Multiple sequence alignment - TraesCS7D01G358500

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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 TraesCS7D01G358500 chr7D 100.000 2918 0 0 1782 4699 461401140 461398223 0.000000e+00 5389
1 TraesCS7D01G358500 chr7D 100.000 1388 0 0 1 1388 461402921 461401534 0.000000e+00 2564
2 TraesCS7D01G358500 chr7D 79.680 1314 259 8 1 1309 469238565 469237255 0.000000e+00 941
3 TraesCS7D01G358500 chr7D 99.592 245 1 0 1782 2026 461401778 461401534 9.280000e-122 448
4 TraesCS7D01G358500 chr7B 95.022 1386 58 5 3297 4673 483866417 483865034 0.000000e+00 2167
5 TraesCS7D01G358500 chr7B 95.833 1344 47 2 1956 3296 483867827 483866490 0.000000e+00 2163
6 TraesCS7D01G358500 chr7B 87.553 1173 118 18 1942 3104 483891144 483889990 0.000000e+00 1332
7 TraesCS7D01G358500 chr7B 81.590 918 121 36 3095 3993 483889892 483889004 0.000000e+00 715
8 TraesCS7D01G358500 chr7B 86.286 175 12 8 1782 1947 372326500 372326671 3.740000e-41 180
9 TraesCS7D01G358500 chr5A 96.107 1310 50 1 1 1309 591973549 591974858 0.000000e+00 2135
10 TraesCS7D01G358500 chr5A 92.771 166 12 0 1782 1947 591974693 591974858 1.690000e-59 241
11 TraesCS7D01G358500 chr5A 89.781 137 14 0 2253 2389 76491296 76491432 4.830000e-40 176
12 TraesCS7D01G358500 chr5A 90.840 131 12 0 2259 2389 77791589 77791459 4.830000e-40 176
13 TraesCS7D01G358500 chr5A 89.051 137 15 0 2253 2389 75338660 75338796 2.250000e-38 171
14 TraesCS7D01G358500 chr4B 95.187 1309 61 2 1 1308 638132944 638131637 0.000000e+00 2067
15 TraesCS7D01G358500 chr4B 93.939 165 10 0 1782 1946 638131801 638131637 2.810000e-62 250
16 TraesCS7D01G358500 chr3B 94.733 1310 66 3 1 1307 433754542 433753233 0.000000e+00 2034
17 TraesCS7D01G358500 chr3B 93.902 164 10 0 1782 1945 433753396 433753233 1.010000e-61 248
18 TraesCS7D01G358500 chr7A 85.256 1621 176 31 2443 4048 538733635 538735207 0.000000e+00 1611
19 TraesCS7D01G358500 chr7A 79.040 1312 265 10 1 1306 513560197 513561504 0.000000e+00 891
20 TraesCS7D01G358500 chr7A 92.549 510 26 3 1942 2447 538711168 538711669 0.000000e+00 721
21 TraesCS7D01G358500 chr7A 85.682 440 41 11 4077 4501 538734974 538735406 1.200000e-120 444
22 TraesCS7D01G358500 chr3D 80.395 1316 249 9 1 1311 349874547 349875858 0.000000e+00 992
23 TraesCS7D01G358500 chr2B 78.767 1314 259 19 5 1307 474408538 474407234 0.000000e+00 863
24 TraesCS7D01G358500 chr1A 78.490 1311 267 14 5 1307 368200467 368199164 0.000000e+00 845
25 TraesCS7D01G358500 chr1B 77.407 1319 263 20 5 1310 169682084 169683380 0.000000e+00 752
26 TraesCS7D01G358500 chr1B 89.130 138 15 0 2254 2391 667058756 667058619 6.250000e-39 172
27 TraesCS7D01G358500 chr5B 89.781 137 14 0 2253 2389 88859223 88859359 4.830000e-40 176
28 TraesCS7D01G358500 chr5D 89.051 137 15 0 2253 2389 80299800 80299936 2.250000e-38 171


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 TraesCS7D01G358500 chr7D 461398223 461402921 4698 True 2800.333333 5389 99.8640 1 4699 3 chr7D.!!$R2 4698
1 TraesCS7D01G358500 chr7D 469237255 469238565 1310 True 941.000000 941 79.6800 1 1309 1 chr7D.!!$R1 1308
2 TraesCS7D01G358500 chr7B 483865034 483867827 2793 True 2165.000000 2167 95.4275 1956 4673 2 chr7B.!!$R1 2717
3 TraesCS7D01G358500 chr7B 483889004 483891144 2140 True 1023.500000 1332 84.5715 1942 3993 2 chr7B.!!$R2 2051
4 TraesCS7D01G358500 chr5A 591973549 591974858 1309 False 1188.000000 2135 94.4390 1 1947 2 chr5A.!!$F3 1946
5 TraesCS7D01G358500 chr4B 638131637 638132944 1307 True 1158.500000 2067 94.5630 1 1946 2 chr4B.!!$R1 1945
6 TraesCS7D01G358500 chr3B 433753233 433754542 1309 True 1141.000000 2034 94.3175 1 1945 2 chr3B.!!$R1 1944
7 TraesCS7D01G358500 chr7A 538733635 538735406 1771 False 1027.500000 1611 85.4690 2443 4501 2 chr7A.!!$F3 2058
8 TraesCS7D01G358500 chr7A 513560197 513561504 1307 False 891.000000 891 79.0400 1 1306 1 chr7A.!!$F1 1305
9 TraesCS7D01G358500 chr7A 538711168 538711669 501 False 721.000000 721 92.5490 1942 2447 1 chr7A.!!$F2 505
10 TraesCS7D01G358500 chr3D 349874547 349875858 1311 False 992.000000 992 80.3950 1 1311 1 chr3D.!!$F1 1310
11 TraesCS7D01G358500 chr2B 474407234 474408538 1304 True 863.000000 863 78.7670 5 1307 1 chr2B.!!$R1 1302
12 TraesCS7D01G358500 chr1A 368199164 368200467 1303 True 845.000000 845 78.4900 5 1307 1 chr1A.!!$R1 1302
13 TraesCS7D01G358500 chr1B 169682084 169683380 1296 False 752.000000 752 77.4070 5 1310 1 chr1B.!!$F1 1305

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
811 816 0.035439 AGGATTTGAACCGCGGACAT 60.035 50.000 35.90 17.93 0.0 3.06 F
1345 1351 0.040067 CACAAGCTTCAAACCCTCGC 60.040 55.000 0.00 0.00 0.0 5.03 F
1888 1894 0.032267 TTGACGGCGTGTGTGTATCA 59.968 50.000 21.19 2.86 0.0 2.15 F
1889 1895 0.032267 TGACGGCGTGTGTGTATCAA 59.968 50.000 21.19 0.00 0.0 2.57 F
1890 1896 1.141645 GACGGCGTGTGTGTATCAAA 58.858 50.000 21.19 0.00 0.0 2.69 F
1892 1898 1.262151 ACGGCGTGTGTGTATCAAAAC 59.738 47.619 13.76 0.00 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1875 0.032267 TGATACACACACGCCGTCAA 59.968 50.000 0.00 0.0 0.00 3.18 R
2898 2919 2.334023 AGGGGCATCCTCAATAGAGAC 58.666 52.381 0.00 0.0 44.06 3.36 R
3517 3731 1.215423 ACCAGCCTTGAACCTCAAACT 59.785 47.619 0.00 0.0 35.73 2.66 R
3518 3732 1.338020 CACCAGCCTTGAACCTCAAAC 59.662 52.381 0.00 0.0 35.73 2.93 R
3628 3842 2.154462 CCTCAAGTTTGCGGAGACATT 58.846 47.619 0.00 0.0 35.05 2.71 R
3874 4093 2.332063 GCCTAGGCACAATTAGCTGA 57.668 50.000 29.33 0.0 41.49 4.26 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
75 76 2.345991 GTCCTTACCGCAGTGGCA 59.654 61.111 0.00 0.00 43.94 4.92
102 103 2.501316 TCATATCACACCACTGGACCTG 59.499 50.000 0.71 0.00 0.00 4.00
128 129 3.503748 GTGGAGGTTCTCAAGACAATTGG 59.496 47.826 10.83 0.00 31.08 3.16
161 162 2.371658 GCCTATCTTTGGGCTGGAAT 57.628 50.000 0.00 0.00 45.63 3.01
348 350 3.798646 CACGCCTTGCATGAAACAT 57.201 47.368 0.00 0.00 0.00 2.71
367 369 3.005155 ACATGATCATGATCTCTTCGCGA 59.995 43.478 36.37 3.71 41.20 5.87
386 388 4.980805 TGCGACCAAGGTGACGGC 62.981 66.667 0.00 0.00 0.00 5.68
423 425 2.038952 AGCAAAATTTTGGGCCTCTTCC 59.961 45.455 27.60 11.04 38.57 3.46
702 706 1.801178 GCTTATATGGCGCAGTTCTCC 59.199 52.381 10.83 0.00 0.00 3.71
703 707 2.806745 GCTTATATGGCGCAGTTCTCCA 60.807 50.000 10.83 0.00 33.45 3.86
811 816 0.035439 AGGATTTGAACCGCGGACAT 60.035 50.000 35.90 17.93 0.00 3.06
833 838 2.819984 TTCAACGCAGAGGATGGCCC 62.820 60.000 0.00 0.00 33.31 5.80
965 970 1.302033 GCATATCCCCACGGCTCTG 60.302 63.158 0.00 0.00 0.00 3.35
1062 1067 5.368145 TGTCTTCTGCATTACTTCTTGTGT 58.632 37.500 0.00 0.00 0.00 3.72
1075 1080 6.126863 ACTTCTTGTGTGATGGGAAATCTA 57.873 37.500 0.00 0.00 0.00 1.98
1208 1213 3.173668 AGTAATGTAATGCCGCGAGAA 57.826 42.857 8.23 0.00 0.00 2.87
1215 1220 4.623002 TGTAATGCCGCGAGAATAATACA 58.377 39.130 8.23 4.85 0.00 2.29
1324 1330 1.717032 AAAAACTTGGAGCCCTTCCC 58.283 50.000 0.00 0.00 46.19 3.97
1325 1331 0.860457 AAAACTTGGAGCCCTTCCCT 59.140 50.000 0.00 0.00 46.19 4.20
1326 1332 0.405973 AAACTTGGAGCCCTTCCCTC 59.594 55.000 0.00 0.00 46.19 4.30
1327 1333 0.772124 AACTTGGAGCCCTTCCCTCA 60.772 55.000 0.00 0.00 46.19 3.86
1328 1334 1.301293 CTTGGAGCCCTTCCCTCAC 59.699 63.158 0.00 0.00 46.19 3.51
1329 1335 1.463214 TTGGAGCCCTTCCCTCACA 60.463 57.895 0.00 0.00 46.19 3.58
1330 1336 1.065410 TTGGAGCCCTTCCCTCACAA 61.065 55.000 0.00 0.00 46.19 3.33
1331 1337 1.301293 GGAGCCCTTCCCTCACAAG 59.699 63.158 0.00 0.00 40.37 3.16
1332 1338 1.377856 GAGCCCTTCCCTCACAAGC 60.378 63.158 0.00 0.00 0.00 4.01
1333 1339 1.846712 GAGCCCTTCCCTCACAAGCT 61.847 60.000 0.00 0.00 0.00 3.74
1334 1340 1.075659 GCCCTTCCCTCACAAGCTT 59.924 57.895 0.00 0.00 0.00 3.74
1335 1341 0.962855 GCCCTTCCCTCACAAGCTTC 60.963 60.000 0.00 0.00 0.00 3.86
1336 1342 0.401738 CCCTTCCCTCACAAGCTTCA 59.598 55.000 0.00 0.00 0.00 3.02
1337 1343 1.202927 CCCTTCCCTCACAAGCTTCAA 60.203 52.381 0.00 0.00 0.00 2.69
1338 1344 2.586425 CCTTCCCTCACAAGCTTCAAA 58.414 47.619 0.00 0.00 0.00 2.69
1339 1345 2.294512 CCTTCCCTCACAAGCTTCAAAC 59.705 50.000 0.00 0.00 0.00 2.93
1340 1346 1.981256 TCCCTCACAAGCTTCAAACC 58.019 50.000 0.00 0.00 0.00 3.27
1341 1347 0.961753 CCCTCACAAGCTTCAAACCC 59.038 55.000 0.00 0.00 0.00 4.11
1342 1348 1.479389 CCCTCACAAGCTTCAAACCCT 60.479 52.381 0.00 0.00 0.00 4.34
1343 1349 1.882623 CCTCACAAGCTTCAAACCCTC 59.117 52.381 0.00 0.00 0.00 4.30
1344 1350 1.532868 CTCACAAGCTTCAAACCCTCG 59.467 52.381 0.00 0.00 0.00 4.63
1345 1351 0.040067 CACAAGCTTCAAACCCTCGC 60.040 55.000 0.00 0.00 0.00 5.03
1346 1352 1.172812 ACAAGCTTCAAACCCTCGCC 61.173 55.000 0.00 0.00 0.00 5.54
1347 1353 1.150536 AAGCTTCAAACCCTCGCCA 59.849 52.632 0.00 0.00 0.00 5.69
1348 1354 1.172812 AAGCTTCAAACCCTCGCCAC 61.173 55.000 0.00 0.00 0.00 5.01
1349 1355 1.896660 GCTTCAAACCCTCGCCACA 60.897 57.895 0.00 0.00 0.00 4.17
1350 1356 1.949257 CTTCAAACCCTCGCCACAC 59.051 57.895 0.00 0.00 0.00 3.82
1351 1357 1.841663 CTTCAAACCCTCGCCACACG 61.842 60.000 0.00 0.00 45.62 4.49
1362 1368 2.986311 GCCACACGAACTGTTCTGA 58.014 52.632 17.60 0.00 0.00 3.27
1363 1369 1.295792 GCCACACGAACTGTTCTGAA 58.704 50.000 17.60 0.00 0.00 3.02
1364 1370 1.668751 GCCACACGAACTGTTCTGAAA 59.331 47.619 17.60 0.00 0.00 2.69
1365 1371 2.096819 GCCACACGAACTGTTCTGAAAA 59.903 45.455 17.60 0.00 0.00 2.29
1366 1372 3.426963 GCCACACGAACTGTTCTGAAAAA 60.427 43.478 17.60 0.00 0.00 1.94
1382 1388 1.439679 AAAAATGTCCGAGAGACCGC 58.560 50.000 0.00 0.00 45.68 5.68
1383 1389 0.736325 AAAATGTCCGAGAGACCGCG 60.736 55.000 0.00 0.00 45.68 6.46
1801 1807 3.923017 AAAGAGGAAATGTCGCTTTGG 57.077 42.857 2.55 0.00 31.62 3.28
1802 1808 1.826385 AGAGGAAATGTCGCTTTGGG 58.174 50.000 0.00 0.00 0.00 4.12
1803 1809 0.171231 GAGGAAATGTCGCTTTGGGC 59.829 55.000 0.00 0.00 37.64 5.36
1804 1810 1.215382 GGAAATGTCGCTTTGGGCC 59.785 57.895 0.00 0.00 37.74 5.80
1805 1811 1.531739 GGAAATGTCGCTTTGGGCCA 61.532 55.000 0.00 0.00 37.74 5.36
1806 1812 0.532115 GAAATGTCGCTTTGGGCCAT 59.468 50.000 7.26 0.00 37.74 4.40
1807 1813 0.975887 AAATGTCGCTTTGGGCCATT 59.024 45.000 7.26 0.00 35.42 3.16
1808 1814 0.247185 AATGTCGCTTTGGGCCATTG 59.753 50.000 7.26 4.24 33.66 2.82
1809 1815 2.125952 GTCGCTTTGGGCCATTGC 60.126 61.111 7.26 14.18 37.74 3.56
1810 1816 3.746889 TCGCTTTGGGCCATTGCG 61.747 61.111 33.23 33.23 46.71 4.85
1811 1817 4.799824 CGCTTTGGGCCATTGCGG 62.800 66.667 32.17 20.02 42.46 5.69
1812 1818 4.455906 GCTTTGGGCCATTGCGGG 62.456 66.667 7.26 0.00 38.85 6.13
1813 1819 2.996734 CTTTGGGCCATTGCGGGT 60.997 61.111 7.26 0.00 38.85 5.28
1814 1820 3.299524 CTTTGGGCCATTGCGGGTG 62.300 63.158 7.26 0.00 38.85 4.61
1819 1825 4.440127 GCCATTGCGGGTGCCAAG 62.440 66.667 0.00 0.00 41.78 3.61
1820 1826 4.440127 CCATTGCGGGTGCCAAGC 62.440 66.667 1.85 1.85 41.78 4.01
1821 1827 3.682885 CATTGCGGGTGCCAAGCA 61.683 61.111 6.53 6.53 41.78 3.91
1837 1843 6.851609 TGCCAAGCACTTAAGTAATGTAATG 58.148 36.000 8.04 1.46 31.71 1.90
1838 1844 5.743872 GCCAAGCACTTAAGTAATGTAATGC 59.256 40.000 8.04 5.09 0.00 3.56
1839 1845 6.265577 CCAAGCACTTAAGTAATGTAATGCC 58.734 40.000 8.04 0.00 32.19 4.40
1840 1846 5.734855 AGCACTTAAGTAATGTAATGCCG 57.265 39.130 8.04 0.00 32.19 5.69
1841 1847 4.035208 AGCACTTAAGTAATGTAATGCCGC 59.965 41.667 8.04 3.00 32.19 6.53
1842 1848 4.514506 CACTTAAGTAATGTAATGCCGCG 58.485 43.478 8.04 0.00 0.00 6.46
1843 1849 4.269123 CACTTAAGTAATGTAATGCCGCGA 59.731 41.667 8.23 0.00 0.00 5.87
1844 1850 4.506654 ACTTAAGTAATGTAATGCCGCGAG 59.493 41.667 8.23 0.00 0.00 5.03
1845 1851 2.882927 AGTAATGTAATGCCGCGAGA 57.117 45.000 8.23 0.00 0.00 4.04
1846 1852 3.173668 AGTAATGTAATGCCGCGAGAA 57.826 42.857 8.23 0.00 0.00 2.87
1847 1853 3.728845 AGTAATGTAATGCCGCGAGAAT 58.271 40.909 8.23 0.00 0.00 2.40
1848 1854 4.878439 AGTAATGTAATGCCGCGAGAATA 58.122 39.130 8.23 0.00 0.00 1.75
1849 1855 5.294356 AGTAATGTAATGCCGCGAGAATAA 58.706 37.500 8.23 0.00 0.00 1.40
1850 1856 5.932303 AGTAATGTAATGCCGCGAGAATAAT 59.068 36.000 8.23 0.00 0.00 1.28
1851 1857 7.094631 AGTAATGTAATGCCGCGAGAATAATA 58.905 34.615 8.23 0.00 0.00 0.98
1852 1858 5.779806 ATGTAATGCCGCGAGAATAATAC 57.220 39.130 8.23 2.10 0.00 1.89
1853 1859 4.623002 TGTAATGCCGCGAGAATAATACA 58.377 39.130 8.23 4.85 0.00 2.29
1854 1860 5.234752 TGTAATGCCGCGAGAATAATACAT 58.765 37.500 8.23 0.00 0.00 2.29
1855 1861 4.928661 AATGCCGCGAGAATAATACATC 57.071 40.909 8.23 0.00 0.00 3.06
1856 1862 3.660501 TGCCGCGAGAATAATACATCT 57.339 42.857 8.23 0.00 0.00 2.90
1857 1863 4.776795 TGCCGCGAGAATAATACATCTA 57.223 40.909 8.23 0.00 0.00 1.98
1858 1864 4.733850 TGCCGCGAGAATAATACATCTAG 58.266 43.478 8.23 0.00 0.00 2.43
1859 1865 4.217767 TGCCGCGAGAATAATACATCTAGT 59.782 41.667 8.23 0.00 0.00 2.57
1860 1866 4.559251 GCCGCGAGAATAATACATCTAGTG 59.441 45.833 8.23 0.00 0.00 2.74
1861 1867 5.700846 CCGCGAGAATAATACATCTAGTGT 58.299 41.667 8.23 3.91 44.95 3.55
1862 1868 6.150318 CCGCGAGAATAATACATCTAGTGTT 58.850 40.000 8.23 0.00 42.29 3.32
1863 1869 6.641314 CCGCGAGAATAATACATCTAGTGTTT 59.359 38.462 8.23 2.58 42.29 2.83
1864 1870 7.358435 CCGCGAGAATAATACATCTAGTGTTTG 60.358 40.741 8.23 0.00 42.29 2.93
1865 1871 7.284351 GCGAGAATAATACATCTAGTGTTTGC 58.716 38.462 3.77 0.00 42.29 3.68
1866 1872 7.569591 GCGAGAATAATACATCTAGTGTTTGCC 60.570 40.741 3.77 0.00 42.29 4.52
1867 1873 7.358435 CGAGAATAATACATCTAGTGTTTGCCG 60.358 40.741 3.77 0.00 42.29 5.69
1868 1874 5.924475 ATAATACATCTAGTGTTTGCCGC 57.076 39.130 3.77 0.00 42.29 6.53
1869 1875 3.543680 ATACATCTAGTGTTTGCCGCT 57.456 42.857 3.77 0.00 42.29 5.52
1870 1876 2.185004 ACATCTAGTGTTTGCCGCTT 57.815 45.000 0.00 0.00 38.01 4.68
1871 1877 1.806542 ACATCTAGTGTTTGCCGCTTG 59.193 47.619 0.00 0.00 38.01 4.01
1872 1878 2.076100 CATCTAGTGTTTGCCGCTTGA 58.924 47.619 0.00 0.00 39.24 3.02
1873 1879 1.508632 TCTAGTGTTTGCCGCTTGAC 58.491 50.000 0.00 0.00 35.05 3.18
1874 1880 0.163788 CTAGTGTTTGCCGCTTGACG 59.836 55.000 0.00 0.00 43.15 4.35
1884 1890 3.269347 GCTTGACGGCGTGTGTGT 61.269 61.111 21.19 0.00 0.00 3.72
1885 1891 1.952133 GCTTGACGGCGTGTGTGTA 60.952 57.895 21.19 0.00 0.00 2.90
1886 1892 1.289109 GCTTGACGGCGTGTGTGTAT 61.289 55.000 21.19 0.00 0.00 2.29
1887 1893 0.713883 CTTGACGGCGTGTGTGTATC 59.286 55.000 21.19 0.00 0.00 2.24
1888 1894 0.032267 TTGACGGCGTGTGTGTATCA 59.968 50.000 21.19 2.86 0.00 2.15
1889 1895 0.032267 TGACGGCGTGTGTGTATCAA 59.968 50.000 21.19 0.00 0.00 2.57
1890 1896 1.141645 GACGGCGTGTGTGTATCAAA 58.858 50.000 21.19 0.00 0.00 2.69
1891 1897 1.527736 GACGGCGTGTGTGTATCAAAA 59.472 47.619 21.19 0.00 0.00 2.44
1892 1898 1.262151 ACGGCGTGTGTGTATCAAAAC 59.738 47.619 13.76 0.00 0.00 2.43
1893 1899 1.529438 CGGCGTGTGTGTATCAAAACT 59.471 47.619 0.00 0.00 0.00 2.66
1894 1900 2.411031 CGGCGTGTGTGTATCAAAACTC 60.411 50.000 0.00 0.00 0.00 3.01
1895 1901 2.806244 GGCGTGTGTGTATCAAAACTCT 59.194 45.455 0.00 0.00 0.00 3.24
1896 1902 3.120649 GGCGTGTGTGTATCAAAACTCTC 60.121 47.826 0.00 0.00 0.00 3.20
1897 1903 3.741344 GCGTGTGTGTATCAAAACTCTCT 59.259 43.478 0.00 0.00 0.00 3.10
1898 1904 4.211374 GCGTGTGTGTATCAAAACTCTCTT 59.789 41.667 0.00 0.00 0.00 2.85
1899 1905 5.612709 GCGTGTGTGTATCAAAACTCTCTTC 60.613 44.000 0.00 0.00 0.00 2.87
1900 1906 5.692204 CGTGTGTGTATCAAAACTCTCTTCT 59.308 40.000 0.00 0.00 0.00 2.85
1901 1907 6.201044 CGTGTGTGTATCAAAACTCTCTTCTT 59.799 38.462 0.00 0.00 0.00 2.52
1902 1908 7.381408 CGTGTGTGTATCAAAACTCTCTTCTTA 59.619 37.037 0.00 0.00 0.00 2.10
1903 1909 9.042008 GTGTGTGTATCAAAACTCTCTTCTTAA 57.958 33.333 0.00 0.00 0.00 1.85
1904 1910 9.778741 TGTGTGTATCAAAACTCTCTTCTTAAT 57.221 29.630 0.00 0.00 0.00 1.40
1917 1923 8.951243 ACTCTCTTCTTAATTAATGAAACTGGC 58.049 33.333 0.00 0.00 0.00 4.85
1918 1924 8.862325 TCTCTTCTTAATTAATGAAACTGGCA 57.138 30.769 0.00 0.00 0.00 4.92
1919 1925 9.295825 TCTCTTCTTAATTAATGAAACTGGCAA 57.704 29.630 0.00 0.00 0.00 4.52
1920 1926 9.912634 CTCTTCTTAATTAATGAAACTGGCAAA 57.087 29.630 0.00 0.00 0.00 3.68
1928 1934 5.678132 AATGAAACTGGCAAATCTTTTGC 57.322 34.783 14.88 14.88 44.22 3.68
1971 1978 1.846712 GAGCCCTTCCCTCACAAGCT 61.847 60.000 0.00 0.00 0.00 3.74
1982 1989 1.532868 CTCACAAGCTTCAAACCCTCG 59.467 52.381 0.00 0.00 0.00 4.63
2211 2226 3.030308 CGCCCGAATCCGACATCG 61.030 66.667 0.00 0.00 38.22 3.84
2249 2267 3.787001 GGAGGGGCAGAAGACGGG 61.787 72.222 0.00 0.00 0.00 5.28
2700 2721 1.369091 CCAGACGCTTCATTTCCCCG 61.369 60.000 0.00 0.00 0.00 5.73
2756 2777 3.462025 CTCGGAAGGTTCTCTGCAGAGA 61.462 54.545 36.94 36.94 43.47 3.10
2898 2919 5.296035 GGATACCGAGGTAAATTGGTGAAAG 59.704 44.000 6.04 0.00 37.53 2.62
3270 3409 5.163258 CCTGCTTGGAGAAGTTGTATATCCT 60.163 44.000 0.00 0.00 38.35 3.24
3283 3422 5.936187 TGTATATCCTGGTAACCGTTCAA 57.064 39.130 0.00 0.00 0.00 2.69
3305 3516 8.500753 TCAACTGTGATTTGTAGTGTTAACTT 57.499 30.769 7.22 0.00 37.88 2.66
3317 3528 8.822652 TGTAGTGTTAACTTTTAAGCTACTCC 57.177 34.615 7.22 0.00 37.88 3.85
3351 3562 9.750125 AACTTTTGTCTTTCCATTTTCAGATAC 57.250 29.630 0.00 0.00 0.00 2.24
3359 3573 4.811908 TCCATTTTCAGATACGTTCGTCA 58.188 39.130 0.00 0.00 0.00 4.35
3378 3592 2.777692 TCAGGGAGAAAGAGTTTGTGGT 59.222 45.455 0.00 0.00 0.00 4.16
3608 3822 1.376466 GGCTTCCAGAGGTGCTCAA 59.624 57.895 0.00 0.00 32.06 3.02
3744 3963 6.551385 ACTTTGATGAGTTACTCTTGCTTG 57.449 37.500 13.86 3.26 0.00 4.01
3760 3979 9.899226 ACTCTTGCTTGTCTAATTATTTGTTTC 57.101 29.630 0.00 0.00 0.00 2.78
3782 4001 5.195940 TCATCCAAATTTGATCAGGTCTCC 58.804 41.667 19.86 0.00 0.00 3.71
3818 4037 2.632996 TGAAGTTCCTAGTGTCCTGGTG 59.367 50.000 0.00 0.00 0.00 4.17
3820 4039 0.977395 GTTCCTAGTGTCCTGGTGCT 59.023 55.000 0.00 0.00 0.00 4.40
3865 4084 5.559770 TGCAGAATCTGTAAAAGATGTGGA 58.440 37.500 12.29 0.00 45.37 4.02
3968 4187 5.407387 TCTGTACGTTTTCTTAACATCCTGC 59.593 40.000 0.00 0.00 0.00 4.85
3999 4218 7.787904 TCCCTAAAACTGAGCTACATCCTATAA 59.212 37.037 0.00 0.00 0.00 0.98
4121 4340 9.823647 AACCAATTATGTAGAATGTGTAGAGAG 57.176 33.333 0.00 0.00 0.00 3.20
4174 4396 1.002033 CAAGGTCTGTGAGTGCAAAGC 60.002 52.381 0.00 0.00 28.90 3.51
4199 4421 9.561270 GCTTGAAACCATTCTCTTTCTTAATAC 57.439 33.333 0.00 0.00 36.48 1.89
4260 4487 7.321153 TCTAAAACTGAGCTACATCCTACAAC 58.679 38.462 0.00 0.00 0.00 3.32
4474 4711 3.961408 TCTATCTAGCCTTGGTTGGAGTC 59.039 47.826 0.00 0.00 0.00 3.36
4486 4723 2.932614 GGTTGGAGTCGAGACATGATTG 59.067 50.000 0.00 0.00 0.00 2.67
4583 4823 0.179936 CCCTTCATCTGTCTGCTCCC 59.820 60.000 0.00 0.00 0.00 4.30
4598 4838 1.228862 TCCCTTTTGCCCTTCCAGC 60.229 57.895 0.00 0.00 0.00 4.85
4694 4940 9.394767 TCATAGTACAATTTACTTCATGCATGT 57.605 29.630 25.43 9.95 0.00 3.21
4697 4943 8.746922 AGTACAATTTACTTCATGCATGTTTG 57.253 30.769 25.43 17.83 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 4.092529 GTGATATGATAGATTGCCACTGCG 59.907 45.833 0.00 0.00 41.78 5.18
75 76 6.239714 GGTCCAGTGGTGTGATATGATAGATT 60.240 42.308 9.54 0.00 0.00 2.40
102 103 1.376037 CTTGAGAACCTCCACCGGC 60.376 63.158 0.00 0.00 0.00 6.13
161 162 1.208706 TCCACCTGTCACTTTGTCCA 58.791 50.000 0.00 0.00 0.00 4.02
348 350 2.620585 AGTCGCGAAGAGATCATGATCA 59.379 45.455 31.99 10.67 39.40 2.92
367 369 2.029073 CGTCACCTTGGTCGCAGT 59.971 61.111 0.00 0.00 0.00 4.40
386 388 7.910441 AATTTTGCTTTATTTCCATCACCAG 57.090 32.000 0.00 0.00 0.00 4.00
423 425 3.795041 CTGAGCCCCTCCAGCCAG 61.795 72.222 0.00 0.00 0.00 4.85
702 706 3.305629 GCAAGCTTGAACGAGATAGTCTG 59.694 47.826 30.39 0.00 0.00 3.51
703 707 3.056536 TGCAAGCTTGAACGAGATAGTCT 60.057 43.478 30.39 0.00 0.00 3.24
800 805 1.599518 TTGAAGCATGTCCGCGGTT 60.600 52.632 27.15 11.07 36.85 4.44
811 816 0.674581 CCATCCTCTGCGTTGAAGCA 60.675 55.000 0.00 0.00 45.96 3.91
965 970 4.279043 GTGCCAAACCGGTGCCAC 62.279 66.667 8.52 9.65 36.97 5.01
1062 1067 6.891306 TCTTTCCTTCTAGATTTCCCATCA 57.109 37.500 0.00 0.00 0.00 3.07
1075 1080 1.197721 CGTGCGCATTTCTTTCCTTCT 59.802 47.619 15.91 0.00 0.00 2.85
1187 1192 3.173668 TCTCGCGGCATTACATTACTT 57.826 42.857 6.13 0.00 0.00 2.24
1208 1213 5.611374 AGCGGCAAACACTAGATGTATTAT 58.389 37.500 1.45 0.00 42.31 1.28
1215 1220 2.076863 GTCAAGCGGCAAACACTAGAT 58.923 47.619 1.45 0.00 0.00 1.98
1313 1319 1.301293 CTTGTGAGGGAAGGGCTCC 59.699 63.158 0.00 0.00 44.54 4.70
1314 1320 1.377856 GCTTGTGAGGGAAGGGCTC 60.378 63.158 0.00 0.00 0.00 4.70
1315 1321 1.430369 AAGCTTGTGAGGGAAGGGCT 61.430 55.000 0.00 0.00 0.00 5.19
1316 1322 0.962855 GAAGCTTGTGAGGGAAGGGC 60.963 60.000 2.10 0.00 0.00 5.19
1317 1323 0.401738 TGAAGCTTGTGAGGGAAGGG 59.598 55.000 2.10 0.00 0.00 3.95
1318 1324 2.276732 TTGAAGCTTGTGAGGGAAGG 57.723 50.000 2.10 0.00 0.00 3.46
1319 1325 2.294512 GGTTTGAAGCTTGTGAGGGAAG 59.705 50.000 2.10 0.00 0.00 3.46
1320 1326 2.306847 GGTTTGAAGCTTGTGAGGGAA 58.693 47.619 2.10 0.00 0.00 3.97
1321 1327 1.478654 GGGTTTGAAGCTTGTGAGGGA 60.479 52.381 2.10 0.00 0.00 4.20
1322 1328 0.961753 GGGTTTGAAGCTTGTGAGGG 59.038 55.000 2.10 0.00 0.00 4.30
1323 1329 1.882623 GAGGGTTTGAAGCTTGTGAGG 59.117 52.381 2.10 0.00 0.00 3.86
1324 1330 1.532868 CGAGGGTTTGAAGCTTGTGAG 59.467 52.381 2.10 0.00 0.00 3.51
1325 1331 1.593196 CGAGGGTTTGAAGCTTGTGA 58.407 50.000 2.10 0.00 0.00 3.58
1326 1332 0.040067 GCGAGGGTTTGAAGCTTGTG 60.040 55.000 2.10 0.00 0.00 3.33
1327 1333 1.172812 GGCGAGGGTTTGAAGCTTGT 61.173 55.000 2.10 0.00 0.00 3.16
1328 1334 1.172180 TGGCGAGGGTTTGAAGCTTG 61.172 55.000 2.10 0.00 0.00 4.01
1329 1335 1.150536 TGGCGAGGGTTTGAAGCTT 59.849 52.632 0.00 0.00 0.00 3.74
1330 1336 1.600916 GTGGCGAGGGTTTGAAGCT 60.601 57.895 0.00 0.00 0.00 3.74
1331 1337 1.896660 TGTGGCGAGGGTTTGAAGC 60.897 57.895 0.00 0.00 0.00 3.86
1332 1338 1.841663 CGTGTGGCGAGGGTTTGAAG 61.842 60.000 0.00 0.00 44.77 3.02
1333 1339 1.890041 CGTGTGGCGAGGGTTTGAA 60.890 57.895 0.00 0.00 44.77 2.69
1334 1340 2.280524 CGTGTGGCGAGGGTTTGA 60.281 61.111 0.00 0.00 44.77 2.69
1335 1341 2.280524 TCGTGTGGCGAGGGTTTG 60.281 61.111 0.00 0.00 45.68 2.93
1343 1349 0.874175 TCAGAACAGTTCGTGTGGCG 60.874 55.000 7.68 0.00 40.26 5.69
1344 1350 1.295792 TTCAGAACAGTTCGTGTGGC 58.704 50.000 7.68 0.00 40.26 5.01
1345 1351 4.349663 TTTTTCAGAACAGTTCGTGTGG 57.650 40.909 7.68 0.00 40.26 4.17
1363 1369 1.439679 GCGGTCTCTCGGACATTTTT 58.560 50.000 0.00 0.00 46.16 1.94
1364 1370 0.736325 CGCGGTCTCTCGGACATTTT 60.736 55.000 0.00 0.00 46.16 1.82
1365 1371 1.153823 CGCGGTCTCTCGGACATTT 60.154 57.895 0.00 0.00 46.16 2.32
1366 1372 2.490217 CGCGGTCTCTCGGACATT 59.510 61.111 0.00 0.00 46.16 2.71
1781 1787 2.558359 CCCAAAGCGACATTTCCTCTTT 59.442 45.455 0.00 0.00 0.00 2.52
1782 1788 2.162681 CCCAAAGCGACATTTCCTCTT 58.837 47.619 0.00 0.00 0.00 2.85
1783 1789 1.826385 CCCAAAGCGACATTTCCTCT 58.174 50.000 0.00 0.00 0.00 3.69
1784 1790 0.171231 GCCCAAAGCGACATTTCCTC 59.829 55.000 0.00 0.00 0.00 3.71
1785 1791 1.250840 GGCCCAAAGCGACATTTCCT 61.251 55.000 0.00 0.00 45.17 3.36
1786 1792 1.215382 GGCCCAAAGCGACATTTCC 59.785 57.895 0.00 0.00 45.17 3.13
1787 1793 0.532115 ATGGCCCAAAGCGACATTTC 59.468 50.000 0.00 0.00 45.17 2.17
1788 1794 0.975887 AATGGCCCAAAGCGACATTT 59.024 45.000 0.00 0.00 45.17 2.32
1789 1795 0.247185 CAATGGCCCAAAGCGACATT 59.753 50.000 0.00 0.00 45.17 2.71
1790 1796 1.892338 CAATGGCCCAAAGCGACAT 59.108 52.632 0.00 0.00 45.17 3.06
1791 1797 2.929903 GCAATGGCCCAAAGCGACA 61.930 57.895 0.00 0.00 45.17 4.35
1792 1798 2.125952 GCAATGGCCCAAAGCGAC 60.126 61.111 0.00 0.00 45.17 5.19
1795 1801 4.455906 CCCGCAATGGCCCAAAGC 62.456 66.667 0.00 0.00 42.60 3.51
1796 1802 2.996734 ACCCGCAATGGCCCAAAG 60.997 61.111 0.00 0.00 36.38 2.77
1797 1803 3.309506 CACCCGCAATGGCCCAAA 61.310 61.111 0.00 0.00 36.38 3.28
1802 1808 4.440127 CTTGGCACCCGCAATGGC 62.440 66.667 0.00 0.00 41.24 4.40
1803 1809 4.440127 GCTTGGCACCCGCAATGG 62.440 66.667 0.00 0.00 41.24 3.16
1804 1810 3.682885 TGCTTGGCACCCGCAATG 61.683 61.111 3.17 0.00 41.24 2.82
1813 1819 6.624861 GCATTACATTACTTAAGTGCTTGGCA 60.625 38.462 18.56 4.73 35.60 4.92
1814 1820 5.743872 GCATTACATTACTTAAGTGCTTGGC 59.256 40.000 18.56 7.74 0.00 4.52
1815 1821 6.265577 GGCATTACATTACTTAAGTGCTTGG 58.734 40.000 18.56 5.83 0.00 3.61
1816 1822 5.965334 CGGCATTACATTACTTAAGTGCTTG 59.035 40.000 18.56 13.94 0.00 4.01
1817 1823 5.448632 GCGGCATTACATTACTTAAGTGCTT 60.449 40.000 18.56 2.59 0.00 3.91
1818 1824 4.035208 GCGGCATTACATTACTTAAGTGCT 59.965 41.667 18.56 2.19 0.00 4.40
1819 1825 4.279659 GCGGCATTACATTACTTAAGTGC 58.720 43.478 18.56 9.83 0.00 4.40
1820 1826 4.269123 TCGCGGCATTACATTACTTAAGTG 59.731 41.667 18.56 4.21 0.00 3.16
1821 1827 4.435425 TCGCGGCATTACATTACTTAAGT 58.565 39.130 13.68 13.68 0.00 2.24
1822 1828 4.743151 TCTCGCGGCATTACATTACTTAAG 59.257 41.667 6.13 0.00 0.00 1.85
1823 1829 4.684877 TCTCGCGGCATTACATTACTTAA 58.315 39.130 6.13 0.00 0.00 1.85
1824 1830 4.310357 TCTCGCGGCATTACATTACTTA 57.690 40.909 6.13 0.00 0.00 2.24
1825 1831 3.173668 TCTCGCGGCATTACATTACTT 57.826 42.857 6.13 0.00 0.00 2.24
1826 1832 2.882927 TCTCGCGGCATTACATTACT 57.117 45.000 6.13 0.00 0.00 2.24
1827 1833 5.585500 TTATTCTCGCGGCATTACATTAC 57.415 39.130 6.13 0.00 0.00 1.89
1828 1834 6.869388 TGTATTATTCTCGCGGCATTACATTA 59.131 34.615 6.13 0.00 0.00 1.90
1829 1835 5.699001 TGTATTATTCTCGCGGCATTACATT 59.301 36.000 6.13 0.00 0.00 2.71
1830 1836 5.234752 TGTATTATTCTCGCGGCATTACAT 58.765 37.500 6.13 0.00 0.00 2.29
1831 1837 4.623002 TGTATTATTCTCGCGGCATTACA 58.377 39.130 6.13 3.33 0.00 2.41
1832 1838 5.577164 AGATGTATTATTCTCGCGGCATTAC 59.423 40.000 6.13 0.63 0.00 1.89
1833 1839 5.720202 AGATGTATTATTCTCGCGGCATTA 58.280 37.500 6.13 0.00 0.00 1.90
1834 1840 4.569943 AGATGTATTATTCTCGCGGCATT 58.430 39.130 6.13 0.00 0.00 3.56
1835 1841 4.193826 AGATGTATTATTCTCGCGGCAT 57.806 40.909 6.13 0.00 0.00 4.40
1836 1842 3.660501 AGATGTATTATTCTCGCGGCA 57.339 42.857 6.13 0.00 0.00 5.69
1837 1843 4.559251 CACTAGATGTATTATTCTCGCGGC 59.441 45.833 6.13 0.00 0.00 6.53
1838 1844 5.700846 ACACTAGATGTATTATTCTCGCGG 58.299 41.667 6.13 0.00 40.88 6.46
1839 1845 7.494130 CAAACACTAGATGTATTATTCTCGCG 58.506 38.462 0.00 0.00 42.31 5.87
1840 1846 7.284351 GCAAACACTAGATGTATTATTCTCGC 58.716 38.462 0.00 0.00 42.31 5.03
1841 1847 7.358435 CGGCAAACACTAGATGTATTATTCTCG 60.358 40.741 0.00 0.00 42.31 4.04
1842 1848 7.569591 GCGGCAAACACTAGATGTATTATTCTC 60.570 40.741 0.00 0.00 42.31 2.87
1843 1849 6.202954 GCGGCAAACACTAGATGTATTATTCT 59.797 38.462 0.00 0.00 42.31 2.40
1844 1850 6.202954 AGCGGCAAACACTAGATGTATTATTC 59.797 38.462 1.45 0.00 42.31 1.75
1845 1851 6.055588 AGCGGCAAACACTAGATGTATTATT 58.944 36.000 1.45 0.00 42.31 1.40
1846 1852 5.611374 AGCGGCAAACACTAGATGTATTAT 58.389 37.500 1.45 0.00 42.31 1.28
1847 1853 5.018539 AGCGGCAAACACTAGATGTATTA 57.981 39.130 1.45 0.00 42.31 0.98
1848 1854 3.873910 AGCGGCAAACACTAGATGTATT 58.126 40.909 1.45 0.00 42.31 1.89
1849 1855 3.543680 AGCGGCAAACACTAGATGTAT 57.456 42.857 1.45 0.00 42.31 2.29
1850 1856 3.000041 CAAGCGGCAAACACTAGATGTA 59.000 45.455 1.45 0.00 42.31 2.29
1851 1857 1.806542 CAAGCGGCAAACACTAGATGT 59.193 47.619 1.45 0.00 46.42 3.06
1852 1858 2.076100 TCAAGCGGCAAACACTAGATG 58.924 47.619 1.45 0.00 0.00 2.90
1853 1859 2.076863 GTCAAGCGGCAAACACTAGAT 58.923 47.619 1.45 0.00 0.00 1.98
1854 1860 1.508632 GTCAAGCGGCAAACACTAGA 58.491 50.000 1.45 0.00 0.00 2.43
1855 1861 0.163788 CGTCAAGCGGCAAACACTAG 59.836 55.000 1.45 0.00 36.85 2.57
1856 1862 2.230892 CGTCAAGCGGCAAACACTA 58.769 52.632 1.45 0.00 36.85 2.74
1857 1863 3.022287 CGTCAAGCGGCAAACACT 58.978 55.556 1.45 0.00 36.85 3.55
1867 1873 1.289109 ATACACACACGCCGTCAAGC 61.289 55.000 0.00 0.00 0.00 4.01
1868 1874 0.713883 GATACACACACGCCGTCAAG 59.286 55.000 0.00 0.00 0.00 3.02
1869 1875 0.032267 TGATACACACACGCCGTCAA 59.968 50.000 0.00 0.00 0.00 3.18
1870 1876 0.032267 TTGATACACACACGCCGTCA 59.968 50.000 0.00 0.00 0.00 4.35
1871 1877 1.141645 TTTGATACACACACGCCGTC 58.858 50.000 0.00 0.00 0.00 4.79
1872 1878 1.262151 GTTTTGATACACACACGCCGT 59.738 47.619 0.00 0.00 0.00 5.68
1873 1879 1.529438 AGTTTTGATACACACACGCCG 59.471 47.619 0.00 0.00 0.00 6.46
1874 1880 2.806244 AGAGTTTTGATACACACACGCC 59.194 45.455 0.00 0.00 0.00 5.68
1875 1881 3.741344 AGAGAGTTTTGATACACACACGC 59.259 43.478 0.00 0.00 0.00 5.34
1876 1882 5.692204 AGAAGAGAGTTTTGATACACACACG 59.308 40.000 0.00 0.00 0.00 4.49
1877 1883 7.484035 AAGAAGAGAGTTTTGATACACACAC 57.516 36.000 0.00 0.00 0.00 3.82
1878 1884 9.778741 ATTAAGAAGAGAGTTTTGATACACACA 57.221 29.630 0.00 0.00 0.00 3.72
1891 1897 8.951243 GCCAGTTTCATTAATTAAGAAGAGAGT 58.049 33.333 3.94 0.00 0.00 3.24
1892 1898 8.950210 TGCCAGTTTCATTAATTAAGAAGAGAG 58.050 33.333 3.94 1.72 0.00 3.20
1893 1899 8.862325 TGCCAGTTTCATTAATTAAGAAGAGA 57.138 30.769 3.94 0.00 0.00 3.10
1894 1900 9.912634 TTTGCCAGTTTCATTAATTAAGAAGAG 57.087 29.630 3.94 3.01 0.00 2.85
1902 1908 8.291740 GCAAAAGATTTGCCAGTTTCATTAATT 58.708 29.630 15.12 0.00 39.38 1.40
1903 1909 7.809665 GCAAAAGATTTGCCAGTTTCATTAAT 58.190 30.769 15.12 0.00 39.38 1.40
1904 1910 7.188468 GCAAAAGATTTGCCAGTTTCATTAA 57.812 32.000 15.12 0.00 39.38 1.40
1905 1911 6.783892 GCAAAAGATTTGCCAGTTTCATTA 57.216 33.333 15.12 0.00 39.38 1.90
1906 1912 5.678132 GCAAAAGATTTGCCAGTTTCATT 57.322 34.783 15.12 0.00 39.38 2.57
1971 1978 1.890041 CGTGTGGCGAGGGTTTGAA 60.890 57.895 0.00 0.00 44.77 2.69
1982 1989 1.295792 TTCAGAACAGTTCGTGTGGC 58.704 50.000 7.68 0.00 40.26 5.01
2237 2255 3.379445 TCGACCCCGTCTTCTGCC 61.379 66.667 0.00 0.00 37.05 4.85
2249 2267 2.509336 CCGCTGATGTGGTCGACC 60.509 66.667 28.17 28.17 38.95 4.79
2898 2919 2.334023 AGGGGCATCCTCAATAGAGAC 58.666 52.381 0.00 0.00 44.06 3.36
3270 3409 2.983907 TCACAGTTGAACGGTTACCA 57.016 45.000 1.13 0.00 0.00 3.25
3305 3516 5.560724 AGTTCATGCAAGGAGTAGCTTAAA 58.439 37.500 0.00 0.00 0.00 1.52
3317 3528 5.350633 TGGAAAGACAAAAGTTCATGCAAG 58.649 37.500 0.00 0.00 0.00 4.01
3351 3562 1.269998 ACTCTTTCTCCCTGACGAACG 59.730 52.381 0.00 0.00 0.00 3.95
3359 3573 2.509964 ACACCACAAACTCTTTCTCCCT 59.490 45.455 0.00 0.00 0.00 4.20
3378 3592 2.427812 TGTGACTCTGGTGTTTACGACA 59.572 45.455 0.00 0.00 35.42 4.35
3517 3731 1.215423 ACCAGCCTTGAACCTCAAACT 59.785 47.619 0.00 0.00 35.73 2.66
3518 3732 1.338020 CACCAGCCTTGAACCTCAAAC 59.662 52.381 0.00 0.00 35.73 2.93
3628 3842 2.154462 CCTCAAGTTTGCGGAGACATT 58.846 47.619 0.00 0.00 35.05 2.71
3760 3979 5.198965 AGGAGACCTGATCAAATTTGGATG 58.801 41.667 17.90 6.42 29.57 3.51
3782 4001 5.529060 AGGAACTTCAAAGCACTAGAAACAG 59.471 40.000 0.00 0.00 27.25 3.16
3818 4037 7.905493 GCATAGTTAGTCTAAACATCACAAAGC 59.095 37.037 0.00 0.00 31.94 3.51
3820 4039 8.840833 TGCATAGTTAGTCTAAACATCACAAA 57.159 30.769 0.00 0.00 31.94 2.83
3874 4093 2.332063 GCCTAGGCACAATTAGCTGA 57.668 50.000 29.33 0.00 41.49 4.26
3903 4122 4.869861 AGAATGGTTTCAAACTTTGCACAC 59.130 37.500 0.00 0.00 34.08 3.82
3904 4123 5.083533 AGAATGGTTTCAAACTTTGCACA 57.916 34.783 0.00 0.00 34.08 4.57
3943 4162 6.401153 GCAGGATGTTAAGAAAACGTACAGAG 60.401 42.308 0.00 0.00 39.31 3.35
3945 4164 5.618561 GCAGGATGTTAAGAAAACGTACAG 58.381 41.667 0.00 0.00 39.31 2.74
3968 4187 2.767505 AGCTCAGTTTTAGGGAACACG 58.232 47.619 0.00 0.00 31.94 4.49
3999 4218 8.328758 TGGAACATTCAGATAAAATAGACCTGT 58.671 33.333 0.00 0.00 0.00 4.00
4032 4251 4.499188 GCCAAGACACAAAGTAAAGTTCCC 60.499 45.833 0.00 0.00 0.00 3.97
4121 4340 0.898326 AGCCGGAAATTTGTCCCCAC 60.898 55.000 5.05 0.00 33.74 4.61
4199 4421 9.944663 AAAGTGTACACAACATAACAAATACTG 57.055 29.630 27.06 0.00 41.10 2.74
4208 4430 8.185505 GGAAACAAGAAAGTGTACACAACATAA 58.814 33.333 27.06 0.00 41.10 1.90
4275 4502 1.879380 TCCCTGTGCTTGAAACATTCG 59.121 47.619 0.00 0.00 0.00 3.34
4403 4639 6.122850 TGATACTCTCAAATGCAAAATCCG 57.877 37.500 0.00 0.00 0.00 4.18
4474 4711 2.200067 GCTCTCACCAATCATGTCTCG 58.800 52.381 0.00 0.00 0.00 4.04
4486 4723 0.798776 CATGTGGAAACGCTCTCACC 59.201 55.000 0.00 0.00 42.82 4.02
4542 4782 5.510520 GGGACAAATGTTACAGGAAATGCAA 60.511 40.000 0.00 0.00 0.00 4.08
4583 4823 0.829182 ACAGGCTGGAAGGGCAAAAG 60.829 55.000 20.34 0.00 0.00 2.27
4598 4838 2.438021 TGCTTACCTAAGGGCATACAGG 59.562 50.000 0.00 0.00 35.63 4.00
4673 4919 7.447430 GCAAACATGCATGAAGTAAATTGTAC 58.553 34.615 32.75 9.67 34.41 2.90
4674 4920 7.579589 GCAAACATGCATGAAGTAAATTGTA 57.420 32.000 32.75 0.00 34.41 2.41
4675 4921 6.470557 GCAAACATGCATGAAGTAAATTGT 57.529 33.333 32.75 4.95 34.41 2.71


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

AutoCloner maintained by Alex Coulton.