Multiple sequence alignment - TraesCS4D01G048800

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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 TraesCS4D01G048800 chr4D 100.000 3005 0 0 1 3005 25195492 25192488 0.000000e+00 5550.0
1 TraesCS4D01G048800 chr4D 89.372 1035 100 8 983 2008 25364013 25362980 0.000000e+00 1293.0
2 TraesCS4D01G048800 chr4D 85.546 1017 126 12 983 1989 25321271 25320266 0.000000e+00 1044.0
3 TraesCS4D01G048800 chr4D 77.321 851 163 21 1134 1976 25159691 25160519 2.710000e-130 475.0
4 TraesCS4D01G048800 chr4A 92.992 2483 137 15 542 3005 578233128 578235592 0.000000e+00 3587.0
5 TraesCS4D01G048800 chr4A 89.672 1036 96 8 983 2008 578176207 578175173 0.000000e+00 1310.0
6 TraesCS4D01G048800 chr4A 88.114 1018 111 8 983 1990 578006996 578008013 0.000000e+00 1201.0
7 TraesCS4D01G048800 chr4B 92.926 1654 88 4 580 2215 37174876 37173234 0.000000e+00 2379.0
8 TraesCS4D01G048800 chr4B 90.048 1035 93 8 983 2008 37297448 37296415 0.000000e+00 1332.0
9 TraesCS4D01G048800 chr4B 92.413 804 53 6 2209 3005 37150617 37149815 0.000000e+00 1140.0
10 TraesCS4D01G048800 chr4B 89.078 412 41 4 88 498 37194135 37193727 2.670000e-140 508.0
11 TraesCS4D01G048800 chr3B 89.275 1035 101 7 983 2008 39545166 39546199 0.000000e+00 1288.0
12 TraesCS4D01G048800 chr3B 94.286 35 2 0 495 529 445147511 445147545 2.000000e-03 54.7
13 TraesCS4D01G048800 chr5D 100.000 48 0 0 495 542 481805625 481805672 4.130000e-14 89.8
14 TraesCS4D01G048800 chr5B 98.000 50 1 0 495 544 655642 655691 1.480000e-13 87.9
15 TraesCS4D01G048800 chr5B 97.727 44 1 0 495 538 394252488 394252445 3.210000e-10 76.8
16 TraesCS4D01G048800 chr1A 84.524 84 11 2 281 363 546226820 546226738 6.900000e-12 82.4
17 TraesCS4D01G048800 chr1D 85.135 74 9 1 295 368 451665167 451665096 1.160000e-09 75.0
18 TraesCS4D01G048800 chr1B 80.220 91 17 1 264 354 621352777 621352866 1.930000e-07 67.6


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 TraesCS4D01G048800 chr4D 25192488 25195492 3004 True 5550 5550 100.000 1 3005 1 chr4D.!!$R1 3004
1 TraesCS4D01G048800 chr4D 25362980 25364013 1033 True 1293 1293 89.372 983 2008 1 chr4D.!!$R3 1025
2 TraesCS4D01G048800 chr4D 25320266 25321271 1005 True 1044 1044 85.546 983 1989 1 chr4D.!!$R2 1006
3 TraesCS4D01G048800 chr4D 25159691 25160519 828 False 475 475 77.321 1134 1976 1 chr4D.!!$F1 842
4 TraesCS4D01G048800 chr4A 578233128 578235592 2464 False 3587 3587 92.992 542 3005 1 chr4A.!!$F2 2463
5 TraesCS4D01G048800 chr4A 578175173 578176207 1034 True 1310 1310 89.672 983 2008 1 chr4A.!!$R1 1025
6 TraesCS4D01G048800 chr4A 578006996 578008013 1017 False 1201 1201 88.114 983 1990 1 chr4A.!!$F1 1007
7 TraesCS4D01G048800 chr4B 37173234 37174876 1642 True 2379 2379 92.926 580 2215 1 chr4B.!!$R2 1635
8 TraesCS4D01G048800 chr4B 37296415 37297448 1033 True 1332 1332 90.048 983 2008 1 chr4B.!!$R4 1025
9 TraesCS4D01G048800 chr4B 37149815 37150617 802 True 1140 1140 92.413 2209 3005 1 chr4B.!!$R1 796
10 TraesCS4D01G048800 chr3B 39545166 39546199 1033 False 1288 1288 89.275 983 2008 1 chr3B.!!$F1 1025

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
81 82 0.110056 GCACTCATTTGGCAGTCGTG 60.110 55.0 0.00 0.00 0.00 4.35 F
82 83 1.229428 CACTCATTTGGCAGTCGTGT 58.771 50.0 0.00 0.00 0.00 4.49 F
1824 1849 0.809241 CCATCTGCTTCGGTGAGCTC 60.809 60.0 6.82 6.82 43.11 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1561 0.320374 AGTCGCCGATTTTGACCTGA 59.680 50.000 0.00 0.00 33.09 3.86 R
1878 1904 1.518903 GGTGGTCTTTCTGCAGGCAC 61.519 60.000 15.13 5.35 0.00 5.01 R
2880 2937 2.092968 TGCAGAATGTAAAGCGGGAGAT 60.093 45.455 0.00 0.00 39.31 2.75 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.416154 TTCGTATTAATAGGCCAAAATCTCG 57.584 36.000 5.01 7.77 0.00 4.04
34 35 6.518493 TCGTATTAATAGGCCAAAATCTCGT 58.482 36.000 5.01 0.00 0.00 4.18
35 36 7.660112 TCGTATTAATAGGCCAAAATCTCGTA 58.340 34.615 5.01 0.00 0.00 3.43
36 37 7.596248 TCGTATTAATAGGCCAAAATCTCGTAC 59.404 37.037 5.01 0.00 0.00 3.67
37 38 7.383029 CGTATTAATAGGCCAAAATCTCGTACA 59.617 37.037 5.01 0.00 0.00 2.90
38 39 6.913873 TTAATAGGCCAAAATCTCGTACAC 57.086 37.500 5.01 0.00 0.00 2.90
39 40 1.722011 AGGCCAAAATCTCGTACACG 58.278 50.000 5.01 0.00 41.45 4.49
54 55 6.380111 TCGTACACGATTAGTTACAAAAGC 57.620 37.500 0.00 0.00 44.22 3.51
55 56 6.151691 TCGTACACGATTAGTTACAAAAGCT 58.848 36.000 0.00 0.00 44.22 3.74
56 57 6.306356 TCGTACACGATTAGTTACAAAAGCTC 59.694 38.462 0.00 0.00 44.22 4.09
57 58 5.511088 ACACGATTAGTTACAAAAGCTCG 57.489 39.130 0.00 0.00 0.00 5.03
58 59 5.224888 ACACGATTAGTTACAAAAGCTCGA 58.775 37.500 0.00 0.00 0.00 4.04
59 60 5.118203 ACACGATTAGTTACAAAAGCTCGAC 59.882 40.000 0.00 0.00 0.00 4.20
60 61 5.118050 CACGATTAGTTACAAAAGCTCGACA 59.882 40.000 0.00 0.00 0.00 4.35
61 62 5.693104 ACGATTAGTTACAAAAGCTCGACAA 59.307 36.000 0.00 0.00 0.00 3.18
62 63 6.128902 ACGATTAGTTACAAAAGCTCGACAAG 60.129 38.462 0.00 0.00 0.00 3.16
73 74 2.888513 CTCGACAAGCACTCATTTGG 57.111 50.000 0.00 0.00 0.00 3.28
74 75 0.874390 TCGACAAGCACTCATTTGGC 59.126 50.000 0.00 0.00 0.00 4.52
75 76 0.592637 CGACAAGCACTCATTTGGCA 59.407 50.000 0.00 0.00 31.67 4.92
76 77 1.400629 CGACAAGCACTCATTTGGCAG 60.401 52.381 0.00 0.00 31.67 4.85
77 78 1.610522 GACAAGCACTCATTTGGCAGT 59.389 47.619 0.00 0.00 32.50 4.40
78 79 1.610522 ACAAGCACTCATTTGGCAGTC 59.389 47.619 0.00 0.00 0.00 3.51
79 80 0.877071 AAGCACTCATTTGGCAGTCG 59.123 50.000 0.00 0.00 0.00 4.18
80 81 0.250467 AGCACTCATTTGGCAGTCGT 60.250 50.000 0.00 0.00 0.00 4.34
81 82 0.110056 GCACTCATTTGGCAGTCGTG 60.110 55.000 0.00 0.00 0.00 4.35
82 83 1.229428 CACTCATTTGGCAGTCGTGT 58.771 50.000 0.00 0.00 0.00 4.49
83 84 2.412870 CACTCATTTGGCAGTCGTGTA 58.587 47.619 0.00 0.00 0.00 2.90
84 85 2.805671 CACTCATTTGGCAGTCGTGTAA 59.194 45.455 0.00 0.00 0.00 2.41
85 86 3.249799 CACTCATTTGGCAGTCGTGTAAA 59.750 43.478 0.00 0.00 0.00 2.01
86 87 3.250040 ACTCATTTGGCAGTCGTGTAAAC 59.750 43.478 0.00 0.00 0.00 2.01
87 88 2.550606 TCATTTGGCAGTCGTGTAAACC 59.449 45.455 0.00 0.00 0.00 3.27
88 89 2.039818 TTTGGCAGTCGTGTAAACCA 57.960 45.000 0.00 0.00 0.00 3.67
89 90 2.039818 TTGGCAGTCGTGTAAACCAA 57.960 45.000 0.00 0.00 34.91 3.67
90 91 2.039818 TGGCAGTCGTGTAAACCAAA 57.960 45.000 0.00 0.00 0.00 3.28
91 92 2.366533 TGGCAGTCGTGTAAACCAAAA 58.633 42.857 0.00 0.00 0.00 2.44
92 93 2.753452 TGGCAGTCGTGTAAACCAAAAA 59.247 40.909 0.00 0.00 0.00 1.94
93 94 3.181495 TGGCAGTCGTGTAAACCAAAAAG 60.181 43.478 0.00 0.00 0.00 2.27
94 95 2.787129 GCAGTCGTGTAAACCAAAAAGC 59.213 45.455 0.00 0.00 0.00 3.51
95 96 3.732471 GCAGTCGTGTAAACCAAAAAGCA 60.732 43.478 0.00 0.00 0.00 3.91
96 97 4.416620 CAGTCGTGTAAACCAAAAAGCAA 58.583 39.130 0.00 0.00 0.00 3.91
97 98 5.040635 CAGTCGTGTAAACCAAAAAGCAAT 58.959 37.500 0.00 0.00 0.00 3.56
98 99 5.173131 CAGTCGTGTAAACCAAAAAGCAATC 59.827 40.000 0.00 0.00 0.00 2.67
99 100 5.038033 GTCGTGTAAACCAAAAAGCAATCA 58.962 37.500 0.00 0.00 0.00 2.57
100 101 5.517054 GTCGTGTAAACCAAAAAGCAATCAA 59.483 36.000 0.00 0.00 0.00 2.57
101 102 6.200097 GTCGTGTAAACCAAAAAGCAATCAAT 59.800 34.615 0.00 0.00 0.00 2.57
102 103 7.380065 GTCGTGTAAACCAAAAAGCAATCAATA 59.620 33.333 0.00 0.00 0.00 1.90
103 104 7.921214 TCGTGTAAACCAAAAAGCAATCAATAA 59.079 29.630 0.00 0.00 0.00 1.40
104 105 8.543774 CGTGTAAACCAAAAAGCAATCAATAAA 58.456 29.630 0.00 0.00 0.00 1.40
118 119 9.807649 AGCAATCAATAAATAAGAACACATTCC 57.192 29.630 0.00 0.00 35.18 3.01
119 120 9.034544 GCAATCAATAAATAAGAACACATTCCC 57.965 33.333 0.00 0.00 35.18 3.97
122 123 9.699410 ATCAATAAATAAGAACACATTCCCTCA 57.301 29.630 0.00 0.00 35.18 3.86
123 124 9.527157 TCAATAAATAAGAACACATTCCCTCAA 57.473 29.630 0.00 0.00 35.18 3.02
128 129 5.728637 AAGAACACATTCCCTCAAATTCC 57.271 39.130 0.00 0.00 35.18 3.01
129 130 4.089361 AGAACACATTCCCTCAAATTCCC 58.911 43.478 0.00 0.00 35.18 3.97
130 131 2.820178 ACACATTCCCTCAAATTCCCC 58.180 47.619 0.00 0.00 0.00 4.81
131 132 2.111613 ACACATTCCCTCAAATTCCCCA 59.888 45.455 0.00 0.00 0.00 4.96
132 133 3.172339 CACATTCCCTCAAATTCCCCAA 58.828 45.455 0.00 0.00 0.00 4.12
133 134 3.582208 CACATTCCCTCAAATTCCCCAAA 59.418 43.478 0.00 0.00 0.00 3.28
134 135 4.041444 CACATTCCCTCAAATTCCCCAAAA 59.959 41.667 0.00 0.00 0.00 2.44
135 136 4.662650 ACATTCCCTCAAATTCCCCAAAAA 59.337 37.500 0.00 0.00 0.00 1.94
163 164 8.950208 AATTCTATCAAACTGGAGCTAGTAAC 57.050 34.615 0.00 0.00 0.00 2.50
164 165 6.466885 TCTATCAAACTGGAGCTAGTAACC 57.533 41.667 0.00 0.00 0.00 2.85
165 166 5.955959 TCTATCAAACTGGAGCTAGTAACCA 59.044 40.000 0.00 0.00 0.00 3.67
166 167 4.967084 TCAAACTGGAGCTAGTAACCAA 57.033 40.909 0.00 0.00 33.14 3.67
167 168 5.499004 TCAAACTGGAGCTAGTAACCAAT 57.501 39.130 0.00 0.00 33.14 3.16
168 169 5.488341 TCAAACTGGAGCTAGTAACCAATC 58.512 41.667 0.00 0.00 33.14 2.67
169 170 5.248477 TCAAACTGGAGCTAGTAACCAATCT 59.752 40.000 0.00 0.00 33.14 2.40
170 171 5.346181 AACTGGAGCTAGTAACCAATCTC 57.654 43.478 0.00 0.00 33.14 2.75
171 172 4.353777 ACTGGAGCTAGTAACCAATCTCA 58.646 43.478 0.00 0.00 33.14 3.27
172 173 4.777896 ACTGGAGCTAGTAACCAATCTCAA 59.222 41.667 0.00 0.00 33.14 3.02
173 174 5.086104 TGGAGCTAGTAACCAATCTCAAC 57.914 43.478 0.00 0.00 0.00 3.18
174 175 4.530553 TGGAGCTAGTAACCAATCTCAACA 59.469 41.667 0.00 0.00 0.00 3.33
175 176 5.189736 TGGAGCTAGTAACCAATCTCAACAT 59.810 40.000 0.00 0.00 0.00 2.71
176 177 6.116126 GGAGCTAGTAACCAATCTCAACATT 58.884 40.000 0.00 0.00 0.00 2.71
177 178 6.037610 GGAGCTAGTAACCAATCTCAACATTG 59.962 42.308 0.00 0.00 34.06 2.82
178 179 6.711277 AGCTAGTAACCAATCTCAACATTGA 58.289 36.000 0.00 0.00 36.03 2.57
179 180 7.168219 AGCTAGTAACCAATCTCAACATTGAA 58.832 34.615 0.00 0.00 36.03 2.69
180 181 7.665559 AGCTAGTAACCAATCTCAACATTGAAA 59.334 33.333 0.00 0.00 36.03 2.69
181 182 8.462016 GCTAGTAACCAATCTCAACATTGAAAT 58.538 33.333 0.00 0.00 36.03 2.17
224 225 7.565323 ACAAGAAATCTCAAATATCCTGAGC 57.435 36.000 9.08 0.00 40.18 4.26
225 226 7.114754 ACAAGAAATCTCAAATATCCTGAGCA 58.885 34.615 9.08 1.74 40.18 4.26
226 227 7.282675 ACAAGAAATCTCAAATATCCTGAGCAG 59.717 37.037 9.08 0.00 40.18 4.24
240 241 3.769201 GCAGGTGCTCAGGCTTTT 58.231 55.556 0.00 0.00 39.59 2.27
241 242 2.044452 GCAGGTGCTCAGGCTTTTT 58.956 52.632 0.00 0.00 39.59 1.94
288 289 7.637709 AAAGATTGACGTCAAATTTTTAGGC 57.362 32.000 32.69 13.95 39.55 3.93
289 290 6.325919 AGATTGACGTCAAATTTTTAGGCA 57.674 33.333 32.69 7.85 39.55 4.75
290 291 6.924111 AGATTGACGTCAAATTTTTAGGCAT 58.076 32.000 32.69 13.26 39.55 4.40
291 292 7.378181 AGATTGACGTCAAATTTTTAGGCATT 58.622 30.769 32.69 13.05 39.55 3.56
292 293 6.761731 TTGACGTCAAATTTTTAGGCATTG 57.238 33.333 27.94 0.00 32.11 2.82
293 294 4.683781 TGACGTCAAATTTTTAGGCATTGC 59.316 37.500 17.62 0.00 0.00 3.56
294 295 4.626042 ACGTCAAATTTTTAGGCATTGCA 58.374 34.783 11.39 0.00 0.00 4.08
295 296 5.053145 ACGTCAAATTTTTAGGCATTGCAA 58.947 33.333 11.39 0.00 0.00 4.08
296 297 5.525378 ACGTCAAATTTTTAGGCATTGCAAA 59.475 32.000 11.39 2.70 0.00 3.68
297 298 6.204495 ACGTCAAATTTTTAGGCATTGCAAAT 59.796 30.769 11.39 5.02 0.00 2.32
298 299 6.737750 CGTCAAATTTTTAGGCATTGCAAATC 59.262 34.615 11.39 0.00 0.00 2.17
299 300 7.360269 CGTCAAATTTTTAGGCATTGCAAATCT 60.360 33.333 11.39 3.99 0.00 2.40
300 301 7.747357 GTCAAATTTTTAGGCATTGCAAATCTG 59.253 33.333 11.39 5.25 0.00 2.90
301 302 7.660617 TCAAATTTTTAGGCATTGCAAATCTGA 59.339 29.630 11.39 7.40 0.00 3.27
302 303 6.973229 ATTTTTAGGCATTGCAAATCTGAC 57.027 33.333 11.39 0.00 0.00 3.51
303 304 5.465532 TTTTAGGCATTGCAAATCTGACA 57.534 34.783 11.39 0.00 0.00 3.58
304 305 5.664294 TTTAGGCATTGCAAATCTGACAT 57.336 34.783 11.39 0.00 0.00 3.06
305 306 5.664294 TTAGGCATTGCAAATCTGACATT 57.336 34.783 11.39 0.00 0.00 2.71
306 307 4.546829 AGGCATTGCAAATCTGACATTT 57.453 36.364 11.39 0.00 0.00 2.32
307 308 4.901868 AGGCATTGCAAATCTGACATTTT 58.098 34.783 11.39 0.00 0.00 1.82
308 309 5.310451 AGGCATTGCAAATCTGACATTTTT 58.690 33.333 11.39 0.00 0.00 1.94
309 310 5.410439 AGGCATTGCAAATCTGACATTTTTC 59.590 36.000 11.39 0.00 0.00 2.29
310 311 5.179742 GGCATTGCAAATCTGACATTTTTCA 59.820 36.000 11.39 0.00 0.00 2.69
311 312 6.128117 GGCATTGCAAATCTGACATTTTTCAT 60.128 34.615 11.39 0.00 0.00 2.57
312 313 6.740905 GCATTGCAAATCTGACATTTTTCATG 59.259 34.615 1.71 0.00 0.00 3.07
313 314 7.360522 GCATTGCAAATCTGACATTTTTCATGA 60.361 33.333 1.71 0.00 0.00 3.07
314 315 7.410800 TTGCAAATCTGACATTTTTCATGAC 57.589 32.000 0.00 0.00 0.00 3.06
315 316 6.514063 TGCAAATCTGACATTTTTCATGACA 58.486 32.000 0.00 0.00 0.00 3.58
316 317 6.985059 TGCAAATCTGACATTTTTCATGACAA 59.015 30.769 0.00 0.00 0.00 3.18
317 318 7.658167 TGCAAATCTGACATTTTTCATGACAAT 59.342 29.630 0.00 0.00 0.00 2.71
318 319 8.500773 GCAAATCTGACATTTTTCATGACAATT 58.499 29.630 0.00 0.00 0.00 2.32
330 331 7.890879 TTTCATGACAATTTATATTGACGCG 57.109 32.000 3.53 3.53 43.12 6.01
331 332 6.597262 TCATGACAATTTATATTGACGCGT 57.403 33.333 13.85 13.85 43.12 6.01
332 333 7.010697 TCATGACAATTTATATTGACGCGTT 57.989 32.000 15.53 0.00 43.12 4.84
333 334 6.904543 TCATGACAATTTATATTGACGCGTTG 59.095 34.615 15.53 5.88 43.12 4.10
334 335 6.410243 TGACAATTTATATTGACGCGTTGA 57.590 33.333 15.53 5.42 43.12 3.18
335 336 7.010697 TGACAATTTATATTGACGCGTTGAT 57.989 32.000 15.53 13.32 43.12 2.57
336 337 6.904543 TGACAATTTATATTGACGCGTTGATG 59.095 34.615 15.53 4.04 43.12 3.07
337 338 7.010697 ACAATTTATATTGACGCGTTGATGA 57.989 32.000 15.53 0.00 43.12 2.92
338 339 7.639039 ACAATTTATATTGACGCGTTGATGAT 58.361 30.769 15.53 6.52 43.12 2.45
339 340 8.769891 ACAATTTATATTGACGCGTTGATGATA 58.230 29.630 15.53 8.20 43.12 2.15
340 341 9.592720 CAATTTATATTGACGCGTTGATGATAA 57.407 29.630 15.53 11.30 43.12 1.75
348 349 8.903570 TTGACGCGTTGATGATAATTTTATTT 57.096 26.923 15.53 0.00 0.00 1.40
349 350 8.903570 TGACGCGTTGATGATAATTTTATTTT 57.096 26.923 15.53 0.00 0.00 1.82
350 351 8.793472 TGACGCGTTGATGATAATTTTATTTTG 58.207 29.630 15.53 0.00 0.00 2.44
351 352 7.608755 ACGCGTTGATGATAATTTTATTTTGC 58.391 30.769 5.58 0.00 0.00 3.68
352 353 7.274468 ACGCGTTGATGATAATTTTATTTTGCA 59.726 29.630 5.58 0.00 0.00 4.08
353 354 8.106956 CGCGTTGATGATAATTTTATTTTGCAA 58.893 29.630 0.00 0.00 0.00 4.08
354 355 9.412390 GCGTTGATGATAATTTTATTTTGCAAG 57.588 29.630 0.00 0.00 0.00 4.01
371 372 5.421212 TGCAAGAATGGCAAAATTTCAAC 57.579 34.783 0.00 0.00 46.27 3.18
372 373 5.124645 TGCAAGAATGGCAAAATTTCAACT 58.875 33.333 0.00 0.00 46.27 3.16
373 374 6.286758 TGCAAGAATGGCAAAATTTCAACTA 58.713 32.000 0.00 0.00 46.27 2.24
374 375 6.765036 TGCAAGAATGGCAAAATTTCAACTAA 59.235 30.769 0.00 0.00 46.27 2.24
375 376 7.281774 TGCAAGAATGGCAAAATTTCAACTAAA 59.718 29.630 0.00 0.00 46.27 1.85
376 377 7.587392 GCAAGAATGGCAAAATTTCAACTAAAC 59.413 33.333 0.00 0.00 32.79 2.01
377 378 8.829612 CAAGAATGGCAAAATTTCAACTAAACT 58.170 29.630 0.00 0.00 0.00 2.66
378 379 8.962884 AGAATGGCAAAATTTCAACTAAACTT 57.037 26.923 0.00 0.00 0.00 2.66
379 380 8.829612 AGAATGGCAAAATTTCAACTAAACTTG 58.170 29.630 0.00 0.00 0.00 3.16
380 381 6.356757 TGGCAAAATTTCAACTAAACTTGC 57.643 33.333 0.00 9.16 42.81 4.01
382 383 6.356757 GCAAAATTTCAACTAAACTTGCCA 57.643 33.333 0.00 0.00 40.30 4.92
383 384 6.421405 GCAAAATTTCAACTAAACTTGCCAG 58.579 36.000 0.00 0.00 40.30 4.85
384 385 6.421405 CAAAATTTCAACTAAACTTGCCAGC 58.579 36.000 0.00 0.00 0.00 4.85
385 386 3.726291 TTTCAACTAAACTTGCCAGCC 57.274 42.857 0.00 0.00 0.00 4.85
386 387 2.656947 TCAACTAAACTTGCCAGCCT 57.343 45.000 0.00 0.00 0.00 4.58
387 388 2.944129 TCAACTAAACTTGCCAGCCTT 58.056 42.857 0.00 0.00 0.00 4.35
388 389 4.093472 TCAACTAAACTTGCCAGCCTTA 57.907 40.909 0.00 0.00 0.00 2.69
389 390 4.465886 TCAACTAAACTTGCCAGCCTTAA 58.534 39.130 0.00 0.00 0.00 1.85
390 391 4.890581 TCAACTAAACTTGCCAGCCTTAAA 59.109 37.500 0.00 0.00 0.00 1.52
391 392 5.361285 TCAACTAAACTTGCCAGCCTTAAAA 59.639 36.000 0.00 0.00 0.00 1.52
392 393 5.862678 ACTAAACTTGCCAGCCTTAAAAA 57.137 34.783 0.00 0.00 0.00 1.94
426 427 8.641499 TTACCATGAAAAATATTCGATTTGCC 57.359 30.769 0.00 0.00 0.00 4.52
427 428 6.638610 ACCATGAAAAATATTCGATTTGCCA 58.361 32.000 0.00 0.00 0.00 4.92
428 429 7.274447 ACCATGAAAAATATTCGATTTGCCAT 58.726 30.769 0.00 0.00 0.00 4.40
429 430 7.225145 ACCATGAAAAATATTCGATTTGCCATG 59.775 33.333 0.00 12.86 34.76 3.66
430 431 7.307514 CCATGAAAAATATTCGATTTGCCATGG 60.308 37.037 18.86 18.86 40.72 3.66
431 432 6.638610 TGAAAAATATTCGATTTGCCATGGT 58.361 32.000 14.67 0.00 0.00 3.55
432 433 7.776107 TGAAAAATATTCGATTTGCCATGGTA 58.224 30.769 14.67 5.86 0.00 3.25
433 434 8.253810 TGAAAAATATTCGATTTGCCATGGTAA 58.746 29.630 11.68 11.68 0.00 2.85
434 435 9.092876 GAAAAATATTCGATTTGCCATGGTAAA 57.907 29.630 27.23 27.23 34.50 2.01
435 436 9.442047 AAAAATATTCGATTTGCCATGGTAAAA 57.558 25.926 28.47 21.13 33.78 1.52
436 437 9.442047 AAAATATTCGATTTGCCATGGTAAAAA 57.558 25.926 28.47 19.56 33.78 1.94
462 463 6.106648 TCTGGCATCAGATTTATAGTGGAG 57.893 41.667 0.00 0.00 44.39 3.86
463 464 5.604231 TCTGGCATCAGATTTATAGTGGAGT 59.396 40.000 0.00 0.00 44.39 3.85
464 465 5.858381 TGGCATCAGATTTATAGTGGAGTC 58.142 41.667 0.00 0.00 0.00 3.36
465 466 5.221722 TGGCATCAGATTTATAGTGGAGTCC 60.222 44.000 0.73 0.73 0.00 3.85
466 467 5.012561 GGCATCAGATTTATAGTGGAGTCCT 59.987 44.000 11.33 0.00 0.00 3.85
467 468 6.465035 GGCATCAGATTTATAGTGGAGTCCTT 60.465 42.308 11.33 1.17 0.00 3.36
468 469 6.995091 GCATCAGATTTATAGTGGAGTCCTTT 59.005 38.462 11.33 0.79 0.00 3.11
469 470 7.500559 GCATCAGATTTATAGTGGAGTCCTTTT 59.499 37.037 11.33 0.00 0.00 2.27
470 471 9.401058 CATCAGATTTATAGTGGAGTCCTTTTT 57.599 33.333 11.33 0.00 0.00 1.94
495 496 9.880157 TTTTATCCCATACTAAACTCTGTGTAC 57.120 33.333 0.00 0.00 0.00 2.90
496 497 5.927281 TCCCATACTAAACTCTGTGTACC 57.073 43.478 0.00 0.00 0.00 3.34
497 498 5.335261 TCCCATACTAAACTCTGTGTACCA 58.665 41.667 0.00 0.00 0.00 3.25
498 499 5.186409 TCCCATACTAAACTCTGTGTACCAC 59.814 44.000 0.00 0.00 34.56 4.16
499 500 5.187186 CCCATACTAAACTCTGTGTACCACT 59.813 44.000 0.00 0.00 35.11 4.00
500 501 6.295688 CCCATACTAAACTCTGTGTACCACTT 60.296 42.308 0.00 0.00 35.11 3.16
501 502 6.590292 CCATACTAAACTCTGTGTACCACTTG 59.410 42.308 0.00 0.00 35.11 3.16
502 503 5.864418 ACTAAACTCTGTGTACCACTTGA 57.136 39.130 0.00 0.00 35.11 3.02
503 504 6.229936 ACTAAACTCTGTGTACCACTTGAA 57.770 37.500 0.00 0.00 35.11 2.69
504 505 6.646267 ACTAAACTCTGTGTACCACTTGAAA 58.354 36.000 0.00 0.00 35.11 2.69
505 506 5.813080 AAACTCTGTGTACCACTTGAAAC 57.187 39.130 0.00 0.00 35.11 2.78
506 507 3.454375 ACTCTGTGTACCACTTGAAACG 58.546 45.455 0.00 0.00 35.11 3.60
507 508 3.131577 ACTCTGTGTACCACTTGAAACGA 59.868 43.478 0.00 0.00 35.11 3.85
508 509 3.713288 TCTGTGTACCACTTGAAACGAG 58.287 45.455 0.00 0.00 35.11 4.18
509 510 3.131577 TCTGTGTACCACTTGAAACGAGT 59.868 43.478 0.00 0.00 35.11 4.18
510 511 3.191669 TGTGTACCACTTGAAACGAGTG 58.808 45.455 11.00 11.00 43.19 3.51
516 517 3.521524 CACTTGAAACGAGTGGTTAGC 57.478 47.619 10.31 0.00 40.58 3.09
517 518 3.131396 CACTTGAAACGAGTGGTTAGCT 58.869 45.455 10.31 0.00 40.58 3.32
518 519 4.304110 CACTTGAAACGAGTGGTTAGCTA 58.696 43.478 10.31 0.00 40.58 3.32
519 520 4.929808 CACTTGAAACGAGTGGTTAGCTAT 59.070 41.667 10.31 0.00 40.58 2.97
520 521 5.062308 CACTTGAAACGAGTGGTTAGCTATC 59.938 44.000 10.31 0.00 40.58 2.08
521 522 5.047235 ACTTGAAACGAGTGGTTAGCTATCT 60.047 40.000 0.00 0.00 38.08 1.98
522 523 4.995124 TGAAACGAGTGGTTAGCTATCTC 58.005 43.478 0.00 0.46 38.08 2.75
523 524 4.461431 TGAAACGAGTGGTTAGCTATCTCA 59.539 41.667 0.00 0.00 38.08 3.27
524 525 5.047590 TGAAACGAGTGGTTAGCTATCTCAA 60.048 40.000 0.00 0.00 38.08 3.02
525 526 5.401531 AACGAGTGGTTAGCTATCTCAAA 57.598 39.130 0.00 0.00 37.00 2.69
526 527 5.401531 ACGAGTGGTTAGCTATCTCAAAA 57.598 39.130 0.00 0.00 0.00 2.44
527 528 5.790593 ACGAGTGGTTAGCTATCTCAAAAA 58.209 37.500 0.00 0.00 0.00 1.94
528 529 5.638234 ACGAGTGGTTAGCTATCTCAAAAAC 59.362 40.000 0.00 0.00 0.00 2.43
529 530 5.637810 CGAGTGGTTAGCTATCTCAAAAACA 59.362 40.000 0.00 0.00 0.00 2.83
530 531 6.183360 CGAGTGGTTAGCTATCTCAAAAACAG 60.183 42.308 0.00 0.00 0.00 3.16
531 532 6.534634 AGTGGTTAGCTATCTCAAAAACAGT 58.465 36.000 0.00 0.00 0.00 3.55
532 533 6.651225 AGTGGTTAGCTATCTCAAAAACAGTC 59.349 38.462 0.00 0.00 0.00 3.51
533 534 6.426937 GTGGTTAGCTATCTCAAAAACAGTCA 59.573 38.462 0.00 0.00 0.00 3.41
534 535 6.995686 TGGTTAGCTATCTCAAAAACAGTCAA 59.004 34.615 0.00 0.00 0.00 3.18
535 536 7.041372 TGGTTAGCTATCTCAAAAACAGTCAAC 60.041 37.037 0.00 0.00 0.00 3.18
536 537 7.041372 GGTTAGCTATCTCAAAAACAGTCAACA 60.041 37.037 0.00 0.00 0.00 3.33
537 538 6.942532 AGCTATCTCAAAAACAGTCAACAA 57.057 33.333 0.00 0.00 0.00 2.83
538 539 6.729187 AGCTATCTCAAAAACAGTCAACAAC 58.271 36.000 0.00 0.00 0.00 3.32
539 540 6.318648 AGCTATCTCAAAAACAGTCAACAACA 59.681 34.615 0.00 0.00 0.00 3.33
540 541 6.972328 GCTATCTCAAAAACAGTCAACAACAA 59.028 34.615 0.00 0.00 0.00 2.83
551 552 9.783256 AAACAGTCAACAACAAATACTAAACTC 57.217 29.630 0.00 0.00 0.00 3.01
553 554 8.612619 ACAGTCAACAACAAATACTAAACTCTG 58.387 33.333 0.00 0.00 0.00 3.35
555 556 8.612619 AGTCAACAACAAATACTAAACTCTGTG 58.387 33.333 0.00 0.00 0.00 3.66
607 614 4.387026 TCCCAAAGATCCTCATGTGTTT 57.613 40.909 0.00 0.00 0.00 2.83
635 642 5.434408 TCTGAAATCATCATTCTCCAGGTG 58.566 41.667 0.00 0.00 37.44 4.00
640 647 4.160642 TCATCATTCTCCAGGTGATTGG 57.839 45.455 11.69 0.00 39.70 3.16
712 719 7.618137 TCCACCAAACTCCTAAAATAGTAGAC 58.382 38.462 0.00 0.00 0.00 2.59
716 723 7.876582 ACCAAACTCCTAAAATAGTAGACACAC 59.123 37.037 0.00 0.00 0.00 3.82
780 787 8.576442 GGCTAAGCTAATTAAGAATTGCCATTA 58.424 33.333 0.00 0.00 35.94 1.90
781 788 9.399403 GCTAAGCTAATTAAGAATTGCCATTAC 57.601 33.333 0.00 0.00 32.38 1.89
911 921 1.919654 TCCATCATTCCCCCGAAAAGA 59.080 47.619 0.00 0.00 0.00 2.52
974 986 5.295540 AGCTTCCAAATTCGATCTTAAGAGC 59.704 40.000 10.76 10.76 0.00 4.09
1205 1218 2.108362 CGGGACCGTCCATAAGGC 59.892 66.667 19.43 0.00 38.64 4.35
1245 1258 2.373938 GCTGTACGCGCTCAAGATT 58.626 52.632 5.73 0.00 0.00 2.40
1545 1561 3.953775 CTGGTCAACAGGGCCGGT 61.954 66.667 2.53 2.53 43.70 5.28
1569 1585 1.017177 TCAAAATCGGCGACTTCGGG 61.017 55.000 13.76 0.96 40.23 5.14
1824 1849 0.809241 CCATCTGCTTCGGTGAGCTC 60.809 60.000 6.82 6.82 43.11 4.09
1843 1869 4.379243 CAGCACTTCCCGACGGCT 62.379 66.667 8.86 0.00 34.64 5.52
1890 1916 4.617520 TCCGCGTGCCTGCAGAAA 62.618 61.111 17.39 0.00 34.15 2.52
1905 1931 1.301479 GAAAGACCACCGGAAGCGT 60.301 57.895 9.46 0.00 0.00 5.07
1914 1940 2.034879 CCGGAAGCGTGCATCAGTT 61.035 57.895 0.00 0.00 0.00 3.16
2077 2103 6.183360 GCAGATACAGATAGTGGAAGAACTCA 60.183 42.308 0.00 0.00 0.00 3.41
2376 2426 7.118723 TCTGTTTTAGCATGATAATTCTGGGT 58.881 34.615 3.91 0.00 0.00 4.51
2381 2431 4.858850 AGCATGATAATTCTGGGTGTTCA 58.141 39.130 0.00 0.00 0.00 3.18
2433 2483 6.721321 TCTTTTGACATTTCCGAAGTTGTAC 58.279 36.000 0.00 0.00 0.00 2.90
2511 2562 7.918562 TCAACTACACATTTCAAAACCTAAAGC 59.081 33.333 0.00 0.00 0.00 3.51
2598 2649 4.448210 TCTTGAGGTACAACAAGTCCAAC 58.552 43.478 21.76 0.00 42.27 3.77
2608 2659 4.141287 CAACAAGTCCAACAATCACCCTA 58.859 43.478 0.00 0.00 0.00 3.53
2609 2660 3.751518 ACAAGTCCAACAATCACCCTAC 58.248 45.455 0.00 0.00 0.00 3.18
2641 2692 9.953697 TTTGTTGTACCTTAAATATTGTCACAC 57.046 29.630 0.00 0.00 0.00 3.82
2850 2907 9.346725 GACAACAAAGCCTCTTGATTAAATTAG 57.653 33.333 0.00 0.00 0.00 1.73
2880 2937 5.530915 ACATCAAAGTTCTTCCAATTCGTCA 59.469 36.000 0.00 0.00 0.00 4.35
2969 3026 2.347731 GCAAAAGCTAGACTAACCGCT 58.652 47.619 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.504005 CGAGATTTTGGCCTATTAATACGAATT 58.496 33.333 3.32 0.00 0.00 2.17
8 9 7.660208 ACGAGATTTTGGCCTATTAATACGAAT 59.340 33.333 3.32 0.00 0.00 3.34
9 10 6.987992 ACGAGATTTTGGCCTATTAATACGAA 59.012 34.615 3.32 0.00 0.00 3.85
10 11 6.518493 ACGAGATTTTGGCCTATTAATACGA 58.482 36.000 3.32 0.00 0.00 3.43
11 12 6.780706 ACGAGATTTTGGCCTATTAATACG 57.219 37.500 3.32 6.70 0.00 3.06
12 13 8.493547 GTGTACGAGATTTTGGCCTATTAATAC 58.506 37.037 3.32 0.00 0.00 1.89
13 14 7.383029 CGTGTACGAGATTTTGGCCTATTAATA 59.617 37.037 3.32 0.00 43.02 0.98
14 15 6.202188 CGTGTACGAGATTTTGGCCTATTAAT 59.798 38.462 3.32 0.00 43.02 1.40
15 16 5.521010 CGTGTACGAGATTTTGGCCTATTAA 59.479 40.000 3.32 0.00 43.02 1.40
16 17 5.045215 CGTGTACGAGATTTTGGCCTATTA 58.955 41.667 3.32 0.00 43.02 0.98
17 18 3.869246 CGTGTACGAGATTTTGGCCTATT 59.131 43.478 3.32 0.00 43.02 1.73
18 19 3.131577 TCGTGTACGAGATTTTGGCCTAT 59.868 43.478 3.32 0.00 44.22 2.57
19 20 2.492881 TCGTGTACGAGATTTTGGCCTA 59.507 45.455 3.32 0.00 44.22 3.93
20 21 1.274167 TCGTGTACGAGATTTTGGCCT 59.726 47.619 3.32 0.00 44.22 5.19
21 22 1.717194 TCGTGTACGAGATTTTGGCC 58.283 50.000 2.55 0.00 44.22 5.36
32 33 6.385537 AGCTTTTGTAACTAATCGTGTACG 57.614 37.500 0.00 0.00 41.45 3.67
33 34 6.306356 TCGAGCTTTTGTAACTAATCGTGTAC 59.694 38.462 0.00 0.00 0.00 2.90
34 35 6.306356 GTCGAGCTTTTGTAACTAATCGTGTA 59.694 38.462 0.00 0.00 0.00 2.90
35 36 5.118203 GTCGAGCTTTTGTAACTAATCGTGT 59.882 40.000 0.00 0.00 0.00 4.49
36 37 5.118050 TGTCGAGCTTTTGTAACTAATCGTG 59.882 40.000 0.00 0.00 0.00 4.35
37 38 5.224888 TGTCGAGCTTTTGTAACTAATCGT 58.775 37.500 0.00 0.00 0.00 3.73
38 39 5.756950 TGTCGAGCTTTTGTAACTAATCG 57.243 39.130 0.00 0.00 0.00 3.34
54 55 1.135859 GCCAAATGAGTGCTTGTCGAG 60.136 52.381 0.00 0.00 0.00 4.04
55 56 0.874390 GCCAAATGAGTGCTTGTCGA 59.126 50.000 0.00 0.00 0.00 4.20
56 57 0.592637 TGCCAAATGAGTGCTTGTCG 59.407 50.000 0.00 0.00 0.00 4.35
57 58 1.610522 ACTGCCAAATGAGTGCTTGTC 59.389 47.619 0.00 0.00 0.00 3.18
58 59 1.610522 GACTGCCAAATGAGTGCTTGT 59.389 47.619 0.00 0.00 0.00 3.16
59 60 1.400629 CGACTGCCAAATGAGTGCTTG 60.401 52.381 0.00 0.00 0.00 4.01
60 61 0.877071 CGACTGCCAAATGAGTGCTT 59.123 50.000 0.00 0.00 0.00 3.91
61 62 0.250467 ACGACTGCCAAATGAGTGCT 60.250 50.000 0.00 0.00 0.00 4.40
62 63 0.110056 CACGACTGCCAAATGAGTGC 60.110 55.000 0.00 0.00 0.00 4.40
63 64 1.229428 ACACGACTGCCAAATGAGTG 58.771 50.000 0.00 0.00 0.00 3.51
64 65 2.831685 TACACGACTGCCAAATGAGT 57.168 45.000 0.00 0.00 0.00 3.41
65 66 3.364964 GGTTTACACGACTGCCAAATGAG 60.365 47.826 0.00 0.00 0.00 2.90
66 67 2.550606 GGTTTACACGACTGCCAAATGA 59.449 45.455 0.00 0.00 0.00 2.57
67 68 2.292016 TGGTTTACACGACTGCCAAATG 59.708 45.455 0.00 0.00 0.00 2.32
68 69 2.577700 TGGTTTACACGACTGCCAAAT 58.422 42.857 0.00 0.00 0.00 2.32
69 70 2.039818 TGGTTTACACGACTGCCAAA 57.960 45.000 0.00 0.00 0.00 3.28
70 71 2.039818 TTGGTTTACACGACTGCCAA 57.960 45.000 0.00 0.00 34.12 4.52
71 72 2.039818 TTTGGTTTACACGACTGCCA 57.960 45.000 0.00 0.00 0.00 4.92
72 73 3.368495 CTTTTTGGTTTACACGACTGCC 58.632 45.455 0.00 0.00 0.00 4.85
73 74 2.787129 GCTTTTTGGTTTACACGACTGC 59.213 45.455 0.00 0.00 0.00 4.40
74 75 4.022464 TGCTTTTTGGTTTACACGACTG 57.978 40.909 0.00 0.00 0.00 3.51
75 76 4.705337 TTGCTTTTTGGTTTACACGACT 57.295 36.364 0.00 0.00 0.00 4.18
76 77 5.038033 TGATTGCTTTTTGGTTTACACGAC 58.962 37.500 0.00 0.00 0.00 4.34
77 78 5.250235 TGATTGCTTTTTGGTTTACACGA 57.750 34.783 0.00 0.00 0.00 4.35
78 79 5.957910 TTGATTGCTTTTTGGTTTACACG 57.042 34.783 0.00 0.00 0.00 4.49
92 93 9.807649 GGAATGTGTTCTTATTTATTGATTGCT 57.192 29.630 0.00 0.00 34.68 3.91
93 94 9.034544 GGGAATGTGTTCTTATTTATTGATTGC 57.965 33.333 0.00 0.00 34.68 3.56
96 97 9.699410 TGAGGGAATGTGTTCTTATTTATTGAT 57.301 29.630 0.00 0.00 34.68 2.57
97 98 9.527157 TTGAGGGAATGTGTTCTTATTTATTGA 57.473 29.630 0.00 0.00 34.68 2.57
102 103 8.314021 GGAATTTGAGGGAATGTGTTCTTATTT 58.686 33.333 0.00 0.00 34.68 1.40
103 104 7.093333 GGGAATTTGAGGGAATGTGTTCTTATT 60.093 37.037 0.00 0.00 34.68 1.40
104 105 6.381133 GGGAATTTGAGGGAATGTGTTCTTAT 59.619 38.462 0.00 0.00 34.68 1.73
105 106 5.714806 GGGAATTTGAGGGAATGTGTTCTTA 59.285 40.000 0.00 0.00 34.68 2.10
106 107 4.528206 GGGAATTTGAGGGAATGTGTTCTT 59.472 41.667 0.00 0.00 34.68 2.52
107 108 4.089361 GGGAATTTGAGGGAATGTGTTCT 58.911 43.478 0.00 0.00 34.68 3.01
108 109 3.195610 GGGGAATTTGAGGGAATGTGTTC 59.804 47.826 0.00 0.00 0.00 3.18
109 110 3.173151 GGGGAATTTGAGGGAATGTGTT 58.827 45.455 0.00 0.00 0.00 3.32
110 111 2.111613 TGGGGAATTTGAGGGAATGTGT 59.888 45.455 0.00 0.00 0.00 3.72
111 112 2.818921 TGGGGAATTTGAGGGAATGTG 58.181 47.619 0.00 0.00 0.00 3.21
112 113 3.558608 TTGGGGAATTTGAGGGAATGT 57.441 42.857 0.00 0.00 0.00 2.71
113 114 4.906747 TTTTGGGGAATTTGAGGGAATG 57.093 40.909 0.00 0.00 0.00 2.67
138 139 7.988028 GGTTACTAGCTCCAGTTTGATAGAATT 59.012 37.037 0.00 0.00 0.00 2.17
139 140 7.125811 TGGTTACTAGCTCCAGTTTGATAGAAT 59.874 37.037 0.00 0.00 0.00 2.40
140 141 6.439375 TGGTTACTAGCTCCAGTTTGATAGAA 59.561 38.462 0.00 0.00 0.00 2.10
141 142 5.955959 TGGTTACTAGCTCCAGTTTGATAGA 59.044 40.000 0.00 0.00 0.00 1.98
142 143 6.222038 TGGTTACTAGCTCCAGTTTGATAG 57.778 41.667 0.00 0.00 0.00 2.08
143 144 6.614694 TTGGTTACTAGCTCCAGTTTGATA 57.385 37.500 0.00 0.00 32.63 2.15
144 145 5.499004 TTGGTTACTAGCTCCAGTTTGAT 57.501 39.130 0.00 0.00 32.63 2.57
145 146 4.967084 TTGGTTACTAGCTCCAGTTTGA 57.033 40.909 0.00 0.00 32.63 2.69
146 147 5.491982 AGATTGGTTACTAGCTCCAGTTTG 58.508 41.667 0.00 0.00 32.63 2.93
147 148 5.248477 TGAGATTGGTTACTAGCTCCAGTTT 59.752 40.000 0.00 0.00 34.64 2.66
148 149 4.777896 TGAGATTGGTTACTAGCTCCAGTT 59.222 41.667 0.00 0.00 34.64 3.16
149 150 4.353777 TGAGATTGGTTACTAGCTCCAGT 58.646 43.478 0.00 0.00 34.64 4.00
150 151 5.112686 GTTGAGATTGGTTACTAGCTCCAG 58.887 45.833 0.00 0.00 34.64 3.86
151 152 4.530553 TGTTGAGATTGGTTACTAGCTCCA 59.469 41.667 0.00 0.00 34.64 3.86
152 153 5.086104 TGTTGAGATTGGTTACTAGCTCC 57.914 43.478 0.00 0.00 34.64 4.70
153 154 6.818644 TCAATGTTGAGATTGGTTACTAGCTC 59.181 38.462 0.00 0.00 35.81 4.09
154 155 6.711277 TCAATGTTGAGATTGGTTACTAGCT 58.289 36.000 0.00 0.00 34.58 3.32
155 156 6.985188 TCAATGTTGAGATTGGTTACTAGC 57.015 37.500 1.64 0.00 34.58 3.42
198 199 8.465201 GCTCAGGATATTTGAGATTTCTTGTTT 58.535 33.333 17.60 0.00 43.75 2.83
199 200 7.613022 TGCTCAGGATATTTGAGATTTCTTGTT 59.387 33.333 17.60 0.00 43.75 2.83
200 201 7.114754 TGCTCAGGATATTTGAGATTTCTTGT 58.885 34.615 17.60 0.00 43.75 3.16
201 202 7.563888 TGCTCAGGATATTTGAGATTTCTTG 57.436 36.000 17.60 0.00 43.75 3.02
202 203 7.804843 CTGCTCAGGATATTTGAGATTTCTT 57.195 36.000 17.60 0.00 43.75 2.52
223 224 2.044452 AAAAAGCCTGAGCACCTGC 58.956 52.632 0.00 0.00 43.56 4.85
262 263 9.187455 GCCTAAAAATTTGACGTCAATCTTTTA 57.813 29.630 31.17 31.17 34.59 1.52
263 264 7.708752 TGCCTAAAAATTTGACGTCAATCTTTT 59.291 29.630 31.83 31.83 35.74 2.27
264 265 7.206687 TGCCTAAAAATTTGACGTCAATCTTT 58.793 30.769 30.10 26.00 35.55 2.52
265 266 6.744112 TGCCTAAAAATTTGACGTCAATCTT 58.256 32.000 30.10 22.40 35.55 2.40
266 267 6.325919 TGCCTAAAAATTTGACGTCAATCT 57.674 33.333 30.10 18.20 35.55 2.40
267 268 7.447430 CAATGCCTAAAAATTTGACGTCAATC 58.553 34.615 30.10 11.79 35.55 2.67
268 269 6.128580 GCAATGCCTAAAAATTTGACGTCAAT 60.129 34.615 30.10 17.85 35.55 2.57
269 270 5.176590 GCAATGCCTAAAAATTTGACGTCAA 59.823 36.000 26.53 26.53 0.00 3.18
270 271 4.683781 GCAATGCCTAAAAATTTGACGTCA 59.316 37.500 15.76 15.76 0.00 4.35
271 272 4.683781 TGCAATGCCTAAAAATTTGACGTC 59.316 37.500 9.11 9.11 0.00 4.34
272 273 4.626042 TGCAATGCCTAAAAATTTGACGT 58.374 34.783 1.53 0.00 0.00 4.34
273 274 5.588568 TTGCAATGCCTAAAAATTTGACG 57.411 34.783 1.53 0.00 0.00 4.35
274 275 7.747357 CAGATTTGCAATGCCTAAAAATTTGAC 59.253 33.333 11.31 0.00 28.80 3.18
275 276 7.660617 TCAGATTTGCAATGCCTAAAAATTTGA 59.339 29.630 13.87 13.87 32.28 2.69
276 277 7.747357 GTCAGATTTGCAATGCCTAAAAATTTG 59.253 33.333 1.53 7.71 0.00 2.32
277 278 7.444792 TGTCAGATTTGCAATGCCTAAAAATTT 59.555 29.630 1.53 0.00 0.00 1.82
278 279 6.935771 TGTCAGATTTGCAATGCCTAAAAATT 59.064 30.769 1.53 0.00 0.00 1.82
279 280 6.465948 TGTCAGATTTGCAATGCCTAAAAAT 58.534 32.000 1.53 1.58 0.00 1.82
280 281 5.851720 TGTCAGATTTGCAATGCCTAAAAA 58.148 33.333 1.53 0.00 0.00 1.94
281 282 5.465532 TGTCAGATTTGCAATGCCTAAAA 57.534 34.783 1.53 0.00 0.00 1.52
282 283 5.664294 ATGTCAGATTTGCAATGCCTAAA 57.336 34.783 1.53 0.00 0.00 1.85
283 284 5.664294 AATGTCAGATTTGCAATGCCTAA 57.336 34.783 1.53 0.00 0.00 2.69
284 285 5.664294 AAATGTCAGATTTGCAATGCCTA 57.336 34.783 1.53 0.00 0.00 3.93
285 286 4.546829 AAATGTCAGATTTGCAATGCCT 57.453 36.364 1.53 0.00 0.00 4.75
286 287 5.179742 TGAAAAATGTCAGATTTGCAATGCC 59.820 36.000 1.53 0.00 0.00 4.40
287 288 6.230849 TGAAAAATGTCAGATTTGCAATGC 57.769 33.333 0.00 0.00 0.00 3.56
288 289 7.955324 GTCATGAAAAATGTCAGATTTGCAATG 59.045 33.333 0.00 0.00 28.28 2.82
289 290 7.658167 TGTCATGAAAAATGTCAGATTTGCAAT 59.342 29.630 0.00 0.00 28.28 3.56
290 291 6.985059 TGTCATGAAAAATGTCAGATTTGCAA 59.015 30.769 0.00 0.00 28.28 4.08
291 292 6.514063 TGTCATGAAAAATGTCAGATTTGCA 58.486 32.000 0.00 0.00 0.00 4.08
292 293 7.410800 TTGTCATGAAAAATGTCAGATTTGC 57.589 32.000 0.00 0.00 0.00 3.68
304 305 8.793472 CGCGTCAATATAAATTGTCATGAAAAA 58.207 29.630 1.55 0.00 42.66 1.94
305 306 7.965655 ACGCGTCAATATAAATTGTCATGAAAA 59.034 29.630 5.58 0.00 42.66 2.29
306 307 7.468441 ACGCGTCAATATAAATTGTCATGAAA 58.532 30.769 5.58 0.00 42.66 2.69
307 308 7.010697 ACGCGTCAATATAAATTGTCATGAA 57.989 32.000 5.58 0.00 42.66 2.57
308 309 6.597262 ACGCGTCAATATAAATTGTCATGA 57.403 33.333 5.58 0.00 42.66 3.07
309 310 6.904543 TCAACGCGTCAATATAAATTGTCATG 59.095 34.615 14.44 0.00 42.66 3.07
310 311 7.010697 TCAACGCGTCAATATAAATTGTCAT 57.989 32.000 14.44 0.00 42.66 3.06
311 312 6.410243 TCAACGCGTCAATATAAATTGTCA 57.590 33.333 14.44 0.00 42.66 3.58
312 313 7.123190 TCATCAACGCGTCAATATAAATTGTC 58.877 34.615 14.44 0.00 42.66 3.18
313 314 7.010697 TCATCAACGCGTCAATATAAATTGT 57.989 32.000 14.44 0.00 42.66 2.71
314 315 9.592720 TTATCATCAACGCGTCAATATAAATTG 57.407 29.630 14.44 2.50 43.32 2.32
322 323 9.515020 AAATAAAATTATCATCAACGCGTCAAT 57.485 25.926 14.44 6.32 0.00 2.57
323 324 8.903570 AAATAAAATTATCATCAACGCGTCAA 57.096 26.923 14.44 3.58 0.00 3.18
324 325 8.793472 CAAAATAAAATTATCATCAACGCGTCA 58.207 29.630 14.44 1.83 0.00 4.35
325 326 7.782955 GCAAAATAAAATTATCATCAACGCGTC 59.217 33.333 14.44 0.00 0.00 5.19
326 327 7.274468 TGCAAAATAAAATTATCATCAACGCGT 59.726 29.630 5.58 5.58 0.00 6.01
327 328 7.607880 TGCAAAATAAAATTATCATCAACGCG 58.392 30.769 3.53 3.53 0.00 6.01
328 329 9.412390 CTTGCAAAATAAAATTATCATCAACGC 57.588 29.630 0.00 0.00 0.00 4.84
335 336 9.445878 TGCCATTCTTGCAAAATAAAATTATCA 57.554 25.926 0.00 0.00 35.40 2.15
348 349 5.589452 AGTTGAAATTTTGCCATTCTTGCAA 59.411 32.000 0.00 0.00 46.30 4.08
349 350 5.124645 AGTTGAAATTTTGCCATTCTTGCA 58.875 33.333 0.00 0.00 36.84 4.08
350 351 5.678132 AGTTGAAATTTTGCCATTCTTGC 57.322 34.783 0.00 0.00 0.00 4.01
351 352 8.829612 AGTTTAGTTGAAATTTTGCCATTCTTG 58.170 29.630 0.00 0.00 0.00 3.02
352 353 8.962884 AGTTTAGTTGAAATTTTGCCATTCTT 57.037 26.923 0.00 0.00 0.00 2.52
353 354 8.829612 CAAGTTTAGTTGAAATTTTGCCATTCT 58.170 29.630 0.00 0.00 0.00 2.40
354 355 7.587392 GCAAGTTTAGTTGAAATTTTGCCATTC 59.413 33.333 1.56 0.00 40.73 2.67
355 356 7.416817 GCAAGTTTAGTTGAAATTTTGCCATT 58.583 30.769 1.56 0.00 40.73 3.16
356 357 6.958255 GCAAGTTTAGTTGAAATTTTGCCAT 58.042 32.000 1.56 0.00 40.73 4.40
357 358 6.356757 GCAAGTTTAGTTGAAATTTTGCCA 57.643 33.333 1.56 0.00 40.73 4.92
359 360 6.356757 TGGCAAGTTTAGTTGAAATTTTGC 57.643 33.333 1.56 10.96 43.10 3.68
360 361 6.421405 GCTGGCAAGTTTAGTTGAAATTTTG 58.579 36.000 1.56 0.00 32.13 2.44
361 362 5.527214 GGCTGGCAAGTTTAGTTGAAATTTT 59.473 36.000 0.00 0.00 0.00 1.82
362 363 5.056480 GGCTGGCAAGTTTAGTTGAAATTT 58.944 37.500 0.00 0.00 0.00 1.82
363 364 4.344968 AGGCTGGCAAGTTTAGTTGAAATT 59.655 37.500 3.38 0.00 0.00 1.82
364 365 3.897505 AGGCTGGCAAGTTTAGTTGAAAT 59.102 39.130 3.38 0.00 0.00 2.17
365 366 3.295973 AGGCTGGCAAGTTTAGTTGAAA 58.704 40.909 3.38 0.00 0.00 2.69
366 367 2.944129 AGGCTGGCAAGTTTAGTTGAA 58.056 42.857 3.38 0.00 0.00 2.69
367 368 2.656947 AGGCTGGCAAGTTTAGTTGA 57.343 45.000 3.38 0.00 0.00 3.18
368 369 4.846779 TTAAGGCTGGCAAGTTTAGTTG 57.153 40.909 3.38 0.00 0.00 3.16
369 370 5.862678 TTTTAAGGCTGGCAAGTTTAGTT 57.137 34.783 3.38 0.00 0.00 2.24
370 371 5.862678 TTTTTAAGGCTGGCAAGTTTAGT 57.137 34.783 3.38 0.00 0.00 2.24
400 401 9.092876 GGCAAATCGAATATTTTTCATGGTAAA 57.907 29.630 0.00 0.00 0.00 2.01
401 402 8.253810 TGGCAAATCGAATATTTTTCATGGTAA 58.746 29.630 0.00 0.00 0.00 2.85
402 403 7.776107 TGGCAAATCGAATATTTTTCATGGTA 58.224 30.769 0.00 0.00 0.00 3.25
403 404 6.638610 TGGCAAATCGAATATTTTTCATGGT 58.361 32.000 0.00 0.00 0.00 3.55
404 405 7.307514 CCATGGCAAATCGAATATTTTTCATGG 60.308 37.037 17.62 17.62 39.59 3.66
405 406 7.225145 ACCATGGCAAATCGAATATTTTTCATG 59.775 33.333 13.04 2.81 33.50 3.07
406 407 7.274447 ACCATGGCAAATCGAATATTTTTCAT 58.726 30.769 13.04 0.00 0.00 2.57
407 408 6.638610 ACCATGGCAAATCGAATATTTTTCA 58.361 32.000 13.04 0.00 0.00 2.69
408 409 8.641499 TTACCATGGCAAATCGAATATTTTTC 57.359 30.769 13.04 0.00 0.00 2.29
409 410 9.442047 TTTTACCATGGCAAATCGAATATTTTT 57.558 25.926 13.04 0.00 0.00 1.94
410 411 9.442047 TTTTTACCATGGCAAATCGAATATTTT 57.558 25.926 13.04 0.00 0.00 1.82
440 441 5.862845 ACTCCACTATAAATCTGATGCCAG 58.137 41.667 0.00 0.00 41.74 4.85
441 442 5.221722 GGACTCCACTATAAATCTGATGCCA 60.222 44.000 0.00 0.00 0.00 4.92
442 443 5.012561 AGGACTCCACTATAAATCTGATGCC 59.987 44.000 0.00 0.00 0.00 4.40
443 444 6.107901 AGGACTCCACTATAAATCTGATGC 57.892 41.667 0.00 0.00 0.00 3.91
444 445 8.970859 AAAAGGACTCCACTATAAATCTGATG 57.029 34.615 0.00 0.00 0.00 3.07
469 470 9.880157 GTACACAGAGTTTAGTATGGGATAAAA 57.120 33.333 0.00 0.00 0.00 1.52
470 471 8.480501 GGTACACAGAGTTTAGTATGGGATAAA 58.519 37.037 0.00 0.00 0.00 1.40
471 472 7.620491 TGGTACACAGAGTTTAGTATGGGATAA 59.380 37.037 0.00 0.00 0.00 1.75
472 473 7.127405 TGGTACACAGAGTTTAGTATGGGATA 58.873 38.462 0.00 0.00 0.00 2.59
473 474 5.962031 TGGTACACAGAGTTTAGTATGGGAT 59.038 40.000 0.00 0.00 0.00 3.85
474 475 5.335261 TGGTACACAGAGTTTAGTATGGGA 58.665 41.667 0.00 0.00 0.00 4.37
475 476 5.670792 TGGTACACAGAGTTTAGTATGGG 57.329 43.478 0.00 0.00 0.00 4.00
496 497 3.131396 AGCTAACCACTCGTTTCAAGTG 58.869 45.455 0.00 0.00 43.04 3.16
497 498 3.470645 AGCTAACCACTCGTTTCAAGT 57.529 42.857 0.00 0.00 35.79 3.16
498 499 5.411781 AGATAGCTAACCACTCGTTTCAAG 58.588 41.667 0.00 0.00 35.79 3.02
499 500 5.047590 TGAGATAGCTAACCACTCGTTTCAA 60.048 40.000 0.00 0.00 35.79 2.69
500 501 4.461431 TGAGATAGCTAACCACTCGTTTCA 59.539 41.667 0.00 0.00 35.79 2.69
501 502 4.995124 TGAGATAGCTAACCACTCGTTTC 58.005 43.478 0.00 0.00 35.79 2.78
502 503 5.401531 TTGAGATAGCTAACCACTCGTTT 57.598 39.130 0.00 0.00 35.79 3.60
503 504 5.401531 TTTGAGATAGCTAACCACTCGTT 57.598 39.130 0.00 0.00 38.57 3.85
504 505 5.401531 TTTTGAGATAGCTAACCACTCGT 57.598 39.130 0.00 0.00 0.00 4.18
505 506 5.637810 TGTTTTTGAGATAGCTAACCACTCG 59.362 40.000 0.00 0.00 0.00 4.18
506 507 6.651225 ACTGTTTTTGAGATAGCTAACCACTC 59.349 38.462 0.00 5.69 0.00 3.51
507 508 6.534634 ACTGTTTTTGAGATAGCTAACCACT 58.465 36.000 0.00 0.00 0.00 4.00
508 509 6.426937 TGACTGTTTTTGAGATAGCTAACCAC 59.573 38.462 0.00 0.00 0.00 4.16
509 510 6.530120 TGACTGTTTTTGAGATAGCTAACCA 58.470 36.000 0.00 0.00 0.00 3.67
510 511 7.041372 TGTTGACTGTTTTTGAGATAGCTAACC 60.041 37.037 0.00 0.00 0.00 2.85
511 512 7.861630 TGTTGACTGTTTTTGAGATAGCTAAC 58.138 34.615 0.00 0.00 0.00 2.34
512 513 8.342634 GTTGTTGACTGTTTTTGAGATAGCTAA 58.657 33.333 0.00 0.00 0.00 3.09
513 514 7.497579 TGTTGTTGACTGTTTTTGAGATAGCTA 59.502 33.333 0.00 0.00 0.00 3.32
514 515 6.318648 TGTTGTTGACTGTTTTTGAGATAGCT 59.681 34.615 0.00 0.00 0.00 3.32
515 516 6.494842 TGTTGTTGACTGTTTTTGAGATAGC 58.505 36.000 0.00 0.00 0.00 2.97
516 517 8.909708 TTTGTTGTTGACTGTTTTTGAGATAG 57.090 30.769 0.00 0.00 0.00 2.08
518 519 9.301153 GTATTTGTTGTTGACTGTTTTTGAGAT 57.699 29.630 0.00 0.00 0.00 2.75
519 520 8.519526 AGTATTTGTTGTTGACTGTTTTTGAGA 58.480 29.630 0.00 0.00 0.00 3.27
520 521 8.687824 AGTATTTGTTGTTGACTGTTTTTGAG 57.312 30.769 0.00 0.00 0.00 3.02
525 526 9.783256 GAGTTTAGTATTTGTTGTTGACTGTTT 57.217 29.630 0.00 0.00 0.00 2.83
526 527 9.174166 AGAGTTTAGTATTTGTTGTTGACTGTT 57.826 29.630 0.00 0.00 0.00 3.16
527 528 8.612619 CAGAGTTTAGTATTTGTTGTTGACTGT 58.387 33.333 0.00 0.00 0.00 3.55
528 529 8.612619 ACAGAGTTTAGTATTTGTTGTTGACTG 58.387 33.333 0.00 0.00 0.00 3.51
529 530 8.612619 CACAGAGTTTAGTATTTGTTGTTGACT 58.387 33.333 0.00 0.00 0.00 3.41
530 531 8.395633 ACACAGAGTTTAGTATTTGTTGTTGAC 58.604 33.333 0.00 0.00 0.00 3.18
531 532 8.500753 ACACAGAGTTTAGTATTTGTTGTTGA 57.499 30.769 0.00 0.00 0.00 3.18
534 535 9.772973 TGATACACAGAGTTTAGTATTTGTTGT 57.227 29.630 0.00 0.00 0.00 3.32
607 614 7.094075 CCTGGAGAATGATGATTTCAGAACAAA 60.094 37.037 0.00 0.00 37.89 2.83
635 642 6.279882 TGTTGAAATTGACAGGAAACCAATC 58.720 36.000 0.00 0.00 30.93 2.67
640 647 6.863126 CCTACATGTTGAAATTGACAGGAAAC 59.137 38.462 2.30 0.00 32.40 2.78
712 719 5.045215 GTGGATATGCATGGAATTTGTGTG 58.955 41.667 10.16 0.00 0.00 3.82
716 723 6.340962 AGATGTGGATATGCATGGAATTTG 57.659 37.500 10.16 0.00 0.00 2.32
780 787 2.380064 TCCTTGGAAAGCAATGTGGT 57.620 45.000 0.00 0.00 44.44 4.16
781 788 3.321682 TCTTTCCTTGGAAAGCAATGTGG 59.678 43.478 28.11 10.86 44.44 4.17
807 814 1.402720 CGAGTAACGGCCGTCCTTTTA 60.403 52.381 34.29 17.51 38.46 1.52
1245 1258 2.110213 GGATGGCCGCGGTGAATA 59.890 61.111 28.70 9.20 0.00 1.75
1545 1561 0.320374 AGTCGCCGATTTTGACCTGA 59.680 50.000 0.00 0.00 33.09 3.86
1824 1849 4.760047 CCGTCGGGAAGTGCTGGG 62.760 72.222 2.34 0.00 34.06 4.45
1857 1883 2.637383 GGACACGAAGCTCCGGAGT 61.637 63.158 31.43 14.17 0.00 3.85
1878 1904 1.518903 GGTGGTCTTTCTGCAGGCAC 61.519 60.000 15.13 5.35 0.00 5.01
1890 1916 4.681978 GCACGCTTCCGGTGGTCT 62.682 66.667 0.00 0.00 39.22 3.85
2077 2103 8.801882 TGTTATCTGGTCGATTTAAAATTCCT 57.198 30.769 0.00 0.00 33.48 3.36
2319 2367 5.067674 GTCATGCTATTGTAAGGGATTTGCA 59.932 40.000 0.00 0.00 0.00 4.08
2365 2415 4.927267 TCCAGTGAACACCCAGAATTAT 57.073 40.909 1.11 0.00 0.00 1.28
2376 2426 9.130661 TCAGATTTTTAAGATTTCCAGTGAACA 57.869 29.630 0.00 0.00 0.00 3.18
2381 2431 7.745620 ACGTCAGATTTTTAAGATTTCCAGT 57.254 32.000 0.00 0.00 0.00 4.00
2415 2465 5.917541 TTCAGTACAACTTCGGAAATGTC 57.082 39.130 10.92 5.44 0.00 3.06
2423 2473 8.062448 CCTTTCTAAAGTTTCAGTACAACTTCG 58.938 37.037 9.51 5.66 42.47 3.79
2433 2483 4.978580 GCAGTTGCCTTTCTAAAGTTTCAG 59.021 41.667 0.00 0.00 34.20 3.02
2479 2530 4.431416 TGAAATGTGTAGTTGAGTGGGT 57.569 40.909 0.00 0.00 0.00 4.51
2483 2534 8.514330 TTAGGTTTTGAAATGTGTAGTTGAGT 57.486 30.769 0.00 0.00 0.00 3.41
2598 2649 5.221422 ACAACAAAACATGGTAGGGTGATTG 60.221 40.000 6.62 0.00 0.00 2.67
2713 2765 4.667519 AAGTATCAACCCATACCGAGAC 57.332 45.455 0.00 0.00 30.49 3.36
2823 2880 6.959639 TTTAATCAAGAGGCTTTGTTGTCT 57.040 33.333 0.00 0.00 32.20 3.41
2880 2937 2.092968 TGCAGAATGTAAAGCGGGAGAT 60.093 45.455 0.00 0.00 39.31 2.75
2969 3026 6.770303 TGTCACATGTAGATTTCAAACCTTGA 59.230 34.615 0.00 0.00 38.04 3.02


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

AutoCloner maintained by Alex Coulton.