Multiple sequence alignment - TraesCS2B01G540100

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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 TraesCS2B01G540100 chr2B 100.000 5432 0 0 1 5432 736242757 736248188 0.000000e+00 10032.0
1 TraesCS2B01G540100 chr2B 89.928 278 28 0 5155 5432 239855660 239855937 5.170000e-95 359.0
2 TraesCS2B01G540100 chr2B 89.928 278 28 0 5155 5432 239857043 239857320 5.170000e-95 359.0
3 TraesCS2B01G540100 chr2B 99.398 166 1 0 2126 2291 594834040 594833875 8.840000e-78 302.0
4 TraesCS2B01G540100 chr2B 90.909 187 15 2 4820 5005 239855066 239855251 3.250000e-62 250.0
5 TraesCS2B01G540100 chr2B 90.909 187 14 3 4820 5005 239856450 239856634 1.170000e-61 248.0
6 TraesCS2B01G540100 chr2B 88.525 183 15 3 4820 5002 772614602 772614778 3.290000e-52 217.0
7 TraesCS2B01G540100 chr2B 92.727 55 3 1 5000 5054 475569402 475569349 1.620000e-10 78.7
8 TraesCS2B01G540100 chr2B 94.872 39 2 0 5004 5042 194942083 194942121 1.630000e-05 62.1
9 TraesCS2B01G540100 chr2A 95.460 2445 78 15 2290 4717 737047171 737049599 0.000000e+00 3869.0
10 TraesCS2B01G540100 chr2A 90.836 1735 97 38 433 2128 737045461 737047172 0.000000e+00 2266.0
11 TraesCS2B01G540100 chr2A 97.260 73 2 0 1963 2035 737046969 737047041 2.050000e-24 124.0
12 TraesCS2B01G540100 chr2A 100.000 29 0 0 2036 2064 737047056 737047084 3.000000e-03 54.7
13 TraesCS2B01G540100 chr2D 96.701 1364 34 5 3460 4821 605712385 605713739 0.000000e+00 2259.0
14 TraesCS2B01G540100 chr2D 97.377 1182 17 3 2290 3458 605711078 605712258 0.000000e+00 1999.0
15 TraesCS2B01G540100 chr2D 89.707 1399 82 35 768 2128 605709705 605711079 0.000000e+00 1729.0
16 TraesCS2B01G540100 chr2D 89.634 492 31 16 291 775 605709206 605709684 4.650000e-170 608.0
17 TraesCS2B01G540100 chr2D 79.726 656 83 31 878 1525 646259253 646258640 3.890000e-116 429.0
18 TraesCS2B01G540100 chr2D 79.211 659 93 23 878 1531 646271979 646271360 8.420000e-113 418.0
19 TraesCS2B01G540100 chr2D 86.395 294 23 11 1 291 605708776 605709055 6.840000e-79 305.0
20 TraesCS2B01G540100 chr2D 98.802 167 2 0 2126 2292 425286932 425287098 1.140000e-76 298.0
21 TraesCS2B01G540100 chr2D 98.802 167 2 0 2125 2291 560959483 560959649 1.140000e-76 298.0
22 TraesCS2B01G540100 chr2D 98.630 73 1 0 1963 2035 605710877 605710949 4.420000e-26 130.0
23 TraesCS2B01G540100 chr2D 100.000 28 0 0 5004 5031 636892440 636892413 1.000000e-02 52.8
24 TraesCS2B01G540100 chr3B 91.039 279 25 0 5154 5432 676888767 676888489 1.430000e-100 377.0
25 TraesCS2B01G540100 chr3B 90.449 178 12 2 4825 5002 676889337 676889165 4.230000e-56 230.0
26 TraesCS2B01G540100 chr3B 93.000 100 7 0 5056 5155 675407886 675407787 4.380000e-31 147.0
27 TraesCS2B01G540100 chr5B 90.681 279 26 0 5154 5432 665829703 665829425 6.640000e-99 372.0
28 TraesCS2B01G540100 chr1B 90.323 279 27 0 5154 5432 563447284 563447006 3.090000e-97 366.0
29 TraesCS2B01G540100 chr1B 90.110 182 16 2 4821 5002 531218842 531219021 9.100000e-58 235.0
30 TraesCS2B01G540100 chr1B 90.110 182 14 2 4821 5002 453319871 453320048 3.270000e-57 233.0
31 TraesCS2B01G540100 chr1B 88.710 186 15 5 4823 5002 686409464 686409649 7.080000e-54 222.0
32 TraesCS2B01G540100 chr1B 93.000 100 7 0 5056 5155 478262369 478262468 4.380000e-31 147.0
33 TraesCS2B01G540100 chr4B 89.606 279 26 2 5154 5432 72172440 72172165 8.660000e-93 351.0
34 TraesCS2B01G540100 chr4B 89.170 277 30 0 5154 5430 554312701 554312425 4.030000e-91 346.0
35 TraesCS2B01G540100 chr4B 93.000 100 7 0 5056 5155 416621609 416621510 4.380000e-31 147.0
36 TraesCS2B01G540100 chr4B 90.196 51 5 0 5004 5054 57172022 57171972 3.510000e-07 67.6
37 TraesCS2B01G540100 chr4B 90.196 51 5 0 5004 5054 637419320 637419270 3.510000e-07 67.6
38 TraesCS2B01G540100 chr4A 89.286 280 28 2 5154 5432 698913299 698913577 3.110000e-92 350.0
39 TraesCS2B01G540100 chr6D 87.814 279 34 0 5154 5432 65708359 65708637 1.460000e-85 327.0
40 TraesCS2B01G540100 chr6D 97.661 171 3 1 2125 2295 13557564 13557733 5.320000e-75 292.0
41 TraesCS2B01G540100 chr5A 98.802 167 2 0 2127 2293 115664680 115664846 1.140000e-76 298.0
42 TraesCS2B01G540100 chr3D 97.674 172 4 0 2127 2298 79558541 79558712 4.110000e-76 296.0
43 TraesCS2B01G540100 chr3D 89.888 178 13 3 4826 5002 567908846 567909019 1.970000e-54 224.0
44 TraesCS2B01G540100 chr3D 94.737 95 5 0 5061 5155 593458690 593458596 1.220000e-31 148.0
45 TraesCS2B01G540100 chr7B 96.610 177 5 1 2119 2295 92045851 92046026 5.320000e-75 292.0
46 TraesCS2B01G540100 chr7B 95.000 100 5 0 5056 5155 681598398 681598299 2.030000e-34 158.0
47 TraesCS2B01G540100 chr6A 97.126 174 4 1 2119 2292 24072067 24071895 5.320000e-75 292.0
48 TraesCS2B01G540100 chr6A 94.737 95 5 0 5061 5155 504899683 504899777 1.220000e-31 148.0
49 TraesCS2B01G540100 chr5D 96.988 166 5 0 2126 2291 559372240 559372075 4.140000e-71 279.0
50 TraesCS2B01G540100 chr5D 89.529 191 13 6 4818 5002 370635294 370635483 9.100000e-58 235.0
51 TraesCS2B01G540100 chr6B 95.789 95 4 0 5061 5155 34445977 34446071 2.620000e-33 154.0
52 TraesCS2B01G540100 chr7D 94.737 95 5 0 5061 5155 198028438 198028344 1.220000e-31 148.0
53 TraesCS2B01G540100 chr7D 92.857 98 7 0 5056 5153 18996604 18996507 5.670000e-30 143.0
54 TraesCS2B01G540100 chr7D 89.474 57 5 1 5000 5056 30455745 30455690 2.710000e-08 71.3
55 TraesCS2B01G540100 chr7A 92.157 51 4 0 5004 5054 690067100 690067050 7.550000e-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 TraesCS2B01G540100 chr2B 736242757 736248188 5431 False 10032.000000 10032 100.0000 1 5432 1 chr2B.!!$F2 5431
1 TraesCS2B01G540100 chr2B 239855066 239857320 2254 False 304.000000 359 90.4185 4820 5432 4 chr2B.!!$F4 612
2 TraesCS2B01G540100 chr2A 737045461 737049599 4138 False 1578.425000 3869 95.8890 433 4717 4 chr2A.!!$F1 4284
3 TraesCS2B01G540100 chr2D 605708776 605713739 4963 False 1171.666667 2259 93.0740 1 4821 6 chr2D.!!$F3 4820
4 TraesCS2B01G540100 chr2D 646258640 646259253 613 True 429.000000 429 79.7260 878 1525 1 chr2D.!!$R2 647
5 TraesCS2B01G540100 chr2D 646271360 646271979 619 True 418.000000 418 79.2110 878 1531 1 chr2D.!!$R3 653
6 TraesCS2B01G540100 chr3B 676888489 676889337 848 True 303.500000 377 90.7440 4825 5432 2 chr3B.!!$R2 607

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
328 482 0.034089 AAGCCCATTCTAGTGCCCAC 60.034 55.0 0.00 0.0 0.00 4.61 F
341 495 0.544223 TGCCCACGGTGCTATATTGT 59.456 50.0 1.68 0.0 0.00 2.71 F
2132 2407 0.179081 GGCGGTCATTGTCTACTCCC 60.179 60.0 0.00 0.0 0.00 4.30 F
2141 2416 0.702902 TGTCTACTCCCTCCGTTCCT 59.297 55.0 0.00 0.0 0.00 3.36 F
3714 4132 0.690192 TGACCTTTCGGAAGCATCCA 59.310 50.0 8.98 0.0 46.97 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1838 0.453793 TGGCACGTTGACCAACAAAG 59.546 50.000 12.64 0.00 41.20 2.77 R
2275 2550 1.076677 TCAACTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.00 3.36 R
3383 3674 0.795085 GATAGGCATGATGAGCGCAC 59.205 55.000 11.47 3.13 0.00 5.34 R
4012 4430 1.000607 TCGTTGTAGCTGTCACAGACC 60.001 52.381 9.70 0.00 32.44 3.85 R
4847 5267 0.695462 TATGATGCAGAGGCCAGGGT 60.695 55.000 5.01 0.00 40.13 4.34 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
35 36 0.110486 TCCTTCTTTTCGCTGCCCTT 59.890 50.000 0.00 0.00 0.00 3.95
55 57 4.779733 TCCACCCTCCTCTCCCGC 62.780 72.222 0.00 0.00 0.00 6.13
68 70 1.542915 TCTCCCGCGTATAATGGCTAC 59.457 52.381 4.92 0.00 0.00 3.58
69 71 0.604578 TCCCGCGTATAATGGCTACC 59.395 55.000 4.92 0.00 0.00 3.18
70 72 0.319083 CCCGCGTATAATGGCTACCA 59.681 55.000 4.92 0.00 38.19 3.25
72 74 2.268298 CCGCGTATAATGGCTACCATC 58.732 52.381 4.92 0.00 44.40 3.51
73 75 1.917955 CGCGTATAATGGCTACCATCG 59.082 52.381 0.00 0.60 44.40 3.84
74 76 2.268298 GCGTATAATGGCTACCATCGG 58.732 52.381 0.00 0.00 44.40 4.18
75 77 2.094390 GCGTATAATGGCTACCATCGGA 60.094 50.000 0.00 0.00 44.40 4.55
76 78 3.430374 GCGTATAATGGCTACCATCGGAT 60.430 47.826 0.00 0.00 44.40 4.18
77 79 4.360563 CGTATAATGGCTACCATCGGATC 58.639 47.826 0.00 0.00 44.40 3.36
78 80 4.098044 CGTATAATGGCTACCATCGGATCT 59.902 45.833 0.00 0.00 44.40 2.75
79 81 5.298527 CGTATAATGGCTACCATCGGATCTA 59.701 44.000 0.00 0.00 44.40 1.98
80 82 6.016192 CGTATAATGGCTACCATCGGATCTAT 60.016 42.308 0.00 0.00 44.40 1.98
81 83 4.744795 AATGGCTACCATCGGATCTATC 57.255 45.455 0.00 0.00 44.40 2.08
106 108 0.752658 CTACCCATCATGGCGTCTCA 59.247 55.000 0.00 0.00 35.79 3.27
114 116 2.034878 TCATGGCGTCTCAGCTCTTAT 58.965 47.619 0.00 0.00 37.29 1.73
127 129 3.879295 CAGCTCTTATGTGGTTACCATGG 59.121 47.826 11.19 11.19 35.28 3.66
129 131 3.877508 GCTCTTATGTGGTTACCATGGTC 59.122 47.826 23.76 8.00 35.28 4.02
145 147 1.346722 TGGTCGAAGGAGGGAGAAAAC 59.653 52.381 0.00 0.00 0.00 2.43
146 148 1.346722 GGTCGAAGGAGGGAGAAAACA 59.653 52.381 0.00 0.00 0.00 2.83
147 149 2.613223 GGTCGAAGGAGGGAGAAAACAG 60.613 54.545 0.00 0.00 0.00 3.16
148 150 2.037381 GTCGAAGGAGGGAGAAAACAGT 59.963 50.000 0.00 0.00 0.00 3.55
149 151 2.704065 TCGAAGGAGGGAGAAAACAGTT 59.296 45.455 0.00 0.00 0.00 3.16
150 152 3.899360 TCGAAGGAGGGAGAAAACAGTTA 59.101 43.478 0.00 0.00 0.00 2.24
151 153 4.530946 TCGAAGGAGGGAGAAAACAGTTAT 59.469 41.667 0.00 0.00 0.00 1.89
195 198 6.034898 GCCCAAATTTTAATGTCGATGAAGTG 59.965 38.462 0.00 0.00 0.00 3.16
221 224 3.308530 GAAATTGCCTGAAGTTTCACCG 58.691 45.455 0.00 0.00 32.90 4.94
242 245 3.491267 CGAGAGGTGTCACTTCTGTTTTC 59.509 47.826 21.26 6.76 34.47 2.29
259 263 7.565680 TCTGTTTTCTAGGAGAAGACAACTTT 58.434 34.615 12.12 0.00 45.03 2.66
266 270 9.529823 TTCTAGGAGAAGACAACTTTACTCATA 57.470 33.333 0.00 0.00 36.39 2.15
306 460 8.743099 GCTACAAATTGCGATAAAATAAAGTCC 58.257 33.333 0.00 0.00 0.00 3.85
307 461 7.734538 ACAAATTGCGATAAAATAAAGTCCG 57.265 32.000 0.00 0.00 0.00 4.79
311 465 5.728351 TGCGATAAAATAAAGTCCGGAAG 57.272 39.130 5.23 0.00 0.00 3.46
320 474 1.580059 AAGTCCGGAAGCCCATTCTA 58.420 50.000 5.23 0.00 38.07 2.10
322 476 0.831307 GTCCGGAAGCCCATTCTAGT 59.169 55.000 5.23 0.00 38.07 2.57
328 482 0.034089 AAGCCCATTCTAGTGCCCAC 60.034 55.000 0.00 0.00 0.00 4.61
333 487 1.078426 ATTCTAGTGCCCACGGTGC 60.078 57.895 1.68 0.00 36.20 5.01
341 495 0.544223 TGCCCACGGTGCTATATTGT 59.456 50.000 1.68 0.00 0.00 2.71
348 502 3.309682 CACGGTGCTATATTGTGGTTCTG 59.690 47.826 0.00 0.00 0.00 3.02
359 513 9.793252 CTATATTGTGGTTCTGAAAGGAAATTG 57.207 33.333 0.00 0.00 0.00 2.32
381 535 4.116238 GAGCAAGGCAGTTACTAGCTAAG 58.884 47.826 0.00 0.00 0.00 2.18
391 545 6.310711 GCAGTTACTAGCTAAGAACGATGTTT 59.689 38.462 10.32 0.00 0.00 2.83
395 549 9.351570 GTTACTAGCTAAGAACGATGTTTTACT 57.648 33.333 0.00 0.00 0.00 2.24
402 556 8.391106 GCTAAGAACGATGTTTTACTCATGAAT 58.609 33.333 0.00 0.00 0.00 2.57
445 599 7.872163 TTGCAAATTTCTACACATGAACATC 57.128 32.000 0.00 0.00 0.00 3.06
512 666 4.217497 CGCAGCTCAAAGAAGAAGAAAAG 58.783 43.478 0.00 0.00 0.00 2.27
513 667 4.260948 CGCAGCTCAAAGAAGAAGAAAAGT 60.261 41.667 0.00 0.00 0.00 2.66
589 752 3.312890 TCCTTCTCATCTCCAATCCTCC 58.687 50.000 0.00 0.00 0.00 4.30
733 900 2.348104 CCCATCCTGTCGACGTCCA 61.348 63.158 10.58 1.84 0.00 4.02
750 917 3.383505 CGTCCATGACACCTTCTACCATA 59.616 47.826 0.00 0.00 32.09 2.74
1317 1518 2.184579 GAGGAGTACCGCAGCACC 59.815 66.667 0.00 0.00 41.83 5.01
1613 1838 6.027749 CCAATCTGTTGCGTAAATTAGGAAC 58.972 40.000 0.00 6.12 38.82 3.62
1687 1912 2.963432 ACTTGCAATAATTGGTGCTGC 58.037 42.857 14.14 0.00 41.48 5.25
1733 1963 2.619074 GGACAGTGAAAAGGGGGATCTG 60.619 54.545 0.00 0.00 0.00 2.90
1740 1970 3.291584 GAAAAGGGGGATCTGTGATTCC 58.708 50.000 0.00 0.00 0.00 3.01
1742 1972 2.219216 AGGGGGATCTGTGATTCCAT 57.781 50.000 7.15 0.00 33.43 3.41
1822 2055 9.924650 TTTTTGTAGGATGTCTTAGTTAGTCTC 57.075 33.333 0.00 0.00 0.00 3.36
1855 2092 6.981762 ATAGAGTCATTCAGTTTTCAGCAG 57.018 37.500 0.00 0.00 0.00 4.24
1857 2094 2.555757 AGTCATTCAGTTTTCAGCAGCC 59.444 45.455 0.00 0.00 0.00 4.85
1879 2116 4.574828 CCGGGACACCTTATTTTCAGTATG 59.425 45.833 0.00 0.00 32.82 2.39
1882 2119 5.163652 GGGACACCTTATTTTCAGTATGTGC 60.164 44.000 0.00 0.00 37.40 4.57
1890 2127 7.335422 CCTTATTTTCAGTATGTGCTTCTGTCT 59.665 37.037 0.00 0.00 37.40 3.41
1897 2134 2.533266 TGTGCTTCTGTCTGAACTCC 57.467 50.000 0.00 0.00 0.00 3.85
1898 2135 2.042464 TGTGCTTCTGTCTGAACTCCT 58.958 47.619 0.00 0.00 0.00 3.69
1899 2136 2.435805 TGTGCTTCTGTCTGAACTCCTT 59.564 45.455 0.00 0.00 0.00 3.36
1900 2137 2.805099 GTGCTTCTGTCTGAACTCCTTG 59.195 50.000 0.00 0.00 0.00 3.61
1901 2138 2.435805 TGCTTCTGTCTGAACTCCTTGT 59.564 45.455 0.00 0.00 0.00 3.16
1924 2161 7.390823 TGTATCACTTGCTAAATTCAGTGGTA 58.609 34.615 0.00 0.00 0.00 3.25
1925 2162 6.992063 ATCACTTGCTAAATTCAGTGGTAG 57.008 37.500 0.00 0.00 0.00 3.18
1926 2163 5.865085 TCACTTGCTAAATTCAGTGGTAGT 58.135 37.500 0.00 0.00 0.00 2.73
1927 2164 6.999950 TCACTTGCTAAATTCAGTGGTAGTA 58.000 36.000 0.00 0.00 0.00 1.82
1928 2165 6.872020 TCACTTGCTAAATTCAGTGGTAGTAC 59.128 38.462 0.00 0.00 0.00 2.73
1929 2166 6.092259 CACTTGCTAAATTCAGTGGTAGTACC 59.908 42.308 12.80 12.80 39.22 3.34
1930 2167 4.751060 TGCTAAATTCAGTGGTAGTACCG 58.249 43.478 14.67 0.67 42.58 4.02
1931 2168 4.463539 TGCTAAATTCAGTGGTAGTACCGA 59.536 41.667 14.67 3.19 42.58 4.69
1932 2169 5.128171 TGCTAAATTCAGTGGTAGTACCGAT 59.872 40.000 14.67 2.58 42.58 4.18
1933 2170 6.047231 GCTAAATTCAGTGGTAGTACCGATT 58.953 40.000 14.67 6.81 42.58 3.34
1934 2171 6.018994 GCTAAATTCAGTGGTAGTACCGATTG 60.019 42.308 14.67 11.95 42.58 2.67
1935 2172 5.670792 AATTCAGTGGTAGTACCGATTGA 57.329 39.130 14.67 13.88 42.58 2.57
1936 2173 5.871396 ATTCAGTGGTAGTACCGATTGAT 57.129 39.130 14.67 3.56 42.58 2.57
1937 2174 5.670792 TTCAGTGGTAGTACCGATTGATT 57.329 39.130 14.67 0.00 42.58 2.57
1938 2175 5.670792 TCAGTGGTAGTACCGATTGATTT 57.329 39.130 14.67 0.00 42.58 2.17
1939 2176 6.778834 TCAGTGGTAGTACCGATTGATTTA 57.221 37.500 14.67 0.00 42.58 1.40
1940 2177 6.567050 TCAGTGGTAGTACCGATTGATTTAC 58.433 40.000 14.67 3.93 42.58 2.01
1941 2178 6.379133 TCAGTGGTAGTACCGATTGATTTACT 59.621 38.462 14.67 6.15 42.58 2.24
1942 2179 7.557358 TCAGTGGTAGTACCGATTGATTTACTA 59.443 37.037 14.67 0.00 42.58 1.82
1943 2180 7.646922 CAGTGGTAGTACCGATTGATTTACTAC 59.353 40.741 14.67 13.26 42.58 2.73
1944 2181 7.559170 AGTGGTAGTACCGATTGATTTACTACT 59.441 37.037 14.67 4.78 43.27 2.57
1945 2182 7.646922 GTGGTAGTACCGATTGATTTACTACTG 59.353 40.741 14.67 0.00 43.27 2.74
1946 2183 7.340232 TGGTAGTACCGATTGATTTACTACTGT 59.660 37.037 14.67 0.00 43.27 3.55
1947 2184 8.840321 GGTAGTACCGATTGATTTACTACTGTA 58.160 37.037 2.90 0.00 43.27 2.74
2120 2395 7.015877 AGGAAAATTATATAGTAGTGGCGGTCA 59.984 37.037 0.00 0.00 0.00 4.02
2126 2401 1.267121 AGTAGTGGCGGTCATTGTCT 58.733 50.000 0.00 0.00 0.00 3.41
2127 2402 2.453521 AGTAGTGGCGGTCATTGTCTA 58.546 47.619 0.00 0.00 0.00 2.59
2128 2403 2.165845 AGTAGTGGCGGTCATTGTCTAC 59.834 50.000 1.16 1.16 0.00 2.59
2129 2404 1.267121 AGTGGCGGTCATTGTCTACT 58.733 50.000 0.00 0.00 0.00 2.57
2130 2405 1.204941 AGTGGCGGTCATTGTCTACTC 59.795 52.381 0.00 0.00 0.00 2.59
2131 2406 0.535335 TGGCGGTCATTGTCTACTCC 59.465 55.000 0.00 0.00 0.00 3.85
2132 2407 0.179081 GGCGGTCATTGTCTACTCCC 60.179 60.000 0.00 0.00 0.00 4.30
2133 2408 0.824759 GCGGTCATTGTCTACTCCCT 59.175 55.000 0.00 0.00 0.00 4.20
2134 2409 1.202428 GCGGTCATTGTCTACTCCCTC 60.202 57.143 0.00 0.00 0.00 4.30
2135 2410 1.409427 CGGTCATTGTCTACTCCCTCC 59.591 57.143 0.00 0.00 0.00 4.30
2136 2411 1.409427 GGTCATTGTCTACTCCCTCCG 59.591 57.143 0.00 0.00 0.00 4.63
2137 2412 2.100989 GTCATTGTCTACTCCCTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
2138 2413 2.496470 GTCATTGTCTACTCCCTCCGTT 59.504 50.000 0.00 0.00 0.00 4.44
2139 2414 2.758979 TCATTGTCTACTCCCTCCGTTC 59.241 50.000 0.00 0.00 0.00 3.95
2140 2415 1.553706 TTGTCTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
2141 2416 0.702902 TGTCTACTCCCTCCGTTCCT 59.297 55.000 0.00 0.00 0.00 3.36
2142 2417 1.918262 TGTCTACTCCCTCCGTTCCTA 59.082 52.381 0.00 0.00 0.00 2.94
2143 2418 2.309755 TGTCTACTCCCTCCGTTCCTAA 59.690 50.000 0.00 0.00 0.00 2.69
2144 2419 3.245371 TGTCTACTCCCTCCGTTCCTAAA 60.245 47.826 0.00 0.00 0.00 1.85
2145 2420 3.959449 GTCTACTCCCTCCGTTCCTAAAT 59.041 47.826 0.00 0.00 0.00 1.40
2146 2421 5.136105 GTCTACTCCCTCCGTTCCTAAATA 58.864 45.833 0.00 0.00 0.00 1.40
2147 2422 5.774184 GTCTACTCCCTCCGTTCCTAAATAT 59.226 44.000 0.00 0.00 0.00 1.28
2148 2423 6.267242 GTCTACTCCCTCCGTTCCTAAATATT 59.733 42.308 0.00 0.00 0.00 1.28
2149 2424 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2150 2425 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2151 2426 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2152 2427 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2153 2428 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2154 2429 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2155 2430 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2156 2431 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2157 2432 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2172 2447 9.971922 ATTTGTCTTTTTAGAGAGTTCAAATGG 57.028 29.630 0.00 0.00 32.96 3.16
2173 2448 8.746052 TTGTCTTTTTAGAGAGTTCAAATGGA 57.254 30.769 0.00 0.00 0.00 3.41
2174 2449 8.154649 TGTCTTTTTAGAGAGTTCAAATGGAC 57.845 34.615 0.00 0.00 0.00 4.02
2175 2450 7.993183 TGTCTTTTTAGAGAGTTCAAATGGACT 59.007 33.333 0.00 0.00 0.00 3.85
2176 2451 9.490379 GTCTTTTTAGAGAGTTCAAATGGACTA 57.510 33.333 0.00 0.00 0.00 2.59
2177 2452 9.490379 TCTTTTTAGAGAGTTCAAATGGACTAC 57.510 33.333 0.00 0.00 0.00 2.73
2178 2453 8.617290 TTTTTAGAGAGTTCAAATGGACTACC 57.383 34.615 0.00 0.00 0.00 3.18
2191 2466 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2192 2467 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2193 2468 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2194 2469 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2195 2470 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2196 2471 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
2197 2472 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
2198 2473 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2199 2474 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
2200 2475 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2202 2477 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2231 2506 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2232 2507 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2233 2508 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2234 2509 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2235 2510 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2236 2511 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2237 2512 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2238 2513 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2239 2514 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2240 2515 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2241 2516 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2242 2517 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2243 2518 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2244 2519 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2245 2520 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2246 2521 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2247 2522 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2248 2523 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2249 2524 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2250 2525 4.460034 TGCTCCGTATGTAGTCACTTGTTA 59.540 41.667 0.00 0.00 0.00 2.41
2251 2526 5.047872 TGCTCCGTATGTAGTCACTTGTTAA 60.048 40.000 0.00 0.00 0.00 2.01
2252 2527 5.865552 GCTCCGTATGTAGTCACTTGTTAAA 59.134 40.000 0.00 0.00 0.00 1.52
2253 2528 6.366877 GCTCCGTATGTAGTCACTTGTTAAAA 59.633 38.462 0.00 0.00 0.00 1.52
2254 2529 7.064253 GCTCCGTATGTAGTCACTTGTTAAAAT 59.936 37.037 0.00 0.00 0.00 1.82
2255 2530 8.470040 TCCGTATGTAGTCACTTGTTAAAATC 57.530 34.615 0.00 0.00 0.00 2.17
2256 2531 8.308931 TCCGTATGTAGTCACTTGTTAAAATCT 58.691 33.333 0.00 0.00 0.00 2.40
2257 2532 8.592998 CCGTATGTAGTCACTTGTTAAAATCTC 58.407 37.037 0.00 0.00 0.00 2.75
2258 2533 9.355215 CGTATGTAGTCACTTGTTAAAATCTCT 57.645 33.333 0.00 0.00 0.00 3.10
2282 2557 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2283 2558 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2284 2559 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2285 2560 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2286 2561 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2287 2562 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2288 2563 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2307 2582 1.831736 AGTAGTTGATAAGCTGGCGGT 59.168 47.619 0.00 0.00 0.00 5.68
2432 2719 2.688446 CGTCTGATTGGTAGCAGGTCTA 59.312 50.000 9.75 0.00 38.33 2.59
2571 2859 7.723616 TCTGATATTTGTTTGTCTTTTCCAGGA 59.276 33.333 0.00 0.00 0.00 3.86
2827 3115 5.371526 AGGTATCATCCGTCTTCGTAGTTA 58.628 41.667 0.00 0.00 35.01 2.24
2828 3116 5.238214 AGGTATCATCCGTCTTCGTAGTTAC 59.762 44.000 0.00 0.00 35.01 2.50
3589 4005 6.648879 TTGATCAAACAGTAAAAGGGGAAG 57.351 37.500 5.45 0.00 0.00 3.46
3596 4012 3.077359 CAGTAAAAGGGGAAGTGCAGAG 58.923 50.000 0.00 0.00 0.00 3.35
3604 4020 2.338500 GGGAAGTGCAGAGTACGAAAG 58.662 52.381 0.00 0.00 0.00 2.62
3659 4076 6.645415 ACTGTTGTCAATTAGTAAACTCCTCG 59.355 38.462 4.23 0.00 0.00 4.63
3712 4130 2.814336 AGTTTGACCTTTCGGAAGCATC 59.186 45.455 0.00 0.00 0.00 3.91
3714 4132 0.690192 TGACCTTTCGGAAGCATCCA 59.310 50.000 8.98 0.00 46.97 3.41
3716 4134 1.740025 GACCTTTCGGAAGCATCCAAG 59.260 52.381 8.98 5.02 46.97 3.61
3757 4175 7.011382 TCCTATTCTCTTAGGGTATCTTCACC 58.989 42.308 0.00 0.00 39.45 4.02
3985 4403 4.435970 CCTAACCCCGGCCCAACC 62.436 72.222 0.00 0.00 0.00 3.77
4042 4460 4.382320 TACAACGAGTGCCCCGCC 62.382 66.667 0.00 0.00 0.00 6.13
4215 4633 3.877508 GCGGTAATAGCTCAGACCATTTT 59.122 43.478 10.50 0.00 31.89 1.82
4287 4705 5.540719 AGCAAGTTGACTAAGAGTCTTAGGT 59.459 40.000 33.15 22.58 45.27 3.08
4288 4706 6.720288 AGCAAGTTGACTAAGAGTCTTAGGTA 59.280 38.462 33.15 22.59 45.27 3.08
4289 4707 6.807720 GCAAGTTGACTAAGAGTCTTAGGTAC 59.192 42.308 33.15 26.77 45.27 3.34
4311 4729 9.668497 GGTACTATCTGATTCTAACTGGTTTTT 57.332 33.333 0.00 0.00 0.00 1.94
4776 5194 1.279558 TGCCCGCTGGTCAATTACTTA 59.720 47.619 0.00 0.00 0.00 2.24
4777 5195 1.940613 GCCCGCTGGTCAATTACTTAG 59.059 52.381 0.00 0.00 0.00 2.18
4802 5220 6.091305 GCTTTGAATTTTATTGCCTCTGGAAC 59.909 38.462 0.00 0.00 0.00 3.62
4817 5236 0.038892 GGAACGTTCGTGTGGAGCTA 60.039 55.000 21.34 0.00 0.00 3.32
4821 5240 3.795623 ACGTTCGTGTGGAGCTATTAT 57.204 42.857 0.00 0.00 0.00 1.28
4822 5241 3.444916 ACGTTCGTGTGGAGCTATTATG 58.555 45.455 0.00 0.00 0.00 1.90
4823 5242 3.129813 ACGTTCGTGTGGAGCTATTATGA 59.870 43.478 0.00 0.00 0.00 2.15
4851 5271 1.353022 TGAAAATGGAGGCGTAACCCT 59.647 47.619 0.00 0.00 40.58 4.34
4897 5317 8.689061 TGCATGCAGTCATCTTATTAAAAGATT 58.311 29.630 18.46 0.00 34.96 2.40
4970 6773 7.266617 CGAAACTAGAAAAAGAAAACAATGCG 58.733 34.615 0.00 0.00 0.00 4.73
4985 6788 3.186047 GCGGACGATCACAACCGG 61.186 66.667 0.00 0.00 44.61 5.28
5019 6941 3.537795 AGGTAGTGAGTAAGGACCACA 57.462 47.619 0.00 0.00 32.33 4.17
5054 6976 3.632604 CGGTAGCTCTAAAGATGACCTGA 59.367 47.826 0.00 0.00 0.00 3.86
5059 7046 7.870445 GGTAGCTCTAAAGATGACCTGAATAAG 59.130 40.741 0.00 0.00 0.00 1.73
5061 7048 7.725251 AGCTCTAAAGATGACCTGAATAAGAG 58.275 38.462 0.00 0.00 0.00 2.85
5078 7065 3.867055 AGAGCGCACATATTTCAATCG 57.133 42.857 11.47 0.00 0.00 3.34
5084 7071 4.846137 GCGCACATATTTCAATCGGAATAC 59.154 41.667 0.30 0.00 34.91 1.89
5085 7072 5.559991 GCGCACATATTTCAATCGGAATACA 60.560 40.000 0.30 0.00 34.91 2.29
5111 7098 2.743183 GCAGTAGTATGCTCAACCCCAG 60.743 54.545 0.00 0.00 43.07 4.45
5147 7134 5.007234 CCAAACAACGACTCAATGTCAACTA 59.993 40.000 0.00 0.00 45.60 2.24
5159 7222 8.105829 ACTCAATGTCAACTAGAGGATTTCATT 58.894 33.333 0.00 0.00 0.00 2.57
5170 7233 9.775854 ACTAGAGGATTTCATTATGATCACAAG 57.224 33.333 0.00 0.00 0.00 3.16
5227 7290 5.063204 TGATTAAGTTGTCCTTGGTGAGTG 58.937 41.667 0.00 0.00 34.46 3.51
5237 7300 3.118038 TCCTTGGTGAGTGTTACTTGCTT 60.118 43.478 0.00 0.00 0.00 3.91
5306 7369 4.227512 TCCAAATATGCAATGATCGTGC 57.772 40.909 12.96 12.96 42.55 5.34
5317 7380 2.045438 ATCGTGCGATTGGGCCAA 60.045 55.556 23.33 23.33 0.00 4.52
5356 7419 9.124807 CCAAATAGAAGGATTTGAACGTAAAAC 57.875 33.333 9.82 0.00 45.70 2.43
5362 7425 3.057104 GGATTTGAACGTAAAACCCCCAG 60.057 47.826 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.934459 CGGGAGAGGAGGGTGGAGTA 61.934 65.000 0.00 0.00 0.00 2.59
55 57 3.861276 TCCGATGGTAGCCATTATACG 57.139 47.619 1.88 1.68 45.26 3.06
56 58 5.599999 AGATCCGATGGTAGCCATTATAC 57.400 43.478 1.88 0.00 45.26 1.47
73 75 9.959585 CCATGATGGGTAGCAATGGATAGATCC 62.960 48.148 2.79 1.24 39.65 3.36
74 76 5.426689 TGATGGGTAGCAATGGATAGATC 57.573 43.478 0.00 0.00 0.00 2.75
75 77 5.339778 CCATGATGGGTAGCAATGGATAGAT 60.340 44.000 2.79 0.00 32.67 1.98
76 78 4.019051 CCATGATGGGTAGCAATGGATAGA 60.019 45.833 2.79 0.00 32.67 1.98
77 79 4.267536 CCATGATGGGTAGCAATGGATAG 58.732 47.826 2.79 0.00 32.67 2.08
78 80 3.561960 GCCATGATGGGTAGCAATGGATA 60.562 47.826 14.26 0.00 38.19 2.59
79 81 2.820485 GCCATGATGGGTAGCAATGGAT 60.820 50.000 14.26 0.00 38.19 3.41
80 82 1.479205 GCCATGATGGGTAGCAATGGA 60.479 52.381 14.26 0.00 38.19 3.41
81 83 0.963962 GCCATGATGGGTAGCAATGG 59.036 55.000 14.26 9.54 38.19 3.16
106 108 3.523564 ACCATGGTAACCACATAAGAGCT 59.476 43.478 18.10 0.00 35.80 4.09
114 116 1.002659 CCTTCGACCATGGTAACCACA 59.997 52.381 19.80 0.00 35.80 4.17
127 129 2.037381 ACTGTTTTCTCCCTCCTTCGAC 59.963 50.000 0.00 0.00 0.00 4.20
129 131 2.841442 ACTGTTTTCTCCCTCCTTCG 57.159 50.000 0.00 0.00 0.00 3.79
157 160 8.980481 TTAAAATTTGGGCCAAAATTGTTCTA 57.020 26.923 33.40 17.85 39.20 2.10
167 170 4.873746 TCGACATTAAAATTTGGGCCAA 57.126 36.364 16.66 16.66 0.00 4.52
170 173 6.034898 CACTTCATCGACATTAAAATTTGGGC 59.965 38.462 0.00 0.00 0.00 5.36
195 198 1.168714 ACTTCAGGCAATTTCCTCGC 58.831 50.000 0.00 0.00 33.25 5.03
221 224 4.698575 AGAAAACAGAAGTGACACCTCTC 58.301 43.478 3.62 0.00 0.00 3.20
235 238 7.793927 AAAGTTGTCTTCTCCTAGAAAACAG 57.206 36.000 8.83 0.00 42.41 3.16
237 240 8.890124 AGTAAAGTTGTCTTCTCCTAGAAAAC 57.110 34.615 0.00 0.00 40.97 2.43
272 276 2.228582 TCGCAATTTGTAGCAATGCTGT 59.771 40.909 19.25 0.00 40.10 4.40
275 279 5.947503 TTTATCGCAATTTGTAGCAATGC 57.052 34.783 0.00 0.00 0.00 3.56
281 285 8.943925 CGGACTTTATTTTATCGCAATTTGTAG 58.056 33.333 0.00 0.00 0.00 2.74
282 286 7.911205 CCGGACTTTATTTTATCGCAATTTGTA 59.089 33.333 0.00 0.00 0.00 2.41
287 291 6.687081 TTCCGGACTTTATTTTATCGCAAT 57.313 33.333 1.83 0.00 0.00 3.56
289 293 4.034742 GCTTCCGGACTTTATTTTATCGCA 59.965 41.667 1.83 0.00 0.00 5.10
306 460 0.815615 GGCACTAGAATGGGCTTCCG 60.816 60.000 0.00 0.00 36.45 4.30
307 461 0.466372 GGGCACTAGAATGGGCTTCC 60.466 60.000 0.00 0.00 36.45 3.46
311 465 1.819632 CGTGGGCACTAGAATGGGC 60.820 63.158 0.00 0.00 35.23 5.36
320 474 0.837272 AATATAGCACCGTGGGCACT 59.163 50.000 0.00 0.00 0.00 4.40
322 476 0.544223 ACAATATAGCACCGTGGGCA 59.456 50.000 0.00 0.00 0.00 5.36
328 482 3.792401 TCAGAACCACAATATAGCACCG 58.208 45.455 0.00 0.00 0.00 4.94
333 487 9.793252 CAATTTCCTTTCAGAACCACAATATAG 57.207 33.333 0.00 0.00 0.00 1.31
341 495 4.214310 TGCTCAATTTCCTTTCAGAACCA 58.786 39.130 0.00 0.00 0.00 3.67
343 497 5.225642 CCTTGCTCAATTTCCTTTCAGAAC 58.774 41.667 0.00 0.00 0.00 3.01
348 502 3.006217 ACTGCCTTGCTCAATTTCCTTTC 59.994 43.478 0.00 0.00 0.00 2.62
359 513 2.682155 AGCTAGTAACTGCCTTGCTC 57.318 50.000 0.00 0.00 36.50 4.26
417 571 9.107177 TGTTCATGTGTAGAAATTTGCAAAAAT 57.893 25.926 17.19 7.91 0.00 1.82
418 572 8.484641 TGTTCATGTGTAGAAATTTGCAAAAA 57.515 26.923 17.19 0.00 0.00 1.94
420 574 7.114670 CGATGTTCATGTGTAGAAATTTGCAAA 59.885 33.333 15.44 15.44 0.00 3.68
421 575 6.581919 CGATGTTCATGTGTAGAAATTTGCAA 59.418 34.615 0.00 0.00 0.00 4.08
422 576 6.072783 TCGATGTTCATGTGTAGAAATTTGCA 60.073 34.615 0.00 0.00 0.00 4.08
423 577 6.314018 TCGATGTTCATGTGTAGAAATTTGC 58.686 36.000 0.00 0.00 0.00 3.68
424 578 7.521529 ACTCGATGTTCATGTGTAGAAATTTG 58.478 34.615 0.00 0.00 0.00 2.32
425 579 7.672983 ACTCGATGTTCATGTGTAGAAATTT 57.327 32.000 0.00 0.00 0.00 1.82
426 580 8.656849 GTTACTCGATGTTCATGTGTAGAAATT 58.343 33.333 0.00 0.00 0.00 1.82
427 581 7.277981 GGTTACTCGATGTTCATGTGTAGAAAT 59.722 37.037 0.00 0.00 0.00 2.17
428 582 6.588756 GGTTACTCGATGTTCATGTGTAGAAA 59.411 38.462 0.00 0.00 0.00 2.52
429 583 6.097356 GGTTACTCGATGTTCATGTGTAGAA 58.903 40.000 0.00 0.00 0.00 2.10
430 584 5.393787 GGGTTACTCGATGTTCATGTGTAGA 60.394 44.000 0.00 0.00 0.00 2.59
431 585 4.804139 GGGTTACTCGATGTTCATGTGTAG 59.196 45.833 0.00 0.00 0.00 2.74
445 599 6.803154 AAGAAAAAGAAGATGGGTTACTCG 57.197 37.500 0.00 0.00 0.00 4.18
512 666 6.218019 GGTGGGTTTTAATTTACTTGTGGAC 58.782 40.000 0.00 0.00 0.00 4.02
513 667 5.009811 CGGTGGGTTTTAATTTACTTGTGGA 59.990 40.000 0.00 0.00 0.00 4.02
589 752 1.134401 AGATAAGGTGCCGTGTGGATG 60.134 52.381 0.00 0.00 37.49 3.51
655 818 8.196771 TGTGAAATGGTTCATTATAAATGCTCC 58.803 33.333 0.00 1.68 45.38 4.70
669 836 4.219033 GACGTGTTCATGTGAAATGGTTC 58.781 43.478 0.00 0.00 35.58 3.62
733 900 8.472007 TTTTTGTTTATGGTAGAAGGTGTCAT 57.528 30.769 0.00 0.00 0.00 3.06
790 991 4.560716 CGCTGGACCAATCGGATATTTCTA 60.561 45.833 0.00 0.00 35.59 2.10
791 992 3.744660 GCTGGACCAATCGGATATTTCT 58.255 45.455 0.00 0.00 35.59 2.52
1613 1838 0.453793 TGGCACGTTGACCAACAAAG 59.546 50.000 12.64 0.00 41.20 2.77
1687 1912 2.231478 TCGTTTAGGTGAAGCCTCTCAG 59.769 50.000 0.00 0.00 46.96 3.35
1733 1963 6.942576 ACCTTATATGCCTAACATGGAATCAC 59.057 38.462 0.00 0.00 40.06 3.06
1740 1970 8.535335 ACTATCTGACCTTATATGCCTAACATG 58.465 37.037 0.00 0.00 40.06 3.21
1742 1972 9.596308 TTACTATCTGACCTTATATGCCTAACA 57.404 33.333 0.00 0.00 0.00 2.41
1800 2033 8.770322 ACTAGAGACTAACTAAGACATCCTACA 58.230 37.037 0.00 0.00 0.00 2.74
1845 2082 1.896660 TGTCCCGGCTGCTGAAAAC 60.897 57.895 10.70 5.55 0.00 2.43
1855 2092 1.743394 CTGAAAATAAGGTGTCCCGGC 59.257 52.381 0.00 0.00 35.12 6.13
1857 2094 5.064707 CACATACTGAAAATAAGGTGTCCCG 59.935 44.000 0.00 0.00 35.12 5.14
1879 2116 2.805099 CAAGGAGTTCAGACAGAAGCAC 59.195 50.000 0.00 0.00 36.78 4.40
1882 2119 5.866633 GTGATACAAGGAGTTCAGACAGAAG 59.133 44.000 0.00 0.00 36.78 2.85
1890 2127 4.623932 AGCAAGTGATACAAGGAGTTCA 57.376 40.909 0.00 0.00 0.00 3.18
1897 2134 7.094634 ACCACTGAATTTAGCAAGTGATACAAG 60.095 37.037 3.32 0.00 0.00 3.16
1898 2135 6.714810 ACCACTGAATTTAGCAAGTGATACAA 59.285 34.615 3.32 0.00 0.00 2.41
1899 2136 6.237901 ACCACTGAATTTAGCAAGTGATACA 58.762 36.000 3.32 0.00 0.00 2.29
1900 2137 6.743575 ACCACTGAATTTAGCAAGTGATAC 57.256 37.500 3.32 0.00 0.00 2.24
1901 2138 7.620880 ACTACCACTGAATTTAGCAAGTGATA 58.379 34.615 3.32 0.00 0.00 2.15
1936 2173 8.698210 TCTGAACTTCCAGTTTACAGTAGTAAA 58.302 33.333 0.00 0.00 38.80 2.01
1937 2174 8.241497 TCTGAACTTCCAGTTTACAGTAGTAA 57.759 34.615 0.00 0.00 38.80 2.24
1938 2175 7.504911 ACTCTGAACTTCCAGTTTACAGTAGTA 59.495 37.037 0.00 0.00 38.80 1.82
1939 2176 6.324254 ACTCTGAACTTCCAGTTTACAGTAGT 59.676 38.462 0.00 0.00 38.80 2.73
1940 2177 6.750148 ACTCTGAACTTCCAGTTTACAGTAG 58.250 40.000 0.00 0.00 38.80 2.57
1941 2178 6.726490 ACTCTGAACTTCCAGTTTACAGTA 57.274 37.500 0.00 0.00 38.80 2.74
1942 2179 5.615925 ACTCTGAACTTCCAGTTTACAGT 57.384 39.130 0.00 0.00 38.80 3.55
1943 2180 6.642950 CAGTACTCTGAACTTCCAGTTTACAG 59.357 42.308 0.00 0.00 43.76 2.74
1944 2181 6.322969 TCAGTACTCTGAACTTCCAGTTTACA 59.677 38.462 0.00 0.00 46.17 2.41
1945 2182 6.746120 TCAGTACTCTGAACTTCCAGTTTAC 58.254 40.000 0.00 0.00 46.17 2.01
1946 2183 6.971726 TCAGTACTCTGAACTTCCAGTTTA 57.028 37.500 0.00 0.00 46.17 2.01
1947 2184 5.871396 TCAGTACTCTGAACTTCCAGTTT 57.129 39.130 0.00 0.00 46.17 2.66
2106 2381 2.453521 AGACAATGACCGCCACTACTA 58.546 47.619 0.00 0.00 0.00 1.82
2120 2395 2.108970 GGAACGGAGGGAGTAGACAAT 58.891 52.381 0.00 0.00 0.00 2.71
2126 2401 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2127 2402 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2128 2403 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2129 2404 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2130 2405 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2131 2406 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2146 2421 9.971922 CCATTTGAACTCTCTAAAAAGACAAAT 57.028 29.630 0.00 0.00 35.63 2.32
2147 2422 9.184523 TCCATTTGAACTCTCTAAAAAGACAAA 57.815 29.630 0.00 0.00 32.31 2.83
2148 2423 8.621286 GTCCATTTGAACTCTCTAAAAAGACAA 58.379 33.333 0.00 0.00 0.00 3.18
2149 2424 7.993183 AGTCCATTTGAACTCTCTAAAAAGACA 59.007 33.333 0.00 0.00 0.00 3.41
2150 2425 8.384607 AGTCCATTTGAACTCTCTAAAAAGAC 57.615 34.615 0.00 0.00 0.00 3.01
2151 2426 9.490379 GTAGTCCATTTGAACTCTCTAAAAAGA 57.510 33.333 0.00 0.00 0.00 2.52
2152 2427 8.722394 GGTAGTCCATTTGAACTCTCTAAAAAG 58.278 37.037 0.00 0.00 0.00 2.27
2153 2428 8.215050 TGGTAGTCCATTTGAACTCTCTAAAAA 58.785 33.333 0.00 0.00 39.03 1.94
2154 2429 7.660208 GTGGTAGTCCATTTGAACTCTCTAAAA 59.340 37.037 0.00 0.00 46.20 1.52
2155 2430 7.159372 GTGGTAGTCCATTTGAACTCTCTAAA 58.841 38.462 0.00 0.00 46.20 1.85
2156 2431 6.269077 TGTGGTAGTCCATTTGAACTCTCTAA 59.731 38.462 0.00 0.00 46.20 2.10
2157 2432 5.778241 TGTGGTAGTCCATTTGAACTCTCTA 59.222 40.000 0.00 0.00 46.20 2.43
2158 2433 4.593206 TGTGGTAGTCCATTTGAACTCTCT 59.407 41.667 0.00 0.00 46.20 3.10
2159 2434 4.894784 TGTGGTAGTCCATTTGAACTCTC 58.105 43.478 0.00 0.00 46.20 3.20
2160 2435 4.974645 TGTGGTAGTCCATTTGAACTCT 57.025 40.909 0.00 0.00 46.20 3.24
2161 2436 5.291128 CGTATGTGGTAGTCCATTTGAACTC 59.709 44.000 0.00 0.00 46.20 3.01
2162 2437 5.175859 CGTATGTGGTAGTCCATTTGAACT 58.824 41.667 0.00 0.00 46.20 3.01
2163 2438 4.331717 CCGTATGTGGTAGTCCATTTGAAC 59.668 45.833 0.00 0.00 46.20 3.18
2164 2439 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
2165 2440 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2166 2441 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2167 2442 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2168 2443 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2169 2444 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2170 2445 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2171 2446 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2172 2447 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
2173 2448 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2174 2449 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2176 2451 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2209 2484 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2210 2485 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2211 2486 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2212 2487 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2213 2488 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2214 2489 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2215 2490 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2216 2491 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2217 2492 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2218 2493 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2219 2494 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2220 2495 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2221 2496 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2222 2497 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2223 2498 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2224 2499 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2225 2500 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2226 2501 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2227 2502 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2228 2503 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2229 2504 7.878477 TTTTAACAAGTGACTACATACGGAG 57.122 36.000 0.00 0.00 0.00 4.63
2230 2505 8.308931 AGATTTTAACAAGTGACTACATACGGA 58.691 33.333 0.00 0.00 0.00 4.69
2231 2506 8.475331 AGATTTTAACAAGTGACTACATACGG 57.525 34.615 0.00 0.00 0.00 4.02
2232 2507 9.355215 AGAGATTTTAACAAGTGACTACATACG 57.645 33.333 0.00 0.00 0.00 3.06
2256 2531 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2257 2532 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2258 2533 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2259 2534 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2260 2535 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2261 2536 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2262 2537 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2263 2538 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2264 2539 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2265 2540 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2266 2541 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2267 2542 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2268 2543 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2269 2544 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2270 2545 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2271 2546 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2272 2547 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2273 2548 3.094572 CAACTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
2274 2549 2.309755 TCAACTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 0.00 2.94
2275 2550 1.076677 TCAACTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.00 3.36
2276 2551 1.553706 TCAACTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
2277 2552 4.737055 GCTTATCAACTACTCCCTCCGTTC 60.737 50.000 0.00 0.00 0.00 3.95
2278 2553 3.132467 GCTTATCAACTACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
2279 2554 2.694109 GCTTATCAACTACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
2280 2555 2.959707 AGCTTATCAACTACTCCCTCCG 59.040 50.000 0.00 0.00 0.00 4.63
2281 2556 3.070302 CCAGCTTATCAACTACTCCCTCC 59.930 52.174 0.00 0.00 0.00 4.30
2282 2557 3.493524 GCCAGCTTATCAACTACTCCCTC 60.494 52.174 0.00 0.00 0.00 4.30
2283 2558 2.436173 GCCAGCTTATCAACTACTCCCT 59.564 50.000 0.00 0.00 0.00 4.20
2284 2559 2.803492 CGCCAGCTTATCAACTACTCCC 60.803 54.545 0.00 0.00 0.00 4.30
2285 2560 2.474816 CGCCAGCTTATCAACTACTCC 58.525 52.381 0.00 0.00 0.00 3.85
2286 2561 2.159085 ACCGCCAGCTTATCAACTACTC 60.159 50.000 0.00 0.00 0.00 2.59
2287 2562 1.831736 ACCGCCAGCTTATCAACTACT 59.168 47.619 0.00 0.00 0.00 2.57
2288 2563 2.202566 GACCGCCAGCTTATCAACTAC 58.797 52.381 0.00 0.00 0.00 2.73
2307 2582 5.011533 CCAACAAATAACAGGACAAATGGGA 59.988 40.000 0.00 0.00 0.00 4.37
2432 2719 9.199982 CTACAAATTTCTTGAAATTGCAGATGT 57.800 29.630 18.37 18.51 33.08 3.06
2827 3115 5.298276 TGCACGTTCTTAAAATTCAGAAGGT 59.702 36.000 8.74 8.74 44.86 3.50
2828 3116 5.757886 TGCACGTTCTTAAAATTCAGAAGG 58.242 37.500 7.76 7.76 39.66 3.46
3383 3674 0.795085 GATAGGCATGATGAGCGCAC 59.205 55.000 11.47 3.13 0.00 5.34
3532 3948 6.514376 GCGAAAAGGGTTTAAACATCTTCAGA 60.514 38.462 19.57 0.00 0.00 3.27
3589 4005 4.270325 AGTTGTTTCTTTCGTACTCTGCAC 59.730 41.667 0.00 0.00 0.00 4.57
3596 4012 7.349711 TGCTATTTGAGTTGTTTCTTTCGTAC 58.650 34.615 0.00 0.00 0.00 3.67
3604 4020 7.810658 TCTGAAGATGCTATTTGAGTTGTTTC 58.189 34.615 0.00 0.00 0.00 2.78
3659 4076 4.927425 TCAAAATGCTAGTTACACCTCGTC 59.073 41.667 0.00 0.00 0.00 4.20
3757 4175 1.227823 TGCTGTTCCACAGGTTCCG 60.228 57.895 6.05 0.00 46.01 4.30
3967 4385 3.332385 GTTGGGCCGGGGTTAGGA 61.332 66.667 2.18 0.00 0.00 2.94
4012 4430 1.000607 TCGTTGTAGCTGTCACAGACC 60.001 52.381 9.70 0.00 32.44 3.85
4311 4729 1.702182 TGGCCTGTTCATGAAGCAAA 58.298 45.000 8.80 0.00 0.00 3.68
4507 4925 2.475466 CCATGCTGCGCCTTCGATT 61.475 57.895 4.18 0.00 38.10 3.34
4729 5147 7.596621 ACATAAGCATCATACACGAGAACTATG 59.403 37.037 0.00 0.00 0.00 2.23
4776 5194 5.481473 TCCAGAGGCAATAAAATTCAAAGCT 59.519 36.000 0.00 0.00 0.00 3.74
4777 5195 5.723295 TCCAGAGGCAATAAAATTCAAAGC 58.277 37.500 0.00 0.00 0.00 3.51
4791 5209 1.300620 CACGAACGTTCCAGAGGCA 60.301 57.895 22.07 0.00 0.00 4.75
4802 5220 3.702330 TCATAATAGCTCCACACGAACG 58.298 45.455 0.00 0.00 0.00 3.95
4833 5252 1.615919 CCAGGGTTACGCCTCCATTTT 60.616 52.381 0.00 0.00 37.43 1.82
4847 5267 0.695462 TATGATGCAGAGGCCAGGGT 60.695 55.000 5.01 0.00 40.13 4.34
4851 5271 3.418047 CATCATTATGATGCAGAGGCCA 58.582 45.455 20.33 0.00 46.37 5.36
4970 6773 0.799534 CGTACCGGTTGTGATCGTCC 60.800 60.000 15.04 0.00 0.00 4.79
4985 6788 4.940463 TCACTACCTTCATATTGCCGTAC 58.060 43.478 0.00 0.00 0.00 3.67
4989 6792 5.992217 CCTTACTCACTACCTTCATATTGCC 59.008 44.000 0.00 0.00 0.00 4.52
4995 6798 4.466726 GTGGTCCTTACTCACTACCTTCAT 59.533 45.833 0.00 0.00 0.00 2.57
5002 6805 5.773091 TCCATATGTGGTCCTTACTCACTA 58.227 41.667 8.51 0.00 46.16 2.74
5019 6941 4.357325 AGAGCTACCGATTGGATCCATAT 58.643 43.478 17.06 11.94 39.21 1.78
5031 6953 3.632604 CAGGTCATCTTTAGAGCTACCGA 59.367 47.826 0.00 0.00 41.51 4.69
5054 6976 6.365839 CGATTGAAATATGTGCGCTCTTATT 58.634 36.000 19.15 19.15 0.00 1.40
5059 7046 2.543848 TCCGATTGAAATATGTGCGCTC 59.456 45.455 9.73 5.51 0.00 5.03
5061 7048 3.332761 TTCCGATTGAAATATGTGCGC 57.667 42.857 0.00 0.00 0.00 6.09
5078 7065 2.311124 ACTACTGCGGCTTGTATTCC 57.689 50.000 0.00 0.00 0.00 3.01
5084 7071 1.212616 GAGCATACTACTGCGGCTTG 58.787 55.000 0.00 0.00 46.86 4.01
5085 7072 0.824109 TGAGCATACTACTGCGGCTT 59.176 50.000 0.00 0.00 46.86 4.35
5111 7098 2.723209 GTTGTTTGGAACGTGGTTAGC 58.277 47.619 0.00 0.00 0.00 3.09
5147 7134 9.118300 GTTCTTGTGATCATAATGAAATCCTCT 57.882 33.333 5.26 0.00 0.00 3.69
5159 7222 5.755861 TCACGTTGTTGTTCTTGTGATCATA 59.244 36.000 0.00 0.00 31.93 2.15
5170 7233 1.400494 AGGCAGTTCACGTTGTTGTTC 59.600 47.619 0.00 0.00 0.00 3.18
5227 7290 2.032290 GGTTCGTCCACAAGCAAGTAAC 60.032 50.000 0.00 0.00 35.97 2.50
5284 7347 4.614306 CGCACGATCATTGCATATTTGGAT 60.614 41.667 14.83 0.00 40.20 3.41
5306 7369 6.478673 GGATTTAATTAACTTTGGCCCAATCG 59.521 38.462 0.00 0.00 0.00 3.34
5356 7419 6.867519 ATGGAAATTAACTAAAACTGGGGG 57.132 37.500 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.