Multiple sequence alignment - TraesCS5D01G177800

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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 TraesCS5D01G177800 chr5D 100.000 5899 0 0 1 5899 277564843 277558945 0.000000e+00 10894.0
1 TraesCS5D01G177800 chr5D 88.506 174 14 4 1 173 535305069 535304901 7.750000e-49 206.0
2 TraesCS5D01G177800 chr5D 74.890 227 37 15 2964 3184 286187755 286187543 1.050000e-12 86.1
3 TraesCS5D01G177800 chr5D 89.062 64 6 1 3122 3184 240088125 240088062 1.760000e-10 78.7
4 TraesCS5D01G177800 chr5A 96.031 5769 174 24 170 5899 366638572 366632820 0.000000e+00 9334.0
5 TraesCS5D01G177800 chr5A 91.720 157 13 0 3234 3390 86662175 86662019 9.950000e-53 219.0
6 TraesCS5D01G177800 chr5A 89.062 64 6 1 3122 3184 313876828 313876891 1.760000e-10 78.7
7 TraesCS5D01G177800 chr5B 95.603 2570 82 7 3342 5899 315615623 315613073 0.000000e+00 4091.0
8 TraesCS5D01G177800 chr5B 93.846 1560 61 12 179 1710 315618761 315617209 0.000000e+00 2316.0
9 TraesCS5D01G177800 chr5B 94.094 1507 51 14 1728 3200 315617156 315615654 0.000000e+00 2255.0
10 TraesCS5D01G177800 chr5B 92.357 157 12 0 3234 3390 98663334 98663178 2.140000e-54 224.0
11 TraesCS5D01G177800 chr5B 85.057 87 12 1 3127 3213 710654471 710654556 2.930000e-13 87.9
12 TraesCS5D01G177800 chr5B 89.831 59 6 0 3126 3184 263518835 263518893 6.340000e-10 76.8
13 TraesCS5D01G177800 chr7D 93.506 154 9 1 3238 3390 436961795 436961948 1.650000e-55 228.0
14 TraesCS5D01G177800 chr7B 93.506 154 9 1 3238 3390 453623290 453623443 1.650000e-55 228.0
15 TraesCS5D01G177800 chr7B 84.071 113 14 1 3128 3240 675998769 675998877 8.090000e-19 106.0
16 TraesCS5D01G177800 chr7B 87.879 66 8 0 3162 3227 89917599 89917534 1.760000e-10 78.7
17 TraesCS5D01G177800 chr7A 92.949 156 11 0 3235 3390 462978584 462978739 1.650000e-55 228.0
18 TraesCS5D01G177800 chr7A 92.857 154 10 1 3238 3390 486929940 486930093 7.690000e-54 222.0
19 TraesCS5D01G177800 chr3D 90.588 170 10 4 1 169 149291672 149291508 2.770000e-53 220.0
20 TraesCS5D01G177800 chr2D 92.667 150 11 0 3241 3390 79056316 79056167 3.580000e-52 217.0
21 TraesCS5D01G177800 chr2D 92.208 154 11 1 3238 3390 88290055 88290208 3.580000e-52 217.0
22 TraesCS5D01G177800 chr2D 88.824 170 17 2 1 169 371842053 371842221 2.150000e-49 207.0
23 TraesCS5D01G177800 chr1D 89.412 170 16 2 1 169 235506664 235506832 4.630000e-51 213.0
24 TraesCS5D01G177800 chr4D 89.349 169 17 1 1 169 344076532 344076699 1.670000e-50 211.0
25 TraesCS5D01G177800 chr6D 89.412 170 12 4 1 169 270476666 270476502 5.990000e-50 209.0
26 TraesCS5D01G177800 chr6B 89.881 168 9 6 4 169 628985302 628985141 5.990000e-50 209.0
27 TraesCS5D01G177800 chr2A 88.571 175 13 5 1 174 616524501 616524333 7.750000e-49 206.0
28 TraesCS5D01G177800 chr2A 81.818 88 14 2 2984 3070 707078196 707078282 8.200000e-09 73.1
29 TraesCS5D01G177800 chr1A 88.506 174 14 4 1 173 160151455 160151623 7.750000e-49 206.0
30 TraesCS5D01G177800 chr3B 91.892 37 3 0 3032 3068 788164154 788164118 1.100000e-02 52.8


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 TraesCS5D01G177800 chr5D 277558945 277564843 5898 True 10894.000000 10894 100.000000 1 5899 1 chr5D.!!$R2 5898
1 TraesCS5D01G177800 chr5A 366632820 366638572 5752 True 9334.000000 9334 96.031000 170 5899 1 chr5A.!!$R2 5729
2 TraesCS5D01G177800 chr5B 315613073 315618761 5688 True 2887.333333 4091 94.514333 179 5899 3 chr5B.!!$R2 5720

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
736 767 0.108945 GCTGGCTTCTTCATTGGTGC 60.109 55.000 0.00 0.0 0.00 5.01 F
839 870 0.241213 TCTTGAGAGACGCCGTTCAG 59.759 55.000 0.00 0.0 0.00 3.02 F
2255 2334 1.196012 GGGACTTGTACAGGAGGGAG 58.804 60.000 12.54 0.0 0.00 4.30 F
3403 3508 2.037144 GGGAGTAGGACGCAAGGATAA 58.963 52.381 0.00 0.0 46.39 1.75 F
3406 3511 3.118884 GGAGTAGGACGCAAGGATAACAA 60.119 47.826 0.00 0.0 46.39 2.83 F
3667 3772 3.325135 CCTGTTGAGAGTAAGGGTTCTGT 59.675 47.826 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 1892 2.455674 ACGCACTAGATGAAGCAACA 57.544 45.000 0.00 0.0 0.00 3.33 R
2286 2365 3.694072 GTGTAATGGCTGCAAAGATGGTA 59.306 43.478 0.50 0.0 0.00 3.25 R
3667 3772 3.826524 TGAGTTGACCAAAATGCACCTA 58.173 40.909 0.00 0.0 0.00 3.08 R
4674 4782 0.810648 TTGCTTTGCGATGCCCTTAG 59.189 50.000 9.22 0.0 0.00 2.18 R
4685 4793 2.597713 GCCGGCTTTGTTGCTTTGC 61.598 57.895 22.15 0.0 0.00 3.68 R
5431 5551 1.673920 GTGCAAGGAAACCTGACGAAA 59.326 47.619 0.00 0.0 32.13 3.46 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
25 26 5.858381 CATGGGCATGTTACTAGTCTATGT 58.142 41.667 0.00 0.00 34.23 2.29
26 27 5.950544 TGGGCATGTTACTAGTCTATGTT 57.049 39.130 0.00 0.00 0.00 2.71
27 28 7.441836 CATGGGCATGTTACTAGTCTATGTTA 58.558 38.462 0.00 0.00 34.23 2.41
28 29 6.812998 TGGGCATGTTACTAGTCTATGTTAC 58.187 40.000 0.00 0.00 0.00 2.50
29 30 6.610020 TGGGCATGTTACTAGTCTATGTTACT 59.390 38.462 0.00 0.00 0.00 2.24
30 31 7.781219 TGGGCATGTTACTAGTCTATGTTACTA 59.219 37.037 0.00 0.00 0.00 1.82
31 32 8.081025 GGGCATGTTACTAGTCTATGTTACTAC 58.919 40.741 0.00 0.00 0.00 2.73
32 33 8.081025 GGCATGTTACTAGTCTATGTTACTACC 58.919 40.741 0.00 0.00 0.00 3.18
33 34 8.081025 GCATGTTACTAGTCTATGTTACTACCC 58.919 40.741 0.00 0.00 0.00 3.69
34 35 9.128404 CATGTTACTAGTCTATGTTACTACCCA 57.872 37.037 0.00 0.00 0.00 4.51
35 36 9.878737 ATGTTACTAGTCTATGTTACTACCCAT 57.121 33.333 0.00 0.00 0.00 4.00
36 37 9.705103 TGTTACTAGTCTATGTTACTACCCATT 57.295 33.333 0.00 0.00 0.00 3.16
37 38 9.962783 GTTACTAGTCTATGTTACTACCCATTG 57.037 37.037 0.00 0.00 0.00 2.82
38 39 9.705103 TTACTAGTCTATGTTACTACCCATTGT 57.295 33.333 0.00 0.00 0.00 2.71
39 40 8.008513 ACTAGTCTATGTTACTACCCATTGTG 57.991 38.462 0.00 0.00 0.00 3.33
40 41 6.235231 AGTCTATGTTACTACCCATTGTGG 57.765 41.667 0.00 0.00 37.25 4.17
41 42 4.814771 GTCTATGTTACTACCCATTGTGGC 59.185 45.833 0.00 0.00 35.79 5.01
42 43 4.719773 TCTATGTTACTACCCATTGTGGCT 59.280 41.667 0.00 0.00 35.79 4.75
43 44 5.900699 TCTATGTTACTACCCATTGTGGCTA 59.099 40.000 0.00 0.00 35.79 3.93
44 45 4.481368 TGTTACTACCCATTGTGGCTAG 57.519 45.455 0.00 0.00 35.79 3.42
45 46 3.841845 TGTTACTACCCATTGTGGCTAGT 59.158 43.478 8.55 8.55 35.79 2.57
46 47 4.081309 TGTTACTACCCATTGTGGCTAGTC 60.081 45.833 7.13 0.00 35.79 2.59
47 48 2.834113 ACTACCCATTGTGGCTAGTCT 58.166 47.619 0.00 0.00 35.79 3.24
48 49 3.990369 ACTACCCATTGTGGCTAGTCTA 58.010 45.455 0.00 0.00 35.79 2.59
49 50 4.359105 ACTACCCATTGTGGCTAGTCTAA 58.641 43.478 0.00 0.00 35.79 2.10
50 51 3.629142 ACCCATTGTGGCTAGTCTAAC 57.371 47.619 0.00 0.00 35.79 2.34
51 52 3.182152 ACCCATTGTGGCTAGTCTAACT 58.818 45.455 0.00 0.00 35.79 2.24
52 53 4.359105 ACCCATTGTGGCTAGTCTAACTA 58.641 43.478 0.00 0.00 35.79 2.24
69 70 8.569641 AGTCTAACTAGCTATGTTACTACATGC 58.430 37.037 10.09 3.61 44.56 4.06
70 71 8.350722 GTCTAACTAGCTATGTTACTACATGCA 58.649 37.037 10.09 0.00 44.56 3.96
71 72 9.078990 TCTAACTAGCTATGTTACTACATGCAT 57.921 33.333 0.00 0.00 44.56 3.96
72 73 9.347934 CTAACTAGCTATGTTACTACATGCATC 57.652 37.037 0.00 0.00 44.56 3.91
73 74 7.531857 ACTAGCTATGTTACTACATGCATCT 57.468 36.000 0.00 0.00 44.56 2.90
74 75 7.957002 ACTAGCTATGTTACTACATGCATCTT 58.043 34.615 0.00 0.00 44.56 2.40
75 76 8.424918 ACTAGCTATGTTACTACATGCATCTTT 58.575 33.333 0.00 0.00 44.56 2.52
76 77 9.265901 CTAGCTATGTTACTACATGCATCTTTT 57.734 33.333 0.00 0.00 44.56 2.27
77 78 8.511604 AGCTATGTTACTACATGCATCTTTTT 57.488 30.769 0.00 0.00 44.56 1.94
78 79 8.616076 AGCTATGTTACTACATGCATCTTTTTC 58.384 33.333 0.00 0.00 44.56 2.29
79 80 8.616076 GCTATGTTACTACATGCATCTTTTTCT 58.384 33.333 0.00 0.00 44.56 2.52
82 83 8.389779 TGTTACTACATGCATCTTTTTCTTCA 57.610 30.769 0.00 0.00 0.00 3.02
83 84 9.013229 TGTTACTACATGCATCTTTTTCTTCAT 57.987 29.630 0.00 0.00 0.00 2.57
84 85 9.846248 GTTACTACATGCATCTTTTTCTTCATT 57.154 29.630 0.00 0.00 0.00 2.57
90 91 8.662141 ACATGCATCTTTTTCTTCATTTATTGC 58.338 29.630 0.00 0.00 0.00 3.56
91 92 8.879759 CATGCATCTTTTTCTTCATTTATTGCT 58.120 29.630 0.00 0.00 0.00 3.91
92 93 8.836268 TGCATCTTTTTCTTCATTTATTGCTT 57.164 26.923 0.00 0.00 0.00 3.91
93 94 8.714179 TGCATCTTTTTCTTCATTTATTGCTTG 58.286 29.630 0.00 0.00 0.00 4.01
94 95 7.691050 GCATCTTTTTCTTCATTTATTGCTTGC 59.309 33.333 0.00 0.00 0.00 4.01
95 96 7.656707 TCTTTTTCTTCATTTATTGCTTGCC 57.343 32.000 0.00 0.00 0.00 4.52
96 97 7.215789 TCTTTTTCTTCATTTATTGCTTGCCA 58.784 30.769 0.00 0.00 0.00 4.92
97 98 6.783892 TTTTCTTCATTTATTGCTTGCCAC 57.216 33.333 0.00 0.00 0.00 5.01
98 99 5.465532 TTCTTCATTTATTGCTTGCCACA 57.534 34.783 0.00 0.00 0.00 4.17
99 100 5.664294 TCTTCATTTATTGCTTGCCACAT 57.336 34.783 0.00 0.00 0.00 3.21
100 101 5.653507 TCTTCATTTATTGCTTGCCACATC 58.346 37.500 0.00 0.00 0.00 3.06
101 102 5.185442 TCTTCATTTATTGCTTGCCACATCA 59.815 36.000 0.00 0.00 0.00 3.07
102 103 5.601583 TCATTTATTGCTTGCCACATCAT 57.398 34.783 0.00 0.00 0.00 2.45
103 104 5.593968 TCATTTATTGCTTGCCACATCATC 58.406 37.500 0.00 0.00 0.00 2.92
104 105 5.361571 TCATTTATTGCTTGCCACATCATCT 59.638 36.000 0.00 0.00 0.00 2.90
105 106 6.546772 TCATTTATTGCTTGCCACATCATCTA 59.453 34.615 0.00 0.00 0.00 1.98
106 107 6.964807 TTTATTGCTTGCCACATCATCTAT 57.035 33.333 0.00 0.00 0.00 1.98
107 108 6.964807 TTATTGCTTGCCACATCATCTATT 57.035 33.333 0.00 0.00 0.00 1.73
108 109 5.864418 ATTGCTTGCCACATCATCTATTT 57.136 34.783 0.00 0.00 0.00 1.40
109 110 5.664294 TTGCTTGCCACATCATCTATTTT 57.336 34.783 0.00 0.00 0.00 1.82
110 111 6.772360 TTGCTTGCCACATCATCTATTTTA 57.228 33.333 0.00 0.00 0.00 1.52
111 112 6.964807 TGCTTGCCACATCATCTATTTTAT 57.035 33.333 0.00 0.00 0.00 1.40
112 113 7.350744 TGCTTGCCACATCATCTATTTTATT 57.649 32.000 0.00 0.00 0.00 1.40
113 114 7.784037 TGCTTGCCACATCATCTATTTTATTT 58.216 30.769 0.00 0.00 0.00 1.40
114 115 8.911965 TGCTTGCCACATCATCTATTTTATTTA 58.088 29.630 0.00 0.00 0.00 1.40
115 116 9.748708 GCTTGCCACATCATCTATTTTATTTAA 57.251 29.630 0.00 0.00 0.00 1.52
159 160 8.190326 TCTACTGTATGTTACTCCATTATGGG 57.810 38.462 11.76 4.88 38.32 4.00
160 161 6.824958 ACTGTATGTTACTCCATTATGGGT 57.175 37.500 11.76 10.49 38.32 4.51
161 162 7.924358 ACTGTATGTTACTCCATTATGGGTA 57.076 36.000 11.76 9.53 38.32 3.69
162 163 7.963532 ACTGTATGTTACTCCATTATGGGTAG 58.036 38.462 11.76 4.93 38.32 3.18
163 164 7.567622 ACTGTATGTTACTCCATTATGGGTAGT 59.432 37.037 11.76 10.72 38.32 2.73
164 165 7.959175 TGTATGTTACTCCATTATGGGTAGTC 58.041 38.462 11.76 9.59 38.32 2.59
165 166 7.787904 TGTATGTTACTCCATTATGGGTAGTCT 59.212 37.037 11.76 4.23 38.32 3.24
166 167 9.305555 GTATGTTACTCCATTATGGGTAGTCTA 57.694 37.037 11.76 0.00 38.32 2.59
167 168 8.792830 ATGTTACTCCATTATGGGTAGTCTAA 57.207 34.615 11.76 0.00 38.32 2.10
168 169 8.246430 TGTTACTCCATTATGGGTAGTCTAAG 57.754 38.462 11.76 1.24 38.32 2.18
173 174 5.844516 TCCATTATGGGTAGTCTAAGGAAGG 59.155 44.000 11.76 0.00 38.32 3.46
186 187 0.976641 AGGAAGGACAGATGCGACAA 59.023 50.000 0.00 0.00 0.00 3.18
249 253 4.475527 GGAACGTGCTTGGGAACT 57.524 55.556 0.00 0.00 0.00 3.01
251 255 1.515521 GGAACGTGCTTGGGAACTGG 61.516 60.000 0.00 0.00 0.00 4.00
459 476 2.282958 AGCTGTCGAGTCCCGGAA 60.283 61.111 0.73 0.00 39.14 4.30
477 494 2.045926 CCTACCACACCTGCTGCC 60.046 66.667 0.00 0.00 0.00 4.85
527 544 3.970410 CTTCCTGGCTGGCCACCA 61.970 66.667 21.25 21.25 41.89 4.17
618 635 0.395586 TGGTTGCTGCTGACTTGGTT 60.396 50.000 0.00 0.00 0.00 3.67
729 760 1.071299 TTGCTCGCTGGCTTCTTCA 59.929 52.632 0.00 0.00 0.00 3.02
736 767 0.108945 GCTGGCTTCTTCATTGGTGC 60.109 55.000 0.00 0.00 0.00 5.01
741 772 1.945819 GCTTCTTCATTGGTGCTCGGA 60.946 52.381 0.00 0.00 0.00 4.55
771 802 1.881324 GGTAGGTAGATCTGCTCGGAC 59.119 57.143 10.82 4.07 0.00 4.79
773 804 1.008309 GGTAGATCTGCTCGGACGC 60.008 63.158 10.82 0.00 0.00 5.19
835 866 0.453793 CAGATCTTGAGAGACGCCGT 59.546 55.000 0.00 0.00 33.99 5.68
839 870 0.241213 TCTTGAGAGACGCCGTTCAG 59.759 55.000 0.00 0.00 0.00 3.02
855 886 4.379243 AGTGTTCTGCCGCTCGGG 62.379 66.667 10.57 0.00 39.58 5.14
905 936 4.706962 AGCTTTACCATGTTGAGAAATCCC 59.293 41.667 0.00 0.00 0.00 3.85
954 985 1.494721 AGGTTTCTGAGGCTGAACCAA 59.505 47.619 16.31 0.00 43.14 3.67
955 986 2.108952 AGGTTTCTGAGGCTGAACCAAT 59.891 45.455 16.31 0.50 43.14 3.16
1254 1285 3.706373 ACGGTGATGAGGGCGCTT 61.706 61.111 7.64 0.00 0.00 4.68
1304 1335 1.557443 GCGCACGCCATACTGGATAC 61.557 60.000 0.30 0.00 40.96 2.24
1372 1403 1.856265 GCTGGTTTCTGCCTTGGACG 61.856 60.000 0.00 0.00 32.58 4.79
1668 1699 7.545265 GTCACTCCATCTTATCTTGAGCATATC 59.455 40.741 0.00 0.00 0.00 1.63
1669 1700 7.454066 TCACTCCATCTTATCTTGAGCATATCT 59.546 37.037 0.00 0.00 0.00 1.98
1699 1730 9.486497 CATCTGTATCAGAATACTGTATTGCTT 57.514 33.333 17.21 1.15 44.04 3.91
1718 1749 7.428282 TTGCTTTCTGATGTACATCGTTAAA 57.572 32.000 26.56 22.79 40.63 1.52
1758 1824 7.290857 ACACAAGTATGTCAATAACATCGAC 57.709 36.000 0.00 0.00 45.78 4.20
1791 1857 7.970614 GCAGCTTTAGTTTTGCATAATTCTACT 59.029 33.333 0.00 0.00 36.59 2.57
1811 1877 7.786030 TCTACTCTGTTTCATATAGCTTTGCT 58.214 34.615 0.00 0.00 43.41 3.91
1814 1880 7.108847 ACTCTGTTTCATATAGCTTTGCTCTT 58.891 34.615 0.00 0.00 40.44 2.85
1826 1892 3.565902 GCTTTGCTCTTAGTCTTGGTTGT 59.434 43.478 0.00 0.00 0.00 3.32
1844 1910 2.068519 TGTGTTGCTTCATCTAGTGCG 58.931 47.619 0.00 0.00 0.00 5.34
1943 2009 4.094887 TGATCCTTCAAGAAATTGCTACGC 59.905 41.667 0.00 0.00 0.00 4.42
1987 2059 5.709164 GCAAATCTATTCTATGTGCAGGGAT 59.291 40.000 0.00 0.00 37.49 3.85
2186 2265 7.851228 TCAACCTATTATGAGCTCTTTCTCAA 58.149 34.615 16.19 0.05 45.17 3.02
2190 2269 8.713036 ACCTATTATGAGCTCTTTCTCAATTCT 58.287 33.333 16.19 0.00 45.17 2.40
2200 2279 9.896645 AGCTCTTTCTCAATTCTTTCACATATA 57.103 29.630 0.00 0.00 0.00 0.86
2255 2334 1.196012 GGGACTTGTACAGGAGGGAG 58.804 60.000 12.54 0.00 0.00 4.30
2654 2735 5.886609 TCACTTCCATGAATTTAGGTTGGA 58.113 37.500 0.00 0.00 34.74 3.53
2655 2736 6.493166 TCACTTCCATGAATTTAGGTTGGAT 58.507 36.000 0.00 0.00 36.42 3.41
2657 2738 8.112822 TCACTTCCATGAATTTAGGTTGGATTA 58.887 33.333 0.00 0.00 36.42 1.75
2786 2879 2.064628 ATCCCCATCTGGATCAGCG 58.935 57.895 0.00 0.00 41.38 5.18
2793 2886 2.096496 CCATCTGGATCAGCGTTTGAAC 59.904 50.000 0.00 0.00 39.77 3.18
2828 2921 2.165998 GATGAAGGTTTGGCTTCTGCT 58.834 47.619 0.00 0.00 39.59 4.24
3306 3411 4.982916 GGACTACATACGGATTGACATGAC 59.017 45.833 0.00 0.00 0.00 3.06
3330 3435 5.383958 TGAACAAACACACTAAAACGTGTC 58.616 37.500 0.00 0.00 45.74 3.67
3334 3439 6.711579 ACAAACACACTAAAACGTGTCTATG 58.288 36.000 0.00 0.00 45.74 2.23
3403 3508 2.037144 GGGAGTAGGACGCAAGGATAA 58.963 52.381 0.00 0.00 46.39 1.75
3406 3511 3.118884 GGAGTAGGACGCAAGGATAACAA 60.119 47.826 0.00 0.00 46.39 2.83
3667 3772 3.325135 CCTGTTGAGAGTAAGGGTTCTGT 59.675 47.826 0.00 0.00 0.00 3.41
3713 3818 3.354089 GCACAAGAACTAGCTTTTGCA 57.646 42.857 13.27 0.00 45.88 4.08
3890 3995 6.325993 TCTCCAAATGGTTCAGAATATGGA 57.674 37.500 0.00 0.00 36.34 3.41
4293 4398 5.711036 ACTCCGGTATGATTACTCCTACATC 59.289 44.000 0.00 0.00 0.00 3.06
4318 4424 9.742144 TCTCTAACTTATCTTCTCACTGTACTT 57.258 33.333 0.00 0.00 0.00 2.24
4449 4557 5.124776 CGGTGTTTCCAATTCCATAGCTAAA 59.875 40.000 0.00 0.00 35.57 1.85
4461 4569 8.879427 ATTCCATAGCTAAATTACCCATTACC 57.121 34.615 0.00 0.00 0.00 2.85
4685 4793 0.744874 TCCGAACTCTAAGGGCATCG 59.255 55.000 0.00 0.00 0.00 3.84
4910 5018 3.616219 TGGGTTTTAATGTGCTATCGCT 58.384 40.909 0.00 0.00 36.97 4.93
5079 5187 1.976045 CGTTCGCCAATGCTTTTGTAC 59.024 47.619 0.00 0.00 34.43 2.90
5086 5194 4.979197 CGCCAATGCTTTTGTACAAGTTTA 59.021 37.500 8.56 0.00 34.43 2.01
5431 5551 4.021229 TGCAAGCATGAGAATCCATCTTT 58.979 39.130 0.00 0.00 38.96 2.52
5457 5577 1.542915 CAGGTTTCCTTGCACTGATGG 59.457 52.381 0.00 0.00 0.00 3.51
5506 5626 1.631388 TCATACGCAGAAAAAGGGGGA 59.369 47.619 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.858381 ACATAGACTAGTAACATGCCCATG 58.142 41.667 6.71 6.71 44.15 3.66
3 4 6.500589 AACATAGACTAGTAACATGCCCAT 57.499 37.500 0.00 0.00 0.00 4.00
4 5 5.950544 AACATAGACTAGTAACATGCCCA 57.049 39.130 0.00 0.00 0.00 5.36
5 6 7.052142 AGTAACATAGACTAGTAACATGCCC 57.948 40.000 0.00 0.00 0.00 5.36
6 7 8.081025 GGTAGTAACATAGACTAGTAACATGCC 58.919 40.741 0.00 0.00 30.08 4.40
7 8 8.081025 GGGTAGTAACATAGACTAGTAACATGC 58.919 40.741 0.00 0.00 30.08 4.06
8 9 9.128404 TGGGTAGTAACATAGACTAGTAACATG 57.872 37.037 0.00 2.36 30.08 3.21
9 10 9.878737 ATGGGTAGTAACATAGACTAGTAACAT 57.121 33.333 0.00 0.00 30.08 2.71
10 11 9.705103 AATGGGTAGTAACATAGACTAGTAACA 57.295 33.333 0.00 0.00 30.08 2.41
11 12 9.962783 CAATGGGTAGTAACATAGACTAGTAAC 57.037 37.037 0.00 0.00 30.08 2.50
12 13 9.705103 ACAATGGGTAGTAACATAGACTAGTAA 57.295 33.333 0.00 0.00 30.08 2.24
13 14 9.128404 CACAATGGGTAGTAACATAGACTAGTA 57.872 37.037 0.00 0.00 30.08 1.82
14 15 7.069578 CCACAATGGGTAGTAACATAGACTAGT 59.930 40.741 0.00 0.00 32.67 2.57
15 16 7.434492 CCACAATGGGTAGTAACATAGACTAG 58.566 42.308 0.00 0.00 32.67 2.57
16 17 6.183360 GCCACAATGGGTAGTAACATAGACTA 60.183 42.308 0.00 0.00 38.19 2.59
17 18 5.396436 GCCACAATGGGTAGTAACATAGACT 60.396 44.000 0.00 0.00 38.19 3.24
18 19 4.814771 GCCACAATGGGTAGTAACATAGAC 59.185 45.833 0.00 0.00 38.19 2.59
19 20 5.031066 GCCACAATGGGTAGTAACATAGA 57.969 43.478 0.00 0.00 38.19 1.98
31 32 3.914426 AGTTAGACTAGCCACAATGGG 57.086 47.619 0.00 0.00 38.19 4.00
43 44 8.569641 GCATGTAGTAACATAGCTAGTTAGACT 58.430 37.037 12.98 12.58 44.70 3.24
44 45 8.350722 TGCATGTAGTAACATAGCTAGTTAGAC 58.649 37.037 12.98 13.50 44.70 2.59
45 46 8.459911 TGCATGTAGTAACATAGCTAGTTAGA 57.540 34.615 12.98 5.43 44.70 2.10
46 47 9.347934 GATGCATGTAGTAACATAGCTAGTTAG 57.652 37.037 2.46 1.35 44.70 2.34
47 48 9.078990 AGATGCATGTAGTAACATAGCTAGTTA 57.921 33.333 2.46 5.74 44.70 2.24
48 49 7.957002 AGATGCATGTAGTAACATAGCTAGTT 58.043 34.615 2.46 6.69 44.70 2.24
49 50 7.531857 AGATGCATGTAGTAACATAGCTAGT 57.468 36.000 2.46 0.00 44.70 2.57
50 51 8.824159 AAAGATGCATGTAGTAACATAGCTAG 57.176 34.615 2.46 0.00 44.70 3.42
51 52 9.613428 AAAAAGATGCATGTAGTAACATAGCTA 57.387 29.630 2.46 0.00 44.70 3.32
52 53 8.511604 AAAAAGATGCATGTAGTAACATAGCT 57.488 30.769 2.46 0.00 44.70 3.32
53 54 8.616076 AGAAAAAGATGCATGTAGTAACATAGC 58.384 33.333 2.46 0.00 44.70 2.97
57 58 8.389779 TGAAGAAAAAGATGCATGTAGTAACA 57.610 30.769 2.46 0.00 40.69 2.41
58 59 9.846248 AATGAAGAAAAAGATGCATGTAGTAAC 57.154 29.630 2.46 0.00 0.00 2.50
64 65 8.662141 GCAATAAATGAAGAAAAAGATGCATGT 58.338 29.630 2.46 0.00 0.00 3.21
65 66 8.879759 AGCAATAAATGAAGAAAAAGATGCATG 58.120 29.630 2.46 0.00 0.00 4.06
66 67 9.444600 AAGCAATAAATGAAGAAAAAGATGCAT 57.555 25.926 0.00 0.00 0.00 3.96
67 68 8.714179 CAAGCAATAAATGAAGAAAAAGATGCA 58.286 29.630 0.00 0.00 0.00 3.96
68 69 7.691050 GCAAGCAATAAATGAAGAAAAAGATGC 59.309 33.333 0.00 0.00 0.00 3.91
69 70 8.173130 GGCAAGCAATAAATGAAGAAAAAGATG 58.827 33.333 0.00 0.00 0.00 2.90
70 71 7.879160 TGGCAAGCAATAAATGAAGAAAAAGAT 59.121 29.630 0.00 0.00 0.00 2.40
71 72 7.171337 GTGGCAAGCAATAAATGAAGAAAAAGA 59.829 33.333 0.00 0.00 0.00 2.52
72 73 7.041916 TGTGGCAAGCAATAAATGAAGAAAAAG 60.042 33.333 0.00 0.00 0.00 2.27
73 74 6.765036 TGTGGCAAGCAATAAATGAAGAAAAA 59.235 30.769 0.00 0.00 0.00 1.94
74 75 6.286758 TGTGGCAAGCAATAAATGAAGAAAA 58.713 32.000 0.00 0.00 0.00 2.29
75 76 5.851720 TGTGGCAAGCAATAAATGAAGAAA 58.148 33.333 0.00 0.00 0.00 2.52
76 77 5.465532 TGTGGCAAGCAATAAATGAAGAA 57.534 34.783 0.00 0.00 0.00 2.52
77 78 5.185442 TGATGTGGCAAGCAATAAATGAAGA 59.815 36.000 0.00 0.00 0.00 2.87
78 79 5.412640 TGATGTGGCAAGCAATAAATGAAG 58.587 37.500 0.00 0.00 0.00 3.02
79 80 5.402997 TGATGTGGCAAGCAATAAATGAA 57.597 34.783 0.00 0.00 0.00 2.57
80 81 5.361571 AGATGATGTGGCAAGCAATAAATGA 59.638 36.000 0.00 0.00 0.00 2.57
81 82 5.597806 AGATGATGTGGCAAGCAATAAATG 58.402 37.500 0.00 0.00 0.00 2.32
82 83 5.864418 AGATGATGTGGCAAGCAATAAAT 57.136 34.783 0.00 0.00 0.00 1.40
83 84 6.964807 ATAGATGATGTGGCAAGCAATAAA 57.035 33.333 0.00 0.00 0.00 1.40
84 85 6.964807 AATAGATGATGTGGCAAGCAATAA 57.035 33.333 0.00 0.00 0.00 1.40
85 86 6.964807 AAATAGATGATGTGGCAAGCAATA 57.035 33.333 0.00 0.00 0.00 1.90
86 87 5.864418 AAATAGATGATGTGGCAAGCAAT 57.136 34.783 0.00 0.00 0.00 3.56
87 88 5.664294 AAAATAGATGATGTGGCAAGCAA 57.336 34.783 0.00 0.00 0.00 3.91
88 89 6.964807 ATAAAATAGATGATGTGGCAAGCA 57.035 33.333 0.00 0.00 0.00 3.91
89 90 9.748708 TTAAATAAAATAGATGATGTGGCAAGC 57.251 29.630 0.00 0.00 0.00 4.01
133 134 8.816894 CCCATAATGGAGTAACATACAGTAGAT 58.183 37.037 0.00 0.00 40.96 1.98
134 135 7.787904 ACCCATAATGGAGTAACATACAGTAGA 59.212 37.037 0.00 0.00 40.96 2.59
135 136 7.963532 ACCCATAATGGAGTAACATACAGTAG 58.036 38.462 0.00 0.00 40.96 2.57
136 137 7.924358 ACCCATAATGGAGTAACATACAGTA 57.076 36.000 0.00 0.00 40.96 2.74
137 138 6.824958 ACCCATAATGGAGTAACATACAGT 57.175 37.500 0.00 0.00 40.96 3.55
138 139 7.963532 ACTACCCATAATGGAGTAACATACAG 58.036 38.462 0.00 0.00 40.96 2.74
139 140 7.787904 AGACTACCCATAATGGAGTAACATACA 59.212 37.037 0.00 0.00 40.96 2.29
140 141 8.191534 AGACTACCCATAATGGAGTAACATAC 57.808 38.462 0.00 0.00 40.96 2.39
141 142 9.886337 TTAGACTACCCATAATGGAGTAACATA 57.114 33.333 0.00 0.00 40.96 2.29
142 143 8.792830 TTAGACTACCCATAATGGAGTAACAT 57.207 34.615 0.00 0.00 40.96 2.71
143 144 7.289317 CCTTAGACTACCCATAATGGAGTAACA 59.711 40.741 0.00 0.00 40.96 2.41
144 145 7.508296 TCCTTAGACTACCCATAATGGAGTAAC 59.492 40.741 0.00 0.00 40.96 2.50
145 146 7.598248 TCCTTAGACTACCCATAATGGAGTAA 58.402 38.462 0.00 0.00 40.96 2.24
146 147 7.170554 TCCTTAGACTACCCATAATGGAGTA 57.829 40.000 0.00 0.00 40.96 2.59
147 148 6.039415 TCCTTAGACTACCCATAATGGAGT 57.961 41.667 0.00 0.00 40.96 3.85
148 149 6.014156 CCTTCCTTAGACTACCCATAATGGAG 60.014 46.154 0.00 0.00 40.96 3.86
149 150 5.844516 CCTTCCTTAGACTACCCATAATGGA 59.155 44.000 0.00 0.00 40.96 3.41
150 151 5.844516 TCCTTCCTTAGACTACCCATAATGG 59.155 44.000 0.00 0.00 37.25 3.16
151 152 6.326583 TGTCCTTCCTTAGACTACCCATAATG 59.673 42.308 0.00 0.00 34.02 1.90
152 153 6.449956 TGTCCTTCCTTAGACTACCCATAAT 58.550 40.000 0.00 0.00 34.02 1.28
153 154 5.845734 TGTCCTTCCTTAGACTACCCATAA 58.154 41.667 0.00 0.00 34.02 1.90
154 155 5.195146 TCTGTCCTTCCTTAGACTACCCATA 59.805 44.000 0.00 0.00 34.02 2.74
155 156 4.016479 TCTGTCCTTCCTTAGACTACCCAT 60.016 45.833 0.00 0.00 34.02 4.00
156 157 3.335786 TCTGTCCTTCCTTAGACTACCCA 59.664 47.826 0.00 0.00 34.02 4.51
157 158 3.978610 TCTGTCCTTCCTTAGACTACCC 58.021 50.000 0.00 0.00 34.02 3.69
158 159 4.202172 GCATCTGTCCTTCCTTAGACTACC 60.202 50.000 0.00 0.00 34.02 3.18
159 160 4.498345 CGCATCTGTCCTTCCTTAGACTAC 60.498 50.000 0.00 0.00 34.02 2.73
160 161 3.632604 CGCATCTGTCCTTCCTTAGACTA 59.367 47.826 0.00 0.00 34.02 2.59
161 162 2.428890 CGCATCTGTCCTTCCTTAGACT 59.571 50.000 0.00 0.00 34.02 3.24
162 163 2.427453 TCGCATCTGTCCTTCCTTAGAC 59.573 50.000 0.00 0.00 0.00 2.59
163 164 2.427453 GTCGCATCTGTCCTTCCTTAGA 59.573 50.000 0.00 0.00 0.00 2.10
164 165 2.166459 TGTCGCATCTGTCCTTCCTTAG 59.834 50.000 0.00 0.00 0.00 2.18
165 166 2.176045 TGTCGCATCTGTCCTTCCTTA 58.824 47.619 0.00 0.00 0.00 2.69
166 167 0.976641 TGTCGCATCTGTCCTTCCTT 59.023 50.000 0.00 0.00 0.00 3.36
167 168 0.976641 TTGTCGCATCTGTCCTTCCT 59.023 50.000 0.00 0.00 0.00 3.36
168 169 1.667724 CATTGTCGCATCTGTCCTTCC 59.332 52.381 0.00 0.00 0.00 3.46
173 174 1.466167 AGTTGCATTGTCGCATCTGTC 59.534 47.619 0.00 0.00 42.62 3.51
186 187 1.614317 GGACAGGCTGGTTAGTTGCAT 60.614 52.381 20.34 0.00 0.00 3.96
447 464 1.379044 GGTAGGTTCCGGGACTCGA 60.379 63.158 13.96 0.00 42.43 4.04
459 476 2.750350 GCAGCAGGTGTGGTAGGT 59.250 61.111 0.66 0.00 31.49 3.08
524 541 1.342672 AAGAACTGGTCGTGGGTGGT 61.343 55.000 0.00 0.00 0.00 4.16
525 542 0.884704 CAAGAACTGGTCGTGGGTGG 60.885 60.000 0.33 0.00 32.59 4.61
526 543 0.105964 TCAAGAACTGGTCGTGGGTG 59.894 55.000 8.73 0.00 36.48 4.61
527 544 1.002087 GATCAAGAACTGGTCGTGGGT 59.998 52.381 8.73 0.00 36.48 4.51
618 635 3.779183 AGCAATGGAAGAAGAGGAGATCA 59.221 43.478 0.00 0.00 0.00 2.92
729 760 0.107654 GCTTACCTCCGAGCACCAAT 60.108 55.000 0.00 0.00 38.73 3.16
736 767 1.033574 CTACCTGGCTTACCTCCGAG 58.966 60.000 0.00 0.00 36.63 4.63
741 772 3.467863 AGATCTACCTACCTGGCTTACCT 59.532 47.826 0.00 0.00 40.22 3.08
771 802 3.853330 CTGTCGAATGGCCGTGCG 61.853 66.667 20.19 20.19 0.00 5.34
773 804 1.497278 CAACTGTCGAATGGCCGTG 59.503 57.895 0.00 0.00 0.00 4.94
835 866 1.664649 CGAGCGGCAGAACACTGAA 60.665 57.895 1.45 0.00 33.94 3.02
855 886 1.659098 CTACGAATCAACAAGGTCCGC 59.341 52.381 0.00 0.00 0.00 5.54
862 893 3.679980 GCTTGAGAGCTACGAATCAACAA 59.320 43.478 0.00 0.00 45.65 2.83
894 925 2.373169 ACACTCAGCAGGGATTTCTCAA 59.627 45.455 0.00 0.00 0.00 3.02
905 936 4.153117 GTGAAGTTTATCCACACTCAGCAG 59.847 45.833 0.00 0.00 0.00 4.24
954 985 2.154462 CCCTCACAAGTCAAAAGCGAT 58.846 47.619 0.00 0.00 0.00 4.58
955 986 1.593196 CCCTCACAAGTCAAAAGCGA 58.407 50.000 0.00 0.00 0.00 4.93
1211 1242 2.401699 CTTCTGCACCAGGTCCAGCA 62.402 60.000 5.51 4.22 35.43 4.41
1254 1285 2.924101 ACGTTCGGGTGCCCCTTA 60.924 61.111 8.43 0.00 42.67 2.69
1281 1312 2.358125 AGTATGGCGTGCGCAACA 60.358 55.556 14.00 12.88 44.11 3.33
1372 1403 1.137282 GAACCCTGCAGTACCTCTAGC 59.863 57.143 13.81 0.00 0.00 3.42
1573 1604 4.171005 CAAAGCAATGGAGTTACATGCAG 58.829 43.478 0.00 0.00 31.66 4.41
1699 1730 8.766000 TTAGCTTTTAACGATGTACATCAGAA 57.234 30.769 30.15 19.17 37.69 3.02
1718 1749 9.113838 CATACTTGTGTCCTGATAATTTAGCTT 57.886 33.333 0.00 0.00 0.00 3.74
1758 1824 3.319755 CAAAACTAAAGCTGCCACATGG 58.680 45.455 0.00 0.00 38.53 3.66
1791 1857 8.260818 ACTAAGAGCAAAGCTATATGAAACAGA 58.739 33.333 0.00 0.00 39.88 3.41
1811 1877 4.150897 AGCAACACAACCAAGACTAAGA 57.849 40.909 0.00 0.00 0.00 2.10
1814 1880 3.879998 TGAAGCAACACAACCAAGACTA 58.120 40.909 0.00 0.00 0.00 2.59
1826 1892 2.455674 ACGCACTAGATGAAGCAACA 57.544 45.000 0.00 0.00 0.00 3.33
1943 2009 4.891260 TGCTGTGATGCCTCTATAATGAG 58.109 43.478 0.00 0.00 0.00 2.90
1987 2059 5.072741 AGAAGCACATTTTCAGCCTTTAGA 58.927 37.500 0.00 0.00 0.00 2.10
2286 2365 3.694072 GTGTAATGGCTGCAAAGATGGTA 59.306 43.478 0.50 0.00 0.00 3.25
2329 2410 5.335191 CCAGTTCAAAGAACAAGATAGGTGC 60.335 44.000 11.92 0.00 0.00 5.01
2330 2411 5.765182 ACCAGTTCAAAGAACAAGATAGGTG 59.235 40.000 11.92 0.00 0.00 4.00
2677 2770 9.836864 ACAGTACATGCATCAATATTAGAGAAA 57.163 29.630 0.00 0.00 0.00 2.52
2793 2886 4.999950 ACCTTCATCTTCAGTAGTTTGCAG 59.000 41.667 0.00 0.00 0.00 4.41
2828 2921 8.998377 GCTTCAATTCTTAAAAAGGGCAAAATA 58.002 29.630 0.00 0.00 0.00 1.40
2938 3034 7.858498 TGCCTTTATCTAGTAGGTAAGCTTTT 58.142 34.615 3.20 0.00 0.00 2.27
3242 3347 6.069684 ACGTCTTATAATAGTGAACGGAGG 57.930 41.667 0.00 0.00 0.00 4.30
3257 3362 9.787532 CATATTGAAACATCCAAAACGTCTTAT 57.212 29.630 0.00 0.00 0.00 1.73
3261 3366 6.526674 GTCCATATTGAAACATCCAAAACGTC 59.473 38.462 0.00 0.00 0.00 4.34
3306 3411 5.908240 CACGTTTTAGTGTGTTTGTTCAG 57.092 39.130 0.00 0.00 37.35 3.02
3667 3772 3.826524 TGAGTTGACCAAAATGCACCTA 58.173 40.909 0.00 0.00 0.00 3.08
3890 3995 7.067859 GGTTTAGTGTTTTGGGTTTTCTCTAGT 59.932 37.037 0.00 0.00 0.00 2.57
4052 4157 6.169557 TGCTCCTTGAGTAAAGTTACTTCA 57.830 37.500 5.24 3.12 43.64 3.02
4353 4459 9.823098 GTTCGACTTATGTATATCTGTTACGAT 57.177 33.333 0.00 0.00 0.00 3.73
4449 4557 4.953579 AGATTGTTTGCGGTAATGGGTAAT 59.046 37.500 0.00 0.00 0.00 1.89
4461 4569 3.670627 GCTAAGGGTTCAGATTGTTTGCG 60.671 47.826 0.00 0.00 0.00 4.85
4674 4782 0.810648 TTGCTTTGCGATGCCCTTAG 59.189 50.000 9.22 0.00 0.00 2.18
4685 4793 2.597713 GCCGGCTTTGTTGCTTTGC 61.598 57.895 22.15 0.00 0.00 3.68
5086 5194 9.077885 ACATGTCACTAAATTTCAGTACCAAAT 57.922 29.630 0.00 0.00 0.00 2.32
5238 5347 2.941064 CCATGTCACATGTGTCCAGATC 59.059 50.000 24.63 8.80 0.00 2.75
5286 5405 3.260632 TGGTATGTGTACATGCTGTGTCT 59.739 43.478 11.83 0.00 42.29 3.41
5351 5471 7.694388 TTCTCGACATTGCATATTACTGTAC 57.306 36.000 0.00 0.00 0.00 2.90
5354 5474 8.430828 CAGTATTCTCGACATTGCATATTACTG 58.569 37.037 0.00 0.00 0.00 2.74
5431 5551 1.673920 GTGCAAGGAAACCTGACGAAA 59.326 47.619 0.00 0.00 32.13 3.46
5457 5577 1.740025 GCTTGCAGGATGAGGTTACAC 59.260 52.381 0.00 0.00 39.69 2.90
5565 5685 8.480643 ACAGTAAGCACTTTGTCTAATCATAC 57.519 34.615 0.00 0.00 30.46 2.39
5667 5787 1.461268 TGTGGAACAGAGGGCCTGA 60.461 57.895 12.95 0.00 45.67 3.86


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

AutoCloner maintained by Alex Coulton.