Multiple sequence alignment - TraesCS5D01G330900

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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 TraesCS5D01G330900 chr5D 100.000 5161 0 0 1 5161 422004258 421999098 0.000000e+00 9531.0
1 TraesCS5D01G330900 chr5D 79.303 1836 323 47 2245 4050 421987819 421986011 0.000000e+00 1232.0
2 TraesCS5D01G330900 chr5D 78.252 1922 316 59 2166 4051 422012627 422010772 0.000000e+00 1140.0
3 TraesCS5D01G330900 chr5D 83.617 1117 181 2 2955 4070 421992882 421991767 0.000000e+00 1048.0
4 TraesCS5D01G330900 chr5D 78.231 588 89 28 2115 2688 421994272 421993710 1.780000e-89 340.0
5 TraesCS5D01G330900 chr5D 82.911 316 48 6 4708 5021 391806081 391805770 3.940000e-71 279.0
6 TraesCS5D01G330900 chr5D 81.940 299 43 8 4718 5010 232042831 232042538 5.160000e-60 243.0
7 TraesCS5D01G330900 chr5D 81.544 298 50 3 4704 4997 102280939 102281235 1.860000e-59 241.0
8 TraesCS5D01G330900 chr5A 93.960 1788 74 8 2886 4662 535555107 535553343 0.000000e+00 2673.0
9 TraesCS5D01G330900 chr5A 94.128 1124 60 4 732 1851 535558734 535557613 0.000000e+00 1705.0
10 TraesCS5D01G330900 chr5A 88.766 997 70 17 1901 2884 535557402 535556435 0.000000e+00 1182.0
11 TraesCS5D01G330900 chr5A 83.333 1218 197 5 2858 4071 535529565 535528350 0.000000e+00 1120.0
12 TraesCS5D01G330900 chr5A 83.008 1177 194 5 2893 4066 535520925 535519752 0.000000e+00 1061.0
13 TraesCS5D01G330900 chr5A 93.320 509 30 3 4657 5161 535535295 535534787 0.000000e+00 749.0
14 TraesCS5D01G330900 chr5A 87.250 549 43 15 146 667 535559322 535558774 7.390000e-168 601.0
15 TraesCS5D01G330900 chr5A 76.962 586 82 33 2115 2688 535530369 535529825 8.460000e-73 285.0
16 TraesCS5D01G330900 chr5A 80.583 309 49 8 4709 5010 324082275 324082579 1.450000e-55 228.0
17 TraesCS5D01G330900 chr5B 93.388 1452 88 6 732 2178 508732623 508731175 0.000000e+00 2143.0
18 TraesCS5D01G330900 chr5B 93.930 1285 63 5 3187 4462 508713578 508712300 0.000000e+00 1927.0
19 TraesCS5D01G330900 chr5B 79.979 1948 319 46 2160 4070 508682550 508680637 0.000000e+00 1371.0
20 TraesCS5D01G330900 chr5B 82.648 1216 199 9 2840 4047 508676601 508675390 0.000000e+00 1066.0
21 TraesCS5D01G330900 chr5B 94.349 637 32 4 2168 2803 508730710 508730077 0.000000e+00 974.0
22 TraesCS5D01G330900 chr5B 88.124 421 27 11 296 695 508733042 508732624 3.610000e-131 479.0
23 TraesCS5D01G330900 chr5B 82.653 294 43 5 2314 2604 508782570 508782282 2.390000e-63 254.0
24 TraesCS5D01G330900 chr5B 80.984 305 50 8 4708 5010 472214846 472214548 8.640000e-58 235.0
25 TraesCS5D01G330900 chr5B 77.882 321 69 2 3732 4051 508780213 508779894 1.130000e-46 198.0
26 TraesCS5D01G330900 chr5B 93.939 99 5 1 4585 4682 508701413 508701315 1.160000e-31 148.0
27 TraesCS5D01G330900 chr5B 91.818 110 1 2 4460 4568 508712097 508711995 4.160000e-31 147.0
28 TraesCS5D01G330900 chr5B 91.429 105 8 1 5012 5115 508701317 508701213 5.390000e-30 143.0
29 TraesCS5D01G330900 chr1D 83.893 298 41 6 4716 5010 490402959 490403252 1.420000e-70 278.0
30 TraesCS5D01G330900 chr2D 83.274 281 41 3 4745 5021 566647967 566647689 2.390000e-63 254.0
31 TraesCS5D01G330900 chr1A 81.350 311 51 5 4703 5010 307398349 307398655 3.990000e-61 246.0
32 TraesCS5D01G330900 chr1A 88.889 54 5 1 108 160 75721219 75721272 1.200000e-06 65.8
33 TraesCS5D01G330900 chr2A 87.963 108 11 2 41 147 598964964 598965070 5.430000e-25 126.0
34 TraesCS5D01G330900 chr7D 90.741 54 4 1 42 95 257759393 257759445 2.580000e-08 71.3
35 TraesCS5D01G330900 chr7B 90.741 54 4 1 42 95 571205880 571205828 2.580000e-08 71.3
36 TraesCS5D01G330900 chr7B 90.566 53 4 1 43 95 253085028 253085079 9.270000e-08 69.4
37 TraesCS5D01G330900 chr6A 92.000 50 4 0 48 97 586359670 586359719 2.580000e-08 71.3
38 TraesCS5D01G330900 chr1B 90.741 54 4 1 42 95 428022932 428022880 2.580000e-08 71.3
39 TraesCS5D01G330900 chr2B 90.385 52 5 0 44 95 377539177 377539228 9.270000e-08 69.4
40 TraesCS5D01G330900 chr2B 100.000 28 0 0 124 151 526898866 526898839 9.000000e-03 52.8
41 TraesCS5D01G330900 chr6B 91.667 48 4 0 48 95 667204377 667204330 3.340000e-07 67.6
42 TraesCS5D01G330900 chr4D 89.796 49 5 0 47 95 244878161 244878113 4.310000e-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 TraesCS5D01G330900 chr5D 421999098 422004258 5160 True 9531.000000 9531 100.000000 1 5161 1 chr5D.!!$R3 5160
1 TraesCS5D01G330900 chr5D 422010772 422012627 1855 True 1140.000000 1140 78.252000 2166 4051 1 chr5D.!!$R4 1885
2 TraesCS5D01G330900 chr5D 421986011 421994272 8261 True 873.333333 1232 80.383667 2115 4070 3 chr5D.!!$R5 1955
3 TraesCS5D01G330900 chr5A 535553343 535559322 5979 True 1540.250000 2673 91.026000 146 4662 4 chr5A.!!$R4 4516
4 TraesCS5D01G330900 chr5A 535519752 535520925 1173 True 1061.000000 1061 83.008000 2893 4066 1 chr5A.!!$R1 1173
5 TraesCS5D01G330900 chr5A 535534787 535535295 508 True 749.000000 749 93.320000 4657 5161 1 chr5A.!!$R2 504
6 TraesCS5D01G330900 chr5A 535528350 535530369 2019 True 702.500000 1120 80.147500 2115 4071 2 chr5A.!!$R3 1956
7 TraesCS5D01G330900 chr5B 508680637 508682550 1913 True 1371.000000 1371 79.979000 2160 4070 1 chr5B.!!$R3 1910
8 TraesCS5D01G330900 chr5B 508730077 508733042 2965 True 1198.666667 2143 91.953667 296 2803 3 chr5B.!!$R6 2507
9 TraesCS5D01G330900 chr5B 508675390 508676601 1211 True 1066.000000 1066 82.648000 2840 4047 1 chr5B.!!$R2 1207
10 TraesCS5D01G330900 chr5B 508711995 508713578 1583 True 1037.000000 1927 92.874000 3187 4568 2 chr5B.!!$R5 1381
11 TraesCS5D01G330900 chr5B 508779894 508782570 2676 True 226.000000 254 80.267500 2314 4051 2 chr5B.!!$R7 1737

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
141 142 0.104304 CAGGTAATTCCGGACGGAGG 59.896 60.0 13.64 0.0 46.06 4.30 F
492 520 0.107897 ATCGTTCCATACAAGGCGCA 60.108 50.0 10.83 0.0 0.00 6.09 F
1023 1066 0.176680 CCTCAGTGCTATTGCTCGGT 59.823 55.0 0.00 0.0 40.48 4.69 F
1362 1405 0.532573 ATCGGTTCTCAGACGTGCAT 59.467 50.0 0.00 0.0 0.00 3.96 F
2399 3137 1.256812 GGGATCAGGTGTTGTTTGGG 58.743 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
1079 1122 0.961019 ACCGCAATGTGTTCTGCATT 59.039 45.000 0.00 0.00 38.52 3.56 R
1770 1813 1.011242 CACGCACACTGTGTTTCCG 60.011 57.895 11.40 15.66 39.36 4.30 R
2705 4230 0.107654 AACCTCTCTACATTGCCGGC 60.108 55.000 22.73 22.73 0.00 6.13 R
2985 6414 0.328258 CCTTGGTTCCACCTTCGGAT 59.672 55.000 0.00 0.00 39.58 4.18 R
4354 13747 1.830477 AGAGAGATCACAACAGGGAGC 59.170 52.381 0.00 0.00 0.00 4.70 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
39 40 9.567848 TTCTAATATTCAAAGTTCATTTTCCGC 57.432 29.630 0.00 0.00 0.00 5.54
40 41 8.956426 TCTAATATTCAAAGTTCATTTTCCGCT 58.044 29.630 0.00 0.00 0.00 5.52
52 53 9.654663 AGTTCATTTTCCGCTATTATATACTCC 57.345 33.333 0.00 0.00 0.00 3.85
53 54 8.880750 GTTCATTTTCCGCTATTATATACTCCC 58.119 37.037 0.00 0.00 0.00 4.30
54 55 8.375493 TCATTTTCCGCTATTATATACTCCCT 57.625 34.615 0.00 0.00 0.00 4.20
55 56 8.822805 TCATTTTCCGCTATTATATACTCCCTT 58.177 33.333 0.00 0.00 0.00 3.95
56 57 9.099454 CATTTTCCGCTATTATATACTCCCTTC 57.901 37.037 0.00 0.00 0.00 3.46
57 58 6.446781 TTCCGCTATTATATACTCCCTTCG 57.553 41.667 0.00 0.00 0.00 3.79
58 59 5.503927 TCCGCTATTATATACTCCCTTCGT 58.496 41.667 0.00 0.00 0.00 3.85
59 60 5.587844 TCCGCTATTATATACTCCCTTCGTC 59.412 44.000 0.00 0.00 0.00 4.20
60 61 5.221009 CCGCTATTATATACTCCCTTCGTCC 60.221 48.000 0.00 0.00 0.00 4.79
61 62 5.356190 CGCTATTATATACTCCCTTCGTCCA 59.644 44.000 0.00 0.00 0.00 4.02
62 63 6.458478 CGCTATTATATACTCCCTTCGTCCAG 60.458 46.154 0.00 0.00 0.00 3.86
63 64 6.602406 GCTATTATATACTCCCTTCGTCCAGA 59.398 42.308 0.00 0.00 0.00 3.86
64 65 7.122353 GCTATTATATACTCCCTTCGTCCAGAA 59.878 40.741 0.00 0.00 37.31 3.02
65 66 7.850935 ATTATATACTCCCTTCGTCCAGAAA 57.149 36.000 0.00 0.00 38.57 2.52
66 67 7.850935 TTATATACTCCCTTCGTCCAGAAAT 57.149 36.000 0.00 0.00 38.57 2.17
67 68 8.945195 TTATATACTCCCTTCGTCCAGAAATA 57.055 34.615 0.00 0.00 38.57 1.40
68 69 3.889520 ACTCCCTTCGTCCAGAAATAC 57.110 47.619 0.00 0.00 38.57 1.89
69 70 3.442076 ACTCCCTTCGTCCAGAAATACT 58.558 45.455 0.00 0.00 38.57 2.12
70 71 3.838903 ACTCCCTTCGTCCAGAAATACTT 59.161 43.478 0.00 0.00 38.57 2.24
71 72 4.184629 CTCCCTTCGTCCAGAAATACTTG 58.815 47.826 0.00 0.00 38.57 3.16
72 73 3.581332 TCCCTTCGTCCAGAAATACTTGT 59.419 43.478 0.00 0.00 38.57 3.16
73 74 3.933332 CCCTTCGTCCAGAAATACTTGTC 59.067 47.826 0.00 0.00 38.57 3.18
74 75 3.612860 CCTTCGTCCAGAAATACTTGTCG 59.387 47.826 0.00 0.00 38.57 4.35
75 76 3.928727 TCGTCCAGAAATACTTGTCGT 57.071 42.857 0.00 0.00 0.00 4.34
76 77 4.247267 TCGTCCAGAAATACTTGTCGTT 57.753 40.909 0.00 0.00 0.00 3.85
77 78 5.375417 TCGTCCAGAAATACTTGTCGTTA 57.625 39.130 0.00 0.00 0.00 3.18
78 79 5.771469 TCGTCCAGAAATACTTGTCGTTAA 58.229 37.500 0.00 0.00 0.00 2.01
79 80 6.215121 TCGTCCAGAAATACTTGTCGTTAAA 58.785 36.000 0.00 0.00 0.00 1.52
80 81 6.700960 TCGTCCAGAAATACTTGTCGTTAAAA 59.299 34.615 0.00 0.00 0.00 1.52
81 82 7.385752 TCGTCCAGAAATACTTGTCGTTAAAAT 59.614 33.333 0.00 0.00 0.00 1.82
82 83 7.477422 CGTCCAGAAATACTTGTCGTTAAAATG 59.523 37.037 0.00 0.00 0.00 2.32
83 84 8.500773 GTCCAGAAATACTTGTCGTTAAAATGA 58.499 33.333 0.00 0.00 0.00 2.57
84 85 9.058174 TCCAGAAATACTTGTCGTTAAAATGAA 57.942 29.630 0.00 0.00 0.00 2.57
85 86 9.840427 CCAGAAATACTTGTCGTTAAAATGAAT 57.160 29.630 0.00 0.00 0.00 2.57
97 98 9.798885 GTCGTTAAAATGAATGTATCTAGATGC 57.201 33.333 15.79 14.54 0.00 3.91
98 99 9.541143 TCGTTAAAATGAATGTATCTAGATGCA 57.459 29.630 23.38 23.38 37.79 3.96
102 103 8.929260 AAAATGAATGTATCTAGATGCATCCA 57.071 30.769 29.32 25.55 42.07 3.41
103 104 9.529823 AAAATGAATGTATCTAGATGCATCCAT 57.470 29.630 29.32 26.43 39.66 3.41
104 105 9.529823 AAATGAATGTATCTAGATGCATCCATT 57.470 29.630 29.68 29.68 45.35 3.16
105 106 9.529823 AATGAATGTATCTAGATGCATCCATTT 57.470 29.630 29.68 19.17 42.67 2.32
106 107 8.929260 TGAATGTATCTAGATGCATCCATTTT 57.071 30.769 29.32 17.47 42.07 1.82
107 108 9.006839 TGAATGTATCTAGATGCATCCATTTTC 57.993 33.333 29.32 23.20 42.07 2.29
108 109 8.929260 AATGTATCTAGATGCATCCATTTTCA 57.071 30.769 29.32 15.43 42.07 2.69
109 110 9.529823 AATGTATCTAGATGCATCCATTTTCAT 57.470 29.630 29.32 16.81 42.07 2.57
110 111 8.557592 TGTATCTAGATGCATCCATTTTCATC 57.442 34.615 23.06 6.69 36.49 2.92
111 112 7.609146 TGTATCTAGATGCATCCATTTTCATCC 59.391 37.037 23.06 2.95 36.81 3.51
112 113 5.944135 TCTAGATGCATCCATTTTCATCCA 58.056 37.500 23.06 0.00 36.81 3.41
113 114 6.549242 TCTAGATGCATCCATTTTCATCCAT 58.451 36.000 23.06 2.35 36.81 3.41
114 115 7.008332 TCTAGATGCATCCATTTTCATCCATT 58.992 34.615 23.06 1.91 36.81 3.16
115 116 6.494666 AGATGCATCCATTTTCATCCATTT 57.505 33.333 23.06 0.00 36.81 2.32
116 117 7.606135 AGATGCATCCATTTTCATCCATTTA 57.394 32.000 23.06 0.00 36.81 1.40
117 118 8.202461 AGATGCATCCATTTTCATCCATTTAT 57.798 30.769 23.06 0.00 36.81 1.40
118 119 8.094548 AGATGCATCCATTTTCATCCATTTATG 58.905 33.333 23.06 0.00 36.81 1.90
119 120 5.992829 TGCATCCATTTTCATCCATTTATGC 59.007 36.000 0.00 0.00 37.19 3.14
120 121 5.992829 GCATCCATTTTCATCCATTTATGCA 59.007 36.000 0.00 0.00 36.79 3.96
121 122 6.483974 GCATCCATTTTCATCCATTTATGCAA 59.516 34.615 0.00 0.00 36.79 4.08
122 123 7.519328 GCATCCATTTTCATCCATTTATGCAAC 60.519 37.037 0.00 0.00 36.79 4.17
123 124 6.944096 TCCATTTTCATCCATTTATGCAACA 58.056 32.000 0.00 0.00 0.00 3.33
124 125 7.042950 TCCATTTTCATCCATTTATGCAACAG 58.957 34.615 0.00 0.00 0.00 3.16
125 126 6.259167 CCATTTTCATCCATTTATGCAACAGG 59.741 38.462 0.00 0.00 0.00 4.00
126 127 5.999205 TTTCATCCATTTATGCAACAGGT 57.001 34.783 0.00 0.00 0.00 4.00
127 128 7.473735 TTTTCATCCATTTATGCAACAGGTA 57.526 32.000 0.00 0.00 0.00 3.08
128 129 7.473735 TTTCATCCATTTATGCAACAGGTAA 57.526 32.000 0.00 0.00 0.00 2.85
129 130 7.658525 TTCATCCATTTATGCAACAGGTAAT 57.341 32.000 0.00 0.00 0.00 1.89
130 131 7.658525 TCATCCATTTATGCAACAGGTAATT 57.341 32.000 0.00 0.00 0.00 1.40
131 132 7.715657 TCATCCATTTATGCAACAGGTAATTC 58.284 34.615 0.00 0.00 0.00 2.17
132 133 6.463995 TCCATTTATGCAACAGGTAATTCC 57.536 37.500 0.00 0.00 0.00 3.01
133 134 5.067153 TCCATTTATGCAACAGGTAATTCCG 59.933 40.000 0.00 0.00 41.99 4.30
134 135 4.974368 TTTATGCAACAGGTAATTCCGG 57.026 40.909 0.00 0.00 41.99 5.14
135 136 2.799126 ATGCAACAGGTAATTCCGGA 57.201 45.000 0.00 0.00 41.99 5.14
136 137 1.816074 TGCAACAGGTAATTCCGGAC 58.184 50.000 1.83 0.00 41.99 4.79
137 138 0.725117 GCAACAGGTAATTCCGGACG 59.275 55.000 1.83 0.00 41.99 4.79
138 139 1.365699 CAACAGGTAATTCCGGACGG 58.634 55.000 1.83 3.96 41.99 4.79
139 140 1.066716 CAACAGGTAATTCCGGACGGA 60.067 52.381 1.83 9.76 43.52 4.69
140 141 0.822164 ACAGGTAATTCCGGACGGAG 59.178 55.000 13.64 3.15 46.06 4.63
141 142 0.104304 CAGGTAATTCCGGACGGAGG 59.896 60.000 13.64 0.00 46.06 4.30
142 143 1.047034 AGGTAATTCCGGACGGAGGG 61.047 60.000 13.64 0.00 46.06 4.30
143 144 1.044790 GGTAATTCCGGACGGAGGGA 61.045 60.000 13.64 0.00 46.06 4.20
144 145 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
159 160 4.262617 GGAGGGAGTATGTTCCAAAAGTC 58.737 47.826 0.47 0.00 39.09 3.01
164 165 5.501156 GGAGTATGTTCCAAAAGTCCTCAT 58.499 41.667 0.00 0.00 37.20 2.90
168 169 5.712152 ATGTTCCAAAAGTCCTCATCAAC 57.288 39.130 0.00 0.00 0.00 3.18
177 178 7.318141 CAAAAGTCCTCATCAACTGCAATTAT 58.682 34.615 0.00 0.00 0.00 1.28
180 181 6.182627 AGTCCTCATCAACTGCAATTATGAA 58.817 36.000 0.00 0.00 0.00 2.57
184 185 6.127814 CCTCATCAACTGCAATTATGAACACT 60.128 38.462 0.00 0.00 0.00 3.55
185 186 6.845302 TCATCAACTGCAATTATGAACACTC 58.155 36.000 0.00 0.00 0.00 3.51
186 187 6.430616 TCATCAACTGCAATTATGAACACTCA 59.569 34.615 0.00 0.00 35.56 3.41
192 193 4.280425 TGCAATTATGAACACTCAAAGCCA 59.720 37.500 0.00 0.00 34.49 4.75
196 197 3.788227 ATGAACACTCAAAGCCACCTA 57.212 42.857 0.00 0.00 34.49 3.08
231 232 7.456725 CCTCCCTGACTATGATTAATCATGTT 58.543 38.462 32.15 21.74 46.34 2.71
245 246 8.619146 ATTAATCATGTTGTACTGCAATTTCG 57.381 30.769 0.00 0.00 39.55 3.46
254 255 3.791973 ACTGCAATTTCGTTTGGTTCA 57.208 38.095 0.00 0.00 0.00 3.18
277 278 9.926158 TTCAAACATTAGTAATTCACATGCATT 57.074 25.926 0.00 0.00 0.00 3.56
375 396 8.155821 TCCAACATTAGTAATTCACGTTTTGA 57.844 30.769 0.00 0.00 0.00 2.69
492 520 0.107897 ATCGTTCCATACAAGGCGCA 60.108 50.000 10.83 0.00 0.00 6.09
534 562 1.289276 GCACAACAACCCAAAAGCAG 58.711 50.000 0.00 0.00 0.00 4.24
654 682 9.554724 CACATTAATTGACGTTGCTTTAGTATT 57.445 29.630 0.00 0.00 0.00 1.89
688 727 8.122952 ACTAAAGCAGCGTGAATTAATATGAAC 58.877 33.333 0.00 0.00 0.00 3.18
695 734 4.741185 CGTGAATTAATATGAACCGGACGA 59.259 41.667 9.46 0.00 0.00 4.20
696 735 5.232626 CGTGAATTAATATGAACCGGACGAA 59.767 40.000 9.46 0.00 0.00 3.85
697 736 6.561533 CGTGAATTAATATGAACCGGACGAAG 60.562 42.308 9.46 0.00 0.00 3.79
716 755 7.582435 ACGAAGTATATGTTTTGTCTGACAG 57.418 36.000 10.77 0.00 41.94 3.51
717 756 6.090898 ACGAAGTATATGTTTTGTCTGACAGC 59.909 38.462 10.77 6.40 41.94 4.40
718 757 6.090763 CGAAGTATATGTTTTGTCTGACAGCA 59.909 38.462 10.77 11.46 0.00 4.41
719 758 7.360017 CGAAGTATATGTTTTGTCTGACAGCAA 60.360 37.037 10.77 5.59 0.00 3.91
720 759 7.744087 AGTATATGTTTTGTCTGACAGCAAA 57.256 32.000 10.77 16.22 33.40 3.68
721 760 7.584987 AGTATATGTTTTGTCTGACAGCAAAC 58.415 34.615 22.25 22.25 34.77 2.93
722 761 4.989279 ATGTTTTGTCTGACAGCAAACT 57.011 36.364 26.09 15.68 32.75 2.66
723 762 4.782019 TGTTTTGTCTGACAGCAAACTT 57.218 36.364 26.09 0.00 32.75 2.66
724 763 4.484236 TGTTTTGTCTGACAGCAAACTTG 58.516 39.130 26.09 0.00 32.75 3.16
768 807 9.622004 CATTTAACATGCCATTTTATTTGCAAA 57.378 25.926 15.44 15.44 37.27 3.68
798 837 8.253113 ACTGCCCTTTGATACAAATATTGAAAG 58.747 33.333 0.00 0.00 0.00 2.62
825 864 9.143631 CCATTCATTCAACCTTGTTCTTATTTC 57.856 33.333 0.00 0.00 0.00 2.17
826 865 9.143631 CATTCATTCAACCTTGTTCTTATTTCC 57.856 33.333 0.00 0.00 0.00 3.13
827 866 6.908825 TCATTCAACCTTGTTCTTATTTCCG 58.091 36.000 0.00 0.00 0.00 4.30
849 888 4.911610 CGAGGTTGTTGTTTCTTTAGCATG 59.088 41.667 0.00 0.00 0.00 4.06
855 897 7.306574 GGTTGTTGTTTCTTTAGCATGTAAAGC 60.307 37.037 16.55 8.58 35.22 3.51
961 1004 5.403897 TTCTGTTCTTCTTTAGCACAACG 57.596 39.130 0.00 0.00 29.49 4.10
966 1009 3.390135 TCTTCTTTAGCACAACGGACAG 58.610 45.455 0.00 0.00 0.00 3.51
1008 1051 8.853126 CAATTTCAGAGAATTAATATGGCCTCA 58.147 33.333 3.32 0.00 0.00 3.86
1009 1052 8.632906 ATTTCAGAGAATTAATATGGCCTCAG 57.367 34.615 3.32 0.00 0.00 3.35
1012 1055 5.180868 CAGAGAATTAATATGGCCTCAGTGC 59.819 44.000 3.32 0.00 0.00 4.40
1015 1058 7.025520 AGAATTAATATGGCCTCAGTGCTAT 57.974 36.000 3.32 0.00 36.35 2.97
1023 1066 0.176680 CCTCAGTGCTATTGCTCGGT 59.823 55.000 0.00 0.00 40.48 4.69
1027 1070 1.745115 GTGCTATTGCTCGGTGCCA 60.745 57.895 0.00 0.00 42.00 4.92
1039 1082 2.744202 CTCGGTGCCATTATAATCCTGC 59.256 50.000 0.00 0.02 0.00 4.85
1079 1122 0.752009 TTGGCGCAACCTAACCACAA 60.752 50.000 10.83 0.00 40.22 3.33
1107 1150 1.952990 ACACATTGCGGTGACATTGAA 59.047 42.857 9.58 0.00 41.32 2.69
1140 1183 2.758736 TTGGCATTGGTATTGGTTGC 57.241 45.000 0.00 0.00 0.00 4.17
1175 1218 0.880278 TTCGAGGTCAACTGCAGCAC 60.880 55.000 15.27 8.10 0.00 4.40
1236 1279 4.003648 AGGAGGTTCTAAACATTTCAGCG 58.996 43.478 0.00 0.00 0.00 5.18
1295 1338 9.896645 CCCATCATATTGCTACAATTCTAGTAT 57.103 33.333 0.00 0.00 0.00 2.12
1313 1356 9.693739 TTCTAGTATAGGAAAAATGGATTTGCA 57.306 29.630 0.00 0.00 39.78 4.08
1353 1396 1.543208 GCATGGCCATATCGGTTCTCA 60.543 52.381 20.30 0.00 36.97 3.27
1362 1405 0.532573 ATCGGTTCTCAGACGTGCAT 59.467 50.000 0.00 0.00 0.00 3.96
1461 1504 2.112297 GTGTGTTGGAGCCCGGAA 59.888 61.111 0.73 0.00 0.00 4.30
1479 1522 2.165998 GAAGAACTGGCAAATGGCTCT 58.834 47.619 8.50 0.36 44.01 4.09
1482 1525 1.615392 GAACTGGCAAATGGCTCTTGT 59.385 47.619 8.50 0.19 44.01 3.16
1620 1663 3.586543 TCCATGGTGGTGGAAGCA 58.413 55.556 12.58 0.00 45.03 3.91
1680 1723 6.036083 CGACAAGGTTCAATGATACCTACAAG 59.964 42.308 14.37 9.40 43.88 3.16
1692 1735 3.561120 CTACAAGGGGCGGCAACCA 62.561 63.158 12.47 0.00 0.00 3.67
1733 1776 2.147958 TGGAAATGTAACGTGTGAGGC 58.852 47.619 0.00 0.00 0.00 4.70
1770 1813 1.412710 TCTTCCTATGCATGTCGGACC 59.587 52.381 10.16 0.00 0.00 4.46
1890 1933 1.839894 CAAGCCCCCACCTAGATCC 59.160 63.158 0.00 0.00 0.00 3.36
1916 2120 9.075519 CGTATGAATTTTCATGTGTAGCATTTT 57.924 29.630 14.54 0.00 46.68 1.82
1936 2140 4.914177 TTCCCTCTCATATATGCATGCA 57.086 40.909 25.04 25.04 0.00 3.96
1937 2141 4.914177 TCCCTCTCATATATGCATGCAA 57.086 40.909 26.68 14.46 0.00 4.08
1995 2201 9.396022 AGGGTTATAATATGTGAGTTTTGTCTG 57.604 33.333 0.00 0.00 0.00 3.51
2096 2302 8.786826 TGTAAAAGGAGAACAAATCGTCATAT 57.213 30.769 0.00 0.00 0.00 1.78
2102 2308 6.037610 AGGAGAACAAATCGTCATATTCAAGC 59.962 38.462 0.00 0.00 0.00 4.01
2191 2873 4.933400 GCATCTTGAATGCCATTTCAGTTT 59.067 37.500 0.00 0.00 39.01 2.66
2194 2876 5.531634 TCTTGAATGCCATTTCAGTTTCAC 58.468 37.500 0.00 0.00 36.97 3.18
2351 3062 6.067217 ACTAATACCCCAATCTGCATATCC 57.933 41.667 0.00 0.00 0.00 2.59
2367 3102 8.535335 TCTGCATATCCTTCTTATCTTACATCC 58.465 37.037 0.00 0.00 0.00 3.51
2393 3128 2.038952 TCTCACTTGGGATCAGGTGTTG 59.961 50.000 8.15 4.24 46.84 3.33
2399 3137 1.256812 GGGATCAGGTGTTGTTTGGG 58.743 55.000 0.00 0.00 0.00 4.12
2449 3187 2.121963 AGTCCAAGTCCCTGCCCA 60.122 61.111 0.00 0.00 0.00 5.36
2689 4213 6.058833 TGTTTTGGTGAGAGCAACATAGTAA 58.941 36.000 0.00 0.00 42.28 2.24
2731 4343 3.126000 GCAATGTAGAGAGGTTTGTCAGC 59.874 47.826 0.00 0.00 0.00 4.26
2966 6395 8.052748 TGTGGTATTGGAGTTCTATTTATTGCT 58.947 33.333 0.00 0.00 0.00 3.91
2985 6414 5.574891 TGCTTTAGTTTCAGCTTTGTTGA 57.425 34.783 0.00 0.00 36.92 3.18
3048 6477 1.535462 CGCACTTCCGGAGAAACAAAT 59.465 47.619 3.34 0.00 0.00 2.32
3308 6737 6.859508 CCATTATGTCACAAATCAATCATCGG 59.140 38.462 0.00 0.00 0.00 4.18
3427 6859 1.416401 TGACAACCTCAGTTCCAGGAC 59.584 52.381 0.00 0.00 32.45 3.85
4180 13554 6.454795 GCTAAATTGTCACATTTTCCCTTCA 58.545 36.000 0.91 0.00 0.00 3.02
4189 13563 7.451255 TGTCACATTTTCCCTTCATTTGATAGT 59.549 33.333 0.00 0.00 0.00 2.12
4354 13747 4.865365 GTCCTCTCCAAAAGTTCGTATCAG 59.135 45.833 0.00 0.00 0.00 2.90
4409 13802 3.674997 TGAACTCTCCATTTGGCACTAC 58.325 45.455 0.00 0.00 34.44 2.73
4444 13837 4.277239 CGATGACAACCCGCAAGA 57.723 55.556 0.00 0.00 43.02 3.02
4488 14086 4.629200 GTCTCGACAAAGAAGCATCTCATT 59.371 41.667 0.00 0.00 33.77 2.57
4514 14112 9.810545 TTAATGTGATTGTAACGATGTGATCTA 57.189 29.630 0.00 0.00 0.00 1.98
4515 14113 7.936950 ATGTGATTGTAACGATGTGATCTAG 57.063 36.000 0.00 0.00 0.00 2.43
4516 14114 6.863275 TGTGATTGTAACGATGTGATCTAGT 58.137 36.000 0.00 0.00 0.00 2.57
4517 14115 7.992008 TGTGATTGTAACGATGTGATCTAGTA 58.008 34.615 0.00 0.00 0.00 1.82
4518 14116 8.463607 TGTGATTGTAACGATGTGATCTAGTAA 58.536 33.333 0.00 0.00 0.00 2.24
4519 14117 8.959058 GTGATTGTAACGATGTGATCTAGTAAG 58.041 37.037 0.00 0.00 0.00 2.34
4520 14118 7.648112 TGATTGTAACGATGTGATCTAGTAAGC 59.352 37.037 0.00 0.00 0.00 3.09
4598 14197 0.719015 TGGAAGAGAGGGGAGATGGT 59.281 55.000 0.00 0.00 0.00 3.55
4647 14246 8.009622 TCAGATATAAAGGCATTTGCATGAAA 57.990 30.769 6.60 0.00 44.36 2.69
4741 14340 1.378762 GGTTACCTTGGCCTCTGCA 59.621 57.895 3.32 0.00 40.13 4.41
4782 14383 9.722184 ACATCCATCTCTATGTTTATTCATCAG 57.278 33.333 0.00 0.00 32.43 2.90
4812 14413 6.790285 ACAAAATGAATGCAAAGATCAACC 57.210 33.333 0.00 0.00 0.00 3.77
4834 14435 2.358247 GCCACCTTCGAGGCGAAA 60.358 61.111 3.77 0.00 45.23 3.46
4877 14478 2.410322 AAAGATGTGCCCTGACCGCA 62.410 55.000 0.00 0.00 0.00 5.69
4885 14486 1.003355 CCCTGACCGCATCAACTGT 60.003 57.895 0.00 0.00 36.69 3.55
4908 14509 5.594725 GTCACTATCTAATCCAGTGTCCTCA 59.405 44.000 0.00 0.00 40.44 3.86
4916 14517 0.322008 CCAGTGTCCTCAAGAAGCCC 60.322 60.000 0.00 0.00 0.00 5.19
4941 14543 2.927014 GCCTGACAAGTTGAGAGTACCG 60.927 54.545 10.54 0.00 0.00 4.02
4998 14600 4.365505 GCTCTAGGATCCGCCGCC 62.366 72.222 5.98 0.00 43.43 6.13
5011 14613 2.505982 CCGCCGTCCCATCTTCAT 59.494 61.111 0.00 0.00 0.00 2.57
5037 14639 4.881850 GGGGTCAGGTAATGTTACAATCTG 59.118 45.833 5.38 0.00 35.37 2.90
5043 14645 7.499232 GTCAGGTAATGTTACAATCTGGCTATT 59.501 37.037 5.38 0.00 35.37 1.73
5062 14664 5.060446 GCTATTTGGACAAACGTAAATGCAC 59.940 40.000 0.00 0.00 32.51 4.57
5082 14684 4.442893 GCACACATGCCTGTCTAGGTTATA 60.443 45.833 0.00 0.00 46.97 0.98
5141 14743 1.976045 CCGTAAACGCAGCAAAATGTC 59.024 47.619 0.00 0.00 38.18 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.567848 GCGGAAAATGAACTTTGAATATTAGAA 57.432 29.630 0.00 0.00 0.00 2.10
14 15 8.956426 AGCGGAAAATGAACTTTGAATATTAGA 58.044 29.630 0.00 0.00 0.00 2.10
26 27 9.654663 GGAGTATATAATAGCGGAAAATGAACT 57.345 33.333 0.00 0.00 0.00 3.01
27 28 8.880750 GGGAGTATATAATAGCGGAAAATGAAC 58.119 37.037 0.00 0.00 0.00 3.18
28 29 8.822805 AGGGAGTATATAATAGCGGAAAATGAA 58.177 33.333 0.00 0.00 0.00 2.57
29 30 8.375493 AGGGAGTATATAATAGCGGAAAATGA 57.625 34.615 0.00 0.00 0.00 2.57
30 31 9.099454 GAAGGGAGTATATAATAGCGGAAAATG 57.901 37.037 0.00 0.00 0.00 2.32
31 32 7.980099 CGAAGGGAGTATATAATAGCGGAAAAT 59.020 37.037 0.00 0.00 0.00 1.82
32 33 7.039504 ACGAAGGGAGTATATAATAGCGGAAAA 60.040 37.037 0.00 0.00 0.00 2.29
33 34 6.435277 ACGAAGGGAGTATATAATAGCGGAAA 59.565 38.462 0.00 0.00 0.00 3.13
34 35 5.948162 ACGAAGGGAGTATATAATAGCGGAA 59.052 40.000 0.00 0.00 0.00 4.30
35 36 5.503927 ACGAAGGGAGTATATAATAGCGGA 58.496 41.667 0.00 0.00 0.00 5.54
36 37 5.221009 GGACGAAGGGAGTATATAATAGCGG 60.221 48.000 0.00 0.00 0.00 5.52
37 38 5.356190 TGGACGAAGGGAGTATATAATAGCG 59.644 44.000 0.00 0.00 0.00 4.26
38 39 6.602406 TCTGGACGAAGGGAGTATATAATAGC 59.398 42.308 0.00 0.00 0.00 2.97
39 40 8.577048 TTCTGGACGAAGGGAGTATATAATAG 57.423 38.462 0.00 0.00 0.00 1.73
40 41 8.945195 TTTCTGGACGAAGGGAGTATATAATA 57.055 34.615 0.00 0.00 32.21 0.98
41 42 7.850935 TTTCTGGACGAAGGGAGTATATAAT 57.149 36.000 0.00 0.00 32.21 1.28
42 43 7.850935 ATTTCTGGACGAAGGGAGTATATAA 57.149 36.000 0.00 0.00 32.21 0.98
43 44 8.168725 AGTATTTCTGGACGAAGGGAGTATATA 58.831 37.037 0.00 0.00 32.21 0.86
44 45 7.011382 AGTATTTCTGGACGAAGGGAGTATAT 58.989 38.462 0.00 0.00 32.21 0.86
45 46 6.371278 AGTATTTCTGGACGAAGGGAGTATA 58.629 40.000 0.00 0.00 32.21 1.47
46 47 5.209659 AGTATTTCTGGACGAAGGGAGTAT 58.790 41.667 0.00 0.00 32.21 2.12
47 48 4.607239 AGTATTTCTGGACGAAGGGAGTA 58.393 43.478 0.00 0.00 32.21 2.59
48 49 3.442076 AGTATTTCTGGACGAAGGGAGT 58.558 45.455 0.00 0.00 32.21 3.85
49 50 4.184629 CAAGTATTTCTGGACGAAGGGAG 58.815 47.826 0.00 0.00 32.21 4.30
50 51 3.581332 ACAAGTATTTCTGGACGAAGGGA 59.419 43.478 0.00 0.00 32.21 4.20
51 52 3.933332 GACAAGTATTTCTGGACGAAGGG 59.067 47.826 0.00 0.00 32.21 3.95
52 53 3.612860 CGACAAGTATTTCTGGACGAAGG 59.387 47.826 0.00 0.00 37.43 3.46
53 54 4.235360 ACGACAAGTATTTCTGGACGAAG 58.765 43.478 0.00 0.00 37.43 3.79
54 55 4.247267 ACGACAAGTATTTCTGGACGAA 57.753 40.909 0.00 0.00 37.43 3.85
55 56 3.928727 ACGACAAGTATTTCTGGACGA 57.071 42.857 0.00 0.00 37.43 4.20
56 57 6.456447 TTTAACGACAAGTATTTCTGGACG 57.544 37.500 0.00 0.00 40.13 4.79
57 58 8.500773 TCATTTTAACGACAAGTATTTCTGGAC 58.499 33.333 0.00 0.00 0.00 4.02
58 59 8.610248 TCATTTTAACGACAAGTATTTCTGGA 57.390 30.769 0.00 0.00 0.00 3.86
59 60 9.840427 ATTCATTTTAACGACAAGTATTTCTGG 57.160 29.630 0.00 0.00 0.00 3.86
71 72 9.798885 GCATCTAGATACATTCATTTTAACGAC 57.201 33.333 4.54 0.00 0.00 4.34
72 73 9.541143 TGCATCTAGATACATTCATTTTAACGA 57.459 29.630 4.54 0.00 0.00 3.85
77 78 8.929260 TGGATGCATCTAGATACATTCATTTT 57.071 30.769 25.28 0.00 27.72 1.82
78 79 9.529823 AATGGATGCATCTAGATACATTCATTT 57.470 29.630 30.91 21.15 43.37 2.32
79 80 9.529823 AAATGGATGCATCTAGATACATTCATT 57.470 29.630 30.91 30.91 45.81 2.57
80 81 9.529823 AAAATGGATGCATCTAGATACATTCAT 57.470 29.630 25.38 25.38 40.73 2.57
81 82 8.929260 AAAATGGATGCATCTAGATACATTCA 57.071 30.769 23.61 23.61 35.23 2.57
82 83 9.006839 TGAAAATGGATGCATCTAGATACATTC 57.993 33.333 25.28 16.39 0.00 2.67
83 84 8.929260 TGAAAATGGATGCATCTAGATACATT 57.071 30.769 25.28 20.08 0.00 2.71
84 85 9.175312 GATGAAAATGGATGCATCTAGATACAT 57.825 33.333 25.28 16.84 35.46 2.29
85 86 7.609146 GGATGAAAATGGATGCATCTAGATACA 59.391 37.037 25.28 17.66 37.77 2.29
86 87 7.609146 TGGATGAAAATGGATGCATCTAGATAC 59.391 37.037 25.28 13.22 37.77 2.24
87 88 7.692172 TGGATGAAAATGGATGCATCTAGATA 58.308 34.615 25.28 8.33 37.77 1.98
88 89 6.549242 TGGATGAAAATGGATGCATCTAGAT 58.451 36.000 25.28 10.64 37.77 1.98
89 90 5.944135 TGGATGAAAATGGATGCATCTAGA 58.056 37.500 25.28 10.86 37.77 2.43
90 91 6.835819 ATGGATGAAAATGGATGCATCTAG 57.164 37.500 25.28 0.00 37.77 2.43
91 92 7.606135 AAATGGATGAAAATGGATGCATCTA 57.394 32.000 25.28 20.79 37.77 1.98
92 93 6.494666 AAATGGATGAAAATGGATGCATCT 57.505 33.333 25.28 5.84 37.77 2.90
93 94 7.148474 GCATAAATGGATGAAAATGGATGCATC 60.148 37.037 18.81 18.81 36.75 3.91
94 95 6.653320 GCATAAATGGATGAAAATGGATGCAT 59.347 34.615 0.00 0.00 36.75 3.96
95 96 5.992829 GCATAAATGGATGAAAATGGATGCA 59.007 36.000 0.00 0.00 36.75 3.96
96 97 5.992829 TGCATAAATGGATGAAAATGGATGC 59.007 36.000 0.00 0.00 37.16 3.91
97 98 7.496263 TGTTGCATAAATGGATGAAAATGGATG 59.504 33.333 0.00 0.00 0.00 3.51
98 99 7.566569 TGTTGCATAAATGGATGAAAATGGAT 58.433 30.769 0.00 0.00 0.00 3.41
99 100 6.944096 TGTTGCATAAATGGATGAAAATGGA 58.056 32.000 0.00 0.00 0.00 3.41
100 101 6.259167 CCTGTTGCATAAATGGATGAAAATGG 59.741 38.462 0.00 0.00 0.00 3.16
101 102 6.819649 ACCTGTTGCATAAATGGATGAAAATG 59.180 34.615 0.00 0.00 0.00 2.32
102 103 6.949715 ACCTGTTGCATAAATGGATGAAAAT 58.050 32.000 0.00 0.00 0.00 1.82
103 104 6.357579 ACCTGTTGCATAAATGGATGAAAA 57.642 33.333 0.00 0.00 0.00 2.29
104 105 5.999205 ACCTGTTGCATAAATGGATGAAA 57.001 34.783 0.00 0.00 0.00 2.69
105 106 7.658525 ATTACCTGTTGCATAAATGGATGAA 57.341 32.000 0.00 0.00 0.00 2.57
106 107 7.201902 GGAATTACCTGTTGCATAAATGGATGA 60.202 37.037 0.00 0.00 35.41 2.92
107 108 6.925165 GGAATTACCTGTTGCATAAATGGATG 59.075 38.462 0.00 0.00 35.41 3.51
108 109 6.239008 CGGAATTACCTGTTGCATAAATGGAT 60.239 38.462 0.00 0.00 36.31 3.41
109 110 5.067153 CGGAATTACCTGTTGCATAAATGGA 59.933 40.000 0.00 0.00 36.31 3.41
110 111 5.280945 CGGAATTACCTGTTGCATAAATGG 58.719 41.667 0.00 0.00 36.31 3.16
111 112 5.067153 TCCGGAATTACCTGTTGCATAAATG 59.933 40.000 0.00 0.00 36.31 2.32
112 113 5.067283 GTCCGGAATTACCTGTTGCATAAAT 59.933 40.000 5.23 0.00 36.31 1.40
113 114 4.396790 GTCCGGAATTACCTGTTGCATAAA 59.603 41.667 5.23 0.00 36.31 1.40
114 115 3.942748 GTCCGGAATTACCTGTTGCATAA 59.057 43.478 5.23 0.00 36.31 1.90
115 116 3.537580 GTCCGGAATTACCTGTTGCATA 58.462 45.455 5.23 0.00 36.31 3.14
116 117 2.365582 GTCCGGAATTACCTGTTGCAT 58.634 47.619 5.23 0.00 36.31 3.96
117 118 1.816074 GTCCGGAATTACCTGTTGCA 58.184 50.000 5.23 0.00 36.31 4.08
118 119 0.725117 CGTCCGGAATTACCTGTTGC 59.275 55.000 5.23 0.00 36.31 4.17
119 120 1.066716 TCCGTCCGGAATTACCTGTTG 60.067 52.381 5.23 0.00 42.05 3.33
120 121 1.206371 CTCCGTCCGGAATTACCTGTT 59.794 52.381 5.23 0.00 44.66 3.16
121 122 0.822164 CTCCGTCCGGAATTACCTGT 59.178 55.000 5.23 0.00 44.66 4.00
122 123 0.104304 CCTCCGTCCGGAATTACCTG 59.896 60.000 5.23 0.00 44.66 4.00
123 124 1.047034 CCCTCCGTCCGGAATTACCT 61.047 60.000 5.23 0.00 44.66 3.08
124 125 1.044790 TCCCTCCGTCCGGAATTACC 61.045 60.000 5.23 0.00 44.66 2.85
125 126 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
126 127 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
127 128 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
128 129 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.00 44.66 3.01
129 130 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
130 131 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
131 132 1.041447 AACATACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
132 133 0.384669 GAACATACTCCCTCCGTCCG 59.615 60.000 0.00 0.00 0.00 4.79
133 134 0.751452 GGAACATACTCCCTCCGTCC 59.249 60.000 0.00 0.00 0.00 4.79
134 135 1.481871 TGGAACATACTCCCTCCGTC 58.518 55.000 0.00 0.00 34.22 4.79
135 136 1.946984 TTGGAACATACTCCCTCCGT 58.053 50.000 0.00 0.00 39.30 4.69
136 137 3.270877 CTTTTGGAACATACTCCCTCCG 58.729 50.000 0.00 0.00 39.30 4.63
137 138 4.262617 GACTTTTGGAACATACTCCCTCC 58.737 47.826 0.00 0.00 39.30 4.30
138 139 4.019231 AGGACTTTTGGAACATACTCCCTC 60.019 45.833 0.00 0.00 39.30 4.30
139 140 3.916989 AGGACTTTTGGAACATACTCCCT 59.083 43.478 0.00 0.00 39.30 4.20
140 141 4.262617 GAGGACTTTTGGAACATACTCCC 58.737 47.826 0.00 0.00 39.30 4.30
141 142 4.906618 TGAGGACTTTTGGAACATACTCC 58.093 43.478 0.00 0.00 39.30 3.85
142 143 6.173339 TGATGAGGACTTTTGGAACATACTC 58.827 40.000 0.00 0.00 39.30 2.59
143 144 6.126863 TGATGAGGACTTTTGGAACATACT 57.873 37.500 0.00 0.00 39.30 2.12
144 145 6.431234 AGTTGATGAGGACTTTTGGAACATAC 59.569 38.462 0.00 0.00 39.30 2.39
159 160 6.032094 GTGTTCATAATTGCAGTTGATGAGG 58.968 40.000 4.47 0.00 0.00 3.86
164 165 6.631971 TTGAGTGTTCATAATTGCAGTTGA 57.368 33.333 4.47 0.00 32.27 3.18
168 169 4.860907 GGCTTTGAGTGTTCATAATTGCAG 59.139 41.667 0.00 0.00 32.27 4.41
177 178 2.438021 ACTAGGTGGCTTTGAGTGTTCA 59.562 45.455 0.00 0.00 0.00 3.18
180 181 3.507411 TCTACTAGGTGGCTTTGAGTGT 58.493 45.455 0.00 0.00 0.00 3.55
184 185 3.306780 GCAACTCTACTAGGTGGCTTTGA 60.307 47.826 0.00 0.00 43.74 2.69
185 186 3.003480 GCAACTCTACTAGGTGGCTTTG 58.997 50.000 0.00 0.00 43.74 2.77
186 187 3.336138 GCAACTCTACTAGGTGGCTTT 57.664 47.619 0.00 0.00 43.74 3.51
231 232 4.096532 TGAACCAAACGAAATTGCAGTACA 59.903 37.500 0.00 0.00 0.00 2.90
254 255 8.530311 TGGAATGCATGTGAATTACTAATGTTT 58.470 29.630 0.00 0.00 0.00 2.83
263 264 9.451002 AAATTTTCATGGAATGCATGTGAATTA 57.549 25.926 20.62 1.99 46.21 1.40
268 269 6.149640 TCCAAAATTTTCATGGAATGCATGTG 59.850 34.615 14.23 3.81 46.21 3.21
277 278 7.209475 GTGTCTTCTTCCAAAATTTTCATGGA 58.791 34.615 6.06 6.06 41.36 3.41
375 396 8.723311 CACAACATCAAAATTATCAAGCCAAAT 58.277 29.630 0.00 0.00 0.00 2.32
422 443 8.529424 AAGATCCATGACATGTGAATTATTGT 57.471 30.769 14.26 0.00 0.00 2.71
423 444 9.811995 AAAAGATCCATGACATGTGAATTATTG 57.188 29.630 14.26 0.00 0.00 1.90
492 520 5.008316 GCGTCCCTTTCGTCCAAAATATATT 59.992 40.000 0.00 0.00 0.00 1.28
534 562 9.891828 TTCGTTTATATGTTCAATAATGCATCC 57.108 29.630 0.00 0.00 0.00 3.51
618 646 7.630242 ACGTCAATTAATGTGGATCAGATTT 57.370 32.000 0.00 0.00 30.18 2.17
619 647 7.475015 CAACGTCAATTAATGTGGATCAGATT 58.525 34.615 0.00 0.00 32.25 2.40
620 648 6.458751 GCAACGTCAATTAATGTGGATCAGAT 60.459 38.462 0.00 0.00 0.00 2.90
623 651 4.699735 AGCAACGTCAATTAATGTGGATCA 59.300 37.500 0.00 0.00 0.00 2.92
654 682 4.873817 TCACGCTGCTTTAGTACAAAGTA 58.126 39.130 14.90 11.41 0.00 2.24
657 696 5.682943 AATTCACGCTGCTTTAGTACAAA 57.317 34.783 0.00 0.00 0.00 2.83
670 709 4.510340 GTCCGGTTCATATTAATTCACGCT 59.490 41.667 0.00 0.00 0.00 5.07
688 727 5.005394 CAGACAAAACATATACTTCGTCCGG 59.995 44.000 0.00 0.00 0.00 5.14
695 734 7.744087 TTGCTGTCAGACAAAACATATACTT 57.256 32.000 4.41 0.00 0.00 2.24
696 735 7.445402 AGTTTGCTGTCAGACAAAACATATACT 59.555 33.333 23.73 14.16 37.50 2.12
697 736 7.584987 AGTTTGCTGTCAGACAAAACATATAC 58.415 34.615 23.73 12.81 37.50 1.47
698 737 7.744087 AGTTTGCTGTCAGACAAAACATATA 57.256 32.000 23.73 1.83 37.50 0.86
699 738 6.639632 AGTTTGCTGTCAGACAAAACATAT 57.360 33.333 23.73 8.56 37.50 1.78
700 739 6.264832 CAAGTTTGCTGTCAGACAAAACATA 58.735 36.000 23.73 9.19 37.50 2.29
701 740 4.989279 AGTTTGCTGTCAGACAAAACAT 57.011 36.364 23.73 12.10 37.50 2.71
702 741 4.484236 CAAGTTTGCTGTCAGACAAAACA 58.516 39.130 23.73 12.79 37.50 2.83
717 756 3.378112 TGGTCAGTCTCTTTGCAAGTTTG 59.622 43.478 0.00 0.00 0.00 2.93
718 757 3.620488 TGGTCAGTCTCTTTGCAAGTTT 58.380 40.909 0.00 0.00 0.00 2.66
719 758 3.281727 TGGTCAGTCTCTTTGCAAGTT 57.718 42.857 0.00 0.00 0.00 2.66
720 759 3.281727 TTGGTCAGTCTCTTTGCAAGT 57.718 42.857 0.00 0.00 0.00 3.16
721 760 3.378112 TGTTTGGTCAGTCTCTTTGCAAG 59.622 43.478 0.00 0.00 0.00 4.01
722 761 3.351740 TGTTTGGTCAGTCTCTTTGCAA 58.648 40.909 0.00 0.00 0.00 4.08
723 762 2.997980 TGTTTGGTCAGTCTCTTTGCA 58.002 42.857 0.00 0.00 0.00 4.08
724 763 4.574599 AATGTTTGGTCAGTCTCTTTGC 57.425 40.909 0.00 0.00 0.00 3.68
725 764 7.479980 TGTTAAATGTTTGGTCAGTCTCTTTG 58.520 34.615 0.00 0.00 0.00 2.77
726 765 7.639113 TGTTAAATGTTTGGTCAGTCTCTTT 57.361 32.000 0.00 0.00 0.00 2.52
727 766 7.651808 CATGTTAAATGTTTGGTCAGTCTCTT 58.348 34.615 0.00 0.00 0.00 2.85
728 767 6.294176 GCATGTTAAATGTTTGGTCAGTCTCT 60.294 38.462 0.00 0.00 0.00 3.10
729 768 5.858581 GCATGTTAAATGTTTGGTCAGTCTC 59.141 40.000 0.00 0.00 0.00 3.36
730 769 5.278957 GGCATGTTAAATGTTTGGTCAGTCT 60.279 40.000 0.00 0.00 0.00 3.24
740 779 8.790718 TGCAAATAAAATGGCATGTTAAATGTT 58.209 25.926 13.85 1.66 0.00 2.71
742 781 9.622004 TTTGCAAATAAAATGGCATGTTAAATG 57.378 25.926 13.85 15.12 35.98 2.32
798 837 4.525912 AGAACAAGGTTGAATGAATGGC 57.474 40.909 0.00 0.00 0.00 4.40
825 864 3.314080 TGCTAAAGAAACAACAACCTCGG 59.686 43.478 0.00 0.00 0.00 4.63
826 865 4.545823 TGCTAAAGAAACAACAACCTCG 57.454 40.909 0.00 0.00 0.00 4.63
827 866 5.831997 ACATGCTAAAGAAACAACAACCTC 58.168 37.500 0.00 0.00 0.00 3.85
948 991 2.902705 ACTGTCCGTTGTGCTAAAGA 57.097 45.000 0.00 0.00 0.00 2.52
961 1004 4.499037 GGTGTCACCAAATTAACTGTCC 57.501 45.455 17.59 0.00 38.42 4.02
1008 1051 4.208632 GCACCGAGCAATAGCACT 57.791 55.556 0.00 0.00 45.49 4.40
1023 1066 4.141181 AGGTTCAGCAGGATTATAATGGCA 60.141 41.667 1.78 0.00 0.00 4.92
1027 1070 4.202357 TGCGAGGTTCAGCAGGATTATAAT 60.202 41.667 0.00 0.00 38.59 1.28
1039 1082 3.443099 TGACATAGATGCGAGGTTCAG 57.557 47.619 0.00 0.00 0.00 3.02
1079 1122 0.961019 ACCGCAATGTGTTCTGCATT 59.039 45.000 0.00 0.00 38.52 3.56
1107 1150 2.938428 TGCCAAATGGGTAGGGAATT 57.062 45.000 0.90 0.00 39.65 2.17
1140 1183 3.676091 GAACCTTTGTTCGATGGCG 57.324 52.632 0.00 0.00 41.35 5.69
1175 1218 2.864946 CTCTCAATTCCATCAGCAGTCG 59.135 50.000 0.00 0.00 0.00 4.18
1181 1224 2.723322 TGGCCTCTCAATTCCATCAG 57.277 50.000 3.32 0.00 0.00 2.90
1236 1279 2.511600 CTGGATTGACCGCGGGAC 60.512 66.667 31.76 22.80 42.61 4.46
1295 1338 4.424842 AGGGTGCAAATCCATTTTTCCTA 58.575 39.130 0.00 0.00 0.00 2.94
1298 1341 3.752747 CCAAGGGTGCAAATCCATTTTTC 59.247 43.478 0.00 0.00 0.00 2.29
1313 1356 5.005628 TGCTAAGTAAAAATCCCAAGGGT 57.994 39.130 4.80 0.00 36.47 4.34
1353 1396 5.163854 GCTTATGAACTTGTTATGCACGTCT 60.164 40.000 0.00 0.00 0.00 4.18
1461 1504 1.891150 CAAGAGCCATTTGCCAGTTCT 59.109 47.619 0.00 0.00 42.71 3.01
1692 1735 2.113986 GCCCAGTCAAGCACCACT 59.886 61.111 0.00 0.00 0.00 4.00
1733 1776 1.714794 AGACATGTTTCTTCTCGCCG 58.285 50.000 0.00 0.00 0.00 6.46
1740 1783 6.446781 CATGCATAGGAAGACATGTTTCTT 57.553 37.500 0.00 0.00 38.60 2.52
1770 1813 1.011242 CACGCACACTGTGTTTCCG 60.011 57.895 11.40 15.66 39.36 4.30
1813 1856 1.480545 TCCGCTAGAGCAGTTGCATAA 59.519 47.619 6.90 0.00 45.16 1.90
1890 1933 8.619146 AAATGCTACACATGAAAATTCATACG 57.381 30.769 8.24 5.61 45.62 3.06
1916 2120 4.914177 TTGCATGCATATATGAGAGGGA 57.086 40.909 23.37 0.00 0.00 4.20
1952 2158 5.712152 AACCCTTACTTTGCATTTCTCTG 57.288 39.130 0.00 0.00 0.00 3.35
2066 2272 7.768240 ACGATTTGTTCTCCTTTTACAGTTTT 58.232 30.769 0.00 0.00 0.00 2.43
2071 2277 8.786826 ATATGACGATTTGTTCTCCTTTTACA 57.213 30.769 0.00 0.00 0.00 2.41
2072 2278 9.704098 GAATATGACGATTTGTTCTCCTTTTAC 57.296 33.333 0.00 0.00 0.00 2.01
2088 2294 5.105513 TGAGTACAAGGCTTGAATATGACGA 60.106 40.000 32.50 9.83 0.00 4.20
2153 2360 6.882610 TCAAGATGCAAGACAAGTACAATT 57.117 33.333 0.00 0.00 0.00 2.32
2157 2364 5.091431 GCATTCAAGATGCAAGACAAGTAC 58.909 41.667 6.15 0.00 44.00 2.73
2257 2968 6.917533 AGAAATGAGTTGCAATTCTACTTGG 58.082 36.000 20.91 0.00 43.24 3.61
2344 3055 9.507329 TTTGGATGTAAGATAAGAAGGATATGC 57.493 33.333 0.00 0.00 0.00 3.14
2351 3062 9.092876 GTGAGACTTTGGATGTAAGATAAGAAG 57.907 37.037 0.00 0.00 0.00 2.85
2367 3102 3.244700 ACCTGATCCCAAGTGAGACTTTG 60.245 47.826 0.00 0.00 36.03 2.77
2393 3128 3.181476 ACATCTGCAGTGAAAACCCAAAC 60.181 43.478 14.67 0.00 0.00 2.93
2399 3137 5.112220 TCATTGACATCTGCAGTGAAAAC 57.888 39.130 14.67 2.85 30.47 2.43
2449 3187 3.261580 GTTTTGGCAAGTTGCAGACTTT 58.738 40.909 28.10 0.00 46.34 2.66
2488 3226 3.161866 ACCGCCAAAAGGACATAAACAT 58.838 40.909 0.00 0.00 0.00 2.71
2656 4177 9.076596 GTTGCTCTCACCAAAACATAAATATTC 57.923 33.333 0.00 0.00 0.00 1.75
2689 4213 2.615240 GCCGGCCCAATGAAAAGAAAAT 60.615 45.455 18.11 0.00 0.00 1.82
2705 4230 0.107654 AACCTCTCTACATTGCCGGC 60.108 55.000 22.73 22.73 0.00 6.13
2731 4343 1.153745 GGCAGTCGGCTAGTGACAG 60.154 63.158 16.32 11.04 44.01 3.51
2789 4413 0.734889 GATTCAGTGGACCAATGCCG 59.265 55.000 17.13 0.00 29.02 5.69
2966 6395 5.529430 TCGGATCAACAAAGCTGAAACTAAA 59.471 36.000 0.00 0.00 0.00 1.85
2985 6414 0.328258 CCTTGGTTCCACCTTCGGAT 59.672 55.000 0.00 0.00 39.58 4.18
3013 6442 1.425412 GTGCGCCTTTCGAACTCTAA 58.575 50.000 4.18 0.00 43.44 2.10
3048 6477 4.214986 TCAGTTGTTCCAAGACAAGACA 57.785 40.909 0.00 0.00 39.97 3.41
3071 6500 2.488204 TGGCACTTTCATCGGATGAA 57.512 45.000 25.39 25.39 46.77 2.57
3308 6737 6.705825 AGCATCCAAAAAGTTTTACCACATTC 59.294 34.615 0.24 0.00 0.00 2.67
3427 6859 3.123804 CGATCGTCCCATGTTAAAGAGG 58.876 50.000 7.03 0.00 0.00 3.69
3656 12863 3.637229 CTGTGTGGTAATACTCGGGATCT 59.363 47.826 0.00 0.00 0.00 2.75
4354 13747 1.830477 AGAGAGATCACAACAGGGAGC 59.170 52.381 0.00 0.00 0.00 4.70
4444 13837 7.971168 CGAGACTATTAATTCGGCTATCTCAAT 59.029 37.037 0.00 0.00 32.21 2.57
4488 14086 8.716646 AGATCACATCGTTACAATCACATTAA 57.283 30.769 0.00 0.00 0.00 1.40
4519 14117 6.487689 AACTTCACTTGATAAGCTTACTGC 57.512 37.500 8.70 2.17 43.29 4.40
4662 14261 6.072728 TGTTGTTCAGGCATGTCATTAACTAC 60.073 38.462 0.00 8.31 0.00 2.73
4663 14262 6.000840 TGTTGTTCAGGCATGTCATTAACTA 58.999 36.000 0.00 0.00 0.00 2.24
4664 14263 4.826733 TGTTGTTCAGGCATGTCATTAACT 59.173 37.500 0.00 0.00 0.00 2.24
4665 14264 5.119931 TGTTGTTCAGGCATGTCATTAAC 57.880 39.130 0.00 1.21 0.00 2.01
4730 14329 2.527497 TCATTTTGATGCAGAGGCCAA 58.473 42.857 5.01 0.00 40.13 4.52
4756 14355 9.722184 CTGATGAATAAACATAGAGATGGATGT 57.278 33.333 0.00 0.00 37.39 3.06
4759 14358 9.152327 ACTCTGATGAATAAACATAGAGATGGA 57.848 33.333 0.00 0.00 37.39 3.41
4788 14389 6.205270 GGGTTGATCTTTGCATTCATTTTGTT 59.795 34.615 0.00 0.00 0.00 2.83
4808 14409 0.821711 TCGAAGGTGGCTTTGGGTTG 60.822 55.000 0.00 0.00 0.00 3.77
4811 14412 1.675641 CCTCGAAGGTGGCTTTGGG 60.676 63.158 0.00 0.00 0.00 4.12
4812 14413 2.335712 GCCTCGAAGGTGGCTTTGG 61.336 63.158 6.18 0.00 42.31 3.28
4854 14455 3.807209 GCGGTCAGGGCACATCTTTATAT 60.807 47.826 0.00 0.00 0.00 0.86
4877 14478 7.124901 ACACTGGATTAGATAGTGACAGTTGAT 59.875 37.037 10.24 0.00 43.35 2.57
4885 14486 5.766590 TGAGGACACTGGATTAGATAGTGA 58.233 41.667 10.24 0.00 43.35 3.41
4916 14517 1.672356 CTCAACTTGTCAGGCGGGG 60.672 63.158 0.00 0.00 0.00 5.73
4924 14525 2.667724 CGGTCGGTACTCTCAACTTGTC 60.668 54.545 0.00 0.00 0.00 3.18
4941 14543 0.167689 GTGAGACGTCTACACCGGTC 59.832 60.000 25.21 11.80 0.00 4.79
4980 14582 4.708968 GCGGCGGATCCTAGAGCG 62.709 72.222 9.78 3.87 0.00 5.03
4998 14600 3.694364 CCCTCATGAAGATGGGACG 57.306 57.895 11.55 0.00 37.05 4.79
5011 14613 3.522759 TGTAACATTACCTGACCCCTCA 58.477 45.455 0.00 0.00 32.72 3.86
5037 14639 4.561213 GCATTTACGTTTGTCCAAATAGCC 59.439 41.667 0.00 0.00 32.36 3.93
5043 14645 3.128764 TGTGTGCATTTACGTTTGTCCAA 59.871 39.130 0.00 0.00 0.00 3.53
5082 14684 8.511748 AGTATAGGAGGATGGTTAAATCACAT 57.488 34.615 0.00 0.00 0.00 3.21
5141 14743 1.163554 GCCTTCTTTGTGAGCTCTGG 58.836 55.000 16.19 5.45 0.00 3.86


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

AutoCloner maintained by Alex Coulton.