Multiple sequence alignment - TraesCS4B01G193400

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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 TraesCS4B01G193400 chr4B 100.000 3030 0 0 1 3030 416442787 416439758 0.000000e+00 5596
1 TraesCS4B01G193400 chr4B 95.614 114 5 0 76 189 522075318 522075431 1.860000e-42 183
2 TraesCS4B01G193400 chr4B 92.308 104 7 1 2215 2317 608669008 608668905 2.430000e-31 147
3 TraesCS4B01G193400 chr4A 90.077 1814 98 35 1249 3028 135353966 135355731 0.000000e+00 2278
4 TraesCS4B01G193400 chr4A 95.447 571 23 2 187 754 135346290 135346860 0.000000e+00 907
5 TraesCS4B01G193400 chr4A 90.909 275 18 6 858 1130 135353574 135353843 2.220000e-96 363
6 TraesCS4B01G193400 chr4A 98.148 108 2 0 81 188 314669069 314669176 3.990000e-44 189
7 TraesCS4B01G193400 chr4A 91.346 104 9 0 1150 1253 135353836 135353939 3.150000e-30 143
8 TraesCS4B01G193400 chr4A 95.181 83 4 0 1 83 135346209 135346291 6.820000e-27 132
9 TraesCS4B01G193400 chr4D 91.212 1593 66 29 1249 2828 337261427 337259896 0.000000e+00 2098
10 TraesCS4B01G193400 chr4D 89.315 964 62 23 187 1128 337262499 337261555 0.000000e+00 1171
11 TraesCS4B01G193400 chr4D 94.382 89 5 0 1165 1253 337261542 337261454 1.470000e-28 137
12 TraesCS4B01G193400 chr5B 98.131 107 2 0 82 188 531200069 531199963 1.430000e-43 187
13 TraesCS4B01G193400 chr3D 94.958 119 6 0 79 197 384141168 384141050 1.430000e-43 187
14 TraesCS4B01G193400 chr2A 97.273 110 3 0 80 189 205919887 205919778 1.430000e-43 187
15 TraesCS4B01G193400 chr1A 94.262 122 6 1 76 196 168552601 168552722 5.160000e-43 185
16 TraesCS4B01G193400 chr1A 94.792 96 5 0 2213 2308 335544594 335544499 1.880000e-32 150
17 TraesCS4B01G193400 chr7A 94.915 118 4 1 71 188 645026050 645026165 1.860000e-42 183
18 TraesCS4B01G193400 chr7A 91.339 127 9 2 892 1016 20999878 21000004 4.020000e-39 172
19 TraesCS4B01G193400 chr7B 94.828 116 6 0 80 195 514050722 514050607 6.670000e-42 182
20 TraesCS4B01G193400 chr2B 92.800 125 7 2 81 204 154146013 154145890 2.400000e-41 180
21 TraesCS4B01G193400 chr2B 92.233 103 5 3 2215 2317 258656170 258656071 3.150000e-30 143
22 TraesCS4B01G193400 chr5A 92.453 106 5 2 2215 2320 662731561 662731663 6.770000e-32 148
23 TraesCS4B01G193400 chr1D 92.381 105 6 2 2213 2317 267593029 267593131 6.770000e-32 148
24 TraesCS4B01G193400 chr5D 93.000 100 6 1 2223 2321 545224408 545224507 8.760000e-31 145
25 TraesCS4B01G193400 chr6D 92.157 102 3 3 2221 2322 82588545 82588641 4.070000e-29 139


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 TraesCS4B01G193400 chr4B 416439758 416442787 3029 True 5596.000000 5596 100.000000 1 3030 1 chr4B.!!$R1 3029
1 TraesCS4B01G193400 chr4A 135353574 135355731 2157 False 928.000000 2278 90.777333 858 3028 3 chr4A.!!$F3 2170
2 TraesCS4B01G193400 chr4A 135346209 135346860 651 False 519.500000 907 95.314000 1 754 2 chr4A.!!$F2 753
3 TraesCS4B01G193400 chr4D 337259896 337262499 2603 True 1135.333333 2098 91.636333 187 2828 3 chr4D.!!$R1 2641

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
846 884 0.390124 GGTGTGGACCGTGTTCACTA 59.61 55.0 14.18 1.99 42.16 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2151 0.040067 CCACGCAGAGAAAGCCAAAC 60.04 55.0 0.0 0.0 0.0 2.93 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
29 30 3.551635 TCCCCCTTAAAGCCAATTTGA 57.448 42.857 0.00 0.00 32.01 2.69
33 34 3.447229 CCCCTTAAAGCCAATTTGACGAT 59.553 43.478 0.00 0.00 32.01 3.73
37 38 5.687285 CCTTAAAGCCAATTTGACGATATGC 59.313 40.000 0.00 0.00 32.01 3.14
81 82 2.694397 TCCTGCCTAGCCACATTATCT 58.306 47.619 0.00 0.00 0.00 1.98
82 83 3.856900 TCCTGCCTAGCCACATTATCTA 58.143 45.455 0.00 0.00 0.00 1.98
83 84 3.578716 TCCTGCCTAGCCACATTATCTAC 59.421 47.826 0.00 0.00 0.00 2.59
84 85 3.580458 CCTGCCTAGCCACATTATCTACT 59.420 47.826 0.00 0.00 0.00 2.57
85 86 4.322349 CCTGCCTAGCCACATTATCTACTC 60.322 50.000 0.00 0.00 0.00 2.59
86 87 3.578716 TGCCTAGCCACATTATCTACTCC 59.421 47.826 0.00 0.00 0.00 3.85
87 88 3.055747 GCCTAGCCACATTATCTACTCCC 60.056 52.174 0.00 0.00 0.00 4.30
88 89 4.421131 CCTAGCCACATTATCTACTCCCT 58.579 47.826 0.00 0.00 0.00 4.20
89 90 4.464597 CCTAGCCACATTATCTACTCCCTC 59.535 50.000 0.00 0.00 0.00 4.30
90 91 4.206244 AGCCACATTATCTACTCCCTCT 57.794 45.455 0.00 0.00 0.00 3.69
91 92 3.900601 AGCCACATTATCTACTCCCTCTG 59.099 47.826 0.00 0.00 0.00 3.35
92 93 3.643792 GCCACATTATCTACTCCCTCTGT 59.356 47.826 0.00 0.00 0.00 3.41
93 94 4.101741 GCCACATTATCTACTCCCTCTGTT 59.898 45.833 0.00 0.00 0.00 3.16
94 95 5.740513 GCCACATTATCTACTCCCTCTGTTC 60.741 48.000 0.00 0.00 0.00 3.18
95 96 5.508153 CCACATTATCTACTCCCTCTGTTCG 60.508 48.000 0.00 0.00 0.00 3.95
96 97 4.585162 ACATTATCTACTCCCTCTGTTCGG 59.415 45.833 0.00 0.00 0.00 4.30
97 98 4.515028 TTATCTACTCCCTCTGTTCGGA 57.485 45.455 0.00 0.00 0.00 4.55
98 99 2.893215 TCTACTCCCTCTGTTCGGAA 57.107 50.000 0.00 0.00 0.00 4.30
99 100 3.383698 TCTACTCCCTCTGTTCGGAAT 57.616 47.619 0.00 0.00 0.00 3.01
100 101 3.709587 TCTACTCCCTCTGTTCGGAATT 58.290 45.455 0.00 0.00 0.00 2.17
101 102 4.863548 TCTACTCCCTCTGTTCGGAATTA 58.136 43.478 0.00 0.00 0.00 1.40
102 103 3.889520 ACTCCCTCTGTTCGGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
103 104 3.442076 ACTCCCTCTGTTCGGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
104 105 3.838903 ACTCCCTCTGTTCGGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
105 106 4.184629 CTCCCTCTGTTCGGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
106 107 3.581332 TCCCTCTGTTCGGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
107 108 3.933332 CCCTCTGTTCGGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
108 109 3.612860 CCTCTGTTCGGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
109 110 2.991190 TCTGTTCGGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
110 111 2.734606 CTGTTCGGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
111 112 2.734606 TGTTCGGAATTACTTGTCGCAG 59.265 45.455 0.00 0.00 0.00 5.18
112 113 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
113 114 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
114 115 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
115 116 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
116 117 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
117 118 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
118 119 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
119 120 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
120 121 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
121 122 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
122 123 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
123 124 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
124 125 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
125 126 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
126 127 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
127 128 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
128 129 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
129 130 5.631512 GTCGCAGAAATGGATGTATCTAGAC 59.368 44.000 0.00 0.00 39.69 2.59
130 131 5.301805 TCGCAGAAATGGATGTATCTAGACA 59.698 40.000 0.00 0.00 0.00 3.41
131 132 6.015095 TCGCAGAAATGGATGTATCTAGACAT 60.015 38.462 0.00 0.00 42.82 3.06
132 133 7.176690 TCGCAGAAATGGATGTATCTAGACATA 59.823 37.037 0.00 0.00 40.18 2.29
133 134 7.978414 CGCAGAAATGGATGTATCTAGACATAT 59.022 37.037 0.00 0.00 40.18 1.78
134 135 9.664332 GCAGAAATGGATGTATCTAGACATATT 57.336 33.333 0.00 0.00 40.18 1.28
161 162 9.529325 TTAGTTCTAGATACATCCATTTTCACG 57.471 33.333 0.00 0.00 0.00 4.35
162 163 7.782049 AGTTCTAGATACATCCATTTTCACGA 58.218 34.615 0.00 0.00 0.00 4.35
163 164 7.707035 AGTTCTAGATACATCCATTTTCACGAC 59.293 37.037 0.00 0.00 0.00 4.34
164 165 7.107639 TCTAGATACATCCATTTTCACGACA 57.892 36.000 0.00 0.00 0.00 4.35
165 166 7.552459 TCTAGATACATCCATTTTCACGACAA 58.448 34.615 0.00 0.00 0.00 3.18
166 167 6.668541 AGATACATCCATTTTCACGACAAG 57.331 37.500 0.00 0.00 0.00 3.16
167 168 6.173339 AGATACATCCATTTTCACGACAAGT 58.827 36.000 0.00 0.00 0.00 3.16
168 169 7.327975 AGATACATCCATTTTCACGACAAGTA 58.672 34.615 0.00 0.00 0.00 2.24
169 170 7.822334 AGATACATCCATTTTCACGACAAGTAA 59.178 33.333 0.00 0.00 0.00 2.24
170 171 6.817765 ACATCCATTTTCACGACAAGTAAT 57.182 33.333 0.00 0.00 0.00 1.89
171 172 7.214467 ACATCCATTTTCACGACAAGTAATT 57.786 32.000 0.00 0.00 0.00 1.40
172 173 7.305474 ACATCCATTTTCACGACAAGTAATTC 58.695 34.615 0.00 0.00 0.00 2.17
173 174 6.249035 TCCATTTTCACGACAAGTAATTCC 57.751 37.500 0.00 0.00 0.00 3.01
174 175 5.086058 CCATTTTCACGACAAGTAATTCCG 58.914 41.667 0.00 0.00 0.00 4.30
175 176 5.106869 CCATTTTCACGACAAGTAATTCCGA 60.107 40.000 0.00 0.00 0.00 4.55
176 177 5.987777 TTTTCACGACAAGTAATTCCGAA 57.012 34.783 0.00 0.00 0.00 4.30
177 178 4.977741 TTCACGACAAGTAATTCCGAAC 57.022 40.909 0.00 0.00 0.00 3.95
178 179 2.981805 TCACGACAAGTAATTCCGAACG 59.018 45.455 0.00 0.00 0.00 3.95
179 180 2.091588 CACGACAAGTAATTCCGAACGG 59.908 50.000 6.94 6.94 0.00 4.44
180 181 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
181 182 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
182 183 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
183 184 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
184 185 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
185 186 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
257 259 2.938428 AGAAGACTCTGATCAGGGGT 57.062 50.000 26.23 21.40 31.73 4.95
268 270 2.111384 GATCAGGGGTCAGAGCTACAA 58.889 52.381 0.00 0.00 0.00 2.41
371 373 1.765230 AGTCGTCCGATAAGCTCCTT 58.235 50.000 0.00 0.00 0.00 3.36
372 374 2.928334 AGTCGTCCGATAAGCTCCTTA 58.072 47.619 0.00 0.00 0.00 2.69
389 391 0.868602 TTATCGCGTACAAGCCTCGC 60.869 55.000 5.77 0.00 45.28 5.03
601 606 2.766263 GGGGATGTAGTGTGTGATCTGA 59.234 50.000 0.00 0.00 0.00 3.27
673 684 2.039084 GACTCAGATTTGTGGACTGGGT 59.961 50.000 0.00 0.00 46.16 4.51
700 711 6.097839 ACGGGAATACATACTGACATGTTACT 59.902 38.462 0.00 0.00 39.77 2.24
704 715 9.982651 GGAATACATACTGACATGTTACTATGT 57.017 33.333 19.48 19.48 43.61 2.29
730 741 2.977914 TGTGCATAGTTCTCTGGCTTC 58.022 47.619 0.00 0.00 0.00 3.86
732 743 3.008375 TGTGCATAGTTCTCTGGCTTCTT 59.992 43.478 0.00 0.00 0.00 2.52
734 745 5.178797 GTGCATAGTTCTCTGGCTTCTTTA 58.821 41.667 0.00 0.00 0.00 1.85
735 746 5.819901 GTGCATAGTTCTCTGGCTTCTTTAT 59.180 40.000 0.00 0.00 0.00 1.40
738 749 7.394359 TGCATAGTTCTCTGGCTTCTTTATTTT 59.606 33.333 0.00 0.00 0.00 1.82
755 766 8.749354 TCTTTATTTTAGGGAAATTTCTCTGGC 58.251 33.333 27.53 6.82 38.75 4.85
756 767 8.664669 TTTATTTTAGGGAAATTTCTCTGGCT 57.335 30.769 27.53 13.27 38.75 4.75
757 768 8.664669 TTATTTTAGGGAAATTTCTCTGGCTT 57.335 30.769 27.53 13.72 38.75 4.35
758 769 6.994421 TTTTAGGGAAATTTCTCTGGCTTT 57.006 33.333 27.53 5.72 38.75 3.51
759 770 5.982890 TTAGGGAAATTTCTCTGGCTTTG 57.017 39.130 27.53 0.00 38.75 2.77
760 771 3.849527 AGGGAAATTTCTCTGGCTTTGT 58.150 40.909 19.93 0.00 36.45 2.83
761 772 3.829026 AGGGAAATTTCTCTGGCTTTGTC 59.171 43.478 19.93 0.00 36.45 3.18
762 773 3.573967 GGGAAATTTCTCTGGCTTTGTCA 59.426 43.478 17.42 0.00 0.00 3.58
763 774 4.321527 GGGAAATTTCTCTGGCTTTGTCAG 60.322 45.833 17.42 0.00 36.50 3.51
764 775 4.279420 GGAAATTTCTCTGGCTTTGTCAGT 59.721 41.667 17.42 0.00 36.55 3.41
765 776 5.473504 GGAAATTTCTCTGGCTTTGTCAGTA 59.526 40.000 17.42 0.00 36.55 2.74
766 777 6.348868 GGAAATTTCTCTGGCTTTGTCAGTAG 60.349 42.308 17.42 0.00 36.55 2.57
767 778 4.689612 TTTCTCTGGCTTTGTCAGTAGT 57.310 40.909 0.00 0.00 36.55 2.73
768 779 4.689612 TTCTCTGGCTTTGTCAGTAGTT 57.310 40.909 0.00 0.00 36.55 2.24
769 780 4.258702 TCTCTGGCTTTGTCAGTAGTTC 57.741 45.455 0.00 0.00 36.55 3.01
770 781 3.641436 TCTCTGGCTTTGTCAGTAGTTCA 59.359 43.478 0.00 0.00 36.55 3.18
771 782 3.993081 CTCTGGCTTTGTCAGTAGTTCAG 59.007 47.826 0.00 0.00 36.55 3.02
772 783 3.388024 TCTGGCTTTGTCAGTAGTTCAGT 59.612 43.478 0.00 0.00 36.55 3.41
773 784 4.587262 TCTGGCTTTGTCAGTAGTTCAGTA 59.413 41.667 0.00 0.00 36.55 2.74
774 785 4.628074 TGGCTTTGTCAGTAGTTCAGTAC 58.372 43.478 0.00 0.00 0.00 2.73
775 786 4.100344 TGGCTTTGTCAGTAGTTCAGTACA 59.900 41.667 0.00 0.00 0.00 2.90
776 787 5.054477 GGCTTTGTCAGTAGTTCAGTACAA 58.946 41.667 0.00 0.00 0.00 2.41
777 788 5.050295 GGCTTTGTCAGTAGTTCAGTACAAC 60.050 44.000 0.00 0.00 0.00 3.32
778 789 5.522460 GCTTTGTCAGTAGTTCAGTACAACA 59.478 40.000 0.00 0.00 0.00 3.33
779 790 6.202954 GCTTTGTCAGTAGTTCAGTACAACAT 59.797 38.462 0.00 0.00 0.00 2.71
780 791 7.569591 GCTTTGTCAGTAGTTCAGTACAACATC 60.570 40.741 0.00 0.00 0.00 3.06
781 792 5.779922 TGTCAGTAGTTCAGTACAACATCC 58.220 41.667 0.00 0.00 0.00 3.51
782 793 5.538813 TGTCAGTAGTTCAGTACAACATCCT 59.461 40.000 0.00 0.00 0.00 3.24
783 794 5.864474 GTCAGTAGTTCAGTACAACATCCTG 59.136 44.000 0.00 0.48 0.00 3.86
784 795 5.538813 TCAGTAGTTCAGTACAACATCCTGT 59.461 40.000 0.00 0.00 0.00 4.00
785 796 5.635280 CAGTAGTTCAGTACAACATCCTGTG 59.365 44.000 0.00 0.00 0.00 3.66
786 797 4.008074 AGTTCAGTACAACATCCTGTGG 57.992 45.455 0.00 0.00 0.00 4.17
787 798 2.472695 TCAGTACAACATCCTGTGGC 57.527 50.000 0.00 0.00 0.00 5.01
788 799 1.003118 TCAGTACAACATCCTGTGGCC 59.997 52.381 0.00 0.00 0.00 5.36
789 800 1.064003 AGTACAACATCCTGTGGCCA 58.936 50.000 0.00 0.00 0.00 5.36
790 801 1.635487 AGTACAACATCCTGTGGCCAT 59.365 47.619 9.72 0.00 0.00 4.40
791 802 2.843730 AGTACAACATCCTGTGGCCATA 59.156 45.455 9.72 4.92 0.00 2.74
792 803 2.425143 ACAACATCCTGTGGCCATAG 57.575 50.000 21.96 21.96 0.00 2.23
823 861 1.981256 TTTGAGAACTTCCTGTGGCC 58.019 50.000 0.00 0.00 0.00 5.36
827 865 2.237143 TGAGAACTTCCTGTGGCCATAG 59.763 50.000 21.96 21.96 0.00 2.23
845 883 1.145377 GGTGTGGACCGTGTTCACT 59.855 57.895 14.18 0.00 42.16 3.41
846 884 0.390124 GGTGTGGACCGTGTTCACTA 59.610 55.000 14.18 1.99 42.16 2.74
847 885 1.494824 GTGTGGACCGTGTTCACTAC 58.505 55.000 14.18 8.63 42.16 2.73
849 887 1.481363 TGTGGACCGTGTTCACTACAA 59.519 47.619 14.18 0.00 42.16 2.41
1036 1086 0.614979 CGGTTCCTCTCCCTCCAAGA 60.615 60.000 0.00 0.00 0.00 3.02
1037 1087 0.906066 GGTTCCTCTCCCTCCAAGAC 59.094 60.000 0.00 0.00 0.00 3.01
1061 1111 0.321653 ACTGCCAAAGTAAGCTCCCG 60.322 55.000 0.00 0.00 37.36 5.14
1081 1138 2.355108 CGCTTCATCTTCTTCCTTCCCA 60.355 50.000 0.00 0.00 0.00 4.37
1082 1139 3.683847 CGCTTCATCTTCTTCCTTCCCAT 60.684 47.826 0.00 0.00 0.00 4.00
1083 1140 3.882288 GCTTCATCTTCTTCCTTCCCATC 59.118 47.826 0.00 0.00 0.00 3.51
1084 1141 4.459330 CTTCATCTTCTTCCTTCCCATCC 58.541 47.826 0.00 0.00 0.00 3.51
1085 1142 3.740780 TCATCTTCTTCCTTCCCATCCT 58.259 45.455 0.00 0.00 0.00 3.24
1086 1143 4.114597 TCATCTTCTTCCTTCCCATCCTT 58.885 43.478 0.00 0.00 0.00 3.36
1087 1144 4.541714 TCATCTTCTTCCTTCCCATCCTTT 59.458 41.667 0.00 0.00 0.00 3.11
1088 1145 5.015603 TCATCTTCTTCCTTCCCATCCTTTT 59.984 40.000 0.00 0.00 0.00 2.27
1089 1146 5.339423 TCTTCTTCCTTCCCATCCTTTTT 57.661 39.130 0.00 0.00 0.00 1.94
1090 1147 5.325239 TCTTCTTCCTTCCCATCCTTTTTC 58.675 41.667 0.00 0.00 0.00 2.29
1091 1148 4.740154 TCTTCCTTCCCATCCTTTTTCA 57.260 40.909 0.00 0.00 0.00 2.69
1098 1155 2.986019 TCCCATCCTTTTTCACTCCTCA 59.014 45.455 0.00 0.00 0.00 3.86
1101 1158 3.192212 CCATCCTTTTTCACTCCTCAAGC 59.808 47.826 0.00 0.00 0.00 4.01
1130 1190 3.700130 ATCGTGTCGTCGTTTGAATTC 57.300 42.857 0.00 0.00 0.00 2.17
1132 1192 2.722629 TCGTGTCGTCGTTTGAATTCTC 59.277 45.455 7.05 0.00 0.00 2.87
1133 1193 2.724690 CGTGTCGTCGTTTGAATTCTCT 59.275 45.455 7.05 0.00 0.00 3.10
1134 1194 3.420544 CGTGTCGTCGTTTGAATTCTCTG 60.421 47.826 7.05 0.00 0.00 3.35
1135 1195 2.475111 TGTCGTCGTTTGAATTCTCTGC 59.525 45.455 7.05 0.00 0.00 4.26
1136 1196 2.731976 GTCGTCGTTTGAATTCTCTGCT 59.268 45.455 7.05 0.00 0.00 4.24
1137 1197 3.184581 GTCGTCGTTTGAATTCTCTGCTT 59.815 43.478 7.05 0.00 0.00 3.91
1138 1198 3.428870 TCGTCGTTTGAATTCTCTGCTTC 59.571 43.478 7.05 0.00 0.00 3.86
1139 1199 3.184379 CGTCGTTTGAATTCTCTGCTTCA 59.816 43.478 7.05 0.00 0.00 3.02
1141 1201 5.615544 CGTCGTTTGAATTCTCTGCTTCAAT 60.616 40.000 7.05 0.00 40.13 2.57
1142 1202 6.401047 CGTCGTTTGAATTCTCTGCTTCAATA 60.401 38.462 7.05 0.00 40.13 1.90
1143 1203 7.467623 GTCGTTTGAATTCTCTGCTTCAATAT 58.532 34.615 7.05 0.00 40.13 1.28
1144 1204 7.965107 GTCGTTTGAATTCTCTGCTTCAATATT 59.035 33.333 7.05 0.00 40.13 1.28
1145 1205 8.514594 TCGTTTGAATTCTCTGCTTCAATATTT 58.485 29.630 7.05 0.00 40.13 1.40
1146 1206 9.132521 CGTTTGAATTCTCTGCTTCAATATTTT 57.867 29.630 7.05 0.00 40.13 1.82
1210 1270 3.704512 TGTAACGAGTTTAGTGCACGAA 58.295 40.909 12.01 10.15 0.00 3.85
1211 1271 4.111198 TGTAACGAGTTTAGTGCACGAAA 58.889 39.130 19.51 19.51 0.00 3.46
1242 1302 0.788995 CTGCTGCTCAGTTCAGTTCG 59.211 55.000 0.00 0.00 38.02 3.95
1328 1428 9.868277 AAAATTGTTGGCGAAATGAGATAATTA 57.132 25.926 0.00 0.00 0.00 1.40
1332 1432 6.318648 TGTTGGCGAAATGAGATAATTAGCTT 59.681 34.615 4.45 0.00 0.00 3.74
1465 1565 0.107654 ACAAGATAGGAACCGCTGCC 60.108 55.000 0.00 0.00 0.00 4.85
1468 1568 4.547367 ATAGGAACCGCTGCCGCC 62.547 66.667 0.00 0.00 0.00 6.13
1559 1662 2.577059 CGGAGGCGCAGGAAAGTA 59.423 61.111 10.83 0.00 0.00 2.24
1561 1664 1.295423 GGAGGCGCAGGAAAGTACA 59.705 57.895 10.83 0.00 0.00 2.90
1573 1676 2.076863 GAAAGTACAACCATCAGCGCT 58.923 47.619 2.64 2.64 0.00 5.92
1735 1838 2.665603 GCGGACAAGAAGGGCTCT 59.334 61.111 0.00 0.00 35.13 4.09
2028 2137 4.259810 CGCCATACATTTCAACGAGTACTG 60.260 45.833 0.00 0.00 0.00 2.74
2029 2138 4.868171 GCCATACATTTCAACGAGTACTGA 59.132 41.667 0.00 0.00 0.00 3.41
2030 2139 5.523916 GCCATACATTTCAACGAGTACTGAT 59.476 40.000 0.00 0.00 0.00 2.90
2031 2140 6.037172 GCCATACATTTCAACGAGTACTGATT 59.963 38.462 0.00 0.00 0.00 2.57
2032 2141 7.223971 GCCATACATTTCAACGAGTACTGATTA 59.776 37.037 0.00 0.00 0.00 1.75
2033 2142 9.093970 CCATACATTTCAACGAGTACTGATTAA 57.906 33.333 0.00 0.00 0.00 1.40
2036 2145 8.771920 ACATTTCAACGAGTACTGATTAATCA 57.228 30.769 17.07 17.07 35.16 2.57
2037 2146 9.214957 ACATTTCAACGAGTACTGATTAATCAA 57.785 29.630 18.47 2.75 36.18 2.57
2038 2147 9.694520 CATTTCAACGAGTACTGATTAATCAAG 57.305 33.333 18.47 14.30 36.18 3.02
2039 2148 6.887376 TCAACGAGTACTGATTAATCAAGC 57.113 37.500 18.47 11.33 36.18 4.01
2040 2149 5.810587 TCAACGAGTACTGATTAATCAAGCC 59.189 40.000 18.47 9.14 36.18 4.35
2041 2150 5.599999 ACGAGTACTGATTAATCAAGCCT 57.400 39.130 18.47 13.23 36.18 4.58
2042 2151 5.352284 ACGAGTACTGATTAATCAAGCCTG 58.648 41.667 18.47 9.41 36.18 4.85
2043 2152 5.105310 ACGAGTACTGATTAATCAAGCCTGT 60.105 40.000 18.47 14.25 36.18 4.00
2044 2153 5.812642 CGAGTACTGATTAATCAAGCCTGTT 59.187 40.000 18.47 0.08 36.18 3.16
2045 2154 6.313905 CGAGTACTGATTAATCAAGCCTGTTT 59.686 38.462 18.47 5.67 36.18 2.83
2046 2155 7.383102 AGTACTGATTAATCAAGCCTGTTTG 57.617 36.000 18.47 6.78 36.18 2.93
2070 2179 3.462483 TTCTCTGCGTGGTTCTGTAAA 57.538 42.857 0.00 0.00 0.00 2.01
2130 2243 2.747446 GCACAGGAATACACCGTGATTT 59.253 45.455 5.28 0.00 36.96 2.17
2134 2247 5.410132 CACAGGAATACACCGTGATTTGTAA 59.590 40.000 5.28 0.00 36.96 2.41
2155 2268 8.804688 TGTAAGAATTAAACCCAACGATTTTG 57.195 30.769 0.00 0.00 28.70 2.44
2156 2269 6.779115 AAGAATTAAACCCAACGATTTTGC 57.221 33.333 0.00 0.00 0.00 3.68
2174 2287 9.651718 CGATTTTGCTGGAGTATTATAGAAAAC 57.348 33.333 0.00 0.00 0.00 2.43
2207 2322 7.639945 AGATGTTAAGTAACTTTTCTGTGTGC 58.360 34.615 3.07 0.00 37.12 4.57
2208 2323 6.126568 TGTTAAGTAACTTTTCTGTGTGCC 57.873 37.500 3.07 0.00 37.12 5.01
2209 2324 5.066764 TGTTAAGTAACTTTTCTGTGTGCCC 59.933 40.000 3.07 0.00 37.12 5.36
2210 2325 2.583143 AGTAACTTTTCTGTGTGCCCC 58.417 47.619 0.00 0.00 0.00 5.80
2217 2332 0.478072 TTCTGTGTGCCCCTGAACAT 59.522 50.000 0.00 0.00 0.00 2.71
2219 2334 0.037303 CTGTGTGCCCCTGAACATCT 59.963 55.000 0.00 0.00 0.00 2.90
2230 2345 3.005554 CCTGAACATCTAAGTGGCTGTG 58.994 50.000 0.00 0.00 0.00 3.66
2294 2409 2.401766 CGAATCCCAGCAGCCACAC 61.402 63.158 0.00 0.00 0.00 3.82
2305 2420 2.162681 GCAGCCACACCTCACTATTTT 58.837 47.619 0.00 0.00 0.00 1.82
2306 2421 2.558359 GCAGCCACACCTCACTATTTTT 59.442 45.455 0.00 0.00 0.00 1.94
2333 2448 7.936496 TTTTTGCTTTTCCAATCCTTCTTTT 57.064 28.000 0.00 0.00 0.00 2.27
2338 2453 8.415950 TGCTTTTCCAATCCTTCTTTTACATA 57.584 30.769 0.00 0.00 0.00 2.29
2339 2454 8.865090 TGCTTTTCCAATCCTTCTTTTACATAA 58.135 29.630 0.00 0.00 0.00 1.90
2340 2455 9.140286 GCTTTTCCAATCCTTCTTTTACATAAC 57.860 33.333 0.00 0.00 0.00 1.89
2341 2456 9.341899 CTTTTCCAATCCTTCTTTTACATAACG 57.658 33.333 0.00 0.00 0.00 3.18
2342 2457 6.431198 TCCAATCCTTCTTTTACATAACGC 57.569 37.500 0.00 0.00 0.00 4.84
2343 2458 6.177610 TCCAATCCTTCTTTTACATAACGCT 58.822 36.000 0.00 0.00 0.00 5.07
2344 2459 6.093495 TCCAATCCTTCTTTTACATAACGCTG 59.907 38.462 0.00 0.00 0.00 5.18
2369 2484 4.051922 CGATTAACGGCTCTGATTAGCTT 58.948 43.478 0.00 0.00 42.37 3.74
2370 2485 5.220381 CGATTAACGGCTCTGATTAGCTTA 58.780 41.667 0.00 0.00 42.37 3.09
2371 2486 5.343593 CGATTAACGGCTCTGATTAGCTTAG 59.656 44.000 0.00 0.00 42.37 2.18
2372 2487 2.517650 ACGGCTCTGATTAGCTTAGC 57.482 50.000 0.00 0.00 42.37 3.09
2373 2488 2.035632 ACGGCTCTGATTAGCTTAGCT 58.964 47.619 12.67 12.67 42.37 3.32
2385 2500 1.342819 AGCTTAGCTCTTATGGAGGCG 59.657 52.381 0.00 0.00 42.08 5.52
2403 2518 2.667418 CTGACAGCCAGACCCCAG 59.333 66.667 0.00 0.00 45.78 4.45
2419 2534 2.660552 AGACCGTTTGCACGTCGG 60.661 61.111 17.87 17.87 45.62 4.79
2438 2553 2.287194 CCCCACCCATCCCCTCTT 60.287 66.667 0.00 0.00 0.00 2.85
2440 2555 1.308216 CCCACCCATCCCCTCTTCT 60.308 63.158 0.00 0.00 0.00 2.85
2442 2557 1.348775 CCACCCATCCCCTCTTCTCC 61.349 65.000 0.00 0.00 0.00 3.71
2499 2624 4.416601 CCCCCGGTCCCTCTCCTT 62.417 72.222 0.00 0.00 0.00 3.36
2513 2638 1.160137 CTCCTTTGGAGTTTCTGCGG 58.840 55.000 5.50 0.00 44.25 5.69
2605 2731 2.429610 CCCCTTTTCCTCGTCTAATCGA 59.570 50.000 0.00 0.00 38.19 3.59
2850 2976 1.671328 CGCTCCATTCTCTCTACGTGA 59.329 52.381 0.00 0.00 0.00 4.35
2860 2986 7.095857 CCATTCTCTCTACGTGATAATTTGCTC 60.096 40.741 0.00 0.00 0.00 4.26
2861 2987 6.451064 TCTCTCTACGTGATAATTTGCTCA 57.549 37.500 0.00 0.00 0.00 4.26
2864 2990 3.796717 TCTACGTGATAATTTGCTCAGCG 59.203 43.478 0.00 0.00 0.00 5.18
2865 2991 2.346803 ACGTGATAATTTGCTCAGCGT 58.653 42.857 0.00 0.00 0.00 5.07
2866 2992 2.742053 ACGTGATAATTTGCTCAGCGTT 59.258 40.909 0.00 0.00 30.57 4.84
2867 2993 3.093574 CGTGATAATTTGCTCAGCGTTG 58.906 45.455 0.00 0.00 0.00 4.10
2868 2994 3.429085 GTGATAATTTGCTCAGCGTTGG 58.571 45.455 0.00 0.00 0.00 3.77
2888 3014 0.250684 TGCCATTGCTTTCCGTCTCA 60.251 50.000 0.00 0.00 38.71 3.27
2890 3016 1.813513 CCATTGCTTTCCGTCTCAGT 58.186 50.000 0.00 0.00 0.00 3.41
2891 3017 2.154462 CCATTGCTTTCCGTCTCAGTT 58.846 47.619 0.00 0.00 0.00 3.16
2892 3018 2.095567 CCATTGCTTTCCGTCTCAGTTG 60.096 50.000 0.00 0.00 0.00 3.16
2908 3034 6.426328 GTCTCAGTTGTGAATTTGATGTCTCT 59.574 38.462 0.00 0.00 30.14 3.10
2926 3052 5.593010 GTCTCTAGACAAGCATTCCGTAAT 58.407 41.667 5.24 0.00 44.18 1.89
2950 3076 1.315690 AATGCGGGCTCATCTGATTG 58.684 50.000 0.00 0.00 0.00 2.67
2957 3083 1.407979 GGCTCATCTGATTGGGCTTTG 59.592 52.381 10.36 0.00 42.94 2.77
2961 3087 4.142004 GCTCATCTGATTGGGCTTTGAAAT 60.142 41.667 5.16 0.00 40.09 2.17
2965 3091 3.004862 CTGATTGGGCTTTGAAATTGCC 58.995 45.455 0.00 0.00 45.42 4.52
2975 3101 6.238456 GGGCTTTGAAATTGCCTATATTTTGC 60.238 38.462 7.92 0.00 45.45 3.68
3007 3134 9.974980 TTTTTAATGGATCACTACTTTGAAACC 57.025 29.630 0.00 0.00 0.00 3.27
3028 3155 4.158025 ACCGTAGTTTCAGTCTCATGGTAG 59.842 45.833 0.00 0.00 0.00 3.18
3029 3156 4.106197 CGTAGTTTCAGTCTCATGGTAGC 58.894 47.826 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.003580 TGGCTAGGCAGGAAGAACAAG 59.996 52.381 16.16 0.00 0.00 3.16
81 82 4.607239 AGTAATTCCGAACAGAGGGAGTA 58.393 43.478 0.00 0.00 33.01 2.59
82 83 3.442076 AGTAATTCCGAACAGAGGGAGT 58.558 45.455 0.00 0.00 33.01 3.85
83 84 4.184629 CAAGTAATTCCGAACAGAGGGAG 58.815 47.826 0.00 0.00 33.01 4.30
84 85 3.581332 ACAAGTAATTCCGAACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
85 86 3.933332 GACAAGTAATTCCGAACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
86 87 3.612860 CGACAAGTAATTCCGAACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
87 88 3.060895 GCGACAAGTAATTCCGAACAGAG 59.939 47.826 0.00 0.00 0.00 3.35
88 89 2.991190 GCGACAAGTAATTCCGAACAGA 59.009 45.455 0.00 0.00 0.00 3.41
89 90 2.734606 TGCGACAAGTAATTCCGAACAG 59.265 45.455 0.00 0.00 0.00 3.16
90 91 2.734606 CTGCGACAAGTAATTCCGAACA 59.265 45.455 0.00 0.00 0.00 3.18
91 92 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
92 93 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
93 94 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
94 95 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
95 96 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
96 97 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
97 98 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
98 99 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
99 100 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
100 101 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
101 102 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
102 103 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
103 104 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
104 105 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
105 106 5.631512 GTCTAGATACATCCATTTCTGCGAC 59.368 44.000 0.00 0.00 0.00 5.19
106 107 5.301805 TGTCTAGATACATCCATTTCTGCGA 59.698 40.000 0.00 0.00 0.00 5.10
107 108 5.532557 TGTCTAGATACATCCATTTCTGCG 58.467 41.667 0.00 0.00 0.00 5.18
108 109 9.664332 AATATGTCTAGATACATCCATTTCTGC 57.336 33.333 0.00 0.00 40.52 4.26
135 136 9.529325 CGTGAAAATGGATGTATCTAGAACTAA 57.471 33.333 0.00 0.00 0.00 2.24
136 137 8.909923 TCGTGAAAATGGATGTATCTAGAACTA 58.090 33.333 0.00 0.00 0.00 2.24
137 138 7.707035 GTCGTGAAAATGGATGTATCTAGAACT 59.293 37.037 0.00 0.00 0.00 3.01
138 139 7.491372 TGTCGTGAAAATGGATGTATCTAGAAC 59.509 37.037 0.00 0.00 0.00 3.01
139 140 7.552459 TGTCGTGAAAATGGATGTATCTAGAA 58.448 34.615 0.00 0.00 0.00 2.10
140 141 7.107639 TGTCGTGAAAATGGATGTATCTAGA 57.892 36.000 0.00 0.00 0.00 2.43
141 142 7.492669 ACTTGTCGTGAAAATGGATGTATCTAG 59.507 37.037 0.00 0.00 0.00 2.43
142 143 7.327975 ACTTGTCGTGAAAATGGATGTATCTA 58.672 34.615 0.00 0.00 0.00 1.98
143 144 6.173339 ACTTGTCGTGAAAATGGATGTATCT 58.827 36.000 0.00 0.00 0.00 1.98
144 145 6.422776 ACTTGTCGTGAAAATGGATGTATC 57.577 37.500 0.00 0.00 0.00 2.24
145 146 7.915293 TTACTTGTCGTGAAAATGGATGTAT 57.085 32.000 0.00 0.00 0.00 2.29
146 147 7.915293 ATTACTTGTCGTGAAAATGGATGTA 57.085 32.000 0.00 0.00 0.00 2.29
147 148 6.817765 ATTACTTGTCGTGAAAATGGATGT 57.182 33.333 0.00 0.00 0.00 3.06
148 149 6.747280 GGAATTACTTGTCGTGAAAATGGATG 59.253 38.462 0.00 0.00 0.00 3.51
149 150 6.403200 CGGAATTACTTGTCGTGAAAATGGAT 60.403 38.462 0.00 0.00 0.00 3.41
150 151 5.106869 CGGAATTACTTGTCGTGAAAATGGA 60.107 40.000 0.00 0.00 0.00 3.41
151 152 5.086058 CGGAATTACTTGTCGTGAAAATGG 58.914 41.667 0.00 0.00 0.00 3.16
152 153 5.922546 TCGGAATTACTTGTCGTGAAAATG 58.077 37.500 0.00 0.00 0.00 2.32
153 154 6.368213 GTTCGGAATTACTTGTCGTGAAAAT 58.632 36.000 0.00 0.00 0.00 1.82
154 155 5.556758 CGTTCGGAATTACTTGTCGTGAAAA 60.557 40.000 0.00 0.00 0.00 2.29
155 156 4.084952 CGTTCGGAATTACTTGTCGTGAAA 60.085 41.667 0.00 0.00 0.00 2.69
156 157 3.426191 CGTTCGGAATTACTTGTCGTGAA 59.574 43.478 0.00 0.00 0.00 3.18
157 158 2.981805 CGTTCGGAATTACTTGTCGTGA 59.018 45.455 0.00 0.00 0.00 4.35
158 159 2.091588 CCGTTCGGAATTACTTGTCGTG 59.908 50.000 5.19 0.00 0.00 4.35
159 160 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
160 161 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
161 162 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
162 163 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
163 164 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
164 165 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
165 166 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
166 167 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
167 168 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
168 169 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
169 170 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
170 171 1.318158 GCTACTCCCTCCGTTCGGAA 61.318 60.000 14.79 0.04 33.41 4.30
171 172 1.751927 GCTACTCCCTCCGTTCGGA 60.752 63.158 13.34 13.34 0.00 4.55
172 173 1.321074 AAGCTACTCCCTCCGTTCGG 61.321 60.000 4.74 4.74 0.00 4.30
173 174 0.100861 GAAGCTACTCCCTCCGTTCG 59.899 60.000 0.00 0.00 0.00 3.95
174 175 1.476477 AGAAGCTACTCCCTCCGTTC 58.524 55.000 0.00 0.00 0.00 3.95
175 176 2.759535 GTTAGAAGCTACTCCCTCCGTT 59.240 50.000 0.00 0.00 0.00 4.44
176 177 2.377073 GTTAGAAGCTACTCCCTCCGT 58.623 52.381 0.00 0.00 0.00 4.69
177 178 1.334243 CGTTAGAAGCTACTCCCTCCG 59.666 57.143 0.00 0.00 0.00 4.63
178 179 1.067364 GCGTTAGAAGCTACTCCCTCC 59.933 57.143 0.00 0.00 0.00 4.30
179 180 1.749634 TGCGTTAGAAGCTACTCCCTC 59.250 52.381 0.00 0.00 35.28 4.30
180 181 1.848652 TGCGTTAGAAGCTACTCCCT 58.151 50.000 0.00 0.00 35.28 4.20
181 182 2.159085 ACATGCGTTAGAAGCTACTCCC 60.159 50.000 0.00 0.00 35.28 4.30
182 183 3.117046 GACATGCGTTAGAAGCTACTCC 58.883 50.000 0.00 0.00 35.28 3.85
183 184 4.035278 AGACATGCGTTAGAAGCTACTC 57.965 45.455 0.00 0.00 35.28 2.59
184 185 4.177026 CAAGACATGCGTTAGAAGCTACT 58.823 43.478 0.00 0.00 35.28 2.57
185 186 3.927142 ACAAGACATGCGTTAGAAGCTAC 59.073 43.478 0.00 0.00 35.28 3.58
268 270 1.072331 AGGTGATTGCGTTTCCAGAGT 59.928 47.619 0.00 0.00 0.00 3.24
371 373 1.298863 GCGAGGCTTGTACGCGATA 60.299 57.895 15.93 0.00 42.65 2.92
372 374 2.582498 GCGAGGCTTGTACGCGAT 60.582 61.111 15.93 0.00 42.65 4.58
492 494 5.419471 TCTTCTACCTAAGAACTGGCTTCTC 59.581 44.000 0.00 0.00 39.36 2.87
601 606 3.116096 TCAACTATGTACAGGCCCTCT 57.884 47.619 0.00 0.00 0.00 3.69
673 684 6.474140 ACATGTCAGTATGTATTCCCGTAA 57.526 37.500 0.00 0.00 39.40 3.18
700 711 8.306761 CCAGAGAACTATGCACATGTATACATA 58.693 37.037 17.86 6.63 34.26 2.29
704 715 5.305386 AGCCAGAGAACTATGCACATGTATA 59.695 40.000 0.00 0.00 0.00 1.47
713 724 6.934048 AATAAAGAAGCCAGAGAACTATGC 57.066 37.500 0.00 0.00 0.00 3.14
718 729 6.884836 TCCCTAAAATAAAGAAGCCAGAGAAC 59.115 38.462 0.00 0.00 0.00 3.01
730 741 8.753133 AGCCAGAGAAATTTCCCTAAAATAAAG 58.247 33.333 14.61 0.00 36.54 1.85
732 743 8.664669 AAGCCAGAGAAATTTCCCTAAAATAA 57.335 30.769 14.61 0.00 36.54 1.40
734 745 7.016563 ACAAAGCCAGAGAAATTTCCCTAAAAT 59.983 33.333 14.61 0.00 39.30 1.82
735 746 6.326323 ACAAAGCCAGAGAAATTTCCCTAAAA 59.674 34.615 14.61 0.00 0.00 1.52
738 749 4.998051 ACAAAGCCAGAGAAATTTCCCTA 58.002 39.130 14.61 0.00 0.00 3.53
754 765 5.522460 TGTTGTACTGAACTACTGACAAAGC 59.478 40.000 0.00 0.00 35.21 3.51
755 766 7.095607 GGATGTTGTACTGAACTACTGACAAAG 60.096 40.741 0.00 0.00 35.21 2.77
756 767 6.704493 GGATGTTGTACTGAACTACTGACAAA 59.296 38.462 0.00 0.00 35.21 2.83
757 768 6.041637 AGGATGTTGTACTGAACTACTGACAA 59.958 38.462 0.00 0.00 35.21 3.18
758 769 5.538813 AGGATGTTGTACTGAACTACTGACA 59.461 40.000 0.00 0.00 35.21 3.58
759 770 5.864474 CAGGATGTTGTACTGAACTACTGAC 59.136 44.000 0.00 0.00 41.74 3.51
760 771 6.025749 CAGGATGTTGTACTGAACTACTGA 57.974 41.667 0.00 0.00 41.74 3.41
813 851 0.327924 CACACCTATGGCCACAGGAA 59.672 55.000 36.90 5.20 35.76 3.36
823 861 1.001520 TGAACACGGTCCACACCTATG 59.998 52.381 0.00 0.00 41.17 2.23
827 865 0.390124 TAGTGAACACGGTCCACACC 59.610 55.000 0.00 0.00 39.69 4.16
838 876 6.149973 ACGCTGTAGTAGTATTGTAGTGAACA 59.850 38.462 0.00 0.00 35.88 3.18
841 879 6.258727 GGTACGCTGTAGTAGTATTGTAGTGA 59.741 42.308 0.00 0.00 0.00 3.41
842 880 6.425504 GGTACGCTGTAGTAGTATTGTAGTG 58.574 44.000 0.00 0.00 0.00 2.74
843 881 6.610741 GGTACGCTGTAGTAGTATTGTAGT 57.389 41.667 0.00 0.00 0.00 2.73
1018 1068 0.906066 GTCTTGGAGGGAGAGGAACC 59.094 60.000 0.00 0.00 0.00 3.62
1036 1086 1.609208 CTTACTTTGGCAGTGGCAGT 58.391 50.000 19.65 16.87 43.71 4.40
1037 1087 0.242017 GCTTACTTTGGCAGTGGCAG 59.758 55.000 19.65 11.71 43.71 4.85
1061 1111 3.356529 TGGGAAGGAAGAAGATGAAGC 57.643 47.619 0.00 0.00 0.00 3.86
1081 1138 4.077822 CAGCTTGAGGAGTGAAAAAGGAT 58.922 43.478 0.00 0.00 0.00 3.24
1082 1139 3.480470 CAGCTTGAGGAGTGAAAAAGGA 58.520 45.455 0.00 0.00 0.00 3.36
1083 1140 2.030451 GCAGCTTGAGGAGTGAAAAAGG 60.030 50.000 0.00 0.00 0.00 3.11
1084 1141 2.883386 AGCAGCTTGAGGAGTGAAAAAG 59.117 45.455 0.00 0.00 0.00 2.27
1085 1142 2.936202 AGCAGCTTGAGGAGTGAAAAA 58.064 42.857 0.00 0.00 0.00 1.94
1086 1143 2.645838 AGCAGCTTGAGGAGTGAAAA 57.354 45.000 0.00 0.00 0.00 2.29
1087 1144 2.027745 CCTAGCAGCTTGAGGAGTGAAA 60.028 50.000 5.35 0.00 31.45 2.69
1088 1145 1.552337 CCTAGCAGCTTGAGGAGTGAA 59.448 52.381 5.35 0.00 31.45 3.18
1089 1146 1.189752 CCTAGCAGCTTGAGGAGTGA 58.810 55.000 5.35 0.00 31.45 3.41
1090 1147 1.189752 TCCTAGCAGCTTGAGGAGTG 58.810 55.000 9.61 0.00 34.36 3.51
1091 1148 1.944177 TTCCTAGCAGCTTGAGGAGT 58.056 50.000 12.85 0.00 40.45 3.85
1098 1155 1.469940 CGACACGATTCCTAGCAGCTT 60.470 52.381 0.00 0.00 0.00 3.74
1101 1158 1.828832 GACGACACGATTCCTAGCAG 58.171 55.000 0.00 0.00 0.00 4.24
1148 1208 9.522804 CGGCATAACTTTGGCTATAATTTAAAA 57.477 29.630 0.00 0.00 39.86 1.52
1149 1209 8.138712 CCGGCATAACTTTGGCTATAATTTAAA 58.861 33.333 0.00 0.00 39.86 1.52
1150 1210 7.653647 CCGGCATAACTTTGGCTATAATTTAA 58.346 34.615 0.00 0.00 39.86 1.52
1151 1211 6.294286 GCCGGCATAACTTTGGCTATAATTTA 60.294 38.462 24.80 0.00 42.44 1.40
1152 1212 5.508994 GCCGGCATAACTTTGGCTATAATTT 60.509 40.000 24.80 0.00 42.44 1.82
1153 1213 4.022329 GCCGGCATAACTTTGGCTATAATT 60.022 41.667 24.80 0.00 42.44 1.40
1154 1214 3.506067 GCCGGCATAACTTTGGCTATAAT 59.494 43.478 24.80 0.00 42.44 1.28
1155 1215 2.882137 GCCGGCATAACTTTGGCTATAA 59.118 45.455 24.80 0.00 42.44 0.98
1156 1216 2.500229 GCCGGCATAACTTTGGCTATA 58.500 47.619 24.80 0.00 42.44 1.31
1157 1217 1.318576 GCCGGCATAACTTTGGCTAT 58.681 50.000 24.80 0.00 42.44 2.97
1158 1218 0.750182 GGCCGGCATAACTTTGGCTA 60.750 55.000 30.85 0.00 45.06 3.93
1159 1219 2.052104 GGCCGGCATAACTTTGGCT 61.052 57.895 30.85 0.00 45.06 4.75
1160 1220 1.675720 ATGGCCGGCATAACTTTGGC 61.676 55.000 30.85 6.94 44.98 4.52
1161 1221 0.102844 CATGGCCGGCATAACTTTGG 59.897 55.000 30.85 2.39 0.00 3.28
1162 1222 0.528249 GCATGGCCGGCATAACTTTG 60.528 55.000 30.85 14.52 0.00 2.77
1163 1223 1.675720 GGCATGGCCGGCATAACTTT 61.676 55.000 30.85 0.51 39.62 2.66
1164 1224 2.127232 GGCATGGCCGGCATAACTT 61.127 57.895 30.85 5.83 39.62 2.66
1165 1225 2.519302 GGCATGGCCGGCATAACT 60.519 61.111 30.85 3.97 39.62 2.24
1184 1244 5.195379 GTGCACTAAACTCGTTACAACAAG 58.805 41.667 10.32 0.00 0.00 3.16
1210 1270 5.717078 TGAGCAGCAGAATTTCAATCTTT 57.283 34.783 0.00 0.00 0.00 2.52
1328 1428 5.474876 CCAAGAACCAAAGATTCAGTAAGCT 59.525 40.000 0.00 0.00 31.06 3.74
1332 1432 3.751175 CGCCAAGAACCAAAGATTCAGTA 59.249 43.478 0.00 0.00 0.00 2.74
1343 1443 3.283684 CGGTTGCGCCAAGAACCA 61.284 61.111 22.63 0.00 41.61 3.67
1468 1568 1.379044 ATTCTGAGGCCTTTGCGGG 60.379 57.895 6.77 0.00 38.85 6.13
1474 1574 1.283347 TGAGCTCATTCTGAGGCCTT 58.717 50.000 13.74 0.00 44.43 4.35
1549 1649 2.162408 GCTGATGGTTGTACTTTCCTGC 59.838 50.000 0.00 0.00 0.00 4.85
1559 1662 3.058160 GCCAGCGCTGATGGTTGT 61.058 61.111 38.06 0.00 41.69 3.32
1561 1664 4.704833 ACGCCAGCGCTGATGGTT 62.705 61.111 38.06 14.49 41.69 3.67
1735 1838 1.218047 CTCCGGCTTGGACGATGAA 59.782 57.895 0.00 0.00 43.74 2.57
1738 1841 1.218316 GAACTCCGGCTTGGACGAT 59.782 57.895 0.00 0.00 43.74 3.73
2039 2148 0.239347 CGCAGAGAAAGCCAAACAGG 59.761 55.000 0.00 0.00 41.84 4.00
2040 2149 0.947244 ACGCAGAGAAAGCCAAACAG 59.053 50.000 0.00 0.00 0.00 3.16
2041 2150 0.662619 CACGCAGAGAAAGCCAAACA 59.337 50.000 0.00 0.00 0.00 2.83
2042 2151 0.040067 CCACGCAGAGAAAGCCAAAC 60.040 55.000 0.00 0.00 0.00 2.93
2043 2152 0.465460 ACCACGCAGAGAAAGCCAAA 60.465 50.000 0.00 0.00 0.00 3.28
2044 2153 0.465460 AACCACGCAGAGAAAGCCAA 60.465 50.000 0.00 0.00 0.00 4.52
2045 2154 0.884704 GAACCACGCAGAGAAAGCCA 60.885 55.000 0.00 0.00 0.00 4.75
2046 2155 0.603975 AGAACCACGCAGAGAAAGCC 60.604 55.000 0.00 0.00 0.00 4.35
2056 2165 4.561213 GGCATTATTTTTACAGAACCACGC 59.439 41.667 0.00 0.00 0.00 5.34
2130 2243 7.382759 GCAAAATCGTTGGGTTTAATTCTTACA 59.617 33.333 0.00 0.00 0.00 2.41
2134 2247 5.925969 CAGCAAAATCGTTGGGTTTAATTCT 59.074 36.000 0.00 0.00 0.00 2.40
2143 2256 1.247567 ACTCCAGCAAAATCGTTGGG 58.752 50.000 0.00 0.00 37.81 4.12
2155 2268 8.193250 TGAAACGTTTTCTATAATACTCCAGC 57.807 34.615 15.89 0.00 0.00 4.85
2198 2313 0.478072 ATGTTCAGGGGCACACAGAA 59.522 50.000 0.00 0.00 0.00 3.02
2207 2322 1.561542 AGCCACTTAGATGTTCAGGGG 59.438 52.381 0.00 0.00 33.76 4.79
2208 2323 2.026822 ACAGCCACTTAGATGTTCAGGG 60.027 50.000 0.00 0.00 0.00 4.45
2209 2324 3.005554 CACAGCCACTTAGATGTTCAGG 58.994 50.000 0.00 0.00 0.00 3.86
2210 2325 3.005554 CCACAGCCACTTAGATGTTCAG 58.994 50.000 0.00 0.00 0.00 3.02
2217 2332 3.244422 CCACTAAACCACAGCCACTTAGA 60.244 47.826 0.00 0.00 0.00 2.10
2219 2334 2.440253 ACCACTAAACCACAGCCACTTA 59.560 45.455 0.00 0.00 0.00 2.24
2305 2420 9.625747 AAGAAGGATTGGAAAAGCAAAAATAAA 57.374 25.926 0.00 0.00 0.00 1.40
2306 2421 9.625747 AAAGAAGGATTGGAAAAGCAAAAATAA 57.374 25.926 0.00 0.00 0.00 1.40
2307 2422 9.625747 AAAAGAAGGATTGGAAAAGCAAAAATA 57.374 25.926 0.00 0.00 0.00 1.40
2308 2423 8.523915 AAAAGAAGGATTGGAAAAGCAAAAAT 57.476 26.923 0.00 0.00 0.00 1.82
2309 2424 7.936496 AAAAGAAGGATTGGAAAAGCAAAAA 57.064 28.000 0.00 0.00 0.00 1.94
2310 2425 8.043710 TGTAAAAGAAGGATTGGAAAAGCAAAA 58.956 29.630 0.00 0.00 0.00 2.44
2311 2426 7.560368 TGTAAAAGAAGGATTGGAAAAGCAAA 58.440 30.769 0.00 0.00 0.00 3.68
2315 2430 9.341899 CGTTATGTAAAAGAAGGATTGGAAAAG 57.658 33.333 0.00 0.00 0.00 2.27
2321 2436 7.072177 TCAGCGTTATGTAAAAGAAGGATTG 57.928 36.000 0.00 0.00 0.00 2.67
2325 2440 5.119588 TCGTTCAGCGTTATGTAAAAGAAGG 59.880 40.000 0.00 0.00 42.13 3.46
2326 2441 6.148270 TCGTTCAGCGTTATGTAAAAGAAG 57.852 37.500 0.00 0.00 42.13 2.85
2329 2444 7.159818 CGTTAATCGTTCAGCGTTATGTAAAAG 59.840 37.037 0.00 0.00 42.13 2.27
2333 2448 4.500117 CCGTTAATCGTTCAGCGTTATGTA 59.500 41.667 0.00 0.00 42.13 2.29
2338 2453 0.441145 GCCGTTAATCGTTCAGCGTT 59.559 50.000 0.00 0.00 42.13 4.84
2339 2454 0.389426 AGCCGTTAATCGTTCAGCGT 60.389 50.000 0.00 0.00 42.13 5.07
2340 2455 0.297820 GAGCCGTTAATCGTTCAGCG 59.702 55.000 0.00 0.00 43.01 5.18
2341 2456 1.324736 CAGAGCCGTTAATCGTTCAGC 59.675 52.381 0.00 0.00 37.94 4.26
2342 2457 2.876091 TCAGAGCCGTTAATCGTTCAG 58.124 47.619 0.00 0.00 37.94 3.02
2343 2458 3.520290 ATCAGAGCCGTTAATCGTTCA 57.480 42.857 0.00 0.00 37.94 3.18
2344 2459 4.085004 GCTAATCAGAGCCGTTAATCGTTC 60.085 45.833 0.00 0.00 36.38 3.95
2369 2484 0.676184 CAGCGCCTCCATAAGAGCTA 59.324 55.000 2.29 0.00 41.74 3.32
2370 2485 1.045350 TCAGCGCCTCCATAAGAGCT 61.045 55.000 2.29 0.00 41.74 4.09
2371 2486 0.878086 GTCAGCGCCTCCATAAGAGC 60.878 60.000 2.29 0.00 41.74 4.09
2372 2487 0.461548 TGTCAGCGCCTCCATAAGAG 59.538 55.000 2.29 0.00 42.83 2.85
2373 2488 0.461548 CTGTCAGCGCCTCCATAAGA 59.538 55.000 2.29 0.00 0.00 2.10
2385 2500 3.618780 CTGGGGTCTGGCTGTCAGC 62.619 68.421 16.93 16.93 43.06 4.26
2403 2518 4.364409 GCCGACGTGCAAACGGTC 62.364 66.667 22.04 11.98 46.95 4.79
2425 2540 1.004891 GGGAGAAGAGGGGATGGGT 59.995 63.158 0.00 0.00 0.00 4.51
2426 2541 1.772156 GGGGAGAAGAGGGGATGGG 60.772 68.421 0.00 0.00 0.00 4.00
2442 2557 2.510906 CTATGGCGGAAGTGGGGG 59.489 66.667 0.00 0.00 0.00 5.40
2499 2624 1.533625 CATTCCCGCAGAAACTCCAA 58.466 50.000 0.00 0.00 38.21 3.53
2513 2638 1.598130 CTTCGCCGGGATCCATTCC 60.598 63.158 15.23 0.00 44.62 3.01
2605 2731 2.351276 GGGTGGCACTGGTTCGAT 59.649 61.111 18.45 0.00 0.00 3.59
2850 2976 2.415893 GCACCAACGCTGAGCAAATTAT 60.416 45.455 4.88 0.00 0.00 1.28
2860 2986 2.424705 AAGCAATGGCACCAACGCTG 62.425 55.000 14.77 2.91 44.61 5.18
2861 2987 1.747325 AAAGCAATGGCACCAACGCT 61.747 50.000 9.70 9.70 44.61 5.07
2864 2990 0.667184 CGGAAAGCAATGGCACCAAC 60.667 55.000 0.00 0.00 44.61 3.77
2865 2991 1.112315 ACGGAAAGCAATGGCACCAA 61.112 50.000 0.00 0.00 44.61 3.67
2866 2992 1.523154 GACGGAAAGCAATGGCACCA 61.523 55.000 0.00 0.00 44.61 4.17
2867 2993 1.212751 GACGGAAAGCAATGGCACC 59.787 57.895 0.00 0.00 44.61 5.01
2868 2994 0.169009 GAGACGGAAAGCAATGGCAC 59.831 55.000 0.00 0.00 44.61 5.01
2888 3014 7.897575 GTCTAGAGACATCAAATTCACAACT 57.102 36.000 4.77 0.00 44.18 3.16
2983 3109 7.446013 ACGGTTTCAAAGTAGTGATCCATTAAA 59.554 33.333 0.00 0.00 0.00 1.52
2987 3113 4.906618 ACGGTTTCAAAGTAGTGATCCAT 58.093 39.130 0.00 0.00 0.00 3.41
3007 3134 4.106197 GCTACCATGAGACTGAAACTACG 58.894 47.826 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.