Multiple sequence alignment - TraesCS3B01G130000

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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 TraesCS3B01G130000 chr3B 100.000 3989 0 0 1 3989 112265782 112261794 0.000000e+00 7367.0
1 TraesCS3B01G130000 chr3D 89.542 4064 227 84 4 3989 67461758 67457815 0.000000e+00 4968.0
2 TraesCS3B01G130000 chr3A 90.013 3845 214 66 200 3989 78720445 78716716 0.000000e+00 4817.0
3 TraesCS3B01G130000 chr1D 85.185 243 34 2 2231 2472 473857519 473857760 8.560000e-62 248.0
4 TraesCS3B01G130000 chrUn 84.127 252 38 2 2231 2481 1493064 1492814 3.980000e-60 243.0
5 TraesCS3B01G130000 chr1B 84.362 243 36 2 2231 2472 658909953 658910194 1.850000e-58 237.0
6 TraesCS3B01G130000 chr7D 92.473 93 7 0 2231 2323 55389149 55389241 2.500000e-27 134.0
7 TraesCS3B01G130000 chr6B 93.182 44 2 1 3848 3890 591192457 591192414 3.330000e-06 63.9


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 TraesCS3B01G130000 chr3B 112261794 112265782 3988 True 7367 7367 100.000 1 3989 1 chr3B.!!$R1 3988
1 TraesCS3B01G130000 chr3D 67457815 67461758 3943 True 4968 4968 89.542 4 3989 1 chr3D.!!$R1 3985
2 TraesCS3B01G130000 chr3A 78716716 78720445 3729 True 4817 4817 90.013 200 3989 1 chr3A.!!$R1 3789

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
174 193 0.037605 AATTGGACAGACCGACCGAC 60.038 55.0 0.00 0.00 42.61 4.79 F
610 647 0.103208 CTTACCTCACCCGCTAGCAG 59.897 60.0 16.45 7.92 0.00 4.24 F
1281 1360 0.178944 TGGTCCTCGAGAGTTTCCCA 60.179 55.0 15.71 7.25 0.00 4.37 F
2388 2494 0.824109 TGTCCATCCTGATCACGACC 59.176 55.0 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2003 0.539986 TGAGGTTCATAAGGGGCGTC 59.460 55.000 0.00 0.00 0.00 5.19 R
2229 2335 1.210234 TGGCATCCATCGTTCATCTGT 59.790 47.619 0.00 0.00 0.00 3.41 R
2811 2917 0.240411 ACGTTCTCTGCAGGTACGAC 59.760 55.000 29.35 15.63 34.29 4.34 R
3803 3917 0.036732 AACTGCATTCGGCTCTCCAA 59.963 50.000 0.00 0.00 45.15 3.53 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
18 19 3.814577 CAGTGACCGATCCGAGTTT 57.185 52.632 0.00 0.00 0.00 2.66
24 25 0.736325 ACCGATCCGAGTTTTCGCTG 60.736 55.000 0.00 0.00 45.38 5.18
40 41 1.723003 CGCTGTTACTACGTTTGACCC 59.277 52.381 0.00 0.00 0.00 4.46
66 67 3.065233 GCATGCACGTAAATCCTGAATCA 59.935 43.478 14.21 0.00 0.00 2.57
67 68 4.787563 GCATGCACGTAAATCCTGAATCAG 60.788 45.833 14.21 2.68 0.00 2.90
72 73 5.005779 GCACGTAAATCCTGAATCAGTACTG 59.994 44.000 17.17 17.17 0.00 2.74
77 78 1.893137 TCCTGAATCAGTACTGCGTGT 59.107 47.619 18.45 2.68 0.00 4.49
104 109 0.524862 ACTCACGTCGAGGCGTTATT 59.475 50.000 16.04 0.00 46.98 1.40
105 110 1.189403 CTCACGTCGAGGCGTTATTC 58.811 55.000 4.75 0.00 43.83 1.75
106 111 0.521867 TCACGTCGAGGCGTTATTCG 60.522 55.000 4.75 0.00 43.83 3.34
113 118 3.179992 GTCGAGGCGTTATTCGAGAATTC 59.820 47.826 3.49 0.00 45.38 2.17
114 119 3.113322 CGAGGCGTTATTCGAGAATTCA 58.887 45.455 8.44 0.00 42.86 2.57
115 120 3.180584 CGAGGCGTTATTCGAGAATTCAG 59.819 47.826 8.44 1.28 42.86 3.02
116 121 4.360563 GAGGCGTTATTCGAGAATTCAGA 58.639 43.478 8.44 3.87 42.86 3.27
118 123 3.245519 GGCGTTATTCGAGAATTCAGACC 59.754 47.826 8.44 0.11 42.86 3.85
163 182 4.780815 ACAGTTCAGACTCAAATTGGACA 58.219 39.130 0.00 0.00 32.54 4.02
169 188 2.632996 AGACTCAAATTGGACAGACCGA 59.367 45.455 0.00 0.00 42.61 4.69
174 193 0.037605 AATTGGACAGACCGACCGAC 60.038 55.000 0.00 0.00 42.61 4.79
175 194 1.885163 ATTGGACAGACCGACCGACC 61.885 60.000 0.00 0.00 42.61 4.79
177 196 3.052082 GACAGACCGACCGACCGA 61.052 66.667 0.00 0.00 0.00 4.69
178 197 3.319926 GACAGACCGACCGACCGAC 62.320 68.421 0.00 0.00 0.00 4.79
179 198 4.112341 CAGACCGACCGACCGACC 62.112 72.222 0.00 0.00 0.00 4.79
183 202 4.547905 CCGACCGACCGACCGATG 62.548 72.222 5.35 0.00 0.00 3.84
184 203 4.547905 CGACCGACCGACCGATGG 62.548 72.222 0.00 0.00 0.00 3.51
185 204 4.867599 GACCGACCGACCGATGGC 62.868 72.222 0.00 0.00 0.00 4.40
187 206 4.873129 CCGACCGACCGATGGCTG 62.873 72.222 0.00 0.00 0.00 4.85
188 207 4.873129 CGACCGACCGATGGCTGG 62.873 72.222 0.00 0.00 0.00 4.85
192 211 4.147449 CGACCGATGGCTGGCTGA 62.147 66.667 2.00 0.00 0.00 4.26
193 212 2.268920 GACCGATGGCTGGCTGAA 59.731 61.111 2.00 0.00 0.00 3.02
194 213 2.045926 ACCGATGGCTGGCTGAAC 60.046 61.111 2.00 0.00 0.00 3.18
195 214 2.046023 CCGATGGCTGGCTGAACA 60.046 61.111 2.00 0.00 0.00 3.18
196 215 1.675310 CCGATGGCTGGCTGAACAA 60.675 57.895 2.00 0.00 0.00 2.83
197 216 1.033746 CCGATGGCTGGCTGAACAAT 61.034 55.000 2.00 0.00 0.00 2.71
198 217 0.813184 CGATGGCTGGCTGAACAATT 59.187 50.000 2.00 0.00 0.00 2.32
199 218 1.202222 CGATGGCTGGCTGAACAATTC 60.202 52.381 2.00 0.00 0.00 2.17
200 219 1.135721 GATGGCTGGCTGAACAATTCC 59.864 52.381 2.00 0.00 0.00 3.01
201 220 1.243342 TGGCTGGCTGAACAATTCCG 61.243 55.000 2.00 0.00 0.00 4.30
202 221 0.960364 GGCTGGCTGAACAATTCCGA 60.960 55.000 0.00 0.00 0.00 4.55
203 222 1.098050 GCTGGCTGAACAATTCCGAT 58.902 50.000 0.00 0.00 0.00 4.18
204 223 1.064654 GCTGGCTGAACAATTCCGATC 59.935 52.381 0.00 0.00 0.00 3.69
205 224 2.358957 CTGGCTGAACAATTCCGATCA 58.641 47.619 0.00 0.00 0.00 2.92
261 281 2.203294 AACACACAAGACGGCCCC 60.203 61.111 0.00 0.00 0.00 5.80
329 361 4.890088 ACGCTAACCAAGAACACATCTAA 58.110 39.130 0.00 0.00 37.42 2.10
330 362 4.929808 ACGCTAACCAAGAACACATCTAAG 59.070 41.667 0.00 0.00 37.42 2.18
331 363 4.201724 CGCTAACCAAGAACACATCTAAGC 60.202 45.833 0.00 0.00 37.42 3.09
332 364 4.938226 GCTAACCAAGAACACATCTAAGCT 59.062 41.667 0.00 0.00 37.42 3.74
333 365 6.106673 GCTAACCAAGAACACATCTAAGCTA 58.893 40.000 0.00 0.00 37.42 3.32
356 388 3.733684 GCTAAGTCAAAGCCTCTCTCTCG 60.734 52.174 0.00 0.00 33.73 4.04
381 413 3.825328 CGAAAGGGAAGGATGATTGGAT 58.175 45.455 0.00 0.00 0.00 3.41
382 414 3.567164 CGAAAGGGAAGGATGATTGGATG 59.433 47.826 0.00 0.00 0.00 3.51
383 415 4.540715 GAAAGGGAAGGATGATTGGATGT 58.459 43.478 0.00 0.00 0.00 3.06
384 416 5.687441 CGAAAGGGAAGGATGATTGGATGTA 60.687 44.000 0.00 0.00 0.00 2.29
385 417 5.937492 AAGGGAAGGATGATTGGATGTAT 57.063 39.130 0.00 0.00 0.00 2.29
386 418 5.252586 AGGGAAGGATGATTGGATGTATG 57.747 43.478 0.00 0.00 0.00 2.39
387 419 4.915809 AGGGAAGGATGATTGGATGTATGA 59.084 41.667 0.00 0.00 0.00 2.15
388 420 5.373555 AGGGAAGGATGATTGGATGTATGAA 59.626 40.000 0.00 0.00 0.00 2.57
389 421 5.709164 GGGAAGGATGATTGGATGTATGAAG 59.291 44.000 0.00 0.00 0.00 3.02
390 422 5.182760 GGAAGGATGATTGGATGTATGAAGC 59.817 44.000 0.00 0.00 0.00 3.86
402 434 0.457853 TATGAAGCAGGTCGCACGTC 60.458 55.000 0.00 0.00 46.13 4.34
601 638 1.746991 GCAGCCTGCTTACCTCACC 60.747 63.158 10.04 0.00 40.96 4.02
606 643 1.327690 CCTGCTTACCTCACCCGCTA 61.328 60.000 0.00 0.00 0.00 4.26
609 646 1.956629 GCTTACCTCACCCGCTAGCA 61.957 60.000 16.45 0.00 0.00 3.49
610 647 0.103208 CTTACCTCACCCGCTAGCAG 59.897 60.000 16.45 7.92 0.00 4.24
613 650 3.774528 CTCACCCGCTAGCAGGCA 61.775 66.667 17.26 2.99 0.00 4.75
614 651 3.729965 CTCACCCGCTAGCAGGCAG 62.730 68.421 17.26 10.07 0.00 4.85
620 657 4.106925 GCTAGCAGGCAGGCAGGT 62.107 66.667 10.63 0.00 35.83 4.00
621 658 2.188994 CTAGCAGGCAGGCAGGTC 59.811 66.667 0.00 0.00 35.83 3.85
622 659 2.284921 TAGCAGGCAGGCAGGTCT 60.285 61.111 0.00 0.00 35.83 3.85
625 662 3.324930 CAGGCAGGCAGGTCTGGA 61.325 66.667 2.75 0.00 36.86 3.86
627 664 4.767255 GGCAGGCAGGTCTGGACG 62.767 72.222 2.75 0.00 35.43 4.79
629 666 4.087892 CAGGCAGGTCTGGACGGG 62.088 72.222 0.00 0.00 0.00 5.28
630 667 4.640690 AGGCAGGTCTGGACGGGT 62.641 66.667 0.00 0.00 0.00 5.28
631 668 4.394712 GGCAGGTCTGGACGGGTG 62.395 72.222 0.00 0.00 0.00 4.61
632 669 3.311110 GCAGGTCTGGACGGGTGA 61.311 66.667 0.00 0.00 0.00 4.02
633 670 2.973899 CAGGTCTGGACGGGTGAG 59.026 66.667 0.00 0.00 0.00 3.51
634 671 2.283966 AGGTCTGGACGGGTGAGG 60.284 66.667 0.00 0.00 0.00 3.86
636 673 1.304713 GGTCTGGACGGGTGAGGTA 60.305 63.158 0.00 0.00 0.00 3.08
700 756 2.805353 GCTCGTTTGCTCGCTCGA 60.805 61.111 0.00 0.00 0.00 4.04
943 1015 1.396301 GTCTCTTGCTCATCCAAAGCG 59.604 52.381 0.00 0.00 42.83 4.68
958 1030 0.606673 AAGCGAACAAAGCTCCCTCC 60.607 55.000 0.00 0.00 45.31 4.30
959 1031 1.302511 GCGAACAAAGCTCCCTCCA 60.303 57.895 0.00 0.00 0.00 3.86
962 1034 1.065854 CGAACAAAGCTCCCTCCATCT 60.066 52.381 0.00 0.00 0.00 2.90
963 1035 2.637947 GAACAAAGCTCCCTCCATCTC 58.362 52.381 0.00 0.00 0.00 2.75
966 1038 0.539051 AAAGCTCCCTCCATCTCGTG 59.461 55.000 0.00 0.00 0.00 4.35
974 1046 4.746361 CCATCTCGTGGCTAGCTG 57.254 61.111 15.72 5.25 42.12 4.24
975 1047 1.593750 CCATCTCGTGGCTAGCTGC 60.594 63.158 15.72 6.83 42.12 5.25
976 1048 1.440893 CATCTCGTGGCTAGCTGCT 59.559 57.895 15.72 7.57 42.39 4.24
977 1049 0.179089 CATCTCGTGGCTAGCTGCTT 60.179 55.000 15.72 0.00 42.39 3.91
978 1050 0.179089 ATCTCGTGGCTAGCTGCTTG 60.179 55.000 15.72 7.19 42.39 4.01
979 1051 1.216444 CTCGTGGCTAGCTGCTTGA 59.784 57.895 15.72 5.22 42.39 3.02
980 1052 0.179089 CTCGTGGCTAGCTGCTTGAT 60.179 55.000 15.72 0.00 42.39 2.57
981 1053 0.179100 TCGTGGCTAGCTGCTTGATC 60.179 55.000 15.72 6.61 42.39 2.92
982 1054 0.179089 CGTGGCTAGCTGCTTGATCT 60.179 55.000 15.72 0.00 42.39 2.75
983 1055 1.741732 CGTGGCTAGCTGCTTGATCTT 60.742 52.381 15.72 0.00 42.39 2.40
984 1056 2.363683 GTGGCTAGCTGCTTGATCTTT 58.636 47.619 15.72 0.00 42.39 2.52
996 1068 4.005650 GCTTGATCTTTGTGACTGATCCA 58.994 43.478 0.00 1.63 36.65 3.41
1087 1161 4.256920 ACACACACATAATCTGCTCCTTC 58.743 43.478 0.00 0.00 0.00 3.46
1088 1162 4.019860 ACACACACATAATCTGCTCCTTCT 60.020 41.667 0.00 0.00 0.00 2.85
1101 1175 4.642429 TGCTCCTTCTCTTTAAGTTGTCC 58.358 43.478 0.00 0.00 0.00 4.02
1153 1232 4.980434 GTGCATCACCATGAATAATTGAGC 59.020 41.667 0.00 0.00 30.57 4.26
1156 1235 5.769367 CATCACCATGAATAATTGAGCTGG 58.231 41.667 0.00 0.00 30.57 4.85
1167 1246 3.548745 ATTGAGCTGGTGATCGATGAA 57.451 42.857 0.54 0.00 32.02 2.57
1192 1271 5.564259 CGTGTACCCTATAGCTACATGTTCC 60.564 48.000 2.30 0.00 0.00 3.62
1207 1286 4.221703 ACATGTTCCTTCTTGAGATCGAGT 59.778 41.667 0.00 0.00 0.00 4.18
1210 1289 4.039245 TGTTCCTTCTTGAGATCGAGTTGT 59.961 41.667 0.00 0.00 0.00 3.32
1215 1294 6.015350 TCCTTCTTGAGATCGAGTTGTAACTT 60.015 38.462 0.00 0.00 39.88 2.66
1281 1360 0.178944 TGGTCCTCGAGAGTTTCCCA 60.179 55.000 15.71 7.25 0.00 4.37
1338 1423 7.942990 AGGTACTACTACAAACTATGATCTGC 58.057 38.462 0.00 0.00 36.02 4.26
1347 1432 6.672147 ACAAACTATGATCTGCAAGTCAAAC 58.328 36.000 4.95 0.00 33.76 2.93
1370 1455 6.402222 ACTGAGAGCTGTTTAATTAGGAGTG 58.598 40.000 0.00 0.00 0.00 3.51
1372 1457 5.046304 TGAGAGCTGTTTAATTAGGAGTGCT 60.046 40.000 0.00 0.00 0.00 4.40
1378 1463 7.928706 AGCTGTTTAATTAGGAGTGCTATGTAG 59.071 37.037 0.00 0.00 0.00 2.74
1379 1464 7.711339 GCTGTTTAATTAGGAGTGCTATGTAGT 59.289 37.037 0.00 0.00 0.00 2.73
1389 1474 8.770010 AGGAGTGCTATGTAGTAAGAAATAGT 57.230 34.615 0.00 0.00 0.00 2.12
1390 1475 9.863650 AGGAGTGCTATGTAGTAAGAAATAGTA 57.136 33.333 0.00 0.00 0.00 1.82
1391 1476 9.896263 GGAGTGCTATGTAGTAAGAAATAGTAC 57.104 37.037 0.00 0.00 39.78 2.73
1441 1528 8.034215 TGAATTGCACCAAATTAAAGATCGAAT 58.966 29.630 0.00 0.00 29.89 3.34
1448 1535 7.433131 CACCAAATTAAAGATCGAATCATGTGG 59.567 37.037 0.00 0.00 0.00 4.17
1450 1537 7.201812 CCAAATTAAAGATCGAATCATGTGGGA 60.202 37.037 0.00 0.00 0.00 4.37
1478 1566 8.783999 ATTTACGAAGAATCACTAGTACGATG 57.216 34.615 0.00 0.00 0.00 3.84
1481 1573 6.713520 ACGAAGAATCACTAGTACGATGTAC 58.286 40.000 0.00 0.00 0.00 2.90
1487 1579 7.553402 AGAATCACTAGTACGATGTACAGTTCT 59.447 37.037 0.33 0.81 0.00 3.01
1698 1790 4.704833 GCCGACAAGCTCCCTGCA 62.705 66.667 0.00 0.00 45.94 4.41
1702 1794 3.255397 ACAAGCTCCCTGCAGCCT 61.255 61.111 8.66 0.00 45.94 4.58
1806 1904 4.081030 TCGCTGTCGTCGTCGTCC 62.081 66.667 1.33 0.00 38.33 4.79
1812 1910 4.377708 TCGTCGTCGTCCTCCGGA 62.378 66.667 2.93 2.93 38.33 5.14
1879 1977 4.357947 GCTCCACTGACGGCGACA 62.358 66.667 16.62 14.00 0.00 4.35
1889 1987 4.988598 CGGCGACAACAGGCAGGT 62.989 66.667 0.00 0.00 0.00 4.00
2143 2249 6.035220 GCGCATAGTACAACATACAGTACAAA 59.965 38.462 0.30 0.00 42.26 2.83
2149 2255 8.160521 AGTACAACATACAGTACAAAATTGCA 57.839 30.769 0.00 0.00 42.26 4.08
2151 2257 7.872163 ACAACATACAGTACAAAATTGCATG 57.128 32.000 0.00 0.00 0.00 4.06
2153 2259 5.410067 ACATACAGTACAAAATTGCATGCC 58.590 37.500 16.68 0.00 0.00 4.40
2154 2260 5.047448 ACATACAGTACAAAATTGCATGCCA 60.047 36.000 16.68 4.04 0.00 4.92
2155 2261 3.652274 ACAGTACAAAATTGCATGCCAC 58.348 40.909 16.68 0.36 0.00 5.01
2156 2262 3.069300 ACAGTACAAAATTGCATGCCACA 59.931 39.130 16.68 0.00 0.00 4.17
2157 2263 4.056740 CAGTACAAAATTGCATGCCACAA 58.943 39.130 16.68 2.88 0.00 3.33
2158 2264 4.150980 CAGTACAAAATTGCATGCCACAAG 59.849 41.667 16.68 3.39 0.00 3.16
2159 2265 3.472283 ACAAAATTGCATGCCACAAGA 57.528 38.095 16.68 0.00 0.00 3.02
2160 2266 3.806380 ACAAAATTGCATGCCACAAGAA 58.194 36.364 16.68 1.18 0.00 2.52
2162 2268 4.639310 ACAAAATTGCATGCCACAAGAAAA 59.361 33.333 16.68 0.00 0.00 2.29
2163 2269 5.299782 ACAAAATTGCATGCCACAAGAAAAT 59.700 32.000 16.68 2.30 0.00 1.82
2165 2271 6.484818 AAATTGCATGCCACAAGAAAATAC 57.515 33.333 16.68 0.00 0.00 1.89
2166 2272 4.870123 TTGCATGCCACAAGAAAATACT 57.130 36.364 16.68 0.00 0.00 2.12
2167 2273 4.870123 TGCATGCCACAAGAAAATACTT 57.130 36.364 16.68 0.00 0.00 2.24
2168 2274 5.212532 TGCATGCCACAAGAAAATACTTT 57.787 34.783 16.68 0.00 0.00 2.66
2169 2275 5.609423 TGCATGCCACAAGAAAATACTTTT 58.391 33.333 16.68 0.00 35.12 2.27
2170 2276 5.466058 TGCATGCCACAAGAAAATACTTTTG 59.534 36.000 16.68 0.00 31.94 2.44
2171 2277 5.695816 GCATGCCACAAGAAAATACTTTTGA 59.304 36.000 6.36 0.00 31.66 2.69
2173 2279 7.095102 GCATGCCACAAGAAAATACTTTTGAAT 60.095 33.333 6.36 0.00 31.66 2.57
2175 2281 8.140677 TGCCACAAGAAAATACTTTTGAATTG 57.859 30.769 0.00 0.00 31.66 2.32
2176 2282 7.226325 TGCCACAAGAAAATACTTTTGAATTGG 59.774 33.333 0.00 0.00 31.66 3.16
2205 2311 9.744468 TGAATTCAAAATCATGATGAGCTAATG 57.256 29.630 9.46 1.72 0.00 1.90
2207 2313 9.967346 AATTCAAAATCATGATGAGCTAATGAG 57.033 29.630 9.46 0.00 34.02 2.90
2208 2314 8.515695 TTCAAAATCATGATGAGCTAATGAGT 57.484 30.769 9.46 0.00 34.02 3.41
2210 2316 8.618677 TCAAAATCATGATGAGCTAATGAGTTC 58.381 33.333 9.46 0.00 37.57 3.01
2211 2317 8.622157 CAAAATCATGATGAGCTAATGAGTTCT 58.378 33.333 9.46 3.94 37.57 3.01
2212 2318 7.966246 AATCATGATGAGCTAATGAGTTCTC 57.034 36.000 9.46 0.00 34.02 2.87
2215 2321 4.691175 TGATGAGCTAATGAGTTCTCTGC 58.309 43.478 0.00 1.78 34.19 4.26
2229 2335 3.317603 TCTCTGCGTGTTGATGATGAA 57.682 42.857 0.00 0.00 0.00 2.57
2244 2350 4.470334 TGATGAACAGATGAACGATGGA 57.530 40.909 0.00 0.00 0.00 3.41
2388 2494 0.824109 TGTCCATCCTGATCACGACC 59.176 55.000 0.00 0.00 0.00 4.79
2502 2608 4.334118 TCGTCCTCGTCCCACGGA 62.334 66.667 0.00 0.00 42.81 4.69
2526 2632 4.735132 CTCCCTTTCGCGTCCGCA 62.735 66.667 12.58 0.00 42.06 5.69
2739 2845 3.640407 AAGAGCTCCTTGCCGGCA 61.640 61.111 29.03 29.03 44.23 5.69
3002 3108 0.663688 AAGTGATCGATCGACCTCGG 59.336 55.000 22.06 0.00 39.13 4.63
3005 3111 3.596667 GATCGATCGACCTCGGGCG 62.597 68.421 22.06 4.45 39.13 6.13
3090 3200 6.200097 ACTTCGTTTTGGTGTTATGAAATTGC 59.800 34.615 0.00 0.00 0.00 3.56
3145 3257 8.643324 AGTCTAGGGATTAGTTGATGTACAATC 58.357 37.037 0.00 0.00 40.76 2.67
3209 3323 5.240891 TGTGAGAAAGAAAGCGATCAGATT 58.759 37.500 0.00 0.00 0.00 2.40
3305 3419 4.960469 ACTTGATCTTAGGGTTCCATACGA 59.040 41.667 0.00 0.00 0.00 3.43
3392 3506 7.235935 TCATATAAATACCAGGGTTACTCCG 57.764 40.000 0.00 0.00 37.00 4.63
3412 3526 3.447586 CCGTCTCACTGAGAAATAGGGAA 59.552 47.826 10.45 0.00 40.59 3.97
3416 3530 6.039941 CGTCTCACTGAGAAATAGGGAACTAT 59.960 42.308 10.45 0.00 43.61 2.12
3442 3556 3.866651 ACATAGAGGCACAAGACATCAC 58.133 45.455 0.00 0.00 0.00 3.06
3464 3578 5.872617 CACCGAGGTGTTCTTATCAATAACA 59.127 40.000 13.82 0.00 40.91 2.41
3487 3601 7.170965 ACACAGGAATGATTAAAGTGAGACAT 58.829 34.615 9.39 0.00 0.00 3.06
3530 3644 6.724893 TTAGGATTACAACGAGATGGATGA 57.275 37.500 0.00 0.00 0.00 2.92
3561 3675 1.802960 GTCGATGGCATGGATGATGAC 59.197 52.381 15.38 0.00 41.10 3.06
3562 3676 1.162698 CGATGGCATGGATGATGACC 58.837 55.000 3.81 0.00 39.75 4.02
3632 3746 3.197983 AGACCCTTATGTTGATTCCCCA 58.802 45.455 0.00 0.00 0.00 4.96
3644 3758 2.876033 ATTCCCCATCCGGACCCCTT 62.876 60.000 6.12 0.00 0.00 3.95
3690 3804 5.655090 TGTTTCGTATGGTGGAATCTCTCTA 59.345 40.000 0.00 0.00 0.00 2.43
3703 3817 6.612863 TGGAATCTCTCTATTTGTCAGATCCA 59.387 38.462 0.00 0.00 0.00 3.41
3717 3831 3.117436 TCAGATCCAATTGCATGGGATGA 60.117 43.478 16.37 10.55 41.39 2.92
3725 3839 5.105228 CCAATTGCATGGGATGAAAGTAGTT 60.105 40.000 0.00 0.00 36.79 2.24
3738 3852 1.657804 AGTAGTTGACCCAAGGGAGG 58.342 55.000 13.15 0.00 38.96 4.30
3771 3885 0.532640 TATGACCGCCGCTACGAGTA 60.533 55.000 0.00 0.00 34.06 2.59
3803 3917 5.410746 TCGTACTACACATCGTCTTCTCTTT 59.589 40.000 0.00 0.00 0.00 2.52
3862 3976 3.199677 TCGTATGGAAGGTTTTATGGCG 58.800 45.455 0.00 0.00 0.00 5.69
3881 3995 4.142271 TGGCGTCCAATCAACATATTTTCC 60.142 41.667 0.00 0.00 0.00 3.13
3965 4079 3.040147 TCAAACAAAAACGGGCAAACA 57.960 38.095 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.993370 GAAAACTCGGATCGGTCACTG 59.007 52.381 0.00 0.00 0.00 3.66
1 2 1.402456 CGAAAACTCGGATCGGTCACT 60.402 52.381 0.00 0.00 33.15 3.41
2 3 0.989890 CGAAAACTCGGATCGGTCAC 59.010 55.000 0.00 0.00 33.15 3.67
9 10 3.314541 AGTAACAGCGAAAACTCGGAT 57.685 42.857 0.00 0.00 0.00 4.18
17 18 3.490526 GGTCAAACGTAGTAACAGCGAAA 59.509 43.478 0.00 0.00 45.00 3.46
18 19 3.052036 GGTCAAACGTAGTAACAGCGAA 58.948 45.455 0.00 0.00 45.00 4.70
24 25 1.723003 CAGCGGGTCAAACGTAGTAAC 59.277 52.381 0.00 0.00 45.00 2.50
66 67 1.660575 GACGCACACACGCAGTACT 60.661 57.895 0.00 0.00 41.61 2.73
67 68 1.947146 TGACGCACACACGCAGTAC 60.947 57.895 0.00 0.00 41.61 2.73
104 109 7.762615 ACGTAAAAATATGGTCTGAATTCTCGA 59.237 33.333 7.05 0.53 0.00 4.04
105 110 7.846107 CACGTAAAAATATGGTCTGAATTCTCG 59.154 37.037 7.05 0.00 0.00 4.04
106 111 8.122952 CCACGTAAAAATATGGTCTGAATTCTC 58.877 37.037 7.05 0.00 0.00 2.87
113 118 5.523916 CCTCTCCACGTAAAAATATGGTCTG 59.476 44.000 0.00 0.00 33.67 3.51
114 119 5.424252 TCCTCTCCACGTAAAAATATGGTCT 59.576 40.000 0.00 0.00 33.67 3.85
115 120 5.667466 TCCTCTCCACGTAAAAATATGGTC 58.333 41.667 0.00 0.00 33.67 4.02
116 121 5.424252 TCTCCTCTCCACGTAAAAATATGGT 59.576 40.000 0.00 0.00 33.67 3.55
118 123 6.816640 TGTTCTCCTCTCCACGTAAAAATATG 59.183 38.462 0.00 0.00 0.00 1.78
175 194 3.664025 TTCAGCCAGCCATCGGTCG 62.664 63.158 0.00 0.00 0.00 4.79
177 196 2.045926 GTTCAGCCAGCCATCGGT 60.046 61.111 0.00 0.00 0.00 4.69
178 197 1.033746 ATTGTTCAGCCAGCCATCGG 61.034 55.000 0.00 0.00 0.00 4.18
179 198 0.813184 AATTGTTCAGCCAGCCATCG 59.187 50.000 0.00 0.00 0.00 3.84
180 199 1.135721 GGAATTGTTCAGCCAGCCATC 59.864 52.381 0.00 0.00 0.00 3.51
181 200 1.188863 GGAATTGTTCAGCCAGCCAT 58.811 50.000 0.00 0.00 0.00 4.40
182 201 1.243342 CGGAATTGTTCAGCCAGCCA 61.243 55.000 0.00 0.00 0.00 4.75
183 202 0.960364 TCGGAATTGTTCAGCCAGCC 60.960 55.000 0.00 0.00 0.00 4.85
184 203 1.064654 GATCGGAATTGTTCAGCCAGC 59.935 52.381 0.00 0.00 0.00 4.85
185 204 2.096496 GTGATCGGAATTGTTCAGCCAG 59.904 50.000 0.00 0.00 0.00 4.85
186 205 2.083774 GTGATCGGAATTGTTCAGCCA 58.916 47.619 0.00 0.00 0.00 4.75
187 206 1.401905 GGTGATCGGAATTGTTCAGCC 59.598 52.381 0.00 0.00 32.57 4.85
188 207 2.083774 TGGTGATCGGAATTGTTCAGC 58.916 47.619 1.81 1.81 36.87 4.26
189 208 3.338249 ACTGGTGATCGGAATTGTTCAG 58.662 45.455 0.00 0.00 0.00 3.02
190 209 3.417069 ACTGGTGATCGGAATTGTTCA 57.583 42.857 0.00 0.00 0.00 3.18
191 210 3.670627 GCAACTGGTGATCGGAATTGTTC 60.671 47.826 0.00 0.00 0.00 3.18
192 211 2.228822 GCAACTGGTGATCGGAATTGTT 59.771 45.455 0.00 0.00 0.00 2.83
193 212 1.812571 GCAACTGGTGATCGGAATTGT 59.187 47.619 0.00 0.00 0.00 2.71
194 213 2.086869 AGCAACTGGTGATCGGAATTG 58.913 47.619 0.00 0.00 0.00 2.32
195 214 2.489329 CAAGCAACTGGTGATCGGAATT 59.511 45.455 0.00 0.00 0.00 2.17
196 215 2.086869 CAAGCAACTGGTGATCGGAAT 58.913 47.619 0.00 0.00 0.00 3.01
197 216 1.522668 CAAGCAACTGGTGATCGGAA 58.477 50.000 0.00 0.00 0.00 4.30
198 217 0.955428 GCAAGCAACTGGTGATCGGA 60.955 55.000 0.00 0.00 0.00 4.55
199 218 0.957395 AGCAAGCAACTGGTGATCGG 60.957 55.000 0.00 0.00 0.00 4.18
200 219 0.877071 AAGCAAGCAACTGGTGATCG 59.123 50.000 0.00 0.00 0.00 3.69
201 220 2.157738 AGAAGCAAGCAACTGGTGATC 58.842 47.619 0.00 0.00 0.00 2.92
202 221 2.157738 GAGAAGCAAGCAACTGGTGAT 58.842 47.619 0.00 0.00 0.00 3.06
203 222 1.597742 GAGAAGCAAGCAACTGGTGA 58.402 50.000 0.00 0.00 0.00 4.02
204 223 0.595095 GGAGAAGCAAGCAACTGGTG 59.405 55.000 0.00 0.00 0.00 4.17
205 224 0.886490 CGGAGAAGCAAGCAACTGGT 60.886 55.000 0.00 0.00 0.00 4.00
249 268 2.593436 CGTTTGGGGCCGTCTTGT 60.593 61.111 0.00 0.00 0.00 3.16
250 269 1.241315 ATTCGTTTGGGGCCGTCTTG 61.241 55.000 0.00 0.00 0.00 3.02
253 272 1.238625 TGAATTCGTTTGGGGCCGTC 61.239 55.000 0.00 0.00 0.00 4.79
261 281 3.155998 CAGCTAGCGTTGAATTCGTTTG 58.844 45.455 9.55 0.00 0.00 2.93
329 361 3.103742 AGAGGCTTTGACTTAGCTAGCT 58.896 45.455 23.12 23.12 38.67 3.32
330 362 3.132111 AGAGAGGCTTTGACTTAGCTAGC 59.868 47.826 6.62 6.62 38.67 3.42
331 363 4.644685 AGAGAGAGGCTTTGACTTAGCTAG 59.355 45.833 0.00 0.00 38.67 3.42
332 364 4.605183 AGAGAGAGGCTTTGACTTAGCTA 58.395 43.478 0.00 0.00 38.67 3.32
333 365 3.440127 AGAGAGAGGCTTTGACTTAGCT 58.560 45.455 0.00 0.00 38.67 3.32
356 388 0.541863 TCATCCTTCCCTTTCGCTCC 59.458 55.000 0.00 0.00 0.00 4.70
381 413 0.735978 CGTGCGACCTGCTTCATACA 60.736 55.000 0.00 0.00 46.63 2.29
382 414 0.736325 ACGTGCGACCTGCTTCATAC 60.736 55.000 0.00 0.00 46.63 2.39
383 415 0.457853 GACGTGCGACCTGCTTCATA 60.458 55.000 0.00 0.00 46.63 2.15
384 416 1.738099 GACGTGCGACCTGCTTCAT 60.738 57.895 0.00 0.00 46.63 2.57
385 417 2.355837 GACGTGCGACCTGCTTCA 60.356 61.111 0.00 0.00 46.63 3.02
386 418 3.112709 GGACGTGCGACCTGCTTC 61.113 66.667 0.00 0.00 46.63 3.86
606 643 4.031129 CAGACCTGCCTGCCTGCT 62.031 66.667 0.00 0.00 0.00 4.24
609 646 3.325753 GTCCAGACCTGCCTGCCT 61.326 66.667 0.00 0.00 32.97 4.75
610 647 4.767255 CGTCCAGACCTGCCTGCC 62.767 72.222 0.00 0.00 32.97 4.85
613 650 4.640690 ACCCGTCCAGACCTGCCT 62.641 66.667 0.00 0.00 0.00 4.75
614 651 4.394712 CACCCGTCCAGACCTGCC 62.395 72.222 0.00 0.00 0.00 4.85
617 654 1.797018 TACCTCACCCGTCCAGACCT 61.797 60.000 0.00 0.00 0.00 3.85
618 655 1.304713 TACCTCACCCGTCCAGACC 60.305 63.158 0.00 0.00 0.00 3.85
620 657 1.681327 GCTACCTCACCCGTCCAGA 60.681 63.158 0.00 0.00 0.00 3.86
621 658 1.682684 AGCTACCTCACCCGTCCAG 60.683 63.158 0.00 0.00 0.00 3.86
622 659 1.982395 CAGCTACCTCACCCGTCCA 60.982 63.158 0.00 0.00 0.00 4.02
624 661 2.184579 GCAGCTACCTCACCCGTC 59.815 66.667 0.00 0.00 0.00 4.79
625 662 3.391382 GGCAGCTACCTCACCCGT 61.391 66.667 0.00 0.00 0.00 5.28
627 664 2.378634 ATGGGCAGCTACCTCACCC 61.379 63.158 2.19 0.19 41.24 4.61
629 666 0.179062 CTCATGGGCAGCTACCTCAC 60.179 60.000 2.19 0.00 0.00 3.51
630 667 1.340399 CCTCATGGGCAGCTACCTCA 61.340 60.000 2.19 0.00 0.00 3.86
631 668 1.449353 CCTCATGGGCAGCTACCTC 59.551 63.158 2.19 0.00 0.00 3.85
632 669 3.652687 CCTCATGGGCAGCTACCT 58.347 61.111 2.19 0.00 0.00 3.08
700 756 1.537889 TGGTTCCCGTCCAGACCAT 60.538 57.895 0.00 0.00 37.26 3.55
726 788 2.024590 AACCTACTATCACGGCGGCC 62.025 60.000 13.24 9.54 0.00 6.13
738 800 1.205055 GCCTGGCTCCTTAACCTACT 58.795 55.000 12.43 0.00 0.00 2.57
805 874 3.469739 GCCGGGGATTAAACTAATCGAA 58.530 45.455 2.18 0.00 44.24 3.71
808 877 3.064931 CTCGCCGGGGATTAAACTAATC 58.935 50.000 22.85 0.00 42.94 1.75
943 1015 2.637947 GAGATGGAGGGAGCTTTGTTC 58.362 52.381 0.00 0.00 0.00 3.18
958 1030 4.024698 GCAGCTAGCCACGAGATG 57.975 61.111 12.13 1.95 37.23 2.90
967 1039 3.005554 TCACAAAGATCAAGCAGCTAGC 58.994 45.455 6.62 6.62 46.19 3.42
969 1041 3.999001 CAGTCACAAAGATCAAGCAGCTA 59.001 43.478 0.00 0.00 0.00 3.32
970 1042 2.812591 CAGTCACAAAGATCAAGCAGCT 59.187 45.455 0.00 0.00 0.00 4.24
971 1043 2.810274 TCAGTCACAAAGATCAAGCAGC 59.190 45.455 0.00 0.00 0.00 5.25
972 1044 4.094590 GGATCAGTCACAAAGATCAAGCAG 59.905 45.833 0.00 0.00 39.85 4.24
974 1046 4.005650 TGGATCAGTCACAAAGATCAAGC 58.994 43.478 0.00 0.00 39.85 4.01
975 1047 5.296283 GGATGGATCAGTCACAAAGATCAAG 59.704 44.000 0.00 0.00 39.85 3.02
976 1048 5.188434 GGATGGATCAGTCACAAAGATCAA 58.812 41.667 0.00 0.00 39.85 2.57
977 1049 4.225717 TGGATGGATCAGTCACAAAGATCA 59.774 41.667 0.00 0.00 39.85 2.92
978 1050 4.774124 TGGATGGATCAGTCACAAAGATC 58.226 43.478 0.00 0.00 37.91 2.75
979 1051 4.849813 TGGATGGATCAGTCACAAAGAT 57.150 40.909 0.00 0.00 0.00 2.40
980 1052 4.520179 CATGGATGGATCAGTCACAAAGA 58.480 43.478 0.00 0.00 0.00 2.52
981 1053 4.895224 CATGGATGGATCAGTCACAAAG 57.105 45.455 0.00 0.00 0.00 2.77
1066 1138 4.511527 AGAAGGAGCAGATTATGTGTGTG 58.488 43.478 0.00 0.00 0.00 3.82
1087 1161 6.166279 TGCATCTAGTGGACAACTTAAAGAG 58.834 40.000 0.00 0.00 40.56 2.85
1088 1162 6.109156 TGCATCTAGTGGACAACTTAAAGA 57.891 37.500 0.00 0.00 40.56 2.52
1101 1175 2.872245 CCGGGTTAACATGCATCTAGTG 59.128 50.000 8.10 0.00 0.00 2.74
1153 1232 1.996292 ACACGTTCATCGATCACCAG 58.004 50.000 0.00 0.00 42.86 4.00
1156 1235 2.159282 AGGGTACACGTTCATCGATCAC 60.159 50.000 0.00 0.00 42.86 3.06
1192 1271 8.744008 TTAAGTTACAACTCGATCTCAAGAAG 57.256 34.615 0.00 0.00 38.57 2.85
1215 1294 6.816140 GCAGGCCAAACAATTAAAGCTAATTA 59.184 34.615 5.01 0.00 35.88 1.40
1281 1360 3.689161 TGATCGAATTTCTTTGCGTGGAT 59.311 39.130 0.00 0.00 0.00 3.41
1322 1401 7.661437 AGTTTGACTTGCAGATCATAGTTTGTA 59.339 33.333 3.09 0.00 0.00 2.41
1324 1403 6.800408 CAGTTTGACTTGCAGATCATAGTTTG 59.200 38.462 3.09 0.00 0.00 2.93
1325 1404 6.712095 TCAGTTTGACTTGCAGATCATAGTTT 59.288 34.615 3.09 0.00 0.00 2.66
1338 1423 4.889832 AAACAGCTCTCAGTTTGACTTG 57.110 40.909 0.00 0.00 36.65 3.16
1347 1432 5.293079 GCACTCCTAATTAAACAGCTCTCAG 59.707 44.000 0.00 0.00 0.00 3.35
1387 1472 9.956640 TCTTAACTTGCTTCTACTACTAGTACT 57.043 33.333 0.00 0.00 0.00 2.73
1396 1481 8.239998 GCAATTCATTCTTAACTTGCTTCTACT 58.760 33.333 0.00 0.00 36.83 2.57
1397 1482 8.023128 TGCAATTCATTCTTAACTTGCTTCTAC 58.977 33.333 6.62 0.00 39.64 2.59
1398 1483 8.023128 GTGCAATTCATTCTTAACTTGCTTCTA 58.977 33.333 6.62 0.00 39.64 2.10
1410 1495 9.729281 ATCTTTAATTTGGTGCAATTCATTCTT 57.271 25.926 0.00 0.00 0.00 2.52
1441 1528 7.990314 TGATTCTTCGTAAATAATCCCACATGA 59.010 33.333 0.00 0.00 30.68 3.07
1474 1562 8.078596 TCATTAGATGATGAGAACTGTACATCG 58.921 37.037 0.00 0.00 41.95 3.84
1806 1904 2.749044 TCGGTCTCGGTTCCGGAG 60.749 66.667 3.34 7.67 45.79 4.63
1812 1910 4.666253 TCGGGGTCGGTCTCGGTT 62.666 66.667 0.00 0.00 36.95 4.44
1869 1967 4.228567 TGCCTGTTGTCGCCGTCA 62.229 61.111 0.00 0.00 0.00 4.35
1902 2000 1.153429 GTTCATAAGGGGCGTCGCT 60.153 57.895 18.11 0.00 37.82 4.93
1905 2003 0.539986 TGAGGTTCATAAGGGGCGTC 59.460 55.000 0.00 0.00 0.00 5.19
2117 2215 4.118093 ACTGTATGTTGTACTATGCGCA 57.882 40.909 14.96 14.96 0.00 6.09
2143 2249 5.797051 AGTATTTTCTTGTGGCATGCAATT 58.203 33.333 21.36 2.43 0.00 2.32
2169 2275 9.557061 TCATGATTTTGAATTCAAACCAATTCA 57.443 25.926 28.78 23.61 46.44 2.57
2173 2279 9.210329 CTCATCATGATTTTGAATTCAAACCAA 57.790 29.630 28.78 17.44 44.56 3.67
2175 2281 7.548075 AGCTCATCATGATTTTGAATTCAAACC 59.452 33.333 28.78 22.93 44.56 3.27
2176 2282 8.475331 AGCTCATCATGATTTTGAATTCAAAC 57.525 30.769 28.78 19.98 44.56 2.93
2204 2310 2.035832 TCATCAACACGCAGAGAACTCA 59.964 45.455 4.64 0.00 0.00 3.41
2205 2311 2.677199 TCATCAACACGCAGAGAACTC 58.323 47.619 0.00 0.00 0.00 3.01
2207 2313 2.995939 TCATCATCAACACGCAGAGAAC 59.004 45.455 0.00 0.00 0.00 3.01
2208 2314 3.317603 TCATCATCAACACGCAGAGAA 57.682 42.857 0.00 0.00 0.00 2.87
2210 2316 2.738314 TGTTCATCATCAACACGCAGAG 59.262 45.455 0.00 0.00 0.00 3.35
2211 2317 2.738314 CTGTTCATCATCAACACGCAGA 59.262 45.455 0.00 0.00 30.49 4.26
2212 2318 2.738314 TCTGTTCATCATCAACACGCAG 59.262 45.455 0.00 0.00 30.49 5.18
2215 2321 5.319139 GTTCATCTGTTCATCATCAACACG 58.681 41.667 0.00 0.00 30.49 4.49
2229 2335 1.210234 TGGCATCCATCGTTCATCTGT 59.790 47.619 0.00 0.00 0.00 3.41
2268 2374 1.641192 GGGTTCCCCTTGGAGATCTTT 59.359 52.381 0.00 0.00 43.07 2.52
2388 2494 2.507102 CTGTGCGTGCCCTCGTAG 60.507 66.667 0.00 0.00 0.00 3.51
2502 2608 2.430367 GCGAAAGGGAGGTGGTGT 59.570 61.111 0.00 0.00 0.00 4.16
2739 2845 2.724273 GCCGAAATGCTGCCCCATT 61.724 57.895 0.00 0.00 37.03 3.16
2811 2917 0.240411 ACGTTCTCTGCAGGTACGAC 59.760 55.000 29.35 15.63 34.29 4.34
2906 3012 2.203788 ACTGGAAGCTCGGGTCCA 60.204 61.111 4.80 4.80 41.72 4.02
3022 3128 6.527423 GGATAAATCCACGGACCTATAAACA 58.473 40.000 4.04 0.00 46.38 2.83
3084 3192 2.290896 TGTCGATCTCCCAAGGCAATTT 60.291 45.455 0.00 0.00 0.00 1.82
3090 3200 0.833287 ACCATGTCGATCTCCCAAGG 59.167 55.000 0.00 0.00 0.00 3.61
3145 3257 3.319689 TCCATGCCATCTATGTGCAATTG 59.680 43.478 0.00 0.00 37.46 2.32
3157 3269 2.617308 CAGTTGACTCATCCATGCCATC 59.383 50.000 0.00 0.00 0.00 3.51
3209 3323 1.836802 TGTGCATATACAGCTGGGACA 59.163 47.619 19.93 14.01 0.00 4.02
3392 3506 5.669164 AGTTCCCTATTTCTCAGTGAGAC 57.331 43.478 22.57 8.39 38.51 3.36
3412 3526 5.189736 TCTTGTGCCTCTATGTCCAAATAGT 59.810 40.000 0.00 0.00 32.82 2.12
3416 3530 3.072330 TGTCTTGTGCCTCTATGTCCAAA 59.928 43.478 0.00 0.00 0.00 3.28
3418 3532 2.256306 TGTCTTGTGCCTCTATGTCCA 58.744 47.619 0.00 0.00 0.00 4.02
3419 3533 3.118629 TGATGTCTTGTGCCTCTATGTCC 60.119 47.826 0.00 0.00 0.00 4.02
3464 3578 8.641498 AAATGTCTCACTTTAATCATTCCTGT 57.359 30.769 0.00 0.00 0.00 4.00
3530 3644 1.202758 TGCCATCGACACCAACTCTTT 60.203 47.619 0.00 0.00 0.00 2.52
3561 3675 0.592500 CACGACGTCGATCTCCATGG 60.593 60.000 41.52 4.97 43.02 3.66
3562 3676 0.592500 CCACGACGTCGATCTCCATG 60.593 60.000 41.52 26.52 43.02 3.66
3644 3758 0.041238 ATCAGAACCTCAGGACCGGA 59.959 55.000 9.46 0.00 0.00 5.14
3648 3762 5.292101 CGAAACAATATCAGAACCTCAGGAC 59.708 44.000 0.00 0.00 0.00 3.85
3650 3764 5.178797 ACGAAACAATATCAGAACCTCAGG 58.821 41.667 0.00 0.00 0.00 3.86
3651 3765 7.042456 CCATACGAAACAATATCAGAACCTCAG 60.042 40.741 0.00 0.00 0.00 3.35
3690 3804 4.141801 CCCATGCAATTGGATCTGACAAAT 60.142 41.667 9.80 0.00 39.25 2.32
3703 3817 5.716228 TCAACTACTTTCATCCCATGCAATT 59.284 36.000 0.00 0.00 0.00 2.32
3717 3831 2.375509 CCTCCCTTGGGTCAACTACTTT 59.624 50.000 5.51 0.00 0.00 2.66
3761 3875 1.536149 GAGCACAACTACTCGTAGCG 58.464 55.000 4.08 0.00 36.66 4.26
3771 3885 3.669824 CGATGTGTAGTACGAGCACAACT 60.670 47.826 18.69 8.15 44.73 3.16
3785 3899 5.462530 TCCAAAAGAGAAGACGATGTGTA 57.537 39.130 0.00 0.00 0.00 2.90
3803 3917 0.036732 AACTGCATTCGGCTCTCCAA 59.963 50.000 0.00 0.00 45.15 3.53
3862 3976 6.279513 TGGTGGAAAATATGTTGATTGGAC 57.720 37.500 0.00 0.00 0.00 4.02
3881 3995 7.874940 TCATTAGAGAACACTCATTTTTGGTG 58.125 34.615 0.00 0.00 37.05 4.17


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

AutoCloner maintained by Alex Coulton.