Multiple sequence alignment - TraesCS4A01G046300

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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 TraesCS4A01G046300 chr4A 100.000 2297 0 0 1 2297 37829723 37832019 0.000000e+00 4242
1 TraesCS4A01G046300 chr4A 94.203 69 3 1 1 69 37829298 37829231 1.120000e-18 104
2 TraesCS4A01G046300 chr4B 91.143 2213 133 35 66 2233 526956869 526959063 0.000000e+00 2942
3 TraesCS4A01G046300 chr4D 91.944 993 53 17 1260 2236 428560945 428559964 0.000000e+00 1365
4 TraesCS4A01G046300 chr4D 94.737 456 18 4 836 1286 428562670 428562216 0.000000e+00 704
5 TraesCS4A01G046300 chr4D 83.081 792 72 32 66 839 428563484 428562737 0.000000e+00 664
6 TraesCS4A01G046300 chr6A 95.714 70 3 0 1 70 11041008 11041077 1.870000e-21 113
7 TraesCS4A01G046300 chr6A 95.714 70 1 2 1 68 560823147 560823078 6.710000e-21 111
8 TraesCS4A01G046300 chr6A 100.000 58 0 0 1 58 11040183 11040126 8.680000e-20 108
9 TraesCS4A01G046300 chr2A 100.000 61 0 0 1 61 55475707 55475767 1.870000e-21 113
10 TraesCS4A01G046300 chr7A 100.000 59 0 0 1 59 645313104 645313046 2.410000e-20 110
11 TraesCS4A01G046300 chr2B 100.000 59 0 0 1 59 771008055 771007997 2.410000e-20 110
12 TraesCS4A01G046300 chr2B 100.000 58 0 0 1 58 771008884 771008941 8.680000e-20 108
13 TraesCS4A01G046300 chr3A 100.000 58 0 0 1 58 31240443 31240500 8.680000e-20 108


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 TraesCS4A01G046300 chr4A 37829723 37832019 2296 False 4242 4242 100.000000 1 2297 1 chr4A.!!$F1 2296
1 TraesCS4A01G046300 chr4B 526956869 526959063 2194 False 2942 2942 91.143000 66 2233 1 chr4B.!!$F1 2167
2 TraesCS4A01G046300 chr4D 428559964 428563484 3520 True 911 1365 89.920667 66 2236 3 chr4D.!!$R1 2170

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
42 43 0.038526 GCGAAGAGTTGAGGGACGAA 60.039 55.000 0.00 0.0 0.00 3.85 F
43 44 1.604693 GCGAAGAGTTGAGGGACGAAA 60.605 52.381 0.00 0.0 0.00 3.46 F
173 181 1.894699 AGTAGAACCCAGGGGAATCC 58.105 55.000 11.37 0.0 38.96 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 1196 1.130054 ACTGGGCCTGACATCTGTGT 61.130 55.0 18.12 0.00 42.49 3.72 R
1116 1234 1.511850 TTGTGATCTTGTCTGCGTGG 58.488 50.0 0.00 0.00 0.00 4.94 R
2088 3518 0.039256 CCACAAACGGCCTGTTCATG 60.039 55.0 12.33 12.55 40.84 3.07 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
23 24 5.744666 TGAGGGACGAAAACTAAACTTTG 57.255 39.130 0.00 0.00 0.00 2.77
24 25 4.035909 TGAGGGACGAAAACTAAACTTTGC 59.964 41.667 0.00 0.00 0.00 3.68
25 26 3.002965 AGGGACGAAAACTAAACTTTGCG 59.997 43.478 0.00 0.00 0.00 4.85
26 27 3.002553 GGGACGAAAACTAAACTTTGCGA 59.997 43.478 0.00 0.00 0.00 5.10
27 28 4.496175 GGGACGAAAACTAAACTTTGCGAA 60.496 41.667 0.00 0.00 0.00 4.70
28 29 4.669283 GGACGAAAACTAAACTTTGCGAAG 59.331 41.667 12.41 12.41 38.87 3.79
29 30 5.473796 ACGAAAACTAAACTTTGCGAAGA 57.526 34.783 20.86 0.00 36.69 2.87
30 31 5.499047 ACGAAAACTAAACTTTGCGAAGAG 58.501 37.500 20.86 9.77 36.69 2.85
31 32 5.064325 ACGAAAACTAAACTTTGCGAAGAGT 59.936 36.000 20.86 10.42 36.69 3.24
32 33 5.963586 CGAAAACTAAACTTTGCGAAGAGTT 59.036 36.000 20.86 15.53 37.69 3.01
33 34 6.076092 CGAAAACTAAACTTTGCGAAGAGTTG 60.076 38.462 20.86 10.22 36.31 3.16
34 35 6.431198 AAACTAAACTTTGCGAAGAGTTGA 57.569 33.333 20.86 0.00 36.31 3.18
35 36 5.659048 ACTAAACTTTGCGAAGAGTTGAG 57.341 39.130 20.86 9.29 39.34 3.02
36 37 3.971032 AAACTTTGCGAAGAGTTGAGG 57.029 42.857 20.86 0.00 36.31 3.86
37 38 1.884235 ACTTTGCGAAGAGTTGAGGG 58.116 50.000 20.86 0.00 36.69 4.30
38 39 1.416401 ACTTTGCGAAGAGTTGAGGGA 59.584 47.619 20.86 0.00 36.69 4.20
39 40 1.801178 CTTTGCGAAGAGTTGAGGGAC 59.199 52.381 8.08 0.00 34.71 4.46
40 41 0.319555 TTGCGAAGAGTTGAGGGACG 60.320 55.000 0.00 0.00 0.00 4.79
41 42 1.176619 TGCGAAGAGTTGAGGGACGA 61.177 55.000 0.00 0.00 0.00 4.20
42 43 0.038526 GCGAAGAGTTGAGGGACGAA 60.039 55.000 0.00 0.00 0.00 3.85
43 44 1.604693 GCGAAGAGTTGAGGGACGAAA 60.605 52.381 0.00 0.00 0.00 3.46
44 45 2.750948 CGAAGAGTTGAGGGACGAAAA 58.249 47.619 0.00 0.00 0.00 2.29
45 46 2.731976 CGAAGAGTTGAGGGACGAAAAG 59.268 50.000 0.00 0.00 0.00 2.27
46 47 3.729966 GAAGAGTTGAGGGACGAAAAGT 58.270 45.455 0.00 0.00 0.00 2.66
47 48 4.558095 CGAAGAGTTGAGGGACGAAAAGTA 60.558 45.833 0.00 0.00 0.00 2.24
48 49 5.480205 GAAGAGTTGAGGGACGAAAAGTAT 58.520 41.667 0.00 0.00 0.00 2.12
49 50 6.600882 AAGAGTTGAGGGACGAAAAGTATA 57.399 37.500 0.00 0.00 0.00 1.47
50 51 5.963594 AGAGTTGAGGGACGAAAAGTATAC 58.036 41.667 0.00 0.00 0.00 1.47
51 52 5.715753 AGAGTTGAGGGACGAAAAGTATACT 59.284 40.000 0.00 0.00 0.00 2.12
52 53 6.210984 AGAGTTGAGGGACGAAAAGTATACTT 59.789 38.462 12.50 12.50 37.91 2.24
90 92 2.076863 CAAGTCTTTGGATGGGTCGTC 58.923 52.381 0.00 0.00 0.00 4.20
99 101 3.605634 TGGATGGGTCGTCTGTAAATTG 58.394 45.455 0.00 0.00 0.00 2.32
106 108 6.231951 TGGGTCGTCTGTAAATTGTCAAATA 58.768 36.000 0.00 0.00 0.00 1.40
109 111 6.248631 GTCGTCTGTAAATTGTCAAATAGGC 58.751 40.000 0.00 0.00 0.00 3.93
115 117 8.296713 TCTGTAAATTGTCAAATAGGCTTGTTC 58.703 33.333 0.00 0.00 0.00 3.18
148 150 3.560636 ATTCGAGTAGACCCCAATTGG 57.439 47.619 18.21 18.21 0.00 3.16
149 151 1.946984 TCGAGTAGACCCCAATTGGT 58.053 50.000 22.91 5.44 42.79 3.67
151 153 2.640826 TCGAGTAGACCCCAATTGGTTT 59.359 45.455 22.91 9.23 39.24 3.27
152 154 3.839490 TCGAGTAGACCCCAATTGGTTTA 59.161 43.478 22.91 7.00 39.24 2.01
153 155 4.472108 TCGAGTAGACCCCAATTGGTTTAT 59.528 41.667 22.91 9.09 39.24 1.40
154 156 5.662208 TCGAGTAGACCCCAATTGGTTTATA 59.338 40.000 22.91 8.12 39.24 0.98
157 159 7.201938 CGAGTAGACCCCAATTGGTTTATAGTA 60.202 40.741 22.91 2.86 39.24 1.82
158 160 8.030913 AGTAGACCCCAATTGGTTTATAGTAG 57.969 38.462 22.91 4.30 39.24 2.57
159 161 7.847848 AGTAGACCCCAATTGGTTTATAGTAGA 59.152 37.037 22.91 0.49 39.24 2.59
160 162 7.519347 AGACCCCAATTGGTTTATAGTAGAA 57.481 36.000 22.91 0.00 39.24 2.10
161 163 7.344134 AGACCCCAATTGGTTTATAGTAGAAC 58.656 38.462 22.91 2.76 39.24 3.01
162 164 6.429151 ACCCCAATTGGTTTATAGTAGAACC 58.571 40.000 22.91 10.04 44.40 3.62
163 165 5.831525 CCCCAATTGGTTTATAGTAGAACCC 59.168 44.000 22.91 0.74 43.69 4.11
164 166 6.428295 CCCAATTGGTTTATAGTAGAACCCA 58.572 40.000 22.91 3.22 43.69 4.51
166 168 6.546034 CCAATTGGTTTATAGTAGAACCCAGG 59.454 42.308 16.90 1.13 43.69 4.45
173 181 1.894699 AGTAGAACCCAGGGGAATCC 58.105 55.000 11.37 0.00 38.96 3.01
179 187 2.189521 CCAGGGGAATCCGAACCG 59.810 66.667 0.00 0.00 41.52 4.44
219 228 2.432510 CCAGGTGTCTCCCTTGTATCTC 59.567 54.545 0.00 0.00 36.75 2.75
240 249 6.936279 TCTCGAGGTTGATTATTTCTTCAGT 58.064 36.000 13.56 0.00 0.00 3.41
268 285 5.032170 AGAAAATAGAAAATGCCATGGGGT 58.968 37.500 15.13 0.00 36.17 4.95
601 631 6.722301 CACTATGCTGTATTCAGATTTGTGG 58.278 40.000 3.14 0.00 43.76 4.17
602 632 6.317140 CACTATGCTGTATTCAGATTTGTGGT 59.683 38.462 3.14 0.00 43.76 4.16
603 633 5.571784 ATGCTGTATTCAGATTTGTGGTG 57.428 39.130 3.14 0.00 43.76 4.17
665 707 5.066246 GCTTCTTAGTACTCCACTATGTCGT 59.934 44.000 0.00 0.00 39.51 4.34
745 787 3.567164 CACAGCTGTTTCCTCAATTCTGT 59.433 43.478 18.94 0.00 34.29 3.41
808 851 2.673368 CTGCTGGTTAGACGTGGAATTC 59.327 50.000 0.00 0.00 0.00 2.17
820 863 3.054166 CGTGGAATTCGTGTGTACTTCA 58.946 45.455 0.00 0.00 0.00 3.02
859 972 6.732896 ACTGTTTATCTAATCAGATCCCGT 57.267 37.500 12.66 0.00 40.81 5.28
1059 1177 2.034879 CAAGCGTGGGTTCAGCGAT 61.035 57.895 0.00 0.00 35.78 4.58
1078 1196 2.928036 TGAGGATGAGGAGGAAGTGA 57.072 50.000 0.00 0.00 0.00 3.41
1116 1234 3.571748 GGACTTAAAGGAGGCCACC 57.428 57.895 11.96 11.96 44.80 4.61
1170 1288 2.851263 AGGTTATCGTGCACAGGAAA 57.149 45.000 18.64 2.17 0.00 3.13
1187 1305 2.738213 AAAGCGTCTGCCCTGACAGG 62.738 60.000 15.15 15.15 44.31 4.00
1428 2843 5.575157 TGTGTATGGTGGTTTGGATGTTAT 58.425 37.500 0.00 0.00 0.00 1.89
1593 3008 3.256631 GGAGAATGTTTGCATCAACAGGT 59.743 43.478 9.64 0.97 33.50 4.00
1594 3009 4.262164 GGAGAATGTTTGCATCAACAGGTT 60.262 41.667 9.64 0.85 33.50 3.50
1595 3010 5.280654 AGAATGTTTGCATCAACAGGTTT 57.719 34.783 9.64 0.20 33.50 3.27
1596 3011 5.673514 AGAATGTTTGCATCAACAGGTTTT 58.326 33.333 9.64 0.00 33.50 2.43
1698 3113 2.054799 TGAAACTGGCTGAAGGGTACT 58.945 47.619 0.00 0.00 0.00 2.73
1699 3114 2.224523 TGAAACTGGCTGAAGGGTACTG 60.225 50.000 0.00 0.00 0.00 2.74
1833 3253 1.741145 GTTTGTCTTTGTCGTGGTGGT 59.259 47.619 0.00 0.00 0.00 4.16
1837 3257 1.821759 CTTTGTCGTGGTGGTGGCA 60.822 57.895 0.00 0.00 0.00 4.92
1879 3304 4.222886 GAGATGATCGTATGTTCGTCTGG 58.777 47.826 18.40 0.00 39.28 3.86
1884 3309 2.156917 TCGTATGTTCGTCTGGTGTCT 58.843 47.619 0.00 0.00 0.00 3.41
1886 3311 3.943381 TCGTATGTTCGTCTGGTGTCTAT 59.057 43.478 0.00 0.00 0.00 1.98
1901 3326 4.641989 GGTGTCTATGAAAATCCTGCATGT 59.358 41.667 0.00 0.00 0.00 3.21
1919 3344 1.952133 TTCGGTCGTTTGTCTGCCG 60.952 57.895 0.00 0.00 43.32 5.69
1935 3360 0.654683 GCCGCTCTTGTGATGTCATC 59.345 55.000 5.83 5.83 0.00 2.92
1936 3361 2.008543 GCCGCTCTTGTGATGTCATCA 61.009 52.381 11.62 11.62 36.84 3.07
1960 3385 7.173735 TCACCTTATTCTTTTAACCTTTCGTCC 59.826 37.037 0.00 0.00 0.00 4.79
1971 3397 2.867975 ACCTTTCGTCCGTGTTAACAAG 59.132 45.455 10.51 12.39 0.00 3.16
2013 3440 0.666374 CTTTTTCCGCGGAAACAGGT 59.334 50.000 44.14 0.00 42.88 4.00
2088 3518 5.912528 TCTTTTAATCTCTTGAACGAACGC 58.087 37.500 0.00 0.00 0.00 4.84
2153 3591 4.904724 CGTTCGCCGCTAGATATATGATAC 59.095 45.833 0.00 0.00 0.00 2.24
2193 3633 0.035458 ACAACAGCTCCTAGTGCCAC 59.965 55.000 0.00 0.00 0.00 5.01
2194 3634 0.674895 CAACAGCTCCTAGTGCCACC 60.675 60.000 0.00 0.00 0.00 4.61
2202 3642 1.009060 TCCTAGTGCCACCATTCCCTA 59.991 52.381 0.00 0.00 0.00 3.53
2203 3643 2.057922 CCTAGTGCCACCATTCCCTAT 58.942 52.381 0.00 0.00 0.00 2.57
2204 3644 3.116512 TCCTAGTGCCACCATTCCCTATA 60.117 47.826 0.00 0.00 0.00 1.31
2211 3651 4.836736 TGCCACCATTCCCTATAGTAGTAC 59.163 45.833 0.00 0.00 0.00 2.73
2233 3673 4.917415 ACTAAAACGCAAGCATGATTTCAC 59.083 37.500 0.00 0.00 45.62 3.18
2234 3674 3.367992 AAACGCAAGCATGATTTCACA 57.632 38.095 0.00 0.00 45.62 3.58
2235 3675 2.624316 ACGCAAGCATGATTTCACAG 57.376 45.000 0.00 0.00 45.62 3.66
2236 3676 1.881973 ACGCAAGCATGATTTCACAGT 59.118 42.857 0.00 0.00 45.62 3.55
2237 3677 2.294233 ACGCAAGCATGATTTCACAGTT 59.706 40.909 0.00 0.00 45.62 3.16
2238 3678 2.912967 CGCAAGCATGATTTCACAGTTC 59.087 45.455 0.00 0.00 0.00 3.01
2239 3679 3.609879 CGCAAGCATGATTTCACAGTTCA 60.610 43.478 0.00 0.00 0.00 3.18
2240 3680 3.671928 GCAAGCATGATTTCACAGTTCAC 59.328 43.478 0.00 0.00 0.00 3.18
2241 3681 4.793678 GCAAGCATGATTTCACAGTTCACA 60.794 41.667 0.00 0.00 0.00 3.58
2242 3682 5.466819 CAAGCATGATTTCACAGTTCACAT 58.533 37.500 0.00 0.00 0.00 3.21
2243 3683 5.717078 AGCATGATTTCACAGTTCACATT 57.283 34.783 0.00 0.00 0.00 2.71
2244 3684 6.822667 AGCATGATTTCACAGTTCACATTA 57.177 33.333 0.00 0.00 0.00 1.90
2245 3685 6.849502 AGCATGATTTCACAGTTCACATTAG 58.150 36.000 0.00 0.00 0.00 1.73
2246 3686 6.432162 AGCATGATTTCACAGTTCACATTAGT 59.568 34.615 0.00 0.00 0.00 2.24
2248 3688 7.587629 CATGATTTCACAGTTCACATTAGTGT 58.412 34.615 0.00 0.00 46.01 3.55
2249 3689 7.189693 TGATTTCACAGTTCACATTAGTGTC 57.810 36.000 0.00 0.00 46.01 3.67
2250 3690 6.992123 TGATTTCACAGTTCACATTAGTGTCT 59.008 34.615 0.00 0.00 46.01 3.41
2251 3691 8.147704 TGATTTCACAGTTCACATTAGTGTCTA 58.852 33.333 0.00 0.00 46.01 2.59
2252 3692 7.946655 TTTCACAGTTCACATTAGTGTCTAG 57.053 36.000 0.00 0.00 46.01 2.43
2253 3693 5.470368 TCACAGTTCACATTAGTGTCTAGC 58.530 41.667 0.00 0.00 46.01 3.42
2254 3694 5.010617 TCACAGTTCACATTAGTGTCTAGCA 59.989 40.000 0.00 0.00 46.01 3.49
2255 3695 5.696270 CACAGTTCACATTAGTGTCTAGCAA 59.304 40.000 0.00 0.00 46.01 3.91
2256 3696 5.696724 ACAGTTCACATTAGTGTCTAGCAAC 59.303 40.000 0.00 0.00 46.01 4.17
2257 3697 4.923871 AGTTCACATTAGTGTCTAGCAACG 59.076 41.667 0.00 0.00 46.01 4.10
2258 3698 4.514781 TCACATTAGTGTCTAGCAACGT 57.485 40.909 0.00 0.00 46.01 3.99
2259 3699 4.482386 TCACATTAGTGTCTAGCAACGTC 58.518 43.478 0.00 0.00 46.01 4.34
2260 3700 4.022676 TCACATTAGTGTCTAGCAACGTCA 60.023 41.667 0.00 0.00 46.01 4.35
2261 3701 4.090066 CACATTAGTGTCTAGCAACGTCAC 59.910 45.833 0.00 0.00 40.92 3.67
2262 3702 3.293311 TTAGTGTCTAGCAACGTCACC 57.707 47.619 0.00 0.00 0.00 4.02
2263 3703 0.039437 AGTGTCTAGCAACGTCACCG 60.039 55.000 0.00 0.00 40.83 4.94
2264 3704 1.372499 TGTCTAGCAACGTCACCGC 60.372 57.895 0.00 0.00 37.70 5.68
2265 3705 1.372499 GTCTAGCAACGTCACCGCA 60.372 57.895 0.00 0.00 37.70 5.69
2266 3706 1.080772 TCTAGCAACGTCACCGCAG 60.081 57.895 0.00 0.00 37.70 5.18
2267 3707 2.730672 CTAGCAACGTCACCGCAGC 61.731 63.158 0.00 0.00 37.70 5.25
2268 3708 3.507597 TAGCAACGTCACCGCAGCA 62.508 57.895 0.00 0.00 38.97 4.41
2269 3709 4.374702 GCAACGTCACCGCAGCAG 62.375 66.667 0.00 0.00 37.20 4.24
2270 3710 4.374702 CAACGTCACCGCAGCAGC 62.375 66.667 0.00 0.00 37.70 5.25
2271 3711 4.908687 AACGTCACCGCAGCAGCA 62.909 61.111 0.82 0.00 42.27 4.41
2274 3714 3.720193 GTCACCGCAGCAGCACAG 61.720 66.667 0.82 0.00 42.27 3.66
2277 3717 4.007644 ACCGCAGCAGCACAGCTA 62.008 61.111 0.82 0.00 44.54 3.32
2278 3718 3.494336 CCGCAGCAGCACAGCTAC 61.494 66.667 0.82 0.00 44.54 3.58
2279 3719 2.433838 CGCAGCAGCACAGCTACT 60.434 61.111 0.82 0.00 44.54 2.57
2284 3724 2.486472 AGCAGCACAGCTACTGAATT 57.514 45.000 13.23 0.00 44.50 2.17
2285 3725 2.787994 AGCAGCACAGCTACTGAATTT 58.212 42.857 13.23 0.00 44.50 1.82
2286 3726 3.942829 AGCAGCACAGCTACTGAATTTA 58.057 40.909 13.23 0.00 44.50 1.40
2287 3727 3.686726 AGCAGCACAGCTACTGAATTTAC 59.313 43.478 13.23 0.00 44.50 2.01
2288 3728 3.686726 GCAGCACAGCTACTGAATTTACT 59.313 43.478 13.23 0.00 36.40 2.24
2289 3729 4.201763 GCAGCACAGCTACTGAATTTACTC 60.202 45.833 13.23 0.00 36.40 2.59
2290 3730 4.331168 CAGCACAGCTACTGAATTTACTCC 59.669 45.833 0.78 0.00 36.40 3.85
2291 3731 3.623510 GCACAGCTACTGAATTTACTCCC 59.376 47.826 0.78 0.00 35.18 4.30
2292 3732 4.624125 GCACAGCTACTGAATTTACTCCCT 60.624 45.833 0.78 0.00 35.18 4.20
2293 3733 5.491982 CACAGCTACTGAATTTACTCCCTT 58.508 41.667 0.78 0.00 35.18 3.95
2294 3734 5.940470 CACAGCTACTGAATTTACTCCCTTT 59.060 40.000 0.78 0.00 35.18 3.11
2295 3735 6.092807 CACAGCTACTGAATTTACTCCCTTTC 59.907 42.308 0.78 0.00 35.18 2.62
2296 3736 6.173339 CAGCTACTGAATTTACTCCCTTTCA 58.827 40.000 0.00 0.00 32.44 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.449451 GCAAAGTTTAGTTTTCGTCCCTCAA 60.449 40.000 0.00 0.00 0.00 3.02
1 2 4.035909 GCAAAGTTTAGTTTTCGTCCCTCA 59.964 41.667 0.00 0.00 0.00 3.86
2 3 4.534168 GCAAAGTTTAGTTTTCGTCCCTC 58.466 43.478 0.00 0.00 0.00 4.30
3 4 3.002965 CGCAAAGTTTAGTTTTCGTCCCT 59.997 43.478 0.00 0.00 0.00 4.20
4 5 3.002553 TCGCAAAGTTTAGTTTTCGTCCC 59.997 43.478 2.91 0.00 0.00 4.46
5 6 4.199840 TCGCAAAGTTTAGTTTTCGTCC 57.800 40.909 2.91 0.00 0.00 4.79
6 7 5.495502 TCTTCGCAAAGTTTAGTTTTCGTC 58.504 37.500 2.91 0.00 33.95 4.20
7 8 5.064325 ACTCTTCGCAAAGTTTAGTTTTCGT 59.936 36.000 2.91 0.00 33.95 3.85
8 9 5.499047 ACTCTTCGCAAAGTTTAGTTTTCG 58.501 37.500 0.00 0.00 33.95 3.46
9 10 6.964934 TCAACTCTTCGCAAAGTTTAGTTTTC 59.035 34.615 0.00 0.00 33.53 2.29
10 11 6.848451 TCAACTCTTCGCAAAGTTTAGTTTT 58.152 32.000 0.00 0.00 33.53 2.43
11 12 6.431198 TCAACTCTTCGCAAAGTTTAGTTT 57.569 33.333 0.00 0.00 33.53 2.66
12 13 5.007724 CCTCAACTCTTCGCAAAGTTTAGTT 59.992 40.000 0.00 0.00 33.53 2.24
13 14 4.511826 CCTCAACTCTTCGCAAAGTTTAGT 59.488 41.667 0.00 0.00 33.53 2.24
14 15 4.083802 CCCTCAACTCTTCGCAAAGTTTAG 60.084 45.833 0.00 0.00 33.53 1.85
15 16 3.813166 CCCTCAACTCTTCGCAAAGTTTA 59.187 43.478 0.00 0.00 33.53 2.01
16 17 2.618709 CCCTCAACTCTTCGCAAAGTTT 59.381 45.455 0.00 0.00 33.53 2.66
17 18 2.158813 TCCCTCAACTCTTCGCAAAGTT 60.159 45.455 0.00 0.00 36.16 2.66
18 19 1.416401 TCCCTCAACTCTTCGCAAAGT 59.584 47.619 0.00 0.00 33.95 2.66
19 20 1.801178 GTCCCTCAACTCTTCGCAAAG 59.199 52.381 0.00 0.00 0.00 2.77
20 21 1.872237 CGTCCCTCAACTCTTCGCAAA 60.872 52.381 0.00 0.00 0.00 3.68
21 22 0.319555 CGTCCCTCAACTCTTCGCAA 60.320 55.000 0.00 0.00 0.00 4.85
22 23 1.176619 TCGTCCCTCAACTCTTCGCA 61.177 55.000 0.00 0.00 0.00 5.10
23 24 0.038526 TTCGTCCCTCAACTCTTCGC 60.039 55.000 0.00 0.00 0.00 4.70
24 25 2.433868 TTTCGTCCCTCAACTCTTCG 57.566 50.000 0.00 0.00 0.00 3.79
25 26 3.729966 ACTTTTCGTCCCTCAACTCTTC 58.270 45.455 0.00 0.00 0.00 2.87
26 27 3.840124 ACTTTTCGTCCCTCAACTCTT 57.160 42.857 0.00 0.00 0.00 2.85
27 28 5.715753 AGTATACTTTTCGTCCCTCAACTCT 59.284 40.000 0.00 0.00 0.00 3.24
28 29 5.963594 AGTATACTTTTCGTCCCTCAACTC 58.036 41.667 0.00 0.00 0.00 3.01
29 30 5.997384 AGTATACTTTTCGTCCCTCAACT 57.003 39.130 0.00 0.00 0.00 3.16
58 59 9.838339 CCATCCAAAGACTTGTAATACTAGAAT 57.162 33.333 8.74 0.00 0.00 2.40
59 60 8.265055 CCCATCCAAAGACTTGTAATACTAGAA 58.735 37.037 8.74 0.00 0.00 2.10
60 61 7.402071 ACCCATCCAAAGACTTGTAATACTAGA 59.598 37.037 8.74 0.00 0.00 2.43
61 62 7.565680 ACCCATCCAAAGACTTGTAATACTAG 58.434 38.462 0.49 0.49 0.00 2.57
62 63 7.504926 ACCCATCCAAAGACTTGTAATACTA 57.495 36.000 0.00 0.00 0.00 1.82
63 64 6.388619 ACCCATCCAAAGACTTGTAATACT 57.611 37.500 0.00 0.00 0.00 2.12
64 65 5.293569 CGACCCATCCAAAGACTTGTAATAC 59.706 44.000 0.00 0.00 0.00 1.89
90 92 8.081633 TGAACAAGCCTATTTGACAATTTACAG 58.918 33.333 0.00 0.00 0.00 2.74
99 101 5.095490 CGGAATTGAACAAGCCTATTTGAC 58.905 41.667 0.00 0.00 0.00 3.18
106 108 0.598065 GCACGGAATTGAACAAGCCT 59.402 50.000 0.00 0.00 0.00 4.58
109 111 4.788100 CGAATTAGCACGGAATTGAACAAG 59.212 41.667 0.00 0.00 0.00 3.16
115 117 5.041287 TCTACTCGAATTAGCACGGAATTG 58.959 41.667 0.00 0.00 0.00 2.32
148 150 5.963214 TTCCCCTGGGTTCTACTATAAAC 57.037 43.478 12.71 0.00 36.47 2.01
149 151 5.609708 GGATTCCCCTGGGTTCTACTATAAA 59.390 44.000 12.71 0.00 36.47 1.40
151 153 4.755106 CGGATTCCCCTGGGTTCTACTATA 60.755 50.000 12.71 0.00 36.47 1.31
152 154 3.599348 GGATTCCCCTGGGTTCTACTAT 58.401 50.000 12.71 0.00 36.47 2.12
153 155 2.691850 CGGATTCCCCTGGGTTCTACTA 60.692 54.545 12.71 0.00 36.47 1.82
154 156 1.894699 GGATTCCCCTGGGTTCTACT 58.105 55.000 12.71 0.00 36.47 2.57
157 159 0.549169 TTCGGATTCCCCTGGGTTCT 60.549 55.000 12.71 0.00 36.47 3.01
158 160 0.393944 GTTCGGATTCCCCTGGGTTC 60.394 60.000 12.71 5.54 36.47 3.62
159 161 1.689412 GTTCGGATTCCCCTGGGTT 59.311 57.895 12.71 0.00 36.47 4.11
160 162 2.306384 GGTTCGGATTCCCCTGGGT 61.306 63.158 12.71 0.00 36.47 4.51
161 163 2.595655 GGTTCGGATTCCCCTGGG 59.404 66.667 5.50 5.50 0.00 4.45
162 164 2.189521 CGGTTCGGATTCCCCTGG 59.810 66.667 0.00 0.00 0.00 4.45
173 181 1.669779 TGTAAACCAAACACCGGTTCG 59.330 47.619 2.97 0.00 46.12 3.95
219 228 8.879342 ATCTACTGAAGAAATAATCAACCTCG 57.121 34.615 0.00 0.00 37.89 4.63
240 249 9.300681 CCCATGGCATTTTCTATTTTCTATCTA 57.699 33.333 6.09 0.00 0.00 1.98
268 285 6.375174 CACCATATCTCAAAGTCACCAATCAA 59.625 38.462 0.00 0.00 0.00 2.57
581 611 5.012239 ACACCACAAATCTGAATACAGCAT 58.988 37.500 0.00 0.00 43.17 3.79
665 707 5.178096 ACATTGTCCATGTGGATAACTGA 57.822 39.130 12.58 0.00 45.89 3.41
719 761 0.111061 TGAGGAAACAGCTGTGGCAT 59.889 50.000 22.49 13.24 41.70 4.40
808 851 5.856126 AACACCAATATGAAGTACACACG 57.144 39.130 0.00 0.00 0.00 4.49
857 970 4.174009 AGCTACAACAACTATGTGCTACG 58.826 43.478 0.00 0.00 40.46 3.51
859 972 6.931838 ACTAAGCTACAACAACTATGTGCTA 58.068 36.000 0.00 0.00 40.46 3.49
908 1024 5.177511 TGATGCTTCAGAGACAAACGTAAAG 59.822 40.000 0.00 0.00 0.00 1.85
1059 1177 2.225369 TGTCACTTCCTCCTCATCCTCA 60.225 50.000 0.00 0.00 0.00 3.86
1078 1196 1.130054 ACTGGGCCTGACATCTGTGT 61.130 55.000 18.12 0.00 42.49 3.72
1116 1234 1.511850 TTGTGATCTTGTCTGCGTGG 58.488 50.000 0.00 0.00 0.00 4.94
1158 1276 1.956170 AGACGCTTTCCTGTGCACG 60.956 57.895 13.13 7.03 0.00 5.34
1170 1288 3.699894 CCTGTCAGGGCAGACGCT 61.700 66.667 11.46 0.00 41.41 5.07
1354 2769 7.234355 ACCCCATCCTTTATTCATGTTAGATC 58.766 38.462 0.00 0.00 0.00 2.75
1363 2778 5.492524 AGAGAGAAACCCCATCCTTTATTCA 59.507 40.000 0.00 0.00 0.00 2.57
1428 2843 5.588648 AGACATCGAAAGTTTTGAAACCAGA 59.411 36.000 9.62 0.00 39.71 3.86
1479 2894 7.628234 AGAGATCAGACATCATGTAAACCTTT 58.372 34.615 0.00 0.00 0.00 3.11
1619 3034 5.285401 TGATCACCATTAGGAAGGGAACTA 58.715 41.667 0.00 0.00 37.98 2.24
1698 3113 3.053917 GCTTCTCCCCTTACCATTTACCA 60.054 47.826 0.00 0.00 0.00 3.25
1699 3114 3.202373 AGCTTCTCCCCTTACCATTTACC 59.798 47.826 0.00 0.00 0.00 2.85
1833 3253 4.639755 ACATGAACACGAAATCATATGCCA 59.360 37.500 0.00 0.00 34.61 4.92
1837 3257 7.712205 TCATCTCACATGAACACGAAATCATAT 59.288 33.333 0.00 0.00 34.61 1.78
1879 3304 5.824904 ACATGCAGGATTTTCATAGACAC 57.175 39.130 4.84 0.00 0.00 3.67
1884 3309 4.269183 ACCGAACATGCAGGATTTTCATA 58.731 39.130 4.84 0.00 0.00 2.15
1886 3311 2.487762 GACCGAACATGCAGGATTTTCA 59.512 45.455 4.84 0.00 0.00 2.69
1901 3326 1.952133 CGGCAGACAAACGACCGAA 60.952 57.895 0.00 0.00 41.80 4.30
1935 3360 7.303261 GGACGAAAGGTTAAAAGAATAAGGTG 58.697 38.462 0.00 0.00 0.00 4.00
1936 3361 6.148315 CGGACGAAAGGTTAAAAGAATAAGGT 59.852 38.462 0.00 0.00 0.00 3.50
1941 3366 4.818005 ACACGGACGAAAGGTTAAAAGAAT 59.182 37.500 0.00 0.00 0.00 2.40
1960 3385 3.579147 TGAACGAAGCTTGTTAACACG 57.421 42.857 8.07 10.72 0.00 4.49
1971 3397 7.066374 AGAACATTTCTAAGATGAACGAAGC 57.934 36.000 0.00 0.00 38.49 3.86
2013 3440 5.068460 TGATCAATGATCATGCATCTTGCAA 59.932 36.000 20.85 0.00 45.72 4.08
2088 3518 0.039256 CCACAAACGGCCTGTTCATG 60.039 55.000 12.33 12.55 40.84 3.07
2137 3575 4.377153 CGCTTGCGTATCATATATCTAGCG 59.623 45.833 6.86 9.82 41.13 4.26
2138 3576 4.147306 GCGCTTGCGTATCATATATCTAGC 59.853 45.833 16.38 0.00 0.00 3.42
2139 3577 5.273944 TGCGCTTGCGTATCATATATCTAG 58.726 41.667 16.38 0.00 43.34 2.43
2140 3578 5.243426 TGCGCTTGCGTATCATATATCTA 57.757 39.130 16.38 0.00 43.34 1.98
2141 3579 4.110036 TGCGCTTGCGTATCATATATCT 57.890 40.909 16.38 0.00 43.34 1.98
2142 3580 4.562789 TCTTGCGCTTGCGTATCATATATC 59.437 41.667 16.38 0.00 43.34 1.63
2143 3581 4.494484 TCTTGCGCTTGCGTATCATATAT 58.506 39.130 16.38 0.00 43.34 0.86
2144 3582 3.908213 TCTTGCGCTTGCGTATCATATA 58.092 40.909 16.38 0.00 43.34 0.86
2153 3591 1.083806 TATGGTCTCTTGCGCTTGCG 61.084 55.000 9.73 10.90 43.34 4.85
2193 3633 7.811713 GCGTTTTAGTACTACTATAGGGAATGG 59.188 40.741 0.91 0.00 29.64 3.16
2194 3634 8.355169 TGCGTTTTAGTACTACTATAGGGAATG 58.645 37.037 0.91 0.00 29.64 2.67
2202 3642 7.262772 TCATGCTTGCGTTTTAGTACTACTAT 58.737 34.615 0.91 0.00 29.64 2.12
2203 3643 6.623486 TCATGCTTGCGTTTTAGTACTACTA 58.377 36.000 0.91 0.00 0.00 1.82
2204 3644 5.475719 TCATGCTTGCGTTTTAGTACTACT 58.524 37.500 0.91 0.00 0.00 2.57
2211 3651 4.916831 TGTGAAATCATGCTTGCGTTTTAG 59.083 37.500 0.00 0.00 0.00 1.85
2233 3673 5.164051 CGTTGCTAGACACTAATGTGAACTG 60.164 44.000 3.03 0.67 46.55 3.16
2234 3674 4.923871 CGTTGCTAGACACTAATGTGAACT 59.076 41.667 3.03 4.96 46.55 3.01
2235 3675 4.684703 ACGTTGCTAGACACTAATGTGAAC 59.315 41.667 3.03 0.00 46.55 3.18
2236 3676 4.878439 ACGTTGCTAGACACTAATGTGAA 58.122 39.130 3.03 0.00 46.55 3.18
2237 3677 4.022676 TGACGTTGCTAGACACTAATGTGA 60.023 41.667 3.03 0.00 46.55 3.58
2239 3679 4.235360 GTGACGTTGCTAGACACTAATGT 58.765 43.478 0.00 0.00 43.71 2.71
2240 3680 3.612860 GGTGACGTTGCTAGACACTAATG 59.387 47.826 0.00 0.00 35.32 1.90
2241 3681 3.846360 GGTGACGTTGCTAGACACTAAT 58.154 45.455 0.00 0.00 35.32 1.73
2242 3682 3.293311 GGTGACGTTGCTAGACACTAA 57.707 47.619 0.00 0.00 35.32 2.24
2244 3684 3.888093 GGTGACGTTGCTAGACACT 57.112 52.632 0.00 0.00 35.32 3.55
2257 3697 3.720193 CTGTGCTGCTGCGGTGAC 61.720 66.667 10.62 7.94 43.34 3.67
2260 3700 4.007644 TAGCTGTGCTGCTGCGGT 62.008 61.111 10.62 5.12 45.21 5.68
2261 3701 3.494336 GTAGCTGTGCTGCTGCGG 61.494 66.667 11.21 3.55 45.21 5.69
2266 3706 3.686726 AGTAAATTCAGTAGCTGTGCTGC 59.313 43.478 0.00 0.66 40.10 5.25
2267 3707 4.331168 GGAGTAAATTCAGTAGCTGTGCTG 59.669 45.833 0.00 2.23 40.10 4.41
2268 3708 4.508662 GGAGTAAATTCAGTAGCTGTGCT 58.491 43.478 0.00 0.00 43.41 4.40
2269 3709 3.623510 GGGAGTAAATTCAGTAGCTGTGC 59.376 47.826 0.00 0.00 32.61 4.57
2270 3710 5.091261 AGGGAGTAAATTCAGTAGCTGTG 57.909 43.478 0.00 0.00 32.61 3.66
2271 3711 5.763876 AAGGGAGTAAATTCAGTAGCTGT 57.236 39.130 0.00 0.00 32.61 4.40
2272 3712 6.173339 TGAAAGGGAGTAAATTCAGTAGCTG 58.827 40.000 0.00 0.00 0.00 4.24
2273 3713 6.374417 TGAAAGGGAGTAAATTCAGTAGCT 57.626 37.500 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.