Multiple sequence alignment - TraesCS5B01G123000

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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 TraesCS5B01G123000 chr5B 100.000 7303 0 0 1 7303 221899460 221906762 0.000000e+00 13487.0
1 TraesCS5B01G123000 chr5B 96.386 83 3 0 3586 3668 82872429 82872347 3.550000e-28 137.0
2 TraesCS5B01G123000 chr5D 97.458 3186 66 7 3666 6840 208510017 208513198 0.000000e+00 5421.0
3 TraesCS5B01G123000 chr5D 96.468 2010 52 14 1592 3586 208508013 208510018 0.000000e+00 3301.0
4 TraesCS5B01G123000 chr5D 95.428 1028 34 6 456 1481 208506490 208507506 0.000000e+00 1626.0
5 TraesCS5B01G123000 chr5D 85.400 500 43 12 8 480 208493050 208493546 6.580000e-135 492.0
6 TraesCS5B01G123000 chr5D 79.915 468 39 22 6879 7291 208513196 208513663 7.170000e-75 292.0
7 TraesCS5B01G123000 chr5A 96.462 3307 71 19 3666 6934 269277305 269280603 0.000000e+00 5417.0
8 TraesCS5B01G123000 chr5A 95.666 3207 98 20 393 3586 269274128 269277306 0.000000e+00 5114.0
9 TraesCS5B01G123000 chr5A 86.634 404 35 7 6916 7303 269280879 269281279 5.240000e-116 429.0
10 TraesCS5B01G123000 chr5A 86.923 260 33 1 8 267 269273493 269273751 2.580000e-74 291.0
11 TraesCS5B01G123000 chr5A 80.435 368 54 3 8 357 623529038 623528671 1.560000e-66 265.0
12 TraesCS5B01G123000 chr4B 75.527 1328 257 54 4460 5749 126334257 126335554 2.270000e-164 590.0
13 TraesCS5B01G123000 chr4B 93.878 98 6 0 3586 3683 519352457 519352554 1.640000e-31 148.0
14 TraesCS5B01G123000 chr4D 75.133 1319 269 45 4460 5749 89430299 89431587 1.380000e-156 564.0
15 TraesCS5B01G123000 chr4D 86.364 198 24 2 167 362 152817861 152817665 5.740000e-51 213.0
16 TraesCS5B01G123000 chr4D 87.500 184 21 1 181 362 152799154 152798971 2.060000e-50 211.0
17 TraesCS5B01G123000 chr4D 83.886 211 31 3 2553 2761 89428694 89428903 1.610000e-46 198.0
18 TraesCS5B01G123000 chr4D 90.000 140 14 0 8 147 152799574 152799435 1.620000e-41 182.0
19 TraesCS5B01G123000 chr4A 74.981 1327 273 46 4452 5749 501970513 501971809 2.300000e-154 556.0
20 TraesCS5B01G123000 chr4A 82.938 211 33 3 2553 2761 501968861 501969070 3.480000e-43 187.0
21 TraesCS5B01G123000 chr4A 96.703 91 3 0 3586 3676 42254276 42254366 1.270000e-32 152.0
22 TraesCS5B01G123000 chr3A 89.888 356 34 2 8 362 635115729 635115375 2.400000e-124 457.0
23 TraesCS5B01G123000 chr1A 85.559 367 41 3 8 362 58410929 58410563 2.490000e-99 374.0
24 TraesCS5B01G123000 chr1A 86.802 197 24 1 168 362 58415634 58415438 1.230000e-52 219.0
25 TraesCS5B01G123000 chr2D 88.325 197 21 1 168 362 81981241 81981437 1.220000e-57 235.0
26 TraesCS5B01G123000 chr2D 87.432 183 20 2 182 362 81994998 81995179 2.670000e-49 207.0
27 TraesCS5B01G123000 chr2D 94.949 99 2 3 3586 3683 113490490 113490394 1.270000e-32 152.0
28 TraesCS5B01G123000 chr3D 86.391 169 23 0 6134 6302 547895630 547895462 1.250000e-42 185.0
29 TraesCS5B01G123000 chr3D 78.761 226 30 13 5411 5631 547907954 547907742 1.280000e-27 135.0
30 TraesCS5B01G123000 chr6D 94.898 98 3 2 3586 3682 379808971 379809067 1.270000e-32 152.0
31 TraesCS5B01G123000 chr7A 93.878 98 5 1 3586 3683 558288806 558288710 5.900000e-31 147.0
32 TraesCS5B01G123000 chr3B 93.000 100 5 2 3586 3685 250576013 250575916 2.120000e-30 145.0
33 TraesCS5B01G123000 chr2B 89.286 112 10 2 3569 3679 77775754 77775644 9.880000e-29 139.0
34 TraesCS5B01G123000 chr7B 89.381 113 6 6 3557 3668 697607618 697607725 3.550000e-28 137.0
35 TraesCS5B01G123000 chr1D 94.595 37 0 1 358 394 329502226 329502192 1.000000e-03 56.5


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 TraesCS5B01G123000 chr5B 221899460 221906762 7302 False 13487.00 13487 100.00000 1 7303 1 chr5B.!!$F1 7302
1 TraesCS5B01G123000 chr5D 208506490 208513663 7173 False 2660.00 5421 92.31725 456 7291 4 chr5D.!!$F2 6835
2 TraesCS5B01G123000 chr5A 269273493 269281279 7786 False 2812.75 5417 91.42125 8 7303 4 chr5A.!!$F1 7295
3 TraesCS5B01G123000 chr4B 126334257 126335554 1297 False 590.00 590 75.52700 4460 5749 1 chr4B.!!$F1 1289
4 TraesCS5B01G123000 chr4D 89428694 89431587 2893 False 381.00 564 79.50950 2553 5749 2 chr4D.!!$F1 3196
5 TraesCS5B01G123000 chr4A 501968861 501971809 2948 False 371.50 556 78.95950 2553 5749 2 chr4A.!!$F2 3196

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
456 743 0.392595 GCTACCTGCTTGTGTACCCC 60.393 60.000 0.0 0.0 38.95 4.95 F
1261 1548 0.109086 CGTGTCTCGTGGAGATGCTT 60.109 55.000 0.0 0.0 40.98 3.91 F
2828 3528 1.602851 CAGCCTTATGAGAGCACATGC 59.397 52.381 0.0 0.0 42.49 4.06 F
3594 4459 0.620556 AGCAATCATGTCCCTCCGTT 59.379 50.000 0.0 0.0 0.00 4.44 F
3595 4460 1.017387 GCAATCATGTCCCTCCGTTC 58.983 55.000 0.0 0.0 0.00 3.95 F
4002 4929 1.173913 CTTCAAAACCCGTCCATCCC 58.826 55.000 0.0 0.0 0.00 3.85 F
5787 6760 2.616960 TGTACTCGCTGCCAACTTATG 58.383 47.619 0.0 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1789 0.974010 TTAGGCCAGTACGAGGGTGG 60.974 60.000 5.01 2.02 0.00 4.61 R
2834 3534 1.039856 GCTGCTGGACCCTTGAAAAA 58.960 50.000 0.00 0.00 0.00 1.94 R
3727 4592 0.333993 ATCAGGTTGCCAGAGCCATT 59.666 50.000 0.00 0.00 38.69 3.16 R
5089 6056 2.346847 GCACAAAGATGACAGCTCGTAG 59.653 50.000 0.00 0.00 0.00 3.51 R
5775 6748 5.670485 TGTATCTGGTACATAAGTTGGCAG 58.330 41.667 0.00 0.00 38.37 4.85 R
5939 6912 5.279406 CCAGCTTATAGTTCAGATCCTCAGG 60.279 48.000 0.00 0.00 0.00 3.86 R
6932 8233 0.464916 AACCTTCGGACACCAACACC 60.465 55.000 0.00 0.00 0.00 4.16 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 2.363788 ATTGCTTGTACGCGAGAAGA 57.636 45.000 15.93 0.00 29.68 2.87
39 40 4.043435 AGAAGATAGCCTTGGGACACTTTT 59.957 41.667 0.00 0.00 39.29 2.27
41 42 3.074538 AGATAGCCTTGGGACACTTTTGT 59.925 43.478 0.00 0.00 39.29 2.83
83 84 2.679336 TCATCAACTTGCGGACATCATG 59.321 45.455 0.00 0.00 0.00 3.07
85 86 2.989909 TCAACTTGCGGACATCATGAT 58.010 42.857 1.18 1.18 0.00 2.45
90 91 3.758023 ACTTGCGGACATCATGATCAAAA 59.242 39.130 4.86 0.00 0.00 2.44
110 111 4.440839 AAGGCTTCCGACAAATTCATTC 57.559 40.909 0.00 0.00 0.00 2.67
111 112 2.420022 AGGCTTCCGACAAATTCATTCG 59.580 45.455 0.00 0.00 0.00 3.34
115 116 3.740044 TCCGACAAATTCATTCGAAGC 57.260 42.857 3.35 0.00 34.62 3.86
116 117 3.070748 TCCGACAAATTCATTCGAAGCA 58.929 40.909 3.35 0.00 34.62 3.91
140 141 3.017442 TCGATCGAGTCTTGGAATCACT 58.983 45.455 15.15 0.00 0.00 3.41
143 144 3.217599 TCGAGTCTTGGAATCACTTCG 57.782 47.619 0.00 0.00 31.75 3.79
149 150 6.240549 AGTCTTGGAATCACTTCGGATTAT 57.759 37.500 0.00 0.00 37.61 1.28
151 152 5.817816 GTCTTGGAATCACTTCGGATTATGT 59.182 40.000 0.00 0.00 37.61 2.29
152 153 6.018669 GTCTTGGAATCACTTCGGATTATGTC 60.019 42.308 0.00 0.00 37.61 3.06
154 155 5.601662 TGGAATCACTTCGGATTATGTCTC 58.398 41.667 0.00 0.00 37.61 3.36
157 158 4.288670 TCACTTCGGATTATGTCTCGAC 57.711 45.455 0.00 0.00 32.04 4.20
159 160 5.121105 TCACTTCGGATTATGTCTCGACTA 58.879 41.667 0.00 0.00 32.04 2.59
161 162 4.025061 ACTTCGGATTATGTCTCGACTACG 60.025 45.833 0.00 0.00 41.26 3.51
203 204 7.876936 CAGCATGCATTAGGGATATTCTTAT 57.123 36.000 21.98 0.00 0.00 1.73
231 232 9.339850 GTAATCTTTTCCCTTCCTATCTAAACC 57.660 37.037 0.00 0.00 0.00 3.27
235 236 4.637288 TCCCTTCCTATCTAAACCTCCA 57.363 45.455 0.00 0.00 0.00 3.86
244 245 6.954684 TCCTATCTAAACCTCCACATCTATCC 59.045 42.308 0.00 0.00 0.00 2.59
252 253 4.410555 ACCTCCACATCTATCCTTTCCTTC 59.589 45.833 0.00 0.00 0.00 3.46
267 268 7.189794 TCCTTTCCTTCTCAACTAGGATTAGA 58.810 38.462 0.00 0.00 40.15 2.10
268 269 7.846823 TCCTTTCCTTCTCAACTAGGATTAGAT 59.153 37.037 0.00 0.00 40.15 1.98
269 270 8.147704 CCTTTCCTTCTCAACTAGGATTAGATC 58.852 40.741 0.00 0.00 40.15 2.75
270 271 8.846423 TTTCCTTCTCAACTAGGATTAGATCT 57.154 34.615 0.00 0.00 40.15 2.75
271 272 8.846423 TTCCTTCTCAACTAGGATTAGATCTT 57.154 34.615 0.00 0.00 40.15 2.40
272 273 8.243961 TCCTTCTCAACTAGGATTAGATCTTG 57.756 38.462 0.00 0.00 35.66 3.02
273 274 7.288852 TCCTTCTCAACTAGGATTAGATCTTGG 59.711 40.741 0.00 0.00 35.66 3.61
274 275 7.288852 CCTTCTCAACTAGGATTAGATCTTGGA 59.711 40.741 0.00 0.00 33.13 3.53
275 276 7.831691 TCTCAACTAGGATTAGATCTTGGAG 57.168 40.000 0.00 0.00 0.00 3.86
276 277 6.780031 TCTCAACTAGGATTAGATCTTGGAGG 59.220 42.308 0.00 0.00 0.00 4.30
277 278 6.683537 TCAACTAGGATTAGATCTTGGAGGA 58.316 40.000 0.00 0.00 0.00 3.71
278 279 6.551601 TCAACTAGGATTAGATCTTGGAGGAC 59.448 42.308 0.00 0.00 0.00 3.85
279 280 6.031964 ACTAGGATTAGATCTTGGAGGACA 57.968 41.667 0.00 0.00 0.00 4.02
280 281 6.444704 ACTAGGATTAGATCTTGGAGGACAA 58.555 40.000 0.00 0.00 37.55 3.18
288 289 3.882131 TTGGAGGACAAGCATAGGC 57.118 52.632 0.00 0.00 41.61 3.93
301 302 2.723273 GCATAGGCTGGTTTTGTAGGT 58.277 47.619 0.00 0.00 36.96 3.08
308 309 2.817258 GCTGGTTTTGTAGGTGTGCATA 59.183 45.455 0.00 0.00 0.00 3.14
309 310 3.365969 GCTGGTTTTGTAGGTGTGCATAC 60.366 47.826 4.79 4.79 32.98 2.39
336 598 0.754472 CTTTGGGCCCTAATGCATGG 59.246 55.000 25.70 4.69 0.00 3.66
361 623 7.017254 GGGATTGATATTCTCCCAAACCTACTA 59.983 40.741 11.43 0.00 46.70 1.82
363 625 6.401047 TGATATTCTCCCAAACCTACTACG 57.599 41.667 0.00 0.00 0.00 3.51
373 653 7.491682 TCCCAAACCTACTACGATTATGTTAC 58.508 38.462 0.00 0.00 0.00 2.50
376 656 7.650903 CCAAACCTACTACGATTATGTTACTCC 59.349 40.741 0.00 0.00 0.00 3.85
384 664 6.971726 ACGATTATGTTACTCCCACTATGA 57.028 37.500 0.00 0.00 0.00 2.15
388 668 9.574458 CGATTATGTTACTCCCACTATGAATAG 57.426 37.037 0.00 0.00 36.46 1.73
391 671 6.726490 TGTTACTCCCACTATGAATAGTCC 57.274 41.667 0.00 0.00 41.44 3.85
392 672 5.301045 TGTTACTCCCACTATGAATAGTCCG 59.699 44.000 0.00 0.00 41.44 4.79
393 673 4.180377 ACTCCCACTATGAATAGTCCGA 57.820 45.455 0.00 0.00 41.44 4.55
395 675 4.960469 ACTCCCACTATGAATAGTCCGAAA 59.040 41.667 0.00 0.00 41.44 3.46
435 722 4.077184 CCGCCAGCCCTAACGACA 62.077 66.667 0.00 0.00 0.00 4.35
456 743 0.392595 GCTACCTGCTTGTGTACCCC 60.393 60.000 0.00 0.00 38.95 4.95
620 907 1.691823 CCTTCCCACCTTTCTCCCC 59.308 63.158 0.00 0.00 0.00 4.81
621 908 1.691823 CTTCCCACCTTTCTCCCCC 59.308 63.158 0.00 0.00 0.00 5.40
801 1088 2.043980 CCGCCGCCATTAACCAACT 61.044 57.895 0.00 0.00 0.00 3.16
841 1128 1.009829 CGATCTGCCAACTAGCCAAC 58.990 55.000 0.00 0.00 0.00 3.77
844 1131 1.678970 CTGCCAACTAGCCAACCCC 60.679 63.158 0.00 0.00 0.00 4.95
919 1206 1.227674 CTTGCATCCTACTCCCGCC 60.228 63.158 0.00 0.00 0.00 6.13
926 1213 4.835891 CTACTCCCGCCGGGTCCT 62.836 72.222 23.92 8.15 44.74 3.85
928 1215 2.710237 CTACTCCCGCCGGGTCCTAT 62.710 65.000 23.92 6.84 44.74 2.57
1237 1524 2.024176 TCTCTTCCAGCAAGGGTACA 57.976 50.000 0.00 0.00 33.68 2.90
1238 1525 2.551270 TCTCTTCCAGCAAGGGTACAT 58.449 47.619 0.00 0.00 33.68 2.29
1261 1548 0.109086 CGTGTCTCGTGGAGATGCTT 60.109 55.000 0.00 0.00 40.98 3.91
1271 1558 2.819608 GTGGAGATGCTTGCTTTTGGTA 59.180 45.455 0.00 0.00 0.00 3.25
1280 1567 7.716560 AGATGCTTGCTTTTGGTATTTTCTTTT 59.283 29.630 0.00 0.00 0.00 2.27
1287 1574 4.857509 TTGGTATTTTCTTTTCCGTGGG 57.142 40.909 0.00 0.00 0.00 4.61
1291 1578 3.726291 ATTTTCTTTTCCGTGGGTGTG 57.274 42.857 0.00 0.00 0.00 3.82
1350 1637 5.011738 TCTGACTACTAAAGTTCCAAGTGGG 59.988 44.000 0.00 0.00 39.07 4.61
1358 1645 3.382083 AGTTCCAAGTGGGTTGAGTTT 57.618 42.857 0.00 0.00 38.60 2.66
1436 1724 6.538945 ACAAACTTAGTCAATGGTTTTGGT 57.461 33.333 0.00 0.00 30.78 3.67
1500 1789 3.963383 TTTTGCGAGTCAGACCTTTTC 57.037 42.857 0.00 0.00 0.00 2.29
1531 1820 4.373156 ACTGGCCTAATTCTGAGTTTGT 57.627 40.909 3.32 0.00 0.00 2.83
1556 1845 9.482627 GTCCATACACATTTTTGTCCATTTTTA 57.517 29.630 0.00 0.00 0.00 1.52
1571 1860 1.748950 TTTTATGCTGCGAGATGGCA 58.251 45.000 0.00 0.00 41.45 4.92
1620 2305 6.713276 TGGATCTCCGAACCTTTTGTATTTA 58.287 36.000 0.00 0.00 39.43 1.40
1645 2330 4.347000 TGTTAACTAGGGAGTGCTGTTCTT 59.653 41.667 7.22 0.00 35.52 2.52
1797 2482 3.118592 CCATCTCTTCTAACCAGGGACAC 60.119 52.174 0.00 0.00 0.00 3.67
1799 2484 4.669866 TCTCTTCTAACCAGGGACACTA 57.330 45.455 0.00 0.00 0.00 2.74
1832 2517 4.252073 CTCTGCTTCAGTGCTTCTGTTAT 58.748 43.478 8.75 0.00 43.97 1.89
1892 2579 6.203723 TGTTTAAATTGGTACCTTTGCAATGC 59.796 34.615 14.36 0.00 0.00 3.56
1893 2580 4.348863 AAATTGGTACCTTTGCAATGCA 57.651 36.364 14.36 2.72 36.47 3.96
1917 2604 7.466050 GCATGTAGTGAGCTAAAAGTTCATACC 60.466 40.741 0.00 0.00 37.76 2.73
1982 2669 6.115448 AGAACCATGCTACTGTTTTCTAGT 57.885 37.500 0.00 0.00 0.00 2.57
2027 2717 9.088512 GTCTACCTATGTAAATGAGACTTTGTG 57.911 37.037 0.00 0.00 0.00 3.33
2086 2776 5.001232 TCAACCTACCTTGTTGCAATCTAC 58.999 41.667 0.59 0.00 42.17 2.59
2087 2777 4.910458 ACCTACCTTGTTGCAATCTACT 57.090 40.909 0.59 0.00 0.00 2.57
2088 2778 5.242795 ACCTACCTTGTTGCAATCTACTT 57.757 39.130 0.59 0.00 0.00 2.24
2177 2867 9.921637 TCAATGTCGTGCACTATAATTATCATA 57.078 29.630 16.19 0.00 0.00 2.15
2179 2869 7.812309 TGTCGTGCACTATAATTATCATAGC 57.188 36.000 16.19 3.57 30.45 2.97
2180 2870 7.375053 TGTCGTGCACTATAATTATCATAGCA 58.625 34.615 16.19 6.04 30.45 3.49
2231 2923 5.305644 GGAGGCTTGTATTCCTTCTAGATGA 59.694 44.000 7.19 0.00 31.71 2.92
2232 2924 6.183361 GGAGGCTTGTATTCCTTCTAGATGAA 60.183 42.308 7.19 7.34 31.71 2.57
2233 2925 6.587273 AGGCTTGTATTCCTTCTAGATGAAC 58.413 40.000 7.19 0.00 0.00 3.18
2234 2926 6.385467 AGGCTTGTATTCCTTCTAGATGAACT 59.615 38.462 7.19 1.63 0.00 3.01
2425 3124 8.183104 TGGTGAAAATGTTGTACCAAATATCA 57.817 30.769 0.00 0.00 38.39 2.15
2426 3125 8.642432 TGGTGAAAATGTTGTACCAAATATCAA 58.358 29.630 0.00 0.00 38.39 2.57
2430 3129 7.754069 AAATGTTGTACCAAATATCAATGCG 57.246 32.000 0.00 0.00 0.00 4.73
2828 3528 1.602851 CAGCCTTATGAGAGCACATGC 59.397 52.381 0.00 0.00 42.49 4.06
2902 3602 4.534647 AATATATGCCCCAACACTGGAA 57.465 40.909 0.00 0.00 46.92 3.53
3150 3885 2.616330 ATTCCACGCGGTGCTTGTG 61.616 57.895 12.47 0.00 31.34 3.33
3168 3903 6.707608 TGCTTGTGGATCTGACATTACATATC 59.292 38.462 0.00 0.00 0.00 1.63
3309 4170 6.793492 AACTAGATGCTCTGAACAACTTTC 57.207 37.500 0.00 0.00 0.00 2.62
3413 4274 6.968263 TCTATTCCTGATCTACCACTTGAG 57.032 41.667 0.00 0.00 0.00 3.02
3417 4278 7.921041 ATTCCTGATCTACCACTTGAGATTA 57.079 36.000 0.00 0.00 32.47 1.75
3423 4284 8.367660 TGATCTACCACTTGAGATTAAACTCT 57.632 34.615 13.24 0.00 37.73 3.24
3590 4455 3.911661 GCATTAGCAATCATGTCCCTC 57.088 47.619 0.00 0.00 41.58 4.30
3591 4456 2.555757 GCATTAGCAATCATGTCCCTCC 59.444 50.000 0.00 0.00 41.58 4.30
3592 4457 2.620251 TTAGCAATCATGTCCCTCCG 57.380 50.000 0.00 0.00 0.00 4.63
3593 4458 1.496060 TAGCAATCATGTCCCTCCGT 58.504 50.000 0.00 0.00 0.00 4.69
3594 4459 0.620556 AGCAATCATGTCCCTCCGTT 59.379 50.000 0.00 0.00 0.00 4.44
3595 4460 1.017387 GCAATCATGTCCCTCCGTTC 58.983 55.000 0.00 0.00 0.00 3.95
3596 4461 1.668419 CAATCATGTCCCTCCGTTCC 58.332 55.000 0.00 0.00 0.00 3.62
3597 4462 1.210478 CAATCATGTCCCTCCGTTCCT 59.790 52.381 0.00 0.00 0.00 3.36
3598 4463 2.434336 CAATCATGTCCCTCCGTTCCTA 59.566 50.000 0.00 0.00 0.00 2.94
3599 4464 2.241281 TCATGTCCCTCCGTTCCTAA 57.759 50.000 0.00 0.00 0.00 2.69
3600 4465 2.542550 TCATGTCCCTCCGTTCCTAAA 58.457 47.619 0.00 0.00 0.00 1.85
3601 4466 3.112263 TCATGTCCCTCCGTTCCTAAAT 58.888 45.455 0.00 0.00 0.00 1.40
3602 4467 4.291792 TCATGTCCCTCCGTTCCTAAATA 58.708 43.478 0.00 0.00 0.00 1.40
3603 4468 4.344102 TCATGTCCCTCCGTTCCTAAATAG 59.656 45.833 0.00 0.00 0.00 1.73
3604 4469 3.985127 TGTCCCTCCGTTCCTAAATAGA 58.015 45.455 0.00 0.00 0.00 1.98
3605 4470 4.553678 TGTCCCTCCGTTCCTAAATAGAT 58.446 43.478 0.00 0.00 0.00 1.98
3606 4471 4.344102 TGTCCCTCCGTTCCTAAATAGATG 59.656 45.833 0.00 0.00 0.00 2.90
3607 4472 4.587684 GTCCCTCCGTTCCTAAATAGATGA 59.412 45.833 0.00 0.00 0.00 2.92
3608 4473 4.587684 TCCCTCCGTTCCTAAATAGATGAC 59.412 45.833 0.00 0.00 0.00 3.06
3609 4474 4.589374 CCCTCCGTTCCTAAATAGATGACT 59.411 45.833 0.00 0.00 0.00 3.41
3610 4475 5.279056 CCCTCCGTTCCTAAATAGATGACTC 60.279 48.000 0.00 0.00 0.00 3.36
3611 4476 5.302059 CCTCCGTTCCTAAATAGATGACTCA 59.698 44.000 0.00 0.00 0.00 3.41
3612 4477 6.183360 CCTCCGTTCCTAAATAGATGACTCAA 60.183 42.308 0.00 0.00 0.00 3.02
3613 4478 6.570692 TCCGTTCCTAAATAGATGACTCAAC 58.429 40.000 0.00 0.00 0.00 3.18
3614 4479 6.380274 TCCGTTCCTAAATAGATGACTCAACT 59.620 38.462 0.00 0.00 0.00 3.16
3615 4480 7.042335 CCGTTCCTAAATAGATGACTCAACTT 58.958 38.462 0.00 0.00 0.00 2.66
3616 4481 7.549488 CCGTTCCTAAATAGATGACTCAACTTT 59.451 37.037 0.00 0.00 0.00 2.66
3617 4482 8.383619 CGTTCCTAAATAGATGACTCAACTTTG 58.616 37.037 0.00 0.00 0.00 2.77
3618 4483 9.220767 GTTCCTAAATAGATGACTCAACTTTGT 57.779 33.333 0.00 0.00 0.00 2.83
3620 4485 9.871238 TCCTAAATAGATGACTCAACTTTGTAC 57.129 33.333 0.00 0.00 0.00 2.90
3621 4486 9.877178 CCTAAATAGATGACTCAACTTTGTACT 57.123 33.333 0.00 0.00 0.00 2.73
3644 4509 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
3645 4510 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
3646 4511 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
3647 4512 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
3648 4513 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
3649 4514 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
3650 4515 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
3651 4516 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
3652 4517 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
3653 4518 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
3654 4519 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
3655 4520 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
3656 4521 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
3657 4522 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
3658 4523 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
3659 4524 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
3660 4525 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
3661 4526 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
3662 4527 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
3663 4528 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3664 4529 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3727 4592 9.895138 GTAGTCCAGTATAAGTTTCCCAATTAA 57.105 33.333 0.00 0.00 0.00 1.40
3982 4909 7.819900 GTCTTGGTAAATATGAGTCACTTCAGT 59.180 37.037 0.00 0.00 0.00 3.41
3993 4920 4.200092 AGTCACTTCAGTCTTCAAAACCC 58.800 43.478 0.00 0.00 0.00 4.11
4002 4929 1.173913 CTTCAAAACCCGTCCATCCC 58.826 55.000 0.00 0.00 0.00 3.85
4134 5061 4.104383 ATGTGTTCATGATATGGGGACC 57.896 45.455 0.00 0.00 40.46 4.46
4212 5147 2.930826 ACAGAGACCCAACGATGTTT 57.069 45.000 0.00 0.00 0.00 2.83
4423 5359 6.800408 GGTTTCTCAGTTAACCTATTTTTCGC 59.200 38.462 0.88 0.00 40.50 4.70
4457 5393 4.633565 TGCCCAACATTGTTTTCTTGTTTC 59.366 37.500 0.00 0.00 31.48 2.78
5157 6124 4.222124 TCTGCTTTAATTCCCTGGAGTC 57.778 45.455 0.00 0.00 0.00 3.36
5775 6748 3.001736 GCTTCATTCTGGAATGTACTCGC 59.998 47.826 18.86 12.74 46.15 5.03
5787 6760 2.616960 TGTACTCGCTGCCAACTTATG 58.383 47.619 0.00 0.00 0.00 1.90
5914 6887 4.023193 GTCACCACAGGTTAGTCCATTTTG 60.023 45.833 0.00 0.00 39.02 2.44
5939 6912 6.635641 GTCCTTTTGAACGACTTCAATTTACC 59.364 38.462 2.44 0.00 44.24 2.85
5940 6913 5.918576 CCTTTTGAACGACTTCAATTTACCC 59.081 40.000 2.44 0.00 44.24 3.69
6218 7191 2.009774 CGGAACCTGAACACCATGATC 58.990 52.381 0.00 0.00 0.00 2.92
6359 7337 3.494048 GCATGATGTTCCAAACCAAACCA 60.494 43.478 0.00 0.00 0.00 3.67
6360 7338 4.701765 CATGATGTTCCAAACCAAACCAA 58.298 39.130 0.00 0.00 0.00 3.67
6361 7339 4.826274 TGATGTTCCAAACCAAACCAAA 57.174 36.364 0.00 0.00 0.00 3.28
6362 7340 4.508662 TGATGTTCCAAACCAAACCAAAC 58.491 39.130 0.00 0.00 0.00 2.93
6363 7341 3.336138 TGTTCCAAACCAAACCAAACC 57.664 42.857 0.00 0.00 0.00 3.27
6364 7342 2.637872 TGTTCCAAACCAAACCAAACCA 59.362 40.909 0.00 0.00 0.00 3.67
6651 7642 8.524870 AAGCATGACATGTGTTTTATTTTCTC 57.475 30.769 16.62 0.00 0.00 2.87
6713 7704 4.281435 TCTTGCCATGTCATGTTGTTGATT 59.719 37.500 11.84 0.00 0.00 2.57
6773 7764 4.881273 AGTGTGCAGTCAAACTTGTATGAA 59.119 37.500 0.00 0.00 37.49 2.57
6774 7765 5.008019 AGTGTGCAGTCAAACTTGTATGAAG 59.992 40.000 0.00 0.00 37.49 3.02
6880 7881 8.999431 TCTTATTTTCAGTGATCTAAACGCTTT 58.001 29.630 0.00 0.00 0.00 3.51
6882 7883 9.959749 TTATTTTCAGTGATCTAAACGCTTTTT 57.040 25.926 0.00 0.00 0.00 1.94
6909 7918 6.894682 AGAGGGAGTATTTCTTTTCCATCTC 58.105 40.000 1.09 0.00 44.88 2.75
6912 7921 7.797062 AGGGAGTATTTCTTTTCCATCTCTAC 58.203 38.462 0.00 0.00 0.00 2.59
6932 8233 8.740906 TCTCTACCGAATAGCTAATGATAAAGG 58.259 37.037 0.00 0.00 0.00 3.11
7122 8438 8.761575 TTTTCTTTCAAATGTGAATGATAGGC 57.238 30.769 13.43 0.00 43.56 3.93
7125 8441 8.125978 TCTTTCAAATGTGAATGATAGGCTTT 57.874 30.769 9.58 0.00 43.29 3.51
7134 8450 6.038161 TGTGAATGATAGGCTTTTATTCCACG 59.962 38.462 16.05 0.00 0.00 4.94
7137 8453 7.771361 TGAATGATAGGCTTTTATTCCACGTAA 59.229 33.333 16.05 0.00 0.00 3.18
7144 8491 7.562135 AGGCTTTTATTCCACGTAAGAATAGA 58.438 34.615 15.73 11.30 37.47 1.98
7156 8503 7.171678 CCACGTAAGAATAGAAATCCATTCCTC 59.828 40.741 0.00 0.00 38.92 3.71
7172 8519 5.163478 CCATTCCTCCAATCAAATGACTTCC 60.163 44.000 0.00 0.00 32.14 3.46
7228 8600 6.060788 CAGAATTCCTATAAGGCTTGAAGCT 58.939 40.000 17.59 0.12 41.99 3.74
7271 8643 6.064717 AGATTATAAGGCCTCATTTGGTGTC 58.935 40.000 5.23 0.00 0.00 3.67
7272 8644 2.507407 TAAGGCCTCATTTGGTGTCC 57.493 50.000 5.23 0.00 0.00 4.02
7291 8663 3.006644 GTCCGTGTTTTTCTACTCCCTCT 59.993 47.826 0.00 0.00 0.00 3.69
7294 8666 3.988517 CGTGTTTTTCTACTCCCTCTGTC 59.011 47.826 0.00 0.00 0.00 3.51
7296 8668 3.971305 TGTTTTTCTACTCCCTCTGTCCA 59.029 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.666508 TCTTCTCGCGTACAAGCAATTC 59.333 45.455 5.77 0.00 36.85 2.17
1 2 2.683968 TCTTCTCGCGTACAAGCAATT 58.316 42.857 5.77 0.00 36.85 2.32
2 3 2.363788 TCTTCTCGCGTACAAGCAAT 57.636 45.000 5.77 0.00 36.85 3.56
4 5 2.794981 GCTATCTTCTCGCGTACAAGCA 60.795 50.000 5.77 0.00 36.85 3.91
6 7 2.033550 AGGCTATCTTCTCGCGTACAAG 59.966 50.000 5.77 7.05 0.00 3.16
14 15 1.757118 TGTCCCAAGGCTATCTTCTCG 59.243 52.381 0.00 0.00 32.41 4.04
21 22 3.157087 CACAAAAGTGTCCCAAGGCTAT 58.843 45.455 0.00 0.00 35.07 2.97
39 40 1.600013 CGTCGAACCATGGAAAACACA 59.400 47.619 21.47 0.00 0.00 3.72
41 42 1.231221 CCGTCGAACCATGGAAAACA 58.769 50.000 21.47 0.00 0.00 2.83
45 46 1.079405 GAGCCGTCGAACCATGGAA 60.079 57.895 21.47 0.00 0.00 3.53
50 51 0.669318 GTTGATGAGCCGTCGAACCA 60.669 55.000 0.00 0.00 0.00 3.67
52 53 1.126846 CAAGTTGATGAGCCGTCGAAC 59.873 52.381 0.00 0.00 0.00 3.95
83 84 3.915437 TTTGTCGGAAGCCTTTTGATC 57.085 42.857 0.00 0.00 0.00 2.92
85 86 3.634448 TGAATTTGTCGGAAGCCTTTTGA 59.366 39.130 0.00 0.00 0.00 2.69
90 91 2.420022 CGAATGAATTTGTCGGAAGCCT 59.580 45.455 0.00 0.00 0.00 4.58
111 112 3.000724 CCAAGACTCGATCGAAATGCTTC 59.999 47.826 19.92 8.51 0.00 3.86
115 116 4.805719 TGATTCCAAGACTCGATCGAAATG 59.194 41.667 19.92 14.22 0.00 2.32
116 117 4.806247 GTGATTCCAAGACTCGATCGAAAT 59.194 41.667 19.92 13.42 0.00 2.17
123 124 2.094700 CCGAAGTGATTCCAAGACTCGA 60.095 50.000 0.00 0.00 0.00 4.04
140 141 3.249320 CCGTAGTCGAGACATAATCCGAA 59.751 47.826 5.99 0.00 39.71 4.30
143 144 2.228343 CCCCGTAGTCGAGACATAATCC 59.772 54.545 5.99 0.00 39.71 3.01
166 167 2.974165 GCATGCTGCGTATTCTTACAC 58.026 47.619 11.37 0.00 31.71 2.90
179 180 7.876936 ATAAGAATATCCCTAATGCATGCTG 57.123 36.000 20.33 6.43 0.00 4.41
217 218 6.739331 AGATGTGGAGGTTTAGATAGGAAG 57.261 41.667 0.00 0.00 0.00 3.46
225 226 6.100424 AGGAAAGGATAGATGTGGAGGTTTAG 59.900 42.308 0.00 0.00 0.00 1.85
231 232 5.365025 TGAGAAGGAAAGGATAGATGTGGAG 59.635 44.000 0.00 0.00 0.00 3.86
235 236 6.882768 AGTTGAGAAGGAAAGGATAGATGT 57.117 37.500 0.00 0.00 0.00 3.06
244 245 8.923270 AGATCTAATCCTAGTTGAGAAGGAAAG 58.077 37.037 0.00 0.00 44.87 2.62
252 253 6.780031 TCCTCCAAGATCTAATCCTAGTTGAG 59.220 42.308 0.00 0.00 0.00 3.02
270 271 3.882131 GCCTATGCTTGTCCTCCAA 57.118 52.632 0.00 0.00 33.53 3.53
281 282 2.423538 CACCTACAAAACCAGCCTATGC 59.576 50.000 0.00 0.00 37.95 3.14
282 283 3.440173 CACACCTACAAAACCAGCCTATG 59.560 47.826 0.00 0.00 0.00 2.23
283 284 3.686016 CACACCTACAAAACCAGCCTAT 58.314 45.455 0.00 0.00 0.00 2.57
284 285 2.812613 GCACACCTACAAAACCAGCCTA 60.813 50.000 0.00 0.00 0.00 3.93
285 286 1.981256 CACACCTACAAAACCAGCCT 58.019 50.000 0.00 0.00 0.00 4.58
286 287 0.313987 GCACACCTACAAAACCAGCC 59.686 55.000 0.00 0.00 0.00 4.85
287 288 1.028905 TGCACACCTACAAAACCAGC 58.971 50.000 0.00 0.00 0.00 4.85
288 289 3.818210 TGTATGCACACCTACAAAACCAG 59.182 43.478 0.00 0.00 0.00 4.00
289 290 3.821748 TGTATGCACACCTACAAAACCA 58.178 40.909 0.00 0.00 0.00 3.67
336 598 6.842676 AGTAGGTTTGGGAGAATATCAATCC 58.157 40.000 0.00 0.00 33.03 3.01
351 613 7.650903 GGGAGTAACATAATCGTAGTAGGTTTG 59.349 40.741 0.00 0.00 29.15 2.93
361 623 6.971726 TCATAGTGGGAGTAACATAATCGT 57.028 37.500 0.00 0.00 0.00 3.73
373 653 5.531122 TTTCGGACTATTCATAGTGGGAG 57.469 43.478 4.13 0.00 43.27 4.30
376 656 4.209288 CGCTTTTCGGACTATTCATAGTGG 59.791 45.833 4.13 0.00 43.27 4.00
456 743 3.441496 TTTATGGCCGTAACTCTACCG 57.559 47.619 17.25 0.00 0.00 4.02
582 869 3.052186 AGGGGATTTTTAATGGCTGGCTA 60.052 43.478 2.00 0.00 0.00 3.93
624 911 3.151022 GAGGGTGAGAGGAGGGCG 61.151 72.222 0.00 0.00 0.00 6.13
625 912 2.766229 GGAGGGTGAGAGGAGGGC 60.766 72.222 0.00 0.00 0.00 5.19
626 913 1.075600 GAGGAGGGTGAGAGGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
627 914 0.338120 AAGAGGAGGGTGAGAGGAGG 59.662 60.000 0.00 0.00 0.00 4.30
801 1088 2.783510 GGGAAGGAATGATGGGAGGTAA 59.216 50.000 0.00 0.00 0.00 2.85
902 1189 2.908015 GGCGGGAGTAGGATGCAA 59.092 61.111 0.00 0.00 0.00 4.08
926 1213 0.105658 AGCTCTAGGGTTCGGGCATA 60.106 55.000 0.00 0.00 0.00 3.14
928 1215 2.038975 AGCTCTAGGGTTCGGGCA 59.961 61.111 0.00 0.00 0.00 5.36
1130 1417 0.034670 GAAGCAGATGGCCCTCTTGT 60.035 55.000 7.97 0.00 46.50 3.16
1237 1524 1.751032 ATCTCCACGAGACACGGCTAT 60.751 52.381 0.00 0.00 41.76 2.97
1238 1525 0.393944 ATCTCCACGAGACACGGCTA 60.394 55.000 0.00 0.00 41.76 3.93
1261 1548 5.751028 CACGGAAAAGAAAATACCAAAAGCA 59.249 36.000 0.00 0.00 0.00 3.91
1271 1558 3.028130 ACACACCCACGGAAAAGAAAAT 58.972 40.909 0.00 0.00 0.00 1.82
1280 1567 1.210967 AGAAAAGAACACACCCACGGA 59.789 47.619 0.00 0.00 0.00 4.69
1287 1574 6.203808 ACTAAACCCAAGAAAAGAACACAC 57.796 37.500 0.00 0.00 0.00 3.82
1291 1578 7.751047 GTGAAACTAAACCCAAGAAAAGAAC 57.249 36.000 0.00 0.00 0.00 3.01
1493 1782 1.346722 CAGTACGAGGGTGGAAAAGGT 59.653 52.381 0.00 0.00 0.00 3.50
1500 1789 0.974010 TTAGGCCAGTACGAGGGTGG 60.974 60.000 5.01 2.02 0.00 4.61
1620 2305 4.910458 ACAGCACTCCCTAGTTAACATT 57.090 40.909 8.61 0.00 31.97 2.71
1645 2330 4.200874 ACCCAATACTCGTTTCACAACAA 58.799 39.130 0.00 0.00 32.54 2.83
1797 2482 3.252400 GAAGCAGAGGATCGCATCATAG 58.748 50.000 0.00 0.00 42.67 2.23
1799 2484 1.415289 TGAAGCAGAGGATCGCATCAT 59.585 47.619 0.00 0.00 42.67 2.45
1832 2517 7.287512 TGGAAACATCTTGAAATCATGTGAA 57.712 32.000 0.00 0.00 33.40 3.18
1892 2579 7.549134 TGGTATGAACTTTTAGCTCACTACATG 59.451 37.037 0.00 0.00 0.00 3.21
1893 2580 7.620880 TGGTATGAACTTTTAGCTCACTACAT 58.379 34.615 0.00 0.00 0.00 2.29
1917 2604 9.247126 TGAATATTGACAACAATCAAACAGTTG 57.753 29.630 0.00 0.00 44.34 3.16
1982 2669 7.178628 AGGTAGACTTCATTTTCTGCACTACTA 59.821 37.037 0.00 0.00 0.00 1.82
2027 2717 4.944317 AGCAAGGTAGAGCTTAAAACCATC 59.056 41.667 9.51 0.70 38.01 3.51
2086 2776 9.748708 CTCTTGATGTTATCTAAGAAGGAGAAG 57.251 37.037 0.00 0.00 31.20 2.85
2087 2777 8.700051 CCTCTTGATGTTATCTAAGAAGGAGAA 58.300 37.037 0.00 0.00 31.20 2.87
2088 2778 7.201956 GCCTCTTGATGTTATCTAAGAAGGAGA 60.202 40.741 0.00 0.00 31.20 3.71
2231 2923 8.331730 ACTCACCGCAATTTAATAAGTTAGTT 57.668 30.769 0.00 0.00 0.00 2.24
2232 2924 7.916914 ACTCACCGCAATTTAATAAGTTAGT 57.083 32.000 0.00 0.00 0.00 2.24
2233 2925 9.309516 TCTACTCACCGCAATTTAATAAGTTAG 57.690 33.333 0.00 0.00 0.00 2.34
2234 2926 9.656040 TTCTACTCACCGCAATTTAATAAGTTA 57.344 29.630 0.00 0.00 0.00 2.24
2251 2947 4.757149 AGACAAGGTGCATTTTCTACTCAC 59.243 41.667 0.00 0.00 0.00 3.51
2280 2977 3.838120 TCAGCTTACTGTCATTGTCTCG 58.162 45.455 0.00 0.00 44.77 4.04
2425 3124 2.939103 GTGATTTAGGTGAGAGCGCATT 59.061 45.455 11.47 0.00 0.00 3.56
2426 3125 2.093500 TGTGATTTAGGTGAGAGCGCAT 60.093 45.455 11.47 0.00 0.00 4.73
2430 3129 7.559590 AAACATATGTGATTTAGGTGAGAGC 57.440 36.000 9.63 0.00 0.00 4.09
2479 3178 8.287439 TCTTGGAATCTTAACACTTGTTTTCA 57.713 30.769 0.00 0.00 39.31 2.69
2548 3248 7.693132 TCTATTAGCTAATGATTGGCAAGGAT 58.307 34.615 25.99 6.30 39.92 3.24
2635 3335 6.015095 TGTTATCAGCGTCATCTATTCTCCAT 60.015 38.462 0.00 0.00 0.00 3.41
2743 3443 3.374042 TTTCCAACCTCTTGTTCACCA 57.626 42.857 0.00 0.00 34.00 4.17
2789 3489 7.889589 AGGCTGCAATTAGTTAATTCAAAAC 57.110 32.000 0.50 0.00 33.88 2.43
2834 3534 1.039856 GCTGCTGGACCCTTGAAAAA 58.960 50.000 0.00 0.00 0.00 1.94
3150 3885 6.807230 GGTACACGATATGTAATGTCAGATCC 59.193 42.308 0.00 0.00 45.51 3.36
3168 3903 1.148310 CACCAGCTTTCAGGTACACG 58.852 55.000 0.00 0.00 36.07 4.49
3254 3990 2.038952 TCACACAAGTTGCATAGGAGCT 59.961 45.455 1.81 0.00 34.99 4.09
3309 4170 4.055360 TCTATGGTTGTGTGACTTTGTCG 58.945 43.478 0.00 0.00 34.95 4.35
3413 4274 6.903883 TCCGCTCATTTGTAGAGTTTAATC 57.096 37.500 0.00 0.00 35.55 1.75
3417 4278 6.575162 AAATTCCGCTCATTTGTAGAGTTT 57.425 33.333 0.00 0.00 35.55 2.66
3455 4316 1.152830 ACCGCTTGGGAATTGTGGT 59.847 52.632 0.00 0.00 39.45 4.16
3498 4359 7.440523 AAGAGCTGAAAGTAAATCAACGATT 57.559 32.000 0.00 0.00 35.30 3.34
3544 4405 6.013032 AGCATAAACTACAGCCTGATGGATAT 60.013 38.462 0.00 0.00 34.57 1.63
3549 4410 3.003068 GCAGCATAAACTACAGCCTGATG 59.997 47.826 0.00 0.00 0.00 3.07
3551 4412 2.027285 TGCAGCATAAACTACAGCCTGA 60.027 45.455 0.00 0.00 0.00 3.86
3552 4413 2.358957 TGCAGCATAAACTACAGCCTG 58.641 47.619 0.00 0.00 0.00 4.85
3553 4414 2.787473 TGCAGCATAAACTACAGCCT 57.213 45.000 0.00 0.00 0.00 4.58
3584 4449 4.587684 TCATCTATTTAGGAACGGAGGGAC 59.412 45.833 0.00 0.00 0.00 4.46
3585 4450 4.587684 GTCATCTATTTAGGAACGGAGGGA 59.412 45.833 0.00 0.00 0.00 4.20
3586 4451 4.589374 AGTCATCTATTTAGGAACGGAGGG 59.411 45.833 0.00 0.00 0.00 4.30
3587 4452 5.302059 TGAGTCATCTATTTAGGAACGGAGG 59.698 44.000 0.00 0.00 0.00 4.30
3588 4453 6.392625 TGAGTCATCTATTTAGGAACGGAG 57.607 41.667 0.00 0.00 0.00 4.63
3589 4454 6.380274 AGTTGAGTCATCTATTTAGGAACGGA 59.620 38.462 1.70 0.00 0.00 4.69
3590 4455 6.574350 AGTTGAGTCATCTATTTAGGAACGG 58.426 40.000 1.70 0.00 0.00 4.44
3591 4456 8.383619 CAAAGTTGAGTCATCTATTTAGGAACG 58.616 37.037 4.14 0.00 0.00 3.95
3592 4457 9.220767 ACAAAGTTGAGTCATCTATTTAGGAAC 57.779 33.333 4.14 0.00 0.00 3.62
3594 4459 9.871238 GTACAAAGTTGAGTCATCTATTTAGGA 57.129 33.333 4.14 0.00 0.00 2.94
3595 4460 9.877178 AGTACAAAGTTGAGTCATCTATTTAGG 57.123 33.333 4.14 0.00 0.00 2.69
3618 4483 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
3619 4484 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
3620 4485 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
3621 4486 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
3623 4488 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
3624 4489 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
3625 4490 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
3626 4491 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
3627 4492 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
3628 4493 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
3629 4494 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
3630 4495 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
3631 4496 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
3632 4497 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
3633 4498 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
3634 4499 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
3635 4500 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
3636 4501 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
3637 4502 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
3638 4503 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
3639 4504 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
3640 4505 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
3641 4506 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3642 4507 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3643 4508 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3644 4509 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3645 4510 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3646 4511 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3647 4512 5.502089 TTTACTCCCTCCGTTCCAAAATA 57.498 39.130 0.00 0.00 0.00 1.40
3648 4513 4.376225 TTTACTCCCTCCGTTCCAAAAT 57.624 40.909 0.00 0.00 0.00 1.82
3649 4514 3.860968 TTTACTCCCTCCGTTCCAAAA 57.139 42.857 0.00 0.00 0.00 2.44
3650 4515 3.328343 TCATTTACTCCCTCCGTTCCAAA 59.672 43.478 0.00 0.00 0.00 3.28
3651 4516 2.907696 TCATTTACTCCCTCCGTTCCAA 59.092 45.455 0.00 0.00 0.00 3.53
3652 4517 2.235402 GTCATTTACTCCCTCCGTTCCA 59.765 50.000 0.00 0.00 0.00 3.53
3653 4518 2.235402 TGTCATTTACTCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
3654 4519 3.604875 TGTCATTTACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
3655 4520 3.517901 TGATGTCATTTACTCCCTCCGTT 59.482 43.478 0.00 0.00 0.00 4.44
3656 4521 3.104512 TGATGTCATTTACTCCCTCCGT 58.895 45.455 0.00 0.00 0.00 4.69
3657 4522 3.819564 TGATGTCATTTACTCCCTCCG 57.180 47.619 0.00 0.00 0.00 4.63
3658 4523 5.104259 AGTTGATGTCATTTACTCCCTCC 57.896 43.478 0.00 0.00 0.00 4.30
3659 4524 6.881602 AGAAAGTTGATGTCATTTACTCCCTC 59.118 38.462 2.38 1.62 0.00 4.30
3660 4525 6.784031 AGAAAGTTGATGTCATTTACTCCCT 58.216 36.000 2.38 1.37 0.00 4.20
3661 4526 8.738645 ATAGAAAGTTGATGTCATTTACTCCC 57.261 34.615 2.38 0.00 0.00 4.30
3662 4527 8.543774 CGATAGAAAGTTGATGTCATTTACTCC 58.456 37.037 2.38 0.00 39.76 3.85
3663 4528 8.058915 GCGATAGAAAGTTGATGTCATTTACTC 58.941 37.037 0.00 0.00 39.76 2.59
3664 4529 7.766278 AGCGATAGAAAGTTGATGTCATTTACT 59.234 33.333 0.00 0.00 39.76 2.24
3727 4592 0.333993 ATCAGGTTGCCAGAGCCATT 59.666 50.000 0.00 0.00 38.69 3.16
3728 4593 0.395311 CATCAGGTTGCCAGAGCCAT 60.395 55.000 0.00 0.00 38.69 4.40
3771 4636 9.778993 CATGTTTACAAGGAGAAAGTAATCATG 57.221 33.333 15.36 15.36 42.80 3.07
3982 4909 1.271707 GGGATGGACGGGTTTTGAAGA 60.272 52.381 0.00 0.00 0.00 2.87
3993 4920 1.037493 TACCAGAATCGGGATGGACG 58.963 55.000 6.40 0.00 37.54 4.79
4002 4929 4.760204 ACAGGGAAAACTTTACCAGAATCG 59.240 41.667 6.22 0.00 43.99 3.34
4143 5070 3.804036 CAAGTCCAGTACACCAACTCAA 58.196 45.455 0.00 0.00 0.00 3.02
4144 5071 2.484770 GCAAGTCCAGTACACCAACTCA 60.485 50.000 0.00 0.00 0.00 3.41
4153 5088 3.334583 TCCAATCAGCAAGTCCAGTAC 57.665 47.619 0.00 0.00 0.00 2.73
4212 5147 3.719268 ACCATCACTAGTGCCATCAAA 57.281 42.857 18.45 0.00 0.00 2.69
4423 5359 5.909477 ACAATGTTGGGCAAATGATATCTG 58.091 37.500 3.98 0.00 0.00 2.90
4457 5393 7.202016 TCTTAGTTTTATTTGTCCTGCAGTG 57.798 36.000 13.81 4.33 0.00 3.66
4917 5884 5.404946 TCTATAAGAACAACAGGTACACGC 58.595 41.667 0.00 0.00 0.00 5.34
5089 6056 2.346847 GCACAAAGATGACAGCTCGTAG 59.653 50.000 0.00 0.00 0.00 3.51
5775 6748 5.670485 TGTATCTGGTACATAAGTTGGCAG 58.330 41.667 0.00 0.00 38.37 4.85
5787 6760 9.614792 ATTCTTACTGGAAAATGTATCTGGTAC 57.385 33.333 0.00 0.00 0.00 3.34
5832 6805 5.479716 TTCGACTGAAGGAAGAAAACAAC 57.520 39.130 0.00 0.00 0.00 3.32
5939 6912 5.279406 CCAGCTTATAGTTCAGATCCTCAGG 60.279 48.000 0.00 0.00 0.00 3.86
5940 6913 5.279406 CCCAGCTTATAGTTCAGATCCTCAG 60.279 48.000 0.00 0.00 0.00 3.35
6363 7341 4.393062 CAGTAGTGCAGTATCCAGGTTTTG 59.607 45.833 4.19 0.00 0.00 2.44
6364 7342 4.286032 TCAGTAGTGCAGTATCCAGGTTTT 59.714 41.667 4.19 0.00 0.00 2.43
6651 7642 6.519382 TCTGCCTGATGTAGTGATCATTAAG 58.481 40.000 0.00 0.00 31.88 1.85
6713 7704 8.298854 CAATGAATCCTCAACATTCAGTTACAA 58.701 33.333 1.93 0.00 42.23 2.41
6880 7881 9.822727 ATGGAAAAGAAATACTCCCTCTAAAAA 57.177 29.630 0.00 0.00 0.00 1.94
6882 7883 8.836735 AGATGGAAAAGAAATACTCCCTCTAAA 58.163 33.333 0.00 0.00 32.94 1.85
6883 7884 8.393959 AGATGGAAAAGAAATACTCCCTCTAA 57.606 34.615 0.00 0.00 32.94 2.10
6909 7918 7.545965 CACCCTTTATCATTAGCTATTCGGTAG 59.454 40.741 0.00 0.00 0.00 3.18
6912 7921 6.231211 ACACCCTTTATCATTAGCTATTCGG 58.769 40.000 0.00 0.00 0.00 4.30
6932 8233 0.464916 AACCTTCGGACACCAACACC 60.465 55.000 0.00 0.00 0.00 4.16
7129 8445 6.990349 GGAATGGATTTCTATTCTTACGTGGA 59.010 38.462 14.01 0.00 41.68 4.02
7134 8450 8.980481 TTGGAGGAATGGATTTCTATTCTTAC 57.020 34.615 14.01 9.43 41.68 2.34
7137 8453 7.819500 TGATTGGAGGAATGGATTTCTATTCT 58.180 34.615 14.01 3.58 41.68 2.40
7144 8491 6.670902 AGTCATTTGATTGGAGGAATGGATTT 59.329 34.615 0.00 0.00 31.97 2.17
7156 8503 5.927281 ATCCTTGGAAGTCATTTGATTGG 57.073 39.130 0.00 0.00 0.00 3.16
7204 8551 6.060788 AGCTTCAAGCCTTATAGGAATTCTG 58.939 40.000 5.53 0.00 43.77 3.02
7212 8559 6.349300 TCACCTTAAGCTTCAAGCCTTATAG 58.651 40.000 5.53 5.25 43.77 1.31
7271 8643 3.244112 ACAGAGGGAGTAGAAAAACACGG 60.244 47.826 0.00 0.00 0.00 4.94
7272 8644 3.988517 GACAGAGGGAGTAGAAAAACACG 59.011 47.826 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.