Multiple sequence alignment - TraesCS3D01G039400

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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 TraesCS3D01G039400 chr3D 100.000 3074 0 0 1 3074 14997882 15000955 0.000000e+00 5677.0
1 TraesCS3D01G039400 chr3D 95.248 926 14 10 2170 3074 14971647 14972563 0.000000e+00 1439.0
2 TraesCS3D01G039400 chr3D 89.604 1087 87 4 998 2083 14948681 14947620 0.000000e+00 1358.0
3 TraesCS3D01G039400 chr3D 78.689 549 44 31 116 650 14965579 14966068 6.440000e-77 298.0
4 TraesCS3D01G039400 chr3D 75.940 399 78 10 1629 2012 569977162 569977557 4.050000e-44 189.0
5 TraesCS3D01G039400 chr3D 96.190 105 3 1 2710 2813 14972078 14972182 1.470000e-38 171.0
6 TraesCS3D01G039400 chr3D 84.524 168 16 4 791 958 14948850 14948693 1.140000e-34 158.0
7 TraesCS3D01G039400 chr3D 93.396 106 5 2 2609 2714 14972178 14972281 4.100000e-34 156.0
8 TraesCS3D01G039400 chr3D 76.203 374 38 18 138 500 14952141 14952474 1.910000e-32 150.0
9 TraesCS3D01G039400 chr3D 80.193 207 29 8 2516 2713 582850600 582850397 8.880000e-31 145.0
10 TraesCS3D01G039400 chr3D 96.970 33 0 1 2848 2880 263812186 263812155 2.000000e-03 54.7
11 TraesCS3D01G039400 chr3B 90.480 1187 100 8 904 2089 22130549 22129375 0.000000e+00 1554.0
12 TraesCS3D01G039400 chr3B 89.002 1182 92 18 906 2083 22101628 22100481 0.000000e+00 1428.0
13 TraesCS3D01G039400 chr3B 85.437 103 9 5 2884 2985 137608064 137607967 5.420000e-18 102.0
14 TraesCS3D01G039400 chr3B 81.905 105 15 3 1298 1400 757456825 757456723 5.460000e-13 86.1
15 TraesCS3D01G039400 chr3B 82.653 98 13 3 1298 1393 757286069 757285974 1.960000e-12 84.2
16 TraesCS3D01G039400 chr3A 90.917 1123 43 21 1999 3074 21319886 21318776 0.000000e+00 1454.0
17 TraesCS3D01G039400 chr3A 86.553 1294 115 20 791 2083 21323735 21324970 0.000000e+00 1371.0
18 TraesCS3D01G039400 chr3A 81.591 679 63 30 255 918 21320513 21319882 3.540000e-139 505.0
19 TraesCS3D01G039400 chr3A 94.393 107 4 2 2609 2714 21319163 21319058 2.450000e-36 163.0
20 TraesCS3D01G039400 chr3A 94.286 105 5 1 2710 2813 21319263 21319159 3.170000e-35 159.0
21 TraesCS3D01G039400 chr3A 75.278 360 75 8 1629 1975 702571202 702571560 3.170000e-35 159.0
22 TraesCS3D01G039400 chr6A 82.751 458 65 7 995 1444 49088510 49088059 2.220000e-106 396.0
23 TraesCS3D01G039400 chr4B 79.902 204 35 5 2511 2713 44311617 44311419 8.880000e-31 145.0
24 TraesCS3D01G039400 chr7A 79.535 215 33 8 2509 2714 291813233 291813445 3.200000e-30 143.0
25 TraesCS3D01G039400 chr7A 79.412 204 32 5 2516 2713 646553766 646553965 5.350000e-28 135.0
26 TraesCS3D01G039400 chr1D 79.812 213 27 11 2509 2713 410746444 410746240 1.150000e-29 141.0
27 TraesCS3D01G039400 chr7D 85.600 125 17 1 2312 2436 412655839 412655962 2.490000e-26 130.0
28 TraesCS3D01G039400 chr7D 100.000 31 0 0 2246 2276 614354675 614354645 1.190000e-04 58.4
29 TraesCS3D01G039400 chr4D 77.596 183 24 12 2250 2431 8394294 8394128 9.070000e-16 95.3
30 TraesCS3D01G039400 chr2D 80.292 137 14 9 2245 2381 305997108 305996985 1.170000e-14 91.6
31 TraesCS3D01G039400 chr5A 79.825 114 21 2 2325 2438 291792576 291792465 7.060000e-12 82.4
32 TraesCS3D01G039400 chr5B 90.385 52 4 1 2246 2297 396394804 396394854 1.980000e-07 67.6
33 TraesCS3D01G039400 chr2B 75.449 167 22 9 2242 2404 374105919 374105768 2.560000e-06 63.9


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 TraesCS3D01G039400 chr3D 14997882 15000955 3073 False 5677.000000 5677 100.000000 1 3074 1 chr3D.!!$F3 3073
1 TraesCS3D01G039400 chr3D 14947620 14948850 1230 True 758.000000 1358 87.064000 791 2083 2 chr3D.!!$R3 1292
2 TraesCS3D01G039400 chr3D 14971647 14972563 916 False 588.666667 1439 94.944667 2170 3074 3 chr3D.!!$F5 904
3 TraesCS3D01G039400 chr3B 22129375 22130549 1174 True 1554.000000 1554 90.480000 904 2089 1 chr3B.!!$R2 1185
4 TraesCS3D01G039400 chr3B 22100481 22101628 1147 True 1428.000000 1428 89.002000 906 2083 1 chr3B.!!$R1 1177
5 TraesCS3D01G039400 chr3A 21323735 21324970 1235 False 1371.000000 1371 86.553000 791 2083 1 chr3A.!!$F1 1292
6 TraesCS3D01G039400 chr3A 21318776 21320513 1737 True 570.250000 1454 90.296750 255 3074 4 chr3A.!!$R1 2819

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
345 346 0.028505 CACCAAGTGCTGCATATCGC 59.971 55.0 5.27 0.0 42.89 4.58 F
954 970 0.178767 CACAGCATCGATCCTCCCAA 59.821 55.0 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1767 0.460987 GTAGCACAGCTCGAATGGCT 60.461 55.000 13.77 13.77 40.44 4.75 R
2301 2333 2.059541 CCGTCACGGTTCTTCTTCTTC 58.940 52.381 8.54 0.00 42.73 2.87 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
25 26 7.819644 AGAGATCGATCTAGTCAAATCATCTG 58.180 38.462 27.36 0.00 37.25 2.90
26 27 7.665145 AGAGATCGATCTAGTCAAATCATCTGA 59.335 37.037 27.36 0.00 37.25 3.27
27 28 7.592938 AGATCGATCTAGTCAAATCATCTGAC 58.407 38.462 26.27 0.00 42.95 3.51
34 35 3.942829 GTCAAATCATCTGACTGGTGGA 58.057 45.455 0.00 0.00 40.10 4.02
35 36 3.686726 GTCAAATCATCTGACTGGTGGAC 59.313 47.826 0.00 0.00 40.10 4.02
36 37 3.327464 TCAAATCATCTGACTGGTGGACA 59.673 43.478 0.00 0.00 0.00 4.02
47 48 2.015456 TGGTGGACAGAGACAGATGT 57.985 50.000 0.00 0.00 0.00 3.06
48 49 3.169512 TGGTGGACAGAGACAGATGTA 57.830 47.619 0.00 0.00 0.00 2.29
49 50 2.826128 TGGTGGACAGAGACAGATGTAC 59.174 50.000 0.00 0.00 0.00 2.90
50 51 3.093057 GGTGGACAGAGACAGATGTACT 58.907 50.000 0.00 0.00 31.14 2.73
66 67 3.121559 GTACTGTACGTACGCATCACA 57.878 47.619 20.18 13.02 39.15 3.58
67 68 2.933495 ACTGTACGTACGCATCACAT 57.067 45.000 20.18 0.00 0.00 3.21
68 69 2.793933 ACTGTACGTACGCATCACATC 58.206 47.619 20.18 0.00 0.00 3.06
69 70 2.162809 ACTGTACGTACGCATCACATCA 59.837 45.455 20.18 2.60 0.00 3.07
70 71 3.181490 ACTGTACGTACGCATCACATCAT 60.181 43.478 20.18 0.00 0.00 2.45
71 72 4.035909 ACTGTACGTACGCATCACATCATA 59.964 41.667 20.18 0.00 0.00 2.15
72 73 5.116069 TGTACGTACGCATCACATCATAT 57.884 39.130 20.18 0.00 0.00 1.78
73 74 6.072893 ACTGTACGTACGCATCACATCATATA 60.073 38.462 20.18 0.00 0.00 0.86
74 75 6.311723 TGTACGTACGCATCACATCATATAG 58.688 40.000 20.18 0.00 0.00 1.31
75 76 4.733850 ACGTACGCATCACATCATATAGG 58.266 43.478 16.72 0.00 0.00 2.57
76 77 4.217767 ACGTACGCATCACATCATATAGGT 59.782 41.667 16.72 0.00 0.00 3.08
77 78 5.413523 ACGTACGCATCACATCATATAGGTA 59.586 40.000 16.72 0.00 0.00 3.08
78 79 6.095021 ACGTACGCATCACATCATATAGGTAT 59.905 38.462 16.72 0.00 0.00 2.73
79 80 6.414987 CGTACGCATCACATCATATAGGTATG 59.585 42.308 0.52 0.00 39.25 2.39
91 92 7.423844 TCATATAGGTATGAATGCTACCTGG 57.576 40.000 10.99 0.00 46.63 4.45
92 93 2.938956 AGGTATGAATGCTACCTGGC 57.061 50.000 1.00 0.00 45.72 4.85
93 94 2.126882 AGGTATGAATGCTACCTGGCA 58.873 47.619 1.00 0.00 45.72 4.92
94 95 2.158755 AGGTATGAATGCTACCTGGCAC 60.159 50.000 1.00 0.00 45.72 5.01
95 96 2.421388 GGTATGAATGCTACCTGGCACA 60.421 50.000 0.00 0.00 45.36 4.57
96 97 1.755179 ATGAATGCTACCTGGCACAC 58.245 50.000 0.00 0.00 45.36 3.82
97 98 0.692476 TGAATGCTACCTGGCACACT 59.308 50.000 0.00 0.00 45.36 3.55
98 99 1.905894 TGAATGCTACCTGGCACACTA 59.094 47.619 0.00 0.00 45.36 2.74
99 100 2.280628 GAATGCTACCTGGCACACTAC 58.719 52.381 0.00 0.00 45.36 2.73
100 101 0.541863 ATGCTACCTGGCACACTACC 59.458 55.000 0.00 0.00 45.36 3.18
101 102 1.221021 GCTACCTGGCACACTACCC 59.779 63.158 0.00 0.00 0.00 3.69
102 103 1.265454 GCTACCTGGCACACTACCCT 61.265 60.000 0.00 0.00 0.00 4.34
103 104 0.537188 CTACCTGGCACACTACCCTG 59.463 60.000 0.00 0.00 0.00 4.45
104 105 0.907704 TACCTGGCACACTACCCTGG 60.908 60.000 0.00 0.00 43.58 4.45
105 106 2.045926 CTGGCACACTACCCTGGC 60.046 66.667 0.00 0.00 0.00 4.85
106 107 3.628646 CTGGCACACTACCCTGGCC 62.629 68.421 0.00 0.00 44.82 5.36
107 108 3.646715 GGCACACTACCCTGGCCA 61.647 66.667 4.71 4.71 44.01 5.36
108 109 2.677228 GCACACTACCCTGGCCAT 59.323 61.111 5.51 0.00 0.00 4.40
109 110 1.750399 GCACACTACCCTGGCCATG 60.750 63.158 5.51 2.45 0.00 3.66
110 111 1.077501 CACACTACCCTGGCCATGG 60.078 63.158 24.26 24.26 0.00 3.66
111 112 2.124151 CACTACCCTGGCCATGGC 60.124 66.667 29.47 29.47 41.06 4.40
112 113 3.797353 ACTACCCTGGCCATGGCG 61.797 66.667 29.90 18.50 43.06 5.69
113 114 3.797353 CTACCCTGGCCATGGCGT 61.797 66.667 29.90 23.10 43.06 5.68
114 115 2.365768 TACCCTGGCCATGGCGTA 60.366 61.111 29.90 22.06 43.06 4.42
115 116 2.660258 CTACCCTGGCCATGGCGTAC 62.660 65.000 29.90 17.11 43.06 3.67
117 118 4.467084 CCTGGCCATGGCGTACGT 62.467 66.667 29.90 0.00 43.06 3.57
118 119 3.195002 CTGGCCATGGCGTACGTG 61.195 66.667 29.90 12.00 43.06 4.49
119 120 3.950794 CTGGCCATGGCGTACGTGT 62.951 63.158 29.90 0.00 43.06 4.49
120 121 2.184836 GGCCATGGCGTACGTGTA 59.815 61.111 29.90 3.90 43.06 2.90
121 122 1.881252 GGCCATGGCGTACGTGTAG 60.881 63.158 29.90 5.11 43.06 2.74
122 123 1.881252 GCCATGGCGTACGTGTAGG 60.881 63.158 23.48 14.69 34.14 3.18
123 124 1.514087 CCATGGCGTACGTGTAGGT 59.486 57.895 17.90 0.00 34.14 3.08
124 125 0.740149 CCATGGCGTACGTGTAGGTA 59.260 55.000 17.90 0.00 34.14 3.08
125 126 1.268896 CCATGGCGTACGTGTAGGTAG 60.269 57.143 17.90 0.00 34.14 3.18
126 127 1.027357 ATGGCGTACGTGTAGGTAGG 58.973 55.000 17.90 0.00 0.00 3.18
127 128 0.035534 TGGCGTACGTGTAGGTAGGA 60.036 55.000 17.90 0.00 31.64 2.94
128 129 1.094785 GGCGTACGTGTAGGTAGGAA 58.905 55.000 17.90 0.00 31.64 3.36
129 130 1.202188 GGCGTACGTGTAGGTAGGAAC 60.202 57.143 17.90 0.00 31.64 3.62
130 131 1.529826 GCGTACGTGTAGGTAGGAACG 60.530 57.143 17.90 0.00 41.64 3.95
131 132 1.062587 CGTACGTGTAGGTAGGAACGG 59.937 57.143 7.22 0.00 40.25 4.44
132 133 2.356135 GTACGTGTAGGTAGGAACGGA 58.644 52.381 0.00 0.00 40.25 4.69
133 134 1.457346 ACGTGTAGGTAGGAACGGAG 58.543 55.000 0.00 0.00 40.25 4.63
134 135 0.737219 CGTGTAGGTAGGAACGGAGG 59.263 60.000 0.00 0.00 32.55 4.30
135 136 1.109609 GTGTAGGTAGGAACGGAGGG 58.890 60.000 0.00 0.00 0.00 4.30
136 137 1.002069 TGTAGGTAGGAACGGAGGGA 58.998 55.000 0.00 0.00 0.00 4.20
137 138 1.341383 TGTAGGTAGGAACGGAGGGAC 60.341 57.143 0.00 0.00 0.00 4.46
138 139 0.259938 TAGGTAGGAACGGAGGGACC 59.740 60.000 0.00 0.00 0.00 4.46
139 140 2.062777 GGTAGGAACGGAGGGACCC 61.063 68.421 0.59 0.59 34.64 4.46
140 141 1.001376 GTAGGAACGGAGGGACCCT 59.999 63.158 14.79 14.79 36.03 4.34
150 151 0.106967 GAGGGACCCTCCTTCAATGC 60.107 60.000 28.16 1.56 44.36 3.56
151 152 1.076705 GGGACCCTCCTTCAATGCC 60.077 63.158 2.09 0.00 36.57 4.40
152 153 1.575447 GGGACCCTCCTTCAATGCCT 61.575 60.000 2.09 0.00 36.57 4.75
153 154 0.394899 GGACCCTCCTTCAATGCCTG 60.395 60.000 0.00 0.00 32.53 4.85
154 155 0.394899 GACCCTCCTTCAATGCCTGG 60.395 60.000 0.00 0.00 0.00 4.45
155 156 1.142688 ACCCTCCTTCAATGCCTGGT 61.143 55.000 0.00 0.00 0.00 4.00
156 157 0.040204 CCCTCCTTCAATGCCTGGTT 59.960 55.000 0.00 0.00 0.00 3.67
157 158 1.284785 CCCTCCTTCAATGCCTGGTTA 59.715 52.381 0.00 0.00 0.00 2.85
158 159 2.291540 CCCTCCTTCAATGCCTGGTTAA 60.292 50.000 0.00 0.00 0.00 2.01
159 160 3.430453 CCTCCTTCAATGCCTGGTTAAA 58.570 45.455 0.00 0.00 0.00 1.52
160 161 3.193479 CCTCCTTCAATGCCTGGTTAAAC 59.807 47.826 0.00 0.00 0.00 2.01
161 162 3.826157 CTCCTTCAATGCCTGGTTAAACA 59.174 43.478 0.00 0.00 0.00 2.83
162 163 4.219115 TCCTTCAATGCCTGGTTAAACAA 58.781 39.130 0.00 0.00 0.00 2.83
163 164 4.837860 TCCTTCAATGCCTGGTTAAACAAT 59.162 37.500 0.00 0.00 0.00 2.71
164 165 5.047377 TCCTTCAATGCCTGGTTAAACAATC 60.047 40.000 0.00 0.00 0.00 2.67
165 166 4.433186 TCAATGCCTGGTTAAACAATCG 57.567 40.909 0.00 0.00 0.00 3.34
166 167 2.923020 CAATGCCTGGTTAAACAATCGC 59.077 45.455 0.00 0.00 0.00 4.58
167 168 1.610363 TGCCTGGTTAAACAATCGCA 58.390 45.000 5.67 5.67 0.00 5.10
168 169 2.166829 TGCCTGGTTAAACAATCGCAT 58.833 42.857 5.67 0.00 0.00 4.73
169 170 2.094803 TGCCTGGTTAAACAATCGCATG 60.095 45.455 5.67 0.00 0.00 4.06
170 171 2.735126 GCCTGGTTAAACAATCGCATGG 60.735 50.000 0.00 0.00 0.00 3.66
171 172 2.491693 CCTGGTTAAACAATCGCATGGT 59.508 45.455 0.00 0.00 0.00 3.55
172 173 3.500982 CTGGTTAAACAATCGCATGGTG 58.499 45.455 0.00 0.00 0.00 4.17
173 174 2.887783 TGGTTAAACAATCGCATGGTGT 59.112 40.909 0.00 0.00 0.00 4.16
174 175 3.241701 GGTTAAACAATCGCATGGTGTG 58.758 45.455 0.00 0.00 0.00 3.82
182 183 2.562912 GCATGGTGTGCGGTTCAG 59.437 61.111 0.00 0.00 45.23 3.02
183 184 2.562912 CATGGTGTGCGGTTCAGC 59.437 61.111 0.00 0.00 37.71 4.26
184 185 3.049674 ATGGTGTGCGGTTCAGCG 61.050 61.111 0.00 0.00 40.67 5.18
193 194 3.741476 GGTTCAGCGGCTGCCAAG 61.741 66.667 24.78 7.58 44.31 3.61
202 203 2.561373 GCTGCCAAGCCAACGTAC 59.439 61.111 0.00 0.00 44.22 3.67
203 204 2.860293 CTGCCAAGCCAACGTACG 59.140 61.111 15.01 15.01 0.00 3.67
204 205 1.959226 CTGCCAAGCCAACGTACGT 60.959 57.895 16.72 16.72 0.00 3.57
205 206 1.503818 CTGCCAAGCCAACGTACGTT 61.504 55.000 27.15 27.15 39.13 3.99
206 207 1.096386 TGCCAAGCCAACGTACGTTT 61.096 50.000 29.91 14.27 36.00 3.60
207 208 0.029700 GCCAAGCCAACGTACGTTTT 59.970 50.000 29.91 19.28 36.00 2.43
208 209 1.534385 GCCAAGCCAACGTACGTTTTT 60.534 47.619 29.91 20.42 36.00 1.94
229 230 3.505835 TTTTTGAGGGAGCCAACGT 57.494 47.368 0.00 0.00 0.00 3.99
230 231 2.642154 TTTTTGAGGGAGCCAACGTA 57.358 45.000 0.00 0.00 0.00 3.57
231 232 1.886886 TTTTGAGGGAGCCAACGTAC 58.113 50.000 0.00 0.00 0.00 3.67
232 233 0.320073 TTTGAGGGAGCCAACGTACG 60.320 55.000 15.01 15.01 0.00 3.67
233 234 1.466025 TTGAGGGAGCCAACGTACGT 61.466 55.000 16.72 16.72 0.00 3.57
234 235 1.291272 GAGGGAGCCAACGTACGTT 59.709 57.895 27.15 27.15 39.13 3.99
235 236 0.320160 GAGGGAGCCAACGTACGTTT 60.320 55.000 29.91 16.90 36.00 3.60
236 237 0.107268 AGGGAGCCAACGTACGTTTT 59.893 50.000 29.91 18.37 36.00 2.43
237 238 0.514255 GGGAGCCAACGTACGTTTTC 59.486 55.000 29.91 24.22 36.00 2.29
247 248 5.583158 CAACGTACGTTTTCGAGTCTTCGA 61.583 45.833 29.91 0.00 44.14 3.71
248 249 6.830854 CAACGTACGTTTTCGAGTCTTCGAT 61.831 44.000 29.91 1.33 44.67 3.59
249 250 8.512141 CAACGTACGTTTTCGAGTCTTCGATC 62.512 46.154 29.91 0.00 44.67 3.69
271 272 3.338249 GAGTTCCACATGTACACTGCAT 58.662 45.455 0.00 0.00 0.00 3.96
274 275 1.811965 TCCACATGTACACTGCATTGC 59.188 47.619 3.61 0.46 0.00 3.56
289 290 0.971959 ATTGCAATGGGACGTGGCAT 60.972 50.000 12.09 0.00 34.03 4.40
291 292 3.067480 GCAATGGGACGTGGCATGG 62.067 63.158 12.05 0.00 0.00 3.66
292 293 2.755469 AATGGGACGTGGCATGGC 60.755 61.111 13.29 13.29 0.00 4.40
293 294 3.582242 AATGGGACGTGGCATGGCA 62.582 57.895 19.43 19.43 0.00 4.92
302 303 1.072332 TGGCATGGCACGTACAACT 59.928 52.632 19.43 0.00 0.00 3.16
305 306 1.086696 GCATGGCACGTACAACTGAT 58.913 50.000 0.00 0.00 0.00 2.90
306 307 2.276201 GCATGGCACGTACAACTGATA 58.724 47.619 0.00 0.00 0.00 2.15
307 308 2.030457 GCATGGCACGTACAACTGATAC 59.970 50.000 0.00 0.00 0.00 2.24
308 309 2.373540 TGGCACGTACAACTGATACC 57.626 50.000 0.00 0.00 0.00 2.73
309 310 1.274596 GGCACGTACAACTGATACCG 58.725 55.000 0.00 0.00 0.00 4.02
310 311 1.135315 GGCACGTACAACTGATACCGA 60.135 52.381 0.00 0.00 0.00 4.69
311 312 1.916000 GCACGTACAACTGATACCGAC 59.084 52.381 0.00 0.00 0.00 4.79
312 313 2.171567 CACGTACAACTGATACCGACG 58.828 52.381 0.00 0.00 35.10 5.12
313 314 1.186030 CGTACAACTGATACCGACGC 58.814 55.000 0.00 0.00 0.00 5.19
314 315 1.553308 GTACAACTGATACCGACGCC 58.447 55.000 0.00 0.00 0.00 5.68
315 316 0.099259 TACAACTGATACCGACGCCG 59.901 55.000 0.00 0.00 0.00 6.46
316 317 1.138036 CAACTGATACCGACGCCGA 59.862 57.895 0.00 0.00 38.22 5.54
317 318 1.138047 CAACTGATACCGACGCCGAC 61.138 60.000 0.00 0.00 38.22 4.79
318 319 1.588824 AACTGATACCGACGCCGACA 61.589 55.000 0.00 0.00 38.22 4.35
319 320 1.585521 CTGATACCGACGCCGACAC 60.586 63.158 0.00 0.00 38.22 3.67
320 321 2.261172 CTGATACCGACGCCGACACA 62.261 60.000 0.00 0.00 38.22 3.72
328 329 3.698463 CGCCGACACAACCGACAC 61.698 66.667 0.00 0.00 0.00 3.67
330 331 2.107343 CCGACACAACCGACACCA 59.893 61.111 0.00 0.00 0.00 4.17
335 336 1.355210 CACAACCGACACCAAGTGC 59.645 57.895 0.00 0.00 36.98 4.40
337 338 1.095228 ACAACCGACACCAAGTGCTG 61.095 55.000 0.00 0.00 36.98 4.41
345 346 0.028505 CACCAAGTGCTGCATATCGC 59.971 55.000 5.27 0.00 42.89 4.58
346 347 1.277739 CCAAGTGCTGCATATCGCG 59.722 57.895 5.27 0.00 46.97 5.87
349 350 0.460109 AAGTGCTGCATATCGCGTCA 60.460 50.000 5.27 0.00 46.97 4.35
350 351 1.148157 AGTGCTGCATATCGCGTCAC 61.148 55.000 5.27 3.08 46.97 3.67
351 352 1.882625 TGCTGCATATCGCGTCACC 60.883 57.895 5.77 0.00 46.97 4.02
352 353 1.592669 GCTGCATATCGCGTCACCT 60.593 57.895 5.77 0.00 46.97 4.00
353 354 1.552348 GCTGCATATCGCGTCACCTC 61.552 60.000 5.77 0.00 46.97 3.85
354 355 0.941463 CTGCATATCGCGTCACCTCC 60.941 60.000 5.77 0.00 46.97 4.30
361 362 2.581354 GCGTCACCTCCTGCATCT 59.419 61.111 0.00 0.00 0.00 2.90
371 372 5.059833 CACCTCCTGCATCTTATCTTAACC 58.940 45.833 0.00 0.00 0.00 2.85
372 373 4.103311 ACCTCCTGCATCTTATCTTAACCC 59.897 45.833 0.00 0.00 0.00 4.11
378 382 3.248602 GCATCTTATCTTAACCCGTGCAG 59.751 47.826 0.00 0.00 0.00 4.41
410 414 4.155310 GGAACACATCCGTAGTTTTTGG 57.845 45.455 0.00 0.00 38.79 3.28
411 415 3.566742 GGAACACATCCGTAGTTTTTGGT 59.433 43.478 0.00 0.00 38.79 3.67
412 416 4.037089 GGAACACATCCGTAGTTTTTGGTT 59.963 41.667 0.00 0.00 38.79 3.67
413 417 5.239087 GGAACACATCCGTAGTTTTTGGTTA 59.761 40.000 0.00 0.00 38.79 2.85
414 418 5.934935 ACACATCCGTAGTTTTTGGTTAG 57.065 39.130 0.00 0.00 0.00 2.34
415 419 4.214758 ACACATCCGTAGTTTTTGGTTAGC 59.785 41.667 0.00 0.00 0.00 3.09
416 420 4.214545 CACATCCGTAGTTTTTGGTTAGCA 59.785 41.667 0.00 0.00 0.00 3.49
417 421 4.822896 ACATCCGTAGTTTTTGGTTAGCAA 59.177 37.500 0.00 0.00 0.00 3.91
418 422 5.475564 ACATCCGTAGTTTTTGGTTAGCAAT 59.524 36.000 0.00 0.00 0.00 3.56
419 423 5.616488 TCCGTAGTTTTTGGTTAGCAATC 57.384 39.130 0.00 0.00 0.00 2.67
440 444 2.202222 GCACGCACACGCAAGATC 60.202 61.111 0.00 0.00 45.53 2.75
441 445 2.953605 GCACGCACACGCAAGATCA 61.954 57.895 0.00 0.00 45.53 2.92
446 450 1.926510 CGCACACGCAAGATCATTAGA 59.073 47.619 0.00 0.00 43.62 2.10
456 460 5.450171 GCAAGATCATTAGACATGTCATGC 58.550 41.667 27.02 16.69 0.00 4.06
457 461 5.008316 GCAAGATCATTAGACATGTCATGCA 59.992 40.000 27.02 12.73 0.00 3.96
458 462 6.294010 GCAAGATCATTAGACATGTCATGCAT 60.294 38.462 27.02 16.07 38.60 3.96
465 469 3.641031 CATGTCATGCATGGCACTG 57.359 52.632 34.69 26.59 46.22 3.66
466 470 0.527600 CATGTCATGCATGGCACTGC 60.528 55.000 34.69 14.00 46.22 4.40
503 507 5.082723 GCTTAGACTTTGAATGCGACTTTC 58.917 41.667 0.00 0.00 0.00 2.62
507 511 3.617669 ACTTTGAATGCGACTTTCAACG 58.382 40.909 15.32 15.50 41.45 4.10
508 512 3.064820 ACTTTGAATGCGACTTTCAACGT 59.935 39.130 16.45 16.45 41.45 3.99
513 517 2.941891 TGCGACTTTCAACGTGAATC 57.058 45.000 0.00 0.00 36.11 2.52
514 518 2.205911 TGCGACTTTCAACGTGAATCA 58.794 42.857 0.00 0.00 36.11 2.57
515 519 2.805671 TGCGACTTTCAACGTGAATCAT 59.194 40.909 0.00 0.00 36.11 2.45
516 520 3.155998 GCGACTTTCAACGTGAATCATG 58.844 45.455 0.12 0.12 36.11 3.07
524 528 1.009335 CGTGAATCATGCATGGCCG 60.009 57.895 25.97 16.07 0.00 6.13
531 535 0.884259 TCATGCATGGCCGGATAACG 60.884 55.000 25.97 0.00 43.80 3.18
536 540 1.539496 GCATGGCCGGATAACGTAGAA 60.539 52.381 5.05 0.00 42.24 2.10
578 582 3.376546 GTCCTCATTCCTCAAGCAACATC 59.623 47.826 0.00 0.00 0.00 3.06
582 586 1.159285 TTCCTCAAGCAACATCGCAG 58.841 50.000 0.00 0.00 0.00 5.18
586 590 0.883153 TCAAGCAACATCGCAGCATT 59.117 45.000 0.00 0.00 0.00 3.56
587 591 0.989164 CAAGCAACATCGCAGCATTG 59.011 50.000 0.00 0.00 0.00 2.82
588 592 0.883153 AAGCAACATCGCAGCATTGA 59.117 45.000 0.00 0.00 0.00 2.57
592 596 2.543031 GCAACATCGCAGCATTGATCAT 60.543 45.455 0.00 0.00 0.00 2.45
615 619 1.328680 GAACACGCATGCATCGATCTT 59.671 47.619 19.57 10.60 0.00 2.40
622 626 2.602211 GCATGCATCGATCTTATCTCCG 59.398 50.000 14.21 0.00 0.00 4.63
637 641 4.129737 CCGCATCGGTCGACCTGT 62.130 66.667 30.92 17.06 42.73 4.00
641 645 1.139734 CATCGGTCGACCTGTGGAG 59.860 63.158 30.92 15.20 0.00 3.86
644 648 2.603776 GGTCGACCTGTGGAGGGT 60.604 66.667 27.64 0.00 44.84 4.34
648 652 4.035102 GACCTGTGGAGGGTGGGC 62.035 72.222 0.00 0.00 44.84 5.36
650 654 4.351054 CCTGTGGAGGGTGGGCAC 62.351 72.222 0.00 0.00 35.40 5.01
676 680 4.531332 GCACTTTGCAATGCTATAGTAGC 58.469 43.478 16.07 10.23 46.86 3.58
677 681 4.274459 GCACTTTGCAATGCTATAGTAGCT 59.726 41.667 16.07 0.00 46.83 3.32
678 682 5.559799 GCACTTTGCAATGCTATAGTAGCTC 60.560 44.000 16.07 0.00 46.83 4.09
679 683 7.888812 GCACTTTGCAATGCTATAGTAGCTCA 61.889 42.308 16.07 0.00 46.83 4.26
709 724 7.781548 ACCCGAATAAGAACACATATGTAAC 57.218 36.000 8.32 3.23 38.45 2.50
716 731 4.843728 AGAACACATATGTAACCACAGGG 58.156 43.478 8.32 0.00 38.45 4.45
735 750 2.288518 GGGAAAAACGCATGCTACCAAA 60.289 45.455 17.13 0.00 0.00 3.28
738 753 5.164954 GGAAAAACGCATGCTACCAAATAA 58.835 37.500 17.13 0.00 0.00 1.40
756 771 3.948380 TGCGCGCATGCAAAATTT 58.052 44.444 33.09 0.00 43.02 1.82
787 802 4.681744 GAGGAGAATCATCTGTGACTGTC 58.318 47.826 0.00 0.00 43.72 3.51
803 819 5.628606 GTGACTGTCATGATGTGATCGATAG 59.371 44.000 14.37 0.00 39.48 2.08
852 868 1.617755 AAGCAACACTGATCGCGACG 61.618 55.000 12.93 5.54 0.00 5.12
865 881 1.132640 GCGACGAATGTTGACCAGC 59.867 57.895 0.00 0.00 0.00 4.85
950 966 1.137872 ACCTTCACAGCATCGATCCTC 59.862 52.381 0.00 0.00 0.00 3.71
954 970 0.178767 CACAGCATCGATCCTCCCAA 59.821 55.000 0.00 0.00 0.00 4.12
955 971 0.179000 ACAGCATCGATCCTCCCAAC 59.821 55.000 0.00 0.00 0.00 3.77
956 972 0.467384 CAGCATCGATCCTCCCAACT 59.533 55.000 0.00 0.00 0.00 3.16
957 973 0.755686 AGCATCGATCCTCCCAACTC 59.244 55.000 0.00 0.00 0.00 3.01
958 974 0.250081 GCATCGATCCTCCCAACTCC 60.250 60.000 0.00 0.00 0.00 3.85
959 975 1.418334 CATCGATCCTCCCAACTCCT 58.582 55.000 0.00 0.00 0.00 3.69
1024 1052 1.673665 CAGTCCAAGCCAGTCCTGC 60.674 63.158 0.00 0.00 0.00 4.85
1029 1057 1.376942 CAAGCCAGTCCTGCTCCTG 60.377 63.158 0.00 0.00 38.34 3.86
1095 1123 1.276421 CTCACGAAGATCACCAAGGGT 59.724 52.381 0.00 0.00 35.62 4.34
1119 1147 3.755628 TCCACGGCGCTCTACACC 61.756 66.667 6.90 0.00 0.00 4.16
1350 1378 3.310860 ATCGTTCCCGGCACAGGTC 62.311 63.158 0.00 0.00 33.95 3.85
1359 1387 2.342279 GCACAGGTCGCCAGTACA 59.658 61.111 0.00 0.00 0.00 2.90
1560 1588 1.447314 GAACCCCGGCTACTTCGTG 60.447 63.158 0.00 0.00 0.00 4.35
1561 1589 1.880819 GAACCCCGGCTACTTCGTGA 61.881 60.000 0.00 0.00 0.00 4.35
1563 1591 2.183555 CCCGGCTACTTCGTGACC 59.816 66.667 0.00 0.00 0.00 4.02
2337 2369 1.334869 GACGGATTTTGCCATGCTAGG 59.665 52.381 0.00 0.00 0.00 3.02
2565 2614 6.764308 CTCCCTAATGAGCAGAAAAATCAA 57.236 37.500 0.00 0.00 0.00 2.57
2566 2615 7.161773 CTCCCTAATGAGCAGAAAAATCAAA 57.838 36.000 0.00 0.00 0.00 2.69
2674 2723 2.503331 TGCATTCATGAAAGTCGTGGT 58.497 42.857 13.09 0.00 34.27 4.16
2675 2724 3.669536 TGCATTCATGAAAGTCGTGGTA 58.330 40.909 13.09 0.00 34.27 3.25
3064 3136 2.486592 ACATGTTTAACGCTAAGCACCC 59.513 45.455 0.00 0.00 31.90 4.61
3065 3137 2.257691 TGTTTAACGCTAAGCACCCA 57.742 45.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.665145 TCAGATGATTTGACTAGATCGATCTCT 59.335 37.037 30.49 17.21 38.32 3.10
1 2 7.750458 GTCAGATGATTTGACTAGATCGATCTC 59.250 40.741 30.49 17.43 41.29 2.75
2 3 7.592938 GTCAGATGATTTGACTAGATCGATCT 58.407 38.462 29.58 29.58 41.29 2.75
3 4 7.795431 GTCAGATGATTTGACTAGATCGATC 57.205 40.000 17.91 17.91 41.29 3.69
13 14 3.686726 GTCCACCAGTCAGATGATTTGAC 59.313 47.826 7.94 7.94 44.09 3.18
14 15 3.327464 TGTCCACCAGTCAGATGATTTGA 59.673 43.478 0.00 0.00 0.00 2.69
15 16 3.678289 TGTCCACCAGTCAGATGATTTG 58.322 45.455 0.00 0.00 0.00 2.32
16 17 3.584406 TCTGTCCACCAGTCAGATGATTT 59.416 43.478 0.00 0.00 42.19 2.17
17 18 3.176411 TCTGTCCACCAGTCAGATGATT 58.824 45.455 0.00 0.00 42.19 2.57
18 19 2.765135 CTCTGTCCACCAGTCAGATGAT 59.235 50.000 0.00 0.00 42.19 2.45
19 20 2.174360 CTCTGTCCACCAGTCAGATGA 58.826 52.381 0.00 0.00 42.19 2.92
20 21 2.094286 GTCTCTGTCCACCAGTCAGATG 60.094 54.545 0.00 0.00 42.19 2.90
21 22 2.175202 GTCTCTGTCCACCAGTCAGAT 58.825 52.381 0.00 0.00 42.19 2.90
22 23 1.133482 TGTCTCTGTCCACCAGTCAGA 60.133 52.381 0.00 0.00 42.19 3.27
23 24 1.271934 CTGTCTCTGTCCACCAGTCAG 59.728 57.143 0.00 0.00 42.19 3.51
24 25 1.133482 TCTGTCTCTGTCCACCAGTCA 60.133 52.381 0.00 0.00 42.19 3.41
25 26 1.621992 TCTGTCTCTGTCCACCAGTC 58.378 55.000 0.00 0.00 42.19 3.51
26 27 1.898472 CATCTGTCTCTGTCCACCAGT 59.102 52.381 0.00 0.00 42.19 4.00
27 28 1.898472 ACATCTGTCTCTGTCCACCAG 59.102 52.381 0.00 0.00 42.97 4.00
28 29 2.015456 ACATCTGTCTCTGTCCACCA 57.985 50.000 0.00 0.00 0.00 4.17
29 30 3.093057 AGTACATCTGTCTCTGTCCACC 58.907 50.000 0.00 0.00 0.00 4.61
30 31 4.103365 CAGTACATCTGTCTCTGTCCAC 57.897 50.000 0.00 0.00 39.17 4.02
47 48 3.374678 TGATGTGATGCGTACGTACAGTA 59.625 43.478 24.50 16.41 0.00 2.74
48 49 2.162809 TGATGTGATGCGTACGTACAGT 59.837 45.455 24.50 10.03 0.00 3.55
49 50 2.792749 TGATGTGATGCGTACGTACAG 58.207 47.619 24.50 17.43 0.00 2.74
50 51 2.923605 TGATGTGATGCGTACGTACA 57.076 45.000 24.50 16.27 0.00 2.90
51 52 5.737757 CCTATATGATGTGATGCGTACGTAC 59.262 44.000 17.90 15.90 0.00 3.67
52 53 5.413523 ACCTATATGATGTGATGCGTACGTA 59.586 40.000 17.90 13.65 0.00 3.57
53 54 4.217767 ACCTATATGATGTGATGCGTACGT 59.782 41.667 17.90 0.00 0.00 3.57
54 55 4.733850 ACCTATATGATGTGATGCGTACG 58.266 43.478 11.84 11.84 0.00 3.67
55 56 7.480810 TCATACCTATATGATGTGATGCGTAC 58.519 38.462 0.00 0.00 41.91 3.67
56 57 7.639113 TCATACCTATATGATGTGATGCGTA 57.361 36.000 0.00 0.00 41.91 4.42
57 58 6.530019 TCATACCTATATGATGTGATGCGT 57.470 37.500 0.00 0.00 41.91 5.24
58 59 7.517893 GCATTCATACCTATATGATGTGATGCG 60.518 40.741 12.44 0.00 45.29 4.73
59 60 7.498239 AGCATTCATACCTATATGATGTGATGC 59.502 37.037 16.68 16.68 46.78 3.91
60 61 8.959705 AGCATTCATACCTATATGATGTGATG 57.040 34.615 11.41 7.73 45.29 3.07
62 63 8.478066 GGTAGCATTCATACCTATATGATGTGA 58.522 37.037 11.41 0.00 45.29 3.58
63 64 8.654230 GGTAGCATTCATACCTATATGATGTG 57.346 38.462 0.00 2.96 45.29 3.21
74 75 2.222027 GTGCCAGGTAGCATTCATACC 58.778 52.381 0.00 0.00 46.24 2.73
75 76 2.614057 GTGTGCCAGGTAGCATTCATAC 59.386 50.000 0.00 0.00 46.24 2.39
76 77 2.505407 AGTGTGCCAGGTAGCATTCATA 59.495 45.455 0.00 0.00 46.24 2.15
77 78 1.283029 AGTGTGCCAGGTAGCATTCAT 59.717 47.619 0.00 0.00 46.24 2.57
78 79 0.692476 AGTGTGCCAGGTAGCATTCA 59.308 50.000 0.00 0.00 46.24 2.57
79 80 2.280628 GTAGTGTGCCAGGTAGCATTC 58.719 52.381 0.00 0.00 46.24 2.67
80 81 1.065418 GGTAGTGTGCCAGGTAGCATT 60.065 52.381 0.00 0.00 46.24 3.56
81 82 0.541863 GGTAGTGTGCCAGGTAGCAT 59.458 55.000 0.00 0.00 46.24 3.79
82 83 1.550130 GGGTAGTGTGCCAGGTAGCA 61.550 60.000 0.00 0.00 41.46 3.49
83 84 1.221021 GGGTAGTGTGCCAGGTAGC 59.779 63.158 0.00 0.00 0.00 3.58
84 85 0.537188 CAGGGTAGTGTGCCAGGTAG 59.463 60.000 0.00 0.00 0.00 3.18
85 86 0.907704 CCAGGGTAGTGTGCCAGGTA 60.908 60.000 0.00 0.00 0.00 3.08
86 87 2.224159 CCAGGGTAGTGTGCCAGGT 61.224 63.158 0.00 0.00 0.00 4.00
87 88 2.671070 CCAGGGTAGTGTGCCAGG 59.329 66.667 0.00 0.00 0.00 4.45
88 89 2.045926 GCCAGGGTAGTGTGCCAG 60.046 66.667 0.00 0.00 0.00 4.85
89 90 3.646715 GGCCAGGGTAGTGTGCCA 61.647 66.667 0.00 0.00 41.76 4.92
90 91 2.983879 ATGGCCAGGGTAGTGTGCC 61.984 63.158 13.05 0.00 42.49 5.01
91 92 1.750399 CATGGCCAGGGTAGTGTGC 60.750 63.158 13.05 0.00 0.00 4.57
92 93 1.077501 CCATGGCCAGGGTAGTGTG 60.078 63.158 28.59 10.10 0.00 3.82
93 94 2.983879 GCCATGGCCAGGGTAGTGT 61.984 63.158 35.31 1.00 34.16 3.55
94 95 2.124151 GCCATGGCCAGGGTAGTG 60.124 66.667 35.31 16.31 34.16 2.74
95 96 3.797353 CGCCATGGCCAGGGTAGT 61.797 66.667 35.31 2.77 37.98 2.73
96 97 2.439960 TACGCCATGGCCAGGGTAG 61.440 63.158 35.31 29.71 37.98 3.18
97 98 2.365768 TACGCCATGGCCAGGGTA 60.366 61.111 35.31 24.64 37.98 3.69
98 99 4.109675 GTACGCCATGGCCAGGGT 62.110 66.667 35.31 25.66 37.98 4.34
100 101 4.467084 ACGTACGCCATGGCCAGG 62.467 66.667 30.79 23.98 37.98 4.45
101 102 2.566057 TACACGTACGCCATGGCCAG 62.566 60.000 30.79 19.97 37.98 4.85
102 103 2.566057 CTACACGTACGCCATGGCCA 62.566 60.000 30.79 16.36 37.98 5.36
103 104 1.881252 CTACACGTACGCCATGGCC 60.881 63.158 30.79 16.00 37.98 5.36
104 105 1.881252 CCTACACGTACGCCATGGC 60.881 63.158 27.67 27.67 37.85 4.40
105 106 0.740149 TACCTACACGTACGCCATGG 59.260 55.000 16.72 7.63 0.00 3.66
106 107 1.268896 CCTACCTACACGTACGCCATG 60.269 57.143 16.72 9.09 0.00 3.66
107 108 1.027357 CCTACCTACACGTACGCCAT 58.973 55.000 16.72 3.26 0.00 4.40
108 109 0.035534 TCCTACCTACACGTACGCCA 60.036 55.000 16.72 0.00 0.00 5.69
109 110 1.094785 TTCCTACCTACACGTACGCC 58.905 55.000 16.72 0.00 0.00 5.68
110 111 1.529826 CGTTCCTACCTACACGTACGC 60.530 57.143 16.72 0.00 0.00 4.42
111 112 1.062587 CCGTTCCTACCTACACGTACG 59.937 57.143 15.01 15.01 0.00 3.67
112 113 2.352960 CTCCGTTCCTACCTACACGTAC 59.647 54.545 0.00 0.00 0.00 3.67
113 114 2.632377 CTCCGTTCCTACCTACACGTA 58.368 52.381 0.00 0.00 0.00 3.57
114 115 1.457346 CTCCGTTCCTACCTACACGT 58.543 55.000 0.00 0.00 0.00 4.49
115 116 0.737219 CCTCCGTTCCTACCTACACG 59.263 60.000 0.00 0.00 0.00 4.49
116 117 1.109609 CCCTCCGTTCCTACCTACAC 58.890 60.000 0.00 0.00 0.00 2.90
117 118 1.002069 TCCCTCCGTTCCTACCTACA 58.998 55.000 0.00 0.00 0.00 2.74
118 119 1.397672 GTCCCTCCGTTCCTACCTAC 58.602 60.000 0.00 0.00 0.00 3.18
119 120 0.259938 GGTCCCTCCGTTCCTACCTA 59.740 60.000 0.00 0.00 0.00 3.08
120 121 1.001376 GGTCCCTCCGTTCCTACCT 59.999 63.158 0.00 0.00 0.00 3.08
121 122 2.062777 GGGTCCCTCCGTTCCTACC 61.063 68.421 0.00 0.00 37.00 3.18
122 123 1.001376 AGGGTCCCTCCGTTCCTAC 59.999 63.158 3.85 0.00 37.00 3.18
123 124 1.309006 GAGGGTCCCTCCGTTCCTA 59.691 63.158 25.89 0.00 44.36 2.94
124 125 2.039137 GAGGGTCCCTCCGTTCCT 59.961 66.667 25.89 0.00 44.36 3.36
132 133 1.575447 GGCATTGAAGGAGGGTCCCT 61.575 60.000 11.38 11.38 37.19 4.20
133 134 1.076705 GGCATTGAAGGAGGGTCCC 60.077 63.158 0.00 0.00 37.19 4.46
134 135 0.394899 CAGGCATTGAAGGAGGGTCC 60.395 60.000 0.00 0.00 36.58 4.46
135 136 0.394899 CCAGGCATTGAAGGAGGGTC 60.395 60.000 0.00 0.00 0.00 4.46
136 137 1.142688 ACCAGGCATTGAAGGAGGGT 61.143 55.000 0.00 0.00 0.00 4.34
137 138 0.040204 AACCAGGCATTGAAGGAGGG 59.960 55.000 0.00 0.00 0.00 4.30
138 139 2.806945 TAACCAGGCATTGAAGGAGG 57.193 50.000 0.00 0.00 0.00 4.30
139 140 3.826157 TGTTTAACCAGGCATTGAAGGAG 59.174 43.478 0.00 0.00 0.00 3.69
140 141 3.838565 TGTTTAACCAGGCATTGAAGGA 58.161 40.909 0.00 0.00 0.00 3.36
141 142 4.599047 TTGTTTAACCAGGCATTGAAGG 57.401 40.909 0.00 0.00 0.00 3.46
142 143 4.858692 CGATTGTTTAACCAGGCATTGAAG 59.141 41.667 0.00 0.00 0.00 3.02
143 144 4.804108 CGATTGTTTAACCAGGCATTGAA 58.196 39.130 0.00 0.00 0.00 2.69
144 145 3.366883 GCGATTGTTTAACCAGGCATTGA 60.367 43.478 0.00 0.00 0.00 2.57
145 146 2.923020 GCGATTGTTTAACCAGGCATTG 59.077 45.455 0.00 0.00 0.00 2.82
146 147 2.560542 TGCGATTGTTTAACCAGGCATT 59.439 40.909 0.00 0.00 0.00 3.56
147 148 2.166829 TGCGATTGTTTAACCAGGCAT 58.833 42.857 0.00 0.00 0.00 4.40
148 149 1.610363 TGCGATTGTTTAACCAGGCA 58.390 45.000 0.00 0.00 0.00 4.75
149 150 2.529151 CATGCGATTGTTTAACCAGGC 58.471 47.619 0.00 0.00 0.00 4.85
150 151 2.491693 ACCATGCGATTGTTTAACCAGG 59.508 45.455 0.00 0.00 0.00 4.45
151 152 3.057596 ACACCATGCGATTGTTTAACCAG 60.058 43.478 0.00 0.00 0.00 4.00
152 153 2.887783 ACACCATGCGATTGTTTAACCA 59.112 40.909 0.00 0.00 0.00 3.67
153 154 3.241701 CACACCATGCGATTGTTTAACC 58.758 45.455 0.00 0.00 0.00 2.85
154 155 2.661195 GCACACCATGCGATTGTTTAAC 59.339 45.455 0.00 0.00 46.55 2.01
155 156 2.940147 GCACACCATGCGATTGTTTAA 58.060 42.857 0.00 0.00 46.55 1.52
156 157 2.627863 GCACACCATGCGATTGTTTA 57.372 45.000 0.00 0.00 46.55 2.01
157 158 3.495124 GCACACCATGCGATTGTTT 57.505 47.368 0.00 0.00 46.55 2.83
166 167 2.562912 GCTGAACCGCACACCATG 59.437 61.111 0.00 0.00 0.00 3.66
167 168 3.049674 CGCTGAACCGCACACCAT 61.050 61.111 0.00 0.00 0.00 3.55
176 177 3.741476 CTTGGCAGCCGCTGAACC 61.741 66.667 24.80 16.36 38.60 3.62
177 178 4.410743 GCTTGGCAGCCGCTGAAC 62.411 66.667 24.80 15.53 40.61 3.18
185 186 2.561373 GTACGTTGGCTTGGCAGC 59.439 61.111 0.00 1.21 46.52 5.25
186 187 1.503818 AACGTACGTTGGCTTGGCAG 61.504 55.000 31.29 0.00 36.91 4.85
187 188 1.096386 AAACGTACGTTGGCTTGGCA 61.096 50.000 32.31 0.00 38.47 4.92
188 189 0.029700 AAAACGTACGTTGGCTTGGC 59.970 50.000 32.31 0.00 38.47 4.52
189 190 2.478547 AAAAACGTACGTTGGCTTGG 57.521 45.000 32.31 0.00 38.47 3.61
211 212 2.223745 GTACGTTGGCTCCCTCAAAAA 58.776 47.619 0.00 0.00 0.00 1.94
212 213 1.874739 CGTACGTTGGCTCCCTCAAAA 60.875 52.381 7.22 0.00 0.00 2.44
213 214 0.320073 CGTACGTTGGCTCCCTCAAA 60.320 55.000 7.22 0.00 0.00 2.69
214 215 1.290955 CGTACGTTGGCTCCCTCAA 59.709 57.895 7.22 0.00 0.00 3.02
215 216 1.466025 AACGTACGTTGGCTCCCTCA 61.466 55.000 31.29 0.00 36.91 3.86
216 217 0.320160 AAACGTACGTTGGCTCCCTC 60.320 55.000 32.31 0.00 38.47 4.30
217 218 0.107268 AAAACGTACGTTGGCTCCCT 59.893 50.000 32.31 13.56 38.47 4.20
218 219 0.514255 GAAAACGTACGTTGGCTCCC 59.486 55.000 32.31 14.63 38.47 4.30
219 220 0.162294 CGAAAACGTACGTTGGCTCC 59.838 55.000 32.31 18.02 38.47 4.70
220 221 1.123756 CTCGAAAACGTACGTTGGCTC 59.876 52.381 32.31 25.06 38.47 4.70
221 222 1.134226 CTCGAAAACGTACGTTGGCT 58.866 50.000 32.31 20.14 38.47 4.75
222 223 0.854705 ACTCGAAAACGTACGTTGGC 59.145 50.000 32.31 24.31 38.47 4.52
223 224 2.388121 AGACTCGAAAACGTACGTTGG 58.612 47.619 32.31 23.29 38.47 3.77
224 225 4.020039 GAAGACTCGAAAACGTACGTTG 57.980 45.455 32.31 21.50 38.47 4.10
237 238 1.397343 TGGAACTCGATCGAAGACTCG 59.603 52.381 19.92 8.73 46.87 4.18
238 239 2.161808 TGTGGAACTCGATCGAAGACTC 59.838 50.000 19.92 12.13 37.14 3.36
239 240 2.160205 TGTGGAACTCGATCGAAGACT 58.840 47.619 19.92 3.45 37.14 3.24
240 241 2.631418 TGTGGAACTCGATCGAAGAC 57.369 50.000 19.92 12.12 37.14 3.01
241 242 2.492088 ACATGTGGAACTCGATCGAAGA 59.508 45.455 19.92 2.41 38.75 2.87
242 243 2.881074 ACATGTGGAACTCGATCGAAG 58.119 47.619 19.92 14.98 38.04 3.79
243 244 3.191791 TGTACATGTGGAACTCGATCGAA 59.808 43.478 19.92 2.21 38.04 3.71
244 245 2.750712 TGTACATGTGGAACTCGATCGA 59.249 45.455 18.32 18.32 38.04 3.59
245 246 2.852413 GTGTACATGTGGAACTCGATCG 59.148 50.000 9.36 9.36 38.04 3.69
246 247 3.859961 CAGTGTACATGTGGAACTCGATC 59.140 47.826 9.11 0.00 38.04 3.69
247 248 3.849911 CAGTGTACATGTGGAACTCGAT 58.150 45.455 9.11 0.00 38.04 3.59
248 249 2.609491 GCAGTGTACATGTGGAACTCGA 60.609 50.000 9.11 0.00 38.04 4.04
249 250 1.726791 GCAGTGTACATGTGGAACTCG 59.273 52.381 9.11 5.76 38.04 4.18
250 251 2.766313 TGCAGTGTACATGTGGAACTC 58.234 47.619 9.11 0.00 38.04 3.01
251 252 2.928801 TGCAGTGTACATGTGGAACT 57.071 45.000 9.11 6.35 38.04 3.01
252 253 3.825308 CAATGCAGTGTACATGTGGAAC 58.175 45.455 9.11 3.95 37.35 3.62
253 254 2.228582 GCAATGCAGTGTACATGTGGAA 59.771 45.455 16.47 0.00 0.00 3.53
271 272 1.606025 ATGCCACGTCCCATTGCAA 60.606 52.632 0.00 0.00 35.30 4.08
274 275 3.067480 GCCATGCCACGTCCCATTG 62.067 63.158 0.00 0.00 0.00 2.82
289 290 1.403116 CGGTATCAGTTGTACGTGCCA 60.403 52.381 0.00 0.00 0.00 4.92
291 292 1.916000 GTCGGTATCAGTTGTACGTGC 59.084 52.381 0.00 0.00 0.00 5.34
292 293 2.171567 CGTCGGTATCAGTTGTACGTG 58.828 52.381 0.00 0.00 0.00 4.49
293 294 1.466360 GCGTCGGTATCAGTTGTACGT 60.466 52.381 0.00 0.00 0.00 3.57
294 295 1.186030 GCGTCGGTATCAGTTGTACG 58.814 55.000 0.00 0.00 0.00 3.67
295 296 1.553308 GGCGTCGGTATCAGTTGTAC 58.447 55.000 0.00 0.00 0.00 2.90
297 298 1.153901 CGGCGTCGGTATCAGTTGT 60.154 57.895 0.00 0.00 0.00 3.32
298 299 1.138036 TCGGCGTCGGTATCAGTTG 59.862 57.895 10.62 0.00 36.95 3.16
299 300 1.138247 GTCGGCGTCGGTATCAGTT 59.862 57.895 10.62 0.00 36.95 3.16
302 303 1.864725 TTGTGTCGGCGTCGGTATCA 61.865 55.000 10.62 1.19 36.95 2.15
305 306 2.050168 GTTGTGTCGGCGTCGGTA 60.050 61.111 10.62 0.00 36.95 4.02
306 307 4.955774 GGTTGTGTCGGCGTCGGT 62.956 66.667 10.62 0.00 36.95 4.69
308 309 4.986587 TCGGTTGTGTCGGCGTCG 62.987 66.667 1.15 1.15 37.82 5.12
309 310 3.400590 GTCGGTTGTGTCGGCGTC 61.401 66.667 6.85 0.72 0.00 5.19
310 311 4.210093 TGTCGGTTGTGTCGGCGT 62.210 61.111 6.85 0.00 34.67 5.68
311 312 3.698463 GTGTCGGTTGTGTCGGCG 61.698 66.667 0.00 0.00 34.67 6.46
312 313 3.343421 GGTGTCGGTTGTGTCGGC 61.343 66.667 0.00 0.00 0.00 5.54
313 314 1.495584 CTTGGTGTCGGTTGTGTCGG 61.496 60.000 0.00 0.00 0.00 4.79
314 315 0.808453 ACTTGGTGTCGGTTGTGTCG 60.808 55.000 0.00 0.00 0.00 4.35
315 316 0.655733 CACTTGGTGTCGGTTGTGTC 59.344 55.000 0.00 0.00 0.00 3.67
316 317 1.373590 GCACTTGGTGTCGGTTGTGT 61.374 55.000 0.00 0.00 35.75 3.72
317 318 1.095228 AGCACTTGGTGTCGGTTGTG 61.095 55.000 0.00 0.00 35.75 3.33
318 319 1.095228 CAGCACTTGGTGTCGGTTGT 61.095 55.000 0.07 0.00 38.61 3.32
319 320 1.648720 CAGCACTTGGTGTCGGTTG 59.351 57.895 0.07 0.00 38.61 3.77
320 321 2.186826 GCAGCACTTGGTGTCGGTT 61.187 57.895 9.98 0.00 44.70 4.44
328 329 1.277739 CGCGATATGCAGCACTTGG 59.722 57.895 0.00 0.00 46.97 3.61
330 331 0.460109 TGACGCGATATGCAGCACTT 60.460 50.000 15.93 0.00 46.97 3.16
335 336 0.941463 GGAGGTGACGCGATATGCAG 60.941 60.000 15.93 0.00 46.97 4.41
337 338 0.941463 CAGGAGGTGACGCGATATGC 60.941 60.000 15.93 0.00 41.47 3.14
345 346 2.363680 AGATAAGATGCAGGAGGTGACG 59.636 50.000 0.00 0.00 0.00 4.35
346 347 4.414337 AAGATAAGATGCAGGAGGTGAC 57.586 45.455 0.00 0.00 0.00 3.67
349 350 4.103311 GGGTTAAGATAAGATGCAGGAGGT 59.897 45.833 0.00 0.00 0.00 3.85
350 351 4.646572 GGGTTAAGATAAGATGCAGGAGG 58.353 47.826 0.00 0.00 0.00 4.30
351 352 4.202264 ACGGGTTAAGATAAGATGCAGGAG 60.202 45.833 0.00 0.00 0.00 3.69
352 353 3.709653 ACGGGTTAAGATAAGATGCAGGA 59.290 43.478 0.00 0.00 0.00 3.86
353 354 3.809832 CACGGGTTAAGATAAGATGCAGG 59.190 47.826 0.00 0.00 0.00 4.85
354 355 3.248602 GCACGGGTTAAGATAAGATGCAG 59.751 47.826 0.00 0.00 0.00 4.41
361 362 2.568062 TGACCTGCACGGGTTAAGATAA 59.432 45.455 1.93 0.00 40.06 1.75
371 372 1.371337 CCATCACATGACCTGCACGG 61.371 60.000 0.00 1.16 39.35 4.94
372 373 0.391528 TCCATCACATGACCTGCACG 60.392 55.000 0.00 0.00 0.00 5.34
395 399 5.365403 TTGCTAACCAAAAACTACGGATG 57.635 39.130 0.00 0.00 0.00 3.51
398 402 5.048991 ACTGATTGCTAACCAAAAACTACGG 60.049 40.000 0.00 0.00 36.92 4.02
415 419 1.439201 CGTGTGCGTGCACTGATTG 60.439 57.895 23.86 0.00 46.30 2.67
416 420 2.938253 CGTGTGCGTGCACTGATT 59.062 55.556 23.86 0.00 46.30 2.57
417 421 3.716006 GCGTGTGCGTGCACTGAT 61.716 61.111 23.86 0.00 46.30 2.90
465 469 0.677731 TAAGCTCCATGCACAGTGGC 60.678 55.000 1.84 0.00 45.94 5.01
466 470 1.065926 TCTAAGCTCCATGCACAGTGG 60.066 52.381 1.84 0.00 45.94 4.00
503 507 1.552226 GCCATGCATGATTCACGTTG 58.448 50.000 28.31 8.75 0.00 4.10
507 511 1.102809 TCCGGCCATGCATGATTCAC 61.103 55.000 28.31 11.04 0.00 3.18
508 512 0.178984 ATCCGGCCATGCATGATTCA 60.179 50.000 28.31 7.93 0.00 2.57
513 517 1.165907 ACGTTATCCGGCCATGCATG 61.166 55.000 20.19 20.19 42.24 4.06
514 518 0.394938 TACGTTATCCGGCCATGCAT 59.605 50.000 2.24 0.00 42.24 3.96
515 519 0.249699 CTACGTTATCCGGCCATGCA 60.250 55.000 2.24 0.00 42.24 3.96
516 520 0.032952 TCTACGTTATCCGGCCATGC 59.967 55.000 2.24 0.00 42.24 4.06
524 528 8.543862 TTTTCTCTCCTTTTTCTACGTTATCC 57.456 34.615 0.00 0.00 0.00 2.59
531 535 9.278978 ACTCTGAATTTTCTCTCCTTTTTCTAC 57.721 33.333 0.00 0.00 0.00 2.59
536 540 6.846988 AGGACTCTGAATTTTCTCTCCTTTT 58.153 36.000 0.00 0.00 0.00 2.27
578 582 0.939419 TTCGGATGATCAATGCTGCG 59.061 50.000 0.00 0.00 0.00 5.18
582 586 1.595489 GCGTGTTCGGATGATCAATGC 60.595 52.381 0.00 0.00 37.56 3.56
586 590 3.758715 ATGCGTGTTCGGATGATCA 57.241 47.368 0.00 0.00 45.61 2.92
592 596 2.451990 CGATGCATGCGTGTTCGGA 61.452 57.895 19.18 0.00 42.23 4.55
622 626 2.509336 CCACAGGTCGACCGATGC 60.509 66.667 28.26 4.70 42.08 3.91
629 633 2.603473 CCACCCTCCACAGGTCGA 60.603 66.667 0.00 0.00 38.30 4.20
633 637 4.351054 GTGCCCACCCTCCACAGG 62.351 72.222 0.00 0.00 39.98 4.00
636 640 1.903404 CAAAGTGCCCACCCTCCAC 60.903 63.158 0.00 0.00 0.00 4.02
637 641 2.520458 CAAAGTGCCCACCCTCCA 59.480 61.111 0.00 0.00 0.00 3.86
641 645 1.685355 AAAGTGCAAAGTGCCCACCC 61.685 55.000 0.00 0.00 44.23 4.61
644 648 1.143620 GCAAAGTGCAAAGTGCCCA 59.856 52.632 5.63 0.00 44.23 5.36
673 677 4.897076 TCTTATTCGGGTATGGTTGAGCTA 59.103 41.667 0.00 0.00 0.00 3.32
674 678 3.709653 TCTTATTCGGGTATGGTTGAGCT 59.290 43.478 0.00 0.00 0.00 4.09
676 680 5.293569 GTGTTCTTATTCGGGTATGGTTGAG 59.706 44.000 0.00 0.00 0.00 3.02
677 681 5.180271 GTGTTCTTATTCGGGTATGGTTGA 58.820 41.667 0.00 0.00 0.00 3.18
678 682 4.938832 TGTGTTCTTATTCGGGTATGGTTG 59.061 41.667 0.00 0.00 0.00 3.77
679 683 5.168647 TGTGTTCTTATTCGGGTATGGTT 57.831 39.130 0.00 0.00 0.00 3.67
681 685 6.934645 ACATATGTGTTCTTATTCGGGTATGG 59.065 38.462 7.78 0.00 34.01 2.74
682 686 7.962964 ACATATGTGTTCTTATTCGGGTATG 57.037 36.000 7.78 0.00 34.01 2.39
683 687 9.485206 GTTACATATGTGTTCTTATTCGGGTAT 57.515 33.333 18.81 0.00 39.77 2.73
688 703 8.192068 TGTGGTTACATATGTGTTCTTATTCG 57.808 34.615 18.81 0.00 39.77 3.34
709 724 0.667184 GCATGCGTTTTTCCCTGTGG 60.667 55.000 0.00 0.00 0.00 4.17
716 731 6.695245 CATTATTTGGTAGCATGCGTTTTTC 58.305 36.000 13.01 1.01 0.00 2.29
735 750 1.855513 ATTTTGCATGCGCGCATTAT 58.144 40.000 41.73 25.24 42.62 1.28
738 753 0.797542 AAAATTTTGCATGCGCGCAT 59.202 40.000 39.13 39.13 42.62 4.73
755 770 7.772292 CACAGATGATTCTCCTCTAATCCAAAA 59.228 37.037 0.00 0.00 33.28 2.44
756 771 7.126268 TCACAGATGATTCTCCTCTAATCCAAA 59.874 37.037 0.00 0.00 33.28 3.28
787 802 8.976986 TTCTATGTTCTATCGATCACATCATG 57.023 34.615 16.88 11.04 32.15 3.07
803 819 8.538409 AACCAGAATTGCATTTTTCTATGTTC 57.462 30.769 6.72 0.00 31.15 3.18
804 820 7.329226 CGAACCAGAATTGCATTTTTCTATGTT 59.671 33.333 14.60 14.60 32.91 2.71
805 821 6.808212 CGAACCAGAATTGCATTTTTCTATGT 59.192 34.615 6.72 5.45 31.15 2.29
806 822 6.237648 GCGAACCAGAATTGCATTTTTCTATG 60.238 38.462 6.72 4.99 31.15 2.23
807 823 5.807011 GCGAACCAGAATTGCATTTTTCTAT 59.193 36.000 6.72 0.00 31.15 1.98
852 868 0.889994 TGCATGGCTGGTCAACATTC 59.110 50.000 0.00 0.00 0.00 2.67
930 946 1.137872 GAGGATCGATGCTGTGAAGGT 59.862 52.381 25.17 0.00 0.00 3.50
976 992 2.358125 CGGTGATGTGTTGGGCGA 60.358 61.111 0.00 0.00 0.00 5.54
978 994 3.747976 GCCGGTGATGTGTTGGGC 61.748 66.667 1.90 0.00 0.00 5.36
988 1010 3.770589 CCACATTTTGGCCGGTGA 58.229 55.556 1.90 0.00 39.07 4.02
1024 1052 4.527583 GGCGAGCAGGAGCAGGAG 62.528 72.222 0.00 0.00 45.49 3.69
1344 1372 0.826256 TCTGTGTACTGGCGACCTGT 60.826 55.000 11.74 11.74 39.06 4.00
1350 1378 0.670546 CCACCTTCTGTGTACTGGCG 60.671 60.000 0.00 0.00 43.85 5.69
1356 1384 1.071699 GAGTTGGCCACCTTCTGTGTA 59.928 52.381 3.88 0.00 43.85 2.90
1359 1387 1.071471 CGAGTTGGCCACCTTCTGT 59.929 57.895 3.88 0.00 0.00 3.41
1494 1522 1.812922 GTCGGAGAGGAGCGTCGTA 60.813 63.158 0.00 0.00 36.95 3.43
1734 1762 0.674895 ACAGCTCGAATGGCTTCACC 60.675 55.000 0.00 0.00 38.03 4.02
1739 1767 0.460987 GTAGCACAGCTCGAATGGCT 60.461 55.000 13.77 13.77 40.44 4.75
1743 1771 0.811915 AGTCGTAGCACAGCTCGAAT 59.188 50.000 12.53 10.04 40.44 3.34
2142 2174 8.918202 AAGTGTCACTTCAATTGGATTTAGTA 57.082 30.769 12.62 0.00 31.77 1.82
2153 2185 5.065988 AGCGTAAACAAAGTGTCACTTCAAT 59.934 36.000 18.42 8.25 37.47 2.57
2298 2330 3.425858 CGTCACGGTTCTTCTTCTTCTTC 59.574 47.826 0.00 0.00 0.00 2.87
2299 2331 3.381949 CGTCACGGTTCTTCTTCTTCTT 58.618 45.455 0.00 0.00 0.00 2.52
2300 2332 2.288273 CCGTCACGGTTCTTCTTCTTCT 60.288 50.000 8.54 0.00 42.73 2.85
2301 2333 2.059541 CCGTCACGGTTCTTCTTCTTC 58.940 52.381 8.54 0.00 42.73 2.87
2337 2369 3.994392 TCGAGGATGACAAGTTTAGTTGC 59.006 43.478 0.00 0.00 0.00 4.17
2736 2785 5.926214 TGCATTTCATGTTGACATTTTGG 57.074 34.783 0.00 0.00 33.61 3.28


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

AutoCloner maintained by Alex Coulton.