Multiple sequence alignment - TraesCS3B01G166900

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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 TraesCS3B01G166900 chr3B 100.000 2816 0 0 1 2816 166716756 166713941 0.000000e+00 5201.0
1 TraesCS3B01G166900 chr3D 92.862 1429 47 18 686 2108 114074749 114076128 0.000000e+00 2023.0
2 TraesCS3B01G166900 chr3D 85.863 672 37 29 2156 2816 114076127 114076751 0.000000e+00 662.0
3 TraesCS3B01G166900 chr3D 97.297 37 1 0 651 687 114074629 114074665 2.340000e-06 63.9
4 TraesCS3B01G166900 chr3A 91.395 1290 71 21 654 1926 109867862 109869128 0.000000e+00 1731.0
5 TraesCS3B01G166900 chr3A 85.151 431 37 10 2400 2816 109869317 109869734 1.560000e-112 416.0
6 TraesCS3B01G166900 chr3A 85.714 147 15 2 1964 2104 109869120 109869266 1.750000e-32 150.0
7 TraesCS3B01G166900 chr2D 89.570 604 41 4 40 636 598626690 598627278 0.000000e+00 747.0
8 TraesCS3B01G166900 chr6B 82.580 597 90 9 40 628 87583588 87584178 5.380000e-142 514.0
9 TraesCS3B01G166900 chr6B 92.661 109 8 0 1066 1174 10902561 10902669 1.040000e-34 158.0
10 TraesCS3B01G166900 chr6B 92.523 107 7 1 1068 1174 10937317 10937212 4.860000e-33 152.0
11 TraesCS3B01G166900 chr7A 77.889 597 115 11 40 626 149263149 149263738 3.450000e-94 355.0
12 TraesCS3B01G166900 chr5A 91.346 104 9 0 1066 1169 528481094 528480991 2.920000e-30 143.0


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 TraesCS3B01G166900 chr3B 166713941 166716756 2815 True 5201.000000 5201 100.000000 1 2816 1 chr3B.!!$R1 2815
1 TraesCS3B01G166900 chr3D 114074629 114076751 2122 False 916.300000 2023 92.007333 651 2816 3 chr3D.!!$F1 2165
2 TraesCS3B01G166900 chr3A 109867862 109869734 1872 False 765.666667 1731 87.420000 654 2816 3 chr3A.!!$F1 2162
3 TraesCS3B01G166900 chr2D 598626690 598627278 588 False 747.000000 747 89.570000 40 636 1 chr2D.!!$F1 596
4 TraesCS3B01G166900 chr6B 87583588 87584178 590 False 514.000000 514 82.580000 40 628 1 chr6B.!!$F2 588
5 TraesCS3B01G166900 chr7A 149263149 149263738 589 False 355.000000 355 77.889000 40 626 1 chr7A.!!$F1 586

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
637 645 0.033699 ATCCCCTTCAAGCTTGCCTC 60.034 55.0 21.99 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2482 0.03563 CTGAAGGAACTGGCTGGGAG 60.036 60.0 0.0 0.0 40.86 4.3 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
25 26 3.057548 CTTGGTCAGCATGCGCCA 61.058 61.111 21.82 21.82 38.66 5.69
26 27 2.361483 TTGGTCAGCATGCGCCAT 60.361 55.556 24.68 2.13 39.74 4.40
27 28 2.607668 CTTGGTCAGCATGCGCCATG 62.608 60.000 24.68 22.66 43.91 3.66
34 35 4.201679 CATGCGCCATGCCTGTGG 62.202 66.667 4.18 0.00 45.60 4.17
35 36 4.746309 ATGCGCCATGCCTGTGGT 62.746 61.111 4.18 0.00 45.60 4.16
131 132 8.092687 AGCCAATGCATCATATTATTTTTCTCC 58.907 33.333 0.00 0.00 41.13 3.71
136 137 8.922931 TGCATCATATTATTTTTCTCCTGCTA 57.077 30.769 0.00 0.00 0.00 3.49
170 171 8.152898 CAGAACCTACAGATCATCATTCCAATA 58.847 37.037 0.00 0.00 0.00 1.90
215 216 4.397417 AGATCAAAGCAGGACATAGCAAAC 59.603 41.667 0.00 0.00 0.00 2.93
225 226 3.006940 GACATAGCAAACGTTGGGATGA 58.993 45.455 0.00 0.00 0.00 2.92
231 232 0.179004 AAACGTTGGGATGACCTGCA 60.179 50.000 0.00 0.00 41.11 4.41
303 304 1.620323 GCCAACCCTGAATTTTCTGCT 59.380 47.619 0.00 0.00 0.00 4.24
310 311 6.313519 ACCCTGAATTTTCTGCTAGATACA 57.686 37.500 0.00 0.00 0.00 2.29
346 347 4.561105 TCAAAAACGTGTTTCCTTGCTTT 58.439 34.783 0.00 0.00 31.45 3.51
362 363 2.304470 TGCTTTGCCTACATACACTGGA 59.696 45.455 0.00 0.00 0.00 3.86
368 369 2.092914 GCCTACATACACTGGAAAGCCT 60.093 50.000 0.00 0.00 34.31 4.58
369 370 3.134081 GCCTACATACACTGGAAAGCCTA 59.866 47.826 0.00 0.00 34.31 3.93
370 371 4.740934 GCCTACATACACTGGAAAGCCTAG 60.741 50.000 0.00 0.00 34.31 3.02
371 372 4.649674 CCTACATACACTGGAAAGCCTAGA 59.350 45.833 0.00 0.00 34.31 2.43
374 375 6.163135 ACATACACTGGAAAGCCTAGATAC 57.837 41.667 0.00 0.00 34.31 2.24
437 445 3.131155 TGCCTTTGCACTTGGCTG 58.869 55.556 20.07 0.00 44.23 4.85
446 454 1.133945 TGCACTTGGCTGGTGTTCTTA 60.134 47.619 10.83 0.00 45.15 2.10
503 511 0.685097 GGCCCGAGCATACCTCATAA 59.315 55.000 0.00 0.00 40.78 1.90
541 549 2.165234 GCAGTGATGTAGCACTCTCTCA 59.835 50.000 0.00 0.00 45.54 3.27
553 561 3.122111 GCACTCTCTCACGAAGCTTTAAC 59.878 47.826 0.00 0.00 0.00 2.01
602 610 2.296073 AATGGTTAAAACTCGGGGCA 57.704 45.000 0.00 0.00 0.00 5.36
632 640 3.933861 ATACGAATCCCCTTCAAGCTT 57.066 42.857 0.00 0.00 33.10 3.74
633 641 1.826385 ACGAATCCCCTTCAAGCTTG 58.174 50.000 20.81 20.81 33.10 4.01
635 643 0.820226 GAATCCCCTTCAAGCTTGCC 59.180 55.000 21.99 0.00 33.78 4.52
636 644 0.411058 AATCCCCTTCAAGCTTGCCT 59.589 50.000 21.99 0.00 0.00 4.75
637 645 0.033699 ATCCCCTTCAAGCTTGCCTC 60.034 55.000 21.99 0.00 0.00 4.70
638 646 1.075482 CCCCTTCAAGCTTGCCTCA 59.925 57.895 21.99 0.99 0.00 3.86
639 647 0.964358 CCCCTTCAAGCTTGCCTCAG 60.964 60.000 21.99 13.38 0.00 3.35
640 648 0.964358 CCCTTCAAGCTTGCCTCAGG 60.964 60.000 21.99 20.35 0.00 3.86
650 658 3.719121 GCCTCAGGCCTCTTCAGA 58.281 61.111 3.37 0.00 44.06 3.27
651 659 1.521616 GCCTCAGGCCTCTTCAGAG 59.478 63.158 3.37 6.12 44.06 3.35
652 660 0.975040 GCCTCAGGCCTCTTCAGAGA 60.975 60.000 16.65 2.82 44.06 3.10
697 790 6.595794 CCTCGAGCGTTCTAAATTTTAACAA 58.404 36.000 6.99 0.00 0.00 2.83
705 798 9.716484 GCGTTCTAAATTTTAACAAAAATACCG 57.284 29.630 13.41 0.00 33.47 4.02
736 829 9.845214 AGTATTATCCCACCTTCAGATATTACT 57.155 33.333 0.00 0.00 36.16 2.24
787 881 2.251893 GCTTCTACTGTCTACGTGTGC 58.748 52.381 0.00 0.00 0.00 4.57
923 1024 1.873698 CCGTATTTATCCCACCACCG 58.126 55.000 0.00 0.00 0.00 4.94
934 1036 0.964860 CCACCACCGCCAATCAATCA 60.965 55.000 0.00 0.00 0.00 2.57
935 1037 0.887247 CACCACCGCCAATCAATCAA 59.113 50.000 0.00 0.00 0.00 2.57
938 1040 1.402720 CCACCGCCAATCAATCAACAC 60.403 52.381 0.00 0.00 0.00 3.32
941 1043 1.811965 CCGCCAATCAATCAACACAGA 59.188 47.619 0.00 0.00 0.00 3.41
969 1075 2.824041 CCCGAGCCCCACAATTCG 60.824 66.667 0.00 0.00 0.00 3.34
986 1092 2.063979 CGCATCCCCCACTCCACTA 61.064 63.158 0.00 0.00 0.00 2.74
987 1093 1.410850 CGCATCCCCCACTCCACTAT 61.411 60.000 0.00 0.00 0.00 2.12
1124 1231 1.008652 CGTACGACGTGGTGGACAA 60.009 57.895 10.44 0.00 36.74 3.18
1197 1304 1.369321 GCCCATCGAGGACATCTCC 59.631 63.158 0.00 0.00 41.22 3.71
1260 1367 2.045045 TCCCTTCGCCATTGCCAG 60.045 61.111 0.00 0.00 0.00 4.85
1261 1368 2.045045 CCCTTCGCCATTGCCAGA 60.045 61.111 0.00 0.00 0.00 3.86
1262 1369 1.454479 CCCTTCGCCATTGCCAGAT 60.454 57.895 0.00 0.00 0.00 2.90
1263 1370 1.450531 CCCTTCGCCATTGCCAGATC 61.451 60.000 0.00 0.00 0.00 2.75
1264 1371 0.749091 CCTTCGCCATTGCCAGATCA 60.749 55.000 0.00 0.00 0.00 2.92
1265 1372 0.379669 CTTCGCCATTGCCAGATCAC 59.620 55.000 0.00 0.00 0.00 3.06
1266 1373 1.368345 TTCGCCATTGCCAGATCACG 61.368 55.000 0.00 0.00 0.00 4.35
1267 1374 2.410469 GCCATTGCCAGATCACGC 59.590 61.111 0.00 0.00 0.00 5.34
1268 1375 2.711311 CCATTGCCAGATCACGCG 59.289 61.111 3.53 3.53 0.00 6.01
1269 1376 2.023741 CATTGCCAGATCACGCGC 59.976 61.111 5.73 0.00 0.00 6.86
1270 1377 2.436469 ATTGCCAGATCACGCGCA 60.436 55.556 5.73 0.00 0.00 6.09
1271 1378 2.039974 ATTGCCAGATCACGCGCAA 61.040 52.632 5.73 10.03 44.62 4.85
1272 1379 2.257286 ATTGCCAGATCACGCGCAAC 62.257 55.000 5.73 0.00 43.44 4.17
1273 1380 3.121030 GCCAGATCACGCGCAACT 61.121 61.111 5.73 0.00 0.00 3.16
1274 1381 2.680913 GCCAGATCACGCGCAACTT 61.681 57.895 5.73 0.00 0.00 2.66
1275 1382 1.133253 CCAGATCACGCGCAACTTG 59.867 57.895 5.73 0.00 0.00 3.16
1276 1383 1.510623 CAGATCACGCGCAACTTGC 60.511 57.895 5.73 3.44 40.69 4.01
1277 1384 1.669115 AGATCACGCGCAACTTGCT 60.669 52.632 5.73 0.00 42.25 3.91
1278 1385 1.225854 GATCACGCGCAACTTGCTC 60.226 57.895 5.73 2.90 42.25 4.26
1361 1475 3.201266 TGGGATAACAATAACGGGCTTCT 59.799 43.478 0.00 0.00 0.00 2.85
1369 1483 4.215613 ACAATAACGGGCTTCTCTTGTTTC 59.784 41.667 0.00 0.00 0.00 2.78
1531 1645 2.809601 CGAAGAACCAGGCGGACG 60.810 66.667 2.43 0.00 35.59 4.79
1743 1857 1.663388 CGTGGCGCAGTACAACTCA 60.663 57.895 10.83 0.00 0.00 3.41
1817 1931 0.736325 GCCGCGTCTGACATGTAACT 60.736 55.000 4.92 0.00 0.00 2.24
1818 1932 0.992072 CCGCGTCTGACATGTAACTG 59.008 55.000 4.92 0.00 0.00 3.16
1819 1933 1.668919 CCGCGTCTGACATGTAACTGT 60.669 52.381 4.92 0.00 0.00 3.55
1820 1934 1.386748 CGCGTCTGACATGTAACTGTG 59.613 52.381 8.73 0.00 0.00 3.66
1821 1935 1.126846 GCGTCTGACATGTAACTGTGC 59.873 52.381 8.73 0.00 0.00 4.57
1822 1936 2.403259 CGTCTGACATGTAACTGTGCA 58.597 47.619 8.73 0.00 0.00 4.57
1823 1937 2.799978 CGTCTGACATGTAACTGTGCAA 59.200 45.455 8.73 0.00 0.00 4.08
1824 1938 3.120889 CGTCTGACATGTAACTGTGCAAG 60.121 47.826 8.73 0.00 0.00 4.01
1825 1939 2.807967 TCTGACATGTAACTGTGCAAGC 59.192 45.455 0.00 0.00 0.00 4.01
1826 1940 2.810274 CTGACATGTAACTGTGCAAGCT 59.190 45.455 0.00 0.00 0.00 3.74
1827 1941 3.213506 TGACATGTAACTGTGCAAGCTT 58.786 40.909 0.00 0.00 0.00 3.74
1828 1942 3.003585 TGACATGTAACTGTGCAAGCTTG 59.996 43.478 22.44 22.44 0.00 4.01
1829 1943 2.951642 ACATGTAACTGTGCAAGCTTGT 59.048 40.909 26.55 9.15 0.00 3.16
1830 1944 3.381272 ACATGTAACTGTGCAAGCTTGTT 59.619 39.130 26.55 15.16 0.00 2.83
1831 1945 3.419264 TGTAACTGTGCAAGCTTGTTG 57.581 42.857 26.55 16.03 0.00 3.33
1832 1946 2.119457 GTAACTGTGCAAGCTTGTTGC 58.881 47.619 26.55 14.89 45.11 4.17
1863 1994 7.327275 GGCTAGATTAATCAGTGAACTCGTATG 59.673 40.741 17.56 0.00 0.00 2.39
1889 2022 7.631717 AAGAGTGTCTTGTCTTTTAAGCTTT 57.368 32.000 3.20 0.00 34.98 3.51
1894 2027 8.994170 AGTGTCTTGTCTTTTAAGCTTTCTATC 58.006 33.333 3.20 0.00 0.00 2.08
1917 2050 1.145803 GCCGACGAATAATGGTAGCC 58.854 55.000 0.00 0.00 0.00 3.93
1929 2065 7.148573 CGAATAATGGTAGCCTATAAACTGCTG 60.149 40.741 0.00 0.00 36.57 4.41
1934 2070 2.924421 AGCCTATAAACTGCTGAAGCC 58.076 47.619 0.00 0.00 41.18 4.35
1937 2073 3.181496 GCCTATAAACTGCTGAAGCCAAC 60.181 47.826 0.00 0.00 41.18 3.77
1940 2076 5.294552 CCTATAAACTGCTGAAGCCAACTAC 59.705 44.000 0.00 0.00 41.18 2.73
1942 2078 2.464157 ACTGCTGAAGCCAACTACTC 57.536 50.000 0.00 0.00 41.18 2.59
1943 2079 1.002544 ACTGCTGAAGCCAACTACTCC 59.997 52.381 0.00 0.00 41.18 3.85
1944 2080 1.277557 CTGCTGAAGCCAACTACTCCT 59.722 52.381 0.00 0.00 41.18 3.69
1945 2081 2.497675 CTGCTGAAGCCAACTACTCCTA 59.502 50.000 0.00 0.00 41.18 2.94
1946 2082 2.497675 TGCTGAAGCCAACTACTCCTAG 59.502 50.000 0.00 0.00 41.18 3.02
1947 2083 2.498078 GCTGAAGCCAACTACTCCTAGT 59.502 50.000 0.00 0.00 32.76 2.57
1948 2084 3.677424 GCTGAAGCCAACTACTCCTAGTG 60.677 52.174 0.00 0.00 32.17 2.74
1949 2085 3.507411 TGAAGCCAACTACTCCTAGTGT 58.493 45.455 0.00 0.00 33.14 3.55
1971 2107 1.535028 CTGTTTTGCGCTGTATGGACA 59.465 47.619 9.73 3.22 0.00 4.02
1990 2126 0.740737 ATGCGAGCAATAAAGTGCCC 59.259 50.000 0.57 0.00 46.14 5.36
2043 2185 0.998727 GCCTGTTGCTTTCTTTCGCG 60.999 55.000 0.00 0.00 36.87 5.87
2054 2196 3.854286 TTCTTTCGCGTTTGAGAAGAC 57.146 42.857 5.77 0.00 35.28 3.01
2061 2203 1.531578 GCGTTTGAGAAGACTGTTCCC 59.468 52.381 0.00 0.00 0.00 3.97
2088 2230 8.674925 TGATACGTTTCCTATAAATATCCCCT 57.325 34.615 0.00 0.00 0.00 4.79
2104 2246 2.586079 CTGCTATCACACCGGCGG 60.586 66.667 27.06 27.06 0.00 6.13
2114 2256 4.096003 ACCGGCGGTGCTGCTAAT 62.096 61.111 33.71 1.44 32.98 1.73
2115 2257 2.824041 CCGGCGGTGCTGCTAATT 60.824 61.111 19.97 0.00 32.89 1.40
2116 2258 2.406616 CCGGCGGTGCTGCTAATTT 61.407 57.895 19.97 0.00 32.89 1.82
2117 2259 1.506262 CGGCGGTGCTGCTAATTTT 59.494 52.632 0.00 0.00 34.52 1.82
2118 2260 0.109319 CGGCGGTGCTGCTAATTTTT 60.109 50.000 0.00 0.00 34.52 1.94
2142 2284 5.772825 TTTTCTTTCCATGGACTGTTCTG 57.227 39.130 15.91 0.00 0.00 3.02
2143 2285 2.783135 TCTTTCCATGGACTGTTCTGC 58.217 47.619 15.91 0.00 0.00 4.26
2144 2286 2.373169 TCTTTCCATGGACTGTTCTGCT 59.627 45.455 15.91 0.00 0.00 4.24
2145 2287 2.189594 TTCCATGGACTGTTCTGCTG 57.810 50.000 15.91 0.00 0.00 4.41
2146 2288 0.321919 TCCATGGACTGTTCTGCTGC 60.322 55.000 11.44 0.00 0.00 5.25
2148 2290 1.065926 CCATGGACTGTTCTGCTGCTA 60.066 52.381 5.56 0.00 0.00 3.49
2149 2291 2.421107 CCATGGACTGTTCTGCTGCTAT 60.421 50.000 5.56 0.00 0.00 2.97
2151 2293 3.423539 TGGACTGTTCTGCTGCTATTT 57.576 42.857 0.00 0.00 0.00 1.40
2152 2294 3.076621 TGGACTGTTCTGCTGCTATTTG 58.923 45.455 0.00 0.00 0.00 2.32
2154 2296 3.126000 GGACTGTTCTGCTGCTATTTGTC 59.874 47.826 0.00 2.86 0.00 3.18
2155 2297 2.738846 ACTGTTCTGCTGCTATTTGTCG 59.261 45.455 0.00 0.00 0.00 4.35
2173 2315 1.806542 TCGCAGCTGAAGAATCAAACC 59.193 47.619 20.43 0.00 34.49 3.27
2178 2320 2.039084 AGCTGAAGAATCAAACCGAGGT 59.961 45.455 0.00 0.00 34.49 3.85
2182 2324 2.474410 AGAATCAAACCGAGGTGTCC 57.526 50.000 0.00 0.00 0.00 4.02
2183 2325 1.076332 GAATCAAACCGAGGTGTCCG 58.924 55.000 0.00 0.00 0.00 4.79
2184 2326 0.682852 AATCAAACCGAGGTGTCCGA 59.317 50.000 0.00 0.00 0.00 4.55
2185 2327 0.682852 ATCAAACCGAGGTGTCCGAA 59.317 50.000 0.00 0.00 0.00 4.30
2186 2328 0.682852 TCAAACCGAGGTGTCCGAAT 59.317 50.000 0.00 0.00 0.00 3.34
2188 2330 0.036671 AAACCGAGGTGTCCGAATCC 60.037 55.000 0.00 0.00 0.00 3.01
2189 2331 1.189524 AACCGAGGTGTCCGAATCCA 61.190 55.000 0.00 0.00 0.00 3.41
2190 2332 1.189524 ACCGAGGTGTCCGAATCCAA 61.190 55.000 0.00 0.00 0.00 3.53
2204 2346 3.123621 CGAATCCAAGTTTCTTCCGTCAG 59.876 47.826 0.00 0.00 0.00 3.51
2210 2352 2.484889 AGTTTCTTCCGTCAGCTCAAC 58.515 47.619 0.00 0.00 0.00 3.18
2216 2358 0.976641 TCCGTCAGCTCAACCAGAAT 59.023 50.000 0.00 0.00 0.00 2.40
2239 2381 3.065510 CGGTGATTCTCACTACATCGACT 59.934 47.826 7.17 0.00 46.19 4.18
2240 2382 4.355437 GGTGATTCTCACTACATCGACTG 58.645 47.826 7.17 0.00 46.19 3.51
2241 2383 3.794028 GTGATTCTCACTACATCGACTGC 59.206 47.826 0.00 0.00 43.73 4.40
2242 2384 3.443681 TGATTCTCACTACATCGACTGCA 59.556 43.478 0.00 0.00 0.00 4.41
2243 2385 3.494045 TTCTCACTACATCGACTGCAG 57.506 47.619 13.48 13.48 0.00 4.41
2250 2392 0.250038 ACATCGACTGCAGTGCACTT 60.250 50.000 27.27 1.55 33.79 3.16
2265 2407 2.224597 TGCACTTTCTCTTGGAGCATCA 60.225 45.455 0.00 0.00 36.25 3.07
2268 2410 3.436015 CACTTTCTCTTGGAGCATCACTG 59.564 47.826 0.00 0.00 36.25 3.66
2269 2411 2.775911 TTCTCTTGGAGCATCACTGG 57.224 50.000 0.00 0.00 36.25 4.00
2270 2412 0.251354 TCTCTTGGAGCATCACTGGC 59.749 55.000 0.00 0.00 36.25 4.85
2271 2413 0.252479 CTCTTGGAGCATCACTGGCT 59.748 55.000 0.00 0.00 46.07 4.75
2272 2414 1.483827 CTCTTGGAGCATCACTGGCTA 59.516 52.381 0.00 0.00 42.78 3.93
2273 2415 1.208052 TCTTGGAGCATCACTGGCTAC 59.792 52.381 0.00 0.00 42.78 3.58
2276 2418 2.338577 GGAGCATCACTGGCTACAAT 57.661 50.000 0.00 0.00 41.99 2.71
2286 2428 2.501723 ACTGGCTACAATAGGGAGTGTG 59.498 50.000 0.00 0.00 34.10 3.82
2287 2429 2.501723 CTGGCTACAATAGGGAGTGTGT 59.498 50.000 0.00 0.00 34.10 3.72
2288 2430 3.704566 CTGGCTACAATAGGGAGTGTGTA 59.295 47.826 0.00 0.00 34.10 2.90
2289 2431 3.449737 TGGCTACAATAGGGAGTGTGTAC 59.550 47.826 0.00 0.00 34.10 2.90
2290 2432 3.490419 GGCTACAATAGGGAGTGTGTACG 60.490 52.174 0.00 0.00 34.10 3.67
2303 2445 1.069296 TGTGTACGTACGTGCTACCAC 60.069 52.381 31.45 24.98 38.62 4.16
2310 2452 2.186350 TACGTGCTACCACCGACGTG 62.186 60.000 0.00 0.00 44.32 4.49
2324 2466 4.047030 CGTGGCGACGTACAGTAC 57.953 61.111 13.58 0.00 40.91 2.73
2341 2483 6.187125 ACAGTACGTACATAACATCGAACT 57.813 37.500 26.55 0.48 0.00 3.01
2343 2485 5.680229 CAGTACGTACATAACATCGAACTCC 59.320 44.000 26.55 0.00 0.00 3.85
2344 2486 4.037858 ACGTACATAACATCGAACTCCC 57.962 45.455 0.00 0.00 0.00 4.30
2345 2487 3.444742 ACGTACATAACATCGAACTCCCA 59.555 43.478 0.00 0.00 0.00 4.37
2346 2488 4.042398 CGTACATAACATCGAACTCCCAG 58.958 47.826 0.00 0.00 0.00 4.45
2347 2489 2.906354 ACATAACATCGAACTCCCAGC 58.094 47.619 0.00 0.00 0.00 4.85
2348 2490 2.213499 CATAACATCGAACTCCCAGCC 58.787 52.381 0.00 0.00 0.00 4.85
2349 2491 1.271856 TAACATCGAACTCCCAGCCA 58.728 50.000 0.00 0.00 0.00 4.75
2350 2492 0.036010 AACATCGAACTCCCAGCCAG 60.036 55.000 0.00 0.00 0.00 4.85
2351 2493 1.194781 ACATCGAACTCCCAGCCAGT 61.195 55.000 0.00 0.00 0.00 4.00
2352 2494 0.036010 CATCGAACTCCCAGCCAGTT 60.036 55.000 0.00 0.00 36.77 3.16
2353 2495 0.250513 ATCGAACTCCCAGCCAGTTC 59.749 55.000 0.00 2.98 44.35 3.01
2354 2496 1.376037 CGAACTCCCAGCCAGTTCC 60.376 63.158 6.93 0.00 44.78 3.62
2355 2497 1.831652 CGAACTCCCAGCCAGTTCCT 61.832 60.000 6.93 0.00 44.78 3.36
2356 2498 0.402121 GAACTCCCAGCCAGTTCCTT 59.598 55.000 1.76 0.00 42.73 3.36
2357 2499 0.402121 AACTCCCAGCCAGTTCCTTC 59.598 55.000 0.00 0.00 27.00 3.46
2358 2500 0.768221 ACTCCCAGCCAGTTCCTTCA 60.768 55.000 0.00 0.00 0.00 3.02
2359 2501 0.035630 CTCCCAGCCAGTTCCTTCAG 60.036 60.000 0.00 0.00 0.00 3.02
2360 2502 1.676967 CCCAGCCAGTTCCTTCAGC 60.677 63.158 0.00 0.00 0.00 4.26
2361 2503 2.037136 CCAGCCAGTTCCTTCAGCG 61.037 63.158 0.00 0.00 0.00 5.18
2362 2504 1.004560 CAGCCAGTTCCTTCAGCGA 60.005 57.895 0.00 0.00 0.00 4.93
2363 2505 0.392193 CAGCCAGTTCCTTCAGCGAT 60.392 55.000 0.00 0.00 0.00 4.58
2364 2506 0.107945 AGCCAGTTCCTTCAGCGATC 60.108 55.000 0.00 0.00 0.00 3.69
2365 2507 1.424493 GCCAGTTCCTTCAGCGATCG 61.424 60.000 11.69 11.69 0.00 3.69
2366 2508 0.807667 CCAGTTCCTTCAGCGATCGG 60.808 60.000 18.30 0.48 0.00 4.18
2367 2509 0.108615 CAGTTCCTTCAGCGATCGGT 60.109 55.000 15.21 15.21 0.00 4.69
2368 2510 0.173708 AGTTCCTTCAGCGATCGGTC 59.826 55.000 18.38 4.23 0.00 4.79
2394 2536 3.873952 GCAGCTCATTTTTCTCTCCGTAT 59.126 43.478 0.00 0.00 0.00 3.06
2395 2537 5.050490 GCAGCTCATTTTTCTCTCCGTATA 58.950 41.667 0.00 0.00 0.00 1.47
2408 2550 0.179156 CCGTATAACAGACGTGCGGT 60.179 55.000 0.00 0.00 38.65 5.68
2489 2637 3.299190 CCGATCTCCTCTCCCCGC 61.299 72.222 0.00 0.00 0.00 6.13
2518 2666 1.328279 TCACTCGGCTCAAAGAGTCA 58.672 50.000 0.00 0.00 44.98 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.412323 ATGGCGCATGCTGACCAAG 61.412 57.895 22.67 5.25 42.25 3.61
9 10 2.361483 ATGGCGCATGCTGACCAA 60.361 55.556 22.67 10.47 42.25 3.67
10 11 3.135457 CATGGCGCATGCTGACCA 61.135 61.111 21.56 21.56 42.25 4.02
18 19 4.746309 ACCACAGGCATGGCGCAT 62.746 61.111 14.30 0.00 44.33 4.73
21 22 3.974835 TAGCACCACAGGCATGGCG 62.975 63.158 14.30 11.27 44.33 5.69
22 23 1.660560 CTTAGCACCACAGGCATGGC 61.661 60.000 12.14 12.14 44.33 4.40
23 24 1.660560 GCTTAGCACCACAGGCATGG 61.661 60.000 2.31 6.28 46.10 3.66
24 25 1.660560 GGCTTAGCACCACAGGCATG 61.661 60.000 6.53 0.00 33.36 4.06
25 26 1.379044 GGCTTAGCACCACAGGCAT 60.379 57.895 6.53 0.00 33.36 4.40
26 27 2.034066 GGCTTAGCACCACAGGCA 59.966 61.111 6.53 0.00 33.36 4.75
27 28 2.515996 TACGGCTTAGCACCACAGGC 62.516 60.000 6.53 0.00 0.00 4.85
28 29 0.460284 CTACGGCTTAGCACCACAGG 60.460 60.000 6.53 0.00 0.00 4.00
29 30 0.530744 TCTACGGCTTAGCACCACAG 59.469 55.000 6.53 0.00 0.00 3.66
30 31 1.134818 CATCTACGGCTTAGCACCACA 60.135 52.381 6.53 0.00 0.00 4.17
31 32 1.134788 ACATCTACGGCTTAGCACCAC 60.135 52.381 6.53 0.00 0.00 4.16
32 33 1.136305 GACATCTACGGCTTAGCACCA 59.864 52.381 6.53 0.00 0.00 4.17
33 34 1.854227 GACATCTACGGCTTAGCACC 58.146 55.000 6.53 0.00 0.00 5.01
34 35 1.478137 CGACATCTACGGCTTAGCAC 58.522 55.000 6.53 0.00 0.00 4.40
35 36 0.248907 GCGACATCTACGGCTTAGCA 60.249 55.000 6.53 0.00 0.00 3.49
36 37 1.269444 CGCGACATCTACGGCTTAGC 61.269 60.000 0.00 0.00 0.00 3.09
37 38 0.660595 CCGCGACATCTACGGCTTAG 60.661 60.000 8.23 0.00 40.55 2.18
38 39 1.096967 TCCGCGACATCTACGGCTTA 61.097 55.000 8.23 0.00 46.49 3.09
70 71 1.140052 TGACAAAGCCGAAGAAGGACA 59.860 47.619 0.00 0.00 0.00 4.02
131 132 0.749454 GGTTCTGGTGGGCATAGCAG 60.749 60.000 12.27 12.27 45.14 4.24
136 137 0.620556 CTGTAGGTTCTGGTGGGCAT 59.379 55.000 0.00 0.00 0.00 4.40
170 171 1.072331 ACCAAGACGCTTTGTGAGGAT 59.928 47.619 0.00 0.00 0.00 3.24
215 216 1.302431 TGTGCAGGTCATCCCAACG 60.302 57.895 0.00 0.00 34.66 4.10
225 226 2.680974 ATCAAGGCGTGTGTGCAGGT 62.681 55.000 0.00 0.00 36.28 4.00
231 232 3.671008 TGTACTAATCAAGGCGTGTGT 57.329 42.857 0.00 0.00 0.00 3.72
310 311 9.541143 AACACGTTTTTGAATATTTGAAGGATT 57.459 25.926 0.00 0.00 0.00 3.01
346 347 2.355716 GGCTTTCCAGTGTATGTAGGCA 60.356 50.000 0.00 0.00 0.00 4.75
362 363 4.767928 CGGAGAGGTATGTATCTAGGCTTT 59.232 45.833 0.00 0.00 0.00 3.51
368 369 5.241064 GCAAAGACGGAGAGGTATGTATCTA 59.759 44.000 0.00 0.00 0.00 1.98
369 370 4.038162 GCAAAGACGGAGAGGTATGTATCT 59.962 45.833 0.00 0.00 0.00 1.98
370 371 4.299978 GCAAAGACGGAGAGGTATGTATC 58.700 47.826 0.00 0.00 0.00 2.24
371 372 3.069729 GGCAAAGACGGAGAGGTATGTAT 59.930 47.826 0.00 0.00 0.00 2.29
374 375 1.482593 AGGCAAAGACGGAGAGGTATG 59.517 52.381 0.00 0.00 0.00 2.39
446 454 5.069119 TGACAAGTACTCTGTCATGTTCAGT 59.931 40.000 24.58 7.30 37.61 3.41
462 470 6.072175 GGCCAAGTTGTGAATTATGACAAGTA 60.072 38.462 0.00 0.00 35.19 2.24
541 549 2.150397 AGTGCTCGTTAAAGCTTCGT 57.850 45.000 0.00 0.00 42.94 3.85
553 561 1.268285 CGGATGACTCACTAGTGCTCG 60.268 57.143 18.45 10.95 35.56 5.03
602 610 1.400494 GGGATTCGTATTTGCAACGCT 59.600 47.619 0.00 0.00 40.12 5.07
635 643 3.692257 TTTTCTCTGAAGAGGCCTGAG 57.308 47.619 12.00 10.82 42.30 3.35
636 644 4.647564 ATTTTTCTCTGAAGAGGCCTGA 57.352 40.909 12.00 0.00 42.30 3.86
637 645 7.121759 TGAATTATTTTTCTCTGAAGAGGCCTG 59.878 37.037 12.00 0.00 42.30 4.85
638 646 7.177878 TGAATTATTTTTCTCTGAAGAGGCCT 58.822 34.615 3.86 3.86 42.30 5.19
639 647 7.396540 TGAATTATTTTTCTCTGAAGAGGCC 57.603 36.000 7.47 0.00 42.30 5.19
648 656 9.348476 GGCCTCTCTATTGAATTATTTTTCTCT 57.652 33.333 0.00 0.00 0.00 3.10
649 657 9.348476 AGGCCTCTCTATTGAATTATTTTTCTC 57.652 33.333 0.00 0.00 0.00 2.87
650 658 9.348476 GAGGCCTCTCTATTGAATTATTTTTCT 57.652 33.333 26.25 0.00 37.07 2.52
651 659 8.286097 CGAGGCCTCTCTATTGAATTATTTTTC 58.714 37.037 29.73 0.00 37.86 2.29
652 660 7.993183 TCGAGGCCTCTCTATTGAATTATTTTT 59.007 33.333 29.73 0.00 37.86 1.94
697 790 8.537858 GGTGGGATAATACTATCTCGGTATTTT 58.462 37.037 4.76 0.00 37.79 1.82
705 798 8.602472 ATCTGAAGGTGGGATAATACTATCTC 57.398 38.462 0.00 0.00 35.78 2.75
719 812 7.921786 TTTTCACAGTAATATCTGAAGGTGG 57.078 36.000 0.65 0.00 38.63 4.61
733 826 7.255451 GGTGGTTTTGAGATGATTTTCACAGTA 60.255 37.037 0.00 0.00 0.00 2.74
736 829 5.362143 TGGTGGTTTTGAGATGATTTTCACA 59.638 36.000 0.00 0.00 0.00 3.58
923 1024 3.568538 GTGTCTGTGTTGATTGATTGGC 58.431 45.455 0.00 0.00 0.00 4.52
934 1036 2.510464 TGCGTGCGTGTCTGTGTT 60.510 55.556 0.00 0.00 0.00 3.32
935 1037 3.261951 GTGCGTGCGTGTCTGTGT 61.262 61.111 0.00 0.00 0.00 3.72
969 1075 0.398318 GATAGTGGAGTGGGGGATGC 59.602 60.000 0.00 0.00 0.00 3.91
986 1092 0.607620 CGCCATGGTTTTTGGTGGAT 59.392 50.000 14.67 0.00 40.36 3.41
987 1093 2.045280 CGCCATGGTTTTTGGTGGA 58.955 52.632 14.67 0.00 40.36 4.02
1015 1122 1.743321 GCGAGTAGGAGGAGCATGCT 61.743 60.000 22.92 22.92 42.52 3.79
1124 1231 2.830704 GATCTCGAACCCGTTGGCGT 62.831 60.000 0.00 0.00 37.05 5.68
1275 1382 3.191539 GGCACTACTGCTGCGAGC 61.192 66.667 0.00 1.70 43.66 5.03
1276 1383 1.808799 CTGGCACTACTGCTGCGAG 60.809 63.158 0.00 0.00 43.66 5.03
1277 1384 2.262603 CTGGCACTACTGCTGCGA 59.737 61.111 0.00 0.00 43.66 5.10
1278 1385 2.047844 ACTGGCACTACTGCTGCG 60.048 61.111 0.00 0.00 43.66 5.18
1361 1475 1.340991 GCCTGGCCCATAGAAACAAGA 60.341 52.381 7.66 0.00 0.00 3.02
1369 1483 1.753073 CTTGAAAAGCCTGGCCCATAG 59.247 52.381 16.57 1.93 36.98 2.23
1743 1857 2.049433 CCGCTGAACTCGAACGGT 60.049 61.111 0.00 0.00 39.05 4.83
1831 1945 3.497640 CACTGATTAATCTAGCCAGCAGC 59.502 47.826 16.24 0.00 44.25 5.25
1832 1946 4.953667 TCACTGATTAATCTAGCCAGCAG 58.046 43.478 16.24 6.08 0.00 4.24
1833 1947 5.104776 AGTTCACTGATTAATCTAGCCAGCA 60.105 40.000 16.24 0.00 0.00 4.41
1834 1948 5.363939 AGTTCACTGATTAATCTAGCCAGC 58.636 41.667 16.24 5.24 0.00 4.85
1835 1949 5.689514 CGAGTTCACTGATTAATCTAGCCAG 59.310 44.000 16.24 8.07 0.00 4.85
1863 1994 7.716768 AGCTTAAAAGACAAGACACTCTTAC 57.283 36.000 0.00 0.00 33.78 2.34
1889 2022 5.475909 ACCATTATTCGTCGGCTTAGATAGA 59.524 40.000 0.00 0.00 0.00 1.98
1894 2027 3.673809 GCTACCATTATTCGTCGGCTTAG 59.326 47.826 0.00 0.00 0.00 2.18
1917 2050 6.109359 AGTAGTTGGCTTCAGCAGTTTATAG 58.891 40.000 0.30 0.00 44.36 1.31
1929 2065 4.705991 AGTACACTAGGAGTAGTTGGCTTC 59.294 45.833 0.00 0.00 37.40 3.86
1934 2070 6.145696 GCAAAACAGTACACTAGGAGTAGTTG 59.854 42.308 0.00 1.93 37.40 3.16
1937 2073 4.857588 CGCAAAACAGTACACTAGGAGTAG 59.142 45.833 0.00 0.00 0.00 2.57
1940 2076 2.412089 GCGCAAAACAGTACACTAGGAG 59.588 50.000 0.30 0.00 0.00 3.69
1942 2078 2.157668 CAGCGCAAAACAGTACACTAGG 59.842 50.000 11.47 0.00 0.00 3.02
1943 2079 2.800544 ACAGCGCAAAACAGTACACTAG 59.199 45.455 11.47 0.00 0.00 2.57
1944 2080 2.828877 ACAGCGCAAAACAGTACACTA 58.171 42.857 11.47 0.00 0.00 2.74
1945 2081 1.663695 ACAGCGCAAAACAGTACACT 58.336 45.000 11.47 0.00 0.00 3.55
1946 2082 3.479006 CATACAGCGCAAAACAGTACAC 58.521 45.455 11.47 0.00 0.00 2.90
1947 2083 2.482336 CCATACAGCGCAAAACAGTACA 59.518 45.455 11.47 0.00 0.00 2.90
1948 2084 2.739913 TCCATACAGCGCAAAACAGTAC 59.260 45.455 11.47 0.00 0.00 2.73
1949 2085 2.739913 GTCCATACAGCGCAAAACAGTA 59.260 45.455 11.47 2.70 0.00 2.74
1971 2107 0.740737 GGGCACTTTATTGCTCGCAT 59.259 50.000 0.00 0.00 42.56 4.73
1990 2126 2.671130 ACAGTTTGTTGCACCAAAGG 57.329 45.000 9.94 8.06 35.13 3.11
2061 2203 9.326413 GGGGATATTTATAGGAAACGTATCATG 57.674 37.037 0.00 0.00 0.00 3.07
2088 2230 3.387091 ACCGCCGGTGTGATAGCA 61.387 61.111 8.62 0.00 32.98 3.49
2119 2261 5.451798 GCAGAACAGTCCATGGAAAGAAAAA 60.452 40.000 18.20 0.00 0.00 1.94
2120 2262 4.037923 GCAGAACAGTCCATGGAAAGAAAA 59.962 41.667 18.20 0.00 0.00 2.29
2121 2263 3.569701 GCAGAACAGTCCATGGAAAGAAA 59.430 43.478 18.20 0.00 0.00 2.52
2122 2264 3.149196 GCAGAACAGTCCATGGAAAGAA 58.851 45.455 18.20 0.00 0.00 2.52
2123 2265 2.373169 AGCAGAACAGTCCATGGAAAGA 59.627 45.455 18.20 0.00 0.00 2.52
2124 2266 2.486982 CAGCAGAACAGTCCATGGAAAG 59.513 50.000 18.20 14.50 0.00 2.62
2125 2267 2.507484 CAGCAGAACAGTCCATGGAAA 58.493 47.619 18.20 0.00 0.00 3.13
2126 2268 1.883638 GCAGCAGAACAGTCCATGGAA 60.884 52.381 18.20 0.00 0.00 3.53
2127 2269 0.321919 GCAGCAGAACAGTCCATGGA 60.322 55.000 11.44 11.44 0.00 3.41
2128 2270 0.322277 AGCAGCAGAACAGTCCATGG 60.322 55.000 4.97 4.97 0.00 3.66
2129 2271 2.391616 TAGCAGCAGAACAGTCCATG 57.608 50.000 0.00 0.00 0.00 3.66
2130 2272 3.641434 AATAGCAGCAGAACAGTCCAT 57.359 42.857 0.00 0.00 0.00 3.41
2131 2273 3.076621 CAAATAGCAGCAGAACAGTCCA 58.923 45.455 0.00 0.00 0.00 4.02
2132 2274 3.077359 ACAAATAGCAGCAGAACAGTCC 58.923 45.455 0.00 0.00 0.00 3.85
2134 2276 2.738846 CGACAAATAGCAGCAGAACAGT 59.261 45.455 0.00 0.00 0.00 3.55
2135 2277 2.475187 GCGACAAATAGCAGCAGAACAG 60.475 50.000 0.00 0.00 0.00 3.16
2137 2279 1.464608 TGCGACAAATAGCAGCAGAAC 59.535 47.619 0.00 0.00 38.59 3.01
2138 2280 1.807139 TGCGACAAATAGCAGCAGAA 58.193 45.000 0.00 0.00 38.59 3.02
2144 2286 1.733912 CTTCAGCTGCGACAAATAGCA 59.266 47.619 9.47 0.00 39.84 3.49
2145 2287 2.002586 TCTTCAGCTGCGACAAATAGC 58.997 47.619 9.47 0.00 37.71 2.97
2146 2288 4.330894 TGATTCTTCAGCTGCGACAAATAG 59.669 41.667 9.47 0.00 0.00 1.73
2148 2290 3.076621 TGATTCTTCAGCTGCGACAAAT 58.923 40.909 9.47 4.21 0.00 2.32
2149 2291 2.493035 TGATTCTTCAGCTGCGACAAA 58.507 42.857 9.47 0.00 0.00 2.83
2151 2293 2.168326 TTGATTCTTCAGCTGCGACA 57.832 45.000 9.47 0.77 32.27 4.35
2152 2294 2.413371 GGTTTGATTCTTCAGCTGCGAC 60.413 50.000 9.47 0.00 32.27 5.19
2154 2296 1.464687 CGGTTTGATTCTTCAGCTGCG 60.465 52.381 9.47 2.34 32.27 5.18
2155 2297 1.806542 TCGGTTTGATTCTTCAGCTGC 59.193 47.619 9.47 0.00 32.27 5.25
2158 2300 2.160417 CACCTCGGTTTGATTCTTCAGC 59.840 50.000 0.00 0.00 32.27 4.26
2173 2315 0.246635 ACTTGGATTCGGACACCTCG 59.753 55.000 0.00 0.00 0.00 4.63
2178 2320 3.408634 GGAAGAAACTTGGATTCGGACA 58.591 45.455 0.00 0.00 32.04 4.02
2182 2324 3.064207 TGACGGAAGAAACTTGGATTCG 58.936 45.455 0.00 0.00 32.04 3.34
2183 2325 3.120165 GCTGACGGAAGAAACTTGGATTC 60.120 47.826 0.00 0.00 0.00 2.52
2184 2326 2.814336 GCTGACGGAAGAAACTTGGATT 59.186 45.455 0.00 0.00 0.00 3.01
2185 2327 2.039084 AGCTGACGGAAGAAACTTGGAT 59.961 45.455 0.00 0.00 0.00 3.41
2186 2328 1.416401 AGCTGACGGAAGAAACTTGGA 59.584 47.619 0.00 0.00 0.00 3.53
2188 2330 2.483876 TGAGCTGACGGAAGAAACTTG 58.516 47.619 0.00 0.00 0.00 3.16
2189 2331 2.872858 GTTGAGCTGACGGAAGAAACTT 59.127 45.455 0.00 0.00 0.00 2.66
2190 2332 2.484889 GTTGAGCTGACGGAAGAAACT 58.515 47.619 0.00 0.00 0.00 2.66
2204 2346 2.029838 ATCACCGATTCTGGTTGAGC 57.970 50.000 0.00 0.00 41.38 4.26
2234 2376 0.104855 AGAAAGTGCACTGCAGTCGA 59.895 50.000 22.49 2.85 41.77 4.20
2239 2381 1.134128 TCCAAGAGAAAGTGCACTGCA 60.134 47.619 22.49 0.00 35.60 4.41
2240 2382 1.534595 CTCCAAGAGAAAGTGCACTGC 59.465 52.381 22.49 15.81 0.00 4.40
2241 2383 1.534595 GCTCCAAGAGAAAGTGCACTG 59.465 52.381 22.49 6.57 0.00 3.66
2242 2384 1.141657 TGCTCCAAGAGAAAGTGCACT 59.858 47.619 15.25 15.25 0.00 4.40
2243 2385 1.597742 TGCTCCAAGAGAAAGTGCAC 58.402 50.000 9.40 9.40 0.00 4.57
2250 2392 1.339438 GCCAGTGATGCTCCAAGAGAA 60.339 52.381 0.00 0.00 0.00 2.87
2265 2407 2.501723 CACACTCCCTATTGTAGCCAGT 59.498 50.000 0.00 0.00 0.00 4.00
2268 2410 3.490419 CGTACACACTCCCTATTGTAGCC 60.490 52.174 0.00 0.00 0.00 3.93
2269 2411 3.129988 ACGTACACACTCCCTATTGTAGC 59.870 47.826 0.00 0.00 0.00 3.58
2270 2412 4.978083 ACGTACACACTCCCTATTGTAG 57.022 45.455 0.00 0.00 0.00 2.74
2271 2413 4.332543 CGTACGTACACACTCCCTATTGTA 59.667 45.833 24.50 0.00 0.00 2.41
2272 2414 3.127548 CGTACGTACACACTCCCTATTGT 59.872 47.826 24.50 0.00 0.00 2.71
2273 2415 3.127548 ACGTACGTACACACTCCCTATTG 59.872 47.826 21.41 6.68 0.00 1.90
2276 2418 2.076100 CACGTACGTACACACTCCCTA 58.924 52.381 22.34 0.00 0.00 3.53
2286 2428 0.521242 CGGTGGTAGCACGTACGTAC 60.521 60.000 22.34 16.33 31.59 3.67
2287 2429 0.672091 TCGGTGGTAGCACGTACGTA 60.672 55.000 22.34 2.28 31.59 3.57
2288 2430 1.965930 TCGGTGGTAGCACGTACGT 60.966 57.895 16.72 16.72 31.59 3.57
2289 2431 1.512734 GTCGGTGGTAGCACGTACG 60.513 63.158 18.23 15.01 31.59 3.67
2290 2432 1.512734 CGTCGGTGGTAGCACGTAC 60.513 63.158 18.23 16.32 0.00 3.67
2319 2461 5.680229 GGAGTTCGATGTTATGTACGTACTG 59.320 44.000 25.12 6.41 36.77 2.74
2321 2463 4.972440 GGGAGTTCGATGTTATGTACGTAC 59.028 45.833 18.90 18.90 0.00 3.67
2322 2464 4.639755 TGGGAGTTCGATGTTATGTACGTA 59.360 41.667 0.00 0.00 0.00 3.57
2323 2465 3.444742 TGGGAGTTCGATGTTATGTACGT 59.555 43.478 0.00 0.00 0.00 3.57
2324 2466 4.036567 TGGGAGTTCGATGTTATGTACG 57.963 45.455 0.00 0.00 0.00 3.67
2325 2467 3.802685 GCTGGGAGTTCGATGTTATGTAC 59.197 47.826 0.00 0.00 0.00 2.90
2327 2469 2.420129 GGCTGGGAGTTCGATGTTATGT 60.420 50.000 0.00 0.00 0.00 2.29
2328 2470 2.213499 GGCTGGGAGTTCGATGTTATG 58.787 52.381 0.00 0.00 0.00 1.90
2329 2471 1.837439 TGGCTGGGAGTTCGATGTTAT 59.163 47.619 0.00 0.00 0.00 1.89
2330 2472 1.207089 CTGGCTGGGAGTTCGATGTTA 59.793 52.381 0.00 0.00 0.00 2.41
2331 2473 0.036010 CTGGCTGGGAGTTCGATGTT 60.036 55.000 0.00 0.00 0.00 2.71
2332 2474 1.194781 ACTGGCTGGGAGTTCGATGT 61.195 55.000 0.00 0.00 0.00 3.06
2336 2478 1.376037 GGAACTGGCTGGGAGTTCG 60.376 63.158 8.73 0.00 46.98 3.95
2337 2479 0.402121 AAGGAACTGGCTGGGAGTTC 59.598 55.000 6.85 6.85 45.83 3.01
2338 2480 0.402121 GAAGGAACTGGCTGGGAGTT 59.598 55.000 0.00 0.00 40.86 3.01
2340 2482 0.035630 CTGAAGGAACTGGCTGGGAG 60.036 60.000 0.00 0.00 40.86 4.30
2341 2483 2.069776 CTGAAGGAACTGGCTGGGA 58.930 57.895 0.00 0.00 40.86 4.37
2343 2485 2.037136 CGCTGAAGGAACTGGCTGG 61.037 63.158 0.00 0.00 40.86 4.85
2344 2486 0.392193 ATCGCTGAAGGAACTGGCTG 60.392 55.000 0.00 0.00 40.86 4.85
2345 2487 0.107945 GATCGCTGAAGGAACTGGCT 60.108 55.000 0.00 0.00 40.86 4.75
2346 2488 1.424493 CGATCGCTGAAGGAACTGGC 61.424 60.000 0.26 0.00 40.86 4.85
2347 2489 0.807667 CCGATCGCTGAAGGAACTGG 60.808 60.000 10.32 0.00 40.86 4.00
2348 2490 0.108615 ACCGATCGCTGAAGGAACTG 60.109 55.000 10.32 0.00 40.86 3.16
2349 2491 3.467650 CGACCGATCGCTGAAGGAACT 62.468 57.143 10.32 0.00 42.43 3.01
2350 2492 1.140407 CGACCGATCGCTGAAGGAAC 61.140 60.000 10.32 0.00 42.43 3.62
2351 2493 1.138883 CGACCGATCGCTGAAGGAA 59.861 57.895 10.32 0.00 42.43 3.36
2352 2494 2.798689 CGACCGATCGCTGAAGGA 59.201 61.111 10.32 0.00 42.43 3.36
2365 2507 2.200170 AAAAATGAGCTGCCGCGACC 62.200 55.000 8.23 0.00 42.32 4.79
2366 2508 0.794605 GAAAAATGAGCTGCCGCGAC 60.795 55.000 8.23 0.00 42.32 5.19
2367 2509 0.955428 AGAAAAATGAGCTGCCGCGA 60.955 50.000 8.23 0.00 42.32 5.87
2368 2510 0.522076 GAGAAAAATGAGCTGCCGCG 60.522 55.000 0.00 0.00 42.32 6.46
2369 2511 0.807496 AGAGAAAAATGAGCTGCCGC 59.193 50.000 0.00 0.00 0.00 6.53
2394 2536 3.038946 GCATACCGCACGTCTGTTA 57.961 52.632 0.00 0.00 41.79 2.41
2395 2537 3.870606 GCATACCGCACGTCTGTT 58.129 55.556 0.00 0.00 41.79 3.16
2408 2550 2.584064 CTGCCGTGGTCCTGCATA 59.416 61.111 0.00 0.00 33.97 3.14
2496 2644 1.895798 ACTCTTTGAGCCGAGTGATCA 59.104 47.619 0.00 0.00 38.94 2.92
2505 2653 4.800471 CAGTTTGTTTTGACTCTTTGAGCC 59.200 41.667 0.00 0.00 32.04 4.70
2518 2666 2.162809 GACGTGTCACCCAGTTTGTTTT 59.837 45.455 0.00 0.00 0.00 2.43
2765 2922 2.278013 CGGGTAGTCGAAGAGCGC 60.278 66.667 0.00 0.00 36.95 5.92
2776 2933 4.602696 CCGTAGTCGCGCGGGTAG 62.603 72.222 31.69 17.07 43.85 3.18


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

AutoCloner maintained by Alex Coulton.