Multiple sequence alignment - TraesCS7A01G500000

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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 TraesCS7A01G500000 chr7A 100.000 3334 0 0 1 3334 690196816 690193483 0.000000e+00 6157.0
1 TraesCS7A01G500000 chr7A 82.558 1376 205 21 976 2340 690517229 690518580 0.000000e+00 1179.0
2 TraesCS7A01G500000 chr7A 78.864 1831 275 61 575 2342 690424913 690426694 0.000000e+00 1134.0
3 TraesCS7A01G500000 chr7A 76.488 1731 301 67 727 2434 690399543 690401190 0.000000e+00 845.0
4 TraesCS7A01G500000 chr7A 83.261 693 86 18 879 1544 690438591 690439280 7.910000e-171 610.0
5 TraesCS7A01G500000 chr7A 80.649 801 135 15 1663 2454 690412994 690413783 1.320000e-168 603.0
6 TraesCS7A01G500000 chr7A 89.024 164 17 1 753 916 690438419 690438581 5.640000e-48 202.0
7 TraesCS7A01G500000 chr7B 89.232 2201 167 23 319 2490 676211739 676209580 0.000000e+00 2687.0
8 TraesCS7A01G500000 chr7B 89.861 1292 87 12 319 1585 676217692 676216420 0.000000e+00 1620.0
9 TraesCS7A01G500000 chr7B 81.841 1564 227 23 804 2340 676535176 676533643 0.000000e+00 1262.0
10 TraesCS7A01G500000 chr7B 90.999 711 47 4 1775 2477 676215590 676214889 0.000000e+00 942.0
11 TraesCS7A01G500000 chr7B 88.674 777 55 28 318 1083 676220266 676219512 0.000000e+00 917.0
12 TraesCS7A01G500000 chr7B 78.018 1433 225 51 1041 2454 676424153 676425514 0.000000e+00 819.0
13 TraesCS7A01G500000 chr7B 81.439 695 118 10 1655 2342 676452933 676453623 2.910000e-155 558.0
14 TraesCS7A01G500000 chr7B 82.748 626 89 10 976 1585 676452279 676452901 1.050000e-149 540.0
15 TraesCS7A01G500000 chr7B 85.024 414 43 14 2507 2903 676209532 676209121 1.440000e-108 403.0
16 TraesCS7A01G500000 chr7B 96.500 200 6 1 1584 1782 676216257 676216058 2.480000e-86 329.0
17 TraesCS7A01G500000 chr7B 78.905 493 51 15 673 1128 676987994 676988470 5.440000e-73 285.0
18 TraesCS7A01G500000 chr7D 98.426 1271 18 1 1220 2490 597965351 597966619 0.000000e+00 2235.0
19 TraesCS7A01G500000 chr7D 82.162 1822 255 41 575 2340 597570735 597568928 0.000000e+00 1500.0
20 TraesCS7A01G500000 chr7D 95.322 855 31 5 2489 3334 597966656 597967510 0.000000e+00 1349.0
21 TraesCS7A01G500000 chr7D 92.299 935 38 15 318 1228 597962866 597963790 0.000000e+00 1297.0
22 TraesCS7A01G500000 chr7D 82.529 1471 216 17 891 2340 597546574 597545124 0.000000e+00 1254.0
23 TraesCS7A01G500000 chr7D 77.993 1445 233 50 1026 2454 597654327 597652952 0.000000e+00 828.0
24 TraesCS7A01G500000 chr7D 80.855 1029 162 17 1316 2342 597574871 597573876 0.000000e+00 776.0
25 TraesCS7A01G500000 chr7D 94.545 275 8 1 2 276 597926804 597927071 5.140000e-113 418.0
26 TraesCS7A01G500000 chr5A 86.885 61 8 0 2861 2921 586313388 586313328 5.970000e-08 69.4
27 TraesCS7A01G500000 chr3B 89.583 48 4 1 2856 2903 574328736 574328690 3.590000e-05 60.2


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 TraesCS7A01G500000 chr7A 690193483 690196816 3333 True 6157.000000 6157 100.000000 1 3334 1 chr7A.!!$R1 3333
1 TraesCS7A01G500000 chr7A 690517229 690518580 1351 False 1179.000000 1179 82.558000 976 2340 1 chr7A.!!$F4 1364
2 TraesCS7A01G500000 chr7A 690424913 690426694 1781 False 1134.000000 1134 78.864000 575 2342 1 chr7A.!!$F3 1767
3 TraesCS7A01G500000 chr7A 690399543 690401190 1647 False 845.000000 845 76.488000 727 2434 1 chr7A.!!$F1 1707
4 TraesCS7A01G500000 chr7A 690412994 690413783 789 False 603.000000 603 80.649000 1663 2454 1 chr7A.!!$F2 791
5 TraesCS7A01G500000 chr7A 690438419 690439280 861 False 406.000000 610 86.142500 753 1544 2 chr7A.!!$F5 791
6 TraesCS7A01G500000 chr7B 676533643 676535176 1533 True 1262.000000 1262 81.841000 804 2340 1 chr7B.!!$R1 1536
7 TraesCS7A01G500000 chr7B 676209121 676220266 11145 True 1149.666667 2687 90.048333 318 2903 6 chr7B.!!$R2 2585
8 TraesCS7A01G500000 chr7B 676424153 676425514 1361 False 819.000000 819 78.018000 1041 2454 1 chr7B.!!$F1 1413
9 TraesCS7A01G500000 chr7B 676452279 676453623 1344 False 549.000000 558 82.093500 976 2342 2 chr7B.!!$F3 1366
10 TraesCS7A01G500000 chr7D 597962866 597967510 4644 False 1627.000000 2235 95.349000 318 3334 3 chr7D.!!$F2 3016
11 TraesCS7A01G500000 chr7D 597545124 597546574 1450 True 1254.000000 1254 82.529000 891 2340 1 chr7D.!!$R1 1449
12 TraesCS7A01G500000 chr7D 597568928 597574871 5943 True 1138.000000 1500 81.508500 575 2342 2 chr7D.!!$R3 1767
13 TraesCS7A01G500000 chr7D 597652952 597654327 1375 True 828.000000 828 77.993000 1026 2454 1 chr7D.!!$R2 1428

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
210 211 0.034756 TCTAGGTGTGTGCGCATGTT 59.965 50.0 15.91 0.0 0.00 2.71 F
274 275 0.042188 GCATGTGTGTCGTGTGTGAC 60.042 55.0 0.00 0.0 39.37 3.67 F
1517 9438 0.107945 GGAGCCTCAACGATCAGCTT 60.108 55.0 0.00 0.0 32.97 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 9231 0.239879 ACGCACCAAATTTAGCACGG 59.760 50.000 9.27 1.14 0.00 4.94 R
2222 16096 1.228154 GTCCCAGTTGGCGAACCTT 60.228 57.895 8.09 0.00 36.63 3.50 R
2889 16834 0.036306 TTTGTCTCTTCTTCGCCCCC 59.964 55.000 0.00 0.00 0.00 5.40 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
22 23 4.956085 TCTTTTGCTATATTAGAGGCGCA 58.044 39.130 10.83 0.00 0.00 6.09
23 24 5.551233 TCTTTTGCTATATTAGAGGCGCAT 58.449 37.500 10.83 0.00 0.00 4.73
24 25 5.409520 TCTTTTGCTATATTAGAGGCGCATG 59.590 40.000 10.83 0.00 0.00 4.06
25 26 4.535526 TTGCTATATTAGAGGCGCATGA 57.464 40.909 10.83 0.00 0.00 3.07
26 27 4.743057 TGCTATATTAGAGGCGCATGAT 57.257 40.909 10.83 0.00 0.00 2.45
27 28 5.852282 TGCTATATTAGAGGCGCATGATA 57.148 39.130 10.83 1.42 0.00 2.15
28 29 6.410942 TGCTATATTAGAGGCGCATGATAT 57.589 37.500 10.83 9.10 0.00 1.63
29 30 6.820335 TGCTATATTAGAGGCGCATGATATT 58.180 36.000 10.83 0.00 0.00 1.28
30 31 7.275183 TGCTATATTAGAGGCGCATGATATTT 58.725 34.615 10.83 0.00 0.00 1.40
31 32 7.770433 TGCTATATTAGAGGCGCATGATATTTT 59.230 33.333 10.83 0.00 0.00 1.82
32 33 8.616076 GCTATATTAGAGGCGCATGATATTTTT 58.384 33.333 10.83 0.00 0.00 1.94
34 35 8.798859 ATATTAGAGGCGCATGATATTTTTCT 57.201 30.769 10.83 0.00 0.00 2.52
35 36 9.890629 ATATTAGAGGCGCATGATATTTTTCTA 57.109 29.630 10.83 0.00 0.00 2.10
36 37 7.658179 TTAGAGGCGCATGATATTTTTCTAG 57.342 36.000 10.83 0.00 0.00 2.43
37 38 5.615289 AGAGGCGCATGATATTTTTCTAGT 58.385 37.500 10.83 0.00 0.00 2.57
39 40 6.203723 AGAGGCGCATGATATTTTTCTAGTTC 59.796 38.462 10.83 0.00 0.00 3.01
40 41 5.822519 AGGCGCATGATATTTTTCTAGTTCA 59.177 36.000 10.83 0.00 0.00 3.18
41 42 6.318648 AGGCGCATGATATTTTTCTAGTTCAA 59.681 34.615 10.83 0.00 0.00 2.69
42 43 7.013655 AGGCGCATGATATTTTTCTAGTTCAAT 59.986 33.333 10.83 0.00 0.00 2.57
43 44 7.113965 GGCGCATGATATTTTTCTAGTTCAATG 59.886 37.037 10.83 0.00 0.00 2.82
44 45 7.857389 GCGCATGATATTTTTCTAGTTCAATGA 59.143 33.333 0.30 0.00 0.00 2.57
45 46 9.720667 CGCATGATATTTTTCTAGTTCAATGAA 57.279 29.630 0.00 0.00 0.00 2.57
61 62 9.147732 AGTTCAATGAATTTCCTTCTTTTACCT 57.852 29.630 0.00 0.00 34.75 3.08
62 63 9.764363 GTTCAATGAATTTCCTTCTTTTACCTT 57.236 29.630 0.00 0.00 34.75 3.50
71 72 8.940768 TTTCCTTCTTTTACCTTTTTCATGTG 57.059 30.769 0.00 0.00 0.00 3.21
72 73 7.654022 TCCTTCTTTTACCTTTTTCATGTGT 57.346 32.000 0.00 0.00 0.00 3.72
74 75 7.123547 TCCTTCTTTTACCTTTTTCATGTGTGT 59.876 33.333 0.00 0.00 0.00 3.72
75 76 7.763985 CCTTCTTTTACCTTTTTCATGTGTGTT 59.236 33.333 0.00 0.00 0.00 3.32
76 77 9.150348 CTTCTTTTACCTTTTTCATGTGTGTTT 57.850 29.630 0.00 0.00 0.00 2.83
77 78 8.472683 TCTTTTACCTTTTTCATGTGTGTTTG 57.527 30.769 0.00 0.00 0.00 2.93
78 79 6.654793 TTTACCTTTTTCATGTGTGTTTGC 57.345 33.333 0.00 0.00 0.00 3.68
79 80 4.470334 ACCTTTTTCATGTGTGTTTGCT 57.530 36.364 0.00 0.00 0.00 3.91
80 81 4.831107 ACCTTTTTCATGTGTGTTTGCTT 58.169 34.783 0.00 0.00 0.00 3.91
81 82 5.244755 ACCTTTTTCATGTGTGTTTGCTTT 58.755 33.333 0.00 0.00 0.00 3.51
82 83 5.704978 ACCTTTTTCATGTGTGTTTGCTTTT 59.295 32.000 0.00 0.00 0.00 2.27
83 84 6.876257 ACCTTTTTCATGTGTGTTTGCTTTTA 59.124 30.769 0.00 0.00 0.00 1.52
85 86 7.064490 CCTTTTTCATGTGTGTTTGCTTTTAGT 59.936 33.333 0.00 0.00 0.00 2.24
87 88 6.449635 TTCATGTGTGTTTGCTTTTAGTCT 57.550 33.333 0.00 0.00 0.00 3.24
88 89 6.449635 TCATGTGTGTTTGCTTTTAGTCTT 57.550 33.333 0.00 0.00 0.00 3.01
91 92 7.816995 TCATGTGTGTTTGCTTTTAGTCTTTTT 59.183 29.630 0.00 0.00 0.00 1.94
93 94 7.375053 TGTGTGTTTGCTTTTAGTCTTTTTCT 58.625 30.769 0.00 0.00 0.00 2.52
94 95 7.870445 TGTGTGTTTGCTTTTAGTCTTTTTCTT 59.130 29.630 0.00 0.00 0.00 2.52
95 96 8.373256 GTGTGTTTGCTTTTAGTCTTTTTCTTC 58.627 33.333 0.00 0.00 0.00 2.87
96 97 8.303876 TGTGTTTGCTTTTAGTCTTTTTCTTCT 58.696 29.630 0.00 0.00 0.00 2.85
97 98 9.140286 GTGTTTGCTTTTAGTCTTTTTCTTCTT 57.860 29.630 0.00 0.00 0.00 2.52
98 99 9.705290 TGTTTGCTTTTAGTCTTTTTCTTCTTT 57.295 25.926 0.00 0.00 0.00 2.52
109 110 9.036671 AGTCTTTTTCTTCTTTCTTCTTAGTCG 57.963 33.333 0.00 0.00 0.00 4.18
110 111 9.032420 GTCTTTTTCTTCTTTCTTCTTAGTCGA 57.968 33.333 0.00 0.00 0.00 4.20
111 112 9.765795 TCTTTTTCTTCTTTCTTCTTAGTCGAT 57.234 29.630 0.00 0.00 0.00 3.59
151 152 9.778741 TCTTTCTTTTTCTGTATATGTGAGTGT 57.221 29.630 0.00 0.00 0.00 3.55
152 153 9.817365 CTTTCTTTTTCTGTATATGTGAGTGTG 57.183 33.333 0.00 0.00 0.00 3.82
153 154 8.902540 TTCTTTTTCTGTATATGTGAGTGTGT 57.097 30.769 0.00 0.00 0.00 3.72
155 156 7.387673 TCTTTTTCTGTATATGTGAGTGTGTGG 59.612 37.037 0.00 0.00 0.00 4.17
156 157 4.736126 TCTGTATATGTGAGTGTGTGGG 57.264 45.455 0.00 0.00 0.00 4.61
158 159 4.530553 TCTGTATATGTGAGTGTGTGGGTT 59.469 41.667 0.00 0.00 0.00 4.11
159 160 5.012664 TCTGTATATGTGAGTGTGTGGGTTT 59.987 40.000 0.00 0.00 0.00 3.27
160 161 6.211785 TCTGTATATGTGAGTGTGTGGGTTTA 59.788 38.462 0.00 0.00 0.00 2.01
162 163 6.821160 TGTATATGTGAGTGTGTGGGTTTATG 59.179 38.462 0.00 0.00 0.00 1.90
163 164 3.569194 TGTGAGTGTGTGGGTTTATGT 57.431 42.857 0.00 0.00 0.00 2.29
165 166 3.211045 GTGAGTGTGTGGGTTTATGTGT 58.789 45.455 0.00 0.00 0.00 3.72
167 168 3.211045 GAGTGTGTGGGTTTATGTGTGT 58.789 45.455 0.00 0.00 0.00 3.72
168 169 2.948979 AGTGTGTGGGTTTATGTGTGTG 59.051 45.455 0.00 0.00 0.00 3.82
169 170 2.685897 GTGTGTGGGTTTATGTGTGTGT 59.314 45.455 0.00 0.00 0.00 3.72
170 171 2.685388 TGTGTGGGTTTATGTGTGTGTG 59.315 45.455 0.00 0.00 0.00 3.82
171 172 2.946329 GTGTGGGTTTATGTGTGTGTGA 59.054 45.455 0.00 0.00 0.00 3.58
172 173 2.946329 TGTGGGTTTATGTGTGTGTGAC 59.054 45.455 0.00 0.00 0.00 3.67
173 174 2.032377 GTGGGTTTATGTGTGTGTGACG 60.032 50.000 0.00 0.00 0.00 4.35
174 175 1.069500 GGGTTTATGTGTGTGTGACGC 60.069 52.381 0.00 0.00 35.45 5.19
192 193 3.786955 CACGCTTGCATGTCGTATC 57.213 52.632 17.00 0.00 34.81 2.24
194 195 2.459934 CACGCTTGCATGTCGTATCTA 58.540 47.619 17.00 0.00 34.81 1.98
195 196 2.469147 CACGCTTGCATGTCGTATCTAG 59.531 50.000 17.00 5.92 34.81 2.43
197 198 2.543861 CGCTTGCATGTCGTATCTAGGT 60.544 50.000 1.14 0.00 0.00 3.08
198 199 2.797156 GCTTGCATGTCGTATCTAGGTG 59.203 50.000 1.14 0.00 0.00 4.00
199 200 3.738281 GCTTGCATGTCGTATCTAGGTGT 60.738 47.826 1.14 0.00 0.00 4.16
201 202 2.758423 TGCATGTCGTATCTAGGTGTGT 59.242 45.455 0.00 0.00 0.00 3.72
202 203 3.116300 GCATGTCGTATCTAGGTGTGTG 58.884 50.000 0.00 0.00 0.00 3.82
203 204 2.933495 TGTCGTATCTAGGTGTGTGC 57.067 50.000 0.00 0.00 0.00 4.57
204 205 1.131693 TGTCGTATCTAGGTGTGTGCG 59.868 52.381 0.00 0.00 0.00 5.34
205 206 0.099968 TCGTATCTAGGTGTGTGCGC 59.900 55.000 0.00 0.00 0.00 6.09
206 207 0.179148 CGTATCTAGGTGTGTGCGCA 60.179 55.000 5.66 5.66 0.00 6.09
208 209 1.860950 GTATCTAGGTGTGTGCGCATG 59.139 52.381 15.91 0.00 0.00 4.06
209 210 0.250234 ATCTAGGTGTGTGCGCATGT 59.750 50.000 15.91 0.00 0.00 3.21
210 211 0.034756 TCTAGGTGTGTGCGCATGTT 59.965 50.000 15.91 0.00 0.00 2.71
211 212 0.874390 CTAGGTGTGTGCGCATGTTT 59.126 50.000 15.91 0.00 0.00 2.83
212 213 0.590682 TAGGTGTGTGCGCATGTTTG 59.409 50.000 15.91 0.00 0.00 2.93
213 214 2.302230 GGTGTGTGCGCATGTTTGC 61.302 57.895 15.91 0.00 45.78 3.68
227 228 4.681744 CATGTTTGCTTTTGTACACAGGT 58.318 39.130 0.00 0.00 28.98 4.00
228 229 4.103365 TGTTTGCTTTTGTACACAGGTG 57.897 40.909 0.00 0.00 0.00 4.00
230 231 4.102649 GTTTGCTTTTGTACACAGGTGTC 58.897 43.478 8.56 2.15 43.74 3.67
231 232 1.937223 TGCTTTTGTACACAGGTGTCG 59.063 47.619 8.56 0.00 43.74 4.35
233 234 2.286184 GCTTTTGTACACAGGTGTCGTG 60.286 50.000 8.56 0.00 43.74 4.35
238 239 4.513519 CACAGGTGTCGTGTGTGT 57.486 55.556 12.44 0.00 42.79 3.72
240 241 1.813753 ACAGGTGTCGTGTGTGTGC 60.814 57.895 0.00 0.00 31.07 4.57
242 243 1.227263 AGGTGTCGTGTGTGTGCTC 60.227 57.895 0.00 0.00 0.00 4.26
243 244 1.227263 GGTGTCGTGTGTGTGCTCT 60.227 57.895 0.00 0.00 0.00 4.09
245 246 0.301687 GTGTCGTGTGTGTGCTCTTG 59.698 55.000 0.00 0.00 0.00 3.02
246 247 0.108377 TGTCGTGTGTGTGCTCTTGT 60.108 50.000 0.00 0.00 0.00 3.16
248 249 0.809636 TCGTGTGTGTGCTCTTGTGG 60.810 55.000 0.00 0.00 0.00 4.17
249 250 1.775039 CGTGTGTGTGCTCTTGTGGG 61.775 60.000 0.00 0.00 0.00 4.61
250 251 0.748005 GTGTGTGTGCTCTTGTGGGT 60.748 55.000 0.00 0.00 0.00 4.51
251 252 0.747644 TGTGTGTGCTCTTGTGGGTG 60.748 55.000 0.00 0.00 0.00 4.61
252 253 0.463654 GTGTGTGCTCTTGTGGGTGA 60.464 55.000 0.00 0.00 0.00 4.02
253 254 0.179048 TGTGTGCTCTTGTGGGTGAG 60.179 55.000 0.00 0.00 0.00 3.51
256 257 3.426568 GCTCTTGTGGGTGAGCGC 61.427 66.667 0.00 0.00 44.72 5.92
257 258 2.031012 CTCTTGTGGGTGAGCGCA 59.969 61.111 11.47 0.00 35.07 6.09
258 259 1.376424 CTCTTGTGGGTGAGCGCAT 60.376 57.895 11.47 0.00 39.75 4.73
259 260 1.642037 CTCTTGTGGGTGAGCGCATG 61.642 60.000 11.47 0.00 39.75 4.06
260 261 1.968017 CTTGTGGGTGAGCGCATGT 60.968 57.895 11.47 0.00 39.75 3.21
261 262 2.191354 CTTGTGGGTGAGCGCATGTG 62.191 60.000 11.47 0.66 39.75 3.21
262 263 2.669569 GTGGGTGAGCGCATGTGT 60.670 61.111 11.47 0.00 39.75 3.72
263 264 2.669229 TGGGTGAGCGCATGTGTG 60.669 61.111 11.47 0.00 32.36 3.82
264 265 2.669569 GGGTGAGCGCATGTGTGT 60.670 61.111 11.47 0.00 0.00 3.72
265 266 2.680913 GGGTGAGCGCATGTGTGTC 61.681 63.158 11.47 6.01 0.00 3.67
266 267 2.471607 GTGAGCGCATGTGTGTCG 59.528 61.111 11.47 0.00 0.00 4.35
267 268 2.028925 TGAGCGCATGTGTGTCGT 59.971 55.556 11.47 0.00 0.00 4.34
270 271 2.127646 GCGCATGTGTGTCGTGTG 60.128 61.111 0.30 0.00 43.87 3.82
271 272 2.881266 GCGCATGTGTGTCGTGTGT 61.881 57.895 0.30 0.00 43.22 3.72
272 273 1.083465 CGCATGTGTGTCGTGTGTG 60.083 57.895 0.00 0.00 38.37 3.82
273 274 1.486644 CGCATGTGTGTCGTGTGTGA 61.487 55.000 0.00 0.00 38.37 3.58
274 275 0.042188 GCATGTGTGTCGTGTGTGAC 60.042 55.000 0.00 0.00 39.37 3.67
275 276 0.581529 CATGTGTGTCGTGTGTGACC 59.418 55.000 0.00 0.00 38.11 4.02
276 277 0.176910 ATGTGTGTCGTGTGTGACCA 59.823 50.000 0.00 0.00 38.11 4.02
277 278 0.176910 TGTGTGTCGTGTGTGACCAT 59.823 50.000 0.00 0.00 38.11 3.55
280 281 1.144936 TGTCGTGTGTGACCATGCA 59.855 52.632 0.00 0.00 38.11 3.96
282 283 0.166597 GTCGTGTGTGACCATGCATG 59.833 55.000 20.19 20.19 32.61 4.06
285 286 1.527034 GTGTGTGACCATGCATGTCT 58.473 50.000 24.58 9.79 0.00 3.41
286 287 1.198408 GTGTGTGACCATGCATGTCTG 59.802 52.381 24.58 12.42 0.00 3.51
287 288 1.202794 TGTGTGACCATGCATGTCTGT 60.203 47.619 24.58 15.58 0.00 3.41
288 289 1.198408 GTGTGACCATGCATGTCTGTG 59.802 52.381 24.58 11.70 0.00 3.66
290 291 2.038295 TGTGACCATGCATGTCTGTGTA 59.962 45.455 24.58 5.24 0.00 2.90
291 292 2.674852 GTGACCATGCATGTCTGTGTAG 59.325 50.000 24.58 9.57 0.00 2.74
292 293 2.302733 TGACCATGCATGTCTGTGTAGT 59.697 45.455 24.58 12.70 0.00 2.73
295 296 4.445453 ACCATGCATGTCTGTGTAGTATG 58.555 43.478 24.58 7.48 0.00 2.39
298 299 3.261580 TGCATGTCTGTGTAGTATGTGC 58.738 45.455 0.00 0.00 0.00 4.57
299 300 3.261580 GCATGTCTGTGTAGTATGTGCA 58.738 45.455 0.00 0.00 0.00 4.57
300 301 3.062639 GCATGTCTGTGTAGTATGTGCAC 59.937 47.826 10.75 10.75 41.90 4.57
386 387 9.926158 ATTCTTACATATTGTGAAAATGTGCAA 57.074 25.926 0.00 0.00 35.54 4.08
387 388 9.926158 TTCTTACATATTGTGAAAATGTGCAAT 57.074 25.926 0.00 0.00 35.54 3.56
388 389 9.926158 TCTTACATATTGTGAAAATGTGCAATT 57.074 25.926 0.00 0.00 35.54 2.32
391 392 8.836268 ACATATTGTGAAAATGTGCAATTTCT 57.164 26.923 16.95 4.86 36.68 2.52
392 393 8.714179 ACATATTGTGAAAATGTGCAATTTCTG 58.286 29.630 16.95 10.74 36.68 3.02
393 394 8.714179 CATATTGTGAAAATGTGCAATTTCTGT 58.286 29.630 16.95 7.32 36.68 3.41
394 395 6.981762 TTGTGAAAATGTGCAATTTCTGTT 57.018 29.167 16.95 1.34 36.68 3.16
395 396 6.586868 TGTGAAAATGTGCAATTTCTGTTC 57.413 33.333 16.95 8.51 36.68 3.18
396 397 6.104665 TGTGAAAATGTGCAATTTCTGTTCA 58.895 32.000 16.95 10.24 36.68 3.18
397 398 6.762187 TGTGAAAATGTGCAATTTCTGTTCAT 59.238 30.769 16.95 0.00 36.68 2.57
399 400 6.762187 TGAAAATGTGCAATTTCTGTTCATGT 59.238 30.769 16.95 0.00 36.68 3.21
400 401 7.280428 TGAAAATGTGCAATTTCTGTTCATGTT 59.720 29.630 16.95 3.68 36.68 2.71
401 402 7.556733 AAATGTGCAATTTCTGTTCATGTTT 57.443 28.000 0.00 0.00 0.00 2.83
402 403 7.556733 AATGTGCAATTTCTGTTCATGTTTT 57.443 28.000 0.00 0.00 0.00 2.43
403 404 6.981762 TGTGCAATTTCTGTTCATGTTTTT 57.018 29.167 0.00 0.00 0.00 1.94
404 405 6.773080 TGTGCAATTTCTGTTCATGTTTTTG 58.227 32.000 0.00 0.00 0.00 2.44
405 406 6.370994 TGTGCAATTTCTGTTCATGTTTTTGT 59.629 30.769 0.00 0.00 0.00 2.83
406 407 6.901357 GTGCAATTTCTGTTCATGTTTTTGTC 59.099 34.615 0.00 0.00 0.00 3.18
408 409 7.280428 TGCAATTTCTGTTCATGTTTTTGTCAT 59.720 29.630 0.00 0.00 0.00 3.06
409 410 7.795272 GCAATTTCTGTTCATGTTTTTGTCATC 59.205 33.333 0.00 0.00 0.00 2.92
411 412 9.550406 AATTTCTGTTCATGTTTTTGTCATCAT 57.450 25.926 0.00 0.00 0.00 2.45
412 413 8.945481 TTTCTGTTCATGTTTTTGTCATCATT 57.055 26.923 0.00 0.00 0.00 2.57
413 414 8.945481 TTCTGTTCATGTTTTTGTCATCATTT 57.055 26.923 0.00 0.00 0.00 2.32
417 418 9.381033 TGTTCATGTTTTTGTCATCATTTCTTT 57.619 25.926 0.00 0.00 0.00 2.52
500 501 7.876936 AGTTTCAGTATATAGTCTTGTCGGA 57.123 36.000 0.00 0.00 0.00 4.55
501 502 8.289939 AGTTTCAGTATATAGTCTTGTCGGAA 57.710 34.615 0.00 0.00 0.00 4.30
502 503 8.746530 AGTTTCAGTATATAGTCTTGTCGGAAA 58.253 33.333 0.00 0.00 0.00 3.13
505 506 8.515695 TCAGTATATAGTCTTGTCGGAAAAGA 57.484 34.615 6.52 6.52 0.00 2.52
508 509 8.968969 AGTATATAGTCTTGTCGGAAAAGAAGT 58.031 33.333 12.11 5.86 35.50 3.01
509 510 9.021863 GTATATAGTCTTGTCGGAAAAGAAGTG 57.978 37.037 12.11 0.00 35.50 3.16
510 511 4.138487 AGTCTTGTCGGAAAAGAAGTGT 57.862 40.909 12.11 0.00 35.50 3.55
513 514 5.696724 AGTCTTGTCGGAAAAGAAGTGTATG 59.303 40.000 12.11 0.00 35.50 2.39
514 515 5.465724 GTCTTGTCGGAAAAGAAGTGTATGT 59.534 40.000 12.11 0.00 35.50 2.29
515 516 5.694910 TCTTGTCGGAAAAGAAGTGTATGTC 59.305 40.000 8.17 0.00 30.79 3.06
516 517 4.951254 TGTCGGAAAAGAAGTGTATGTCA 58.049 39.130 0.00 0.00 0.00 3.58
517 518 5.547465 TGTCGGAAAAGAAGTGTATGTCAT 58.453 37.500 0.00 0.00 0.00 3.06
518 519 5.408299 TGTCGGAAAAGAAGTGTATGTCATG 59.592 40.000 0.00 0.00 0.00 3.07
519 520 5.408604 GTCGGAAAAGAAGTGTATGTCATGT 59.591 40.000 0.00 0.00 0.00 3.21
520 521 5.637810 TCGGAAAAGAAGTGTATGTCATGTC 59.362 40.000 0.00 0.00 0.00 3.06
521 522 5.408299 CGGAAAAGAAGTGTATGTCATGTCA 59.592 40.000 0.00 0.00 0.00 3.58
522 523 6.073276 CGGAAAAGAAGTGTATGTCATGTCAA 60.073 38.462 0.00 0.00 0.00 3.18
523 524 7.519809 CGGAAAAGAAGTGTATGTCATGTCAAA 60.520 37.037 0.00 0.00 0.00 2.69
524 525 8.134895 GGAAAAGAAGTGTATGTCATGTCAAAA 58.865 33.333 0.00 0.00 0.00 2.44
525 526 9.515020 GAAAAGAAGTGTATGTCATGTCAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
548 549 6.506500 AATTCCATCACTTGTTAAGCAGAG 57.493 37.500 0.00 0.00 0.00 3.35
549 550 3.942829 TCCATCACTTGTTAAGCAGAGG 58.057 45.455 0.00 0.00 0.00 3.69
550 551 3.582647 TCCATCACTTGTTAAGCAGAGGA 59.417 43.478 0.00 0.00 0.00 3.71
551 552 4.041567 TCCATCACTTGTTAAGCAGAGGAA 59.958 41.667 0.00 0.00 0.00 3.36
552 553 4.394300 CCATCACTTGTTAAGCAGAGGAAG 59.606 45.833 0.00 0.00 0.00 3.46
553 554 4.955811 TCACTTGTTAAGCAGAGGAAGA 57.044 40.909 0.00 0.00 0.00 2.87
554 555 5.290493 TCACTTGTTAAGCAGAGGAAGAA 57.710 39.130 0.00 0.00 0.00 2.52
555 556 5.300752 TCACTTGTTAAGCAGAGGAAGAAG 58.699 41.667 0.00 0.00 31.60 2.85
557 558 5.760253 CACTTGTTAAGCAGAGGAAGAAGAA 59.240 40.000 0.00 0.00 30.32 2.52
558 559 5.994668 ACTTGTTAAGCAGAGGAAGAAGAAG 59.005 40.000 0.00 0.00 30.32 2.85
560 561 2.488204 AAGCAGAGGAAGAAGAAGGC 57.512 50.000 0.00 0.00 0.00 4.35
561 562 1.356124 AGCAGAGGAAGAAGAAGGCA 58.644 50.000 0.00 0.00 0.00 4.75
562 563 1.278699 AGCAGAGGAAGAAGAAGGCAG 59.721 52.381 0.00 0.00 0.00 4.85
563 564 1.277557 GCAGAGGAAGAAGAAGGCAGA 59.722 52.381 0.00 0.00 0.00 4.26
566 567 2.504996 AGAGGAAGAAGAAGGCAGATGG 59.495 50.000 0.00 0.00 0.00 3.51
881 7107 8.417106 AGACATCTTGATATACACAATTCGACT 58.583 33.333 0.00 0.00 0.00 4.18
916 7190 5.584551 ACTATAAATGGGGATGAAGGGAC 57.415 43.478 0.00 0.00 0.00 4.46
1020 7320 1.227383 GGGGAGTTCCAATCGCCAT 59.773 57.895 2.70 0.00 46.28 4.40
1035 7335 2.023673 CGCCATTGCTCCATTTCCTTA 58.976 47.619 0.00 0.00 34.43 2.69
1312 9231 7.067728 GTGTTCTAACAGTTCAATTTCGTACC 58.932 38.462 0.00 0.00 40.05 3.34
1407 9328 1.671742 GAGAAGACGGGGCAGTTCA 59.328 57.895 0.00 0.00 0.00 3.18
1506 9427 1.299648 CCGTTTCCATGGAGCCTCA 59.700 57.895 15.53 0.00 0.00 3.86
1517 9438 0.107945 GGAGCCTCAACGATCAGCTT 60.108 55.000 0.00 0.00 32.97 3.74
1522 9443 2.200067 CCTCAACGATCAGCTTGCTAG 58.800 52.381 0.00 0.00 0.00 3.42
1597 9682 2.899303 AAACATACCTTGGGGTCAGG 57.101 50.000 0.00 0.00 45.98 3.86
2170 16044 3.642503 TGGTGGTAACGGGCCCTG 61.643 66.667 22.43 16.23 42.51 4.45
2222 16096 3.053291 GTTTGCCGCGACCCATCA 61.053 61.111 8.23 0.00 0.00 3.07
2281 16155 0.933097 GCATACAGTGTCATCGCCAG 59.067 55.000 0.00 0.00 0.00 4.85
2395 16283 5.451937 CCACCAAGATCTGATACGCTTCTTA 60.452 44.000 0.00 0.00 0.00 2.10
2513 16443 3.074412 GTTGTATAGTTGCAGTGCCAGT 58.926 45.455 13.72 7.26 0.00 4.00
2578 16509 5.048507 CGGTAACTTGCTATAGGGTCTTTC 58.951 45.833 1.04 0.00 0.00 2.62
2584 16515 7.676683 ACTTGCTATAGGGTCTTTCTCATTA 57.323 36.000 1.04 0.00 0.00 1.90
2741 16686 6.262273 GGATGTGTTAGGTGAAAACTCAAAGA 59.738 38.462 0.00 0.00 34.94 2.52
2814 16759 5.476945 AGCCAGTTATAAGACCCACAAAAAG 59.523 40.000 0.00 0.00 0.00 2.27
2869 16814 1.606885 TAAACGTAGTCAGGGGCGGG 61.607 60.000 0.00 0.00 45.00 6.13
2889 16834 4.709250 GGGGCTAAGATTTAGACTTGAGG 58.291 47.826 2.03 0.00 0.00 3.86
2948 16893 6.183360 GCCAAGCAATAATCACTACAGGAAAT 60.183 38.462 0.00 0.00 0.00 2.17
2982 16927 5.587043 CCCTAGTATCTGACTATAAGCCGAG 59.413 48.000 0.00 0.00 39.98 4.63
3044 16989 4.398044 CGAGTACCAAACCCTAAAATGCAT 59.602 41.667 0.00 0.00 0.00 3.96
3046 16991 5.329399 AGTACCAAACCCTAAAATGCATGA 58.671 37.500 0.00 0.00 0.00 3.07
3064 17009 4.455533 GCATGACACAAATACTGACCTCAA 59.544 41.667 0.00 0.00 0.00 3.02
3105 17050 5.536161 CCAAGAATCAGGAAAAGAACCTCAA 59.464 40.000 0.00 0.00 35.35 3.02
3106 17051 6.442112 CAAGAATCAGGAAAAGAACCTCAAC 58.558 40.000 0.00 0.00 35.35 3.18
3163 17108 3.878160 CTCGGCTTAGAGTTCCTTCTT 57.122 47.619 0.00 0.00 33.75 2.52
3200 17145 1.391577 GTGGCCATCACATATGTGCA 58.608 50.000 27.71 17.62 45.39 4.57
3257 17202 6.928492 TGCTTGAAAGATGCGTGACATATATA 59.072 34.615 0.00 0.00 39.84 0.86
3258 17203 7.603784 TGCTTGAAAGATGCGTGACATATATAT 59.396 33.333 0.00 0.00 39.84 0.86
3317 17262 6.587608 GCTTACACTTTGCATCTTATTTGCTT 59.412 34.615 0.00 0.00 40.77 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.409520 TCATGCGCCTCTAATATAGCAAAAG 59.590 40.000 4.18 0.00 38.15 2.27
2 3 5.304778 TCATGCGCCTCTAATATAGCAAAA 58.695 37.500 4.18 0.00 38.15 2.44
4 5 4.535526 TCATGCGCCTCTAATATAGCAA 57.464 40.909 4.18 0.00 38.15 3.91
5 6 4.743057 ATCATGCGCCTCTAATATAGCA 57.257 40.909 4.18 0.00 39.02 3.49
6 7 7.721286 AAATATCATGCGCCTCTAATATAGC 57.279 36.000 4.18 0.00 0.00 2.97
9 10 8.798859 AGAAAAATATCATGCGCCTCTAATAT 57.201 30.769 4.18 0.00 0.00 1.28
10 11 9.371136 CTAGAAAAATATCATGCGCCTCTAATA 57.629 33.333 4.18 0.00 0.00 0.98
11 12 7.880195 ACTAGAAAAATATCATGCGCCTCTAAT 59.120 33.333 4.18 0.00 0.00 1.73
13 14 6.759272 ACTAGAAAAATATCATGCGCCTCTA 58.241 36.000 4.18 0.00 0.00 2.43
14 15 5.615289 ACTAGAAAAATATCATGCGCCTCT 58.385 37.500 4.18 0.00 0.00 3.69
16 17 5.822519 TGAACTAGAAAAATATCATGCGCCT 59.177 36.000 4.18 0.00 0.00 5.52
18 19 7.857389 TCATTGAACTAGAAAAATATCATGCGC 59.143 33.333 0.00 0.00 0.00 6.09
19 20 9.720667 TTCATTGAACTAGAAAAATATCATGCG 57.279 29.630 0.00 0.00 0.00 4.73
35 36 9.147732 AGGTAAAAGAAGGAAATTCATTGAACT 57.852 29.630 0.15 0.00 40.67 3.01
36 37 9.764363 AAGGTAAAAGAAGGAAATTCATTGAAC 57.236 29.630 0.15 0.00 40.67 3.18
45 46 9.546428 CACATGAAAAAGGTAAAAGAAGGAAAT 57.454 29.630 0.00 0.00 0.00 2.17
46 47 8.536175 ACACATGAAAAAGGTAAAAGAAGGAAA 58.464 29.630 0.00 0.00 0.00 3.13
47 48 7.978975 CACACATGAAAAAGGTAAAAGAAGGAA 59.021 33.333 0.00 0.00 0.00 3.36
48 49 7.123547 ACACACATGAAAAAGGTAAAAGAAGGA 59.876 33.333 0.00 0.00 0.00 3.36
49 50 7.264947 ACACACATGAAAAAGGTAAAAGAAGG 58.735 34.615 0.00 0.00 0.00 3.46
52 53 7.064016 GCAAACACACATGAAAAAGGTAAAAGA 59.936 33.333 0.00 0.00 0.00 2.52
55 56 6.402222 AGCAAACACACATGAAAAAGGTAAA 58.598 32.000 0.00 0.00 0.00 2.01
56 57 5.971763 AGCAAACACACATGAAAAAGGTAA 58.028 33.333 0.00 0.00 0.00 2.85
57 58 5.590530 AGCAAACACACATGAAAAAGGTA 57.409 34.783 0.00 0.00 0.00 3.08
58 59 4.470334 AGCAAACACACATGAAAAAGGT 57.530 36.364 0.00 0.00 0.00 3.50
61 62 7.816995 AGACTAAAAGCAAACACACATGAAAAA 59.183 29.630 0.00 0.00 0.00 1.94
62 63 7.319646 AGACTAAAAGCAAACACACATGAAAA 58.680 30.769 0.00 0.00 0.00 2.29
63 64 6.862209 AGACTAAAAGCAAACACACATGAAA 58.138 32.000 0.00 0.00 0.00 2.69
64 65 6.449635 AGACTAAAAGCAAACACACATGAA 57.550 33.333 0.00 0.00 0.00 2.57
65 66 6.449635 AAGACTAAAAGCAAACACACATGA 57.550 33.333 0.00 0.00 0.00 3.07
66 67 7.524294 AAAAGACTAAAAGCAAACACACATG 57.476 32.000 0.00 0.00 0.00 3.21
67 68 8.034804 AGAAAAAGACTAAAAGCAAACACACAT 58.965 29.630 0.00 0.00 0.00 3.21
68 69 7.375053 AGAAAAAGACTAAAAGCAAACACACA 58.625 30.769 0.00 0.00 0.00 3.72
69 70 7.812309 AGAAAAAGACTAAAAGCAAACACAC 57.188 32.000 0.00 0.00 0.00 3.82
70 71 8.303876 AGAAGAAAAAGACTAAAAGCAAACACA 58.696 29.630 0.00 0.00 0.00 3.72
71 72 8.689251 AGAAGAAAAAGACTAAAAGCAAACAC 57.311 30.769 0.00 0.00 0.00 3.32
72 73 9.705290 AAAGAAGAAAAAGACTAAAAGCAAACA 57.295 25.926 0.00 0.00 0.00 2.83
76 77 9.788960 GAAGAAAGAAGAAAAAGACTAAAAGCA 57.211 29.630 0.00 0.00 0.00 3.91
83 84 9.036671 CGACTAAGAAGAAAGAAGAAAAAGACT 57.963 33.333 0.00 0.00 0.00 3.24
85 86 9.765795 ATCGACTAAGAAGAAAGAAGAAAAAGA 57.234 29.630 0.00 0.00 0.00 2.52
125 126 9.778741 ACACTCACATATACAGAAAAAGAAAGA 57.221 29.630 0.00 0.00 0.00 2.52
127 128 9.337396 ACACACTCACATATACAGAAAAAGAAA 57.663 29.630 0.00 0.00 0.00 2.52
128 129 8.773645 CACACACTCACATATACAGAAAAAGAA 58.226 33.333 0.00 0.00 0.00 2.52
129 130 7.387673 CCACACACTCACATATACAGAAAAAGA 59.612 37.037 0.00 0.00 0.00 2.52
130 131 7.361201 CCCACACACTCACATATACAGAAAAAG 60.361 40.741 0.00 0.00 0.00 2.27
131 132 6.429692 CCCACACACTCACATATACAGAAAAA 59.570 38.462 0.00 0.00 0.00 1.94
133 134 5.012664 ACCCACACACTCACATATACAGAAA 59.987 40.000 0.00 0.00 0.00 2.52
134 135 4.530553 ACCCACACACTCACATATACAGAA 59.469 41.667 0.00 0.00 0.00 3.02
135 136 4.093743 ACCCACACACTCACATATACAGA 58.906 43.478 0.00 0.00 0.00 3.41
137 138 4.901197 AACCCACACACTCACATATACA 57.099 40.909 0.00 0.00 0.00 2.29
138 139 6.821665 ACATAAACCCACACACTCACATATAC 59.178 38.462 0.00 0.00 0.00 1.47
139 140 6.821160 CACATAAACCCACACACTCACATATA 59.179 38.462 0.00 0.00 0.00 0.86
141 142 5.000591 CACATAAACCCACACACTCACATA 58.999 41.667 0.00 0.00 0.00 2.29
142 143 3.820467 CACATAAACCCACACACTCACAT 59.180 43.478 0.00 0.00 0.00 3.21
144 145 3.003275 CACACATAAACCCACACACTCAC 59.997 47.826 0.00 0.00 0.00 3.51
145 146 3.210227 CACACATAAACCCACACACTCA 58.790 45.455 0.00 0.00 0.00 3.41
146 147 3.003275 CACACACATAAACCCACACACTC 59.997 47.826 0.00 0.00 0.00 3.51
147 148 2.948979 CACACACATAAACCCACACACT 59.051 45.455 0.00 0.00 0.00 3.55
148 149 2.685897 ACACACACATAAACCCACACAC 59.314 45.455 0.00 0.00 0.00 3.82
149 150 2.685388 CACACACACATAAACCCACACA 59.315 45.455 0.00 0.00 0.00 3.72
150 151 2.946329 TCACACACACATAAACCCACAC 59.054 45.455 0.00 0.00 0.00 3.82
151 152 2.946329 GTCACACACACATAAACCCACA 59.054 45.455 0.00 0.00 0.00 4.17
152 153 2.032377 CGTCACACACACATAAACCCAC 60.032 50.000 0.00 0.00 0.00 4.61
153 154 2.214347 CGTCACACACACATAAACCCA 58.786 47.619 0.00 0.00 0.00 4.51
155 156 1.600013 TGCGTCACACACACATAAACC 59.400 47.619 0.00 0.00 0.00 3.27
174 175 1.280982 AGATACGACATGCAAGCGTG 58.719 50.000 18.20 12.42 38.84 5.34
175 176 2.543861 CCTAGATACGACATGCAAGCGT 60.544 50.000 14.63 14.63 41.58 5.07
176 177 2.054363 CCTAGATACGACATGCAAGCG 58.946 52.381 0.00 0.00 0.00 4.68
177 178 2.797156 CACCTAGATACGACATGCAAGC 59.203 50.000 0.00 0.00 0.00 4.01
178 179 3.798878 CACACCTAGATACGACATGCAAG 59.201 47.826 0.00 0.00 0.00 4.01
180 181 2.758423 ACACACCTAGATACGACATGCA 59.242 45.455 0.00 0.00 0.00 3.96
182 183 3.116300 GCACACACCTAGATACGACATG 58.884 50.000 0.00 0.00 0.00 3.21
183 184 2.223502 CGCACACACCTAGATACGACAT 60.224 50.000 0.00 0.00 0.00 3.06
184 185 1.131693 CGCACACACCTAGATACGACA 59.868 52.381 0.00 0.00 0.00 4.35
185 186 1.823828 CGCACACACCTAGATACGAC 58.176 55.000 0.00 0.00 0.00 4.34
189 190 1.480545 ACATGCGCACACACCTAGATA 59.519 47.619 14.90 0.00 0.00 1.98
190 191 0.250234 ACATGCGCACACACCTAGAT 59.750 50.000 14.90 0.00 0.00 1.98
191 192 0.034756 AACATGCGCACACACCTAGA 59.965 50.000 14.90 0.00 0.00 2.43
192 193 0.874390 AAACATGCGCACACACCTAG 59.126 50.000 14.90 0.00 0.00 3.02
194 195 1.359833 CAAACATGCGCACACACCT 59.640 52.632 14.90 0.00 0.00 4.00
195 196 2.302230 GCAAACATGCGCACACACC 61.302 57.895 14.90 0.00 0.00 4.16
197 198 0.179116 AAAGCAAACATGCGCACACA 60.179 45.000 14.90 0.00 40.27 3.72
198 199 0.929615 AAAAGCAAACATGCGCACAC 59.070 45.000 14.90 0.00 40.27 3.82
199 200 0.928922 CAAAAGCAAACATGCGCACA 59.071 45.000 14.90 0.00 40.27 4.57
201 202 2.123342 GTACAAAAGCAAACATGCGCA 58.877 42.857 14.96 14.96 40.27 6.09
202 203 2.097444 GTGTACAAAAGCAAACATGCGC 60.097 45.455 0.00 0.00 40.27 6.09
203 204 3.111838 TGTGTACAAAAGCAAACATGCG 58.888 40.909 0.00 0.00 40.27 4.73
204 205 3.490526 CCTGTGTACAAAAGCAAACATGC 59.509 43.478 0.00 0.00 0.00 4.06
205 206 4.503734 CACCTGTGTACAAAAGCAAACATG 59.496 41.667 0.00 0.00 0.00 3.21
206 207 4.159506 ACACCTGTGTACAAAAGCAAACAT 59.840 37.500 0.00 0.00 42.90 2.71
208 209 4.102649 GACACCTGTGTACAAAAGCAAAC 58.897 43.478 2.35 0.00 45.05 2.93
209 210 3.181505 CGACACCTGTGTACAAAAGCAAA 60.182 43.478 2.35 0.00 45.05 3.68
210 211 2.353269 CGACACCTGTGTACAAAAGCAA 59.647 45.455 2.35 0.00 45.05 3.91
211 212 1.937223 CGACACCTGTGTACAAAAGCA 59.063 47.619 2.35 0.00 45.05 3.91
212 213 1.937899 ACGACACCTGTGTACAAAAGC 59.062 47.619 2.35 0.00 45.05 3.51
213 214 3.585748 CACGACACCTGTGTACAAAAG 57.414 47.619 2.35 0.00 45.05 2.27
221 222 2.005995 CACACACACGACACCTGTG 58.994 57.895 1.88 1.88 43.99 3.66
222 223 1.813753 GCACACACACGACACCTGT 60.814 57.895 0.00 0.00 0.00 4.00
223 224 1.490693 GAGCACACACACGACACCTG 61.491 60.000 0.00 0.00 0.00 4.00
224 225 1.227263 GAGCACACACACGACACCT 60.227 57.895 0.00 0.00 0.00 4.00
227 228 0.108377 ACAAGAGCACACACACGACA 60.108 50.000 0.00 0.00 0.00 4.35
228 229 0.301687 CACAAGAGCACACACACGAC 59.698 55.000 0.00 0.00 0.00 4.34
230 231 1.643292 CCACAAGAGCACACACACG 59.357 57.895 0.00 0.00 0.00 4.49
231 232 0.748005 ACCCACAAGAGCACACACAC 60.748 55.000 0.00 0.00 0.00 3.82
233 234 0.463654 TCACCCACAAGAGCACACAC 60.464 55.000 0.00 0.00 0.00 3.82
234 235 0.179048 CTCACCCACAAGAGCACACA 60.179 55.000 0.00 0.00 0.00 3.72
240 241 1.376424 ATGCGCTCACCCACAAGAG 60.376 57.895 9.73 0.00 35.01 2.85
242 243 1.968017 ACATGCGCTCACCCACAAG 60.968 57.895 9.73 0.00 0.00 3.16
243 244 2.112928 ACATGCGCTCACCCACAA 59.887 55.556 9.73 0.00 0.00 3.33
245 246 2.669569 ACACATGCGCTCACCCAC 60.670 61.111 9.73 0.00 0.00 4.61
246 247 2.669229 CACACATGCGCTCACCCA 60.669 61.111 9.73 0.00 0.00 4.51
248 249 2.863153 GACACACATGCGCTCACC 59.137 61.111 9.73 0.00 0.00 4.02
249 250 2.310233 ACGACACACATGCGCTCAC 61.310 57.895 9.73 0.00 0.00 3.51
250 251 2.028925 ACGACACACATGCGCTCA 59.971 55.556 9.73 0.00 0.00 4.26
251 252 2.310233 ACACGACACACATGCGCTC 61.310 57.895 9.73 0.00 0.00 5.03
252 253 2.280119 ACACGACACACATGCGCT 60.280 55.556 9.73 0.00 0.00 5.92
253 254 2.127646 CACACGACACACATGCGC 60.128 61.111 0.00 0.00 0.00 6.09
254 255 1.083465 CACACACGACACACATGCG 60.083 57.895 0.00 0.00 0.00 4.73
255 256 0.042188 GTCACACACGACACACATGC 60.042 55.000 0.00 0.00 35.88 4.06
256 257 0.581529 GGTCACACACGACACACATG 59.418 55.000 0.00 0.00 37.66 3.21
257 258 0.176910 TGGTCACACACGACACACAT 59.823 50.000 0.00 0.00 37.66 3.21
258 259 0.176910 ATGGTCACACACGACACACA 59.823 50.000 0.00 0.00 37.66 3.72
259 260 0.581529 CATGGTCACACACGACACAC 59.418 55.000 0.00 0.00 37.66 3.82
260 261 1.157257 GCATGGTCACACACGACACA 61.157 55.000 0.00 0.00 37.66 3.72
261 262 1.157257 TGCATGGTCACACACGACAC 61.157 55.000 0.00 0.00 37.66 3.67
262 263 0.250252 ATGCATGGTCACACACGACA 60.250 50.000 0.00 0.00 37.66 4.35
263 264 0.166597 CATGCATGGTCACACACGAC 59.833 55.000 19.40 0.00 35.03 4.34
264 265 0.250252 ACATGCATGGTCACACACGA 60.250 50.000 29.41 0.00 0.00 4.35
265 266 0.166597 GACATGCATGGTCACACACG 59.833 55.000 29.41 1.63 35.36 4.49
266 267 1.198408 CAGACATGCATGGTCACACAC 59.802 52.381 29.41 10.46 37.74 3.82
267 268 1.202794 ACAGACATGCATGGTCACACA 60.203 47.619 29.41 0.00 37.74 3.72
270 271 1.527034 ACACAGACATGCATGGTCAC 58.473 50.000 29.41 17.05 37.74 3.67
271 272 2.302733 ACTACACAGACATGCATGGTCA 59.697 45.455 29.41 8.09 37.74 4.02
272 273 2.977914 ACTACACAGACATGCATGGTC 58.022 47.619 29.41 22.20 35.50 4.02
273 274 4.080919 ACATACTACACAGACATGCATGGT 60.081 41.667 29.41 18.99 0.00 3.55
274 275 4.271776 CACATACTACACAGACATGCATGG 59.728 45.833 29.41 14.96 0.00 3.66
275 276 4.260497 GCACATACTACACAGACATGCATG 60.260 45.833 25.09 25.09 0.00 4.06
276 277 3.873361 GCACATACTACACAGACATGCAT 59.127 43.478 0.00 0.00 0.00 3.96
277 278 3.261580 GCACATACTACACAGACATGCA 58.738 45.455 0.00 0.00 0.00 3.96
280 281 4.535526 TGTGCACATACTACACAGACAT 57.464 40.909 17.42 0.00 39.29 3.06
282 283 5.621422 CATTTGTGCACATACTACACAGAC 58.379 41.667 22.39 0.00 44.46 3.51
285 286 3.120373 CGCATTTGTGCACATACTACACA 60.120 43.478 22.39 0.00 42.27 3.72
286 287 3.124466 TCGCATTTGTGCACATACTACAC 59.876 43.478 22.39 6.03 34.86 2.90
287 288 3.330267 TCGCATTTGTGCACATACTACA 58.670 40.909 22.39 0.45 34.41 2.74
288 289 4.536364 ATCGCATTTGTGCACATACTAC 57.464 40.909 22.39 8.73 34.41 2.73
290 291 5.756195 AATATCGCATTTGTGCACATACT 57.244 34.783 22.39 5.38 34.41 2.12
291 292 9.773328 ATATTAATATCGCATTTGTGCACATAC 57.227 29.630 22.39 9.46 34.41 2.39
292 293 9.771915 CATATTAATATCGCATTTGTGCACATA 57.228 29.630 22.39 17.13 34.41 2.29
295 296 6.581919 TGCATATTAATATCGCATTTGTGCAC 59.418 34.615 19.74 10.75 33.36 4.57
361 362 9.926158 ATTGCACATTTTCACAATATGTAAGAA 57.074 25.926 0.00 0.00 31.20 2.52
366 367 8.714179 CAGAAATTGCACATTTTCACAATATGT 58.286 29.630 16.17 0.00 34.74 2.29
367 368 8.714179 ACAGAAATTGCACATTTTCACAATATG 58.286 29.630 16.17 9.39 34.74 1.78
368 369 8.836268 ACAGAAATTGCACATTTTCACAATAT 57.164 26.923 16.17 0.00 34.74 1.28
369 370 8.659925 AACAGAAATTGCACATTTTCACAATA 57.340 26.923 16.17 0.00 34.74 1.90
370 371 7.280428 TGAACAGAAATTGCACATTTTCACAAT 59.720 29.630 16.17 0.00 34.74 2.71
371 372 6.592994 TGAACAGAAATTGCACATTTTCACAA 59.407 30.769 16.17 0.00 34.74 3.33
372 373 6.104665 TGAACAGAAATTGCACATTTTCACA 58.895 32.000 16.17 9.84 34.74 3.58
373 374 6.586868 TGAACAGAAATTGCACATTTTCAC 57.413 33.333 16.17 8.17 34.74 3.18
374 375 6.762187 ACATGAACAGAAATTGCACATTTTCA 59.238 30.769 16.17 11.12 34.74 2.69
376 377 7.556733 AACATGAACAGAAATTGCACATTTT 57.443 28.000 0.00 0.00 0.00 1.82
377 378 7.556733 AAACATGAACAGAAATTGCACATTT 57.443 28.000 0.00 6.57 0.00 2.32
378 379 7.556733 AAAACATGAACAGAAATTGCACATT 57.443 28.000 0.00 0.00 0.00 2.71
381 382 6.774084 ACAAAAACATGAACAGAAATTGCAC 58.226 32.000 0.00 0.00 0.00 4.57
382 383 6.592994 TGACAAAAACATGAACAGAAATTGCA 59.407 30.769 0.00 0.00 0.00 4.08
383 384 7.002816 TGACAAAAACATGAACAGAAATTGC 57.997 32.000 0.00 0.00 0.00 3.56
384 385 8.819015 TGATGACAAAAACATGAACAGAAATTG 58.181 29.630 0.00 0.00 0.00 2.32
385 386 8.945481 TGATGACAAAAACATGAACAGAAATT 57.055 26.923 0.00 0.00 0.00 1.82
386 387 9.550406 AATGATGACAAAAACATGAACAGAAAT 57.450 25.926 0.00 0.00 0.00 2.17
387 388 8.945481 AATGATGACAAAAACATGAACAGAAA 57.055 26.923 0.00 0.00 0.00 2.52
388 389 8.945481 AAATGATGACAAAAACATGAACAGAA 57.055 26.923 0.00 0.00 0.00 3.02
389 390 8.415553 AGAAATGATGACAAAAACATGAACAGA 58.584 29.630 0.00 0.00 0.00 3.41
390 391 8.583810 AGAAATGATGACAAAAACATGAACAG 57.416 30.769 0.00 0.00 0.00 3.16
391 392 8.945481 AAGAAATGATGACAAAAACATGAACA 57.055 26.923 0.00 0.00 0.00 3.18
474 475 9.399797 TCCGACAAGACTATATACTGAAACTAA 57.600 33.333 0.00 0.00 0.00 2.24
475 476 8.969260 TCCGACAAGACTATATACTGAAACTA 57.031 34.615 0.00 0.00 0.00 2.24
476 477 7.876936 TCCGACAAGACTATATACTGAAACT 57.123 36.000 0.00 0.00 0.00 2.66
478 479 9.582431 CTTTTCCGACAAGACTATATACTGAAA 57.418 33.333 0.00 0.00 0.00 2.69
481 482 9.239002 CTTCTTTTCCGACAAGACTATATACTG 57.761 37.037 0.00 0.00 29.70 2.74
482 483 8.968969 ACTTCTTTTCCGACAAGACTATATACT 58.031 33.333 0.00 0.00 29.70 2.12
483 484 9.021863 CACTTCTTTTCCGACAAGACTATATAC 57.978 37.037 0.00 0.00 29.70 1.47
484 485 8.746530 ACACTTCTTTTCCGACAAGACTATATA 58.253 33.333 0.00 0.00 29.70 0.86
485 486 7.612677 ACACTTCTTTTCCGACAAGACTATAT 58.387 34.615 0.00 0.00 29.70 0.86
486 487 6.989659 ACACTTCTTTTCCGACAAGACTATA 58.010 36.000 0.00 0.00 29.70 1.31
491 492 5.607477 ACATACACTTCTTTTCCGACAAGA 58.393 37.500 0.00 0.00 0.00 3.02
493 494 5.361427 TGACATACACTTCTTTTCCGACAA 58.639 37.500 0.00 0.00 0.00 3.18
494 495 4.951254 TGACATACACTTCTTTTCCGACA 58.049 39.130 0.00 0.00 0.00 4.35
495 496 5.408604 ACATGACATACACTTCTTTTCCGAC 59.591 40.000 0.00 0.00 0.00 4.79
496 497 5.547465 ACATGACATACACTTCTTTTCCGA 58.453 37.500 0.00 0.00 0.00 4.55
497 498 5.408299 TGACATGACATACACTTCTTTTCCG 59.592 40.000 0.00 0.00 0.00 4.30
498 499 6.801539 TGACATGACATACACTTCTTTTCC 57.198 37.500 0.00 0.00 0.00 3.13
522 523 7.725251 TCTGCTTAACAAGTGATGGAATTTTT 58.275 30.769 0.00 0.00 0.00 1.94
523 524 7.288810 TCTGCTTAACAAGTGATGGAATTTT 57.711 32.000 0.00 0.00 0.00 1.82
524 525 6.071728 CCTCTGCTTAACAAGTGATGGAATTT 60.072 38.462 0.00 0.00 0.00 1.82
525 526 5.416952 CCTCTGCTTAACAAGTGATGGAATT 59.583 40.000 0.00 0.00 0.00 2.17
527 528 4.041567 TCCTCTGCTTAACAAGTGATGGAA 59.958 41.667 0.00 0.00 0.00 3.53
528 529 3.582647 TCCTCTGCTTAACAAGTGATGGA 59.417 43.478 0.00 0.00 0.00 3.41
529 530 3.942829 TCCTCTGCTTAACAAGTGATGG 58.057 45.455 0.00 0.00 0.00 3.51
531 532 5.489792 TCTTCCTCTGCTTAACAAGTGAT 57.510 39.130 0.00 0.00 0.00 3.06
532 533 4.955811 TCTTCCTCTGCTTAACAAGTGA 57.044 40.909 0.00 0.00 0.00 3.41
533 534 5.300752 TCTTCTTCCTCTGCTTAACAAGTG 58.699 41.667 0.00 0.00 0.00 3.16
534 535 5.552870 TCTTCTTCCTCTGCTTAACAAGT 57.447 39.130 0.00 0.00 0.00 3.16
540 541 2.906389 TGCCTTCTTCTTCCTCTGCTTA 59.094 45.455 0.00 0.00 0.00 3.09
541 542 1.701847 TGCCTTCTTCTTCCTCTGCTT 59.298 47.619 0.00 0.00 0.00 3.91
542 543 1.278699 CTGCCTTCTTCTTCCTCTGCT 59.721 52.381 0.00 0.00 0.00 4.24
544 545 3.533547 CATCTGCCTTCTTCTTCCTCTG 58.466 50.000 0.00 0.00 0.00 3.35
545 546 2.504996 CCATCTGCCTTCTTCTTCCTCT 59.495 50.000 0.00 0.00 0.00 3.69
548 549 2.021208 GCCCATCTGCCTTCTTCTTCC 61.021 57.143 0.00 0.00 0.00 3.46
549 550 1.387539 GCCCATCTGCCTTCTTCTTC 58.612 55.000 0.00 0.00 0.00 2.87
550 551 3.584947 GCCCATCTGCCTTCTTCTT 57.415 52.632 0.00 0.00 0.00 2.52
644 4298 7.568349 TCTGATTTTCAGTCAGTTGCCTATAT 58.432 34.615 4.56 0.00 44.58 0.86
645 4299 6.946340 TCTGATTTTCAGTCAGTTGCCTATA 58.054 36.000 4.56 0.00 44.58 1.31
723 4383 6.772716 ACTTCTTTCCAAATGCAGTCTTTCTA 59.227 34.615 0.00 0.00 0.00 2.10
881 7107 6.932400 CCCCATTTATAGTAGAACGTTATGCA 59.068 38.462 13.42 0.00 0.00 3.96
916 7190 6.455113 CGTTTCGTTTAGTATTCCACATGAGG 60.455 42.308 2.20 2.20 0.00 3.86
1020 7320 3.347216 GACAGCTAAGGAAATGGAGCAA 58.653 45.455 0.00 0.00 37.40 3.91
1035 7335 1.544314 GCAAAGACCAAGAGGACAGCT 60.544 52.381 0.00 0.00 38.69 4.24
1312 9231 0.239879 ACGCACCAAATTTAGCACGG 59.760 50.000 9.27 1.14 0.00 4.94
1407 9328 1.675720 GCAAAGTTGGCACCAGTGGT 61.676 55.000 9.70 9.70 35.62 4.16
1506 9427 3.664107 TGAAACTAGCAAGCTGATCGTT 58.336 40.909 4.53 0.60 0.00 3.85
1517 9438 3.944650 TGAGCACTTTGTTGAAACTAGCA 59.055 39.130 0.00 0.00 0.00 3.49
1522 9443 2.845967 CGTGTGAGCACTTTGTTGAAAC 59.154 45.455 1.99 0.00 43.16 2.78
2201 16075 4.038080 GGGTCGCGGCAAACCTTG 62.038 66.667 14.93 0.00 35.78 3.61
2222 16096 1.228154 GTCCCAGTTGGCGAACCTT 60.228 57.895 8.09 0.00 36.63 3.50
2281 16155 3.070576 GGCCATTGAGCACCCCAC 61.071 66.667 0.00 0.00 0.00 4.61
2434 16326 4.701651 TGTGACAGATCCAACCATTTCATC 59.298 41.667 0.00 0.00 0.00 2.92
2490 16382 1.396996 GGCACTGCAACTATACAACGG 59.603 52.381 2.82 0.00 0.00 4.44
2492 16384 3.074412 ACTGGCACTGCAACTATACAAC 58.926 45.455 2.82 0.00 0.00 3.32
2494 16386 2.301583 TGACTGGCACTGCAACTATACA 59.698 45.455 2.82 0.00 0.00 2.29
2513 16443 2.026729 AGTGAGTCCAGTCTCGAGATGA 60.027 50.000 19.90 12.80 37.28 2.92
2788 16733 4.650972 TGTGGGTCTTATAACTGGCTTT 57.349 40.909 0.00 0.00 0.00 3.51
2789 16734 4.650972 TTGTGGGTCTTATAACTGGCTT 57.349 40.909 0.00 0.00 0.00 4.35
2814 16759 5.403466 GTCACAACATTGGATTTCTTTCTGC 59.597 40.000 0.00 0.00 0.00 4.26
2859 16804 3.714078 ATCTTAGCCCCGCCCCTGA 62.714 63.158 0.00 0.00 0.00 3.86
2869 16814 4.445019 CCCCCTCAAGTCTAAATCTTAGCC 60.445 50.000 0.00 0.00 0.00 3.93
2889 16834 0.036306 TTTGTCTCTTCTTCGCCCCC 59.964 55.000 0.00 0.00 0.00 5.40
2963 16908 5.692613 ACACTCGGCTTATAGTCAGATAC 57.307 43.478 0.00 0.00 0.00 2.24
2982 16927 3.370061 GCAGAGTACCGGTGAAATAACAC 59.630 47.826 19.93 4.26 39.70 3.32
3044 16989 4.055360 CGTTGAGGTCAGTATTTGTGTCA 58.945 43.478 0.00 0.00 0.00 3.58
3046 16991 4.067972 ACGTTGAGGTCAGTATTTGTGT 57.932 40.909 0.00 0.00 0.00 3.72
3073 17018 7.458397 TCTTTTCCTGATTCTTGGCTTAGTTA 58.542 34.615 0.00 0.00 0.00 2.24
3105 17050 7.859325 ATATGCCGAGTGTTTTTATGTAAGT 57.141 32.000 0.00 0.00 0.00 2.24
3106 17051 8.181573 ACAATATGCCGAGTGTTTTTATGTAAG 58.818 33.333 0.00 0.00 0.00 2.34
3163 17108 4.717233 CCACATGGCAATAACTTTGCTA 57.283 40.909 9.86 4.67 44.36 3.49
3257 17202 9.553064 CTATTTTGTGCACTCCTCTTCTATTAT 57.447 33.333 19.41 0.00 0.00 1.28
3258 17203 7.987458 CCTATTTTGTGCACTCCTCTTCTATTA 59.013 37.037 19.41 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.