Multiple sequence alignment - TraesCS4B01G245900

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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 TraesCS4B01G245900 chr4B 100.000 5913 0 0 1 5913 509038336 509032424 0.000000e+00 10920.0
1 TraesCS4B01G245900 chr4B 85.135 74 8 3 3446 3516 445322961 445323034 8.220000e-09 73.1
2 TraesCS4B01G245900 chr4D 95.333 2164 72 17 1 2149 412718735 412716586 0.000000e+00 3410.0
3 TraesCS4B01G245900 chr4D 90.324 1788 119 18 3515 5266 412715371 412713602 0.000000e+00 2294.0
4 TraesCS4B01G245900 chr4D 92.857 896 45 9 2159 3040 412716626 412715736 0.000000e+00 1282.0
5 TraesCS4B01G245900 chr4D 93.386 378 23 2 3099 3474 412715743 412715366 5.180000e-155 558.0
6 TraesCS4B01G245900 chr4A 94.529 2175 75 19 1 2141 51136936 51139100 0.000000e+00 3317.0
7 TraesCS4B01G245900 chr4A 91.341 1640 86 20 3670 5266 51140692 51142318 0.000000e+00 2191.0
8 TraesCS4B01G245900 chr4A 91.470 891 53 8 2172 3040 51139073 51139962 0.000000e+00 1203.0
9 TraesCS4B01G245900 chr4A 92.126 381 28 2 3096 3474 51139952 51140332 2.430000e-148 536.0
10 TraesCS4B01G245900 chr4A 88.272 162 15 4 3515 3672 51140327 51140488 2.170000e-44 191.0
11 TraesCS4B01G245900 chr4A 95.918 49 2 0 5844 5892 51142379 51142427 4.910000e-11 80.5
12 TraesCS4B01G245900 chr5B 96.127 568 22 0 5269 5836 489098513 489099080 0.000000e+00 928.0
13 TraesCS4B01G245900 chr5B 95.629 572 25 0 5265 5836 621505615 621506186 0.000000e+00 918.0
14 TraesCS4B01G245900 chr5B 95.606 569 25 0 5268 5836 321568787 321568219 0.000000e+00 913.0
15 TraesCS4B01G245900 chr5B 95.606 569 25 0 5268 5836 610019035 610018467 0.000000e+00 913.0
16 TraesCS4B01G245900 chr5B 94.921 571 29 0 5265 5835 689459264 689459834 0.000000e+00 894.0
17 TraesCS4B01G245900 chr6B 95.965 570 22 1 5268 5836 23042472 23041903 0.000000e+00 924.0
18 TraesCS4B01G245900 chr6B 95.288 573 26 1 5264 5836 41567769 41568340 0.000000e+00 907.0
19 TraesCS4B01G245900 chr1B 95.629 572 25 0 5265 5836 24112852 24113423 0.000000e+00 918.0
20 TraesCS4B01G245900 chr3B 94.755 572 30 0 5265 5836 142285940 142286511 0.000000e+00 891.0
21 TraesCS4B01G245900 chrUn 92.453 53 2 2 3475 3526 45258325 45258274 2.290000e-09 75.0
22 TraesCS4B01G245900 chrUn 92.453 53 2 2 3475 3526 378001444 378001393 2.290000e-09 75.0
23 TraesCS4B01G245900 chrUn 92.453 53 2 2 3475 3526 378185197 378185146 2.290000e-09 75.0
24 TraesCS4B01G245900 chrUn 83.333 84 10 4 3446 3526 404872003 404872085 2.290000e-09 75.0
25 TraesCS4B01G245900 chrUn 85.135 74 8 3 3446 3516 269554242 269554315 8.220000e-09 73.1
26 TraesCS4B01G245900 chr7D 97.674 43 0 1 3475 3516 47905522 47905480 8.220000e-09 73.1
27 TraesCS4B01G245900 chr6A 85.135 74 8 3 3446 3516 46103656 46103729 8.220000e-09 73.1
28 TraesCS4B01G245900 chr6A 85.135 74 8 3 3446 3516 46134576 46134649 8.220000e-09 73.1


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 TraesCS4B01G245900 chr4B 509032424 509038336 5912 True 10920.000000 10920 100.000 1 5913 1 chr4B.!!$R1 5912
1 TraesCS4B01G245900 chr4D 412713602 412718735 5133 True 1886.000000 3410 92.975 1 5266 4 chr4D.!!$R1 5265
2 TraesCS4B01G245900 chr4A 51136936 51142427 5491 False 1253.083333 3317 92.276 1 5892 6 chr4A.!!$F1 5891
3 TraesCS4B01G245900 chr5B 489098513 489099080 567 False 928.000000 928 96.127 5269 5836 1 chr5B.!!$F1 567
4 TraesCS4B01G245900 chr5B 621505615 621506186 571 False 918.000000 918 95.629 5265 5836 1 chr5B.!!$F2 571
5 TraesCS4B01G245900 chr5B 321568219 321568787 568 True 913.000000 913 95.606 5268 5836 1 chr5B.!!$R1 568
6 TraesCS4B01G245900 chr5B 610018467 610019035 568 True 913.000000 913 95.606 5268 5836 1 chr5B.!!$R2 568
7 TraesCS4B01G245900 chr5B 689459264 689459834 570 False 894.000000 894 94.921 5265 5835 1 chr5B.!!$F3 570
8 TraesCS4B01G245900 chr6B 23041903 23042472 569 True 924.000000 924 95.965 5268 5836 1 chr6B.!!$R1 568
9 TraesCS4B01G245900 chr6B 41567769 41568340 571 False 907.000000 907 95.288 5264 5836 1 chr6B.!!$F1 572
10 TraesCS4B01G245900 chr1B 24112852 24113423 571 False 918.000000 918 95.629 5265 5836 1 chr1B.!!$F1 571
11 TraesCS4B01G245900 chr3B 142285940 142286511 571 False 891.000000 891 94.755 5265 5836 1 chr3B.!!$F1 571

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
938 961 0.036022 GCCCAAGCTCACTCTTGACT 59.964 55.0 5.19 0.00 44.61 3.41 F
1827 1861 0.372334 GTCTCACTCTCGTCTCGCTC 59.628 60.0 0.00 0.00 0.00 5.03 F
3027 3091 0.108520 TGGGAGTTTACGGCGCTTAG 60.109 55.0 6.90 1.39 0.00 2.18 F
3028 3092 0.174162 GGGAGTTTACGGCGCTTAGA 59.826 55.0 6.90 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2404 0.607620 AAAACCCCATGAATGCCACG 59.392 50.000 0.00 0.0 0.00 4.94 R
3722 3997 1.069432 GTGTTGCTGCATGTCTGTCAG 60.069 52.381 1.84 0.0 32.82 3.51 R
4161 4470 0.111061 TGACCTCAAGGCACAGCAAT 59.889 50.000 0.00 0.0 39.32 3.56 R
4912 5227 0.601558 CCAGCATGCTTATGATGCCC 59.398 55.000 19.98 0.0 46.24 5.36 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
41 42 0.741915 ACACCAACGGCGAAAACAAT 59.258 45.000 16.62 0.00 0.00 2.71
60 61 7.603963 AACAATAGCGTAACACACATGATAA 57.396 32.000 0.00 0.00 0.00 1.75
171 174 0.251354 AGCAGGCGATCACACTCATT 59.749 50.000 0.00 0.00 0.00 2.57
210 213 8.446714 ATAGGATCCTATGAGTGAATTCACAT 57.553 34.615 33.92 23.64 41.83 3.21
226 229 2.159435 TCACATGACGACCATACGTGAG 60.159 50.000 0.00 0.00 46.52 3.51
377 385 2.677542 AGGCCTACACCGATAGATCA 57.322 50.000 1.29 0.00 39.76 2.92
472 480 3.159615 TGGATGTGCCACTGCTCA 58.840 55.556 0.00 0.00 43.33 4.26
538 546 1.874231 CTCGATCGGAAGTAGCAGCTA 59.126 52.381 16.41 0.00 0.00 3.32
539 547 2.486203 CTCGATCGGAAGTAGCAGCTAT 59.514 50.000 16.41 0.00 0.00 2.97
576 584 2.039624 GGAGGAGGTGGAGCAGGA 59.960 66.667 0.00 0.00 0.00 3.86
599 611 4.699522 GGCCGGGGTGTGACAGTC 62.700 72.222 2.18 0.00 0.00 3.51
718 730 4.181578 CAACTTTATGGGTGTCCGTCTAG 58.818 47.826 0.00 0.00 35.24 2.43
827 841 2.885266 GACCTCTCTACACACACACTCA 59.115 50.000 0.00 0.00 0.00 3.41
882 905 0.935194 CTACCTCCCACCCTCCTACT 59.065 60.000 0.00 0.00 0.00 2.57
902 925 3.054287 ACTCTCCACATCCTCGTCTTCTA 60.054 47.826 0.00 0.00 0.00 2.10
914 937 2.753452 TCGTCTTCTATTGGCTCTTCGT 59.247 45.455 0.00 0.00 0.00 3.85
916 939 3.427638 CGTCTTCTATTGGCTCTTCGTGA 60.428 47.826 0.00 0.00 0.00 4.35
938 961 0.036022 GCCCAAGCTCACTCTTGACT 59.964 55.000 5.19 0.00 44.61 3.41
1106 1133 1.064357 CTCGAGAAACCGGAGCTACTC 59.936 57.143 9.46 8.52 0.00 2.59
1131 1158 2.111384 CTGGGCTAGTAGGAGCTTTGA 58.889 52.381 0.00 0.00 42.43 2.69
1166 1193 6.928492 TGGATTTTGTTTTGTCCTAGCATTTC 59.072 34.615 0.00 0.00 0.00 2.17
1171 1198 7.769272 TTGTTTTGTCCTAGCATTTCTTTTG 57.231 32.000 0.00 0.00 0.00 2.44
1235 1262 1.138661 CTTCTTGCTAGCTCTCCCTGG 59.861 57.143 17.23 0.00 0.00 4.45
1246 1273 1.081092 CTCCCTGGTTGGAGGAGGA 59.919 63.158 0.00 0.00 46.85 3.71
1260 1287 4.044317 TGGAGGAGGAGACACTTACTAGTT 59.956 45.833 0.00 0.00 30.26 2.24
1274 1301 9.062524 ACACTTACTAGTTTTATTGTTCATGCA 57.937 29.630 0.00 0.00 30.26 3.96
1524 1551 1.607178 CTCTTTGGCATGCACCCCA 60.607 57.895 21.36 5.00 0.00 4.96
1590 1617 4.917474 GCGCCATGCAAAGGAATT 57.083 50.000 12.36 0.00 45.45 2.17
1629 1663 4.434520 TCACACAGTTTACGTCATTGTGA 58.565 39.130 22.48 16.24 41.12 3.58
1816 1850 1.079750 GCCGTTCCAGGTCTCACTC 60.080 63.158 0.00 0.00 0.00 3.51
1827 1861 0.372334 GTCTCACTCTCGTCTCGCTC 59.628 60.000 0.00 0.00 0.00 5.03
1935 1969 7.164230 TCTTGTTATGAGGAGAGAGAAAGTC 57.836 40.000 0.00 0.00 0.00 3.01
1939 1973 6.127225 TGTTATGAGGAGAGAGAAAGTCATGG 60.127 42.308 0.00 0.00 0.00 3.66
1961 1995 0.739813 ACGAACGGTGCAGGATAAGC 60.740 55.000 0.00 0.00 0.00 3.09
1963 1997 1.448985 GAACGGTGCAGGATAAGCAA 58.551 50.000 0.00 0.00 44.64 3.91
1973 2007 2.676839 CAGGATAAGCAACTGCACTGAG 59.323 50.000 4.22 0.00 45.16 3.35
2009 2050 8.379457 AGTAAAACACACAAAGAAGTAGATCC 57.621 34.615 0.00 0.00 0.00 3.36
2054 2095 5.459536 TCTCATGAAATATGGTCCTCTCG 57.540 43.478 0.00 0.00 0.00 4.04
2055 2096 4.281941 TCTCATGAAATATGGTCCTCTCGG 59.718 45.833 0.00 0.00 0.00 4.63
2081 2124 2.177394 TTCAGATTGCGCCAGTGTTA 57.823 45.000 4.18 0.00 0.00 2.41
2087 2130 0.948678 TTGCGCCAGTGTTACCTTTC 59.051 50.000 4.18 0.00 0.00 2.62
2107 2150 5.789643 TTCCTTTGCTATCTTTGTTTGCT 57.210 34.783 0.00 0.00 0.00 3.91
2108 2151 5.376854 TCCTTTGCTATCTTTGTTTGCTC 57.623 39.130 0.00 0.00 0.00 4.26
2109 2152 5.072741 TCCTTTGCTATCTTTGTTTGCTCT 58.927 37.500 0.00 0.00 0.00 4.09
2110 2153 5.182001 TCCTTTGCTATCTTTGTTTGCTCTC 59.818 40.000 0.00 0.00 0.00 3.20
2111 2154 5.182760 CCTTTGCTATCTTTGTTTGCTCTCT 59.817 40.000 0.00 0.00 0.00 3.10
2112 2155 5.869753 TTGCTATCTTTGTTTGCTCTCTC 57.130 39.130 0.00 0.00 0.00 3.20
2113 2156 5.157940 TGCTATCTTTGTTTGCTCTCTCT 57.842 39.130 0.00 0.00 0.00 3.10
2114 2157 5.174395 TGCTATCTTTGTTTGCTCTCTCTC 58.826 41.667 0.00 0.00 0.00 3.20
2115 2158 5.046735 TGCTATCTTTGTTTGCTCTCTCTCT 60.047 40.000 0.00 0.00 0.00 3.10
2116 2159 5.519927 GCTATCTTTGTTTGCTCTCTCTCTC 59.480 44.000 0.00 0.00 0.00 3.20
2117 2160 5.743636 ATCTTTGTTTGCTCTCTCTCTCT 57.256 39.130 0.00 0.00 0.00 3.10
2118 2161 5.132897 TCTTTGTTTGCTCTCTCTCTCTC 57.867 43.478 0.00 0.00 0.00 3.20
2119 2162 4.832266 TCTTTGTTTGCTCTCTCTCTCTCT 59.168 41.667 0.00 0.00 0.00 3.10
2120 2163 4.782019 TTGTTTGCTCTCTCTCTCTCTC 57.218 45.455 0.00 0.00 0.00 3.20
2121 2164 4.032960 TGTTTGCTCTCTCTCTCTCTCT 57.967 45.455 0.00 0.00 0.00 3.10
2122 2165 4.009675 TGTTTGCTCTCTCTCTCTCTCTC 58.990 47.826 0.00 0.00 0.00 3.20
2123 2166 4.263462 TGTTTGCTCTCTCTCTCTCTCTCT 60.263 45.833 0.00 0.00 0.00 3.10
2124 2167 4.574674 TTGCTCTCTCTCTCTCTCTCTT 57.425 45.455 0.00 0.00 0.00 2.85
2125 2168 4.574674 TGCTCTCTCTCTCTCTCTCTTT 57.425 45.455 0.00 0.00 0.00 2.52
2166 2209 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2167 2210 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2168 2211 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2169 2212 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2170 2213 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
2171 2214 5.960811 TCTCTCTCTCTCTCTCTCTCTCTTT 59.039 44.000 0.00 0.00 0.00 2.52
2172 2215 6.097554 TCTCTCTCTCTCTCTCTCTCTCTTTC 59.902 46.154 0.00 0.00 0.00 2.62
2173 2216 5.960811 TCTCTCTCTCTCTCTCTCTCTTTCT 59.039 44.000 0.00 0.00 0.00 2.52
2174 2217 6.097554 TCTCTCTCTCTCTCTCTCTCTTTCTC 59.902 46.154 0.00 0.00 0.00 2.87
2175 2218 5.960811 TCTCTCTCTCTCTCTCTCTTTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2176 2219 6.097554 TCTCTCTCTCTCTCTCTCTTTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2177 2220 5.960811 TCTCTCTCTCTCTCTCTTTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2178 2221 6.097554 TCTCTCTCTCTCTCTCTTTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2179 2222 5.960811 TCTCTCTCTCTCTCTTTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2180 2223 6.097554 TCTCTCTCTCTCTCTTTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2181 2224 5.960811 TCTCTCTCTCTCTTTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2182 2225 6.097554 TCTCTCTCTCTCTTTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2183 2226 5.960811 TCTCTCTCTCTTTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2184 2227 6.097554 TCTCTCTCTCTTTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2185 2228 5.960811 TCTCTCTCTTTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2186 2229 6.097554 TCTCTCTCTTTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2187 2230 5.960811 TCTCTCTTTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2188 2231 6.097554 TCTCTCTTTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2189 2232 5.960811 TCTCTTTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2190 2233 6.097554 TCTCTTTCTCTCTCTCTCTCTCTCTC 59.902 46.154 0.00 0.00 0.00 3.20
2191 2234 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
2192 2235 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
2193 2236 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2194 2237 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2195 2238 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2196 2239 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2197 2240 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2210 2253 1.826720 CTCTCTCTCCTTGAGCTGCTT 59.173 52.381 2.53 0.00 42.38 3.91
2319 2362 0.752009 TGCAAAAGCCGGTTGGTGTA 60.752 50.000 1.90 0.00 37.67 2.90
2346 2389 2.046604 AGCATGCAGAAGCGAGCA 60.047 55.556 21.98 0.00 46.23 4.26
2382 2431 2.425539 GTGGCATTCATGGGGTTTTTG 58.574 47.619 0.00 0.00 0.00 2.44
2481 2534 2.478831 GCTCGTGAAGATCTGGGAATC 58.521 52.381 0.00 0.00 0.00 2.52
2548 2610 5.578336 AGATGTTGATTCTGATGTGTACACG 59.422 40.000 20.61 6.89 0.00 4.49
2555 2617 7.320399 TGATTCTGATGTGTACACGTATTTCT 58.680 34.615 20.49 6.28 0.00 2.52
2561 2623 2.093783 GTGTACACGTATTTCTGGCTGC 59.906 50.000 10.84 0.00 0.00 5.25
2680 2742 5.348997 AGCGTAAGTAGCAAGAAACTTCATC 59.651 40.000 0.00 0.00 37.19 2.92
2704 2766 7.217906 TCACCTCTTCCTTCTTTTCTTTCTAC 58.782 38.462 0.00 0.00 0.00 2.59
2719 2783 7.440523 TTCTTTCTACTTTTGCTCTTCCATC 57.559 36.000 0.00 0.00 0.00 3.51
2729 2793 1.140652 GCTCTTCCATCCTTCTGGAGG 59.859 57.143 0.00 0.00 45.80 4.30
2876 2940 0.981183 AGAAACACCGCCTACCATCA 59.019 50.000 0.00 0.00 0.00 3.07
2921 2985 6.315393 GGTGAGAAGGCGTTTCTATATTTTCA 59.685 38.462 4.62 0.00 46.12 2.69
2942 3006 5.472148 TCATTTTAGGCTGTTCAAATGCAG 58.528 37.500 13.91 0.00 36.81 4.41
2955 3019 2.942376 CAAATGCAGCGTACATCCCTAA 59.058 45.455 0.00 0.00 0.00 2.69
2991 3055 8.831715 ACATGCGACATAATTTATGATGTCTA 57.168 30.769 20.54 7.27 46.45 2.59
3012 3076 8.215050 TGTCTAGTTTATTCTCTTTGTTTGGGA 58.785 33.333 0.00 0.00 0.00 4.37
3022 3086 0.945813 TTGTTTGGGAGTTTACGGCG 59.054 50.000 4.80 4.80 0.00 6.46
3027 3091 0.108520 TGGGAGTTTACGGCGCTTAG 60.109 55.000 6.90 1.39 0.00 2.18
3028 3092 0.174162 GGGAGTTTACGGCGCTTAGA 59.826 55.000 6.90 0.00 0.00 2.10
3030 3094 2.035066 GGGAGTTTACGGCGCTTAGATA 59.965 50.000 6.90 0.00 0.00 1.98
3031 3095 3.491447 GGGAGTTTACGGCGCTTAGATAA 60.491 47.826 6.90 0.00 0.00 1.75
3032 3096 3.488678 GGAGTTTACGGCGCTTAGATAAC 59.511 47.826 6.90 5.03 0.00 1.89
3033 3097 4.357996 GAGTTTACGGCGCTTAGATAACT 58.642 43.478 6.90 9.87 0.00 2.24
3034 3098 4.110482 AGTTTACGGCGCTTAGATAACTG 58.890 43.478 6.90 0.00 0.00 3.16
3035 3099 4.107622 GTTTACGGCGCTTAGATAACTGA 58.892 43.478 6.90 0.00 0.00 3.41
3036 3100 4.579454 TTACGGCGCTTAGATAACTGAT 57.421 40.909 6.90 0.00 0.00 2.90
3037 3101 3.014604 ACGGCGCTTAGATAACTGATC 57.985 47.619 6.90 0.00 34.40 2.92
3039 3103 3.068307 ACGGCGCTTAGATAACTGATCTT 59.932 43.478 6.90 0.00 42.70 2.40
3040 3104 4.051922 CGGCGCTTAGATAACTGATCTTT 58.948 43.478 7.64 0.00 42.70 2.52
3041 3105 4.508124 CGGCGCTTAGATAACTGATCTTTT 59.492 41.667 7.64 0.00 42.70 2.27
3042 3106 5.006746 CGGCGCTTAGATAACTGATCTTTTT 59.993 40.000 7.64 0.00 42.70 1.94
3119 3183 8.153550 ACAATTGAGTCTTATCATAGGATCCAC 58.846 37.037 15.82 0.00 34.89 4.02
3125 3189 7.182760 AGTCTTATCATAGGATCCACGGATTA 58.817 38.462 15.82 6.33 34.60 1.75
3128 3193 9.355916 TCTTATCATAGGATCCACGGATTATAG 57.644 37.037 15.82 10.66 34.60 1.31
3178 3243 7.492352 AAGTCATCACAAGTTAGGTGTTTAC 57.508 36.000 0.00 0.00 37.52 2.01
3200 3265 5.445964 ACTTGTAAAAATGTGGACAGACCT 58.554 37.500 0.00 0.00 39.86 3.85
3294 3359 5.067153 TCAACCAAGTACAAATCCTTGTGTG 59.933 40.000 0.00 0.00 45.53 3.82
3309 3374 1.337447 TGTGTGCGGAAACCTAGCTAC 60.337 52.381 0.00 0.00 0.00 3.58
3314 3379 2.224329 TGCGGAAACCTAGCTACAACAA 60.224 45.455 0.00 0.00 0.00 2.83
3407 3472 7.918033 TGCACAAACCATATTTTCCGTATAATG 59.082 33.333 0.00 0.00 0.00 1.90
3439 3505 6.531503 TTCAACTCTCTAACATCCTACCAG 57.468 41.667 0.00 0.00 0.00 4.00
3458 3524 6.831664 ACCAGGAGATATGTGTTCCTTATT 57.168 37.500 0.00 0.00 39.28 1.40
3496 3562 7.649370 AGCTTTATGATATGAATGAGACACG 57.351 36.000 0.00 0.00 0.00 4.49
3497 3563 7.212976 AGCTTTATGATATGAATGAGACACGT 58.787 34.615 0.00 0.00 0.00 4.49
3498 3564 8.360390 AGCTTTATGATATGAATGAGACACGTA 58.640 33.333 0.00 0.00 0.00 3.57
3499 3565 9.144747 GCTTTATGATATGAATGAGACACGTAT 57.855 33.333 0.00 0.00 0.00 3.06
3503 3569 8.988064 ATGATATGAATGAGACACGTATTACC 57.012 34.615 0.00 0.00 0.00 2.85
3504 3570 7.947282 TGATATGAATGAGACACGTATTACCA 58.053 34.615 0.00 0.00 0.00 3.25
3505 3571 8.585018 TGATATGAATGAGACACGTATTACCAT 58.415 33.333 0.00 0.00 0.00 3.55
3506 3572 8.763049 ATATGAATGAGACACGTATTACCATG 57.237 34.615 0.00 0.00 0.00 3.66
3507 3573 6.215495 TGAATGAGACACGTATTACCATGA 57.785 37.500 0.00 0.00 0.00 3.07
3508 3574 6.635755 TGAATGAGACACGTATTACCATGAA 58.364 36.000 0.00 0.00 0.00 2.57
3509 3575 7.100409 TGAATGAGACACGTATTACCATGAAA 58.900 34.615 0.00 0.00 0.00 2.69
3510 3576 7.604545 TGAATGAGACACGTATTACCATGAAAA 59.395 33.333 0.00 0.00 0.00 2.29
3511 3577 7.915293 ATGAGACACGTATTACCATGAAAAA 57.085 32.000 0.00 0.00 0.00 1.94
3549 3615 6.697019 GGTGCTAGCCACAAACAAAATATATG 59.303 38.462 13.29 0.00 46.50 1.78
3596 3663 0.758685 TGCCAGTTTGGAACCAAGGG 60.759 55.000 6.39 10.39 40.96 3.95
3600 3667 1.341209 CAGTTTGGAACCAAGGGAAGC 59.659 52.381 6.39 0.00 37.24 3.86
3601 3668 1.063266 AGTTTGGAACCAAGGGAAGCA 60.063 47.619 6.39 0.00 37.24 3.91
3622 3689 7.516198 AGCAGGCATTTAATTATTAGGTCAG 57.484 36.000 0.00 0.00 0.00 3.51
3626 3693 8.902806 CAGGCATTTAATTATTAGGTCAGTTCA 58.097 33.333 0.00 0.00 0.00 3.18
3729 4004 9.996554 TTACAAATTAAATCAGTCTCTGACAGA 57.003 29.630 4.78 4.78 43.63 3.41
3737 4012 3.828657 TCTCTGACAGACATGCAGC 57.171 52.632 0.00 0.00 33.35 5.25
3756 4031 4.261572 GCAGCAACACATTTTACTTCCTCA 60.262 41.667 0.00 0.00 0.00 3.86
3786 4061 2.499197 ACAATGCACACCACACGAATA 58.501 42.857 0.00 0.00 0.00 1.75
3801 4077 4.036498 ACACGAATAACTATCAGGGAGTCG 59.964 45.833 0.00 0.00 0.00 4.18
3834 4117 6.877611 ATTGTGTGTTAAAGGATCGAGTTT 57.122 33.333 0.00 0.00 0.00 2.66
3835 4118 6.687081 TTGTGTGTTAAAGGATCGAGTTTT 57.313 33.333 0.00 0.00 0.00 2.43
3887 4170 4.878971 TCTTTGTTTCATGTTTCGAGTGGA 59.121 37.500 0.00 0.00 0.00 4.02
3891 4174 4.638421 TGTTTCATGTTTCGAGTGGAGTTT 59.362 37.500 0.00 0.00 0.00 2.66
3915 4198 5.258216 TGCCTAGGTACCCAACAATTTTA 57.742 39.130 11.31 0.00 0.00 1.52
3930 4213 7.064966 CCAACAATTTTATCAAATCCTTGCTCC 59.935 37.037 0.00 0.00 30.80 4.70
3933 4216 4.963276 TTTATCAAATCCTTGCTCCGTG 57.037 40.909 0.00 0.00 32.14 4.94
3935 4218 1.808411 TCAAATCCTTGCTCCGTGAC 58.192 50.000 0.00 0.00 32.14 3.67
3991 4274 9.052759 TCCATTTAAAACAAGAGAAGTGACTAC 57.947 33.333 0.00 0.00 0.00 2.73
4008 4293 8.974060 AGTGACTACCTATTTGAAGTTTTGAA 57.026 30.769 0.00 0.00 0.00 2.69
4039 4341 1.745653 GTGCTACTGGATTTGCCCTTC 59.254 52.381 0.00 0.00 34.97 3.46
4082 4387 8.483758 TGGACTTACCCTTAATGAATAGAGTTC 58.516 37.037 0.00 0.00 38.00 3.01
4083 4388 8.483758 GGACTTACCCTTAATGAATAGAGTTCA 58.516 37.037 0.00 0.00 0.00 3.18
4092 4397 6.899393 AATGAATAGAGTTCAAAGTGGCAA 57.101 33.333 0.00 0.00 31.55 4.52
4097 4402 4.311816 AGAGTTCAAAGTGGCAAATGTG 57.688 40.909 0.00 0.00 0.00 3.21
4112 4417 5.867174 GGCAAATGTGGAACTAACCATTAAC 59.133 40.000 0.00 0.00 42.17 2.01
4114 4423 6.586082 GCAAATGTGGAACTAACCATTAACAG 59.414 38.462 0.00 0.00 42.17 3.16
4161 4470 7.118723 AGAAAATGCACCATCCTAGTTTCATA 58.881 34.615 0.00 0.00 0.00 2.15
4187 4496 3.476552 TGTGCCTTGAGGTCAGTTTTAG 58.523 45.455 0.00 0.00 37.57 1.85
4198 4507 6.325545 TGAGGTCAGTTTTAGTTAGAACTCCA 59.674 38.462 0.00 0.00 41.23 3.86
4219 4528 4.293415 CAATTCTAATCCCGCAATTGCTC 58.707 43.478 26.86 0.76 39.32 4.26
4261 4571 9.406828 CTTCACTAAAATAAAAACTTGGTAGGC 57.593 33.333 0.00 0.00 0.00 3.93
4278 4588 1.065126 AGGCCCTTCACAATACTGCTC 60.065 52.381 0.00 0.00 0.00 4.26
4306 4618 7.334421 CAGAGAGAGAACTAGTGAGATATAGCC 59.666 44.444 0.00 0.00 0.00 3.93
4312 4624 0.178932 AGTGAGATATAGCCGGGCCA 60.179 55.000 17.02 1.09 0.00 5.36
4348 4660 7.011773 CGCATGACATAAATAAGCAGTCATAC 58.988 38.462 0.00 0.88 45.26 2.39
4402 4714 4.037208 ACATACCGCGTATATATACCTGCC 59.963 45.833 15.70 3.30 0.00 4.85
4474 4788 1.133976 CCTGCCAGGGAGGAAATACAG 60.134 57.143 22.97 0.00 41.22 2.74
4550 4864 6.087522 GCTGCTAAGAACGTAAGATCGATAT 58.912 40.000 0.00 0.00 44.80 1.63
4582 4897 2.012673 CCCTACATGCTGTTCAGCTTC 58.987 52.381 22.44 0.00 35.49 3.86
4586 4901 0.725686 CATGCTGTTCAGCTTCTCCG 59.274 55.000 22.44 4.42 35.49 4.63
4636 4951 4.439305 AAACAATCCCATTGATCACACG 57.561 40.909 0.00 0.00 42.83 4.49
4821 5136 2.082231 ACTGAATGTCTGTCTGCATGC 58.918 47.619 11.82 11.82 0.00 4.06
4952 5267 6.463897 GCTGGGATTAATTAGTACTGCTACCA 60.464 42.308 5.39 2.67 0.00 3.25
4958 5273 2.863401 TAGTACTGCTACCACATGCG 57.137 50.000 5.39 0.00 0.00 4.73
4962 5277 1.153842 CTGCTACCACATGCGTCGA 60.154 57.895 0.00 0.00 0.00 4.20
5025 5340 6.820459 TGCATATATATAATGCATAAGCGCG 58.180 36.000 19.74 0.00 45.14 6.86
5082 5397 1.597663 GCTGCTGTGTCGTTAAGTTGT 59.402 47.619 0.00 0.00 0.00 3.32
5085 5400 3.263261 TGCTGTGTCGTTAAGTTGTTGA 58.737 40.909 0.00 0.00 0.00 3.18
5117 5433 6.651643 TGTTATATTTGTTGTTGGAGCGTACT 59.348 34.615 0.00 0.00 0.00 2.73
5190 5507 5.008019 CGCAATTGTTCTTGGCTGTATATCT 59.992 40.000 7.40 0.00 0.00 1.98
5222 5547 7.033185 GGTTACAGGTAATTGGTTTGCATAAG 58.967 38.462 0.00 0.00 0.00 1.73
5266 5591 6.069963 ACGGTATATATAGTACCTCTTCCGGT 60.070 42.308 0.00 0.00 39.55 5.28
5322 5647 3.802139 TGTCACAAAGTGAACTCGACATC 59.198 43.478 0.82 0.00 44.49 3.06
5337 5662 5.345202 ACTCGACATCAAAGTATTTCACGAC 59.655 40.000 0.00 0.00 35.03 4.34
5389 5714 3.991773 GGCGTTTCTTCCCCAAATAAAAC 59.008 43.478 0.00 0.00 0.00 2.43
5394 5719 2.176045 CTTCCCCAAATAAAACCGCCT 58.824 47.619 0.00 0.00 0.00 5.52
5571 5897 3.817709 TGCCAAAGTAAAAAGCTGCTT 57.182 38.095 9.53 9.53 0.00 3.91
5580 5906 3.643159 AAAAAGCTGCTTCTAAACCCG 57.357 42.857 16.28 0.00 0.00 5.28
5772 6098 4.501071 GTTGCTAAAAGGGTCAGATCGTA 58.499 43.478 0.00 0.00 0.00 3.43
5800 6126 5.116180 ACTTTCATGTCGAGTTCACTTTGA 58.884 37.500 0.00 0.00 0.00 2.69
5894 6251 9.623000 TTTAAGAATATCCAAGTAAGTAAGGGC 57.377 33.333 0.00 0.00 0.00 5.19
5895 6252 6.824958 AGAATATCCAAGTAAGTAAGGGCA 57.175 37.500 0.00 0.00 0.00 5.36
5896 6253 7.394144 AGAATATCCAAGTAAGTAAGGGCAT 57.606 36.000 0.00 0.00 0.00 4.40
5897 6254 7.816411 AGAATATCCAAGTAAGTAAGGGCATT 58.184 34.615 0.00 0.00 0.00 3.56
5898 6255 8.282256 AGAATATCCAAGTAAGTAAGGGCATTT 58.718 33.333 0.00 0.00 0.00 2.32
5899 6256 8.465273 AATATCCAAGTAAGTAAGGGCATTTC 57.535 34.615 0.00 0.00 0.00 2.17
5900 6257 5.514500 TCCAAGTAAGTAAGGGCATTTCT 57.486 39.130 0.00 0.00 0.00 2.52
5901 6258 6.630203 TCCAAGTAAGTAAGGGCATTTCTA 57.370 37.500 0.00 0.00 0.00 2.10
5902 6259 6.650120 TCCAAGTAAGTAAGGGCATTTCTAG 58.350 40.000 0.00 0.00 0.00 2.43
5903 6260 5.297029 CCAAGTAAGTAAGGGCATTTCTAGC 59.703 44.000 0.00 0.00 0.00 3.42
5904 6261 5.959583 AGTAAGTAAGGGCATTTCTAGCT 57.040 39.130 0.00 0.00 0.00 3.32
5905 6262 5.675538 AGTAAGTAAGGGCATTTCTAGCTG 58.324 41.667 0.00 0.00 0.00 4.24
5906 6263 4.844349 AAGTAAGGGCATTTCTAGCTGA 57.156 40.909 0.00 0.00 0.00 4.26
5907 6264 5.379706 AAGTAAGGGCATTTCTAGCTGAT 57.620 39.130 0.00 0.00 0.00 2.90
5908 6265 4.967036 AGTAAGGGCATTTCTAGCTGATC 58.033 43.478 0.00 0.00 0.00 2.92
5909 6266 2.947127 AGGGCATTTCTAGCTGATCC 57.053 50.000 0.00 0.00 0.00 3.36
5910 6267 1.423161 AGGGCATTTCTAGCTGATCCC 59.577 52.381 0.00 0.00 0.00 3.85
5911 6268 1.546548 GGGCATTTCTAGCTGATCCCC 60.547 57.143 0.00 0.00 0.00 4.81
5912 6269 1.143684 GGCATTTCTAGCTGATCCCCA 59.856 52.381 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.172205 TGCTTTATCATGTGTGTTACGCTA 58.828 37.500 0.00 0.00 0.00 4.26
60 61 1.833630 TCGAGTTCCCATCTGATGCTT 59.166 47.619 12.17 0.00 0.00 3.91
171 174 3.255888 GGATCCTATGTACTGCGATGTGA 59.744 47.826 3.84 0.00 0.00 3.58
210 213 1.509463 GCCTCACGTATGGTCGTCA 59.491 57.895 7.67 0.00 42.27 4.35
226 229 3.499737 CTTGTCCATCGGTGCGCC 61.500 66.667 6.11 6.11 0.00 6.53
350 354 0.318445 CGGTGTAGGCCTATGTACGC 60.318 60.000 17.38 12.18 0.00 4.42
377 385 0.325602 TACCCGGCTTTTGATCGGTT 59.674 50.000 0.00 0.00 41.98 4.44
538 546 1.364328 CTCCTAGCCCCTCCATCCTAT 59.636 57.143 0.00 0.00 0.00 2.57
539 547 0.787084 CTCCTAGCCCCTCCATCCTA 59.213 60.000 0.00 0.00 0.00 2.94
599 611 0.391793 GCGTCTCAAGGGAAAGAGGG 60.392 60.000 0.00 0.00 32.76 4.30
882 905 2.516227 AGAAGACGAGGATGTGGAGA 57.484 50.000 0.00 0.00 0.00 3.71
916 939 2.888447 AAGAGTGAGCTTGGGCGCT 61.888 57.895 7.64 0.00 44.33 5.92
979 1006 2.104331 CGCTAGCCAACGGACGAT 59.896 61.111 9.66 0.00 0.00 3.73
1068 1095 1.373748 GGAGTTTACCGCGAGCACA 60.374 57.895 8.23 0.00 0.00 4.57
1131 1158 6.690530 ACAAAACAAAATCCATGATCATCGT 58.309 32.000 4.86 0.00 0.00 3.73
1166 1193 4.083484 CCCTTGCGAGTAAGGTAACAAAAG 60.083 45.833 16.66 0.00 44.65 2.27
1171 1198 2.494870 TCTCCCTTGCGAGTAAGGTAAC 59.505 50.000 16.66 0.00 44.65 2.50
1235 1262 3.166679 AGTAAGTGTCTCCTCCTCCAAC 58.833 50.000 0.00 0.00 0.00 3.77
1274 1301 3.814842 ACACACGACACATCAATCATGTT 59.185 39.130 0.00 0.00 43.89 2.71
1408 1435 7.578203 AGGAGAAAAATAAAGAGTATGGAGGG 58.422 38.462 0.00 0.00 0.00 4.30
1584 1611 2.170187 CCACTCAGCTCAGCTAATTCCT 59.830 50.000 0.00 0.00 36.40 3.36
1590 1617 1.273606 GTGAACCACTCAGCTCAGCTA 59.726 52.381 0.00 0.00 36.40 3.32
1619 1653 5.121298 ACACAAGATCAATCTCACAATGACG 59.879 40.000 0.00 0.00 35.76 4.35
1629 1663 5.388654 ACCCAGAAAACACAAGATCAATCT 58.611 37.500 0.00 0.00 39.22 2.40
1849 1883 4.186856 ACCCCAAATTAAAGTTGATGCG 57.813 40.909 4.29 0.00 0.00 4.73
1911 1945 6.721668 TGACTTTCTCTCTCCTCATAACAAGA 59.278 38.462 0.00 0.00 0.00 3.02
1935 1969 3.124921 GCACCGTTCGTCCCCATG 61.125 66.667 0.00 0.00 0.00 3.66
1939 1973 1.952102 TATCCTGCACCGTTCGTCCC 61.952 60.000 0.00 0.00 0.00 4.46
2027 2068 9.784531 GAGAGGACCATATTTCATGAGAAAATA 57.215 33.333 0.00 0.00 46.06 1.40
2081 2124 6.515832 CAAACAAAGATAGCAAAGGAAAGGT 58.484 36.000 0.00 0.00 0.00 3.50
2087 2130 5.182760 AGAGAGCAAACAAAGATAGCAAAGG 59.817 40.000 0.00 0.00 0.00 3.11
2107 2150 5.960811 AGAGAGAAAGAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
2108 2151 6.098124 AGAGAGAGAAAGAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
2109 2152 5.960811 AGAGAGAGAAAGAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
2110 2153 6.098124 AGAGAGAGAGAAAGAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
2111 2154 5.960811 AGAGAGAGAGAAAGAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
2112 2155 6.098124 AGAGAGAGAGAGAAAGAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
2113 2156 5.960811 AGAGAGAGAGAGAAAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
2114 2157 6.098124 AGAGAGAGAGAGAGAAAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
2115 2158 5.960811 AGAGAGAGAGAGAGAAAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
2116 2159 6.098124 AGAGAGAGAGAGAGAGAAAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
2117 2160 5.960811 AGAGAGAGAGAGAGAGAAAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
2118 2161 6.098124 AGAGAGAGAGAGAGAGAGAAAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
2119 2162 5.960811 AGAGAGAGAGAGAGAGAGAAAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
2120 2163 6.098124 AGAGAGAGAGAGAGAGAGAGAAAGAG 59.902 46.154 0.00 0.00 0.00 2.85
2121 2164 5.960811 AGAGAGAGAGAGAGAGAGAGAAAGA 59.039 44.000 0.00 0.00 0.00 2.52
2122 2165 6.098124 AGAGAGAGAGAGAGAGAGAGAGAAAG 59.902 46.154 0.00 0.00 0.00 2.62
2123 2166 5.960811 AGAGAGAGAGAGAGAGAGAGAGAAA 59.039 44.000 0.00 0.00 0.00 2.52
2124 2167 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
2125 2168 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2166 2209 6.098124 AGAGAGAGAGAGAGAGAGAGAAAGAG 59.902 46.154 0.00 0.00 0.00 2.85
2167 2210 5.960811 AGAGAGAGAGAGAGAGAGAGAAAGA 59.039 44.000 0.00 0.00 0.00 2.52
2168 2211 6.098124 AGAGAGAGAGAGAGAGAGAGAGAAAG 59.902 46.154 0.00 0.00 0.00 2.62
2169 2212 5.960811 AGAGAGAGAGAGAGAGAGAGAGAAA 59.039 44.000 0.00 0.00 0.00 2.52
2170 2213 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
2171 2214 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2172 2215 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2173 2216 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2174 2217 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2175 2218 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2176 2219 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
2177 2220 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
2178 2221 4.222336 AGGAGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
2179 2222 4.271807 AGGAGAGAGAGAGAGAGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
2180 2223 4.406972 TCAAGGAGAGAGAGAGAGAGAGAG 59.593 50.000 0.00 0.00 0.00 3.20
2181 2224 4.361783 TCAAGGAGAGAGAGAGAGAGAGA 58.638 47.826 0.00 0.00 0.00 3.10
2182 2225 4.760530 TCAAGGAGAGAGAGAGAGAGAG 57.239 50.000 0.00 0.00 0.00 3.20
2195 2238 4.357918 ACTTTTAAGCAGCTCAAGGAGA 57.642 40.909 0.00 0.00 0.00 3.71
2196 2239 5.241662 AGTACTTTTAAGCAGCTCAAGGAG 58.758 41.667 0.00 0.00 0.00 3.69
2197 2240 5.228945 AGTACTTTTAAGCAGCTCAAGGA 57.771 39.130 0.00 0.00 0.00 3.36
2319 2362 3.677976 GCTTCTGCATGCTGCCTTAAAAT 60.678 43.478 20.33 0.00 44.23 1.82
2361 2404 0.607620 AAAACCCCATGAATGCCACG 59.392 50.000 0.00 0.00 0.00 4.94
2364 2407 2.857186 ACAAAAACCCCATGAATGCC 57.143 45.000 0.00 0.00 0.00 4.40
2382 2431 1.077915 CATGAATGCCCCGCAAAAAC 58.922 50.000 0.00 0.00 43.62 2.43
2449 2502 3.994392 TCTTCACGAGCCATCAAAACTAC 59.006 43.478 0.00 0.00 0.00 2.73
2504 2566 6.544931 ACATCTCAAAATGACATGTAGGGATG 59.455 38.462 16.55 16.55 34.87 3.51
2528 2590 6.887376 ATACGTGTACACATCAGAATCAAC 57.113 37.500 24.98 0.00 0.00 3.18
2548 2610 3.406764 CATCCCTAGCAGCCAGAAATAC 58.593 50.000 0.00 0.00 0.00 1.89
2555 2617 1.997311 AGTGCATCCCTAGCAGCCA 60.997 57.895 0.00 0.00 43.63 4.75
2680 2742 7.220740 AGTAGAAAGAAAAGAAGGAAGAGGTG 58.779 38.462 0.00 0.00 0.00 4.00
2704 2766 3.442977 CCAGAAGGATGGAAGAGCAAAAG 59.557 47.826 0.00 0.00 43.57 2.27
2828 2892 6.252995 TGGGGCTACAGTCAAATTAAAAGAT 58.747 36.000 0.00 0.00 0.00 2.40
2876 2940 2.484417 CCTCATGAAGCGATTGTAGGCT 60.484 50.000 0.00 0.00 42.33 4.58
2942 3006 8.950210 TGTACTAATAGTATTAGGGATGTACGC 58.050 37.037 26.39 10.90 32.65 4.42
2985 3049 9.014297 CCCAAACAAAGAGAATAAACTAGACAT 57.986 33.333 0.00 0.00 0.00 3.06
2991 3055 7.898014 AACTCCCAAACAAAGAGAATAAACT 57.102 32.000 0.00 0.00 0.00 2.66
3010 3074 2.220479 ATCTAAGCGCCGTAAACTCC 57.780 50.000 2.29 0.00 0.00 3.85
3012 3076 4.110482 CAGTTATCTAAGCGCCGTAAACT 58.890 43.478 2.29 4.13 0.00 2.66
3078 3142 9.394767 AGACTCAATTGTTTGTATACATATGCA 57.605 29.630 6.36 0.00 34.32 3.96
3089 3153 9.911788 ATCCTATGATAAGACTCAATTGTTTGT 57.088 29.630 5.13 3.45 34.32 2.83
3091 3155 9.566432 GGATCCTATGATAAGACTCAATTGTTT 57.434 33.333 3.84 0.00 0.00 2.83
3092 3156 8.717717 TGGATCCTATGATAAGACTCAATTGTT 58.282 33.333 14.23 0.00 0.00 2.83
3093 3157 8.153550 GTGGATCCTATGATAAGACTCAATTGT 58.846 37.037 14.23 0.00 0.00 2.71
3094 3158 7.330454 CGTGGATCCTATGATAAGACTCAATTG 59.670 40.741 14.23 0.00 0.00 2.32
3097 3161 5.243954 CCGTGGATCCTATGATAAGACTCAA 59.756 44.000 14.23 0.00 0.00 3.02
3119 3183 7.507956 TGGGGTCCATATGTATACTATAATCCG 59.492 40.741 4.17 0.00 0.00 4.18
3139 3204 8.918202 TGTGATGACTTAAAATATATGGGGTC 57.082 34.615 0.00 0.00 0.00 4.46
3172 3237 8.185505 GTCTGTCCACATTTTTACAAGTAAACA 58.814 33.333 4.97 0.00 35.05 2.83
3178 3243 5.299279 ACAGGTCTGTCCACATTTTTACAAG 59.701 40.000 0.00 0.00 40.24 3.16
3200 3265 5.530915 GCTGGCTTCAATATATTGTACCACA 59.469 40.000 21.89 15.01 38.84 4.17
3268 3333 5.299279 CACAAGGATTTGTACTTGGTTGACT 59.701 40.000 8.97 0.00 45.53 3.41
3294 3359 2.088950 TGTTGTAGCTAGGTTTCCGC 57.911 50.000 0.00 0.00 0.00 5.54
3309 3374 8.576442 ACAAAATAAGATCCCTGTACTTTGTTG 58.424 33.333 0.00 0.00 32.19 3.33
3314 3379 9.802039 TGTAAACAAAATAAGATCCCTGTACTT 57.198 29.630 0.00 0.00 0.00 2.24
3353 3418 5.739752 TTGCATCAAATCCGAAGTCATAG 57.260 39.130 0.00 0.00 0.00 2.23
3432 3498 4.227197 AGGAACACATATCTCCTGGTAGG 58.773 47.826 0.00 0.00 38.19 3.18
3439 3505 6.064717 AGCCAAATAAGGAACACATATCTCC 58.935 40.000 0.00 0.00 0.00 3.71
3470 3536 9.196552 CGTGTCTCATTCATATCATAAAGCTAA 57.803 33.333 0.00 0.00 0.00 3.09
3471 3537 8.360390 ACGTGTCTCATTCATATCATAAAGCTA 58.640 33.333 0.00 0.00 0.00 3.32
3472 3538 7.212976 ACGTGTCTCATTCATATCATAAAGCT 58.787 34.615 0.00 0.00 0.00 3.74
3473 3539 7.413475 ACGTGTCTCATTCATATCATAAAGC 57.587 36.000 0.00 0.00 0.00 3.51
3478 3544 8.585018 TGGTAATACGTGTCTCATTCATATCAT 58.415 33.333 0.00 0.00 0.00 2.45
3479 3545 7.947282 TGGTAATACGTGTCTCATTCATATCA 58.053 34.615 0.00 0.00 0.00 2.15
3480 3546 8.864024 CATGGTAATACGTGTCTCATTCATATC 58.136 37.037 0.00 0.00 0.00 1.63
3481 3547 8.585018 TCATGGTAATACGTGTCTCATTCATAT 58.415 33.333 0.00 0.00 0.00 1.78
3482 3548 7.947282 TCATGGTAATACGTGTCTCATTCATA 58.053 34.615 0.00 0.00 0.00 2.15
3483 3549 6.816136 TCATGGTAATACGTGTCTCATTCAT 58.184 36.000 0.00 0.00 0.00 2.57
3484 3550 6.215495 TCATGGTAATACGTGTCTCATTCA 57.785 37.500 0.00 0.00 0.00 2.57
3485 3551 7.534085 TTTCATGGTAATACGTGTCTCATTC 57.466 36.000 0.00 0.00 0.00 2.67
3486 3552 7.915293 TTTTCATGGTAATACGTGTCTCATT 57.085 32.000 0.00 0.00 0.00 2.57
3487 3553 7.915293 TTTTTCATGGTAATACGTGTCTCAT 57.085 32.000 0.00 0.00 0.00 2.90
3511 3577 6.492087 TGTGGCTAGCACCTTTACTAATTTTT 59.508 34.615 18.24 0.00 0.00 1.94
3512 3578 6.007703 TGTGGCTAGCACCTTTACTAATTTT 58.992 36.000 18.24 0.00 0.00 1.82
3513 3579 5.566469 TGTGGCTAGCACCTTTACTAATTT 58.434 37.500 18.24 0.00 0.00 1.82
3596 3663 7.940850 TGACCTAATAATTAAATGCCTGCTTC 58.059 34.615 0.00 0.00 0.00 3.86
3600 3667 8.902806 TGAACTGACCTAATAATTAAATGCCTG 58.097 33.333 0.00 0.00 0.00 4.85
3601 3668 9.646522 ATGAACTGACCTAATAATTAAATGCCT 57.353 29.630 0.00 0.00 0.00 4.75
3721 3996 1.202675 TGTTGCTGCATGTCTGTCAGA 60.203 47.619 1.84 0.00 31.94 3.27
3722 3997 1.069432 GTGTTGCTGCATGTCTGTCAG 60.069 52.381 1.84 0.00 32.82 3.51
3726 4001 2.717580 AATGTGTTGCTGCATGTCTG 57.282 45.000 1.84 0.00 0.00 3.51
3728 4003 4.549458 AGTAAAATGTGTTGCTGCATGTC 58.451 39.130 1.84 0.00 0.00 3.06
3729 4004 4.589216 AGTAAAATGTGTTGCTGCATGT 57.411 36.364 1.84 0.00 0.00 3.21
3737 4012 6.583806 GCTCAATGAGGAAGTAAAATGTGTTG 59.416 38.462 12.66 0.00 0.00 3.33
3756 4031 2.548493 GGTGTGCATTGTTTGGCTCAAT 60.548 45.455 0.00 0.00 35.58 2.57
3786 4061 4.383118 CCATTTGACGACTCCCTGATAGTT 60.383 45.833 0.00 0.00 0.00 2.24
3801 4077 7.206687 TCCTTTAACACACAATTCCATTTGAC 58.793 34.615 0.00 0.00 0.00 3.18
3881 4164 3.141767 ACCTAGGCAAAAACTCCACTC 57.858 47.619 9.30 0.00 0.00 3.51
3915 4198 2.026822 AGTCACGGAGCAAGGATTTGAT 60.027 45.455 0.00 0.00 36.36 2.57
3930 4213 8.655970 TCAGTATGATTTTATGTTTCAGTCACG 58.344 33.333 0.00 0.00 42.56 4.35
3991 4274 9.023967 CAAAGACTGTTCAAAACTTCAAATAGG 57.976 33.333 0.00 0.00 0.00 2.57
4008 4293 2.434336 TCCAGTAGCACACAAAGACTGT 59.566 45.455 0.00 0.00 39.56 3.55
4039 4341 9.155975 GGTAAGTCCAGTAGCATATAATTCATG 57.844 37.037 0.00 0.00 35.97 3.07
4082 4387 3.457610 AGTTCCACATTTGCCACTTTG 57.542 42.857 0.00 0.00 0.00 2.77
4083 4388 4.202212 GGTTAGTTCCACATTTGCCACTTT 60.202 41.667 0.00 0.00 0.00 2.66
4092 4397 8.650143 ATTCTGTTAATGGTTAGTTCCACATT 57.350 30.769 0.00 0.00 40.51 2.71
4097 4402 8.674607 CAACCTATTCTGTTAATGGTTAGTTCC 58.325 37.037 0.00 0.00 36.22 3.62
4112 4417 4.042062 TCCATGCCCTATCAACCTATTCTG 59.958 45.833 0.00 0.00 0.00 3.02
4114 4423 4.640771 TCCATGCCCTATCAACCTATTC 57.359 45.455 0.00 0.00 0.00 1.75
4161 4470 0.111061 TGACCTCAAGGCACAGCAAT 59.889 50.000 0.00 0.00 39.32 3.56
4238 4547 7.039293 AGGGCCTACCAAGTTTTTATTTTAGTG 60.039 37.037 2.82 0.00 43.89 2.74
4243 4552 5.841783 TGAAGGGCCTACCAAGTTTTTATTT 59.158 36.000 6.41 0.00 43.89 1.40
4244 4553 5.245301 GTGAAGGGCCTACCAAGTTTTTATT 59.755 40.000 6.41 0.00 43.89 1.40
4245 4554 4.770531 GTGAAGGGCCTACCAAGTTTTTAT 59.229 41.667 6.41 0.00 43.89 1.40
4246 4555 4.146564 GTGAAGGGCCTACCAAGTTTTTA 58.853 43.478 6.41 0.00 43.89 1.52
4261 4571 1.009829 GCGAGCAGTATTGTGAAGGG 58.990 55.000 0.00 0.00 0.00 3.95
4278 4588 3.266636 TCTCACTAGTTCTCTCTCTGCG 58.733 50.000 0.00 0.00 0.00 5.18
4306 4618 1.068194 TGCGTTCTTATTTTTGGCCCG 60.068 47.619 0.00 0.00 0.00 6.13
4474 4788 1.262882 GCTTTGCAGCTTTGATACGC 58.737 50.000 0.00 0.00 43.51 4.42
4550 4864 2.126882 CATGTAGGGGGAGAATGGACA 58.873 52.381 0.00 0.00 0.00 4.02
4582 4897 7.548196 TCAGTAAATAATTTAACTGGCGGAG 57.452 36.000 0.00 0.00 31.33 4.63
4636 4951 3.618594 CCACTGCATATGTACATATCCGC 59.381 47.826 22.81 22.56 31.98 5.54
4789 5104 8.458052 AGACAGACATTCAGTATCGATCATATC 58.542 37.037 0.00 0.00 0.00 1.63
4821 5136 4.245660 CAGCTACGTCCCCATGTATATTG 58.754 47.826 0.00 0.00 0.00 1.90
4907 5222 2.553904 GCATGCTTATGATGCCCTAGGT 60.554 50.000 11.37 0.00 40.37 3.08
4912 5227 0.601558 CCAGCATGCTTATGATGCCC 59.398 55.000 19.98 0.00 46.24 5.36
4952 5267 3.375642 CTGATAAGTGATCGACGCATGT 58.624 45.455 0.00 0.00 37.38 3.21
4958 5273 4.023622 TGAGCTAGCTGATAAGTGATCGAC 60.024 45.833 24.99 2.40 37.38 4.20
4962 5277 6.210984 TGATGATGAGCTAGCTGATAAGTGAT 59.789 38.462 24.99 6.88 0.00 3.06
5025 5340 2.536393 ACCAAACACAAATTAAACGCGC 59.464 40.909 5.73 0.00 0.00 6.86
5082 5397 9.676195 CAACAACAAATATAACAGACACATCAA 57.324 29.630 0.00 0.00 0.00 2.57
5085 5400 8.402798 TCCAACAACAAATATAACAGACACAT 57.597 30.769 0.00 0.00 0.00 3.21
5117 5433 6.403855 GCTGTTCATAATTAAAGGGTGCGTAA 60.404 38.462 0.00 0.00 0.00 3.18
5190 5507 3.766591 CCAATTACCTGTAACCCATGCAA 59.233 43.478 0.00 0.00 0.00 4.08
5222 5547 4.021368 ACCGTATAACTAGGACCATGCATC 60.021 45.833 0.00 0.00 0.00 3.91
5266 5591 6.549736 TGATAGGGTCAGAATAGTGATTTCGA 59.450 38.462 0.00 0.00 31.80 3.71
5322 5647 3.435671 GGGTCAGGTCGTGAAATACTTTG 59.564 47.826 0.00 0.00 36.74 2.77
5337 5662 0.521735 GCGTTGCTAAAAGGGTCAGG 59.478 55.000 0.00 0.00 0.00 3.86
5389 5714 1.797211 AACGCTAGCTAGCTAGGCGG 61.797 60.000 39.79 30.52 46.85 6.13
5394 5719 1.948145 GACAGGAACGCTAGCTAGCTA 59.052 52.381 36.02 22.85 46.85 3.32
5413 5738 0.948678 CTCGGCGTTTTTCCTTTGGA 59.051 50.000 6.85 0.00 0.00 3.53
5422 5747 0.806492 GCTAGCTAGCTCGGCGTTTT 60.806 55.000 33.71 0.00 45.62 2.43
5571 5897 0.620030 GTTTAGGCCCCGGGTTTAGA 59.380 55.000 21.85 0.83 0.00 2.10
5772 6098 7.730364 AGTGAACTCGACATGAAAGTATTTT 57.270 32.000 0.00 0.00 39.27 1.82
5837 6163 9.778741 TTAAGATCAAAGGCTAGGTACATAATG 57.221 33.333 0.00 0.00 0.00 1.90
5879 6236 5.297029 GCTAGAAATGCCCTTACTTACTTGG 59.703 44.000 0.00 0.00 0.00 3.61
5892 6249 1.143684 TGGGGATCAGCTAGAAATGCC 59.856 52.381 0.00 0.00 0.00 4.40
5893 6250 2.645838 TGGGGATCAGCTAGAAATGC 57.354 50.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.