Multiple sequence alignment - TraesCS2A01G110400

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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 TraesCS2A01G110400 chr2A 100.000 3691 0 0 512 4202 62264924 62268614 0.000000e+00 6817
1 TraesCS2A01G110400 chr2A 100.000 188 0 0 1 188 62264413 62264600 8.650000e-92 348
2 TraesCS2A01G110400 chr2A 82.993 147 24 1 610 755 16619865 16619719 9.480000e-27 132
3 TraesCS2A01G110400 chr2A 82.313 147 24 2 610 755 16605414 16605269 4.410000e-25 126
4 TraesCS2A01G110400 chr2D 94.357 3048 116 18 787 3793 61796021 61799053 0.000000e+00 4625
5 TraesCS2A01G110400 chr2D 97.214 323 9 0 3880 4202 61800226 61800548 7.940000e-152 547
6 TraesCS2A01G110400 chr2D 89.270 233 24 1 512 744 61795683 61795914 1.480000e-74 291
7 TraesCS2A01G110400 chr2D 92.090 177 13 1 13 188 555383867 555383691 9.020000e-62 248
8 TraesCS2A01G110400 chr2B 95.980 2388 81 6 856 3240 96596343 96598718 0.000000e+00 3864
9 TraesCS2A01G110400 chr2B 93.320 494 17 7 3387 3879 96599094 96599572 0.000000e+00 715
10 TraesCS2A01G110400 chr2B 95.046 323 16 0 3880 4202 96600714 96601036 3.750000e-140 508
11 TraesCS2A01G110400 chr2B 93.296 179 12 0 3227 3405 96598735 96598913 8.960000e-67 265
12 TraesCS2A01G110400 chr2B 90.909 187 16 1 3 188 182966583 182966397 2.510000e-62 250
13 TraesCS2A01G110400 chr2B 83.212 137 21 2 609 744 142450898 142450763 1.590000e-24 124
14 TraesCS2A01G110400 chr6D 91.444 187 15 1 3 188 461377781 461377595 5.390000e-64 255
15 TraesCS2A01G110400 chr6D 90.426 188 15 3 3 188 8996982 8997168 1.170000e-60 244
16 TraesCS2A01G110400 chr7D 91.398 186 14 2 3 187 599081832 599081648 1.940000e-63 254
17 TraesCS2A01G110400 chr7D 90.374 187 16 2 3 188 45931658 45931843 1.170000e-60 244
18 TraesCS2A01G110400 chr5D 92.265 181 11 2 10 188 507861800 507861979 1.940000e-63 254
19 TraesCS2A01G110400 chr5D 80.952 147 27 1 609 755 251938102 251937957 9.550000e-22 115
20 TraesCS2A01G110400 chr5D 87.755 98 11 1 637 733 33077390 33077293 3.430000e-21 113
21 TraesCS2A01G110400 chr4D 90.909 187 16 1 3 188 293366452 293366266 2.510000e-62 250
22 TraesCS2A01G110400 chr4D 90.909 187 15 2 3 188 434459704 434459519 2.510000e-62 250
23 TraesCS2A01G110400 chr5B 85.135 148 21 1 609 756 335201146 335201292 2.620000e-32 150
24 TraesCS2A01G110400 chr7B 88.119 101 11 1 644 744 621296644 621296743 7.380000e-23 119
25 TraesCS2A01G110400 chr3A 85.714 98 12 2 623 719 585013044 585012948 7.430000e-18 102


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 TraesCS2A01G110400 chr2A 62264413 62268614 4201 False 3582.5 6817 100.000000 1 4202 2 chr2A.!!$F1 4201
1 TraesCS2A01G110400 chr2D 61795683 61800548 4865 False 1821.0 4625 93.613667 512 4202 3 chr2D.!!$F1 3690
2 TraesCS2A01G110400 chr2B 96596343 96601036 4693 False 1338.0 3864 94.410500 856 4202 4 chr2B.!!$F1 3346

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
747 748 0.107831 TACAACCGGGCATATGAGGC 59.892 55.000 6.32 0.0 0.00 4.70 F
787 827 0.996462 CGGTGCGGTGTGTATAACAG 59.004 55.000 0.00 0.0 40.26 3.16 F
788 828 1.670674 CGGTGCGGTGTGTATAACAGT 60.671 52.381 0.00 0.0 40.26 3.55 F
2466 2548 0.173481 GCATCACTGCCGACTCTGTA 59.827 55.000 0.00 0.0 42.88 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1672 0.461135 ACTGCACAAGGTTGGCAAAG 59.539 50.000 0.00 0.0 35.19 2.77 R
1619 1701 1.003118 CAATGTGGAAGAACCCCTCGA 59.997 52.381 0.00 0.0 38.00 4.04 R
2775 2857 1.066573 AGAATCCTCCAAGTCACAGCG 60.067 52.381 0.00 0.0 0.00 5.18 R
3974 5431 0.464452 GGCTTGGCGTAGACTATGGT 59.536 55.000 3.89 0.0 34.59 3.55 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
24 25 4.056125 CCGCTGTGTCCGAGCAGA 62.056 66.667 4.54 0.00 36.12 4.26
25 26 2.049156 CGCTGTGTCCGAGCAGAA 60.049 61.111 4.54 0.00 36.12 3.02
26 27 2.375766 CGCTGTGTCCGAGCAGAAC 61.376 63.158 4.54 0.00 36.12 3.01
27 28 2.029844 GCTGTGTCCGAGCAGAACC 61.030 63.158 4.54 0.00 36.40 3.62
28 29 1.374758 CTGTGTCCGAGCAGAACCC 60.375 63.158 0.00 0.00 34.87 4.11
29 30 2.432628 GTGTCCGAGCAGAACCCG 60.433 66.667 0.00 0.00 0.00 5.28
30 31 4.373116 TGTCCGAGCAGAACCCGC 62.373 66.667 0.00 0.00 0.00 6.13
31 32 4.373116 GTCCGAGCAGAACCCGCA 62.373 66.667 0.00 0.00 0.00 5.69
32 33 4.069232 TCCGAGCAGAACCCGCAG 62.069 66.667 0.00 0.00 0.00 5.18
33 34 4.069232 CCGAGCAGAACCCGCAGA 62.069 66.667 0.00 0.00 0.00 4.26
34 35 2.048222 CGAGCAGAACCCGCAGAA 60.048 61.111 0.00 0.00 0.00 3.02
35 36 2.097038 CGAGCAGAACCCGCAGAAG 61.097 63.158 0.00 0.00 0.00 2.85
36 37 2.359230 AGCAGAACCCGCAGAAGC 60.359 61.111 0.00 0.00 37.42 3.86
37 38 3.435186 GCAGAACCCGCAGAAGCC 61.435 66.667 0.00 0.00 37.52 4.35
38 39 3.121030 CAGAACCCGCAGAAGCCG 61.121 66.667 0.00 0.00 37.52 5.52
39 40 3.311110 AGAACCCGCAGAAGCCGA 61.311 61.111 0.00 0.00 37.52 5.54
40 41 3.119096 GAACCCGCAGAAGCCGAC 61.119 66.667 0.00 0.00 37.52 4.79
41 42 4.699522 AACCCGCAGAAGCCGACC 62.700 66.667 0.00 0.00 37.52 4.79
45 46 4.124351 CGCAGAAGCCGACCCGTA 62.124 66.667 0.00 0.00 37.52 4.02
46 47 2.263540 GCAGAAGCCGACCCGTAA 59.736 61.111 0.00 0.00 33.58 3.18
47 48 1.375013 GCAGAAGCCGACCCGTAAA 60.375 57.895 0.00 0.00 33.58 2.01
48 49 0.952010 GCAGAAGCCGACCCGTAAAA 60.952 55.000 0.00 0.00 33.58 1.52
49 50 1.515081 CAGAAGCCGACCCGTAAAAA 58.485 50.000 0.00 0.00 0.00 1.94
94 95 4.710167 CGGGTCCGTTTGGGGGTC 62.710 72.222 0.55 0.00 36.01 4.46
95 96 3.254617 GGGTCCGTTTGGGGGTCT 61.255 66.667 0.00 0.00 36.01 3.85
96 97 2.033602 GGTCCGTTTGGGGGTCTG 59.966 66.667 0.00 0.00 36.01 3.51
97 98 2.671963 GTCCGTTTGGGGGTCTGC 60.672 66.667 0.00 0.00 36.01 4.26
98 99 3.172106 TCCGTTTGGGGGTCTGCA 61.172 61.111 0.00 0.00 36.01 4.41
99 100 2.035626 CCGTTTGGGGGTCTGCAT 59.964 61.111 0.00 0.00 0.00 3.96
100 101 2.046285 CCGTTTGGGGGTCTGCATC 61.046 63.158 0.00 0.00 0.00 3.91
101 102 1.002134 CGTTTGGGGGTCTGCATCT 60.002 57.895 0.00 0.00 0.00 2.90
102 103 1.308069 CGTTTGGGGGTCTGCATCTG 61.308 60.000 0.00 0.00 0.00 2.90
103 104 0.251341 GTTTGGGGGTCTGCATCTGT 60.251 55.000 0.00 0.00 0.00 3.41
104 105 0.251297 TTTGGGGGTCTGCATCTGTG 60.251 55.000 0.00 0.00 0.00 3.66
105 106 1.133181 TTGGGGGTCTGCATCTGTGA 61.133 55.000 0.00 0.00 0.00 3.58
106 107 1.078143 GGGGGTCTGCATCTGTGAC 60.078 63.158 0.00 0.00 0.00 3.67
107 108 1.679311 GGGGTCTGCATCTGTGACA 59.321 57.895 5.52 0.00 32.84 3.58
108 109 0.392193 GGGGTCTGCATCTGTGACAG 60.392 60.000 6.18 6.18 33.55 3.51
109 110 1.023513 GGGTCTGCATCTGTGACAGC 61.024 60.000 7.93 0.00 32.83 4.40
110 111 1.023513 GGTCTGCATCTGTGACAGCC 61.024 60.000 7.93 0.00 32.83 4.85
111 112 1.023513 GTCTGCATCTGTGACAGCCC 61.024 60.000 7.93 0.00 32.83 5.19
112 113 2.046988 TGCATCTGTGACAGCCCG 60.047 61.111 7.93 0.00 0.00 6.13
113 114 2.265739 GCATCTGTGACAGCCCGA 59.734 61.111 7.93 0.00 0.00 5.14
114 115 1.812922 GCATCTGTGACAGCCCGAG 60.813 63.158 7.93 0.00 0.00 4.63
115 116 1.812922 CATCTGTGACAGCCCGAGC 60.813 63.158 7.93 0.00 40.32 5.03
116 117 3.023949 ATCTGTGACAGCCCGAGCC 62.024 63.158 7.93 0.00 41.25 4.70
117 118 4.007644 CTGTGACAGCCCGAGCCA 62.008 66.667 0.00 0.00 41.25 4.75
118 119 3.947132 CTGTGACAGCCCGAGCCAG 62.947 68.421 0.00 0.00 41.25 4.85
128 129 4.183686 CGAGCCAGCCCGCAAATG 62.184 66.667 0.00 0.00 0.00 2.32
129 130 4.503314 GAGCCAGCCCGCAAATGC 62.503 66.667 0.00 0.00 37.78 3.56
145 146 3.566273 TGCGGTTTTGCATGAACTG 57.434 47.368 14.69 14.69 40.62 3.16
154 155 4.920662 CATGAACTGCAAACGCGT 57.079 50.000 5.58 5.58 0.00 6.01
155 156 3.162499 CATGAACTGCAAACGCGTT 57.838 47.368 20.79 20.79 0.00 4.84
156 157 1.476074 CATGAACTGCAAACGCGTTT 58.524 45.000 30.36 30.36 0.00 3.60
157 158 1.851666 CATGAACTGCAAACGCGTTTT 59.148 42.857 33.05 19.44 0.00 2.43
158 159 1.263776 TGAACTGCAAACGCGTTTTG 58.736 45.000 33.05 26.38 46.57 2.44
169 170 4.741781 CGTTTTGCGAGCCGGCTG 62.742 66.667 38.41 26.20 44.77 4.85
170 171 4.404654 GTTTTGCGAGCCGGCTGG 62.405 66.667 38.41 34.73 38.77 4.85
171 172 4.634703 TTTTGCGAGCCGGCTGGA 62.635 61.111 38.72 25.97 37.49 3.86
172 173 3.918253 TTTTGCGAGCCGGCTGGAT 62.918 57.895 38.72 15.00 37.49 3.41
182 183 4.864334 GGCTGGATGCGGGGTCTG 62.864 72.222 0.00 0.00 44.05 3.51
184 185 3.790437 CTGGATGCGGGGTCTGCT 61.790 66.667 0.30 0.00 0.00 4.24
185 186 2.364973 TGGATGCGGGGTCTGCTA 60.365 61.111 0.30 0.00 0.00 3.49
186 187 2.374830 CTGGATGCGGGGTCTGCTAG 62.375 65.000 0.30 0.00 0.00 3.42
187 188 2.134287 GGATGCGGGGTCTGCTAGA 61.134 63.158 0.00 0.00 0.00 2.43
534 535 2.031616 ATGGCGGCGATGGATCAG 59.968 61.111 12.98 0.00 0.00 2.90
541 542 1.118356 GGCGATGGATCAGAGGTCCT 61.118 60.000 0.00 0.00 36.68 3.85
548 549 1.407258 GGATCAGAGGTCCTTCTCGTG 59.593 57.143 0.00 0.00 38.71 4.35
552 553 0.820871 AGAGGTCCTTCTCGTGCATC 59.179 55.000 0.00 0.00 38.71 3.91
563 564 0.607620 TCGTGCATCTGTGGTCATCA 59.392 50.000 0.00 0.00 0.00 3.07
567 568 2.095567 GTGCATCTGTGGTCATCAACAC 60.096 50.000 0.00 0.00 38.08 3.32
568 569 2.153645 GCATCTGTGGTCATCAACACA 58.846 47.619 0.00 0.00 44.60 3.72
579 580 2.750712 TCATCAACACATAGGACGACGA 59.249 45.455 0.00 0.00 0.00 4.20
596 597 3.677700 CGACGACCATGGTTTCCATTCTA 60.678 47.826 20.85 0.00 42.23 2.10
607 608 5.066593 GGTTTCCATTCTATCTCCCATGAC 58.933 45.833 0.00 0.00 0.00 3.06
614 615 5.604758 TTCTATCTCCCATGACAGTTCAG 57.395 43.478 0.00 0.00 34.35 3.02
632 633 9.167311 ACAGTTCAGATATGTCAAAAACTATCC 57.833 33.333 0.00 0.00 0.00 2.59
676 677 4.836825 AGTATGAATGGATATCGCTTGGG 58.163 43.478 0.00 0.00 0.00 4.12
737 738 4.688511 TTTTGATCGAAATACAACCGGG 57.311 40.909 6.32 0.00 0.00 5.73
744 745 3.135225 CGAAATACAACCGGGCATATGA 58.865 45.455 6.32 0.00 0.00 2.15
747 748 0.107831 TACAACCGGGCATATGAGGC 59.892 55.000 6.32 0.00 0.00 4.70
762 802 2.818274 GGCCAGCTTTACGGTCCG 60.818 66.667 10.48 10.48 0.00 4.79
763 803 3.497031 GCCAGCTTTACGGTCCGC 61.497 66.667 12.28 0.00 0.00 5.54
784 824 4.915298 CCGGTGCGGTGTGTATAA 57.085 55.556 0.00 0.00 42.73 0.98
785 825 2.375981 CCGGTGCGGTGTGTATAAC 58.624 57.895 0.00 0.00 42.73 1.89
787 827 0.996462 CGGTGCGGTGTGTATAACAG 59.004 55.000 0.00 0.00 40.26 3.16
788 828 1.670674 CGGTGCGGTGTGTATAACAGT 60.671 52.381 0.00 0.00 40.26 3.55
790 830 2.610976 GGTGCGGTGTGTATAACAGTGA 60.611 50.000 0.00 0.00 40.26 3.41
791 831 3.061322 GTGCGGTGTGTATAACAGTGAA 58.939 45.455 0.00 0.00 40.26 3.18
796 863 5.061808 GCGGTGTGTATAACAGTGAAAGTAG 59.938 44.000 0.00 0.00 40.26 2.57
799 866 7.148853 CGGTGTGTATAACAGTGAAAGTAGAAC 60.149 40.741 0.00 0.00 40.26 3.01
800 867 7.148853 GGTGTGTATAACAGTGAAAGTAGAACG 60.149 40.741 0.00 0.00 40.26 3.95
806 873 8.912787 ATAACAGTGAAAGTAGAACGAGTATG 57.087 34.615 0.00 0.00 0.00 2.39
815 882 6.125327 AGTAGAACGAGTATGTGATCACAG 57.875 41.667 30.63 19.91 45.48 3.66
857 936 6.166982 AGCTAGTAACCTGAACTGAATTGTC 58.833 40.000 0.00 0.00 0.00 3.18
882 961 3.195698 CGCTAAGTTCAGGCGGGC 61.196 66.667 9.09 0.00 44.32 6.13
998 1077 3.771160 GCCTCCTTTCGCCTCCGA 61.771 66.667 0.00 0.00 42.66 4.55
1114 1193 4.116585 TCGCGCTCCTCCTCTCCT 62.117 66.667 5.56 0.00 0.00 3.69
1115 1194 3.591835 CGCGCTCCTCCTCTCCTC 61.592 72.222 5.56 0.00 0.00 3.71
1116 1195 3.223589 GCGCTCCTCCTCTCCTCC 61.224 72.222 0.00 0.00 0.00 4.30
1117 1196 2.904866 CGCTCCTCCTCTCCTCCG 60.905 72.222 0.00 0.00 0.00 4.63
1118 1197 3.223589 GCTCCTCCTCTCCTCCGC 61.224 72.222 0.00 0.00 0.00 5.54
1119 1198 2.277072 CTCCTCCTCTCCTCCGCA 59.723 66.667 0.00 0.00 0.00 5.69
1307 1389 4.814041 GCCCTGGCTCCTCCTCCT 62.814 72.222 0.00 0.00 38.26 3.69
1308 1390 2.445654 CCCTGGCTCCTCCTCCTC 60.446 72.222 0.00 0.00 35.26 3.71
1532 1614 2.126580 GGACCTCGTCGACAACCG 60.127 66.667 17.16 0.96 40.25 4.44
1619 1701 4.854924 TGTGCAGTGCCTGTGCGT 62.855 61.111 13.72 0.00 44.35 5.24
2161 2243 4.485163 TGTGATCACTATGAACACTGTCG 58.515 43.478 25.55 0.00 46.31 4.35
2230 2312 2.571212 TGGACGACATGATTAATGGGC 58.429 47.619 0.00 0.00 40.94 5.36
2274 2356 2.224079 CACCTTCACCACACTCATTTCG 59.776 50.000 0.00 0.00 0.00 3.46
2466 2548 0.173481 GCATCACTGCCGACTCTGTA 59.827 55.000 0.00 0.00 42.88 2.74
2468 2550 2.263077 CATCACTGCCGACTCTGTAAC 58.737 52.381 0.00 0.00 0.00 2.50
2497 2579 1.327303 GGTGATCAAAGGGTTGTGCA 58.673 50.000 0.00 0.00 36.07 4.57
2541 2623 3.737559 AAGGCATTCTGGGACAATGTA 57.262 42.857 0.00 0.00 38.70 2.29
2628 2710 0.610232 GGAAACTGGAGCAGGCATGT 60.610 55.000 0.00 0.00 35.51 3.21
2637 2719 2.421952 GGAGCAGGCATGTGATTTCCTA 60.422 50.000 0.00 0.00 0.00 2.94
2654 2736 4.944619 TCCTATATGAGTTGGCAGACTG 57.055 45.455 0.00 0.00 0.00 3.51
2775 2857 1.313091 GGAATGGCCTTTCACCGGAC 61.313 60.000 27.32 9.74 0.00 4.79
2826 2908 3.444742 TGCACCTTTATGGCAATGAAGAG 59.555 43.478 7.17 1.22 40.22 2.85
2852 2937 1.151899 AGCACCAGGTCCCCACTTA 60.152 57.895 0.00 0.00 0.00 2.24
2857 2942 3.045634 CACCAGGTCCCCACTTATCATA 58.954 50.000 0.00 0.00 0.00 2.15
2893 2978 2.034558 GCAGATGACAGAGTAGAGCCTC 59.965 54.545 0.00 0.00 0.00 4.70
2901 2986 1.834896 AGAGTAGAGCCTCTCGTCTCA 59.165 52.381 17.50 0.00 37.20 3.27
2948 3033 2.561733 TCGTCATCATCGTCAGAACC 57.438 50.000 0.00 0.00 0.00 3.62
3014 3099 1.072965 AGCTGGAAGGTCACCAGAAAG 59.927 52.381 16.63 0.00 44.61 2.62
3051 3136 3.622163 CAGATCTTACTGAGCCAGCAAAG 59.378 47.826 0.00 6.77 39.94 2.77
3212 3297 3.815401 GGCTTGCTCTAGAACAAGAACAA 59.185 43.478 30.97 10.56 44.89 2.83
3314 3429 1.272490 TGAAGGCCGAGTTAGTGACAG 59.728 52.381 0.00 0.00 0.00 3.51
3316 3431 1.185618 AGGCCGAGTTAGTGACAGCA 61.186 55.000 0.00 0.00 0.00 4.41
3384 3499 5.050363 GCTTGACTGACACGACTGATTTTTA 60.050 40.000 0.00 0.00 0.00 1.52
3389 3504 4.377021 TGACACGACTGATTTTTAGCTGT 58.623 39.130 0.00 0.00 0.00 4.40
3658 3972 2.751806 CTGGGCTCTTTTGGATGAAGAC 59.248 50.000 0.00 0.00 0.00 3.01
3690 4004 1.203994 GCTTGCAAGCCTGTGAATCAT 59.796 47.619 36.21 0.00 46.20 2.45
3695 4009 3.512329 TGCAAGCCTGTGAATCATTGATT 59.488 39.130 11.64 11.64 34.71 2.57
3713 4027 4.478203 TGATTCAAGACATTGGGGTTTCA 58.522 39.130 0.00 0.00 37.02 2.69
3724 4038 9.354673 AGACATTGGGGTTTCAATATATGTAAG 57.645 33.333 0.00 0.00 35.78 2.34
3771 4085 4.423625 AGGTACTTATCACTTCATGGGC 57.576 45.455 0.00 0.00 27.25 5.36
3803 4117 0.179134 GCGTCGCAAGGTATGAGAGT 60.179 55.000 13.44 0.00 38.61 3.24
3813 4127 5.008613 GCAAGGTATGAGAGTGTTTTGACAA 59.991 40.000 0.00 0.00 0.00 3.18
3833 4147 1.103803 GGACTGATGCTACTGTCGGA 58.896 55.000 11.75 0.00 38.82 4.55
3854 4168 4.142816 GGACTTGTTAACTGTATGCTGCTG 60.143 45.833 7.22 0.00 0.00 4.41
3916 5373 4.647615 CGCCTCATCTACGCCGGG 62.648 72.222 2.18 0.00 0.00 5.73
3974 5431 0.179094 GATGATTGACCGTGGGCGTA 60.179 55.000 0.00 0.00 36.15 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.573772 TTCTGCTCGGACACAGCGG 62.574 63.158 0.00 0.00 43.65 5.52
8 9 2.049156 TTCTGCTCGGACACAGCG 60.049 61.111 0.00 0.00 40.01 5.18
9 10 2.029844 GGTTCTGCTCGGACACAGC 61.030 63.158 0.00 0.00 37.40 4.40
10 11 1.374758 GGGTTCTGCTCGGACACAG 60.375 63.158 0.00 0.00 35.15 3.66
11 12 2.741092 GGGTTCTGCTCGGACACA 59.259 61.111 0.00 0.00 0.00 3.72
12 13 2.432628 CGGGTTCTGCTCGGACAC 60.433 66.667 0.00 0.00 37.44 3.67
13 14 4.373116 GCGGGTTCTGCTCGGACA 62.373 66.667 0.00 0.00 42.38 4.02
14 15 4.373116 TGCGGGTTCTGCTCGGAC 62.373 66.667 0.30 0.00 42.38 4.79
15 16 4.069232 CTGCGGGTTCTGCTCGGA 62.069 66.667 0.30 0.00 42.38 4.55
16 17 3.589654 TTCTGCGGGTTCTGCTCGG 62.590 63.158 0.00 0.00 42.38 4.63
17 18 2.048222 TTCTGCGGGTTCTGCTCG 60.048 61.111 0.00 0.00 45.55 5.03
18 19 2.394563 GCTTCTGCGGGTTCTGCTC 61.395 63.158 0.00 0.00 0.00 4.26
19 20 2.359230 GCTTCTGCGGGTTCTGCT 60.359 61.111 0.00 0.00 0.00 4.24
20 21 3.435186 GGCTTCTGCGGGTTCTGC 61.435 66.667 0.00 0.00 40.82 4.26
21 22 3.121030 CGGCTTCTGCGGGTTCTG 61.121 66.667 0.00 0.00 40.82 3.02
22 23 3.311110 TCGGCTTCTGCGGGTTCT 61.311 61.111 0.00 0.00 40.82 3.01
23 24 3.119096 GTCGGCTTCTGCGGGTTC 61.119 66.667 0.00 0.00 40.82 3.62
24 25 4.699522 GGTCGGCTTCTGCGGGTT 62.700 66.667 0.00 0.00 40.82 4.11
28 29 3.636313 TTACGGGTCGGCTTCTGCG 62.636 63.158 0.00 0.00 40.82 5.18
29 30 0.952010 TTTTACGGGTCGGCTTCTGC 60.952 55.000 0.00 0.00 38.76 4.26
30 31 1.515081 TTTTTACGGGTCGGCTTCTG 58.485 50.000 0.00 0.00 0.00 3.02
77 78 4.710167 GACCCCCAAACGGACCCG 62.710 72.222 6.94 6.94 46.03 5.28
78 79 3.254617 AGACCCCCAAACGGACCC 61.255 66.667 0.00 0.00 0.00 4.46
79 80 2.033602 CAGACCCCCAAACGGACC 59.966 66.667 0.00 0.00 0.00 4.46
80 81 2.671963 GCAGACCCCCAAACGGAC 60.672 66.667 0.00 0.00 0.00 4.79
81 82 2.478335 GATGCAGACCCCCAAACGGA 62.478 60.000 0.00 0.00 0.00 4.69
82 83 2.035626 ATGCAGACCCCCAAACGG 59.964 61.111 0.00 0.00 0.00 4.44
83 84 1.002134 AGATGCAGACCCCCAAACG 60.002 57.895 0.00 0.00 0.00 3.60
84 85 0.251341 ACAGATGCAGACCCCCAAAC 60.251 55.000 0.00 0.00 0.00 2.93
85 86 0.251297 CACAGATGCAGACCCCCAAA 60.251 55.000 0.00 0.00 0.00 3.28
86 87 1.133181 TCACAGATGCAGACCCCCAA 61.133 55.000 0.00 0.00 0.00 4.12
87 88 1.538629 TCACAGATGCAGACCCCCA 60.539 57.895 0.00 0.00 0.00 4.96
88 89 1.078143 GTCACAGATGCAGACCCCC 60.078 63.158 0.00 0.00 0.00 5.40
89 90 0.392193 CTGTCACAGATGCAGACCCC 60.392 60.000 0.00 0.00 34.03 4.95
90 91 1.023513 GCTGTCACAGATGCAGACCC 61.024 60.000 9.70 0.00 34.03 4.46
91 92 1.023513 GGCTGTCACAGATGCAGACC 61.024 60.000 9.70 0.00 34.00 3.85
92 93 1.023513 GGGCTGTCACAGATGCAGAC 61.024 60.000 9.70 0.00 37.30 3.51
93 94 1.297689 GGGCTGTCACAGATGCAGA 59.702 57.895 9.70 0.00 34.03 4.26
94 95 2.104859 CGGGCTGTCACAGATGCAG 61.105 63.158 9.70 0.00 34.79 4.41
95 96 2.046988 CGGGCTGTCACAGATGCA 60.047 61.111 9.70 0.00 32.44 3.96
96 97 1.812922 CTCGGGCTGTCACAGATGC 60.813 63.158 9.70 0.00 32.44 3.91
97 98 1.812922 GCTCGGGCTGTCACAGATG 60.813 63.158 9.70 0.00 32.44 2.90
98 99 2.581354 GCTCGGGCTGTCACAGAT 59.419 61.111 9.70 0.00 32.44 2.90
99 100 3.695606 GGCTCGGGCTGTCACAGA 61.696 66.667 9.70 0.00 38.73 3.41
100 101 3.947132 CTGGCTCGGGCTGTCACAG 62.947 68.421 7.48 0.00 38.73 3.66
101 102 4.007644 CTGGCTCGGGCTGTCACA 62.008 66.667 7.48 0.00 38.73 3.58
111 112 4.183686 CATTTGCGGGCTGGCTCG 62.184 66.667 10.73 10.73 43.79 5.03
112 113 4.503314 GCATTTGCGGGCTGGCTC 62.503 66.667 0.00 0.00 0.00 4.70
137 138 1.476074 AAACGCGTTTGCAGTTCATG 58.524 45.000 34.36 0.00 42.97 3.07
138 139 1.851666 CAAAACGCGTTTGCAGTTCAT 59.148 42.857 35.31 16.10 40.25 2.57
139 140 1.263776 CAAAACGCGTTTGCAGTTCA 58.736 45.000 35.31 0.00 40.25 3.18
152 153 4.741781 CAGCCGGCTCGCAAAACG 62.742 66.667 30.29 9.21 45.62 3.60
153 154 4.404654 CCAGCCGGCTCGCAAAAC 62.405 66.667 30.29 0.00 0.00 2.43
154 155 3.918253 ATCCAGCCGGCTCGCAAAA 62.918 57.895 30.29 3.83 0.00 2.44
155 156 4.408821 ATCCAGCCGGCTCGCAAA 62.409 61.111 30.29 10.77 0.00 3.68
165 166 4.864334 CAGACCCCGCATCCAGCC 62.864 72.222 0.00 0.00 41.38 4.85
167 168 2.374830 CTAGCAGACCCCGCATCCAG 62.375 65.000 0.00 0.00 0.00 3.86
168 169 2.364973 TAGCAGACCCCGCATCCA 60.365 61.111 0.00 0.00 0.00 3.41
169 170 2.134287 TCTAGCAGACCCCGCATCC 61.134 63.158 0.00 0.00 0.00 3.51
170 171 3.538614 TCTAGCAGACCCCGCATC 58.461 61.111 0.00 0.00 0.00 3.91
514 515 2.281070 ATCCATCGCCGCCATGAC 60.281 61.111 0.00 0.00 0.00 3.06
526 527 2.315176 CGAGAAGGACCTCTGATCCAT 58.685 52.381 0.00 0.00 38.86 3.41
534 535 0.820871 AGATGCACGAGAAGGACCTC 59.179 55.000 0.00 0.00 0.00 3.85
541 542 0.678950 TGACCACAGATGCACGAGAA 59.321 50.000 0.00 0.00 0.00 2.87
548 549 2.153645 TGTGTTGATGACCACAGATGC 58.846 47.619 0.00 0.00 0.00 3.91
552 553 3.935203 GTCCTATGTGTTGATGACCACAG 59.065 47.826 0.00 0.00 0.00 3.66
563 564 1.250328 TGGTCGTCGTCCTATGTGTT 58.750 50.000 9.90 0.00 0.00 3.32
567 568 0.744874 ACCATGGTCGTCGTCCTATG 59.255 55.000 13.00 10.69 0.00 2.23
568 569 1.481871 AACCATGGTCGTCGTCCTAT 58.518 50.000 20.07 0.00 0.00 2.57
579 580 4.141158 GGGAGATAGAATGGAAACCATGGT 60.141 45.833 13.00 13.00 44.40 3.55
596 597 5.605908 ACATATCTGAACTGTCATGGGAGAT 59.394 40.000 0.00 0.00 31.85 2.75
607 608 8.331022 CGGATAGTTTTTGACATATCTGAACTG 58.669 37.037 0.00 0.00 34.35 3.16
669 670 4.489810 TGCATATTTAAACAACCCAAGCG 58.510 39.130 0.00 0.00 0.00 4.68
672 673 9.512588 AATTTGATGCATATTTAAACAACCCAA 57.487 25.926 0.00 0.00 0.00 4.12
673 674 9.512588 AAATTTGATGCATATTTAAACAACCCA 57.487 25.926 0.00 0.00 0.00 4.51
719 720 1.066071 TGCCCGGTTGTATTTCGATCA 60.066 47.619 0.00 0.00 0.00 2.92
720 721 1.658994 TGCCCGGTTGTATTTCGATC 58.341 50.000 0.00 0.00 0.00 3.69
724 725 3.502211 CCTCATATGCCCGGTTGTATTTC 59.498 47.826 0.00 0.00 0.00 2.17
729 730 1.152963 GCCTCATATGCCCGGTTGT 60.153 57.895 0.00 0.00 0.00 3.32
737 738 1.532868 CGTAAAGCTGGCCTCATATGC 59.467 52.381 3.32 0.00 0.00 3.14
744 745 2.669240 GGACCGTAAAGCTGGCCT 59.331 61.111 3.32 0.00 0.00 5.19
747 748 3.186047 CGCGGACCGTAAAGCTGG 61.186 66.667 16.73 0.00 0.00 4.85
748 749 3.186047 CCGCGGACCGTAAAGCTG 61.186 66.667 24.07 0.00 34.38 4.24
750 751 3.184003 GTCCGCGGACCGTAAAGC 61.184 66.667 41.88 19.15 39.08 3.51
770 810 2.679450 TCACTGTTATACACACCGCAC 58.321 47.619 0.00 0.00 0.00 5.34
780 820 9.999009 CATACTCGTTCTACTTTCACTGTTATA 57.001 33.333 0.00 0.00 0.00 0.98
781 821 8.521176 ACATACTCGTTCTACTTTCACTGTTAT 58.479 33.333 0.00 0.00 0.00 1.89
782 822 7.806487 CACATACTCGTTCTACTTTCACTGTTA 59.194 37.037 0.00 0.00 0.00 2.41
783 823 6.641314 CACATACTCGTTCTACTTTCACTGTT 59.359 38.462 0.00 0.00 0.00 3.16
784 824 6.016527 TCACATACTCGTTCTACTTTCACTGT 60.017 38.462 0.00 0.00 0.00 3.55
785 825 6.379386 TCACATACTCGTTCTACTTTCACTG 58.621 40.000 0.00 0.00 0.00 3.66
787 827 7.008447 GTGATCACATACTCGTTCTACTTTCAC 59.992 40.741 21.07 0.00 0.00 3.18
788 828 7.027760 GTGATCACATACTCGTTCTACTTTCA 58.972 38.462 21.07 0.00 0.00 2.69
790 830 6.920817 TGTGATCACATACTCGTTCTACTTT 58.079 36.000 24.56 0.00 36.21 2.66
791 831 6.510879 TGTGATCACATACTCGTTCTACTT 57.489 37.500 24.56 0.00 36.21 2.24
796 863 3.511699 TGCTGTGATCACATACTCGTTC 58.488 45.455 28.00 10.61 41.01 3.95
799 866 4.926860 TTTTGCTGTGATCACATACTCG 57.073 40.909 28.00 17.01 41.01 4.18
800 867 7.280876 TCCTTATTTTGCTGTGATCACATACTC 59.719 37.037 28.00 17.06 41.01 2.59
805 872 6.647334 TTTCCTTATTTTGCTGTGATCACA 57.353 33.333 26.33 26.33 39.32 3.58
806 873 7.945033 TTTTTCCTTATTTTGCTGTGATCAC 57.055 32.000 19.27 19.27 0.00 3.06
832 899 6.534634 ACAATTCAGTTCAGGTTACTAGCTT 58.465 36.000 0.00 0.00 0.00 3.74
835 902 7.588143 CTGACAATTCAGTTCAGGTTACTAG 57.412 40.000 0.00 0.00 43.95 2.57
879 958 4.699522 GCATCGTATCGGGGGCCC 62.700 72.222 15.76 15.76 0.00 5.80
962 1041 3.061260 GCAGGGTCGAGACGGTACC 62.061 68.421 0.16 0.16 0.00 3.34
994 1073 4.545706 GGCCGCCATCATGTCGGA 62.546 66.667 12.29 0.00 45.53 4.55
1235 1314 3.995809 TAGTTGGGGAGGGAGGGCG 62.996 68.421 0.00 0.00 0.00 6.13
1590 1672 0.461135 ACTGCACAAGGTTGGCAAAG 59.539 50.000 0.00 0.00 35.19 2.77
1619 1701 1.003118 CAATGTGGAAGAACCCCTCGA 59.997 52.381 0.00 0.00 38.00 4.04
1686 1768 1.095807 GGGCATAGGCAAACTCGTCC 61.096 60.000 0.15 0.00 43.71 4.79
1968 2050 1.661463 TCAGCTCCAGGACATCCTTT 58.339 50.000 0.00 0.00 46.09 3.11
2016 2098 2.716017 CCTGGTCTCCTCGTCAGGC 61.716 68.421 0.00 0.00 40.04 4.85
2106 2188 2.334946 CCCCTGCAACATGGACACG 61.335 63.158 0.00 0.00 0.00 4.49
2161 2243 3.054878 CAACTTTGCAGAAGCCATGAAC 58.945 45.455 0.00 0.00 41.13 3.18
2230 2312 3.504906 ACAACATCAGGAGCACAGAATTG 59.495 43.478 0.00 0.00 0.00 2.32
2541 2623 1.344393 TGTATCCCTGATGGCCAGACT 60.344 52.381 13.05 0.00 45.78 3.24
2628 2710 6.100279 AGTCTGCCAACTCATATAGGAAATCA 59.900 38.462 0.00 0.00 0.00 2.57
2637 2719 2.092753 CCCACAGTCTGCCAACTCATAT 60.093 50.000 0.00 0.00 0.00 1.78
2775 2857 1.066573 AGAATCCTCCAAGTCACAGCG 60.067 52.381 0.00 0.00 0.00 5.18
2826 2908 1.376553 GACCTGGTGCTCCTCTTGC 60.377 63.158 2.82 0.00 34.23 4.01
2852 2937 6.519382 TCTGCAGAACTTTGATCGATATGAT 58.481 36.000 15.67 0.00 41.06 2.45
2857 2942 4.569966 GTCATCTGCAGAACTTTGATCGAT 59.430 41.667 22.50 0.00 0.00 3.59
2916 3001 2.029380 TGATGACGATGACAACGAAGGT 60.029 45.455 12.41 0.00 34.70 3.50
3014 3099 3.037549 AGATCTGATGGGTTCTCAGTCC 58.962 50.000 0.00 0.00 40.79 3.85
3051 3136 5.534654 ACTGTCTATCAGATAGTTCTGCTCC 59.465 44.000 15.85 0.00 42.91 4.70
3212 3297 2.489073 CCCCTTCTAACCAGCAACACTT 60.489 50.000 0.00 0.00 0.00 3.16
3287 3402 2.270352 AACTCGGCCTTCATTGACAA 57.730 45.000 0.00 0.00 0.00 3.18
3316 3431 1.545651 GGACAGGTAACCAGCTTTGCT 60.546 52.381 0.00 0.00 40.77 3.91
3384 3499 4.899502 ACAAGCTTATGTCAAGTACAGCT 58.100 39.130 0.00 0.00 42.70 4.24
3520 3834 3.613432 GCAAAACTGGAGCAATCTGAAGG 60.613 47.826 0.00 0.00 0.00 3.46
3658 3972 1.676529 CTTGCAAGCATCTCCATGAGG 59.323 52.381 14.65 0.00 30.57 3.86
3690 4004 4.898265 TGAAACCCCAATGTCTTGAATCAA 59.102 37.500 0.00 0.00 34.04 2.57
3695 4009 7.838696 ACATATATTGAAACCCCAATGTCTTGA 59.161 33.333 0.00 0.00 37.34 3.02
3713 4027 9.632638 ACCTTTTGACATGCTCTTACATATATT 57.367 29.630 0.00 0.00 0.00 1.28
3724 4038 2.158449 CGTCTCACCTTTTGACATGCTC 59.842 50.000 0.00 0.00 0.00 4.26
3734 4048 1.073199 CCTTGGCCGTCTCACCTTT 59.927 57.895 0.00 0.00 0.00 3.11
3771 4085 2.398036 GACGCGCCAACAATACCG 59.602 61.111 5.73 0.00 0.00 4.02
3803 4117 3.554934 AGCATCAGTCCTTGTCAAAACA 58.445 40.909 0.00 0.00 0.00 2.83
3813 4127 1.107114 CCGACAGTAGCATCAGTCCT 58.893 55.000 0.00 0.00 0.00 3.85
3833 4147 3.753272 CCAGCAGCATACAGTTAACAAGT 59.247 43.478 8.61 8.54 0.00 3.16
3854 4168 3.389329 TCTTCATAGATGAACTCCAGGCC 59.611 47.826 0.00 0.00 41.51 5.19
3974 5431 0.464452 GGCTTGGCGTAGACTATGGT 59.536 55.000 3.89 0.00 34.59 3.55


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

AutoCloner maintained by Alex Coulton.