Multiple sequence alignment - TraesCS1D01G210200

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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 TraesCS1D01G210200 chr1D 100.000 6889 0 0 1 6889 296272337 296279225 0.000000e+00 12722.0
1 TraesCS1D01G210200 chr1D 84.507 710 98 8 6187 6889 100453199 100453903 0.000000e+00 691.0
2 TraesCS1D01G210200 chr1D 85.922 206 20 4 3414 3613 296275521 296275723 1.950000e-50 211.0
3 TraesCS1D01G210200 chr1D 85.922 206 20 4 3185 3387 296275750 296275949 1.950000e-50 211.0
4 TraesCS1D01G210200 chr1D 89.216 102 11 0 3513 3614 487198692 487198591 2.020000e-25 128.0
5 TraesCS1D01G210200 chr1D 94.286 35 1 1 1608 1641 404135902 404135868 1.200000e-02 52.8
6 TraesCS1D01G210200 chr1A 95.187 4654 168 28 1560 6187 369049685 369054308 0.000000e+00 7302.0
7 TraesCS1D01G210200 chr1A 94.525 621 15 5 892 1512 369048993 369049594 0.000000e+00 941.0
8 TraesCS1D01G210200 chr1A 85.085 704 85 17 6189 6889 344296067 344296753 0.000000e+00 701.0
9 TraesCS1D01G210200 chr1A 83.230 644 51 29 1 633 369047966 369048563 7.860000e-149 538.0
10 TraesCS1D01G210200 chr1A 85.437 206 21 4 3414 3613 369051314 369051516 9.060000e-49 206.0
11 TraesCS1D01G210200 chr1A 85.437 206 21 5 3185 3387 369051543 369051742 9.060000e-49 206.0
12 TraesCS1D01G210200 chr1A 84.043 94 15 0 3502 3595 235358872 235358965 2.650000e-14 91.6
13 TraesCS1D01G210200 chr1B 95.035 3726 134 21 1551 5258 397792607 397796299 0.000000e+00 5808.0
14 TraesCS1D01G210200 chr1B 91.213 1525 77 30 1 1504 397791032 397792520 0.000000e+00 2021.0
15 TraesCS1D01G210200 chr1B 89.258 391 24 10 5807 6187 397797005 397797387 2.250000e-129 473.0
16 TraesCS1D01G210200 chr1B 85.460 337 38 9 5431 5765 397796585 397796912 2.380000e-89 340.0
17 TraesCS1D01G210200 chr1B 89.000 200 19 2 3414 3613 397794235 397794431 1.920000e-60 244.0
18 TraesCS1D01G210200 chr1B 84.804 204 22 7 3185 3385 397794458 397794655 5.450000e-46 196.0
19 TraesCS1D01G210200 chr1B 92.105 114 9 0 5526 5639 211335057 211335170 1.990000e-35 161.0
20 TraesCS1D01G210200 chr1B 90.411 73 7 0 5325 5397 179997414 179997342 5.690000e-16 97.1
21 TraesCS1D01G210200 chr1B 85.227 88 11 1 3510 3595 230715955 230715868 9.520000e-14 89.8
22 TraesCS1D01G210200 chr1B 95.238 42 2 0 5528 5569 292050415 292050374 4.460000e-07 67.6
23 TraesCS1D01G210200 chr6D 86.676 713 78 8 6189 6889 65107536 65108243 0.000000e+00 774.0
24 TraesCS1D01G210200 chr6D 90.000 140 8 3 5431 5564 95895398 95895259 7.100000e-40 176.0
25 TraesCS1D01G210200 chr6D 91.892 74 6 0 5324 5397 77394876 77394803 3.400000e-18 104.0
26 TraesCS1D01G210200 chr6B 86.563 707 86 6 6189 6889 514660420 514659717 0.000000e+00 771.0
27 TraesCS1D01G210200 chr6B 84.463 708 97 8 6189 6889 510707716 510707015 0.000000e+00 686.0
28 TraesCS1D01G210200 chr6B 91.892 74 6 0 5324 5397 425430516 425430589 3.400000e-18 104.0
29 TraesCS1D01G210200 chr7D 86.080 704 86 11 6189 6889 461392216 461391522 0.000000e+00 747.0
30 TraesCS1D01G210200 chr3A 85.915 710 85 12 6186 6889 682009056 682009756 0.000000e+00 743.0
31 TraesCS1D01G210200 chr2D 85.196 716 88 10 6182 6889 293684798 293685503 0.000000e+00 719.0
32 TraesCS1D01G210200 chr2D 84.724 707 94 14 6187 6889 563024178 563024874 0.000000e+00 695.0
33 TraesCS1D01G210200 chr3B 88.991 109 10 2 5431 5537 410368455 410368563 4.330000e-27 134.0
34 TraesCS1D01G210200 chr3B 87.963 108 11 2 5431 5536 341341694 341341587 7.250000e-25 126.0
35 TraesCS1D01G210200 chrUn 91.892 74 6 0 5324 5397 88746813 88746886 3.400000e-18 104.0
36 TraesCS1D01G210200 chr4B 91.892 74 6 0 5324 5397 299463085 299463012 3.400000e-18 104.0
37 TraesCS1D01G210200 chr5A 84.112 107 15 2 3510 3615 367594130 367594235 1.220000e-17 102.0
38 TraesCS1D01G210200 chr5B 90.541 74 7 0 5324 5397 692099477 692099550 1.580000e-16 99.0
39 TraesCS1D01G210200 chr5B 87.302 63 8 0 3068 3130 698067758 698067820 9.580000e-09 73.1
40 TraesCS1D01G210200 chr7B 90.141 71 7 0 5327 5397 120491328 120491258 7.360000e-15 93.5
41 TraesCS1D01G210200 chr5D 96.000 50 2 0 5505 5554 378344679 378344728 1.590000e-11 82.4


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 TraesCS1D01G210200 chr1D 296272337 296279225 6888 False 4381.333333 12722 90.614667 1 6889 3 chr1D.!!$F2 6888
1 TraesCS1D01G210200 chr1D 100453199 100453903 704 False 691.000000 691 84.507000 6187 6889 1 chr1D.!!$F1 702
2 TraesCS1D01G210200 chr1A 369047966 369054308 6342 False 1838.600000 7302 88.763200 1 6187 5 chr1A.!!$F3 6186
3 TraesCS1D01G210200 chr1A 344296067 344296753 686 False 701.000000 701 85.085000 6189 6889 1 chr1A.!!$F2 700
4 TraesCS1D01G210200 chr1B 397791032 397797387 6355 False 1513.666667 5808 89.128333 1 6187 6 chr1B.!!$F2 6186
5 TraesCS1D01G210200 chr6D 65107536 65108243 707 False 774.000000 774 86.676000 6189 6889 1 chr6D.!!$F1 700
6 TraesCS1D01G210200 chr6B 514659717 514660420 703 True 771.000000 771 86.563000 6189 6889 1 chr6B.!!$R2 700
7 TraesCS1D01G210200 chr6B 510707015 510707716 701 True 686.000000 686 84.463000 6189 6889 1 chr6B.!!$R1 700
8 TraesCS1D01G210200 chr7D 461391522 461392216 694 True 747.000000 747 86.080000 6189 6889 1 chr7D.!!$R1 700
9 TraesCS1D01G210200 chr3A 682009056 682009756 700 False 743.000000 743 85.915000 6186 6889 1 chr3A.!!$F1 703
10 TraesCS1D01G210200 chr2D 293684798 293685503 705 False 719.000000 719 85.196000 6182 6889 1 chr2D.!!$F1 707
11 TraesCS1D01G210200 chr2D 563024178 563024874 696 False 695.000000 695 84.724000 6187 6889 1 chr2D.!!$F2 702

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
836 886 0.533755 CGTTGGGGATGGAGATGCTC 60.534 60.000 0.00 0.00 0.00 4.26 F
1504 1803 0.450184 GACGGTGTGCTCTCTCTCTC 59.550 60.000 0.00 0.00 0.00 3.20 F
1829 2174 0.173708 GTCGGTGTAGCTCCTTCCAG 59.826 60.000 0.00 0.00 0.00 3.86 F
2333 2681 3.194542 AGCTCGAGACTTATGCTTTGAGT 59.805 43.478 18.75 0.00 0.00 3.41 F
3856 4225 2.567615 AGGTTCTGTACTGACATGGACC 59.432 50.000 10.88 10.88 34.76 4.46 F
4699 5071 0.454600 GCAGTGTCCAGGCATGAATG 59.545 55.000 0.00 0.00 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 2149 0.460284 GGAGCTACACCGACACCATG 60.460 60.000 0.0 0.0 0.00 3.66 R
2959 3326 3.511540 GGGAAAGATGAAAAACCCTGAGG 59.488 47.826 0.0 0.0 40.04 3.86 R
3604 3972 8.665685 ACTGTGTTCGAAATAGGCTAATTTTAG 58.334 33.333 0.0 0.0 0.00 1.85 R
3993 4362 3.263261 GCTTTCCTTAGTGCTACTGGAC 58.737 50.000 0.0 0.0 34.56 4.02 R
5191 5564 1.476891 GTCTGCCCGTGAGAGATACAA 59.523 52.381 0.0 0.0 0.00 2.41 R
6178 6749 0.037232 GAGTTGCTCTAAGCCCACGT 60.037 55.000 0.0 0.0 41.51 4.49 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
84 87 8.815141 TTTGTTATGAATCTGTGACCATTTTG 57.185 30.769 0.00 0.00 0.00 2.44
100 103 7.496920 TGACCATTTTGCAAATTGACAAACATA 59.503 29.630 27.41 5.15 35.60 2.29
135 138 6.193776 CGCGAACATATTTTTATCTTTTGCGA 59.806 34.615 0.00 0.00 44.43 5.10
172 177 9.985318 GAATTGTGAACATTTGTTTTTGAATCA 57.015 25.926 0.00 0.00 38.56 2.57
179 184 5.051774 ACATTTGTTTTTGAATCAGCGAACG 60.052 36.000 0.00 0.00 0.00 3.95
242 248 7.935338 TGAATCAGCAAACTTTTTCTGAATC 57.065 32.000 7.92 9.43 42.14 2.52
244 250 4.858935 TCAGCAAACTTTTTCTGAATCGG 58.141 39.130 2.09 0.00 37.47 4.18
255 261 5.452078 TTTCTGAATCGGTGAGCATTTTT 57.548 34.783 0.00 0.00 0.00 1.94
393 403 9.912634 ACACGAAACATTTAATGATTTCAGATT 57.087 25.926 21.00 2.36 33.70 2.40
439 449 1.982073 GAAACATTCCAGCCCGCTCG 61.982 60.000 0.00 0.00 0.00 5.03
497 508 1.909700 ATGCATCACCCGTTGAAACT 58.090 45.000 0.00 0.00 37.92 2.66
499 510 0.951558 GCATCACCCGTTGAAACTGT 59.048 50.000 0.00 0.00 37.92 3.55
564 578 4.794278 AGCATCATTTCTGCACATTTGA 57.206 36.364 0.00 0.00 42.15 2.69
746 789 6.678878 AGCTAAGAAATATGAATAGACGCGA 58.321 36.000 15.93 0.00 0.00 5.87
759 802 7.411274 TGAATAGACGCGAAAAAGAAAAGAAA 58.589 30.769 15.93 0.00 0.00 2.52
760 803 8.073768 TGAATAGACGCGAAAAAGAAAAGAAAT 58.926 29.630 15.93 0.00 0.00 2.17
806 849 7.071698 AGAGGCTCTATATTTGAAGATGTGGAA 59.928 37.037 17.09 0.00 0.00 3.53
807 850 7.753630 AGGCTCTATATTTGAAGATGTGGAAT 58.246 34.615 0.00 0.00 0.00 3.01
823 873 2.207788 GAATTTGACGGGCCGTTGGG 62.208 60.000 34.58 2.80 41.37 4.12
830 880 4.506255 GGGCCGTTGGGGATGGAG 62.506 72.222 0.00 0.00 38.47 3.86
831 881 3.407967 GGCCGTTGGGGATGGAGA 61.408 66.667 0.00 0.00 38.47 3.71
832 882 2.757124 GGCCGTTGGGGATGGAGAT 61.757 63.158 0.00 0.00 38.47 2.75
833 883 1.526917 GCCGTTGGGGATGGAGATG 60.527 63.158 0.00 0.00 38.47 2.90
834 884 1.526917 CCGTTGGGGATGGAGATGC 60.527 63.158 0.00 0.00 38.47 3.91
835 885 1.528824 CGTTGGGGATGGAGATGCT 59.471 57.895 0.00 0.00 0.00 3.79
836 886 0.533755 CGTTGGGGATGGAGATGCTC 60.534 60.000 0.00 0.00 0.00 4.26
837 887 0.548031 GTTGGGGATGGAGATGCTCA 59.452 55.000 0.00 0.00 31.08 4.26
857 907 1.445238 GCTCTCACAGTCTCACGCC 60.445 63.158 0.00 0.00 0.00 5.68
858 908 1.959848 CTCTCACAGTCTCACGCCA 59.040 57.895 0.00 0.00 0.00 5.69
864 914 1.066858 CACAGTCTCACGCCAATACCT 60.067 52.381 0.00 0.00 0.00 3.08
1044 1343 2.047443 GTTCGCGTCTCCTCCTCCT 61.047 63.158 5.77 0.00 0.00 3.69
1224 1523 1.097547 GGAACGACGACTCGGGGATA 61.098 60.000 0.00 0.00 44.80 2.59
1504 1803 0.450184 GACGGTGTGCTCTCTCTCTC 59.550 60.000 0.00 0.00 0.00 3.20
1506 1805 0.732571 CGGTGTGCTCTCTCTCTCTC 59.267 60.000 0.00 0.00 0.00 3.20
1512 1811 3.118629 TGTGCTCTCTCTCTCTCTCTCTC 60.119 52.174 0.00 0.00 0.00 3.20
1513 1812 3.133721 GTGCTCTCTCTCTCTCTCTCTCT 59.866 52.174 0.00 0.00 0.00 3.10
1515 1814 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
1516 1815 4.100808 GCTCTCTCTCTCTCTCTCTCTCTT 59.899 50.000 0.00 0.00 0.00 2.85
1517 1816 5.396213 GCTCTCTCTCTCTCTCTCTCTCTTT 60.396 48.000 0.00 0.00 0.00 2.52
1518 1817 6.227298 TCTCTCTCTCTCTCTCTCTCTTTC 57.773 45.833 0.00 0.00 0.00 2.62
1519 1818 5.960811 TCTCTCTCTCTCTCTCTCTCTTTCT 59.039 44.000 0.00 0.00 0.00 2.52
1520 1819 6.097554 TCTCTCTCTCTCTCTCTCTCTTTCTC 59.902 46.154 0.00 0.00 0.00 2.87
1522 1821 6.213397 TCTCTCTCTCTCTCTCTCTTTCTCAA 59.787 42.308 0.00 0.00 0.00 3.02
1524 1823 7.405292 TCTCTCTCTCTCTCTCTTTCTCAAAT 58.595 38.462 0.00 0.00 0.00 2.32
1525 1824 7.337689 TCTCTCTCTCTCTCTCTTTCTCAAATG 59.662 40.741 0.00 0.00 0.00 2.32
1526 1825 5.964758 TCTCTCTCTCTCTTTCTCAAATGC 58.035 41.667 0.00 0.00 0.00 3.56
1527 1826 5.716228 TCTCTCTCTCTCTTTCTCAAATGCT 59.284 40.000 0.00 0.00 0.00 3.79
1529 1828 7.560991 TCTCTCTCTCTCTTTCTCAAATGCTAT 59.439 37.037 0.00 0.00 0.00 2.97
1530 1829 8.759481 TCTCTCTCTCTTTCTCAAATGCTATA 57.241 34.615 0.00 0.00 0.00 1.31
1532 1831 7.432869 TCTCTCTCTTTCTCAAATGCTATAGC 58.567 38.462 18.18 18.18 42.50 2.97
1534 1833 4.747108 TCTCTTTCTCAAATGCTATAGCGC 59.253 41.667 19.55 0.00 45.83 5.92
1535 1834 3.809832 TCTTTCTCAAATGCTATAGCGCC 59.190 43.478 19.55 0.00 45.83 6.53
1536 1835 3.475566 TTCTCAAATGCTATAGCGCCT 57.524 42.857 19.55 4.45 45.83 5.52
1537 1836 3.032017 TCTCAAATGCTATAGCGCCTC 57.968 47.619 19.55 0.00 45.83 4.70
1538 1837 2.365293 TCTCAAATGCTATAGCGCCTCA 59.635 45.455 19.55 2.08 45.83 3.86
1539 1838 3.133691 CTCAAATGCTATAGCGCCTCAA 58.866 45.455 19.55 1.31 45.83 3.02
1540 1839 3.540617 TCAAATGCTATAGCGCCTCAAA 58.459 40.909 19.55 0.55 45.83 2.69
1542 1841 5.304778 TCAAATGCTATAGCGCCTCAAATA 58.695 37.500 19.55 0.00 45.83 1.40
1543 1842 5.179368 TCAAATGCTATAGCGCCTCAAATAC 59.821 40.000 19.55 0.00 45.83 1.89
1544 1843 4.543590 ATGCTATAGCGCCTCAAATACT 57.456 40.909 19.55 0.00 45.83 2.12
1545 1844 3.914312 TGCTATAGCGCCTCAAATACTC 58.086 45.455 19.55 0.00 45.83 2.59
1546 1845 2.917971 GCTATAGCGCCTCAAATACTCG 59.082 50.000 9.40 0.00 0.00 4.18
1547 1846 3.612004 GCTATAGCGCCTCAAATACTCGT 60.612 47.826 9.40 0.00 0.00 4.18
1548 1847 4.379186 GCTATAGCGCCTCAAATACTCGTA 60.379 45.833 9.40 0.00 0.00 3.43
1549 1848 2.953466 AGCGCCTCAAATACTCGTAA 57.047 45.000 2.29 0.00 0.00 3.18
1550 1849 2.537401 AGCGCCTCAAATACTCGTAAC 58.463 47.619 2.29 0.00 0.00 2.50
1552 1851 2.028883 GCGCCTCAAATACTCGTAACAC 59.971 50.000 0.00 0.00 0.00 3.32
1556 1855 5.163893 CGCCTCAAATACTCGTAACACAATT 60.164 40.000 0.00 0.00 0.00 2.32
1557 1856 6.608610 GCCTCAAATACTCGTAACACAATTT 58.391 36.000 0.00 0.00 0.00 1.82
1558 1857 6.523201 GCCTCAAATACTCGTAACACAATTTG 59.477 38.462 0.00 0.00 36.25 2.32
1559 1858 7.572353 GCCTCAAATACTCGTAACACAATTTGA 60.572 37.037 2.79 7.74 39.64 2.69
1560 1859 8.865753 CTCAAATACTCGTAACACAATTTGAG 57.134 34.615 16.62 16.62 46.44 3.02
1561 1860 7.802738 TCAAATACTCGTAACACAATTTGAGG 58.197 34.615 2.79 0.00 38.02 3.86
1585 1928 8.107095 AGGCACATAACTTTTGTCCTAAGATAA 58.893 33.333 0.00 0.00 0.00 1.75
1586 1929 8.398665 GGCACATAACTTTTGTCCTAAGATAAG 58.601 37.037 0.00 0.00 0.00 1.73
1675 2018 6.320434 TGGAAACATATTCCACTGTGGATA 57.680 37.500 28.76 21.30 43.17 2.59
1676 2019 6.910191 TGGAAACATATTCCACTGTGGATAT 58.090 36.000 28.76 23.72 43.17 1.63
1713 2056 9.821662 GTTTGGTATTGTAGATGTAACAGTTTC 57.178 33.333 0.00 0.00 0.00 2.78
1731 2076 6.811665 ACAGTTTCTTTTTCTGTAAACTTGGC 59.188 34.615 0.00 0.00 39.50 4.52
1749 2094 2.428890 TGGCCAACCTTACACAAGTTTG 59.571 45.455 0.61 0.00 34.78 2.93
1783 2128 6.110411 ACAGTTATACACCTTACTTGCTGT 57.890 37.500 0.00 0.00 0.00 4.40
1784 2129 6.531021 ACAGTTATACACCTTACTTGCTGTT 58.469 36.000 0.00 0.00 30.50 3.16
1785 2130 6.426937 ACAGTTATACACCTTACTTGCTGTTG 59.573 38.462 0.00 0.00 30.50 3.33
1786 2131 5.411669 AGTTATACACCTTACTTGCTGTTGC 59.588 40.000 0.00 0.00 40.20 4.17
1787 2132 2.348411 ACACCTTACTTGCTGTTGCT 57.652 45.000 0.00 0.00 40.48 3.91
1788 2133 1.949525 ACACCTTACTTGCTGTTGCTG 59.050 47.619 0.00 0.00 40.48 4.41
1793 2138 4.637534 ACCTTACTTGCTGTTGCTGATATG 59.362 41.667 0.00 0.00 40.48 1.78
1804 2149 5.541845 TGTTGCTGATATGCTATCTGGTAC 58.458 41.667 10.05 0.00 0.00 3.34
1813 2158 2.100749 TGCTATCTGGTACATGGTGTCG 59.899 50.000 0.00 0.00 38.20 4.35
1821 2166 1.203994 GTACATGGTGTCGGTGTAGCT 59.796 52.381 0.00 0.00 0.00 3.32
1829 2174 0.173708 GTCGGTGTAGCTCCTTCCAG 59.826 60.000 0.00 0.00 0.00 3.86
1841 2186 3.775202 CTCCTTCCAGTATGACTTCACG 58.225 50.000 0.00 0.00 39.69 4.35
1973 2318 6.126863 AGATCTTTTGATAACCAGACCACA 57.873 37.500 0.00 0.00 39.67 4.17
1980 2326 3.392947 TGATAACCAGACCACAACCTCAA 59.607 43.478 0.00 0.00 0.00 3.02
1989 2335 3.795877 ACCACAACCTCAATTTTGCTTG 58.204 40.909 0.00 0.00 0.00 4.01
2270 2618 8.233190 CACAAAAGATTTCTCTCAGTAATGGTC 58.767 37.037 0.00 0.00 0.00 4.02
2333 2681 3.194542 AGCTCGAGACTTATGCTTTGAGT 59.805 43.478 18.75 0.00 0.00 3.41
2714 3063 6.370718 ACACAATAAGGAATACCGTTGAAGAC 59.629 38.462 0.00 0.00 41.83 3.01
2738 3087 7.167535 ACCTAATTACAAAATGCAAGGCAATT 58.832 30.769 0.00 0.00 43.62 2.32
2866 3215 9.394477 GTTTATCTCGAGCTAAAACAATGTTTT 57.606 29.630 24.77 24.77 31.85 2.43
2989 3356 8.343787 AGGGTTTTTCATCTTTCCCTTATGATA 58.656 33.333 0.00 0.00 42.00 2.15
3254 3622 9.384764 GAATACTAATTTTACTGCAAGGACTCT 57.615 33.333 0.00 0.00 39.30 3.24
3856 4225 2.567615 AGGTTCTGTACTGACATGGACC 59.432 50.000 10.88 10.88 34.76 4.46
3993 4362 2.550830 AGTGTTACACTGCTGAAGGG 57.449 50.000 17.92 0.00 43.63 3.95
4272 4641 5.308825 ACAAGGTTAAGACTGGTCAAGATG 58.691 41.667 3.51 0.00 0.00 2.90
4546 4918 4.383173 TGCTGCCTACACTGATGATATTG 58.617 43.478 0.00 0.00 0.00 1.90
4548 4920 4.450419 GCTGCCTACACTGATGATATTGTC 59.550 45.833 0.00 0.00 0.00 3.18
4554 4926 7.570140 GCCTACACTGATGATATTGTCGATTTG 60.570 40.741 0.00 0.00 0.00 2.32
4575 4947 9.139174 GATTTGTGATACCAAACTACCAATTTG 57.861 33.333 0.00 0.00 37.16 2.32
4582 4954 6.412362 ACCAAACTACCAATTTGCACAATA 57.588 33.333 0.00 0.00 36.01 1.90
4594 4966 8.533965 CCAATTTGCACAATAAGAATGATAACG 58.466 33.333 0.00 0.00 0.00 3.18
4618 4990 9.877178 ACGTGAACTAAGAGAAATTCTTATCAT 57.123 29.630 0.00 0.00 45.07 2.45
4675 5047 5.066593 TCTGTCTACTGCATATCGTCATCT 58.933 41.667 0.00 0.00 0.00 2.90
4677 5049 6.039829 TCTGTCTACTGCATATCGTCATCTTT 59.960 38.462 0.00 0.00 0.00 2.52
4699 5071 0.454600 GCAGTGTCCAGGCATGAATG 59.545 55.000 0.00 0.00 0.00 2.67
4705 5077 1.684983 GTCCAGGCATGAATGAATGGG 59.315 52.381 0.00 1.25 36.30 4.00
4833 5205 4.281688 CCCATTCCAAATGAGTCAAACACT 59.718 41.667 0.00 0.00 38.45 3.55
4878 5250 8.443953 ACCTTGAGATACATTCTTTTATGCTC 57.556 34.615 0.00 0.00 33.74 4.26
4954 5327 5.368230 TCTTTTTGCCAGGTTTATCCCTTTT 59.632 36.000 0.00 0.00 36.75 2.27
5132 5505 6.904626 AGGAAGCACTATCCAATTACTTCAT 58.095 36.000 0.00 0.00 39.55 2.57
5145 5518 6.529125 CCAATTACTTCATTGTCTTGTGCATC 59.471 38.462 0.00 0.00 32.95 3.91
5191 5564 9.257651 GCGATAGAGGTACAAACTATAAAACAT 57.742 33.333 0.00 0.00 39.76 2.71
5277 5790 9.587772 TCTTAGTATGAGTTTGTTTAGATCAGC 57.412 33.333 0.00 0.00 0.00 4.26
5386 5899 6.820656 AGTCTAGTGAAATTGCAATCTGTAGG 59.179 38.462 13.38 1.55 0.00 3.18
5397 5910 4.041075 TGCAATCTGTAGGTTTAGTCACCA 59.959 41.667 0.00 0.00 39.62 4.17
5398 5911 5.001232 GCAATCTGTAGGTTTAGTCACCAA 58.999 41.667 0.00 0.00 39.62 3.67
5456 5969 5.221581 ACAAACGGTGAAGGATACAAGTAGT 60.222 40.000 0.00 0.00 41.41 2.73
5467 5980 4.797349 GGATACAAGTAGTACTGCACGTTC 59.203 45.833 13.75 9.09 35.05 3.95
5603 6116 3.416156 AGTCAATTGAGACCAAGCTTCC 58.584 45.455 8.80 0.00 39.34 3.46
5639 6152 5.245531 CCCTATGCTACACTTTCTGTTTCA 58.754 41.667 0.00 0.00 33.91 2.69
5798 6339 8.189119 ACAGATTATCAAGAATACCTCTCTCC 57.811 38.462 0.00 0.00 31.02 3.71
5803 6344 5.923733 TCAAGAATACCTCTCTCCAGTTC 57.076 43.478 0.00 0.00 31.02 3.01
5828 6393 4.287720 CAGAATGATCCAACATGCATTCG 58.712 43.478 0.00 0.00 46.78 3.34
5849 6414 8.507249 CATTCGGTGATTACTTTTCTTCTTCTT 58.493 33.333 0.00 0.00 0.00 2.52
5850 6415 7.653767 TCGGTGATTACTTTTCTTCTTCTTC 57.346 36.000 0.00 0.00 0.00 2.87
5851 6416 7.442656 TCGGTGATTACTTTTCTTCTTCTTCT 58.557 34.615 0.00 0.00 0.00 2.85
5852 6417 7.385205 TCGGTGATTACTTTTCTTCTTCTTCTG 59.615 37.037 0.00 0.00 0.00 3.02
5853 6418 7.385205 CGGTGATTACTTTTCTTCTTCTTCTGA 59.615 37.037 0.00 0.00 0.00 3.27
5854 6419 9.225436 GGTGATTACTTTTCTTCTTCTTCTGAT 57.775 33.333 0.00 0.00 0.00 2.90
5923 6488 4.658063 CAAAACAGGGTGGGATTAGTACA 58.342 43.478 0.00 0.00 0.00 2.90
5990 6555 9.828852 CAATTAAATTTGGACATGTTTGGAATG 57.171 29.630 0.00 0.00 0.00 2.67
6010 6575 6.424812 GGAATGTTTCCTTGTCCAGAAATTTG 59.575 38.462 0.00 0.00 46.57 2.32
6011 6576 6.729690 ATGTTTCCTTGTCCAGAAATTTGA 57.270 33.333 0.00 0.00 34.69 2.69
6012 6577 6.147864 TGTTTCCTTGTCCAGAAATTTGAG 57.852 37.500 0.00 0.00 34.69 3.02
6013 6578 5.890985 TGTTTCCTTGTCCAGAAATTTGAGA 59.109 36.000 0.00 0.00 34.69 3.27
6014 6579 6.550854 TGTTTCCTTGTCCAGAAATTTGAGAT 59.449 34.615 0.00 0.00 34.69 2.75
6015 6580 7.723616 TGTTTCCTTGTCCAGAAATTTGAGATA 59.276 33.333 0.00 0.00 34.69 1.98
6016 6581 7.687941 TTCCTTGTCCAGAAATTTGAGATAC 57.312 36.000 0.00 0.00 0.00 2.24
6017 6582 6.180472 TCCTTGTCCAGAAATTTGAGATACC 58.820 40.000 0.00 0.00 0.00 2.73
6018 6583 6.012508 TCCTTGTCCAGAAATTTGAGATACCT 60.013 38.462 0.00 0.00 0.00 3.08
6019 6584 6.317391 CCTTGTCCAGAAATTTGAGATACCTC 59.683 42.308 0.00 0.00 39.86 3.85
6020 6585 6.627087 TGTCCAGAAATTTGAGATACCTCT 57.373 37.500 0.00 0.00 40.10 3.69
6021 6586 6.644347 TGTCCAGAAATTTGAGATACCTCTC 58.356 40.000 0.00 0.00 46.89 3.20
6022 6587 6.441924 TGTCCAGAAATTTGAGATACCTCTCT 59.558 38.462 0.00 0.00 46.84 3.10
6024 6589 7.494298 GTCCAGAAATTTGAGATACCTCTCTTC 59.506 40.741 0.00 0.66 46.84 2.87
6025 6590 7.180946 TCCAGAAATTTGAGATACCTCTCTTCA 59.819 37.037 0.00 0.00 46.84 3.02
6026 6591 7.495279 CCAGAAATTTGAGATACCTCTCTTCAG 59.505 40.741 0.00 0.00 46.84 3.02
6060 6628 1.908619 TCAGCAGGTTCCAGCTATCAA 59.091 47.619 8.34 0.00 39.50 2.57
6135 6706 8.964420 ATTTTGACAGTTAATGTAAATCGGTG 57.036 30.769 0.00 0.00 44.17 4.94
6154 6725 3.811497 GGTGGTACCTTGTCTGTTTGTAC 59.189 47.826 14.36 0.00 34.73 2.90
6176 6747 1.882623 GTTCCCTTTTCCAGCAGAGTG 59.117 52.381 0.00 0.00 0.00 3.51
6178 6749 2.334977 TCCCTTTTCCAGCAGAGTGTA 58.665 47.619 0.00 0.00 0.00 2.90
6230 6801 1.447838 ATTTCGTCCATGCGCGTCT 60.448 52.632 8.43 0.00 0.00 4.18
6302 6873 3.474806 CGCGTCCGCTTTTCATCT 58.525 55.556 10.21 0.00 39.32 2.90
6320 6891 4.115199 GCCTGCCGACCCATTCCT 62.115 66.667 0.00 0.00 0.00 3.36
6367 6938 2.202743 CGTGGACATGCGACGGAT 60.203 61.111 13.79 0.00 43.78 4.18
6370 6941 3.272334 GGACATGCGACGGATGCC 61.272 66.667 26.64 23.11 0.00 4.40
6395 6974 4.798682 CCGCCTACTCCCCCTGGT 62.799 72.222 0.00 0.00 0.00 4.00
6397 6976 2.369001 GCCTACTCCCCCTGGTCT 59.631 66.667 0.00 0.00 0.00 3.85
6428 7007 0.106819 GCACATTGGCCATCCTCTCT 60.107 55.000 6.09 0.00 0.00 3.10
6436 7015 1.202746 GGCCATCCTCTCTCATTCCAC 60.203 57.143 0.00 0.00 0.00 4.02
6449 7028 2.091610 TCATTCCACCAACAAACCCTCA 60.092 45.455 0.00 0.00 0.00 3.86
6450 7029 2.534042 TTCCACCAACAAACCCTCAA 57.466 45.000 0.00 0.00 0.00 3.02
6454 7034 0.033894 ACCAACAAACCCTCAACCGT 60.034 50.000 0.00 0.00 0.00 4.83
6457 7037 2.021457 CAACAAACCCTCAACCGTCTT 58.979 47.619 0.00 0.00 0.00 3.01
6461 7041 2.949644 CAAACCCTCAACCGTCTTCTTT 59.050 45.455 0.00 0.00 0.00 2.52
6467 7047 0.234884 CAACCGTCTTCTTTGTCGCC 59.765 55.000 0.00 0.00 0.00 5.54
6468 7048 0.179067 AACCGTCTTCTTTGTCGCCA 60.179 50.000 0.00 0.00 0.00 5.69
6469 7049 0.878961 ACCGTCTTCTTTGTCGCCAC 60.879 55.000 0.00 0.00 0.00 5.01
6472 7058 0.878961 GTCTTCTTTGTCGCCACCGT 60.879 55.000 0.00 0.00 35.54 4.83
6534 7129 0.674581 TCGCAACATCCCTTCTGCAG 60.675 55.000 7.63 7.63 34.39 4.41
6536 7131 1.246056 GCAACATCCCTTCTGCAGCA 61.246 55.000 9.47 0.00 34.87 4.41
6584 7180 2.267961 GTCTTGCCGTCGGGGAAT 59.732 61.111 14.38 0.00 43.29 3.01
6602 7205 2.536997 ATCGAAAGCTTCCCACCCCG 62.537 60.000 0.00 0.00 0.00 5.73
6604 7207 3.569200 GAAAGCTTCCCACCCCGCT 62.569 63.158 0.00 0.00 0.00 5.52
6605 7208 3.569200 AAAGCTTCCCACCCCGCTC 62.569 63.158 0.00 0.00 31.30 5.03
6618 7221 4.056125 CGCTCCTCCGACACAGCA 62.056 66.667 0.00 0.00 0.00 4.41
6627 7230 3.712881 GACACAGCAACGACCGCC 61.713 66.667 0.00 0.00 0.00 6.13
6646 7249 2.280552 ACCAAGAAGCCGCCTCGTA 61.281 57.895 0.00 0.00 0.00 3.43
6752 7356 1.429825 CGTCTCCTTCGTCGATGCT 59.570 57.895 0.00 0.00 0.00 3.79
6796 7404 3.071892 TCAAGGTACAAAATGGACTCCGT 59.928 43.478 0.00 0.00 30.12 4.69
6854 7465 2.095008 CGACGATTCCTCATCCGATGAT 60.095 50.000 11.53 0.00 38.85 2.45
6870 7481 4.280425 CCGATGATGAGGAGAAGATCTTGA 59.720 45.833 14.00 0.00 0.00 3.02
6871 7482 5.463286 CGATGATGAGGAGAAGATCTTGAG 58.537 45.833 14.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 228 4.442073 CACCGATTCAGAAAAAGTTTGCTG 59.558 41.667 5.52 5.52 43.80 4.41
224 229 4.338118 TCACCGATTCAGAAAAAGTTTGCT 59.662 37.500 0.00 0.00 0.00 3.91
226 231 4.676924 GCTCACCGATTCAGAAAAAGTTTG 59.323 41.667 0.00 0.00 0.00 2.93
227 232 4.338118 TGCTCACCGATTCAGAAAAAGTTT 59.662 37.500 0.00 0.00 0.00 2.66
242 248 4.225984 TGAATTTCGAAAAATGCTCACCG 58.774 39.130 15.66 0.00 35.27 4.94
244 250 6.932901 TCATGAATTTCGAAAAATGCTCAC 57.067 33.333 15.66 1.68 35.27 3.51
367 377 9.912634 AATCTGAAATCATTAAATGTTTCGTGT 57.087 25.926 0.00 0.00 35.24 4.49
439 449 1.747355 GAGCATATGCATATGGCCCAC 59.253 52.381 36.01 23.79 45.16 4.61
806 849 2.675075 CCCAACGGCCCGTCAAAT 60.675 61.111 10.32 0.00 39.99 2.32
807 850 4.958897 CCCCAACGGCCCGTCAAA 62.959 66.667 10.32 0.00 39.99 2.69
823 873 1.348366 AGAGCATGAGCATCTCCATCC 59.652 52.381 0.00 0.00 45.49 3.51
830 880 2.159071 AGACTGTGAGAGCATGAGCATC 60.159 50.000 0.00 0.00 45.49 3.91
831 881 1.832366 AGACTGTGAGAGCATGAGCAT 59.168 47.619 0.00 0.00 45.49 3.79
832 882 1.204231 GAGACTGTGAGAGCATGAGCA 59.796 52.381 0.00 0.00 45.49 4.26
833 883 1.204231 TGAGACTGTGAGAGCATGAGC 59.796 52.381 0.00 0.00 42.56 4.26
834 884 2.731654 CGTGAGACTGTGAGAGCATGAG 60.732 54.545 0.00 0.00 0.00 2.90
835 885 1.200948 CGTGAGACTGTGAGAGCATGA 59.799 52.381 0.00 0.00 0.00 3.07
836 886 1.626747 CGTGAGACTGTGAGAGCATG 58.373 55.000 0.00 0.00 0.00 4.06
837 887 0.108898 GCGTGAGACTGTGAGAGCAT 60.109 55.000 0.00 0.00 0.00 3.79
857 907 3.209097 CGGGGGCGCAAGGTATTG 61.209 66.667 10.83 0.00 39.57 1.90
884 934 3.493303 GAGGATGAGGTGGGCCCC 61.493 72.222 22.27 10.91 34.57 5.80
885 935 1.988982 GAAGAGGATGAGGTGGGCCC 61.989 65.000 17.59 17.59 34.57 5.80
886 936 1.529309 GAAGAGGATGAGGTGGGCC 59.471 63.158 0.00 0.00 0.00 5.80
887 937 0.985490 AGGAAGAGGATGAGGTGGGC 60.985 60.000 0.00 0.00 0.00 5.36
888 938 1.127343 GAGGAAGAGGATGAGGTGGG 58.873 60.000 0.00 0.00 0.00 4.61
890 940 3.373830 AGAAGAGGAAGAGGATGAGGTG 58.626 50.000 0.00 0.00 0.00 4.00
891 941 3.272020 AGAGAAGAGGAAGAGGATGAGGT 59.728 47.826 0.00 0.00 0.00 3.85
892 942 3.891366 GAGAGAAGAGGAAGAGGATGAGG 59.109 52.174 0.00 0.00 0.00 3.86
893 943 4.796606 AGAGAGAAGAGGAAGAGGATGAG 58.203 47.826 0.00 0.00 0.00 2.90
1173 1472 2.574736 GAGCGAGACAGCGACGTC 60.575 66.667 5.18 5.18 43.00 4.34
1504 1803 5.969423 AGCATTTGAGAAAGAGAGAGAGAG 58.031 41.667 0.00 0.00 0.00 3.20
1506 1805 7.596248 GCTATAGCATTTGAGAAAGAGAGAGAG 59.404 40.741 20.01 0.00 41.59 3.20
1512 1811 4.084118 GGCGCTATAGCATTTGAGAAAGAG 60.084 45.833 23.99 4.49 42.21 2.85
1513 1812 3.809832 GGCGCTATAGCATTTGAGAAAGA 59.190 43.478 23.99 0.00 42.21 2.52
1515 1814 3.808728 AGGCGCTATAGCATTTGAGAAA 58.191 40.909 23.99 0.00 42.21 2.52
1516 1815 3.181466 TGAGGCGCTATAGCATTTGAGAA 60.181 43.478 23.99 0.00 42.21 2.87
1517 1816 2.365293 TGAGGCGCTATAGCATTTGAGA 59.635 45.455 23.99 0.00 42.21 3.27
1518 1817 2.759191 TGAGGCGCTATAGCATTTGAG 58.241 47.619 23.99 8.00 42.21 3.02
1519 1818 2.908688 TGAGGCGCTATAGCATTTGA 57.091 45.000 23.99 2.29 42.21 2.69
1520 1819 3.969117 TTTGAGGCGCTATAGCATTTG 57.031 42.857 23.99 9.08 42.21 2.32
1522 1821 4.899502 AGTATTTGAGGCGCTATAGCATT 58.100 39.130 23.99 8.78 42.21 3.56
1524 1823 3.611766 CGAGTATTTGAGGCGCTATAGCA 60.612 47.826 23.99 3.32 42.21 3.49
1525 1824 2.917971 CGAGTATTTGAGGCGCTATAGC 59.082 50.000 15.09 15.09 37.78 2.97
1526 1825 4.162096 ACGAGTATTTGAGGCGCTATAG 57.838 45.455 7.64 0.00 0.00 1.31
1527 1826 5.008911 TGTTACGAGTATTTGAGGCGCTATA 59.991 40.000 7.64 0.00 0.00 1.31
1529 1828 3.129113 TGTTACGAGTATTTGAGGCGCTA 59.871 43.478 7.64 0.00 0.00 4.26
1530 1829 2.094390 TGTTACGAGTATTTGAGGCGCT 60.094 45.455 7.64 0.00 0.00 5.92
1532 1831 3.247442 TGTGTTACGAGTATTTGAGGCG 58.753 45.455 0.00 0.00 0.00 5.52
1534 1833 7.802738 TCAAATTGTGTTACGAGTATTTGAGG 58.197 34.615 0.00 0.00 37.19 3.86
1535 1834 8.865753 CTCAAATTGTGTTACGAGTATTTGAG 57.134 34.615 16.31 16.31 45.62 3.02
1536 1835 7.572353 GCCTCAAATTGTGTTACGAGTATTTGA 60.572 37.037 0.00 0.00 38.77 2.69
1537 1836 6.523201 GCCTCAAATTGTGTTACGAGTATTTG 59.477 38.462 0.00 0.00 35.42 2.32
1538 1837 6.205853 TGCCTCAAATTGTGTTACGAGTATTT 59.794 34.615 0.00 0.00 0.00 1.40
1539 1838 5.703592 TGCCTCAAATTGTGTTACGAGTATT 59.296 36.000 0.00 0.00 0.00 1.89
1540 1839 5.121768 GTGCCTCAAATTGTGTTACGAGTAT 59.878 40.000 0.00 0.00 0.00 2.12
1542 1841 3.250040 GTGCCTCAAATTGTGTTACGAGT 59.750 43.478 0.00 0.00 0.00 4.18
1543 1842 3.249799 TGTGCCTCAAATTGTGTTACGAG 59.750 43.478 0.00 0.00 0.00 4.18
1544 1843 3.206964 TGTGCCTCAAATTGTGTTACGA 58.793 40.909 0.00 0.00 0.00 3.43
1545 1844 3.617540 TGTGCCTCAAATTGTGTTACG 57.382 42.857 0.00 0.00 0.00 3.18
1546 1845 6.677913 AGTTATGTGCCTCAAATTGTGTTAC 58.322 36.000 0.00 0.00 0.00 2.50
1547 1846 6.892658 AGTTATGTGCCTCAAATTGTGTTA 57.107 33.333 0.00 0.00 0.00 2.41
1548 1847 5.789643 AGTTATGTGCCTCAAATTGTGTT 57.210 34.783 0.00 0.00 0.00 3.32
1549 1848 5.789643 AAGTTATGTGCCTCAAATTGTGT 57.210 34.783 0.00 0.00 0.00 3.72
1550 1849 6.479660 ACAAAAGTTATGTGCCTCAAATTGTG 59.520 34.615 0.00 0.00 0.00 3.33
1552 1851 6.146021 GGACAAAAGTTATGTGCCTCAAATTG 59.854 38.462 0.00 0.00 33.54 2.32
1556 1855 4.469657 AGGACAAAAGTTATGTGCCTCAA 58.530 39.130 0.00 0.00 39.65 3.02
1557 1856 4.098914 AGGACAAAAGTTATGTGCCTCA 57.901 40.909 0.00 0.00 39.65 3.86
1558 1857 5.938125 TCTTAGGACAAAAGTTATGTGCCTC 59.062 40.000 0.00 0.00 39.65 4.70
1559 1858 5.876357 TCTTAGGACAAAAGTTATGTGCCT 58.124 37.500 0.00 0.00 39.65 4.75
1560 1859 6.759497 ATCTTAGGACAAAAGTTATGTGCC 57.241 37.500 0.00 0.00 39.65 5.01
1561 1860 7.910683 GCTTATCTTAGGACAAAAGTTATGTGC 59.089 37.037 0.00 0.00 39.17 4.57
1664 2007 6.122277 ACCAAAATCAGTATATCCACAGTGG 58.878 40.000 14.19 14.19 39.43 4.00
1667 2010 7.122650 ACCAAACCAAAATCAGTATATCCACAG 59.877 37.037 0.00 0.00 0.00 3.66
1668 2011 6.951198 ACCAAACCAAAATCAGTATATCCACA 59.049 34.615 0.00 0.00 0.00 4.17
1669 2012 7.404671 ACCAAACCAAAATCAGTATATCCAC 57.595 36.000 0.00 0.00 0.00 4.02
1675 2018 9.747898 TCTACAATACCAAACCAAAATCAGTAT 57.252 29.630 0.00 0.00 0.00 2.12
1676 2019 9.747898 ATCTACAATACCAAACCAAAATCAGTA 57.252 29.630 0.00 0.00 0.00 2.74
1713 2056 4.808895 GGTTGGCCAAGTTTACAGAAAAAG 59.191 41.667 21.21 0.00 34.09 2.27
1721 2066 3.633065 TGTGTAAGGTTGGCCAAGTTTAC 59.367 43.478 28.77 28.77 37.19 2.01
1749 2094 8.828688 AAGGTGTATAACTGTTGTCTTAAGTC 57.171 34.615 2.69 0.00 0.00 3.01
1783 2128 5.806654 TGTACCAGATAGCATATCAGCAA 57.193 39.130 0.00 0.00 36.85 3.91
1784 2129 5.337813 CCATGTACCAGATAGCATATCAGCA 60.338 44.000 0.00 0.00 36.85 4.41
1785 2130 5.114780 CCATGTACCAGATAGCATATCAGC 58.885 45.833 0.00 0.00 0.00 4.26
1786 2131 6.104665 CACCATGTACCAGATAGCATATCAG 58.895 44.000 0.00 0.00 0.00 2.90
1787 2132 5.543790 ACACCATGTACCAGATAGCATATCA 59.456 40.000 0.00 0.00 0.00 2.15
1788 2133 6.042638 ACACCATGTACCAGATAGCATATC 57.957 41.667 0.00 0.00 0.00 1.63
1793 2138 2.545952 CCGACACCATGTACCAGATAGC 60.546 54.545 0.00 0.00 0.00 2.97
1804 2149 0.460284 GGAGCTACACCGACACCATG 60.460 60.000 0.00 0.00 0.00 3.66
1813 2158 3.031736 TCATACTGGAAGGAGCTACACC 58.968 50.000 0.00 1.40 39.30 4.16
1821 2166 2.496070 CCGTGAAGTCATACTGGAAGGA 59.504 50.000 0.00 0.00 39.30 3.36
1829 2174 5.759963 CACCTATAGTCCGTGAAGTCATAC 58.240 45.833 0.00 0.00 0.00 2.39
1841 2186 1.689273 CCAGTCCAGCACCTATAGTCC 59.311 57.143 0.00 0.00 0.00 3.85
1930 2275 6.542370 AGATCTACTCTAGTTCTGAGTCTTGC 59.458 42.308 0.00 0.00 42.95 4.01
1966 2311 3.299503 AGCAAAATTGAGGTTGTGGTCT 58.700 40.909 0.00 0.00 0.00 3.85
1973 2318 4.141233 ACAAGCAAGCAAAATTGAGGTT 57.859 36.364 0.00 0.00 31.55 3.50
1980 2326 7.551035 TTTCACAAATACAAGCAAGCAAAAT 57.449 28.000 0.00 0.00 0.00 1.82
2039 2385 4.043310 TGAGTGTCCTCCTGAATTCCATTT 59.957 41.667 2.27 0.00 36.86 2.32
2040 2386 3.588842 TGAGTGTCCTCCTGAATTCCATT 59.411 43.478 2.27 0.00 36.86 3.16
2041 2387 3.054802 GTGAGTGTCCTCCTGAATTCCAT 60.055 47.826 2.27 0.00 36.86 3.41
2047 2393 3.527507 ACTAGTGAGTGTCCTCCTGAA 57.472 47.619 0.00 0.00 36.86 3.02
2105 2451 4.767409 GTGAATTAGAGGTGGGAAGCTTTT 59.233 41.667 0.00 0.00 0.00 2.27
2270 2618 6.738200 CAGCACATTTACAGAACACTTTATCG 59.262 38.462 0.00 0.00 0.00 2.92
2333 2681 4.947388 GCTTCCATATTAACAGGTTCACCA 59.053 41.667 0.00 0.00 38.89 4.17
2366 2714 5.030295 CCAATCACATCTAACGTCATTTGC 58.970 41.667 0.00 0.00 0.00 3.68
2657 3006 7.627300 GCTTTTTCTGCTTTTATCTGTCTAGGG 60.627 40.741 0.00 0.00 0.00 3.53
2714 3063 7.119553 ACAATTGCCTTGCATTTTGTAATTAGG 59.880 33.333 5.05 0.00 40.68 2.69
2738 3087 7.391275 TCAATCTGTTCATTTTCAGCATCTACA 59.609 33.333 0.00 0.00 0.00 2.74
2959 3326 3.511540 GGGAAAGATGAAAAACCCTGAGG 59.488 47.826 0.00 0.00 40.04 3.86
3604 3972 8.665685 ACTGTGTTCGAAATAGGCTAATTTTAG 58.334 33.333 0.00 0.00 0.00 1.85
3856 4225 8.919145 AGGAGTACCTTACTGAGAAGATAAATG 58.081 37.037 0.00 0.00 45.36 2.32
3993 4362 3.263261 GCTTTCCTTAGTGCTACTGGAC 58.737 50.000 0.00 0.00 34.56 4.02
4546 4918 5.640357 TGGTAGTTTGGTATCACAAATCGAC 59.360 40.000 0.00 0.00 41.80 4.20
4548 4920 6.489127 TTGGTAGTTTGGTATCACAAATCG 57.511 37.500 0.00 0.00 41.80 3.34
4554 4926 5.861787 GTGCAAATTGGTAGTTTGGTATCAC 59.138 40.000 0.00 0.00 37.12 3.06
4575 4947 7.464358 AGTTCACGTTATCATTCTTATTGTGC 58.536 34.615 0.00 0.00 0.00 4.57
4582 4954 9.706691 TTTCTCTTAGTTCACGTTATCATTCTT 57.293 29.630 0.00 0.00 0.00 2.52
4675 5047 2.203480 GCCTGGACACTGCCCAAA 60.203 61.111 0.00 0.00 32.53 3.28
4677 5049 3.259314 ATGCCTGGACACTGCCCA 61.259 61.111 0.00 0.00 0.00 5.36
4705 5077 7.171848 TGCAATGATAAAATATTGGAATGCTGC 59.828 33.333 0.00 0.00 35.40 5.25
4833 5205 6.187727 AGGTTACTTTCTGACCTGAAATCA 57.812 37.500 3.20 0.00 42.04 2.57
4954 5327 3.056107 CACATTTTCGAGGACCTCCACTA 60.056 47.826 16.13 0.00 38.89 2.74
5132 5505 3.144657 ACCTGATGATGCACAAGACAA 57.855 42.857 0.00 0.00 0.00 3.18
5145 5518 3.122278 CGCAAATTGAAAGCAACCTGATG 59.878 43.478 0.00 0.00 36.72 3.07
5191 5564 1.476891 GTCTGCCCGTGAGAGATACAA 59.523 52.381 0.00 0.00 0.00 2.41
5227 5600 5.885912 ACCAACATGAACATAATCACCTACC 59.114 40.000 0.00 0.00 30.82 3.18
5277 5790 2.424956 GGCATAAACTGGGAGCTTTCAG 59.575 50.000 13.53 13.53 37.07 3.02
5397 5910 3.735208 CGTGCAGTACTACAGCAGCTATT 60.735 47.826 6.53 0.00 41.29 1.73
5398 5911 2.223595 CGTGCAGTACTACAGCAGCTAT 60.224 50.000 6.53 0.00 41.29 2.97
5456 5969 2.159014 AGTGTTTCAGGAACGTGCAGTA 60.159 45.455 0.00 0.00 41.29 2.74
5467 5980 5.728351 TTGTTTTAGTCGAGTGTTTCAGG 57.272 39.130 2.10 0.00 0.00 3.86
5569 6082 5.771153 TCAATTGACTTGAGACATGCAAA 57.229 34.783 3.38 0.00 38.97 3.68
5583 6096 2.160417 CGGAAGCTTGGTCTCAATTGAC 59.840 50.000 2.10 0.00 36.31 3.18
5603 6116 2.158755 AGCATAGGGGAAGGAATGAACG 60.159 50.000 0.00 0.00 0.00 3.95
5657 6170 6.881602 AGTCCCTGTTGAAGAGAATATTTGTC 59.118 38.462 0.00 0.00 0.00 3.18
5673 6186 8.090788 ACTTACATTCATATACAGTCCCTGTT 57.909 34.615 1.74 0.00 42.59 3.16
5781 6322 5.584913 AGAACTGGAGAGAGGTATTCTTGA 58.415 41.667 0.00 0.00 35.87 3.02
5798 6339 4.582869 TGTTGGATCATTCTGGAGAACTG 58.417 43.478 0.00 0.00 36.80 3.16
5803 6344 3.284617 TGCATGTTGGATCATTCTGGAG 58.715 45.455 0.00 0.00 0.00 3.86
5828 6393 8.608844 TCAGAAGAAGAAGAAAAGTAATCACC 57.391 34.615 0.00 0.00 0.00 4.02
5849 6414 5.239744 GCACGAGAGGAGTAGATAAATCAGA 59.760 44.000 0.00 0.00 0.00 3.27
5850 6415 5.009110 TGCACGAGAGGAGTAGATAAATCAG 59.991 44.000 0.00 0.00 0.00 2.90
5851 6416 4.887655 TGCACGAGAGGAGTAGATAAATCA 59.112 41.667 0.00 0.00 0.00 2.57
5852 6417 5.009210 ACTGCACGAGAGGAGTAGATAAATC 59.991 44.000 0.00 0.00 38.49 2.17
5853 6418 4.890581 ACTGCACGAGAGGAGTAGATAAAT 59.109 41.667 0.00 0.00 38.49 1.40
5854 6419 4.270834 ACTGCACGAGAGGAGTAGATAAA 58.729 43.478 0.00 0.00 38.49 1.40
5923 6488 1.202976 ACAATTCTGTTGCCTCTGCCT 60.203 47.619 0.00 0.00 36.33 4.75
5990 6555 6.391227 TCTCAAATTTCTGGACAAGGAAAC 57.609 37.500 0.00 0.00 34.83 2.78
6011 6576 8.058847 AGATACAAGAACTGAAGAGAGGTATCT 58.941 37.037 0.00 0.00 39.75 1.98
6012 6577 8.232913 AGATACAAGAACTGAAGAGAGGTATC 57.767 38.462 0.00 0.00 36.47 2.24
6013 6578 8.602472 AAGATACAAGAACTGAAGAGAGGTAT 57.398 34.615 0.00 0.00 0.00 2.73
6014 6579 8.423906 AAAGATACAAGAACTGAAGAGAGGTA 57.576 34.615 0.00 0.00 0.00 3.08
6015 6580 6.926630 AAGATACAAGAACTGAAGAGAGGT 57.073 37.500 0.00 0.00 0.00 3.85
6016 6581 7.875041 TGAAAAGATACAAGAACTGAAGAGAGG 59.125 37.037 0.00 0.00 0.00 3.69
6017 6582 8.824159 TGAAAAGATACAAGAACTGAAGAGAG 57.176 34.615 0.00 0.00 0.00 3.20
6018 6583 7.386299 GCTGAAAAGATACAAGAACTGAAGAGA 59.614 37.037 0.00 0.00 0.00 3.10
6019 6584 7.172190 TGCTGAAAAGATACAAGAACTGAAGAG 59.828 37.037 0.00 0.00 0.00 2.85
6020 6585 6.992123 TGCTGAAAAGATACAAGAACTGAAGA 59.008 34.615 0.00 0.00 0.00 2.87
6021 6586 7.194607 TGCTGAAAAGATACAAGAACTGAAG 57.805 36.000 0.00 0.00 0.00 3.02
6022 6587 6.205464 CCTGCTGAAAAGATACAAGAACTGAA 59.795 38.462 0.00 0.00 0.00 3.02
6024 6589 5.471456 ACCTGCTGAAAAGATACAAGAACTG 59.529 40.000 0.00 0.00 0.00 3.16
6025 6590 5.625150 ACCTGCTGAAAAGATACAAGAACT 58.375 37.500 0.00 0.00 0.00 3.01
6026 6591 5.948992 ACCTGCTGAAAAGATACAAGAAC 57.051 39.130 0.00 0.00 0.00 3.01
6060 6628 4.574828 CAGTTTACGCAACCTATTAGCCAT 59.425 41.667 0.00 0.00 35.77 4.40
6135 6706 3.062042 CCGTACAAACAGACAAGGTACC 58.938 50.000 2.73 2.73 32.70 3.34
6176 6747 1.067071 AGTTGCTCTAAGCCCACGTAC 60.067 52.381 0.00 0.00 41.51 3.67
6178 6749 0.037232 GAGTTGCTCTAAGCCCACGT 60.037 55.000 0.00 0.00 41.51 4.49
6299 6870 2.615227 GAATGGGTCGGCAGGCAGAT 62.615 60.000 0.00 0.00 0.00 2.90
6302 6873 4.424711 GGAATGGGTCGGCAGGCA 62.425 66.667 0.00 0.00 0.00 4.75
6320 6891 5.792741 CAAATCCAACTCAAAAATGGGCTA 58.207 37.500 0.00 0.00 34.89 3.93
6380 6958 2.066999 CAGACCAGGGGGAGTAGGC 61.067 68.421 0.00 0.00 38.05 3.93
6381 6959 2.066999 GCAGACCAGGGGGAGTAGG 61.067 68.421 0.00 0.00 38.05 3.18
6384 6962 2.608988 CAGCAGACCAGGGGGAGT 60.609 66.667 0.00 0.00 38.05 3.85
6395 6974 1.902765 ATGTGCCATCGACCAGCAGA 61.903 55.000 6.12 5.86 37.15 4.26
6397 6976 1.002257 AATGTGCCATCGACCAGCA 60.002 52.632 1.97 1.97 0.00 4.41
6428 7007 2.091610 TGAGGGTTTGTTGGTGGAATGA 60.092 45.455 0.00 0.00 0.00 2.57
6436 7015 0.666374 GACGGTTGAGGGTTTGTTGG 59.334 55.000 0.00 0.00 0.00 3.77
6449 7028 0.179067 TGGCGACAAAGAAGACGGTT 60.179 50.000 0.00 0.00 37.44 4.44
6450 7029 0.878961 GTGGCGACAAAGAAGACGGT 60.879 55.000 0.00 0.00 46.06 4.83
6454 7034 0.599204 GACGGTGGCGACAAAGAAGA 60.599 55.000 0.00 0.00 46.06 2.87
6457 7037 2.355363 CGACGGTGGCGACAAAGA 60.355 61.111 0.00 0.00 46.06 2.52
6472 7058 4.408821 AGAAATGGGCGGCAGCGA 62.409 61.111 12.47 0.00 46.35 4.93
6515 7110 0.674581 CTGCAGAAGGGATGTTGCGA 60.675 55.000 8.42 0.00 39.34 5.10
6536 7131 4.295119 GACGTGTGAGGTGGCGGT 62.295 66.667 0.00 0.00 0.00 5.68
6584 7180 2.754375 GGGGTGGGAAGCTTTCGA 59.246 61.111 0.00 0.00 0.00 3.71
6602 7205 2.029844 GTTGCTGTGTCGGAGGAGC 61.030 63.158 0.00 0.00 0.00 4.70
6604 7207 2.197605 TCGTTGCTGTGTCGGAGGA 61.198 57.895 0.00 0.00 0.00 3.71
6605 7208 2.022129 GTCGTTGCTGTGTCGGAGG 61.022 63.158 0.00 0.00 0.00 4.30
6606 7209 2.022129 GGTCGTTGCTGTGTCGGAG 61.022 63.158 0.00 0.00 0.00 4.63
6607 7210 2.028484 GGTCGTTGCTGTGTCGGA 59.972 61.111 0.00 0.00 0.00 4.55
6618 7221 1.597027 CTTCTTGGTGGCGGTCGTT 60.597 57.895 0.00 0.00 0.00 3.85
6627 7230 2.501223 TACGAGGCGGCTTCTTGGTG 62.501 60.000 14.76 0.00 0.00 4.17
6752 7356 3.936653 CTGTCGAACAGCTTGCGA 58.063 55.556 0.00 0.00 39.62 5.10
6854 7465 2.499289 GGCACTCAAGATCTTCTCCTCA 59.501 50.000 4.57 0.00 0.00 3.86
6855 7466 2.481104 CGGCACTCAAGATCTTCTCCTC 60.481 54.545 4.57 0.00 0.00 3.71
6856 7467 1.480137 CGGCACTCAAGATCTTCTCCT 59.520 52.381 4.57 0.00 0.00 3.69
6861 7472 2.146342 CAACACGGCACTCAAGATCTT 58.854 47.619 0.88 0.88 0.00 2.40
6870 7481 1.302511 GATGGACCAACACGGCACT 60.303 57.895 0.00 0.00 39.03 4.40
6871 7482 3.263941 GATGGACCAACACGGCAC 58.736 61.111 0.00 0.00 39.03 5.01


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

AutoCloner maintained by Alex Coulton.