Multiple sequence alignment - TraesCS4A01G328300

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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 TraesCS4A01G328300 chr4A 100.000 2517 0 0 1 2517 614028976 614031492 0.000000e+00 4649
1 TraesCS4A01G328300 chr5D 85.250 1200 79 42 999 2173 554504493 554503367 0.000000e+00 1146
2 TraesCS4A01G328300 chr5D 92.288 765 32 7 193 950 554505332 554504588 0.000000e+00 1061
3 TraesCS4A01G328300 chr5D 82.275 378 33 12 2170 2517 554503310 554502937 1.890000e-76 296
4 TraesCS4A01G328300 chr5B 92.439 820 33 14 195 1003 696177822 696178623 0.000000e+00 1144
5 TraesCS4A01G328300 chr5B 85.586 666 37 23 1460 2088 696179012 696179655 0.000000e+00 643
6 TraesCS4A01G328300 chr5B 80.214 374 44 16 2170 2517 696179770 696180139 1.160000e-63 254
7 TraesCS4A01G328300 chr5B 92.727 110 8 0 1337 1446 696178803 696178912 2.590000e-35 159
8 TraesCS4A01G328300 chr2B 86.957 184 22 2 183 366 674066543 674066724 3.280000e-49 206
9 TraesCS4A01G328300 chr4B 86.413 184 23 2 183 366 563997533 563997714 1.530000e-47 200
10 TraesCS4A01G328300 chr3B 86.441 177 22 2 199 375 543184354 543184180 2.560000e-45 193
11 TraesCS4A01G328300 chr3B 89.928 139 14 0 2280 2418 74282866 74282728 1.990000e-41 180
12 TraesCS4A01G328300 chr3D 89.928 139 14 0 2280 2418 47481681 47481543 1.990000e-41 180
13 TraesCS4A01G328300 chr3A 89.437 142 15 0 2277 2418 59519432 59519291 1.990000e-41 180


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 TraesCS4A01G328300 chr4A 614028976 614031492 2516 False 4649.000000 4649 100.000000 1 2517 1 chr4A.!!$F1 2516
1 TraesCS4A01G328300 chr5D 554502937 554505332 2395 True 834.333333 1146 86.604333 193 2517 3 chr5D.!!$R1 2324
2 TraesCS4A01G328300 chr5B 696177822 696180139 2317 False 550.000000 1144 87.741500 195 2517 4 chr5B.!!$F1 2322

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
35 36 0.109132 GGCCCGAAGCATCAAAACAG 60.109 55.0 0.0 0.0 46.5 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2088 0.24746 GCCCCAAAGAAGATGTTGCC 59.753 55.0 0.0 0.0 0.0 4.52 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
20 21 2.651382 ATTAATGTAACCGAGGGCCC 57.349 50.000 16.46 16.46 0.00 5.80
21 22 0.178533 TTAATGTAACCGAGGGCCCG 59.821 55.000 18.44 5.04 0.00 6.13
22 23 0.687098 TAATGTAACCGAGGGCCCGA 60.687 55.000 18.44 0.00 0.00 5.14
23 24 1.555477 AATGTAACCGAGGGCCCGAA 61.555 55.000 18.44 0.00 0.00 4.30
24 25 1.968050 ATGTAACCGAGGGCCCGAAG 61.968 60.000 18.44 11.56 0.00 3.79
25 26 3.777910 TAACCGAGGGCCCGAAGC 61.778 66.667 18.44 6.52 42.60 3.86
28 29 4.918201 CCGAGGGCCCGAAGCATC 62.918 72.222 18.44 6.22 46.50 3.91
29 30 4.161295 CGAGGGCCCGAAGCATCA 62.161 66.667 18.44 0.00 46.50 3.07
30 31 2.272146 GAGGGCCCGAAGCATCAA 59.728 61.111 18.44 0.00 46.50 2.57
31 32 1.378514 GAGGGCCCGAAGCATCAAA 60.379 57.895 18.44 0.00 46.50 2.69
32 33 0.965363 GAGGGCCCGAAGCATCAAAA 60.965 55.000 18.44 0.00 46.50 2.44
33 34 1.215382 GGGCCCGAAGCATCAAAAC 59.785 57.895 5.69 0.00 46.50 2.43
34 35 1.531739 GGGCCCGAAGCATCAAAACA 61.532 55.000 5.69 0.00 46.50 2.83
35 36 0.109132 GGCCCGAAGCATCAAAACAG 60.109 55.000 0.00 0.00 46.50 3.16
36 37 0.881118 GCCCGAAGCATCAAAACAGA 59.119 50.000 0.00 0.00 42.97 3.41
37 38 1.269448 GCCCGAAGCATCAAAACAGAA 59.731 47.619 0.00 0.00 42.97 3.02
38 39 2.669391 GCCCGAAGCATCAAAACAGAAG 60.669 50.000 0.00 0.00 42.97 2.85
39 40 2.589014 CCGAAGCATCAAAACAGAAGC 58.411 47.619 0.00 0.00 32.72 3.86
40 41 2.030893 CCGAAGCATCAAAACAGAAGCA 60.031 45.455 0.00 0.00 34.86 3.91
41 42 3.231965 CGAAGCATCAAAACAGAAGCAG 58.768 45.455 0.00 0.00 34.86 4.24
42 43 3.058708 CGAAGCATCAAAACAGAAGCAGA 60.059 43.478 0.00 0.00 34.86 4.26
43 44 3.911661 AGCATCAAAACAGAAGCAGAC 57.088 42.857 0.00 0.00 34.86 3.51
44 45 3.216800 AGCATCAAAACAGAAGCAGACA 58.783 40.909 0.00 0.00 34.86 3.41
45 46 3.825014 AGCATCAAAACAGAAGCAGACAT 59.175 39.130 0.00 0.00 34.86 3.06
46 47 3.918591 GCATCAAAACAGAAGCAGACATG 59.081 43.478 0.00 0.00 32.81 3.21
47 48 4.482386 CATCAAAACAGAAGCAGACATGG 58.518 43.478 0.00 0.00 0.00 3.66
48 49 3.554934 TCAAAACAGAAGCAGACATGGT 58.445 40.909 0.00 0.00 39.32 3.55
49 50 4.713553 TCAAAACAGAAGCAGACATGGTA 58.286 39.130 0.00 0.00 35.69 3.25
50 51 5.316167 TCAAAACAGAAGCAGACATGGTAT 58.684 37.500 0.00 0.00 35.69 2.73
51 52 5.412594 TCAAAACAGAAGCAGACATGGTATC 59.587 40.000 0.00 0.00 35.69 2.24
52 53 3.550437 ACAGAAGCAGACATGGTATCC 57.450 47.619 0.00 0.00 35.69 2.59
53 54 2.159043 ACAGAAGCAGACATGGTATCCG 60.159 50.000 0.00 0.00 35.69 4.18
54 55 2.111384 AGAAGCAGACATGGTATCCGT 58.889 47.619 0.00 0.00 35.69 4.69
55 56 2.101582 AGAAGCAGACATGGTATCCGTC 59.898 50.000 0.00 0.00 35.69 4.79
56 57 1.485124 AGCAGACATGGTATCCGTCA 58.515 50.000 0.00 0.00 34.74 4.35
57 58 1.410517 AGCAGACATGGTATCCGTCAG 59.589 52.381 0.00 0.00 34.74 3.51
58 59 1.409064 GCAGACATGGTATCCGTCAGA 59.591 52.381 0.00 0.00 31.92 3.27
59 60 2.544694 GCAGACATGGTATCCGTCAGAG 60.545 54.545 0.00 0.00 31.92 3.35
60 61 1.683917 AGACATGGTATCCGTCAGAGC 59.316 52.381 0.00 0.00 31.92 4.09
61 62 1.409064 GACATGGTATCCGTCAGAGCA 59.591 52.381 0.00 0.00 0.00 4.26
62 63 2.036475 GACATGGTATCCGTCAGAGCAT 59.964 50.000 0.00 0.00 0.00 3.79
63 64 2.036475 ACATGGTATCCGTCAGAGCATC 59.964 50.000 0.00 0.00 0.00 3.91
76 77 2.048444 GAGCATCTGAAATGGAGGCA 57.952 50.000 3.40 0.00 42.03 4.75
77 78 2.372264 GAGCATCTGAAATGGAGGCAA 58.628 47.619 3.40 0.00 42.03 4.52
78 79 2.756760 GAGCATCTGAAATGGAGGCAAA 59.243 45.455 3.40 0.00 42.03 3.68
79 80 3.167485 AGCATCTGAAATGGAGGCAAAA 58.833 40.909 3.40 0.00 42.03 2.44
80 81 3.056322 AGCATCTGAAATGGAGGCAAAAC 60.056 43.478 3.40 0.00 42.03 2.43
81 82 3.056322 GCATCTGAAATGGAGGCAAAACT 60.056 43.478 0.00 0.00 39.79 2.66
82 83 4.491676 CATCTGAAATGGAGGCAAAACTG 58.508 43.478 0.00 0.00 0.00 3.16
83 84 2.297033 TCTGAAATGGAGGCAAAACTGC 59.703 45.455 0.00 0.00 0.00 4.40
84 85 2.298163 CTGAAATGGAGGCAAAACTGCT 59.702 45.455 0.00 0.00 34.73 4.24
85 86 2.297033 TGAAATGGAGGCAAAACTGCTC 59.703 45.455 0.00 0.00 34.73 4.26
86 87 1.260544 AATGGAGGCAAAACTGCTCC 58.739 50.000 0.00 0.00 34.75 4.70
87 88 0.613012 ATGGAGGCAAAACTGCTCCC 60.613 55.000 0.00 7.06 33.90 4.30
88 89 2.335712 GGAGGCAAAACTGCTCCCG 61.336 63.158 0.00 0.00 34.73 5.14
89 90 1.302511 GAGGCAAAACTGCTCCCGA 60.303 57.895 0.00 0.00 34.73 5.14
90 91 0.889186 GAGGCAAAACTGCTCCCGAA 60.889 55.000 0.00 0.00 34.73 4.30
91 92 0.467290 AGGCAAAACTGCTCCCGAAA 60.467 50.000 0.00 0.00 34.73 3.46
92 93 0.387565 GGCAAAACTGCTCCCGAAAA 59.612 50.000 0.00 0.00 34.73 2.29
93 94 1.202475 GGCAAAACTGCTCCCGAAAAA 60.202 47.619 0.00 0.00 34.73 1.94
113 114 3.317603 AAACATTTGTATGCACTGCCC 57.682 42.857 0.00 0.00 35.03 5.36
114 115 1.921982 ACATTTGTATGCACTGCCCA 58.078 45.000 0.00 0.00 35.03 5.36
115 116 1.820519 ACATTTGTATGCACTGCCCAG 59.179 47.619 0.00 0.00 35.03 4.45
116 117 2.093890 CATTTGTATGCACTGCCCAGA 58.906 47.619 1.69 0.00 0.00 3.86
117 118 2.284754 TTTGTATGCACTGCCCAGAA 57.715 45.000 1.69 0.00 0.00 3.02
118 119 1.825090 TTGTATGCACTGCCCAGAAG 58.175 50.000 1.69 0.00 0.00 2.85
119 120 0.983467 TGTATGCACTGCCCAGAAGA 59.017 50.000 1.69 0.00 0.00 2.87
120 121 1.350684 TGTATGCACTGCCCAGAAGAA 59.649 47.619 1.69 0.00 0.00 2.52
121 122 2.025981 TGTATGCACTGCCCAGAAGAAT 60.026 45.455 1.69 0.00 0.00 2.40
122 123 1.471119 ATGCACTGCCCAGAAGAATG 58.529 50.000 1.69 0.00 0.00 2.67
123 124 0.111061 TGCACTGCCCAGAAGAATGT 59.889 50.000 1.69 0.00 0.00 2.71
124 125 1.350684 TGCACTGCCCAGAAGAATGTA 59.649 47.619 1.69 0.00 0.00 2.29
125 126 1.740025 GCACTGCCCAGAAGAATGTAC 59.260 52.381 1.69 0.00 0.00 2.90
126 127 2.616510 GCACTGCCCAGAAGAATGTACT 60.617 50.000 1.69 0.00 0.00 2.73
127 128 3.679389 CACTGCCCAGAAGAATGTACTT 58.321 45.455 1.69 0.00 0.00 2.24
128 129 4.832248 CACTGCCCAGAAGAATGTACTTA 58.168 43.478 1.69 0.00 0.00 2.24
129 130 5.431765 CACTGCCCAGAAGAATGTACTTAT 58.568 41.667 1.69 0.00 0.00 1.73
130 131 5.525378 CACTGCCCAGAAGAATGTACTTATC 59.475 44.000 1.69 0.00 0.00 1.75
131 132 5.189736 ACTGCCCAGAAGAATGTACTTATCA 59.810 40.000 1.69 0.00 0.00 2.15
132 133 5.674525 TGCCCAGAAGAATGTACTTATCAG 58.325 41.667 0.00 0.00 0.00 2.90
133 134 5.059833 GCCCAGAAGAATGTACTTATCAGG 58.940 45.833 0.00 0.00 0.00 3.86
134 135 5.396884 GCCCAGAAGAATGTACTTATCAGGT 60.397 44.000 0.00 0.00 0.00 4.00
135 136 6.653989 CCCAGAAGAATGTACTTATCAGGTT 58.346 40.000 0.00 0.00 0.00 3.50
136 137 7.635089 GCCCAGAAGAATGTACTTATCAGGTTA 60.635 40.741 0.00 0.00 0.00 2.85
137 138 8.432805 CCCAGAAGAATGTACTTATCAGGTTAT 58.567 37.037 0.00 0.00 0.00 1.89
138 139 9.482627 CCAGAAGAATGTACTTATCAGGTTATC 57.517 37.037 0.00 0.00 0.00 1.75
154 155 7.545362 CAGGTTATCAAAACTGTCCATCTAG 57.455 40.000 0.00 0.00 44.11 2.43
155 156 6.540189 CAGGTTATCAAAACTGTCCATCTAGG 59.460 42.308 0.00 0.00 44.11 3.02
156 157 5.823045 GGTTATCAAAACTGTCCATCTAGGG 59.177 44.000 0.00 0.00 38.24 3.53
157 158 4.510167 ATCAAAACTGTCCATCTAGGGG 57.490 45.455 0.00 0.00 38.24 4.79
158 159 3.526899 TCAAAACTGTCCATCTAGGGGA 58.473 45.455 0.46 0.46 38.24 4.81
159 160 4.111577 TCAAAACTGTCCATCTAGGGGAT 58.888 43.478 7.24 0.00 36.67 3.85
160 161 4.164221 TCAAAACTGTCCATCTAGGGGATC 59.836 45.833 7.24 0.00 36.67 3.36
161 162 3.715648 AACTGTCCATCTAGGGGATCT 57.284 47.619 7.24 0.00 36.67 2.75
162 163 2.969628 ACTGTCCATCTAGGGGATCTG 58.030 52.381 7.24 7.74 36.67 2.90
163 164 2.248686 ACTGTCCATCTAGGGGATCTGT 59.751 50.000 7.24 8.19 36.67 3.41
164 165 3.467483 ACTGTCCATCTAGGGGATCTGTA 59.533 47.826 7.24 0.00 36.67 2.74
165 166 4.078571 ACTGTCCATCTAGGGGATCTGTAA 60.079 45.833 7.24 0.00 36.67 2.41
166 167 4.223953 TGTCCATCTAGGGGATCTGTAAC 58.776 47.826 7.24 0.00 36.67 2.50
167 168 4.078571 TGTCCATCTAGGGGATCTGTAACT 60.079 45.833 7.24 0.00 36.67 2.24
168 169 4.525100 GTCCATCTAGGGGATCTGTAACTC 59.475 50.000 7.24 0.00 36.67 3.01
169 170 3.835395 CCATCTAGGGGATCTGTAACTCC 59.165 52.174 0.00 0.00 31.27 3.85
175 176 2.197465 GGGATCTGTAACTCCCCAAGT 58.803 52.381 0.00 0.00 44.68 3.16
176 177 3.381335 GGGATCTGTAACTCCCCAAGTA 58.619 50.000 0.00 0.00 44.68 2.24
177 178 3.778629 GGGATCTGTAACTCCCCAAGTAA 59.221 47.826 0.00 0.00 44.68 2.24
178 179 4.412528 GGGATCTGTAACTCCCCAAGTAAT 59.587 45.833 0.00 0.00 44.68 1.89
179 180 5.104067 GGGATCTGTAACTCCCCAAGTAATT 60.104 44.000 0.00 0.00 44.68 1.40
180 181 5.823045 GGATCTGTAACTCCCCAAGTAATTG 59.177 44.000 0.00 0.00 37.17 2.32
181 182 5.836024 TCTGTAACTCCCCAAGTAATTGT 57.164 39.130 1.80 0.00 37.17 2.71
182 183 5.801380 TCTGTAACTCCCCAAGTAATTGTC 58.199 41.667 1.80 0.00 37.17 3.18
183 184 5.308497 TCTGTAACTCCCCAAGTAATTGTCA 59.692 40.000 1.80 0.00 37.17 3.58
184 185 5.942961 TGTAACTCCCCAAGTAATTGTCAA 58.057 37.500 1.80 0.00 37.17 3.18
185 186 6.366340 TGTAACTCCCCAAGTAATTGTCAAA 58.634 36.000 1.80 0.00 37.17 2.69
186 187 7.007723 TGTAACTCCCCAAGTAATTGTCAAAT 58.992 34.615 1.80 0.00 37.17 2.32
187 188 6.994421 AACTCCCCAAGTAATTGTCAAATT 57.006 33.333 1.80 0.00 37.17 1.82
188 189 6.590234 ACTCCCCAAGTAATTGTCAAATTC 57.410 37.500 1.80 0.00 37.23 2.17
189 190 6.314917 ACTCCCCAAGTAATTGTCAAATTCT 58.685 36.000 1.80 0.00 37.23 2.40
190 191 6.209391 ACTCCCCAAGTAATTGTCAAATTCTG 59.791 38.462 1.80 0.00 37.23 3.02
191 192 6.074648 TCCCCAAGTAATTGTCAAATTCTGT 58.925 36.000 1.80 0.00 37.23 3.41
196 197 9.612620 CCAAGTAATTGTCAAATTCTGTTACTC 57.387 33.333 1.80 0.00 37.23 2.59
214 215 1.137675 CTCACCATTCGGCAGATGAGA 59.862 52.381 8.89 2.18 36.50 3.27
220 221 1.960040 TTCGGCAGATGAGACGCCAT 61.960 55.000 0.00 0.00 46.60 4.40
256 257 2.431771 CCGAACATGGCGACGTCA 60.432 61.111 17.16 3.85 0.00 4.35
787 797 3.484806 ACCGCCGCCATGGGATTA 61.485 61.111 15.13 0.00 38.63 1.75
795 805 0.251077 GCCATGGGATTAGGAGCAGG 60.251 60.000 15.13 0.00 0.00 4.85
821 837 0.460987 GTCAGATGAGTCCAAGCGGG 60.461 60.000 0.00 0.00 38.37 6.13
822 838 1.153289 CAGATGAGTCCAAGCGGGG 60.153 63.158 0.00 0.00 37.22 5.73
823 839 1.306141 AGATGAGTCCAAGCGGGGA 60.306 57.895 0.00 0.00 37.22 4.81
824 840 1.144936 GATGAGTCCAAGCGGGGAG 59.855 63.158 0.00 0.00 37.71 4.30
867 893 2.202892 GGCGACGGGGAAGATGAC 60.203 66.667 0.00 0.00 0.00 3.06
922 949 1.264672 GAGACGAGAGCGAAAGAAGC 58.735 55.000 0.00 0.00 41.64 3.86
955 982 0.878961 AAACAAGACAGCGACGGGTC 60.879 55.000 0.00 0.00 0.00 4.46
956 983 2.432628 CAAGACAGCGACGGGTCC 60.433 66.667 0.00 0.00 34.58 4.46
1171 1262 2.966309 CTTTCACCGGGCACGAAGC 61.966 63.158 11.66 0.00 44.60 3.86
1205 1296 2.978824 CGGAGCCGGGAAGAAGAA 59.021 61.111 2.18 0.00 35.56 2.52
1206 1297 1.295423 CGGAGCCGGGAAGAAGAAA 59.705 57.895 2.18 0.00 35.56 2.52
1207 1298 0.321298 CGGAGCCGGGAAGAAGAAAA 60.321 55.000 2.18 0.00 35.56 2.29
1208 1299 1.454201 GGAGCCGGGAAGAAGAAAAG 58.546 55.000 2.18 0.00 0.00 2.27
1216 1307 4.505039 CCGGGAAGAAGAAAAGGAAGAAGA 60.505 45.833 0.00 0.00 0.00 2.87
1221 1312 6.072230 GGAAGAAGAAAAGGAAGAAGATGGTG 60.072 42.308 0.00 0.00 0.00 4.17
1228 1319 3.165875 AGGAAGAAGATGGTGAAGACGA 58.834 45.455 0.00 0.00 0.00 4.20
1234 1325 1.751924 AGATGGTGAAGACGAGGCTAC 59.248 52.381 0.00 0.00 0.00 3.58
1307 1398 4.717629 CGACGACGAGCTGGCCAA 62.718 66.667 7.01 0.00 42.66 4.52
1319 1410 3.712907 GGCCAAGCGTCCCAGGTA 61.713 66.667 0.00 0.00 0.00 3.08
1320 1411 2.436115 GCCAAGCGTCCCAGGTAC 60.436 66.667 0.00 0.00 0.00 3.34
1322 1413 1.610554 GCCAAGCGTCCCAGGTACTA 61.611 60.000 0.00 0.00 36.02 1.82
1326 1417 2.803479 CGTCCCAGGTACTACCGC 59.197 66.667 0.00 0.00 44.90 5.68
1463 1640 1.026584 GAGTCGGAGGAGAACTAGCC 58.973 60.000 0.00 0.00 0.00 3.93
1465 1642 0.741915 GTCGGAGGAGAACTAGCCAG 59.258 60.000 0.00 0.00 0.00 4.85
1525 1708 2.565841 GGCTCGTGCTGAATAATTCCT 58.434 47.619 9.61 0.00 39.59 3.36
1526 1709 3.728845 GGCTCGTGCTGAATAATTCCTA 58.271 45.455 9.61 0.00 39.59 2.94
1527 1710 3.743396 GGCTCGTGCTGAATAATTCCTAG 59.257 47.826 9.61 0.00 39.59 3.02
1528 1711 4.372656 GCTCGTGCTGAATAATTCCTAGT 58.627 43.478 1.41 0.00 36.03 2.57
1529 1712 5.509163 GGCTCGTGCTGAATAATTCCTAGTA 60.509 44.000 9.61 0.00 39.59 1.82
1591 1774 9.899661 TGTTATTATCACACCTTAATTGCTAGT 57.100 29.630 0.00 0.00 0.00 2.57
1601 1784 8.414778 ACACCTTAATTGCTAGTACTAGTGATC 58.585 37.037 26.76 13.42 35.65 2.92
1618 1813 3.385755 GTGATCCCATTGCTATTTTGGCT 59.614 43.478 0.00 0.00 0.00 4.75
1634 1829 2.177734 TGGCTGCAAGAAATTGGCATA 58.822 42.857 0.50 0.00 36.87 3.14
1670 1866 3.996825 GGCACCAAATAGCACGAAG 57.003 52.632 0.00 0.00 0.00 3.79
1725 1921 6.625362 AGAACACACATGATGACTACTACTG 58.375 40.000 0.00 0.00 0.00 2.74
1726 1922 5.984695 ACACACATGATGACTACTACTGT 57.015 39.130 0.00 0.00 0.00 3.55
1881 2088 0.738389 AACAACACTTCAGCCCAACG 59.262 50.000 0.00 0.00 0.00 4.10
1911 2118 2.969628 TCTTTGGGGCCATCTTTTTCA 58.030 42.857 4.39 0.00 0.00 2.69
1919 2126 3.554960 GGGCCATCTTTTTCACCACTTTC 60.555 47.826 4.39 0.00 0.00 2.62
1936 2143 9.450807 CACCACTTTCTTTACATTTCTTTGTAG 57.549 33.333 0.00 0.00 33.81 2.74
1938 2145 9.884465 CCACTTTCTTTACATTTCTTTGTAGAG 57.116 33.333 0.00 0.00 36.26 2.43
2088 2311 0.671472 GGGCTGGCTTTCAATGTTGC 60.671 55.000 0.00 0.00 0.00 4.17
2089 2312 0.671472 GGCTGGCTTTCAATGTTGCC 60.671 55.000 0.00 0.00 45.10 4.52
2091 2314 3.860717 GGCTTTCAATGTTGCCGC 58.139 55.556 0.00 0.00 35.79 6.53
2092 2315 1.006337 GGCTTTCAATGTTGCCGCA 60.006 52.632 0.00 0.00 35.79 5.69
2093 2316 1.284297 GGCTTTCAATGTTGCCGCAC 61.284 55.000 0.00 0.00 35.79 5.34
2095 2318 1.869342 GCTTTCAATGTTGCCGCACTT 60.869 47.619 0.00 0.00 0.00 3.16
2096 2319 1.788308 CTTTCAATGTTGCCGCACTTG 59.212 47.619 0.00 0.00 0.00 3.16
2097 2320 0.597118 TTCAATGTTGCCGCACTTGC 60.597 50.000 0.00 0.00 37.78 4.01
2118 2341 1.131883 GGTAATGAACAGCAGCAGCAG 59.868 52.381 3.17 0.00 45.49 4.24
2149 2374 1.291132 GCAGGTTCGTCTAGCCAATC 58.709 55.000 0.00 0.00 0.00 2.67
2162 2387 2.636830 AGCCAATCGACCATCTTTCAG 58.363 47.619 0.00 0.00 0.00 3.02
2178 2464 5.477510 TCTTTCAGAGATGTCTTCTTGCTC 58.522 41.667 0.00 0.00 33.74 4.26
2180 2466 3.439154 TCAGAGATGTCTTCTTGCTCCT 58.561 45.455 0.00 0.00 33.74 3.69
2182 2468 2.765699 AGAGATGTCTTCTTGCTCCTCC 59.234 50.000 0.00 0.00 33.74 4.30
2188 2474 3.392616 TGTCTTCTTGCTCCTCCTTTCTT 59.607 43.478 0.00 0.00 0.00 2.52
2191 2477 1.630878 TCTTGCTCCTCCTTTCTTCCC 59.369 52.381 0.00 0.00 0.00 3.97
2197 2483 1.346722 TCCTCCTTTCTTCCCGTGAAC 59.653 52.381 0.00 0.00 0.00 3.18
2199 2485 2.486548 CCTCCTTTCTTCCCGTGAACAA 60.487 50.000 0.00 0.00 0.00 2.83
2212 2498 4.221342 CCGTGAACAACAGATCACAAATG 58.779 43.478 6.70 0.00 44.84 2.32
2304 2597 5.933463 CCTTCTCATGCCTTATCTCTGAATC 59.067 44.000 0.00 0.00 0.00 2.52
2305 2598 6.464039 CCTTCTCATGCCTTATCTCTGAATCA 60.464 42.308 0.00 0.00 0.00 2.57
2307 2600 6.286758 TCTCATGCCTTATCTCTGAATCAAC 58.713 40.000 0.00 0.00 0.00 3.18
2336 2629 4.338879 CCAACAAATCCCAGTGAGATCTT 58.661 43.478 0.00 0.00 0.00 2.40
2344 2637 1.554160 CCAGTGAGATCTTCAGCACCT 59.446 52.381 8.29 0.00 36.21 4.00
2345 2638 2.418471 CCAGTGAGATCTTCAGCACCTC 60.418 54.545 8.29 0.00 36.21 3.85
2352 2645 0.397941 TCTTCAGCACCTCCACCAAG 59.602 55.000 0.00 0.00 0.00 3.61
2356 2649 2.149383 AGCACCTCCACCAAGAGCA 61.149 57.895 0.00 0.00 32.17 4.26
2357 2650 1.001641 GCACCTCCACCAAGAGCAT 60.002 57.895 0.00 0.00 32.17 3.79
2358 2651 0.610232 GCACCTCCACCAAGAGCATT 60.610 55.000 0.00 0.00 32.17 3.56
2382 2675 1.470996 GCACCAAACATGCCTCCCAA 61.471 55.000 0.00 0.00 37.08 4.12
2383 2676 1.047002 CACCAAACATGCCTCCCAAA 58.953 50.000 0.00 0.00 0.00 3.28
2384 2677 1.624813 CACCAAACATGCCTCCCAAAT 59.375 47.619 0.00 0.00 0.00 2.32
2385 2678 1.624813 ACCAAACATGCCTCCCAAATG 59.375 47.619 0.00 0.00 0.00 2.32
2395 2695 2.555227 GCCTCCCAAATGGACAAGAAGA 60.555 50.000 0.00 0.00 38.61 2.87
2399 2699 3.084786 CCCAAATGGACAAGAAGAGGAC 58.915 50.000 0.00 0.00 37.39 3.85
2400 2700 3.498481 CCCAAATGGACAAGAAGAGGACA 60.498 47.826 0.00 0.00 37.39 4.02
2439 2755 5.627499 TCAGCACCAATACATTCTGAAAC 57.373 39.130 0.00 0.00 0.00 2.78
2455 2771 3.149196 TGAAACACAGCTCCAGATTTCC 58.851 45.455 0.00 0.00 0.00 3.13
2479 2795 2.106684 GGGTTCAGGAGTTCAGGAGTTT 59.893 50.000 0.00 0.00 0.00 2.66
2480 2796 3.142174 GGTTCAGGAGTTCAGGAGTTTG 58.858 50.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.747135 CGGGCCCTCGGTTACATTAATT 60.747 50.000 22.43 0.00 0.00 1.40
1 2 1.202722 CGGGCCCTCGGTTACATTAAT 60.203 52.381 22.43 0.00 0.00 1.40
2 3 0.178533 CGGGCCCTCGGTTACATTAA 59.821 55.000 22.43 0.00 0.00 1.40
3 4 0.687098 TCGGGCCCTCGGTTACATTA 60.687 55.000 22.43 0.00 0.00 1.90
4 5 1.555477 TTCGGGCCCTCGGTTACATT 61.555 55.000 22.43 0.00 0.00 2.71
5 6 1.968050 CTTCGGGCCCTCGGTTACAT 61.968 60.000 22.43 0.00 0.00 2.29
6 7 2.604079 TTCGGGCCCTCGGTTACA 60.604 61.111 22.43 0.00 0.00 2.41
7 8 2.186125 CTTCGGGCCCTCGGTTAC 59.814 66.667 22.43 0.00 0.00 2.50
8 9 3.777910 GCTTCGGGCCCTCGGTTA 61.778 66.667 22.43 0.00 34.27 2.85
11 12 4.918201 GATGCTTCGGGCCCTCGG 62.918 72.222 22.43 10.32 40.92 4.63
12 13 3.680620 TTGATGCTTCGGGCCCTCG 62.681 63.158 22.43 7.80 40.92 4.63
13 14 0.965363 TTTTGATGCTTCGGGCCCTC 60.965 55.000 22.43 10.14 40.92 4.30
14 15 1.076549 TTTTGATGCTTCGGGCCCT 59.923 52.632 22.43 0.00 40.92 5.19
15 16 1.215382 GTTTTGATGCTTCGGGCCC 59.785 57.895 13.57 13.57 40.92 5.80
16 17 0.109132 CTGTTTTGATGCTTCGGGCC 60.109 55.000 0.00 0.00 40.92 5.80
17 18 0.881118 TCTGTTTTGATGCTTCGGGC 59.119 50.000 0.00 0.00 42.22 6.13
18 19 2.669391 GCTTCTGTTTTGATGCTTCGGG 60.669 50.000 0.00 0.00 35.22 5.14
19 20 2.030893 TGCTTCTGTTTTGATGCTTCGG 60.031 45.455 0.00 0.00 37.79 4.30
20 21 3.058708 TCTGCTTCTGTTTTGATGCTTCG 60.059 43.478 0.00 0.00 37.79 3.79
21 22 4.225208 GTCTGCTTCTGTTTTGATGCTTC 58.775 43.478 0.00 0.00 37.79 3.86
22 23 3.633525 TGTCTGCTTCTGTTTTGATGCTT 59.366 39.130 0.00 0.00 37.79 3.91
23 24 3.216800 TGTCTGCTTCTGTTTTGATGCT 58.783 40.909 0.00 0.00 37.79 3.79
24 25 3.631145 TGTCTGCTTCTGTTTTGATGC 57.369 42.857 0.00 0.00 37.55 3.91
25 26 4.022589 ACCATGTCTGCTTCTGTTTTGATG 60.023 41.667 0.00 0.00 0.00 3.07
26 27 4.147321 ACCATGTCTGCTTCTGTTTTGAT 58.853 39.130 0.00 0.00 0.00 2.57
27 28 3.554934 ACCATGTCTGCTTCTGTTTTGA 58.445 40.909 0.00 0.00 0.00 2.69
28 29 3.996150 ACCATGTCTGCTTCTGTTTTG 57.004 42.857 0.00 0.00 0.00 2.44
29 30 4.702131 GGATACCATGTCTGCTTCTGTTTT 59.298 41.667 0.00 0.00 0.00 2.43
30 31 4.265073 GGATACCATGTCTGCTTCTGTTT 58.735 43.478 0.00 0.00 0.00 2.83
31 32 3.679917 CGGATACCATGTCTGCTTCTGTT 60.680 47.826 0.00 0.00 0.00 3.16
32 33 2.159043 CGGATACCATGTCTGCTTCTGT 60.159 50.000 0.00 0.00 0.00 3.41
33 34 2.159043 ACGGATACCATGTCTGCTTCTG 60.159 50.000 0.00 0.00 0.00 3.02
34 35 2.101582 GACGGATACCATGTCTGCTTCT 59.898 50.000 0.00 0.00 0.00 2.85
35 36 2.159099 TGACGGATACCATGTCTGCTTC 60.159 50.000 0.00 0.00 33.81 3.86
36 37 1.831106 TGACGGATACCATGTCTGCTT 59.169 47.619 0.00 0.00 33.81 3.91
37 38 1.410517 CTGACGGATACCATGTCTGCT 59.589 52.381 0.00 0.00 33.81 4.24
38 39 1.409064 TCTGACGGATACCATGTCTGC 59.591 52.381 0.00 0.00 33.28 4.26
39 40 2.544694 GCTCTGACGGATACCATGTCTG 60.545 54.545 0.00 0.00 33.81 3.51
40 41 1.683917 GCTCTGACGGATACCATGTCT 59.316 52.381 0.00 0.00 33.81 3.41
41 42 1.409064 TGCTCTGACGGATACCATGTC 59.591 52.381 0.00 0.00 0.00 3.06
42 43 1.485124 TGCTCTGACGGATACCATGT 58.515 50.000 0.00 0.00 0.00 3.21
43 44 2.298446 AGATGCTCTGACGGATACCATG 59.702 50.000 0.00 0.00 0.00 3.66
44 45 2.603021 AGATGCTCTGACGGATACCAT 58.397 47.619 0.00 0.00 0.00 3.55
45 46 2.073252 AGATGCTCTGACGGATACCA 57.927 50.000 0.00 0.00 0.00 3.25
55 56 1.948145 GCCTCCATTTCAGATGCTCTG 59.052 52.381 6.79 6.79 45.59 3.35
56 57 1.562942 TGCCTCCATTTCAGATGCTCT 59.437 47.619 0.00 0.00 0.00 4.09
57 58 2.048444 TGCCTCCATTTCAGATGCTC 57.952 50.000 0.00 0.00 0.00 4.26
58 59 2.519771 TTGCCTCCATTTCAGATGCT 57.480 45.000 0.00 0.00 0.00 3.79
59 60 3.056322 AGTTTTGCCTCCATTTCAGATGC 60.056 43.478 0.00 0.00 0.00 3.91
60 61 4.491676 CAGTTTTGCCTCCATTTCAGATG 58.508 43.478 0.00 0.00 0.00 2.90
61 62 3.056322 GCAGTTTTGCCTCCATTTCAGAT 60.056 43.478 0.00 0.00 44.74 2.90
62 63 2.297033 GCAGTTTTGCCTCCATTTCAGA 59.703 45.455 0.00 0.00 44.74 3.27
63 64 2.680577 GCAGTTTTGCCTCCATTTCAG 58.319 47.619 0.00 0.00 44.74 3.02
64 65 2.818130 GCAGTTTTGCCTCCATTTCA 57.182 45.000 0.00 0.00 44.74 2.69
91 92 4.064388 GGGCAGTGCATACAAATGTTTTT 58.936 39.130 18.61 0.00 35.38 1.94
92 93 3.070734 TGGGCAGTGCATACAAATGTTTT 59.929 39.130 18.61 0.00 35.38 2.43
93 94 2.632028 TGGGCAGTGCATACAAATGTTT 59.368 40.909 18.61 0.00 35.38 2.83
94 95 2.231964 CTGGGCAGTGCATACAAATGTT 59.768 45.455 18.61 0.00 35.38 2.71
95 96 1.820519 CTGGGCAGTGCATACAAATGT 59.179 47.619 18.61 0.00 35.38 2.71
96 97 2.093890 TCTGGGCAGTGCATACAAATG 58.906 47.619 18.61 1.74 36.09 2.32
97 98 2.512692 TCTGGGCAGTGCATACAAAT 57.487 45.000 18.61 0.00 0.00 2.32
98 99 2.161855 CTTCTGGGCAGTGCATACAAA 58.838 47.619 18.61 8.66 0.00 2.83
99 100 1.350684 TCTTCTGGGCAGTGCATACAA 59.649 47.619 18.61 3.12 0.00 2.41
100 101 0.983467 TCTTCTGGGCAGTGCATACA 59.017 50.000 18.61 11.53 0.00 2.29
101 102 2.113860 TTCTTCTGGGCAGTGCATAC 57.886 50.000 18.61 7.10 0.00 2.39
102 103 2.025981 ACATTCTTCTGGGCAGTGCATA 60.026 45.455 18.61 3.77 0.00 3.14
103 104 1.272313 ACATTCTTCTGGGCAGTGCAT 60.272 47.619 18.61 0.00 0.00 3.96
104 105 0.111061 ACATTCTTCTGGGCAGTGCA 59.889 50.000 18.61 0.00 0.00 4.57
105 106 1.740025 GTACATTCTTCTGGGCAGTGC 59.260 52.381 6.55 6.55 0.00 4.40
106 107 3.340814 AGTACATTCTTCTGGGCAGTG 57.659 47.619 0.00 0.00 0.00 3.66
107 108 5.189736 TGATAAGTACATTCTTCTGGGCAGT 59.810 40.000 0.00 0.00 0.00 4.40
108 109 5.674525 TGATAAGTACATTCTTCTGGGCAG 58.325 41.667 0.00 0.00 0.00 4.85
109 110 5.396772 CCTGATAAGTACATTCTTCTGGGCA 60.397 44.000 0.00 0.00 0.00 5.36
110 111 5.059833 CCTGATAAGTACATTCTTCTGGGC 58.940 45.833 0.00 0.00 0.00 5.36
111 112 6.240549 ACCTGATAAGTACATTCTTCTGGG 57.759 41.667 0.00 0.00 31.65 4.45
112 113 9.482627 GATAACCTGATAAGTACATTCTTCTGG 57.517 37.037 0.00 1.30 32.71 3.86
120 121 9.959721 ACAGTTTTGATAACCTGATAAGTACAT 57.040 29.630 0.00 0.00 0.00 2.29
121 122 9.431887 GACAGTTTTGATAACCTGATAAGTACA 57.568 33.333 0.00 0.00 0.00 2.90
122 123 8.880750 GGACAGTTTTGATAACCTGATAAGTAC 58.119 37.037 0.00 0.00 0.00 2.73
123 124 8.598916 TGGACAGTTTTGATAACCTGATAAGTA 58.401 33.333 0.00 0.00 0.00 2.24
124 125 7.458397 TGGACAGTTTTGATAACCTGATAAGT 58.542 34.615 0.00 0.00 0.00 2.24
125 126 7.921786 TGGACAGTTTTGATAACCTGATAAG 57.078 36.000 0.00 0.00 0.00 1.73
126 127 8.328758 AGATGGACAGTTTTGATAACCTGATAA 58.671 33.333 0.00 0.00 0.00 1.75
127 128 7.861629 AGATGGACAGTTTTGATAACCTGATA 58.138 34.615 0.00 0.00 0.00 2.15
128 129 6.725364 AGATGGACAGTTTTGATAACCTGAT 58.275 36.000 0.00 0.00 0.00 2.90
129 130 6.126863 AGATGGACAGTTTTGATAACCTGA 57.873 37.500 0.00 0.00 0.00 3.86
130 131 6.540189 CCTAGATGGACAGTTTTGATAACCTG 59.460 42.308 0.00 0.00 38.35 4.00
131 132 6.353082 CCCTAGATGGACAGTTTTGATAACCT 60.353 42.308 0.00 0.00 38.35 3.50
132 133 5.823045 CCCTAGATGGACAGTTTTGATAACC 59.177 44.000 0.00 0.00 38.35 2.85
133 134 5.823045 CCCCTAGATGGACAGTTTTGATAAC 59.177 44.000 0.00 0.00 38.35 1.89
134 135 5.729229 TCCCCTAGATGGACAGTTTTGATAA 59.271 40.000 0.00 0.00 38.35 1.75
135 136 5.285401 TCCCCTAGATGGACAGTTTTGATA 58.715 41.667 0.00 0.00 38.35 2.15
136 137 4.111577 TCCCCTAGATGGACAGTTTTGAT 58.888 43.478 0.00 0.00 38.35 2.57
137 138 3.526899 TCCCCTAGATGGACAGTTTTGA 58.473 45.455 0.00 0.00 38.35 2.69
138 139 4.164988 AGATCCCCTAGATGGACAGTTTTG 59.835 45.833 3.38 0.00 38.35 2.44
139 140 4.164988 CAGATCCCCTAGATGGACAGTTTT 59.835 45.833 3.38 0.00 38.35 2.43
140 141 3.713764 CAGATCCCCTAGATGGACAGTTT 59.286 47.826 3.38 0.00 38.35 2.66
141 142 3.310954 ACAGATCCCCTAGATGGACAGTT 60.311 47.826 3.38 0.00 38.35 3.16
142 143 2.248686 ACAGATCCCCTAGATGGACAGT 59.751 50.000 3.38 1.23 38.35 3.55
143 144 2.969628 ACAGATCCCCTAGATGGACAG 58.030 52.381 3.38 0.71 38.35 3.51
144 145 4.078571 AGTTACAGATCCCCTAGATGGACA 60.079 45.833 3.38 0.00 38.35 4.02
145 146 4.484912 AGTTACAGATCCCCTAGATGGAC 58.515 47.826 3.38 0.00 38.35 4.02
146 147 4.449376 GGAGTTACAGATCCCCTAGATGGA 60.449 50.000 3.75 3.75 38.35 3.41
147 148 3.835395 GGAGTTACAGATCCCCTAGATGG 59.165 52.174 0.00 0.00 34.42 3.51
156 157 5.632034 ATTACTTGGGGAGTTACAGATCC 57.368 43.478 0.00 0.00 39.86 3.36
157 158 6.415573 ACAATTACTTGGGGAGTTACAGATC 58.584 40.000 0.00 0.00 39.86 2.75
158 159 6.012858 TGACAATTACTTGGGGAGTTACAGAT 60.013 38.462 0.00 0.00 39.86 2.90
159 160 5.308497 TGACAATTACTTGGGGAGTTACAGA 59.692 40.000 0.00 0.00 39.86 3.41
160 161 5.556915 TGACAATTACTTGGGGAGTTACAG 58.443 41.667 0.00 0.00 39.86 2.74
161 162 5.570205 TGACAATTACTTGGGGAGTTACA 57.430 39.130 0.00 0.00 39.86 2.41
162 163 6.887626 TTTGACAATTACTTGGGGAGTTAC 57.112 37.500 0.00 0.00 39.86 2.50
163 164 7.947890 AGAATTTGACAATTACTTGGGGAGTTA 59.052 33.333 0.00 0.00 39.86 2.24
164 165 6.782494 AGAATTTGACAATTACTTGGGGAGTT 59.218 34.615 0.00 0.00 39.86 3.01
165 166 6.209391 CAGAATTTGACAATTACTTGGGGAGT 59.791 38.462 0.00 0.00 42.55 3.85
166 167 6.209391 ACAGAATTTGACAATTACTTGGGGAG 59.791 38.462 0.00 0.00 36.64 4.30
167 168 6.074648 ACAGAATTTGACAATTACTTGGGGA 58.925 36.000 0.00 0.00 36.64 4.81
168 169 6.345096 ACAGAATTTGACAATTACTTGGGG 57.655 37.500 0.00 0.00 36.64 4.96
169 170 8.576442 AGTAACAGAATTTGACAATTACTTGGG 58.424 33.333 4.52 0.00 36.64 4.12
170 171 9.612620 GAGTAACAGAATTTGACAATTACTTGG 57.387 33.333 9.75 0.00 36.64 3.61
173 174 8.784043 GGTGAGTAACAGAATTTGACAATTACT 58.216 33.333 8.62 8.62 34.85 2.24
174 175 8.564574 TGGTGAGTAACAGAATTTGACAATTAC 58.435 33.333 0.00 0.00 32.35 1.89
175 176 8.684386 TGGTGAGTAACAGAATTTGACAATTA 57.316 30.769 0.00 0.00 32.35 1.40
176 177 7.581213 TGGTGAGTAACAGAATTTGACAATT 57.419 32.000 0.00 0.00 35.12 2.32
177 178 7.765695 ATGGTGAGTAACAGAATTTGACAAT 57.234 32.000 0.00 0.00 0.00 2.71
178 179 7.519809 CGAATGGTGAGTAACAGAATTTGACAA 60.520 37.037 0.00 0.00 0.00 3.18
179 180 6.073276 CGAATGGTGAGTAACAGAATTTGACA 60.073 38.462 0.00 0.00 0.00 3.58
180 181 6.307155 CGAATGGTGAGTAACAGAATTTGAC 58.693 40.000 0.00 0.00 0.00 3.18
181 182 5.411361 CCGAATGGTGAGTAACAGAATTTGA 59.589 40.000 0.00 0.00 0.00 2.69
182 183 5.631026 CCGAATGGTGAGTAACAGAATTTG 58.369 41.667 0.00 0.00 0.00 2.32
183 184 4.156008 GCCGAATGGTGAGTAACAGAATTT 59.844 41.667 0.00 0.00 37.67 1.82
184 185 3.689649 GCCGAATGGTGAGTAACAGAATT 59.310 43.478 0.00 0.00 37.67 2.17
185 186 3.270877 GCCGAATGGTGAGTAACAGAAT 58.729 45.455 0.00 0.00 37.67 2.40
186 187 2.037902 TGCCGAATGGTGAGTAACAGAA 59.962 45.455 0.00 0.00 37.67 3.02
187 188 1.621317 TGCCGAATGGTGAGTAACAGA 59.379 47.619 0.00 0.00 37.67 3.41
188 189 2.002586 CTGCCGAATGGTGAGTAACAG 58.997 52.381 0.00 0.00 37.67 3.16
189 190 1.621317 TCTGCCGAATGGTGAGTAACA 59.379 47.619 0.00 0.00 37.67 2.41
190 191 2.380084 TCTGCCGAATGGTGAGTAAC 57.620 50.000 0.00 0.00 37.67 2.50
191 192 2.499693 TCATCTGCCGAATGGTGAGTAA 59.500 45.455 0.00 0.00 37.67 2.24
196 197 1.293924 GTCTCATCTGCCGAATGGTG 58.706 55.000 0.00 0.00 37.67 4.17
220 221 3.454447 TCGGGAAGAAGGATTATCAGCAA 59.546 43.478 0.00 0.00 0.00 3.91
256 257 1.371389 GTTCAACGTCGTCGAGCCT 60.371 57.895 9.47 0.00 40.62 4.58
769 779 3.765894 TAATCCCATGGCGGCGGTG 62.766 63.158 9.78 5.80 0.00 4.94
770 780 3.476031 CTAATCCCATGGCGGCGGT 62.476 63.158 9.78 0.00 0.00 5.68
786 796 2.037367 ACGACTGCCCTGCTCCTA 59.963 61.111 0.00 0.00 0.00 2.94
787 797 3.386237 GACGACTGCCCTGCTCCT 61.386 66.667 0.00 0.00 0.00 3.69
795 805 0.179124 GGACTCATCTGACGACTGCC 60.179 60.000 0.00 0.00 0.00 4.85
821 837 2.457366 TTGACTTCTTTCTCCGCTCC 57.543 50.000 0.00 0.00 0.00 4.70
822 838 3.394719 ACTTTGACTTCTTTCTCCGCTC 58.605 45.455 0.00 0.00 0.00 5.03
823 839 3.477210 ACTTTGACTTCTTTCTCCGCT 57.523 42.857 0.00 0.00 0.00 5.52
824 840 4.553756 AAACTTTGACTTCTTTCTCCGC 57.446 40.909 0.00 0.00 0.00 5.54
825 841 5.065988 TCCAAAACTTTGACTTCTTTCTCCG 59.934 40.000 3.72 0.00 40.55 4.63
826 842 6.451064 TCCAAAACTTTGACTTCTTTCTCC 57.549 37.500 3.72 0.00 40.55 3.71
827 843 6.499172 CCTCCAAAACTTTGACTTCTTTCTC 58.501 40.000 3.72 0.00 40.55 2.87
828 844 5.163509 GCCTCCAAAACTTTGACTTCTTTCT 60.164 40.000 3.72 0.00 40.55 2.52
829 845 5.043903 GCCTCCAAAACTTTGACTTCTTTC 58.956 41.667 3.72 0.00 40.55 2.62
830 846 4.440112 CGCCTCCAAAACTTTGACTTCTTT 60.440 41.667 3.72 0.00 40.55 2.52
831 847 3.066760 CGCCTCCAAAACTTTGACTTCTT 59.933 43.478 3.72 0.00 40.55 2.52
832 848 2.618709 CGCCTCCAAAACTTTGACTTCT 59.381 45.455 3.72 0.00 40.55 2.85
867 893 3.443045 AAGGCCGCCGCAATCTTG 61.443 61.111 3.05 0.00 36.38 3.02
945 972 1.597027 CAAAACAGGACCCGTCGCT 60.597 57.895 0.00 0.00 0.00 4.93
955 982 1.281656 GACGGTTCGCCAAAACAGG 59.718 57.895 0.00 0.00 37.00 4.00
956 983 0.316689 GTGACGGTTCGCCAAAACAG 60.317 55.000 0.00 0.00 37.00 3.16
1060 1151 4.500116 GAGGAGAGCGCGGTCACC 62.500 72.222 37.03 37.03 0.00 4.02
1061 1152 4.838486 CGAGGAGAGCGCGGTCAC 62.838 72.222 36.38 30.46 0.00 3.67
1148 1239 2.106683 GTGCCCGGTGAAAGATCCG 61.107 63.158 0.00 0.00 45.42 4.18
1149 1240 2.106683 CGTGCCCGGTGAAAGATCC 61.107 63.158 0.00 0.00 0.00 3.36
1151 1242 0.673644 CTTCGTGCCCGGTGAAAGAT 60.674 55.000 0.00 0.00 33.95 2.40
1152 1243 1.301401 CTTCGTGCCCGGTGAAAGA 60.301 57.895 0.00 0.00 33.95 2.52
1188 1279 0.321298 TTTTCTTCTTCCCGGCTCCG 60.321 55.000 0.00 0.48 39.44 4.63
1189 1280 1.454201 CTTTTCTTCTTCCCGGCTCC 58.546 55.000 0.00 0.00 0.00 4.70
1190 1281 1.003233 TCCTTTTCTTCTTCCCGGCTC 59.997 52.381 0.00 0.00 0.00 4.70
1191 1282 1.064825 TCCTTTTCTTCTTCCCGGCT 58.935 50.000 0.00 0.00 0.00 5.52
1192 1283 1.813178 CTTCCTTTTCTTCTTCCCGGC 59.187 52.381 0.00 0.00 0.00 6.13
1193 1284 3.418684 TCTTCCTTTTCTTCTTCCCGG 57.581 47.619 0.00 0.00 0.00 5.73
1194 1285 4.642429 TCTTCTTCCTTTTCTTCTTCCCG 58.358 43.478 0.00 0.00 0.00 5.14
1195 1286 5.417266 CCATCTTCTTCCTTTTCTTCTTCCC 59.583 44.000 0.00 0.00 0.00 3.97
1196 1287 6.007076 ACCATCTTCTTCCTTTTCTTCTTCC 58.993 40.000 0.00 0.00 0.00 3.46
1197 1288 6.712547 TCACCATCTTCTTCCTTTTCTTCTTC 59.287 38.462 0.00 0.00 0.00 2.87
1198 1289 6.605119 TCACCATCTTCTTCCTTTTCTTCTT 58.395 36.000 0.00 0.00 0.00 2.52
1199 1290 6.192970 TCACCATCTTCTTCCTTTTCTTCT 57.807 37.500 0.00 0.00 0.00 2.85
1200 1291 6.712547 TCTTCACCATCTTCTTCCTTTTCTTC 59.287 38.462 0.00 0.00 0.00 2.87
1201 1292 6.488344 GTCTTCACCATCTTCTTCCTTTTCTT 59.512 38.462 0.00 0.00 0.00 2.52
1202 1293 6.000840 GTCTTCACCATCTTCTTCCTTTTCT 58.999 40.000 0.00 0.00 0.00 2.52
1203 1294 5.106908 CGTCTTCACCATCTTCTTCCTTTTC 60.107 44.000 0.00 0.00 0.00 2.29
1204 1295 4.757149 CGTCTTCACCATCTTCTTCCTTTT 59.243 41.667 0.00 0.00 0.00 2.27
1205 1296 4.040461 TCGTCTTCACCATCTTCTTCCTTT 59.960 41.667 0.00 0.00 0.00 3.11
1206 1297 3.578716 TCGTCTTCACCATCTTCTTCCTT 59.421 43.478 0.00 0.00 0.00 3.36
1207 1298 3.165875 TCGTCTTCACCATCTTCTTCCT 58.834 45.455 0.00 0.00 0.00 3.36
1208 1299 3.516615 CTCGTCTTCACCATCTTCTTCC 58.483 50.000 0.00 0.00 0.00 3.46
1216 1307 0.824759 GGTAGCCTCGTCTTCACCAT 59.175 55.000 0.00 0.00 0.00 3.55
1221 1312 1.226717 CTGCGGTAGCCTCGTCTTC 60.227 63.158 0.00 0.00 44.33 2.87
1248 1339 0.526954 GGCTCGCCATCATTTGCTTG 60.527 55.000 2.41 0.00 35.81 4.01
1249 1340 1.669999 GGGCTCGCCATCATTTGCTT 61.670 55.000 10.51 0.00 37.98 3.91
1254 1345 1.344953 TGTAGGGGCTCGCCATCATT 61.345 55.000 10.51 0.00 37.98 2.57
1307 1398 1.751927 CGGTAGTACCTGGGACGCT 60.752 63.158 17.29 0.00 35.66 5.07
1319 1410 1.427020 GCGTAGAACTCGCGGTAGT 59.573 57.895 6.13 0.00 43.94 2.73
1320 1411 4.281946 GCGTAGAACTCGCGGTAG 57.718 61.111 6.13 0.00 43.94 3.18
1326 1417 1.805945 GGCTGTGGCGTAGAACTCG 60.806 63.158 0.00 0.00 39.81 4.18
1339 1430 2.507944 GGCTCGATCCATGGCTGT 59.492 61.111 6.96 0.00 0.00 4.40
1390 1481 2.747686 CCTGGCCACGTACTGGTT 59.252 61.111 0.00 0.00 42.99 3.67
1463 1640 2.765250 CTTTGCTTGCTGCTGCCCTG 62.765 60.000 13.47 4.35 43.37 4.45
1465 1642 2.048503 CTTTGCTTGCTGCTGCCC 60.049 61.111 13.47 2.32 43.37 5.36
1487 1664 2.357009 AGCCGATGAACATCTTGAATGC 59.643 45.455 12.05 5.97 35.72 3.56
1546 1729 4.938575 ACATCAGGGTGGTAATTGGTAA 57.061 40.909 0.00 0.00 0.00 2.85
1547 1730 4.938575 AACATCAGGGTGGTAATTGGTA 57.061 40.909 0.00 0.00 0.00 3.25
1548 1731 3.825908 AACATCAGGGTGGTAATTGGT 57.174 42.857 0.00 0.00 0.00 3.67
1549 1732 7.723616 TGATAATAACATCAGGGTGGTAATTGG 59.276 37.037 0.00 0.00 31.34 3.16
1550 1733 8.567948 GTGATAATAACATCAGGGTGGTAATTG 58.432 37.037 0.00 0.00 35.63 2.32
1551 1734 8.278639 TGTGATAATAACATCAGGGTGGTAATT 58.721 33.333 0.00 0.00 35.63 1.40
1552 1735 7.719633 GTGTGATAATAACATCAGGGTGGTAAT 59.280 37.037 0.00 0.00 35.63 1.89
1590 1773 7.041098 CCAAAATAGCAATGGGATCACTAGTAC 60.041 40.741 0.00 0.00 0.00 2.73
1591 1774 6.998074 CCAAAATAGCAATGGGATCACTAGTA 59.002 38.462 0.00 0.00 0.00 1.82
1592 1775 5.829924 CCAAAATAGCAATGGGATCACTAGT 59.170 40.000 0.00 0.00 0.00 2.57
1601 1784 1.207570 TGCAGCCAAAATAGCAATGGG 59.792 47.619 0.00 0.00 34.71 4.00
1618 1813 4.567971 CAAGGTTATGCCAATTTCTTGCA 58.432 39.130 0.00 0.00 40.61 4.08
1634 1829 0.611896 CCCCGAAATGAGGCAAGGTT 60.612 55.000 0.00 0.00 0.00 3.50
1649 1844 2.760159 CGTGCTATTTGGTGCCCCG 61.760 63.158 0.00 0.00 0.00 5.73
1668 1864 1.537202 GCTGCAATTTCCTGTCGACTT 59.463 47.619 17.92 0.00 0.00 3.01
1670 1866 0.874390 TGCTGCAATTTCCTGTCGAC 59.126 50.000 9.11 9.11 0.00 4.20
1731 1927 3.475575 TGTGCTGTTTGCTGTCATAGAA 58.524 40.909 0.00 0.00 43.37 2.10
1757 1953 9.498176 TCTGGATTGTTGAACTATATGATGATG 57.502 33.333 0.00 0.00 0.00 3.07
1881 2088 0.247460 GCCCCAAAGAAGATGTTGCC 59.753 55.000 0.00 0.00 0.00 4.52
1911 2118 9.403583 TCTACAAAGAAATGTAAAGAAAGTGGT 57.596 29.630 0.00 0.00 35.48 4.16
1919 2126 9.387123 GCTGTTTCTCTACAAAGAAATGTAAAG 57.613 33.333 2.72 0.00 44.64 1.85
1936 2143 1.303155 AGCCAGGCAGCTGTTTCTC 60.303 57.895 15.80 2.52 42.95 2.87
1938 2145 1.303155 AGAGCCAGGCAGCTGTTTC 60.303 57.895 15.80 5.68 45.15 2.78
1942 2155 1.973816 ATCTCAGAGCCAGGCAGCTG 61.974 60.000 22.30 22.30 45.15 4.24
2091 2314 1.535028 TGCTGTTCATTACCGCAAGTG 59.465 47.619 0.00 0.00 42.90 3.16
2092 2315 1.806542 CTGCTGTTCATTACCGCAAGT 59.193 47.619 0.00 0.00 44.75 3.16
2093 2316 1.466360 GCTGCTGTTCATTACCGCAAG 60.466 52.381 0.00 0.00 44.75 4.01
2095 2318 0.605050 TGCTGCTGTTCATTACCGCA 60.605 50.000 0.00 0.00 43.52 5.69
2096 2319 0.097674 CTGCTGCTGTTCATTACCGC 59.902 55.000 0.00 0.00 37.48 5.68
2097 2320 0.097674 GCTGCTGCTGTTCATTACCG 59.902 55.000 8.53 0.00 36.03 4.02
2098 2321 1.131883 CTGCTGCTGCTGTTCATTACC 59.868 52.381 17.00 0.00 40.48 2.85
2099 2322 1.467035 GCTGCTGCTGCTGTTCATTAC 60.467 52.381 22.10 2.21 39.81 1.89
2100 2323 0.806868 GCTGCTGCTGCTGTTCATTA 59.193 50.000 22.10 0.00 39.81 1.90
2101 2324 1.585006 GCTGCTGCTGCTGTTCATT 59.415 52.632 22.10 0.00 39.81 2.57
2102 2325 3.275088 GCTGCTGCTGCTGTTCAT 58.725 55.556 22.10 0.00 39.81 2.57
2118 2341 1.394917 CGAACCTGCATGTGTAGAAGC 59.605 52.381 0.00 0.00 0.00 3.86
2162 2387 2.765699 AGGAGGAGCAAGAAGACATCTC 59.234 50.000 0.00 0.00 37.42 2.75
2167 2392 3.694043 AGAAAGGAGGAGCAAGAAGAC 57.306 47.619 0.00 0.00 0.00 3.01
2168 2393 3.008485 GGAAGAAAGGAGGAGCAAGAAGA 59.992 47.826 0.00 0.00 0.00 2.87
2173 2398 0.324943 CGGGAAGAAAGGAGGAGCAA 59.675 55.000 0.00 0.00 0.00 3.91
2174 2399 0.836400 ACGGGAAGAAAGGAGGAGCA 60.836 55.000 0.00 0.00 0.00 4.26
2178 2464 1.071699 TGTTCACGGGAAGAAAGGAGG 59.928 52.381 0.00 0.00 32.62 4.30
2180 2466 2.092861 TGTTGTTCACGGGAAGAAAGGA 60.093 45.455 12.05 0.00 37.94 3.36
2182 2468 3.202906 TCTGTTGTTCACGGGAAGAAAG 58.797 45.455 12.05 11.36 37.94 2.62
2188 2474 1.414550 TGTGATCTGTTGTTCACGGGA 59.585 47.619 0.00 0.00 42.66 5.14
2191 2477 4.847633 ACATTTGTGATCTGTTGTTCACG 58.152 39.130 0.00 0.00 42.66 4.35
2291 2584 6.541278 TGGCAATCAGTTGATTCAGAGATAAG 59.459 38.462 4.43 0.00 42.41 1.73
2304 2597 3.244146 TGGGATTTGTTGGCAATCAGTTG 60.244 43.478 1.92 0.00 38.39 3.16
2305 2598 2.971330 TGGGATTTGTTGGCAATCAGTT 59.029 40.909 1.92 0.00 34.18 3.16
2307 2600 2.564062 ACTGGGATTTGTTGGCAATCAG 59.436 45.455 1.92 5.88 34.18 2.90
2336 2629 2.061220 CTCTTGGTGGAGGTGCTGA 58.939 57.895 0.00 0.00 0.00 4.26
2344 2637 1.883638 GCTGTCAATGCTCTTGGTGGA 60.884 52.381 0.70 0.00 0.00 4.02
2345 2638 0.524862 GCTGTCAATGCTCTTGGTGG 59.475 55.000 0.70 0.00 0.00 4.61
2352 2645 1.337703 TGTTTGGTGCTGTCAATGCTC 59.662 47.619 0.00 0.00 0.00 4.26
2356 2649 1.001181 GGCATGTTTGGTGCTGTCAAT 59.999 47.619 0.00 0.00 42.16 2.57
2357 2650 0.388659 GGCATGTTTGGTGCTGTCAA 59.611 50.000 0.00 0.00 42.16 3.18
2358 2651 0.467844 AGGCATGTTTGGTGCTGTCA 60.468 50.000 0.00 0.00 42.16 3.58
2382 2675 3.648067 TCAGTGTCCTCTTCTTGTCCATT 59.352 43.478 0.00 0.00 0.00 3.16
2383 2676 3.242867 TCAGTGTCCTCTTCTTGTCCAT 58.757 45.455 0.00 0.00 0.00 3.41
2384 2677 2.677914 TCAGTGTCCTCTTCTTGTCCA 58.322 47.619 0.00 0.00 0.00 4.02
2385 2678 3.594134 CATCAGTGTCCTCTTCTTGTCC 58.406 50.000 0.00 0.00 0.00 4.02
2399 2699 5.871524 GTGCTGATATATACACCCATCAGTG 59.128 44.000 10.96 0.00 44.04 3.66
2400 2700 5.046304 GGTGCTGATATATACACCCATCAGT 60.046 44.000 16.17 0.00 45.56 3.41
2429 2745 3.405831 TCTGGAGCTGTGTTTCAGAATG 58.594 45.455 0.00 0.00 46.27 2.67
2455 2771 0.326264 CCTGAACTCCTGAACCCCAG 59.674 60.000 0.00 0.00 42.55 4.45
2458 2774 1.353091 ACTCCTGAACTCCTGAACCC 58.647 55.000 0.00 0.00 0.00 4.11
2479 2795 1.830587 CTAGAGCCCTGTGTGCACCA 61.831 60.000 15.69 10.97 0.00 4.17
2480 2796 1.078848 CTAGAGCCCTGTGTGCACC 60.079 63.158 15.69 6.37 0.00 5.01


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

AutoCloner maintained by Alex Coulton.