Multiple sequence alignment - TraesCS2B01G001400

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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 TraesCS2B01G001400 chr2B 100.000 4902 0 0 1 4902 1170680 1175581 0.000000e+00 9053
1 TraesCS2B01G001400 chr2B 92.261 2830 196 13 222 3031 4882277 4885103 0.000000e+00 3991
2 TraesCS2B01G001400 chr2B 95.354 2497 107 8 2409 4902 1266390 1263900 0.000000e+00 3960
3 TraesCS2B01G001400 chr2B 85.731 3406 462 12 373 3774 1248921 1252306 0.000000e+00 3576
4 TraesCS2B01G001400 chr2B 81.309 3467 594 38 350 3804 2643174 2639750 0.000000e+00 2763
5 TraesCS2B01G001400 chr2B 84.329 2795 411 19 1039 3809 1309961 1307170 0.000000e+00 2710
6 TraesCS2B01G001400 chr2B 84.029 2805 410 23 1039 3809 3685294 3688094 0.000000e+00 2663
7 TraesCS2B01G001400 chr2B 88.092 1646 160 14 3033 4670 4886406 4888023 0.000000e+00 1921
8 TraesCS2B01G001400 chr2B 80.039 516 86 11 272 774 1310515 1310004 2.790000e-97 366
9 TraesCS2B01G001400 chr2B 80.039 516 86 11 272 774 3684740 3685251 2.790000e-97 366
10 TraesCS2B01G001400 chr2B 90.164 244 21 2 4659 4902 4903125 4903365 1.020000e-81 315
11 TraesCS2B01G001400 chr2B 84.848 297 29 10 4187 4471 3655289 3654997 8.030000e-73 285
12 TraesCS2B01G001400 chr2B 91.707 205 13 3 4223 4426 3657411 3657210 1.040000e-71 281
13 TraesCS2B01G001400 chr2B 84.175 297 32 8 4187 4471 3473535 3473242 1.740000e-69 274
14 TraesCS2B01G001400 chr2B 83.607 244 26 8 3941 4181 1306936 1306704 2.970000e-52 217
15 TraesCS2B01G001400 chr2B 83.607 244 26 8 3941 4181 3688328 3688560 2.970000e-52 217
16 TraesCS2B01G001400 chr2B 82.787 244 28 8 3941 4181 3657737 3657505 6.430000e-49 206
17 TraesCS2B01G001400 chr2B 87.387 111 13 1 3923 4032 1252522 1252632 5.150000e-25 126
18 TraesCS2B01G001400 chr2D 94.006 4705 246 23 222 4902 6593714 6598406 0.000000e+00 7094
19 TraesCS2B01G001400 chr2D 87.249 2690 329 12 1081 3764 6523003 6525684 0.000000e+00 3055
20 TraesCS2B01G001400 chr2D 85.088 2783 399 14 1039 3809 6600557 6603335 0.000000e+00 2826
21 TraesCS2B01G001400 chr2D 85.119 504 72 2 370 870 6522502 6523005 3.380000e-141 512
22 TraesCS2B01G001400 chr2D 84.746 295 30 9 4187 4469 6526302 6526593 1.040000e-71 281
23 TraesCS2B01G001400 chr2D 84.677 124 15 3 3921 4040 6603530 6603653 2.400000e-23 121
24 TraesCS2B01G001400 chr2A 94.976 4180 197 12 695 4869 4937423 4941594 0.000000e+00 6543
25 TraesCS2B01G001400 chr2A 85.043 2788 396 16 1039 3809 4944747 4947530 0.000000e+00 2819
26 TraesCS2B01G001400 chr2A 97.719 263 3 2 4640 4902 4942203 4942462 2.690000e-122 449
27 TraesCS2B01G001400 chr2A 79.871 621 106 7 267 871 4920136 4920753 2.100000e-118 436
28 TraesCS2B01G001400 chr2A 88.739 222 19 4 4225 4443 4949594 4949812 2.910000e-67 267
29 TraesCS2B01G001400 chrUn 80.039 516 86 11 272 774 321154808 321154297 2.790000e-97 366


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 TraesCS2B01G001400 chr2B 1170680 1175581 4901 False 9053.000000 9053 100.000000 1 4902 1 chr2B.!!$F1 4901
1 TraesCS2B01G001400 chr2B 1263900 1266390 2490 True 3960.000000 3960 95.354000 2409 4902 1 chr2B.!!$R1 2493
2 TraesCS2B01G001400 chr2B 4882277 4888023 5746 False 2956.000000 3991 90.176500 222 4670 2 chr2B.!!$F5 4448
3 TraesCS2B01G001400 chr2B 2639750 2643174 3424 True 2763.000000 2763 81.309000 350 3804 1 chr2B.!!$R2 3454
4 TraesCS2B01G001400 chr2B 1248921 1252632 3711 False 1851.000000 3576 86.559000 373 4032 2 chr2B.!!$F3 3659
5 TraesCS2B01G001400 chr2B 1306704 1310515 3811 True 1097.666667 2710 82.658333 272 4181 3 chr2B.!!$R4 3909
6 TraesCS2B01G001400 chr2B 3684740 3688560 3820 False 1082.000000 2663 82.558333 272 4181 3 chr2B.!!$F4 3909
7 TraesCS2B01G001400 chr2B 3654997 3657737 2740 True 257.333333 285 86.447333 3941 4471 3 chr2B.!!$R5 530
8 TraesCS2B01G001400 chr2D 6593714 6603653 9939 False 3347.000000 7094 87.923667 222 4902 3 chr2D.!!$F2 4680
9 TraesCS2B01G001400 chr2D 6522502 6526593 4091 False 1282.666667 3055 85.704667 370 4469 3 chr2D.!!$F1 4099
10 TraesCS2B01G001400 chr2A 4937423 4949812 12389 False 2519.500000 6543 91.619250 695 4902 4 chr2A.!!$F2 4207
11 TraesCS2B01G001400 chr2A 4920136 4920753 617 False 436.000000 436 79.871000 267 871 1 chr2A.!!$F1 604
12 TraesCS2B01G001400 chrUn 321154297 321154808 511 True 366.000000 366 80.039000 272 774 1 chrUn.!!$R1 502

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
68 69 0.101399 AGACGTCGAGGATGTGATGC 59.899 55.0 12.85 0.0 31.35 3.91 F
93 94 0.321564 CACTTTCCTGCACGGATGGA 60.322 55.0 5.83 0.0 42.70 3.41 F
97 98 0.617935 TTCCTGCACGGATGGATGAA 59.382 50.0 5.83 0.0 42.70 2.57 F
345 351 0.902531 TAGCTTTGAACCCCTCCTCG 59.097 55.0 0.00 0.0 0.00 4.63 F
465 490 1.089112 CCTCGCATGATTTCTGCACA 58.911 50.0 0.00 0.0 39.64 4.57 F
2255 9272 0.546747 TTCCTCGGGACCTTCACCAT 60.547 55.0 0.00 0.0 0.00 3.55 F
2389 9406 1.388547 TTTTGCGGAACAAGAGCTGT 58.611 45.0 0.00 0.0 40.06 4.40 F
3632 17973 0.739112 TGCAATGCGCGATGTCTACA 60.739 50.0 12.10 0.0 46.97 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1548 1.350684 TCAGCAGCTGGGTACAATTCA 59.649 47.619 22.62 0.0 31.51 2.57 R
1621 1658 2.158623 TGCCAGAGATGTTGTTTGACCT 60.159 45.455 0.00 0.0 0.00 3.85 R
1839 1876 2.426522 CTTCCACTCAGCCGATTTTCA 58.573 47.619 0.00 0.0 0.00 2.69 R
1849 1886 3.616956 TTCAGGTATGCTTCCACTCAG 57.383 47.619 0.00 0.0 0.00 3.35 R
2389 9406 3.430374 GGTACCGAAGCAAAGCATCTAGA 60.430 47.826 0.00 0.0 0.00 2.43 R
3614 17955 0.042708 CTGTAGACATCGCGCATTGC 60.043 55.000 8.75 0.0 41.47 3.56 R
3703 18044 0.239879 TTCATCGACCGCCTTTTTGC 59.760 50.000 0.00 0.0 0.00 3.68 R
4765 20949 0.397675 TCTCATCCGATGCCAGAGGT 60.398 55.000 3.25 0.0 0.00 3.85 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
21 22 2.398498 GATCTATATATGCCGCCGCTG 58.602 52.381 0.00 0.00 35.36 5.18
22 23 1.470051 TCTATATATGCCGCCGCTGA 58.530 50.000 0.00 0.00 35.36 4.26
23 24 1.822371 TCTATATATGCCGCCGCTGAA 59.178 47.619 0.00 0.00 35.36 3.02
25 26 0.608130 ATATATGCCGCCGCTGAAGA 59.392 50.000 0.00 0.00 35.36 2.87
27 28 3.921475 TATATGCCGCCGCTGAAGACG 62.921 57.143 0.00 0.00 35.36 4.18
30 31 3.777925 CCGCCGCTGAAGACGTTG 61.778 66.667 0.00 0.00 0.00 4.10
33 34 2.668280 GCCGCTGAAGACGTTGACC 61.668 63.158 0.00 0.00 0.00 4.02
34 35 1.300620 CCGCTGAAGACGTTGACCA 60.301 57.895 0.00 0.00 0.00 4.02
35 36 0.670546 CCGCTGAAGACGTTGACCAT 60.671 55.000 0.00 0.00 0.00 3.55
36 37 0.439985 CGCTGAAGACGTTGACCATG 59.560 55.000 0.00 0.00 0.00 3.66
38 39 1.461127 GCTGAAGACGTTGACCATGAC 59.539 52.381 0.00 0.00 0.00 3.06
39 40 2.868044 GCTGAAGACGTTGACCATGACT 60.868 50.000 0.00 0.00 0.00 3.41
40 41 2.989840 CTGAAGACGTTGACCATGACTC 59.010 50.000 0.00 0.00 0.00 3.36
41 42 2.288825 TGAAGACGTTGACCATGACTCC 60.289 50.000 0.00 0.00 0.00 3.85
42 43 1.338107 AGACGTTGACCATGACTCCA 58.662 50.000 0.00 0.00 0.00 3.86
53 54 0.826715 ATGACTCCATGACCCAGACG 59.173 55.000 0.00 0.00 0.00 4.18
55 56 0.173708 GACTCCATGACCCAGACGTC 59.826 60.000 7.70 7.70 0.00 4.34
56 57 1.139734 CTCCATGACCCAGACGTCG 59.860 63.158 10.46 5.16 35.40 5.12
57 58 1.303806 TCCATGACCCAGACGTCGA 60.304 57.895 10.46 0.00 35.40 4.20
58 59 1.139734 CCATGACCCAGACGTCGAG 59.860 63.158 10.46 7.00 35.40 4.04
59 60 1.139734 CATGACCCAGACGTCGAGG 59.860 63.158 21.15 21.15 35.40 4.63
60 61 1.001269 ATGACCCAGACGTCGAGGA 60.001 57.895 27.25 11.77 35.40 3.71
61 62 0.395862 ATGACCCAGACGTCGAGGAT 60.396 55.000 27.25 14.42 35.40 3.24
62 63 1.313091 TGACCCAGACGTCGAGGATG 61.313 60.000 27.25 15.93 35.40 3.51
64 65 1.139734 CCCAGACGTCGAGGATGTG 59.860 63.158 25.56 10.92 31.35 3.21
65 66 1.313091 CCCAGACGTCGAGGATGTGA 61.313 60.000 25.56 0.00 31.35 3.58
66 67 0.741326 CCAGACGTCGAGGATGTGAT 59.259 55.000 21.12 0.00 31.35 3.06
67 68 1.534805 CCAGACGTCGAGGATGTGATG 60.535 57.143 21.12 5.80 31.35 3.07
68 69 0.101399 AGACGTCGAGGATGTGATGC 59.899 55.000 12.85 0.00 31.35 3.91
69 70 1.202973 GACGTCGAGGATGTGATGCG 61.203 60.000 12.85 0.00 31.35 4.73
71 72 1.519234 GTCGAGGATGTGATGCGCA 60.519 57.895 14.96 14.96 0.00 6.09
72 73 0.877649 GTCGAGGATGTGATGCGCAT 60.878 55.000 25.66 25.66 37.29 4.73
73 74 0.877213 TCGAGGATGTGATGCGCATG 60.877 55.000 30.76 10.09 34.53 4.06
74 75 1.281960 GAGGATGTGATGCGCATGC 59.718 57.895 30.76 20.21 41.74 4.06
84 85 2.505557 GCGCATGCACTTTCCTGC 60.506 61.111 19.57 6.33 42.15 4.85
89 90 2.508436 TGCACTTTCCTGCACGGA 59.492 55.556 1.25 1.25 42.36 4.69
90 91 1.073025 TGCACTTTCCTGCACGGAT 59.927 52.632 5.83 0.00 42.36 4.18
91 92 1.236616 TGCACTTTCCTGCACGGATG 61.237 55.000 5.83 3.66 42.36 3.51
92 93 1.926511 GCACTTTCCTGCACGGATGG 61.927 60.000 5.83 0.00 42.70 3.51
93 94 0.321564 CACTTTCCTGCACGGATGGA 60.322 55.000 5.83 0.00 42.70 3.41
94 95 0.620556 ACTTTCCTGCACGGATGGAT 59.379 50.000 5.83 0.00 42.70 3.41
95 96 1.019673 CTTTCCTGCACGGATGGATG 58.980 55.000 5.83 0.00 42.70 3.51
97 98 0.617935 TTCCTGCACGGATGGATGAA 59.382 50.000 5.83 0.00 42.70 2.57
98 99 0.617935 TCCTGCACGGATGGATGAAA 59.382 50.000 1.25 0.00 36.69 2.69
99 100 1.019673 CCTGCACGGATGGATGAAAG 58.980 55.000 0.00 0.00 33.16 2.62
101 102 1.938577 CTGCACGGATGGATGAAAGAG 59.061 52.381 0.00 0.00 0.00 2.85
103 104 2.027285 TGCACGGATGGATGAAAGAGAA 60.027 45.455 0.00 0.00 0.00 2.87
104 105 3.209410 GCACGGATGGATGAAAGAGAAT 58.791 45.455 0.00 0.00 0.00 2.40
105 106 3.003068 GCACGGATGGATGAAAGAGAATG 59.997 47.826 0.00 0.00 0.00 2.67
106 107 3.003068 CACGGATGGATGAAAGAGAATGC 59.997 47.826 0.00 0.00 0.00 3.56
107 108 3.208594 CGGATGGATGAAAGAGAATGCA 58.791 45.455 0.00 0.00 0.00 3.96
108 109 3.003068 CGGATGGATGAAAGAGAATGCAC 59.997 47.826 0.00 0.00 0.00 4.57
109 110 4.205587 GGATGGATGAAAGAGAATGCACT 58.794 43.478 0.00 0.00 0.00 4.40
110 111 4.036498 GGATGGATGAAAGAGAATGCACTG 59.964 45.833 0.00 0.00 0.00 3.66
111 112 2.751259 TGGATGAAAGAGAATGCACTGC 59.249 45.455 0.00 0.00 0.00 4.40
112 113 2.751259 GGATGAAAGAGAATGCACTGCA 59.249 45.455 6.09 6.09 44.86 4.41
113 114 3.181499 GGATGAAAGAGAATGCACTGCAG 60.181 47.826 13.48 13.48 43.65 4.41
116 117 2.283145 AAGAGAATGCACTGCAGGTT 57.717 45.000 19.93 7.13 43.65 3.50
117 118 1.818642 AGAGAATGCACTGCAGGTTC 58.181 50.000 19.93 15.41 43.65 3.62
118 119 1.072806 AGAGAATGCACTGCAGGTTCA 59.927 47.619 19.93 12.65 43.65 3.18
119 120 1.881973 GAGAATGCACTGCAGGTTCAA 59.118 47.619 19.93 0.00 43.65 2.69
121 122 2.230508 AGAATGCACTGCAGGTTCAATG 59.769 45.455 19.93 7.04 43.65 2.82
132 133 5.954296 GCAGGTTCAATGCATGATACTAT 57.046 39.130 0.00 0.00 43.31 2.12
133 134 5.936054 GCAGGTTCAATGCATGATACTATC 58.064 41.667 0.00 0.00 43.31 2.08
134 135 5.106396 GCAGGTTCAATGCATGATACTATCC 60.106 44.000 0.00 0.00 43.31 2.59
135 136 5.413833 CAGGTTCAATGCATGATACTATCCC 59.586 44.000 0.00 0.00 38.03 3.85
136 137 4.393062 GGTTCAATGCATGATACTATCCCG 59.607 45.833 0.00 0.00 38.03 5.14
138 139 5.227569 TCAATGCATGATACTATCCCGTT 57.772 39.130 0.00 0.00 31.50 4.44
140 141 6.398095 TCAATGCATGATACTATCCCGTTAG 58.602 40.000 0.00 0.00 31.50 2.34
141 142 6.014584 TCAATGCATGATACTATCCCGTTAGT 60.015 38.462 0.00 0.00 33.30 2.24
142 143 5.134202 TGCATGATACTATCCCGTTAGTG 57.866 43.478 0.00 0.00 34.35 2.74
154 155 3.515330 CCGTTAGTGGGATCTTAACGT 57.485 47.619 20.04 0.00 41.02 3.99
155 156 4.637483 CCGTTAGTGGGATCTTAACGTA 57.363 45.455 20.04 0.00 41.02 3.57
156 157 4.997565 CCGTTAGTGGGATCTTAACGTAA 58.002 43.478 20.04 6.37 41.02 3.18
157 158 5.410067 CCGTTAGTGGGATCTTAACGTAAA 58.590 41.667 20.04 0.00 41.02 2.01
158 159 6.044682 CCGTTAGTGGGATCTTAACGTAAAT 58.955 40.000 20.04 0.00 41.02 1.40
159 160 6.019318 CCGTTAGTGGGATCTTAACGTAAATG 60.019 42.308 20.04 9.27 41.02 2.32
161 162 7.043590 CGTTAGTGGGATCTTAACGTAAATGAG 60.044 40.741 16.64 0.00 38.74 2.90
162 163 5.671493 AGTGGGATCTTAACGTAAATGAGG 58.329 41.667 0.00 0.00 0.00 3.86
163 164 5.424252 AGTGGGATCTTAACGTAAATGAGGA 59.576 40.000 0.00 0.00 0.00 3.71
164 165 6.099845 AGTGGGATCTTAACGTAAATGAGGAT 59.900 38.462 0.00 0.00 0.00 3.24
165 166 6.424207 GTGGGATCTTAACGTAAATGAGGATC 59.576 42.308 0.00 0.00 0.00 3.36
179 180 4.063998 TGAGGATCATGTACATGCTCAC 57.936 45.455 30.56 24.64 42.56 3.51
180 181 3.055591 GAGGATCATGTACATGCTCACG 58.944 50.000 30.56 11.12 36.09 4.35
182 183 2.797156 GGATCATGTACATGCTCACGTC 59.203 50.000 30.56 19.68 36.09 4.34
184 185 3.150848 TCATGTACATGCTCACGTCTC 57.849 47.619 27.71 0.00 38.65 3.36
185 186 2.491693 TCATGTACATGCTCACGTCTCA 59.508 45.455 27.71 6.70 38.65 3.27
186 187 3.056891 TCATGTACATGCTCACGTCTCAA 60.057 43.478 27.71 6.21 38.65 3.02
187 188 2.672714 TGTACATGCTCACGTCTCAAC 58.327 47.619 0.00 0.00 0.00 3.18
188 189 2.296190 TGTACATGCTCACGTCTCAACT 59.704 45.455 0.00 0.00 0.00 3.16
189 190 2.071688 ACATGCTCACGTCTCAACTC 57.928 50.000 0.00 0.00 0.00 3.01
190 191 1.615883 ACATGCTCACGTCTCAACTCT 59.384 47.619 0.00 0.00 0.00 3.24
191 192 2.820197 ACATGCTCACGTCTCAACTCTA 59.180 45.455 0.00 0.00 0.00 2.43
192 193 3.445450 ACATGCTCACGTCTCAACTCTAT 59.555 43.478 0.00 0.00 0.00 1.98
193 194 4.081972 ACATGCTCACGTCTCAACTCTATT 60.082 41.667 0.00 0.00 0.00 1.73
197 198 6.093404 TGCTCACGTCTCAACTCTATTAAAG 58.907 40.000 0.00 0.00 0.00 1.85
198 199 5.004916 GCTCACGTCTCAACTCTATTAAAGC 59.995 44.000 0.00 0.00 0.00 3.51
200 201 6.631016 TCACGTCTCAACTCTATTAAAGCAT 58.369 36.000 0.00 0.00 0.00 3.79
201 202 6.531594 TCACGTCTCAACTCTATTAAAGCATG 59.468 38.462 0.00 0.00 0.00 4.06
202 203 5.292101 ACGTCTCAACTCTATTAAAGCATGC 59.708 40.000 10.51 10.51 0.00 4.06
204 205 5.520288 GTCTCAACTCTATTAAAGCATGCGA 59.480 40.000 13.01 0.14 0.00 5.10
205 206 5.520288 TCTCAACTCTATTAAAGCATGCGAC 59.480 40.000 13.01 0.00 0.00 5.19
206 207 5.175127 TCAACTCTATTAAAGCATGCGACA 58.825 37.500 13.01 0.00 0.00 4.35
207 208 5.063438 TCAACTCTATTAAAGCATGCGACAC 59.937 40.000 13.01 0.00 0.00 3.67
208 209 4.503910 ACTCTATTAAAGCATGCGACACA 58.496 39.130 13.01 0.00 0.00 3.72
209 210 5.118990 ACTCTATTAAAGCATGCGACACAT 58.881 37.500 13.01 4.94 40.66 3.21
210 211 6.280643 ACTCTATTAAAGCATGCGACACATA 58.719 36.000 13.01 5.85 36.64 2.29
211 212 6.201044 ACTCTATTAAAGCATGCGACACATAC 59.799 38.462 13.01 0.00 36.64 2.39
212 213 4.552166 ATTAAAGCATGCGACACATACC 57.448 40.909 13.01 0.00 36.64 2.73
213 214 2.113860 AAAGCATGCGACACATACCT 57.886 45.000 13.01 0.00 36.64 3.08
214 215 1.372582 AAGCATGCGACACATACCTG 58.627 50.000 13.01 0.00 36.64 4.00
216 217 2.016961 CATGCGACACATACCTGCC 58.983 57.895 0.00 0.00 36.64 4.85
217 218 1.153168 ATGCGACACATACCTGCCC 60.153 57.895 0.00 0.00 37.17 5.36
218 219 2.513897 GCGACACATACCTGCCCC 60.514 66.667 0.00 0.00 0.00 5.80
219 220 2.202878 CGACACATACCTGCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
220 221 2.189521 GACACATACCTGCCCCGG 59.810 66.667 0.00 0.00 0.00 5.73
276 279 2.157834 TCATGTCCACCACGTTACAC 57.842 50.000 0.00 0.00 0.00 2.90
313 319 5.536916 GTCTGTCCTATGTTAGTAGCCATCT 59.463 44.000 0.00 0.00 0.00 2.90
316 322 6.136857 TGTCCTATGTTAGTAGCCATCTTCT 58.863 40.000 0.00 0.00 0.00 2.85
324 330 2.428890 AGTAGCCATCTTCTTCCTGTCG 59.571 50.000 0.00 0.00 0.00 4.35
326 332 1.625818 AGCCATCTTCTTCCTGTCGTT 59.374 47.619 0.00 0.00 0.00 3.85
341 347 2.074576 GTCGTTAGCTTTGAACCCCTC 58.925 52.381 0.00 0.00 0.00 4.30
342 348 1.002773 TCGTTAGCTTTGAACCCCTCC 59.997 52.381 0.00 0.00 0.00 4.30
345 351 0.902531 TAGCTTTGAACCCCTCCTCG 59.097 55.000 0.00 0.00 0.00 4.63
375 393 2.031516 CACCGCAGACAAGAGCAGG 61.032 63.158 0.00 0.00 0.00 4.85
452 477 2.110213 GAACCACACCACCTCGCA 59.890 61.111 0.00 0.00 0.00 5.10
453 478 1.302511 GAACCACACCACCTCGCAT 60.303 57.895 0.00 0.00 0.00 4.73
465 490 1.089112 CCTCGCATGATTTCTGCACA 58.911 50.000 0.00 0.00 39.64 4.57
491 519 2.887568 CGTCTCATGCGCCAGGAC 60.888 66.667 4.18 7.37 0.00 3.85
963 991 4.474651 ACCATCATGGAGATACACCTTTGA 59.525 41.667 11.90 0.00 40.96 2.69
1132 1160 2.173519 ACCAGTTGCAAGGATCCATTG 58.826 47.619 15.82 15.70 0.00 2.82
1206 1234 1.556911 CTGTCAGGAATAGTGCCACCT 59.443 52.381 0.00 0.00 0.00 4.00
1294 1322 3.801698 CCTTCTGACATGGGTATCACAG 58.198 50.000 0.00 0.00 0.00 3.66
1311 1339 2.806244 CACAGTTCCTAACCTCCAAACG 59.194 50.000 0.00 0.00 0.00 3.60
1368 1396 1.616725 CCTGCCTCCCTACAAAATGCA 60.617 52.381 0.00 0.00 0.00 3.96
1418 1455 1.484444 AACTCTCTGACTGGGGTGGC 61.484 60.000 0.00 0.00 0.00 5.01
1511 1548 3.652869 TGGACATTCTTCTCCTCTTTGGT 59.347 43.478 0.00 0.00 37.07 3.67
1621 1658 3.090037 AGCTTGACCGCTCTAACTCTTA 58.910 45.455 0.00 0.00 34.57 2.10
1796 1833 5.254032 ACAAATTTTCAGGAGAGATACCCCT 59.746 40.000 0.00 0.00 0.00 4.79
1839 1876 5.477984 TCAACTGGAAGAGCTTTATTTGCAT 59.522 36.000 0.00 0.00 37.43 3.96
1849 1886 4.567959 AGCTTTATTTGCATGAAAATCGGC 59.432 37.500 15.21 16.11 32.16 5.54
2255 9272 0.546747 TTCCTCGGGACCTTCACCAT 60.547 55.000 0.00 0.00 0.00 3.55
2389 9406 1.388547 TTTTGCGGAACAAGAGCTGT 58.611 45.000 0.00 0.00 40.06 4.40
2683 15707 2.933492 GCACAAGATGGTACGGTTGCTA 60.933 50.000 0.00 0.00 0.00 3.49
2689 15713 6.655848 ACAAGATGGTACGGTTGCTATTAAAA 59.344 34.615 0.00 0.00 0.00 1.52
2838 15862 3.093057 TGAGTTCAGGGCTCTAGTCTTC 58.907 50.000 0.00 0.00 34.30 2.87
2844 15868 2.614983 CAGGGCTCTAGTCTTCGAGTAC 59.385 54.545 0.00 0.00 0.00 2.73
2931 15955 5.350640 CGCAGTGATATGCATATCAGTTGAT 59.649 40.000 37.69 23.78 46.14 2.57
2949 15973 7.020010 CAGTTGATATTTCTTGTGCTCTTGAC 58.980 38.462 0.00 0.00 0.00 3.18
2963 15987 6.607600 TGTGCTCTTGACTACCTACATAATCT 59.392 38.462 0.00 0.00 0.00 2.40
3025 16049 5.238432 AGCAACATACTTTTCGACAATGACA 59.762 36.000 0.00 0.00 0.00 3.58
3307 17648 1.961394 GTCGCAGAGTATGGTATGGGA 59.039 52.381 0.00 0.00 36.95 4.37
3359 17700 8.518430 TTATAGCTATGGCATTGTTCTTTTGA 57.482 30.769 16.77 0.00 41.70 2.69
3365 17706 7.095102 GCTATGGCATTGTTCTTTTGAAAATGT 60.095 33.333 4.78 0.00 38.15 2.71
3373 17714 8.744008 TTGTTCTTTTGAAAATGTTAACACGA 57.256 26.923 11.22 0.00 40.53 4.35
3459 17800 3.485463 TTCACGAACCCAAGACATTCT 57.515 42.857 0.00 0.00 0.00 2.40
3460 17801 3.485463 TCACGAACCCAAGACATTCTT 57.515 42.857 0.00 0.00 37.14 2.52
3462 17803 3.138304 CACGAACCCAAGACATTCTTCA 58.862 45.455 0.00 0.00 33.78 3.02
3463 17804 3.563808 CACGAACCCAAGACATTCTTCAA 59.436 43.478 0.00 0.00 33.78 2.69
3465 17806 3.058224 CGAACCCAAGACATTCTTCAACC 60.058 47.826 0.00 0.00 33.78 3.77
3466 17807 2.876581 ACCCAAGACATTCTTCAACCC 58.123 47.619 0.00 0.00 33.78 4.11
3467 17808 1.812571 CCCAAGACATTCTTCAACCCG 59.187 52.381 0.00 0.00 33.78 5.28
3468 17809 1.812571 CCAAGACATTCTTCAACCCGG 59.187 52.381 0.00 0.00 33.78 5.73
3476 17817 1.903404 CTTCAACCCGGCCTTGCTT 60.903 57.895 0.00 0.00 0.00 3.91
3482 17823 4.697756 CCGGCCTTGCTTCGGTGA 62.698 66.667 0.00 0.00 39.04 4.02
3517 17858 7.280652 CAGTTTGTTGATCAAATCCCAAACTTT 59.719 33.333 31.88 20.36 46.61 2.66
3545 17886 2.129607 GCAACACATTTGCACTGAAGG 58.870 47.619 4.12 0.00 44.34 3.46
3632 17973 0.739112 TGCAATGCGCGATGTCTACA 60.739 50.000 12.10 0.00 46.97 2.74
3658 17999 5.164080 CGAAGTAACTGAAGTAAAAGAGGCG 60.164 44.000 0.00 0.00 0.00 5.52
3677 18018 3.181490 GGCGTTTTTCTCCATGGATAACC 60.181 47.826 16.63 7.73 0.00 2.85
3685 18026 2.614057 CTCCATGGATAACCGAAGCAAC 59.386 50.000 16.63 0.00 39.42 4.17
3726 18067 2.403252 AAAGGCGGTCGATGAAGATT 57.597 45.000 0.00 0.00 0.00 2.40
3746 18087 2.853914 GCTCGTTGCTTCGACCAC 59.146 61.111 0.00 0.00 38.95 4.16
3764 18105 3.119173 ACCACGGCATGAAAATATGTTGG 60.119 43.478 0.00 0.00 33.99 3.77
3769 18110 5.827797 ACGGCATGAAAATATGTTGGTATCT 59.172 36.000 0.00 0.00 0.00 1.98
3770 18111 6.321181 ACGGCATGAAAATATGTTGGTATCTT 59.679 34.615 0.00 0.00 0.00 2.40
3801 18142 4.433186 TTTTGTGAGCCAATATGTTCGG 57.567 40.909 0.00 0.00 31.81 4.30
3825 18166 0.036388 CTGCGGTGAAGAGCCCTTTA 60.036 55.000 0.00 0.00 31.62 1.85
3854 18195 7.570982 TGATAATGATGGGTTTCTACTAGGGAA 59.429 37.037 0.00 0.00 0.00 3.97
3855 18196 6.652205 AATGATGGGTTTCTACTAGGGAAA 57.348 37.500 8.44 8.44 0.00 3.13
3857 18198 6.001449 TGATGGGTTTCTACTAGGGAAATG 57.999 41.667 13.56 0.00 35.55 2.32
3862 18203 7.757611 TGGGTTTCTACTAGGGAAATGTTTTA 58.242 34.615 13.56 0.73 35.55 1.52
3945 18288 2.159099 ACAGTTCGAACAGTGAAGCTCA 60.159 45.455 28.78 0.00 0.00 4.26
3949 18507 4.576463 AGTTCGAACAGTGAAGCTCATTTT 59.424 37.500 28.78 0.40 0.00 1.82
3972 18533 0.761323 TTCACCTCTCCCCACGAACA 60.761 55.000 0.00 0.00 0.00 3.18
4140 20252 0.109723 CACTTTTGGGGGAACTCGGA 59.890 55.000 0.00 0.00 0.00 4.55
4273 20446 6.463995 AACTGCAAAAGGATTAAGTGAACA 57.536 33.333 0.00 0.00 0.00 3.18
4279 20452 8.203485 TGCAAAAGGATTAAGTGAACAAATCTT 58.797 29.630 0.00 0.00 31.66 2.40
4454 20633 3.156293 TGATAAATCATGCATTCCGGGG 58.844 45.455 0.00 0.00 0.00 5.73
4508 20691 1.064979 GTGGTGGGTCCCGAATGTAAT 60.065 52.381 2.65 0.00 34.77 1.89
4509 20692 1.636519 TGGTGGGTCCCGAATGTAATT 59.363 47.619 2.65 0.00 35.31 1.40
4569 20752 5.578776 GGAGGGCATGTAACTAATTTTTCG 58.421 41.667 0.00 0.00 0.00 3.46
4738 20922 1.558233 AAGAGTAAGGCTGCGTAGGT 58.442 50.000 1.76 0.00 0.00 3.08
4765 20949 5.105716 GCTAGTCTCCACTCTACACATTTCA 60.106 44.000 0.00 0.00 33.62 2.69
4869 21053 5.946942 AGACTGTGTATTCTGGATCATGT 57.053 39.130 0.00 0.00 0.00 3.21
4870 21054 5.668471 AGACTGTGTATTCTGGATCATGTG 58.332 41.667 0.00 0.00 0.00 3.21
4878 21062 9.325198 GTGTATTCTGGATCATGTGTTGTAATA 57.675 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.001268 AGCGGCGGCATATATAGATCG 60.001 52.381 19.21 0.00 43.41 3.69
2 3 2.031870 TCAGCGGCGGCATATATAGAT 58.968 47.619 19.21 0.00 43.41 1.98
5 6 1.822371 TCTTCAGCGGCGGCATATATA 59.178 47.619 19.21 0.00 43.41 0.86
6 7 0.608130 TCTTCAGCGGCGGCATATAT 59.392 50.000 19.21 0.00 43.41 0.86
8 9 1.595382 GTCTTCAGCGGCGGCATAT 60.595 57.895 19.21 0.00 43.41 1.78
13 14 3.777925 CAACGTCTTCAGCGGCGG 61.778 66.667 9.78 0.00 0.00 6.13
14 15 2.733218 TCAACGTCTTCAGCGGCG 60.733 61.111 0.51 0.51 0.00 6.46
15 16 2.668280 GGTCAACGTCTTCAGCGGC 61.668 63.158 0.00 0.00 0.00 6.53
16 17 0.670546 ATGGTCAACGTCTTCAGCGG 60.671 55.000 0.00 0.00 0.00 5.52
17 18 0.439985 CATGGTCAACGTCTTCAGCG 59.560 55.000 0.00 0.00 0.00 5.18
18 19 1.461127 GTCATGGTCAACGTCTTCAGC 59.539 52.381 0.00 0.00 0.00 4.26
21 22 2.288825 TGGAGTCATGGTCAACGTCTTC 60.289 50.000 0.00 0.00 0.00 2.87
22 23 1.691976 TGGAGTCATGGTCAACGTCTT 59.308 47.619 0.00 0.00 0.00 3.01
23 24 1.338107 TGGAGTCATGGTCAACGTCT 58.662 50.000 0.00 0.00 0.00 4.18
25 26 2.099141 CATGGAGTCATGGTCAACGT 57.901 50.000 0.00 0.00 45.19 3.99
34 35 0.826715 CGTCTGGGTCATGGAGTCAT 59.173 55.000 0.00 0.00 0.00 3.06
35 36 0.541998 ACGTCTGGGTCATGGAGTCA 60.542 55.000 0.00 0.00 0.00 3.41
36 37 0.173708 GACGTCTGGGTCATGGAGTC 59.826 60.000 8.70 0.00 36.91 3.36
38 39 1.139734 CGACGTCTGGGTCATGGAG 59.860 63.158 14.70 0.00 36.73 3.86
39 40 1.303806 TCGACGTCTGGGTCATGGA 60.304 57.895 14.70 0.00 36.73 3.41
40 41 1.139734 CTCGACGTCTGGGTCATGG 59.860 63.158 14.70 0.00 36.73 3.66
41 42 1.139734 CCTCGACGTCTGGGTCATG 59.860 63.158 14.70 0.00 36.73 3.07
42 43 0.395862 ATCCTCGACGTCTGGGTCAT 60.396 55.000 14.70 3.44 36.73 3.06
44 45 1.313812 ACATCCTCGACGTCTGGGTC 61.314 60.000 14.70 0.00 0.00 4.46
46 47 1.139734 CACATCCTCGACGTCTGGG 59.860 63.158 14.70 14.78 0.00 4.45
48 49 1.832600 CATCACATCCTCGACGTCTG 58.167 55.000 14.70 7.10 0.00 3.51
50 51 1.202973 CGCATCACATCCTCGACGTC 61.203 60.000 5.18 5.18 0.00 4.34
52 53 2.580470 GCGCATCACATCCTCGACG 61.580 63.158 0.30 0.00 0.00 5.12
53 54 0.877649 ATGCGCATCACATCCTCGAC 60.878 55.000 19.28 0.00 0.00 4.20
55 56 1.568025 CATGCGCATCACATCCTCG 59.432 57.895 22.51 1.48 0.00 4.63
56 57 1.281960 GCATGCGCATCACATCCTC 59.718 57.895 22.51 0.00 38.36 3.71
57 58 1.452470 TGCATGCGCATCACATCCT 60.452 52.632 22.51 0.00 45.36 3.24
58 59 3.112842 TGCATGCGCATCACATCC 58.887 55.556 22.51 5.39 45.36 3.51
67 68 2.505557 GCAGGAAAGTGCATGCGC 60.506 61.111 23.64 23.64 43.41 6.09
80 81 1.019673 CTTTCATCCATCCGTGCAGG 58.980 55.000 0.00 0.00 42.97 4.85
81 82 1.938577 CTCTTTCATCCATCCGTGCAG 59.061 52.381 0.00 0.00 0.00 4.41
82 83 1.554617 TCTCTTTCATCCATCCGTGCA 59.445 47.619 0.00 0.00 0.00 4.57
83 84 2.315925 TCTCTTTCATCCATCCGTGC 57.684 50.000 0.00 0.00 0.00 5.34
84 85 3.003068 GCATTCTCTTTCATCCATCCGTG 59.997 47.826 0.00 0.00 0.00 4.94
85 86 3.209410 GCATTCTCTTTCATCCATCCGT 58.791 45.455 0.00 0.00 0.00 4.69
88 89 4.497674 GCAGTGCATTCTCTTTCATCCATC 60.498 45.833 11.09 0.00 0.00 3.51
89 90 3.380637 GCAGTGCATTCTCTTTCATCCAT 59.619 43.478 11.09 0.00 0.00 3.41
90 91 2.751259 GCAGTGCATTCTCTTTCATCCA 59.249 45.455 11.09 0.00 0.00 3.41
91 92 2.751259 TGCAGTGCATTCTCTTTCATCC 59.249 45.455 15.37 0.00 31.71 3.51
92 93 3.181499 CCTGCAGTGCATTCTCTTTCATC 60.181 47.826 20.10 0.00 38.13 2.92
93 94 2.753452 CCTGCAGTGCATTCTCTTTCAT 59.247 45.455 20.10 0.00 38.13 2.57
94 95 2.156917 CCTGCAGTGCATTCTCTTTCA 58.843 47.619 20.10 0.00 38.13 2.69
95 96 2.157738 ACCTGCAGTGCATTCTCTTTC 58.842 47.619 20.10 0.00 38.13 2.62
97 98 2.157738 GAACCTGCAGTGCATTCTCTT 58.842 47.619 20.10 5.48 38.13 2.85
98 99 1.072806 TGAACCTGCAGTGCATTCTCT 59.927 47.619 24.59 8.51 38.13 3.10
99 100 1.527034 TGAACCTGCAGTGCATTCTC 58.473 50.000 24.59 18.25 38.13 2.87
101 102 2.602878 CATTGAACCTGCAGTGCATTC 58.397 47.619 20.10 20.01 38.13 2.67
103 104 0.245539 GCATTGAACCTGCAGTGCAT 59.754 50.000 20.10 3.27 46.74 3.96
104 105 1.661480 GCATTGAACCTGCAGTGCA 59.339 52.632 18.58 18.58 46.74 4.57
105 106 4.565531 GCATTGAACCTGCAGTGC 57.434 55.556 13.81 8.58 42.78 4.40
110 111 5.106396 GGATAGTATCATGCATTGAACCTGC 60.106 44.000 12.19 0.00 38.03 4.85
111 112 5.413833 GGGATAGTATCATGCATTGAACCTG 59.586 44.000 12.19 0.00 38.03 4.00
112 113 5.564550 GGGATAGTATCATGCATTGAACCT 58.435 41.667 12.19 2.01 38.03 3.50
113 114 4.393062 CGGGATAGTATCATGCATTGAACC 59.607 45.833 12.19 0.00 38.03 3.62
116 117 4.890158 ACGGGATAGTATCATGCATTGA 57.110 40.909 12.19 0.00 39.12 2.57
117 118 6.091305 CACTAACGGGATAGTATCATGCATTG 59.909 42.308 12.19 0.00 34.40 2.82
118 119 6.166279 CACTAACGGGATAGTATCATGCATT 58.834 40.000 12.19 2.05 34.40 3.56
119 120 5.337571 CCACTAACGGGATAGTATCATGCAT 60.338 44.000 12.19 0.00 34.40 3.96
121 122 4.495422 CCACTAACGGGATAGTATCATGC 58.505 47.826 12.19 0.00 34.40 4.06
134 135 3.515330 ACGTTAAGATCCCACTAACGG 57.485 47.619 21.21 10.52 45.11 4.44
135 136 6.753279 TCATTTACGTTAAGATCCCACTAACG 59.247 38.462 18.10 18.10 45.92 3.18
136 137 7.224167 CCTCATTTACGTTAAGATCCCACTAAC 59.776 40.741 0.00 0.00 0.00 2.34
138 139 6.608405 TCCTCATTTACGTTAAGATCCCACTA 59.392 38.462 0.00 0.00 0.00 2.74
140 141 5.667466 TCCTCATTTACGTTAAGATCCCAC 58.333 41.667 0.00 0.00 0.00 4.61
141 142 5.943349 TCCTCATTTACGTTAAGATCCCA 57.057 39.130 0.00 0.00 0.00 4.37
142 143 6.522054 TGATCCTCATTTACGTTAAGATCCC 58.478 40.000 0.00 0.00 0.00 3.85
144 145 8.594881 ACATGATCCTCATTTACGTTAAGATC 57.405 34.615 0.00 0.18 34.28 2.75
145 146 9.477484 GTACATGATCCTCATTTACGTTAAGAT 57.523 33.333 0.00 0.00 34.28 2.40
146 147 8.471609 TGTACATGATCCTCATTTACGTTAAGA 58.528 33.333 0.00 0.00 40.86 2.10
147 148 8.642908 TGTACATGATCCTCATTTACGTTAAG 57.357 34.615 0.00 0.00 40.86 1.85
148 149 9.040939 CATGTACATGATCCTCATTTACGTTAA 57.959 33.333 28.41 0.00 40.86 2.01
149 150 7.170828 GCATGTACATGATCCTCATTTACGTTA 59.829 37.037 34.65 0.00 40.86 3.18
150 151 6.017934 GCATGTACATGATCCTCATTTACGTT 60.018 38.462 34.65 0.00 40.86 3.99
151 152 5.466728 GCATGTACATGATCCTCATTTACGT 59.533 40.000 34.65 0.00 40.86 3.57
152 153 5.698089 AGCATGTACATGATCCTCATTTACG 59.302 40.000 34.65 7.73 40.86 3.18
153 154 7.126726 GAGCATGTACATGATCCTCATTTAC 57.873 40.000 33.84 15.59 45.59 2.01
163 164 3.131046 TGAGACGTGAGCATGTACATGAT 59.869 43.478 34.65 30.53 41.20 2.45
164 165 2.491693 TGAGACGTGAGCATGTACATGA 59.508 45.455 34.65 14.97 41.20 3.07
165 166 2.879826 TGAGACGTGAGCATGTACATG 58.120 47.619 28.07 28.07 41.60 3.21
166 167 3.056536 AGTTGAGACGTGAGCATGTACAT 60.057 43.478 1.41 1.41 0.00 2.29
167 168 2.296190 AGTTGAGACGTGAGCATGTACA 59.704 45.455 0.00 0.00 0.00 2.90
168 169 2.917971 GAGTTGAGACGTGAGCATGTAC 59.082 50.000 0.00 0.00 0.00 2.90
169 170 2.820197 AGAGTTGAGACGTGAGCATGTA 59.180 45.455 0.00 0.00 0.00 2.29
170 171 1.615883 AGAGTTGAGACGTGAGCATGT 59.384 47.619 0.00 0.00 0.00 3.21
171 172 2.360553 AGAGTTGAGACGTGAGCATG 57.639 50.000 0.00 0.00 0.00 4.06
172 173 4.727507 AATAGAGTTGAGACGTGAGCAT 57.272 40.909 0.00 0.00 0.00 3.79
174 175 5.004916 GCTTTAATAGAGTTGAGACGTGAGC 59.995 44.000 0.00 0.00 0.00 4.26
176 177 6.020971 TGCTTTAATAGAGTTGAGACGTGA 57.979 37.500 0.00 0.00 0.00 4.35
179 180 5.555256 CGCATGCTTTAATAGAGTTGAGACG 60.555 44.000 17.13 0.00 0.00 4.18
180 181 5.520288 TCGCATGCTTTAATAGAGTTGAGAC 59.480 40.000 17.13 0.00 0.00 3.36
182 183 5.291858 TGTCGCATGCTTTAATAGAGTTGAG 59.708 40.000 17.13 0.00 0.00 3.02
184 185 5.163864 TGTGTCGCATGCTTTAATAGAGTTG 60.164 40.000 17.13 0.00 0.00 3.16
185 186 4.935205 TGTGTCGCATGCTTTAATAGAGTT 59.065 37.500 17.13 0.00 0.00 3.01
186 187 4.503910 TGTGTCGCATGCTTTAATAGAGT 58.496 39.130 17.13 0.00 0.00 3.24
187 188 5.663795 ATGTGTCGCATGCTTTAATAGAG 57.336 39.130 17.13 0.00 36.26 2.43
188 189 5.465390 GGTATGTGTCGCATGCTTTAATAGA 59.535 40.000 17.13 0.03 39.66 1.98
189 190 5.466728 AGGTATGTGTCGCATGCTTTAATAG 59.533 40.000 17.13 0.00 39.66 1.73
190 191 5.236263 CAGGTATGTGTCGCATGCTTTAATA 59.764 40.000 17.13 4.67 39.66 0.98
191 192 4.035558 CAGGTATGTGTCGCATGCTTTAAT 59.964 41.667 17.13 5.63 39.66 1.40
192 193 3.373748 CAGGTATGTGTCGCATGCTTTAA 59.626 43.478 17.13 0.00 39.66 1.52
193 194 2.935849 CAGGTATGTGTCGCATGCTTTA 59.064 45.455 17.13 0.00 39.66 1.85
197 198 1.353103 GCAGGTATGTGTCGCATGC 59.647 57.895 7.91 7.91 38.47 4.06
198 199 1.439353 GGGCAGGTATGTGTCGCATG 61.439 60.000 9.20 0.00 38.47 4.06
200 201 2.267642 GGGCAGGTATGTGTCGCA 59.732 61.111 0.00 0.00 0.00 5.10
201 202 2.513897 GGGGCAGGTATGTGTCGC 60.514 66.667 0.00 0.00 0.00 5.19
202 203 2.202878 CGGGGCAGGTATGTGTCG 60.203 66.667 0.00 0.00 0.00 4.35
204 205 4.109675 GCCGGGGCAGGTATGTGT 62.110 66.667 2.18 0.00 41.49 3.72
205 206 4.875713 GGCCGGGGCAGGTATGTG 62.876 72.222 16.76 0.00 44.11 3.21
207 208 4.569180 CAGGCCGGGGCAGGTATG 62.569 72.222 23.67 7.89 44.11 2.39
208 209 4.815973 TCAGGCCGGGGCAGGTAT 62.816 66.667 23.67 0.00 44.11 2.73
212 213 3.164269 ATACTCAGGCCGGGGCAG 61.164 66.667 23.67 15.41 44.11 4.85
213 214 3.161450 GATACTCAGGCCGGGGCA 61.161 66.667 23.67 1.09 44.11 5.36
214 215 2.265467 TTTGATACTCAGGCCGGGGC 62.265 60.000 13.58 13.58 41.06 5.80
216 217 0.179045 CCTTTGATACTCAGGCCGGG 60.179 60.000 2.18 0.00 0.00 5.73
217 218 0.815615 GCCTTTGATACTCAGGCCGG 60.816 60.000 0.00 0.00 39.57 6.13
218 219 0.107703 TGCCTTTGATACTCAGGCCG 60.108 55.000 6.96 0.00 44.42 6.13
219 220 1.383523 GTGCCTTTGATACTCAGGCC 58.616 55.000 6.96 0.00 44.42 5.19
220 221 1.340017 TGGTGCCTTTGATACTCAGGC 60.340 52.381 2.29 2.29 45.19 4.85
313 319 4.330944 TCAAAGCTAACGACAGGAAGAA 57.669 40.909 0.00 0.00 0.00 2.52
316 322 3.135994 GGTTCAAAGCTAACGACAGGAA 58.864 45.455 0.00 0.00 0.00 3.36
324 330 2.712709 GAGGAGGGGTTCAAAGCTAAC 58.287 52.381 0.00 0.00 0.00 2.34
326 332 0.902531 CGAGGAGGGGTTCAAAGCTA 59.097 55.000 0.00 0.00 0.00 3.32
361 379 1.375098 GCATCCCTGCTCTTGTCTGC 61.375 60.000 0.00 0.00 45.32 4.26
375 393 1.227615 GAGGCAGAGCAGAGCATCC 60.228 63.158 0.00 0.00 35.69 3.51
428 446 0.179004 GGTGGTGTGGTTCCATGTGA 60.179 55.000 0.00 0.00 37.30 3.58
465 490 4.152644 CATGAGACGCCATGCCAT 57.847 55.556 0.00 0.00 37.68 4.40
963 991 3.023119 TGCACCAGAAAGATTGTTGTGT 58.977 40.909 0.00 0.00 0.00 3.72
1132 1160 2.671070 CGGCAAGTTTACCCAAATCTGC 60.671 50.000 0.00 0.00 35.18 4.26
1294 1322 1.804748 CAGCGTTTGGAGGTTAGGAAC 59.195 52.381 0.00 0.00 0.00 3.62
1311 1339 1.875514 TGATTATTCGCCATGCTCAGC 59.124 47.619 0.00 0.00 0.00 4.26
1323 1351 6.980397 GGATGTCACCCACAAAATGATTATTC 59.020 38.462 0.00 0.00 38.97 1.75
1368 1396 6.470278 CATATGGATATACATCATGCCGGAT 58.530 40.000 5.05 0.00 32.32 4.18
1418 1455 3.623906 TCATGGAGCTGAAAGAAGGAG 57.376 47.619 0.00 0.00 34.07 3.69
1511 1548 1.350684 TCAGCAGCTGGGTACAATTCA 59.649 47.619 22.62 0.00 31.51 2.57
1621 1658 2.158623 TGCCAGAGATGTTGTTTGACCT 60.159 45.455 0.00 0.00 0.00 3.85
1839 1876 2.426522 CTTCCACTCAGCCGATTTTCA 58.573 47.619 0.00 0.00 0.00 2.69
1849 1886 3.616956 TTCAGGTATGCTTCCACTCAG 57.383 47.619 0.00 0.00 0.00 3.35
2255 9272 6.239217 AGGACATATTCAGATACTGCAACA 57.761 37.500 0.00 0.00 0.00 3.33
2378 9395 4.550076 AAGCATCTAGACAGCTCTTGTT 57.450 40.909 18.73 3.80 41.05 2.83
2389 9406 3.430374 GGTACCGAAGCAAAGCATCTAGA 60.430 47.826 0.00 0.00 0.00 2.43
2710 15734 1.315690 ATGAAGCTATGCAATGCGCT 58.684 45.000 9.73 0.00 43.06 5.92
2838 15862 2.460918 CTTCCGTTAGCCATGTACTCG 58.539 52.381 0.00 0.00 0.00 4.18
2931 15955 6.360370 AGGTAGTCAAGAGCACAAGAAATA 57.640 37.500 0.00 0.00 0.00 1.40
2935 15959 4.149598 TGTAGGTAGTCAAGAGCACAAGA 58.850 43.478 0.00 0.00 0.00 3.02
2949 15973 5.012046 TGGGATGCACAGATTATGTAGGTAG 59.988 44.000 0.00 0.00 41.41 3.18
2963 15987 2.282110 CAACCGGTGGGATGCACA 60.282 61.111 8.52 0.00 36.97 4.57
3025 16049 0.038618 TCGCAGACACGTGCAGTATT 60.039 50.000 17.22 0.00 44.21 1.89
3116 17441 3.799590 TGTACCCAATAGACCCCCTTA 57.200 47.619 0.00 0.00 0.00 2.69
3219 17545 7.133891 ACATGCTAGTGTTAGTAAAAGCAAG 57.866 36.000 11.99 10.73 42.64 4.01
3233 17562 6.293298 GGAGCTCATAATGAAACATGCTAGTG 60.293 42.308 17.19 0.00 0.00 2.74
3289 17630 1.273606 CCTCCCATACCATACTCTGCG 59.726 57.143 0.00 0.00 0.00 5.18
3307 17648 1.912043 CCCTCAGTGGAGATTTCACCT 59.088 52.381 0.00 0.00 44.26 4.00
3359 17700 3.797796 GGCCGTTTTCGTGTTAACATTTT 59.202 39.130 12.26 0.00 42.35 1.82
3365 17706 3.110447 AGTAGGCCGTTTTCGTGTTAA 57.890 42.857 0.00 0.00 42.35 2.01
3373 17714 6.657541 TGAATTCTTCATTAGTAGGCCGTTTT 59.342 34.615 7.05 0.00 34.08 2.43
3459 17800 1.901464 GAAGCAAGGCCGGGTTGAA 60.901 57.895 17.72 0.00 0.00 2.69
3460 17801 2.282180 GAAGCAAGGCCGGGTTGA 60.282 61.111 17.72 0.00 0.00 3.18
3466 17807 3.423154 GTCACCGAAGCAAGGCCG 61.423 66.667 0.00 0.00 0.00 6.13
3467 17808 3.423154 CGTCACCGAAGCAAGGCC 61.423 66.667 0.00 0.00 35.63 5.19
3468 17809 3.423154 CCGTCACCGAAGCAAGGC 61.423 66.667 0.00 0.00 35.63 4.35
3476 17817 0.611062 AACTGATCTCCCGTCACCGA 60.611 55.000 0.00 0.00 35.63 4.69
3480 17821 2.367241 TCAACAAACTGATCTCCCGTCA 59.633 45.455 0.00 0.00 0.00 4.35
3482 17823 3.600388 GATCAACAAACTGATCTCCCGT 58.400 45.455 6.38 0.00 45.56 5.28
3495 17836 6.882656 TGAAAGTTTGGGATTTGATCAACAA 58.117 32.000 7.89 6.38 36.65 2.83
3505 17846 5.549742 TGCATTCTTGAAAGTTTGGGATT 57.450 34.783 0.00 0.00 0.00 3.01
3508 17849 4.270808 GTGTTGCATTCTTGAAAGTTTGGG 59.729 41.667 0.00 0.00 0.00 4.12
3545 17886 2.287909 GGAGACGGAGAGCACACATATC 60.288 54.545 0.00 0.00 0.00 1.63
3601 17942 2.028130 CATTGCAGGGCGATCCTTC 58.972 57.895 0.00 0.00 45.47 3.46
3614 17955 0.042708 CTGTAGACATCGCGCATTGC 60.043 55.000 8.75 0.00 41.47 3.56
3616 17957 1.482621 CGCTGTAGACATCGCGCATT 61.483 55.000 8.75 0.00 39.11 3.56
3622 17963 3.786576 CAGTTACTTCGCTGTAGACATCG 59.213 47.826 0.00 0.00 36.89 3.84
3632 17973 5.927115 CCTCTTTTACTTCAGTTACTTCGCT 59.073 40.000 0.00 0.00 0.00 4.93
3635 17976 5.695363 ACGCCTCTTTTACTTCAGTTACTTC 59.305 40.000 0.00 0.00 0.00 3.01
3658 17999 5.676331 GCTTCGGTTATCCATGGAGAAAAAC 60.676 44.000 22.98 19.65 0.00 2.43
3677 18018 5.464965 AATAATGTAAGGTCGTTGCTTCG 57.535 39.130 0.00 0.00 0.00 3.79
3703 18044 0.239879 TTCATCGACCGCCTTTTTGC 59.760 50.000 0.00 0.00 0.00 3.68
3715 18056 3.551890 GCAACGAGCTTAATCTTCATCGA 59.448 43.478 0.00 0.00 41.15 3.59
3746 18087 6.317789 AGATACCAACATATTTTCATGCCG 57.682 37.500 0.00 0.00 0.00 5.69
3782 18123 1.742831 GCCGAACATATTGGCTCACAA 59.257 47.619 0.00 0.00 45.40 3.33
3790 18131 1.004610 CGCAGTGAGCCGAACATATTG 60.005 52.381 0.00 0.00 41.38 1.90
3825 18166 8.378565 CCTAGTAGAAACCCATCATTATCATGT 58.621 37.037 0.00 0.00 0.00 3.21
3930 18273 4.024556 ACTGAAAATGAGCTTCACTGTTCG 60.025 41.667 0.00 0.00 0.00 3.95
3945 18288 2.716424 TGGGGAGAGGTGAACTGAAAAT 59.284 45.455 0.00 0.00 0.00 1.82
3949 18507 1.185618 CGTGGGGAGAGGTGAACTGA 61.186 60.000 0.00 0.00 0.00 3.41
4103 20215 9.439500 CCAAAAGTGAAATAATTCATGGATGTT 57.561 29.630 5.32 0.00 46.67 2.71
4156 20269 4.050315 GGGAAAGTAATTTGGTACCCCA 57.950 45.455 10.07 0.00 39.65 4.96
4160 20273 4.083565 TGCAGGGGAAAGTAATTTGGTAC 58.916 43.478 0.00 0.00 0.00 3.34
4161 20274 4.390129 TGCAGGGGAAAGTAATTTGGTA 57.610 40.909 0.00 0.00 0.00 3.25
4164 20277 3.055963 TGCATGCAGGGGAAAGTAATTTG 60.056 43.478 18.46 0.00 0.00 2.32
4215 20385 3.255642 TGATTTGAAACTGCCAGGCTTAC 59.744 43.478 14.15 0.52 0.00 2.34
4273 20446 6.611236 TGGAAAACTTGAAAGAGGGAAGATTT 59.389 34.615 0.00 0.00 0.00 2.17
4279 20452 7.610305 GTGTATATGGAAAACTTGAAAGAGGGA 59.390 37.037 0.00 0.00 0.00 4.20
4454 20633 2.285834 GCTGTAGTTGATGTACATGCGC 60.286 50.000 14.43 0.00 30.07 6.09
4508 20691 1.143277 TGCCGTCTCCTTTGGGTTAAA 59.857 47.619 0.00 0.00 0.00 1.52
4509 20692 0.766131 TGCCGTCTCCTTTGGGTTAA 59.234 50.000 0.00 0.00 0.00 2.01
4569 20752 1.209504 TCTATGCCACTACCACTTGCC 59.790 52.381 0.00 0.00 0.00 4.52
4723 20907 2.662150 CGAACCTACGCAGCCTTAC 58.338 57.895 0.00 0.00 0.00 2.34
4738 20922 3.008330 GTGTAGAGTGGAGACTAGCGAA 58.992 50.000 0.00 0.00 30.16 4.70
4765 20949 0.397675 TCTCATCCGATGCCAGAGGT 60.398 55.000 3.25 0.00 0.00 3.85
4837 21021 8.758829 TCCAGAATACACAGTCTAATACACATT 58.241 33.333 0.00 0.00 0.00 2.71
4838 21022 8.306313 TCCAGAATACACAGTCTAATACACAT 57.694 34.615 0.00 0.00 0.00 3.21
4839 21023 7.712204 TCCAGAATACACAGTCTAATACACA 57.288 36.000 0.00 0.00 0.00 3.72
4840 21024 8.414003 TGATCCAGAATACACAGTCTAATACAC 58.586 37.037 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.