Multiple sequence alignment - TraesCS1D01G057900

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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 TraesCS1D01G057900 chr1D 100.000 3718 0 0 1 3718 38249211 38252928 0.000000e+00 6866.0
1 TraesCS1D01G057900 chr1D 96.290 1644 42 12 274 1903 38293235 38294873 0.000000e+00 2680.0
2 TraesCS1D01G057900 chr1D 91.903 988 57 13 1900 2886 38294901 38295866 0.000000e+00 1360.0
3 TraesCS1D01G057900 chr1D 81.362 778 130 13 1106 1875 38655210 38655980 1.470000e-173 619.0
4 TraesCS1D01G057900 chr1D 80.959 688 115 6 1199 1883 39651489 39652163 7.070000e-147 531.0
5 TraesCS1D01G057900 chr1D 85.241 332 33 6 2894 3214 234030763 234031089 9.960000e-86 327.0
6 TraesCS1D01G057900 chr1D 92.157 51 2 2 551 600 39648967 39649016 1.850000e-08 71.3
7 TraesCS1D01G057900 chr1B 95.962 1783 52 9 1900 3672 57783474 57785246 0.000000e+00 2876.0
8 TraesCS1D01G057900 chr1B 95.602 1137 42 6 772 1903 57782313 57783446 0.000000e+00 1816.0
9 TraesCS1D01G057900 chr1B 88.629 941 93 8 965 1903 58031333 58032261 0.000000e+00 1133.0
10 TraesCS1D01G057900 chr1B 87.029 717 78 10 968 1681 58107641 58108345 0.000000e+00 795.0
11 TraesCS1D01G057900 chr1B 93.529 510 23 4 274 773 57781718 57782227 0.000000e+00 750.0
12 TraesCS1D01G057900 chr1B 92.131 521 36 3 1900 2420 58032289 58032804 0.000000e+00 730.0
13 TraesCS1D01G057900 chr1B 86.169 629 73 8 965 1591 58080198 58080814 0.000000e+00 667.0
14 TraesCS1D01G057900 chr1B 81.545 764 126 5 1123 1883 58752941 58753692 1.900000e-172 616.0
15 TraesCS1D01G057900 chr1B 81.050 781 120 20 1106 1875 58540115 58540878 6.870000e-167 597.0
16 TraesCS1D01G057900 chr1B 76.171 491 92 17 1900 2381 58540934 58541408 6.210000e-58 235.0
17 TraesCS1D01G057900 chr1B 96.154 78 2 1 3631 3707 57785232 57785309 3.900000e-25 126.0
18 TraesCS1D01G057900 chr1B 88.889 72 5 3 826 895 58080073 58080143 6.620000e-13 86.1
19 TraesCS1D01G057900 chr1B 86.111 72 7 3 826 895 58031208 58031278 1.430000e-09 75.0
20 TraesCS1D01G057900 chr1A 89.243 1664 95 38 312 1903 37465762 37467413 0.000000e+00 2004.0
21 TraesCS1D01G057900 chr1A 79.008 1210 210 32 1106 2299 38359213 38360394 0.000000e+00 787.0
22 TraesCS1D01G057900 chr1A 86.463 687 66 13 1900 2577 37467441 37468109 0.000000e+00 728.0
23 TraesCS1D01G057900 chr1A 91.304 276 23 1 3 277 572733826 572733551 3.510000e-100 375.0
24 TraesCS1D01G057900 chr1A 90.647 278 25 1 1 277 572737123 572736846 5.870000e-98 368.0
25 TraesCS1D01G057900 chr1A 85.319 361 35 7 2894 3241 313293738 313293383 1.270000e-94 357.0
26 TraesCS1D01G057900 chr4A 94.909 275 13 1 1 274 643087607 643087881 2.650000e-116 429.0
27 TraesCS1D01G057900 chr5A 93.091 275 17 2 1 274 632351484 632351757 5.780000e-108 401.0
28 TraesCS1D01G057900 chr7D 92.473 279 19 2 1 279 76597097 76597373 7.480000e-107 398.0
29 TraesCS1D01G057900 chr6A 91.197 284 23 2 1 282 555251167 555251450 5.820000e-103 385.0
30 TraesCS1D01G057900 chr6A 92.222 270 20 1 1 269 534661160 534660891 7.540000e-102 381.0
31 TraesCS1D01G057900 chr3B 91.429 280 22 2 1 278 822996279 822996000 2.100000e-102 383.0
32 TraesCS1D01G057900 chr3A 91.071 280 23 2 1 278 59525579 59525300 9.750000e-101 377.0
33 TraesCS1D01G057900 chr2D 81.612 397 40 10 2926 3308 382186023 382186400 7.810000e-77 298.0
34 TraesCS1D01G057900 chr2A 81.842 380 38 10 2943 3308 516471119 516471481 1.310000e-74 291.0


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 TraesCS1D01G057900 chr1D 38249211 38252928 3717 False 6866.00 6866 100.00000 1 3718 1 chr1D.!!$F1 3717
1 TraesCS1D01G057900 chr1D 38293235 38295866 2631 False 2020.00 2680 94.09650 274 2886 2 chr1D.!!$F4 2612
2 TraesCS1D01G057900 chr1D 38655210 38655980 770 False 619.00 619 81.36200 1106 1875 1 chr1D.!!$F2 769
3 TraesCS1D01G057900 chr1D 39648967 39652163 3196 False 301.15 531 86.55800 551 1883 2 chr1D.!!$F5 1332
4 TraesCS1D01G057900 chr1B 57781718 57785309 3591 False 1392.00 2876 95.31175 274 3707 4 chr1B.!!$F3 3433
5 TraesCS1D01G057900 chr1B 58107641 58108345 704 False 795.00 795 87.02900 968 1681 1 chr1B.!!$F1 713
6 TraesCS1D01G057900 chr1B 58031208 58032804 1596 False 646.00 1133 88.95700 826 2420 3 chr1B.!!$F4 1594
7 TraesCS1D01G057900 chr1B 58752941 58753692 751 False 616.00 616 81.54500 1123 1883 1 chr1B.!!$F2 760
8 TraesCS1D01G057900 chr1B 58540115 58541408 1293 False 416.00 597 78.61050 1106 2381 2 chr1B.!!$F6 1275
9 TraesCS1D01G057900 chr1B 58080073 58080814 741 False 376.55 667 87.52900 826 1591 2 chr1B.!!$F5 765
10 TraesCS1D01G057900 chr1A 37465762 37468109 2347 False 1366.00 2004 87.85300 312 2577 2 chr1A.!!$F2 2265
11 TraesCS1D01G057900 chr1A 38359213 38360394 1181 False 787.00 787 79.00800 1106 2299 1 chr1A.!!$F1 1193
12 TraesCS1D01G057900 chr1A 572733551 572737123 3572 True 371.50 375 90.97550 1 277 2 chr1A.!!$R2 276

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
219 220 0.033405 CTCCTCGGAGGGTCCTTGTA 60.033 60.000 23.39 0.96 38.51 2.41 F
222 223 0.172803 CTCGGAGGGTCCTTGTAACG 59.827 60.000 0.00 0.00 33.30 3.18 F
225 226 0.323957 GGAGGGTCCTTGTAACGCTT 59.676 55.000 0.00 0.00 39.70 4.68 F
375 384 0.712775 CGAGCAAAGAAGAGACAGCG 59.287 55.000 0.00 0.00 0.00 5.18 F
1895 5316 1.003545 CAGATCATAAGTTTGCCGCCG 60.004 52.381 0.00 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 6585 2.235402 TGTATCTCGTTGAGTTTCCCCC 59.765 50.000 0.00 0.00 0.00 5.40 R
2318 6701 1.753930 TCCACAGATGCGCATTGAAT 58.246 45.000 26.12 8.43 0.00 2.57 R
2337 6720 1.871676 CAGCATATCGCAGCAGAACAT 59.128 47.619 0.00 0.00 46.13 2.71 R
2541 6938 2.088423 ACAAACAGAGCCAAACGAACA 58.912 42.857 0.00 0.00 0.00 3.18 R
2886 7690 0.857675 ACCAAACAAGGCCTAGGGTT 59.142 50.000 5.16 8.77 0.00 4.11 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
26 27 5.944007 GGTGAAAACCTAAGATTTGGCTAGA 59.056 40.000 0.00 0.00 0.00 2.43
37 38 1.310030 TGGCTAGACCAGATCGGGT 59.690 57.895 18.14 18.14 46.36 5.28
38 39 1.043116 TGGCTAGACCAGATCGGGTG 61.043 60.000 23.04 9.28 46.36 4.61
39 40 0.755698 GGCTAGACCAGATCGGGTGA 60.756 60.000 23.04 9.00 42.53 4.02
40 41 0.386113 GCTAGACCAGATCGGGTGAC 59.614 60.000 23.04 8.91 42.53 3.67
41 42 1.763968 CTAGACCAGATCGGGTGACA 58.236 55.000 23.04 6.00 42.53 3.58
42 43 1.678627 CTAGACCAGATCGGGTGACAG 59.321 57.143 23.04 11.73 42.53 3.51
43 44 0.251832 AGACCAGATCGGGTGACAGT 60.252 55.000 23.04 0.00 42.53 3.55
44 45 0.108615 GACCAGATCGGGTGACAGTG 60.109 60.000 23.04 0.00 42.53 3.66
45 46 0.832135 ACCAGATCGGGTGACAGTGT 60.832 55.000 17.39 0.00 40.44 3.55
46 47 0.321671 CCAGATCGGGTGACAGTGTT 59.678 55.000 3.35 0.00 0.00 3.32
47 48 1.432514 CAGATCGGGTGACAGTGTTG 58.567 55.000 0.00 0.00 0.00 3.33
48 49 1.048601 AGATCGGGTGACAGTGTTGT 58.951 50.000 0.00 0.00 41.18 3.32
59 60 4.371855 GACAGTGTTGTCCTCGATATCA 57.628 45.455 3.12 0.00 46.47 2.15
60 61 4.106197 GACAGTGTTGTCCTCGATATCAC 58.894 47.826 3.12 0.00 46.47 3.06
61 62 3.764434 ACAGTGTTGTCCTCGATATCACT 59.236 43.478 3.12 0.00 35.28 3.41
62 63 4.142359 ACAGTGTTGTCCTCGATATCACTC 60.142 45.833 3.12 0.00 33.60 3.51
63 64 3.381908 AGTGTTGTCCTCGATATCACTCC 59.618 47.826 3.12 0.00 31.43 3.85
64 65 2.693591 TGTTGTCCTCGATATCACTCCC 59.306 50.000 3.12 0.00 0.00 4.30
65 66 2.959707 GTTGTCCTCGATATCACTCCCT 59.040 50.000 3.12 0.00 0.00 4.20
66 67 2.865079 TGTCCTCGATATCACTCCCTC 58.135 52.381 3.12 0.00 0.00 4.30
67 68 2.164338 GTCCTCGATATCACTCCCTCC 58.836 57.143 3.12 0.00 0.00 4.30
68 69 2.066592 TCCTCGATATCACTCCCTCCT 58.933 52.381 3.12 0.00 0.00 3.69
69 70 2.447429 TCCTCGATATCACTCCCTCCTT 59.553 50.000 3.12 0.00 0.00 3.36
70 71 3.117093 TCCTCGATATCACTCCCTCCTTT 60.117 47.826 3.12 0.00 0.00 3.11
71 72 3.006323 CCTCGATATCACTCCCTCCTTTG 59.994 52.174 3.12 0.00 0.00 2.77
72 73 3.891977 CTCGATATCACTCCCTCCTTTGA 59.108 47.826 3.12 0.00 0.00 2.69
73 74 3.891977 TCGATATCACTCCCTCCTTTGAG 59.108 47.826 3.12 0.00 38.42 3.02
81 82 2.269241 CTCCTTTGAGGCGTCCCC 59.731 66.667 3.56 0.00 34.61 4.81
83 84 1.842381 CTCCTTTGAGGCGTCCCCTT 61.842 60.000 3.56 0.00 46.60 3.95
84 85 1.675641 CCTTTGAGGCGTCCCCTTG 60.676 63.158 3.56 0.00 46.60 3.61
85 86 1.675641 CTTTGAGGCGTCCCCTTGG 60.676 63.158 3.56 0.00 46.60 3.61
86 87 2.124507 CTTTGAGGCGTCCCCTTGGA 62.125 60.000 3.56 0.00 46.60 3.53
87 88 2.124507 TTTGAGGCGTCCCCTTGGAG 62.125 60.000 3.56 0.00 46.60 3.86
88 89 3.787001 GAGGCGTCCCCTTGGAGG 61.787 72.222 0.00 0.00 46.60 4.30
98 99 4.195334 CTTGGAGGCCCGGGGATG 62.195 72.222 25.28 0.00 34.29 3.51
102 103 4.191015 GAGGCCCGGGGATGGTTC 62.191 72.222 25.28 2.42 0.00 3.62
114 115 2.767505 GGATGGTTCCCGATGATGTAC 58.232 52.381 0.00 0.00 35.84 2.90
115 116 2.104111 GGATGGTTCCCGATGATGTACA 59.896 50.000 0.00 0.00 35.84 2.90
116 117 3.244561 GGATGGTTCCCGATGATGTACAT 60.245 47.826 8.43 8.43 37.75 2.29
117 118 3.192541 TGGTTCCCGATGATGTACATG 57.807 47.619 14.43 0.00 39.56 3.21
118 119 2.158827 TGGTTCCCGATGATGTACATGG 60.159 50.000 14.43 7.97 39.56 3.66
119 120 1.873591 GTTCCCGATGATGTACATGGC 59.126 52.381 14.43 0.00 39.56 4.40
120 121 1.423584 TCCCGATGATGTACATGGCT 58.576 50.000 14.43 0.00 39.56 4.75
121 122 1.768275 TCCCGATGATGTACATGGCTT 59.232 47.619 14.43 0.00 39.56 4.35
122 123 1.875514 CCCGATGATGTACATGGCTTG 59.124 52.381 14.43 1.45 39.56 4.01
123 124 2.564771 CCGATGATGTACATGGCTTGT 58.435 47.619 14.43 11.04 39.56 3.16
124 125 2.545526 CCGATGATGTACATGGCTTGTC 59.454 50.000 14.43 0.00 39.56 3.18
125 126 2.219445 CGATGATGTACATGGCTTGTCG 59.781 50.000 14.43 9.39 39.56 4.35
126 127 2.022764 TGATGTACATGGCTTGTCGG 57.977 50.000 14.43 0.00 39.87 4.79
127 128 1.277842 TGATGTACATGGCTTGTCGGT 59.722 47.619 14.43 0.00 39.87 4.69
128 129 1.665679 GATGTACATGGCTTGTCGGTG 59.334 52.381 14.43 0.00 39.87 4.94
129 130 0.321210 TGTACATGGCTTGTCGGTGG 60.321 55.000 9.52 0.00 39.87 4.61
130 131 0.036765 GTACATGGCTTGTCGGTGGA 60.037 55.000 9.52 0.00 39.87 4.02
131 132 0.249120 TACATGGCTTGTCGGTGGAG 59.751 55.000 9.52 0.00 39.87 3.86
132 133 2.045926 ATGGCTTGTCGGTGGAGC 60.046 61.111 0.00 0.00 35.71 4.70
133 134 2.596851 ATGGCTTGTCGGTGGAGCT 61.597 57.895 0.00 0.00 36.66 4.09
134 135 2.032681 GGCTTGTCGGTGGAGCTT 59.967 61.111 0.00 0.00 36.66 3.74
135 136 1.295423 GGCTTGTCGGTGGAGCTTA 59.705 57.895 0.00 0.00 36.66 3.09
136 137 0.741221 GGCTTGTCGGTGGAGCTTAG 60.741 60.000 0.00 0.00 36.66 2.18
137 138 0.741221 GCTTGTCGGTGGAGCTTAGG 60.741 60.000 0.00 0.00 33.72 2.69
138 139 0.608640 CTTGTCGGTGGAGCTTAGGT 59.391 55.000 0.00 0.00 0.00 3.08
139 140 1.002087 CTTGTCGGTGGAGCTTAGGTT 59.998 52.381 0.00 0.00 0.00 3.50
140 141 1.053424 TGTCGGTGGAGCTTAGGTTT 58.947 50.000 0.00 0.00 0.00 3.27
141 142 1.270625 TGTCGGTGGAGCTTAGGTTTG 60.271 52.381 0.00 0.00 0.00 2.93
142 143 1.053424 TCGGTGGAGCTTAGGTTTGT 58.947 50.000 0.00 0.00 0.00 2.83
143 144 1.156736 CGGTGGAGCTTAGGTTTGTG 58.843 55.000 0.00 0.00 0.00 3.33
144 145 1.534729 GGTGGAGCTTAGGTTTGTGG 58.465 55.000 0.00 0.00 0.00 4.17
145 146 1.202891 GGTGGAGCTTAGGTTTGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
146 147 1.880027 GTGGAGCTTAGGTTTGTGGTG 59.120 52.381 0.00 0.00 0.00 4.17
147 148 1.202879 TGGAGCTTAGGTTTGTGGTGG 60.203 52.381 0.00 0.00 0.00 4.61
148 149 1.202891 GGAGCTTAGGTTTGTGGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
149 150 1.880027 GAGCTTAGGTTTGTGGTGGTG 59.120 52.381 0.00 0.00 0.00 4.17
150 151 0.313987 GCTTAGGTTTGTGGTGGTGC 59.686 55.000 0.00 0.00 0.00 5.01
151 152 0.958822 CTTAGGTTTGTGGTGGTGCC 59.041 55.000 0.00 0.00 37.90 5.01
152 153 0.820074 TTAGGTTTGTGGTGGTGCCG 60.820 55.000 0.00 0.00 41.21 5.69
153 154 1.697082 TAGGTTTGTGGTGGTGCCGA 61.697 55.000 0.00 0.00 41.21 5.54
154 155 2.719354 GTTTGTGGTGGTGCCGAC 59.281 61.111 0.00 0.00 41.21 4.79
155 156 1.822186 GTTTGTGGTGGTGCCGACT 60.822 57.895 0.00 0.00 41.21 4.18
156 157 1.077357 TTTGTGGTGGTGCCGACTT 60.077 52.632 0.00 0.00 41.21 3.01
157 158 0.681564 TTTGTGGTGGTGCCGACTTT 60.682 50.000 0.00 0.00 41.21 2.66
158 159 0.681564 TTGTGGTGGTGCCGACTTTT 60.682 50.000 0.00 0.00 41.21 2.27
159 160 0.681564 TGTGGTGGTGCCGACTTTTT 60.682 50.000 0.00 0.00 41.21 1.94
195 196 3.708563 TTCACTAACCTTTTGCTGTGC 57.291 42.857 0.00 0.00 0.00 4.57
196 197 2.930950 TCACTAACCTTTTGCTGTGCT 58.069 42.857 0.00 0.00 0.00 4.40
197 198 3.287222 TCACTAACCTTTTGCTGTGCTT 58.713 40.909 0.00 0.00 0.00 3.91
198 199 3.699038 TCACTAACCTTTTGCTGTGCTTT 59.301 39.130 0.00 0.00 0.00 3.51
199 200 4.044426 CACTAACCTTTTGCTGTGCTTTC 58.956 43.478 0.00 0.00 0.00 2.62
200 201 2.602257 AACCTTTTGCTGTGCTTTCC 57.398 45.000 0.00 0.00 0.00 3.13
201 202 1.780503 ACCTTTTGCTGTGCTTTCCT 58.219 45.000 0.00 0.00 0.00 3.36
202 203 1.683385 ACCTTTTGCTGTGCTTTCCTC 59.317 47.619 0.00 0.00 0.00 3.71
203 204 1.000171 CCTTTTGCTGTGCTTTCCTCC 60.000 52.381 0.00 0.00 0.00 4.30
204 205 1.959282 CTTTTGCTGTGCTTTCCTCCT 59.041 47.619 0.00 0.00 0.00 3.69
205 206 1.609208 TTTGCTGTGCTTTCCTCCTC 58.391 50.000 0.00 0.00 0.00 3.71
206 207 0.603707 TTGCTGTGCTTTCCTCCTCG 60.604 55.000 0.00 0.00 0.00 4.63
207 208 1.743252 GCTGTGCTTTCCTCCTCGG 60.743 63.158 0.00 0.00 0.00 4.63
208 209 1.975327 CTGTGCTTTCCTCCTCGGA 59.025 57.895 0.00 0.00 41.06 4.55
209 210 0.108424 CTGTGCTTTCCTCCTCGGAG 60.108 60.000 5.97 5.97 44.28 4.63
217 218 3.622514 CTCCTCGGAGGGTCCTTG 58.377 66.667 23.39 4.35 38.51 3.61
218 219 1.305381 CTCCTCGGAGGGTCCTTGT 60.305 63.158 23.39 0.00 38.51 3.16
219 220 0.033405 CTCCTCGGAGGGTCCTTGTA 60.033 60.000 23.39 0.96 38.51 2.41
220 221 0.410663 TCCTCGGAGGGTCCTTGTAA 59.589 55.000 23.39 0.00 35.59 2.41
221 222 0.535797 CCTCGGAGGGTCCTTGTAAC 59.464 60.000 16.59 0.00 33.30 2.50
222 223 0.172803 CTCGGAGGGTCCTTGTAACG 59.827 60.000 0.00 0.00 33.30 3.18
223 224 1.447314 CGGAGGGTCCTTGTAACGC 60.447 63.158 0.00 0.00 33.30 4.84
224 225 1.885163 CGGAGGGTCCTTGTAACGCT 61.885 60.000 0.00 0.00 41.99 5.07
225 226 0.323957 GGAGGGTCCTTGTAACGCTT 59.676 55.000 0.00 0.00 39.70 4.68
226 227 1.675116 GGAGGGTCCTTGTAACGCTTC 60.675 57.143 0.00 0.00 39.70 3.86
227 228 1.275573 GAGGGTCCTTGTAACGCTTCT 59.724 52.381 0.00 0.00 39.70 2.85
228 229 1.697982 AGGGTCCTTGTAACGCTTCTT 59.302 47.619 0.00 0.00 36.62 2.52
229 230 2.074576 GGGTCCTTGTAACGCTTCTTC 58.925 52.381 0.00 0.00 0.00 2.87
230 231 2.289506 GGGTCCTTGTAACGCTTCTTCT 60.290 50.000 0.00 0.00 0.00 2.85
231 232 2.737252 GGTCCTTGTAACGCTTCTTCTG 59.263 50.000 0.00 0.00 0.00 3.02
232 233 3.554337 GGTCCTTGTAACGCTTCTTCTGA 60.554 47.826 0.00 0.00 0.00 3.27
233 234 4.246458 GTCCTTGTAACGCTTCTTCTGAT 58.754 43.478 0.00 0.00 0.00 2.90
234 235 4.327627 GTCCTTGTAACGCTTCTTCTGATC 59.672 45.833 0.00 0.00 0.00 2.92
235 236 4.021456 TCCTTGTAACGCTTCTTCTGATCA 60.021 41.667 0.00 0.00 0.00 2.92
236 237 4.690748 CCTTGTAACGCTTCTTCTGATCAA 59.309 41.667 0.00 0.00 0.00 2.57
237 238 5.352569 CCTTGTAACGCTTCTTCTGATCAAT 59.647 40.000 0.00 0.00 0.00 2.57
238 239 5.784750 TGTAACGCTTCTTCTGATCAATG 57.215 39.130 0.00 0.00 0.00 2.82
239 240 5.478407 TGTAACGCTTCTTCTGATCAATGA 58.522 37.500 0.00 0.00 0.00 2.57
240 241 5.931724 TGTAACGCTTCTTCTGATCAATGAA 59.068 36.000 0.00 0.00 0.00 2.57
241 242 6.595326 TGTAACGCTTCTTCTGATCAATGAAT 59.405 34.615 0.00 0.00 0.00 2.57
242 243 6.506500 AACGCTTCTTCTGATCAATGAATT 57.493 33.333 0.00 0.00 0.00 2.17
243 244 6.506500 ACGCTTCTTCTGATCAATGAATTT 57.493 33.333 0.00 0.00 0.00 1.82
244 245 6.320171 ACGCTTCTTCTGATCAATGAATTTG 58.680 36.000 0.00 0.00 36.61 2.32
245 246 5.742453 CGCTTCTTCTGATCAATGAATTTGG 59.258 40.000 0.00 0.00 35.92 3.28
246 247 5.519206 GCTTCTTCTGATCAATGAATTTGGC 59.481 40.000 0.00 0.00 35.92 4.52
247 248 6.593268 TTCTTCTGATCAATGAATTTGGCA 57.407 33.333 0.00 0.00 35.92 4.92
248 249 6.203808 TCTTCTGATCAATGAATTTGGCAG 57.796 37.500 0.00 0.00 38.44 4.85
249 250 4.380841 TCTGATCAATGAATTTGGCAGC 57.619 40.909 0.00 0.00 37.71 5.25
250 251 4.021229 TCTGATCAATGAATTTGGCAGCT 58.979 39.130 0.00 0.00 37.71 4.24
251 252 4.097437 TCTGATCAATGAATTTGGCAGCTC 59.903 41.667 0.00 0.00 37.71 4.09
252 253 4.021229 TGATCAATGAATTTGGCAGCTCT 58.979 39.130 0.00 0.00 35.92 4.09
253 254 5.195185 TGATCAATGAATTTGGCAGCTCTA 58.805 37.500 0.00 0.00 35.92 2.43
254 255 4.970662 TCAATGAATTTGGCAGCTCTAC 57.029 40.909 0.00 0.00 35.92 2.59
255 256 4.592942 TCAATGAATTTGGCAGCTCTACT 58.407 39.130 0.00 0.00 35.92 2.57
256 257 4.397103 TCAATGAATTTGGCAGCTCTACTG 59.603 41.667 0.00 0.00 40.67 2.74
263 264 4.996976 CAGCTCTACTGCCAACGT 57.003 55.556 0.00 0.00 40.19 3.99
264 265 3.217242 CAGCTCTACTGCCAACGTT 57.783 52.632 0.00 0.00 40.19 3.99
265 266 1.512926 CAGCTCTACTGCCAACGTTT 58.487 50.000 0.00 0.00 40.19 3.60
266 267 2.683968 CAGCTCTACTGCCAACGTTTA 58.316 47.619 0.00 0.00 40.19 2.01
267 268 3.064207 CAGCTCTACTGCCAACGTTTAA 58.936 45.455 0.00 0.00 40.19 1.52
268 269 3.496884 CAGCTCTACTGCCAACGTTTAAA 59.503 43.478 0.00 0.00 40.19 1.52
269 270 4.024387 CAGCTCTACTGCCAACGTTTAAAA 60.024 41.667 0.00 0.00 40.19 1.52
270 271 4.760204 AGCTCTACTGCCAACGTTTAAAAT 59.240 37.500 0.00 0.00 0.00 1.82
271 272 5.935789 AGCTCTACTGCCAACGTTTAAAATA 59.064 36.000 0.00 0.00 0.00 1.40
272 273 6.428771 AGCTCTACTGCCAACGTTTAAAATAA 59.571 34.615 0.00 0.00 0.00 1.40
337 338 6.262193 ACTTCAAAAGGTTCGACTTGAAAA 57.738 33.333 0.00 0.00 38.60 2.29
338 339 6.090783 ACTTCAAAAGGTTCGACTTGAAAAC 58.909 36.000 0.00 0.00 38.60 2.43
375 384 0.712775 CGAGCAAAGAAGAGACAGCG 59.287 55.000 0.00 0.00 0.00 5.18
409 418 1.308069 CGATCCCAACAAGGCCACAG 61.308 60.000 5.01 0.00 35.39 3.66
421 430 2.200337 GCCACAGAACCCACAACCC 61.200 63.158 0.00 0.00 0.00 4.11
422 431 1.536676 CCACAGAACCCACAACCCT 59.463 57.895 0.00 0.00 0.00 4.34
509 523 1.696097 GCGGCCTATTTCCTCCTCCA 61.696 60.000 0.00 0.00 0.00 3.86
679 740 5.531634 TCTTTGTGCTTGATTTTCATCCAC 58.468 37.500 0.00 0.00 32.13 4.02
680 741 3.557577 TGTGCTTGATTTTCATCCACG 57.442 42.857 0.00 0.00 33.33 4.94
753 821 3.186409 CGAGAAACAGAAATTTCGAGCCA 59.814 43.478 12.42 0.00 42.37 4.75
1685 5100 3.088532 TGTCCATGGTTTGATACTTGGC 58.911 45.455 12.58 0.00 33.02 4.52
1895 5316 1.003545 CAGATCATAAGTTTGCCGCCG 60.004 52.381 0.00 0.00 0.00 6.46
1955 5654 1.026182 GCCACATGAGAATGGTCGCA 61.026 55.000 0.00 0.00 38.34 5.10
1990 5689 4.837298 TGGACATTGGATGATTTTGGTCAA 59.163 37.500 0.00 0.00 0.00 3.18
2202 6585 7.798596 AGCTTCTTTCATACAATATCAGTGG 57.201 36.000 0.00 0.00 0.00 4.00
2318 6701 6.227522 TCGGTTCAGTGAATGTCAAATTCTA 58.772 36.000 9.18 0.00 0.00 2.10
2337 6720 1.753930 ATTCAATGCGCATCTGTGGA 58.246 45.000 25.53 14.01 0.00 4.02
2382 6768 3.005897 CCACCTTGTATATCACGCTAGCT 59.994 47.826 13.93 0.00 0.00 3.32
2383 6769 4.217767 CCACCTTGTATATCACGCTAGCTA 59.782 45.833 13.93 0.00 0.00 3.32
2384 6770 5.394802 CACCTTGTATATCACGCTAGCTAG 58.605 45.833 16.84 16.84 0.00 3.42
2385 6771 5.048643 CACCTTGTATATCACGCTAGCTAGT 60.049 44.000 21.62 0.65 0.00 2.57
2879 7683 2.081161 GGGATCCCATGGGCAGAGT 61.081 63.158 27.41 8.98 35.81 3.24
2882 7686 1.494721 GGATCCCATGGGCAGAGTAAA 59.505 52.381 27.41 6.44 34.68 2.01
2886 7690 2.580322 TCCCATGGGCAGAGTAAAATCA 59.420 45.455 27.41 0.08 34.68 2.57
2887 7691 3.011144 TCCCATGGGCAGAGTAAAATCAA 59.989 43.478 27.41 0.00 34.68 2.57
2979 7783 1.328279 CCTTCTTGTCACCCAAACCC 58.672 55.000 0.00 0.00 31.20 4.11
2995 7799 5.104569 CCCAAACCCTGCAATACCAATTAAT 60.105 40.000 0.00 0.00 0.00 1.40
3000 7804 8.409358 AACCCTGCAATACCAATTAATATCTC 57.591 34.615 0.00 0.00 0.00 2.75
3012 7819 9.326413 ACCAATTAATATCTCGTTTGGTTCTAG 57.674 33.333 0.00 0.00 43.08 2.43
3076 7883 0.397816 GGAAGAGAGGGAGCAGCCTA 60.398 60.000 0.00 0.00 36.66 3.93
3080 7887 0.184933 GAGAGGGAGCAGCCTAGAGA 59.815 60.000 0.00 0.00 36.66 3.10
3090 7897 0.396417 AGCCTAGAGACGTGCCTCAT 60.396 55.000 0.00 0.00 35.68 2.90
3119 7926 2.567615 GGTTCCACGGATCATAGGCTAT 59.432 50.000 0.00 0.00 0.00 2.97
3150 7957 1.486310 CCCGTGGATTGAAGGAGATCA 59.514 52.381 0.00 0.00 0.00 2.92
3153 7960 2.604914 CGTGGATTGAAGGAGATCAACG 59.395 50.000 0.00 0.00 41.78 4.10
3154 7961 2.352960 GTGGATTGAAGGAGATCAACGC 59.647 50.000 0.00 0.00 41.78 4.84
3251 8058 1.660607 CAGAATGAACCACGTGGATCG 59.339 52.381 40.21 20.13 39.57 3.69
3380 8187 7.161404 AGGGGCAACAAATATTTTTCTTCTTC 58.839 34.615 0.00 0.00 39.74 2.87
3417 8224 6.662414 TTTCTTAATCGGTACTCTTGCATG 57.338 37.500 0.00 0.00 0.00 4.06
3419 8226 6.459670 TCTTAATCGGTACTCTTGCATGTA 57.540 37.500 0.00 0.00 0.00 2.29
3424 8231 9.850628 TTAATCGGTACTCTTGCATGTATATAC 57.149 33.333 5.89 5.89 0.00 1.47
3687 8731 5.378230 TGCTCCTTCCAGAACATATGATT 57.622 39.130 10.38 0.00 0.00 2.57
3713 8757 8.834749 AAGAAAGATGAACTGTTTAGTACTCC 57.165 34.615 0.00 0.00 35.69 3.85
3714 8758 7.387643 AGAAAGATGAACTGTTTAGTACTCCC 58.612 38.462 0.00 0.00 35.69 4.30
3715 8759 6.936968 AAGATGAACTGTTTAGTACTCCCT 57.063 37.500 0.00 0.00 35.69 4.20
3716 8760 6.532988 AGATGAACTGTTTAGTACTCCCTC 57.467 41.667 0.00 0.00 35.69 4.30
3717 8761 6.257586 AGATGAACTGTTTAGTACTCCCTCT 58.742 40.000 0.00 0.00 35.69 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.832135 ACACTGTCACCCGATCTGGT 60.832 55.000 2.44 2.44 39.96 4.00
39 40 3.764434 AGTGATATCGAGGACAACACTGT 59.236 43.478 0.00 0.00 38.98 3.55
40 41 4.355437 GAGTGATATCGAGGACAACACTG 58.645 47.826 0.00 0.00 37.27 3.66
41 42 3.381908 GGAGTGATATCGAGGACAACACT 59.618 47.826 0.00 0.00 39.32 3.55
42 43 3.491104 GGGAGTGATATCGAGGACAACAC 60.491 52.174 0.00 0.00 0.00 3.32
43 44 2.693591 GGGAGTGATATCGAGGACAACA 59.306 50.000 0.00 0.00 0.00 3.33
44 45 2.959707 AGGGAGTGATATCGAGGACAAC 59.040 50.000 0.00 0.00 0.00 3.32
45 46 3.223435 GAGGGAGTGATATCGAGGACAA 58.777 50.000 0.00 0.00 0.00 3.18
46 47 2.489255 GGAGGGAGTGATATCGAGGACA 60.489 54.545 0.00 0.00 0.00 4.02
47 48 2.164338 GGAGGGAGTGATATCGAGGAC 58.836 57.143 0.00 0.00 0.00 3.85
48 49 2.066592 AGGAGGGAGTGATATCGAGGA 58.933 52.381 0.00 0.00 0.00 3.71
49 50 2.595750 AGGAGGGAGTGATATCGAGG 57.404 55.000 0.00 0.00 0.00 4.63
50 51 3.891977 TCAAAGGAGGGAGTGATATCGAG 59.108 47.826 0.00 0.00 0.00 4.04
51 52 3.891977 CTCAAAGGAGGGAGTGATATCGA 59.108 47.826 0.00 0.00 37.51 3.59
52 53 4.250116 CTCAAAGGAGGGAGTGATATCG 57.750 50.000 0.00 0.00 37.51 2.92
64 65 1.842381 AAGGGGACGCCTCAAAGGAG 61.842 60.000 12.13 0.00 41.31 3.69
65 66 1.846124 AAGGGGACGCCTCAAAGGA 60.846 57.895 12.13 0.00 37.67 3.36
66 67 1.675641 CAAGGGGACGCCTCAAAGG 60.676 63.158 12.13 0.00 38.80 3.11
67 68 1.675641 CCAAGGGGACGCCTCAAAG 60.676 63.158 12.13 2.75 35.59 2.77
68 69 2.124507 CTCCAAGGGGACGCCTCAAA 62.125 60.000 12.13 0.00 38.64 2.69
69 70 2.528127 TCCAAGGGGACGCCTCAA 60.528 61.111 12.13 0.00 38.64 3.02
70 71 3.003173 CTCCAAGGGGACGCCTCA 61.003 66.667 12.13 0.00 38.64 3.86
71 72 3.787001 CCTCCAAGGGGACGCCTC 61.787 72.222 12.13 0.00 38.64 4.70
81 82 4.195334 CATCCCCGGGCCTCCAAG 62.195 72.222 17.73 0.00 0.00 3.61
85 86 4.191015 GAACCATCCCCGGGCCTC 62.191 72.222 17.73 0.08 0.00 4.70
94 95 5.336107 CATGTACATCATCGGGAACCATCC 61.336 50.000 5.07 0.00 41.73 3.51
95 96 3.748048 CATGTACATCATCGGGAACCATC 59.252 47.826 5.07 0.00 41.73 3.51
96 97 3.496692 CCATGTACATCATCGGGAACCAT 60.497 47.826 5.07 0.00 41.73 3.55
97 98 2.158827 CCATGTACATCATCGGGAACCA 60.159 50.000 5.07 0.00 41.73 3.67
98 99 2.494059 CCATGTACATCATCGGGAACC 58.506 52.381 5.07 0.00 39.19 3.62
99 100 1.873591 GCCATGTACATCATCGGGAAC 59.126 52.381 5.07 0.00 34.09 3.62
100 101 1.768275 AGCCATGTACATCATCGGGAA 59.232 47.619 5.07 0.00 34.09 3.97
101 102 1.423584 AGCCATGTACATCATCGGGA 58.576 50.000 5.07 0.00 34.09 5.14
102 103 1.875514 CAAGCCATGTACATCATCGGG 59.124 52.381 5.07 5.07 34.09 5.14
103 104 2.545526 GACAAGCCATGTACATCATCGG 59.454 50.000 5.07 5.46 44.12 4.18
104 105 2.219445 CGACAAGCCATGTACATCATCG 59.781 50.000 5.07 5.60 44.12 3.84
105 106 2.545526 CCGACAAGCCATGTACATCATC 59.454 50.000 5.07 0.00 44.12 2.92
106 107 2.092968 ACCGACAAGCCATGTACATCAT 60.093 45.455 5.07 0.00 44.12 2.45
107 108 1.277842 ACCGACAAGCCATGTACATCA 59.722 47.619 5.07 0.00 44.12 3.07
108 109 1.665679 CACCGACAAGCCATGTACATC 59.334 52.381 5.07 0.00 44.12 3.06
109 110 1.678728 CCACCGACAAGCCATGTACAT 60.679 52.381 1.41 1.41 44.12 2.29
110 111 0.321210 CCACCGACAAGCCATGTACA 60.321 55.000 0.00 0.00 44.12 2.90
111 112 0.036765 TCCACCGACAAGCCATGTAC 60.037 55.000 0.00 0.00 44.12 2.90
112 113 0.249120 CTCCACCGACAAGCCATGTA 59.751 55.000 0.00 0.00 44.12 2.29
114 115 2.401766 GCTCCACCGACAAGCCATG 61.402 63.158 0.00 0.00 0.00 3.66
115 116 2.045926 GCTCCACCGACAAGCCAT 60.046 61.111 0.00 0.00 0.00 4.40
116 117 1.476845 TAAGCTCCACCGACAAGCCA 61.477 55.000 0.00 0.00 36.69 4.75
117 118 0.741221 CTAAGCTCCACCGACAAGCC 60.741 60.000 0.00 0.00 36.69 4.35
118 119 0.741221 CCTAAGCTCCACCGACAAGC 60.741 60.000 0.00 0.00 36.27 4.01
119 120 0.608640 ACCTAAGCTCCACCGACAAG 59.391 55.000 0.00 0.00 0.00 3.16
120 121 1.053424 AACCTAAGCTCCACCGACAA 58.947 50.000 0.00 0.00 0.00 3.18
121 122 1.053424 AAACCTAAGCTCCACCGACA 58.947 50.000 0.00 0.00 0.00 4.35
122 123 1.270678 ACAAACCTAAGCTCCACCGAC 60.271 52.381 0.00 0.00 0.00 4.79
123 124 1.053424 ACAAACCTAAGCTCCACCGA 58.947 50.000 0.00 0.00 0.00 4.69
124 125 1.156736 CACAAACCTAAGCTCCACCG 58.843 55.000 0.00 0.00 0.00 4.94
125 126 1.202891 ACCACAAACCTAAGCTCCACC 60.203 52.381 0.00 0.00 0.00 4.61
126 127 1.880027 CACCACAAACCTAAGCTCCAC 59.120 52.381 0.00 0.00 0.00 4.02
127 128 1.202879 CCACCACAAACCTAAGCTCCA 60.203 52.381 0.00 0.00 0.00 3.86
128 129 1.202891 ACCACCACAAACCTAAGCTCC 60.203 52.381 0.00 0.00 0.00 4.70
129 130 1.880027 CACCACCACAAACCTAAGCTC 59.120 52.381 0.00 0.00 0.00 4.09
130 131 1.981256 CACCACCACAAACCTAAGCT 58.019 50.000 0.00 0.00 0.00 3.74
131 132 0.313987 GCACCACCACAAACCTAAGC 59.686 55.000 0.00 0.00 0.00 3.09
132 133 0.958822 GGCACCACCACAAACCTAAG 59.041 55.000 0.00 0.00 38.86 2.18
133 134 0.820074 CGGCACCACCACAAACCTAA 60.820 55.000 0.00 0.00 39.03 2.69
134 135 1.228003 CGGCACCACCACAAACCTA 60.228 57.895 0.00 0.00 39.03 3.08
135 136 2.518349 CGGCACCACCACAAACCT 60.518 61.111 0.00 0.00 39.03 3.50
136 137 2.517402 TCGGCACCACCACAAACC 60.517 61.111 0.00 0.00 39.03 3.27
137 138 1.381165 AAGTCGGCACCACCACAAAC 61.381 55.000 0.00 0.00 39.03 2.93
138 139 0.681564 AAAGTCGGCACCACCACAAA 60.682 50.000 0.00 0.00 39.03 2.83
139 140 0.681564 AAAAGTCGGCACCACCACAA 60.682 50.000 0.00 0.00 39.03 3.33
140 141 0.681564 AAAAAGTCGGCACCACCACA 60.682 50.000 0.00 0.00 39.03 4.17
141 142 2.112029 AAAAAGTCGGCACCACCAC 58.888 52.632 0.00 0.00 39.03 4.16
142 143 4.668151 AAAAAGTCGGCACCACCA 57.332 50.000 0.00 0.00 39.03 4.17
172 173 4.867608 GCACAGCAAAAGGTTAGTGAAAAA 59.132 37.500 0.00 0.00 0.00 1.94
173 174 4.159506 AGCACAGCAAAAGGTTAGTGAAAA 59.840 37.500 0.00 0.00 0.00 2.29
174 175 3.699038 AGCACAGCAAAAGGTTAGTGAAA 59.301 39.130 0.00 0.00 0.00 2.69
175 176 3.287222 AGCACAGCAAAAGGTTAGTGAA 58.713 40.909 0.00 0.00 0.00 3.18
176 177 2.930950 AGCACAGCAAAAGGTTAGTGA 58.069 42.857 0.00 0.00 0.00 3.41
177 178 3.715628 AAGCACAGCAAAAGGTTAGTG 57.284 42.857 0.00 0.00 0.00 2.74
178 179 3.068165 GGAAAGCACAGCAAAAGGTTAGT 59.932 43.478 0.00 0.00 0.00 2.24
179 180 3.319122 AGGAAAGCACAGCAAAAGGTTAG 59.681 43.478 0.00 0.00 0.00 2.34
180 181 3.295973 AGGAAAGCACAGCAAAAGGTTA 58.704 40.909 0.00 0.00 0.00 2.85
181 182 2.101415 GAGGAAAGCACAGCAAAAGGTT 59.899 45.455 0.00 0.00 0.00 3.50
182 183 1.683385 GAGGAAAGCACAGCAAAAGGT 59.317 47.619 0.00 0.00 0.00 3.50
183 184 1.000171 GGAGGAAAGCACAGCAAAAGG 60.000 52.381 0.00 0.00 0.00 3.11
184 185 1.959282 AGGAGGAAAGCACAGCAAAAG 59.041 47.619 0.00 0.00 0.00 2.27
185 186 1.956477 GAGGAGGAAAGCACAGCAAAA 59.044 47.619 0.00 0.00 0.00 2.44
186 187 1.609208 GAGGAGGAAAGCACAGCAAA 58.391 50.000 0.00 0.00 0.00 3.68
187 188 0.603707 CGAGGAGGAAAGCACAGCAA 60.604 55.000 0.00 0.00 0.00 3.91
188 189 1.004560 CGAGGAGGAAAGCACAGCA 60.005 57.895 0.00 0.00 0.00 4.41
189 190 1.743252 CCGAGGAGGAAAGCACAGC 60.743 63.158 0.00 0.00 45.00 4.40
190 191 4.606071 CCGAGGAGGAAAGCACAG 57.394 61.111 0.00 0.00 45.00 3.66
200 201 0.033405 TACAAGGACCCTCCGAGGAG 60.033 60.000 16.69 12.06 42.75 3.69
201 202 0.410663 TTACAAGGACCCTCCGAGGA 59.589 55.000 16.69 0.00 42.75 3.71
202 203 0.535797 GTTACAAGGACCCTCCGAGG 59.464 60.000 7.56 7.56 42.75 4.63
203 204 0.172803 CGTTACAAGGACCCTCCGAG 59.827 60.000 0.00 0.00 42.75 4.63
204 205 1.880819 GCGTTACAAGGACCCTCCGA 61.881 60.000 0.00 0.00 42.75 4.55
205 206 1.447314 GCGTTACAAGGACCCTCCG 60.447 63.158 0.00 0.00 42.75 4.63
206 207 0.323957 AAGCGTTACAAGGACCCTCC 59.676 55.000 0.00 0.00 36.58 4.30
207 208 1.275573 AGAAGCGTTACAAGGACCCTC 59.724 52.381 0.00 0.00 0.00 4.30
208 209 1.349067 AGAAGCGTTACAAGGACCCT 58.651 50.000 0.00 0.00 0.00 4.34
209 210 2.074576 GAAGAAGCGTTACAAGGACCC 58.925 52.381 0.00 0.00 0.00 4.46
210 211 2.737252 CAGAAGAAGCGTTACAAGGACC 59.263 50.000 0.00 0.00 0.00 4.46
211 212 3.650139 TCAGAAGAAGCGTTACAAGGAC 58.350 45.455 0.00 0.00 0.00 3.85
212 213 4.021456 TGATCAGAAGAAGCGTTACAAGGA 60.021 41.667 0.00 0.00 0.00 3.36
213 214 4.245660 TGATCAGAAGAAGCGTTACAAGG 58.754 43.478 0.00 0.00 0.00 3.61
214 215 5.845985 TTGATCAGAAGAAGCGTTACAAG 57.154 39.130 0.00 0.00 0.00 3.16
215 216 5.931724 TCATTGATCAGAAGAAGCGTTACAA 59.068 36.000 0.00 0.00 0.00 2.41
216 217 5.478407 TCATTGATCAGAAGAAGCGTTACA 58.522 37.500 0.00 0.00 0.00 2.41
217 218 6.408858 TTCATTGATCAGAAGAAGCGTTAC 57.591 37.500 0.00 0.00 0.00 2.50
218 219 7.615582 AATTCATTGATCAGAAGAAGCGTTA 57.384 32.000 10.81 0.00 0.00 3.18
219 220 6.506500 AATTCATTGATCAGAAGAAGCGTT 57.493 33.333 10.81 1.37 0.00 4.84
220 221 6.320171 CAAATTCATTGATCAGAAGAAGCGT 58.680 36.000 10.81 0.00 41.85 5.07
221 222 5.742453 CCAAATTCATTGATCAGAAGAAGCG 59.258 40.000 10.81 0.00 41.85 4.68
222 223 5.519206 GCCAAATTCATTGATCAGAAGAAGC 59.481 40.000 10.81 6.46 41.85 3.86
223 224 6.627243 TGCCAAATTCATTGATCAGAAGAAG 58.373 36.000 10.81 1.62 41.85 2.85
224 225 6.593268 TGCCAAATTCATTGATCAGAAGAA 57.407 33.333 0.00 2.38 41.85 2.52
225 226 5.393787 GCTGCCAAATTCATTGATCAGAAGA 60.394 40.000 0.00 0.00 41.85 2.87
226 227 4.804139 GCTGCCAAATTCATTGATCAGAAG 59.196 41.667 0.00 0.00 41.85 2.85
227 228 4.464951 AGCTGCCAAATTCATTGATCAGAA 59.535 37.500 0.00 0.00 41.85 3.02
228 229 4.021229 AGCTGCCAAATTCATTGATCAGA 58.979 39.130 0.00 0.00 41.85 3.27
229 230 4.098044 AGAGCTGCCAAATTCATTGATCAG 59.902 41.667 0.00 0.00 41.85 2.90
230 231 4.021229 AGAGCTGCCAAATTCATTGATCA 58.979 39.130 0.00 0.00 41.85 2.92
231 232 4.650754 AGAGCTGCCAAATTCATTGATC 57.349 40.909 0.00 0.00 41.85 2.92
232 233 5.067413 CAGTAGAGCTGCCAAATTCATTGAT 59.933 40.000 0.00 0.00 38.67 2.57
233 234 4.397103 CAGTAGAGCTGCCAAATTCATTGA 59.603 41.667 0.00 0.00 38.67 2.57
234 235 4.669318 CAGTAGAGCTGCCAAATTCATTG 58.331 43.478 0.00 0.00 38.52 2.82
235 236 4.978083 CAGTAGAGCTGCCAAATTCATT 57.022 40.909 0.00 0.00 38.52 2.57
247 248 3.396260 TTAAACGTTGGCAGTAGAGCT 57.604 42.857 0.00 0.00 34.17 4.09
248 249 4.477302 TTTTAAACGTTGGCAGTAGAGC 57.523 40.909 0.00 0.00 0.00 4.09
350 352 0.248843 CTCTTCTTTGCTCGGAGGCT 59.751 55.000 7.20 0.00 0.00 4.58
409 418 0.618981 CTAGGGAGGGTTGTGGGTTC 59.381 60.000 0.00 0.00 0.00 3.62
421 430 2.501610 GGCGAAGGTGCTAGGGAG 59.498 66.667 0.00 0.00 34.52 4.30
422 431 3.458163 CGGCGAAGGTGCTAGGGA 61.458 66.667 0.00 0.00 34.52 4.20
448 462 1.215673 AGCAGGGGACGAGAGAGATAA 59.784 52.381 0.00 0.00 0.00 1.75
509 523 2.897972 GGCTTGTATCCGGTCGGT 59.102 61.111 9.36 0.06 36.47 4.69
1071 1261 8.058915 CGAAACAAAGAGACTTAAAAGAGACAG 58.941 37.037 0.00 0.00 0.00 3.51
1685 5100 4.201851 CGGAATATCTCAAGTTTGCTGGTG 60.202 45.833 0.00 0.00 0.00 4.17
1955 5654 3.634448 TCCAATGTCCAAACAACAATCGT 59.366 39.130 0.00 0.00 39.30 3.73
1990 5689 5.762179 TCTTAGTCCAAGTCCATGAATGT 57.238 39.130 0.00 0.00 35.58 2.71
2202 6585 2.235402 TGTATCTCGTTGAGTTTCCCCC 59.765 50.000 0.00 0.00 0.00 5.40
2318 6701 1.753930 TCCACAGATGCGCATTGAAT 58.246 45.000 26.12 8.43 0.00 2.57
2337 6720 1.871676 CAGCATATCGCAGCAGAACAT 59.128 47.619 0.00 0.00 46.13 2.71
2540 6937 2.097466 ACAAACAGAGCCAAACGAACAG 59.903 45.455 0.00 0.00 0.00 3.16
2541 6938 2.088423 ACAAACAGAGCCAAACGAACA 58.912 42.857 0.00 0.00 0.00 3.18
2542 6939 2.450160 CACAAACAGAGCCAAACGAAC 58.550 47.619 0.00 0.00 0.00 3.95
2629 7433 7.713507 AGGATTGTAATGCCAATTCAATTCATG 59.286 33.333 0.00 0.00 35.24 3.07
2879 7683 4.668138 ACAAGGCCTAGGGTTGATTTTA 57.332 40.909 5.16 0.00 0.00 1.52
2882 7686 3.165071 CAAACAAGGCCTAGGGTTGATT 58.835 45.455 24.04 9.67 0.00 2.57
2886 7690 0.857675 ACCAAACAAGGCCTAGGGTT 59.142 50.000 5.16 8.77 0.00 4.11
2887 7691 0.857675 AACCAAACAAGGCCTAGGGT 59.142 50.000 5.16 6.81 0.00 4.34
2979 7783 9.385902 CAAACGAGATATTAATTGGTATTGCAG 57.614 33.333 0.00 0.00 0.00 4.41
3012 7819 2.686816 CCATTGTTGCGTCCGGGTC 61.687 63.158 0.00 0.00 0.00 4.46
3076 7883 0.900182 TCCACATGAGGCACGTCTCT 60.900 55.000 3.98 0.00 34.98 3.10
3080 7887 1.153568 CGATCCACATGAGGCACGT 60.154 57.895 3.98 0.00 0.00 4.49
3153 7960 3.373565 CTTCCCAGCCCAAACCGC 61.374 66.667 0.00 0.00 0.00 5.68
3154 7961 1.524008 GAACTTCCCAGCCCAAACCG 61.524 60.000 0.00 0.00 0.00 4.44
3191 7998 1.535462 GGATCCCAGTTGACGTGTTTG 59.465 52.381 0.00 0.00 0.00 2.93
3279 8086 4.709886 GGCCTTGTTTGGTTAGGATACAAT 59.290 41.667 0.00 0.00 41.41 2.71
3286 8093 2.620627 CCTAGGGCCTTGTTTGGTTAGG 60.621 54.545 13.45 4.85 0.00 2.69
3330 8137 1.407979 GCTCATTTGATTGCTGGGGAG 59.592 52.381 0.00 0.00 0.00 4.30
3380 8187 9.420551 ACCGATTAAGAAAAACTCTACTAACTG 57.579 33.333 0.00 0.00 32.46 3.16
3385 8192 9.022884 AGAGTACCGATTAAGAAAAACTCTACT 57.977 33.333 9.57 0.00 40.35 2.57
3387 8194 9.635520 CAAGAGTACCGATTAAGAAAAACTCTA 57.364 33.333 10.99 0.00 41.04 2.43
3392 8199 7.174253 ACATGCAAGAGTACCGATTAAGAAAAA 59.826 33.333 0.00 0.00 0.00 1.94
3393 8200 6.653320 ACATGCAAGAGTACCGATTAAGAAAA 59.347 34.615 0.00 0.00 0.00 2.29
3424 8231 7.624360 TGCAAGTAAACCCTGAAAGTATATG 57.376 36.000 0.00 0.00 0.00 1.78
3545 8356 5.616488 TTTACATAAAAGGAGAACGGCAC 57.384 39.130 0.00 0.00 0.00 5.01
3546 8357 6.657541 AGATTTTACATAAAAGGAGAACGGCA 59.342 34.615 3.42 0.00 38.42 5.69
3687 8731 9.924650 GGAGTACTAAACAGTTCATCTTTCTTA 57.075 33.333 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.