Multiple sequence alignment - TraesCS6B01G355100

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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 TraesCS6B01G355100 chr6B 100.000 2816 0 0 1 2816 623439297 623442112 0.000000e+00 5201
1 TraesCS6B01G355100 chr6B 91.215 1844 159 2 1 1841 708391820 708389977 0.000000e+00 2505
2 TraesCS6B01G355100 chr6B 95.968 124 3 2 2080 2203 128924766 128924887 1.710000e-47 200
3 TraesCS6B01G355100 chr7B 91.933 1847 143 5 1 1842 621912354 621910509 0.000000e+00 2580
4 TraesCS6B01G355100 chr7B 85.985 1848 250 8 1 1842 248687995 248686151 0.000000e+00 1969
5 TraesCS6B01G355100 chr1B 91.363 1841 153 5 1 1839 539122596 539124432 0.000000e+00 2514
6 TraesCS6B01G355100 chr7D 88.997 1845 193 4 1 1841 205160397 205158559 0.000000e+00 2274
7 TraesCS6B01G355100 chr1D 88.341 1844 212 2 1 1841 442380074 442378231 0.000000e+00 2211
8 TraesCS6B01G355100 chr4B 90.613 1566 145 1 277 1840 514184001 514182436 0.000000e+00 2076
9 TraesCS6B01G355100 chr4B 98.291 117 2 0 2087 2203 13941695 13941811 3.680000e-49 206
10 TraesCS6B01G355100 chrUn 86.533 1849 245 3 1 1845 307306238 307308086 0.000000e+00 2032
11 TraesCS6B01G355100 chr2B 85.985 1848 248 10 1 1841 115905827 115903984 0.000000e+00 1967
12 TraesCS6B01G355100 chr2B 97.500 120 3 0 2085 2204 719530496 719530615 3.680000e-49 206
13 TraesCS6B01G355100 chr2B 96.721 122 3 1 2082 2203 245689731 245689851 4.760000e-48 202
14 TraesCS6B01G355100 chr6A 80.068 592 67 14 2200 2756 558930863 558931438 2.630000e-105 392
15 TraesCS6B01G355100 chr6A 91.200 250 17 3 1844 2088 558930617 558930866 4.490000e-88 335
16 TraesCS6B01G355100 chr6A 77.249 189 35 6 1907 2090 558926188 558926373 1.380000e-18 104
17 TraesCS6B01G355100 chr5B 96.850 127 4 0 2077 2203 70795781 70795655 2.200000e-51 213
18 TraesCS6B01G355100 chr5B 93.431 137 7 2 2068 2203 522656723 522656858 4.760000e-48 202
19 TraesCS6B01G355100 chr5B 95.238 126 6 0 2078 2203 403545843 403545718 1.710000e-47 200
20 TraesCS6B01G355100 chr3B 97.521 121 3 0 2083 2203 659785846 659785966 1.020000e-49 207
21 TraesCS6B01G355100 chr3D 96.694 121 4 0 2084 2204 346837564 346837444 4.760000e-48 202


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 TraesCS6B01G355100 chr6B 623439297 623442112 2815 False 5201.0 5201 100.000 1 2816 1 chr6B.!!$F2 2815
1 TraesCS6B01G355100 chr6B 708389977 708391820 1843 True 2505.0 2505 91.215 1 1841 1 chr6B.!!$R1 1840
2 TraesCS6B01G355100 chr7B 621910509 621912354 1845 True 2580.0 2580 91.933 1 1842 1 chr7B.!!$R2 1841
3 TraesCS6B01G355100 chr7B 248686151 248687995 1844 True 1969.0 1969 85.985 1 1842 1 chr7B.!!$R1 1841
4 TraesCS6B01G355100 chr1B 539122596 539124432 1836 False 2514.0 2514 91.363 1 1839 1 chr1B.!!$F1 1838
5 TraesCS6B01G355100 chr7D 205158559 205160397 1838 True 2274.0 2274 88.997 1 1841 1 chr7D.!!$R1 1840
6 TraesCS6B01G355100 chr1D 442378231 442380074 1843 True 2211.0 2211 88.341 1 1841 1 chr1D.!!$R1 1840
7 TraesCS6B01G355100 chr4B 514182436 514184001 1565 True 2076.0 2076 90.613 277 1840 1 chr4B.!!$R1 1563
8 TraesCS6B01G355100 chrUn 307306238 307308086 1848 False 2032.0 2032 86.533 1 1845 1 chrUn.!!$F1 1844
9 TraesCS6B01G355100 chr2B 115903984 115905827 1843 True 1967.0 1967 85.985 1 1841 1 chr2B.!!$R1 1840
10 TraesCS6B01G355100 chr6A 558930617 558931438 821 False 363.5 392 85.634 1844 2756 2 chr6A.!!$F2 912

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
909 916 0.105964 CCTTCCGACACTTGGTGACA 59.894 55.0 4.62 0.0 36.96 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2184 0.030369 CCGGAAATACTCGTCGGAGG 59.97 60.0 0.0 0.0 44.93 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
104 106 2.092861 TGAGTGTTTTCAAACTCCCGGA 60.093 45.455 0.73 0.00 41.79 5.14
178 182 2.907042 AGAACGGGAAGAAGAAGATGGT 59.093 45.455 0.00 0.00 0.00 3.55
456 461 2.960129 GGCGAGTCGGTAATGGCG 60.960 66.667 15.52 0.00 0.00 5.69
466 471 2.093921 TCGGTAATGGCGTGAAGATTCA 60.094 45.455 0.00 0.00 34.20 2.57
716 721 0.249911 GGTTGACGGTGAGAAGTGCT 60.250 55.000 0.00 0.00 0.00 4.40
814 821 0.600782 GTGGAACTACGTTTGGCGGA 60.601 55.000 0.00 0.00 46.52 5.54
815 822 0.106335 TGGAACTACGTTTGGCGGAA 59.894 50.000 0.00 0.00 46.52 4.30
816 823 1.228533 GGAACTACGTTTGGCGGAAA 58.771 50.000 0.00 0.00 46.52 3.13
905 912 0.182775 AAAGCCTTCCGACACTTGGT 59.817 50.000 0.00 0.00 0.00 3.67
909 916 0.105964 CCTTCCGACACTTGGTGACA 59.894 55.000 4.62 0.00 36.96 3.58
1004 1011 4.323417 AGAACGTTCTGGACAAATATGCA 58.677 39.130 29.24 0.00 35.89 3.96
1025 1032 2.672996 CCGTTGGCCACTTCCTGG 60.673 66.667 3.88 0.00 44.08 4.45
1137 1144 3.364442 TGGCGGATTTGGCAGTTG 58.636 55.556 0.00 0.00 39.79 3.16
1153 1160 3.365868 GCAGTTGCGTAATGATTTGACCA 60.366 43.478 0.00 0.00 0.00 4.02
1362 1369 1.300931 GCTGGTGCTGTCAGTCGAA 60.301 57.895 0.93 0.00 34.89 3.71
1527 1534 2.122783 TGGCCCTAGCATTACAACAC 57.877 50.000 0.00 0.00 42.56 3.32
1604 1611 3.254166 ACAAATGATGCACTTCTTCGCTT 59.746 39.130 0.00 0.00 0.00 4.68
1649 1656 7.815840 TGGAGATCAAGTCACTCTTAGATAG 57.184 40.000 0.00 0.00 34.66 2.08
1869 1877 3.405831 TCTGATTGTTCACTTCTGGCTG 58.594 45.455 0.00 0.00 0.00 4.85
1897 1905 9.424319 ACTTAATTTGCATACTACATAGATCGG 57.576 33.333 0.00 0.00 0.00 4.18
1985 1993 7.518161 CATTGGTAAACATGTACTACACTGTG 58.482 38.462 16.01 6.19 0.00 3.66
1990 1999 7.277098 GGTAAACATGTACTACACTGTGGTATG 59.723 40.741 13.09 7.55 32.57 2.39
1993 2002 3.101437 TGTACTACACTGTGGTATGGGG 58.899 50.000 13.09 0.00 32.57 4.96
1999 2008 0.034186 ACTGTGGTATGGGGCACATG 60.034 55.000 13.70 0.00 40.82 3.21
2003 2012 0.395586 TGGTATGGGGCACATGAAGC 60.396 55.000 13.70 3.33 40.82 3.86
2018 2029 4.202357 ACATGAAGCGGGAGAATAGCAATA 60.202 41.667 0.00 0.00 0.00 1.90
2088 2101 9.582431 TGCAAGTTATCTTTCACAGTATAGTAC 57.418 33.333 0.00 0.00 0.00 2.73
2092 2105 9.134055 AGTTATCTTTCACAGTATAGTACTCCC 57.866 37.037 0.00 0.00 36.76 4.30
2093 2106 9.134055 GTTATCTTTCACAGTATAGTACTCCCT 57.866 37.037 0.00 0.00 36.76 4.20
2094 2107 7.826918 ATCTTTCACAGTATAGTACTCCCTC 57.173 40.000 0.00 0.00 36.76 4.30
2095 2108 6.127793 TCTTTCACAGTATAGTACTCCCTCC 58.872 44.000 0.00 0.00 36.76 4.30
2096 2109 4.082665 TCACAGTATAGTACTCCCTCCG 57.917 50.000 0.00 0.00 36.76 4.63
2097 2110 3.457380 TCACAGTATAGTACTCCCTCCGT 59.543 47.826 0.00 0.00 36.76 4.69
2098 2111 3.814283 CACAGTATAGTACTCCCTCCGTC 59.186 52.174 0.00 0.00 36.76 4.79
2099 2112 3.181446 ACAGTATAGTACTCCCTCCGTCC 60.181 52.174 0.00 0.00 36.76 4.79
2100 2113 2.038295 AGTATAGTACTCCCTCCGTCCG 59.962 54.545 0.00 0.00 32.47 4.79
2101 2114 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
2102 2115 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2103 2116 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2104 2117 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2105 2118 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2106 2119 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2107 2120 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2108 2121 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2109 2122 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2110 2123 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2111 2124 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2112 2125 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2113 2126 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2114 2127 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
2115 2128 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
2116 2129 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
2117 2130 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
2118 2131 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
2119 2132 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
2120 2133 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
2121 2134 5.127519 TCCGGAAATACTTGTCGGAGAAATA 59.872 40.000 0.00 0.00 43.84 1.40
2122 2135 5.233689 CCGGAAATACTTGTCGGAGAAATAC 59.766 44.000 0.00 0.00 42.94 1.89
2123 2136 5.808540 CGGAAATACTTGTCGGAGAAATACA 59.191 40.000 0.00 0.00 39.69 2.29
2124 2137 6.479001 CGGAAATACTTGTCGGAGAAATACAT 59.521 38.462 0.00 0.00 39.69 2.29
2125 2138 7.650504 CGGAAATACTTGTCGGAGAAATACATA 59.349 37.037 0.00 0.00 39.69 2.29
2126 2139 9.321562 GGAAATACTTGTCGGAGAAATACATAA 57.678 33.333 0.00 0.00 39.69 1.90
2132 2145 9.226606 ACTTGTCGGAGAAATACATAAAAATGA 57.773 29.630 0.00 0.00 39.69 2.57
2178 2191 6.576662 TCTAGATACATTCATTCCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
2179 2192 4.244425 AGATACATTCATTCCTCCGACG 57.756 45.455 0.00 0.00 0.00 5.12
2180 2193 3.889538 AGATACATTCATTCCTCCGACGA 59.110 43.478 0.00 0.00 0.00 4.20
2181 2194 2.586258 ACATTCATTCCTCCGACGAG 57.414 50.000 0.00 0.00 35.72 4.18
2182 2195 1.825474 ACATTCATTCCTCCGACGAGT 59.175 47.619 0.00 0.00 33.93 4.18
2183 2196 3.021695 ACATTCATTCCTCCGACGAGTA 58.978 45.455 0.00 0.00 33.93 2.59
2184 2197 3.637229 ACATTCATTCCTCCGACGAGTAT 59.363 43.478 0.00 0.00 33.93 2.12
2185 2198 4.099573 ACATTCATTCCTCCGACGAGTATT 59.900 41.667 0.00 0.00 33.93 1.89
2186 2199 4.730949 TTCATTCCTCCGACGAGTATTT 57.269 40.909 0.00 0.00 33.93 1.40
2187 2200 4.303086 TCATTCCTCCGACGAGTATTTC 57.697 45.455 0.00 0.00 33.93 2.17
2188 2201 3.067742 TCATTCCTCCGACGAGTATTTCC 59.932 47.826 0.00 0.00 33.93 3.13
2189 2202 1.019673 TCCTCCGACGAGTATTTCCG 58.980 55.000 0.00 0.00 33.93 4.30
2190 2203 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.000 0.00 0.00 41.36 5.14
2191 2204 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
2192 2205 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
2193 2206 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
2194 2207 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
2195 2208 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
2196 2209 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
2197 2210 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
2198 2211 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
2199 2212 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2200 2213 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2201 2214 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2202 2215 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2203 2216 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
2204 2217 3.217743 CCGGACGGAGGGAGTAGC 61.218 72.222 4.40 0.00 37.50 3.58
2205 2218 2.124236 CGGACGGAGGGAGTAGCT 60.124 66.667 0.00 0.00 0.00 3.32
2206 2219 2.482333 CGGACGGAGGGAGTAGCTG 61.482 68.421 0.00 0.00 0.00 4.24
2207 2220 2.787567 GGACGGAGGGAGTAGCTGC 61.788 68.421 0.00 0.00 0.00 5.25
2229 2242 4.797275 GCTGCATTAAACCAAACTTGCTCT 60.797 41.667 0.00 0.00 0.00 4.09
2230 2243 5.564651 GCTGCATTAAACCAAACTTGCTCTA 60.565 40.000 0.00 0.00 0.00 2.43
2240 2253 5.163237 ACCAAACTTGCTCTACTTTACTCCA 60.163 40.000 0.00 0.00 0.00 3.86
2290 2304 2.696989 TACAGACCGACCATACGAGA 57.303 50.000 0.00 0.00 35.09 4.04
2295 2309 2.358267 AGACCGACCATACGAGAATCAC 59.642 50.000 0.00 0.00 35.09 3.06
2305 2319 2.767505 ACGAGAATCACACAAAGACCC 58.232 47.619 0.00 0.00 33.17 4.46
2319 2333 4.023193 ACAAAGACCCAATGCGAGTTTTAG 60.023 41.667 0.00 0.00 0.00 1.85
2324 2338 2.159379 CCCAATGCGAGTTTTAGGCTTC 60.159 50.000 0.00 0.00 0.00 3.86
2327 2341 1.144969 TGCGAGTTTTAGGCTTCGTG 58.855 50.000 7.31 0.00 0.00 4.35
2328 2342 0.179222 GCGAGTTTTAGGCTTCGTGC 60.179 55.000 7.31 0.00 41.94 5.34
2362 2376 5.788450 AGCACATAGTAGCCACATAGAATC 58.212 41.667 0.00 0.00 0.00 2.52
2370 2384 3.041211 AGCCACATAGAATCTGTAGGCA 58.959 45.455 19.27 0.00 40.34 4.75
2371 2385 3.649981 AGCCACATAGAATCTGTAGGCAT 59.350 43.478 19.27 6.94 40.34 4.40
2372 2386 3.750130 GCCACATAGAATCTGTAGGCATG 59.250 47.826 14.58 3.12 39.01 4.06
2373 2387 4.503817 GCCACATAGAATCTGTAGGCATGA 60.504 45.833 14.58 0.00 39.01 3.07
2374 2388 5.236282 CCACATAGAATCTGTAGGCATGAG 58.764 45.833 0.00 0.00 0.00 2.90
2375 2389 5.011431 CCACATAGAATCTGTAGGCATGAGA 59.989 44.000 0.00 0.00 0.00 3.27
2376 2390 6.157904 CACATAGAATCTGTAGGCATGAGAG 58.842 44.000 0.00 0.00 0.00 3.20
2377 2391 5.245751 ACATAGAATCTGTAGGCATGAGAGG 59.754 44.000 0.00 0.00 0.00 3.69
2378 2392 2.368221 AGAATCTGTAGGCATGAGAGGC 59.632 50.000 0.00 0.00 0.00 4.70
2379 2393 1.798626 ATCTGTAGGCATGAGAGGCA 58.201 50.000 0.00 0.00 36.37 4.75
2392 2406 3.378512 TGAGAGGCATGAGGAACATAGT 58.621 45.455 0.00 0.00 37.46 2.12
2393 2407 3.133542 TGAGAGGCATGAGGAACATAGTG 59.866 47.826 0.00 0.00 37.46 2.74
2395 2409 3.972638 AGAGGCATGAGGAACATAGTGAT 59.027 43.478 0.00 0.00 37.46 3.06
2402 2416 5.627503 CATGAGGAACATAGTGATCACCACA 60.628 44.000 22.21 10.17 41.67 4.17
2420 2434 3.055094 CCACACCTAGGCATACTTTCAGT 60.055 47.826 9.30 0.00 0.00 3.41
2430 2456 6.485171 AGGCATACTTTCAGTTTTAGATGGT 58.515 36.000 0.00 0.00 0.00 3.55
2445 2471 3.110705 AGATGGTGTTCCTGCTAGATGT 58.889 45.455 0.00 0.00 34.23 3.06
2447 2473 1.339055 TGGTGTTCCTGCTAGATGTGC 60.339 52.381 0.00 0.00 34.23 4.57
2456 2482 3.129871 CTGCTAGATGTGCCTTCTTAGC 58.870 50.000 0.00 0.00 0.00 3.09
2471 2519 0.817634 TTAGCTGGCACACAAAGCGT 60.818 50.000 0.00 0.00 41.88 5.07
2472 2520 0.817634 TAGCTGGCACACAAAGCGTT 60.818 50.000 0.00 0.00 41.88 4.84
2482 2530 4.597079 CACACAAAGCGTTGTATTTCTGT 58.403 39.130 17.71 7.85 46.47 3.41
2484 2532 5.034152 ACACAAAGCGTTGTATTTCTGTTG 58.966 37.500 17.71 5.15 46.47 3.33
2490 2538 4.574828 AGCGTTGTATTTCTGTTGTTCTGT 59.425 37.500 0.00 0.00 0.00 3.41
2491 2539 5.065988 AGCGTTGTATTTCTGTTGTTCTGTT 59.934 36.000 0.00 0.00 0.00 3.16
2498 2546 9.042008 TGTATTTCTGTTGTTCTGTTTAGACTC 57.958 33.333 0.00 0.00 31.21 3.36
2507 2555 3.682696 TCTGTTTAGACTCTAGACGCCA 58.317 45.455 0.00 0.00 0.00 5.69
2508 2556 4.077108 TCTGTTTAGACTCTAGACGCCAA 58.923 43.478 0.00 0.00 0.00 4.52
2509 2557 4.156190 TCTGTTTAGACTCTAGACGCCAAG 59.844 45.833 0.00 0.00 0.00 3.61
2551 2599 7.390027 AGAGTAGTTCTATGAAGCACATGTTT 58.610 34.615 0.00 0.00 39.77 2.83
2553 2601 5.051891 AGTTCTATGAAGCACATGTTTGC 57.948 39.130 0.00 0.00 43.34 3.68
2562 2610 0.109781 CACATGTTTGCTACCACGGC 60.110 55.000 0.00 0.00 0.00 5.68
2569 2617 2.358737 GCTACCACGGCTTGCAGT 60.359 61.111 0.00 0.00 0.00 4.40
2611 2659 4.329545 GGTCCTTGCACCCGCTCA 62.330 66.667 0.00 0.00 39.64 4.26
2647 2695 4.122143 TCATGTCATGATGTAAGCACGA 57.878 40.909 11.62 0.00 30.93 4.35
2651 2699 1.474879 TCATGATGTAAGCACGACGGA 59.525 47.619 0.00 0.00 30.93 4.69
2671 2719 4.724697 CGCAAGCTGTCAACGCCG 62.725 66.667 0.00 0.00 0.00 6.46
2697 2745 2.972505 GGGTGTCACGTGTGCCTG 60.973 66.667 16.51 0.00 0.00 4.85
2703 2751 1.087202 GTCACGTGTGCCTGTGAACA 61.087 55.000 16.51 0.00 45.84 3.18
2705 2753 1.078778 ACGTGTGCCTGTGAACACA 60.079 52.632 7.42 7.42 45.61 3.72
2709 2757 1.286880 GTGCCTGTGAACACATGGC 59.713 57.895 25.89 25.89 46.36 4.40
2728 2776 3.830755 TGGCGTAGGAGAAGAACTTTAGT 59.169 43.478 0.00 0.00 0.00 2.24
2729 2777 4.174762 GGCGTAGGAGAAGAACTTTAGTG 58.825 47.826 0.00 0.00 0.00 2.74
2731 2779 5.467705 GCGTAGGAGAAGAACTTTAGTGAA 58.532 41.667 0.00 0.00 0.00 3.18
2745 2793 2.736670 AGTGAAGTGGCAACTTTCCT 57.263 45.000 8.18 4.28 46.84 3.36
2747 2795 2.952310 AGTGAAGTGGCAACTTTCCTTC 59.048 45.455 8.18 6.38 46.84 3.46
2748 2796 2.034685 GTGAAGTGGCAACTTTCCTTCC 59.965 50.000 8.18 0.00 46.84 3.46
2750 2798 0.853530 AGTGGCAACTTTCCTTCCCT 59.146 50.000 0.00 0.00 30.14 4.20
2751 2799 2.062636 AGTGGCAACTTTCCTTCCCTA 58.937 47.619 0.00 0.00 30.14 3.53
2752 2800 2.649816 AGTGGCAACTTTCCTTCCCTAT 59.350 45.455 0.00 0.00 30.14 2.57
2753 2801 3.017442 GTGGCAACTTTCCTTCCCTATC 58.983 50.000 0.00 0.00 37.61 2.08
2754 2802 2.025321 TGGCAACTTTCCTTCCCTATCC 60.025 50.000 0.00 0.00 37.61 2.59
2755 2803 2.289565 GCAACTTTCCTTCCCTATCCG 58.710 52.381 0.00 0.00 0.00 4.18
2756 2804 2.355818 GCAACTTTCCTTCCCTATCCGT 60.356 50.000 0.00 0.00 0.00 4.69
2757 2805 3.872630 GCAACTTTCCTTCCCTATCCGTT 60.873 47.826 0.00 0.00 0.00 4.44
2758 2806 3.629142 ACTTTCCTTCCCTATCCGTTG 57.371 47.619 0.00 0.00 0.00 4.10
2759 2807 2.910977 ACTTTCCTTCCCTATCCGTTGT 59.089 45.455 0.00 0.00 0.00 3.32
2760 2808 3.270877 CTTTCCTTCCCTATCCGTTGTG 58.729 50.000 0.00 0.00 0.00 3.33
2761 2809 1.946984 TCCTTCCCTATCCGTTGTGT 58.053 50.000 0.00 0.00 0.00 3.72
2762 2810 1.553248 TCCTTCCCTATCCGTTGTGTG 59.447 52.381 0.00 0.00 0.00 3.82
2763 2811 1.369625 CTTCCCTATCCGTTGTGTGC 58.630 55.000 0.00 0.00 0.00 4.57
2764 2812 0.981183 TTCCCTATCCGTTGTGTGCT 59.019 50.000 0.00 0.00 0.00 4.40
2765 2813 0.535335 TCCCTATCCGTTGTGTGCTC 59.465 55.000 0.00 0.00 0.00 4.26
2766 2814 0.806102 CCCTATCCGTTGTGTGCTCG 60.806 60.000 0.00 0.00 0.00 5.03
2767 2815 0.108804 CCTATCCGTTGTGTGCTCGT 60.109 55.000 0.00 0.00 0.00 4.18
2768 2816 1.671850 CCTATCCGTTGTGTGCTCGTT 60.672 52.381 0.00 0.00 0.00 3.85
2769 2817 2.066262 CTATCCGTTGTGTGCTCGTTT 58.934 47.619 0.00 0.00 0.00 3.60
2770 2818 1.305201 ATCCGTTGTGTGCTCGTTTT 58.695 45.000 0.00 0.00 0.00 2.43
2771 2819 0.653636 TCCGTTGTGTGCTCGTTTTC 59.346 50.000 0.00 0.00 0.00 2.29
2772 2820 0.655733 CCGTTGTGTGCTCGTTTTCT 59.344 50.000 0.00 0.00 0.00 2.52
2773 2821 1.063469 CCGTTGTGTGCTCGTTTTCTT 59.937 47.619 0.00 0.00 0.00 2.52
2774 2822 2.477189 CCGTTGTGTGCTCGTTTTCTTT 60.477 45.455 0.00 0.00 0.00 2.52
2775 2823 3.168193 CGTTGTGTGCTCGTTTTCTTTT 58.832 40.909 0.00 0.00 0.00 2.27
2776 2824 3.002149 CGTTGTGTGCTCGTTTTCTTTTG 60.002 43.478 0.00 0.00 0.00 2.44
2777 2825 4.162812 GTTGTGTGCTCGTTTTCTTTTGA 58.837 39.130 0.00 0.00 0.00 2.69
2778 2826 4.014847 TGTGTGCTCGTTTTCTTTTGAG 57.985 40.909 0.00 0.00 0.00 3.02
2779 2827 3.181501 TGTGTGCTCGTTTTCTTTTGAGG 60.182 43.478 0.00 0.00 0.00 3.86
2780 2828 2.223479 TGTGCTCGTTTTCTTTTGAGGC 60.223 45.455 0.00 0.00 0.00 4.70
2781 2829 1.002900 TGCTCGTTTTCTTTTGAGGCG 60.003 47.619 0.00 0.00 0.00 5.52
2782 2830 1.263217 GCTCGTTTTCTTTTGAGGCGA 59.737 47.619 0.00 0.00 0.00 5.54
2783 2831 2.095718 GCTCGTTTTCTTTTGAGGCGAT 60.096 45.455 0.00 0.00 31.48 4.58
2784 2832 3.737305 CTCGTTTTCTTTTGAGGCGATC 58.263 45.455 0.00 0.00 31.48 3.69
2785 2833 2.482721 TCGTTTTCTTTTGAGGCGATCC 59.517 45.455 0.00 0.00 0.00 3.36
2797 2845 3.703001 AGGCGATCCTCTTTCTTTTCA 57.297 42.857 0.00 0.00 38.72 2.69
2798 2846 3.604582 AGGCGATCCTCTTTCTTTTCAG 58.395 45.455 0.00 0.00 38.72 3.02
2799 2847 2.680339 GGCGATCCTCTTTCTTTTCAGG 59.320 50.000 0.00 0.00 0.00 3.86
2800 2848 3.600388 GCGATCCTCTTTCTTTTCAGGA 58.400 45.455 0.00 0.00 39.42 3.86
2801 2849 3.620821 GCGATCCTCTTTCTTTTCAGGAG 59.379 47.826 0.00 0.00 38.47 3.69
2802 2850 4.621747 GCGATCCTCTTTCTTTTCAGGAGA 60.622 45.833 0.00 0.00 38.47 3.71
2803 2851 5.669477 CGATCCTCTTTCTTTTCAGGAGAT 58.331 41.667 0.00 0.00 38.47 2.75
2804 2852 6.112058 CGATCCTCTTTCTTTTCAGGAGATT 58.888 40.000 0.00 0.00 38.47 2.40
2805 2853 6.257630 CGATCCTCTTTCTTTTCAGGAGATTC 59.742 42.308 0.00 0.00 38.47 2.52
2806 2854 6.694445 TCCTCTTTCTTTTCAGGAGATTCT 57.306 37.500 0.00 0.00 31.10 2.40
2807 2855 7.084268 TCCTCTTTCTTTTCAGGAGATTCTT 57.916 36.000 0.00 0.00 31.10 2.52
2808 2856 7.521669 TCCTCTTTCTTTTCAGGAGATTCTTT 58.478 34.615 0.00 0.00 31.10 2.52
2809 2857 7.446625 TCCTCTTTCTTTTCAGGAGATTCTTTG 59.553 37.037 0.00 0.00 31.10 2.77
2810 2858 7.309073 CCTCTTTCTTTTCAGGAGATTCTTTGG 60.309 40.741 0.00 0.00 0.00 3.28
2811 2859 6.491403 TCTTTCTTTTCAGGAGATTCTTTGGG 59.509 38.462 0.00 0.00 0.00 4.12
2812 2860 5.582950 TCTTTTCAGGAGATTCTTTGGGA 57.417 39.130 0.00 0.00 0.00 4.37
2813 2861 5.952387 TCTTTTCAGGAGATTCTTTGGGAA 58.048 37.500 0.00 0.00 38.41 3.97
2814 2862 5.770162 TCTTTTCAGGAGATTCTTTGGGAAC 59.230 40.000 0.00 0.00 36.70 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 6.554419 TGAAAACACTCATAACATATGCTGC 58.446 36.000 1.58 0.00 0.00 5.25
104 106 5.598416 TGTTAGATCATCACAGACCGAAT 57.402 39.130 0.00 0.00 0.00 3.34
178 182 3.135348 CAGTTTATCCCAGCTCATCCAGA 59.865 47.826 0.00 0.00 0.00 3.86
305 310 0.461870 TCAGCAGACACGCACAAAGT 60.462 50.000 0.00 0.00 0.00 2.66
456 461 5.220931 GGTCATGCCAAGTATGAATCTTCAC 60.221 44.000 0.00 0.00 36.52 3.18
466 471 1.686115 GCCAAGGGTCATGCCAAGTAT 60.686 52.381 8.20 0.00 39.65 2.12
526 531 5.449553 AGACCCTGTTGAAAAGACAGATTT 58.550 37.500 5.87 0.00 45.72 2.17
529 534 3.711704 AGAGACCCTGTTGAAAAGACAGA 59.288 43.478 5.87 0.00 45.72 3.41
535 540 5.694995 AGAAATCAGAGACCCTGTTGAAAA 58.305 37.500 0.00 0.00 43.38 2.29
692 697 2.032071 CTCACCGTCAACCCACCC 59.968 66.667 0.00 0.00 0.00 4.61
701 706 2.433868 TGTAAGCACTTCTCACCGTC 57.566 50.000 0.00 0.00 0.00 4.79
716 721 7.643569 ATGATCACATGTAGCCAATTTGTAA 57.356 32.000 0.00 0.00 35.21 2.41
814 821 4.463050 TCATTTTCTGTGGTACCCCTTT 57.537 40.909 10.07 0.00 0.00 3.11
815 822 4.463050 TTCATTTTCTGTGGTACCCCTT 57.537 40.909 10.07 0.00 0.00 3.95
816 823 4.463050 TTTCATTTTCTGTGGTACCCCT 57.537 40.909 10.07 0.00 0.00 4.79
825 832 6.978343 CATGCATGGATTTTCATTTTCTGT 57.022 33.333 19.40 0.00 0.00 3.41
877 884 5.655532 AGTGTCGGAAGGCTTTATAACTCTA 59.344 40.000 0.00 0.00 36.07 2.43
909 916 1.670811 CAAAGCAGACAGGTTGAACGT 59.329 47.619 0.00 0.00 38.12 3.99
988 995 4.129380 CGGAGATGCATATTTGTCCAGAA 58.871 43.478 0.00 0.00 0.00 3.02
1004 1011 1.201429 AGGAAGTGGCCAACGGAGAT 61.201 55.000 7.24 0.00 0.00 2.75
1025 1032 4.462508 TCATGGATAAGGAGATCATCGC 57.537 45.455 0.00 0.00 0.00 4.58
1092 1099 5.171339 ACATAATCAGCATATCCTGGACC 57.829 43.478 0.00 0.00 33.64 4.46
1135 1142 3.365465 CCGTTGGTCAAATCATTACGCAA 60.365 43.478 0.00 0.00 0.00 4.85
1137 1144 2.477189 CCCGTTGGTCAAATCATTACGC 60.477 50.000 0.00 0.00 0.00 4.42
1153 1160 2.529389 AGGCACCTCCTTCCCGTT 60.529 61.111 0.00 0.00 44.75 4.44
1230 1237 3.118482 TGATCTCCTCCGTAGAGTAACGT 60.118 47.826 0.00 0.00 41.27 3.99
1294 1301 4.680237 CGGCGGCTTGACACCTGA 62.680 66.667 7.61 0.00 0.00 3.86
1349 1356 1.290324 GAGCCTTCGACTGACAGCA 59.710 57.895 1.25 0.00 0.00 4.41
1362 1369 0.255318 CCTCATGCAGAAAGGAGCCT 59.745 55.000 6.03 0.00 31.44 4.58
1527 1534 1.278127 ACCACCACCGGTAAATCAGAG 59.722 52.381 6.87 0.00 37.57 3.35
1604 1611 2.981921 AGATGATCTGTCCATAGGCCA 58.018 47.619 5.01 0.00 0.00 5.36
1842 1850 6.541641 GCCAGAAGTGAACAATCAGATATTCT 59.458 38.462 8.23 0.00 35.88 2.40
1885 1893 1.215647 GGGCGGCCGATCTATGTAG 59.784 63.158 33.48 0.00 0.00 2.74
1887 1895 3.626924 GGGGCGGCCGATCTATGT 61.627 66.667 33.48 0.00 0.00 2.29
1905 1913 1.200948 GCTTCCTTGTGATGGTTGCTC 59.799 52.381 0.00 0.00 0.00 4.26
1944 1952 5.520376 ACCAATGCTTATATGCAACCTTC 57.480 39.130 16.33 0.00 46.61 3.46
1956 1964 8.098286 AGTGTAGTACATGTTTACCAATGCTTA 58.902 33.333 2.30 0.00 0.00 3.09
1985 1993 1.447317 CGCTTCATGTGCCCCATACC 61.447 60.000 7.61 0.00 30.71 2.73
1990 1999 4.424711 TCCCGCTTCATGTGCCCC 62.425 66.667 7.61 0.00 0.00 5.80
1993 2002 1.869767 CTATTCTCCCGCTTCATGTGC 59.130 52.381 0.00 0.00 0.00 4.57
1999 2008 4.569943 TCATATTGCTATTCTCCCGCTTC 58.430 43.478 0.00 0.00 0.00 3.86
2076 2089 3.814283 GACGGAGGGAGTACTATACTGTG 59.186 52.174 0.00 0.00 39.59 3.66
2088 2101 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2090 2103 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2091 2104 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2092 2105 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2093 2106 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2094 2107 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2095 2108 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
2096 2109 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
2097 2110 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
2098 2111 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
2099 2112 5.808540 TGTATTTCTCCGACAAGTATTTCCG 59.191 40.000 0.00 0.00 0.00 4.30
2100 2113 7.787725 ATGTATTTCTCCGACAAGTATTTCC 57.212 36.000 0.00 0.00 0.00 3.13
2106 2119 9.226606 TCATTTTTATGTATTTCTCCGACAAGT 57.773 29.630 0.00 0.00 0.00 3.16
2152 2165 8.908903 GTCGGAGGAATGAATGTATCTAGATAT 58.091 37.037 15.43 0.00 0.00 1.63
2153 2166 7.065923 CGTCGGAGGAATGAATGTATCTAGATA 59.934 40.741 8.44 8.44 0.00 1.98
2154 2167 6.127869 CGTCGGAGGAATGAATGTATCTAGAT 60.128 42.308 10.73 10.73 0.00 1.98
2155 2168 5.181433 CGTCGGAGGAATGAATGTATCTAGA 59.819 44.000 0.00 0.00 0.00 2.43
2156 2169 5.181433 TCGTCGGAGGAATGAATGTATCTAG 59.819 44.000 0.00 0.00 0.00 2.43
2157 2170 5.067954 TCGTCGGAGGAATGAATGTATCTA 58.932 41.667 0.00 0.00 0.00 1.98
2158 2171 3.889538 TCGTCGGAGGAATGAATGTATCT 59.110 43.478 0.00 0.00 0.00 1.98
2159 2172 4.230657 CTCGTCGGAGGAATGAATGTATC 58.769 47.826 1.73 0.00 36.61 2.24
2160 2173 3.637229 ACTCGTCGGAGGAATGAATGTAT 59.363 43.478 1.73 0.00 44.93 2.29
2161 2174 3.021695 ACTCGTCGGAGGAATGAATGTA 58.978 45.455 1.73 0.00 44.93 2.29
2162 2175 1.825474 ACTCGTCGGAGGAATGAATGT 59.175 47.619 1.73 0.00 44.93 2.71
2163 2176 2.586258 ACTCGTCGGAGGAATGAATG 57.414 50.000 1.73 0.00 44.93 2.67
2164 2177 4.939052 AATACTCGTCGGAGGAATGAAT 57.061 40.909 1.73 0.00 44.93 2.57
2165 2178 4.441079 GGAAATACTCGTCGGAGGAATGAA 60.441 45.833 1.73 0.00 44.93 2.57
2166 2179 3.067742 GGAAATACTCGTCGGAGGAATGA 59.932 47.826 1.73 0.00 44.93 2.57
2167 2180 3.381949 GGAAATACTCGTCGGAGGAATG 58.618 50.000 1.73 0.00 44.93 2.67
2168 2181 2.034305 CGGAAATACTCGTCGGAGGAAT 59.966 50.000 1.73 0.00 44.93 3.01
2169 2182 1.402968 CGGAAATACTCGTCGGAGGAA 59.597 52.381 1.73 0.00 44.93 3.36
2170 2183 1.019673 CGGAAATACTCGTCGGAGGA 58.980 55.000 0.00 0.00 44.93 3.71
2171 2184 0.030369 CCGGAAATACTCGTCGGAGG 59.970 60.000 0.00 0.00 44.93 4.30
2172 2185 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
2173 2186 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
2174 2187 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
2175 2188 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
2176 2189 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
2177 2190 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
2178 2191 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
2179 2192 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
2180 2193 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2181 2194 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2182 2195 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2183 2196 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2184 2197 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
2185 2198 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2186 2199 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
2187 2200 3.217743 GCTACTCCCTCCGTCCGG 61.218 72.222 0.00 0.00 0.00 5.14
2188 2201 2.124236 AGCTACTCCCTCCGTCCG 60.124 66.667 0.00 0.00 0.00 4.79
2189 2202 2.787567 GCAGCTACTCCCTCCGTCC 61.788 68.421 0.00 0.00 0.00 4.79
2190 2203 1.755008 AGCAGCTACTCCCTCCGTC 60.755 63.158 0.00 0.00 0.00 4.79
2191 2204 2.055042 CAGCAGCTACTCCCTCCGT 61.055 63.158 0.00 0.00 0.00 4.69
2192 2205 2.811101 CAGCAGCTACTCCCTCCG 59.189 66.667 0.00 0.00 0.00 4.63
2193 2206 1.694133 ATGCAGCAGCTACTCCCTCC 61.694 60.000 0.00 0.00 42.74 4.30
2194 2207 0.179936 AATGCAGCAGCTACTCCCTC 59.820 55.000 0.00 0.00 42.74 4.30
2195 2208 1.500474 TAATGCAGCAGCTACTCCCT 58.500 50.000 0.00 0.00 42.74 4.20
2196 2209 2.332063 TTAATGCAGCAGCTACTCCC 57.668 50.000 0.00 0.00 42.74 4.30
2197 2210 2.356069 GGTTTAATGCAGCAGCTACTCC 59.644 50.000 0.00 0.00 42.74 3.85
2198 2211 3.009723 TGGTTTAATGCAGCAGCTACTC 58.990 45.455 0.00 0.00 42.74 2.59
2199 2212 3.071874 TGGTTTAATGCAGCAGCTACT 57.928 42.857 0.00 0.00 42.74 2.57
2200 2213 3.848272 TTGGTTTAATGCAGCAGCTAC 57.152 42.857 0.00 0.00 42.74 3.58
2201 2214 3.826157 AGTTTGGTTTAATGCAGCAGCTA 59.174 39.130 0.00 0.00 42.74 3.32
2202 2215 2.629617 AGTTTGGTTTAATGCAGCAGCT 59.370 40.909 0.00 0.00 42.74 4.24
2203 2216 3.030668 AGTTTGGTTTAATGCAGCAGC 57.969 42.857 0.00 0.00 42.57 5.25
2204 2217 3.184986 GCAAGTTTGGTTTAATGCAGCAG 59.815 43.478 0.00 0.00 34.10 4.24
2205 2218 3.129871 GCAAGTTTGGTTTAATGCAGCA 58.870 40.909 0.00 0.00 34.10 4.41
2206 2219 3.392882 AGCAAGTTTGGTTTAATGCAGC 58.607 40.909 0.00 0.00 34.89 5.25
2207 2220 4.874970 AGAGCAAGTTTGGTTTAATGCAG 58.125 39.130 0.00 0.00 39.30 4.41
2267 2281 4.063689 CTCGTATGGTCGGTCTGTATAGT 58.936 47.826 0.00 0.00 0.00 2.12
2268 2282 4.313282 TCTCGTATGGTCGGTCTGTATAG 58.687 47.826 0.00 0.00 0.00 1.31
2273 2287 2.357952 TGATTCTCGTATGGTCGGTCTG 59.642 50.000 0.00 0.00 0.00 3.51
2278 2292 3.145212 TGTGTGATTCTCGTATGGTCG 57.855 47.619 0.00 0.00 0.00 4.79
2290 2304 2.030007 CGCATTGGGTCTTTGTGTGATT 60.030 45.455 0.00 0.00 0.00 2.57
2295 2309 1.238439 ACTCGCATTGGGTCTTTGTG 58.762 50.000 0.24 0.00 0.00 3.33
2305 2319 2.159627 ACGAAGCCTAAAACTCGCATTG 59.840 45.455 0.00 0.00 0.00 2.82
2327 2341 0.463654 TATGTGCTCCCAACATCGGC 60.464 55.000 0.00 0.00 0.00 5.54
2328 2342 1.134401 ACTATGTGCTCCCAACATCGG 60.134 52.381 0.00 0.00 0.00 4.18
2333 2347 1.209504 TGGCTACTATGTGCTCCCAAC 59.790 52.381 0.00 0.00 0.00 3.77
2362 2376 1.880271 CATGCCTCTCATGCCTACAG 58.120 55.000 0.00 0.00 45.20 2.74
2370 2384 3.972638 ACTATGTTCCTCATGCCTCTCAT 59.027 43.478 0.00 0.00 37.91 2.90
2371 2385 3.133542 CACTATGTTCCTCATGCCTCTCA 59.866 47.826 0.00 0.00 37.91 3.27
2372 2386 3.386078 TCACTATGTTCCTCATGCCTCTC 59.614 47.826 0.00 0.00 37.91 3.20
2373 2387 3.378512 TCACTATGTTCCTCATGCCTCT 58.621 45.455 0.00 0.00 37.91 3.69
2374 2388 3.827008 TCACTATGTTCCTCATGCCTC 57.173 47.619 0.00 0.00 37.91 4.70
2375 2389 3.713248 TGATCACTATGTTCCTCATGCCT 59.287 43.478 0.00 0.00 37.91 4.75
2376 2390 3.812053 GTGATCACTATGTTCCTCATGCC 59.188 47.826 18.83 0.00 37.91 4.40
2377 2391 3.812053 GGTGATCACTATGTTCCTCATGC 59.188 47.826 24.50 0.00 37.91 4.06
2378 2392 4.813161 GTGGTGATCACTATGTTCCTCATG 59.187 45.833 24.50 0.00 42.86 3.07
2379 2393 4.471025 TGTGGTGATCACTATGTTCCTCAT 59.529 41.667 24.50 0.00 46.20 2.90
2392 2406 1.583556 ATGCCTAGGTGTGGTGATCA 58.416 50.000 11.31 0.00 0.00 2.92
2393 2407 2.700897 AGTATGCCTAGGTGTGGTGATC 59.299 50.000 11.31 0.00 0.00 2.92
2395 2409 2.247699 AGTATGCCTAGGTGTGGTGA 57.752 50.000 11.31 0.00 0.00 4.02
2420 2434 5.755409 TCTAGCAGGAACACCATCTAAAA 57.245 39.130 0.00 0.00 0.00 1.52
2430 2456 1.279496 AGGCACATCTAGCAGGAACA 58.721 50.000 0.00 0.00 0.00 3.18
2447 2473 1.896220 TTGTGTGCCAGCTAAGAAGG 58.104 50.000 0.00 0.00 0.00 3.46
2456 2482 0.660488 TACAACGCTTTGTGTGCCAG 59.340 50.000 18.06 0.00 45.91 4.85
2471 2519 9.391006 AGTCTAAACAGAACAACAGAAATACAA 57.609 29.630 0.00 0.00 0.00 2.41
2472 2520 8.958119 AGTCTAAACAGAACAACAGAAATACA 57.042 30.769 0.00 0.00 0.00 2.29
2482 2530 5.458891 GCGTCTAGAGTCTAAACAGAACAA 58.541 41.667 4.56 0.00 0.00 2.83
2484 2532 4.082895 TGGCGTCTAGAGTCTAAACAGAAC 60.083 45.833 4.56 0.00 0.00 3.01
2490 2538 2.823747 TGCTTGGCGTCTAGAGTCTAAA 59.176 45.455 1.70 0.00 0.00 1.85
2491 2539 2.443416 TGCTTGGCGTCTAGAGTCTAA 58.557 47.619 1.70 0.00 0.00 2.10
2498 2546 2.283298 ACATGATTGCTTGGCGTCTAG 58.717 47.619 0.00 0.00 0.00 2.43
2523 2571 7.558081 ACATGTGCTTCATAGAACTACTCTAGA 59.442 37.037 0.00 0.00 40.06 2.43
2528 2576 6.128172 GCAAACATGTGCTTCATAGAACTACT 60.128 38.462 0.00 0.00 41.51 2.57
2529 2577 6.024049 GCAAACATGTGCTTCATAGAACTAC 58.976 40.000 0.00 0.00 41.51 2.73
2531 2579 5.051891 GCAAACATGTGCTTCATAGAACT 57.948 39.130 0.00 0.00 41.51 3.01
2542 2590 0.109781 CCGTGGTAGCAAACATGTGC 60.110 55.000 0.00 0.00 45.28 4.57
2551 2599 2.358615 CTGCAAGCCGTGGTAGCA 60.359 61.111 0.00 0.00 0.00 3.49
2553 2601 2.680913 GCACTGCAAGCCGTGGTAG 61.681 63.158 16.43 0.00 37.60 3.18
2557 2605 4.374702 GTCGCACTGCAAGCCGTG 62.375 66.667 11.55 11.55 37.60 4.94
2610 2658 1.009078 ATGATCATGAACACGCCGTG 58.991 50.000 16.94 16.94 39.75 4.94
2611 2659 1.009078 CATGATCATGAACACGCCGT 58.991 50.000 28.37 0.00 41.20 5.68
2647 2695 3.121030 GACAGCTTGCGCATCCGT 61.121 61.111 12.75 6.43 39.10 4.69
2651 2699 2.557805 CGTTGACAGCTTGCGCAT 59.442 55.556 12.75 0.00 39.10 4.73
2669 2717 2.509336 GACACCCAGATCGCACGG 60.509 66.667 0.00 0.00 0.00 4.94
2671 2719 2.094659 CGTGACACCCAGATCGCAC 61.095 63.158 0.00 0.00 0.00 5.34
2676 2724 1.301716 GCACACGTGACACCCAGAT 60.302 57.895 25.01 0.00 0.00 2.90
2697 2745 1.067142 TCTCCTACGCCATGTGTTCAC 60.067 52.381 0.00 0.00 0.00 3.18
2703 2751 2.180276 AGTTCTTCTCCTACGCCATGT 58.820 47.619 0.00 0.00 0.00 3.21
2705 2753 3.983044 AAAGTTCTTCTCCTACGCCAT 57.017 42.857 0.00 0.00 0.00 4.40
2707 2755 4.082354 TCACTAAAGTTCTTCTCCTACGCC 60.082 45.833 0.00 0.00 0.00 5.68
2709 2757 6.583050 CACTTCACTAAAGTTCTTCTCCTACG 59.417 42.308 0.00 0.00 46.26 3.51
2728 2776 2.306847 GGAAGGAAAGTTGCCACTTCA 58.693 47.619 1.70 0.00 42.89 3.02
2729 2777 1.613925 GGGAAGGAAAGTTGCCACTTC 59.386 52.381 1.70 0.00 42.89 3.01
2731 2779 0.853530 AGGGAAGGAAAGTTGCCACT 59.146 50.000 1.70 0.00 40.31 4.00
2740 2788 2.640826 ACACAACGGATAGGGAAGGAAA 59.359 45.455 0.00 0.00 0.00 3.13
2745 2793 0.981183 AGCACACAACGGATAGGGAA 59.019 50.000 0.00 0.00 0.00 3.97
2747 2795 0.806102 CGAGCACACAACGGATAGGG 60.806 60.000 0.00 0.00 0.00 3.53
2748 2796 0.108804 ACGAGCACACAACGGATAGG 60.109 55.000 0.00 0.00 0.00 2.57
2750 2798 2.157834 AAACGAGCACACAACGGATA 57.842 45.000 0.00 0.00 0.00 2.59
2751 2799 1.263217 GAAAACGAGCACACAACGGAT 59.737 47.619 0.00 0.00 0.00 4.18
2752 2800 0.653636 GAAAACGAGCACACAACGGA 59.346 50.000 0.00 0.00 0.00 4.69
2753 2801 0.655733 AGAAAACGAGCACACAACGG 59.344 50.000 0.00 0.00 0.00 4.44
2754 2802 2.452006 AAGAAAACGAGCACACAACG 57.548 45.000 0.00 0.00 0.00 4.10
2755 2803 4.162812 TCAAAAGAAAACGAGCACACAAC 58.837 39.130 0.00 0.00 0.00 3.32
2756 2804 4.411327 CTCAAAAGAAAACGAGCACACAA 58.589 39.130 0.00 0.00 0.00 3.33
2757 2805 3.181501 CCTCAAAAGAAAACGAGCACACA 60.182 43.478 0.00 0.00 0.00 3.72
2758 2806 3.363178 CCTCAAAAGAAAACGAGCACAC 58.637 45.455 0.00 0.00 0.00 3.82
2759 2807 2.223479 GCCTCAAAAGAAAACGAGCACA 60.223 45.455 0.00 0.00 0.00 4.57
2760 2808 2.385315 GCCTCAAAAGAAAACGAGCAC 58.615 47.619 0.00 0.00 0.00 4.40
2761 2809 1.002900 CGCCTCAAAAGAAAACGAGCA 60.003 47.619 0.00 0.00 0.00 4.26
2762 2810 1.263217 TCGCCTCAAAAGAAAACGAGC 59.737 47.619 0.00 0.00 0.00 5.03
2763 2811 3.424962 GGATCGCCTCAAAAGAAAACGAG 60.425 47.826 0.00 0.00 0.00 4.18
2764 2812 2.482721 GGATCGCCTCAAAAGAAAACGA 59.517 45.455 0.00 0.00 0.00 3.85
2765 2813 2.484264 AGGATCGCCTCAAAAGAAAACG 59.516 45.455 0.00 0.00 42.19 3.60
2778 2826 2.680339 CCTGAAAAGAAAGAGGATCGCC 59.320 50.000 0.00 0.00 42.67 5.54
2779 2827 3.600388 TCCTGAAAAGAAAGAGGATCGC 58.400 45.455 0.00 0.00 42.67 4.58
2780 2828 5.078411 TCTCCTGAAAAGAAAGAGGATCG 57.922 43.478 0.00 0.00 42.67 3.69
2781 2829 7.337938 AGAATCTCCTGAAAAGAAAGAGGATC 58.662 38.462 0.00 0.00 34.07 3.36
2782 2830 7.269522 AGAATCTCCTGAAAAGAAAGAGGAT 57.730 36.000 0.00 0.00 34.07 3.24
2783 2831 6.694445 AGAATCTCCTGAAAAGAAAGAGGA 57.306 37.500 0.00 0.00 33.45 3.71
2784 2832 7.309073 CCAAAGAATCTCCTGAAAAGAAAGAGG 60.309 40.741 0.00 0.00 0.00 3.69
2785 2833 7.309073 CCCAAAGAATCTCCTGAAAAGAAAGAG 60.309 40.741 0.00 0.00 0.00 2.85
2786 2834 6.491403 CCCAAAGAATCTCCTGAAAAGAAAGA 59.509 38.462 0.00 0.00 0.00 2.52
2787 2835 6.491403 TCCCAAAGAATCTCCTGAAAAGAAAG 59.509 38.462 0.00 0.00 0.00 2.62
2788 2836 6.372931 TCCCAAAGAATCTCCTGAAAAGAAA 58.627 36.000 0.00 0.00 0.00 2.52
2789 2837 5.952387 TCCCAAAGAATCTCCTGAAAAGAA 58.048 37.500 0.00 0.00 0.00 2.52
2790 2838 5.582950 TCCCAAAGAATCTCCTGAAAAGA 57.417 39.130 0.00 0.00 0.00 2.52
2791 2839 5.047731 GGTTCCCAAAGAATCTCCTGAAAAG 60.048 44.000 0.00 0.00 36.69 2.27
2792 2840 4.832823 GGTTCCCAAAGAATCTCCTGAAAA 59.167 41.667 0.00 0.00 36.69 2.29
2793 2841 4.407365 GGTTCCCAAAGAATCTCCTGAAA 58.593 43.478 0.00 0.00 36.69 2.69
2794 2842 4.034285 GGTTCCCAAAGAATCTCCTGAA 57.966 45.455 0.00 0.00 36.69 3.02
2795 2843 3.721087 GGTTCCCAAAGAATCTCCTGA 57.279 47.619 0.00 0.00 36.69 3.86


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

AutoCloner maintained by Alex Coulton.