Multiple sequence alignment - TraesCS4B01G326400

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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 TraesCS4B01G326400 chr4B 100.000 3687 0 0 679 4365 617379572 617383258 0.000000e+00 6809.0
1 TraesCS4B01G326400 chr4B 100.000 128 0 0 1 128 617378894 617379021 2.030000e-58 237.0
2 TraesCS4B01G326400 chr4B 82.123 179 15 7 4195 4365 617392077 617392246 2.120000e-28 137.0
3 TraesCS4B01G326400 chr5A 92.357 2944 146 33 761 3659 665611812 665614721 0.000000e+00 4117.0
4 TraesCS4B01G326400 chr5A 90.637 534 42 5 3646 4176 665614823 665615351 0.000000e+00 702.0
5 TraesCS4B01G326400 chr5A 97.541 122 3 0 4244 4365 665615361 665615482 4.420000e-50 209.0
6 TraesCS4B01G326400 chr5A 87.692 130 8 2 4244 4365 665701811 665701940 1.270000e-30 145.0
7 TraesCS4B01G326400 chr5A 86.607 112 13 1 3904 4013 665695856 665695967 5.930000e-24 122.0
8 TraesCS4B01G326400 chr4D 91.808 2832 154 40 1583 4365 484688913 484691715 0.000000e+00 3873.0
9 TraesCS4B01G326400 chr4D 88.490 808 46 21 761 1531 484688031 484688828 0.000000e+00 933.0
10 TraesCS4B01G326400 chr4D 89.286 168 18 0 1162 1329 62772199 62772366 1.230000e-50 211.0
11 TraesCS4B01G326400 chr4D 88.462 130 7 2 4244 4365 484705462 484705591 2.720000e-32 150.0
12 TraesCS4B01G326400 chr1D 91.429 245 21 0 1162 1406 11241427 11241183 1.940000e-88 337.0
13 TraesCS4B01G326400 chr6B 92.188 64 3 2 4 66 711317800 711317738 6.010000e-14 89.8


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 TraesCS4B01G326400 chr4B 617378894 617383258 4364 False 3523 6809 100.000000 1 4365 2 chr4B.!!$F2 4364
1 TraesCS4B01G326400 chr5A 665611812 665615482 3670 False 1676 4117 93.511667 761 4365 3 chr5A.!!$F3 3604
2 TraesCS4B01G326400 chr4D 484688031 484691715 3684 False 2403 3873 90.149000 761 4365 2 chr4D.!!$F3 3604

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
25 26 0.033208 CTCCTCTCTCAGTCCCAGCT 60.033 60.0 0.0 0.0 0.0 4.24 F
28 29 0.033208 CTCTCTCAGTCCCAGCTCCT 60.033 60.0 0.0 0.0 0.0 3.69 F
1157 1189 0.041238 TCCTCTGATTCCGTGGTCCT 59.959 55.0 0.0 0.0 0.0 3.85 F
1567 1661 0.181350 GAGATCCGGTGCCCATTCTT 59.819 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2126 0.106708 AGGAACACGCTGAAGCAGAA 59.893 50.0 2.79 0.0 42.21 3.02 R
2013 2129 0.106708 AAGAGGAACACGCTGAAGCA 59.893 50.0 2.79 0.0 42.21 3.91 R
2014 2130 0.793250 GAAGAGGAACACGCTGAAGC 59.207 55.0 0.00 0.0 37.78 3.86 R
3475 3608 1.288188 TGCACCTCATCTGGGATGAA 58.712 50.0 10.75 0.0 0.00 2.57 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
18 19 3.998560 CAGGTCCTCCTCTCTCAGT 57.001 57.895 0.00 0.00 43.07 3.41
19 20 1.762708 CAGGTCCTCCTCTCTCAGTC 58.237 60.000 0.00 0.00 43.07 3.51
20 21 0.629058 AGGTCCTCCTCTCTCAGTCC 59.371 60.000 0.00 0.00 40.58 3.85
21 22 0.396556 GGTCCTCCTCTCTCAGTCCC 60.397 65.000 0.00 0.00 0.00 4.46
22 23 0.333312 GTCCTCCTCTCTCAGTCCCA 59.667 60.000 0.00 0.00 0.00 4.37
23 24 0.628522 TCCTCCTCTCTCAGTCCCAG 59.371 60.000 0.00 0.00 0.00 4.45
24 25 1.042559 CCTCCTCTCTCAGTCCCAGC 61.043 65.000 0.00 0.00 0.00 4.85
25 26 0.033208 CTCCTCTCTCAGTCCCAGCT 60.033 60.000 0.00 0.00 0.00 4.24
26 27 0.033601 TCCTCTCTCAGTCCCAGCTC 60.034 60.000 0.00 0.00 0.00 4.09
27 28 1.042559 CCTCTCTCAGTCCCAGCTCC 61.043 65.000 0.00 0.00 0.00 4.70
28 29 0.033208 CTCTCTCAGTCCCAGCTCCT 60.033 60.000 0.00 0.00 0.00 3.69
29 30 0.411452 TCTCTCAGTCCCAGCTCCTT 59.589 55.000 0.00 0.00 0.00 3.36
30 31 0.823460 CTCTCAGTCCCAGCTCCTTC 59.177 60.000 0.00 0.00 0.00 3.46
31 32 0.115152 TCTCAGTCCCAGCTCCTTCA 59.885 55.000 0.00 0.00 0.00 3.02
32 33 1.202330 CTCAGTCCCAGCTCCTTCAT 58.798 55.000 0.00 0.00 0.00 2.57
33 34 1.138661 CTCAGTCCCAGCTCCTTCATC 59.861 57.143 0.00 0.00 0.00 2.92
34 35 0.907486 CAGTCCCAGCTCCTTCATCA 59.093 55.000 0.00 0.00 0.00 3.07
35 36 1.489649 CAGTCCCAGCTCCTTCATCAT 59.510 52.381 0.00 0.00 0.00 2.45
36 37 1.767681 AGTCCCAGCTCCTTCATCATC 59.232 52.381 0.00 0.00 0.00 2.92
37 38 1.767681 GTCCCAGCTCCTTCATCATCT 59.232 52.381 0.00 0.00 0.00 2.90
38 39 1.767088 TCCCAGCTCCTTCATCATCTG 59.233 52.381 0.00 0.00 0.00 2.90
39 40 1.595466 CCAGCTCCTTCATCATCTGC 58.405 55.000 0.00 0.00 0.00 4.26
40 41 1.141254 CCAGCTCCTTCATCATCTGCT 59.859 52.381 0.00 0.00 0.00 4.24
41 42 2.485903 CAGCTCCTTCATCATCTGCTC 58.514 52.381 0.00 0.00 0.00 4.26
42 43 1.068895 AGCTCCTTCATCATCTGCTCG 59.931 52.381 0.00 0.00 0.00 5.03
43 44 1.068281 GCTCCTTCATCATCTGCTCGA 59.932 52.381 0.00 0.00 0.00 4.04
44 45 2.741612 CTCCTTCATCATCTGCTCGAC 58.258 52.381 0.00 0.00 0.00 4.20
45 46 2.100418 CTCCTTCATCATCTGCTCGACA 59.900 50.000 0.00 0.00 0.00 4.35
46 47 2.697229 TCCTTCATCATCTGCTCGACAT 59.303 45.455 0.00 0.00 0.00 3.06
47 48 3.058450 CCTTCATCATCTGCTCGACATC 58.942 50.000 0.00 0.00 0.00 3.06
48 49 3.492137 CCTTCATCATCTGCTCGACATCA 60.492 47.826 0.00 0.00 0.00 3.07
49 50 3.089573 TCATCATCTGCTCGACATCAC 57.910 47.619 0.00 0.00 0.00 3.06
50 51 2.692041 TCATCATCTGCTCGACATCACT 59.308 45.455 0.00 0.00 0.00 3.41
51 52 3.885297 TCATCATCTGCTCGACATCACTA 59.115 43.478 0.00 0.00 0.00 2.74
52 53 4.339247 TCATCATCTGCTCGACATCACTAA 59.661 41.667 0.00 0.00 0.00 2.24
53 54 4.926140 TCATCTGCTCGACATCACTAAT 57.074 40.909 0.00 0.00 0.00 1.73
54 55 5.268118 TCATCTGCTCGACATCACTAATT 57.732 39.130 0.00 0.00 0.00 1.40
55 56 5.284864 TCATCTGCTCGACATCACTAATTC 58.715 41.667 0.00 0.00 0.00 2.17
56 57 4.046938 TCTGCTCGACATCACTAATTCC 57.953 45.455 0.00 0.00 0.00 3.01
57 58 3.126831 CTGCTCGACATCACTAATTCCC 58.873 50.000 0.00 0.00 0.00 3.97
58 59 2.128035 GCTCGACATCACTAATTCCCG 58.872 52.381 0.00 0.00 0.00 5.14
59 60 2.223735 GCTCGACATCACTAATTCCCGA 60.224 50.000 0.00 0.00 0.00 5.14
60 61 3.633235 CTCGACATCACTAATTCCCGAG 58.367 50.000 0.00 0.00 36.74 4.63
61 62 2.361119 TCGACATCACTAATTCCCGAGG 59.639 50.000 0.00 0.00 0.00 4.63
62 63 2.361119 CGACATCACTAATTCCCGAGGA 59.639 50.000 0.00 0.00 0.00 3.71
63 64 3.181479 CGACATCACTAATTCCCGAGGAA 60.181 47.826 7.67 7.67 46.39 3.36
64 65 4.120589 GACATCACTAATTCCCGAGGAAC 58.879 47.826 7.42 0.00 45.07 3.62
65 66 3.775316 ACATCACTAATTCCCGAGGAACT 59.225 43.478 7.42 0.35 45.07 3.01
76 77 2.683933 AGGAACTCGATGCCCCGT 60.684 61.111 0.00 0.00 0.00 5.28
77 78 2.202892 GGAACTCGATGCCCCGTC 60.203 66.667 0.00 0.00 0.00 4.79
78 79 2.582498 GAACTCGATGCCCCGTCG 60.582 66.667 0.66 0.66 43.28 5.12
79 80 4.143333 AACTCGATGCCCCGTCGG 62.143 66.667 3.60 3.60 42.34 4.79
81 82 3.833645 CTCGATGCCCCGTCGGAA 61.834 66.667 14.39 0.00 42.34 4.30
82 83 3.774959 CTCGATGCCCCGTCGGAAG 62.775 68.421 14.39 4.74 42.34 3.46
87 88 4.796495 GCCCCGTCGGAAGCCATT 62.796 66.667 14.39 0.00 0.00 3.16
88 89 2.904905 CCCCGTCGGAAGCCATTA 59.095 61.111 14.39 0.00 0.00 1.90
89 90 1.227556 CCCCGTCGGAAGCCATTAG 60.228 63.158 14.39 0.00 0.00 1.73
90 91 1.682451 CCCCGTCGGAAGCCATTAGA 61.682 60.000 14.39 0.00 0.00 2.10
91 92 0.177141 CCCGTCGGAAGCCATTAGAA 59.823 55.000 14.39 0.00 0.00 2.10
92 93 1.287425 CCGTCGGAAGCCATTAGAAC 58.713 55.000 4.91 0.00 0.00 3.01
93 94 1.134788 CCGTCGGAAGCCATTAGAACT 60.135 52.381 4.91 0.00 0.00 3.01
94 95 2.194271 CGTCGGAAGCCATTAGAACTC 58.806 52.381 0.00 0.00 0.00 3.01
95 96 2.159226 CGTCGGAAGCCATTAGAACTCT 60.159 50.000 0.00 0.00 0.00 3.24
96 97 3.190874 GTCGGAAGCCATTAGAACTCTG 58.809 50.000 0.00 0.00 0.00 3.35
97 98 2.168521 TCGGAAGCCATTAGAACTCTGG 59.831 50.000 0.00 0.00 0.00 3.86
101 102 3.386543 CCATTAGAACTCTGGCCCG 57.613 57.895 0.00 0.00 0.00 6.13
102 103 0.830648 CCATTAGAACTCTGGCCCGA 59.169 55.000 0.00 0.00 0.00 5.14
103 104 1.209504 CCATTAGAACTCTGGCCCGAA 59.790 52.381 0.00 0.00 0.00 4.30
104 105 2.555199 CATTAGAACTCTGGCCCGAAG 58.445 52.381 0.00 0.00 0.00 3.79
105 106 1.933021 TTAGAACTCTGGCCCGAAGA 58.067 50.000 0.00 0.00 0.00 2.87
106 107 1.933021 TAGAACTCTGGCCCGAAGAA 58.067 50.000 0.00 0.00 0.00 2.52
107 108 1.056660 AGAACTCTGGCCCGAAGAAA 58.943 50.000 0.00 0.00 0.00 2.52
108 109 1.420138 AGAACTCTGGCCCGAAGAAAA 59.580 47.619 0.00 0.00 0.00 2.29
109 110 1.807142 GAACTCTGGCCCGAAGAAAAG 59.193 52.381 0.00 0.00 0.00 2.27
110 111 1.056660 ACTCTGGCCCGAAGAAAAGA 58.943 50.000 0.00 0.00 0.00 2.52
111 112 1.630878 ACTCTGGCCCGAAGAAAAGAT 59.369 47.619 0.00 0.00 0.00 2.40
112 113 2.284190 CTCTGGCCCGAAGAAAAGATC 58.716 52.381 0.00 0.00 0.00 2.75
113 114 1.009829 CTGGCCCGAAGAAAAGATCG 58.990 55.000 0.00 0.00 38.74 3.69
114 115 0.611200 TGGCCCGAAGAAAAGATCGA 59.389 50.000 0.00 0.00 41.43 3.59
115 116 1.209504 TGGCCCGAAGAAAAGATCGAT 59.790 47.619 0.00 0.00 41.43 3.59
116 117 1.867865 GGCCCGAAGAAAAGATCGATC 59.132 52.381 17.91 17.91 41.43 3.69
117 118 1.523095 GCCCGAAGAAAAGATCGATCG 59.477 52.381 19.33 9.36 41.43 3.69
118 119 2.798499 GCCCGAAGAAAAGATCGATCGA 60.798 50.000 21.86 21.86 41.68 3.59
119 120 3.046390 CCCGAAGAAAAGATCGATCGAG 58.954 50.000 23.84 5.37 41.68 4.04
120 121 3.489398 CCCGAAGAAAAGATCGATCGAGT 60.489 47.826 23.84 10.44 41.68 4.18
121 122 4.106197 CCGAAGAAAAGATCGATCGAGTT 58.894 43.478 23.84 15.88 41.68 3.01
122 123 4.027295 CCGAAGAAAAGATCGATCGAGTTG 60.027 45.833 23.84 6.41 41.68 3.16
123 124 4.547210 CGAAGAAAAGATCGATCGAGTTGC 60.547 45.833 23.84 15.00 41.68 4.17
124 125 4.116747 AGAAAAGATCGATCGAGTTGCT 57.883 40.909 23.84 16.88 0.00 3.91
125 126 4.499183 AGAAAAGATCGATCGAGTTGCTT 58.501 39.130 23.84 18.70 0.00 3.91
126 127 4.328440 AGAAAAGATCGATCGAGTTGCTTG 59.672 41.667 23.84 0.00 0.00 4.01
127 128 2.215907 AGATCGATCGAGTTGCTTGG 57.784 50.000 23.84 0.00 0.00 3.61
712 713 2.613390 AAAAAGACTCGACGGTGGC 58.387 52.632 0.00 0.00 0.00 5.01
713 714 0.106149 AAAAAGACTCGACGGTGGCT 59.894 50.000 0.00 0.00 0.00 4.75
714 715 0.963962 AAAAGACTCGACGGTGGCTA 59.036 50.000 0.00 0.00 0.00 3.93
715 716 0.526662 AAAGACTCGACGGTGGCTAG 59.473 55.000 0.00 0.00 0.00 3.42
716 717 0.322277 AAGACTCGACGGTGGCTAGA 60.322 55.000 0.00 0.00 0.00 2.43
717 718 0.107116 AGACTCGACGGTGGCTAGAT 60.107 55.000 0.00 0.00 0.00 1.98
718 719 0.308376 GACTCGACGGTGGCTAGATC 59.692 60.000 0.00 0.00 0.00 2.75
719 720 1.280142 CTCGACGGTGGCTAGATCG 59.720 63.158 0.00 0.00 0.00 3.69
720 721 2.353607 CGACGGTGGCTAGATCGC 60.354 66.667 0.00 0.00 0.00 4.58
728 729 3.686045 GCTAGATCGCCCCGGGAG 61.686 72.222 26.32 16.47 0.00 4.30
729 730 2.115480 CTAGATCGCCCCGGGAGA 59.885 66.667 26.32 21.75 35.71 3.71
730 731 1.530891 CTAGATCGCCCCGGGAGAA 60.531 63.158 26.32 6.59 34.75 2.87
731 732 1.807495 CTAGATCGCCCCGGGAGAAC 61.807 65.000 26.32 19.25 34.75 3.01
732 733 2.294170 TAGATCGCCCCGGGAGAACT 62.294 60.000 26.32 24.90 38.12 3.01
733 734 1.831286 GATCGCCCCGGGAGAACTA 60.831 63.158 26.32 0.52 34.75 2.24
734 735 1.807495 GATCGCCCCGGGAGAACTAG 61.807 65.000 26.32 3.67 34.75 2.57
735 736 2.294170 ATCGCCCCGGGAGAACTAGA 62.294 60.000 26.32 10.39 34.75 2.43
736 737 2.491022 CGCCCCGGGAGAACTAGAG 61.491 68.421 26.32 1.85 0.00 2.43
737 738 1.076192 GCCCCGGGAGAACTAGAGA 60.076 63.158 26.32 0.00 0.00 3.10
738 739 0.686769 GCCCCGGGAGAACTAGAGAA 60.687 60.000 26.32 0.00 0.00 2.87
739 740 1.861982 CCCCGGGAGAACTAGAGAAA 58.138 55.000 26.32 0.00 0.00 2.52
740 741 1.481363 CCCCGGGAGAACTAGAGAAAC 59.519 57.143 26.32 0.00 0.00 2.78
741 742 1.481363 CCCGGGAGAACTAGAGAAACC 59.519 57.143 18.48 0.00 0.00 3.27
742 743 1.481363 CCGGGAGAACTAGAGAAACCC 59.519 57.143 0.00 1.88 0.00 4.11
743 744 2.458620 CGGGAGAACTAGAGAAACCCT 58.541 52.381 0.00 0.00 34.35 4.34
744 745 3.626729 CCGGGAGAACTAGAGAAACCCTA 60.627 52.174 0.00 0.00 34.35 3.53
745 746 4.021916 CGGGAGAACTAGAGAAACCCTAA 58.978 47.826 0.00 0.00 34.35 2.69
746 747 4.142204 CGGGAGAACTAGAGAAACCCTAAC 60.142 50.000 0.00 0.00 34.35 2.34
747 748 5.024785 GGGAGAACTAGAGAAACCCTAACT 58.975 45.833 0.00 0.00 33.79 2.24
748 749 6.193504 GGGAGAACTAGAGAAACCCTAACTA 58.806 44.000 0.00 0.00 33.79 2.24
749 750 6.321945 GGGAGAACTAGAGAAACCCTAACTAG 59.678 46.154 0.00 0.00 37.25 2.57
750 751 7.118060 GGAGAACTAGAGAAACCCTAACTAGA 58.882 42.308 0.00 0.00 35.80 2.43
751 752 7.283807 GGAGAACTAGAGAAACCCTAACTAGAG 59.716 44.444 0.00 0.00 35.80 2.43
752 753 7.120716 AGAACTAGAGAAACCCTAACTAGAGG 58.879 42.308 0.00 0.00 35.80 3.69
789 790 4.630644 TTCTTCTGCAGTGAGAATTCCT 57.369 40.909 22.56 0.00 31.51 3.36
800 801 2.158564 TGAGAATTCCTGCCATCATCCC 60.159 50.000 0.65 0.00 0.00 3.85
801 802 1.854939 AGAATTCCTGCCATCATCCCA 59.145 47.619 0.65 0.00 0.00 4.37
802 803 2.449730 AGAATTCCTGCCATCATCCCAT 59.550 45.455 0.65 0.00 0.00 4.00
803 804 3.116862 AGAATTCCTGCCATCATCCCATT 60.117 43.478 0.65 0.00 0.00 3.16
804 805 2.076207 TTCCTGCCATCATCCCATTG 57.924 50.000 0.00 0.00 0.00 2.82
827 828 3.677527 CAAGGTTGCTGGCTCCAG 58.322 61.111 11.47 11.47 46.15 3.86
828 829 1.073722 CAAGGTTGCTGGCTCCAGA 59.926 57.895 19.45 2.44 46.30 3.86
829 830 0.538057 CAAGGTTGCTGGCTCCAGAA 60.538 55.000 19.45 6.28 46.30 3.02
830 831 0.185901 AAGGTTGCTGGCTCCAGAAA 59.814 50.000 19.45 12.56 46.30 2.52
831 832 0.185901 AGGTTGCTGGCTCCAGAAAA 59.814 50.000 19.45 9.73 42.67 2.29
832 833 1.039856 GGTTGCTGGCTCCAGAAAAA 58.960 50.000 19.45 7.43 42.67 1.94
833 834 1.620323 GGTTGCTGGCTCCAGAAAAAT 59.380 47.619 19.45 0.00 42.67 1.82
834 835 2.037641 GGTTGCTGGCTCCAGAAAAATT 59.962 45.455 19.45 0.00 42.67 1.82
835 836 3.062042 GTTGCTGGCTCCAGAAAAATTG 58.938 45.455 19.45 0.00 42.67 2.32
868 883 2.733956 GTGTTATTTGATGGGCCCAGA 58.266 47.619 31.97 16.96 0.00 3.86
924 939 1.085091 CAGTAAGCAAGCTCAGCTGG 58.915 55.000 15.13 0.00 42.53 4.85
986 1012 1.872197 GCGAGCTCTCACCACTCACT 61.872 60.000 12.85 0.00 0.00 3.41
1027 1053 1.076412 ATCTCCGCAGCTCTCTCCA 60.076 57.895 0.00 0.00 0.00 3.86
1113 1145 0.178941 AGGTAAGACCCACACCGTCT 60.179 55.000 0.00 0.00 42.41 4.18
1121 1153 1.069765 CCACACCGTCTGCACTTCT 59.930 57.895 0.00 0.00 0.00 2.85
1157 1189 0.041238 TCCTCTGATTCCGTGGTCCT 59.959 55.000 0.00 0.00 0.00 3.85
1192 1224 2.110835 TTCAGGTGCTGCGCAGAA 59.889 55.556 40.21 29.84 40.08 3.02
1207 1239 1.160145 AGAACCTCCTTCCCCGGAA 59.840 57.895 0.73 0.00 31.44 4.30
1220 1252 2.286523 CCGGAACAGCAGGAGACCT 61.287 63.158 0.00 0.00 33.08 3.85
1230 1262 4.516195 GGAGACCTCCGCGCCTTC 62.516 72.222 0.00 0.00 40.36 3.46
1288 1320 4.680237 TCCACAAGCGCCTGGACG 62.680 66.667 11.35 1.52 31.20 4.79
1497 1549 4.823157 TGCTTTCATTATGCTTGCATTGT 58.177 34.783 13.52 0.45 0.00 2.71
1498 1550 4.865925 TGCTTTCATTATGCTTGCATTGTC 59.134 37.500 13.52 0.91 0.00 3.18
1499 1551 4.865925 GCTTTCATTATGCTTGCATTGTCA 59.134 37.500 13.52 0.00 0.00 3.58
1500 1552 5.005394 GCTTTCATTATGCTTGCATTGTCAG 59.995 40.000 13.52 8.20 0.00 3.51
1501 1553 5.648178 TTCATTATGCTTGCATTGTCAGT 57.352 34.783 13.52 0.00 0.00 3.41
1502 1554 6.756299 TTCATTATGCTTGCATTGTCAGTA 57.244 33.333 13.52 0.00 0.00 2.74
1503 1555 6.122850 TCATTATGCTTGCATTGTCAGTAC 57.877 37.500 13.52 0.00 0.00 2.73
1507 1559 3.678289 TGCTTGCATTGTCAGTACTCAT 58.322 40.909 0.00 0.00 0.00 2.90
1531 1586 9.219603 CATTATGTAGGTAGGATTGTGTATTGG 57.780 37.037 0.00 0.00 0.00 3.16
1567 1661 0.181350 GAGATCCGGTGCCCATTCTT 59.819 55.000 0.00 0.00 0.00 2.52
1574 1668 2.403259 CGGTGCCCATTCTTTTTCAAC 58.597 47.619 0.00 0.00 0.00 3.18
1581 1675 3.809279 CCCATTCTTTTTCAACTGTTGCC 59.191 43.478 15.52 0.00 0.00 4.52
1593 1687 2.162338 CTGTTGCCCATGGTTGCAGG 62.162 60.000 11.73 4.93 38.95 4.85
1645 1741 3.016736 CCCTTTTATCATTCTGCCGTGT 58.983 45.455 0.00 0.00 0.00 4.49
1646 1742 3.181497 CCCTTTTATCATTCTGCCGTGTG 60.181 47.826 0.00 0.00 0.00 3.82
1647 1743 3.429085 CTTTTATCATTCTGCCGTGTGC 58.571 45.455 0.00 0.00 41.77 4.57
1648 1744 1.378531 TTATCATTCTGCCGTGTGCC 58.621 50.000 0.00 0.00 40.16 5.01
1649 1745 0.809636 TATCATTCTGCCGTGTGCCG 60.810 55.000 0.00 0.00 40.16 5.69
1651 1747 3.049674 ATTCTGCCGTGTGCCGTG 61.050 61.111 0.00 0.00 40.16 4.94
1652 1748 3.825160 ATTCTGCCGTGTGCCGTGT 62.825 57.895 0.00 0.00 40.16 4.49
1669 1765 2.799978 CGTGTTGTGTGTGCTGAGATAA 59.200 45.455 0.00 0.00 0.00 1.75
1703 1814 9.526713 CATAATACAGTACTATGGATGCTCATC 57.473 37.037 0.00 1.35 37.11 2.92
1704 1815 7.544804 AATACAGTACTATGGATGCTCATCA 57.455 36.000 11.49 0.00 39.54 3.07
1718 1830 4.507710 TGCTCATCAGTAACATTGGTCTC 58.492 43.478 0.00 0.00 0.00 3.36
1719 1831 3.553511 GCTCATCAGTAACATTGGTCTCG 59.446 47.826 0.00 0.00 0.00 4.04
1725 1837 5.730550 TCAGTAACATTGGTCTCGCTTTAT 58.269 37.500 0.00 0.00 0.00 1.40
1792 1908 2.698274 TGTGGTGACTGCACTTTCTCTA 59.302 45.455 0.00 0.00 44.52 2.43
1897 2013 3.241804 CGACTGCGAGTGCTTATTTTCTC 60.242 47.826 0.00 0.00 43.34 2.87
1909 2025 7.833183 AGTGCTTATTTTCTCTTCATCCTGAAT 59.167 33.333 0.00 0.00 35.59 2.57
1927 2043 4.658063 TGAATACCAAATTTGTCGGGACT 58.342 39.130 16.73 0.00 0.00 3.85
1945 2061 3.873952 GGACTTCTTGCTTATACTGCCTG 59.126 47.826 0.00 0.00 0.00 4.85
2002 2118 2.289002 CAGACTGAAGGTGTGTGCTTTC 59.711 50.000 0.00 0.00 34.91 2.62
2003 2119 2.171448 AGACTGAAGGTGTGTGCTTTCT 59.829 45.455 0.00 0.00 0.00 2.52
2005 2121 4.127171 GACTGAAGGTGTGTGCTTTCTTA 58.873 43.478 0.00 0.00 0.00 2.10
2008 2124 5.163652 ACTGAAGGTGTGTGCTTTCTTAAAC 60.164 40.000 0.00 0.00 0.00 2.01
2009 2125 4.702612 TGAAGGTGTGTGCTTTCTTAAACA 59.297 37.500 0.00 0.00 0.00 2.83
2010 2126 5.359576 TGAAGGTGTGTGCTTTCTTAAACAT 59.640 36.000 0.00 0.00 0.00 2.71
2012 2128 5.831997 AGGTGTGTGCTTTCTTAAACATTC 58.168 37.500 0.00 0.00 0.00 2.67
2013 2129 5.594317 AGGTGTGTGCTTTCTTAAACATTCT 59.406 36.000 0.00 0.00 0.00 2.40
2014 2130 5.687285 GGTGTGTGCTTTCTTAAACATTCTG 59.313 40.000 0.00 0.00 0.00 3.02
2015 2131 5.173854 GTGTGTGCTTTCTTAAACATTCTGC 59.826 40.000 0.00 0.00 0.00 4.26
2016 2132 5.067674 TGTGTGCTTTCTTAAACATTCTGCT 59.932 36.000 0.00 0.00 0.00 4.24
2067 2183 2.032680 TTGGTAATCAAGTAGCCCGC 57.967 50.000 0.00 0.00 0.00 6.13
2225 2341 5.152934 ACTCAGTTAAAGGGGTGAGACTTA 58.847 41.667 5.24 0.00 39.04 2.24
2292 2408 7.431084 CAGCGAAAATACAAATTATAAGGCGTT 59.569 33.333 0.00 0.00 0.00 4.84
2335 2453 0.234625 TCATCGAACGTGCAGCAAAC 59.765 50.000 0.00 0.00 0.00 2.93
2404 2528 8.437360 AATTTCTCTTTTGGACAACCATTTTC 57.563 30.769 0.00 0.00 46.34 2.29
2493 2617 7.488471 CGTAGTTCGTTTCCTTTAAGATCATCT 59.512 37.037 0.00 0.00 34.52 2.90
2535 2660 9.264719 CTTTCTTTTTCCTTCATTTTATGCAGT 57.735 29.630 0.00 0.00 0.00 4.40
2699 2824 9.533253 CCAAAAACAAGTATGAGTTCTTTCATT 57.467 29.630 0.00 0.00 38.65 2.57
2743 2868 7.651027 TTAATAGTTACTACCACAGGACCTC 57.349 40.000 0.00 0.00 0.00 3.85
2922 3049 2.437200 AAATGGCCAACGAATGTGTG 57.563 45.000 10.96 0.00 0.00 3.82
3028 3155 2.577563 TCCATGATGTCACCCATTCAGT 59.422 45.455 0.00 0.00 32.56 3.41
3045 3172 6.392354 CATTCAGTGTTTTATGTTGAGGCAT 58.608 36.000 0.00 0.00 0.00 4.40
3068 3195 4.391830 TGATTTAAGTTCTCGGTGCACATC 59.608 41.667 20.43 8.66 0.00 3.06
3089 3216 3.691118 TCTGCATTTCTGTCAGTATTGGC 59.309 43.478 0.00 0.19 32.09 4.52
3090 3217 3.689347 TGCATTTCTGTCAGTATTGGCT 58.311 40.909 0.00 0.00 0.00 4.75
3145 3273 4.859304 TCCTCTGTTTTACTTCGCAGTA 57.141 40.909 0.00 0.00 34.06 2.74
3149 3277 4.566004 TCTGTTTTACTTCGCAGTAGCAT 58.434 39.130 0.00 0.00 42.27 3.79
3154 3282 2.602257 ACTTCGCAGTAGCATGCATA 57.398 45.000 21.98 6.62 46.87 3.14
3162 3290 4.668431 CGCAGTAGCATGCATATAGCTTTG 60.668 45.833 21.98 13.64 46.87 2.77
3169 3297 5.361857 AGCATGCATATAGCTTTGGTTTTCT 59.638 36.000 21.98 0.00 45.94 2.52
3174 3302 7.706159 TGCATATAGCTTTGGTTTTCTACATG 58.294 34.615 0.00 0.00 45.94 3.21
3191 3319 1.464608 CATGTGATGTTGTCGGTCACC 59.535 52.381 0.00 0.00 41.09 4.02
3197 3325 0.179094 TGTTGTCGGTCACCACACTC 60.179 55.000 0.00 0.00 0.00 3.51
3211 3339 3.923864 ACTCCGTCGTGGCTTGCA 61.924 61.111 0.00 0.00 37.80 4.08
3255 3384 3.561725 GCACTATGCTTCCTATGTGTTCC 59.438 47.826 0.00 0.00 40.96 3.62
3264 3393 3.104512 TCCTATGTGTTCCCGAACTGAT 58.895 45.455 8.91 3.85 41.67 2.90
3373 3503 0.183014 AGCAATCCTGAGGCATGGAG 59.817 55.000 0.00 0.00 35.63 3.86
3379 3509 1.747145 CTGAGGCATGGAGCTCGAT 59.253 57.895 7.83 6.51 44.79 3.59
3395 3525 1.817099 GATGAGCAGAAGCACCCCG 60.817 63.158 0.00 0.00 45.49 5.73
3400 3530 4.697756 CAGAAGCACCCCGCCGAA 62.698 66.667 0.00 0.00 44.04 4.30
3407 3537 3.072468 ACCCCGCCGAATCGAAGA 61.072 61.111 3.36 0.00 45.75 2.87
3450 3583 1.000938 CAAGAACCTGAAGCTTGTGGC 60.001 52.381 2.10 0.00 42.19 5.01
3463 3596 2.731217 CTTGTGGCAGTTAACAGCAAC 58.269 47.619 20.46 20.46 33.46 4.17
3464 3597 1.756430 TGTGGCAGTTAACAGCAACA 58.244 45.000 24.66 24.66 39.54 3.33
3475 3608 6.091986 CAGTTAACAGCAACACCACAAAAATT 59.908 34.615 8.61 0.00 0.00 1.82
3593 3732 2.315925 TTGTCCTCTCATCGAATGGC 57.684 50.000 0.00 0.00 0.00 4.40
3613 3752 1.148759 GCGGAAGGAGAGCATCGAAC 61.149 60.000 0.00 0.00 42.67 3.95
3633 3772 1.366366 CCGGGGGCGAATGTACTAG 59.634 63.158 0.00 0.00 0.00 2.57
3671 3925 4.791734 GCCTGTAGTTTGTGCTGTAAAACC 60.792 45.833 0.00 0.00 37.04 3.27
3690 3944 2.986728 ACCTGTAGTCCTGGAAAACCAT 59.013 45.455 0.00 0.00 36.11 3.55
3691 3945 3.397955 ACCTGTAGTCCTGGAAAACCATT 59.602 43.478 0.00 0.00 36.11 3.16
3752 4012 1.275573 GTCCTGGGGAAGTACACTGTC 59.724 57.143 0.00 0.00 31.38 3.51
3763 4023 2.047844 CACTGTCTGTGCCCTCCG 60.048 66.667 0.00 0.00 40.06 4.63
3832 4092 1.542472 TGAGCTCCACAACGTCGATAA 59.458 47.619 12.15 0.00 0.00 1.75
3855 4115 4.970662 TGAGCCATTGATACTTTCTTGC 57.029 40.909 0.00 0.00 0.00 4.01
3893 4154 3.243501 GCCTGATTTGTGCAGAAAGTCAA 60.244 43.478 14.83 0.00 35.39 3.18
3948 4210 1.157585 GAAGCAAAACCGTCTCCCTC 58.842 55.000 0.00 0.00 0.00 4.30
3987 4249 7.665145 TGGATATGTGAATTCACTTTTGTCTCA 59.335 33.333 32.57 20.73 46.55 3.27
4087 4349 9.341899 TCTTTATTTTCAGCTTAAGAAATTCGC 57.658 29.630 6.67 0.00 35.17 4.70
4088 4350 9.128107 CTTTATTTTCAGCTTAAGAAATTCGCA 57.872 29.630 6.67 0.00 35.17 5.10
4100 4362 5.565592 AGAAATTCGCAATATGCACTTCA 57.434 34.783 2.99 0.00 45.36 3.02
4109 4371 0.323302 TATGCACTTCAGGGTTGCGA 59.677 50.000 0.00 0.00 0.00 5.10
4129 4391 4.142138 GCGAAAAATGTAGAGAGAGGGAGA 60.142 45.833 0.00 0.00 0.00 3.71
4133 4395 5.725551 AAATGTAGAGAGAGGGAGAGAGA 57.274 43.478 0.00 0.00 0.00 3.10
4137 4399 3.136641 AGAGAGAGGGAGAGAGAGAGT 57.863 52.381 0.00 0.00 0.00 3.24
4160 4422 0.394352 GCACAGTTGGGGGTATCAGG 60.394 60.000 0.00 0.00 0.00 3.86
4200 4462 9.765795 ACTTTGTTTGGACAGCTATATATAGAC 57.234 33.333 21.65 13.17 37.04 2.59
4238 4500 6.833342 TTCTAAAAACGGAGAACACACTAC 57.167 37.500 0.00 0.00 0.00 2.73
4239 4501 6.152932 TCTAAAAACGGAGAACACACTACT 57.847 37.500 0.00 0.00 0.00 2.57
4240 4502 5.981315 TCTAAAAACGGAGAACACACTACTG 59.019 40.000 0.00 0.00 0.00 2.74
4241 4503 3.814005 AAACGGAGAACACACTACTGT 57.186 42.857 0.00 0.00 0.00 3.55
4242 4504 4.924305 AAACGGAGAACACACTACTGTA 57.076 40.909 0.00 0.00 0.00 2.74
4309 4571 1.007038 AAATGCACTGTGGCGCTTG 60.007 52.632 7.64 0.00 36.28 4.01
4314 4576 1.580845 GCACTGTGGCGCTTGATTCT 61.581 55.000 7.64 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.396556 GGGACTGAGAGAGGAGGACC 60.397 65.000 0.00 0.00 0.00 4.46
3 4 0.333312 TGGGACTGAGAGAGGAGGAC 59.667 60.000 0.00 0.00 0.00 3.85
4 5 0.628522 CTGGGACTGAGAGAGGAGGA 59.371 60.000 0.00 0.00 0.00 3.71
5 6 1.042559 GCTGGGACTGAGAGAGGAGG 61.043 65.000 0.00 0.00 0.00 4.30
6 7 0.033208 AGCTGGGACTGAGAGAGGAG 60.033 60.000 0.00 0.00 0.00 3.69
7 8 0.033601 GAGCTGGGACTGAGAGAGGA 60.034 60.000 0.00 0.00 0.00 3.71
8 9 1.042559 GGAGCTGGGACTGAGAGAGG 61.043 65.000 0.00 0.00 0.00 3.69
9 10 0.033208 AGGAGCTGGGACTGAGAGAG 60.033 60.000 0.00 0.00 0.00 3.20
10 11 0.411452 AAGGAGCTGGGACTGAGAGA 59.589 55.000 0.00 0.00 0.00 3.10
11 12 0.823460 GAAGGAGCTGGGACTGAGAG 59.177 60.000 0.00 0.00 0.00 3.20
12 13 0.115152 TGAAGGAGCTGGGACTGAGA 59.885 55.000 0.00 0.00 0.00 3.27
13 14 1.138661 GATGAAGGAGCTGGGACTGAG 59.861 57.143 0.00 0.00 0.00 3.35
14 15 1.198713 GATGAAGGAGCTGGGACTGA 58.801 55.000 0.00 0.00 0.00 3.41
15 16 0.907486 TGATGAAGGAGCTGGGACTG 59.093 55.000 0.00 0.00 0.00 3.51
16 17 1.767681 GATGATGAAGGAGCTGGGACT 59.232 52.381 0.00 0.00 0.00 3.85
17 18 1.767681 AGATGATGAAGGAGCTGGGAC 59.232 52.381 0.00 0.00 0.00 4.46
18 19 1.767088 CAGATGATGAAGGAGCTGGGA 59.233 52.381 0.00 0.00 0.00 4.37
19 20 1.814634 GCAGATGATGAAGGAGCTGGG 60.815 57.143 0.00 0.00 0.00 4.45
20 21 1.141254 AGCAGATGATGAAGGAGCTGG 59.859 52.381 0.00 0.00 0.00 4.85
21 22 2.485903 GAGCAGATGATGAAGGAGCTG 58.514 52.381 0.00 0.00 0.00 4.24
22 23 1.068895 CGAGCAGATGATGAAGGAGCT 59.931 52.381 0.00 0.00 0.00 4.09
23 24 1.068281 TCGAGCAGATGATGAAGGAGC 59.932 52.381 0.00 0.00 0.00 4.70
24 25 2.100418 TGTCGAGCAGATGATGAAGGAG 59.900 50.000 0.00 0.00 0.00 3.69
25 26 2.102578 TGTCGAGCAGATGATGAAGGA 58.897 47.619 0.00 0.00 0.00 3.36
26 27 2.591571 TGTCGAGCAGATGATGAAGG 57.408 50.000 0.00 0.00 0.00 3.46
27 28 3.490155 GTGATGTCGAGCAGATGATGAAG 59.510 47.826 0.00 0.00 0.00 3.02
28 29 3.131755 AGTGATGTCGAGCAGATGATGAA 59.868 43.478 0.00 0.00 0.00 2.57
29 30 2.692041 AGTGATGTCGAGCAGATGATGA 59.308 45.455 0.00 0.00 0.00 2.92
30 31 3.095102 AGTGATGTCGAGCAGATGATG 57.905 47.619 0.00 0.00 0.00 3.07
31 32 4.926140 TTAGTGATGTCGAGCAGATGAT 57.074 40.909 0.00 0.00 0.00 2.45
32 33 4.926140 ATTAGTGATGTCGAGCAGATGA 57.074 40.909 0.00 0.00 0.00 2.92
33 34 4.447054 GGAATTAGTGATGTCGAGCAGATG 59.553 45.833 0.00 0.00 0.00 2.90
34 35 4.502259 GGGAATTAGTGATGTCGAGCAGAT 60.502 45.833 0.00 0.00 0.00 2.90
35 36 3.181475 GGGAATTAGTGATGTCGAGCAGA 60.181 47.826 0.00 0.00 0.00 4.26
36 37 3.126831 GGGAATTAGTGATGTCGAGCAG 58.873 50.000 0.00 0.00 0.00 4.24
37 38 2.481276 CGGGAATTAGTGATGTCGAGCA 60.481 50.000 0.00 0.00 0.00 4.26
38 39 2.128035 CGGGAATTAGTGATGTCGAGC 58.872 52.381 0.00 0.00 0.00 5.03
39 40 3.551046 CCTCGGGAATTAGTGATGTCGAG 60.551 52.174 0.00 0.00 41.41 4.04
40 41 2.361119 CCTCGGGAATTAGTGATGTCGA 59.639 50.000 0.00 0.00 0.00 4.20
41 42 2.361119 TCCTCGGGAATTAGTGATGTCG 59.639 50.000 0.00 0.00 0.00 4.35
42 43 4.120589 GTTCCTCGGGAATTAGTGATGTC 58.879 47.826 8.36 0.00 44.04 3.06
43 44 3.775316 AGTTCCTCGGGAATTAGTGATGT 59.225 43.478 8.36 0.00 44.04 3.06
44 45 4.372656 GAGTTCCTCGGGAATTAGTGATG 58.627 47.826 8.36 0.00 44.04 3.07
45 46 4.674281 GAGTTCCTCGGGAATTAGTGAT 57.326 45.455 8.36 0.00 44.04 3.06
58 59 2.107141 CGGGGCATCGAGTTCCTC 59.893 66.667 0.00 0.00 0.00 3.71
59 60 2.683933 ACGGGGCATCGAGTTCCT 60.684 61.111 6.49 0.00 0.00 3.36
60 61 2.202892 GACGGGGCATCGAGTTCC 60.203 66.667 6.49 0.00 0.00 3.62
61 62 2.582498 CGACGGGGCATCGAGTTC 60.582 66.667 6.49 0.00 42.25 3.01
62 63 4.143333 CCGACGGGGCATCGAGTT 62.143 66.667 5.81 0.00 42.25 3.01
64 65 3.774959 CTTCCGACGGGGCATCGAG 62.775 68.421 15.25 0.00 42.25 4.04
65 66 3.833645 CTTCCGACGGGGCATCGA 61.834 66.667 15.25 0.00 42.25 3.59
70 71 3.394635 TAATGGCTTCCGACGGGGC 62.395 63.158 15.25 17.82 34.94 5.80
71 72 1.227556 CTAATGGCTTCCGACGGGG 60.228 63.158 15.25 8.68 37.02 5.73
72 73 0.177141 TTCTAATGGCTTCCGACGGG 59.823 55.000 15.25 0.00 0.00 5.28
73 74 1.134788 AGTTCTAATGGCTTCCGACGG 60.135 52.381 7.84 7.84 0.00 4.79
74 75 2.159226 AGAGTTCTAATGGCTTCCGACG 60.159 50.000 0.00 0.00 0.00 5.12
75 76 3.190874 CAGAGTTCTAATGGCTTCCGAC 58.809 50.000 0.00 0.00 0.00 4.79
76 77 2.168521 CCAGAGTTCTAATGGCTTCCGA 59.831 50.000 0.00 0.00 0.00 4.55
77 78 2.555199 CCAGAGTTCTAATGGCTTCCG 58.445 52.381 0.00 0.00 0.00 4.30
83 84 0.830648 TCGGGCCAGAGTTCTAATGG 59.169 55.000 4.39 0.00 37.15 3.16
84 85 2.168521 TCTTCGGGCCAGAGTTCTAATG 59.831 50.000 4.39 0.00 0.00 1.90
85 86 2.467880 TCTTCGGGCCAGAGTTCTAAT 58.532 47.619 4.39 0.00 0.00 1.73
86 87 1.933021 TCTTCGGGCCAGAGTTCTAA 58.067 50.000 4.39 0.00 0.00 2.10
87 88 1.933021 TTCTTCGGGCCAGAGTTCTA 58.067 50.000 4.39 0.00 0.00 2.10
88 89 1.056660 TTTCTTCGGGCCAGAGTTCT 58.943 50.000 4.39 0.00 0.00 3.01
89 90 1.807142 CTTTTCTTCGGGCCAGAGTTC 59.193 52.381 4.39 0.00 0.00 3.01
90 91 1.420138 TCTTTTCTTCGGGCCAGAGTT 59.580 47.619 4.39 0.00 0.00 3.01
91 92 1.056660 TCTTTTCTTCGGGCCAGAGT 58.943 50.000 4.39 0.00 0.00 3.24
92 93 2.284190 GATCTTTTCTTCGGGCCAGAG 58.716 52.381 4.39 0.00 0.00 3.35
93 94 1.405526 CGATCTTTTCTTCGGGCCAGA 60.406 52.381 4.39 1.93 0.00 3.86
94 95 1.009829 CGATCTTTTCTTCGGGCCAG 58.990 55.000 4.39 0.00 0.00 4.85
95 96 0.611200 TCGATCTTTTCTTCGGGCCA 59.389 50.000 4.39 0.00 36.08 5.36
96 97 1.867865 GATCGATCTTTTCTTCGGGCC 59.132 52.381 18.29 0.00 36.08 5.80
97 98 1.523095 CGATCGATCTTTTCTTCGGGC 59.477 52.381 22.43 0.00 36.08 6.13
98 99 3.046390 CTCGATCGATCTTTTCTTCGGG 58.954 50.000 19.78 5.05 36.08 5.14
99 100 3.696898 ACTCGATCGATCTTTTCTTCGG 58.303 45.455 19.78 4.64 36.08 4.30
100 101 4.547210 GCAACTCGATCGATCTTTTCTTCG 60.547 45.833 19.78 9.03 36.72 3.79
101 102 4.564769 AGCAACTCGATCGATCTTTTCTTC 59.435 41.667 19.78 6.96 0.00 2.87
102 103 4.499183 AGCAACTCGATCGATCTTTTCTT 58.501 39.130 19.78 4.67 0.00 2.52
103 104 4.116747 AGCAACTCGATCGATCTTTTCT 57.883 40.909 19.78 9.13 0.00 2.52
104 105 4.493220 CCAAGCAACTCGATCGATCTTTTC 60.493 45.833 19.78 6.99 0.00 2.29
105 106 3.372206 CCAAGCAACTCGATCGATCTTTT 59.628 43.478 19.78 9.99 0.00 2.27
106 107 2.932614 CCAAGCAACTCGATCGATCTTT 59.067 45.455 19.78 9.46 0.00 2.52
107 108 2.544685 CCAAGCAACTCGATCGATCTT 58.455 47.619 19.78 15.48 0.00 2.40
108 109 2.215907 CCAAGCAACTCGATCGATCT 57.784 50.000 19.78 10.49 0.00 2.75
694 695 0.106149 AGCCACCGTCGAGTCTTTTT 59.894 50.000 0.00 0.00 0.00 1.94
695 696 0.963962 TAGCCACCGTCGAGTCTTTT 59.036 50.000 0.00 0.00 0.00 2.27
696 697 0.526662 CTAGCCACCGTCGAGTCTTT 59.473 55.000 0.00 0.00 0.00 2.52
697 698 0.322277 TCTAGCCACCGTCGAGTCTT 60.322 55.000 0.00 0.00 0.00 3.01
698 699 0.107116 ATCTAGCCACCGTCGAGTCT 60.107 55.000 0.00 0.00 0.00 3.24
699 700 0.308376 GATCTAGCCACCGTCGAGTC 59.692 60.000 0.00 0.00 0.00 3.36
700 701 1.437772 CGATCTAGCCACCGTCGAGT 61.438 60.000 0.00 0.00 34.46 4.18
701 702 1.280142 CGATCTAGCCACCGTCGAG 59.720 63.158 0.00 0.00 34.46 4.04
702 703 2.831366 GCGATCTAGCCACCGTCGA 61.831 63.158 0.00 0.00 34.46 4.20
703 704 2.353607 GCGATCTAGCCACCGTCG 60.354 66.667 0.00 0.00 35.56 5.12
711 712 3.686045 CTCCCGGGGCGATCTAGC 61.686 72.222 23.50 0.00 0.00 3.42
712 713 1.530891 TTCTCCCGGGGCGATCTAG 60.531 63.158 23.50 8.94 0.00 2.43
713 714 1.831286 GTTCTCCCGGGGCGATCTA 60.831 63.158 23.50 0.00 0.00 1.98
714 715 2.294170 TAGTTCTCCCGGGGCGATCT 62.294 60.000 23.50 21.65 0.00 2.75
715 716 1.807495 CTAGTTCTCCCGGGGCGATC 61.807 65.000 23.50 16.00 0.00 3.69
716 717 1.833049 CTAGTTCTCCCGGGGCGAT 60.833 63.158 23.50 5.99 0.00 4.58
717 718 2.441532 CTAGTTCTCCCGGGGCGA 60.442 66.667 23.50 15.25 0.00 5.54
718 719 2.441532 TCTAGTTCTCCCGGGGCG 60.442 66.667 23.50 12.84 0.00 6.13
719 720 0.686769 TTCTCTAGTTCTCCCGGGGC 60.687 60.000 23.50 8.94 0.00 5.80
720 721 1.481363 GTTTCTCTAGTTCTCCCGGGG 59.519 57.143 23.50 12.05 0.00 5.73
721 722 1.481363 GGTTTCTCTAGTTCTCCCGGG 59.519 57.143 16.85 16.85 0.00 5.73
722 723 1.481363 GGGTTTCTCTAGTTCTCCCGG 59.519 57.143 0.00 0.00 0.00 5.73
723 724 2.458620 AGGGTTTCTCTAGTTCTCCCG 58.541 52.381 0.00 0.00 38.52 5.14
724 725 5.024785 AGTTAGGGTTTCTCTAGTTCTCCC 58.975 45.833 0.00 0.00 0.00 4.30
725 726 7.118060 TCTAGTTAGGGTTTCTCTAGTTCTCC 58.882 42.308 0.00 0.00 32.57 3.71
726 727 7.283807 CCTCTAGTTAGGGTTTCTCTAGTTCTC 59.716 44.444 0.00 0.00 32.55 2.87
727 728 7.120716 CCTCTAGTTAGGGTTTCTCTAGTTCT 58.879 42.308 0.00 0.00 32.55 3.01
728 729 7.337480 CCTCTAGTTAGGGTTTCTCTAGTTC 57.663 44.000 0.00 0.00 32.55 3.01
741 742 3.309296 TGAGCCATTCCCTCTAGTTAGG 58.691 50.000 0.00 0.00 36.30 2.69
742 743 3.964031 ACTGAGCCATTCCCTCTAGTTAG 59.036 47.826 0.00 0.00 0.00 2.34
743 744 3.995636 ACTGAGCCATTCCCTCTAGTTA 58.004 45.455 0.00 0.00 0.00 2.24
744 745 2.839228 ACTGAGCCATTCCCTCTAGTT 58.161 47.619 0.00 0.00 0.00 2.24
745 746 2.559381 ACTGAGCCATTCCCTCTAGT 57.441 50.000 0.00 0.00 0.00 2.57
746 747 5.559148 AAATACTGAGCCATTCCCTCTAG 57.441 43.478 0.00 0.00 0.00 2.43
747 748 5.667626 AGAAAATACTGAGCCATTCCCTCTA 59.332 40.000 0.00 0.00 0.00 2.43
748 749 4.476479 AGAAAATACTGAGCCATTCCCTCT 59.524 41.667 0.00 0.00 0.00 3.69
749 750 4.786425 AGAAAATACTGAGCCATTCCCTC 58.214 43.478 0.00 0.00 0.00 4.30
750 751 4.870021 AGAAAATACTGAGCCATTCCCT 57.130 40.909 0.00 0.00 0.00 4.20
751 752 5.067023 CAGAAGAAAATACTGAGCCATTCCC 59.933 44.000 0.00 0.00 34.07 3.97
752 753 5.449725 GCAGAAGAAAATACTGAGCCATTCC 60.450 44.000 0.00 0.00 34.07 3.01
753 754 5.124457 TGCAGAAGAAAATACTGAGCCATTC 59.876 40.000 0.00 0.00 34.07 2.67
754 755 5.012239 TGCAGAAGAAAATACTGAGCCATT 58.988 37.500 0.00 0.00 34.07 3.16
755 756 4.592942 TGCAGAAGAAAATACTGAGCCAT 58.407 39.130 0.00 0.00 34.07 4.40
756 757 4.005650 CTGCAGAAGAAAATACTGAGCCA 58.994 43.478 8.42 0.00 34.07 4.75
757 758 4.006319 ACTGCAGAAGAAAATACTGAGCC 58.994 43.478 23.35 0.00 34.07 4.70
758 759 4.692625 TCACTGCAGAAGAAAATACTGAGC 59.307 41.667 23.35 0.00 34.07 4.26
759 760 6.162079 TCTCACTGCAGAAGAAAATACTGAG 58.838 40.000 23.35 17.68 34.07 3.35
789 790 2.521126 CTATGCAATGGGATGATGGCA 58.479 47.619 0.00 0.00 35.54 4.92
843 858 3.243401 GGGCCCATCAAATAACACGATTC 60.243 47.826 19.95 0.00 0.00 2.52
846 861 1.004862 TGGGCCCATCAAATAACACGA 59.995 47.619 24.45 0.00 0.00 4.35
1027 1053 4.565850 GGGCGGGAGGAGGGAGAT 62.566 72.222 0.00 0.00 0.00 2.75
1189 1221 1.160145 TTCCGGGGAAGGAGGTTCT 59.840 57.895 0.00 0.00 41.98 3.01
1192 1224 1.918800 CTGTTCCGGGGAAGGAGGT 60.919 63.158 0.00 0.00 41.98 3.85
1247 1279 4.760047 CCACAGGGACGAAGGCGG 62.760 72.222 0.00 0.00 43.17 6.13
1497 1549 9.078990 CAATCCTACCTACATAATGAGTACTGA 57.921 37.037 0.00 0.00 0.00 3.41
1498 1550 8.861086 ACAATCCTACCTACATAATGAGTACTG 58.139 37.037 0.00 0.00 0.00 2.74
1499 1551 8.861086 CACAATCCTACCTACATAATGAGTACT 58.139 37.037 0.00 0.00 0.00 2.73
1500 1552 8.639761 ACACAATCCTACCTACATAATGAGTAC 58.360 37.037 0.00 0.00 0.00 2.73
1501 1553 8.777578 ACACAATCCTACCTACATAATGAGTA 57.222 34.615 0.00 0.00 0.00 2.59
1502 1554 7.676683 ACACAATCCTACCTACATAATGAGT 57.323 36.000 0.00 0.00 0.00 3.41
1507 1559 8.326765 ACCAATACACAATCCTACCTACATAA 57.673 34.615 0.00 0.00 0.00 1.90
1531 1586 4.745620 GGATCTCGAATGTGGCTAAGTTAC 59.254 45.833 0.00 0.00 0.00 2.50
1567 1661 2.114616 ACCATGGGCAACAGTTGAAAA 58.885 42.857 17.99 1.17 39.74 2.29
1574 1668 1.290955 CTGCAACCATGGGCAACAG 59.709 57.895 18.09 13.63 39.93 3.16
1581 1675 1.619654 TTCTGAACCTGCAACCATGG 58.380 50.000 11.19 11.19 0.00 3.66
1622 1718 3.065371 CACGGCAGAATGATAAAAGGGAC 59.935 47.826 0.00 0.00 39.69 4.46
1645 1741 2.437537 AGCACACACAACACGGCA 60.438 55.556 0.00 0.00 0.00 5.69
1646 1742 2.024588 CAGCACACACAACACGGC 59.975 61.111 0.00 0.00 0.00 5.68
1647 1743 0.809636 TCTCAGCACACACAACACGG 60.810 55.000 0.00 0.00 0.00 4.94
1648 1744 1.220529 ATCTCAGCACACACAACACG 58.779 50.000 0.00 0.00 0.00 4.49
1649 1745 4.273480 AGTTTATCTCAGCACACACAACAC 59.727 41.667 0.00 0.00 0.00 3.32
1651 1747 5.424121 AAGTTTATCTCAGCACACACAAC 57.576 39.130 0.00 0.00 0.00 3.32
1652 1748 5.588246 TGAAAGTTTATCTCAGCACACACAA 59.412 36.000 0.00 0.00 0.00 3.33
1688 1799 5.876651 TGTTACTGATGAGCATCCATAGT 57.123 39.130 7.92 7.40 37.02 2.12
1703 1814 6.422776 AATAAAGCGAGACCAATGTTACTG 57.577 37.500 0.00 0.00 0.00 2.74
1704 1815 6.879458 AGAAATAAAGCGAGACCAATGTTACT 59.121 34.615 0.00 0.00 0.00 2.24
1718 1830 4.065789 GGGATCCCTACAGAAATAAAGCG 58.934 47.826 24.69 0.00 0.00 4.68
1719 1831 5.311844 AGGGATCCCTACAGAAATAAAGC 57.688 43.478 33.08 0.00 46.14 3.51
1792 1908 3.840124 AACTCCTCTCCGTTTTCTTGT 57.160 42.857 0.00 0.00 0.00 3.16
1909 2025 4.360951 AGAAGTCCCGACAAATTTGGTA 57.639 40.909 21.74 0.22 0.00 3.25
1927 2043 3.056107 ACGACAGGCAGTATAAGCAAGAA 60.056 43.478 0.00 0.00 0.00 2.52
1945 2061 4.268884 GTGAAGGAGATAAATGCTGACGAC 59.731 45.833 0.00 0.00 0.00 4.34
2002 2118 4.153986 CACGCTGAAGCAGAATGTTTAAG 58.846 43.478 2.79 0.00 40.56 1.85
2003 2119 3.563808 ACACGCTGAAGCAGAATGTTTAA 59.436 39.130 2.79 0.00 40.56 1.52
2005 2121 1.949525 ACACGCTGAAGCAGAATGTTT 59.050 42.857 2.79 0.00 44.25 2.83
2008 2124 1.135859 GGAACACGCTGAAGCAGAATG 60.136 52.381 2.79 0.00 42.21 2.67
2009 2125 1.160137 GGAACACGCTGAAGCAGAAT 58.840 50.000 2.79 0.00 42.21 2.40
2010 2126 0.106708 AGGAACACGCTGAAGCAGAA 59.893 50.000 2.79 0.00 42.21 3.02
2012 2128 0.320247 AGAGGAACACGCTGAAGCAG 60.320 55.000 2.79 0.00 42.21 4.24
2013 2129 0.106708 AAGAGGAACACGCTGAAGCA 59.893 50.000 2.79 0.00 42.21 3.91
2014 2130 0.793250 GAAGAGGAACACGCTGAAGC 59.207 55.000 0.00 0.00 37.78 3.86
2015 2131 2.447244 AGAAGAGGAACACGCTGAAG 57.553 50.000 0.00 0.00 0.00 3.02
2016 2132 2.102420 TGAAGAAGAGGAACACGCTGAA 59.898 45.455 0.00 0.00 0.00 3.02
2067 2183 1.202879 TGGAGCACAAGGTTAGTTGGG 60.203 52.381 0.00 0.00 33.63 4.12
2097 2213 1.818959 GCCAAGCCAATGTCCTGCAA 61.819 55.000 0.00 0.00 0.00 4.08
2225 2341 6.932400 TCAACGTTAATTACCAATGTGAGAGT 59.068 34.615 0.00 0.00 0.00 3.24
2239 2355 6.042143 GCAATCCCATCATTCAACGTTAATT 58.958 36.000 0.00 0.00 0.00 1.40
2335 2453 9.193133 CATACAACCATAATAGAGAGTTAACGG 57.807 37.037 0.00 0.00 0.00 4.44
2535 2660 7.172868 TGGTTCTAATACGAAATCACCTGTA 57.827 36.000 0.00 0.00 0.00 2.74
2699 2824 9.912634 CTATTAAAAGCTGTTGATTCAAGGAAA 57.087 29.630 0.00 0.00 0.00 3.13
2743 2868 3.311871 GGAGATCTAGCACAGCAACAATG 59.688 47.826 0.00 0.00 0.00 2.82
2922 3049 2.069165 AACCTTCCAGACCAGTGGCC 62.069 60.000 9.78 0.00 37.53 5.36
3028 3155 8.584157 ACTTAAATCATGCCTCAACATAAAACA 58.416 29.630 0.00 0.00 0.00 2.83
3045 3172 3.734463 TGTGCACCGAGAACTTAAATCA 58.266 40.909 15.69 0.00 0.00 2.57
3068 3195 3.693085 AGCCAATACTGACAGAAATGCAG 59.307 43.478 10.08 0.00 35.81 4.41
3079 3206 4.223700 AGATTCAGTGTGAGCCAATACTGA 59.776 41.667 10.58 10.58 45.45 3.41
3089 3216 2.096220 AGCTGCAGATTCAGTGTGAG 57.904 50.000 20.43 0.00 36.49 3.51
3090 3217 2.556144 AAGCTGCAGATTCAGTGTGA 57.444 45.000 20.43 0.00 36.49 3.58
3145 3273 5.361857 AGAAAACCAAAGCTATATGCATGCT 59.638 36.000 20.33 6.84 45.94 3.79
3149 3277 7.339212 ACATGTAGAAAACCAAAGCTATATGCA 59.661 33.333 0.00 0.00 45.94 3.96
3154 3282 7.394359 ACATCACATGTAGAAAACCAAAGCTAT 59.606 33.333 0.00 0.00 42.78 2.97
3162 3290 5.382303 CGACAACATCACATGTAGAAAACC 58.618 41.667 0.00 0.00 44.07 3.27
3169 3297 3.322369 GTGACCGACAACATCACATGTA 58.678 45.455 0.00 0.00 44.07 2.29
3174 3302 3.299050 TGGTGACCGACAACATCAC 57.701 52.632 0.00 0.00 41.68 3.06
3211 3339 4.820716 GCTTTCATCATCTAGGAAGCATGT 59.179 41.667 0.00 0.00 0.00 3.21
3255 3384 3.641906 AGGGAGGTACATAATCAGTTCGG 59.358 47.826 0.00 0.00 0.00 4.30
3264 3393 4.030913 CTGAGTGGAAGGGAGGTACATAA 58.969 47.826 0.00 0.00 0.00 1.90
3379 3509 4.704833 GCGGGGTGCTTCTGCTCA 62.705 66.667 0.00 0.00 41.73 4.26
3395 3525 1.359848 TTTCTGCTCTTCGATTCGGC 58.640 50.000 6.18 2.18 0.00 5.54
3400 3530 3.608316 AGCTCTTTTCTGCTCTTCGAT 57.392 42.857 0.00 0.00 33.90 3.59
3407 3537 3.701040 CCTCTAGAGAGCTCTTTTCTGCT 59.299 47.826 21.76 11.52 40.93 4.24
3450 3583 3.773860 TTGTGGTGTTGCTGTTAACTG 57.226 42.857 7.22 7.67 0.00 3.16
3463 3596 5.212532 TCTGGGATGAAATTTTTGTGGTG 57.787 39.130 0.00 0.00 0.00 4.17
3464 3597 5.543405 TCATCTGGGATGAAATTTTTGTGGT 59.457 36.000 7.64 0.00 0.00 4.16
3475 3608 1.288188 TGCACCTCATCTGGGATGAA 58.712 50.000 10.75 0.00 0.00 2.57
3567 3706 4.920640 TCGATGAGAGGACAAATAGGTC 57.079 45.455 0.00 0.00 37.06 3.85
3593 3732 2.613739 TTCGATGCTCTCCTTCCGCG 62.614 60.000 0.00 0.00 0.00 6.46
3622 3761 7.318141 TCTACAAAAAGGTCCTAGTACATTCG 58.682 38.462 0.00 0.00 0.00 3.34
3633 3772 3.141767 ACAGGCTCTACAAAAAGGTCC 57.858 47.619 0.00 0.00 0.00 4.46
3690 3944 8.213812 GCAAAGTATTACGTACTACGAAAACAA 58.786 33.333 15.49 2.19 46.05 2.83
3691 3945 7.380870 TGCAAAGTATTACGTACTACGAAAACA 59.619 33.333 15.49 9.73 46.05 2.83
3703 3959 4.382291 TGTCCAAGTGCAAAGTATTACGT 58.618 39.130 0.00 0.00 0.00 3.57
3804 4064 2.783135 GTTGTGGAGCTCAGGAATTCA 58.217 47.619 17.19 0.00 0.00 2.57
3832 4092 5.655532 AGCAAGAAAGTATCAATGGCTCAAT 59.344 36.000 0.00 0.00 0.00 2.57
3855 4115 7.869429 ACAAATCAGGCAGAAATTCAGTTTTAG 59.131 33.333 0.00 0.00 0.00 1.85
3893 4154 8.250143 AGAATTAGACCATTTCCTTGTGTTTT 57.750 30.769 0.00 0.00 0.00 2.43
3969 4231 7.403312 TTTTCCTGAGACAAAAGTGAATTCA 57.597 32.000 3.38 3.38 0.00 2.57
4012 4274 4.005650 CCAGAAACATGAGTATGCACACT 58.994 43.478 0.00 0.00 37.85 3.55
4070 4332 6.201517 GCATATTGCGAATTTCTTAAGCTGA 58.798 36.000 0.00 0.00 31.71 4.26
4071 4333 6.430048 GCATATTGCGAATTTCTTAAGCTG 57.570 37.500 0.00 0.00 31.71 4.24
4087 4349 2.478370 CGCAACCCTGAAGTGCATATTG 60.478 50.000 0.00 0.00 0.00 1.90
4088 4350 1.745087 CGCAACCCTGAAGTGCATATT 59.255 47.619 0.00 0.00 0.00 1.28
4100 4362 4.003648 CTCTCTACATTTTTCGCAACCCT 58.996 43.478 0.00 0.00 0.00 4.34
4109 4371 6.498538 TCTCTCTCCCTCTCTCTACATTTTT 58.501 40.000 0.00 0.00 0.00 1.94
4129 4391 2.499289 CCAACTGTGCCATACTCTCTCT 59.501 50.000 0.00 0.00 0.00 3.10
4133 4395 0.620556 CCCCAACTGTGCCATACTCT 59.379 55.000 0.00 0.00 0.00 3.24
4137 4399 1.493022 GATACCCCCAACTGTGCCATA 59.507 52.381 0.00 0.00 0.00 2.74
4188 4450 7.094975 CCAGAGTGGCTATCGTCTATATATAGC 60.095 44.444 14.03 8.88 44.74 2.97
4200 4462 4.386867 TTTAGAACCAGAGTGGCTATCG 57.613 45.455 0.00 0.00 42.67 2.92
4261 4523 5.115480 TGCTTTTCACAATCCTTCAAAACC 58.885 37.500 0.00 0.00 0.00 3.27
4309 4571 9.481340 AAGAAAAATAAAGGTTTCTGCAGAATC 57.519 29.630 28.89 25.97 41.98 2.52
4314 4576 6.581712 AGCAAGAAAAATAAAGGTTTCTGCA 58.418 32.000 15.89 0.00 41.98 4.41


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

AutoCloner maintained by Alex Coulton.