Multiple sequence alignment - TraesCS4D01G002600

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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 TraesCS4D01G002600 chr4D 100.000 2735 0 0 1 2735 1312597 1309863 0.000000e+00 5051
1 TraesCS4D01G002600 chr4D 100.000 146 0 0 1 146 18411806 18411661 1.250000e-68 270
2 TraesCS4D01G002600 chr4D 100.000 146 0 0 1 146 323071633 323071778 1.250000e-68 270
3 TraesCS4D01G002600 chr4D 98.013 151 3 0 1 151 2387046 2386896 2.090000e-66 263
4 TraesCS4D01G002600 chr4D 75.394 508 97 20 1237 1726 1333532 1333035 1.270000e-53 220
5 TraesCS4D01G002600 chr4D 73.231 650 123 28 1237 1847 1337999 1337362 3.600000e-44 189
6 TraesCS4D01G002600 chr4A 95.433 1248 56 1 861 2108 603469064 603470310 0.000000e+00 1988
7 TraesCS4D01G002600 chr4A 95.477 1238 55 1 866 2103 603389945 603388709 0.000000e+00 1975
8 TraesCS4D01G002600 chr4B 93.276 1279 83 2 860 2138 1767768 1766493 0.000000e+00 1882
9 TraesCS4D01G002600 chr4B 87.910 488 49 4 2140 2619 1761496 1761011 1.420000e-157 566
10 TraesCS4D01G002600 chr4B 93.548 93 4 1 2643 2733 1761015 1760923 1.320000e-28 137
11 TraesCS4D01G002600 chr6D 97.568 699 16 1 162 859 385683502 385682804 0.000000e+00 1195
12 TraesCS4D01G002600 chr6D 97.425 699 17 1 162 859 385674013 385673315 0.000000e+00 1190
13 TraesCS4D01G002600 chr6D 99.315 146 1 0 1 146 77561843 77561698 5.810000e-67 265
14 TraesCS4D01G002600 chr6D 99.315 146 1 0 1 146 94655707 94655852 5.810000e-67 265
15 TraesCS4D01G002600 chr1D 97.425 699 17 1 162 859 68648105 68647407 0.000000e+00 1190
16 TraesCS4D01G002600 chr1D 97.282 699 18 1 162 859 435956678 435955980 0.000000e+00 1184
17 TraesCS4D01G002600 chr1D 97.143 700 19 1 162 860 68638495 68637796 0.000000e+00 1181
18 TraesCS4D01G002600 chr5D 97.286 700 18 1 162 860 3848305 3847606 0.000000e+00 1186
19 TraesCS4D01G002600 chr5D 96.624 711 22 2 162 870 448968736 448968026 0.000000e+00 1179
20 TraesCS4D01G002600 chr5D 100.000 146 0 0 1 146 513029724 513029579 1.250000e-68 270
21 TraesCS4D01G002600 chr5D 98.013 151 3 0 1 151 391171198 391171348 2.090000e-66 263
22 TraesCS4D01G002600 chr2D 97.282 699 17 2 162 859 549804628 549805325 0.000000e+00 1184
23 TraesCS4D01G002600 chr2D 81.197 234 30 8 860 1090 426434399 426434177 2.800000e-40 176
24 TraesCS4D01G002600 chr7D 97.013 703 20 1 162 863 508867496 508866794 0.000000e+00 1181
25 TraesCS4D01G002600 chr3D 100.000 146 0 0 1 146 41884332 41884477 1.250000e-68 270
26 TraesCS4D01G002600 chr3D 98.013 151 3 0 1 151 495665779 495665629 2.090000e-66 263
27 TraesCS4D01G002600 chr2B 81.197 234 30 8 860 1090 503453504 503453282 2.800000e-40 176
28 TraesCS4D01G002600 chr2A 81.223 229 30 7 860 1086 562508560 562508777 3.620000e-39 172
29 TraesCS4D01G002600 chr5A 86.335 161 14 4 2501 2653 171204193 171204353 4.680000e-38 169
30 TraesCS4D01G002600 chr5A 84.177 158 17 3 2501 2650 171174678 171174835 2.190000e-31 147


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 TraesCS4D01G002600 chr4D 1309863 1312597 2734 True 5051.0 5051 100.0000 1 2735 1 chr4D.!!$R1 2734
1 TraesCS4D01G002600 chr4D 1333035 1337999 4964 True 204.5 220 74.3125 1237 1847 2 chr4D.!!$R4 610
2 TraesCS4D01G002600 chr4A 603469064 603470310 1246 False 1988.0 1988 95.4330 861 2108 1 chr4A.!!$F1 1247
3 TraesCS4D01G002600 chr4A 603388709 603389945 1236 True 1975.0 1975 95.4770 866 2103 1 chr4A.!!$R1 1237
4 TraesCS4D01G002600 chr4B 1766493 1767768 1275 True 1882.0 1882 93.2760 860 2138 1 chr4B.!!$R1 1278
5 TraesCS4D01G002600 chr4B 1760923 1761496 573 True 351.5 566 90.7290 2140 2733 2 chr4B.!!$R2 593
6 TraesCS4D01G002600 chr6D 385682804 385683502 698 True 1195.0 1195 97.5680 162 859 1 chr6D.!!$R3 697
7 TraesCS4D01G002600 chr6D 385673315 385674013 698 True 1190.0 1190 97.4250 162 859 1 chr6D.!!$R2 697
8 TraesCS4D01G002600 chr1D 68647407 68648105 698 True 1190.0 1190 97.4250 162 859 1 chr1D.!!$R2 697
9 TraesCS4D01G002600 chr1D 435955980 435956678 698 True 1184.0 1184 97.2820 162 859 1 chr1D.!!$R3 697
10 TraesCS4D01G002600 chr1D 68637796 68638495 699 True 1181.0 1181 97.1430 162 860 1 chr1D.!!$R1 698
11 TraesCS4D01G002600 chr5D 3847606 3848305 699 True 1186.0 1186 97.2860 162 860 1 chr5D.!!$R1 698
12 TraesCS4D01G002600 chr5D 448968026 448968736 710 True 1179.0 1179 96.6240 162 870 1 chr5D.!!$R2 708
13 TraesCS4D01G002600 chr2D 549804628 549805325 697 False 1184.0 1184 97.2820 162 859 1 chr2D.!!$F1 697
14 TraesCS4D01G002600 chr7D 508866794 508867496 702 True 1181.0 1181 97.0130 162 863 1 chr7D.!!$R1 701

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
147 148 0.039074 CTTCTTGACGTCAGCGACCT 60.039 55.000 19.11 0.00 42.00 3.85 F
151 152 0.520404 TTGACGTCAGCGACCTAGTC 59.480 55.000 19.11 5.95 42.00 2.59 F
903 907 2.361357 AGGCTCGCCTACGTCACT 60.361 61.111 9.06 0.00 46.14 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1066 0.459899 CGATGATGACTGGTTCCCGA 59.540 55.0 0.0 0.0 0.0 5.14 R
1519 1540 1.051812 ATGCCTTGATCCCTACCTCG 58.948 55.0 0.0 0.0 0.0 4.63 R
2635 6415 0.108138 GCGTCTAGTGTTGGATGGCT 60.108 55.0 0.0 0.0 0.0 4.75 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
24 25 5.122328 GTGGATACTTAACACGCTTAACG 57.878 43.478 0.00 0.00 43.61 3.18
25 26 4.858692 GTGGATACTTAACACGCTTAACGA 59.141 41.667 0.00 0.00 41.05 3.85
26 27 5.004156 GTGGATACTTAACACGCTTAACGAG 59.996 44.000 0.00 0.33 41.05 4.18
27 28 5.106197 TGGATACTTAACACGCTTAACGAGA 60.106 40.000 0.00 0.00 41.05 4.04
28 29 6.405065 TGGATACTTAACACGCTTAACGAGAT 60.405 38.462 0.00 0.00 41.05 2.75
29 30 8.152118 TGGATACTTAACACGCTTAACGAGATC 61.152 40.741 0.00 0.00 41.05 2.75
40 41 6.903883 GCTTAACGAGATCTTGGTATTTGA 57.096 37.500 14.65 0.00 0.00 2.69
41 42 7.484035 GCTTAACGAGATCTTGGTATTTGAT 57.516 36.000 14.65 0.00 0.00 2.57
42 43 7.568433 GCTTAACGAGATCTTGGTATTTGATC 58.432 38.462 14.65 0.00 37.46 2.92
43 44 7.439655 GCTTAACGAGATCTTGGTATTTGATCT 59.560 37.037 14.65 4.64 46.44 2.75
44 45 8.648557 TTAACGAGATCTTGGTATTTGATCTG 57.351 34.615 14.65 5.27 44.58 2.90
45 46 6.471233 ACGAGATCTTGGTATTTGATCTGA 57.529 37.500 14.65 0.00 44.58 3.27
46 47 6.511416 ACGAGATCTTGGTATTTGATCTGAG 58.489 40.000 14.65 6.22 44.58 3.35
47 48 6.097554 ACGAGATCTTGGTATTTGATCTGAGT 59.902 38.462 14.65 6.73 44.58 3.41
48 49 6.640499 CGAGATCTTGGTATTTGATCTGAGTC 59.360 42.308 9.10 0.00 44.58 3.36
49 50 7.469870 CGAGATCTTGGTATTTGATCTGAGTCT 60.470 40.741 9.10 0.00 44.58 3.24
50 51 7.499292 AGATCTTGGTATTTGATCTGAGTCTG 58.501 38.462 0.00 0.00 43.42 3.51
51 52 5.982356 TCTTGGTATTTGATCTGAGTCTGG 58.018 41.667 0.00 0.00 0.00 3.86
52 53 4.142609 TGGTATTTGATCTGAGTCTGGC 57.857 45.455 0.00 0.00 0.00 4.85
53 54 3.118261 TGGTATTTGATCTGAGTCTGGCC 60.118 47.826 0.00 0.00 0.00 5.36
54 55 3.118261 GGTATTTGATCTGAGTCTGGCCA 60.118 47.826 4.71 4.71 0.00 5.36
55 56 3.947612 ATTTGATCTGAGTCTGGCCAT 57.052 42.857 5.51 0.00 0.00 4.40
56 57 3.726557 TTTGATCTGAGTCTGGCCATT 57.273 42.857 5.51 0.00 0.00 3.16
57 58 3.726557 TTGATCTGAGTCTGGCCATTT 57.273 42.857 5.51 0.00 0.00 2.32
58 59 2.995283 TGATCTGAGTCTGGCCATTTG 58.005 47.619 5.51 0.00 0.00 2.32
59 60 2.295885 GATCTGAGTCTGGCCATTTGG 58.704 52.381 5.51 0.00 38.53 3.28
60 61 1.067295 TCTGAGTCTGGCCATTTGGT 58.933 50.000 5.51 0.00 37.57 3.67
61 62 1.003580 TCTGAGTCTGGCCATTTGGTC 59.996 52.381 5.51 0.00 41.09 4.02
62 63 1.004044 CTGAGTCTGGCCATTTGGTCT 59.996 52.381 5.51 0.00 41.34 3.85
63 64 2.237143 CTGAGTCTGGCCATTTGGTCTA 59.763 50.000 5.51 0.00 41.34 2.59
64 65 2.846206 TGAGTCTGGCCATTTGGTCTAT 59.154 45.455 5.51 0.00 41.34 1.98
65 66 4.037222 TGAGTCTGGCCATTTGGTCTATA 58.963 43.478 5.51 0.00 41.34 1.31
66 67 4.141711 TGAGTCTGGCCATTTGGTCTATAC 60.142 45.833 5.51 0.00 41.34 1.47
67 68 3.131396 GTCTGGCCATTTGGTCTATACG 58.869 50.000 5.51 0.00 41.34 3.06
68 69 1.873591 CTGGCCATTTGGTCTATACGC 59.126 52.381 5.51 0.00 41.34 4.42
69 70 1.210722 TGGCCATTTGGTCTATACGCA 59.789 47.619 0.00 0.00 41.34 5.24
70 71 1.602377 GGCCATTTGGTCTATACGCAC 59.398 52.381 0.00 0.00 36.72 5.34
71 72 2.561569 GCCATTTGGTCTATACGCACT 58.438 47.619 0.00 0.00 37.57 4.40
72 73 3.493699 GGCCATTTGGTCTATACGCACTA 60.494 47.826 0.00 0.00 36.72 2.74
73 74 3.741344 GCCATTTGGTCTATACGCACTAG 59.259 47.826 0.00 0.00 37.57 2.57
74 75 3.741344 CCATTTGGTCTATACGCACTAGC 59.259 47.826 0.00 0.00 37.42 3.42
75 76 3.447918 TTTGGTCTATACGCACTAGCC 57.552 47.619 0.00 0.00 37.52 3.93
76 77 2.061509 TGGTCTATACGCACTAGCCA 57.938 50.000 0.00 0.00 37.52 4.75
77 78 2.594131 TGGTCTATACGCACTAGCCAT 58.406 47.619 0.00 0.00 37.52 4.40
78 79 2.557056 TGGTCTATACGCACTAGCCATC 59.443 50.000 0.00 0.00 37.52 3.51
79 80 2.820787 GGTCTATACGCACTAGCCATCT 59.179 50.000 0.00 0.00 37.52 2.90
80 81 4.008330 GGTCTATACGCACTAGCCATCTA 58.992 47.826 0.00 0.00 37.52 1.98
81 82 4.142643 GGTCTATACGCACTAGCCATCTAC 60.143 50.000 0.00 0.00 37.52 2.59
82 83 2.991434 ATACGCACTAGCCATCTACG 57.009 50.000 0.00 0.00 37.52 3.51
83 84 0.309922 TACGCACTAGCCATCTACGC 59.690 55.000 0.00 0.00 37.52 4.42
84 85 2.011349 CGCACTAGCCATCTACGCG 61.011 63.158 3.53 3.53 36.16 6.01
85 86 1.661821 GCACTAGCCATCTACGCGG 60.662 63.158 12.47 0.00 33.58 6.46
86 87 1.007271 CACTAGCCATCTACGCGGG 60.007 63.158 12.47 1.71 0.00 6.13
87 88 1.152819 ACTAGCCATCTACGCGGGA 60.153 57.895 12.47 8.98 0.00 5.14
88 89 1.173444 ACTAGCCATCTACGCGGGAG 61.173 60.000 12.47 7.61 0.00 4.30
89 90 1.152819 TAGCCATCTACGCGGGAGT 60.153 57.895 12.47 0.00 0.00 3.85
90 91 0.109153 TAGCCATCTACGCGGGAGTA 59.891 55.000 12.47 0.00 0.00 2.59
91 92 1.173444 AGCCATCTACGCGGGAGTAG 61.173 60.000 12.47 2.66 43.97 2.57
92 93 1.453762 GCCATCTACGCGGGAGTAGT 61.454 60.000 12.47 0.00 43.31 2.73
93 94 1.030457 CCATCTACGCGGGAGTAGTT 58.970 55.000 12.47 0.00 43.31 2.24
94 95 2.224606 CCATCTACGCGGGAGTAGTTA 58.775 52.381 12.47 0.00 43.31 2.24
95 96 2.818432 CCATCTACGCGGGAGTAGTTAT 59.182 50.000 12.47 0.00 43.31 1.89
96 97 3.366070 CCATCTACGCGGGAGTAGTTATG 60.366 52.174 12.47 6.51 43.31 1.90
97 98 2.224606 TCTACGCGGGAGTAGTTATGG 58.775 52.381 12.47 0.00 43.31 2.74
98 99 1.268899 CTACGCGGGAGTAGTTATGGG 59.731 57.143 12.47 0.00 39.27 4.00
99 100 0.685458 ACGCGGGAGTAGTTATGGGT 60.685 55.000 12.47 0.00 0.00 4.51
100 101 1.321474 CGCGGGAGTAGTTATGGGTA 58.679 55.000 0.00 0.00 0.00 3.69
101 102 1.891150 CGCGGGAGTAGTTATGGGTAT 59.109 52.381 0.00 0.00 0.00 2.73
102 103 2.094854 CGCGGGAGTAGTTATGGGTATC 60.095 54.545 0.00 0.00 0.00 2.24
103 104 2.233186 GCGGGAGTAGTTATGGGTATCC 59.767 54.545 0.00 0.00 0.00 2.59
104 105 2.830321 CGGGAGTAGTTATGGGTATCCC 59.170 54.545 0.00 0.00 45.71 3.85
113 114 4.580551 GGGTATCCCGGCGTCGTG 62.581 72.222 9.28 0.00 32.13 4.35
114 115 4.580551 GGTATCCCGGCGTCGTGG 62.581 72.222 9.28 9.84 33.95 4.94
115 116 3.830192 GTATCCCGGCGTCGTGGT 61.830 66.667 9.28 0.00 33.95 4.16
116 117 2.124362 TATCCCGGCGTCGTGGTA 60.124 61.111 9.28 0.00 33.95 3.25
117 118 1.529010 TATCCCGGCGTCGTGGTAT 60.529 57.895 9.28 7.69 33.95 2.73
118 119 1.518056 TATCCCGGCGTCGTGGTATC 61.518 60.000 9.28 0.00 33.95 2.24
119 120 3.829044 CCCGGCGTCGTGGTATCA 61.829 66.667 9.28 0.00 33.95 2.15
120 121 2.278596 CCGGCGTCGTGGTATCAG 60.279 66.667 9.28 0.00 33.95 2.90
121 122 2.954868 CGGCGTCGTGGTATCAGC 60.955 66.667 0.00 0.00 0.00 4.26
122 123 2.585247 GGCGTCGTGGTATCAGCC 60.585 66.667 0.00 0.00 37.61 4.85
123 124 2.954868 GCGTCGTGGTATCAGCCG 60.955 66.667 0.00 0.00 0.00 5.52
124 125 2.795973 CGTCGTGGTATCAGCCGA 59.204 61.111 0.00 0.00 0.00 5.54
125 126 1.138036 CGTCGTGGTATCAGCCGAA 59.862 57.895 0.00 0.00 0.00 4.30
126 127 0.866061 CGTCGTGGTATCAGCCGAAG 60.866 60.000 0.00 0.00 0.00 3.79
127 128 1.141019 TCGTGGTATCAGCCGAAGC 59.859 57.895 0.00 0.00 40.32 3.86
128 129 1.883084 CGTGGTATCAGCCGAAGCC 60.883 63.158 0.00 0.00 41.25 4.35
129 130 1.522569 GTGGTATCAGCCGAAGCCT 59.477 57.895 0.00 0.00 41.25 4.58
130 131 0.107654 GTGGTATCAGCCGAAGCCTT 60.108 55.000 0.00 0.00 41.25 4.35
131 132 0.178068 TGGTATCAGCCGAAGCCTTC 59.822 55.000 0.00 0.00 41.25 3.46
132 133 0.466124 GGTATCAGCCGAAGCCTTCT 59.534 55.000 2.49 0.00 41.25 2.85
133 134 1.134371 GGTATCAGCCGAAGCCTTCTT 60.134 52.381 2.49 0.00 41.25 2.52
134 135 1.936547 GTATCAGCCGAAGCCTTCTTG 59.063 52.381 2.49 0.00 41.25 3.02
135 136 0.615331 ATCAGCCGAAGCCTTCTTGA 59.385 50.000 2.49 4.53 41.25 3.02
136 137 0.320771 TCAGCCGAAGCCTTCTTGAC 60.321 55.000 2.49 0.00 41.25 3.18
137 138 1.374758 AGCCGAAGCCTTCTTGACG 60.375 57.895 2.49 0.00 41.25 4.35
138 139 1.668151 GCCGAAGCCTTCTTGACGT 60.668 57.895 2.49 0.00 31.48 4.34
139 140 1.627550 GCCGAAGCCTTCTTGACGTC 61.628 60.000 9.11 9.11 31.48 4.34
140 141 0.319555 CCGAAGCCTTCTTGACGTCA 60.320 55.000 15.76 15.76 31.48 4.35
141 142 1.063806 CGAAGCCTTCTTGACGTCAG 58.936 55.000 19.11 12.86 31.48 3.51
142 143 0.793250 GAAGCCTTCTTGACGTCAGC 59.207 55.000 19.11 17.62 31.48 4.26
143 144 0.946221 AAGCCTTCTTGACGTCAGCG 60.946 55.000 19.11 13.83 44.93 5.18
144 145 1.372997 GCCTTCTTGACGTCAGCGA 60.373 57.895 19.11 15.91 42.00 4.93
145 146 1.618640 GCCTTCTTGACGTCAGCGAC 61.619 60.000 19.11 4.12 42.00 5.19
146 147 1.009389 CCTTCTTGACGTCAGCGACC 61.009 60.000 19.11 0.00 42.00 4.79
147 148 0.039074 CTTCTTGACGTCAGCGACCT 60.039 55.000 19.11 0.00 42.00 3.85
148 149 1.199327 CTTCTTGACGTCAGCGACCTA 59.801 52.381 19.11 0.60 42.00 3.08
149 150 0.803117 TCTTGACGTCAGCGACCTAG 59.197 55.000 19.11 11.38 42.00 3.02
150 151 0.522180 CTTGACGTCAGCGACCTAGT 59.478 55.000 19.11 0.00 42.00 2.57
151 152 0.520404 TTGACGTCAGCGACCTAGTC 59.480 55.000 19.11 5.95 42.00 2.59
196 197 2.381911 GGATCGCCGGGTAGGATTATA 58.618 52.381 2.18 0.00 45.00 0.98
845 849 4.390603 TGCATGATTAGTGTACGGTCAAAC 59.609 41.667 0.00 0.00 0.00 2.93
903 907 2.361357 AGGCTCGCCTACGTCACT 60.361 61.111 9.06 0.00 46.14 3.41
1096 1100 2.456577 TCATCGAGGACCAGACATCAA 58.543 47.619 0.00 0.00 0.00 2.57
1519 1540 1.413077 GTGTCTACTGGATAGGTGGGC 59.587 57.143 0.00 0.00 0.00 5.36
1578 1600 2.483889 CGGGAAATCTAGACCTTGCCTC 60.484 54.545 18.96 4.38 0.00 4.70
1646 1668 1.208293 CTGGTACTTTCTGAGGGAGGC 59.792 57.143 0.00 0.00 0.00 4.70
1721 1744 2.715005 TGCTCAACGTGCACAAGC 59.285 55.556 18.64 18.49 42.57 4.01
1731 1754 0.039798 GTGCACAAGCCATGTCACAG 60.040 55.000 13.17 0.00 41.46 3.66
1772 1802 0.246360 TGGTGACATAGTGAGCACCG 59.754 55.000 15.94 0.00 43.69 4.94
2045 2100 7.010367 GTCTGAGATGATCAATGTCTTGAGAAC 59.990 40.741 0.00 0.00 44.32 3.01
2085 2543 5.606348 ACATGGTATGTTGTGTTGGTTTT 57.394 34.783 0.00 0.00 41.63 2.43
2104 2562 5.170748 GTTTTAGTTCCCATGCTTGGATTG 58.829 41.667 19.85 3.75 46.92 2.67
2122 2580 4.153117 GGATTGTGTCTCATGTTCAGTGAC 59.847 45.833 0.00 0.00 0.00 3.67
2208 2666 2.329379 GTATAATCTTCCAGCTCGGCG 58.671 52.381 0.00 0.00 33.14 6.46
2274 4705 7.472334 AAAGCATAAATGAGTTCTTCCACAT 57.528 32.000 0.00 0.00 0.00 3.21
2326 6098 4.139038 GGTGATCCTGAGTACTACCTCTC 58.861 52.174 0.00 0.00 32.50 3.20
2327 6099 4.141344 GGTGATCCTGAGTACTACCTCTCT 60.141 50.000 0.00 0.00 32.50 3.10
2331 6103 4.846040 TCCTGAGTACTACCTCTCTGTTC 58.154 47.826 0.00 0.00 32.50 3.18
2335 6107 5.382616 TGAGTACTACCTCTCTGTTCAACA 58.617 41.667 0.00 0.00 32.50 3.33
2339 6111 5.615925 ACTACCTCTCTGTTCAACAACTT 57.384 39.130 0.00 0.00 33.17 2.66
2375 6147 5.005490 GGCACGAGTTTATACTGTAGAAAGC 59.995 44.000 7.79 7.49 33.84 3.51
2429 6208 7.245419 ACCAAAACTTATTCAACATTGTTGC 57.755 32.000 22.02 0.00 0.00 4.17
2444 6223 1.075374 TGTTGCAGGGAAGCATAGGTT 59.925 47.619 0.00 0.00 45.19 3.50
2462 6241 7.765307 CATAGGTTGCTGACAATATCTTTTGT 58.235 34.615 0.00 0.00 42.37 2.83
2467 6246 4.826733 TGCTGACAATATCTTTTGTGTGGT 59.173 37.500 0.00 0.00 39.85 4.16
2469 6248 5.048782 GCTGACAATATCTTTTGTGTGGTGA 60.049 40.000 0.00 0.00 39.85 4.02
2472 6251 6.204688 TGACAATATCTTTTGTGTGGTGAGTC 59.795 38.462 0.00 0.00 39.85 3.36
2519 6298 2.109425 AATTACGTCACCCCTTGAGC 57.891 50.000 0.00 0.00 33.71 4.26
2526 6305 1.215423 GTCACCCCTTGAGCCCATATT 59.785 52.381 0.00 0.00 33.71 1.28
2527 6306 1.494721 TCACCCCTTGAGCCCATATTC 59.505 52.381 0.00 0.00 0.00 1.75
2532 6311 2.421388 CCCTTGAGCCCATATTCGACAA 60.421 50.000 0.00 0.00 0.00 3.18
2537 6316 4.002982 TGAGCCCATATTCGACAATATGC 58.997 43.478 10.42 2.68 45.93 3.14
2548 6327 4.692228 TCGACAATATGCAGCACTATTCA 58.308 39.130 0.00 0.00 0.00 2.57
2562 6341 9.918630 GCAGCACTATTCATGGAAATAAAATAT 57.081 29.630 0.00 0.00 0.00 1.28
2594 6374 7.448748 AGTTTACACTGGAATAATTGTGTCC 57.551 36.000 0.00 0.00 41.87 4.02
2602 6382 4.457603 TGGAATAATTGTGTCCGGAAAGTG 59.542 41.667 5.23 0.00 33.87 3.16
2614 6394 1.119684 GGAAAGTGTGCCCCTTGTTT 58.880 50.000 0.00 0.00 0.00 2.83
2615 6395 2.312390 GGAAAGTGTGCCCCTTGTTTA 58.688 47.619 0.00 0.00 0.00 2.01
2616 6396 2.696187 GGAAAGTGTGCCCCTTGTTTAA 59.304 45.455 0.00 0.00 0.00 1.52
2617 6397 3.491964 GGAAAGTGTGCCCCTTGTTTAAC 60.492 47.826 0.00 0.00 0.00 2.01
2618 6398 2.445682 AGTGTGCCCCTTGTTTAACA 57.554 45.000 0.00 0.00 0.00 2.41
2619 6399 2.306847 AGTGTGCCCCTTGTTTAACAG 58.693 47.619 0.00 0.00 0.00 3.16
2620 6400 2.028876 GTGTGCCCCTTGTTTAACAGT 58.971 47.619 0.00 0.00 0.00 3.55
2621 6401 2.034179 GTGTGCCCCTTGTTTAACAGTC 59.966 50.000 0.00 0.00 0.00 3.51
2622 6402 2.092103 TGTGCCCCTTGTTTAACAGTCT 60.092 45.455 0.00 0.00 0.00 3.24
2623 6403 2.956333 GTGCCCCTTGTTTAACAGTCTT 59.044 45.455 0.00 0.00 0.00 3.01
2624 6404 2.955660 TGCCCCTTGTTTAACAGTCTTG 59.044 45.455 0.00 0.00 0.00 3.02
2625 6405 2.956333 GCCCCTTGTTTAACAGTCTTGT 59.044 45.455 0.00 0.00 39.87 3.16
2626 6406 3.004419 GCCCCTTGTTTAACAGTCTTGTC 59.996 47.826 0.00 0.00 36.23 3.18
2627 6407 3.568430 CCCCTTGTTTAACAGTCTTGTCC 59.432 47.826 0.00 0.00 36.23 4.02
2628 6408 4.204012 CCCTTGTTTAACAGTCTTGTCCA 58.796 43.478 0.00 0.00 36.23 4.02
2629 6409 4.827284 CCCTTGTTTAACAGTCTTGTCCAT 59.173 41.667 0.00 0.00 36.23 3.41
2630 6410 6.001460 CCCTTGTTTAACAGTCTTGTCCATA 58.999 40.000 0.00 0.00 36.23 2.74
2631 6411 6.072673 CCCTTGTTTAACAGTCTTGTCCATAC 60.073 42.308 0.00 0.00 36.23 2.39
2632 6412 6.072673 CCTTGTTTAACAGTCTTGTCCATACC 60.073 42.308 0.00 0.00 36.23 2.73
2633 6413 5.310451 TGTTTAACAGTCTTGTCCATACCC 58.690 41.667 0.00 0.00 36.23 3.69
2634 6414 5.163184 TGTTTAACAGTCTTGTCCATACCCA 60.163 40.000 0.00 0.00 36.23 4.51
2635 6415 5.570205 TTAACAGTCTTGTCCATACCCAA 57.430 39.130 0.00 0.00 36.23 4.12
2636 6416 3.703001 ACAGTCTTGTCCATACCCAAG 57.297 47.619 0.00 0.00 39.50 3.61
2637 6417 2.290323 ACAGTCTTGTCCATACCCAAGC 60.290 50.000 0.00 0.00 38.33 4.01
2638 6418 1.282157 AGTCTTGTCCATACCCAAGCC 59.718 52.381 0.00 0.00 38.33 4.35
2639 6419 1.004277 GTCTTGTCCATACCCAAGCCA 59.996 52.381 0.00 0.00 38.33 4.75
2640 6420 1.922447 TCTTGTCCATACCCAAGCCAT 59.078 47.619 0.00 0.00 38.33 4.40
2641 6421 2.092429 TCTTGTCCATACCCAAGCCATC 60.092 50.000 0.00 0.00 38.33 3.51
2653 6433 2.002586 CAAGCCATCCAACACTAGACG 58.997 52.381 0.00 0.00 0.00 4.18
2661 6441 2.094700 TCCAACACTAGACGCTTAGCAG 60.095 50.000 4.70 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.858692 TCGTTAAGCGTGTTAAGTATCCAC 59.141 41.667 0.00 0.00 42.13 4.02
3 4 5.058149 TCGTTAAGCGTGTTAAGTATCCA 57.942 39.130 0.00 0.00 42.13 3.41
4 5 5.335127 TCTCGTTAAGCGTGTTAAGTATCC 58.665 41.667 0.00 0.00 42.13 2.59
5 6 6.911511 AGATCTCGTTAAGCGTGTTAAGTATC 59.088 38.462 0.00 0.00 42.13 2.24
6 7 6.793349 AGATCTCGTTAAGCGTGTTAAGTAT 58.207 36.000 0.00 0.00 42.13 2.12
7 8 6.187125 AGATCTCGTTAAGCGTGTTAAGTA 57.813 37.500 0.00 0.00 42.13 2.24
8 9 5.056894 AGATCTCGTTAAGCGTGTTAAGT 57.943 39.130 0.00 0.00 42.13 2.24
9 10 5.220228 CCAAGATCTCGTTAAGCGTGTTAAG 60.220 44.000 0.00 0.00 42.13 1.85
10 11 4.624024 CCAAGATCTCGTTAAGCGTGTTAA 59.376 41.667 0.00 0.00 42.13 2.01
11 12 4.171005 CCAAGATCTCGTTAAGCGTGTTA 58.829 43.478 0.00 0.00 42.13 2.41
12 13 2.993899 CCAAGATCTCGTTAAGCGTGTT 59.006 45.455 0.00 0.00 42.13 3.32
13 14 2.029290 ACCAAGATCTCGTTAAGCGTGT 60.029 45.455 0.00 0.00 42.13 4.49
14 15 2.607187 ACCAAGATCTCGTTAAGCGTG 58.393 47.619 0.00 0.00 42.13 5.34
15 16 4.650754 ATACCAAGATCTCGTTAAGCGT 57.349 40.909 0.00 0.00 42.13 5.07
16 17 5.518847 TCAAATACCAAGATCTCGTTAAGCG 59.481 40.000 0.00 0.00 43.01 4.68
17 18 6.903883 TCAAATACCAAGATCTCGTTAAGC 57.096 37.500 0.00 0.00 0.00 3.09
18 19 8.759641 CAGATCAAATACCAAGATCTCGTTAAG 58.240 37.037 0.00 0.00 44.84 1.85
19 20 8.474831 TCAGATCAAATACCAAGATCTCGTTAA 58.525 33.333 0.00 0.00 44.84 2.01
20 21 8.007405 TCAGATCAAATACCAAGATCTCGTTA 57.993 34.615 0.00 0.00 44.84 3.18
21 22 6.878317 TCAGATCAAATACCAAGATCTCGTT 58.122 36.000 0.00 0.00 44.84 3.85
22 23 6.097554 ACTCAGATCAAATACCAAGATCTCGT 59.902 38.462 0.00 0.00 44.84 4.18
23 24 6.511416 ACTCAGATCAAATACCAAGATCTCG 58.489 40.000 0.00 0.00 44.84 4.04
24 25 7.652909 CAGACTCAGATCAAATACCAAGATCTC 59.347 40.741 0.00 0.00 44.84 2.75
25 26 7.418827 CCAGACTCAGATCAAATACCAAGATCT 60.419 40.741 0.00 0.00 46.90 2.75
26 27 6.705381 CCAGACTCAGATCAAATACCAAGATC 59.295 42.308 0.00 0.00 38.70 2.75
27 28 6.590068 CCAGACTCAGATCAAATACCAAGAT 58.410 40.000 0.00 0.00 0.00 2.40
28 29 5.627735 GCCAGACTCAGATCAAATACCAAGA 60.628 44.000 0.00 0.00 0.00 3.02
29 30 4.574013 GCCAGACTCAGATCAAATACCAAG 59.426 45.833 0.00 0.00 0.00 3.61
30 31 4.517285 GCCAGACTCAGATCAAATACCAA 58.483 43.478 0.00 0.00 0.00 3.67
31 32 3.118261 GGCCAGACTCAGATCAAATACCA 60.118 47.826 0.00 0.00 0.00 3.25
32 33 3.118261 TGGCCAGACTCAGATCAAATACC 60.118 47.826 0.00 0.00 0.00 2.73
33 34 4.142609 TGGCCAGACTCAGATCAAATAC 57.857 45.455 0.00 0.00 0.00 1.89
34 35 5.378230 AATGGCCAGACTCAGATCAAATA 57.622 39.130 13.05 0.00 0.00 1.40
35 36 3.947612 ATGGCCAGACTCAGATCAAAT 57.052 42.857 13.05 0.00 0.00 2.32
36 37 3.726557 AATGGCCAGACTCAGATCAAA 57.273 42.857 13.05 0.00 0.00 2.69
37 38 3.349927 CAAATGGCCAGACTCAGATCAA 58.650 45.455 13.05 0.00 0.00 2.57
38 39 2.356432 CCAAATGGCCAGACTCAGATCA 60.356 50.000 13.05 0.00 0.00 2.92
39 40 2.295885 CCAAATGGCCAGACTCAGATC 58.704 52.381 13.05 0.00 0.00 2.75
40 41 1.637553 ACCAAATGGCCAGACTCAGAT 59.362 47.619 13.05 0.00 39.32 2.90
41 42 1.003580 GACCAAATGGCCAGACTCAGA 59.996 52.381 13.05 0.00 39.32 3.27
42 43 1.004044 AGACCAAATGGCCAGACTCAG 59.996 52.381 13.05 0.00 39.32 3.35
43 44 1.067295 AGACCAAATGGCCAGACTCA 58.933 50.000 13.05 0.00 39.32 3.41
44 45 3.567478 ATAGACCAAATGGCCAGACTC 57.433 47.619 13.05 0.83 39.32 3.36
45 46 3.181465 CGTATAGACCAAATGGCCAGACT 60.181 47.826 13.05 5.73 39.32 3.24
46 47 3.131396 CGTATAGACCAAATGGCCAGAC 58.869 50.000 13.05 0.00 39.32 3.51
47 48 2.484770 GCGTATAGACCAAATGGCCAGA 60.485 50.000 13.05 0.00 39.32 3.86
48 49 1.873591 GCGTATAGACCAAATGGCCAG 59.126 52.381 13.05 0.00 39.32 4.85
49 50 1.210722 TGCGTATAGACCAAATGGCCA 59.789 47.619 8.56 8.56 39.32 5.36
50 51 1.602377 GTGCGTATAGACCAAATGGCC 59.398 52.381 0.00 0.00 39.32 5.36
51 52 2.561569 AGTGCGTATAGACCAAATGGC 58.438 47.619 0.00 0.00 39.32 4.40
52 53 3.741344 GCTAGTGCGTATAGACCAAATGG 59.259 47.826 0.00 0.00 42.17 3.16
53 54 3.741344 GGCTAGTGCGTATAGACCAAATG 59.259 47.826 0.00 0.00 40.82 2.32
54 55 3.386726 TGGCTAGTGCGTATAGACCAAAT 59.613 43.478 0.00 0.00 40.82 2.32
55 56 2.761767 TGGCTAGTGCGTATAGACCAAA 59.238 45.455 0.00 0.00 40.82 3.28
56 57 2.380941 TGGCTAGTGCGTATAGACCAA 58.619 47.619 0.00 0.00 40.82 3.67
57 58 2.061509 TGGCTAGTGCGTATAGACCA 57.938 50.000 0.00 0.00 40.82 4.02
58 59 2.820787 AGATGGCTAGTGCGTATAGACC 59.179 50.000 0.00 0.00 40.82 3.85
59 60 4.435784 CGTAGATGGCTAGTGCGTATAGAC 60.436 50.000 0.00 0.00 40.82 2.59
60 61 3.683340 CGTAGATGGCTAGTGCGTATAGA 59.317 47.826 0.00 0.00 40.82 1.98
61 62 3.728268 GCGTAGATGGCTAGTGCGTATAG 60.728 52.174 0.00 0.00 40.82 1.31
62 63 2.161012 GCGTAGATGGCTAGTGCGTATA 59.839 50.000 0.00 0.00 40.82 1.47
63 64 1.068472 GCGTAGATGGCTAGTGCGTAT 60.068 52.381 0.00 0.00 40.82 3.06
64 65 0.309922 GCGTAGATGGCTAGTGCGTA 59.690 55.000 0.00 0.00 40.82 4.42
65 66 1.065928 GCGTAGATGGCTAGTGCGT 59.934 57.895 0.00 0.00 40.82 5.24
66 67 2.011349 CGCGTAGATGGCTAGTGCG 61.011 63.158 0.00 0.00 42.45 5.34
67 68 1.661821 CCGCGTAGATGGCTAGTGC 60.662 63.158 4.92 0.00 38.76 4.40
68 69 1.007271 CCCGCGTAGATGGCTAGTG 60.007 63.158 4.92 0.00 0.00 2.74
69 70 1.152819 TCCCGCGTAGATGGCTAGT 60.153 57.895 4.92 0.00 0.00 2.57
70 71 1.173444 ACTCCCGCGTAGATGGCTAG 61.173 60.000 4.92 0.00 0.00 3.42
71 72 0.109153 TACTCCCGCGTAGATGGCTA 59.891 55.000 4.92 0.00 0.00 3.93
72 73 1.152819 TACTCCCGCGTAGATGGCT 60.153 57.895 4.92 0.00 0.00 4.75
73 74 1.286260 CTACTCCCGCGTAGATGGC 59.714 63.158 4.92 0.00 39.33 4.40
74 75 1.030457 AACTACTCCCGCGTAGATGG 58.970 55.000 4.92 0.00 39.33 3.51
75 76 3.366070 CCATAACTACTCCCGCGTAGATG 60.366 52.174 4.92 1.23 39.33 2.90
76 77 2.818432 CCATAACTACTCCCGCGTAGAT 59.182 50.000 4.92 0.00 39.33 1.98
77 78 2.224606 CCATAACTACTCCCGCGTAGA 58.775 52.381 4.92 0.00 39.33 2.59
78 79 1.268899 CCCATAACTACTCCCGCGTAG 59.731 57.143 4.92 4.57 41.98 3.51
79 80 1.321474 CCCATAACTACTCCCGCGTA 58.679 55.000 4.92 0.00 0.00 4.42
80 81 0.685458 ACCCATAACTACTCCCGCGT 60.685 55.000 4.92 0.00 0.00 6.01
81 82 1.321474 TACCCATAACTACTCCCGCG 58.679 55.000 0.00 0.00 0.00 6.46
82 83 2.233186 GGATACCCATAACTACTCCCGC 59.767 54.545 0.00 0.00 0.00 6.13
98 99 1.799258 ATACCACGACGCCGGGATAC 61.799 60.000 2.18 0.00 43.04 2.24
99 100 1.518056 GATACCACGACGCCGGGATA 61.518 60.000 2.18 0.00 43.04 2.59
100 101 2.836360 ATACCACGACGCCGGGAT 60.836 61.111 2.18 2.54 43.04 3.85
101 102 3.520862 GATACCACGACGCCGGGA 61.521 66.667 2.18 0.03 43.04 5.14
102 103 3.768185 CTGATACCACGACGCCGGG 62.768 68.421 2.18 0.00 40.78 5.73
103 104 2.278596 CTGATACCACGACGCCGG 60.279 66.667 0.00 0.00 40.78 6.13
104 105 2.954868 GCTGATACCACGACGCCG 60.955 66.667 0.00 0.00 42.50 6.46
105 106 2.585247 GGCTGATACCACGACGCC 60.585 66.667 0.00 0.00 0.00 5.68
106 107 2.877360 TTCGGCTGATACCACGACGC 62.877 60.000 0.00 0.00 34.82 5.19
107 108 0.866061 CTTCGGCTGATACCACGACG 60.866 60.000 0.00 0.00 34.82 5.12
108 109 1.146358 GCTTCGGCTGATACCACGAC 61.146 60.000 0.00 0.00 38.08 4.34
109 110 1.141019 GCTTCGGCTGATACCACGA 59.859 57.895 0.00 0.00 38.08 4.35
110 111 1.883084 GGCTTCGGCTGATACCACG 60.883 63.158 9.03 0.00 41.44 4.94
111 112 0.107654 AAGGCTTCGGCTGATACCAC 60.108 55.000 14.90 0.00 38.81 4.16
112 113 0.178068 GAAGGCTTCGGCTGATACCA 59.822 55.000 12.12 0.00 38.81 3.25
113 114 0.466124 AGAAGGCTTCGGCTGATACC 59.534 55.000 20.78 0.46 38.81 2.73
114 115 1.936547 CAAGAAGGCTTCGGCTGATAC 59.063 52.381 20.78 0.00 38.81 2.24
115 116 1.831106 TCAAGAAGGCTTCGGCTGATA 59.169 47.619 20.78 3.56 38.81 2.15
116 117 0.615331 TCAAGAAGGCTTCGGCTGAT 59.385 50.000 20.78 0.00 38.81 2.90
117 118 0.320771 GTCAAGAAGGCTTCGGCTGA 60.321 55.000 20.78 19.88 38.81 4.26
118 119 1.630244 CGTCAAGAAGGCTTCGGCTG 61.630 60.000 20.78 18.15 38.81 4.85
119 120 1.374758 CGTCAAGAAGGCTTCGGCT 60.375 57.895 20.78 7.58 41.24 5.52
120 121 1.627550 GACGTCAAGAAGGCTTCGGC 61.628 60.000 20.78 8.48 40.88 5.54
121 122 0.319555 TGACGTCAAGAAGGCTTCGG 60.320 55.000 17.62 16.83 30.14 4.30
122 123 1.063806 CTGACGTCAAGAAGGCTTCG 58.936 55.000 20.49 12.20 30.14 3.79
123 124 0.793250 GCTGACGTCAAGAAGGCTTC 59.207 55.000 20.49 19.53 30.14 3.86
124 125 0.946221 CGCTGACGTCAAGAAGGCTT 60.946 55.000 20.49 0.00 31.87 4.35
125 126 1.373497 CGCTGACGTCAAGAAGGCT 60.373 57.895 20.49 0.00 33.53 4.58
126 127 1.372997 TCGCTGACGTCAAGAAGGC 60.373 57.895 20.49 17.24 41.18 4.35
127 128 1.009389 GGTCGCTGACGTCAAGAAGG 61.009 60.000 20.49 8.56 41.18 3.46
128 129 0.039074 AGGTCGCTGACGTCAAGAAG 60.039 55.000 20.49 8.96 41.18 2.85
129 130 1.199327 CTAGGTCGCTGACGTCAAGAA 59.801 52.381 20.49 4.50 41.18 2.52
130 131 0.803117 CTAGGTCGCTGACGTCAAGA 59.197 55.000 20.49 18.18 41.18 3.02
131 132 0.522180 ACTAGGTCGCTGACGTCAAG 59.478 55.000 20.49 16.15 41.18 3.02
132 133 0.520404 GACTAGGTCGCTGACGTCAA 59.480 55.000 20.49 1.33 41.18 3.18
133 134 2.168947 GACTAGGTCGCTGACGTCA 58.831 57.895 18.88 18.88 41.18 4.35
143 144 2.011222 CCTCACTCAGTCGACTAGGTC 58.989 57.143 19.57 0.00 0.00 3.85
144 145 1.340211 CCCTCACTCAGTCGACTAGGT 60.340 57.143 23.46 19.07 0.00 3.08
145 146 1.384525 CCCTCACTCAGTCGACTAGG 58.615 60.000 19.57 19.91 0.00 3.02
146 147 0.736053 GCCCTCACTCAGTCGACTAG 59.264 60.000 19.57 17.26 0.00 2.57
147 148 1.025113 CGCCCTCACTCAGTCGACTA 61.025 60.000 19.57 6.17 0.00 2.59
148 149 2.336478 CGCCCTCACTCAGTCGACT 61.336 63.158 13.58 13.58 0.00 4.18
149 150 2.179517 CGCCCTCACTCAGTCGAC 59.820 66.667 7.70 7.70 0.00 4.20
150 151 2.033602 TCGCCCTCACTCAGTCGA 59.966 61.111 0.00 0.00 0.00 4.20
151 152 2.179517 GTCGCCCTCACTCAGTCG 59.820 66.667 0.00 0.00 0.00 4.18
152 153 2.179517 CGTCGCCCTCACTCAGTC 59.820 66.667 0.00 0.00 0.00 3.51
153 154 2.282251 TCGTCGCCCTCACTCAGT 60.282 61.111 0.00 0.00 0.00 3.41
154 155 2.487428 CTCGTCGCCCTCACTCAG 59.513 66.667 0.00 0.00 0.00 3.35
155 156 3.062466 CCTCGTCGCCCTCACTCA 61.062 66.667 0.00 0.00 0.00 3.41
156 157 2.750637 TCCTCGTCGCCCTCACTC 60.751 66.667 0.00 0.00 0.00 3.51
157 158 2.752238 CTCCTCGTCGCCCTCACT 60.752 66.667 0.00 0.00 0.00 3.41
158 159 3.827898 CCTCCTCGTCGCCCTCAC 61.828 72.222 0.00 0.00 0.00 3.51
196 197 1.065701 CTCCAAGTAGCATCGCGTAGT 59.934 52.381 5.77 0.00 0.00 2.73
923 927 4.047059 GGACGCGGTCAAGGACGA 62.047 66.667 12.47 0.00 33.68 4.20
950 954 0.466372 ATCGATGAGCTGGTCTCCGA 60.466 55.000 19.71 19.71 41.18 4.55
1021 1025 3.209410 GGAGCACATAGACATTCCCAAG 58.791 50.000 0.00 0.00 0.00 3.61
1062 1066 0.459899 CGATGATGACTGGTTCCCGA 59.540 55.000 0.00 0.00 0.00 5.14
1071 1075 2.028130 GTCTGGTCCTCGATGATGACT 58.972 52.381 11.25 0.00 30.09 3.41
1096 1100 2.025155 ACGCGATACAAGATCCTCTGT 58.975 47.619 15.93 0.00 0.00 3.41
1340 1344 8.314751 CAAATATTTCATCCTCCTCTATACGGT 58.685 37.037 0.00 0.00 0.00 4.83
1519 1540 1.051812 ATGCCTTGATCCCTACCTCG 58.948 55.000 0.00 0.00 0.00 4.63
1704 1727 2.715005 GCTTGTGCACGTTGAGCA 59.285 55.556 21.72 0.00 40.19 4.26
1731 1754 1.594862 GCTATCTTGGCGACACATCAC 59.405 52.381 0.00 0.00 42.67 3.06
1772 1802 2.825836 CATCACTTCCAGGCCGGC 60.826 66.667 21.18 21.18 33.14 6.13
2104 2562 6.974932 ATTATGTCACTGAACATGAGACAC 57.025 37.500 0.00 0.00 41.43 3.67
2174 2632 7.622081 TGGAAGATTATACCAAACTCTCCTACA 59.378 37.037 0.00 0.00 0.00 2.74
2208 2666 0.319813 GACTTGTGCCATGGTTTGCC 60.320 55.000 14.67 0.00 0.00 4.52
2216 2674 1.959085 CGCCAAAGACTTGTGCCAT 59.041 52.632 4.20 0.00 0.00 4.40
2221 2679 1.526917 AGCAGCGCCAAAGACTTGT 60.527 52.632 2.29 0.00 0.00 3.16
2229 2687 4.284123 CTACTTCAGCAGCGCCAA 57.716 55.556 2.29 0.00 0.00 4.52
2261 4692 7.993183 TCCTGGAAATATTATGTGGAAGAACTC 59.007 37.037 0.00 0.00 0.00 3.01
2264 4695 8.966868 GTTTCCTGGAAATATTATGTGGAAGAA 58.033 33.333 23.60 0.00 33.97 2.52
2283 5967 6.071447 TCACCATGATAAACCATTGTTTCCTG 60.071 38.462 0.00 0.00 43.50 3.86
2410 6189 5.304101 TCCCTGCAACAATGTTGAATAAGTT 59.696 36.000 28.10 0.00 0.00 2.66
2415 6194 3.555586 GCTTCCCTGCAACAATGTTGAAT 60.556 43.478 28.10 0.00 0.00 2.57
2416 6195 2.224018 GCTTCCCTGCAACAATGTTGAA 60.224 45.455 28.10 18.13 0.00 2.69
2444 6223 4.826733 ACCACACAAAAGATATTGTCAGCA 59.173 37.500 0.00 0.00 41.44 4.41
2448 6227 6.560253 ACTCACCACACAAAAGATATTGTC 57.440 37.500 0.00 0.00 41.44 3.18
2449 6228 5.179368 CGACTCACCACACAAAAGATATTGT 59.821 40.000 0.00 0.00 44.08 2.71
2462 6241 3.804786 TTAGTGAAACGACTCACCACA 57.195 42.857 15.01 2.55 45.77 4.17
2467 6246 4.510340 GCTTTCCTTTAGTGAAACGACTCA 59.490 41.667 0.00 0.00 45.86 3.41
2469 6248 3.813724 GGCTTTCCTTTAGTGAAACGACT 59.186 43.478 0.00 0.00 45.86 4.18
2472 6251 3.058224 CCTGGCTTTCCTTTAGTGAAACG 60.058 47.826 0.00 0.00 45.86 3.60
2519 6298 3.752747 TGCTGCATATTGTCGAATATGGG 59.247 43.478 15.55 0.00 46.43 4.00
2526 6305 4.692228 TGAATAGTGCTGCATATTGTCGA 58.308 39.130 5.27 0.00 0.00 4.20
2527 6306 5.379827 CATGAATAGTGCTGCATATTGTCG 58.620 41.667 5.27 0.00 0.00 4.35
2532 6311 8.640063 TTATTTCCATGAATAGTGCTGCATAT 57.360 30.769 5.27 0.00 0.00 1.78
2567 6346 9.988350 GACACAATTATTCCAGTGTAAACTATG 57.012 33.333 0.00 0.00 44.48 2.23
2589 6369 2.258726 GGGCACACTTTCCGGACAC 61.259 63.158 1.83 0.00 0.00 3.67
2594 6374 1.106944 AACAAGGGGCACACTTTCCG 61.107 55.000 0.00 0.00 0.00 4.30
2602 6382 2.583143 AGACTGTTAAACAAGGGGCAC 58.417 47.619 0.00 0.00 0.00 5.01
2614 6394 4.564821 GCTTGGGTATGGACAAGACTGTTA 60.565 45.833 8.45 0.00 45.22 2.41
2615 6395 3.810743 GCTTGGGTATGGACAAGACTGTT 60.811 47.826 8.45 0.00 45.22 3.16
2616 6396 2.290323 GCTTGGGTATGGACAAGACTGT 60.290 50.000 8.45 0.00 45.22 3.55
2617 6397 2.359900 GCTTGGGTATGGACAAGACTG 58.640 52.381 8.45 0.00 45.22 3.51
2618 6398 1.282157 GGCTTGGGTATGGACAAGACT 59.718 52.381 8.45 0.00 46.67 3.24
2619 6399 1.751437 GGCTTGGGTATGGACAAGAC 58.249 55.000 8.45 1.54 45.22 3.01
2620 6400 1.367346 TGGCTTGGGTATGGACAAGA 58.633 50.000 8.45 0.00 45.22 3.02
2621 6401 2.301346 GATGGCTTGGGTATGGACAAG 58.699 52.381 0.00 0.00 45.19 3.16
2622 6402 1.064017 GGATGGCTTGGGTATGGACAA 60.064 52.381 0.00 0.00 0.00 3.18
2623 6403 0.550914 GGATGGCTTGGGTATGGACA 59.449 55.000 0.00 0.00 0.00 4.02
2624 6404 0.550914 TGGATGGCTTGGGTATGGAC 59.449 55.000 0.00 0.00 0.00 4.02
2625 6405 1.064017 GTTGGATGGCTTGGGTATGGA 60.064 52.381 0.00 0.00 0.00 3.41
2626 6406 1.341877 TGTTGGATGGCTTGGGTATGG 60.342 52.381 0.00 0.00 0.00 2.74
2627 6407 1.750778 GTGTTGGATGGCTTGGGTATG 59.249 52.381 0.00 0.00 0.00 2.39
2628 6408 1.640670 AGTGTTGGATGGCTTGGGTAT 59.359 47.619 0.00 0.00 0.00 2.73
2629 6409 1.072266 AGTGTTGGATGGCTTGGGTA 58.928 50.000 0.00 0.00 0.00 3.69
2630 6410 1.004745 CTAGTGTTGGATGGCTTGGGT 59.995 52.381 0.00 0.00 0.00 4.51
2631 6411 1.281867 TCTAGTGTTGGATGGCTTGGG 59.718 52.381 0.00 0.00 0.00 4.12
2632 6412 2.359900 GTCTAGTGTTGGATGGCTTGG 58.640 52.381 0.00 0.00 0.00 3.61
2633 6413 2.002586 CGTCTAGTGTTGGATGGCTTG 58.997 52.381 0.00 0.00 0.00 4.01
2634 6414 1.676014 GCGTCTAGTGTTGGATGGCTT 60.676 52.381 0.00 0.00 0.00 4.35
2635 6415 0.108138 GCGTCTAGTGTTGGATGGCT 60.108 55.000 0.00 0.00 0.00 4.75
2636 6416 0.108138 AGCGTCTAGTGTTGGATGGC 60.108 55.000 0.00 0.00 0.00 4.40
2637 6417 2.386661 AAGCGTCTAGTGTTGGATGG 57.613 50.000 0.00 0.00 0.00 3.51
2638 6418 2.860735 GCTAAGCGTCTAGTGTTGGATG 59.139 50.000 0.00 0.00 0.00 3.51
2639 6419 2.496070 TGCTAAGCGTCTAGTGTTGGAT 59.504 45.455 0.00 0.00 0.00 3.41
2640 6420 1.890489 TGCTAAGCGTCTAGTGTTGGA 59.110 47.619 0.00 0.00 0.00 3.53
2641 6421 2.094700 TCTGCTAAGCGTCTAGTGTTGG 60.095 50.000 0.00 0.00 0.00 3.77
2653 6433 6.458888 GGTCAATTTCATTACCTCTGCTAAGC 60.459 42.308 0.00 0.00 0.00 3.09
2661 6441 9.956720 CTCATAATTGGTCAATTTCATTACCTC 57.043 33.333 13.24 0.00 40.99 3.85


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

AutoCloner maintained by Alex Coulton.