Multiple sequence alignment - TraesCS2A01G402200

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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 TraesCS2A01G402200 chr2A 100.000 3998 0 0 1 3998 656238869 656242866 0.000000e+00 7384.0
1 TraesCS2A01G402200 chr2D 93.092 3923 135 57 142 3998 512684946 512688798 0.000000e+00 5618.0
2 TraesCS2A01G402200 chr2B 91.827 3952 175 63 142 3998 602761503 602765401 0.000000e+00 5373.0
3 TraesCS2A01G402200 chr1B 92.286 1750 55 24 2257 3947 332586679 332584951 0.000000e+00 2410.0
4 TraesCS2A01G402200 chr6A 93.954 1257 41 14 2276 3503 441441550 441442800 0.000000e+00 1868.0
5 TraesCS2A01G402200 chr6A 79.236 602 91 24 2079 2662 473575567 473574982 4.850000e-104 388.0
6 TraesCS2A01G402200 chr6A 92.308 260 11 1 2276 2535 441443048 441442798 1.060000e-95 361.0
7 TraesCS2A01G402200 chr6A 86.500 200 27 0 2073 2272 500083817 500083618 1.870000e-53 220.0
8 TraesCS2A01G402200 chr6A 85.946 185 21 4 2109 2289 520355715 520355532 4.080000e-45 193.0
9 TraesCS2A01G402200 chr6A 84.043 94 10 3 3862 3954 473573758 473573669 7.120000e-13 86.1
10 TraesCS2A01G402200 chr6B 79.264 598 86 23 2079 2656 486224664 486225243 2.250000e-102 383.0
11 TraesCS2A01G402200 chr6B 86.000 200 28 0 2073 2272 539727742 539727543 8.700000e-52 215.0
12 TraesCS2A01G402200 chr6B 84.043 94 10 3 3862 3954 486226492 486226581 7.120000e-13 86.1
13 TraesCS2A01G402200 chr6D 78.904 602 93 25 2079 2662 334227663 334227078 1.050000e-100 377.0
14 TraesCS2A01G402200 chr6D 86.154 195 27 0 2078 2272 358326193 358325999 1.130000e-50 211.0
15 TraesCS2A01G402200 chr6D 78.723 94 10 6 3862 3954 334225830 334225746 2.000000e-03 54.7
16 TraesCS2A01G402200 chr7A 97.101 138 4 0 2 139 519564098 519563961 2.400000e-57 233.0
17 TraesCS2A01G402200 chr3A 97.101 138 4 0 2 139 746407816 746407953 2.400000e-57 233.0
18 TraesCS2A01G402200 chr3B 96.377 138 5 0 2 139 829350554 829350691 1.120000e-55 228.0
19 TraesCS2A01G402200 chr3D 95.683 139 5 1 2 139 611658854 611658992 5.200000e-54 222.0
20 TraesCS2A01G402200 chr1A 98.824 85 1 0 2 86 534024039 534024123 6.920000e-33 152.0


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 TraesCS2A01G402200 chr2A 656238869 656242866 3997 False 7384.00 7384 100.0000 1 3998 1 chr2A.!!$F1 3997
1 TraesCS2A01G402200 chr2D 512684946 512688798 3852 False 5618.00 5618 93.0920 142 3998 1 chr2D.!!$F1 3856
2 TraesCS2A01G402200 chr2B 602761503 602765401 3898 False 5373.00 5373 91.8270 142 3998 1 chr2B.!!$F1 3856
3 TraesCS2A01G402200 chr1B 332584951 332586679 1728 True 2410.00 2410 92.2860 2257 3947 1 chr1B.!!$R1 1690
4 TraesCS2A01G402200 chr6A 441441550 441442800 1250 False 1868.00 1868 93.9540 2276 3503 1 chr6A.!!$F1 1227
5 TraesCS2A01G402200 chr6A 473573669 473575567 1898 True 237.05 388 81.6395 2079 3954 2 chr6A.!!$R4 1875
6 TraesCS2A01G402200 chr6B 486224664 486226581 1917 False 234.55 383 81.6535 2079 3954 2 chr6B.!!$F1 1875
7 TraesCS2A01G402200 chr6D 334225746 334227663 1917 True 215.85 377 78.8135 2079 3954 2 chr6D.!!$R2 1875

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
111 112 0.032678 CTAGTCCTACGCCATGGCAG 59.967 60.000 34.93 27.71 42.06 4.85 F
140 141 0.037232 CCTTGGTCTCTTGGTCGTCC 60.037 60.000 0.00 0.00 0.00 4.79 F
650 681 0.109458 TCACAGTACGTCGCACATCC 60.109 55.000 0.00 0.00 0.00 3.51 F
1033 1097 0.183731 CTGGCCCCAGGTAAATCTCC 59.816 60.000 0.00 0.00 40.17 3.71 F
1239 1321 0.393537 CACAATCAGCACCCCTCTCC 60.394 60.000 0.00 0.00 0.00 3.71 F
1269 1357 1.144913 AGGCTTTAAGGTGCAGGTGAA 59.855 47.619 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1137 0.467804 GAGAGGAGGATGAACAGGCC 59.532 60.000 0.00 0.00 0.00 5.19 R
1871 1975 0.614979 TAGCCCCTGAGGACACAGAC 60.615 60.000 0.00 0.00 39.94 3.51 R
1905 2012 1.424302 CCCATCAGCATCTCCTCCATT 59.576 52.381 0.00 0.00 0.00 3.16 R
1936 2043 1.597854 CTTGCACCTGCTGGTTCGA 60.598 57.895 13.36 7.37 46.05 3.71 R
2055 2162 2.436115 GTGCTACCCGCTCCAACC 60.436 66.667 0.00 0.00 40.11 3.77 R
3027 3287 2.809174 CGCACAGCCGACGATGAA 60.809 61.111 0.00 0.00 0.00 2.57 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
22 23 5.798125 TCTAGCCATGAAGGTGAAGATAG 57.202 43.478 0.00 0.00 40.61 2.08
23 24 5.211973 TCTAGCCATGAAGGTGAAGATAGT 58.788 41.667 0.00 0.00 40.61 2.12
24 25 4.414337 AGCCATGAAGGTGAAGATAGTC 57.586 45.455 0.00 0.00 40.61 2.59
25 26 3.776969 AGCCATGAAGGTGAAGATAGTCA 59.223 43.478 0.00 0.00 40.61 3.41
26 27 4.225942 AGCCATGAAGGTGAAGATAGTCAA 59.774 41.667 0.00 0.00 40.61 3.18
27 28 4.574013 GCCATGAAGGTGAAGATAGTCAAG 59.426 45.833 0.00 0.00 40.61 3.02
28 29 4.574013 CCATGAAGGTGAAGATAGTCAAGC 59.426 45.833 0.00 0.00 0.00 4.01
29 30 5.426504 CATGAAGGTGAAGATAGTCAAGCT 58.573 41.667 0.00 0.00 0.00 3.74
30 31 5.489792 TGAAGGTGAAGATAGTCAAGCTT 57.510 39.130 0.00 0.00 0.00 3.74
31 32 5.240891 TGAAGGTGAAGATAGTCAAGCTTG 58.759 41.667 20.81 20.81 0.00 4.01
32 33 4.213564 AGGTGAAGATAGTCAAGCTTGG 57.786 45.455 25.73 8.01 0.00 3.61
33 34 3.584848 AGGTGAAGATAGTCAAGCTTGGT 59.415 43.478 25.73 15.80 0.00 3.67
34 35 3.686726 GGTGAAGATAGTCAAGCTTGGTG 59.313 47.826 25.73 1.51 0.00 4.17
35 36 3.126000 GTGAAGATAGTCAAGCTTGGTGC 59.874 47.826 25.73 15.80 43.29 5.01
36 37 3.244526 TGAAGATAGTCAAGCTTGGTGCA 60.245 43.478 25.73 9.66 45.94 4.57
37 38 2.983229 AGATAGTCAAGCTTGGTGCAG 58.017 47.619 25.73 0.00 45.94 4.41
38 39 2.568956 AGATAGTCAAGCTTGGTGCAGA 59.431 45.455 25.73 2.68 45.94 4.26
39 40 2.169832 TAGTCAAGCTTGGTGCAGAC 57.830 50.000 25.73 15.14 45.94 3.51
40 41 0.181114 AGTCAAGCTTGGTGCAGACA 59.819 50.000 25.73 1.09 45.27 3.41
41 42 0.590195 GTCAAGCTTGGTGCAGACAG 59.410 55.000 25.73 0.00 43.60 3.51
42 43 0.535780 TCAAGCTTGGTGCAGACAGG 60.536 55.000 25.73 0.00 45.94 4.00
43 44 0.820891 CAAGCTTGGTGCAGACAGGT 60.821 55.000 19.14 0.00 45.94 4.00
44 45 0.536006 AAGCTTGGTGCAGACAGGTC 60.536 55.000 0.00 0.00 45.94 3.85
45 46 2.320587 GCTTGGTGCAGACAGGTCG 61.321 63.158 0.00 0.00 42.31 4.79
46 47 1.367471 CTTGGTGCAGACAGGTCGA 59.633 57.895 0.00 0.00 34.09 4.20
47 48 0.668706 CTTGGTGCAGACAGGTCGAG 60.669 60.000 0.00 0.00 34.09 4.04
48 49 2.099652 TTGGTGCAGACAGGTCGAGG 62.100 60.000 0.00 0.00 34.09 4.63
49 50 2.574955 GGTGCAGACAGGTCGAGGT 61.575 63.158 0.00 0.00 34.09 3.85
50 51 1.367840 GTGCAGACAGGTCGAGGTT 59.632 57.895 0.00 0.00 34.09 3.50
51 52 0.667792 GTGCAGACAGGTCGAGGTTC 60.668 60.000 0.00 0.00 34.09 3.62
52 53 1.112916 TGCAGACAGGTCGAGGTTCA 61.113 55.000 0.00 0.00 34.09 3.18
53 54 0.389166 GCAGACAGGTCGAGGTTCAG 60.389 60.000 0.00 0.00 34.09 3.02
54 55 0.389166 CAGACAGGTCGAGGTTCAGC 60.389 60.000 0.00 0.00 34.09 4.26
55 56 0.540830 AGACAGGTCGAGGTTCAGCT 60.541 55.000 0.00 0.00 34.09 4.24
56 57 0.318762 GACAGGTCGAGGTTCAGCTT 59.681 55.000 0.00 0.00 0.00 3.74
57 58 1.544691 GACAGGTCGAGGTTCAGCTTA 59.455 52.381 0.00 0.00 0.00 3.09
58 59 1.968493 ACAGGTCGAGGTTCAGCTTAA 59.032 47.619 0.00 0.00 0.00 1.85
59 60 2.567615 ACAGGTCGAGGTTCAGCTTAAT 59.432 45.455 0.00 0.00 0.00 1.40
60 61 3.767673 ACAGGTCGAGGTTCAGCTTAATA 59.232 43.478 0.00 0.00 0.00 0.98
61 62 4.142138 ACAGGTCGAGGTTCAGCTTAATAG 60.142 45.833 0.00 0.00 0.00 1.73
62 63 4.024670 AGGTCGAGGTTCAGCTTAATAGT 58.975 43.478 0.00 0.00 0.00 2.12
63 64 4.113354 GGTCGAGGTTCAGCTTAATAGTG 58.887 47.826 0.00 0.00 0.00 2.74
64 65 4.142227 GGTCGAGGTTCAGCTTAATAGTGA 60.142 45.833 0.00 0.00 0.00 3.41
65 66 5.408356 GTCGAGGTTCAGCTTAATAGTGAA 58.592 41.667 0.00 0.00 0.00 3.18
66 67 5.517054 GTCGAGGTTCAGCTTAATAGTGAAG 59.483 44.000 0.00 0.00 30.94 3.02
67 68 5.417894 TCGAGGTTCAGCTTAATAGTGAAGA 59.582 40.000 0.00 0.00 30.94 2.87
68 69 6.096987 TCGAGGTTCAGCTTAATAGTGAAGAT 59.903 38.462 0.00 0.00 30.94 2.40
69 70 6.199908 CGAGGTTCAGCTTAATAGTGAAGATG 59.800 42.308 0.00 0.00 40.79 2.90
70 71 7.187824 AGGTTCAGCTTAATAGTGAAGATGA 57.812 36.000 0.00 0.00 45.07 2.92
76 77 9.725019 TCAGCTTAATAGTGAAGATGAAGAAAA 57.275 29.630 1.13 0.00 44.11 2.29
77 78 9.766277 CAGCTTAATAGTGAAGATGAAGAAAAC 57.234 33.333 0.00 0.00 41.73 2.43
78 79 8.660373 AGCTTAATAGTGAAGATGAAGAAAACG 58.340 33.333 0.00 0.00 0.00 3.60
79 80 8.656849 GCTTAATAGTGAAGATGAAGAAAACGA 58.343 33.333 0.00 0.00 0.00 3.85
80 81 9.959775 CTTAATAGTGAAGATGAAGAAAACGAC 57.040 33.333 0.00 0.00 0.00 4.34
81 82 6.969828 ATAGTGAAGATGAAGAAAACGACC 57.030 37.500 0.00 0.00 0.00 4.79
82 83 4.703897 AGTGAAGATGAAGAAAACGACCA 58.296 39.130 0.00 0.00 0.00 4.02
83 84 5.123227 AGTGAAGATGAAGAAAACGACCAA 58.877 37.500 0.00 0.00 0.00 3.67
84 85 5.237344 AGTGAAGATGAAGAAAACGACCAAG 59.763 40.000 0.00 0.00 0.00 3.61
85 86 4.024048 TGAAGATGAAGAAAACGACCAAGC 60.024 41.667 0.00 0.00 0.00 4.01
86 87 3.744660 AGATGAAGAAAACGACCAAGCT 58.255 40.909 0.00 0.00 0.00 3.74
87 88 4.137543 AGATGAAGAAAACGACCAAGCTT 58.862 39.130 0.00 0.00 0.00 3.74
88 89 3.963383 TGAAGAAAACGACCAAGCTTC 57.037 42.857 0.00 0.00 34.04 3.86
89 90 2.616842 TGAAGAAAACGACCAAGCTTCC 59.383 45.455 0.00 0.00 32.84 3.46
90 91 2.640316 AGAAAACGACCAAGCTTCCT 57.360 45.000 0.00 0.00 0.00 3.36
91 92 2.932261 AGAAAACGACCAAGCTTCCTT 58.068 42.857 0.00 0.00 0.00 3.36
92 93 2.879026 AGAAAACGACCAAGCTTCCTTC 59.121 45.455 0.00 0.00 0.00 3.46
93 94 2.640316 AAACGACCAAGCTTCCTTCT 57.360 45.000 0.00 0.00 0.00 2.85
94 95 3.764237 AAACGACCAAGCTTCCTTCTA 57.236 42.857 0.00 0.00 0.00 2.10
95 96 3.320673 AACGACCAAGCTTCCTTCTAG 57.679 47.619 0.00 0.00 0.00 2.43
96 97 2.249139 ACGACCAAGCTTCCTTCTAGT 58.751 47.619 0.00 0.00 0.00 2.57
97 98 2.231721 ACGACCAAGCTTCCTTCTAGTC 59.768 50.000 0.00 0.00 0.00 2.59
98 99 2.417515 CGACCAAGCTTCCTTCTAGTCC 60.418 54.545 0.00 0.00 0.00 3.85
99 100 2.835156 GACCAAGCTTCCTTCTAGTCCT 59.165 50.000 0.00 0.00 0.00 3.85
100 101 4.024670 GACCAAGCTTCCTTCTAGTCCTA 58.975 47.826 0.00 0.00 0.00 2.94
101 102 3.770388 ACCAAGCTTCCTTCTAGTCCTAC 59.230 47.826 0.00 0.00 0.00 3.18
102 103 3.181485 CCAAGCTTCCTTCTAGTCCTACG 60.181 52.174 0.00 0.00 0.00 3.51
103 104 2.025898 AGCTTCCTTCTAGTCCTACGC 58.974 52.381 0.00 0.00 0.00 4.42
104 105 1.067364 GCTTCCTTCTAGTCCTACGCC 59.933 57.143 0.00 0.00 0.00 5.68
105 106 2.376109 CTTCCTTCTAGTCCTACGCCA 58.624 52.381 0.00 0.00 0.00 5.69
106 107 2.750141 TCCTTCTAGTCCTACGCCAT 57.250 50.000 0.00 0.00 0.00 4.40
107 108 2.307768 TCCTTCTAGTCCTACGCCATG 58.692 52.381 0.00 0.00 0.00 3.66
108 109 1.341531 CCTTCTAGTCCTACGCCATGG 59.658 57.143 7.63 7.63 0.00 3.66
109 110 0.750850 TTCTAGTCCTACGCCATGGC 59.249 55.000 27.67 27.67 37.85 4.40
110 111 0.396556 TCTAGTCCTACGCCATGGCA 60.397 55.000 34.93 16.95 42.06 4.92
111 112 0.032678 CTAGTCCTACGCCATGGCAG 59.967 60.000 34.93 27.71 42.06 4.85
112 113 1.399744 TAGTCCTACGCCATGGCAGG 61.400 60.000 34.93 31.86 42.06 4.85
113 114 3.479203 TCCTACGCCATGGCAGGG 61.479 66.667 32.37 28.66 42.06 4.45
114 115 3.797353 CCTACGCCATGGCAGGGT 61.797 66.667 34.93 25.97 42.06 4.34
115 116 2.439960 CCTACGCCATGGCAGGGTA 61.440 63.158 34.93 25.71 42.06 3.69
116 117 1.754745 CTACGCCATGGCAGGGTAT 59.245 57.895 34.93 15.34 42.06 2.73
117 118 0.108585 CTACGCCATGGCAGGGTATT 59.891 55.000 34.93 14.07 42.06 1.89
118 119 0.107831 TACGCCATGGCAGGGTATTC 59.892 55.000 34.93 3.77 42.06 1.75
119 120 1.149174 CGCCATGGCAGGGTATTCT 59.851 57.895 34.93 0.00 42.06 2.40
120 121 0.466189 CGCCATGGCAGGGTATTCTT 60.466 55.000 34.93 0.00 42.06 2.52
121 122 1.322442 GCCATGGCAGGGTATTCTTC 58.678 55.000 32.08 0.00 41.49 2.87
122 123 1.986882 CCATGGCAGGGTATTCTTCC 58.013 55.000 10.66 0.00 0.00 3.46
123 124 1.496429 CCATGGCAGGGTATTCTTCCT 59.504 52.381 10.66 0.00 0.00 3.36
124 125 2.091665 CCATGGCAGGGTATTCTTCCTT 60.092 50.000 10.66 0.00 0.00 3.36
125 126 2.806945 TGGCAGGGTATTCTTCCTTG 57.193 50.000 0.00 0.00 35.56 3.61
126 127 1.284785 TGGCAGGGTATTCTTCCTTGG 59.715 52.381 0.00 0.00 33.51 3.61
127 128 1.285078 GGCAGGGTATTCTTCCTTGGT 59.715 52.381 0.00 0.00 33.51 3.67
128 129 2.644676 GCAGGGTATTCTTCCTTGGTC 58.355 52.381 0.00 0.00 33.51 4.02
129 130 2.239907 GCAGGGTATTCTTCCTTGGTCT 59.760 50.000 0.00 0.00 33.51 3.85
130 131 3.682999 GCAGGGTATTCTTCCTTGGTCTC 60.683 52.174 0.00 0.00 33.51 3.36
131 132 3.777522 CAGGGTATTCTTCCTTGGTCTCT 59.222 47.826 0.00 0.00 0.00 3.10
132 133 4.226168 CAGGGTATTCTTCCTTGGTCTCTT 59.774 45.833 0.00 0.00 0.00 2.85
133 134 4.226168 AGGGTATTCTTCCTTGGTCTCTTG 59.774 45.833 0.00 0.00 0.00 3.02
134 135 4.518249 GGTATTCTTCCTTGGTCTCTTGG 58.482 47.826 0.00 0.00 0.00 3.61
135 136 4.019231 GGTATTCTTCCTTGGTCTCTTGGT 60.019 45.833 0.00 0.00 0.00 3.67
136 137 3.771577 TTCTTCCTTGGTCTCTTGGTC 57.228 47.619 0.00 0.00 0.00 4.02
137 138 1.618837 TCTTCCTTGGTCTCTTGGTCG 59.381 52.381 0.00 0.00 0.00 4.79
138 139 1.344763 CTTCCTTGGTCTCTTGGTCGT 59.655 52.381 0.00 0.00 0.00 4.34
139 140 0.966920 TCCTTGGTCTCTTGGTCGTC 59.033 55.000 0.00 0.00 0.00 4.20
140 141 0.037232 CCTTGGTCTCTTGGTCGTCC 60.037 60.000 0.00 0.00 0.00 4.79
177 178 5.627367 CCATGCATTTTGTTTTGAAGCAATG 59.373 36.000 0.00 0.00 33.91 2.82
180 181 6.256686 TGCATTTTGTTTTGAAGCAATGTTC 58.743 32.000 0.00 0.00 0.00 3.18
183 184 5.467902 TTTGTTTTGAAGCAATGTTCTGC 57.532 34.783 0.00 0.00 42.97 4.26
242 247 1.081906 GAACCGTACACGAGCACGA 60.082 57.895 11.40 0.00 43.02 4.35
265 270 7.279313 ACGACTTAAAAGCTAAAACTCTTGACA 59.721 33.333 0.00 0.00 0.00 3.58
278 283 5.108385 ACTCTTGACAAATTTTGTAGCCG 57.892 39.130 14.49 7.05 45.52 5.52
352 364 5.511088 AATTACGCTGTAGACTGAAAACG 57.489 39.130 0.00 0.00 0.00 3.60
356 368 2.408704 CGCTGTAGACTGAAAACGAAGG 59.591 50.000 0.00 0.00 0.00 3.46
383 395 2.027688 GTGCACTGTCGCGTAATAGAAC 59.972 50.000 10.32 0.00 33.35 3.01
394 406 5.061311 TCGCGTAATAGAACGGAAAAGAAAG 59.939 40.000 5.77 0.00 43.06 2.62
494 514 2.573340 CAAACCGCCATTCCCAGC 59.427 61.111 0.00 0.00 0.00 4.85
495 515 1.978617 CAAACCGCCATTCCCAGCT 60.979 57.895 0.00 0.00 0.00 4.24
496 516 1.978617 AAACCGCCATTCCCAGCTG 60.979 57.895 6.78 6.78 0.00 4.24
517 537 1.001641 CTTCCTCCCTTGGTGCCTG 60.002 63.158 0.00 0.00 0.00 4.85
518 538 3.210012 TTCCTCCCTTGGTGCCTGC 62.210 63.158 0.00 0.00 0.00 4.85
519 539 4.748144 CCTCCCTTGGTGCCTGCC 62.748 72.222 0.00 0.00 0.00 4.85
520 540 3.655211 CTCCCTTGGTGCCTGCCT 61.655 66.667 0.00 0.00 0.00 4.75
605 632 0.603569 TCGAGCAAGAACACCTCTCC 59.396 55.000 0.00 0.00 31.02 3.71
616 643 2.692741 CCTCTCCACCCCCTTCCC 60.693 72.222 0.00 0.00 0.00 3.97
645 676 0.240145 CTTCCTCACAGTACGTCGCA 59.760 55.000 0.00 0.00 0.00 5.10
650 681 0.109458 TCACAGTACGTCGCACATCC 60.109 55.000 0.00 0.00 0.00 3.51
797 861 0.527817 CGTATGTGGGAAGAGCGGAC 60.528 60.000 0.00 0.00 0.00 4.79
823 887 1.168714 GGGACAATTCCACTCACTGC 58.831 55.000 0.00 0.00 44.98 4.40
844 908 3.553095 AACCACAGCGCCTTCCTCC 62.553 63.158 2.29 0.00 0.00 4.30
845 909 3.710722 CCACAGCGCCTTCCTCCT 61.711 66.667 2.29 0.00 0.00 3.69
859 923 1.292941 CCTCCTCTCTCTCCCCTCCA 61.293 65.000 0.00 0.00 0.00 3.86
886 950 4.332268 GCTCAAGAAATCTACCAGAAGCAG 59.668 45.833 0.00 0.00 0.00 4.24
887 951 4.256920 TCAAGAAATCTACCAGAAGCAGC 58.743 43.478 0.00 0.00 0.00 5.25
888 952 4.019860 TCAAGAAATCTACCAGAAGCAGCT 60.020 41.667 0.00 0.00 0.00 4.24
889 953 4.135747 AGAAATCTACCAGAAGCAGCTC 57.864 45.455 0.00 0.00 0.00 4.09
894 958 0.686789 TACCAGAAGCAGCTCAGCAA 59.313 50.000 0.00 0.00 36.85 3.91
895 959 0.605860 ACCAGAAGCAGCTCAGCAAG 60.606 55.000 0.00 0.00 36.85 4.01
931 995 4.790861 GTCTTCCGGCCGTCGTCC 62.791 72.222 26.12 4.90 37.11 4.79
939 1003 3.827898 GCCGTCGTCCTCCTCCTG 61.828 72.222 0.00 0.00 0.00 3.86
953 1017 4.657969 CCTCCTCCTGGTATTCAGATTTCT 59.342 45.833 0.00 0.00 46.18 2.52
956 1020 4.445448 CCTCCTGGTATTCAGATTTCTGGG 60.445 50.000 7.68 0.01 46.18 4.45
958 1022 3.459598 CCTGGTATTCAGATTTCTGGGGA 59.540 47.826 7.68 0.00 46.18 4.81
985 1049 2.966732 TTTGGGAGGTAGCCTGGCG 61.967 63.158 13.96 0.00 31.76 5.69
1033 1097 0.183731 CTGGCCCCAGGTAAATCTCC 59.816 60.000 0.00 0.00 40.17 3.71
1051 1115 4.431661 CTCCTTGTGAGAATTTGGCTTC 57.568 45.455 0.00 0.00 44.42 3.86
1067 1131 3.450457 TGGCTTCTCTTCTCCTTGATCTC 59.550 47.826 0.00 0.00 0.00 2.75
1073 1137 2.613739 TTCTCCTTGATCTCGCCGCG 62.614 60.000 6.39 6.39 0.00 6.46
1156 1230 2.113807 CATGATCTCCCTCTGTGTGGA 58.886 52.381 0.00 0.00 0.00 4.02
1239 1321 0.393537 CACAATCAGCACCCCTCTCC 60.394 60.000 0.00 0.00 0.00 3.71
1262 1350 3.560636 TCTCCATAGGCTTTAAGGTGC 57.439 47.619 0.00 0.00 0.00 5.01
1269 1357 1.144913 AGGCTTTAAGGTGCAGGTGAA 59.855 47.619 0.00 0.00 0.00 3.18
1270 1358 1.541588 GGCTTTAAGGTGCAGGTGAAG 59.458 52.381 0.00 0.00 0.00 3.02
1271 1359 1.541588 GCTTTAAGGTGCAGGTGAAGG 59.458 52.381 0.00 0.00 0.00 3.46
1272 1360 2.863809 CTTTAAGGTGCAGGTGAAGGT 58.136 47.619 0.00 0.00 0.00 3.50
1273 1361 2.270352 TTAAGGTGCAGGTGAAGGTG 57.730 50.000 0.00 0.00 0.00 4.00
1274 1362 1.429930 TAAGGTGCAGGTGAAGGTGA 58.570 50.000 0.00 0.00 0.00 4.02
1374 1463 7.178573 CCTTTCTTTTCCCCTCTTTCTAATCT 58.821 38.462 0.00 0.00 0.00 2.40
1437 1527 2.047296 ACCTCCCCCTTCCTTTCTCATA 59.953 50.000 0.00 0.00 0.00 2.15
1454 1544 6.463995 TCTCATAGCTTTTCTTCTCTCTCC 57.536 41.667 0.00 0.00 0.00 3.71
1455 1545 6.194235 TCTCATAGCTTTTCTTCTCTCTCCT 58.806 40.000 0.00 0.00 0.00 3.69
1456 1546 6.667414 TCTCATAGCTTTTCTTCTCTCTCCTT 59.333 38.462 0.00 0.00 0.00 3.36
1457 1547 6.638610 TCATAGCTTTTCTTCTCTCTCCTTG 58.361 40.000 0.00 0.00 0.00 3.61
1757 1861 3.935203 CTCGCTCACCACATGTTATCTTT 59.065 43.478 0.00 0.00 0.00 2.52
1760 1864 4.393062 CGCTCACCACATGTTATCTTTCTT 59.607 41.667 0.00 0.00 0.00 2.52
1762 1866 5.412594 GCTCACCACATGTTATCTTTCTTCA 59.587 40.000 0.00 0.00 0.00 3.02
1763 1867 6.621596 GCTCACCACATGTTATCTTTCTTCAC 60.622 42.308 0.00 0.00 0.00 3.18
1765 1869 6.427853 TCACCACATGTTATCTTTCTTCACTG 59.572 38.462 0.00 0.00 0.00 3.66
1810 1914 1.959042 CTAGCTTGGCATGTAGTGGG 58.041 55.000 0.00 0.00 0.00 4.61
1828 1932 1.812571 GGGCTTGTGTTGATCATCGTT 59.187 47.619 0.00 0.00 0.00 3.85
1841 1945 6.228273 TGATCATCGTTTGTTCTCAACTTC 57.772 37.500 0.00 0.00 32.93 3.01
1871 1975 1.875514 AAGTGCTGCACTATGTGTGTG 59.124 47.619 33.11 0.00 44.62 3.82
2115 2222 1.270907 AGGAGAAGGCGATCAACTGT 58.729 50.000 0.00 0.00 0.00 3.55
3027 3287 2.558286 GCGCCCATGCATGCATAGT 61.558 57.895 31.73 9.93 37.32 2.12
3155 3452 6.659242 TCTTTCTTTCTTTCTGGTGTTCTTGT 59.341 34.615 0.00 0.00 0.00 3.16
3156 3453 6.834168 TTCTTTCTTTCTGGTGTTCTTGTT 57.166 33.333 0.00 0.00 0.00 2.83
3157 3454 6.436843 TCTTTCTTTCTGGTGTTCTTGTTC 57.563 37.500 0.00 0.00 0.00 3.18
3158 3455 6.180472 TCTTTCTTTCTGGTGTTCTTGTTCT 58.820 36.000 0.00 0.00 0.00 3.01
3196 3500 2.084546 GGAATTGTGCTCTAGCCGTTT 58.915 47.619 0.00 0.00 41.18 3.60
3258 3578 9.283768 CTCTAACACATCAGACTATCAGAGTAT 57.716 37.037 0.00 0.00 39.06 2.12
3300 3623 1.893808 CGGTGCCATGGATGCTACC 60.894 63.158 18.40 13.39 0.00 3.18
3301 3624 1.227102 GGTGCCATGGATGCTACCA 59.773 57.895 18.40 0.00 44.41 3.25
3312 3635 2.420687 GGATGCTACCATATGCTAGCCC 60.421 54.545 21.85 15.06 35.45 5.19
3313 3636 1.728323 TGCTACCATATGCTAGCCCA 58.272 50.000 21.85 6.74 35.45 5.36
3324 3647 1.559219 TGCTAGCCCATGTGAAGCTTA 59.441 47.619 13.29 0.00 38.06 3.09
3325 3648 2.173356 TGCTAGCCCATGTGAAGCTTAT 59.827 45.455 13.29 0.00 38.06 1.73
3371 3698 1.991121 CTAGGCCTCGGTACATACCA 58.009 55.000 9.68 0.00 46.80 3.25
3372 3699 1.612463 CTAGGCCTCGGTACATACCAC 59.388 57.143 9.68 0.00 46.80 4.16
3373 3700 1.047034 AGGCCTCGGTACATACCACC 61.047 60.000 0.00 4.09 46.80 4.61
3374 3701 1.047034 GGCCTCGGTACATACCACCT 61.047 60.000 8.76 0.00 46.80 4.00
3375 3702 1.696063 GCCTCGGTACATACCACCTA 58.304 55.000 8.76 0.00 46.80 3.08
3376 3703 2.245582 GCCTCGGTACATACCACCTAT 58.754 52.381 8.76 0.00 46.80 2.57
3377 3704 2.230750 GCCTCGGTACATACCACCTATC 59.769 54.545 8.76 0.00 46.80 2.08
3378 3705 2.824341 CCTCGGTACATACCACCTATCC 59.176 54.545 8.76 0.00 46.80 2.59
3380 3707 3.493334 TCGGTACATACCACCTATCCAG 58.507 50.000 8.76 0.00 46.80 3.86
3571 3967 3.120199 CGATGGCTTCCAAGTTTGTAGTG 60.120 47.826 0.00 0.00 36.95 2.74
3644 4041 7.550551 ACAATGAGTACAAGTACCATCATCTTG 59.449 37.037 12.61 11.67 42.60 3.02
3691 4088 6.003326 TCCTCTTCATTATTGTGCTTGTTGA 58.997 36.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.211973 ACTATCTTCACCTTCATGGCTAGA 58.788 41.667 0.00 0.00 40.22 2.43
1 2 5.069648 TGACTATCTTCACCTTCATGGCTAG 59.930 44.000 0.00 0.00 40.22 3.42
2 3 4.962362 TGACTATCTTCACCTTCATGGCTA 59.038 41.667 0.00 0.00 40.22 3.93
3 4 3.776969 TGACTATCTTCACCTTCATGGCT 59.223 43.478 0.00 0.00 40.22 4.75
5 6 4.574013 GCTTGACTATCTTCACCTTCATGG 59.426 45.833 0.00 0.00 42.93 3.66
6 7 5.426504 AGCTTGACTATCTTCACCTTCATG 58.573 41.667 0.00 0.00 0.00 3.07
7 8 5.690464 AGCTTGACTATCTTCACCTTCAT 57.310 39.130 0.00 0.00 0.00 2.57
8 9 5.240891 CAAGCTTGACTATCTTCACCTTCA 58.759 41.667 22.31 0.00 0.00 3.02
9 10 4.633565 CCAAGCTTGACTATCTTCACCTTC 59.366 45.833 28.05 0.00 0.00 3.46
10 11 4.042187 ACCAAGCTTGACTATCTTCACCTT 59.958 41.667 28.05 0.00 0.00 3.50
11 12 3.584848 ACCAAGCTTGACTATCTTCACCT 59.415 43.478 28.05 0.00 0.00 4.00
12 13 3.686726 CACCAAGCTTGACTATCTTCACC 59.313 47.826 28.05 0.00 0.00 4.02
13 14 3.126000 GCACCAAGCTTGACTATCTTCAC 59.874 47.826 28.05 1.49 41.15 3.18
14 15 3.244526 TGCACCAAGCTTGACTATCTTCA 60.245 43.478 28.05 10.26 45.94 3.02
15 16 3.338249 TGCACCAAGCTTGACTATCTTC 58.662 45.455 28.05 7.97 45.94 2.87
16 17 3.008375 TCTGCACCAAGCTTGACTATCTT 59.992 43.478 28.05 0.00 45.94 2.40
17 18 2.568956 TCTGCACCAAGCTTGACTATCT 59.431 45.455 28.05 0.00 45.94 1.98
18 19 2.675348 GTCTGCACCAAGCTTGACTATC 59.325 50.000 28.05 11.70 45.94 2.08
19 20 2.038952 TGTCTGCACCAAGCTTGACTAT 59.961 45.455 28.05 7.31 45.94 2.12
20 21 1.416030 TGTCTGCACCAAGCTTGACTA 59.584 47.619 28.05 9.84 45.94 2.59
21 22 0.181114 TGTCTGCACCAAGCTTGACT 59.819 50.000 28.05 9.37 45.94 3.41
22 23 0.590195 CTGTCTGCACCAAGCTTGAC 59.410 55.000 28.05 16.36 45.94 3.18
23 24 0.535780 CCTGTCTGCACCAAGCTTGA 60.536 55.000 28.05 6.71 45.94 3.02
24 25 0.820891 ACCTGTCTGCACCAAGCTTG 60.821 55.000 19.93 19.93 45.94 4.01
25 26 0.536006 GACCTGTCTGCACCAAGCTT 60.536 55.000 0.00 0.00 45.94 3.74
26 27 1.072159 GACCTGTCTGCACCAAGCT 59.928 57.895 0.00 0.00 45.94 3.74
27 28 2.320587 CGACCTGTCTGCACCAAGC 61.321 63.158 0.00 0.00 45.96 4.01
28 29 0.668706 CTCGACCTGTCTGCACCAAG 60.669 60.000 0.00 0.00 0.00 3.61
29 30 1.367471 CTCGACCTGTCTGCACCAA 59.633 57.895 0.00 0.00 0.00 3.67
30 31 2.574018 CCTCGACCTGTCTGCACCA 61.574 63.158 0.00 0.00 0.00 4.17
31 32 2.100879 AACCTCGACCTGTCTGCACC 62.101 60.000 0.00 0.00 0.00 5.01
32 33 0.667792 GAACCTCGACCTGTCTGCAC 60.668 60.000 0.00 0.00 0.00 4.57
33 34 1.112916 TGAACCTCGACCTGTCTGCA 61.113 55.000 0.00 0.00 0.00 4.41
34 35 0.389166 CTGAACCTCGACCTGTCTGC 60.389 60.000 0.00 0.00 0.00 4.26
35 36 0.389166 GCTGAACCTCGACCTGTCTG 60.389 60.000 0.00 0.00 0.00 3.51
36 37 0.540830 AGCTGAACCTCGACCTGTCT 60.541 55.000 0.00 0.00 0.00 3.41
37 38 0.318762 AAGCTGAACCTCGACCTGTC 59.681 55.000 0.00 0.00 0.00 3.51
38 39 1.629043 TAAGCTGAACCTCGACCTGT 58.371 50.000 0.00 0.00 0.00 4.00
39 40 2.743636 TTAAGCTGAACCTCGACCTG 57.256 50.000 0.00 0.00 0.00 4.00
40 41 4.024670 ACTATTAAGCTGAACCTCGACCT 58.975 43.478 0.00 0.00 0.00 3.85
41 42 4.113354 CACTATTAAGCTGAACCTCGACC 58.887 47.826 0.00 0.00 0.00 4.79
42 43 4.995124 TCACTATTAAGCTGAACCTCGAC 58.005 43.478 0.00 0.00 0.00 4.20
43 44 5.417894 TCTTCACTATTAAGCTGAACCTCGA 59.582 40.000 0.00 0.00 0.00 4.04
44 45 5.651530 TCTTCACTATTAAGCTGAACCTCG 58.348 41.667 0.00 0.00 0.00 4.63
45 46 7.268586 TCATCTTCACTATTAAGCTGAACCTC 58.731 38.462 0.00 0.00 28.92 3.85
46 47 7.187824 TCATCTTCACTATTAAGCTGAACCT 57.812 36.000 0.00 0.00 28.92 3.50
47 48 7.766278 TCTTCATCTTCACTATTAAGCTGAACC 59.234 37.037 0.00 0.00 35.36 3.62
48 49 8.709386 TCTTCATCTTCACTATTAAGCTGAAC 57.291 34.615 0.00 0.00 35.36 3.18
49 50 9.725019 TTTCTTCATCTTCACTATTAAGCTGAA 57.275 29.630 0.00 0.00 36.97 3.02
50 51 9.725019 TTTTCTTCATCTTCACTATTAAGCTGA 57.275 29.630 0.00 0.00 29.70 4.26
51 52 9.766277 GTTTTCTTCATCTTCACTATTAAGCTG 57.234 33.333 0.00 0.00 0.00 4.24
52 53 8.660373 CGTTTTCTTCATCTTCACTATTAAGCT 58.340 33.333 0.00 0.00 0.00 3.74
53 54 8.656849 TCGTTTTCTTCATCTTCACTATTAAGC 58.343 33.333 0.00 0.00 0.00 3.09
54 55 9.959775 GTCGTTTTCTTCATCTTCACTATTAAG 57.040 33.333 0.00 0.00 0.00 1.85
55 56 8.932791 GGTCGTTTTCTTCATCTTCACTATTAA 58.067 33.333 0.00 0.00 0.00 1.40
56 57 8.092068 TGGTCGTTTTCTTCATCTTCACTATTA 58.908 33.333 0.00 0.00 0.00 0.98
57 58 6.934645 TGGTCGTTTTCTTCATCTTCACTATT 59.065 34.615 0.00 0.00 0.00 1.73
58 59 6.464222 TGGTCGTTTTCTTCATCTTCACTAT 58.536 36.000 0.00 0.00 0.00 2.12
59 60 5.849510 TGGTCGTTTTCTTCATCTTCACTA 58.150 37.500 0.00 0.00 0.00 2.74
60 61 4.703897 TGGTCGTTTTCTTCATCTTCACT 58.296 39.130 0.00 0.00 0.00 3.41
61 62 5.418310 TTGGTCGTTTTCTTCATCTTCAC 57.582 39.130 0.00 0.00 0.00 3.18
62 63 4.024048 GCTTGGTCGTTTTCTTCATCTTCA 60.024 41.667 0.00 0.00 0.00 3.02
63 64 4.214332 AGCTTGGTCGTTTTCTTCATCTTC 59.786 41.667 0.00 0.00 0.00 2.87
64 65 4.137543 AGCTTGGTCGTTTTCTTCATCTT 58.862 39.130 0.00 0.00 0.00 2.40
65 66 3.744660 AGCTTGGTCGTTTTCTTCATCT 58.255 40.909 0.00 0.00 0.00 2.90
66 67 4.467735 GAAGCTTGGTCGTTTTCTTCATC 58.532 43.478 2.10 0.00 32.53 2.92
67 68 3.253432 GGAAGCTTGGTCGTTTTCTTCAT 59.747 43.478 2.10 0.00 33.56 2.57
68 69 2.616842 GGAAGCTTGGTCGTTTTCTTCA 59.383 45.455 2.10 0.00 33.56 3.02
69 70 2.879026 AGGAAGCTTGGTCGTTTTCTTC 59.121 45.455 2.10 0.00 0.00 2.87
70 71 2.932261 AGGAAGCTTGGTCGTTTTCTT 58.068 42.857 2.10 0.00 0.00 2.52
71 72 2.640316 AGGAAGCTTGGTCGTTTTCT 57.360 45.000 2.10 0.00 0.00 2.52
72 73 2.879026 AGAAGGAAGCTTGGTCGTTTTC 59.121 45.455 2.10 0.00 0.00 2.29
73 74 2.932261 AGAAGGAAGCTTGGTCGTTTT 58.068 42.857 2.10 0.00 0.00 2.43
74 75 2.640316 AGAAGGAAGCTTGGTCGTTT 57.360 45.000 2.10 0.00 0.00 3.60
75 76 2.633481 ACTAGAAGGAAGCTTGGTCGTT 59.367 45.455 2.10 0.00 0.00 3.85
76 77 2.231721 GACTAGAAGGAAGCTTGGTCGT 59.768 50.000 2.10 0.00 0.00 4.34
77 78 2.417515 GGACTAGAAGGAAGCTTGGTCG 60.418 54.545 2.10 0.00 0.00 4.79
78 79 2.835156 AGGACTAGAAGGAAGCTTGGTC 59.165 50.000 2.10 0.00 0.00 4.02
79 80 2.909217 AGGACTAGAAGGAAGCTTGGT 58.091 47.619 2.10 0.00 0.00 3.67
80 81 3.181485 CGTAGGACTAGAAGGAAGCTTGG 60.181 52.174 2.10 0.00 0.00 3.61
81 82 3.735514 GCGTAGGACTAGAAGGAAGCTTG 60.736 52.174 2.10 0.00 0.00 4.01
82 83 2.427812 GCGTAGGACTAGAAGGAAGCTT 59.572 50.000 0.00 0.00 0.00 3.74
83 84 2.025898 GCGTAGGACTAGAAGGAAGCT 58.974 52.381 0.00 0.00 0.00 3.74
84 85 1.067364 GGCGTAGGACTAGAAGGAAGC 59.933 57.143 0.00 0.00 0.00 3.86
85 86 2.376109 TGGCGTAGGACTAGAAGGAAG 58.624 52.381 0.00 0.00 0.00 3.46
86 87 2.519771 TGGCGTAGGACTAGAAGGAA 57.480 50.000 0.00 0.00 0.00 3.36
87 88 2.307768 CATGGCGTAGGACTAGAAGGA 58.692 52.381 0.00 0.00 0.00 3.36
88 89 1.341531 CCATGGCGTAGGACTAGAAGG 59.658 57.143 0.00 0.00 0.00 3.46
89 90 1.269831 GCCATGGCGTAGGACTAGAAG 60.270 57.143 23.48 0.00 0.00 2.85
90 91 0.750850 GCCATGGCGTAGGACTAGAA 59.249 55.000 23.48 0.00 0.00 2.10
91 92 0.396556 TGCCATGGCGTAGGACTAGA 60.397 55.000 30.87 7.13 45.51 2.43
92 93 0.032678 CTGCCATGGCGTAGGACTAG 59.967 60.000 30.87 16.43 45.51 2.57
93 94 1.399744 CCTGCCATGGCGTAGGACTA 61.400 60.000 30.78 12.45 45.51 2.59
94 95 2.735772 CCTGCCATGGCGTAGGACT 61.736 63.158 30.78 0.00 45.51 3.85
95 96 2.203070 CCTGCCATGGCGTAGGAC 60.203 66.667 30.78 6.78 45.51 3.85
96 97 2.882403 TACCCTGCCATGGCGTAGGA 62.882 60.000 34.29 19.97 45.51 2.94
97 98 1.768684 ATACCCTGCCATGGCGTAGG 61.769 60.000 28.60 28.60 45.51 3.18
98 99 0.108585 AATACCCTGCCATGGCGTAG 59.891 55.000 30.87 22.85 45.51 3.51
99 100 0.107831 GAATACCCTGCCATGGCGTA 59.892 55.000 30.87 25.24 45.51 4.42
100 101 1.152963 GAATACCCTGCCATGGCGT 60.153 57.895 30.87 23.97 45.51 5.68
101 102 0.466189 AAGAATACCCTGCCATGGCG 60.466 55.000 30.87 23.82 45.51 5.69
102 103 1.322442 GAAGAATACCCTGCCATGGC 58.678 55.000 30.54 30.54 42.35 4.40
103 104 1.496429 AGGAAGAATACCCTGCCATGG 59.504 52.381 7.63 7.63 34.08 3.66
104 105 2.954318 CAAGGAAGAATACCCTGCCATG 59.046 50.000 0.00 0.00 34.08 3.66
105 106 2.091665 CCAAGGAAGAATACCCTGCCAT 60.092 50.000 0.00 0.00 34.08 4.40
106 107 1.284785 CCAAGGAAGAATACCCTGCCA 59.715 52.381 0.00 0.00 34.08 4.92
107 108 1.285078 ACCAAGGAAGAATACCCTGCC 59.715 52.381 0.00 0.00 32.12 4.85
108 109 2.239907 AGACCAAGGAAGAATACCCTGC 59.760 50.000 0.00 0.00 32.12 4.85
109 110 3.777522 AGAGACCAAGGAAGAATACCCTG 59.222 47.826 0.00 0.00 32.12 4.45
110 111 4.081695 AGAGACCAAGGAAGAATACCCT 57.918 45.455 0.00 0.00 0.00 4.34
111 112 4.518249 CAAGAGACCAAGGAAGAATACCC 58.482 47.826 0.00 0.00 0.00 3.69
112 113 4.019231 ACCAAGAGACCAAGGAAGAATACC 60.019 45.833 0.00 0.00 0.00 2.73
113 114 5.167303 ACCAAGAGACCAAGGAAGAATAC 57.833 43.478 0.00 0.00 0.00 1.89
114 115 4.081642 CGACCAAGAGACCAAGGAAGAATA 60.082 45.833 0.00 0.00 0.00 1.75
115 116 3.307059 CGACCAAGAGACCAAGGAAGAAT 60.307 47.826 0.00 0.00 0.00 2.40
116 117 2.037251 CGACCAAGAGACCAAGGAAGAA 59.963 50.000 0.00 0.00 0.00 2.52
117 118 1.618837 CGACCAAGAGACCAAGGAAGA 59.381 52.381 0.00 0.00 0.00 2.87
118 119 1.344763 ACGACCAAGAGACCAAGGAAG 59.655 52.381 0.00 0.00 0.00 3.46
119 120 1.343465 GACGACCAAGAGACCAAGGAA 59.657 52.381 0.00 0.00 0.00 3.36
120 121 0.966920 GACGACCAAGAGACCAAGGA 59.033 55.000 0.00 0.00 0.00 3.36
121 122 0.037232 GGACGACCAAGAGACCAAGG 60.037 60.000 0.00 0.00 35.97 3.61
122 123 0.388649 CGGACGACCAAGAGACCAAG 60.389 60.000 4.48 0.00 35.59 3.61
123 124 1.663739 CGGACGACCAAGAGACCAA 59.336 57.895 4.48 0.00 35.59 3.67
124 125 2.927580 GCGGACGACCAAGAGACCA 61.928 63.158 4.48 0.00 35.59 4.02
125 126 2.126031 GCGGACGACCAAGAGACC 60.126 66.667 4.48 0.00 35.59 3.85
126 127 0.454600 TATGCGGACGACCAAGAGAC 59.545 55.000 4.48 0.00 35.59 3.36
127 128 1.399714 ATATGCGGACGACCAAGAGA 58.600 50.000 4.48 0.00 35.59 3.10
128 129 3.577649 ATATATGCGGACGACCAAGAG 57.422 47.619 4.48 0.00 35.59 2.85
129 130 5.407502 CAATATATATGCGGACGACCAAGA 58.592 41.667 4.48 0.00 35.59 3.02
130 131 4.032900 GCAATATATATGCGGACGACCAAG 59.967 45.833 4.48 0.00 33.57 3.61
131 132 3.930229 GCAATATATATGCGGACGACCAA 59.070 43.478 4.48 0.00 33.57 3.67
132 133 3.517602 GCAATATATATGCGGACGACCA 58.482 45.455 4.48 0.00 33.57 4.02
133 134 2.864343 GGCAATATATATGCGGACGACC 59.136 50.000 0.00 0.00 44.75 4.79
134 135 3.517602 TGGCAATATATATGCGGACGAC 58.482 45.455 0.00 0.00 44.75 4.34
135 136 3.878160 TGGCAATATATATGCGGACGA 57.122 42.857 0.00 0.00 44.75 4.20
136 137 3.303329 GCATGGCAATATATATGCGGACG 60.303 47.826 0.00 0.00 44.75 4.79
137 138 3.627123 TGCATGGCAATATATATGCGGAC 59.373 43.478 11.67 0.00 46.61 4.79
138 139 3.883669 TGCATGGCAATATATATGCGGA 58.116 40.909 11.67 4.30 46.61 5.54
139 140 4.841443 ATGCATGGCAATATATATGCGG 57.159 40.909 0.00 6.91 46.61 5.69
140 141 6.532302 ACAAAATGCATGGCAATATATATGCG 59.468 34.615 0.00 2.72 46.61 4.73
177 178 4.925068 ACTTGAATGAAGTGTTGCAGAAC 58.075 39.130 0.00 0.00 43.71 3.01
219 220 2.988493 GTGCTCGTGTACGGTTCAAATA 59.012 45.455 4.44 0.00 40.29 1.40
220 221 1.796459 GTGCTCGTGTACGGTTCAAAT 59.204 47.619 4.44 0.00 40.29 2.32
265 270 2.224784 GTCGACACCGGCTACAAAATTT 59.775 45.455 11.55 0.00 37.44 1.82
278 283 0.782384 GTCATGTTGTCGTCGACACC 59.218 55.000 26.95 20.97 42.60 4.16
352 364 2.674380 CAGTGCACCTGCCCCTTC 60.674 66.667 14.63 0.00 41.18 3.46
517 537 1.065709 TCGACCATTGTAAGGGAAGGC 60.066 52.381 1.88 0.00 33.23 4.35
518 538 3.206150 CATCGACCATTGTAAGGGAAGG 58.794 50.000 1.88 0.00 33.23 3.46
519 539 3.118408 TCCATCGACCATTGTAAGGGAAG 60.118 47.826 1.88 0.00 33.23 3.46
520 540 2.841266 TCCATCGACCATTGTAAGGGAA 59.159 45.455 1.88 0.00 33.23 3.97
576 596 3.074369 TTGCTCGATCGGAGGCCA 61.074 61.111 16.41 6.78 43.36 5.36
620 651 1.196012 GTACTGTGAGGAAGGAGGGG 58.804 60.000 0.00 0.00 0.00 4.79
621 652 0.818296 CGTACTGTGAGGAAGGAGGG 59.182 60.000 0.00 0.00 0.00 4.30
622 653 1.473278 GACGTACTGTGAGGAAGGAGG 59.527 57.143 0.00 0.00 0.00 4.30
623 654 1.130749 CGACGTACTGTGAGGAAGGAG 59.869 57.143 0.00 0.00 0.00 3.69
624 655 1.162698 CGACGTACTGTGAGGAAGGA 58.837 55.000 0.00 0.00 0.00 3.36
625 656 0.456312 GCGACGTACTGTGAGGAAGG 60.456 60.000 0.00 0.00 0.00 3.46
626 657 0.240145 TGCGACGTACTGTGAGGAAG 59.760 55.000 0.00 0.00 0.00 3.46
627 658 0.039798 GTGCGACGTACTGTGAGGAA 60.040 55.000 8.95 0.00 0.00 3.36
628 659 1.167781 TGTGCGACGTACTGTGAGGA 61.168 55.000 16.98 0.00 0.00 3.71
645 676 1.514983 TGGAGCAGATGGATGGATGT 58.485 50.000 0.00 0.00 0.00 3.06
650 681 2.940158 TGGATTTGGAGCAGATGGATG 58.060 47.619 0.00 0.00 0.00 3.51
797 861 3.455910 TGAGTGGAATTGTCCCTCCTATG 59.544 47.826 8.07 0.00 44.23 2.23
823 887 3.365265 GAAGGCGCTGTGGTTGGG 61.365 66.667 7.64 0.00 0.00 4.12
844 908 0.539438 CGGATGGAGGGGAGAGAGAG 60.539 65.000 0.00 0.00 0.00 3.20
845 909 1.539165 CGGATGGAGGGGAGAGAGA 59.461 63.158 0.00 0.00 0.00 3.10
859 923 3.706594 TCTGGTAGATTTCTTGAGCGGAT 59.293 43.478 0.00 0.00 0.00 4.18
887 951 2.818714 CTCCTGCGGCTTGCTGAG 60.819 66.667 5.52 8.03 46.63 3.35
931 995 5.454471 CCAGAAATCTGAATACCAGGAGGAG 60.454 48.000 11.94 0.00 46.59 3.69
939 1003 5.755849 TCTTTCCCCAGAAATCTGAATACC 58.244 41.667 11.94 0.00 46.59 2.73
953 1017 3.238597 CTCCCAAACAATTCTTTCCCCA 58.761 45.455 0.00 0.00 0.00 4.96
956 1020 4.082190 GCTACCTCCCAAACAATTCTTTCC 60.082 45.833 0.00 0.00 0.00 3.13
958 1022 3.832490 GGCTACCTCCCAAACAATTCTTT 59.168 43.478 0.00 0.00 0.00 2.52
985 1049 0.464373 TCCATGCGAAGGCTCCAATC 60.464 55.000 0.00 0.00 40.82 2.67
1051 1115 1.268999 CGGCGAGATCAAGGAGAAGAG 60.269 57.143 0.00 0.00 0.00 2.85
1073 1137 0.467804 GAGAGGAGGATGAACAGGCC 59.532 60.000 0.00 0.00 0.00 5.19
1075 1139 2.168106 CACAGAGAGGAGGATGAACAGG 59.832 54.545 0.00 0.00 0.00 4.00
1156 1230 1.002087 GAACACGACCCAAGAGGACAT 59.998 52.381 0.00 0.00 39.89 3.06
1239 1321 4.455606 CACCTTAAAGCCTATGGAGAAGG 58.544 47.826 0.00 0.00 38.34 3.46
1262 1350 2.352805 GGGGCTCACCTTCACCTG 59.647 66.667 0.00 0.00 40.03 4.00
1374 1463 1.846439 GGATGATGGTGAGGAAAGGGA 59.154 52.381 0.00 0.00 0.00 4.20
1437 1527 4.972751 ACAAGGAGAGAGAAGAAAAGCT 57.027 40.909 0.00 0.00 0.00 3.74
1455 1545 1.952990 TCTTTTGATGCGAGGCAACAA 59.047 42.857 8.88 8.88 46.43 2.83
1456 1546 1.536766 CTCTTTTGATGCGAGGCAACA 59.463 47.619 0.00 0.00 43.62 3.33
1457 1547 1.135575 CCTCTTTTGATGCGAGGCAAC 60.136 52.381 0.00 0.00 43.62 4.17
1719 1812 1.153208 GAGCATGCAGAGGTCAGGG 60.153 63.158 21.98 0.00 33.87 4.45
1722 1815 2.125391 GCGAGCATGCAGAGGTCA 60.125 61.111 21.98 0.00 33.29 4.02
1723 1816 1.882167 GAGCGAGCATGCAGAGGTC 60.882 63.158 21.98 19.77 37.31 3.85
1757 1861 2.355756 GCAAGCAAGAACACAGTGAAGA 59.644 45.455 7.81 0.00 0.00 2.87
1760 1864 1.942657 GAGCAAGCAAGAACACAGTGA 59.057 47.619 7.81 0.00 0.00 3.41
1762 1866 2.338577 AGAGCAAGCAAGAACACAGT 57.661 45.000 0.00 0.00 0.00 3.55
1763 1867 2.740981 CCTAGAGCAAGCAAGAACACAG 59.259 50.000 0.00 0.00 0.00 3.66
1765 1869 2.481952 CACCTAGAGCAAGCAAGAACAC 59.518 50.000 0.00 0.00 0.00 3.32
1810 1914 3.888934 ACAAACGATGATCAACACAAGC 58.111 40.909 0.00 0.00 0.00 4.01
1828 1932 5.917462 TGATCAGTCAGAAGTTGAGAACAA 58.083 37.500 0.00 0.00 36.21 2.83
1841 1945 1.463831 GTGCAGCACTTGATCAGTCAG 59.536 52.381 18.92 0.00 35.39 3.51
1871 1975 0.614979 TAGCCCCTGAGGACACAGAC 60.615 60.000 0.00 0.00 39.94 3.51
1905 2012 1.424302 CCCATCAGCATCTCCTCCATT 59.576 52.381 0.00 0.00 0.00 3.16
1936 2043 1.597854 CTTGCACCTGCTGGTTCGA 60.598 57.895 13.36 7.37 46.05 3.71
2055 2162 2.436115 GTGCTACCCGCTCCAACC 60.436 66.667 0.00 0.00 40.11 3.77
2057 2164 4.077184 CCGTGCTACCCGCTCCAA 62.077 66.667 0.00 0.00 40.11 3.53
2115 2222 3.948719 GTGGAGTTGCACCGGGGA 61.949 66.667 8.67 0.00 0.00 4.81
3027 3287 2.809174 CGCACAGCCGACGATGAA 60.809 61.111 0.00 0.00 0.00 2.57
3155 3452 6.500589 TCCAAGGAAGAAGAAGAAGAAGAA 57.499 37.500 0.00 0.00 0.00 2.52
3156 3453 6.500589 TTCCAAGGAAGAAGAAGAAGAAGA 57.499 37.500 0.00 0.00 0.00 2.87
3157 3454 7.230309 ACAATTCCAAGGAAGAAGAAGAAGAAG 59.770 37.037 7.69 0.00 37.56 2.85
3158 3455 7.013655 CACAATTCCAAGGAAGAAGAAGAAGAA 59.986 37.037 7.69 0.00 37.56 2.52
3196 3500 5.049060 CCAAGTCGATCACCAAACACAAATA 60.049 40.000 0.00 0.00 0.00 1.40
3258 3578 7.011389 CCGATCAACAGAGATTAAAATGCTGTA 59.989 37.037 0.00 0.00 38.74 2.74
3279 3599 0.035317 TAGCATCCATGGCACCGATC 59.965 55.000 6.96 0.00 0.00 3.69
3300 3623 2.486982 GCTTCACATGGGCTAGCATATG 59.513 50.000 18.24 20.47 0.00 1.78
3301 3624 2.374504 AGCTTCACATGGGCTAGCATAT 59.625 45.455 18.24 7.10 34.31 1.78
3302 3625 1.770658 AGCTTCACATGGGCTAGCATA 59.229 47.619 18.24 4.68 34.31 3.14
3312 3635 6.038356 CCAGCCTAAAAATAAGCTTCACATG 58.962 40.000 0.00 0.00 31.93 3.21
3313 3636 5.394553 GCCAGCCTAAAAATAAGCTTCACAT 60.395 40.000 0.00 0.00 31.93 3.21
3324 3647 3.175438 ACTCCAAGCCAGCCTAAAAAT 57.825 42.857 0.00 0.00 0.00 1.82
3325 3648 2.675658 ACTCCAAGCCAGCCTAAAAA 57.324 45.000 0.00 0.00 0.00 1.94
3371 3698 2.626743 GCCATGTACGTACTGGATAGGT 59.373 50.000 31.34 8.93 35.98 3.08
3372 3699 2.351447 CGCCATGTACGTACTGGATAGG 60.351 54.545 31.34 21.79 31.38 2.57
3373 3700 2.921069 GCGCCATGTACGTACTGGATAG 60.921 54.545 31.34 24.37 31.38 2.08
3374 3701 1.001048 GCGCCATGTACGTACTGGATA 60.001 52.381 31.34 14.41 31.38 2.59
3375 3702 0.249322 GCGCCATGTACGTACTGGAT 60.249 55.000 31.34 16.33 31.38 3.41
3376 3703 1.140161 GCGCCATGTACGTACTGGA 59.860 57.895 31.34 15.02 31.38 3.86
3377 3704 0.529773 ATGCGCCATGTACGTACTGG 60.530 55.000 26.67 26.67 0.00 4.00
3378 3705 0.576798 CATGCGCCATGTACGTACTG 59.423 55.000 25.12 19.08 37.12 2.74
3552 3948 2.092103 ACCACTACAAACTTGGAAGCCA 60.092 45.455 0.00 0.00 34.24 4.75
3658 4055 9.807649 GCACAATAATGAAGAGGAATTTGTAAT 57.192 29.630 0.00 0.00 0.00 1.89
3659 4056 9.023962 AGCACAATAATGAAGAGGAATTTGTAA 57.976 29.630 0.00 0.00 0.00 2.41
3691 4088 9.925545 TTTGGATGAGCCTATATATGCATAAAT 57.074 29.630 11.13 0.00 37.63 1.40


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

AutoCloner maintained by Alex Coulton.