Multiple sequence alignment - TraesCS7B01G141200

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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 TraesCS7B01G141200 chr7B 100.000 3002 0 0 1 3002 179252835 179255836 0 5544
1 TraesCS7B01G141200 chr7D 95.654 2623 74 19 400 3002 220279739 220277137 0 4176
2 TraesCS7B01G141200 chr7A 93.827 1944 75 19 400 2319 232591261 232589339 0 2883
3 TraesCS7B01G141200 chr7A 95.683 695 28 2 2309 3002 232589319 232588626 0 1116


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 TraesCS7B01G141200 chr7B 179252835 179255836 3001 False 5544.0 5544 100.000 1 3002 1 chr7B.!!$F1 3001
1 TraesCS7B01G141200 chr7D 220277137 220279739 2602 True 4176.0 4176 95.654 400 3002 1 chr7D.!!$R1 2602
2 TraesCS7B01G141200 chr7A 232588626 232591261 2635 True 1999.5 2883 94.755 400 3002 2 chr7A.!!$R1 2602

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
22 23 0.034896 ACGTGGTGTTAAGAGCCTGG 59.965 55.0 0.00 0.00 0.0 4.45 F
26 27 0.035343 GGTGTTAAGAGCCTGGGGAC 60.035 60.0 0.00 0.00 0.0 4.46 F
64 65 0.034896 GAGTTGAGGGACGAAAGCCA 59.965 55.0 0.00 0.00 0.0 4.75 F
323 324 0.184451 ACTGATAGCCTGGCATTGGG 59.816 55.0 22.65 10.16 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1454 1.142748 GCTGTAGCTGATGAGGCGT 59.857 57.895 0.00 0.00 38.21 5.68 R
1725 1754 3.028850 AGCCACCAATTTCATGATCTGG 58.971 45.455 13.87 13.87 0.00 3.86 R
1903 1932 4.629200 CCTTGAGTTCATCTGCTTGAGTAC 59.371 45.833 0.00 0.00 0.00 2.73 R
2197 2228 5.163513 CACGCTTTGCTTGGAAGAAATATT 58.836 37.500 0.00 0.00 0.00 1.28 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
20 21 2.522185 TCTACGTGGTGTTAAGAGCCT 58.478 47.619 0.00 0.00 0.00 4.58
21 22 2.230508 TCTACGTGGTGTTAAGAGCCTG 59.769 50.000 0.00 0.00 0.00 4.85
22 23 0.034896 ACGTGGTGTTAAGAGCCTGG 59.965 55.000 0.00 0.00 0.00 4.45
23 24 0.673644 CGTGGTGTTAAGAGCCTGGG 60.674 60.000 0.00 0.00 0.00 4.45
24 25 0.322546 GTGGTGTTAAGAGCCTGGGG 60.323 60.000 0.00 0.00 0.00 4.96
25 26 0.474854 TGGTGTTAAGAGCCTGGGGA 60.475 55.000 0.00 0.00 0.00 4.81
26 27 0.035343 GGTGTTAAGAGCCTGGGGAC 60.035 60.000 0.00 0.00 0.00 4.46
27 28 0.690762 GTGTTAAGAGCCTGGGGACA 59.309 55.000 0.00 0.00 39.59 4.02
28 29 1.073284 GTGTTAAGAGCCTGGGGACAA 59.927 52.381 0.00 0.00 42.06 3.18
29 30 1.777878 TGTTAAGAGCCTGGGGACAAA 59.222 47.619 0.00 0.00 42.06 2.83
30 31 2.378547 TGTTAAGAGCCTGGGGACAAAT 59.621 45.455 0.00 0.00 42.06 2.32
31 32 2.755103 GTTAAGAGCCTGGGGACAAATG 59.245 50.000 0.00 0.00 42.06 2.32
32 33 0.779997 AAGAGCCTGGGGACAAATGT 59.220 50.000 0.00 0.00 42.06 2.71
33 34 0.329596 AGAGCCTGGGGACAAATGTC 59.670 55.000 4.96 4.96 42.06 3.06
34 35 1.002134 AGCCTGGGGACAAATGTCG 60.002 57.895 7.42 0.00 45.65 4.35
40 41 3.274067 GGACAAATGTCGCACCCC 58.726 61.111 7.42 0.00 45.65 4.95
41 42 1.602323 GGACAAATGTCGCACCCCA 60.602 57.895 7.42 0.00 45.65 4.96
42 43 1.175983 GGACAAATGTCGCACCCCAA 61.176 55.000 7.42 0.00 45.65 4.12
43 44 0.671251 GACAAATGTCGCACCCCAAA 59.329 50.000 0.00 0.00 35.12 3.28
44 45 1.067821 GACAAATGTCGCACCCCAAAA 59.932 47.619 0.00 0.00 35.12 2.44
45 46 1.068434 ACAAATGTCGCACCCCAAAAG 59.932 47.619 0.00 0.00 0.00 2.27
46 47 1.339610 CAAATGTCGCACCCCAAAAGA 59.660 47.619 0.00 0.00 0.00 2.52
47 48 1.247567 AATGTCGCACCCCAAAAGAG 58.752 50.000 0.00 0.00 0.00 2.85
48 49 0.110486 ATGTCGCACCCCAAAAGAGT 59.890 50.000 0.00 0.00 0.00 3.24
49 50 0.106918 TGTCGCACCCCAAAAGAGTT 60.107 50.000 0.00 0.00 0.00 3.01
50 51 0.310854 GTCGCACCCCAAAAGAGTTG 59.689 55.000 0.00 0.00 0.00 3.16
51 52 0.181587 TCGCACCCCAAAAGAGTTGA 59.818 50.000 0.00 0.00 0.00 3.18
52 53 0.593128 CGCACCCCAAAAGAGTTGAG 59.407 55.000 0.00 0.00 0.00 3.02
53 54 0.961753 GCACCCCAAAAGAGTTGAGG 59.038 55.000 0.00 0.00 0.00 3.86
54 55 1.620822 CACCCCAAAAGAGTTGAGGG 58.379 55.000 9.69 9.69 39.29 4.30
55 56 1.144913 CACCCCAAAAGAGTTGAGGGA 59.855 52.381 15.37 0.00 42.25 4.20
56 57 1.145119 ACCCCAAAAGAGTTGAGGGAC 59.855 52.381 15.37 0.00 42.25 4.46
57 58 1.523758 CCCAAAAGAGTTGAGGGACG 58.476 55.000 0.00 0.00 42.25 4.79
58 59 1.071699 CCCAAAAGAGTTGAGGGACGA 59.928 52.381 0.00 0.00 42.25 4.20
59 60 2.486548 CCCAAAAGAGTTGAGGGACGAA 60.487 50.000 0.00 0.00 42.25 3.85
60 61 3.211045 CCAAAAGAGTTGAGGGACGAAA 58.789 45.455 0.00 0.00 0.00 3.46
61 62 3.251004 CCAAAAGAGTTGAGGGACGAAAG 59.749 47.826 0.00 0.00 0.00 2.62
62 63 2.171341 AAGAGTTGAGGGACGAAAGC 57.829 50.000 0.00 0.00 0.00 3.51
63 64 0.321996 AGAGTTGAGGGACGAAAGCC 59.678 55.000 0.00 0.00 0.00 4.35
64 65 0.034896 GAGTTGAGGGACGAAAGCCA 59.965 55.000 0.00 0.00 0.00 4.75
65 66 0.250338 AGTTGAGGGACGAAAGCCAC 60.250 55.000 0.00 0.00 0.00 5.01
66 67 0.534203 GTTGAGGGACGAAAGCCACA 60.534 55.000 0.00 0.00 0.00 4.17
67 68 0.534203 TTGAGGGACGAAAGCCACAC 60.534 55.000 0.00 0.00 0.00 3.82
68 69 1.371558 GAGGGACGAAAGCCACACT 59.628 57.895 0.00 0.00 0.00 3.55
69 70 0.250338 GAGGGACGAAAGCCACACTT 60.250 55.000 0.00 0.00 41.70 3.16
70 71 0.250338 AGGGACGAAAGCCACACTTC 60.250 55.000 0.00 0.00 37.75 3.01
71 72 0.534203 GGGACGAAAGCCACACTTCA 60.534 55.000 0.00 0.00 37.75 3.02
72 73 0.586802 GGACGAAAGCCACACTTCAC 59.413 55.000 0.00 0.00 37.75 3.18
73 74 1.295792 GACGAAAGCCACACTTCACA 58.704 50.000 0.00 0.00 37.75 3.58
74 75 1.668751 GACGAAAGCCACACTTCACAA 59.331 47.619 0.00 0.00 37.75 3.33
75 76 2.290641 GACGAAAGCCACACTTCACAAT 59.709 45.455 0.00 0.00 37.75 2.71
76 77 3.472652 ACGAAAGCCACACTTCACAATA 58.527 40.909 0.00 0.00 37.75 1.90
77 78 3.880490 ACGAAAGCCACACTTCACAATAA 59.120 39.130 0.00 0.00 37.75 1.40
78 79 4.024048 ACGAAAGCCACACTTCACAATAAG 60.024 41.667 0.00 0.00 37.75 1.73
79 80 4.024048 CGAAAGCCACACTTCACAATAAGT 60.024 41.667 0.00 0.00 40.33 2.24
80 81 5.505654 CGAAAGCCACACTTCACAATAAGTT 60.506 40.000 0.00 0.00 37.61 2.66
81 82 4.836125 AGCCACACTTCACAATAAGTTG 57.164 40.909 0.00 0.00 37.61 3.16
82 83 4.460263 AGCCACACTTCACAATAAGTTGA 58.540 39.130 0.00 0.00 37.61 3.18
83 84 4.516698 AGCCACACTTCACAATAAGTTGAG 59.483 41.667 0.00 0.00 37.61 3.02
84 85 4.320494 GCCACACTTCACAATAAGTTGAGG 60.320 45.833 0.00 0.00 37.61 3.86
85 86 4.216257 CCACACTTCACAATAAGTTGAGGG 59.784 45.833 0.00 0.00 37.61 4.30
86 87 5.063204 CACACTTCACAATAAGTTGAGGGA 58.937 41.667 0.00 0.00 37.61 4.20
87 88 5.049405 CACACTTCACAATAAGTTGAGGGAC 60.049 44.000 0.00 0.00 37.61 4.46
88 89 4.152402 CACTTCACAATAAGTTGAGGGACG 59.848 45.833 0.00 0.00 37.61 4.79
89 90 4.039973 ACTTCACAATAAGTTGAGGGACGA 59.960 41.667 0.00 0.00 36.26 4.20
90 91 4.610605 TCACAATAAGTTGAGGGACGAA 57.389 40.909 0.00 0.00 38.71 3.85
91 92 4.963373 TCACAATAAGTTGAGGGACGAAA 58.037 39.130 0.00 0.00 38.71 3.46
92 93 5.369833 TCACAATAAGTTGAGGGACGAAAA 58.630 37.500 0.00 0.00 38.71 2.29
93 94 5.823570 TCACAATAAGTTGAGGGACGAAAAA 59.176 36.000 0.00 0.00 38.71 1.94
94 95 6.488683 TCACAATAAGTTGAGGGACGAAAAAT 59.511 34.615 0.00 0.00 38.71 1.82
95 96 7.662258 TCACAATAAGTTGAGGGACGAAAAATA 59.338 33.333 0.00 0.00 38.71 1.40
96 97 7.749126 CACAATAAGTTGAGGGACGAAAAATAC 59.251 37.037 0.00 0.00 38.71 1.89
97 98 7.446013 ACAATAAGTTGAGGGACGAAAAATACA 59.554 33.333 0.00 0.00 38.71 2.29
98 99 5.684550 AAGTTGAGGGACGAAAAATACAC 57.315 39.130 0.00 0.00 0.00 2.90
99 100 4.969484 AGTTGAGGGACGAAAAATACACT 58.031 39.130 0.00 0.00 0.00 3.55
100 101 5.374071 AGTTGAGGGACGAAAAATACACTT 58.626 37.500 0.00 0.00 0.00 3.16
101 102 5.826208 AGTTGAGGGACGAAAAATACACTTT 59.174 36.000 0.00 0.00 0.00 2.66
102 103 6.993902 AGTTGAGGGACGAAAAATACACTTTA 59.006 34.615 0.00 0.00 0.00 1.85
103 104 7.664318 AGTTGAGGGACGAAAAATACACTTTAT 59.336 33.333 0.00 0.00 0.00 1.40
104 105 7.605410 TGAGGGACGAAAAATACACTTTATC 57.395 36.000 0.00 0.00 0.00 1.75
105 106 6.596497 TGAGGGACGAAAAATACACTTTATCC 59.404 38.462 0.00 0.00 0.00 2.59
106 107 6.718294 AGGGACGAAAAATACACTTTATCCT 58.282 36.000 0.00 0.00 0.00 3.24
107 108 7.173032 AGGGACGAAAAATACACTTTATCCTT 58.827 34.615 0.00 0.00 0.00 3.36
108 109 7.668469 AGGGACGAAAAATACACTTTATCCTTT 59.332 33.333 0.00 0.00 0.00 3.11
109 110 8.949177 GGGACGAAAAATACACTTTATCCTTTA 58.051 33.333 0.00 0.00 0.00 1.85
136 137 8.841444 AATGTTCAAATAATATTCACAGACGC 57.159 30.769 0.00 0.00 0.00 5.19
137 138 7.609760 TGTTCAAATAATATTCACAGACGCT 57.390 32.000 0.00 0.00 0.00 5.07
138 139 8.039603 TGTTCAAATAATATTCACAGACGCTT 57.960 30.769 0.00 0.00 0.00 4.68
139 140 8.511321 TGTTCAAATAATATTCACAGACGCTTT 58.489 29.630 0.00 0.00 0.00 3.51
140 141 9.982291 GTTCAAATAATATTCACAGACGCTTTA 57.018 29.630 0.00 0.00 0.00 1.85
149 150 9.769093 ATATTCACAGACGCTTTAAAAATGTAC 57.231 29.630 0.00 0.00 0.00 2.90
150 151 6.606234 TCACAGACGCTTTAAAAATGTACA 57.394 33.333 0.00 0.00 0.00 2.90
151 152 6.423862 TCACAGACGCTTTAAAAATGTACAC 58.576 36.000 0.00 0.00 0.00 2.90
152 153 5.335949 CACAGACGCTTTAAAAATGTACACG 59.664 40.000 0.00 0.00 0.00 4.49
153 154 5.006941 ACAGACGCTTTAAAAATGTACACGT 59.993 36.000 0.00 0.00 0.00 4.49
154 155 5.905181 CAGACGCTTTAAAAATGTACACGTT 59.095 36.000 0.00 0.00 0.00 3.99
155 156 6.412653 CAGACGCTTTAAAAATGTACACGTTT 59.587 34.615 0.00 4.24 36.70 3.60
156 157 6.968335 AGACGCTTTAAAAATGTACACGTTTT 59.032 30.769 18.22 18.22 44.33 2.43
197 198 9.981114 TCAAAATTTAAAAAGACATCTTCTCCC 57.019 29.630 0.00 0.00 34.61 4.30
198 199 9.762933 CAAAATTTAAAAAGACATCTTCTCCCA 57.237 29.630 0.00 0.00 34.61 4.37
200 201 9.933723 AAATTTAAAAAGACATCTTCTCCCATG 57.066 29.630 0.00 0.00 34.61 3.66
201 202 8.655935 ATTTAAAAAGACATCTTCTCCCATGT 57.344 30.769 0.00 0.00 35.88 3.21
202 203 8.477419 TTTAAAAAGACATCTTCTCCCATGTT 57.523 30.769 0.00 0.00 33.22 2.71
203 204 6.581171 AAAAAGACATCTTCTCCCATGTTC 57.419 37.500 0.00 0.00 33.22 3.18
204 205 4.916041 AAGACATCTTCTCCCATGTTCA 57.084 40.909 0.00 0.00 33.22 3.18
205 206 5.447778 AAGACATCTTCTCCCATGTTCAT 57.552 39.130 0.00 0.00 33.22 2.57
206 207 5.447778 AGACATCTTCTCCCATGTTCATT 57.552 39.130 0.00 0.00 33.22 2.57
207 208 5.824421 AGACATCTTCTCCCATGTTCATTT 58.176 37.500 0.00 0.00 33.22 2.32
208 209 6.251471 AGACATCTTCTCCCATGTTCATTTT 58.749 36.000 0.00 0.00 33.22 1.82
209 210 6.723052 AGACATCTTCTCCCATGTTCATTTTT 59.277 34.615 0.00 0.00 33.22 1.94
210 211 6.694447 ACATCTTCTCCCATGTTCATTTTTG 58.306 36.000 0.00 0.00 28.27 2.44
211 212 6.494491 ACATCTTCTCCCATGTTCATTTTTGA 59.506 34.615 0.00 0.00 28.27 2.69
212 213 6.975196 TCTTCTCCCATGTTCATTTTTGAA 57.025 33.333 0.00 0.00 0.00 2.69
213 214 7.358770 TCTTCTCCCATGTTCATTTTTGAAA 57.641 32.000 0.00 0.00 0.00 2.69
214 215 7.436118 TCTTCTCCCATGTTCATTTTTGAAAG 58.564 34.615 0.00 0.00 0.00 2.62
215 216 6.975196 TCTCCCATGTTCATTTTTGAAAGA 57.025 33.333 0.00 0.00 0.00 2.52
216 217 7.358770 TCTCCCATGTTCATTTTTGAAAGAA 57.641 32.000 0.00 0.00 0.00 2.52
217 218 7.209475 TCTCCCATGTTCATTTTTGAAAGAAC 58.791 34.615 0.00 0.00 40.45 3.01
218 219 5.982516 TCCCATGTTCATTTTTGAAAGAACG 59.017 36.000 0.00 0.00 42.35 3.95
219 220 5.982516 CCCATGTTCATTTTTGAAAGAACGA 59.017 36.000 0.00 0.00 42.35 3.85
220 221 6.478344 CCCATGTTCATTTTTGAAAGAACGAA 59.522 34.615 0.00 0.00 42.35 3.85
221 222 7.171337 CCCATGTTCATTTTTGAAAGAACGAAT 59.829 33.333 0.00 0.00 42.35 3.34
222 223 9.190858 CCATGTTCATTTTTGAAAGAACGAATA 57.809 29.630 0.00 0.00 42.35 1.75
251 252 5.954296 AAAACTCGCTACAGTAGACTACA 57.046 39.130 12.15 0.00 0.00 2.74
252 253 5.548706 AAACTCGCTACAGTAGACTACAG 57.451 43.478 12.15 9.30 0.00 2.74
253 254 4.468765 ACTCGCTACAGTAGACTACAGA 57.531 45.455 12.15 3.81 0.00 3.41
254 255 4.829968 ACTCGCTACAGTAGACTACAGAA 58.170 43.478 12.15 0.00 0.00 3.02
255 256 5.243981 ACTCGCTACAGTAGACTACAGAAA 58.756 41.667 12.15 1.02 0.00 2.52
256 257 5.122082 ACTCGCTACAGTAGACTACAGAAAC 59.878 44.000 12.15 0.92 0.00 2.78
257 258 4.394300 TCGCTACAGTAGACTACAGAAACC 59.606 45.833 12.15 0.00 0.00 3.27
258 259 4.395542 CGCTACAGTAGACTACAGAAACCT 59.604 45.833 12.15 0.00 0.00 3.50
259 260 5.447548 CGCTACAGTAGACTACAGAAACCTC 60.448 48.000 12.15 0.00 0.00 3.85
260 261 5.447548 GCTACAGTAGACTACAGAAACCTCG 60.448 48.000 12.15 0.00 0.00 4.63
261 262 3.190953 ACAGTAGACTACAGAAACCTCGC 59.809 47.826 14.95 0.00 0.00 5.03
262 263 2.754002 AGTAGACTACAGAAACCTCGCC 59.246 50.000 14.95 0.00 0.00 5.54
263 264 1.629043 AGACTACAGAAACCTCGCCA 58.371 50.000 0.00 0.00 0.00 5.69
264 265 2.180276 AGACTACAGAAACCTCGCCAT 58.820 47.619 0.00 0.00 0.00 4.40
265 266 2.567615 AGACTACAGAAACCTCGCCATT 59.432 45.455 0.00 0.00 0.00 3.16
266 267 2.673368 GACTACAGAAACCTCGCCATTG 59.327 50.000 0.00 0.00 0.00 2.82
267 268 2.009774 CTACAGAAACCTCGCCATTGG 58.990 52.381 0.00 0.00 0.00 3.16
268 269 0.609131 ACAGAAACCTCGCCATTGGG 60.609 55.000 4.53 0.00 37.18 4.12
290 291 2.672996 CCCAGTTGAAGGGTGGCG 60.673 66.667 0.00 0.00 41.61 5.69
291 292 2.429930 CCAGTTGAAGGGTGGCGA 59.570 61.111 0.00 0.00 0.00 5.54
292 293 1.228124 CCAGTTGAAGGGTGGCGAA 60.228 57.895 0.00 0.00 0.00 4.70
293 294 0.821711 CCAGTTGAAGGGTGGCGAAA 60.822 55.000 0.00 0.00 0.00 3.46
294 295 0.310854 CAGTTGAAGGGTGGCGAAAC 59.689 55.000 0.00 0.00 0.00 2.78
295 296 1.164041 AGTTGAAGGGTGGCGAAACG 61.164 55.000 0.00 0.00 0.00 3.60
296 297 1.153127 TTGAAGGGTGGCGAAACGT 60.153 52.632 0.00 0.00 0.00 3.99
297 298 1.440938 TTGAAGGGTGGCGAAACGTG 61.441 55.000 0.00 0.00 0.00 4.49
298 299 2.593436 AAGGGTGGCGAAACGTGG 60.593 61.111 0.00 0.00 0.00 4.94
299 300 3.409605 AAGGGTGGCGAAACGTGGT 62.410 57.895 0.00 0.00 0.00 4.16
300 301 3.351416 GGGTGGCGAAACGTGGTC 61.351 66.667 0.00 0.00 0.00 4.02
301 302 3.351416 GGTGGCGAAACGTGGTCC 61.351 66.667 0.00 0.00 0.00 4.46
302 303 2.589442 GTGGCGAAACGTGGTCCA 60.589 61.111 0.00 0.00 0.00 4.02
303 304 2.181521 GTGGCGAAACGTGGTCCAA 61.182 57.895 0.00 0.00 0.00 3.53
304 305 1.451567 TGGCGAAACGTGGTCCAAA 60.452 52.632 0.00 0.00 0.00 3.28
305 306 1.009335 GGCGAAACGTGGTCCAAAC 60.009 57.895 0.00 0.00 0.00 2.93
306 307 1.441732 GGCGAAACGTGGTCCAAACT 61.442 55.000 0.00 0.00 0.00 2.66
307 308 0.316689 GCGAAACGTGGTCCAAACTG 60.317 55.000 0.00 0.00 0.00 3.16
308 309 1.292061 CGAAACGTGGTCCAAACTGA 58.708 50.000 0.00 0.00 0.00 3.41
309 310 1.871039 CGAAACGTGGTCCAAACTGAT 59.129 47.619 0.00 0.00 0.00 2.90
310 311 3.061322 CGAAACGTGGTCCAAACTGATA 58.939 45.455 0.00 0.00 0.00 2.15
311 312 3.122948 CGAAACGTGGTCCAAACTGATAG 59.877 47.826 0.00 0.00 0.00 2.08
312 313 2.094762 ACGTGGTCCAAACTGATAGC 57.905 50.000 0.00 0.00 0.00 2.97
313 314 1.338769 ACGTGGTCCAAACTGATAGCC 60.339 52.381 0.00 0.00 0.00 3.93
314 315 1.066143 CGTGGTCCAAACTGATAGCCT 60.066 52.381 0.00 0.00 0.00 4.58
315 316 2.359900 GTGGTCCAAACTGATAGCCTG 58.640 52.381 0.00 0.00 0.00 4.85
316 317 1.281867 TGGTCCAAACTGATAGCCTGG 59.718 52.381 0.00 0.00 0.00 4.45
317 318 1.383523 GTCCAAACTGATAGCCTGGC 58.616 55.000 11.65 11.65 0.00 4.85
318 319 0.991146 TCCAAACTGATAGCCTGGCA 59.009 50.000 22.65 7.39 0.00 4.92
319 320 1.565759 TCCAAACTGATAGCCTGGCAT 59.434 47.619 22.65 12.20 0.00 4.40
320 321 2.025037 TCCAAACTGATAGCCTGGCATT 60.025 45.455 22.65 7.33 0.00 3.56
321 322 2.100252 CCAAACTGATAGCCTGGCATTG 59.900 50.000 22.65 12.60 0.00 2.82
322 323 2.062971 AACTGATAGCCTGGCATTGG 57.937 50.000 22.65 9.09 0.00 3.16
323 324 0.184451 ACTGATAGCCTGGCATTGGG 59.816 55.000 22.65 10.16 0.00 4.12
324 325 0.538977 CTGATAGCCTGGCATTGGGG 60.539 60.000 22.65 2.37 0.00 4.96
325 326 1.228675 GATAGCCTGGCATTGGGGG 60.229 63.158 22.65 0.00 0.00 5.40
343 344 4.751431 GCTTCTCAGCCCATGGTT 57.249 55.556 11.73 0.00 40.61 3.67
344 345 2.967270 GCTTCTCAGCCCATGGTTT 58.033 52.632 11.73 0.00 40.61 3.27
345 346 2.128771 GCTTCTCAGCCCATGGTTTA 57.871 50.000 11.73 0.00 40.61 2.01
346 347 2.659428 GCTTCTCAGCCCATGGTTTAT 58.341 47.619 11.73 0.00 40.61 1.40
347 348 3.820557 GCTTCTCAGCCCATGGTTTATA 58.179 45.455 11.73 0.00 40.61 0.98
348 349 3.817647 GCTTCTCAGCCCATGGTTTATAG 59.182 47.826 11.73 1.60 40.61 1.31
349 350 4.687219 GCTTCTCAGCCCATGGTTTATAGT 60.687 45.833 11.73 0.00 40.61 2.12
350 351 4.689612 TCTCAGCCCATGGTTTATAGTC 57.310 45.455 11.73 0.00 0.00 2.59
351 352 3.391296 TCTCAGCCCATGGTTTATAGTCC 59.609 47.826 11.73 0.00 0.00 3.85
352 353 2.441750 TCAGCCCATGGTTTATAGTCCC 59.558 50.000 11.73 0.00 0.00 4.46
353 354 2.174639 CAGCCCATGGTTTATAGTCCCA 59.825 50.000 11.73 0.00 0.00 4.37
354 355 2.174854 AGCCCATGGTTTATAGTCCCAC 59.825 50.000 11.73 0.00 0.00 4.61
355 356 2.846193 CCCATGGTTTATAGTCCCACG 58.154 52.381 11.73 0.00 0.00 4.94
356 357 2.436542 CCCATGGTTTATAGTCCCACGA 59.563 50.000 11.73 0.00 0.00 4.35
357 358 3.072476 CCCATGGTTTATAGTCCCACGAT 59.928 47.826 11.73 0.00 0.00 3.73
358 359 4.285003 CCCATGGTTTATAGTCCCACGATA 59.715 45.833 11.73 0.00 0.00 2.92
359 360 5.045869 CCCATGGTTTATAGTCCCACGATAT 60.046 44.000 11.73 0.00 0.00 1.63
360 361 6.106673 CCATGGTTTATAGTCCCACGATATC 58.893 44.000 2.57 0.00 0.00 1.63
361 362 5.733620 TGGTTTATAGTCCCACGATATCC 57.266 43.478 0.00 0.00 0.00 2.59
362 363 4.529377 TGGTTTATAGTCCCACGATATCCC 59.471 45.833 0.00 0.00 0.00 3.85
363 364 4.381292 GGTTTATAGTCCCACGATATCCCG 60.381 50.000 0.00 0.00 0.00 5.14
364 365 2.893215 ATAGTCCCACGATATCCCGA 57.107 50.000 0.00 0.00 0.00 5.14
365 366 2.195741 TAGTCCCACGATATCCCGAG 57.804 55.000 0.00 0.00 0.00 4.63
366 367 1.179814 AGTCCCACGATATCCCGAGC 61.180 60.000 0.00 0.00 0.00 5.03
367 368 1.906824 TCCCACGATATCCCGAGCC 60.907 63.158 0.00 0.00 0.00 4.70
368 369 2.657237 CCACGATATCCCGAGCCC 59.343 66.667 0.00 0.00 0.00 5.19
369 370 1.908793 CCACGATATCCCGAGCCCT 60.909 63.158 0.00 0.00 0.00 5.19
370 371 1.587054 CACGATATCCCGAGCCCTC 59.413 63.158 0.00 0.00 0.00 4.30
391 392 4.659172 CCAGCCCGGCCAACAAGA 62.659 66.667 5.55 0.00 0.00 3.02
392 393 2.597217 CAGCCCGGCCAACAAGAA 60.597 61.111 5.55 0.00 0.00 2.52
393 394 2.597510 AGCCCGGCCAACAAGAAC 60.598 61.111 5.55 0.00 0.00 3.01
394 395 4.038080 GCCCGGCCAACAAGAACG 62.038 66.667 2.24 0.00 0.00 3.95
395 396 4.038080 CCCGGCCAACAAGAACGC 62.038 66.667 2.24 0.00 0.00 4.84
396 397 4.038080 CCGGCCAACAAGAACGCC 62.038 66.667 2.24 0.00 38.07 5.68
397 398 3.283684 CGGCCAACAAGAACGCCA 61.284 61.111 2.24 0.00 41.71 5.69
398 399 2.335011 GGCCAACAAGAACGCCAC 59.665 61.111 0.00 0.00 41.25 5.01
440 445 1.290203 AATCACACATGCCGTCGATC 58.710 50.000 0.00 0.00 0.00 3.69
445 450 0.594796 CACATGCCGTCGATCGATGA 60.595 55.000 33.40 18.27 42.86 2.92
451 456 1.267383 GCCGTCGATCGATGAAAAACC 60.267 52.381 33.40 12.70 42.86 3.27
452 457 1.006391 CCGTCGATCGATGAAAAACCG 60.006 52.381 33.40 22.34 42.86 4.44
453 458 1.589022 CGTCGATCGATGAAAAACCGC 60.589 52.381 29.26 8.11 42.86 5.68
460 465 4.857871 TCGATGAAAAACCGCAGATAAG 57.142 40.909 0.00 0.00 0.00 1.73
461 466 4.500127 TCGATGAAAAACCGCAGATAAGA 58.500 39.130 0.00 0.00 0.00 2.10
462 467 4.328983 TCGATGAAAAACCGCAGATAAGAC 59.671 41.667 0.00 0.00 0.00 3.01
474 479 4.552767 CGCAGATAAGACGCCATTTTTAGG 60.553 45.833 0.00 0.00 0.00 2.69
502 512 2.283532 ACTCGCTCCAGGCTCAGT 60.284 61.111 0.00 0.00 39.13 3.41
542 552 1.745320 TTATCCTCCTCTTCCGCGGC 61.745 60.000 23.51 0.00 0.00 6.53
555 565 2.616330 CGCGGCCACACTTCACATT 61.616 57.895 2.24 0.00 0.00 2.71
560 570 0.240945 GCCACACTTCACATTTCCGG 59.759 55.000 0.00 0.00 0.00 5.14
572 582 3.125316 CACATTTCCGGCTTCTTCTACAC 59.875 47.826 0.00 0.00 0.00 2.90
573 583 3.008049 ACATTTCCGGCTTCTTCTACACT 59.992 43.478 0.00 0.00 0.00 3.55
604 614 0.768622 TGGATCGACAAGGTGGGTTT 59.231 50.000 0.00 0.00 0.00 3.27
605 615 1.165270 GGATCGACAAGGTGGGTTTG 58.835 55.000 0.00 0.00 0.00 2.93
606 616 1.165270 GATCGACAAGGTGGGTTTGG 58.835 55.000 0.00 0.00 0.00 3.28
607 617 0.251165 ATCGACAAGGTGGGTTTGGG 60.251 55.000 0.00 0.00 0.00 4.12
608 618 1.152839 CGACAAGGTGGGTTTGGGT 60.153 57.895 0.00 0.00 0.00 4.51
609 619 0.753848 CGACAAGGTGGGTTTGGGTT 60.754 55.000 0.00 0.00 0.00 4.11
620 630 3.076785 TGGGTTTGGGTTACATCCTCATT 59.923 43.478 0.00 0.00 0.00 2.57
650 660 2.550978 CCTCCGCTGTGTTCGATTATT 58.449 47.619 0.00 0.00 0.00 1.40
654 669 4.496360 TCCGCTGTGTTCGATTATTGTAA 58.504 39.130 0.00 0.00 0.00 2.41
655 670 5.113383 TCCGCTGTGTTCGATTATTGTAAT 58.887 37.500 0.00 0.00 0.00 1.89
656 671 5.583061 TCCGCTGTGTTCGATTATTGTAATT 59.417 36.000 0.00 0.00 0.00 1.40
685 700 5.450965 CCAATTTCCACCATGCTGTAGATTC 60.451 44.000 0.00 0.00 0.00 2.52
702 720 2.456073 TTCGGGGGAAGAAAAACCAA 57.544 45.000 0.00 0.00 0.00 3.67
705 723 1.611977 CGGGGGAAGAAAAACCAACTC 59.388 52.381 0.00 0.00 0.00 3.01
815 842 6.207221 TGTGCATATGATGATATGAACCAACC 59.793 38.462 17.73 0.23 45.53 3.77
835 862 5.592104 ACCGAACCTTCTTGTTTGATTTT 57.408 34.783 0.00 0.00 32.32 1.82
836 863 5.972935 ACCGAACCTTCTTGTTTGATTTTT 58.027 33.333 0.00 0.00 32.32 1.94
837 864 5.810074 ACCGAACCTTCTTGTTTGATTTTTG 59.190 36.000 0.00 0.00 32.32 2.44
838 865 6.039616 CCGAACCTTCTTGTTTGATTTTTGA 58.960 36.000 0.00 0.00 32.32 2.69
840 867 7.306749 CCGAACCTTCTTGTTTGATTTTTGATG 60.307 37.037 0.00 0.00 32.32 3.07
904 933 3.503748 ACTGCCATGTTTCTTAGCTGAAC 59.496 43.478 0.00 0.00 0.00 3.18
921 950 1.696097 AACGAGTGCACCAGGGTTCT 61.696 55.000 14.63 0.00 0.00 3.01
948 977 5.046304 ACTGGTAGCCTGGCATTATATGTAG 60.046 44.000 22.65 8.44 0.00 2.74
949 978 4.225042 TGGTAGCCTGGCATTATATGTAGG 59.775 45.833 22.65 0.00 38.75 3.18
950 979 4.469945 GGTAGCCTGGCATTATATGTAGGA 59.530 45.833 22.65 0.00 38.31 2.94
951 980 4.833478 AGCCTGGCATTATATGTAGGAG 57.167 45.455 22.65 0.00 38.31 3.69
952 981 4.171234 AGCCTGGCATTATATGTAGGAGT 58.829 43.478 22.65 0.00 38.31 3.85
953 982 5.342017 AGCCTGGCATTATATGTAGGAGTA 58.658 41.667 22.65 0.00 38.31 2.59
987 1016 3.490155 CGCATTTCAATTGTTGTGCAGAA 59.510 39.130 21.89 0.00 33.09 3.02
1036 1065 1.094073 CGATGCCAAGAAGAGCCTGG 61.094 60.000 0.00 0.00 0.00 4.45
1039 1068 2.437359 CCAAGAAGAGCCTGGCGG 60.437 66.667 13.96 2.27 0.00 6.13
1251 1280 1.450312 CGACAAGCTCATCCCCACC 60.450 63.158 0.00 0.00 0.00 4.61
1581 1610 4.435436 CGGCTGCGTCCTACTGCA 62.435 66.667 0.00 0.00 39.13 4.41
1903 1932 1.079127 CTGGAGTACCGCCACAAGG 60.079 63.158 1.11 0.00 39.42 3.61
2043 2073 4.009675 TCAGTTCCCATGTAGCATGTTTC 58.990 43.478 8.11 0.00 0.00 2.78
2127 2157 5.172934 GCATTGAGAATCCAAGCATTTTGA 58.827 37.500 0.00 0.00 0.00 2.69
2197 2228 8.511321 CAACAAGTGGCTTGAGTATGTATTTTA 58.489 33.333 14.81 0.00 43.42 1.52
2310 2342 6.926826 CACAGTCACCTAATTACACAGTTACA 59.073 38.462 0.00 0.00 0.00 2.41
2319 2351 6.935741 AATTACACAGTTACACACACACAT 57.064 33.333 0.00 0.00 0.00 3.21
2602 2664 5.319453 AGAAAAATGATCTGCTTCCTGACA 58.681 37.500 0.00 0.00 0.00 3.58
2936 2999 2.664436 GCGTGCGAACCCACTGTAC 61.664 63.158 0.00 0.00 33.60 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.230508 CAGGCTCTTAACACCACGTAGA 59.769 50.000 0.00 0.00 0.00 2.59
1 2 2.607187 CAGGCTCTTAACACCACGTAG 58.393 52.381 0.00 0.00 0.00 3.51
2 3 1.274167 CCAGGCTCTTAACACCACGTA 59.726 52.381 0.00 0.00 0.00 3.57
3 4 0.034896 CCAGGCTCTTAACACCACGT 59.965 55.000 0.00 0.00 0.00 4.49
4 5 0.673644 CCCAGGCTCTTAACACCACG 60.674 60.000 0.00 0.00 0.00 4.94
5 6 0.322546 CCCCAGGCTCTTAACACCAC 60.323 60.000 0.00 0.00 0.00 4.16
6 7 0.474854 TCCCCAGGCTCTTAACACCA 60.475 55.000 0.00 0.00 0.00 4.17
7 8 0.035343 GTCCCCAGGCTCTTAACACC 60.035 60.000 0.00 0.00 0.00 4.16
8 9 0.690762 TGTCCCCAGGCTCTTAACAC 59.309 55.000 0.00 0.00 0.00 3.32
9 10 1.440618 TTGTCCCCAGGCTCTTAACA 58.559 50.000 0.00 0.00 0.00 2.41
10 11 2.579410 TTTGTCCCCAGGCTCTTAAC 57.421 50.000 0.00 0.00 0.00 2.01
11 12 2.378547 ACATTTGTCCCCAGGCTCTTAA 59.621 45.455 0.00 0.00 0.00 1.85
12 13 1.992557 ACATTTGTCCCCAGGCTCTTA 59.007 47.619 0.00 0.00 0.00 2.10
13 14 0.779997 ACATTTGTCCCCAGGCTCTT 59.220 50.000 0.00 0.00 0.00 2.85
14 15 0.329596 GACATTTGTCCCCAGGCTCT 59.670 55.000 0.00 0.00 39.07 4.09
15 16 1.026718 CGACATTTGTCCCCAGGCTC 61.027 60.000 5.17 0.00 41.86 4.70
16 17 1.002134 CGACATTTGTCCCCAGGCT 60.002 57.895 5.17 0.00 41.86 4.58
17 18 2.700773 GCGACATTTGTCCCCAGGC 61.701 63.158 5.17 0.00 41.86 4.85
18 19 1.303236 TGCGACATTTGTCCCCAGG 60.303 57.895 5.17 0.00 41.86 4.45
19 20 1.586154 GGTGCGACATTTGTCCCCAG 61.586 60.000 5.17 0.00 41.86 4.45
20 21 1.602323 GGTGCGACATTTGTCCCCA 60.602 57.895 5.17 0.70 41.86 4.96
21 22 2.340328 GGGTGCGACATTTGTCCCC 61.340 63.158 5.17 6.47 41.86 4.81
22 23 2.340328 GGGGTGCGACATTTGTCCC 61.340 63.158 5.17 1.38 41.86 4.46
23 24 1.175983 TTGGGGTGCGACATTTGTCC 61.176 55.000 5.17 0.00 41.86 4.02
24 25 0.671251 TTTGGGGTGCGACATTTGTC 59.329 50.000 0.46 0.46 41.47 3.18
25 26 1.068434 CTTTTGGGGTGCGACATTTGT 59.932 47.619 0.00 0.00 0.00 2.83
26 27 1.339610 TCTTTTGGGGTGCGACATTTG 59.660 47.619 0.00 0.00 0.00 2.32
27 28 1.613437 CTCTTTTGGGGTGCGACATTT 59.387 47.619 0.00 0.00 0.00 2.32
28 29 1.247567 CTCTTTTGGGGTGCGACATT 58.752 50.000 0.00 0.00 0.00 2.71
29 30 0.110486 ACTCTTTTGGGGTGCGACAT 59.890 50.000 0.00 0.00 0.00 3.06
30 31 0.106918 AACTCTTTTGGGGTGCGACA 60.107 50.000 0.00 0.00 0.00 4.35
31 32 0.310854 CAACTCTTTTGGGGTGCGAC 59.689 55.000 0.00 0.00 26.79 5.19
32 33 0.181587 TCAACTCTTTTGGGGTGCGA 59.818 50.000 0.00 0.00 37.58 5.10
33 34 0.593128 CTCAACTCTTTTGGGGTGCG 59.407 55.000 0.00 0.00 37.58 5.34
34 35 0.961753 CCTCAACTCTTTTGGGGTGC 59.038 55.000 0.00 0.00 37.58 5.01
35 36 1.144913 TCCCTCAACTCTTTTGGGGTG 59.855 52.381 2.29 0.00 38.39 4.61
36 37 1.145119 GTCCCTCAACTCTTTTGGGGT 59.855 52.381 2.29 0.00 38.39 4.95
37 38 1.882352 CGTCCCTCAACTCTTTTGGGG 60.882 57.143 0.00 0.00 39.77 4.96
38 39 1.071699 TCGTCCCTCAACTCTTTTGGG 59.928 52.381 0.00 0.00 39.22 4.12
39 40 2.543777 TCGTCCCTCAACTCTTTTGG 57.456 50.000 0.00 0.00 0.00 3.28
40 41 3.304057 GCTTTCGTCCCTCAACTCTTTTG 60.304 47.826 0.00 0.00 0.00 2.44
41 42 2.879026 GCTTTCGTCCCTCAACTCTTTT 59.121 45.455 0.00 0.00 0.00 2.27
42 43 2.495084 GCTTTCGTCCCTCAACTCTTT 58.505 47.619 0.00 0.00 0.00 2.52
43 44 1.270893 GGCTTTCGTCCCTCAACTCTT 60.271 52.381 0.00 0.00 0.00 2.85
44 45 0.321996 GGCTTTCGTCCCTCAACTCT 59.678 55.000 0.00 0.00 0.00 3.24
45 46 0.034896 TGGCTTTCGTCCCTCAACTC 59.965 55.000 0.00 0.00 0.00 3.01
46 47 0.250338 GTGGCTTTCGTCCCTCAACT 60.250 55.000 0.00 0.00 0.00 3.16
47 48 0.534203 TGTGGCTTTCGTCCCTCAAC 60.534 55.000 0.00 0.00 0.00 3.18
48 49 0.534203 GTGTGGCTTTCGTCCCTCAA 60.534 55.000 0.00 0.00 0.00 3.02
49 50 1.070786 GTGTGGCTTTCGTCCCTCA 59.929 57.895 0.00 0.00 0.00 3.86
50 51 0.250338 AAGTGTGGCTTTCGTCCCTC 60.250 55.000 0.00 0.00 32.57 4.30
51 52 0.250338 GAAGTGTGGCTTTCGTCCCT 60.250 55.000 0.00 0.00 37.59 4.20
52 53 0.534203 TGAAGTGTGGCTTTCGTCCC 60.534 55.000 0.00 0.00 37.59 4.46
53 54 0.586802 GTGAAGTGTGGCTTTCGTCC 59.413 55.000 0.00 0.00 37.59 4.79
54 55 1.295792 TGTGAAGTGTGGCTTTCGTC 58.704 50.000 0.00 0.00 37.59 4.20
55 56 1.745232 TTGTGAAGTGTGGCTTTCGT 58.255 45.000 0.00 0.00 37.59 3.85
56 57 4.024048 ACTTATTGTGAAGTGTGGCTTTCG 60.024 41.667 0.00 0.00 38.25 3.46
57 58 5.438761 ACTTATTGTGAAGTGTGGCTTTC 57.561 39.130 0.00 0.00 38.25 2.62
58 59 5.359576 TCAACTTATTGTGAAGTGTGGCTTT 59.640 36.000 0.00 0.00 39.62 3.51
59 60 4.887071 TCAACTTATTGTGAAGTGTGGCTT 59.113 37.500 0.00 0.00 39.62 4.35
60 61 4.460263 TCAACTTATTGTGAAGTGTGGCT 58.540 39.130 0.00 0.00 39.62 4.75
61 62 4.320494 CCTCAACTTATTGTGAAGTGTGGC 60.320 45.833 0.00 0.00 39.62 5.01
62 63 4.216257 CCCTCAACTTATTGTGAAGTGTGG 59.784 45.833 0.00 0.00 39.62 4.17
63 64 5.049405 GTCCCTCAACTTATTGTGAAGTGTG 60.049 44.000 0.00 0.00 39.62 3.82
64 65 5.063880 GTCCCTCAACTTATTGTGAAGTGT 58.936 41.667 0.00 0.00 39.62 3.55
65 66 4.152402 CGTCCCTCAACTTATTGTGAAGTG 59.848 45.833 0.00 0.00 39.62 3.16
66 67 4.039973 TCGTCCCTCAACTTATTGTGAAGT 59.960 41.667 0.00 0.00 41.50 3.01
67 68 4.566004 TCGTCCCTCAACTTATTGTGAAG 58.434 43.478 0.00 0.00 37.11 3.02
68 69 4.610605 TCGTCCCTCAACTTATTGTGAA 57.389 40.909 0.00 0.00 37.11 3.18
69 70 4.610605 TTCGTCCCTCAACTTATTGTGA 57.389 40.909 0.00 0.00 37.11 3.58
70 71 5.682943 TTTTCGTCCCTCAACTTATTGTG 57.317 39.130 0.00 0.00 37.11 3.33
71 72 6.894339 ATTTTTCGTCCCTCAACTTATTGT 57.106 33.333 0.00 0.00 37.11 2.71
72 73 7.749126 GTGTATTTTTCGTCCCTCAACTTATTG 59.251 37.037 0.00 0.00 37.14 1.90
73 74 7.664318 AGTGTATTTTTCGTCCCTCAACTTATT 59.336 33.333 0.00 0.00 0.00 1.40
74 75 7.166167 AGTGTATTTTTCGTCCCTCAACTTAT 58.834 34.615 0.00 0.00 0.00 1.73
75 76 6.527423 AGTGTATTTTTCGTCCCTCAACTTA 58.473 36.000 0.00 0.00 0.00 2.24
76 77 5.374071 AGTGTATTTTTCGTCCCTCAACTT 58.626 37.500 0.00 0.00 0.00 2.66
77 78 4.969484 AGTGTATTTTTCGTCCCTCAACT 58.031 39.130 0.00 0.00 0.00 3.16
78 79 5.684550 AAGTGTATTTTTCGTCCCTCAAC 57.315 39.130 0.00 0.00 0.00 3.18
79 80 7.120138 GGATAAAGTGTATTTTTCGTCCCTCAA 59.880 37.037 0.00 0.00 0.00 3.02
80 81 6.596497 GGATAAAGTGTATTTTTCGTCCCTCA 59.404 38.462 0.00 0.00 0.00 3.86
81 82 6.822170 AGGATAAAGTGTATTTTTCGTCCCTC 59.178 38.462 0.00 0.00 0.00 4.30
82 83 6.718294 AGGATAAAGTGTATTTTTCGTCCCT 58.282 36.000 0.00 0.00 0.00 4.20
83 84 6.997239 AGGATAAAGTGTATTTTTCGTCCC 57.003 37.500 0.00 0.00 0.00 4.46
110 111 9.289303 GCGTCTGTGAATATTATTTGAACATTT 57.711 29.630 0.00 0.00 0.00 2.32
111 112 8.677300 AGCGTCTGTGAATATTATTTGAACATT 58.323 29.630 0.00 0.00 0.00 2.71
112 113 8.213518 AGCGTCTGTGAATATTATTTGAACAT 57.786 30.769 0.00 0.00 0.00 2.71
113 114 7.609760 AGCGTCTGTGAATATTATTTGAACA 57.390 32.000 0.00 0.00 0.00 3.18
114 115 8.895932 AAAGCGTCTGTGAATATTATTTGAAC 57.104 30.769 0.00 0.00 0.00 3.18
123 124 9.769093 GTACATTTTTAAAGCGTCTGTGAATAT 57.231 29.630 0.00 0.00 0.00 1.28
124 125 8.775527 TGTACATTTTTAAAGCGTCTGTGAATA 58.224 29.630 0.00 0.00 0.00 1.75
125 126 7.589954 GTGTACATTTTTAAAGCGTCTGTGAAT 59.410 33.333 0.00 0.00 0.00 2.57
126 127 6.908284 GTGTACATTTTTAAAGCGTCTGTGAA 59.092 34.615 0.00 0.00 0.00 3.18
127 128 6.423862 GTGTACATTTTTAAAGCGTCTGTGA 58.576 36.000 0.00 0.00 0.00 3.58
128 129 5.335949 CGTGTACATTTTTAAAGCGTCTGTG 59.664 40.000 0.00 0.00 0.00 3.66
129 130 5.006941 ACGTGTACATTTTTAAAGCGTCTGT 59.993 36.000 0.00 0.00 0.00 3.41
130 131 5.437263 ACGTGTACATTTTTAAAGCGTCTG 58.563 37.500 0.00 0.00 0.00 3.51
131 132 5.662211 ACGTGTACATTTTTAAAGCGTCT 57.338 34.783 0.00 0.00 0.00 4.18
132 133 6.721442 AAACGTGTACATTTTTAAAGCGTC 57.279 33.333 0.00 0.00 0.00 5.19
133 134 7.509050 AAAAACGTGTACATTTTTAAAGCGT 57.491 28.000 15.11 7.21 36.49 5.07
171 172 9.981114 GGGAGAAGATGTCTTTTTAAATTTTGA 57.019 29.630 0.00 0.00 36.41 2.69
172 173 9.762933 TGGGAGAAGATGTCTTTTTAAATTTTG 57.237 29.630 0.00 0.00 36.41 2.44
174 175 9.933723 CATGGGAGAAGATGTCTTTTTAAATTT 57.066 29.630 0.00 0.00 36.41 1.82
175 176 9.093458 ACATGGGAGAAGATGTCTTTTTAAATT 57.907 29.630 0.00 0.00 36.41 1.82
176 177 8.655935 ACATGGGAGAAGATGTCTTTTTAAAT 57.344 30.769 0.00 0.00 36.41 1.40
177 178 8.477419 AACATGGGAGAAGATGTCTTTTTAAA 57.523 30.769 0.00 0.00 36.41 1.52
178 179 7.723616 TGAACATGGGAGAAGATGTCTTTTTAA 59.276 33.333 0.00 0.00 36.41 1.52
179 180 7.230747 TGAACATGGGAGAAGATGTCTTTTTA 58.769 34.615 0.00 0.00 36.41 1.52
180 181 6.070656 TGAACATGGGAGAAGATGTCTTTTT 58.929 36.000 0.00 0.00 36.41 1.94
181 182 5.634118 TGAACATGGGAGAAGATGTCTTTT 58.366 37.500 0.00 0.00 36.41 2.27
182 183 5.246981 TGAACATGGGAGAAGATGTCTTT 57.753 39.130 0.00 0.00 36.41 2.52
183 184 4.916041 TGAACATGGGAGAAGATGTCTT 57.084 40.909 0.00 0.00 36.41 3.01
184 185 5.447778 AATGAACATGGGAGAAGATGTCT 57.552 39.130 0.00 0.00 40.25 3.41
185 186 6.521151 AAAATGAACATGGGAGAAGATGTC 57.479 37.500 0.00 0.00 31.43 3.06
186 187 6.494491 TCAAAAATGAACATGGGAGAAGATGT 59.506 34.615 0.00 0.00 34.16 3.06
187 188 6.927416 TCAAAAATGAACATGGGAGAAGATG 58.073 36.000 0.00 0.00 0.00 2.90
188 189 7.543359 TTCAAAAATGAACATGGGAGAAGAT 57.457 32.000 0.00 0.00 0.00 2.40
189 190 6.975196 TTCAAAAATGAACATGGGAGAAGA 57.025 33.333 0.00 0.00 0.00 2.87
190 191 7.436118 TCTTTCAAAAATGAACATGGGAGAAG 58.564 34.615 0.00 0.00 0.00 2.85
191 192 7.358770 TCTTTCAAAAATGAACATGGGAGAA 57.641 32.000 0.00 0.00 0.00 2.87
192 193 6.975196 TCTTTCAAAAATGAACATGGGAGA 57.025 33.333 0.00 0.00 0.00 3.71
193 194 6.144402 CGTTCTTTCAAAAATGAACATGGGAG 59.856 38.462 13.77 0.00 44.09 4.30
194 195 5.982516 CGTTCTTTCAAAAATGAACATGGGA 59.017 36.000 13.77 0.00 44.09 4.37
195 196 5.982516 TCGTTCTTTCAAAAATGAACATGGG 59.017 36.000 13.77 2.58 44.09 4.00
196 197 7.462109 TTCGTTCTTTCAAAAATGAACATGG 57.538 32.000 13.77 2.83 44.09 3.66
228 229 6.206243 TCTGTAGTCTACTGTAGCGAGTTTTT 59.794 38.462 9.98 0.00 0.00 1.94
229 230 5.704515 TCTGTAGTCTACTGTAGCGAGTTTT 59.295 40.000 9.98 0.00 0.00 2.43
230 231 5.243981 TCTGTAGTCTACTGTAGCGAGTTT 58.756 41.667 9.98 0.00 0.00 2.66
231 232 4.829968 TCTGTAGTCTACTGTAGCGAGTT 58.170 43.478 9.98 0.00 0.00 3.01
232 233 4.468765 TCTGTAGTCTACTGTAGCGAGT 57.531 45.455 9.98 0.38 0.00 4.18
233 234 5.447548 GGTTTCTGTAGTCTACTGTAGCGAG 60.448 48.000 9.98 0.00 0.00 5.03
234 235 4.394300 GGTTTCTGTAGTCTACTGTAGCGA 59.606 45.833 9.98 0.00 0.00 4.93
235 236 4.395542 AGGTTTCTGTAGTCTACTGTAGCG 59.604 45.833 9.98 0.00 0.00 4.26
236 237 5.447548 CGAGGTTTCTGTAGTCTACTGTAGC 60.448 48.000 9.98 11.66 0.00 3.58
237 238 5.447548 GCGAGGTTTCTGTAGTCTACTGTAG 60.448 48.000 11.28 8.55 0.00 2.74
238 239 4.394300 GCGAGGTTTCTGTAGTCTACTGTA 59.606 45.833 11.28 2.24 0.00 2.74
239 240 3.190953 GCGAGGTTTCTGTAGTCTACTGT 59.809 47.826 11.28 0.00 0.00 3.55
240 241 3.427773 GGCGAGGTTTCTGTAGTCTACTG 60.428 52.174 11.28 10.58 0.00 2.74
241 242 2.754002 GGCGAGGTTTCTGTAGTCTACT 59.246 50.000 11.28 0.00 0.00 2.57
242 243 2.490903 TGGCGAGGTTTCTGTAGTCTAC 59.509 50.000 2.81 2.81 0.00 2.59
243 244 2.799017 TGGCGAGGTTTCTGTAGTCTA 58.201 47.619 0.00 0.00 0.00 2.59
244 245 1.629043 TGGCGAGGTTTCTGTAGTCT 58.371 50.000 0.00 0.00 0.00 3.24
245 246 2.673368 CAATGGCGAGGTTTCTGTAGTC 59.327 50.000 0.00 0.00 0.00 2.59
246 247 2.615493 CCAATGGCGAGGTTTCTGTAGT 60.615 50.000 0.00 0.00 0.00 2.73
247 248 2.009774 CCAATGGCGAGGTTTCTGTAG 58.990 52.381 0.00 0.00 0.00 2.74
248 249 1.339631 CCCAATGGCGAGGTTTCTGTA 60.340 52.381 0.00 0.00 0.00 2.74
249 250 0.609131 CCCAATGGCGAGGTTTCTGT 60.609 55.000 0.00 0.00 0.00 3.41
250 251 2.183409 CCCAATGGCGAGGTTTCTG 58.817 57.895 0.00 0.00 0.00 3.02
251 252 4.743018 CCCAATGGCGAGGTTTCT 57.257 55.556 0.00 0.00 0.00 2.52
274 275 0.821711 TTTCGCCACCCTTCAACTGG 60.822 55.000 0.00 0.00 0.00 4.00
275 276 0.310854 GTTTCGCCACCCTTCAACTG 59.689 55.000 0.00 0.00 0.00 3.16
276 277 1.164041 CGTTTCGCCACCCTTCAACT 61.164 55.000 0.00 0.00 0.00 3.16
277 278 1.281656 CGTTTCGCCACCCTTCAAC 59.718 57.895 0.00 0.00 0.00 3.18
278 279 1.153127 ACGTTTCGCCACCCTTCAA 60.153 52.632 0.00 0.00 0.00 2.69
279 280 1.890041 CACGTTTCGCCACCCTTCA 60.890 57.895 0.00 0.00 0.00 3.02
280 281 2.613506 CCACGTTTCGCCACCCTTC 61.614 63.158 0.00 0.00 0.00 3.46
281 282 2.593436 CCACGTTTCGCCACCCTT 60.593 61.111 0.00 0.00 0.00 3.95
282 283 3.819877 GACCACGTTTCGCCACCCT 62.820 63.158 0.00 0.00 0.00 4.34
283 284 3.351416 GACCACGTTTCGCCACCC 61.351 66.667 0.00 0.00 0.00 4.61
284 285 3.351416 GGACCACGTTTCGCCACC 61.351 66.667 0.00 0.00 0.00 4.61
285 286 1.716826 TTTGGACCACGTTTCGCCAC 61.717 55.000 0.00 0.00 0.00 5.01
286 287 1.451567 TTTGGACCACGTTTCGCCA 60.452 52.632 0.00 0.00 0.00 5.69
287 288 1.009335 GTTTGGACCACGTTTCGCC 60.009 57.895 0.00 0.00 0.00 5.54
288 289 0.316689 CAGTTTGGACCACGTTTCGC 60.317 55.000 0.00 0.00 0.00 4.70
289 290 1.292061 TCAGTTTGGACCACGTTTCG 58.708 50.000 0.00 0.00 0.00 3.46
290 291 3.120304 GCTATCAGTTTGGACCACGTTTC 60.120 47.826 0.00 0.00 0.00 2.78
291 292 2.812011 GCTATCAGTTTGGACCACGTTT 59.188 45.455 0.00 0.00 0.00 3.60
292 293 2.423577 GCTATCAGTTTGGACCACGTT 58.576 47.619 0.00 0.00 0.00 3.99
293 294 1.338769 GGCTATCAGTTTGGACCACGT 60.339 52.381 0.00 0.00 0.00 4.49
294 295 1.066143 AGGCTATCAGTTTGGACCACG 60.066 52.381 0.00 0.00 0.00 4.94
295 296 2.359900 CAGGCTATCAGTTTGGACCAC 58.640 52.381 0.00 0.00 0.00 4.16
296 297 1.281867 CCAGGCTATCAGTTTGGACCA 59.718 52.381 0.00 0.00 0.00 4.02
297 298 2.019156 GCCAGGCTATCAGTTTGGACC 61.019 57.143 3.29 0.00 0.00 4.46
298 299 1.340017 TGCCAGGCTATCAGTTTGGAC 60.340 52.381 14.15 0.00 0.00 4.02
299 300 0.991146 TGCCAGGCTATCAGTTTGGA 59.009 50.000 14.15 0.00 0.00 3.53
300 301 2.062971 ATGCCAGGCTATCAGTTTGG 57.937 50.000 14.15 0.00 0.00 3.28
301 302 2.100252 CCAATGCCAGGCTATCAGTTTG 59.900 50.000 14.15 5.23 0.00 2.93
302 303 2.381911 CCAATGCCAGGCTATCAGTTT 58.618 47.619 14.15 0.00 0.00 2.66
303 304 1.410648 CCCAATGCCAGGCTATCAGTT 60.411 52.381 14.15 0.00 0.00 3.16
304 305 0.184451 CCCAATGCCAGGCTATCAGT 59.816 55.000 14.15 0.00 0.00 3.41
305 306 0.538977 CCCCAATGCCAGGCTATCAG 60.539 60.000 14.15 0.00 0.00 2.90
306 307 1.538167 CCCCAATGCCAGGCTATCA 59.462 57.895 14.15 0.00 0.00 2.15
307 308 1.228675 CCCCCAATGCCAGGCTATC 60.229 63.158 14.15 0.00 0.00 2.08
308 309 2.937650 CCCCCAATGCCAGGCTAT 59.062 61.111 14.15 1.45 0.00 2.97
326 327 2.128771 TAAACCATGGGCTGAGAAGC 57.871 50.000 18.09 0.00 0.00 3.86
327 328 5.041191 ACTATAAACCATGGGCTGAGAAG 57.959 43.478 18.09 6.94 0.00 2.85
328 329 4.141482 GGACTATAAACCATGGGCTGAGAA 60.141 45.833 18.09 0.00 0.00 2.87
329 330 3.391296 GGACTATAAACCATGGGCTGAGA 59.609 47.826 18.09 0.00 0.00 3.27
330 331 3.496870 GGGACTATAAACCATGGGCTGAG 60.497 52.174 18.09 8.89 0.00 3.35
331 332 2.441750 GGGACTATAAACCATGGGCTGA 59.558 50.000 18.09 0.00 0.00 4.26
332 333 2.174639 TGGGACTATAAACCATGGGCTG 59.825 50.000 18.09 2.43 0.00 4.85
333 334 2.174854 GTGGGACTATAAACCATGGGCT 59.825 50.000 18.09 4.76 36.54 5.19
334 335 2.583143 GTGGGACTATAAACCATGGGC 58.417 52.381 18.09 0.00 36.54 5.36
335 336 2.436542 TCGTGGGACTATAAACCATGGG 59.563 50.000 18.09 0.00 40.77 4.00
336 337 3.830744 TCGTGGGACTATAAACCATGG 57.169 47.619 11.19 11.19 40.77 3.66
337 338 6.106673 GGATATCGTGGGACTATAAACCATG 58.893 44.000 0.00 0.00 41.55 3.66
338 339 5.189145 GGGATATCGTGGGACTATAAACCAT 59.811 44.000 0.00 0.00 36.54 3.55
339 340 4.529377 GGGATATCGTGGGACTATAAACCA 59.471 45.833 0.00 0.00 0.00 3.67
340 341 4.381292 CGGGATATCGTGGGACTATAAACC 60.381 50.000 0.00 0.00 0.00 3.27
341 342 4.460382 TCGGGATATCGTGGGACTATAAAC 59.540 45.833 0.00 0.00 0.00 2.01
342 343 4.665451 TCGGGATATCGTGGGACTATAAA 58.335 43.478 0.00 0.00 0.00 1.40
343 344 4.267536 CTCGGGATATCGTGGGACTATAA 58.732 47.826 0.00 0.00 0.00 0.98
344 345 3.882444 CTCGGGATATCGTGGGACTATA 58.118 50.000 0.00 0.00 0.00 1.31
345 346 2.724454 CTCGGGATATCGTGGGACTAT 58.276 52.381 0.00 0.00 0.00 2.12
346 347 1.885359 GCTCGGGATATCGTGGGACTA 60.885 57.143 0.00 0.00 0.00 2.59
347 348 1.179814 GCTCGGGATATCGTGGGACT 61.180 60.000 0.00 0.00 0.00 3.85
348 349 1.289380 GCTCGGGATATCGTGGGAC 59.711 63.158 0.00 0.00 0.00 4.46
349 350 1.906824 GGCTCGGGATATCGTGGGA 60.907 63.158 0.00 0.00 0.00 4.37
350 351 2.657237 GGCTCGGGATATCGTGGG 59.343 66.667 0.00 0.00 0.00 4.61
351 352 1.878656 GAGGGCTCGGGATATCGTGG 61.879 65.000 0.00 0.00 0.00 4.94
352 353 1.587054 GAGGGCTCGGGATATCGTG 59.413 63.158 0.00 0.00 0.00 4.35
353 354 4.098847 GAGGGCTCGGGATATCGT 57.901 61.111 0.00 0.00 0.00 3.73
374 375 4.659172 TCTTGTTGGCCGGGCTGG 62.659 66.667 29.87 8.39 42.50 4.85
375 376 2.597217 TTCTTGTTGGCCGGGCTG 60.597 61.111 29.87 13.47 0.00 4.85
376 377 2.597510 GTTCTTGTTGGCCGGGCT 60.598 61.111 29.87 0.00 0.00 5.19
377 378 4.038080 CGTTCTTGTTGGCCGGGC 62.038 66.667 23.42 23.42 0.00 6.13
378 379 4.038080 GCGTTCTTGTTGGCCGGG 62.038 66.667 2.18 0.00 0.00 5.73
379 380 4.038080 GGCGTTCTTGTTGGCCGG 62.038 66.667 0.00 0.00 35.59 6.13
381 382 2.335011 GTGGCGTTCTTGTTGGCC 59.665 61.111 0.00 0.00 45.76 5.36
382 383 2.335011 GGTGGCGTTCTTGTTGGC 59.665 61.111 0.00 0.00 0.00 4.52
383 384 2.637025 CGGTGGCGTTCTTGTTGG 59.363 61.111 0.00 0.00 0.00 3.77
384 385 2.637025 CCGGTGGCGTTCTTGTTG 59.363 61.111 0.00 0.00 0.00 3.33
385 386 3.284449 GCCGGTGGCGTTCTTGTT 61.284 61.111 1.90 0.00 39.62 2.83
395 396 2.700407 TAACCAGTTTGGGCCGGTGG 62.700 60.000 1.90 2.90 43.37 4.61
396 397 0.824182 TTAACCAGTTTGGGCCGGTG 60.824 55.000 1.90 0.00 43.37 4.94
397 398 0.106116 TTTAACCAGTTTGGGCCGGT 60.106 50.000 1.90 0.00 43.37 5.28
398 399 1.203758 GATTTAACCAGTTTGGGCCGG 59.796 52.381 0.00 0.00 43.37 6.13
440 445 4.578601 GTCTTATCTGCGGTTTTTCATCG 58.421 43.478 0.00 0.00 0.00 3.84
445 450 1.467342 GGCGTCTTATCTGCGGTTTTT 59.533 47.619 0.00 0.00 0.00 1.94
451 456 3.405170 AAAAATGGCGTCTTATCTGCG 57.595 42.857 0.00 0.00 0.00 5.18
452 457 4.789802 GCCTAAAAATGGCGTCTTATCTGC 60.790 45.833 0.00 0.00 41.03 4.26
453 458 4.848757 GCCTAAAAATGGCGTCTTATCTG 58.151 43.478 0.00 0.00 41.03 2.90
502 512 0.341258 AGAGGATGAGGAAGCCCTGA 59.659 55.000 0.00 0.00 44.53 3.86
542 552 0.240945 GCCGGAAATGTGAAGTGTGG 59.759 55.000 5.05 0.00 0.00 4.17
555 565 1.549170 GGAGTGTAGAAGAAGCCGGAA 59.451 52.381 5.05 0.00 0.00 4.30
560 570 0.533032 AGGCGGAGTGTAGAAGAAGC 59.467 55.000 0.00 0.00 0.00 3.86
572 582 1.583986 GATCCAGATCGAGGCGGAG 59.416 63.158 5.79 0.00 0.00 4.63
573 583 3.765051 GATCCAGATCGAGGCGGA 58.235 61.111 2.32 2.32 0.00 5.54
604 614 6.230472 CGATATTCAATGAGGATGTAACCCA 58.770 40.000 0.00 0.00 0.00 4.51
605 615 5.122396 GCGATATTCAATGAGGATGTAACCC 59.878 44.000 0.00 0.00 0.00 4.11
606 616 5.122396 GGCGATATTCAATGAGGATGTAACC 59.878 44.000 0.00 0.00 0.00 2.85
607 617 5.122396 GGGCGATATTCAATGAGGATGTAAC 59.878 44.000 0.00 0.00 0.00 2.50
608 618 5.013079 AGGGCGATATTCAATGAGGATGTAA 59.987 40.000 0.00 0.00 0.00 2.41
609 619 4.532126 AGGGCGATATTCAATGAGGATGTA 59.468 41.667 0.00 0.00 0.00 2.29
655 670 2.564947 GCATGGTGGAAATTGGGTACAA 59.435 45.455 0.00 0.00 41.59 2.41
656 671 2.175202 GCATGGTGGAAATTGGGTACA 58.825 47.619 0.00 0.00 0.00 2.90
685 700 1.611977 GAGTTGGTTTTTCTTCCCCCG 59.388 52.381 0.00 0.00 0.00 5.73
770 789 3.119459 ACACACTGATCTGATGGTACGAC 60.119 47.826 6.60 0.00 0.00 4.34
815 842 7.222611 ACATCAAAAATCAAACAAGAAGGTTCG 59.777 33.333 0.00 0.00 0.00 3.95
835 862 2.637382 TGCAGGTGACTAAGGACATCAA 59.363 45.455 0.00 0.00 40.21 2.57
836 863 2.028112 GTGCAGGTGACTAAGGACATCA 60.028 50.000 0.00 0.00 40.21 3.07
837 864 2.234908 AGTGCAGGTGACTAAGGACATC 59.765 50.000 0.00 0.00 40.21 3.06
838 865 2.027745 CAGTGCAGGTGACTAAGGACAT 60.028 50.000 0.00 0.00 40.21 3.06
840 867 1.344763 ACAGTGCAGGTGACTAAGGAC 59.655 52.381 2.98 0.00 40.21 3.85
904 933 0.320374 TTAGAACCCTGGTGCACTCG 59.680 55.000 17.98 7.85 0.00 4.18
921 950 4.788925 ATAATGCCAGGCTACCAGTTTA 57.211 40.909 14.15 0.28 0.00 2.01
928 957 5.187967 ACTCCTACATATAATGCCAGGCTAC 59.812 44.000 14.15 0.00 36.33 3.58
948 977 2.759191 TGCGATGAAGCATCATACTCC 58.241 47.619 4.06 0.00 46.30 3.85
974 1003 3.834231 AGGGCTAATTTCTGCACAACAAT 59.166 39.130 3.52 0.00 34.58 2.71
1039 1068 1.219393 CTTTCTCCCCGAGCCACTC 59.781 63.158 0.00 0.00 0.00 3.51
1251 1280 2.357517 GTGGTGAGGCACTGGACG 60.358 66.667 0.00 0.00 41.55 4.79
1425 1454 1.142748 GCTGTAGCTGATGAGGCGT 59.857 57.895 0.00 0.00 38.21 5.68
1725 1754 3.028850 AGCCACCAATTTCATGATCTGG 58.971 45.455 13.87 13.87 0.00 3.86
1903 1932 4.629200 CCTTGAGTTCATCTGCTTGAGTAC 59.371 45.833 0.00 0.00 0.00 2.73
2127 2157 9.696917 GAACATTCAGAAAACATCCAGTTAAAT 57.303 29.630 0.00 0.00 40.26 1.40
2197 2228 5.163513 CACGCTTTGCTTGGAAGAAATATT 58.836 37.500 0.00 0.00 0.00 1.28
2310 2342 8.402798 TGGAAATCATTAACTTATGTGTGTGT 57.597 30.769 0.00 0.00 0.00 3.72
2936 2999 1.004927 GCGCTAACAAGCTAATGGTCG 60.005 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.