Multiple sequence alignment - TraesCS6B01G135500

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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 TraesCS6B01G135500 chr6B 100.000 3035 0 0 1 3035 132677953 132680987 0.000000e+00 5605.0
1 TraesCS6B01G135500 chr6B 88.734 1935 174 14 290 2188 132904682 132906608 0.000000e+00 2326.0
2 TraesCS6B01G135500 chr6B 95.283 212 10 0 1 212 132904473 132904684 1.350000e-88 337.0
3 TraesCS6B01G135500 chr6B 90.233 215 19 2 2821 3035 469769764 469769976 2.300000e-71 279.0
4 TraesCS6B01G135500 chr6B 90.610 213 15 1 2821 3028 262047607 262047819 8.290000e-71 278.0
5 TraesCS6B01G135500 chr6B 89.189 222 17 4 2820 3035 471171826 471171606 1.390000e-68 270.0
6 TraesCS6B01G135500 chr6B 91.228 171 13 2 2275 2445 132906633 132906801 6.540000e-57 231.0
7 TraesCS6B01G135500 chr6B 88.776 98 7 2 211 305 270366045 270366141 1.910000e-22 117.0
8 TraesCS6B01G135500 chr6A 93.724 1689 77 9 789 2477 74974892 74973233 0.000000e+00 2505.0
9 TraesCS6B01G135500 chr6A 95.137 329 12 3 2482 2810 74972937 74972613 1.610000e-142 516.0
10 TraesCS6B01G135500 chr6A 95.257 253 6 4 489 737 74975161 74974911 2.190000e-106 396.0
11 TraesCS6B01G135500 chr6A 98.710 155 1 1 1 155 74976723 74976570 1.070000e-69 274.0
12 TraesCS6B01G135500 chr6A 96.711 152 5 0 338 489 74975339 74975188 1.400000e-63 254.0
13 TraesCS6B01G135500 chr6A 92.308 91 4 1 209 296 142784312 142784222 3.180000e-25 126.0
14 TraesCS6B01G135500 chr6A 88.462 104 8 2 198 298 15768138 15768240 4.110000e-24 122.0
15 TraesCS6B01G135500 chr6A 95.161 62 3 0 151 212 74975862 74975801 6.920000e-17 99.0
16 TraesCS6B01G135500 chr6D 88.889 2025 164 25 290 2276 59424174 59426175 0.000000e+00 2436.0
17 TraesCS6B01G135500 chr6D 94.592 1054 52 2 1226 2276 59024598 59023547 0.000000e+00 1626.0
18 TraesCS6B01G135500 chr6D 91.030 903 41 19 290 1162 59066878 59065986 0.000000e+00 1182.0
19 TraesCS6B01G135500 chr6D 97.642 212 4 1 1 212 59067086 59066876 2.220000e-96 363.0
20 TraesCS6B01G135500 chr6D 94.340 212 11 1 1 212 59423966 59424176 1.050000e-84 324.0
21 TraesCS6B01G135500 chr6D 92.742 124 7 2 2275 2397 59023445 59023323 8.650000e-41 178.0
22 TraesCS6B01G135500 chr6D 87.619 105 9 2 191 292 103601835 103601938 5.320000e-23 119.0
23 TraesCS6B01G135500 chr6D 96.875 64 2 0 1158 1221 59026470 59026407 1.150000e-19 108.0
24 TraesCS6B01G135500 chr7B 91.827 208 17 0 2821 3028 128905431 128905224 1.060000e-74 291.0
25 TraesCS6B01G135500 chr5A 91.549 213 13 1 2821 3028 126953939 126953727 3.830000e-74 289.0
26 TraesCS6B01G135500 chr5A 91.080 213 14 1 2821 3028 387095266 387095054 1.780000e-72 283.0
27 TraesCS6B01G135500 chr2A 90.654 214 15 1 2820 3028 453796655 453796868 2.300000e-71 279.0
28 TraesCS6B01G135500 chr2A 80.292 137 19 7 52 181 559105721 559105586 2.490000e-16 97.1
29 TraesCS6B01G135500 chr2A 79.021 143 20 8 46 182 618970096 618970234 4.170000e-14 89.8
30 TraesCS6B01G135500 chr7A 89.767 215 21 1 2821 3035 700795326 700795113 1.070000e-69 274.0
31 TraesCS6B01G135500 chr7A 78.472 144 19 10 45 179 533325406 533325266 1.940000e-12 84.2
32 TraesCS6B01G135500 chr7A 76.923 143 27 5 45 181 518506354 518506212 3.240000e-10 76.8
33 TraesCS6B01G135500 chr3B 89.545 220 15 4 2821 3035 479293484 479293268 3.860000e-69 272.0
34 TraesCS6B01G135500 chr4A 91.304 92 5 1 211 299 95187556 95187465 4.110000e-24 122.0
35 TraesCS6B01G135500 chr2B 90.526 95 5 2 202 292 478114366 478114460 4.110000e-24 122.0
36 TraesCS6B01G135500 chr2B 77.536 138 23 7 47 176 747822508 747822645 3.240000e-10 76.8
37 TraesCS6B01G135500 chr1D 89.320 103 4 4 204 300 222023899 222023798 4.110000e-24 122.0
38 TraesCS6B01G135500 chr3D 88.235 102 6 4 201 297 362238383 362238283 1.910000e-22 117.0
39 TraesCS6B01G135500 chr4D 86.667 105 11 1 193 294 437508878 437508982 2.470000e-21 113.0
40 TraesCS6B01G135500 chr4D 85.586 111 7 5 188 293 109272500 109272606 1.150000e-19 108.0


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 TraesCS6B01G135500 chr6B 132677953 132680987 3034 False 5605.000000 5605 100.000000 1 3035 1 chr6B.!!$F1 3034
1 TraesCS6B01G135500 chr6B 132904473 132906801 2328 False 964.666667 2326 91.748333 1 2445 3 chr6B.!!$F5 2444
2 TraesCS6B01G135500 chr6A 74972613 74976723 4110 True 674.000000 2505 95.783333 1 2810 6 chr6A.!!$R2 2809
3 TraesCS6B01G135500 chr6D 59423966 59426175 2209 False 1380.000000 2436 91.614500 1 2276 2 chr6D.!!$F2 2275
4 TraesCS6B01G135500 chr6D 59065986 59067086 1100 True 772.500000 1182 94.336000 1 1162 2 chr6D.!!$R2 1161
5 TraesCS6B01G135500 chr6D 59023323 59026470 3147 True 637.333333 1626 94.736333 1158 2397 3 chr6D.!!$R1 1239

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
671 1837 0.43883 CTTGGTCTGTTTACGCGAGC 59.561 55.0 15.93 0.0 0.0 5.03 F
1419 4391 0.03563 AGATTGGGAGTGCAGCAGAC 60.036 55.0 0.00 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 4553 0.252696 ACCTCCTCAGCATGGTACCA 60.253 55.0 18.99 18.99 36.16 3.25 R
2863 6237 0.036732 TTGTGTCAGGCTTGGCTAGG 59.963 55.0 0.92 0.00 0.00 3.02 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
182 895 4.431378 TCCCCACTATGACCAGTCTAAAA 58.569 43.478 0.00 0.00 0.00 1.52
212 925 7.320443 TGTGATCTGCCAATTAAATGAGTAC 57.680 36.000 0.00 0.00 0.00 2.73
213 926 7.112122 TGTGATCTGCCAATTAAATGAGTACT 58.888 34.615 0.00 0.00 0.00 2.73
214 927 7.280876 TGTGATCTGCCAATTAAATGAGTACTC 59.719 37.037 16.32 16.32 0.00 2.59
215 928 6.767902 TGATCTGCCAATTAAATGAGTACTCC 59.232 38.462 20.11 3.06 0.00 3.85
216 929 5.437060 TCTGCCAATTAAATGAGTACTCCC 58.563 41.667 20.11 0.00 0.00 4.30
217 930 5.191722 TCTGCCAATTAAATGAGTACTCCCT 59.808 40.000 20.11 4.85 0.00 4.20
218 931 5.437060 TGCCAATTAAATGAGTACTCCCTC 58.563 41.667 20.11 0.00 0.00 4.30
219 932 4.822350 GCCAATTAAATGAGTACTCCCTCC 59.178 45.833 20.11 0.00 0.00 4.30
220 933 5.631481 GCCAATTAAATGAGTACTCCCTCCA 60.631 44.000 20.11 1.84 0.00 3.86
221 934 6.605119 CCAATTAAATGAGTACTCCCTCCAT 58.395 40.000 20.11 4.33 0.00 3.41
222 935 7.062957 CCAATTAAATGAGTACTCCCTCCATT 58.937 38.462 20.11 10.27 0.00 3.16
223 936 7.229506 CCAATTAAATGAGTACTCCCTCCATTC 59.770 40.741 20.11 0.00 0.00 2.67
224 937 4.779993 AAATGAGTACTCCCTCCATTCC 57.220 45.455 20.11 0.00 0.00 3.01
225 938 2.940514 TGAGTACTCCCTCCATTCCA 57.059 50.000 20.11 0.00 0.00 3.53
226 939 3.421394 TGAGTACTCCCTCCATTCCAT 57.579 47.619 20.11 0.00 0.00 3.41
227 940 4.552883 TGAGTACTCCCTCCATTCCATA 57.447 45.455 20.11 0.00 0.00 2.74
228 941 4.890988 TGAGTACTCCCTCCATTCCATAA 58.109 43.478 20.11 0.00 0.00 1.90
229 942 5.476983 TGAGTACTCCCTCCATTCCATAAT 58.523 41.667 20.11 0.00 0.00 1.28
230 943 5.307976 TGAGTACTCCCTCCATTCCATAATG 59.692 44.000 20.11 0.00 41.90 1.90
231 944 5.227593 AGTACTCCCTCCATTCCATAATGT 58.772 41.667 0.00 0.00 40.84 2.71
232 945 6.390504 AGTACTCCCTCCATTCCATAATGTA 58.609 40.000 0.00 0.00 40.84 2.29
233 946 6.849697 AGTACTCCCTCCATTCCATAATGTAA 59.150 38.462 0.00 0.00 40.84 2.41
234 947 6.192970 ACTCCCTCCATTCCATAATGTAAG 57.807 41.667 0.00 0.00 40.84 2.34
235 948 5.911178 ACTCCCTCCATTCCATAATGTAAGA 59.089 40.000 0.00 0.00 40.84 2.10
236 949 6.183361 ACTCCCTCCATTCCATAATGTAAGAC 60.183 42.308 0.00 0.00 40.84 3.01
237 950 4.997395 CCCTCCATTCCATAATGTAAGACG 59.003 45.833 0.00 0.00 40.84 4.18
238 951 5.454755 CCCTCCATTCCATAATGTAAGACGT 60.455 44.000 0.00 0.00 40.84 4.34
239 952 6.055588 CCTCCATTCCATAATGTAAGACGTT 58.944 40.000 0.00 0.00 40.84 3.99
240 953 6.542370 CCTCCATTCCATAATGTAAGACGTTT 59.458 38.462 0.00 0.00 40.84 3.60
241 954 7.067008 CCTCCATTCCATAATGTAAGACGTTTT 59.933 37.037 0.00 0.00 40.84 2.43
242 955 8.343168 TCCATTCCATAATGTAAGACGTTTTT 57.657 30.769 0.00 0.00 40.84 1.94
286 999 4.796038 AACGTATATTATGGGACGGAGG 57.204 45.455 0.00 0.00 39.57 4.30
287 1000 3.094572 ACGTATATTATGGGACGGAGGG 58.905 50.000 0.00 0.00 39.57 4.30
288 1001 3.094572 CGTATATTATGGGACGGAGGGT 58.905 50.000 0.00 0.00 0.00 4.34
289 1002 3.119245 CGTATATTATGGGACGGAGGGTG 60.119 52.174 0.00 0.00 0.00 4.61
290 1003 2.482414 TATTATGGGACGGAGGGTGT 57.518 50.000 0.00 0.00 0.00 4.16
291 1004 2.482414 ATTATGGGACGGAGGGTGTA 57.518 50.000 0.00 0.00 0.00 2.90
295 1008 0.472352 TGGGACGGAGGGTGTAGTTT 60.472 55.000 0.00 0.00 0.00 2.66
451 1583 8.251026 TGTTGACTCCACTAATTACTGATGTAG 58.749 37.037 0.00 0.00 0.00 2.74
478 1610 6.921914 AGTACTGTAGTTCGATTTAGTTGCT 58.078 36.000 0.00 0.00 0.00 3.91
514 1673 9.193133 ACAGTATTAAATCGGAGTTATGAATCG 57.807 33.333 0.00 0.00 0.00 3.34
543 1702 4.632153 GTGCTGAAAACTAAGAGGAGACA 58.368 43.478 0.00 0.00 0.00 3.41
544 1703 4.449405 GTGCTGAAAACTAAGAGGAGACAC 59.551 45.833 0.00 0.00 0.00 3.67
632 1798 2.535166 GTGTGCGTGTTGTTTAGACGTA 59.465 45.455 0.00 0.00 44.66 3.57
655 1821 2.216046 TCTGTTTCAGTGCTCTGCTTG 58.784 47.619 10.95 0.46 41.10 4.01
671 1837 0.438830 CTTGGTCTGTTTACGCGAGC 59.561 55.000 15.93 0.00 0.00 5.03
753 1920 8.837099 AAACAATATGGTATTCTGAATCCCAA 57.163 30.769 17.17 8.49 0.00 4.12
764 1932 3.264193 TCTGAATCCCAAGCACATACACT 59.736 43.478 0.00 0.00 0.00 3.55
1231 4203 2.742372 GTCGCATTGACCTGCCGT 60.742 61.111 0.00 0.00 42.04 5.68
1264 4236 2.520536 AAGCAAGGGGTGACTCGCT 61.521 57.895 0.00 0.00 34.16 4.93
1295 4267 1.306825 AGATGGCAGCCCTCTCACT 60.307 57.895 13.30 0.00 0.00 3.41
1407 4379 0.833287 ATCACTGGACCGAGATTGGG 59.167 55.000 0.00 0.00 0.00 4.12
1419 4391 0.035630 AGATTGGGAGTGCAGCAGAC 60.036 55.000 0.00 0.00 0.00 3.51
1482 4454 3.131223 TCCTCACGTCCAATGAAGATCTC 59.869 47.826 0.00 0.00 0.00 2.75
1581 4553 5.422970 GGATGATCTCTATGAAGCTCAGGAT 59.577 44.000 0.00 0.00 0.00 3.24
1668 4643 3.119316 AGACTCATTGTAGCAAGAGGACG 60.119 47.826 0.00 0.00 32.52 4.79
1713 4691 3.499737 GTTGACGATGCCGGCCAG 61.500 66.667 26.77 17.60 44.97 4.85
1782 4760 3.387962 AGGTCAGGCTTCTTCCATATCA 58.612 45.455 0.00 0.00 0.00 2.15
1845 4823 0.820871 GTCTGGTGAAGAGCGAGGAT 59.179 55.000 0.00 0.00 34.84 3.24
1935 4913 2.220133 CAGTTACCGAACACCAAACGAG 59.780 50.000 0.00 0.00 38.10 4.18
2024 5002 0.842635 GAGCCCCAGTCTGATGGATT 59.157 55.000 11.39 0.70 43.57 3.01
2094 5072 0.883833 CCAGCTCCGCTTGTTTTCAT 59.116 50.000 0.00 0.00 36.40 2.57
2162 5140 2.167281 AGAGTGTGCTAGCTGTATGTGG 59.833 50.000 17.23 0.00 0.00 4.17
2390 5473 3.146066 AGCTTGGACATCAACGCTTTAA 58.854 40.909 0.00 0.00 36.89 1.52
2414 5497 7.944729 ATATGCTGACCAGAATTAAGTGTTT 57.055 32.000 0.47 0.00 0.00 2.83
2435 5518 8.480853 GTGTTTATGACTATAGAATGCGTCTTC 58.519 37.037 6.78 0.00 37.84 2.87
2477 5560 3.181503 CGAGCATTTGACTCCCTTTCATG 60.182 47.826 0.00 0.00 0.00 3.07
2478 5561 3.094572 AGCATTTGACTCCCTTTCATGG 58.905 45.455 0.00 0.00 0.00 3.66
2479 5562 2.417787 GCATTTGACTCCCTTTCATGGC 60.418 50.000 0.00 0.00 0.00 4.40
2566 5940 6.034591 ACAAATCGACTACAATAAGACCTCG 58.965 40.000 0.00 0.00 0.00 4.63
2567 5941 4.832590 ATCGACTACAATAAGACCTCGG 57.167 45.455 0.00 0.00 0.00 4.63
2586 5960 3.309582 GGTGCTCATCCGAGGGAA 58.690 61.111 0.00 0.00 39.88 3.97
2601 5975 6.138263 TCCGAGGGAATTACAGTATTAAGGA 58.862 40.000 0.00 0.00 0.00 3.36
2602 5976 6.267014 TCCGAGGGAATTACAGTATTAAGGAG 59.733 42.308 0.00 0.00 0.00 3.69
2612 5986 8.680039 TTACAGTATTAAGGAGAGAGAGTAGC 57.320 38.462 0.00 0.00 0.00 3.58
2657 6031 7.574967 CGTTGCTAAGTTTCCAATCAAATACCT 60.575 37.037 0.00 0.00 0.00 3.08
2690 6064 2.125753 CTCGGTGAGAGCAGTGGC 60.126 66.667 0.00 0.00 40.54 5.01
2715 6089 1.971695 GTGGCGGAGGGTTTCTTGG 60.972 63.158 0.00 0.00 0.00 3.61
2717 6091 1.074248 GGCGGAGGGTTTCTTGGAA 59.926 57.895 0.00 0.00 0.00 3.53
2718 6092 0.960861 GGCGGAGGGTTTCTTGGAAG 60.961 60.000 0.00 0.00 0.00 3.46
2741 6115 2.018515 TCTGGTCGTTTGGTTTTGGTC 58.981 47.619 0.00 0.00 0.00 4.02
2785 6159 1.966451 GTCGGCCTGGGTGTTTGAG 60.966 63.158 0.00 0.00 0.00 3.02
2810 6184 2.362077 GTCAACAGTGAGGCATTTGGTT 59.638 45.455 0.00 0.00 33.27 3.67
2811 6185 2.361757 TCAACAGTGAGGCATTTGGTTG 59.638 45.455 0.00 0.00 36.42 3.77
2812 6186 1.331214 ACAGTGAGGCATTTGGTTGG 58.669 50.000 0.00 0.00 0.00 3.77
2813 6187 1.331214 CAGTGAGGCATTTGGTTGGT 58.669 50.000 0.00 0.00 0.00 3.67
2814 6188 1.270550 CAGTGAGGCATTTGGTTGGTC 59.729 52.381 0.00 0.00 0.00 4.02
2815 6189 0.240945 GTGAGGCATTTGGTTGGTCG 59.759 55.000 0.00 0.00 0.00 4.79
2816 6190 1.212751 GAGGCATTTGGTTGGTCGC 59.787 57.895 0.00 0.00 0.00 5.19
2817 6191 1.523154 GAGGCATTTGGTTGGTCGCA 61.523 55.000 0.00 0.00 0.00 5.10
2818 6192 0.899717 AGGCATTTGGTTGGTCGCAT 60.900 50.000 0.00 0.00 0.00 4.73
2819 6193 0.458370 GGCATTTGGTTGGTCGCATC 60.458 55.000 0.00 0.00 0.00 3.91
2820 6194 0.527565 GCATTTGGTTGGTCGCATCT 59.472 50.000 0.00 0.00 0.00 2.90
2821 6195 1.742831 GCATTTGGTTGGTCGCATCTA 59.257 47.619 0.00 0.00 0.00 1.98
2822 6196 2.358898 GCATTTGGTTGGTCGCATCTAT 59.641 45.455 0.00 0.00 0.00 1.98
2823 6197 3.563808 GCATTTGGTTGGTCGCATCTATA 59.436 43.478 0.00 0.00 0.00 1.31
2824 6198 4.554723 GCATTTGGTTGGTCGCATCTATAC 60.555 45.833 0.00 0.00 0.00 1.47
2825 6199 2.902705 TGGTTGGTCGCATCTATACC 57.097 50.000 0.00 0.00 0.00 2.73
2826 6200 2.394632 TGGTTGGTCGCATCTATACCT 58.605 47.619 0.00 0.00 34.23 3.08
2827 6201 2.102420 TGGTTGGTCGCATCTATACCTG 59.898 50.000 0.00 0.00 34.23 4.00
2828 6202 2.548067 GGTTGGTCGCATCTATACCTGG 60.548 54.545 0.00 0.00 34.23 4.45
2829 6203 0.679505 TGGTCGCATCTATACCTGGC 59.320 55.000 0.00 0.00 34.23 4.85
2830 6204 0.037232 GGTCGCATCTATACCTGGCC 60.037 60.000 0.00 0.00 0.00 5.36
2831 6205 0.679505 GTCGCATCTATACCTGGCCA 59.320 55.000 4.71 4.71 0.00 5.36
2832 6206 1.070134 GTCGCATCTATACCTGGCCAA 59.930 52.381 7.01 0.00 0.00 4.52
2833 6207 1.765904 TCGCATCTATACCTGGCCAAA 59.234 47.619 7.01 0.00 0.00 3.28
2834 6208 1.873591 CGCATCTATACCTGGCCAAAC 59.126 52.381 7.01 0.00 0.00 2.93
2835 6209 2.230660 GCATCTATACCTGGCCAAACC 58.769 52.381 7.01 0.00 39.84 3.27
2836 6210 2.158608 GCATCTATACCTGGCCAAACCT 60.159 50.000 7.01 0.00 40.22 3.50
2837 6211 3.744660 CATCTATACCTGGCCAAACCTC 58.255 50.000 7.01 0.00 40.22 3.85
2838 6212 1.760613 TCTATACCTGGCCAAACCTCG 59.239 52.381 7.01 0.00 40.22 4.63
2839 6213 0.834612 TATACCTGGCCAAACCTCGG 59.165 55.000 7.01 5.79 40.22 4.63
2840 6214 1.921869 ATACCTGGCCAAACCTCGGG 61.922 60.000 7.01 4.92 40.22 5.14
2879 6253 2.671070 GCCTAGCCAAGCCTGACA 59.329 61.111 0.00 0.00 0.00 3.58
2880 6254 1.746991 GCCTAGCCAAGCCTGACAC 60.747 63.158 0.00 0.00 0.00 3.67
2881 6255 1.679311 CCTAGCCAAGCCTGACACA 59.321 57.895 0.00 0.00 0.00 3.72
2882 6256 0.036732 CCTAGCCAAGCCTGACACAA 59.963 55.000 0.00 0.00 0.00 3.33
2883 6257 1.545428 CCTAGCCAAGCCTGACACAAA 60.545 52.381 0.00 0.00 0.00 2.83
2884 6258 2.229792 CTAGCCAAGCCTGACACAAAA 58.770 47.619 0.00 0.00 0.00 2.44
2885 6259 1.484038 AGCCAAGCCTGACACAAAAA 58.516 45.000 0.00 0.00 0.00 1.94
2899 6273 2.036731 AAAAACCTAGGCCCGGGC 59.963 61.111 38.57 38.57 41.06 6.13
2926 6300 3.590824 CCATCGGGCCTGTGTTTC 58.409 61.111 12.43 0.00 0.00 2.78
2927 6301 1.002134 CCATCGGGCCTGTGTTTCT 60.002 57.895 12.43 0.00 0.00 2.52
2928 6302 0.251916 CCATCGGGCCTGTGTTTCTA 59.748 55.000 12.43 0.00 0.00 2.10
2929 6303 1.656652 CATCGGGCCTGTGTTTCTAG 58.343 55.000 12.43 0.00 0.00 2.43
2930 6304 0.541863 ATCGGGCCTGTGTTTCTAGG 59.458 55.000 12.43 0.00 37.14 3.02
2936 6310 2.393271 CCTGTGTTTCTAGGCCTGAG 57.607 55.000 17.99 9.21 0.00 3.35
2937 6311 1.677217 CCTGTGTTTCTAGGCCTGAGC 60.677 57.143 17.99 3.93 38.76 4.26
2954 6328 4.376176 CCCGGCCCGAACACGTAA 62.376 66.667 3.71 0.00 0.00 3.18
2955 6329 2.357275 CCGGCCCGAACACGTAAA 60.357 61.111 3.71 0.00 0.00 2.01
2956 6330 1.960250 CCGGCCCGAACACGTAAAA 60.960 57.895 3.71 0.00 0.00 1.52
2957 6331 1.494189 CGGCCCGAACACGTAAAAG 59.506 57.895 0.00 0.00 0.00 2.27
2958 6332 1.208358 GGCCCGAACACGTAAAAGC 59.792 57.895 0.00 0.00 0.00 3.51
2959 6333 1.208358 GCCCGAACACGTAAAAGCC 59.792 57.895 0.00 0.00 0.00 4.35
2960 6334 1.871077 CCCGAACACGTAAAAGCCC 59.129 57.895 0.00 0.00 0.00 5.19
2961 6335 1.494189 CCGAACACGTAAAAGCCCG 59.506 57.895 0.00 0.00 0.00 6.13
2962 6336 1.223417 CCGAACACGTAAAAGCCCGT 61.223 55.000 0.00 0.00 37.90 5.28
2963 6337 0.162294 CGAACACGTAAAAGCCCGTC 59.838 55.000 0.00 0.00 34.59 4.79
2964 6338 0.162294 GAACACGTAAAAGCCCGTCG 59.838 55.000 0.00 0.00 34.59 5.12
2965 6339 1.223417 AACACGTAAAAGCCCGTCGG 61.223 55.000 3.60 3.60 34.59 4.79
2994 6368 4.785453 GCCCGGCCTGACCTTCAG 62.785 72.222 0.00 0.00 43.91 3.02
3013 6387 9.471084 ACCTTCAGAAAAATACAAAAATAACGG 57.529 29.630 0.00 0.00 0.00 4.44
3014 6388 8.921670 CCTTCAGAAAAATACAAAAATAACGGG 58.078 33.333 0.00 0.00 0.00 5.28
3015 6389 7.876896 TCAGAAAAATACAAAAATAACGGGC 57.123 32.000 0.00 0.00 0.00 6.13
3016 6390 6.869388 TCAGAAAAATACAAAAATAACGGGCC 59.131 34.615 0.00 0.00 0.00 5.80
3017 6391 6.091577 CAGAAAAATACAAAAATAACGGGCCC 59.908 38.462 13.57 13.57 0.00 5.80
3018 6392 3.786516 AATACAAAAATAACGGGCCCG 57.213 42.857 42.17 42.17 46.03 6.13
3019 6393 1.461559 TACAAAAATAACGGGCCCGG 58.538 50.000 44.99 27.73 44.69 5.73
3020 6394 1.252215 ACAAAAATAACGGGCCCGGG 61.252 55.000 44.99 24.93 44.69 5.73
3021 6395 2.352821 AAAAATAACGGGCCCGGGC 61.353 57.895 44.99 38.57 44.69 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.182627 AGGGTGCATATGTGATGGTATAATG 58.817 40.000 4.29 0.00 0.00 1.90
36 37 4.287067 AGACTCATTTTCTCTTAGGGTGCA 59.713 41.667 0.00 0.00 0.00 4.57
182 895 3.323774 AATTGGCAGATCACATCCCAT 57.676 42.857 0.00 0.00 0.00 4.00
212 925 6.234177 GTCTTACATTATGGAATGGAGGGAG 58.766 44.000 0.00 0.00 45.83 4.30
213 926 5.221641 CGTCTTACATTATGGAATGGAGGGA 60.222 44.000 0.00 0.00 45.83 4.20
214 927 4.997395 CGTCTTACATTATGGAATGGAGGG 59.003 45.833 0.00 0.00 45.83 4.30
215 928 5.611374 ACGTCTTACATTATGGAATGGAGG 58.389 41.667 0.00 0.00 45.83 4.30
216 929 7.553881 AAACGTCTTACATTATGGAATGGAG 57.446 36.000 0.00 1.17 45.83 3.86
217 930 7.931578 AAAACGTCTTACATTATGGAATGGA 57.068 32.000 0.00 0.00 45.83 3.41
262 975 5.993441 CCTCCGTCCCATAATATACGTTTTT 59.007 40.000 0.00 0.00 33.63 1.94
263 976 5.511888 CCCTCCGTCCCATAATATACGTTTT 60.512 44.000 0.00 0.00 33.63 2.43
264 977 4.020839 CCCTCCGTCCCATAATATACGTTT 60.021 45.833 0.00 0.00 33.63 3.60
265 978 3.512724 CCCTCCGTCCCATAATATACGTT 59.487 47.826 0.00 0.00 33.63 3.99
266 979 3.094572 CCCTCCGTCCCATAATATACGT 58.905 50.000 0.00 0.00 33.63 3.57
267 980 3.094572 ACCCTCCGTCCCATAATATACG 58.905 50.000 0.00 0.00 35.20 3.06
268 981 3.836562 ACACCCTCCGTCCCATAATATAC 59.163 47.826 0.00 0.00 0.00 1.47
269 982 4.136341 ACACCCTCCGTCCCATAATATA 57.864 45.455 0.00 0.00 0.00 0.86
270 983 2.986050 ACACCCTCCGTCCCATAATAT 58.014 47.619 0.00 0.00 0.00 1.28
271 984 2.482414 ACACCCTCCGTCCCATAATA 57.518 50.000 0.00 0.00 0.00 0.98
272 985 2.326428 CTACACCCTCCGTCCCATAAT 58.674 52.381 0.00 0.00 0.00 1.28
273 986 1.007479 ACTACACCCTCCGTCCCATAA 59.993 52.381 0.00 0.00 0.00 1.90
274 987 0.632835 ACTACACCCTCCGTCCCATA 59.367 55.000 0.00 0.00 0.00 2.74
275 988 0.252558 AACTACACCCTCCGTCCCAT 60.253 55.000 0.00 0.00 0.00 4.00
276 989 0.472352 AAACTACACCCTCCGTCCCA 60.472 55.000 0.00 0.00 0.00 4.37
277 990 1.205655 GTAAACTACACCCTCCGTCCC 59.794 57.143 0.00 0.00 0.00 4.46
278 991 1.895131 TGTAAACTACACCCTCCGTCC 59.105 52.381 0.00 0.00 32.89 4.79
279 992 3.665745 TTGTAAACTACACCCTCCGTC 57.334 47.619 0.00 0.00 38.63 4.79
280 993 4.129380 GTTTTGTAAACTACACCCTCCGT 58.871 43.478 0.00 0.00 38.63 4.69
281 994 4.128643 TGTTTTGTAAACTACACCCTCCG 58.871 43.478 4.19 0.00 38.63 4.63
282 995 6.644248 ATTGTTTTGTAAACTACACCCTCC 57.356 37.500 4.19 0.00 38.63 4.30
283 996 9.620660 CAATATTGTTTTGTAAACTACACCCTC 57.379 33.333 7.32 0.00 38.63 4.30
284 997 9.138596 ACAATATTGTTTTGTAAACTACACCCT 57.861 29.630 15.47 0.00 38.47 4.34
322 1035 8.276453 ACCAAAGTAAGCCATTATACTCCTAT 57.724 34.615 0.00 0.00 31.31 2.57
333 1046 5.815581 TGATGTAAGACCAAAGTAAGCCAT 58.184 37.500 0.00 0.00 0.00 4.40
367 1499 9.958180 TGATTATTACAGAAAGGAAGATTGTCA 57.042 29.630 0.00 0.00 0.00 3.58
451 1583 7.445836 CAACTAAATCGAACTACAGTACTTGC 58.554 38.462 0.00 0.00 0.00 4.01
478 1610 7.561251 TCCGATTTAATACTGTGGAAGATGAA 58.439 34.615 0.00 0.00 0.00 2.57
514 1673 0.887387 TAGTTTTCAGCACGGGCCAC 60.887 55.000 5.73 0.00 42.56 5.01
543 1702 6.068670 AGTAAAACTGACTTGCCTATTTGGT 58.931 36.000 0.00 0.00 38.35 3.67
544 1703 6.575162 AGTAAAACTGACTTGCCTATTTGG 57.425 37.500 0.00 0.00 39.35 3.28
632 1798 2.302445 AGCAGAGCACTGAAACAGAGAT 59.698 45.455 15.88 0.00 46.03 2.75
655 1821 1.852895 CTATGCTCGCGTAAACAGACC 59.147 52.381 5.77 0.00 0.00 3.85
737 1904 3.620488 TGTGCTTGGGATTCAGAATACC 58.380 45.455 16.98 16.98 42.69 2.73
753 1920 0.670546 GGACGTGCAGTGTATGTGCT 60.671 55.000 16.04 0.00 41.78 4.40
764 1932 2.674563 CTTTGGGGAGTGGACGTGCA 62.675 60.000 5.33 5.33 0.00 4.57
803 1971 1.801178 GAAGCAGGTTGAGCACACTAC 59.199 52.381 0.00 0.00 0.00 2.73
1132 2300 2.080336 ATGAATACCCATGGCCCCCG 62.080 60.000 6.09 0.00 0.00 5.73
1231 4203 3.325870 CTTGCTTGTCCAGTATCGTCAA 58.674 45.455 0.00 0.00 0.00 3.18
1264 4236 2.046023 CATCTCAACCCTGGCGCA 60.046 61.111 10.83 0.00 0.00 6.09
1270 4242 2.679716 GGCTGCCATCTCAACCCT 59.320 61.111 15.17 0.00 0.00 4.34
1407 4379 1.670406 CACCCTGTCTGCTGCACTC 60.670 63.158 0.00 0.00 0.00 3.51
1419 4391 1.331214 ACAAAATGTCCAGCACCCTG 58.669 50.000 0.00 0.00 38.85 4.45
1482 4454 0.745845 CCTCCGGAACAAGCCTGATG 60.746 60.000 5.23 0.00 0.00 3.07
1564 4536 4.021544 GGTACCATCCTGAGCTTCATAGAG 60.022 50.000 7.15 0.00 0.00 2.43
1581 4553 0.252696 ACCTCCTCAGCATGGTACCA 60.253 55.000 18.99 18.99 36.16 3.25
1668 4643 6.072673 ACAGACGGAAAACTTTGATATCAACC 60.073 38.462 17.76 12.96 35.28 3.77
1713 4691 1.077716 GTAGTGGACCCATGTGGCC 60.078 63.158 0.00 0.00 37.83 5.36
1719 4697 2.708861 TGTGTTCTTGTAGTGGACCCAT 59.291 45.455 0.00 0.00 0.00 4.00
1782 4760 1.274728 GGCTCAGACTGAGTGACACAT 59.725 52.381 28.76 0.00 45.94 3.21
1809 4787 3.127548 CCAGACGGTCATCAAGAAAATGG 59.872 47.826 11.27 1.28 0.00 3.16
1935 4913 2.365617 TCGATAGCTGAACCTGGATTCC 59.634 50.000 0.00 0.00 0.00 3.01
1965 4943 0.733150 CGTCAGTCGCTCCTATGTCA 59.267 55.000 0.00 0.00 0.00 3.58
2024 5002 1.696884 TGGCAGTCAGTCACATGGTAA 59.303 47.619 0.00 0.00 0.00 2.85
2094 5072 6.012508 AGAGAGAAAAGGGTAATGTCAATCCA 60.013 38.462 0.00 0.00 0.00 3.41
2142 5120 2.166459 TCCACATACAGCTAGCACACTC 59.834 50.000 18.83 0.00 0.00 3.51
2143 5121 2.179427 TCCACATACAGCTAGCACACT 58.821 47.619 18.83 0.00 0.00 3.55
2162 5140 5.824904 TTGCAATCCTAGAAAGCAGAATC 57.175 39.130 0.00 0.00 36.47 2.52
2390 5473 7.944729 AAACACTTAATTCTGGTCAGCATAT 57.055 32.000 0.00 0.00 0.00 1.78
2414 5497 6.808704 GCATGAAGACGCATTCTATAGTCATA 59.191 38.462 0.00 0.00 36.18 2.15
2427 5510 1.302752 AAGCTGGCATGAAGACGCA 60.303 52.632 0.00 0.00 0.00 5.24
2435 5518 3.811497 TCGAGAAATATCAAGCTGGCATG 59.189 43.478 0.00 0.00 0.00 4.06
2477 5560 0.743097 GATGTGCTTGAGGAATGGCC 59.257 55.000 0.00 0.00 0.00 5.36
2478 5561 1.466856 TGATGTGCTTGAGGAATGGC 58.533 50.000 0.00 0.00 0.00 4.40
2479 5562 2.361119 CCATGATGTGCTTGAGGAATGG 59.639 50.000 0.00 0.00 0.00 3.16
2586 5960 9.292195 GCTACTCTCTCTCCTTAATACTGTAAT 57.708 37.037 0.00 0.00 0.00 1.89
2601 5975 2.785562 AGTGTGTTCGCTACTCTCTCT 58.214 47.619 0.00 0.00 32.17 3.10
2602 5976 3.238441 CAAGTGTGTTCGCTACTCTCTC 58.762 50.000 0.00 0.00 33.71 3.20
2612 5986 1.280746 CTGCAGCCAAGTGTGTTCG 59.719 57.895 0.00 0.00 0.00 3.95
2657 6031 0.391927 CGAGTCAATTAACGGCCCCA 60.392 55.000 0.00 0.00 0.00 4.96
2693 6067 3.501040 GAAACCCTCCGCCACCCAA 62.501 63.158 0.00 0.00 0.00 4.12
2702 6076 0.778083 ACCCTTCCAAGAAACCCTCC 59.222 55.000 0.00 0.00 0.00 4.30
2705 6079 1.547901 CCAGACCCTTCCAAGAAACCC 60.548 57.143 0.00 0.00 0.00 4.11
2715 6089 0.108019 ACCAAACGACCAGACCCTTC 59.892 55.000 0.00 0.00 0.00 3.46
2717 6091 0.549469 AAACCAAACGACCAGACCCT 59.451 50.000 0.00 0.00 0.00 4.34
2718 6092 1.066454 CAAAACCAAACGACCAGACCC 59.934 52.381 0.00 0.00 0.00 4.46
2741 6115 2.163211 TCTCGCTGAGATGACAGACTTG 59.837 50.000 0.00 0.00 39.94 3.16
2785 6159 2.191128 ATGCCTCACTGTTGACTTCC 57.809 50.000 0.00 0.00 0.00 3.46
2810 6184 0.679505 GCCAGGTATAGATGCGACCA 59.320 55.000 0.00 0.00 35.56 4.02
2811 6185 0.037232 GGCCAGGTATAGATGCGACC 60.037 60.000 0.00 0.00 0.00 4.79
2812 6186 0.679505 TGGCCAGGTATAGATGCGAC 59.320 55.000 0.00 0.00 0.00 5.19
2813 6187 1.419381 TTGGCCAGGTATAGATGCGA 58.581 50.000 5.11 0.00 0.00 5.10
2814 6188 1.873591 GTTTGGCCAGGTATAGATGCG 59.126 52.381 5.11 0.00 0.00 4.73
2815 6189 2.158608 AGGTTTGGCCAGGTATAGATGC 60.159 50.000 5.11 0.00 40.61 3.91
2816 6190 3.744660 GAGGTTTGGCCAGGTATAGATG 58.255 50.000 5.11 0.00 40.61 2.90
2817 6191 2.368875 CGAGGTTTGGCCAGGTATAGAT 59.631 50.000 5.11 0.00 40.61 1.98
2818 6192 1.760613 CGAGGTTTGGCCAGGTATAGA 59.239 52.381 5.11 0.00 40.61 1.98
2819 6193 1.202651 CCGAGGTTTGGCCAGGTATAG 60.203 57.143 5.11 0.00 40.61 1.31
2820 6194 0.834612 CCGAGGTTTGGCCAGGTATA 59.165 55.000 5.11 0.00 40.61 1.47
2821 6195 1.607612 CCGAGGTTTGGCCAGGTAT 59.392 57.895 5.11 0.00 40.61 2.73
2822 6196 2.598787 CCCGAGGTTTGGCCAGGTA 61.599 63.158 5.11 0.00 40.61 3.08
2823 6197 3.966543 CCCGAGGTTTGGCCAGGT 61.967 66.667 5.11 0.00 40.61 4.00
2863 6237 0.036732 TTGTGTCAGGCTTGGCTAGG 59.963 55.000 0.92 0.00 0.00 3.02
2864 6238 1.896220 TTTGTGTCAGGCTTGGCTAG 58.104 50.000 0.92 0.00 0.00 3.42
2865 6239 2.356665 TTTTGTGTCAGGCTTGGCTA 57.643 45.000 0.92 0.00 0.00 3.93
2866 6240 1.484038 TTTTTGTGTCAGGCTTGGCT 58.516 45.000 0.92 0.00 0.00 4.75
2882 6256 2.036731 GCCCGGGCCTAGGTTTTT 59.963 61.111 36.64 0.00 34.56 1.94
2909 6283 0.251916 TAGAAACACAGGCCCGATGG 59.748 55.000 0.00 0.00 0.00 3.51
2910 6284 1.656652 CTAGAAACACAGGCCCGATG 58.343 55.000 0.00 0.00 0.00 3.84
2911 6285 0.541863 CCTAGAAACACAGGCCCGAT 59.458 55.000 0.00 0.00 0.00 4.18
2912 6286 1.980052 CCTAGAAACACAGGCCCGA 59.020 57.895 0.00 0.00 0.00 5.14
2913 6287 4.617875 CCTAGAAACACAGGCCCG 57.382 61.111 0.00 0.00 0.00 6.13
2917 6291 1.677217 GCTCAGGCCTAGAAACACAGG 60.677 57.143 3.98 0.00 34.85 4.00
2918 6292 1.731720 GCTCAGGCCTAGAAACACAG 58.268 55.000 3.98 0.00 0.00 3.66
2919 6293 3.935993 GCTCAGGCCTAGAAACACA 57.064 52.632 3.98 0.00 0.00 3.72
2937 6311 3.880162 TTTACGTGTTCGGGCCGGG 62.880 63.158 27.98 12.73 41.85 5.73
2938 6312 1.903783 CTTTTACGTGTTCGGGCCGG 61.904 60.000 27.98 12.18 41.85 6.13
2939 6313 1.494189 CTTTTACGTGTTCGGGCCG 59.506 57.895 22.51 22.51 41.85 6.13
2940 6314 1.208358 GCTTTTACGTGTTCGGGCC 59.792 57.895 0.00 0.00 41.85 5.80
2941 6315 1.208358 GGCTTTTACGTGTTCGGGC 59.792 57.895 0.00 0.00 41.85 6.13
2942 6316 1.871077 GGGCTTTTACGTGTTCGGG 59.129 57.895 0.00 0.00 41.85 5.14
2943 6317 1.223417 ACGGGCTTTTACGTGTTCGG 61.223 55.000 0.00 0.00 42.39 4.30
2944 6318 0.162294 GACGGGCTTTTACGTGTTCG 59.838 55.000 0.00 0.00 44.24 3.95
2945 6319 0.162294 CGACGGGCTTTTACGTGTTC 59.838 55.000 0.00 0.00 44.24 3.18
2946 6320 1.223417 CCGACGGGCTTTTACGTGTT 61.223 55.000 5.81 0.00 44.24 3.32
2947 6321 1.665599 CCGACGGGCTTTTACGTGT 60.666 57.895 5.81 0.00 44.24 4.49
2948 6322 2.385091 CCCGACGGGCTTTTACGTG 61.385 63.158 22.37 0.00 44.24 4.49
2977 6351 4.785453 CTGAAGGTCAGGCCGGGC 62.785 72.222 22.67 22.67 40.71 6.13
2978 6352 2.124507 TTTCTGAAGGTCAGGCCGGG 62.125 60.000 2.18 0.00 44.39 5.73
2979 6353 0.250727 TTTTCTGAAGGTCAGGCCGG 60.251 55.000 0.00 0.00 44.39 6.13
2980 6354 1.604604 TTTTTCTGAAGGTCAGGCCG 58.395 50.000 0.00 0.00 44.39 6.13
2981 6355 4.079253 TGTATTTTTCTGAAGGTCAGGCC 58.921 43.478 0.00 0.00 44.39 5.19
2982 6356 5.705609 TTGTATTTTTCTGAAGGTCAGGC 57.294 39.130 5.46 0.00 44.39 4.85
2987 6361 9.471084 CCGTTATTTTTGTATTTTTCTGAAGGT 57.529 29.630 0.00 0.00 0.00 3.50
2988 6362 8.921670 CCCGTTATTTTTGTATTTTTCTGAAGG 58.078 33.333 0.00 0.00 0.00 3.46
2989 6363 8.432359 GCCCGTTATTTTTGTATTTTTCTGAAG 58.568 33.333 0.00 0.00 0.00 3.02
2990 6364 7.385478 GGCCCGTTATTTTTGTATTTTTCTGAA 59.615 33.333 0.00 0.00 0.00 3.02
2991 6365 6.869388 GGCCCGTTATTTTTGTATTTTTCTGA 59.131 34.615 0.00 0.00 0.00 3.27
2992 6366 6.091577 GGGCCCGTTATTTTTGTATTTTTCTG 59.908 38.462 5.69 0.00 0.00 3.02
2993 6367 6.167685 GGGCCCGTTATTTTTGTATTTTTCT 58.832 36.000 5.69 0.00 0.00 2.52
2994 6368 5.062433 CGGGCCCGTTATTTTTGTATTTTTC 59.938 40.000 36.64 0.00 34.35 2.29
2995 6369 4.930405 CGGGCCCGTTATTTTTGTATTTTT 59.070 37.500 36.64 0.00 34.35 1.94
2996 6370 4.496360 CGGGCCCGTTATTTTTGTATTTT 58.504 39.130 36.64 0.00 34.35 1.82
2997 6371 3.119065 CCGGGCCCGTTATTTTTGTATTT 60.119 43.478 40.52 0.00 37.81 1.40
2998 6372 2.427812 CCGGGCCCGTTATTTTTGTATT 59.572 45.455 40.52 0.00 37.81 1.89
2999 6373 2.025898 CCGGGCCCGTTATTTTTGTAT 58.974 47.619 40.52 0.00 37.81 2.29
3000 6374 1.461559 CCGGGCCCGTTATTTTTGTA 58.538 50.000 40.52 0.00 37.81 2.41
3001 6375 1.252215 CCCGGGCCCGTTATTTTTGT 61.252 55.000 40.52 0.00 37.81 2.83
3002 6376 1.513622 CCCGGGCCCGTTATTTTTG 59.486 57.895 40.52 23.20 37.81 2.44
3003 6377 2.352821 GCCCGGGCCCGTTATTTTT 61.353 57.895 40.52 0.00 37.81 1.94
3004 6378 2.756691 GCCCGGGCCCGTTATTTT 60.757 61.111 40.52 0.00 37.81 1.82


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

AutoCloner maintained by Alex Coulton.