Multiple sequence alignment - TraesCS5A01G066800

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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 TraesCS5A01G066800 chr5A 100.000 4539 0 0 1 4539 74495131 74499669 0.000000e+00 8383.0
1 TraesCS5A01G066800 chr5A 89.139 1068 105 9 1491 2553 74590826 74591887 0.000000e+00 1319.0
2 TraesCS5A01G066800 chr5A 82.239 1599 195 44 2672 4248 74591885 74593416 0.000000e+00 1297.0
3 TraesCS5A01G066800 chr5A 83.170 1224 167 24 2672 3867 74673763 74674975 0.000000e+00 1083.0
4 TraesCS5A01G066800 chr5A 86.075 991 123 9 1491 2471 74672723 74673708 0.000000e+00 1051.0
5 TraesCS5A01G066800 chr5A 92.123 457 35 1 1035 1490 74672212 74672668 1.060000e-180 643.0
6 TraesCS5A01G066800 chr5A 89.716 457 46 1 1035 1490 74590315 74590771 2.350000e-162 582.0
7 TraesCS5A01G066800 chr5A 83.168 101 7 5 230 320 74671553 74671653 2.910000e-12 84.2
8 TraesCS5A01G066800 chr5D 95.724 3555 130 12 382 3929 77736602 77740141 0.000000e+00 5703.0
9 TraesCS5A01G066800 chr5D 89.727 1061 101 7 1491 2548 78010985 78012040 0.000000e+00 1349.0
10 TraesCS5A01G066800 chr5D 84.375 1248 148 24 2675 3914 78012046 78013254 0.000000e+00 1181.0
11 TraesCS5A01G066800 chr5D 83.740 1230 160 26 2672 3873 78054099 78055316 0.000000e+00 1127.0
12 TraesCS5A01G066800 chr5D 86.869 990 117 9 1491 2471 78053063 78054048 0.000000e+00 1096.0
13 TraesCS5A01G066800 chr5D 91.032 591 23 4 3951 4539 77740128 77740690 0.000000e+00 771.0
14 TraesCS5A01G066800 chr5D 92.560 457 33 1 1035 1490 78052552 78053008 0.000000e+00 654.0
15 TraesCS5A01G066800 chr5D 90.110 455 44 1 1037 1490 78010476 78010930 1.410000e-164 590.0
16 TraesCS5A01G066800 chr5D 89.163 406 11 13 1 388 77736048 77736438 4.110000e-130 475.0
17 TraesCS5A01G066800 chr5D 78.733 442 58 23 3951 4383 78055337 78055751 3.480000e-66 263.0
18 TraesCS5A01G066800 chr5D 89.151 212 19 1 828 1035 78052272 78052483 1.250000e-65 261.0
19 TraesCS5A01G066800 chr5D 92.437 119 8 1 2555 2672 324424531 324424413 7.810000e-38 169.0
20 TraesCS5A01G066800 chr5D 88.372 86 7 3 348 432 78052303 78052386 2.890000e-17 100.0
21 TraesCS5A01G066800 chr5D 82.222 90 12 2 494 583 76996932 76996847 1.750000e-09 75.0
22 TraesCS5A01G066800 chr5D 81.188 101 9 5 230 320 78051887 78051987 6.300000e-09 73.1
23 TraesCS5A01G066800 chr5D 84.746 59 7 2 382 440 78009667 78009723 1.760000e-04 58.4
24 TraesCS5A01G066800 chr5B 96.887 2281 67 4 1652 3928 87292924 87295204 0.000000e+00 3816.0
25 TraesCS5A01G066800 chr5B 91.928 1722 46 20 1 1665 87290020 87291705 0.000000e+00 2324.0
26 TraesCS5A01G066800 chr5B 90.122 1063 95 8 1491 2548 87651093 87652150 0.000000e+00 1373.0
27 TraesCS5A01G066800 chr5B 85.012 1221 138 24 2676 3889 87652157 87653339 0.000000e+00 1199.0
28 TraesCS5A01G066800 chr5B 87.563 989 112 6 1491 2471 87765305 87766290 0.000000e+00 1134.0
29 TraesCS5A01G066800 chr5B 83.538 1221 166 20 2672 3867 87970362 87971572 0.000000e+00 1109.0
30 TraesCS5A01G066800 chr5B 82.463 1283 182 25 2672 3929 87766345 87767609 0.000000e+00 1083.0
31 TraesCS5A01G066800 chr5B 94.435 593 28 5 3951 4539 87295192 87295783 0.000000e+00 907.0
32 TraesCS5A01G066800 chr5B 87.250 651 78 4 1491 2140 87969131 87969777 0.000000e+00 737.0
33 TraesCS5A01G066800 chr5B 91.904 457 36 1 1035 1490 87764794 87765250 4.950000e-179 638.0
34 TraesCS5A01G066800 chr5B 91.247 457 39 1 1035 1490 87968620 87969076 4.990000e-174 621.0
35 TraesCS5A01G066800 chr5B 89.497 457 47 1 1035 1490 87650582 87651038 1.090000e-160 577.0
36 TraesCS5A01G066800 chr5B 87.023 393 44 3 2168 2553 87969972 87970364 1.940000e-118 436.0
37 TraesCS5A01G066800 chr5B 88.208 212 20 2 828 1035 87968341 87968551 9.750000e-62 248.0
38 TraesCS5A01G066800 chr5B 78.947 380 50 17 473 833 87649937 87650305 9.820000e-57 231.0
39 TraesCS5A01G066800 chr5B 80.805 323 38 17 4088 4398 87971709 87972019 9.820000e-57 231.0
40 TraesCS5A01G066800 chr5B 86.364 132 13 2 707 833 87968185 87968316 6.120000e-29 139.0
41 TraesCS5A01G066800 chr5B 86.275 102 8 5 348 445 87968371 87968470 6.210000e-19 106.0
42 TraesCS5A01G066800 chr5B 81.915 94 14 1 349 439 87650119 87650212 4.870000e-10 76.8
43 TraesCS5A01G066800 chr5B 89.831 59 4 2 526 583 85905717 85905660 1.750000e-09 75.0
44 TraesCS5A01G066800 chr3B 93.220 118 8 0 2555 2672 92322168 92322051 1.680000e-39 174.0
45 TraesCS5A01G066800 chr4D 92.500 120 8 1 2554 2672 123428043 123427924 2.170000e-38 171.0
46 TraesCS5A01G066800 chrUn 92.437 119 8 1 2555 2672 457168619 457168501 7.810000e-38 169.0
47 TraesCS5A01G066800 chrUn 92.437 119 8 1 2555 2672 459542343 459542461 7.810000e-38 169.0
48 TraesCS5A01G066800 chrUn 90.566 53 5 0 781 833 45881375 45881427 2.270000e-08 71.3
49 TraesCS5A01G066800 chr6A 92.437 119 8 1 2555 2672 84438479 84438361 7.810000e-38 169.0
50 TraesCS5A01G066800 chr2D 92.437 119 8 1 2555 2672 291725723 291725841 7.810000e-38 169.0


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 TraesCS5A01G066800 chr5A 74495131 74499669 4538 False 8383.000000 8383 100.000000 1 4539 1 chr5A.!!$F1 4538
1 TraesCS5A01G066800 chr5A 74590315 74593416 3101 False 1066.000000 1319 87.031333 1035 4248 3 chr5A.!!$F2 3213
2 TraesCS5A01G066800 chr5A 74671553 74674975 3422 False 715.300000 1083 86.134000 230 3867 4 chr5A.!!$F3 3637
3 TraesCS5A01G066800 chr5D 77736048 77740690 4642 False 2316.333333 5703 91.973000 1 4539 3 chr5D.!!$F1 4538
4 TraesCS5A01G066800 chr5D 78009667 78013254 3587 False 794.600000 1349 87.239500 382 3914 4 chr5D.!!$F2 3532
5 TraesCS5A01G066800 chr5D 78051887 78055751 3864 False 510.585714 1127 85.801857 230 4383 7 chr5D.!!$F3 4153
6 TraesCS5A01G066800 chr5B 87290020 87295783 5763 False 2349.000000 3816 94.416667 1 4539 3 chr5B.!!$F1 4538
7 TraesCS5A01G066800 chr5B 87764794 87767609 2815 False 951.666667 1134 87.310000 1035 3929 3 chr5B.!!$F3 2894
8 TraesCS5A01G066800 chr5B 87649937 87653339 3402 False 691.360000 1373 85.098600 349 3889 5 chr5B.!!$F2 3540
9 TraesCS5A01G066800 chr5B 87968185 87972019 3834 False 453.375000 1109 86.338750 348 4398 8 chr5B.!!$F4 4050

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
463 488 0.243095 GCTCTTTTGCTCTGGGCTTG 59.757 55.000 0.0 0.0 42.39 4.01 F
465 490 0.540365 TCTTTTGCTCTGGGCTTGGG 60.540 55.000 0.0 0.0 42.39 4.12 F
2310 4499 1.134401 CGGGGTGCAATCTGACTACAT 60.134 52.381 0.0 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 4499 1.000163 GTCGACTTCTGCCTTCTGTGA 60.000 52.381 8.70 0.0 0.00 3.58 R
2399 4588 1.136891 TGCACACATACCAGAGATCCG 59.863 52.381 0.00 0.0 0.00 4.18 R
3828 6056 0.178767 ATGGATGCAGCTACGCAGAA 59.821 50.000 0.22 0.0 46.99 3.02 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
192 204 4.557942 GCATCGTTGGCAACTTGG 57.442 55.556 26.26 16.11 37.61 3.61
193 205 1.734117 GCATCGTTGGCAACTTGGC 60.734 57.895 26.26 21.11 44.03 4.52
207 219 1.823169 CTTGGCATTGTGGCTGGCTT 61.823 55.000 2.00 0.00 44.10 4.35
208 220 2.102109 TTGGCATTGTGGCTGGCTTG 62.102 55.000 2.00 0.00 44.10 4.01
209 221 2.263540 GCATTGTGGCTGGCTTGG 59.736 61.111 2.00 0.00 0.00 3.61
212 224 0.966875 CATTGTGGCTGGCTTGGCTA 60.967 55.000 2.00 0.00 0.00 3.93
224 236 1.066573 GCTTGGCTACTTCTCTGCAGA 60.067 52.381 17.19 17.19 0.00 4.26
225 237 2.613977 GCTTGGCTACTTCTCTGCAGAA 60.614 50.000 18.85 2.48 37.11 3.02
226 238 3.668447 CTTGGCTACTTCTCTGCAGAAA 58.332 45.455 18.85 13.40 38.23 2.52
227 239 3.988976 TGGCTACTTCTCTGCAGAAAT 57.011 42.857 18.85 5.93 38.23 2.17
228 240 3.866651 TGGCTACTTCTCTGCAGAAATC 58.133 45.455 18.85 2.90 38.23 2.17
258 270 2.716217 CTCTTGGCAAAGGTAAGAGGG 58.284 52.381 0.00 0.00 42.19 4.30
321 346 4.046286 TGGATCTTGTTTATGGTGGCTT 57.954 40.909 0.00 0.00 0.00 4.35
409 434 2.170397 TGAAGTTGGAACAGACTGCTGA 59.830 45.455 1.25 0.00 45.17 4.26
410 435 3.181451 TGAAGTTGGAACAGACTGCTGAT 60.181 43.478 1.25 0.00 45.17 2.90
411 436 4.040339 TGAAGTTGGAACAGACTGCTGATA 59.960 41.667 1.25 0.00 45.17 2.15
412 437 4.623932 AGTTGGAACAGACTGCTGATAA 57.376 40.909 1.25 0.00 45.17 1.75
413 438 4.319177 AGTTGGAACAGACTGCTGATAAC 58.681 43.478 1.25 2.64 45.17 1.89
414 439 4.065088 GTTGGAACAGACTGCTGATAACA 58.935 43.478 1.25 0.00 45.17 2.41
416 441 4.713553 TGGAACAGACTGCTGATAACAAA 58.286 39.130 1.25 0.00 45.17 2.83
417 442 5.316167 TGGAACAGACTGCTGATAACAAAT 58.684 37.500 1.25 0.00 45.17 2.32
418 443 6.472016 TGGAACAGACTGCTGATAACAAATA 58.528 36.000 1.25 0.00 45.17 1.40
419 444 7.112122 TGGAACAGACTGCTGATAACAAATAT 58.888 34.615 1.25 0.00 45.17 1.28
420 445 7.611467 TGGAACAGACTGCTGATAACAAATATT 59.389 33.333 1.25 0.00 45.17 1.28
421 446 9.109393 GGAACAGACTGCTGATAACAAATATTA 57.891 33.333 1.25 0.00 45.17 0.98
422 447 9.922305 GAACAGACTGCTGATAACAAATATTAC 57.078 33.333 1.25 0.00 45.17 1.89
445 470 6.292150 ACTACTTCATCCTATTTTAGGCTGC 58.708 40.000 0.00 0.00 45.82 5.25
447 472 5.372373 ACTTCATCCTATTTTAGGCTGCTC 58.628 41.667 0.00 0.00 45.82 4.26
448 473 5.131809 ACTTCATCCTATTTTAGGCTGCTCT 59.868 40.000 0.00 0.00 45.82 4.09
449 474 5.636903 TCATCCTATTTTAGGCTGCTCTT 57.363 39.130 0.00 0.00 45.82 2.85
451 476 6.426587 TCATCCTATTTTAGGCTGCTCTTTT 58.573 36.000 0.00 0.00 45.82 2.27
452 477 6.319658 TCATCCTATTTTAGGCTGCTCTTTTG 59.680 38.462 0.00 0.00 45.82 2.44
453 478 4.399303 TCCTATTTTAGGCTGCTCTTTTGC 59.601 41.667 0.00 0.00 45.82 3.68
454 479 4.400567 CCTATTTTAGGCTGCTCTTTTGCT 59.599 41.667 0.00 0.00 39.48 3.91
455 480 3.923017 TTTTAGGCTGCTCTTTTGCTC 57.077 42.857 0.00 0.00 0.00 4.26
456 481 2.867109 TTAGGCTGCTCTTTTGCTCT 57.133 45.000 0.00 0.00 0.00 4.09
457 482 2.105006 TAGGCTGCTCTTTTGCTCTG 57.895 50.000 0.00 0.00 0.00 3.35
458 483 0.608582 AGGCTGCTCTTTTGCTCTGG 60.609 55.000 0.00 0.00 0.00 3.86
459 484 1.593296 GGCTGCTCTTTTGCTCTGGG 61.593 60.000 0.00 0.00 0.00 4.45
460 485 1.881602 CTGCTCTTTTGCTCTGGGC 59.118 57.895 0.00 0.00 42.22 5.36
463 488 0.243095 GCTCTTTTGCTCTGGGCTTG 59.757 55.000 0.00 0.00 42.39 4.01
464 489 0.886563 CTCTTTTGCTCTGGGCTTGG 59.113 55.000 0.00 0.00 42.39 3.61
465 490 0.540365 TCTTTTGCTCTGGGCTTGGG 60.540 55.000 0.00 0.00 42.39 4.12
466 491 1.533753 TTTTGCTCTGGGCTTGGGG 60.534 57.895 0.00 0.00 42.39 4.96
467 492 2.310930 TTTTGCTCTGGGCTTGGGGT 62.311 55.000 0.00 0.00 42.39 4.95
468 493 2.310930 TTTGCTCTGGGCTTGGGGTT 62.311 55.000 0.00 0.00 42.39 4.11
469 494 2.118294 GCTCTGGGCTTGGGGTTT 59.882 61.111 0.00 0.00 38.06 3.27
470 495 1.979155 GCTCTGGGCTTGGGGTTTC 60.979 63.158 0.00 0.00 38.06 2.78
471 496 1.304464 CTCTGGGCTTGGGGTTTCC 60.304 63.158 0.00 0.00 0.00 3.13
473 498 4.986708 TGGGCTTGGGGTTTCCGC 62.987 66.667 0.00 0.00 38.76 5.54
474 499 4.986708 GGGCTTGGGGTTTCCGCA 62.987 66.667 1.46 1.46 44.70 5.69
476 501 2.710902 GGCTTGGGGTTTCCGCATC 61.711 63.158 6.38 2.67 45.64 3.91
486 511 1.956477 GTTTCCGCATCCTTGGCATAT 59.044 47.619 0.00 0.00 0.00 1.78
503 528 4.563168 GGCATATAGACTGCTTCTCTGCAT 60.563 45.833 14.30 0.32 42.48 3.96
516 541 5.277731 GCTTCTCTGCATAAGTATTGGCTTC 60.278 44.000 0.00 0.00 32.02 3.86
528 553 5.320277 AGTATTGGCTTCTTCAAAGAGCTT 58.680 37.500 11.37 0.00 36.22 3.74
559 584 4.900684 AGGTAAGAGGCTTCTTGTCTTTC 58.099 43.478 20.48 4.44 43.41 2.62
567 592 4.068599 GGCTTCTTGTCTTTCTACTTGCT 58.931 43.478 0.00 0.00 0.00 3.91
587 612 9.035607 ACTTGCTACATCTTTAGATCATAAACG 57.964 33.333 0.00 0.00 31.21 3.60
590 624 9.378551 TGCTACATCTTTAGATCATAAACGTTT 57.621 29.630 18.90 18.90 31.21 3.60
876 1252 5.010012 GGACACCTTTGATTTGTCTGACATT 59.990 40.000 11.86 2.32 39.72 2.71
964 1624 4.907879 ATTTTAGGCTGCTGTATCTTGC 57.092 40.909 0.00 0.00 0.00 4.01
966 1626 2.609427 TAGGCTGCTGTATCTTGCTG 57.391 50.000 0.00 0.00 0.00 4.41
1050 1780 6.450545 AGATAACAGTCATGTGGATGATACG 58.549 40.000 0.00 0.00 40.78 3.06
1080 1810 3.902881 TTTTTCAAGTGCATGGTTGGT 57.097 38.095 0.00 0.00 0.00 3.67
1317 2049 3.695060 TCTGAACAAGATAGTCCTCGGAC 59.305 47.826 8.03 8.03 44.86 4.79
1643 2430 3.073650 GGATGATAATGCCCTTCCTGACT 59.926 47.826 0.00 0.00 0.00 3.41
1749 3770 7.707893 CAGAAATTTGTGAACAATTTCAGAGGT 59.292 33.333 9.67 7.86 42.60 3.85
2079 4100 3.000041 TGGATCACACGATAACAACAGC 59.000 45.455 0.00 0.00 29.66 4.40
2165 4189 7.485913 GCTAACTGATGTACATTTTCATTGGTG 59.514 37.037 10.30 0.00 0.00 4.17
2310 4499 1.134401 CGGGGTGCAATCTGACTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2393 4582 1.610522 ACAGCCATGAACAAGACAAGC 59.389 47.619 0.00 0.00 0.00 4.01
3241 5463 2.094957 CGAGGAAGAGGAGAGTGACAAC 60.095 54.545 0.00 0.00 0.00 3.32
3246 5468 2.588620 AGAGGAGAGTGACAACGAACT 58.411 47.619 0.00 0.00 0.00 3.01
3296 5524 2.731571 GCCTATGACCTGACCGGCA 61.732 63.158 0.00 0.00 37.48 5.69
3352 5580 2.708861 TCAACAGGGCAATCCGGTATAT 59.291 45.455 0.00 0.00 43.17 0.86
3361 5589 0.963962 ATCCGGTATATGTCGCCGTT 59.036 50.000 0.00 0.00 43.56 4.44
3418 5646 1.867233 CTGGTCAGTTCAGTTGTTCCG 59.133 52.381 0.00 0.00 0.00 4.30
3484 5712 4.092771 TGATAGACTTTCTGAACCGTCG 57.907 45.455 11.21 0.00 0.00 5.12
3489 5717 1.886861 CTTTCTGAACCGTCGGTGCG 61.887 60.000 19.67 12.51 32.81 5.34
3648 5876 3.631227 GCGTGAGGTACTACTACCATTCT 59.369 47.826 1.95 0.00 44.75 2.40
3748 5976 3.727726 TGTGTCTTCGAGCTGATGAAAA 58.272 40.909 0.00 0.00 33.05 2.29
3752 5980 0.443869 TTCGAGCTGATGAAAAGCGC 59.556 50.000 0.00 0.00 45.59 5.92
3875 6108 4.383774 TTGTCGTTGAATAACTGAAGCG 57.616 40.909 0.00 0.00 34.60 4.68
3889 6123 4.643387 AGCGGTTGCCACTGGGAC 62.643 66.667 0.00 0.00 44.31 4.46
3916 6150 4.727507 ATGAGAGTAGCTTGTGTACCAG 57.272 45.455 0.00 0.00 0.00 4.00
3917 6151 2.231478 TGAGAGTAGCTTGTGTACCAGC 59.769 50.000 0.00 0.19 0.00 4.85
3918 6152 2.231478 GAGAGTAGCTTGTGTACCAGCA 59.769 50.000 10.24 0.00 0.00 4.41
3919 6153 2.232452 AGAGTAGCTTGTGTACCAGCAG 59.768 50.000 10.24 0.00 0.00 4.24
3920 6154 2.231478 GAGTAGCTTGTGTACCAGCAGA 59.769 50.000 10.24 0.00 0.00 4.26
3921 6155 2.632996 AGTAGCTTGTGTACCAGCAGAA 59.367 45.455 10.24 0.00 0.00 3.02
3922 6156 2.175878 AGCTTGTGTACCAGCAGAAG 57.824 50.000 10.24 0.00 41.10 2.85
3923 6157 1.417890 AGCTTGTGTACCAGCAGAAGT 59.582 47.619 10.24 0.00 40.52 3.01
3924 6158 2.632996 AGCTTGTGTACCAGCAGAAGTA 59.367 45.455 10.24 0.00 40.52 2.24
3925 6159 2.996621 GCTTGTGTACCAGCAGAAGTAG 59.003 50.000 3.49 0.00 40.52 2.57
3926 6160 3.555168 GCTTGTGTACCAGCAGAAGTAGT 60.555 47.826 3.49 0.00 40.52 2.73
3927 6161 4.632153 CTTGTGTACCAGCAGAAGTAGTT 58.368 43.478 0.00 0.00 35.72 2.24
3928 6162 3.990092 TGTGTACCAGCAGAAGTAGTTG 58.010 45.455 0.00 0.00 0.00 3.16
3929 6163 2.737252 GTGTACCAGCAGAAGTAGTTGC 59.263 50.000 0.00 0.00 40.57 4.17
3930 6164 2.289444 TGTACCAGCAGAAGTAGTTGCC 60.289 50.000 0.00 0.00 41.17 4.52
3931 6165 1.059913 ACCAGCAGAAGTAGTTGCCT 58.940 50.000 0.00 0.00 41.17 4.75
3932 6166 1.421646 ACCAGCAGAAGTAGTTGCCTT 59.578 47.619 0.00 0.00 41.17 4.35
3933 6167 2.158608 ACCAGCAGAAGTAGTTGCCTTT 60.159 45.455 0.00 0.00 41.17 3.11
3934 6168 2.887152 CCAGCAGAAGTAGTTGCCTTTT 59.113 45.455 0.00 0.00 41.17 2.27
3935 6169 3.319122 CCAGCAGAAGTAGTTGCCTTTTT 59.681 43.478 0.00 0.00 41.17 1.94
3965 6224 5.895807 TGAGGGGAAGTAGAAGTAGTTGTA 58.104 41.667 0.00 0.00 0.00 2.41
3978 6237 6.426937 AGAAGTAGTTGTAGAAACGTACCGTA 59.573 38.462 0.00 0.00 39.99 4.02
4003 6263 3.126001 TGTTCACTCCTGATTCACCAC 57.874 47.619 0.00 0.00 0.00 4.16
4004 6264 2.705658 TGTTCACTCCTGATTCACCACT 59.294 45.455 0.00 0.00 0.00 4.00
4193 6466 2.036604 TGCACATGTTACTCGAGGACAA 59.963 45.455 22.30 9.50 0.00 3.18
4273 6546 4.149598 GGTGGGTTCTTTAAGTGGTGATT 58.850 43.478 0.00 0.00 0.00 2.57
4302 6576 6.681777 AGGAGAAATTAATTGTCTGTTGCAC 58.318 36.000 13.94 3.55 32.09 4.57
4383 6658 4.329801 TGATATGAAGCGTGTAGTTGCAAG 59.670 41.667 0.00 0.00 0.00 4.01
4426 6701 5.976458 TCTGGTTTTGCAAATTCAGAAACT 58.024 33.333 27.87 0.00 32.39 2.66
4535 6811 1.153046 ATGTAAACCGCCGGATGGG 60.153 57.895 11.71 5.15 39.58 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 89 3.820467 CTGCCATCACACCTTCAACTAAA 59.180 43.478 0.00 0.00 0.00 1.85
131 143 9.819267 ACATAGATATATGCAGATGAATGACAG 57.181 33.333 3.54 0.00 0.00 3.51
187 199 2.576832 GCCAGCCACAATGCCAAGT 61.577 57.895 0.00 0.00 0.00 3.16
188 200 1.823169 AAGCCAGCCACAATGCCAAG 61.823 55.000 0.00 0.00 0.00 3.61
189 201 1.837947 AAGCCAGCCACAATGCCAA 60.838 52.632 0.00 0.00 0.00 4.52
190 202 2.203669 AAGCCAGCCACAATGCCA 60.204 55.556 0.00 0.00 0.00 4.92
191 203 2.263540 CAAGCCAGCCACAATGCC 59.736 61.111 0.00 0.00 0.00 4.40
192 204 2.263540 CCAAGCCAGCCACAATGC 59.736 61.111 0.00 0.00 0.00 3.56
193 205 0.966875 TAGCCAAGCCAGCCACAATG 60.967 55.000 0.00 0.00 0.00 2.82
194 206 0.967380 GTAGCCAAGCCAGCCACAAT 60.967 55.000 0.00 0.00 0.00 2.71
207 219 3.261643 TGATTTCTGCAGAGAAGTAGCCA 59.738 43.478 17.43 5.21 39.44 4.75
208 220 3.866651 TGATTTCTGCAGAGAAGTAGCC 58.133 45.455 17.43 2.75 39.44 3.93
209 221 4.934602 ACTTGATTTCTGCAGAGAAGTAGC 59.065 41.667 17.43 5.03 39.44 3.58
212 224 6.373774 CCAATACTTGATTTCTGCAGAGAAGT 59.626 38.462 24.11 24.11 39.44 3.01
224 236 4.088634 TGCCAAGAGCCAATACTTGATTT 58.911 39.130 0.00 0.00 43.98 2.17
225 237 3.700538 TGCCAAGAGCCAATACTTGATT 58.299 40.909 0.00 0.00 43.98 2.57
226 238 3.370840 TGCCAAGAGCCAATACTTGAT 57.629 42.857 0.00 0.00 43.98 2.57
227 239 2.877097 TGCCAAGAGCCAATACTTGA 57.123 45.000 0.00 0.00 43.98 3.02
228 240 3.367703 CCTTTGCCAAGAGCCAATACTTG 60.368 47.826 0.00 0.00 42.71 3.16
258 270 9.940166 GCTCTAAGATGTAGTAGAAAGTAGAAC 57.060 37.037 0.00 0.00 0.00 3.01
430 455 5.807721 AGCAAAAGAGCAGCCTAAAATAGGA 60.808 40.000 7.61 0.00 42.13 2.94
433 458 5.124457 CAGAGCAAAAGAGCAGCCTAAAATA 59.876 40.000 0.00 0.00 36.85 1.40
435 460 3.254166 CAGAGCAAAAGAGCAGCCTAAAA 59.746 43.478 0.00 0.00 36.85 1.52
436 461 2.816087 CAGAGCAAAAGAGCAGCCTAAA 59.184 45.455 0.00 0.00 36.85 1.85
439 464 0.608582 CCAGAGCAAAAGAGCAGCCT 60.609 55.000 0.00 0.00 36.85 4.58
441 466 1.881602 CCCAGAGCAAAAGAGCAGC 59.118 57.895 0.00 0.00 36.85 5.25
442 467 1.881602 GCCCAGAGCAAAAGAGCAG 59.118 57.895 0.00 0.00 42.97 4.24
443 468 4.085876 GCCCAGAGCAAAAGAGCA 57.914 55.556 0.00 0.00 42.97 4.26
452 477 1.979155 GAAACCCCAAGCCCAGAGC 60.979 63.158 0.00 0.00 44.25 4.09
453 478 1.304464 GGAAACCCCAAGCCCAGAG 60.304 63.158 0.00 0.00 34.14 3.35
454 479 2.851045 GGAAACCCCAAGCCCAGA 59.149 61.111 0.00 0.00 34.14 3.86
455 480 2.676471 CGGAAACCCCAAGCCCAG 60.676 66.667 0.00 0.00 34.14 4.45
456 481 4.986708 GCGGAAACCCCAAGCCCA 62.987 66.667 0.00 0.00 34.14 5.36
457 482 4.986708 TGCGGAAACCCCAAGCCC 62.987 66.667 0.00 0.00 34.14 5.19
458 483 2.679996 ATGCGGAAACCCCAAGCC 60.680 61.111 0.00 0.00 34.14 4.35
459 484 2.710902 GGATGCGGAAACCCCAAGC 61.711 63.158 0.00 0.00 34.14 4.01
460 485 0.611896 AAGGATGCGGAAACCCCAAG 60.612 55.000 0.42 0.00 34.14 3.61
463 488 2.052104 CCAAGGATGCGGAAACCCC 61.052 63.158 0.42 0.00 0.00 4.95
464 489 2.710902 GCCAAGGATGCGGAAACCC 61.711 63.158 0.00 0.00 0.00 4.11
465 490 1.322538 ATGCCAAGGATGCGGAAACC 61.323 55.000 0.00 0.00 0.00 3.27
466 491 1.388547 TATGCCAAGGATGCGGAAAC 58.611 50.000 0.00 0.00 0.00 2.78
467 492 2.363306 ATATGCCAAGGATGCGGAAA 57.637 45.000 0.00 0.00 0.00 3.13
468 493 2.637382 TCTATATGCCAAGGATGCGGAA 59.363 45.455 0.00 0.00 0.00 4.30
469 494 2.028112 GTCTATATGCCAAGGATGCGGA 60.028 50.000 0.00 0.00 0.00 5.54
470 495 2.027745 AGTCTATATGCCAAGGATGCGG 60.028 50.000 0.00 0.00 0.00 5.69
471 496 2.998670 CAGTCTATATGCCAAGGATGCG 59.001 50.000 0.00 0.00 0.00 4.73
473 498 4.283363 AGCAGTCTATATGCCAAGGATG 57.717 45.455 0.00 0.00 44.97 3.51
474 499 4.596643 AGAAGCAGTCTATATGCCAAGGAT 59.403 41.667 0.00 0.00 44.97 3.24
476 501 4.040217 AGAGAAGCAGTCTATATGCCAAGG 59.960 45.833 0.00 0.00 44.97 3.61
503 528 6.476378 AGCTCTTTGAAGAAGCCAATACTTA 58.524 36.000 9.83 0.00 34.03 2.24
516 541 3.996150 TTGCCAAGAAGCTCTTTGAAG 57.004 42.857 10.75 0.00 33.78 3.02
528 553 1.705186 AGCCTCTTACCTTTGCCAAGA 59.295 47.619 0.00 0.00 30.57 3.02
586 611 6.852853 GTGCCATCATAAACATCATCTAAACG 59.147 38.462 0.00 0.00 0.00 3.60
587 612 7.645340 GTGTGCCATCATAAACATCATCTAAAC 59.355 37.037 0.00 0.00 0.00 2.01
590 624 6.355747 TGTGTGCCATCATAAACATCATCTA 58.644 36.000 0.00 0.00 0.00 1.98
595 629 4.395854 TGTCTGTGTGCCATCATAAACATC 59.604 41.667 0.00 0.00 0.00 3.06
616 650 3.508845 ATGCACTTTAGGTTCCTGTGT 57.491 42.857 1.12 0.00 0.00 3.72
617 651 4.579869 ACTATGCACTTTAGGTTCCTGTG 58.420 43.478 1.12 2.93 0.00 3.66
618 652 4.910458 ACTATGCACTTTAGGTTCCTGT 57.090 40.909 1.12 0.00 0.00 4.00
619 653 5.491982 AGAACTATGCACTTTAGGTTCCTG 58.508 41.667 1.12 0.00 0.00 3.86
620 654 5.763876 AGAACTATGCACTTTAGGTTCCT 57.236 39.130 0.00 0.00 0.00 3.36
621 655 8.398665 CAAATAGAACTATGCACTTTAGGTTCC 58.601 37.037 0.00 0.00 0.00 3.62
876 1252 6.130692 ACCTCACATGGATGCATATATTCA 57.869 37.500 0.00 0.00 0.00 2.57
964 1624 2.814805 ATGGTGGGGAATCAAGACAG 57.185 50.000 0.00 0.00 0.00 3.51
966 1626 3.831911 TCAAAATGGTGGGGAATCAAGAC 59.168 43.478 0.00 0.00 0.00 3.01
1178 1910 2.109128 TGGTATGGCCTGAAGGAACAAA 59.891 45.455 3.32 0.00 38.35 2.83
1187 1919 1.656587 ACTTCTGTGGTATGGCCTGA 58.343 50.000 3.32 0.00 38.35 3.86
1456 2188 1.942657 CATTAGGGTCGCAGTTCATGG 59.057 52.381 0.00 0.00 0.00 3.66
1643 2430 5.815222 TCAAAAGACGACACTTCATCAAGAA 59.185 36.000 0.00 0.00 33.34 2.52
1702 3721 1.065926 TGGTATGCTCTGCAGGAACAG 60.066 52.381 15.13 4.69 43.65 3.16
1749 3770 4.646945 AGCTTCATAACTTCAGAGATCCGA 59.353 41.667 0.00 0.00 0.00 4.55
1966 3987 3.612479 GCATGGTTCAAGACAATGTGGAC 60.612 47.826 0.00 0.00 41.10 4.02
2058 4079 3.000041 GCTGTTGTTATCGTGTGATCCA 59.000 45.455 0.00 0.00 35.99 3.41
2079 4100 7.229506 ACCAGAGTCATCTTTTTAGTTTTCCTG 59.770 37.037 0.00 0.00 31.64 3.86
2165 4189 4.878397 AGACATCAGTTAGCAATTACAGGC 59.122 41.667 0.00 0.00 0.00 4.85
2272 4461 2.167693 CCCGTTGCTAGGACATAGTGAA 59.832 50.000 0.00 0.00 33.65 3.18
2310 4499 1.000163 GTCGACTTCTGCCTTCTGTGA 60.000 52.381 8.70 0.00 0.00 3.58
2393 4582 2.630098 ACATACCAGAGATCCGGACATG 59.370 50.000 6.12 2.86 0.00 3.21
2399 4588 1.136891 TGCACACATACCAGAGATCCG 59.863 52.381 0.00 0.00 0.00 4.18
2632 4829 9.067986 CCATTAGTAAGAAAAACTCCAGTTTCT 57.932 33.333 5.17 0.00 46.47 2.52
3241 5463 1.871080 AGTTGGACTCAGCAAGTTCG 58.129 50.000 0.00 0.00 38.74 3.95
3246 5468 5.322754 AGTAGTAGTAGTTGGACTCAGCAA 58.677 41.667 0.00 0.00 0.00 3.91
3296 5524 4.347583 CCTGAATATCTCCTCTTGCTCCTT 59.652 45.833 0.00 0.00 0.00 3.36
3352 5580 3.573772 CTCCTGCAGAACGGCGACA 62.574 63.158 17.39 2.39 36.28 4.35
3361 5589 3.198417 TGCTAACATGATTCTCCTGCAGA 59.802 43.478 17.39 0.00 0.00 4.26
3418 5646 4.327680 AGGTCTTCCAGTTTGTGATTAGC 58.672 43.478 0.00 0.00 35.89 3.09
3484 5712 2.143925 AGTACAGAAAGCTTTCGCACC 58.856 47.619 28.67 19.33 41.92 5.01
3648 5876 5.221722 GCTGAAACCCTGTATCCTCATCATA 60.222 44.000 0.00 0.00 0.00 2.15
3752 5980 2.167219 ATCATCGTCGCCTTGCACG 61.167 57.895 0.00 0.00 35.60 5.34
3827 6055 0.460811 TGGATGCAGCTACGCAGAAG 60.461 55.000 0.22 0.00 46.99 2.85
3828 6056 0.178767 ATGGATGCAGCTACGCAGAA 59.821 50.000 0.22 0.00 46.99 3.02
3875 6108 2.282462 CAGGTCCCAGTGGCAACC 60.282 66.667 19.50 19.50 0.00 3.77
3889 6123 4.573900 ACACAAGCTACTCTCATTTCAGG 58.426 43.478 0.00 0.00 0.00 3.86
3933 6167 7.123383 ACTTCTACTTCCCCTCAAAAGAAAAA 58.877 34.615 0.00 0.00 0.00 1.94
3934 6168 6.669631 ACTTCTACTTCCCCTCAAAAGAAAA 58.330 36.000 0.00 0.00 0.00 2.29
3935 6169 6.262056 ACTTCTACTTCCCCTCAAAAGAAA 57.738 37.500 0.00 0.00 0.00 2.52
3936 6170 5.906772 ACTTCTACTTCCCCTCAAAAGAA 57.093 39.130 0.00 0.00 0.00 2.52
3937 6171 6.082707 ACTACTTCTACTTCCCCTCAAAAGA 58.917 40.000 0.00 0.00 0.00 2.52
3938 6172 6.361768 ACTACTTCTACTTCCCCTCAAAAG 57.638 41.667 0.00 0.00 0.00 2.27
3939 6173 6.100714 ACAACTACTTCTACTTCCCCTCAAAA 59.899 38.462 0.00 0.00 0.00 2.44
3940 6174 5.605488 ACAACTACTTCTACTTCCCCTCAAA 59.395 40.000 0.00 0.00 0.00 2.69
3941 6175 5.152934 ACAACTACTTCTACTTCCCCTCAA 58.847 41.667 0.00 0.00 0.00 3.02
3942 6176 4.748701 ACAACTACTTCTACTTCCCCTCA 58.251 43.478 0.00 0.00 0.00 3.86
3943 6177 6.186234 TCTACAACTACTTCTACTTCCCCTC 58.814 44.000 0.00 0.00 0.00 4.30
3944 6178 6.150034 TCTACAACTACTTCTACTTCCCCT 57.850 41.667 0.00 0.00 0.00 4.79
3945 6179 6.847421 TTCTACAACTACTTCTACTTCCCC 57.153 41.667 0.00 0.00 0.00 4.81
3946 6180 6.805760 CGTTTCTACAACTACTTCTACTTCCC 59.194 42.308 0.00 0.00 0.00 3.97
3947 6181 7.366513 ACGTTTCTACAACTACTTCTACTTCC 58.633 38.462 0.00 0.00 0.00 3.46
3948 6182 9.323963 GTACGTTTCTACAACTACTTCTACTTC 57.676 37.037 0.00 0.00 0.00 3.01
3949 6183 8.293157 GGTACGTTTCTACAACTACTTCTACTT 58.707 37.037 0.00 0.00 0.00 2.24
3950 6184 7.811653 GGTACGTTTCTACAACTACTTCTACT 58.188 38.462 0.00 0.00 0.00 2.57
3978 6237 4.946157 GGTGAATCAGGAGTGAACATTCAT 59.054 41.667 0.00 0.00 39.73 2.57
4003 6263 4.999311 TGGTTCTGAAATCACAGTCATGAG 59.001 41.667 0.00 0.00 38.79 2.90
4004 6264 4.971939 TGGTTCTGAAATCACAGTCATGA 58.028 39.130 0.00 0.00 38.79 3.07
4193 6466 1.334243 GTCGCCGATTAGCTGAGTAGT 59.666 52.381 0.00 0.00 0.00 2.73
4273 6546 9.219603 CAACAGACAATTAATTTCTCCTAGTCA 57.780 33.333 12.44 0.00 0.00 3.41
4294 6567 1.728971 GAGAACCAGATCGTGCAACAG 59.271 52.381 0.00 0.00 35.74 3.16
4302 6576 2.956964 GCCGCGAGAACCAGATCG 60.957 66.667 8.23 0.00 41.79 3.69
4383 6658 6.489361 ACCAGATAAAGAGCCATTGATGAATC 59.511 38.462 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.