Multiple sequence alignment - TraesCS3B01G355700

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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 TraesCS3B01G355700 chr3B 100.000 3687 0 0 1 3687 566160282 566163968 0.000000e+00 6809.0
1 TraesCS3B01G355700 chr3B 97.297 37 1 0 2193 2229 729804887 729804923 3.070000e-06 63.9
2 TraesCS3B01G355700 chr3D 94.594 3015 115 24 403 3399 433413722 433416706 0.000000e+00 4621.0
3 TraesCS3B01G355700 chr3D 87.209 258 28 5 3433 3687 433416702 433416957 4.660000e-74 289.0
4 TraesCS3B01G355700 chr3A 93.842 2858 133 25 860 3687 571790212 571793056 0.000000e+00 4263.0
5 TraesCS3B01G355700 chr3A 91.538 520 25 5 403 920 571789713 571790215 0.000000e+00 699.0
6 TraesCS3B01G355700 chr5D 93.781 402 22 1 1 402 460195990 460195592 5.270000e-168 601.0
7 TraesCS3B01G355700 chr5D 93.564 404 21 3 1 403 201656369 201656768 6.820000e-167 597.0
8 TraesCS3B01G355700 chr5D 93.532 402 23 1 1 402 352348793 352349191 2.450000e-166 595.0
9 TraesCS3B01G355700 chr5D 97.500 40 1 0 2203 2242 72902348 72902309 6.610000e-08 69.4
10 TraesCS3B01G355700 chr2D 93.781 402 22 2 1 402 431966503 431966901 5.270000e-168 601.0
11 TraesCS3B01G355700 chr2D 93.564 404 23 1 1 404 448453295 448453695 1.890000e-167 599.0
12 TraesCS3B01G355700 chr2D 81.481 81 15 0 1722 1802 121704762 121704682 2.380000e-07 67.6
13 TraesCS3B01G355700 chr2B 93.766 401 22 2 4 403 254624675 254624277 1.890000e-167 599.0
14 TraesCS3B01G355700 chr2B 80.247 81 16 0 1722 1802 174829932 174829852 1.110000e-05 62.1
15 TraesCS3B01G355700 chr7D 93.333 405 24 1 1 405 431080432 431080031 2.450000e-166 595.0
16 TraesCS3B01G355700 chr7D 96.875 32 1 0 1782 1813 618488597 618488628 2.000000e-03 54.7
17 TraesCS3B01G355700 chr2A 93.532 402 22 2 1 402 620205018 620205415 2.450000e-166 595.0
18 TraesCS3B01G355700 chr1A 92.944 411 24 3 1 409 413779578 413779985 8.820000e-166 593.0
19 TraesCS3B01G355700 chr1A 100.000 32 0 0 1776 1807 453074401 453074432 3.980000e-05 60.2
20 TraesCS3B01G355700 chr4B 85.271 129 19 0 2128 2256 178071960 178072088 2.310000e-27 134.0
21 TraesCS3B01G355700 chr5A 95.652 46 2 0 2197 2242 67471167 67471122 1.420000e-09 75.0
22 TraesCS3B01G355700 chr4A 91.111 45 4 0 2193 2237 294300211 294300255 1.110000e-05 62.1
23 TraesCS3B01G355700 chr6B 94.595 37 2 0 1776 1812 216356328 216356364 1.430000e-04 58.4
24 TraesCS3B01G355700 chr6A 94.595 37 2 0 1776 1812 160475787 160475823 1.430000e-04 58.4
25 TraesCS3B01G355700 chr1B 96.875 32 1 0 1779 1810 474835275 474835244 2.000000e-03 54.7


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 TraesCS3B01G355700 chr3B 566160282 566163968 3686 False 6809 6809 100.0000 1 3687 1 chr3B.!!$F1 3686
1 TraesCS3B01G355700 chr3D 433413722 433416957 3235 False 2455 4621 90.9015 403 3687 2 chr3D.!!$F1 3284
2 TraesCS3B01G355700 chr3A 571789713 571793056 3343 False 2481 4263 92.6900 403 3687 2 chr3A.!!$F1 3284

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
33 34 0.251916 CACAAGGCATTCCTCCGGTA 59.748 55.0 0.00 0.0 43.40 4.02 F
1887 1959 0.250640 GGCTTGGCTGATCGATGGAT 60.251 55.0 0.54 0.0 34.96 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1965 0.034059 CCCGGGAGATCTGCATGTAC 59.966 60.0 18.48 0.0 0.0 2.90 R
2957 3039 0.331278 TGATGGAAAAGGATGGCGGT 59.669 50.0 0.00 0.0 0.0 5.68 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
20 21 2.384382 GACGTTTGATTGCACACAAGG 58.616 47.619 0.00 0.00 39.69 3.61
21 22 1.130955 CGTTTGATTGCACACAAGGC 58.869 50.000 0.00 0.00 39.69 4.35
22 23 1.535649 CGTTTGATTGCACACAAGGCA 60.536 47.619 0.00 0.00 39.69 4.75
23 24 2.758009 GTTTGATTGCACACAAGGCAT 58.242 42.857 0.00 0.00 41.58 4.40
24 25 3.132925 GTTTGATTGCACACAAGGCATT 58.867 40.909 0.00 0.00 41.58 3.56
25 26 2.728690 TGATTGCACACAAGGCATTC 57.271 45.000 0.00 0.00 41.58 2.67
26 27 1.273048 TGATTGCACACAAGGCATTCC 59.727 47.619 0.00 0.00 41.58 3.01
28 29 0.961019 TTGCACACAAGGCATTCCTC 59.039 50.000 0.00 0.00 43.40 3.71
29 30 0.895100 TGCACACAAGGCATTCCTCC 60.895 55.000 0.00 0.00 43.40 4.30
30 31 1.926511 GCACACAAGGCATTCCTCCG 61.927 60.000 0.00 0.00 43.40 4.63
31 32 1.002134 ACACAAGGCATTCCTCCGG 60.002 57.895 0.00 0.00 43.40 5.14
32 33 1.002134 CACAAGGCATTCCTCCGGT 60.002 57.895 0.00 0.00 43.40 5.28
33 34 0.251916 CACAAGGCATTCCTCCGGTA 59.748 55.000 0.00 0.00 43.40 4.02
34 35 1.134098 CACAAGGCATTCCTCCGGTAT 60.134 52.381 0.00 0.00 43.40 2.73
35 36 1.564348 ACAAGGCATTCCTCCGGTATT 59.436 47.619 0.00 0.00 43.40 1.89
36 37 2.222027 CAAGGCATTCCTCCGGTATTC 58.778 52.381 0.00 0.00 43.40 1.75
37 38 0.393077 AGGCATTCCTCCGGTATTCG 59.607 55.000 0.00 0.00 38.72 3.34
46 47 4.924019 CGGTATTCGGGAGTTGCA 57.076 55.556 0.00 0.00 34.75 4.08
47 48 3.379650 CGGTATTCGGGAGTTGCAT 57.620 52.632 0.00 0.00 34.75 3.96
48 49 2.519377 CGGTATTCGGGAGTTGCATA 57.481 50.000 0.00 0.00 34.75 3.14
49 50 2.828877 CGGTATTCGGGAGTTGCATAA 58.171 47.619 0.00 0.00 34.75 1.90
50 51 2.542595 CGGTATTCGGGAGTTGCATAAC 59.457 50.000 0.00 0.00 34.56 1.89
51 52 2.876550 GGTATTCGGGAGTTGCATAACC 59.123 50.000 0.00 0.00 37.52 2.85
52 53 3.433173 GGTATTCGGGAGTTGCATAACCT 60.433 47.826 0.00 0.00 37.52 3.50
53 54 2.396590 TTCGGGAGTTGCATAACCTC 57.603 50.000 0.00 0.00 37.52 3.85
54 55 1.271856 TCGGGAGTTGCATAACCTCA 58.728 50.000 0.00 0.00 37.52 3.86
55 56 1.837439 TCGGGAGTTGCATAACCTCAT 59.163 47.619 0.00 0.00 37.52 2.90
56 57 3.035363 TCGGGAGTTGCATAACCTCATA 58.965 45.455 0.00 0.00 37.52 2.15
57 58 3.069586 TCGGGAGTTGCATAACCTCATAG 59.930 47.826 0.00 0.00 37.52 2.23
58 59 3.181465 CGGGAGTTGCATAACCTCATAGT 60.181 47.826 0.00 0.00 37.52 2.12
59 60 4.381411 GGGAGTTGCATAACCTCATAGTC 58.619 47.826 0.00 0.00 37.52 2.59
60 61 4.051922 GGAGTTGCATAACCTCATAGTCG 58.948 47.826 0.00 0.00 37.52 4.18
61 62 4.202121 GGAGTTGCATAACCTCATAGTCGA 60.202 45.833 0.00 0.00 37.52 4.20
62 63 5.339008 AGTTGCATAACCTCATAGTCGAA 57.661 39.130 0.00 0.00 37.52 3.71
63 64 5.352284 AGTTGCATAACCTCATAGTCGAAG 58.648 41.667 0.00 0.00 37.52 3.79
64 65 5.127194 AGTTGCATAACCTCATAGTCGAAGA 59.873 40.000 0.00 0.00 37.52 2.87
65 66 5.592104 TGCATAACCTCATAGTCGAAGAA 57.408 39.130 0.00 0.00 39.69 2.52
66 67 5.972935 TGCATAACCTCATAGTCGAAGAAA 58.027 37.500 0.00 0.00 39.69 2.52
67 68 6.582636 TGCATAACCTCATAGTCGAAGAAAT 58.417 36.000 0.00 0.00 39.69 2.17
68 69 7.722363 TGCATAACCTCATAGTCGAAGAAATA 58.278 34.615 0.00 0.00 39.69 1.40
69 70 8.367911 TGCATAACCTCATAGTCGAAGAAATAT 58.632 33.333 0.00 0.00 39.69 1.28
70 71 8.651588 GCATAACCTCATAGTCGAAGAAATATG 58.348 37.037 0.00 0.00 39.69 1.78
71 72 9.698309 CATAACCTCATAGTCGAAGAAATATGT 57.302 33.333 0.00 0.00 39.69 2.29
82 83 9.599866 AGTCGAAGAAATATGTATTTGACATGA 57.400 29.630 18.72 0.00 44.33 3.07
95 96 7.970061 TGTATTTGACATGAAGAAAGCAATAGC 59.030 33.333 0.00 0.00 35.11 2.97
96 97 5.963176 TTGACATGAAGAAAGCAATAGCA 57.037 34.783 0.00 0.00 45.49 3.49
97 98 5.963176 TGACATGAAGAAAGCAATAGCAA 57.037 34.783 0.00 0.00 45.49 3.91
98 99 6.519679 TGACATGAAGAAAGCAATAGCAAT 57.480 33.333 0.00 0.00 45.49 3.56
99 100 7.628769 TGACATGAAGAAAGCAATAGCAATA 57.371 32.000 0.00 0.00 45.49 1.90
100 101 8.054152 TGACATGAAGAAAGCAATAGCAATAA 57.946 30.769 0.00 0.00 45.49 1.40
101 102 8.522003 TGACATGAAGAAAGCAATAGCAATAAA 58.478 29.630 0.00 0.00 45.49 1.40
102 103 9.525409 GACATGAAGAAAGCAATAGCAATAAAT 57.475 29.630 0.00 0.00 45.49 1.40
103 104 9.880157 ACATGAAGAAAGCAATAGCAATAAATT 57.120 25.926 0.00 0.00 45.49 1.82
106 107 9.926158 TGAAGAAAGCAATAGCAATAAATTGAA 57.074 25.926 6.87 0.00 45.49 2.69
108 109 8.398491 AGAAAGCAATAGCAATAAATTGAACG 57.602 30.769 6.87 0.00 45.49 3.95
109 110 8.243426 AGAAAGCAATAGCAATAAATTGAACGA 58.757 29.630 6.87 0.00 45.49 3.85
110 111 8.931385 AAAGCAATAGCAATAAATTGAACGAT 57.069 26.923 6.87 0.00 45.49 3.73
111 112 8.566008 AAGCAATAGCAATAAATTGAACGATC 57.434 30.769 6.87 0.00 45.49 3.69
112 113 7.706159 AGCAATAGCAATAAATTGAACGATCA 58.294 30.769 6.87 0.00 45.49 2.92
113 114 8.355169 AGCAATAGCAATAAATTGAACGATCAT 58.645 29.630 6.87 0.00 45.49 2.45
114 115 8.971321 GCAATAGCAATAAATTGAACGATCATT 58.029 29.630 6.87 0.00 40.14 2.57
118 119 8.511465 AGCAATAAATTGAACGATCATTATGC 57.489 30.769 6.87 5.98 40.14 3.14
119 120 8.355169 AGCAATAAATTGAACGATCATTATGCT 58.645 29.630 6.87 13.62 40.14 3.79
120 121 9.611284 GCAATAAATTGAACGATCATTATGCTA 57.389 29.630 6.87 0.00 40.14 3.49
123 124 9.831737 ATAAATTGAACGATCATTATGCTAAGC 57.168 29.630 0.00 0.00 34.96 3.09
124 125 7.502120 AATTGAACGATCATTATGCTAAGCT 57.498 32.000 0.00 0.00 34.96 3.74
125 126 8.607441 AATTGAACGATCATTATGCTAAGCTA 57.393 30.769 0.00 0.00 34.96 3.32
126 127 8.607441 ATTGAACGATCATTATGCTAAGCTAA 57.393 30.769 0.00 0.00 34.96 3.09
127 128 7.408132 TGAACGATCATTATGCTAAGCTAAC 57.592 36.000 0.00 0.00 0.00 2.34
128 129 6.143919 TGAACGATCATTATGCTAAGCTAACG 59.856 38.462 0.00 0.00 0.00 3.18
129 130 4.923871 ACGATCATTATGCTAAGCTAACGG 59.076 41.667 0.00 0.00 0.00 4.44
130 131 5.161358 CGATCATTATGCTAAGCTAACGGA 58.839 41.667 0.00 0.00 0.00 4.69
131 132 5.807520 CGATCATTATGCTAAGCTAACGGAT 59.192 40.000 0.00 0.00 0.00 4.18
132 133 6.237675 CGATCATTATGCTAAGCTAACGGATG 60.238 42.308 0.00 0.00 0.00 3.51
133 134 5.237815 TCATTATGCTAAGCTAACGGATGG 58.762 41.667 0.00 0.00 0.00 3.51
134 135 2.550830 ATGCTAAGCTAACGGATGGG 57.449 50.000 0.00 0.00 0.00 4.00
135 136 1.200519 TGCTAAGCTAACGGATGGGT 58.799 50.000 0.00 0.00 0.00 4.51
136 137 1.138266 TGCTAAGCTAACGGATGGGTC 59.862 52.381 0.00 0.00 0.00 4.46
137 138 1.413077 GCTAAGCTAACGGATGGGTCT 59.587 52.381 0.00 0.00 0.00 3.85
138 139 2.158943 GCTAAGCTAACGGATGGGTCTT 60.159 50.000 0.00 0.00 0.00 3.01
139 140 2.403252 AAGCTAACGGATGGGTCTTG 57.597 50.000 0.00 0.00 0.00 3.02
140 141 1.276622 AGCTAACGGATGGGTCTTGT 58.723 50.000 0.00 0.00 0.00 3.16
141 142 1.207329 AGCTAACGGATGGGTCTTGTC 59.793 52.381 0.00 0.00 0.00 3.18
142 143 1.742750 GCTAACGGATGGGTCTTGTCC 60.743 57.143 0.00 0.00 0.00 4.02
143 144 1.553248 CTAACGGATGGGTCTTGTCCA 59.447 52.381 0.00 0.00 38.82 4.02
144 145 0.991920 AACGGATGGGTCTTGTCCAT 59.008 50.000 0.00 0.00 46.73 3.41
150 151 2.787473 TGGGTCTTGTCCATCACATC 57.213 50.000 0.00 0.00 33.90 3.06
151 152 1.984424 TGGGTCTTGTCCATCACATCA 59.016 47.619 0.00 0.00 33.90 3.07
152 153 2.577563 TGGGTCTTGTCCATCACATCAT 59.422 45.455 0.00 0.00 33.90 2.45
153 154 3.010472 TGGGTCTTGTCCATCACATCATT 59.990 43.478 0.00 0.00 33.90 2.57
154 155 3.629398 GGGTCTTGTCCATCACATCATTC 59.371 47.826 0.00 0.00 33.90 2.67
155 156 4.521146 GGTCTTGTCCATCACATCATTCT 58.479 43.478 0.00 0.00 33.90 2.40
156 157 4.574013 GGTCTTGTCCATCACATCATTCTC 59.426 45.833 0.00 0.00 33.90 2.87
157 158 4.574013 GTCTTGTCCATCACATCATTCTCC 59.426 45.833 0.00 0.00 33.90 3.71
158 159 4.472470 TCTTGTCCATCACATCATTCTCCT 59.528 41.667 0.00 0.00 33.90 3.69
159 160 5.662657 TCTTGTCCATCACATCATTCTCCTA 59.337 40.000 0.00 0.00 33.90 2.94
160 161 5.955961 TGTCCATCACATCATTCTCCTAA 57.044 39.130 0.00 0.00 0.00 2.69
161 162 6.505048 TGTCCATCACATCATTCTCCTAAT 57.495 37.500 0.00 0.00 0.00 1.73
162 163 6.293698 TGTCCATCACATCATTCTCCTAATG 58.706 40.000 0.00 0.00 0.00 1.90
163 164 6.100134 TGTCCATCACATCATTCTCCTAATGA 59.900 38.462 3.13 3.13 40.50 2.57
164 165 7.166851 GTCCATCACATCATTCTCCTAATGAT 58.833 38.462 7.28 7.28 45.40 2.45
172 173 5.787380 TCATTCTCCTAATGATGTGATCCG 58.213 41.667 0.00 0.00 32.21 4.18
173 174 4.607293 TTCTCCTAATGATGTGATCCGG 57.393 45.455 0.00 0.00 0.00 5.14
174 175 3.576861 TCTCCTAATGATGTGATCCGGT 58.423 45.455 0.00 0.00 0.00 5.28
175 176 3.967326 TCTCCTAATGATGTGATCCGGTT 59.033 43.478 0.00 0.00 0.00 4.44
176 177 5.144832 TCTCCTAATGATGTGATCCGGTTA 58.855 41.667 0.00 0.00 0.00 2.85
177 178 5.780282 TCTCCTAATGATGTGATCCGGTTAT 59.220 40.000 0.00 0.00 0.00 1.89
178 179 6.037786 TCCTAATGATGTGATCCGGTTATC 57.962 41.667 0.00 0.00 0.00 1.75
179 180 5.542251 TCCTAATGATGTGATCCGGTTATCA 59.458 40.000 0.00 0.58 33.48 2.15
180 181 6.042666 TCCTAATGATGTGATCCGGTTATCAA 59.957 38.462 7.37 0.27 37.61 2.57
181 182 6.710295 CCTAATGATGTGATCCGGTTATCAAA 59.290 38.462 7.37 3.08 37.61 2.69
182 183 7.391554 CCTAATGATGTGATCCGGTTATCAAAT 59.608 37.037 8.25 8.25 36.67 2.32
183 184 6.564709 ATGATGTGATCCGGTTATCAAATG 57.435 37.500 12.42 0.00 34.56 2.32
184 185 5.679601 TGATGTGATCCGGTTATCAAATGA 58.320 37.500 12.42 2.97 34.56 2.57
185 186 5.527214 TGATGTGATCCGGTTATCAAATGAC 59.473 40.000 12.42 2.03 34.56 3.06
186 187 4.837972 TGTGATCCGGTTATCAAATGACA 58.162 39.130 7.37 0.00 37.61 3.58
187 188 5.249420 TGTGATCCGGTTATCAAATGACAA 58.751 37.500 7.37 0.00 37.61 3.18
188 189 5.123186 TGTGATCCGGTTATCAAATGACAAC 59.877 40.000 7.37 0.00 37.61 3.32
189 190 5.354234 GTGATCCGGTTATCAAATGACAACT 59.646 40.000 7.37 0.00 37.61 3.16
190 191 5.943416 TGATCCGGTTATCAAATGACAACTT 59.057 36.000 0.00 0.00 32.41 2.66
191 192 7.065324 GTGATCCGGTTATCAAATGACAACTTA 59.935 37.037 7.37 0.00 37.61 2.24
192 193 7.773224 TGATCCGGTTATCAAATGACAACTTAT 59.227 33.333 0.00 0.00 32.41 1.73
193 194 7.315247 TCCGGTTATCAAATGACAACTTATG 57.685 36.000 0.00 0.00 32.41 1.90
217 218 8.669055 TGTCTATAGTTAGGAAACCTTAACCA 57.331 34.615 0.00 0.00 36.15 3.67
218 219 9.275572 TGTCTATAGTTAGGAAACCTTAACCAT 57.724 33.333 0.00 0.00 36.15 3.55
219 220 9.761504 GTCTATAGTTAGGAAACCTTAACCATC 57.238 37.037 0.00 0.00 36.15 3.51
220 221 9.725206 TCTATAGTTAGGAAACCTTAACCATCT 57.275 33.333 0.00 0.00 36.15 2.90
224 225 8.777578 AGTTAGGAAACCTTAACCATCTTTTT 57.222 30.769 0.00 0.00 36.15 1.94
245 246 5.899120 TTTGATCAACGAGCTAGTCTAGT 57.101 39.130 7.89 0.00 31.68 2.57
246 247 6.997239 TTTGATCAACGAGCTAGTCTAGTA 57.003 37.500 7.89 0.00 30.15 1.82
247 248 6.606234 TTGATCAACGAGCTAGTCTAGTAG 57.394 41.667 3.38 3.39 30.15 2.57
248 249 5.915175 TGATCAACGAGCTAGTCTAGTAGA 58.085 41.667 8.68 0.00 30.15 2.59
249 250 5.986741 TGATCAACGAGCTAGTCTAGTAGAG 59.013 44.000 8.68 1.49 30.15 2.43
250 251 4.695396 TCAACGAGCTAGTCTAGTAGAGG 58.305 47.826 8.68 0.00 30.15 3.69
251 252 3.116079 ACGAGCTAGTCTAGTAGAGGC 57.884 52.381 8.68 5.92 0.00 4.70
252 253 2.701951 ACGAGCTAGTCTAGTAGAGGCT 59.298 50.000 17.02 17.02 44.48 4.58
253 254 3.064207 CGAGCTAGTCTAGTAGAGGCTG 58.936 54.545 20.15 12.17 41.49 4.85
254 255 3.243941 CGAGCTAGTCTAGTAGAGGCTGA 60.244 52.174 20.15 0.00 41.49 4.26
255 256 4.062991 GAGCTAGTCTAGTAGAGGCTGAC 58.937 52.174 20.15 8.71 41.49 3.51
256 257 3.714798 AGCTAGTCTAGTAGAGGCTGACT 59.285 47.826 16.56 7.87 41.49 3.41
257 258 4.903049 AGCTAGTCTAGTAGAGGCTGACTA 59.097 45.833 16.56 9.09 41.49 2.59
259 260 4.699925 AGTCTAGTAGAGGCTGACTAGG 57.300 50.000 23.35 11.73 43.57 3.02
260 261 3.393278 AGTCTAGTAGAGGCTGACTAGGG 59.607 52.174 23.35 8.72 43.57 3.53
261 262 3.391955 GTCTAGTAGAGGCTGACTAGGGA 59.608 52.174 23.35 10.35 43.57 4.20
262 263 2.740506 AGTAGAGGCTGACTAGGGAC 57.259 55.000 0.00 0.00 0.00 4.46
263 264 1.923850 AGTAGAGGCTGACTAGGGACA 59.076 52.381 0.00 0.00 0.00 4.02
264 265 2.025898 GTAGAGGCTGACTAGGGACAC 58.974 57.143 0.00 0.00 0.00 3.67
265 266 0.681564 AGAGGCTGACTAGGGACACG 60.682 60.000 0.00 0.00 0.00 4.49
266 267 1.668101 GAGGCTGACTAGGGACACGG 61.668 65.000 0.00 0.00 0.00 4.94
267 268 1.982938 GGCTGACTAGGGACACGGT 60.983 63.158 0.00 0.00 0.00 4.83
268 269 0.682209 GGCTGACTAGGGACACGGTA 60.682 60.000 0.00 0.00 0.00 4.02
269 270 1.400737 GCTGACTAGGGACACGGTAT 58.599 55.000 0.00 0.00 0.00 2.73
270 271 1.755380 GCTGACTAGGGACACGGTATT 59.245 52.381 0.00 0.00 0.00 1.89
271 272 2.223758 GCTGACTAGGGACACGGTATTC 60.224 54.545 0.00 0.00 0.00 1.75
272 273 2.019249 TGACTAGGGACACGGTATTCG 58.981 52.381 0.00 0.00 45.88 3.34
287 288 6.206600 CGGTATTCGTTTATGTATCCACAC 57.793 41.667 0.00 0.00 37.54 3.82
288 289 5.749588 CGGTATTCGTTTATGTATCCACACA 59.250 40.000 0.00 0.00 37.54 3.72
289 290 6.422701 CGGTATTCGTTTATGTATCCACACAT 59.577 38.462 0.00 0.00 41.88 3.21
290 291 7.568679 CGGTATTCGTTTATGTATCCACACATG 60.569 40.741 0.00 0.00 39.46 3.21
291 292 7.225931 GGTATTCGTTTATGTATCCACACATGT 59.774 37.037 0.00 0.00 39.46 3.21
292 293 9.251792 GTATTCGTTTATGTATCCACACATGTA 57.748 33.333 0.00 0.00 39.46 2.29
293 294 8.902540 ATTCGTTTATGTATCCACACATGTAT 57.097 30.769 0.00 0.00 39.46 2.29
294 295 8.725405 TTCGTTTATGTATCCACACATGTATT 57.275 30.769 0.00 0.00 39.46 1.89
295 296 8.725405 TCGTTTATGTATCCACACATGTATTT 57.275 30.769 0.00 0.00 39.46 1.40
296 297 9.819267 TCGTTTATGTATCCACACATGTATTTA 57.181 29.630 0.00 0.00 39.46 1.40
305 306 8.925161 ATCCACACATGTATTTAAATTTTCGG 57.075 30.769 5.91 0.00 0.00 4.30
306 307 7.887381 TCCACACATGTATTTAAATTTTCGGT 58.113 30.769 5.91 0.00 0.00 4.69
307 308 8.024285 TCCACACATGTATTTAAATTTTCGGTC 58.976 33.333 5.91 0.00 0.00 4.79
308 309 7.810282 CCACACATGTATTTAAATTTTCGGTCA 59.190 33.333 5.91 0.00 0.00 4.02
309 310 9.186323 CACACATGTATTTAAATTTTCGGTCAA 57.814 29.630 5.91 0.00 0.00 3.18
310 311 9.921637 ACACATGTATTTAAATTTTCGGTCAAT 57.078 25.926 5.91 0.00 0.00 2.57
321 322 8.911247 AAATTTTCGGTCAATACAATTCTAGC 57.089 30.769 0.00 0.00 0.00 3.42
322 323 7.624360 ATTTTCGGTCAATACAATTCTAGCA 57.376 32.000 0.00 0.00 0.00 3.49
323 324 7.624360 TTTTCGGTCAATACAATTCTAGCAT 57.376 32.000 0.00 0.00 0.00 3.79
324 325 6.603237 TTCGGTCAATACAATTCTAGCATG 57.397 37.500 0.00 0.00 0.00 4.06
325 326 5.670485 TCGGTCAATACAATTCTAGCATGT 58.330 37.500 0.00 0.00 0.00 3.21
326 327 6.811954 TCGGTCAATACAATTCTAGCATGTA 58.188 36.000 0.00 5.08 34.35 2.29
327 328 7.441836 TCGGTCAATACAATTCTAGCATGTAT 58.558 34.615 8.30 8.30 40.89 2.29
328 329 8.581578 TCGGTCAATACAATTCTAGCATGTATA 58.418 33.333 12.38 0.00 38.85 1.47
329 330 9.203421 CGGTCAATACAATTCTAGCATGTATAA 57.797 33.333 12.38 5.17 38.85 0.98
388 389 7.839680 AACCATTTTATTATTGCCTCTAGGG 57.160 36.000 0.00 0.00 35.18 3.53
401 402 4.916041 CCTCTAGGGCATATTTCCATCA 57.084 45.455 0.00 0.00 0.00 3.07
405 406 7.405292 CCTCTAGGGCATATTTCCATCAATAA 58.595 38.462 0.00 0.00 0.00 1.40
592 594 8.751335 GTTATACAAATTTCCATGTAATTGCCG 58.249 33.333 4.39 1.06 35.79 5.69
776 779 2.735237 CGTCCGCTCCCTATTCCC 59.265 66.667 0.00 0.00 0.00 3.97
782 785 2.421739 CTCCCTATTCCCGGTGCG 59.578 66.667 0.00 0.00 0.00 5.34
857 860 3.864983 TTTGGGTCCTCGCCTCCCT 62.865 63.158 0.00 0.00 41.58 4.20
890 893 1.212935 AGCTTTAGCATTCCCGTCCAT 59.787 47.619 4.33 0.00 45.16 3.41
928 988 6.715280 CATGGCTGTTCAAGTATATATCCCT 58.285 40.000 0.00 0.00 0.00 4.20
929 989 6.114187 TGGCTGTTCAAGTATATATCCCTG 57.886 41.667 0.00 0.00 0.00 4.45
1230 1290 2.437359 GCAGAGTGCGAGGCCATT 60.437 61.111 5.01 0.00 31.71 3.16
1329 1389 3.311322 GGTTTGATGCCGATATTTGACGA 59.689 43.478 0.00 0.00 0.00 4.20
1370 1430 1.673033 GCTGCAGACGTTACCAGTCAT 60.673 52.381 20.43 0.00 40.84 3.06
1371 1431 1.995484 CTGCAGACGTTACCAGTCATG 59.005 52.381 8.42 0.00 40.84 3.07
1535 1595 0.668535 GGCACTTCAAGGACACCAAC 59.331 55.000 0.00 0.00 0.00 3.77
1618 1686 4.096532 TCTCATGTAACGTGGATGAGTCTC 59.903 45.833 21.82 0.00 42.48 3.36
1735 1803 3.607370 GAGCCACCCCAACCTCGTC 62.607 68.421 0.00 0.00 0.00 4.20
1742 1810 1.026718 CCCCAACCTCGTCAATCTGC 61.027 60.000 0.00 0.00 0.00 4.26
1847 1915 1.862123 CTGTTGCATGCGTTCGAGT 59.138 52.632 14.09 0.00 0.00 4.18
1884 1956 1.227350 TCGGCTTGGCTGATCGATG 60.227 57.895 0.54 0.00 39.19 3.84
1887 1959 0.250640 GGCTTGGCTGATCGATGGAT 60.251 55.000 0.54 0.00 34.96 3.41
1897 1969 3.898517 GATCGATGGATCTGTCGTACA 57.101 47.619 0.54 2.76 44.66 2.90
1898 1970 4.427096 GATCGATGGATCTGTCGTACAT 57.573 45.455 0.54 6.48 44.66 2.29
1912 1985 0.034059 GTACATGCAGATCTCCCGGG 59.966 60.000 16.85 16.85 0.00 5.73
2156 2229 2.754658 ACCTACGGCTACTGCGCT 60.755 61.111 9.73 0.00 40.82 5.92
2195 2268 0.445436 GCAAGCTCACCAAGATGTCG 59.555 55.000 0.00 0.00 0.00 4.35
2348 2421 6.153067 TCGAACGTTTAATCCAATGCAAATT 58.847 32.000 0.46 0.00 0.00 1.82
2362 2440 7.120579 TCCAATGCAAATTACTAACAAGATCGT 59.879 33.333 0.00 0.00 0.00 3.73
2369 2447 5.717078 TTACTAACAAGATCGTGACCACT 57.283 39.130 15.90 0.00 0.00 4.00
2425 2503 0.250901 AAATGTTCGTGAGGCTGGCT 60.251 50.000 2.24 2.24 0.00 4.75
2443 2521 0.322456 CTGATCCGTTGCTGGGGAAA 60.322 55.000 0.00 0.00 35.60 3.13
2702 2781 2.437281 AGATGAGCCAGACAACCATAGG 59.563 50.000 0.00 0.00 0.00 2.57
2828 2910 2.417933 GCAGCAACGAATCATCTTGACT 59.582 45.455 0.00 0.00 0.00 3.41
2928 3010 0.817634 CCAAGGACTGCCACGTTCAA 60.818 55.000 0.00 0.00 36.29 2.69
2958 3040 8.545229 AGCTTCTAGATCAACATATATGCAAC 57.455 34.615 12.79 1.06 0.00 4.17
2959 3041 7.605691 AGCTTCTAGATCAACATATATGCAACC 59.394 37.037 12.79 0.00 0.00 3.77
2960 3042 7.412346 GCTTCTAGATCAACATATATGCAACCG 60.412 40.741 12.79 0.00 0.00 4.44
2962 3044 3.753272 AGATCAACATATATGCAACCGCC 59.247 43.478 12.79 0.00 37.32 6.13
2963 3045 2.924421 TCAACATATATGCAACCGCCA 58.076 42.857 12.79 0.00 37.32 5.69
2964 3046 3.485394 TCAACATATATGCAACCGCCAT 58.515 40.909 12.79 0.00 37.32 4.40
2965 3047 3.501828 TCAACATATATGCAACCGCCATC 59.498 43.478 12.79 0.00 37.32 3.51
2966 3048 2.436417 ACATATATGCAACCGCCATCC 58.564 47.619 12.79 0.00 37.32 3.51
2986 3068 5.261040 TCCTTTTCCATCATTCTGGTCTT 57.739 39.130 0.00 0.00 37.57 3.01
3020 3103 9.113838 TCTAAAATCTATGTGAGAAGGATTTGC 57.886 33.333 0.00 0.00 37.85 3.68
3033 3116 4.918810 AGGATTTGCGGAATTGATAACC 57.081 40.909 0.00 0.00 0.00 2.85
3090 3175 9.941325 TTGAAGTTGCAAATAATTATTGGATGT 57.059 25.926 15.57 0.00 0.00 3.06
3374 3470 8.325787 AGTTATGATACACACTATTTTGGGACA 58.674 33.333 0.00 0.00 0.00 4.02
3413 3509 3.835395 TCATTTTTGTTGGGTGGGGATAC 59.165 43.478 0.00 0.00 0.00 2.24
3421 3517 1.493022 TGGGTGGGGATACTGTATTGC 59.507 52.381 1.22 0.00 0.00 3.56
3491 3588 3.681593 TCCCTCACTTCCAAAATAACCG 58.318 45.455 0.00 0.00 0.00 4.44
3492 3589 3.073356 TCCCTCACTTCCAAAATAACCGT 59.927 43.478 0.00 0.00 0.00 4.83
3495 3592 4.517453 CCTCACTTCCAAAATAACCGTGAA 59.483 41.667 0.00 0.00 30.60 3.18
3505 3602 9.819267 TCCAAAATAACCGTGAAACTTATTTTT 57.181 25.926 0.00 0.00 40.88 1.94
3543 3640 5.890110 TTCATAAGAGCGAGAATTTAGCG 57.110 39.130 0.00 0.00 35.78 4.26
3575 3673 2.435586 ACGCCAGCTCATGACAGC 60.436 61.111 0.00 0.00 39.99 4.40
3592 3690 2.502947 ACAGCTGGCTCATCACTATCAA 59.497 45.455 19.93 0.00 0.00 2.57
3602 3700 3.947196 TCATCACTATCAAATTTGCCGCT 59.053 39.130 13.54 1.11 0.00 5.52
3637 3736 0.881796 TCCGCTAGCTATCATCACCG 59.118 55.000 13.93 0.00 0.00 4.94
3655 3754 3.934579 CACCGTCAAGATCACATCAATCA 59.065 43.478 0.00 0.00 0.00 2.57
3659 3758 5.065602 CCGTCAAGATCACATCAATCACATT 59.934 40.000 0.00 0.00 0.00 2.71
3660 3759 6.258507 CCGTCAAGATCACATCAATCACATTA 59.741 38.462 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.384382 CCTTGTGTGCAATCAAACGTC 58.616 47.619 0.00 0.00 33.01 4.34
1 2 1.535860 GCCTTGTGTGCAATCAAACGT 60.536 47.619 0.00 0.00 33.01 3.99
2 3 1.130955 GCCTTGTGTGCAATCAAACG 58.869 50.000 0.00 0.00 33.01 3.60
3 4 2.222007 TGCCTTGTGTGCAATCAAAC 57.778 45.000 0.00 0.00 35.40 2.93
4 5 3.391965 GAATGCCTTGTGTGCAATCAAA 58.608 40.909 0.00 0.00 42.92 2.69
5 6 2.288948 GGAATGCCTTGTGTGCAATCAA 60.289 45.455 0.00 0.00 42.92 2.57
6 7 1.273048 GGAATGCCTTGTGTGCAATCA 59.727 47.619 0.00 0.00 42.92 2.57
7 8 1.547372 AGGAATGCCTTGTGTGCAATC 59.453 47.619 0.00 0.00 43.90 2.67
8 9 1.636148 AGGAATGCCTTGTGTGCAAT 58.364 45.000 0.00 0.00 43.90 3.56
9 10 3.130264 AGGAATGCCTTGTGTGCAA 57.870 47.368 0.00 0.00 43.90 4.08
10 11 4.927557 AGGAATGCCTTGTGTGCA 57.072 50.000 0.00 0.00 43.90 4.57
29 30 2.519377 TATGCAACTCCCGAATACCG 57.481 50.000 0.00 0.00 38.18 4.02
30 31 2.876550 GGTTATGCAACTCCCGAATACC 59.123 50.000 0.00 0.00 34.88 2.73
31 32 3.805207 AGGTTATGCAACTCCCGAATAC 58.195 45.455 0.00 0.00 34.88 1.89
32 33 3.452990 TGAGGTTATGCAACTCCCGAATA 59.547 43.478 0.00 0.00 34.88 1.75
33 34 2.238646 TGAGGTTATGCAACTCCCGAAT 59.761 45.455 0.00 0.00 34.88 3.34
34 35 1.626321 TGAGGTTATGCAACTCCCGAA 59.374 47.619 0.00 0.00 34.88 4.30
35 36 1.271856 TGAGGTTATGCAACTCCCGA 58.728 50.000 0.00 0.00 34.88 5.14
36 37 2.332063 ATGAGGTTATGCAACTCCCG 57.668 50.000 0.00 0.00 34.88 5.14
37 38 4.381411 GACTATGAGGTTATGCAACTCCC 58.619 47.826 0.00 0.00 34.88 4.30
38 39 4.051922 CGACTATGAGGTTATGCAACTCC 58.948 47.826 0.00 0.00 34.88 3.85
39 40 4.933330 TCGACTATGAGGTTATGCAACTC 58.067 43.478 0.00 0.00 34.88 3.01
40 41 5.127194 TCTTCGACTATGAGGTTATGCAACT 59.873 40.000 0.00 0.00 34.88 3.16
41 42 5.348986 TCTTCGACTATGAGGTTATGCAAC 58.651 41.667 0.00 0.00 0.00 4.17
42 43 5.592104 TCTTCGACTATGAGGTTATGCAA 57.408 39.130 0.00 0.00 0.00 4.08
43 44 5.592104 TTCTTCGACTATGAGGTTATGCA 57.408 39.130 0.00 0.00 0.00 3.96
44 45 8.651588 CATATTTCTTCGACTATGAGGTTATGC 58.348 37.037 0.00 0.00 0.00 3.14
45 46 9.698309 ACATATTTCTTCGACTATGAGGTTATG 57.302 33.333 0.00 0.00 0.00 1.90
69 70 7.970061 GCTATTGCTTTCTTCATGTCAAATACA 59.030 33.333 0.00 0.00 38.22 2.29
70 71 7.970061 TGCTATTGCTTTCTTCATGTCAAATAC 59.030 33.333 0.00 0.00 40.48 1.89
71 72 8.054152 TGCTATTGCTTTCTTCATGTCAAATA 57.946 30.769 0.00 0.00 40.48 1.40
72 73 6.927416 TGCTATTGCTTTCTTCATGTCAAAT 58.073 32.000 0.00 0.00 40.48 2.32
73 74 6.330004 TGCTATTGCTTTCTTCATGTCAAA 57.670 33.333 0.00 0.00 40.48 2.69
74 75 5.963176 TGCTATTGCTTTCTTCATGTCAA 57.037 34.783 0.00 0.00 40.48 3.18
75 76 5.963176 TTGCTATTGCTTTCTTCATGTCA 57.037 34.783 0.00 0.00 40.48 3.58
76 77 8.915871 TTTATTGCTATTGCTTTCTTCATGTC 57.084 30.769 0.00 0.00 40.48 3.06
77 78 9.880157 AATTTATTGCTATTGCTTTCTTCATGT 57.120 25.926 0.00 0.00 40.48 3.21
80 81 9.926158 TTCAATTTATTGCTATTGCTTTCTTCA 57.074 25.926 0.00 0.00 40.48 3.02
82 83 8.863049 CGTTCAATTTATTGCTATTGCTTTCTT 58.137 29.630 0.00 0.00 40.48 2.52
83 84 8.243426 TCGTTCAATTTATTGCTATTGCTTTCT 58.757 29.630 0.00 0.00 40.48 2.52
84 85 8.393395 TCGTTCAATTTATTGCTATTGCTTTC 57.607 30.769 0.00 0.00 40.48 2.62
85 86 8.931385 ATCGTTCAATTTATTGCTATTGCTTT 57.069 26.923 0.00 0.00 40.48 3.51
86 87 8.190122 TGATCGTTCAATTTATTGCTATTGCTT 58.810 29.630 0.00 0.00 40.48 3.91
87 88 7.706159 TGATCGTTCAATTTATTGCTATTGCT 58.294 30.769 0.00 0.00 40.48 3.91
88 89 7.912949 TGATCGTTCAATTTATTGCTATTGC 57.087 32.000 0.00 0.00 37.68 3.56
92 93 9.611284 GCATAATGATCGTTCAATTTATTGCTA 57.389 29.630 2.72 0.00 37.68 3.49
93 94 8.355169 AGCATAATGATCGTTCAATTTATTGCT 58.645 29.630 2.72 9.37 37.68 3.91
94 95 8.511465 AGCATAATGATCGTTCAATTTATTGC 57.489 30.769 2.72 7.73 37.68 3.56
97 98 9.831737 GCTTAGCATAATGATCGTTCAATTTAT 57.168 29.630 2.72 0.00 34.96 1.40
98 99 9.056005 AGCTTAGCATAATGATCGTTCAATTTA 57.944 29.630 7.07 0.00 34.96 1.40
99 100 7.934457 AGCTTAGCATAATGATCGTTCAATTT 58.066 30.769 7.07 0.00 34.96 1.82
100 101 7.502120 AGCTTAGCATAATGATCGTTCAATT 57.498 32.000 7.07 0.00 34.96 2.32
101 102 8.499162 GTTAGCTTAGCATAATGATCGTTCAAT 58.501 33.333 7.07 0.00 34.96 2.57
102 103 7.306574 CGTTAGCTTAGCATAATGATCGTTCAA 60.307 37.037 7.07 0.00 34.96 2.69
103 104 6.143919 CGTTAGCTTAGCATAATGATCGTTCA 59.856 38.462 7.07 0.00 36.00 3.18
104 105 6.400091 CCGTTAGCTTAGCATAATGATCGTTC 60.400 42.308 7.07 0.00 0.00 3.95
105 106 5.405571 CCGTTAGCTTAGCATAATGATCGTT 59.594 40.000 7.07 5.33 0.00 3.85
106 107 4.923871 CCGTTAGCTTAGCATAATGATCGT 59.076 41.667 7.07 0.00 0.00 3.73
107 108 5.161358 TCCGTTAGCTTAGCATAATGATCG 58.839 41.667 7.07 2.92 0.00 3.69
108 109 6.036517 CCATCCGTTAGCTTAGCATAATGATC 59.963 42.308 7.07 0.00 0.00 2.92
109 110 5.877012 CCATCCGTTAGCTTAGCATAATGAT 59.123 40.000 7.07 0.00 0.00 2.45
110 111 5.237815 CCATCCGTTAGCTTAGCATAATGA 58.762 41.667 7.07 0.00 0.00 2.57
111 112 4.393062 CCCATCCGTTAGCTTAGCATAATG 59.607 45.833 7.07 7.64 0.00 1.90
112 113 4.041691 ACCCATCCGTTAGCTTAGCATAAT 59.958 41.667 7.07 0.00 0.00 1.28
113 114 3.389983 ACCCATCCGTTAGCTTAGCATAA 59.610 43.478 7.07 0.00 0.00 1.90
114 115 2.969950 ACCCATCCGTTAGCTTAGCATA 59.030 45.455 7.07 0.00 0.00 3.14
115 116 1.768870 ACCCATCCGTTAGCTTAGCAT 59.231 47.619 7.07 0.00 0.00 3.79
116 117 1.138266 GACCCATCCGTTAGCTTAGCA 59.862 52.381 7.07 0.00 0.00 3.49
117 118 1.413077 AGACCCATCCGTTAGCTTAGC 59.587 52.381 0.00 0.00 0.00 3.09
118 119 3.118738 ACAAGACCCATCCGTTAGCTTAG 60.119 47.826 0.00 0.00 0.00 2.18
119 120 2.835764 ACAAGACCCATCCGTTAGCTTA 59.164 45.455 0.00 0.00 0.00 3.09
120 121 1.628846 ACAAGACCCATCCGTTAGCTT 59.371 47.619 0.00 0.00 0.00 3.74
121 122 1.207329 GACAAGACCCATCCGTTAGCT 59.793 52.381 0.00 0.00 0.00 3.32
122 123 1.653151 GACAAGACCCATCCGTTAGC 58.347 55.000 0.00 0.00 0.00 3.09
123 124 1.553248 TGGACAAGACCCATCCGTTAG 59.447 52.381 0.00 0.00 35.06 2.34
124 125 1.646912 TGGACAAGACCCATCCGTTA 58.353 50.000 0.00 0.00 35.06 3.18
125 126 0.991920 ATGGACAAGACCCATCCGTT 59.008 50.000 0.00 0.00 40.16 4.44
126 127 2.696864 ATGGACAAGACCCATCCGT 58.303 52.632 0.00 0.00 40.16 4.69
130 131 2.577563 TGATGTGATGGACAAGACCCAT 59.422 45.455 0.00 0.00 46.40 4.00
131 132 1.984424 TGATGTGATGGACAAGACCCA 59.016 47.619 0.00 0.00 38.36 4.51
132 133 2.787473 TGATGTGATGGACAAGACCC 57.213 50.000 0.00 0.00 38.36 4.46
133 134 4.521146 AGAATGATGTGATGGACAAGACC 58.479 43.478 0.00 0.00 38.36 3.85
134 135 4.574013 GGAGAATGATGTGATGGACAAGAC 59.426 45.833 0.00 0.00 38.36 3.01
135 136 4.472470 AGGAGAATGATGTGATGGACAAGA 59.528 41.667 0.00 0.00 38.36 3.02
136 137 4.778579 AGGAGAATGATGTGATGGACAAG 58.221 43.478 0.00 0.00 38.36 3.16
137 138 4.849813 AGGAGAATGATGTGATGGACAA 57.150 40.909 0.00 0.00 38.36 3.18
138 139 5.955961 TTAGGAGAATGATGTGATGGACA 57.044 39.130 0.00 0.00 39.53 4.02
139 140 6.528321 TCATTAGGAGAATGATGTGATGGAC 58.472 40.000 0.00 0.00 32.21 4.02
140 141 6.752285 TCATTAGGAGAATGATGTGATGGA 57.248 37.500 0.00 0.00 32.21 3.41
148 149 6.404708 CGGATCACATCATTAGGAGAATGAT 58.595 40.000 6.90 6.90 45.40 2.45
149 150 5.279657 CCGGATCACATCATTAGGAGAATGA 60.280 44.000 0.00 2.66 40.50 2.57
150 151 4.934001 CCGGATCACATCATTAGGAGAATG 59.066 45.833 0.00 0.00 0.00 2.67
151 152 4.594920 ACCGGATCACATCATTAGGAGAAT 59.405 41.667 9.46 0.00 0.00 2.40
152 153 3.967326 ACCGGATCACATCATTAGGAGAA 59.033 43.478 9.46 0.00 0.00 2.87
153 154 3.576861 ACCGGATCACATCATTAGGAGA 58.423 45.455 9.46 0.00 0.00 3.71
154 155 4.342862 AACCGGATCACATCATTAGGAG 57.657 45.455 9.46 0.00 0.00 3.69
155 156 5.542251 TGATAACCGGATCACATCATTAGGA 59.458 40.000 9.46 0.00 30.75 2.94
156 157 5.793817 TGATAACCGGATCACATCATTAGG 58.206 41.667 9.46 0.00 30.75 2.69
157 158 7.728847 TTTGATAACCGGATCACATCATTAG 57.271 36.000 9.46 0.00 35.56 1.73
158 159 7.936301 TCATTTGATAACCGGATCACATCATTA 59.064 33.333 9.46 0.00 35.56 1.90
159 160 6.772233 TCATTTGATAACCGGATCACATCATT 59.228 34.615 9.46 0.00 35.56 2.57
160 161 6.205464 GTCATTTGATAACCGGATCACATCAT 59.795 38.462 9.46 0.00 35.56 2.45
161 162 5.527214 GTCATTTGATAACCGGATCACATCA 59.473 40.000 9.46 6.29 35.56 3.07
162 163 5.527214 TGTCATTTGATAACCGGATCACATC 59.473 40.000 9.46 3.51 35.56 3.06
163 164 5.436175 TGTCATTTGATAACCGGATCACAT 58.564 37.500 9.46 3.44 35.56 3.21
164 165 4.837972 TGTCATTTGATAACCGGATCACA 58.162 39.130 9.46 0.60 35.56 3.58
165 166 5.354234 AGTTGTCATTTGATAACCGGATCAC 59.646 40.000 9.46 0.00 44.11 3.06
166 167 5.496556 AGTTGTCATTTGATAACCGGATCA 58.503 37.500 9.46 4.78 44.11 2.92
167 168 6.436843 AAGTTGTCATTTGATAACCGGATC 57.563 37.500 9.46 1.36 44.11 3.36
168 169 7.556275 ACATAAGTTGTCATTTGATAACCGGAT 59.444 33.333 9.46 0.00 44.11 4.18
169 170 6.882140 ACATAAGTTGTCATTTGATAACCGGA 59.118 34.615 9.46 0.00 44.11 5.14
170 171 7.083875 ACATAAGTTGTCATTTGATAACCGG 57.916 36.000 14.25 0.00 44.11 5.28
191 192 9.275572 TGGTTAAGGTTTCCTAACTATAGACAT 57.724 33.333 6.78 0.00 34.59 3.06
192 193 8.669055 TGGTTAAGGTTTCCTAACTATAGACA 57.331 34.615 6.78 0.00 34.59 3.41
193 194 9.761504 GATGGTTAAGGTTTCCTAACTATAGAC 57.238 37.037 6.78 0.00 34.59 2.59
194 195 9.725206 AGATGGTTAAGGTTTCCTAACTATAGA 57.275 33.333 6.78 0.00 34.59 1.98
198 199 9.871175 AAAAAGATGGTTAAGGTTTCCTAACTA 57.129 29.630 0.00 0.00 34.59 2.24
199 200 8.777578 AAAAAGATGGTTAAGGTTTCCTAACT 57.222 30.769 0.00 0.00 34.59 2.24
221 222 6.688578 ACTAGACTAGCTCGTTGATCAAAAA 58.311 36.000 10.35 0.07 0.00 1.94
222 223 6.268825 ACTAGACTAGCTCGTTGATCAAAA 57.731 37.500 10.35 0.46 0.00 2.44
223 224 5.899120 ACTAGACTAGCTCGTTGATCAAA 57.101 39.130 10.35 0.00 0.00 2.69
224 225 6.346896 TCTACTAGACTAGCTCGTTGATCAA 58.653 40.000 9.52 3.38 0.00 2.57
225 226 5.915175 TCTACTAGACTAGCTCGTTGATCA 58.085 41.667 9.52 0.00 0.00 2.92
226 227 5.407387 CCTCTACTAGACTAGCTCGTTGATC 59.593 48.000 9.52 0.00 0.00 2.92
227 228 5.302360 CCTCTACTAGACTAGCTCGTTGAT 58.698 45.833 9.52 0.00 0.00 2.57
228 229 4.695396 CCTCTACTAGACTAGCTCGTTGA 58.305 47.826 9.52 0.00 0.00 3.18
229 230 3.249080 GCCTCTACTAGACTAGCTCGTTG 59.751 52.174 9.52 0.00 0.00 4.10
230 231 3.135167 AGCCTCTACTAGACTAGCTCGTT 59.865 47.826 9.52 0.00 0.00 3.85
231 232 2.701951 AGCCTCTACTAGACTAGCTCGT 59.298 50.000 9.52 0.00 0.00 4.18
232 233 3.064207 CAGCCTCTACTAGACTAGCTCG 58.936 54.545 9.52 0.00 0.00 5.03
233 234 4.062991 GTCAGCCTCTACTAGACTAGCTC 58.937 52.174 9.52 0.00 0.00 4.09
234 235 3.714798 AGTCAGCCTCTACTAGACTAGCT 59.285 47.826 9.52 0.00 37.75 3.32
235 236 4.081322 AGTCAGCCTCTACTAGACTAGC 57.919 50.000 9.52 0.00 37.75 3.42
237 238 4.594062 CCCTAGTCAGCCTCTACTAGACTA 59.406 50.000 10.88 0.00 45.29 2.59
238 239 3.393278 CCCTAGTCAGCCTCTACTAGACT 59.607 52.174 10.88 0.00 45.29 3.24
239 240 3.391955 TCCCTAGTCAGCCTCTACTAGAC 59.608 52.174 10.88 0.00 45.29 2.59
240 241 3.391955 GTCCCTAGTCAGCCTCTACTAGA 59.608 52.174 10.88 0.00 45.29 2.43
241 242 3.136809 TGTCCCTAGTCAGCCTCTACTAG 59.863 52.174 0.00 0.00 43.15 2.57
242 243 3.117963 GTGTCCCTAGTCAGCCTCTACTA 60.118 52.174 0.00 0.00 0.00 1.82
243 244 1.923850 TGTCCCTAGTCAGCCTCTACT 59.076 52.381 0.00 0.00 0.00 2.57
244 245 2.025898 GTGTCCCTAGTCAGCCTCTAC 58.974 57.143 0.00 0.00 0.00 2.59
245 246 1.408405 CGTGTCCCTAGTCAGCCTCTA 60.408 57.143 0.00 0.00 0.00 2.43
246 247 0.681564 CGTGTCCCTAGTCAGCCTCT 60.682 60.000 0.00 0.00 0.00 3.69
247 248 1.668101 CCGTGTCCCTAGTCAGCCTC 61.668 65.000 0.00 0.00 0.00 4.70
248 249 1.682684 CCGTGTCCCTAGTCAGCCT 60.683 63.158 0.00 0.00 0.00 4.58
249 250 0.682209 TACCGTGTCCCTAGTCAGCC 60.682 60.000 0.00 0.00 0.00 4.85
250 251 1.400737 ATACCGTGTCCCTAGTCAGC 58.599 55.000 0.00 0.00 0.00 4.26
251 252 2.033049 CGAATACCGTGTCCCTAGTCAG 59.967 54.545 0.00 0.00 0.00 3.51
252 253 2.019249 CGAATACCGTGTCCCTAGTCA 58.981 52.381 0.00 0.00 0.00 3.41
253 254 2.770699 CGAATACCGTGTCCCTAGTC 57.229 55.000 0.00 0.00 0.00 2.59
280 281 8.527810 ACCGAAAATTTAAATACATGTGTGGAT 58.472 29.630 9.11 0.00 0.00 3.41
281 282 7.887381 ACCGAAAATTTAAATACATGTGTGGA 58.113 30.769 9.11 0.00 0.00 4.02
282 283 7.810282 TGACCGAAAATTTAAATACATGTGTGG 59.190 33.333 9.11 0.00 0.00 4.17
283 284 8.735303 TGACCGAAAATTTAAATACATGTGTG 57.265 30.769 9.11 0.00 0.00 3.82
284 285 9.921637 ATTGACCGAAAATTTAAATACATGTGT 57.078 25.926 9.11 0.00 0.00 3.72
295 296 9.997482 GCTAGAATTGTATTGACCGAAAATTTA 57.003 29.630 0.00 0.00 0.00 1.40
296 297 8.519526 TGCTAGAATTGTATTGACCGAAAATTT 58.480 29.630 0.00 0.00 0.00 1.82
297 298 8.050778 TGCTAGAATTGTATTGACCGAAAATT 57.949 30.769 0.00 0.00 0.00 1.82
298 299 7.624360 TGCTAGAATTGTATTGACCGAAAAT 57.376 32.000 0.00 0.00 0.00 1.82
299 300 7.120579 ACATGCTAGAATTGTATTGACCGAAAA 59.879 33.333 0.00 0.00 0.00 2.29
300 301 6.597672 ACATGCTAGAATTGTATTGACCGAAA 59.402 34.615 0.00 0.00 0.00 3.46
301 302 6.112734 ACATGCTAGAATTGTATTGACCGAA 58.887 36.000 0.00 0.00 0.00 4.30
302 303 5.670485 ACATGCTAGAATTGTATTGACCGA 58.330 37.500 0.00 0.00 0.00 4.69
303 304 5.991328 ACATGCTAGAATTGTATTGACCG 57.009 39.130 0.00 0.00 0.00 4.79
362 363 9.533831 CCCTAGAGGCAATAATAAAATGGTTAT 57.466 33.333 0.00 0.00 0.00 1.89
363 364 8.934023 CCCTAGAGGCAATAATAAAATGGTTA 57.066 34.615 0.00 0.00 0.00 2.85
364 365 7.839680 CCCTAGAGGCAATAATAAAATGGTT 57.160 36.000 0.00 0.00 0.00 3.67
380 381 4.916041 TGATGGAAATATGCCCTAGAGG 57.084 45.455 0.00 0.00 39.47 3.69
381 382 8.324306 TCTTATTGATGGAAATATGCCCTAGAG 58.676 37.037 0.00 0.00 0.00 2.43
382 383 8.218423 TCTTATTGATGGAAATATGCCCTAGA 57.782 34.615 0.00 0.00 0.00 2.43
383 384 7.555554 CCTCTTATTGATGGAAATATGCCCTAG 59.444 40.741 0.00 0.00 0.00 3.02
384 385 7.405292 CCTCTTATTGATGGAAATATGCCCTA 58.595 38.462 0.00 0.00 0.00 3.53
385 386 6.251471 CCTCTTATTGATGGAAATATGCCCT 58.749 40.000 0.00 0.00 0.00 5.19
386 387 5.105595 GCCTCTTATTGATGGAAATATGCCC 60.106 44.000 0.00 0.00 0.00 5.36
387 388 5.105595 GGCCTCTTATTGATGGAAATATGCC 60.106 44.000 0.00 0.00 0.00 4.40
388 389 5.392380 CGGCCTCTTATTGATGGAAATATGC 60.392 44.000 0.00 0.00 0.00 3.14
389 390 5.124457 CCGGCCTCTTATTGATGGAAATATG 59.876 44.000 0.00 0.00 0.00 1.78
390 391 5.014123 TCCGGCCTCTTATTGATGGAAATAT 59.986 40.000 0.00 0.00 0.00 1.28
391 392 4.349636 TCCGGCCTCTTATTGATGGAAATA 59.650 41.667 0.00 0.00 0.00 1.40
392 393 3.138283 TCCGGCCTCTTATTGATGGAAAT 59.862 43.478 0.00 0.00 0.00 2.17
393 394 2.507886 TCCGGCCTCTTATTGATGGAAA 59.492 45.455 0.00 0.00 0.00 3.13
394 395 2.123589 TCCGGCCTCTTATTGATGGAA 58.876 47.619 0.00 0.00 0.00 3.53
395 396 1.801242 TCCGGCCTCTTATTGATGGA 58.199 50.000 0.00 0.00 0.00 3.41
396 397 2.867109 ATCCGGCCTCTTATTGATGG 57.133 50.000 0.00 0.00 0.00 3.51
397 398 5.738909 AGAATATCCGGCCTCTTATTGATG 58.261 41.667 0.00 0.00 0.00 3.07
398 399 6.176183 CAAGAATATCCGGCCTCTTATTGAT 58.824 40.000 0.00 0.00 0.00 2.57
399 400 5.071788 ACAAGAATATCCGGCCTCTTATTGA 59.928 40.000 15.35 0.00 0.00 2.57
400 401 5.180117 CACAAGAATATCCGGCCTCTTATTG 59.820 44.000 0.00 4.27 0.00 1.90
401 402 5.071788 TCACAAGAATATCCGGCCTCTTATT 59.928 40.000 0.00 0.69 0.00 1.40
405 406 2.366916 CTCACAAGAATATCCGGCCTCT 59.633 50.000 0.00 0.00 0.00 3.69
543 545 4.379339 TTTTTGGTGAGAAAACCTTCCG 57.621 40.909 0.00 0.00 41.16 4.30
592 594 5.887754 TCCATTTGCCTAATACCTAATCCC 58.112 41.667 0.00 0.00 0.00 3.85
653 655 5.405935 AATTCTAGGGCCAACAAATGTTC 57.594 39.130 6.18 0.00 35.83 3.18
782 785 2.251371 GCCACGGCGTCAACTTTC 59.749 61.111 10.85 0.00 0.00 2.62
800 803 2.671963 GGTTCCGGTTCCTGCCAC 60.672 66.667 0.00 0.00 0.00 5.01
801 804 2.690653 CTTGGTTCCGGTTCCTGCCA 62.691 60.000 15.95 7.87 0.00 4.92
802 805 1.971695 CTTGGTTCCGGTTCCTGCC 60.972 63.158 15.95 5.75 0.00 4.85
803 806 0.955919 CTCTTGGTTCCGGTTCCTGC 60.956 60.000 15.95 0.00 0.00 4.85
804 807 0.955919 GCTCTTGGTTCCGGTTCCTG 60.956 60.000 15.95 10.33 0.00 3.86
857 860 4.917385 TGCTAAAGCTTATTTGGTCCTCA 58.083 39.130 0.00 0.00 42.66 3.86
864 867 5.248870 ACGGGAATGCTAAAGCTTATTTG 57.751 39.130 0.00 0.00 42.66 2.32
890 893 1.561076 AGCCATGCACACAAGGATCTA 59.439 47.619 0.00 0.00 36.75 1.98
956 1016 0.324091 AGGACACCCTCGTACCGATT 60.324 55.000 0.00 0.00 38.86 3.34
999 1059 1.745489 GGACGACAACAGCCCCATC 60.745 63.158 0.00 0.00 0.00 3.51
1215 1275 2.437359 GCAATGGCCTCGCACTCT 60.437 61.111 3.32 0.00 0.00 3.24
1329 1389 2.051076 CACGCGCATGTTGCAGTT 60.051 55.556 5.73 0.00 45.36 3.16
1371 1431 4.849329 CTCCTCGGCCGCGTACAC 62.849 72.222 23.51 0.00 0.00 2.90
1535 1595 2.061773 CTTGTTGCAGTAGTCACCTCG 58.938 52.381 0.00 0.00 0.00 4.63
1584 1644 5.235186 CACGTTACATGAGAAGGGAATGATC 59.765 44.000 0.00 0.00 0.00 2.92
1618 1686 5.345202 GGCGATATCCTACGTTACAAAGATG 59.655 44.000 0.00 0.00 0.00 2.90
1627 1695 1.311859 TCACGGCGATATCCTACGTT 58.688 50.000 16.62 0.00 35.36 3.99
1690 1758 2.104859 CAGCATCAGCACCTCCACG 61.105 63.158 0.00 0.00 45.49 4.94
1735 1803 0.460811 TGCTGTAGCCGAGCAGATTG 60.461 55.000 0.80 0.00 41.56 2.67
1847 1915 2.670229 CGACGACAAGGAAGGAATCGAA 60.670 50.000 0.00 0.00 36.64 3.71
1884 1956 2.871182 TCTGCATGTACGACAGATCC 57.129 50.000 7.89 0.00 35.58 3.36
1887 1959 2.359214 GGAGATCTGCATGTACGACAGA 59.641 50.000 9.69 12.84 44.06 3.41
1888 1960 2.544694 GGGAGATCTGCATGTACGACAG 60.545 54.545 16.72 3.82 0.00 3.51
1889 1961 1.409064 GGGAGATCTGCATGTACGACA 59.591 52.381 16.72 0.00 0.00 4.35
1891 1963 0.668535 CGGGAGATCTGCATGTACGA 59.331 55.000 16.72 0.00 0.00 3.43
1892 1964 0.319040 CCGGGAGATCTGCATGTACG 60.319 60.000 16.72 9.46 0.00 3.67
1893 1965 0.034059 CCCGGGAGATCTGCATGTAC 59.966 60.000 18.48 0.00 0.00 2.90
1894 1966 1.121407 CCCCGGGAGATCTGCATGTA 61.121 60.000 26.32 0.00 0.00 2.29
1896 1968 1.699054 TTCCCCGGGAGATCTGCATG 61.699 60.000 26.32 7.60 31.21 4.06
1897 1969 1.384502 TTCCCCGGGAGATCTGCAT 60.385 57.895 26.32 0.00 31.21 3.96
1898 1970 2.040442 TTCCCCGGGAGATCTGCA 59.960 61.111 26.32 0.00 31.21 4.41
2156 2229 2.420568 GGTCATGGCGTACTCGGGA 61.421 63.158 0.00 0.00 37.56 5.14
2195 2268 0.872021 CGCCGAAGCTGTAGATGTCC 60.872 60.000 0.00 0.00 36.60 4.02
2348 2421 5.475909 AGAAGTGGTCACGATCTTGTTAGTA 59.524 40.000 0.00 0.00 36.20 1.82
2359 2432 3.068165 CCTGCATATAGAAGTGGTCACGA 59.932 47.826 0.00 0.00 36.20 4.35
2362 2440 2.224042 CGCCTGCATATAGAAGTGGTCA 60.224 50.000 0.00 0.00 0.00 4.02
2386 2464 0.712979 TCCTGTCCCTGATCAGAGGT 59.287 55.000 24.62 0.00 34.02 3.85
2425 2503 0.322456 CTTTCCCCAGCAACGGATCA 60.322 55.000 0.00 0.00 0.00 2.92
2485 2563 0.467474 CCTCCTGCATGCACATGGAT 60.467 55.000 23.15 0.00 38.47 3.41
2828 2910 7.362315 CCTTGACTAACAAATCAGCATCATCAA 60.362 37.037 0.00 0.00 38.08 2.57
2950 3032 2.071778 AAAGGATGGCGGTTGCATAT 57.928 45.000 0.00 0.00 45.35 1.78
2951 3033 1.748493 GAAAAGGATGGCGGTTGCATA 59.252 47.619 0.00 0.00 45.35 3.14
2953 3035 1.531739 GGAAAAGGATGGCGGTTGCA 61.532 55.000 0.00 0.00 45.35 4.08
2954 3036 1.215382 GGAAAAGGATGGCGGTTGC 59.785 57.895 0.00 0.00 41.71 4.17
2957 3039 0.331278 TGATGGAAAAGGATGGCGGT 59.669 50.000 0.00 0.00 0.00 5.68
2958 3040 1.696063 ATGATGGAAAAGGATGGCGG 58.304 50.000 0.00 0.00 0.00 6.13
2959 3041 2.954318 AGAATGATGGAAAAGGATGGCG 59.046 45.455 0.00 0.00 0.00 5.69
2960 3042 3.069158 CCAGAATGATGGAAAAGGATGGC 59.931 47.826 0.00 0.00 43.57 4.40
2962 3044 5.198965 AGACCAGAATGATGGAAAAGGATG 58.801 41.667 3.52 0.00 43.57 3.51
2963 3045 5.463051 AGACCAGAATGATGGAAAAGGAT 57.537 39.130 3.52 0.00 43.57 3.24
2964 3046 4.934797 AGACCAGAATGATGGAAAAGGA 57.065 40.909 3.52 0.00 43.57 3.36
2965 3047 5.012239 TGAAGACCAGAATGATGGAAAAGG 58.988 41.667 3.52 0.00 43.57 3.11
2966 3048 6.152323 ACATGAAGACCAGAATGATGGAAAAG 59.848 38.462 0.00 0.00 43.57 2.27
3006 3088 3.440173 TCAATTCCGCAAATCCTTCTCAC 59.560 43.478 0.00 0.00 0.00 3.51
3007 3089 3.684908 TCAATTCCGCAAATCCTTCTCA 58.315 40.909 0.00 0.00 0.00 3.27
3008 3090 4.907879 ATCAATTCCGCAAATCCTTCTC 57.092 40.909 0.00 0.00 0.00 2.87
3009 3091 5.067805 GGTTATCAATTCCGCAAATCCTTCT 59.932 40.000 0.00 0.00 0.00 2.85
3010 3092 5.281727 GGTTATCAATTCCGCAAATCCTTC 58.718 41.667 0.00 0.00 0.00 3.46
3020 3103 6.700520 GTGTTCTACTAGGGTTATCAATTCCG 59.299 42.308 0.00 0.00 0.00 4.30
3065 3150 9.368674 CACATCCAATAATTATTTGCAACTTCA 57.631 29.630 8.01 0.00 0.00 3.02
3090 3175 4.331443 CCGTTATTCAATCACGGTTCATCA 59.669 41.667 14.06 0.00 46.90 3.07
3135 3220 4.096532 TGCTCTCTATATTATTCGGCCGAG 59.903 45.833 29.20 14.27 0.00 4.63
3168 3253 7.540745 GTCAAAGTTTGTGAAGCTTGACTTTTA 59.459 33.333 17.14 7.79 39.29 1.52
3171 3256 5.183904 AGTCAAAGTTTGTGAAGCTTGACTT 59.816 36.000 17.14 9.56 42.98 3.01
3315 3411 9.507280 GTCAACATATGTAAACTTTGATGGATG 57.493 33.333 9.21 0.00 0.00 3.51
3316 3412 9.466497 AGTCAACATATGTAAACTTTGATGGAT 57.534 29.630 9.21 0.00 0.00 3.41
3349 3445 8.500753 TGTCCCAAAATAGTGTGTATCATAAC 57.499 34.615 0.00 0.00 0.00 1.89
3352 3448 6.957631 TCTGTCCCAAAATAGTGTGTATCAT 58.042 36.000 0.00 0.00 0.00 2.45
3505 3602 9.614792 GCTCTTATGAAATACTTCCTCCTTTTA 57.385 33.333 0.00 0.00 0.00 1.52
3509 3606 5.598830 TCGCTCTTATGAAATACTTCCTCCT 59.401 40.000 0.00 0.00 0.00 3.69
3543 3640 1.569479 GGCGTGGTCTTCAGAGTTGC 61.569 60.000 0.00 0.00 0.00 4.17
3575 3673 5.279384 GCAAATTTGATAGTGATGAGCCAG 58.721 41.667 22.31 0.00 0.00 4.85
3576 3674 4.098349 GGCAAATTTGATAGTGATGAGCCA 59.902 41.667 22.31 0.00 37.23 4.75
3602 3700 2.815211 GAGGCGCGTCAGATGCAA 60.815 61.111 24.22 0.00 0.00 4.08
3629 3728 3.195396 TGATGTGATCTTGACGGTGATGA 59.805 43.478 0.00 0.00 0.00 2.92
3637 3736 8.429493 TCTAATGTGATTGATGTGATCTTGAC 57.571 34.615 0.00 0.00 0.00 3.18
3655 3754 2.094762 GGCACCACGAGTTCTAATGT 57.905 50.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.