Multiple sequence alignment - TraesCS3B01G030200

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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 TraesCS3B01G030200 chr3B 100.000 2609 0 0 1 2609 13826701 13824093 0.000000e+00 4819.0
1 TraesCS3B01G030200 chr3B 82.357 1553 228 23 309 1832 13856574 13855039 0.000000e+00 1308.0
2 TraesCS3B01G030200 chr3B 100.000 31 0 0 1844 1874 46781530 46781560 1.010000e-04 58.4
3 TraesCS3B01G030200 chr3D 93.027 1305 82 2 291 1594 5058892 5060188 0.000000e+00 1897.0
4 TraesCS3B01G030200 chr3D 90.254 1262 105 11 337 1594 9620728 9619481 0.000000e+00 1633.0
5 TraesCS3B01G030200 chr3D 84.331 1621 206 24 308 1890 5051765 5053375 0.000000e+00 1543.0
6 TraesCS3B01G030200 chr3D 89.109 303 22 6 1 293 5058510 5058811 1.480000e-97 366.0
7 TraesCS3B01G030200 chr3D 91.579 95 7 1 1885 1978 81420947 81421041 2.110000e-26 130.0
8 TraesCS3B01G030200 chr3D 91.579 95 7 1 1885 1978 204189683 204189777 2.110000e-26 130.0
9 TraesCS3B01G030200 chr3D 100.000 31 0 0 1844 1874 27933241 27933271 1.010000e-04 58.4
10 TraesCS3B01G030200 chr3D 100.000 30 0 0 1845 1874 28222156 28222127 3.630000e-04 56.5
11 TraesCS3B01G030200 chr3D 100.000 28 0 0 1847 1874 4651747 4651774 5.000000e-03 52.8
12 TraesCS3B01G030200 chrUn 92.890 1308 83 7 288 1594 36498600 36499898 0.000000e+00 1892.0
13 TraesCS3B01G030200 chrUn 91.722 302 15 5 1 292 36497430 36497731 6.720000e-111 411.0
14 TraesCS3B01G030200 chrUn 82.738 168 15 7 7 161 35487494 35487660 1.260000e-28 137.0
15 TraesCS3B01G030200 chrUn 77.907 172 35 2 437 605 105551674 105551845 1.280000e-18 104.0
16 TraesCS3B01G030200 chrUn 100.000 28 0 0 1847 1874 34597132 34597159 5.000000e-03 52.8
17 TraesCS3B01G030200 chrUn 100.000 28 0 0 1847 1874 226970370 226970343 5.000000e-03 52.8
18 TraesCS3B01G030200 chrUn 100.000 28 0 0 1847 1874 250251544 250251517 5.000000e-03 52.8
19 TraesCS3B01G030200 chrUn 100.000 28 0 0 1847 1874 253533595 253533622 5.000000e-03 52.8
20 TraesCS3B01G030200 chr3A 87.413 1573 172 19 306 1861 11513538 11515101 0.000000e+00 1784.0
21 TraesCS3B01G030200 chr3A 88.469 1483 152 7 419 1890 10719976 10721450 0.000000e+00 1773.0
22 TraesCS3B01G030200 chr3A 88.402 1483 153 7 419 1890 10750016 10751490 0.000000e+00 1768.0
23 TraesCS3B01G030200 chr3A 84.024 1496 200 27 426 1890 11535804 11537291 0.000000e+00 1402.0
24 TraesCS3B01G030200 chr3A 93.463 872 42 6 290 1154 11538179 11539042 0.000000e+00 1280.0
25 TraesCS3B01G030200 chr3A 89.501 962 88 6 940 1890 10775883 10776842 0.000000e+00 1205.0
26 TraesCS3B01G030200 chr3A 86.408 515 62 6 419 932 10775059 10775566 8.160000e-155 556.0
27 TraesCS3B01G030200 chr3A 90.667 375 33 2 1977 2351 414901866 414902238 5.010000e-137 497.0
28 TraesCS3B01G030200 chr3A 89.508 305 19 7 1 293 11537803 11538106 8.820000e-100 374.0
29 TraesCS3B01G030200 chr3A 79.310 232 29 13 1649 1873 10943686 10943905 7.530000e-31 145.0
30 TraesCS3B01G030200 chr3A 77.385 283 26 12 13 293 10719523 10719769 1.630000e-27 134.0
31 TraesCS3B01G030200 chr7D 93.803 355 19 2 1996 2350 206996543 206996192 4.940000e-147 531.0
32 TraesCS3B01G030200 chr7D 91.579 95 7 1 1885 1978 210089587 210089681 2.110000e-26 130.0
33 TraesCS3B01G030200 chr5D 91.467 375 28 4 1978 2350 502109837 502110209 1.790000e-141 512.0
34 TraesCS3B01G030200 chr5D 91.200 375 29 4 1978 2350 502108615 502108987 8.330000e-140 507.0
35 TraesCS3B01G030200 chr5D 90.957 376 28 6 1977 2350 275621663 275621292 3.880000e-138 501.0
36 TraesCS3B01G030200 chr7A 91.176 374 31 2 1981 2353 490997741 490997369 8.330000e-140 507.0
37 TraesCS3B01G030200 chr2B 92.011 363 26 3 1981 2342 33865513 33865153 8.330000e-140 507.0
38 TraesCS3B01G030200 chr2B 91.576 368 30 1 1981 2348 193835234 193834868 8.330000e-140 507.0
39 TraesCS3B01G030200 chr2B 90.625 96 7 2 1885 1978 136642286 136642381 2.730000e-25 126.0
40 TraesCS3B01G030200 chr4D 90.860 372 33 1 1981 2351 110952305 110951934 5.010000e-137 497.0
41 TraesCS3B01G030200 chr4D 92.473 93 7 0 1885 1977 464124910 464124818 1.630000e-27 134.0
42 TraesCS3B01G030200 chr4A 82.366 465 64 13 1899 2350 58227103 58227562 3.150000e-104 388.0
43 TraesCS3B01G030200 chr1D 81.777 439 63 15 1898 2323 399562922 399563356 4.130000e-93 351.0
44 TraesCS3B01G030200 chr2A 80.818 391 58 14 1939 2323 477346806 477346427 9.130000e-75 291.0
45 TraesCS3B01G030200 chr6B 79.028 391 65 14 1939 2321 525776100 525775719 4.310000e-63 252.0
46 TraesCS3B01G030200 chr6B 96.970 33 0 1 2542 2574 532164362 532164393 1.000000e-03 54.7
47 TraesCS3B01G030200 chr4B 92.222 90 6 1 1890 1978 551961541 551961452 2.730000e-25 126.0
48 TraesCS3B01G030200 chr7B 90.526 95 8 1 1885 1978 361553007 361553101 9.800000e-25 124.0
49 TraesCS3B01G030200 chr1A 100.000 28 0 0 2547 2574 574940915 574940888 5.000000e-03 52.8


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 TraesCS3B01G030200 chr3B 13824093 13826701 2608 True 4819.000000 4819 100.000000 1 2609 1 chr3B.!!$R1 2608
1 TraesCS3B01G030200 chr3B 13855039 13856574 1535 True 1308.000000 1308 82.357000 309 1832 1 chr3B.!!$R2 1523
2 TraesCS3B01G030200 chr3D 9619481 9620728 1247 True 1633.000000 1633 90.254000 337 1594 1 chr3D.!!$R1 1257
3 TraesCS3B01G030200 chr3D 5051765 5053375 1610 False 1543.000000 1543 84.331000 308 1890 1 chr3D.!!$F2 1582
4 TraesCS3B01G030200 chr3D 5058510 5060188 1678 False 1131.500000 1897 91.068000 1 1594 2 chr3D.!!$F6 1593
5 TraesCS3B01G030200 chrUn 36497430 36499898 2468 False 1151.500000 1892 92.306000 1 1594 2 chrUn.!!$F5 1593
6 TraesCS3B01G030200 chr3A 11513538 11515101 1563 False 1784.000000 1784 87.413000 306 1861 1 chr3A.!!$F3 1555
7 TraesCS3B01G030200 chr3A 10750016 10751490 1474 False 1768.000000 1768 88.402000 419 1890 1 chr3A.!!$F1 1471
8 TraesCS3B01G030200 chr3A 11535804 11539042 3238 False 1018.666667 1402 88.998333 1 1890 3 chr3A.!!$F7 1889
9 TraesCS3B01G030200 chr3A 10719523 10721450 1927 False 953.500000 1773 82.927000 13 1890 2 chr3A.!!$F5 1877
10 TraesCS3B01G030200 chr3A 10775059 10776842 1783 False 880.500000 1205 87.954500 419 1890 2 chr3A.!!$F6 1471
11 TraesCS3B01G030200 chr5D 502108615 502110209 1594 False 509.500000 512 91.333500 1978 2350 2 chr5D.!!$F1 372

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
83 84 0.460987 CTGAAAGGCGGCGATTCTCT 60.461 55.0 23.62 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 3083 0.109827 CCACATGATGCGCGACAAAA 60.11 50.0 12.1 0.44 0.0 2.44 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
21 22 1.068417 CCACCGGACTGTTGTCGAA 59.932 57.895 9.46 0.00 43.79 3.71
83 84 0.460987 CTGAAAGGCGGCGATTCTCT 60.461 55.000 23.62 0.00 0.00 3.10
84 85 0.740868 TGAAAGGCGGCGATTCTCTG 60.741 55.000 23.62 0.00 0.00 3.35
129 138 4.115199 GCTGGGCTCCGATTGGGT 62.115 66.667 0.00 0.00 37.00 4.51
135 144 2.670148 GCTCCGATTGGGTGGGTCT 61.670 63.158 0.00 0.00 37.00 3.85
136 145 1.991230 CTCCGATTGGGTGGGTCTT 59.009 57.895 0.00 0.00 37.00 3.01
140 149 1.019278 CGATTGGGTGGGTCTTCACG 61.019 60.000 0.00 0.00 38.46 4.35
389 1343 2.556144 AGAAACCCACCCTTACGTTC 57.444 50.000 0.00 0.00 0.00 3.95
392 1346 1.337118 AACCCACCCTTACGTTCGTA 58.663 50.000 0.00 0.78 0.00 3.43
487 1449 3.113514 TTGGCCGTGCTGGAAGACA 62.114 57.895 0.00 0.00 42.00 3.41
609 1571 1.672356 CAGGTTCCTCCGCCAGTTG 60.672 63.158 0.00 0.00 41.99 3.16
630 1592 0.471191 ATCAGCATCATCGGAAGCCA 59.529 50.000 0.00 0.00 38.48 4.75
634 1596 1.224315 CATCATCGGAAGCCACCCA 59.776 57.895 0.00 0.00 0.00 4.51
708 1670 0.539901 CTCCCGACCGTATCCATCCT 60.540 60.000 0.00 0.00 0.00 3.24
742 1704 1.366366 GTACGATATGGCGGCCACT 59.634 57.895 26.48 15.15 35.80 4.00
957 2231 1.441729 CGATCAGGGCCACGTACAT 59.558 57.895 6.18 0.00 0.00 2.29
1075 2361 1.204704 CGGAGACTAACACATGGAGCA 59.795 52.381 0.00 0.00 0.00 4.26
1138 2424 0.690762 TGGTCCTAGCACCCTTGTTC 59.309 55.000 0.00 0.00 35.26 3.18
1277 2568 1.202782 CCAGATCATCCAGGCAGAAGG 60.203 57.143 0.00 0.00 0.00 3.46
1281 2572 0.842030 TCATCCAGGCAGAAGGTGGT 60.842 55.000 0.00 0.00 32.73 4.16
1334 2625 1.398390 CCTTCAACTATGGCAGCGAAC 59.602 52.381 0.00 0.00 0.00 3.95
1338 2629 0.321298 AACTATGGCAGCGAACGGTT 60.321 50.000 0.00 0.00 0.00 4.44
1382 2673 2.290641 GGTTGTCGTGCAAGATTGTTCT 59.709 45.455 5.42 0.00 37.83 3.01
1389 2680 2.848302 GTGCAAGATTGTTCTATTGCGC 59.152 45.455 0.00 0.00 38.17 6.09
1617 2911 8.296713 GGTTACTTGCAGAAGTGATGATTTTAA 58.703 33.333 1.14 0.00 42.66 1.52
1643 2937 9.850628 AAATGATAAAGTGATCATGAGTTTGTG 57.149 29.630 0.00 0.00 44.15 3.33
1834 3164 3.368248 ACTGAATGCATATGCCTTGGTT 58.632 40.909 24.54 11.33 41.18 3.67
1837 3167 5.599656 ACTGAATGCATATGCCTTGGTTTAT 59.400 36.000 24.54 6.17 41.18 1.40
1878 3209 6.320171 CAAGATGCTTTTGAATACCTCAGTG 58.680 40.000 0.00 0.00 34.81 3.66
1886 3217 6.509418 TTTGAATACCTCAGTGTTAATGCC 57.491 37.500 0.00 0.00 34.81 4.40
1888 3219 5.565509 TGAATACCTCAGTGTTAATGCCAA 58.434 37.500 0.00 0.00 0.00 4.52
1889 3220 5.647658 TGAATACCTCAGTGTTAATGCCAAG 59.352 40.000 0.00 0.00 0.00 3.61
1890 3221 2.795329 ACCTCAGTGTTAATGCCAAGG 58.205 47.619 0.00 0.00 0.00 3.61
1891 3222 1.474077 CCTCAGTGTTAATGCCAAGGC 59.526 52.381 3.61 3.61 42.35 4.35
1907 3238 3.727387 GCAGGAGCCCAAGTAGGA 58.273 61.111 0.00 0.00 41.22 2.94
1908 3239 2.225792 GCAGGAGCCCAAGTAGGAT 58.774 57.895 0.00 0.00 41.22 3.24
1909 3240 0.548510 GCAGGAGCCCAAGTAGGATT 59.451 55.000 0.00 0.00 41.22 3.01
1910 3241 1.475930 GCAGGAGCCCAAGTAGGATTC 60.476 57.143 0.00 0.00 41.22 2.52
1911 3242 1.839994 CAGGAGCCCAAGTAGGATTCA 59.160 52.381 0.00 0.00 41.22 2.57
1912 3243 2.122768 AGGAGCCCAAGTAGGATTCAG 58.877 52.381 0.00 0.00 41.22 3.02
1913 3244 1.475930 GGAGCCCAAGTAGGATTCAGC 60.476 57.143 0.00 0.00 41.22 4.26
1914 3245 0.548510 AGCCCAAGTAGGATTCAGCC 59.451 55.000 0.00 0.00 41.22 4.85
1916 3247 1.064389 GCCCAAGTAGGATTCAGCCTT 60.064 52.381 0.00 0.00 41.22 4.35
1917 3248 2.172717 GCCCAAGTAGGATTCAGCCTTA 59.827 50.000 0.00 0.00 41.22 2.69
1918 3249 3.809905 CCCAAGTAGGATTCAGCCTTAC 58.190 50.000 0.00 0.00 41.22 2.34
1919 3250 3.433740 CCCAAGTAGGATTCAGCCTTACC 60.434 52.174 0.00 0.00 41.22 2.85
1920 3251 3.456277 CCAAGTAGGATTCAGCCTTACCT 59.544 47.826 0.00 0.00 41.22 3.08
1921 3252 4.446371 CAAGTAGGATTCAGCCTTACCTG 58.554 47.826 0.00 0.00 39.50 4.00
1922 3253 3.041946 AGTAGGATTCAGCCTTACCTGG 58.958 50.000 0.00 0.00 39.50 4.45
1923 3254 1.216990 AGGATTCAGCCTTACCTGGG 58.783 55.000 0.00 0.00 33.46 4.45
1924 3255 0.183731 GGATTCAGCCTTACCTGGGG 59.816 60.000 0.00 0.00 33.64 4.96
1930 3261 4.489771 CCTTACCTGGGGCGCCTG 62.490 72.222 28.56 20.01 0.00 4.85
1945 3276 4.486503 CTGCTGGCTGCTCCCCTC 62.487 72.222 17.45 0.00 43.37 4.30
1947 3278 4.173924 GCTGGCTGCTCCCCTCTC 62.174 72.222 9.31 0.00 38.95 3.20
1948 3279 3.478274 CTGGCTGCTCCCCTCTCC 61.478 72.222 0.00 0.00 0.00 3.71
1952 3283 4.421554 CTGCTCCCCTCTCCCCCA 62.422 72.222 0.00 0.00 0.00 4.96
1953 3284 4.741239 TGCTCCCCTCTCCCCCAC 62.741 72.222 0.00 0.00 0.00 4.61
1955 3286 3.700350 CTCCCCTCTCCCCCACCT 61.700 72.222 0.00 0.00 0.00 4.00
1956 3287 2.204721 TCCCCTCTCCCCCACCTA 60.205 66.667 0.00 0.00 0.00 3.08
1957 3288 1.632269 TCCCCTCTCCCCCACCTAT 60.632 63.158 0.00 0.00 0.00 2.57
1958 3289 0.331137 TCCCCTCTCCCCCACCTATA 60.331 60.000 0.00 0.00 0.00 1.31
1959 3290 0.800239 CCCCTCTCCCCCACCTATAT 59.200 60.000 0.00 0.00 0.00 0.86
1960 3291 2.016096 CCCCTCTCCCCCACCTATATA 58.984 57.143 0.00 0.00 0.00 0.86
1961 3292 2.597304 CCCCTCTCCCCCACCTATATAT 59.403 54.545 0.00 0.00 0.00 0.86
1962 3293 3.803644 CCCCTCTCCCCCACCTATATATA 59.196 52.174 0.00 0.00 0.00 0.86
1963 3294 4.427406 CCCCTCTCCCCCACCTATATATAT 59.573 50.000 0.00 0.00 0.00 0.86
1964 3295 5.407049 CCCTCTCCCCCACCTATATATATG 58.593 50.000 5.44 0.00 0.00 1.78
1965 3296 5.102609 CCCTCTCCCCCACCTATATATATGT 60.103 48.000 5.44 0.00 0.00 2.29
1966 3297 6.105740 CCCTCTCCCCCACCTATATATATGTA 59.894 46.154 5.44 0.00 0.00 2.29
1967 3298 7.242359 CCTCTCCCCCACCTATATATATGTAG 58.758 46.154 9.04 9.04 0.00 2.74
1968 3299 7.175635 TCTCCCCCACCTATATATATGTAGG 57.824 44.000 26.02 26.02 44.47 3.18
1969 3300 6.924058 TCTCCCCCACCTATATATATGTAGGA 59.076 42.308 31.50 14.45 42.36 2.94
1970 3301 7.075138 TCTCCCCCACCTATATATATGTAGGAG 59.925 44.444 31.50 25.43 42.36 3.69
1971 3302 6.105740 TCCCCCACCTATATATATGTAGGAGG 59.894 46.154 31.50 30.48 45.42 4.30
1974 3305 6.323737 CCACCTATATATATGTAGGAGGGGG 58.676 48.000 31.50 23.37 43.60 5.40
2002 3333 4.712829 TCATAGTTTTGTCCCTCGGTCATA 59.287 41.667 0.00 0.00 0.00 2.15
2059 4909 0.911769 ATCACCATCACCGTCACCAT 59.088 50.000 0.00 0.00 0.00 3.55
2063 4913 1.083806 CCATCACCGTCACCATGTCG 61.084 60.000 0.00 0.00 0.00 4.35
2065 4915 0.108804 ATCACCGTCACCATGTCGTC 60.109 55.000 0.00 0.00 0.00 4.20
2096 4946 2.159028 GGACTCATCCACTACTTGGCTC 60.159 54.545 0.00 0.00 46.47 4.70
2144 5021 1.299850 CACCGAGCTGAACGTGTGA 60.300 57.895 0.00 0.00 35.60 3.58
2159 5036 1.080093 GTGATGAACGCGGAGGTGA 60.080 57.895 12.47 0.00 0.00 4.02
2160 5037 0.460284 GTGATGAACGCGGAGGTGAT 60.460 55.000 12.47 0.00 0.00 3.06
2168 5045 1.066430 ACGCGGAGGTGATGTACATTT 60.066 47.619 12.47 0.00 0.00 2.32
2197 5074 0.457853 TCGGTTGGATCGCGAAGAAG 60.458 55.000 15.24 1.14 0.00 2.85
2215 5092 3.255149 AGAAGTTCGACTACATCAACCGT 59.745 43.478 0.00 0.00 0.00 4.83
2226 5103 6.514947 ACTACATCAACCGTGTTACTAAACA 58.485 36.000 0.00 0.00 43.32 2.83
2273 5151 1.081481 TAGACACACTCTCCCCCTCA 58.919 55.000 0.00 0.00 0.00 3.86
2350 5228 2.896685 TCCATCCAATGTTTCCCAACAC 59.103 45.455 0.00 0.00 45.88 3.32
2352 5230 4.085733 CCATCCAATGTTTCCCAACACTA 58.914 43.478 0.00 0.00 45.88 2.74
2353 5231 4.158394 CCATCCAATGTTTCCCAACACTAG 59.842 45.833 0.00 0.00 45.88 2.57
2354 5232 3.761897 TCCAATGTTTCCCAACACTAGG 58.238 45.455 0.00 0.00 45.88 3.02
2355 5233 3.139397 TCCAATGTTTCCCAACACTAGGT 59.861 43.478 0.00 0.00 45.88 3.08
2357 5235 2.943036 TGTTTCCCAACACTAGGTCC 57.057 50.000 0.00 0.00 38.03 4.46
2358 5236 1.422402 TGTTTCCCAACACTAGGTCCC 59.578 52.381 0.00 0.00 38.03 4.46
2360 5238 2.107726 GTTTCCCAACACTAGGTCCCTT 59.892 50.000 0.00 0.00 32.54 3.95
2361 5239 1.358152 TCCCAACACTAGGTCCCTTG 58.642 55.000 0.00 0.00 0.00 3.61
2362 5240 0.328258 CCCAACACTAGGTCCCTTGG 59.672 60.000 0.00 0.00 0.00 3.61
2363 5241 0.322546 CCAACACTAGGTCCCTTGGC 60.323 60.000 0.00 0.00 0.00 4.52
2364 5242 0.322546 CAACACTAGGTCCCTTGGCC 60.323 60.000 0.00 0.00 0.00 5.36
2365 5243 1.498176 AACACTAGGTCCCTTGGCCC 61.498 60.000 0.00 0.00 0.00 5.80
2366 5244 1.923395 CACTAGGTCCCTTGGCCCA 60.923 63.158 0.00 0.00 0.00 5.36
2367 5245 1.151677 ACTAGGTCCCTTGGCCCAA 60.152 57.895 0.00 0.00 0.00 4.12
2369 5247 2.211468 CTAGGTCCCTTGGCCCAACC 62.211 65.000 0.00 0.10 39.84 3.77
2370 5248 4.696805 GGTCCCTTGGCCCAACCC 62.697 72.222 0.00 0.00 37.83 4.11
2371 5249 3.909651 GTCCCTTGGCCCAACCCA 61.910 66.667 0.00 0.00 37.83 4.51
2376 5254 2.841988 TTGGCCCAACCCAAGTGC 60.842 61.111 0.00 0.00 39.85 4.40
2379 5257 2.203480 GCCCAACCCAAGTGCTCA 60.203 61.111 0.00 0.00 0.00 4.26
2380 5258 1.607467 GCCCAACCCAAGTGCTCAT 60.607 57.895 0.00 0.00 0.00 2.90
2381 5259 1.187567 GCCCAACCCAAGTGCTCATT 61.188 55.000 0.00 0.00 0.00 2.57
2383 5261 1.273327 CCCAACCCAAGTGCTCATTTC 59.727 52.381 0.00 0.00 0.00 2.17
2385 5263 1.068333 CAACCCAAGTGCTCATTTCCG 60.068 52.381 0.00 0.00 0.00 4.30
2386 5264 0.609131 ACCCAAGTGCTCATTTCCGG 60.609 55.000 0.00 0.00 0.00 5.14
2387 5265 0.609131 CCCAAGTGCTCATTTCCGGT 60.609 55.000 0.00 0.00 0.00 5.28
2389 5267 2.432444 CCAAGTGCTCATTTCCGGTTA 58.568 47.619 0.00 0.00 0.00 2.85
2390 5268 2.420022 CCAAGTGCTCATTTCCGGTTAG 59.580 50.000 0.00 0.00 0.00 2.34
2391 5269 2.403252 AGTGCTCATTTCCGGTTAGG 57.597 50.000 0.00 0.00 42.97 2.69
2392 5270 1.065418 AGTGCTCATTTCCGGTTAGGG 60.065 52.381 0.00 0.00 41.52 3.53
2393 5271 1.065709 GTGCTCATTTCCGGTTAGGGA 60.066 52.381 0.00 0.00 41.52 4.20
2394 5272 1.631388 TGCTCATTTCCGGTTAGGGAA 59.369 47.619 0.00 0.00 42.94 3.97
2395 5273 2.289565 GCTCATTTCCGGTTAGGGAAG 58.710 52.381 0.00 0.00 46.23 3.46
2396 5274 2.919228 CTCATTTCCGGTTAGGGAAGG 58.081 52.381 0.00 0.00 46.23 3.46
2397 5275 2.238898 CTCATTTCCGGTTAGGGAAGGT 59.761 50.000 0.00 0.00 46.23 3.50
2398 5276 2.645797 TCATTTCCGGTTAGGGAAGGTT 59.354 45.455 0.00 0.00 46.23 3.50
2399 5277 2.865119 TTTCCGGTTAGGGAAGGTTC 57.135 50.000 0.00 0.00 46.23 3.62
2401 5279 2.925966 TCCGGTTAGGGAAGGTTCTA 57.074 50.000 0.00 0.00 41.52 2.10
2403 5281 2.312741 TCCGGTTAGGGAAGGTTCTAGA 59.687 50.000 0.00 0.00 41.52 2.43
2404 5282 3.102204 CCGGTTAGGGAAGGTTCTAGAA 58.898 50.000 0.00 0.00 35.97 2.10
2405 5283 3.118847 CCGGTTAGGGAAGGTTCTAGAAC 60.119 52.174 24.73 24.73 37.16 3.01
2406 5284 3.512724 CGGTTAGGGAAGGTTCTAGAACA 59.487 47.826 31.30 11.05 42.85 3.18
2411 5289 3.562343 GGAAGGTTCTAGAACATCCCC 57.438 52.381 30.97 25.41 42.85 4.81
2412 5290 2.844348 GGAAGGTTCTAGAACATCCCCA 59.156 50.000 30.97 1.22 42.85 4.96
2414 5292 4.263771 GGAAGGTTCTAGAACATCCCCAAA 60.264 45.833 30.97 0.00 42.85 3.28
2415 5293 5.510430 GAAGGTTCTAGAACATCCCCAAAT 58.490 41.667 31.30 12.19 42.85 2.32
2416 5294 5.117406 AGGTTCTAGAACATCCCCAAATC 57.883 43.478 31.30 13.69 42.85 2.17
2417 5295 3.877508 GGTTCTAGAACATCCCCAAATCG 59.122 47.826 31.30 0.00 42.85 3.34
2418 5296 4.383770 GGTTCTAGAACATCCCCAAATCGA 60.384 45.833 31.30 0.00 42.85 3.59
2420 5298 5.630415 TCTAGAACATCCCCAAATCGATT 57.370 39.130 4.39 4.39 0.00 3.34
2421 5299 6.001449 TCTAGAACATCCCCAAATCGATTT 57.999 37.500 17.60 17.60 0.00 2.17
2424 5302 5.965922 AGAACATCCCCAAATCGATTTTTC 58.034 37.500 20.56 17.92 0.00 2.29
2428 5306 6.768483 ACATCCCCAAATCGATTTTTCTTTT 58.232 32.000 20.56 2.37 0.00 2.27
2429 5307 7.223584 ACATCCCCAAATCGATTTTTCTTTTT 58.776 30.769 20.56 1.49 0.00 1.94
2479 5357 9.692749 ATCCTTTCTCTTTTAATTTCGGTTTTC 57.307 29.630 0.00 0.00 0.00 2.29
2480 5358 8.139350 TCCTTTCTCTTTTAATTTCGGTTTTCC 58.861 33.333 0.00 0.00 0.00 3.13
2481 5359 7.384115 CCTTTCTCTTTTAATTTCGGTTTTCCC 59.616 37.037 0.00 0.00 36.42 3.97
2495 6234 9.451002 TTTCGGTTTTCCCTTTTTATTTTTCTT 57.549 25.926 0.00 0.00 36.42 2.52
2496 6235 9.451002 TTCGGTTTTCCCTTTTTATTTTTCTTT 57.549 25.926 0.00 0.00 36.42 2.52
2522 6261 8.940768 TTTCTTTTCTGTGTCCAAATTAAAGG 57.059 30.769 0.00 0.00 0.00 3.11
2524 6263 8.299990 TCTTTTCTGTGTCCAAATTAAAGGAA 57.700 30.769 0.00 0.00 35.29 3.36
2526 6265 9.546428 CTTTTCTGTGTCCAAATTAAAGGAATT 57.454 29.630 0.00 0.00 39.56 2.17
2527 6266 9.898152 TTTTCTGTGTCCAAATTAAAGGAATTT 57.102 25.926 0.00 0.00 46.60 1.82
2528 6267 9.898152 TTTCTGTGTCCAAATTAAAGGAATTTT 57.102 25.926 0.00 0.00 43.83 1.82
2529 6268 9.898152 TTCTGTGTCCAAATTAAAGGAATTTTT 57.102 25.926 0.00 0.00 43.83 1.94
2551 6290 6.676237 TTTTGAAAGCTGGGAACATTTTTC 57.324 33.333 0.00 0.00 41.51 2.29
2552 6291 5.350504 TTGAAAGCTGGGAACATTTTTCA 57.649 34.783 0.00 0.00 44.15 2.69
2553 6292 5.350504 TGAAAGCTGGGAACATTTTTCAA 57.649 34.783 0.00 0.00 43.52 2.69
2554 6293 5.738909 TGAAAGCTGGGAACATTTTTCAAA 58.261 33.333 0.00 0.00 43.52 2.69
2555 6294 6.355747 TGAAAGCTGGGAACATTTTTCAAAT 58.644 32.000 0.00 0.00 43.52 2.32
2556 6295 6.482973 TGAAAGCTGGGAACATTTTTCAAATC 59.517 34.615 0.00 0.00 43.52 2.17
2557 6296 5.549742 AGCTGGGAACATTTTTCAAATCA 57.450 34.783 0.00 0.00 41.51 2.57
2558 6297 5.927819 AGCTGGGAACATTTTTCAAATCAA 58.072 33.333 0.00 0.00 41.51 2.57
2559 6298 6.536447 AGCTGGGAACATTTTTCAAATCAAT 58.464 32.000 0.00 0.00 41.51 2.57
2560 6299 6.428771 AGCTGGGAACATTTTTCAAATCAATG 59.571 34.615 0.00 0.00 41.51 2.82
2561 6300 6.427547 GCTGGGAACATTTTTCAAATCAATGA 59.572 34.615 2.19 0.00 41.51 2.57
2562 6301 7.041235 GCTGGGAACATTTTTCAAATCAATGAA 60.041 33.333 2.19 0.00 41.51 2.57
2563 6302 8.152309 TGGGAACATTTTTCAAATCAATGAAC 57.848 30.769 2.19 0.00 35.54 3.18
2564 6303 7.772292 TGGGAACATTTTTCAAATCAATGAACA 59.228 29.630 2.19 0.00 35.54 3.18
2565 6304 8.785946 GGGAACATTTTTCAAATCAATGAACAT 58.214 29.630 2.19 0.00 38.95 2.71
2592 6331 3.544615 GTCAGTGGACGTTTTTGGC 57.455 52.632 0.00 0.00 33.68 4.52
2593 6332 0.736053 GTCAGTGGACGTTTTTGGCA 59.264 50.000 0.00 0.00 33.68 4.92
2594 6333 1.133407 GTCAGTGGACGTTTTTGGCAA 59.867 47.619 0.00 0.00 33.68 4.52
2595 6334 1.133407 TCAGTGGACGTTTTTGGCAAC 59.867 47.619 0.00 0.00 0.00 4.17
2596 6335 1.134175 CAGTGGACGTTTTTGGCAACT 59.866 47.619 0.00 0.00 37.61 3.16
2597 6336 1.404035 AGTGGACGTTTTTGGCAACTC 59.596 47.619 0.00 0.00 37.61 3.01
2598 6337 1.133407 GTGGACGTTTTTGGCAACTCA 59.867 47.619 0.00 0.00 37.61 3.41
2599 6338 1.819288 TGGACGTTTTTGGCAACTCAA 59.181 42.857 0.00 0.00 37.61 3.02
2600 6339 2.231478 TGGACGTTTTTGGCAACTCAAA 59.769 40.909 0.00 0.00 35.15 2.69
2601 6340 3.254892 GGACGTTTTTGGCAACTCAAAA 58.745 40.909 0.00 0.00 42.63 2.44
2602 6341 3.868661 GGACGTTTTTGGCAACTCAAAAT 59.131 39.130 0.00 0.00 43.42 1.82
2603 6342 4.331443 GGACGTTTTTGGCAACTCAAAATT 59.669 37.500 0.00 0.00 43.42 1.82
2604 6343 5.163804 GGACGTTTTTGGCAACTCAAAATTT 60.164 36.000 0.00 0.00 43.42 1.82
2605 6344 5.626211 ACGTTTTTGGCAACTCAAAATTTG 58.374 33.333 0.00 0.00 43.42 2.32
2606 6345 5.180304 ACGTTTTTGGCAACTCAAAATTTGT 59.820 32.000 0.00 0.00 43.42 2.83
2607 6346 6.082984 CGTTTTTGGCAACTCAAAATTTGTT 58.917 32.000 0.00 0.00 43.42 2.83
2608 6347 6.248210 CGTTTTTGGCAACTCAAAATTTGTTC 59.752 34.615 0.00 0.00 43.42 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 1.911357 ACCAGAGAATCATGCTCACCA 59.089 47.619 0.00 0.00 37.82 4.17
84 85 2.093288 TCACCAGAGAATCATGCTCACC 60.093 50.000 0.00 0.00 37.82 4.02
129 138 1.978455 AACCACTGCGTGAAGACCCA 61.978 55.000 9.75 0.00 35.23 4.51
135 144 2.254546 ATTCAGAACCACTGCGTGAA 57.745 45.000 9.75 0.00 45.38 3.18
136 145 2.254546 AATTCAGAACCACTGCGTGA 57.745 45.000 9.75 0.00 45.38 4.35
140 149 4.082733 GGTTAGGAAATTCAGAACCACTGC 60.083 45.833 17.94 0.00 45.38 4.40
315 1258 6.768483 TCTTTGTGTACTGGATTTGATCTCA 58.232 36.000 0.00 0.00 0.00 3.27
389 1343 2.554272 GCTGGGTGCAAACGTACG 59.446 61.111 15.01 15.01 42.31 3.67
394 1348 3.558099 GAAGGCGCTGGGTGCAAAC 62.558 63.158 7.64 0.00 41.25 2.93
399 1353 2.892425 GATCGAAGGCGCTGGGTG 60.892 66.667 7.64 0.00 37.46 4.61
400 1354 4.514577 CGATCGAAGGCGCTGGGT 62.515 66.667 10.26 0.00 37.46 4.51
408 1370 2.333225 CTCTCGGCCGATCGAAGG 59.667 66.667 31.19 16.35 38.77 3.46
469 1431 2.281484 GTCTTCCAGCACGGCCAA 60.281 61.111 2.24 0.00 33.14 4.52
609 1571 2.072298 GGCTTCCGATGATGCTGATAC 58.928 52.381 0.00 0.00 40.52 2.24
634 1596 3.181489 CGGTACTCGAAGAAGCCAAGTAT 60.181 47.826 0.00 0.00 42.43 2.12
708 1670 0.942410 GTACAAGGTCGAAGCGCACA 60.942 55.000 11.47 0.00 0.00 4.57
742 1704 1.513373 GCACGCTGTCATCGTCGTA 60.513 57.895 0.00 0.00 38.19 3.43
828 1793 2.909006 ACACACAATGACCTCTCTCCAT 59.091 45.455 0.00 0.00 0.00 3.41
890 1855 1.196012 CCACTCCCTCTGTAACTCCC 58.804 60.000 0.00 0.00 0.00 4.30
970 2244 1.749258 CCACCTTAAAGGGGCTCGC 60.749 63.158 0.00 0.00 37.50 5.03
1029 2315 1.024579 AAACACGGGCGATGGATGAC 61.025 55.000 0.00 0.00 0.00 3.06
1033 2319 1.658994 GAATAAACACGGGCGATGGA 58.341 50.000 0.00 0.00 0.00 3.41
1075 2361 6.003950 GTGAAGCCTCTATAGAGATGAGACT 58.996 44.000 28.04 13.30 44.74 3.24
1138 2424 3.261981 AGGCCAGTAAAGGACATTACG 57.738 47.619 5.01 0.00 40.05 3.18
1277 2568 1.211709 GCAATACCAACGGCACCAC 59.788 57.895 0.00 0.00 0.00 4.16
1281 2572 2.032834 ACGGCAATACCAACGGCA 59.967 55.556 0.00 0.00 39.03 5.69
1382 2673 5.009210 GGGATGTTAATAAGGTTGCGCAATA 59.991 40.000 27.79 15.32 0.00 1.90
1389 2680 5.057149 CGAGGAGGGATGTTAATAAGGTTG 58.943 45.833 0.00 0.00 0.00 3.77
1617 2911 9.850628 CACAAACTCATGATCACTTTATCATTT 57.149 29.630 0.00 0.00 42.63 2.32
1756 3083 0.109827 CCACATGATGCGCGACAAAA 60.110 50.000 12.10 0.44 0.00 2.44
1801 3129 7.970061 GCATATGCATTCAGTAAGTTTCTTCAA 59.030 33.333 22.84 0.00 41.59 2.69
1837 3167 7.953158 GCATCTTGCTACATTAGAACATAGA 57.047 36.000 0.00 0.00 40.96 1.98
1873 3204 2.161855 CTGCCTTGGCATTAACACTGA 58.838 47.619 15.21 0.00 0.00 3.41
1874 3205 1.203052 CCTGCCTTGGCATTAACACTG 59.797 52.381 15.21 0.74 0.00 3.66
1878 3209 0.457443 GCTCCTGCCTTGGCATTAAC 59.543 55.000 15.21 2.30 0.00 2.01
1890 3221 0.548510 AATCCTACTTGGGCTCCTGC 59.451 55.000 0.00 0.00 36.20 4.85
1891 3222 1.839994 TGAATCCTACTTGGGCTCCTG 59.160 52.381 0.00 0.00 36.20 3.86
1893 3224 1.475930 GCTGAATCCTACTTGGGCTCC 60.476 57.143 0.00 0.00 36.20 4.70
1894 3225 1.475930 GGCTGAATCCTACTTGGGCTC 60.476 57.143 0.00 0.00 36.20 4.70
1895 3226 0.548510 GGCTGAATCCTACTTGGGCT 59.451 55.000 0.00 0.00 36.20 5.19
1896 3227 0.548510 AGGCTGAATCCTACTTGGGC 59.451 55.000 0.00 0.00 33.95 5.36
1897 3228 3.433740 GGTAAGGCTGAATCCTACTTGGG 60.434 52.174 0.00 0.00 34.82 4.12
1898 3229 3.456277 AGGTAAGGCTGAATCCTACTTGG 59.544 47.826 0.00 0.00 34.82 3.61
1899 3230 4.446371 CAGGTAAGGCTGAATCCTACTTG 58.554 47.826 0.00 0.00 34.82 3.16
1900 3231 3.456277 CCAGGTAAGGCTGAATCCTACTT 59.544 47.826 0.00 0.00 34.82 2.24
1902 3233 2.104963 CCCAGGTAAGGCTGAATCCTAC 59.895 54.545 0.00 0.00 34.82 3.18
1903 3234 2.408565 CCCAGGTAAGGCTGAATCCTA 58.591 52.381 0.00 0.00 34.82 2.94
1904 3235 1.216990 CCCAGGTAAGGCTGAATCCT 58.783 55.000 0.00 0.00 38.31 3.24
1906 3237 0.466372 GCCCCAGGTAAGGCTGAATC 60.466 60.000 0.00 0.00 46.14 2.52
1907 3238 1.615262 GCCCCAGGTAAGGCTGAAT 59.385 57.895 0.00 0.00 46.14 2.57
1908 3239 3.087065 GCCCCAGGTAAGGCTGAA 58.913 61.111 0.00 0.00 46.14 3.02
1913 3244 4.489771 CAGGCGCCCCAGGTAAGG 62.490 72.222 26.15 0.00 0.00 2.69
1930 3261 4.173924 GAGAGGGGAGCAGCCAGC 62.174 72.222 0.00 0.00 46.19 4.85
1931 3262 3.478274 GGAGAGGGGAGCAGCCAG 61.478 72.222 0.00 0.00 38.95 4.85
1935 3266 4.421554 TGGGGGAGAGGGGAGCAG 62.422 72.222 0.00 0.00 0.00 4.24
1936 3267 4.741239 GTGGGGGAGAGGGGAGCA 62.741 72.222 0.00 0.00 0.00 4.26
1938 3269 1.679969 ATAGGTGGGGGAGAGGGGAG 61.680 65.000 0.00 0.00 0.00 4.30
1939 3270 0.331137 TATAGGTGGGGGAGAGGGGA 60.331 60.000 0.00 0.00 0.00 4.81
1940 3271 0.800239 ATATAGGTGGGGGAGAGGGG 59.200 60.000 0.00 0.00 0.00 4.79
1941 3272 5.102609 ACATATATATAGGTGGGGGAGAGGG 60.103 48.000 9.17 0.00 0.00 4.30
1942 3273 6.044411 ACATATATATAGGTGGGGGAGAGG 57.956 45.833 9.17 0.00 0.00 3.69
1943 3274 7.075138 TCCTACATATATATAGGTGGGGGAGAG 59.925 44.444 28.83 14.04 43.22 3.20
1944 3275 6.924058 TCCTACATATATATAGGTGGGGGAGA 59.076 42.308 28.83 14.40 43.22 3.71
1945 3276 7.175635 TCCTACATATATATAGGTGGGGGAG 57.824 44.000 28.83 15.14 43.22 4.30
1946 3277 6.105740 CCTCCTACATATATATAGGTGGGGGA 59.894 46.154 30.68 23.85 45.49 4.81
1947 3278 6.323737 CCTCCTACATATATATAGGTGGGGG 58.676 48.000 28.83 27.07 43.25 5.40
1950 3281 6.323737 CCCCCTCCTACATATATATAGGTGG 58.676 48.000 23.21 23.21 45.76 4.61
1971 3302 2.100197 GACAAAACTATGAAGGCCCCC 58.900 52.381 0.00 0.00 0.00 5.40
1972 3303 2.100197 GGACAAAACTATGAAGGCCCC 58.900 52.381 0.00 0.00 0.00 5.80
1973 3304 2.100197 GGGACAAAACTATGAAGGCCC 58.900 52.381 0.00 0.00 0.00 5.80
1974 3305 3.017442 GAGGGACAAAACTATGAAGGCC 58.983 50.000 0.00 0.00 0.00 5.19
1975 3306 2.678336 CGAGGGACAAAACTATGAAGGC 59.322 50.000 0.00 0.00 0.00 4.35
1976 3307 3.270877 CCGAGGGACAAAACTATGAAGG 58.729 50.000 0.00 0.00 0.00 3.46
1979 3310 2.901192 TGACCGAGGGACAAAACTATGA 59.099 45.455 0.00 0.00 0.00 2.15
1982 3313 5.687166 AATATGACCGAGGGACAAAACTA 57.313 39.130 0.00 0.00 30.61 2.24
1988 3319 2.498481 ACGAAAATATGACCGAGGGACA 59.502 45.455 0.00 0.00 0.00 4.02
2002 3333 3.241067 TCGCCTAAGCACTACGAAAAT 57.759 42.857 0.00 0.00 39.83 1.82
2065 4915 1.517257 GATGAGTCCCGTCAGCACG 60.517 63.158 0.00 0.00 46.29 5.34
2092 4942 0.391661 TTGATCCAGCAAGACGAGCC 60.392 55.000 0.00 0.00 0.00 4.70
2129 4979 1.125021 GTTCATCACACGTTCAGCTCG 59.875 52.381 0.00 0.00 0.00 5.03
2144 5021 0.821517 TACATCACCTCCGCGTTCAT 59.178 50.000 4.92 0.00 0.00 2.57
2168 5045 2.159156 CGATCCAACCGATCAAGTACCA 60.159 50.000 0.00 0.00 46.85 3.25
2197 5074 2.669364 ACACGGTTGATGTAGTCGAAC 58.331 47.619 0.00 0.00 0.00 3.95
2215 5092 4.681025 CGTAAGCGGAAGTGTTTAGTAACA 59.319 41.667 0.00 0.00 41.82 2.41
2273 5151 3.801307 TCCATGGAGATGCATAGCAAT 57.199 42.857 11.44 0.00 43.62 3.56
2299 5177 3.341857 AAAATTCTACGCACACGCAAA 57.658 38.095 0.00 0.00 45.53 3.68
2334 5212 3.496331 ACCTAGTGTTGGGAAACATTGG 58.504 45.455 0.00 1.42 34.86 3.16
2354 5232 3.460478 TTGGGTTGGGCCAAGGGAC 62.460 63.158 21.62 8.58 39.65 4.46
2355 5233 3.113477 TTGGGTTGGGCCAAGGGA 61.113 61.111 21.62 2.74 39.65 4.20
2357 5235 2.201210 ACTTGGGTTGGGCCAAGG 59.799 61.111 21.62 10.05 45.19 3.61
2358 5236 2.871253 GCACTTGGGTTGGGCCAAG 61.871 63.158 21.62 10.22 46.02 3.61
2360 5238 3.808218 GAGCACTTGGGTTGGGCCA 62.808 63.158 0.00 0.00 39.65 5.36
2361 5239 2.991540 GAGCACTTGGGTTGGGCC 60.992 66.667 0.00 0.00 0.00 5.80
2362 5240 1.187567 AATGAGCACTTGGGTTGGGC 61.188 55.000 0.00 0.00 0.00 5.36
2363 5241 1.273327 GAAATGAGCACTTGGGTTGGG 59.727 52.381 0.00 0.00 0.00 4.12
2364 5242 1.273327 GGAAATGAGCACTTGGGTTGG 59.727 52.381 0.00 0.00 0.00 3.77
2365 5243 1.068333 CGGAAATGAGCACTTGGGTTG 60.068 52.381 0.00 0.00 0.00 3.77
2366 5244 1.247567 CGGAAATGAGCACTTGGGTT 58.752 50.000 0.00 0.00 0.00 4.11
2367 5245 0.609131 CCGGAAATGAGCACTTGGGT 60.609 55.000 0.00 0.00 0.00 4.51
2369 5247 1.247567 AACCGGAAATGAGCACTTGG 58.752 50.000 9.46 0.00 0.00 3.61
2370 5248 2.420022 CCTAACCGGAAATGAGCACTTG 59.580 50.000 9.46 0.00 33.16 3.16
2371 5249 2.618045 CCCTAACCGGAAATGAGCACTT 60.618 50.000 9.46 0.00 33.16 3.16
2373 5251 1.065709 TCCCTAACCGGAAATGAGCAC 60.066 52.381 9.46 0.00 33.16 4.40
2374 5252 1.281419 TCCCTAACCGGAAATGAGCA 58.719 50.000 9.46 0.00 33.16 4.26
2375 5253 2.289565 CTTCCCTAACCGGAAATGAGC 58.710 52.381 9.46 0.00 41.40 4.26
2376 5254 2.238898 ACCTTCCCTAACCGGAAATGAG 59.761 50.000 9.46 0.00 41.40 2.90
2379 5257 2.917600 AGAACCTTCCCTAACCGGAAAT 59.082 45.455 9.46 0.00 41.40 2.17
2380 5258 2.341695 AGAACCTTCCCTAACCGGAAA 58.658 47.619 9.46 0.00 41.40 3.13
2381 5259 2.034436 AGAACCTTCCCTAACCGGAA 57.966 50.000 9.46 0.00 39.67 4.30
2383 5261 2.743553 TCTAGAACCTTCCCTAACCGG 58.256 52.381 0.00 0.00 0.00 5.28
2385 5263 5.396548 GGATGTTCTAGAACCTTCCCTAACC 60.397 48.000 28.38 16.73 40.46 2.85
2386 5264 5.672503 GGATGTTCTAGAACCTTCCCTAAC 58.327 45.833 28.38 12.99 40.46 2.34
2387 5265 5.952347 GGATGTTCTAGAACCTTCCCTAA 57.048 43.478 28.38 14.03 40.46 2.69
2390 5268 3.562343 GGGATGTTCTAGAACCTTCCC 57.438 52.381 35.10 35.10 46.31 3.97
2391 5269 2.844348 TGGGGATGTTCTAGAACCTTCC 59.156 50.000 29.58 29.58 40.46 3.46
2392 5270 4.569719 TTGGGGATGTTCTAGAACCTTC 57.430 45.455 28.43 23.64 40.46 3.46
2393 5271 5.510430 GATTTGGGGATGTTCTAGAACCTT 58.490 41.667 28.43 18.04 40.46 3.50
2394 5272 4.384208 CGATTTGGGGATGTTCTAGAACCT 60.384 45.833 28.43 20.95 40.46 3.50
2395 5273 3.877508 CGATTTGGGGATGTTCTAGAACC 59.122 47.826 28.43 15.95 40.46 3.62
2396 5274 4.766375 TCGATTTGGGGATGTTCTAGAAC 58.234 43.478 25.73 25.73 41.50 3.01
2397 5275 5.630415 ATCGATTTGGGGATGTTCTAGAA 57.370 39.130 0.00 0.00 0.00 2.10
2398 5276 5.630415 AATCGATTTGGGGATGTTCTAGA 57.370 39.130 4.39 0.00 0.00 2.43
2399 5277 6.699575 AAAATCGATTTGGGGATGTTCTAG 57.300 37.500 23.38 0.00 0.00 2.43
2401 5279 5.716703 AGAAAAATCGATTTGGGGATGTTCT 59.283 36.000 23.38 20.76 0.00 3.01
2403 5281 6.358974 AAGAAAAATCGATTTGGGGATGTT 57.641 33.333 23.38 12.13 0.00 2.71
2404 5282 6.358974 AAAGAAAAATCGATTTGGGGATGT 57.641 33.333 23.38 3.70 0.00 3.06
2405 5283 7.671495 AAAAAGAAAAATCGATTTGGGGATG 57.329 32.000 23.38 0.00 0.00 3.51
2453 5331 9.692749 GAAAACCGAAATTAAAAGAGAAAGGAT 57.307 29.630 0.00 0.00 0.00 3.24
2456 5334 8.141909 AGGGAAAACCGAAATTAAAAGAGAAAG 58.858 33.333 0.00 0.00 46.96 2.62
2457 5335 8.014070 AGGGAAAACCGAAATTAAAAGAGAAA 57.986 30.769 0.00 0.00 46.96 2.52
2458 5336 7.591421 AGGGAAAACCGAAATTAAAAGAGAA 57.409 32.000 0.00 0.00 46.96 2.87
2459 5337 7.591421 AAGGGAAAACCGAAATTAAAAGAGA 57.409 32.000 0.00 0.00 46.96 3.10
2460 5338 8.657074 AAAAGGGAAAACCGAAATTAAAAGAG 57.343 30.769 0.00 0.00 46.96 2.85
2469 5347 9.451002 AAGAAAAATAAAAAGGGAAAACCGAAA 57.549 25.926 0.00 0.00 46.96 3.46
2470 5348 9.451002 AAAGAAAAATAAAAAGGGAAAACCGAA 57.549 25.926 0.00 0.00 46.96 4.30
2496 6235 9.377312 CCTTTAATTTGGACACAGAAAAGAAAA 57.623 29.630 0.00 0.00 0.00 2.29
2498 6237 8.299990 TCCTTTAATTTGGACACAGAAAAGAA 57.700 30.769 0.00 0.00 0.00 2.52
2499 6238 7.889873 TCCTTTAATTTGGACACAGAAAAGA 57.110 32.000 0.00 0.00 0.00 2.52
2501 6240 9.898152 AAATTCCTTTAATTTGGACACAGAAAA 57.102 25.926 0.00 0.00 44.36 2.29
2502 6241 9.898152 AAAATTCCTTTAATTTGGACACAGAAA 57.102 25.926 0.00 0.00 45.12 2.52
2503 6242 9.898152 AAAAATTCCTTTAATTTGGACACAGAA 57.102 25.926 0.00 0.00 45.12 3.02
2527 6266 6.656693 TGAAAAATGTTCCCAGCTTTCAAAAA 59.343 30.769 0.00 0.00 34.60 1.94
2528 6267 6.176183 TGAAAAATGTTCCCAGCTTTCAAAA 58.824 32.000 0.00 0.00 34.60 2.44
2529 6268 5.738909 TGAAAAATGTTCCCAGCTTTCAAA 58.261 33.333 0.00 0.00 34.60 2.69
2530 6269 5.350504 TGAAAAATGTTCCCAGCTTTCAA 57.649 34.783 0.00 0.00 34.60 2.69
2531 6270 5.350504 TTGAAAAATGTTCCCAGCTTTCA 57.649 34.783 0.00 0.00 35.19 2.69
2532 6271 6.482973 TGATTTGAAAAATGTTCCCAGCTTTC 59.517 34.615 0.00 0.00 0.00 2.62
2533 6272 6.355747 TGATTTGAAAAATGTTCCCAGCTTT 58.644 32.000 0.00 0.00 0.00 3.51
2534 6273 5.927819 TGATTTGAAAAATGTTCCCAGCTT 58.072 33.333 0.00 0.00 0.00 3.74
2535 6274 5.549742 TGATTTGAAAAATGTTCCCAGCT 57.450 34.783 0.00 0.00 0.00 4.24
2536 6275 6.427547 TCATTGATTTGAAAAATGTTCCCAGC 59.572 34.615 3.18 0.00 33.84 4.85
2537 6276 7.966246 TCATTGATTTGAAAAATGTTCCCAG 57.034 32.000 3.18 0.00 33.84 4.45
2538 6277 7.772292 TGTTCATTGATTTGAAAAATGTTCCCA 59.228 29.630 3.18 0.00 37.36 4.37
2539 6278 8.152309 TGTTCATTGATTTGAAAAATGTTCCC 57.848 30.769 3.18 0.00 37.36 3.97
2566 6305 5.379732 AAAACGTCCACTGACTTGAAAAA 57.620 34.783 0.00 0.00 39.47 1.94
2567 6306 5.157781 CAAAAACGTCCACTGACTTGAAAA 58.842 37.500 0.00 0.00 39.47 2.29
2568 6307 4.380023 CCAAAAACGTCCACTGACTTGAAA 60.380 41.667 0.00 0.00 39.47 2.69
2569 6308 3.127895 CCAAAAACGTCCACTGACTTGAA 59.872 43.478 0.00 0.00 39.47 2.69
2570 6309 2.680841 CCAAAAACGTCCACTGACTTGA 59.319 45.455 0.00 0.00 39.47 3.02
2571 6310 2.794631 GCCAAAAACGTCCACTGACTTG 60.795 50.000 0.00 0.00 39.47 3.16
2572 6311 1.404035 GCCAAAAACGTCCACTGACTT 59.596 47.619 0.00 0.00 39.47 3.01
2573 6312 1.021968 GCCAAAAACGTCCACTGACT 58.978 50.000 0.00 0.00 39.47 3.41
2574 6313 0.736053 TGCCAAAAACGTCCACTGAC 59.264 50.000 0.00 0.00 38.18 3.51
2575 6314 1.133407 GTTGCCAAAAACGTCCACTGA 59.867 47.619 0.00 0.00 0.00 3.41
2576 6315 1.134175 AGTTGCCAAAAACGTCCACTG 59.866 47.619 0.00 0.00 35.13 3.66
2577 6316 1.404035 GAGTTGCCAAAAACGTCCACT 59.596 47.619 0.00 0.00 35.13 4.00
2578 6317 1.133407 TGAGTTGCCAAAAACGTCCAC 59.867 47.619 0.00 0.00 35.13 4.02
2579 6318 1.464734 TGAGTTGCCAAAAACGTCCA 58.535 45.000 0.00 0.00 35.13 4.02
2580 6319 2.570442 TTGAGTTGCCAAAAACGTCC 57.430 45.000 0.00 0.00 35.13 4.79
2581 6320 5.463499 AATTTTGAGTTGCCAAAAACGTC 57.537 34.783 5.99 0.00 45.54 4.34
2582 6321 5.180304 ACAAATTTTGAGTTGCCAAAAACGT 59.820 32.000 15.81 0.00 45.54 3.99
2583 6322 5.626211 ACAAATTTTGAGTTGCCAAAAACG 58.374 33.333 15.81 0.00 45.54 3.60
2584 6323 7.491254 GAACAAATTTTGAGTTGCCAAAAAC 57.509 32.000 15.81 0.00 45.54 2.43


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

AutoCloner maintained by Alex Coulton.