Multiple sequence alignment - TraesCS3D01G458600

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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 TraesCS3D01G458600 chr3D 100.000 6643 0 0 1 6643 563869977 563863335 0.000000e+00 12268.0
1 TraesCS3D01G458600 chr3D 95.833 48 2 0 5982 6029 563863886 563863839 1.990000e-10 78.7
2 TraesCS3D01G458600 chr3D 95.833 48 2 0 6092 6139 563863996 563863949 1.990000e-10 78.7
3 TraesCS3D01G458600 chr2A 97.998 4246 74 3 1785 6029 7927801 7923566 0.000000e+00 7360.0
4 TraesCS3D01G458600 chr2A 95.620 1644 49 9 111 1735 7929438 7927799 0.000000e+00 2615.0
5 TraesCS3D01G458600 chr2A 96.920 552 17 0 6092 6643 7923613 7923062 0.000000e+00 926.0
6 TraesCS3D01G458600 chr2A 93.043 115 8 0 3672 3786 8175943 8176057 1.150000e-37 169.0
7 TraesCS3D01G458600 chr2A 91.304 115 10 0 3672 3786 8349920 8350034 2.480000e-34 158.0
8 TraesCS3D01G458600 chr2A 95.122 82 4 0 1 82 7929598 7929517 5.410000e-26 130.0
9 TraesCS3D01G458600 chr2A 91.837 49 4 0 703 751 8174028 8174076 1.200000e-07 69.4
10 TraesCS3D01G458600 chr4B 88.819 957 76 14 1451 2382 672238428 672237478 0.000000e+00 1146.0
11 TraesCS3D01G458600 chr4B 87.062 1028 96 17 1385 2382 185230293 185229273 0.000000e+00 1127.0
12 TraesCS3D01G458600 chr4B 87.853 955 87 13 1451 2379 599643319 599642368 0.000000e+00 1094.0
13 TraesCS3D01G458600 chr4B 87.762 956 87 12 1451 2379 599552670 599551718 0.000000e+00 1090.0
14 TraesCS3D01G458600 chr4B 87.080 774 65 15 2370 3126 672237258 672236503 0.000000e+00 843.0
15 TraesCS3D01G458600 chr4B 89.489 666 59 9 2483 3141 185228949 185228288 0.000000e+00 832.0
16 TraesCS3D01G458600 chr4B 83.796 901 95 30 2370 3230 43728092 43728981 0.000000e+00 808.0
17 TraesCS3D01G458600 chr4B 86.154 260 23 6 2370 2625 599642135 599641885 1.100000e-67 268.0
18 TraesCS3D01G458600 chr4B 85.000 260 26 6 2370 2625 599551485 599551235 1.110000e-62 252.0
19 TraesCS3D01G458600 chrUn 87.329 1026 92 17 1389 2382 100082847 100083866 0.000000e+00 1140.0
20 TraesCS3D01G458600 chrUn 87.327 797 73 15 2370 3149 100084095 100084880 0.000000e+00 887.0
21 TraesCS3D01G458600 chr4A 86.906 1031 97 16 1385 2382 448518439 448519464 0.000000e+00 1122.0
22 TraesCS3D01G458600 chr4A 85.629 1009 111 15 1404 2382 572564863 572563859 0.000000e+00 1029.0
23 TraesCS3D01G458600 chr4A 84.694 882 98 24 2370 3230 448519689 448520554 0.000000e+00 846.0
24 TraesCS3D01G458600 chr4A 84.868 793 88 20 2370 3136 572563630 572562844 0.000000e+00 771.0
25 TraesCS3D01G458600 chr4D 86.952 1027 96 15 1385 2377 122196564 122195542 0.000000e+00 1120.0
26 TraesCS3D01G458600 chr4D 84.857 1017 111 21 1404 2382 30405579 30406590 0.000000e+00 985.0
27 TraesCS3D01G458600 chr4D 84.642 879 101 23 2370 3230 122195311 122194449 0.000000e+00 845.0
28 TraesCS3D01G458600 chr4D 85.268 801 75 26 2370 3131 30406820 30407616 0.000000e+00 785.0
29 TraesCS3D01G458600 chr7A 86.210 1008 99 21 1407 2382 213097393 213096394 0.000000e+00 1055.0
30 TraesCS3D01G458600 chr7A 94.545 660 24 4 311 958 466531077 466530418 0.000000e+00 1009.0
31 TraesCS3D01G458600 chr7A 93.593 437 24 2 1321 1753 466525463 466525027 0.000000e+00 649.0
32 TraesCS3D01G458600 chr7A 80.795 880 106 27 2370 3230 213096167 213095332 1.220000e-176 630.0
33 TraesCS3D01G458600 chr7A 94.915 177 3 3 87 258 466531359 466531184 8.490000e-69 272.0
34 TraesCS3D01G458600 chr7A 93.902 82 5 0 1 82 466531503 466531422 2.520000e-24 124.0
35 TraesCS3D01G458600 chr7A 91.463 82 7 0 1 82 466536024 466535943 5.440000e-21 113.0
36 TraesCS3D01G458600 chr7A 98.039 51 1 0 270 320 466531145 466531095 9.180000e-14 89.8
37 TraesCS3D01G458600 chr2B 97.104 587 14 3 2969 3555 12053122 12053705 0.000000e+00 987.0
38 TraesCS3D01G458600 chr2B 95.522 469 21 0 2462 2930 12052654 12053122 0.000000e+00 750.0
39 TraesCS3D01G458600 chr2B 87.952 581 27 13 585 1139 12051674 12052237 0.000000e+00 645.0
40 TraesCS3D01G458600 chr2B 90.476 315 26 2 1445 1755 12053700 12054014 4.790000e-111 412.0
41 TraesCS3D01G458600 chr2B 91.304 115 10 0 3672 3786 12011540 12011654 2.480000e-34 158.0
42 TraesCS3D01G458600 chr2B 90.244 82 8 0 1 82 12045186 12045267 2.530000e-19 108.0
43 TraesCS3D01G458600 chr2B 89.796 49 5 0 703 751 12008331 12008379 5.560000e-06 63.9
44 TraesCS3D01G458600 chr7B 81.725 881 97 29 2370 3230 171994291 171995127 0.000000e+00 676.0
45 TraesCS3D01G458600 chr6B 90.566 159 11 4 3628 3786 17227619 17227465 2.430000e-49 207.0
46 TraesCS3D01G458600 chr6A 89.222 167 12 6 3622 3786 11272979 11273141 3.140000e-48 204.0
47 TraesCS3D01G458600 chr6D 89.937 159 12 4 3628 3786 9248777 9248623 1.130000e-47 202.0
48 TraesCS3D01G458600 chr2D 94.495 109 6 0 3678 3786 8776641 8776533 1.150000e-37 169.0
49 TraesCS3D01G458600 chr2D 91.837 49 4 0 703 751 8778622 8778574 1.200000e-07 69.4


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 TraesCS3D01G458600 chr3D 563863335 563869977 6642 True 12268.00 12268 100.00000 1 6643 1 chr3D.!!$R1 6642
1 TraesCS3D01G458600 chr2A 7923062 7929598 6536 True 2757.75 7360 96.41500 1 6643 4 chr2A.!!$R1 6642
2 TraesCS3D01G458600 chr4B 672236503 672238428 1925 True 994.50 1146 87.94950 1451 3126 2 chr4B.!!$R4 1675
3 TraesCS3D01G458600 chr4B 185228288 185230293 2005 True 979.50 1127 88.27550 1385 3141 2 chr4B.!!$R1 1756
4 TraesCS3D01G458600 chr4B 43728092 43728981 889 False 808.00 808 83.79600 2370 3230 1 chr4B.!!$F1 860
5 TraesCS3D01G458600 chr4B 599641885 599643319 1434 True 681.00 1094 87.00350 1451 2625 2 chr4B.!!$R3 1174
6 TraesCS3D01G458600 chr4B 599551235 599552670 1435 True 671.00 1090 86.38100 1451 2625 2 chr4B.!!$R2 1174
7 TraesCS3D01G458600 chrUn 100082847 100084880 2033 False 1013.50 1140 87.32800 1389 3149 2 chrUn.!!$F1 1760
8 TraesCS3D01G458600 chr4A 448518439 448520554 2115 False 984.00 1122 85.80000 1385 3230 2 chr4A.!!$F1 1845
9 TraesCS3D01G458600 chr4A 572562844 572564863 2019 True 900.00 1029 85.24850 1404 3136 2 chr4A.!!$R1 1732
10 TraesCS3D01G458600 chr4D 122194449 122196564 2115 True 982.50 1120 85.79700 1385 3230 2 chr4D.!!$R1 1845
11 TraesCS3D01G458600 chr4D 30405579 30407616 2037 False 885.00 985 85.06250 1404 3131 2 chr4D.!!$F1 1727
12 TraesCS3D01G458600 chr7A 213095332 213097393 2061 True 842.50 1055 83.50250 1407 3230 2 chr7A.!!$R3 1823
13 TraesCS3D01G458600 chr7A 466530418 466531503 1085 True 373.70 1009 95.35025 1 958 4 chr7A.!!$R4 957
14 TraesCS3D01G458600 chr2B 12051674 12054014 2340 False 698.50 987 92.76350 585 3555 4 chr2B.!!$F3 2970
15 TraesCS3D01G458600 chr7B 171994291 171995127 836 False 676.00 676 81.72500 2370 3230 1 chr7B.!!$F1 860

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
338 459 1.028330 GTTGGGTAGGGTTTAGCGGC 61.028 60.000 0.00 0.0 0.00 6.53 F
1142 1308 0.693049 TGGCCTTCTCCCTTGTTCTC 59.307 55.000 3.32 0.0 0.00 2.87 F
2119 2358 2.038659 GAATAGAGGCTGAGCTGGAGT 58.961 52.381 3.72 0.0 0.00 3.85 F
2871 3442 0.106894 GGATCAACTAAGGGAGGCGG 59.893 60.000 0.00 0.0 0.00 6.13 F
4576 5171 1.658409 GTTTTGCAGTGCTGGTCGC 60.658 57.895 17.60 0.0 39.77 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1319 0.110056 CAGCAGAATTTCAAGCGCGT 60.110 50.000 8.43 0.0 0.00 6.01 R
2847 3418 3.495806 GCCTCCCTTAGTTGATCCTGATG 60.496 52.174 0.00 0.0 0.00 3.07 R
3656 4250 1.880027 GAGAAATGCACAACCCGAACT 59.120 47.619 0.00 0.0 0.00 3.01 R
4798 5393 0.235665 GCACATTACCATCGGCATCG 59.764 55.000 0.00 0.0 37.82 3.84 R
6441 7036 0.764271 TCACTGGTGCATCCAAGACA 59.236 50.000 8.96 0.0 46.59 3.41 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
82 144 3.064207 GACAGTGAACGGTAGAAATGCA 58.936 45.455 0.00 0.00 0.00 3.96
134 196 1.762460 CCGGATCTGCTACACCCCT 60.762 63.158 0.00 0.00 0.00 4.79
320 441 3.330720 CCCCTCCCTTTCCGCTGT 61.331 66.667 0.00 0.00 0.00 4.40
338 459 1.028330 GTTGGGTAGGGTTTAGCGGC 61.028 60.000 0.00 0.00 0.00 6.53
420 541 2.123640 GAGGGGGAGGACGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
717 850 3.681835 GACGGTGAGGGCACGTCT 61.682 66.667 8.94 0.00 46.09 4.18
773 912 4.789075 CTACACCGACACCCCGCG 62.789 72.222 0.00 0.00 0.00 6.46
853 992 2.759795 GGGGCCAGAAGAGCAAGT 59.240 61.111 4.39 0.00 0.00 3.16
1142 1308 0.693049 TGGCCTTCTCCCTTGTTCTC 59.307 55.000 3.32 0.00 0.00 2.87
1273 1443 2.644707 GTTTATGTGAGCGCGCGC 60.645 61.111 45.10 45.10 42.33 6.86
1497 1678 4.375305 GCGTTGCATGAATTCTTTTGACAC 60.375 41.667 7.05 2.46 0.00 3.67
1505 1686 6.266168 TGAATTCTTTTGACACGCCATATT 57.734 33.333 7.05 0.00 0.00 1.28
1750 1949 8.879759 TGCTAAATTACACTGCAATACTTCTAC 58.120 33.333 0.00 0.00 0.00 2.59
1764 1985 7.042187 GCAATACTTCTACTACTGCGTACTCTA 60.042 40.741 0.00 0.00 0.00 2.43
1778 2000 4.250464 CGTACTCTAATGCTCCAAACCAA 58.750 43.478 0.00 0.00 0.00 3.67
1903 2136 6.151144 GCAAATGTAGGAAGTAATTGGTGACT 59.849 38.462 0.00 0.00 0.00 3.41
1986 2219 9.669353 CATGGTATGCTGTGATTCTTTTTATAC 57.331 33.333 0.00 0.00 0.00 1.47
2119 2358 2.038659 GAATAGAGGCTGAGCTGGAGT 58.961 52.381 3.72 0.00 0.00 3.85
2290 2534 5.784177 ACATATGGGCTTTGTAGATCTACG 58.216 41.667 24.32 13.54 38.85 3.51
2871 3442 0.106894 GGATCAACTAAGGGAGGCGG 59.893 60.000 0.00 0.00 0.00 6.13
3089 3668 6.349300 AGTAGTGTCCGCATCATCTAAAAAT 58.651 36.000 0.00 0.00 0.00 1.82
3812 4406 5.799213 AGCAAACAACAGCTCTTCTACTAT 58.201 37.500 0.00 0.00 36.00 2.12
4304 4898 5.051891 ACTGTAAATTGTGAGCTGAATGC 57.948 39.130 0.00 0.00 43.29 3.56
4576 5171 1.658409 GTTTTGCAGTGCTGGTCGC 60.658 57.895 17.60 0.00 39.77 5.19
4653 5248 1.702699 TGGGACCTACTTCTCCCCTA 58.297 55.000 0.00 0.00 45.30 3.53
4659 5254 4.403734 GACCTACTTCTCCCCTATCAGAG 58.596 52.174 0.00 0.00 0.00 3.35
4660 5255 3.161866 CCTACTTCTCCCCTATCAGAGC 58.838 54.545 0.00 0.00 0.00 4.09
4661 5256 2.856760 ACTTCTCCCCTATCAGAGCA 57.143 50.000 0.00 0.00 0.00 4.26
4662 5257 3.121929 ACTTCTCCCCTATCAGAGCAA 57.878 47.619 0.00 0.00 0.00 3.91
4663 5258 3.037549 ACTTCTCCCCTATCAGAGCAAG 58.962 50.000 0.00 0.00 0.00 4.01
4664 5259 3.303938 CTTCTCCCCTATCAGAGCAAGA 58.696 50.000 0.00 0.00 0.00 3.02
4665 5260 3.627041 TCTCCCCTATCAGAGCAAGAT 57.373 47.619 0.00 0.00 0.00 2.40
4666 5261 4.749048 TCTCCCCTATCAGAGCAAGATA 57.251 45.455 0.00 0.00 0.00 1.98
4667 5262 4.411927 TCTCCCCTATCAGAGCAAGATAC 58.588 47.826 0.00 0.00 0.00 2.24
4793 5388 3.006217 AGGCTTCACTTCCAAGCAAATTC 59.994 43.478 6.74 0.00 46.94 2.17
4798 5393 5.695851 TCACTTCCAAGCAAATTCTCTTC 57.304 39.130 0.00 0.00 0.00 2.87
4815 5410 2.102420 TCTTCGATGCCGATGGTAATGT 59.898 45.455 0.00 0.00 45.10 2.71
4851 5446 4.646945 TGCTCCTCAAGAGTATAGTCAAGG 59.353 45.833 10.21 12.23 45.21 3.61
4905 5500 5.063204 TGGAATATTTGACGATGCCTTAGG 58.937 41.667 0.00 0.00 0.00 2.69
4980 5575 4.661222 TCAAATGGTCCTGCTGTTGATTA 58.339 39.130 0.00 0.00 0.00 1.75
5090 5685 2.221169 TGTTGCTTACAAGGCTCAGTG 58.779 47.619 3.11 0.00 36.16 3.66
5114 5709 5.486735 AGATGATTCAGAGGCCTTGATAG 57.513 43.478 6.77 0.00 0.00 2.08
5115 5710 3.482156 TGATTCAGAGGCCTTGATAGC 57.518 47.619 6.77 7.39 0.00 2.97
5119 5714 6.019108 TGATTCAGAGGCCTTGATAGCTATA 58.981 40.000 6.77 0.00 0.00 1.31
5152 5747 1.867595 ATTGGGGGAGCAGGTTGGAG 61.868 60.000 0.00 0.00 0.00 3.86
5181 5776 1.611006 TGCAATGCACCACACGTATTT 59.389 42.857 2.72 0.00 31.71 1.40
5199 5794 5.872617 CGTATTTCTTTCACTGGTGGTATGA 59.127 40.000 0.70 0.00 0.00 2.15
5262 5857 5.177326 AGTCAGCTTGCTCAAATTCTCTAG 58.823 41.667 0.00 0.00 0.00 2.43
5374 5969 1.821332 CTTCCGATGCAGGGCTTCC 60.821 63.158 1.72 0.00 30.42 3.46
5520 6115 7.325660 TCAGGCTTTTATTGATGAAGTGATC 57.674 36.000 0.00 0.00 0.00 2.92
5522 6117 6.037500 CAGGCTTTTATTGATGAAGTGATCGA 59.962 38.462 0.00 0.00 0.00 3.59
5738 6333 1.089481 ATGCATGTCTAACACCGGCG 61.089 55.000 0.00 0.00 0.00 6.46
5924 6519 2.167487 GACTAGCCTAGCTTTGCTCTGT 59.833 50.000 12.40 12.33 40.44 3.41
6025 6620 8.413229 TCAAGAGTGATGATAAACGATGATGTA 58.587 33.333 0.00 0.00 0.00 2.29
6026 6621 9.201127 CAAGAGTGATGATAAACGATGATGTAT 57.799 33.333 0.00 0.00 0.00 2.29
6027 6622 8.978564 AGAGTGATGATAAACGATGATGTATC 57.021 34.615 0.00 0.00 0.00 2.24
6028 6623 8.579863 AGAGTGATGATAAACGATGATGTATCA 58.420 33.333 0.00 0.00 41.70 2.15
6030 6625 9.716531 AGTGATGATAAACGATGATGTATCATT 57.283 29.630 8.62 0.00 46.84 2.57
6063 6658 8.705134 TGACGTATTAAACTATTGATTATGCCG 58.295 33.333 0.00 0.00 0.00 5.69
6064 6659 8.597662 ACGTATTAAACTATTGATTATGCCGT 57.402 30.769 0.00 0.00 0.00 5.68
6065 6660 9.695526 ACGTATTAAACTATTGATTATGCCGTA 57.304 29.630 0.00 0.00 0.00 4.02
6074 6669 8.883731 ACTATTGATTATGCCGTATAAAGATGC 58.116 33.333 0.00 0.00 35.03 3.91
6075 6670 7.928307 ATTGATTATGCCGTATAAAGATGCT 57.072 32.000 0.00 0.00 35.03 3.79
6076 6671 7.744087 TTGATTATGCCGTATAAAGATGCTT 57.256 32.000 0.00 0.00 35.03 3.91
6077 6672 7.364522 TGATTATGCCGTATAAAGATGCTTC 57.635 36.000 0.00 0.00 35.03 3.86
6078 6673 6.371548 TGATTATGCCGTATAAAGATGCTTCC 59.628 38.462 0.00 0.00 35.03 3.46
6079 6674 3.552132 TGCCGTATAAAGATGCTTCCA 57.448 42.857 0.00 0.00 0.00 3.53
6080 6675 4.085357 TGCCGTATAAAGATGCTTCCAT 57.915 40.909 0.00 0.00 0.00 3.41
6081 6676 3.814842 TGCCGTATAAAGATGCTTCCATG 59.185 43.478 0.00 0.00 0.00 3.66
6082 6677 3.815401 GCCGTATAAAGATGCTTCCATGT 59.185 43.478 0.00 0.00 0.00 3.21
6083 6678 4.994852 GCCGTATAAAGATGCTTCCATGTA 59.005 41.667 0.00 0.00 0.00 2.29
6084 6679 5.107065 GCCGTATAAAGATGCTTCCATGTAC 60.107 44.000 0.00 0.00 0.00 2.90
6085 6680 5.408604 CCGTATAAAGATGCTTCCATGTACC 59.591 44.000 0.00 0.00 0.00 3.34
6086 6681 5.989168 CGTATAAAGATGCTTCCATGTACCA 59.011 40.000 0.00 0.00 0.00 3.25
6087 6682 6.650807 CGTATAAAGATGCTTCCATGTACCAT 59.349 38.462 0.00 0.00 0.00 3.55
6088 6683 7.817478 CGTATAAAGATGCTTCCATGTACCATA 59.183 37.037 0.00 0.00 0.00 2.74
6089 6684 9.672673 GTATAAAGATGCTTCCATGTACCATAT 57.327 33.333 0.00 0.00 0.00 1.78
6098 6693 9.487442 TGCTTCCATGTACCATATATATACAGA 57.513 33.333 12.27 5.34 32.58 3.41
6118 6713 7.630242 ACAGATGTTTTCTTTTCAAGAGTGA 57.370 32.000 0.00 0.00 39.03 3.41
6119 6714 8.230472 ACAGATGTTTTCTTTTCAAGAGTGAT 57.770 30.769 0.00 0.00 39.03 3.06
6120 6715 8.133627 ACAGATGTTTTCTTTTCAAGAGTGATG 58.866 33.333 0.00 0.00 39.03 3.07
6121 6716 8.347771 CAGATGTTTTCTTTTCAAGAGTGATGA 58.652 33.333 0.00 0.00 39.03 2.92
6122 6717 9.075678 AGATGTTTTCTTTTCAAGAGTGATGAT 57.924 29.630 0.00 0.00 39.03 2.45
6127 6722 9.663904 TTTTCTTTTCAAGAGTGATGATAAACG 57.336 29.630 0.00 0.00 39.03 3.60
6128 6723 8.601845 TTCTTTTCAAGAGTGATGATAAACGA 57.398 30.769 0.00 0.00 39.03 3.85
6129 6724 8.777865 TCTTTTCAAGAGTGATGATAAACGAT 57.222 30.769 0.00 0.00 32.48 3.73
6130 6725 8.659491 TCTTTTCAAGAGTGATGATAAACGATG 58.341 33.333 0.00 0.00 32.48 3.84
6131 6726 8.546597 TTTTCAAGAGTGATGATAAACGATGA 57.453 30.769 0.00 0.00 32.48 2.92
6132 6727 8.722480 TTTCAAGAGTGATGATAAACGATGAT 57.278 30.769 0.00 0.00 32.48 2.45
6133 6728 7.704789 TCAAGAGTGATGATAAACGATGATG 57.295 36.000 0.00 0.00 0.00 3.07
6134 6729 6.201615 TCAAGAGTGATGATAAACGATGATGC 59.798 38.462 0.00 0.00 0.00 3.91
6188 6783 7.243604 TGAATGGCATTACCTCAAGAAAAAT 57.756 32.000 13.65 0.00 40.22 1.82
6214 6809 6.630071 ACAGGGCATAAACAAATCATTACAC 58.370 36.000 0.00 0.00 0.00 2.90
6261 6856 0.181350 CAAGGCCGCCTTAAGGAGAT 59.819 55.000 26.21 8.58 42.67 2.75
6283 6878 7.923888 AGATGAATTATAGCACACATCACAAC 58.076 34.615 0.00 0.00 37.27 3.32
6291 6886 2.795681 GCACACATCACAACCACAACAG 60.796 50.000 0.00 0.00 0.00 3.16
6403 6998 0.536233 TGCCTAAAAGTGCTTGCCGA 60.536 50.000 0.00 0.00 0.00 5.54
6441 7036 5.160607 TGGTCGGTCTTGAGAAATGTATT 57.839 39.130 0.00 0.00 0.00 1.89
6574 7169 6.069673 ACACAATACTCCCAACATAGGAATGA 60.070 38.462 0.00 0.00 36.54 2.57
6601 7196 3.640000 CACCGCCATCGCCGATTC 61.640 66.667 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.802553 ATAACTAGCCGGGATGTGGT 58.197 50.000 2.18 0.00 0.00 4.16
82 144 1.140375 GGAACGGACGGCTACGATT 59.860 57.895 0.00 0.00 44.60 3.34
134 196 4.792068 ACACCCTTGTTCATTCAGAGAAA 58.208 39.130 0.00 0.00 28.43 2.52
217 279 2.114411 TTTCCGTTGGCTGGGTCC 59.886 61.111 0.00 0.00 0.00 4.46
320 441 1.300634 GCCGCTAAACCCTACCCAA 59.699 57.895 0.00 0.00 0.00 4.12
338 459 3.522731 CGAGACCTCCCTCAGCCG 61.523 72.222 0.00 0.00 32.86 5.52
753 892 2.939261 CGGGGTGTCGGTGTAGCTT 61.939 63.158 0.00 0.00 0.00 3.74
848 987 2.397252 GCATCTCGTCGCACTTGC 59.603 61.111 0.00 0.00 37.78 4.01
935 1074 2.597510 GCACCAGGCTCGGGTTTT 60.598 61.111 7.70 0.00 40.25 2.43
1153 1319 0.110056 CAGCAGAATTTCAAGCGCGT 60.110 50.000 8.43 0.00 0.00 6.01
1161 1327 6.914757 GCATATTGTAACTCCAGCAGAATTTC 59.085 38.462 0.00 0.00 0.00 2.17
1273 1443 7.148641 GGAATGCACGTCCCTCATATATATAG 58.851 42.308 6.97 0.00 0.00 1.31
1497 1678 7.439157 TCTGATCCAGAAATAAAATATGGCG 57.561 36.000 0.00 0.00 37.57 5.69
1505 1686 9.330063 GTGTCATACATCTGATCCAGAAATAAA 57.670 33.333 0.43 0.00 44.04 1.40
1764 1985 4.262420 GGTACATGTTTGGTTTGGAGCATT 60.262 41.667 2.30 0.00 32.51 3.56
1778 2000 5.116084 AGTTCAGCATATGGGTACATGTT 57.884 39.130 2.30 0.00 37.97 2.71
2119 2358 9.801873 GGCTAATTTTATTTCTTGTGCAGATAA 57.198 29.630 0.00 0.00 0.00 1.75
2290 2534 4.979197 CGATACAACTCTTACAGGATCAGC 59.021 45.833 0.00 0.00 0.00 4.26
2847 3418 3.495806 GCCTCCCTTAGTTGATCCTGATG 60.496 52.174 0.00 0.00 0.00 3.07
2871 3442 3.982576 TTCTTTGCCCGTTTTCTTCTC 57.017 42.857 0.00 0.00 0.00 2.87
3201 3795 6.189859 TCATTATTGGCAGACTCTGGAAAAT 58.810 36.000 8.17 0.00 31.21 1.82
3536 4130 7.110155 AGGTCACAAACAGAATATCGGTTTAT 58.890 34.615 8.00 0.00 41.53 1.40
3656 4250 1.880027 GAGAAATGCACAACCCGAACT 59.120 47.619 0.00 0.00 0.00 3.01
3837 4431 3.396260 GGCAGTACCTGAACAGTGTTA 57.604 47.619 8.88 0.00 32.44 2.41
4069 4663 2.734346 GCACACCGGCAAACATGC 60.734 61.111 0.00 0.00 0.00 4.06
4304 4898 5.413309 ACCAAGAATCAGTACTTCAGGAG 57.587 43.478 10.02 0.00 0.00 3.69
4459 5054 4.890088 ACAGTTAACAGCAATCTAACGGA 58.110 39.130 8.61 0.00 32.06 4.69
4653 5248 2.223923 GCTGGACGTATCTTGCTCTGAT 60.224 50.000 0.00 0.00 0.00 2.90
4659 5254 2.279741 TCATTGCTGGACGTATCTTGC 58.720 47.619 0.00 0.00 0.00 4.01
4660 5255 4.393062 ACTTTCATTGCTGGACGTATCTTG 59.607 41.667 0.00 0.00 0.00 3.02
4661 5256 4.393062 CACTTTCATTGCTGGACGTATCTT 59.607 41.667 0.00 0.00 0.00 2.40
4662 5257 3.935203 CACTTTCATTGCTGGACGTATCT 59.065 43.478 0.00 0.00 0.00 1.98
4663 5258 3.684788 ACACTTTCATTGCTGGACGTATC 59.315 43.478 0.00 0.00 0.00 2.24
4664 5259 3.436704 CACACTTTCATTGCTGGACGTAT 59.563 43.478 0.00 0.00 0.00 3.06
4665 5260 2.805671 CACACTTTCATTGCTGGACGTA 59.194 45.455 0.00 0.00 0.00 3.57
4666 5261 1.603802 CACACTTTCATTGCTGGACGT 59.396 47.619 0.00 0.00 0.00 4.34
4667 5262 1.069022 CCACACTTTCATTGCTGGACG 60.069 52.381 0.00 0.00 0.00 4.79
4798 5393 0.235665 GCACATTACCATCGGCATCG 59.764 55.000 0.00 0.00 37.82 3.84
4851 5446 5.979517 GCACCATAATCAAATAAGGCAAGTC 59.020 40.000 0.00 0.00 0.00 3.01
4864 5459 4.299586 TCCAGAAACTGCACCATAATCA 57.700 40.909 0.00 0.00 0.00 2.57
4905 5500 7.068716 AGGTTGGATATTTGTTAATTCCAGCTC 59.931 37.037 0.00 0.00 35.31 4.09
4950 5545 4.891756 CAGCAGGACCATTTGATAGGAAAT 59.108 41.667 0.00 0.00 0.00 2.17
4957 5552 3.159213 TCAACAGCAGGACCATTTGAT 57.841 42.857 0.00 0.00 0.00 2.57
4964 5559 3.179443 TCGATAATCAACAGCAGGACC 57.821 47.619 0.00 0.00 0.00 4.46
4980 5575 2.939103 GCAATCACAGCCTTACTTCGAT 59.061 45.455 0.00 0.00 0.00 3.59
5018 5613 5.271625 TCGAGAATATGTTAACAGCGAGAC 58.728 41.667 14.65 3.91 0.00 3.36
5019 5614 5.494632 TCGAGAATATGTTAACAGCGAGA 57.505 39.130 14.65 4.45 0.00 4.04
5090 5685 4.148128 TCAAGGCCTCTGAATCATCTTC 57.852 45.455 5.23 0.00 0.00 2.87
5114 5709 8.360390 CCCCCAATAGAAATTTTCAAGTATAGC 58.640 37.037 11.53 0.00 0.00 2.97
5115 5710 9.640952 TCCCCCAATAGAAATTTTCAAGTATAG 57.359 33.333 11.53 0.00 0.00 1.31
5119 5714 5.187772 GCTCCCCCAATAGAAATTTTCAAGT 59.812 40.000 11.53 0.00 0.00 3.16
5133 5728 1.856873 TCCAACCTGCTCCCCCAAT 60.857 57.895 0.00 0.00 0.00 3.16
5152 5747 0.244721 GGTGCATTGCAGGAACCTTC 59.755 55.000 12.53 0.00 40.08 3.46
5181 5776 5.163405 GCTCTATCATACCACCAGTGAAAGA 60.163 44.000 0.00 0.00 0.00 2.52
5199 5794 4.097418 GGTACATATGGTCCCAGCTCTAT 58.903 47.826 7.80 0.00 0.00 1.98
5272 5867 8.397906 GCTAAACATCTTACATTGTGATGCTTA 58.602 33.333 14.01 11.97 40.66 3.09
5374 5969 0.249657 GCATCCCGCTGTTCTAGAGG 60.250 60.000 0.00 0.00 45.13 3.69
5383 5978 3.434319 AAACGCTGCATCCCGCTG 61.434 61.111 0.00 0.00 43.06 5.18
5520 6115 2.283298 AGTGCCATAGCTCACATTTCG 58.717 47.619 6.11 0.00 40.80 3.46
5522 6117 3.689347 TCAAGTGCCATAGCTCACATTT 58.311 40.909 6.11 0.00 40.80 2.32
5738 6333 3.740832 GCTTACAACAACAGCAATTTCCC 59.259 43.478 0.00 0.00 33.45 3.97
6037 6632 8.705134 CGGCATAATCAATAGTTTAATACGTCA 58.295 33.333 0.00 0.00 0.00 4.35
6038 6633 8.706035 ACGGCATAATCAATAGTTTAATACGTC 58.294 33.333 0.00 0.00 0.00 4.34
6039 6634 8.597662 ACGGCATAATCAATAGTTTAATACGT 57.402 30.769 0.00 0.00 0.00 3.57
6048 6643 8.883731 GCATCTTTATACGGCATAATCAATAGT 58.116 33.333 0.00 0.00 0.00 2.12
6049 6644 9.102757 AGCATCTTTATACGGCATAATCAATAG 57.897 33.333 0.00 0.00 0.00 1.73
6050 6645 9.448438 AAGCATCTTTATACGGCATAATCAATA 57.552 29.630 0.00 0.00 0.00 1.90
6051 6646 7.928307 AGCATCTTTATACGGCATAATCAAT 57.072 32.000 0.00 0.00 0.00 2.57
6052 6647 7.094805 GGAAGCATCTTTATACGGCATAATCAA 60.095 37.037 0.00 0.00 0.00 2.57
6053 6648 6.371548 GGAAGCATCTTTATACGGCATAATCA 59.628 38.462 0.00 0.00 0.00 2.57
6054 6649 6.371548 TGGAAGCATCTTTATACGGCATAATC 59.628 38.462 0.00 0.00 0.00 1.75
6055 6650 6.237901 TGGAAGCATCTTTATACGGCATAAT 58.762 36.000 0.00 0.00 0.00 1.28
6056 6651 5.616270 TGGAAGCATCTTTATACGGCATAA 58.384 37.500 0.00 0.00 0.00 1.90
6057 6652 5.222079 TGGAAGCATCTTTATACGGCATA 57.778 39.130 0.00 0.00 0.00 3.14
6058 6653 4.085357 TGGAAGCATCTTTATACGGCAT 57.915 40.909 0.00 0.00 0.00 4.40
6059 6654 3.552132 TGGAAGCATCTTTATACGGCA 57.448 42.857 0.00 0.00 0.00 5.69
6060 6655 3.815401 ACATGGAAGCATCTTTATACGGC 59.185 43.478 0.00 0.00 0.00 5.68
6061 6656 5.408604 GGTACATGGAAGCATCTTTATACGG 59.591 44.000 0.00 0.00 0.00 4.02
6062 6657 5.989168 TGGTACATGGAAGCATCTTTATACG 59.011 40.000 0.00 0.00 0.00 3.06
6106 6701 8.546597 TCATCGTTTATCATCACTCTTGAAAA 57.453 30.769 0.00 0.00 34.61 2.29
6107 6702 8.606602 CATCATCGTTTATCATCACTCTTGAAA 58.393 33.333 0.00 0.00 34.61 2.69
6108 6703 7.254556 GCATCATCGTTTATCATCACTCTTGAA 60.255 37.037 0.00 0.00 34.61 2.69
6109 6704 6.201615 GCATCATCGTTTATCATCACTCTTGA 59.798 38.462 0.00 0.00 35.73 3.02
6110 6705 6.018507 TGCATCATCGTTTATCATCACTCTTG 60.019 38.462 0.00 0.00 0.00 3.02
6111 6706 6.051074 TGCATCATCGTTTATCATCACTCTT 58.949 36.000 0.00 0.00 0.00 2.85
6112 6707 5.604565 TGCATCATCGTTTATCATCACTCT 58.395 37.500 0.00 0.00 0.00 3.24
6113 6708 5.912360 TGCATCATCGTTTATCATCACTC 57.088 39.130 0.00 0.00 0.00 3.51
6114 6709 5.993441 TGATGCATCATCGTTTATCATCACT 59.007 36.000 25.42 0.00 43.14 3.41
6115 6710 6.073385 ACTGATGCATCATCGTTTATCATCAC 60.073 38.462 28.81 0.00 43.14 3.06
6116 6711 5.993441 ACTGATGCATCATCGTTTATCATCA 59.007 36.000 28.81 3.25 43.14 3.07
6117 6712 6.073385 ACACTGATGCATCATCGTTTATCATC 60.073 38.462 28.81 0.00 43.14 2.92
6118 6713 5.761726 ACACTGATGCATCATCGTTTATCAT 59.238 36.000 28.81 3.70 43.14 2.45
6119 6714 5.118286 ACACTGATGCATCATCGTTTATCA 58.882 37.500 28.81 4.47 43.14 2.15
6120 6715 5.663795 ACACTGATGCATCATCGTTTATC 57.336 39.130 28.81 0.00 43.14 1.75
6121 6716 6.093909 TCAAACACTGATGCATCATCGTTTAT 59.906 34.615 33.70 22.18 43.14 1.40
6122 6717 5.411053 TCAAACACTGATGCATCATCGTTTA 59.589 36.000 33.70 25.07 43.14 2.01
6123 6718 4.216042 TCAAACACTGATGCATCATCGTTT 59.784 37.500 31.38 31.38 43.14 3.60
6124 6719 3.752747 TCAAACACTGATGCATCATCGTT 59.247 39.130 28.81 27.35 43.14 3.85
6125 6720 3.337358 TCAAACACTGATGCATCATCGT 58.663 40.909 28.81 23.78 43.14 3.73
6126 6721 4.142752 ACTTCAAACACTGATGCATCATCG 60.143 41.667 28.81 23.17 43.14 3.84
6127 6722 5.306532 ACTTCAAACACTGATGCATCATC 57.693 39.130 28.81 4.11 40.88 2.92
6128 6723 5.242171 TGAACTTCAAACACTGATGCATCAT 59.758 36.000 28.81 16.25 36.02 2.45
6129 6724 4.579753 TGAACTTCAAACACTGATGCATCA 59.420 37.500 27.10 27.10 33.45 3.07
6130 6725 5.112220 TGAACTTCAAACACTGATGCATC 57.888 39.130 20.14 20.14 33.45 3.91
6131 6726 5.518848 TTGAACTTCAAACACTGATGCAT 57.481 34.783 0.00 0.00 32.71 3.96
6132 6727 4.979943 TTGAACTTCAAACACTGATGCA 57.020 36.364 1.47 0.00 32.71 3.96
6133 6728 5.522456 TGATTGAACTTCAAACACTGATGC 58.478 37.500 8.28 0.00 40.12 3.91
6134 6729 6.143438 GCTTGATTGAACTTCAAACACTGATG 59.857 38.462 12.62 4.66 38.58 3.07
6188 6783 8.247562 GTGTAATGATTTGTTTATGCCCTGTTA 58.752 33.333 0.00 0.00 0.00 2.41
6214 6809 2.322161 GCTTGTGCTATGCTTGTTGTG 58.678 47.619 0.00 0.00 36.03 3.33
6261 6856 5.942826 TGGTTGTGATGTGTGCTATAATTCA 59.057 36.000 0.00 0.00 0.00 2.57
6283 6878 1.338769 GGTAGGCACCTACTGTTGTGG 60.339 57.143 22.79 3.33 45.88 4.17
6291 6886 2.190538 TGGTTTAGGGTAGGCACCTAC 58.809 52.381 17.04 17.04 45.04 3.18
6345 6940 5.918426 TGATTACATAAGTCACGGTGGTA 57.082 39.130 8.50 0.00 0.00 3.25
6403 6998 3.133003 CCGACCAAGTCCTGACATCTATT 59.867 47.826 0.00 0.00 0.00 1.73
6441 7036 0.764271 TCACTGGTGCATCCAAGACA 59.236 50.000 8.96 0.00 46.59 3.41
6513 7108 1.209275 GAGATCCGGTGTTGCGATCG 61.209 60.000 11.69 11.69 37.95 3.69
6553 7148 5.130477 ACGTCATTCCTATGTTGGGAGTATT 59.870 40.000 0.00 0.00 34.06 1.89
6601 7196 3.683340 GTGAAAGGCTAGGTTTAGTTCCG 59.317 47.826 0.00 0.00 0.00 4.30
6602 7197 3.683340 CGTGAAAGGCTAGGTTTAGTTCC 59.317 47.826 0.00 0.00 0.00 3.62
6616 7211 0.457166 TGTCGTATCCGCGTGAAAGG 60.457 55.000 4.92 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.