Multiple sequence alignment - TraesCS5A01G159400

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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 TraesCS5A01G159400 chr5A 100.000 6825 0 0 509 7333 340130201 340137025 0.000000e+00 12604.0
1 TraesCS5A01G159400 chr5A 98.454 194 1 1 2007 2198 227709774 227709967 2.530000e-89 340.0
2 TraesCS5A01G159400 chr5A 100.000 132 0 0 1 132 340129693 340129824 2.040000e-60 244.0
3 TraesCS5A01G159400 chr5A 95.312 64 3 0 1906 1969 340131535 340131598 1.300000e-17 102.0
4 TraesCS5A01G159400 chr5A 95.312 64 3 0 1843 1906 340131598 340131661 1.300000e-17 102.0
5 TraesCS5A01G159400 chr5A 88.889 72 1 3 7262 7333 340142483 340142547 1.700000e-11 82.4
6 TraesCS5A01G159400 chr5B 95.424 4502 144 25 2198 6651 289704551 289709038 0.000000e+00 7116.0
7 TraesCS5A01G159400 chr5B 90.855 1520 119 14 512 2018 289703051 289704563 0.000000e+00 2019.0
8 TraesCS5A01G159400 chr5B 87.044 548 38 14 6816 7333 289733155 289733699 8.200000e-164 588.0
9 TraesCS5A01G159400 chr5B 96.341 82 3 0 6733 6814 289733040 289733121 1.280000e-27 135.0
10 TraesCS5A01G159400 chr5B 93.750 64 1 1 1906 1969 289704389 289704449 7.830000e-15 93.5
11 TraesCS5A01G159400 chr5B 100.000 44 0 0 6638 6681 289732931 289732974 1.700000e-11 82.4
12 TraesCS5A01G159400 chr5D 96.234 1673 53 3 2198 3861 255943741 255945412 0.000000e+00 2732.0
13 TraesCS5A01G159400 chr5D 94.366 994 30 9 4862 5847 255946728 255947703 0.000000e+00 1502.0
14 TraesCS5A01G159400 chr5D 92.757 994 35 12 5832 6817 255947723 255948687 0.000000e+00 1402.0
15 TraesCS5A01G159400 chr5D 95.928 614 19 6 3897 4508 255945614 255946223 0.000000e+00 990.0
16 TraesCS5A01G159400 chr5D 94.679 639 29 4 1272 1908 255943073 255943708 0.000000e+00 987.0
17 TraesCS5A01G159400 chr5D 98.131 428 8 0 4436 4863 255946210 255946637 0.000000e+00 747.0
18 TraesCS5A01G159400 chr5D 89.562 594 43 7 696 1272 255942442 255943033 0.000000e+00 736.0
19 TraesCS5A01G159400 chr5D 97.980 99 2 0 6816 6914 255948718 255948816 9.780000e-39 172.0
20 TraesCS5A01G159400 chr5D 93.162 117 7 1 7065 7181 255951717 255951832 3.520000e-38 171.0
21 TraesCS5A01G159400 chr5D 91.803 122 7 1 6950 7071 255948939 255949057 4.550000e-37 167.0
22 TraesCS5A01G159400 chr5D 92.035 113 8 1 1906 2018 255943642 255943753 2.740000e-34 158.0
23 TraesCS5A01G159400 chr5D 90.000 110 6 2 7229 7333 255951825 255951934 3.570000e-28 137.0
24 TraesCS5A01G159400 chr1D 88.329 1191 85 28 5400 6569 8731432 8732589 0.000000e+00 1380.0
25 TraesCS5A01G159400 chr1D 92.537 536 36 2 4385 4916 8730909 8731444 0.000000e+00 765.0
26 TraesCS5A01G159400 chr1D 77.895 285 20 12 6542 6817 8732595 8732845 3.570000e-28 137.0
27 TraesCS5A01G159400 chr1B 100.000 188 0 0 2012 2199 288394633 288394446 1.510000e-91 348.0
28 TraesCS5A01G159400 chr1B 100.000 186 0 0 2014 2199 80963832 80964017 1.960000e-90 344.0
29 TraesCS5A01G159400 chr1A 100.000 187 0 0 2013 2199 97954911 97955097 5.450000e-91 346.0
30 TraesCS5A01G159400 chr1A 99.468 188 1 0 2012 2199 333878722 333878909 7.040000e-90 342.0
31 TraesCS5A01G159400 chr7B 99.471 189 1 0 2011 2199 51073642 51073830 1.960000e-90 344.0
32 TraesCS5A01G159400 chr3A 100.000 186 0 0 2014 2199 329511723 329511538 1.960000e-90 344.0
33 TraesCS5A01G159400 chr2B 100.000 186 0 0 2013 2198 66807726 66807541 1.960000e-90 344.0
34 TraesCS5A01G159400 chr2B 83.491 212 28 5 3677 3882 522087159 522087369 2.700000e-44 191.0
35 TraesCS5A01G159400 chr2B 88.889 81 9 0 3673 3753 723400081 723400001 4.680000e-17 100.0
36 TraesCS5A01G159400 chr2B 100.000 28 0 0 668 695 33963705 33963732 1.300000e-02 52.8
37 TraesCS5A01G159400 chr4B 100.000 185 0 0 2014 2198 351874619 351874803 7.040000e-90 342.0
38 TraesCS5A01G159400 chr4B 100.000 28 0 0 668 695 603292680 603292653 1.300000e-02 52.8
39 TraesCS5A01G159400 chr2D 82.407 216 31 6 3673 3882 442986242 442986456 1.630000e-41 182.0
40 TraesCS5A01G159400 chr3B 79.710 138 17 9 636 766 803062314 803062447 1.010000e-13 89.8
41 TraesCS5A01G159400 chr7D 100.000 28 0 0 668 695 491802364 491802337 1.300000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G159400 chr5A 340129693 340137025 7332 False 6424.000000 12604 100.000000 1 7333 2 chr5A.!!$F3 7332
1 TraesCS5A01G159400 chr5B 289703051 289709038 5987 False 3076.166667 7116 93.343000 512 6651 3 chr5B.!!$F1 6139
2 TraesCS5A01G159400 chr5B 289732931 289733699 768 False 268.466667 588 94.461667 6638 7333 3 chr5B.!!$F2 695
3 TraesCS5A01G159400 chr5D 255942442 255951934 9492 False 825.083333 2732 93.886417 696 7333 12 chr5D.!!$F1 6637
4 TraesCS5A01G159400 chr1D 8730909 8732845 1936 False 760.666667 1380 86.253667 4385 6817 3 chr1D.!!$F1 2432

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
920 950 0.032952 TATCTTCACCGCCGCATACC 59.967 55.0 0.00 0.0 0.00 2.73 F
1127 1165 0.110104 AGCTTCTTGGAGCAGCAACT 59.890 50.0 3.54 0.0 45.12 3.16 F
2039 2121 0.108041 TTAAAGGCGTCCCTAAGGCG 60.108 55.0 0.00 0.0 41.90 5.52 F
2104 2186 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.0 0.00 0.0 44.64 4.12 F
2105 2187 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.0 0.00 0.0 45.45 5.36 F
2782 2864 0.937304 TTGAGAACTTGCAGCACGAC 59.063 50.0 5.78 0.0 0.00 4.34 F
3519 3619 1.698165 TGCTTGAAAGTAGCGAGACG 58.302 50.0 0.00 0.0 41.54 4.18 F
3902 4169 2.099756 GCATTGCCTAACCCTGAATGAC 59.900 50.0 0.00 0.0 0.00 3.06 F
5295 5715 1.928706 GCCGTATTGCTTGGCCGAAA 61.929 55.0 0.00 0.0 43.06 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2102 0.108041 CGCCTTAGGGACGCCTTTAA 60.108 55.000 0.00 0.0 33.58 1.52 R
2085 2167 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.0 30.80 3.13 R
3043 3143 1.622312 TGCTGCATAATTTGGGCAACA 59.378 42.857 0.00 0.0 37.06 3.33 R
3457 3557 1.972872 CCTCAATGATGTAGGGTGGC 58.027 55.000 0.00 0.0 0.00 5.01 R
3831 3932 2.614829 GGCTCGATAAGGCCTAAACA 57.385 50.000 5.16 0.0 44.69 2.83 R
4186 4454 3.769739 ATAGAAGTATTGGATGGCGCA 57.230 42.857 10.83 0.0 0.00 6.09 R
5295 5715 0.038310 GGCTAAAGAGTGGTGGGCTT 59.962 55.000 0.00 0.0 0.00 4.35 R
5554 5980 1.683943 GAGCATGCTAAGGCCAATGA 58.316 50.000 22.74 0.0 37.74 2.57 R
7061 7763 0.036010 ACTGTAGGGTGCATGTGAGC 60.036 55.000 0.00 0.0 0.00 4.26 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
34 35 4.992511 CCCAACCCGCCGAAACGA 62.993 66.667 0.00 0.00 34.06 3.85
35 36 2.973600 CCAACCCGCCGAAACGAA 60.974 61.111 0.00 0.00 34.06 3.85
36 37 2.554272 CAACCCGCCGAAACGAAG 59.446 61.111 0.00 0.00 34.06 3.79
37 38 3.351416 AACCCGCCGAAACGAAGC 61.351 61.111 0.00 0.00 34.06 3.86
40 41 3.350612 CCGCCGAAACGAAGCCAA 61.351 61.111 0.00 0.00 34.06 4.52
41 42 2.127383 CGCCGAAACGAAGCCAAC 60.127 61.111 0.00 0.00 34.06 3.77
42 43 2.604174 CGCCGAAACGAAGCCAACT 61.604 57.895 0.00 0.00 34.06 3.16
43 44 1.286354 CGCCGAAACGAAGCCAACTA 61.286 55.000 0.00 0.00 34.06 2.24
44 45 0.442699 GCCGAAACGAAGCCAACTAG 59.557 55.000 0.00 0.00 0.00 2.57
45 46 0.442699 CCGAAACGAAGCCAACTAGC 59.557 55.000 0.00 0.00 0.00 3.42
46 47 0.442699 CGAAACGAAGCCAACTAGCC 59.557 55.000 0.00 0.00 0.00 3.93
47 48 1.519408 GAAACGAAGCCAACTAGCCA 58.481 50.000 0.00 0.00 0.00 4.75
48 49 1.877443 GAAACGAAGCCAACTAGCCAA 59.123 47.619 0.00 0.00 0.00 4.52
49 50 1.523758 AACGAAGCCAACTAGCCAAG 58.476 50.000 0.00 0.00 0.00 3.61
50 51 0.685097 ACGAAGCCAACTAGCCAAGA 59.315 50.000 0.00 0.00 0.00 3.02
51 52 1.079503 CGAAGCCAACTAGCCAAGAC 58.920 55.000 0.00 0.00 0.00 3.01
52 53 1.079503 GAAGCCAACTAGCCAAGACG 58.920 55.000 0.00 0.00 0.00 4.18
53 54 0.955919 AAGCCAACTAGCCAAGACGC 60.956 55.000 0.00 0.00 0.00 5.19
54 55 2.399356 GCCAACTAGCCAAGACGCC 61.399 63.158 0.00 0.00 0.00 5.68
55 56 1.003839 CCAACTAGCCAAGACGCCA 60.004 57.895 0.00 0.00 0.00 5.69
56 57 0.392998 CCAACTAGCCAAGACGCCAT 60.393 55.000 0.00 0.00 0.00 4.40
57 58 1.009829 CAACTAGCCAAGACGCCATC 58.990 55.000 0.00 0.00 0.00 3.51
58 59 0.460284 AACTAGCCAAGACGCCATCG 60.460 55.000 0.00 0.00 42.43 3.84
59 60 1.592669 CTAGCCAAGACGCCATCGG 60.593 63.158 0.00 0.00 40.69 4.18
60 61 2.016393 CTAGCCAAGACGCCATCGGA 62.016 60.000 0.00 0.00 40.69 4.55
61 62 2.292794 TAGCCAAGACGCCATCGGAC 62.293 60.000 0.00 0.00 40.69 4.79
62 63 2.885644 CCAAGACGCCATCGGACG 60.886 66.667 0.00 0.00 40.69 4.79
63 64 2.885644 CAAGACGCCATCGGACGG 60.886 66.667 0.00 0.00 40.69 4.79
64 65 4.143333 AAGACGCCATCGGACGGG 62.143 66.667 0.00 0.00 40.69 5.28
66 67 4.570663 GACGCCATCGGACGGGAG 62.571 72.222 1.93 1.28 40.69 4.30
70 71 3.781307 CCATCGGACGGGAGCCAA 61.781 66.667 0.00 0.00 0.00 4.52
71 72 2.511600 CATCGGACGGGAGCCAAC 60.512 66.667 0.00 0.00 0.00 3.77
72 73 3.000819 ATCGGACGGGAGCCAACA 61.001 61.111 0.00 0.00 0.00 3.33
73 74 2.367202 ATCGGACGGGAGCCAACAT 61.367 57.895 0.00 0.00 0.00 2.71
74 75 2.311688 ATCGGACGGGAGCCAACATC 62.312 60.000 0.00 0.00 0.00 3.06
75 76 2.124695 GGACGGGAGCCAACATCC 60.125 66.667 0.00 0.00 35.99 3.51
82 83 1.972872 GGAGCCAACATCCCATGTAG 58.027 55.000 0.00 0.00 44.07 2.74
83 84 1.490490 GGAGCCAACATCCCATGTAGA 59.510 52.381 0.00 0.00 44.07 2.59
84 85 2.486191 GGAGCCAACATCCCATGTAGAG 60.486 54.545 0.00 0.00 44.07 2.43
85 86 2.435805 GAGCCAACATCCCATGTAGAGA 59.564 50.000 0.00 0.00 44.07 3.10
86 87 2.437281 AGCCAACATCCCATGTAGAGAG 59.563 50.000 0.00 0.00 44.07 3.20
87 88 2.486191 GCCAACATCCCATGTAGAGAGG 60.486 54.545 0.00 0.00 44.07 3.69
88 89 2.486191 CCAACATCCCATGTAGAGAGGC 60.486 54.545 0.00 0.00 44.07 4.70
89 90 1.428869 ACATCCCATGTAGAGAGGCC 58.571 55.000 0.00 0.00 42.78 5.19
90 91 0.319728 CATCCCATGTAGAGAGGCCG 59.680 60.000 0.00 0.00 0.00 6.13
91 92 1.476007 ATCCCATGTAGAGAGGCCGC 61.476 60.000 0.00 0.00 0.00 6.53
92 93 2.423446 CCATGTAGAGAGGCCGCC 59.577 66.667 1.49 0.00 0.00 6.13
93 94 2.423446 CATGTAGAGAGGCCGCCC 59.577 66.667 5.55 0.00 0.00 6.13
94 95 3.227276 ATGTAGAGAGGCCGCCCG 61.227 66.667 5.55 0.00 35.76 6.13
526 527 2.182842 GCCATGTGACCGCTCCATC 61.183 63.158 0.00 0.00 0.00 3.51
531 532 1.221840 GTGACCGCTCCATCACCAT 59.778 57.895 0.00 0.00 39.49 3.55
539 540 0.677731 CTCCATCACCATGCAACCGT 60.678 55.000 0.00 0.00 0.00 4.83
567 568 4.659172 CGCCTTGCCCTGGGTCAA 62.659 66.667 15.56 16.87 0.00 3.18
578 579 2.671963 GGGTCAACGAAGCACCCC 60.672 66.667 0.00 0.00 43.79 4.95
579 580 2.671963 GGTCAACGAAGCACCCCC 60.672 66.667 0.00 0.00 0.00 5.40
589 590 3.399181 GCACCCCCGATCCAGACA 61.399 66.667 0.00 0.00 0.00 3.41
591 592 2.121832 ACCCCCGATCCAGACACA 59.878 61.111 0.00 0.00 0.00 3.72
596 597 4.018609 CGATCCAGACACATCGGC 57.981 61.111 0.00 0.00 38.60 5.54
598 599 1.227674 GATCCAGACACATCGGCCC 60.228 63.158 0.00 0.00 0.00 5.80
697 700 1.234529 CGAGGGAGGAGGAAGGGAT 59.765 63.158 0.00 0.00 0.00 3.85
702 705 1.414866 GGAGGAGGAAGGGATGGAGC 61.415 65.000 0.00 0.00 0.00 4.70
745 748 1.375326 GTTTCCTCCCTGTCGCCTT 59.625 57.895 0.00 0.00 0.00 4.35
834 862 8.830580 CCCTCTGTAAACAAATATATGACACTG 58.169 37.037 0.00 0.00 0.00 3.66
842 870 9.479549 AAACAAATATATGACACTGATTTCCCT 57.520 29.630 0.00 0.00 0.00 4.20
911 941 1.927174 CGCTCAACCTTATCTTCACCG 59.073 52.381 0.00 0.00 0.00 4.94
920 950 0.032952 TATCTTCACCGCCGCATACC 59.967 55.000 0.00 0.00 0.00 2.73
927 957 3.861797 CGCCGCATACCCCCTCTT 61.862 66.667 0.00 0.00 0.00 2.85
935 965 1.689273 CATACCCCCTCTTCCTTCTCG 59.311 57.143 0.00 0.00 0.00 4.04
1082 1120 1.002366 CAACGATTCAGCCTTCCTCG 58.998 55.000 0.00 0.00 35.56 4.63
1127 1165 0.110104 AGCTTCTTGGAGCAGCAACT 59.890 50.000 3.54 0.00 45.12 3.16
1195 1233 0.760945 AGGCCCTCTTCATACCCTCG 60.761 60.000 0.00 0.00 0.00 4.63
1266 1304 7.864379 GGATGGATGTATTTAATTGTTCTGCAG 59.136 37.037 7.63 7.63 0.00 4.41
1277 1355 3.275617 TGTTCTGCAGTTACACAGGTT 57.724 42.857 14.67 0.00 34.57 3.50
1413 1491 3.421844 AGTTTCAGTAGGGGACATTTGC 58.578 45.455 0.00 0.00 0.00 3.68
1428 1506 7.068955 GGGACATTTGCGAAATTTAGTTTTTG 58.931 34.615 0.13 0.00 0.00 2.44
1456 1534 8.795786 TTGCAACAGTTAATAGTTTGAACATC 57.204 30.769 0.00 0.00 0.00 3.06
1481 1559 6.473455 CGAATGCTTTTTCACAAGAAGTTTCT 59.527 34.615 0.00 0.00 39.74 2.52
1502 1580 7.661536 TTCTAGTGTATTTCTGCAGTCCTAT 57.338 36.000 14.67 5.82 0.00 2.57
1534 1612 3.947196 CCAAGATTATGTAACTGCCTGCA 59.053 43.478 0.00 0.00 0.00 4.41
1673 1752 1.743772 GCAATGGGCTACACGATGACT 60.744 52.381 0.00 0.00 40.25 3.41
1778 1857 2.271800 GAGTGGCAAAGATACAGACCG 58.728 52.381 0.00 0.00 0.00 4.79
1823 1902 6.398918 AGTGTGTATAGATGTGGAAACTGAC 58.601 40.000 0.00 0.00 0.00 3.51
1946 2025 9.004717 AGAAAAGTAAAGAAGGTATGCTCTTTC 57.995 33.333 2.07 0.00 40.27 2.62
2010 2092 1.223487 GTCTTTATGGCCGGCCTCA 59.777 57.895 43.34 29.06 36.94 3.86
2011 2093 0.393808 GTCTTTATGGCCGGCCTCAA 60.394 55.000 43.34 32.57 36.94 3.02
2012 2094 0.393808 TCTTTATGGCCGGCCTCAAC 60.394 55.000 43.34 19.89 36.94 3.18
2013 2095 1.379309 TTTATGGCCGGCCTCAACC 60.379 57.895 43.34 19.10 36.94 3.77
2014 2096 1.858739 TTTATGGCCGGCCTCAACCT 61.859 55.000 43.34 23.14 36.94 3.50
2015 2097 0.983905 TTATGGCCGGCCTCAACCTA 60.984 55.000 43.34 24.35 36.94 3.08
2016 2098 0.766674 TATGGCCGGCCTCAACCTAT 60.767 55.000 43.34 28.95 36.94 2.57
2017 2099 2.203209 GGCCGGCCTCAACCTATG 60.203 66.667 38.76 0.00 0.00 2.23
2018 2100 2.590092 GCCGGCCTCAACCTATGT 59.410 61.111 18.11 0.00 0.00 2.29
2019 2101 1.077716 GCCGGCCTCAACCTATGTT 60.078 57.895 18.11 0.00 34.14 2.71
2020 2102 0.679960 GCCGGCCTCAACCTATGTTT 60.680 55.000 18.11 0.00 30.42 2.83
2021 2103 1.834188 CCGGCCTCAACCTATGTTTT 58.166 50.000 0.00 0.00 30.42 2.43
2022 2104 2.942306 GCCGGCCTCAACCTATGTTTTA 60.942 50.000 18.11 0.00 30.42 1.52
2023 2105 3.349022 CCGGCCTCAACCTATGTTTTAA 58.651 45.455 0.00 0.00 30.42 1.52
2024 2106 3.759618 CCGGCCTCAACCTATGTTTTAAA 59.240 43.478 0.00 0.00 30.42 1.52
2025 2107 4.142469 CCGGCCTCAACCTATGTTTTAAAG 60.142 45.833 0.00 0.00 30.42 1.85
2026 2108 4.142469 CGGCCTCAACCTATGTTTTAAAGG 60.142 45.833 0.00 0.00 36.42 3.11
2027 2109 4.381612 GGCCTCAACCTATGTTTTAAAGGC 60.382 45.833 0.00 11.65 39.87 4.35
2028 2110 4.674362 GCCTCAACCTATGTTTTAAAGGCG 60.674 45.833 0.00 0.00 35.44 5.52
2029 2111 4.457949 CCTCAACCTATGTTTTAAAGGCGT 59.542 41.667 0.00 0.00 33.42 5.68
2030 2112 5.391629 CCTCAACCTATGTTTTAAAGGCGTC 60.392 44.000 0.00 0.00 33.42 5.19
2031 2113 4.456566 TCAACCTATGTTTTAAAGGCGTCC 59.543 41.667 0.00 0.00 33.42 4.79
2032 2114 3.349927 ACCTATGTTTTAAAGGCGTCCC 58.650 45.455 0.00 0.00 33.42 4.46
2033 2115 3.009805 ACCTATGTTTTAAAGGCGTCCCT 59.990 43.478 0.00 0.00 45.77 4.20
2034 2116 4.225717 ACCTATGTTTTAAAGGCGTCCCTA 59.774 41.667 0.00 0.00 41.90 3.53
2035 2117 5.187687 CCTATGTTTTAAAGGCGTCCCTAA 58.812 41.667 0.00 0.00 41.90 2.69
2036 2118 5.296035 CCTATGTTTTAAAGGCGTCCCTAAG 59.704 44.000 0.00 0.00 41.90 2.18
2037 2119 3.414269 TGTTTTAAAGGCGTCCCTAAGG 58.586 45.455 0.00 0.00 41.90 2.69
2038 2120 2.118313 TTTAAAGGCGTCCCTAAGGC 57.882 50.000 0.00 0.00 41.90 4.35
2039 2121 0.108041 TTAAAGGCGTCCCTAAGGCG 60.108 55.000 0.00 0.00 41.90 5.52
2040 2122 0.971959 TAAAGGCGTCCCTAAGGCGA 60.972 55.000 0.00 0.00 41.90 5.54
2041 2123 2.517484 AAAGGCGTCCCTAAGGCGAC 62.517 60.000 0.00 0.00 41.90 5.19
2078 2160 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
2086 2168 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
2096 2178 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
2097 2179 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
2098 2180 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
2099 2181 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
2100 2182 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
2101 2183 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
2102 2184 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
2103 2185 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
2104 2186 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
2105 2187 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
2123 2205 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
2131 2213 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
2132 2214 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
2174 2256 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
2175 2257 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
2176 2258 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
2177 2259 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
2178 2260 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
2197 2279 3.047613 GGCGTCGCCTTAAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
2198 2280 2.223180 GGCGTCGCCTTAAAAACATAGG 60.223 50.000 28.98 0.00 46.69 2.57
2264 2346 4.427312 CATCCTTGCCAATTTAAGTCTGC 58.573 43.478 0.00 0.00 0.00 4.26
2383 2465 3.806521 CGCCATAGTCAATCAAGAGAAGG 59.193 47.826 0.00 0.00 0.00 3.46
2515 2597 4.449068 CCCACTGATATCAACGCTATTGTC 59.551 45.833 6.90 0.00 0.00 3.18
2518 2600 3.712187 TGATATCAACGCTATTGTCGCA 58.288 40.909 1.98 0.00 0.00 5.10
2536 2618 3.537793 GCAAGACGACGAAAGGATTTT 57.462 42.857 0.00 0.00 39.27 1.82
2542 2624 4.021719 AGACGACGAAAGGATTTTACTGGA 60.022 41.667 0.00 0.00 39.27 3.86
2560 2642 2.093973 TGGAGACTTCTTCCGCAATCTC 60.094 50.000 0.00 0.00 33.36 2.75
2782 2864 0.937304 TTGAGAACTTGCAGCACGAC 59.063 50.000 5.78 0.00 0.00 4.34
2819 2901 9.586435 AACAGTCAGAAAAGTAAATGAAAAAGG 57.414 29.630 0.00 0.00 0.00 3.11
2904 2994 4.646492 GGCTGGTCATTTAATTCATCCAGT 59.354 41.667 9.50 0.00 41.77 4.00
3036 3136 7.551262 TGGTCTTATTTTTCTTATCTGCGCTTA 59.449 33.333 9.73 0.00 0.00 3.09
3043 3143 8.810652 TTTTTCTTATCTGCGCTTATTTTGTT 57.189 26.923 9.73 0.00 0.00 2.83
3044 3144 7.795431 TTTCTTATCTGCGCTTATTTTGTTG 57.205 32.000 9.73 0.00 0.00 3.33
3192 3292 6.478016 TGAATTCTTCTTCACTAGATGATGCG 59.522 38.462 7.05 0.00 37.04 4.73
3457 3557 7.170320 GCATTATGCTGATTTTCCCACTATTTG 59.830 37.037 10.27 0.00 40.96 2.32
3519 3619 1.698165 TGCTTGAAAGTAGCGAGACG 58.302 50.000 0.00 0.00 41.54 4.18
3595 3695 2.101582 AGCACTTCTGCCTATACTTCCG 59.898 50.000 0.00 0.00 45.53 4.30
3614 3714 4.785417 TCCGCCACGTTTACATTTTTAAG 58.215 39.130 0.00 0.00 0.00 1.85
3831 3932 2.174360 GCTTGCCCTCTTTCTTTCCAT 58.826 47.619 0.00 0.00 0.00 3.41
3894 3997 4.398319 AGTATATGTGCATTGCCTAACCC 58.602 43.478 6.12 0.00 0.00 4.11
3902 4169 2.099756 GCATTGCCTAACCCTGAATGAC 59.900 50.000 0.00 0.00 0.00 3.06
4186 4454 7.125391 TGCTTCAGTATTTGGGAATAAAGGAT 58.875 34.615 0.00 0.00 29.89 3.24
4461 4730 7.693952 TCCAAATTTGTATTAGTCGCATTCTC 58.306 34.615 16.73 0.00 0.00 2.87
4491 4815 6.942005 TGATCACATATTAGATTTGCCGGATT 59.058 34.615 5.05 0.00 0.00 3.01
4906 5324 2.947652 AGTTCATCGATTCATTGGCTGG 59.052 45.455 0.00 0.00 0.00 4.85
4908 5326 3.497103 TCATCGATTCATTGGCTGGAT 57.503 42.857 0.00 0.00 0.00 3.41
4943 5361 4.486125 TTGAAGAAAGGCAAAAGGCTTT 57.514 36.364 15.52 15.52 44.69 3.51
5037 5455 3.318275 GGGAAAACCCACTGAAGAGAAAC 59.682 47.826 0.00 0.00 36.34 2.78
5273 5693 3.094498 GGGTCCCTATGCCCCGTT 61.094 66.667 0.00 0.00 38.99 4.44
5295 5715 1.928706 GCCGTATTGCTTGGCCGAAA 61.929 55.000 0.00 0.00 43.06 3.46
5438 5864 6.016360 TGTCCATGCAGTATAATATGTTTGCC 60.016 38.462 0.00 0.00 0.00 4.52
5489 5915 5.856126 TTCTTGTCCATTCGTTATGTCAC 57.144 39.130 0.00 0.00 31.99 3.67
5514 5940 7.119846 ACAAGTATTTGAGTTGATTGGAGTAGC 59.880 37.037 4.81 0.00 40.46 3.58
5591 6020 6.631016 CATGCTCCACTGAACTACTTACTAA 58.369 40.000 0.00 0.00 0.00 2.24
5839 6268 4.253685 TCCTGCTTATCCAGAAAAAGACG 58.746 43.478 0.00 0.00 34.77 4.18
5889 6355 5.652452 GGCCAGGATAATATTATGTTGACCC 59.348 44.000 12.74 6.61 0.00 4.46
5983 6457 5.699001 AGCATGTATGTTGTTACGTCTTGAA 59.301 36.000 0.00 0.00 0.00 2.69
6105 6586 6.294473 CCAGACCTGCTAATTAGACATCATT 58.706 40.000 16.85 0.00 0.00 2.57
6131 6612 1.149148 GCAGAACTCCCAACGAACTC 58.851 55.000 0.00 0.00 0.00 3.01
6155 6636 4.218200 CACAAGTGGATCAAAATGGTGCTA 59.782 41.667 0.00 0.00 0.00 3.49
6322 6803 2.398754 TCAGAGGACAGGGAAGAACA 57.601 50.000 0.00 0.00 0.00 3.18
6372 6863 6.535150 TGAATCGGTGATGTTTGTAGAAGATC 59.465 38.462 0.00 0.00 0.00 2.75
6395 6886 2.738587 TGTTTTGTAGGTTGCCAGGA 57.261 45.000 0.00 0.00 0.00 3.86
6484 6976 7.793036 AGGTAAGGTTTAGCTAGAACTTATGG 58.207 38.462 21.04 0.00 0.00 2.74
6566 7095 5.567915 GCATGCAGTCAATATTTCATCATCG 59.432 40.000 14.21 0.00 0.00 3.84
6567 7096 6.567132 GCATGCAGTCAATATTTCATCATCGA 60.567 38.462 14.21 0.00 0.00 3.59
6568 7097 7.527457 CATGCAGTCAATATTTCATCATCGAT 58.473 34.615 0.00 0.00 0.00 3.59
6569 7098 7.125536 TGCAGTCAATATTTCATCATCGATC 57.874 36.000 0.00 0.00 0.00 3.69
6726 7260 5.554437 TGACTGGTTTGTATACCACTTGA 57.446 39.130 0.00 0.00 43.14 3.02
6727 7261 5.931294 TGACTGGTTTGTATACCACTTGAA 58.069 37.500 0.00 0.00 43.14 2.69
6728 7262 6.358178 TGACTGGTTTGTATACCACTTGAAA 58.642 36.000 0.00 0.00 43.14 2.69
6729 7263 6.485313 TGACTGGTTTGTATACCACTTGAAAG 59.515 38.462 0.00 0.00 43.14 2.62
6730 7264 6.362248 ACTGGTTTGTATACCACTTGAAAGT 58.638 36.000 0.00 0.00 43.14 2.66
6748 7318 6.980593 TGAAAGTTGAAACCACATTATCTGG 58.019 36.000 0.00 0.00 34.62 3.86
6757 7327 7.816995 TGAAACCACATTATCTGGCATAAAAAC 59.183 33.333 0.00 0.00 31.13 2.43
6985 7687 5.279456 GGGTGACATTAAAGGCTGAAAACAT 60.279 40.000 0.00 0.00 0.00 2.71
6992 7694 8.421002 ACATTAAAGGCTGAAAACATAACTTGT 58.579 29.630 0.00 0.00 41.53 3.16
6997 7699 5.536161 AGGCTGAAAACATAACTTGTCATGT 59.464 36.000 0.00 0.00 37.68 3.21
7061 7763 2.886862 ATGGAGTTCATGAGCTCGAG 57.113 50.000 26.99 8.45 39.23 4.04
7153 10518 0.612744 TCGTGATGGAGTGGCATTCA 59.387 50.000 12.30 1.25 0.00 2.57
7207 10590 5.360714 AGACTGTTTTGAAGCATTTTGGAGA 59.639 36.000 0.00 0.00 0.00 3.71
7226 10609 5.104109 TGGAGAATCGATTATGTTTTCCCCT 60.104 40.000 10.53 0.00 34.37 4.79
7227 10610 6.100569 TGGAGAATCGATTATGTTTTCCCCTA 59.899 38.462 10.53 0.00 34.37 3.53
7260 10643 5.341993 TGAATGTCGTTCGATTGCAAAAATC 59.658 36.000 1.71 0.00 39.80 2.17
7321 10714 5.722021 AATTTTACTGTAGCAAAGGGTGG 57.278 39.130 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.992511 TCGTTTCGGCGGGTTGGG 62.993 66.667 7.21 0.00 0.00 4.12
18 19 2.961669 CTTCGTTTCGGCGGGTTGG 61.962 63.158 7.21 0.00 0.00 3.77
19 20 2.554272 CTTCGTTTCGGCGGGTTG 59.446 61.111 7.21 0.00 0.00 3.77
20 21 3.351416 GCTTCGTTTCGGCGGGTT 61.351 61.111 7.21 0.00 0.00 4.11
23 24 3.350612 TTGGCTTCGTTTCGGCGG 61.351 61.111 7.21 0.00 0.00 6.13
24 25 1.286354 TAGTTGGCTTCGTTTCGGCG 61.286 55.000 0.00 0.00 0.00 6.46
25 26 0.442699 CTAGTTGGCTTCGTTTCGGC 59.557 55.000 0.00 0.00 0.00 5.54
26 27 0.442699 GCTAGTTGGCTTCGTTTCGG 59.557 55.000 0.00 0.00 0.00 4.30
27 28 0.442699 GGCTAGTTGGCTTCGTTTCG 59.557 55.000 0.00 0.00 38.32 3.46
28 29 1.519408 TGGCTAGTTGGCTTCGTTTC 58.481 50.000 0.00 0.00 42.34 2.78
29 30 1.880027 CTTGGCTAGTTGGCTTCGTTT 59.120 47.619 0.00 0.00 42.34 3.60
30 31 1.071699 TCTTGGCTAGTTGGCTTCGTT 59.928 47.619 0.00 0.00 42.34 3.85
31 32 0.685097 TCTTGGCTAGTTGGCTTCGT 59.315 50.000 0.00 0.00 42.34 3.85
32 33 1.079503 GTCTTGGCTAGTTGGCTTCG 58.920 55.000 0.00 0.00 42.34 3.79
33 34 1.079503 CGTCTTGGCTAGTTGGCTTC 58.920 55.000 0.00 0.00 42.34 3.86
34 35 0.955919 GCGTCTTGGCTAGTTGGCTT 60.956 55.000 0.00 0.00 42.34 4.35
35 36 1.376037 GCGTCTTGGCTAGTTGGCT 60.376 57.895 0.00 0.00 42.34 4.75
36 37 2.399356 GGCGTCTTGGCTAGTTGGC 61.399 63.158 0.00 0.00 40.72 4.52
37 38 0.392998 ATGGCGTCTTGGCTAGTTGG 60.393 55.000 0.00 0.00 45.14 3.77
38 39 1.009829 GATGGCGTCTTGGCTAGTTG 58.990 55.000 0.00 0.00 45.14 3.16
39 40 0.460284 CGATGGCGTCTTGGCTAGTT 60.460 55.000 5.00 0.00 45.14 2.24
40 41 1.141881 CGATGGCGTCTTGGCTAGT 59.858 57.895 5.00 0.00 45.14 2.57
41 42 1.592669 CCGATGGCGTCTTGGCTAG 60.593 63.158 5.00 0.00 45.14 3.42
42 43 2.055633 TCCGATGGCGTCTTGGCTA 61.056 57.895 5.00 0.00 45.14 3.93
43 44 3.390521 TCCGATGGCGTCTTGGCT 61.391 61.111 5.00 0.00 45.14 4.75
44 45 3.195698 GTCCGATGGCGTCTTGGC 61.196 66.667 5.00 0.00 45.12 4.52
45 46 2.885644 CGTCCGATGGCGTCTTGG 60.886 66.667 5.00 0.00 35.23 3.61
46 47 2.885644 CCGTCCGATGGCGTCTTG 60.886 66.667 5.00 0.00 35.23 3.02
47 48 4.143333 CCCGTCCGATGGCGTCTT 62.143 66.667 5.00 0.00 35.23 3.01
49 50 4.570663 CTCCCGTCCGATGGCGTC 62.571 72.222 0.46 0.00 35.23 5.19
53 54 3.781307 TTGGCTCCCGTCCGATGG 61.781 66.667 0.00 0.00 0.00 3.51
54 55 2.511600 GTTGGCTCCCGTCCGATG 60.512 66.667 0.00 0.00 0.00 3.84
55 56 2.311688 GATGTTGGCTCCCGTCCGAT 62.312 60.000 0.00 0.00 0.00 4.18
56 57 3.000819 ATGTTGGCTCCCGTCCGA 61.001 61.111 0.00 0.00 0.00 4.55
57 58 2.511600 GATGTTGGCTCCCGTCCG 60.512 66.667 0.00 0.00 0.00 4.79
58 59 2.124695 GGATGTTGGCTCCCGTCC 60.125 66.667 0.00 0.00 0.00 4.79
59 60 2.124695 GGGATGTTGGCTCCCGTC 60.125 66.667 0.00 0.00 42.94 4.79
63 64 1.490490 TCTACATGGGATGTTGGCTCC 59.510 52.381 0.00 0.00 41.63 4.70
64 65 2.435805 TCTCTACATGGGATGTTGGCTC 59.564 50.000 0.00 0.00 41.63 4.70
65 66 2.437281 CTCTCTACATGGGATGTTGGCT 59.563 50.000 0.00 0.00 41.63 4.75
66 67 2.486191 CCTCTCTACATGGGATGTTGGC 60.486 54.545 0.00 0.00 41.63 4.52
67 68 2.486191 GCCTCTCTACATGGGATGTTGG 60.486 54.545 0.00 0.00 41.63 3.77
68 69 2.486191 GGCCTCTCTACATGGGATGTTG 60.486 54.545 0.00 0.00 41.63 3.33
69 70 1.771255 GGCCTCTCTACATGGGATGTT 59.229 52.381 0.00 0.00 41.63 2.71
70 71 1.428869 GGCCTCTCTACATGGGATGT 58.571 55.000 0.00 0.00 46.92 3.06
71 72 0.319728 CGGCCTCTCTACATGGGATG 59.680 60.000 0.00 0.00 0.00 3.51
72 73 1.476007 GCGGCCTCTCTACATGGGAT 61.476 60.000 0.00 0.00 0.00 3.85
73 74 2.134287 GCGGCCTCTCTACATGGGA 61.134 63.158 0.00 0.00 0.00 4.37
74 75 2.423446 GCGGCCTCTCTACATGGG 59.577 66.667 0.00 0.00 0.00 4.00
75 76 2.423446 GGCGGCCTCTCTACATGG 59.577 66.667 12.87 0.00 0.00 3.66
76 77 2.423446 GGGCGGCCTCTCTACATG 59.577 66.667 22.87 0.00 0.00 3.21
77 78 3.227276 CGGGCGGCCTCTCTACAT 61.227 66.667 27.04 0.00 0.00 2.29
508 509 2.124570 ATGGAGCGGTCACATGGC 60.125 61.111 17.59 0.00 0.00 4.40
509 510 1.091771 GTGATGGAGCGGTCACATGG 61.092 60.000 17.59 0.00 43.20 3.66
510 511 1.091771 GGTGATGGAGCGGTCACATG 61.092 60.000 17.59 0.00 44.99 3.21
514 515 1.221566 CATGGTGATGGAGCGGTCA 59.778 57.895 17.59 3.01 0.00 4.02
519 520 1.811860 GGTTGCATGGTGATGGAGC 59.188 57.895 0.00 0.00 30.64 4.70
521 522 0.959867 CACGGTTGCATGGTGATGGA 60.960 55.000 6.48 0.00 33.58 3.41
555 556 2.429930 CTTCGTTGACCCAGGGCA 59.570 61.111 4.91 1.25 0.00 5.36
567 568 3.782443 GGATCGGGGGTGCTTCGT 61.782 66.667 0.00 0.00 0.00 3.85
579 580 1.592669 GGCCGATGTGTCTGGATCG 60.593 63.158 0.00 0.00 40.94 3.69
621 622 4.645809 GGCGAGGCCTTCTCATTT 57.354 55.556 6.77 0.00 46.69 2.32
684 687 0.692419 TGCTCCATCCCTTCCTCCTC 60.692 60.000 0.00 0.00 0.00 3.71
685 688 0.693767 CTGCTCCATCCCTTCCTCCT 60.694 60.000 0.00 0.00 0.00 3.69
692 695 3.329093 GCTTCCTGCTCCATCCCT 58.671 61.111 0.00 0.00 38.95 4.20
702 705 3.123620 GTCGCAGCCAGCTTCCTG 61.124 66.667 6.10 6.10 42.61 3.86
728 731 1.374947 CAAGGCGACAGGGAGGAAA 59.625 57.895 0.00 0.00 0.00 3.13
772 775 2.347755 GCGAGGATTGTTACGGACTTTC 59.652 50.000 0.00 0.00 0.00 2.62
780 783 3.851098 ACTCAAGAGCGAGGATTGTTAC 58.149 45.455 0.00 0.00 37.34 2.50
828 854 5.765182 TCTTTCTTTCAGGGAAATCAGTGTC 59.235 40.000 0.00 0.00 33.12 3.67
830 856 5.048434 GGTCTTTCTTTCAGGGAAATCAGTG 60.048 44.000 0.00 0.00 33.12 3.66
834 862 3.440522 CCGGTCTTTCTTTCAGGGAAATC 59.559 47.826 0.00 0.00 33.12 2.17
842 870 6.512342 TTTTTGTTACCGGTCTTTCTTTCA 57.488 33.333 12.40 0.00 0.00 2.69
911 941 2.111251 GAAGAGGGGGTATGCGGC 59.889 66.667 0.00 0.00 0.00 6.53
920 950 0.324943 TTTGCGAGAAGGAAGAGGGG 59.675 55.000 0.00 0.00 0.00 4.79
927 957 3.181491 CCAAAGTTTGTTTGCGAGAAGGA 60.181 43.478 14.36 0.00 0.00 3.36
935 965 5.122239 AGCTTTTCTTCCAAAGTTTGTTTGC 59.878 36.000 14.36 7.03 36.32 3.68
1069 1107 2.573869 CGCTCGAGGAAGGCTGAA 59.426 61.111 15.58 0.00 0.00 3.02
1111 1149 2.027745 CCTCTAGTTGCTGCTCCAAGAA 60.028 50.000 0.00 0.00 0.00 2.52
1127 1165 2.683572 TGCCGGCTGCTTCCTCTA 60.684 61.111 29.70 0.00 42.00 2.43
1195 1233 1.270068 GCCTCGTCGTTAGAGAAAGC 58.730 55.000 6.22 0.00 37.93 3.51
1227 1265 1.289160 TCCATCCTGGACAAGAAGGG 58.711 55.000 0.00 0.00 42.67 3.95
1266 1304 3.264964 TCCCCAATAGGAACCTGTGTAAC 59.735 47.826 3.36 0.00 38.24 2.50
1277 1355 5.104277 ACACAATTATTCGTCCCCAATAGGA 60.104 40.000 0.00 0.00 38.24 2.94
1393 1471 2.161609 CGCAAATGTCCCCTACTGAAAC 59.838 50.000 0.00 0.00 0.00 2.78
1413 1491 9.146270 CTGTTGCAATTCAAAAACTAAATTTCG 57.854 29.630 0.59 0.00 36.26 3.46
1428 1506 9.243637 TGTTCAAACTATTAACTGTTGCAATTC 57.756 29.630 0.59 0.00 0.00 2.17
1456 1534 6.473455 AGAAACTTCTTGTGAAAAAGCATTCG 59.527 34.615 0.00 0.00 32.55 3.34
1481 1559 8.946085 CAAAAATAGGACTGCAGAAATACACTA 58.054 33.333 23.35 11.16 0.00 2.74
1534 1612 2.945984 CACAAAGTGGATGCGCGT 59.054 55.556 8.43 0.00 0.00 6.01
1584 1663 1.672356 CCACACACCCTGCAGTAGC 60.672 63.158 13.81 0.00 42.57 3.58
1673 1752 9.739276 AACTCAATAAACCTATCACAGATTTGA 57.261 29.630 0.00 0.00 0.00 2.69
1778 1857 0.110192 GGCAACGCTTGTAGAAGTGC 60.110 55.000 12.73 8.80 42.55 4.40
1911 1990 7.089538 ACCTTCTTTACTTTTCTAGCGAGTAC 58.910 38.462 0.00 0.00 0.00 2.73
2010 2092 3.760151 GGGACGCCTTTAAAACATAGGTT 59.240 43.478 0.00 0.00 39.43 3.50
2011 2093 3.009805 AGGGACGCCTTTAAAACATAGGT 59.990 43.478 0.00 0.00 0.00 3.08
2012 2094 3.617284 AGGGACGCCTTTAAAACATAGG 58.383 45.455 0.00 0.00 0.00 2.57
2013 2095 5.296035 CCTTAGGGACGCCTTTAAAACATAG 59.704 44.000 0.00 0.00 33.58 2.23
2014 2096 5.187687 CCTTAGGGACGCCTTTAAAACATA 58.812 41.667 0.00 0.00 33.58 2.29
2015 2097 4.014406 CCTTAGGGACGCCTTTAAAACAT 58.986 43.478 0.00 0.00 33.58 2.71
2016 2098 3.414269 CCTTAGGGACGCCTTTAAAACA 58.586 45.455 0.00 0.00 33.58 2.83
2017 2099 2.163010 GCCTTAGGGACGCCTTTAAAAC 59.837 50.000 0.00 0.00 33.58 2.43
2018 2100 2.439409 GCCTTAGGGACGCCTTTAAAA 58.561 47.619 0.00 0.00 33.58 1.52
2019 2101 1.676615 CGCCTTAGGGACGCCTTTAAA 60.677 52.381 0.00 0.00 33.58 1.52
2020 2102 0.108041 CGCCTTAGGGACGCCTTTAA 60.108 55.000 0.00 0.00 33.58 1.52
2021 2103 0.971959 TCGCCTTAGGGACGCCTTTA 60.972 55.000 0.00 0.00 34.09 1.85
2022 2104 2.267961 CGCCTTAGGGACGCCTTT 59.732 61.111 0.00 0.00 33.58 3.11
2023 2105 2.682494 TCGCCTTAGGGACGCCTT 60.682 61.111 0.00 0.00 34.09 4.35
2024 2106 3.459063 GTCGCCTTAGGGACGCCT 61.459 66.667 0.00 0.00 44.82 5.52
2061 2143 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
2069 2151 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
2070 2152 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
2077 2159 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
2078 2160 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
2079 2161 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
2080 2162 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
2081 2163 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
2082 2164 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
2083 2165 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
2084 2166 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
2085 2167 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
2086 2168 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
2087 2169 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
2088 2170 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
2106 2188 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
2114 2196 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
2115 2197 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
2161 2243 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
2162 2244 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
2163 2245 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
2164 2246 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
2165 2247 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
2166 2248 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
2178 2260 2.790123 GCCTATGTTTTTAAGGCGACGC 60.790 50.000 12.43 12.43 45.82 5.19
2179 2261 3.047613 GCCTATGTTTTTAAGGCGACG 57.952 47.619 0.00 0.00 45.82 5.12
2184 2266 7.556275 TCATAGTTGAGGCCTATGTTTTTAAGG 59.444 37.037 4.42 0.00 41.55 2.69
2185 2267 8.506168 TCATAGTTGAGGCCTATGTTTTTAAG 57.494 34.615 4.42 0.00 41.55 1.85
2186 2268 8.506168 CTCATAGTTGAGGCCTATGTTTTTAA 57.494 34.615 4.42 0.00 44.78 1.52
2201 2283 6.299805 AGAACATAGTTGGCTCATAGTTGA 57.700 37.500 0.00 0.00 0.00 3.18
2383 2465 5.630680 CAGAAAACTACAATGCACATGAACC 59.369 40.000 0.00 0.00 0.00 3.62
2515 2597 1.068474 AATCCTTTCGTCGTCTTGCG 58.932 50.000 0.00 0.00 43.01 4.85
2518 2600 4.689345 CCAGTAAAATCCTTTCGTCGTCTT 59.311 41.667 0.00 0.00 0.00 3.01
2536 2618 1.919240 TGCGGAAGAAGTCTCCAGTA 58.081 50.000 0.00 0.00 0.00 2.74
2542 2624 3.685139 TTGAGATTGCGGAAGAAGTCT 57.315 42.857 0.00 0.00 0.00 3.24
2584 2666 1.068753 ATCTCGCTCATCAAGGCCG 59.931 57.895 0.00 0.00 0.00 6.13
2724 2806 4.447138 TTGGTGGGTCTGTTTCAGTAAT 57.553 40.909 0.00 0.00 32.61 1.89
2917 3007 6.215845 TGATATACATGACACACATTCTCGG 58.784 40.000 0.00 0.00 37.07 4.63
3036 3136 5.533903 TGCATAATTTGGGCAACAACAAAAT 59.466 32.000 0.00 0.00 39.69 1.82
3041 3141 2.416202 GCTGCATAATTTGGGCAACAAC 59.584 45.455 0.00 0.00 39.19 3.32
3043 3143 1.622312 TGCTGCATAATTTGGGCAACA 59.378 42.857 0.00 0.00 37.06 3.33
3044 3144 2.383368 TGCTGCATAATTTGGGCAAC 57.617 45.000 0.00 0.00 37.06 4.17
3192 3292 7.617041 AGCTAATCCTTTTATCTTGTCACAC 57.383 36.000 0.00 0.00 0.00 3.82
3414 3514 6.016024 GCATAATGCCTGATGGATTAAAGTGA 60.016 38.462 0.00 0.00 37.42 3.41
3457 3557 1.972872 CCTCAATGATGTAGGGTGGC 58.027 55.000 0.00 0.00 0.00 5.01
3595 3695 7.688478 AACTTCTTAAAAATGTAAACGTGGC 57.312 32.000 0.00 0.00 0.00 5.01
3831 3932 2.614829 GGCTCGATAAGGCCTAAACA 57.385 50.000 5.16 0.00 44.69 2.83
3902 4169 8.774586 CGGGGAATCATCTAGTTTTATTAAGTG 58.225 37.037 0.00 0.00 0.00 3.16
4084 4352 7.622893 AGAAAATGAAAGAGAGGAATAGCAC 57.377 36.000 0.00 0.00 0.00 4.40
4144 4412 6.316140 ACTGAAGCAAATTTTCTTGGAAAACC 59.684 34.615 7.85 0.00 0.00 3.27
4186 4454 3.769739 ATAGAAGTATTGGATGGCGCA 57.230 42.857 10.83 0.00 0.00 6.09
4355 4624 6.600822 ACGAAGCTCAAGTATTACCACTAGTA 59.399 38.462 0.00 0.00 0.00 1.82
4358 4627 5.163581 GGACGAAGCTCAAGTATTACCACTA 60.164 44.000 0.00 0.00 0.00 2.74
4461 4730 7.592533 CGGCAAATCTAATATGTGATCAAAAGG 59.407 37.037 0.00 0.00 0.00 3.11
4625 4951 5.821204 AGTGTAAACAAACATTCTCTGCAC 58.179 37.500 0.00 0.00 0.00 4.57
4943 5361 7.874252 TCCCCTACTTAATTAATGTAAAGGCA 58.126 34.615 0.00 0.00 0.00 4.75
5037 5455 2.950781 TGGGTACAGGCTCTCTATGAG 58.049 52.381 0.00 0.00 45.33 2.90
5165 5585 2.350522 GACCATTCTGTCGCAACTCAT 58.649 47.619 0.00 0.00 0.00 2.90
5273 5693 3.809775 GCCAAGCAATACGGCGCA 61.810 61.111 10.83 0.00 39.27 6.09
5277 5697 0.523966 TTTTCGGCCAAGCAATACGG 59.476 50.000 2.24 0.00 0.00 4.02
5295 5715 0.038310 GGCTAAAGAGTGGTGGGCTT 59.962 55.000 0.00 0.00 0.00 4.35
5438 5864 4.389992 AGATGCATCCGACGCAATAAATAG 59.610 41.667 23.06 0.00 43.84 1.73
5489 5915 7.414540 GGCTACTCCAATCAACTCAAATACTTG 60.415 40.741 0.00 0.00 34.01 3.16
5514 5940 8.472413 AGTCATAGAATCAACATTTCCAATTGG 58.528 33.333 19.08 19.08 0.00 3.16
5554 5980 1.683943 GAGCATGCTAAGGCCAATGA 58.316 50.000 22.74 0.00 37.74 2.57
5591 6020 6.369059 GCTCAATGCTTACATGTCAGTATT 57.631 37.500 15.18 15.18 36.36 1.89
5724 6153 8.095792 TGTGGTTTCCGTAAATATAACTCTCAA 58.904 33.333 0.00 0.00 0.00 3.02
5741 6170 5.863935 GCAAGAATTATGAAGTGTGGTTTCC 59.136 40.000 0.00 0.00 0.00 3.13
5839 6268 7.437267 CCATTTAGCATTCATTGTCAAATCCTC 59.563 37.037 0.00 0.00 0.00 3.71
5983 6457 0.474184 AGCAGTTTGTGGTGCCTAGT 59.526 50.000 0.00 0.00 40.81 2.57
6058 6539 8.853077 TGGGTAAAATGCATAGAGATTATGAG 57.147 34.615 0.00 0.00 0.00 2.90
6105 6586 2.811431 CGTTGGGAGTTCTGCATAAACA 59.189 45.455 12.93 0.00 0.00 2.83
6131 6612 3.861886 GCACCATTTTGATCCACTTGTGG 60.862 47.826 13.24 13.24 0.00 4.17
6155 6636 4.466370 TCCTTGTTGAGATGGTACGAATCT 59.534 41.667 8.92 8.92 37.09 2.40
6322 6803 4.280929 GGGTGTTACAGGCTCAAAATTCTT 59.719 41.667 0.00 0.00 0.00 2.52
6372 6863 3.057315 CCTGGCAACCTACAAAACATCTG 60.057 47.826 0.00 0.00 0.00 2.90
6395 6886 7.959175 TGTAACTTCATAAGACCAACACTAGT 58.041 34.615 0.00 0.00 0.00 2.57
6566 7095 6.369890 TGATGACACACTTGCTCTAAAAGATC 59.630 38.462 0.00 0.00 0.00 2.75
6567 7096 6.233434 TGATGACACACTTGCTCTAAAAGAT 58.767 36.000 0.00 0.00 0.00 2.40
6568 7097 5.610398 TGATGACACACTTGCTCTAAAAGA 58.390 37.500 0.00 0.00 0.00 2.52
6569 7098 5.698089 TCTGATGACACACTTGCTCTAAAAG 59.302 40.000 0.00 0.00 0.00 2.27
6684 7218 9.726232 CCAGTCATTTTTATGTCAGATAATGTG 57.274 33.333 0.00 0.00 0.00 3.21
6685 7219 9.466497 ACCAGTCATTTTTATGTCAGATAATGT 57.534 29.630 0.00 0.00 0.00 2.71
6689 7223 9.295825 ACAAACCAGTCATTTTTATGTCAGATA 57.704 29.630 0.00 0.00 0.00 1.98
6690 7224 8.181904 ACAAACCAGTCATTTTTATGTCAGAT 57.818 30.769 0.00 0.00 0.00 2.90
6691 7225 7.581213 ACAAACCAGTCATTTTTATGTCAGA 57.419 32.000 0.00 0.00 0.00 3.27
6694 7228 9.783256 GGTATACAAACCAGTCATTTTTATGTC 57.217 33.333 5.01 0.00 39.50 3.06
6695 7229 9.303116 TGGTATACAAACCAGTCATTTTTATGT 57.697 29.630 5.01 0.00 44.68 2.29
6709 7243 7.266922 TCAACTTTCAAGTGGTATACAAACC 57.733 36.000 5.01 0.00 39.66 3.27
6719 7253 4.448537 TGTGGTTTCAACTTTCAAGTGG 57.551 40.909 0.00 0.00 39.66 4.00
6726 7260 5.304101 TGCCAGATAATGTGGTTTCAACTTT 59.696 36.000 0.00 0.00 37.40 2.66
6727 7261 4.832266 TGCCAGATAATGTGGTTTCAACTT 59.168 37.500 0.00 0.00 37.40 2.66
6728 7262 4.406456 TGCCAGATAATGTGGTTTCAACT 58.594 39.130 0.00 0.00 37.40 3.16
6729 7263 4.782019 TGCCAGATAATGTGGTTTCAAC 57.218 40.909 0.00 0.00 37.40 3.18
6730 7264 7.473735 TTTATGCCAGATAATGTGGTTTCAA 57.526 32.000 0.00 0.00 37.40 2.69
6748 7318 4.347813 AGTTGTGTGTGTCGTTTTTATGC 58.652 39.130 0.00 0.00 0.00 3.14
6757 7327 7.411912 CCAGATTAATTCTAGTTGTGTGTGTCG 60.412 40.741 0.00 0.00 31.77 4.35
6985 7687 7.601130 GTCTGGTACATGTTACATGACAAGTTA 59.399 37.037 29.17 9.30 38.20 2.24
6992 7694 5.859495 TGTTGTCTGGTACATGTTACATGA 58.141 37.500 29.17 11.94 38.10 3.07
6997 7699 5.037383 TGGTTGTTGTCTGGTACATGTTA 57.963 39.130 2.30 0.00 38.10 2.41
7061 7763 0.036010 ACTGTAGGGTGCATGTGAGC 60.036 55.000 0.00 0.00 0.00 4.26
7187 10570 5.691305 CGATTCTCCAAAATGCTTCAAAACA 59.309 36.000 0.00 0.00 0.00 2.83
7207 10590 6.101296 AGGTCTAGGGGAAAACATAATCGATT 59.899 38.462 16.15 16.15 0.00 3.34
7226 10609 3.181490 CGAACGACATTCATGGAGGTCTA 60.181 47.826 16.36 0.00 37.12 2.59
7227 10610 2.417379 CGAACGACATTCATGGAGGTCT 60.417 50.000 16.36 0.00 37.12 3.85
7260 10643 4.880886 TGTCTGTTTCACATGTGTTCAG 57.119 40.909 24.63 25.34 0.00 3.02


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

AutoCloner maintained by Alex Coulton.