Multiple sequence alignment - TraesCS1A01G057300

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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 TraesCS1A01G057300 chr1A 100.000 4857 0 0 1 4857 37505986 37501130 0.000000e+00 8970.0
1 TraesCS1A01G057300 chr1A 84.986 2471 346 21 662 3113 36613181 36615645 0.000000e+00 2484.0
2 TraesCS1A01G057300 chr1A 84.292 2572 355 39 542 3087 36635431 36637979 0.000000e+00 2466.0
3 TraesCS1A01G057300 chr1A 86.613 620 78 3 648 1266 36605138 36605753 0.000000e+00 680.0
4 TraesCS1A01G057300 chr1D 95.539 4259 90 32 420 4659 38560511 38556334 0.000000e+00 6721.0
5 TraesCS1A01G057300 chr1D 88.716 3146 285 43 1 3100 38584688 38581567 0.000000e+00 3779.0
6 TraesCS1A01G057300 chr1D 88.914 2607 252 15 562 3155 38368107 38365525 0.000000e+00 3179.0
7 TraesCS1A01G057300 chr1D 84.840 2909 365 38 505 3373 38259855 38256983 0.000000e+00 2859.0
8 TraesCS1A01G057300 chr1D 85.657 2510 322 23 617 3094 36624669 36622166 0.000000e+00 2606.0
9 TraesCS1A01G057300 chr1D 84.624 2608 351 27 546 3116 37423706 37426300 0.000000e+00 2549.0
10 TraesCS1A01G057300 chr1D 90.476 357 22 9 1 349 38560887 38560535 1.230000e-125 460.0
11 TraesCS1A01G057300 chr1D 88.350 206 7 5 4652 4857 38555905 38555717 1.050000e-56 231.0
12 TraesCS1A01G057300 chr1B 91.340 3210 229 29 52 3231 58329289 58326099 0.000000e+00 4342.0
13 TraesCS1A01G057300 chr1B 84.232 2911 377 36 505 3373 57791811 57788941 0.000000e+00 2758.0
14 TraesCS1A01G057300 chr1B 85.131 2475 339 18 662 3116 56501803 56499338 0.000000e+00 2505.0
15 TraesCS1A01G057300 chr1B 84.942 2424 344 16 662 3070 57130232 57132649 0.000000e+00 2435.0
16 TraesCS1A01G057300 chr1B 90.183 438 39 4 3990 4424 58326094 58325658 7.050000e-158 568.0
17 TraesCS1A01G057300 chr1B 80.645 558 98 7 2890 3442 58048776 58048224 1.620000e-114 424.0
18 TraesCS1A01G057300 chr1B 80.645 558 98 7 2890 3442 58087710 58087158 1.620000e-114 424.0
19 TraesCS1A01G057300 chr1B 80.501 559 97 9 2890 3442 58114355 58113803 7.520000e-113 418.0
20 TraesCS1A01G057300 chr3A 76.947 321 56 12 22 336 672183622 672183930 3.010000e-37 167.0
21 TraesCS1A01G057300 chr7B 100.000 29 0 0 3364 3392 537732607 537732635 2.000000e-03 54.7


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 TraesCS1A01G057300 chr1A 37501130 37505986 4856 True 8970.000000 8970 100.0000 1 4857 1 chr1A.!!$R1 4856
1 TraesCS1A01G057300 chr1A 36613181 36615645 2464 False 2484.000000 2484 84.9860 662 3113 1 chr1A.!!$F2 2451
2 TraesCS1A01G057300 chr1A 36635431 36637979 2548 False 2466.000000 2466 84.2920 542 3087 1 chr1A.!!$F3 2545
3 TraesCS1A01G057300 chr1A 36605138 36605753 615 False 680.000000 680 86.6130 648 1266 1 chr1A.!!$F1 618
4 TraesCS1A01G057300 chr1D 38581567 38584688 3121 True 3779.000000 3779 88.7160 1 3100 1 chr1D.!!$R4 3099
5 TraesCS1A01G057300 chr1D 38365525 38368107 2582 True 3179.000000 3179 88.9140 562 3155 1 chr1D.!!$R3 2593
6 TraesCS1A01G057300 chr1D 38256983 38259855 2872 True 2859.000000 2859 84.8400 505 3373 1 chr1D.!!$R2 2868
7 TraesCS1A01G057300 chr1D 36622166 36624669 2503 True 2606.000000 2606 85.6570 617 3094 1 chr1D.!!$R1 2477
8 TraesCS1A01G057300 chr1D 37423706 37426300 2594 False 2549.000000 2549 84.6240 546 3116 1 chr1D.!!$F1 2570
9 TraesCS1A01G057300 chr1D 38555717 38560887 5170 True 2470.666667 6721 91.4550 1 4857 3 chr1D.!!$R5 4856
10 TraesCS1A01G057300 chr1B 57788941 57791811 2870 True 2758.000000 2758 84.2320 505 3373 1 chr1B.!!$R2 2868
11 TraesCS1A01G057300 chr1B 56499338 56501803 2465 True 2505.000000 2505 85.1310 662 3116 1 chr1B.!!$R1 2454
12 TraesCS1A01G057300 chr1B 58325658 58329289 3631 True 2455.000000 4342 90.7615 52 4424 2 chr1B.!!$R6 4372
13 TraesCS1A01G057300 chr1B 57130232 57132649 2417 False 2435.000000 2435 84.9420 662 3070 1 chr1B.!!$F1 2408
14 TraesCS1A01G057300 chr1B 58048224 58048776 552 True 424.000000 424 80.6450 2890 3442 1 chr1B.!!$R3 552
15 TraesCS1A01G057300 chr1B 58087158 58087710 552 True 424.000000 424 80.6450 2890 3442 1 chr1B.!!$R4 552
16 TraesCS1A01G057300 chr1B 58113803 58114355 552 True 418.000000 418 80.5010 2890 3442 1 chr1B.!!$R5 552

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
490 506 0.179073 CACCTCCACCTAAGCCATCG 60.179 60.000 0.0 0.0 0.00 3.84 F
1150 1287 0.033504 GACGGAAGAGGCTGTGAACA 59.966 55.000 0.0 0.0 0.00 3.18 F
1409 1588 1.066929 TGATCCTGATGTGGTGACGTG 60.067 52.381 0.0 0.0 0.00 4.49 F
1512 1691 2.371841 TGTTCAGCCCAATACAGTGACT 59.628 45.455 0.0 0.0 0.00 3.41 F
1723 1902 2.690778 AAACCGAATGCTGCCTCGC 61.691 57.895 13.8 0.0 33.70 5.03 F
2628 2808 4.142816 GCAGACGAAGCAATCACACTATTT 60.143 41.667 0.0 0.0 0.00 1.40 F
3646 3838 0.179048 CACTGGTGGAGTCTGTTGCA 60.179 55.000 0.0 0.0 29.75 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1721 0.955919 CCTCTTTCAACCGCCCTGAC 60.956 60.000 0.00 0.00 0.00 3.51 R
2476 2656 1.580942 CAGCACGGAACAACCCATG 59.419 57.895 0.00 0.00 34.64 3.66 R
3172 3360 1.271656 ACTTTCTGCAAGCAGGCAATC 59.728 47.619 20.78 0.00 44.40 2.67 R
3393 3585 5.503927 AGATTGCAAAATCTCAGGAAGCTA 58.496 37.500 1.71 0.00 34.60 3.32 R
3535 3727 1.739067 GTTCTTCCAGGACCCATTCG 58.261 55.000 0.00 0.00 0.00 3.34 R
3867 4059 0.027716 ACATACGCGTACGAGAGCAG 59.972 55.000 25.90 13.59 43.93 4.24 R
4576 4774 0.249531 TGCGTTCCTGTTTCTGCGTA 60.250 50.000 0.00 0.00 0.00 4.42 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
35 36 2.633488 CCATTCTCGAAAGTCCCCTTC 58.367 52.381 0.00 0.00 0.00 3.46
41 42 3.010361 TCTCGAAAGTCCCCTTCTACTCT 59.990 47.826 0.00 0.00 0.00 3.24
44 45 2.146920 AAGTCCCCTTCTACTCTCGG 57.853 55.000 0.00 0.00 0.00 4.63
152 154 3.836949 ACAAATATTTTGAGTGCCTGCG 58.163 40.909 6.96 0.00 0.00 5.18
166 168 1.856597 GCCTGCGAATTTTCATCATGC 59.143 47.619 0.00 0.00 0.00 4.06
168 170 2.855963 CCTGCGAATTTTCATCATGCAC 59.144 45.455 0.00 0.00 0.00 4.57
238 243 9.567848 TCCAAAATTCTTTCGTAAATAGCATTC 57.432 29.630 0.00 0.00 0.00 2.67
239 244 8.807581 CCAAAATTCTTTCGTAAATAGCATTCC 58.192 33.333 0.00 0.00 0.00 3.01
240 245 8.523464 CAAAATTCTTTCGTAAATAGCATTCCG 58.477 33.333 0.00 0.00 0.00 4.30
241 246 4.789095 TCTTTCGTAAATAGCATTCCGC 57.211 40.909 0.00 0.00 42.91 5.54
242 247 4.185394 TCTTTCGTAAATAGCATTCCGCA 58.815 39.130 0.00 0.00 46.13 5.69
244 249 4.948608 TTCGTAAATAGCATTCCGCAAA 57.051 36.364 0.00 0.00 46.13 3.68
245 250 4.948608 TCGTAAATAGCATTCCGCAAAA 57.051 36.364 0.00 0.00 46.13 2.44
246 251 5.493133 TCGTAAATAGCATTCCGCAAAAT 57.507 34.783 0.00 0.00 46.13 1.82
247 252 5.270083 TCGTAAATAGCATTCCGCAAAATG 58.730 37.500 4.14 4.14 46.13 2.32
248 253 5.065346 TCGTAAATAGCATTCCGCAAAATGA 59.935 36.000 11.22 0.00 46.13 2.57
416 431 1.134280 AGCATTTGAGATCGGGACTGG 60.134 52.381 0.00 0.00 0.00 4.00
417 432 1.134401 GCATTTGAGATCGGGACTGGA 60.134 52.381 0.00 0.00 0.00 3.86
418 433 2.680805 GCATTTGAGATCGGGACTGGAA 60.681 50.000 0.00 0.00 0.00 3.53
463 479 3.144506 CACTTTCTCAGTGCAGAACCAT 58.855 45.455 0.00 0.00 46.70 3.55
464 480 3.188048 CACTTTCTCAGTGCAGAACCATC 59.812 47.826 0.00 0.00 46.70 3.51
465 481 2.479566 TTCTCAGTGCAGAACCATCC 57.520 50.000 0.00 0.00 0.00 3.51
466 482 0.247460 TCTCAGTGCAGAACCATCCG 59.753 55.000 0.00 0.00 0.00 4.18
467 483 1.364626 CTCAGTGCAGAACCATCCGC 61.365 60.000 0.00 0.00 0.00 5.54
469 485 2.045926 GTGCAGAACCATCCGCCT 60.046 61.111 0.00 0.00 0.00 5.52
472 488 2.989639 CAGAACCATCCGCCTCCA 59.010 61.111 0.00 0.00 0.00 3.86
473 489 1.450312 CAGAACCATCCGCCTCCAC 60.450 63.158 0.00 0.00 0.00 4.02
474 490 2.124695 GAACCATCCGCCTCCACC 60.125 66.667 0.00 0.00 0.00 4.61
475 491 2.610859 AACCATCCGCCTCCACCT 60.611 61.111 0.00 0.00 0.00 4.00
476 492 2.595009 GAACCATCCGCCTCCACCTC 62.595 65.000 0.00 0.00 0.00 3.85
478 494 3.083349 CATCCGCCTCCACCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
482 498 2.363795 CGCCTCCACCTCCACCTA 60.364 66.667 0.00 0.00 0.00 3.08
483 499 1.987855 CGCCTCCACCTCCACCTAA 60.988 63.158 0.00 0.00 0.00 2.69
484 500 1.908483 GCCTCCACCTCCACCTAAG 59.092 63.158 0.00 0.00 0.00 2.18
485 501 1.908483 CCTCCACCTCCACCTAAGC 59.092 63.158 0.00 0.00 0.00 3.09
486 502 1.627297 CCTCCACCTCCACCTAAGCC 61.627 65.000 0.00 0.00 0.00 4.35
487 503 0.909610 CTCCACCTCCACCTAAGCCA 60.910 60.000 0.00 0.00 0.00 4.75
488 504 0.253160 TCCACCTCCACCTAAGCCAT 60.253 55.000 0.00 0.00 0.00 4.40
489 505 0.181350 CCACCTCCACCTAAGCCATC 59.819 60.000 0.00 0.00 0.00 3.51
490 506 0.179073 CACCTCCACCTAAGCCATCG 60.179 60.000 0.00 0.00 0.00 3.84
491 507 1.227674 CCTCCACCTAAGCCATCGC 60.228 63.158 0.00 0.00 0.00 4.58
1092 1229 3.306641 GCCTGAAGACAGAACAGATCACT 60.307 47.826 0.00 0.00 46.03 3.41
1150 1287 0.033504 GACGGAAGAGGCTGTGAACA 59.966 55.000 0.00 0.00 0.00 3.18
1252 1389 1.689243 TAGCATGAGTCAGCGGGCAT 61.689 55.000 0.00 0.00 35.48 4.40
1266 1435 2.109126 GGCATTCGACCTGCTCCAC 61.109 63.158 16.32 0.00 39.60 4.02
1269 1438 1.078848 ATTCGACCTGCTCCACAGC 60.079 57.895 0.00 0.00 45.78 4.40
1409 1588 1.066929 TGATCCTGATGTGGTGACGTG 60.067 52.381 0.00 0.00 0.00 4.49
1423 1602 2.921121 GTGACGTGCAACTCGATCATTA 59.079 45.455 0.00 0.00 31.75 1.90
1497 1676 4.568359 CAGATGGTCGATAAAGGTGTTCAG 59.432 45.833 0.00 0.00 0.00 3.02
1512 1691 2.371841 TGTTCAGCCCAATACAGTGACT 59.628 45.455 0.00 0.00 0.00 3.41
1642 1821 5.556915 ACAATTCGTTGATGACTTCCCTTA 58.443 37.500 0.00 0.00 0.00 2.69
1723 1902 2.690778 AAACCGAATGCTGCCTCGC 61.691 57.895 13.80 0.00 33.70 5.03
2476 2656 5.702670 ACTGTTACATATGGCATCATACTGC 59.297 40.000 1.65 0.00 38.53 4.40
2628 2808 4.142816 GCAGACGAAGCAATCACACTATTT 60.143 41.667 0.00 0.00 0.00 1.40
3071 3253 7.332678 GCTTCCTGCAAAGTATCAATTTTTCAT 59.667 33.333 0.36 0.00 42.31 2.57
3106 3288 8.400947 GTTGATTAGTTGATGCATTGTCTATGT 58.599 33.333 0.00 0.00 36.57 2.29
3172 3360 5.296151 TCCTGCCAGTAAAAGATATCCAG 57.704 43.478 0.00 0.00 0.00 3.86
3398 3590 8.567285 ACTAATGCAATCTTTTGTAGTAGCTT 57.433 30.769 9.94 0.00 44.65 3.74
3535 3727 7.665561 GAGATATTTTCTCTATTGTCAGGGC 57.334 40.000 0.00 0.00 46.33 5.19
3572 3764 1.741401 CGATGTTTGAGCGGGCTGA 60.741 57.895 0.00 0.00 0.00 4.26
3646 3838 0.179048 CACTGGTGGAGTCTGTTGCA 60.179 55.000 0.00 0.00 29.75 4.08
3725 3917 3.922375 TCAACCACTTTCCTTCCCAAAT 58.078 40.909 0.00 0.00 0.00 2.32
3853 4045 6.086095 AGGAGAGAGAATTGATGGATCTGAT 58.914 40.000 0.00 0.00 0.00 2.90
3854 4046 6.559539 AGGAGAGAGAATTGATGGATCTGATT 59.440 38.462 0.00 0.00 0.00 2.57
3855 4047 6.651643 GGAGAGAGAATTGATGGATCTGATTG 59.348 42.308 0.00 0.00 0.00 2.67
3856 4048 7.376335 AGAGAGAATTGATGGATCTGATTGA 57.624 36.000 0.00 0.00 0.00 2.57
3857 4049 7.980032 AGAGAGAATTGATGGATCTGATTGAT 58.020 34.615 0.00 0.00 38.27 2.57
3858 4050 7.880713 AGAGAGAATTGATGGATCTGATTGATG 59.119 37.037 0.00 0.00 35.14 3.07
3859 4051 7.746703 AGAGAATTGATGGATCTGATTGATGA 58.253 34.615 0.00 0.00 35.14 2.92
3860 4052 7.880713 AGAGAATTGATGGATCTGATTGATGAG 59.119 37.037 0.00 0.00 35.14 2.90
3861 4053 7.746703 AGAATTGATGGATCTGATTGATGAGA 58.253 34.615 0.00 0.00 35.14 3.27
3862 4054 7.662258 AGAATTGATGGATCTGATTGATGAGAC 59.338 37.037 0.00 0.00 35.14 3.36
3863 4055 5.224821 TGATGGATCTGATTGATGAGACC 57.775 43.478 0.00 0.00 35.14 3.85
3864 4056 3.740631 TGGATCTGATTGATGAGACCG 57.259 47.619 0.00 0.00 35.14 4.79
3865 4057 3.033909 TGGATCTGATTGATGAGACCGT 58.966 45.455 0.00 0.00 35.14 4.83
3866 4058 3.068732 TGGATCTGATTGATGAGACCGTC 59.931 47.826 0.00 0.00 35.14 4.79
3867 4059 3.553922 GGATCTGATTGATGAGACCGTCC 60.554 52.174 0.00 0.00 35.14 4.79
3868 4060 2.739943 TCTGATTGATGAGACCGTCCT 58.260 47.619 0.00 0.00 0.00 3.85
3869 4061 2.428530 TCTGATTGATGAGACCGTCCTG 59.571 50.000 0.00 0.00 0.00 3.86
3870 4062 1.134699 TGATTGATGAGACCGTCCTGC 60.135 52.381 0.00 0.00 0.00 4.85
3871 4063 1.137872 GATTGATGAGACCGTCCTGCT 59.862 52.381 0.00 0.00 0.00 4.24
3872 4064 0.532573 TTGATGAGACCGTCCTGCTC 59.467 55.000 0.00 0.00 0.00 4.26
3873 4065 0.323816 TGATGAGACCGTCCTGCTCT 60.324 55.000 0.00 0.00 0.00 4.09
3874 4066 0.383949 GATGAGACCGTCCTGCTCTC 59.616 60.000 0.00 0.00 0.00 3.20
3875 4067 1.380403 ATGAGACCGTCCTGCTCTCG 61.380 60.000 0.00 0.00 34.30 4.04
3876 4068 2.034376 AGACCGTCCTGCTCTCGT 59.966 61.111 0.00 0.00 0.00 4.18
3877 4069 0.743701 GAGACCGTCCTGCTCTCGTA 60.744 60.000 0.00 0.00 0.00 3.43
3878 4070 1.025647 AGACCGTCCTGCTCTCGTAC 61.026 60.000 0.00 0.00 0.00 3.67
3879 4071 2.307137 GACCGTCCTGCTCTCGTACG 62.307 65.000 9.53 9.53 0.00 3.67
3880 4072 2.277373 CGTCCTGCTCTCGTACGC 60.277 66.667 11.24 0.00 0.00 4.42
3881 4073 2.277373 GTCCTGCTCTCGTACGCG 60.277 66.667 11.24 3.53 39.92 6.01
3882 4074 2.745100 TCCTGCTCTCGTACGCGT 60.745 61.111 19.17 19.17 39.49 6.01
3883 4075 1.448365 TCCTGCTCTCGTACGCGTA 60.448 57.895 16.41 16.41 39.49 4.42
3884 4076 0.812811 TCCTGCTCTCGTACGCGTAT 60.813 55.000 23.56 0.00 39.49 3.06
3885 4077 0.657659 CCTGCTCTCGTACGCGTATG 60.658 60.000 28.46 28.46 39.49 2.39
4007 4199 2.885135 TTGGTCATCCAGTGCTCAAT 57.115 45.000 0.00 0.00 45.22 2.57
4096 4288 1.082679 GTTTACGCCTCTCCGCTTCC 61.083 60.000 0.00 0.00 0.00 3.46
4231 4424 1.908299 TCGCTCTGCCCTTCTCACA 60.908 57.895 0.00 0.00 0.00 3.58
4283 4476 4.515432 GCTGAGACGTAAACTGTGTTTTC 58.485 43.478 0.94 0.00 0.00 2.29
4305 4499 5.012239 TCAAGGAATTGAGGTGGATTGAAG 58.988 41.667 0.00 0.00 0.00 3.02
4330 4524 4.201724 CGCAGGTGAATTTACTAGAACTGC 60.202 45.833 14.46 14.46 43.74 4.40
4371 4565 1.823169 GCTGTAGGTGGTTGTCCCGA 61.823 60.000 0.00 0.00 35.15 5.14
4377 4571 1.982958 AGGTGGTTGTCCCGATAACTT 59.017 47.619 4.61 0.00 33.64 2.66
4476 4671 9.364989 GCATTCAGCCAAATTACTTTTTGTATA 57.635 29.630 0.00 0.00 35.30 1.47
4489 4684 4.932268 TTTTGTATACAGCTGGCGTAAC 57.068 40.909 19.93 9.10 0.00 2.50
4521 4716 7.433131 TGTTTCTCTATACGGTGTTATTTAGCG 59.567 37.037 0.00 0.00 43.90 4.26
4548 4743 4.871513 TGTCTGTAGTGTTCAGCTGTTAG 58.128 43.478 14.67 2.35 33.48 2.34
4604 4802 1.967319 ACAGGAACGCAGACATGTTT 58.033 45.000 0.00 0.00 30.88 2.83
4620 4818 6.095440 AGACATGTTTCTGTTGTTGCTAACTT 59.905 34.615 0.00 0.00 0.00 2.66
4626 4824 5.984233 TCTGTTGTTGCTAACTTGTAGTG 57.016 39.130 0.00 0.00 0.00 2.74
4644 4842 9.708222 CTTGTAGTGCTAAGCAATTAATTGTAG 57.292 33.333 25.15 20.22 41.47 2.74
4697 5331 3.830744 TCTTTCAGAACTGTTCCCGAA 57.169 42.857 16.48 15.75 0.00 4.30
4698 5332 4.145365 TCTTTCAGAACTGTTCCCGAAA 57.855 40.909 23.33 23.33 33.31 3.46
4702 5336 3.664107 TCAGAACTGTTCCCGAAAGATG 58.336 45.455 16.48 6.40 0.00 2.90
4707 5341 2.305927 ACTGTTCCCGAAAGATGGATGT 59.694 45.455 0.00 0.00 0.00 3.06
4713 5347 2.292267 CCGAAAGATGGATGTGGAAGG 58.708 52.381 0.00 0.00 0.00 3.46
4754 5388 3.203161 GCCACACGAAAAGGAAATCTC 57.797 47.619 0.00 0.00 0.00 2.75
4755 5389 2.552315 GCCACACGAAAAGGAAATCTCA 59.448 45.455 0.00 0.00 0.00 3.27
4756 5390 3.609409 GCCACACGAAAAGGAAATCTCAC 60.609 47.826 0.00 0.00 0.00 3.51
4757 5391 3.563808 CCACACGAAAAGGAAATCTCACA 59.436 43.478 0.00 0.00 0.00 3.58
4758 5392 4.319766 CCACACGAAAAGGAAATCTCACAG 60.320 45.833 0.00 0.00 0.00 3.66
4759 5393 4.511454 CACACGAAAAGGAAATCTCACAGA 59.489 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.090952 CTCAAATGAGCCCGAGAGTAG 57.909 52.381 0.00 0.00 35.13 2.57
127 129 5.346822 GCAGGCACTCAAAATATTTGTCAAG 59.653 40.000 0.39 0.40 34.60 3.02
152 154 6.257193 GGGATTTCAGTGCATGATGAAAATTC 59.743 38.462 21.14 16.53 45.61 2.17
166 168 3.077359 GTGACTTCCAGGGATTTCAGTG 58.923 50.000 0.00 0.00 0.00 3.66
168 170 3.341823 CTGTGACTTCCAGGGATTTCAG 58.658 50.000 0.00 0.00 0.00 3.02
393 408 1.139853 GTCCCGATCTCAAATGCTCCT 59.860 52.381 0.00 0.00 0.00 3.69
416 431 0.311477 GCCGGACGAGGAGTATCTTC 59.689 60.000 5.05 0.00 37.94 2.87
417 432 1.108132 GGCCGGACGAGGAGTATCTT 61.108 60.000 5.05 0.00 33.73 2.40
418 433 1.528776 GGCCGGACGAGGAGTATCT 60.529 63.158 5.05 0.00 33.73 1.98
459 475 3.083997 GAGGTGGAGGCGGATGGT 61.084 66.667 0.00 0.00 0.00 3.55
464 480 3.976490 TAGGTGGAGGTGGAGGCGG 62.976 68.421 0.00 0.00 0.00 6.13
465 481 1.961180 CTTAGGTGGAGGTGGAGGCG 61.961 65.000 0.00 0.00 0.00 5.52
466 482 1.908483 CTTAGGTGGAGGTGGAGGC 59.092 63.158 0.00 0.00 0.00 4.70
467 483 1.627297 GGCTTAGGTGGAGGTGGAGG 61.627 65.000 0.00 0.00 0.00 4.30
469 485 0.253160 ATGGCTTAGGTGGAGGTGGA 60.253 55.000 0.00 0.00 0.00 4.02
472 488 1.972660 GCGATGGCTTAGGTGGAGGT 61.973 60.000 0.00 0.00 35.83 3.85
473 489 1.227674 GCGATGGCTTAGGTGGAGG 60.228 63.158 0.00 0.00 35.83 4.30
474 490 1.227674 GGCGATGGCTTAGGTGGAG 60.228 63.158 0.00 0.00 39.81 3.86
475 491 1.344953 ATGGCGATGGCTTAGGTGGA 61.345 55.000 0.00 0.00 39.81 4.02
476 492 0.886490 GATGGCGATGGCTTAGGTGG 60.886 60.000 0.00 0.00 39.81 4.61
478 494 1.451936 GGATGGCGATGGCTTAGGT 59.548 57.895 0.00 0.00 39.81 3.08
480 496 1.302832 GGGGATGGCGATGGCTTAG 60.303 63.158 0.00 0.00 39.81 2.18
481 497 1.426251 ATGGGGATGGCGATGGCTTA 61.426 55.000 0.00 0.00 39.81 3.09
482 498 2.703675 GATGGGGATGGCGATGGCTT 62.704 60.000 0.00 0.00 39.81 4.35
483 499 3.180799 ATGGGGATGGCGATGGCT 61.181 61.111 0.00 0.00 39.81 4.75
484 500 2.674380 GATGGGGATGGCGATGGC 60.674 66.667 0.00 0.00 38.90 4.40
485 501 2.034687 GGATGGGGATGGCGATGG 59.965 66.667 0.00 0.00 0.00 3.51
486 502 2.359107 CGGATGGGGATGGCGATG 60.359 66.667 0.00 0.00 0.00 3.84
487 503 4.335647 GCGGATGGGGATGGCGAT 62.336 66.667 0.00 0.00 0.00 4.58
1019 1156 3.536917 CTAGGTCCGGGCGATGCA 61.537 66.667 0.00 0.00 0.00 3.96
1092 1229 0.550914 ACTTGAGGAAGGTGTTGGCA 59.449 50.000 0.00 0.00 32.95 4.92
1150 1287 1.688772 GACATCCCATGAAGCAGCAT 58.311 50.000 0.00 0.00 0.00 3.79
1252 1389 2.343758 GCTGTGGAGCAGGTCGAA 59.656 61.111 0.00 0.00 45.46 3.71
1269 1438 4.803426 GAGCAGGTCGAGTGCCCG 62.803 72.222 14.60 0.00 42.24 6.13
1271 1440 1.004440 AAAGAGCAGGTCGAGTGCC 60.004 57.895 14.60 7.73 42.24 5.01
1273 1442 1.000283 ACTGAAAGAGCAGGTCGAGTG 60.000 52.381 0.00 0.00 40.20 3.51
1274 1443 1.000283 CACTGAAAGAGCAGGTCGAGT 60.000 52.381 0.00 0.00 40.20 4.18
1275 1444 1.000283 ACACTGAAAGAGCAGGTCGAG 60.000 52.381 0.00 0.00 40.20 4.04
1276 1445 1.040646 ACACTGAAAGAGCAGGTCGA 58.959 50.000 0.00 0.00 40.20 4.20
1277 1446 1.143305 CACACTGAAAGAGCAGGTCG 58.857 55.000 0.00 0.00 40.20 4.79
1278 1447 1.202698 ACCACACTGAAAGAGCAGGTC 60.203 52.381 0.00 0.00 40.20 3.85
1409 1588 5.172591 CACAATGCATTAATGATCGAGTTGC 59.827 40.000 19.73 2.26 0.00 4.17
1497 1676 6.039270 TGCAATTATAAGTCACTGTATTGGGC 59.961 38.462 0.00 0.00 0.00 5.36
1542 1721 0.955919 CCTCTTTCAACCGCCCTGAC 60.956 60.000 0.00 0.00 0.00 3.51
1642 1821 1.527034 TTGCTTCTTCGATGCTTGCT 58.473 45.000 0.00 0.00 34.46 3.91
1723 1902 4.712122 ACCCATTAAGCAAAATACGGTG 57.288 40.909 0.00 0.00 0.00 4.94
2476 2656 1.580942 CAGCACGGAACAACCCATG 59.419 57.895 0.00 0.00 34.64 3.66
2628 2808 6.885918 TGACATTCATTGCTCCTAATTTCTGA 59.114 34.615 0.00 0.00 0.00 3.27
3071 3253 6.014755 TGCATCAACTAATCAACCAAATCCAA 60.015 34.615 0.00 0.00 0.00 3.53
3172 3360 1.271656 ACTTTCTGCAAGCAGGCAATC 59.728 47.619 20.78 0.00 44.40 2.67
3393 3585 5.503927 AGATTGCAAAATCTCAGGAAGCTA 58.496 37.500 1.71 0.00 34.60 3.32
3516 3708 4.487714 TCGCCCTGACAATAGAGAAAAT 57.512 40.909 0.00 0.00 0.00 1.82
3535 3727 1.739067 GTTCTTCCAGGACCCATTCG 58.261 55.000 0.00 0.00 0.00 3.34
3572 3764 8.542926 TGTATATCCAATACTTGAGCATAGCAT 58.457 33.333 0.00 0.00 0.00 3.79
3853 4045 0.532573 GAGCAGGACGGTCTCATCAA 59.467 55.000 8.23 0.00 39.15 2.57
3854 4046 2.193532 GAGCAGGACGGTCTCATCA 58.806 57.895 8.23 0.00 39.15 3.07
3860 4052 1.428620 GTACGAGAGCAGGACGGTC 59.571 63.158 0.00 0.00 42.76 4.79
3861 4053 2.396955 CGTACGAGAGCAGGACGGT 61.397 63.158 10.44 0.00 0.00 4.83
3862 4054 2.403987 CGTACGAGAGCAGGACGG 59.596 66.667 10.44 0.00 0.00 4.79
3863 4055 2.277373 GCGTACGAGAGCAGGACG 60.277 66.667 21.65 0.00 36.62 4.79
3864 4056 1.699656 TACGCGTACGAGAGCAGGAC 61.700 60.000 25.90 0.00 43.93 3.85
3865 4057 0.812811 ATACGCGTACGAGAGCAGGA 60.813 55.000 25.90 0.00 43.93 3.86
3866 4058 0.657659 CATACGCGTACGAGAGCAGG 60.658 60.000 25.90 7.98 43.93 4.85
3867 4059 0.027716 ACATACGCGTACGAGAGCAG 59.972 55.000 25.90 13.59 43.93 4.24
3868 4060 0.448990 AACATACGCGTACGAGAGCA 59.551 50.000 25.90 10.23 43.93 4.26
3869 4061 0.838229 CAACATACGCGTACGAGAGC 59.162 55.000 25.90 2.98 43.93 4.09
3870 4062 1.838345 CACAACATACGCGTACGAGAG 59.162 52.381 25.90 15.90 43.93 3.20
3871 4063 1.886037 CACAACATACGCGTACGAGA 58.114 50.000 25.90 9.60 43.93 4.04
3872 4064 0.293723 GCACAACATACGCGTACGAG 59.706 55.000 23.19 19.58 43.93 4.18
3873 4065 0.386985 TGCACAACATACGCGTACGA 60.387 50.000 23.19 0.59 43.93 3.43
3874 4066 1.059979 AATGCACAACATACGCGTACG 59.940 47.619 23.19 17.16 41.51 3.67
3875 4067 2.536130 GGAATGCACAACATACGCGTAC 60.536 50.000 23.19 7.50 38.34 3.67
3876 4068 1.661617 GGAATGCACAACATACGCGTA 59.338 47.619 22.94 22.94 38.34 4.42
3877 4069 0.446222 GGAATGCACAACATACGCGT 59.554 50.000 19.17 19.17 38.34 6.01
3878 4070 0.726827 AGGAATGCACAACATACGCG 59.273 50.000 3.53 3.53 38.34 6.01
3879 4071 2.009774 AGAGGAATGCACAACATACGC 58.990 47.619 0.00 0.00 38.34 4.42
3880 4072 2.609459 GGAGAGGAATGCACAACATACG 59.391 50.000 0.00 0.00 38.34 3.06
3881 4073 3.609853 TGGAGAGGAATGCACAACATAC 58.390 45.455 0.00 0.00 38.34 2.39
3882 4074 3.998913 TGGAGAGGAATGCACAACATA 57.001 42.857 0.00 0.00 38.34 2.29
3883 4075 2.885135 TGGAGAGGAATGCACAACAT 57.115 45.000 0.00 0.00 42.30 2.71
3884 4076 2.885135 ATGGAGAGGAATGCACAACA 57.115 45.000 0.00 0.00 0.00 3.33
3885 4077 3.760684 AGAAATGGAGAGGAATGCACAAC 59.239 43.478 0.00 0.00 0.00 3.32
4007 4199 7.222417 CAGTGTGATTTAATCAGCAACAAAACA 59.778 33.333 8.00 0.00 40.53 2.83
4096 4288 6.038985 CCTCATTGTATATATGTGAGCTCCG 58.961 44.000 12.15 0.00 36.00 4.63
4231 4424 5.128919 GTCCATCCATGATTAAGCAAGAGT 58.871 41.667 0.00 0.00 0.00 3.24
4264 4457 5.292589 TCCTTGAAAACACAGTTTACGTCTC 59.707 40.000 0.00 0.00 0.00 3.36
4283 4476 4.159135 CCTTCAATCCACCTCAATTCCTTG 59.841 45.833 0.00 0.00 0.00 3.61
4305 4499 2.901249 TCTAGTAAATTCACCTGCGCC 58.099 47.619 4.18 0.00 0.00 6.53
4330 4524 8.200792 ACAGCTACTTCTAGAGTTCCATATTTG 58.799 37.037 0.00 0.00 39.86 2.32
4371 4565 8.680903 CATACAGAATGAAGCCTTTCAAGTTAT 58.319 33.333 0.00 0.00 45.82 1.89
4377 4571 5.335897 GCAACATACAGAATGAAGCCTTTCA 60.336 40.000 0.00 0.00 46.67 2.69
4432 4627 6.634805 TGAATGCTTAGCTAGATATGCTACC 58.365 40.000 21.92 13.07 41.95 3.18
4476 4671 2.289444 ACATGTAAGTTACGCCAGCTGT 60.289 45.455 13.81 0.00 0.00 4.40
4489 4684 9.745880 ATAACACCGTATAGAGAAACATGTAAG 57.254 33.333 0.00 0.00 0.00 2.34
4518 4713 3.936453 TGAACACTACAGACAAAAACGCT 59.064 39.130 0.00 0.00 0.00 5.07
4521 4716 5.163754 ACAGCTGAACACTACAGACAAAAAC 60.164 40.000 23.35 0.00 37.54 2.43
4524 4719 4.137116 ACAGCTGAACACTACAGACAAA 57.863 40.909 23.35 0.00 37.54 2.83
4526 4721 3.819564 AACAGCTGAACACTACAGACA 57.180 42.857 23.35 0.00 37.54 3.41
4576 4774 0.249531 TGCGTTCCTGTTTCTGCGTA 60.250 50.000 0.00 0.00 0.00 4.42
4604 4802 4.272504 GCACTACAAGTTAGCAACAACAGA 59.727 41.667 0.00 0.00 0.00 3.41
4620 4818 7.335673 TGCTACAATTAATTGCTTAGCACTACA 59.664 33.333 30.62 18.33 42.43 2.74
4626 4824 6.698766 AGCATTGCTACAATTAATTGCTTAGC 59.301 34.615 27.78 27.78 40.19 3.09
4644 4842 2.203401 TCAGCACAAACAAAGCATTGC 58.797 42.857 0.68 0.00 40.34 3.56
4697 5331 3.054802 GTGAGTCCTTCCACATCCATCTT 60.055 47.826 0.00 0.00 33.72 2.40
4698 5332 2.503356 GTGAGTCCTTCCACATCCATCT 59.497 50.000 0.00 0.00 33.72 2.90
4702 5336 1.677217 GCAGTGAGTCCTTCCACATCC 60.677 57.143 0.00 0.00 35.84 3.51
4707 5341 1.131638 ACTTGCAGTGAGTCCTTCCA 58.868 50.000 0.00 0.00 0.00 3.53
4713 5347 3.238441 CGAGTTCTACTTGCAGTGAGTC 58.762 50.000 0.00 0.00 0.00 3.36
4734 5368 2.552315 TGAGATTTCCTTTTCGTGTGGC 59.448 45.455 0.00 0.00 0.00 5.01
4742 5376 7.777440 AGAGAACTTTCTGTGAGATTTCCTTTT 59.223 33.333 0.00 0.00 37.73 2.27
4743 5377 7.286313 AGAGAACTTTCTGTGAGATTTCCTTT 58.714 34.615 0.00 0.00 37.73 3.11
4744 5378 6.836242 AGAGAACTTTCTGTGAGATTTCCTT 58.164 36.000 0.00 0.00 37.73 3.36
4745 5379 6.432403 AGAGAACTTTCTGTGAGATTTCCT 57.568 37.500 0.00 0.00 37.73 3.36
4746 5380 7.503521 AAAGAGAACTTTCTGTGAGATTTCC 57.496 36.000 0.00 0.00 41.80 3.13
4747 5381 8.401709 ACAAAAGAGAACTTTCTGTGAGATTTC 58.598 33.333 0.00 0.00 44.32 2.17
4748 5382 8.186821 CACAAAAGAGAACTTTCTGTGAGATTT 58.813 33.333 19.82 0.13 44.94 2.17
4749 5383 7.680588 GCACAAAAGAGAACTTTCTGTGAGATT 60.681 37.037 23.94 0.00 44.94 2.40
4750 5384 6.238593 GCACAAAAGAGAACTTTCTGTGAGAT 60.239 38.462 23.94 0.75 44.94 2.75
4751 5385 5.065218 GCACAAAAGAGAACTTTCTGTGAGA 59.935 40.000 23.94 0.00 44.94 3.27
4752 5386 5.269313 GCACAAAAGAGAACTTTCTGTGAG 58.731 41.667 23.94 10.91 44.94 3.51
4753 5387 4.096382 GGCACAAAAGAGAACTTTCTGTGA 59.904 41.667 23.94 0.00 44.94 3.58
4754 5388 4.096984 AGGCACAAAAGAGAACTTTCTGTG 59.903 41.667 20.00 20.00 44.32 3.66
4755 5389 4.273318 AGGCACAAAAGAGAACTTTCTGT 58.727 39.130 0.00 0.00 44.32 3.41
4756 5390 4.907879 AGGCACAAAAGAGAACTTTCTG 57.092 40.909 0.00 0.00 44.32 3.02
4757 5391 4.440663 GCAAGGCACAAAAGAGAACTTTCT 60.441 41.667 0.00 0.00 44.32 2.52
4758 5392 3.798878 GCAAGGCACAAAAGAGAACTTTC 59.201 43.478 0.00 0.00 44.32 2.62
4759 5393 3.195396 TGCAAGGCACAAAAGAGAACTTT 59.805 39.130 0.00 0.00 39.72 2.66


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

AutoCloner maintained by Alex Coulton.