Multiple sequence alignment - TraesCS1A01G015900

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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 TraesCS1A01G015900 chr1A 100.000 4499 0 0 1 4499 8326147 8330645 0.000000e+00 8309.0
1 TraesCS1A01G015900 chr1A 84.933 2761 329 41 821 3537 8144670 8141953 0.000000e+00 2713.0
2 TraesCS1A01G015900 chr1A 83.253 2681 353 39 920 3556 8159929 8157301 0.000000e+00 2375.0
3 TraesCS1A01G015900 chr1A 83.577 2594 353 42 982 3537 7834665 7837223 0.000000e+00 2362.0
4 TraesCS1A01G015900 chr1A 78.840 293 31 11 463 724 8089150 8088858 7.740000e-38 169.0
5 TraesCS1A01G015900 chr1A 92.424 66 5 0 821 886 8326813 8326878 1.330000e-15 95.3
6 TraesCS1A01G015900 chr1A 92.424 66 5 0 667 732 8326967 8327032 1.330000e-15 95.3
7 TraesCS1A01G015900 chr1A 79.845 129 24 2 422 549 8336995 8337122 4.790000e-15 93.5
8 TraesCS1A01G015900 chr1A 100.000 29 0 0 3715 3743 7833921 7833949 2.000000e-03 54.7
9 TraesCS1A01G015900 chr1D 92.465 3716 206 36 1 3670 6897441 6901128 0.000000e+00 5243.0
10 TraesCS1A01G015900 chr1D 84.540 2943 342 50 663 3537 6714958 6712061 0.000000e+00 2809.0
11 TraesCS1A01G015900 chr1D 84.208 2590 342 30 982 3538 407672562 407670007 0.000000e+00 2455.0
12 TraesCS1A01G015900 chr1D 83.119 2719 352 46 822 3491 6721749 6719089 0.000000e+00 2379.0
13 TraesCS1A01G015900 chr1D 77.534 365 57 15 383 724 6692309 6691947 3.550000e-46 196.0
14 TraesCS1A01G015900 chr5B 91.303 3162 213 36 591 3732 549547587 549550706 0.000000e+00 4259.0
15 TraesCS1A01G015900 chr5B 91.593 226 18 1 3920 4144 117960300 117960525 1.220000e-80 311.0
16 TraesCS1A01G015900 chr5B 82.090 201 32 4 4001 4198 549551113 549551312 7.740000e-38 169.0
17 TraesCS1A01G015900 chr5B 94.915 59 2 1 4183 4241 549551455 549551512 1.720000e-14 91.6
18 TraesCS1A01G015900 chr1B 88.772 3429 284 43 383 3743 548200530 548197135 0.000000e+00 4106.0
19 TraesCS1A01G015900 chr1B 91.827 2288 148 17 880 3159 9175260 9177516 0.000000e+00 3153.0
20 TraesCS1A01G015900 chr1B 83.796 2592 334 43 982 3538 548193703 548191163 0.000000e+00 2381.0
21 TraesCS1A01G015900 chr1B 82.740 2781 361 47 821 3556 9161650 9164356 0.000000e+00 2366.0
22 TraesCS1A01G015900 chr1B 82.892 2683 356 40 921 3556 8867301 8864675 0.000000e+00 2316.0
23 TraesCS1A01G015900 chr1B 81.262 2583 363 69 982 3494 10007504 10004973 0.000000e+00 1977.0
24 TraesCS1A01G015900 chr1B 95.052 869 33 4 884 1750 9281161 9282021 0.000000e+00 1358.0
25 TraesCS1A01G015900 chr1B 92.885 506 28 4 295 793 9280657 9281161 0.000000e+00 728.0
26 TraesCS1A01G015900 chr1B 84.047 514 55 12 3833 4333 548196861 548196362 1.890000e-128 470.0
27 TraesCS1A01G015900 chr1B 83.381 349 33 13 4060 4404 569855513 569855186 2.630000e-77 300.0
28 TraesCS1A01G015900 chr1B 78.906 384 49 12 383 735 8867674 8867292 9.730000e-57 231.0
29 TraesCS1A01G015900 chr1B 93.836 146 9 0 3920 4065 569869015 569868870 2.110000e-53 220.0
30 TraesCS1A01G015900 chr1B 86.667 105 8 3 157 256 9280542 9280645 1.320000e-20 111.0
31 TraesCS1A01G015900 chr2A 82.801 2628 341 46 917 3491 733628833 733631402 0.000000e+00 2246.0
32 TraesCS1A01G015900 chr2A 78.287 327 37 19 4200 4497 733632209 733632530 3.580000e-41 180.0
33 TraesCS1A01G015900 chr2D 83.144 2557 331 43 988 3491 599926413 599928922 0.000000e+00 2242.0
34 TraesCS1A01G015900 chr2D 94.845 97 3 2 4403 4497 599929953 599930049 2.800000e-32 150.0
35 TraesCS1A01G015900 chr2B 82.686 2628 340 52 918 3491 729766526 729769092 0.000000e+00 2226.0
36 TraesCS1A01G015900 chr7B 86.037 487 47 9 3920 4404 20345758 20345291 1.870000e-138 503.0
37 TraesCS1A01G015900 chr4B 85.361 485 47 12 3920 4401 240107818 240108281 8.750000e-132 481.0
38 TraesCS1A01G015900 chr4B 80.804 448 47 22 383 800 36636304 36635866 9.390000e-82 315.0


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 TraesCS1A01G015900 chr1A 8326147 8330645 4498 False 2833.200000 8309 94.949333 1 4499 3 chr1A.!!$F3 4498
1 TraesCS1A01G015900 chr1A 8141953 8144670 2717 True 2713.000000 2713 84.933000 821 3537 1 chr1A.!!$R2 2716
2 TraesCS1A01G015900 chr1A 8157301 8159929 2628 True 2375.000000 2375 83.253000 920 3556 1 chr1A.!!$R3 2636
3 TraesCS1A01G015900 chr1A 7833921 7837223 3302 False 1208.350000 2362 91.788500 982 3743 2 chr1A.!!$F2 2761
4 TraesCS1A01G015900 chr1D 6897441 6901128 3687 False 5243.000000 5243 92.465000 1 3670 1 chr1D.!!$F1 3669
5 TraesCS1A01G015900 chr1D 6712061 6714958 2897 True 2809.000000 2809 84.540000 663 3537 1 chr1D.!!$R2 2874
6 TraesCS1A01G015900 chr1D 407670007 407672562 2555 True 2455.000000 2455 84.208000 982 3538 1 chr1D.!!$R4 2556
7 TraesCS1A01G015900 chr1D 6719089 6721749 2660 True 2379.000000 2379 83.119000 822 3491 1 chr1D.!!$R3 2669
8 TraesCS1A01G015900 chr5B 549547587 549551512 3925 False 1506.533333 4259 89.436000 591 4241 3 chr5B.!!$F2 3650
9 TraesCS1A01G015900 chr1B 9175260 9177516 2256 False 3153.000000 3153 91.827000 880 3159 1 chr1B.!!$F2 2279
10 TraesCS1A01G015900 chr1B 9161650 9164356 2706 False 2366.000000 2366 82.740000 821 3556 1 chr1B.!!$F1 2735
11 TraesCS1A01G015900 chr1B 548191163 548200530 9367 True 2319.000000 4106 85.538333 383 4333 3 chr1B.!!$R5 3950
12 TraesCS1A01G015900 chr1B 10004973 10007504 2531 True 1977.000000 1977 81.262000 982 3494 1 chr1B.!!$R1 2512
13 TraesCS1A01G015900 chr1B 8864675 8867674 2999 True 1273.500000 2316 80.899000 383 3556 2 chr1B.!!$R4 3173
14 TraesCS1A01G015900 chr1B 9280542 9282021 1479 False 732.333333 1358 91.534667 157 1750 3 chr1B.!!$F3 1593
15 TraesCS1A01G015900 chr2A 733628833 733632530 3697 False 1213.000000 2246 80.544000 917 4497 2 chr2A.!!$F1 3580
16 TraesCS1A01G015900 chr2D 599926413 599930049 3636 False 1196.000000 2242 88.994500 988 4497 2 chr2D.!!$F1 3509
17 TraesCS1A01G015900 chr2B 729766526 729769092 2566 False 2226.000000 2226 82.686000 918 3491 1 chr2B.!!$F1 2573

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
801 1044 0.036448 AACAGCAGAGCAGAGCACAT 59.964 50.0 0.0 0.0 0.00 3.21 F
978 1430 0.390124 ATAGCAGAGCAGAGCAGAGC 59.610 55.0 0.0 0.0 0.00 4.09 F
2097 2637 0.537188 TTGAGGATCGAACAGGAGGC 59.463 55.0 0.0 0.0 38.61 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2649 0.464870 TGCTGCAATGCAAAGGTGTT 59.535 45.0 9.92 0.0 40.29 3.32 R
2607 3183 0.771755 AACCACCTCCTCCCAGTTTC 59.228 55.0 0.00 0.0 0.00 2.78 R
3830 4671 0.036732 ATGTTTCCTTCGCAGCCAGA 59.963 50.0 0.00 0.0 0.00 3.86 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
82 83 5.556915 TGGTCAACTAGTTGGATTTCGAAT 58.443 37.500 30.35 0.00 40.78 3.34
85 86 6.238130 GGTCAACTAGTTGGATTTCGAATAGC 60.238 42.308 30.35 15.46 40.78 2.97
86 87 6.312918 GTCAACTAGTTGGATTTCGAATAGCA 59.687 38.462 30.35 7.63 40.78 3.49
119 120 6.882610 TCTGCAGTTGACATGTAGAAATTT 57.117 33.333 14.67 0.00 36.61 1.82
155 156 0.391597 GGCGACGAAATGATCCCCTA 59.608 55.000 0.00 0.00 0.00 3.53
160 161 4.127171 CGACGAAATGATCCCCTAAACAT 58.873 43.478 0.00 0.00 0.00 2.71
202 204 3.872771 CCATTGAAGCAAATATTGTGGGC 59.127 43.478 0.00 0.00 0.00 5.36
215 222 7.971368 AATATTGTGGGCTGGTTAGTAAAAT 57.029 32.000 0.00 0.00 0.00 1.82
262 269 6.357367 AGACCACCCTTGAATATGTCAATAC 58.643 40.000 0.00 0.00 45.27 1.89
263 270 5.445964 ACCACCCTTGAATATGTCAATACC 58.554 41.667 0.00 0.00 45.27 2.73
692 905 1.475403 GCCACTGCTGTCCTAGTCTA 58.525 55.000 0.00 0.00 33.53 2.59
784 1027 9.482627 CTACATATACATCCTCTTCCTTTGAAC 57.517 37.037 0.00 0.00 0.00 3.18
799 1042 0.602106 TGAACAGCAGAGCAGAGCAC 60.602 55.000 0.00 0.00 0.00 4.40
801 1044 0.036448 AACAGCAGAGCAGAGCACAT 59.964 50.000 0.00 0.00 0.00 3.21
816 1063 4.581824 AGAGCACATTTCACATTCACACTT 59.418 37.500 0.00 0.00 0.00 3.16
845 1092 0.464554 GGCCACTGCTGTCCTAATCC 60.465 60.000 0.00 0.00 37.74 3.01
914 1343 5.922053 ACAGTCAGCTGAGCATATTATTGA 58.078 37.500 18.89 0.00 45.28 2.57
975 1427 1.066757 TCGAATAGCAGAGCAGAGCAG 59.933 52.381 0.00 0.00 0.00 4.24
976 1428 1.066757 CGAATAGCAGAGCAGAGCAGA 59.933 52.381 0.00 0.00 0.00 4.26
977 1429 2.746269 GAATAGCAGAGCAGAGCAGAG 58.254 52.381 0.00 0.00 0.00 3.35
978 1430 0.390124 ATAGCAGAGCAGAGCAGAGC 59.610 55.000 0.00 0.00 0.00 4.09
979 1431 0.969409 TAGCAGAGCAGAGCAGAGCA 60.969 55.000 0.00 0.00 0.00 4.26
980 1432 2.101835 GCAGAGCAGAGCAGAGCAC 61.102 63.158 0.00 0.00 0.00 4.40
1188 1662 4.817517 CAACGACCACCATTAGTAAGTCT 58.182 43.478 0.00 0.00 31.65 3.24
2097 2637 0.537188 TTGAGGATCGAACAGGAGGC 59.463 55.000 0.00 0.00 38.61 4.70
2109 2649 1.074405 ACAGGAGGCTGCATCAGAAAA 59.926 47.619 16.67 0.00 32.44 2.29
2607 3183 6.150318 TCGTGCTACTAAAAACTTCTCAGAG 58.850 40.000 0.00 0.00 0.00 3.35
2852 3431 6.261826 GGTTCTCTTGATGGTCATCTATTTGG 59.738 42.308 11.62 0.00 38.60 3.28
2859 3438 5.667172 TGATGGTCATCTATTTGGGAAGAGA 59.333 40.000 11.62 0.00 37.50 3.10
2860 3439 6.158520 TGATGGTCATCTATTTGGGAAGAGAA 59.841 38.462 11.62 0.00 36.75 2.87
2861 3440 6.387192 TGGTCATCTATTTGGGAAGAGAAA 57.613 37.500 0.00 0.00 36.75 2.52
2864 3446 6.830838 GGTCATCTATTTGGGAAGAGAAACAT 59.169 38.462 0.00 0.00 36.75 2.71
3001 3596 3.378427 GCCAGGAAACATACTTGTGGATC 59.622 47.826 0.00 0.00 35.83 3.36
3006 3601 5.192522 AGGAAACATACTTGTGGATCCATCT 59.807 40.000 19.62 3.23 36.82 2.90
3075 3670 3.596214 GGATTTTAGCCGAGTTCTGACA 58.404 45.455 0.00 0.00 0.00 3.58
3140 3735 0.798776 GGAGTTGCAATCACACCGAG 59.201 55.000 0.59 0.00 0.00 4.63
3183 3778 4.646492 GGCATGGTACTTCTGGAAATCATT 59.354 41.667 0.00 0.00 0.00 2.57
3229 3824 8.011673 CACTTGAAACATCATACAACACTAGTG 58.988 37.037 21.44 21.44 0.00 2.74
3234 3829 4.020218 ACATCATACAACACTAGTGGCAGT 60.020 41.667 26.12 21.09 34.19 4.40
3239 3837 2.289072 ACAACACTAGTGGCAGTAGCAG 60.289 50.000 26.12 20.59 44.61 4.24
3240 3838 1.633774 ACACTAGTGGCAGTAGCAGT 58.366 50.000 26.12 21.16 44.61 4.40
3241 3839 1.971357 ACACTAGTGGCAGTAGCAGTT 59.029 47.619 26.12 6.80 44.61 3.16
3330 3934 1.137479 GTGGATCCACAATTGCATGGG 59.863 52.381 35.21 7.32 45.53 4.00
3409 4013 1.295792 TAATGAGTTTGATCGGCCGC 58.704 50.000 23.51 8.29 0.00 6.53
3416 4020 1.978455 TTTGATCGGCCGCCTATGGT 61.978 55.000 23.51 0.00 0.00 3.55
3492 4096 5.715429 CAAGACTACTTGCAGCTCTAATG 57.285 43.478 0.00 0.00 45.19 1.90
3493 4097 4.399004 AGACTACTTGCAGCTCTAATGG 57.601 45.455 0.00 0.00 0.00 3.16
3494 4098 3.772025 AGACTACTTGCAGCTCTAATGGT 59.228 43.478 0.00 0.00 0.00 3.55
3495 4099 4.116238 GACTACTTGCAGCTCTAATGGTC 58.884 47.826 0.00 0.00 0.00 4.02
3496 4100 3.772025 ACTACTTGCAGCTCTAATGGTCT 59.228 43.478 0.00 0.00 0.00 3.85
3497 4101 4.956700 ACTACTTGCAGCTCTAATGGTCTA 59.043 41.667 0.00 0.00 0.00 2.59
3498 4102 4.826274 ACTTGCAGCTCTAATGGTCTAA 57.174 40.909 0.00 0.00 0.00 2.10
3505 4109 4.024670 AGCTCTAATGGTCTAACGGAACT 58.975 43.478 0.00 0.00 31.77 3.01
3512 4116 2.960384 TGGTCTAACGGAACTGTCTGAA 59.040 45.455 0.00 0.00 33.93 3.02
3564 4171 2.153645 AGAGTGTTTCGCATGCAATCA 58.846 42.857 19.57 12.77 30.74 2.57
3573 4180 6.034790 TGTTTCGCATGCAATCAATGTTATTC 59.965 34.615 19.57 0.00 0.00 1.75
3584 4191 9.962759 GCAATCAATGTTATTCATCTTTGTTTC 57.037 29.630 0.00 0.00 35.48 2.78
3587 4194 8.746922 TCAATGTTATTCATCTTTGTTTCAGC 57.253 30.769 0.00 0.00 35.48 4.26
3588 4195 8.358895 TCAATGTTATTCATCTTTGTTTCAGCA 58.641 29.630 0.00 0.00 35.48 4.41
3589 4196 8.430063 CAATGTTATTCATCTTTGTTTCAGCAC 58.570 33.333 0.00 0.00 35.48 4.40
3590 4197 7.036996 TGTTATTCATCTTTGTTTCAGCACA 57.963 32.000 0.00 0.00 0.00 4.57
3591 4198 7.660112 TGTTATTCATCTTTGTTTCAGCACAT 58.340 30.769 0.00 0.00 0.00 3.21
3592 4199 8.143193 TGTTATTCATCTTTGTTTCAGCACATT 58.857 29.630 0.00 0.00 0.00 2.71
3601 4231 6.645700 TTGTTTCAGCACATTCTTGAAAAC 57.354 33.333 0.97 0.00 31.51 2.43
3610 4240 7.436080 CAGCACATTCTTGAAAACTGTAATGTT 59.564 33.333 0.00 0.00 35.87 2.71
3635 4273 4.219288 AGTGGAAGGAATAAAGCAAGCTTG 59.781 41.667 22.44 22.44 36.26 4.01
3649 4287 3.904571 CAAGCTTGCAGTTGCTAAATCA 58.095 40.909 14.65 0.00 42.66 2.57
3653 4291 5.188434 AGCTTGCAGTTGCTAAATCATCTA 58.812 37.500 8.79 0.00 42.66 1.98
3660 4298 9.955208 TGCAGTTGCTAAATCATCTATTATTTG 57.045 29.630 5.62 0.00 42.66 2.32
3661 4299 8.909671 GCAGTTGCTAAATCATCTATTATTTGC 58.090 33.333 0.00 0.00 38.21 3.68
3671 4310 9.853555 AATCATCTATTATTTGCGTTTTTGTGA 57.146 25.926 0.00 0.00 0.00 3.58
3714 4355 9.403110 CAAAATATGGCAGAACTAGAAATATGC 57.597 33.333 0.00 1.34 0.00 3.14
3715 4356 8.696043 AAATATGGCAGAACTAGAAATATGCA 57.304 30.769 13.49 0.00 35.40 3.96
3752 4478 2.891580 GGATAGTTCGATAGCCTGGTCA 59.108 50.000 0.00 0.00 0.00 4.02
3774 4502 1.301558 CTCATGCTCCCTCGATGGC 60.302 63.158 1.18 0.00 0.00 4.40
3776 4504 3.933722 ATGCTCCCTCGATGGCGG 61.934 66.667 1.18 0.00 38.28 6.13
3793 4521 2.268920 GGGCCTCTTCATGCACGA 59.731 61.111 0.84 0.00 0.00 4.35
3796 4524 1.738099 GCCTCTTCATGCACGACGT 60.738 57.895 0.00 0.00 0.00 4.34
3798 4526 0.388520 CCTCTTCATGCACGACGTCA 60.389 55.000 17.16 0.00 0.00 4.35
3817 4545 2.033141 CAGCCTGGACCCACAGTG 59.967 66.667 0.00 0.00 36.75 3.66
3818 4546 3.958860 AGCCTGGACCCACAGTGC 61.959 66.667 0.00 0.00 36.75 4.40
3855 4703 1.129998 CTGCGAAGGAAACATGCTCAG 59.870 52.381 0.00 0.00 0.00 3.35
3878 4726 6.854892 CAGACGAATGATAAAATGAATCCAGC 59.145 38.462 0.00 0.00 0.00 4.85
3879 4727 6.016777 AGACGAATGATAAAATGAATCCAGCC 60.017 38.462 0.00 0.00 0.00 4.85
3900 4748 3.129988 CCTTGAAGATGGCCAAAGATGAC 59.870 47.826 10.96 0.00 0.00 3.06
3905 4753 3.972133 AGATGGCCAAAGATGACATGAA 58.028 40.909 10.96 0.00 0.00 2.57
3924 4772 9.325198 GACATGAAGGTATGTAATATGTTGACA 57.675 33.333 0.00 0.00 41.15 3.58
3966 4816 6.020360 GCACTTGTTCTGTGTTGATTTTTCTC 60.020 38.462 0.00 0.00 37.70 2.87
3997 4847 9.217278 CACCATCTTCTCTTGAGGATATTATTG 57.783 37.037 0.00 0.00 36.98 1.90
4086 4953 5.217978 TGCAATGCATTCTTTCTTTCCTT 57.782 34.783 9.53 0.00 31.71 3.36
4118 4993 7.492352 TTTTCTCAGAAGTAACTTGGCTAAC 57.508 36.000 0.00 0.00 0.00 2.34
4123 4998 6.296026 TCAGAAGTAACTTGGCTAACAATGT 58.704 36.000 0.00 0.00 38.65 2.71
4125 5000 6.204688 CAGAAGTAACTTGGCTAACAATGTCA 59.795 38.462 0.00 0.00 38.65 3.58
4137 5012 8.694540 TGGCTAACAATGTCATTTTTATATGCT 58.305 29.630 4.95 0.00 0.00 3.79
4268 5312 9.742144 TGTAATAACTACATCTGGGCTTTTAAA 57.258 29.630 0.00 0.00 35.50 1.52
4317 5362 2.941720 GGATTCTCTACCAGCAGCAAAG 59.058 50.000 0.00 0.00 0.00 2.77
4339 5384 5.836347 AGAACTGTTTCTCTTTTGATTGCC 58.164 37.500 0.00 0.00 37.55 4.52
4340 5385 4.590850 ACTGTTTCTCTTTTGATTGCCC 57.409 40.909 0.00 0.00 0.00 5.36
4342 5387 3.575687 CTGTTTCTCTTTTGATTGCCCCT 59.424 43.478 0.00 0.00 0.00 4.79
4376 5429 4.681483 GCCTTTCTACTGTTTGCAAATGTC 59.319 41.667 16.21 3.08 0.00 3.06
4380 5433 2.514205 ACTGTTTGCAAATGTCCTGC 57.486 45.000 16.21 0.73 40.35 4.85
4400 5453 5.335897 CCTGCTGTATTTATGTGCTGTGTTT 60.336 40.000 0.00 0.00 0.00 2.83
4401 5454 6.083098 TGCTGTATTTATGTGCTGTGTTTT 57.917 33.333 0.00 0.00 0.00 2.43
4465 5542 3.584657 TGCATTGCACTGTGCTTACACA 61.585 45.455 30.43 19.47 43.81 3.72
4497 5576 1.971481 TGCTGAGAAAAAGCTGCAGA 58.029 45.000 20.43 0.00 41.42 4.26
4498 5577 2.300433 TGCTGAGAAAAAGCTGCAGAA 58.700 42.857 20.43 0.00 41.42 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.661552 CATGACCGTACGGATCGAGT 59.338 55.000 39.52 17.31 38.96 4.18
49 50 5.641209 CCAACTAGTTGACCAAGATTCAGAG 59.359 44.000 32.50 10.14 42.93 3.35
85 86 8.239314 ACATGTCAACTGCAGAAAGTAATTATG 58.761 33.333 23.35 13.81 33.31 1.90
86 87 8.340618 ACATGTCAACTGCAGAAAGTAATTAT 57.659 30.769 23.35 0.02 0.00 1.28
140 141 5.373812 AGATGTTTAGGGGATCATTTCGT 57.626 39.130 0.00 0.00 0.00 3.85
155 156 6.147328 GTCTAGGAACGCAACTAAAGATGTTT 59.853 38.462 0.00 0.00 0.00 2.83
160 161 3.575256 TGGTCTAGGAACGCAACTAAAGA 59.425 43.478 0.00 0.00 0.00 2.52
231 238 4.664688 ATTCAAGGGTGGTCTTCAGATT 57.335 40.909 0.00 0.00 0.00 2.40
262 269 4.436242 GCAATAGCCTGAATGATCATGG 57.564 45.455 9.46 7.58 34.37 3.66
312 325 9.890629 ATATGAAGAAACAGAGTACAAGCAATA 57.109 29.630 0.00 0.00 0.00 1.90
351 369 4.899616 TCGCGAATACGAAAAAGTTTTGTC 59.100 37.500 6.20 1.70 39.54 3.18
608 651 4.201950 GCAGGCAGTATACCATGAAAACTG 60.202 45.833 0.00 3.79 40.38 3.16
692 905 5.839517 TCCATTTGGGACCAATCAAATTT 57.160 34.783 4.36 0.00 42.15 1.82
784 1027 1.130749 GAAATGTGCTCTGCTCTGCTG 59.869 52.381 0.00 0.00 0.00 4.41
799 1042 7.627585 ATTCGAAAAGTGTGAATGTGAAATG 57.372 32.000 0.00 0.00 31.46 2.32
801 1044 6.475076 CCAATTCGAAAAGTGTGAATGTGAAA 59.525 34.615 0.00 0.00 32.91 2.69
816 1063 0.539438 AGCAGTGGCCCAATTCGAAA 60.539 50.000 0.00 0.00 42.56 3.46
975 1427 5.163713 GGGAAAGAGTGTGAATAATGTGCTC 60.164 44.000 0.00 0.00 0.00 4.26
976 1428 4.702131 GGGAAAGAGTGTGAATAATGTGCT 59.298 41.667 0.00 0.00 0.00 4.40
977 1429 4.458989 TGGGAAAGAGTGTGAATAATGTGC 59.541 41.667 0.00 0.00 0.00 4.57
978 1430 6.558009 CATGGGAAAGAGTGTGAATAATGTG 58.442 40.000 0.00 0.00 0.00 3.21
979 1431 5.126061 GCATGGGAAAGAGTGTGAATAATGT 59.874 40.000 0.00 0.00 0.00 2.71
980 1432 5.450965 GGCATGGGAAAGAGTGTGAATAATG 60.451 44.000 0.00 0.00 0.00 1.90
1845 2367 1.341531 GACGATGATTCCTCCGGTGAT 59.658 52.381 4.76 0.00 0.00 3.06
2097 2637 3.492011 GCAAAGGTGTTTTTCTGATGCAG 59.508 43.478 0.00 0.00 31.29 4.41
2109 2649 0.464870 TGCTGCAATGCAAAGGTGTT 59.535 45.000 9.92 0.00 40.29 3.32
2520 3078 7.556275 CCAGTACCTTGATTGTTGTATAATGGT 59.444 37.037 0.00 0.00 0.00 3.55
2607 3183 0.771755 AACCACCTCCTCCCAGTTTC 59.228 55.000 0.00 0.00 0.00 2.78
2829 3408 6.158520 TCCCAAATAGATGACCATCAAGAGAA 59.841 38.462 12.01 0.00 40.22 2.87
2852 3431 3.005155 AGCAACAGCAATGTTTCTCTTCC 59.995 43.478 0.00 0.00 0.00 3.46
2859 3438 2.034124 AGGACAGCAACAGCAATGTTT 58.966 42.857 0.00 0.00 0.00 2.83
2860 3439 1.696063 AGGACAGCAACAGCAATGTT 58.304 45.000 0.00 0.00 0.00 2.71
2861 3440 2.566833 TAGGACAGCAACAGCAATGT 57.433 45.000 0.00 0.00 0.00 2.71
2864 3446 3.005684 CCAATTTAGGACAGCAACAGCAA 59.994 43.478 0.00 0.00 0.00 3.91
3001 3596 7.116805 GTCTGCAATTTTAGGAACAAAAGATGG 59.883 37.037 0.00 0.00 31.29 3.51
3006 3601 7.279758 CCAAAGTCTGCAATTTTAGGAACAAAA 59.720 33.333 0.00 0.00 0.00 2.44
3075 3670 2.107204 ACCAGCAGTTCCTCTGAATGTT 59.893 45.455 0.00 0.00 46.27 2.71
3140 3735 3.612423 GCCAAAGCCATAAACGTCAATTC 59.388 43.478 0.00 0.00 0.00 2.17
3234 3829 3.138884 TCAACATTCTGGCAACTGCTA 57.861 42.857 1.06 0.00 41.70 3.49
3239 3837 5.812127 GGGAAATATTCAACATTCTGGCAAC 59.188 40.000 0.00 0.00 0.00 4.17
3240 3838 5.721000 AGGGAAATATTCAACATTCTGGCAA 59.279 36.000 0.00 0.00 0.00 4.52
3241 3839 5.127519 CAGGGAAATATTCAACATTCTGGCA 59.872 40.000 0.00 0.00 0.00 4.92
3330 3934 4.463891 TCAGCCTCTTCCAAATTGAAATCC 59.536 41.667 0.00 0.00 0.00 3.01
3409 4013 1.406887 CCGGACCACTTCAACCATAGG 60.407 57.143 0.00 0.00 0.00 2.57
3416 4020 0.841289 AAGAACCCGGACCACTTCAA 59.159 50.000 0.73 0.00 0.00 2.69
3491 4095 2.589720 TCAGACAGTTCCGTTAGACCA 58.410 47.619 0.00 0.00 0.00 4.02
3492 4096 3.655276 TTCAGACAGTTCCGTTAGACC 57.345 47.619 0.00 0.00 0.00 3.85
3493 4097 4.859798 CAGATTCAGACAGTTCCGTTAGAC 59.140 45.833 0.00 0.00 0.00 2.59
3494 4098 4.618460 GCAGATTCAGACAGTTCCGTTAGA 60.618 45.833 0.00 0.00 0.00 2.10
3495 4099 3.614616 GCAGATTCAGACAGTTCCGTTAG 59.385 47.826 0.00 0.00 0.00 2.34
3496 4100 3.006430 TGCAGATTCAGACAGTTCCGTTA 59.994 43.478 0.00 0.00 0.00 3.18
3497 4101 2.224281 TGCAGATTCAGACAGTTCCGTT 60.224 45.455 0.00 0.00 0.00 4.44
3498 4102 1.344438 TGCAGATTCAGACAGTTCCGT 59.656 47.619 0.00 0.00 0.00 4.69
3505 4109 4.823442 ACATTGAAGTTGCAGATTCAGACA 59.177 37.500 13.38 3.12 36.81 3.41
3541 4145 3.745332 TTGCATGCGAAACACTCTATG 57.255 42.857 14.09 0.00 0.00 2.23
3542 4146 3.940852 TGATTGCATGCGAAACACTCTAT 59.059 39.130 12.68 0.00 0.00 1.98
3543 4147 3.333804 TGATTGCATGCGAAACACTCTA 58.666 40.909 12.68 0.00 0.00 2.43
3554 4161 7.709269 AAGATGAATAACATTGATTGCATGC 57.291 32.000 11.82 11.82 39.56 4.06
3564 4171 8.143193 TGTGCTGAAACAAAGATGAATAACATT 58.857 29.630 0.00 0.00 39.56 2.71
3573 4180 6.210796 TCAAGAATGTGCTGAAACAAAGATG 58.789 36.000 0.00 0.00 32.81 2.90
3584 4191 6.919662 ACATTACAGTTTTCAAGAATGTGCTG 59.080 34.615 0.00 0.00 36.45 4.41
3585 4192 7.042797 ACATTACAGTTTTCAAGAATGTGCT 57.957 32.000 0.00 0.00 36.45 4.40
3586 4193 7.434897 TCAACATTACAGTTTTCAAGAATGTGC 59.565 33.333 0.00 0.00 37.53 4.57
3587 4194 8.854979 TCAACATTACAGTTTTCAAGAATGTG 57.145 30.769 0.00 0.00 37.53 3.21
3588 4195 8.686334 ACTCAACATTACAGTTTTCAAGAATGT 58.314 29.630 0.00 0.00 38.74 2.71
3589 4196 8.961092 CACTCAACATTACAGTTTTCAAGAATG 58.039 33.333 0.00 0.00 0.00 2.67
3590 4197 8.137437 CCACTCAACATTACAGTTTTCAAGAAT 58.863 33.333 0.00 0.00 0.00 2.40
3591 4198 7.338196 TCCACTCAACATTACAGTTTTCAAGAA 59.662 33.333 0.00 0.00 0.00 2.52
3592 4199 6.826231 TCCACTCAACATTACAGTTTTCAAGA 59.174 34.615 0.00 0.00 0.00 3.02
3601 4231 7.921786 TTATTCCTTCCACTCAACATTACAG 57.078 36.000 0.00 0.00 0.00 2.74
3610 4240 3.758554 GCTTGCTTTATTCCTTCCACTCA 59.241 43.478 0.00 0.00 0.00 3.41
3635 4273 8.909671 GCAAATAATAGATGATTTAGCAACTGC 58.090 33.333 0.00 0.00 42.49 4.40
3653 4291 7.881643 TGCTTATCACAAAAACGCAAATAAT 57.118 28.000 0.00 0.00 0.00 1.28
3660 4298 3.049206 TGCTTGCTTATCACAAAAACGC 58.951 40.909 0.00 0.00 0.00 4.84
3661 4299 5.601582 CAATGCTTGCTTATCACAAAAACG 58.398 37.500 0.00 0.00 0.00 3.60
3685 4326 6.441093 TTCTAGTTCTGCCATATTTTGCTG 57.559 37.500 0.00 0.00 0.00 4.41
3714 4355 7.484641 CGAACTATCCCAACAACAAAACATATG 59.515 37.037 0.00 0.00 0.00 1.78
3715 4356 7.392113 TCGAACTATCCCAACAACAAAACATAT 59.608 33.333 0.00 0.00 0.00 1.78
3728 4369 2.632996 CCAGGCTATCGAACTATCCCAA 59.367 50.000 0.00 0.00 0.00 4.12
3774 4502 2.825836 GTGCATGAAGAGGCCCCG 60.826 66.667 0.00 0.00 0.00 5.73
3776 4504 2.109126 GTCGTGCATGAAGAGGCCC 61.109 63.158 10.93 0.00 0.00 5.80
3793 4521 4.008933 GGTCCAGGCTGCTGACGT 62.009 66.667 9.56 0.00 0.00 4.34
3796 4524 3.640407 GTGGGTCCAGGCTGCTGA 61.640 66.667 9.56 0.00 0.00 4.26
3798 4526 3.644606 CTGTGGGTCCAGGCTGCT 61.645 66.667 9.56 0.00 0.00 4.24
3822 4550 4.994471 CGCAGCCAGACAGCCACA 62.994 66.667 0.00 0.00 0.00 4.17
3826 4667 3.123620 CCTTCGCAGCCAGACAGC 61.124 66.667 0.00 0.00 0.00 4.40
3828 4669 0.884704 GTTTCCTTCGCAGCCAGACA 60.885 55.000 0.00 0.00 0.00 3.41
3830 4671 0.036732 ATGTTTCCTTCGCAGCCAGA 59.963 50.000 0.00 0.00 0.00 3.86
3831 4672 0.169672 CATGTTTCCTTCGCAGCCAG 59.830 55.000 0.00 0.00 0.00 4.85
3855 4703 6.016777 AGGCTGGATTCATTTTATCATTCGTC 60.017 38.462 0.00 0.00 0.00 4.20
3878 4726 3.129988 GTCATCTTTGGCCATCTTCAAGG 59.870 47.826 6.09 0.00 0.00 3.61
3879 4727 3.760151 TGTCATCTTTGGCCATCTTCAAG 59.240 43.478 6.09 7.08 0.00 3.02
3928 4776 8.668353 CACAGAACAAGTGCATTTATATGTAGT 58.332 33.333 6.80 0.00 34.12 2.73
3948 4796 7.174946 GGTGATAGGAGAAAAATCAACACAGAA 59.825 37.037 0.00 0.00 37.31 3.02
3950 4798 6.430925 TGGTGATAGGAGAAAAATCAACACAG 59.569 38.462 0.00 0.00 41.24 3.66
3966 4816 4.898265 TCCTCAAGAGAAGATGGTGATAGG 59.102 45.833 0.00 0.00 0.00 2.57
3997 4847 8.627208 TCATCATTATAATCTCCAAGAAAGGC 57.373 34.615 0.00 0.00 0.00 4.35
4101 4976 6.296026 TGACATTGTTAGCCAAGTTACTTCT 58.704 36.000 0.00 0.00 36.25 2.85
4102 4977 6.554334 TGACATTGTTAGCCAAGTTACTTC 57.446 37.500 0.00 0.00 36.25 3.01
4112 4987 8.971321 CAGCATATAAAAATGACATTGTTAGCC 58.029 33.333 14.61 5.10 0.00 3.93
4118 4993 7.493320 AGGTTGCAGCATATAAAAATGACATTG 59.507 33.333 0.34 0.00 0.00 2.82
4123 4998 8.518430 TTCTAGGTTGCAGCATATAAAAATGA 57.482 30.769 2.05 0.00 0.00 2.57
4125 5000 8.752005 TCTTCTAGGTTGCAGCATATAAAAAT 57.248 30.769 2.05 0.00 0.00 1.82
4137 5012 2.158682 TGGCTGTTTCTTCTAGGTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
4234 5275 7.039644 CCCAGATGTAGTTATTACAGTAGGAGG 60.040 44.444 0.00 0.00 45.05 4.30
4302 5346 2.104792 ACAGTTCTTTGCTGCTGGTAGA 59.895 45.455 0.00 0.00 37.47 2.59
4303 5347 2.498167 ACAGTTCTTTGCTGCTGGTAG 58.502 47.619 0.00 0.00 37.47 3.18
4304 5348 2.638480 ACAGTTCTTTGCTGCTGGTA 57.362 45.000 0.00 0.00 37.47 3.25
4317 5362 4.984785 GGGCAATCAAAAGAGAAACAGTTC 59.015 41.667 0.00 0.00 0.00 3.01
4352 5397 4.099266 ACATTTGCAAACAGTAGAAAGGCA 59.901 37.500 15.41 0.00 0.00 4.75
4353 5398 4.620982 ACATTTGCAAACAGTAGAAAGGC 58.379 39.130 15.41 0.00 0.00 4.35
4376 5429 3.691118 ACACAGCACATAAATACAGCAGG 59.309 43.478 0.00 0.00 0.00 4.85
4380 5433 5.345741 GCCAAAACACAGCACATAAATACAG 59.654 40.000 0.00 0.00 0.00 2.74
4400 5453 0.250684 TGCTTCGTTCCAGATGCCAA 60.251 50.000 3.10 0.00 39.61 4.52
4401 5454 0.035152 ATGCTTCGTTCCAGATGCCA 60.035 50.000 3.10 0.00 39.61 4.92
4427 5504 4.826274 ATGCAGTACCTTGAGAAGCTTA 57.174 40.909 0.00 0.00 0.00 3.09
4465 5542 8.239998 GCTTTTTCTCAGCAATTTAGTATGAGT 58.760 33.333 0.00 0.00 38.76 3.41


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

AutoCloner maintained by Alex Coulton.