Multiple sequence alignment - TraesCS1D01G287300

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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 TraesCS1D01G287300 chr1D 100.000 6126 0 0 1 6126 385629207 385623082 0.000000e+00 11313
1 TraesCS1D01G287300 chr1B 91.611 5102 239 89 462 5466 517913806 517908797 0.000000e+00 6876
2 TraesCS1D01G287300 chr1A 92.210 4724 209 63 836 5466 485349561 485344904 0.000000e+00 6538
3 TraesCS1D01G287300 chr1A 96.515 660 22 1 5467 6126 548283425 548282767 0.000000e+00 1090
4 TraesCS1D01G287300 chr1A 92.771 332 11 9 462 787 485349896 485349572 9.300000e-128 468
5 TraesCS1D01G287300 chr1A 83.262 466 52 8 1 465 485350654 485350214 7.390000e-109 405
6 TraesCS1D01G287300 chr3B 89.996 2629 206 27 2031 4634 744211981 744214577 0.000000e+00 3345
7 TraesCS1D01G287300 chr3B 86.258 815 75 18 4681 5466 744215047 744215853 0.000000e+00 850
8 TraesCS1D01G287300 chr3B 84.466 103 12 3 5295 5393 747496010 747495908 1.410000e-16 99
9 TraesCS1D01G287300 chr3D 90.762 2100 162 18 2514 4591 560106702 560108791 0.000000e+00 2774
10 TraesCS1D01G287300 chr3D 90.347 518 40 5 4672 5186 560109223 560109733 0.000000e+00 671
11 TraesCS1D01G287300 chr3D 90.080 373 24 6 2029 2391 560106304 560106673 7.190000e-129 472
12 TraesCS1D01G287300 chr3D 90.094 212 16 4 5258 5466 560109853 560110062 2.810000e-68 270
13 TraesCS1D01G287300 chr3D 88.679 212 17 5 5258 5466 259363230 259363023 1.020000e-62 252
14 TraesCS1D01G287300 chr3D 85.714 231 22 6 1629 1859 560106087 560106306 3.690000e-57 233
15 TraesCS1D01G287300 chr3D 89.655 145 6 3 4997 5132 560231829 560231973 6.310000e-40 176
16 TraesCS1D01G287300 chr3A 89.820 1670 133 23 2029 3676 696239791 696241445 0.000000e+00 2108
17 TraesCS1D01G287300 chr3A 89.586 941 80 7 3704 4634 696241442 696242374 0.000000e+00 1179
18 TraesCS1D01G287300 chr3A 85.907 816 74 19 4681 5466 696242843 696243647 0.000000e+00 832
19 TraesCS1D01G287300 chr3A 89.941 507 43 5 4681 5186 629013541 629014040 0.000000e+00 647
20 TraesCS1D01G287300 chr3A 90.759 303 26 1 4332 4634 629012772 629013072 2.660000e-108 403
21 TraesCS1D01G287300 chr3A 85.517 290 40 2 3372 3659 629015834 629016123 9.980000e-78 302
22 TraesCS1D01G287300 chr3A 84.932 292 40 3 3372 3659 696245082 696245373 6.010000e-75 292
23 TraesCS1D01G287300 chr3A 88.208 212 20 4 5258 5466 629014161 629014370 1.320000e-61 248
24 TraesCS1D01G287300 chr3A 76.429 420 60 27 4977 5369 629090373 629089966 2.250000e-44 191
25 TraesCS1D01G287300 chr3A 84.000 175 12 9 4974 5133 696330462 696330635 2.960000e-33 154
26 TraesCS1D01G287300 chr3A 79.904 209 23 13 5191 5391 696267042 696267239 1.070000e-27 135
27 TraesCS1D01G287300 chr3A 79.426 209 24 13 5191 5391 629016125 629016322 4.980000e-26 130
28 TraesCS1D01G287300 chr7D 97.576 660 16 0 5467 6126 629118994 629119653 0.000000e+00 1131
29 TraesCS1D01G287300 chr2A 96.212 660 24 1 5467 6126 62612941 62613599 0.000000e+00 1079
30 TraesCS1D01G287300 chr4D 97.297 407 11 0 5466 5872 10483112 10482706 0.000000e+00 691
31 TraesCS1D01G287300 chr4D 97.701 261 6 0 5866 6126 10476295 10476035 3.370000e-122 449
32 TraesCS1D01G287300 chr4A 85.000 400 48 8 2045 2442 706496134 706495745 4.450000e-106 396
33 TraesCS1D01G287300 chr4A 92.571 175 13 0 5465 5639 545768080 545768254 1.020000e-62 252
34 TraesCS1D01G287300 chr4A 91.304 115 10 0 1656 1770 706496574 706496460 2.290000e-34 158
35 TraesCS1D01G287300 chr7A 93.889 180 8 3 2045 2223 23898289 23898466 1.010000e-67 268
36 TraesCS1D01G287300 chr7A 93.333 180 9 3 2045 2223 24283517 24283694 4.710000e-66 263
37 TraesCS1D01G287300 chr7A 92.857 182 8 4 2045 2223 24097944 24098123 6.090000e-65 259
38 TraesCS1D01G287300 chr7A 89.151 212 16 5 5258 5466 671908093 671907886 2.190000e-64 257
39 TraesCS1D01G287300 chr7A 88.889 117 13 0 1653 1769 23897846 23897962 1.780000e-30 145
40 TraesCS1D01G287300 chr7A 88.889 117 13 0 1653 1769 24097501 24097617 1.780000e-30 145
41 TraesCS1D01G287300 chr7A 88.034 117 14 0 1653 1769 23789817 23789933 8.280000e-29 139
42 TraesCS1D01G287300 chr6D 82.938 211 31 4 1552 1761 21353667 21353873 1.050000e-42 185


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 TraesCS1D01G287300 chr1D 385623082 385629207 6125 True 11313.000000 11313 100.000000 1 6126 1 chr1D.!!$R1 6125
1 TraesCS1D01G287300 chr1B 517908797 517913806 5009 True 6876.000000 6876 91.611000 462 5466 1 chr1B.!!$R1 5004
2 TraesCS1D01G287300 chr1A 485344904 485350654 5750 True 2470.333333 6538 89.414333 1 5466 3 chr1A.!!$R2 5465
3 TraesCS1D01G287300 chr1A 548282767 548283425 658 True 1090.000000 1090 96.515000 5467 6126 1 chr1A.!!$R1 659
4 TraesCS1D01G287300 chr3B 744211981 744215853 3872 False 2097.500000 3345 88.127000 2031 5466 2 chr3B.!!$F1 3435
5 TraesCS1D01G287300 chr3D 560106087 560110062 3975 False 884.000000 2774 89.399400 1629 5466 5 chr3D.!!$F2 3837
6 TraesCS1D01G287300 chr3A 696239791 696245373 5582 False 1102.750000 2108 87.561250 2029 5466 4 chr3A.!!$F4 3437
7 TraesCS1D01G287300 chr3A 629012772 629016322 3550 False 346.000000 647 86.770200 3372 5466 5 chr3A.!!$F3 2094
8 TraesCS1D01G287300 chr7D 629118994 629119653 659 False 1131.000000 1131 97.576000 5467 6126 1 chr7D.!!$F1 659
9 TraesCS1D01G287300 chr2A 62612941 62613599 658 False 1079.000000 1079 96.212000 5467 6126 1 chr2A.!!$F1 659
10 TraesCS1D01G287300 chr4A 706495745 706496574 829 True 277.000000 396 88.152000 1656 2442 2 chr4A.!!$R1 786
11 TraesCS1D01G287300 chr7A 23897846 23898466 620 False 206.500000 268 91.389000 1653 2223 2 chr7A.!!$F3 570
12 TraesCS1D01G287300 chr7A 24097501 24098123 622 False 202.000000 259 90.873000 1653 2223 2 chr7A.!!$F4 570

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
450 452 0.023229 CGTGTATGTGCGCAACTACG 59.977 55.000 14.00 15.17 0.0 3.51 F
821 1156 0.613292 AGGACGACAGGACTGCAGAT 60.613 55.000 23.35 4.35 0.0 2.90 F
1771 2241 0.606401 CGTTTGTGCTGTGGGATCCT 60.606 55.000 12.58 0.00 0.0 3.24 F
2707 3224 0.108207 AGCATGGCATAGGTGAGAGC 59.892 55.000 0.00 0.00 0.0 4.09 F
4145 4701 1.003928 TGTTCCTGCATGCTCATCTGT 59.996 47.619 20.33 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 2138 1.168714 GAGGATCCCACAGCACAAAC 58.831 55.000 8.55 0.00 0.00 2.93 R
2361 2867 2.408271 TCAGATCCACATGCACCTTC 57.592 50.000 0.00 0.00 0.00 3.46 R
2988 3508 1.815196 CAACAACTGCAACCAGCCA 59.185 52.632 0.00 0.00 43.02 4.75 R
4395 4960 0.320771 ACTGTTGAGCTAGCCAACCG 60.321 55.000 29.91 27.31 42.23 4.44 R
5302 6365 0.323360 TAGCACATGGCCCTGGTTTC 60.323 55.000 13.03 0.00 46.50 2.78 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
24 25 3.740115 TCAGTGCCAAGTTTAGGACTTC 58.260 45.455 0.00 0.00 45.40 3.01
28 29 3.883489 GTGCCAAGTTTAGGACTTCAAGT 59.117 43.478 0.00 0.00 45.40 3.16
66 67 7.979444 TTCACAAGAAACCTAACCATCTAAG 57.021 36.000 0.00 0.00 0.00 2.18
71 72 5.983540 AGAAACCTAACCATCTAAGCTCAG 58.016 41.667 0.00 0.00 0.00 3.35
77 78 4.623932 AACCATCTAAGCTCAGTTCACA 57.376 40.909 0.00 0.00 0.00 3.58
78 79 4.833478 ACCATCTAAGCTCAGTTCACAT 57.167 40.909 0.00 0.00 0.00 3.21
79 80 4.511527 ACCATCTAAGCTCAGTTCACATG 58.488 43.478 0.00 0.00 0.00 3.21
84 85 2.393271 AGCTCAGTTCACATGCTACC 57.607 50.000 0.00 0.00 31.71 3.18
101 102 3.680458 GCTACCTTATTATTGCCTCTCGC 59.320 47.826 0.00 0.00 38.31 5.03
154 155 6.043358 TGGTATGAAATTACCATCCCGACATA 59.957 38.462 0.00 0.00 45.23 2.29
163 164 8.618240 ATTACCATCCCGACATATTTATCCTA 57.382 34.615 0.00 0.00 0.00 2.94
166 167 7.394816 ACCATCCCGACATATTTATCCTAAAG 58.605 38.462 0.00 0.00 0.00 1.85
167 168 6.823689 CCATCCCGACATATTTATCCTAAAGG 59.176 42.308 0.00 0.00 0.00 3.11
195 197 1.543802 CGGGTTTTCAATTGGCAGCTA 59.456 47.619 5.42 0.00 0.00 3.32
203 205 2.487762 TCAATTGGCAGCTAAAAGTCCG 59.512 45.455 5.42 0.00 0.00 4.79
208 210 0.442699 GCAGCTAAAAGTCCGGTTCG 59.557 55.000 0.00 0.00 0.00 3.95
219 221 4.261578 AGTCCGGTTCGTCAATCTTAAA 57.738 40.909 0.00 0.00 0.00 1.52
226 228 5.788531 CGGTTCGTCAATCTTAAAATGTGAC 59.211 40.000 0.00 0.00 36.17 3.67
240 242 1.588674 TGTGACGTCGGCTCAATTTT 58.411 45.000 11.62 0.00 0.00 1.82
243 245 1.798223 TGACGTCGGCTCAATTTTCTG 59.202 47.619 11.62 0.00 0.00 3.02
247 249 1.200020 GTCGGCTCAATTTTCTGGTGG 59.800 52.381 0.00 0.00 0.00 4.61
248 250 0.527565 CGGCTCAATTTTCTGGTGGG 59.472 55.000 0.00 0.00 0.00 4.61
250 252 1.260544 GCTCAATTTTCTGGTGGGCT 58.739 50.000 0.00 0.00 35.79 5.19
253 255 0.971386 CAATTTTCTGGTGGGCTGCT 59.029 50.000 0.00 0.00 0.00 4.24
259 261 0.253044 TCTGGTGGGCTGCTTATGTC 59.747 55.000 0.00 0.00 0.00 3.06
268 270 3.755378 GGGCTGCTTATGTCCATTCATAG 59.245 47.826 0.00 0.00 32.85 2.23
280 282 7.392766 TGTCCATTCATAGGGATGAGTTTAT 57.607 36.000 0.00 0.00 43.03 1.40
284 286 7.000472 CCATTCATAGGGATGAGTTTATGTGT 59.000 38.462 0.00 0.00 43.03 3.72
285 287 8.156820 CCATTCATAGGGATGAGTTTATGTGTA 58.843 37.037 0.00 0.00 43.03 2.90
290 292 9.605275 CATAGGGATGAGTTTATGTGTATATGG 57.395 37.037 0.00 0.00 34.73 2.74
293 295 8.502738 AGGGATGAGTTTATGTGTATATGGTTT 58.497 33.333 0.00 0.00 0.00 3.27
335 337 4.790810 TGTAAGCATCTACGAGACTACG 57.209 45.455 0.00 0.00 39.31 3.51
336 338 4.436332 TGTAAGCATCTACGAGACTACGA 58.564 43.478 0.00 0.00 37.03 3.43
337 339 3.948196 AAGCATCTACGAGACTACGAC 57.052 47.619 0.00 0.00 37.03 4.34
342 344 3.865011 TCTACGAGACTACGACTGTCT 57.135 47.619 6.21 8.81 46.17 3.41
356 358 0.881796 CTGTCTCGTGTAGGTGCTCA 59.118 55.000 0.00 0.00 0.00 4.26
360 362 2.033550 GTCTCGTGTAGGTGCTCATAGG 59.966 54.545 0.00 0.00 0.00 2.57
371 373 1.294068 TGCTCATAGGGGTAGGGTCTT 59.706 52.381 0.00 0.00 0.00 3.01
372 374 1.694696 GCTCATAGGGGTAGGGTCTTG 59.305 57.143 0.00 0.00 0.00 3.02
373 375 1.694696 CTCATAGGGGTAGGGTCTTGC 59.305 57.143 0.00 0.00 0.00 4.01
390 392 3.809279 TCTTGCGTATGTGCATTCATAGG 59.191 43.478 10.91 10.91 45.78 2.57
392 394 2.103941 TGCGTATGTGCATTCATAGGGA 59.896 45.455 14.97 11.21 40.62 4.20
393 395 2.480419 GCGTATGTGCATTCATAGGGAC 59.520 50.000 14.97 0.51 36.95 4.46
394 396 2.731451 CGTATGTGCATTCATAGGGACG 59.269 50.000 8.43 3.56 34.54 4.79
395 397 3.552068 CGTATGTGCATTCATAGGGACGA 60.552 47.826 8.43 0.00 34.54 4.20
396 398 2.602257 TGTGCATTCATAGGGACGAG 57.398 50.000 0.00 0.00 0.00 4.18
397 399 1.831106 TGTGCATTCATAGGGACGAGT 59.169 47.619 0.00 0.00 0.00 4.18
398 400 2.236146 TGTGCATTCATAGGGACGAGTT 59.764 45.455 0.00 0.00 0.00 3.01
399 401 3.270877 GTGCATTCATAGGGACGAGTTT 58.729 45.455 0.00 0.00 0.00 2.66
400 402 4.081365 TGTGCATTCATAGGGACGAGTTTA 60.081 41.667 0.00 0.00 0.00 2.01
401 403 5.057149 GTGCATTCATAGGGACGAGTTTAT 58.943 41.667 0.00 0.00 0.00 1.40
402 404 5.050091 GTGCATTCATAGGGACGAGTTTATG 60.050 44.000 0.00 0.00 0.00 1.90
403 405 5.057149 GCATTCATAGGGACGAGTTTATGT 58.943 41.667 0.00 0.00 0.00 2.29
404 406 5.527582 GCATTCATAGGGACGAGTTTATGTT 59.472 40.000 0.00 0.00 0.00 2.71
405 407 6.292919 GCATTCATAGGGACGAGTTTATGTTC 60.293 42.308 0.00 0.00 0.00 3.18
406 408 5.925506 TCATAGGGACGAGTTTATGTTCA 57.074 39.130 0.00 0.00 0.00 3.18
441 443 2.095768 AGAAACATGTGCGTGTATGTGC 60.096 45.455 0.00 0.00 37.57 4.57
450 452 0.023229 CGTGTATGTGCGCAACTACG 59.977 55.000 14.00 15.17 0.00 3.51
455 457 1.438651 ATGTGCGCAACTACGATTGT 58.561 45.000 14.00 0.00 34.06 2.71
491 814 6.736853 CGAAAATTTGAGGAAAACTAGCGTAG 59.263 38.462 0.00 0.00 0.00 3.51
561 884 4.966787 GCCTCCGGCCACCAACAA 62.967 66.667 2.24 0.00 44.06 2.83
562 885 2.983592 CCTCCGGCCACCAACAAC 60.984 66.667 2.24 0.00 0.00 3.32
563 886 2.203280 CTCCGGCCACCAACAACA 60.203 61.111 2.24 0.00 0.00 3.33
818 1153 2.574018 CCAGGACGACAGGACTGCA 61.574 63.158 0.00 0.00 0.00 4.41
821 1156 0.613292 AGGACGACAGGACTGCAGAT 60.613 55.000 23.35 4.35 0.00 2.90
827 1162 3.474570 AGGACTGCAGATCCCGGC 61.475 66.667 23.35 0.00 36.86 6.13
828 1163 4.554036 GGACTGCAGATCCCGGCC 62.554 72.222 23.35 0.00 32.32 6.13
829 1164 4.899239 GACTGCAGATCCCGGCCG 62.899 72.222 23.35 21.04 32.32 6.13
831 1166 4.473520 CTGCAGATCCCGGCCGTT 62.474 66.667 26.12 8.48 32.32 4.44
834 1169 4.473520 CAGATCCCGGCCGTTGCT 62.474 66.667 26.12 12.72 37.74 3.91
842 1184 4.742201 GGCCGTTGCTCAGCTCGA 62.742 66.667 14.51 0.00 37.74 4.04
878 1220 7.281100 GCCAAGTATGTCTTTTTAGCTGACTAT 59.719 37.037 0.00 0.00 33.63 2.12
879 1221 9.817809 CCAAGTATGTCTTTTTAGCTGACTATA 57.182 33.333 0.00 0.00 33.63 1.31
881 1223 9.819267 AAGTATGTCTTTTTAGCTGACTATACC 57.181 33.333 0.00 0.00 32.21 2.73
904 1246 7.532571 ACCTATCAATTTACGGTTTTTAGTGC 58.467 34.615 0.00 0.00 0.00 4.40
1056 1404 1.753078 CACATCCCTCTCCCGTCGA 60.753 63.158 0.00 0.00 0.00 4.20
1116 1464 1.750351 GCGCGACGAGTCAATATACA 58.250 50.000 12.10 0.00 0.00 2.29
1117 1465 2.316792 GCGCGACGAGTCAATATACAT 58.683 47.619 12.10 0.00 0.00 2.29
1118 1466 3.485633 GCGCGACGAGTCAATATACATA 58.514 45.455 12.10 0.00 0.00 2.29
1119 1467 4.096311 GCGCGACGAGTCAATATACATAT 58.904 43.478 12.10 0.00 0.00 1.78
1120 1468 5.260900 GCGCGACGAGTCAATATACATATA 58.739 41.667 12.10 0.00 0.00 0.86
1216 1564 1.077716 GGTGCGCAGGGAGGTAATT 60.078 57.895 12.22 0.00 0.00 1.40
1234 1582 7.068702 AGGTAATTGGATTGGCTTTGATATGA 58.931 34.615 0.00 0.00 0.00 2.15
1235 1583 7.731688 AGGTAATTGGATTGGCTTTGATATGAT 59.268 33.333 0.00 0.00 0.00 2.45
1236 1584 8.370182 GGTAATTGGATTGGCTTTGATATGATT 58.630 33.333 0.00 0.00 0.00 2.57
1272 1620 7.069085 AGGAATTTGGAATACTCACATTGGATG 59.931 37.037 0.00 0.00 0.00 3.51
1327 1676 2.422597 TCTACCAGCGGTTTCAATGTG 58.577 47.619 5.57 0.00 37.09 3.21
1391 1744 5.130145 CCATCACTTGATTCTCCTTCCTACT 59.870 44.000 0.00 0.00 31.21 2.57
1400 1753 4.081322 TCTCCTTCCTACTTGCGTTTTT 57.919 40.909 0.00 0.00 0.00 1.94
1401 1754 3.813166 TCTCCTTCCTACTTGCGTTTTTG 59.187 43.478 0.00 0.00 0.00 2.44
1402 1755 3.811083 TCCTTCCTACTTGCGTTTTTGA 58.189 40.909 0.00 0.00 0.00 2.69
1403 1756 4.394729 TCCTTCCTACTTGCGTTTTTGAT 58.605 39.130 0.00 0.00 0.00 2.57
1404 1757 4.215399 TCCTTCCTACTTGCGTTTTTGATG 59.785 41.667 0.00 0.00 0.00 3.07
1409 1762 5.935206 TCCTACTTGCGTTTTTGATGTGATA 59.065 36.000 0.00 0.00 0.00 2.15
1416 1769 8.785468 TTGCGTTTTTGATGTGATATGATATG 57.215 30.769 0.00 0.00 0.00 1.78
1419 1772 7.535258 GCGTTTTTGATGTGATATGATATGACC 59.465 37.037 0.00 0.00 0.00 4.02
1556 1941 9.864034 CTTGTTACAACTCATGTGTTTAAGTAG 57.136 33.333 10.36 1.79 43.77 2.57
1562 1947 6.787085 ACTCATGTGTTTAAGTAGTCAAGC 57.213 37.500 0.00 0.00 0.00 4.01
1617 2002 8.894409 TTCATTTTACGTTTTCTCATGCATAG 57.106 30.769 0.00 0.00 0.00 2.23
1753 2138 0.895530 TCAGAGCTTGGGGTAACTCG 59.104 55.000 0.00 0.00 44.09 4.18
1771 2241 0.606401 CGTTTGTGCTGTGGGATCCT 60.606 55.000 12.58 0.00 0.00 3.24
1797 2267 4.823442 TGCATCACCATGGAGAATTATGTC 59.177 41.667 21.47 8.08 0.00 3.06
1804 2274 7.014808 TCACCATGGAGAATTATGTCGTACATA 59.985 37.037 21.47 4.30 39.88 2.29
1830 2300 4.077300 CCTAATTCAGGCAGTGCTGATA 57.923 45.455 16.11 6.43 37.70 2.15
2051 2531 6.319658 CCGTTCTAGTTATGTAGGGTCTTACA 59.680 42.308 0.00 0.00 37.89 2.41
2244 2729 9.812347 TTTATCCAGGCATGATTTATCATAGTT 57.188 29.630 0.00 0.00 45.23 2.24
2284 2782 6.592994 TGAATCAAATTTGTTGCAAGTGTTGA 59.407 30.769 17.47 6.42 0.00 3.18
2322 2820 4.151689 TGAAATGTTTCTGTAGCACGCTAC 59.848 41.667 19.93 19.93 40.58 3.58
2361 2867 3.849911 AGTGTGATGTCCATTCGTGTAG 58.150 45.455 0.00 0.00 0.00 2.74
2545 3062 5.703130 GGCAGGTCATTTAGAGGATATTGAC 59.297 44.000 0.00 0.00 34.24 3.18
2707 3224 0.108207 AGCATGGCATAGGTGAGAGC 59.892 55.000 0.00 0.00 0.00 4.09
2772 3292 8.853126 TCTTCCAATTATCATGCCATTAAAGAG 58.147 33.333 0.00 0.00 0.00 2.85
3107 3652 7.356089 ACTCGTGGGATCAATGTAATAGTTA 57.644 36.000 0.00 0.00 0.00 2.24
3113 3658 8.922676 GTGGGATCAATGTAATAGTTATGTACG 58.077 37.037 0.00 0.00 0.00 3.67
3180 3725 8.180267 CAGAATCATAAGGATGTTCTTGTTGTC 58.820 37.037 0.00 0.00 36.02 3.18
3207 3752 5.514484 GGATCATCATGATTACCCTGCTCTT 60.514 44.000 5.16 0.00 37.20 2.85
3339 3884 3.998341 GGAAGCAAACGAACAGTGGTATA 59.002 43.478 0.00 0.00 0.00 1.47
3383 3928 8.375506 TGGTCCAATACATATCTGATAGTTTCC 58.624 37.037 3.48 0.00 0.00 3.13
3692 4238 1.277273 CTCTTCTGAGATGGTGCCACA 59.723 52.381 0.00 0.00 42.73 4.17
3709 4256 3.128242 GCCACAAATTCCATGTCTCTCAG 59.872 47.826 0.00 0.00 0.00 3.35
3831 4384 2.430694 GGGTTTTCATAACTGGCATCCC 59.569 50.000 0.00 0.00 0.00 3.85
3891 4444 1.852942 CTGATGCTGCATGGAATTGC 58.147 50.000 21.53 4.02 43.07 3.56
3924 4477 4.497291 TGAGAACCCTACTTGTGTTGTT 57.503 40.909 0.00 0.00 0.00 2.83
4002 4555 7.064016 GCATATAGATTAGCTGTAAAGGCAGAC 59.936 40.741 0.00 0.00 38.70 3.51
4101 4655 3.015934 TCGCAAGCTCTAACGTTTGTA 57.984 42.857 5.91 0.00 37.18 2.41
4145 4701 1.003928 TGTTCCTGCATGCTCATCTGT 59.996 47.619 20.33 0.00 0.00 3.41
4147 4703 2.609427 TCCTGCATGCTCATCTGTAC 57.391 50.000 20.33 0.00 0.00 2.90
4162 4718 7.629437 GCTCATCTGTACATTCTCAGTTAGTCA 60.629 40.741 0.00 0.00 33.89 3.41
4329 4894 3.073946 AGGTCCTCAAAGGGAAATCGAAA 59.926 43.478 0.00 0.00 37.10 3.46
4368 4933 2.820197 GGCGAAGAGAAGTGGGAAAAAT 59.180 45.455 0.00 0.00 0.00 1.82
4392 4957 1.811679 GTCGCTCAGGCAGGTAAGC 60.812 63.158 0.00 0.00 38.60 3.09
4395 4960 2.512515 CTCAGGCAGGTAAGCGGC 60.513 66.667 0.00 0.00 34.64 6.53
4411 4976 2.399356 GGCGGTTGGCTAGCTCAAC 61.399 63.158 27.43 27.43 42.53 3.18
4416 4981 1.270839 GGTTGGCTAGCTCAACAGTCA 60.271 52.381 31.93 14.10 44.38 3.41
4596 5162 2.170607 CCAAGGAAAAGATAGGGCGAGA 59.829 50.000 0.00 0.00 0.00 4.04
4613 5179 4.448732 GGCGAGAAAATTTCAGTTTGCAAT 59.551 37.500 8.55 0.00 0.00 3.56
4751 5755 3.643320 TGACTTGACTGATCCTCTTGTGT 59.357 43.478 0.00 0.00 0.00 3.72
4883 5887 1.305930 GCGACGCCTTCTTCCCATTT 61.306 55.000 9.14 0.00 0.00 2.32
4901 5910 5.174395 CCATTTGGTGAGAACAAAACAACA 58.826 37.500 0.00 0.00 40.74 3.33
4902 5911 5.641209 CCATTTGGTGAGAACAAAACAACAA 59.359 36.000 0.00 0.00 40.74 2.83
4903 5912 6.402011 CCATTTGGTGAGAACAAAACAACAAC 60.402 38.462 0.00 0.00 40.21 3.32
4904 5913 4.181309 TGGTGAGAACAAAACAACAACC 57.819 40.909 0.00 0.00 0.00 3.77
4905 5914 3.056465 TGGTGAGAACAAAACAACAACCC 60.056 43.478 0.00 0.00 0.00 4.11
4906 5915 3.175929 GTGAGAACAAAACAACAACCCG 58.824 45.455 0.00 0.00 0.00 5.28
4907 5916 2.164624 TGAGAACAAAACAACAACCCGG 59.835 45.455 0.00 0.00 0.00 5.73
4932 5941 3.653539 TTCGATTCGACCAAGTGAGAA 57.346 42.857 8.55 0.00 34.89 2.87
5236 6275 3.857157 ATAATTGTATGACAGGGGCGT 57.143 42.857 0.00 0.00 0.00 5.68
5248 6287 1.226184 GGGGCGTAATCGTTTTGCG 60.226 57.895 6.90 6.90 43.01 4.85
5302 6365 5.424252 TGAGTGGGTAATAACTAAGGTCAGG 59.576 44.000 0.00 0.00 0.00 3.86
5315 6391 1.384191 GTCAGGAAACCAGGGCCAT 59.616 57.895 6.18 0.00 0.00 4.40
5316 6392 0.967380 GTCAGGAAACCAGGGCCATG 60.967 60.000 11.33 11.33 0.00 3.66
5317 6393 1.077265 CAGGAAACCAGGGCCATGT 59.923 57.895 17.55 1.30 0.00 3.21
5318 6394 1.077265 AGGAAACCAGGGCCATGTG 59.923 57.895 17.55 10.40 0.00 3.21
5319 6395 2.649129 GGAAACCAGGGCCATGTGC 61.649 63.158 17.55 0.00 40.16 4.57
5320 6396 1.607467 GAAACCAGGGCCATGTGCT 60.607 57.895 17.55 0.00 40.92 4.40
5321 6397 0.323360 GAAACCAGGGCCATGTGCTA 60.323 55.000 17.55 0.00 40.92 3.49
5322 6398 0.323725 AAACCAGGGCCATGTGCTAG 60.324 55.000 17.55 2.57 40.92 3.42
5323 6399 1.500783 AACCAGGGCCATGTGCTAGT 61.501 55.000 17.55 3.29 40.92 2.57
5324 6400 1.304282 CCAGGGCCATGTGCTAGTT 59.696 57.895 17.55 0.00 40.92 2.24
5325 6401 0.546122 CCAGGGCCATGTGCTAGTTA 59.454 55.000 17.55 0.00 40.92 2.24
5326 6402 1.064758 CCAGGGCCATGTGCTAGTTAA 60.065 52.381 17.55 0.00 40.92 2.01
5338 6414 7.413438 CCATGTGCTAGTTAAACTAAGCAGAAG 60.413 40.741 8.77 5.92 36.37 2.85
5430 6509 4.660105 GTGATCTCTGCTTGAAGATTTGC 58.340 43.478 0.00 0.00 0.00 3.68
5548 6627 3.058914 GCGAAATTCATCCATCTTACCCG 60.059 47.826 0.00 0.00 0.00 5.28
5645 6724 9.822185 ATGATTTATAGGCATTTTTCTTTGTCC 57.178 29.630 0.00 0.00 0.00 4.02
5665 6744 4.329256 GTCCGTAGCCAGTTTTATTCACTC 59.671 45.833 0.00 0.00 0.00 3.51
5792 6871 0.107017 CCATCGACTCCTTGCCCATT 60.107 55.000 0.00 0.00 0.00 3.16
5847 6926 1.273327 TGATCGAGTTTGAGCTGAGCA 59.727 47.619 7.39 0.00 0.00 4.26
5897 6976 2.623889 GCGTCCTTCTCCTATTCTAGCA 59.376 50.000 0.00 0.00 0.00 3.49
5901 6980 4.647399 GTCCTTCTCCTATTCTAGCACTGT 59.353 45.833 0.00 0.00 0.00 3.55
6118 7244 4.870123 AGGCACTTGCAAATTGATGTAA 57.130 36.364 11.11 0.00 44.36 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.065371 GTGAAACCAACTCACCAGACTTG 59.935 47.826 0.00 0.00 37.77 3.16
28 29 3.054728 TCTTGTGAAACCAACTCACCAGA 60.055 43.478 3.40 3.40 41.04 3.86
43 44 5.938125 GCTTAGATGGTTAGGTTTCTTGTGA 59.062 40.000 0.00 0.00 0.00 3.58
61 62 3.969287 AGCATGTGAACTGAGCTTAGA 57.031 42.857 13.21 0.00 29.98 2.10
62 63 3.868077 GGTAGCATGTGAACTGAGCTTAG 59.132 47.826 3.53 3.53 36.80 2.18
66 67 2.393271 AGGTAGCATGTGAACTGAGC 57.607 50.000 0.00 0.00 0.00 4.26
71 72 6.263168 AGGCAATAATAAGGTAGCATGTGAAC 59.737 38.462 0.00 0.00 0.00 3.18
77 78 5.482908 CGAGAGGCAATAATAAGGTAGCAT 58.517 41.667 0.00 0.00 0.00 3.79
78 79 4.799586 GCGAGAGGCAATAATAAGGTAGCA 60.800 45.833 0.00 0.00 42.87 3.49
79 80 3.680458 GCGAGAGGCAATAATAAGGTAGC 59.320 47.826 0.00 0.00 42.87 3.58
84 85 2.408050 AGCGCGAGAGGCAATAATAAG 58.592 47.619 12.10 0.00 43.84 1.73
101 102 8.868744 TTATTGTTTTATTTCGTAGTCAAGCG 57.131 30.769 0.00 0.00 0.00 4.68
154 155 6.102762 ACCCGAGAATTCCCTTTAGGATAAAT 59.897 38.462 0.65 0.00 46.94 1.40
158 159 3.394645 ACCCGAGAATTCCCTTTAGGAT 58.605 45.455 0.65 0.00 46.94 3.24
163 164 3.839778 TGAAAACCCGAGAATTCCCTTT 58.160 40.909 0.65 0.00 0.00 3.11
166 167 4.494484 CAATTGAAAACCCGAGAATTCCC 58.506 43.478 0.00 0.00 0.00 3.97
167 168 4.494484 CCAATTGAAAACCCGAGAATTCC 58.506 43.478 7.12 0.00 0.00 3.01
173 175 1.669795 GCTGCCAATTGAAAACCCGAG 60.670 52.381 7.12 0.00 0.00 4.63
175 177 0.318120 AGCTGCCAATTGAAAACCCG 59.682 50.000 7.12 0.00 0.00 5.28
176 178 3.676291 TTAGCTGCCAATTGAAAACCC 57.324 42.857 7.12 0.00 0.00 4.11
195 197 3.121738 AGATTGACGAACCGGACTTTT 57.878 42.857 9.46 0.00 0.00 2.27
208 210 5.313623 CCGACGTCACATTTTAAGATTGAC 58.686 41.667 17.16 9.37 34.48 3.18
219 221 1.808411 AATTGAGCCGACGTCACATT 58.192 45.000 17.16 3.92 0.00 2.71
226 228 1.135972 CACCAGAAAATTGAGCCGACG 60.136 52.381 0.00 0.00 0.00 5.12
240 242 0.253044 GACATAAGCAGCCCACCAGA 59.747 55.000 0.00 0.00 0.00 3.86
243 245 0.106519 ATGGACATAAGCAGCCCACC 60.107 55.000 0.00 0.00 0.00 4.61
247 249 3.755378 CCTATGAATGGACATAAGCAGCC 59.245 47.826 0.00 0.00 33.26 4.85
248 250 3.755378 CCCTATGAATGGACATAAGCAGC 59.245 47.826 0.00 0.00 33.26 5.25
250 252 5.310331 TCATCCCTATGAATGGACATAAGCA 59.690 40.000 0.00 0.00 39.20 3.91
253 255 7.392766 AACTCATCCCTATGAATGGACATAA 57.607 36.000 0.00 0.00 41.57 1.90
259 261 7.000472 ACACATAAACTCATCCCTATGAATGG 59.000 38.462 0.00 0.00 41.57 3.16
268 270 8.691661 AAACCATATACACATAAACTCATCCC 57.308 34.615 0.00 0.00 0.00 3.85
293 295 5.826586 ACATCTACGCACATGTTTCAAAAA 58.173 33.333 0.00 0.00 28.27 1.94
296 298 5.390461 GCTTACATCTACGCACATGTTTCAA 60.390 40.000 0.00 0.00 34.92 2.69
297 299 4.092821 GCTTACATCTACGCACATGTTTCA 59.907 41.667 0.00 0.00 34.92 2.69
298 300 4.092821 TGCTTACATCTACGCACATGTTTC 59.907 41.667 0.00 0.00 34.92 2.78
335 337 0.882474 AGCACCTACACGAGACAGTC 59.118 55.000 0.00 0.00 0.00 3.51
336 338 0.882474 GAGCACCTACACGAGACAGT 59.118 55.000 0.00 0.00 0.00 3.55
337 339 0.881796 TGAGCACCTACACGAGACAG 59.118 55.000 0.00 0.00 0.00 3.51
342 344 1.399714 CCCTATGAGCACCTACACGA 58.600 55.000 0.00 0.00 0.00 4.35
346 348 2.249139 CCTACCCCTATGAGCACCTAC 58.751 57.143 0.00 0.00 0.00 3.18
356 358 0.031414 ACGCAAGACCCTACCCCTAT 60.031 55.000 0.00 0.00 43.62 2.57
360 362 0.828677 ACATACGCAAGACCCTACCC 59.171 55.000 0.00 0.00 43.62 3.69
372 374 2.480419 GTCCCTATGAATGCACATACGC 59.520 50.000 0.00 0.00 0.00 4.42
373 375 2.731451 CGTCCCTATGAATGCACATACG 59.269 50.000 0.00 0.00 0.00 3.06
390 392 6.903883 ACATACATGAACATAAACTCGTCC 57.096 37.500 0.00 0.00 0.00 4.79
432 434 1.342555 TCGTAGTTGCGCACATACAC 58.657 50.000 23.58 14.67 0.00 2.90
433 435 2.287393 ATCGTAGTTGCGCACATACA 57.713 45.000 23.58 14.63 0.00 2.29
434 436 2.347452 ACAATCGTAGTTGCGCACATAC 59.653 45.455 11.12 15.28 32.32 2.39
441 443 0.734942 ACGGGACAATCGTAGTTGCG 60.735 55.000 0.00 0.00 39.22 4.85
450 452 2.083167 TTCGGTAACACGGGACAATC 57.917 50.000 0.00 0.00 0.00 2.67
455 457 3.474600 TCAAATTTTCGGTAACACGGGA 58.525 40.909 0.00 0.00 0.00 5.14
512 835 1.883021 CCTTGGGCCACGACAATTC 59.117 57.895 12.26 0.00 0.00 2.17
818 1153 4.162690 GAGCAACGGCCGGGATCT 62.163 66.667 31.76 19.86 42.56 2.75
827 1162 2.049156 TGTCGAGCTGAGCAACGG 60.049 61.111 19.63 1.71 33.43 4.44
828 1163 2.724708 GCTGTCGAGCTGAGCAACG 61.725 63.158 7.39 12.39 42.52 4.10
829 1164 1.224069 TTGCTGTCGAGCTGAGCAAC 61.224 55.000 7.39 2.23 45.46 4.17
830 1165 2.736531 TGCTGTCGAGCTGAGCAA 59.263 55.556 7.39 0.00 46.39 3.91
831 1166 1.665916 GTTGCTGTCGAGCTGAGCA 60.666 57.895 7.39 0.00 46.39 4.26
833 1168 2.091112 CGGTTGCTGTCGAGCTGAG 61.091 63.158 0.00 0.00 46.39 3.35
834 1169 2.049156 CGGTTGCTGTCGAGCTGA 60.049 61.111 0.00 0.00 46.39 4.26
842 1184 0.960364 CATACTTGGCCGGTTGCTGT 60.960 55.000 1.90 0.00 40.92 4.40
847 1189 2.579410 AAAGACATACTTGGCCGGTT 57.421 45.000 1.90 0.00 38.98 4.44
878 1220 8.667463 GCACTAAAAACCGTAAATTGATAGGTA 58.333 33.333 0.00 0.00 34.35 3.08
879 1221 7.175293 TGCACTAAAAACCGTAAATTGATAGGT 59.825 33.333 0.00 0.00 36.66 3.08
880 1222 7.531716 TGCACTAAAAACCGTAAATTGATAGG 58.468 34.615 0.00 0.00 0.00 2.57
881 1223 8.447833 TCTGCACTAAAAACCGTAAATTGATAG 58.552 33.333 0.00 0.00 0.00 2.08
887 1229 6.617879 GGATTCTGCACTAAAAACCGTAAAT 58.382 36.000 0.00 0.00 0.00 1.40
893 1235 2.817844 ACCGGATTCTGCACTAAAAACC 59.182 45.455 9.46 0.00 0.00 3.27
900 1242 2.154462 CTGAAAACCGGATTCTGCACT 58.846 47.619 9.46 0.00 0.00 4.40
901 1243 1.880027 ACTGAAAACCGGATTCTGCAC 59.120 47.619 21.87 5.55 31.26 4.57
902 1244 2.270352 ACTGAAAACCGGATTCTGCA 57.730 45.000 21.87 11.02 31.26 4.41
903 1245 4.394920 TGATAACTGAAAACCGGATTCTGC 59.605 41.667 21.87 12.12 31.26 4.26
904 1246 5.643777 AGTGATAACTGAAAACCGGATTCTG 59.356 40.000 9.46 17.71 33.49 3.02
1095 1443 0.385098 TATATTGACTCGTCGCGCGG 60.385 55.000 31.69 16.53 41.72 6.46
1115 1463 2.226437 GCAACCCGGCTCATTGTATATG 59.774 50.000 0.00 0.00 0.00 1.78
1116 1464 2.504367 GCAACCCGGCTCATTGTATAT 58.496 47.619 0.00 0.00 0.00 0.86
1117 1465 1.808512 CGCAACCCGGCTCATTGTATA 60.809 52.381 0.00 0.00 0.00 1.47
1118 1466 1.095228 CGCAACCCGGCTCATTGTAT 61.095 55.000 0.00 0.00 0.00 2.29
1119 1467 1.743623 CGCAACCCGGCTCATTGTA 60.744 57.895 0.00 0.00 0.00 2.41
1120 1468 3.055719 CGCAACCCGGCTCATTGT 61.056 61.111 0.00 0.00 0.00 2.71
1291 1639 6.071840 CGCTGGTAGAAGGAATAAGCTACTAT 60.072 42.308 0.00 0.00 34.95 2.12
1327 1676 8.514594 TCATTCATCAGTTCAACAACCTATTTC 58.485 33.333 0.00 0.00 32.22 2.17
1391 1744 8.619546 TCATATCATATCACATCAAAAACGCAA 58.380 29.630 0.00 0.00 0.00 4.85
1400 1753 8.118600 AGTAGGAGGTCATATCATATCACATCA 58.881 37.037 0.00 0.00 0.00 3.07
1401 1754 8.532186 AGTAGGAGGTCATATCATATCACATC 57.468 38.462 0.00 0.00 0.00 3.06
1402 1755 8.756927 CAAGTAGGAGGTCATATCATATCACAT 58.243 37.037 0.00 0.00 0.00 3.21
1403 1756 7.310052 GCAAGTAGGAGGTCATATCATATCACA 60.310 40.741 0.00 0.00 0.00 3.58
1404 1757 7.038659 GCAAGTAGGAGGTCATATCATATCAC 58.961 42.308 0.00 0.00 0.00 3.06
1409 1762 5.455326 GGTTGCAAGTAGGAGGTCATATCAT 60.455 44.000 0.00 0.00 0.00 2.45
1416 1769 2.152016 GTTGGTTGCAAGTAGGAGGTC 58.848 52.381 0.00 0.00 0.00 3.85
1419 1772 1.880027 GTGGTTGGTTGCAAGTAGGAG 59.120 52.381 0.00 0.00 0.00 3.69
1504 1889 9.929722 GATTAATCGATTAGCACATAACAACAA 57.070 29.630 16.89 0.84 0.00 2.83
1537 1922 7.072030 GCTTGACTACTTAAACACATGAGTTG 58.928 38.462 9.37 0.18 0.00 3.16
1556 1941 2.489938 TAGGACCCATGTTGCTTGAC 57.510 50.000 0.00 0.00 0.00 3.18
1562 1947 4.021102 ACAACTCTTAGGACCCATGTTG 57.979 45.455 0.00 0.00 39.11 3.33
1753 2138 1.168714 GAGGATCCCACAGCACAAAC 58.831 55.000 8.55 0.00 0.00 2.93
1771 2241 3.588210 ATTCTCCATGGTGATGCATGA 57.412 42.857 16.93 0.00 0.00 3.07
1813 2283 5.494390 TGATATATCAGCACTGCCTGAAT 57.506 39.130 11.49 1.97 44.34 2.57
1852 2322 6.183360 GCTACTGTGAGCAATGCATAACTTTA 60.183 38.462 8.35 0.00 42.36 1.85
2322 2820 5.643348 TCACACTTGCCAACTATATCAACTG 59.357 40.000 0.00 0.00 0.00 3.16
2361 2867 2.408271 TCAGATCCACATGCACCTTC 57.592 50.000 0.00 0.00 0.00 3.46
2419 2925 8.546083 ACTATTGTGAGGATTCAAGAGACTAT 57.454 34.615 6.55 0.00 36.69 2.12
2420 2926 7.962995 ACTATTGTGAGGATTCAAGAGACTA 57.037 36.000 6.55 0.00 36.69 2.59
2475 2991 3.710209 AGTGGGATGACAAGAGGAAAG 57.290 47.619 0.00 0.00 0.00 2.62
2479 2996 3.274288 GCTAAAGTGGGATGACAAGAGG 58.726 50.000 0.00 0.00 0.00 3.69
2562 3079 8.650490 ACCAAAACAGAAATGTAAATGGAGATT 58.350 29.630 11.61 0.00 0.00 2.40
2988 3508 1.815196 CAACAACTGCAACCAGCCA 59.185 52.632 0.00 0.00 43.02 4.75
3107 3652 4.720649 AAGCTGTACATCAGTCGTACAT 57.279 40.909 0.00 0.00 45.97 2.29
3180 3725 3.999001 CAGGGTAATCATGATGATCCACG 59.001 47.826 22.56 10.59 35.76 4.94
3207 3752 9.410556 GCTTGCTTTTCTTGTAGATATTTCAAA 57.589 29.630 0.00 0.00 0.00 2.69
3282 3827 5.105023 TGAGACAGCTGAATCATAAGAAGCT 60.105 40.000 23.35 0.00 44.83 3.74
3339 3884 4.528206 GGACCATTCACCAAAAGAAGGATT 59.472 41.667 0.00 0.00 0.00 3.01
3383 3928 8.893219 TGTGATATCCAATAAAAGTAGCAGAG 57.107 34.615 0.00 0.00 0.00 3.35
3445 3990 2.557056 GAGGGGAACAGTAAAACTTGGC 59.443 50.000 0.00 0.00 0.00 4.52
3692 4238 7.114754 TGCTAAATCTGAGAGACATGGAATTT 58.885 34.615 0.00 0.00 0.00 1.82
3891 4444 2.135933 GGGTTCTCAAACTCTGACACG 58.864 52.381 0.00 0.00 32.75 4.49
3924 4477 1.876799 CACGGATTGGTGTGCTTAACA 59.123 47.619 0.00 0.00 36.04 2.41
4002 4555 1.252904 CCCCAAATGCACTCACAGGG 61.253 60.000 0.00 0.00 33.22 4.45
4101 4655 1.820519 CATGGGCAGCAACACAACTAT 59.179 47.619 0.00 0.00 0.00 2.12
4145 4701 7.010460 CGCAATTCATGACTAACTGAGAATGTA 59.990 37.037 0.00 0.00 0.00 2.29
4147 4703 6.190264 CGCAATTCATGACTAACTGAGAATG 58.810 40.000 0.00 0.00 0.00 2.67
4162 4718 1.000233 TTGCCCCTCCGCAATTCAT 60.000 52.632 0.00 0.00 43.65 2.57
4329 4894 0.539051 CCTCAAGGATCCTCAGCGTT 59.461 55.000 16.52 0.00 37.39 4.84
4392 4957 3.950794 TTGAGCTAGCCAACCGCCG 62.951 63.158 12.13 0.00 38.78 6.46
4395 4960 0.320771 ACTGTTGAGCTAGCCAACCG 60.321 55.000 29.91 27.31 42.23 4.44
4411 4976 0.671251 GGGGCTAGATCGTCTGACTG 59.329 60.000 6.21 0.01 0.00 3.51
4416 4981 1.215673 TCTTCTGGGGCTAGATCGTCT 59.784 52.381 0.00 0.00 0.00 4.18
4596 5162 8.491331 ACAGTTGTATTGCAAACTGAAATTTT 57.509 26.923 27.51 8.33 39.03 1.82
4613 5179 3.766676 TTTTTGCTTGCGACAGTTGTA 57.233 38.095 0.00 0.00 0.00 2.41
4638 5205 2.338577 ACTGACAGCAGCAAGTCTTT 57.661 45.000 16.25 3.76 46.26 2.52
4641 5208 3.499918 ACAAATACTGACAGCAGCAAGTC 59.500 43.478 1.25 10.27 46.26 3.01
4883 5887 3.056465 GGGTTGTTGTTTTGTTCTCACCA 60.056 43.478 0.00 0.00 0.00 4.17
4901 5910 1.453197 GAATCGAATGGGCCGGGTT 60.453 57.895 2.18 0.00 0.00 4.11
4902 5911 2.192175 GAATCGAATGGGCCGGGT 59.808 61.111 2.18 0.00 0.00 5.28
4903 5912 2.972505 CGAATCGAATGGGCCGGG 60.973 66.667 2.18 0.00 0.00 5.73
4904 5913 2.108157 TCGAATCGAATGGGCCGG 59.892 61.111 1.57 0.00 31.06 6.13
4905 5914 2.244651 GGTCGAATCGAATGGGCCG 61.245 63.158 7.01 0.00 37.72 6.13
4906 5915 0.746563 TTGGTCGAATCGAATGGGCC 60.747 55.000 7.01 4.49 37.72 5.80
4907 5916 0.657840 CTTGGTCGAATCGAATGGGC 59.342 55.000 7.01 0.00 37.72 5.36
4932 5941 5.622460 CGAGTCAGTTTATCAGCCTGTAAGT 60.622 44.000 0.00 0.00 0.00 2.24
5186 6198 3.244770 TGGACTCAAAACCACCTGTATCC 60.245 47.826 0.00 0.00 0.00 2.59
5187 6199 4.015872 TGGACTCAAAACCACCTGTATC 57.984 45.455 0.00 0.00 0.00 2.24
5188 6200 4.141251 AGTTGGACTCAAAACCACCTGTAT 60.141 41.667 0.00 0.00 35.81 2.29
5190 6202 2.025321 AGTTGGACTCAAAACCACCTGT 60.025 45.455 0.00 0.00 35.81 4.00
5248 6287 4.497006 GGCTCAGCAATGTGATACAACATC 60.497 45.833 0.00 0.00 39.89 3.06
5278 6341 5.424252 CCTGACCTTAGTTATTACCCACTCA 59.576 44.000 0.00 0.00 0.00 3.41
5302 6365 0.323360 TAGCACATGGCCCTGGTTTC 60.323 55.000 13.03 0.00 46.50 2.78
5315 6391 5.408604 GCTTCTGCTTAGTTTAACTAGCACA 59.591 40.000 18.23 11.71 34.04 4.57
5316 6392 5.859557 GCTTCTGCTTAGTTTAACTAGCAC 58.140 41.667 18.23 8.70 34.04 4.40
5338 6414 3.123621 CGAGGTCTGAATACAAACACAGC 59.876 47.826 0.00 0.00 0.00 4.40
5430 6509 1.081892 CTGAAGGTTGCTGGTGATCG 58.918 55.000 0.00 0.00 0.00 3.69
5645 6724 3.621715 GGGAGTGAATAAAACTGGCTACG 59.378 47.826 0.00 0.00 0.00 3.51
5665 6744 4.873129 CGGATGTGCGGTCGAGGG 62.873 72.222 0.00 0.00 0.00 4.30
5792 6871 2.095213 CGCGCAAAATGGCTAAACTAGA 59.905 45.455 8.75 0.00 0.00 2.43
5859 6938 3.015293 GCCGAGCATGTCACACACG 62.015 63.158 0.00 0.00 0.00 4.49
5871 6950 1.457009 ATAGGAGAAGGACGCCGAGC 61.457 60.000 0.00 0.00 43.25 5.03


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

AutoCloner maintained by Alex Coulton.