTATTCT 58.828 41.667 0.00 0.00 0.00 2.40
611 676 0.719465 ACCTCGATTTAAGCGTTGCG 59.281 50.000 1.83 0.00 0.00 4.85
646 711 4.994852 GGTGGGAAACTTTCTTTATTTGCC 59.005 41.667 1.57 0.00 42.41 4.52
736 801 0.172352 GAGAGAGCTGGAGTGGTTCG 59.828 60.000 0.00 0.00 0.00 3.95
776 841 1.226859 GCACTACGCATCGTGGCTA 60.227 57.895 1.77 0.00 41.87 3.93
855 920 3.314635 CCCTGCTACTTACTACAGTACCG 59.685 52.174 0.00 0.00 0.00 4.02
908 973 0.179081 GCAAGGTATCGACAGGTCCC 60.179 60.000 0.00 0.00 0.00 4.46
1113 1178 0.602905 GCACGTTGTAGCCCTTCTGT 60.603 55.000 0.00 0.00 0.00 3.41
1163 1228 6.712998 AGATGAACTCGAGTGTGCTACTATAT 59.287 38.462 20.85 0.00 40.53 0.86
1164 1229 6.056236 AGATGAACTCGAGTGTGCTACTATA 58.944 40.000 20.85 0.00 40.53 1.31
1167 1232 3.085533 AGATGAACTCGAGTGTGCTACT 58.914 45.455 20.85 11.08 44.02 2.57
1169 1234 3.838120 CAAGATGAACTCGAGTGTGCTA 58.162 45.455 20.85 4.42 0.00 3.49
1171 1236 1.127582 GCAAGATGAACTCGAGTGTGC 59.872 52.381 20.85 16.82 0.00 4.57
1172 1237 2.407090 TGCAAGATGAACTCGAGTGTG 58.593 47.619 20.85 11.33 0.00 3.82
1173 1238 2.820059 TGCAAGATGAACTCGAGTGT 57.180 45.000 20.85 9.42 0.00 3.55
1174 1239 3.122613 GTCTTGCAAGATGAACTCGAGTG 59.877 47.826 30.65 5.66 37.39 3.51
1176 1241 3.122613 GTGTCTTGCAAGATGAACTCGAG 59.877 47.826 30.65 11.84 37.39 4.04
1177 1242 3.059884 GTGTCTTGCAAGATGAACTCGA 58.940 45.455 30.65 3.70 37.39 4.04
1178 1243 3.062763 AGTGTCTTGCAAGATGAACTCG 58.937 45.455 30.65 1.04 37.39 4.18
1210 1283 1.891178 CGAACGATCGTGTTAGCAGA 58.109 50.000 23.51 0.00 44.06 4.26
1231 1311 2.079925 GGATCAACTGCCAGAAGTCAC 58.920 52.381 0.00 0.00 0.00 3.67
1357 1437 2.268920 GCGTGGAAGATGCCCTCA 59.731 61.111 0.00 0.00 0.00 3.86
1425 1505 4.021981 AGTTTCCAAGCAGGTTAGCAATTC 60.022 41.667 0.00 0.00 39.02 2.17
1440 1520 5.026038 TCGGTCAGAAGTTTAGTTTCCAA 57.974 39.130 0.00 0.00 0.00 3.53
1454 1534 1.043116 CCTGGTAGCCATCGGTCAGA 61.043 60.000 0.00 0.00 30.82 3.27
1456 1536 1.001120 TCCTGGTAGCCATCGGTCA 59.999 57.895 0.00 0.00 30.82 4.02
1459 1539 0.390860 CTTCTCCTGGTAGCCATCGG 59.609 60.000 0.00 0.00 30.82 4.18
1511 1594 2.743538 GCGGCTGCAGTGATCACA 60.744 61.111 27.02 6.47 42.15 3.58
1550 1633 0.319555 CGATGGTGGACGTGAACACT 60.320 55.000 12.54 0.00 37.72 3.55
1590 1673 2.846532 CTTGCTGGGGTCCCTGTT 59.153 61.111 8.15 0.00 37.37 3.16
1665 1748 9.088512 TGTATGTGAACAAAACAAACAATTACC 57.911 29.630 0.88 0.00 0.00 2.85
1686 1957 6.914215 GCAATGGATTATTGTGTCACTGTATG 59.086 38.462 4.27 0.00 46.35 2.39
1693 1964 8.978874 ATAAGTAGCAATGGATTATTGTGTCA 57.021 30.769 0.00 0.00 46.35 3.58
1706 1977 7.064609 TCCGAGTTTCAAAGATAAGTAGCAATG 59.935 37.037 0.00 0.00 0.00 2.82
1710 1981 6.963049 TTCCGAGTTTCAAAGATAAGTAGC 57.037 37.500 0.00 0.00 0.00 3.58
1730 2001 7.716560 ACAGTAAACATATATTACCGGGTTTCC 59.283 37.037 4.31 0.00 34.50 3.13
1743 2014 8.867097 GGAGGGAGTATTCACAGTAAACATATA 58.133 37.037 0.00 0.00 0.00 0.86
1744 2015 7.471539 CGGAGGGAGTATTCACAGTAAACATAT 60.472 40.741 0.00 0.00 0.00 1.78
1745 2016 6.183360 CGGAGGGAGTATTCACAGTAAACATA 60.183 42.308 0.00 0.00 0.00 2.29
1746 2017 5.395324 CGGAGGGAGTATTCACAGTAAACAT 60.395 44.000 0.00 0.00 0.00 2.71
1747 2018 4.081862 CGGAGGGAGTATTCACAGTAAACA 60.082 45.833 0.00 0.00 0.00 2.83
1748 2019 4.081807 ACGGAGGGAGTATTCACAGTAAAC 60.082 45.833 0.00 0.00 0.00 2.01
1749 2020 4.091549 ACGGAGGGAGTATTCACAGTAAA 58.908 43.478 0.00 0.00 0.00 2.01
1750 2021 3.705051 ACGGAGGGAGTATTCACAGTAA 58.295 45.455 0.00 0.00 0.00 2.24
1751 2022 3.377253 ACGGAGGGAGTATTCACAGTA 57.623 47.619 0.00 0.00 0.00 2.74
1752 2023 2.233305 ACGGAGGGAGTATTCACAGT 57.767 50.000 0.00 0.00 0.00 3.55
1753 2024 3.056107 TGAAACGGAGGGAGTATTCACAG 60.056 47.826 0.00 0.00 0.00 3.66
1754 2025 2.901192 TGAAACGGAGGGAGTATTCACA 59.099 45.455 0.00 0.00 0.00 3.58
1755 2026 3.604875 TGAAACGGAGGGAGTATTCAC 57.395 47.619 0.00 0.00 0.00 3.18
1756 2027 4.627284 TTTGAAACGGAGGGAGTATTCA 57.373 40.909 0.00 0.00 0.00 2.57
1757 2028 6.822170 AGTAATTTGAAACGGAGGGAGTATTC 59.178 38.462 0.00 0.00 0.00 1.75
1758 2029 6.718294 AGTAATTTGAAACGGAGGGAGTATT 58.282 36.000 0.00 0.00 0.00 1.89
1759 2030 6.309389 AGTAATTTGAAACGGAGGGAGTAT 57.691 37.500 0.00 0.00 0.00 2.12
1760 2031 5.750352 AGTAATTTGAAACGGAGGGAGTA 57.250 39.130 0.00 0.00 0.00 2.59
1761 2032 4.635699 AGTAATTTGAAACGGAGGGAGT 57.364 40.909 0.00 0.00 0.00 3.85
1762 2033 4.760204 ACAAGTAATTTGAAACGGAGGGAG 59.240 41.667 0.00 0.00 39.21 4.30
1763 2034 4.721132 ACAAGTAATTTGAAACGGAGGGA 58.279 39.130 0.00 0.00 39.21 4.20
1764 2035 4.378046 CGACAAGTAATTTGAAACGGAGGG 60.378 45.833 0.00 0.00 39.21 4.30
1765 2036 4.212636 ACGACAAGTAATTTGAAACGGAGG 59.787 41.667 0.00 0.00 39.21 4.30
1766 2037 5.137403 CACGACAAGTAATTTGAAACGGAG 58.863 41.667 0.00 0.00 39.21 4.63
1767 2038 4.024725 CCACGACAAGTAATTTGAAACGGA 60.025 41.667 0.00 0.00 39.21 4.69
1768 2039 4.215965 CCACGACAAGTAATTTGAAACGG 58.784 43.478 0.00 0.00 39.21 4.44
1769 2040 4.839796 ACCACGACAAGTAATTTGAAACG 58.160 39.130 0.00 0.00 39.21 3.60
1770 2041 7.514573 AAAACCACGACAAGTAATTTGAAAC 57.485 32.000 0.00 0.00 39.21 2.78
1771 2042 9.804758 ATTAAAACCACGACAAGTAATTTGAAA 57.195 25.926 0.00 0.00 39.21 2.69
1772 2043 9.804758 AATTAAAACCACGACAAGTAATTTGAA 57.195 25.926 0.00 0.00 39.21 2.69
1773 2044 9.453325 GAATTAAAACCACGACAAGTAATTTGA 57.547 29.630 0.00 0.00 39.21 2.69
1774 2045 9.239002 TGAATTAAAACCACGACAAGTAATTTG 57.761 29.630 0.00 0.00 42.68 2.32
1775 2046 9.804758 TTGAATTAAAACCACGACAAGTAATTT 57.195 25.926 0.00 0.00 0.00 1.82
1776 2047 9.804758 TTTGAATTAAAACCACGACAAGTAATT 57.195 25.926 0.00 0.00 0.00 1.40
1777 2048 9.974980 ATTTGAATTAAAACCACGACAAGTAAT 57.025 25.926 0.00 0.00 0.00 1.89
1778 2049 9.804758 AATTTGAATTAAAACCACGACAAGTAA 57.195 25.926 0.00 0.00 0.00 2.24
1779 2050 9.804758 AAATTTGAATTAAAACCACGACAAGTA 57.195 25.926 0.00 0.00 0.00 2.24
1780 2051 8.599774 CAAATTTGAATTAAAACCACGACAAGT 58.400 29.630 13.08 0.00 0.00 3.16
1781 2052 8.812329 TCAAATTTGAATTAAAACCACGACAAG 58.188 29.630 18.45 0.00 33.55 3.16
1782 2053 8.703604 TCAAATTTGAATTAAAACCACGACAA 57.296 26.923 18.45 0.00 33.55 3.18
1783 2054 8.703604 TTCAAATTTGAATTAAAACCACGACA 57.296 26.923 26.01 2.16 41.88 4.35
1797 2068 7.313646 TGTCGTGGTTTTAGTTCAAATTTGAA 58.686 30.769 26.01 26.01 44.31 2.69
1798 2069 6.853720 TGTCGTGGTTTTAGTTCAAATTTGA 58.146 32.000 16.91 16.91 34.92 2.69
1799 2070 7.274686 ACTTGTCGTGGTTTTAGTTCAAATTTG 59.725 33.333 12.15 12.15 0.00 2.32
1800 2071 7.317390 ACTTGTCGTGGTTTTAGTTCAAATTT 58.683 30.769 0.00 0.00 0.00 1.82
1801 2072 6.859017 ACTTGTCGTGGTTTTAGTTCAAATT 58.141 32.000 0.00 0.00 0.00 1.82
1802 2073 6.445357 ACTTGTCGTGGTTTTAGTTCAAAT 57.555 33.333 0.00 0.00 0.00 2.32
1803 2074 5.883503 ACTTGTCGTGGTTTTAGTTCAAA 57.116 34.783 0.00 0.00 0.00 2.69
1804 2075 6.981762 TTACTTGTCGTGGTTTTAGTTCAA 57.018 33.333 0.00 0.00 0.00 2.69
1805 2076 7.556733 AATTACTTGTCGTGGTTTTAGTTCA 57.443 32.000 0.00 0.00 0.00 3.18
1806 2077 7.377662 CCAAATTACTTGTCGTGGTTTTAGTTC 59.622 37.037 0.00 0.00 32.65 3.01
1807 2078 7.067251 TCCAAATTACTTGTCGTGGTTTTAGTT 59.933 33.333 0.00 0.00 32.65 2.24
1808 2079 6.543100 TCCAAATTACTTGTCGTGGTTTTAGT 59.457 34.615 0.00 0.00 32.65 2.24
1809 2080 6.961576 TCCAAATTACTTGTCGTGGTTTTAG 58.038 36.000 0.00 0.00 32.65 1.85
1810 2081 6.939132 TCCAAATTACTTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 32.65 1.52
1811 2082 5.838531 TCCAAATTACTTGTCGTGGTTTT 57.161 34.783 0.00 0.00 32.65 2.43
1812 2083 5.838531 TTCCAAATTACTTGTCGTGGTTT 57.161 34.783 0.00 0.00 32.65 3.27
1813 2084 5.221165 CCTTTCCAAATTACTTGTCGTGGTT 60.221 40.000 0.00 0.00 32.65 3.67
1814 2085 4.277423 CCTTTCCAAATTACTTGTCGTGGT 59.723 41.667 0.00 0.00 32.65 4.16
1815 2086 4.517453 TCCTTTCCAAATTACTTGTCGTGG 59.483 41.667 0.00 0.00 32.65 4.94
1816 2087 5.334879 CCTCCTTTCCAAATTACTTGTCGTG 60.335 44.000 0.00 0.00 32.65 4.35
1817 2088 4.760204 CCTCCTTTCCAAATTACTTGTCGT 59.240 41.667 0.00 0.00 32.65 4.34
1818 2089 4.156008 CCCTCCTTTCCAAATTACTTGTCG 59.844 45.833 0.00 0.00 32.65 4.35
1819 2090 5.321927 TCCCTCCTTTCCAAATTACTTGTC 58.678 41.667 0.00 0.00 32.65 3.18
1820 2091 5.162980 ACTCCCTCCTTTCCAAATTACTTGT 60.163 40.000 0.00 0.00 32.65 3.16
1821 2092 5.325239 ACTCCCTCCTTTCCAAATTACTTG 58.675 41.667 0.00 0.00 34.52 3.16
1822 2093 5.600669 ACTCCCTCCTTTCCAAATTACTT 57.399 39.130 0.00 0.00 0.00 2.24
1823 2094 5.791141 ACTACTCCCTCCTTTCCAAATTACT 59.209 40.000 0.00 0.00 0.00 2.24
1824 2095 6.063496 ACTACTCCCTCCTTTCCAAATTAC 57.937 41.667 0.00 0.00 0.00 1.89
1825 2096 6.964086 AGTACTACTCCCTCCTTTCCAAATTA 59.036 38.462 0.00 0.00 0.00 1.40
1826 2097 5.791141 AGTACTACTCCCTCCTTTCCAAATT 59.209 40.000 0.00 0.00 0.00 1.82
1827 2098 5.351405 AGTACTACTCCCTCCTTTCCAAAT 58.649 41.667 0.00 0.00 0.00 2.32
1828 2099 4.759953 AGTACTACTCCCTCCTTTCCAAA 58.240 43.478 0.00 0.00 0.00 3.28
1829 2100 4.415224 AGTACTACTCCCTCCTTTCCAA 57.585 45.455 0.00 0.00 0.00 3.53
1830 2101 5.745988 ATAGTACTACTCCCTCCTTTCCA 57.254 43.478 4.31 0.00 0.00 3.53
1831 2102 5.704978 CGTATAGTACTACTCCCTCCTTTCC 59.295 48.000 4.31 0.00 0.00 3.13
1832 2103 6.295249 ACGTATAGTACTACTCCCTCCTTTC 58.705 44.000 4.31 0.00 0.00 2.62
1833 2104 6.259346 ACGTATAGTACTACTCCCTCCTTT 57.741 41.667 4.31 0.00 0.00 3.11
1834 2105 5.903198 ACGTATAGTACTACTCCCTCCTT 57.097 43.478 4.31 0.00 0.00 3.36
1835 2106 6.728164 TCATACGTATAGTACTACTCCCTCCT 59.272 42.308 7.96 0.00 38.29 3.69
1836 2107 6.940739 TCATACGTATAGTACTACTCCCTCC 58.059 44.000 7.96 0.00 38.29 4.30
1838 2109 9.883142 GTAATCATACGTATAGTACTACTCCCT 57.117 37.037 7.96 0.00 38.29 4.20
1839 2110 9.883142 AGTAATCATACGTATAGTACTACTCCC 57.117 37.037 17.12 0.00 38.29 4.30
1854 2125 7.651704 TGTACCATCATTGACAGTAATCATACG 59.348 37.037 0.00 0.00 37.11 3.06
1856 2127 8.482128 TGTGTACCATCATTGACAGTAATCATA 58.518 33.333 0.00 0.00 0.00 2.15
1860 2131 7.994425 TTTGTGTACCATCATTGACAGTAAT 57.006 32.000 0.00 0.00 0.00 1.89
1867 2138 5.241662 TCGACATTTGTGTACCATCATTGA 58.758 37.500 0.00 0.00 0.00 2.57
1880 2184 2.631160 TGGTGAACCTCGACATTTGT 57.369 45.000 0.37 0.00 36.82 2.83
2041 2345 1.806247 GCAAAAGGTGTTTGGAGTGGC 60.806 52.381 1.38 0.00 0.00 5.01
2182 2490 1.196808 CAAAAAGTGGATGACCGACCG 59.803 52.381 0.00 0.00 39.42 4.79
2183 2491 2.484264 CTCAAAAAGTGGATGACCGACC 59.516 50.000 0.00 0.00 39.42 4.79
2184 2492 3.139077 ACTCAAAAAGTGGATGACCGAC 58.861 45.455 0.00 0.00 36.65 4.79
2185 2493 3.485463 ACTCAAAAAGTGGATGACCGA 57.515 42.857 0.00 0.00 36.65 4.69
2260 2568 9.361315 TCATGCATGCTATGATTTAAATATTGC 57.639 29.630 22.25 8.37 30.03 3.56
2633 2941 0.902984 TACTCGGGGAAGAGCTTGCA 60.903 55.000 4.17 0.00 41.77 4.08
2732 3041 6.020440 GCATGTGTTAATGATCAAATCAACCG 60.020 38.462 0.00 0.00 43.50 4.44
2757 3067 1.567537 CACCTACACACCAAACGCG 59.432 57.895 3.53 3.53 0.00 6.01
3054 3368 0.459899 TGACCGATCGAATGGACAGG 59.540 55.000 18.66 0.00 0.00 4.00
3083 3397 5.737290 GCCAATTAAAAGTGCATACGTGTAG 59.263 40.000 0.00 0.00 0.00 2.74
3152 3474 3.444703 ACAGCACTGATCGATCCTTAC 57.555 47.619 22.31 9.81 0.00 2.34
3277 3601 2.493035 CCACTGCAATGCACGGATATA 58.507 47.619 2.72 0.00 33.79 0.86
3281 3605 2.672651 CCCACTGCAATGCACGGA 60.673 61.111 17.78 0.00 33.79 4.69
3313 3638 7.805071 CACCTTTGAGTTAGATCACATTTGAAC 59.195 37.037 0.00 0.00 34.61 3.18
3324 3649 7.429374 TGAGATCATCACCTTTGAGTTAGAT 57.571 36.000 0.00 0.00 34.35 1.98
3329 3654 3.370315 GGCTGAGATCATCACCTTTGAGT 60.370 47.826 0.00 0.00 34.35 3.41
3359 3684 3.367292 GCATGGTTCAATTGTGGGTGTAG 60.367 47.826 5.13 0.00 0.00 2.74
3412 3738 1.938577 CATCCCAGCTCAACGAGATTG 59.061 52.381 0.00 0.00 39.94 2.67
3421 3747 1.676678 GCGGTAGTCATCCCAGCTCA 61.677 60.000 0.00 0.00 0.00 4.26
3476 3802 1.136891 TGAGTGCGGGTATGAGTGATG 59.863 52.381 0.00 0.00 0.00 3.07
3477 3803 1.137086 GTGAGTGCGGGTATGAGTGAT 59.863 52.381 0.00 0.00 0.00 3.06
3623 3951 4.701171 TCATGCAATTCTGTTCACATGCTA 59.299 37.500 0.00 0.00 35.89 3.49
3764 4404 8.831550 GTGTTGGTGCCTTTTGAAAAATATTAA 58.168 29.630 0.00 0.00 0.00 1.40
3884 4560 5.509498 AGAAGGAATGCATGGCTAACTTAA 58.491 37.500 0.00 0.00 0.00 1.85
3922 4605 3.434637 CGGCAAAAATGATAAACTCCGG 58.565 45.455 0.00 0.00 0.00 5.14
3968 4651 7.777910 TGTCTCAGGAAGGAAATGAACTAAAAA 59.222 33.333 0.00 0.00 0.00 1.94
3969 4652 7.287061 TGTCTCAGGAAGGAAATGAACTAAAA 58.713 34.615 0.00 0.00 0.00 1.52
3970 4653 6.837312 TGTCTCAGGAAGGAAATGAACTAAA 58.163 36.000 0.00 0.00 0.00 1.85
3971 4654 6.433847 TGTCTCAGGAAGGAAATGAACTAA 57.566 37.500 0.00 0.00 0.00 2.24
3972 4655 6.627087 ATGTCTCAGGAAGGAAATGAACTA 57.373 37.500 0.00 0.00 0.00 2.24
3973 4656 4.982241 TGTCTCAGGAAGGAAATGAACT 57.018 40.909 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.