Multiple sequence alignment - TraesCS7B01G204800

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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 TraesCS7B01G204800 chr7B 100.000 2291 0 0 1953 4243 375190705 375192995 0.000000e+00 4231.0
1 TraesCS7B01G204800 chr7B 100.000 1496 0 0 1 1496 375188753 375190248 0.000000e+00 2763.0
2 TraesCS7B01G204800 chr7B 94.536 183 8 2 58 238 705489234 705489052 8.980000e-72 281.0
3 TraesCS7B01G204800 chr7B 92.308 52 0 3 1 50 375188655 375188606 2.120000e-08 71.3
4 TraesCS7B01G204800 chr7B 93.750 48 0 2 1 48 11441271 11441315 7.610000e-08 69.4
5 TraesCS7B01G204800 chr7D 94.943 2294 75 17 1959 4240 380145412 380147676 0.000000e+00 3555.0
6 TraesCS7B01G204800 chr7D 97.625 1263 22 6 234 1496 380144119 380145373 0.000000e+00 2159.0
7 TraesCS7B01G204800 chr7A 93.377 2295 77 31 1966 4240 428810315 428812554 0.000000e+00 3326.0
8 TraesCS7B01G204800 chr7A 96.212 1267 34 8 234 1496 428809014 428810270 0.000000e+00 2061.0
9 TraesCS7B01G204800 chr7A 83.744 203 26 6 71 270 669660909 669661107 7.240000e-43 185.0
10 TraesCS7B01G204800 chr3A 96.571 175 4 2 64 237 12424257 12424430 5.370000e-74 289.0
11 TraesCS7B01G204800 chr3A 94.915 59 3 0 2492 2550 330698744 330698802 4.520000e-15 93.5
12 TraesCS7B01G204800 chr3A 91.071 56 5 0 1313 1368 476385479 476385534 4.550000e-10 76.8
13 TraesCS7B01G204800 chr2B 95.082 183 9 0 64 246 357152501 357152319 5.370000e-74 289.0
14 TraesCS7B01G204800 chr5B 95.954 173 7 0 66 238 656461770 656461942 8.980000e-72 281.0
15 TraesCS7B01G204800 chr5B 81.982 111 18 2 1305 1414 211146258 211146367 4.520000e-15 93.5
16 TraesCS7B01G204800 chr5A 95.954 173 7 0 65 237 362177068 362176896 8.980000e-72 281.0
17 TraesCS7B01G204800 chr5A 94.118 187 7 4 65 248 685871065 685871250 8.980000e-72 281.0
18 TraesCS7B01G204800 chr5A 82.883 111 17 2 1305 1414 214166634 214166743 9.710000e-17 99.0
19 TraesCS7B01G204800 chr5A 93.878 49 0 3 1 47 526657824 526657777 2.120000e-08 71.3
20 TraesCS7B01G204800 chr3B 96.471 170 5 1 72 241 306557559 306557391 3.230000e-71 279.0
21 TraesCS7B01G204800 chr3B 94.915 59 3 0 2492 2550 304277919 304277977 4.520000e-15 93.5
22 TraesCS7B01G204800 chr3B 91.071 56 5 0 1313 1368 458343140 458343195 4.550000e-10 76.8
23 TraesCS7B01G204800 chr3B 95.652 46 1 1 1 45 781341636 781341591 5.880000e-09 73.1
24 TraesCS7B01G204800 chr3B 86.885 61 4 4 1 60 474143937 474143880 9.850000e-07 65.8
25 TraesCS7B01G204800 chr6A 94.475 181 9 1 59 238 1829839 1830019 1.160000e-70 278.0
26 TraesCS7B01G204800 chr6A 87.719 57 7 0 2479 2535 1133639 1133695 2.740000e-07 67.6
27 TraesCS7B01G204800 chr2A 94.022 184 9 2 71 254 609646491 609646310 1.160000e-70 278.0
28 TraesCS7B01G204800 chr4B 89.730 185 15 3 71 254 338425782 338425963 2.550000e-57 233.0
29 TraesCS7B01G204800 chr4B 81.081 111 21 0 1313 1423 100576667 100576777 5.840000e-14 89.8
30 TraesCS7B01G204800 chr4B 84.507 71 11 0 2465 2535 405906885 405906955 2.120000e-08 71.3
31 TraesCS7B01G204800 chr4D 82.456 114 14 5 1313 1423 68053418 68053528 1.260000e-15 95.3
32 TraesCS7B01G204800 chr4A 82.456 114 14 5 1313 1423 517884598 517884708 1.260000e-15 95.3
33 TraesCS7B01G204800 chr3D 94.915 59 3 0 2492 2550 253340047 253339989 4.520000e-15 93.5
34 TraesCS7B01G204800 chr3D 85.714 56 8 0 2492 2547 48071129 48071184 4.580000e-05 60.2
35 TraesCS7B01G204800 chr3D 90.909 44 4 0 2492 2535 360048663 360048620 4.580000e-05 60.2
36 TraesCS7B01G204800 chr5D 81.081 111 19 2 1305 1414 200501287 200501396 2.100000e-13 87.9
37 TraesCS7B01G204800 chr1D 88.571 70 8 0 2466 2535 8096554 8096623 7.560000e-13 86.1
38 TraesCS7B01G204800 chr1D 84.127 63 10 0 2468 2530 474510211 474510149 1.270000e-05 62.1
39 TraesCS7B01G204800 chr1D 97.059 34 1 0 2497 2530 22437082 22437049 1.650000e-04 58.4
40 TraesCS7B01G204800 chr2D 95.652 46 0 2 1 45 146303527 146303571 5.880000e-09 73.1
41 TraesCS7B01G204800 chr2D 87.931 58 5 2 1308 1364 471450876 471450820 2.740000e-07 67.6
42 TraesCS7B01G204800 chr1B 90.741 54 5 0 2482 2535 10569228 10569175 5.880000e-09 73.1
43 TraesCS7B01G204800 chr6D 93.617 47 1 2 1 46 161722601 161722646 7.610000e-08 69.4
44 TraesCS7B01G204800 chr6D 84.722 72 7 4 1 69 305359758 305359828 7.610000e-08 69.4
45 TraesCS7B01G204800 chr6D 90.566 53 2 3 1 50 29839601 29839549 2.740000e-07 67.6
46 TraesCS7B01G204800 chr1A 85.714 63 9 0 2468 2530 569139252 569139190 2.740000e-07 67.6
47 TraesCS7B01G204800 chr1A 94.595 37 2 0 2494 2530 23340019 23340055 1.650000e-04 58.4


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 TraesCS7B01G204800 chr7B 375188753 375192995 4242 False 3497.0 4231 100.0000 1 4243 2 chr7B.!!$F2 4242
1 TraesCS7B01G204800 chr7D 380144119 380147676 3557 False 2857.0 3555 96.2840 234 4240 2 chr7D.!!$F1 4006
2 TraesCS7B01G204800 chr7A 428809014 428812554 3540 False 2693.5 3326 94.7945 234 4240 2 chr7A.!!$F2 4006

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
67 68 0.248702 TGTCGCGCGTGCTTCATATA 60.249 50.0 30.98 2.41 39.65 0.86 F
68 69 1.060713 GTCGCGCGTGCTTCATATAT 58.939 50.0 30.98 0.00 39.65 0.86 F
1974 1979 0.933796 GGAGAGCTGCGCTTATCAAC 59.066 55.0 9.73 2.48 39.88 3.18 F
2160 2166 0.249073 TTTCTCTGGAGCGCGCTATC 60.249 55.0 36.69 28.08 0.00 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 1979 0.392193 GGCACAGGTCAGATGAGTGG 60.392 60.000 0.00 0.00 0.00 4.00 R
2038 2044 2.159114 TGCATGCGACATTAGCTACAGA 60.159 45.455 14.09 0.00 35.28 3.41 R
3110 3123 1.270414 ACTGCTCATGCTGCCCTAGT 61.270 55.000 0.00 3.16 41.07 2.57 R
3954 3982 1.868713 TCTCTATTACCACCCCGCAA 58.131 50.000 0.00 0.00 0.00 4.85 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
28 29 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
29 30 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
30 31 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
31 32 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
32 33 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
33 34 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
34 35 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
35 36 9.471702 CTTATATTTAGGAACGGAGGGAGTATA 57.528 37.037 0.00 0.00 0.00 1.47
36 37 7.715266 ATATTTAGGAACGGAGGGAGTATAC 57.285 40.000 0.00 0.00 0.00 1.47
37 38 4.524802 TTAGGAACGGAGGGAGTATACA 57.475 45.455 5.50 0.00 0.00 2.29
38 39 3.614568 AGGAACGGAGGGAGTATACAT 57.385 47.619 5.50 0.00 0.00 2.29
39 40 3.231818 AGGAACGGAGGGAGTATACATG 58.768 50.000 5.50 0.00 0.00 3.21
40 41 2.963782 GGAACGGAGGGAGTATACATGT 59.036 50.000 2.69 2.69 0.00 3.21
41 42 3.243771 GGAACGGAGGGAGTATACATGTG 60.244 52.174 9.11 0.00 0.00 3.21
42 43 1.687123 ACGGAGGGAGTATACATGTGC 59.313 52.381 9.11 0.00 0.00 4.57
43 44 1.686587 CGGAGGGAGTATACATGTGCA 59.313 52.381 9.11 0.00 0.00 4.57
44 45 2.300152 CGGAGGGAGTATACATGTGCAT 59.700 50.000 9.11 0.00 0.00 3.96
45 46 3.509967 CGGAGGGAGTATACATGTGCATA 59.490 47.826 9.11 0.00 0.00 3.14
46 47 4.618460 CGGAGGGAGTATACATGTGCATAC 60.618 50.000 9.11 9.53 0.00 2.39
47 48 4.283467 GGAGGGAGTATACATGTGCATACA 59.717 45.833 17.18 0.00 41.89 2.29
55 56 1.643292 ATGTGCATACATGTCGCGC 59.357 52.632 20.99 20.99 45.54 6.86
56 57 2.053984 GTGCATACATGTCGCGCG 60.054 61.111 26.76 26.76 0.00 6.86
57 58 2.508215 TGCATACATGTCGCGCGT 60.508 55.556 30.98 12.90 0.00 6.01
58 59 2.053984 GCATACATGTCGCGCGTG 60.054 61.111 30.98 22.98 39.90 5.34
59 60 2.053984 CATACATGTCGCGCGTGC 60.054 61.111 30.98 23.08 37.62 5.34
60 61 2.202743 ATACATGTCGCGCGTGCT 60.203 55.556 30.98 12.34 39.65 4.40
61 62 1.809619 ATACATGTCGCGCGTGCTT 60.810 52.632 30.98 18.08 39.65 3.91
62 63 1.752501 ATACATGTCGCGCGTGCTTC 61.753 55.000 30.98 15.73 39.65 3.86
63 64 3.776849 CATGTCGCGCGTGCTTCA 61.777 61.111 30.98 20.42 39.65 3.02
64 65 2.815211 ATGTCGCGCGTGCTTCAT 60.815 55.556 30.98 21.58 39.65 2.57
65 66 1.518352 ATGTCGCGCGTGCTTCATA 60.518 52.632 30.98 7.87 39.65 2.15
66 67 0.875908 ATGTCGCGCGTGCTTCATAT 60.876 50.000 30.98 10.11 39.65 1.78
67 68 0.248702 TGTCGCGCGTGCTTCATATA 60.249 50.000 30.98 2.41 39.65 0.86
68 69 1.060713 GTCGCGCGTGCTTCATATAT 58.939 50.000 30.98 0.00 39.65 0.86
69 70 2.247637 GTCGCGCGTGCTTCATATATA 58.752 47.619 30.98 1.54 39.65 0.86
70 71 2.026507 GTCGCGCGTGCTTCATATATAC 59.973 50.000 30.98 11.80 39.65 1.47
71 72 2.095415 TCGCGCGTGCTTCATATATACT 60.095 45.455 30.98 0.00 39.65 2.12
72 73 3.125658 TCGCGCGTGCTTCATATATACTA 59.874 43.478 30.98 0.00 39.65 1.82
73 74 3.237660 CGCGCGTGCTTCATATATACTAC 59.762 47.826 24.19 0.00 39.65 2.73
74 75 4.413087 GCGCGTGCTTCATATATACTACT 58.587 43.478 15.02 0.00 38.39 2.57
75 76 4.496183 GCGCGTGCTTCATATATACTACTC 59.504 45.833 15.02 0.00 38.39 2.59
76 77 5.674068 GCGCGTGCTTCATATATACTACTCT 60.674 44.000 15.02 0.00 38.39 3.24
77 78 5.960683 CGCGTGCTTCATATATACTACTCTC 59.039 44.000 0.00 0.00 0.00 3.20
78 79 6.183360 CGCGTGCTTCATATATACTACTCTCT 60.183 42.308 0.00 0.00 0.00 3.10
79 80 7.184106 GCGTGCTTCATATATACTACTCTCTC 58.816 42.308 0.00 0.00 0.00 3.20
80 81 7.677747 GCGTGCTTCATATATACTACTCTCTCC 60.678 44.444 0.00 0.00 0.00 3.71
81 82 7.464844 CGTGCTTCATATATACTACTCTCTCCG 60.465 44.444 0.00 0.00 0.00 4.63
82 83 7.334921 GTGCTTCATATATACTACTCTCTCCGT 59.665 40.741 0.00 0.00 0.00 4.69
83 84 7.883833 TGCTTCATATATACTACTCTCTCCGTT 59.116 37.037 0.00 0.00 0.00 4.44
84 85 8.392612 GCTTCATATATACTACTCTCTCCGTTC 58.607 40.741 0.00 0.00 0.00 3.95
85 86 8.789825 TTCATATATACTACTCTCTCCGTTCC 57.210 38.462 0.00 0.00 0.00 3.62
86 87 8.148437 TCATATATACTACTCTCTCCGTTCCT 57.852 38.462 0.00 0.00 0.00 3.36
87 88 9.264653 TCATATATACTACTCTCTCCGTTCCTA 57.735 37.037 0.00 0.00 0.00 2.94
88 89 9.887629 CATATATACTACTCTCTCCGTTCCTAA 57.112 37.037 0.00 0.00 0.00 2.69
93 94 9.810870 ATACTACTCTCTCCGTTCCTAAATATT 57.189 33.333 0.00 0.00 0.00 1.28
94 95 8.536340 ACTACTCTCTCCGTTCCTAAATATTT 57.464 34.615 5.89 5.89 0.00 1.40
95 96 8.414778 ACTACTCTCTCCGTTCCTAAATATTTG 58.585 37.037 11.05 1.40 0.00 2.32
96 97 7.184067 ACTCTCTCCGTTCCTAAATATTTGT 57.816 36.000 11.05 0.00 0.00 2.83
97 98 7.266400 ACTCTCTCCGTTCCTAAATATTTGTC 58.734 38.462 11.05 0.00 0.00 3.18
98 99 7.124448 ACTCTCTCCGTTCCTAAATATTTGTCT 59.876 37.037 11.05 0.00 0.00 3.41
99 100 7.848128 TCTCTCCGTTCCTAAATATTTGTCTT 58.152 34.615 11.05 0.00 0.00 3.01
100 101 8.319146 TCTCTCCGTTCCTAAATATTTGTCTTT 58.681 33.333 11.05 0.00 0.00 2.52
101 102 8.488651 TCTCCGTTCCTAAATATTTGTCTTTC 57.511 34.615 11.05 0.00 0.00 2.62
102 103 8.319146 TCTCCGTTCCTAAATATTTGTCTTTCT 58.681 33.333 11.05 0.00 0.00 2.52
103 104 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
104 105 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
105 106 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
134 135 8.583810 TTCAAATAACTACTACATACGGATGC 57.416 34.615 7.78 0.00 36.43 3.91
135 136 7.718525 TCAAATAACTACTACATACGGATGCA 58.281 34.615 7.78 0.00 36.43 3.96
136 137 8.364894 TCAAATAACTACTACATACGGATGCAT 58.635 33.333 7.78 0.00 36.43 3.96
137 138 8.435430 CAAATAACTACTACATACGGATGCATG 58.565 37.037 7.78 0.25 36.43 4.06
138 139 5.531122 AACTACTACATACGGATGCATGT 57.469 39.130 7.78 6.76 38.81 3.21
139 140 6.644248 AACTACTACATACGGATGCATGTA 57.356 37.500 7.78 7.57 36.74 2.29
144 145 4.607293 ACATACGGATGCATGTAGACAT 57.393 40.909 7.78 0.00 36.43 3.06
145 146 5.722021 ACATACGGATGCATGTAGACATA 57.278 39.130 7.78 0.00 36.43 2.29
146 147 6.286240 ACATACGGATGCATGTAGACATAT 57.714 37.500 7.78 0.00 36.43 1.78
147 148 6.701340 ACATACGGATGCATGTAGACATATT 58.299 36.000 7.78 0.00 36.43 1.28
148 149 7.161404 ACATACGGATGCATGTAGACATATTT 58.839 34.615 7.78 0.00 36.43 1.40
149 150 7.661437 ACATACGGATGCATGTAGACATATTTT 59.339 33.333 7.78 0.00 36.43 1.82
150 151 9.150348 CATACGGATGCATGTAGACATATTTTA 57.850 33.333 2.46 0.00 34.26 1.52
151 152 7.658179 ACGGATGCATGTAGACATATTTTAG 57.342 36.000 2.46 0.00 34.26 1.85
152 153 7.441836 ACGGATGCATGTAGACATATTTTAGA 58.558 34.615 2.46 0.00 34.26 2.10
153 154 7.600375 ACGGATGCATGTAGACATATTTTAGAG 59.400 37.037 2.46 0.00 34.26 2.43
154 155 7.600375 CGGATGCATGTAGACATATTTTAGAGT 59.400 37.037 2.46 0.00 34.26 3.24
155 156 8.715998 GGATGCATGTAGACATATTTTAGAGTG 58.284 37.037 2.46 0.00 34.26 3.51
156 157 9.265901 GATGCATGTAGACATATTTTAGAGTGT 57.734 33.333 2.46 0.00 34.26 3.55
158 159 9.750125 TGCATGTAGACATATTTTAGAGTGTAG 57.250 33.333 0.00 0.00 34.26 2.74
159 160 9.967346 GCATGTAGACATATTTTAGAGTGTAGA 57.033 33.333 0.00 0.00 34.26 2.59
176 177 7.440523 AGTGTAGATTCACTCATTTTGTTCC 57.559 36.000 0.00 0.00 44.07 3.62
177 178 6.147821 AGTGTAGATTCACTCATTTTGTTCCG 59.852 38.462 0.00 0.00 44.07 4.30
178 179 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
179 180 7.117236 GTGTAGATTCACTCATTTTGTTCCGTA 59.883 37.037 0.00 0.00 35.68 4.02
180 181 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
181 182 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
182 183 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
183 184 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
184 185 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
185 186 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
186 187 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
187 188 6.367695 CACTCATTTTGTTCCGTATGTAGTCA 59.632 38.462 0.00 0.00 0.00 3.41
188 189 6.367969 ACTCATTTTGTTCCGTATGTAGTCAC 59.632 38.462 0.00 0.00 0.00 3.67
189 190 6.460781 TCATTTTGTTCCGTATGTAGTCACT 58.539 36.000 0.00 0.00 0.00 3.41
190 191 6.932400 TCATTTTGTTCCGTATGTAGTCACTT 59.068 34.615 0.00 0.00 0.00 3.16
191 192 6.533819 TTTTGTTCCGTATGTAGTCACTTG 57.466 37.500 0.00 0.00 0.00 3.16
192 193 4.859304 TGTTCCGTATGTAGTCACTTGT 57.141 40.909 0.00 0.00 0.00 3.16
193 194 5.204409 TGTTCCGTATGTAGTCACTTGTT 57.796 39.130 0.00 0.00 0.00 2.83
194 195 6.330004 TGTTCCGTATGTAGTCACTTGTTA 57.670 37.500 0.00 0.00 0.00 2.41
195 196 6.747125 TGTTCCGTATGTAGTCACTTGTTAA 58.253 36.000 0.00 0.00 0.00 2.01
196 197 7.208777 TGTTCCGTATGTAGTCACTTGTTAAA 58.791 34.615 0.00 0.00 0.00 1.52
197 198 7.710044 TGTTCCGTATGTAGTCACTTGTTAAAA 59.290 33.333 0.00 0.00 0.00 1.52
198 199 8.715088 GTTCCGTATGTAGTCACTTGTTAAAAT 58.285 33.333 0.00 0.00 0.00 1.82
199 200 8.246908 TCCGTATGTAGTCACTTGTTAAAATG 57.753 34.615 0.00 0.00 0.00 2.32
200 201 7.874016 TCCGTATGTAGTCACTTGTTAAAATGT 59.126 33.333 0.00 0.00 0.00 2.71
201 202 8.166706 CCGTATGTAGTCACTTGTTAAAATGTC 58.833 37.037 0.00 0.00 0.00 3.06
202 203 8.922676 CGTATGTAGTCACTTGTTAAAATGTCT 58.077 33.333 0.00 0.00 0.00 3.41
209 210 9.832445 AGTCACTTGTTAAAATGTCTAGAAAGA 57.168 29.630 0.00 0.00 0.00 2.52
226 227 8.248945 TCTAGAAAGACAAGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
227 228 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
228 229 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
229 230 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
230 231 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
231 232 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
232 233 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
250 251 7.833183 CGGAGGGAGTAGTATAAATACCACTAT 59.167 40.741 1.88 0.00 35.79 2.12
268 269 8.650143 ACCACTATTTGACAATCTTGGTTTAT 57.350 30.769 5.77 0.00 35.46 1.40
383 384 1.190643 TCACTGTCATGCATCCGGTA 58.809 50.000 0.00 0.00 0.00 4.02
1095 1096 1.449601 CCGCTACATCACCACCCAC 60.450 63.158 0.00 0.00 0.00 4.61
1098 1099 1.895020 GCTACATCACCACCCACGGA 61.895 60.000 0.00 0.00 0.00 4.69
1161 1162 6.183360 CGTAATCTTGATCCGTCTATCTCGAT 60.183 42.308 0.00 0.00 0.00 3.59
1254 1255 1.344191 AAGATGGGGCTCTCTGGCTC 61.344 60.000 0.00 0.00 42.84 4.70
1974 1979 0.933796 GGAGAGCTGCGCTTATCAAC 59.066 55.000 9.73 2.48 39.88 3.18
2077 2083 4.305989 TGCAGGTGACAAAAGTGATTTC 57.694 40.909 0.00 0.00 0.00 2.17
2110 2116 7.969508 CCTAAAAAGAAACGGTGTTTTGAAGTA 59.030 33.333 0.00 0.00 33.24 2.24
2113 2119 7.749539 AAAGAAACGGTGTTTTGAAGTATTG 57.250 32.000 0.00 0.00 0.00 1.90
2160 2166 0.249073 TTTCTCTGGAGCGCGCTATC 60.249 55.000 36.69 28.08 0.00 2.08
2202 2208 9.807921 TTCCAAGTTAATTAAGATTTCTGGTCT 57.192 29.630 0.00 0.00 0.00 3.85
2317 2323 2.735134 GCACGACTACCCTAACAACAAG 59.265 50.000 0.00 0.00 0.00 3.16
2341 2353 5.798934 GTCAATGAAGTGGTACGTACTACTG 59.201 44.000 35.85 25.93 45.56 2.74
2342 2354 3.837213 TGAAGTGGTACGTACTACTGC 57.163 47.619 35.85 34.20 45.56 4.40
2344 2356 3.058016 TGAAGTGGTACGTACTACTGCAC 60.058 47.826 36.11 29.08 45.10 4.57
2345 2357 2.507484 AGTGGTACGTACTACTGCACA 58.493 47.619 35.07 16.98 44.76 4.57
2346 2358 2.886523 AGTGGTACGTACTACTGCACAA 59.113 45.455 35.07 0.00 44.76 3.33
2352 2365 3.834610 ACGTACTACTGCACAAAGCTAG 58.165 45.455 0.00 0.00 45.94 3.42
2353 2366 2.599082 CGTACTACTGCACAAAGCTAGC 59.401 50.000 6.62 6.62 45.94 3.42
2354 2367 3.673594 CGTACTACTGCACAAAGCTAGCT 60.674 47.826 12.68 12.68 45.94 3.32
2371 2384 4.500716 GCTAGCTAGCTAGGGTTTCTTCAG 60.501 50.000 39.60 21.65 45.62 3.02
2379 2392 1.499007 AGGGTTTCTTCAGGGCAAAGA 59.501 47.619 0.00 0.00 0.00 2.52
2381 2394 3.333680 AGGGTTTCTTCAGGGCAAAGATA 59.666 43.478 0.00 0.00 33.01 1.98
2388 2401 4.522789 TCTTCAGGGCAAAGATACCAAAAC 59.477 41.667 0.00 0.00 0.00 2.43
2425 2438 8.206189 AGTGATGACAAAAGGAAAAATTCACAT 58.794 29.630 0.00 0.00 33.87 3.21
2449 2462 6.535274 AATGACTTTACTGACGTAAACACC 57.465 37.500 0.00 0.00 39.87 4.16
2450 2463 5.266733 TGACTTTACTGACGTAAACACCT 57.733 39.130 0.00 0.00 39.87 4.00
2452 2465 6.108015 TGACTTTACTGACGTAAACACCTTT 58.892 36.000 0.00 0.00 39.87 3.11
2453 2466 7.264221 TGACTTTACTGACGTAAACACCTTTA 58.736 34.615 0.00 0.00 39.87 1.85
2454 2467 7.222611 TGACTTTACTGACGTAAACACCTTTAC 59.777 37.037 0.00 0.00 39.87 2.01
2585 2598 2.160853 GGCGCCGAACGTAACTACC 61.161 63.158 12.58 0.00 46.11 3.18
2586 2599 1.444212 GCGCCGAACGTAACTACCA 60.444 57.895 0.00 0.00 46.11 3.25
2587 2600 1.677353 GCGCCGAACGTAACTACCAC 61.677 60.000 0.00 0.00 46.11 4.16
2603 2616 2.520020 ACCACCTCGTCCACGACA 60.520 61.111 0.00 0.00 44.22 4.35
3110 3123 2.041265 GAGGAGGAGGGGGAGCAA 59.959 66.667 0.00 0.00 0.00 3.91
3208 3221 2.047939 GGCCATGCAAAGTGGTGC 60.048 61.111 6.68 0.00 45.15 5.01
3247 3260 1.299541 GGACCAAACGCATGATCGAT 58.700 50.000 0.00 0.00 0.00 3.59
3258 3271 2.223611 GCATGATCGATCAGAAAGCTGG 59.776 50.000 30.11 13.98 42.53 4.85
3261 3274 4.944619 TGATCGATCAGAAAGCTGGTAT 57.055 40.909 23.99 0.00 42.53 2.73
3341 3360 1.969923 CTCCCCCTCTCACATCTGATC 59.030 57.143 0.00 0.00 0.00 2.92
3433 3452 9.632807 GGTGCACTTAATTTATTGTGTTTGATA 57.367 29.630 17.98 0.00 33.44 2.15
3612 3636 2.615747 GGAAGGAAGAAAGGGAACTCCG 60.616 54.545 0.00 0.00 42.68 4.63
3705 3729 6.884836 AGGGATCAATGTGTACCTTTTTAGTC 59.115 38.462 0.00 0.00 0.00 2.59
3793 3819 7.401955 AACGATTTACACTAGCTACTAAGGT 57.598 36.000 0.00 0.00 37.23 3.50
4196 4226 7.040823 AGCAAAGATAAGAGAGACTGGTTTTTG 60.041 37.037 0.00 0.00 0.00 2.44
4235 4265 1.159285 CGTGTGTGCATTCACCATCT 58.841 50.000 15.20 0.00 42.46 2.90
4240 4270 2.751259 GTGTGCATTCACCATCTGTCAT 59.249 45.455 0.00 0.00 42.46 3.06
4241 4271 3.192001 GTGTGCATTCACCATCTGTCATT 59.808 43.478 0.00 0.00 42.46 2.57
4242 4272 3.191791 TGTGCATTCACCATCTGTCATTG 59.808 43.478 0.00 0.00 42.46 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3 4 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4 5 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
5 6 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
6 7 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
7 8 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
8 9 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
9 10 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
10 11 9.247861 GTATACTCCCTCCGTTCCTAAATATAA 57.752 37.037 0.00 0.00 0.00 0.98
11 12 8.393259 TGTATACTCCCTCCGTTCCTAAATATA 58.607 37.037 4.17 0.00 0.00 0.86
12 13 7.243824 TGTATACTCCCTCCGTTCCTAAATAT 58.756 38.462 4.17 0.00 0.00 1.28
13 14 6.613699 TGTATACTCCCTCCGTTCCTAAATA 58.386 40.000 4.17 0.00 0.00 1.40
14 15 5.461327 TGTATACTCCCTCCGTTCCTAAAT 58.539 41.667 4.17 0.00 0.00 1.40
15 16 4.870636 TGTATACTCCCTCCGTTCCTAAA 58.129 43.478 4.17 0.00 0.00 1.85
16 17 4.524802 TGTATACTCCCTCCGTTCCTAA 57.475 45.455 4.17 0.00 0.00 2.69
17 18 4.141088 ACATGTATACTCCCTCCGTTCCTA 60.141 45.833 0.00 0.00 0.00 2.94
18 19 3.231818 CATGTATACTCCCTCCGTTCCT 58.768 50.000 4.17 0.00 0.00 3.36
19 20 2.963782 ACATGTATACTCCCTCCGTTCC 59.036 50.000 0.00 0.00 0.00 3.62
20 21 3.799232 GCACATGTATACTCCCTCCGTTC 60.799 52.174 0.00 0.00 0.00 3.95
21 22 2.102588 GCACATGTATACTCCCTCCGTT 59.897 50.000 0.00 0.00 0.00 4.44
22 23 1.687123 GCACATGTATACTCCCTCCGT 59.313 52.381 0.00 0.00 0.00 4.69
23 24 1.686587 TGCACATGTATACTCCCTCCG 59.313 52.381 0.00 0.00 0.00 4.63
24 25 4.283467 TGTATGCACATGTATACTCCCTCC 59.717 45.833 17.46 0.00 41.94 4.30
25 26 5.468540 TGTATGCACATGTATACTCCCTC 57.531 43.478 17.46 0.00 41.94 4.30
37 38 1.643292 GCGCGACATGTATGCACAT 59.357 52.632 12.10 0.00 46.58 3.21
38 39 2.797462 CGCGCGACATGTATGCACA 61.797 57.895 28.94 0.00 39.52 4.57
39 40 2.053984 CGCGCGACATGTATGCAC 60.054 61.111 28.94 10.82 0.00 4.57
40 41 2.508215 ACGCGCGACATGTATGCA 60.508 55.556 39.36 0.00 0.00 3.96
41 42 2.053984 CACGCGCGACATGTATGC 60.054 61.111 39.36 11.54 0.00 3.14
42 43 2.024226 AAGCACGCGCGACATGTATG 62.024 55.000 39.36 23.13 45.49 2.39
43 44 1.752501 GAAGCACGCGCGACATGTAT 61.753 55.000 39.36 16.74 45.49 2.29
44 45 2.431771 AAGCACGCGCGACATGTA 60.432 55.556 39.36 0.00 45.49 2.29
45 46 3.777925 GAAGCACGCGCGACATGT 61.778 61.111 39.36 17.16 45.49 3.21
46 47 1.751536 TATGAAGCACGCGCGACATG 61.752 55.000 39.36 25.53 45.49 3.21
47 48 0.875908 ATATGAAGCACGCGCGACAT 60.876 50.000 39.36 28.89 45.49 3.06
48 49 0.248702 TATATGAAGCACGCGCGACA 60.249 50.000 39.36 25.05 45.49 4.35
49 50 1.060713 ATATATGAAGCACGCGCGAC 58.939 50.000 39.36 27.09 45.49 5.19
50 51 2.095415 AGTATATATGAAGCACGCGCGA 60.095 45.455 39.36 14.00 45.49 5.87
51 52 2.251040 AGTATATATGAAGCACGCGCG 58.749 47.619 30.96 30.96 45.49 6.86
52 53 4.413087 AGTAGTATATATGAAGCACGCGC 58.587 43.478 5.73 0.00 38.99 6.86
53 54 5.870444 AGAGTAGTATATATGAAGCACGCG 58.130 41.667 3.53 3.53 0.00 6.01
54 55 7.079182 AGAGAGTAGTATATATGAAGCACGC 57.921 40.000 0.00 0.00 0.00 5.34
55 56 7.464844 CGGAGAGAGTAGTATATATGAAGCACG 60.465 44.444 0.00 0.00 0.00 5.34
56 57 7.334921 ACGGAGAGAGTAGTATATATGAAGCAC 59.665 40.741 0.00 0.00 0.00 4.40
57 58 7.395617 ACGGAGAGAGTAGTATATATGAAGCA 58.604 38.462 0.00 0.00 0.00 3.91
58 59 7.852971 ACGGAGAGAGTAGTATATATGAAGC 57.147 40.000 0.00 0.00 0.00 3.86
59 60 8.885722 GGAACGGAGAGAGTAGTATATATGAAG 58.114 40.741 0.00 0.00 0.00 3.02
60 61 8.604184 AGGAACGGAGAGAGTAGTATATATGAA 58.396 37.037 0.00 0.00 0.00 2.57
61 62 8.148437 AGGAACGGAGAGAGTAGTATATATGA 57.852 38.462 0.00 0.00 0.00 2.15
62 63 9.887629 TTAGGAACGGAGAGAGTAGTATATATG 57.112 37.037 0.00 0.00 0.00 1.78
67 68 9.810870 AATATTTAGGAACGGAGAGAGTAGTAT 57.189 33.333 0.00 0.00 0.00 2.12
68 69 9.638176 AAATATTTAGGAACGGAGAGAGTAGTA 57.362 33.333 0.00 0.00 0.00 1.82
69 70 8.414778 CAAATATTTAGGAACGGAGAGAGTAGT 58.585 37.037 0.00 0.00 0.00 2.73
70 71 8.414778 ACAAATATTTAGGAACGGAGAGAGTAG 58.585 37.037 0.00 0.00 0.00 2.57
71 72 8.302515 ACAAATATTTAGGAACGGAGAGAGTA 57.697 34.615 0.00 0.00 0.00 2.59
72 73 7.124448 AGACAAATATTTAGGAACGGAGAGAGT 59.876 37.037 0.00 0.00 0.00 3.24
73 74 7.493367 AGACAAATATTTAGGAACGGAGAGAG 58.507 38.462 0.00 0.00 0.00 3.20
74 75 7.419711 AGACAAATATTTAGGAACGGAGAGA 57.580 36.000 0.00 0.00 0.00 3.10
75 76 8.494016 AAAGACAAATATTTAGGAACGGAGAG 57.506 34.615 0.00 0.00 0.00 3.20
76 77 8.319146 AGAAAGACAAATATTTAGGAACGGAGA 58.681 33.333 0.00 0.00 0.00 3.71
77 78 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
78 79 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
79 80 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
108 109 9.037737 GCATCCGTATGTAGTAGTTATTTGAAA 57.962 33.333 0.00 0.00 35.38 2.69
109 110 8.198778 TGCATCCGTATGTAGTAGTTATTTGAA 58.801 33.333 0.00 0.00 35.38 2.69
110 111 7.718525 TGCATCCGTATGTAGTAGTTATTTGA 58.281 34.615 0.00 0.00 35.38 2.69
111 112 7.940178 TGCATCCGTATGTAGTAGTTATTTG 57.060 36.000 0.00 0.00 35.38 2.32
112 113 8.148351 ACATGCATCCGTATGTAGTAGTTATTT 58.852 33.333 0.00 0.00 45.37 1.40
113 114 7.667557 ACATGCATCCGTATGTAGTAGTTATT 58.332 34.615 0.00 0.00 45.37 1.40
114 115 7.228314 ACATGCATCCGTATGTAGTAGTTAT 57.772 36.000 0.00 0.00 45.37 1.89
115 116 6.644248 ACATGCATCCGTATGTAGTAGTTA 57.356 37.500 0.00 0.00 45.37 2.24
116 117 5.531122 ACATGCATCCGTATGTAGTAGTT 57.469 39.130 0.00 0.00 45.37 2.24
122 123 5.722021 ATGTCTACATGCATCCGTATGTA 57.278 39.130 0.00 0.00 45.37 2.29
124 125 7.601073 AAATATGTCTACATGCATCCGTATG 57.399 36.000 0.00 0.00 40.73 2.39
125 126 9.371136 CTAAAATATGTCTACATGCATCCGTAT 57.629 33.333 0.00 0.00 37.15 3.06
126 127 8.581578 TCTAAAATATGTCTACATGCATCCGTA 58.418 33.333 0.00 0.00 37.15 4.02
127 128 7.441836 TCTAAAATATGTCTACATGCATCCGT 58.558 34.615 0.00 0.00 37.15 4.69
128 129 7.600375 ACTCTAAAATATGTCTACATGCATCCG 59.400 37.037 0.00 0.00 37.15 4.18
129 130 8.715998 CACTCTAAAATATGTCTACATGCATCC 58.284 37.037 0.00 0.00 37.15 3.51
130 131 9.265901 ACACTCTAAAATATGTCTACATGCATC 57.734 33.333 0.00 0.00 37.15 3.91
132 133 9.750125 CTACACTCTAAAATATGTCTACATGCA 57.250 33.333 5.85 0.00 37.15 3.96
133 134 9.967346 TCTACACTCTAAAATATGTCTACATGC 57.033 33.333 5.85 0.00 37.15 4.06
153 154 6.073222 ACGGAACAAAATGAGTGAATCTACAC 60.073 38.462 0.00 0.00 40.60 2.90
154 155 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
155 156 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
156 157 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
157 158 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
158 159 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
159 160 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
160 161 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
161 162 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
162 163 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
163 164 6.367969 GTGACTACATACGGAACAAAATGAGT 59.632 38.462 0.00 0.00 0.00 3.41
164 165 6.590292 AGTGACTACATACGGAACAAAATGAG 59.410 38.462 0.00 0.00 0.00 2.90
165 166 6.460781 AGTGACTACATACGGAACAAAATGA 58.539 36.000 0.00 0.00 0.00 2.57
166 167 6.721571 AGTGACTACATACGGAACAAAATG 57.278 37.500 0.00 0.00 0.00 2.32
167 168 6.708949 ACAAGTGACTACATACGGAACAAAAT 59.291 34.615 0.00 0.00 0.00 1.82
168 169 6.050432 ACAAGTGACTACATACGGAACAAAA 58.950 36.000 0.00 0.00 0.00 2.44
169 170 5.603596 ACAAGTGACTACATACGGAACAAA 58.396 37.500 0.00 0.00 0.00 2.83
170 171 5.204409 ACAAGTGACTACATACGGAACAA 57.796 39.130 0.00 0.00 0.00 2.83
171 172 4.859304 ACAAGTGACTACATACGGAACA 57.141 40.909 0.00 0.00 0.00 3.18
172 173 7.642071 TTTAACAAGTGACTACATACGGAAC 57.358 36.000 0.00 0.00 0.00 3.62
173 174 8.714179 CATTTTAACAAGTGACTACATACGGAA 58.286 33.333 0.00 0.00 0.00 4.30
174 175 7.874016 ACATTTTAACAAGTGACTACATACGGA 59.126 33.333 0.00 0.00 0.00 4.69
175 176 8.025243 ACATTTTAACAAGTGACTACATACGG 57.975 34.615 0.00 0.00 0.00 4.02
176 177 8.922676 AGACATTTTAACAAGTGACTACATACG 58.077 33.333 0.00 0.00 0.00 3.06
183 184 9.832445 TCTTTCTAGACATTTTAACAAGTGACT 57.168 29.630 0.00 0.00 31.45 3.41
200 201 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
201 202 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
202 203 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
203 204 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
204 205 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
205 206 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
206 207 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
207 208 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
208 209 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
209 210 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
210 211 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
211 212 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
212 213 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
213 214 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
214 215 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
215 216 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
216 217 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
217 218 4.803329 ATACTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
218 219 5.912149 TTATACTACTCCCTCCGTTCCTA 57.088 43.478 0.00 0.00 0.00 2.94
219 220 4.803329 TTATACTACTCCCTCCGTTCCT 57.197 45.455 0.00 0.00 0.00 3.36
220 221 6.071672 GGTATTTATACTACTCCCTCCGTTCC 60.072 46.154 0.37 0.00 33.81 3.62
221 222 6.491403 TGGTATTTATACTACTCCCTCCGTTC 59.509 42.308 0.37 0.00 33.81 3.95
222 223 6.266330 GTGGTATTTATACTACTCCCTCCGTT 59.734 42.308 8.59 0.00 40.35 4.44
223 224 5.772169 GTGGTATTTATACTACTCCCTCCGT 59.228 44.000 8.59 0.00 40.35 4.69
224 225 6.264841 GTGGTATTTATACTACTCCCTCCG 57.735 45.833 8.59 0.00 40.35 4.63
268 269 8.400186 CAAATCAACATGATCATGCTAGTTGTA 58.600 33.333 31.17 18.05 42.39 2.41
349 350 3.027412 ACAGTGATCTTGAGGAGCGTAT 58.973 45.455 0.00 0.00 32.20 3.06
350 351 2.423892 GACAGTGATCTTGAGGAGCGTA 59.576 50.000 0.00 0.00 32.20 4.42
1095 1096 1.670406 GCTCCAGCAGCCATATCCG 60.670 63.158 0.00 0.00 43.17 4.18
1098 1099 1.370437 CTCGCTCCAGCAGCCATAT 59.630 57.895 0.00 0.00 46.74 1.78
1141 1142 3.680458 CGATCGAGATAGACGGATCAAGA 59.320 47.826 10.26 0.00 35.02 3.02
1161 1162 3.531207 CCTGATCGAGGCAGCCGA 61.531 66.667 5.55 0.11 40.53 5.54
1176 1177 3.706594 TGTTAATCGAATGAGAGAGGCCT 59.293 43.478 3.86 3.86 0.00 5.19
1254 1255 6.651755 ATTAAGCAAAGCAAATGAATTCCG 57.348 33.333 2.27 0.00 0.00 4.30
1391 1392 2.539432 TGATGAGCTTCTCCTCCTCA 57.461 50.000 0.00 0.00 39.65 3.86
1961 1966 1.725641 TGAGTGGTTGATAAGCGCAG 58.274 50.000 11.47 0.00 41.58 5.18
1962 1967 2.093500 AGATGAGTGGTTGATAAGCGCA 60.093 45.455 11.47 0.00 41.58 6.09
1963 1968 2.286294 CAGATGAGTGGTTGATAAGCGC 59.714 50.000 0.00 0.00 39.55 5.92
1964 1969 3.553511 GTCAGATGAGTGGTTGATAAGCG 59.446 47.826 0.00 0.00 0.00 4.68
1974 1979 0.392193 GGCACAGGTCAGATGAGTGG 60.392 60.000 0.00 0.00 0.00 4.00
2038 2044 2.159114 TGCATGCGACATTAGCTACAGA 60.159 45.455 14.09 0.00 35.28 3.41
2077 2083 6.735130 ACACCGTTTCTTTTTAGGAGATTTG 58.265 36.000 0.00 0.00 0.00 2.32
2110 2116 0.596577 GCCATGCATGATCGAGCAAT 59.403 50.000 28.31 0.00 44.88 3.56
2113 2119 1.895231 TGGCCATGCATGATCGAGC 60.895 57.895 28.31 20.51 0.00 5.03
2194 2200 9.674068 CATATACATAGACTAGCTAGACCAGAA 57.326 37.037 27.45 7.56 31.33 3.02
2196 2202 7.554476 TGCATATACATAGACTAGCTAGACCAG 59.446 40.741 27.45 14.89 31.33 4.00
2197 2203 7.402862 TGCATATACATAGACTAGCTAGACCA 58.597 38.462 27.45 10.84 31.33 4.02
2198 2204 7.867305 TGCATATACATAGACTAGCTAGACC 57.133 40.000 27.45 16.99 31.33 3.85
2199 2205 8.731605 TGTTGCATATACATAGACTAGCTAGAC 58.268 37.037 27.45 20.68 31.33 2.59
2200 2206 8.863872 TGTTGCATATACATAGACTAGCTAGA 57.136 34.615 27.45 5.35 31.33 2.43
2201 2207 9.729023 GATGTTGCATATACATAGACTAGCTAG 57.271 37.037 19.44 19.44 36.41 3.42
2202 2208 9.243105 TGATGTTGCATATACATAGACTAGCTA 57.757 33.333 2.52 0.00 36.41 3.32
2203 2209 8.127150 TGATGTTGCATATACATAGACTAGCT 57.873 34.615 2.52 0.00 36.41 3.32
2204 2210 7.009999 GCTGATGTTGCATATACATAGACTAGC 59.990 40.741 2.52 5.21 36.41 3.42
2296 2302 2.443887 TGTTGTTAGGGTAGTCGTGC 57.556 50.000 0.00 0.00 0.00 5.34
2317 2323 5.798934 CAGTAGTACGTACCACTTCATTGAC 59.201 44.000 21.84 1.30 31.06 3.18
2352 2365 2.158885 CCCTGAAGAAACCCTAGCTAGC 60.159 54.545 15.74 6.62 0.00 3.42
2353 2366 2.158885 GCCCTGAAGAAACCCTAGCTAG 60.159 54.545 14.20 14.20 0.00 3.42
2354 2367 1.838077 GCCCTGAAGAAACCCTAGCTA 59.162 52.381 0.00 0.00 0.00 3.32
2371 2384 4.017126 AGCTAGTTTTGGTATCTTTGCCC 58.983 43.478 0.00 0.00 0.00 5.36
2379 2392 7.419711 TCACTAAGCTAGCTAGTTTTGGTAT 57.580 36.000 25.25 7.64 0.00 2.73
2381 2394 5.740290 TCACTAAGCTAGCTAGTTTTGGT 57.260 39.130 25.25 20.66 0.00 3.67
2388 2401 6.478344 CCTTTTGTCATCACTAAGCTAGCTAG 59.522 42.308 19.70 16.84 0.00 3.42
2449 2462 2.029244 CACCTGCAATACGAGCGTAAAG 59.971 50.000 6.84 4.12 33.99 1.85
2450 2463 1.996898 CACCTGCAATACGAGCGTAAA 59.003 47.619 6.84 0.00 33.99 2.01
2452 2465 0.179121 CCACCTGCAATACGAGCGTA 60.179 55.000 5.12 5.12 34.87 4.42
2453 2466 1.447838 CCACCTGCAATACGAGCGT 60.448 57.895 0.00 0.00 33.85 5.07
2454 2467 2.173669 CCCACCTGCAATACGAGCG 61.174 63.158 0.00 0.00 33.85 5.03
2455 2468 2.472909 GCCCACCTGCAATACGAGC 61.473 63.158 0.00 0.00 0.00 5.03
2456 2469 1.819632 GGCCCACCTGCAATACGAG 60.820 63.158 0.00 0.00 0.00 4.18
2457 2470 2.270850 GGCCCACCTGCAATACGA 59.729 61.111 0.00 0.00 0.00 3.43
2603 2616 0.968901 TGTTAGGTGGGCTCGTCGAT 60.969 55.000 0.00 0.00 0.00 3.59
2813 2826 2.816360 CGGGCAGTGATGCGACATG 61.816 63.158 0.00 0.00 35.24 3.21
2885 2898 2.360350 ATGAACGGGTGCTGCTGG 60.360 61.111 0.00 0.00 0.00 4.85
3110 3123 1.270414 ACTGCTCATGCTGCCCTAGT 61.270 55.000 0.00 3.16 41.07 2.57
3208 3221 3.010138 TCCCATAAAAAGGAGGGAGTGTG 59.990 47.826 0.00 0.00 45.15 3.82
3341 3360 5.068198 AGCAGAATGAGCTAGAGAGAGAAAG 59.932 44.000 0.00 0.00 41.32 2.62
3440 3459 9.987272 AACCAAAAGATTAGGAAAATTTGAGAG 57.013 29.630 0.00 0.00 31.23 3.20
3458 3477 6.340522 ACATTCTTCACTCCAAAACCAAAAG 58.659 36.000 0.00 0.00 0.00 2.27
3612 3636 4.263018 AGAATCCAAAAGAGCAAAAGGC 57.737 40.909 0.00 0.00 45.30 4.35
3733 3757 5.357257 TGTCCTTAGAGAACAGAACAACAC 58.643 41.667 0.00 0.00 0.00 3.32
3793 3819 2.616001 GGGCCGTGTGTGGTAGATTTTA 60.616 50.000 0.00 0.00 0.00 1.52
3877 3903 4.481930 TTCAAGACGGCTTAAACACATG 57.518 40.909 1.37 0.00 31.81 3.21
3888 3914 6.857964 CCATACATATTGATTTTCAAGACGGC 59.142 38.462 0.00 0.00 40.05 5.68
3954 3982 1.868713 TCTCTATTACCACCCCGCAA 58.131 50.000 0.00 0.00 0.00 4.85
4093 4123 4.208045 TGGGGATGATCTCCTCTTGAAGG 61.208 52.174 13.41 0.00 45.90 3.46
4100 4130 3.099141 GAGAGATGGGGATGATCTCCTC 58.901 54.545 13.41 7.70 44.82 3.71
4220 4250 2.565046 TGACAGATGGTGAATGCACA 57.435 45.000 6.08 0.00 46.96 4.57


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

AutoCloner maintained by Alex Coulton.