Multiple sequence alignment - TraesCS6D01G212700

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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 TraesCS6D01G212700 chr6D 100.000 4511 0 0 1 4511 301267010 301271520 0.000000e+00 8331
1 TraesCS6D01G212700 chr6B 93.740 3690 116 42 761 4401 466695338 466698961 0.000000e+00 5428
2 TraesCS6D01G212700 chr6B 95.044 343 15 2 1 343 466671599 466671939 5.130000e-149 538
3 TraesCS6D01G212700 chr6B 93.352 361 24 0 329 689 466679250 466679610 6.640000e-148 534
4 TraesCS6D01G212700 chr6A 95.521 3282 100 20 827 4071 415908072 415904801 0.000000e+00 5203
5 TraesCS6D01G212700 chr6A 92.489 679 42 2 1 671 415909010 415908333 0.000000e+00 963
6 TraesCS6D01G212700 chr6A 91.831 355 13 5 4070 4408 415904548 415904194 8.780000e-132 481
7 TraesCS6D01G212700 chr6A 96.296 81 2 1 761 841 415908180 415908101 1.020000e-26 132
8 TraesCS6D01G212700 chr2A 80.057 1058 161 36 1254 2287 623564709 623563678 0.000000e+00 739
9 TraesCS6D01G212700 chr2B 80.197 1015 163 28 1285 2283 563924023 563923031 0.000000e+00 726
10 TraesCS6D01G212700 chr2D 79.807 1035 162 34 1276 2287 480778603 480777593 0.000000e+00 710
11 TraesCS6D01G212700 chr7D 80.831 626 101 19 1280 1900 556120975 556121586 1.470000e-129 473
12 TraesCS6D01G212700 chr7A 80.284 634 99 22 1280 1900 641581291 641580671 5.320000e-124 455
13 TraesCS6D01G212700 chr1A 77.612 670 112 30 1261 1902 278141914 278142573 5.510000e-99 372
14 TraesCS6D01G212700 chr1B 77.581 678 107 35 1261 1902 310927094 310927762 7.130000e-98 368


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 TraesCS6D01G212700 chr6D 301267010 301271520 4510 False 8331.00 8331 100.00000 1 4511 1 chr6D.!!$F1 4510
1 TraesCS6D01G212700 chr6B 466695338 466698961 3623 False 5428.00 5428 93.74000 761 4401 1 chr6B.!!$F3 3640
2 TraesCS6D01G212700 chr6A 415904194 415909010 4816 True 1694.75 5203 94.03425 1 4408 4 chr6A.!!$R1 4407
3 TraesCS6D01G212700 chr2A 623563678 623564709 1031 True 739.00 739 80.05700 1254 2287 1 chr2A.!!$R1 1033
4 TraesCS6D01G212700 chr2B 563923031 563924023 992 True 726.00 726 80.19700 1285 2283 1 chr2B.!!$R1 998
5 TraesCS6D01G212700 chr2D 480777593 480778603 1010 True 710.00 710 79.80700 1276 2287 1 chr2D.!!$R1 1011
6 TraesCS6D01G212700 chr7D 556120975 556121586 611 False 473.00 473 80.83100 1280 1900 1 chr7D.!!$F1 620
7 TraesCS6D01G212700 chr7A 641580671 641581291 620 True 455.00 455 80.28400 1280 1900 1 chr7A.!!$R1 620
8 TraesCS6D01G212700 chr1A 278141914 278142573 659 False 372.00 372 77.61200 1261 1902 1 chr1A.!!$F1 641
9 TraesCS6D01G212700 chr1B 310927094 310927762 668 False 368.00 368 77.58100 1261 1902 1 chr1B.!!$F1 641

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
468 477 0.109689 ACTCGTTGCACTAGCTCGAC 60.110 55.0 0.0 0.0 40.5 4.20 F
1096 1211 0.232303 GCCGTTCGTTGTGAGAGTTG 59.768 55.0 0.0 0.0 0.0 3.16 F
2309 2486 0.970427 ACCCCCGCCAACAAATCATC 60.970 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1684 1.269723 GCGACATCGTCCTGGATATCA 59.730 52.381 4.83 0.00 42.22 2.15 R
2587 2771 0.460284 GATGGTAGCTGTCGGTGTGG 60.460 60.000 0.00 0.00 0.00 4.17 R
3555 3767 0.656259 CTCATTGAGCTGCACGGATG 59.344 55.000 1.02 4.78 0.00 3.51 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
65 66 7.615582 TCTTCAAACTTGACATGATATCCAC 57.384 36.000 0.00 0.00 36.83 4.02
71 72 6.222038 ACTTGACATGATATCCACGTAACT 57.778 37.500 0.00 0.00 0.00 2.24
168 169 4.141181 CCACTTAGGATCATCCCCATCAAA 60.141 45.833 0.00 0.00 41.22 2.69
170 171 5.475909 CACTTAGGATCATCCCCATCAAATG 59.524 44.000 0.00 0.00 37.19 2.32
190 191 3.071479 TGGAGTAAAATTCGTGTGAGGC 58.929 45.455 0.00 0.00 0.00 4.70
198 199 2.051345 CGTGTGAGGCGTTTTGGC 60.051 61.111 0.00 0.00 45.27 4.52
226 227 4.092237 CCAAAATAACGCCCCGAATTTTTC 59.908 41.667 10.36 0.00 35.60 2.29
237 238 4.332828 CCCGAATTTTTCCCTACTTCAGT 58.667 43.478 0.00 0.00 0.00 3.41
292 293 3.097162 GTGGGGGTGGGGGAGATC 61.097 72.222 0.00 0.00 0.00 2.75
327 336 3.066814 GCCCAAGGCTTGCCTCTG 61.067 66.667 21.77 13.93 46.69 3.35
352 361 3.885297 CCTGAATGGTTCTTGTCACAACT 59.115 43.478 0.00 0.00 0.00 3.16
375 384 2.127609 GTGCTTCGCTGCAACGTC 60.128 61.111 9.64 1.26 45.12 4.34
385 394 4.012895 GCAACGTCGTGCCCACTG 62.013 66.667 0.00 0.00 38.66 3.66
445 454 2.290641 TGGTGGCGTAGATTCCAACATT 60.291 45.455 0.00 0.00 44.48 2.71
465 474 0.243907 TCCACTCGTTGCACTAGCTC 59.756 55.000 0.00 0.00 42.74 4.09
468 477 0.109689 ACTCGTTGCACTAGCTCGAC 60.110 55.000 0.00 0.00 40.50 4.20
517 526 0.602638 TCAGCAACCGTGTCACCATC 60.603 55.000 0.00 0.00 0.00 3.51
523 532 2.677003 CCGTGTCACCATCGTTGCC 61.677 63.158 0.00 0.00 0.00 4.52
528 537 1.374125 TCACCATCGTTGCCGTCTG 60.374 57.895 0.00 0.00 35.01 3.51
565 574 0.250467 TTGCAGACTGGGACTTGAGC 60.250 55.000 4.26 0.00 0.00 4.26
577 586 2.421424 GGACTTGAGCACATCATCAACC 59.579 50.000 0.00 0.00 37.89 3.77
582 591 4.558226 TGAGCACATCATCAACCTTACT 57.442 40.909 0.00 0.00 31.12 2.24
585 594 2.609459 GCACATCATCAACCTTACTCGG 59.391 50.000 0.00 0.00 0.00 4.63
588 597 2.672961 TCATCAACCTTACTCGGCAG 57.327 50.000 0.00 0.00 0.00 4.85
602 611 0.807667 CGGCAGAGTTTCGATCTGGG 60.808 60.000 14.63 0.69 43.61 4.45
604 613 1.424493 GCAGAGTTTCGATCTGGGCG 61.424 60.000 14.63 0.00 43.61 6.13
608 617 1.068741 GAGTTTCGATCTGGGCGGTAT 59.931 52.381 0.00 0.00 0.00 2.73
609 618 1.202533 AGTTTCGATCTGGGCGGTATG 60.203 52.381 0.00 0.00 0.00 2.39
637 646 1.929836 GAAGTCGTAGCAGCAATGAGG 59.070 52.381 0.00 0.00 0.00 3.86
646 655 1.336125 GCAGCAATGAGGTATTGGAGC 59.664 52.381 0.00 0.00 45.09 4.70
675 715 1.908340 GACAGCTCTGCACCCTCCAT 61.908 60.000 0.00 0.00 0.00 3.41
694 734 4.806481 CGCGTCGTCGATGTCGGT 62.806 66.667 22.30 0.00 40.29 4.69
708 748 1.079405 TCGGTTTGGTGGATCTCGC 60.079 57.895 0.00 0.00 0.00 5.03
730 770 0.251916 TGGTGAAGGTTATCCGGCAG 59.748 55.000 0.00 0.00 39.05 4.85
747 787 0.804989 CAGTTCAACCGAATCCAGGC 59.195 55.000 0.00 0.00 32.61 4.85
751 791 0.321564 TCAACCGAATCCAGGCACAG 60.322 55.000 0.00 0.00 0.00 3.66
754 794 2.110967 CCGAATCCAGGCACAGCAG 61.111 63.158 0.00 0.00 0.00 4.24
772 844 2.242043 CAGAGGTGTTTTGCTGGGAAT 58.758 47.619 0.00 0.00 0.00 3.01
917 1032 4.465016 GTGTCAGTAGTTCAGTACGAGTG 58.535 47.826 0.00 0.00 35.00 3.51
983 1098 2.203728 TGTAGCCACTGGTCCCGT 60.204 61.111 0.00 0.00 0.00 5.28
1096 1211 0.232303 GCCGTTCGTTGTGAGAGTTG 59.768 55.000 0.00 0.00 0.00 3.16
1728 1882 1.138036 CGTCATCGCCAAGGACGTA 59.862 57.895 11.48 0.00 46.68 3.57
2308 2485 1.078347 ACCCCCGCCAACAAATCAT 59.922 52.632 0.00 0.00 0.00 2.45
2309 2486 0.970427 ACCCCCGCCAACAAATCATC 60.970 55.000 0.00 0.00 0.00 2.92
2310 2487 1.433064 CCCCGCCAACAAATCATCG 59.567 57.895 0.00 0.00 0.00 3.84
2329 2513 5.633601 TCATCGTACAGTTGCTTTTCTGTAG 59.366 40.000 5.46 2.05 44.33 2.74
2550 2734 1.829523 CTAAACCCGTCGTTCCCCCA 61.830 60.000 0.00 0.00 31.78 4.96
2558 2742 1.152715 TCGTTCCCCCAAAACCCAC 60.153 57.895 0.00 0.00 0.00 4.61
2587 2771 1.610522 GGCCATCAGCACCATTATCAC 59.389 52.381 0.00 0.00 46.50 3.06
2615 2799 0.105039 CAGCTACCATCCGTCCTTCC 59.895 60.000 0.00 0.00 0.00 3.46
2694 2878 7.264221 CAATTTGGTCCATTTTTATCGGATCA 58.736 34.615 0.00 0.00 38.17 2.92
2769 2953 0.792640 CATGTCAGTCCTGCAACGAC 59.207 55.000 5.62 5.62 0.00 4.34
3010 3194 0.818040 ACTGGAACACCGACAAAGCC 60.818 55.000 0.00 0.00 0.00 4.35
3067 3251 1.733399 GAACAGTGGCTCGACCGAC 60.733 63.158 0.00 0.00 43.94 4.79
3088 3272 2.362503 ACATCGCCGGAGAGACCA 60.363 61.111 14.81 0.00 38.90 4.02
3097 3281 1.079750 GGAGAGACCACGGCTGTTC 60.080 63.158 0.00 0.00 38.79 3.18
3155 3339 1.526575 CGGGCAATGCAAGGTGTTCT 61.527 55.000 7.79 0.00 0.00 3.01
3222 3406 2.214347 CTCGTTCGAGGAGCTCTATGA 58.786 52.381 14.64 5.97 0.00 2.15
3284 3468 2.879907 GCCGTGTGCTCTACCGTA 59.120 61.111 0.00 0.00 36.87 4.02
3331 3515 1.301716 TGACGAGCCTTTCAGGTGC 60.302 57.895 0.00 0.00 37.80 5.01
3348 3550 4.449743 CAGGTGCGTTAAACTTGCTAGTAA 59.550 41.667 0.00 0.00 33.17 2.24
3428 3635 3.649073 GCACCACGCTTTTAATTTCCTT 58.351 40.909 0.00 0.00 37.77 3.36
3555 3767 1.132588 GAGCATCGTTCGTCCATAGC 58.867 55.000 0.00 0.00 0.00 2.97
3757 3980 5.840243 TCTTGAAATTAGATGCATGTGGG 57.160 39.130 2.46 0.00 0.00 4.61
4154 4643 2.291741 CTCAGGGCGAGAAATTATTGCC 59.708 50.000 10.30 10.30 45.45 4.52
4341 4844 1.663135 CGGTTGGGTTTTGTTGCTTTG 59.337 47.619 0.00 0.00 0.00 2.77
4408 4915 0.036952 AGCTGTTCCCTCGTCACATG 60.037 55.000 0.00 0.00 0.00 3.21
4409 4916 0.320771 GCTGTTCCCTCGTCACATGT 60.321 55.000 0.00 0.00 0.00 3.21
4410 4917 1.067142 GCTGTTCCCTCGTCACATGTA 60.067 52.381 0.00 0.00 0.00 2.29
4411 4918 2.418746 GCTGTTCCCTCGTCACATGTAT 60.419 50.000 0.00 0.00 0.00 2.29
4412 4919 3.448686 CTGTTCCCTCGTCACATGTATC 58.551 50.000 0.00 0.00 0.00 2.24
4413 4920 3.096852 TGTTCCCTCGTCACATGTATCT 58.903 45.455 0.00 0.00 0.00 1.98
4414 4921 3.130516 TGTTCCCTCGTCACATGTATCTC 59.869 47.826 0.00 0.00 0.00 2.75
4415 4922 3.012934 TCCCTCGTCACATGTATCTCA 57.987 47.619 0.00 0.00 0.00 3.27
4416 4923 3.566351 TCCCTCGTCACATGTATCTCAT 58.434 45.455 0.00 0.00 37.22 2.90
4417 4924 4.725490 TCCCTCGTCACATGTATCTCATA 58.275 43.478 0.00 0.00 34.67 2.15
4418 4925 5.325239 TCCCTCGTCACATGTATCTCATAT 58.675 41.667 0.00 0.00 34.67 1.78
4419 4926 5.416013 TCCCTCGTCACATGTATCTCATATC 59.584 44.000 0.00 0.00 34.67 1.63
4420 4927 5.393569 CCCTCGTCACATGTATCTCATATCC 60.394 48.000 0.00 0.00 34.67 2.59
4421 4928 5.296813 TCGTCACATGTATCTCATATCCG 57.703 43.478 0.00 0.00 34.67 4.18
4422 4929 4.156008 TCGTCACATGTATCTCATATCCGG 59.844 45.833 0.00 0.00 34.67 5.14
4423 4930 4.177026 GTCACATGTATCTCATATCCGGC 58.823 47.826 0.00 0.00 34.67 6.13
4424 4931 3.831911 TCACATGTATCTCATATCCGGCA 59.168 43.478 0.00 0.00 34.67 5.69
4425 4932 3.928992 CACATGTATCTCATATCCGGCAC 59.071 47.826 0.00 0.00 34.67 5.01
4426 4933 3.578282 ACATGTATCTCATATCCGGCACA 59.422 43.478 0.00 0.00 34.67 4.57
4427 4934 3.660501 TGTATCTCATATCCGGCACAC 57.339 47.619 0.00 0.00 0.00 3.82
4428 4935 3.230976 TGTATCTCATATCCGGCACACT 58.769 45.455 0.00 0.00 0.00 3.55
4429 4936 4.403734 TGTATCTCATATCCGGCACACTA 58.596 43.478 0.00 0.00 0.00 2.74
4430 4937 5.016831 TGTATCTCATATCCGGCACACTAT 58.983 41.667 0.00 0.00 0.00 2.12
4431 4938 6.184789 TGTATCTCATATCCGGCACACTATA 58.815 40.000 0.00 0.00 0.00 1.31
4432 4939 6.833933 TGTATCTCATATCCGGCACACTATAT 59.166 38.462 0.00 0.00 0.00 0.86
4433 4940 6.798427 ATCTCATATCCGGCACACTATATT 57.202 37.500 0.00 0.00 0.00 1.28
4434 4941 6.605471 TCTCATATCCGGCACACTATATTT 57.395 37.500 0.00 0.00 0.00 1.40
4435 4942 7.712204 TCTCATATCCGGCACACTATATTTA 57.288 36.000 0.00 0.00 0.00 1.40
4436 4943 8.306313 TCTCATATCCGGCACACTATATTTAT 57.694 34.615 0.00 0.00 0.00 1.40
4437 4944 9.416284 TCTCATATCCGGCACACTATATTTATA 57.584 33.333 0.00 0.00 0.00 0.98
4438 4945 9.464714 CTCATATCCGGCACACTATATTTATAC 57.535 37.037 0.00 0.00 0.00 1.47
4439 4946 8.973182 TCATATCCGGCACACTATATTTATACA 58.027 33.333 0.00 0.00 0.00 2.29
4440 4947 9.594478 CATATCCGGCACACTATATTTATACAA 57.406 33.333 0.00 0.00 0.00 2.41
4443 4950 8.911918 TCCGGCACACTATATTTATACAAATT 57.088 30.769 0.00 0.00 35.88 1.82
4444 4951 8.995220 TCCGGCACACTATATTTATACAAATTC 58.005 33.333 0.00 0.00 35.88 2.17
4445 4952 8.779303 CCGGCACACTATATTTATACAAATTCA 58.221 33.333 0.00 0.00 35.88 2.57
4458 4965 9.549509 TTTATACAAATTCATGCAAACGTAGTC 57.450 29.630 0.00 0.00 45.00 2.59
4459 4966 4.794169 ACAAATTCATGCAAACGTAGTCC 58.206 39.130 0.00 0.00 45.00 3.85
4460 4967 4.277174 ACAAATTCATGCAAACGTAGTCCA 59.723 37.500 0.00 0.00 45.00 4.02
4461 4968 5.048083 ACAAATTCATGCAAACGTAGTCCAT 60.048 36.000 0.00 0.00 45.00 3.41
4462 4969 6.150307 ACAAATTCATGCAAACGTAGTCCATA 59.850 34.615 0.00 0.00 45.00 2.74
4463 4970 5.991328 ATTCATGCAAACGTAGTCCATAG 57.009 39.130 0.00 0.00 45.00 2.23
4464 4971 4.729227 TCATGCAAACGTAGTCCATAGA 57.271 40.909 0.00 0.00 45.00 1.98
4465 4972 5.276461 TCATGCAAACGTAGTCCATAGAT 57.724 39.130 0.00 0.00 45.00 1.98
4466 4973 5.289595 TCATGCAAACGTAGTCCATAGATC 58.710 41.667 0.00 0.00 45.00 2.75
4467 4974 4.729227 TGCAAACGTAGTCCATAGATCA 57.271 40.909 0.00 0.00 45.00 2.92
4468 4975 5.276461 TGCAAACGTAGTCCATAGATCAT 57.724 39.130 0.00 0.00 45.00 2.45
4469 4976 5.289595 TGCAAACGTAGTCCATAGATCATC 58.710 41.667 0.00 0.00 45.00 2.92
4470 4977 5.163457 TGCAAACGTAGTCCATAGATCATCA 60.163 40.000 0.00 0.00 45.00 3.07
4471 4978 5.753438 GCAAACGTAGTCCATAGATCATCAA 59.247 40.000 0.00 0.00 45.00 2.57
4472 4979 6.257849 GCAAACGTAGTCCATAGATCATCAAA 59.742 38.462 0.00 0.00 45.00 2.69
4473 4980 7.621991 CAAACGTAGTCCATAGATCATCAAAC 58.378 38.462 0.00 0.00 45.00 2.93
4474 4981 5.520632 ACGTAGTCCATAGATCATCAAACG 58.479 41.667 0.00 0.00 29.74 3.60
4475 4982 5.298527 ACGTAGTCCATAGATCATCAAACGA 59.701 40.000 0.00 0.00 29.74 3.85
4476 4983 6.016192 ACGTAGTCCATAGATCATCAAACGAT 60.016 38.462 0.00 0.00 29.74 3.73
4477 4984 6.524933 CGTAGTCCATAGATCATCAAACGATC 59.475 42.308 0.00 0.00 39.71 3.69
4478 4985 6.410942 AGTCCATAGATCATCAAACGATCA 57.589 37.500 0.00 0.00 41.49 2.92
4479 4986 6.820335 AGTCCATAGATCATCAAACGATCAA 58.180 36.000 0.00 0.00 41.49 2.57
4480 4987 7.275183 AGTCCATAGATCATCAAACGATCAAA 58.725 34.615 0.00 0.00 41.49 2.69
4481 4988 7.770433 AGTCCATAGATCATCAAACGATCAAAA 59.230 33.333 0.00 0.00 41.49 2.44
4482 4989 8.562892 GTCCATAGATCATCAAACGATCAAAAT 58.437 33.333 0.00 0.00 41.49 1.82
4483 4990 9.123902 TCCATAGATCATCAAACGATCAAAATT 57.876 29.630 0.00 0.00 41.49 1.82
4484 4991 9.177304 CCATAGATCATCAAACGATCAAAATTG 57.823 33.333 0.00 0.00 41.49 2.32
4485 4992 9.940166 CATAGATCATCAAACGATCAAAATTGA 57.060 29.630 0.00 0.00 41.49 2.57
4486 4993 9.941664 ATAGATCATCAAACGATCAAAATTGAC 57.058 29.630 0.00 0.00 41.49 3.18
4487 4994 7.819644 AGATCATCAAACGATCAAAATTGACA 58.180 30.769 0.00 0.00 41.49 3.58
4488 4995 7.966753 AGATCATCAAACGATCAAAATTGACAG 59.033 33.333 0.00 0.00 41.49 3.51
4489 4996 7.200778 TCATCAAACGATCAAAATTGACAGA 57.799 32.000 0.00 0.00 40.49 3.41
4490 4997 7.647228 TCATCAAACGATCAAAATTGACAGAA 58.353 30.769 0.00 0.00 40.49 3.02
4491 4998 8.134261 TCATCAAACGATCAAAATTGACAGAAA 58.866 29.630 0.00 0.00 40.49 2.52
4492 4999 8.754096 CATCAAACGATCAAAATTGACAGAAAA 58.246 29.630 0.00 0.00 40.49 2.29
4493 5000 8.114359 TCAAACGATCAAAATTGACAGAAAAC 57.886 30.769 0.00 0.00 40.49 2.43
4494 5001 7.757173 TCAAACGATCAAAATTGACAGAAAACA 59.243 29.630 0.00 0.00 40.49 2.83
4495 5002 7.684062 AACGATCAAAATTGACAGAAAACAG 57.316 32.000 0.00 0.00 40.49 3.16
4496 5003 7.026631 ACGATCAAAATTGACAGAAAACAGA 57.973 32.000 0.00 0.00 40.49 3.41
4497 5004 6.912591 ACGATCAAAATTGACAGAAAACAGAC 59.087 34.615 0.00 0.00 40.49 3.51
4498 5005 6.912051 CGATCAAAATTGACAGAAAACAGACA 59.088 34.615 0.00 0.00 40.49 3.41
4499 5006 7.592533 CGATCAAAATTGACAGAAAACAGACAT 59.407 33.333 0.00 0.00 40.49 3.06
4500 5007 9.897744 GATCAAAATTGACAGAAAACAGACATA 57.102 29.630 0.00 0.00 40.49 2.29
4506 5013 9.950496 AATTGACAGAAAACAGACATATAGACT 57.050 29.630 0.00 0.00 0.00 3.24
4507 5014 8.763049 TTGACAGAAAACAGACATATAGACTG 57.237 34.615 0.00 0.00 44.11 3.51
4508 5015 8.122472 TGACAGAAAACAGACATATAGACTGA 57.878 34.615 0.00 0.00 41.64 3.41
4509 5016 8.753133 TGACAGAAAACAGACATATAGACTGAT 58.247 33.333 0.00 0.00 41.64 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 7.851822 ACTTGCAACAATTATTCAAGTTACG 57.148 32.000 0.00 0.00 43.09 3.18
168 169 3.689649 GCCTCACACGAATTTTACTCCAT 59.310 43.478 0.00 0.00 0.00 3.41
170 171 2.093783 CGCCTCACACGAATTTTACTCC 59.906 50.000 0.00 0.00 0.00 3.85
174 175 4.283678 CAAAACGCCTCACACGAATTTTA 58.716 39.130 0.00 0.00 0.00 1.52
182 183 0.664166 CATGCCAAAACGCCTCACAC 60.664 55.000 0.00 0.00 0.00 3.82
198 199 1.202245 CGGGGCGTTATTTTGGTCATG 60.202 52.381 0.00 0.00 0.00 3.07
206 207 3.368635 GGGAAAAATTCGGGGCGTTATTT 60.369 43.478 0.00 0.00 0.00 1.40
210 211 0.541063 AGGGAAAAATTCGGGGCGTT 60.541 50.000 0.00 0.00 0.00 4.84
226 227 8.842358 TTATTTGTCACTTTACTGAAGTAGGG 57.158 34.615 0.00 0.00 46.75 3.53
250 251 2.831526 CTCCCCGGTCCATTTTTCAATT 59.168 45.455 0.00 0.00 0.00 2.32
278 279 1.697754 ACATGATCTCCCCCACCCC 60.698 63.158 0.00 0.00 0.00 4.95
292 293 1.575922 CCAAGGACACACGCACATG 59.424 57.895 0.00 0.00 0.00 3.21
431 440 4.935808 ACGAGTGGAAATGTTGGAATCTAC 59.064 41.667 0.00 0.00 0.00 2.59
445 454 0.679505 AGCTAGTGCAACGAGTGGAA 59.320 50.000 0.00 0.00 45.86 3.53
485 494 3.067833 GGTTGCTGACCTCAACTAACTC 58.932 50.000 5.94 0.00 45.55 3.01
523 532 3.256558 TCTCATTGAGCATTGTCAGACG 58.743 45.455 8.89 0.00 0.00 4.18
528 537 4.740268 TGCAATTCTCATTGAGCATTGTC 58.260 39.130 28.03 22.50 42.31 3.18
551 560 1.002430 TGATGTGCTCAAGTCCCAGTC 59.998 52.381 0.00 0.00 0.00 3.51
565 574 2.609459 GCCGAGTAAGGTTGATGATGTG 59.391 50.000 0.00 0.00 0.00 3.21
582 591 0.173481 CCAGATCGAAACTCTGCCGA 59.827 55.000 8.69 0.00 39.04 5.54
585 594 1.424493 CGCCCAGATCGAAACTCTGC 61.424 60.000 8.69 6.22 39.04 4.26
588 597 0.458669 TACCGCCCAGATCGAAACTC 59.541 55.000 0.00 0.00 0.00 3.01
591 600 1.116308 TCATACCGCCCAGATCGAAA 58.884 50.000 0.00 0.00 0.00 3.46
594 603 1.800586 CAAATCATACCGCCCAGATCG 59.199 52.381 0.00 0.00 0.00 3.69
596 605 3.072915 TCATCAAATCATACCGCCCAGAT 59.927 43.478 0.00 0.00 0.00 2.90
598 607 2.849942 TCATCAAATCATACCGCCCAG 58.150 47.619 0.00 0.00 0.00 4.45
602 611 3.555956 ACGACTTCATCAAATCATACCGC 59.444 43.478 0.00 0.00 0.00 5.68
604 613 5.753438 TGCTACGACTTCATCAAATCATACC 59.247 40.000 0.00 0.00 0.00 2.73
608 617 3.618594 GCTGCTACGACTTCATCAAATCA 59.381 43.478 0.00 0.00 0.00 2.57
609 618 3.618594 TGCTGCTACGACTTCATCAAATC 59.381 43.478 0.00 0.00 0.00 2.17
637 646 1.004277 CGATCCGCGAGCTCCAATAC 61.004 60.000 8.23 0.00 44.57 1.89
680 720 0.665369 ACCAAACCGACATCGACGAC 60.665 55.000 0.00 0.00 43.02 4.34
682 722 1.623081 CCACCAAACCGACATCGACG 61.623 60.000 2.09 0.00 43.02 5.12
694 734 1.375396 CACGGCGAGATCCACCAAA 60.375 57.895 16.62 0.00 0.00 3.28
708 748 0.461339 CCGGATAACCTTCACCACGG 60.461 60.000 0.00 0.00 0.00 4.94
730 770 0.521735 GTGCCTGGATTCGGTTGAAC 59.478 55.000 0.00 0.00 36.81 3.18
742 782 2.359602 CACCTCTGCTGTGCCTGG 60.360 66.667 0.00 0.00 0.00 4.45
747 787 1.027357 AGCAAAACACCTCTGCTGTG 58.973 50.000 0.00 0.00 44.56 3.66
751 791 0.823356 TCCCAGCAAAACACCTCTGC 60.823 55.000 0.00 0.00 36.29 4.26
754 794 3.751479 AAATTCCCAGCAAAACACCTC 57.249 42.857 0.00 0.00 0.00 3.85
917 1032 4.157958 GCGCTAGCACTGCACAGC 62.158 66.667 16.45 14.63 44.35 4.40
983 1098 0.174845 CATCGCGAGGAAACAGGGTA 59.825 55.000 17.12 0.00 0.00 3.69
1009 1124 1.154197 CGGCTCGTGGATATAGTCGA 58.846 55.000 0.00 0.00 40.66 4.20
1533 1684 1.269723 GCGACATCGTCCTGGATATCA 59.730 52.381 4.83 0.00 42.22 2.15
1701 1855 2.432456 GCGATGACGGTCTGCACA 60.432 61.111 9.88 0.00 40.15 4.57
2308 2485 5.190992 TCTACAGAAAAGCAACTGTACGA 57.809 39.130 0.00 0.00 44.06 3.43
2309 2486 4.386049 CCTCTACAGAAAAGCAACTGTACG 59.614 45.833 0.00 0.00 44.06 3.67
2310 2487 5.298347 ACCTCTACAGAAAAGCAACTGTAC 58.702 41.667 0.00 0.00 44.06 2.90
2329 2513 1.865865 TGACAAGTGAGCGAAACCTC 58.134 50.000 0.00 0.00 0.00 3.85
2558 2742 3.129502 CTGATGGCCGTGCACCAG 61.130 66.667 12.15 7.70 41.46 4.00
2587 2771 0.460284 GATGGTAGCTGTCGGTGTGG 60.460 60.000 0.00 0.00 0.00 4.17
2694 2878 1.772567 TGCAGGTGGGTAAGGTGGT 60.773 57.895 0.00 0.00 0.00 4.16
2769 2953 1.006998 TGATTCTTGGTGGGAATGGGG 59.993 52.381 0.00 0.00 34.09 4.96
2857 3041 3.119096 GCGTCGTTGGGCCTCTTC 61.119 66.667 4.53 0.00 0.00 2.87
2890 3074 2.435059 GTCTGCCCGAAGAGCACC 60.435 66.667 0.00 0.00 35.30 5.01
3010 3194 4.260355 CCCTGCGATGCATTGCCG 62.260 66.667 31.45 25.82 38.13 5.69
3067 3251 1.078759 GTCTCTCCGGCGATGTGTTG 61.079 60.000 9.30 0.00 0.00 3.33
3088 3272 0.892755 TATTGTCTCCGAACAGCCGT 59.107 50.000 0.00 0.00 0.00 5.68
3097 3281 0.456221 AGACGTGGCTATTGTCTCCG 59.544 55.000 0.00 0.00 38.55 4.63
3155 3339 1.100510 CCGACGGTATCTGACTCCAA 58.899 55.000 5.48 0.00 0.00 3.53
3157 3341 1.359475 GCCGACGGTATCTGACTCC 59.641 63.158 16.73 0.00 0.00 3.85
3291 3475 2.954753 GCGTGCTTCACTTCACCGG 61.955 63.158 0.00 0.00 31.34 5.28
3416 3623 7.148885 CGCTGAAATACGCAAAGGAAATTAAAA 60.149 33.333 0.00 0.00 0.00 1.52
3428 3635 4.627900 TGATAAACTCGCTGAAATACGCAA 59.372 37.500 0.00 0.00 0.00 4.85
3497 3704 1.441311 GCTCTCTAGCTCCCTGTGC 59.559 63.158 0.00 0.00 45.85 4.57
3555 3767 0.656259 CTCATTGAGCTGCACGGATG 59.344 55.000 1.02 4.78 0.00 3.51
3611 3823 8.364142 TGGTTCCGAAATCAATTAAAAGAACAT 58.636 29.630 0.00 0.00 34.26 2.71
3620 3832 5.298276 GCCATACTGGTTCCGAAATCAATTA 59.702 40.000 0.00 0.00 40.46 1.40
3757 3980 2.678336 CGGGAATTCAAGAACTACTGCC 59.322 50.000 7.93 0.00 0.00 4.85
4118 4606 2.206515 CTGAGCGAGCAAGAGGACGT 62.207 60.000 0.00 0.00 0.00 4.34
4341 4844 0.383231 AGCAGCCAAAATATCAGCGC 59.617 50.000 0.00 0.00 0.00 5.92
4387 4894 0.601558 TGTGACGAGGGAACAGCTAC 59.398 55.000 0.00 0.00 0.00 3.58
4408 4915 3.944055 AGTGTGCCGGATATGAGATAC 57.056 47.619 5.05 0.00 0.00 2.24
4409 4916 7.898014 AATATAGTGTGCCGGATATGAGATA 57.102 36.000 5.05 0.00 0.00 1.98
4410 4917 6.798427 AATATAGTGTGCCGGATATGAGAT 57.202 37.500 5.05 0.00 0.00 2.75
4411 4918 6.605471 AAATATAGTGTGCCGGATATGAGA 57.395 37.500 5.05 0.00 0.00 3.27
4412 4919 9.464714 GTATAAATATAGTGTGCCGGATATGAG 57.535 37.037 5.05 0.00 0.00 2.90
4413 4920 8.973182 TGTATAAATATAGTGTGCCGGATATGA 58.027 33.333 5.05 0.00 0.00 2.15
4414 4921 9.594478 TTGTATAAATATAGTGTGCCGGATATG 57.406 33.333 5.05 0.00 0.00 1.78
4417 4924 9.515226 AATTTGTATAAATATAGTGTGCCGGAT 57.485 29.630 5.05 0.00 35.50 4.18
4418 4925 8.911918 AATTTGTATAAATATAGTGTGCCGGA 57.088 30.769 5.05 0.00 35.50 5.14
4419 4926 8.779303 TGAATTTGTATAAATATAGTGTGCCGG 58.221 33.333 0.00 0.00 35.50 6.13
4432 4939 9.549509 GACTACGTTTGCATGAATTTGTATAAA 57.450 29.630 0.00 0.00 0.00 1.40
4433 4940 8.178964 GGACTACGTTTGCATGAATTTGTATAA 58.821 33.333 0.00 0.00 0.00 0.98
4434 4941 7.334671 TGGACTACGTTTGCATGAATTTGTATA 59.665 33.333 0.00 0.00 0.00 1.47
4435 4942 6.150307 TGGACTACGTTTGCATGAATTTGTAT 59.850 34.615 0.00 0.00 0.00 2.29
4436 4943 5.470437 TGGACTACGTTTGCATGAATTTGTA 59.530 36.000 0.00 0.00 0.00 2.41
4437 4944 4.277174 TGGACTACGTTTGCATGAATTTGT 59.723 37.500 0.00 0.00 0.00 2.83
4438 4945 4.793071 TGGACTACGTTTGCATGAATTTG 58.207 39.130 0.00 0.00 0.00 2.32
4439 4946 5.643379 ATGGACTACGTTTGCATGAATTT 57.357 34.783 0.00 0.00 0.00 1.82
4440 4947 6.112734 TCTATGGACTACGTTTGCATGAATT 58.887 36.000 12.34 0.00 0.00 2.17
4441 4948 5.670485 TCTATGGACTACGTTTGCATGAAT 58.330 37.500 12.34 0.00 0.00 2.57
4442 4949 5.079689 TCTATGGACTACGTTTGCATGAA 57.920 39.130 12.34 0.00 0.00 2.57
4443 4950 4.729227 TCTATGGACTACGTTTGCATGA 57.271 40.909 12.34 6.71 0.00 3.07
4444 4951 5.049828 TGATCTATGGACTACGTTTGCATG 58.950 41.667 12.34 0.00 0.00 4.06
4445 4952 5.276461 TGATCTATGGACTACGTTTGCAT 57.724 39.130 0.00 0.61 0.00 3.96
4446 4953 4.729227 TGATCTATGGACTACGTTTGCA 57.271 40.909 0.00 0.00 0.00 4.08
4447 4954 5.289595 TGATGATCTATGGACTACGTTTGC 58.710 41.667 0.00 0.00 0.00 3.68
4448 4955 7.515215 CGTTTGATGATCTATGGACTACGTTTG 60.515 40.741 0.00 0.00 0.00 2.93
4449 4956 6.475727 CGTTTGATGATCTATGGACTACGTTT 59.524 38.462 0.00 0.00 0.00 3.60
4450 4957 5.977725 CGTTTGATGATCTATGGACTACGTT 59.022 40.000 0.00 0.00 0.00 3.99
4451 4958 5.298527 TCGTTTGATGATCTATGGACTACGT 59.701 40.000 0.00 0.00 0.00 3.57
4452 4959 5.758924 TCGTTTGATGATCTATGGACTACG 58.241 41.667 0.00 0.00 0.00 3.51
4453 4960 7.371159 TGATCGTTTGATGATCTATGGACTAC 58.629 38.462 10.50 0.00 40.43 2.73
4454 4961 7.524717 TGATCGTTTGATGATCTATGGACTA 57.475 36.000 10.50 0.00 40.43 2.59
4455 4962 6.410942 TGATCGTTTGATGATCTATGGACT 57.589 37.500 10.50 0.00 40.43 3.85
4456 4963 7.482654 TTTGATCGTTTGATGATCTATGGAC 57.517 36.000 10.50 0.00 40.43 4.02
4457 4964 8.681486 ATTTTGATCGTTTGATGATCTATGGA 57.319 30.769 10.50 0.00 40.43 3.41
4458 4965 9.177304 CAATTTTGATCGTTTGATGATCTATGG 57.823 33.333 10.50 0.00 40.43 2.74
4459 4966 9.940166 TCAATTTTGATCGTTTGATGATCTATG 57.060 29.630 10.50 1.52 40.43 2.23
4460 4967 9.941664 GTCAATTTTGATCGTTTGATGATCTAT 57.058 29.630 10.50 1.54 40.43 1.98
4461 4968 8.945057 TGTCAATTTTGATCGTTTGATGATCTA 58.055 29.630 10.50 2.01 40.43 1.98
4462 4969 7.819644 TGTCAATTTTGATCGTTTGATGATCT 58.180 30.769 10.50 0.00 40.43 2.75
4463 4970 7.964559 TCTGTCAATTTTGATCGTTTGATGATC 59.035 33.333 0.00 3.72 40.25 2.92
4464 4971 7.819644 TCTGTCAATTTTGATCGTTTGATGAT 58.180 30.769 0.00 0.00 39.73 2.45
4465 4972 7.200778 TCTGTCAATTTTGATCGTTTGATGA 57.799 32.000 0.00 3.66 39.73 2.92
4466 4973 7.856492 TTCTGTCAATTTTGATCGTTTGATG 57.144 32.000 0.00 2.01 39.73 3.07
4467 4974 8.755018 GTTTTCTGTCAATTTTGATCGTTTGAT 58.245 29.630 0.00 0.00 39.73 2.57
4468 4975 7.757173 TGTTTTCTGTCAATTTTGATCGTTTGA 59.243 29.630 0.00 0.00 39.73 2.69
4469 4976 7.893824 TGTTTTCTGTCAATTTTGATCGTTTG 58.106 30.769 0.00 0.00 39.73 2.93
4470 4977 7.973388 TCTGTTTTCTGTCAATTTTGATCGTTT 59.027 29.630 0.00 0.00 39.73 3.60
4471 4978 7.432252 GTCTGTTTTCTGTCAATTTTGATCGTT 59.568 33.333 0.00 0.00 39.73 3.85
4472 4979 6.912591 GTCTGTTTTCTGTCAATTTTGATCGT 59.087 34.615 0.00 0.00 39.73 3.73
4473 4980 6.912051 TGTCTGTTTTCTGTCAATTTTGATCG 59.088 34.615 0.00 0.00 39.73 3.69
4474 4981 8.807667 ATGTCTGTTTTCTGTCAATTTTGATC 57.192 30.769 0.00 0.00 39.73 2.92
4480 4987 9.950496 AGTCTATATGTCTGTTTTCTGTCAATT 57.050 29.630 0.00 0.00 0.00 2.32
4481 4988 9.376075 CAGTCTATATGTCTGTTTTCTGTCAAT 57.624 33.333 0.00 0.00 0.00 2.57
4482 4989 8.585018 TCAGTCTATATGTCTGTTTTCTGTCAA 58.415 33.333 0.00 0.00 34.30 3.18
4483 4990 8.122472 TCAGTCTATATGTCTGTTTTCTGTCA 57.878 34.615 0.00 0.00 34.30 3.58


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

AutoCloner maintained by Alex Coulton.