Multiple sequence alignment - TraesCS7B01G336900

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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 TraesCS7B01G336900 chr7B 100.000 2471 0 0 1 2471 591948528 591950998 0.000000e+00 4564.0
1 TraesCS7B01G336900 chr7B 88.874 1456 99 32 794 2242 592348555 592347156 0.000000e+00 1733.0
2 TraesCS7B01G336900 chr7B 85.069 1306 96 45 356 1572 591723240 591724535 0.000000e+00 1240.0
3 TraesCS7B01G336900 chr7B 90.464 797 36 19 794 1572 592355540 592354766 0.000000e+00 1014.0
4 TraesCS7B01G336900 chr7B 91.416 233 17 3 356 587 591718247 591718477 1.430000e-82 316.0
5 TraesCS7B01G336900 chr7B 92.056 214 11 5 1573 1782 592354861 592354650 1.860000e-76 296.0
6 TraesCS7B01G336900 chr7B 92.143 140 11 0 2332 2471 615378207 615378068 5.390000e-47 198.0
7 TraesCS7B01G336900 chr7B 91.176 136 12 0 2333 2468 497083647 497083782 4.200000e-43 185.0
8 TraesCS7B01G336900 chr7B 85.417 144 20 1 215 357 719719300 719719443 5.510000e-32 148.0
9 TraesCS7B01G336900 chr7B 80.000 220 16 15 684 875 591718630 591718849 1.190000e-28 137.0
10 TraesCS7B01G336900 chr7B 83.516 91 9 2 712 796 592355659 592355569 2.040000e-11 80.5
11 TraesCS7B01G336900 chr7A 91.881 1010 64 9 794 1796 632551317 632550319 0.000000e+00 1395.0
12 TraesCS7B01G336900 chr7A 91.482 857 42 15 939 1782 632526569 632527407 0.000000e+00 1149.0
13 TraesCS7B01G336900 chr7A 91.447 795 46 14 791 1572 632531900 632532685 0.000000e+00 1072.0
14 TraesCS7B01G336900 chr7A 89.529 764 43 19 794 1540 632581912 632581169 0.000000e+00 933.0
15 TraesCS7B01G336900 chr7A 85.714 210 18 5 1576 1782 632581230 632581030 6.920000e-51 211.0
16 TraesCS7B01G336900 chr7A 97.590 83 2 0 1997 2079 632550150 632550068 2.560000e-30 143.0
17 TraesCS7B01G336900 chr7A 78.626 131 21 6 466 591 3422314 3422442 2.040000e-11 80.5
18 TraesCS7B01G336900 chr7A 81.609 87 9 6 356 442 652610751 652610830 5.700000e-07 65.8
19 TraesCS7B01G336900 chr7D 89.321 1002 58 18 619 1572 548708660 548709660 0.000000e+00 1212.0
20 TraesCS7B01G336900 chr7D 89.415 992 54 20 794 1772 548776808 548775855 0.000000e+00 1203.0
21 TraesCS7B01G336900 chr7D 91.017 757 40 18 794 1540 548782226 548781488 0.000000e+00 996.0
22 TraesCS7B01G336900 chr7D 91.845 233 17 2 356 587 548708298 548708529 8.520000e-85 324.0
23 TraesCS7B01G336900 chr7D 89.224 232 17 6 356 587 548711401 548711624 1.450000e-72 283.0
24 TraesCS7B01G336900 chr7D 83.069 189 13 8 1573 1751 548781552 548781373 1.180000e-33 154.0
25 TraesCS7B01G336900 chr5D 92.754 138 10 0 2334 2471 450172640 450172777 1.500000e-47 200.0
26 TraesCS7B01G336900 chr2B 92.701 137 10 0 2332 2468 142869615 142869751 5.390000e-47 198.0
27 TraesCS7B01G336900 chr2B 77.885 104 18 5 115 216 55856974 55856874 2.650000e-05 60.2
28 TraesCS7B01G336900 chr4D 92.593 135 10 0 2334 2468 105122891 105123025 6.970000e-46 195.0
29 TraesCS7B01G336900 chr4D 91.111 135 12 0 2334 2468 77371197 77371331 1.510000e-42 183.0
30 TraesCS7B01G336900 chr2A 91.912 136 11 0 2333 2468 339090565 339090700 9.020000e-45 191.0
31 TraesCS7B01G336900 chr2A 82.418 91 13 3 101 190 717413954 717413866 2.640000e-10 76.8
32 TraesCS7B01G336900 chr1D 90.580 138 13 0 2334 2471 473119303 473119166 1.510000e-42 183.0
33 TraesCS7B01G336900 chr1D 83.784 148 18 6 211 355 365716911 365717055 4.290000e-28 135.0
34 TraesCS7B01G336900 chr1D 87.302 63 7 1 124 186 438359652 438359591 1.230000e-08 71.3
35 TraesCS7B01G336900 chr6D 89.189 148 13 3 212 357 363384208 363384354 5.430000e-42 182.0
36 TraesCS7B01G336900 chr6D 79.528 127 15 9 96 216 455881846 455881725 2.040000e-11 80.5
37 TraesCS7B01G336900 chr5A 89.362 141 15 0 2328 2468 449776430 449776570 7.020000e-41 178.0
38 TraesCS7B01G336900 chr3B 87.248 149 15 3 213 359 815372927 815372781 1.520000e-37 167.0
39 TraesCS7B01G336900 chr1B 87.162 148 14 4 215 357 352890033 352890180 1.970000e-36 163.0
40 TraesCS7B01G336900 chr1B 83.439 157 21 4 214 368 491543492 491543339 9.210000e-30 141.0
41 TraesCS7B01G336900 chr1B 83.007 153 22 3 212 360 427473134 427472982 4.290000e-28 135.0
42 TraesCS7B01G336900 chr1B 77.863 131 21 8 82 208 137451112 137450986 9.480000e-10 75.0
43 TraesCS7B01G336900 chr1B 96.774 31 1 0 472 502 114692451 114692421 4.000000e-03 52.8
44 TraesCS7B01G336900 chr1A 86.000 150 16 4 215 360 409855022 409855170 3.290000e-34 156.0
45 TraesCS7B01G336900 chr1A 81.319 91 14 3 124 213 278366413 278366501 1.230000e-08 71.3
46 TraesCS7B01G336900 chr1A 83.333 78 9 4 133 208 78959973 78959898 4.410000e-08 69.4
47 TraesCS7B01G336900 chr5B 86.232 138 16 3 222 357 549680613 549680749 1.980000e-31 147.0
48 TraesCS7B01G336900 chr3A 77.914 163 30 4 380 539 621986055 621985896 2.020000e-16 97.1
49 TraesCS7B01G336900 chr2D 86.207 58 6 2 131 187 501269500 501269556 7.380000e-06 62.1
50 TraesCS7B01G336900 chr4B 85.246 61 5 3 159 216 580793302 580793243 2.650000e-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 TraesCS7B01G336900 chr7B 591948528 591950998 2470 False 4564.000000 4564 100.000000 1 2471 1 chr7B.!!$F3 2470
1 TraesCS7B01G336900 chr7B 592347156 592348555 1399 True 1733.000000 1733 88.874000 794 2242 1 chr7B.!!$R1 1448
2 TraesCS7B01G336900 chr7B 591723240 591724535 1295 False 1240.000000 1240 85.069000 356 1572 1 chr7B.!!$F2 1216
3 TraesCS7B01G336900 chr7B 592354650 592355659 1009 True 463.500000 1014 88.678667 712 1782 3 chr7B.!!$R3 1070
4 TraesCS7B01G336900 chr7B 591718247 591718849 602 False 226.500000 316 85.708000 356 875 2 chr7B.!!$F5 519
5 TraesCS7B01G336900 chr7A 632526569 632527407 838 False 1149.000000 1149 91.482000 939 1782 1 chr7A.!!$F2 843
6 TraesCS7B01G336900 chr7A 632531900 632532685 785 False 1072.000000 1072 91.447000 791 1572 1 chr7A.!!$F3 781
7 TraesCS7B01G336900 chr7A 632550068 632551317 1249 True 769.000000 1395 94.735500 794 2079 2 chr7A.!!$R1 1285
8 TraesCS7B01G336900 chr7A 632581030 632581912 882 True 572.000000 933 87.621500 794 1782 2 chr7A.!!$R2 988
9 TraesCS7B01G336900 chr7D 548775855 548776808 953 True 1203.000000 1203 89.415000 794 1772 1 chr7D.!!$R1 978
10 TraesCS7B01G336900 chr7D 548708298 548711624 3326 False 606.333333 1212 90.130000 356 1572 3 chr7D.!!$F1 1216
11 TraesCS7B01G336900 chr7D 548781373 548782226 853 True 575.000000 996 87.043000 794 1751 2 chr7D.!!$R2 957

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
751 871 1.358152 TGAGGGTCGGTTTGGAGATT 58.642 50.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 2216 0.03563 GCTCCAACAGACCATGCTCT 60.036 55.0 0.0 0.0 0.0 4.09 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
21 22 4.487714 ACTCCTCATTTCTATTTCCGCA 57.512 40.909 0.00 0.00 0.00 5.69
22 23 4.192317 ACTCCTCATTTCTATTTCCGCAC 58.808 43.478 0.00 0.00 0.00 5.34
23 24 4.080863 ACTCCTCATTTCTATTTCCGCACT 60.081 41.667 0.00 0.00 0.00 4.40
24 25 4.843728 TCCTCATTTCTATTTCCGCACTT 58.156 39.130 0.00 0.00 0.00 3.16
25 26 5.984725 TCCTCATTTCTATTTCCGCACTTA 58.015 37.500 0.00 0.00 0.00 2.24
26 27 5.815740 TCCTCATTTCTATTTCCGCACTTAC 59.184 40.000 0.00 0.00 0.00 2.34
27 28 5.817816 CCTCATTTCTATTTCCGCACTTACT 59.182 40.000 0.00 0.00 0.00 2.24
28 29 6.316390 CCTCATTTCTATTTCCGCACTTACTT 59.684 38.462 0.00 0.00 0.00 2.24
29 30 7.148239 CCTCATTTCTATTTCCGCACTTACTTT 60.148 37.037 0.00 0.00 0.00 2.66
30 31 8.106247 TCATTTCTATTTCCGCACTTACTTTT 57.894 30.769 0.00 0.00 0.00 2.27
31 32 8.573035 TCATTTCTATTTCCGCACTTACTTTTT 58.427 29.630 0.00 0.00 0.00 1.94
32 33 9.834628 CATTTCTATTTCCGCACTTACTTTTTA 57.165 29.630 0.00 0.00 0.00 1.52
36 37 9.221933 TCTATTTCCGCACTTACTTTTTATTCA 57.778 29.630 0.00 0.00 0.00 2.57
37 38 9.834628 CTATTTCCGCACTTACTTTTTATTCAA 57.165 29.630 0.00 0.00 0.00 2.69
39 40 9.705290 ATTTCCGCACTTACTTTTTATTCAATT 57.295 25.926 0.00 0.00 0.00 2.32
40 41 8.736751 TTCCGCACTTACTTTTTATTCAATTC 57.263 30.769 0.00 0.00 0.00 2.17
41 42 8.106247 TCCGCACTTACTTTTTATTCAATTCT 57.894 30.769 0.00 0.00 0.00 2.40
42 43 8.234546 TCCGCACTTACTTTTTATTCAATTCTC 58.765 33.333 0.00 0.00 0.00 2.87
43 44 7.484959 CCGCACTTACTTTTTATTCAATTCTCC 59.515 37.037 0.00 0.00 0.00 3.71
44 45 8.237267 CGCACTTACTTTTTATTCAATTCTCCT 58.763 33.333 0.00 0.00 0.00 3.69
45 46 9.561270 GCACTTACTTTTTATTCAATTCTCCTC 57.439 33.333 0.00 0.00 0.00 3.71
49 50 7.946381 ACTTTTTATTCAATTCTCCTCCTCC 57.054 36.000 0.00 0.00 0.00 4.30
50 51 7.470192 ACTTTTTATTCAATTCTCCTCCTCCA 58.530 34.615 0.00 0.00 0.00 3.86
51 52 7.950124 ACTTTTTATTCAATTCTCCTCCTCCAA 59.050 33.333 0.00 0.00 0.00 3.53
52 53 8.899887 TTTTTATTCAATTCTCCTCCTCCAAT 57.100 30.769 0.00 0.00 0.00 3.16
53 54 8.899887 TTTTATTCAATTCTCCTCCTCCAATT 57.100 30.769 0.00 0.00 0.00 2.32
54 55 8.899887 TTTATTCAATTCTCCTCCTCCAATTT 57.100 30.769 0.00 0.00 0.00 1.82
55 56 8.899887 TTATTCAATTCTCCTCCTCCAATTTT 57.100 30.769 0.00 0.00 0.00 1.82
56 57 6.840780 TTCAATTCTCCTCCTCCAATTTTC 57.159 37.500 0.00 0.00 0.00 2.29
57 58 5.891198 TCAATTCTCCTCCTCCAATTTTCA 58.109 37.500 0.00 0.00 0.00 2.69
58 59 6.496743 TCAATTCTCCTCCTCCAATTTTCAT 58.503 36.000 0.00 0.00 0.00 2.57
59 60 6.955851 TCAATTCTCCTCCTCCAATTTTCATT 59.044 34.615 0.00 0.00 0.00 2.57
60 61 7.455638 TCAATTCTCCTCCTCCAATTTTCATTT 59.544 33.333 0.00 0.00 0.00 2.32
61 62 7.803487 ATTCTCCTCCTCCAATTTTCATTTT 57.197 32.000 0.00 0.00 0.00 1.82
62 63 7.616528 TTCTCCTCCTCCAATTTTCATTTTT 57.383 32.000 0.00 0.00 0.00 1.94
63 64 8.719645 TTCTCCTCCTCCAATTTTCATTTTTA 57.280 30.769 0.00 0.00 0.00 1.52
64 65 8.719645 TCTCCTCCTCCAATTTTCATTTTTAA 57.280 30.769 0.00 0.00 0.00 1.52
65 66 9.153479 TCTCCTCCTCCAATTTTCATTTTTAAA 57.847 29.630 0.00 0.00 0.00 1.52
66 67 9.777297 CTCCTCCTCCAATTTTCATTTTTAAAA 57.223 29.630 0.00 0.00 0.00 1.52
67 68 9.777297 TCCTCCTCCAATTTTCATTTTTAAAAG 57.223 29.630 0.14 0.00 29.93 2.27
68 69 9.559732 CCTCCTCCAATTTTCATTTTTAAAAGT 57.440 29.630 0.14 0.00 29.93 2.66
70 71 9.898152 TCCTCCAATTTTCATTTTTAAAAGTGT 57.102 25.926 19.27 1.88 39.18 3.55
77 78 8.867248 TTTTCATTTTTAAAAGTGTTCAACGC 57.133 26.923 19.27 0.00 0.00 4.84
78 79 7.582435 TTCATTTTTAAAAGTGTTCAACGCA 57.418 28.000 19.27 0.00 0.00 5.24
79 80 7.763172 TCATTTTTAAAAGTGTTCAACGCAT 57.237 28.000 19.27 0.00 0.00 4.73
80 81 8.190888 TCATTTTTAAAAGTGTTCAACGCATT 57.809 26.923 19.27 0.00 0.00 3.56
81 82 8.660373 TCATTTTTAAAAGTGTTCAACGCATTT 58.340 25.926 19.27 9.12 34.49 2.32
82 83 9.907576 CATTTTTAAAAGTGTTCAACGCATTTA 57.092 25.926 13.66 7.29 32.70 1.40
86 87 9.959775 TTTAAAAGTGTTCAACGCATTTAAAAG 57.040 25.926 24.29 0.00 42.98 2.27
87 88 7.589574 AAAAGTGTTCAACGCATTTAAAAGT 57.410 28.000 3.43 0.00 29.25 2.66
88 89 8.690680 AAAAGTGTTCAACGCATTTAAAAGTA 57.309 26.923 3.43 0.00 29.25 2.24
89 90 8.865590 AAAGTGTTCAACGCATTTAAAAGTAT 57.134 26.923 3.43 0.00 0.00 2.12
90 91 9.953697 AAAGTGTTCAACGCATTTAAAAGTATA 57.046 25.926 3.43 0.00 0.00 1.47
184 185 9.283768 ACAATGTGTATGAAAAAGTAGTCATCA 57.716 29.630 0.00 0.00 36.00 3.07
188 189 9.944663 TGTGTATGAAAAAGTAGTCATCAAAAC 57.055 29.630 0.00 0.00 36.00 2.43
189 190 9.944663 GTGTATGAAAAAGTAGTCATCAAAACA 57.055 29.630 0.00 0.00 36.00 2.83
198 199 9.912634 AAAGTAGTCATCAAAACATGTATTTGG 57.087 29.630 22.19 13.50 38.12 3.28
199 200 8.862325 AGTAGTCATCAAAACATGTATTTGGA 57.138 30.769 22.19 10.38 38.12 3.53
200 201 9.295825 AGTAGTCATCAAAACATGTATTTGGAA 57.704 29.630 22.19 11.97 38.12 3.53
201 202 9.906660 GTAGTCATCAAAACATGTATTTGGAAA 57.093 29.630 22.19 11.51 38.12 3.13
205 206 9.775854 TCATCAAAACATGTATTTGGAAAATGT 57.224 25.926 22.19 0.00 38.12 2.71
221 222 8.934023 TGGAAAATGTTAATCATATACTCCCC 57.066 34.615 0.00 0.00 35.48 4.81
222 223 7.947890 TGGAAAATGTTAATCATATACTCCCCC 59.052 37.037 0.00 0.00 35.48 5.40
223 224 7.120726 GGAAAATGTTAATCATATACTCCCCCG 59.879 40.741 0.00 0.00 35.48 5.73
224 225 6.697641 AATGTTAATCATATACTCCCCCGT 57.302 37.500 0.00 0.00 35.48 5.28
225 226 6.697641 ATGTTAATCATATACTCCCCCGTT 57.302 37.500 0.00 0.00 34.67 4.44
226 227 6.105397 TGTTAATCATATACTCCCCCGTTC 57.895 41.667 0.00 0.00 0.00 3.95
227 228 5.012354 TGTTAATCATATACTCCCCCGTTCC 59.988 44.000 0.00 0.00 0.00 3.62
228 229 3.562108 ATCATATACTCCCCCGTTCCT 57.438 47.619 0.00 0.00 0.00 3.36
229 230 4.687262 ATCATATACTCCCCCGTTCCTA 57.313 45.455 0.00 0.00 0.00 2.94
230 231 4.474303 TCATATACTCCCCCGTTCCTAA 57.526 45.455 0.00 0.00 0.00 2.69
231 232 4.818447 TCATATACTCCCCCGTTCCTAAA 58.182 43.478 0.00 0.00 0.00 1.85
232 233 4.590222 TCATATACTCCCCCGTTCCTAAAC 59.410 45.833 0.00 0.00 0.00 2.01
233 234 2.323999 TACTCCCCCGTTCCTAAACA 57.676 50.000 0.00 0.00 34.93 2.83
234 235 1.665137 ACTCCCCCGTTCCTAAACAT 58.335 50.000 0.00 0.00 34.93 2.71
235 236 2.836667 ACTCCCCCGTTCCTAAACATA 58.163 47.619 0.00 0.00 34.93 2.29
236 237 3.183801 ACTCCCCCGTTCCTAAACATAA 58.816 45.455 0.00 0.00 34.93 1.90
237 238 3.199289 ACTCCCCCGTTCCTAAACATAAG 59.801 47.826 0.00 0.00 34.93 1.73
238 239 3.183801 TCCCCCGTTCCTAAACATAAGT 58.816 45.455 0.00 0.00 34.93 2.24
239 240 3.198417 TCCCCCGTTCCTAAACATAAGTC 59.802 47.826 0.00 0.00 34.93 3.01
240 241 3.199289 CCCCCGTTCCTAAACATAAGTCT 59.801 47.826 0.00 0.00 34.93 3.24
241 242 4.324022 CCCCCGTTCCTAAACATAAGTCTT 60.324 45.833 0.00 0.00 34.93 3.01
242 243 5.250982 CCCCGTTCCTAAACATAAGTCTTT 58.749 41.667 0.00 0.00 34.93 2.52
243 244 5.708697 CCCCGTTCCTAAACATAAGTCTTTT 59.291 40.000 0.00 0.00 34.93 2.27
244 245 6.208007 CCCCGTTCCTAAACATAAGTCTTTTT 59.792 38.462 0.00 0.00 34.93 1.94
245 246 7.391275 CCCCGTTCCTAAACATAAGTCTTTTTA 59.609 37.037 0.00 0.00 34.93 1.52
246 247 8.448615 CCCGTTCCTAAACATAAGTCTTTTTAG 58.551 37.037 7.75 7.75 34.93 1.85
247 248 9.211485 CCGTTCCTAAACATAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 34.70 2.10
278 279 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
279 280 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
280 281 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
281 282 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
282 283 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
283 284 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
284 285 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
285 286 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
286 287 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
287 288 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
288 289 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
289 290 2.749621 ACGGAGCAAAATGAGTGAATCC 59.250 45.455 0.00 0.00 0.00 3.01
290 291 2.749076 CGGAGCAAAATGAGTGAATCCA 59.251 45.455 0.00 0.00 0.00 3.41
291 292 3.426695 CGGAGCAAAATGAGTGAATCCAC 60.427 47.826 0.00 0.00 43.50 4.02
292 293 3.507233 GGAGCAAAATGAGTGAATCCACA 59.493 43.478 0.00 0.00 45.54 4.17
293 294 4.479619 GAGCAAAATGAGTGAATCCACAC 58.520 43.478 0.00 0.00 45.54 3.82
312 313 9.959721 ATCCACACTCTAAAATATGTTAGTTGT 57.040 29.630 11.66 12.43 32.95 3.32
663 770 1.397692 GTGTTTGGAAAACACGTCCGA 59.602 47.619 17.38 0.00 40.72 4.55
677 784 1.743958 CGTCCGAACCAGACTGTAGAT 59.256 52.381 0.93 0.00 31.83 1.98
678 785 2.163815 CGTCCGAACCAGACTGTAGATT 59.836 50.000 0.93 0.00 31.83 2.40
679 786 3.367087 CGTCCGAACCAGACTGTAGATTT 60.367 47.826 0.93 0.00 31.83 2.17
704 823 5.739935 GCTGGATGACAAAACAGGTTCAAAT 60.740 40.000 6.55 0.00 0.00 2.32
741 861 2.033602 GGGTGGTTTGAGGGTCGG 59.966 66.667 0.00 0.00 0.00 4.79
751 871 1.358152 TGAGGGTCGGTTTGGAGATT 58.642 50.000 0.00 0.00 0.00 2.40
792 948 5.661056 TGATTAAACCACCAACAAACACA 57.339 34.783 0.00 0.00 0.00 3.72
895 1051 3.243177 GTCGCTTTAAATACTCAGCCTCG 59.757 47.826 0.00 0.00 0.00 4.63
1035 1206 4.516195 GGAGCCGGAGCGAAGTCC 62.516 72.222 5.05 0.00 46.67 3.85
1278 1449 0.034896 ACAAGAAGTCCCGCATCGTT 59.965 50.000 0.00 0.00 0.00 3.85
1458 1638 2.530661 TCCCCCAAGAAGGCCGAA 60.531 61.111 0.00 0.00 35.39 4.30
1489 1732 1.265462 GACAGAGACGCGCATCGATC 61.265 60.000 5.73 4.05 41.67 3.69
1490 1733 2.051793 AGAGACGCGCATCGATCG 60.052 61.111 9.36 9.36 41.67 3.69
1491 1734 2.052148 GAGACGCGCATCGATCGA 60.052 61.111 21.86 21.86 41.67 3.59
1492 1735 1.441182 GAGACGCGCATCGATCGAT 60.441 57.895 24.60 24.60 41.67 3.59
1525 1783 5.392703 CGTGCTCTGTAGAACTAATGGTGTA 60.393 44.000 0.00 0.00 0.00 2.90
1719 2011 5.980698 TTTGGTGTTGCAATGTTAACATG 57.019 34.783 21.46 15.57 38.84 3.21
1728 2020 1.459450 ATGTTAACATGGGTGCGGTC 58.541 50.000 20.19 0.00 34.83 4.79
1756 2048 4.935885 ACTCAGATCTGTTCGAATTTGC 57.064 40.909 21.92 0.00 0.00 3.68
1791 2115 0.947244 GTGGTGCTGAGTGGAGTTTG 59.053 55.000 0.00 0.00 0.00 2.93
1793 2117 0.536006 GGTGCTGAGTGGAGTTTGCT 60.536 55.000 0.00 0.00 0.00 3.91
1821 2145 0.749091 TTCAGCGATGCCCAAGATGG 60.749 55.000 0.00 0.00 37.25 3.51
1838 2162 4.739793 AGATGGAAGTGAACCCAAATCAA 58.260 39.130 0.00 0.00 35.85 2.57
1844 2168 5.473039 GAAGTGAACCCAAATCAATTGAGG 58.527 41.667 14.54 11.66 41.85 3.86
1848 2172 3.541242 ACCCAAATCAATTGAGGTCCA 57.459 42.857 14.54 0.00 41.85 4.02
1849 2173 3.855668 ACCCAAATCAATTGAGGTCCAA 58.144 40.909 14.54 0.00 41.85 3.53
1851 2175 3.834231 CCCAAATCAATTGAGGTCCAAGT 59.166 43.478 14.54 0.00 41.85 3.16
1867 2191 1.879380 CAAGTGAATTCCCACGCAGAA 59.121 47.619 2.27 0.00 41.67 3.02
1894 2219 0.030101 GCAGGAGCAGCGTACTAGAG 59.970 60.000 0.00 0.00 41.58 2.43
1895 2220 0.030101 CAGGAGCAGCGTACTAGAGC 59.970 60.000 0.00 0.00 0.00 4.09
1896 2221 0.394488 AGGAGCAGCGTACTAGAGCA 60.394 55.000 0.00 0.00 35.48 4.26
1897 2222 0.671251 GGAGCAGCGTACTAGAGCAT 59.329 55.000 0.00 0.00 35.48 3.79
1898 2223 1.601663 GGAGCAGCGTACTAGAGCATG 60.602 57.143 0.00 0.00 35.48 4.06
1899 2224 0.387202 AGCAGCGTACTAGAGCATGG 59.613 55.000 0.00 0.00 35.48 3.66
1902 2227 1.678627 CAGCGTACTAGAGCATGGTCT 59.321 52.381 28.82 28.82 35.48 3.85
1927 2254 2.419297 GGAGCCAACCATGAGTCTGTAG 60.419 54.545 0.00 0.00 0.00 2.74
1958 2285 1.165270 GACAACCCCAGTGAAATCGG 58.835 55.000 0.00 0.00 0.00 4.18
2003 2736 2.103432 TCAAGCGAAAAGTAGACACCCA 59.897 45.455 0.00 0.00 0.00 4.51
2087 2820 3.120060 GGCATCTTCAATCGCCATACATC 60.120 47.826 0.00 0.00 44.25 3.06
2098 2831 2.032894 CGCCATACATCAAATCGGACAC 60.033 50.000 0.00 0.00 0.00 3.67
2183 3130 2.603652 CCGGATTTGAACAAACACGGAC 60.604 50.000 25.65 7.64 46.65 4.79
2199 3146 1.173043 GGACCGAATTCATGCAACCA 58.827 50.000 6.22 0.00 0.00 3.67
2203 3150 2.026641 CCGAATTCATGCAACCAGGAT 58.973 47.619 6.22 0.00 31.06 3.24
2261 3533 9.610705 CTAGGAGTAGTAGATACTTTGTGTACA 57.389 37.037 0.00 0.00 45.06 2.90
2263 3535 9.305555 AGGAGTAGTAGATACTTTGTGTACAAA 57.694 33.333 9.56 9.56 45.06 2.83
2275 3547 3.403968 TGTGTACAAAGTGTGTGTGTGT 58.596 40.909 0.00 0.00 41.89 3.72
2276 3548 3.187432 TGTGTACAAAGTGTGTGTGTGTG 59.813 43.478 0.00 0.00 41.89 3.82
2278 3550 2.987413 ACAAAGTGTGTGTGTGTGTG 57.013 45.000 0.00 0.00 39.72 3.82
2279 3551 2.226330 ACAAAGTGTGTGTGTGTGTGT 58.774 42.857 0.00 0.00 39.72 3.72
2280 3552 2.031245 ACAAAGTGTGTGTGTGTGTGTG 60.031 45.455 0.00 0.00 39.72 3.82
2281 3553 1.890876 AAGTGTGTGTGTGTGTGTGT 58.109 45.000 0.00 0.00 0.00 3.72
2284 3556 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2285 3557 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2286 3558 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2287 3559 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2288 3560 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2289 3561 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2290 3562 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2291 3563 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2293 3565 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2294 3566 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2295 3567 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2296 3568 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2297 3569 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2299 3571 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2300 3572 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2301 3573 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2302 3574 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2303 3575 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2305 3577 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2306 3578 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2307 3579 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2309 3581 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2310 3582 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2311 3583 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2312 3584 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2313 3585 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2314 3586 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2315 3587 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2316 3588 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
2317 3589 1.265365 TGTGTGTGTGTGTGTGTGTTG 59.735 47.619 0.00 0.00 0.00 3.33
2321 3593 1.271108 TGTGTGTGTGTGTGTTGACCT 60.271 47.619 0.00 0.00 0.00 3.85
2322 3594 2.028020 TGTGTGTGTGTGTGTTGACCTA 60.028 45.455 0.00 0.00 0.00 3.08
2323 3595 2.607635 GTGTGTGTGTGTGTTGACCTAG 59.392 50.000 0.00 0.00 0.00 3.02
2324 3596 1.597663 GTGTGTGTGTGTTGACCTAGC 59.402 52.381 0.00 0.00 0.00 3.42
2326 3598 2.696187 TGTGTGTGTGTTGACCTAGCTA 59.304 45.455 0.00 0.00 0.00 3.32
2327 3599 3.323691 TGTGTGTGTGTTGACCTAGCTAT 59.676 43.478 0.00 0.00 0.00 2.97
2328 3600 3.679980 GTGTGTGTGTTGACCTAGCTATG 59.320 47.826 0.00 0.00 0.00 2.23
2330 3602 3.056107 GTGTGTGTTGACCTAGCTATGGA 60.056 47.826 14.03 0.00 0.00 3.41
2331 3603 3.774766 TGTGTGTTGACCTAGCTATGGAT 59.225 43.478 14.03 1.77 0.00 3.41
2332 3604 4.122776 GTGTGTTGACCTAGCTATGGATG 58.877 47.826 14.03 0.00 0.00 3.51
2333 3605 3.774766 TGTGTTGACCTAGCTATGGATGT 59.225 43.478 14.03 0.00 0.00 3.06
2334 3606 4.959839 TGTGTTGACCTAGCTATGGATGTA 59.040 41.667 14.03 0.00 0.00 2.29
2336 3608 5.069251 GTGTTGACCTAGCTATGGATGTACT 59.931 44.000 14.03 0.00 0.00 2.73
2338 3610 4.408276 TGACCTAGCTATGGATGTACTCC 58.592 47.826 14.03 0.00 45.19 3.85
2341 3613 2.031495 AGCTATGGATGTACTCCCCC 57.969 55.000 8.36 0.00 44.23 5.40
2358 3656 1.808343 CCCCCGTTTCTTTTTACTCCG 59.192 52.381 0.00 0.00 0.00 4.63
2359 3657 1.198408 CCCCGTTTCTTTTTACTCCGC 59.802 52.381 0.00 0.00 0.00 5.54
2360 3658 1.198408 CCCGTTTCTTTTTACTCCGCC 59.802 52.381 0.00 0.00 0.00 6.13
2361 3659 2.148768 CCGTTTCTTTTTACTCCGCCT 58.851 47.619 0.00 0.00 0.00 5.52
2362 3660 3.328505 CCGTTTCTTTTTACTCCGCCTA 58.671 45.455 0.00 0.00 0.00 3.93
2364 3662 5.111293 CCGTTTCTTTTTACTCCGCCTATA 58.889 41.667 0.00 0.00 0.00 1.31
2367 3665 7.178074 CGTTTCTTTTTACTCCGCCTATAAAG 58.822 38.462 0.00 0.00 0.00 1.85
2371 3669 8.036273 TCTTTTTACTCCGCCTATAAAGTTTG 57.964 34.615 0.00 0.00 0.00 2.93
2372 3670 6.746745 TTTTACTCCGCCTATAAAGTTTGG 57.253 37.500 0.00 0.00 0.00 3.28
2374 3672 3.606687 ACTCCGCCTATAAAGTTTGGTG 58.393 45.455 0.00 0.00 0.00 4.17
2378 3676 4.616181 CGCCTATAAAGTTTGGTGGAAG 57.384 45.455 0.00 0.00 0.00 3.46
2379 3677 4.007659 CGCCTATAAAGTTTGGTGGAAGT 58.992 43.478 0.00 0.00 0.00 3.01
2381 3679 5.007682 GCCTATAAAGTTTGGTGGAAGTCA 58.992 41.667 0.00 0.00 0.00 3.41
2382 3680 5.475564 GCCTATAAAGTTTGGTGGAAGTCAA 59.524 40.000 0.00 0.00 0.00 3.18
2383 3681 6.015772 GCCTATAAAGTTTGGTGGAAGTCAAA 60.016 38.462 0.00 0.00 0.00 2.69
2390 3688 5.923665 GTTTGGTGGAAGTCAAACTATACG 58.076 41.667 10.51 0.00 45.28 3.06
2391 3689 5.471556 TTGGTGGAAGTCAAACTATACGA 57.528 39.130 0.00 0.00 0.00 3.43
2393 3691 5.475719 TGGTGGAAGTCAAACTATACGAAG 58.524 41.667 0.00 0.00 0.00 3.79
2395 3693 5.930569 GGTGGAAGTCAAACTATACGAAGTT 59.069 40.000 0.00 0.00 37.78 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.080863 AGTGCGGAAATAGAAATGAGGAGT 60.081 41.667 0.00 0.00 0.00 3.85
1 2 4.446371 AGTGCGGAAATAGAAATGAGGAG 58.554 43.478 0.00 0.00 0.00 3.69
2 3 4.487714 AGTGCGGAAATAGAAATGAGGA 57.512 40.909 0.00 0.00 0.00 3.71
3 4 5.817816 AGTAAGTGCGGAAATAGAAATGAGG 59.182 40.000 0.00 0.00 0.00 3.86
4 5 6.910536 AGTAAGTGCGGAAATAGAAATGAG 57.089 37.500 0.00 0.00 0.00 2.90
5 6 7.681939 AAAGTAAGTGCGGAAATAGAAATGA 57.318 32.000 0.00 0.00 0.00 2.57
6 7 8.742554 AAAAAGTAAGTGCGGAAATAGAAATG 57.257 30.769 0.00 0.00 0.00 2.32
10 11 9.221933 TGAATAAAAAGTAAGTGCGGAAATAGA 57.778 29.630 0.00 0.00 0.00 1.98
11 12 9.834628 TTGAATAAAAAGTAAGTGCGGAAATAG 57.165 29.630 0.00 0.00 0.00 1.73
13 14 9.705290 AATTGAATAAAAAGTAAGTGCGGAAAT 57.295 25.926 0.00 0.00 0.00 2.17
14 15 9.187455 GAATTGAATAAAAAGTAAGTGCGGAAA 57.813 29.630 0.00 0.00 0.00 3.13
15 16 8.573035 AGAATTGAATAAAAAGTAAGTGCGGAA 58.427 29.630 0.00 0.00 0.00 4.30
16 17 8.106247 AGAATTGAATAAAAAGTAAGTGCGGA 57.894 30.769 0.00 0.00 0.00 5.54
17 18 7.484959 GGAGAATTGAATAAAAAGTAAGTGCGG 59.515 37.037 0.00 0.00 0.00 5.69
18 19 8.237267 AGGAGAATTGAATAAAAAGTAAGTGCG 58.763 33.333 0.00 0.00 0.00 5.34
19 20 9.561270 GAGGAGAATTGAATAAAAAGTAAGTGC 57.439 33.333 0.00 0.00 0.00 4.40
23 24 9.462606 GGAGGAGGAGAATTGAATAAAAAGTAA 57.537 33.333 0.00 0.00 0.00 2.24
24 25 8.611257 TGGAGGAGGAGAATTGAATAAAAAGTA 58.389 33.333 0.00 0.00 0.00 2.24
25 26 7.470192 TGGAGGAGGAGAATTGAATAAAAAGT 58.530 34.615 0.00 0.00 0.00 2.66
26 27 7.944729 TGGAGGAGGAGAATTGAATAAAAAG 57.055 36.000 0.00 0.00 0.00 2.27
27 28 8.899887 ATTGGAGGAGGAGAATTGAATAAAAA 57.100 30.769 0.00 0.00 0.00 1.94
28 29 8.899887 AATTGGAGGAGGAGAATTGAATAAAA 57.100 30.769 0.00 0.00 0.00 1.52
29 30 8.899887 AAATTGGAGGAGGAGAATTGAATAAA 57.100 30.769 0.00 0.00 0.00 1.40
30 31 8.899887 AAAATTGGAGGAGGAGAATTGAATAA 57.100 30.769 0.00 0.00 0.00 1.40
31 32 8.115384 TGAAAATTGGAGGAGGAGAATTGAATA 58.885 33.333 0.00 0.00 0.00 1.75
32 33 6.955851 TGAAAATTGGAGGAGGAGAATTGAAT 59.044 34.615 0.00 0.00 0.00 2.57
33 34 6.314120 TGAAAATTGGAGGAGGAGAATTGAA 58.686 36.000 0.00 0.00 0.00 2.69
34 35 5.891198 TGAAAATTGGAGGAGGAGAATTGA 58.109 37.500 0.00 0.00 0.00 2.57
35 36 6.786967 ATGAAAATTGGAGGAGGAGAATTG 57.213 37.500 0.00 0.00 0.00 2.32
36 37 7.803487 AAATGAAAATTGGAGGAGGAGAATT 57.197 32.000 0.00 0.00 0.00 2.17
37 38 7.803487 AAAATGAAAATTGGAGGAGGAGAAT 57.197 32.000 0.00 0.00 0.00 2.40
38 39 7.616528 AAAAATGAAAATTGGAGGAGGAGAA 57.383 32.000 0.00 0.00 0.00 2.87
39 40 8.719645 TTAAAAATGAAAATTGGAGGAGGAGA 57.280 30.769 0.00 0.00 0.00 3.71
40 41 9.777297 TTTTAAAAATGAAAATTGGAGGAGGAG 57.223 29.630 0.00 0.00 0.00 3.69
41 42 9.777297 CTTTTAAAAATGAAAATTGGAGGAGGA 57.223 29.630 1.66 0.00 0.00 3.71
42 43 9.559732 ACTTTTAAAAATGAAAATTGGAGGAGG 57.440 29.630 1.66 0.00 0.00 4.30
44 45 9.898152 ACACTTTTAAAAATGAAAATTGGAGGA 57.102 25.926 15.75 0.00 33.24 3.71
51 52 9.484326 GCGTTGAACACTTTTAAAAATGAAAAT 57.516 25.926 15.75 0.00 0.00 1.82
52 53 8.495949 TGCGTTGAACACTTTTAAAAATGAAAA 58.504 25.926 15.75 4.67 0.00 2.29
53 54 8.018677 TGCGTTGAACACTTTTAAAAATGAAA 57.981 26.923 15.75 4.98 0.00 2.69
54 55 7.582435 TGCGTTGAACACTTTTAAAAATGAA 57.418 28.000 15.75 0.00 0.00 2.57
55 56 7.763172 ATGCGTTGAACACTTTTAAAAATGA 57.237 28.000 15.75 0.00 0.00 2.57
56 57 8.819152 AAATGCGTTGAACACTTTTAAAAATG 57.181 26.923 7.80 7.80 0.00 2.32
60 61 9.959775 CTTTTAAATGCGTTGAACACTTTTAAA 57.040 25.926 18.04 18.04 32.71 1.52
61 62 9.141400 ACTTTTAAATGCGTTGAACACTTTTAA 57.859 25.926 10.95 10.95 0.00 1.52
62 63 8.690680 ACTTTTAAATGCGTTGAACACTTTTA 57.309 26.923 0.00 0.00 0.00 1.52
63 64 7.589574 ACTTTTAAATGCGTTGAACACTTTT 57.410 28.000 0.00 0.00 0.00 2.27
64 65 8.865590 ATACTTTTAAATGCGTTGAACACTTT 57.134 26.923 0.00 0.00 0.00 2.66
158 159 9.283768 TGATGACTACTTTTTCATACACATTGT 57.716 29.630 0.00 0.00 32.43 2.71
162 163 9.944663 GTTTTGATGACTACTTTTTCATACACA 57.055 29.630 0.00 0.00 32.43 3.72
163 164 9.944663 TGTTTTGATGACTACTTTTTCATACAC 57.055 29.630 0.00 0.00 32.43 2.90
172 173 9.912634 CCAAATACATGTTTTGATGACTACTTT 57.087 29.630 23.47 0.00 36.40 2.66
173 174 9.295825 TCCAAATACATGTTTTGATGACTACTT 57.704 29.630 23.47 0.00 36.40 2.24
174 175 8.862325 TCCAAATACATGTTTTGATGACTACT 57.138 30.769 23.47 0.00 36.40 2.57
175 176 9.906660 TTTCCAAATACATGTTTTGATGACTAC 57.093 29.630 23.47 0.00 36.40 2.73
179 180 9.775854 ACATTTTCCAAATACATGTTTTGATGA 57.224 25.926 23.47 15.35 36.40 2.92
195 196 9.362151 GGGGAGTATATGATTAACATTTTCCAA 57.638 33.333 0.00 0.00 40.07 3.53
196 197 7.947890 GGGGGAGTATATGATTAACATTTTCCA 59.052 37.037 0.00 0.00 40.07 3.53
197 198 7.120726 CGGGGGAGTATATGATTAACATTTTCC 59.879 40.741 0.00 0.00 40.07 3.13
198 199 7.664318 ACGGGGGAGTATATGATTAACATTTTC 59.336 37.037 0.00 0.00 40.07 2.29
199 200 7.523415 ACGGGGGAGTATATGATTAACATTTT 58.477 34.615 0.00 0.00 40.07 1.82
200 201 7.086685 ACGGGGGAGTATATGATTAACATTT 57.913 36.000 0.00 0.00 40.07 2.32
201 202 6.697641 ACGGGGGAGTATATGATTAACATT 57.302 37.500 0.00 0.00 40.07 2.71
202 203 6.296259 GGAACGGGGGAGTATATGATTAACAT 60.296 42.308 0.00 0.00 42.39 2.71
203 204 5.012354 GGAACGGGGGAGTATATGATTAACA 59.988 44.000 0.00 0.00 0.00 2.41
204 205 5.247792 AGGAACGGGGGAGTATATGATTAAC 59.752 44.000 0.00 0.00 0.00 2.01
205 206 5.408824 AGGAACGGGGGAGTATATGATTAA 58.591 41.667 0.00 0.00 0.00 1.40
206 207 5.019657 AGGAACGGGGGAGTATATGATTA 57.980 43.478 0.00 0.00 0.00 1.75
207 208 3.870559 AGGAACGGGGGAGTATATGATT 58.129 45.455 0.00 0.00 0.00 2.57
208 209 3.562108 AGGAACGGGGGAGTATATGAT 57.438 47.619 0.00 0.00 0.00 2.45
209 210 4.474303 TTAGGAACGGGGGAGTATATGA 57.526 45.455 0.00 0.00 0.00 2.15
210 211 4.345837 TGTTTAGGAACGGGGGAGTATATG 59.654 45.833 0.00 0.00 38.65 1.78
211 212 4.559726 TGTTTAGGAACGGGGGAGTATAT 58.440 43.478 0.00 0.00 38.65 0.86
212 213 3.992999 TGTTTAGGAACGGGGGAGTATA 58.007 45.455 0.00 0.00 38.65 1.47
213 214 2.836667 TGTTTAGGAACGGGGGAGTAT 58.163 47.619 0.00 0.00 38.65 2.12
214 215 2.323999 TGTTTAGGAACGGGGGAGTA 57.676 50.000 0.00 0.00 38.65 2.59
215 216 1.665137 ATGTTTAGGAACGGGGGAGT 58.335 50.000 0.00 0.00 38.65 3.85
216 217 3.199289 ACTTATGTTTAGGAACGGGGGAG 59.801 47.826 0.00 0.00 38.65 4.30
217 218 3.183801 ACTTATGTTTAGGAACGGGGGA 58.816 45.455 0.00 0.00 38.65 4.81
218 219 3.199289 AGACTTATGTTTAGGAACGGGGG 59.801 47.826 0.00 0.00 38.65 5.40
219 220 4.482952 AGACTTATGTTTAGGAACGGGG 57.517 45.455 0.00 0.00 38.65 5.73
220 221 6.812879 AAAAGACTTATGTTTAGGAACGGG 57.187 37.500 0.00 0.00 38.65 5.28
221 222 9.211485 TCTAAAAAGACTTATGTTTAGGAACGG 57.789 33.333 13.94 0.00 38.65 4.44
256 257 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
257 258 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
258 259 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
259 260 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
260 261 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
261 262 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
262 263 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
263 264 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
264 265 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
265 266 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
266 267 4.576463 GGATTCACTCATTTTGCTCCGTAT 59.424 41.667 0.00 0.00 0.00 3.06
267 268 3.938963 GGATTCACTCATTTTGCTCCGTA 59.061 43.478 0.00 0.00 0.00 4.02
268 269 2.749621 GGATTCACTCATTTTGCTCCGT 59.250 45.455 0.00 0.00 0.00 4.69
269 270 2.749076 TGGATTCACTCATTTTGCTCCG 59.251 45.455 0.00 0.00 0.00 4.63
270 271 3.507233 TGTGGATTCACTCATTTTGCTCC 59.493 43.478 5.55 0.00 43.94 4.70
271 272 4.217118 AGTGTGGATTCACTCATTTTGCTC 59.783 41.667 5.55 0.00 44.07 4.26
272 273 4.147321 AGTGTGGATTCACTCATTTTGCT 58.853 39.130 5.55 0.00 44.07 3.91
273 274 4.510038 AGTGTGGATTCACTCATTTTGC 57.490 40.909 5.55 0.00 44.07 3.68
286 287 9.959721 ACAACTAACATATTTTAGAGTGTGGAT 57.040 29.630 14.21 0.00 33.48 3.41
392 393 9.991388 TGTACATTTTTCATATACGCCTTAAAC 57.009 29.630 0.00 0.00 0.00 2.01
594 678 8.896320 TTTGTACATGTTCTAGCAGTAGAAAA 57.104 30.769 2.30 0.00 45.08 2.29
648 755 0.107800 TGGTTCGGACGTGTTTTCCA 60.108 50.000 0.00 0.00 31.94 3.53
650 757 1.259770 GTCTGGTTCGGACGTGTTTTC 59.740 52.381 0.00 0.00 29.77 2.29
663 770 3.327757 TCCAGCAAATCTACAGTCTGGTT 59.672 43.478 4.53 0.00 41.24 3.67
677 784 3.030291 ACCTGTTTTGTCATCCAGCAAA 58.970 40.909 0.00 0.00 33.40 3.68
678 785 2.665165 ACCTGTTTTGTCATCCAGCAA 58.335 42.857 0.00 0.00 0.00 3.91
679 786 2.363306 ACCTGTTTTGTCATCCAGCA 57.637 45.000 0.00 0.00 0.00 4.41
704 823 0.037697 CAACCATTCGGACCTCACGA 60.038 55.000 0.00 0.00 38.78 4.35
741 861 6.420903 GGTGCTTGTTTTTCTAATCTCCAAAC 59.579 38.462 0.00 0.00 0.00 2.93
751 871 6.811253 AATCATACGGTGCTTGTTTTTCTA 57.189 33.333 0.00 0.00 0.00 2.10
792 948 2.581354 GGCTGCGATGTCCTCTGT 59.419 61.111 0.00 0.00 0.00 3.41
895 1051 0.107752 CTGCTTGGGAAGAGAGAGGC 60.108 60.000 0.00 0.00 0.00 4.70
1458 1638 3.615351 GCGTCTCTGTCTAAGCCTTCTTT 60.615 47.826 0.00 0.00 33.85 2.52
1472 1652 2.353074 CGATCGATGCGCGTCTCTG 61.353 63.158 26.02 11.92 41.80 3.35
1489 1732 1.585668 CAGAGCACGACAAGCTAATCG 59.414 52.381 15.85 15.85 43.58 3.34
1490 1733 2.611518 ACAGAGCACGACAAGCTAATC 58.388 47.619 0.00 0.00 43.58 1.75
1491 1734 2.751166 ACAGAGCACGACAAGCTAAT 57.249 45.000 0.00 0.00 43.58 1.73
1492 1735 2.817844 TCTACAGAGCACGACAAGCTAA 59.182 45.455 0.00 0.00 43.58 3.09
1525 1783 4.713814 TCTTGGAAGCACAGATCTACATCT 59.286 41.667 0.00 0.00 40.32 2.90
1719 2011 1.848932 GAGTTTTTCCGACCGCACCC 61.849 60.000 0.00 0.00 0.00 4.61
1728 2020 3.987868 TCGAACAGATCTGAGTTTTTCCG 59.012 43.478 29.27 17.03 0.00 4.30
1756 2048 3.803778 GCACCACAAGAAAGAAATGTTGG 59.196 43.478 0.00 0.00 0.00 3.77
1791 2115 2.589014 CATCGCTGAAACTTCCAAAGC 58.411 47.619 0.00 0.00 0.00 3.51
1793 2117 1.269448 GGCATCGCTGAAACTTCCAAA 59.731 47.619 0.00 0.00 0.00 3.28
1821 2145 5.011023 ACCTCAATTGATTTGGGTTCACTTC 59.989 40.000 8.96 0.00 36.21 3.01
1838 2162 3.075882 TGGGAATTCACTTGGACCTCAAT 59.924 43.478 9.56 0.00 34.45 2.57
1844 2168 0.521735 GCGTGGGAATTCACTTGGAC 59.478 55.000 9.56 0.00 35.63 4.02
1848 2172 2.270352 TTCTGCGTGGGAATTCACTT 57.730 45.000 9.56 0.00 35.63 3.16
1849 2173 2.496899 ATTCTGCGTGGGAATTCACT 57.503 45.000 9.56 0.00 35.63 3.41
1851 2175 5.913137 AAATTATTCTGCGTGGGAATTCA 57.087 34.783 7.93 0.00 35.40 2.57
1854 2178 4.081752 TGCAAAATTATTCTGCGTGGGAAT 60.082 37.500 0.00 0.00 38.97 3.01
1883 2208 1.678627 CAGACCATGCTCTAGTACGCT 59.321 52.381 0.00 0.00 0.00 5.07
1889 2214 2.741228 GCTCCAACAGACCATGCTCTAG 60.741 54.545 0.00 0.00 0.00 2.43
1890 2215 1.208052 GCTCCAACAGACCATGCTCTA 59.792 52.381 0.00 0.00 0.00 2.43
1891 2216 0.035630 GCTCCAACAGACCATGCTCT 60.036 55.000 0.00 0.00 0.00 4.09
1894 2219 0.895100 TTGGCTCCAACAGACCATGC 60.895 55.000 0.00 0.00 30.95 4.06
1895 2220 3.344703 TTGGCTCCAACAGACCATG 57.655 52.632 0.00 0.00 30.95 3.66
1927 2254 0.876342 GGGTTGTCATCCTCGATCGC 60.876 60.000 11.09 0.00 0.00 4.58
1958 2285 3.891366 ACCATGCTTAGTATTTGCCCATC 59.109 43.478 0.00 0.00 0.00 3.51
2003 2736 6.306987 ACTCTGTTTATTTGATGGTTCCTGT 58.693 36.000 0.00 0.00 0.00 4.00
2087 2820 1.404047 GCATTTGGGGTGTCCGATTTG 60.404 52.381 0.00 0.00 38.76 2.32
2117 2850 3.680786 CGAGGCGGTGTCCAGACA 61.681 66.667 0.00 0.00 39.32 3.41
2132 2865 2.048222 CTCGCAGTTGGCTTCCGA 60.048 61.111 0.00 0.00 41.67 4.55
2135 2868 2.359230 AGGCTCGCAGTTGGCTTC 60.359 61.111 0.00 0.00 41.67 3.86
2147 2880 1.821216 TCCGGTTTGAAATGAGGCTC 58.179 50.000 7.79 7.79 0.00 4.70
2183 3130 1.462616 TCCTGGTTGCATGAATTCGG 58.537 50.000 0.00 0.00 0.00 4.30
2235 3507 9.610705 TGTACACAAAGTATCTACTACTCCTAG 57.389 37.037 0.00 0.00 39.87 3.02
2252 3524 4.276183 ACACACACACACTTTGTACACAAA 59.724 37.500 7.28 7.28 42.90 2.83
2255 3527 3.187637 ACACACACACACACTTTGTACAC 59.812 43.478 0.00 0.00 35.67 2.90
2256 3528 3.187432 CACACACACACACACTTTGTACA 59.813 43.478 0.00 0.00 35.67 2.90
2257 3529 3.187637 ACACACACACACACACTTTGTAC 59.812 43.478 0.00 0.00 35.67 2.90
2258 3530 3.187432 CACACACACACACACACTTTGTA 59.813 43.478 0.00 0.00 35.67 2.41
2259 3531 2.031245 CACACACACACACACACTTTGT 60.031 45.455 0.00 0.00 39.97 2.83
2261 3533 2.031245 CACACACACACACACACACTTT 60.031 45.455 0.00 0.00 0.00 2.66
2263 3535 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
2264 3536 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2265 3537 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2266 3538 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2267 3539 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2270 3542 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2272 3544 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2275 3547 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2276 3548 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2278 3550 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2279 3551 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2280 3552 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2281 3553 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2284 3556 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2285 3557 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2286 3558 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2287 3559 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2288 3560 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2289 3561 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2290 3562 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2291 3563 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2293 3565 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2294 3566 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2295 3567 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2296 3568 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2297 3569 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
2299 3571 1.533299 GTCAACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
2300 3572 1.135803 GGTCAACACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
2301 3573 1.160989 GGTCAACACACACACACACA 58.839 50.000 0.00 0.00 0.00 3.72
2302 3574 1.448985 AGGTCAACACACACACACAC 58.551 50.000 0.00 0.00 0.00 3.82
2303 3575 2.899976 CTAGGTCAACACACACACACA 58.100 47.619 0.00 0.00 0.00 3.72
2305 3577 1.484653 AGCTAGGTCAACACACACACA 59.515 47.619 0.00 0.00 0.00 3.72
2306 3578 2.240493 AGCTAGGTCAACACACACAC 57.760 50.000 0.00 0.00 0.00 3.82
2307 3579 3.306710 CCATAGCTAGGTCAACACACACA 60.307 47.826 4.47 0.00 0.00 3.72
2309 3581 3.169908 TCCATAGCTAGGTCAACACACA 58.830 45.455 4.47 0.00 0.00 3.72
2310 3582 3.887621 TCCATAGCTAGGTCAACACAC 57.112 47.619 4.47 0.00 0.00 3.82
2311 3583 3.774766 ACATCCATAGCTAGGTCAACACA 59.225 43.478 4.47 0.00 0.00 3.72
2312 3584 4.408182 ACATCCATAGCTAGGTCAACAC 57.592 45.455 4.47 0.00 0.00 3.32
2313 3585 5.208890 AGTACATCCATAGCTAGGTCAACA 58.791 41.667 4.47 0.00 0.00 3.33
2314 3586 5.774630 GAGTACATCCATAGCTAGGTCAAC 58.225 45.833 4.47 0.00 0.00 3.18
2338 3610 1.808343 CGGAGTAAAAAGAAACGGGGG 59.192 52.381 0.00 0.00 0.00 5.40
2341 3613 2.148768 AGGCGGAGTAAAAAGAAACGG 58.851 47.619 0.00 0.00 0.00 4.44
2343 3615 8.037382 ACTTTATAGGCGGAGTAAAAAGAAAC 57.963 34.615 0.00 0.00 0.00 2.78
2353 3651 3.606687 CACCAAACTTTATAGGCGGAGT 58.393 45.455 0.00 0.00 0.00 3.85
2356 3654 2.993937 TCCACCAAACTTTATAGGCGG 58.006 47.619 0.00 0.00 0.00 6.13
2357 3655 4.007659 ACTTCCACCAAACTTTATAGGCG 58.992 43.478 0.00 0.00 0.00 5.52
2358 3656 5.007682 TGACTTCCACCAAACTTTATAGGC 58.992 41.667 0.00 0.00 0.00 3.93
2359 3657 7.368059 GTTTGACTTCCACCAAACTTTATAGG 58.632 38.462 0.00 0.00 45.05 2.57
2371 3669 5.476614 ACTTCGTATAGTTTGACTTCCACC 58.523 41.667 0.00 0.00 0.00 4.61
2372 3670 7.417496 AAACTTCGTATAGTTTGACTTCCAC 57.583 36.000 10.63 0.00 44.42 4.02


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

AutoCloner maintained by Alex Coulton.