Multiple sequence alignment - TraesCS3D01G506900

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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 TraesCS3D01G506900 chr3D 100.000 4730 0 0 1 4730 593657335 593652606 0.000000e+00 8735.0
1 TraesCS3D01G506900 chr3D 81.863 2812 434 49 1028 3796 593687842 593690620 0.000000e+00 2298.0
2 TraesCS3D01G506900 chr3D 90.525 781 72 2 3020 3798 593666827 593667607 0.000000e+00 1031.0
3 TraesCS3D01G506900 chr3D 78.103 1708 306 39 1009 2679 593663119 593664795 0.000000e+00 1020.0
4 TraesCS3D01G506900 chr3D 81.346 1233 204 18 2522 3747 593707815 593709028 0.000000e+00 979.0
5 TraesCS3D01G506900 chr3D 76.620 1497 259 47 1006 2480 593706304 593707731 0.000000e+00 741.0
6 TraesCS3D01G506900 chr3D 75.637 1178 213 47 1097 2219 373603433 373602275 7.020000e-143 518.0
7 TraesCS3D01G506900 chr3D 84.000 325 31 11 3972 4278 501893648 501893327 4.630000e-75 292.0
8 TraesCS3D01G506900 chrUn 94.522 4107 197 7 632 4728 41924657 41928745 0.000000e+00 6312.0
9 TraesCS3D01G506900 chrUn 81.517 1239 199 18 2522 3749 41909187 41907968 0.000000e+00 992.0
10 TraesCS3D01G506900 chrUn 84.615 325 29 10 3972 4278 223717170 223716849 2.140000e-78 303.0
11 TraesCS3D01G506900 chrUn 84.615 325 29 10 3972 4278 257853951 257854272 2.140000e-78 303.0
12 TraesCS3D01G506900 chrUn 97.260 73 1 1 575 646 41924573 41924645 6.430000e-24 122.0
13 TraesCS3D01G506900 chr3A 89.598 2067 152 20 717 2756 724540947 724542977 0.000000e+00 2567.0
14 TraesCS3D01G506900 chr3A 90.207 1981 129 18 2791 4730 724542974 724544930 0.000000e+00 2523.0
15 TraesCS3D01G506900 chr3A 81.619 1964 303 37 2595 4520 724561251 724563194 0.000000e+00 1574.0
16 TraesCS3D01G506900 chr3A 90.090 888 55 12 3860 4730 724549959 724550830 0.000000e+00 1122.0
17 TraesCS3D01G506900 chr3A 81.818 1232 198 18 2522 3746 724697494 724698706 0.000000e+00 1011.0
18 TraesCS3D01G506900 chr3A 77.279 1404 262 30 1097 2470 724559687 724561063 0.000000e+00 773.0
19 TraesCS3D01G506900 chr3B 77.509 538 115 5 3208 3741 487441142 487440607 7.640000e-83 318.0
20 TraesCS3D01G506900 chr5B 84.615 325 29 10 3972 4278 127796650 127796971 2.140000e-78 303.0
21 TraesCS3D01G506900 chr5A 84.984 313 28 9 3983 4278 667731070 667731380 2.770000e-77 300.0
22 TraesCS3D01G506900 chr5A 86.538 104 10 4 4629 4730 34692259 34692158 1.390000e-20 111.0
23 TraesCS3D01G506900 chr4D 84.308 325 30 10 3972 4278 123729577 123729898 9.950000e-77 298.0
24 TraesCS3D01G506900 chr4D 85.714 98 12 2 4629 4725 9743042 9743138 8.370000e-18 102.0
25 TraesCS3D01G506900 chr7B 74.425 782 135 41 1399 2161 518463815 518464550 4.660000e-70 276.0
26 TraesCS3D01G506900 chr7B 76.066 305 63 6 1099 1398 518463485 518463784 2.950000e-32 150.0
27 TraesCS3D01G506900 chr7A 74.425 782 135 37 1399 2161 556557886 556558621 4.660000e-70 276.0
28 TraesCS3D01G506900 chr1B 97.059 34 0 1 3837 3870 547297701 547297669 6.610000e-04 56.5


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 TraesCS3D01G506900 chr3D 593652606 593657335 4729 True 8735.0 8735 100.0000 1 4730 1 chr3D.!!$R3 4729
1 TraesCS3D01G506900 chr3D 593687842 593690620 2778 False 2298.0 2298 81.8630 1028 3796 1 chr3D.!!$F1 2768
2 TraesCS3D01G506900 chr3D 593663119 593667607 4488 False 1025.5 1031 84.3140 1009 3798 2 chr3D.!!$F2 2789
3 TraesCS3D01G506900 chr3D 593706304 593709028 2724 False 860.0 979 78.9830 1006 3747 2 chr3D.!!$F3 2741
4 TraesCS3D01G506900 chr3D 373602275 373603433 1158 True 518.0 518 75.6370 1097 2219 1 chr3D.!!$R1 1122
5 TraesCS3D01G506900 chrUn 41924573 41928745 4172 False 3217.0 6312 95.8910 575 4728 2 chrUn.!!$F2 4153
6 TraesCS3D01G506900 chrUn 41907968 41909187 1219 True 992.0 992 81.5170 2522 3749 1 chrUn.!!$R1 1227
7 TraesCS3D01G506900 chr3A 724540947 724544930 3983 False 2545.0 2567 89.9025 717 4730 2 chr3A.!!$F3 4013
8 TraesCS3D01G506900 chr3A 724559687 724563194 3507 False 1173.5 1574 79.4490 1097 4520 2 chr3A.!!$F4 3423
9 TraesCS3D01G506900 chr3A 724549959 724550830 871 False 1122.0 1122 90.0900 3860 4730 1 chr3A.!!$F1 870
10 TraesCS3D01G506900 chr3A 724697494 724698706 1212 False 1011.0 1011 81.8180 2522 3746 1 chr3A.!!$F2 1224
11 TraesCS3D01G506900 chr3B 487440607 487441142 535 True 318.0 318 77.5090 3208 3741 1 chr3B.!!$R1 533
12 TraesCS3D01G506900 chr7B 518463485 518464550 1065 False 213.0 276 75.2455 1099 2161 2 chr7B.!!$F1 1062
13 TraesCS3D01G506900 chr7A 556557886 556558621 735 False 276.0 276 74.4250 1399 2161 1 chr7A.!!$F1 762

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
80 81 0.036306 CGTTGTTTCCTGGGCTACCT 59.964 55.0 0.00 0.00 37.76 3.08 F
984 1012 0.329596 ACTCCCTCGGGTAAGTACGT 59.670 55.0 1.18 0.00 36.47 3.57 F
1962 2100 0.386478 GACGACGCTTCTTGGTACGT 60.386 55.0 0.00 0.00 42.27 3.57 F
3261 5282 0.249073 CATTGTACGCTCTCGGAGGG 60.249 60.0 4.96 2.09 46.05 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1665 2.110006 GCGAGGCTGGGAGGATTC 59.890 66.667 0.00 0.0 0.00 2.52 R
2709 2940 1.042229 ACTGCACCGTTACCAGTGTA 58.958 50.000 2.83 0.0 38.32 2.90 R
3375 5429 0.695462 AGCCATCCAGTATCAGCCCA 60.695 55.000 0.00 0.0 0.00 5.36 R
4259 6363 4.618227 GCTGGCTTCATATTTTTCGTGGTT 60.618 41.667 0.00 0.0 0.00 3.67 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
27 28 3.597550 GCCTAGAGAGGGCGAATTC 57.402 57.895 0.00 0.00 43.97 2.17
28 29 1.044611 GCCTAGAGAGGGCGAATTCT 58.955 55.000 3.52 0.00 43.97 2.40
29 30 1.000394 GCCTAGAGAGGGCGAATTCTC 60.000 57.143 3.52 0.00 43.97 2.87
30 31 2.311463 CCTAGAGAGGGCGAATTCTCA 58.689 52.381 3.52 0.58 41.78 3.27
31 32 2.695666 CCTAGAGAGGGCGAATTCTCAA 59.304 50.000 3.52 0.00 41.78 3.02
32 33 2.977772 AGAGAGGGCGAATTCTCAAG 57.022 50.000 3.52 0.00 41.78 3.02
33 34 2.461695 AGAGAGGGCGAATTCTCAAGA 58.538 47.619 3.52 0.00 41.78 3.02
34 35 2.834549 AGAGAGGGCGAATTCTCAAGAA 59.165 45.455 3.52 0.00 41.78 2.52
35 36 3.261897 AGAGAGGGCGAATTCTCAAGAAA 59.738 43.478 3.52 0.00 41.78 2.52
36 37 4.003648 GAGAGGGCGAATTCTCAAGAAAA 58.996 43.478 3.52 0.00 39.65 2.29
37 38 4.398319 AGAGGGCGAATTCTCAAGAAAAA 58.602 39.130 3.52 0.00 37.61 1.94
57 58 4.947077 AAACAAAATTTGCTCGCTAACG 57.053 36.364 5.52 0.00 42.01 3.18
58 59 3.619233 ACAAAATTTGCTCGCTAACGT 57.381 38.095 5.52 0.00 41.18 3.99
59 60 3.959943 ACAAAATTTGCTCGCTAACGTT 58.040 36.364 5.88 5.88 41.18 3.99
60 61 5.098218 ACAAAATTTGCTCGCTAACGTTA 57.902 34.783 7.94 7.94 41.18 3.18
61 62 4.907582 ACAAAATTTGCTCGCTAACGTTAC 59.092 37.500 3.29 1.11 41.18 2.50
62 63 3.363788 AATTTGCTCGCTAACGTTACG 57.636 42.857 18.15 18.15 41.18 3.18
63 64 1.769733 TTTGCTCGCTAACGTTACGT 58.230 45.000 21.21 3.95 43.97 3.57
74 75 1.585297 ACGTTACGTTGTTTCCTGGG 58.415 50.000 3.95 0.00 36.35 4.45
75 76 0.236449 CGTTACGTTGTTTCCTGGGC 59.764 55.000 0.00 0.00 0.00 5.36
76 77 1.601166 GTTACGTTGTTTCCTGGGCT 58.399 50.000 0.00 0.00 0.00 5.19
77 78 2.769893 GTTACGTTGTTTCCTGGGCTA 58.230 47.619 0.00 0.00 0.00 3.93
78 79 2.460757 TACGTTGTTTCCTGGGCTAC 57.539 50.000 0.00 0.00 0.00 3.58
79 80 0.250597 ACGTTGTTTCCTGGGCTACC 60.251 55.000 0.00 0.00 37.24 3.18
80 81 0.036306 CGTTGTTTCCTGGGCTACCT 59.964 55.000 0.00 0.00 37.76 3.08
81 82 1.822506 GTTGTTTCCTGGGCTACCTC 58.177 55.000 0.00 0.00 37.76 3.85
82 83 1.073284 GTTGTTTCCTGGGCTACCTCA 59.927 52.381 0.00 0.00 37.76 3.86
83 84 1.668826 TGTTTCCTGGGCTACCTCAT 58.331 50.000 0.00 0.00 37.76 2.90
84 85 1.992557 TGTTTCCTGGGCTACCTCATT 59.007 47.619 0.00 0.00 37.76 2.57
85 86 2.290896 TGTTTCCTGGGCTACCTCATTG 60.291 50.000 0.00 0.00 37.76 2.82
86 87 0.918983 TTCCTGGGCTACCTCATTGG 59.081 55.000 0.00 0.00 42.93 3.16
87 88 1.152881 CCTGGGCTACCTCATTGGC 60.153 63.158 0.00 0.00 40.22 4.52
88 89 1.639635 CCTGGGCTACCTCATTGGCT 61.640 60.000 0.00 0.00 40.22 4.75
89 90 1.131638 CTGGGCTACCTCATTGGCTA 58.868 55.000 0.00 0.00 40.22 3.93
90 91 1.701847 CTGGGCTACCTCATTGGCTAT 59.298 52.381 0.00 0.00 40.22 2.97
91 92 2.906389 CTGGGCTACCTCATTGGCTATA 59.094 50.000 0.00 0.00 40.22 1.31
92 93 3.322862 TGGGCTACCTCATTGGCTATAA 58.677 45.455 0.00 0.00 40.22 0.98
93 94 3.916349 TGGGCTACCTCATTGGCTATAAT 59.084 43.478 0.00 0.00 40.22 1.28
94 95 4.263462 TGGGCTACCTCATTGGCTATAATG 60.263 45.833 0.00 0.00 40.22 1.90
95 96 4.263506 GGGCTACCTCATTGGCTATAATGT 60.264 45.833 0.00 0.00 38.77 2.71
96 97 4.938226 GGCTACCTCATTGGCTATAATGTC 59.062 45.833 0.00 0.00 38.77 3.06
97 98 5.513094 GGCTACCTCATTGGCTATAATGTCA 60.513 44.000 0.00 0.00 38.77 3.58
98 99 5.997746 GCTACCTCATTGGCTATAATGTCAA 59.002 40.000 0.00 0.00 38.77 3.18
99 100 6.073003 GCTACCTCATTGGCTATAATGTCAAC 60.073 42.308 0.00 0.00 38.77 3.18
100 101 5.754782 ACCTCATTGGCTATAATGTCAACA 58.245 37.500 0.00 0.00 38.77 3.33
101 102 5.590259 ACCTCATTGGCTATAATGTCAACAC 59.410 40.000 0.00 0.00 38.77 3.32
102 103 5.589855 CCTCATTGGCTATAATGTCAACACA 59.410 40.000 0.00 0.00 38.77 3.72
103 104 6.435430 TCATTGGCTATAATGTCAACACAC 57.565 37.500 0.00 0.00 38.77 3.82
104 105 5.942826 TCATTGGCTATAATGTCAACACACA 59.057 36.000 0.00 0.00 38.77 3.72
105 106 6.602803 TCATTGGCTATAATGTCAACACACAT 59.397 34.615 0.00 0.00 38.74 3.21
106 107 6.832520 TTGGCTATAATGTCAACACACATT 57.167 33.333 4.37 4.37 46.54 2.71
107 108 6.193514 TGGCTATAATGTCAACACACATTG 57.806 37.500 8.72 0.00 44.92 2.82
108 109 5.709631 TGGCTATAATGTCAACACACATTGT 59.290 36.000 8.72 5.22 44.92 2.71
121 122 3.309410 CACACATTGTGGTTTTTGGAAGC 59.691 43.478 20.33 0.00 44.27 3.86
122 123 3.197549 ACACATTGTGGTTTTTGGAAGCT 59.802 39.130 20.33 0.00 37.94 3.74
123 124 4.404073 ACACATTGTGGTTTTTGGAAGCTA 59.596 37.500 20.33 0.00 37.94 3.32
124 125 4.744631 CACATTGTGGTTTTTGGAAGCTAC 59.255 41.667 9.00 0.00 0.00 3.58
125 126 4.202212 ACATTGTGGTTTTTGGAAGCTACC 60.202 41.667 0.00 0.00 28.57 3.18
126 127 3.019799 TGTGGTTTTTGGAAGCTACCA 57.980 42.857 0.00 0.00 36.58 3.25
127 128 2.955660 TGTGGTTTTTGGAAGCTACCAG 59.044 45.455 2.45 0.00 39.40 4.00
128 129 3.219281 GTGGTTTTTGGAAGCTACCAGA 58.781 45.455 2.45 0.00 39.40 3.86
129 130 3.634910 GTGGTTTTTGGAAGCTACCAGAA 59.365 43.478 2.45 0.00 39.40 3.02
130 131 3.634910 TGGTTTTTGGAAGCTACCAGAAC 59.365 43.478 0.00 0.00 41.19 3.01
131 132 3.889538 GGTTTTTGGAAGCTACCAGAACT 59.110 43.478 0.00 0.00 41.19 3.01
132 133 4.341235 GGTTTTTGGAAGCTACCAGAACTT 59.659 41.667 0.00 0.00 41.19 2.66
133 134 5.163447 GGTTTTTGGAAGCTACCAGAACTTT 60.163 40.000 0.00 0.00 41.19 2.66
134 135 6.338146 GTTTTTGGAAGCTACCAGAACTTTT 58.662 36.000 0.00 0.00 41.19 2.27
135 136 5.767816 TTTGGAAGCTACCAGAACTTTTC 57.232 39.130 0.00 0.00 41.19 2.29
136 137 3.399330 TGGAAGCTACCAGAACTTTTCG 58.601 45.455 0.00 0.00 34.77 3.46
137 138 3.181458 TGGAAGCTACCAGAACTTTTCGT 60.181 43.478 0.00 0.00 34.77 3.85
138 139 3.432592 GGAAGCTACCAGAACTTTTCGTC 59.567 47.826 0.00 0.00 34.02 4.20
139 140 3.041508 AGCTACCAGAACTTTTCGTCC 57.958 47.619 0.00 0.00 34.02 4.79
140 141 2.367567 AGCTACCAGAACTTTTCGTCCA 59.632 45.455 0.00 0.00 34.02 4.02
141 142 2.737252 GCTACCAGAACTTTTCGTCCAG 59.263 50.000 0.00 0.00 34.02 3.86
142 143 3.802675 GCTACCAGAACTTTTCGTCCAGT 60.803 47.826 0.00 0.00 34.02 4.00
143 144 3.277142 ACCAGAACTTTTCGTCCAGTT 57.723 42.857 0.00 0.00 35.88 3.16
144 145 3.617284 ACCAGAACTTTTCGTCCAGTTT 58.383 40.909 0.00 0.00 33.22 2.66
145 146 4.014406 ACCAGAACTTTTCGTCCAGTTTT 58.986 39.130 0.00 0.00 33.22 2.43
146 147 4.142469 ACCAGAACTTTTCGTCCAGTTTTG 60.142 41.667 6.81 6.81 35.74 2.44
147 148 4.351192 CAGAACTTTTCGTCCAGTTTTGG 58.649 43.478 0.00 0.00 39.27 3.28
148 149 3.380320 AGAACTTTTCGTCCAGTTTTGGG 59.620 43.478 0.00 0.00 38.78 4.12
149 150 3.007473 ACTTTTCGTCCAGTTTTGGGA 57.993 42.857 0.00 0.00 45.10 4.37
150 151 3.358118 ACTTTTCGTCCAGTTTTGGGAA 58.642 40.909 0.00 0.00 45.10 3.97
151 152 3.958147 ACTTTTCGTCCAGTTTTGGGAAT 59.042 39.130 0.00 0.00 45.10 3.01
152 153 4.202111 ACTTTTCGTCCAGTTTTGGGAATG 60.202 41.667 0.00 0.00 45.10 2.67
153 154 2.649531 TCGTCCAGTTTTGGGAATGT 57.350 45.000 0.00 0.00 45.10 2.71
154 155 2.500229 TCGTCCAGTTTTGGGAATGTC 58.500 47.619 0.00 0.00 45.10 3.06
155 156 1.539827 CGTCCAGTTTTGGGAATGTCC 59.460 52.381 0.00 0.00 45.10 4.02
156 157 2.814097 CGTCCAGTTTTGGGAATGTCCT 60.814 50.000 0.00 0.00 45.10 3.85
157 158 3.558321 CGTCCAGTTTTGGGAATGTCCTA 60.558 47.826 0.00 0.00 45.10 2.94
158 159 4.010349 GTCCAGTTTTGGGAATGTCCTAG 58.990 47.826 0.00 0.00 45.10 3.02
159 160 3.913799 TCCAGTTTTGGGAATGTCCTAGA 59.086 43.478 0.00 0.00 45.10 2.43
160 161 4.352595 TCCAGTTTTGGGAATGTCCTAGAA 59.647 41.667 0.00 0.00 45.10 2.10
161 162 4.702131 CCAGTTTTGGGAATGTCCTAGAAG 59.298 45.833 0.00 0.00 41.05 2.85
162 163 5.316987 CAGTTTTGGGAATGTCCTAGAAGT 58.683 41.667 0.00 0.00 36.57 3.01
163 164 5.770162 CAGTTTTGGGAATGTCCTAGAAGTT 59.230 40.000 0.00 0.00 36.57 2.66
164 165 6.265422 CAGTTTTGGGAATGTCCTAGAAGTTT 59.735 38.462 0.00 0.00 36.57 2.66
165 166 6.490381 AGTTTTGGGAATGTCCTAGAAGTTTC 59.510 38.462 0.00 0.00 36.57 2.78
166 167 5.843019 TTGGGAATGTCCTAGAAGTTTCT 57.157 39.130 0.00 0.00 36.57 2.52
167 168 5.843019 TGGGAATGTCCTAGAAGTTTCTT 57.157 39.130 0.00 0.00 36.57 2.52
168 169 6.200878 TGGGAATGTCCTAGAAGTTTCTTT 57.799 37.500 0.00 0.00 36.57 2.52
169 170 6.610830 TGGGAATGTCCTAGAAGTTTCTTTT 58.389 36.000 0.00 0.00 36.57 2.27
170 171 7.066781 TGGGAATGTCCTAGAAGTTTCTTTTT 58.933 34.615 0.00 0.00 36.57 1.94
192 193 7.832503 TTTTCTTTCTTCTTTGGCTTTTCTG 57.167 32.000 0.00 0.00 0.00 3.02
193 194 5.520376 TCTTTCTTCTTTGGCTTTTCTGG 57.480 39.130 0.00 0.00 0.00 3.86
194 195 4.956075 TCTTTCTTCTTTGGCTTTTCTGGT 59.044 37.500 0.00 0.00 0.00 4.00
195 196 5.422012 TCTTTCTTCTTTGGCTTTTCTGGTT 59.578 36.000 0.00 0.00 0.00 3.67
196 197 5.675684 TTCTTCTTTGGCTTTTCTGGTTT 57.324 34.783 0.00 0.00 0.00 3.27
197 198 5.675684 TCTTCTTTGGCTTTTCTGGTTTT 57.324 34.783 0.00 0.00 0.00 2.43
198 199 6.048732 TCTTCTTTGGCTTTTCTGGTTTTT 57.951 33.333 0.00 0.00 0.00 1.94
199 200 6.106003 TCTTCTTTGGCTTTTCTGGTTTTTC 58.894 36.000 0.00 0.00 0.00 2.29
200 201 5.413309 TCTTTGGCTTTTCTGGTTTTTCA 57.587 34.783 0.00 0.00 0.00 2.69
201 202 5.988287 TCTTTGGCTTTTCTGGTTTTTCAT 58.012 33.333 0.00 0.00 0.00 2.57
202 203 6.413892 TCTTTGGCTTTTCTGGTTTTTCATT 58.586 32.000 0.00 0.00 0.00 2.57
203 204 6.883756 TCTTTGGCTTTTCTGGTTTTTCATTT 59.116 30.769 0.00 0.00 0.00 2.32
204 205 7.392953 TCTTTGGCTTTTCTGGTTTTTCATTTT 59.607 29.630 0.00 0.00 0.00 1.82
205 206 6.676237 TGGCTTTTCTGGTTTTTCATTTTC 57.324 33.333 0.00 0.00 0.00 2.29
206 207 6.413892 TGGCTTTTCTGGTTTTTCATTTTCT 58.586 32.000 0.00 0.00 0.00 2.52
207 208 6.315891 TGGCTTTTCTGGTTTTTCATTTTCTG 59.684 34.615 0.00 0.00 0.00 3.02
208 209 6.316140 GGCTTTTCTGGTTTTTCATTTTCTGT 59.684 34.615 0.00 0.00 0.00 3.41
209 210 7.148255 GGCTTTTCTGGTTTTTCATTTTCTGTT 60.148 33.333 0.00 0.00 0.00 3.16
210 211 8.236586 GCTTTTCTGGTTTTTCATTTTCTGTTT 58.763 29.630 0.00 0.00 0.00 2.83
213 214 9.500785 TTTCTGGTTTTTCATTTTCTGTTTTCT 57.499 25.926 0.00 0.00 0.00 2.52
214 215 9.500785 TTCTGGTTTTTCATTTTCTGTTTTCTT 57.499 25.926 0.00 0.00 0.00 2.52
215 216 9.500785 TCTGGTTTTTCATTTTCTGTTTTCTTT 57.499 25.926 0.00 0.00 0.00 2.52
216 217 9.759259 CTGGTTTTTCATTTTCTGTTTTCTTTC 57.241 29.630 0.00 0.00 0.00 2.62
217 218 8.726068 TGGTTTTTCATTTTCTGTTTTCTTTCC 58.274 29.630 0.00 0.00 0.00 3.13
218 219 8.946085 GGTTTTTCATTTTCTGTTTTCTTTCCT 58.054 29.630 0.00 0.00 0.00 3.36
221 222 9.942850 TTTTCATTTTCTGTTTTCTTTCCTTCT 57.057 25.926 0.00 0.00 0.00 2.85
222 223 9.586435 TTTCATTTTCTGTTTTCTTTCCTTCTC 57.414 29.630 0.00 0.00 0.00 2.87
223 224 8.292444 TCATTTTCTGTTTTCTTTCCTTCTCA 57.708 30.769 0.00 0.00 0.00 3.27
224 225 8.917088 TCATTTTCTGTTTTCTTTCCTTCTCAT 58.083 29.630 0.00 0.00 0.00 2.90
225 226 9.189723 CATTTTCTGTTTTCTTTCCTTCTCATC 57.810 33.333 0.00 0.00 0.00 2.92
226 227 8.525290 TTTTCTGTTTTCTTTCCTTCTCATCT 57.475 30.769 0.00 0.00 0.00 2.90
227 228 7.502120 TTCTGTTTTCTTTCCTTCTCATCTG 57.498 36.000 0.00 0.00 0.00 2.90
228 229 6.595682 TCTGTTTTCTTTCCTTCTCATCTGT 58.404 36.000 0.00 0.00 0.00 3.41
229 230 7.735917 TCTGTTTTCTTTCCTTCTCATCTGTA 58.264 34.615 0.00 0.00 0.00 2.74
230 231 8.378565 TCTGTTTTCTTTCCTTCTCATCTGTAT 58.621 33.333 0.00 0.00 0.00 2.29
231 232 8.553459 TGTTTTCTTTCCTTCTCATCTGTATC 57.447 34.615 0.00 0.00 0.00 2.24
232 233 7.607991 TGTTTTCTTTCCTTCTCATCTGTATCC 59.392 37.037 0.00 0.00 0.00 2.59
233 234 5.878406 TCTTTCCTTCTCATCTGTATCCC 57.122 43.478 0.00 0.00 0.00 3.85
234 235 5.533112 TCTTTCCTTCTCATCTGTATCCCT 58.467 41.667 0.00 0.00 0.00 4.20
235 236 5.966935 TCTTTCCTTCTCATCTGTATCCCTT 59.033 40.000 0.00 0.00 0.00 3.95
236 237 6.445139 TCTTTCCTTCTCATCTGTATCCCTTT 59.555 38.462 0.00 0.00 0.00 3.11
237 238 5.878406 TCCTTCTCATCTGTATCCCTTTC 57.122 43.478 0.00 0.00 0.00 2.62
238 239 5.533112 TCCTTCTCATCTGTATCCCTTTCT 58.467 41.667 0.00 0.00 0.00 2.52
239 240 5.966935 TCCTTCTCATCTGTATCCCTTTCTT 59.033 40.000 0.00 0.00 0.00 2.52
240 241 6.098982 TCCTTCTCATCTGTATCCCTTTCTTC 59.901 42.308 0.00 0.00 0.00 2.87
241 242 6.126940 CCTTCTCATCTGTATCCCTTTCTTCA 60.127 42.308 0.00 0.00 0.00 3.02
242 243 7.419981 CCTTCTCATCTGTATCCCTTTCTTCAT 60.420 40.741 0.00 0.00 0.00 2.57
243 244 7.443302 TCTCATCTGTATCCCTTTCTTCATT 57.557 36.000 0.00 0.00 0.00 2.57
244 245 7.865820 TCTCATCTGTATCCCTTTCTTCATTT 58.134 34.615 0.00 0.00 0.00 2.32
245 246 8.331740 TCTCATCTGTATCCCTTTCTTCATTTT 58.668 33.333 0.00 0.00 0.00 1.82
246 247 8.511604 TCATCTGTATCCCTTTCTTCATTTTC 57.488 34.615 0.00 0.00 0.00 2.29
247 248 8.331740 TCATCTGTATCCCTTTCTTCATTTTCT 58.668 33.333 0.00 0.00 0.00 2.52
248 249 8.964772 CATCTGTATCCCTTTCTTCATTTTCTT 58.035 33.333 0.00 0.00 0.00 2.52
316 317 8.789881 ATTTGTGAACATTTTTGCAATTCATG 57.210 26.923 13.82 11.88 32.30 3.07
317 318 7.549615 TTGTGAACATTTTTGCAATTCATGA 57.450 28.000 13.82 0.00 32.30 3.07
318 319 7.549615 TGTGAACATTTTTGCAATTCATGAA 57.450 28.000 11.26 11.26 32.30 2.57
319 320 8.155821 TGTGAACATTTTTGCAATTCATGAAT 57.844 26.923 15.36 15.36 32.30 2.57
320 321 9.269453 TGTGAACATTTTTGCAATTCATGAATA 57.731 25.926 21.00 3.28 32.30 1.75
338 339 9.993454 TCATGAATATTTTTCAAATCCACAACA 57.007 25.926 0.00 0.00 31.55 3.33
352 353 8.945930 CAAATCCACAACAATTTTTCAAATTCG 58.054 29.630 0.00 0.00 0.00 3.34
353 354 7.784633 ATCCACAACAATTTTTCAAATTCGT 57.215 28.000 0.00 0.00 0.00 3.85
354 355 6.998338 TCCACAACAATTTTTCAAATTCGTG 58.002 32.000 7.84 7.84 0.00 4.35
355 356 6.813649 TCCACAACAATTTTTCAAATTCGTGA 59.186 30.769 12.78 0.00 0.00 4.35
356 357 7.493971 TCCACAACAATTTTTCAAATTCGTGAT 59.506 29.630 12.78 0.00 0.00 3.06
357 358 8.121708 CCACAACAATTTTTCAAATTCGTGATT 58.878 29.630 12.78 0.00 0.00 2.57
374 375 7.646446 TCGTGATTAATATTTACATCCGTGG 57.354 36.000 0.00 0.00 0.00 4.94
375 376 7.435305 TCGTGATTAATATTTACATCCGTGGA 58.565 34.615 0.00 0.00 0.00 4.02
376 377 7.383029 TCGTGATTAATATTTACATCCGTGGAC 59.617 37.037 0.00 0.00 0.00 4.02
377 378 7.170151 CGTGATTAATATTTACATCCGTGGACA 59.830 37.037 0.00 0.00 0.00 4.02
378 379 8.999431 GTGATTAATATTTACATCCGTGGACAT 58.001 33.333 0.00 0.00 0.00 3.06
476 477 9.574458 TTCACTAATTTTTCAAATTCGTGAACA 57.426 25.926 24.17 13.08 42.32 3.18
477 478 9.574458 TCACTAATTTTTCAAATTCGTGAACAA 57.426 25.926 19.26 5.04 38.52 2.83
497 498 9.681692 TGAACAAAAATTCACAATGATCTACTG 57.318 29.630 0.00 0.00 33.62 2.74
498 499 9.683069 GAACAAAAATTCACAATGATCTACTGT 57.317 29.630 0.00 0.00 0.00 3.55
567 568 6.187727 TGGGACAATCTAAGAACTTTCAGT 57.812 37.500 0.00 0.00 31.92 3.41
568 569 7.311092 TGGGACAATCTAAGAACTTTCAGTA 57.689 36.000 0.00 0.00 31.92 2.74
569 570 7.159372 TGGGACAATCTAAGAACTTTCAGTAC 58.841 38.462 0.00 0.00 31.92 2.73
570 571 7.016268 TGGGACAATCTAAGAACTTTCAGTACT 59.984 37.037 0.00 0.00 31.92 2.73
571 572 7.878644 GGGACAATCTAAGAACTTTCAGTACTT 59.121 37.037 0.00 0.00 0.00 2.24
572 573 9.274206 GGACAATCTAAGAACTTTCAGTACTTT 57.726 33.333 0.00 0.00 0.00 2.66
574 575 9.832445 ACAATCTAAGAACTTTCAGTACTTTGA 57.168 29.630 0.00 0.00 0.00 2.69
658 685 6.175471 AGGTTACCCCGTTAATTAACTTGAG 58.825 40.000 22.57 12.68 38.74 3.02
674 701 4.978099 ACTTGAGTATGATTATGGGCAGG 58.022 43.478 0.00 0.00 0.00 4.85
681 708 0.603975 GATTATGGGCAGGGCTCGTC 60.604 60.000 0.00 0.00 28.12 4.20
701 728 0.601057 AATGAAAACGAAAGGCCGGG 59.399 50.000 2.18 0.00 0.00 5.73
703 730 0.752376 TGAAAACGAAAGGCCGGGTT 60.752 50.000 2.18 0.00 0.00 4.11
750 777 5.009610 TGAAAAACCAGGACAAGATAAGTGC 59.990 40.000 0.00 0.00 0.00 4.40
764 791 3.747976 GTGCGTGGACCCATTGGC 61.748 66.667 0.00 0.00 33.59 4.52
767 794 2.044053 CGTGGACCCATTGGCCAT 60.044 61.111 6.09 0.00 39.17 4.40
768 795 1.682005 CGTGGACCCATTGGCCATT 60.682 57.895 6.09 0.00 39.17 3.16
790 817 5.692115 TCCATTATGCTTCTCACCACTAA 57.308 39.130 0.00 0.00 0.00 2.24
830 857 6.631766 CGATATTTCCTCCCAACTTTCCACTA 60.632 42.308 0.00 0.00 0.00 2.74
832 859 3.269592 TCCTCCCAACTTTCCACTAGA 57.730 47.619 0.00 0.00 0.00 2.43
894 921 2.278854 ACATGCAAGTTGCCAACAAAC 58.721 42.857 24.59 0.00 44.23 2.93
900 927 3.583806 CAAGTTGCCAACAAACAAGTCA 58.416 40.909 10.69 0.00 37.58 3.41
978 1006 3.118531 AGTCTAGTACTCCCTCGGGTAA 58.881 50.000 0.00 0.00 30.33 2.85
982 1010 3.289407 AGTACTCCCTCGGGTAAGTAC 57.711 52.381 19.13 19.13 41.80 2.73
984 1012 0.329596 ACTCCCTCGGGTAAGTACGT 59.670 55.000 1.18 0.00 36.47 3.57
986 1014 2.216898 CTCCCTCGGGTAAGTACGTAG 58.783 57.143 0.00 0.00 36.47 3.51
987 1015 1.559682 TCCCTCGGGTAAGTACGTAGT 59.440 52.381 0.00 0.00 39.89 2.73
1160 1194 1.482593 CACCGCTTCCTCTTACTCCAT 59.517 52.381 0.00 0.00 0.00 3.41
1221 1257 3.119096 GCTGACGACGCCCTTTCC 61.119 66.667 0.00 0.00 0.00 3.13
1323 1377 0.884704 ACAATGACCGCTCGTTTGCT 60.885 50.000 0.00 0.00 0.00 3.91
1383 1437 3.625897 CTCCACCTCACCGCCACA 61.626 66.667 0.00 0.00 0.00 4.17
1493 1595 2.068821 AGCTCTGCATGGTCGGGAT 61.069 57.895 0.00 0.00 0.00 3.85
1639 1741 1.741770 CTTGGGACTTTCCGCCTCG 60.742 63.158 0.00 0.00 37.43 4.63
1680 1782 0.807496 ACTACAAGTACGGCTCCGAC 59.193 55.000 15.95 8.76 42.83 4.79
1855 1987 3.848301 AACCAGATGCGCTGCACCA 62.848 57.895 9.73 0.00 43.04 4.17
1962 2100 0.386478 GACGACGCTTCTTGGTACGT 60.386 55.000 0.00 0.00 42.27 3.57
2113 2263 4.344865 GCTTCTGGTTCCCGGCCA 62.345 66.667 2.24 0.00 34.42 5.36
2232 2388 1.048601 TGGACGACCAAAGAAGCTCT 58.951 50.000 3.49 0.00 43.91 4.09
2238 2394 3.008049 ACGACCAAAGAAGCTCTACCAAT 59.992 43.478 0.00 0.00 0.00 3.16
2312 2468 2.240667 AGCACTACCTGGAAATCAGCAT 59.759 45.455 0.00 0.00 42.05 3.79
2341 2497 0.391263 GAAGATCACGGGGTCACACC 60.391 60.000 0.00 0.00 37.60 4.16
2383 2539 2.351726 ACTGTCAGTGACTTTGCGTTTC 59.648 45.455 23.29 0.00 33.15 2.78
2439 2595 1.296392 CCCAGTCACAATCGGCTCA 59.704 57.895 0.00 0.00 0.00 4.26
2592 2805 3.181463 GGGTGCGTCCTACCAATATGTTA 60.181 47.826 0.00 0.00 40.03 2.41
2709 2940 4.148825 GGCTCGACGGACTGCCAT 62.149 66.667 6.26 0.00 44.34 4.40
2781 4802 1.614241 GCACGGGGGTGATCAGTAGT 61.614 60.000 0.00 0.00 0.00 2.73
2838 4859 2.100989 GTCGACTTCACCTCCTATGGT 58.899 52.381 8.70 0.00 41.77 3.55
2889 4910 1.063642 TCGAGGATGGACATGGAGAGT 60.064 52.381 0.00 0.00 0.00 3.24
2964 4985 1.142870 CTCCACACAAAGAGGAACCCA 59.857 52.381 0.00 0.00 36.50 4.51
3042 5063 2.705821 CCCTCTCGCGCTCAACTCT 61.706 63.158 5.56 0.00 0.00 3.24
3166 5187 2.341101 GCCTTCATGCTGCAGCTGT 61.341 57.895 36.61 23.56 42.66 4.40
3261 5282 0.249073 CATTGTACGCTCTCGGAGGG 60.249 60.000 4.96 2.09 46.05 4.30
3329 5383 1.009829 GACCCGTCAATGATCAGCAC 58.990 55.000 0.09 0.00 0.00 4.40
3375 5429 1.177256 AGGACCTTGTGTCGTACGCT 61.177 55.000 11.24 0.00 45.46 5.07
3593 5649 3.822607 GTGACCTCTTCAGCATCGT 57.177 52.632 0.00 0.00 33.71 3.73
3772 5830 4.202243 CCTTCAAGGAAACAAAGGATGCAA 60.202 41.667 0.00 0.00 37.67 4.08
4259 6363 6.272822 ACTGCTATAACTCGCATGATATGA 57.727 37.500 0.00 0.00 35.32 2.15
4298 6402 2.048877 GCTGGCCATGTTGTGTGC 60.049 61.111 5.51 0.00 0.00 4.57
4361 6471 6.479660 GTGAAATGGATTGTTTTCATGTGTGT 59.520 34.615 1.89 0.00 42.12 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.311463 TGAGAATTCGCCCTCTCTAGG 58.689 52.381 6.73 0.00 43.25 3.02
11 12 3.634448 TCTTGAGAATTCGCCCTCTCTAG 59.366 47.826 6.73 10.42 40.64 2.43
12 13 3.632333 TCTTGAGAATTCGCCCTCTCTA 58.368 45.455 6.73 0.00 39.11 2.43
13 14 2.461695 TCTTGAGAATTCGCCCTCTCT 58.538 47.619 6.73 0.00 39.11 3.10
14 15 2.969628 TCTTGAGAATTCGCCCTCTC 57.030 50.000 6.73 0.00 38.87 3.20
15 16 3.703001 TTTCTTGAGAATTCGCCCTCT 57.297 42.857 6.73 0.00 33.54 3.69
16 17 4.766404 TTTTTCTTGAGAATTCGCCCTC 57.234 40.909 6.73 0.00 33.54 4.30
34 35 5.289917 ACGTTAGCGAGCAAATTTTGTTTTT 59.710 32.000 5.81 0.00 42.00 1.94
35 36 4.801516 ACGTTAGCGAGCAAATTTTGTTTT 59.198 33.333 5.81 0.00 42.00 2.43
36 37 4.356289 ACGTTAGCGAGCAAATTTTGTTT 58.644 34.783 5.81 0.17 42.00 2.83
37 38 3.959943 ACGTTAGCGAGCAAATTTTGTT 58.040 36.364 5.81 4.60 42.00 2.83
38 39 3.619233 ACGTTAGCGAGCAAATTTTGT 57.381 38.095 5.81 0.00 42.00 2.83
39 40 4.027556 CGTAACGTTAGCGAGCAAATTTTG 59.972 41.667 18.96 4.72 42.00 2.44
40 41 4.145997 CGTAACGTTAGCGAGCAAATTTT 58.854 39.130 18.96 0.00 42.00 1.82
41 42 3.184986 ACGTAACGTTAGCGAGCAAATTT 59.815 39.130 25.92 7.96 36.35 1.82
42 43 2.733026 ACGTAACGTTAGCGAGCAAATT 59.267 40.909 25.92 8.48 36.35 1.82
43 44 2.331194 ACGTAACGTTAGCGAGCAAAT 58.669 42.857 25.92 8.99 36.35 2.32
44 45 1.769733 ACGTAACGTTAGCGAGCAAA 58.230 45.000 25.92 0.00 36.35 3.68
45 46 3.477504 ACGTAACGTTAGCGAGCAA 57.522 47.368 25.92 0.00 36.35 3.91
55 56 1.585297 CCCAGGAAACAACGTAACGT 58.415 50.000 0.00 0.00 43.97 3.99
56 57 0.236449 GCCCAGGAAACAACGTAACG 59.764 55.000 0.00 0.00 0.00 3.18
57 58 1.601166 AGCCCAGGAAACAACGTAAC 58.399 50.000 0.00 0.00 0.00 2.50
58 59 2.550639 GGTAGCCCAGGAAACAACGTAA 60.551 50.000 0.00 0.00 0.00 3.18
59 60 1.002315 GGTAGCCCAGGAAACAACGTA 59.998 52.381 0.00 0.00 0.00 3.57
60 61 0.250597 GGTAGCCCAGGAAACAACGT 60.251 55.000 0.00 0.00 0.00 3.99
61 62 0.036306 AGGTAGCCCAGGAAACAACG 59.964 55.000 0.00 0.00 0.00 4.10
62 63 1.073284 TGAGGTAGCCCAGGAAACAAC 59.927 52.381 0.00 0.00 0.00 3.32
63 64 1.440618 TGAGGTAGCCCAGGAAACAA 58.559 50.000 0.00 0.00 0.00 2.83
64 65 1.668826 ATGAGGTAGCCCAGGAAACA 58.331 50.000 0.00 0.00 0.00 2.83
65 66 2.369394 CAATGAGGTAGCCCAGGAAAC 58.631 52.381 0.00 0.00 0.00 2.78
66 67 1.284785 CCAATGAGGTAGCCCAGGAAA 59.715 52.381 0.00 0.00 0.00 3.13
67 68 0.918983 CCAATGAGGTAGCCCAGGAA 59.081 55.000 0.00 0.00 0.00 3.36
68 69 1.635817 GCCAATGAGGTAGCCCAGGA 61.636 60.000 0.00 0.00 40.61 3.86
69 70 1.152881 GCCAATGAGGTAGCCCAGG 60.153 63.158 0.00 0.00 40.61 4.45
70 71 1.131638 TAGCCAATGAGGTAGCCCAG 58.868 55.000 0.00 0.00 40.61 4.45
71 72 1.819753 ATAGCCAATGAGGTAGCCCA 58.180 50.000 0.00 0.00 40.61 5.36
72 73 4.263506 ACATTATAGCCAATGAGGTAGCCC 60.264 45.833 9.55 0.00 38.01 5.19
73 74 4.911390 ACATTATAGCCAATGAGGTAGCC 58.089 43.478 9.55 0.00 38.01 3.93
74 75 5.551233 TGACATTATAGCCAATGAGGTAGC 58.449 41.667 9.55 0.00 38.01 3.58
75 76 6.992123 TGTTGACATTATAGCCAATGAGGTAG 59.008 38.462 9.55 0.00 38.01 3.18
76 77 6.765989 GTGTTGACATTATAGCCAATGAGGTA 59.234 38.462 9.55 0.00 38.01 3.08
77 78 5.590259 GTGTTGACATTATAGCCAATGAGGT 59.410 40.000 9.55 0.00 38.01 3.85
78 79 5.589855 TGTGTTGACATTATAGCCAATGAGG 59.410 40.000 9.55 0.00 38.01 3.86
79 80 6.093909 TGTGTGTTGACATTATAGCCAATGAG 59.906 38.462 9.55 0.00 38.01 2.90
80 81 5.942826 TGTGTGTTGACATTATAGCCAATGA 59.057 36.000 9.55 0.00 38.01 2.57
81 82 6.193514 TGTGTGTTGACATTATAGCCAATG 57.806 37.500 2.62 2.62 40.93 2.82
82 83 7.093814 ACAATGTGTGTTGACATTATAGCCAAT 60.094 33.333 0.00 0.00 43.29 3.16
83 84 6.208402 ACAATGTGTGTTGACATTATAGCCAA 59.792 34.615 0.00 0.00 43.29 4.52
84 85 5.709631 ACAATGTGTGTTGACATTATAGCCA 59.290 36.000 0.00 0.00 43.29 4.75
85 86 6.029607 CACAATGTGTGTTGACATTATAGCC 58.970 40.000 5.00 0.00 43.29 3.93
86 87 6.029607 CCACAATGTGTGTTGACATTATAGC 58.970 40.000 12.79 0.00 46.45 2.97
87 88 7.144722 ACCACAATGTGTGTTGACATTATAG 57.855 36.000 12.79 0.00 46.45 1.31
88 89 7.517614 AACCACAATGTGTGTTGACATTATA 57.482 32.000 12.79 0.00 46.45 0.98
89 90 6.403866 AACCACAATGTGTGTTGACATTAT 57.596 33.333 12.79 0.00 46.45 1.28
90 91 5.843673 AACCACAATGTGTGTTGACATTA 57.156 34.783 12.79 0.00 46.45 1.90
91 92 4.734398 AACCACAATGTGTGTTGACATT 57.266 36.364 12.79 0.00 46.45 2.71
92 93 4.734398 AAACCACAATGTGTGTTGACAT 57.266 36.364 16.74 3.58 46.45 3.06
93 94 4.527509 AAAACCACAATGTGTGTTGACA 57.472 36.364 16.74 0.00 46.45 3.58
94 95 4.092675 CCAAAAACCACAATGTGTGTTGAC 59.907 41.667 16.74 0.00 46.45 3.18
95 96 4.021104 TCCAAAAACCACAATGTGTGTTGA 60.021 37.500 16.74 9.65 46.45 3.18
96 97 4.248859 TCCAAAAACCACAATGTGTGTTG 58.751 39.130 16.74 9.50 46.45 3.33
97 98 4.543590 TCCAAAAACCACAATGTGTGTT 57.456 36.364 12.79 12.50 46.45 3.32
98 99 4.502962 CTTCCAAAAACCACAATGTGTGT 58.497 39.130 12.79 7.12 46.45 3.72
100 101 3.197549 AGCTTCCAAAAACCACAATGTGT 59.802 39.130 12.79 0.00 0.00 3.72
101 102 3.795877 AGCTTCCAAAAACCACAATGTG 58.204 40.909 6.37 6.37 0.00 3.21
102 103 4.202212 GGTAGCTTCCAAAAACCACAATGT 60.202 41.667 4.19 0.00 0.00 2.71
103 104 4.202202 TGGTAGCTTCCAAAAACCACAATG 60.202 41.667 10.01 0.00 35.34 2.82
104 105 3.964031 TGGTAGCTTCCAAAAACCACAAT 59.036 39.130 10.01 0.00 35.34 2.71
105 106 3.366396 TGGTAGCTTCCAAAAACCACAA 58.634 40.909 10.01 0.00 35.34 3.33
106 107 2.955660 CTGGTAGCTTCCAAAAACCACA 59.044 45.455 13.60 0.00 35.34 4.17
107 108 3.219281 TCTGGTAGCTTCCAAAAACCAC 58.781 45.455 13.60 0.00 35.34 4.16
108 109 3.586470 TCTGGTAGCTTCCAAAAACCA 57.414 42.857 13.60 7.77 37.88 3.67
109 110 3.889538 AGTTCTGGTAGCTTCCAAAAACC 59.110 43.478 22.92 11.64 37.01 3.27
110 111 5.515797 AAGTTCTGGTAGCTTCCAAAAAC 57.484 39.130 20.75 20.75 37.01 2.43
111 112 6.538945 AAAAGTTCTGGTAGCTTCCAAAAA 57.461 33.333 13.60 7.98 37.01 1.94
112 113 5.220970 CGAAAAGTTCTGGTAGCTTCCAAAA 60.221 40.000 13.60 3.55 37.01 2.44
113 114 4.274950 CGAAAAGTTCTGGTAGCTTCCAAA 59.725 41.667 13.60 7.97 37.01 3.28
114 115 3.813166 CGAAAAGTTCTGGTAGCTTCCAA 59.187 43.478 13.60 2.20 37.01 3.53
115 116 3.181458 ACGAAAAGTTCTGGTAGCTTCCA 60.181 43.478 12.01 12.01 36.00 3.53
116 117 3.400255 ACGAAAAGTTCTGGTAGCTTCC 58.600 45.455 1.68 1.68 0.00 3.46
117 118 3.432592 GGACGAAAAGTTCTGGTAGCTTC 59.567 47.826 0.00 0.00 0.00 3.86
118 119 3.181458 TGGACGAAAAGTTCTGGTAGCTT 60.181 43.478 0.00 0.00 0.00 3.74
119 120 2.367567 TGGACGAAAAGTTCTGGTAGCT 59.632 45.455 0.00 0.00 0.00 3.32
120 121 2.737252 CTGGACGAAAAGTTCTGGTAGC 59.263 50.000 0.00 0.00 0.00 3.58
121 122 3.991367 ACTGGACGAAAAGTTCTGGTAG 58.009 45.455 0.00 0.00 32.15 3.18
122 123 4.411256 AACTGGACGAAAAGTTCTGGTA 57.589 40.909 0.00 0.00 30.87 3.25
123 124 3.277142 AACTGGACGAAAAGTTCTGGT 57.723 42.857 0.00 0.00 30.87 4.00
124 125 4.351192 CAAAACTGGACGAAAAGTTCTGG 58.649 43.478 0.00 0.00 35.60 3.86
125 126 4.351192 CCAAAACTGGACGAAAAGTTCTG 58.649 43.478 0.00 0.00 35.60 3.02
126 127 3.380320 CCCAAAACTGGACGAAAAGTTCT 59.620 43.478 0.00 0.00 35.60 3.01
127 128 3.379057 TCCCAAAACTGGACGAAAAGTTC 59.621 43.478 0.00 0.00 35.60 3.01
128 129 3.358118 TCCCAAAACTGGACGAAAAGTT 58.642 40.909 0.00 0.00 38.25 2.66
129 130 3.007473 TCCCAAAACTGGACGAAAAGT 57.993 42.857 0.00 0.00 0.00 2.66
130 131 4.202111 ACATTCCCAAAACTGGACGAAAAG 60.202 41.667 0.00 0.00 0.00 2.27
131 132 3.702045 ACATTCCCAAAACTGGACGAAAA 59.298 39.130 0.00 0.00 0.00 2.29
132 133 3.292460 ACATTCCCAAAACTGGACGAAA 58.708 40.909 0.00 0.00 0.00 3.46
133 134 2.882137 GACATTCCCAAAACTGGACGAA 59.118 45.455 0.00 0.00 0.00 3.85
134 135 2.500229 GACATTCCCAAAACTGGACGA 58.500 47.619 0.00 0.00 0.00 4.20
135 136 1.539827 GGACATTCCCAAAACTGGACG 59.460 52.381 0.00 0.00 0.00 4.79
136 137 2.876581 AGGACATTCCCAAAACTGGAC 58.123 47.619 0.00 0.00 37.19 4.02
137 138 3.913799 TCTAGGACATTCCCAAAACTGGA 59.086 43.478 0.00 0.00 37.19 3.86
138 139 4.301072 TCTAGGACATTCCCAAAACTGG 57.699 45.455 0.00 0.00 37.19 4.00
139 140 5.316987 ACTTCTAGGACATTCCCAAAACTG 58.683 41.667 0.00 0.00 37.19 3.16
140 141 5.584551 ACTTCTAGGACATTCCCAAAACT 57.415 39.130 0.00 0.00 37.19 2.66
141 142 6.490381 AGAAACTTCTAGGACATTCCCAAAAC 59.510 38.462 0.00 0.00 37.19 2.43
142 143 6.610830 AGAAACTTCTAGGACATTCCCAAAA 58.389 36.000 0.00 0.00 37.19 2.44
143 144 6.200878 AGAAACTTCTAGGACATTCCCAAA 57.799 37.500 0.00 0.00 37.19 3.28
144 145 5.843019 AGAAACTTCTAGGACATTCCCAA 57.157 39.130 0.00 0.00 37.19 4.12
145 146 5.843019 AAGAAACTTCTAGGACATTCCCA 57.157 39.130 0.00 0.00 34.91 4.37
146 147 7.526142 AAAAAGAAACTTCTAGGACATTCCC 57.474 36.000 0.00 0.00 34.91 3.97
167 168 7.334171 CCAGAAAAGCCAAAGAAGAAAGAAAAA 59.666 33.333 0.00 0.00 0.00 1.94
168 169 6.818142 CCAGAAAAGCCAAAGAAGAAAGAAAA 59.182 34.615 0.00 0.00 0.00 2.29
169 170 6.070824 ACCAGAAAAGCCAAAGAAGAAAGAAA 60.071 34.615 0.00 0.00 0.00 2.52
170 171 5.422012 ACCAGAAAAGCCAAAGAAGAAAGAA 59.578 36.000 0.00 0.00 0.00 2.52
171 172 4.956075 ACCAGAAAAGCCAAAGAAGAAAGA 59.044 37.500 0.00 0.00 0.00 2.52
172 173 5.268118 ACCAGAAAAGCCAAAGAAGAAAG 57.732 39.130 0.00 0.00 0.00 2.62
173 174 5.675684 AACCAGAAAAGCCAAAGAAGAAA 57.324 34.783 0.00 0.00 0.00 2.52
174 175 5.675684 AAACCAGAAAAGCCAAAGAAGAA 57.324 34.783 0.00 0.00 0.00 2.52
175 176 5.675684 AAAACCAGAAAAGCCAAAGAAGA 57.324 34.783 0.00 0.00 0.00 2.87
176 177 5.874261 TGAAAAACCAGAAAAGCCAAAGAAG 59.126 36.000 0.00 0.00 0.00 2.85
177 178 5.799213 TGAAAAACCAGAAAAGCCAAAGAA 58.201 33.333 0.00 0.00 0.00 2.52
178 179 5.413309 TGAAAAACCAGAAAAGCCAAAGA 57.587 34.783 0.00 0.00 0.00 2.52
179 180 6.682423 AATGAAAAACCAGAAAAGCCAAAG 57.318 33.333 0.00 0.00 0.00 2.77
180 181 7.392953 AGAAAATGAAAAACCAGAAAAGCCAAA 59.607 29.630 0.00 0.00 0.00 3.28
181 182 6.883756 AGAAAATGAAAAACCAGAAAAGCCAA 59.116 30.769 0.00 0.00 0.00 4.52
182 183 6.315891 CAGAAAATGAAAAACCAGAAAAGCCA 59.684 34.615 0.00 0.00 0.00 4.75
183 184 6.316140 ACAGAAAATGAAAAACCAGAAAAGCC 59.684 34.615 0.00 0.00 0.00 4.35
184 185 7.307493 ACAGAAAATGAAAAACCAGAAAAGC 57.693 32.000 0.00 0.00 0.00 3.51
187 188 9.500785 AGAAAACAGAAAATGAAAAACCAGAAA 57.499 25.926 0.00 0.00 0.00 2.52
188 189 9.500785 AAGAAAACAGAAAATGAAAAACCAGAA 57.499 25.926 0.00 0.00 0.00 3.02
189 190 9.500785 AAAGAAAACAGAAAATGAAAAACCAGA 57.499 25.926 0.00 0.00 0.00 3.86
190 191 9.759259 GAAAGAAAACAGAAAATGAAAAACCAG 57.241 29.630 0.00 0.00 0.00 4.00
191 192 8.726068 GGAAAGAAAACAGAAAATGAAAAACCA 58.274 29.630 0.00 0.00 0.00 3.67
192 193 8.946085 AGGAAAGAAAACAGAAAATGAAAAACC 58.054 29.630 0.00 0.00 0.00 3.27
195 196 9.942850 AGAAGGAAAGAAAACAGAAAATGAAAA 57.057 25.926 0.00 0.00 0.00 2.29
196 197 9.586435 GAGAAGGAAAGAAAACAGAAAATGAAA 57.414 29.630 0.00 0.00 0.00 2.69
197 198 8.748412 TGAGAAGGAAAGAAAACAGAAAATGAA 58.252 29.630 0.00 0.00 0.00 2.57
198 199 8.292444 TGAGAAGGAAAGAAAACAGAAAATGA 57.708 30.769 0.00 0.00 0.00 2.57
199 200 9.189723 GATGAGAAGGAAAGAAAACAGAAAATG 57.810 33.333 0.00 0.00 0.00 2.32
200 201 9.140874 AGATGAGAAGGAAAGAAAACAGAAAAT 57.859 29.630 0.00 0.00 0.00 1.82
201 202 8.408601 CAGATGAGAAGGAAAGAAAACAGAAAA 58.591 33.333 0.00 0.00 0.00 2.29
202 203 7.557719 ACAGATGAGAAGGAAAGAAAACAGAAA 59.442 33.333 0.00 0.00 0.00 2.52
203 204 7.056635 ACAGATGAGAAGGAAAGAAAACAGAA 58.943 34.615 0.00 0.00 0.00 3.02
204 205 6.595682 ACAGATGAGAAGGAAAGAAAACAGA 58.404 36.000 0.00 0.00 0.00 3.41
205 206 6.874288 ACAGATGAGAAGGAAAGAAAACAG 57.126 37.500 0.00 0.00 0.00 3.16
206 207 7.607991 GGATACAGATGAGAAGGAAAGAAAACA 59.392 37.037 0.00 0.00 0.00 2.83
207 208 7.066404 GGGATACAGATGAGAAGGAAAGAAAAC 59.934 40.741 0.00 0.00 39.74 2.43
208 209 7.037297 AGGGATACAGATGAGAAGGAAAGAAAA 60.037 37.037 0.00 0.00 39.74 2.29
209 210 6.445139 AGGGATACAGATGAGAAGGAAAGAAA 59.555 38.462 0.00 0.00 39.74 2.52
210 211 5.966935 AGGGATACAGATGAGAAGGAAAGAA 59.033 40.000 0.00 0.00 39.74 2.52
211 212 5.533112 AGGGATACAGATGAGAAGGAAAGA 58.467 41.667 0.00 0.00 39.74 2.52
212 213 5.885449 AGGGATACAGATGAGAAGGAAAG 57.115 43.478 0.00 0.00 39.74 2.62
213 214 6.445139 AGAAAGGGATACAGATGAGAAGGAAA 59.555 38.462 0.00 0.00 39.74 3.13
214 215 5.966935 AGAAAGGGATACAGATGAGAAGGAA 59.033 40.000 0.00 0.00 39.74 3.36
215 216 5.533112 AGAAAGGGATACAGATGAGAAGGA 58.467 41.667 0.00 0.00 39.74 3.36
216 217 5.885449 AGAAAGGGATACAGATGAGAAGG 57.115 43.478 0.00 0.00 39.74 3.46
217 218 6.882656 TGAAGAAAGGGATACAGATGAGAAG 58.117 40.000 0.00 0.00 39.74 2.85
218 219 6.874278 TGAAGAAAGGGATACAGATGAGAA 57.126 37.500 0.00 0.00 39.74 2.87
219 220 7.443302 AATGAAGAAAGGGATACAGATGAGA 57.557 36.000 0.00 0.00 39.74 3.27
220 221 8.517062 AAAATGAAGAAAGGGATACAGATGAG 57.483 34.615 0.00 0.00 39.74 2.90
221 222 8.331740 AGAAAATGAAGAAAGGGATACAGATGA 58.668 33.333 0.00 0.00 39.74 2.92
222 223 8.517062 AGAAAATGAAGAAAGGGATACAGATG 57.483 34.615 0.00 0.00 39.74 2.90
290 291 9.239002 CATGAATTGCAAAAATGTTCACAAATT 57.761 25.926 13.17 0.00 32.30 1.82
291 292 8.622157 TCATGAATTGCAAAAATGTTCACAAAT 58.378 25.926 13.17 0.00 32.30 2.32
292 293 7.982224 TCATGAATTGCAAAAATGTTCACAAA 58.018 26.923 13.17 1.92 32.30 2.83
293 294 7.549615 TCATGAATTGCAAAAATGTTCACAA 57.450 28.000 13.17 3.95 32.30 3.33
294 295 7.549615 TTCATGAATTGCAAAAATGTTCACA 57.450 28.000 13.17 2.85 32.30 3.58
312 313 9.993454 TGTTGTGGATTTGAAAAATATTCATGA 57.007 25.926 0.00 0.00 0.00 3.07
326 327 8.945930 CGAATTTGAAAAATTGTTGTGGATTTG 58.054 29.630 2.82 0.00 0.00 2.32
327 328 8.672815 ACGAATTTGAAAAATTGTTGTGGATTT 58.327 25.926 0.00 0.00 0.00 2.17
328 329 8.121708 CACGAATTTGAAAAATTGTTGTGGATT 58.878 29.630 0.00 0.00 0.00 3.01
329 330 7.493971 TCACGAATTTGAAAAATTGTTGTGGAT 59.506 29.630 0.00 0.00 0.00 3.41
330 331 6.813649 TCACGAATTTGAAAAATTGTTGTGGA 59.186 30.769 0.00 6.38 0.00 4.02
331 332 6.998338 TCACGAATTTGAAAAATTGTTGTGG 58.002 32.000 0.00 5.04 0.00 4.17
348 349 8.717821 CCACGGATGTAAATATTAATCACGAAT 58.282 33.333 15.38 0.00 0.00 3.34
349 350 7.927092 TCCACGGATGTAAATATTAATCACGAA 59.073 33.333 15.38 0.00 0.00 3.85
350 351 7.383029 GTCCACGGATGTAAATATTAATCACGA 59.617 37.037 15.38 0.00 0.00 4.35
351 352 7.170151 TGTCCACGGATGTAAATATTAATCACG 59.830 37.037 0.00 2.75 0.00 4.35
352 353 8.373048 TGTCCACGGATGTAAATATTAATCAC 57.627 34.615 0.00 0.00 0.00 3.06
451 452 9.574458 TTGTTCACGAATTTGAAAAATTAGTGA 57.426 25.926 24.77 24.77 44.54 3.41
459 460 9.535270 GTGAATTTTTGTTCACGAATTTGAAAA 57.465 25.926 0.00 0.00 45.76 2.29
471 472 9.681692 CAGTAGATCATTGTGAATTTTTGTTCA 57.318 29.630 0.00 0.00 35.84 3.18
472 473 9.683069 ACAGTAGATCATTGTGAATTTTTGTTC 57.317 29.630 0.00 0.00 0.00 3.18
534 535 8.847196 GTTCTTAGATTGTCCCAAGTTAAACTT 58.153 33.333 0.00 0.00 39.39 2.66
535 536 8.218488 AGTTCTTAGATTGTCCCAAGTTAAACT 58.782 33.333 0.00 0.00 0.00 2.66
536 537 8.392372 AGTTCTTAGATTGTCCCAAGTTAAAC 57.608 34.615 0.00 0.00 0.00 2.01
537 538 8.990163 AAGTTCTTAGATTGTCCCAAGTTAAA 57.010 30.769 0.00 0.00 0.00 1.52
538 539 8.990163 AAAGTTCTTAGATTGTCCCAAGTTAA 57.010 30.769 0.00 0.00 0.00 2.01
539 540 8.215050 TGAAAGTTCTTAGATTGTCCCAAGTTA 58.785 33.333 0.00 0.00 0.00 2.24
540 541 7.060421 TGAAAGTTCTTAGATTGTCCCAAGTT 58.940 34.615 0.00 0.00 0.00 2.66
541 542 6.601332 TGAAAGTTCTTAGATTGTCCCAAGT 58.399 36.000 0.00 0.00 0.00 3.16
542 543 7.138692 CTGAAAGTTCTTAGATTGTCCCAAG 57.861 40.000 0.00 0.00 0.00 3.61
575 576 3.886505 TGCTTCACACGTATTCCCTTTTT 59.113 39.130 0.00 0.00 0.00 1.94
576 577 3.482436 TGCTTCACACGTATTCCCTTTT 58.518 40.909 0.00 0.00 0.00 2.27
577 578 3.134574 TGCTTCACACGTATTCCCTTT 57.865 42.857 0.00 0.00 0.00 3.11
578 579 2.851263 TGCTTCACACGTATTCCCTT 57.149 45.000 0.00 0.00 0.00 3.95
658 685 2.716217 GAGCCCTGCCCATAATCATAC 58.284 52.381 0.00 0.00 0.00 2.39
681 708 1.668628 CCCGGCCTTTCGTTTTCATTG 60.669 52.381 0.00 0.00 0.00 2.82
701 728 1.283736 AACGTCAACGGTCAGTGAAC 58.716 50.000 7.53 0.00 44.95 3.18
703 730 2.099592 AGTAAACGTCAACGGTCAGTGA 59.900 45.455 7.53 0.00 39.00 3.41
750 777 1.666209 GAATGGCCAATGGGTCCACG 61.666 60.000 10.96 0.00 41.24 4.94
764 791 4.037208 GTGGTGAGAAGCATAATGGAATGG 59.963 45.833 0.00 0.00 0.00 3.16
765 792 4.885907 AGTGGTGAGAAGCATAATGGAATG 59.114 41.667 0.00 0.00 0.00 2.67
766 793 5.121380 AGTGGTGAGAAGCATAATGGAAT 57.879 39.130 0.00 0.00 0.00 3.01
767 794 4.574674 AGTGGTGAGAAGCATAATGGAA 57.425 40.909 0.00 0.00 0.00 3.53
768 795 5.692115 TTAGTGGTGAGAAGCATAATGGA 57.308 39.130 0.00 0.00 0.00 3.41
848 875 6.300703 TCGAAGAAAAGTTGGGAGGAAATAA 58.699 36.000 0.00 0.00 0.00 1.40
894 921 1.399440 CGATGTGGAATGGCTGACTTG 59.601 52.381 0.00 0.00 0.00 3.16
900 927 2.117156 GCTGCGATGTGGAATGGCT 61.117 57.895 0.00 0.00 0.00 4.75
931 958 2.736670 AGAAAACTGCAGGGTGAAGT 57.263 45.000 19.93 0.00 38.05 3.01
984 1012 4.015764 TGGCCATGTGTTAGTACGTACTA 58.984 43.478 27.51 27.51 37.73 1.82
986 1014 3.235157 TGGCCATGTGTTAGTACGTAC 57.765 47.619 18.10 18.10 0.00 3.67
987 1015 3.431068 CCATGGCCATGTGTTAGTACGTA 60.431 47.826 37.30 0.00 37.11 3.57
989 1017 1.939934 CCATGGCCATGTGTTAGTACG 59.060 52.381 37.30 19.19 37.11 3.67
1186 1220 4.955774 GTCGGTGTGGCGGTCGTT 62.956 66.667 0.00 0.00 0.00 3.85
1206 1242 2.920912 AGGGAAAGGGCGTCGTCA 60.921 61.111 0.00 0.00 0.00 4.35
1221 1257 3.003173 TGGAAGGAGCGGGTGAGG 61.003 66.667 0.00 0.00 0.00 3.86
1510 1612 2.960688 GCTTGAGGGAGCCGTCCTT 61.961 63.158 6.75 0.00 43.36 3.36
1563 1665 2.110006 GCGAGGCTGGGAGGATTC 59.890 66.667 0.00 0.00 0.00 2.52
1697 1799 4.329545 GGTGCTTCGGTGGCCTGA 62.330 66.667 3.32 0.00 0.00 3.86
1872 2007 3.261951 GCATATGCGCGGACGTGT 61.262 61.111 12.82 0.00 42.83 4.49
1893 2028 2.330372 CCCGGTGTCGTTCGAGAGA 61.330 63.158 0.00 0.00 39.20 3.10
2113 2263 1.293498 GCTCCCGCATCGTCCATAT 59.707 57.895 0.00 0.00 35.78 1.78
2232 2388 2.118313 TCACGTCGGAGAGATTGGTA 57.882 50.000 0.00 0.00 36.95 3.25
2238 2394 2.074576 CTGTACTTCACGTCGGAGAGA 58.925 52.381 0.00 0.00 36.95 3.10
2312 2468 1.555075 CCGTGATCTTCTTCTTCCCCA 59.445 52.381 0.00 0.00 0.00 4.96
2341 2497 3.121738 ACAGTTAAAGTCAGGGAACGG 57.878 47.619 0.00 0.00 0.00 4.44
2592 2805 6.211584 TCTTCTCATAGCCAACTGAGTAGTTT 59.788 38.462 6.22 0.00 44.57 2.66
2709 2940 1.042229 ACTGCACCGTTACCAGTGTA 58.958 50.000 2.83 0.00 38.32 2.90
2781 4802 1.535833 GGTCCGTCTTGTCTCTGAGA 58.464 55.000 2.58 2.58 0.00 3.27
2838 4859 6.413783 TCAAACACTTGTGAGGAGTACATA 57.586 37.500 7.83 0.00 33.94 2.29
2889 4910 3.005539 GAGGCCAGCAGGAGGACA 61.006 66.667 5.01 0.00 36.27 4.02
3042 5063 2.202395 GCTTGCAAACAGGGCCTCA 61.202 57.895 0.95 0.00 0.00 3.86
3375 5429 0.695462 AGCCATCCAGTATCAGCCCA 60.695 55.000 0.00 0.00 0.00 5.36
3576 5632 0.969149 ACACGATGCTGAAGAGGTCA 59.031 50.000 0.00 0.00 34.17 4.02
3593 5649 1.941377 AGGTATAACCACGTCCCACA 58.059 50.000 0.00 0.00 41.95 4.17
3772 5830 7.118723 AGTACATGTTATCCATCAACCACAAT 58.881 34.615 2.30 0.00 0.00 2.71
4259 6363 4.618227 GCTGGCTTCATATTTTTCGTGGTT 60.618 41.667 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.