Multiple sequence alignment - TraesCS2D01G417800

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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 TraesCS2D01G417800 chr2D 100.000 5766 0 0 1 5766 531934778 531929013 0.000000e+00 10648
1 TraesCS2D01G417800 chr2A 91.975 5869 292 84 1 5766 676388168 676382376 0.000000e+00 8063
2 TraesCS2D01G417800 chr2B 94.848 2640 89 21 1987 4593 631725907 631723282 0.000000e+00 4078
3 TraesCS2D01G417800 chr2B 93.301 612 26 7 4599 5205 631723103 631722502 0.000000e+00 889
4 TraesCS2D01G417800 chr2B 83.954 779 66 31 542 1277 631727305 631726543 0.000000e+00 691
5 TraesCS2D01G417800 chr2B 88.304 513 27 9 5255 5766 631722492 631722012 8.330000e-163 584
6 TraesCS2D01G417800 chr2B 86.337 344 38 5 1563 1903 631726242 631725905 3.280000e-97 366
7 TraesCS2D01G417800 chr2B 82.374 278 17 13 60 311 53413286 53413557 4.530000e-51 213
8 TraesCS2D01G417800 chr7A 77.929 367 49 19 1 341 121044447 121044087 3.520000e-47 200
9 TraesCS2D01G417800 chr4B 82.960 223 23 11 77 287 645894784 645894565 2.740000e-43 187
10 TraesCS2D01G417800 chr1A 79.927 274 30 12 74 328 260838044 260837777 1.650000e-40 178
11 TraesCS2D01G417800 chr1A 82.353 204 26 9 132 330 32292777 32292975 9.940000e-38 169
12 TraesCS2D01G417800 chr1A 80.952 231 28 10 129 348 462013192 462012967 9.940000e-38 169
13 TraesCS2D01G417800 chr1A 81.921 177 26 5 159 330 62255970 62256145 1.670000e-30 145
14 TraesCS2D01G417800 chr4A 82.039 206 24 8 138 337 637840784 637840586 4.620000e-36 163
15 TraesCS2D01G417800 chr4A 79.208 202 30 10 135 330 55919934 55920129 4.690000e-26 130
16 TraesCS2D01G417800 chr5B 80.734 218 28 10 73 278 549630420 549630205 2.150000e-34 158
17 TraesCS2D01G417800 chr7B 81.068 206 23 13 136 330 380731245 380731045 3.600000e-32 150
18 TraesCS2D01G417800 chr3B 78.151 238 29 8 25 243 708025546 708025779 4.690000e-26 130
19 TraesCS2D01G417800 chr3D 74.632 272 45 13 68 318 26208658 26208926 1.320000e-16 99


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 TraesCS2D01G417800 chr2D 531929013 531934778 5765 True 10648.0 10648 100.0000 1 5766 1 chr2D.!!$R1 5765
1 TraesCS2D01G417800 chr2A 676382376 676388168 5792 True 8063.0 8063 91.9750 1 5766 1 chr2A.!!$R1 5765
2 TraesCS2D01G417800 chr2B 631722012 631727305 5293 True 1321.6 4078 89.3488 542 5766 5 chr2B.!!$R1 5224

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
524 551 0.030908 CTATGTTCTCGCGAGTCCCC 59.969 60.000 33.33 19.77 0.00 4.81 F
686 722 0.179134 CACGAGGAGGAAGCGTTAGG 60.179 60.000 0.00 0.00 35.90 2.69 F
980 1040 0.182775 AGTGCTTATTTAGGGCGGGG 59.817 55.000 0.00 0.00 0.00 5.73 F
1924 2048 0.113580 TTTTACCTTGGCCCTGTCCC 59.886 55.000 0.00 0.00 0.00 4.46 F
1994 2118 0.835276 TGACTGCAGCAGATATGCCT 59.165 50.000 29.70 4.02 43.18 4.75 F
2275 2436 1.667212 CGTAATCTTTACGGGGTTGCC 59.333 52.381 11.02 0.00 37.29 4.52 F
3656 3819 1.002430 TGACTGGATGTTGTCTGCCTC 59.998 52.381 0.00 0.00 34.57 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1552 0.890542 TGGAGCATGCCGATATTGCC 60.891 55.0 15.66 3.96 37.07 4.52 R
1916 2040 1.584724 AATGGTAGAGTGGGACAGGG 58.415 55.0 0.00 0.00 41.80 4.45 R
1973 2097 1.660167 GCATATCTGCTGCAGTCACA 58.340 50.0 27.24 10.28 45.32 3.58 R
2824 2987 2.424956 CCAGCTCAGGATTTAAAGGCAC 59.575 50.0 0.00 0.00 0.00 5.01 R
2837 3000 2.740981 CAGCAAGTTACTTCCAGCTCAG 59.259 50.0 5.60 0.00 0.00 3.35 R
4237 4404 0.815213 GCCAATGCTGGACTATGCGA 60.815 55.0 0.00 0.00 46.92 5.10 R
5468 5849 0.179936 GTAGCTGCTTGCCTGATCCT 59.820 55.0 7.79 0.00 44.23 3.24 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
40 41 7.337689 TCCATCGAGACTGAATTTGAAATGATT 59.662 33.333 0.00 0.00 0.00 2.57
110 113 8.339720 AGGGACATAATATACAAGGGTGTAAA 57.660 34.615 0.00 0.00 43.41 2.01
120 123 5.784578 ACAAGGGTGTAAATTTTCAGGAC 57.215 39.130 0.00 0.00 35.72 3.85
127 130 7.025365 GGGTGTAAATTTTCAGGACGAAATAC 58.975 38.462 0.00 0.00 43.12 1.89
168 174 4.215399 TCTGTGGCTTTTTAGTACATGCAC 59.785 41.667 0.00 0.00 0.00 4.57
190 196 5.530171 CACTATTCATCCTCAAAGTCCATGG 59.470 44.000 4.97 4.97 0.00 3.66
191 197 4.598036 ATTCATCCTCAAAGTCCATGGT 57.402 40.909 12.58 0.00 0.00 3.55
192 198 4.387026 TTCATCCTCAAAGTCCATGGTT 57.613 40.909 12.58 0.00 0.00 3.67
193 199 3.689347 TCATCCTCAAAGTCCATGGTTG 58.311 45.455 12.58 9.44 0.00 3.77
199 205 4.810491 CCTCAAAGTCCATGGTTGTTTTTG 59.190 41.667 12.58 14.89 0.00 2.44
232 238 8.181487 CTTGCATTTCAAGGTATTTCATCTTG 57.819 34.615 0.00 0.00 46.50 3.02
233 239 7.465353 TGCATTTCAAGGTATTTCATCTTGA 57.535 32.000 0.00 0.00 43.25 3.02
261 267 1.135888 CACACGCACATCACATCCTTG 60.136 52.381 0.00 0.00 0.00 3.61
266 272 4.751600 CACGCACATCACATCCTTGTATAT 59.248 41.667 0.00 0.00 33.76 0.86
267 273 5.237127 CACGCACATCACATCCTTGTATATT 59.763 40.000 0.00 0.00 33.76 1.28
524 551 0.030908 CTATGTTCTCGCGAGTCCCC 59.969 60.000 33.33 19.77 0.00 4.81
533 560 2.802792 CGAGTCCCCGCATCGTTA 59.197 61.111 0.00 0.00 0.00 3.18
534 561 1.299165 CGAGTCCCCGCATCGTTAG 60.299 63.158 0.00 0.00 0.00 2.34
579 606 3.751246 CCCGAGCCGTCGTACCAA 61.751 66.667 0.00 0.00 45.30 3.67
581 608 1.804326 CCGAGCCGTCGTACCAAAG 60.804 63.158 0.00 0.00 45.30 2.77
602 629 3.087906 ACGCCCCTACATCCCACC 61.088 66.667 0.00 0.00 0.00 4.61
621 648 3.842925 GACAGCCGGGTCCAGCAAA 62.843 63.158 1.27 0.00 0.00 3.68
652 679 3.746045 TCCCTGTCAGTGAAACAGTAC 57.254 47.619 10.21 0.00 42.08 2.73
653 680 3.305720 TCCCTGTCAGTGAAACAGTACT 58.694 45.455 10.21 0.00 42.08 2.73
685 721 0.802607 GCACGAGGAGGAAGCGTTAG 60.803 60.000 0.00 0.00 35.90 2.34
686 722 0.179134 CACGAGGAGGAAGCGTTAGG 60.179 60.000 0.00 0.00 35.90 2.69
687 723 1.321074 ACGAGGAGGAAGCGTTAGGG 61.321 60.000 0.00 0.00 34.12 3.53
724 760 3.033873 GTCCGTTCGCTCTTTGTTTTTC 58.966 45.455 0.00 0.00 0.00 2.29
796 840 3.668142 CCCCACCCCCGTCCAAAT 61.668 66.667 0.00 0.00 0.00 2.32
814 859 2.579410 ATCCGGGCAAACCATATACC 57.421 50.000 0.00 0.00 40.22 2.73
819 864 1.328279 GGCAAACCATATACCCCAGC 58.672 55.000 0.00 0.00 35.26 4.85
820 865 1.133482 GGCAAACCATATACCCCAGCT 60.133 52.381 0.00 0.00 35.26 4.24
821 866 2.107552 GGCAAACCATATACCCCAGCTA 59.892 50.000 0.00 0.00 35.26 3.32
822 867 3.146847 GCAAACCATATACCCCAGCTAC 58.853 50.000 0.00 0.00 0.00 3.58
825 870 0.902531 CCATATACCCCAGCTACCCG 59.097 60.000 0.00 0.00 0.00 5.28
939 994 2.429767 CCTCGCCCTCTCATGCTGA 61.430 63.158 0.00 0.00 0.00 4.26
940 995 1.747145 CTCGCCCTCTCATGCTGAT 59.253 57.895 0.00 0.00 0.00 2.90
949 1004 3.344215 CATGCTGATCTCGCGGCC 61.344 66.667 6.13 0.00 39.43 6.13
980 1040 0.182775 AGTGCTTATTTAGGGCGGGG 59.817 55.000 0.00 0.00 0.00 5.73
1163 1235 3.978571 GAGGCCGGGAACAAGGAGC 62.979 68.421 2.18 0.00 0.00 4.70
1237 1309 1.078848 GCAGTTCGATGCCTCCACT 60.079 57.895 0.00 0.00 40.43 4.00
1244 1316 0.882042 CGATGCCTCCACTGGTATGC 60.882 60.000 0.00 0.00 32.59 3.14
1251 1323 0.970427 TCCACTGGTATGCGCAGAGA 60.970 55.000 18.32 0.00 0.00 3.10
1254 1326 0.608130 ACTGGTATGCGCAGAGAACA 59.392 50.000 18.32 11.81 0.00 3.18
1255 1327 1.002366 CTGGTATGCGCAGAGAACAC 58.998 55.000 18.32 6.38 0.00 3.32
1256 1328 0.735978 TGGTATGCGCAGAGAACACG 60.736 55.000 18.32 0.00 0.00 4.49
1279 1351 3.309296 TCCTTCCTTGTCTCTGTCTGTT 58.691 45.455 0.00 0.00 0.00 3.16
1315 1387 6.017357 TGAGCTAATAGATTGCTGAATTGCTG 60.017 38.462 0.00 0.00 37.16 4.41
1322 1394 2.275134 TGCTGAATTGCTGGAGAACA 57.725 45.000 0.00 0.00 0.00 3.18
1380 1452 6.575162 AAGTAAGCAAACAATGAAGGGTAG 57.425 37.500 0.00 0.00 0.00 3.18
1391 1463 6.597562 ACAATGAAGGGTAGACTGTTTTGTA 58.402 36.000 0.00 0.00 0.00 2.41
1396 1468 6.014070 TGAAGGGTAGACTGTTTTGTATGCTA 60.014 38.462 0.00 0.00 0.00 3.49
1427 1506 4.910195 TGCTTGTGTGATGATTAGAAGGT 58.090 39.130 0.00 0.00 0.00 3.50
1428 1507 5.316167 TGCTTGTGTGATGATTAGAAGGTT 58.684 37.500 0.00 0.00 0.00 3.50
1429 1508 5.181811 TGCTTGTGTGATGATTAGAAGGTTG 59.818 40.000 0.00 0.00 0.00 3.77
1448 1527 4.498009 GGTTGGTATCTGGAAATTGATGCG 60.498 45.833 0.00 0.00 0.00 4.73
1487 1566 1.677576 ACACTTGGCAATATCGGCATG 59.322 47.619 0.00 2.01 41.62 4.06
1508 1587 6.420008 GCATGCTCCATCTGAATTAATGTTTC 59.580 38.462 11.37 0.00 0.00 2.78
1554 1633 2.761208 AGCAGCTCGTAGGTATTTCACT 59.239 45.455 0.00 0.00 0.00 3.41
1555 1634 3.195825 AGCAGCTCGTAGGTATTTCACTT 59.804 43.478 0.00 0.00 0.00 3.16
1556 1635 3.933332 GCAGCTCGTAGGTATTTCACTTT 59.067 43.478 0.00 0.00 0.00 2.66
1558 1637 5.446073 GCAGCTCGTAGGTATTTCACTTTTC 60.446 44.000 0.00 0.00 0.00 2.29
1559 1638 4.863131 AGCTCGTAGGTATTTCACTTTTCG 59.137 41.667 0.00 0.00 0.00 3.46
1560 1639 4.624452 GCTCGTAGGTATTTCACTTTTCGT 59.376 41.667 0.00 0.00 0.00 3.85
1568 1689 7.439381 AGGTATTTCACTTTTCGTAGACTTCA 58.561 34.615 0.00 0.00 34.32 3.02
1606 1730 3.196685 ACTCAGTAGGCATGTTCCTTCTC 59.803 47.826 0.00 0.00 37.66 2.87
1619 1743 3.520290 TCCTTCTCGTCGCATGTTATT 57.480 42.857 0.00 0.00 0.00 1.40
1678 1802 5.156355 GTCATTTGATGCCAAACTACTGTG 58.844 41.667 0.00 0.00 44.16 3.66
1696 1820 2.224744 TGTGATGGAGCAGGCAAAACTA 60.225 45.455 0.00 0.00 0.00 2.24
1731 1855 1.651987 AAATACGCATCACTGTCCCG 58.348 50.000 0.00 0.00 0.00 5.14
1916 2040 4.016444 TCATCTGATGGTTTTACCTTGGC 58.984 43.478 17.06 0.00 39.58 4.52
1924 2048 0.113580 TTTTACCTTGGCCCTGTCCC 59.886 55.000 0.00 0.00 0.00 4.46
1931 2055 1.198759 TTGGCCCTGTCCCACTCTAC 61.199 60.000 0.00 0.00 30.65 2.59
1932 2056 2.368011 GGCCCTGTCCCACTCTACC 61.368 68.421 0.00 0.00 0.00 3.18
1934 2058 0.983378 GCCCTGTCCCACTCTACCAT 60.983 60.000 0.00 0.00 0.00 3.55
1935 2059 1.584724 CCCTGTCCCACTCTACCATT 58.415 55.000 0.00 0.00 0.00 3.16
1936 2060 2.759355 CCCTGTCCCACTCTACCATTA 58.241 52.381 0.00 0.00 0.00 1.90
1937 2061 2.700897 CCCTGTCCCACTCTACCATTAG 59.299 54.545 0.00 0.00 0.00 1.73
1938 2062 2.103263 CCTGTCCCACTCTACCATTAGC 59.897 54.545 0.00 0.00 0.00 3.09
1939 2063 2.766263 CTGTCCCACTCTACCATTAGCA 59.234 50.000 0.00 0.00 0.00 3.49
1940 2064 2.766263 TGTCCCACTCTACCATTAGCAG 59.234 50.000 0.00 0.00 0.00 4.24
1941 2065 2.766828 GTCCCACTCTACCATTAGCAGT 59.233 50.000 0.00 0.00 0.00 4.40
1942 2066 3.958798 GTCCCACTCTACCATTAGCAGTA 59.041 47.826 0.00 0.00 0.00 2.74
1943 2067 4.038162 GTCCCACTCTACCATTAGCAGTAG 59.962 50.000 0.00 0.00 37.83 2.57
1944 2068 3.961408 CCCACTCTACCATTAGCAGTAGT 59.039 47.826 0.00 0.00 37.73 2.73
1945 2069 5.103813 TCCCACTCTACCATTAGCAGTAGTA 60.104 44.000 0.00 0.00 37.73 1.82
1946 2070 5.241949 CCCACTCTACCATTAGCAGTAGTAG 59.758 48.000 0.00 0.00 37.73 2.57
1947 2071 5.828859 CCACTCTACCATTAGCAGTAGTAGT 59.171 44.000 0.00 0.00 37.73 2.73
1948 2072 6.996879 CCACTCTACCATTAGCAGTAGTAGTA 59.003 42.308 0.00 0.00 37.73 1.82
1949 2073 7.501559 CCACTCTACCATTAGCAGTAGTAGTAA 59.498 40.741 0.00 0.00 37.73 2.24
1950 2074 8.900781 CACTCTACCATTAGCAGTAGTAGTAAA 58.099 37.037 0.00 0.00 37.73 2.01
1951 2075 9.643735 ACTCTACCATTAGCAGTAGTAGTAAAT 57.356 33.333 0.00 0.00 37.73 1.40
1953 2077 9.636789 TCTACCATTAGCAGTAGTAGTAAATCA 57.363 33.333 0.00 0.00 37.73 2.57
1954 2078 9.900710 CTACCATTAGCAGTAGTAGTAAATCAG 57.099 37.037 0.00 0.00 32.90 2.90
1955 2079 8.307582 ACCATTAGCAGTAGTAGTAAATCAGT 57.692 34.615 0.00 0.00 0.00 3.41
1956 2080 8.198109 ACCATTAGCAGTAGTAGTAAATCAGTG 58.802 37.037 0.00 0.00 0.00 3.66
1957 2081 8.414003 CCATTAGCAGTAGTAGTAAATCAGTGA 58.586 37.037 0.00 0.00 0.00 3.41
1958 2082 9.239002 CATTAGCAGTAGTAGTAAATCAGTGAC 57.761 37.037 0.00 0.00 0.00 3.67
1959 2083 8.577048 TTAGCAGTAGTAGTAAATCAGTGACT 57.423 34.615 0.00 0.00 0.00 3.41
1967 2091 5.730296 AGTAAATCAGTGACTGCAGTAGT 57.270 39.130 21.73 8.49 44.02 2.73
1973 2097 5.984695 TCAGTGACTGCAGTAGTAAATCT 57.015 39.130 21.73 7.59 40.53 2.40
1976 2100 5.347093 CAGTGACTGCAGTAGTAAATCTGTG 59.653 44.000 21.73 3.61 40.53 3.66
1991 2115 3.175109 TCTGTGACTGCAGCAGATATG 57.825 47.619 29.70 13.79 34.72 1.78
1993 2117 0.942962 GTGACTGCAGCAGATATGCC 59.057 55.000 29.70 10.34 43.18 4.40
1994 2118 0.835276 TGACTGCAGCAGATATGCCT 59.165 50.000 29.70 4.02 43.18 4.75
2148 2281 4.216687 CGCCAAAGTAACAGGTAAATTCCA 59.783 41.667 0.00 0.00 0.00 3.53
2180 2313 6.320434 TCCCTGTTTTGTATATGTCATCCA 57.680 37.500 0.00 0.00 0.00 3.41
2244 2402 3.600448 ATTTGGTGGCCATGCTAGTAT 57.400 42.857 9.72 0.00 31.53 2.12
2256 2417 5.573282 GCCATGCTAGTATGTGTATAGAACG 59.427 44.000 18.08 1.91 0.00 3.95
2275 2436 1.667212 CGTAATCTTTACGGGGTTGCC 59.333 52.381 11.02 0.00 37.29 4.52
2371 2533 7.698970 TCGGAAACACTTGACAAATTTTCTAAC 59.301 33.333 12.24 0.00 0.00 2.34
2497 2659 4.855715 TGTGAGTACTTCTCCAGTTCTG 57.144 45.455 0.00 0.00 42.12 3.02
2557 2720 3.607775 CGTGCCATGCTTAGATAATGTGC 60.608 47.826 0.00 0.00 0.00 4.57
2730 2893 4.760530 TGCTACAGTGGAAGCTTGATAT 57.239 40.909 2.10 0.00 39.53 1.63
2824 2987 7.254795 CCAAGGGATACTAATTTTAACTGCGAG 60.255 40.741 0.00 0.00 0.00 5.03
2837 3000 2.084546 ACTGCGAGTGCCTTTAAATCC 58.915 47.619 0.00 0.00 41.78 3.01
3159 3322 3.264193 ACACCATTGCTACAGATCTGGAA 59.736 43.478 26.08 13.04 34.19 3.53
3205 3368 2.789409 AAAGTGCCATACTGGAGTCC 57.211 50.000 0.73 0.73 40.96 3.85
3280 3443 7.288810 TGAGGTGAATCTTTTGCACTTAAAT 57.711 32.000 0.00 0.00 33.25 1.40
3511 3674 9.281371 ACTGTTTGGTACTTTACTATCTTTTCC 57.719 33.333 0.00 0.00 0.00 3.13
3531 3694 9.678941 CTTTTCCACTTCTGGTTTTAATTCTAC 57.321 33.333 0.00 0.00 38.90 2.59
3593 3756 4.764050 TCCACTGAAGTTTGGTTGACTA 57.236 40.909 0.00 0.00 34.19 2.59
3656 3819 1.002430 TGACTGGATGTTGTCTGCCTC 59.998 52.381 0.00 0.00 34.57 4.70
3689 3852 7.562135 TCTGGGGTTAATAGTGCTTAGTAAAG 58.438 38.462 0.00 0.00 35.68 1.85
3824 3987 6.374333 CCTAAAGTTGTGTAATGTGTATGCCT 59.626 38.462 0.00 0.00 0.00 4.75
3983 4146 1.341581 GCACCAAGTAGCCCCCATTTA 60.342 52.381 0.00 0.00 0.00 1.40
4136 4303 6.350445 GGAAATATGCACTGTGGAAAATGAGT 60.350 38.462 5.98 0.00 0.00 3.41
4143 4310 5.621422 CACTGTGGAAAATGAGTGTAATCG 58.379 41.667 0.00 0.00 32.74 3.34
4213 4380 3.695606 GCTGCTGACCACCGAGGA 61.696 66.667 0.00 0.00 41.22 3.71
4282 4449 1.149854 GGGTGAACCTGACCCGTTT 59.850 57.895 0.00 0.00 43.87 3.60
4402 4569 1.967066 GAGATCATCTCCCACACCGAT 59.033 52.381 2.84 0.00 37.55 4.18
4451 4618 2.511373 CTGCTATGGTTGGCGCGA 60.511 61.111 12.10 0.00 30.65 5.87
4588 4755 2.432123 GGTGGCTAGCTATGGGCC 59.568 66.667 15.72 14.13 45.45 5.80
4594 4761 0.528470 GCTAGCTATGGGCCTACTCG 59.472 60.000 7.70 0.00 43.05 4.18
4595 4762 0.528470 CTAGCTATGGGCCTACTCGC 59.472 60.000 4.53 0.00 43.05 5.03
4603 4770 3.486285 GGCCTACTCGCCGTATAAC 57.514 57.895 0.00 0.00 39.64 1.89
4605 4772 1.339291 GGCCTACTCGCCGTATAACTT 59.661 52.381 0.00 0.00 39.64 2.66
4794 5140 3.412386 GATTACCAGCTTGTCACCTTGT 58.588 45.455 0.00 0.00 0.00 3.16
4795 5141 4.564821 GGATTACCAGCTTGTCACCTTGTA 60.565 45.833 0.00 0.00 35.97 2.41
4796 5142 2.256117 ACCAGCTTGTCACCTTGTAC 57.744 50.000 0.00 0.00 0.00 2.90
4867 5217 4.331968 CTTGTTTAGGTCCAAGCCATACA 58.668 43.478 0.00 0.00 32.46 2.29
4903 5253 3.998341 TCCTGTGTTGCTACCGATTTAAC 59.002 43.478 0.00 0.00 0.00 2.01
4948 5316 8.715190 TGGTTATTATGTCAGGTATAGTGCTA 57.285 34.615 0.00 0.00 0.00 3.49
5003 5372 9.651718 GCTGTAAGTATCGAATATTTCCAAAAG 57.348 33.333 0.00 0.00 35.30 2.27
5055 5424 4.407365 ACCTATGGACAAACAAAAGAGGG 58.593 43.478 0.00 0.00 0.00 4.30
5103 5474 3.067106 CGTAGGTTGCTTTGTGACATCT 58.933 45.455 0.00 0.00 0.00 2.90
5116 5487 2.481952 GTGACATCTGAGGAACAGCAAC 59.518 50.000 0.00 0.00 45.38 4.17
5161 5532 5.558846 GCAATGGCAAAAACTCAACTGGAG 61.559 45.833 0.00 0.00 44.21 3.86
5162 5533 7.688325 GCAATGGCAAAAACTCAACTGGAGA 62.688 44.000 0.00 0.00 42.52 3.71
5176 5547 7.016153 TCAACTGGAGAATAAATGTACTGGT 57.984 36.000 0.00 0.00 0.00 4.00
5182 5553 5.066505 GGAGAATAAATGTACTGGTTGCTGG 59.933 44.000 0.00 0.00 0.00 4.85
5210 5581 3.251729 ACTCGCACATATCCAATTCATGC 59.748 43.478 0.00 0.00 0.00 4.06
5225 5596 5.999205 ATTCATGCCCAACAAATTACAGA 57.001 34.783 0.00 0.00 0.00 3.41
5226 5597 5.798125 TTCATGCCCAACAAATTACAGAA 57.202 34.783 0.00 0.00 0.00 3.02
5227 5598 5.389859 TCATGCCCAACAAATTACAGAAG 57.610 39.130 0.00 0.00 0.00 2.85
5230 5601 3.161866 GCCCAACAAATTACAGAAGGGA 58.838 45.455 0.00 0.00 37.22 4.20
5232 5603 3.763897 CCCAACAAATTACAGAAGGGAGG 59.236 47.826 0.00 0.00 37.22 4.30
5235 5606 5.316987 CAACAAATTACAGAAGGGAGGTCT 58.683 41.667 0.00 0.00 0.00 3.85
5236 5607 5.167303 ACAAATTACAGAAGGGAGGTCTC 57.833 43.478 0.00 0.00 0.00 3.36
5237 5608 4.846940 ACAAATTACAGAAGGGAGGTCTCT 59.153 41.667 0.00 0.00 0.00 3.10
5238 5609 5.181748 CAAATTACAGAAGGGAGGTCTCTG 58.818 45.833 0.00 0.00 34.85 3.35
5239 5610 1.853963 TACAGAAGGGAGGTCTCTGC 58.146 55.000 0.00 0.00 32.16 4.26
5240 5611 0.116143 ACAGAAGGGAGGTCTCTGCT 59.884 55.000 0.00 0.00 32.16 4.24
5241 5612 1.359474 ACAGAAGGGAGGTCTCTGCTA 59.641 52.381 0.00 0.00 32.16 3.49
5242 5613 2.225394 ACAGAAGGGAGGTCTCTGCTAA 60.225 50.000 0.00 0.00 32.16 3.09
5268 5639 5.049828 AGCAAGCAACAACAAAGTAAATCC 58.950 37.500 0.00 0.00 0.00 3.01
5274 5645 5.458779 GCAACAACAAAGTAAATCCACTGAC 59.541 40.000 0.00 0.00 0.00 3.51
5320 5697 7.615365 TGATACAGAATTAAGCCAAATCCAAGT 59.385 33.333 0.00 0.00 0.00 3.16
5337 5714 1.981256 AGTTGTGCCAAGGAAACGAT 58.019 45.000 0.00 0.00 0.00 3.73
5468 5849 9.868277 AGATCAAAACAAACAAAACATACAGAA 57.132 25.926 0.00 0.00 0.00 3.02
5476 5857 6.824305 AACAAAACATACAGAAGGATCAGG 57.176 37.500 0.00 0.00 0.00 3.86
5478 5859 4.574674 AAACATACAGAAGGATCAGGCA 57.425 40.909 0.00 0.00 0.00 4.75
5480 5861 4.148128 ACATACAGAAGGATCAGGCAAG 57.852 45.455 0.00 0.00 0.00 4.01
5489 5870 1.297664 GATCAGGCAAGCAGCTACTG 58.702 55.000 13.05 13.05 44.79 2.74
5504 5885 4.220821 CAGCTACTGATACGGGTAATGGAT 59.779 45.833 0.00 0.00 32.44 3.41
5751 6138 2.813200 GGCTGGTAGTAGTCGGCC 59.187 66.667 7.34 7.34 46.54 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.314648 TCATTTCAAATTCAGTCTCGATGGAG 59.685 38.462 0.00 0.00 41.89 3.86
81 84 7.571357 ACACCCTTGTATATTATGTCCCTAAGT 59.429 37.037 0.00 0.00 32.60 2.24
96 99 6.150474 CGTCCTGAAAATTTACACCCTTGTAT 59.850 38.462 0.00 0.00 38.05 2.29
102 105 5.441709 TTTCGTCCTGAAAATTTACACCC 57.558 39.130 0.00 0.00 43.46 4.61
139 142 7.341445 TGTACTAAAAAGCCACAGATGTTTT 57.659 32.000 0.00 0.00 0.00 2.43
143 146 5.106197 TGCATGTACTAAAAAGCCACAGATG 60.106 40.000 0.00 0.00 0.00 2.90
145 148 4.215399 GTGCATGTACTAAAAAGCCACAGA 59.785 41.667 6.69 0.00 0.00 3.41
146 149 4.216257 AGTGCATGTACTAAAAAGCCACAG 59.784 41.667 15.40 0.00 0.00 3.66
147 150 4.141287 AGTGCATGTACTAAAAAGCCACA 58.859 39.130 15.40 0.00 0.00 4.17
148 151 4.766404 AGTGCATGTACTAAAAAGCCAC 57.234 40.909 15.40 0.00 0.00 5.01
149 152 6.657117 TGAATAGTGCATGTACTAAAAAGCCA 59.343 34.615 24.69 13.98 36.78 4.75
150 153 7.083875 TGAATAGTGCATGTACTAAAAAGCC 57.916 36.000 24.69 12.05 36.78 4.35
162 168 5.008415 GGACTTTGAGGATGAATAGTGCATG 59.992 44.000 0.00 0.00 0.00 4.06
168 174 5.688807 ACCATGGACTTTGAGGATGAATAG 58.311 41.667 21.47 0.00 0.00 1.73
190 196 3.372869 CAAGCTGTGCACAAAAACAAC 57.627 42.857 21.98 4.54 0.00 3.32
229 235 5.685068 TGATGTGCGTGTGTAAAATTTCAAG 59.315 36.000 0.00 0.00 0.00 3.02
230 236 5.457148 GTGATGTGCGTGTGTAAAATTTCAA 59.543 36.000 0.00 0.00 0.00 2.69
231 237 4.973051 GTGATGTGCGTGTGTAAAATTTCA 59.027 37.500 0.00 0.00 0.00 2.69
232 238 4.973051 TGTGATGTGCGTGTGTAAAATTTC 59.027 37.500 0.00 0.00 0.00 2.17
233 239 4.926244 TGTGATGTGCGTGTGTAAAATTT 58.074 34.783 0.00 0.00 0.00 1.82
234 240 4.560136 TGTGATGTGCGTGTGTAAAATT 57.440 36.364 0.00 0.00 0.00 1.82
235 241 4.379394 GGATGTGATGTGCGTGTGTAAAAT 60.379 41.667 0.00 0.00 0.00 1.82
236 242 3.058570 GGATGTGATGTGCGTGTGTAAAA 60.059 43.478 0.00 0.00 0.00 1.52
237 243 2.482336 GGATGTGATGTGCGTGTGTAAA 59.518 45.455 0.00 0.00 0.00 2.01
238 244 2.073056 GGATGTGATGTGCGTGTGTAA 58.927 47.619 0.00 0.00 0.00 2.41
239 245 1.275010 AGGATGTGATGTGCGTGTGTA 59.725 47.619 0.00 0.00 0.00 2.90
240 246 0.035317 AGGATGTGATGTGCGTGTGT 59.965 50.000 0.00 0.00 0.00 3.72
241 247 1.135888 CAAGGATGTGATGTGCGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
242 248 1.159285 CAAGGATGTGATGTGCGTGT 58.841 50.000 0.00 0.00 0.00 4.49
243 249 1.159285 ACAAGGATGTGATGTGCGTG 58.841 50.000 0.00 0.00 38.69 5.34
244 250 2.760634 TACAAGGATGTGATGTGCGT 57.239 45.000 0.00 0.00 40.84 5.24
245 251 5.929697 AATATACAAGGATGTGATGTGCG 57.070 39.130 0.00 0.00 40.84 5.34
246 252 7.031226 ACAAATATACAAGGATGTGATGTGC 57.969 36.000 0.00 0.00 40.84 4.57
340 362 2.876550 GTTTGACTGAGTAGGGCGTTTT 59.123 45.455 0.00 0.00 0.00 2.43
547 574 4.410400 GGGCTCCGGGGAGTTGTG 62.410 72.222 4.80 0.00 43.70 3.33
579 606 4.096003 ATGTAGGGGCGTGCGCTT 62.096 61.111 16.21 5.36 41.60 4.68
632 659 3.069586 CAGTACTGTTTCACTGACAGGGA 59.930 47.826 15.06 2.37 46.77 4.20
685 721 2.437895 GGGAAGTAAGCCACGCCC 60.438 66.667 0.00 0.00 38.79 6.13
686 722 2.818274 CGGGAAGTAAGCCACGCC 60.818 66.667 0.00 0.00 0.00 5.68
687 723 2.047560 ACGGGAAGTAAGCCACGC 60.048 61.111 0.00 0.00 0.00 5.34
796 840 0.475044 GGGTATATGGTTTGCCCGGA 59.525 55.000 0.73 0.00 35.15 5.14
949 1004 1.899437 TAAGCACTCTCAAGCCCCCG 61.899 60.000 0.00 0.00 0.00 5.73
961 1016 0.182775 CCCCGCCCTAAATAAGCACT 59.817 55.000 0.00 0.00 0.00 4.40
1237 1309 0.735978 CGTGTTCTCTGCGCATACCA 60.736 55.000 12.24 0.35 0.00 3.25
1244 1316 0.784778 GAAGGAACGTGTTCTCTGCG 59.215 55.000 12.10 0.00 39.45 5.18
1251 1323 2.434702 AGAGACAAGGAAGGAACGTGTT 59.565 45.455 0.00 0.00 30.85 3.32
1254 1326 2.036089 GACAGAGACAAGGAAGGAACGT 59.964 50.000 0.00 0.00 0.00 3.99
1255 1327 2.297597 AGACAGAGACAAGGAAGGAACG 59.702 50.000 0.00 0.00 0.00 3.95
1256 1328 3.070302 ACAGACAGAGACAAGGAAGGAAC 59.930 47.826 0.00 0.00 0.00 3.62
1294 1366 6.709397 TCTCCAGCAATTCAGCAATCTATTAG 59.291 38.462 0.00 0.00 36.85 1.73
1315 1387 8.388484 ACAATCAAGCTCATATAATGTTCTCC 57.612 34.615 0.00 0.00 0.00 3.71
1380 1452 4.389077 AGCGTTCTAGCATACAAAACAGTC 59.611 41.667 0.00 0.00 40.15 3.51
1391 1463 2.095567 CACAAGCAAAGCGTTCTAGCAT 60.096 45.455 0.00 0.00 40.15 3.79
1396 1468 1.378531 TCACACAAGCAAAGCGTTCT 58.621 45.000 0.00 0.00 0.00 3.01
1427 1506 3.631686 CCGCATCAATTTCCAGATACCAA 59.368 43.478 0.00 0.00 0.00 3.67
1428 1507 3.213506 CCGCATCAATTTCCAGATACCA 58.786 45.455 0.00 0.00 0.00 3.25
1429 1508 2.030805 GCCGCATCAATTTCCAGATACC 60.031 50.000 0.00 0.00 0.00 2.73
1448 1527 2.166664 TGTTTACCAAACCACACAAGCC 59.833 45.455 0.00 0.00 40.67 4.35
1473 1552 0.890542 TGGAGCATGCCGATATTGCC 60.891 55.000 15.66 3.96 37.07 4.52
1487 1566 5.066505 ACGGAAACATTAATTCAGATGGAGC 59.933 40.000 0.00 0.00 0.00 4.70
1550 1629 7.780008 TTCAATTGAAGTCTACGAAAAGTGA 57.220 32.000 16.91 0.00 0.00 3.41
1554 1633 9.284594 CAGTTTTTCAATTGAAGTCTACGAAAA 57.715 29.630 19.64 12.30 35.21 2.29
1555 1634 7.431084 GCAGTTTTTCAATTGAAGTCTACGAAA 59.569 33.333 19.64 12.94 35.21 3.46
1556 1635 6.910433 GCAGTTTTTCAATTGAAGTCTACGAA 59.090 34.615 19.64 7.87 35.21 3.85
1558 1637 5.625311 GGCAGTTTTTCAATTGAAGTCTACG 59.375 40.000 19.64 10.14 35.21 3.51
1559 1638 5.625311 CGGCAGTTTTTCAATTGAAGTCTAC 59.375 40.000 19.64 15.32 35.21 2.59
1560 1639 5.529430 TCGGCAGTTTTTCAATTGAAGTCTA 59.471 36.000 19.64 3.68 35.21 2.59
1568 1689 3.632145 ACTGAGTCGGCAGTTTTTCAATT 59.368 39.130 0.00 0.00 46.42 2.32
1606 1730 3.305897 TCAGCACTAAATAACATGCGACG 59.694 43.478 0.00 0.00 42.98 5.12
1678 1802 4.400567 AGAAATAGTTTTGCCTGCTCCATC 59.599 41.667 0.00 0.00 0.00 3.51
1696 1820 5.647658 TGCGTATTTTCTCATCCACAGAAAT 59.352 36.000 0.00 0.00 39.16 2.17
1731 1855 4.381718 GCGTACAATCCATACCTATCCTCC 60.382 50.000 0.00 0.00 0.00 4.30
1891 2015 6.321181 GCCAAGGTAAAACCATCAGATGATAA 59.679 38.462 12.41 0.00 41.95 1.75
1914 2038 2.368011 GGTAGAGTGGGACAGGGCC 61.368 68.421 0.00 0.00 41.80 5.80
1916 2040 1.584724 AATGGTAGAGTGGGACAGGG 58.415 55.000 0.00 0.00 41.80 4.45
1924 2048 6.945938 ACTACTACTGCTAATGGTAGAGTG 57.054 41.667 11.11 0.82 38.82 3.51
1931 2055 8.414003 TCACTGATTTACTACTACTGCTAATGG 58.586 37.037 0.00 0.00 0.00 3.16
1932 2056 9.239002 GTCACTGATTTACTACTACTGCTAATG 57.761 37.037 0.00 0.00 0.00 1.90
1934 2058 8.459635 CAGTCACTGATTTACTACTACTGCTAA 58.540 37.037 0.00 0.00 32.44 3.09
1935 2059 7.986562 CAGTCACTGATTTACTACTACTGCTA 58.013 38.462 0.00 0.00 32.44 3.49
1936 2060 6.857956 CAGTCACTGATTTACTACTACTGCT 58.142 40.000 0.00 0.00 32.44 4.24
1938 2062 6.621613 TGCAGTCACTGATTTACTACTACTG 58.378 40.000 9.70 0.00 35.94 2.74
1939 2063 6.434652 ACTGCAGTCACTGATTTACTACTACT 59.565 38.462 15.25 0.00 32.44 2.57
1940 2064 6.622549 ACTGCAGTCACTGATTTACTACTAC 58.377 40.000 15.25 0.00 32.44 2.73
1941 2065 6.835819 ACTGCAGTCACTGATTTACTACTA 57.164 37.500 15.25 0.00 32.44 1.82
1942 2066 5.730296 ACTGCAGTCACTGATTTACTACT 57.270 39.130 15.25 0.00 32.44 2.57
1943 2067 6.622549 ACTACTGCAGTCACTGATTTACTAC 58.377 40.000 25.56 0.00 32.44 2.73
1944 2068 6.835819 ACTACTGCAGTCACTGATTTACTA 57.164 37.500 25.56 0.00 32.44 1.82
1945 2069 5.730296 ACTACTGCAGTCACTGATTTACT 57.270 39.130 25.56 0.00 32.44 2.24
1946 2070 7.884816 TTTACTACTGCAGTCACTGATTTAC 57.115 36.000 25.56 0.00 38.80 2.01
1947 2071 8.531982 AGATTTACTACTGCAGTCACTGATTTA 58.468 33.333 25.56 0.59 38.80 1.40
1948 2072 7.332926 CAGATTTACTACTGCAGTCACTGATTT 59.667 37.037 25.56 6.18 38.80 2.17
1949 2073 6.815641 CAGATTTACTACTGCAGTCACTGATT 59.184 38.462 25.56 1.79 38.80 2.57
1950 2074 6.071108 ACAGATTTACTACTGCAGTCACTGAT 60.071 38.462 25.56 13.26 38.80 2.90
1951 2075 5.243954 ACAGATTTACTACTGCAGTCACTGA 59.756 40.000 25.56 8.63 38.80 3.41
1952 2076 5.347093 CACAGATTTACTACTGCAGTCACTG 59.653 44.000 25.56 21.54 38.80 3.66
1953 2077 5.243954 TCACAGATTTACTACTGCAGTCACT 59.756 40.000 25.56 9.36 38.80 3.41
1954 2078 5.346281 GTCACAGATTTACTACTGCAGTCAC 59.654 44.000 25.56 8.01 38.80 3.67
1955 2079 5.243954 AGTCACAGATTTACTACTGCAGTCA 59.756 40.000 25.56 7.17 38.80 3.41
1956 2080 5.574830 CAGTCACAGATTTACTACTGCAGTC 59.425 44.000 25.56 7.02 38.80 3.51
1957 2081 5.473931 CAGTCACAGATTTACTACTGCAGT 58.526 41.667 25.12 25.12 41.62 4.40
1967 2091 3.683365 TCTGCTGCAGTCACAGATTTA 57.317 42.857 27.24 2.95 40.25 1.40
1973 2097 1.660167 GCATATCTGCTGCAGTCACA 58.340 50.000 27.24 10.28 45.32 3.58
1991 2115 8.286097 GCAAATTTAGAAGTATATGAGTGAGGC 58.714 37.037 0.00 0.00 0.00 4.70
2148 2281 8.494433 ACATATACAAAACAGGGATACAGATGT 58.506 33.333 0.00 0.00 39.74 3.06
2244 2402 7.195646 CCCGTAAAGATTACGTTCTATACACA 58.804 38.462 18.06 0.00 39.09 3.72
2256 2417 2.995283 AGGCAACCCCGTAAAGATTAC 58.005 47.619 0.00 0.00 39.21 1.89
2371 2533 5.067153 AGCTGTGTATACTGACTCTAGCTTG 59.933 44.000 4.17 0.00 35.65 4.01
2497 2659 5.072741 TCATCAGAGGCCCAAAATATAAGC 58.927 41.667 0.00 0.00 0.00 3.09
2824 2987 2.424956 CCAGCTCAGGATTTAAAGGCAC 59.575 50.000 0.00 0.00 0.00 5.01
2837 3000 2.740981 CAGCAAGTTACTTCCAGCTCAG 59.259 50.000 5.60 0.00 0.00 3.35
3159 3322 4.080695 TGCCATTGTCATCTAAGCTCTCTT 60.081 41.667 0.00 0.00 36.35 2.85
3205 3368 8.442632 TCTTTATTGCTTCATCTGGTTCATAG 57.557 34.615 0.00 0.00 0.00 2.23
3531 3694 7.951530 ATTGGCACATGAAAAGAACTAAAAG 57.048 32.000 0.00 0.00 39.30 2.27
3630 3793 4.142730 GCAGACAACATCCAGTCAATTCTC 60.143 45.833 0.00 0.00 37.23 2.87
3656 3819 4.336433 CACTATTAACCCCAGAACATGCTG 59.664 45.833 0.00 0.00 35.66 4.41
3689 3852 7.312899 TCTTTTGGAAAAAGTTCAGAACTCAC 58.687 34.615 16.44 8.04 41.91 3.51
3824 3987 8.370266 TGCAAAGAGAAGGGTATTACTAACTA 57.630 34.615 0.00 0.00 0.00 2.24
4136 4303 5.468746 CCTGACAAAAGAAAGGACGATTACA 59.531 40.000 0.00 0.00 30.92 2.41
4143 4310 1.266989 CCGCCTGACAAAAGAAAGGAC 59.733 52.381 0.00 0.00 30.92 3.85
4237 4404 0.815213 GCCAATGCTGGACTATGCGA 60.815 55.000 0.00 0.00 46.92 5.10
4282 4449 1.081242 GTCGTTGAGCGGGTCGTAA 60.081 57.895 2.41 0.00 41.72 3.18
4435 4602 2.179547 CATCGCGCCAACCATAGCA 61.180 57.895 0.00 0.00 0.00 3.49
4451 4618 1.446792 CCTCGCAAGACGCAGACAT 60.447 57.895 0.00 0.00 45.01 3.06
4463 4630 2.742116 GGCCATCCTTACCCTCGCA 61.742 63.158 0.00 0.00 0.00 5.10
4483 4650 4.221422 GCCTGCGCCTCGTCCATA 62.221 66.667 4.18 0.00 0.00 2.74
4531 4698 3.044059 GACTTCCACATGCTGCCGC 62.044 63.158 0.00 0.00 0.00 6.53
4588 4755 5.105834 AGCTAAAGTTATACGGCGAGTAG 57.894 43.478 16.62 3.97 38.94 2.57
4594 4761 3.324117 GCCCTAGCTAAAGTTATACGGC 58.676 50.000 0.00 0.00 35.50 5.68
4595 4762 3.254166 TCGCCCTAGCTAAAGTTATACGG 59.746 47.826 0.00 0.00 36.60 4.02
4596 4763 4.494350 TCGCCCTAGCTAAAGTTATACG 57.506 45.455 0.00 0.00 36.60 3.06
4597 4764 5.120363 GCAATCGCCCTAGCTAAAGTTATAC 59.880 44.000 0.00 0.00 36.60 1.47
4599 4766 4.065789 GCAATCGCCCTAGCTAAAGTTAT 58.934 43.478 0.00 0.00 36.60 1.89
4602 4769 1.209504 TGCAATCGCCCTAGCTAAAGT 59.790 47.619 0.00 0.00 37.32 2.66
4603 4770 1.599542 GTGCAATCGCCCTAGCTAAAG 59.400 52.381 0.00 0.00 37.32 1.85
4605 4772 0.539518 TGTGCAATCGCCCTAGCTAA 59.460 50.000 0.00 0.00 37.32 3.09
4660 5003 8.794553 CGTATTTACAGAGACATATTCCCTACT 58.205 37.037 0.00 0.00 0.00 2.57
4794 5140 4.891168 TCAACCAACAGACAGACAGTAGTA 59.109 41.667 0.00 0.00 0.00 1.82
4795 5141 3.704566 TCAACCAACAGACAGACAGTAGT 59.295 43.478 0.00 0.00 0.00 2.73
4796 5142 4.322080 TCAACCAACAGACAGACAGTAG 57.678 45.455 0.00 0.00 0.00 2.57
4903 5253 6.980051 ACCAAACTAATACGGAAAAGCTAG 57.020 37.500 0.00 0.00 0.00 3.42
4941 5309 6.148976 CCGTGAGCTGTACTATAATAGCACTA 59.851 42.308 0.00 0.00 38.59 2.74
4942 5310 5.048643 CCGTGAGCTGTACTATAATAGCACT 60.049 44.000 0.00 0.00 38.59 4.40
4948 5316 4.873746 ATGCCGTGAGCTGTACTATAAT 57.126 40.909 0.00 0.00 44.23 1.28
5003 5372 4.207019 GGCAAACATAATAAATGCGTGCTC 59.793 41.667 11.14 0.00 37.88 4.26
5055 5424 0.251341 AGGGTGCCAAATGTCAGACC 60.251 55.000 0.00 0.00 0.00 3.85
5161 5532 6.509418 TTCCAGCAACCAGTACATTTATTC 57.491 37.500 0.00 0.00 0.00 1.75
5162 5533 6.909550 TTTCCAGCAACCAGTACATTTATT 57.090 33.333 0.00 0.00 0.00 1.40
5163 5534 8.466798 GTTATTTCCAGCAACCAGTACATTTAT 58.533 33.333 0.00 0.00 0.00 1.40
5164 5535 7.668052 AGTTATTTCCAGCAACCAGTACATTTA 59.332 33.333 0.00 0.00 0.00 1.40
5176 5547 2.499197 TGTGCGAGTTATTTCCAGCAA 58.501 42.857 0.00 0.00 36.32 3.91
5182 5553 7.639039 TGAATTGGATATGTGCGAGTTATTTC 58.361 34.615 0.00 0.00 0.00 2.17
5210 5581 3.763897 CCTCCCTTCTGTAATTTGTTGGG 59.236 47.826 0.00 0.00 34.98 4.12
5225 5596 3.389656 GCTTATTAGCAGAGACCTCCCTT 59.610 47.826 0.00 0.00 46.95 3.95
5226 5597 2.969262 GCTTATTAGCAGAGACCTCCCT 59.031 50.000 0.00 0.00 46.95 4.20
5227 5598 3.394674 GCTTATTAGCAGAGACCTCCC 57.605 52.381 0.00 0.00 46.95 4.30
5239 5610 8.795786 TTACTTTGTTGTTGCTTGCTTATTAG 57.204 30.769 0.00 0.00 0.00 1.73
5240 5611 9.757227 ATTTACTTTGTTGTTGCTTGCTTATTA 57.243 25.926 0.00 0.00 0.00 0.98
5241 5612 8.661352 ATTTACTTTGTTGTTGCTTGCTTATT 57.339 26.923 0.00 0.00 0.00 1.40
5242 5613 7.384932 GGATTTACTTTGTTGTTGCTTGCTTAT 59.615 33.333 0.00 0.00 0.00 1.73
5247 5618 6.019640 CAGTGGATTTACTTTGTTGTTGCTTG 60.020 38.462 0.00 0.00 0.00 4.01
5251 5622 6.692681 CAGTCAGTGGATTTACTTTGTTGTTG 59.307 38.462 0.00 0.00 0.00 3.33
5253 5624 6.377327 CAGTCAGTGGATTTACTTTGTTGT 57.623 37.500 0.00 0.00 0.00 3.32
5268 5639 1.269723 TCGCTCAGTTACCAGTCAGTG 59.730 52.381 0.00 0.00 0.00 3.66
5274 5645 1.066858 ACCATGTCGCTCAGTTACCAG 60.067 52.381 0.00 0.00 0.00 4.00
5337 5714 1.227468 GCTGCTCGCCATCAGATCA 60.227 57.895 0.00 0.00 32.26 2.92
5468 5849 0.179936 GTAGCTGCTTGCCTGATCCT 59.820 55.000 7.79 0.00 44.23 3.24
5476 5857 1.212616 CCGTATCAGTAGCTGCTTGC 58.787 55.000 7.79 1.21 43.29 4.01
5478 5859 1.486211 ACCCGTATCAGTAGCTGCTT 58.514 50.000 7.79 0.00 0.00 3.91
5480 5861 3.318017 CATTACCCGTATCAGTAGCTGC 58.682 50.000 0.00 0.00 0.00 5.25
5489 5870 6.537660 GCATACCTAAATCCATTACCCGTATC 59.462 42.308 0.00 0.00 0.00 2.24
5504 5885 2.433662 TGCCTGCATGCATACCTAAA 57.566 45.000 22.97 0.00 36.04 1.85
5649 6036 3.830192 AACTACTACCCGCCGCCG 61.830 66.667 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.