Multiple sequence alignment - TraesCS3D01G243300

Loading Multiple Alignment...

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 TraesCS3D01G243300 chr3D 100.000 3174 0 0 1 3174 338493570 338490397 0 5862
1 TraesCS3D01G243300 chr3A 93.640 1871 77 17 1321 3174 456778289 456776444 0 2758
2 TraesCS3D01G243300 chr3A 90.832 1178 76 12 148 1303 456779442 456778275 0 1548
3 TraesCS3D01G243300 chr3B 92.238 1868 93 29 1327 3174 436742509 436740674 0 2599
4 TraesCS3D01G243300 chr3B 93.135 874 40 7 438 1297 436743368 436742501 0 1264


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 TraesCS3D01G243300 chr3D 338490397 338493570 3173 True 5862.0 5862 100.0000 1 3174 1 chr3D.!!$R1 3173
1 TraesCS3D01G243300 chr3A 456776444 456779442 2998 True 2153.0 2758 92.2360 148 3174 2 chr3A.!!$R1 3026
2 TraesCS3D01G243300 chr3B 436740674 436743368 2694 True 1931.5 2599 92.6865 438 3174 2 chr3B.!!$R1 2736

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
75 76 0.312416 TTTTGCGGGTCAAATGACGG 59.688 50.0 7.42 3.65 45.65 4.79 F
1044 1065 0.104855 TGCTCGTTCTGTGCACTTCT 59.895 50.0 19.41 0.00 41.83 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1356 0.109272 TTCTAGGCGTCAACTGCGAG 60.109 55.0 0.0 0.0 0.0 5.03 R
2894 2953 0.392595 CCAAGGTTAGCGGGAGGAAC 60.393 60.0 0.0 0.0 0.0 3.62 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
32 33 4.499037 AAAAGATTTCGAGAAAACCCCG 57.501 40.909 2.17 0.00 33.56 5.73
33 34 1.450025 AGATTTCGAGAAAACCCCGC 58.550 50.000 2.17 0.00 33.56 6.13
34 35 1.161843 GATTTCGAGAAAACCCCGCA 58.838 50.000 2.17 0.00 33.56 5.69
35 36 1.130561 GATTTCGAGAAAACCCCGCAG 59.869 52.381 2.17 0.00 33.56 5.18
36 37 2.219484 ATTTCGAGAAAACCCCGCAGG 61.219 52.381 2.17 0.00 40.04 4.85
61 62 4.965042 ACGAAACCGATTTCATTTTTGC 57.035 36.364 2.58 0.00 43.90 3.68
62 63 3.423867 ACGAAACCGATTTCATTTTTGCG 59.576 39.130 2.58 0.00 43.90 4.85
63 64 3.181545 CGAAACCGATTTCATTTTTGCGG 60.182 43.478 2.58 0.00 43.90 5.69
64 65 2.362169 ACCGATTTCATTTTTGCGGG 57.638 45.000 0.00 0.00 42.76 6.13
65 66 1.616374 ACCGATTTCATTTTTGCGGGT 59.384 42.857 0.00 0.00 42.76 5.28
66 67 2.258755 CCGATTTCATTTTTGCGGGTC 58.741 47.619 0.00 0.00 35.42 4.46
67 68 2.352225 CCGATTTCATTTTTGCGGGTCA 60.352 45.455 0.00 0.00 35.42 4.02
68 69 3.312828 CGATTTCATTTTTGCGGGTCAA 58.687 40.909 0.00 0.00 0.00 3.18
69 70 3.738282 CGATTTCATTTTTGCGGGTCAAA 59.262 39.130 0.00 0.00 42.50 2.69
70 71 4.388469 CGATTTCATTTTTGCGGGTCAAAT 59.612 37.500 0.00 0.00 43.53 2.32
71 72 5.610235 ATTTCATTTTTGCGGGTCAAATG 57.390 34.783 0.00 0.00 43.53 2.32
72 73 4.327982 TTCATTTTTGCGGGTCAAATGA 57.672 36.364 3.05 3.05 43.53 2.57
73 74 3.648009 TCATTTTTGCGGGTCAAATGAC 58.352 40.909 4.96 4.96 43.53 3.06
74 75 2.126914 TTTTTGCGGGTCAAATGACG 57.873 45.000 7.42 0.00 45.65 4.35
75 76 0.312416 TTTTGCGGGTCAAATGACGG 59.688 50.000 7.42 3.65 45.65 4.79
76 77 0.535328 TTTGCGGGTCAAATGACGGA 60.535 50.000 7.42 0.00 45.65 4.69
77 78 0.535328 TTGCGGGTCAAATGACGGAA 60.535 50.000 7.42 2.41 45.65 4.30
78 79 0.535328 TGCGGGTCAAATGACGGAAA 60.535 50.000 7.42 0.00 45.65 3.13
79 80 0.594110 GCGGGTCAAATGACGGAAAA 59.406 50.000 7.42 0.00 45.65 2.29
80 81 1.664874 GCGGGTCAAATGACGGAAAAC 60.665 52.381 7.42 0.00 45.65 2.43
81 82 1.877443 CGGGTCAAATGACGGAAAACT 59.123 47.619 7.42 0.00 45.65 2.66
82 83 2.292292 CGGGTCAAATGACGGAAAACTT 59.708 45.455 7.42 0.00 45.65 2.66
83 84 3.608474 CGGGTCAAATGACGGAAAACTTC 60.608 47.826 7.42 0.00 45.65 3.01
84 85 3.316868 GGGTCAAATGACGGAAAACTTCA 59.683 43.478 7.42 0.00 45.65 3.02
85 86 4.537015 GGTCAAATGACGGAAAACTTCAG 58.463 43.478 7.42 0.00 45.65 3.02
86 87 4.036380 GGTCAAATGACGGAAAACTTCAGT 59.964 41.667 7.42 0.00 45.65 3.41
87 88 4.970003 GTCAAATGACGGAAAACTTCAGTG 59.030 41.667 0.00 0.00 38.20 3.66
88 89 4.878971 TCAAATGACGGAAAACTTCAGTGA 59.121 37.500 0.00 0.00 38.20 3.41
89 90 5.355630 TCAAATGACGGAAAACTTCAGTGAA 59.644 36.000 5.25 5.25 38.20 3.18
90 91 6.039270 TCAAATGACGGAAAACTTCAGTGAAT 59.961 34.615 5.91 0.00 38.20 2.57
91 92 6.391227 AATGACGGAAAACTTCAGTGAATT 57.609 33.333 5.91 0.00 38.20 2.17
92 93 5.828299 TGACGGAAAACTTCAGTGAATTT 57.172 34.783 5.91 4.19 38.20 1.82
93 94 5.577835 TGACGGAAAACTTCAGTGAATTTG 58.422 37.500 5.91 0.00 38.20 2.32
94 95 4.359706 ACGGAAAACTTCAGTGAATTTGC 58.640 39.130 5.91 9.36 36.72 3.68
95 96 4.097892 ACGGAAAACTTCAGTGAATTTGCT 59.902 37.500 16.54 6.32 36.72 3.91
96 97 5.298276 ACGGAAAACTTCAGTGAATTTGCTA 59.702 36.000 16.54 0.00 36.72 3.49
97 98 5.625311 CGGAAAACTTCAGTGAATTTGCTAC 59.375 40.000 16.54 6.31 0.00 3.58
98 99 6.503524 GGAAAACTTCAGTGAATTTGCTACA 58.496 36.000 5.91 0.00 0.00 2.74
99 100 6.978080 GGAAAACTTCAGTGAATTTGCTACAA 59.022 34.615 5.91 0.00 0.00 2.41
100 101 7.168135 GGAAAACTTCAGTGAATTTGCTACAAG 59.832 37.037 5.91 0.00 0.00 3.16
101 102 5.113502 ACTTCAGTGAATTTGCTACAAGC 57.886 39.130 5.91 0.00 42.82 4.01
102 103 4.022849 ACTTCAGTGAATTTGCTACAAGCC 60.023 41.667 5.91 0.00 41.51 4.35
103 104 3.485394 TCAGTGAATTTGCTACAAGCCA 58.515 40.909 0.00 0.00 41.51 4.75
104 105 3.253188 TCAGTGAATTTGCTACAAGCCAC 59.747 43.478 0.00 0.00 41.51 5.01
105 106 3.004629 CAGTGAATTTGCTACAAGCCACA 59.995 43.478 7.61 0.00 41.51 4.17
106 107 3.254166 AGTGAATTTGCTACAAGCCACAG 59.746 43.478 7.61 0.00 41.51 3.66
107 108 2.557924 TGAATTTGCTACAAGCCACAGG 59.442 45.455 0.00 0.00 41.51 4.00
108 109 2.292828 ATTTGCTACAAGCCACAGGT 57.707 45.000 0.00 0.00 41.51 4.00
109 110 1.604604 TTTGCTACAAGCCACAGGTC 58.395 50.000 0.00 0.00 41.51 3.85
110 111 0.472044 TTGCTACAAGCCACAGGTCA 59.528 50.000 0.00 0.00 41.51 4.02
111 112 0.472044 TGCTACAAGCCACAGGTCAA 59.528 50.000 0.00 0.00 41.51 3.18
112 113 1.160137 GCTACAAGCCACAGGTCAAG 58.840 55.000 0.00 0.00 34.48 3.02
113 114 1.270839 GCTACAAGCCACAGGTCAAGA 60.271 52.381 0.00 0.00 34.48 3.02
114 115 2.693069 CTACAAGCCACAGGTCAAGAG 58.307 52.381 0.00 0.00 0.00 2.85
115 116 1.131638 ACAAGCCACAGGTCAAGAGA 58.868 50.000 0.00 0.00 0.00 3.10
116 117 1.071385 ACAAGCCACAGGTCAAGAGAG 59.929 52.381 0.00 0.00 0.00 3.20
117 118 1.071385 CAAGCCACAGGTCAAGAGAGT 59.929 52.381 0.00 0.00 0.00 3.24
118 119 0.683973 AGCCACAGGTCAAGAGAGTG 59.316 55.000 0.00 0.00 0.00 3.51
119 120 0.394565 GCCACAGGTCAAGAGAGTGT 59.605 55.000 0.00 0.00 0.00 3.55
120 121 1.606737 GCCACAGGTCAAGAGAGTGTC 60.607 57.143 0.00 0.00 0.00 3.67
121 122 1.688735 CCACAGGTCAAGAGAGTGTCA 59.311 52.381 0.00 0.00 0.00 3.58
122 123 2.301296 CCACAGGTCAAGAGAGTGTCAT 59.699 50.000 0.00 0.00 0.00 3.06
123 124 3.583806 CACAGGTCAAGAGAGTGTCATC 58.416 50.000 0.00 0.00 0.00 2.92
124 125 2.564947 ACAGGTCAAGAGAGTGTCATCC 59.435 50.000 0.00 0.00 0.00 3.51
125 126 2.564504 CAGGTCAAGAGAGTGTCATCCA 59.435 50.000 0.00 0.00 0.00 3.41
126 127 2.564947 AGGTCAAGAGAGTGTCATCCAC 59.435 50.000 0.00 0.00 44.89 4.02
161 162 3.213264 CGGAAACCCTAGCCGCTA 58.787 61.111 0.00 0.00 38.46 4.26
177 178 0.683179 GCTACCGCCCCCAAAAATCT 60.683 55.000 0.00 0.00 0.00 2.40
189 190 4.268359 CCCAAAAATCTCCTCTTCCTCTG 58.732 47.826 0.00 0.00 0.00 3.35
190 191 4.263683 CCCAAAAATCTCCTCTTCCTCTGT 60.264 45.833 0.00 0.00 0.00 3.41
197 198 3.853181 TCTCCTCTTCCTCTGTCCTTCTA 59.147 47.826 0.00 0.00 0.00 2.10
203 204 1.006519 TCCTCTGTCCTTCTAGCTGCT 59.993 52.381 7.57 7.57 0.00 4.24
205 206 2.159114 CCTCTGTCCTTCTAGCTGCTTC 60.159 54.545 7.79 0.00 0.00 3.86
226 227 2.093764 CAGGATGACACTGGAAGAGGTC 60.094 54.545 0.00 0.00 39.69 3.85
232 233 1.152312 ACTGGAAGAGGTCGGGTGT 60.152 57.895 0.00 0.00 37.43 4.16
236 237 1.746517 GAAGAGGTCGGGTGTGTGT 59.253 57.895 0.00 0.00 0.00 3.72
240 241 1.764134 AGAGGTCGGGTGTGTGTTTAA 59.236 47.619 0.00 0.00 0.00 1.52
241 242 2.370849 AGAGGTCGGGTGTGTGTTTAAT 59.629 45.455 0.00 0.00 0.00 1.40
252 253 6.474102 GGGTGTGTGTTTAATGTGTTTGTAAG 59.526 38.462 0.00 0.00 0.00 2.34
257 258 6.749578 TGTGTTTAATGTGTTTGTAAGCACTG 59.250 34.615 11.84 0.00 40.30 3.66
342 343 5.482686 TTGCTTTGTTTTGCTGGATTTTC 57.517 34.783 0.00 0.00 0.00 2.29
366 367 9.816787 TTCTTATTAGGTGGGTAAAATCTTTGT 57.183 29.630 0.00 0.00 0.00 2.83
372 373 7.520451 AGGTGGGTAAAATCTTTGTTAAGAC 57.480 36.000 0.00 0.00 42.91 3.01
385 386 8.251750 TCTTTGTTAAGACATATCCTGAAACG 57.748 34.615 0.00 0.00 35.49 3.60
401 402 3.192422 TGAAACGTTAGGCCAAATCCATG 59.808 43.478 5.01 0.00 0.00 3.66
404 405 3.161866 ACGTTAGGCCAAATCCATGTTT 58.838 40.909 5.01 0.00 0.00 2.83
571 580 1.163554 CAAGGAGAGCAAGCAGTTCC 58.836 55.000 0.00 0.00 0.00 3.62
615 624 2.103042 CGGCAAAAGCCTCTCCTCG 61.103 63.158 4.85 0.00 0.00 4.63
872 893 2.427506 ACCTCCACTTCAGAATTTCGC 58.572 47.619 0.00 0.00 0.00 4.70
876 897 3.486383 TCCACTTCAGAATTTCGCCTTT 58.514 40.909 0.00 0.00 0.00 3.11
909 930 3.963428 TTTTCTCCCTCCTCTTCTTCG 57.037 47.619 0.00 0.00 0.00 3.79
940 961 1.262683 GTCGCTGGCATAGAATCTTGC 59.737 52.381 8.29 8.29 38.14 4.01
976 997 0.690762 TTGTTTCTTCGGAGGAGGGG 59.309 55.000 0.00 0.00 0.00 4.79
1041 1062 0.598680 GACTGCTCGTTCTGTGCACT 60.599 55.000 19.41 0.00 41.83 4.40
1042 1063 0.179073 ACTGCTCGTTCTGTGCACTT 60.179 50.000 19.41 0.00 41.83 3.16
1043 1064 0.510359 CTGCTCGTTCTGTGCACTTC 59.490 55.000 19.41 4.88 41.83 3.01
1044 1065 0.104855 TGCTCGTTCTGTGCACTTCT 59.895 50.000 19.41 0.00 41.83 2.85
1089 1110 3.822192 CCGTCCGATGGCTCGTCA 61.822 66.667 0.00 0.00 43.49 4.35
1114 1135 2.432146 TCCACGGAGGATCTCAATCAAG 59.568 50.000 0.00 0.00 43.07 3.02
1168 1189 1.001487 TCACAGCGGTTTTCTTGCATG 60.001 47.619 0.00 0.00 0.00 4.06
1170 1191 0.388907 CAGCGGTTTTCTTGCATGGG 60.389 55.000 0.00 0.00 0.00 4.00
1176 1197 1.872952 GTTTTCTTGCATGGGGTTTGC 59.127 47.619 0.00 0.00 40.55 3.68
1180 1201 2.768503 CTTGCATGGGGTTTGCGGTG 62.769 60.000 0.00 0.00 43.10 4.94
1190 1211 1.812571 GGTTTGCGGTGTTCTGATCAT 59.187 47.619 0.00 0.00 0.00 2.45
1191 1212 2.159517 GGTTTGCGGTGTTCTGATCATC 60.160 50.000 0.00 0.00 0.00 2.92
1192 1213 2.470983 TTGCGGTGTTCTGATCATCA 57.529 45.000 0.00 0.00 0.00 3.07
1193 1214 1.725641 TGCGGTGTTCTGATCATCAC 58.274 50.000 13.73 13.73 0.00 3.06
1194 1215 0.647410 GCGGTGTTCTGATCATCACG 59.353 55.000 14.89 12.35 0.00 4.35
1199 1221 2.602211 GTGTTCTGATCATCACGCTCTG 59.398 50.000 0.00 0.00 0.00 3.35
1200 1222 2.200067 GTTCTGATCATCACGCTCTGG 58.800 52.381 0.00 0.00 0.00 3.86
1216 1238 3.107601 CTCTGGGATACTTGGTTCTGGA 58.892 50.000 0.00 0.00 0.00 3.86
1225 1247 7.054124 GGATACTTGGTTCTGGATTACATTCA 58.946 38.462 0.00 0.00 0.00 2.57
1303 1326 5.126061 AGCAACAAATCTCTCTCTCTCTCTC 59.874 44.000 0.00 0.00 0.00 3.20
1304 1327 5.126061 GCAACAAATCTCTCTCTCTCTCTCT 59.874 44.000 0.00 0.00 0.00 3.10
1305 1328 6.678900 GCAACAAATCTCTCTCTCTCTCTCTC 60.679 46.154 0.00 0.00 0.00 3.20
1306 1329 6.319048 ACAAATCTCTCTCTCTCTCTCTCT 57.681 41.667 0.00 0.00 0.00 3.10
1307 1330 6.352516 ACAAATCTCTCTCTCTCTCTCTCTC 58.647 44.000 0.00 0.00 0.00 3.20
1308 1331 6.157645 ACAAATCTCTCTCTCTCTCTCTCTCT 59.842 42.308 0.00 0.00 0.00 3.10
1309 1332 6.418057 AATCTCTCTCTCTCTCTCTCTCTC 57.582 45.833 0.00 0.00 0.00 3.20
1310 1333 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1311 1334 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1312 1335 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1313 1336 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1314 1337 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1315 1338 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1316 1339 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1317 1340 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1318 1341 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1319 1342 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1320 1343 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1321 1344 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1322 1345 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1323 1346 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1324 1347 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1325 1348 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1326 1349 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1327 1350 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1328 1351 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1329 1352 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1330 1353 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1331 1354 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1332 1355 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1333 1356 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1334 1357 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1335 1358 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1447 1470 1.998315 CTGGTCAGAATGTCGAGCAAG 59.002 52.381 0.00 0.00 39.01 4.01
1450 1473 1.651138 GTCAGAATGTCGAGCAAGTCG 59.349 52.381 0.00 0.00 42.73 4.18
1510 1533 6.678900 GCCATGTCATTTCTCAGGTTTGTATC 60.679 42.308 0.00 0.00 0.00 2.24
1512 1535 7.121759 CCATGTCATTTCTCAGGTTTGTATCTT 59.878 37.037 0.00 0.00 0.00 2.40
1513 1536 7.672983 TGTCATTTCTCAGGTTTGTATCTTC 57.327 36.000 0.00 0.00 0.00 2.87
1515 1538 7.604164 TGTCATTTCTCAGGTTTGTATCTTCTC 59.396 37.037 0.00 0.00 0.00 2.87
1518 1541 9.092876 CATTTCTCAGGTTTGTATCTTCTCTAC 57.907 37.037 0.00 0.00 0.00 2.59
1519 1542 7.776618 TTCTCAGGTTTGTATCTTCTCTACA 57.223 36.000 0.00 0.00 0.00 2.74
1520 1543 7.776618 TCTCAGGTTTGTATCTTCTCTACAA 57.223 36.000 0.00 0.00 37.32 2.41
1521 1544 7.603651 TCTCAGGTTTGTATCTTCTCTACAAC 58.396 38.462 0.00 0.00 38.46 3.32
1522 1545 6.698380 TCAGGTTTGTATCTTCTCTACAACC 58.302 40.000 0.00 0.00 38.46 3.77
1523 1546 6.497259 TCAGGTTTGTATCTTCTCTACAACCT 59.503 38.462 0.00 0.00 38.46 3.50
1524 1547 6.591834 CAGGTTTGTATCTTCTCTACAACCTG 59.408 42.308 18.88 18.88 42.90 4.00
1525 1548 5.875359 GGTTTGTATCTTCTCTACAACCTGG 59.125 44.000 0.00 0.00 38.46 4.45
1526 1549 6.295688 GGTTTGTATCTTCTCTACAACCTGGA 60.296 42.308 0.00 0.00 38.46 3.86
1527 1550 6.531503 TTGTATCTTCTCTACAACCTGGAG 57.468 41.667 0.00 0.00 34.90 3.86
1528 1551 5.580998 TGTATCTTCTCTACAACCTGGAGT 58.419 41.667 0.00 0.79 28.14 3.85
1529 1552 5.419155 TGTATCTTCTCTACAACCTGGAGTG 59.581 44.000 0.00 0.08 28.14 3.51
1530 1553 3.165875 TCTTCTCTACAACCTGGAGTGG 58.834 50.000 0.00 0.62 28.14 4.00
1531 1554 2.696526 TCTCTACAACCTGGAGTGGT 57.303 50.000 0.00 0.00 43.11 4.16
1532 1555 3.820195 TCTCTACAACCTGGAGTGGTA 57.180 47.619 0.00 0.00 39.83 3.25
1533 1556 4.332683 TCTCTACAACCTGGAGTGGTAT 57.667 45.455 0.00 0.00 39.83 2.73
1534 1557 4.684724 TCTCTACAACCTGGAGTGGTATT 58.315 43.478 0.00 0.00 39.83 1.89
1535 1558 5.091552 TCTCTACAACCTGGAGTGGTATTT 58.908 41.667 0.00 0.00 39.83 1.40
1536 1559 5.546499 TCTCTACAACCTGGAGTGGTATTTT 59.454 40.000 0.00 0.00 39.83 1.82
1537 1560 5.556915 TCTACAACCTGGAGTGGTATTTTG 58.443 41.667 0.00 0.00 39.83 2.44
1538 1561 4.447138 ACAACCTGGAGTGGTATTTTGA 57.553 40.909 0.00 0.00 39.83 2.69
1580 1608 5.787953 TTCTTTCATGTTTCATGGAGCAA 57.212 34.783 9.39 0.00 0.00 3.91
1583 1611 5.244402 TCTTTCATGTTTCATGGAGCAACAT 59.756 36.000 9.39 1.63 40.94 2.71
1587 1615 4.669206 TGTTTCATGGAGCAACATGTTT 57.331 36.364 8.77 0.00 46.39 2.83
1615 1643 6.732531 TTTGTGCTCTACTGAATCTGAATG 57.267 37.500 0.00 0.00 0.00 2.67
1674 1702 3.006247 GGCTCTGTCCTTGATGAACTTC 58.994 50.000 0.00 0.00 0.00 3.01
1722 1750 5.053145 CAGAGAGTAGGATTGGCATTGTAC 58.947 45.833 0.00 0.00 0.00 2.90
1790 1818 9.847224 AGAAAGGTGAGAAAAACTACTTTCATA 57.153 29.630 14.31 0.00 41.25 2.15
1848 1888 2.777692 TCATACCTGAACCTGAATCCCC 59.222 50.000 0.00 0.00 0.00 4.81
1879 1923 2.103153 ACAGAGGTGTCAAGGGAAGA 57.897 50.000 0.00 0.00 26.76 2.87
1983 2027 1.592400 TACCACGAGAGAACCGCCAG 61.592 60.000 0.00 0.00 0.00 4.85
2086 2130 1.089920 ACATGATCAAGCAAGGACGC 58.910 50.000 0.00 0.00 0.00 5.19
2181 2225 1.795286 GGTGCAAGAGTGAAGTCTTCG 59.205 52.381 8.06 0.00 34.38 3.79
2193 2237 6.626302 AGTGAAGTCTTCGAATAAGAGAAGG 58.374 40.000 8.06 0.00 42.85 3.46
2319 2363 5.396362 CGTTTGAACAAGATTGTACAGCTTG 59.604 40.000 26.21 26.21 41.31 4.01
2350 2394 2.686915 GTTGAGATTGCAGAGGATTGGG 59.313 50.000 0.00 0.00 0.00 4.12
2375 2419 4.380531 CTCTGGTGTTGTAGCTTGAGAAA 58.619 43.478 0.00 0.00 33.33 2.52
2488 2532 9.833182 GAAGAAATTATCAGAAGTTTCAGAACC 57.167 33.333 0.00 0.00 36.39 3.62
2506 2550 0.673437 CCGTGGTTGAAATGCACCTT 59.327 50.000 0.00 0.00 0.00 3.50
2560 2605 7.763985 TCTTCAGATTGTCAATATCAAAGCGTA 59.236 33.333 0.00 0.00 0.00 4.42
2563 2608 4.850859 TTGTCAATATCAAAGCGTACGG 57.149 40.909 18.39 0.00 0.00 4.02
2564 2609 3.852286 TGTCAATATCAAAGCGTACGGT 58.148 40.909 15.34 15.34 0.00 4.83
2565 2610 3.615056 TGTCAATATCAAAGCGTACGGTG 59.385 43.478 22.08 9.67 0.00 4.94
2567 2612 2.596904 ATATCAAAGCGTACGGTGCT 57.403 45.000 22.08 8.66 46.68 4.40
2568 2613 3.720949 ATATCAAAGCGTACGGTGCTA 57.279 42.857 22.08 9.44 43.14 3.49
2569 2614 2.373540 ATCAAAGCGTACGGTGCTAA 57.626 45.000 22.08 7.60 43.14 3.09
2730 2789 3.525537 ACAGACATACAATTCTCTGGCG 58.474 45.455 0.00 0.00 35.43 5.69
2828 2887 4.286032 TGGACATAACCAGTTAAGACAGCT 59.714 41.667 0.17 0.00 34.77 4.24
2831 2890 6.480320 GGACATAACCAGTTAAGACAGCTATG 59.520 42.308 0.17 0.00 0.00 2.23
2894 2953 1.863880 CGCGAAGAAGACCGAGTCG 60.864 63.158 0.00 5.29 37.67 4.18
3045 3104 2.283529 CCCCTGTCACCGTACAGCT 61.284 63.158 4.70 0.00 44.56 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.794981 GCGGGGTTTTCTCGAAATCTTTTT 60.795 41.667 0.00 0.00 0.00 1.94
11 12 3.305131 GCGGGGTTTTCTCGAAATCTTTT 60.305 43.478 0.00 0.00 0.00 2.27
12 13 2.228103 GCGGGGTTTTCTCGAAATCTTT 59.772 45.455 0.00 0.00 0.00 2.52
13 14 1.810755 GCGGGGTTTTCTCGAAATCTT 59.189 47.619 0.00 0.00 0.00 2.40
14 15 1.271163 TGCGGGGTTTTCTCGAAATCT 60.271 47.619 0.00 0.00 0.00 2.40
15 16 1.130561 CTGCGGGGTTTTCTCGAAATC 59.869 52.381 0.00 0.00 0.00 2.17
16 17 1.165270 CTGCGGGGTTTTCTCGAAAT 58.835 50.000 0.00 0.00 0.00 2.17
17 18 0.887387 CCTGCGGGGTTTTCTCGAAA 60.887 55.000 2.57 0.00 0.00 3.46
18 19 1.302192 CCTGCGGGGTTTTCTCGAA 60.302 57.895 2.57 0.00 0.00 3.71
19 20 2.345991 CCTGCGGGGTTTTCTCGA 59.654 61.111 2.57 0.00 0.00 4.04
28 29 1.871077 GTTTCGTAAACCTGCGGGG 59.129 57.895 18.00 5.11 41.89 5.73
36 37 6.783759 GCAAAAATGAAATCGGTTTCGTAAAC 59.216 34.615 15.98 1.96 45.34 2.01
37 38 6.345093 CGCAAAAATGAAATCGGTTTCGTAAA 60.345 34.615 15.98 0.00 45.34 2.01
38 39 5.115773 CGCAAAAATGAAATCGGTTTCGTAA 59.884 36.000 15.98 0.00 45.34 3.18
39 40 4.613448 CGCAAAAATGAAATCGGTTTCGTA 59.387 37.500 15.98 0.00 45.34 3.43
40 41 3.423867 CGCAAAAATGAAATCGGTTTCGT 59.576 39.130 16.01 13.19 45.34 3.85
41 42 3.181545 CCGCAAAAATGAAATCGGTTTCG 60.182 43.478 16.01 2.44 45.34 3.46
42 43 3.122780 CCCGCAAAAATGAAATCGGTTTC 59.877 43.478 14.35 14.35 43.22 2.78
43 44 3.063485 CCCGCAAAAATGAAATCGGTTT 58.937 40.909 0.00 0.00 35.52 3.27
44 45 2.036604 ACCCGCAAAAATGAAATCGGTT 59.963 40.909 0.00 0.00 35.52 4.44
45 46 1.616374 ACCCGCAAAAATGAAATCGGT 59.384 42.857 0.00 0.00 35.52 4.69
46 47 2.258755 GACCCGCAAAAATGAAATCGG 58.741 47.619 0.00 0.00 36.90 4.18
47 48 2.940147 TGACCCGCAAAAATGAAATCG 58.060 42.857 0.00 0.00 0.00 3.34
58 59 0.535328 TTCCGTCATTTGACCCGCAA 60.535 50.000 5.17 0.00 41.86 4.85
59 60 0.535328 TTTCCGTCATTTGACCCGCA 60.535 50.000 5.17 0.00 41.86 5.69
60 61 0.594110 TTTTCCGTCATTTGACCCGC 59.406 50.000 5.17 0.00 41.86 6.13
61 62 1.877443 AGTTTTCCGTCATTTGACCCG 59.123 47.619 5.17 0.00 41.86 5.28
62 63 3.316868 TGAAGTTTTCCGTCATTTGACCC 59.683 43.478 5.17 0.00 41.86 4.46
63 64 4.036380 ACTGAAGTTTTCCGTCATTTGACC 59.964 41.667 5.17 0.00 41.86 4.02
64 65 4.970003 CACTGAAGTTTTCCGTCATTTGAC 59.030 41.667 0.46 0.46 41.47 3.18
65 66 4.878971 TCACTGAAGTTTTCCGTCATTTGA 59.121 37.500 0.00 0.00 0.00 2.69
66 67 5.168526 TCACTGAAGTTTTCCGTCATTTG 57.831 39.130 0.00 0.00 0.00 2.32
67 68 5.828299 TTCACTGAAGTTTTCCGTCATTT 57.172 34.783 0.00 0.00 0.00 2.32
68 69 6.391227 AATTCACTGAAGTTTTCCGTCATT 57.609 33.333 0.00 0.00 0.00 2.57
69 70 6.208644 CAAATTCACTGAAGTTTTCCGTCAT 58.791 36.000 1.70 0.00 27.08 3.06
70 71 5.577835 CAAATTCACTGAAGTTTTCCGTCA 58.422 37.500 1.70 0.00 27.08 4.35
71 72 4.441087 GCAAATTCACTGAAGTTTTCCGTC 59.559 41.667 1.70 0.00 27.08 4.79
72 73 4.097892 AGCAAATTCACTGAAGTTTTCCGT 59.902 37.500 1.70 0.00 27.08 4.69
73 74 4.610945 AGCAAATTCACTGAAGTTTTCCG 58.389 39.130 1.70 0.00 27.08 4.30
74 75 6.503524 TGTAGCAAATTCACTGAAGTTTTCC 58.496 36.000 1.70 0.00 27.08 3.13
75 76 7.306225 GCTTGTAGCAAATTCACTGAAGTTTTC 60.306 37.037 1.70 0.00 41.89 2.29
76 77 6.476706 GCTTGTAGCAAATTCACTGAAGTTTT 59.523 34.615 1.70 0.00 41.89 2.43
77 78 5.979517 GCTTGTAGCAAATTCACTGAAGTTT 59.020 36.000 1.70 0.00 41.89 2.66
78 79 5.507985 GGCTTGTAGCAAATTCACTGAAGTT 60.508 40.000 0.00 0.00 44.75 2.66
79 80 4.022849 GGCTTGTAGCAAATTCACTGAAGT 60.023 41.667 0.67 0.00 44.75 3.01
80 81 4.022935 TGGCTTGTAGCAAATTCACTGAAG 60.023 41.667 0.67 0.00 44.75 3.02
81 82 3.888323 TGGCTTGTAGCAAATTCACTGAA 59.112 39.130 0.67 0.00 44.75 3.02
82 83 3.253188 GTGGCTTGTAGCAAATTCACTGA 59.747 43.478 0.67 0.00 44.75 3.41
83 84 3.004629 TGTGGCTTGTAGCAAATTCACTG 59.995 43.478 0.67 0.00 44.75 3.66
84 85 3.221771 TGTGGCTTGTAGCAAATTCACT 58.778 40.909 0.67 0.00 44.75 3.41
85 86 3.568538 CTGTGGCTTGTAGCAAATTCAC 58.431 45.455 0.67 0.35 44.75 3.18
86 87 2.557924 CCTGTGGCTTGTAGCAAATTCA 59.442 45.455 0.67 0.00 44.75 2.57
87 88 2.558359 ACCTGTGGCTTGTAGCAAATTC 59.442 45.455 0.67 0.00 44.75 2.17
88 89 2.558359 GACCTGTGGCTTGTAGCAAATT 59.442 45.455 0.67 0.00 44.75 1.82
89 90 2.162681 GACCTGTGGCTTGTAGCAAAT 58.837 47.619 0.67 0.00 44.75 2.32
90 91 1.133945 TGACCTGTGGCTTGTAGCAAA 60.134 47.619 0.67 0.00 44.75 3.68
91 92 0.472044 TGACCTGTGGCTTGTAGCAA 59.528 50.000 0.67 0.00 44.75 3.91
92 93 0.472044 TTGACCTGTGGCTTGTAGCA 59.528 50.000 0.67 0.00 44.75 3.49
93 94 1.160137 CTTGACCTGTGGCTTGTAGC 58.840 55.000 0.00 0.00 41.46 3.58
94 95 2.300152 TCTCTTGACCTGTGGCTTGTAG 59.700 50.000 0.00 0.00 0.00 2.74
95 96 2.300152 CTCTCTTGACCTGTGGCTTGTA 59.700 50.000 0.00 0.00 0.00 2.41
96 97 1.071385 CTCTCTTGACCTGTGGCTTGT 59.929 52.381 0.00 0.00 0.00 3.16
97 98 1.071385 ACTCTCTTGACCTGTGGCTTG 59.929 52.381 0.00 0.00 0.00 4.01
98 99 1.071385 CACTCTCTTGACCTGTGGCTT 59.929 52.381 0.00 0.00 0.00 4.35
99 100 0.683973 CACTCTCTTGACCTGTGGCT 59.316 55.000 0.00 0.00 0.00 4.75
100 101 0.394565 ACACTCTCTTGACCTGTGGC 59.605 55.000 0.00 0.00 33.44 5.01
101 102 1.688735 TGACACTCTCTTGACCTGTGG 59.311 52.381 0.00 0.00 33.44 4.17
102 103 3.583806 GATGACACTCTCTTGACCTGTG 58.416 50.000 0.00 0.00 35.09 3.66
103 104 2.564947 GGATGACACTCTCTTGACCTGT 59.435 50.000 0.00 0.00 0.00 4.00
104 105 2.564504 TGGATGACACTCTCTTGACCTG 59.435 50.000 0.00 0.00 0.00 4.00
105 106 2.564947 GTGGATGACACTCTCTTGACCT 59.435 50.000 0.00 0.00 46.72 3.85
106 107 2.966050 GTGGATGACACTCTCTTGACC 58.034 52.381 0.00 0.00 46.72 4.02
144 145 1.227176 GTAGCGGCTAGGGTTTCCG 60.227 63.158 10.54 1.76 45.46 4.30
145 146 1.145598 GGTAGCGGCTAGGGTTTCC 59.854 63.158 10.54 3.08 0.00 3.13
146 147 1.227176 CGGTAGCGGCTAGGGTTTC 60.227 63.158 10.54 0.00 0.00 2.78
161 162 1.304962 GGAGATTTTTGGGGGCGGT 60.305 57.895 0.00 0.00 0.00 5.68
172 173 4.073425 AGGACAGAGGAAGAGGAGATTT 57.927 45.455 0.00 0.00 0.00 2.17
177 178 3.626222 GCTAGAAGGACAGAGGAAGAGGA 60.626 52.174 0.00 0.00 0.00 3.71
189 190 1.827969 TCCTGAAGCAGCTAGAAGGAC 59.172 52.381 14.08 0.00 0.00 3.85
190 191 2.238084 TCCTGAAGCAGCTAGAAGGA 57.762 50.000 14.08 14.08 0.00 3.36
197 198 0.982704 AGTGTCATCCTGAAGCAGCT 59.017 50.000 0.00 0.00 0.00 4.24
203 204 2.568956 CCTCTTCCAGTGTCATCCTGAA 59.431 50.000 0.00 0.00 31.38 3.02
205 206 1.905215 ACCTCTTCCAGTGTCATCCTG 59.095 52.381 0.00 0.00 0.00 3.86
214 215 1.152312 ACACCCGACCTCTTCCAGT 60.152 57.895 0.00 0.00 0.00 4.00
219 220 0.544697 AAACACACACCCGACCTCTT 59.455 50.000 0.00 0.00 0.00 2.85
226 227 3.701532 AACACATTAAACACACACCCG 57.298 42.857 0.00 0.00 0.00 5.28
232 233 6.749578 CAGTGCTTACAAACACATTAAACACA 59.250 34.615 0.00 0.00 39.30 3.72
236 237 6.701145 TCCAGTGCTTACAAACACATTAAA 57.299 33.333 0.00 0.00 39.30 1.52
240 241 4.771590 CATCCAGTGCTTACAAACACAT 57.228 40.909 0.00 0.00 39.30 3.21
314 315 3.181508 CCAGCAAAACAAAGCAAAAGTGG 60.182 43.478 0.00 0.00 0.00 4.00
361 362 8.029642 ACGTTTCAGGATATGTCTTAACAAAG 57.970 34.615 0.00 0.00 39.30 2.77
364 365 7.762615 CCTAACGTTTCAGGATATGTCTTAACA 59.237 37.037 11.07 0.00 35.30 2.41
366 367 6.759827 GCCTAACGTTTCAGGATATGTCTTAA 59.240 38.462 19.25 0.00 33.42 1.85
368 369 5.116882 GCCTAACGTTTCAGGATATGTCTT 58.883 41.667 19.25 0.00 33.42 3.01
370 371 3.808174 GGCCTAACGTTTCAGGATATGTC 59.192 47.826 19.25 2.25 33.42 3.06
372 373 3.804036 TGGCCTAACGTTTCAGGATATG 58.196 45.455 19.25 0.00 33.42 1.78
377 378 2.163613 GGATTTGGCCTAACGTTTCAGG 59.836 50.000 5.91 9.68 34.85 3.86
384 385 3.510719 CAAACATGGATTTGGCCTAACG 58.489 45.455 3.32 0.00 36.17 3.18
419 420 7.359595 GGGCCATGTTTGTTTCTTTATTTTTC 58.640 34.615 4.39 0.00 0.00 2.29
433 434 3.814268 CTCGCGGGGCCATGTTTG 61.814 66.667 6.13 0.00 0.00 2.93
538 540 1.071471 CCTTGGTTGGTGCGTCTCT 59.929 57.895 0.00 0.00 0.00 3.10
615 624 0.842635 TAGGGACGGTAGGGAGAGTC 59.157 60.000 0.00 0.00 0.00 3.36
872 893 3.821033 AGAAAATCCCGTGAACTGAAAGG 59.179 43.478 0.00 0.00 39.30 3.11
876 897 3.053831 GGAGAAAATCCCGTGAACTGA 57.946 47.619 0.00 0.00 43.01 3.41
909 930 1.696832 GCCAGCGACGAAGAATGACC 61.697 60.000 0.00 0.00 0.00 4.02
940 961 1.024579 CAAACCGACGAGAATGGGGG 61.025 60.000 0.00 0.00 0.00 5.40
1009 1030 2.885861 CAGTCGTCTTCTCCCGGG 59.114 66.667 16.85 16.85 0.00 5.73
1041 1062 4.398044 AGAAGCGAAAGAACCACAAAAGAA 59.602 37.500 0.00 0.00 0.00 2.52
1042 1063 3.945285 AGAAGCGAAAGAACCACAAAAGA 59.055 39.130 0.00 0.00 0.00 2.52
1043 1064 4.201910 TGAGAAGCGAAAGAACCACAAAAG 60.202 41.667 0.00 0.00 0.00 2.27
1044 1065 3.692101 TGAGAAGCGAAAGAACCACAAAA 59.308 39.130 0.00 0.00 0.00 2.44
1151 1172 0.388907 CCCATGCAAGAAAACCGCTG 60.389 55.000 0.00 0.00 0.00 5.18
1152 1173 1.535204 CCCCATGCAAGAAAACCGCT 61.535 55.000 0.00 0.00 0.00 5.52
1168 1189 0.893727 ATCAGAACACCGCAAACCCC 60.894 55.000 0.00 0.00 0.00 4.95
1170 1191 1.234821 TGATCAGAACACCGCAAACC 58.765 50.000 0.00 0.00 0.00 3.27
1176 1197 0.647410 GCGTGATGATCAGAACACCG 59.353 55.000 18.21 15.19 0.00 4.94
1180 1201 2.200067 CCAGAGCGTGATGATCAGAAC 58.800 52.381 0.09 0.83 34.70 3.01
1190 1211 0.824109 CCAAGTATCCCAGAGCGTGA 59.176 55.000 0.00 0.00 0.00 4.35
1191 1212 0.537188 ACCAAGTATCCCAGAGCGTG 59.463 55.000 0.00 0.00 0.00 5.34
1192 1213 1.207329 GAACCAAGTATCCCAGAGCGT 59.793 52.381 0.00 0.00 0.00 5.07
1193 1214 1.482593 AGAACCAAGTATCCCAGAGCG 59.517 52.381 0.00 0.00 0.00 5.03
1194 1215 2.420687 CCAGAACCAAGTATCCCAGAGC 60.421 54.545 0.00 0.00 0.00 4.09
1199 1221 5.367945 TGTAATCCAGAACCAAGTATCCC 57.632 43.478 0.00 0.00 0.00 3.85
1200 1222 7.054124 TGAATGTAATCCAGAACCAAGTATCC 58.946 38.462 0.00 0.00 0.00 2.59
1216 1238 6.725364 AGACCTGTTCTCCAATGAATGTAAT 58.275 36.000 0.00 0.00 0.00 1.89
1225 1247 4.141158 ACCAAGAAAGACCTGTTCTCCAAT 60.141 41.667 0.00 0.00 34.19 3.16
1303 1326 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1304 1327 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1305 1328 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1306 1329 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1307 1330 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1308 1331 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1309 1332 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1310 1333 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1311 1334 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1312 1335 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1313 1336 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
1314 1337 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
1315 1338 3.551863 GCGAGAGAGAGAGAGAGAGAGAG 60.552 56.522 0.00 0.00 0.00 3.20
1316 1339 2.362397 GCGAGAGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
1317 1340 2.101415 TGCGAGAGAGAGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
1318 1341 2.101415 CTGCGAGAGAGAGAGAGAGAGA 59.899 54.545 0.00 0.00 0.00 3.10
1319 1342 2.159043 ACTGCGAGAGAGAGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
1320 1343 1.831106 ACTGCGAGAGAGAGAGAGAGA 59.169 52.381 0.00 0.00 0.00 3.10
1321 1344 2.315925 ACTGCGAGAGAGAGAGAGAG 57.684 55.000 0.00 0.00 0.00 3.20
1322 1345 2.027653 TCAACTGCGAGAGAGAGAGAGA 60.028 50.000 0.00 0.00 0.00 3.10
1323 1346 2.095853 GTCAACTGCGAGAGAGAGAGAG 59.904 54.545 0.00 0.00 0.00 3.20
1324 1347 2.080693 GTCAACTGCGAGAGAGAGAGA 58.919 52.381 0.00 0.00 0.00 3.10
1325 1348 1.202020 CGTCAACTGCGAGAGAGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
1326 1349 0.799393 CGTCAACTGCGAGAGAGAGA 59.201 55.000 0.00 0.00 0.00 3.10
1327 1350 0.796491 GCGTCAACTGCGAGAGAGAG 60.796 60.000 0.00 0.00 0.00 3.20
1328 1351 1.210413 GCGTCAACTGCGAGAGAGA 59.790 57.895 0.00 0.00 0.00 3.10
1329 1352 1.803519 GGCGTCAACTGCGAGAGAG 60.804 63.158 0.00 0.00 0.00 3.20
1330 1353 0.958876 TAGGCGTCAACTGCGAGAGA 60.959 55.000 0.00 0.00 0.00 3.10
1331 1354 0.524392 CTAGGCGTCAACTGCGAGAG 60.524 60.000 0.00 0.00 0.00 3.20
1332 1355 0.958876 TCTAGGCGTCAACTGCGAGA 60.959 55.000 0.00 0.00 0.00 4.04
1333 1356 0.109272 TTCTAGGCGTCAACTGCGAG 60.109 55.000 0.00 0.00 0.00 5.03
1334 1357 0.388134 GTTCTAGGCGTCAACTGCGA 60.388 55.000 0.00 0.00 0.00 5.10
1335 1358 0.666274 TGTTCTAGGCGTCAACTGCG 60.666 55.000 0.00 0.00 0.00 5.18
1447 1470 1.226128 GCATCTGCCGCTTTTCGAC 60.226 57.895 0.00 0.00 41.67 4.20
1450 1473 1.515736 GCTGCATCTGCCGCTTTTC 60.516 57.895 10.79 0.00 45.80 2.29
1510 1533 2.900546 ACCACTCCAGGTTGTAGAGAAG 59.099 50.000 0.00 0.00 39.34 2.85
1512 1535 2.696526 ACCACTCCAGGTTGTAGAGA 57.303 50.000 0.00 0.00 39.34 3.10
1513 1536 5.422214 AAATACCACTCCAGGTTGTAGAG 57.578 43.478 0.00 0.00 43.08 2.43
1515 1538 5.411669 GTCAAAATACCACTCCAGGTTGTAG 59.588 44.000 0.00 0.00 43.08 2.74
1518 1541 3.188460 CGTCAAAATACCACTCCAGGTTG 59.812 47.826 0.00 0.00 43.08 3.77
1519 1542 3.071892 TCGTCAAAATACCACTCCAGGTT 59.928 43.478 0.00 0.00 43.08 3.50
1520 1543 2.635915 TCGTCAAAATACCACTCCAGGT 59.364 45.455 0.00 0.00 45.72 4.00
1521 1544 3.056107 TCTCGTCAAAATACCACTCCAGG 60.056 47.826 0.00 0.00 0.00 4.45
1522 1545 4.082190 TCTCTCGTCAAAATACCACTCCAG 60.082 45.833 0.00 0.00 0.00 3.86
1523 1546 3.830178 TCTCTCGTCAAAATACCACTCCA 59.170 43.478 0.00 0.00 0.00 3.86
1524 1547 4.451629 TCTCTCGTCAAAATACCACTCC 57.548 45.455 0.00 0.00 0.00 3.85
1525 1548 5.411781 ACATCTCTCGTCAAAATACCACTC 58.588 41.667 0.00 0.00 0.00 3.51
1526 1549 5.407407 ACATCTCTCGTCAAAATACCACT 57.593 39.130 0.00 0.00 0.00 4.00
1527 1550 6.369065 AGAAACATCTCTCGTCAAAATACCAC 59.631 38.462 0.00 0.00 0.00 4.16
1528 1551 6.368791 CAGAAACATCTCTCGTCAAAATACCA 59.631 38.462 0.00 0.00 0.00 3.25
1529 1552 6.369065 ACAGAAACATCTCTCGTCAAAATACC 59.631 38.462 0.00 0.00 0.00 2.73
1530 1553 7.352719 ACAGAAACATCTCTCGTCAAAATAC 57.647 36.000 0.00 0.00 0.00 1.89
1531 1554 7.962964 AACAGAAACATCTCTCGTCAAAATA 57.037 32.000 0.00 0.00 0.00 1.40
1532 1555 6.867662 AACAGAAACATCTCTCGTCAAAAT 57.132 33.333 0.00 0.00 0.00 1.82
1533 1556 6.677781 AAACAGAAACATCTCTCGTCAAAA 57.322 33.333 0.00 0.00 0.00 2.44
1534 1557 6.677781 AAAACAGAAACATCTCTCGTCAAA 57.322 33.333 0.00 0.00 0.00 2.69
1535 1558 6.677781 AAAAACAGAAACATCTCTCGTCAA 57.322 33.333 0.00 0.00 0.00 3.18
1560 1588 4.873817 TGTTGCTCCATGAAACATGAAAG 58.126 39.130 12.46 10.21 39.19 2.62
1595 1623 4.033817 GCACATTCAGATTCAGTAGAGCAC 59.966 45.833 0.00 0.00 0.00 4.40
1596 1624 4.186926 GCACATTCAGATTCAGTAGAGCA 58.813 43.478 0.00 0.00 0.00 4.26
1597 1625 4.186926 TGCACATTCAGATTCAGTAGAGC 58.813 43.478 0.00 0.00 0.00 4.09
1598 1626 5.658468 TCTGCACATTCAGATTCAGTAGAG 58.342 41.667 0.00 0.00 38.11 2.43
1599 1627 5.665916 TCTGCACATTCAGATTCAGTAGA 57.334 39.130 0.00 0.00 38.11 2.59
1629 1657 1.269166 CGCCAGTAGCAAGAAGTACG 58.731 55.000 0.00 0.00 44.04 3.67
1674 1702 4.023107 TGACTGTTACTGAAGGAGTTCTCG 60.023 45.833 0.00 0.00 35.96 4.04
1722 1750 0.379669 GCTGAAGCCACATGAATCCG 59.620 55.000 0.00 0.00 34.31 4.18
1790 1818 3.700538 TGAAAAGGATGCAAGGTGCTAT 58.299 40.909 0.00 0.00 45.31 2.97
1848 1888 4.464244 TGACACCTCTGTAGAGATGGAAAG 59.536 45.833 10.40 0.00 40.06 2.62
1879 1923 1.494721 TGGAAGAAGAACCACAGGCTT 59.505 47.619 0.00 0.00 0.00 4.35
1938 1982 2.097825 GGAGGCCAGAGTAGACGTTTA 58.902 52.381 5.01 0.00 0.00 2.01
1983 2027 2.035442 GTCCAAAGGCTCACGCTCC 61.035 63.158 0.00 0.00 36.09 4.70
2181 2225 5.580297 CACTGACTTCTGCCTTCTCTTATTC 59.420 44.000 0.00 0.00 0.00 1.75
2193 2237 4.060900 TCAATCTTCACACTGACTTCTGC 58.939 43.478 0.00 0.00 0.00 4.26
2319 2363 6.036517 CCTCTGCAATCTCAACACAAGTATAC 59.963 42.308 0.00 0.00 0.00 1.47
2350 2394 2.037251 TCAAGCTACAACACCAGAGGTC 59.963 50.000 0.00 0.00 31.02 3.85
2488 2532 2.507339 AAAGGTGCATTTCAACCACG 57.493 45.000 0.00 0.00 30.95 4.94
2506 2550 6.094742 TGTTGCACAAAGAACATGAAGACTAA 59.905 34.615 0.00 0.00 0.00 2.24
2541 2586 4.873827 ACCGTACGCTTTGATATTGACAAT 59.126 37.500 10.49 5.87 0.00 2.71
2560 2605 5.124936 GGGTCAAAAATAAGATTAGCACCGT 59.875 40.000 0.00 0.00 0.00 4.83
2563 2608 6.603599 AGGAGGGTCAAAAATAAGATTAGCAC 59.396 38.462 0.00 0.00 0.00 4.40
2564 2609 6.731467 AGGAGGGTCAAAAATAAGATTAGCA 58.269 36.000 0.00 0.00 0.00 3.49
2565 2610 7.122799 ACAAGGAGGGTCAAAAATAAGATTAGC 59.877 37.037 0.00 0.00 0.00 3.09
2567 2612 8.802267 CAACAAGGAGGGTCAAAAATAAGATTA 58.198 33.333 0.00 0.00 0.00 1.75
2568 2613 7.508977 TCAACAAGGAGGGTCAAAAATAAGATT 59.491 33.333 0.00 0.00 0.00 2.40
2569 2614 7.010160 TCAACAAGGAGGGTCAAAAATAAGAT 58.990 34.615 0.00 0.00 0.00 2.40
2623 2682 9.295825 TGGCATAAGTATGTTTTATCCATTAGG 57.704 33.333 0.54 0.00 36.11 2.69
2828 2887 3.343617 GCCTATCGCCATTTTAGCCATA 58.656 45.455 0.00 0.00 0.00 2.74
2831 2890 0.517316 CGCCTATCGCCATTTTAGCC 59.483 55.000 0.00 0.00 0.00 3.93
2894 2953 0.392595 CCAAGGTTAGCGGGAGGAAC 60.393 60.000 0.00 0.00 0.00 3.62
3045 3104 0.684479 ATCCGTGAGCAGCTGGTAGA 60.684 55.000 20.22 13.51 0.00 2.59
3095 3154 3.389329 TCCCCTTATGCTCAGAGAATGAC 59.611 47.826 0.00 0.00 33.22 3.06


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

AutoCloner maintained by Alex Coulton.