Multiple sequence alignment - TraesCS3D01G040800

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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 TraesCS3D01G040800 chr3D 100.000 4556 0 0 1 4556 15398213 15393658 0.000000e+00 8414.0
1 TraesCS3D01G040800 chr3D 84.943 1853 189 45 2249 4052 15372591 15370780 0.000000e+00 1794.0
2 TraesCS3D01G040800 chr3D 83.759 1293 171 34 2279 3561 15348878 15347615 0.000000e+00 1188.0
3 TraesCS3D01G040800 chr3D 86.997 969 105 11 986 1936 15373890 15372925 0.000000e+00 1072.0
4 TraesCS3D01G040800 chr3D 85.526 380 39 11 208 578 523940248 523939876 2.570000e-102 383.0
5 TraesCS3D01G040800 chr3D 86.747 249 27 5 2271 2517 15388176 15387932 5.810000e-69 272.0
6 TraesCS3D01G040800 chr3D 83.902 205 12 9 577 772 15374278 15374086 4.680000e-40 176.0
7 TraesCS3D01G040800 chr3A 95.292 3653 109 22 706 4308 20834148 20837787 0.000000e+00 5734.0
8 TraesCS3D01G040800 chr3A 87.476 1589 150 28 2249 3802 20896859 20898433 0.000000e+00 1786.0
9 TraesCS3D01G040800 chr3A 86.204 1167 121 20 986 2115 20895582 20896745 0.000000e+00 1227.0
10 TraesCS3D01G040800 chr3A 83.604 1293 175 26 2278 3561 20933816 20935080 0.000000e+00 1179.0
11 TraesCS3D01G040800 chr3A 95.154 227 8 1 1 227 20832727 20832950 5.610000e-94 355.0
12 TraesCS3D01G040800 chr3A 92.308 247 14 4 4315 4556 20838060 20838306 3.370000e-91 346.0
13 TraesCS3D01G040800 chr3A 88.060 201 16 2 578 770 20895127 20895327 9.860000e-57 231.0
14 TraesCS3D01G040800 chr3A 86.243 189 7 3 685 861 20833111 20833292 2.160000e-43 187.0
15 TraesCS3D01G040800 chr3A 94.915 118 6 0 601 718 20833882 20833999 7.780000e-43 185.0
16 TraesCS3D01G040800 chr3A 90.265 113 8 1 114 226 20833776 20833885 1.320000e-30 145.0
17 TraesCS3D01G040800 chr3A 86.885 122 8 4 2 121 20874494 20874609 3.700000e-26 130.0
18 TraesCS3D01G040800 chr3A 96.000 75 3 0 43 117 20833431 20833505 6.190000e-24 122.0
19 TraesCS3D01G040800 chr3A 95.312 64 2 1 858 920 20833336 20833399 2.900000e-17 100.0
20 TraesCS3D01G040800 chr3A 98.077 52 1 0 591 642 20833053 20833104 1.750000e-14 91.6
21 TraesCS3D01G040800 chr3A 92.857 56 4 0 1550 1605 20937397 20937452 1.050000e-11 82.4
22 TraesCS3D01G040800 chr3B 84.978 1824 192 47 2278 4052 22511868 22513658 0.000000e+00 1775.0
23 TraesCS3D01G040800 chr3B 86.723 1175 117 23 975 2115 22510560 22511729 0.000000e+00 1269.0
24 TraesCS3D01G040800 chr3B 83.836 1293 166 29 2278 3561 22473319 22472061 0.000000e+00 1190.0
25 TraesCS3D01G040800 chr3B 80.887 1465 210 50 2280 3697 22345332 22343891 0.000000e+00 1090.0
26 TraesCS3D01G040800 chr3B 81.513 1163 167 29 989 2115 22349067 22347917 0.000000e+00 913.0
27 TraesCS3D01G040800 chr3B 84.572 538 76 6 986 1518 22506538 22507073 1.120000e-145 527.0
28 TraesCS3D01G040800 chr3B 84.073 383 43 15 208 580 699268197 699267823 2.020000e-93 353.0
29 TraesCS3D01G040800 chr3B 92.105 114 9 0 597 710 22502588 22502701 1.310000e-35 161.0
30 TraesCS3D01G040800 chr3B 93.103 58 4 0 1548 1605 22460885 22460828 8.120000e-13 86.1
31 TraesCS3D01G040800 chr4A 85.622 925 111 15 2649 3561 611269511 611268597 0.000000e+00 952.0
32 TraesCS3D01G040800 chr4A 74.728 368 65 18 1771 2115 722324596 722324958 6.150000e-29 139.0
33 TraesCS3D01G040800 chr5D 84.712 955 122 20 2620 3561 558346861 558345918 0.000000e+00 933.0
34 TraesCS3D01G040800 chr5D 80.695 777 121 13 1028 1779 558348789 558348017 1.100000e-160 577.0
35 TraesCS3D01G040800 chr5D 85.904 376 39 9 209 577 67871357 67871725 5.530000e-104 388.0
36 TraesCS3D01G040800 chr5B 83.112 977 119 33 2621 3561 704302974 704303940 0.000000e+00 848.0
37 TraesCS3D01G040800 chr5B 80.402 796 120 26 1017 1779 704301328 704302120 1.420000e-159 573.0
38 TraesCS3D01G040800 chr6A 78.767 1314 228 41 2277 3556 528359723 528361019 0.000000e+00 833.0
39 TraesCS3D01G040800 chr2B 85.752 379 41 8 208 578 51674683 51675056 5.530000e-104 388.0
40 TraesCS3D01G040800 chr2B 84.225 374 52 4 209 577 749825119 749824748 1.560000e-94 357.0
41 TraesCS3D01G040800 chr5A 84.840 376 46 9 209 577 19634087 19633716 7.200000e-98 368.0
42 TraesCS3D01G040800 chr6D 84.635 384 42 13 203 577 99213962 99213587 2.590000e-97 366.0
43 TraesCS3D01G040800 chr1D 84.840 376 43 12 210 578 74410060 74409692 2.590000e-97 366.0
44 TraesCS3D01G040800 chr1A 84.127 378 46 11 209 577 556140878 556141250 2.020000e-93 353.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G040800 chr3D 15393658 15398213 4555 True 8414.000000 8414 100.000000 1 4556 1 chr3D.!!$R3 4555
1 TraesCS3D01G040800 chr3D 15347615 15348878 1263 True 1188.000000 1188 83.759000 2279 3561 1 chr3D.!!$R1 1282
2 TraesCS3D01G040800 chr3D 15370780 15374278 3498 True 1014.000000 1794 85.280667 577 4052 3 chr3D.!!$R5 3475
3 TraesCS3D01G040800 chr3A 20895127 20898433 3306 False 1081.333333 1786 87.246667 578 3802 3 chr3A.!!$F3 3224
4 TraesCS3D01G040800 chr3A 20832727 20838306 5579 False 807.288889 5734 93.729556 1 4556 9 chr3A.!!$F2 4555
5 TraesCS3D01G040800 chr3A 20933816 20937452 3636 False 630.700000 1179 88.230500 1550 3561 2 chr3A.!!$F4 2011
6 TraesCS3D01G040800 chr3B 22472061 22473319 1258 True 1190.000000 1190 83.836000 2278 3561 1 chr3B.!!$R2 1283
7 TraesCS3D01G040800 chr3B 22343891 22349067 5176 True 1001.500000 1090 81.200000 989 3697 2 chr3B.!!$R4 2708
8 TraesCS3D01G040800 chr3B 22502588 22513658 11070 False 933.000000 1775 87.094500 597 4052 4 chr3B.!!$F1 3455
9 TraesCS3D01G040800 chr4A 611268597 611269511 914 True 952.000000 952 85.622000 2649 3561 1 chr4A.!!$R1 912
10 TraesCS3D01G040800 chr5D 558345918 558348789 2871 True 755.000000 933 82.703500 1028 3561 2 chr5D.!!$R1 2533
11 TraesCS3D01G040800 chr5B 704301328 704303940 2612 False 710.500000 848 81.757000 1017 3561 2 chr5B.!!$F1 2544
12 TraesCS3D01G040800 chr6A 528359723 528361019 1296 False 833.000000 833 78.767000 2277 3556 1 chr6A.!!$F1 1279

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
255 256 0.101759 GCAACCAGCTATGCCATGTG 59.898 55.0 6.99 0.0 41.15 3.21 F
543 544 0.179059 TGCGCACAACTTCCTCTCAA 60.179 50.0 5.66 0.0 0.00 3.02 F
1443 10133 0.390603 CCCGCATCGTCAACCTTACA 60.391 55.0 0.00 0.0 0.00 2.41 F
2434 13823 0.035881 TCTTGGGCTGTTGCTCTCAG 59.964 55.0 0.00 0.0 41.13 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 10385 1.941325 GGGCACCGTAGAAATGAGAG 58.059 55.000 0.0 0.0 40.86 3.20 R
2374 13763 1.020437 GGAGTTTGGCTATGAGCTGC 58.980 55.000 0.0 0.0 41.99 5.25 R
2721 14167 2.357637 TGCTACGCCTTCAATTATTGCC 59.642 45.455 0.0 0.0 0.00 4.52 R
4344 16713 0.321122 CCTTCGCCATCTCATAGCCC 60.321 60.000 0.0 0.0 0.00 5.19 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
138 139 2.464157 ATCTATTCTAGCAAGCCGGC 57.536 50.000 21.89 21.89 0.00 6.13
179 180 3.191162 CCTCCAATTCACGAAATTCAGCA 59.809 43.478 0.00 0.00 35.32 4.41
182 183 3.861113 CCAATTCACGAAATTCAGCATGG 59.139 43.478 0.00 0.00 35.32 3.66
187 188 1.067635 ACGAAATTCAGCATGGTTGGC 60.068 47.619 0.00 0.00 36.16 4.52
200 201 1.134694 GTTGGCGCCTTGATCGTTC 59.865 57.895 29.70 3.49 0.00 3.95
214 215 9.313118 GCCTTGATCGTTCCAAAATAATTAAAT 57.687 29.630 0.00 0.00 0.00 1.40
229 230 9.607285 AAATAATTAAATCCATTAAGCTACGCG 57.393 29.630 3.53 3.53 36.94 6.01
230 231 6.613755 AATTAAATCCATTAAGCTACGCGT 57.386 33.333 19.17 19.17 36.94 6.01
231 232 3.944422 AAATCCATTAAGCTACGCGTG 57.056 42.857 24.59 13.17 0.00 5.34
232 233 2.882927 ATCCATTAAGCTACGCGTGA 57.117 45.000 24.59 7.36 0.00 4.35
233 234 2.658373 TCCATTAAGCTACGCGTGAA 57.342 45.000 24.59 8.37 0.00 3.18
235 236 1.593006 CCATTAAGCTACGCGTGAAGG 59.407 52.381 24.59 10.35 0.00 3.46
236 237 1.593006 CATTAAGCTACGCGTGAAGGG 59.407 52.381 24.59 7.77 38.93 3.95
239 240 2.725203 AAGCTACGCGTGAAGGGCAA 62.725 55.000 24.59 0.00 36.05 4.52
240 241 3.023591 GCTACGCGTGAAGGGCAAC 62.024 63.158 24.59 0.00 36.05 4.17
254 255 2.496942 GCAACCAGCTATGCCATGT 58.503 52.632 6.99 0.00 41.15 3.21
255 256 0.101759 GCAACCAGCTATGCCATGTG 59.898 55.000 6.99 0.00 41.15 3.21
256 257 0.742505 CAACCAGCTATGCCATGTGG 59.257 55.000 0.00 0.00 38.53 4.17
276 277 4.047059 CAAGCTGGTTGGCCGCAG 62.047 66.667 11.59 0.00 36.97 5.18
277 278 4.586235 AAGCTGGTTGGCCGCAGT 62.586 61.111 0.00 0.00 36.97 4.40
280 281 3.052082 CTGGTTGGCCGCAGTGAG 61.052 66.667 0.00 0.00 37.67 3.51
282 283 2.281484 GGTTGGCCGCAGTGAGAA 60.281 61.111 0.00 0.00 0.00 2.87
283 284 1.675641 GGTTGGCCGCAGTGAGAAT 60.676 57.895 0.00 0.00 0.00 2.40
286 287 1.000274 GTTGGCCGCAGTGAGAATTTT 60.000 47.619 0.00 0.00 0.00 1.82
287 288 1.327303 TGGCCGCAGTGAGAATTTTT 58.673 45.000 0.00 0.00 0.00 1.94
360 361 7.687941 TCATTTTTAGATGAAAGTGAGGACC 57.312 36.000 0.00 0.00 32.50 4.46
361 362 7.461749 TCATTTTTAGATGAAAGTGAGGACCT 58.538 34.615 0.00 0.00 32.50 3.85
362 363 7.607991 TCATTTTTAGATGAAAGTGAGGACCTC 59.392 37.037 15.13 15.13 32.50 3.85
363 364 6.688073 TTTTAGATGAAAGTGAGGACCTCT 57.312 37.500 22.14 1.52 0.00 3.69
364 365 5.667539 TTAGATGAAAGTGAGGACCTCTG 57.332 43.478 22.14 0.00 0.00 3.35
365 366 3.784178 AGATGAAAGTGAGGACCTCTGA 58.216 45.455 22.14 0.00 0.00 3.27
366 367 4.360889 AGATGAAAGTGAGGACCTCTGAT 58.639 43.478 22.14 1.56 0.00 2.90
367 368 5.523588 AGATGAAAGTGAGGACCTCTGATA 58.476 41.667 22.14 0.00 0.00 2.15
368 369 6.142498 AGATGAAAGTGAGGACCTCTGATAT 58.858 40.000 22.14 9.15 0.00 1.63
369 370 6.614906 AGATGAAAGTGAGGACCTCTGATATT 59.385 38.462 22.14 10.02 0.00 1.28
370 371 6.627087 TGAAAGTGAGGACCTCTGATATTT 57.373 37.500 22.14 14.22 0.00 1.40
371 372 7.020827 TGAAAGTGAGGACCTCTGATATTTT 57.979 36.000 22.14 10.74 0.00 1.82
372 373 7.461749 TGAAAGTGAGGACCTCTGATATTTTT 58.538 34.615 22.14 11.18 0.00 1.94
395 396 9.921637 TTTTTAAATAGAGGGTTATGCAAAGTG 57.078 29.630 0.00 0.00 0.00 3.16
396 397 7.639113 TTAAATAGAGGGTTATGCAAAGTGG 57.361 36.000 0.00 0.00 0.00 4.00
397 398 1.839424 AGAGGGTTATGCAAAGTGGC 58.161 50.000 0.00 0.00 0.00 5.01
404 405 2.203195 TGCAAAGTGGCACTCGCT 60.203 55.556 30.33 12.89 39.25 4.93
406 407 1.370900 GCAAAGTGGCACTCGCTTG 60.371 57.895 26.14 23.55 44.63 4.01
407 408 2.024918 CAAAGTGGCACTCGCTTGT 58.975 52.632 22.31 0.07 44.63 3.16
408 409 1.225855 CAAAGTGGCACTCGCTTGTA 58.774 50.000 22.31 0.00 44.63 2.41
409 410 1.195448 CAAAGTGGCACTCGCTTGTAG 59.805 52.381 22.31 1.23 44.63 2.74
410 411 0.320771 AAGTGGCACTCGCTTGTAGG 60.321 55.000 22.31 0.00 43.82 3.18
411 412 2.047274 TGGCACTCGCTTGTAGGC 60.047 61.111 0.00 0.00 38.60 3.93
412 413 2.266055 GGCACTCGCTTGTAGGCT 59.734 61.111 0.00 0.00 38.60 4.58
413 414 1.811679 GGCACTCGCTTGTAGGCTC 60.812 63.158 0.00 0.00 38.60 4.70
414 415 1.216710 GCACTCGCTTGTAGGCTCT 59.783 57.895 0.00 0.00 34.30 4.09
415 416 1.080995 GCACTCGCTTGTAGGCTCTG 61.081 60.000 0.00 0.00 34.30 3.35
416 417 0.459237 CACTCGCTTGTAGGCTCTGG 60.459 60.000 0.00 0.00 0.00 3.86
417 418 0.900647 ACTCGCTTGTAGGCTCTGGT 60.901 55.000 0.00 0.00 0.00 4.00
418 419 0.459237 CTCGCTTGTAGGCTCTGGTG 60.459 60.000 0.00 0.00 0.00 4.17
419 420 1.448540 CGCTTGTAGGCTCTGGTGG 60.449 63.158 0.00 0.00 0.00 4.61
420 421 1.679898 GCTTGTAGGCTCTGGTGGT 59.320 57.895 0.00 0.00 0.00 4.16
421 422 0.902531 GCTTGTAGGCTCTGGTGGTA 59.097 55.000 0.00 0.00 0.00 3.25
422 423 1.278127 GCTTGTAGGCTCTGGTGGTAA 59.722 52.381 0.00 0.00 0.00 2.85
423 424 2.092914 GCTTGTAGGCTCTGGTGGTAAT 60.093 50.000 0.00 0.00 0.00 1.89
424 425 3.622455 GCTTGTAGGCTCTGGTGGTAATT 60.622 47.826 0.00 0.00 0.00 1.40
425 426 4.589908 CTTGTAGGCTCTGGTGGTAATTT 58.410 43.478 0.00 0.00 0.00 1.82
426 427 4.650972 TGTAGGCTCTGGTGGTAATTTT 57.349 40.909 0.00 0.00 0.00 1.82
427 428 4.993028 TGTAGGCTCTGGTGGTAATTTTT 58.007 39.130 0.00 0.00 0.00 1.94
497 498 2.358939 TTTTAGACGGAGGCGAGAAC 57.641 50.000 0.00 0.00 0.00 3.01
498 499 1.542492 TTTAGACGGAGGCGAGAACT 58.458 50.000 0.00 0.00 0.00 3.01
499 500 1.093159 TTAGACGGAGGCGAGAACTC 58.907 55.000 0.00 0.00 0.00 3.01
500 501 0.252479 TAGACGGAGGCGAGAACTCT 59.748 55.000 0.00 0.00 35.34 3.24
501 502 0.252479 AGACGGAGGCGAGAACTCTA 59.748 55.000 0.00 0.00 35.34 2.43
502 503 1.134037 AGACGGAGGCGAGAACTCTAT 60.134 52.381 0.00 0.00 35.34 1.98
503 504 1.002251 GACGGAGGCGAGAACTCTATG 60.002 57.143 0.00 0.00 35.34 2.23
504 505 1.025812 CGGAGGCGAGAACTCTATGT 58.974 55.000 0.00 0.00 35.34 2.29
505 506 1.268794 CGGAGGCGAGAACTCTATGTG 60.269 57.143 0.00 0.00 35.34 3.21
506 507 1.751924 GGAGGCGAGAACTCTATGTGT 59.248 52.381 0.00 0.00 35.34 3.72
507 508 2.166664 GGAGGCGAGAACTCTATGTGTT 59.833 50.000 0.00 0.00 35.34 3.32
508 509 3.368531 GGAGGCGAGAACTCTATGTGTTT 60.369 47.826 0.00 0.00 35.34 2.83
509 510 4.246458 GAGGCGAGAACTCTATGTGTTTT 58.754 43.478 0.00 0.00 32.28 2.43
510 511 4.642429 AGGCGAGAACTCTATGTGTTTTT 58.358 39.130 0.00 0.00 0.00 1.94
531 532 4.469625 TTTTAAATAGAACGTGCGCACA 57.530 36.364 37.03 20.07 0.00 4.57
532 533 4.469625 TTTAAATAGAACGTGCGCACAA 57.530 36.364 37.03 19.20 0.00 3.33
533 534 2.309898 AAATAGAACGTGCGCACAAC 57.690 45.000 37.03 26.12 0.00 3.32
534 535 1.508632 AATAGAACGTGCGCACAACT 58.491 45.000 37.03 30.48 0.00 3.16
535 536 1.508632 ATAGAACGTGCGCACAACTT 58.491 45.000 37.03 24.75 0.00 2.66
536 537 0.856641 TAGAACGTGCGCACAACTTC 59.143 50.000 37.03 29.89 0.00 3.01
537 538 1.368850 GAACGTGCGCACAACTTCC 60.369 57.895 37.03 17.02 0.00 3.46
538 539 1.772063 GAACGTGCGCACAACTTCCT 61.772 55.000 37.03 14.48 0.00 3.36
539 540 1.772063 AACGTGCGCACAACTTCCTC 61.772 55.000 37.03 10.05 0.00 3.71
540 541 1.956170 CGTGCGCACAACTTCCTCT 60.956 57.895 37.03 0.00 0.00 3.69
541 542 1.862806 GTGCGCACAACTTCCTCTC 59.137 57.895 34.52 2.71 0.00 3.20
542 543 0.880278 GTGCGCACAACTTCCTCTCA 60.880 55.000 34.52 0.00 0.00 3.27
543 544 0.179059 TGCGCACAACTTCCTCTCAA 60.179 50.000 5.66 0.00 0.00 3.02
544 545 0.514691 GCGCACAACTTCCTCTCAAG 59.485 55.000 0.30 0.00 0.00 3.02
545 546 0.514691 CGCACAACTTCCTCTCAAGC 59.485 55.000 0.00 0.00 0.00 4.01
546 547 0.514691 GCACAACTTCCTCTCAAGCG 59.485 55.000 0.00 0.00 0.00 4.68
547 548 1.151668 CACAACTTCCTCTCAAGCGG 58.848 55.000 0.00 0.00 0.00 5.52
548 549 0.759346 ACAACTTCCTCTCAAGCGGT 59.241 50.000 0.00 0.00 0.00 5.68
549 550 1.151668 CAACTTCCTCTCAAGCGGTG 58.848 55.000 0.00 0.00 0.00 4.94
550 551 0.603975 AACTTCCTCTCAAGCGGTGC 60.604 55.000 0.00 0.00 0.00 5.01
551 552 1.743252 CTTCCTCTCAAGCGGTGCC 60.743 63.158 0.00 0.00 0.00 5.01
552 553 2.454832 CTTCCTCTCAAGCGGTGCCA 62.455 60.000 0.00 0.00 0.00 4.92
553 554 2.731691 TTCCTCTCAAGCGGTGCCAC 62.732 60.000 0.00 0.00 0.00 5.01
554 555 2.031012 CTCTCAAGCGGTGCCACA 59.969 61.111 0.00 0.00 0.00 4.17
555 556 2.031012 TCTCAAGCGGTGCCACAG 59.969 61.111 0.00 0.00 0.00 3.66
556 557 3.052082 CTCAAGCGGTGCCACAGG 61.052 66.667 0.00 0.00 0.00 4.00
557 558 3.535629 CTCAAGCGGTGCCACAGGA 62.536 63.158 0.00 0.00 0.00 3.86
558 559 2.360350 CAAGCGGTGCCACAGGAT 60.360 61.111 0.00 0.00 0.00 3.24
559 560 2.360350 AAGCGGTGCCACAGGATG 60.360 61.111 0.00 0.00 46.00 3.51
560 561 2.894257 AAGCGGTGCCACAGGATGA 61.894 57.895 0.00 0.00 39.69 2.92
561 562 2.359850 GCGGTGCCACAGGATGAA 60.360 61.111 0.00 0.00 39.69 2.57
562 563 2.401766 GCGGTGCCACAGGATGAAG 61.402 63.158 0.00 0.00 39.69 3.02
563 564 2.401766 CGGTGCCACAGGATGAAGC 61.402 63.158 0.00 0.00 39.69 3.86
564 565 2.048603 GGTGCCACAGGATGAAGCC 61.049 63.158 0.00 0.00 39.69 4.35
565 566 2.048603 GTGCCACAGGATGAAGCCC 61.049 63.158 0.00 0.00 39.69 5.19
566 567 2.440980 GCCACAGGATGAAGCCCC 60.441 66.667 0.00 0.00 39.69 5.80
567 568 3.089838 CCACAGGATGAAGCCCCA 58.910 61.111 0.00 0.00 39.69 4.96
568 569 1.383799 CCACAGGATGAAGCCCCAA 59.616 57.895 0.00 0.00 39.69 4.12
569 570 0.967380 CCACAGGATGAAGCCCCAAC 60.967 60.000 0.00 0.00 39.69 3.77
570 571 0.967380 CACAGGATGAAGCCCCAACC 60.967 60.000 0.00 0.00 39.69 3.77
571 572 1.383799 CAGGATGAAGCCCCAACCA 59.616 57.895 5.31 0.00 39.69 3.67
572 573 0.967380 CAGGATGAAGCCCCAACCAC 60.967 60.000 5.31 0.00 39.69 4.16
573 574 1.142688 AGGATGAAGCCCCAACCACT 61.143 55.000 5.31 0.00 32.11 4.00
574 575 0.623723 GGATGAAGCCCCAACCACTA 59.376 55.000 0.00 0.00 0.00 2.74
575 576 1.408822 GGATGAAGCCCCAACCACTAG 60.409 57.143 0.00 0.00 0.00 2.57
576 577 1.282157 GATGAAGCCCCAACCACTAGT 59.718 52.381 0.00 0.00 0.00 2.57
579 580 2.916934 TGAAGCCCCAACCACTAGTAAT 59.083 45.455 0.00 0.00 0.00 1.89
632 633 3.181451 ACTGAAAGCAACTGAGATGACCA 60.181 43.478 0.00 0.00 37.60 4.02
830 2502 1.621672 GCTAGCTGGCTTGACCTCCT 61.622 60.000 15.78 0.00 40.22 3.69
920 9519 5.138276 ACTAGGACCGATAGTGATTTGCTA 58.862 41.667 0.00 0.00 32.27 3.49
921 9520 4.592485 AGGACCGATAGTGATTTGCTAG 57.408 45.455 0.00 0.00 0.00 3.42
922 9521 3.060602 GGACCGATAGTGATTTGCTAGC 58.939 50.000 8.10 8.10 0.00 3.42
959 9565 1.556911 ACCTTCGTTCATCATCTGGCT 59.443 47.619 0.00 0.00 0.00 4.75
999 9648 1.219393 GCTCGGCTGTTAGCTTCCT 59.781 57.895 0.00 0.00 41.99 3.36
1443 10133 0.390603 CCCGCATCGTCAACCTTACA 60.391 55.000 0.00 0.00 0.00 2.41
1695 10385 2.934553 GTGTTATTTCAGGTACGAGGCC 59.065 50.000 0.00 0.00 0.00 5.19
2122 11887 7.376615 GCTGTCTACAAGGTAAATCGGTATAT 58.623 38.462 0.00 0.00 0.00 0.86
2123 11888 7.541437 GCTGTCTACAAGGTAAATCGGTATATC 59.459 40.741 0.00 0.00 0.00 1.63
2125 11890 9.797642 TGTCTACAAGGTAAATCGGTATATCTA 57.202 33.333 0.00 0.00 0.00 1.98
2139 11904 9.765795 ATCGGTATATCTAAAAGGCTAATATGC 57.234 33.333 0.00 0.00 0.00 3.14
2221 13596 9.420551 GTAAATGGTAGAGGAGGATTAATTACG 57.579 37.037 0.00 0.00 0.00 3.18
2237 13624 9.486857 GATTAATTACGACAAGCCTAGTTTTTC 57.513 33.333 0.00 0.00 0.00 2.29
2272 13660 3.071874 TGAGCCTAACTTTGGACCATG 57.928 47.619 0.00 0.00 0.00 3.66
2274 13662 3.010420 GAGCCTAACTTTGGACCATGTC 58.990 50.000 0.00 0.00 0.00 3.06
2422 13811 1.852633 ATTTGGTTAGGCTCTTGGGC 58.147 50.000 0.00 0.00 41.20 5.36
2434 13823 0.035881 TCTTGGGCTGTTGCTCTCAG 59.964 55.000 0.00 0.00 41.13 3.35
2503 13892 6.772716 GCCTGGATTTCTTCATCTTTGGTATA 59.227 38.462 0.00 0.00 0.00 1.47
2504 13893 7.449704 GCCTGGATTTCTTCATCTTTGGTATAT 59.550 37.037 0.00 0.00 0.00 0.86
2721 14167 3.318839 TGCTGGATTGGACAAAACTTCTG 59.681 43.478 0.00 0.00 0.00 3.02
2925 14371 6.054860 AGAAGAGTTGTTGGCACATAGTAT 57.945 37.500 0.00 0.00 39.30 2.12
3015 14473 8.671384 TGACACTTACCATATACCATTTTAGC 57.329 34.615 0.00 0.00 0.00 3.09
3176 14634 8.504815 CAATCTTCTTGGATATGTGAGCTTATG 58.495 37.037 0.00 0.00 0.00 1.90
3561 15064 8.035394 TCTATCACAAGTCCAAGATAGTGTTTC 58.965 37.037 0.00 0.00 40.34 2.78
3577 15095 4.272504 AGTGTTTCTGTGTATTGTCCGTTG 59.727 41.667 0.00 0.00 0.00 4.10
3594 15112 3.062909 CCGTTGGTAATACATTCACACCG 59.937 47.826 0.00 0.00 31.64 4.94
3640 15161 8.726988 TGTTAGTTTAAGTGGTATCTCAAATGC 58.273 33.333 0.00 0.00 0.00 3.56
3831 15400 0.740149 TGGATCGTGCCAAATGATGC 59.260 50.000 0.00 0.00 41.69 3.91
3841 15410 4.035558 GTGCCAAATGATGCTTCGATTCTA 59.964 41.667 0.00 0.00 0.00 2.10
3855 15424 7.389330 TGCTTCGATTCTATTAAGTTGTTCCAA 59.611 33.333 0.00 0.00 0.00 3.53
3881 15450 8.980832 AGATAATGATTTGGTATCTAGGGAGT 57.019 34.615 0.00 0.00 33.74 3.85
3888 15457 6.360370 TTTGGTATCTAGGGAGTATGATGC 57.640 41.667 0.00 0.00 0.00 3.91
3889 15458 5.276694 TGGTATCTAGGGAGTATGATGCT 57.723 43.478 0.00 0.00 0.00 3.79
3908 15486 5.385509 TGCTTGGCTATAAAAAGAACACC 57.614 39.130 0.00 0.00 0.00 4.16
3916 15494 7.502895 TGGCTATAAAAAGAACACCACAAACTA 59.497 33.333 0.00 0.00 0.00 2.24
4041 15628 0.527565 CCGGCTTTTGTTCCTCCATG 59.472 55.000 0.00 0.00 0.00 3.66
4079 15666 3.244249 GGCAGGTACATGAATCCTCTACC 60.244 52.174 12.53 0.00 0.00 3.18
4081 15668 3.889538 CAGGTACATGAATCCTCTACCGA 59.110 47.826 0.00 0.00 33.39 4.69
4083 15670 3.305471 GGTACATGAATCCTCTACCGAGC 60.305 52.174 0.00 0.00 35.90 5.03
4085 15672 1.609072 CATGAATCCTCTACCGAGCGA 59.391 52.381 0.00 0.00 35.90 4.93
4122 15709 8.847196 GTTCCTTGTACTAAGATTGGTTTTCTT 58.153 33.333 0.00 0.00 37.25 2.52
4123 15710 8.391075 TCCTTGTACTAAGATTGGTTTTCTTG 57.609 34.615 0.00 0.00 35.19 3.02
4156 15743 7.566569 TCCAAATATCGTATGGGTAGTTTTCA 58.433 34.615 0.00 0.00 34.89 2.69
4188 15775 4.587976 TTAGAGTACAGCTAGGTGAGGT 57.412 45.455 27.87 11.18 35.84 3.85
4213 15800 5.305675 TCTAGAAGGCCCCTTGGATATAT 57.694 43.478 3.91 0.00 36.26 0.86
4215 15802 6.444704 TCTAGAAGGCCCCTTGGATATATAG 58.555 44.000 3.91 0.00 36.26 1.31
4223 15810 6.670902 GGCCCCTTGGATATATAGTAGTTGTA 59.329 42.308 0.00 0.00 0.00 2.41
4258 15845 9.039870 GTAGTCAGATTGATTCTATCTTTGGTG 57.960 37.037 7.74 0.00 31.77 4.17
4261 15848 7.550551 GTCAGATTGATTCTATCTTTGGTGTCA 59.449 37.037 7.74 0.00 31.77 3.58
4289 15876 5.377358 GTTTGTTGAGATGAAGATGTGTCG 58.623 41.667 0.00 0.00 0.00 4.35
4295 15882 6.267496 TGAGATGAAGATGTGTCGAGTTAA 57.733 37.500 0.00 0.00 0.00 2.01
4300 15887 8.633561 AGATGAAGATGTGTCGAGTTAATCATA 58.366 33.333 0.00 0.00 0.00 2.15
4302 15889 6.697455 TGAAGATGTGTCGAGTTAATCATAGC 59.303 38.462 0.00 0.00 0.00 2.97
4308 15895 3.997021 GTCGAGTTAATCATAGCCATGGG 59.003 47.826 15.13 0.00 32.61 4.00
4309 15896 3.901222 TCGAGTTAATCATAGCCATGGGA 59.099 43.478 15.13 1.87 32.61 4.37
4310 15897 4.346709 TCGAGTTAATCATAGCCATGGGAA 59.653 41.667 15.13 0.00 32.61 3.97
4311 15898 5.063204 CGAGTTAATCATAGCCATGGGAAA 58.937 41.667 15.13 0.00 32.61 3.13
4312 15899 5.530915 CGAGTTAATCATAGCCATGGGAAAA 59.469 40.000 15.13 0.00 32.61 2.29
4313 15900 6.293626 CGAGTTAATCATAGCCATGGGAAAAG 60.294 42.308 15.13 0.00 32.61 2.27
4342 16711 0.390472 GGAGTGGGACGAAAGCAGAG 60.390 60.000 0.00 0.00 0.00 3.35
4344 16713 1.376037 GTGGGACGAAAGCAGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
4366 16735 1.051812 CTATGAGATGGCGAAGGGGT 58.948 55.000 0.00 0.00 0.00 4.95
4400 17361 2.401583 TGGGTGATGTCCGAAATCAG 57.598 50.000 1.09 0.00 34.78 2.90
4403 17364 3.262151 TGGGTGATGTCCGAAATCAGTTA 59.738 43.478 1.09 0.00 34.78 2.24
4407 17368 5.235186 GGTGATGTCCGAAATCAGTTATCTG 59.765 44.000 1.09 0.00 42.54 2.90
4435 17396 5.416271 ACGACTTTGAATTAGGCTTCCTA 57.584 39.130 0.00 0.00 34.61 2.94
4470 17432 5.416952 TCCCATTTGTTGTTGTGCAAATTTT 59.583 32.000 0.00 0.00 41.62 1.82
4482 17446 7.600375 TGTTGTGCAAATTTTGTTGTTCTTCTA 59.400 29.630 10.65 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.109597 CTGGCCTGCACAAATTCGTC 60.110 55.000 3.32 0.00 0.00 4.20
75 76 2.185004 AAGCATGCACTTAGTTCGGT 57.815 45.000 21.98 0.00 0.00 4.69
78 79 4.756084 AGACAAAGCATGCACTTAGTTC 57.244 40.909 21.98 9.50 0.00 3.01
138 139 1.197721 GGTTCCACTTGCACTTGATCG 59.802 52.381 0.00 0.00 0.00 3.69
179 180 2.114670 CGATCAAGGCGCCAACCAT 61.115 57.895 31.54 14.70 0.00 3.55
182 183 1.134694 GAACGATCAAGGCGCCAAC 59.865 57.895 31.54 13.32 0.00 3.77
187 188 2.919666 ATTTTGGAACGATCAAGGCG 57.080 45.000 0.00 0.00 0.00 5.52
227 228 4.043200 GCTGGTTGCCCTTCACGC 62.043 66.667 0.00 0.00 35.15 5.34
229 230 1.098050 CATAGCTGGTTGCCCTTCAC 58.902 55.000 0.00 0.00 44.23 3.18
230 231 0.680921 GCATAGCTGGTTGCCCTTCA 60.681 55.000 0.00 0.00 44.23 3.02
231 232 2.110296 GCATAGCTGGTTGCCCTTC 58.890 57.895 0.00 0.00 44.23 3.46
232 233 4.344237 GCATAGCTGGTTGCCCTT 57.656 55.556 0.00 0.00 44.23 3.95
236 237 0.101759 CACATGGCATAGCTGGTTGC 59.898 55.000 0.00 2.72 43.29 4.17
239 240 4.993307 CCACATGGCATAGCTGGT 57.007 55.556 0.00 0.00 0.00 4.00
249 250 4.124351 CCAGCTTGCGCCACATGG 62.124 66.667 4.18 4.49 36.60 3.66
251 252 2.598394 AACCAGCTTGCGCCACAT 60.598 55.556 4.18 0.00 36.60 3.21
252 253 3.594775 CAACCAGCTTGCGCCACA 61.595 61.111 4.18 0.00 36.60 4.17
253 254 4.347453 CCAACCAGCTTGCGCCAC 62.347 66.667 4.18 0.00 36.60 5.01
259 260 4.047059 CTGCGGCCAACCAGCTTG 62.047 66.667 2.24 0.00 36.71 4.01
263 264 3.052082 CTCACTGCGGCCAACCAG 61.052 66.667 2.24 8.59 34.57 4.00
264 265 2.410322 ATTCTCACTGCGGCCAACCA 62.410 55.000 2.24 0.00 34.57 3.67
265 266 1.244019 AATTCTCACTGCGGCCAACC 61.244 55.000 2.24 0.00 0.00 3.77
267 268 1.327303 AAAATTCTCACTGCGGCCAA 58.673 45.000 2.24 0.00 0.00 4.52
268 269 1.327303 AAAAATTCTCACTGCGGCCA 58.673 45.000 2.24 0.00 0.00 5.36
335 336 7.944554 AGGTCCTCACTTTCATCTAAAAATGAA 59.055 33.333 0.00 0.00 42.42 2.57
336 337 7.461749 AGGTCCTCACTTTCATCTAAAAATGA 58.538 34.615 0.00 0.00 33.88 2.57
337 338 7.609532 AGAGGTCCTCACTTTCATCTAAAAATG 59.390 37.037 21.26 0.00 32.06 2.32
338 339 7.609532 CAGAGGTCCTCACTTTCATCTAAAAAT 59.390 37.037 21.26 0.00 32.06 1.82
339 340 6.936900 CAGAGGTCCTCACTTTCATCTAAAAA 59.063 38.462 21.26 0.00 32.06 1.94
340 341 6.270000 TCAGAGGTCCTCACTTTCATCTAAAA 59.730 38.462 21.26 0.00 32.06 1.52
341 342 5.780282 TCAGAGGTCCTCACTTTCATCTAAA 59.220 40.000 21.26 0.00 32.06 1.85
342 343 5.333581 TCAGAGGTCCTCACTTTCATCTAA 58.666 41.667 21.26 0.00 32.06 2.10
343 344 4.935578 TCAGAGGTCCTCACTTTCATCTA 58.064 43.478 21.26 0.00 32.06 1.98
344 345 3.784178 TCAGAGGTCCTCACTTTCATCT 58.216 45.455 21.26 0.00 32.06 2.90
345 346 4.751767 ATCAGAGGTCCTCACTTTCATC 57.248 45.455 21.26 0.00 32.06 2.92
346 347 6.821616 AATATCAGAGGTCCTCACTTTCAT 57.178 37.500 21.26 5.74 32.06 2.57
347 348 6.627087 AAATATCAGAGGTCCTCACTTTCA 57.373 37.500 21.26 1.37 32.06 2.69
348 349 7.929941 AAAAATATCAGAGGTCCTCACTTTC 57.070 36.000 21.26 0.00 32.06 2.62
369 370 9.921637 CACTTTGCATAACCCTCTATTTAAAAA 57.078 29.630 0.00 0.00 0.00 1.94
370 371 8.527810 CCACTTTGCATAACCCTCTATTTAAAA 58.472 33.333 0.00 0.00 0.00 1.52
371 372 7.363443 GCCACTTTGCATAACCCTCTATTTAAA 60.363 37.037 0.00 0.00 0.00 1.52
372 373 6.096282 GCCACTTTGCATAACCCTCTATTTAA 59.904 38.462 0.00 0.00 0.00 1.52
373 374 5.592688 GCCACTTTGCATAACCCTCTATTTA 59.407 40.000 0.00 0.00 0.00 1.40
374 375 4.402474 GCCACTTTGCATAACCCTCTATTT 59.598 41.667 0.00 0.00 0.00 1.40
375 376 3.954258 GCCACTTTGCATAACCCTCTATT 59.046 43.478 0.00 0.00 0.00 1.73
376 377 3.053693 TGCCACTTTGCATAACCCTCTAT 60.054 43.478 0.00 0.00 36.04 1.98
377 378 2.307392 TGCCACTTTGCATAACCCTCTA 59.693 45.455 0.00 0.00 36.04 2.43
378 379 1.075374 TGCCACTTTGCATAACCCTCT 59.925 47.619 0.00 0.00 36.04 3.69
379 380 1.202348 GTGCCACTTTGCATAACCCTC 59.798 52.381 0.00 0.00 44.30 4.30
380 381 1.203050 AGTGCCACTTTGCATAACCCT 60.203 47.619 0.00 0.00 44.30 4.34
381 382 1.202348 GAGTGCCACTTTGCATAACCC 59.798 52.381 0.00 0.00 44.30 4.11
382 383 1.135689 CGAGTGCCACTTTGCATAACC 60.136 52.381 0.00 0.00 44.30 2.85
383 384 1.729149 GCGAGTGCCACTTTGCATAAC 60.729 52.381 15.52 0.00 44.30 1.89
384 385 0.521291 GCGAGTGCCACTTTGCATAA 59.479 50.000 15.52 0.00 44.30 1.90
385 386 0.321564 AGCGAGTGCCACTTTGCATA 60.322 50.000 20.52 0.00 44.30 3.14
386 387 1.174712 AAGCGAGTGCCACTTTGCAT 61.175 50.000 20.52 9.61 44.30 3.96
387 388 1.823470 AAGCGAGTGCCACTTTGCA 60.823 52.632 20.52 0.41 44.31 4.08
388 389 1.370900 CAAGCGAGTGCCACTTTGC 60.371 57.895 13.31 13.31 44.31 3.68
389 390 1.195448 CTACAAGCGAGTGCCACTTTG 59.805 52.381 0.00 2.29 44.31 2.77
390 391 1.512926 CTACAAGCGAGTGCCACTTT 58.487 50.000 0.00 0.00 44.31 2.66
391 392 0.320771 CCTACAAGCGAGTGCCACTT 60.321 55.000 0.00 0.00 44.31 3.16
392 393 1.293498 CCTACAAGCGAGTGCCACT 59.707 57.895 0.00 0.00 44.31 4.00
393 394 2.391389 GCCTACAAGCGAGTGCCAC 61.391 63.158 0.00 0.00 44.31 5.01
394 395 2.047274 GCCTACAAGCGAGTGCCA 60.047 61.111 0.00 0.00 44.31 4.92
395 396 1.811679 GAGCCTACAAGCGAGTGCC 60.812 63.158 0.00 0.00 44.31 5.01
396 397 1.080995 CAGAGCCTACAAGCGAGTGC 61.081 60.000 0.00 0.00 43.24 4.40
397 398 0.459237 CCAGAGCCTACAAGCGAGTG 60.459 60.000 0.00 0.00 38.01 3.51
398 399 0.900647 ACCAGAGCCTACAAGCGAGT 60.901 55.000 0.00 0.00 38.01 4.18
399 400 0.459237 CACCAGAGCCTACAAGCGAG 60.459 60.000 0.00 0.00 38.01 5.03
400 401 1.591703 CACCAGAGCCTACAAGCGA 59.408 57.895 0.00 0.00 38.01 4.93
401 402 1.448540 CCACCAGAGCCTACAAGCG 60.449 63.158 0.00 0.00 38.01 4.68
402 403 0.902531 TACCACCAGAGCCTACAAGC 59.097 55.000 0.00 0.00 0.00 4.01
403 404 3.914426 ATTACCACCAGAGCCTACAAG 57.086 47.619 0.00 0.00 0.00 3.16
404 405 4.650972 AAATTACCACCAGAGCCTACAA 57.349 40.909 0.00 0.00 0.00 2.41
405 406 4.650972 AAAATTACCACCAGAGCCTACA 57.349 40.909 0.00 0.00 0.00 2.74
477 478 2.298163 AGTTCTCGCCTCCGTCTAAAAA 59.702 45.455 0.00 0.00 35.54 1.94
478 479 1.891150 AGTTCTCGCCTCCGTCTAAAA 59.109 47.619 0.00 0.00 35.54 1.52
479 480 1.471684 GAGTTCTCGCCTCCGTCTAAA 59.528 52.381 0.00 0.00 35.54 1.85
480 481 1.093159 GAGTTCTCGCCTCCGTCTAA 58.907 55.000 0.00 0.00 35.54 2.10
481 482 0.252479 AGAGTTCTCGCCTCCGTCTA 59.748 55.000 0.00 0.00 35.54 2.59
482 483 0.252479 TAGAGTTCTCGCCTCCGTCT 59.748 55.000 0.00 0.00 35.54 4.18
483 484 1.002251 CATAGAGTTCTCGCCTCCGTC 60.002 57.143 0.00 0.00 35.54 4.79
484 485 1.025812 CATAGAGTTCTCGCCTCCGT 58.974 55.000 0.00 0.00 35.54 4.69
485 486 1.025812 ACATAGAGTTCTCGCCTCCG 58.974 55.000 0.00 0.00 0.00 4.63
486 487 1.751924 ACACATAGAGTTCTCGCCTCC 59.248 52.381 0.00 0.00 0.00 4.30
487 488 3.512033 AACACATAGAGTTCTCGCCTC 57.488 47.619 0.00 0.00 0.00 4.70
488 489 3.963428 AAACACATAGAGTTCTCGCCT 57.037 42.857 0.00 0.00 0.00 5.52
509 510 4.845387 TGTGCGCACGTTCTATTTAAAAA 58.155 34.783 33.22 9.66 0.00 1.94
510 511 4.469625 TGTGCGCACGTTCTATTTAAAA 57.530 36.364 33.22 10.12 0.00 1.52
511 512 4.024725 AGTTGTGCGCACGTTCTATTTAAA 60.025 37.500 33.22 16.28 0.00 1.52
512 513 3.495377 AGTTGTGCGCACGTTCTATTTAA 59.505 39.130 33.22 17.00 0.00 1.52
513 514 3.061322 AGTTGTGCGCACGTTCTATTTA 58.939 40.909 33.22 11.66 0.00 1.40
514 515 1.871039 AGTTGTGCGCACGTTCTATTT 59.129 42.857 33.22 11.47 0.00 1.40
515 516 1.508632 AGTTGTGCGCACGTTCTATT 58.491 45.000 33.22 12.99 0.00 1.73
516 517 1.459592 GAAGTTGTGCGCACGTTCTAT 59.540 47.619 33.22 18.07 0.00 1.98
517 518 0.856641 GAAGTTGTGCGCACGTTCTA 59.143 50.000 33.22 14.79 0.00 2.10
518 519 1.641677 GAAGTTGTGCGCACGTTCT 59.358 52.632 33.22 26.10 0.00 3.01
519 520 1.368850 GGAAGTTGTGCGCACGTTC 60.369 57.895 33.22 30.44 0.00 3.95
520 521 1.772063 GAGGAAGTTGTGCGCACGTT 61.772 55.000 33.22 25.65 0.00 3.99
521 522 2.203015 AGGAAGTTGTGCGCACGT 60.203 55.556 33.22 19.03 0.00 4.49
522 523 1.891060 GAGAGGAAGTTGTGCGCACG 61.891 60.000 33.22 0.00 0.00 5.34
523 524 0.880278 TGAGAGGAAGTTGTGCGCAC 60.880 55.000 33.11 33.11 0.00 5.34
524 525 0.179059 TTGAGAGGAAGTTGTGCGCA 60.179 50.000 5.66 5.66 0.00 6.09
525 526 0.514691 CTTGAGAGGAAGTTGTGCGC 59.485 55.000 0.00 0.00 0.00 6.09
526 527 0.514691 GCTTGAGAGGAAGTTGTGCG 59.485 55.000 0.00 0.00 0.00 5.34
527 528 0.514691 CGCTTGAGAGGAAGTTGTGC 59.485 55.000 0.00 0.00 0.00 4.57
528 529 1.151668 CCGCTTGAGAGGAAGTTGTG 58.848 55.000 0.00 0.00 37.14 3.33
529 530 0.759346 ACCGCTTGAGAGGAAGTTGT 59.241 50.000 7.82 0.00 38.45 3.32
530 531 1.151668 CACCGCTTGAGAGGAAGTTG 58.848 55.000 7.82 0.00 38.45 3.16
531 532 0.603975 GCACCGCTTGAGAGGAAGTT 60.604 55.000 7.82 0.00 38.45 2.66
532 533 1.004440 GCACCGCTTGAGAGGAAGT 60.004 57.895 7.82 0.00 38.45 3.01
533 534 1.743252 GGCACCGCTTGAGAGGAAG 60.743 63.158 7.82 1.41 38.45 3.46
534 535 2.347490 GGCACCGCTTGAGAGGAA 59.653 61.111 7.82 0.00 38.45 3.36
535 536 2.922503 TGGCACCGCTTGAGAGGA 60.923 61.111 7.82 0.00 38.45 3.71
536 537 2.743928 GTGGCACCGCTTGAGAGG 60.744 66.667 6.29 0.00 41.06 3.69
537 538 2.031012 TGTGGCACCGCTTGAGAG 59.969 61.111 16.26 0.00 0.00 3.20
538 539 2.031012 CTGTGGCACCGCTTGAGA 59.969 61.111 16.26 0.00 0.00 3.27
539 540 2.809861 ATCCTGTGGCACCGCTTGAG 62.810 60.000 16.26 4.21 0.00 3.02
540 541 2.894257 ATCCTGTGGCACCGCTTGA 61.894 57.895 16.26 4.73 0.00 3.02
541 542 2.360350 ATCCTGTGGCACCGCTTG 60.360 61.111 16.26 0.00 0.00 4.01
542 543 2.360350 CATCCTGTGGCACCGCTT 60.360 61.111 16.26 0.00 0.00 4.68
543 544 2.809861 CTTCATCCTGTGGCACCGCT 62.810 60.000 16.26 0.00 0.00 5.52
544 545 2.359850 TTCATCCTGTGGCACCGC 60.360 61.111 16.26 0.00 0.00 5.68
545 546 2.401766 GCTTCATCCTGTGGCACCG 61.402 63.158 16.26 8.85 0.00 4.94
546 547 2.048603 GGCTTCATCCTGTGGCACC 61.049 63.158 16.26 0.00 0.00 5.01
547 548 2.048603 GGGCTTCATCCTGTGGCAC 61.049 63.158 11.55 11.55 0.00 5.01
548 549 2.356278 GGGCTTCATCCTGTGGCA 59.644 61.111 0.00 0.00 0.00 4.92
549 550 2.440980 GGGGCTTCATCCTGTGGC 60.441 66.667 0.00 0.00 0.00 5.01
550 551 0.967380 GTTGGGGCTTCATCCTGTGG 60.967 60.000 0.00 0.00 0.00 4.17
551 552 0.967380 GGTTGGGGCTTCATCCTGTG 60.967 60.000 0.00 0.00 0.00 3.66
552 553 1.384191 GGTTGGGGCTTCATCCTGT 59.616 57.895 0.00 0.00 0.00 4.00
553 554 0.967380 GTGGTTGGGGCTTCATCCTG 60.967 60.000 8.91 0.00 0.00 3.86
554 555 1.142688 AGTGGTTGGGGCTTCATCCT 61.143 55.000 8.91 0.00 0.00 3.24
555 556 0.623723 TAGTGGTTGGGGCTTCATCC 59.376 55.000 0.00 0.00 0.00 3.51
556 557 1.282157 ACTAGTGGTTGGGGCTTCATC 59.718 52.381 0.00 0.00 0.00 2.92
557 558 1.372501 ACTAGTGGTTGGGGCTTCAT 58.627 50.000 0.00 0.00 0.00 2.57
558 559 2.032965 TACTAGTGGTTGGGGCTTCA 57.967 50.000 5.39 0.00 0.00 3.02
559 560 3.646736 ATTACTAGTGGTTGGGGCTTC 57.353 47.619 5.39 0.00 0.00 3.86
560 561 5.523883 TTAATTACTAGTGGTTGGGGCTT 57.476 39.130 5.39 0.00 0.00 4.35
561 562 5.523883 TTTAATTACTAGTGGTTGGGGCT 57.476 39.130 5.39 0.00 0.00 5.19
562 563 6.785337 ATTTTAATTACTAGTGGTTGGGGC 57.215 37.500 5.39 0.00 0.00 5.80
564 565 9.797556 GCTTAATTTTAATTACTAGTGGTTGGG 57.202 33.333 5.39 0.00 31.03 4.12
579 580 9.158233 ACTAGCGAACATGTAGCTTAATTTTAA 57.842 29.630 26.72 10.87 41.88 1.52
632 633 1.074889 AGTTAATTTCCCACCGCCACT 59.925 47.619 0.00 0.00 0.00 4.00
830 2502 5.355630 TCTTGAATCGTTCACTTGGTTTTGA 59.644 36.000 0.76 0.00 39.87 2.69
959 9565 0.319900 GACCAGCTGCTGAACGAAGA 60.320 55.000 30.10 0.00 32.44 2.87
1695 10385 1.941325 GGGCACCGTAGAAATGAGAG 58.059 55.000 0.00 0.00 40.86 3.20
2122 11887 6.841601 AGGTCATGCATATTAGCCTTTTAGA 58.158 36.000 0.00 0.00 0.00 2.10
2123 11888 7.516198 AAGGTCATGCATATTAGCCTTTTAG 57.484 36.000 0.00 0.00 31.59 1.85
2125 11890 6.796785 AAAGGTCATGCATATTAGCCTTTT 57.203 33.333 18.29 6.48 40.61 2.27
2139 11904 9.345517 CATACTTGTTTCATACAAAAGGTCATG 57.654 33.333 0.00 0.00 45.69 3.07
2221 13596 9.797556 TTCTTAAAAAGAAAAACTAGGCTTGTC 57.202 29.630 1.23 0.00 44.10 3.18
2237 13624 9.750125 AAGTTAGGCTCATTGTTTCTTAAAAAG 57.250 29.630 0.00 0.00 0.00 2.27
2374 13763 1.020437 GGAGTTTGGCTATGAGCTGC 58.980 55.000 0.00 0.00 41.99 5.25
2434 13823 5.685520 AGACCAGTATTTTCTCCTCTTCC 57.314 43.478 0.00 0.00 0.00 3.46
2688 14134 2.824341 CCAATCCAGCAAAGCTCTTCTT 59.176 45.455 0.00 0.00 36.40 2.52
2721 14167 2.357637 TGCTACGCCTTCAATTATTGCC 59.642 45.455 0.00 0.00 0.00 4.52
2925 14371 9.823647 TTGCAATTGGAGTTTTATTAAGAAACA 57.176 25.926 7.72 1.23 38.99 2.83
2963 14412 6.509418 TTGCCTTATCTGGTTGAAATGTAC 57.491 37.500 0.00 0.00 0.00 2.90
3176 14634 3.726291 TTCCCAAGCTTAAGTTTGTGC 57.274 42.857 24.78 2.96 34.95 4.57
3561 15064 5.870433 TGTATTACCAACGGACAATACACAG 59.130 40.000 15.00 0.00 38.19 3.66
3577 15095 7.542534 TTTATGTCGGTGTGAATGTATTACC 57.457 36.000 0.00 0.00 0.00 2.85
3640 15161 6.806388 ACTTTTTAGGGTACATAAACCACG 57.194 37.500 0.00 0.00 41.67 4.94
3798 15367 4.808895 GCACGATCCATAGTTGTATTGTGA 59.191 41.667 0.00 0.00 36.31 3.58
3855 15424 9.398921 ACTCCCTAGATACCAAATCATTATCTT 57.601 33.333 0.00 0.00 34.90 2.40
3881 15450 8.405531 GTGTTCTTTTTATAGCCAAGCATCATA 58.594 33.333 0.00 0.00 0.00 2.15
3888 15457 6.325919 TGTGGTGTTCTTTTTATAGCCAAG 57.674 37.500 0.00 0.00 0.00 3.61
3889 15458 6.716934 TTGTGGTGTTCTTTTTATAGCCAA 57.283 33.333 0.00 0.00 0.00 4.52
3908 15486 7.870826 TGACCATTTAGACATTGTAGTTTGTG 58.129 34.615 0.00 0.00 0.00 3.33
3916 15494 6.306987 ACTCCTTTGACCATTTAGACATTGT 58.693 36.000 0.00 0.00 0.00 2.71
4005 15591 1.217882 CGGTTCATATTGGACGAGCC 58.782 55.000 0.00 0.00 37.10 4.70
4081 15668 4.157840 ACAAGGAACAAAAAGAGTTTCGCT 59.842 37.500 0.00 0.00 29.67 4.93
4083 15670 6.782150 AGTACAAGGAACAAAAAGAGTTTCG 58.218 36.000 0.00 0.00 29.67 3.46
4085 15672 9.457436 TCTTAGTACAAGGAACAAAAAGAGTTT 57.543 29.630 0.00 0.00 0.00 2.66
4123 15710 5.186198 CCATACGATATTTGGAATCCCTCC 58.814 45.833 0.00 0.00 45.64 4.30
4188 15775 2.354328 TCCAAGGGGCCTTCTAGAAAA 58.646 47.619 6.63 0.00 33.42 2.29
4223 15810 7.220030 AGAATCAATCTGACTACAAGTTGTGT 58.780 34.615 18.90 13.73 39.72 3.72
4253 15840 1.740585 CAACAAACGGAGTGACACCAA 59.259 47.619 0.84 0.00 45.00 3.67
4254 15841 1.066071 TCAACAAACGGAGTGACACCA 60.066 47.619 0.84 0.00 45.00 4.17
4258 15845 3.390135 TCATCTCAACAAACGGAGTGAC 58.610 45.455 0.00 0.00 45.00 3.67
4289 15876 6.772716 TCTTTTCCCATGGCTATGATTAACTC 59.227 38.462 12.26 0.00 36.36 3.01
4295 15882 5.393068 TTCTCTTTTCCCATGGCTATGAT 57.607 39.130 12.26 0.00 36.36 2.45
4300 15887 3.243359 TGTTTCTCTTTTCCCATGGCT 57.757 42.857 6.09 0.00 0.00 4.75
4302 15889 4.588528 TCCTTTGTTTCTCTTTTCCCATGG 59.411 41.667 4.14 4.14 0.00 3.66
4308 15895 4.887655 TCCCACTCCTTTGTTTCTCTTTTC 59.112 41.667 0.00 0.00 0.00 2.29
4309 15896 4.645136 GTCCCACTCCTTTGTTTCTCTTTT 59.355 41.667 0.00 0.00 0.00 2.27
4310 15897 4.207955 GTCCCACTCCTTTGTTTCTCTTT 58.792 43.478 0.00 0.00 0.00 2.52
4311 15898 3.744530 CGTCCCACTCCTTTGTTTCTCTT 60.745 47.826 0.00 0.00 0.00 2.85
4312 15899 2.224305 CGTCCCACTCCTTTGTTTCTCT 60.224 50.000 0.00 0.00 0.00 3.10
4313 15900 2.143925 CGTCCCACTCCTTTGTTTCTC 58.856 52.381 0.00 0.00 0.00 2.87
4342 16711 1.768684 TTCGCCATCTCATAGCCCCC 61.769 60.000 0.00 0.00 0.00 5.40
4344 16713 0.321122 CCTTCGCCATCTCATAGCCC 60.321 60.000 0.00 0.00 0.00 5.19
4366 16735 3.035363 TCACCCAACTAGTCAGAACACA 58.965 45.455 0.00 0.00 0.00 3.72
4400 17361 6.780706 TTCAAAGTCGTTCCTTCAGATAAC 57.219 37.500 0.00 0.00 0.00 1.89
4403 17364 6.595716 CCTAATTCAAAGTCGTTCCTTCAGAT 59.404 38.462 0.00 0.00 0.00 2.90
4407 17368 4.695928 AGCCTAATTCAAAGTCGTTCCTTC 59.304 41.667 0.00 0.00 0.00 3.46
4435 17396 0.971386 CAAATGGGAAAGCCTGCTGT 59.029 50.000 0.00 0.00 0.00 4.40
4470 17432 7.284261 TCACATGTCCAAATTAGAAGAACAACA 59.716 33.333 0.00 0.00 0.00 3.33
4482 17446 7.769970 ACAAGAACAAAATCACATGTCCAAATT 59.230 29.630 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.