Multiple sequence alignment - TraesCS2D01G178400

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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 TraesCS2D01G178400 chr2D 100.000 2963 0 0 1 2963 122038727 122035765 0.000000e+00 5472.0
1 TraesCS2D01G178400 chr2D 93.475 1885 94 7 287 2144 532132475 532134357 0.000000e+00 2772.0
2 TraesCS2D01G178400 chr2D 97.360 303 6 2 1 302 626005742 626006043 5.660000e-142 514.0
3 TraesCS2D01G178400 chr6A 94.271 1885 79 8 287 2144 457606000 457604118 0.000000e+00 2856.0
4 TraesCS2D01G178400 chr6A 94.058 1885 85 7 287 2145 457588597 457586714 0.000000e+00 2835.0
5 TraesCS2D01G178400 chr1B 94.214 1884 82 6 287 2144 374332763 374334645 0.000000e+00 2850.0
6 TraesCS2D01G178400 chr1B 92.781 1884 108 12 287 2144 53736141 53738022 0.000000e+00 2700.0
7 TraesCS2D01G178400 chr3B 94.168 1886 82 7 287 2145 725370743 725372627 0.000000e+00 2848.0
8 TraesCS2D01G178400 chr5A 93.849 1886 87 8 287 2145 704587313 704585430 0.000000e+00 2813.0
9 TraesCS2D01G178400 chr3D 92.589 1889 103 9 287 2151 194685592 194687467 0.000000e+00 2678.0
10 TraesCS2D01G178400 chr3D 96.764 309 9 1 1 308 423493326 423493018 5.660000e-142 514.0
11 TraesCS2D01G178400 chrUn 95.309 1535 65 6 615 2145 62695869 62694338 0.000000e+00 2429.0
12 TraesCS2D01G178400 chrUn 89.203 389 19 3 287 652 62696258 62695870 5.780000e-127 464.0
13 TraesCS2D01G178400 chr2A 85.474 833 99 13 2145 2963 126476722 126475898 0.000000e+00 848.0
14 TraesCS2D01G178400 chr5D 99.310 290 2 0 1 290 304813135 304812846 2.620000e-145 525.0
15 TraesCS2D01G178400 chr5D 97.068 307 5 3 1 303 253514674 253514980 5.660000e-142 514.0
16 TraesCS2D01G178400 chr5D 98.955 287 3 0 1 287 257109254 257109540 5.660000e-142 514.0
17 TraesCS2D01G178400 chr5D 96.743 307 8 1 1 305 125883841 125883535 7.330000e-141 510.0
18 TraesCS2D01G178400 chr6D 98.644 295 4 0 1 295 83777969 83777675 9.410000e-145 523.0
19 TraesCS2D01G178400 chr4D 98.316 297 4 1 1 296 51453796 51454092 1.220000e-143 520.0
20 TraesCS2D01G178400 chr1D 97.360 303 6 2 1 301 58071571 58071269 5.660000e-142 514.0
21 TraesCS2D01G178400 chr2B 84.601 539 52 21 2433 2963 175063196 175062681 9.480000e-140 507.0
22 TraesCS2D01G178400 chr2B 90.608 181 17 0 2145 2325 175066728 175066548 1.060000e-59 241.0
23 TraesCS2D01G178400 chr2B 83.178 107 9 5 2048 2146 744184715 744184820 4.070000e-14 89.8
24 TraesCS2D01G178400 chr7A 91.667 60 5 0 2088 2147 128211634 128211575 1.890000e-12 84.2


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 TraesCS2D01G178400 chr2D 122035765 122038727 2962 True 5472.0 5472 100.0000 1 2963 1 chr2D.!!$R1 2962
1 TraesCS2D01G178400 chr2D 532132475 532134357 1882 False 2772.0 2772 93.4750 287 2144 1 chr2D.!!$F1 1857
2 TraesCS2D01G178400 chr6A 457604118 457606000 1882 True 2856.0 2856 94.2710 287 2144 1 chr6A.!!$R2 1857
3 TraesCS2D01G178400 chr6A 457586714 457588597 1883 True 2835.0 2835 94.0580 287 2145 1 chr6A.!!$R1 1858
4 TraesCS2D01G178400 chr1B 374332763 374334645 1882 False 2850.0 2850 94.2140 287 2144 1 chr1B.!!$F2 1857
5 TraesCS2D01G178400 chr1B 53736141 53738022 1881 False 2700.0 2700 92.7810 287 2144 1 chr1B.!!$F1 1857
6 TraesCS2D01G178400 chr3B 725370743 725372627 1884 False 2848.0 2848 94.1680 287 2145 1 chr3B.!!$F1 1858
7 TraesCS2D01G178400 chr5A 704585430 704587313 1883 True 2813.0 2813 93.8490 287 2145 1 chr5A.!!$R1 1858
8 TraesCS2D01G178400 chr3D 194685592 194687467 1875 False 2678.0 2678 92.5890 287 2151 1 chr3D.!!$F1 1864
9 TraesCS2D01G178400 chrUn 62694338 62696258 1920 True 1446.5 2429 92.2560 287 2145 2 chrUn.!!$R1 1858
10 TraesCS2D01G178400 chr2A 126475898 126476722 824 True 848.0 848 85.4740 2145 2963 1 chr2A.!!$R1 818
11 TraesCS2D01G178400 chr2B 175062681 175066728 4047 True 374.0 507 87.6045 2145 2963 2 chr2B.!!$R1 818

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
99 100 0.036164 TGTCCATGGTCAGGAAACCG 59.964 55.0 12.58 0.0 42.62 4.44 F
100 101 0.036306 GTCCATGGTCAGGAAACCGT 59.964 55.0 12.58 0.0 42.62 4.83 F
1331 1399 0.037326 CTAGAGTTCCGCACCAAGCA 60.037 55.0 0.00 0.0 46.13 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1381 2.054458 TGCTTGGTGCGGAACTCTA 58.946 52.632 0.0 0.0 46.63 2.43 R
1552 1620 3.888323 TCAAGATTAACACAAGCAGCCAA 59.112 39.130 0.0 0.0 0.00 4.52 R
2898 6298 0.174845 AGACGCTTATGCCGCTGTAA 59.825 50.000 0.0 0.0 35.36 2.41 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
21 22 4.142609 TCTTGTGCTAGGCTTAGGATTG 57.857 45.455 4.88 0.00 29.47 2.67
22 23 3.118261 TCTTGTGCTAGGCTTAGGATTGG 60.118 47.826 4.88 0.00 29.47 3.16
23 24 1.490490 TGTGCTAGGCTTAGGATTGGG 59.510 52.381 4.88 0.00 29.47 4.12
24 25 1.490910 GTGCTAGGCTTAGGATTGGGT 59.509 52.381 4.88 0.00 29.47 4.51
25 26 1.768870 TGCTAGGCTTAGGATTGGGTC 59.231 52.381 4.88 0.00 0.00 4.46
26 27 2.050918 GCTAGGCTTAGGATTGGGTCT 58.949 52.381 4.88 0.00 0.00 3.85
27 28 2.037902 GCTAGGCTTAGGATTGGGTCTC 59.962 54.545 4.88 0.00 0.00 3.36
28 29 1.123928 AGGCTTAGGATTGGGTCTCG 58.876 55.000 0.00 0.00 0.00 4.04
29 30 0.831307 GGCTTAGGATTGGGTCTCGT 59.169 55.000 0.00 0.00 0.00 4.18
30 31 1.202545 GGCTTAGGATTGGGTCTCGTC 60.203 57.143 0.00 0.00 0.00 4.20
31 32 1.202545 GCTTAGGATTGGGTCTCGTCC 60.203 57.143 0.00 0.00 0.00 4.79
32 33 2.108168 CTTAGGATTGGGTCTCGTCCA 58.892 52.381 0.00 0.00 33.12 4.02
33 34 2.471815 TAGGATTGGGTCTCGTCCAT 57.528 50.000 0.00 0.00 33.82 3.41
34 35 1.123928 AGGATTGGGTCTCGTCCATC 58.876 55.000 0.00 0.00 33.82 3.51
35 36 0.830648 GGATTGGGTCTCGTCCATCA 59.169 55.000 0.00 0.00 33.82 3.07
36 37 1.473434 GGATTGGGTCTCGTCCATCAC 60.473 57.143 0.00 0.00 33.82 3.06
37 38 1.207089 GATTGGGTCTCGTCCATCACA 59.793 52.381 0.00 0.00 33.82 3.58
38 39 1.275666 TTGGGTCTCGTCCATCACAT 58.724 50.000 0.00 0.00 33.82 3.21
39 40 0.824109 TGGGTCTCGTCCATCACATC 59.176 55.000 0.00 0.00 0.00 3.06
40 41 0.824109 GGGTCTCGTCCATCACATCA 59.176 55.000 0.00 0.00 0.00 3.07
41 42 1.414181 GGGTCTCGTCCATCACATCAT 59.586 52.381 0.00 0.00 0.00 2.45
42 43 2.158900 GGGTCTCGTCCATCACATCATT 60.159 50.000 0.00 0.00 0.00 2.57
43 44 3.126831 GGTCTCGTCCATCACATCATTC 58.873 50.000 0.00 0.00 0.00 2.67
44 45 3.181471 GGTCTCGTCCATCACATCATTCT 60.181 47.826 0.00 0.00 0.00 2.40
45 46 4.047822 GTCTCGTCCATCACATCATTCTC 58.952 47.826 0.00 0.00 0.00 2.87
46 47 3.068732 TCTCGTCCATCACATCATTCTCC 59.931 47.826 0.00 0.00 0.00 3.71
47 48 3.033909 TCGTCCATCACATCATTCTCCT 58.966 45.455 0.00 0.00 0.00 3.69
48 49 4.215109 TCGTCCATCACATCATTCTCCTA 58.785 43.478 0.00 0.00 0.00 2.94
49 50 4.649218 TCGTCCATCACATCATTCTCCTAA 59.351 41.667 0.00 0.00 0.00 2.69
50 51 5.305386 TCGTCCATCACATCATTCTCCTAAT 59.695 40.000 0.00 0.00 0.00 1.73
51 52 5.407691 CGTCCATCACATCATTCTCCTAATG 59.592 44.000 0.00 0.00 0.00 1.90
52 53 6.528321 GTCCATCACATCATTCTCCTAATGA 58.472 40.000 3.13 3.13 40.50 2.57
53 54 7.166851 GTCCATCACATCATTCTCCTAATGAT 58.833 38.462 7.28 7.28 45.40 2.45
61 62 6.119240 TCATTCTCCTAATGATGTGATCCC 57.881 41.667 0.00 0.00 32.21 3.85
62 63 4.607293 TTCTCCTAATGATGTGATCCCG 57.393 45.455 0.00 0.00 0.00 5.14
63 64 3.576861 TCTCCTAATGATGTGATCCCGT 58.423 45.455 0.00 0.00 0.00 5.28
64 65 3.967326 TCTCCTAATGATGTGATCCCGTT 59.033 43.478 0.00 0.00 0.00 4.44
65 66 5.144832 TCTCCTAATGATGTGATCCCGTTA 58.855 41.667 0.00 0.00 0.00 3.18
66 67 5.780282 TCTCCTAATGATGTGATCCCGTTAT 59.220 40.000 0.00 0.00 0.00 1.89
67 68 6.037786 TCCTAATGATGTGATCCCGTTATC 57.962 41.667 0.00 0.00 0.00 1.75
68 69 5.542251 TCCTAATGATGTGATCCCGTTATCA 59.458 40.000 0.00 0.00 33.48 2.15
69 70 6.042666 TCCTAATGATGTGATCCCGTTATCAA 59.957 38.462 0.00 0.00 37.61 2.57
70 71 6.147821 CCTAATGATGTGATCCCGTTATCAAC 59.852 42.308 0.00 0.00 37.61 3.18
92 93 3.008835 ACATCCAATGTCCATGGTCAG 57.991 47.619 16.79 4.75 39.92 3.51
93 94 2.304092 CATCCAATGTCCATGGTCAGG 58.696 52.381 16.79 13.14 39.09 3.86
94 95 1.667595 TCCAATGTCCATGGTCAGGA 58.332 50.000 16.79 15.06 39.09 3.86
95 96 1.991813 TCCAATGTCCATGGTCAGGAA 59.008 47.619 16.79 0.75 39.09 3.36
96 97 2.378208 TCCAATGTCCATGGTCAGGAAA 59.622 45.455 16.79 1.08 39.09 3.13
97 98 2.493278 CCAATGTCCATGGTCAGGAAAC 59.507 50.000 16.79 4.30 36.80 2.78
98 99 2.493278 CAATGTCCATGGTCAGGAAACC 59.507 50.000 16.79 0.00 36.80 3.27
99 100 0.036164 TGTCCATGGTCAGGAAACCG 59.964 55.000 12.58 0.00 42.62 4.44
100 101 0.036306 GTCCATGGTCAGGAAACCGT 59.964 55.000 12.58 0.00 42.62 4.83
101 102 1.276989 GTCCATGGTCAGGAAACCGTA 59.723 52.381 12.58 0.00 42.62 4.02
102 103 1.979308 TCCATGGTCAGGAAACCGTAA 59.021 47.619 12.58 0.00 42.62 3.18
103 104 2.081462 CCATGGTCAGGAAACCGTAAC 58.919 52.381 2.57 0.00 42.62 2.50
104 105 2.081462 CATGGTCAGGAAACCGTAACC 58.919 52.381 0.00 0.00 42.62 2.85
105 106 1.129917 TGGTCAGGAAACCGTAACCA 58.870 50.000 0.00 0.00 42.62 3.67
106 107 1.700739 TGGTCAGGAAACCGTAACCAT 59.299 47.619 0.00 0.00 42.62 3.55
107 108 2.289819 TGGTCAGGAAACCGTAACCATC 60.290 50.000 0.00 0.00 42.62 3.51
108 109 2.027469 GGTCAGGAAACCGTAACCATCT 60.027 50.000 0.00 0.00 0.00 2.90
109 110 3.196254 GGTCAGGAAACCGTAACCATCTA 59.804 47.826 0.00 0.00 0.00 1.98
110 111 4.141779 GGTCAGGAAACCGTAACCATCTAT 60.142 45.833 0.00 0.00 0.00 1.98
111 112 5.425630 GTCAGGAAACCGTAACCATCTATT 58.574 41.667 0.00 0.00 0.00 1.73
112 113 5.293569 GTCAGGAAACCGTAACCATCTATTG 59.706 44.000 0.00 0.00 0.00 1.90
113 114 5.188163 TCAGGAAACCGTAACCATCTATTGA 59.812 40.000 0.00 0.00 0.00 2.57
114 115 6.055588 CAGGAAACCGTAACCATCTATTGAT 58.944 40.000 0.00 0.00 0.00 2.57
115 116 6.202954 CAGGAAACCGTAACCATCTATTGATC 59.797 42.308 0.00 0.00 0.00 2.92
116 117 6.053005 GGAAACCGTAACCATCTATTGATCA 58.947 40.000 0.00 0.00 0.00 2.92
117 118 6.540914 GGAAACCGTAACCATCTATTGATCAA 59.459 38.462 11.26 11.26 0.00 2.57
118 119 6.920569 AACCGTAACCATCTATTGATCAAC 57.079 37.500 11.07 0.00 0.00 3.18
119 120 5.047847 ACCGTAACCATCTATTGATCAACG 58.952 41.667 11.07 6.28 0.00 4.10
120 121 5.163488 ACCGTAACCATCTATTGATCAACGA 60.163 40.000 11.07 10.80 0.00 3.85
121 122 5.402568 CCGTAACCATCTATTGATCAACGAG 59.597 44.000 11.07 11.28 0.00 4.18
122 123 5.107837 CGTAACCATCTATTGATCAACGAGC 60.108 44.000 11.07 0.00 0.00 5.03
123 124 4.679373 ACCATCTATTGATCAACGAGCT 57.321 40.909 11.07 0.00 0.00 4.09
124 125 5.791336 ACCATCTATTGATCAACGAGCTA 57.209 39.130 11.07 0.00 0.00 3.32
125 126 5.777802 ACCATCTATTGATCAACGAGCTAG 58.222 41.667 11.07 8.38 0.00 3.42
126 127 5.303078 ACCATCTATTGATCAACGAGCTAGT 59.697 40.000 11.07 6.23 0.00 2.57
127 128 5.861251 CCATCTATTGATCAACGAGCTAGTC 59.139 44.000 11.07 0.00 0.00 2.59
128 129 6.442112 CATCTATTGATCAACGAGCTAGTCA 58.558 40.000 11.07 0.00 0.00 3.41
129 130 6.451064 TCTATTGATCAACGAGCTAGTCAA 57.549 37.500 11.07 0.55 0.00 3.18
130 131 6.266323 TCTATTGATCAACGAGCTAGTCAAC 58.734 40.000 11.07 0.00 0.00 3.18
131 132 4.521130 TTGATCAACGAGCTAGTCAACT 57.479 40.909 3.38 0.00 0.00 3.16
132 133 5.638596 TTGATCAACGAGCTAGTCAACTA 57.361 39.130 3.38 0.00 0.00 2.24
133 134 5.236655 TGATCAACGAGCTAGTCAACTAG 57.763 43.478 11.99 11.99 46.63 2.57
134 135 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
135 136 4.948608 TCAACGAGCTAGTCAACTAGAG 57.051 45.455 19.03 11.89 46.80 2.43
136 137 3.690139 TCAACGAGCTAGTCAACTAGAGG 59.310 47.826 19.03 10.05 46.80 3.69
137 138 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
138 139 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
139 140 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
140 141 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
141 142 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
142 143 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
143 144 4.642885 AGCTAGTCAACTAGAGGCTTACTG 59.357 45.833 19.03 0.00 46.80 2.74
144 145 4.202070 GCTAGTCAACTAGAGGCTTACTGG 60.202 50.000 19.03 0.00 46.80 4.00
145 146 3.100671 AGTCAACTAGAGGCTTACTGGG 58.899 50.000 0.00 0.00 0.00 4.45
146 147 2.168728 GTCAACTAGAGGCTTACTGGGG 59.831 54.545 0.00 0.00 0.00 4.96
147 148 2.043939 TCAACTAGAGGCTTACTGGGGA 59.956 50.000 0.00 0.00 0.00 4.81
148 149 2.162264 ACTAGAGGCTTACTGGGGAC 57.838 55.000 0.00 0.00 0.00 4.46
149 150 1.361543 ACTAGAGGCTTACTGGGGACA 59.638 52.381 0.00 0.00 39.59 4.02
150 151 2.022918 ACTAGAGGCTTACTGGGGACAT 60.023 50.000 0.00 0.00 41.51 3.06
151 152 1.207791 AGAGGCTTACTGGGGACATG 58.792 55.000 0.00 0.00 41.51 3.21
152 153 0.181350 GAGGCTTACTGGGGACATGG 59.819 60.000 0.00 0.00 41.51 3.66
153 154 0.550147 AGGCTTACTGGGGACATGGT 60.550 55.000 0.00 0.00 41.51 3.55
154 155 0.394352 GGCTTACTGGGGACATGGTG 60.394 60.000 0.00 0.00 41.51 4.17
155 156 0.328258 GCTTACTGGGGACATGGTGT 59.672 55.000 0.00 0.00 41.51 4.16
156 157 1.271926 GCTTACTGGGGACATGGTGTT 60.272 52.381 0.00 0.00 41.51 3.32
157 158 2.436417 CTTACTGGGGACATGGTGTTG 58.564 52.381 0.00 0.00 41.51 3.33
158 159 1.440618 TACTGGGGACATGGTGTTGT 58.559 50.000 0.00 0.00 41.51 3.32
159 160 0.110486 ACTGGGGACATGGTGTTGTC 59.890 55.000 0.00 0.00 44.27 3.18
160 161 0.401738 CTGGGGACATGGTGTTGTCT 59.598 55.000 0.00 0.00 44.39 3.41
161 162 1.628340 CTGGGGACATGGTGTTGTCTA 59.372 52.381 0.00 0.00 44.39 2.59
162 163 2.239654 CTGGGGACATGGTGTTGTCTAT 59.760 50.000 0.00 0.00 44.39 1.98
163 164 2.026356 TGGGGACATGGTGTTGTCTATG 60.026 50.000 0.00 0.00 44.39 2.23
164 165 2.017049 GGGACATGGTGTTGTCTATGC 58.983 52.381 0.00 0.00 44.39 3.14
165 166 2.617788 GGGACATGGTGTTGTCTATGCA 60.618 50.000 0.00 0.00 44.39 3.96
166 167 3.282021 GGACATGGTGTTGTCTATGCAT 58.718 45.455 3.79 3.79 44.39 3.96
167 168 3.313526 GGACATGGTGTTGTCTATGCATC 59.686 47.826 0.19 0.00 44.39 3.91
168 169 3.282021 ACATGGTGTTGTCTATGCATCC 58.718 45.455 0.19 0.00 0.00 3.51
169 170 3.281158 CATGGTGTTGTCTATGCATCCA 58.719 45.455 0.19 1.54 0.00 3.41
170 171 2.710377 TGGTGTTGTCTATGCATCCAC 58.290 47.619 0.19 1.15 0.00 4.02
171 172 2.039613 TGGTGTTGTCTATGCATCCACA 59.960 45.455 0.19 4.28 0.00 4.17
172 173 2.420022 GGTGTTGTCTATGCATCCACAC 59.580 50.000 0.19 7.55 0.00 3.82
173 174 3.073678 GTGTTGTCTATGCATCCACACA 58.926 45.455 0.19 5.90 0.00 3.72
174 175 3.691118 GTGTTGTCTATGCATCCACACAT 59.309 43.478 0.19 0.00 0.00 3.21
175 176 3.690628 TGTTGTCTATGCATCCACACATG 59.309 43.478 0.19 0.00 0.00 3.21
176 177 3.632643 TGTCTATGCATCCACACATGT 57.367 42.857 0.19 0.00 0.00 3.21
177 178 4.751767 TGTCTATGCATCCACACATGTA 57.248 40.909 0.19 0.00 0.00 2.29
178 179 5.294734 TGTCTATGCATCCACACATGTAT 57.705 39.130 0.19 0.00 34.00 2.29
179 180 5.299949 TGTCTATGCATCCACACATGTATC 58.700 41.667 0.19 0.00 32.10 2.24
180 181 5.070847 TGTCTATGCATCCACACATGTATCT 59.929 40.000 0.19 0.00 32.10 1.98
181 182 5.407691 GTCTATGCATCCACACATGTATCTG 59.592 44.000 0.19 0.00 32.10 2.90
182 183 3.910568 TGCATCCACACATGTATCTGA 57.089 42.857 0.00 0.00 0.00 3.27
183 184 3.800531 TGCATCCACACATGTATCTGAG 58.199 45.455 0.00 0.00 0.00 3.35
184 185 3.198417 TGCATCCACACATGTATCTGAGT 59.802 43.478 0.00 0.00 0.00 3.41
185 186 4.194640 GCATCCACACATGTATCTGAGTT 58.805 43.478 0.00 0.00 0.00 3.01
186 187 4.637534 GCATCCACACATGTATCTGAGTTT 59.362 41.667 0.00 0.00 0.00 2.66
187 188 5.220739 GCATCCACACATGTATCTGAGTTTC 60.221 44.000 0.00 0.00 0.00 2.78
188 189 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
189 190 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
190 191 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
191 192 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
192 193 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
193 194 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
194 195 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
195 196 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
196 197 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
197 198 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
198 199 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
206 207 9.547753 TGAGTTTCCTATCAATACAATTCTAGC 57.452 33.333 0.00 0.00 0.00 3.42
207 208 9.547753 GAGTTTCCTATCAATACAATTCTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
210 211 8.853077 TTCCTATCAATACAATTCTAGCATGG 57.147 34.615 0.00 0.00 0.00 3.66
211 212 8.206126 TCCTATCAATACAATTCTAGCATGGA 57.794 34.615 0.00 0.00 0.00 3.41
212 213 8.829746 TCCTATCAATACAATTCTAGCATGGAT 58.170 33.333 0.00 0.00 0.00 3.41
221 222 8.902540 ACAATTCTAGCATGGATAATAAACGA 57.097 30.769 0.00 0.00 0.00 3.85
222 223 9.507329 ACAATTCTAGCATGGATAATAAACGAT 57.493 29.630 0.00 0.00 0.00 3.73
324 325 4.210331 CAATGGGAATTTCCTAGGACTGG 58.790 47.826 12.22 0.00 36.57 4.00
330 331 5.510430 GGAATTTCCTAGGACTGGTTGAAT 58.490 41.667 12.22 3.74 32.53 2.57
394 396 5.360714 ACCGCATCACCAATGATAAAATTCT 59.639 36.000 0.00 0.00 44.13 2.40
455 457 6.764308 ATAAATATGCTCGCTATTGCCATT 57.236 33.333 0.00 0.00 35.36 3.16
456 458 4.691860 AATATGCTCGCTATTGCCATTC 57.308 40.909 0.00 0.00 35.36 2.67
461 463 0.464036 TCGCTATTGCCATTCGGTCT 59.536 50.000 0.00 0.00 35.36 3.85
539 541 0.809385 CTGATGCAAGCCACCAAGAG 59.191 55.000 0.00 0.00 0.00 2.85
542 544 1.248785 ATGCAAGCCACCAAGAGCAG 61.249 55.000 0.00 0.00 35.26 4.24
546 548 0.964358 AAGCCACCAAGAGCAGATGC 60.964 55.000 0.00 0.00 42.49 3.91
559 561 7.039923 CCAAGAGCAGATGCCTTTGATAATTAT 60.040 37.037 16.17 0.00 43.38 1.28
563 565 8.332996 AGCAGATGCCTTTGATAATTATGTAG 57.667 34.615 1.78 0.00 43.38 2.74
564 566 8.159447 AGCAGATGCCTTTGATAATTATGTAGA 58.841 33.333 1.78 0.00 43.38 2.59
582 607 7.798596 ATGTAGATGCATCGAAGAATCTTTT 57.201 32.000 16.02 1.63 43.58 2.27
620 646 2.301346 GAATGATACCACTGGGCAAGG 58.699 52.381 0.00 0.00 37.90 3.61
639 665 7.084486 GGCAAGGTTTGTTTAATGTTCTAGAG 58.916 38.462 0.00 0.00 0.00 2.43
750 815 8.499288 AAGGGGTACAAAATAAATTTCTGGAA 57.501 30.769 0.00 0.00 0.00 3.53
808 873 5.664457 TGTCATAGTCTAAATCTGGCACTG 58.336 41.667 0.00 0.00 0.00 3.66
854 919 4.376340 AAAGCAACACACTTCTTTGGAG 57.624 40.909 0.00 0.00 0.00 3.86
1034 1100 2.305052 GGGAGGCTTTACTACAAGTGGT 59.695 50.000 0.00 0.00 0.00 4.16
1111 1177 6.923928 ATGAACTTGGTGGTTTTGAATTTG 57.076 33.333 0.00 0.00 0.00 2.32
1230 1296 4.353777 AGTCTATACAGGGTCTGCTTTCA 58.646 43.478 0.00 0.00 34.37 2.69
1277 1344 3.058708 GGCTTTTCAAAAGCATTGGAAGC 60.059 43.478 31.07 21.67 44.71 3.86
1331 1399 0.037326 CTAGAGTTCCGCACCAAGCA 60.037 55.000 0.00 0.00 46.13 3.91
1429 1497 8.971073 AGTCATTTAGGGTCAATTATTTTCTGG 58.029 33.333 0.00 0.00 0.00 3.86
1484 1552 3.782523 AGGAGGTTTGAGCAATATCAGGA 59.217 43.478 0.00 0.00 0.00 3.86
1540 1608 2.533266 TAGGCTGCGATCTTTGGATC 57.467 50.000 0.00 0.00 43.48 3.36
1552 1620 6.037610 GCGATCTTTGGATCATAAGAGTTTGT 59.962 38.462 12.49 0.00 46.30 2.83
1581 1649 4.439289 GCTTGTGTTAATCTTGAGGATGCC 60.439 45.833 0.00 0.00 34.45 4.40
1673 1741 7.724061 GGATTTAGTTAAGAAATCTATGGGCCA 59.276 37.037 9.61 9.61 41.22 5.36
1674 1742 9.301897 GATTTAGTTAAGAAATCTATGGGCCAT 57.698 33.333 24.69 24.69 39.29 4.40
1762 1830 9.016438 GGATTTTGTTAACCATTCCTGTAACTA 57.984 33.333 2.48 0.00 0.00 2.24
1809 1877 8.154649 TCTCTAAACTCAAGTTGTTGAAATCC 57.845 34.615 2.11 0.00 42.27 3.01
1854 1922 3.565307 AGAAAGACTCAATGGTTTGGCA 58.435 40.909 0.00 0.00 33.44 4.92
1958 2027 4.631813 ACGGATGACACTTTTCAATAGAGC 59.368 41.667 0.00 0.00 0.00 4.09
2071 2140 8.668353 CATAATTAGGTGATTATGCTTGCGTAT 58.332 33.333 5.09 0.00 40.86 3.06
2075 2144 3.730715 GGTGATTATGCTTGCGTATTTGC 59.269 43.478 0.00 0.00 0.00 3.68
2078 2147 5.459762 GTGATTATGCTTGCGTATTTGCATT 59.540 36.000 12.43 0.00 45.78 3.56
2119 2192 0.752376 TTTTCTTTTCGCACCGGGGT 60.752 50.000 5.12 0.00 0.00 4.95
2179 2252 0.173708 CTAGGACCTCCAAGTCGTGC 59.826 60.000 0.00 0.00 37.66 5.34
2216 2289 2.367241 TCCCAACAGAAGAACGACATCA 59.633 45.455 0.00 0.00 0.00 3.07
2221 2294 4.543590 ACAGAAGAACGACATCAAGGAT 57.456 40.909 0.00 0.00 0.00 3.24
2224 2297 2.029838 AGAACGACATCAAGGATGCC 57.970 50.000 6.15 0.00 43.15 4.40
2285 2358 5.059161 CAGAGACAACCAATCAAGTGAGAA 58.941 41.667 0.00 0.00 0.00 2.87
2297 2398 3.706594 TCAAGTGAGAAAGAGTGAGGTGT 59.293 43.478 0.00 0.00 0.00 4.16
2312 2413 1.520564 GTGTCGACACACCACAGCA 60.521 57.895 37.16 2.18 46.49 4.41
2315 2416 1.087202 GTCGACACACCACAGCAACA 61.087 55.000 11.55 0.00 0.00 3.33
2316 2417 0.179059 TCGACACACCACAGCAACAT 60.179 50.000 0.00 0.00 0.00 2.71
2317 2418 0.235665 CGACACACCACAGCAACATC 59.764 55.000 0.00 0.00 0.00 3.06
2318 2419 1.597742 GACACACCACAGCAACATCT 58.402 50.000 0.00 0.00 0.00 2.90
2319 2420 1.532868 GACACACCACAGCAACATCTC 59.467 52.381 0.00 0.00 0.00 2.75
2320 2421 0.877071 CACACCACAGCAACATCTCC 59.123 55.000 0.00 0.00 0.00 3.71
2321 2422 0.473755 ACACCACAGCAACATCTCCA 59.526 50.000 0.00 0.00 0.00 3.86
2322 2423 1.133823 ACACCACAGCAACATCTCCAA 60.134 47.619 0.00 0.00 0.00 3.53
2323 2424 1.538512 CACCACAGCAACATCTCCAAG 59.461 52.381 0.00 0.00 0.00 3.61
2324 2425 1.171308 CCACAGCAACATCTCCAAGG 58.829 55.000 0.00 0.00 0.00 3.61
2325 2426 0.524862 CACAGCAACATCTCCAAGGC 59.475 55.000 0.00 0.00 0.00 4.35
2326 2427 0.957395 ACAGCAACATCTCCAAGGCG 60.957 55.000 0.00 0.00 0.00 5.52
2327 2428 2.042831 AGCAACATCTCCAAGGCGC 61.043 57.895 0.00 0.00 0.00 6.53
2328 2429 2.042831 GCAACATCTCCAAGGCGCT 61.043 57.895 7.64 0.00 0.00 5.92
2329 2430 0.744414 GCAACATCTCCAAGGCGCTA 60.744 55.000 7.64 0.00 0.00 4.26
2330 2431 1.959042 CAACATCTCCAAGGCGCTAT 58.041 50.000 7.64 0.00 0.00 2.97
2331 2432 1.869767 CAACATCTCCAAGGCGCTATC 59.130 52.381 7.64 0.00 0.00 2.08
2332 2433 1.418334 ACATCTCCAAGGCGCTATCT 58.582 50.000 7.64 0.00 0.00 1.98
2333 2434 1.342819 ACATCTCCAAGGCGCTATCTC 59.657 52.381 7.64 0.00 0.00 2.75
2334 2435 0.972883 ATCTCCAAGGCGCTATCTCC 59.027 55.000 7.64 0.00 0.00 3.71
2335 2436 0.397114 TCTCCAAGGCGCTATCTCCA 60.397 55.000 7.64 0.00 0.00 3.86
2336 2437 0.465705 CTCCAAGGCGCTATCTCCAA 59.534 55.000 7.64 0.00 0.00 3.53
2337 2438 0.908910 TCCAAGGCGCTATCTCCAAA 59.091 50.000 7.64 0.00 0.00 3.28
2338 2439 1.280710 TCCAAGGCGCTATCTCCAAAA 59.719 47.619 7.64 0.00 0.00 2.44
2339 2440 2.091541 CCAAGGCGCTATCTCCAAAAA 58.908 47.619 7.64 0.00 0.00 1.94
2416 2517 1.446907 CAGCCAAAGACGAGCAAGAT 58.553 50.000 0.00 0.00 0.00 2.40
2439 2540 4.497473 TTCATCCGAATTGTCACAAACC 57.503 40.909 0.00 0.00 0.00 3.27
2440 2541 3.750371 TCATCCGAATTGTCACAAACCT 58.250 40.909 0.00 0.00 0.00 3.50
2460 5839 1.355718 ATCCCTGCCCATCGGAATGT 61.356 55.000 0.00 0.00 0.00 2.71
2486 5865 7.290014 TGGTACACCATCATTAGACATGATACT 59.710 37.037 0.00 0.00 42.01 2.12
2487 5866 8.150945 GGTACACCATCATTAGACATGATACTT 58.849 37.037 0.00 0.00 36.69 2.24
2611 6001 1.132453 CACTCGTCCTTACATCTCGCA 59.868 52.381 0.00 0.00 0.00 5.10
2621 6011 4.438336 CCTTACATCTCGCAACGAACTCTA 60.438 45.833 0.00 0.00 34.74 2.43
2629 6019 2.673043 CGCAACGAACTCTAAAGCCCTA 60.673 50.000 0.00 0.00 0.00 3.53
2641 6031 4.733542 GCCCTAAGCCGCCACCAA 62.734 66.667 0.00 0.00 34.35 3.67
2670 6060 2.979676 CGCTGCTGCCAAAGTCCA 60.980 61.111 10.24 0.00 35.36 4.02
2673 6063 1.798735 CTGCTGCCAAAGTCCATCG 59.201 57.895 0.00 0.00 0.00 3.84
2676 6066 0.955428 GCTGCCAAAGTCCATCGTCA 60.955 55.000 0.00 0.00 0.00 4.35
2694 6084 0.106335 CAAGCAAAACCCATGTGGCA 59.894 50.000 0.00 0.00 37.83 4.92
2717 6115 1.153369 CGGTGCGGGATGATCTGTT 60.153 57.895 0.00 0.00 0.00 3.16
2762 6160 2.203056 CCGGATGCGGCAGATCAA 60.203 61.111 14.38 0.00 0.00 2.57
2765 6163 2.550101 GGATGCGGCAGATCAAGGC 61.550 63.158 9.25 0.00 0.00 4.35
2771 6169 1.300963 GGCAGATCAAGGCTGGTGA 59.699 57.895 0.00 0.00 34.00 4.02
2772 6170 0.106819 GGCAGATCAAGGCTGGTGAT 60.107 55.000 1.34 1.34 38.44 3.06
2783 6181 1.668419 GCTGGTGATAGCGGTTGATT 58.332 50.000 0.00 0.00 33.46 2.57
2795 6193 1.721489 CGGTTGATTTGTGTTCGAGCG 60.721 52.381 0.00 0.00 40.73 5.03
2818 6216 1.610624 GGCAATTCTCAACCGAGGACA 60.611 52.381 0.00 0.00 39.95 4.02
2829 6227 1.153823 CGAGGACACTTACAGGCGG 60.154 63.158 0.00 0.00 0.00 6.13
2898 6298 1.849039 ACCTCTGGCTCATATTTGGCT 59.151 47.619 0.00 0.00 0.00 4.75
2905 6305 2.031682 GGCTCATATTTGGCTTACAGCG 60.032 50.000 0.00 0.00 43.62 5.18
2911 6311 1.827681 TTTGGCTTACAGCGGCATAA 58.172 45.000 1.45 0.00 43.62 1.90
2925 6325 2.351350 CGGCATAAGCGTCTTGGTTTTT 60.351 45.455 2.86 0.00 43.41 1.94
2942 6342 9.549078 CTTGGTTTTTATTTAGCCTGGTTTTAA 57.451 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.118261 CCAATCCTAAGCCTAGCACAAGA 60.118 47.826 0.00 0.00 0.00 3.02
1 2 3.209410 CCAATCCTAAGCCTAGCACAAG 58.791 50.000 0.00 0.00 0.00 3.16
2 3 2.092429 CCCAATCCTAAGCCTAGCACAA 60.092 50.000 0.00 0.00 0.00 3.33
3 4 1.490490 CCCAATCCTAAGCCTAGCACA 59.510 52.381 0.00 0.00 0.00 4.57
4 5 1.490910 ACCCAATCCTAAGCCTAGCAC 59.509 52.381 0.00 0.00 0.00 4.40
5 6 1.768870 GACCCAATCCTAAGCCTAGCA 59.231 52.381 0.00 0.00 0.00 3.49
6 7 2.037902 GAGACCCAATCCTAAGCCTAGC 59.962 54.545 0.00 0.00 0.00 3.42
7 8 2.297597 CGAGACCCAATCCTAAGCCTAG 59.702 54.545 0.00 0.00 0.00 3.02
8 9 2.317040 CGAGACCCAATCCTAAGCCTA 58.683 52.381 0.00 0.00 0.00 3.93
9 10 1.123928 CGAGACCCAATCCTAAGCCT 58.876 55.000 0.00 0.00 0.00 4.58
10 11 0.831307 ACGAGACCCAATCCTAAGCC 59.169 55.000 0.00 0.00 0.00 4.35
11 12 1.202545 GGACGAGACCCAATCCTAAGC 60.203 57.143 0.00 0.00 0.00 3.09
12 13 2.108168 TGGACGAGACCCAATCCTAAG 58.892 52.381 0.00 0.00 32.06 2.18
13 14 2.241281 TGGACGAGACCCAATCCTAA 57.759 50.000 0.00 0.00 32.06 2.69
14 15 2.317040 GATGGACGAGACCCAATCCTA 58.683 52.381 0.00 0.00 37.22 2.94
15 16 1.123928 GATGGACGAGACCCAATCCT 58.876 55.000 0.00 0.00 37.22 3.24
16 17 0.830648 TGATGGACGAGACCCAATCC 59.169 55.000 0.00 0.00 37.22 3.01
17 18 1.207089 TGTGATGGACGAGACCCAATC 59.793 52.381 0.00 0.00 37.22 2.67
18 19 1.275666 TGTGATGGACGAGACCCAAT 58.724 50.000 0.00 0.00 37.22 3.16
19 20 1.207089 GATGTGATGGACGAGACCCAA 59.793 52.381 0.00 0.00 37.22 4.12
20 21 0.824109 GATGTGATGGACGAGACCCA 59.176 55.000 0.00 0.00 38.19 4.51
21 22 0.824109 TGATGTGATGGACGAGACCC 59.176 55.000 0.00 0.00 0.00 4.46
22 23 2.898729 ATGATGTGATGGACGAGACC 57.101 50.000 0.00 0.00 0.00 3.85
23 24 4.047822 GAGAATGATGTGATGGACGAGAC 58.952 47.826 0.00 0.00 0.00 3.36
24 25 3.068732 GGAGAATGATGTGATGGACGAGA 59.931 47.826 0.00 0.00 0.00 4.04
25 26 3.069300 AGGAGAATGATGTGATGGACGAG 59.931 47.826 0.00 0.00 0.00 4.18
26 27 3.033909 AGGAGAATGATGTGATGGACGA 58.966 45.455 0.00 0.00 0.00 4.20
27 28 3.465742 AGGAGAATGATGTGATGGACG 57.534 47.619 0.00 0.00 0.00 4.79
28 29 6.528321 TCATTAGGAGAATGATGTGATGGAC 58.472 40.000 0.00 0.00 32.21 4.02
29 30 6.752285 TCATTAGGAGAATGATGTGATGGA 57.248 37.500 0.00 0.00 32.21 3.41
37 38 6.575847 CGGGATCACATCATTAGGAGAATGAT 60.576 42.308 6.90 6.90 45.40 2.45
38 39 5.279657 CGGGATCACATCATTAGGAGAATGA 60.280 44.000 0.00 2.66 40.50 2.57
39 40 4.934001 CGGGATCACATCATTAGGAGAATG 59.066 45.833 0.00 0.00 0.00 2.67
40 41 4.594920 ACGGGATCACATCATTAGGAGAAT 59.405 41.667 0.00 0.00 0.00 2.40
41 42 3.967326 ACGGGATCACATCATTAGGAGAA 59.033 43.478 0.00 0.00 0.00 2.87
42 43 3.576861 ACGGGATCACATCATTAGGAGA 58.423 45.455 0.00 0.00 0.00 3.71
43 44 4.342862 AACGGGATCACATCATTAGGAG 57.657 45.455 0.00 0.00 0.00 3.69
44 45 5.542251 TGATAACGGGATCACATCATTAGGA 59.458 40.000 0.00 0.00 30.75 2.94
45 46 5.793817 TGATAACGGGATCACATCATTAGG 58.206 41.667 0.00 0.00 30.75 2.69
46 47 7.121974 GTTGATAACGGGATCACATCATTAG 57.878 40.000 0.00 0.00 35.56 1.73
73 74 2.092267 TCCTGACCATGGACATTGGATG 60.092 50.000 21.47 5.31 0.00 3.51
74 75 2.207988 TCCTGACCATGGACATTGGAT 58.792 47.619 21.47 0.00 0.00 3.41
75 76 1.667595 TCCTGACCATGGACATTGGA 58.332 50.000 21.47 18.93 0.00 3.53
76 77 2.493278 GTTTCCTGACCATGGACATTGG 59.507 50.000 21.47 16.85 32.65 3.16
77 78 2.493278 GGTTTCCTGACCATGGACATTG 59.507 50.000 21.47 12.72 39.57 2.82
78 79 2.807676 GGTTTCCTGACCATGGACATT 58.192 47.619 21.47 0.00 39.57 2.71
79 80 1.340017 CGGTTTCCTGACCATGGACAT 60.340 52.381 21.47 0.00 39.78 3.06
80 81 0.036164 CGGTTTCCTGACCATGGACA 59.964 55.000 21.47 18.47 39.78 4.02
81 82 0.036306 ACGGTTTCCTGACCATGGAC 59.964 55.000 21.47 13.94 39.78 4.02
82 83 1.646912 TACGGTTTCCTGACCATGGA 58.353 50.000 21.47 0.00 39.78 3.41
83 84 2.081462 GTTACGGTTTCCTGACCATGG 58.919 52.381 11.19 11.19 39.78 3.66
84 85 2.081462 GGTTACGGTTTCCTGACCATG 58.919 52.381 0.00 0.00 39.78 3.66
85 86 1.700739 TGGTTACGGTTTCCTGACCAT 59.299 47.619 0.00 0.00 39.78 3.55
86 87 1.129917 TGGTTACGGTTTCCTGACCA 58.870 50.000 0.00 0.00 39.78 4.02
87 88 2.027469 AGATGGTTACGGTTTCCTGACC 60.027 50.000 0.00 0.00 36.31 4.02
88 89 3.329929 AGATGGTTACGGTTTCCTGAC 57.670 47.619 0.00 0.00 0.00 3.51
89 90 5.188163 TCAATAGATGGTTACGGTTTCCTGA 59.812 40.000 0.00 0.00 0.00 3.86
90 91 5.424757 TCAATAGATGGTTACGGTTTCCTG 58.575 41.667 0.00 0.00 0.00 3.86
91 92 5.687166 TCAATAGATGGTTACGGTTTCCT 57.313 39.130 0.00 0.00 0.00 3.36
92 93 6.053005 TGATCAATAGATGGTTACGGTTTCC 58.947 40.000 0.00 0.00 33.72 3.13
93 94 7.407337 GTTGATCAATAGATGGTTACGGTTTC 58.593 38.462 12.12 0.00 33.72 2.78
94 95 6.036735 CGTTGATCAATAGATGGTTACGGTTT 59.963 38.462 12.12 0.00 33.72 3.27
95 96 5.522460 CGTTGATCAATAGATGGTTACGGTT 59.478 40.000 12.12 0.00 33.72 4.44
96 97 5.047847 CGTTGATCAATAGATGGTTACGGT 58.952 41.667 12.12 0.00 33.72 4.83
97 98 5.286438 TCGTTGATCAATAGATGGTTACGG 58.714 41.667 12.12 0.00 33.72 4.02
98 99 5.107837 GCTCGTTGATCAATAGATGGTTACG 60.108 44.000 19.51 12.22 33.72 3.18
99 100 5.986135 AGCTCGTTGATCAATAGATGGTTAC 59.014 40.000 19.51 1.79 33.72 2.50
100 101 6.161855 AGCTCGTTGATCAATAGATGGTTA 57.838 37.500 19.51 0.00 33.72 2.85
101 102 5.028549 AGCTCGTTGATCAATAGATGGTT 57.971 39.130 19.51 6.05 33.72 3.67
102 103 4.679373 AGCTCGTTGATCAATAGATGGT 57.321 40.909 19.51 14.02 33.72 3.55
103 104 5.777802 ACTAGCTCGTTGATCAATAGATGG 58.222 41.667 19.51 17.62 33.72 3.51
104 105 6.442112 TGACTAGCTCGTTGATCAATAGATG 58.558 40.000 19.51 12.48 33.72 2.90
105 106 6.641169 TGACTAGCTCGTTGATCAATAGAT 57.359 37.500 19.51 16.66 37.13 1.98
106 107 6.095580 AGTTGACTAGCTCGTTGATCAATAGA 59.904 38.462 19.51 16.55 0.00 1.98
107 108 6.269315 AGTTGACTAGCTCGTTGATCAATAG 58.731 40.000 12.12 13.07 0.00 1.73
108 109 6.208988 AGTTGACTAGCTCGTTGATCAATA 57.791 37.500 12.12 2.38 0.00 1.90
109 110 5.078411 AGTTGACTAGCTCGTTGATCAAT 57.922 39.130 12.12 0.00 0.00 2.57
110 111 4.521130 AGTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
111 112 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
112 113 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
113 114 4.336993 CCTCTAGTTGACTAGCTCGTTGAT 59.663 45.833 12.30 0.00 44.24 2.57
114 115 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
115 116 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
116 117 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
117 118 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
118 119 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
119 120 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
120 121 4.642885 CAGTAAGCCTCTAGTTGACTAGCT 59.357 45.833 12.30 5.64 44.24 3.32
121 122 4.202070 CCAGTAAGCCTCTAGTTGACTAGC 60.202 50.000 12.30 3.61 44.24 3.42
122 123 4.339814 CCCAGTAAGCCTCTAGTTGACTAG 59.660 50.000 11.14 11.14 45.57 2.57
123 124 4.279145 CCCAGTAAGCCTCTAGTTGACTA 58.721 47.826 0.00 0.00 0.00 2.59
124 125 3.100671 CCCAGTAAGCCTCTAGTTGACT 58.899 50.000 0.00 0.00 0.00 3.41
125 126 2.168728 CCCCAGTAAGCCTCTAGTTGAC 59.831 54.545 0.00 0.00 0.00 3.18
126 127 2.043939 TCCCCAGTAAGCCTCTAGTTGA 59.956 50.000 0.00 0.00 0.00 3.18
127 128 2.168728 GTCCCCAGTAAGCCTCTAGTTG 59.831 54.545 0.00 0.00 0.00 3.16
128 129 2.225547 TGTCCCCAGTAAGCCTCTAGTT 60.226 50.000 0.00 0.00 0.00 2.24
129 130 1.361543 TGTCCCCAGTAAGCCTCTAGT 59.638 52.381 0.00 0.00 0.00 2.57
130 131 2.160721 TGTCCCCAGTAAGCCTCTAG 57.839 55.000 0.00 0.00 0.00 2.43
131 132 2.398588 CATGTCCCCAGTAAGCCTCTA 58.601 52.381 0.00 0.00 0.00 2.43
132 133 1.207791 CATGTCCCCAGTAAGCCTCT 58.792 55.000 0.00 0.00 0.00 3.69
133 134 0.181350 CCATGTCCCCAGTAAGCCTC 59.819 60.000 0.00 0.00 0.00 4.70
134 135 0.550147 ACCATGTCCCCAGTAAGCCT 60.550 55.000 0.00 0.00 0.00 4.58
135 136 0.394352 CACCATGTCCCCAGTAAGCC 60.394 60.000 0.00 0.00 0.00 4.35
136 137 0.328258 ACACCATGTCCCCAGTAAGC 59.672 55.000 0.00 0.00 0.00 3.09
137 138 2.224769 ACAACACCATGTCCCCAGTAAG 60.225 50.000 0.00 0.00 0.00 2.34
138 139 1.777878 ACAACACCATGTCCCCAGTAA 59.222 47.619 0.00 0.00 0.00 2.24
139 140 1.349688 GACAACACCATGTCCCCAGTA 59.650 52.381 0.00 0.00 43.11 2.74
140 141 0.110486 GACAACACCATGTCCCCAGT 59.890 55.000 0.00 0.00 43.11 4.00
141 142 2.946947 GACAACACCATGTCCCCAG 58.053 57.895 0.00 0.00 43.11 4.45
147 148 3.282021 GGATGCATAGACAACACCATGT 58.718 45.455 0.00 0.00 35.90 3.21
148 149 3.065786 GTGGATGCATAGACAACACCATG 59.934 47.826 0.00 0.00 0.00 3.66
149 150 3.282021 GTGGATGCATAGACAACACCAT 58.718 45.455 0.00 0.00 0.00 3.55
150 151 2.039613 TGTGGATGCATAGACAACACCA 59.960 45.455 0.00 0.00 33.22 4.17
151 152 2.420022 GTGTGGATGCATAGACAACACC 59.580 50.000 11.70 2.23 33.22 4.16
152 153 3.073678 TGTGTGGATGCATAGACAACAC 58.926 45.455 14.68 14.68 34.17 3.32
153 154 3.415457 TGTGTGGATGCATAGACAACA 57.585 42.857 10.96 1.40 0.00 3.33
154 155 3.691118 ACATGTGTGGATGCATAGACAAC 59.309 43.478 10.96 0.00 0.00 3.32
155 156 3.954200 ACATGTGTGGATGCATAGACAA 58.046 40.909 10.96 4.23 0.00 3.18
156 157 3.632643 ACATGTGTGGATGCATAGACA 57.367 42.857 0.00 2.24 0.00 3.41
157 158 5.407691 CAGATACATGTGTGGATGCATAGAC 59.592 44.000 9.11 0.00 0.00 2.59
158 159 5.305128 TCAGATACATGTGTGGATGCATAGA 59.695 40.000 9.11 0.00 0.00 1.98
159 160 5.544650 TCAGATACATGTGTGGATGCATAG 58.455 41.667 9.11 0.00 0.00 2.23
160 161 5.070847 ACTCAGATACATGTGTGGATGCATA 59.929 40.000 9.11 0.00 0.00 3.14
161 162 4.141551 ACTCAGATACATGTGTGGATGCAT 60.142 41.667 9.11 0.00 0.00 3.96
162 163 3.198417 ACTCAGATACATGTGTGGATGCA 59.802 43.478 9.11 0.00 0.00 3.96
163 164 3.801698 ACTCAGATACATGTGTGGATGC 58.198 45.455 9.11 0.00 0.00 3.91
164 165 5.295292 GGAAACTCAGATACATGTGTGGATG 59.705 44.000 9.11 0.76 0.00 3.51
165 166 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
166 167 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
167 168 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
168 169 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
169 170 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
170 171 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
171 172 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
172 173 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
180 181 9.547753 GCTAGAATTGTATTGATAGGAAACTCA 57.452 33.333 0.00 0.00 43.67 3.41
181 182 9.547753 TGCTAGAATTGTATTGATAGGAAACTC 57.452 33.333 0.00 0.00 43.67 3.01
184 185 9.288576 CCATGCTAGAATTGTATTGATAGGAAA 57.711 33.333 0.00 0.00 0.00 3.13
185 186 8.659527 TCCATGCTAGAATTGTATTGATAGGAA 58.340 33.333 0.00 0.00 0.00 3.36
186 187 8.206126 TCCATGCTAGAATTGTATTGATAGGA 57.794 34.615 0.00 0.00 0.00 2.94
195 196 9.990360 TCGTTTATTATCCATGCTAGAATTGTA 57.010 29.630 0.00 0.00 0.00 2.41
196 197 8.902540 TCGTTTATTATCCATGCTAGAATTGT 57.097 30.769 0.00 0.00 0.00 2.71
265 266 4.141390 ACTGTTGGAAATATGCCCTAGAGG 60.141 45.833 0.00 0.00 39.47 3.69
266 267 5.041191 ACTGTTGGAAATATGCCCTAGAG 57.959 43.478 0.00 0.00 0.00 2.43
267 268 5.192927 CAACTGTTGGAAATATGCCCTAGA 58.807 41.667 12.66 0.00 0.00 2.43
268 269 4.949856 ACAACTGTTGGAAATATGCCCTAG 59.050 41.667 23.15 0.00 34.12 3.02
269 270 4.929479 ACAACTGTTGGAAATATGCCCTA 58.071 39.130 23.15 0.00 34.12 3.53
270 271 3.778265 ACAACTGTTGGAAATATGCCCT 58.222 40.909 23.15 0.00 34.12 5.19
271 272 4.142249 GGTACAACTGTTGGAAATATGCCC 60.142 45.833 23.15 7.87 34.12 5.36
272 273 4.461081 TGGTACAACTGTTGGAAATATGCC 59.539 41.667 23.15 14.21 31.92 4.40
273 274 5.637006 TGGTACAACTGTTGGAAATATGC 57.363 39.130 23.15 5.90 31.92 3.14
324 325 5.050159 GGTCAAATTCAGCCAACAATTCAAC 60.050 40.000 0.00 0.00 0.00 3.18
330 331 2.364970 CTGGGTCAAATTCAGCCAACAA 59.635 45.455 9.04 0.00 40.89 2.83
386 387 5.815740 GCCGAGGTAGTGATCAAGAATTTTA 59.184 40.000 0.00 0.00 0.00 1.52
394 396 0.325296 AGGGCCGAGGTAGTGATCAA 60.325 55.000 0.00 0.00 0.00 2.57
407 409 3.322254 ACTCATTCTGTATAGAAGGGCCG 59.678 47.826 13.00 5.86 45.53 6.13
448 450 3.904800 TGATTCTAGACCGAATGGCAA 57.095 42.857 0.00 0.00 39.70 4.52
455 457 6.049955 ACCTTTTCAATGATTCTAGACCGA 57.950 37.500 0.00 0.00 0.00 4.69
456 458 7.843490 TTACCTTTTCAATGATTCTAGACCG 57.157 36.000 0.00 0.00 0.00 4.79
461 463 8.739972 GCTTCCTTTACCTTTTCAATGATTCTA 58.260 33.333 0.00 0.00 0.00 2.10
539 541 8.327941 TCTACATAATTATCAAAGGCATCTGC 57.672 34.615 0.00 0.00 41.14 4.26
542 544 8.733458 TGCATCTACATAATTATCAAAGGCATC 58.267 33.333 0.00 0.00 0.00 3.91
546 548 9.154847 TCGATGCATCTACATAATTATCAAAGG 57.845 33.333 23.73 2.52 0.00 3.11
559 561 7.615582 AAAAAGATTCTTCGATGCATCTACA 57.384 32.000 23.73 5.50 0.00 2.74
582 607 5.144100 TCATTCACCTCCAAAAAGCCTAAA 58.856 37.500 0.00 0.00 0.00 1.85
620 646 7.878644 ACTCCTCCTCTAGAACATTAAACAAAC 59.121 37.037 0.00 0.00 0.00 2.93
639 665 6.181206 AGGCTAAGATTATTCAACTCCTCC 57.819 41.667 0.00 0.00 0.00 4.30
754 819 7.199167 AGCTAAATAAAATGCCCTTGGATTT 57.801 32.000 0.00 0.00 0.00 2.17
774 839 6.599356 TTAGACTATGACAACCACAAGCTA 57.401 37.500 0.00 0.00 0.00 3.32
808 873 1.258982 CAAGACTTCGCCATATCGCAC 59.741 52.381 0.00 0.00 0.00 5.34
842 907 5.178623 TGCGTTGTATAACTCCAAAGAAGTG 59.821 40.000 0.65 0.00 34.60 3.16
1034 1100 7.174413 TGTCAATGGATCCTTATCAGTTTCAA 58.826 34.615 14.23 0.00 33.41 2.69
1149 1215 3.305608 GCTGCTTGCTGACCAAATTAACT 60.306 43.478 3.71 0.00 38.95 2.24
1179 1245 6.973843 TGCAATATCAATAAGCATGTCCTTC 58.026 36.000 0.00 0.00 0.00 3.46
1313 1381 2.054458 TGCTTGGTGCGGAACTCTA 58.946 52.632 0.00 0.00 46.63 2.43
1331 1399 9.455847 CGAATTGTCTTCTTCTTTTGATTTTCT 57.544 29.630 0.00 0.00 0.00 2.52
1385 1453 6.611613 ATGACTCCTCTGTAGATTGTGAAA 57.388 37.500 0.00 0.00 0.00 2.69
1429 1497 5.189659 ACTATAGCTTGATCGACCACTTC 57.810 43.478 0.00 0.00 0.00 3.01
1540 1608 4.232221 CAAGCAGCCAACAAACTCTTATG 58.768 43.478 0.00 0.00 0.00 1.90
1552 1620 3.888323 TCAAGATTAACACAAGCAGCCAA 59.112 39.130 0.00 0.00 0.00 4.52
1581 1649 5.467063 GTCTTTGTGTTCTCCACTCTTAAGG 59.533 44.000 1.85 0.00 44.81 2.69
1674 1742 9.895138 TTCATCAGAATCTCAAGAATATCAACA 57.105 29.630 0.00 0.00 0.00 3.33
1773 1841 6.042666 ACTTGAGTTTAGAGAAGCTCCTTTCT 59.957 38.462 0.00 0.00 41.03 2.52
1809 1877 6.164408 TGTGTCATAGTTGAACGCAAATAG 57.836 37.500 0.00 0.00 37.89 1.73
1854 1922 7.889469 AGACATCATTTTCAAGTGCTATTGTT 58.111 30.769 2.14 0.00 0.00 2.83
1958 2027 8.110860 ACTAAAACCAATAAACTGACCTCATG 57.889 34.615 0.00 0.00 0.00 3.07
2119 2192 1.327690 CCGTCTCCAGGAATTCGGGA 61.328 60.000 14.61 14.61 37.40 5.14
2179 2252 2.459644 TGGGATCATTGCTTTTGGAGG 58.540 47.619 0.00 0.00 0.00 4.30
2216 2289 2.124151 GGTGATGGCGGCATCCTT 60.124 61.111 39.14 15.93 0.00 3.36
2221 2294 4.545706 GGATCGGTGATGGCGGCA 62.546 66.667 16.34 16.34 0.00 5.69
2263 2336 4.963318 TCTCACTTGATTGGTTGTCTCT 57.037 40.909 0.00 0.00 0.00 3.10
2264 2337 5.760253 TCTTTCTCACTTGATTGGTTGTCTC 59.240 40.000 0.00 0.00 0.00 3.36
2285 2358 1.067212 GTGTGTCGACACCTCACTCTT 59.933 52.381 38.12 0.00 45.96 2.85
2297 2398 0.179059 ATGTTGCTGTGGTGTGTCGA 60.179 50.000 0.00 0.00 0.00 4.20
2312 2413 1.765314 AGATAGCGCCTTGGAGATGTT 59.235 47.619 2.29 0.00 0.00 2.71
2315 2416 0.972883 GGAGATAGCGCCTTGGAGAT 59.027 55.000 2.29 0.00 0.00 2.75
2316 2417 0.397114 TGGAGATAGCGCCTTGGAGA 60.397 55.000 2.29 0.00 34.70 3.71
2317 2418 0.465705 TTGGAGATAGCGCCTTGGAG 59.534 55.000 2.29 0.00 34.70 3.86
2318 2419 0.908910 TTTGGAGATAGCGCCTTGGA 59.091 50.000 2.29 0.00 34.70 3.53
2319 2420 1.750193 TTTTGGAGATAGCGCCTTGG 58.250 50.000 2.29 0.00 34.70 3.61
2337 2438 1.754226 TCCTTGAAGGCGTTGCTTTTT 59.246 42.857 6.30 0.00 34.61 1.94
2338 2439 1.338020 CTCCTTGAAGGCGTTGCTTTT 59.662 47.619 6.30 0.00 34.61 2.27
2339 2440 0.954452 CTCCTTGAAGGCGTTGCTTT 59.046 50.000 6.30 0.00 34.61 3.51
2340 2441 0.890996 CCTCCTTGAAGGCGTTGCTT 60.891 55.000 6.30 0.00 34.61 3.91
2341 2442 1.302832 CCTCCTTGAAGGCGTTGCT 60.303 57.895 6.30 0.00 34.61 3.91
2342 2443 2.335712 CCCTCCTTGAAGGCGTTGC 61.336 63.158 6.30 0.00 34.61 4.17
2343 2444 1.675641 CCCCTCCTTGAAGGCGTTG 60.676 63.158 6.30 0.00 34.61 4.10
2344 2445 1.423794 TTCCCCTCCTTGAAGGCGTT 61.424 55.000 6.30 0.00 34.61 4.84
2345 2446 1.423794 TTTCCCCTCCTTGAAGGCGT 61.424 55.000 6.30 0.00 34.61 5.68
2346 2447 0.960861 GTTTCCCCTCCTTGAAGGCG 60.961 60.000 6.30 0.00 34.61 5.52
2351 2452 0.395312 GTGTCGTTTCCCCTCCTTGA 59.605 55.000 0.00 0.00 0.00 3.02
2409 2510 5.183713 TGACAATTCGGATGAAAATCTTGCT 59.816 36.000 0.00 0.00 37.71 3.91
2416 2517 5.068460 AGGTTTGTGACAATTCGGATGAAAA 59.932 36.000 0.00 0.00 37.71 2.29
2439 2540 0.987294 ATTCCGATGGGCAGGGATAG 59.013 55.000 0.00 0.00 0.00 2.08
2440 2541 0.692476 CATTCCGATGGGCAGGGATA 59.308 55.000 0.00 0.00 0.00 2.59
2570 5960 6.579865 AGTGAATCAGGTTAGGTAATTACGG 58.420 40.000 9.46 0.00 0.00 4.02
2611 6001 3.597255 GCTTAGGGCTTTAGAGTTCGTT 58.403 45.455 0.00 0.00 38.06 3.85
2621 6011 2.361230 GTGGCGGCTTAGGGCTTT 60.361 61.111 11.43 0.00 41.46 3.51
2629 6019 2.111460 TAACGTTGGTGGCGGCTT 59.889 55.556 11.99 0.00 0.00 4.35
2670 6060 2.030007 CACATGGGTTTTGCTTGACGAT 60.030 45.455 0.00 0.00 0.00 3.73
2673 6063 1.873486 GCCACATGGGTTTTGCTTGAC 60.873 52.381 0.00 0.00 39.65 3.18
2676 6066 1.002315 GATGCCACATGGGTTTTGCTT 59.998 47.619 0.00 0.00 39.65 3.91
2694 6084 2.721971 GATCATCCCGCACCGCAGAT 62.722 60.000 0.00 0.00 0.00 2.90
2705 6095 3.118112 ACTCCATGTGAACAGATCATCCC 60.118 47.826 0.00 0.00 40.97 3.85
2760 6158 0.392998 AACCGCTATCACCAGCCTTG 60.393 55.000 0.00 0.00 38.37 3.61
2762 6160 1.221840 CAACCGCTATCACCAGCCT 59.778 57.895 0.00 0.00 38.37 4.58
2765 6163 3.009723 ACAAATCAACCGCTATCACCAG 58.990 45.455 0.00 0.00 0.00 4.00
2771 6169 3.331150 TCGAACACAAATCAACCGCTAT 58.669 40.909 0.00 0.00 0.00 2.97
2772 6170 2.734606 CTCGAACACAAATCAACCGCTA 59.265 45.455 0.00 0.00 0.00 4.26
2795 6193 1.982073 CTCGGTTGAGAATTGCCGCC 61.982 60.000 0.00 0.00 45.57 6.13
2812 6210 0.389948 CACCGCCTGTAAGTGTCCTC 60.390 60.000 0.00 0.00 0.00 3.71
2813 6211 1.671742 CACCGCCTGTAAGTGTCCT 59.328 57.895 0.00 0.00 0.00 3.85
2818 6216 0.903454 AGGTAGCACCGCCTGTAAGT 60.903 55.000 0.00 0.00 44.90 2.24
2898 6298 0.174845 AGACGCTTATGCCGCTGTAA 59.825 50.000 0.00 0.00 35.36 2.41
2905 6305 3.297830 AAAAACCAAGACGCTTATGCC 57.702 42.857 0.00 0.00 35.36 4.40
2911 6311 4.765339 AGGCTAAATAAAAACCAAGACGCT 59.235 37.500 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.