Multiple sequence alignment - TraesCS5D01G304200

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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 TraesCS5D01G304200 chr5D 100.000 2794 0 0 1 2794 399326700 399329493 0.000000e+00 5160.0
1 TraesCS5D01G304200 chr5D 97.917 48 1 0 1202 1249 399327852 399327899 1.780000e-12 84.2
2 TraesCS5D01G304200 chr5D 97.917 48 1 0 1153 1200 399327901 399327948 1.780000e-12 84.2
3 TraesCS5D01G304200 chr5B 93.898 1606 58 21 1202 2794 479715178 479716756 0.000000e+00 2386.0
4 TraesCS5D01G304200 chr5B 94.540 348 15 4 856 1199 479714877 479715224 4.100000e-148 534.0
5 TraesCS5D01G304200 chr5A 91.116 923 61 10 1202 2114 504955392 504956303 0.000000e+00 1230.0
6 TraesCS5D01G304200 chr5A 97.092 619 15 3 129 745 671959502 671960119 0.000000e+00 1040.0
7 TraesCS5D01G304200 chr5A 89.969 638 52 5 2161 2789 504956283 504956917 0.000000e+00 813.0
8 TraesCS5D01G304200 chr5A 88.403 457 38 8 747 1200 504954995 504955439 1.140000e-148 536.0
9 TraesCS5D01G304200 chr3D 97.756 624 12 2 126 748 69661815 69661193 0.000000e+00 1074.0
10 TraesCS5D01G304200 chr3D 79.807 931 126 25 1209 2114 51686788 51685895 3.060000e-174 621.0
11 TraesCS5D01G304200 chr3D 84.861 251 32 4 953 1200 51686995 51686748 5.980000e-62 248.0
12 TraesCS5D01G304200 chr1A 97.444 626 12 4 126 748 493005064 493004440 0.000000e+00 1064.0
13 TraesCS5D01G304200 chr1A 97.092 619 15 3 129 745 551939910 551940527 0.000000e+00 1040.0
14 TraesCS5D01G304200 chr1A 94.231 52 3 0 2115 2166 123551410 123551359 2.310000e-11 80.5
15 TraesCS5D01G304200 chr7B 97.419 620 13 3 130 748 84528646 84528029 0.000000e+00 1053.0
16 TraesCS5D01G304200 chr6B 97.254 619 15 2 128 745 49400198 49400815 0.000000e+00 1048.0
17 TraesCS5D01G304200 chr6B 96.945 622 17 2 128 748 695058037 695057417 0.000000e+00 1042.0
18 TraesCS5D01G304200 chr6B 95.918 49 2 0 2115 2163 415119632 415119584 2.310000e-11 80.5
19 TraesCS5D01G304200 chr4A 97.097 620 15 3 128 745 652267024 652267642 0.000000e+00 1042.0
20 TraesCS5D01G304200 chr4A 96.226 53 2 0 2115 2167 705816597 705816649 1.380000e-13 87.9
21 TraesCS5D01G304200 chr6A 96.940 621 17 2 129 748 532871506 532870887 0.000000e+00 1040.0
22 TraesCS5D01G304200 chr3B 80.543 920 126 25 1209 2114 82629889 82629009 0.000000e+00 658.0
23 TraesCS5D01G304200 chr3B 85.259 251 31 4 953 1200 82630096 82629849 1.280000e-63 254.0
24 TraesCS5D01G304200 chr3A 80.153 917 136 19 1209 2114 64285359 64284478 0.000000e+00 643.0
25 TraesCS5D01G304200 chr3A 82.996 247 37 4 957 1200 64285563 64285319 4.690000e-53 219.0
26 TraesCS5D01G304200 chr7A 94.444 54 3 0 2115 2168 316454762 316454709 1.780000e-12 84.2
27 TraesCS5D01G304200 chr2D 95.918 49 2 0 2115 2163 350750632 350750680 2.310000e-11 80.5
28 TraesCS5D01G304200 chr1D 95.918 49 2 0 2115 2163 345263345 345263393 2.310000e-11 80.5
29 TraesCS5D01G304200 chr1B 94.231 52 3 0 2115 2166 465702376 465702325 2.310000e-11 80.5
30 TraesCS5D01G304200 chrUn 95.833 48 2 0 2115 2162 85312940 85312987 8.300000e-11 78.7


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 TraesCS5D01G304200 chr5D 399326700 399329493 2793 False 1776.133333 5160 98.611333 1 2794 3 chr5D.!!$F1 2793
1 TraesCS5D01G304200 chr5B 479714877 479716756 1879 False 1460.000000 2386 94.219000 856 2794 2 chr5B.!!$F1 1938
2 TraesCS5D01G304200 chr5A 671959502 671960119 617 False 1040.000000 1040 97.092000 129 745 1 chr5A.!!$F1 616
3 TraesCS5D01G304200 chr5A 504954995 504956917 1922 False 859.666667 1230 89.829333 747 2789 3 chr5A.!!$F2 2042
4 TraesCS5D01G304200 chr3D 69661193 69661815 622 True 1074.000000 1074 97.756000 126 748 1 chr3D.!!$R1 622
5 TraesCS5D01G304200 chr3D 51685895 51686995 1100 True 434.500000 621 82.334000 953 2114 2 chr3D.!!$R2 1161
6 TraesCS5D01G304200 chr1A 493004440 493005064 624 True 1064.000000 1064 97.444000 126 748 1 chr1A.!!$R2 622
7 TraesCS5D01G304200 chr1A 551939910 551940527 617 False 1040.000000 1040 97.092000 129 745 1 chr1A.!!$F1 616
8 TraesCS5D01G304200 chr7B 84528029 84528646 617 True 1053.000000 1053 97.419000 130 748 1 chr7B.!!$R1 618
9 TraesCS5D01G304200 chr6B 49400198 49400815 617 False 1048.000000 1048 97.254000 128 745 1 chr6B.!!$F1 617
10 TraesCS5D01G304200 chr6B 695057417 695058037 620 True 1042.000000 1042 96.945000 128 748 1 chr6B.!!$R2 620
11 TraesCS5D01G304200 chr4A 652267024 652267642 618 False 1042.000000 1042 97.097000 128 745 1 chr4A.!!$F1 617
12 TraesCS5D01G304200 chr6A 532870887 532871506 619 True 1040.000000 1040 96.940000 129 748 1 chr6A.!!$R1 619
13 TraesCS5D01G304200 chr3B 82629009 82630096 1087 True 456.000000 658 82.901000 953 2114 2 chr3B.!!$R1 1161
14 TraesCS5D01G304200 chr3A 64284478 64285563 1085 True 431.000000 643 81.574500 957 2114 2 chr3A.!!$R1 1157

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
837 839 0.179076 CAGTGAGGCAGTGACACACA 60.179 55.0 25.73 7.77 36.99 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2566 2642 0.108585 GAGGCCACAACAGAGAACCA 59.891 55.0 5.01 0.0 0.0 3.67 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
52 53 9.234384 CAATCTTGACATCTATTCAATTTCTGC 57.766 33.333 0.00 0.00 32.57 4.26
53 54 8.749026 ATCTTGACATCTATTCAATTTCTGCT 57.251 30.769 0.00 0.00 32.57 4.24
54 55 9.842775 ATCTTGACATCTATTCAATTTCTGCTA 57.157 29.630 0.00 0.00 32.57 3.49
55 56 9.322773 TCTTGACATCTATTCAATTTCTGCTAG 57.677 33.333 0.00 0.00 32.57 3.42
56 57 9.322773 CTTGACATCTATTCAATTTCTGCTAGA 57.677 33.333 0.00 0.00 32.57 2.43
57 58 9.842775 TTGACATCTATTCAATTTCTGCTAGAT 57.157 29.630 0.00 0.00 33.45 1.98
82 83 6.832549 GCTAAAGCGTGTAGTTTGTTTATG 57.167 37.500 0.00 0.00 0.00 1.90
83 84 6.368213 GCTAAAGCGTGTAGTTTGTTTATGT 58.632 36.000 0.00 0.00 0.00 2.29
84 85 7.512297 GCTAAAGCGTGTAGTTTGTTTATGTA 58.488 34.615 0.00 0.00 0.00 2.29
85 86 8.173130 GCTAAAGCGTGTAGTTTGTTTATGTAT 58.827 33.333 0.00 0.00 0.00 2.29
90 91 8.823818 AGCGTGTAGTTTGTTTATGTATAATCC 58.176 33.333 0.00 0.00 0.00 3.01
91 92 8.605746 GCGTGTAGTTTGTTTATGTATAATCCA 58.394 33.333 0.00 0.00 0.00 3.41
109 110 8.922931 ATAATCCAATGTAATCATGTACTGCA 57.077 30.769 0.00 0.00 34.19 4.41
110 111 7.643569 AATCCAATGTAATCATGTACTGCAA 57.356 32.000 0.00 0.00 34.19 4.08
111 112 7.643569 ATCCAATGTAATCATGTACTGCAAA 57.356 32.000 0.00 0.00 34.19 3.68
112 113 7.643569 TCCAATGTAATCATGTACTGCAAAT 57.356 32.000 0.00 0.00 34.19 2.32
113 114 7.482474 TCCAATGTAATCATGTACTGCAAATG 58.518 34.615 0.00 0.00 34.19 2.32
114 115 7.122501 TCCAATGTAATCATGTACTGCAAATGT 59.877 33.333 0.00 0.00 34.19 2.71
115 116 7.221259 CCAATGTAATCATGTACTGCAAATGTG 59.779 37.037 0.00 0.00 34.19 3.21
116 117 6.816134 TGTAATCATGTACTGCAAATGTGT 57.184 33.333 0.00 0.00 0.00 3.72
117 118 7.213216 TGTAATCATGTACTGCAAATGTGTT 57.787 32.000 0.00 0.00 0.00 3.32
118 119 8.329203 TGTAATCATGTACTGCAAATGTGTTA 57.671 30.769 0.00 0.00 0.00 2.41
119 120 8.955388 TGTAATCATGTACTGCAAATGTGTTAT 58.045 29.630 0.00 0.00 0.00 1.89
509 511 1.014564 CGAGTCGAAGCAAAGGTCCC 61.015 60.000 6.73 0.00 0.00 4.46
745 747 5.627499 TGATATGCGCTTTGAGTTTCTTT 57.373 34.783 9.73 0.00 0.00 2.52
749 751 2.163412 TGCGCTTTGAGTTTCTTTGTGT 59.837 40.909 9.73 0.00 0.00 3.72
786 788 9.740710 ATTAATTAGCTCAGAACTTAACCAACT 57.259 29.630 0.00 0.00 0.00 3.16
822 824 7.602644 AGAAACTGTATTGTACATGTACCAGTG 59.397 37.037 29.99 19.65 36.06 3.66
824 826 6.631016 ACTGTATTGTACATGTACCAGTGAG 58.369 40.000 29.32 22.30 38.15 3.51
825 827 5.972935 TGTATTGTACATGTACCAGTGAGG 58.027 41.667 28.67 0.00 37.28 3.86
828 830 2.233676 TGTACATGTACCAGTGAGGCAG 59.766 50.000 28.67 0.00 43.14 4.85
829 831 1.352083 ACATGTACCAGTGAGGCAGT 58.648 50.000 0.00 0.00 43.14 4.40
830 832 1.002430 ACATGTACCAGTGAGGCAGTG 59.998 52.381 0.00 0.00 43.14 3.66
831 833 1.276138 CATGTACCAGTGAGGCAGTGA 59.724 52.381 3.92 0.00 43.14 3.41
832 834 0.679505 TGTACCAGTGAGGCAGTGAC 59.320 55.000 3.92 0.00 43.14 3.67
833 835 0.679505 GTACCAGTGAGGCAGTGACA 59.320 55.000 0.00 0.00 43.14 3.58
834 836 0.679505 TACCAGTGAGGCAGTGACAC 59.320 55.000 0.00 0.00 43.14 3.67
835 837 1.337384 ACCAGTGAGGCAGTGACACA 61.337 55.000 8.59 0.00 43.14 3.72
836 838 0.882042 CCAGTGAGGCAGTGACACAC 60.882 60.000 17.90 17.90 36.99 3.82
837 839 0.179076 CAGTGAGGCAGTGACACACA 60.179 55.000 25.73 7.77 36.99 3.72
838 840 0.761187 AGTGAGGCAGTGACACACAT 59.239 50.000 25.73 10.29 36.74 3.21
839 841 1.151668 GTGAGGCAGTGACACACATC 58.848 55.000 20.26 7.30 36.74 3.06
840 842 0.319813 TGAGGCAGTGACACACATCG 60.320 55.000 8.59 0.00 36.74 3.84
841 843 0.319900 GAGGCAGTGACACACATCGT 60.320 55.000 8.59 0.00 36.74 3.73
852 854 1.716050 CACACATCGTGTCTCAGTTCG 59.284 52.381 0.00 0.00 43.92 3.95
905 909 1.965643 TGCTACAGTTTACCTGACGGT 59.034 47.619 0.00 0.00 44.49 4.83
994 998 2.171940 CAGACAAGCGCTGCGTTC 59.828 61.111 24.04 14.22 0.00 3.95
1173 1182 7.039082 AGGCTCCTTTTAATTAAGATGTTTGCA 60.039 33.333 0.00 0.00 0.00 4.08
1191 1200 4.870123 TGCATCTGGCTTTTGTTGTTAT 57.130 36.364 0.00 0.00 45.15 1.89
1192 1201 5.973899 TGCATCTGGCTTTTGTTGTTATA 57.026 34.783 0.00 0.00 45.15 0.98
1193 1202 5.953183 TGCATCTGGCTTTTGTTGTTATAG 58.047 37.500 0.00 0.00 45.15 1.31
1194 1203 4.800471 GCATCTGGCTTTTGTTGTTATAGC 59.200 41.667 0.00 0.00 40.25 2.97
1195 1204 5.393461 GCATCTGGCTTTTGTTGTTATAGCT 60.393 40.000 0.00 0.00 40.25 3.32
1196 1205 6.624423 CATCTGGCTTTTGTTGTTATAGCTT 58.376 36.000 0.00 0.00 32.58 3.74
1197 1206 6.254281 TCTGGCTTTTGTTGTTATAGCTTC 57.746 37.500 0.00 0.00 32.58 3.86
1198 1207 5.183140 TCTGGCTTTTGTTGTTATAGCTTCC 59.817 40.000 0.00 0.00 32.58 3.46
1199 1208 4.219725 TGGCTTTTGTTGTTATAGCTTCCC 59.780 41.667 0.00 0.00 32.58 3.97
1200 1209 4.412207 GCTTTTGTTGTTATAGCTTCCCG 58.588 43.478 0.00 0.00 0.00 5.14
1201 1210 4.412207 CTTTTGTTGTTATAGCTTCCCGC 58.588 43.478 0.00 0.00 39.57 6.13
1202 1211 2.032680 TGTTGTTATAGCTTCCCGCC 57.967 50.000 0.00 0.00 40.39 6.13
1203 1212 1.557832 TGTTGTTATAGCTTCCCGCCT 59.442 47.619 0.00 0.00 40.39 5.52
1204 1213 2.026636 TGTTGTTATAGCTTCCCGCCTT 60.027 45.455 0.00 0.00 40.39 4.35
1205 1214 3.014623 GTTGTTATAGCTTCCCGCCTTT 58.985 45.455 0.00 0.00 40.39 3.11
1206 1215 3.359695 TGTTATAGCTTCCCGCCTTTT 57.640 42.857 0.00 0.00 40.39 2.27
1207 1216 4.490899 TGTTATAGCTTCCCGCCTTTTA 57.509 40.909 0.00 0.00 40.39 1.52
1208 1217 4.846040 TGTTATAGCTTCCCGCCTTTTAA 58.154 39.130 0.00 0.00 40.39 1.52
1209 1218 5.442391 TGTTATAGCTTCCCGCCTTTTAAT 58.558 37.500 0.00 0.00 40.39 1.40
1210 1219 5.889289 TGTTATAGCTTCCCGCCTTTTAATT 59.111 36.000 0.00 0.00 40.39 1.40
1211 1220 7.055378 TGTTATAGCTTCCCGCCTTTTAATTA 58.945 34.615 0.00 0.00 40.39 1.40
1212 1221 7.556996 TGTTATAGCTTCCCGCCTTTTAATTAA 59.443 33.333 0.00 0.00 40.39 1.40
1213 1222 4.983671 AGCTTCCCGCCTTTTAATTAAG 57.016 40.909 0.00 0.00 40.39 1.85
1214 1223 4.595986 AGCTTCCCGCCTTTTAATTAAGA 58.404 39.130 0.00 0.00 40.39 2.10
1215 1224 5.201243 AGCTTCCCGCCTTTTAATTAAGAT 58.799 37.500 0.00 0.00 40.39 2.40
1216 1225 5.067805 AGCTTCCCGCCTTTTAATTAAGATG 59.932 40.000 0.00 0.00 40.39 2.90
1217 1226 5.067283 GCTTCCCGCCTTTTAATTAAGATGA 59.933 40.000 0.00 0.00 0.00 2.92
1218 1227 6.239036 GCTTCCCGCCTTTTAATTAAGATGAT 60.239 38.462 0.00 0.00 0.00 2.45
1219 1228 7.654022 TTCCCGCCTTTTAATTAAGATGATT 57.346 32.000 0.00 0.00 0.00 2.57
1220 1229 7.038154 TCCCGCCTTTTAATTAAGATGATTG 57.962 36.000 0.00 0.00 0.00 2.67
1221 1230 5.691754 CCCGCCTTTTAATTAAGATGATTGC 59.308 40.000 0.00 0.00 0.00 3.56
1222 1231 6.272318 CCGCCTTTTAATTAAGATGATTGCA 58.728 36.000 0.00 0.00 0.00 4.08
1223 1232 6.925165 CCGCCTTTTAATTAAGATGATTGCAT 59.075 34.615 0.00 0.00 37.47 3.96
1234 1243 4.119442 GATGATTGCATCTGGCTTTTGT 57.881 40.909 0.00 0.00 45.93 2.83
1235 1244 4.501071 GATGATTGCATCTGGCTTTTGTT 58.499 39.130 0.00 0.00 45.93 2.83
1236 1245 3.655486 TGATTGCATCTGGCTTTTGTTG 58.345 40.909 0.00 0.00 45.15 3.33
1237 1246 3.069872 TGATTGCATCTGGCTTTTGTTGT 59.930 39.130 0.00 0.00 45.15 3.32
1238 1247 3.540314 TTGCATCTGGCTTTTGTTGTT 57.460 38.095 0.00 0.00 45.15 2.83
1239 1248 4.662468 TTGCATCTGGCTTTTGTTGTTA 57.338 36.364 0.00 0.00 45.15 2.41
1384 1410 2.872858 GTCCTAGCAGCCTAATTTTCCG 59.127 50.000 0.00 0.00 0.00 4.30
2051 2094 7.959651 GTGTTCAAGACATGTCTGCTATTTTAG 59.040 37.037 28.52 10.25 41.10 1.85
2107 2150 2.309528 TTCTGCGCGGTATCATCTTT 57.690 45.000 17.37 0.00 0.00 2.52
2112 2155 1.934589 CGCGGTATCATCTTTGGTGA 58.065 50.000 0.00 0.00 0.00 4.02
2153 2196 5.364157 TGTTTGGGGCTAAATACTTTGTTGT 59.636 36.000 0.00 0.00 0.00 3.32
2154 2197 6.127026 TGTTTGGGGCTAAATACTTTGTTGTT 60.127 34.615 0.00 0.00 0.00 2.83
2155 2198 5.461032 TGGGGCTAAATACTTTGTTGTTG 57.539 39.130 0.00 0.00 0.00 3.33
2314 2358 2.143925 GACAAAGTTCTGAACCCCTCG 58.856 52.381 16.48 4.56 0.00 4.63
2338 2382 8.946085 TCGTGATTAGCAAAAGATCATTAAACT 58.054 29.630 0.00 0.00 32.92 2.66
2347 2391 9.516314 GCAAAAGATCATTAAACTACCAATACC 57.484 33.333 0.00 0.00 0.00 2.73
2352 2396 9.920946 AGATCATTAAACTACCAATACCATTGT 57.079 29.630 0.00 0.00 0.00 2.71
2355 2399 8.247562 TCATTAAACTACCAATACCATTGTTGC 58.752 33.333 0.00 0.00 0.00 4.17
2356 2400 7.768807 TTAAACTACCAATACCATTGTTGCT 57.231 32.000 0.00 0.00 0.00 3.91
2357 2401 5.897377 AACTACCAATACCATTGTTGCTC 57.103 39.130 0.00 0.00 0.00 4.26
2358 2402 4.270008 ACTACCAATACCATTGTTGCTCC 58.730 43.478 0.00 0.00 0.00 4.70
2359 2403 3.168035 ACCAATACCATTGTTGCTCCA 57.832 42.857 0.00 0.00 0.00 3.86
2360 2404 3.711863 ACCAATACCATTGTTGCTCCAT 58.288 40.909 0.00 0.00 0.00 3.41
2361 2405 3.448301 ACCAATACCATTGTTGCTCCATG 59.552 43.478 0.00 0.00 0.00 3.66
2362 2406 3.448301 CCAATACCATTGTTGCTCCATGT 59.552 43.478 0.00 0.00 0.00 3.21
2363 2407 4.081531 CCAATACCATTGTTGCTCCATGTT 60.082 41.667 0.00 0.00 0.00 2.71
2364 2408 5.481105 CAATACCATTGTTGCTCCATGTTT 58.519 37.500 0.00 0.00 0.00 2.83
2365 2409 6.350864 CCAATACCATTGTTGCTCCATGTTTA 60.351 38.462 0.00 0.00 0.00 2.01
2477 2550 1.300931 GTTGGCAGCAGACAGTCGA 60.301 57.895 0.00 0.00 31.60 4.20
2519 2592 1.227734 CCGACGGGGACTTGTTTGT 60.228 57.895 5.81 0.00 38.47 2.83
2547 2620 0.877649 CATCATCTTCTCCGGCACCG 60.878 60.000 1.02 1.02 39.44 4.94
2577 2653 2.430367 GCCCCGTGGTTCTCTGTT 59.570 61.111 0.00 0.00 0.00 3.16
2579 2655 1.450211 CCCCGTGGTTCTCTGTTGT 59.550 57.895 0.00 0.00 0.00 3.32
2580 2656 0.884704 CCCCGTGGTTCTCTGTTGTG 60.885 60.000 0.00 0.00 0.00 3.33
2589 2665 0.471780 TCTCTGTTGTGGCCTCCTCA 60.472 55.000 3.32 1.50 0.00 3.86
2699 2779 0.532573 ACACTGTCAGGGTAGATGCG 59.467 55.000 5.76 0.00 23.74 4.73
2724 2804 7.542477 CGGGTAGTAGCTATCATGAATGTTTAG 59.458 40.741 0.00 0.00 0.00 1.85
2729 2809 4.665009 AGCTATCATGAATGTTTAGGGGGA 59.335 41.667 0.00 0.00 0.00 4.81
2744 2829 1.686587 GGGGGAAACACAAACTGAAGG 59.313 52.381 0.00 0.00 32.66 3.46
2746 2831 2.623416 GGGGAAACACAAACTGAAGGAG 59.377 50.000 0.00 0.00 0.00 3.69
2789 2874 1.236616 TGAGACCAATTGCAGTGCCG 61.237 55.000 13.72 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.234384 GCAGAAATTGAATAGATGTCAAGATTG 57.766 33.333 0.00 0.00 38.34 2.67
27 28 9.186837 AGCAGAAATTGAATAGATGTCAAGATT 57.813 29.630 0.00 0.00 38.34 2.40
28 29 8.749026 AGCAGAAATTGAATAGATGTCAAGAT 57.251 30.769 0.00 0.00 38.34 2.40
29 30 9.322773 CTAGCAGAAATTGAATAGATGTCAAGA 57.677 33.333 0.00 0.00 38.34 3.02
30 31 9.322773 TCTAGCAGAAATTGAATAGATGTCAAG 57.677 33.333 0.00 0.00 38.34 3.02
31 32 9.842775 ATCTAGCAGAAATTGAATAGATGTCAA 57.157 29.630 0.00 0.00 36.64 3.18
52 53 6.973474 ACAAACTACACGCTTTAGCTATCTAG 59.027 38.462 0.00 0.00 39.32 2.43
53 54 6.860080 ACAAACTACACGCTTTAGCTATCTA 58.140 36.000 0.00 0.00 39.32 1.98
54 55 5.721232 ACAAACTACACGCTTTAGCTATCT 58.279 37.500 0.00 0.00 39.32 1.98
55 56 6.404712 AACAAACTACACGCTTTAGCTATC 57.595 37.500 0.00 0.00 39.32 2.08
56 57 6.796705 AAACAAACTACACGCTTTAGCTAT 57.203 33.333 0.00 0.00 39.32 2.97
57 58 7.385752 ACATAAACAAACTACACGCTTTAGCTA 59.614 33.333 0.00 0.00 39.32 3.32
58 59 6.204108 ACATAAACAAACTACACGCTTTAGCT 59.796 34.615 0.00 0.00 39.32 3.32
59 60 6.368213 ACATAAACAAACTACACGCTTTAGC 58.632 36.000 0.00 0.00 37.78 3.09
64 65 8.823818 GGATTATACATAAACAAACTACACGCT 58.176 33.333 0.00 0.00 0.00 5.07
65 66 8.605746 TGGATTATACATAAACAAACTACACGC 58.394 33.333 0.00 0.00 0.00 5.34
84 85 8.922931 TGCAGTACATGATTACATTGGATTAT 57.077 30.769 0.00 0.00 34.15 1.28
85 86 8.744568 TTGCAGTACATGATTACATTGGATTA 57.255 30.769 0.00 0.00 34.15 1.75
86 87 7.643569 TTGCAGTACATGATTACATTGGATT 57.356 32.000 0.00 0.00 34.15 3.01
87 88 7.643569 TTTGCAGTACATGATTACATTGGAT 57.356 32.000 0.00 0.00 34.15 3.41
88 89 7.122501 ACATTTGCAGTACATGATTACATTGGA 59.877 33.333 0.00 0.00 34.15 3.53
89 90 7.221259 CACATTTGCAGTACATGATTACATTGG 59.779 37.037 0.00 0.00 34.15 3.16
90 91 7.756272 ACACATTTGCAGTACATGATTACATTG 59.244 33.333 0.00 0.00 34.15 2.82
91 92 7.829725 ACACATTTGCAGTACATGATTACATT 58.170 30.769 0.00 0.00 34.15 2.71
92 93 7.395190 ACACATTTGCAGTACATGATTACAT 57.605 32.000 0.00 0.00 37.19 2.29
93 94 6.816134 ACACATTTGCAGTACATGATTACA 57.184 33.333 0.00 0.00 0.00 2.41
158 159 9.897349 GTAAACGATGCTACTTTACTTATGAAC 57.103 33.333 0.00 0.00 30.75 3.18
304 306 5.720371 TGTCATTAGGTTTTTCCCATGTG 57.280 39.130 0.00 0.00 36.75 3.21
509 511 2.724349 GCGGCTGCTAATGAAAAGATG 58.276 47.619 11.21 0.00 38.39 2.90
816 818 1.337384 TGTGTCACTGCCTCACTGGT 61.337 55.000 4.27 0.00 38.35 4.00
822 824 0.319900 ACGATGTGTGTCACTGCCTC 60.320 55.000 4.27 0.00 35.11 4.70
824 826 1.862123 CACGATGTGTGTCACTGCC 59.138 57.895 4.27 0.00 43.88 4.85
834 836 1.340658 CCGAACTGAGACACGATGTG 58.659 55.000 0.00 0.00 39.75 3.21
835 837 0.388649 GCCGAACTGAGACACGATGT 60.389 55.000 0.00 0.00 0.00 3.06
836 838 1.078759 GGCCGAACTGAGACACGATG 61.079 60.000 0.00 0.00 0.00 3.84
837 839 1.215647 GGCCGAACTGAGACACGAT 59.784 57.895 0.00 0.00 0.00 3.73
838 840 2.142357 CTGGCCGAACTGAGACACGA 62.142 60.000 0.00 0.00 0.00 4.35
839 841 1.734477 CTGGCCGAACTGAGACACG 60.734 63.158 0.00 0.00 0.00 4.49
840 842 0.601558 TACTGGCCGAACTGAGACAC 59.398 55.000 0.00 0.00 0.00 3.67
841 843 0.888619 CTACTGGCCGAACTGAGACA 59.111 55.000 0.00 0.00 0.00 3.41
873 875 6.263168 GGTAAACTGTAGCAGCATCCATTATT 59.737 38.462 0.00 0.00 34.37 1.40
905 909 2.828661 TTCCTAGAGCAGGCAGTAGA 57.171 50.000 0.00 0.00 45.10 2.59
991 995 6.291377 TGAATATGTGCTTCATCTAGGGAAC 58.709 40.000 0.00 0.00 37.91 3.62
994 998 6.528321 TCTTGAATATGTGCTTCATCTAGGG 58.472 40.000 0.00 0.00 37.91 3.53
1121 1129 8.085296 TCTCTTCTTCAAGACATTAGAAGTGAC 58.915 37.037 0.00 0.00 42.54 3.67
1173 1182 6.127619 GGAAGCTATAACAACAAAAGCCAGAT 60.128 38.462 0.00 0.00 33.63 2.90
1194 1203 6.693315 TCATCTTAATTAAAAGGCGGGAAG 57.307 37.500 0.00 0.00 0.00 3.46
1195 1204 7.488322 CAATCATCTTAATTAAAAGGCGGGAA 58.512 34.615 0.00 0.00 0.00 3.97
1196 1205 6.460953 GCAATCATCTTAATTAAAAGGCGGGA 60.461 38.462 0.00 0.00 0.00 5.14
1197 1206 5.691754 GCAATCATCTTAATTAAAAGGCGGG 59.308 40.000 0.00 0.00 0.00 6.13
1198 1207 6.272318 TGCAATCATCTTAATTAAAAGGCGG 58.728 36.000 0.00 0.00 0.00 6.13
1199 1208 7.935338 ATGCAATCATCTTAATTAAAAGGCG 57.065 32.000 0.00 0.00 0.00 5.52
1216 1225 3.656559 ACAACAAAAGCCAGATGCAATC 58.343 40.909 0.00 0.00 46.04 2.67
1217 1226 3.756933 ACAACAAAAGCCAGATGCAAT 57.243 38.095 0.00 0.00 44.83 3.56
1218 1227 3.540314 AACAACAAAAGCCAGATGCAA 57.460 38.095 0.00 0.00 44.83 4.08
1219 1228 4.870123 ATAACAACAAAAGCCAGATGCA 57.130 36.364 0.00 0.00 44.83 3.96
1220 1229 4.800471 GCTATAACAACAAAAGCCAGATGC 59.200 41.667 0.00 0.00 41.71 3.91
1221 1230 6.199937 AGCTATAACAACAAAAGCCAGATG 57.800 37.500 0.00 0.00 33.63 2.90
1222 1231 6.127619 GGAAGCTATAACAACAAAAGCCAGAT 60.128 38.462 0.00 0.00 33.63 2.90
1223 1232 5.183140 GGAAGCTATAACAACAAAAGCCAGA 59.817 40.000 0.00 0.00 33.63 3.86
1224 1233 5.402398 GGAAGCTATAACAACAAAAGCCAG 58.598 41.667 0.00 0.00 33.63 4.85
1225 1234 4.219725 GGGAAGCTATAACAACAAAAGCCA 59.780 41.667 0.00 0.00 33.63 4.75
1226 1235 4.219725 TGGGAAGCTATAACAACAAAAGCC 59.780 41.667 0.00 0.00 33.63 4.35
1227 1236 5.385509 TGGGAAGCTATAACAACAAAAGC 57.614 39.130 0.00 0.00 0.00 3.51
1228 1237 7.396540 AGATGGGAAGCTATAACAACAAAAG 57.603 36.000 0.00 0.00 0.00 2.27
1229 1238 8.107095 AGTAGATGGGAAGCTATAACAACAAAA 58.893 33.333 0.00 0.00 0.00 2.44
1230 1239 7.630082 AGTAGATGGGAAGCTATAACAACAAA 58.370 34.615 0.00 0.00 0.00 2.83
1231 1240 7.195374 AGTAGATGGGAAGCTATAACAACAA 57.805 36.000 0.00 0.00 0.00 2.83
1232 1241 6.808321 AGTAGATGGGAAGCTATAACAACA 57.192 37.500 0.00 0.00 0.00 3.33
1233 1242 6.483640 CCAAGTAGATGGGAAGCTATAACAAC 59.516 42.308 0.00 0.00 36.79 3.32
1234 1243 6.157994 ACCAAGTAGATGGGAAGCTATAACAA 59.842 38.462 0.00 0.00 45.18 2.83
1235 1244 5.665812 ACCAAGTAGATGGGAAGCTATAACA 59.334 40.000 0.00 0.00 45.18 2.41
1236 1245 6.176014 ACCAAGTAGATGGGAAGCTATAAC 57.824 41.667 0.00 0.00 45.18 1.89
1237 1246 7.015292 CACTACCAAGTAGATGGGAAGCTATAA 59.985 40.741 8.70 0.00 45.18 0.98
1238 1247 6.493802 CACTACCAAGTAGATGGGAAGCTATA 59.506 42.308 8.70 0.00 45.18 1.31
1239 1248 5.305644 CACTACCAAGTAGATGGGAAGCTAT 59.694 44.000 8.70 0.00 45.18 2.97
1384 1410 6.073440 TGGAAATAAGACTGCGTAGACAAAAC 60.073 38.462 7.78 0.00 0.00 2.43
1630 1656 2.298729 TCAGGTGGCTTGGTTTATTTGC 59.701 45.455 0.00 0.00 0.00 3.68
1677 1705 4.280677 TGGGAAGAAACCAAACATGTGATC 59.719 41.667 0.00 0.00 34.44 2.92
1810 1839 6.072286 AGCTTCAAACTGGTCATGAAACATAG 60.072 38.462 0.00 0.00 33.08 2.23
2051 2094 3.507233 TCCAGTGATGAAAACCAGATTGC 59.493 43.478 0.00 0.00 0.00 3.56
2107 2150 1.562475 GTTGGGGTAGGCTAATCACCA 59.438 52.381 2.12 2.12 33.78 4.17
2112 2155 4.086457 CAAACAAGTTGGGGTAGGCTAAT 58.914 43.478 7.96 0.00 33.18 1.73
2153 2196 6.348132 CGCCAAAGATGATACTACAACAACAA 60.348 38.462 0.00 0.00 0.00 2.83
2154 2197 5.121611 CGCCAAAGATGATACTACAACAACA 59.878 40.000 0.00 0.00 0.00 3.33
2155 2198 5.350365 TCGCCAAAGATGATACTACAACAAC 59.650 40.000 0.00 0.00 0.00 3.32
2338 2382 4.308526 TGGAGCAACAATGGTATTGGTA 57.691 40.909 6.51 0.00 36.70 3.25
2339 2383 3.168035 TGGAGCAACAATGGTATTGGT 57.832 42.857 6.51 0.00 39.16 3.67
2340 2384 3.448301 ACATGGAGCAACAATGGTATTGG 59.552 43.478 0.00 0.00 37.41 3.16
2341 2385 4.724074 ACATGGAGCAACAATGGTATTG 57.276 40.909 0.00 0.28 37.41 1.90
2343 2387 5.714333 TGTAAACATGGAGCAACAATGGTAT 59.286 36.000 0.00 0.00 37.41 2.73
2344 2388 5.073428 TGTAAACATGGAGCAACAATGGTA 58.927 37.500 0.00 0.00 37.41 3.25
2345 2389 3.894427 TGTAAACATGGAGCAACAATGGT 59.106 39.130 0.00 0.00 40.72 3.55
2346 2390 4.517952 TGTAAACATGGAGCAACAATGG 57.482 40.909 0.00 0.00 0.00 3.16
2347 2391 6.257411 TGTTTTGTAAACATGGAGCAACAATG 59.743 34.615 0.00 0.00 0.00 2.82
2348 2392 6.344500 TGTTTTGTAAACATGGAGCAACAAT 58.656 32.000 0.00 0.00 0.00 2.71
2349 2393 5.724328 TGTTTTGTAAACATGGAGCAACAA 58.276 33.333 0.00 0.00 0.00 2.83
2350 2394 5.330455 TGTTTTGTAAACATGGAGCAACA 57.670 34.783 0.00 0.00 0.00 3.33
2351 2395 6.843069 ATTGTTTTGTAAACATGGAGCAAC 57.157 33.333 5.88 0.00 0.00 4.17
2352 2396 6.820656 ACAATTGTTTTGTAAACATGGAGCAA 59.179 30.769 4.92 0.00 0.00 3.91
2353 2397 6.344500 ACAATTGTTTTGTAAACATGGAGCA 58.656 32.000 4.92 0.00 0.00 4.26
2354 2398 6.843069 ACAATTGTTTTGTAAACATGGAGC 57.157 33.333 4.92 0.00 0.00 4.70
2355 2399 9.743057 TTCTACAATTGTTTTGTAAACATGGAG 57.257 29.630 17.78 10.03 34.84 3.86
2363 2407 9.743057 CTGGTTCATTCTACAATTGTTTTGTAA 57.257 29.630 17.78 4.98 34.84 2.41
2364 2408 8.908903 ACTGGTTCATTCTACAATTGTTTTGTA 58.091 29.630 17.78 0.00 34.11 2.41
2365 2409 7.781056 ACTGGTTCATTCTACAATTGTTTTGT 58.219 30.769 17.78 0.00 36.49 2.83
2519 2592 1.757118 GAGAAGATGATGGACCGGACA 59.243 52.381 9.46 7.37 0.00 4.02
2563 2636 1.507141 GCCACAACAGAGAACCACGG 61.507 60.000 0.00 0.00 0.00 4.94
2564 2640 1.507141 GGCCACAACAGAGAACCACG 61.507 60.000 0.00 0.00 0.00 4.94
2566 2642 0.108585 GAGGCCACAACAGAGAACCA 59.891 55.000 5.01 0.00 0.00 3.67
2577 2653 1.956636 GCAATTGATGAGGAGGCCACA 60.957 52.381 10.34 0.00 0.00 4.17
2579 2655 0.749091 CGCAATTGATGAGGAGGCCA 60.749 55.000 10.34 0.00 0.00 5.36
2580 2656 2.028130 CGCAATTGATGAGGAGGCC 58.972 57.895 10.34 0.00 0.00 5.19
2589 2665 0.322816 AGGTCACAGGCGCAATTGAT 60.323 50.000 10.83 0.00 0.00 2.57
2699 2779 7.819900 CCTAAACATTCATGATAGCTACTACCC 59.180 40.741 0.00 0.00 0.00 3.69
2724 2804 1.686587 CCTTCAGTTTGTGTTTCCCCC 59.313 52.381 0.00 0.00 0.00 5.40
2729 2809 4.589908 ACTGTCTCCTTCAGTTTGTGTTT 58.410 39.130 0.00 0.00 42.50 2.83
2735 2820 5.615925 ACAAGTACTGTCTCCTTCAGTTT 57.384 39.130 0.00 0.00 42.50 2.66
2744 2829 8.439993 TCATCTACTCATACAAGTACTGTCTC 57.560 38.462 0.00 0.00 39.64 3.36
2746 2831 8.841300 TCATCATCTACTCATACAAGTACTGTC 58.159 37.037 0.00 0.00 39.64 3.51


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

AutoCloner maintained by Alex Coulton.