Multiple sequence alignment - TraesCS5A01G314200

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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 TraesCS5A01G314200 chr5A 100.000 6425 0 0 1 6425 524687666 524681242 0.000000e+00 11865
1 TraesCS5A01G314200 chr5A 95.246 6248 234 32 196 6425 398469775 398475977 0.000000e+00 9834
2 TraesCS5A01G314200 chr5A 98.492 199 3 0 1 199 588367028 588366830 1.020000e-92 351
3 TraesCS5A01G314200 chr4A 95.866 6265 218 16 196 6425 37340517 37334259 0.000000e+00 10096
4 TraesCS5A01G314200 chr4A 83.871 465 53 17 205 661 527897900 527897450 2.140000e-114 424
5 TraesCS5A01G314200 chr4A 93.640 283 5 3 196 467 578191198 578191478 1.670000e-110 411
6 TraesCS5A01G314200 chr4A 98.995 199 2 0 1 199 202263437 202263635 2.200000e-94 357
7 TraesCS5A01G314200 chr4A 99.487 195 1 0 1 195 486608491 486608297 7.920000e-94 355
8 TraesCS5A01G314200 chr3A 95.817 6263 215 26 197 6425 711566421 711572670 0.000000e+00 10070
9 TraesCS5A01G314200 chr3A 95.507 6010 220 20 239 6210 653952586 653946589 0.000000e+00 9557
10 TraesCS5A01G314200 chr3A 91.864 295 18 4 6134 6425 745762110 745761819 2.160000e-109 407
11 TraesCS5A01G314200 chr3A 91.216 296 18 5 6134 6425 653946710 653946419 4.670000e-106 396
12 TraesCS5A01G314200 chr3A 98.492 199 3 0 1 199 527500988 527500790 1.020000e-92 351
13 TraesCS5A01G314200 chr1A 95.857 6251 202 18 196 6425 365643139 365636925 0.000000e+00 10056
14 TraesCS5A01G314200 chr2A 95.785 6264 194 26 196 6425 619869817 619876044 0.000000e+00 10041
15 TraesCS5A01G314200 chr2A 93.866 6260 256 41 196 6425 58490117 58496278 0.000000e+00 9315
16 TraesCS5A01G314200 chr2A 98.500 200 2 1 1 199 130009695 130009496 1.020000e-92 351
17 TraesCS5A01G314200 chr6A 96.005 6007 198 20 239 6210 494436830 494430831 0.000000e+00 9725
18 TraesCS5A01G314200 chr6A 95.066 6181 231 33 198 6350 554926644 554920510 0.000000e+00 9657
19 TraesCS5A01G314200 chr6A 95.656 6008 219 19 239 6210 184594581 184600582 0.000000e+00 9611
20 TraesCS5A01G314200 chr6A 98.995 199 2 0 1 199 423676463 423676265 2.200000e-94 357
21 TraesCS5A01G314200 chr6A 98.492 199 3 0 1 199 349062046 349061848 1.020000e-92 351
22 TraesCS5A01G314200 chr2D 93.671 4124 201 40 196 4303 536220002 536215923 0.000000e+00 6115
23 TraesCS5A01G314200 chr7A 94.936 3673 148 11 2757 6425 636925872 636929510 0.000000e+00 5718
24 TraesCS5A01G314200 chr7A 95.075 1726 51 13 196 1889 722664942 722666665 0.000000e+00 2686
25 TraesCS5A01G314200 chr7A 91.523 637 31 9 196 813 701319015 701319647 0.000000e+00 856
26 TraesCS5A01G314200 chr7A 98.492 199 3 0 1 199 271333690 271333492 1.020000e-92 351
27 TraesCS5A01G314200 chr3B 90.547 4115 281 62 211 4303 177757719 177753691 0.000000e+00 5345
28 TraesCS5A01G314200 chr5B 82.990 1552 209 41 206 1745 644394038 644392530 0.000000e+00 1352
29 TraesCS5A01G314200 chr6B 91.429 455 13 12 196 628 21370304 21369854 9.220000e-168 601
30 TraesCS5A01G314200 chrUn 98.500 200 2 1 1 199 277089793 277089992 1.020000e-92 351


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 TraesCS5A01G314200 chr5A 524681242 524687666 6424 True 11865.0 11865 100.0000 1 6425 1 chr5A.!!$R1 6424
1 TraesCS5A01G314200 chr5A 398469775 398475977 6202 False 9834.0 9834 95.2460 196 6425 1 chr5A.!!$F1 6229
2 TraesCS5A01G314200 chr4A 37334259 37340517 6258 True 10096.0 10096 95.8660 196 6425 1 chr4A.!!$R1 6229
3 TraesCS5A01G314200 chr3A 711566421 711572670 6249 False 10070.0 10070 95.8170 197 6425 1 chr3A.!!$F1 6228
4 TraesCS5A01G314200 chr3A 653946419 653952586 6167 True 4976.5 9557 93.3615 239 6425 2 chr3A.!!$R3 6186
5 TraesCS5A01G314200 chr1A 365636925 365643139 6214 True 10056.0 10056 95.8570 196 6425 1 chr1A.!!$R1 6229
6 TraesCS5A01G314200 chr2A 619869817 619876044 6227 False 10041.0 10041 95.7850 196 6425 1 chr2A.!!$F2 6229
7 TraesCS5A01G314200 chr2A 58490117 58496278 6161 False 9315.0 9315 93.8660 196 6425 1 chr2A.!!$F1 6229
8 TraesCS5A01G314200 chr6A 494430831 494436830 5999 True 9725.0 9725 96.0050 239 6210 1 chr6A.!!$R3 5971
9 TraesCS5A01G314200 chr6A 554920510 554926644 6134 True 9657.0 9657 95.0660 198 6350 1 chr6A.!!$R4 6152
10 TraesCS5A01G314200 chr6A 184594581 184600582 6001 False 9611.0 9611 95.6560 239 6210 1 chr6A.!!$F1 5971
11 TraesCS5A01G314200 chr2D 536215923 536220002 4079 True 6115.0 6115 93.6710 196 4303 1 chr2D.!!$R1 4107
12 TraesCS5A01G314200 chr7A 636925872 636929510 3638 False 5718.0 5718 94.9360 2757 6425 1 chr7A.!!$F1 3668
13 TraesCS5A01G314200 chr7A 722664942 722666665 1723 False 2686.0 2686 95.0750 196 1889 1 chr7A.!!$F3 1693
14 TraesCS5A01G314200 chr7A 701319015 701319647 632 False 856.0 856 91.5230 196 813 1 chr7A.!!$F2 617
15 TraesCS5A01G314200 chr3B 177753691 177757719 4028 True 5345.0 5345 90.5470 211 4303 1 chr3B.!!$R1 4092
16 TraesCS5A01G314200 chr5B 644392530 644394038 1508 True 1352.0 1352 82.9900 206 1745 1 chr5B.!!$R1 1539

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
194 195 0.032952 GCCGCATCGAGGGTGTTATA 59.967 55.0 0.0 0.0 0.00 0.98 F
1552 1612 0.618458 TTGGGTCTGGTGCAGATACC 59.382 55.0 0.0 0.0 42.73 2.73 F
3008 3124 0.634465 GGAAGAGGAGGAGGAGGAGT 59.366 60.0 0.0 0.0 0.00 3.85 F
3522 3653 0.752658 GCTTTGCCAACCACCTTTCT 59.247 50.0 0.0 0.0 0.00 2.52 F
4754 4893 0.916086 TTCGGGACCACCTATTGCAT 59.084 50.0 0.0 0.0 36.97 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2249 0.877071 CCACGAATGCTTCAGCTTGT 59.123 50.000 0.0 0.0 42.66 3.16 R
3522 3653 0.108186 ATCGCTGAAATCTGGCACGA 60.108 50.000 0.0 0.0 0.00 4.35 R
4861 5000 0.034186 CCCAATACAAGAGGGCAGCA 60.034 55.000 0.0 0.0 35.44 4.41 R
5069 5210 2.180276 AGTTAGCTCGAAGGGTCACAT 58.820 47.619 0.0 0.0 0.00 3.21 R
5786 5936 0.394192 TGTCCAGTGTCCTGCTTGAG 59.606 55.000 0.0 0.0 37.38 3.02 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
30 31 8.929827 TTGGATGTTGTAATGCTTTATTCATG 57.070 30.769 0.00 0.00 0.00 3.07
31 32 8.065473 TGGATGTTGTAATGCTTTATTCATGT 57.935 30.769 0.00 0.00 0.00 3.21
32 33 9.183368 TGGATGTTGTAATGCTTTATTCATGTA 57.817 29.630 0.00 0.00 0.00 2.29
39 40 9.786105 TGTAATGCTTTATTCATGTATTGTGTG 57.214 29.630 0.00 0.00 0.00 3.82
42 43 9.577110 AATGCTTTATTCATGTATTGTGTGAAG 57.423 29.630 0.00 0.00 35.56 3.02
43 44 8.109705 TGCTTTATTCATGTATTGTGTGAAGT 57.890 30.769 0.00 0.00 35.56 3.01
44 45 8.022550 TGCTTTATTCATGTATTGTGTGAAGTG 58.977 33.333 0.00 0.00 35.56 3.16
45 46 7.485913 GCTTTATTCATGTATTGTGTGAAGTGG 59.514 37.037 0.00 0.00 35.56 4.00
46 47 4.764679 TTCATGTATTGTGTGAAGTGGC 57.235 40.909 0.00 0.00 0.00 5.01
47 48 2.741517 TCATGTATTGTGTGAAGTGGCG 59.258 45.455 0.00 0.00 0.00 5.69
48 49 2.535012 TGTATTGTGTGAAGTGGCGA 57.465 45.000 0.00 0.00 0.00 5.54
49 50 3.052455 TGTATTGTGTGAAGTGGCGAT 57.948 42.857 0.00 0.00 0.00 4.58
50 51 3.407698 TGTATTGTGTGAAGTGGCGATT 58.592 40.909 0.00 0.00 0.00 3.34
51 52 2.995466 ATTGTGTGAAGTGGCGATTG 57.005 45.000 0.00 0.00 0.00 2.67
52 53 1.674359 TTGTGTGAAGTGGCGATTGT 58.326 45.000 0.00 0.00 0.00 2.71
53 54 2.535012 TGTGTGAAGTGGCGATTGTA 57.465 45.000 0.00 0.00 0.00 2.41
54 55 2.839975 TGTGTGAAGTGGCGATTGTAA 58.160 42.857 0.00 0.00 0.00 2.41
55 56 2.805671 TGTGTGAAGTGGCGATTGTAAG 59.194 45.455 0.00 0.00 0.00 2.34
56 57 1.804151 TGTGAAGTGGCGATTGTAAGC 59.196 47.619 0.00 0.00 0.00 3.09
67 68 5.924475 GCGATTGTAAGCCAACTATGTAT 57.076 39.130 0.00 0.00 35.44 2.29
68 69 5.916969 GCGATTGTAAGCCAACTATGTATC 58.083 41.667 0.00 0.00 35.44 2.24
69 70 5.696724 GCGATTGTAAGCCAACTATGTATCT 59.303 40.000 0.00 0.00 35.44 1.98
70 71 6.128795 GCGATTGTAAGCCAACTATGTATCTC 60.129 42.308 0.00 0.00 35.44 2.75
71 72 7.148641 CGATTGTAAGCCAACTATGTATCTCT 58.851 38.462 0.00 0.00 35.44 3.10
72 73 7.653713 CGATTGTAAGCCAACTATGTATCTCTT 59.346 37.037 0.00 0.00 35.44 2.85
73 74 9.331282 GATTGTAAGCCAACTATGTATCTCTTT 57.669 33.333 0.00 0.00 35.44 2.52
74 75 8.718102 TTGTAAGCCAACTATGTATCTCTTTC 57.282 34.615 0.00 0.00 0.00 2.62
75 76 7.272978 TGTAAGCCAACTATGTATCTCTTTCC 58.727 38.462 0.00 0.00 0.00 3.13
76 77 5.297569 AGCCAACTATGTATCTCTTTCCC 57.702 43.478 0.00 0.00 0.00 3.97
77 78 4.971924 AGCCAACTATGTATCTCTTTCCCT 59.028 41.667 0.00 0.00 0.00 4.20
78 79 5.430089 AGCCAACTATGTATCTCTTTCCCTT 59.570 40.000 0.00 0.00 0.00 3.95
79 80 6.615726 AGCCAACTATGTATCTCTTTCCCTTA 59.384 38.462 0.00 0.00 0.00 2.69
80 81 7.293535 AGCCAACTATGTATCTCTTTCCCTTAT 59.706 37.037 0.00 0.00 0.00 1.73
81 82 7.389053 GCCAACTATGTATCTCTTTCCCTTATG 59.611 40.741 0.00 0.00 0.00 1.90
82 83 8.432805 CCAACTATGTATCTCTTTCCCTTATGT 58.567 37.037 0.00 0.00 0.00 2.29
92 93 7.745717 TCTCTTTCCCTTATGTATTACATGGG 58.254 38.462 19.48 19.48 41.04 4.00
93 94 7.349859 TCTCTTTCCCTTATGTATTACATGGGT 59.650 37.037 22.47 3.38 40.71 4.51
94 95 7.878495 TCTTTCCCTTATGTATTACATGGGTT 58.122 34.615 22.47 3.08 40.71 4.11
95 96 7.777910 TCTTTCCCTTATGTATTACATGGGTTG 59.222 37.037 22.47 16.30 40.71 3.77
96 97 6.584471 TCCCTTATGTATTACATGGGTTGT 57.416 37.500 22.47 1.91 40.71 3.32
97 98 6.361433 TCCCTTATGTATTACATGGGTTGTG 58.639 40.000 22.47 11.74 40.71 3.33
98 99 6.069323 TCCCTTATGTATTACATGGGTTGTGT 60.069 38.462 22.47 0.74 40.71 3.72
99 100 6.039270 CCCTTATGTATTACATGGGTTGTGTG 59.961 42.308 17.68 4.59 39.53 3.82
100 101 6.826231 CCTTATGTATTACATGGGTTGTGTGA 59.174 38.462 17.68 0.00 39.53 3.58
101 102 7.338196 CCTTATGTATTACATGGGTTGTGTGAA 59.662 37.037 17.68 1.51 39.53 3.18
102 103 6.757897 ATGTATTACATGGGTTGTGTGAAG 57.242 37.500 8.51 0.00 37.45 3.02
103 104 5.870706 TGTATTACATGGGTTGTGTGAAGA 58.129 37.500 0.00 0.00 39.48 2.87
104 105 6.480763 TGTATTACATGGGTTGTGTGAAGAT 58.519 36.000 0.00 0.00 39.48 2.40
105 106 6.945435 TGTATTACATGGGTTGTGTGAAGATT 59.055 34.615 0.00 0.00 39.48 2.40
106 107 8.103935 TGTATTACATGGGTTGTGTGAAGATTA 58.896 33.333 0.00 0.00 39.48 1.75
107 108 6.811253 TTACATGGGTTGTGTGAAGATTAC 57.189 37.500 0.00 0.00 39.48 1.89
108 109 4.079253 ACATGGGTTGTGTGAAGATTACC 58.921 43.478 0.00 0.00 37.11 2.85
109 110 4.202567 ACATGGGTTGTGTGAAGATTACCT 60.203 41.667 0.00 0.00 37.11 3.08
110 111 4.015872 TGGGTTGTGTGAAGATTACCTC 57.984 45.455 0.00 0.00 0.00 3.85
111 112 3.392947 TGGGTTGTGTGAAGATTACCTCA 59.607 43.478 0.00 0.00 0.00 3.86
112 113 3.751698 GGGTTGTGTGAAGATTACCTCAC 59.248 47.826 0.00 0.00 0.00 3.51
113 114 4.505039 GGGTTGTGTGAAGATTACCTCACT 60.505 45.833 4.07 0.00 34.51 3.41
114 115 5.063880 GGTTGTGTGAAGATTACCTCACTT 58.936 41.667 4.07 0.00 34.51 3.16
115 116 5.049405 GGTTGTGTGAAGATTACCTCACTTG 60.049 44.000 4.07 0.00 34.51 3.16
116 117 4.065088 TGTGTGAAGATTACCTCACTTGC 58.935 43.478 4.07 0.00 34.51 4.01
117 118 3.123621 GTGTGAAGATTACCTCACTTGCG 59.876 47.826 4.07 0.00 34.51 4.85
118 119 3.006430 TGTGAAGATTACCTCACTTGCGA 59.994 43.478 4.07 0.00 34.51 5.10
119 120 3.368236 GTGAAGATTACCTCACTTGCGAC 59.632 47.826 0.00 0.00 0.00 5.19
120 121 3.006430 TGAAGATTACCTCACTTGCGACA 59.994 43.478 0.00 0.00 0.00 4.35
121 122 3.895232 AGATTACCTCACTTGCGACAT 57.105 42.857 0.00 0.00 0.00 3.06
122 123 4.207891 AGATTACCTCACTTGCGACATT 57.792 40.909 0.00 0.00 0.00 2.71
123 124 3.935203 AGATTACCTCACTTGCGACATTG 59.065 43.478 0.00 0.00 0.00 2.82
124 125 1.438651 TACCTCACTTGCGACATTGC 58.561 50.000 0.00 0.00 0.00 3.56
125 126 0.250467 ACCTCACTTGCGACATTGCT 60.250 50.000 0.00 0.00 35.36 3.91
126 127 0.877071 CCTCACTTGCGACATTGCTT 59.123 50.000 0.00 0.00 35.36 3.91
127 128 1.267806 CCTCACTTGCGACATTGCTTT 59.732 47.619 0.00 0.00 35.36 3.51
128 129 2.578495 CTCACTTGCGACATTGCTTTC 58.422 47.619 0.00 0.00 35.36 2.62
129 130 1.946081 TCACTTGCGACATTGCTTTCA 59.054 42.857 0.00 0.00 35.36 2.69
130 131 2.357323 TCACTTGCGACATTGCTTTCAA 59.643 40.909 0.00 0.00 36.51 2.69
131 132 3.004629 TCACTTGCGACATTGCTTTCAAT 59.995 39.130 0.00 0.00 43.31 2.57
141 142 2.276472 TGCTTTCAATGCGGTTATGC 57.724 45.000 0.00 0.00 0.00 3.14
142 143 1.135141 TGCTTTCAATGCGGTTATGCC 60.135 47.619 0.00 0.00 0.00 4.40
143 144 1.134946 GCTTTCAATGCGGTTATGCCT 59.865 47.619 0.00 0.00 34.25 4.75
144 145 2.796032 GCTTTCAATGCGGTTATGCCTC 60.796 50.000 0.00 0.00 34.25 4.70
145 146 2.418368 TTCAATGCGGTTATGCCTCT 57.582 45.000 0.00 0.00 34.25 3.69
146 147 3.552132 TTCAATGCGGTTATGCCTCTA 57.448 42.857 0.00 0.00 34.25 2.43
147 148 3.111853 TCAATGCGGTTATGCCTCTAG 57.888 47.619 0.00 0.00 34.25 2.43
148 149 2.146342 CAATGCGGTTATGCCTCTAGG 58.854 52.381 0.00 0.00 38.53 3.02
149 150 1.424638 ATGCGGTTATGCCTCTAGGT 58.575 50.000 0.00 0.00 37.57 3.08
150 151 0.750850 TGCGGTTATGCCTCTAGGTC 59.249 55.000 0.00 0.00 37.57 3.85
151 152 0.318784 GCGGTTATGCCTCTAGGTCG 60.319 60.000 0.00 0.00 37.57 4.79
152 153 1.030457 CGGTTATGCCTCTAGGTCGT 58.970 55.000 0.00 0.00 37.57 4.34
153 154 1.269102 CGGTTATGCCTCTAGGTCGTG 60.269 57.143 0.00 0.00 37.57 4.35
154 155 1.538419 GGTTATGCCTCTAGGTCGTGC 60.538 57.143 0.00 0.00 37.57 5.34
155 156 1.409427 GTTATGCCTCTAGGTCGTGCT 59.591 52.381 0.00 0.00 37.57 4.40
156 157 1.776662 TATGCCTCTAGGTCGTGCTT 58.223 50.000 0.00 0.00 37.57 3.91
157 158 0.461961 ATGCCTCTAGGTCGTGCTTC 59.538 55.000 0.00 0.00 37.57 3.86
158 159 1.226717 GCCTCTAGGTCGTGCTTCG 60.227 63.158 0.00 0.00 37.57 3.79
159 160 1.654954 GCCTCTAGGTCGTGCTTCGA 61.655 60.000 0.00 0.92 40.04 3.71
168 169 2.028484 GTGCTTCGACACGTGGGA 59.972 61.111 21.57 13.88 0.00 4.37
169 170 2.022129 GTGCTTCGACACGTGGGAG 61.022 63.158 21.57 8.15 0.00 4.30
170 171 2.197605 TGCTTCGACACGTGGGAGA 61.198 57.895 21.57 12.82 0.00 3.71
171 172 1.215647 GCTTCGACACGTGGGAGAT 59.784 57.895 21.57 0.00 0.00 2.75
172 173 0.454600 GCTTCGACACGTGGGAGATA 59.545 55.000 21.57 1.34 0.00 1.98
173 174 1.067212 GCTTCGACACGTGGGAGATAT 59.933 52.381 21.57 0.00 0.00 1.63
174 175 2.292569 GCTTCGACACGTGGGAGATATA 59.707 50.000 21.57 0.63 0.00 0.86
175 176 3.609644 GCTTCGACACGTGGGAGATATAG 60.610 52.174 21.57 11.01 0.00 1.31
176 177 1.878088 TCGACACGTGGGAGATATAGC 59.122 52.381 21.57 0.00 0.00 2.97
177 178 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
178 179 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
179 180 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
180 181 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
181 182 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
182 183 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
183 184 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
184 185 1.103803 GGGAGATATAGCCGCATCGA 58.896 55.000 0.00 0.00 0.00 3.59
185 186 1.066303 GGGAGATATAGCCGCATCGAG 59.934 57.143 0.00 0.00 0.00 4.04
186 187 1.066303 GGAGATATAGCCGCATCGAGG 59.934 57.143 0.00 0.00 0.00 4.63
187 188 1.066303 GAGATATAGCCGCATCGAGGG 59.934 57.143 0.00 0.00 0.00 4.30
188 189 0.818296 GATATAGCCGCATCGAGGGT 59.182 55.000 0.00 0.00 42.74 4.34
189 190 0.532573 ATATAGCCGCATCGAGGGTG 59.467 55.000 0.00 0.00 40.09 4.61
190 191 0.826256 TATAGCCGCATCGAGGGTGT 60.826 55.000 0.00 0.00 40.09 4.16
191 192 1.686325 ATAGCCGCATCGAGGGTGTT 61.686 55.000 0.00 0.00 40.09 3.32
192 193 1.038681 TAGCCGCATCGAGGGTGTTA 61.039 55.000 0.00 0.00 40.09 2.41
193 194 1.227556 GCCGCATCGAGGGTGTTAT 60.228 57.895 0.00 0.00 0.00 1.89
194 195 0.032952 GCCGCATCGAGGGTGTTATA 59.967 55.000 0.00 0.00 0.00 0.98
336 350 5.065090 TGGCATCTTTTCATAGTTGACATCG 59.935 40.000 0.00 0.00 29.95 3.84
347 363 3.074412 AGTTGACATCGGTGGTCATTTC 58.926 45.455 0.00 0.00 44.11 2.17
417 435 3.237268 TGCTGAGGTATGTGGGTTTTT 57.763 42.857 0.00 0.00 0.00 1.94
525 552 6.060028 TGTTGCACATTCACTAGAACTTTC 57.940 37.500 0.00 0.00 36.39 2.62
745 798 9.729023 CTCTTGTGTTTAATGTTTGTGTAATGA 57.271 29.630 0.00 0.00 0.00 2.57
938 992 3.756117 GGGGGCTATTGAACTTATCAGG 58.244 50.000 0.00 0.00 39.77 3.86
1051 1105 1.271001 TGGATGCTGACAGTGTTCAGG 60.271 52.381 18.36 4.02 42.95 3.86
1060 1114 3.911260 TGACAGTGTTCAGGGGGTATTTA 59.089 43.478 0.00 0.00 0.00 1.40
1198 1252 6.575847 GCTCAAGATGATTCAGGATATGGCTA 60.576 42.308 0.00 0.00 0.00 3.93
1214 1268 2.766263 TGGCTAGAAGAACGGATGACAT 59.234 45.455 0.00 0.00 0.00 3.06
1321 1375 5.008415 GGACTTGTGCTAGATCATCAAATGG 59.992 44.000 0.00 0.00 0.00 3.16
1368 1422 5.839262 TTGTAGCAGAACACATTAACGAG 57.161 39.130 0.00 0.00 0.00 4.18
1552 1612 0.618458 TTGGGTCTGGTGCAGATACC 59.382 55.000 0.00 0.00 42.73 2.73
1683 1743 2.095263 CCTGGTGTGTTCGGCAAATTAG 60.095 50.000 0.00 0.00 0.00 1.73
1740 1803 9.436957 GTGTCTTCCTTCTATGTTCTTTTGATA 57.563 33.333 0.00 0.00 0.00 2.15
1836 1902 7.599998 CAGATTGTAGCTTTAAGTTTGGCAATT 59.400 33.333 0.00 0.00 0.00 2.32
2294 2370 3.448093 TTGGCTGGGATGTATGTTCAA 57.552 42.857 0.00 0.00 0.00 2.69
2354 2430 7.394359 ACAGAATTTAGTTGGCTGTGATGTATT 59.606 33.333 0.00 0.00 38.30 1.89
2634 2720 2.942804 TGTGTTGATGCAGAAAAGGGA 58.057 42.857 0.00 0.00 0.00 4.20
2753 2839 7.818997 TCAGATATTGATCCTTACGTACAGT 57.181 36.000 0.00 0.00 31.81 3.55
2822 2908 2.498885 AGACGGGGGTCAACTATACAAC 59.501 50.000 0.00 0.00 0.00 3.32
2877 2963 6.882768 AGAAGATGAGGAAATGGAAGTAGT 57.117 37.500 0.00 0.00 0.00 2.73
2911 2997 1.212751 CGACGAGGACACAGATGCA 59.787 57.895 0.00 0.00 0.00 3.96
2992 3108 1.289530 GAGGAGGAGGAGGAAGAGGAA 59.710 57.143 0.00 0.00 0.00 3.36
2993 3109 1.290732 AGGAGGAGGAGGAAGAGGAAG 59.709 57.143 0.00 0.00 0.00 3.46
2994 3110 1.289530 GGAGGAGGAGGAAGAGGAAGA 59.710 57.143 0.00 0.00 0.00 2.87
2995 3111 2.666317 GAGGAGGAGGAAGAGGAAGAG 58.334 57.143 0.00 0.00 0.00 2.85
2996 3112 1.290732 AGGAGGAGGAAGAGGAAGAGG 59.709 57.143 0.00 0.00 0.00 3.69
2997 3113 1.289530 GGAGGAGGAAGAGGAAGAGGA 59.710 57.143 0.00 0.00 0.00 3.71
3008 3124 0.634465 GGAAGAGGAGGAGGAGGAGT 59.366 60.000 0.00 0.00 0.00 3.85
3303 3434 1.571773 GCCCCTGGTTCTGGTGGTAT 61.572 60.000 0.00 0.00 0.00 2.73
3373 3504 3.128242 GCAGCAGCAATTCATTGAGTAGT 59.872 43.478 3.60 0.00 40.14 2.73
3522 3653 0.752658 GCTTTGCCAACCACCTTTCT 59.247 50.000 0.00 0.00 0.00 2.52
3556 3687 7.841915 TTTCAGCGATAAAGATATGTGTGAA 57.158 32.000 0.00 0.00 0.00 3.18
3602 3733 5.669477 AGAGCCTGTTCTTATCAAGTGATC 58.331 41.667 0.00 0.00 36.05 2.92
3603 3734 5.188555 AGAGCCTGTTCTTATCAAGTGATCA 59.811 40.000 0.00 0.00 36.05 2.92
3629 3760 8.180706 TGAAAAGAATCAAATTGACATGGAGA 57.819 30.769 0.00 0.00 0.00 3.71
3642 3773 2.376518 ACATGGAGAAAGCAGGAAAGGA 59.623 45.455 0.00 0.00 0.00 3.36
3765 3896 1.336517 CGTGGTCCAGAAGCGTAAAGA 60.337 52.381 0.00 0.00 0.00 2.52
3794 3925 5.999600 TCAATGAAGAAGAATCTGCAGTTGA 59.000 36.000 14.67 8.62 44.64 3.18
3827 3958 3.386078 GGAGAAGATGGTGAGTGCAGATA 59.614 47.826 0.00 0.00 0.00 1.98
3917 4048 5.276270 CAACCAATGTCACAGAAGTTCAAG 58.724 41.667 5.50 0.00 0.00 3.02
3925 4056 6.348498 TGTCACAGAAGTTCAAGAGATCAAA 58.652 36.000 5.50 0.00 0.00 2.69
4092 4229 1.443802 GTGCCAAGTTCTGCTAGGTC 58.556 55.000 0.00 0.00 0.00 3.85
4290 4427 5.880901 AGGTGATCCAACTATCAAAGTGTT 58.119 37.500 0.00 0.00 38.88 3.32
4427 4564 1.781025 CGATGCACCCGTGTTTGTGT 61.781 55.000 0.00 0.00 34.94 3.72
4444 4581 0.975556 TGTCGCAAGGAGATGCCCTA 60.976 55.000 0.00 0.00 43.47 3.53
4605 4744 2.329267 TGATGAGTGTGAGTTGGACCT 58.671 47.619 0.00 0.00 0.00 3.85
4661 4800 1.820519 CTGGCAAGGCAATAGCTCAAA 59.179 47.619 0.00 0.00 41.70 2.69
4678 4817 4.670221 GCTCAAAAGCTAGATGTTGGTTCG 60.670 45.833 10.94 0.00 45.55 3.95
4754 4893 0.916086 TTCGGGACCACCTATTGCAT 59.084 50.000 0.00 0.00 36.97 3.96
4821 4960 5.410924 TCCATTCATCGACTACAACAAGAG 58.589 41.667 0.00 0.00 0.00 2.85
4861 5000 3.754965 TGAGGCAGTGAACAAGCTTTAT 58.245 40.909 0.00 0.00 0.00 1.40
4969 5108 8.579850 ACATATCTTTTTCAGTTGCATAGGAA 57.420 30.769 0.00 0.00 0.00 3.36
4972 5111 6.707440 TCTTTTTCAGTTGCATAGGAACAA 57.293 33.333 4.29 0.00 0.00 2.83
5109 5250 8.694394 GCTAACTTGTCTTTTTATTGCTTTCAG 58.306 33.333 0.00 0.00 0.00 3.02
5781 5931 0.942884 GGACGGACGCTTCGAAGTTT 60.943 55.000 25.24 13.14 0.00 2.66
5786 5936 2.636519 GGACGCTTCGAAGTTTTTGAC 58.363 47.619 25.24 6.81 0.00 3.18
5798 5949 3.620488 AGTTTTTGACTCAAGCAGGACA 58.380 40.909 0.00 0.00 31.20 4.02
6125 6299 2.927477 GCGCATAAGTAGTTGCACACTA 59.073 45.455 0.30 0.00 38.80 2.74
6251 6447 4.194640 CAGTAGGACATAAGCAGTTGCAT 58.805 43.478 6.90 0.00 45.16 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.368674 CATGAATAAAGCATTACAACATCCAAA 57.631 29.630 0.00 0.00 0.00 3.28
6 7 8.065473 ACATGAATAAAGCATTACAACATCCA 57.935 30.769 0.00 0.00 0.00 3.41
13 14 9.786105 CACACAATACATGAATAAAGCATTACA 57.214 29.630 0.00 0.00 0.00 2.41
16 17 9.577110 CTTCACACAATACATGAATAAAGCATT 57.423 29.630 0.00 0.00 32.16 3.56
17 18 8.742777 ACTTCACACAATACATGAATAAAGCAT 58.257 29.630 0.00 0.00 32.16 3.79
18 19 8.022550 CACTTCACACAATACATGAATAAAGCA 58.977 33.333 0.00 0.00 32.16 3.91
19 20 7.485913 CCACTTCACACAATACATGAATAAAGC 59.514 37.037 0.00 0.00 32.16 3.51
20 21 7.485913 GCCACTTCACACAATACATGAATAAAG 59.514 37.037 0.00 0.00 32.16 1.85
21 22 7.312154 GCCACTTCACACAATACATGAATAAA 58.688 34.615 0.00 0.00 32.16 1.40
22 23 6.403092 CGCCACTTCACACAATACATGAATAA 60.403 38.462 0.00 0.00 32.16 1.40
23 24 5.064579 CGCCACTTCACACAATACATGAATA 59.935 40.000 0.00 0.00 32.16 1.75
24 25 4.142622 CGCCACTTCACACAATACATGAAT 60.143 41.667 0.00 0.00 32.16 2.57
25 26 3.188254 CGCCACTTCACACAATACATGAA 59.812 43.478 0.00 0.00 0.00 2.57
26 27 2.741517 CGCCACTTCACACAATACATGA 59.258 45.455 0.00 0.00 0.00 3.07
27 28 2.741517 TCGCCACTTCACACAATACATG 59.258 45.455 0.00 0.00 0.00 3.21
28 29 3.052455 TCGCCACTTCACACAATACAT 57.948 42.857 0.00 0.00 0.00 2.29
29 30 2.535012 TCGCCACTTCACACAATACA 57.465 45.000 0.00 0.00 0.00 2.29
30 31 3.188460 ACAATCGCCACTTCACACAATAC 59.812 43.478 0.00 0.00 0.00 1.89
31 32 3.407698 ACAATCGCCACTTCACACAATA 58.592 40.909 0.00 0.00 0.00 1.90
32 33 2.229792 ACAATCGCCACTTCACACAAT 58.770 42.857 0.00 0.00 0.00 2.71
33 34 1.674359 ACAATCGCCACTTCACACAA 58.326 45.000 0.00 0.00 0.00 3.33
34 35 2.535012 TACAATCGCCACTTCACACA 57.465 45.000 0.00 0.00 0.00 3.72
35 36 2.412847 GCTTACAATCGCCACTTCACAC 60.413 50.000 0.00 0.00 0.00 3.82
36 37 1.804151 GCTTACAATCGCCACTTCACA 59.196 47.619 0.00 0.00 0.00 3.58
37 38 1.130561 GGCTTACAATCGCCACTTCAC 59.869 52.381 0.00 0.00 45.59 3.18
38 39 1.448985 GGCTTACAATCGCCACTTCA 58.551 50.000 0.00 0.00 45.59 3.02
44 45 2.943033 ACATAGTTGGCTTACAATCGCC 59.057 45.455 0.00 0.00 46.46 5.54
45 46 5.696724 AGATACATAGTTGGCTTACAATCGC 59.303 40.000 0.00 0.00 41.95 4.58
46 47 7.148641 AGAGATACATAGTTGGCTTACAATCG 58.851 38.462 0.00 0.00 41.95 3.34
47 48 8.894768 AAGAGATACATAGTTGGCTTACAATC 57.105 34.615 0.00 0.00 41.95 2.67
48 49 9.331282 GAAAGAGATACATAGTTGGCTTACAAT 57.669 33.333 0.00 0.00 41.95 2.71
49 50 7.769044 GGAAAGAGATACATAGTTGGCTTACAA 59.231 37.037 0.00 0.00 36.54 2.41
50 51 7.272978 GGAAAGAGATACATAGTTGGCTTACA 58.727 38.462 0.00 0.00 0.00 2.41
51 52 6.706716 GGGAAAGAGATACATAGTTGGCTTAC 59.293 42.308 0.00 0.00 0.00 2.34
52 53 6.615726 AGGGAAAGAGATACATAGTTGGCTTA 59.384 38.462 0.00 0.00 0.00 3.09
53 54 5.430089 AGGGAAAGAGATACATAGTTGGCTT 59.570 40.000 0.00 0.00 0.00 4.35
54 55 4.971924 AGGGAAAGAGATACATAGTTGGCT 59.028 41.667 0.00 0.00 0.00 4.75
55 56 5.297569 AGGGAAAGAGATACATAGTTGGC 57.702 43.478 0.00 0.00 0.00 4.52
56 57 8.432805 ACATAAGGGAAAGAGATACATAGTTGG 58.567 37.037 0.00 0.00 0.00 3.77
66 67 8.386264 CCCATGTAATACATAAGGGAAAGAGAT 58.614 37.037 18.88 0.00 41.79 2.75
67 68 7.349859 ACCCATGTAATACATAAGGGAAAGAGA 59.650 37.037 26.38 0.00 41.79 3.10
68 69 7.518188 ACCCATGTAATACATAAGGGAAAGAG 58.482 38.462 26.38 7.48 41.79 2.85
69 70 7.460214 ACCCATGTAATACATAAGGGAAAGA 57.540 36.000 26.38 0.00 41.79 2.52
70 71 7.559897 ACAACCCATGTAATACATAAGGGAAAG 59.440 37.037 26.38 18.92 41.79 2.62
71 72 7.340743 CACAACCCATGTAATACATAAGGGAAA 59.659 37.037 26.38 0.00 41.79 3.13
72 73 6.831353 CACAACCCATGTAATACATAAGGGAA 59.169 38.462 26.38 0.00 41.79 3.97
73 74 6.069323 ACACAACCCATGTAATACATAAGGGA 60.069 38.462 26.38 0.00 41.79 4.20
74 75 6.039270 CACACAACCCATGTAATACATAAGGG 59.961 42.308 20.91 20.91 43.69 3.95
75 76 6.826231 TCACACAACCCATGTAATACATAAGG 59.174 38.462 15.94 15.94 41.46 2.69
76 77 7.857734 TCACACAACCCATGTAATACATAAG 57.142 36.000 5.49 3.25 41.46 1.73
77 78 8.103935 TCTTCACACAACCCATGTAATACATAA 58.896 33.333 5.49 0.00 41.46 1.90
78 79 7.625469 TCTTCACACAACCCATGTAATACATA 58.375 34.615 5.49 0.00 41.46 2.29
79 80 6.480763 TCTTCACACAACCCATGTAATACAT 58.519 36.000 0.00 0.00 41.46 2.29
80 81 5.870706 TCTTCACACAACCCATGTAATACA 58.129 37.500 0.00 0.00 41.46 2.29
81 82 7.391148 AATCTTCACACAACCCATGTAATAC 57.609 36.000 0.00 0.00 41.46 1.89
82 83 7.554835 GGTAATCTTCACACAACCCATGTAATA 59.445 37.037 0.00 0.00 41.46 0.98
83 84 6.377146 GGTAATCTTCACACAACCCATGTAAT 59.623 38.462 0.00 0.00 41.46 1.89
84 85 5.708230 GGTAATCTTCACACAACCCATGTAA 59.292 40.000 0.00 0.00 41.46 2.41
85 86 5.013704 AGGTAATCTTCACACAACCCATGTA 59.986 40.000 0.00 0.00 41.46 2.29
86 87 4.079253 GGTAATCTTCACACAACCCATGT 58.921 43.478 0.00 0.00 45.34 3.21
87 88 4.335416 AGGTAATCTTCACACAACCCATG 58.665 43.478 0.00 0.00 0.00 3.66
88 89 4.042809 TGAGGTAATCTTCACACAACCCAT 59.957 41.667 0.00 0.00 0.00 4.00
89 90 3.392947 TGAGGTAATCTTCACACAACCCA 59.607 43.478 0.00 0.00 0.00 4.51
90 91 3.751698 GTGAGGTAATCTTCACACAACCC 59.248 47.826 5.78 0.00 45.79 4.11
97 98 3.368236 GTCGCAAGTGAGGTAATCTTCAC 59.632 47.826 2.97 2.97 46.51 3.18
98 99 3.006430 TGTCGCAAGTGAGGTAATCTTCA 59.994 43.478 0.00 0.00 39.48 3.02
99 100 3.585862 TGTCGCAAGTGAGGTAATCTTC 58.414 45.455 0.00 0.00 39.48 2.87
100 101 3.678056 TGTCGCAAGTGAGGTAATCTT 57.322 42.857 0.00 0.00 39.48 2.40
101 102 3.895232 ATGTCGCAAGTGAGGTAATCT 57.105 42.857 0.00 0.00 39.48 2.40
102 103 3.485877 GCAATGTCGCAAGTGAGGTAATC 60.486 47.826 0.00 0.00 39.48 1.75
103 104 2.420022 GCAATGTCGCAAGTGAGGTAAT 59.580 45.455 0.00 0.00 39.48 1.89
104 105 1.804151 GCAATGTCGCAAGTGAGGTAA 59.196 47.619 0.00 0.00 39.48 2.85
105 106 1.001974 AGCAATGTCGCAAGTGAGGTA 59.998 47.619 0.00 0.00 39.48 3.08
106 107 0.250467 AGCAATGTCGCAAGTGAGGT 60.250 50.000 0.00 0.00 39.48 3.85
107 108 0.877071 AAGCAATGTCGCAAGTGAGG 59.123 50.000 0.00 0.00 39.48 3.86
108 109 2.031769 TGAAAGCAATGTCGCAAGTGAG 60.032 45.455 0.00 0.00 39.48 3.51
109 110 1.946081 TGAAAGCAATGTCGCAAGTGA 59.054 42.857 0.00 0.00 39.48 3.41
110 111 2.404265 TGAAAGCAATGTCGCAAGTG 57.596 45.000 0.00 0.00 39.48 3.16
111 112 3.648339 ATTGAAAGCAATGTCGCAAGT 57.352 38.095 0.00 0.00 42.91 3.16
120 121 3.189285 GCATAACCGCATTGAAAGCAAT 58.811 40.909 0.00 0.00 45.33 3.56
121 122 2.605030 GCATAACCGCATTGAAAGCAA 58.395 42.857 0.00 0.00 38.60 3.91
122 123 1.135141 GGCATAACCGCATTGAAAGCA 60.135 47.619 0.00 0.00 0.00 3.91
123 124 1.134946 AGGCATAACCGCATTGAAAGC 59.865 47.619 0.00 0.00 46.52 3.51
124 125 2.684881 AGAGGCATAACCGCATTGAAAG 59.315 45.455 0.00 0.00 46.52 2.62
125 126 2.722094 AGAGGCATAACCGCATTGAAA 58.278 42.857 0.00 0.00 46.52 2.69
126 127 2.418368 AGAGGCATAACCGCATTGAA 57.582 45.000 0.00 0.00 46.52 2.69
127 128 2.224281 CCTAGAGGCATAACCGCATTGA 60.224 50.000 0.00 0.00 46.52 2.57
128 129 2.146342 CCTAGAGGCATAACCGCATTG 58.854 52.381 0.00 0.00 46.52 2.82
129 130 1.768870 ACCTAGAGGCATAACCGCATT 59.231 47.619 0.00 0.00 46.52 3.56
130 131 1.344763 GACCTAGAGGCATAACCGCAT 59.655 52.381 0.00 0.00 46.52 4.73
131 132 0.750850 GACCTAGAGGCATAACCGCA 59.249 55.000 0.00 0.00 46.52 5.69
132 133 0.318784 CGACCTAGAGGCATAACCGC 60.319 60.000 0.00 0.00 46.52 5.68
133 134 1.030457 ACGACCTAGAGGCATAACCG 58.970 55.000 0.00 0.00 46.52 4.44
134 135 1.538419 GCACGACCTAGAGGCATAACC 60.538 57.143 0.00 0.00 39.32 2.85
135 136 1.409427 AGCACGACCTAGAGGCATAAC 59.591 52.381 0.00 0.00 39.32 1.89
136 137 1.776662 AGCACGACCTAGAGGCATAA 58.223 50.000 0.00 0.00 39.32 1.90
137 138 1.681793 GAAGCACGACCTAGAGGCATA 59.318 52.381 0.00 0.00 39.32 3.14
138 139 0.461961 GAAGCACGACCTAGAGGCAT 59.538 55.000 0.00 0.00 39.32 4.40
139 140 1.890894 GAAGCACGACCTAGAGGCA 59.109 57.895 0.00 0.00 39.32 4.75
140 141 1.226717 CGAAGCACGACCTAGAGGC 60.227 63.158 0.00 0.00 45.77 4.70
141 142 2.478989 TCGAAGCACGACCTAGAGG 58.521 57.895 2.09 0.00 46.45 3.69
151 152 2.022129 CTCCCACGTGTCGAAGCAC 61.022 63.158 15.65 0.00 36.12 4.40
152 153 1.532604 ATCTCCCACGTGTCGAAGCA 61.533 55.000 15.65 0.00 0.00 3.91
153 154 0.454600 TATCTCCCACGTGTCGAAGC 59.545 55.000 15.65 0.00 0.00 3.86
154 155 3.609644 GCTATATCTCCCACGTGTCGAAG 60.610 52.174 15.65 6.13 0.00 3.79
155 156 2.292569 GCTATATCTCCCACGTGTCGAA 59.707 50.000 15.65 0.00 0.00 3.71
156 157 1.878088 GCTATATCTCCCACGTGTCGA 59.122 52.381 15.65 8.55 0.00 4.20
157 158 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
158 159 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
159 160 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
160 161 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
161 162 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
162 163 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
163 164 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
164 165 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
165 166 1.066303 CTCGATGCGGCTATATCTCCC 59.934 57.143 0.00 0.00 0.00 4.30
166 167 1.066303 CCTCGATGCGGCTATATCTCC 59.934 57.143 0.00 0.00 0.00 3.71
167 168 1.066303 CCCTCGATGCGGCTATATCTC 59.934 57.143 0.00 0.00 0.00 2.75
168 169 1.107114 CCCTCGATGCGGCTATATCT 58.893 55.000 0.00 0.00 0.00 1.98
169 170 0.818296 ACCCTCGATGCGGCTATATC 59.182 55.000 0.00 0.00 0.00 1.63
170 171 0.532573 CACCCTCGATGCGGCTATAT 59.467 55.000 0.00 0.00 0.00 0.86
171 172 0.826256 ACACCCTCGATGCGGCTATA 60.826 55.000 0.00 0.00 0.00 1.31
172 173 1.686325 AACACCCTCGATGCGGCTAT 61.686 55.000 0.00 0.00 0.00 2.97
173 174 1.038681 TAACACCCTCGATGCGGCTA 61.039 55.000 0.00 0.00 0.00 3.93
174 175 1.686325 ATAACACCCTCGATGCGGCT 61.686 55.000 0.00 0.00 0.00 5.52
175 176 0.032952 TATAACACCCTCGATGCGGC 59.967 55.000 0.00 0.00 0.00 6.53
176 177 2.223971 ACTTATAACACCCTCGATGCGG 60.224 50.000 0.00 0.00 0.00 5.69
177 178 3.093717 ACTTATAACACCCTCGATGCG 57.906 47.619 0.00 0.00 0.00 4.73
178 179 3.489785 CGAACTTATAACACCCTCGATGC 59.510 47.826 0.00 0.00 0.00 3.91
179 180 4.049186 CCGAACTTATAACACCCTCGATG 58.951 47.826 0.00 0.00 0.00 3.84
180 181 3.956199 TCCGAACTTATAACACCCTCGAT 59.044 43.478 0.00 0.00 0.00 3.59
181 182 3.129287 GTCCGAACTTATAACACCCTCGA 59.871 47.826 0.00 0.00 0.00 4.04
182 183 3.442100 GTCCGAACTTATAACACCCTCG 58.558 50.000 0.00 0.00 0.00 4.63
183 184 3.196254 TGGTCCGAACTTATAACACCCTC 59.804 47.826 0.00 0.00 0.00 4.30
184 185 3.055602 GTGGTCCGAACTTATAACACCCT 60.056 47.826 0.00 0.00 0.00 4.34
185 186 3.055602 AGTGGTCCGAACTTATAACACCC 60.056 47.826 0.00 0.00 0.00 4.61
186 187 4.198028 AGTGGTCCGAACTTATAACACC 57.802 45.455 0.00 0.00 0.00 4.16
187 188 7.838771 AAATAGTGGTCCGAACTTATAACAC 57.161 36.000 0.00 0.00 0.00 3.32
188 189 8.723311 CAAAAATAGTGGTCCGAACTTATAACA 58.277 33.333 0.00 0.00 0.00 2.41
189 190 8.724229 ACAAAAATAGTGGTCCGAACTTATAAC 58.276 33.333 0.00 0.00 0.00 1.89
190 191 8.851541 ACAAAAATAGTGGTCCGAACTTATAA 57.148 30.769 0.00 0.00 0.00 0.98
191 192 8.851541 AACAAAAATAGTGGTCCGAACTTATA 57.148 30.769 0.00 0.00 0.00 0.98
192 193 7.754851 AACAAAAATAGTGGTCCGAACTTAT 57.245 32.000 0.00 0.00 0.00 1.73
193 194 7.571080 AAACAAAAATAGTGGTCCGAACTTA 57.429 32.000 0.00 0.00 0.00 2.24
194 195 6.459670 AAACAAAAATAGTGGTCCGAACTT 57.540 33.333 0.00 0.00 0.00 2.66
336 350 1.270550 CCTGCACAAGAAATGACCACC 59.729 52.381 0.00 0.00 0.00 4.61
417 435 6.875948 AATAGCTCATAAACACACACACAA 57.124 33.333 0.00 0.00 0.00 3.33
418 436 6.484977 TCAAATAGCTCATAAACACACACACA 59.515 34.615 0.00 0.00 0.00 3.72
419 437 6.898041 TCAAATAGCTCATAAACACACACAC 58.102 36.000 0.00 0.00 0.00 3.82
525 552 1.140589 CGAGACCTGGCAGCTACAG 59.859 63.158 9.56 9.94 35.74 2.74
745 798 7.243604 TGCCCTGTTGATTAGAAAATGAAAT 57.756 32.000 0.00 0.00 0.00 2.17
938 992 3.050275 GGTCCGCTGGAAGTGTGC 61.050 66.667 0.00 0.00 44.74 4.57
1032 1086 1.446907 CCTGAACACTGTCAGCATCC 58.553 55.000 0.00 0.00 43.18 3.51
1051 1105 4.893524 CCTGTTTGGGAGATTAAATACCCC 59.106 45.833 0.00 0.00 41.44 4.95
1105 1159 3.776969 TGTCTGAATCTCCTAGTGGCATT 59.223 43.478 0.00 0.00 0.00 3.56
1198 1252 9.265901 CATAAAGAATATGTCATCCGTTCTTCT 57.734 33.333 15.49 10.98 37.95 2.85
1214 1268 2.958355 GCAAGCCAGGCCATAAAGAATA 59.042 45.455 8.22 0.00 0.00 1.75
1321 1375 7.617041 AGAGGCAGATGTTTGTATTCTTTAC 57.383 36.000 0.00 0.00 0.00 2.01
1368 1422 1.313091 GGTCCATGTTCCGGAAAGCC 61.313 60.000 20.79 7.47 33.29 4.35
1552 1612 1.787155 GTACGAGCGCATCAAGGTATG 59.213 52.381 11.47 0.00 0.00 2.39
1740 1803 6.739565 GCAATTTCCAAAAAGAGTGACCAGAT 60.740 38.462 0.00 0.00 0.00 2.90
1836 1902 7.637229 CCAATTTAAAATGAACATGTGTGCAA 58.363 30.769 0.00 0.00 37.10 4.08
2013 2083 5.606505 TGTGCAACTACAACAAGATACTGA 58.393 37.500 0.00 0.00 38.04 3.41
2173 2249 0.877071 CCACGAATGCTTCAGCTTGT 59.123 50.000 0.00 0.00 42.66 3.16
2196 2272 7.201661 GCGGATTGTATGTTATTGGTAACTTGA 60.202 37.037 0.73 0.00 40.66 3.02
2354 2430 7.432869 ACAAAAGCTTATATGTGCAACTGAAA 58.567 30.769 0.00 0.00 38.04 2.69
2404 2489 8.687242 TGACAATGGTTGTAAATGAACACTTTA 58.313 29.630 0.00 0.00 45.52 1.85
2631 2717 2.296190 ACCACTTTCGCAATCTTTTCCC 59.704 45.455 0.00 0.00 0.00 3.97
2634 2720 4.647424 TTGACCACTTTCGCAATCTTTT 57.353 36.364 0.00 0.00 0.00 2.27
2729 2815 7.818997 ACTGTACGTAAGGATCAATATCTGA 57.181 36.000 0.00 0.00 46.39 3.27
2753 2839 2.101783 CCCAGTTTGCATTGATGGCTA 58.898 47.619 0.00 0.00 0.00 3.93
2822 2908 6.484643 TCATCCTCAACAAACTCTTCTTCTTG 59.515 38.462 0.00 0.00 0.00 3.02
2877 2963 1.003866 CGTCGTCGTCAGCATCTATCA 60.004 52.381 0.00 0.00 0.00 2.15
2911 2997 3.052262 TGTCCTCCTCCTCTGATTCATCT 60.052 47.826 0.00 0.00 0.00 2.90
2992 3108 1.011545 TCCTACTCCTCCTCCTCCTCT 59.988 57.143 0.00 0.00 0.00 3.69
2993 3109 1.423921 CTCCTACTCCTCCTCCTCCTC 59.576 61.905 0.00 0.00 0.00 3.71
2994 3110 1.529744 CTCCTACTCCTCCTCCTCCT 58.470 60.000 0.00 0.00 0.00 3.69
2995 3111 0.481128 CCTCCTACTCCTCCTCCTCC 59.519 65.000 0.00 0.00 0.00 4.30
2996 3112 1.144298 GTCCTCCTACTCCTCCTCCTC 59.856 61.905 0.00 0.00 0.00 3.71
2997 3113 1.228190 GTCCTCCTACTCCTCCTCCT 58.772 60.000 0.00 0.00 0.00 3.69
3008 3124 4.283722 GTCCTCTTCTTGTTTGTCCTCCTA 59.716 45.833 0.00 0.00 0.00 2.94
3303 3434 2.766263 CTCCTAGATGTGTTGCCACCTA 59.234 50.000 0.00 0.00 41.09 3.08
3373 3504 4.086457 TCAACATCTGTAGTGTGCTCCTA 58.914 43.478 0.00 0.00 0.00 2.94
3489 3620 1.202452 GCAAAGCTGGCTTCAAGTTGT 60.202 47.619 8.33 0.00 34.84 3.32
3522 3653 0.108186 ATCGCTGAAATCTGGCACGA 60.108 50.000 0.00 0.00 0.00 4.35
3556 3687 5.534207 TGTCAATGGCAAAGTTGATCTTT 57.466 34.783 5.40 0.00 45.96 2.52
3602 3733 8.766000 TCCATGTCAATTTGATTCTTTTCATG 57.234 30.769 13.11 13.11 0.00 3.07
3603 3734 8.809066 TCTCCATGTCAATTTGATTCTTTTCAT 58.191 29.630 1.78 0.00 0.00 2.57
3629 3760 4.077822 CAGTCAAGATCCTTTCCTGCTTT 58.922 43.478 0.00 0.00 0.00 3.51
3765 3896 7.014038 ACTGCAGATTCTTCTTCATTGAAACTT 59.986 33.333 23.35 0.00 0.00 2.66
3794 3925 3.395941 ACCATCTTCTCCTTGGTTTGAGT 59.604 43.478 0.00 0.00 40.87 3.41
3827 3958 6.599638 GCTTCCTTGACCATATTTACTTCAGT 59.400 38.462 0.00 0.00 0.00 3.41
4092 4229 2.031516 CCAGTCTGAGTTGGCAGCG 61.032 63.158 0.00 0.00 35.86 5.18
4290 4427 1.072331 GAAAGTCAGCTCTTGGGGACA 59.928 52.381 2.85 0.00 39.83 4.02
4427 4564 0.687757 ACTAGGGCATCTCCTTGCGA 60.688 55.000 0.00 0.00 43.71 5.10
4444 4581 3.236896 TCTTCGTAAGGGTTCAAGGACT 58.763 45.455 0.00 0.00 38.47 3.85
4548 4687 2.083774 CTTCCGCTGTTTCTATTGCCA 58.916 47.619 0.00 0.00 0.00 4.92
4549 4688 1.202188 GCTTCCGCTGTTTCTATTGCC 60.202 52.381 0.00 0.00 0.00 4.52
4574 4713 5.417894 ACTCACACTCATCAATGCAAATCAT 59.582 36.000 0.00 0.00 36.87 2.45
4605 4744 3.054875 ACATCCTTCATTCACAGCTGCTA 60.055 43.478 15.27 0.00 0.00 3.49
4661 4800 1.003118 TGGCGAACCAACATCTAGCTT 59.997 47.619 0.00 0.00 45.37 3.74
4678 4817 1.598701 GGGTGTGGCAATTCTCTGGC 61.599 60.000 0.00 0.00 42.07 4.85
4754 4893 4.962995 CCTTATTACCCTCCTCTGTCTTCA 59.037 45.833 0.00 0.00 0.00 3.02
4821 4960 3.149196 TCATTGGTGCTGAAAGTCTTCC 58.851 45.455 0.00 0.00 35.30 3.46
4861 5000 0.034186 CCCAATACAAGAGGGCAGCA 60.034 55.000 0.00 0.00 35.44 4.41
4969 5108 3.275617 TCTGTGCAACTAAGTGGTTGT 57.724 42.857 9.00 0.00 45.69 3.32
4972 5111 2.618709 GCTTTCTGTGCAACTAAGTGGT 59.381 45.455 0.00 0.00 38.04 4.16
5007 5146 3.818773 GTGCAACTAAAAGCCCTGTTCTA 59.181 43.478 0.00 0.00 0.00 2.10
5069 5210 2.180276 AGTTAGCTCGAAGGGTCACAT 58.820 47.619 0.00 0.00 0.00 3.21
5109 5250 8.627208 TGATTATCTCAGGGCTGATTATTTTC 57.373 34.615 0.00 0.00 39.13 2.29
5429 5574 7.830697 TGTTTATCTCATTCACATTGTGGATCT 59.169 33.333 16.46 1.52 27.74 2.75
5781 5931 2.564771 CAGTGTCCTGCTTGAGTCAAA 58.435 47.619 7.06 0.00 0.00 2.69
5786 5936 0.394192 TGTCCAGTGTCCTGCTTGAG 59.606 55.000 0.00 0.00 37.38 3.02
5798 5949 2.936919 TCAGCTCAATGTTGTCCAGT 57.063 45.000 0.00 0.00 0.00 4.00
6125 6299 0.813610 TGTGCAACTGCTTACGTGCT 60.814 50.000 0.00 0.00 42.66 4.40
6251 6447 8.644374 AAACCAAATAAAGGTAATGCACTCTA 57.356 30.769 0.00 0.00 38.76 2.43


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

AutoCloner maintained by Alex Coulton.