Multiple sequence alignment - TraesCS1D01G205300

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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 TraesCS1D01G205300 chr1D 100.000 2747 0 0 1 2747 290707216 290704470 0.000000e+00 5073.0
1 TraesCS1D01G205300 chr1D 91.351 185 9 3 27 210 290708449 290708627 2.110000e-61 246.0
2 TraesCS1D01G205300 chr1D 85.294 102 11 4 1480 1579 398246679 398246778 4.840000e-18 102.0
3 TraesCS1D01G205300 chr1A 95.652 1840 53 14 334 2152 363007888 363006055 0.000000e+00 2929.0
4 TraesCS1D01G205300 chr1A 87.255 102 9 4 1480 1579 495306919 495307018 2.240000e-21 113.0
5 TraesCS1D01G205300 chr1B 96.540 1532 22 10 642 2152 391962234 391960713 0.000000e+00 2507.0
6 TraesCS1D01G205300 chr1B 96.417 307 11 0 334 640 391964007 391963701 8.780000e-140 507.0
7 TraesCS1D01G205300 chr1B 87.255 102 9 4 1480 1579 533748208 533748307 2.240000e-21 113.0
8 TraesCS1D01G205300 chr7A 90.761 552 49 2 2195 2745 25943238 25942688 0.000000e+00 736.0
9 TraesCS1D01G205300 chr7D 89.150 553 52 6 2195 2745 25058575 25058029 0.000000e+00 682.0
10 TraesCS1D01G205300 chr7D 89.504 524 50 4 2224 2745 154647439 154646919 0.000000e+00 658.0
11 TraesCS1D01G205300 chr5D 87.659 551 68 0 2195 2745 62530497 62529947 2.310000e-180 641.0
12 TraesCS1D01G205300 chr5D 91.398 93 4 1 27 115 560410903 560410995 1.030000e-24 124.0
13 TraesCS1D01G205300 chr4B 87.500 552 66 3 2195 2745 575652890 575652341 3.860000e-178 634.0
14 TraesCS1D01G205300 chr4B 100.000 28 0 0 2171 2198 661255589 661255616 5.000000e-03 52.8
15 TraesCS1D01G205300 chr3B 87.941 539 62 3 2195 2732 775734912 775734376 1.390000e-177 632.0
16 TraesCS1D01G205300 chr4D 87.296 551 70 0 2195 2745 354115467 354114917 4.990000e-177 630.0
17 TraesCS1D01G205300 chr4D 100.000 28 0 0 2171 2198 505724373 505724400 5.000000e-03 52.8
18 TraesCS1D01G205300 chr4A 87.477 551 64 4 2195 2745 708539939 708540484 4.990000e-177 630.0
19 TraesCS1D01G205300 chr4A 85.993 307 39 3 27 329 479410538 479410844 2.640000e-85 326.0
20 TraesCS1D01G205300 chr4A 85.668 307 40 3 27 329 551777668 551777362 1.230000e-83 320.0
21 TraesCS1D01G205300 chr4A 83.401 247 40 1 84 329 479409424 479409178 7.650000e-56 228.0
22 TraesCS1D01G205300 chr4A 82.400 250 43 1 81 329 551778779 551779028 1.660000e-52 217.0
23 TraesCS1D01G205300 chr2A 87.114 551 65 4 2195 2745 564614030 564613486 1.080000e-173 619.0
24 TraesCS1D01G205300 chr3D 86.039 308 38 2 27 329 420011927 420012234 2.640000e-85 326.0
25 TraesCS1D01G205300 chr3D 85.714 161 19 1 27 183 420046501 420046661 1.690000e-37 167.0
26 TraesCS1D01G205300 chr2D 85.382 301 39 2 30 325 75651619 75651319 9.560000e-80 307.0
27 TraesCS1D01G205300 chr7B 84.000 250 39 1 81 329 38682840 38683089 3.540000e-59 239.0
28 TraesCS1D01G205300 chr7B 93.846 65 3 1 27 90 87175037 87174973 2.250000e-16 97.1
29 TraesCS1D01G205300 chr6B 83.889 180 24 5 153 329 100928191 100928014 1.690000e-37 167.0
30 TraesCS1D01G205300 chr5B 78.814 236 47 3 95 328 232264984 232265218 3.660000e-34 156.0
31 TraesCS1D01G205300 chr6D 100.000 28 0 0 2171 2198 391896812 391896839 5.000000e-03 52.8
32 TraesCS1D01G205300 chr3A 100.000 28 0 0 2171 2198 732875312 732875285 5.000000e-03 52.8


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 TraesCS1D01G205300 chr1D 290704470 290707216 2746 True 5073 5073 100.0000 1 2747 1 chr1D.!!$R1 2746
1 TraesCS1D01G205300 chr1A 363006055 363007888 1833 True 2929 2929 95.6520 334 2152 1 chr1A.!!$R1 1818
2 TraesCS1D01G205300 chr1B 391960713 391964007 3294 True 1507 2507 96.4785 334 2152 2 chr1B.!!$R1 1818
3 TraesCS1D01G205300 chr7A 25942688 25943238 550 True 736 736 90.7610 2195 2745 1 chr7A.!!$R1 550
4 TraesCS1D01G205300 chr7D 25058029 25058575 546 True 682 682 89.1500 2195 2745 1 chr7D.!!$R1 550
5 TraesCS1D01G205300 chr7D 154646919 154647439 520 True 658 658 89.5040 2224 2745 1 chr7D.!!$R2 521
6 TraesCS1D01G205300 chr5D 62529947 62530497 550 True 641 641 87.6590 2195 2745 1 chr5D.!!$R1 550
7 TraesCS1D01G205300 chr4B 575652341 575652890 549 True 634 634 87.5000 2195 2745 1 chr4B.!!$R1 550
8 TraesCS1D01G205300 chr3B 775734376 775734912 536 True 632 632 87.9410 2195 2732 1 chr3B.!!$R1 537
9 TraesCS1D01G205300 chr4D 354114917 354115467 550 True 630 630 87.2960 2195 2745 1 chr4D.!!$R1 550
10 TraesCS1D01G205300 chr4A 708539939 708540484 545 False 630 630 87.4770 2195 2745 1 chr4A.!!$F3 550
11 TraesCS1D01G205300 chr2A 564613486 564614030 544 True 619 619 87.1140 2195 2745 1 chr2A.!!$R1 550

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
62 63 0.030235 CATGCATGCATCGGGTCTTG 59.97 55.0 30.07 14.44 33.9 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 3461 1.066215 TCTGATGTCATGTTCCCCACG 60.066 52.381 0.0 0.0 0.0 4.94 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 4.178956 TCTTTTTGAGGGGTAACAAGCT 57.821 40.909 0.00 0.00 39.74 3.74
22 23 5.313280 TCTTTTTGAGGGGTAACAAGCTA 57.687 39.130 0.00 0.00 39.74 3.32
23 24 5.697067 TCTTTTTGAGGGGTAACAAGCTAA 58.303 37.500 0.00 0.00 39.74 3.09
24 25 5.533528 TCTTTTTGAGGGGTAACAAGCTAAC 59.466 40.000 0.00 0.00 39.74 2.34
25 26 4.717279 TTTGAGGGGTAACAAGCTAACT 57.283 40.909 0.00 0.00 39.74 2.24
26 27 3.695830 TGAGGGGTAACAAGCTAACTG 57.304 47.619 0.00 0.00 39.74 3.16
27 28 2.290071 TGAGGGGTAACAAGCTAACTGC 60.290 50.000 0.00 0.00 39.86 4.40
28 29 1.004394 AGGGGTAACAAGCTAACTGCC 59.996 52.381 0.00 0.00 40.34 4.85
29 30 1.271707 GGGGTAACAAGCTAACTGCCA 60.272 52.381 0.00 0.00 40.34 4.92
30 31 1.810755 GGGTAACAAGCTAACTGCCAC 59.189 52.381 0.00 0.00 40.34 5.01
31 32 1.463444 GGTAACAAGCTAACTGCCACG 59.537 52.381 0.00 0.00 44.23 4.94
32 33 2.409975 GTAACAAGCTAACTGCCACGA 58.590 47.619 0.00 0.00 44.23 4.35
33 34 1.226746 AACAAGCTAACTGCCACGAC 58.773 50.000 0.00 0.00 44.23 4.34
34 35 0.944311 ACAAGCTAACTGCCACGACG 60.944 55.000 0.00 0.00 44.23 5.12
35 36 0.944311 CAAGCTAACTGCCACGACGT 60.944 55.000 0.00 0.00 44.23 4.34
36 37 0.599558 AAGCTAACTGCCACGACGTA 59.400 50.000 0.00 0.00 44.23 3.57
37 38 0.109412 AGCTAACTGCCACGACGTAC 60.109 55.000 0.00 0.00 44.23 3.67
38 39 0.109412 GCTAACTGCCACGACGTACT 60.109 55.000 0.00 0.00 35.15 2.73
39 40 1.131126 GCTAACTGCCACGACGTACTA 59.869 52.381 0.00 0.00 35.15 1.82
40 41 2.790468 GCTAACTGCCACGACGTACTAG 60.790 54.545 0.00 1.53 35.15 2.57
41 42 0.109412 AACTGCCACGACGTACTAGC 60.109 55.000 0.00 2.25 0.00 3.42
42 43 1.239296 ACTGCCACGACGTACTAGCA 61.239 55.000 0.00 7.07 0.00 3.49
43 44 0.797249 CTGCCACGACGTACTAGCAC 60.797 60.000 0.00 0.00 0.00 4.40
44 45 1.210931 GCCACGACGTACTAGCACA 59.789 57.895 0.00 0.00 0.00 4.57
45 46 0.179145 GCCACGACGTACTAGCACAT 60.179 55.000 0.00 0.00 0.00 3.21
46 47 1.545759 CCACGACGTACTAGCACATG 58.454 55.000 0.00 0.00 0.00 3.21
47 48 0.914551 CACGACGTACTAGCACATGC 59.085 55.000 0.00 0.00 42.49 4.06
48 49 0.524414 ACGACGTACTAGCACATGCA 59.476 50.000 6.64 0.00 45.16 3.96
49 50 1.134367 ACGACGTACTAGCACATGCAT 59.866 47.619 6.64 0.00 45.16 3.96
50 51 1.518515 CGACGTACTAGCACATGCATG 59.481 52.381 25.09 25.09 45.16 4.06
51 52 1.258982 GACGTACTAGCACATGCATGC 59.741 52.381 26.53 15.62 46.50 4.06
57 58 2.027024 GCACATGCATGCATCGGG 59.973 61.111 30.07 24.73 45.39 5.14
58 59 2.777972 GCACATGCATGCATCGGGT 61.778 57.895 30.07 21.56 45.39 5.28
59 60 1.357690 CACATGCATGCATCGGGTC 59.642 57.895 30.07 0.00 33.90 4.46
60 61 1.099295 CACATGCATGCATCGGGTCT 61.099 55.000 30.07 5.99 33.90 3.85
61 62 0.394762 ACATGCATGCATCGGGTCTT 60.395 50.000 30.07 5.14 33.90 3.01
62 63 0.030235 CATGCATGCATCGGGTCTTG 59.970 55.000 30.07 14.44 33.90 3.02
63 64 1.731433 ATGCATGCATCGGGTCTTGC 61.731 55.000 27.46 0.00 39.33 4.01
64 65 2.117156 GCATGCATCGGGTCTTGCT 61.117 57.895 14.21 0.00 39.60 3.91
65 66 1.725665 CATGCATCGGGTCTTGCTG 59.274 57.895 0.00 0.00 39.60 4.41
66 67 2.117156 ATGCATCGGGTCTTGCTGC 61.117 57.895 0.00 0.00 39.60 5.25
67 68 2.747460 GCATCGGGTCTTGCTGCA 60.747 61.111 0.00 0.00 35.95 4.41
68 69 2.758089 GCATCGGGTCTTGCTGCAG 61.758 63.158 10.11 10.11 35.95 4.41
69 70 2.437359 ATCGGGTCTTGCTGCAGC 60.437 61.111 31.89 31.89 42.50 5.25
79 80 2.952245 GCTGCAGCAACAGTCCTG 59.048 61.111 33.36 0.00 39.96 3.86
82 83 3.730761 GCAGCAACAGTCCTGCCG 61.731 66.667 12.90 0.00 46.59 5.69
83 84 3.730761 CAGCAACAGTCCTGCCGC 61.731 66.667 0.00 0.00 40.86 6.53
86 87 3.357079 CAACAGTCCTGCCGCCAC 61.357 66.667 0.00 0.00 0.00 5.01
87 88 4.643387 AACAGTCCTGCCGCCACC 62.643 66.667 0.00 0.00 0.00 4.61
122 123 4.636435 CCAACACCGGCCTCCGTT 62.636 66.667 0.00 0.00 46.80 4.44
123 124 2.593436 CAACACCGGCCTCCGTTT 60.593 61.111 0.00 0.00 46.80 3.60
124 125 2.281276 AACACCGGCCTCCGTTTC 60.281 61.111 0.00 0.00 46.80 2.78
125 126 4.675029 ACACCGGCCTCCGTTTCG 62.675 66.667 0.00 0.00 46.80 3.46
126 127 4.675029 CACCGGCCTCCGTTTCGT 62.675 66.667 0.00 0.00 46.80 3.85
127 128 2.990967 ACCGGCCTCCGTTTCGTA 60.991 61.111 0.00 0.00 46.80 3.43
128 129 2.202703 CCGGCCTCCGTTTCGTAG 60.203 66.667 0.00 0.00 46.80 3.51
129 130 2.884207 CGGCCTCCGTTTCGTAGC 60.884 66.667 0.00 0.00 42.73 3.58
130 131 2.884207 GGCCTCCGTTTCGTAGCG 60.884 66.667 0.00 0.00 0.00 4.26
131 132 2.180017 GCCTCCGTTTCGTAGCGA 59.820 61.111 0.00 0.00 0.00 4.93
132 133 1.226888 GCCTCCGTTTCGTAGCGAT 60.227 57.895 0.00 0.00 35.23 4.58
133 134 0.804933 GCCTCCGTTTCGTAGCGATT 60.805 55.000 0.00 0.00 35.23 3.34
134 135 1.197910 CCTCCGTTTCGTAGCGATTC 58.802 55.000 0.00 0.00 35.23 2.52
135 136 1.468565 CCTCCGTTTCGTAGCGATTCA 60.469 52.381 0.00 0.00 35.23 2.57
136 137 1.582502 CTCCGTTTCGTAGCGATTCAC 59.417 52.381 0.00 0.00 35.23 3.18
137 138 0.643820 CCGTTTCGTAGCGATTCACC 59.356 55.000 0.00 0.00 35.23 4.02
138 139 1.342555 CGTTTCGTAGCGATTCACCA 58.657 50.000 0.00 0.00 35.23 4.17
139 140 1.058695 CGTTTCGTAGCGATTCACCAC 59.941 52.381 0.00 0.00 35.23 4.16
140 141 2.334838 GTTTCGTAGCGATTCACCACT 58.665 47.619 0.00 0.00 35.23 4.00
141 142 1.990799 TTCGTAGCGATTCACCACTG 58.009 50.000 0.00 0.00 35.23 3.66
142 143 0.172578 TCGTAGCGATTCACCACTGG 59.827 55.000 0.00 0.00 0.00 4.00
143 144 1.421410 CGTAGCGATTCACCACTGGC 61.421 60.000 0.00 0.00 0.00 4.85
144 145 0.108138 GTAGCGATTCACCACTGGCT 60.108 55.000 0.00 0.00 34.69 4.75
145 146 0.108186 TAGCGATTCACCACTGGCTG 60.108 55.000 0.00 0.00 32.29 4.85
146 147 1.672356 GCGATTCACCACTGGCTGT 60.672 57.895 0.00 0.00 0.00 4.40
147 148 1.237285 GCGATTCACCACTGGCTGTT 61.237 55.000 0.00 0.00 0.00 3.16
148 149 1.943968 GCGATTCACCACTGGCTGTTA 60.944 52.381 0.00 0.00 0.00 2.41
149 150 2.632377 CGATTCACCACTGGCTGTTAT 58.368 47.619 0.00 0.00 0.00 1.89
150 151 2.352651 CGATTCACCACTGGCTGTTATG 59.647 50.000 0.00 0.00 0.00 1.90
151 152 2.198827 TTCACCACTGGCTGTTATGG 57.801 50.000 0.00 0.00 38.26 2.74
152 153 0.327924 TCACCACTGGCTGTTATGGG 59.672 55.000 0.00 0.00 36.47 4.00
153 154 1.000896 ACCACTGGCTGTTATGGGC 60.001 57.895 0.00 0.00 36.47 5.36
154 155 1.001020 CCACTGGCTGTTATGGGCA 60.001 57.895 0.00 0.00 37.66 5.36
160 161 3.518003 CTGTTATGGGCAGCCTGC 58.482 61.111 12.43 8.55 44.08 4.85
223 224 3.349006 GCAGGTGCCACGTGTCAG 61.349 66.667 17.81 0.00 36.45 3.51
224 225 3.349006 CAGGTGCCACGTGTCAGC 61.349 66.667 20.17 20.17 0.00 4.26
225 226 3.550431 AGGTGCCACGTGTCAGCT 61.550 61.111 24.12 24.12 36.35 4.24
226 227 3.349006 GGTGCCACGTGTCAGCTG 61.349 66.667 20.43 7.63 0.00 4.24
227 228 2.280119 GTGCCACGTGTCAGCTGA 60.280 61.111 13.74 13.74 0.00 4.26
228 229 1.669115 GTGCCACGTGTCAGCTGAT 60.669 57.895 21.47 0.00 0.00 2.90
229 230 1.668793 TGCCACGTGTCAGCTGATG 60.669 57.895 21.47 13.81 0.00 3.07
230 231 3.031964 GCCACGTGTCAGCTGATGC 62.032 63.158 21.47 14.43 40.05 3.91
231 232 2.733671 CCACGTGTCAGCTGATGCG 61.734 63.158 28.87 28.87 45.42 4.73
232 233 3.114616 ACGTGTCAGCTGATGCGC 61.115 61.111 29.79 20.18 45.42 6.09
233 234 3.857854 CGTGTCAGCTGATGCGCC 61.858 66.667 21.47 7.03 45.42 6.53
234 235 2.435586 GTGTCAGCTGATGCGCCT 60.436 61.111 21.47 0.00 45.42 5.52
235 236 2.435410 TGTCAGCTGATGCGCCTG 60.435 61.111 21.47 4.34 45.42 4.85
236 237 3.873883 GTCAGCTGATGCGCCTGC 61.874 66.667 21.47 6.15 45.42 4.85
257 258 3.966543 CACGGCCCAGGGGTCTTT 61.967 66.667 7.91 0.00 37.84 2.52
258 259 3.182996 ACGGCCCAGGGGTCTTTT 61.183 61.111 7.91 0.00 37.84 2.27
259 260 2.117423 CGGCCCAGGGGTCTTTTT 59.883 61.111 7.91 0.00 37.84 1.94
280 281 4.916041 TTGCCAATATCATCTAGAGGGG 57.084 45.455 4.28 0.00 0.00 4.79
281 282 3.184628 TGCCAATATCATCTAGAGGGGG 58.815 50.000 4.28 0.78 0.00 5.40
282 283 3.185455 GCCAATATCATCTAGAGGGGGT 58.815 50.000 4.28 0.00 0.00 4.95
283 284 3.198853 GCCAATATCATCTAGAGGGGGTC 59.801 52.174 4.28 0.00 0.00 4.46
284 285 4.693420 CCAATATCATCTAGAGGGGGTCT 58.307 47.826 4.28 0.00 39.59 3.85
285 286 5.097234 CCAATATCATCTAGAGGGGGTCTT 58.903 45.833 4.28 0.00 36.64 3.01
286 287 5.549619 CCAATATCATCTAGAGGGGGTCTTT 59.450 44.000 4.28 0.00 36.64 2.52
287 288 6.044871 CCAATATCATCTAGAGGGGGTCTTTT 59.955 42.308 4.28 0.00 36.64 2.27
288 289 7.421853 CCAATATCATCTAGAGGGGGTCTTTTT 60.422 40.741 4.28 0.00 36.64 1.94
308 309 4.448537 TTTGATAATTTCGTTGGGCAGG 57.551 40.909 0.00 0.00 0.00 4.85
309 310 3.080300 TGATAATTTCGTTGGGCAGGT 57.920 42.857 0.00 0.00 0.00 4.00
310 311 2.752354 TGATAATTTCGTTGGGCAGGTG 59.248 45.455 0.00 0.00 0.00 4.00
311 312 1.540267 TAATTTCGTTGGGCAGGTGG 58.460 50.000 0.00 0.00 0.00 4.61
312 313 0.469144 AATTTCGTTGGGCAGGTGGT 60.469 50.000 0.00 0.00 0.00 4.16
313 314 0.893727 ATTTCGTTGGGCAGGTGGTC 60.894 55.000 0.00 0.00 0.00 4.02
314 315 1.990160 TTTCGTTGGGCAGGTGGTCT 61.990 55.000 0.00 0.00 0.00 3.85
315 316 1.990160 TTCGTTGGGCAGGTGGTCTT 61.990 55.000 0.00 0.00 0.00 3.01
316 317 1.528309 CGTTGGGCAGGTGGTCTTT 60.528 57.895 0.00 0.00 0.00 2.52
317 318 1.106944 CGTTGGGCAGGTGGTCTTTT 61.107 55.000 0.00 0.00 0.00 2.27
318 319 1.119684 GTTGGGCAGGTGGTCTTTTT 58.880 50.000 0.00 0.00 0.00 1.94
319 320 1.068588 GTTGGGCAGGTGGTCTTTTTC 59.931 52.381 0.00 0.00 0.00 2.29
320 321 0.260230 TGGGCAGGTGGTCTTTTTCA 59.740 50.000 0.00 0.00 0.00 2.69
321 322 1.342474 TGGGCAGGTGGTCTTTTTCAA 60.342 47.619 0.00 0.00 0.00 2.69
322 323 1.760029 GGGCAGGTGGTCTTTTTCAAA 59.240 47.619 0.00 0.00 0.00 2.69
323 324 2.169561 GGGCAGGTGGTCTTTTTCAAAA 59.830 45.455 0.00 0.00 0.00 2.44
324 325 3.369997 GGGCAGGTGGTCTTTTTCAAAAA 60.370 43.478 0.00 0.00 0.00 1.94
391 392 2.258591 TCGCTGTTCGAGACTGCC 59.741 61.111 17.25 6.55 46.85 4.85
407 408 3.370104 ACTGCCAGGCTATAGCTATAGG 58.630 50.000 32.25 21.85 41.70 2.57
575 577 6.049263 ACTACAGCGAAACTTCTTTCTTTG 57.951 37.500 0.00 0.00 34.62 2.77
578 580 4.035675 ACAGCGAAACTTCTTTCTTTGGAG 59.964 41.667 0.00 0.00 34.62 3.86
640 646 2.533266 ACACGCATCATCCATCTACC 57.467 50.000 0.00 0.00 0.00 3.18
647 2118 2.715763 TCATCCATCTACCCTACCCC 57.284 55.000 0.00 0.00 0.00 4.95
818 2290 2.397044 TTGGGATTTTCCAGCTGGTT 57.603 45.000 31.58 15.38 38.64 3.67
819 2291 1.923356 TGGGATTTTCCAGCTGGTTC 58.077 50.000 31.58 21.81 38.64 3.62
820 2292 1.186200 GGGATTTTCCAGCTGGTTCC 58.814 55.000 31.58 27.84 38.64 3.62
821 2293 0.811281 GGATTTTCCAGCTGGTTCCG 59.189 55.000 31.58 6.61 36.28 4.30
822 2294 0.171231 GATTTTCCAGCTGGTTCCGC 59.829 55.000 31.58 15.91 36.34 5.54
823 2295 1.250840 ATTTTCCAGCTGGTTCCGCC 61.251 55.000 31.58 0.00 36.34 6.13
824 2296 3.860930 TTTCCAGCTGGTTCCGCCC 62.861 63.158 31.58 0.00 36.04 6.13
1560 3049 2.430244 CACGGGTTCCACGTCGAG 60.430 66.667 0.00 0.00 43.58 4.04
1936 3428 1.398692 TTCTGCAACCTTTTTCGCCT 58.601 45.000 0.00 0.00 0.00 5.52
1969 3461 0.388649 CTGCTCCAGTACGTGTGGAC 60.389 60.000 15.54 13.03 39.28 4.02
2016 3508 3.318539 GAGCGTGCGTGGTCTCGTA 62.319 63.158 0.44 0.00 33.66 3.43
2152 3650 4.695928 GTGGAGAAATAGGTGGAAGTTGTC 59.304 45.833 0.00 0.00 0.00 3.18
2153 3651 4.597507 TGGAGAAATAGGTGGAAGTTGTCT 59.402 41.667 0.00 0.00 0.00 3.41
2154 3652 5.073144 TGGAGAAATAGGTGGAAGTTGTCTT 59.927 40.000 0.00 0.00 36.51 3.01
2155 3653 6.004574 GGAGAAATAGGTGGAAGTTGTCTTT 58.995 40.000 0.00 0.00 33.64 2.52
2156 3654 7.166167 GGAGAAATAGGTGGAAGTTGTCTTTA 58.834 38.462 0.00 0.00 33.64 1.85
2157 3655 7.664318 GGAGAAATAGGTGGAAGTTGTCTTTAA 59.336 37.037 0.00 0.00 33.64 1.52
2158 3656 8.990163 AGAAATAGGTGGAAGTTGTCTTTAAA 57.010 30.769 0.00 0.00 33.64 1.52
2159 3657 9.416284 AGAAATAGGTGGAAGTTGTCTTTAAAA 57.584 29.630 0.00 0.00 33.64 1.52
2180 3678 6.731292 AAAAATCTTTGGTACTCTTTGGCT 57.269 33.333 0.00 0.00 0.00 4.75
2181 3679 7.833285 AAAAATCTTTGGTACTCTTTGGCTA 57.167 32.000 0.00 0.00 0.00 3.93
2182 3680 7.454260 AAAATCTTTGGTACTCTTTGGCTAG 57.546 36.000 0.00 0.00 0.00 3.42
2183 3681 4.553330 TCTTTGGTACTCTTTGGCTAGG 57.447 45.455 0.00 0.00 0.00 3.02
2184 3682 3.263425 TCTTTGGTACTCTTTGGCTAGGG 59.737 47.826 0.00 0.00 0.00 3.53
2185 3683 2.337359 TGGTACTCTTTGGCTAGGGT 57.663 50.000 0.00 0.00 32.47 4.34
2186 3684 2.627933 TGGTACTCTTTGGCTAGGGTT 58.372 47.619 0.00 0.00 29.85 4.11
2187 3685 2.983898 TGGTACTCTTTGGCTAGGGTTT 59.016 45.455 0.00 0.00 29.85 3.27
2188 3686 3.008704 TGGTACTCTTTGGCTAGGGTTTC 59.991 47.826 0.00 0.00 29.85 2.78
2189 3687 3.263681 GGTACTCTTTGGCTAGGGTTTCT 59.736 47.826 0.00 0.00 29.85 2.52
2190 3688 3.704800 ACTCTTTGGCTAGGGTTTCTC 57.295 47.619 0.00 0.00 0.00 2.87
2191 3689 2.028020 ACTCTTTGGCTAGGGTTTCTCG 60.028 50.000 0.00 0.00 0.00 4.04
2192 3690 1.975680 TCTTTGGCTAGGGTTTCTCGT 59.024 47.619 0.00 0.00 0.00 4.18
2193 3691 2.076863 CTTTGGCTAGGGTTTCTCGTG 58.923 52.381 0.00 0.00 0.00 4.35
2302 3801 7.463961 TTTGAGTTTTGTTAGGGTTTGTGTA 57.536 32.000 0.00 0.00 0.00 2.90
2308 3807 6.837471 TTTGTTAGGGTTTGTGTACTGTTT 57.163 33.333 0.00 0.00 0.00 2.83
2324 3823 0.810016 GTTTAGAGAGTCGAGGCGGT 59.190 55.000 0.00 0.00 0.00 5.68
2334 3833 4.070552 GAGGCGGTGGCGACTCTT 62.071 66.667 0.00 0.00 41.24 2.85
2342 3841 1.405526 GGTGGCGACTCTTTGCAGATA 60.406 52.381 0.00 0.00 33.08 1.98
2379 3878 2.204013 TTGTCCCCATCCCGGTGA 60.204 61.111 0.00 0.00 0.00 4.02
2400 3899 2.089201 TGTTTCTAGCATCGTCGGAGA 58.911 47.619 0.00 0.00 0.00 3.71
2411 3910 2.033602 TCGGAGAGCGTGTGGAGA 59.966 61.111 0.00 0.00 0.00 3.71
2422 3921 2.610479 GCGTGTGGAGATTTGTCTCTGA 60.610 50.000 5.52 0.00 36.97 3.27
2442 3941 1.502163 CGGATCTTGCGGGATTCAGC 61.502 60.000 0.00 0.00 0.00 4.26
2445 3944 1.971505 ATCTTGCGGGATTCAGCCGA 61.972 55.000 0.00 0.00 0.00 5.54
2501 4000 4.152223 TCTTCGTTCGTCTATGTTCGTGTA 59.848 41.667 0.00 0.00 0.00 2.90
2642 4142 2.511452 CCCGGCTCCGATGAAGGAT 61.511 63.158 10.28 0.00 42.83 3.24
2711 4211 3.068560 GTCGCTAGATGATCTACGGACT 58.931 50.000 17.72 0.00 30.31 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.178956 AGCTTGTTACCCCTCAAAAAGA 57.821 40.909 0.00 0.00 0.00 2.52
1 2 5.535030 AGTTAGCTTGTTACCCCTCAAAAAG 59.465 40.000 0.00 0.00 0.00 2.27
2 3 5.300792 CAGTTAGCTTGTTACCCCTCAAAAA 59.699 40.000 0.00 0.00 0.00 1.94
3 4 4.825085 CAGTTAGCTTGTTACCCCTCAAAA 59.175 41.667 0.00 0.00 0.00 2.44
4 5 4.394729 CAGTTAGCTTGTTACCCCTCAAA 58.605 43.478 0.00 0.00 0.00 2.69
5 6 3.809324 GCAGTTAGCTTGTTACCCCTCAA 60.809 47.826 0.00 0.00 41.15 3.02
6 7 2.290071 GCAGTTAGCTTGTTACCCCTCA 60.290 50.000 0.00 0.00 41.15 3.86
7 8 2.357075 GCAGTTAGCTTGTTACCCCTC 58.643 52.381 0.00 0.00 41.15 4.30
8 9 1.004394 GGCAGTTAGCTTGTTACCCCT 59.996 52.381 0.00 0.00 44.79 4.79
9 10 1.271707 TGGCAGTTAGCTTGTTACCCC 60.272 52.381 0.00 0.00 44.79 4.95
10 11 1.810755 GTGGCAGTTAGCTTGTTACCC 59.189 52.381 0.00 0.00 44.79 3.69
11 12 1.463444 CGTGGCAGTTAGCTTGTTACC 59.537 52.381 0.00 0.00 44.79 2.85
12 13 2.157085 GTCGTGGCAGTTAGCTTGTTAC 59.843 50.000 0.00 0.00 44.79 2.50
13 14 2.409975 GTCGTGGCAGTTAGCTTGTTA 58.590 47.619 0.00 0.00 44.79 2.41
14 15 1.226746 GTCGTGGCAGTTAGCTTGTT 58.773 50.000 0.00 0.00 44.79 2.83
15 16 0.944311 CGTCGTGGCAGTTAGCTTGT 60.944 55.000 0.00 0.00 44.79 3.16
16 17 0.944311 ACGTCGTGGCAGTTAGCTTG 60.944 55.000 0.00 0.00 44.79 4.01
17 18 0.599558 TACGTCGTGGCAGTTAGCTT 59.400 50.000 8.47 0.00 44.79 3.74
18 19 0.109412 GTACGTCGTGGCAGTTAGCT 60.109 55.000 8.47 0.00 44.79 3.32
19 20 0.109412 AGTACGTCGTGGCAGTTAGC 60.109 55.000 8.47 0.00 44.65 3.09
20 21 2.790468 GCTAGTACGTCGTGGCAGTTAG 60.790 54.545 8.47 2.40 0.00 2.34
21 22 1.131126 GCTAGTACGTCGTGGCAGTTA 59.869 52.381 8.47 0.00 0.00 2.24
22 23 0.109412 GCTAGTACGTCGTGGCAGTT 60.109 55.000 8.47 0.00 0.00 3.16
23 24 1.239296 TGCTAGTACGTCGTGGCAGT 61.239 55.000 8.47 0.00 0.00 4.40
24 25 0.797249 GTGCTAGTACGTCGTGGCAG 60.797 60.000 8.47 2.99 0.00 4.85
25 26 1.210931 GTGCTAGTACGTCGTGGCA 59.789 57.895 8.47 10.16 0.00 4.92
26 27 0.179145 ATGTGCTAGTACGTCGTGGC 60.179 55.000 8.47 7.70 0.00 5.01
27 28 1.545759 CATGTGCTAGTACGTCGTGG 58.454 55.000 8.47 0.00 0.00 4.94
28 29 0.914551 GCATGTGCTAGTACGTCGTG 59.085 55.000 8.47 2.50 38.21 4.35
29 30 0.524414 TGCATGTGCTAGTACGTCGT 59.476 50.000 2.21 2.21 42.66 4.34
30 31 1.518515 CATGCATGTGCTAGTACGTCG 59.481 52.381 18.91 1.23 42.66 5.12
31 32 1.258982 GCATGCATGTGCTAGTACGTC 59.741 52.381 26.79 2.80 41.82 4.34
32 33 1.290203 GCATGCATGTGCTAGTACGT 58.710 50.000 26.79 2.93 41.82 3.57
33 34 1.289276 TGCATGCATGTGCTAGTACG 58.711 50.000 26.79 0.00 45.27 3.67
34 35 2.096565 CGATGCATGCATGTGCTAGTAC 60.097 50.000 36.73 17.64 45.27 2.73
35 36 2.137523 CGATGCATGCATGTGCTAGTA 58.862 47.619 36.73 3.35 45.27 1.82
36 37 0.942252 CGATGCATGCATGTGCTAGT 59.058 50.000 36.73 12.27 45.27 2.57
37 38 0.237498 CCGATGCATGCATGTGCTAG 59.763 55.000 36.73 18.71 45.27 3.42
38 39 1.167781 CCCGATGCATGCATGTGCTA 61.168 55.000 36.73 5.92 45.27 3.49
39 40 2.486663 CCCGATGCATGCATGTGCT 61.487 57.895 36.73 14.80 45.27 4.40
40 41 2.027024 CCCGATGCATGCATGTGC 59.973 61.111 36.73 21.20 45.25 4.57
41 42 1.099295 AGACCCGATGCATGCATGTG 61.099 55.000 36.73 26.29 36.70 3.21
42 43 0.394762 AAGACCCGATGCATGCATGT 60.395 50.000 36.73 27.06 36.70 3.21
43 44 0.030235 CAAGACCCGATGCATGCATG 59.970 55.000 36.73 25.69 36.70 4.06
44 45 1.731433 GCAAGACCCGATGCATGCAT 61.731 55.000 32.66 32.66 42.12 3.96
45 46 2.409055 GCAAGACCCGATGCATGCA 61.409 57.895 25.04 25.04 42.12 3.96
46 47 2.117156 AGCAAGACCCGATGCATGC 61.117 57.895 11.82 11.82 44.95 4.06
47 48 1.725665 CAGCAAGACCCGATGCATG 59.274 57.895 2.46 0.00 44.95 4.06
48 49 2.117156 GCAGCAAGACCCGATGCAT 61.117 57.895 0.00 0.00 44.95 3.96
49 50 2.747460 GCAGCAAGACCCGATGCA 60.747 61.111 0.00 0.00 44.95 3.96
50 51 2.747460 TGCAGCAAGACCCGATGC 60.747 61.111 0.00 0.00 42.87 3.91
51 52 2.758089 GCTGCAGCAAGACCCGATG 61.758 63.158 33.36 0.00 41.59 3.84
52 53 2.437359 GCTGCAGCAAGACCCGAT 60.437 61.111 33.36 0.00 41.59 4.18
62 63 2.952245 CAGGACTGTTGCTGCAGC 59.048 61.111 31.89 31.89 39.96 5.25
69 70 3.357079 GTGGCGGCAGGACTGTTG 61.357 66.667 13.91 0.00 0.00 3.33
70 71 4.643387 GGTGGCGGCAGGACTGTT 62.643 66.667 13.91 0.00 0.00 3.16
113 114 2.624437 ATCGCTACGAAACGGAGGCC 62.624 60.000 0.00 0.00 38.40 5.19
114 115 0.804933 AATCGCTACGAAACGGAGGC 60.805 55.000 5.56 1.39 38.40 4.70
115 116 1.197910 GAATCGCTACGAAACGGAGG 58.802 55.000 5.56 0.00 38.40 4.30
116 117 1.582502 GTGAATCGCTACGAAACGGAG 59.417 52.381 0.00 0.00 41.33 4.63
117 118 1.621107 GTGAATCGCTACGAAACGGA 58.379 50.000 0.00 0.00 39.99 4.69
118 119 0.643820 GGTGAATCGCTACGAAACGG 59.356 55.000 0.00 0.00 39.99 4.44
119 120 1.058695 GTGGTGAATCGCTACGAAACG 59.941 52.381 0.00 0.00 39.99 3.60
120 121 2.092211 CAGTGGTGAATCGCTACGAAAC 59.908 50.000 4.70 0.00 39.99 2.78
121 122 2.333926 CAGTGGTGAATCGCTACGAAA 58.666 47.619 4.70 0.00 39.99 3.46
122 123 1.403647 CCAGTGGTGAATCGCTACGAA 60.404 52.381 0.00 0.00 39.99 3.85
123 124 0.172578 CCAGTGGTGAATCGCTACGA 59.827 55.000 0.00 0.00 41.13 3.43
124 125 1.421410 GCCAGTGGTGAATCGCTACG 61.421 60.000 11.74 0.86 30.82 3.51
125 126 0.108138 AGCCAGTGGTGAATCGCTAC 60.108 55.000 11.74 1.90 0.00 3.58
126 127 0.108186 CAGCCAGTGGTGAATCGCTA 60.108 55.000 11.74 0.00 42.66 4.26
127 128 1.376424 CAGCCAGTGGTGAATCGCT 60.376 57.895 11.74 0.00 42.66 4.93
128 129 1.237285 AACAGCCAGTGGTGAATCGC 61.237 55.000 11.74 0.00 42.66 4.58
129 130 2.093306 TAACAGCCAGTGGTGAATCG 57.907 50.000 11.74 0.00 42.66 3.34
130 131 2.684881 CCATAACAGCCAGTGGTGAATC 59.315 50.000 11.74 0.00 42.66 2.52
131 132 2.621407 CCCATAACAGCCAGTGGTGAAT 60.621 50.000 11.74 5.12 42.66 2.57
132 133 1.271871 CCCATAACAGCCAGTGGTGAA 60.272 52.381 11.74 3.13 42.66 3.18
133 134 0.327924 CCCATAACAGCCAGTGGTGA 59.672 55.000 11.74 0.00 42.66 4.02
134 135 1.315257 GCCCATAACAGCCAGTGGTG 61.315 60.000 11.74 10.35 45.50 4.17
135 136 1.000896 GCCCATAACAGCCAGTGGT 60.001 57.895 11.74 0.00 0.00 4.16
136 137 1.001020 TGCCCATAACAGCCAGTGG 60.001 57.895 4.20 4.20 0.00 4.00
137 138 2.485677 CTGCCCATAACAGCCAGTG 58.514 57.895 0.00 0.00 0.00 3.66
143 144 3.518003 GCAGGCTGCCCATAACAG 58.482 61.111 28.87 0.00 37.42 3.16
206 207 3.349006 CTGACACGTGGCACCTGC 61.349 66.667 23.03 7.87 41.14 4.85
207 208 3.349006 GCTGACACGTGGCACCTG 61.349 66.667 23.03 12.88 0.00 4.00
208 209 3.550431 AGCTGACACGTGGCACCT 61.550 61.111 23.03 17.93 0.00 4.00
209 210 3.349006 CAGCTGACACGTGGCACC 61.349 66.667 23.03 15.44 0.00 5.01
210 211 1.669115 ATCAGCTGACACGTGGCAC 60.669 57.895 23.03 17.50 0.00 5.01
211 212 1.668793 CATCAGCTGACACGTGGCA 60.669 57.895 25.31 25.31 0.00 4.92
212 213 3.031964 GCATCAGCTGACACGTGGC 62.032 63.158 20.97 19.24 37.91 5.01
213 214 2.733671 CGCATCAGCTGACACGTGG 61.734 63.158 20.97 5.80 39.10 4.94
214 215 2.774126 CGCATCAGCTGACACGTG 59.226 61.111 20.97 15.48 39.10 4.49
215 216 3.114616 GCGCATCAGCTGACACGT 61.115 61.111 29.93 11.22 39.10 4.49
216 217 3.857854 GGCGCATCAGCTGACACG 61.858 66.667 27.34 27.34 39.10 4.49
217 218 2.435586 AGGCGCATCAGCTGACAC 60.436 61.111 20.97 13.19 39.10 3.67
218 219 2.435410 CAGGCGCATCAGCTGACA 60.435 61.111 20.97 0.00 39.10 3.58
219 220 3.873883 GCAGGCGCATCAGCTGAC 61.874 66.667 20.97 6.39 39.10 3.51
240 241 2.994643 AAAAAGACCCCTGGGCCGTG 62.995 60.000 7.39 0.00 39.32 4.94
241 242 2.774633 AAAAAGACCCCTGGGCCGT 61.775 57.895 7.39 0.00 39.32 5.68
242 243 2.117423 AAAAAGACCCCTGGGCCG 59.883 61.111 7.39 0.00 39.32 6.13
256 257 6.070656 CCCCTCTAGATGATATTGGCAAAAA 58.929 40.000 3.01 0.00 0.00 1.94
257 258 5.458069 CCCCCTCTAGATGATATTGGCAAAA 60.458 44.000 3.01 0.00 0.00 2.44
258 259 4.043310 CCCCCTCTAGATGATATTGGCAAA 59.957 45.833 3.01 0.00 0.00 3.68
259 260 3.588842 CCCCCTCTAGATGATATTGGCAA 59.411 47.826 0.68 0.68 0.00 4.52
260 261 3.184628 CCCCCTCTAGATGATATTGGCA 58.815 50.000 0.00 0.00 0.00 4.92
261 262 3.185455 ACCCCCTCTAGATGATATTGGC 58.815 50.000 0.00 0.00 0.00 4.52
262 263 4.693420 AGACCCCCTCTAGATGATATTGG 58.307 47.826 0.00 0.00 0.00 3.16
263 264 6.694445 AAAGACCCCCTCTAGATGATATTG 57.306 41.667 0.00 0.00 0.00 1.90
264 265 7.713704 AAAAAGACCCCCTCTAGATGATATT 57.286 36.000 0.00 0.00 0.00 1.28
285 286 5.221541 ACCTGCCCAACGAAATTATCAAAAA 60.222 36.000 0.00 0.00 0.00 1.94
286 287 4.282195 ACCTGCCCAACGAAATTATCAAAA 59.718 37.500 0.00 0.00 0.00 2.44
287 288 3.829601 ACCTGCCCAACGAAATTATCAAA 59.170 39.130 0.00 0.00 0.00 2.69
288 289 3.192422 CACCTGCCCAACGAAATTATCAA 59.808 43.478 0.00 0.00 0.00 2.57
289 290 2.752354 CACCTGCCCAACGAAATTATCA 59.248 45.455 0.00 0.00 0.00 2.15
290 291 2.099098 CCACCTGCCCAACGAAATTATC 59.901 50.000 0.00 0.00 0.00 1.75
291 292 2.099405 CCACCTGCCCAACGAAATTAT 58.901 47.619 0.00 0.00 0.00 1.28
292 293 1.202952 ACCACCTGCCCAACGAAATTA 60.203 47.619 0.00 0.00 0.00 1.40
293 294 0.469144 ACCACCTGCCCAACGAAATT 60.469 50.000 0.00 0.00 0.00 1.82
294 295 0.893727 GACCACCTGCCCAACGAAAT 60.894 55.000 0.00 0.00 0.00 2.17
295 296 1.527380 GACCACCTGCCCAACGAAA 60.527 57.895 0.00 0.00 0.00 3.46
296 297 1.990160 AAGACCACCTGCCCAACGAA 61.990 55.000 0.00 0.00 0.00 3.85
297 298 1.990160 AAAGACCACCTGCCCAACGA 61.990 55.000 0.00 0.00 0.00 3.85
298 299 1.106944 AAAAGACCACCTGCCCAACG 61.107 55.000 0.00 0.00 0.00 4.10
299 300 1.068588 GAAAAAGACCACCTGCCCAAC 59.931 52.381 0.00 0.00 0.00 3.77
300 301 1.342474 TGAAAAAGACCACCTGCCCAA 60.342 47.619 0.00 0.00 0.00 4.12
301 302 0.260230 TGAAAAAGACCACCTGCCCA 59.740 50.000 0.00 0.00 0.00 5.36
302 303 1.408969 TTGAAAAAGACCACCTGCCC 58.591 50.000 0.00 0.00 0.00 5.36
303 304 3.535280 TTTTGAAAAAGACCACCTGCC 57.465 42.857 0.00 0.00 0.00 4.85
326 327 0.319405 AGGTCCGTCCGACGATTTTT 59.681 50.000 22.40 1.21 46.05 1.94
327 328 0.389426 CAGGTCCGTCCGACGATTTT 60.389 55.000 22.40 2.61 46.05 1.82
328 329 1.214589 CAGGTCCGTCCGACGATTT 59.785 57.895 22.40 2.25 46.05 2.17
329 330 2.882876 CAGGTCCGTCCGACGATT 59.117 61.111 22.40 1.91 46.05 3.34
330 331 3.823330 GCAGGTCCGTCCGACGAT 61.823 66.667 22.40 2.54 46.05 3.73
391 392 2.962421 GAGGCCCTATAGCTATAGCCTG 59.038 54.545 34.52 24.39 43.38 4.85
435 436 1.487976 ACGATCCCAATCATGAGCAGT 59.512 47.619 0.09 0.00 31.76 4.40
575 577 1.535202 AGGCGATCCCTGATCCTCC 60.535 63.158 2.27 1.34 44.28 4.30
578 580 3.064416 GGAGGCGATCCCTGATCC 58.936 66.667 7.41 0.58 46.60 3.36
640 646 0.620410 TGTGGATGGAGTGGGGTAGG 60.620 60.000 0.00 0.00 0.00 3.18
647 2118 0.742281 CCTTCGCTGTGGATGGAGTG 60.742 60.000 0.00 0.00 34.11 3.51
1560 3049 4.664677 AGCCAGGTGTCGACGCAC 62.665 66.667 28.67 18.21 38.56 5.34
1936 3428 1.568612 GAGCAGTAGCGCAAGTGCAA 61.569 55.000 24.07 0.00 46.28 4.08
1969 3461 1.066215 TCTGATGTCATGTTCCCCACG 60.066 52.381 0.00 0.00 0.00 4.94
2079 3571 4.740334 GCATATTTTTGCCGGATCCACATT 60.740 41.667 13.41 0.00 36.60 2.71
2157 3655 6.731292 AGCCAAAGAGTACCAAAGATTTTT 57.269 33.333 0.00 0.00 0.00 1.94
2158 3656 6.434340 CCTAGCCAAAGAGTACCAAAGATTTT 59.566 38.462 0.00 0.00 0.00 1.82
2159 3657 5.946377 CCTAGCCAAAGAGTACCAAAGATTT 59.054 40.000 0.00 0.00 0.00 2.17
2160 3658 5.501156 CCTAGCCAAAGAGTACCAAAGATT 58.499 41.667 0.00 0.00 0.00 2.40
2161 3659 4.080299 CCCTAGCCAAAGAGTACCAAAGAT 60.080 45.833 0.00 0.00 0.00 2.40
2162 3660 3.263425 CCCTAGCCAAAGAGTACCAAAGA 59.737 47.826 0.00 0.00 0.00 2.52
2163 3661 3.009143 ACCCTAGCCAAAGAGTACCAAAG 59.991 47.826 0.00 0.00 0.00 2.77
2164 3662 2.983898 ACCCTAGCCAAAGAGTACCAAA 59.016 45.455 0.00 0.00 0.00 3.28
2165 3663 2.627933 ACCCTAGCCAAAGAGTACCAA 58.372 47.619 0.00 0.00 0.00 3.67
2166 3664 2.337359 ACCCTAGCCAAAGAGTACCA 57.663 50.000 0.00 0.00 0.00 3.25
2167 3665 3.263681 AGAAACCCTAGCCAAAGAGTACC 59.736 47.826 0.00 0.00 0.00 3.34
2168 3666 4.505808 GAGAAACCCTAGCCAAAGAGTAC 58.494 47.826 0.00 0.00 0.00 2.73
2169 3667 3.194968 CGAGAAACCCTAGCCAAAGAGTA 59.805 47.826 0.00 0.00 0.00 2.59
2170 3668 2.028020 CGAGAAACCCTAGCCAAAGAGT 60.028 50.000 0.00 0.00 0.00 3.24
2171 3669 2.028020 ACGAGAAACCCTAGCCAAAGAG 60.028 50.000 0.00 0.00 0.00 2.85
2172 3670 1.975680 ACGAGAAACCCTAGCCAAAGA 59.024 47.619 0.00 0.00 0.00 2.52
2173 3671 2.076863 CACGAGAAACCCTAGCCAAAG 58.923 52.381 0.00 0.00 0.00 2.77
2174 3672 1.880646 GCACGAGAAACCCTAGCCAAA 60.881 52.381 0.00 0.00 0.00 3.28
2175 3673 0.321298 GCACGAGAAACCCTAGCCAA 60.321 55.000 0.00 0.00 0.00 4.52
2176 3674 1.295423 GCACGAGAAACCCTAGCCA 59.705 57.895 0.00 0.00 0.00 4.75
2177 3675 1.449778 GGCACGAGAAACCCTAGCC 60.450 63.158 0.00 0.00 32.64 3.93
2178 3676 0.460459 GAGGCACGAGAAACCCTAGC 60.460 60.000 0.00 0.00 0.00 3.42
2179 3677 0.179134 CGAGGCACGAGAAACCCTAG 60.179 60.000 0.00 0.00 45.77 3.02
2180 3678 0.896940 ACGAGGCACGAGAAACCCTA 60.897 55.000 12.15 0.00 45.77 3.53
2181 3679 2.156051 GACGAGGCACGAGAAACCCT 62.156 60.000 12.15 0.00 45.77 4.34
2182 3680 1.737008 GACGAGGCACGAGAAACCC 60.737 63.158 12.15 0.00 45.77 4.11
2183 3681 0.319641 AAGACGAGGCACGAGAAACC 60.320 55.000 12.15 0.00 45.77 3.27
2184 3682 1.061485 GAAGACGAGGCACGAGAAAC 58.939 55.000 12.15 0.00 45.77 2.78
2185 3683 0.959553 AGAAGACGAGGCACGAGAAA 59.040 50.000 12.15 0.00 45.77 2.52
2186 3684 0.241213 CAGAAGACGAGGCACGAGAA 59.759 55.000 12.15 0.00 45.77 2.87
2187 3685 0.889638 ACAGAAGACGAGGCACGAGA 60.890 55.000 12.15 0.00 45.77 4.04
2188 3686 0.730834 CACAGAAGACGAGGCACGAG 60.731 60.000 12.15 0.00 45.77 4.18
2189 3687 1.285950 CACAGAAGACGAGGCACGA 59.714 57.895 12.15 0.00 45.77 4.35
2191 3689 0.667792 GACCACAGAAGACGAGGCAC 60.668 60.000 0.00 0.00 0.00 5.01
2192 3690 0.827925 AGACCACAGAAGACGAGGCA 60.828 55.000 0.00 0.00 0.00 4.75
2193 3691 0.318762 AAGACCACAGAAGACGAGGC 59.681 55.000 0.00 0.00 0.00 4.70
2276 3774 7.217906 ACACAAACCCTAACAAAACTCAAAAA 58.782 30.769 0.00 0.00 0.00 1.94
2302 3801 1.469308 CGCCTCGACTCTCTAAACAGT 59.531 52.381 0.00 0.00 0.00 3.55
2308 3807 1.451567 CCACCGCCTCGACTCTCTA 60.452 63.158 0.00 0.00 0.00 2.43
2324 3823 1.824852 TCTATCTGCAAAGAGTCGCCA 59.175 47.619 0.00 0.00 0.00 5.69
2334 3833 6.357367 GGGAAGAACCTTATTCTATCTGCAA 58.643 40.000 0.00 0.00 38.98 4.08
2342 3841 2.197465 AGGCGGGAAGAACCTTATTCT 58.803 47.619 0.00 0.00 38.98 2.40
2379 3878 2.688446 TCTCCGACGATGCTAGAAACAT 59.312 45.455 0.00 0.00 0.00 2.71
2400 3899 2.086054 GAGACAAATCTCCACACGCT 57.914 50.000 0.00 0.00 45.06 5.07
2411 3910 3.265791 GCAAGATCCGTCAGAGACAAAT 58.734 45.455 0.00 0.00 32.09 2.32
2422 3921 0.179073 CTGAATCCCGCAAGATCCGT 60.179 55.000 0.00 0.00 43.02 4.69
2445 3944 1.003233 GGATCCACCGAAGACAAAGGT 59.997 52.381 6.95 0.00 39.12 3.50
2471 3970 5.710984 ACATAGACGAACGAAGACAAGATT 58.289 37.500 0.14 0.00 0.00 2.40
2501 4000 4.537751 TCAGAAGGATCGAACCTGTAGAT 58.462 43.478 15.81 0.00 40.49 1.98


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

AutoCloner maintained by Alex Coulton.