Multiple sequence alignment - TraesCS4A01G385700

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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 TraesCS4A01G385700 chr4A 100.000 2660 0 0 1 2660 662817770 662815111 0.000000e+00 4913.0
1 TraesCS4A01G385700 chr4A 79.819 441 56 12 1298 1711 662727257 662726823 9.310000e-75 291.0
2 TraesCS4A01G385700 chr7A 91.079 1446 121 6 229 1669 50615093 50616535 0.000000e+00 1949.0
3 TraesCS4A01G385700 chr7D 92.626 895 64 2 769 1663 47910344 47911236 0.000000e+00 1286.0
4 TraesCS4A01G385700 chr7D 86.770 514 44 9 1768 2279 137514317 137514808 3.870000e-153 551.0
5 TraesCS4A01G385700 chr7D 86.389 360 30 10 2306 2660 137514804 137515149 2.500000e-100 375.0
6 TraesCS4A01G385700 chr7D 98.148 54 1 0 1717 1770 53965562 53965615 7.840000e-16 95.3
7 TraesCS4A01G385700 chr7D 96.429 56 2 0 1715 1770 505596274 505596219 2.820000e-15 93.5
8 TraesCS4A01G385700 chr1B 93.430 761 38 5 1906 2660 251157850 251157096 0.000000e+00 1118.0
9 TraesCS4A01G385700 chr1B 75.148 676 144 24 775 1437 277769694 277769030 2.000000e-76 296.0
10 TraesCS4A01G385700 chr4D 89.341 910 66 14 1768 2660 403812897 403812002 0.000000e+00 1114.0
11 TraesCS4A01G385700 chr5A 85.218 893 106 14 1769 2656 296074685 296075556 0.000000e+00 894.0
12 TraesCS4A01G385700 chr5A 83.852 514 43 19 1769 2278 125215188 125215665 1.120000e-123 453.0
13 TraesCS4A01G385700 chr3A 81.003 758 99 28 1915 2660 79951949 79952673 6.430000e-156 560.0
14 TraesCS4A01G385700 chr2A 85.255 529 53 10 1758 2283 571487914 571488420 3.030000e-144 521.0
15 TraesCS4A01G385700 chr2A 87.435 382 27 10 1904 2283 591730185 591730547 1.140000e-113 420.0
16 TraesCS4A01G385700 chr6A 84.363 518 59 12 1769 2283 23587802 23587304 3.080000e-134 488.0
17 TraesCS4A01G385700 chrUn 79.819 441 56 12 1298 1711 48710482 48710048 9.310000e-75 291.0
18 TraesCS4A01G385700 chrUn 79.638 442 56 13 1298 1711 188909789 188909354 1.200000e-73 287.0
19 TraesCS4A01G385700 chrUn 79.592 441 57 11 1298 1711 48676278 48675844 4.330000e-73 285.0
20 TraesCS4A01G385700 chrUn 79.577 426 54 12 1313 1711 408575812 408575393 9.380000e-70 274.0
21 TraesCS4A01G385700 chr1A 74.504 655 145 22 796 1438 248434845 248434201 5.650000e-67 265.0
22 TraesCS4A01G385700 chr7B 78.241 216 44 3 1766 1979 254690506 254690720 4.620000e-28 135.0
23 TraesCS4A01G385700 chr6D 95.312 64 1 2 1709 1770 334225735 334225672 1.680000e-17 100.0
24 TraesCS4A01G385700 chr6D 95.082 61 3 0 1710 1770 344353078 344353018 2.180000e-16 97.1
25 TraesCS4A01G385700 chr6D 96.364 55 2 0 1716 1770 334224549 334224603 1.010000e-14 91.6
26 TraesCS4A01G385700 chr3D 98.182 55 1 0 1716 1770 528817481 528817535 2.180000e-16 97.1
27 TraesCS4A01G385700 chr3D 98.148 54 1 0 1717 1770 82124584 82124531 7.840000e-16 95.3
28 TraesCS4A01G385700 chr2D 98.113 53 1 0 1716 1768 623855555 623855607 2.820000e-15 93.5
29 TraesCS4A01G385700 chr2D 93.333 60 3 1 1709 1767 365550063 365550122 1.310000e-13 87.9


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 TraesCS4A01G385700 chr4A 662815111 662817770 2659 True 4913 4913 100.0000 1 2660 1 chr4A.!!$R2 2659
1 TraesCS4A01G385700 chr7A 50615093 50616535 1442 False 1949 1949 91.0790 229 1669 1 chr7A.!!$F1 1440
2 TraesCS4A01G385700 chr7D 47910344 47911236 892 False 1286 1286 92.6260 769 1663 1 chr7D.!!$F1 894
3 TraesCS4A01G385700 chr7D 137514317 137515149 832 False 463 551 86.5795 1768 2660 2 chr7D.!!$F3 892
4 TraesCS4A01G385700 chr1B 251157096 251157850 754 True 1118 1118 93.4300 1906 2660 1 chr1B.!!$R1 754
5 TraesCS4A01G385700 chr1B 277769030 277769694 664 True 296 296 75.1480 775 1437 1 chr1B.!!$R2 662
6 TraesCS4A01G385700 chr4D 403812002 403812897 895 True 1114 1114 89.3410 1768 2660 1 chr4D.!!$R1 892
7 TraesCS4A01G385700 chr5A 296074685 296075556 871 False 894 894 85.2180 1769 2656 1 chr5A.!!$F2 887
8 TraesCS4A01G385700 chr3A 79951949 79952673 724 False 560 560 81.0030 1915 2660 1 chr3A.!!$F1 745
9 TraesCS4A01G385700 chr2A 571487914 571488420 506 False 521 521 85.2550 1758 2283 1 chr2A.!!$F1 525
10 TraesCS4A01G385700 chr1A 248434201 248434845 644 True 265 265 74.5040 796 1438 1 chr1A.!!$R1 642

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
442 443 0.034896 CCAGCCTACAACTTCACCGT 59.965 55.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1683 0.03601 CTTGCACCCGGAGAGACAAT 60.036 55.0 0.73 0.0 0.0 2.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.948341 AAACGGAAAACCAAGCCTAATT 57.052 36.364 0.00 0.00 0.00 1.40
22 23 4.514781 AACGGAAAACCAAGCCTAATTC 57.485 40.909 0.00 0.00 0.00 2.17
23 24 2.486592 ACGGAAAACCAAGCCTAATTCG 59.513 45.455 0.00 0.00 0.00 3.34
24 25 2.159435 CGGAAAACCAAGCCTAATTCGG 60.159 50.000 0.00 0.00 0.00 4.30
25 26 3.086282 GGAAAACCAAGCCTAATTCGGA 58.914 45.455 0.00 0.00 0.00 4.55
26 27 3.119602 GGAAAACCAAGCCTAATTCGGAC 60.120 47.826 0.00 0.00 0.00 4.79
27 28 2.871096 AACCAAGCCTAATTCGGACA 57.129 45.000 0.00 0.00 0.00 4.02
28 29 3.366052 AACCAAGCCTAATTCGGACAT 57.634 42.857 0.00 0.00 0.00 3.06
29 30 2.643551 ACCAAGCCTAATTCGGACATG 58.356 47.619 0.00 0.00 0.00 3.21
30 31 1.334869 CCAAGCCTAATTCGGACATGC 59.665 52.381 0.00 0.00 0.00 4.06
31 32 2.016318 CAAGCCTAATTCGGACATGCA 58.984 47.619 0.00 0.00 0.00 3.96
32 33 2.620115 CAAGCCTAATTCGGACATGCAT 59.380 45.455 0.00 0.00 0.00 3.96
33 34 2.224606 AGCCTAATTCGGACATGCATG 58.775 47.619 25.09 25.09 0.00 4.06
34 35 1.335324 GCCTAATTCGGACATGCATGC 60.335 52.381 26.53 18.01 0.00 4.06
35 36 1.948834 CCTAATTCGGACATGCATGCA 59.051 47.619 26.53 25.04 0.00 3.96
36 37 2.031420 CCTAATTCGGACATGCATGCAG 60.031 50.000 26.69 19.15 0.00 4.41
37 38 1.753930 AATTCGGACATGCATGCAGA 58.246 45.000 26.69 20.15 0.00 4.26
38 39 1.977056 ATTCGGACATGCATGCAGAT 58.023 45.000 26.69 16.32 0.00 2.90
39 40 1.018910 TTCGGACATGCATGCAGATG 58.981 50.000 26.69 21.79 0.00 2.90
40 41 0.107557 TCGGACATGCATGCAGATGT 60.108 50.000 26.69 24.91 31.50 3.06
41 42 1.138661 TCGGACATGCATGCAGATGTA 59.861 47.619 26.69 8.75 31.50 2.29
42 43 1.529865 CGGACATGCATGCAGATGTAG 59.470 52.381 26.69 17.93 31.50 2.74
43 44 1.878088 GGACATGCATGCAGATGTAGG 59.122 52.381 26.69 10.99 32.83 3.18
44 45 2.569059 GACATGCATGCAGATGTAGGT 58.431 47.619 26.69 13.94 41.17 3.08
45 46 2.289820 GACATGCATGCAGATGTAGGTG 59.710 50.000 26.69 18.14 39.00 4.00
46 47 1.001706 CATGCATGCAGATGTAGGTGC 60.002 52.381 26.69 0.00 40.29 5.01
51 52 1.741528 TGCAGATGTAGGTGCATGTG 58.258 50.000 0.00 1.45 44.70 3.21
65 66 3.244670 GCATGTGCAGCTAATTACGAG 57.755 47.619 0.00 0.00 41.59 4.18
66 67 2.032549 GCATGTGCAGCTAATTACGAGG 60.033 50.000 0.00 0.00 41.59 4.63
67 68 3.457234 CATGTGCAGCTAATTACGAGGA 58.543 45.455 0.00 0.00 0.00 3.71
68 69 3.165058 TGTGCAGCTAATTACGAGGAG 57.835 47.619 0.00 0.00 0.00 3.69
69 70 2.758423 TGTGCAGCTAATTACGAGGAGA 59.242 45.455 0.00 0.00 0.00 3.71
70 71 3.194755 TGTGCAGCTAATTACGAGGAGAA 59.805 43.478 0.00 0.00 0.00 2.87
71 72 3.552294 GTGCAGCTAATTACGAGGAGAAC 59.448 47.826 0.00 0.00 0.00 3.01
72 73 3.447586 TGCAGCTAATTACGAGGAGAACT 59.552 43.478 0.00 0.00 0.00 3.01
73 74 4.643334 TGCAGCTAATTACGAGGAGAACTA 59.357 41.667 0.00 0.00 0.00 2.24
74 75 4.977347 GCAGCTAATTACGAGGAGAACTAC 59.023 45.833 0.00 0.00 0.00 2.73
75 76 5.521544 CAGCTAATTACGAGGAGAACTACC 58.478 45.833 0.00 0.00 0.00 3.18
76 77 4.275443 AGCTAATTACGAGGAGAACTACCG 59.725 45.833 0.00 0.00 0.00 4.02
77 78 4.274459 GCTAATTACGAGGAGAACTACCGA 59.726 45.833 0.00 0.00 0.00 4.69
78 79 5.220931 GCTAATTACGAGGAGAACTACCGAA 60.221 44.000 0.00 0.00 0.00 4.30
79 80 4.897025 ATTACGAGGAGAACTACCGAAG 57.103 45.455 0.00 0.00 0.00 3.79
80 81 0.810016 ACGAGGAGAACTACCGAAGC 59.190 55.000 0.00 0.00 0.00 3.86
81 82 0.809385 CGAGGAGAACTACCGAAGCA 59.191 55.000 0.00 0.00 0.00 3.91
82 83 1.467713 CGAGGAGAACTACCGAAGCAC 60.468 57.143 0.00 0.00 0.00 4.40
83 84 0.526662 AGGAGAACTACCGAAGCACG 59.473 55.000 0.00 0.00 42.18 5.34
100 101 2.356673 GGACGTCCGGTTCACCAC 60.357 66.667 20.85 0.00 35.14 4.16
101 102 2.732094 GACGTCCGGTTCACCACG 60.732 66.667 3.51 9.33 40.12 4.94
102 103 3.198236 GACGTCCGGTTCACCACGA 62.198 63.158 16.87 0.00 37.54 4.35
103 104 2.260434 CGTCCGGTTCACCACGAT 59.740 61.111 0.00 0.00 37.54 3.73
104 105 1.804326 CGTCCGGTTCACCACGATC 60.804 63.158 0.00 0.00 37.54 3.69
105 106 1.804326 GTCCGGTTCACCACGATCG 60.804 63.158 14.88 14.88 35.14 3.69
106 107 2.260434 CCGGTTCACCACGATCGT 59.740 61.111 16.60 16.60 35.14 3.73
107 108 2.092291 CCGGTTCACCACGATCGTG 61.092 63.158 35.57 35.57 45.02 4.35
115 116 2.576053 CACGATCGTGGACCGTCG 60.576 66.667 35.09 11.63 42.00 5.12
116 117 4.471726 ACGATCGTGGACCGTCGC 62.472 66.667 22.06 0.00 40.93 5.19
136 137 2.343758 GCTCCACCTCTGCGAACA 59.656 61.111 0.00 0.00 0.00 3.18
137 138 1.301716 GCTCCACCTCTGCGAACAA 60.302 57.895 0.00 0.00 0.00 2.83
138 139 1.294659 GCTCCACCTCTGCGAACAAG 61.295 60.000 0.00 0.00 0.00 3.16
139 140 0.671781 CTCCACCTCTGCGAACAAGG 60.672 60.000 0.00 0.00 36.21 3.61
140 141 2.328099 CCACCTCTGCGAACAAGGC 61.328 63.158 0.00 0.00 33.21 4.35
141 142 1.302033 CACCTCTGCGAACAAGGCT 60.302 57.895 0.00 0.00 33.21 4.58
142 143 1.004440 ACCTCTGCGAACAAGGCTC 60.004 57.895 0.00 0.00 33.21 4.70
143 144 1.004560 CCTCTGCGAACAAGGCTCA 60.005 57.895 0.00 0.00 0.00 4.26
144 145 1.294659 CCTCTGCGAACAAGGCTCAC 61.295 60.000 0.00 0.00 0.00 3.51
145 146 1.621301 CTCTGCGAACAAGGCTCACG 61.621 60.000 0.00 0.00 0.00 4.35
146 147 1.956170 CTGCGAACAAGGCTCACGT 60.956 57.895 0.00 0.00 0.00 4.49
147 148 2.162921 CTGCGAACAAGGCTCACGTG 62.163 60.000 9.94 9.94 34.52 4.49
148 149 2.244651 GCGAACAAGGCTCACGTGT 61.245 57.895 16.51 0.00 43.82 4.49
149 150 1.564622 CGAACAAGGCTCACGTGTG 59.435 57.895 16.51 14.71 41.02 3.82
150 151 1.279840 GAACAAGGCTCACGTGTGC 59.720 57.895 29.40 29.40 41.02 4.57
151 152 1.153168 AACAAGGCTCACGTGTGCT 60.153 52.632 33.61 20.83 41.02 4.40
152 153 1.160329 AACAAGGCTCACGTGTGCTC 61.160 55.000 33.61 25.21 41.02 4.26
153 154 1.595109 CAAGGCTCACGTGTGCTCA 60.595 57.895 33.61 8.06 35.15 4.26
154 155 1.146041 AAGGCTCACGTGTGCTCAA 59.854 52.632 33.61 7.34 35.15 3.02
155 156 0.882042 AAGGCTCACGTGTGCTCAAG 60.882 55.000 33.61 17.03 35.15 3.02
156 157 2.553268 GCTCACGTGTGCTCAAGC 59.447 61.111 29.80 19.73 42.50 4.01
157 158 2.959357 GCTCACGTGTGCTCAAGCC 61.959 63.158 29.80 4.61 41.18 4.35
158 159 2.661537 TCACGTGTGCTCAAGCCG 60.662 61.111 16.51 0.00 41.18 5.52
159 160 4.374702 CACGTGTGCTCAAGCCGC 62.375 66.667 7.58 0.00 41.18 6.53
162 163 3.649986 GTGTGCTCAAGCCGCGTT 61.650 61.111 4.92 0.00 41.18 4.84
163 164 3.345808 TGTGCTCAAGCCGCGTTC 61.346 61.111 4.92 0.00 41.18 3.95
164 165 3.044305 GTGCTCAAGCCGCGTTCT 61.044 61.111 4.92 0.00 41.18 3.01
165 166 2.738521 TGCTCAAGCCGCGTTCTC 60.739 61.111 4.92 0.00 41.18 2.87
166 167 2.433318 GCTCAAGCCGCGTTCTCT 60.433 61.111 4.92 0.00 34.31 3.10
167 168 1.153823 GCTCAAGCCGCGTTCTCTA 60.154 57.895 4.92 0.00 34.31 2.43
168 169 0.528684 GCTCAAGCCGCGTTCTCTAT 60.529 55.000 4.92 0.00 34.31 1.98
169 170 1.269102 GCTCAAGCCGCGTTCTCTATA 60.269 52.381 4.92 0.00 34.31 1.31
170 171 2.608261 GCTCAAGCCGCGTTCTCTATAT 60.608 50.000 4.92 0.00 34.31 0.86
171 172 3.366070 GCTCAAGCCGCGTTCTCTATATA 60.366 47.826 4.92 0.00 34.31 0.86
172 173 4.675671 GCTCAAGCCGCGTTCTCTATATAT 60.676 45.833 4.92 0.00 34.31 0.86
173 174 4.733850 TCAAGCCGCGTTCTCTATATATG 58.266 43.478 4.92 0.00 0.00 1.78
174 175 4.217767 TCAAGCCGCGTTCTCTATATATGT 59.782 41.667 4.92 0.00 0.00 2.29
175 176 4.098055 AGCCGCGTTCTCTATATATGTG 57.902 45.455 4.92 0.00 0.00 3.21
176 177 3.506455 AGCCGCGTTCTCTATATATGTGT 59.494 43.478 4.92 0.00 0.00 3.72
177 178 4.022242 AGCCGCGTTCTCTATATATGTGTT 60.022 41.667 4.92 0.00 0.00 3.32
178 179 4.684703 GCCGCGTTCTCTATATATGTGTTT 59.315 41.667 4.92 0.00 0.00 2.83
179 180 5.860182 GCCGCGTTCTCTATATATGTGTTTA 59.140 40.000 4.92 0.00 0.00 2.01
180 181 6.183359 GCCGCGTTCTCTATATATGTGTTTAC 60.183 42.308 4.92 0.00 0.00 2.01
181 182 7.082602 CCGCGTTCTCTATATATGTGTTTACT 58.917 38.462 4.92 0.00 0.00 2.24
182 183 7.270793 CCGCGTTCTCTATATATGTGTTTACTC 59.729 40.741 4.92 0.00 0.00 2.59
183 184 7.270793 CGCGTTCTCTATATATGTGTTTACTCC 59.729 40.741 0.00 0.00 0.00 3.85
184 185 7.270793 GCGTTCTCTATATATGTGTTTACTCCG 59.729 40.741 0.00 0.00 0.00 4.63
185 186 7.270793 CGTTCTCTATATATGTGTTTACTCCGC 59.729 40.741 0.00 0.00 0.00 5.54
186 187 6.839033 TCTCTATATATGTGTTTACTCCGCG 58.161 40.000 0.00 0.00 0.00 6.46
187 188 5.946298 TCTATATATGTGTTTACTCCGCGG 58.054 41.667 22.12 22.12 0.00 6.46
188 189 2.973694 ATATGTGTTTACTCCGCGGT 57.026 45.000 27.15 9.68 0.00 5.68
189 190 5.710513 ATATATGTGTTTACTCCGCGGTA 57.289 39.130 27.15 8.44 0.00 4.02
190 191 2.000429 ATGTGTTTACTCCGCGGTAC 58.000 50.000 27.15 16.09 0.00 3.34
191 192 0.038343 TGTGTTTACTCCGCGGTACC 60.038 55.000 27.15 0.16 0.00 3.34
192 193 1.072666 GTGTTTACTCCGCGGTACCG 61.073 60.000 30.06 30.06 43.09 4.02
237 238 4.093952 CCGTACGTCGTCACCGCT 62.094 66.667 15.21 0.00 37.94 5.52
258 259 1.474879 GGAGGAGGTCTCAGAGAAACG 59.525 57.143 0.20 0.00 44.19 3.60
280 281 2.840651 TCATTTCTCCTCAGACCCTTCC 59.159 50.000 0.00 0.00 0.00 3.46
356 357 3.468326 GAGCCCCCTCCGCATTCTC 62.468 68.421 0.00 0.00 31.68 2.87
374 375 2.341101 CCTGTACGTCCTCGCCACT 61.341 63.158 0.00 0.00 41.18 4.00
375 376 1.154016 CTGTACGTCCTCGCCACTG 60.154 63.158 0.00 0.00 41.18 3.66
377 378 1.154073 GTACGTCCTCGCCACTGTC 60.154 63.158 0.00 0.00 41.18 3.51
408 409 3.520862 CGGTAGAGGCGCCGGTAA 61.521 66.667 23.20 5.11 43.85 2.85
414 415 1.217244 GAGGCGCCGGTAAAGAAGA 59.783 57.895 23.20 0.00 0.00 2.87
416 417 2.450345 GGCGCCGGTAAAGAAGACG 61.450 63.158 12.58 0.00 0.00 4.18
420 421 2.450345 CCGGTAAAGAAGACGCCGC 61.450 63.158 0.00 0.00 40.94 6.53
421 422 2.450345 CGGTAAAGAAGACGCCGCC 61.450 63.158 0.00 0.00 35.90 6.13
435 436 4.760047 CGCCGCCAGCCTACAACT 62.760 66.667 0.00 0.00 38.78 3.16
442 443 0.034896 CCAGCCTACAACTTCACCGT 59.965 55.000 0.00 0.00 0.00 4.83
443 444 1.274167 CCAGCCTACAACTTCACCGTA 59.726 52.381 0.00 0.00 0.00 4.02
460 461 1.406614 CGTAGACGAGGAGTACTGGGT 60.407 57.143 0.00 0.00 43.02 4.51
541 542 0.884704 GAGCTCAACCGCTTCAACCA 60.885 55.000 9.40 0.00 41.08 3.67
772 776 2.464865 CGAGCTCATCGTCCCTAAAAG 58.535 52.381 15.40 0.00 46.62 2.27
784 788 0.036388 CCTAAAAGAGGCACGCTCCA 60.036 55.000 0.00 0.00 37.64 3.86
821 825 3.470888 CGGCCCCTCTGGATCGTT 61.471 66.667 0.00 0.00 35.39 3.85
851 855 0.249784 CCATGGTGATCAGGCTCTCG 60.250 60.000 2.57 0.00 0.00 4.04
980 987 2.382746 CGTGCACATCCACCACTCG 61.383 63.158 18.64 0.00 32.10 4.18
982 989 3.127533 GCACATCCACCACTCGGC 61.128 66.667 0.00 0.00 34.57 5.54
1093 1100 0.667487 CAGCAACGTGTGGATCGACT 60.667 55.000 9.41 0.00 0.00 4.18
1161 1168 4.077184 TCCACCGCCGTCACCATC 62.077 66.667 0.00 0.00 0.00 3.51
1326 1333 0.868406 GCTTCTTCCACGTGGTGAAG 59.132 55.000 38.04 38.04 42.99 3.02
1398 1405 0.481567 CCATCATCAGCCAGGGGAAT 59.518 55.000 0.00 0.00 0.00 3.01
1407 1414 1.103398 GCCAGGGGAATCGGTTCATG 61.103 60.000 11.19 5.70 36.01 3.07
1570 1577 2.171725 GCGTACGGCAAGATGGACC 61.172 63.158 18.39 0.00 42.87 4.46
1669 1676 4.096984 AGCCATGCTATTAACTTCACTTGC 59.903 41.667 0.00 0.00 36.99 4.01
1670 1677 4.734695 GCCATGCTATTAACTTCACTTGCC 60.735 45.833 0.00 0.00 0.00 4.52
1671 1678 4.496341 CCATGCTATTAACTTCACTTGCCG 60.496 45.833 0.00 0.00 0.00 5.69
1672 1679 3.006940 TGCTATTAACTTCACTTGCCGG 58.993 45.455 0.00 0.00 0.00 6.13
1673 1680 2.223272 GCTATTAACTTCACTTGCCGGC 60.223 50.000 22.73 22.73 0.00 6.13
1674 1681 2.200373 ATTAACTTCACTTGCCGGCT 57.800 45.000 29.70 3.84 0.00 5.52
1675 1682 2.843401 TTAACTTCACTTGCCGGCTA 57.157 45.000 29.70 20.51 0.00 3.93
1676 1683 2.843401 TAACTTCACTTGCCGGCTAA 57.157 45.000 29.70 18.60 0.00 3.09
1677 1684 2.200373 AACTTCACTTGCCGGCTAAT 57.800 45.000 29.70 7.12 0.00 1.73
1678 1685 2.200373 ACTTCACTTGCCGGCTAATT 57.800 45.000 29.70 11.56 0.00 1.40
1679 1686 1.812571 ACTTCACTTGCCGGCTAATTG 59.187 47.619 29.70 21.84 0.00 2.32
1680 1687 1.812571 CTTCACTTGCCGGCTAATTGT 59.187 47.619 29.70 11.90 0.00 2.71
1681 1688 1.448985 TCACTTGCCGGCTAATTGTC 58.551 50.000 29.70 0.00 0.00 3.18
1682 1689 1.003118 TCACTTGCCGGCTAATTGTCT 59.997 47.619 29.70 0.00 0.00 3.41
1683 1690 1.398390 CACTTGCCGGCTAATTGTCTC 59.602 52.381 29.70 0.00 0.00 3.36
1684 1691 1.279271 ACTTGCCGGCTAATTGTCTCT 59.721 47.619 29.70 0.00 0.00 3.10
1685 1692 1.936547 CTTGCCGGCTAATTGTCTCTC 59.063 52.381 29.70 0.00 0.00 3.20
1686 1693 0.178068 TGCCGGCTAATTGTCTCTCC 59.822 55.000 29.70 0.00 0.00 3.71
1687 1694 0.876342 GCCGGCTAATTGTCTCTCCG 60.876 60.000 22.15 0.00 36.90 4.63
1688 1695 3.274393 CGGCTAATTGTCTCTCCGG 57.726 57.895 0.00 0.00 33.85 5.14
1689 1696 0.249489 CGGCTAATTGTCTCTCCGGG 60.249 60.000 0.00 0.00 33.85 5.73
1690 1697 0.831307 GGCTAATTGTCTCTCCGGGT 59.169 55.000 0.00 0.00 0.00 5.28
1691 1698 1.473434 GGCTAATTGTCTCTCCGGGTG 60.473 57.143 0.00 0.00 0.00 4.61
1692 1699 1.941325 CTAATTGTCTCTCCGGGTGC 58.059 55.000 0.00 0.00 0.00 5.01
1693 1700 1.207089 CTAATTGTCTCTCCGGGTGCA 59.793 52.381 0.00 0.00 0.00 4.57
1694 1701 0.400213 AATTGTCTCTCCGGGTGCAA 59.600 50.000 0.00 0.81 0.00 4.08
1695 1702 0.036010 ATTGTCTCTCCGGGTGCAAG 60.036 55.000 0.00 0.00 0.00 4.01
1696 1703 1.407656 TTGTCTCTCCGGGTGCAAGT 61.408 55.000 0.00 0.00 0.00 3.16
1697 1704 1.371558 GTCTCTCCGGGTGCAAGTT 59.628 57.895 0.00 0.00 0.00 2.66
1698 1705 0.951040 GTCTCTCCGGGTGCAAGTTG 60.951 60.000 0.00 0.00 0.00 3.16
1699 1706 1.071471 CTCTCCGGGTGCAAGTTGT 59.929 57.895 0.00 0.00 0.00 3.32
1700 1707 0.535102 CTCTCCGGGTGCAAGTTGTT 60.535 55.000 0.00 0.00 0.00 2.83
1701 1708 0.817634 TCTCCGGGTGCAAGTTGTTG 60.818 55.000 0.00 0.00 36.67 3.33
1702 1709 1.077357 TCCGGGTGCAAGTTGTTGT 60.077 52.632 0.00 0.00 35.92 3.32
1703 1710 1.065600 CCGGGTGCAAGTTGTTGTG 59.934 57.895 4.48 0.00 35.92 3.33
1704 1711 1.380403 CCGGGTGCAAGTTGTTGTGA 61.380 55.000 4.48 0.00 35.92 3.58
1705 1712 0.667993 CGGGTGCAAGTTGTTGTGAT 59.332 50.000 4.48 0.00 35.92 3.06
1706 1713 1.066908 CGGGTGCAAGTTGTTGTGATT 59.933 47.619 4.48 0.00 35.92 2.57
1707 1714 2.292016 CGGGTGCAAGTTGTTGTGATTA 59.708 45.455 4.48 0.00 35.92 1.75
1708 1715 3.243234 CGGGTGCAAGTTGTTGTGATTAA 60.243 43.478 4.48 0.00 35.92 1.40
1709 1716 4.688021 GGGTGCAAGTTGTTGTGATTAAA 58.312 39.130 4.48 0.00 35.92 1.52
1710 1717 5.112686 GGGTGCAAGTTGTTGTGATTAAAA 58.887 37.500 4.48 0.00 35.92 1.52
1711 1718 5.582665 GGGTGCAAGTTGTTGTGATTAAAAA 59.417 36.000 4.48 0.00 35.92 1.94
1712 1719 6.238076 GGGTGCAAGTTGTTGTGATTAAAAAG 60.238 38.462 4.48 0.00 35.92 2.27
1713 1720 6.533367 GGTGCAAGTTGTTGTGATTAAAAAGA 59.467 34.615 4.48 0.00 35.92 2.52
1714 1721 7.391016 GTGCAAGTTGTTGTGATTAAAAAGAC 58.609 34.615 4.48 0.00 35.92 3.01
1715 1722 6.252441 TGCAAGTTGTTGTGATTAAAAAGACG 59.748 34.615 4.48 0.00 35.92 4.18
1716 1723 6.470877 GCAAGTTGTTGTGATTAAAAAGACGA 59.529 34.615 4.48 0.00 35.92 4.20
1717 1724 7.305418 GCAAGTTGTTGTGATTAAAAAGACGAG 60.305 37.037 4.48 0.00 35.92 4.18
1718 1725 7.316544 AGTTGTTGTGATTAAAAAGACGAGT 57.683 32.000 0.00 0.00 0.00 4.18
1719 1726 7.758495 AGTTGTTGTGATTAAAAAGACGAGTT 58.242 30.769 0.00 0.00 0.00 3.01
1720 1727 8.885722 AGTTGTTGTGATTAAAAAGACGAGTTA 58.114 29.630 0.00 0.00 0.00 2.24
1721 1728 9.493206 GTTGTTGTGATTAAAAAGACGAGTTAA 57.507 29.630 0.00 0.00 0.00 2.01
1749 1756 8.181487 ACACTATTAGTACATAAACTTGCACG 57.819 34.615 0.00 0.00 0.00 5.34
1750 1757 7.277098 ACACTATTAGTACATAAACTTGCACGG 59.723 37.037 0.00 0.00 0.00 4.94
1751 1758 7.277098 CACTATTAGTACATAAACTTGCACGGT 59.723 37.037 0.00 0.00 0.00 4.83
1752 1759 5.849357 TTAGTACATAAACTTGCACGGTG 57.151 39.130 3.15 3.15 0.00 4.94
1753 1760 2.482721 AGTACATAAACTTGCACGGTGC 59.517 45.455 25.55 25.55 45.29 5.01
1763 1770 2.995938 GCACGGTGCGTACAAATTC 58.004 52.632 18.35 0.00 38.32 2.17
1764 1771 0.236187 GCACGGTGCGTACAAATTCA 59.764 50.000 18.35 0.00 38.32 2.57
1765 1772 1.135803 GCACGGTGCGTACAAATTCAT 60.136 47.619 18.35 0.00 38.32 2.57
1814 1822 1.210204 TTCCAGCCCCTCAGAGCATT 61.210 55.000 0.00 0.00 0.00 3.56
1816 1824 0.548031 CCAGCCCCTCAGAGCATTAA 59.452 55.000 0.00 0.00 0.00 1.40
1825 1833 3.745975 CCTCAGAGCATTAACGTTCACAA 59.254 43.478 2.82 0.00 0.00 3.33
1876 1884 2.924290 GACCGTCAGATTAGCTGTGAAC 59.076 50.000 0.00 0.00 45.14 3.18
1882 1910 2.036764 GATTAGCTGTGAACCGCGCC 62.037 60.000 0.00 0.00 0.00 6.53
1892 1920 4.587189 ACCGCGCCTAATCTCGGC 62.587 66.667 0.00 0.00 45.23 5.54
1936 1965 4.082523 GTCTGGGCCGCTGCTACA 62.083 66.667 0.00 0.00 37.74 2.74
1974 2003 1.138671 CGCGTTAAATTGGGCCCAG 59.861 57.895 26.87 12.94 0.00 4.45
2044 2081 2.448542 GCATAGGCCCCCTCCTCA 60.449 66.667 0.00 0.00 37.66 3.86
2052 2092 1.690985 CCCCCTCCTCAACTCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
2053 2093 1.394151 CCCCTCCTCAACTCCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
2054 2094 0.689412 CCCCTCCTCAACTCCTCCTC 60.689 65.000 0.00 0.00 0.00 3.71
2055 2095 0.338120 CCCTCCTCAACTCCTCCTCT 59.662 60.000 0.00 0.00 0.00 3.69
2056 2096 1.687996 CCCTCCTCAACTCCTCCTCTC 60.688 61.905 0.00 0.00 0.00 3.20
2229 2274 5.130145 CCCTCTCTGTTGATTTCTCTACCAT 59.870 44.000 0.00 0.00 0.00 3.55
2316 2364 3.865383 CCCTATGCTGCCGCCAGA 61.865 66.667 0.00 0.00 41.77 3.86
2337 2385 2.067932 CTTGTGGTTCTGGAGCCCCA 62.068 60.000 1.22 0.00 40.95 4.96
2439 2488 0.835941 CCCTCTCCTCTGGATGTTGG 59.164 60.000 0.00 0.00 0.00 3.77
2447 2496 3.074390 TCCTCTGGATGTTGGTGTCAAAT 59.926 43.478 0.00 0.00 34.28 2.32
2515 2565 7.148590 GCAAAACTTGTGTTTCTCATTGTCTTT 60.149 33.333 0.00 0.00 44.70 2.52
2526 2576 2.146342 CATTGTCTTTCACTCACGCCT 58.854 47.619 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.557895 CGAATTAGGCTTGGTTTTCCGTTT 60.558 41.667 0.00 0.00 44.36 3.60
3 4 2.159435 CCGAATTAGGCTTGGTTTTCCG 60.159 50.000 0.00 0.00 44.36 4.30
4 5 3.086282 TCCGAATTAGGCTTGGTTTTCC 58.914 45.455 0.00 0.00 41.14 3.13
5 6 3.504520 TGTCCGAATTAGGCTTGGTTTTC 59.495 43.478 0.00 0.00 0.00 2.29
6 7 3.492337 TGTCCGAATTAGGCTTGGTTTT 58.508 40.909 0.00 0.00 0.00 2.43
7 8 3.149005 TGTCCGAATTAGGCTTGGTTT 57.851 42.857 0.00 0.00 0.00 3.27
8 9 2.871096 TGTCCGAATTAGGCTTGGTT 57.129 45.000 0.00 0.00 0.00 3.67
9 10 2.643551 CATGTCCGAATTAGGCTTGGT 58.356 47.619 0.00 0.00 0.00 3.67
10 11 1.334869 GCATGTCCGAATTAGGCTTGG 59.665 52.381 0.00 0.00 0.00 3.61
11 12 2.016318 TGCATGTCCGAATTAGGCTTG 58.984 47.619 0.00 5.42 0.00 4.01
12 13 2.418368 TGCATGTCCGAATTAGGCTT 57.582 45.000 0.00 0.00 0.00 4.35
13 14 2.224606 CATGCATGTCCGAATTAGGCT 58.775 47.619 18.91 0.00 0.00 4.58
14 15 1.335324 GCATGCATGTCCGAATTAGGC 60.335 52.381 26.79 5.04 0.00 3.93
15 16 1.948834 TGCATGCATGTCCGAATTAGG 59.051 47.619 26.79 0.00 0.00 2.69
16 17 2.874086 TCTGCATGCATGTCCGAATTAG 59.126 45.455 26.79 4.74 0.00 1.73
17 18 2.916640 TCTGCATGCATGTCCGAATTA 58.083 42.857 26.79 3.00 0.00 1.40
18 19 1.753930 TCTGCATGCATGTCCGAATT 58.246 45.000 26.79 0.00 0.00 2.17
19 20 1.607148 CATCTGCATGCATGTCCGAAT 59.393 47.619 26.79 11.45 0.00 3.34
20 21 1.018910 CATCTGCATGCATGTCCGAA 58.981 50.000 26.79 9.73 0.00 4.30
21 22 0.107557 ACATCTGCATGCATGTCCGA 60.108 50.000 26.79 19.50 32.57 4.55
22 23 1.529865 CTACATCTGCATGCATGTCCG 59.470 52.381 25.93 16.32 32.57 4.79
23 24 1.878088 CCTACATCTGCATGCATGTCC 59.122 52.381 25.93 12.52 32.57 4.02
24 25 2.289820 CACCTACATCTGCATGCATGTC 59.710 50.000 25.93 18.98 32.57 3.06
25 26 2.294979 CACCTACATCTGCATGCATGT 58.705 47.619 25.58 25.58 32.57 3.21
26 27 1.001706 GCACCTACATCTGCATGCATG 60.002 52.381 22.97 22.70 32.57 4.06
27 28 1.315690 GCACCTACATCTGCATGCAT 58.684 50.000 22.97 9.00 32.57 3.96
28 29 0.035247 TGCACCTACATCTGCATGCA 60.035 50.000 21.29 21.29 38.49 3.96
29 30 2.784547 TGCACCTACATCTGCATGC 58.215 52.632 11.82 11.82 38.49 4.06
32 33 4.837965 TGCACATGCACCTACATCTGCA 62.838 50.000 1.49 3.76 45.73 4.41
33 34 0.379669 GCACATGCACCTACATCTGC 59.620 55.000 0.00 0.00 41.59 4.26
45 46 2.032549 CCTCGTAATTAGCTGCACATGC 60.033 50.000 1.02 0.00 42.50 4.06
46 47 3.457234 TCCTCGTAATTAGCTGCACATG 58.543 45.455 1.02 0.00 0.00 3.21
47 48 3.384789 TCTCCTCGTAATTAGCTGCACAT 59.615 43.478 1.02 0.00 0.00 3.21
48 49 2.758423 TCTCCTCGTAATTAGCTGCACA 59.242 45.455 1.02 0.00 0.00 4.57
49 50 3.438297 TCTCCTCGTAATTAGCTGCAC 57.562 47.619 1.02 0.00 0.00 4.57
50 51 3.447586 AGTTCTCCTCGTAATTAGCTGCA 59.552 43.478 1.02 0.00 0.00 4.41
51 52 4.048241 AGTTCTCCTCGTAATTAGCTGC 57.952 45.455 0.00 0.00 0.00 5.25
52 53 5.521544 GGTAGTTCTCCTCGTAATTAGCTG 58.478 45.833 0.00 0.00 0.00 4.24
53 54 4.275443 CGGTAGTTCTCCTCGTAATTAGCT 59.725 45.833 0.00 0.00 0.00 3.32
54 55 4.274459 TCGGTAGTTCTCCTCGTAATTAGC 59.726 45.833 0.00 0.00 0.00 3.09
55 56 5.998454 TCGGTAGTTCTCCTCGTAATTAG 57.002 43.478 0.00 0.00 0.00 1.73
56 57 5.220931 GCTTCGGTAGTTCTCCTCGTAATTA 60.221 44.000 0.00 0.00 0.00 1.40
57 58 4.439837 GCTTCGGTAGTTCTCCTCGTAATT 60.440 45.833 0.00 0.00 0.00 1.40
58 59 3.066481 GCTTCGGTAGTTCTCCTCGTAAT 59.934 47.826 0.00 0.00 0.00 1.89
59 60 2.421424 GCTTCGGTAGTTCTCCTCGTAA 59.579 50.000 0.00 0.00 0.00 3.18
60 61 2.012673 GCTTCGGTAGTTCTCCTCGTA 58.987 52.381 0.00 0.00 0.00 3.43
61 62 0.810016 GCTTCGGTAGTTCTCCTCGT 59.190 55.000 0.00 0.00 0.00 4.18
62 63 0.809385 TGCTTCGGTAGTTCTCCTCG 59.191 55.000 0.00 0.00 0.00 4.63
63 64 1.467713 CGTGCTTCGGTAGTTCTCCTC 60.468 57.143 0.00 0.00 35.71 3.71
64 65 0.526662 CGTGCTTCGGTAGTTCTCCT 59.473 55.000 0.00 0.00 35.71 3.69
65 66 3.031660 CGTGCTTCGGTAGTTCTCC 57.968 57.895 0.00 0.00 35.71 3.71
83 84 2.356673 GTGGTGAACCGGACGTCC 60.357 66.667 25.28 25.28 39.43 4.79
84 85 2.482296 ATCGTGGTGAACCGGACGTC 62.482 60.000 9.46 7.13 36.93 4.34
85 86 2.482296 GATCGTGGTGAACCGGACGT 62.482 60.000 9.46 0.00 36.93 4.34
86 87 1.804326 GATCGTGGTGAACCGGACG 60.804 63.158 9.46 6.62 39.43 4.79
87 88 1.804326 CGATCGTGGTGAACCGGAC 60.804 63.158 9.46 1.77 39.43 4.79
88 89 2.270257 ACGATCGTGGTGAACCGGA 61.270 57.895 22.06 0.00 39.43 5.14
89 90 2.092291 CACGATCGTGGTGAACCGG 61.092 63.158 35.09 10.91 42.00 5.28
90 91 3.459027 CACGATCGTGGTGAACCG 58.541 61.111 35.09 11.63 42.00 4.44
119 120 1.294659 CTTGTTCGCAGAGGTGGAGC 61.295 60.000 0.00 0.00 38.43 4.70
120 121 0.671781 CCTTGTTCGCAGAGGTGGAG 60.672 60.000 0.00 0.00 38.43 3.86
121 122 1.371183 CCTTGTTCGCAGAGGTGGA 59.629 57.895 0.00 0.00 38.43 4.02
122 123 2.328099 GCCTTGTTCGCAGAGGTGG 61.328 63.158 0.00 0.00 38.43 4.61
123 124 1.294659 GAGCCTTGTTCGCAGAGGTG 61.295 60.000 0.00 0.00 38.43 4.00
124 125 1.004440 GAGCCTTGTTCGCAGAGGT 60.004 57.895 0.00 0.00 38.43 3.85
125 126 1.004560 TGAGCCTTGTTCGCAGAGG 60.005 57.895 0.00 0.00 38.43 3.69
126 127 1.621301 CGTGAGCCTTGTTCGCAGAG 61.621 60.000 0.00 0.00 38.43 3.35
127 128 1.664649 CGTGAGCCTTGTTCGCAGA 60.665 57.895 0.00 0.00 0.00 4.26
128 129 1.956170 ACGTGAGCCTTGTTCGCAG 60.956 57.895 0.00 0.00 0.00 5.18
129 130 2.108157 ACGTGAGCCTTGTTCGCA 59.892 55.556 0.00 0.00 0.00 5.10
130 131 2.244651 ACACGTGAGCCTTGTTCGC 61.245 57.895 25.01 0.00 0.00 4.70
131 132 1.564622 CACACGTGAGCCTTGTTCG 59.435 57.895 25.01 0.00 0.00 3.95
132 133 1.160329 AGCACACGTGAGCCTTGTTC 61.160 55.000 30.26 5.48 31.86 3.18
133 134 1.153168 AGCACACGTGAGCCTTGTT 60.153 52.632 30.26 12.11 31.86 2.83
134 135 1.595382 GAGCACACGTGAGCCTTGT 60.595 57.895 30.26 14.97 31.86 3.16
135 136 1.159713 TTGAGCACACGTGAGCCTTG 61.160 55.000 30.26 15.58 31.86 3.61
136 137 0.882042 CTTGAGCACACGTGAGCCTT 60.882 55.000 30.26 16.04 31.86 4.35
137 138 1.301244 CTTGAGCACACGTGAGCCT 60.301 57.895 30.26 19.19 31.86 4.58
138 139 2.959357 GCTTGAGCACACGTGAGCC 61.959 63.158 30.26 22.24 41.59 4.70
139 140 2.553268 GCTTGAGCACACGTGAGC 59.447 61.111 27.55 27.55 41.59 4.26
140 141 2.661566 CGGCTTGAGCACACGTGAG 61.662 63.158 25.01 16.59 44.36 3.51
141 142 2.661537 CGGCTTGAGCACACGTGA 60.662 61.111 25.01 0.00 44.36 4.35
142 143 4.374702 GCGGCTTGAGCACACGTG 62.375 66.667 15.48 15.48 44.36 4.49
145 146 3.579626 GAACGCGGCTTGAGCACAC 62.580 63.158 12.47 0.00 44.36 3.82
146 147 3.345808 GAACGCGGCTTGAGCACA 61.346 61.111 12.47 0.00 44.36 4.57
147 148 3.016474 GAGAACGCGGCTTGAGCAC 62.016 63.158 12.47 0.00 44.36 4.40
148 149 1.873270 TAGAGAACGCGGCTTGAGCA 61.873 55.000 12.47 0.00 44.36 4.26
149 150 0.528684 ATAGAGAACGCGGCTTGAGC 60.529 55.000 12.47 0.00 41.14 4.26
150 151 2.776312 TATAGAGAACGCGGCTTGAG 57.224 50.000 12.47 0.00 0.00 3.02
151 152 4.217767 ACATATATAGAGAACGCGGCTTGA 59.782 41.667 12.47 0.00 0.00 3.02
152 153 4.324669 CACATATATAGAGAACGCGGCTTG 59.675 45.833 12.47 3.32 0.00 4.01
153 154 4.022242 ACACATATATAGAGAACGCGGCTT 60.022 41.667 12.47 0.00 0.00 4.35
154 155 3.506455 ACACATATATAGAGAACGCGGCT 59.494 43.478 12.47 7.37 0.00 5.52
155 156 3.834610 ACACATATATAGAGAACGCGGC 58.165 45.455 12.47 1.16 0.00 6.53
156 157 7.082602 AGTAAACACATATATAGAGAACGCGG 58.917 38.462 12.47 0.00 0.00 6.46
157 158 7.270793 GGAGTAAACACATATATAGAGAACGCG 59.729 40.741 3.53 3.53 0.00 6.01
158 159 7.270793 CGGAGTAAACACATATATAGAGAACGC 59.729 40.741 0.00 0.00 0.00 4.84
159 160 7.270793 GCGGAGTAAACACATATATAGAGAACG 59.729 40.741 0.00 0.00 0.00 3.95
160 161 7.270793 CGCGGAGTAAACACATATATAGAGAAC 59.729 40.741 0.00 0.00 0.00 3.01
161 162 7.303261 CGCGGAGTAAACACATATATAGAGAA 58.697 38.462 0.00 0.00 0.00 2.87
162 163 6.128090 CCGCGGAGTAAACACATATATAGAGA 60.128 42.308 24.07 0.00 0.00 3.10
163 164 6.028368 CCGCGGAGTAAACACATATATAGAG 58.972 44.000 24.07 0.00 0.00 2.43
164 165 5.474532 ACCGCGGAGTAAACACATATATAGA 59.525 40.000 35.90 0.00 0.00 1.98
165 166 5.706916 ACCGCGGAGTAAACACATATATAG 58.293 41.667 35.90 0.00 0.00 1.31
166 167 5.710513 ACCGCGGAGTAAACACATATATA 57.289 39.130 35.90 0.00 0.00 0.86
167 168 4.595762 ACCGCGGAGTAAACACATATAT 57.404 40.909 35.90 0.00 0.00 0.86
168 169 4.261572 GGTACCGCGGAGTAAACACATATA 60.262 45.833 35.90 5.53 0.00 0.86
169 170 2.973694 ACCGCGGAGTAAACACATAT 57.026 45.000 35.90 0.00 0.00 1.78
170 171 2.159254 GGTACCGCGGAGTAAACACATA 60.159 50.000 35.90 6.39 0.00 2.29
171 172 1.404583 GGTACCGCGGAGTAAACACAT 60.405 52.381 35.90 7.61 0.00 3.21
172 173 0.038343 GGTACCGCGGAGTAAACACA 60.038 55.000 35.90 1.49 0.00 3.72
173 174 1.072666 CGGTACCGCGGAGTAAACAC 61.073 60.000 35.90 15.97 0.00 3.32
174 175 1.212490 CGGTACCGCGGAGTAAACA 59.788 57.895 35.90 4.20 0.00 2.83
175 176 4.077543 CGGTACCGCGGAGTAAAC 57.922 61.111 35.90 19.78 0.00 2.01
229 230 2.997897 ACCTCCTCCAGCGGTGAC 60.998 66.667 17.83 0.00 0.00 3.67
230 231 2.680352 GACCTCCTCCAGCGGTGA 60.680 66.667 17.83 1.17 0.00 4.02
237 238 2.530701 GTTTCTCTGAGACCTCCTCCA 58.469 52.381 6.92 0.00 41.25 3.86
258 259 3.369997 GGAAGGGTCTGAGGAGAAATGAC 60.370 52.174 0.00 0.00 0.00 3.06
302 303 1.154225 CGCCGCCATTGTGAGTTTC 60.154 57.895 0.00 0.00 0.00 2.78
303 304 2.625823 CCGCCGCCATTGTGAGTTT 61.626 57.895 0.00 0.00 0.00 2.66
304 305 3.055719 CCGCCGCCATTGTGAGTT 61.056 61.111 0.00 0.00 0.00 3.01
349 350 1.534175 CGAGGACGTACAGGAGAATGC 60.534 57.143 0.00 0.00 34.56 3.56
356 357 2.181021 GTGGCGAGGACGTACAGG 59.819 66.667 0.00 0.00 41.98 4.00
394 395 0.458669 CTTCTTTACCGGCGCCTCTA 59.541 55.000 26.68 10.52 0.00 2.43
404 405 2.450345 CGGCGGCGTCTTCTTTACC 61.450 63.158 24.74 0.00 0.00 2.85
405 406 3.078560 CGGCGGCGTCTTCTTTAC 58.921 61.111 24.74 0.00 0.00 2.01
406 407 2.812178 GCGGCGGCGTCTTCTTTA 60.812 61.111 32.35 0.00 0.00 1.85
420 421 1.003839 TGAAGTTGTAGGCTGGCGG 60.004 57.895 0.00 0.00 0.00 6.13
421 422 1.298859 GGTGAAGTTGTAGGCTGGCG 61.299 60.000 0.00 0.00 0.00 5.69
425 426 2.230750 GTCTACGGTGAAGTTGTAGGCT 59.769 50.000 0.00 0.00 37.72 4.58
431 432 1.538512 TCCTCGTCTACGGTGAAGTTG 59.461 52.381 2.24 0.00 40.29 3.16
435 436 2.027745 AGTACTCCTCGTCTACGGTGAA 60.028 50.000 2.24 0.00 40.29 3.18
442 443 1.911357 TCACCCAGTACTCCTCGTCTA 59.089 52.381 0.00 0.00 0.00 2.59
443 444 0.697079 TCACCCAGTACTCCTCGTCT 59.303 55.000 0.00 0.00 0.00 4.18
460 461 3.452786 CCTCCTCCGCTCGCTTCA 61.453 66.667 0.00 0.00 0.00 3.02
595 596 4.147322 GGTTCGTCGCCACGCATG 62.147 66.667 0.00 0.00 46.28 4.06
740 744 4.379243 AGCTCGTTGTCGCTGGGG 62.379 66.667 0.00 0.00 34.69 4.96
742 746 1.416813 GATGAGCTCGTTGTCGCTGG 61.417 60.000 10.42 0.00 36.45 4.85
767 771 0.685097 ACTGGAGCGTGCCTCTTTTA 59.315 50.000 0.00 0.00 40.57 1.52
772 776 2.811317 CGAACTGGAGCGTGCCTC 60.811 66.667 0.00 0.00 39.98 4.70
784 788 1.982395 TCCTGGATCACGCCGAACT 60.982 57.895 0.00 0.00 0.00 3.01
812 816 2.020016 CGCGCGAAAACGATCCAG 59.980 61.111 28.94 0.00 34.06 3.86
821 825 4.690719 ACCATGGACCGCGCGAAA 62.691 61.111 34.63 13.97 0.00 3.46
851 855 0.390340 TGTTCACGATGAGCTCCTGC 60.390 55.000 12.15 0.00 40.05 4.85
1059 1066 0.689080 TGCTGGAGGAGAGGATGGAC 60.689 60.000 0.00 0.00 0.00 4.02
1093 1100 0.246360 CAGCTGGACATGGACACGTA 59.754 55.000 5.57 0.00 0.00 3.57
1153 1160 0.036732 TGGCTGTTGGAGATGGTGAC 59.963 55.000 0.00 0.00 0.00 3.67
1159 1166 1.271597 GGTGAAGTGGCTGTTGGAGAT 60.272 52.381 0.00 0.00 0.00 2.75
1161 1168 0.179020 TGGTGAAGTGGCTGTTGGAG 60.179 55.000 0.00 0.00 0.00 3.86
1326 1333 1.615107 GCCAGTGCGTGTAGTCGTTC 61.615 60.000 0.00 0.00 0.00 3.95
1455 1462 1.076024 TCCTTGTACTCGGTGTAGGGT 59.924 52.381 0.00 0.00 0.00 4.34
1507 1514 0.404040 TTGAAGAAGGCCCCGTTCAT 59.596 50.000 11.05 0.00 0.00 2.57
1552 1559 2.171725 GGTCCATCTTGCCGTACGC 61.172 63.158 10.49 6.24 38.31 4.42
1553 1560 0.527817 GAGGTCCATCTTGCCGTACG 60.528 60.000 8.69 8.69 0.00 3.67
1570 1577 2.825836 GTGCTTGGCCGGGATGAG 60.826 66.667 2.18 0.00 0.00 2.90
1592 1599 1.517832 GTGAGCTGCCCGACATACT 59.482 57.895 0.00 0.00 0.00 2.12
1613 1620 4.749310 CGAGAGTGCCGGCAAGCT 62.749 66.667 34.66 30.03 0.00 3.74
1615 1622 2.811317 GTCGAGAGTGCCGGCAAG 60.811 66.667 34.66 19.70 0.00 4.01
1617 1624 4.056125 CAGTCGAGAGTGCCGGCA 62.056 66.667 29.03 29.03 33.55 5.69
1624 1631 2.955402 GACGTGGCAGTCGAGAGT 59.045 61.111 4.40 0.00 0.00 3.24
1650 1657 3.627577 CCGGCAAGTGAAGTTAATAGCAT 59.372 43.478 0.00 0.00 0.00 3.79
1656 1663 2.843401 TAGCCGGCAAGTGAAGTTAA 57.157 45.000 31.54 0.00 0.00 2.01
1665 1672 1.936547 GAGAGACAATTAGCCGGCAAG 59.063 52.381 31.54 15.33 0.00 4.01
1669 1676 3.274393 CGGAGAGACAATTAGCCGG 57.726 57.895 0.00 0.00 35.42 6.13
1670 1677 0.249489 CCCGGAGAGACAATTAGCCG 60.249 60.000 0.73 0.00 38.54 5.52
1671 1678 0.831307 ACCCGGAGAGACAATTAGCC 59.169 55.000 0.73 0.00 0.00 3.93
1672 1679 1.941325 CACCCGGAGAGACAATTAGC 58.059 55.000 0.73 0.00 0.00 3.09
1673 1680 1.207089 TGCACCCGGAGAGACAATTAG 59.793 52.381 0.73 0.00 0.00 1.73
1674 1681 1.271856 TGCACCCGGAGAGACAATTA 58.728 50.000 0.73 0.00 0.00 1.40
1675 1682 0.400213 TTGCACCCGGAGAGACAATT 59.600 50.000 0.73 0.00 0.00 2.32
1676 1683 0.036010 CTTGCACCCGGAGAGACAAT 60.036 55.000 0.73 0.00 0.00 2.71
1677 1684 1.371183 CTTGCACCCGGAGAGACAA 59.629 57.895 0.73 0.00 0.00 3.18
1678 1685 1.407656 AACTTGCACCCGGAGAGACA 61.408 55.000 0.73 0.00 0.00 3.41
1679 1686 0.951040 CAACTTGCACCCGGAGAGAC 60.951 60.000 0.73 0.00 0.00 3.36
1680 1687 1.371183 CAACTTGCACCCGGAGAGA 59.629 57.895 0.73 0.00 0.00 3.10
1681 1688 0.535102 AACAACTTGCACCCGGAGAG 60.535 55.000 0.73 0.00 0.00 3.20
1682 1689 0.817634 CAACAACTTGCACCCGGAGA 60.818 55.000 0.73 0.00 0.00 3.71
1683 1690 1.101049 ACAACAACTTGCACCCGGAG 61.101 55.000 0.73 0.00 0.00 4.63
1684 1691 1.077357 ACAACAACTTGCACCCGGA 60.077 52.632 0.73 0.00 0.00 5.14
1685 1692 1.065600 CACAACAACTTGCACCCGG 59.934 57.895 0.00 0.00 0.00 5.73
1686 1693 0.667993 ATCACAACAACTTGCACCCG 59.332 50.000 0.00 0.00 0.00 5.28
1687 1694 2.888834 AATCACAACAACTTGCACCC 57.111 45.000 0.00 0.00 0.00 4.61
1688 1695 6.533367 TCTTTTTAATCACAACAACTTGCACC 59.467 34.615 0.00 0.00 0.00 5.01
1689 1696 7.391016 GTCTTTTTAATCACAACAACTTGCAC 58.609 34.615 0.00 0.00 0.00 4.57
1690 1697 6.252441 CGTCTTTTTAATCACAACAACTTGCA 59.748 34.615 0.00 0.00 0.00 4.08
1691 1698 6.470877 TCGTCTTTTTAATCACAACAACTTGC 59.529 34.615 0.00 0.00 0.00 4.01
1692 1699 7.696453 ACTCGTCTTTTTAATCACAACAACTTG 59.304 33.333 0.00 0.00 0.00 3.16
1693 1700 7.758495 ACTCGTCTTTTTAATCACAACAACTT 58.242 30.769 0.00 0.00 0.00 2.66
1694 1701 7.316544 ACTCGTCTTTTTAATCACAACAACT 57.683 32.000 0.00 0.00 0.00 3.16
1695 1702 7.964545 AACTCGTCTTTTTAATCACAACAAC 57.035 32.000 0.00 0.00 0.00 3.32
1723 1730 9.292846 CGTGCAAGTTTATGTACTAATAGTGTA 57.707 33.333 2.68 0.00 34.25 2.90
1724 1731 7.277098 CCGTGCAAGTTTATGTACTAATAGTGT 59.723 37.037 2.68 0.00 34.25 3.55
1725 1732 7.277098 ACCGTGCAAGTTTATGTACTAATAGTG 59.723 37.037 2.68 0.00 34.25 2.74
1726 1733 7.277098 CACCGTGCAAGTTTATGTACTAATAGT 59.723 37.037 0.00 0.00 34.25 2.12
1727 1734 7.618442 CACCGTGCAAGTTTATGTACTAATAG 58.382 38.462 0.00 0.00 34.25 1.73
1728 1735 6.036300 GCACCGTGCAAGTTTATGTACTAATA 59.964 38.462 18.79 0.00 44.26 0.98
1729 1736 5.163794 GCACCGTGCAAGTTTATGTACTAAT 60.164 40.000 18.79 0.00 44.26 1.73
1730 1737 4.152759 GCACCGTGCAAGTTTATGTACTAA 59.847 41.667 18.79 0.00 44.26 2.24
1731 1738 3.680937 GCACCGTGCAAGTTTATGTACTA 59.319 43.478 18.79 0.00 44.26 1.82
1732 1739 2.482721 GCACCGTGCAAGTTTATGTACT 59.517 45.455 18.79 0.00 44.26 2.73
1733 1740 2.723618 CGCACCGTGCAAGTTTATGTAC 60.724 50.000 22.89 0.00 45.36 2.90
1734 1741 1.461512 CGCACCGTGCAAGTTTATGTA 59.538 47.619 22.89 0.00 45.36 2.29
1735 1742 0.237235 CGCACCGTGCAAGTTTATGT 59.763 50.000 22.89 0.00 45.36 2.29
1736 1743 0.237235 ACGCACCGTGCAAGTTTATG 59.763 50.000 22.89 6.76 45.36 1.90
1737 1744 1.461897 GTACGCACCGTGCAAGTTTAT 59.538 47.619 22.89 2.25 45.36 1.40
1738 1745 0.860533 GTACGCACCGTGCAAGTTTA 59.139 50.000 22.89 3.45 45.36 2.01
1739 1746 1.644913 GTACGCACCGTGCAAGTTT 59.355 52.632 22.89 4.36 45.36 2.66
1740 1747 3.326109 GTACGCACCGTGCAAGTT 58.674 55.556 22.89 6.72 45.36 2.66
1745 1752 0.236187 TGAATTTGTACGCACCGTGC 59.764 50.000 13.81 13.81 41.39 5.34
1746 1753 2.892373 ATGAATTTGTACGCACCGTG 57.108 45.000 0.00 0.00 41.39 4.94
1747 1754 3.327626 TGTATGAATTTGTACGCACCGT 58.672 40.909 0.00 0.00 44.35 4.83
1748 1755 4.530094 ATGTATGAATTTGTACGCACCG 57.470 40.909 0.00 0.00 0.00 4.94
1749 1756 7.690228 TCTAAATGTATGAATTTGTACGCACC 58.310 34.615 0.00 0.00 32.16 5.01
1777 1784 7.096551 GGCTGGAAAAATGCTCAGTTTTAATA 58.903 34.615 7.84 0.00 38.49 0.98
1792 1799 0.251341 GCTCTGAGGGGCTGGAAAAA 60.251 55.000 6.83 0.00 0.00 1.94
1814 1822 0.383590 TCGGACGGTTGTGAACGTTA 59.616 50.000 0.00 0.00 44.24 3.18
1825 1833 2.088950 AAAATTGACGATCGGACGGT 57.911 45.000 20.98 0.00 37.61 4.83
1882 1910 2.500509 AGCGAAAGAGCCGAGATTAG 57.499 50.000 0.00 0.00 38.01 1.73
1974 2003 2.633481 AGAGGAGACTTGTACAACCCAC 59.367 50.000 3.59 3.08 44.43 4.61
2033 2070 2.285743 AGGAGTTGAGGAGGGGGC 60.286 66.667 0.00 0.00 0.00 5.80
2044 2081 2.246874 TCGGGGGAGAGGAGGAGTT 61.247 63.158 0.00 0.00 0.00 3.01
2052 2092 1.152839 GAGAGAGGTCGGGGGAGAG 60.153 68.421 0.00 0.00 0.00 3.20
2053 2093 2.691779 GGAGAGAGGTCGGGGGAGA 61.692 68.421 0.00 0.00 0.00 3.71
2054 2094 2.123640 GGAGAGAGGTCGGGGGAG 60.124 72.222 0.00 0.00 0.00 4.30
2055 2095 2.617538 AGGAGAGAGGTCGGGGGA 60.618 66.667 0.00 0.00 0.00 4.81
2056 2096 2.123640 GAGGAGAGAGGTCGGGGG 60.124 72.222 0.00 0.00 0.00 5.40
2229 2274 4.357947 GCTCCGAGCACACCGTCA 62.358 66.667 15.78 0.00 41.89 4.35
2439 2488 2.040412 ACCTTGGAGGAGGATTTGACAC 59.960 50.000 0.07 0.00 37.67 3.67
2447 2496 1.435563 TCTGGTTACCTTGGAGGAGGA 59.564 52.381 2.07 0.00 37.67 3.71
2515 2565 4.465632 AATATTGTACAGGCGTGAGTGA 57.534 40.909 14.38 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.