Multiple sequence alignment - TraesCS1D01G300800

Loading Multiple Alignment...

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 TraesCS1D01G300800 chr1D 100.000 2585 0 0 1 2585 398867058 398864474 0.000000e+00 4774.0
1 TraesCS1D01G300800 chr1D 95.311 917 37 2 711 1627 278102166 278101256 0.000000e+00 1450.0
2 TraesCS1D01G300800 chr1D 92.683 287 18 3 436 719 424634899 424635185 6.660000e-111 411.0
3 TraesCS1D01G300800 chr2D 93.257 1216 48 17 444 1627 236134841 236136054 0.000000e+00 1760.0
4 TraesCS1D01G300800 chr2D 97.077 958 27 1 1628 2585 565582310 565581354 0.000000e+00 1613.0
5 TraesCS1D01G300800 chr2D 95.616 958 42 0 1628 2585 194422052 194421095 0.000000e+00 1537.0
6 TraesCS1D01G300800 chr2D 94.896 960 45 3 1628 2585 395447602 395446645 0.000000e+00 1498.0
7 TraesCS1D01G300800 chr2D 94.792 960 46 3 1627 2585 146135463 146136419 0.000000e+00 1493.0
8 TraesCS1D01G300800 chr2D 94.984 917 44 2 711 1627 350066313 350067227 0.000000e+00 1437.0
9 TraesCS1D01G300800 chr2D 94.600 926 48 2 703 1627 619798636 619797712 0.000000e+00 1432.0
10 TraesCS1D01G300800 chr3B 93.103 1189 74 7 444 1627 618438688 618437503 0.000000e+00 1735.0
11 TraesCS1D01G300800 chr3B 95.862 145 5 1 220 364 41644950 41644807 1.550000e-57 233.0
12 TraesCS1D01G300800 chr3B 90.411 146 14 0 219 364 141825639 141825784 2.630000e-45 193.0
13 TraesCS1D01G300800 chr7D 96.455 959 33 1 1628 2585 290462580 290461622 0.000000e+00 1581.0
14 TraesCS1D01G300800 chr7D 94.781 958 49 1 1628 2585 387867128 387868084 0.000000e+00 1491.0
15 TraesCS1D01G300800 chr7D 93.885 278 15 2 444 719 18554230 18553953 3.980000e-113 418.0
16 TraesCS1D01G300800 chr7D 92.908 282 18 2 440 719 54236974 54237255 2.390000e-110 409.0
17 TraesCS1D01G300800 chr4D 96.354 960 31 3 1628 2585 403525136 403524179 0.000000e+00 1576.0
18 TraesCS1D01G300800 chr4D 93.885 278 13 4 444 719 486565780 486565505 1.430000e-112 416.0
19 TraesCS1D01G300800 chr4D 92.606 284 19 2 438 719 419345997 419346280 8.610000e-110 407.0
20 TraesCS1D01G300800 chr4D 99.306 144 1 0 221 364 500090557 500090414 7.090000e-66 261.0
21 TraesCS1D01G300800 chr3D 96.029 957 37 1 1630 2585 466253039 466252083 0.000000e+00 1555.0
22 TraesCS1D01G300800 chr3D 95.202 917 44 0 711 1627 553937052 553936136 0.000000e+00 1450.0
23 TraesCS1D01G300800 chr3D 95.093 917 44 1 711 1627 1283615 1282700 0.000000e+00 1443.0
24 TraesCS1D01G300800 chr3D 94.995 919 41 2 711 1629 580656661 580657574 0.000000e+00 1437.0
25 TraesCS1D01G300800 chr3D 88.019 626 49 15 444 1044 562634781 562635405 0.000000e+00 717.0
26 TraesCS1D01G300800 chr5D 95.407 958 44 0 1625 2582 1655022 1655979 0.000000e+00 1526.0
27 TraesCS1D01G300800 chr5D 93.502 277 17 1 444 719 179972953 179972677 6.660000e-111 411.0
28 TraesCS1D01G300800 chr6D 95.856 917 37 1 711 1627 449137757 449136842 0.000000e+00 1482.0
29 TraesCS1D01G300800 chr2B 93.502 277 16 2 444 719 396181959 396181684 6.660000e-111 411.0
30 TraesCS1D01G300800 chr6B 95.946 148 4 2 218 364 545612895 545612749 3.320000e-59 239.0
31 TraesCS1D01G300800 chr6A 95.775 142 5 1 223 364 50040004 50039864 7.200000e-56 228.0
32 TraesCS1D01G300800 chr6A 90.141 142 14 0 221 362 61676433 61676292 4.390000e-43 185.0
33 TraesCS1D01G300800 chr7B 93.243 148 7 1 220 364 115389161 115389014 5.600000e-52 215.0
34 TraesCS1D01G300800 chr1A 93.289 149 5 2 220 364 577704724 577704577 5.600000e-52 215.0
35 TraesCS1D01G300800 chr7A 90.780 141 12 1 222 362 280824474 280824613 1.220000e-43 187.0
36 TraesCS1D01G300800 chr5B 96.774 31 1 0 370 400 441809871 441809901 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G300800 chr1D 398864474 398867058 2584 True 4774 4774 100.000 1 2585 1 chr1D.!!$R2 2584
1 TraesCS1D01G300800 chr1D 278101256 278102166 910 True 1450 1450 95.311 711 1627 1 chr1D.!!$R1 916
2 TraesCS1D01G300800 chr2D 236134841 236136054 1213 False 1760 1760 93.257 444 1627 1 chr2D.!!$F2 1183
3 TraesCS1D01G300800 chr2D 565581354 565582310 956 True 1613 1613 97.077 1628 2585 1 chr2D.!!$R3 957
4 TraesCS1D01G300800 chr2D 194421095 194422052 957 True 1537 1537 95.616 1628 2585 1 chr2D.!!$R1 957
5 TraesCS1D01G300800 chr2D 395446645 395447602 957 True 1498 1498 94.896 1628 2585 1 chr2D.!!$R2 957
6 TraesCS1D01G300800 chr2D 146135463 146136419 956 False 1493 1493 94.792 1627 2585 1 chr2D.!!$F1 958
7 TraesCS1D01G300800 chr2D 350066313 350067227 914 False 1437 1437 94.984 711 1627 1 chr2D.!!$F3 916
8 TraesCS1D01G300800 chr2D 619797712 619798636 924 True 1432 1432 94.600 703 1627 1 chr2D.!!$R4 924
9 TraesCS1D01G300800 chr3B 618437503 618438688 1185 True 1735 1735 93.103 444 1627 1 chr3B.!!$R2 1183
10 TraesCS1D01G300800 chr7D 290461622 290462580 958 True 1581 1581 96.455 1628 2585 1 chr7D.!!$R2 957
11 TraesCS1D01G300800 chr7D 387867128 387868084 956 False 1491 1491 94.781 1628 2585 1 chr7D.!!$F2 957
12 TraesCS1D01G300800 chr4D 403524179 403525136 957 True 1576 1576 96.354 1628 2585 1 chr4D.!!$R1 957
13 TraesCS1D01G300800 chr3D 466252083 466253039 956 True 1555 1555 96.029 1630 2585 1 chr3D.!!$R2 955
14 TraesCS1D01G300800 chr3D 553936136 553937052 916 True 1450 1450 95.202 711 1627 1 chr3D.!!$R3 916
15 TraesCS1D01G300800 chr3D 1282700 1283615 915 True 1443 1443 95.093 711 1627 1 chr3D.!!$R1 916
16 TraesCS1D01G300800 chr3D 580656661 580657574 913 False 1437 1437 94.995 711 1629 1 chr3D.!!$F2 918
17 TraesCS1D01G300800 chr3D 562634781 562635405 624 False 717 717 88.019 444 1044 1 chr3D.!!$F1 600
18 TraesCS1D01G300800 chr5D 1655022 1655979 957 False 1526 1526 95.407 1625 2582 1 chr5D.!!$F1 957
19 TraesCS1D01G300800 chr6D 449136842 449137757 915 True 1482 1482 95.856 711 1627 1 chr6D.!!$R1 916

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
176 177 0.028242 CCGATGAGAGGACGAAGACG 59.972 60.0 0.0 0.00 45.75 4.18 F
442 443 0.108186 TCGACGGTTCGCTACCTAGA 60.108 55.0 0.0 0.17 45.40 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1339 0.111061 ACATGGCCACTTGCTCTTCA 59.889 50.0 8.16 0.00 40.92 3.02 R
1991 2044 0.759436 GGTTCGGGCCCTCTCTATGA 60.759 60.0 22.43 4.41 0.00 2.15 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
35 36 8.697846 CGTATTGGATATTGGATACGTAATGT 57.302 34.615 0.00 0.00 41.22 2.71
36 37 8.804743 CGTATTGGATATTGGATACGTAATGTC 58.195 37.037 0.00 0.00 41.22 3.06
37 38 9.095065 GTATTGGATATTGGATACGTAATGTCC 57.905 37.037 14.39 14.39 41.93 4.02
38 39 6.928348 TGGATATTGGATACGTAATGTCCT 57.072 37.500 19.26 4.23 42.02 3.85
39 40 6.697395 TGGATATTGGATACGTAATGTCCTG 58.303 40.000 19.26 0.00 42.02 3.86
40 41 5.581085 GGATATTGGATACGTAATGTCCTGC 59.419 44.000 14.12 0.00 39.83 4.85
41 42 3.897141 TTGGATACGTAATGTCCTGCA 57.103 42.857 13.46 0.00 39.36 4.41
42 43 3.173668 TGGATACGTAATGTCCTGCAC 57.826 47.619 13.46 0.00 39.36 4.57
43 44 2.764010 TGGATACGTAATGTCCTGCACT 59.236 45.455 13.46 0.00 39.36 4.40
44 45 3.181479 TGGATACGTAATGTCCTGCACTC 60.181 47.826 13.46 0.00 39.36 3.51
45 46 3.181479 GGATACGTAATGTCCTGCACTCA 60.181 47.826 0.00 0.00 35.70 3.41
46 47 2.080286 ACGTAATGTCCTGCACTCAC 57.920 50.000 0.00 0.00 0.00 3.51
47 48 1.343142 ACGTAATGTCCTGCACTCACA 59.657 47.619 0.00 0.00 0.00 3.58
48 49 2.028112 ACGTAATGTCCTGCACTCACAT 60.028 45.455 0.00 0.00 31.90 3.21
49 50 3.194755 ACGTAATGTCCTGCACTCACATA 59.805 43.478 0.00 0.00 30.37 2.29
50 51 3.551890 CGTAATGTCCTGCACTCACATAC 59.448 47.826 1.75 0.78 30.37 2.39
51 52 2.299993 ATGTCCTGCACTCACATACG 57.700 50.000 0.00 0.00 0.00 3.06
52 53 0.966179 TGTCCTGCACTCACATACGT 59.034 50.000 0.00 0.00 0.00 3.57
53 54 2.164338 TGTCCTGCACTCACATACGTA 58.836 47.619 0.00 0.00 0.00 3.57
54 55 2.758423 TGTCCTGCACTCACATACGTAT 59.242 45.455 1.14 1.14 0.00 3.06
55 56 3.181490 TGTCCTGCACTCACATACGTATC 60.181 47.826 4.74 0.00 0.00 2.24
56 57 3.020984 TCCTGCACTCACATACGTATCA 58.979 45.455 4.74 0.00 0.00 2.15
57 58 3.116300 CCTGCACTCACATACGTATCAC 58.884 50.000 4.74 0.00 0.00 3.06
71 72 4.288132 CGTATCACGTATTGCCGTATTG 57.712 45.455 0.00 0.00 39.45 1.90
72 73 3.421312 CGTATCACGTATTGCCGTATTGC 60.421 47.826 0.00 0.00 39.45 3.56
73 74 1.292061 TCACGTATTGCCGTATTGCC 58.708 50.000 0.00 0.00 39.45 4.52
74 75 0.042535 CACGTATTGCCGTATTGCCG 60.043 55.000 0.00 0.00 39.45 5.69
97 98 3.187058 CGGGTTGCCGGATTTCTG 58.813 61.111 5.05 0.00 0.00 3.02
98 99 2.885113 GGGTTGCCGGATTTCTGC 59.115 61.111 5.05 0.00 0.00 4.26
99 100 2.485122 GGTTGCCGGATTTCTGCG 59.515 61.111 5.05 0.00 35.77 5.18
100 101 2.202479 GTTGCCGGATTTCTGCGC 60.202 61.111 5.05 0.00 34.49 6.09
101 102 3.798650 TTGCCGGATTTCTGCGCG 61.799 61.111 5.05 0.00 34.49 6.86
103 104 2.888534 GCCGGATTTCTGCGCGTA 60.889 61.111 5.05 0.71 34.49 4.42
104 105 2.871427 GCCGGATTTCTGCGCGTAG 61.871 63.158 18.85 18.85 34.49 3.51
124 125 4.980805 GTGACAACCAGCGGCCGA 62.981 66.667 33.48 0.00 0.00 5.54
125 126 4.680237 TGACAACCAGCGGCCGAG 62.680 66.667 33.48 20.67 0.00 4.63
148 149 4.933064 GAGCGACGGGCCGATGAG 62.933 72.222 35.78 20.21 45.17 2.90
151 152 4.907034 CGACGGGCCGATGAGACG 62.907 72.222 35.78 21.39 0.00 4.18
152 153 3.515286 GACGGGCCGATGAGACGA 61.515 66.667 35.78 0.00 35.09 4.20
153 154 3.753070 GACGGGCCGATGAGACGAC 62.753 68.421 35.78 7.88 35.09 4.34
154 155 4.907034 CGGGCCGATGAGACGACG 62.907 72.222 24.41 0.00 35.09 5.12
155 156 3.515286 GGGCCGATGAGACGACGA 61.515 66.667 0.00 0.00 35.09 4.20
156 157 2.024871 GGCCGATGAGACGACGAG 59.975 66.667 0.00 0.00 35.09 4.18
157 158 2.652496 GCCGATGAGACGACGAGC 60.652 66.667 0.00 0.00 35.09 5.03
158 159 2.024871 CCGATGAGACGACGAGCC 59.975 66.667 0.00 0.00 35.09 4.70
159 160 2.351322 CGATGAGACGACGAGCCG 60.351 66.667 0.00 0.00 35.09 5.52
160 161 2.810012 CGATGAGACGACGAGCCGA 61.810 63.158 0.00 0.00 35.09 5.54
161 162 1.649815 GATGAGACGACGAGCCGAT 59.350 57.895 0.00 0.00 0.00 4.18
162 163 0.658829 GATGAGACGACGAGCCGATG 60.659 60.000 0.00 0.00 0.00 3.84
163 164 1.095807 ATGAGACGACGAGCCGATGA 61.096 55.000 0.00 0.00 0.00 2.92
164 165 1.010574 GAGACGACGAGCCGATGAG 60.011 63.158 0.00 0.00 0.00 2.90
165 166 1.429927 GAGACGACGAGCCGATGAGA 61.430 60.000 0.00 0.00 0.00 3.27
166 167 1.010574 GACGACGAGCCGATGAGAG 60.011 63.158 0.00 0.00 0.00 3.20
167 168 2.329690 CGACGAGCCGATGAGAGG 59.670 66.667 1.50 0.00 0.00 3.69
168 169 2.180862 CGACGAGCCGATGAGAGGA 61.181 63.158 1.50 0.00 0.00 3.71
169 170 1.357334 GACGAGCCGATGAGAGGAC 59.643 63.158 1.50 0.00 0.00 3.85
170 171 2.329690 CGAGCCGATGAGAGGACG 59.670 66.667 0.00 0.00 0.00 4.79
171 172 2.180862 CGAGCCGATGAGAGGACGA 61.181 63.158 0.00 0.00 34.14 4.20
172 173 1.715862 CGAGCCGATGAGAGGACGAA 61.716 60.000 0.00 0.00 34.14 3.85
173 174 0.030101 GAGCCGATGAGAGGACGAAG 59.970 60.000 0.00 0.00 0.00 3.79
174 175 0.394488 AGCCGATGAGAGGACGAAGA 60.394 55.000 0.00 0.00 0.00 2.87
175 176 0.248702 GCCGATGAGAGGACGAAGAC 60.249 60.000 0.00 0.00 0.00 3.01
176 177 0.028242 CCGATGAGAGGACGAAGACG 59.972 60.000 0.00 0.00 45.75 4.18
177 178 1.007580 CGATGAGAGGACGAAGACGA 58.992 55.000 0.00 0.00 42.66 4.20
178 179 1.397343 CGATGAGAGGACGAAGACGAA 59.603 52.381 0.00 0.00 42.66 3.85
179 180 2.788030 GATGAGAGGACGAAGACGAAC 58.212 52.381 0.00 0.00 42.66 3.95
180 181 0.879765 TGAGAGGACGAAGACGAACC 59.120 55.000 0.00 0.00 42.66 3.62
181 182 0.179194 GAGAGGACGAAGACGAACCG 60.179 60.000 0.00 0.00 42.66 4.44
182 183 0.604780 AGAGGACGAAGACGAACCGA 60.605 55.000 0.00 0.00 42.66 4.69
183 184 0.450983 GAGGACGAAGACGAACCGAT 59.549 55.000 0.00 0.00 42.66 4.18
184 185 0.170561 AGGACGAAGACGAACCGATG 59.829 55.000 0.00 0.00 42.66 3.84
185 186 0.169672 GGACGAAGACGAACCGATGA 59.830 55.000 0.00 0.00 42.66 2.92
186 187 1.536149 GACGAAGACGAACCGATGAG 58.464 55.000 0.00 0.00 42.66 2.90
187 188 0.456312 ACGAAGACGAACCGATGAGC 60.456 55.000 0.00 0.00 42.66 4.26
188 189 1.464429 CGAAGACGAACCGATGAGCG 61.464 60.000 0.00 0.00 42.66 5.03
189 190 0.179171 GAAGACGAACCGATGAGCGA 60.179 55.000 0.00 0.00 44.57 4.93
190 191 0.456312 AAGACGAACCGATGAGCGAC 60.456 55.000 0.00 0.00 44.57 5.19
191 192 2.202440 ACGAACCGATGAGCGACG 60.202 61.111 0.00 0.00 44.57 5.12
192 193 2.099638 CGAACCGATGAGCGACGA 59.900 61.111 0.00 0.00 44.57 4.20
193 194 1.513373 CGAACCGATGAGCGACGAA 60.513 57.895 0.00 0.00 44.57 3.85
194 195 1.730593 CGAACCGATGAGCGACGAAC 61.731 60.000 0.00 0.00 44.57 3.95
195 196 0.731514 GAACCGATGAGCGACGAACA 60.732 55.000 0.00 0.00 44.57 3.18
196 197 0.732880 AACCGATGAGCGACGAACAG 60.733 55.000 0.00 0.00 44.57 3.16
197 198 1.874019 CCGATGAGCGACGAACAGG 60.874 63.158 0.00 0.00 44.57 4.00
198 199 1.136774 CGATGAGCGACGAACAGGA 59.863 57.895 0.00 0.00 44.57 3.86
199 200 0.456142 CGATGAGCGACGAACAGGAA 60.456 55.000 0.00 0.00 44.57 3.36
200 201 1.272781 GATGAGCGACGAACAGGAAG 58.727 55.000 0.00 0.00 0.00 3.46
201 202 0.737715 ATGAGCGACGAACAGGAAGC 60.738 55.000 0.00 0.00 0.00 3.86
202 203 2.048127 AGCGACGAACAGGAAGCC 60.048 61.111 0.00 0.00 0.00 4.35
203 204 2.357034 GCGACGAACAGGAAGCCA 60.357 61.111 0.00 0.00 0.00 4.75
204 205 2.383527 GCGACGAACAGGAAGCCAG 61.384 63.158 0.00 0.00 0.00 4.85
205 206 1.289066 CGACGAACAGGAAGCCAGA 59.711 57.895 0.00 0.00 0.00 3.86
206 207 0.108615 CGACGAACAGGAAGCCAGAT 60.109 55.000 0.00 0.00 0.00 2.90
207 208 1.363744 GACGAACAGGAAGCCAGATG 58.636 55.000 0.00 0.00 0.00 2.90
208 209 0.687354 ACGAACAGGAAGCCAGATGT 59.313 50.000 0.00 0.00 0.00 3.06
209 210 1.072331 ACGAACAGGAAGCCAGATGTT 59.928 47.619 0.00 0.00 38.53 2.71
210 211 1.734465 CGAACAGGAAGCCAGATGTTC 59.266 52.381 10.73 10.73 45.07 3.18
211 212 2.087646 GAACAGGAAGCCAGATGTTCC 58.912 52.381 9.97 2.34 43.58 3.62
212 213 0.329596 ACAGGAAGCCAGATGTTCCC 59.670 55.000 0.00 0.00 42.97 3.97
213 214 0.329261 CAGGAAGCCAGATGTTCCCA 59.671 55.000 0.00 0.00 42.97 4.37
214 215 1.064166 CAGGAAGCCAGATGTTCCCAT 60.064 52.381 0.00 0.00 42.97 4.00
215 216 1.642762 AGGAAGCCAGATGTTCCCATT 59.357 47.619 0.00 0.00 42.97 3.16
216 217 1.753073 GGAAGCCAGATGTTCCCATTG 59.247 52.381 0.00 0.00 36.92 2.82
217 218 2.621407 GGAAGCCAGATGTTCCCATTGA 60.621 50.000 0.00 0.00 36.92 2.57
218 219 3.294214 GAAGCCAGATGTTCCCATTGAT 58.706 45.455 0.00 0.00 0.00 2.57
219 220 3.393426 AGCCAGATGTTCCCATTGATT 57.607 42.857 0.00 0.00 0.00 2.57
220 221 3.716431 AGCCAGATGTTCCCATTGATTT 58.284 40.909 0.00 0.00 0.00 2.17
221 222 4.098894 AGCCAGATGTTCCCATTGATTTT 58.901 39.130 0.00 0.00 0.00 1.82
222 223 4.533311 AGCCAGATGTTCCCATTGATTTTT 59.467 37.500 0.00 0.00 0.00 1.94
249 250 2.685850 CGGGAAAACCTCTCGGTATT 57.314 50.000 0.00 0.00 44.87 1.89
250 251 2.981898 CGGGAAAACCTCTCGGTATTT 58.018 47.619 0.00 0.00 44.87 1.40
251 252 3.340928 CGGGAAAACCTCTCGGTATTTT 58.659 45.455 0.00 0.00 44.87 1.82
252 253 4.506758 CGGGAAAACCTCTCGGTATTTTA 58.493 43.478 0.00 0.00 44.87 1.52
253 254 5.121105 CGGGAAAACCTCTCGGTATTTTAT 58.879 41.667 0.00 0.00 44.87 1.40
254 255 5.587443 CGGGAAAACCTCTCGGTATTTTATT 59.413 40.000 0.00 0.00 44.87 1.40
255 256 6.094464 CGGGAAAACCTCTCGGTATTTTATTT 59.906 38.462 0.00 0.00 44.87 1.40
256 257 7.478322 GGGAAAACCTCTCGGTATTTTATTTC 58.522 38.462 0.00 0.00 44.73 2.17
257 258 7.338703 GGGAAAACCTCTCGGTATTTTATTTCT 59.661 37.037 0.00 0.00 44.73 2.52
258 259 8.396390 GGAAAACCTCTCGGTATTTTATTTCTC 58.604 37.037 0.00 0.00 44.73 2.87
259 260 8.857694 AAAACCTCTCGGTATTTTATTTCTCA 57.142 30.769 0.00 0.00 44.73 3.27
260 261 8.494016 AAACCTCTCGGTATTTTATTTCTCAG 57.506 34.615 0.00 0.00 44.73 3.35
261 262 6.049790 ACCTCTCGGTATTTTATTTCTCAGC 58.950 40.000 0.00 0.00 43.29 4.26
262 263 6.127026 ACCTCTCGGTATTTTATTTCTCAGCT 60.127 38.462 0.00 0.00 43.29 4.24
263 264 7.069578 ACCTCTCGGTATTTTATTTCTCAGCTA 59.930 37.037 0.00 0.00 43.29 3.32
264 265 7.926555 CCTCTCGGTATTTTATTTCTCAGCTAA 59.073 37.037 0.00 0.00 0.00 3.09
265 266 9.314321 CTCTCGGTATTTTATTTCTCAGCTAAA 57.686 33.333 0.00 0.00 0.00 1.85
266 267 9.661563 TCTCGGTATTTTATTTCTCAGCTAAAA 57.338 29.630 0.00 0.00 0.00 1.52
267 268 9.922305 CTCGGTATTTTATTTCTCAGCTAAAAG 57.078 33.333 0.00 0.00 30.39 2.27
268 269 9.661563 TCGGTATTTTATTTCTCAGCTAAAAGA 57.338 29.630 0.00 0.00 30.39 2.52
269 270 9.922305 CGGTATTTTATTTCTCAGCTAAAAGAG 57.078 33.333 0.00 0.00 30.39 2.85
277 278 8.677148 ATTTCTCAGCTAAAAGAGTTACAACA 57.323 30.769 0.00 0.00 33.63 3.33
278 279 8.677148 TTTCTCAGCTAAAAGAGTTACAACAT 57.323 30.769 0.00 0.00 33.63 2.71
279 280 8.677148 TTCTCAGCTAAAAGAGTTACAACATT 57.323 30.769 0.00 0.00 33.63 2.71
280 281 8.677148 TCTCAGCTAAAAGAGTTACAACATTT 57.323 30.769 0.00 0.00 33.63 2.32
281 282 9.772973 TCTCAGCTAAAAGAGTTACAACATTTA 57.227 29.630 0.00 0.00 33.63 1.40
307 308 8.893563 TTACATAAGGAAGAATGAAATTGGGT 57.106 30.769 0.00 0.00 36.07 4.51
308 309 7.174107 ACATAAGGAAGAATGAAATTGGGTG 57.826 36.000 0.00 0.00 36.07 4.61
309 310 6.155049 ACATAAGGAAGAATGAAATTGGGTGG 59.845 38.462 0.00 0.00 36.07 4.61
310 311 4.402616 AGGAAGAATGAAATTGGGTGGA 57.597 40.909 0.00 0.00 36.07 4.02
311 312 4.951603 AGGAAGAATGAAATTGGGTGGAT 58.048 39.130 0.00 0.00 36.07 3.41
312 313 4.958581 AGGAAGAATGAAATTGGGTGGATC 59.041 41.667 0.00 0.00 36.07 3.36
313 314 4.958581 GGAAGAATGAAATTGGGTGGATCT 59.041 41.667 0.00 0.00 36.07 2.75
314 315 5.068329 GGAAGAATGAAATTGGGTGGATCTC 59.932 44.000 0.00 0.00 36.07 2.75
315 316 4.540715 AGAATGAAATTGGGTGGATCTCC 58.459 43.478 0.00 0.00 36.07 3.71
316 317 4.017222 AGAATGAAATTGGGTGGATCTCCA 60.017 41.667 0.00 0.00 39.63 3.86
317 318 4.887367 AATGAAATTGGGTGGATCTCCAT 58.113 39.130 1.54 0.00 41.53 3.41
318 319 4.897670 AATGAAATTGGGTGGATCTCCATC 59.102 41.667 1.54 1.01 46.41 3.51
330 331 4.796606 GGATCTCCATCCCATTCAAAAGA 58.203 43.478 0.00 0.00 42.91 2.52
331 332 5.203528 GGATCTCCATCCCATTCAAAAGAA 58.796 41.667 0.00 0.00 42.91 2.52
332 333 5.301298 GGATCTCCATCCCATTCAAAAGAAG 59.699 44.000 0.00 0.00 42.91 2.85
333 334 5.519183 TCTCCATCCCATTCAAAAGAAGA 57.481 39.130 0.00 0.00 0.00 2.87
334 335 6.083487 TCTCCATCCCATTCAAAAGAAGAT 57.917 37.500 0.00 0.00 0.00 2.40
335 336 6.496743 TCTCCATCCCATTCAAAAGAAGATT 58.503 36.000 0.00 0.00 0.00 2.40
336 337 6.379133 TCTCCATCCCATTCAAAAGAAGATTG 59.621 38.462 0.00 0.00 0.00 2.67
337 338 6.255287 TCCATCCCATTCAAAAGAAGATTGA 58.745 36.000 0.00 0.00 35.11 2.57
338 339 6.379133 TCCATCCCATTCAAAAGAAGATTGAG 59.621 38.462 0.00 0.00 38.01 3.02
339 340 6.154021 CCATCCCATTCAAAAGAAGATTGAGT 59.846 38.462 0.00 0.00 38.01 3.41
340 341 7.340232 CCATCCCATTCAAAAGAAGATTGAGTA 59.660 37.037 0.00 0.00 38.01 2.59
341 342 8.910944 CATCCCATTCAAAAGAAGATTGAGTAT 58.089 33.333 0.00 0.00 38.01 2.12
342 343 8.511604 TCCCATTCAAAAGAAGATTGAGTATC 57.488 34.615 0.00 0.00 38.01 2.24
358 359 6.090483 TGAGTATCATAAGAGTGCTTAGCC 57.910 41.667 0.29 0.00 42.56 3.93
359 360 5.598417 TGAGTATCATAAGAGTGCTTAGCCA 59.402 40.000 0.29 0.00 42.56 4.75
360 361 6.095432 AGTATCATAAGAGTGCTTAGCCAG 57.905 41.667 0.29 0.00 39.79 4.85
361 362 5.835819 AGTATCATAAGAGTGCTTAGCCAGA 59.164 40.000 0.29 0.00 39.79 3.86
362 363 5.822132 ATCATAAGAGTGCTTAGCCAGAT 57.178 39.130 0.29 0.00 39.79 2.90
363 364 4.953667 TCATAAGAGTGCTTAGCCAGATG 58.046 43.478 0.29 0.00 39.79 2.90
364 365 4.406972 TCATAAGAGTGCTTAGCCAGATGT 59.593 41.667 0.29 0.00 39.79 3.06
365 366 3.710209 AAGAGTGCTTAGCCAGATGTT 57.290 42.857 0.29 0.00 31.07 2.71
366 367 3.258971 AGAGTGCTTAGCCAGATGTTC 57.741 47.619 0.29 0.00 0.00 3.18
367 368 2.093235 AGAGTGCTTAGCCAGATGTTCC 60.093 50.000 0.29 0.00 0.00 3.62
368 369 1.065126 AGTGCTTAGCCAGATGTTCCC 60.065 52.381 0.29 0.00 0.00 3.97
369 370 0.991146 TGCTTAGCCAGATGTTCCCA 59.009 50.000 0.29 0.00 0.00 4.37
370 371 1.565759 TGCTTAGCCAGATGTTCCCAT 59.434 47.619 0.29 0.00 0.00 4.00
371 372 2.025037 TGCTTAGCCAGATGTTCCCATT 60.025 45.455 0.29 0.00 0.00 3.16
372 373 2.360165 GCTTAGCCAGATGTTCCCATTG 59.640 50.000 0.00 0.00 0.00 2.82
373 374 3.889815 CTTAGCCAGATGTTCCCATTGA 58.110 45.455 0.00 0.00 0.00 2.57
374 375 4.467769 CTTAGCCAGATGTTCCCATTGAT 58.532 43.478 0.00 0.00 0.00 2.57
375 376 3.393426 AGCCAGATGTTCCCATTGATT 57.607 42.857 0.00 0.00 0.00 2.57
376 377 3.716431 AGCCAGATGTTCCCATTGATTT 58.284 40.909 0.00 0.00 0.00 2.17
377 378 3.449737 AGCCAGATGTTCCCATTGATTTG 59.550 43.478 0.00 0.00 0.00 2.32
378 379 3.196254 GCCAGATGTTCCCATTGATTTGT 59.804 43.478 0.00 0.00 0.00 2.83
379 380 4.322953 GCCAGATGTTCCCATTGATTTGTT 60.323 41.667 0.00 0.00 0.00 2.83
380 381 5.797051 CCAGATGTTCCCATTGATTTGTTT 58.203 37.500 0.00 0.00 0.00 2.83
381 382 5.870978 CCAGATGTTCCCATTGATTTGTTTC 59.129 40.000 0.00 0.00 0.00 2.78
382 383 6.457355 CAGATGTTCCCATTGATTTGTTTCA 58.543 36.000 0.00 0.00 0.00 2.69
383 384 6.366877 CAGATGTTCCCATTGATTTGTTTCAC 59.633 38.462 0.00 0.00 0.00 3.18
384 385 5.604758 TGTTCCCATTGATTTGTTTCACA 57.395 34.783 0.00 0.00 0.00 3.58
385 386 5.355596 TGTTCCCATTGATTTGTTTCACAC 58.644 37.500 0.00 0.00 0.00 3.82
386 387 4.235939 TCCCATTGATTTGTTTCACACG 57.764 40.909 0.00 0.00 0.00 4.49
387 388 3.634448 TCCCATTGATTTGTTTCACACGT 59.366 39.130 0.00 0.00 0.00 4.49
388 389 4.822350 TCCCATTGATTTGTTTCACACGTA 59.178 37.500 0.00 0.00 0.00 3.57
389 390 4.915085 CCCATTGATTTGTTTCACACGTAC 59.085 41.667 0.00 0.00 0.00 3.67
390 391 4.610951 CCATTGATTTGTTTCACACGTACG 59.389 41.667 15.01 15.01 0.00 3.67
391 392 3.241783 TGATTTGTTTCACACGTACGC 57.758 42.857 16.72 0.00 0.00 4.42
392 393 2.608090 TGATTTGTTTCACACGTACGCA 59.392 40.909 16.72 0.00 0.00 5.24
393 394 3.248841 TGATTTGTTTCACACGTACGCAT 59.751 39.130 16.72 0.00 0.00 4.73
394 395 3.677190 TTTGTTTCACACGTACGCATT 57.323 38.095 16.72 0.00 0.00 3.56
395 396 3.677190 TTGTTTCACACGTACGCATTT 57.323 38.095 16.72 0.00 0.00 2.32
396 397 3.241783 TGTTTCACACGTACGCATTTC 57.758 42.857 16.72 1.05 0.00 2.17
397 398 2.608090 TGTTTCACACGTACGCATTTCA 59.392 40.909 16.72 3.75 0.00 2.69
398 399 3.063588 TGTTTCACACGTACGCATTTCAA 59.936 39.130 16.72 0.00 0.00 2.69
399 400 4.215965 GTTTCACACGTACGCATTTCAAT 58.784 39.130 16.72 0.00 0.00 2.57
400 401 4.475763 TTCACACGTACGCATTTCAATT 57.524 36.364 16.72 0.00 0.00 2.32
401 402 3.804688 TCACACGTACGCATTTCAATTG 58.195 40.909 16.72 5.14 0.00 2.32
402 403 3.248841 TCACACGTACGCATTTCAATTGT 59.751 39.130 16.72 5.84 0.00 2.71
403 404 3.357531 CACACGTACGCATTTCAATTGTG 59.642 43.478 16.72 14.53 0.00 3.33
404 405 2.908009 CACGTACGCATTTCAATTGTGG 59.092 45.455 16.72 0.00 0.00 4.17
405 406 2.550606 ACGTACGCATTTCAATTGTGGT 59.449 40.909 16.72 0.63 0.00 4.16
406 407 3.160545 CGTACGCATTTCAATTGTGGTC 58.839 45.455 0.52 0.00 0.00 4.02
407 408 2.330231 ACGCATTTCAATTGTGGTCG 57.670 45.000 5.13 6.80 0.00 4.79
408 409 1.606668 ACGCATTTCAATTGTGGTCGT 59.393 42.857 5.13 7.39 0.00 4.34
409 410 1.978097 CGCATTTCAATTGTGGTCGTG 59.022 47.619 5.13 0.00 0.00 4.35
410 411 2.604373 CGCATTTCAATTGTGGTCGTGT 60.604 45.455 5.13 0.00 0.00 4.49
411 412 2.725723 GCATTTCAATTGTGGTCGTGTG 59.274 45.455 5.13 0.00 0.00 3.82
412 413 3.549827 GCATTTCAATTGTGGTCGTGTGA 60.550 43.478 5.13 0.00 0.00 3.58
413 414 3.684103 TTTCAATTGTGGTCGTGTGAC 57.316 42.857 5.13 0.00 44.72 3.67
414 415 2.613026 TCAATTGTGGTCGTGTGACT 57.387 45.000 5.13 0.00 44.83 3.41
415 416 2.912771 TCAATTGTGGTCGTGTGACTT 58.087 42.857 5.13 0.00 44.83 3.01
416 417 2.611751 TCAATTGTGGTCGTGTGACTTG 59.388 45.455 5.13 0.00 44.83 3.16
417 418 0.944386 ATTGTGGTCGTGTGACTTGC 59.056 50.000 0.00 0.00 44.83 4.01
418 419 1.425267 TTGTGGTCGTGTGACTTGCG 61.425 55.000 0.00 0.00 44.83 4.85
419 420 1.881252 GTGGTCGTGTGACTTGCGT 60.881 57.895 0.00 0.00 44.83 5.24
420 421 1.880796 TGGTCGTGTGACTTGCGTG 60.881 57.895 0.00 0.00 44.83 5.34
421 422 2.245532 GTCGTGTGACTTGCGTGC 59.754 61.111 0.00 0.00 42.08 5.34
422 423 2.964925 TCGTGTGACTTGCGTGCC 60.965 61.111 0.00 0.00 0.00 5.01
423 424 2.967076 CGTGTGACTTGCGTGCCT 60.967 61.111 0.00 0.00 0.00 4.75
424 425 2.939022 GTGTGACTTGCGTGCCTC 59.061 61.111 0.00 0.00 0.00 4.70
425 426 2.661537 TGTGACTTGCGTGCCTCG 60.662 61.111 0.00 0.00 43.12 4.63
426 427 2.355837 GTGACTTGCGTGCCTCGA 60.356 61.111 2.66 0.00 42.86 4.04
427 428 2.355837 TGACTTGCGTGCCTCGAC 60.356 61.111 2.66 0.00 42.86 4.20
428 429 3.470567 GACTTGCGTGCCTCGACG 61.471 66.667 2.66 0.00 42.86 5.12
431 432 4.595538 TTGCGTGCCTCGACGGTT 62.596 61.111 0.00 0.00 42.86 4.44
435 436 4.719369 GTGCCTCGACGGTTCGCT 62.719 66.667 0.00 0.00 45.46 4.93
436 437 3.057548 TGCCTCGACGGTTCGCTA 61.058 61.111 0.00 0.00 45.46 4.26
437 438 2.578981 GCCTCGACGGTTCGCTAC 60.579 66.667 0.00 0.00 45.46 3.58
438 439 2.101770 CCTCGACGGTTCGCTACC 59.898 66.667 0.00 0.00 45.46 3.18
439 440 2.404995 CCTCGACGGTTCGCTACCT 61.405 63.158 0.00 0.00 45.40 3.08
440 441 1.091771 CCTCGACGGTTCGCTACCTA 61.092 60.000 0.00 0.00 45.40 3.08
441 442 0.304098 CTCGACGGTTCGCTACCTAG 59.696 60.000 0.00 0.00 45.40 3.02
442 443 0.108186 TCGACGGTTCGCTACCTAGA 60.108 55.000 0.00 0.17 45.40 2.43
472 473 2.443390 GCCTGCATCCAGCCCAAT 60.443 61.111 0.00 0.00 44.83 3.16
578 579 1.289066 CCTGACTCGCTGGAAACGA 59.711 57.895 0.00 0.00 37.79 3.85
707 709 2.203070 CCGCGCCAAATCTAGCCT 60.203 61.111 0.00 0.00 0.00 4.58
777 815 1.181786 GATCTATGCTAGAGGCGGCT 58.818 55.000 13.09 13.09 45.43 5.52
820 867 2.851071 GCGGCGGATCTAGTGCTCT 61.851 63.158 9.78 0.00 0.00 4.09
985 1032 1.068417 CCCACTGAACGAACCGTCA 59.932 57.895 0.00 0.00 39.99 4.35
1006 1053 4.707934 TCAATGTCGACTAGGTTATGGACA 59.292 41.667 17.92 0.00 38.59 4.02
1017 1064 1.933853 GTTATGGACACACGGATGAGC 59.066 52.381 0.00 0.00 0.00 4.26
1145 1193 0.109723 TTGTTTCTCCGGGAACAGGG 59.890 55.000 15.19 0.00 33.13 4.45
1182 1230 5.926542 TCTGAACTACATCTACAACTGCAAC 59.073 40.000 0.00 0.00 0.00 4.17
1271 1319 2.273449 CAGGGGGCTGCTACAAGG 59.727 66.667 0.00 0.00 0.00 3.61
1275 1324 1.272554 GGGGGCTGCTACAAGGTAGT 61.273 60.000 0.00 0.00 0.00 2.73
1354 1403 1.630878 AGAGGTTCAGGGTCATTCACC 59.369 52.381 0.00 0.00 45.97 4.02
1575 1624 3.308595 TGTTCAAGTTGAGCACTAACACG 59.691 43.478 17.37 0.00 32.63 4.49
1922 1975 7.633018 TCTAGGGTTTAGCCATTATGATCTT 57.367 36.000 0.26 0.00 39.65 2.40
1991 2044 6.906901 TCAATCAGGAAGTAGGGTATTACCTT 59.093 38.462 12.54 7.74 42.09 3.50
2540 2594 2.368594 TCCGATCTGGAAGGGCCT 59.631 61.111 0.00 0.00 46.38 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.095065 GGACATTACGTATCCAATATCCAATAC 57.905 37.037 8.53 0.00 29.74 1.89
12 13 9.042450 AGGACATTACGTATCCAATATCCAATA 57.958 33.333 14.55 0.00 31.37 1.90
13 14 7.824289 CAGGACATTACGTATCCAATATCCAAT 59.176 37.037 14.55 0.00 31.37 3.16
14 15 7.158697 CAGGACATTACGTATCCAATATCCAA 58.841 38.462 14.55 0.00 31.37 3.53
15 16 6.697395 CAGGACATTACGTATCCAATATCCA 58.303 40.000 14.55 0.00 31.37 3.41
16 17 5.581085 GCAGGACATTACGTATCCAATATCC 59.419 44.000 14.55 7.14 34.73 2.59
17 18 6.090898 GTGCAGGACATTACGTATCCAATATC 59.909 42.308 14.55 0.00 34.73 1.63
18 19 5.932303 GTGCAGGACATTACGTATCCAATAT 59.068 40.000 14.55 0.00 34.73 1.28
19 20 5.069914 AGTGCAGGACATTACGTATCCAATA 59.930 40.000 14.55 0.00 34.73 1.90
20 21 4.127171 GTGCAGGACATTACGTATCCAAT 58.873 43.478 14.55 0.00 34.73 3.16
21 22 3.196901 AGTGCAGGACATTACGTATCCAA 59.803 43.478 14.55 0.00 34.73 3.53
22 23 2.764010 AGTGCAGGACATTACGTATCCA 59.236 45.455 14.55 0.00 34.73 3.41
23 24 3.181479 TGAGTGCAGGACATTACGTATCC 60.181 47.826 5.69 5.69 0.00 2.59
24 25 3.797256 GTGAGTGCAGGACATTACGTATC 59.203 47.826 0.00 0.00 0.00 2.24
25 26 3.194755 TGTGAGTGCAGGACATTACGTAT 59.805 43.478 0.00 0.00 0.00 3.06
26 27 2.559231 TGTGAGTGCAGGACATTACGTA 59.441 45.455 0.00 0.00 0.00 3.57
27 28 1.343142 TGTGAGTGCAGGACATTACGT 59.657 47.619 0.00 0.00 0.00 3.57
28 29 2.078849 TGTGAGTGCAGGACATTACG 57.921 50.000 0.00 0.00 0.00 3.18
29 30 3.551890 CGTATGTGAGTGCAGGACATTAC 59.448 47.826 9.73 6.43 32.59 1.89
30 31 3.194755 ACGTATGTGAGTGCAGGACATTA 59.805 43.478 9.73 0.00 32.59 1.90
31 32 2.028112 ACGTATGTGAGTGCAGGACATT 60.028 45.455 9.73 0.00 32.59 2.71
32 33 1.550524 ACGTATGTGAGTGCAGGACAT 59.449 47.619 9.47 9.47 34.68 3.06
33 34 0.966179 ACGTATGTGAGTGCAGGACA 59.034 50.000 0.00 0.00 0.00 4.02
34 35 2.933495 TACGTATGTGAGTGCAGGAC 57.067 50.000 0.00 0.00 0.00 3.85
35 36 3.020984 TGATACGTATGTGAGTGCAGGA 58.979 45.455 13.97 0.00 0.00 3.86
36 37 3.116300 GTGATACGTATGTGAGTGCAGG 58.884 50.000 13.97 0.00 0.00 4.85
37 38 2.783832 CGTGATACGTATGTGAGTGCAG 59.216 50.000 13.97 0.00 36.74 4.41
38 39 2.792749 CGTGATACGTATGTGAGTGCA 58.207 47.619 13.97 0.00 36.74 4.57
81 82 2.885113 GCAGAAATCCGGCAACCC 59.115 61.111 0.00 0.00 35.96 4.11
82 83 2.485122 CGCAGAAATCCGGCAACC 59.515 61.111 0.00 0.00 35.63 3.77
83 84 2.202479 GCGCAGAAATCCGGCAAC 60.202 61.111 0.30 0.00 35.63 4.17
84 85 3.798650 CGCGCAGAAATCCGGCAA 61.799 61.111 8.75 0.00 35.63 4.52
85 86 3.650907 TACGCGCAGAAATCCGGCA 62.651 57.895 5.73 0.00 35.63 5.69
86 87 2.871427 CTACGCGCAGAAATCCGGC 61.871 63.158 5.73 0.00 0.00 6.13
87 88 2.871427 GCTACGCGCAGAAATCCGG 61.871 63.158 11.36 0.00 38.92 5.14
88 89 2.621000 GCTACGCGCAGAAATCCG 59.379 61.111 11.36 0.00 38.92 4.18
107 108 4.980805 TCGGCCGCTGGTTGTCAC 62.981 66.667 23.51 0.00 0.00 3.67
108 109 4.680237 CTCGGCCGCTGGTTGTCA 62.680 66.667 23.51 0.00 0.00 3.58
131 132 4.933064 CTCATCGGCCCGTCGCTC 62.933 72.222 1.63 0.00 37.74 5.03
134 135 4.907034 CGTCTCATCGGCCCGTCG 62.907 72.222 1.63 0.00 0.00 5.12
135 136 3.515286 TCGTCTCATCGGCCCGTC 61.515 66.667 1.63 0.00 0.00 4.79
136 137 3.823330 GTCGTCTCATCGGCCCGT 61.823 66.667 1.63 0.00 0.00 5.28
137 138 4.907034 CGTCGTCTCATCGGCCCG 62.907 72.222 0.00 0.00 31.35 6.13
138 139 3.471244 CTCGTCGTCTCATCGGCCC 62.471 68.421 0.00 0.00 31.35 5.80
139 140 2.024871 CTCGTCGTCTCATCGGCC 59.975 66.667 0.00 0.00 31.35 6.13
140 141 2.652496 GCTCGTCGTCTCATCGGC 60.652 66.667 0.00 0.00 0.00 5.54
141 142 2.024871 GGCTCGTCGTCTCATCGG 59.975 66.667 0.00 0.00 0.00 4.18
142 143 2.107151 ATCGGCTCGTCGTCTCATCG 62.107 60.000 0.00 0.00 0.00 3.84
143 144 0.658829 CATCGGCTCGTCGTCTCATC 60.659 60.000 0.00 0.00 0.00 2.92
144 145 1.095807 TCATCGGCTCGTCGTCTCAT 61.096 55.000 0.00 0.00 0.00 2.90
145 146 1.706287 CTCATCGGCTCGTCGTCTCA 61.706 60.000 0.00 0.00 0.00 3.27
146 147 1.010574 CTCATCGGCTCGTCGTCTC 60.011 63.158 0.00 0.00 0.00 3.36
147 148 1.433053 CTCTCATCGGCTCGTCGTCT 61.433 60.000 0.00 0.00 0.00 4.18
148 149 1.010574 CTCTCATCGGCTCGTCGTC 60.011 63.158 0.00 0.00 0.00 4.20
149 150 2.473760 CCTCTCATCGGCTCGTCGT 61.474 63.158 0.00 0.00 0.00 4.34
150 151 2.180862 TCCTCTCATCGGCTCGTCG 61.181 63.158 0.00 0.00 0.00 5.12
151 152 1.357334 GTCCTCTCATCGGCTCGTC 59.643 63.158 0.00 0.00 0.00 4.20
152 153 2.473760 CGTCCTCTCATCGGCTCGT 61.474 63.158 0.00 0.00 0.00 4.18
153 154 1.715862 TTCGTCCTCTCATCGGCTCG 61.716 60.000 0.00 0.00 0.00 5.03
154 155 0.030101 CTTCGTCCTCTCATCGGCTC 59.970 60.000 0.00 0.00 0.00 4.70
155 156 0.394488 TCTTCGTCCTCTCATCGGCT 60.394 55.000 0.00 0.00 0.00 5.52
156 157 0.248702 GTCTTCGTCCTCTCATCGGC 60.249 60.000 0.00 0.00 0.00 5.54
157 158 0.028242 CGTCTTCGTCCTCTCATCGG 59.972 60.000 0.00 0.00 0.00 4.18
158 159 1.007580 TCGTCTTCGTCCTCTCATCG 58.992 55.000 0.00 0.00 38.33 3.84
159 160 2.478200 GGTTCGTCTTCGTCCTCTCATC 60.478 54.545 0.00 0.00 38.33 2.92
160 161 1.473278 GGTTCGTCTTCGTCCTCTCAT 59.527 52.381 0.00 0.00 38.33 2.90
161 162 0.879765 GGTTCGTCTTCGTCCTCTCA 59.120 55.000 0.00 0.00 38.33 3.27
162 163 0.179194 CGGTTCGTCTTCGTCCTCTC 60.179 60.000 0.00 0.00 38.33 3.20
163 164 0.604780 TCGGTTCGTCTTCGTCCTCT 60.605 55.000 0.00 0.00 38.33 3.69
164 165 0.450983 ATCGGTTCGTCTTCGTCCTC 59.549 55.000 0.00 0.00 38.33 3.71
165 166 0.170561 CATCGGTTCGTCTTCGTCCT 59.829 55.000 0.00 0.00 38.33 3.85
166 167 0.169672 TCATCGGTTCGTCTTCGTCC 59.830 55.000 0.00 0.00 38.33 4.79
167 168 1.536149 CTCATCGGTTCGTCTTCGTC 58.464 55.000 0.00 0.00 38.33 4.20
168 169 0.456312 GCTCATCGGTTCGTCTTCGT 60.456 55.000 0.00 0.00 38.33 3.85
169 170 1.464429 CGCTCATCGGTTCGTCTTCG 61.464 60.000 0.00 0.00 34.77 3.79
170 171 0.179171 TCGCTCATCGGTTCGTCTTC 60.179 55.000 0.00 0.00 39.05 2.87
171 172 0.456312 GTCGCTCATCGGTTCGTCTT 60.456 55.000 0.00 0.00 39.05 3.01
172 173 1.136984 GTCGCTCATCGGTTCGTCT 59.863 57.895 0.00 0.00 39.05 4.18
173 174 2.215604 CGTCGCTCATCGGTTCGTC 61.216 63.158 0.00 0.00 39.05 4.20
174 175 2.191354 TTCGTCGCTCATCGGTTCGT 62.191 55.000 0.00 0.00 39.05 3.85
175 176 1.513373 TTCGTCGCTCATCGGTTCG 60.513 57.895 0.00 0.00 39.05 3.95
176 177 0.731514 TGTTCGTCGCTCATCGGTTC 60.732 55.000 0.00 0.00 39.05 3.62
177 178 0.732880 CTGTTCGTCGCTCATCGGTT 60.733 55.000 0.00 0.00 39.05 4.44
178 179 1.154016 CTGTTCGTCGCTCATCGGT 60.154 57.895 0.00 0.00 39.05 4.69
179 180 1.874019 CCTGTTCGTCGCTCATCGG 60.874 63.158 0.00 0.00 39.05 4.18
180 181 0.456142 TTCCTGTTCGTCGCTCATCG 60.456 55.000 0.00 0.00 40.15 3.84
181 182 1.272781 CTTCCTGTTCGTCGCTCATC 58.727 55.000 0.00 0.00 0.00 2.92
182 183 0.737715 GCTTCCTGTTCGTCGCTCAT 60.738 55.000 0.00 0.00 0.00 2.90
183 184 1.372997 GCTTCCTGTTCGTCGCTCA 60.373 57.895 0.00 0.00 0.00 4.26
184 185 2.095252 GGCTTCCTGTTCGTCGCTC 61.095 63.158 0.00 0.00 0.00 5.03
185 186 2.048127 GGCTTCCTGTTCGTCGCT 60.048 61.111 0.00 0.00 0.00 4.93
186 187 2.357034 TGGCTTCCTGTTCGTCGC 60.357 61.111 0.00 0.00 0.00 5.19
187 188 0.108615 ATCTGGCTTCCTGTTCGTCG 60.109 55.000 0.00 0.00 0.00 5.12
188 189 1.338200 ACATCTGGCTTCCTGTTCGTC 60.338 52.381 0.00 0.00 0.00 4.20
189 190 0.687354 ACATCTGGCTTCCTGTTCGT 59.313 50.000 0.00 0.00 0.00 3.85
190 191 1.734465 GAACATCTGGCTTCCTGTTCG 59.266 52.381 0.00 0.00 38.43 3.95
191 192 2.087646 GGAACATCTGGCTTCCTGTTC 58.912 52.381 11.66 11.66 44.19 3.18
192 193 1.272147 GGGAACATCTGGCTTCCTGTT 60.272 52.381 2.91 0.00 36.84 3.16
193 194 0.329596 GGGAACATCTGGCTTCCTGT 59.670 55.000 2.91 0.00 36.84 4.00
194 195 0.329261 TGGGAACATCTGGCTTCCTG 59.671 55.000 2.91 0.00 36.84 3.86
195 196 2.791253 TGGGAACATCTGGCTTCCT 58.209 52.632 2.91 0.00 36.84 3.36
223 224 2.614983 CGAGAGGTTTTCCCGTCAAAAA 59.385 45.455 0.00 0.00 41.86 1.94
224 225 2.215196 CGAGAGGTTTTCCCGTCAAAA 58.785 47.619 0.00 0.00 41.86 2.44
225 226 1.873698 CGAGAGGTTTTCCCGTCAAA 58.126 50.000 0.00 0.00 41.86 2.69
226 227 3.599412 CGAGAGGTTTTCCCGTCAA 57.401 52.632 0.00 0.00 41.86 3.18
239 240 8.873215 TTAGCTGAGAAATAAAATACCGAGAG 57.127 34.615 0.00 0.00 0.00 3.20
240 241 9.661563 TTTTAGCTGAGAAATAAAATACCGAGA 57.338 29.630 0.00 0.00 0.00 4.04
241 242 9.922305 CTTTTAGCTGAGAAATAAAATACCGAG 57.078 33.333 0.00 0.00 30.39 4.63
242 243 9.661563 TCTTTTAGCTGAGAAATAAAATACCGA 57.338 29.630 0.00 0.00 30.39 4.69
243 244 9.922305 CTCTTTTAGCTGAGAAATAAAATACCG 57.078 33.333 0.00 0.00 30.39 4.02
251 252 9.772973 TGTTGTAACTCTTTTAGCTGAGAAATA 57.227 29.630 5.84 0.00 34.65 1.40
252 253 8.677148 TGTTGTAACTCTTTTAGCTGAGAAAT 57.323 30.769 5.84 0.00 34.65 2.17
253 254 8.677148 ATGTTGTAACTCTTTTAGCTGAGAAA 57.323 30.769 5.84 0.00 34.65 2.52
254 255 8.677148 AATGTTGTAACTCTTTTAGCTGAGAA 57.323 30.769 5.84 0.00 34.65 2.87
255 256 8.677148 AAATGTTGTAACTCTTTTAGCTGAGA 57.323 30.769 5.84 1.57 34.65 3.27
281 282 9.492730 ACCCAATTTCATTCTTCCTTATGTAAT 57.507 29.630 0.00 0.00 0.00 1.89
282 283 8.748412 CACCCAATTTCATTCTTCCTTATGTAA 58.252 33.333 0.00 0.00 0.00 2.41
283 284 7.341769 CCACCCAATTTCATTCTTCCTTATGTA 59.658 37.037 0.00 0.00 0.00 2.29
284 285 6.155049 CCACCCAATTTCATTCTTCCTTATGT 59.845 38.462 0.00 0.00 0.00 2.29
285 286 6.380846 TCCACCCAATTTCATTCTTCCTTATG 59.619 38.462 0.00 0.00 0.00 1.90
286 287 6.502138 TCCACCCAATTTCATTCTTCCTTAT 58.498 36.000 0.00 0.00 0.00 1.73
287 288 5.898120 TCCACCCAATTTCATTCTTCCTTA 58.102 37.500 0.00 0.00 0.00 2.69
288 289 4.750941 TCCACCCAATTTCATTCTTCCTT 58.249 39.130 0.00 0.00 0.00 3.36
289 290 4.402616 TCCACCCAATTTCATTCTTCCT 57.597 40.909 0.00 0.00 0.00 3.36
290 291 4.958581 AGATCCACCCAATTTCATTCTTCC 59.041 41.667 0.00 0.00 0.00 3.46
291 292 5.068329 GGAGATCCACCCAATTTCATTCTTC 59.932 44.000 0.00 0.00 35.64 2.87
292 293 4.958581 GGAGATCCACCCAATTTCATTCTT 59.041 41.667 0.00 0.00 35.64 2.52
293 294 4.017222 TGGAGATCCACCCAATTTCATTCT 60.017 41.667 0.00 0.00 42.01 2.40
294 295 4.280819 TGGAGATCCACCCAATTTCATTC 58.719 43.478 0.00 0.00 42.01 2.67
295 296 4.335735 TGGAGATCCACCCAATTTCATT 57.664 40.909 0.00 0.00 42.01 2.57
306 307 7.310058 TTCTTTTGAATGGGATGGAGATCCAC 61.310 42.308 3.07 0.00 40.81 4.02
307 308 5.281663 TTCTTTTGAATGGGATGGAGATCCA 60.282 40.000 3.57 3.57 40.81 3.41
308 309 4.796606 TCTTTTGAATGGGATGGAGATCC 58.203 43.478 0.00 0.00 46.99 3.36
309 310 6.125029 TCTTCTTTTGAATGGGATGGAGATC 58.875 40.000 0.00 0.00 37.85 2.75
310 311 6.083487 TCTTCTTTTGAATGGGATGGAGAT 57.917 37.500 0.00 0.00 37.85 2.75
311 312 5.519183 TCTTCTTTTGAATGGGATGGAGA 57.481 39.130 0.00 0.00 37.85 3.71
312 313 6.379133 TCAATCTTCTTTTGAATGGGATGGAG 59.621 38.462 0.00 0.00 37.85 3.86
313 314 6.255287 TCAATCTTCTTTTGAATGGGATGGA 58.745 36.000 0.00 0.00 37.85 3.41
314 315 6.154021 ACTCAATCTTCTTTTGAATGGGATGG 59.846 38.462 0.00 0.00 37.85 3.51
315 316 7.166691 ACTCAATCTTCTTTTGAATGGGATG 57.833 36.000 0.00 0.00 37.85 3.51
316 317 9.129532 GATACTCAATCTTCTTTTGAATGGGAT 57.870 33.333 0.00 0.00 37.85 3.85
317 318 8.108999 TGATACTCAATCTTCTTTTGAATGGGA 58.891 33.333 0.00 0.00 37.85 4.37
318 319 8.284945 TGATACTCAATCTTCTTTTGAATGGG 57.715 34.615 0.00 0.00 37.85 4.00
326 327 9.323985 GCACTCTTATGATACTCAATCTTCTTT 57.676 33.333 0.00 0.00 35.45 2.52
327 328 8.703743 AGCACTCTTATGATACTCAATCTTCTT 58.296 33.333 0.00 0.00 35.45 2.52
328 329 8.248904 AGCACTCTTATGATACTCAATCTTCT 57.751 34.615 0.00 0.00 35.45 2.85
329 330 8.885494 AAGCACTCTTATGATACTCAATCTTC 57.115 34.615 0.00 0.00 35.45 2.87
330 331 9.979578 CTAAGCACTCTTATGATACTCAATCTT 57.020 33.333 0.00 0.00 34.54 2.40
331 332 8.087750 GCTAAGCACTCTTATGATACTCAATCT 58.912 37.037 0.00 0.00 34.54 2.40
332 333 7.330700 GGCTAAGCACTCTTATGATACTCAATC 59.669 40.741 0.00 0.00 34.54 2.67
333 334 7.158021 GGCTAAGCACTCTTATGATACTCAAT 58.842 38.462 0.00 0.00 34.54 2.57
334 335 6.098266 TGGCTAAGCACTCTTATGATACTCAA 59.902 38.462 0.00 0.00 34.54 3.02
335 336 5.598417 TGGCTAAGCACTCTTATGATACTCA 59.402 40.000 0.00 0.00 34.54 3.41
336 337 6.015856 TCTGGCTAAGCACTCTTATGATACTC 60.016 42.308 0.00 0.00 34.54 2.59
337 338 5.835819 TCTGGCTAAGCACTCTTATGATACT 59.164 40.000 0.00 0.00 34.54 2.12
338 339 6.090483 TCTGGCTAAGCACTCTTATGATAC 57.910 41.667 0.00 0.00 34.54 2.24
339 340 6.268617 ACATCTGGCTAAGCACTCTTATGATA 59.731 38.462 0.00 0.00 34.54 2.15
340 341 5.071519 ACATCTGGCTAAGCACTCTTATGAT 59.928 40.000 0.00 0.00 34.54 2.45
341 342 4.406972 ACATCTGGCTAAGCACTCTTATGA 59.593 41.667 0.00 0.00 34.54 2.15
342 343 4.701765 ACATCTGGCTAAGCACTCTTATG 58.298 43.478 0.00 0.00 34.54 1.90
343 344 5.363939 GAACATCTGGCTAAGCACTCTTAT 58.636 41.667 0.00 0.00 34.54 1.73
344 345 4.383118 GGAACATCTGGCTAAGCACTCTTA 60.383 45.833 0.00 0.00 33.85 2.10
345 346 3.604582 GAACATCTGGCTAAGCACTCTT 58.395 45.455 0.00 0.00 36.35 2.85
346 347 2.093235 GGAACATCTGGCTAAGCACTCT 60.093 50.000 0.00 0.00 0.00 3.24
347 348 2.284190 GGAACATCTGGCTAAGCACTC 58.716 52.381 0.00 0.00 0.00 3.51
348 349 1.065126 GGGAACATCTGGCTAAGCACT 60.065 52.381 0.00 0.00 0.00 4.40
349 350 1.340017 TGGGAACATCTGGCTAAGCAC 60.340 52.381 0.00 0.00 33.40 4.40
350 351 0.991146 TGGGAACATCTGGCTAAGCA 59.009 50.000 0.00 0.00 33.40 3.91
351 352 3.882131 TGGGAACATCTGGCTAAGC 57.118 52.632 0.00 0.00 33.40 3.09
357 358 8.478844 GTGAAACAAATCAATGGGAACATCTGG 61.479 40.741 0.00 0.00 44.83 3.86
358 359 6.366877 GTGAAACAAATCAATGGGAACATCTG 59.633 38.462 0.00 0.00 44.83 2.90
359 360 6.458210 GTGAAACAAATCAATGGGAACATCT 58.542 36.000 0.00 0.00 44.83 2.90
360 361 6.710692 GTGAAACAAATCAATGGGAACATC 57.289 37.500 0.00 0.00 44.83 3.06
377 378 3.241783 TGAAATGCGTACGTGTGAAAC 57.758 42.857 17.90 0.00 37.35 2.78
378 379 3.946308 TTGAAATGCGTACGTGTGAAA 57.054 38.095 17.90 2.45 0.00 2.69
379 380 4.215201 CAATTGAAATGCGTACGTGTGAA 58.785 39.130 17.90 3.33 0.00 3.18
380 381 3.248841 ACAATTGAAATGCGTACGTGTGA 59.751 39.130 17.90 0.00 0.00 3.58
381 382 3.357531 CACAATTGAAATGCGTACGTGTG 59.642 43.478 17.90 15.09 0.00 3.82
382 383 3.550561 CACAATTGAAATGCGTACGTGT 58.449 40.909 17.90 6.84 0.00 4.49
383 384 2.908009 CCACAATTGAAATGCGTACGTG 59.092 45.455 17.90 6.16 0.00 4.49
384 385 2.550606 ACCACAATTGAAATGCGTACGT 59.449 40.909 17.90 0.00 0.00 3.57
385 386 3.160545 GACCACAATTGAAATGCGTACG 58.839 45.455 13.59 11.84 0.00 3.67
386 387 3.160545 CGACCACAATTGAAATGCGTAC 58.839 45.455 13.59 0.00 0.00 3.67
387 388 2.809119 ACGACCACAATTGAAATGCGTA 59.191 40.909 13.59 0.00 0.00 4.42
388 389 1.606668 ACGACCACAATTGAAATGCGT 59.393 42.857 13.59 11.62 0.00 5.24
389 390 1.978097 CACGACCACAATTGAAATGCG 59.022 47.619 13.59 11.01 0.00 4.73
390 391 2.725723 CACACGACCACAATTGAAATGC 59.274 45.455 13.59 0.00 0.00 3.56
391 392 3.974401 GTCACACGACCACAATTGAAATG 59.026 43.478 13.59 0.00 36.02 2.32
392 393 3.882888 AGTCACACGACCACAATTGAAAT 59.117 39.130 13.59 0.00 43.73 2.17
393 394 3.275143 AGTCACACGACCACAATTGAAA 58.725 40.909 13.59 0.00 43.73 2.69
394 395 2.912771 AGTCACACGACCACAATTGAA 58.087 42.857 13.59 0.00 43.73 2.69
395 396 2.611751 CAAGTCACACGACCACAATTGA 59.388 45.455 13.59 0.00 43.73 2.57
396 397 2.854424 GCAAGTCACACGACCACAATTG 60.854 50.000 3.24 3.24 43.73 2.32
397 398 1.333619 GCAAGTCACACGACCACAATT 59.666 47.619 0.00 0.00 43.73 2.32
398 399 0.944386 GCAAGTCACACGACCACAAT 59.056 50.000 0.00 0.00 43.73 2.71
399 400 1.425267 CGCAAGTCACACGACCACAA 61.425 55.000 0.00 0.00 43.73 3.33
400 401 1.880796 CGCAAGTCACACGACCACA 60.881 57.895 0.00 0.00 43.73 4.17
401 402 2.928361 CGCAAGTCACACGACCAC 59.072 61.111 0.00 0.00 43.73 4.16
414 415 4.595538 AACCGTCGAGGCACGCAA 62.596 61.111 0.00 0.00 46.52 4.85
433 434 1.067071 ACCAAACACGCTCTAGGTAGC 60.067 52.381 0.00 0.00 39.21 3.58
434 435 2.993899 CAACCAAACACGCTCTAGGTAG 59.006 50.000 0.00 0.00 0.00 3.18
435 436 2.868839 GCAACCAAACACGCTCTAGGTA 60.869 50.000 0.00 0.00 0.00 3.08
436 437 1.878953 CAACCAAACACGCTCTAGGT 58.121 50.000 0.00 0.00 0.00 3.08
437 438 0.517316 GCAACCAAACACGCTCTAGG 59.483 55.000 0.00 0.00 0.00 3.02
438 439 0.517316 GGCAACCAAACACGCTCTAG 59.483 55.000 0.00 0.00 0.00 2.43
439 440 0.107831 AGGCAACCAAACACGCTCTA 59.892 50.000 0.00 0.00 37.17 2.43
440 441 1.152963 AGGCAACCAAACACGCTCT 60.153 52.632 0.00 0.00 37.17 4.09
441 442 1.008538 CAGGCAACCAAACACGCTC 60.009 57.895 0.00 0.00 37.17 5.03
442 443 3.119193 CAGGCAACCAAACACGCT 58.881 55.556 0.00 0.00 37.17 5.07
490 491 0.538287 GCAACCAAACAGGCCTCTCT 60.538 55.000 0.00 0.00 43.14 3.10
578 579 0.249073 CGAGAAACTGCCGATCCGAT 60.249 55.000 0.00 0.00 0.00 4.18
691 693 1.521457 TGAGGCTAGATTTGGCGCG 60.521 57.895 0.00 0.00 32.96 6.86
707 709 1.153565 AGTAGGGAAGAAAGGGGGTGA 59.846 52.381 0.00 0.00 0.00 4.02
820 867 2.203480 GGTGGCCAACAGCAAGGA 60.203 61.111 18.33 0.00 46.64 3.36
985 1032 4.464951 TGTGTCCATAACCTAGTCGACATT 59.535 41.667 19.50 8.80 33.25 2.71
1006 1053 2.037772 GGATTATCAGGCTCATCCGTGT 59.962 50.000 0.00 0.00 40.77 4.49
1145 1193 5.745227 TGTAGTTCAGATTTTGGATCCTCC 58.255 41.667 14.23 0.00 36.96 4.30
1182 1230 2.202362 CACAGAGCCTCGACGTCG 60.202 66.667 31.30 31.30 41.45 5.12
1290 1339 0.111061 ACATGGCCACTTGCTCTTCA 59.889 50.000 8.16 0.00 40.92 3.02
1354 1403 2.674852 CCATTGATCTCCTGAACGTGTG 59.325 50.000 0.00 0.00 0.00 3.82
1465 1514 1.449601 GGCTTCCGCGAATCTTGGA 60.450 57.895 8.23 0.00 36.88 3.53
1618 1667 3.767309 AGGACTCCCTCAATGAGTACT 57.233 47.619 9.63 0.00 46.84 2.73
1665 1714 1.898574 CCGGCCCATGGATAACAGC 60.899 63.158 15.22 6.59 0.00 4.40
1922 1975 6.041637 AGTGTTACAAGAGTTGATCTACCACA 59.958 38.462 3.54 0.00 37.23 4.17
1970 2023 5.845734 TGAAGGTAATACCCTACTTCCTGA 58.154 41.667 5.71 0.00 39.75 3.86
1991 2044 0.759436 GGTTCGGGCCCTCTCTATGA 60.759 60.000 22.43 4.41 0.00 2.15
2019 2072 2.356780 GGAGACGGGGGACACGATT 61.357 63.158 0.00 0.00 34.93 3.34
2540 2594 2.485479 GCCTTTCTGCCGGAGAATATCA 60.485 50.000 5.05 0.00 40.53 2.15


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

AutoCloner maintained by Alex Coulton.