Multiple sequence alignment - TraesCS2D01G435800

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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 TraesCS2D01G435800 chr2D 100.000 2663 0 0 1 2663 546805359 546808021 0.000000e+00 4918.0
1 TraesCS2D01G435800 chr2D 88.895 1972 135 48 316 2232 546681600 546683542 0.000000e+00 2351.0
2 TraesCS2D01G435800 chr2D 87.781 1113 84 33 1000 2085 546733266 546734353 0.000000e+00 1254.0
3 TraesCS2D01G435800 chr2D 93.220 767 40 3 1000 1766 546637504 546638258 0.000000e+00 1118.0
4 TraesCS2D01G435800 chr2D 91.275 149 6 5 1886 2034 546638376 546638517 2.090000e-46 196.0
5 TraesCS2D01G435800 chr2D 97.872 94 2 0 1084 1177 546779249 546779342 2.120000e-36 163.0
6 TraesCS2D01G435800 chr2D 86.429 140 5 4 2089 2228 546734626 546734751 9.940000e-30 141.0
7 TraesCS2D01G435800 chr2A 90.437 1464 89 21 1088 2519 689761526 689760082 0.000000e+00 1881.0
8 TraesCS2D01G435800 chr2A 86.585 984 80 28 1087 2050 689769888 689768937 0.000000e+00 1038.0
9 TraesCS2D01G435800 chr2A 86.410 986 89 28 1088 2050 689805200 689804237 0.000000e+00 1037.0
10 TraesCS2D01G435800 chr2A 94.602 389 21 0 319 707 689781618 689781230 1.050000e-168 603.0
11 TraesCS2D01G435800 chr2B 93.823 858 51 1 870 1725 653592031 653592888 0.000000e+00 1290.0
12 TraesCS2D01G435800 chr2B 87.029 717 88 3 1000 1711 653415583 653416299 0.000000e+00 804.0
13 TraesCS2D01G435800 chr2B 94.605 519 22 3 316 833 653587639 653588152 0.000000e+00 798.0
14 TraesCS2D01G435800 chr2B 91.732 254 10 4 1 243 77945167 77945420 2.540000e-90 342.0
15 TraesCS2D01G435800 chr2B 85.220 318 25 8 2254 2551 653593202 653593517 9.260000e-80 307.0
16 TraesCS2D01G435800 chr2B 93.684 190 12 0 1000 1189 653403644 653403833 4.340000e-73 285.0
17 TraesCS2D01G435800 chr2B 92.814 167 9 1 2497 2663 653593490 653593653 3.430000e-59 239.0
18 TraesCS2D01G435800 chr2B 89.894 188 14 2 3 185 195514946 195514759 1.230000e-58 237.0
19 TraesCS2D01G435800 chr2B 89.175 194 8 5 1857 2047 653592965 653593148 2.060000e-56 230.0
20 TraesCS2D01G435800 chr2B 87.097 155 9 6 2087 2240 653446664 653446808 5.900000e-37 165.0
21 TraesCS2D01G435800 chr2B 97.753 89 2 0 1084 1172 653583377 653583465 1.280000e-33 154.0
22 TraesCS2D01G435800 chr5A 91.775 766 48 4 1001 1766 377361811 377362561 0.000000e+00 1051.0
23 TraesCS2D01G435800 chr5A 85.062 241 23 5 3 243 549387820 549388047 1.590000e-57 233.0
24 TraesCS2D01G435800 chr5A 76.849 311 60 8 321 627 601171075 601171377 5.900000e-37 165.0
25 TraesCS2D01G435800 chr5A 82.090 201 16 10 1894 2085 377363029 377363218 1.280000e-33 154.0
26 TraesCS2D01G435800 chr5A 96.471 85 2 1 236 319 549388075 549388159 3.570000e-29 139.0
27 TraesCS2D01G435800 chr5A 95.062 81 4 0 237 317 317291524 317291604 7.740000e-26 128.0
28 TraesCS2D01G435800 chr5D 92.653 245 14 3 3 243 448151210 448150966 1.520000e-92 350.0
29 TraesCS2D01G435800 chr5D 76.359 368 80 6 322 684 41431835 41431470 9.730000e-45 191.0
30 TraesCS2D01G435800 chr5D 92.222 90 5 2 236 324 446751572 446751660 2.780000e-25 126.0
31 TraesCS2D01G435800 chr6D 92.653 245 12 2 3 243 418737833 418738075 5.460000e-92 348.0
32 TraesCS2D01G435800 chr3B 91.837 245 16 3 3 243 709766477 709766233 3.280000e-89 339.0
33 TraesCS2D01G435800 chr3B 90.612 245 19 3 3 243 671753290 671753534 3.310000e-84 322.0
34 TraesCS2D01G435800 chr3B 95.000 80 4 0 236 315 709766205 709766126 2.780000e-25 126.0
35 TraesCS2D01G435800 chr6B 91.463 246 16 4 3 243 10919218 10919463 1.530000e-87 333.0
36 TraesCS2D01G435800 chr6B 96.250 80 3 0 236 315 10919491 10919570 5.980000e-27 132.0
37 TraesCS2D01G435800 chr7D 90.157 254 14 6 1 243 31588974 31589227 1.190000e-83 320.0
38 TraesCS2D01G435800 chr4A 91.111 180 11 2 3 177 75887824 75887645 3.430000e-59 239.0
39 TraesCS2D01G435800 chr4A 94.000 50 3 0 2158 2207 103333030 103333079 2.840000e-10 76.8
40 TraesCS2D01G435800 chr3A 80.135 297 51 6 319 611 72421093 72420801 5.770000e-52 215.0
41 TraesCS2D01G435800 chr5B 84.314 204 27 4 316 514 461824914 461825117 7.520000e-46 195.0
42 TraesCS2D01G435800 chr5B 85.484 62 8 1 640 700 349526516 349526455 2.210000e-06 63.9
43 TraesCS2D01G435800 chr7A 75.786 318 71 6 415 728 617222207 617222522 3.550000e-34 156.0
44 TraesCS2D01G435800 chr7A 96.203 79 3 0 237 315 49652892 49652814 2.150000e-26 130.0
45 TraesCS2D01G435800 chr7A 96.203 79 3 0 237 315 709894650 709894728 2.150000e-26 130.0
46 TraesCS2D01G435800 chrUn 95.000 80 4 0 236 315 38452511 38452590 2.780000e-25 126.0
47 TraesCS2D01G435800 chr1B 92.941 85 6 0 236 320 22002549 22002633 1.000000e-24 124.0
48 TraesCS2D01G435800 chr4B 92.857 56 4 0 2158 2213 447365331 447365276 6.110000e-12 82.4
49 TraesCS2D01G435800 chr4D 91.071 56 5 0 2158 2213 361978997 361978942 2.840000e-10 76.8


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 TraesCS2D01G435800 chr2D 546805359 546808021 2662 False 4918.0 4918 100.0000 1 2663 1 chr2D.!!$F3 2662
1 TraesCS2D01G435800 chr2D 546681600 546683542 1942 False 2351.0 2351 88.8950 316 2232 1 chr2D.!!$F1 1916
2 TraesCS2D01G435800 chr2D 546733266 546734751 1485 False 697.5 1254 87.1050 1000 2228 2 chr2D.!!$F5 1228
3 TraesCS2D01G435800 chr2D 546637504 546638517 1013 False 657.0 1118 92.2475 1000 2034 2 chr2D.!!$F4 1034
4 TraesCS2D01G435800 chr2A 689760082 689761526 1444 True 1881.0 1881 90.4370 1088 2519 1 chr2A.!!$R1 1431
5 TraesCS2D01G435800 chr2A 689768937 689769888 951 True 1038.0 1038 86.5850 1087 2050 1 chr2A.!!$R2 963
6 TraesCS2D01G435800 chr2A 689804237 689805200 963 True 1037.0 1037 86.4100 1088 2050 1 chr2A.!!$R4 962
7 TraesCS2D01G435800 chr2B 653415583 653416299 716 False 804.0 804 87.0290 1000 1711 1 chr2B.!!$F3 711
8 TraesCS2D01G435800 chr2B 653587639 653593653 6014 False 572.8 1290 91.1274 316 2663 5 chr2B.!!$F6 2347
9 TraesCS2D01G435800 chr5A 377361811 377363218 1407 False 602.5 1051 86.9325 1001 2085 2 chr5A.!!$F3 1084

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
750 752 0.106708 AGCTTGTTTCGACTGGCTGA 59.893 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2533 7122 0.321996 ACAAGGAGAACCGGAGCTTC 59.678 55.0 9.46 0.7 41.83 3.86 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
26 27 8.977505 GCTTTGTTTATTGTTTCTATTCTTGCA 58.022 29.630 0.00 0.00 0.00 4.08
50 51 9.086336 GCATATGCAAACACAAATAATGTAACT 57.914 29.630 22.84 0.00 39.85 2.24
52 53 7.795431 ATGCAAACACAAATAATGTAACTCG 57.205 32.000 0.00 0.00 41.46 4.18
53 54 6.146216 TGCAAACACAAATAATGTAACTCGG 58.854 36.000 0.00 0.00 41.46 4.63
54 55 6.017026 TGCAAACACAAATAATGTAACTCGGA 60.017 34.615 0.00 0.00 41.46 4.55
55 56 6.304683 GCAAACACAAATAATGTAACTCGGAC 59.695 38.462 0.00 0.00 41.46 4.79
56 57 7.356540 CAAACACAAATAATGTAACTCGGACA 58.643 34.615 0.00 0.00 41.46 4.02
57 58 7.681939 AACACAAATAATGTAACTCGGACAT 57.318 32.000 0.00 0.00 41.46 3.06
58 59 7.681939 ACACAAATAATGTAACTCGGACATT 57.318 32.000 6.29 6.29 46.59 2.71
59 60 8.106247 ACACAAATAATGTAACTCGGACATTT 57.894 30.769 6.34 0.00 43.38 2.32
60 61 8.573035 ACACAAATAATGTAACTCGGACATTTT 58.427 29.630 6.34 0.00 43.38 1.82
61 62 9.405587 CACAAATAATGTAACTCGGACATTTTT 57.594 29.630 6.34 3.04 43.38 1.94
62 63 9.405587 ACAAATAATGTAACTCGGACATTTTTG 57.594 29.630 19.99 19.99 43.38 2.44
63 64 8.372521 CAAATAATGTAACTCGGACATTTTTGC 58.627 33.333 6.34 0.00 43.38 3.68
64 65 5.705609 AATGTAACTCGGACATTTTTGCT 57.294 34.783 0.00 0.00 43.38 3.91
65 66 6.811253 AATGTAACTCGGACATTTTTGCTA 57.189 33.333 0.00 0.00 43.38 3.49
66 67 6.811253 ATGTAACTCGGACATTTTTGCTAA 57.189 33.333 0.00 0.00 33.70 3.09
67 68 5.992729 TGTAACTCGGACATTTTTGCTAAC 58.007 37.500 0.00 0.00 0.00 2.34
68 69 5.527951 TGTAACTCGGACATTTTTGCTAACA 59.472 36.000 0.00 0.00 0.00 2.41
69 70 4.483476 ACTCGGACATTTTTGCTAACAC 57.517 40.909 0.00 0.00 0.00 3.32
70 71 3.880490 ACTCGGACATTTTTGCTAACACA 59.120 39.130 0.00 0.00 0.00 3.72
71 72 4.336993 ACTCGGACATTTTTGCTAACACAA 59.663 37.500 0.00 0.00 0.00 3.33
72 73 5.009610 ACTCGGACATTTTTGCTAACACAAT 59.990 36.000 0.00 0.00 0.00 2.71
73 74 6.205853 ACTCGGACATTTTTGCTAACACAATA 59.794 34.615 0.00 0.00 0.00 1.90
74 75 6.971602 TCGGACATTTTTGCTAACACAATAA 58.028 32.000 0.00 0.00 0.00 1.40
75 76 7.598278 TCGGACATTTTTGCTAACACAATAAT 58.402 30.769 0.00 0.00 33.30 1.28
76 77 8.731605 TCGGACATTTTTGCTAACACAATAATA 58.268 29.630 0.00 0.00 31.93 0.98
77 78 9.347934 CGGACATTTTTGCTAACACAATAATAA 57.652 29.630 0.00 0.00 31.93 1.40
101 102 8.655935 AATTAATCACAAGAGGATGGAAAAGT 57.344 30.769 0.00 0.00 0.00 2.66
102 103 8.655935 ATTAATCACAAGAGGATGGAAAAGTT 57.344 30.769 0.00 0.00 0.00 2.66
103 104 6.983906 AATCACAAGAGGATGGAAAAGTTT 57.016 33.333 0.00 0.00 0.00 2.66
104 105 6.581171 ATCACAAGAGGATGGAAAAGTTTC 57.419 37.500 0.00 0.00 36.46 2.78
105 106 5.694995 TCACAAGAGGATGGAAAAGTTTCT 58.305 37.500 3.92 0.00 37.35 2.52
106 107 6.129179 TCACAAGAGGATGGAAAAGTTTCTT 58.871 36.000 3.92 0.00 37.35 2.52
107 108 7.287061 TCACAAGAGGATGGAAAAGTTTCTTA 58.713 34.615 3.92 0.00 37.35 2.10
108 109 7.777910 TCACAAGAGGATGGAAAAGTTTCTTAA 59.222 33.333 3.92 0.00 37.35 1.85
109 110 8.413229 CACAAGAGGATGGAAAAGTTTCTTAAA 58.587 33.333 3.92 0.00 37.35 1.52
110 111 8.977412 ACAAGAGGATGGAAAAGTTTCTTAAAA 58.023 29.630 3.92 0.00 37.35 1.52
111 112 9.816354 CAAGAGGATGGAAAAGTTTCTTAAAAA 57.184 29.630 3.92 0.00 37.35 1.94
130 131 4.647424 AAAAATGAAGACTTCGGCACAA 57.353 36.364 10.56 0.00 0.00 3.33
131 132 3.904136 AAATGAAGACTTCGGCACAAG 57.096 42.857 10.56 0.00 0.00 3.16
132 133 2.839486 ATGAAGACTTCGGCACAAGA 57.161 45.000 10.56 0.00 0.00 3.02
133 134 2.839486 TGAAGACTTCGGCACAAGAT 57.161 45.000 10.56 0.00 0.00 2.40
134 135 2.416747 TGAAGACTTCGGCACAAGATG 58.583 47.619 10.56 0.00 0.00 2.90
135 136 2.037121 TGAAGACTTCGGCACAAGATGA 59.963 45.455 10.56 0.00 0.00 2.92
136 137 3.265791 GAAGACTTCGGCACAAGATGAT 58.734 45.455 0.00 0.00 0.00 2.45
137 138 4.081697 TGAAGACTTCGGCACAAGATGATA 60.082 41.667 10.56 0.00 0.00 2.15
138 139 4.679373 AGACTTCGGCACAAGATGATAT 57.321 40.909 1.08 0.00 0.00 1.63
139 140 5.791336 AGACTTCGGCACAAGATGATATA 57.209 39.130 1.08 0.00 0.00 0.86
140 141 5.777802 AGACTTCGGCACAAGATGATATAG 58.222 41.667 1.08 0.00 0.00 1.31
141 142 4.310769 ACTTCGGCACAAGATGATATAGC 58.689 43.478 1.08 0.00 0.00 2.97
142 143 4.039730 ACTTCGGCACAAGATGATATAGCT 59.960 41.667 0.00 0.00 0.00 3.32
143 144 5.243954 ACTTCGGCACAAGATGATATAGCTA 59.756 40.000 0.00 0.00 0.00 3.32
144 145 5.316327 TCGGCACAAGATGATATAGCTAG 57.684 43.478 0.00 0.00 0.00 3.42
145 146 3.862267 CGGCACAAGATGATATAGCTAGC 59.138 47.826 6.62 6.62 0.00 3.42
146 147 4.187694 GGCACAAGATGATATAGCTAGCC 58.812 47.826 12.13 0.00 32.70 3.93
147 148 4.187694 GCACAAGATGATATAGCTAGCCC 58.812 47.826 12.13 0.00 0.00 5.19
148 149 4.323028 GCACAAGATGATATAGCTAGCCCA 60.323 45.833 12.13 0.00 0.00 5.36
149 150 5.628666 GCACAAGATGATATAGCTAGCCCAT 60.629 44.000 12.13 7.90 0.00 4.00
150 151 6.047870 CACAAGATGATATAGCTAGCCCATC 58.952 44.000 12.13 15.32 0.00 3.51
151 152 5.723405 ACAAGATGATATAGCTAGCCCATCA 59.277 40.000 22.80 19.80 34.49 3.07
152 153 5.867903 AGATGATATAGCTAGCCCATCAC 57.132 43.478 19.88 15.04 34.49 3.06
153 154 5.275630 AGATGATATAGCTAGCCCATCACA 58.724 41.667 19.88 13.48 34.49 3.58
154 155 5.904169 AGATGATATAGCTAGCCCATCACAT 59.096 40.000 19.88 16.38 34.49 3.21
155 156 5.349061 TGATATAGCTAGCCCATCACATG 57.651 43.478 12.13 0.00 0.00 3.21
156 157 5.025453 TGATATAGCTAGCCCATCACATGA 58.975 41.667 12.13 0.00 0.00 3.07
157 158 5.484998 TGATATAGCTAGCCCATCACATGAA 59.515 40.000 12.13 0.00 0.00 2.57
158 159 2.338577 AGCTAGCCCATCACATGAAC 57.661 50.000 12.13 0.00 0.00 3.18
159 160 1.133976 AGCTAGCCCATCACATGAACC 60.134 52.381 12.13 0.00 0.00 3.62
160 161 1.586422 CTAGCCCATCACATGAACCG 58.414 55.000 0.00 0.00 0.00 4.44
161 162 0.180171 TAGCCCATCACATGAACCGG 59.820 55.000 0.00 0.00 0.00 5.28
162 163 1.077787 GCCCATCACATGAACCGGA 60.078 57.895 9.46 0.00 0.00 5.14
163 164 0.466189 GCCCATCACATGAACCGGAT 60.466 55.000 9.46 0.00 0.00 4.18
164 165 1.311859 CCCATCACATGAACCGGATG 58.688 55.000 9.46 3.80 37.48 3.51
165 166 1.134128 CCCATCACATGAACCGGATGA 60.134 52.381 9.46 1.89 39.52 2.92
166 167 2.487805 CCCATCACATGAACCGGATGAT 60.488 50.000 9.46 4.39 39.52 2.45
167 168 3.244526 CCCATCACATGAACCGGATGATA 60.245 47.826 9.46 0.00 39.52 2.15
168 169 3.748048 CCATCACATGAACCGGATGATAC 59.252 47.826 9.46 0.00 39.52 2.24
169 170 4.503817 CCATCACATGAACCGGATGATACT 60.504 45.833 9.46 0.00 39.52 2.12
170 171 4.322080 TCACATGAACCGGATGATACTC 57.678 45.455 9.46 0.00 0.00 2.59
171 172 3.069586 TCACATGAACCGGATGATACTCC 59.930 47.826 9.46 0.00 0.00 3.85
172 173 3.038280 ACATGAACCGGATGATACTCCA 58.962 45.455 9.46 0.00 34.78 3.86
173 174 3.070159 ACATGAACCGGATGATACTCCAG 59.930 47.826 9.46 0.00 34.78 3.86
174 175 1.412710 TGAACCGGATGATACTCCAGC 59.587 52.381 9.46 0.00 34.78 4.85
175 176 1.689273 GAACCGGATGATACTCCAGCT 59.311 52.381 9.46 0.00 34.78 4.24
176 177 1.333177 ACCGGATGATACTCCAGCTC 58.667 55.000 9.46 0.00 34.78 4.09
177 178 0.605589 CCGGATGATACTCCAGCTCC 59.394 60.000 0.00 0.00 34.78 4.70
178 179 1.332195 CGGATGATACTCCAGCTCCA 58.668 55.000 0.00 0.00 34.78 3.86
179 180 1.000283 CGGATGATACTCCAGCTCCAC 60.000 57.143 0.00 0.00 34.78 4.02
180 181 1.346068 GGATGATACTCCAGCTCCACC 59.654 57.143 0.00 0.00 35.24 4.61
181 182 2.042464 GATGATACTCCAGCTCCACCA 58.958 52.381 0.00 0.00 0.00 4.17
182 183 2.180946 TGATACTCCAGCTCCACCAT 57.819 50.000 0.00 0.00 0.00 3.55
183 184 3.328535 TGATACTCCAGCTCCACCATA 57.671 47.619 0.00 0.00 0.00 2.74
184 185 3.861846 TGATACTCCAGCTCCACCATAT 58.138 45.455 0.00 0.00 0.00 1.78
185 186 4.234550 TGATACTCCAGCTCCACCATATT 58.765 43.478 0.00 0.00 0.00 1.28
186 187 4.284490 TGATACTCCAGCTCCACCATATTC 59.716 45.833 0.00 0.00 0.00 1.75
187 188 2.481441 ACTCCAGCTCCACCATATTCA 58.519 47.619 0.00 0.00 0.00 2.57
188 189 2.846206 ACTCCAGCTCCACCATATTCAA 59.154 45.455 0.00 0.00 0.00 2.69
189 190 3.118112 ACTCCAGCTCCACCATATTCAAG 60.118 47.826 0.00 0.00 0.00 3.02
190 191 2.846206 TCCAGCTCCACCATATTCAAGT 59.154 45.455 0.00 0.00 0.00 3.16
191 192 2.947652 CCAGCTCCACCATATTCAAGTG 59.052 50.000 0.00 0.00 0.00 3.16
200 201 6.187125 CACCATATTCAAGTGGAAGTGAAG 57.813 41.667 0.00 0.00 39.30 3.02
201 202 4.702131 ACCATATTCAAGTGGAAGTGAAGC 59.298 41.667 0.00 0.00 39.30 3.86
202 203 4.701651 CCATATTCAAGTGGAAGTGAAGCA 59.298 41.667 0.00 0.00 39.30 3.91
203 204 5.163683 CCATATTCAAGTGGAAGTGAAGCAG 60.164 44.000 0.00 0.00 39.30 4.24
204 205 3.281727 TTCAAGTGGAAGTGAAGCAGT 57.718 42.857 0.00 0.00 30.41 4.40
205 206 3.281727 TCAAGTGGAAGTGAAGCAGTT 57.718 42.857 0.00 0.00 0.00 3.16
206 207 3.620488 TCAAGTGGAAGTGAAGCAGTTT 58.380 40.909 0.00 0.00 0.00 2.66
207 208 4.776349 TCAAGTGGAAGTGAAGCAGTTTA 58.224 39.130 0.00 0.00 0.00 2.01
208 209 5.376625 TCAAGTGGAAGTGAAGCAGTTTAT 58.623 37.500 0.00 0.00 0.00 1.40
209 210 5.827797 TCAAGTGGAAGTGAAGCAGTTTATT 59.172 36.000 0.00 0.00 0.00 1.40
210 211 6.321181 TCAAGTGGAAGTGAAGCAGTTTATTT 59.679 34.615 0.00 0.00 0.00 1.40
211 212 7.500892 TCAAGTGGAAGTGAAGCAGTTTATTTA 59.499 33.333 0.00 0.00 0.00 1.40
212 213 8.299570 CAAGTGGAAGTGAAGCAGTTTATTTAT 58.700 33.333 0.00 0.00 0.00 1.40
213 214 8.409358 AGTGGAAGTGAAGCAGTTTATTTATT 57.591 30.769 0.00 0.00 0.00 1.40
214 215 8.860088 AGTGGAAGTGAAGCAGTTTATTTATTT 58.140 29.630 0.00 0.00 0.00 1.40
215 216 9.476202 GTGGAAGTGAAGCAGTTTATTTATTTT 57.524 29.630 0.00 0.00 0.00 1.82
216 217 9.474920 TGGAAGTGAAGCAGTTTATTTATTTTG 57.525 29.630 0.00 0.00 0.00 2.44
217 218 8.925700 GGAAGTGAAGCAGTTTATTTATTTTGG 58.074 33.333 0.00 0.00 0.00 3.28
218 219 9.476202 GAAGTGAAGCAGTTTATTTATTTTGGT 57.524 29.630 0.00 0.00 0.00 3.67
245 246 8.890410 AGAAATATCCTTGCCATATTATTGCT 57.110 30.769 1.91 0.00 0.00 3.91
246 247 9.317827 AGAAATATCCTTGCCATATTATTGCTT 57.682 29.630 1.91 0.00 0.00 3.91
247 248 9.362539 GAAATATCCTTGCCATATTATTGCTTG 57.637 33.333 1.91 0.00 0.00 4.01
248 249 5.733620 ATCCTTGCCATATTATTGCTTGG 57.266 39.130 1.91 4.11 0.00 3.61
249 250 4.545678 TCCTTGCCATATTATTGCTTGGT 58.454 39.130 1.91 0.00 0.00 3.67
250 251 4.341806 TCCTTGCCATATTATTGCTTGGTG 59.658 41.667 1.91 0.00 0.00 4.17
251 252 4.099881 CCTTGCCATATTATTGCTTGGTGT 59.900 41.667 1.91 0.00 0.00 4.16
252 253 4.916983 TGCCATATTATTGCTTGGTGTC 57.083 40.909 1.91 0.00 0.00 3.67
253 254 3.636300 TGCCATATTATTGCTTGGTGTCC 59.364 43.478 1.91 0.00 0.00 4.02
254 255 3.636300 GCCATATTATTGCTTGGTGTCCA 59.364 43.478 0.00 0.00 0.00 4.02
255 256 4.281688 GCCATATTATTGCTTGGTGTCCAT 59.718 41.667 0.00 0.00 31.53 3.41
256 257 5.565439 GCCATATTATTGCTTGGTGTCCATC 60.565 44.000 0.00 0.00 31.53 3.51
257 258 5.771666 CCATATTATTGCTTGGTGTCCATCT 59.228 40.000 0.00 0.00 31.53 2.90
258 259 6.266103 CCATATTATTGCTTGGTGTCCATCTT 59.734 38.462 0.00 0.00 31.53 2.40
259 260 7.201938 CCATATTATTGCTTGGTGTCCATCTTT 60.202 37.037 0.00 0.00 31.53 2.52
260 261 3.947910 ATTGCTTGGTGTCCATCTTTG 57.052 42.857 0.00 0.00 31.53 2.77
261 262 2.363306 TGCTTGGTGTCCATCTTTGT 57.637 45.000 0.00 0.00 31.53 2.83
262 263 3.500448 TGCTTGGTGTCCATCTTTGTA 57.500 42.857 0.00 0.00 31.53 2.41
263 264 4.032960 TGCTTGGTGTCCATCTTTGTAT 57.967 40.909 0.00 0.00 31.53 2.29
264 265 5.172687 TGCTTGGTGTCCATCTTTGTATA 57.827 39.130 0.00 0.00 31.53 1.47
265 266 5.754782 TGCTTGGTGTCCATCTTTGTATAT 58.245 37.500 0.00 0.00 31.53 0.86
266 267 6.894682 TGCTTGGTGTCCATCTTTGTATATA 58.105 36.000 0.00 0.00 31.53 0.86
267 268 7.517320 TGCTTGGTGTCCATCTTTGTATATAT 58.483 34.615 0.00 0.00 31.53 0.86
268 269 7.445096 TGCTTGGTGTCCATCTTTGTATATATG 59.555 37.037 0.00 0.00 31.53 1.78
269 270 7.661437 GCTTGGTGTCCATCTTTGTATATATGA 59.339 37.037 0.00 0.00 31.53 2.15
270 271 9.730705 CTTGGTGTCCATCTTTGTATATATGAT 57.269 33.333 0.00 0.00 31.53 2.45
271 272 9.506018 TTGGTGTCCATCTTTGTATATATGATG 57.494 33.333 0.00 0.00 35.59 3.07
272 273 8.659527 TGGTGTCCATCTTTGTATATATGATGT 58.340 33.333 0.00 0.00 34.44 3.06
273 274 8.939929 GGTGTCCATCTTTGTATATATGATGTG 58.060 37.037 0.00 0.00 34.44 3.21
274 275 8.446273 GTGTCCATCTTTGTATATATGATGTGC 58.554 37.037 0.00 0.00 34.44 4.57
275 276 8.156165 TGTCCATCTTTGTATATATGATGTGCA 58.844 33.333 0.00 0.00 34.44 4.57
276 277 8.446273 GTCCATCTTTGTATATATGATGTGCAC 58.554 37.037 10.75 10.75 34.44 4.57
277 278 7.331687 TCCATCTTTGTATATATGATGTGCACG 59.668 37.037 13.13 0.00 34.44 5.34
278 279 7.118245 CCATCTTTGTATATATGATGTGCACGT 59.882 37.037 12.38 12.38 34.44 4.49
279 280 7.406799 TCTTTGTATATATGATGTGCACGTG 57.593 36.000 18.17 12.28 0.00 4.49
280 281 6.423604 TCTTTGTATATATGATGTGCACGTGG 59.576 38.462 18.17 0.00 0.00 4.94
281 282 5.461032 TGTATATATGATGTGCACGTGGA 57.539 39.130 18.17 12.78 0.00 4.02
282 283 5.227152 TGTATATATGATGTGCACGTGGAC 58.773 41.667 30.61 30.61 36.87 4.02
287 288 4.901123 TGTGCACGTGGACACCGG 62.901 66.667 35.02 0.00 41.48 5.28
291 292 3.918977 CACGTGGACACCGGGACA 61.919 66.667 7.95 0.00 0.00 4.02
292 293 2.920912 ACGTGGACACCGGGACAT 60.921 61.111 6.32 0.00 0.00 3.06
293 294 2.345991 CGTGGACACCGGGACATT 59.654 61.111 6.32 0.00 0.00 2.71
294 295 1.302192 CGTGGACACCGGGACATTT 60.302 57.895 6.32 0.00 0.00 2.32
295 296 0.887387 CGTGGACACCGGGACATTTT 60.887 55.000 6.32 0.00 0.00 1.82
296 297 1.324383 GTGGACACCGGGACATTTTT 58.676 50.000 6.32 0.00 0.00 1.94
297 298 1.000717 GTGGACACCGGGACATTTTTG 60.001 52.381 6.32 0.00 0.00 2.44
298 299 1.324383 GGACACCGGGACATTTTTGT 58.676 50.000 6.32 0.00 0.00 2.83
299 300 1.684450 GGACACCGGGACATTTTTGTT 59.316 47.619 6.32 0.00 0.00 2.83
300 301 2.287970 GGACACCGGGACATTTTTGTTC 60.288 50.000 6.32 0.00 0.00 3.18
301 302 2.621526 GACACCGGGACATTTTTGTTCT 59.378 45.455 6.32 0.00 0.00 3.01
302 303 2.360801 ACACCGGGACATTTTTGTTCTG 59.639 45.455 6.32 0.00 0.00 3.02
303 304 1.960689 ACCGGGACATTTTTGTTCTGG 59.039 47.619 6.32 10.19 46.89 3.86
304 305 2.235016 CCGGGACATTTTTGTTCTGGA 58.765 47.619 6.43 0.00 44.85 3.86
305 306 2.825532 CCGGGACATTTTTGTTCTGGAT 59.174 45.455 6.43 0.00 44.85 3.41
306 307 3.119495 CCGGGACATTTTTGTTCTGGATC 60.119 47.826 6.43 0.00 44.85 3.36
307 308 3.758554 CGGGACATTTTTGTTCTGGATCT 59.241 43.478 0.00 0.00 0.00 2.75
308 309 4.379813 CGGGACATTTTTGTTCTGGATCTG 60.380 45.833 0.00 0.00 0.00 2.90
309 310 4.488879 GGACATTTTTGTTCTGGATCTGC 58.511 43.478 0.00 0.00 0.00 4.26
310 311 4.488879 GACATTTTTGTTCTGGATCTGCC 58.511 43.478 0.00 0.00 37.10 4.85
311 312 3.259123 ACATTTTTGTTCTGGATCTGCCC 59.741 43.478 0.00 0.00 34.97 5.36
312 313 1.923356 TTTTGTTCTGGATCTGCCCC 58.077 50.000 0.00 0.00 34.97 5.80
313 314 1.075601 TTTGTTCTGGATCTGCCCCT 58.924 50.000 0.00 0.00 34.97 4.79
314 315 0.329261 TTGTTCTGGATCTGCCCCTG 59.671 55.000 0.00 0.00 34.97 4.45
328 329 2.105128 CCTGTCGCCGTCTCATCC 59.895 66.667 0.00 0.00 0.00 3.51
342 343 1.743958 CTCATCCGTGTAGTCCTCGTT 59.256 52.381 0.00 0.00 0.00 3.85
394 395 4.083484 TGCTCGTGTATGTACTCCATATCG 60.083 45.833 0.00 0.00 38.29 2.92
463 464 1.244816 TCACCGAACAGTCGATGAGT 58.755 50.000 0.00 0.00 45.11 3.41
480 481 1.827969 GAGTATGGTGAGTGCCTCAGT 59.172 52.381 5.28 0.00 41.46 3.41
524 525 3.025262 GACGGAGGAGAGGTATGAAACT 58.975 50.000 0.00 0.00 0.00 2.66
531 532 0.459585 GAGGTATGAAACTGCGGCGA 60.460 55.000 12.98 0.00 0.00 5.54
544 545 4.459089 GGCGAAGGAGAAGCGGCT 62.459 66.667 0.00 0.00 45.52 5.52
655 657 4.764823 AGAGTCGAGAGAGAAAACAGATGT 59.235 41.667 0.00 0.00 43.49 3.06
750 752 0.106708 AGCTTGTTTCGACTGGCTGA 59.893 50.000 0.00 0.00 0.00 4.26
761 763 1.142748 CTGGCTGATGTCCGGTCTC 59.857 63.158 0.00 0.00 0.00 3.36
795 797 1.908066 AAATTTGTCCCTCGCGTCGC 61.908 55.000 7.29 7.29 0.00 5.19
828 831 2.026641 GTATGGTGGAGCGGTACAGTA 58.973 52.381 0.00 0.00 0.00 2.74
853 2931 0.393537 AGCTCATTTTCTCAGCCCCG 60.394 55.000 0.00 0.00 33.28 5.73
854 2932 1.379642 GCTCATTTTCTCAGCCCCGG 61.380 60.000 0.00 0.00 0.00 5.73
889 4736 1.214589 GAACTCGGCAGCGTTAGGA 59.785 57.895 0.00 0.00 0.00 2.94
1455 5306 3.084039 GTCCATGCAACAGGAGATCAAA 58.916 45.455 6.19 0.00 33.85 2.69
1617 5468 1.593750 GGCGCTAGAGGACATGCAG 60.594 63.158 7.64 0.00 0.00 4.41
1681 5542 2.435938 TTCCAAGATGGGCGCGTC 60.436 61.111 14.82 14.82 38.32 5.19
1835 5764 8.514330 AATCCTTTGTTTGTAGTTGTTGAGTA 57.486 30.769 0.00 0.00 0.00 2.59
1850 5779 3.752412 TGAGTAATACGTGACGAGGTG 57.248 47.619 13.70 0.00 0.00 4.00
1873 5807 7.443272 GGTGTTTACACTTGTCTGTATTACCTT 59.557 37.037 12.32 0.00 45.73 3.50
1880 5814 8.208903 ACACTTGTCTGTATTACCTTGTAGTTT 58.791 33.333 0.00 0.00 0.00 2.66
1883 5817 9.701098 CTTGTCTGTATTACCTTGTAGTTTGTA 57.299 33.333 0.00 0.00 0.00 2.41
1884 5818 9.480053 TTGTCTGTATTACCTTGTAGTTTGTAC 57.520 33.333 0.00 0.00 0.00 2.90
1885 5819 8.863086 TGTCTGTATTACCTTGTAGTTTGTACT 58.137 33.333 0.00 0.00 38.44 2.73
1971 6214 2.159156 CCTGTGGCTACGTTGTGCTATA 60.159 50.000 0.00 0.00 0.00 1.31
1972 6215 3.492656 CCTGTGGCTACGTTGTGCTATAT 60.493 47.826 0.00 0.00 0.00 0.86
1974 6217 5.462530 TGTGGCTACGTTGTGCTATATAT 57.537 39.130 0.00 0.00 0.00 0.86
1976 6219 4.091509 GTGGCTACGTTGTGCTATATATGC 59.908 45.833 0.00 0.00 0.00 3.14
1977 6220 3.303495 GGCTACGTTGTGCTATATATGCG 59.697 47.826 0.00 0.00 0.00 4.73
1978 6221 3.241678 GCTACGTTGTGCTATATATGCGC 60.242 47.826 0.00 0.00 40.87 6.09
2276 6812 1.918262 TGGAGGTGAAGAAGGATGCAT 59.082 47.619 0.00 0.00 0.00 3.96
2303 6841 1.884579 TCTGTCTGTGAACTCGTACCC 59.115 52.381 0.00 0.00 0.00 3.69
2325 6871 2.046892 GCTCACAGGCGTCACCAT 60.047 61.111 0.00 0.00 43.14 3.55
2521 7083 0.894184 TCGACAAGCTCCGGTTCTCT 60.894 55.000 0.00 0.00 0.00 3.10
2525 7087 1.270893 ACAAGCTCCGGTTCTCTTTCC 60.271 52.381 0.00 0.00 0.00 3.13
2533 7122 2.416162 CCGGTTCTCTTTCCTCTTCGAG 60.416 54.545 0.00 0.00 0.00 4.04
2613 7202 2.126189 CGTCGTCCGTTCTTCCCC 60.126 66.667 0.00 0.00 0.00 4.81
2614 7203 2.126189 GTCGTCCGTTCTTCCCCG 60.126 66.667 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.977505 TGCAAGAATAGAAACAATAAACAAAGC 58.022 29.630 0.00 0.00 0.00 3.51
23 24 8.867935 GTTACATTATTTGTGTTTGCATATGCA 58.132 29.630 26.32 26.32 43.87 3.96
24 25 9.086336 AGTTACATTATTTGTGTTTGCATATGC 57.914 29.630 21.09 21.09 39.48 3.14
26 27 9.502145 CGAGTTACATTATTTGTGTTTGCATAT 57.498 29.630 0.00 0.00 39.48 1.78
27 28 7.965655 CCGAGTTACATTATTTGTGTTTGCATA 59.034 33.333 0.00 0.00 39.48 3.14
28 29 6.806249 CCGAGTTACATTATTTGTGTTTGCAT 59.194 34.615 0.00 0.00 39.48 3.96
29 30 6.017026 TCCGAGTTACATTATTTGTGTTTGCA 60.017 34.615 0.00 0.00 39.48 4.08
30 31 6.304683 GTCCGAGTTACATTATTTGTGTTTGC 59.695 38.462 0.00 0.00 39.48 3.68
31 32 7.356540 TGTCCGAGTTACATTATTTGTGTTTG 58.643 34.615 0.00 0.00 39.48 2.93
32 33 7.499321 TGTCCGAGTTACATTATTTGTGTTT 57.501 32.000 0.00 0.00 39.48 2.83
33 34 7.681939 ATGTCCGAGTTACATTATTTGTGTT 57.318 32.000 0.00 0.00 39.48 3.32
34 35 7.681939 AATGTCCGAGTTACATTATTTGTGT 57.318 32.000 0.00 0.00 43.84 3.72
35 36 8.964420 AAAATGTCCGAGTTACATTATTTGTG 57.036 30.769 2.18 0.00 44.66 3.33
36 37 9.405587 CAAAAATGTCCGAGTTACATTATTTGT 57.594 29.630 17.14 0.00 44.66 2.83
37 38 8.372521 GCAAAAATGTCCGAGTTACATTATTTG 58.627 33.333 18.93 18.93 44.66 2.32
38 39 8.303876 AGCAAAAATGTCCGAGTTACATTATTT 58.696 29.630 2.18 3.70 44.66 1.40
39 40 7.826690 AGCAAAAATGTCCGAGTTACATTATT 58.173 30.769 2.18 0.00 44.66 1.40
40 41 7.391148 AGCAAAAATGTCCGAGTTACATTAT 57.609 32.000 2.18 0.00 44.66 1.28
41 42 6.811253 AGCAAAAATGTCCGAGTTACATTA 57.189 33.333 2.18 0.00 44.66 1.90
42 43 5.705609 AGCAAAAATGTCCGAGTTACATT 57.294 34.783 0.00 0.00 46.77 2.71
43 44 6.205853 TGTTAGCAAAAATGTCCGAGTTACAT 59.794 34.615 0.00 0.00 39.22 2.29
44 45 5.527951 TGTTAGCAAAAATGTCCGAGTTACA 59.472 36.000 0.00 0.00 0.00 2.41
45 46 5.849604 GTGTTAGCAAAAATGTCCGAGTTAC 59.150 40.000 0.00 0.00 0.00 2.50
46 47 5.527951 TGTGTTAGCAAAAATGTCCGAGTTA 59.472 36.000 0.00 0.00 0.00 2.24
47 48 4.336993 TGTGTTAGCAAAAATGTCCGAGTT 59.663 37.500 0.00 0.00 0.00 3.01
48 49 3.880490 TGTGTTAGCAAAAATGTCCGAGT 59.120 39.130 0.00 0.00 0.00 4.18
49 50 4.481930 TGTGTTAGCAAAAATGTCCGAG 57.518 40.909 0.00 0.00 0.00 4.63
50 51 4.902443 TTGTGTTAGCAAAAATGTCCGA 57.098 36.364 0.00 0.00 0.00 4.55
51 52 7.810766 ATTATTGTGTTAGCAAAAATGTCCG 57.189 32.000 0.00 0.00 31.63 4.79
75 76 9.753674 ACTTTTCCATCCTCTTGTGATTAATTA 57.246 29.630 0.00 0.00 0.00 1.40
76 77 8.655935 ACTTTTCCATCCTCTTGTGATTAATT 57.344 30.769 0.00 0.00 0.00 1.40
77 78 8.655935 AACTTTTCCATCCTCTTGTGATTAAT 57.344 30.769 0.00 0.00 0.00 1.40
78 79 8.477419 AAACTTTTCCATCCTCTTGTGATTAA 57.523 30.769 0.00 0.00 0.00 1.40
79 80 7.944554 AGAAACTTTTCCATCCTCTTGTGATTA 59.055 33.333 0.00 0.00 37.92 1.75
80 81 6.779539 AGAAACTTTTCCATCCTCTTGTGATT 59.220 34.615 0.00 0.00 37.92 2.57
81 82 6.310149 AGAAACTTTTCCATCCTCTTGTGAT 58.690 36.000 0.00 0.00 37.92 3.06
82 83 5.694995 AGAAACTTTTCCATCCTCTTGTGA 58.305 37.500 0.00 0.00 37.92 3.58
83 84 6.396829 AAGAAACTTTTCCATCCTCTTGTG 57.603 37.500 0.00 0.00 37.92 3.33
84 85 8.533569 TTTAAGAAACTTTTCCATCCTCTTGT 57.466 30.769 0.00 0.00 37.92 3.16
85 86 9.816354 TTTTTAAGAAACTTTTCCATCCTCTTG 57.184 29.630 0.00 0.00 37.92 3.02
109 110 4.338118 TCTTGTGCCGAAGTCTTCATTTTT 59.662 37.500 12.99 0.00 0.00 1.94
110 111 3.882888 TCTTGTGCCGAAGTCTTCATTTT 59.117 39.130 12.99 0.00 0.00 1.82
111 112 3.476552 TCTTGTGCCGAAGTCTTCATTT 58.523 40.909 12.99 0.00 0.00 2.32
112 113 3.126001 TCTTGTGCCGAAGTCTTCATT 57.874 42.857 12.99 0.00 0.00 2.57
113 114 2.839486 TCTTGTGCCGAAGTCTTCAT 57.161 45.000 12.99 0.00 0.00 2.57
114 115 2.037121 TCATCTTGTGCCGAAGTCTTCA 59.963 45.455 12.99 0.00 0.00 3.02
115 116 2.688507 TCATCTTGTGCCGAAGTCTTC 58.311 47.619 2.18 2.18 0.00 2.87
116 117 2.839486 TCATCTTGTGCCGAAGTCTT 57.161 45.000 0.00 0.00 0.00 3.01
117 118 4.679373 ATATCATCTTGTGCCGAAGTCT 57.321 40.909 0.00 0.00 0.00 3.24
118 119 4.387256 GCTATATCATCTTGTGCCGAAGTC 59.613 45.833 0.00 0.00 0.00 3.01
119 120 4.039730 AGCTATATCATCTTGTGCCGAAGT 59.960 41.667 0.00 0.00 0.00 3.01
120 121 4.564041 AGCTATATCATCTTGTGCCGAAG 58.436 43.478 0.00 0.00 0.00 3.79
121 122 4.607293 AGCTATATCATCTTGTGCCGAA 57.393 40.909 0.00 0.00 0.00 4.30
122 123 4.380973 GCTAGCTATATCATCTTGTGCCGA 60.381 45.833 7.70 0.00 0.00 5.54
123 124 3.862267 GCTAGCTATATCATCTTGTGCCG 59.138 47.826 7.70 0.00 0.00 5.69
124 125 4.187694 GGCTAGCTATATCATCTTGTGCC 58.812 47.826 15.72 0.00 0.00 5.01
125 126 4.187694 GGGCTAGCTATATCATCTTGTGC 58.812 47.826 15.72 0.00 0.00 4.57
126 127 5.411831 TGGGCTAGCTATATCATCTTGTG 57.588 43.478 15.72 0.00 0.00 3.33
127 128 5.723405 TGATGGGCTAGCTATATCATCTTGT 59.277 40.000 15.72 0.00 34.03 3.16
128 129 6.047870 GTGATGGGCTAGCTATATCATCTTG 58.952 44.000 22.43 0.93 34.03 3.02
129 130 5.723405 TGTGATGGGCTAGCTATATCATCTT 59.277 40.000 22.43 1.74 34.03 2.40
130 131 5.275630 TGTGATGGGCTAGCTATATCATCT 58.724 41.667 22.43 2.26 34.03 2.90
131 132 5.604758 TGTGATGGGCTAGCTATATCATC 57.395 43.478 22.43 20.52 31.28 2.92
132 133 5.664457 TCATGTGATGGGCTAGCTATATCAT 59.336 40.000 22.43 16.78 31.28 2.45
133 134 5.025453 TCATGTGATGGGCTAGCTATATCA 58.975 41.667 15.72 17.48 0.00 2.15
134 135 5.604758 TCATGTGATGGGCTAGCTATATC 57.395 43.478 15.72 15.28 0.00 1.63
135 136 5.338708 GGTTCATGTGATGGGCTAGCTATAT 60.339 44.000 15.72 6.64 0.00 0.86
136 137 4.020218 GGTTCATGTGATGGGCTAGCTATA 60.020 45.833 15.72 1.44 0.00 1.31
137 138 3.244700 GGTTCATGTGATGGGCTAGCTAT 60.245 47.826 15.72 9.65 0.00 2.97
138 139 2.104792 GGTTCATGTGATGGGCTAGCTA 59.895 50.000 15.72 4.59 0.00 3.32
139 140 1.133976 GGTTCATGTGATGGGCTAGCT 60.134 52.381 15.72 0.00 0.00 3.32
140 141 1.312815 GGTTCATGTGATGGGCTAGC 58.687 55.000 6.04 6.04 0.00 3.42
141 142 1.586422 CGGTTCATGTGATGGGCTAG 58.414 55.000 0.00 0.00 0.00 3.42
142 143 0.180171 CCGGTTCATGTGATGGGCTA 59.820 55.000 0.00 0.00 0.00 3.93
143 144 1.077501 CCGGTTCATGTGATGGGCT 60.078 57.895 0.00 0.00 0.00 5.19
144 145 0.466189 ATCCGGTTCATGTGATGGGC 60.466 55.000 0.00 0.00 0.00 5.36
145 146 1.134128 TCATCCGGTTCATGTGATGGG 60.134 52.381 0.00 0.00 36.21 4.00
146 147 2.330440 TCATCCGGTTCATGTGATGG 57.670 50.000 0.00 0.00 36.21 3.51
147 148 4.635223 AGTATCATCCGGTTCATGTGATG 58.365 43.478 0.00 0.00 36.73 3.07
148 149 4.262635 GGAGTATCATCCGGTTCATGTGAT 60.263 45.833 0.00 5.98 36.25 3.06
149 150 3.069586 GGAGTATCATCCGGTTCATGTGA 59.930 47.826 0.00 0.00 36.25 3.58
150 151 3.181466 TGGAGTATCATCCGGTTCATGTG 60.181 47.826 0.00 0.00 42.77 3.21
151 152 3.038280 TGGAGTATCATCCGGTTCATGT 58.962 45.455 0.00 0.00 42.77 3.21
152 153 3.657634 CTGGAGTATCATCCGGTTCATG 58.342 50.000 0.00 0.00 42.77 3.07
153 154 2.037772 GCTGGAGTATCATCCGGTTCAT 59.962 50.000 0.00 0.00 46.04 2.57
154 155 1.412710 GCTGGAGTATCATCCGGTTCA 59.587 52.381 0.00 0.00 46.04 3.18
155 156 1.689273 AGCTGGAGTATCATCCGGTTC 59.311 52.381 0.00 0.00 46.04 3.62
156 157 1.689273 GAGCTGGAGTATCATCCGGTT 59.311 52.381 0.00 0.00 46.04 4.44
157 158 1.333177 GAGCTGGAGTATCATCCGGT 58.667 55.000 0.00 0.00 46.04 5.28
158 159 0.605589 GGAGCTGGAGTATCATCCGG 59.394 60.000 0.00 0.00 46.90 5.14
159 160 1.000283 GTGGAGCTGGAGTATCATCCG 60.000 57.143 0.00 0.00 42.77 4.18
160 161 1.346068 GGTGGAGCTGGAGTATCATCC 59.654 57.143 0.00 0.00 40.03 3.51
161 162 2.042464 TGGTGGAGCTGGAGTATCATC 58.958 52.381 0.00 0.00 36.25 2.92
162 163 2.180946 TGGTGGAGCTGGAGTATCAT 57.819 50.000 0.00 0.00 36.25 2.45
163 164 2.180946 ATGGTGGAGCTGGAGTATCA 57.819 50.000 0.00 0.00 36.25 2.15
164 165 4.284490 TGAATATGGTGGAGCTGGAGTATC 59.716 45.833 0.00 0.00 0.00 2.24
165 166 4.234550 TGAATATGGTGGAGCTGGAGTAT 58.765 43.478 0.00 0.00 0.00 2.12
166 167 3.653164 TGAATATGGTGGAGCTGGAGTA 58.347 45.455 0.00 0.00 0.00 2.59
167 168 2.481441 TGAATATGGTGGAGCTGGAGT 58.519 47.619 0.00 0.00 0.00 3.85
168 169 3.118112 ACTTGAATATGGTGGAGCTGGAG 60.118 47.826 0.00 0.00 0.00 3.86
169 170 2.846206 ACTTGAATATGGTGGAGCTGGA 59.154 45.455 0.00 0.00 0.00 3.86
170 171 2.947652 CACTTGAATATGGTGGAGCTGG 59.052 50.000 0.00 0.00 0.00 4.85
177 178 5.392380 GCTTCACTTCCACTTGAATATGGTG 60.392 44.000 0.00 0.00 37.27 4.17
178 179 4.702131 GCTTCACTTCCACTTGAATATGGT 59.298 41.667 0.00 0.00 37.27 3.55
179 180 4.701651 TGCTTCACTTCCACTTGAATATGG 59.298 41.667 0.00 0.00 37.32 2.74
180 181 5.413833 ACTGCTTCACTTCCACTTGAATATG 59.586 40.000 0.00 0.00 31.41 1.78
181 182 5.564550 ACTGCTTCACTTCCACTTGAATAT 58.435 37.500 0.00 0.00 31.41 1.28
182 183 4.973168 ACTGCTTCACTTCCACTTGAATA 58.027 39.130 0.00 0.00 31.41 1.75
183 184 3.825328 ACTGCTTCACTTCCACTTGAAT 58.175 40.909 0.00 0.00 31.41 2.57
184 185 3.281727 ACTGCTTCACTTCCACTTGAA 57.718 42.857 0.00 0.00 0.00 2.69
185 186 3.281727 AACTGCTTCACTTCCACTTGA 57.718 42.857 0.00 0.00 0.00 3.02
186 187 5.695851 ATAAACTGCTTCACTTCCACTTG 57.304 39.130 0.00 0.00 0.00 3.16
187 188 6.715347 AAATAAACTGCTTCACTTCCACTT 57.285 33.333 0.00 0.00 0.00 3.16
188 189 8.409358 AATAAATAAACTGCTTCACTTCCACT 57.591 30.769 0.00 0.00 0.00 4.00
189 190 9.476202 AAAATAAATAAACTGCTTCACTTCCAC 57.524 29.630 0.00 0.00 0.00 4.02
190 191 9.474920 CAAAATAAATAAACTGCTTCACTTCCA 57.525 29.630 0.00 0.00 0.00 3.53
191 192 8.925700 CCAAAATAAATAAACTGCTTCACTTCC 58.074 33.333 0.00 0.00 0.00 3.46
192 193 9.476202 ACCAAAATAAATAAACTGCTTCACTTC 57.524 29.630 0.00 0.00 0.00 3.01
209 210 9.261035 TGGCAAGGATATTTCTTACCAAAATAA 57.739 29.630 8.44 0.00 35.41 1.40
210 211 8.830915 TGGCAAGGATATTTCTTACCAAAATA 57.169 30.769 8.44 0.00 35.41 1.40
211 212 7.732222 TGGCAAGGATATTTCTTACCAAAAT 57.268 32.000 8.44 0.00 35.41 1.82
212 213 7.732222 ATGGCAAGGATATTTCTTACCAAAA 57.268 32.000 12.72 0.00 40.03 2.44
213 214 9.432982 AATATGGCAAGGATATTTCTTACCAAA 57.567 29.630 12.72 0.00 40.03 3.28
219 220 9.317827 AGCAATAATATGGCAAGGATATTTCTT 57.682 29.630 2.08 0.00 30.37 2.52
220 221 8.890410 AGCAATAATATGGCAAGGATATTTCT 57.110 30.769 2.08 0.00 30.37 2.52
221 222 9.362539 CAAGCAATAATATGGCAAGGATATTTC 57.637 33.333 2.08 0.00 30.37 2.17
222 223 8.316214 CCAAGCAATAATATGGCAAGGATATTT 58.684 33.333 2.08 0.00 30.37 1.40
223 224 7.455638 ACCAAGCAATAATATGGCAAGGATATT 59.544 33.333 14.62 0.00 36.37 1.28
224 225 6.955851 ACCAAGCAATAATATGGCAAGGATAT 59.044 34.615 14.62 0.00 36.37 1.63
225 226 6.209192 CACCAAGCAATAATATGGCAAGGATA 59.791 38.462 14.62 0.00 36.37 2.59
226 227 5.011329 CACCAAGCAATAATATGGCAAGGAT 59.989 40.000 14.62 0.72 36.37 3.24
227 228 4.341806 CACCAAGCAATAATATGGCAAGGA 59.658 41.667 14.62 0.00 36.37 3.36
228 229 4.099881 ACACCAAGCAATAATATGGCAAGG 59.900 41.667 2.08 5.72 36.37 3.61
229 230 5.266733 ACACCAAGCAATAATATGGCAAG 57.733 39.130 2.08 0.00 36.37 4.01
230 231 4.099266 GGACACCAAGCAATAATATGGCAA 59.901 41.667 2.08 0.00 36.37 4.52
231 232 3.636300 GGACACCAAGCAATAATATGGCA 59.364 43.478 2.08 0.00 36.37 4.92
232 233 3.636300 TGGACACCAAGCAATAATATGGC 59.364 43.478 0.00 0.00 36.37 4.40
233 234 5.771666 AGATGGACACCAAGCAATAATATGG 59.228 40.000 0.00 0.00 36.95 2.74
234 235 6.889301 AGATGGACACCAAGCAATAATATG 57.111 37.500 0.00 0.00 36.95 1.78
235 236 7.342799 ACAAAGATGGACACCAAGCAATAATAT 59.657 33.333 0.00 0.00 36.95 1.28
236 237 6.663093 ACAAAGATGGACACCAAGCAATAATA 59.337 34.615 0.00 0.00 36.95 0.98
237 238 5.481473 ACAAAGATGGACACCAAGCAATAAT 59.519 36.000 0.00 0.00 36.95 1.28
238 239 4.832266 ACAAAGATGGACACCAAGCAATAA 59.168 37.500 0.00 0.00 36.95 1.40
239 240 4.406456 ACAAAGATGGACACCAAGCAATA 58.594 39.130 0.00 0.00 36.95 1.90
240 241 3.233507 ACAAAGATGGACACCAAGCAAT 58.766 40.909 0.00 0.00 36.95 3.56
241 242 2.665165 ACAAAGATGGACACCAAGCAA 58.335 42.857 0.00 0.00 36.95 3.91
242 243 2.363306 ACAAAGATGGACACCAAGCA 57.637 45.000 0.00 0.00 36.95 3.91
243 244 7.661437 TCATATATACAAAGATGGACACCAAGC 59.339 37.037 0.00 0.00 36.95 4.01
244 245 9.730705 ATCATATATACAAAGATGGACACCAAG 57.269 33.333 0.00 0.00 36.95 3.61
245 246 9.506018 CATCATATATACAAAGATGGACACCAA 57.494 33.333 0.00 0.00 36.95 3.67
246 247 8.659527 ACATCATATATACAAAGATGGACACCA 58.340 33.333 12.24 0.00 40.17 4.17
247 248 8.939929 CACATCATATATACAAAGATGGACACC 58.060 37.037 12.24 0.00 40.17 4.16
248 249 8.446273 GCACATCATATATACAAAGATGGACAC 58.554 37.037 12.24 0.00 40.17 3.67
249 250 8.156165 TGCACATCATATATACAAAGATGGACA 58.844 33.333 12.24 8.16 40.17 4.02
250 251 8.446273 GTGCACATCATATATACAAAGATGGAC 58.554 37.037 13.17 6.38 40.17 4.02
251 252 7.331687 CGTGCACATCATATATACAAAGATGGA 59.668 37.037 18.64 0.00 40.17 3.41
252 253 7.118245 ACGTGCACATCATATATACAAAGATGG 59.882 37.037 18.64 0.00 40.17 3.51
253 254 7.953710 CACGTGCACATCATATATACAAAGATG 59.046 37.037 18.64 7.93 41.28 2.90
254 255 7.118245 CCACGTGCACATCATATATACAAAGAT 59.882 37.037 18.64 0.00 0.00 2.40
255 256 6.423604 CCACGTGCACATCATATATACAAAGA 59.576 38.462 18.64 0.00 0.00 2.52
256 257 6.423604 TCCACGTGCACATCATATATACAAAG 59.576 38.462 18.64 0.00 0.00 2.77
257 258 6.201997 GTCCACGTGCACATCATATATACAAA 59.798 38.462 18.64 0.00 0.00 2.83
258 259 5.694458 GTCCACGTGCACATCATATATACAA 59.306 40.000 18.64 0.00 0.00 2.41
259 260 5.221342 TGTCCACGTGCACATCATATATACA 60.221 40.000 18.64 5.25 0.00 2.29
260 261 5.118664 GTGTCCACGTGCACATCATATATAC 59.881 44.000 16.64 0.00 35.81 1.47
261 262 5.227152 GTGTCCACGTGCACATCATATATA 58.773 41.667 16.64 0.00 35.81 0.86
262 263 4.058124 GTGTCCACGTGCACATCATATAT 58.942 43.478 16.64 0.00 35.81 0.86
263 264 3.453424 GTGTCCACGTGCACATCATATA 58.547 45.455 16.64 0.00 35.81 0.86
264 265 2.279741 GTGTCCACGTGCACATCATAT 58.720 47.619 16.64 0.00 35.81 1.78
265 266 1.674519 GGTGTCCACGTGCACATCATA 60.675 52.381 17.99 0.00 37.35 2.15
266 267 0.955428 GGTGTCCACGTGCACATCAT 60.955 55.000 17.99 0.00 37.35 2.45
267 268 1.596752 GGTGTCCACGTGCACATCA 60.597 57.895 17.99 5.30 37.35 3.07
268 269 2.667318 CGGTGTCCACGTGCACATC 61.667 63.158 16.64 14.78 37.35 3.06
269 270 2.664851 CGGTGTCCACGTGCACAT 60.665 61.111 16.64 0.00 37.35 3.21
270 271 4.901123 CCGGTGTCCACGTGCACA 62.901 66.667 22.35 17.28 37.35 4.57
274 275 2.725203 AATGTCCCGGTGTCCACGTG 62.725 60.000 9.08 9.08 0.00 4.49
275 276 2.047213 AAATGTCCCGGTGTCCACGT 62.047 55.000 0.00 0.00 0.00 4.49
276 277 0.887387 AAAATGTCCCGGTGTCCACG 60.887 55.000 0.00 0.00 0.00 4.94
277 278 1.000717 CAAAAATGTCCCGGTGTCCAC 60.001 52.381 0.00 0.00 0.00 4.02
278 279 1.323412 CAAAAATGTCCCGGTGTCCA 58.677 50.000 0.00 0.00 0.00 4.02
279 280 1.324383 ACAAAAATGTCCCGGTGTCC 58.676 50.000 0.00 0.00 0.00 4.02
280 281 2.621526 AGAACAAAAATGTCCCGGTGTC 59.378 45.455 0.00 0.00 0.00 3.67
281 282 2.360801 CAGAACAAAAATGTCCCGGTGT 59.639 45.455 0.00 0.00 0.00 4.16
282 283 2.288152 CCAGAACAAAAATGTCCCGGTG 60.288 50.000 0.00 0.00 0.00 4.94
283 284 1.960689 CCAGAACAAAAATGTCCCGGT 59.039 47.619 0.00 0.00 0.00 5.28
284 285 2.235016 TCCAGAACAAAAATGTCCCGG 58.765 47.619 0.00 0.00 0.00 5.73
285 286 3.758554 AGATCCAGAACAAAAATGTCCCG 59.241 43.478 0.00 0.00 0.00 5.14
286 287 4.619160 GCAGATCCAGAACAAAAATGTCCC 60.619 45.833 0.00 0.00 0.00 4.46
287 288 4.488879 GCAGATCCAGAACAAAAATGTCC 58.511 43.478 0.00 0.00 0.00 4.02
288 289 4.488879 GGCAGATCCAGAACAAAAATGTC 58.511 43.478 0.00 0.00 34.01 3.06
289 290 3.259123 GGGCAGATCCAGAACAAAAATGT 59.741 43.478 0.00 0.00 36.21 2.71
290 291 3.368739 GGGGCAGATCCAGAACAAAAATG 60.369 47.826 0.00 0.00 36.21 2.32
291 292 2.833943 GGGGCAGATCCAGAACAAAAAT 59.166 45.455 0.00 0.00 36.21 1.82
292 293 2.158325 AGGGGCAGATCCAGAACAAAAA 60.158 45.455 0.00 0.00 36.21 1.94
293 294 1.428912 AGGGGCAGATCCAGAACAAAA 59.571 47.619 0.00 0.00 36.21 2.44
294 295 1.075601 AGGGGCAGATCCAGAACAAA 58.924 50.000 0.00 0.00 36.21 2.83
295 296 0.329261 CAGGGGCAGATCCAGAACAA 59.671 55.000 0.00 0.00 36.21 2.83
296 297 0.842030 ACAGGGGCAGATCCAGAACA 60.842 55.000 0.00 0.00 36.21 3.18
297 298 0.107459 GACAGGGGCAGATCCAGAAC 60.107 60.000 0.00 0.00 36.21 3.01
298 299 1.617018 CGACAGGGGCAGATCCAGAA 61.617 60.000 0.00 0.00 36.21 3.02
299 300 2.060383 CGACAGGGGCAGATCCAGA 61.060 63.158 0.00 0.00 36.21 3.86
300 301 2.503061 CGACAGGGGCAGATCCAG 59.497 66.667 0.00 0.00 36.21 3.86
301 302 3.785859 GCGACAGGGGCAGATCCA 61.786 66.667 0.00 0.00 36.21 3.41
302 303 4.554036 GGCGACAGGGGCAGATCC 62.554 72.222 0.00 0.00 0.00 3.36
303 304 4.899239 CGGCGACAGGGGCAGATC 62.899 72.222 0.00 0.00 0.00 2.75
309 310 3.432051 GATGAGACGGCGACAGGGG 62.432 68.421 16.62 0.00 0.00 4.79
310 311 2.105128 GATGAGACGGCGACAGGG 59.895 66.667 16.62 0.00 0.00 4.45
311 312 2.105128 GGATGAGACGGCGACAGG 59.895 66.667 16.62 0.00 0.00 4.00
312 313 2.278206 CGGATGAGACGGCGACAG 60.278 66.667 16.62 0.00 0.00 3.51
313 314 3.060000 ACGGATGAGACGGCGACA 61.060 61.111 16.62 11.31 35.23 4.35
314 315 1.985447 TACACGGATGAGACGGCGAC 61.985 60.000 16.62 7.87 35.23 5.19
394 395 9.780413 CTCTTCTTCTTTAAAGCAATGTATTCC 57.220 33.333 10.51 0.00 0.00 3.01
480 481 1.669049 CGTACAGGTACCATCCGCCA 61.669 60.000 15.94 0.00 32.61 5.69
531 532 1.298014 CTCCAAGCCGCTTCTCCTT 59.702 57.895 1.56 0.00 0.00 3.36
544 545 2.954684 CGCTACACCTGGGCTCCAA 61.955 63.158 0.00 0.00 30.80 3.53
655 657 8.093307 GTGCATTCATCCTATCATCTTTCTCTA 58.907 37.037 0.00 0.00 0.00 2.43
729 731 0.106708 AGCCAGTCGAAACAAGCTCA 59.893 50.000 0.00 0.00 32.39 4.26
761 763 2.153547 AATTTGGGTTGCTTCGCCGG 62.154 55.000 0.00 0.00 0.00 6.13
828 831 3.080319 GCTGAGAAAATGAGCTTGAGGT 58.920 45.455 0.00 0.00 0.00 3.85
853 2931 2.596904 TCAATTCGAGTCCGATTCCC 57.403 50.000 0.00 0.00 45.10 3.97
854 2932 3.522553 AGTTCAATTCGAGTCCGATTCC 58.477 45.455 0.00 0.00 45.10 3.01
909 4756 2.016704 CGGCTCGATTCCGGATTCG 61.017 63.158 32.66 32.66 42.99 3.34
996 4843 0.108992 CAGCGATGCAAGCCATGTTT 60.109 50.000 13.01 0.00 33.29 2.83
1263 5110 4.415332 TCTGTCGGCTCGGCGAAC 62.415 66.667 17.13 6.36 32.50 3.95
1278 5125 3.314331 CCCACCGTGGAGTGCTCT 61.314 66.667 19.81 0.00 40.96 4.09
1595 5446 0.596083 CATGTCCTCTAGCGCCTTCG 60.596 60.000 2.29 0.00 39.07 3.79
1681 5542 3.752339 GCTTCCGCTTGGCTTGGG 61.752 66.667 0.00 0.00 0.00 4.12
1745 5608 1.086634 GTCGATGAAGCCAGCACCTC 61.087 60.000 0.00 0.00 0.00 3.85
1780 5699 4.508662 CCTCACTACAATCCTTCTGAACC 58.491 47.826 0.00 0.00 0.00 3.62
1781 5700 4.508662 CCCTCACTACAATCCTTCTGAAC 58.491 47.826 0.00 0.00 0.00 3.18
1782 5701 3.055094 GCCCTCACTACAATCCTTCTGAA 60.055 47.826 0.00 0.00 0.00 3.02
1830 5756 3.076621 ACACCTCGTCACGTATTACTCA 58.923 45.455 0.00 0.00 0.00 3.41
1835 5764 3.983344 GTGTAAACACCTCGTCACGTATT 59.017 43.478 0.00 0.00 40.85 1.89
1850 5779 8.374327 ACAAGGTAATACAGACAAGTGTAAAC 57.626 34.615 0.00 0.00 36.51 2.01
1873 5807 8.620416 TCTTGAAACGTACTAGTACAAACTACA 58.380 33.333 28.03 17.59 37.15 2.74
1880 5814 5.922739 TCGTCTTGAAACGTACTAGTACA 57.077 39.130 28.03 9.53 43.08 2.90
1883 5817 5.368256 ACATCGTCTTGAAACGTACTAGT 57.632 39.130 0.00 0.00 43.08 2.57
1884 5818 6.686130 AAACATCGTCTTGAAACGTACTAG 57.314 37.500 0.00 0.00 43.08 2.57
1885 5819 7.324375 CAGTAAACATCGTCTTGAAACGTACTA 59.676 37.037 0.00 0.00 43.08 1.82
1971 6214 4.524316 TTATTACCCTACGTGCGCATAT 57.476 40.909 15.91 7.60 0.00 1.78
1972 6215 4.319139 TTTATTACCCTACGTGCGCATA 57.681 40.909 15.91 0.93 0.00 3.14
1974 6217 2.669300 TTTATTACCCTACGTGCGCA 57.331 45.000 5.66 5.66 0.00 6.09
1976 6219 6.211515 AGTATCTTTTATTACCCTACGTGCG 58.788 40.000 0.00 0.00 0.00 5.34
1977 6220 8.355913 ACTAGTATCTTTTATTACCCTACGTGC 58.644 37.037 0.00 0.00 0.00 5.34
2053 6307 7.064847 ACAACAAAGTACTACACATTTTGACGA 59.935 33.333 7.93 0.00 33.98 4.20
2055 6309 8.905103 AACAACAAAGTACTACACATTTTGAC 57.095 30.769 7.93 0.00 33.98 3.18
2235 6771 2.797866 ATCCTGTGCGTGTCGTCGAC 62.798 60.000 18.51 18.51 0.00 4.20
2276 6812 3.440522 CGAGTTCACAGACAGACATCCTA 59.559 47.826 0.00 0.00 0.00 2.94
2343 6889 2.981909 ACGAGGACGAAGGACGCA 60.982 61.111 0.00 0.00 46.94 5.24
2533 7122 0.321996 ACAAGGAGAACCGGAGCTTC 59.678 55.000 9.46 0.70 41.83 3.86


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

AutoCloner maintained by Alex Coulton.