Multiple sequence alignment - TraesCS3B01G061400

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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 TraesCS3B01G061400 chr3B 100.000 2462 0 0 1 2462 33300087 33297626 0.000000e+00 4547.0
1 TraesCS3B01G061400 chr3B 81.163 1083 136 39 853 1906 32992152 32991109 0.000000e+00 808.0
2 TraesCS3B01G061400 chr3B 79.396 927 131 32 992 1906 33096992 33096114 1.260000e-167 599.0
3 TraesCS3B01G061400 chr3B 82.343 572 62 22 901 1464 33334253 33333713 6.200000e-126 460.0
4 TraesCS3B01G061400 chr3B 76.277 274 38 13 1478 1748 32732897 32732648 1.200000e-23 121.0
5 TraesCS3B01G061400 chr3B 90.000 80 5 1 991 1070 32942608 32942532 1.560000e-17 100.0
6 TraesCS3B01G061400 chr3B 81.553 103 17 2 1000 1101 32801696 32801595 1.570000e-12 84.2
7 TraesCS3B01G061400 chr3A 87.724 1841 137 27 641 2462 28391661 28389891 0.000000e+00 2065.0
8 TraesCS3B01G061400 chr3A 81.803 1209 146 42 744 1906 28231645 28230465 0.000000e+00 946.0
9 TraesCS3B01G061400 chr3A 86.777 847 89 11 1304 2139 28371220 28370386 0.000000e+00 922.0
10 TraesCS3B01G061400 chr3A 85.179 641 60 15 854 1462 28322930 28322293 2.080000e-175 625.0
11 TraesCS3B01G061400 chr3A 89.461 427 31 5 220 644 28392105 28391691 6.030000e-146 527.0
12 TraesCS3B01G061400 chr3A 79.801 302 48 11 1246 1542 28423720 28423427 8.920000e-50 207.0
13 TraesCS3B01G061400 chr3A 79.911 224 36 7 1587 1803 28056777 28056556 3.280000e-34 156.0
14 TraesCS3B01G061400 chr3A 91.250 80 4 1 991 1070 28206767 28206691 3.350000e-19 106.0
15 TraesCS3B01G061400 chr3A 85.714 77 4 4 1461 1530 27766109 27766033 9.440000e-10 75.0
16 TraesCS3B01G061400 chr3A 96.970 33 1 0 1467 1499 28322298 28322266 3.420000e-04 56.5
17 TraesCS3B01G061400 chr4A 87.933 779 66 10 1685 2462 723214956 723214205 0.000000e+00 893.0
18 TraesCS3B01G061400 chr4A 84.664 476 43 12 1984 2457 520877188 520876741 4.830000e-122 448.0
19 TraesCS3B01G061400 chr4A 84.454 476 43 15 1984 2457 549789976 549790422 8.080000e-120 440.0
20 TraesCS3B01G061400 chr4A 84.034 476 45 13 1984 2457 598281512 598281958 1.750000e-116 429.0
21 TraesCS3B01G061400 chr7B 87.147 778 68 12 1685 2459 665490128 665490876 0.000000e+00 854.0
22 TraesCS3B01G061400 chr7B 88.005 742 56 16 1721 2457 728924588 728925301 0.000000e+00 846.0
23 TraesCS3B01G061400 chr5B 87.018 778 71 13 1685 2459 169510018 169510768 0.000000e+00 850.0
24 TraesCS3B01G061400 chr5B 87.995 733 56 12 1729 2457 392923962 392923258 0.000000e+00 837.0
25 TraesCS3B01G061400 chr6B 86.194 775 77 11 1690 2462 666654692 666653946 0.000000e+00 811.0
26 TraesCS3B01G061400 chr3D 80.987 952 121 30 974 1902 20708406 20707492 0.000000e+00 701.0
27 TraesCS3B01G061400 chr3D 85.577 104 11 2 1000 1101 20232904 20232803 3.350000e-19 106.0
28 TraesCS3B01G061400 chr3D 88.750 80 6 1 991 1070 20555549 20555473 7.250000e-16 95.3
29 TraesCS3B01G061400 chr6A 91.827 416 31 3 1685 2100 36994 36582 5.900000e-161 577.0
30 TraesCS3B01G061400 chr7A 84.664 476 42 13 1984 2457 288914702 288915148 1.740000e-121 446.0
31 TraesCS3B01G061400 chr1A 84.664 476 42 15 1984 2457 38158751 38158305 1.740000e-121 446.0
32 TraesCS3B01G061400 chr5A 84.244 476 44 15 1984 2457 405518685 405519131 3.760000e-118 435.0
33 TraesCS3B01G061400 chrUn 87.591 274 29 5 2191 2462 254102856 254102586 1.840000e-81 313.0


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 TraesCS3B01G061400 chr3B 33297626 33300087 2461 True 4547.00 4547 100.0000 1 2462 1 chr3B.!!$R6 2461
1 TraesCS3B01G061400 chr3B 32991109 32992152 1043 True 808.00 808 81.1630 853 1906 1 chr3B.!!$R4 1053
2 TraesCS3B01G061400 chr3B 33096114 33096992 878 True 599.00 599 79.3960 992 1906 1 chr3B.!!$R5 914
3 TraesCS3B01G061400 chr3B 33333713 33334253 540 True 460.00 460 82.3430 901 1464 1 chr3B.!!$R7 563
4 TraesCS3B01G061400 chr3A 28389891 28392105 2214 True 1296.00 2065 88.5925 220 2462 2 chr3A.!!$R8 2242
5 TraesCS3B01G061400 chr3A 28230465 28231645 1180 True 946.00 946 81.8030 744 1906 1 chr3A.!!$R4 1162
6 TraesCS3B01G061400 chr3A 28370386 28371220 834 True 922.00 922 86.7770 1304 2139 1 chr3A.!!$R5 835
7 TraesCS3B01G061400 chr3A 28322266 28322930 664 True 340.75 625 91.0745 854 1499 2 chr3A.!!$R7 645
8 TraesCS3B01G061400 chr4A 723214205 723214956 751 True 893.00 893 87.9330 1685 2462 1 chr4A.!!$R2 777
9 TraesCS3B01G061400 chr7B 665490128 665490876 748 False 854.00 854 87.1470 1685 2459 1 chr7B.!!$F1 774
10 TraesCS3B01G061400 chr7B 728924588 728925301 713 False 846.00 846 88.0050 1721 2457 1 chr7B.!!$F2 736
11 TraesCS3B01G061400 chr5B 169510018 169510768 750 False 850.00 850 87.0180 1685 2459 1 chr5B.!!$F1 774
12 TraesCS3B01G061400 chr5B 392923258 392923962 704 True 837.00 837 87.9950 1729 2457 1 chr5B.!!$R1 728
13 TraesCS3B01G061400 chr6B 666653946 666654692 746 True 811.00 811 86.1940 1690 2462 1 chr6B.!!$R1 772
14 TraesCS3B01G061400 chr3D 20707492 20708406 914 True 701.00 701 80.9870 974 1902 1 chr3D.!!$R3 928

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
741 777 0.03101 AACCAGGCTAGGGAGTAGGG 60.031 60.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 2087 0.254178 ATCCTGGCAGTAGCACCAAG 59.746 55.0 14.43 0.0 44.61 3.61 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.425577 CATTGGACAGAAGTTTGGTAGC 57.574 45.455 0.00 0.00 0.00 3.58
22 23 3.569194 TTGGACAGAAGTTTGGTAGCA 57.431 42.857 0.00 0.00 0.00 3.49
23 24 3.569194 TGGACAGAAGTTTGGTAGCAA 57.431 42.857 2.54 2.54 0.00 3.91
24 25 3.476552 TGGACAGAAGTTTGGTAGCAAG 58.523 45.455 7.51 0.00 0.00 4.01
25 26 2.226674 GGACAGAAGTTTGGTAGCAAGC 59.773 50.000 12.96 12.96 0.00 4.01
26 27 2.878406 GACAGAAGTTTGGTAGCAAGCA 59.122 45.455 21.22 0.00 0.00 3.91
27 28 3.490348 ACAGAAGTTTGGTAGCAAGCAT 58.510 40.909 21.22 11.21 32.06 3.79
28 29 3.503748 ACAGAAGTTTGGTAGCAAGCATC 59.496 43.478 21.22 18.49 32.06 3.91
29 30 3.755378 CAGAAGTTTGGTAGCAAGCATCT 59.245 43.478 19.26 19.26 32.06 2.90
30 31 4.217118 CAGAAGTTTGGTAGCAAGCATCTT 59.783 41.667 21.46 16.61 33.49 2.40
31 32 4.457257 AGAAGTTTGGTAGCAAGCATCTTC 59.543 41.667 19.26 20.74 40.57 2.87
32 33 3.754965 AGTTTGGTAGCAAGCATCTTCA 58.245 40.909 21.22 0.00 32.06 3.02
33 34 3.755378 AGTTTGGTAGCAAGCATCTTCAG 59.245 43.478 21.22 0.00 32.06 3.02
34 35 3.423539 TTGGTAGCAAGCATCTTCAGT 57.576 42.857 2.54 0.00 32.06 3.41
35 36 4.551702 TTGGTAGCAAGCATCTTCAGTA 57.448 40.909 2.54 0.00 32.06 2.74
36 37 4.760530 TGGTAGCAAGCATCTTCAGTAT 57.239 40.909 0.00 0.00 0.00 2.12
37 38 4.697514 TGGTAGCAAGCATCTTCAGTATC 58.302 43.478 0.00 0.00 0.00 2.24
38 39 4.406972 TGGTAGCAAGCATCTTCAGTATCT 59.593 41.667 0.00 0.00 0.00 1.98
39 40 4.749099 GGTAGCAAGCATCTTCAGTATCTG 59.251 45.833 0.00 0.00 0.00 2.90
40 41 3.806380 AGCAAGCATCTTCAGTATCTGG 58.194 45.455 0.00 0.00 31.51 3.86
41 42 3.453717 AGCAAGCATCTTCAGTATCTGGA 59.546 43.478 0.00 0.00 31.51 3.86
42 43 3.559242 GCAAGCATCTTCAGTATCTGGAC 59.441 47.826 0.00 0.00 31.51 4.02
43 44 4.682859 GCAAGCATCTTCAGTATCTGGACT 60.683 45.833 0.00 0.00 31.51 3.85
44 45 4.669206 AGCATCTTCAGTATCTGGACTG 57.331 45.455 0.00 0.00 46.90 3.51
45 46 4.029520 AGCATCTTCAGTATCTGGACTGT 58.970 43.478 3.66 0.00 45.88 3.55
46 47 4.118410 GCATCTTCAGTATCTGGACTGTG 58.882 47.826 3.66 0.00 45.88 3.66
47 48 3.876274 TCTTCAGTATCTGGACTGTGC 57.124 47.619 3.66 0.00 45.88 4.57
48 49 3.435275 TCTTCAGTATCTGGACTGTGCT 58.565 45.455 0.00 0.00 45.88 4.40
49 50 3.834813 TCTTCAGTATCTGGACTGTGCTT 59.165 43.478 0.00 0.00 45.88 3.91
50 51 3.599730 TCAGTATCTGGACTGTGCTTG 57.400 47.619 0.00 0.00 45.88 4.01
51 52 2.234661 TCAGTATCTGGACTGTGCTTGG 59.765 50.000 0.00 0.00 45.88 3.61
52 53 1.065854 AGTATCTGGACTGTGCTTGGC 60.066 52.381 0.00 0.00 0.00 4.52
53 54 0.253044 TATCTGGACTGTGCTTGGCC 59.747 55.000 0.00 0.00 0.00 5.36
54 55 1.495579 ATCTGGACTGTGCTTGGCCT 61.496 55.000 3.32 0.00 0.00 5.19
55 56 1.970114 CTGGACTGTGCTTGGCCTG 60.970 63.158 3.32 0.00 0.00 4.85
56 57 2.401699 CTGGACTGTGCTTGGCCTGA 62.402 60.000 3.32 0.00 0.00 3.86
57 58 1.228245 GGACTGTGCTTGGCCTGAA 60.228 57.895 3.32 0.00 0.00 3.02
58 59 0.823356 GGACTGTGCTTGGCCTGAAA 60.823 55.000 3.32 0.00 0.00 2.69
59 60 1.251251 GACTGTGCTTGGCCTGAAAT 58.749 50.000 3.32 0.00 0.00 2.17
60 61 0.963962 ACTGTGCTTGGCCTGAAATG 59.036 50.000 3.32 0.00 0.00 2.32
61 62 1.250328 CTGTGCTTGGCCTGAAATGA 58.750 50.000 3.32 0.00 0.00 2.57
62 63 1.614903 CTGTGCTTGGCCTGAAATGAA 59.385 47.619 3.32 0.00 0.00 2.57
63 64 2.036217 CTGTGCTTGGCCTGAAATGAAA 59.964 45.455 3.32 0.00 0.00 2.69
64 65 2.633967 TGTGCTTGGCCTGAAATGAAAT 59.366 40.909 3.32 0.00 0.00 2.17
65 66 3.071312 TGTGCTTGGCCTGAAATGAAATT 59.929 39.130 3.32 0.00 38.98 1.82
66 67 3.681417 GTGCTTGGCCTGAAATGAAATTC 59.319 43.478 3.32 0.00 33.67 2.17
67 68 2.925563 GCTTGGCCTGAAATGAAATTCG 59.074 45.455 3.32 0.00 33.67 3.34
68 69 3.514645 CTTGGCCTGAAATGAAATTCGG 58.485 45.455 3.32 0.00 33.67 4.30
73 74 4.981806 CCTGAAATGAAATTCGGGCTAA 57.018 40.909 2.20 0.00 46.06 3.09
74 75 5.323371 CCTGAAATGAAATTCGGGCTAAA 57.677 39.130 2.20 0.00 46.06 1.85
75 76 5.343249 CCTGAAATGAAATTCGGGCTAAAG 58.657 41.667 2.20 0.00 46.06 1.85
76 77 5.125417 CCTGAAATGAAATTCGGGCTAAAGA 59.875 40.000 2.20 0.00 46.06 2.52
77 78 6.350110 CCTGAAATGAAATTCGGGCTAAAGAA 60.350 38.462 2.20 0.00 46.06 2.52
78 79 7.169158 TGAAATGAAATTCGGGCTAAAGAAT 57.831 32.000 0.00 0.00 33.67 2.40
79 80 7.610865 TGAAATGAAATTCGGGCTAAAGAATT 58.389 30.769 0.00 0.00 45.66 2.17
84 85 5.722021 AATTCGGGCTAAAGAATTTGTGT 57.278 34.783 0.00 0.00 42.41 3.72
85 86 5.722021 ATTCGGGCTAAAGAATTTGTGTT 57.278 34.783 0.00 0.00 39.63 3.32
86 87 4.759516 TCGGGCTAAAGAATTTGTGTTC 57.240 40.909 0.00 0.00 39.63 3.18
87 88 4.138290 TCGGGCTAAAGAATTTGTGTTCA 58.862 39.130 0.00 0.00 39.63 3.18
88 89 4.023536 TCGGGCTAAAGAATTTGTGTTCAC 60.024 41.667 0.00 0.00 39.63 3.18
89 90 4.226761 GGGCTAAAGAATTTGTGTTCACG 58.773 43.478 0.00 0.00 39.63 4.35
90 91 4.023536 GGGCTAAAGAATTTGTGTTCACGA 60.024 41.667 0.00 0.00 39.63 4.35
91 92 5.335661 GGGCTAAAGAATTTGTGTTCACGAT 60.336 40.000 0.00 0.00 39.63 3.73
92 93 5.569059 GGCTAAAGAATTTGTGTTCACGATG 59.431 40.000 0.00 0.00 39.63 3.84
93 94 6.370593 GCTAAAGAATTTGTGTTCACGATGA 58.629 36.000 0.00 0.00 39.63 2.92
94 95 6.855914 GCTAAAGAATTTGTGTTCACGATGAA 59.144 34.615 0.00 0.00 39.63 2.57
95 96 7.149128 GCTAAAGAATTTGTGTTCACGATGAAC 60.149 37.037 18.17 18.17 46.87 3.18
96 97 5.977129 AAAGAATTTGTGTTCACGATGAACC 59.023 36.000 20.58 14.87 45.89 3.62
97 98 6.405286 AAAGAATTTGTGTTCACGATGAACCA 60.405 34.615 20.58 16.46 45.89 3.67
98 99 7.684187 AAAGAATTTGTGTTCACGATGAACCAT 60.684 33.333 20.58 10.06 45.89 3.55
104 105 3.610040 TTCACGATGAACCATGCTAGT 57.390 42.857 0.00 0.00 30.26 2.57
105 106 3.165058 TCACGATGAACCATGCTAGTC 57.835 47.619 0.00 0.00 0.00 2.59
106 107 2.760650 TCACGATGAACCATGCTAGTCT 59.239 45.455 0.00 0.00 0.00 3.24
107 108 2.862536 CACGATGAACCATGCTAGTCTG 59.137 50.000 0.00 0.00 0.00 3.51
108 109 2.497675 ACGATGAACCATGCTAGTCTGT 59.502 45.455 0.00 0.00 0.00 3.41
109 110 3.119291 CGATGAACCATGCTAGTCTGTC 58.881 50.000 0.00 0.00 0.00 3.51
110 111 3.181482 CGATGAACCATGCTAGTCTGTCT 60.181 47.826 0.00 0.00 0.00 3.41
111 112 3.599730 TGAACCATGCTAGTCTGTCTG 57.400 47.619 0.00 0.00 0.00 3.51
112 113 2.275318 GAACCATGCTAGTCTGTCTGC 58.725 52.381 0.00 0.00 0.00 4.26
113 114 1.566211 ACCATGCTAGTCTGTCTGCT 58.434 50.000 0.00 0.00 0.00 4.24
114 115 1.905215 ACCATGCTAGTCTGTCTGCTT 59.095 47.619 0.00 0.00 0.00 3.91
115 116 2.277969 CCATGCTAGTCTGTCTGCTTG 58.722 52.381 0.00 0.00 0.00 4.01
116 117 2.277969 CATGCTAGTCTGTCTGCTTGG 58.722 52.381 0.00 0.00 0.00 3.61
117 118 0.036952 TGCTAGTCTGTCTGCTTGGC 60.037 55.000 0.00 0.00 0.00 4.52
118 119 0.036952 GCTAGTCTGTCTGCTTGGCA 60.037 55.000 0.00 0.00 36.92 4.92
119 120 1.609061 GCTAGTCTGTCTGCTTGGCAA 60.609 52.381 0.00 0.00 38.41 4.52
120 121 2.344950 CTAGTCTGTCTGCTTGGCAAG 58.655 52.381 22.75 22.75 38.41 4.01
121 122 0.471617 AGTCTGTCTGCTTGGCAAGT 59.528 50.000 26.71 2.26 38.41 3.16
122 123 1.694150 AGTCTGTCTGCTTGGCAAGTA 59.306 47.619 26.71 22.05 38.41 2.24
123 124 1.801178 GTCTGTCTGCTTGGCAAGTAC 59.199 52.381 26.71 21.23 38.41 2.73
124 125 1.694150 TCTGTCTGCTTGGCAAGTACT 59.306 47.619 26.71 0.00 38.41 2.73
125 126 2.072298 CTGTCTGCTTGGCAAGTACTC 58.928 52.381 26.71 16.04 38.41 2.59
126 127 1.270839 TGTCTGCTTGGCAAGTACTCC 60.271 52.381 26.71 11.44 38.41 3.85
127 128 0.324943 TCTGCTTGGCAAGTACTCCC 59.675 55.000 26.71 10.75 38.41 4.30
128 129 0.326264 CTGCTTGGCAAGTACTCCCT 59.674 55.000 26.71 0.00 38.41 4.20
129 130 0.771127 TGCTTGGCAAGTACTCCCTT 59.229 50.000 26.71 0.00 34.76 3.95
130 131 1.271379 TGCTTGGCAAGTACTCCCTTC 60.271 52.381 26.71 8.68 34.76 3.46
131 132 1.726853 CTTGGCAAGTACTCCCTTCG 58.273 55.000 19.07 0.00 0.00 3.79
132 133 1.002087 CTTGGCAAGTACTCCCTTCGT 59.998 52.381 19.07 0.00 0.00 3.85
133 134 0.606604 TGGCAAGTACTCCCTTCGTC 59.393 55.000 12.28 0.00 0.00 4.20
134 135 0.108281 GGCAAGTACTCCCTTCGTCC 60.108 60.000 0.00 0.00 0.00 4.79
135 136 0.108281 GCAAGTACTCCCTTCGTCCC 60.108 60.000 0.00 0.00 0.00 4.46
136 137 1.263356 CAAGTACTCCCTTCGTCCCA 58.737 55.000 0.00 0.00 0.00 4.37
137 138 1.621814 CAAGTACTCCCTTCGTCCCAA 59.378 52.381 0.00 0.00 0.00 4.12
138 139 2.019807 AGTACTCCCTTCGTCCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
139 140 2.332117 AGTACTCCCTTCGTCCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
140 141 2.910977 AGTACTCCCTTCGTCCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
141 142 4.098894 AGTACTCCCTTCGTCCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
142 143 4.720273 AGTACTCCCTTCGTCCCAAAATAT 59.280 41.667 0.00 0.00 0.00 1.28
143 144 3.886123 ACTCCCTTCGTCCCAAAATATG 58.114 45.455 0.00 0.00 0.00 1.78
144 145 3.265995 ACTCCCTTCGTCCCAAAATATGT 59.734 43.478 0.00 0.00 0.00 2.29
145 146 4.472108 ACTCCCTTCGTCCCAAAATATGTA 59.528 41.667 0.00 0.00 0.00 2.29
146 147 5.132144 ACTCCCTTCGTCCCAAAATATGTAT 59.868 40.000 0.00 0.00 0.00 2.29
147 148 5.617252 TCCCTTCGTCCCAAAATATGTATC 58.383 41.667 0.00 0.00 0.00 2.24
148 149 5.368523 TCCCTTCGTCCCAAAATATGTATCT 59.631 40.000 0.00 0.00 0.00 1.98
149 150 5.701290 CCCTTCGTCCCAAAATATGTATCTC 59.299 44.000 0.00 0.00 0.00 2.75
150 151 6.288294 CCTTCGTCCCAAAATATGTATCTCA 58.712 40.000 0.00 0.00 0.00 3.27
151 152 6.765989 CCTTCGTCCCAAAATATGTATCTCAA 59.234 38.462 0.00 0.00 0.00 3.02
152 153 7.041780 CCTTCGTCCCAAAATATGTATCTCAAG 60.042 40.741 0.00 0.00 0.00 3.02
153 154 6.884832 TCGTCCCAAAATATGTATCTCAAGT 58.115 36.000 0.00 0.00 0.00 3.16
154 155 7.335627 TCGTCCCAAAATATGTATCTCAAGTT 58.664 34.615 0.00 0.00 0.00 2.66
155 156 8.479689 TCGTCCCAAAATATGTATCTCAAGTTA 58.520 33.333 0.00 0.00 0.00 2.24
156 157 9.104965 CGTCCCAAAATATGTATCTCAAGTTAA 57.895 33.333 0.00 0.00 0.00 2.01
232 233 4.439253 AGGGAGTATATTTGGCAGAACC 57.561 45.455 0.00 0.00 39.84 3.62
279 280 1.329292 TGTCTTGAAAACCTGCGTTCG 59.671 47.619 0.00 0.00 0.00 3.95
280 281 0.941542 TCTTGAAAACCTGCGTTCGG 59.058 50.000 0.00 0.00 0.00 4.30
286 287 2.951475 AAACCTGCGTTCGGGCAAGA 62.951 55.000 0.75 0.00 43.39 3.02
308 309 3.266772 ACAGTGGGTATCATGAACATGGT 59.733 43.478 13.67 9.92 39.24 3.55
312 313 2.174639 GGGTATCATGAACATGGTGGGA 59.825 50.000 13.67 0.00 39.24 4.37
323 324 3.134127 GGTGGGAGCATCGGCAAC 61.134 66.667 0.00 0.00 44.61 4.17
337 338 1.299926 GCAACGGTGAGTCTGTCGT 60.300 57.895 3.55 0.00 34.09 4.34
344 345 1.785430 GGTGAGTCTGTCGTCGTTTTC 59.215 52.381 0.00 0.00 0.00 2.29
345 346 2.456989 GTGAGTCTGTCGTCGTTTTCA 58.543 47.619 0.00 0.00 0.00 2.69
346 347 2.855963 GTGAGTCTGTCGTCGTTTTCAA 59.144 45.455 0.00 0.00 0.00 2.69
347 348 2.855963 TGAGTCTGTCGTCGTTTTCAAC 59.144 45.455 0.00 0.00 0.00 3.18
369 370 5.243207 ACGTTAGGACAAAATTCTACCTGG 58.757 41.667 0.00 0.00 32.90 4.45
371 372 5.254115 GTTAGGACAAAATTCTACCTGGCT 58.746 41.667 0.00 0.00 32.90 4.75
376 377 5.453567 ACAAAATTCTACCTGGCTTTGAC 57.546 39.130 0.00 0.00 0.00 3.18
398 399 2.496899 AGCCGTGTTCCAAGATGAAT 57.503 45.000 0.00 0.00 0.00 2.57
411 412 2.187958 AGATGAATGAACACGGAGGGA 58.812 47.619 0.00 0.00 0.00 4.20
425 426 1.039856 GAGGGAGAGAGAGCATGGAC 58.960 60.000 0.00 0.00 0.00 4.02
432 433 3.435275 AGAGAGAGCATGGACAACAGTA 58.565 45.455 0.00 0.00 0.00 2.74
433 434 3.834813 AGAGAGAGCATGGACAACAGTAA 59.165 43.478 0.00 0.00 0.00 2.24
445 446 2.218603 CAACAGTAAGGTCTTGCCGTT 58.781 47.619 0.00 0.00 43.70 4.44
477 478 0.035343 GGCCTAAGACAGAACCCCAC 60.035 60.000 0.00 0.00 0.00 4.61
512 513 4.627058 CATTTCCAAACCCAAACAGTACC 58.373 43.478 0.00 0.00 0.00 3.34
516 517 0.184211 AAACCCAAACAGTACCGCCT 59.816 50.000 0.00 0.00 0.00 5.52
520 521 1.666553 CAAACAGTACCGCCTGCGA 60.667 57.895 13.94 0.00 42.83 5.10
532 533 2.110967 CCTGCGACATCTTGGCCTG 61.111 63.158 3.32 0.00 0.00 4.85
621 624 2.348998 CCCTGCAAGCGTTCCTCT 59.651 61.111 0.00 0.00 0.00 3.69
644 647 1.406887 CCGATTCCCCGATTTGACTGT 60.407 52.381 0.00 0.00 0.00 3.55
645 648 2.356135 CGATTCCCCGATTTGACTGTT 58.644 47.619 0.00 0.00 0.00 3.16
646 649 3.527533 CGATTCCCCGATTTGACTGTTA 58.472 45.455 0.00 0.00 0.00 2.41
653 689 2.744202 CCGATTTGACTGTTAGCAAGCT 59.256 45.455 0.00 0.00 0.00 3.74
660 696 3.249917 GACTGTTAGCAAGCTGAGACTC 58.750 50.000 4.53 0.00 0.00 3.36
666 702 1.066286 AGCAAGCTGAGACTCATGACC 60.066 52.381 5.42 0.00 0.00 4.02
741 777 0.031010 AACCAGGCTAGGGAGTAGGG 60.031 60.000 0.00 0.00 0.00 3.53
742 778 0.929734 ACCAGGCTAGGGAGTAGGGA 60.930 60.000 0.00 0.00 0.00 4.20
755 791 3.833070 GGAGTAGGGAGAGAAGTGTGAAA 59.167 47.826 0.00 0.00 0.00 2.69
764 800 1.070289 AGAAGTGTGAAACCGGACTCC 59.930 52.381 9.46 0.00 34.36 3.85
773 809 2.436115 CCGGACTCCGCTTTTCCC 60.436 66.667 12.37 0.00 46.86 3.97
793 829 2.270527 GCCAAGGCCTCCTCAGTC 59.729 66.667 5.23 0.00 30.89 3.51
794 830 2.993853 CCAAGGCCTCCTCAGTCC 59.006 66.667 5.23 0.00 30.89 3.85
795 831 1.614824 CCAAGGCCTCCTCAGTCCT 60.615 63.158 5.23 0.00 30.89 3.85
828 864 3.791539 GCACGTGCTCATCCTCTG 58.208 61.111 32.55 0.00 38.21 3.35
829 865 2.459442 GCACGTGCTCATCCTCTGC 61.459 63.158 32.55 1.36 38.21 4.26
850 886 1.470979 GCACCCGGAGCATATATACCG 60.471 57.143 0.73 14.29 44.16 4.02
925 962 1.341383 GGTGCACCTCCAATCCAGATT 60.341 52.381 29.12 0.00 0.00 2.40
980 1028 5.273208 AGAAAACAGATAGAGGTAGCCAGA 58.727 41.667 0.00 0.00 0.00 3.86
1545 1675 4.020218 ACACTGCCTCTGCTTCTGTTAATA 60.020 41.667 0.00 0.00 38.71 0.98
1546 1676 4.937620 CACTGCCTCTGCTTCTGTTAATAA 59.062 41.667 0.00 0.00 38.71 1.40
1550 1680 6.003950 TGCCTCTGCTTCTGTTAATAAGTTT 58.996 36.000 0.00 0.00 38.71 2.66
1556 1686 8.349983 TCTGCTTCTGTTAATAAGTTTTGTTCC 58.650 33.333 0.00 0.00 0.00 3.62
1559 1689 7.112984 GCTTCTGTTAATAAGTTTTGTTCCGTG 59.887 37.037 0.00 0.00 0.00 4.94
1589 1750 7.257722 TGCTTTTCTACTCTGTTTTTCCTTTG 58.742 34.615 0.00 0.00 0.00 2.77
1596 1757 5.667466 ACTCTGTTTTTCCTTTGTCGTCTA 58.333 37.500 0.00 0.00 0.00 2.59
1617 1779 2.301346 CTGAAACTGAAAGGCACCTGT 58.699 47.619 0.00 0.00 39.30 4.00
1619 1781 3.476552 TGAAACTGAAAGGCACCTGTAG 58.523 45.455 0.00 0.00 39.30 2.74
1644 1806 0.471780 TGTGAGAGCCAGGAACCAGA 60.472 55.000 0.00 0.00 0.00 3.86
1645 1807 0.908198 GTGAGAGCCAGGAACCAGAT 59.092 55.000 0.00 0.00 0.00 2.90
1648 1810 1.280421 GAGAGCCAGGAACCAGATTGT 59.720 52.381 0.00 0.00 0.00 2.71
1712 1881 0.881118 CGGCACAAATTACAGCACCT 59.119 50.000 0.00 0.00 0.00 4.00
1725 1894 4.584638 ACAGCACCTGGGATATTTTACA 57.415 40.909 0.00 0.00 35.51 2.41
1734 1905 6.603201 ACCTGGGATATTTTACAACTCATGTG 59.397 38.462 0.00 0.00 43.77 3.21
1757 1932 6.250527 GTGTGTGTAGTTGCTTGTTTTTACTG 59.749 38.462 0.00 0.00 0.00 2.74
1784 1962 4.905429 TGTGGCTGCTTTCTTCTTGTATA 58.095 39.130 0.00 0.00 0.00 1.47
1825 2004 7.463961 AAAGCATTTCTGAGATCAAAGATGT 57.536 32.000 0.00 0.00 27.08 3.06
1835 2014 7.551974 TCTGAGATCAAAGATGTTTCCTCATTC 59.448 37.037 10.18 0.00 29.98 2.67
1841 2020 6.813649 TCAAAGATGTTTCCTCATTCTCTACG 59.186 38.462 0.00 0.00 0.00 3.51
1846 2025 3.887621 TTCCTCATTCTCTACGGTTGG 57.112 47.619 0.00 0.00 0.00 3.77
1906 2087 1.202818 ACTCAGTTCCAGGGCTTGAAC 60.203 52.381 0.00 2.31 40.88 3.18
2111 2293 0.613012 GCTTGAAAGAGCCCACCCAT 60.613 55.000 0.00 0.00 36.66 4.00
2112 2294 1.340991 GCTTGAAAGAGCCCACCCATA 60.341 52.381 0.00 0.00 36.66 2.74
2113 2295 2.883888 GCTTGAAAGAGCCCACCCATAA 60.884 50.000 0.00 0.00 36.66 1.90
2116 2298 3.631250 TGAAAGAGCCCACCCATAATTC 58.369 45.455 0.00 0.00 0.00 2.17
2145 2327 2.843701 CCTGAACCATCATACCTGCTC 58.156 52.381 0.00 0.00 34.37 4.26
2162 2344 4.958509 CTGCTCAACATATGATCAGGTCT 58.041 43.478 10.38 0.00 44.74 3.85
2171 2353 7.976135 ACATATGATCAGGTCTAAAATCTGC 57.024 36.000 10.38 0.00 0.00 4.26
2175 2358 7.976135 ATGATCAGGTCTAAAATCTGCATAC 57.024 36.000 0.09 0.00 0.00 2.39
2181 2364 7.334421 TCAGGTCTAAAATCTGCATACTGTTTC 59.666 37.037 0.00 0.00 0.00 2.78
2183 2366 7.335422 AGGTCTAAAATCTGCATACTGTTTCTG 59.665 37.037 0.00 0.00 0.00 3.02
2189 2373 7.935338 AATCTGCATACTGTTTCTGTTTTTG 57.065 32.000 0.00 0.00 0.00 2.44
2192 2376 7.319646 TCTGCATACTGTTTCTGTTTTTGTTT 58.680 30.769 0.00 0.00 0.00 2.83
2193 2377 7.816995 TCTGCATACTGTTTCTGTTTTTGTTTT 59.183 29.630 0.00 0.00 0.00 2.43
2194 2378 8.316640 TGCATACTGTTTCTGTTTTTGTTTTT 57.683 26.923 0.00 0.00 0.00 1.94
2195 2379 8.439286 TGCATACTGTTTCTGTTTTTGTTTTTC 58.561 29.630 0.00 0.00 0.00 2.29
2196 2380 8.655970 GCATACTGTTTCTGTTTTTGTTTTTCT 58.344 29.630 0.00 0.00 0.00 2.52
2204 2388 8.553459 TTCTGTTTTTGTTTTTCTTTGGCATA 57.447 26.923 0.00 0.00 0.00 3.14
2219 2403 2.092323 GGCATAGAAAGGTTCACCCAC 58.908 52.381 0.00 0.00 36.42 4.61
2230 2414 4.344104 AGGTTCACCCACATTTCCATTAG 58.656 43.478 0.00 0.00 36.42 1.73
2241 2425 5.126061 CACATTTCCATTAGGAGAAACCAGG 59.874 44.000 0.00 0.00 46.74 4.45
2324 2509 3.081061 GACAGGTGGCACATATGTTTCA 58.919 45.455 20.82 4.73 44.52 2.69
2368 2554 7.675161 TTTTCTAGAGGGTGATGATGTCATA 57.325 36.000 0.00 0.00 39.48 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.820467 TGCTACCAAACTTCTGTCCAATG 59.180 43.478 0.00 0.00 0.00 2.82
1 2 4.098914 TGCTACCAAACTTCTGTCCAAT 57.901 40.909 0.00 0.00 0.00 3.16
5 6 2.878406 TGCTTGCTACCAAACTTCTGTC 59.122 45.455 0.00 0.00 0.00 3.51
6 7 2.930950 TGCTTGCTACCAAACTTCTGT 58.069 42.857 0.00 0.00 0.00 3.41
8 9 4.026356 AGATGCTTGCTACCAAACTTCT 57.974 40.909 0.00 0.00 30.92 2.85
9 10 4.216257 TGAAGATGCTTGCTACCAAACTTC 59.784 41.667 0.00 0.00 33.22 3.01
11 12 3.754965 TGAAGATGCTTGCTACCAAACT 58.245 40.909 0.00 0.00 0.00 2.66
12 13 3.503748 ACTGAAGATGCTTGCTACCAAAC 59.496 43.478 0.00 0.00 0.00 2.93
13 14 3.754965 ACTGAAGATGCTTGCTACCAAA 58.245 40.909 0.00 0.00 0.00 3.28
14 15 3.423539 ACTGAAGATGCTTGCTACCAA 57.576 42.857 0.00 0.00 0.00 3.67
15 16 4.406972 AGATACTGAAGATGCTTGCTACCA 59.593 41.667 0.00 0.00 0.00 3.25
16 17 4.749099 CAGATACTGAAGATGCTTGCTACC 59.251 45.833 0.00 0.00 32.44 3.18
17 18 4.749099 CCAGATACTGAAGATGCTTGCTAC 59.251 45.833 0.00 0.00 32.44 3.58
18 19 4.651045 TCCAGATACTGAAGATGCTTGCTA 59.349 41.667 0.00 0.00 32.44 3.49
19 20 3.453717 TCCAGATACTGAAGATGCTTGCT 59.546 43.478 0.00 0.00 32.44 3.91
20 21 3.559242 GTCCAGATACTGAAGATGCTTGC 59.441 47.826 0.00 0.00 32.44 4.01
21 22 5.021033 AGTCCAGATACTGAAGATGCTTG 57.979 43.478 0.00 0.00 32.44 4.01
32 33 1.065854 GCCAAGCACAGTCCAGATACT 60.066 52.381 0.00 0.00 0.00 2.12
33 34 1.373570 GCCAAGCACAGTCCAGATAC 58.626 55.000 0.00 0.00 0.00 2.24
34 35 0.253044 GGCCAAGCACAGTCCAGATA 59.747 55.000 0.00 0.00 0.00 1.98
35 36 1.001641 GGCCAAGCACAGTCCAGAT 60.002 57.895 0.00 0.00 0.00 2.90
36 37 2.149383 AGGCCAAGCACAGTCCAGA 61.149 57.895 5.01 0.00 0.00 3.86
37 38 1.970114 CAGGCCAAGCACAGTCCAG 60.970 63.158 5.01 0.00 0.00 3.86
38 39 1.993701 TTCAGGCCAAGCACAGTCCA 61.994 55.000 5.01 0.00 0.00 4.02
39 40 0.823356 TTTCAGGCCAAGCACAGTCC 60.823 55.000 5.01 0.00 0.00 3.85
40 41 1.068055 CATTTCAGGCCAAGCACAGTC 60.068 52.381 5.01 0.00 0.00 3.51
41 42 0.963962 CATTTCAGGCCAAGCACAGT 59.036 50.000 5.01 0.00 0.00 3.55
42 43 1.250328 TCATTTCAGGCCAAGCACAG 58.750 50.000 5.01 0.00 0.00 3.66
43 44 1.702182 TTCATTTCAGGCCAAGCACA 58.298 45.000 5.01 0.00 0.00 4.57
44 45 2.818130 TTTCATTTCAGGCCAAGCAC 57.182 45.000 5.01 0.00 0.00 4.40
45 46 3.614630 CGAATTTCATTTCAGGCCAAGCA 60.615 43.478 5.01 0.00 0.00 3.91
46 47 2.925563 CGAATTTCATTTCAGGCCAAGC 59.074 45.455 5.01 0.00 0.00 4.01
47 48 3.514645 CCGAATTTCATTTCAGGCCAAG 58.485 45.455 5.01 0.00 0.00 3.61
48 49 2.233431 CCCGAATTTCATTTCAGGCCAA 59.767 45.455 5.01 0.00 0.00 4.52
49 50 1.824230 CCCGAATTTCATTTCAGGCCA 59.176 47.619 5.01 0.00 0.00 5.36
50 51 1.471501 GCCCGAATTTCATTTCAGGCC 60.472 52.381 0.00 0.00 41.41 5.19
51 52 1.478105 AGCCCGAATTTCATTTCAGGC 59.522 47.619 3.74 3.74 45.58 4.85
52 53 4.981806 TTAGCCCGAATTTCATTTCAGG 57.018 40.909 0.00 0.00 0.00 3.86
53 54 6.194796 TCTTTAGCCCGAATTTCATTTCAG 57.805 37.500 0.00 0.00 0.00 3.02
54 55 6.582677 TTCTTTAGCCCGAATTTCATTTCA 57.417 33.333 0.00 0.00 0.00 2.69
55 56 8.382875 CAAATTCTTTAGCCCGAATTTCATTTC 58.617 33.333 6.93 0.00 43.91 2.17
56 57 7.877612 ACAAATTCTTTAGCCCGAATTTCATTT 59.122 29.630 6.93 0.00 43.91 2.32
57 58 7.331687 CACAAATTCTTTAGCCCGAATTTCATT 59.668 33.333 6.93 0.00 43.91 2.57
58 59 6.813152 CACAAATTCTTTAGCCCGAATTTCAT 59.187 34.615 6.93 0.00 43.91 2.57
59 60 6.155827 CACAAATTCTTTAGCCCGAATTTCA 58.844 36.000 6.93 0.00 43.91 2.69
60 61 6.156519 ACACAAATTCTTTAGCCCGAATTTC 58.843 36.000 6.93 0.00 43.91 2.17
61 62 6.096673 ACACAAATTCTTTAGCCCGAATTT 57.903 33.333 0.00 0.00 45.59 1.82
62 63 5.722021 ACACAAATTCTTTAGCCCGAATT 57.278 34.783 0.00 0.00 40.50 2.17
63 64 5.242838 TGAACACAAATTCTTTAGCCCGAAT 59.757 36.000 0.00 0.00 0.00 3.34
64 65 4.580995 TGAACACAAATTCTTTAGCCCGAA 59.419 37.500 0.00 0.00 0.00 4.30
65 66 4.023536 GTGAACACAAATTCTTTAGCCCGA 60.024 41.667 0.00 0.00 0.00 5.14
66 67 4.226761 GTGAACACAAATTCTTTAGCCCG 58.773 43.478 0.00 0.00 0.00 6.13
67 68 4.023536 TCGTGAACACAAATTCTTTAGCCC 60.024 41.667 5.80 0.00 0.00 5.19
68 69 5.103290 TCGTGAACACAAATTCTTTAGCC 57.897 39.130 5.80 0.00 0.00 3.93
69 70 6.370593 TCATCGTGAACACAAATTCTTTAGC 58.629 36.000 5.80 0.00 0.00 3.09
84 85 3.195610 AGACTAGCATGGTTCATCGTGAA 59.804 43.478 1.12 0.00 33.32 3.18
85 86 2.760650 AGACTAGCATGGTTCATCGTGA 59.239 45.455 1.12 0.00 0.00 4.35
86 87 2.862536 CAGACTAGCATGGTTCATCGTG 59.137 50.000 1.12 0.00 0.00 4.35
87 88 2.497675 ACAGACTAGCATGGTTCATCGT 59.502 45.455 1.12 0.00 0.00 3.73
88 89 3.119291 GACAGACTAGCATGGTTCATCG 58.881 50.000 1.12 0.00 0.00 3.84
89 90 4.118410 CAGACAGACTAGCATGGTTCATC 58.882 47.826 1.12 0.00 0.00 2.92
90 91 3.681034 GCAGACAGACTAGCATGGTTCAT 60.681 47.826 1.12 0.00 0.00 2.57
91 92 2.354103 GCAGACAGACTAGCATGGTTCA 60.354 50.000 1.12 0.00 0.00 3.18
92 93 2.093764 AGCAGACAGACTAGCATGGTTC 60.094 50.000 1.12 0.00 0.00 3.62
93 94 1.905215 AGCAGACAGACTAGCATGGTT 59.095 47.619 1.12 0.00 0.00 3.67
94 95 1.566211 AGCAGACAGACTAGCATGGT 58.434 50.000 1.62 1.62 0.00 3.55
95 96 2.277969 CAAGCAGACAGACTAGCATGG 58.722 52.381 0.00 0.00 0.00 3.66
96 97 2.277969 CCAAGCAGACAGACTAGCATG 58.722 52.381 0.00 0.00 0.00 4.06
97 98 1.406614 GCCAAGCAGACAGACTAGCAT 60.407 52.381 0.00 0.00 0.00 3.79
98 99 0.036952 GCCAAGCAGACAGACTAGCA 60.037 55.000 0.00 0.00 0.00 3.49
99 100 0.036952 TGCCAAGCAGACAGACTAGC 60.037 55.000 0.00 0.00 33.32 3.42
100 101 2.289320 ACTTGCCAAGCAGACAGACTAG 60.289 50.000 3.88 0.00 40.61 2.57
101 102 1.694150 ACTTGCCAAGCAGACAGACTA 59.306 47.619 3.88 0.00 40.61 2.59
102 103 0.471617 ACTTGCCAAGCAGACAGACT 59.528 50.000 3.88 0.00 40.61 3.24
103 104 1.801178 GTACTTGCCAAGCAGACAGAC 59.199 52.381 3.88 0.00 40.61 3.51
104 105 1.694150 AGTACTTGCCAAGCAGACAGA 59.306 47.619 3.88 0.00 40.61 3.41
105 106 2.072298 GAGTACTTGCCAAGCAGACAG 58.928 52.381 3.88 0.00 40.61 3.51
106 107 1.270839 GGAGTACTTGCCAAGCAGACA 60.271 52.381 3.88 0.00 40.61 3.41
107 108 1.443802 GGAGTACTTGCCAAGCAGAC 58.556 55.000 3.88 0.51 40.61 3.51
108 109 0.324943 GGGAGTACTTGCCAAGCAGA 59.675 55.000 3.88 0.00 40.61 4.26
109 110 0.326264 AGGGAGTACTTGCCAAGCAG 59.674 55.000 3.88 0.00 40.61 4.24
110 111 0.771127 AAGGGAGTACTTGCCAAGCA 59.229 50.000 3.88 0.00 40.38 3.91
111 112 1.454201 GAAGGGAGTACTTGCCAAGC 58.546 55.000 3.88 0.00 40.38 4.01
112 113 1.002087 ACGAAGGGAGTACTTGCCAAG 59.998 52.381 2.11 2.11 40.38 3.61
113 114 1.001633 GACGAAGGGAGTACTTGCCAA 59.998 52.381 0.00 0.00 40.38 4.52
114 115 0.606604 GACGAAGGGAGTACTTGCCA 59.393 55.000 0.00 0.00 40.38 4.92
115 116 0.108281 GGACGAAGGGAGTACTTGCC 60.108 60.000 0.00 0.00 37.61 4.52
116 117 0.108281 GGGACGAAGGGAGTACTTGC 60.108 60.000 0.00 0.00 0.00 4.01
117 118 1.263356 TGGGACGAAGGGAGTACTTG 58.737 55.000 0.00 0.00 0.00 3.16
118 119 2.019807 TTGGGACGAAGGGAGTACTT 57.980 50.000 0.00 0.00 0.00 2.24
119 120 2.019807 TTTGGGACGAAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
120 121 2.845363 TTTTGGGACGAAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
121 122 4.472108 ACATATTTTGGGACGAAGGGAGTA 59.528 41.667 0.00 0.00 0.00 2.59
122 123 3.265995 ACATATTTTGGGACGAAGGGAGT 59.734 43.478 0.00 0.00 0.00 3.85
123 124 3.886123 ACATATTTTGGGACGAAGGGAG 58.114 45.455 0.00 0.00 0.00 4.30
124 125 5.368523 AGATACATATTTTGGGACGAAGGGA 59.631 40.000 0.00 0.00 0.00 4.20
125 126 5.621193 AGATACATATTTTGGGACGAAGGG 58.379 41.667 0.00 0.00 0.00 3.95
126 127 6.288294 TGAGATACATATTTTGGGACGAAGG 58.712 40.000 0.00 0.00 0.00 3.46
127 128 7.495934 ACTTGAGATACATATTTTGGGACGAAG 59.504 37.037 0.00 0.00 0.00 3.79
128 129 7.335627 ACTTGAGATACATATTTTGGGACGAA 58.664 34.615 0.00 0.00 0.00 3.85
129 130 6.884832 ACTTGAGATACATATTTTGGGACGA 58.115 36.000 0.00 0.00 0.00 4.20
130 131 7.553881 AACTTGAGATACATATTTTGGGACG 57.446 36.000 0.00 0.00 0.00 4.79
200 201 9.131791 GCCAAATATACTCCCTTCATTCTAAAA 57.868 33.333 0.00 0.00 0.00 1.52
201 202 8.278639 TGCCAAATATACTCCCTTCATTCTAAA 58.721 33.333 0.00 0.00 0.00 1.85
202 203 7.811282 TGCCAAATATACTCCCTTCATTCTAA 58.189 34.615 0.00 0.00 0.00 2.10
203 204 7.292356 TCTGCCAAATATACTCCCTTCATTCTA 59.708 37.037 0.00 0.00 0.00 2.10
204 205 6.101734 TCTGCCAAATATACTCCCTTCATTCT 59.898 38.462 0.00 0.00 0.00 2.40
205 206 6.299141 TCTGCCAAATATACTCCCTTCATTC 58.701 40.000 0.00 0.00 0.00 2.67
206 207 6.266131 TCTGCCAAATATACTCCCTTCATT 57.734 37.500 0.00 0.00 0.00 2.57
207 208 5.912149 TCTGCCAAATATACTCCCTTCAT 57.088 39.130 0.00 0.00 0.00 2.57
208 209 5.437060 GTTCTGCCAAATATACTCCCTTCA 58.563 41.667 0.00 0.00 0.00 3.02
209 210 4.822350 GGTTCTGCCAAATATACTCCCTTC 59.178 45.833 0.00 0.00 37.17 3.46
210 211 4.229582 TGGTTCTGCCAAATATACTCCCTT 59.770 41.667 0.00 0.00 45.94 3.95
211 212 3.785887 TGGTTCTGCCAAATATACTCCCT 59.214 43.478 0.00 0.00 45.94 4.20
212 213 4.164843 TGGTTCTGCCAAATATACTCCC 57.835 45.455 0.00 0.00 45.94 4.30
240 241 9.349713 TCAAGACAAAGTAGAATTTGGTTATGT 57.650 29.630 7.30 0.00 43.10 2.29
244 245 9.366216 GTTTTCAAGACAAAGTAGAATTTGGTT 57.634 29.630 7.30 0.00 43.10 3.67
255 256 2.752903 ACGCAGGTTTTCAAGACAAAGT 59.247 40.909 0.00 0.00 0.00 2.66
279 280 0.618458 TGATACCCACTGTCTTGCCC 59.382 55.000 0.00 0.00 0.00 5.36
280 281 2.092968 TCATGATACCCACTGTCTTGCC 60.093 50.000 0.00 0.00 0.00 4.52
286 287 3.266772 ACCATGTTCATGATACCCACTGT 59.733 43.478 13.51 0.00 0.00 3.55
308 309 4.776322 CCGTTGCCGATGCTCCCA 62.776 66.667 0.00 0.00 38.71 4.37
312 313 2.434884 CTCACCGTTGCCGATGCT 60.435 61.111 0.00 0.00 38.71 3.79
323 324 0.317603 AAACGACGACAGACTCACCG 60.318 55.000 0.00 0.00 0.00 4.94
327 328 3.484834 GTTGAAAACGACGACAGACTC 57.515 47.619 0.00 0.00 36.92 3.36
344 345 6.348213 CCAGGTAGAATTTTGTCCTAACGTTG 60.348 42.308 11.99 0.68 0.00 4.10
345 346 5.704053 CCAGGTAGAATTTTGTCCTAACGTT 59.296 40.000 5.88 5.88 0.00 3.99
346 347 5.243207 CCAGGTAGAATTTTGTCCTAACGT 58.757 41.667 0.00 0.00 0.00 3.99
347 348 4.094442 GCCAGGTAGAATTTTGTCCTAACG 59.906 45.833 0.00 0.00 0.00 3.18
348 349 5.254115 AGCCAGGTAGAATTTTGTCCTAAC 58.746 41.667 0.00 0.00 0.00 2.34
349 350 5.514500 AGCCAGGTAGAATTTTGTCCTAA 57.486 39.130 0.00 0.00 0.00 2.69
350 351 5.514500 AAGCCAGGTAGAATTTTGTCCTA 57.486 39.130 0.00 0.00 0.00 2.94
351 352 4.388577 AAGCCAGGTAGAATTTTGTCCT 57.611 40.909 0.00 0.00 0.00 3.85
371 372 1.464734 TGGAACACGGCTTTGTCAAA 58.535 45.000 0.00 0.00 0.00 2.69
376 377 1.879380 TCATCTTGGAACACGGCTTTG 59.121 47.619 0.00 0.00 39.29 2.77
381 382 3.501828 TGTTCATTCATCTTGGAACACGG 59.498 43.478 0.00 0.00 43.19 4.94
398 399 0.404426 TCTCTCTCCCTCCGTGTTCA 59.596 55.000 0.00 0.00 0.00 3.18
411 412 2.255406 ACTGTTGTCCATGCTCTCTCT 58.745 47.619 0.00 0.00 0.00 3.10
425 426 1.878953 ACGGCAAGACCTTACTGTTG 58.121 50.000 0.00 0.00 35.61 3.33
432 433 1.611673 CCTCATGAACGGCAAGACCTT 60.612 52.381 0.00 0.00 35.61 3.50
433 434 0.036010 CCTCATGAACGGCAAGACCT 60.036 55.000 0.00 0.00 35.61 3.85
458 459 0.035343 GTGGGGTTCTGTCTTAGGCC 60.035 60.000 0.00 0.00 0.00 5.19
512 513 3.869272 GCCAAGATGTCGCAGGCG 61.869 66.667 7.46 7.46 41.35 5.52
516 517 2.747460 GCAGGCCAAGATGTCGCA 60.747 61.111 5.01 0.00 0.00 5.10
520 521 2.679716 GGAGGCAGGCCAAGATGT 59.320 61.111 13.63 0.00 38.92 3.06
606 607 1.743252 GGGAGAGGAACGCTTGCAG 60.743 63.158 0.00 0.00 39.71 4.41
607 608 2.347490 GGGAGAGGAACGCTTGCA 59.653 61.111 0.00 0.00 39.71 4.08
621 624 0.983905 TCAAATCGGGGAATCGGGGA 60.984 55.000 0.00 0.00 0.00 4.81
644 647 3.368843 GGTCATGAGTCTCAGCTTGCTAA 60.369 47.826 8.82 0.00 0.00 3.09
645 648 2.167281 GGTCATGAGTCTCAGCTTGCTA 59.833 50.000 8.82 0.00 0.00 3.49
646 649 1.066286 GGTCATGAGTCTCAGCTTGCT 60.066 52.381 8.82 0.00 0.00 3.91
653 689 1.186200 CCTTCGGGTCATGAGTCTCA 58.814 55.000 4.68 4.68 0.00 3.27
694 730 1.961277 CCACCTGAAGCGCGTCTTT 60.961 57.895 23.50 1.53 34.56 2.52
741 777 2.036089 AGTCCGGTTTCACACTTCTCTC 59.964 50.000 0.00 0.00 0.00 3.20
742 778 2.036089 GAGTCCGGTTTCACACTTCTCT 59.964 50.000 0.00 0.00 0.00 3.10
764 800 2.639327 CCTTGGCCTGGGAAAAGCG 61.639 63.158 3.32 0.00 0.00 4.68
773 809 3.333219 TGAGGAGGCCTTGGCCTG 61.333 66.667 35.01 0.00 40.79 4.85
788 824 2.643272 GCGACGTGTGAGGACTGA 59.357 61.111 0.00 0.00 0.00 3.41
789 825 2.801162 CGCGACGTGTGAGGACTG 60.801 66.667 0.00 0.00 0.00 3.51
790 826 3.251318 GACGCGACGTGTGAGGACT 62.251 63.158 20.29 0.00 41.37 3.85
791 827 2.799916 GACGCGACGTGTGAGGAC 60.800 66.667 20.29 0.00 41.37 3.85
792 828 4.034258 GGACGCGACGTGTGAGGA 62.034 66.667 20.29 0.00 41.37 3.71
793 829 4.337060 TGGACGCGACGTGTGAGG 62.337 66.667 20.29 0.00 41.37 3.86
794 830 2.801162 CTGGACGCGACGTGTGAG 60.801 66.667 20.29 10.53 41.37 3.51
795 831 4.994201 GCTGGACGCGACGTGTGA 62.994 66.667 20.29 4.22 41.37 3.58
828 864 0.174845 TATATATGCTCCGGGTGCGC 59.825 55.000 15.59 0.00 0.00 6.09
829 865 1.470979 GGTATATATGCTCCGGGTGCG 60.471 57.143 15.59 0.00 0.00 5.34
925 962 4.827835 ACTTGCACTAGACTAGACAAGACA 59.172 41.667 32.85 15.88 41.53 3.41
980 1028 1.040646 TCTTGCTGGTGACTCGACTT 58.959 50.000 0.00 0.00 0.00 3.01
1162 1252 4.740822 GATGGCCGGCTGGTGGTT 62.741 66.667 28.56 3.07 37.67 3.67
1391 1496 2.499205 CGGCGTGCTCCCTATGAA 59.501 61.111 0.00 0.00 0.00 2.57
1545 1675 1.676006 CAGAGCCACGGAACAAAACTT 59.324 47.619 0.00 0.00 0.00 2.66
1546 1676 1.308998 CAGAGCCACGGAACAAAACT 58.691 50.000 0.00 0.00 0.00 2.66
1550 1680 0.465460 AAAGCAGAGCCACGGAACAA 60.465 50.000 0.00 0.00 0.00 2.83
1556 1686 1.996191 GAGTAGAAAAGCAGAGCCACG 59.004 52.381 0.00 0.00 0.00 4.94
1559 1689 3.326836 ACAGAGTAGAAAAGCAGAGCC 57.673 47.619 0.00 0.00 0.00 4.70
1589 1750 3.429207 GCCTTTCAGTTTCAGTAGACGAC 59.571 47.826 0.00 0.00 0.00 4.34
1596 1757 2.301346 CAGGTGCCTTTCAGTTTCAGT 58.699 47.619 0.00 0.00 0.00 3.41
1617 1779 2.041216 TCCTGGCTCTCACACACTACTA 59.959 50.000 0.00 0.00 0.00 1.82
1619 1781 1.257743 TCCTGGCTCTCACACACTAC 58.742 55.000 0.00 0.00 0.00 2.73
1644 1806 5.337009 GGCTCTGATCAAAATCCACAACAAT 60.337 40.000 0.00 0.00 0.00 2.71
1645 1807 4.022068 GGCTCTGATCAAAATCCACAACAA 60.022 41.667 0.00 0.00 0.00 2.83
1648 1810 4.012374 GAGGCTCTGATCAAAATCCACAA 58.988 43.478 7.40 0.00 0.00 3.33
1701 1870 6.668645 TGTAAAATATCCCAGGTGCTGTAAT 58.331 36.000 0.00 0.00 0.00 1.89
1712 1881 6.945435 ACACACATGAGTTGTAAAATATCCCA 59.055 34.615 0.00 0.00 36.57 4.37
1725 1894 3.808728 AGCAACTACACACACATGAGTT 58.191 40.909 0.00 0.00 31.52 3.01
1734 1905 6.319399 ACAGTAAAAACAAGCAACTACACAC 58.681 36.000 0.00 0.00 0.00 3.82
1757 1932 3.142174 AGAAGAAAGCAGCCACAACTAC 58.858 45.455 0.00 0.00 0.00 2.73
1825 2004 3.581332 ACCAACCGTAGAGAATGAGGAAA 59.419 43.478 0.00 0.00 0.00 3.13
1835 2014 2.665649 TGCACATACCAACCGTAGAG 57.334 50.000 0.00 0.00 0.00 2.43
1841 2020 1.885887 ACACACATGCACATACCAACC 59.114 47.619 0.00 0.00 0.00 3.77
1846 2025 1.167851 AGCCACACACATGCACATAC 58.832 50.000 0.00 0.00 0.00 2.39
1906 2087 0.254178 ATCCTGGCAGTAGCACCAAG 59.746 55.000 14.43 0.00 44.61 3.61
2067 2249 1.812571 GATGAGGTGCCAACGAACATT 59.187 47.619 0.00 0.00 0.00 2.71
2073 2255 1.645034 CAGTAGATGAGGTGCCAACG 58.355 55.000 0.00 0.00 0.00 4.10
2111 2293 7.276658 TGATGGTTCAGGCTTAATACGAATTA 58.723 34.615 0.00 0.00 0.00 1.40
2112 2294 6.119536 TGATGGTTCAGGCTTAATACGAATT 58.880 36.000 0.00 0.00 0.00 2.17
2113 2295 5.680619 TGATGGTTCAGGCTTAATACGAAT 58.319 37.500 0.00 0.00 0.00 3.34
2116 2298 5.408604 GGTATGATGGTTCAGGCTTAATACG 59.591 44.000 0.00 0.00 34.73 3.06
2145 2327 8.288208 GCAGATTTTAGACCTGATCATATGTTG 58.712 37.037 1.90 0.00 0.00 3.33
2175 2358 7.323416 GCCAAAGAAAAACAAAAACAGAAACAG 59.677 33.333 0.00 0.00 0.00 3.16
2181 2364 8.195617 TCTATGCCAAAGAAAAACAAAAACAG 57.804 30.769 0.00 0.00 0.00 3.16
2183 2366 9.489393 CTTTCTATGCCAAAGAAAAACAAAAAC 57.511 29.630 6.66 0.00 41.21 2.43
2189 2373 6.983890 TGAACCTTTCTATGCCAAAGAAAAAC 59.016 34.615 6.66 1.64 41.21 2.43
2192 2376 5.010617 GGTGAACCTTTCTATGCCAAAGAAA 59.989 40.000 5.45 5.45 39.91 2.52
2193 2377 4.522789 GGTGAACCTTTCTATGCCAAAGAA 59.477 41.667 0.00 0.00 33.34 2.52
2194 2378 4.079253 GGTGAACCTTTCTATGCCAAAGA 58.921 43.478 0.00 0.00 33.34 2.52
2195 2379 3.193479 GGGTGAACCTTTCTATGCCAAAG 59.807 47.826 0.00 0.00 35.85 2.77
2196 2380 3.161866 GGGTGAACCTTTCTATGCCAAA 58.838 45.455 0.00 0.00 35.85 3.28
2197 2381 2.109128 TGGGTGAACCTTTCTATGCCAA 59.891 45.455 0.00 0.00 41.11 4.52
2198 2382 1.707989 TGGGTGAACCTTTCTATGCCA 59.292 47.619 0.00 0.00 41.11 4.92
2199 2383 2.092323 GTGGGTGAACCTTTCTATGCC 58.908 52.381 0.00 0.00 41.11 4.40
2204 2388 3.230976 GGAAATGTGGGTGAACCTTTCT 58.769 45.455 10.17 0.00 41.11 2.52
2219 2403 5.358160 GTCCTGGTTTCTCCTAATGGAAATG 59.642 44.000 0.00 0.00 42.66 2.32
2230 2414 2.038557 TGTAGCAAGTCCTGGTTTCTCC 59.961 50.000 0.00 0.00 36.95 3.71
2241 2425 6.094061 AGTATTCGAGACTTTGTAGCAAGTC 58.906 40.000 6.56 6.56 44.23 3.01
2279 2464 7.905493 GTCAGGAAATATAGAAACGAAAGCAAG 59.095 37.037 0.00 0.00 0.00 4.01
2280 2465 7.389330 TGTCAGGAAATATAGAAACGAAAGCAA 59.611 33.333 0.00 0.00 0.00 3.91
2288 2473 5.297029 GCCACCTGTCAGGAAATATAGAAAC 59.703 44.000 26.18 0.00 37.67 2.78
2324 2509 4.864704 AAAACCAACAAATATGGCGTCT 57.135 36.364 0.00 0.00 41.89 4.18
2350 2535 4.776837 GGAGATATGACATCATCACCCTCT 59.223 45.833 0.00 0.00 41.24 3.69
2355 2541 5.219343 TGGTGGAGATATGACATCATCAC 57.781 43.478 0.00 0.40 41.24 3.06
2368 2554 8.656806 TCCGTTATTTTAATCTATGGTGGAGAT 58.343 33.333 0.00 0.00 35.08 2.75
2411 2597 9.388506 CATTGTAATTAGTCAAGACATCTCCTT 57.611 33.333 2.72 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.