Multiple sequence alignment - TraesCS7D01G383000

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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 TraesCS7D01G383000 chr7D 100.000 4361 0 0 1 4361 496776296 496780656 0.000000e+00 8054.0
1 TraesCS7D01G383000 chr7A 94.938 3773 153 19 328 4093 562169787 562173528 0.000000e+00 5875.0
2 TraesCS7D01G383000 chr7A 90.120 334 22 4 1 332 98100975 98100651 1.450000e-114 424.0
3 TraesCS7D01G383000 chr7A 91.228 285 11 4 4090 4360 562173657 562173941 4.120000e-100 375.0
4 TraesCS7D01G383000 chr7B 94.363 3743 149 29 367 4072 524906248 524909965 0.000000e+00 5686.0
5 TraesCS7D01G383000 chr7B 93.713 334 16 3 1 332 308667088 308666758 3.030000e-136 496.0
6 TraesCS7D01G383000 chr7B 93.878 245 7 2 4122 4360 524909960 524910202 3.210000e-96 363.0
7 TraesCS7D01G383000 chr7B 85.139 323 40 5 2 322 671278771 671278455 1.510000e-84 324.0
8 TraesCS7D01G383000 chr1B 94.294 333 13 5 1 330 527289554 527289883 5.030000e-139 505.0
9 TraesCS7D01G383000 chr1B 87.681 276 25 8 55 327 432689327 432689596 3.270000e-81 313.0
10 TraesCS7D01G383000 chr5B 94.012 334 15 4 1 332 292490128 292490458 6.510000e-138 501.0
11 TraesCS7D01G383000 chr4B 93.114 334 17 5 1 332 388972462 388972791 6.560000e-133 484.0
12 TraesCS7D01G383000 chr1A 90.663 332 26 3 1 330 393997622 393997294 1.860000e-118 436.0
13 TraesCS7D01G383000 chr5A 84.894 331 42 6 3 330 367594466 367594791 1.170000e-85 327.0
14 TraesCS7D01G383000 chr6B 94.258 209 9 3 26 234 7597758 7597963 2.530000e-82 316.0
15 TraesCS7D01G383000 chr5D 86.747 83 11 0 1009 1091 46083795 46083713 4.640000e-15 93.5
16 TraesCS7D01G383000 chr6D 91.071 56 4 1 4136 4191 68707507 68707561 1.680000e-09 75.0


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 TraesCS7D01G383000 chr7D 496776296 496780656 4360 False 8054.0 8054 100.0000 1 4361 1 chr7D.!!$F1 4360
1 TraesCS7D01G383000 chr7A 562169787 562173941 4154 False 3125.0 5875 93.0830 328 4360 2 chr7A.!!$F1 4032
2 TraesCS7D01G383000 chr7B 524906248 524910202 3954 False 3024.5 5686 94.1205 367 4360 2 chr7B.!!$F1 3993

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
123 124 0.033699 AGCCATGCTTCCCCTCTTTC 60.034 55.000 0.00 0.0 33.89 2.62 F
124 125 0.033699 GCCATGCTTCCCCTCTTTCT 60.034 55.000 0.00 0.0 0.00 2.52 F
804 834 0.632835 ATTCAGATGTGCACCCCCAT 59.367 50.000 15.69 0.0 0.00 4.00 F
2338 2371 1.134753 CAACTGTTGTTTGCCTGCTCA 59.865 47.619 12.30 0.0 33.52 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1218 1.105759 GGATCACATCCCAGCCAAGC 61.106 60.000 0.00 0.0 43.88 4.01 R
1327 1360 1.153823 CCTCCACGTAACCAGCTCG 60.154 63.158 0.00 0.0 0.00 5.03 R
2586 2619 0.171007 CCCCGTGTTGCTGCATTAAG 59.829 55.000 1.84 0.0 0.00 1.85 R
3985 4035 0.251341 CCAGGGTGCCTACTTTGCTT 60.251 55.000 0.00 0.0 29.64 3.91 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 4.450082 ACTAAAATTTTGCCGCTAAGGG 57.550 40.909 13.76 0.00 41.48 3.95
22 23 4.083565 ACTAAAATTTTGCCGCTAAGGGA 58.916 39.130 13.76 0.00 41.48 4.20
23 24 4.709886 ACTAAAATTTTGCCGCTAAGGGAT 59.290 37.500 13.76 0.00 41.19 3.85
24 25 5.889289 ACTAAAATTTTGCCGCTAAGGGATA 59.111 36.000 13.76 0.00 41.19 2.59
25 26 5.669164 AAAATTTTGCCGCTAAGGGATAA 57.331 34.783 1.75 0.00 41.19 1.75
26 27 5.669164 AAATTTTGCCGCTAAGGGATAAA 57.331 34.783 0.00 0.00 41.19 1.40
27 28 5.669164 AATTTTGCCGCTAAGGGATAAAA 57.331 34.783 0.00 0.00 41.19 1.52
28 29 4.443913 TTTTGCCGCTAAGGGATAAAAC 57.556 40.909 0.00 0.00 41.19 2.43
29 30 3.359695 TTGCCGCTAAGGGATAAAACT 57.640 42.857 0.00 0.00 41.19 2.66
30 31 2.914059 TGCCGCTAAGGGATAAAACTC 58.086 47.619 0.00 0.00 41.48 3.01
31 32 2.219458 GCCGCTAAGGGATAAAACTCC 58.781 52.381 0.00 0.00 41.48 3.85
32 33 2.420967 GCCGCTAAGGGATAAAACTCCA 60.421 50.000 0.00 0.00 41.48 3.86
33 34 3.467803 CCGCTAAGGGATAAAACTCCAG 58.532 50.000 0.00 0.00 37.01 3.86
34 35 3.134081 CCGCTAAGGGATAAAACTCCAGA 59.866 47.826 0.00 0.00 37.01 3.86
35 36 4.383770 CCGCTAAGGGATAAAACTCCAGAA 60.384 45.833 0.00 0.00 37.01 3.02
36 37 5.183228 CGCTAAGGGATAAAACTCCAGAAA 58.817 41.667 0.00 0.00 37.01 2.52
37 38 5.064834 CGCTAAGGGATAAAACTCCAGAAAC 59.935 44.000 0.00 0.00 37.01 2.78
38 39 5.064834 GCTAAGGGATAAAACTCCAGAAACG 59.935 44.000 0.00 0.00 37.01 3.60
39 40 4.903045 AGGGATAAAACTCCAGAAACGA 57.097 40.909 0.00 0.00 37.01 3.85
40 41 4.576879 AGGGATAAAACTCCAGAAACGAC 58.423 43.478 0.00 0.00 37.01 4.34
41 42 4.041198 AGGGATAAAACTCCAGAAACGACA 59.959 41.667 0.00 0.00 37.01 4.35
42 43 4.941873 GGGATAAAACTCCAGAAACGACAT 59.058 41.667 0.00 0.00 37.01 3.06
43 44 5.163754 GGGATAAAACTCCAGAAACGACATG 60.164 44.000 0.00 0.00 37.01 3.21
44 45 5.163754 GGATAAAACTCCAGAAACGACATGG 60.164 44.000 0.00 0.00 35.24 3.66
45 46 1.523758 AACTCCAGAAACGACATGGC 58.476 50.000 0.00 0.00 33.92 4.40
46 47 0.670546 ACTCCAGAAACGACATGGCG 60.671 55.000 21.98 21.98 33.92 5.69
47 48 1.361668 CTCCAGAAACGACATGGCGG 61.362 60.000 27.41 6.53 33.92 6.13
48 49 1.671054 CCAGAAACGACATGGCGGT 60.671 57.895 27.41 18.42 35.12 5.68
49 50 1.497278 CAGAAACGACATGGCGGTG 59.503 57.895 27.41 12.98 35.12 4.94
50 51 1.671054 AGAAACGACATGGCGGTGG 60.671 57.895 27.41 0.00 35.12 4.61
51 52 3.322706 GAAACGACATGGCGGTGGC 62.323 63.158 27.41 11.48 38.90 5.01
52 53 4.634703 AACGACATGGCGGTGGCA 62.635 61.111 27.41 0.00 43.52 4.92
53 54 4.634703 ACGACATGGCGGTGGCAA 62.635 61.111 27.41 0.00 42.43 4.52
54 55 4.101790 CGACATGGCGGTGGCAAC 62.102 66.667 14.85 0.00 42.43 4.17
55 56 4.101790 GACATGGCGGTGGCAACG 62.102 66.667 22.75 22.75 42.43 4.10
56 57 4.634703 ACATGGCGGTGGCAACGA 62.635 61.111 31.68 9.41 42.43 3.85
57 58 3.133464 CATGGCGGTGGCAACGAT 61.133 61.111 31.68 11.75 42.43 3.73
58 59 3.133464 ATGGCGGTGGCAACGATG 61.133 61.111 31.68 0.00 42.43 3.84
68 69 1.226773 GCAACGATGGCATGGAAGC 60.227 57.895 16.77 14.40 0.00 3.86
69 70 1.063006 CAACGATGGCATGGAAGCG 59.937 57.895 16.77 10.09 34.64 4.68
70 71 1.078497 AACGATGGCATGGAAGCGA 60.078 52.632 16.77 0.00 34.64 4.93
71 72 0.676466 AACGATGGCATGGAAGCGAA 60.676 50.000 16.77 0.00 34.64 4.70
72 73 1.091771 ACGATGGCATGGAAGCGAAG 61.092 55.000 16.77 0.00 34.64 3.79
73 74 1.779025 CGATGGCATGGAAGCGAAGG 61.779 60.000 3.81 0.00 34.64 3.46
74 75 1.450531 GATGGCATGGAAGCGAAGGG 61.451 60.000 3.81 0.00 34.64 3.95
75 76 2.830370 GGCATGGAAGCGAAGGGG 60.830 66.667 0.00 0.00 34.64 4.79
76 77 2.272146 GCATGGAAGCGAAGGGGA 59.728 61.111 0.00 0.00 0.00 4.81
77 78 1.378514 GCATGGAAGCGAAGGGGAA 60.379 57.895 0.00 0.00 0.00 3.97
78 79 0.753111 GCATGGAAGCGAAGGGGAAT 60.753 55.000 0.00 0.00 0.00 3.01
79 80 1.767759 CATGGAAGCGAAGGGGAATT 58.232 50.000 0.00 0.00 0.00 2.17
80 81 1.406539 CATGGAAGCGAAGGGGAATTG 59.593 52.381 0.00 0.00 0.00 2.32
81 82 0.695924 TGGAAGCGAAGGGGAATTGA 59.304 50.000 0.00 0.00 0.00 2.57
82 83 1.284785 TGGAAGCGAAGGGGAATTGAT 59.715 47.619 0.00 0.00 0.00 2.57
83 84 1.678101 GGAAGCGAAGGGGAATTGATG 59.322 52.381 0.00 0.00 0.00 3.07
84 85 1.066152 GAAGCGAAGGGGAATTGATGC 59.934 52.381 0.00 0.00 0.00 3.91
85 86 1.097547 AGCGAAGGGGAATTGATGCG 61.098 55.000 0.00 0.00 0.00 4.73
86 87 1.095228 GCGAAGGGGAATTGATGCGA 61.095 55.000 0.00 0.00 0.00 5.10
87 88 1.378531 CGAAGGGGAATTGATGCGAA 58.621 50.000 0.00 0.00 0.00 4.70
88 89 1.949525 CGAAGGGGAATTGATGCGAAT 59.050 47.619 0.00 0.00 0.00 3.34
89 90 3.138304 CGAAGGGGAATTGATGCGAATA 58.862 45.455 0.00 0.00 0.00 1.75
90 91 3.187227 CGAAGGGGAATTGATGCGAATAG 59.813 47.826 0.00 0.00 0.00 1.73
91 92 3.864789 AGGGGAATTGATGCGAATAGT 57.135 42.857 0.00 0.00 0.00 2.12
92 93 3.480470 AGGGGAATTGATGCGAATAGTG 58.520 45.455 0.00 0.00 0.00 2.74
93 94 3.136443 AGGGGAATTGATGCGAATAGTGA 59.864 43.478 0.00 0.00 0.00 3.41
94 95 3.499918 GGGGAATTGATGCGAATAGTGAG 59.500 47.826 0.00 0.00 0.00 3.51
95 96 3.499918 GGGAATTGATGCGAATAGTGAGG 59.500 47.826 0.00 0.00 0.00 3.86
96 97 3.499918 GGAATTGATGCGAATAGTGAGGG 59.500 47.826 0.00 0.00 0.00 4.30
97 98 4.380531 GAATTGATGCGAATAGTGAGGGA 58.619 43.478 0.00 0.00 0.00 4.20
98 99 3.904800 TTGATGCGAATAGTGAGGGAA 57.095 42.857 0.00 0.00 0.00 3.97
99 100 3.904800 TGATGCGAATAGTGAGGGAAA 57.095 42.857 0.00 0.00 0.00 3.13
100 101 4.214986 TGATGCGAATAGTGAGGGAAAA 57.785 40.909 0.00 0.00 0.00 2.29
101 102 4.191544 TGATGCGAATAGTGAGGGAAAAG 58.808 43.478 0.00 0.00 0.00 2.27
102 103 3.973206 TGCGAATAGTGAGGGAAAAGA 57.027 42.857 0.00 0.00 0.00 2.52
103 104 4.487714 TGCGAATAGTGAGGGAAAAGAT 57.512 40.909 0.00 0.00 0.00 2.40
104 105 5.607939 TGCGAATAGTGAGGGAAAAGATA 57.392 39.130 0.00 0.00 0.00 1.98
105 106 5.601662 TGCGAATAGTGAGGGAAAAGATAG 58.398 41.667 0.00 0.00 0.00 2.08
106 107 4.449405 GCGAATAGTGAGGGAAAAGATAGC 59.551 45.833 0.00 0.00 0.00 2.97
107 108 4.991687 CGAATAGTGAGGGAAAAGATAGCC 59.008 45.833 0.00 0.00 0.00 3.93
108 109 5.453339 CGAATAGTGAGGGAAAAGATAGCCA 60.453 44.000 0.00 0.00 0.00 4.75
109 110 6.521527 AATAGTGAGGGAAAAGATAGCCAT 57.478 37.500 0.00 0.00 0.00 4.40
110 111 4.162040 AGTGAGGGAAAAGATAGCCATG 57.838 45.455 0.00 0.00 0.00 3.66
111 112 2.620585 GTGAGGGAAAAGATAGCCATGC 59.379 50.000 0.00 0.00 0.00 4.06
112 113 2.511218 TGAGGGAAAAGATAGCCATGCT 59.489 45.455 0.00 0.00 43.41 3.79
113 114 3.053395 TGAGGGAAAAGATAGCCATGCTT 60.053 43.478 0.00 0.00 40.44 3.91
114 115 3.560105 AGGGAAAAGATAGCCATGCTTC 58.440 45.455 0.00 0.00 40.44 3.86
115 116 2.625314 GGGAAAAGATAGCCATGCTTCC 59.375 50.000 0.00 0.00 40.44 3.46
116 117 2.625314 GGAAAAGATAGCCATGCTTCCC 59.375 50.000 0.00 0.00 40.44 3.97
117 118 2.371658 AAAGATAGCCATGCTTCCCC 57.628 50.000 0.00 0.00 40.44 4.81
118 119 1.527457 AAGATAGCCATGCTTCCCCT 58.473 50.000 0.00 0.00 40.44 4.79
119 120 1.063183 AGATAGCCATGCTTCCCCTC 58.937 55.000 0.00 0.00 40.44 4.30
120 121 1.063183 GATAGCCATGCTTCCCCTCT 58.937 55.000 0.00 0.00 40.44 3.69
121 122 1.423161 GATAGCCATGCTTCCCCTCTT 59.577 52.381 0.00 0.00 40.44 2.85
122 123 1.298953 TAGCCATGCTTCCCCTCTTT 58.701 50.000 0.00 0.00 40.44 2.52
123 124 0.033699 AGCCATGCTTCCCCTCTTTC 60.034 55.000 0.00 0.00 33.89 2.62
124 125 0.033699 GCCATGCTTCCCCTCTTTCT 60.034 55.000 0.00 0.00 0.00 2.52
125 126 1.618074 GCCATGCTTCCCCTCTTTCTT 60.618 52.381 0.00 0.00 0.00 2.52
126 127 2.812658 CCATGCTTCCCCTCTTTCTTT 58.187 47.619 0.00 0.00 0.00 2.52
127 128 3.168292 CCATGCTTCCCCTCTTTCTTTT 58.832 45.455 0.00 0.00 0.00 2.27
128 129 4.344104 CCATGCTTCCCCTCTTTCTTTTA 58.656 43.478 0.00 0.00 0.00 1.52
129 130 4.158579 CCATGCTTCCCCTCTTTCTTTTAC 59.841 45.833 0.00 0.00 0.00 2.01
130 131 4.447138 TGCTTCCCCTCTTTCTTTTACA 57.553 40.909 0.00 0.00 0.00 2.41
131 132 4.398319 TGCTTCCCCTCTTTCTTTTACAG 58.602 43.478 0.00 0.00 0.00 2.74
132 133 3.191581 GCTTCCCCTCTTTCTTTTACAGC 59.808 47.826 0.00 0.00 0.00 4.40
133 134 4.657013 CTTCCCCTCTTTCTTTTACAGCT 58.343 43.478 0.00 0.00 0.00 4.24
134 135 4.021102 TCCCCTCTTTCTTTTACAGCTG 57.979 45.455 13.48 13.48 0.00 4.24
135 136 2.489722 CCCCTCTTTCTTTTACAGCTGC 59.510 50.000 15.27 0.00 0.00 5.25
136 137 3.416156 CCCTCTTTCTTTTACAGCTGCT 58.584 45.455 15.27 0.00 0.00 4.24
137 138 3.438434 CCCTCTTTCTTTTACAGCTGCTC 59.562 47.826 15.27 0.00 0.00 4.26
138 139 4.322567 CCTCTTTCTTTTACAGCTGCTCT 58.677 43.478 15.27 0.00 0.00 4.09
168 169 5.638530 AAAAAGAGAGGTCAAGAGGTCTT 57.361 39.130 0.00 0.00 36.45 3.01
169 170 5.638530 AAAAGAGAGGTCAAGAGGTCTTT 57.361 39.130 0.00 0.00 36.13 2.52
170 171 5.638530 AAAGAGAGGTCAAGAGGTCTTTT 57.361 39.130 0.00 0.00 31.73 2.27
171 172 5.638530 AAGAGAGGTCAAGAGGTCTTTTT 57.361 39.130 0.00 0.00 33.11 1.94
216 217 6.413052 TGGTTTGGTAAATACCGCAGTATTA 58.587 36.000 5.76 0.00 46.30 0.98
217 218 6.883217 TGGTTTGGTAAATACCGCAGTATTAA 59.117 34.615 5.76 0.00 46.30 1.40
218 219 7.392673 TGGTTTGGTAAATACCGCAGTATTAAA 59.607 33.333 5.76 1.01 46.30 1.52
219 220 8.242739 GGTTTGGTAAATACCGCAGTATTAAAA 58.757 33.333 5.76 3.28 46.30 1.52
220 221 9.791820 GTTTGGTAAATACCGCAGTATTAAAAT 57.208 29.630 5.76 0.00 46.30 1.82
222 223 8.734218 TGGTAAATACCGCAGTATTAAAATCA 57.266 30.769 5.76 0.00 46.30 2.57
223 224 9.344772 TGGTAAATACCGCAGTATTAAAATCAT 57.655 29.630 5.76 0.00 46.30 2.45
244 245 9.744468 AATCATAGTTTTTAGTGACAACCAAAC 57.256 29.630 0.00 0.00 0.00 2.93
245 246 8.282455 TCATAGTTTTTAGTGACAACCAAACA 57.718 30.769 0.00 0.00 0.00 2.83
246 247 8.402472 TCATAGTTTTTAGTGACAACCAAACAG 58.598 33.333 0.00 0.00 0.00 3.16
247 248 5.407502 AGTTTTTAGTGACAACCAAACAGC 58.592 37.500 0.00 0.00 0.00 4.40
248 249 5.185056 AGTTTTTAGTGACAACCAAACAGCT 59.815 36.000 0.00 0.00 0.00 4.24
249 250 4.893424 TTTAGTGACAACCAAACAGCTC 57.107 40.909 0.00 0.00 0.00 4.09
250 251 2.418368 AGTGACAACCAAACAGCTCA 57.582 45.000 0.00 0.00 0.00 4.26
251 252 2.936202 AGTGACAACCAAACAGCTCAT 58.064 42.857 0.00 0.00 0.00 2.90
252 253 3.290710 AGTGACAACCAAACAGCTCATT 58.709 40.909 0.00 0.00 0.00 2.57
253 254 3.067180 AGTGACAACCAAACAGCTCATTG 59.933 43.478 1.74 1.74 0.00 2.82
254 255 3.023119 TGACAACCAAACAGCTCATTGT 58.977 40.909 7.12 0.00 33.15 2.71
255 256 3.066621 TGACAACCAAACAGCTCATTGTC 59.933 43.478 7.75 7.75 43.90 3.18
256 257 3.023119 ACAACCAAACAGCTCATTGTCA 58.977 40.909 7.12 0.00 0.00 3.58
257 258 3.446873 ACAACCAAACAGCTCATTGTCAA 59.553 39.130 7.12 0.00 0.00 3.18
258 259 4.081752 ACAACCAAACAGCTCATTGTCAAA 60.082 37.500 7.12 0.00 0.00 2.69
259 260 4.734398 ACCAAACAGCTCATTGTCAAAA 57.266 36.364 7.12 0.00 0.00 2.44
260 261 5.083533 ACCAAACAGCTCATTGTCAAAAA 57.916 34.783 7.12 0.00 0.00 1.94
347 348 4.645136 GGGCCTAAGTTTCTAAATTCCTGG 59.355 45.833 0.84 0.00 0.00 4.45
658 685 2.701780 CGACGCCCTAGAGCACTGT 61.702 63.158 0.00 0.00 0.00 3.55
677 704 0.696501 TCTGGACCCCTAGTTTTGGC 59.303 55.000 0.00 0.00 0.00 4.52
696 723 2.158755 GGCTAGGTATGTCCATTGCACT 60.159 50.000 0.00 0.00 39.02 4.40
717 744 3.674997 TGATGCCCTATTTCCGATTAGC 58.325 45.455 0.00 0.00 0.00 3.09
765 792 5.525378 CCTACTCCTACTTTGAATGTCATGC 59.475 44.000 0.00 0.00 0.00 4.06
781 808 3.796717 GTCATGCGACGAATTGAGATGTA 59.203 43.478 0.00 0.00 31.07 2.29
788 818 6.198403 TGCGACGAATTGAGATGTACTAATTC 59.802 38.462 0.00 0.00 36.61 2.17
798 828 6.758416 TGAGATGTACTAATTCAGATGTGCAC 59.242 38.462 10.75 10.75 0.00 4.57
804 834 0.632835 ATTCAGATGTGCACCCCCAT 59.367 50.000 15.69 0.00 0.00 4.00
818 848 5.777732 TGCACCCCCATCCATTAATTTATAC 59.222 40.000 0.00 0.00 0.00 1.47
821 851 7.010160 CACCCCCATCCATTAATTTATACAGT 58.990 38.462 0.00 0.00 0.00 3.55
822 852 8.167392 CACCCCCATCCATTAATTTATACAGTA 58.833 37.037 0.00 0.00 0.00 2.74
823 853 8.390921 ACCCCCATCCATTAATTTATACAGTAG 58.609 37.037 0.00 0.00 0.00 2.57
824 854 8.611257 CCCCCATCCATTAATTTATACAGTAGA 58.389 37.037 0.00 0.00 0.00 2.59
871 901 8.741603 TTTTATTTAGGTAGCAATGGGTAGAC 57.258 34.615 0.00 0.00 0.00 2.59
877 907 1.279496 AGCAATGGGTAGACAGCAGA 58.721 50.000 0.00 0.00 0.00 4.26
927 957 4.524802 TTGATCCTAGCATTGGTGGAAT 57.475 40.909 0.26 0.00 31.87 3.01
959 992 5.064707 TCGAAGGCATAATTTTCTTTCTCGG 59.935 40.000 0.00 0.00 0.00 4.63
965 998 6.308041 GGCATAATTTTCTTTCTCGGTTGTTC 59.692 38.462 0.00 0.00 0.00 3.18
969 1002 3.570912 TTCTTTCTCGGTTGTTCCCTT 57.429 42.857 0.00 0.00 0.00 3.95
1199 1232 4.431131 CGGGCTTGGCTGGGATGT 62.431 66.667 0.00 0.00 0.00 3.06
1242 1275 3.696045 TGGCTTGTATGCACATTTAGGT 58.304 40.909 0.00 0.00 33.76 3.08
1269 1302 2.547855 GCCCGATTCAAGGCTTGTTTTT 60.548 45.455 25.39 9.89 46.14 1.94
1287 1320 7.581213 TGTTTTTCAGAGTATTGTGAATGGT 57.419 32.000 0.00 0.00 36.59 3.55
1299 1332 2.575735 TGTGAATGGTGATCTTGCCCTA 59.424 45.455 0.00 0.00 0.00 3.53
1327 1360 5.596836 TTCTGCCATGGTTGATTATTTCC 57.403 39.130 14.67 0.00 0.00 3.13
1339 1372 4.116961 TGATTATTTCCGAGCTGGTTACG 58.883 43.478 0.00 0.00 39.52 3.18
1449 1482 3.753272 GCACTCAGCTCAGGAATTTGTTA 59.247 43.478 0.00 0.00 41.15 2.41
1587 1620 5.121454 GCGAGTGTTTGAAGAGATCTTTGAT 59.879 40.000 0.00 0.00 36.11 2.57
1622 1655 4.633126 TGCTTACACTTCAATGATCTCTGC 59.367 41.667 0.00 0.00 0.00 4.26
1644 1677 5.366477 TGCCTATTCTGATGTAGTGGATTCA 59.634 40.000 0.00 0.00 0.00 2.57
1650 1683 4.406649 TCTGATGTAGTGGATTCATCTGCA 59.593 41.667 0.00 0.00 38.78 4.41
1716 1749 3.384146 TGGAAGTAAACCGTGTGACACTA 59.616 43.478 14.42 0.00 31.34 2.74
2079 2112 3.667497 TGTGGCTATGCTGCTAGTATC 57.333 47.619 0.00 0.00 0.00 2.24
2109 2142 7.255801 GCCTACTTGATCAGAAGAACTATAGCT 60.256 40.741 0.00 0.00 0.00 3.32
2110 2143 8.081633 CCTACTTGATCAGAAGAACTATAGCTG 58.918 40.741 0.00 0.00 0.00 4.24
2338 2371 1.134753 CAACTGTTGTTTGCCTGCTCA 59.865 47.619 12.30 0.00 33.52 4.26
2365 2398 6.165577 GCTTTTGCTGATCAAAGGGATTTAA 58.834 36.000 6.93 0.00 44.62 1.52
2420 2453 3.442977 AGACATGGCTTTTCTTCAGATGC 59.557 43.478 0.00 0.00 0.00 3.91
2576 2609 1.511850 CGTGCAGATGAGGTTGTTCA 58.488 50.000 0.00 0.00 0.00 3.18
2586 2619 7.246311 CAGATGAGGTTGTTCAATTATGTCAC 58.754 38.462 0.00 0.00 0.00 3.67
2833 2866 1.212688 ACCTGGATTCATGGAATGCGA 59.787 47.619 0.00 0.00 46.21 5.10
3006 3039 8.637099 TGGTGTATTTTTCAGTCAATGATTTCA 58.363 29.630 0.00 0.00 37.89 2.69
3158 3191 0.036577 GCTCTCCTCTCTGCTTGCAA 60.037 55.000 0.00 0.00 0.00 4.08
3380 3413 6.014413 GTCTAGGAAGTAGAGAGGGTGTTTTT 60.014 42.308 0.00 0.00 38.52 1.94
3394 3427 1.136695 TGTTTTTGAGCCCAAGCACAG 59.863 47.619 0.00 0.00 40.81 3.66
3414 3447 2.832201 GCTCCTGCAATCTGGGCC 60.832 66.667 0.00 0.00 39.41 5.80
3448 3481 1.634459 TCGAGGTCTGTAGAGGAAGGT 59.366 52.381 0.00 0.00 0.00 3.50
3449 3482 1.746220 CGAGGTCTGTAGAGGAAGGTG 59.254 57.143 0.00 0.00 0.00 4.00
3450 3483 2.104170 GAGGTCTGTAGAGGAAGGTGG 58.896 57.143 0.00 0.00 0.00 4.61
3451 3484 1.717077 AGGTCTGTAGAGGAAGGTGGA 59.283 52.381 0.00 0.00 0.00 4.02
3452 3485 2.104170 GGTCTGTAGAGGAAGGTGGAG 58.896 57.143 0.00 0.00 0.00 3.86
3453 3486 2.104170 GTCTGTAGAGGAAGGTGGAGG 58.896 57.143 0.00 0.00 0.00 4.30
3454 3487 2.000803 TCTGTAGAGGAAGGTGGAGGA 58.999 52.381 0.00 0.00 0.00 3.71
3455 3488 2.382305 TCTGTAGAGGAAGGTGGAGGAA 59.618 50.000 0.00 0.00 0.00 3.36
3456 3489 2.763448 CTGTAGAGGAAGGTGGAGGAAG 59.237 54.545 0.00 0.00 0.00 3.46
3457 3490 2.112190 GTAGAGGAAGGTGGAGGAAGG 58.888 57.143 0.00 0.00 0.00 3.46
3522 3561 3.328382 AGCTGTGCCGTAGTTCATTTA 57.672 42.857 0.00 0.00 0.00 1.40
3575 3614 0.681243 GAGATGCAACCAGGTTCCCC 60.681 60.000 0.12 0.00 0.00 4.81
3692 3732 4.036852 TCAGTAGGACTATTGCAGATGACG 59.963 45.833 0.00 0.00 0.00 4.35
3722 3762 1.226859 CGAACAGCCGGCGAGATTA 60.227 57.895 23.20 0.00 0.00 1.75
3727 3767 0.103208 CAGCCGGCGAGATTAGAAGT 59.897 55.000 23.20 0.00 0.00 3.01
3746 3786 1.367840 GGGCTCTGACTGTTGTCGT 59.632 57.895 0.00 0.00 45.70 4.34
3914 3963 3.861113 TGTAGACGCGTCATATTTTCACC 59.139 43.478 37.85 10.03 0.00 4.02
3915 3964 3.247006 AGACGCGTCATATTTTCACCT 57.753 42.857 37.85 12.56 0.00 4.00
3942 3991 1.098869 TCTGTTTTTGTCGGCTGCAA 58.901 45.000 0.50 0.00 0.00 4.08
4026 4077 0.765510 AATCTACAGGGGGATTCGCC 59.234 55.000 11.21 11.21 45.38 5.54
4036 4087 0.460311 GGGATTCGCCGAGAAGAGAA 59.540 55.000 0.00 0.00 42.92 2.87
4040 4091 2.519377 TTCGCCGAGAAGAGAAAACA 57.481 45.000 0.00 0.00 34.26 2.83
4315 4506 2.204059 AGGGGAAGCTGAGTGCCT 60.204 61.111 0.00 0.00 44.23 4.75
4344 4541 3.436704 CACGCTGGACATACTGTGATTTT 59.563 43.478 0.00 0.00 0.00 1.82
4360 4557 7.823799 ACTGTGATTTTGTTTTCCAGTGATTTT 59.176 29.630 0.00 0.00 31.01 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.083565 TCCCTTAGCGGCAAAATTTTAGT 58.916 39.130 2.44 0.00 0.00 2.24
1 2 4.712122 TCCCTTAGCGGCAAAATTTTAG 57.288 40.909 2.44 0.00 0.00 1.85
2 3 6.777213 TTATCCCTTAGCGGCAAAATTTTA 57.223 33.333 2.44 0.00 0.00 1.52
3 4 5.669164 TTATCCCTTAGCGGCAAAATTTT 57.331 34.783 1.45 0.00 0.00 1.82
4 5 5.669164 TTTATCCCTTAGCGGCAAAATTT 57.331 34.783 1.45 0.00 0.00 1.82
5 6 5.186992 AGTTTTATCCCTTAGCGGCAAAATT 59.813 36.000 1.45 0.00 0.00 1.82
6 7 4.709886 AGTTTTATCCCTTAGCGGCAAAAT 59.290 37.500 1.45 0.00 0.00 1.82
7 8 4.083565 AGTTTTATCCCTTAGCGGCAAAA 58.916 39.130 1.45 0.00 0.00 2.44
8 9 3.692593 GAGTTTTATCCCTTAGCGGCAAA 59.307 43.478 1.45 0.00 0.00 3.68
9 10 3.275999 GAGTTTTATCCCTTAGCGGCAA 58.724 45.455 1.45 0.00 0.00 4.52
10 11 2.420967 GGAGTTTTATCCCTTAGCGGCA 60.421 50.000 1.45 0.00 32.79 5.69
11 12 2.219458 GGAGTTTTATCCCTTAGCGGC 58.781 52.381 0.00 0.00 32.79 6.53
12 13 3.134081 TCTGGAGTTTTATCCCTTAGCGG 59.866 47.826 0.00 0.00 38.72 5.52
13 14 4.402056 TCTGGAGTTTTATCCCTTAGCG 57.598 45.455 0.00 0.00 38.72 4.26
14 15 5.064834 CGTTTCTGGAGTTTTATCCCTTAGC 59.935 44.000 0.00 0.00 38.72 3.09
15 16 6.313164 GTCGTTTCTGGAGTTTTATCCCTTAG 59.687 42.308 0.00 0.00 38.72 2.18
16 17 6.168389 GTCGTTTCTGGAGTTTTATCCCTTA 58.832 40.000 0.00 0.00 38.72 2.69
17 18 5.001874 GTCGTTTCTGGAGTTTTATCCCTT 58.998 41.667 0.00 0.00 38.72 3.95
18 19 4.041198 TGTCGTTTCTGGAGTTTTATCCCT 59.959 41.667 0.00 0.00 38.72 4.20
19 20 4.320870 TGTCGTTTCTGGAGTTTTATCCC 58.679 43.478 0.00 0.00 38.72 3.85
20 21 5.163754 CCATGTCGTTTCTGGAGTTTTATCC 60.164 44.000 0.00 0.00 40.03 2.59
21 22 5.673818 GCCATGTCGTTTCTGGAGTTTTATC 60.674 44.000 0.00 0.00 31.38 1.75
22 23 4.156008 GCCATGTCGTTTCTGGAGTTTTAT 59.844 41.667 0.00 0.00 31.38 1.40
23 24 3.500680 GCCATGTCGTTTCTGGAGTTTTA 59.499 43.478 0.00 0.00 31.38 1.52
24 25 2.293399 GCCATGTCGTTTCTGGAGTTTT 59.707 45.455 0.00 0.00 31.38 2.43
25 26 1.880027 GCCATGTCGTTTCTGGAGTTT 59.120 47.619 0.00 0.00 31.38 2.66
26 27 1.523758 GCCATGTCGTTTCTGGAGTT 58.476 50.000 0.00 0.00 31.38 3.01
27 28 0.670546 CGCCATGTCGTTTCTGGAGT 60.671 55.000 0.00 0.00 31.38 3.85
28 29 1.361668 CCGCCATGTCGTTTCTGGAG 61.362 60.000 0.00 0.00 31.38 3.86
29 30 1.375396 CCGCCATGTCGTTTCTGGA 60.375 57.895 0.00 0.00 31.38 3.86
30 31 1.671054 ACCGCCATGTCGTTTCTGG 60.671 57.895 0.00 0.00 0.00 3.86
31 32 1.497278 CACCGCCATGTCGTTTCTG 59.503 57.895 0.00 0.00 0.00 3.02
32 33 1.671054 CCACCGCCATGTCGTTTCT 60.671 57.895 0.00 0.00 0.00 2.52
33 34 2.867472 CCACCGCCATGTCGTTTC 59.133 61.111 0.00 0.00 0.00 2.78
34 35 3.361977 GCCACCGCCATGTCGTTT 61.362 61.111 0.00 0.00 0.00 3.60
35 36 4.634703 TGCCACCGCCATGTCGTT 62.635 61.111 0.00 0.00 0.00 3.85
36 37 4.634703 TTGCCACCGCCATGTCGT 62.635 61.111 0.00 0.00 0.00 4.34
37 38 4.101790 GTTGCCACCGCCATGTCG 62.102 66.667 0.00 0.00 0.00 4.35
38 39 4.101790 CGTTGCCACCGCCATGTC 62.102 66.667 0.00 0.00 0.00 3.06
39 40 3.918253 ATCGTTGCCACCGCCATGT 62.918 57.895 0.00 0.00 0.00 3.21
40 41 3.133464 ATCGTTGCCACCGCCATG 61.133 61.111 0.00 0.00 0.00 3.66
41 42 3.133464 CATCGTTGCCACCGCCAT 61.133 61.111 0.00 0.00 0.00 4.40
45 46 3.133464 ATGCCATCGTTGCCACCG 61.133 61.111 0.00 0.00 0.00 4.94
46 47 2.491152 CATGCCATCGTTGCCACC 59.509 61.111 0.00 0.00 0.00 4.61
47 48 1.594194 TTCCATGCCATCGTTGCCAC 61.594 55.000 0.00 0.00 0.00 5.01
48 49 1.303970 TTCCATGCCATCGTTGCCA 60.304 52.632 0.00 0.00 0.00 4.92
49 50 1.434696 CTTCCATGCCATCGTTGCC 59.565 57.895 0.00 0.00 0.00 4.52
50 51 1.226773 GCTTCCATGCCATCGTTGC 60.227 57.895 0.00 0.00 0.00 4.17
51 52 1.063006 CGCTTCCATGCCATCGTTG 59.937 57.895 0.00 0.00 0.00 4.10
52 53 0.676466 TTCGCTTCCATGCCATCGTT 60.676 50.000 0.00 0.00 0.00 3.85
53 54 1.078497 TTCGCTTCCATGCCATCGT 60.078 52.632 0.00 0.00 0.00 3.73
54 55 1.645455 CTTCGCTTCCATGCCATCG 59.355 57.895 0.00 0.00 0.00 3.84
55 56 1.450531 CCCTTCGCTTCCATGCCATC 61.451 60.000 0.00 0.00 0.00 3.51
56 57 1.454479 CCCTTCGCTTCCATGCCAT 60.454 57.895 0.00 0.00 0.00 4.40
57 58 2.045045 CCCTTCGCTTCCATGCCA 60.045 61.111 0.00 0.00 0.00 4.92
58 59 2.830370 CCCCTTCGCTTCCATGCC 60.830 66.667 0.00 0.00 0.00 4.40
59 60 0.753111 ATTCCCCTTCGCTTCCATGC 60.753 55.000 0.00 0.00 0.00 4.06
60 61 1.406539 CAATTCCCCTTCGCTTCCATG 59.593 52.381 0.00 0.00 0.00 3.66
61 62 1.284785 TCAATTCCCCTTCGCTTCCAT 59.715 47.619 0.00 0.00 0.00 3.41
62 63 0.695924 TCAATTCCCCTTCGCTTCCA 59.304 50.000 0.00 0.00 0.00 3.53
63 64 1.678101 CATCAATTCCCCTTCGCTTCC 59.322 52.381 0.00 0.00 0.00 3.46
64 65 1.066152 GCATCAATTCCCCTTCGCTTC 59.934 52.381 0.00 0.00 0.00 3.86
65 66 1.106285 GCATCAATTCCCCTTCGCTT 58.894 50.000 0.00 0.00 0.00 4.68
66 67 1.097547 CGCATCAATTCCCCTTCGCT 61.098 55.000 0.00 0.00 0.00 4.93
67 68 1.095228 TCGCATCAATTCCCCTTCGC 61.095 55.000 0.00 0.00 0.00 4.70
68 69 1.378531 TTCGCATCAATTCCCCTTCG 58.621 50.000 0.00 0.00 0.00 3.79
69 70 4.023707 CACTATTCGCATCAATTCCCCTTC 60.024 45.833 0.00 0.00 0.00 3.46
70 71 3.885297 CACTATTCGCATCAATTCCCCTT 59.115 43.478 0.00 0.00 0.00 3.95
71 72 3.136443 TCACTATTCGCATCAATTCCCCT 59.864 43.478 0.00 0.00 0.00 4.79
72 73 3.476552 TCACTATTCGCATCAATTCCCC 58.523 45.455 0.00 0.00 0.00 4.81
73 74 3.499918 CCTCACTATTCGCATCAATTCCC 59.500 47.826 0.00 0.00 0.00 3.97
74 75 3.499918 CCCTCACTATTCGCATCAATTCC 59.500 47.826 0.00 0.00 0.00 3.01
75 76 4.380531 TCCCTCACTATTCGCATCAATTC 58.619 43.478 0.00 0.00 0.00 2.17
76 77 4.422073 TCCCTCACTATTCGCATCAATT 57.578 40.909 0.00 0.00 0.00 2.32
77 78 4.422073 TTCCCTCACTATTCGCATCAAT 57.578 40.909 0.00 0.00 0.00 2.57
78 79 3.904800 TTCCCTCACTATTCGCATCAA 57.095 42.857 0.00 0.00 0.00 2.57
79 80 3.904800 TTTCCCTCACTATTCGCATCA 57.095 42.857 0.00 0.00 0.00 3.07
80 81 4.442706 TCTTTTCCCTCACTATTCGCATC 58.557 43.478 0.00 0.00 0.00 3.91
81 82 4.487714 TCTTTTCCCTCACTATTCGCAT 57.512 40.909 0.00 0.00 0.00 4.73
82 83 3.973206 TCTTTTCCCTCACTATTCGCA 57.027 42.857 0.00 0.00 0.00 5.10
83 84 4.449405 GCTATCTTTTCCCTCACTATTCGC 59.551 45.833 0.00 0.00 0.00 4.70
84 85 4.991687 GGCTATCTTTTCCCTCACTATTCG 59.008 45.833 0.00 0.00 0.00 3.34
85 86 5.930135 TGGCTATCTTTTCCCTCACTATTC 58.070 41.667 0.00 0.00 0.00 1.75
86 87 5.975988 TGGCTATCTTTTCCCTCACTATT 57.024 39.130 0.00 0.00 0.00 1.73
87 88 5.747248 GCATGGCTATCTTTTCCCTCACTAT 60.747 44.000 0.00 0.00 0.00 2.12
88 89 4.444876 GCATGGCTATCTTTTCCCTCACTA 60.445 45.833 0.00 0.00 0.00 2.74
89 90 3.686691 GCATGGCTATCTTTTCCCTCACT 60.687 47.826 0.00 0.00 0.00 3.41
90 91 2.620585 GCATGGCTATCTTTTCCCTCAC 59.379 50.000 0.00 0.00 0.00 3.51
91 92 2.511218 AGCATGGCTATCTTTTCCCTCA 59.489 45.455 0.00 0.00 36.99 3.86
92 93 3.220674 AGCATGGCTATCTTTTCCCTC 57.779 47.619 0.00 0.00 36.99 4.30
93 94 3.560105 GAAGCATGGCTATCTTTTCCCT 58.440 45.455 0.00 0.00 38.25 4.20
94 95 2.625314 GGAAGCATGGCTATCTTTTCCC 59.375 50.000 0.00 0.00 38.25 3.97
95 96 2.625314 GGGAAGCATGGCTATCTTTTCC 59.375 50.000 0.00 7.74 38.25 3.13
96 97 2.625314 GGGGAAGCATGGCTATCTTTTC 59.375 50.000 0.00 0.00 38.25 2.29
97 98 2.245806 AGGGGAAGCATGGCTATCTTTT 59.754 45.455 0.00 0.00 38.25 2.27
98 99 1.855599 AGGGGAAGCATGGCTATCTTT 59.144 47.619 0.00 0.00 38.25 2.52
99 100 1.423161 GAGGGGAAGCATGGCTATCTT 59.577 52.381 0.00 0.00 38.25 2.40
100 101 1.063183 GAGGGGAAGCATGGCTATCT 58.937 55.000 0.00 0.00 38.25 1.98
101 102 1.063183 AGAGGGGAAGCATGGCTATC 58.937 55.000 0.00 0.00 38.25 2.08
102 103 1.527457 AAGAGGGGAAGCATGGCTAT 58.473 50.000 0.00 0.00 38.25 2.97
103 104 1.212935 GAAAGAGGGGAAGCATGGCTA 59.787 52.381 0.00 0.00 38.25 3.93
104 105 0.033699 GAAAGAGGGGAAGCATGGCT 60.034 55.000 0.00 0.00 42.56 4.75
105 106 0.033699 AGAAAGAGGGGAAGCATGGC 60.034 55.000 0.00 0.00 0.00 4.40
106 107 2.521547 AAGAAAGAGGGGAAGCATGG 57.478 50.000 0.00 0.00 0.00 3.66
107 108 4.766891 TGTAAAAGAAAGAGGGGAAGCATG 59.233 41.667 0.00 0.00 0.00 4.06
108 109 4.998051 TGTAAAAGAAAGAGGGGAAGCAT 58.002 39.130 0.00 0.00 0.00 3.79
109 110 4.398319 CTGTAAAAGAAAGAGGGGAAGCA 58.602 43.478 0.00 0.00 0.00 3.91
110 111 3.191581 GCTGTAAAAGAAAGAGGGGAAGC 59.808 47.826 0.00 0.00 0.00 3.86
111 112 4.457257 CAGCTGTAAAAGAAAGAGGGGAAG 59.543 45.833 5.25 0.00 0.00 3.46
112 113 4.398319 CAGCTGTAAAAGAAAGAGGGGAA 58.602 43.478 5.25 0.00 0.00 3.97
113 114 3.810743 GCAGCTGTAAAAGAAAGAGGGGA 60.811 47.826 16.64 0.00 0.00 4.81
114 115 2.489722 GCAGCTGTAAAAGAAAGAGGGG 59.510 50.000 16.64 0.00 0.00 4.79
115 116 3.416156 AGCAGCTGTAAAAGAAAGAGGG 58.584 45.455 16.64 0.00 0.00 4.30
116 117 4.153835 CAGAGCAGCTGTAAAAGAAAGAGG 59.846 45.833 16.64 0.00 39.85 3.69
117 118 5.280328 CAGAGCAGCTGTAAAAGAAAGAG 57.720 43.478 16.64 0.00 39.85 2.85
146 147 5.638530 AAGACCTCTTGACCTCTCTTTTT 57.361 39.130 0.00 0.00 34.38 1.94
147 148 5.638530 AAAGACCTCTTGACCTCTCTTTT 57.361 39.130 0.00 0.00 36.12 2.27
148 149 5.638530 AAAAGACCTCTTGACCTCTCTTT 57.361 39.130 0.00 0.00 36.12 2.52
149 150 5.638530 AAAAAGACCTCTTGACCTCTCTT 57.361 39.130 0.00 0.00 36.12 2.85
184 185 6.282167 CGGTATTTACCAAACCAAGGTTTTT 58.718 36.000 14.27 7.51 45.32 1.94
185 186 5.739647 GCGGTATTTACCAAACCAAGGTTTT 60.740 40.000 14.27 4.51 45.32 2.43
187 188 3.256383 GCGGTATTTACCAAACCAAGGTT 59.744 43.478 7.50 0.00 46.80 3.50
188 189 2.821378 GCGGTATTTACCAAACCAAGGT 59.179 45.455 7.50 0.00 46.80 3.50
189 190 2.820787 TGCGGTATTTACCAAACCAAGG 59.179 45.455 7.50 0.00 46.80 3.61
190 191 3.504520 ACTGCGGTATTTACCAAACCAAG 59.495 43.478 0.00 0.00 46.80 3.61
191 192 3.488363 ACTGCGGTATTTACCAAACCAA 58.512 40.909 0.00 0.00 46.80 3.67
192 193 3.143211 ACTGCGGTATTTACCAAACCA 57.857 42.857 0.00 0.00 46.80 3.67
193 194 5.823209 AATACTGCGGTATTTACCAAACC 57.177 39.130 22.67 0.00 46.80 3.27
194 195 9.791820 ATTTTAATACTGCGGTATTTACCAAAC 57.208 29.630 30.65 0.00 46.80 2.93
196 197 9.175312 TGATTTTAATACTGCGGTATTTACCAA 57.825 29.630 30.65 18.46 46.80 3.67
197 198 8.734218 TGATTTTAATACTGCGGTATTTACCA 57.266 30.769 30.65 19.45 46.80 3.25
218 219 9.744468 GTTTGGTTGTCACTAAAAACTATGATT 57.256 29.630 0.00 0.00 35.34 2.57
219 220 8.908903 TGTTTGGTTGTCACTAAAAACTATGAT 58.091 29.630 0.00 0.00 35.34 2.45
220 221 8.282455 TGTTTGGTTGTCACTAAAAACTATGA 57.718 30.769 0.00 0.00 35.34 2.15
221 222 7.167468 GCTGTTTGGTTGTCACTAAAAACTATG 59.833 37.037 0.00 0.00 35.34 2.23
222 223 7.068226 AGCTGTTTGGTTGTCACTAAAAACTAT 59.932 33.333 0.00 0.00 35.34 2.12
223 224 6.376018 AGCTGTTTGGTTGTCACTAAAAACTA 59.624 34.615 0.00 0.00 35.34 2.24
224 225 5.185056 AGCTGTTTGGTTGTCACTAAAAACT 59.815 36.000 0.00 0.00 35.34 2.66
225 226 5.407502 AGCTGTTTGGTTGTCACTAAAAAC 58.592 37.500 0.00 0.00 35.34 2.43
226 227 5.184096 TGAGCTGTTTGGTTGTCACTAAAAA 59.816 36.000 0.00 0.00 35.34 1.94
227 228 4.702612 TGAGCTGTTTGGTTGTCACTAAAA 59.297 37.500 0.00 0.00 35.34 1.52
228 229 4.265893 TGAGCTGTTTGGTTGTCACTAAA 58.734 39.130 0.00 0.00 31.33 1.85
229 230 3.879998 TGAGCTGTTTGGTTGTCACTAA 58.120 40.909 0.00 0.00 0.00 2.24
230 231 3.552132 TGAGCTGTTTGGTTGTCACTA 57.448 42.857 0.00 0.00 0.00 2.74
231 232 2.418368 TGAGCTGTTTGGTTGTCACT 57.582 45.000 0.00 0.00 0.00 3.41
232 233 3.181487 ACAATGAGCTGTTTGGTTGTCAC 60.181 43.478 0.00 0.00 0.00 3.67
233 234 3.023119 ACAATGAGCTGTTTGGTTGTCA 58.977 40.909 0.00 0.00 0.00 3.58
234 235 3.066621 TGACAATGAGCTGTTTGGTTGTC 59.933 43.478 0.00 8.61 43.32 3.18
235 236 3.023119 TGACAATGAGCTGTTTGGTTGT 58.977 40.909 0.00 0.00 32.98 3.32
236 237 3.713858 TGACAATGAGCTGTTTGGTTG 57.286 42.857 0.00 0.00 0.00 3.77
237 238 4.734398 TTTGACAATGAGCTGTTTGGTT 57.266 36.364 0.00 0.00 0.00 3.67
238 239 4.734398 TTTTGACAATGAGCTGTTTGGT 57.266 36.364 0.00 0.00 0.00 3.67
301 302 7.988028 GCCCTGTTTGATAGTAGAGTATTTTCT 59.012 37.037 0.00 0.00 0.00 2.52
302 303 7.226918 GGCCCTGTTTGATAGTAGAGTATTTTC 59.773 40.741 0.00 0.00 0.00 2.29
303 304 7.054751 GGCCCTGTTTGATAGTAGAGTATTTT 58.945 38.462 0.00 0.00 0.00 1.82
304 305 6.387220 AGGCCCTGTTTGATAGTAGAGTATTT 59.613 38.462 0.00 0.00 0.00 1.40
305 306 5.905913 AGGCCCTGTTTGATAGTAGAGTATT 59.094 40.000 0.00 0.00 0.00 1.89
306 307 5.468658 AGGCCCTGTTTGATAGTAGAGTAT 58.531 41.667 0.00 0.00 0.00 2.12
307 308 4.880164 AGGCCCTGTTTGATAGTAGAGTA 58.120 43.478 0.00 0.00 0.00 2.59
308 309 3.725634 AGGCCCTGTTTGATAGTAGAGT 58.274 45.455 0.00 0.00 0.00 3.24
309 310 5.364157 ACTTAGGCCCTGTTTGATAGTAGAG 59.636 44.000 0.00 0.00 0.00 2.43
310 311 5.278061 ACTTAGGCCCTGTTTGATAGTAGA 58.722 41.667 0.00 0.00 0.00 2.59
311 312 5.615925 ACTTAGGCCCTGTTTGATAGTAG 57.384 43.478 0.00 0.00 0.00 2.57
312 313 6.214819 AGAAACTTAGGCCCTGTTTGATAGTA 59.785 38.462 18.87 0.00 34.55 1.82
313 314 4.929146 AACTTAGGCCCTGTTTGATAGT 57.071 40.909 0.00 0.00 0.00 2.12
314 315 5.501156 AGAAACTTAGGCCCTGTTTGATAG 58.499 41.667 18.87 0.00 34.55 2.08
315 316 5.514500 AGAAACTTAGGCCCTGTTTGATA 57.486 39.130 18.87 0.00 34.55 2.15
316 317 4.388577 AGAAACTTAGGCCCTGTTTGAT 57.611 40.909 18.87 8.10 34.55 2.57
317 318 3.876309 AGAAACTTAGGCCCTGTTTGA 57.124 42.857 18.87 0.00 34.55 2.69
318 319 6.590234 ATTTAGAAACTTAGGCCCTGTTTG 57.410 37.500 18.87 0.00 34.55 2.93
319 320 6.210784 GGAATTTAGAAACTTAGGCCCTGTTT 59.789 38.462 15.33 15.33 36.73 2.83
320 321 5.715279 GGAATTTAGAAACTTAGGCCCTGTT 59.285 40.000 0.00 0.00 0.00 3.16
321 322 5.015284 AGGAATTTAGAAACTTAGGCCCTGT 59.985 40.000 0.00 0.00 0.00 4.00
322 323 5.358160 CAGGAATTTAGAAACTTAGGCCCTG 59.642 44.000 0.00 0.00 0.00 4.45
323 324 5.510430 CAGGAATTTAGAAACTTAGGCCCT 58.490 41.667 0.00 0.00 0.00 5.19
324 325 4.645136 CCAGGAATTTAGAAACTTAGGCCC 59.355 45.833 0.00 0.00 0.00 5.80
325 326 4.645136 CCCAGGAATTTAGAAACTTAGGCC 59.355 45.833 0.00 0.00 0.00 5.19
326 327 5.506708 TCCCAGGAATTTAGAAACTTAGGC 58.493 41.667 0.00 0.00 0.00 3.93
347 348 5.048434 GCATATCAAGGGCTTCTTTGTATCC 60.048 44.000 0.00 0.00 32.41 2.59
658 685 0.696501 GCCAAAACTAGGGGTCCAGA 59.303 55.000 0.00 0.00 0.00 3.86
677 704 4.406648 TCAGTGCAATGGACATACCTAG 57.593 45.455 15.06 0.00 39.86 3.02
696 723 3.072330 TGCTAATCGGAAATAGGGCATCA 59.928 43.478 0.00 0.00 0.00 3.07
710 737 1.193203 CATAGCCGCTTGTGCTAATCG 59.807 52.381 0.00 0.00 43.96 3.34
717 744 0.391661 ACTGGACATAGCCGCTTGTG 60.392 55.000 0.00 0.76 0.00 3.33
725 752 2.761208 AGTAGGACACACTGGACATAGC 59.239 50.000 0.00 0.00 0.00 2.97
765 792 7.644157 TCTGAATTAGTACATCTCAATTCGTCG 59.356 37.037 0.00 0.00 39.26 5.12
781 808 2.357154 GGGGGTGCACATCTGAATTAGT 60.357 50.000 20.43 0.00 0.00 2.24
788 818 1.454479 GGATGGGGGTGCACATCTG 60.454 63.158 20.43 0.00 42.34 2.90
798 828 8.611257 TCTACTGTATAAATTAATGGATGGGGG 58.389 37.037 0.00 0.00 0.00 5.40
857 887 2.466846 TCTGCTGTCTACCCATTGCTA 58.533 47.619 0.00 0.00 0.00 3.49
877 907 4.726416 CTTTAAAAGCACGACTGCATCAT 58.274 39.130 0.52 0.00 46.97 2.45
895 925 7.765360 CCAATGCTAGGATCAAAAATTGCTTTA 59.235 33.333 0.00 0.00 0.00 1.85
903 933 4.671831 TCCACCAATGCTAGGATCAAAAA 58.328 39.130 0.00 0.00 0.00 1.94
911 941 4.717877 TCACATATTCCACCAATGCTAGG 58.282 43.478 0.00 0.00 0.00 3.02
927 957 8.450578 AGAAAATTATGCCTTCGATTCACATA 57.549 30.769 0.00 0.00 0.00 2.29
980 1013 5.012664 TGCATACTAACTGGAGAAACTTCCA 59.987 40.000 0.00 0.00 44.84 3.53
991 1024 3.895232 ACCAGACTGCATACTAACTGG 57.105 47.619 0.00 0.00 46.78 4.00
1185 1218 1.105759 GGATCACATCCCAGCCAAGC 61.106 60.000 0.00 0.00 43.88 4.01
1199 1232 5.104360 CCAAGAATCTTAGACCCAAGGATCA 60.104 44.000 0.00 0.00 0.00 2.92
1209 1242 5.586243 TGCATACAAGCCAAGAATCTTAGAC 59.414 40.000 0.00 0.00 0.00 2.59
1242 1275 4.001248 CTTGAATCGGGCAAGGCA 57.999 55.556 0.00 0.00 39.18 4.75
1269 1302 6.550938 AGATCACCATTCACAATACTCTGA 57.449 37.500 0.00 0.00 0.00 3.27
1287 1320 4.722220 CAGAATTCCATAGGGCAAGATCA 58.278 43.478 0.65 0.00 0.00 2.92
1299 1332 3.104519 TCAACCATGGCAGAATTCCAT 57.895 42.857 13.04 0.00 45.26 3.41
1327 1360 1.153823 CCTCCACGTAACCAGCTCG 60.154 63.158 0.00 0.00 0.00 5.03
1339 1372 7.094762 CCTGTACAAAAGAATAACTTCCTCCAC 60.095 40.741 0.00 0.00 37.93 4.02
1449 1482 1.407712 GCATGCATTCCTTTGCCCAAT 60.408 47.619 14.21 0.00 42.06 3.16
1469 1502 1.471684 GGCCAAGCTTCAGTGAATCTG 59.528 52.381 9.89 6.10 44.85 2.90
1587 1620 8.856153 TTGAAGTGTAAGCAACAATATCCTTA 57.144 30.769 0.00 0.00 40.63 2.69
1622 1655 7.818446 CAGATGAATCCACTACATCAGAATAGG 59.182 40.741 0.00 0.00 41.64 2.57
1650 1683 4.590918 TGGCAATTTTGAATGCATTCCAT 58.409 34.783 31.35 19.64 44.32 3.41
1663 1696 7.243604 TCCTTATCATTTCACTGGCAATTTT 57.756 32.000 0.00 0.00 0.00 1.82
1797 1830 2.606725 GACTTCATCTGAGACGCCAATG 59.393 50.000 0.00 0.00 0.00 2.82
2044 2077 6.072286 GCATAGCCACAATAGCATAATTCAGT 60.072 38.462 0.00 0.00 0.00 3.41
2079 2112 4.412796 TCTTCTGATCAAGTAGGCATGG 57.587 45.455 0.00 0.00 0.00 3.66
2109 2142 1.686052 GTGGCCAAAACAAGATCCACA 59.314 47.619 7.24 0.00 42.45 4.17
2110 2143 1.963515 AGTGGCCAAAACAAGATCCAC 59.036 47.619 7.24 0.00 43.03 4.02
2338 2371 2.298163 CCCTTTGATCAGCAAAAGCTGT 59.702 45.455 16.10 5.07 45.26 4.40
2365 2398 3.134804 CCGTGAATCCACCTTCCTCTTAT 59.865 47.826 0.00 0.00 40.12 1.73
2420 2453 4.201647 GCAGAATTTGATTTGCAATGTCCG 60.202 41.667 0.00 0.00 36.15 4.79
2576 2609 6.808212 GTGTTGCTGCATTAAGTGACATAATT 59.192 34.615 1.84 0.00 0.00 1.40
2586 2619 0.171007 CCCCGTGTTGCTGCATTAAG 59.829 55.000 1.84 0.00 0.00 1.85
2833 2866 3.181437 TGCATCCCATAAGCACTGATCAT 60.181 43.478 0.00 0.00 32.55 2.45
2913 2946 6.652481 CAGAAGTGAATGTTAACTCATCAGGT 59.348 38.462 7.22 0.31 0.00 4.00
3158 3191 6.127366 CCCAAGCAGTGTATTTCCATATGTTT 60.127 38.462 1.24 0.00 0.00 2.83
3321 3354 4.545208 ACTAGAGCCAGGAAGTTTCTTC 57.455 45.455 0.00 1.39 0.00 2.87
3368 3401 0.555769 TGGGCTCAAAAACACCCTCT 59.444 50.000 0.00 0.00 43.25 3.69
3380 3413 4.728409 CATCTGTGCTTGGGCTCA 57.272 55.556 0.00 0.00 39.25 4.26
3414 3447 0.867753 CCTCGACTCGATTTCCAGCG 60.868 60.000 0.62 0.00 34.61 5.18
3448 3481 1.699634 CAAGAACTCCACCTTCCTCCA 59.300 52.381 0.00 0.00 0.00 3.86
3449 3482 1.611936 GCAAGAACTCCACCTTCCTCC 60.612 57.143 0.00 0.00 0.00 4.30
3450 3483 1.349357 AGCAAGAACTCCACCTTCCTC 59.651 52.381 0.00 0.00 0.00 3.71
3451 3484 1.072965 CAGCAAGAACTCCACCTTCCT 59.927 52.381 0.00 0.00 0.00 3.36
3452 3485 1.528129 CAGCAAGAACTCCACCTTCC 58.472 55.000 0.00 0.00 0.00 3.46
3453 3486 1.072331 TCCAGCAAGAACTCCACCTTC 59.928 52.381 0.00 0.00 0.00 3.46
3454 3487 1.140312 TCCAGCAAGAACTCCACCTT 58.860 50.000 0.00 0.00 0.00 3.50
3455 3488 1.280421 GATCCAGCAAGAACTCCACCT 59.720 52.381 0.00 0.00 0.00 4.00
3456 3489 1.680249 GGATCCAGCAAGAACTCCACC 60.680 57.143 6.95 0.00 0.00 4.61
3457 3490 1.280421 AGGATCCAGCAAGAACTCCAC 59.720 52.381 15.82 0.00 0.00 4.02
3575 3614 1.098050 CCCCCATCGCTTCAAGAAAG 58.902 55.000 0.00 0.00 38.08 2.62
3722 3762 1.071385 CAACAGTCAGAGCCCACTTCT 59.929 52.381 0.00 0.00 0.00 2.85
3727 3767 1.367471 CGACAACAGTCAGAGCCCA 59.633 57.895 0.00 0.00 32.50 5.36
3746 3786 1.299648 CTGGATTCTGCCGTTCCCA 59.700 57.895 0.00 0.00 0.00 4.37
3914 3963 4.776743 CCGACAAAAACAGATGTTCAGAG 58.223 43.478 0.00 0.00 37.25 3.35
3915 3964 3.003275 GCCGACAAAAACAGATGTTCAGA 59.997 43.478 0.00 0.00 37.25 3.27
3942 3991 3.682696 GGAACCGACCCAACTCTAATTT 58.317 45.455 0.00 0.00 0.00 1.82
3985 4035 0.251341 CCAGGGTGCCTACTTTGCTT 60.251 55.000 0.00 0.00 29.64 3.91
3990 4040 1.840635 GATTCTCCAGGGTGCCTACTT 59.159 52.381 0.00 0.00 29.64 2.24
4026 4077 3.629058 TCTGTCGTGTTTTCTCTTCTCG 58.371 45.455 0.00 0.00 0.00 4.04
4315 4506 2.823747 AGTATGTCCAGCGTGTGTTCTA 59.176 45.455 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.