Multiple sequence alignment - TraesCS2D01G087700

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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 TraesCS2D01G087700 chr2D 100.000 3476 0 0 1 3476 37830614 37827139 0.000000e+00 6420
1 TraesCS2D01G087700 chr2B 91.829 3182 176 44 330 3476 66216663 66213531 0.000000e+00 4359
2 TraesCS2D01G087700 chr2A 91.913 2634 150 25 874 3476 42721471 42718870 0.000000e+00 3626
3 TraesCS2D01G087700 chr2A 84.263 502 38 20 330 811 42721947 42721467 5.290000e-123 451
4 TraesCS2D01G087700 chr1A 90.909 517 39 7 2709 3221 564326548 564326036 0.000000e+00 688
5 TraesCS2D01G087700 chr1A 89.963 269 20 5 1147 1408 10501279 10501011 1.190000e-89 340
6 TraesCS2D01G087700 chr6B 90.716 517 40 7 2709 3221 14720700 14720188 0.000000e+00 682
7 TraesCS2D01G087700 chr4D 87.372 586 66 7 1034 1618 177317681 177317103 0.000000e+00 665
8 TraesCS2D01G087700 chr3B 87.500 472 59 0 1147 1618 699575388 699575859 2.360000e-151 545
9 TraesCS2D01G087700 chr1D 90.432 324 31 0 1295 1618 412282502 412282825 8.920000e-116 427
10 TraesCS2D01G087700 chr1D 91.985 262 21 0 1147 1408 486449310 486449049 5.480000e-98 368
11 TraesCS2D01G087700 chr7A 91.321 265 20 1 1147 1408 727763607 727763343 3.300000e-95 359
12 TraesCS2D01G087700 chr7A 88.593 263 28 2 1147 1408 5349059 5348798 5.600000e-83 318
13 TraesCS2D01G087700 chr5D 89.695 262 27 0 1147 1408 391158959 391159220 5.560000e-88 335


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 TraesCS2D01G087700 chr2D 37827139 37830614 3475 True 6420.0 6420 100.000 1 3476 1 chr2D.!!$R1 3475
1 TraesCS2D01G087700 chr2B 66213531 66216663 3132 True 4359.0 4359 91.829 330 3476 1 chr2B.!!$R1 3146
2 TraesCS2D01G087700 chr2A 42718870 42721947 3077 True 2038.5 3626 88.088 330 3476 2 chr2A.!!$R1 3146
3 TraesCS2D01G087700 chr1A 564326036 564326548 512 True 688.0 688 90.909 2709 3221 1 chr1A.!!$R2 512
4 TraesCS2D01G087700 chr6B 14720188 14720700 512 True 682.0 682 90.716 2709 3221 1 chr6B.!!$R1 512
5 TraesCS2D01G087700 chr4D 177317103 177317681 578 True 665.0 665 87.372 1034 1618 1 chr4D.!!$R1 584

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
65 66 0.032017 ATAAGCACCCCCGAGAGACT 60.032 55.0 0.00 0.0 0.00 3.24 F
588 606 0.179032 ACCTCGTGACACAATGGCAA 60.179 50.0 6.37 0.0 36.98 4.52 F
2040 2070 0.681243 GGAAGGGGGTCACATTGCTC 60.681 60.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 1980 1.134220 TCGAAGGTGTGGTTCTGCTTT 60.134 47.619 0.00 0.0 0.00 3.51 R
2097 2127 2.184579 GCCTCGTCCTCCTTTCCG 59.815 66.667 0.00 0.0 0.00 4.30 R
3218 3281 0.308993 GCTTGGATGATTACAGCGCC 59.691 55.000 2.29 0.0 32.75 6.53 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
43 44 4.302559 GGGGGTGAATATGATCTTACCC 57.697 50.000 8.26 8.26 45.50 3.69
47 48 6.893020 GGGTGAATATGATCTTACCCCTAT 57.107 41.667 6.17 0.00 41.46 2.57
48 49 7.989947 GGGTGAATATGATCTTACCCCTATA 57.010 40.000 6.17 0.00 41.46 1.31
49 50 8.388656 GGGTGAATATGATCTTACCCCTATAA 57.611 38.462 6.17 0.00 41.46 0.98
50 51 8.487028 GGGTGAATATGATCTTACCCCTATAAG 58.513 40.741 6.17 0.00 41.46 1.73
51 52 7.988028 GGTGAATATGATCTTACCCCTATAAGC 59.012 40.741 0.00 0.00 32.99 3.09
52 53 8.540388 GTGAATATGATCTTACCCCTATAAGCA 58.460 37.037 0.00 0.00 32.99 3.91
53 54 8.540388 TGAATATGATCTTACCCCTATAAGCAC 58.460 37.037 0.00 0.00 32.99 4.40
54 55 5.763876 ATGATCTTACCCCTATAAGCACC 57.236 43.478 0.00 0.00 32.99 5.01
55 56 3.908103 TGATCTTACCCCTATAAGCACCC 59.092 47.826 0.00 0.00 32.99 4.61
56 57 2.697967 TCTTACCCCTATAAGCACCCC 58.302 52.381 0.00 0.00 32.99 4.95
57 58 1.703513 CTTACCCCTATAAGCACCCCC 59.296 57.143 0.00 0.00 0.00 5.40
58 59 0.472352 TACCCCTATAAGCACCCCCG 60.472 60.000 0.00 0.00 0.00 5.73
59 60 1.460689 CCCCTATAAGCACCCCCGA 60.461 63.158 0.00 0.00 0.00 5.14
60 61 1.481056 CCCCTATAAGCACCCCCGAG 61.481 65.000 0.00 0.00 0.00 4.63
61 62 0.471211 CCCTATAAGCACCCCCGAGA 60.471 60.000 0.00 0.00 0.00 4.04
62 63 0.969894 CCTATAAGCACCCCCGAGAG 59.030 60.000 0.00 0.00 0.00 3.20
63 64 1.480683 CCTATAAGCACCCCCGAGAGA 60.481 57.143 0.00 0.00 0.00 3.10
64 65 1.614413 CTATAAGCACCCCCGAGAGAC 59.386 57.143 0.00 0.00 0.00 3.36
65 66 0.032017 ATAAGCACCCCCGAGAGACT 60.032 55.000 0.00 0.00 0.00 3.24
66 67 0.627451 TAAGCACCCCCGAGAGACTA 59.373 55.000 0.00 0.00 0.00 2.59
67 68 0.252103 AAGCACCCCCGAGAGACTAA 60.252 55.000 0.00 0.00 0.00 2.24
68 69 0.684805 AGCACCCCCGAGAGACTAAG 60.685 60.000 0.00 0.00 0.00 2.18
69 70 0.683504 GCACCCCCGAGAGACTAAGA 60.684 60.000 0.00 0.00 0.00 2.10
70 71 1.848652 CACCCCCGAGAGACTAAGAA 58.151 55.000 0.00 0.00 0.00 2.52
71 72 1.751924 CACCCCCGAGAGACTAAGAAG 59.248 57.143 0.00 0.00 0.00 2.85
72 73 1.358445 ACCCCCGAGAGACTAAGAAGT 59.642 52.381 0.00 0.00 39.21 3.01
73 74 2.225318 ACCCCCGAGAGACTAAGAAGTT 60.225 50.000 0.00 0.00 35.56 2.66
74 75 2.832733 CCCCCGAGAGACTAAGAAGTTT 59.167 50.000 0.00 0.00 35.56 2.66
75 76 3.119065 CCCCCGAGAGACTAAGAAGTTTC 60.119 52.174 0.00 0.00 37.16 2.78
76 77 3.510360 CCCCGAGAGACTAAGAAGTTTCA 59.490 47.826 0.00 0.00 38.91 2.69
77 78 4.021368 CCCCGAGAGACTAAGAAGTTTCAA 60.021 45.833 0.00 0.00 38.91 2.69
78 79 5.510861 CCCCGAGAGACTAAGAAGTTTCAAA 60.511 44.000 0.00 0.00 38.91 2.69
79 80 5.989777 CCCGAGAGACTAAGAAGTTTCAAAA 59.010 40.000 0.00 0.00 38.91 2.44
80 81 6.482308 CCCGAGAGACTAAGAAGTTTCAAAAA 59.518 38.462 0.00 0.00 38.91 1.94
81 82 7.173390 CCCGAGAGACTAAGAAGTTTCAAAAAT 59.827 37.037 0.00 0.00 38.91 1.82
82 83 9.204570 CCGAGAGACTAAGAAGTTTCAAAAATA 57.795 33.333 0.00 0.00 38.91 1.40
98 99 9.900710 TTTCAAAAATACATACATGTGTGTACC 57.099 29.630 30.38 0.00 43.21 3.34
99 100 8.046294 TCAAAAATACATACATGTGTGTACCC 57.954 34.615 30.38 0.00 43.21 3.69
100 101 7.885922 TCAAAAATACATACATGTGTGTACCCT 59.114 33.333 30.38 18.34 43.21 4.34
101 102 8.519526 CAAAAATACATACATGTGTGTACCCTT 58.480 33.333 30.38 21.88 43.21 3.95
102 103 8.644374 AAAATACATACATGTGTGTACCCTTT 57.356 30.769 30.38 24.98 43.21 3.11
103 104 8.644374 AAATACATACATGTGTGTACCCTTTT 57.356 30.769 30.38 23.83 43.21 2.27
104 105 8.644374 AATACATACATGTGTGTACCCTTTTT 57.356 30.769 30.38 19.53 43.21 1.94
105 106 6.325919 ACATACATGTGTGTACCCTTTTTG 57.674 37.500 24.77 0.00 43.21 2.44
106 107 6.065374 ACATACATGTGTGTACCCTTTTTGA 58.935 36.000 24.77 0.00 43.21 2.69
107 108 4.911514 ACATGTGTGTACCCTTTTTGAC 57.088 40.909 0.00 0.00 36.63 3.18
108 109 4.532834 ACATGTGTGTACCCTTTTTGACT 58.467 39.130 0.00 0.00 36.63 3.41
109 110 4.953579 ACATGTGTGTACCCTTTTTGACTT 59.046 37.500 0.00 0.00 36.63 3.01
110 111 5.067283 ACATGTGTGTACCCTTTTTGACTTC 59.933 40.000 0.00 0.00 36.63 3.01
111 112 3.623960 TGTGTGTACCCTTTTTGACTTCG 59.376 43.478 0.00 0.00 0.00 3.79
112 113 3.872771 GTGTGTACCCTTTTTGACTTCGA 59.127 43.478 0.00 0.00 0.00 3.71
113 114 4.333372 GTGTGTACCCTTTTTGACTTCGAA 59.667 41.667 0.00 0.00 0.00 3.71
114 115 4.942483 TGTGTACCCTTTTTGACTTCGAAA 59.058 37.500 0.00 0.00 0.00 3.46
115 116 5.065474 TGTGTACCCTTTTTGACTTCGAAAG 59.935 40.000 0.00 0.00 31.46 2.62
116 117 5.065602 GTGTACCCTTTTTGACTTCGAAAGT 59.934 40.000 0.00 0.00 46.38 2.66
137 138 3.767711 TCTTTCAGAGACCTAGTGAGCA 58.232 45.455 0.00 0.00 0.00 4.26
138 139 4.348486 TCTTTCAGAGACCTAGTGAGCAT 58.652 43.478 0.00 0.00 0.00 3.79
139 140 4.400884 TCTTTCAGAGACCTAGTGAGCATC 59.599 45.833 0.00 0.00 0.00 3.91
140 141 2.660572 TCAGAGACCTAGTGAGCATCC 58.339 52.381 0.00 0.00 0.00 3.51
141 142 1.686052 CAGAGACCTAGTGAGCATCCC 59.314 57.143 0.00 0.00 0.00 3.85
142 143 1.573376 AGAGACCTAGTGAGCATCCCT 59.427 52.381 0.00 0.00 0.00 4.20
143 144 2.023501 AGAGACCTAGTGAGCATCCCTT 60.024 50.000 0.00 0.00 0.00 3.95
144 145 2.364002 GAGACCTAGTGAGCATCCCTTC 59.636 54.545 0.00 0.00 0.00 3.46
145 146 1.067821 GACCTAGTGAGCATCCCTTCG 59.932 57.143 0.00 0.00 0.00 3.79
146 147 0.249657 CCTAGTGAGCATCCCTTCGC 60.250 60.000 0.00 0.00 0.00 4.70
147 148 0.249657 CTAGTGAGCATCCCTTCGCC 60.250 60.000 0.00 0.00 0.00 5.54
148 149 2.016393 TAGTGAGCATCCCTTCGCCG 62.016 60.000 0.00 0.00 0.00 6.46
149 150 4.838152 TGAGCATCCCTTCGCCGC 62.838 66.667 0.00 0.00 0.00 6.53
153 154 3.564027 CATCCCTTCGCCGCGTTC 61.564 66.667 13.39 0.00 0.00 3.95
154 155 3.771160 ATCCCTTCGCCGCGTTCT 61.771 61.111 13.39 0.00 0.00 3.01
155 156 4.735132 TCCCTTCGCCGCGTTCTG 62.735 66.667 13.39 0.89 0.00 3.02
171 172 3.883462 TGCGTAACAGATTGCCCG 58.117 55.556 0.00 0.00 0.00 6.13
172 173 2.395360 TGCGTAACAGATTGCCCGC 61.395 57.895 0.00 0.00 41.34 6.13
173 174 2.106683 GCGTAACAGATTGCCCGCT 61.107 57.895 0.00 0.00 38.22 5.52
174 175 0.808453 GCGTAACAGATTGCCCGCTA 60.808 55.000 0.00 0.00 38.22 4.26
175 176 1.865865 CGTAACAGATTGCCCGCTAT 58.134 50.000 0.00 0.00 0.00 2.97
176 177 1.526887 CGTAACAGATTGCCCGCTATG 59.473 52.381 0.00 0.00 0.00 2.23
177 178 2.801699 CGTAACAGATTGCCCGCTATGA 60.802 50.000 0.00 0.00 0.00 2.15
178 179 2.418368 AACAGATTGCCCGCTATGAA 57.582 45.000 0.00 0.00 0.00 2.57
179 180 1.668419 ACAGATTGCCCGCTATGAAC 58.332 50.000 0.00 0.00 0.00 3.18
180 181 0.583438 CAGATTGCCCGCTATGAACG 59.417 55.000 0.00 0.00 0.00 3.95
187 188 3.436001 CCGCTATGAACGGTGTCTT 57.564 52.632 0.00 0.00 45.70 3.01
188 189 1.278238 CCGCTATGAACGGTGTCTTC 58.722 55.000 0.00 0.00 45.70 2.87
189 190 1.135083 CCGCTATGAACGGTGTCTTCT 60.135 52.381 0.00 0.00 45.70 2.85
190 191 2.098607 CCGCTATGAACGGTGTCTTCTA 59.901 50.000 0.00 0.00 45.70 2.10
191 192 3.243434 CCGCTATGAACGGTGTCTTCTAT 60.243 47.826 0.00 0.00 45.70 1.98
192 193 4.360563 CGCTATGAACGGTGTCTTCTATT 58.639 43.478 0.00 0.00 0.00 1.73
193 194 4.804139 CGCTATGAACGGTGTCTTCTATTT 59.196 41.667 0.00 0.00 0.00 1.40
194 195 5.291128 CGCTATGAACGGTGTCTTCTATTTT 59.709 40.000 0.00 0.00 0.00 1.82
195 196 6.183360 CGCTATGAACGGTGTCTTCTATTTTT 60.183 38.462 0.00 0.00 0.00 1.94
196 197 7.180748 GCTATGAACGGTGTCTTCTATTTTTC 58.819 38.462 0.00 0.00 0.00 2.29
197 198 5.585500 TGAACGGTGTCTTCTATTTTTCG 57.415 39.130 0.00 0.00 0.00 3.46
198 199 5.051816 TGAACGGTGTCTTCTATTTTTCGT 58.948 37.500 0.00 0.00 0.00 3.85
199 200 5.176223 TGAACGGTGTCTTCTATTTTTCGTC 59.824 40.000 0.00 0.00 0.00 4.20
200 201 4.879598 ACGGTGTCTTCTATTTTTCGTCT 58.120 39.130 0.00 0.00 0.00 4.18
201 202 4.922103 ACGGTGTCTTCTATTTTTCGTCTC 59.078 41.667 0.00 0.00 0.00 3.36
202 203 4.921515 CGGTGTCTTCTATTTTTCGTCTCA 59.078 41.667 0.00 0.00 0.00 3.27
203 204 5.577164 CGGTGTCTTCTATTTTTCGTCTCAT 59.423 40.000 0.00 0.00 0.00 2.90
204 205 6.454318 CGGTGTCTTCTATTTTTCGTCTCATG 60.454 42.308 0.00 0.00 0.00 3.07
205 206 6.183360 GGTGTCTTCTATTTTTCGTCTCATGG 60.183 42.308 0.00 0.00 0.00 3.66
206 207 6.590292 GTGTCTTCTATTTTTCGTCTCATGGA 59.410 38.462 0.00 0.00 0.00 3.41
207 208 7.278868 GTGTCTTCTATTTTTCGTCTCATGGAT 59.721 37.037 0.00 0.00 0.00 3.41
208 209 7.278646 TGTCTTCTATTTTTCGTCTCATGGATG 59.721 37.037 0.00 0.00 0.00 3.51
209 210 5.991328 TCTATTTTTCGTCTCATGGATGC 57.009 39.130 0.00 0.00 0.00 3.91
210 211 5.427378 TCTATTTTTCGTCTCATGGATGCA 58.573 37.500 0.00 0.00 0.00 3.96
211 212 6.057533 TCTATTTTTCGTCTCATGGATGCAT 58.942 36.000 0.00 0.00 0.00 3.96
212 213 5.587388 ATTTTTCGTCTCATGGATGCATT 57.413 34.783 0.00 0.00 0.00 3.56
213 214 5.389859 TTTTTCGTCTCATGGATGCATTT 57.610 34.783 0.00 0.00 0.00 2.32
214 215 5.389859 TTTTCGTCTCATGGATGCATTTT 57.610 34.783 0.00 0.00 0.00 1.82
215 216 5.389859 TTTCGTCTCATGGATGCATTTTT 57.610 34.783 0.00 0.00 0.00 1.94
216 217 6.507958 TTTCGTCTCATGGATGCATTTTTA 57.492 33.333 0.00 0.00 0.00 1.52
217 218 5.484173 TCGTCTCATGGATGCATTTTTAC 57.516 39.130 0.00 0.00 0.00 2.01
218 219 4.335315 TCGTCTCATGGATGCATTTTTACC 59.665 41.667 0.00 0.00 0.00 2.85
219 220 4.096231 CGTCTCATGGATGCATTTTTACCA 59.904 41.667 0.00 3.17 35.09 3.25
220 221 5.221106 CGTCTCATGGATGCATTTTTACCAT 60.221 40.000 10.33 10.33 41.25 3.55
224 225 4.368874 TGGATGCATTTTTACCATGTCG 57.631 40.909 0.00 0.00 0.00 4.35
225 226 3.130164 TGGATGCATTTTTACCATGTCGG 59.870 43.478 0.00 0.00 42.50 4.79
242 243 8.560576 CCATGTCGGTTTAAATGTCATTATTC 57.439 34.615 0.00 0.00 0.00 1.75
243 244 7.647715 CCATGTCGGTTTAAATGTCATTATTCC 59.352 37.037 0.00 0.00 0.00 3.01
244 245 6.777101 TGTCGGTTTAAATGTCATTATTCCG 58.223 36.000 17.48 17.48 35.10 4.30
245 246 6.183360 TGTCGGTTTAAATGTCATTATTCCGG 60.183 38.462 20.53 0.00 34.83 5.14
246 247 5.881443 TCGGTTTAAATGTCATTATTCCGGT 59.119 36.000 20.53 0.00 34.83 5.28
247 248 7.011295 GTCGGTTTAAATGTCATTATTCCGGTA 59.989 37.037 20.53 0.00 34.83 4.02
248 249 7.011295 TCGGTTTAAATGTCATTATTCCGGTAC 59.989 37.037 20.53 0.00 34.83 3.34
270 271 9.730420 GGTACGATGCAAGAAAATATATTGTTT 57.270 29.630 0.00 0.00 0.00 2.83
273 274 9.075519 ACGATGCAAGAAAATATATTGTTTGTG 57.924 29.630 0.00 0.00 0.00 3.33
274 275 9.288124 CGATGCAAGAAAATATATTGTTTGTGA 57.712 29.630 0.00 0.00 0.00 3.58
288 289 7.661127 ATTGTTTGTGATGACAATGGAAATG 57.339 32.000 0.00 0.00 42.96 2.32
289 290 5.539979 TGTTTGTGATGACAATGGAAATGG 58.460 37.500 0.00 0.00 41.77 3.16
290 291 5.303845 TGTTTGTGATGACAATGGAAATGGA 59.696 36.000 0.00 0.00 41.77 3.41
291 292 6.183360 TGTTTGTGATGACAATGGAAATGGAA 60.183 34.615 0.00 0.00 41.77 3.53
292 293 5.648178 TGTGATGACAATGGAAATGGAAG 57.352 39.130 0.00 0.00 0.00 3.46
293 294 5.323581 TGTGATGACAATGGAAATGGAAGA 58.676 37.500 0.00 0.00 0.00 2.87
294 295 5.416639 TGTGATGACAATGGAAATGGAAGAG 59.583 40.000 0.00 0.00 0.00 2.85
295 296 4.400251 TGATGACAATGGAAATGGAAGAGC 59.600 41.667 0.00 0.00 0.00 4.09
296 297 3.765381 TGACAATGGAAATGGAAGAGCA 58.235 40.909 0.00 0.00 0.00 4.26
297 298 4.346730 TGACAATGGAAATGGAAGAGCAT 58.653 39.130 0.00 0.00 0.00 3.79
298 299 4.158949 TGACAATGGAAATGGAAGAGCATG 59.841 41.667 0.00 0.00 0.00 4.06
299 300 3.118884 ACAATGGAAATGGAAGAGCATGC 60.119 43.478 10.51 10.51 0.00 4.06
300 301 1.477553 TGGAAATGGAAGAGCATGCC 58.522 50.000 15.66 6.03 0.00 4.40
301 302 1.272592 TGGAAATGGAAGAGCATGCCA 60.273 47.619 15.66 4.89 35.91 4.92
302 303 1.135721 GGAAATGGAAGAGCATGCCAC 59.864 52.381 15.66 9.32 33.93 5.01
303 304 2.097825 GAAATGGAAGAGCATGCCACT 58.902 47.619 15.66 11.70 33.93 4.00
304 305 1.471119 AATGGAAGAGCATGCCACTG 58.529 50.000 15.66 0.00 33.93 3.66
305 306 0.330604 ATGGAAGAGCATGCCACTGT 59.669 50.000 15.66 5.62 33.93 3.55
306 307 0.983467 TGGAAGAGCATGCCACTGTA 59.017 50.000 15.66 2.28 0.00 2.74
307 308 1.350684 TGGAAGAGCATGCCACTGTAA 59.649 47.619 15.66 1.15 0.00 2.41
308 309 2.025981 TGGAAGAGCATGCCACTGTAAT 60.026 45.455 15.66 0.00 0.00 1.89
309 310 3.019564 GGAAGAGCATGCCACTGTAATT 58.980 45.455 15.66 0.00 0.00 1.40
310 311 3.065925 GGAAGAGCATGCCACTGTAATTC 59.934 47.826 15.66 8.11 0.00 2.17
311 312 3.354948 AGAGCATGCCACTGTAATTCA 57.645 42.857 15.66 0.00 0.00 2.57
312 313 3.689347 AGAGCATGCCACTGTAATTCAA 58.311 40.909 15.66 0.00 0.00 2.69
313 314 3.441572 AGAGCATGCCACTGTAATTCAAC 59.558 43.478 15.66 0.00 0.00 3.18
314 315 3.424703 AGCATGCCACTGTAATTCAACT 58.575 40.909 15.66 0.00 0.00 3.16
315 316 3.828451 AGCATGCCACTGTAATTCAACTT 59.172 39.130 15.66 0.00 0.00 2.66
316 317 4.281688 AGCATGCCACTGTAATTCAACTTT 59.718 37.500 15.66 0.00 0.00 2.66
317 318 4.990426 GCATGCCACTGTAATTCAACTTTT 59.010 37.500 6.36 0.00 0.00 2.27
318 319 5.466393 GCATGCCACTGTAATTCAACTTTTT 59.534 36.000 6.36 0.00 0.00 1.94
358 359 5.220209 CGTTGTTTCTTTGCTGGTTCTTTTC 60.220 40.000 0.00 0.00 0.00 2.29
359 360 4.420168 TGTTTCTTTGCTGGTTCTTTTCG 58.580 39.130 0.00 0.00 0.00 3.46
366 367 7.932335 TCTTTGCTGGTTCTTTTCGTTTATTA 58.068 30.769 0.00 0.00 0.00 0.98
368 374 6.004408 TGCTGGTTCTTTTCGTTTATTACC 57.996 37.500 0.00 0.00 0.00 2.85
378 384 9.997482 TCTTTTCGTTTATTACCTATCAATTGC 57.003 29.630 0.00 0.00 0.00 3.56
411 419 4.771590 TGTGAAAACCAGATCATTGCTC 57.228 40.909 0.00 0.00 0.00 4.26
412 420 4.143543 TGTGAAAACCAGATCATTGCTCA 58.856 39.130 0.00 0.00 0.00 4.26
413 421 4.583907 TGTGAAAACCAGATCATTGCTCAA 59.416 37.500 0.00 0.00 0.00 3.02
415 423 5.984926 GTGAAAACCAGATCATTGCTCAAAA 59.015 36.000 0.00 0.00 0.00 2.44
416 424 6.479660 GTGAAAACCAGATCATTGCTCAAAAA 59.520 34.615 0.00 0.00 0.00 1.94
417 425 6.479660 TGAAAACCAGATCATTGCTCAAAAAC 59.520 34.615 0.00 0.00 0.00 2.43
420 428 3.916172 CCAGATCATTGCTCAAAAACGTG 59.084 43.478 0.00 0.00 0.00 4.49
421 429 4.539870 CAGATCATTGCTCAAAAACGTGT 58.460 39.130 0.00 0.00 0.00 4.49
426 434 7.704472 AGATCATTGCTCAAAAACGTGTAAAAA 59.296 29.630 0.00 0.00 0.00 1.94
475 488 9.746711 CATCGCACATTTATTTTCTATAGTAGC 57.253 33.333 0.00 0.00 0.00 3.58
476 489 8.880878 TCGCACATTTATTTTCTATAGTAGCA 57.119 30.769 0.00 0.00 0.00 3.49
477 490 8.978539 TCGCACATTTATTTTCTATAGTAGCAG 58.021 33.333 0.00 0.00 0.00 4.24
478 491 8.765219 CGCACATTTATTTTCTATAGTAGCAGT 58.235 33.333 0.00 0.00 0.00 4.40
510 523 9.201989 ACTTCTTTTTGAGGACCTTTATTTTCT 57.798 29.630 0.00 0.00 0.00 2.52
519 532 5.482878 AGGACCTTTATTTTCTACCGACTCA 59.517 40.000 0.00 0.00 0.00 3.41
546 564 2.631160 TTTTGGAAGCACCGAGAGAA 57.369 45.000 0.00 0.00 42.61 2.87
588 606 0.179032 ACCTCGTGACACAATGGCAA 60.179 50.000 6.37 0.00 36.98 4.52
591 609 2.223688 CCTCGTGACACAATGGCAAAAA 60.224 45.455 6.37 0.00 36.98 1.94
592 610 3.044986 CTCGTGACACAATGGCAAAAAG 58.955 45.455 6.37 0.00 36.98 2.27
696 714 5.285401 TCAATCCAACTCCTATACCTTCCA 58.715 41.667 0.00 0.00 0.00 3.53
702 720 2.866454 ACTCCTATACCTTCCACCTCCT 59.134 50.000 0.00 0.00 0.00 3.69
703 721 3.117054 ACTCCTATACCTTCCACCTCCTC 60.117 52.174 0.00 0.00 0.00 3.71
917 937 2.746277 GCACGCCGGAATCCTGTT 60.746 61.111 5.05 0.00 0.00 3.16
918 938 2.750888 GCACGCCGGAATCCTGTTC 61.751 63.158 5.05 0.00 0.00 3.18
919 939 2.125673 ACGCCGGAATCCTGTTCG 60.126 61.111 5.05 0.00 0.00 3.95
921 941 3.202706 GCCGGAATCCTGTTCGCC 61.203 66.667 5.05 0.00 0.00 5.54
922 942 2.890474 CCGGAATCCTGTTCGCCG 60.890 66.667 0.00 0.00 41.53 6.46
924 944 3.564027 GGAATCCTGTTCGCCGCG 61.564 66.667 6.39 6.39 0.00 6.46
925 945 2.508439 GAATCCTGTTCGCCGCGA 60.508 61.111 12.39 12.39 0.00 5.87
940 961 2.875485 CGACACCGTCCGTCAGAT 59.125 61.111 0.00 0.00 32.72 2.90
953 974 1.900351 TCAGATTCTGACTGGCCGG 59.100 57.895 11.02 11.02 35.39 6.13
982 1003 4.951963 GCTAGATTCGCGGGCGCT 62.952 66.667 7.64 2.58 39.59 5.92
985 1006 2.131294 CTAGATTCGCGGGCGCTAGT 62.131 60.000 7.64 0.00 39.59 2.57
1484 1514 4.180946 CGCCCTCGACTCGTCCAG 62.181 72.222 0.00 0.00 38.10 3.86
1950 1980 1.675219 GTTCCGGAAGCAGTACCCA 59.325 57.895 19.50 0.00 0.00 4.51
2040 2070 0.681243 GGAAGGGGGTCACATTGCTC 60.681 60.000 0.00 0.00 0.00 4.26
2046 2076 0.743345 GGGTCACATTGCTCCCGTAC 60.743 60.000 0.00 0.00 0.00 3.67
2097 2127 1.595382 CGAGATCAATGGCGACCCC 60.595 63.158 0.00 0.00 0.00 4.95
2109 2139 2.987962 GACCCCGGAAAGGAGGAC 59.012 66.667 0.73 0.00 45.00 3.85
2115 2145 2.585153 GGAAAGGAGGACGAGGCC 59.415 66.667 0.00 0.00 0.00 5.19
2488 2518 2.233431 TGGTTTTGATTGCTGCCATACC 59.767 45.455 0.00 0.00 0.00 2.73
2499 2529 3.138098 TGCTGCCATACCCATTCAGAATA 59.862 43.478 0.00 0.00 0.00 1.75
2692 2732 2.745281 GCGTTTAACTGCATTCCCAGTA 59.255 45.455 6.95 0.00 44.86 2.74
2696 2736 6.386654 CGTTTAACTGCATTCCCAGTAAAAT 58.613 36.000 0.00 0.00 44.86 1.82
2815 2863 5.906113 TTTTTGTCAGGTAGTTCTTGCAA 57.094 34.783 0.00 0.00 0.00 4.08
2826 2874 5.221244 GGTAGTTCTTGCAACTCCATTTGTT 60.221 40.000 0.00 0.00 0.00 2.83
2828 2876 5.351458 AGTTCTTGCAACTCCATTTGTTTC 58.649 37.500 0.00 0.00 0.00 2.78
2883 2931 7.275888 TGTAGCAGTCAAATTGTTTCAGAAT 57.724 32.000 0.00 0.00 0.00 2.40
2888 2937 9.768662 AGCAGTCAAATTGTTTCAGAATTTTAT 57.231 25.926 0.00 0.00 31.96 1.40
2959 3008 1.963515 GTGGATTCTGTGGTGCCTTTT 59.036 47.619 0.00 0.00 0.00 2.27
2996 3050 0.251341 ACAAACCATGACCTCCTGGC 60.251 55.000 0.00 0.00 35.88 4.85
2997 3051 1.002134 AAACCATGACCTCCTGGCG 60.002 57.895 0.00 0.00 35.88 5.69
3025 3080 1.551430 TCCGCGGAACCTGAATTTCTA 59.449 47.619 28.99 0.00 0.00 2.10
3138 3195 8.339714 TGTAATTGCAGTAATCGGCTAATTTAC 58.660 33.333 0.00 0.00 35.86 2.01
3145 3204 7.186804 CAGTAATCGGCTAATTTACCAAGTTG 58.813 38.462 0.00 0.00 0.00 3.16
3218 3281 3.043713 AGACATGCGTGTGTGCCG 61.044 61.111 18.17 0.00 39.09 5.69
3230 3293 2.817834 GTGCCGGCGCTGTAATCA 60.818 61.111 32.27 2.34 35.36 2.57
3290 3353 5.588240 CCAGGTTTTGGTCTTTACTTCAAC 58.412 41.667 0.00 0.00 42.41 3.18
3297 3360 3.714798 TGGTCTTTACTTCAACTGAGGGT 59.285 43.478 0.00 0.00 0.00 4.34
3310 3373 3.778265 ACTGAGGGTATGCCAAATTTGT 58.222 40.909 16.73 1.39 36.17 2.83
3344 3407 0.893270 TGTGCGTTTGATTCTGGGGG 60.893 55.000 0.00 0.00 0.00 5.40
3356 3420 4.540099 TGATTCTGGGGGATGTTTCTAACT 59.460 41.667 0.00 0.00 0.00 2.24
3358 3422 4.301072 TCTGGGGGATGTTTCTAACTTG 57.699 45.455 0.00 0.00 0.00 3.16
3393 3457 4.947388 TGGTATGTCTGGCCTTATTTGTTC 59.053 41.667 3.32 0.00 0.00 3.18
3446 3510 4.939509 TTTCTTGCCAAAGATAGTACGC 57.060 40.909 0.00 0.00 42.04 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.302559 GGGTAAGATCATATTCACCCCC 57.697 50.000 0.00 0.00 39.83 5.40
24 25 6.893020 ATAGGGGTAAGATCATATTCACCC 57.107 41.667 0.00 0.00 44.11 4.61
25 26 7.988028 GCTTATAGGGGTAAGATCATATTCACC 59.012 40.741 0.00 0.00 34.34 4.02
26 27 8.540388 TGCTTATAGGGGTAAGATCATATTCAC 58.460 37.037 0.00 0.00 34.34 3.18
27 28 8.540388 GTGCTTATAGGGGTAAGATCATATTCA 58.460 37.037 0.00 0.00 34.34 2.57
28 29 7.988028 GGTGCTTATAGGGGTAAGATCATATTC 59.012 40.741 0.00 0.00 34.34 1.75
29 30 7.092399 GGGTGCTTATAGGGGTAAGATCATATT 60.092 40.741 0.00 0.00 34.34 1.28
30 31 6.387220 GGGTGCTTATAGGGGTAAGATCATAT 59.613 42.308 0.00 0.00 34.34 1.78
31 32 5.724854 GGGTGCTTATAGGGGTAAGATCATA 59.275 44.000 0.00 0.00 34.34 2.15
32 33 4.536489 GGGTGCTTATAGGGGTAAGATCAT 59.464 45.833 0.00 0.00 34.34 2.45
33 34 3.908103 GGGTGCTTATAGGGGTAAGATCA 59.092 47.826 0.00 0.00 34.34 2.92
34 35 3.263681 GGGGTGCTTATAGGGGTAAGATC 59.736 52.174 0.00 0.00 34.34 2.75
35 36 3.257578 GGGGTGCTTATAGGGGTAAGAT 58.742 50.000 0.00 0.00 34.34 2.40
36 37 2.697967 GGGGTGCTTATAGGGGTAAGA 58.302 52.381 0.00 0.00 34.34 2.10
37 38 1.703513 GGGGGTGCTTATAGGGGTAAG 59.296 57.143 0.00 0.00 35.31 2.34
38 39 1.823764 GGGGGTGCTTATAGGGGTAA 58.176 55.000 0.00 0.00 0.00 2.85
39 40 0.472352 CGGGGGTGCTTATAGGGGTA 60.472 60.000 0.00 0.00 0.00 3.69
40 41 1.768888 CGGGGGTGCTTATAGGGGT 60.769 63.158 0.00 0.00 0.00 4.95
41 42 1.460689 TCGGGGGTGCTTATAGGGG 60.461 63.158 0.00 0.00 0.00 4.79
42 43 0.471211 TCTCGGGGGTGCTTATAGGG 60.471 60.000 0.00 0.00 0.00 3.53
43 44 0.969894 CTCTCGGGGGTGCTTATAGG 59.030 60.000 0.00 0.00 0.00 2.57
44 45 1.614413 GTCTCTCGGGGGTGCTTATAG 59.386 57.143 0.00 0.00 0.00 1.31
45 46 1.217183 AGTCTCTCGGGGGTGCTTATA 59.783 52.381 0.00 0.00 0.00 0.98
46 47 0.032017 AGTCTCTCGGGGGTGCTTAT 60.032 55.000 0.00 0.00 0.00 1.73
47 48 0.627451 TAGTCTCTCGGGGGTGCTTA 59.373 55.000 0.00 0.00 0.00 3.09
48 49 0.252103 TTAGTCTCTCGGGGGTGCTT 60.252 55.000 0.00 0.00 0.00 3.91
49 50 0.684805 CTTAGTCTCTCGGGGGTGCT 60.685 60.000 0.00 0.00 0.00 4.40
50 51 0.683504 TCTTAGTCTCTCGGGGGTGC 60.684 60.000 0.00 0.00 0.00 5.01
51 52 1.751924 CTTCTTAGTCTCTCGGGGGTG 59.248 57.143 0.00 0.00 0.00 4.61
52 53 1.358445 ACTTCTTAGTCTCTCGGGGGT 59.642 52.381 0.00 0.00 0.00 4.95
53 54 2.146920 ACTTCTTAGTCTCTCGGGGG 57.853 55.000 0.00 0.00 0.00 5.40
54 55 3.510360 TGAAACTTCTTAGTCTCTCGGGG 59.490 47.826 0.00 0.00 31.99 5.73
55 56 4.785511 TGAAACTTCTTAGTCTCTCGGG 57.214 45.455 0.00 0.00 31.99 5.14
56 57 7.478520 TTTTTGAAACTTCTTAGTCTCTCGG 57.521 36.000 0.00 0.00 31.99 4.63
72 73 9.900710 GGTACACACATGTATGTATTTTTGAAA 57.099 29.630 19.30 0.00 43.21 2.69
73 74 8.516234 GGGTACACACATGTATGTATTTTTGAA 58.484 33.333 19.30 0.00 43.21 2.69
74 75 7.885922 AGGGTACACACATGTATGTATTTTTGA 59.114 33.333 19.30 0.00 43.21 2.69
75 76 8.050778 AGGGTACACACATGTATGTATTTTTG 57.949 34.615 19.30 0.00 43.21 2.44
76 77 8.644374 AAGGGTACACACATGTATGTATTTTT 57.356 30.769 19.30 11.06 43.21 1.94
77 78 8.644374 AAAGGGTACACACATGTATGTATTTT 57.356 30.769 19.30 15.98 43.21 1.82
78 79 8.644374 AAAAGGGTACACACATGTATGTATTT 57.356 30.769 19.30 13.01 43.21 1.40
79 80 8.519526 CAAAAAGGGTACACACATGTATGTATT 58.480 33.333 19.30 7.87 43.21 1.89
80 81 7.885922 TCAAAAAGGGTACACACATGTATGTAT 59.114 33.333 19.30 1.76 43.21 2.29
81 82 7.173562 GTCAAAAAGGGTACACACATGTATGTA 59.826 37.037 12.91 12.91 43.21 2.29
82 83 6.016610 GTCAAAAAGGGTACACACATGTATGT 60.017 38.462 15.18 15.18 43.21 2.29
83 84 6.206634 AGTCAAAAAGGGTACACACATGTATG 59.793 38.462 1.67 1.67 43.21 2.39
84 85 6.303839 AGTCAAAAAGGGTACACACATGTAT 58.696 36.000 0.00 0.00 43.21 2.29
85 86 5.686753 AGTCAAAAAGGGTACACACATGTA 58.313 37.500 0.00 0.00 40.48 2.29
86 87 4.532834 AGTCAAAAAGGGTACACACATGT 58.467 39.130 0.00 0.00 43.30 3.21
87 88 5.514274 AAGTCAAAAAGGGTACACACATG 57.486 39.130 0.00 0.00 0.00 3.21
88 89 4.274950 CGAAGTCAAAAAGGGTACACACAT 59.725 41.667 0.00 0.00 0.00 3.21
89 90 3.623960 CGAAGTCAAAAAGGGTACACACA 59.376 43.478 0.00 0.00 0.00 3.72
90 91 3.872771 TCGAAGTCAAAAAGGGTACACAC 59.127 43.478 0.00 0.00 0.00 3.82
91 92 4.139859 TCGAAGTCAAAAAGGGTACACA 57.860 40.909 0.00 0.00 0.00 3.72
92 93 5.065602 ACTTTCGAAGTCAAAAAGGGTACAC 59.934 40.000 0.00 0.00 37.02 2.90
93 94 5.187687 ACTTTCGAAGTCAAAAAGGGTACA 58.812 37.500 0.00 0.00 37.02 2.90
94 95 5.746307 ACTTTCGAAGTCAAAAAGGGTAC 57.254 39.130 0.00 0.00 37.02 3.34
116 117 3.767711 TGCTCACTAGGTCTCTGAAAGA 58.232 45.455 0.00 0.00 43.69 2.52
117 118 4.441356 GGATGCTCACTAGGTCTCTGAAAG 60.441 50.000 0.00 0.00 0.00 2.62
118 119 3.449018 GGATGCTCACTAGGTCTCTGAAA 59.551 47.826 0.00 0.00 0.00 2.69
119 120 3.027412 GGATGCTCACTAGGTCTCTGAA 58.973 50.000 0.00 0.00 0.00 3.02
120 121 2.660572 GGATGCTCACTAGGTCTCTGA 58.339 52.381 0.00 0.00 0.00 3.27
121 122 1.686052 GGGATGCTCACTAGGTCTCTG 59.314 57.143 0.00 0.00 0.00 3.35
122 123 1.573376 AGGGATGCTCACTAGGTCTCT 59.427 52.381 0.00 0.00 0.00 3.10
123 124 2.080654 AGGGATGCTCACTAGGTCTC 57.919 55.000 0.00 0.00 0.00 3.36
124 125 2.393646 GAAGGGATGCTCACTAGGTCT 58.606 52.381 0.00 0.00 24.29 3.85
125 126 1.067821 CGAAGGGATGCTCACTAGGTC 59.932 57.143 0.00 0.00 24.29 3.85
126 127 1.115467 CGAAGGGATGCTCACTAGGT 58.885 55.000 0.00 0.00 24.29 3.08
127 128 0.249657 GCGAAGGGATGCTCACTAGG 60.250 60.000 0.00 0.00 24.29 3.02
128 129 0.249657 GGCGAAGGGATGCTCACTAG 60.250 60.000 0.00 0.00 24.29 2.57
129 130 1.823295 GGCGAAGGGATGCTCACTA 59.177 57.895 0.00 0.00 24.29 2.74
130 131 2.586792 GGCGAAGGGATGCTCACT 59.413 61.111 0.00 0.00 0.00 3.41
131 132 2.892425 CGGCGAAGGGATGCTCAC 60.892 66.667 0.00 0.00 0.00 3.51
132 133 4.838152 GCGGCGAAGGGATGCTCA 62.838 66.667 12.98 0.00 0.00 4.26
136 137 3.564027 GAACGCGGCGAAGGGATG 61.564 66.667 30.94 0.00 0.00 3.51
137 138 3.771160 AGAACGCGGCGAAGGGAT 61.771 61.111 30.94 1.41 0.00 3.85
138 139 4.735132 CAGAACGCGGCGAAGGGA 62.735 66.667 30.94 0.00 0.00 4.20
153 154 1.715585 CGGGCAATCTGTTACGCAG 59.284 57.895 0.00 0.00 46.34 5.18
154 155 2.395360 GCGGGCAATCTGTTACGCA 61.395 57.895 0.00 0.00 45.57 5.24
155 156 0.808453 TAGCGGGCAATCTGTTACGC 60.808 55.000 0.00 0.00 46.50 4.42
156 157 1.526887 CATAGCGGGCAATCTGTTACG 59.473 52.381 0.00 0.00 0.00 3.18
157 158 2.833794 TCATAGCGGGCAATCTGTTAC 58.166 47.619 0.00 0.00 0.00 2.50
158 159 3.202906 GTTCATAGCGGGCAATCTGTTA 58.797 45.455 0.00 0.00 0.00 2.41
159 160 2.017049 GTTCATAGCGGGCAATCTGTT 58.983 47.619 0.00 0.00 0.00 3.16
160 161 1.668419 GTTCATAGCGGGCAATCTGT 58.332 50.000 0.00 0.00 0.00 3.41
161 162 0.583438 CGTTCATAGCGGGCAATCTG 59.417 55.000 0.00 0.00 0.00 2.90
162 163 0.532862 CCGTTCATAGCGGGCAATCT 60.533 55.000 0.00 0.00 44.98 2.40
163 164 1.941812 CCGTTCATAGCGGGCAATC 59.058 57.895 0.00 0.00 44.98 2.67
164 165 4.141144 CCGTTCATAGCGGGCAAT 57.859 55.556 0.00 0.00 44.98 3.56
170 171 2.279582 AGAAGACACCGTTCATAGCG 57.720 50.000 0.00 0.00 0.00 4.26
171 172 6.663944 AAAATAGAAGACACCGTTCATAGC 57.336 37.500 0.00 0.00 0.00 2.97
172 173 7.063074 ACGAAAAATAGAAGACACCGTTCATAG 59.937 37.037 0.00 0.00 0.00 2.23
173 174 6.869913 ACGAAAAATAGAAGACACCGTTCATA 59.130 34.615 0.00 0.00 0.00 2.15
174 175 5.699458 ACGAAAAATAGAAGACACCGTTCAT 59.301 36.000 0.00 0.00 0.00 2.57
175 176 5.051816 ACGAAAAATAGAAGACACCGTTCA 58.948 37.500 0.00 0.00 0.00 3.18
176 177 5.404667 AGACGAAAAATAGAAGACACCGTTC 59.595 40.000 0.00 0.00 0.00 3.95
177 178 5.295152 AGACGAAAAATAGAAGACACCGTT 58.705 37.500 0.00 0.00 0.00 4.44
178 179 4.879598 AGACGAAAAATAGAAGACACCGT 58.120 39.130 0.00 0.00 0.00 4.83
179 180 4.921515 TGAGACGAAAAATAGAAGACACCG 59.078 41.667 0.00 0.00 0.00 4.94
180 181 6.183360 CCATGAGACGAAAAATAGAAGACACC 60.183 42.308 0.00 0.00 0.00 4.16
181 182 6.590292 TCCATGAGACGAAAAATAGAAGACAC 59.410 38.462 0.00 0.00 0.00 3.67
182 183 6.697395 TCCATGAGACGAAAAATAGAAGACA 58.303 36.000 0.00 0.00 0.00 3.41
183 184 7.625553 CATCCATGAGACGAAAAATAGAAGAC 58.374 38.462 0.00 0.00 0.00 3.01
184 185 6.258727 GCATCCATGAGACGAAAAATAGAAGA 59.741 38.462 0.00 0.00 0.00 2.87
185 186 6.037500 TGCATCCATGAGACGAAAAATAGAAG 59.962 38.462 0.00 0.00 0.00 2.85
186 187 5.879777 TGCATCCATGAGACGAAAAATAGAA 59.120 36.000 0.00 0.00 0.00 2.10
187 188 5.427378 TGCATCCATGAGACGAAAAATAGA 58.573 37.500 0.00 0.00 0.00 1.98
188 189 5.739752 TGCATCCATGAGACGAAAAATAG 57.260 39.130 0.00 0.00 0.00 1.73
189 190 6.698008 AATGCATCCATGAGACGAAAAATA 57.302 33.333 0.00 0.00 0.00 1.40
190 191 5.587388 AATGCATCCATGAGACGAAAAAT 57.413 34.783 0.00 0.00 0.00 1.82
191 192 5.389859 AAATGCATCCATGAGACGAAAAA 57.610 34.783 0.00 0.00 0.00 1.94
192 193 5.389859 AAAATGCATCCATGAGACGAAAA 57.610 34.783 0.00 0.00 0.00 2.29
193 194 5.389859 AAAAATGCATCCATGAGACGAAA 57.610 34.783 0.00 0.00 0.00 3.46
194 195 5.163663 GGTAAAAATGCATCCATGAGACGAA 60.164 40.000 0.00 0.00 0.00 3.85
195 196 4.335315 GGTAAAAATGCATCCATGAGACGA 59.665 41.667 0.00 0.00 0.00 4.20
196 197 4.096231 TGGTAAAAATGCATCCATGAGACG 59.904 41.667 0.00 0.00 0.00 4.18
197 198 5.581126 TGGTAAAAATGCATCCATGAGAC 57.419 39.130 0.00 0.00 0.00 3.36
202 203 4.202141 CCGACATGGTAAAAATGCATCCAT 60.202 41.667 10.33 10.33 39.14 3.41
203 204 3.130164 CCGACATGGTAAAAATGCATCCA 59.870 43.478 0.00 2.56 0.00 3.41
204 205 3.705604 CCGACATGGTAAAAATGCATCC 58.294 45.455 0.00 0.00 0.00 3.51
217 218 7.647715 GGAATAATGACATTTAAACCGACATGG 59.352 37.037 5.89 0.00 46.41 3.66
218 219 7.375808 CGGAATAATGACATTTAAACCGACATG 59.624 37.037 20.47 0.00 36.68 3.21
219 220 7.414436 CGGAATAATGACATTTAAACCGACAT 58.586 34.615 20.47 0.00 36.68 3.06
220 221 6.183360 CCGGAATAATGACATTTAAACCGACA 60.183 38.462 23.79 2.19 36.68 4.35
221 222 6.183360 ACCGGAATAATGACATTTAAACCGAC 60.183 38.462 23.79 0.00 36.68 4.79
222 223 5.881443 ACCGGAATAATGACATTTAAACCGA 59.119 36.000 23.79 3.22 36.68 4.69
223 224 6.126568 ACCGGAATAATGACATTTAAACCG 57.873 37.500 9.46 19.24 35.55 4.44
224 225 7.011295 TCGTACCGGAATAATGACATTTAAACC 59.989 37.037 9.46 4.96 0.00 3.27
225 226 7.908230 TCGTACCGGAATAATGACATTTAAAC 58.092 34.615 9.46 0.00 0.00 2.01
226 227 8.552865 CATCGTACCGGAATAATGACATTTAAA 58.447 33.333 9.46 0.00 0.00 1.52
227 228 7.307514 GCATCGTACCGGAATAATGACATTTAA 60.308 37.037 9.46 0.00 0.00 1.52
228 229 6.146510 GCATCGTACCGGAATAATGACATTTA 59.853 38.462 9.46 0.00 0.00 1.40
229 230 5.049680 GCATCGTACCGGAATAATGACATTT 60.050 40.000 9.46 0.00 0.00 2.32
230 231 4.451096 GCATCGTACCGGAATAATGACATT 59.549 41.667 9.46 5.87 0.00 2.71
231 232 3.994392 GCATCGTACCGGAATAATGACAT 59.006 43.478 9.46 0.00 0.00 3.06
232 233 3.181474 TGCATCGTACCGGAATAATGACA 60.181 43.478 9.46 6.57 0.00 3.58
233 234 3.386486 TGCATCGTACCGGAATAATGAC 58.614 45.455 9.46 4.18 0.00 3.06
234 235 3.737032 TGCATCGTACCGGAATAATGA 57.263 42.857 9.46 1.53 0.00 2.57
235 236 4.055360 TCTTGCATCGTACCGGAATAATG 58.945 43.478 9.46 7.87 0.00 1.90
236 237 4.330944 TCTTGCATCGTACCGGAATAAT 57.669 40.909 9.46 0.00 0.00 1.28
237 238 3.804786 TCTTGCATCGTACCGGAATAA 57.195 42.857 9.46 0.00 0.00 1.40
238 239 3.804786 TTCTTGCATCGTACCGGAATA 57.195 42.857 9.46 0.00 0.00 1.75
239 240 2.684001 TTCTTGCATCGTACCGGAAT 57.316 45.000 9.46 0.00 0.00 3.01
240 241 2.459060 TTTCTTGCATCGTACCGGAA 57.541 45.000 9.46 0.00 0.00 4.30
241 242 2.459060 TTTTCTTGCATCGTACCGGA 57.541 45.000 9.46 0.00 0.00 5.14
242 243 6.721571 ATATATTTTCTTGCATCGTACCGG 57.278 37.500 0.00 0.00 0.00 5.28
243 244 7.572759 ACAATATATTTTCTTGCATCGTACCG 58.427 34.615 0.00 0.00 0.00 4.02
244 245 9.730420 AAACAATATATTTTCTTGCATCGTACC 57.270 29.630 0.00 0.00 0.00 3.34
247 248 9.075519 CACAAACAATATATTTTCTTGCATCGT 57.924 29.630 0.00 0.00 0.00 3.73
248 249 9.288124 TCACAAACAATATATTTTCTTGCATCG 57.712 29.630 0.00 0.00 0.00 3.84
262 263 9.373603 CATTTCCATTGTCATCACAAACAATAT 57.626 29.630 0.00 0.00 45.78 1.28
263 264 7.818446 CCATTTCCATTGTCATCACAAACAATA 59.182 33.333 0.00 0.00 45.78 1.90
264 265 6.651643 CCATTTCCATTGTCATCACAAACAAT 59.348 34.615 0.00 0.00 45.78 2.71
265 266 5.990386 CCATTTCCATTGTCATCACAAACAA 59.010 36.000 0.00 0.00 45.78 2.83
266 267 5.303845 TCCATTTCCATTGTCATCACAAACA 59.696 36.000 0.00 0.00 45.78 2.83
267 268 5.782047 TCCATTTCCATTGTCATCACAAAC 58.218 37.500 0.00 0.00 45.78 2.93
268 269 6.267242 TCTTCCATTTCCATTGTCATCACAAA 59.733 34.615 0.00 0.00 45.78 2.83
269 270 5.774184 TCTTCCATTTCCATTGTCATCACAA 59.226 36.000 0.00 0.00 46.71 3.33
270 271 5.323581 TCTTCCATTTCCATTGTCATCACA 58.676 37.500 0.00 0.00 0.00 3.58
271 272 5.678107 GCTCTTCCATTTCCATTGTCATCAC 60.678 44.000 0.00 0.00 0.00 3.06
272 273 4.400251 GCTCTTCCATTTCCATTGTCATCA 59.600 41.667 0.00 0.00 0.00 3.07
273 274 4.400251 TGCTCTTCCATTTCCATTGTCATC 59.600 41.667 0.00 0.00 0.00 2.92
274 275 4.346730 TGCTCTTCCATTTCCATTGTCAT 58.653 39.130 0.00 0.00 0.00 3.06
275 276 3.765381 TGCTCTTCCATTTCCATTGTCA 58.235 40.909 0.00 0.00 0.00 3.58
276 277 4.679662 CATGCTCTTCCATTTCCATTGTC 58.320 43.478 0.00 0.00 0.00 3.18
277 278 3.118884 GCATGCTCTTCCATTTCCATTGT 60.119 43.478 11.37 0.00 0.00 2.71
278 279 3.454375 GCATGCTCTTCCATTTCCATTG 58.546 45.455 11.37 0.00 0.00 2.82
279 280 2.433239 GGCATGCTCTTCCATTTCCATT 59.567 45.455 18.92 0.00 0.00 3.16
280 281 2.037144 GGCATGCTCTTCCATTTCCAT 58.963 47.619 18.92 0.00 0.00 3.41
281 282 1.272592 TGGCATGCTCTTCCATTTCCA 60.273 47.619 18.92 0.00 0.00 3.53
282 283 1.135721 GTGGCATGCTCTTCCATTTCC 59.864 52.381 18.92 0.00 31.83 3.13
283 284 2.097825 AGTGGCATGCTCTTCCATTTC 58.902 47.619 18.92 0.00 31.83 2.17
284 285 1.822990 CAGTGGCATGCTCTTCCATTT 59.177 47.619 18.92 0.00 31.83 2.32
285 286 1.272313 ACAGTGGCATGCTCTTCCATT 60.272 47.619 18.92 0.00 31.83 3.16
286 287 0.330604 ACAGTGGCATGCTCTTCCAT 59.669 50.000 18.92 0.00 31.83 3.41
287 288 0.983467 TACAGTGGCATGCTCTTCCA 59.017 50.000 18.92 3.25 0.00 3.53
288 289 2.113860 TTACAGTGGCATGCTCTTCC 57.886 50.000 18.92 0.10 0.00 3.46
289 290 3.691118 TGAATTACAGTGGCATGCTCTTC 59.309 43.478 18.92 10.45 0.00 2.87
290 291 3.689347 TGAATTACAGTGGCATGCTCTT 58.311 40.909 18.92 9.59 0.00 2.85
291 292 3.354948 TGAATTACAGTGGCATGCTCT 57.645 42.857 18.92 13.41 0.00 4.09
292 293 3.441572 AGTTGAATTACAGTGGCATGCTC 59.558 43.478 18.92 11.26 0.00 4.26
293 294 3.424703 AGTTGAATTACAGTGGCATGCT 58.575 40.909 18.92 0.00 0.00 3.79
294 295 3.855689 AGTTGAATTACAGTGGCATGC 57.144 42.857 9.90 9.90 0.00 4.06
320 321 9.658475 CAAAGAAACAACGAATACTGATGTTAA 57.342 29.630 0.00 0.00 33.39 2.01
321 322 7.801315 GCAAAGAAACAACGAATACTGATGTTA 59.199 33.333 0.00 0.00 33.39 2.41
322 323 6.636850 GCAAAGAAACAACGAATACTGATGTT 59.363 34.615 0.00 0.00 35.86 2.71
323 324 6.017109 AGCAAAGAAACAACGAATACTGATGT 60.017 34.615 0.00 0.00 0.00 3.06
324 325 6.303970 CAGCAAAGAAACAACGAATACTGATG 59.696 38.462 0.00 0.00 0.00 3.07
325 326 6.373779 CAGCAAAGAAACAACGAATACTGAT 58.626 36.000 0.00 0.00 0.00 2.90
326 327 5.277779 CCAGCAAAGAAACAACGAATACTGA 60.278 40.000 0.00 0.00 0.00 3.41
327 328 4.911610 CCAGCAAAGAAACAACGAATACTG 59.088 41.667 0.00 0.00 0.00 2.74
328 329 4.578928 ACCAGCAAAGAAACAACGAATACT 59.421 37.500 0.00 0.00 0.00 2.12
339 340 4.712122 ACGAAAAGAACCAGCAAAGAAA 57.288 36.364 0.00 0.00 0.00 2.52
342 343 7.114388 GGTAATAAACGAAAAGAACCAGCAAAG 59.886 37.037 0.00 0.00 0.00 2.77
391 397 4.771590 TGAGCAATGATCTGGTTTTCAC 57.228 40.909 0.00 0.00 0.00 3.18
392 398 5.787953 TTTGAGCAATGATCTGGTTTTCA 57.212 34.783 0.00 0.00 0.00 2.69
393 399 6.346040 CGTTTTTGAGCAATGATCTGGTTTTC 60.346 38.462 0.00 0.00 0.00 2.29
396 404 4.037923 ACGTTTTTGAGCAATGATCTGGTT 59.962 37.500 0.00 0.00 0.00 3.67
428 436 7.433719 GCGATGATTATATGCGTATTTCTCTCT 59.566 37.037 3.23 0.00 0.00 3.10
435 448 6.908870 ATGTGCGATGATTATATGCGTATT 57.091 33.333 3.23 0.00 0.00 1.89
472 485 9.251440 TCCTCAAAAAGAAGTATAGTACTGCTA 57.749 33.333 5.39 0.00 44.01 3.49
473 486 8.035984 GTCCTCAAAAAGAAGTATAGTACTGCT 58.964 37.037 5.39 0.00 46.80 4.24
474 487 7.278203 GGTCCTCAAAAAGAAGTATAGTACTGC 59.722 40.741 5.39 0.00 39.39 4.40
475 488 8.532819 AGGTCCTCAAAAAGAAGTATAGTACTG 58.467 37.037 5.39 0.00 39.39 2.74
476 489 8.667592 AGGTCCTCAAAAAGAAGTATAGTACT 57.332 34.615 0.00 0.00 41.73 2.73
477 490 9.722184 AAAGGTCCTCAAAAAGAAGTATAGTAC 57.278 33.333 0.00 0.00 0.00 2.73
493 506 5.482878 AGTCGGTAGAAAATAAAGGTCCTCA 59.517 40.000 0.00 0.00 0.00 3.86
510 523 7.520937 GCTTCCAAAAATAAAGTTGAGTCGGTA 60.521 37.037 0.00 0.00 0.00 4.02
519 532 5.300792 TCTCGGTGCTTCCAAAAATAAAGTT 59.699 36.000 0.00 0.00 35.57 2.66
569 587 0.179032 TTGCCATTGTGTCACGAGGT 60.179 50.000 4.26 0.00 0.00 3.85
588 606 1.897133 GGTTGCCCGGAATTACCTTTT 59.103 47.619 0.73 0.00 36.31 2.27
591 609 1.305287 GGGTTGCCCGGAATTACCT 59.695 57.895 0.73 0.00 32.13 3.08
592 610 1.755395 GGGGTTGCCCGGAATTACC 60.755 63.158 0.73 4.61 46.66 2.85
673 691 5.130477 GTGGAAGGTATAGGAGTTGGATTGA 59.870 44.000 0.00 0.00 0.00 2.57
696 714 4.698625 ACGGCGAAGGGAGGAGGT 62.699 66.667 16.62 0.00 0.00 3.85
902 920 2.125673 CGAACAGGATTCCGGCGT 60.126 61.111 6.01 0.00 0.00 5.68
906 926 3.564027 GCGGCGAACAGGATTCCG 61.564 66.667 12.98 0.00 42.68 4.30
907 927 3.564027 CGCGGCGAACAGGATTCC 61.564 66.667 19.16 0.00 0.00 3.01
909 929 2.813908 GTCGCGGCGAACAGGATT 60.814 61.111 28.14 0.00 37.72 3.01
922 942 2.814183 AATCTGACGGACGGTGTCGC 62.814 60.000 0.00 0.00 39.22 5.19
924 944 0.526662 AGAATCTGACGGACGGTGTC 59.473 55.000 0.00 0.00 36.88 3.67
925 945 0.243907 CAGAATCTGACGGACGGTGT 59.756 55.000 3.77 0.00 32.44 4.16
982 1003 0.981183 ATGCCGACCTCAACCAACTA 59.019 50.000 0.00 0.00 0.00 2.24
985 1006 1.303236 CCATGCCGACCTCAACCAA 60.303 57.895 0.00 0.00 0.00 3.67
989 1010 2.268920 GCTCCATGCCGACCTCAA 59.731 61.111 0.00 0.00 35.15 3.02
1422 1452 2.490685 GAGGACTCGAACGGGAGC 59.509 66.667 0.00 0.00 37.57 4.70
1425 1455 3.198582 GAGGAGGACTCGAACGGG 58.801 66.667 0.00 0.00 36.29 5.28
1950 1980 1.134220 TCGAAGGTGTGGTTCTGCTTT 60.134 47.619 0.00 0.00 0.00 3.51
2046 2076 3.976701 ATTCTTGACCCAGGCGGCG 62.977 63.158 0.51 0.51 33.26 6.46
2097 2127 2.184579 GCCTCGTCCTCCTTTCCG 59.815 66.667 0.00 0.00 0.00 4.30
2196 2226 3.676091 CCACTCGGCGAAATCAAAC 57.324 52.632 12.13 0.00 0.00 2.93
2391 2421 6.827251 ACTCCTCGTATGTGTTCTGATACTTA 59.173 38.462 0.00 0.00 0.00 2.24
2488 2518 5.791666 TCTATCTGCAGCTATTCTGAATGG 58.208 41.667 9.47 11.03 45.72 3.16
2499 2529 2.374184 AGTCGAACTCTATCTGCAGCT 58.626 47.619 9.47 0.82 0.00 4.24
2662 2702 3.468770 TGCAGTTAAACGCTACCTTTCA 58.531 40.909 0.00 0.00 0.00 2.69
2692 2732 3.508744 ATCGCAATCCGCAGAAATTTT 57.491 38.095 0.00 0.00 42.60 1.82
2696 2736 1.164411 ACAATCGCAATCCGCAGAAA 58.836 45.000 0.00 0.00 42.60 2.52
2763 2803 3.404899 GGAAGTGAACATGGTTTCGGTA 58.595 45.455 0.00 0.00 0.00 4.02
2764 2804 2.227194 GGAAGTGAACATGGTTTCGGT 58.773 47.619 0.00 0.00 0.00 4.69
2772 2819 2.566833 TCACAGGGGAAGTGAACATG 57.433 50.000 0.00 0.00 42.57 3.21
2815 2863 2.297033 AGCGCAATGAAACAAATGGAGT 59.703 40.909 11.47 0.00 0.00 3.85
2826 2874 3.688673 TGTGATGAACATAGCGCAATGAA 59.311 39.130 11.47 0.00 32.36 2.57
2828 2876 3.678915 TGTGATGAACATAGCGCAATG 57.321 42.857 11.47 0.00 32.36 2.82
2888 2937 2.233676 CAGTATACAGTCTGGCACACCA 59.766 50.000 5.50 0.00 46.51 4.17
2906 2955 2.884639 CGGTTTTCTTCACCCATTCAGT 59.115 45.455 0.00 0.00 0.00 3.41
2959 3008 3.490439 TGTTGAGAGTCATGGCAGAAA 57.510 42.857 0.00 0.00 0.00 2.52
3025 3080 6.413052 AGAACAGAGCAACATGACTGAATAT 58.587 36.000 0.00 0.00 34.88 1.28
3035 3090 2.157738 GCTTGGAGAACAGAGCAACAT 58.842 47.619 0.00 0.00 35.04 2.71
3130 3187 8.777865 TCAGATCAGTCAACTTGGTAAATTAG 57.222 34.615 0.00 0.00 0.00 1.73
3186 3248 2.268762 TGTCTGCACCAACATAGCAA 57.731 45.000 0.00 0.00 37.89 3.91
3187 3249 2.086094 CATGTCTGCACCAACATAGCA 58.914 47.619 4.73 0.00 34.42 3.49
3218 3281 0.308993 GCTTGGATGATTACAGCGCC 59.691 55.000 2.29 0.00 32.75 6.53
3230 3293 3.393609 TGCAGGAGAATAGATGCTTGGAT 59.606 43.478 0.00 0.00 39.42 3.41
3279 3342 4.636206 GGCATACCCTCAGTTGAAGTAAAG 59.364 45.833 0.00 0.00 0.00 1.85
3286 3349 3.737559 ATTTGGCATACCCTCAGTTGA 57.262 42.857 0.00 0.00 33.59 3.18
3290 3353 3.676873 GCACAAATTTGGCATACCCTCAG 60.677 47.826 21.74 0.00 33.59 3.35
3297 3360 1.993542 CAGCGCACAAATTTGGCATA 58.006 45.000 21.74 0.00 0.00 3.14
3335 3398 5.264395 CAAGTTAGAAACATCCCCCAGAAT 58.736 41.667 0.00 0.00 0.00 2.40
3338 3401 3.245264 ACCAAGTTAGAAACATCCCCCAG 60.245 47.826 0.00 0.00 0.00 4.45
3344 3407 7.824779 AGTATCTTCCACCAAGTTAGAAACATC 59.175 37.037 0.00 0.00 33.27 3.06
3356 3420 5.030147 AGACATACCAGTATCTTCCACCAA 58.970 41.667 0.00 0.00 0.00 3.67
3358 3422 4.202264 CCAGACATACCAGTATCTTCCACC 60.202 50.000 0.00 0.00 0.00 4.61
3446 3510 0.611896 ATTCCAGGGCCAAAAGGACG 60.612 55.000 6.18 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.