Multiple sequence alignment - TraesCS3A01G020000

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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 TraesCS3A01G020000 chr3A 100.000 2515 0 0 1 2515 11897338 11899852 0.000000e+00 4645.0
1 TraesCS3A01G020000 chr3A 99.180 122 1 0 1866 1987 11930991 11931112 1.370000e-53 220.0
2 TraesCS3A01G020000 chr3A 100.000 98 0 0 2844 2941 11900181 11900278 6.470000e-42 182.0
3 TraesCS3A01G020000 chr3D 93.176 1099 48 13 893 1977 9078168 9077083 0.000000e+00 1589.0
4 TraesCS3A01G020000 chr3D 100.000 31 0 0 862 892 559169763 559169733 1.140000e-04 58.4
5 TraesCS3A01G020000 chr3B 93.690 1046 63 2 932 1977 11230899 11229857 0.000000e+00 1563.0
6 TraesCS3A01G020000 chr3B 91.978 1097 79 5 890 1977 11166621 11165525 0.000000e+00 1530.0
7 TraesCS3A01G020000 chr3B 88.446 251 18 5 2265 2515 11229726 11229487 2.870000e-75 292.0
8 TraesCS3A01G020000 chr3B 93.590 78 5 0 2864 2941 11229427 11229350 1.850000e-22 117.0
9 TraesCS3A01G020000 chr2D 91.599 857 63 4 1 849 509952475 509953330 0.000000e+00 1175.0
10 TraesCS3A01G020000 chr2D 90.587 818 69 7 33 844 286455326 286454511 0.000000e+00 1077.0
11 TraesCS3A01G020000 chr2D 86.473 207 26 2 1975 2179 76557616 76557822 2.950000e-55 226.0
12 TraesCS3A01G020000 chr2D 95.000 40 2 0 2186 2225 104868108 104868069 2.450000e-06 63.9
13 TraesCS3A01G020000 chr2D 97.059 34 0 1 860 892 137063844 137063877 4.090000e-04 56.5
14 TraesCS3A01G020000 chr4D 90.170 824 73 7 33 850 462813960 462814781 0.000000e+00 1066.0
15 TraesCS3A01G020000 chr4D 87.179 195 24 1 1989 2182 20141632 20141438 1.370000e-53 220.0
16 TraesCS3A01G020000 chr4D 86.667 195 25 1 1989 2182 20077416 20077222 6.380000e-52 215.0
17 TraesCS3A01G020000 chr4D 98.387 62 1 0 1 62 426646902 426646963 3.100000e-20 110.0
18 TraesCS3A01G020000 chr4D 100.000 31 0 0 862 892 504226955 504226985 1.140000e-04 58.4
19 TraesCS3A01G020000 chr7A 89.202 852 86 5 1 847 59428597 59427747 0.000000e+00 1059.0
20 TraesCS3A01G020000 chr7A 90.196 51 3 2 846 895 156968621 156968572 6.800000e-07 65.8
21 TraesCS3A01G020000 chr7A 94.872 39 1 1 2191 2228 506152594 506152556 3.170000e-05 60.2
22 TraesCS3A01G020000 chr1D 89.964 827 72 8 33 855 77646655 77647474 0.000000e+00 1057.0
23 TraesCS3A01G020000 chr1D 89.390 820 80 6 33 847 60167969 60167152 0.000000e+00 1026.0
24 TraesCS3A01G020000 chr1D 96.774 62 2 0 1 62 423060613 423060552 1.440000e-18 104.0
25 TraesCS3A01G020000 chr1D 93.182 44 1 2 2183 2226 210939957 210939998 2.450000e-06 63.9
26 TraesCS3A01G020000 chr1D 92.500 40 3 0 2186 2225 414298925 414298886 1.140000e-04 58.4
27 TraesCS3A01G020000 chr5A 89.731 818 75 8 33 845 618483073 618483886 0.000000e+00 1037.0
28 TraesCS3A01G020000 chr5A 87.500 192 23 1 1989 2179 544150727 544150918 1.370000e-53 220.0
29 TraesCS3A01G020000 chr5A 92.857 42 2 1 855 895 40813856 40813815 3.170000e-05 60.2
30 TraesCS3A01G020000 chr5A 100.000 31 0 0 862 892 78920069 78920039 1.140000e-04 58.4
31 TraesCS3A01G020000 chr1A 88.575 849 94 3 1 847 539460748 539461595 0.000000e+00 1027.0
32 TraesCS3A01G020000 chr1A 87.986 849 99 3 1 847 539435341 539436188 0.000000e+00 1000.0
33 TraesCS3A01G020000 chr1A 100.000 29 0 0 863 891 398654987 398654959 1.000000e-03 54.7
34 TraesCS3A01G020000 chr5B 88.205 195 22 1 1989 2182 702896900 702896706 6.340000e-57 231.0
35 TraesCS3A01G020000 chr5B 92.308 52 3 1 846 896 484833579 484833528 4.070000e-09 73.1
36 TraesCS3A01G020000 chr2B 88.083 193 21 2 1988 2179 663864241 663864432 8.200000e-56 228.0
37 TraesCS3A01G020000 chr2B 86.802 197 25 1 1989 2184 519387104 519387300 4.940000e-53 219.0
38 TraesCS3A01G020000 chr2B 97.143 35 1 0 862 896 378686801 378686767 3.170000e-05 60.2
39 TraesCS3A01G020000 chr2B 92.500 40 3 0 2186 2225 691415919 691415958 1.140000e-04 58.4
40 TraesCS3A01G020000 chr2B 100.000 28 0 0 2249 2276 250902034 250902007 5.000000e-03 52.8
41 TraesCS3A01G020000 chr7D 87.629 194 19 5 1989 2179 42051495 42051686 1.370000e-53 220.0
42 TraesCS3A01G020000 chr4B 86.735 196 25 1 1989 2183 586574561 586574756 1.770000e-52 217.0
43 TraesCS3A01G020000 chr4B 89.583 48 4 1 848 894 417133583 417133536 3.170000e-05 60.2
44 TraesCS3A01G020000 chr6B 98.387 62 1 0 1 62 686852322 686852261 3.100000e-20 110.0
45 TraesCS3A01G020000 chr5D 96.825 63 1 1 1 62 505952673 505952735 1.440000e-18 104.0
46 TraesCS3A01G020000 chr5D 96.825 63 1 1 1 62 550291452 550291390 1.440000e-18 104.0
47 TraesCS3A01G020000 chr5D 92.857 42 2 1 2186 2227 24619776 24619736 3.170000e-05 60.2
48 TraesCS3A01G020000 chr4A 93.750 48 2 1 848 894 577540028 577540075 1.460000e-08 71.3
49 TraesCS3A01G020000 chr2A 95.122 41 2 0 2186 2226 401915758 401915718 6.800000e-07 65.8
50 TraesCS3A01G020000 chrUn 100.000 31 0 0 862 892 104012901 104012931 1.140000e-04 58.4
51 TraesCS3A01G020000 chr7B 92.683 41 1 2 2186 2226 557711091 557711129 1.140000e-04 58.4
52 TraesCS3A01G020000 chr7B 89.362 47 4 1 847 892 660248949 660248903 1.140000e-04 58.4
53 TraesCS3A01G020000 chr6D 92.500 40 3 0 2186 2225 355275317 355275356 1.140000e-04 58.4


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 TraesCS3A01G020000 chr3A 11897338 11900278 2940 False 2413.500000 4645 100.000000 1 2941 2 chr3A.!!$F2 2940
1 TraesCS3A01G020000 chr3D 9077083 9078168 1085 True 1589.000000 1589 93.176000 893 1977 1 chr3D.!!$R1 1084
2 TraesCS3A01G020000 chr3B 11165525 11166621 1096 True 1530.000000 1530 91.978000 890 1977 1 chr3B.!!$R1 1087
3 TraesCS3A01G020000 chr3B 11229350 11230899 1549 True 657.333333 1563 91.908667 932 2941 3 chr3B.!!$R2 2009
4 TraesCS3A01G020000 chr2D 509952475 509953330 855 False 1175.000000 1175 91.599000 1 849 1 chr2D.!!$F3 848
5 TraesCS3A01G020000 chr2D 286454511 286455326 815 True 1077.000000 1077 90.587000 33 844 1 chr2D.!!$R2 811
6 TraesCS3A01G020000 chr4D 462813960 462814781 821 False 1066.000000 1066 90.170000 33 850 1 chr4D.!!$F2 817
7 TraesCS3A01G020000 chr7A 59427747 59428597 850 True 1059.000000 1059 89.202000 1 847 1 chr7A.!!$R1 846
8 TraesCS3A01G020000 chr1D 77646655 77647474 819 False 1057.000000 1057 89.964000 33 855 1 chr1D.!!$F1 822
9 TraesCS3A01G020000 chr1D 60167152 60167969 817 True 1026.000000 1026 89.390000 33 847 1 chr1D.!!$R1 814
10 TraesCS3A01G020000 chr5A 618483073 618483886 813 False 1037.000000 1037 89.731000 33 845 1 chr5A.!!$F2 812
11 TraesCS3A01G020000 chr1A 539460748 539461595 847 False 1027.000000 1027 88.575000 1 847 1 chr1A.!!$F2 846
12 TraesCS3A01G020000 chr1A 539435341 539436188 847 False 1000.000000 1000 87.986000 1 847 1 chr1A.!!$F1 846

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
44 45 0.036164 TGCTACATGCTTCAACCGGT 59.964 50.0 0.0 0.0 43.37 5.28 F
1061 1093 0.251474 ATGTAGCTCCCGCCGGTATA 60.251 55.0 1.9 0.0 36.60 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1465 0.234884 CGTTGAACTTGAAGACGCCC 59.765 55.0 0.0 0.0 0.00 6.13 R
2127 2194 0.248539 GTAGGCACCTCGTCATCGAC 60.249 60.0 0.0 0.0 41.35 4.20 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
44 45 0.036164 TGCTACATGCTTCAACCGGT 59.964 50.000 0.00 0.00 43.37 5.28
108 111 2.656973 CGGCGTTGTGGTTTTGCC 60.657 61.111 0.00 0.00 42.29 4.52
147 153 6.825944 TTTTGCTACAACTGGCATAATGTA 57.174 33.333 0.00 0.00 38.30 2.29
232 245 3.242543 CGTCGTAGGTATTTGCTACGTCT 60.243 47.826 2.68 0.00 44.42 4.18
312 326 1.027792 ACAACCAGTGAAAACGGCGT 61.028 50.000 6.77 6.77 0.00 5.68
340 354 0.814457 TTTTGCTGCAACCGTGTCTT 59.186 45.000 15.72 0.00 0.00 3.01
361 375 6.636850 GTCTTCATTTTGCTACGACAAACAAT 59.363 34.615 0.00 0.00 39.18 2.71
517 535 3.616721 AAGCGCGGGTGACAGAGT 61.617 61.111 8.83 0.00 0.00 3.24
550 568 1.029408 AGCGCAGATCTCTGACGAGT 61.029 55.000 11.47 9.32 46.59 4.18
557 575 4.056125 CTCTGACGAGTGCGGGCA 62.056 66.667 0.00 0.00 43.17 5.36
661 679 1.598130 GTGGTGCTTCAAGCTCGGT 60.598 57.895 11.57 0.00 42.97 4.69
670 688 3.489229 GCTTCAAGCTCGGTTGTTTTCTT 60.489 43.478 0.71 0.00 38.45 2.52
849 875 3.125607 CGCCTAGTGTCGCCCATA 58.874 61.111 0.00 0.00 0.00 2.74
855 881 3.804036 CCTAGTGTCGCCCATATTGAAA 58.196 45.455 0.00 0.00 0.00 2.69
856 882 4.389374 CCTAGTGTCGCCCATATTGAAAT 58.611 43.478 0.00 0.00 0.00 2.17
857 883 4.214119 CCTAGTGTCGCCCATATTGAAATG 59.786 45.833 0.00 0.00 0.00 2.32
858 884 2.358898 AGTGTCGCCCATATTGAAATGC 59.641 45.455 0.00 0.00 0.00 3.56
859 885 1.680735 TGTCGCCCATATTGAAATGCC 59.319 47.619 0.00 0.00 0.00 4.40
860 886 1.956477 GTCGCCCATATTGAAATGCCT 59.044 47.619 0.00 0.00 0.00 4.75
861 887 3.146066 GTCGCCCATATTGAAATGCCTA 58.854 45.455 0.00 0.00 0.00 3.93
862 888 3.568007 GTCGCCCATATTGAAATGCCTAA 59.432 43.478 0.00 0.00 0.00 2.69
863 889 4.037446 GTCGCCCATATTGAAATGCCTAAA 59.963 41.667 0.00 0.00 0.00 1.85
864 890 4.646945 TCGCCCATATTGAAATGCCTAAAA 59.353 37.500 0.00 0.00 0.00 1.52
865 891 4.984161 CGCCCATATTGAAATGCCTAAAAG 59.016 41.667 0.00 0.00 0.00 2.27
866 892 5.221224 CGCCCATATTGAAATGCCTAAAAGA 60.221 40.000 0.00 0.00 0.00 2.52
867 893 5.985530 GCCCATATTGAAATGCCTAAAAGAC 59.014 40.000 0.00 0.00 0.00 3.01
868 894 6.183360 GCCCATATTGAAATGCCTAAAAGACT 60.183 38.462 0.00 0.00 0.00 3.24
869 895 7.633553 GCCCATATTGAAATGCCTAAAAGACTT 60.634 37.037 0.00 0.00 0.00 3.01
870 896 8.912988 CCCATATTGAAATGCCTAAAAGACTTA 58.087 33.333 0.00 0.00 0.00 2.24
1032 1064 1.656652 GGACAGGGTTGATGTGATCG 58.343 55.000 0.00 0.00 0.00 3.69
1052 1084 5.386958 TCGTGTGAATATATGTAGCTCCC 57.613 43.478 0.00 0.00 0.00 4.30
1061 1093 0.251474 ATGTAGCTCCCGCCGGTATA 60.251 55.000 1.90 0.00 36.60 1.47
1068 1100 2.649034 CCGCCGGTATACATCGCT 59.351 61.111 1.90 0.00 0.00 4.93
1078 1110 5.336213 CCGGTATACATCGCTACAACCTATT 60.336 44.000 5.01 0.00 0.00 1.73
1079 1111 6.127925 CCGGTATACATCGCTACAACCTATTA 60.128 42.308 5.01 0.00 0.00 0.98
1080 1112 6.744537 CGGTATACATCGCTACAACCTATTAC 59.255 42.308 5.01 0.00 0.00 1.89
1269 1306 0.409092 TCCACTACTACCCCAACGGA 59.591 55.000 0.00 0.00 34.64 4.69
1274 1311 1.962100 CTACTACCCCAACGGAGGATC 59.038 57.143 0.00 0.00 34.64 3.36
1548 1585 1.226688 CGTCAGGTGCGACATCGAT 60.227 57.895 5.26 0.00 43.02 3.59
1572 1609 3.807538 GTCACGTCGGCGGCTAGA 61.808 66.667 16.39 4.02 43.45 2.43
1576 1613 3.812019 CGTCGGCGGCTAGAGTGT 61.812 66.667 10.76 0.00 0.00 3.55
1733 1770 3.877126 CGATATCGGGTTGGCGAAGCT 62.877 57.143 17.51 0.00 45.29 3.74
1780 1817 3.697619 AGATGATGATGCATCCGATGT 57.302 42.857 23.67 8.60 44.47 3.06
1789 1826 4.286320 ATCCGATGTCCGCCGCTC 62.286 66.667 0.00 0.00 36.84 5.03
1909 1947 5.957771 ATGGAAACTAGTAGCTCATCCAA 57.042 39.130 14.25 3.48 38.82 3.53
1914 1952 4.333913 ACTAGTAGCTCATCCAATGCAG 57.666 45.455 0.00 0.00 0.00 4.41
1939 1979 8.616076 AGCCTCTCTATAAATTTTGATTTGACG 58.384 33.333 0.00 0.00 0.00 4.35
1956 1996 4.355543 TGACGAGGCAATTATTTTCTGC 57.644 40.909 0.00 0.00 35.28 4.26
1968 2008 8.139989 GCAATTATTTTCTGCCTTCTACATCAT 58.860 33.333 0.00 0.00 0.00 2.45
1977 2017 9.851686 TTCTGCCTTCTACATCATTTTATACAT 57.148 29.630 0.00 0.00 0.00 2.29
1978 2018 9.851686 TCTGCCTTCTACATCATTTTATACATT 57.148 29.630 0.00 0.00 0.00 2.71
2003 2069 8.818141 TTATTAATTTGCGAACCAATTTGTGA 57.182 26.923 0.00 0.00 32.49 3.58
2020 2086 0.539986 TGATTGGACGGTTAGAGGGC 59.460 55.000 0.00 0.00 0.00 5.19
2021 2087 0.831307 GATTGGACGGTTAGAGGGCT 59.169 55.000 0.00 0.00 0.00 5.19
2022 2088 0.541863 ATTGGACGGTTAGAGGGCTG 59.458 55.000 0.00 0.00 0.00 4.85
2023 2089 0.834687 TTGGACGGTTAGAGGGCTGT 60.835 55.000 0.00 0.00 0.00 4.40
2024 2090 1.218316 GGACGGTTAGAGGGCTGTG 59.782 63.158 0.00 0.00 0.00 3.66
2025 2091 1.448013 GACGGTTAGAGGGCTGTGC 60.448 63.158 0.00 0.00 0.00 4.57
2032 2099 3.231818 GTTAGAGGGCTGTGCTATCCTA 58.768 50.000 0.00 0.00 0.00 2.94
2033 2100 2.008242 AGAGGGCTGTGCTATCCTAG 57.992 55.000 0.00 0.00 0.00 3.02
2039 2106 1.356124 CTGTGCTATCCTAGGCCCAT 58.644 55.000 2.96 0.00 0.00 4.00
2064 2131 2.682856 GGTTTAAATCCTGATGCTCGCA 59.317 45.455 0.00 0.00 0.00 5.10
2065 2132 3.316308 GGTTTAAATCCTGATGCTCGCAT 59.684 43.478 3.70 3.70 39.69 4.73
2066 2133 4.202050 GGTTTAAATCCTGATGCTCGCATT 60.202 41.667 5.79 0.00 36.70 3.56
2067 2134 5.343249 GTTTAAATCCTGATGCTCGCATTT 58.657 37.500 5.79 0.00 36.70 2.32
2068 2135 6.459573 GGTTTAAATCCTGATGCTCGCATTTA 60.460 38.462 5.79 0.00 36.70 1.40
2069 2136 6.882610 TTAAATCCTGATGCTCGCATTTAT 57.117 33.333 5.79 0.00 36.70 1.40
2070 2137 5.779529 AAATCCTGATGCTCGCATTTATT 57.220 34.783 5.79 1.98 36.70 1.40
2071 2138 5.779529 AATCCTGATGCTCGCATTTATTT 57.220 34.783 5.79 0.00 36.70 1.40
2072 2139 5.779529 ATCCTGATGCTCGCATTTATTTT 57.220 34.783 5.79 0.00 36.70 1.82
2073 2140 5.581126 TCCTGATGCTCGCATTTATTTTT 57.419 34.783 5.79 0.00 36.70 1.94
2074 2141 5.342433 TCCTGATGCTCGCATTTATTTTTG 58.658 37.500 5.79 0.00 36.70 2.44
2075 2142 5.125257 TCCTGATGCTCGCATTTATTTTTGA 59.875 36.000 5.79 0.00 36.70 2.69
2076 2143 5.806502 CCTGATGCTCGCATTTATTTTTGAA 59.193 36.000 5.79 0.00 36.70 2.69
2077 2144 6.477688 CCTGATGCTCGCATTTATTTTTGAAT 59.522 34.615 5.79 0.00 36.70 2.57
2078 2145 7.010738 CCTGATGCTCGCATTTATTTTTGAATT 59.989 33.333 5.79 0.00 36.70 2.17
2079 2146 8.254178 TGATGCTCGCATTTATTTTTGAATTT 57.746 26.923 5.79 0.00 36.70 1.82
2080 2147 9.363763 TGATGCTCGCATTTATTTTTGAATTTA 57.636 25.926 5.79 0.00 36.70 1.40
2097 2164 8.667987 TTGAATTTATTTCAGAATTTCCGACG 57.332 30.769 0.00 0.00 44.90 5.12
2098 2165 8.035165 TGAATTTATTTCAGAATTTCCGACGA 57.965 30.769 0.00 0.00 39.44 4.20
2099 2166 8.673711 TGAATTTATTTCAGAATTTCCGACGAT 58.326 29.630 0.00 0.00 39.44 3.73
2100 2167 8.841444 AATTTATTTCAGAATTTCCGACGATG 57.159 30.769 0.00 0.00 0.00 3.84
2101 2168 3.740044 TTTCAGAATTTCCGACGATGC 57.260 42.857 0.00 0.00 0.00 3.91
2102 2169 1.277326 TCAGAATTTCCGACGATGCG 58.723 50.000 0.00 0.00 0.00 4.73
2103 2170 0.999406 CAGAATTTCCGACGATGCGT 59.001 50.000 0.00 0.00 45.10 5.24
2104 2171 2.159352 TCAGAATTTCCGACGATGCGTA 60.159 45.455 0.00 0.00 41.37 4.42
2105 2172 2.794910 CAGAATTTCCGACGATGCGTAT 59.205 45.455 0.00 0.00 41.37 3.06
2106 2173 3.245284 CAGAATTTCCGACGATGCGTATT 59.755 43.478 0.00 0.00 41.37 1.89
2107 2174 3.489785 AGAATTTCCGACGATGCGTATTC 59.510 43.478 0.00 0.00 41.37 1.75
2108 2175 2.281140 TTTCCGACGATGCGTATTCA 57.719 45.000 0.00 0.00 41.37 2.57
2109 2176 1.835121 TTCCGACGATGCGTATTCAG 58.165 50.000 0.00 0.00 41.37 3.02
2110 2177 0.736636 TCCGACGATGCGTATTCAGT 59.263 50.000 0.00 0.00 41.37 3.41
2111 2178 1.133598 TCCGACGATGCGTATTCAGTT 59.866 47.619 0.00 0.00 41.37 3.16
2112 2179 1.255342 CCGACGATGCGTATTCAGTTG 59.745 52.381 0.00 0.00 41.37 3.16
2113 2180 2.182014 CGACGATGCGTATTCAGTTGA 58.818 47.619 0.00 0.00 41.37 3.18
2114 2181 2.596862 CGACGATGCGTATTCAGTTGAA 59.403 45.455 0.00 0.00 41.37 2.69
2115 2182 3.301197 CGACGATGCGTATTCAGTTGAAG 60.301 47.826 0.74 0.00 41.37 3.02
2116 2183 3.845178 ACGATGCGTATTCAGTTGAAGA 58.155 40.909 0.74 0.00 38.73 2.87
2117 2184 4.242475 ACGATGCGTATTCAGTTGAAGAA 58.758 39.130 0.74 0.00 38.73 2.52
2118 2185 4.327357 ACGATGCGTATTCAGTTGAAGAAG 59.673 41.667 0.74 0.00 38.73 2.85
2119 2186 4.562789 CGATGCGTATTCAGTTGAAGAAGA 59.437 41.667 6.61 0.00 37.48 2.87
2120 2187 5.499334 CGATGCGTATTCAGTTGAAGAAGAC 60.499 44.000 6.61 0.00 37.48 3.01
2125 2192 6.154451 GTATTCAGTTGAAGAAGACGTTCC 57.846 41.667 0.00 0.00 37.48 3.62
2126 2193 3.107642 TCAGTTGAAGAAGACGTTCCC 57.892 47.619 0.00 0.00 32.48 3.97
2127 2194 1.792949 CAGTTGAAGAAGACGTTCCCG 59.207 52.381 0.00 0.00 40.83 5.14
2128 2195 7.698716 ATTCAGTTGAAGAAGACGTTCCCGT 62.699 44.000 0.00 0.00 43.32 5.28
2145 2212 4.649845 TCGATGACGAGGTGCCTA 57.350 55.556 0.00 0.00 43.81 3.93
2146 2213 2.104267 TCGATGACGAGGTGCCTAC 58.896 57.895 0.00 0.00 43.81 3.18
2147 2214 0.678684 TCGATGACGAGGTGCCTACA 60.679 55.000 0.00 0.00 43.81 2.74
2148 2215 0.248661 CGATGACGAGGTGCCTACAG 60.249 60.000 0.00 0.00 42.66 2.74
2149 2216 0.818296 GATGACGAGGTGCCTACAGT 59.182 55.000 0.00 0.00 0.00 3.55
2150 2217 1.204941 GATGACGAGGTGCCTACAGTT 59.795 52.381 0.00 0.00 0.00 3.16
2151 2218 1.913778 TGACGAGGTGCCTACAGTTA 58.086 50.000 0.00 0.00 0.00 2.24
2152 2219 1.542915 TGACGAGGTGCCTACAGTTAC 59.457 52.381 0.00 0.00 0.00 2.50
2153 2220 1.817447 GACGAGGTGCCTACAGTTACT 59.183 52.381 0.00 0.00 0.00 2.24
2154 2221 2.230750 GACGAGGTGCCTACAGTTACTT 59.769 50.000 0.00 0.00 0.00 2.24
2155 2222 2.230750 ACGAGGTGCCTACAGTTACTTC 59.769 50.000 0.00 0.00 0.00 3.01
2156 2223 2.731341 CGAGGTGCCTACAGTTACTTCG 60.731 54.545 0.00 0.00 36.56 3.79
2157 2224 2.230750 GAGGTGCCTACAGTTACTTCGT 59.769 50.000 0.00 0.00 0.00 3.85
2158 2225 3.424703 AGGTGCCTACAGTTACTTCGTA 58.575 45.455 0.00 0.00 0.00 3.43
2159 2226 3.828451 AGGTGCCTACAGTTACTTCGTAA 59.172 43.478 0.00 0.00 0.00 3.18
2160 2227 4.281688 AGGTGCCTACAGTTACTTCGTAAA 59.718 41.667 0.00 0.00 29.42 2.01
2161 2228 5.046807 AGGTGCCTACAGTTACTTCGTAAAT 60.047 40.000 0.00 0.00 29.42 1.40
2162 2229 5.640783 GGTGCCTACAGTTACTTCGTAAATT 59.359 40.000 0.00 0.00 29.42 1.82
2163 2230 6.148315 GGTGCCTACAGTTACTTCGTAAATTT 59.852 38.462 0.00 0.00 29.42 1.82
2164 2231 7.308169 GGTGCCTACAGTTACTTCGTAAATTTT 60.308 37.037 0.00 0.00 29.42 1.82
2165 2232 8.711457 GTGCCTACAGTTACTTCGTAAATTTTA 58.289 33.333 0.00 0.00 29.42 1.52
2166 2233 9.270640 TGCCTACAGTTACTTCGTAAATTTTAA 57.729 29.630 0.00 0.00 29.42 1.52
2167 2234 9.750882 GCCTACAGTTACTTCGTAAATTTTAAG 57.249 33.333 0.00 1.31 29.42 1.85
2178 2245 9.318041 CTTCGTAAATTTTAAGATGATATGCCG 57.682 33.333 0.00 0.00 0.00 5.69
2179 2246 8.596271 TCGTAAATTTTAAGATGATATGCCGA 57.404 30.769 0.00 0.00 0.00 5.54
2180 2247 8.492748 TCGTAAATTTTAAGATGATATGCCGAC 58.507 33.333 0.00 0.00 0.00 4.79
2181 2248 8.495949 CGTAAATTTTAAGATGATATGCCGACT 58.504 33.333 0.00 0.00 0.00 4.18
2184 2251 7.807977 ATTTTAAGATGATATGCCGACTTGT 57.192 32.000 0.00 0.00 0.00 3.16
2188 2255 3.132824 AGATGATATGCCGACTTGTGTGA 59.867 43.478 0.00 0.00 0.00 3.58
2197 2264 3.261580 CCGACTTGTGTGAATATGAGCA 58.738 45.455 0.00 0.00 0.00 4.26
2201 2268 5.618056 ACTTGTGTGAATATGAGCACTTG 57.382 39.130 0.00 0.00 36.05 3.16
2202 2269 4.083110 ACTTGTGTGAATATGAGCACTTGC 60.083 41.667 0.00 0.00 42.49 4.01
2214 2281 1.741993 GCACTTGCGTTTGTACTGTG 58.258 50.000 0.00 0.00 0.00 3.66
2215 2282 1.063469 GCACTTGCGTTTGTACTGTGT 59.937 47.619 0.00 0.00 0.00 3.72
2216 2283 2.477189 GCACTTGCGTTTGTACTGTGTT 60.477 45.455 0.00 0.00 0.00 3.32
2217 2284 3.753842 CACTTGCGTTTGTACTGTGTTT 58.246 40.909 0.00 0.00 0.00 2.83
2218 2285 4.728307 GCACTTGCGTTTGTACTGTGTTTA 60.728 41.667 0.00 0.00 0.00 2.01
2219 2286 5.325494 CACTTGCGTTTGTACTGTGTTTAA 58.675 37.500 0.00 0.00 0.00 1.52
2220 2287 5.451023 CACTTGCGTTTGTACTGTGTTTAAG 59.549 40.000 0.00 0.00 0.00 1.85
2221 2288 5.352016 ACTTGCGTTTGTACTGTGTTTAAGA 59.648 36.000 0.00 0.00 0.00 2.10
2222 2289 5.798015 TGCGTTTGTACTGTGTTTAAGAA 57.202 34.783 0.00 0.00 0.00 2.52
2223 2290 6.179504 TGCGTTTGTACTGTGTTTAAGAAA 57.820 33.333 0.00 0.00 0.00 2.52
2224 2291 6.609533 TGCGTTTGTACTGTGTTTAAGAAAA 58.390 32.000 0.00 0.00 0.00 2.29
2225 2292 6.523893 TGCGTTTGTACTGTGTTTAAGAAAAC 59.476 34.615 0.00 0.00 44.40 2.43
2239 2306 8.452989 GTTTAAGAAAACACCTGCTATTCATG 57.547 34.615 0.00 0.00 43.73 3.07
2240 2307 7.994425 TTAAGAAAACACCTGCTATTCATGA 57.006 32.000 0.00 0.00 0.00 3.07
2241 2308 5.886960 AGAAAACACCTGCTATTCATGAC 57.113 39.130 0.00 0.00 0.00 3.06
2242 2309 5.316167 AGAAAACACCTGCTATTCATGACA 58.684 37.500 0.00 0.00 0.00 3.58
2243 2310 5.182001 AGAAAACACCTGCTATTCATGACAC 59.818 40.000 0.00 0.00 0.00 3.67
2244 2311 2.991250 ACACCTGCTATTCATGACACC 58.009 47.619 0.00 0.00 0.00 4.16
2245 2312 2.573462 ACACCTGCTATTCATGACACCT 59.427 45.455 0.00 0.00 0.00 4.00
2246 2313 3.774766 ACACCTGCTATTCATGACACCTA 59.225 43.478 0.00 0.00 0.00 3.08
2247 2314 4.141846 ACACCTGCTATTCATGACACCTAG 60.142 45.833 0.00 0.00 0.00 3.02
2248 2315 4.033709 ACCTGCTATTCATGACACCTAGT 58.966 43.478 0.00 0.00 0.00 2.57
2249 2316 5.069119 CACCTGCTATTCATGACACCTAGTA 59.931 44.000 0.00 0.00 0.00 1.82
2250 2317 5.841237 ACCTGCTATTCATGACACCTAGTAT 59.159 40.000 0.00 0.00 0.00 2.12
2251 2318 6.327626 ACCTGCTATTCATGACACCTAGTATT 59.672 38.462 0.00 0.00 0.00 1.89
2252 2319 7.147479 ACCTGCTATTCATGACACCTAGTATTT 60.147 37.037 0.00 0.00 0.00 1.40
2253 2320 7.716998 CCTGCTATTCATGACACCTAGTATTTT 59.283 37.037 0.00 0.00 0.00 1.82
2254 2321 8.437360 TGCTATTCATGACACCTAGTATTTTG 57.563 34.615 0.00 0.00 0.00 2.44
2255 2322 7.498900 TGCTATTCATGACACCTAGTATTTTGG 59.501 37.037 0.00 0.00 0.00 3.28
2256 2323 7.715249 GCTATTCATGACACCTAGTATTTTGGA 59.285 37.037 0.00 0.00 0.00 3.53
2257 2324 9.613428 CTATTCATGACACCTAGTATTTTGGAA 57.387 33.333 0.00 0.00 0.00 3.53
2258 2325 7.681939 TTCATGACACCTAGTATTTTGGAAC 57.318 36.000 0.00 0.00 0.00 3.62
2259 2326 5.872617 TCATGACACCTAGTATTTTGGAACG 59.127 40.000 0.00 0.00 0.00 3.95
2260 2327 4.571919 TGACACCTAGTATTTTGGAACGG 58.428 43.478 0.00 0.00 0.00 4.44
2261 2328 4.283978 TGACACCTAGTATTTTGGAACGGA 59.716 41.667 0.00 0.00 0.00 4.69
2262 2329 4.828829 ACACCTAGTATTTTGGAACGGAG 58.171 43.478 0.00 0.00 0.00 4.63
2263 2330 4.529377 ACACCTAGTATTTTGGAACGGAGA 59.471 41.667 0.00 0.00 0.00 3.71
2291 2358 8.051535 AGTAGCAGATAGTACAAGGTAAGTGTA 58.948 37.037 0.00 0.00 0.00 2.90
2344 2411 4.920927 CACATGACACACTTATACGTCACA 59.079 41.667 0.00 0.00 40.91 3.58
2348 2415 7.172532 ACATGACACACTTATACGTCACAAAAT 59.827 33.333 0.00 0.00 40.91 1.82
2365 2432 7.970061 GTCACAAAATTCTATTGCTAGATTGCA 59.030 33.333 0.00 0.00 41.65 4.08
2377 2444 4.926953 TGCTAGATTGCAATCCGAATTGGA 60.927 41.667 31.05 14.90 44.41 3.53
2386 2453 2.488204 TCCGAATTGGATGAACAGCA 57.512 45.000 0.00 0.00 43.74 4.41
2397 2464 3.932710 GGATGAACAGCACGAACTTCATA 59.067 43.478 0.00 0.00 34.26 2.15
2434 2501 3.318275 TCATAGTAACACATCCGAGGCTC 59.682 47.826 3.87 3.87 0.00 4.70
2441 2508 0.179100 ACATCCGAGGCTCGTGAATG 60.179 55.000 32.41 29.70 38.40 2.67
2442 2509 0.179100 CATCCGAGGCTCGTGAATGT 60.179 55.000 32.41 13.55 38.40 2.71
2443 2510 0.537188 ATCCGAGGCTCGTGAATGTT 59.463 50.000 32.41 13.23 38.40 2.71
2444 2511 0.320374 TCCGAGGCTCGTGAATGTTT 59.680 50.000 32.41 0.00 38.40 2.83
2445 2512 1.156736 CCGAGGCTCGTGAATGTTTT 58.843 50.000 32.41 0.00 38.40 2.43
2446 2513 1.128692 CCGAGGCTCGTGAATGTTTTC 59.871 52.381 32.41 0.00 38.40 2.29
2447 2514 2.069273 CGAGGCTCGTGAATGTTTTCT 58.931 47.619 27.92 0.00 34.72 2.52
2448 2515 2.092838 CGAGGCTCGTGAATGTTTTCTC 59.907 50.000 27.92 0.00 34.72 2.87
2449 2516 3.330267 GAGGCTCGTGAATGTTTTCTCT 58.670 45.455 0.00 0.00 32.78 3.10
2450 2517 3.330267 AGGCTCGTGAATGTTTTCTCTC 58.670 45.455 0.00 0.00 32.78 3.20
2451 2518 3.007398 AGGCTCGTGAATGTTTTCTCTCT 59.993 43.478 0.00 0.00 32.78 3.10
2452 2519 4.220821 AGGCTCGTGAATGTTTTCTCTCTA 59.779 41.667 0.00 0.00 32.78 2.43
2473 2540 8.993121 TCTCTAGTTTTCTCATGATTTGTTGAC 58.007 33.333 0.00 0.00 0.00 3.18
2885 2963 0.317479 CCGTCTCCTCTTTGTCCGTT 59.683 55.000 0.00 0.00 0.00 4.44
2886 2964 1.270147 CCGTCTCCTCTTTGTCCGTTT 60.270 52.381 0.00 0.00 0.00 3.60
2887 2965 2.480845 CGTCTCCTCTTTGTCCGTTTT 58.519 47.619 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.202137 GTGACCCTAGTTGTAGCAAAATCTATA 58.798 37.037 0.00 0.00 0.00 1.31
101 104 3.004734 AGTGATGCTAGTTGTGGCAAAAC 59.995 43.478 12.75 12.75 44.32 2.43
183 189 2.935446 AAAAAGTCGTCGTCGCCGC 61.935 57.895 0.00 0.00 36.96 6.53
232 245 3.502979 GGATGTAACAAAACCCGTTGCTA 59.497 43.478 0.00 0.00 31.17 3.49
340 354 6.066054 TCATTGTTTGTCGTAGCAAAATGA 57.934 33.333 10.24 10.24 39.65 2.57
361 375 1.957177 TGCCCGTTGTAGCATTTTTCA 59.043 42.857 0.00 0.00 33.08 2.69
482 498 0.612453 TTGCCATGGATGCAGCTTCA 60.612 50.000 18.40 0.00 40.35 3.02
509 527 1.352017 ACCATGGATGCAACTCTGTCA 59.648 47.619 21.47 0.00 0.00 3.58
511 529 1.352017 TCACCATGGATGCAACTCTGT 59.648 47.619 21.47 0.00 0.00 3.41
517 535 2.409055 GCGCTCACCATGGATGCAA 61.409 57.895 21.47 0.00 0.00 4.08
557 575 1.822613 CCATGGATGCAGCTTCGCT 60.823 57.895 5.56 0.00 40.77 4.93
617 635 1.304630 TTCCTCATCGTCGGTGGGA 60.305 57.895 7.03 9.19 0.00 4.37
661 679 3.442273 GTCATATCCCCGCAAGAAAACAA 59.558 43.478 0.00 0.00 43.02 2.83
670 688 2.061578 ACCACGTCATATCCCCGCA 61.062 57.895 0.00 0.00 0.00 5.69
839 865 1.680735 GGCATTTCAATATGGGCGACA 59.319 47.619 0.00 0.00 0.00 4.35
871 897 9.476928 AGCTACTACTCTCTTTGTTCCTAAATA 57.523 33.333 0.00 0.00 0.00 1.40
872 898 8.368962 AGCTACTACTCTCTTTGTTCCTAAAT 57.631 34.615 0.00 0.00 0.00 1.40
873 899 7.778185 AGCTACTACTCTCTTTGTTCCTAAA 57.222 36.000 0.00 0.00 0.00 1.85
874 900 7.338957 GGTAGCTACTACTCTCTTTGTTCCTAA 59.661 40.741 22.74 0.00 37.16 2.69
875 901 6.827762 GGTAGCTACTACTCTCTTTGTTCCTA 59.172 42.308 22.74 0.00 37.16 2.94
876 902 5.653330 GGTAGCTACTACTCTCTTTGTTCCT 59.347 44.000 22.74 0.00 37.16 3.36
877 903 5.418209 TGGTAGCTACTACTCTCTTTGTTCC 59.582 44.000 22.74 1.61 37.16 3.62
878 904 6.512342 TGGTAGCTACTACTCTCTTTGTTC 57.488 41.667 22.74 2.30 37.16 3.18
879 905 6.912951 TTGGTAGCTACTACTCTCTTTGTT 57.087 37.500 22.74 0.00 37.16 2.83
880 906 6.071278 CCTTTGGTAGCTACTACTCTCTTTGT 60.071 42.308 22.74 0.00 37.16 2.83
881 907 6.153000 TCCTTTGGTAGCTACTACTCTCTTTG 59.847 42.308 22.74 3.10 37.16 2.77
882 908 6.254522 TCCTTTGGTAGCTACTACTCTCTTT 58.745 40.000 22.74 0.00 37.16 2.52
883 909 5.828871 TCCTTTGGTAGCTACTACTCTCTT 58.171 41.667 22.74 0.00 37.16 2.85
884 910 5.453866 TCCTTTGGTAGCTACTACTCTCT 57.546 43.478 22.74 0.00 37.16 3.10
885 911 6.718522 AATCCTTTGGTAGCTACTACTCTC 57.281 41.667 22.74 6.25 37.16 3.20
886 912 7.618512 TGTAAATCCTTTGGTAGCTACTACTCT 59.381 37.037 22.74 0.66 37.16 3.24
887 913 7.705752 GTGTAAATCCTTTGGTAGCTACTACTC 59.294 40.741 22.74 10.92 37.16 2.59
888 914 7.179694 TGTGTAAATCCTTTGGTAGCTACTACT 59.820 37.037 22.74 0.00 37.16 2.57
927 955 1.508632 CGTCTTGTTGTCCCATCGTT 58.491 50.000 0.00 0.00 0.00 3.85
943 971 1.209640 GACTCCGACTGTCACCGTC 59.790 63.158 8.73 6.60 34.80 4.79
1052 1084 0.239082 TGTAGCGATGTATACCGGCG 59.761 55.000 0.00 0.00 0.00 6.46
1061 1093 4.739735 GCAGGTAATAGGTTGTAGCGATGT 60.740 45.833 0.00 0.00 0.00 3.06
1068 1100 3.884693 TCGATCGCAGGTAATAGGTTGTA 59.115 43.478 11.09 0.00 0.00 2.41
1078 1110 3.408634 TCATCATAGTCGATCGCAGGTA 58.591 45.455 11.09 0.00 0.00 3.08
1079 1111 2.230660 TCATCATAGTCGATCGCAGGT 58.769 47.619 11.09 0.00 0.00 4.00
1080 1112 2.997485 TCATCATAGTCGATCGCAGG 57.003 50.000 11.09 0.00 0.00 4.85
1269 1306 1.375523 GGCGTTGTTCCACGATCCT 60.376 57.895 0.00 0.00 43.15 3.24
1274 1311 4.054455 CGTCGGCGTTGTTCCACG 62.054 66.667 6.85 3.37 43.36 4.94
1428 1465 0.234884 CGTTGAACTTGAAGACGCCC 59.765 55.000 0.00 0.00 0.00 6.13
1572 1609 3.595758 GCCGTGCTGCCAAACACT 61.596 61.111 0.00 0.00 34.58 3.55
1599 1636 1.410517 GCCTCCTCGAGATCATCACAA 59.589 52.381 15.71 0.00 0.00 3.33
1780 1817 0.389948 GAAGAGAAAAGAGCGGCGGA 60.390 55.000 9.78 0.00 0.00 5.54
1789 1826 7.727331 AACATGAGAAGACAGAAGAGAAAAG 57.273 36.000 0.00 0.00 0.00 2.27
1909 1947 8.474710 AATCAAAATTTATAGAGAGGCTGCAT 57.525 30.769 0.50 0.00 0.00 3.96
1914 1952 8.612619 TCGTCAAATCAAAATTTATAGAGAGGC 58.387 33.333 0.00 0.00 33.27 4.70
1977 2017 9.261180 TCACAAATTGGTTCGCAAATTAATAAA 57.739 25.926 0.00 0.00 30.86 1.40
1978 2018 8.818141 TCACAAATTGGTTCGCAAATTAATAA 57.182 26.923 0.00 0.00 30.86 1.40
1979 2019 8.994429 ATCACAAATTGGTTCGCAAATTAATA 57.006 26.923 0.00 0.00 30.86 0.98
1981 2021 7.307632 CCAATCACAAATTGGTTCGCAAATTAA 60.308 33.333 8.35 0.00 42.63 1.40
1987 2053 2.625314 TCCAATCACAAATTGGTTCGCA 59.375 40.909 14.65 0.00 46.47 5.10
1998 2064 2.027561 CCCTCTAACCGTCCAATCACAA 60.028 50.000 0.00 0.00 0.00 3.33
2003 2069 0.541863 CAGCCCTCTAACCGTCCAAT 59.458 55.000 0.00 0.00 0.00 3.16
2009 2075 0.753262 ATAGCACAGCCCTCTAACCG 59.247 55.000 0.00 0.00 0.00 4.44
2020 2086 1.277557 GATGGGCCTAGGATAGCACAG 59.722 57.143 14.75 0.00 37.37 3.66
2021 2087 1.352083 GATGGGCCTAGGATAGCACA 58.648 55.000 14.75 4.23 37.37 4.57
2022 2088 1.277557 CTGATGGGCCTAGGATAGCAC 59.722 57.143 14.75 0.00 37.37 4.40
2023 2089 1.649321 CTGATGGGCCTAGGATAGCA 58.351 55.000 14.75 5.54 37.37 3.49
2024 2090 0.908198 CCTGATGGGCCTAGGATAGC 59.092 60.000 14.75 0.39 37.37 2.97
2047 2114 6.882610 AATAAATGCGAGCATCAGGATTTA 57.117 33.333 11.26 6.42 41.59 1.40
2050 2117 5.779529 AAAATAAATGCGAGCATCAGGAT 57.220 34.783 11.26 0.39 35.31 3.24
2052 2119 5.342433 TCAAAAATAAATGCGAGCATCAGG 58.658 37.500 11.26 0.00 35.31 3.86
2073 2140 8.035165 TCGTCGGAAATTCTGAAATAAATTCA 57.965 30.769 6.03 0.00 45.71 2.57
2074 2141 8.947940 CATCGTCGGAAATTCTGAAATAAATTC 58.052 33.333 6.03 0.00 32.84 2.17
2075 2142 7.432252 GCATCGTCGGAAATTCTGAAATAAATT 59.568 33.333 6.03 0.00 32.84 1.82
2076 2143 6.912591 GCATCGTCGGAAATTCTGAAATAAAT 59.087 34.615 6.03 0.00 32.84 1.40
2077 2144 6.255215 GCATCGTCGGAAATTCTGAAATAAA 58.745 36.000 6.03 0.00 32.84 1.40
2078 2145 5.501736 CGCATCGTCGGAAATTCTGAAATAA 60.502 40.000 6.03 0.00 32.84 1.40
2079 2146 4.026062 CGCATCGTCGGAAATTCTGAAATA 60.026 41.667 6.03 0.00 32.84 1.40
2080 2147 3.242413 CGCATCGTCGGAAATTCTGAAAT 60.242 43.478 6.03 0.99 32.84 2.17
2081 2148 2.093625 CGCATCGTCGGAAATTCTGAAA 59.906 45.455 6.03 0.00 32.84 2.69
2082 2149 1.658596 CGCATCGTCGGAAATTCTGAA 59.341 47.619 6.03 0.00 32.84 3.02
2083 2150 1.277326 CGCATCGTCGGAAATTCTGA 58.723 50.000 0.00 0.00 0.00 3.27
2084 2151 0.999406 ACGCATCGTCGGAAATTCTG 59.001 50.000 0.00 0.00 33.69 3.02
2085 2152 2.572191 TACGCATCGTCGGAAATTCT 57.428 45.000 0.00 0.00 41.54 2.40
2086 2153 3.244345 TGAATACGCATCGTCGGAAATTC 59.756 43.478 0.00 0.65 41.54 2.17
2087 2154 3.191669 TGAATACGCATCGTCGGAAATT 58.808 40.909 0.00 0.00 41.54 1.82
2088 2155 2.794910 CTGAATACGCATCGTCGGAAAT 59.205 45.455 0.00 0.00 41.54 2.17
2089 2156 2.190161 CTGAATACGCATCGTCGGAAA 58.810 47.619 0.00 0.00 41.54 3.13
2090 2157 1.133598 ACTGAATACGCATCGTCGGAA 59.866 47.619 0.00 0.00 41.54 4.30
2091 2158 0.736636 ACTGAATACGCATCGTCGGA 59.263 50.000 0.00 0.00 41.54 4.55
2092 2159 1.255342 CAACTGAATACGCATCGTCGG 59.745 52.381 0.00 0.00 41.54 4.79
2093 2160 2.182014 TCAACTGAATACGCATCGTCG 58.818 47.619 0.00 0.00 41.54 5.12
2094 2161 3.857665 TCTTCAACTGAATACGCATCGTC 59.142 43.478 0.00 0.00 41.54 4.20
2095 2162 3.845178 TCTTCAACTGAATACGCATCGT 58.155 40.909 0.00 0.00 44.35 3.73
2096 2163 4.562789 TCTTCTTCAACTGAATACGCATCG 59.437 41.667 0.00 0.00 33.01 3.84
2097 2164 5.499334 CGTCTTCTTCAACTGAATACGCATC 60.499 44.000 0.00 0.00 37.27 3.91
2098 2165 4.327357 CGTCTTCTTCAACTGAATACGCAT 59.673 41.667 0.00 0.00 37.27 4.73
2099 2166 3.673338 CGTCTTCTTCAACTGAATACGCA 59.327 43.478 0.00 0.00 37.27 5.24
2100 2167 3.673809 ACGTCTTCTTCAACTGAATACGC 59.326 43.478 12.06 0.00 43.16 4.42
2101 2168 5.164080 GGAACGTCTTCTTCAACTGAATACG 60.164 44.000 11.03 11.03 44.15 3.06
2102 2169 5.120363 GGGAACGTCTTCTTCAACTGAATAC 59.880 44.000 0.00 0.00 33.01 1.89
2103 2170 5.235516 GGGAACGTCTTCTTCAACTGAATA 58.764 41.667 0.00 0.00 33.01 1.75
2104 2171 4.065789 GGGAACGTCTTCTTCAACTGAAT 58.934 43.478 0.00 0.00 33.01 2.57
2105 2172 3.463944 GGGAACGTCTTCTTCAACTGAA 58.536 45.455 0.00 0.00 0.00 3.02
2106 2173 3.107642 GGGAACGTCTTCTTCAACTGA 57.892 47.619 0.00 0.00 0.00 3.41
2127 2194 0.248539 GTAGGCACCTCGTCATCGAC 60.249 60.000 0.00 0.00 41.35 4.20
2128 2195 0.678684 TGTAGGCACCTCGTCATCGA 60.679 55.000 0.00 0.00 44.12 3.59
2129 2196 0.248661 CTGTAGGCACCTCGTCATCG 60.249 60.000 0.00 0.00 38.55 3.84
2130 2197 0.818296 ACTGTAGGCACCTCGTCATC 59.182 55.000 0.00 0.00 0.00 2.92
2131 2198 1.267121 AACTGTAGGCACCTCGTCAT 58.733 50.000 0.00 0.00 0.00 3.06
2132 2199 1.542915 GTAACTGTAGGCACCTCGTCA 59.457 52.381 0.00 0.00 0.00 4.35
2133 2200 1.817447 AGTAACTGTAGGCACCTCGTC 59.183 52.381 0.00 0.00 0.00 4.20
2134 2201 1.920610 AGTAACTGTAGGCACCTCGT 58.079 50.000 0.00 0.00 0.00 4.18
2135 2202 2.731341 CGAAGTAACTGTAGGCACCTCG 60.731 54.545 0.00 0.00 0.00 4.63
2136 2203 2.230750 ACGAAGTAACTGTAGGCACCTC 59.769 50.000 0.00 0.00 41.94 3.85
2137 2204 2.245582 ACGAAGTAACTGTAGGCACCT 58.754 47.619 0.00 0.00 41.94 4.00
2138 2205 2.738013 ACGAAGTAACTGTAGGCACC 57.262 50.000 0.00 0.00 41.94 5.01
2152 2219 9.318041 CGGCATATCATCTTAAAATTTACGAAG 57.682 33.333 0.00 0.00 0.00 3.79
2153 2220 9.047371 TCGGCATATCATCTTAAAATTTACGAA 57.953 29.630 0.00 0.00 0.00 3.85
2154 2221 8.492748 GTCGGCATATCATCTTAAAATTTACGA 58.507 33.333 0.00 0.00 0.00 3.43
2155 2222 8.495949 AGTCGGCATATCATCTTAAAATTTACG 58.504 33.333 0.00 0.00 0.00 3.18
2158 2225 8.686334 ACAAGTCGGCATATCATCTTAAAATTT 58.314 29.630 0.00 0.00 0.00 1.82
2159 2226 8.131100 CACAAGTCGGCATATCATCTTAAAATT 58.869 33.333 0.00 0.00 0.00 1.82
2160 2227 7.283127 ACACAAGTCGGCATATCATCTTAAAAT 59.717 33.333 0.00 0.00 0.00 1.82
2161 2228 6.597672 ACACAAGTCGGCATATCATCTTAAAA 59.402 34.615 0.00 0.00 0.00 1.52
2162 2229 6.037062 CACACAAGTCGGCATATCATCTTAAA 59.963 38.462 0.00 0.00 0.00 1.52
2163 2230 5.523552 CACACAAGTCGGCATATCATCTTAA 59.476 40.000 0.00 0.00 0.00 1.85
2164 2231 5.049828 CACACAAGTCGGCATATCATCTTA 58.950 41.667 0.00 0.00 0.00 2.10
2165 2232 3.873361 CACACAAGTCGGCATATCATCTT 59.127 43.478 0.00 0.00 0.00 2.40
2166 2233 3.132824 TCACACAAGTCGGCATATCATCT 59.867 43.478 0.00 0.00 0.00 2.90
2167 2234 3.457234 TCACACAAGTCGGCATATCATC 58.543 45.455 0.00 0.00 0.00 2.92
2168 2235 3.541996 TCACACAAGTCGGCATATCAT 57.458 42.857 0.00 0.00 0.00 2.45
2169 2236 3.326836 TTCACACAAGTCGGCATATCA 57.673 42.857 0.00 0.00 0.00 2.15
2170 2237 5.696270 TCATATTCACACAAGTCGGCATATC 59.304 40.000 0.00 0.00 0.00 1.63
2171 2238 5.610398 TCATATTCACACAAGTCGGCATAT 58.390 37.500 0.00 0.00 0.00 1.78
2172 2239 5.017294 TCATATTCACACAAGTCGGCATA 57.983 39.130 0.00 0.00 0.00 3.14
2173 2240 3.872696 TCATATTCACACAAGTCGGCAT 58.127 40.909 0.00 0.00 0.00 4.40
2174 2241 3.261580 CTCATATTCACACAAGTCGGCA 58.738 45.455 0.00 0.00 0.00 5.69
2175 2242 2.030946 GCTCATATTCACACAAGTCGGC 59.969 50.000 0.00 0.00 0.00 5.54
2176 2243 3.062639 GTGCTCATATTCACACAAGTCGG 59.937 47.826 0.00 0.00 33.63 4.79
2177 2244 3.928992 AGTGCTCATATTCACACAAGTCG 59.071 43.478 0.00 0.00 35.47 4.18
2178 2245 5.625251 CAAGTGCTCATATTCACACAAGTC 58.375 41.667 0.00 0.00 35.47 3.01
2179 2246 4.083110 GCAAGTGCTCATATTCACACAAGT 60.083 41.667 0.00 0.00 38.21 3.16
2180 2247 4.409570 GCAAGTGCTCATATTCACACAAG 58.590 43.478 0.00 0.00 38.21 3.16
2181 2248 3.120234 CGCAAGTGCTCATATTCACACAA 60.120 43.478 1.21 0.00 39.32 3.33
2182 2249 2.416202 CGCAAGTGCTCATATTCACACA 59.584 45.455 1.21 0.00 39.32 3.72
2183 2250 3.043635 CGCAAGTGCTCATATTCACAC 57.956 47.619 1.21 0.00 39.32 3.82
2201 2268 6.523893 TGTTTTCTTAAACACAGTACAAACGC 59.476 34.615 0.00 0.00 46.46 4.84
2214 2281 8.296713 TCATGAATAGCAGGTGTTTTCTTAAAC 58.703 33.333 0.00 0.00 43.17 2.01
2215 2282 8.296713 GTCATGAATAGCAGGTGTTTTCTTAAA 58.703 33.333 0.00 0.00 0.00 1.52
2216 2283 7.446931 TGTCATGAATAGCAGGTGTTTTCTTAA 59.553 33.333 0.00 0.00 0.00 1.85
2217 2284 6.939730 TGTCATGAATAGCAGGTGTTTTCTTA 59.060 34.615 0.00 0.00 0.00 2.10
2218 2285 5.769662 TGTCATGAATAGCAGGTGTTTTCTT 59.230 36.000 0.00 0.00 0.00 2.52
2219 2286 5.182001 GTGTCATGAATAGCAGGTGTTTTCT 59.818 40.000 0.00 0.00 0.00 2.52
2220 2287 5.393962 GTGTCATGAATAGCAGGTGTTTTC 58.606 41.667 0.00 0.00 0.00 2.29
2221 2288 4.218417 GGTGTCATGAATAGCAGGTGTTTT 59.782 41.667 0.00 0.00 0.00 2.43
2222 2289 3.758554 GGTGTCATGAATAGCAGGTGTTT 59.241 43.478 0.00 0.00 0.00 2.83
2223 2290 3.009473 AGGTGTCATGAATAGCAGGTGTT 59.991 43.478 0.00 0.00 0.00 3.32
2224 2291 2.573462 AGGTGTCATGAATAGCAGGTGT 59.427 45.455 0.00 0.00 0.00 4.16
2225 2292 3.272574 AGGTGTCATGAATAGCAGGTG 57.727 47.619 0.00 0.00 0.00 4.00
2226 2293 4.033709 ACTAGGTGTCATGAATAGCAGGT 58.966 43.478 0.00 0.44 0.00 4.00
2227 2294 4.679373 ACTAGGTGTCATGAATAGCAGG 57.321 45.455 0.00 0.00 0.00 4.85
2228 2295 8.554528 CAAAATACTAGGTGTCATGAATAGCAG 58.445 37.037 0.00 3.28 0.00 4.24
2229 2296 7.498900 CCAAAATACTAGGTGTCATGAATAGCA 59.501 37.037 0.00 0.00 0.00 3.49
2230 2297 7.715249 TCCAAAATACTAGGTGTCATGAATAGC 59.285 37.037 0.00 0.00 0.00 2.97
2231 2298 9.613428 TTCCAAAATACTAGGTGTCATGAATAG 57.387 33.333 0.00 0.58 0.00 1.73
2232 2299 9.391006 GTTCCAAAATACTAGGTGTCATGAATA 57.609 33.333 0.00 0.00 0.00 1.75
2233 2300 7.065803 CGTTCCAAAATACTAGGTGTCATGAAT 59.934 37.037 0.00 0.00 0.00 2.57
2234 2301 6.370442 CGTTCCAAAATACTAGGTGTCATGAA 59.630 38.462 0.00 0.00 0.00 2.57
2235 2302 5.872617 CGTTCCAAAATACTAGGTGTCATGA 59.127 40.000 0.00 0.00 0.00 3.07
2236 2303 5.064707 CCGTTCCAAAATACTAGGTGTCATG 59.935 44.000 0.00 0.00 0.00 3.07
2237 2304 5.046159 TCCGTTCCAAAATACTAGGTGTCAT 60.046 40.000 0.00 0.00 0.00 3.06
2238 2305 4.283978 TCCGTTCCAAAATACTAGGTGTCA 59.716 41.667 0.00 0.00 0.00 3.58
2239 2306 4.824289 TCCGTTCCAAAATACTAGGTGTC 58.176 43.478 0.00 0.00 0.00 3.67
2240 2307 4.529377 TCTCCGTTCCAAAATACTAGGTGT 59.471 41.667 0.00 0.00 0.00 4.16
2241 2308 5.080969 TCTCCGTTCCAAAATACTAGGTG 57.919 43.478 0.00 0.00 0.00 4.00
2242 2309 5.021458 TCTCTCCGTTCCAAAATACTAGGT 58.979 41.667 0.00 0.00 0.00 3.08
2243 2310 5.127356 ACTCTCTCCGTTCCAAAATACTAGG 59.873 44.000 0.00 0.00 0.00 3.02
2244 2311 6.210287 ACTCTCTCCGTTCCAAAATACTAG 57.790 41.667 0.00 0.00 0.00 2.57
2245 2312 6.183360 GCTACTCTCTCCGTTCCAAAATACTA 60.183 42.308 0.00 0.00 0.00 1.82
2246 2313 5.394333 GCTACTCTCTCCGTTCCAAAATACT 60.394 44.000 0.00 0.00 0.00 2.12
2247 2314 4.804665 GCTACTCTCTCCGTTCCAAAATAC 59.195 45.833 0.00 0.00 0.00 1.89
2248 2315 4.464951 TGCTACTCTCTCCGTTCCAAAATA 59.535 41.667 0.00 0.00 0.00 1.40
2249 2316 3.260884 TGCTACTCTCTCCGTTCCAAAAT 59.739 43.478 0.00 0.00 0.00 1.82
2250 2317 2.631062 TGCTACTCTCTCCGTTCCAAAA 59.369 45.455 0.00 0.00 0.00 2.44
2251 2318 2.231478 CTGCTACTCTCTCCGTTCCAAA 59.769 50.000 0.00 0.00 0.00 3.28
2252 2319 1.819288 CTGCTACTCTCTCCGTTCCAA 59.181 52.381 0.00 0.00 0.00 3.53
2253 2320 1.004394 TCTGCTACTCTCTCCGTTCCA 59.996 52.381 0.00 0.00 0.00 3.53
2254 2321 1.752683 TCTGCTACTCTCTCCGTTCC 58.247 55.000 0.00 0.00 0.00 3.62
2255 2322 4.131596 ACTATCTGCTACTCTCTCCGTTC 58.868 47.826 0.00 0.00 0.00 3.95
2256 2323 4.159244 ACTATCTGCTACTCTCTCCGTT 57.841 45.455 0.00 0.00 0.00 4.44
2257 2324 3.849563 ACTATCTGCTACTCTCTCCGT 57.150 47.619 0.00 0.00 0.00 4.69
2258 2325 4.633175 TGTACTATCTGCTACTCTCTCCG 58.367 47.826 0.00 0.00 0.00 4.63
2259 2326 5.472137 CCTTGTACTATCTGCTACTCTCTCC 59.528 48.000 0.00 0.00 0.00 3.71
2260 2327 6.059484 ACCTTGTACTATCTGCTACTCTCTC 58.941 44.000 0.00 0.00 0.00 3.20
2261 2328 6.008696 ACCTTGTACTATCTGCTACTCTCT 57.991 41.667 0.00 0.00 0.00 3.10
2262 2329 7.499895 ACTTACCTTGTACTATCTGCTACTCTC 59.500 40.741 0.00 0.00 0.00 3.20
2263 2330 7.283580 CACTTACCTTGTACTATCTGCTACTCT 59.716 40.741 0.00 0.00 0.00 3.24
2291 2358 2.279037 AAACCACCACGGCCTTCTGT 62.279 55.000 0.00 0.00 39.03 3.41
2294 2361 1.515521 CTGAAACCACCACGGCCTTC 61.516 60.000 0.00 0.00 39.03 3.46
2370 2437 3.189287 AGTTCGTGCTGTTCATCCAATTC 59.811 43.478 0.00 0.00 0.00 2.17
2377 2444 4.572389 GGATATGAAGTTCGTGCTGTTCAT 59.428 41.667 7.89 0.00 41.42 2.57
2378 2445 3.932710 GGATATGAAGTTCGTGCTGTTCA 59.067 43.478 7.89 0.00 33.61 3.18
2379 2446 3.932710 TGGATATGAAGTTCGTGCTGTTC 59.067 43.478 7.89 0.00 0.00 3.18
2382 2449 3.873361 ACATGGATATGAAGTTCGTGCTG 59.127 43.478 7.89 1.37 37.73 4.41
2386 2453 3.206150 GCCACATGGATATGAAGTTCGT 58.794 45.455 0.87 2.56 37.73 3.85
2397 2464 1.073444 CTATGAGCTGGCCACATGGAT 59.927 52.381 15.71 0.00 37.39 3.41
2434 2501 8.077836 AGAAAACTAGAGAGAAAACATTCACG 57.922 34.615 0.00 0.00 0.00 4.35
2443 2510 9.784531 ACAAATCATGAGAAAACTAGAGAGAAA 57.215 29.630 0.09 0.00 0.00 2.52
2444 2511 9.784531 AACAAATCATGAGAAAACTAGAGAGAA 57.215 29.630 0.09 0.00 0.00 2.87
2445 2512 9.212641 CAACAAATCATGAGAAAACTAGAGAGA 57.787 33.333 0.09 0.00 0.00 3.10
2446 2513 9.212641 TCAACAAATCATGAGAAAACTAGAGAG 57.787 33.333 0.09 0.00 0.00 3.20
2447 2514 8.993121 GTCAACAAATCATGAGAAAACTAGAGA 58.007 33.333 0.09 0.00 0.00 3.10
2448 2515 8.997323 AGTCAACAAATCATGAGAAAACTAGAG 58.003 33.333 0.09 0.00 0.00 2.43
2449 2516 8.908786 AGTCAACAAATCATGAGAAAACTAGA 57.091 30.769 0.09 0.00 0.00 2.43
2450 2517 9.956720 AAAGTCAACAAATCATGAGAAAACTAG 57.043 29.630 0.09 0.00 0.00 2.57
2452 2519 9.657419 AAAAAGTCAACAAATCATGAGAAAACT 57.343 25.926 0.09 0.00 0.00 2.66
2847 2916 1.146637 GATCATCGGCAGAGATGTGC 58.853 55.000 13.33 0.00 45.96 4.57
2848 2917 1.793258 GGATCATCGGCAGAGATGTG 58.207 55.000 13.33 0.00 45.96 3.21
2849 2918 0.316522 CGGATCATCGGCAGAGATGT 59.683 55.000 13.33 4.35 45.96 3.06
2850 2919 0.316522 ACGGATCATCGGCAGAGATG 59.683 55.000 9.04 9.04 46.90 2.90
2851 2920 0.600557 GACGGATCATCGGCAGAGAT 59.399 55.000 0.00 0.00 38.21 2.75
2852 2921 0.466372 AGACGGATCATCGGCAGAGA 60.466 55.000 0.00 0.00 41.34 3.10


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

AutoCloner maintained by Alex Coulton.