Multiple sequence alignment - TraesCS6A01G372400

Loading Multiple Alignment...

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 TraesCS6A01G372400 chr6A 100.000 3677 0 0 850 4526 596169083 596172759 0.000000e+00 6791
1 TraesCS6A01G372400 chr6A 100.000 622 0 0 1 622 596168234 596168855 0.000000e+00 1149
2 TraesCS6A01G372400 chr6A 92.113 355 19 5 3749 4102 613834827 613835173 4.070000e-135 492
3 TraesCS6A01G372400 chr6D 97.538 3696 70 4 851 4526 450648353 450652047 0.000000e+00 6301
4 TraesCS6A01G372400 chr6D 89.277 401 28 8 225 619 450647945 450648336 5.260000e-134 488
5 TraesCS6A01G372400 chr6D 93.769 321 18 1 3727 4045 467774027 467774347 8.810000e-132 481
6 TraesCS6A01G372400 chr6B 96.038 3660 112 9 852 4491 684410690 684414336 0.000000e+00 5925
7 TraesCS6A01G372400 chr6B 88.651 467 33 6 3727 4183 712994727 712995183 6.620000e-153 551
8 TraesCS6A01G372400 chr7D 92.438 2764 204 2 852 3615 98660570 98663328 0.000000e+00 3941
9 TraesCS6A01G372400 chr7D 95.122 82 3 1 3614 3694 98663368 98663449 1.320000e-25 128
10 TraesCS6A01G372400 chr7A 92.155 2766 200 9 852 3615 101219111 101221861 0.000000e+00 3890
11 TraesCS6A01G372400 chr7A 95.122 82 3 1 3614 3694 101221901 101221982 1.320000e-25 128
12 TraesCS6A01G372400 chr7B 92.979 2407 167 1 1209 3615 54311087 54313491 0.000000e+00 3507
13 TraesCS6A01G372400 chr7B 87.055 309 32 5 911 1218 54310828 54311129 4.340000e-90 342
14 TraesCS6A01G372400 chr7B 95.122 82 3 1 3614 3694 54313531 54313612 1.320000e-25 128
15 TraesCS6A01G372400 chrUn 93.985 399 24 0 2130 2528 478902044 478901646 5.010000e-169 604


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 TraesCS6A01G372400 chr6A 596168234 596172759 4525 False 3970.000000 6791 100.000000 1 4526 2 chr6A.!!$F2 4525
1 TraesCS6A01G372400 chr6D 450647945 450652047 4102 False 3394.500000 6301 93.407500 225 4526 2 chr6D.!!$F2 4301
2 TraesCS6A01G372400 chr6B 684410690 684414336 3646 False 5925.000000 5925 96.038000 852 4491 1 chr6B.!!$F1 3639
3 TraesCS6A01G372400 chr7D 98660570 98663449 2879 False 2034.500000 3941 93.780000 852 3694 2 chr7D.!!$F1 2842
4 TraesCS6A01G372400 chr7A 101219111 101221982 2871 False 2009.000000 3890 93.638500 852 3694 2 chr7A.!!$F1 2842
5 TraesCS6A01G372400 chr7B 54310828 54313612 2784 False 1325.666667 3507 91.718667 911 3694 3 chr7B.!!$F1 2783

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
397 398 0.035739 GCCCGGGACAAGTTCTTGTA 59.964 55.0 29.31 0.00 34.90 2.41 F
550 556 0.371301 GCCGTTCCGTTCCGTTAATC 59.629 55.0 0.00 0.00 0.00 1.75 F
1758 1765 0.179134 ATGCTCACGCGTTAGTCCTC 60.179 55.0 20.60 5.68 39.65 3.71 F
2374 2381 0.605589 GGGTCTGACACCTGACAGAG 59.394 60.0 10.38 0.00 44.70 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1589 2.749621 CAAACAGCCCTATTGTGTCCTC 59.250 50.000 0.00 0.00 0.00 3.71 R
1967 1974 3.144657 TGCATAGCCCATCCATTACTG 57.855 47.619 0.00 0.00 0.00 2.74 R
3376 3383 4.094590 GCAATATCCACATATCAGAGCTGC 59.905 45.833 0.00 0.00 0.00 5.25 R
3890 3939 2.358737 GACCAGTGCCTTGGGACG 60.359 66.667 5.68 1.72 42.76 4.79 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 3.681705 CGCTTGTTGATCGCATGTT 57.318 47.368 0.00 0.00 0.00 2.71
19 20 1.253116 CGCTTGTTGATCGCATGTTG 58.747 50.000 0.00 0.00 0.00 3.33
20 21 1.136000 CGCTTGTTGATCGCATGTTGA 60.136 47.619 0.00 0.00 0.00 3.18
21 22 2.245096 GCTTGTTGATCGCATGTTGAC 58.755 47.619 0.00 0.00 0.00 3.18
22 23 2.498905 CTTGTTGATCGCATGTTGACG 58.501 47.619 0.00 0.00 0.00 4.35
23 24 1.507562 TGTTGATCGCATGTTGACGT 58.492 45.000 0.00 0.00 0.00 4.34
24 25 1.194322 TGTTGATCGCATGTTGACGTG 59.806 47.619 0.00 0.00 36.01 4.49
25 26 1.459209 GTTGATCGCATGTTGACGTGA 59.541 47.619 7.50 0.00 34.90 4.35
26 27 1.789506 TGATCGCATGTTGACGTGAA 58.210 45.000 7.50 0.00 34.90 3.18
27 28 2.139118 TGATCGCATGTTGACGTGAAA 58.861 42.857 7.50 0.00 34.90 2.69
28 29 2.545946 TGATCGCATGTTGACGTGAAAA 59.454 40.909 7.50 0.00 34.90 2.29
29 30 2.376915 TCGCATGTTGACGTGAAAAC 57.623 45.000 7.50 0.00 34.90 2.43
30 31 1.003331 TCGCATGTTGACGTGAAAACC 60.003 47.619 7.50 0.00 34.90 3.27
31 32 1.394697 GCATGTTGACGTGAAAACCG 58.605 50.000 7.50 0.00 34.90 4.44
32 33 1.394697 CATGTTGACGTGAAAACCGC 58.605 50.000 0.00 0.00 34.90 5.68
33 34 1.002900 CATGTTGACGTGAAAACCGCT 60.003 47.619 0.00 0.00 34.90 5.52
34 35 0.653636 TGTTGACGTGAAAACCGCTC 59.346 50.000 0.00 0.00 0.00 5.03
35 36 0.382636 GTTGACGTGAAAACCGCTCG 60.383 55.000 0.00 0.00 0.00 5.03
36 37 2.096481 TTGACGTGAAAACCGCTCGC 62.096 55.000 0.00 0.00 0.00 5.03
37 38 3.291167 GACGTGAAAACCGCTCGCC 62.291 63.158 0.00 0.00 0.00 5.54
38 39 4.084888 CGTGAAAACCGCTCGCCC 62.085 66.667 0.00 0.00 0.00 6.13
39 40 3.733960 GTGAAAACCGCTCGCCCC 61.734 66.667 0.00 0.00 0.00 5.80
40 41 4.257654 TGAAAACCGCTCGCCCCA 62.258 61.111 0.00 0.00 0.00 4.96
41 42 2.981350 GAAAACCGCTCGCCCCAA 60.981 61.111 0.00 0.00 0.00 4.12
42 43 2.519780 AAAACCGCTCGCCCCAAA 60.520 55.556 0.00 0.00 0.00 3.28
43 44 2.742710 GAAAACCGCTCGCCCCAAAC 62.743 60.000 0.00 0.00 0.00 2.93
48 49 2.746277 GCTCGCCCCAAACGACAT 60.746 61.111 0.00 0.00 35.35 3.06
49 50 2.750888 GCTCGCCCCAAACGACATC 61.751 63.158 0.00 0.00 35.35 3.06
50 51 1.079127 CTCGCCCCAAACGACATCT 60.079 57.895 0.00 0.00 35.35 2.90
51 52 0.673644 CTCGCCCCAAACGACATCTT 60.674 55.000 0.00 0.00 35.35 2.40
52 53 0.953471 TCGCCCCAAACGACATCTTG 60.953 55.000 0.00 0.00 33.96 3.02
53 54 1.883021 GCCCCAAACGACATCTTGG 59.117 57.895 0.00 0.00 41.58 3.61
56 57 1.883021 CCAAACGACATCTTGGGGC 59.117 57.895 0.00 0.00 38.77 5.80
57 58 0.609131 CCAAACGACATCTTGGGGCT 60.609 55.000 0.00 0.00 38.77 5.19
58 59 1.247567 CAAACGACATCTTGGGGCTT 58.752 50.000 0.00 0.00 0.00 4.35
59 60 1.068333 CAAACGACATCTTGGGGCTTG 60.068 52.381 0.00 0.00 0.00 4.01
60 61 0.110486 AACGACATCTTGGGGCTTGT 59.890 50.000 0.00 0.00 0.00 3.16
61 62 0.321653 ACGACATCTTGGGGCTTGTC 60.322 55.000 0.00 0.00 36.09 3.18
62 63 0.321564 CGACATCTTGGGGCTTGTCA 60.322 55.000 0.00 0.00 38.68 3.58
63 64 1.881925 CGACATCTTGGGGCTTGTCAA 60.882 52.381 0.00 0.00 38.68 3.18
64 65 2.238521 GACATCTTGGGGCTTGTCAAA 58.761 47.619 0.00 0.00 38.63 2.69
65 66 2.229784 GACATCTTGGGGCTTGTCAAAG 59.770 50.000 0.00 0.00 38.63 2.77
66 67 2.158475 ACATCTTGGGGCTTGTCAAAGA 60.158 45.455 0.00 0.00 35.19 2.52
67 68 2.978156 TCTTGGGGCTTGTCAAAGAT 57.022 45.000 0.00 0.00 35.19 2.40
68 69 2.517959 TCTTGGGGCTTGTCAAAGATG 58.482 47.619 0.00 0.00 35.19 2.90
69 70 2.158475 TCTTGGGGCTTGTCAAAGATGT 60.158 45.455 0.00 0.00 35.19 3.06
70 71 1.909700 TGGGGCTTGTCAAAGATGTC 58.090 50.000 0.00 0.00 35.19 3.06
71 72 1.425066 TGGGGCTTGTCAAAGATGTCT 59.575 47.619 0.00 0.00 35.19 3.41
72 73 2.642311 TGGGGCTTGTCAAAGATGTCTA 59.358 45.455 0.00 0.00 35.19 2.59
73 74 3.010420 GGGGCTTGTCAAAGATGTCTAC 58.990 50.000 0.00 0.00 35.19 2.59
74 75 2.673368 GGGCTTGTCAAAGATGTCTACG 59.327 50.000 0.00 0.00 35.19 3.51
75 76 3.585862 GGCTTGTCAAAGATGTCTACGA 58.414 45.455 0.00 0.00 35.19 3.43
76 77 3.614616 GGCTTGTCAAAGATGTCTACGAG 59.385 47.826 0.00 0.00 35.19 4.18
77 78 3.061429 GCTTGTCAAAGATGTCTACGAGC 59.939 47.826 7.53 7.53 39.62 5.03
78 79 4.489810 CTTGTCAAAGATGTCTACGAGCT 58.510 43.478 0.00 0.00 35.19 4.09
79 80 3.838120 TGTCAAAGATGTCTACGAGCTG 58.162 45.455 0.00 0.00 0.00 4.24
80 81 3.506067 TGTCAAAGATGTCTACGAGCTGA 59.494 43.478 0.00 0.00 0.00 4.26
81 82 4.101942 GTCAAAGATGTCTACGAGCTGAG 58.898 47.826 0.00 0.00 0.00 3.35
82 83 3.129462 TCAAAGATGTCTACGAGCTGAGG 59.871 47.826 0.00 0.00 0.00 3.86
83 84 2.719531 AGATGTCTACGAGCTGAGGA 57.280 50.000 0.00 0.00 0.00 3.71
84 85 2.571212 AGATGTCTACGAGCTGAGGAG 58.429 52.381 0.00 0.00 0.00 3.69
85 86 2.092646 AGATGTCTACGAGCTGAGGAGT 60.093 50.000 0.00 0.00 0.00 3.85
86 87 1.740297 TGTCTACGAGCTGAGGAGTC 58.260 55.000 0.00 0.00 0.00 3.36
87 88 0.653636 GTCTACGAGCTGAGGAGTCG 59.346 60.000 0.00 0.00 39.63 4.18
88 89 0.462225 TCTACGAGCTGAGGAGTCGG 60.462 60.000 0.00 0.00 38.03 4.79
94 95 2.575993 CTGAGGAGTCGGCCTGTG 59.424 66.667 0.00 0.00 38.73 3.66
95 96 2.203640 TGAGGAGTCGGCCTGTGT 60.204 61.111 0.00 0.00 38.73 3.72
96 97 2.262915 GAGGAGTCGGCCTGTGTG 59.737 66.667 0.00 0.00 38.73 3.82
97 98 2.203640 AGGAGTCGGCCTGTGTGA 60.204 61.111 0.00 0.00 36.76 3.58
98 99 1.816863 GAGGAGTCGGCCTGTGTGAA 61.817 60.000 0.00 0.00 38.73 3.18
99 100 1.070786 GGAGTCGGCCTGTGTGAAA 59.929 57.895 0.00 0.00 0.00 2.69
100 101 0.534203 GGAGTCGGCCTGTGTGAAAA 60.534 55.000 0.00 0.00 0.00 2.29
101 102 1.305201 GAGTCGGCCTGTGTGAAAAA 58.695 50.000 0.00 0.00 0.00 1.94
102 103 1.880027 GAGTCGGCCTGTGTGAAAAAT 59.120 47.619 0.00 0.00 0.00 1.82
103 104 2.293399 GAGTCGGCCTGTGTGAAAAATT 59.707 45.455 0.00 0.00 0.00 1.82
104 105 2.693074 AGTCGGCCTGTGTGAAAAATTT 59.307 40.909 0.00 0.00 0.00 1.82
105 106 2.794350 GTCGGCCTGTGTGAAAAATTTG 59.206 45.455 0.00 0.00 0.00 2.32
106 107 2.690497 TCGGCCTGTGTGAAAAATTTGA 59.310 40.909 0.00 0.00 0.00 2.69
107 108 3.131223 TCGGCCTGTGTGAAAAATTTGAA 59.869 39.130 0.00 0.00 0.00 2.69
108 109 3.868077 CGGCCTGTGTGAAAAATTTGAAA 59.132 39.130 0.00 0.00 0.00 2.69
109 110 4.025813 CGGCCTGTGTGAAAAATTTGAAAG 60.026 41.667 0.00 0.00 0.00 2.62
110 111 5.115480 GGCCTGTGTGAAAAATTTGAAAGA 58.885 37.500 0.00 0.00 0.00 2.52
111 112 5.759763 GGCCTGTGTGAAAAATTTGAAAGAT 59.240 36.000 0.00 0.00 0.00 2.40
112 113 6.293027 GGCCTGTGTGAAAAATTTGAAAGATG 60.293 38.462 0.00 0.00 0.00 2.90
113 114 6.258507 GCCTGTGTGAAAAATTTGAAAGATGT 59.741 34.615 0.00 0.00 0.00 3.06
114 115 7.201635 GCCTGTGTGAAAAATTTGAAAGATGTT 60.202 33.333 0.00 0.00 0.00 2.71
115 116 8.330302 CCTGTGTGAAAAATTTGAAAGATGTTC 58.670 33.333 0.00 0.00 0.00 3.18
116 117 8.768957 TGTGTGAAAAATTTGAAAGATGTTCA 57.231 26.923 0.00 0.00 0.00 3.18
117 118 8.655092 TGTGTGAAAAATTTGAAAGATGTTCAC 58.345 29.630 16.51 16.51 42.38 3.18
118 119 8.116136 GTGTGAAAAATTTGAAAGATGTTCACC 58.884 33.333 18.82 11.28 41.72 4.02
119 120 7.009999 TGTGAAAAATTTGAAAGATGTTCACCG 59.990 33.333 18.82 0.00 41.72 4.94
120 121 6.478344 TGAAAAATTTGAAAGATGTTCACCGG 59.522 34.615 0.00 0.00 0.00 5.28
121 122 4.519540 AATTTGAAAGATGTTCACCGGG 57.480 40.909 6.32 0.00 0.00 5.73
122 123 2.649531 TTGAAAGATGTTCACCGGGT 57.350 45.000 6.32 0.00 0.00 5.28
123 124 1.890876 TGAAAGATGTTCACCGGGTG 58.109 50.000 21.27 21.27 34.45 4.61
124 125 1.418264 TGAAAGATGTTCACCGGGTGA 59.582 47.619 25.53 25.53 41.09 4.02
125 126 2.076863 GAAAGATGTTCACCGGGTGAG 58.923 52.381 27.32 3.97 43.69 3.51
126 127 1.348064 AAGATGTTCACCGGGTGAGA 58.652 50.000 27.32 19.17 43.69 3.27
127 128 0.608640 AGATGTTCACCGGGTGAGAC 59.391 55.000 27.32 25.19 43.69 3.36
128 129 0.736325 GATGTTCACCGGGTGAGACG 60.736 60.000 27.32 2.41 43.69 4.18
129 130 1.183030 ATGTTCACCGGGTGAGACGA 61.183 55.000 27.32 12.25 43.69 4.20
130 131 1.364901 GTTCACCGGGTGAGACGAA 59.635 57.895 27.32 11.87 43.69 3.85
131 132 0.037605 GTTCACCGGGTGAGACGAAT 60.038 55.000 27.32 0.00 43.69 3.34
132 133 0.682852 TTCACCGGGTGAGACGAATT 59.317 50.000 27.32 0.00 43.69 2.17
133 134 0.682852 TCACCGGGTGAGACGAATTT 59.317 50.000 25.53 0.00 37.67 1.82
134 135 0.796312 CACCGGGTGAGACGAATTTG 59.204 55.000 22.77 0.00 35.23 2.32
135 136 0.395312 ACCGGGTGAGACGAATTTGT 59.605 50.000 6.32 0.00 0.00 2.83
136 137 1.202722 ACCGGGTGAGACGAATTTGTT 60.203 47.619 6.32 0.00 0.00 2.83
137 138 1.463444 CCGGGTGAGACGAATTTGTTC 59.537 52.381 0.00 1.11 0.00 3.18
138 139 2.139917 CGGGTGAGACGAATTTGTTCA 58.860 47.619 0.00 3.60 0.00 3.18
139 140 2.546368 CGGGTGAGACGAATTTGTTCAA 59.454 45.455 0.00 0.00 0.00 2.69
140 141 3.188460 CGGGTGAGACGAATTTGTTCAAT 59.812 43.478 0.00 0.00 0.00 2.57
141 142 4.475944 GGGTGAGACGAATTTGTTCAATG 58.524 43.478 0.00 0.00 0.00 2.82
142 143 4.215399 GGGTGAGACGAATTTGTTCAATGA 59.785 41.667 0.00 0.00 0.00 2.57
143 144 5.278266 GGGTGAGACGAATTTGTTCAATGAA 60.278 40.000 0.00 0.00 0.00 2.57
144 145 5.853282 GGTGAGACGAATTTGTTCAATGAAG 59.147 40.000 0.00 0.00 0.00 3.02
145 146 6.430451 GTGAGACGAATTTGTTCAATGAAGT 58.570 36.000 0.00 0.00 0.00 3.01
146 147 6.575201 GTGAGACGAATTTGTTCAATGAAGTC 59.425 38.462 0.00 0.00 0.00 3.01
147 148 6.002062 AGACGAATTTGTTCAATGAAGTCC 57.998 37.500 0.00 0.00 29.93 3.85
148 149 5.530915 AGACGAATTTGTTCAATGAAGTCCA 59.469 36.000 0.00 0.00 29.93 4.02
149 150 6.207417 AGACGAATTTGTTCAATGAAGTCCAT 59.793 34.615 0.00 0.00 36.99 3.41
150 151 6.151691 ACGAATTTGTTCAATGAAGTCCATG 58.848 36.000 0.00 0.00 35.24 3.66
151 152 5.574055 CGAATTTGTTCAATGAAGTCCATGG 59.426 40.000 4.97 4.97 35.24 3.66
152 153 6.423776 AATTTGTTCAATGAAGTCCATGGT 57.576 33.333 12.58 0.00 35.24 3.55
153 154 5.452078 TTTGTTCAATGAAGTCCATGGTC 57.548 39.130 12.58 6.20 35.24 4.02
154 155 4.371624 TGTTCAATGAAGTCCATGGTCT 57.628 40.909 12.58 8.95 35.24 3.85
155 156 4.074259 TGTTCAATGAAGTCCATGGTCTG 58.926 43.478 12.50 0.77 35.24 3.51
156 157 4.202451 TGTTCAATGAAGTCCATGGTCTGA 60.202 41.667 12.50 3.22 35.24 3.27
157 158 4.212143 TCAATGAAGTCCATGGTCTGAG 57.788 45.455 12.50 1.92 35.24 3.35
158 159 3.584406 TCAATGAAGTCCATGGTCTGAGT 59.416 43.478 12.50 0.00 35.24 3.41
159 160 4.042062 TCAATGAAGTCCATGGTCTGAGTT 59.958 41.667 12.50 1.48 35.24 3.01
160 161 3.407424 TGAAGTCCATGGTCTGAGTTG 57.593 47.619 12.50 0.00 0.00 3.16
161 162 2.972021 TGAAGTCCATGGTCTGAGTTGA 59.028 45.455 12.50 0.00 0.00 3.18
162 163 3.390967 TGAAGTCCATGGTCTGAGTTGAA 59.609 43.478 12.50 0.00 0.00 2.69
163 164 3.692257 AGTCCATGGTCTGAGTTGAAG 57.308 47.619 12.58 0.00 0.00 3.02
164 165 3.242867 AGTCCATGGTCTGAGTTGAAGA 58.757 45.455 12.58 0.00 0.00 2.87
165 166 3.260380 AGTCCATGGTCTGAGTTGAAGAG 59.740 47.826 12.58 0.00 0.00 2.85
166 167 2.568956 TCCATGGTCTGAGTTGAAGAGG 59.431 50.000 12.58 0.00 0.00 3.69
167 168 2.568956 CCATGGTCTGAGTTGAAGAGGA 59.431 50.000 2.57 0.00 0.00 3.71
168 169 3.594134 CATGGTCTGAGTTGAAGAGGAC 58.406 50.000 0.00 0.00 0.00 3.85
169 170 2.677914 TGGTCTGAGTTGAAGAGGACA 58.322 47.619 0.00 0.00 0.00 4.02
170 171 2.365617 TGGTCTGAGTTGAAGAGGACAC 59.634 50.000 0.00 0.00 0.00 3.67
171 172 2.289133 GGTCTGAGTTGAAGAGGACACC 60.289 54.545 0.00 0.00 0.00 4.16
172 173 1.613925 TCTGAGTTGAAGAGGACACCG 59.386 52.381 0.00 0.00 0.00 4.94
173 174 0.679505 TGAGTTGAAGAGGACACCGG 59.320 55.000 0.00 0.00 0.00 5.28
174 175 0.966920 GAGTTGAAGAGGACACCGGA 59.033 55.000 9.46 0.00 0.00 5.14
175 176 1.343465 GAGTTGAAGAGGACACCGGAA 59.657 52.381 9.46 0.00 0.00 4.30
176 177 1.978580 AGTTGAAGAGGACACCGGAAT 59.021 47.619 9.46 0.00 0.00 3.01
177 178 2.372172 AGTTGAAGAGGACACCGGAATT 59.628 45.455 9.46 0.00 0.00 2.17
178 179 2.742589 GTTGAAGAGGACACCGGAATTC 59.257 50.000 9.46 0.00 0.00 2.17
179 180 1.974957 TGAAGAGGACACCGGAATTCA 59.025 47.619 9.46 4.60 0.00 2.57
180 181 2.370519 TGAAGAGGACACCGGAATTCAA 59.629 45.455 9.46 0.00 0.00 2.69
181 182 3.009033 TGAAGAGGACACCGGAATTCAAT 59.991 43.478 9.46 0.00 0.00 2.57
182 183 3.268023 AGAGGACACCGGAATTCAATC 57.732 47.619 9.46 3.49 0.00 2.67
183 184 1.933853 GAGGACACCGGAATTCAATCG 59.066 52.381 9.46 1.63 0.00 3.34
184 185 1.553248 AGGACACCGGAATTCAATCGA 59.447 47.619 9.46 0.00 0.00 3.59
185 186 2.170607 AGGACACCGGAATTCAATCGAT 59.829 45.455 9.46 0.00 0.00 3.59
186 187 2.287915 GGACACCGGAATTCAATCGATG 59.712 50.000 9.46 1.52 0.00 3.84
187 188 2.936498 GACACCGGAATTCAATCGATGT 59.064 45.455 9.46 5.02 0.00 3.06
188 189 4.116961 GACACCGGAATTCAATCGATGTA 58.883 43.478 9.46 0.00 0.00 2.29
189 190 4.119862 ACACCGGAATTCAATCGATGTAG 58.880 43.478 9.46 0.00 0.00 2.74
190 191 4.119862 CACCGGAATTCAATCGATGTAGT 58.880 43.478 9.46 0.00 0.00 2.73
191 192 4.209288 CACCGGAATTCAATCGATGTAGTC 59.791 45.833 9.46 0.00 0.00 2.59
192 193 4.142026 ACCGGAATTCAATCGATGTAGTCA 60.142 41.667 9.46 0.00 0.00 3.41
193 194 4.991056 CCGGAATTCAATCGATGTAGTCAT 59.009 41.667 7.93 0.00 36.95 3.06
194 195 5.107337 CCGGAATTCAATCGATGTAGTCATG 60.107 44.000 7.93 0.00 34.06 3.07
195 196 5.463392 CGGAATTCAATCGATGTAGTCATGT 59.537 40.000 7.93 0.00 34.06 3.21
196 197 6.346120 CGGAATTCAATCGATGTAGTCATGTC 60.346 42.308 7.93 0.00 34.06 3.06
197 198 6.703607 GGAATTCAATCGATGTAGTCATGTCT 59.296 38.462 7.93 0.00 34.06 3.41
198 199 7.095857 GGAATTCAATCGATGTAGTCATGTCTC 60.096 40.741 7.93 0.00 34.06 3.36
199 200 5.188327 TCAATCGATGTAGTCATGTCTCC 57.812 43.478 0.00 0.00 34.06 3.71
200 201 4.889995 TCAATCGATGTAGTCATGTCTCCT 59.110 41.667 0.00 0.00 34.06 3.69
201 202 4.844998 ATCGATGTAGTCATGTCTCCTG 57.155 45.455 0.00 0.00 34.06 3.86
202 203 2.952310 TCGATGTAGTCATGTCTCCTGG 59.048 50.000 0.00 0.00 34.06 4.45
203 204 2.035193 CGATGTAGTCATGTCTCCTGGG 59.965 54.545 0.00 0.00 34.06 4.45
204 205 1.866015 TGTAGTCATGTCTCCTGGGG 58.134 55.000 0.00 0.00 0.00 4.96
205 206 1.361197 TGTAGTCATGTCTCCTGGGGA 59.639 52.381 0.00 0.00 0.00 4.81
206 207 3.947711 ATGTAGTCATGTCTCCTGGGGAG 60.948 52.174 0.00 7.22 40.73 4.30
216 217 4.697756 CTGGGGAGCGCGGTCAAA 62.698 66.667 35.80 20.78 0.00 2.69
217 218 4.697756 TGGGGAGCGCGGTCAAAG 62.698 66.667 35.80 0.00 0.00 2.77
218 219 4.388499 GGGGAGCGCGGTCAAAGA 62.388 66.667 35.80 0.00 0.00 2.52
219 220 3.119096 GGGAGCGCGGTCAAAGAC 61.119 66.667 35.80 19.89 0.00 3.01
227 228 3.087988 GGTCAAAGACCCCTCCCC 58.912 66.667 4.85 0.00 46.19 4.81
228 229 1.850755 GGTCAAAGACCCCTCCCCA 60.851 63.158 4.85 0.00 46.19 4.96
238 239 4.008933 CCTCCCCATCGCCGGATC 62.009 72.222 5.05 0.00 0.00 3.36
260 261 0.391661 CAAGTGGTGTCATCGAGGGG 60.392 60.000 0.00 0.00 0.00 4.79
284 285 3.738399 CGGCAAATTTTAATCGTCACGA 58.262 40.909 0.28 0.28 41.13 4.35
305 306 2.031157 ACCTTGCTTCCAAACGATTTCG 60.031 45.455 0.00 0.00 46.33 3.46
312 313 4.602995 CTTCCAAACGATTTCGACCAAAA 58.397 39.130 7.01 0.00 43.02 2.44
313 314 4.839668 TCCAAACGATTTCGACCAAAAT 57.160 36.364 7.01 0.00 43.02 1.82
319 320 4.533222 ACGATTTCGACCAAAATGAACAC 58.467 39.130 7.01 0.00 43.02 3.32
326 327 3.682858 CGACCAAAATGAACACGTAGGAT 59.317 43.478 0.00 0.00 0.00 3.24
328 329 5.220340 CGACCAAAATGAACACGTAGGATAC 60.220 44.000 0.00 0.00 38.50 2.24
330 331 6.177610 ACCAAAATGAACACGTAGGATACAT 58.822 36.000 0.00 0.00 43.24 2.29
331 332 6.657541 ACCAAAATGAACACGTAGGATACATT 59.342 34.615 0.00 0.00 43.24 2.71
340 341 5.983720 ACACGTAGGATACATTTAGCATGAC 59.016 40.000 0.00 0.00 43.24 3.06
359 360 6.586082 GCATGACAAAATTCCATTTTACGAGT 59.414 34.615 0.00 0.00 40.27 4.18
374 375 0.982673 CGAGTCCGTGAACTAAAGCG 59.017 55.000 0.00 0.00 0.00 4.68
376 377 0.677842 AGTCCGTGAACTAAAGCGGT 59.322 50.000 0.00 0.00 44.07 5.68
377 378 1.066136 GTCCGTGAACTAAAGCGGTC 58.934 55.000 0.00 0.00 44.07 4.79
378 379 0.387622 TCCGTGAACTAAAGCGGTCG 60.388 55.000 0.00 0.00 44.07 4.79
379 380 1.414897 CGTGAACTAAAGCGGTCGC 59.585 57.895 7.32 7.32 42.33 5.19
391 392 4.324991 GGTCGCCCGGGACAAGTT 62.325 66.667 29.31 0.00 38.70 2.66
392 393 2.741211 GTCGCCCGGGACAAGTTC 60.741 66.667 29.31 2.60 36.91 3.01
397 398 0.035739 GCCCGGGACAAGTTCTTGTA 59.964 55.000 29.31 0.00 34.90 2.41
404 405 4.330074 CGGGACAAGTTCTTGTATCATCAC 59.670 45.833 16.57 5.99 34.90 3.06
511 514 3.346734 CCCAAAGCCCTAGCCCCA 61.347 66.667 0.00 0.00 41.25 4.96
546 552 2.968697 GTGCCGTTCCGTTCCGTT 60.969 61.111 0.00 0.00 0.00 4.44
547 553 1.664333 GTGCCGTTCCGTTCCGTTA 60.664 57.895 0.00 0.00 0.00 3.18
548 554 1.068753 TGCCGTTCCGTTCCGTTAA 59.931 52.632 0.00 0.00 0.00 2.01
550 556 0.371301 GCCGTTCCGTTCCGTTAATC 59.629 55.000 0.00 0.00 0.00 1.75
589 595 2.973034 AATCCCCTCCCCTCCCCT 60.973 66.667 0.00 0.00 0.00 4.79
590 596 3.054557 AATCCCCTCCCCTCCCCTC 62.055 68.421 0.00 0.00 0.00 4.30
1036 1043 4.742201 AATGCGTCGCCGAGTGCT 62.742 61.111 15.88 0.00 38.05 4.40
1437 1444 4.060038 TCTGTTCTCCTTGTTCAGTGAC 57.940 45.455 0.00 0.00 0.00 3.67
1556 1563 1.270252 TGCGACAGACTGCTTGATCAA 60.270 47.619 8.12 8.12 0.00 2.57
1582 1589 0.248743 CACCACTTGTTGCAGTGCAG 60.249 55.000 18.81 9.26 42.63 4.41
1637 1644 3.969250 TTGGAATCGTCCCGGCAGC 62.969 63.158 0.00 0.00 44.23 5.25
1671 1678 5.064441 ACATACTTCTCAAATTTGCAGCC 57.936 39.130 13.54 0.00 0.00 4.85
1758 1765 0.179134 ATGCTCACGCGTTAGTCCTC 60.179 55.000 20.60 5.68 39.65 3.71
1967 1974 5.186198 AGTTGAGGACATGGCTTATAACAC 58.814 41.667 11.35 0.00 0.00 3.32
1968 1975 4.835284 TGAGGACATGGCTTATAACACA 57.165 40.909 0.00 0.00 0.00 3.72
2044 2051 1.202818 AGAACAAGACCAGACAAGGGC 60.203 52.381 0.00 0.00 36.73 5.19
2171 2178 2.425312 TCGAAACAAACTGCCACATTGT 59.575 40.909 0.00 0.00 38.85 2.71
2374 2381 0.605589 GGGTCTGACACCTGACAGAG 59.394 60.000 10.38 0.00 44.70 3.35
2653 2660 6.431234 CCTTAGTGAAGCAGAGGTGTTATTTT 59.569 38.462 0.00 0.00 0.00 1.82
2751 2758 4.503817 GGCTGGACAGATCATGCTTACATA 60.504 45.833 3.00 0.00 33.67 2.29
2961 2968 4.213694 GGAGATATGCACAATGCTCTCTTG 59.786 45.833 14.51 0.00 45.31 3.02
3002 3009 1.129437 GCGAGGACTTTCTGTTGATGC 59.871 52.381 0.00 0.00 0.00 3.91
3009 3016 5.645497 AGGACTTTCTGTTGATGCTATTGTC 59.355 40.000 0.00 0.00 0.00 3.18
3376 3383 5.831997 TGACTCCTGATCAACATGTATACG 58.168 41.667 0.00 0.00 0.00 3.06
3466 3473 4.263594 TGGTAGACAGGGGAATAAAACCAC 60.264 45.833 0.00 0.00 29.85 4.16
3890 3939 3.577415 AGTCTTACAGGAACACAGTACCC 59.423 47.826 0.00 0.00 0.00 3.69
4072 4122 1.133790 GGCAGATGCAAACAGATCACC 59.866 52.381 7.19 0.00 44.36 4.02
4154 4204 7.770433 TGTCATCTAACTAATACTGCATGCTTT 59.230 33.333 20.33 8.07 0.00 3.51
4444 4513 0.461339 AGTGTAAGCCCATAACCGCG 60.461 55.000 0.00 0.00 0.00 6.46
4475 4544 2.171237 TCCAGCATGCATAAGCTAGTGT 59.829 45.455 21.98 0.00 39.50 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.245096 GTCAACATGCGATCAACAAGC 58.755 47.619 0.00 0.00 0.00 4.01
3 4 1.870402 ACGTCAACATGCGATCAACAA 59.130 42.857 0.00 0.00 0.00 2.83
5 6 1.459209 TCACGTCAACATGCGATCAAC 59.541 47.619 0.00 0.00 0.00 3.18
6 7 1.789506 TCACGTCAACATGCGATCAA 58.210 45.000 0.00 0.00 0.00 2.57
7 8 1.789506 TTCACGTCAACATGCGATCA 58.210 45.000 0.00 0.00 0.00 2.92
8 9 2.873170 TTTCACGTCAACATGCGATC 57.127 45.000 0.00 0.00 0.00 3.69
9 10 2.350388 GGTTTTCACGTCAACATGCGAT 60.350 45.455 0.00 0.00 0.00 4.58
10 11 1.003331 GGTTTTCACGTCAACATGCGA 60.003 47.619 0.00 0.00 0.00 5.10
11 12 1.394697 GGTTTTCACGTCAACATGCG 58.605 50.000 0.00 0.00 0.00 4.73
12 13 1.394697 CGGTTTTCACGTCAACATGC 58.605 50.000 0.00 0.00 0.00 4.06
13 14 1.002900 AGCGGTTTTCACGTCAACATG 60.003 47.619 0.00 0.00 0.00 3.21
14 15 1.263217 GAGCGGTTTTCACGTCAACAT 59.737 47.619 0.00 0.00 0.00 2.71
15 16 0.653636 GAGCGGTTTTCACGTCAACA 59.346 50.000 0.00 0.00 0.00 3.33
16 17 0.382636 CGAGCGGTTTTCACGTCAAC 60.383 55.000 0.00 0.00 0.00 3.18
17 18 1.928653 CGAGCGGTTTTCACGTCAA 59.071 52.632 0.00 0.00 0.00 3.18
18 19 2.591311 GCGAGCGGTTTTCACGTCA 61.591 57.895 0.00 0.00 0.00 4.35
19 20 2.170273 GCGAGCGGTTTTCACGTC 59.830 61.111 0.00 0.00 0.00 4.34
20 21 3.343421 GGCGAGCGGTTTTCACGT 61.343 61.111 0.00 0.00 0.00 4.49
21 22 4.084888 GGGCGAGCGGTTTTCACG 62.085 66.667 0.00 0.00 0.00 4.35
22 23 3.733960 GGGGCGAGCGGTTTTCAC 61.734 66.667 0.00 0.00 0.00 3.18
23 24 3.776347 TTGGGGCGAGCGGTTTTCA 62.776 57.895 0.00 0.00 0.00 2.69
24 25 2.557372 TTTGGGGCGAGCGGTTTTC 61.557 57.895 0.00 0.00 0.00 2.29
25 26 2.519780 TTTGGGGCGAGCGGTTTT 60.520 55.556 0.00 0.00 0.00 2.43
26 27 3.292159 GTTTGGGGCGAGCGGTTT 61.292 61.111 0.00 0.00 0.00 3.27
31 32 2.746277 ATGTCGTTTGGGGCGAGC 60.746 61.111 0.00 0.00 39.14 5.03
32 33 0.673644 AAGATGTCGTTTGGGGCGAG 60.674 55.000 0.00 0.00 39.14 5.03
33 34 0.953471 CAAGATGTCGTTTGGGGCGA 60.953 55.000 0.00 0.00 35.89 5.54
34 35 1.501741 CAAGATGTCGTTTGGGGCG 59.498 57.895 0.00 0.00 0.00 6.13
35 36 1.883021 CCAAGATGTCGTTTGGGGC 59.117 57.895 0.00 0.00 40.11 5.80
38 39 0.609131 AGCCCCAAGATGTCGTTTGG 60.609 55.000 0.00 0.00 42.77 3.28
39 40 1.068333 CAAGCCCCAAGATGTCGTTTG 60.068 52.381 0.00 0.00 0.00 2.93
40 41 1.247567 CAAGCCCCAAGATGTCGTTT 58.752 50.000 0.00 0.00 0.00 3.60
41 42 0.110486 ACAAGCCCCAAGATGTCGTT 59.890 50.000 0.00 0.00 0.00 3.85
42 43 0.321653 GACAAGCCCCAAGATGTCGT 60.322 55.000 0.00 0.00 33.62 4.34
43 44 0.321564 TGACAAGCCCCAAGATGTCG 60.322 55.000 0.00 0.00 43.91 4.35
44 45 1.909700 TTGACAAGCCCCAAGATGTC 58.090 50.000 0.00 0.00 41.90 3.06
45 46 2.158475 TCTTTGACAAGCCCCAAGATGT 60.158 45.455 0.00 0.00 0.00 3.06
46 47 2.517959 TCTTTGACAAGCCCCAAGATG 58.482 47.619 0.00 0.00 0.00 2.90
47 48 2.978156 TCTTTGACAAGCCCCAAGAT 57.022 45.000 0.00 0.00 0.00 2.40
48 49 2.158475 ACATCTTTGACAAGCCCCAAGA 60.158 45.455 0.00 0.00 0.00 3.02
49 50 2.229784 GACATCTTTGACAAGCCCCAAG 59.770 50.000 0.00 0.00 0.00 3.61
50 51 2.158475 AGACATCTTTGACAAGCCCCAA 60.158 45.455 0.00 0.00 0.00 4.12
51 52 1.425066 AGACATCTTTGACAAGCCCCA 59.575 47.619 0.00 0.00 0.00 4.96
52 53 2.206576 AGACATCTTTGACAAGCCCC 57.793 50.000 0.00 0.00 0.00 5.80
53 54 2.673368 CGTAGACATCTTTGACAAGCCC 59.327 50.000 0.00 0.00 0.00 5.19
54 55 3.585862 TCGTAGACATCTTTGACAAGCC 58.414 45.455 0.00 0.00 0.00 4.35
55 56 3.061429 GCTCGTAGACATCTTTGACAAGC 59.939 47.826 0.00 0.00 0.00 4.01
56 57 4.325741 CAGCTCGTAGACATCTTTGACAAG 59.674 45.833 0.00 0.00 0.00 3.16
57 58 4.022329 TCAGCTCGTAGACATCTTTGACAA 60.022 41.667 0.00 0.00 0.00 3.18
58 59 3.506067 TCAGCTCGTAGACATCTTTGACA 59.494 43.478 0.00 0.00 0.00 3.58
59 60 4.098055 TCAGCTCGTAGACATCTTTGAC 57.902 45.455 0.00 0.00 0.00 3.18
60 61 3.129462 CCTCAGCTCGTAGACATCTTTGA 59.871 47.826 0.00 0.00 0.00 2.69
61 62 3.129462 TCCTCAGCTCGTAGACATCTTTG 59.871 47.826 0.00 0.00 0.00 2.77
62 63 3.357203 TCCTCAGCTCGTAGACATCTTT 58.643 45.455 0.00 0.00 0.00 2.52
63 64 2.948979 CTCCTCAGCTCGTAGACATCTT 59.051 50.000 0.00 0.00 0.00 2.40
64 65 2.092646 ACTCCTCAGCTCGTAGACATCT 60.093 50.000 0.00 0.00 0.00 2.90
65 66 2.289547 GACTCCTCAGCTCGTAGACATC 59.710 54.545 0.00 0.00 0.00 3.06
66 67 2.294074 GACTCCTCAGCTCGTAGACAT 58.706 52.381 0.00 0.00 0.00 3.06
67 68 1.740297 GACTCCTCAGCTCGTAGACA 58.260 55.000 0.00 0.00 0.00 3.41
68 69 0.653636 CGACTCCTCAGCTCGTAGAC 59.346 60.000 0.00 0.00 0.00 2.59
69 70 0.462225 CCGACTCCTCAGCTCGTAGA 60.462 60.000 0.00 0.00 0.00 2.59
70 71 2.018544 CCGACTCCTCAGCTCGTAG 58.981 63.158 0.00 0.00 0.00 3.51
71 72 2.113433 GCCGACTCCTCAGCTCGTA 61.113 63.158 0.00 0.00 0.00 3.43
72 73 3.444805 GCCGACTCCTCAGCTCGT 61.445 66.667 0.00 0.00 0.00 4.18
73 74 4.200283 GGCCGACTCCTCAGCTCG 62.200 72.222 0.00 0.00 0.00 5.03
74 75 2.757917 AGGCCGACTCCTCAGCTC 60.758 66.667 0.00 0.00 0.00 4.09
75 76 3.073735 CAGGCCGACTCCTCAGCT 61.074 66.667 0.00 0.00 33.25 4.24
76 77 3.386237 ACAGGCCGACTCCTCAGC 61.386 66.667 0.00 0.00 33.25 4.26
77 78 2.279069 ACACAGGCCGACTCCTCAG 61.279 63.158 0.00 0.00 33.25 3.35
78 79 2.203640 ACACAGGCCGACTCCTCA 60.204 61.111 0.00 0.00 33.25 3.86
79 80 1.816863 TTCACACAGGCCGACTCCTC 61.817 60.000 0.00 0.00 33.25 3.71
80 81 1.407656 TTTCACACAGGCCGACTCCT 61.408 55.000 0.00 0.00 36.78 3.69
81 82 0.534203 TTTTCACACAGGCCGACTCC 60.534 55.000 0.00 0.00 0.00 3.85
82 83 1.305201 TTTTTCACACAGGCCGACTC 58.695 50.000 0.00 0.00 0.00 3.36
83 84 1.981256 ATTTTTCACACAGGCCGACT 58.019 45.000 0.00 0.00 0.00 4.18
84 85 2.793278 AATTTTTCACACAGGCCGAC 57.207 45.000 0.00 0.00 0.00 4.79
85 86 2.690497 TCAAATTTTTCACACAGGCCGA 59.310 40.909 0.00 0.00 0.00 5.54
86 87 3.090952 TCAAATTTTTCACACAGGCCG 57.909 42.857 0.00 0.00 0.00 6.13
87 88 5.115480 TCTTTCAAATTTTTCACACAGGCC 58.885 37.500 0.00 0.00 0.00 5.19
88 89 6.258507 ACATCTTTCAAATTTTTCACACAGGC 59.741 34.615 0.00 0.00 0.00 4.85
89 90 7.775397 ACATCTTTCAAATTTTTCACACAGG 57.225 32.000 0.00 0.00 0.00 4.00
90 91 8.871862 TGAACATCTTTCAAATTTTTCACACAG 58.128 29.630 0.00 0.00 0.00 3.66
91 92 8.655092 GTGAACATCTTTCAAATTTTTCACACA 58.345 29.630 17.20 0.00 40.72 3.72
92 93 8.116136 GGTGAACATCTTTCAAATTTTTCACAC 58.884 33.333 20.95 11.96 42.11 3.82
93 94 7.009999 CGGTGAACATCTTTCAAATTTTTCACA 59.990 33.333 20.95 0.00 42.11 3.58
94 95 7.336975 CGGTGAACATCTTTCAAATTTTTCAC 58.663 34.615 15.12 15.12 40.45 3.18
95 96 6.478344 CCGGTGAACATCTTTCAAATTTTTCA 59.522 34.615 0.00 0.00 0.00 2.69
96 97 6.073819 CCCGGTGAACATCTTTCAAATTTTTC 60.074 38.462 0.00 0.00 0.00 2.29
97 98 5.757808 CCCGGTGAACATCTTTCAAATTTTT 59.242 36.000 0.00 0.00 0.00 1.94
98 99 5.163353 ACCCGGTGAACATCTTTCAAATTTT 60.163 36.000 0.00 0.00 0.00 1.82
99 100 4.343814 ACCCGGTGAACATCTTTCAAATTT 59.656 37.500 0.00 0.00 0.00 1.82
100 101 3.895041 ACCCGGTGAACATCTTTCAAATT 59.105 39.130 0.00 0.00 0.00 1.82
101 102 3.255642 CACCCGGTGAACATCTTTCAAAT 59.744 43.478 12.68 0.00 35.23 2.32
102 103 2.621055 CACCCGGTGAACATCTTTCAAA 59.379 45.455 12.68 0.00 35.23 2.69
103 104 2.158740 TCACCCGGTGAACATCTTTCAA 60.159 45.455 18.34 0.00 39.78 2.69
104 105 1.418264 TCACCCGGTGAACATCTTTCA 59.582 47.619 18.34 0.00 39.78 2.69
105 106 2.076863 CTCACCCGGTGAACATCTTTC 58.923 52.381 20.81 0.00 42.26 2.62
106 107 1.697432 TCTCACCCGGTGAACATCTTT 59.303 47.619 20.81 0.00 42.26 2.52
107 108 1.002087 GTCTCACCCGGTGAACATCTT 59.998 52.381 20.81 0.00 42.26 2.40
108 109 0.608640 GTCTCACCCGGTGAACATCT 59.391 55.000 20.81 0.00 42.26 2.90
109 110 0.736325 CGTCTCACCCGGTGAACATC 60.736 60.000 20.81 10.33 42.26 3.06
110 111 1.183030 TCGTCTCACCCGGTGAACAT 61.183 55.000 20.81 0.00 42.26 2.71
111 112 1.393487 TTCGTCTCACCCGGTGAACA 61.393 55.000 20.81 8.13 42.26 3.18
112 113 0.037605 ATTCGTCTCACCCGGTGAAC 60.038 55.000 20.81 18.35 42.26 3.18
113 114 0.682852 AATTCGTCTCACCCGGTGAA 59.317 50.000 20.81 6.53 42.26 3.18
114 115 0.682852 AAATTCGTCTCACCCGGTGA 59.317 50.000 19.39 19.39 40.50 4.02
115 116 0.796312 CAAATTCGTCTCACCCGGTG 59.204 55.000 11.73 11.73 34.45 4.94
116 117 0.395312 ACAAATTCGTCTCACCCGGT 59.605 50.000 0.00 0.00 0.00 5.28
117 118 1.463444 GAACAAATTCGTCTCACCCGG 59.537 52.381 0.00 0.00 0.00 5.73
118 119 2.139917 TGAACAAATTCGTCTCACCCG 58.860 47.619 0.00 0.00 37.69 5.28
119 120 4.215399 TCATTGAACAAATTCGTCTCACCC 59.785 41.667 0.00 0.00 37.69 4.61
120 121 5.356882 TCATTGAACAAATTCGTCTCACC 57.643 39.130 0.00 0.00 37.69 4.02
121 122 6.430451 ACTTCATTGAACAAATTCGTCTCAC 58.570 36.000 0.00 0.00 37.69 3.51
122 123 6.293407 GGACTTCATTGAACAAATTCGTCTCA 60.293 38.462 10.60 0.00 37.69 3.27
123 124 6.080406 GGACTTCATTGAACAAATTCGTCTC 58.920 40.000 10.60 1.71 37.69 3.36
124 125 5.530915 TGGACTTCATTGAACAAATTCGTCT 59.469 36.000 10.60 0.00 37.69 4.18
125 126 5.757886 TGGACTTCATTGAACAAATTCGTC 58.242 37.500 0.00 0.17 37.69 4.20
126 127 5.766150 TGGACTTCATTGAACAAATTCGT 57.234 34.783 0.00 0.00 37.69 3.85
127 128 5.574055 CCATGGACTTCATTGAACAAATTCG 59.426 40.000 5.56 0.00 33.90 3.34
128 129 6.458210 ACCATGGACTTCATTGAACAAATTC 58.542 36.000 21.47 0.00 32.92 2.17
129 130 6.268387 AGACCATGGACTTCATTGAACAAATT 59.732 34.615 21.47 0.00 32.92 1.82
130 131 5.776716 AGACCATGGACTTCATTGAACAAAT 59.223 36.000 21.47 0.00 32.92 2.32
131 132 5.009911 CAGACCATGGACTTCATTGAACAAA 59.990 40.000 21.47 0.00 32.92 2.83
132 133 4.520111 CAGACCATGGACTTCATTGAACAA 59.480 41.667 21.47 0.00 32.92 2.83
133 134 4.074259 CAGACCATGGACTTCATTGAACA 58.926 43.478 21.47 0.00 32.92 3.18
134 135 4.326826 TCAGACCATGGACTTCATTGAAC 58.673 43.478 21.47 0.00 32.92 3.18
135 136 4.042062 ACTCAGACCATGGACTTCATTGAA 59.958 41.667 21.47 0.00 32.92 2.69
136 137 3.584406 ACTCAGACCATGGACTTCATTGA 59.416 43.478 21.47 10.62 32.92 2.57
137 138 3.947868 ACTCAGACCATGGACTTCATTG 58.052 45.455 21.47 6.40 32.92 2.82
138 139 4.042062 TCAACTCAGACCATGGACTTCATT 59.958 41.667 21.47 8.18 32.92 2.57
139 140 3.584406 TCAACTCAGACCATGGACTTCAT 59.416 43.478 21.47 1.70 36.31 2.57
140 141 2.972021 TCAACTCAGACCATGGACTTCA 59.028 45.455 21.47 5.59 0.00 3.02
141 142 3.685139 TCAACTCAGACCATGGACTTC 57.315 47.619 21.47 5.63 0.00 3.01
142 143 3.648067 TCTTCAACTCAGACCATGGACTT 59.352 43.478 21.47 0.00 0.00 3.01
143 144 3.242867 TCTTCAACTCAGACCATGGACT 58.757 45.455 21.47 15.99 0.00 3.85
144 145 3.594134 CTCTTCAACTCAGACCATGGAC 58.406 50.000 21.47 13.40 0.00 4.02
145 146 2.568956 CCTCTTCAACTCAGACCATGGA 59.431 50.000 21.47 0.00 0.00 3.41
146 147 2.568956 TCCTCTTCAACTCAGACCATGG 59.431 50.000 11.19 11.19 0.00 3.66
147 148 3.007290 TGTCCTCTTCAACTCAGACCATG 59.993 47.826 0.00 0.00 0.00 3.66
148 149 3.007398 GTGTCCTCTTCAACTCAGACCAT 59.993 47.826 0.00 0.00 0.00 3.55
149 150 2.365617 GTGTCCTCTTCAACTCAGACCA 59.634 50.000 0.00 0.00 0.00 4.02
150 151 2.289133 GGTGTCCTCTTCAACTCAGACC 60.289 54.545 0.00 0.00 0.00 3.85
151 152 2.608261 CGGTGTCCTCTTCAACTCAGAC 60.608 54.545 0.00 0.00 0.00 3.51
152 153 1.613925 CGGTGTCCTCTTCAACTCAGA 59.386 52.381 0.00 0.00 0.00 3.27
153 154 1.337260 CCGGTGTCCTCTTCAACTCAG 60.337 57.143 0.00 0.00 0.00 3.35
154 155 0.679505 CCGGTGTCCTCTTCAACTCA 59.320 55.000 0.00 0.00 0.00 3.41
155 156 0.966920 TCCGGTGTCCTCTTCAACTC 59.033 55.000 0.00 0.00 0.00 3.01
156 157 1.420430 TTCCGGTGTCCTCTTCAACT 58.580 50.000 0.00 0.00 0.00 3.16
157 158 2.474410 ATTCCGGTGTCCTCTTCAAC 57.526 50.000 0.00 0.00 0.00 3.18
158 159 2.370519 TGAATTCCGGTGTCCTCTTCAA 59.629 45.455 0.00 0.00 0.00 2.69
159 160 1.974957 TGAATTCCGGTGTCCTCTTCA 59.025 47.619 0.00 0.00 0.00 3.02
160 161 2.762535 TGAATTCCGGTGTCCTCTTC 57.237 50.000 0.00 0.00 0.00 2.87
161 162 3.610911 GATTGAATTCCGGTGTCCTCTT 58.389 45.455 0.00 0.00 0.00 2.85
162 163 2.418746 CGATTGAATTCCGGTGTCCTCT 60.419 50.000 0.00 0.00 0.00 3.69
163 164 1.933853 CGATTGAATTCCGGTGTCCTC 59.066 52.381 0.00 0.00 0.00 3.71
164 165 1.553248 TCGATTGAATTCCGGTGTCCT 59.447 47.619 0.00 0.00 0.00 3.85
165 166 2.018542 TCGATTGAATTCCGGTGTCC 57.981 50.000 0.00 0.00 0.00 4.02
166 167 2.936498 ACATCGATTGAATTCCGGTGTC 59.064 45.455 13.56 0.00 43.12 3.67
167 168 2.985896 ACATCGATTGAATTCCGGTGT 58.014 42.857 13.56 13.56 42.03 4.16
168 169 4.119862 ACTACATCGATTGAATTCCGGTG 58.880 43.478 12.48 12.48 39.97 4.94
169 170 4.142026 TGACTACATCGATTGAATTCCGGT 60.142 41.667 0.00 0.00 0.00 5.28
170 171 4.368315 TGACTACATCGATTGAATTCCGG 58.632 43.478 2.27 0.00 0.00 5.14
171 172 5.463392 ACATGACTACATCGATTGAATTCCG 59.537 40.000 0.00 0.00 34.15 4.30
172 173 6.703607 AGACATGACTACATCGATTGAATTCC 59.296 38.462 0.00 0.00 34.15 3.01
173 174 7.095857 GGAGACATGACTACATCGATTGAATTC 60.096 40.741 0.00 0.00 34.15 2.17
174 175 6.703607 GGAGACATGACTACATCGATTGAATT 59.296 38.462 0.00 0.00 34.15 2.17
175 176 6.041409 AGGAGACATGACTACATCGATTGAAT 59.959 38.462 10.12 0.00 34.15 2.57
176 177 5.360999 AGGAGACATGACTACATCGATTGAA 59.639 40.000 10.12 0.00 34.15 2.69
177 178 4.889995 AGGAGACATGACTACATCGATTGA 59.110 41.667 10.12 0.00 34.15 2.57
178 179 4.981054 CAGGAGACATGACTACATCGATTG 59.019 45.833 10.12 0.00 34.15 2.67
179 180 4.038522 CCAGGAGACATGACTACATCGATT 59.961 45.833 10.12 0.00 34.15 3.34
180 181 3.571828 CCAGGAGACATGACTACATCGAT 59.428 47.826 10.12 0.00 34.15 3.59
181 182 2.952310 CCAGGAGACATGACTACATCGA 59.048 50.000 10.12 0.00 34.15 3.59
182 183 2.035193 CCCAGGAGACATGACTACATCG 59.965 54.545 10.12 0.00 34.15 3.84
183 184 2.366916 CCCCAGGAGACATGACTACATC 59.633 54.545 10.12 0.00 34.15 3.06
184 185 2.023015 TCCCCAGGAGACATGACTACAT 60.023 50.000 10.12 0.00 37.19 2.29
185 186 1.361197 TCCCCAGGAGACATGACTACA 59.639 52.381 10.12 0.00 0.00 2.74
186 187 2.160721 TCCCCAGGAGACATGACTAC 57.839 55.000 0.00 0.00 0.00 2.73
199 200 4.697756 TTTGACCGCGCTCCCCAG 62.698 66.667 5.56 0.00 0.00 4.45
200 201 4.697756 CTTTGACCGCGCTCCCCA 62.698 66.667 5.56 0.00 0.00 4.96
201 202 4.388499 TCTTTGACCGCGCTCCCC 62.388 66.667 5.56 0.00 0.00 4.81
202 203 3.119096 GTCTTTGACCGCGCTCCC 61.119 66.667 5.56 0.00 0.00 4.30
203 204 3.119096 GGTCTTTGACCGCGCTCC 61.119 66.667 5.56 0.00 43.14 4.70
211 212 0.256177 GATGGGGAGGGGTCTTTGAC 59.744 60.000 0.00 0.00 0.00 3.18
212 213 1.271840 CGATGGGGAGGGGTCTTTGA 61.272 60.000 0.00 0.00 0.00 2.69
213 214 1.224592 CGATGGGGAGGGGTCTTTG 59.775 63.158 0.00 0.00 0.00 2.77
214 215 2.680370 GCGATGGGGAGGGGTCTTT 61.680 63.158 0.00 0.00 0.00 2.52
215 216 3.090532 GCGATGGGGAGGGGTCTT 61.091 66.667 0.00 0.00 0.00 3.01
221 222 4.008933 GATCCGGCGATGGGGAGG 62.009 72.222 9.30 0.00 35.40 4.30
222 223 1.606601 TAGATCCGGCGATGGGGAG 60.607 63.158 9.30 0.00 35.40 4.30
223 224 1.906824 GTAGATCCGGCGATGGGGA 60.907 63.158 9.30 0.00 36.61 4.81
224 225 1.754380 TTGTAGATCCGGCGATGGGG 61.754 60.000 9.30 0.00 0.00 4.96
225 226 0.319900 CTTGTAGATCCGGCGATGGG 60.320 60.000 9.30 0.00 0.00 4.00
226 227 0.389391 ACTTGTAGATCCGGCGATGG 59.611 55.000 9.30 0.00 0.00 3.51
227 228 1.491670 CACTTGTAGATCCGGCGATG 58.508 55.000 9.30 0.00 0.00 3.84
228 229 0.389391 CCACTTGTAGATCCGGCGAT 59.611 55.000 9.30 0.00 0.00 4.58
238 239 2.417379 CCCTCGATGACACCACTTGTAG 60.417 54.545 0.00 0.00 39.17 2.74
260 261 2.190161 GACGATTAAAATTTGCCGCCC 58.810 47.619 0.00 0.00 0.00 6.13
268 269 4.454504 AGCAAGGTCGTGACGATTAAAATT 59.545 37.500 12.08 0.00 38.42 1.82
284 285 2.031157 CGAAATCGTTTGGAAGCAAGGT 60.031 45.455 0.00 0.00 34.11 3.50
305 306 5.640357 TGTATCCTACGTGTTCATTTTGGTC 59.360 40.000 0.00 0.00 0.00 4.02
312 313 6.578944 TGCTAAATGTATCCTACGTGTTCAT 58.421 36.000 0.00 0.00 0.00 2.57
313 314 5.968254 TGCTAAATGTATCCTACGTGTTCA 58.032 37.500 0.00 0.00 0.00 3.18
319 320 7.477144 TTTGTCATGCTAAATGTATCCTACG 57.523 36.000 0.00 0.00 0.00 3.51
326 327 9.941325 AAATGGAATTTTGTCATGCTAAATGTA 57.059 25.926 9.09 2.84 46.10 2.29
355 356 0.982673 CGCTTTAGTTCACGGACTCG 59.017 55.000 0.00 0.00 43.02 4.18
376 377 2.513259 AAGAACTTGTCCCGGGCGA 61.513 57.895 18.49 10.29 0.00 5.54
377 378 2.032071 AAGAACTTGTCCCGGGCG 59.968 61.111 18.49 6.49 0.00 6.13
378 379 3.668386 CAAGAACTTGTCCCGGGC 58.332 61.111 18.49 12.24 35.92 6.13
386 387 9.552114 GAAATTCAGTGATGATACAAGAACTTG 57.448 33.333 12.22 12.22 45.58 3.16
388 389 8.725148 GTGAAATTCAGTGATGATACAAGAACT 58.275 33.333 0.00 0.00 0.00 3.01
389 390 8.725148 AGTGAAATTCAGTGATGATACAAGAAC 58.275 33.333 2.02 0.00 0.00 3.01
391 392 9.591792 CTAGTGAAATTCAGTGATGATACAAGA 57.408 33.333 13.19 0.00 31.49 3.02
392 393 9.591792 TCTAGTGAAATTCAGTGATGATACAAG 57.408 33.333 13.19 0.16 31.49 3.16
397 398 9.458727 AAATGTCTAGTGAAATTCAGTGATGAT 57.541 29.630 13.19 3.85 29.27 2.45
849 855 3.089874 CGATGGCCCAGGGAGGAA 61.090 66.667 10.89 0.00 41.22 3.36
990 997 1.770658 CACAGGAGCATGGGGATCTAA 59.229 52.381 0.00 0.00 30.93 2.10
1182 1189 0.337082 TCCAGATAACCTCACGGGGA 59.663 55.000 0.00 0.00 40.03 4.81
1186 1193 2.101582 CCCTTCTCCAGATAACCTCACG 59.898 54.545 0.00 0.00 0.00 4.35
1188 1195 2.764269 CCCCTTCTCCAGATAACCTCA 58.236 52.381 0.00 0.00 0.00 3.86
1195 1202 2.739996 CGCAGCCCCTTCTCCAGAT 61.740 63.158 0.00 0.00 0.00 2.90
1226 1233 3.443479 AGCTCCTCCTCCGGGGAT 61.443 66.667 0.37 0.00 44.15 3.85
1228 1235 4.150454 AGAGCTCCTCCTCCGGGG 62.150 72.222 10.93 0.00 32.17 5.73
1582 1589 2.749621 CAAACAGCCCTATTGTGTCCTC 59.250 50.000 0.00 0.00 0.00 3.71
1637 1644 4.756642 TGAGAAGTATGTTGCAAGTCCAAG 59.243 41.667 0.00 0.00 0.00 3.61
1967 1974 3.144657 TGCATAGCCCATCCATTACTG 57.855 47.619 0.00 0.00 0.00 2.74
1968 1975 3.499202 CCTTGCATAGCCCATCCATTACT 60.499 47.826 0.00 0.00 0.00 2.24
2044 2051 9.973450 GCTATAACCATATATATCTGGTGTGAG 57.027 37.037 20.25 17.09 44.97 3.51
2374 2381 5.050769 CCTTGATCACGCATGTATAGTGAAC 60.051 44.000 15.38 13.78 46.22 3.18
2692 2699 4.261994 GCCACAAACCATTGAACTGTACAT 60.262 41.667 0.00 0.00 38.94 2.29
2961 2968 4.496341 CGCTGAACCATATCATGAAACCAC 60.496 45.833 0.00 0.00 0.00 4.16
3009 3016 9.302345 CAGTAACCATTCATTAGTACAGTGTAG 57.698 37.037 2.39 0.00 0.00 2.74
3250 3257 5.074804 GGTGTAAAAGGGTACATCAGGTTT 58.925 41.667 0.00 0.00 35.53 3.27
3376 3383 4.094590 GCAATATCCACATATCAGAGCTGC 59.905 45.833 0.00 0.00 0.00 5.25
3466 3473 7.624360 TTAATACAGAAAAGGCCAGTACATG 57.376 36.000 5.01 0.00 0.00 3.21
3890 3939 2.358737 GACCAGTGCCTTGGGACG 60.359 66.667 5.68 1.72 42.76 4.79
4072 4122 5.567138 ACAAGTGGAGTTCAAAGAAACTG 57.433 39.130 0.00 0.00 39.55 3.16
4224 4291 8.100791 TGGTGCTCTATTTTACAAGTGAGTTAT 58.899 33.333 0.00 0.00 0.00 1.89
4444 4513 1.639298 GCATGCTGGACCGAACAGTC 61.639 60.000 11.37 0.00 38.22 3.51
4454 4523 2.171237 ACACTAGCTTATGCATGCTGGA 59.829 45.455 23.50 5.58 39.63 3.86
4475 4544 7.663905 ACTGCCATAACACTTTGTAATGAGTTA 59.336 33.333 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.