Multiple sequence alignment - TraesCS1B01G383000

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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 TraesCS1B01G383000 chr1B 100.000 2927 0 0 1 2927 615019069 615021995 0.000000e+00 5406.0
1 TraesCS1B01G383000 chr1B 84.828 145 19 3 1177 1321 615020188 615020329 3.040000e-30 143.0
2 TraesCS1B01G383000 chr1B 84.828 145 19 3 1120 1261 615020245 615020389 3.040000e-30 143.0
3 TraesCS1B01G383000 chr1B 97.297 37 1 0 39 75 421334391 421334355 2.440000e-06 63.9
4 TraesCS1B01G383000 chr1D 93.082 2255 85 37 3 2234 449451692 449453898 0.000000e+00 3234.0
5 TraesCS1B01G383000 chr1D 82.843 408 32 19 37 409 449447599 449448003 6.050000e-87 331.0
6 TraesCS1B01G383000 chr1D 87.448 239 19 4 2578 2806 449454295 449454532 6.220000e-67 265.0
7 TraesCS1B01G383000 chr1D 85.417 144 18 3 1120 1260 449452845 449452988 2.350000e-31 147.0
8 TraesCS1B01G383000 chr1D 84.615 143 19 3 1179 1321 449452790 449452929 3.930000e-29 139.0
9 TraesCS1B01G383000 chr1A 91.993 1074 27 22 1253 2322 544583626 544584644 0.000000e+00 1452.0
10 TraesCS1B01G383000 chr1A 89.381 791 45 15 477 1261 544582814 544583571 0.000000e+00 959.0
11 TraesCS1B01G383000 chr1A 90.395 531 37 9 2276 2806 544584662 544585178 0.000000e+00 686.0
12 TraesCS1B01G383000 chr1A 95.166 331 12 2 3 329 544564545 544564875 1.200000e-143 520.0
13 TraesCS1B01G383000 chr1A 89.268 205 19 3 1177 1381 544583430 544583631 1.350000e-63 254.0
14 TraesCS1B01G383000 chr1A 95.683 139 4 2 318 455 544570543 544570680 3.800000e-54 222.0
15 TraesCS1B01G383000 chr1A 97.101 69 2 0 1193 1261 544583626 544583694 1.840000e-22 117.0
16 TraesCS1B01G383000 chr3B 85.047 321 34 10 79 395 606211682 606211992 6.090000e-82 315.0
17 TraesCS1B01G383000 chr3B 96.875 32 1 0 42 73 606211601 606211632 1.000000e-03 54.7
18 TraesCS1B01G383000 chr4B 100.000 37 0 0 39 75 36958228 36958192 5.230000e-08 69.4


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 TraesCS1B01G383000 chr1B 615019069 615021995 2926 False 1897.333333 5406 89.885333 1 2927 3 chr1B.!!$F1 2926
1 TraesCS1B01G383000 chr1D 449447599 449454532 6933 False 823.200000 3234 86.681000 3 2806 5 chr1D.!!$F1 2803
2 TraesCS1B01G383000 chr1A 544582814 544585178 2364 False 693.600000 1452 91.627600 477 2806 5 chr1A.!!$F3 2329

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
270 4364 0.385473 GATTTGGACACACGCCGTTG 60.385 55.0 0.0 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 6209 0.462937 TACAGCACACCACACCACAC 60.463 55.0 0.0 0.0 0.0 3.82 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
97 4189 5.805728 AGGGAAAACACATGTACTCTAAGG 58.194 41.667 0.00 0.00 0.00 2.69
98 4190 5.309806 AGGGAAAACACATGTACTCTAAGGT 59.690 40.000 0.00 0.00 0.00 3.50
99 4191 5.411669 GGGAAAACACATGTACTCTAAGGTG 59.588 44.000 0.00 0.00 0.00 4.00
100 4192 6.228258 GGAAAACACATGTACTCTAAGGTGA 58.772 40.000 0.00 0.00 0.00 4.02
101 4193 6.708949 GGAAAACACATGTACTCTAAGGTGAA 59.291 38.462 0.00 0.00 0.00 3.18
102 4194 7.390718 GGAAAACACATGTACTCTAAGGTGAAT 59.609 37.037 0.00 0.00 0.00 2.57
103 4195 7.672983 AAACACATGTACTCTAAGGTGAATG 57.327 36.000 0.00 0.00 0.00 2.67
104 4196 6.605471 ACACATGTACTCTAAGGTGAATGA 57.395 37.500 0.00 0.00 0.00 2.57
105 4197 7.004555 ACACATGTACTCTAAGGTGAATGAA 57.995 36.000 0.00 0.00 0.00 2.57
106 4198 7.624549 ACACATGTACTCTAAGGTGAATGAAT 58.375 34.615 0.00 0.00 0.00 2.57
107 4199 7.550551 ACACATGTACTCTAAGGTGAATGAATG 59.449 37.037 0.00 0.00 0.00 2.67
108 4200 7.765819 CACATGTACTCTAAGGTGAATGAATGA 59.234 37.037 0.00 0.00 0.00 2.57
109 4201 8.321353 ACATGTACTCTAAGGTGAATGAATGAA 58.679 33.333 0.00 0.00 0.00 2.57
110 4202 8.824781 CATGTACTCTAAGGTGAATGAATGAAG 58.175 37.037 0.00 0.00 0.00 3.02
111 4203 7.331026 TGTACTCTAAGGTGAATGAATGAAGG 58.669 38.462 0.00 0.00 0.00 3.46
112 4204 5.749462 ACTCTAAGGTGAATGAATGAAGGG 58.251 41.667 0.00 0.00 0.00 3.95
270 4364 0.385473 GATTTGGACACACGCCGTTG 60.385 55.000 0.00 0.00 0.00 4.10
293 4387 7.776933 TGAGTCAATTTATAACTGCAGCTAG 57.223 36.000 15.27 0.00 0.00 3.42
297 4391 3.924114 TTTATAACTGCAGCTAGCCCA 57.076 42.857 15.27 8.33 44.83 5.36
346 4440 1.546029 TCTACATGAGTCGTGCAGCTT 59.454 47.619 12.41 0.00 0.00 3.74
347 4441 1.657594 CTACATGAGTCGTGCAGCTTG 59.342 52.381 12.41 0.00 0.00 4.01
390 4484 4.728772 AGGTTGTTGTCCTCATTCATGAA 58.271 39.130 11.26 11.26 36.18 2.57
450 4544 4.557695 CGCCATTAACACAAAAGTTAGGCA 60.558 41.667 13.82 0.00 41.63 4.75
459 4553 4.330074 CACAAAAGTTAGGCATACTCTCGG 59.670 45.833 0.00 0.00 0.00 4.63
460 4554 3.821421 AAAGTTAGGCATACTCTCGGG 57.179 47.619 0.00 0.00 0.00 5.14
461 4555 1.705873 AGTTAGGCATACTCTCGGGG 58.294 55.000 0.00 0.00 0.00 5.73
500 4594 4.581409 TGTGAATCAATAGACATGCATGGG 59.419 41.667 29.41 7.08 0.00 4.00
579 4673 7.562135 TGTGTTAGAGAAAACAAGAACCTAGT 58.438 34.615 0.00 0.00 40.85 2.57
580 4674 8.698210 TGTGTTAGAGAAAACAAGAACCTAGTA 58.302 33.333 0.00 0.00 40.85 1.82
581 4675 9.194271 GTGTTAGAGAAAACAAGAACCTAGTAG 57.806 37.037 0.00 0.00 40.85 2.57
604 4699 4.739046 CAATAATGCTTCCCATCGAGAC 57.261 45.455 0.00 0.00 31.43 3.36
680 4779 1.909781 CCCCTGCACACCAAGCAAT 60.910 57.895 0.00 0.00 42.17 3.56
681 4780 1.474332 CCCCTGCACACCAAGCAATT 61.474 55.000 0.00 0.00 42.17 2.32
684 4783 2.353011 CCCTGCACACCAAGCAATTAAG 60.353 50.000 0.00 0.00 42.17 1.85
690 4790 4.082026 GCACACCAAGCAATTAAGATTCCT 60.082 41.667 0.00 0.00 0.00 3.36
764 4864 0.879090 CCGTGGCCAGACCTTAAAAC 59.121 55.000 5.11 0.00 40.22 2.43
773 4873 1.173913 GACCTTAAAACGCCATGGCT 58.826 50.000 33.07 17.87 39.32 4.75
840 4940 6.604396 TCCTTCCTATATAACTTCGACACACA 59.396 38.462 0.00 0.00 0.00 3.72
1933 6096 0.443088 CAAGAAGCTCTGAGCAAGCG 59.557 55.000 29.49 11.32 45.56 4.68
1934 6097 0.673022 AAGAAGCTCTGAGCAAGCGG 60.673 55.000 29.49 0.00 45.56 5.52
1938 6115 1.886777 GCTCTGAGCAAGCGGATCC 60.887 63.158 24.02 0.00 41.89 3.36
1941 6118 0.179065 TCTGAGCAAGCGGATCCATG 60.179 55.000 13.41 8.63 0.00 3.66
1962 6139 2.803979 TGGAAACACACGATCGACG 58.196 52.632 24.34 14.70 41.56 5.12
1964 6141 1.266446 TGGAAACACACGATCGACGTA 59.734 47.619 24.34 0.00 45.28 3.57
1965 6142 2.095110 TGGAAACACACGATCGACGTAT 60.095 45.455 24.34 4.62 45.28 3.06
1973 6150 1.963747 CGATCGACGTATGCATGCTA 58.036 50.000 20.33 5.73 37.22 3.49
1992 6169 1.206072 GCTATGCTATGCTGCACGC 59.794 57.895 16.16 16.16 46.33 5.34
1997 6174 3.933498 CTATGCTGCACGCGCTGG 61.933 66.667 5.73 0.00 43.27 4.85
2027 6208 1.879380 TCTTGATTTGTGAAGGGCGTG 59.121 47.619 0.00 0.00 0.00 5.34
2028 6209 0.958091 TTGATTTGTGAAGGGCGTGG 59.042 50.000 0.00 0.00 0.00 4.94
2029 6210 0.179004 TGATTTGTGAAGGGCGTGGT 60.179 50.000 0.00 0.00 0.00 4.16
2030 6211 0.240945 GATTTGTGAAGGGCGTGGTG 59.759 55.000 0.00 0.00 0.00 4.17
2031 6212 0.467290 ATTTGTGAAGGGCGTGGTGT 60.467 50.000 0.00 0.00 0.00 4.16
2137 6320 7.591795 GTGCTAGTGTATGTACAAGTATGCTAG 59.408 40.741 0.00 8.56 38.04 3.42
2155 6338 2.629656 GCACGGCAAGCAGGTTGAT 61.630 57.895 16.74 0.00 38.60 2.57
2159 6342 1.699656 CGGCAAGCAGGTTGATCTCG 61.700 60.000 16.74 9.41 38.60 4.04
2210 6393 8.402798 TCAAATGTTACTCTATTTGGCTTTCA 57.597 30.769 0.00 0.00 41.98 2.69
2214 6397 7.391148 TGTTACTCTATTTGGCTTTCATTCC 57.609 36.000 0.00 0.00 0.00 3.01
2248 6431 9.185192 GGAAAATGTCTTCAAAACTATGACTTG 57.815 33.333 0.00 0.00 0.00 3.16
2263 6481 2.037641 TGACTTGATGACTGGAGTGGTG 59.962 50.000 0.00 0.00 0.00 4.17
2291 6509 7.257722 TGACATCTTTCTTTTCTGTGGTTTTC 58.742 34.615 0.00 0.00 0.00 2.29
2358 6640 7.084268 AGGTAGCTATAGCATTCCAGATTTT 57.916 36.000 26.07 3.86 45.16 1.82
2375 6657 8.352201 TCCAGATTTTCATTGTGTTTACTGAAG 58.648 33.333 0.00 0.00 0.00 3.02
2399 6681 5.639931 GGAGAAGAAGTCCACATTAGTTGAC 59.360 44.000 0.00 0.00 39.90 3.18
2484 6766 7.816945 AAACATAGATGCATTGTTAGTTTGC 57.183 32.000 14.06 0.00 33.44 3.68
2534 6816 6.479990 CGAATGGTGAGATATTGAGTTTGCTA 59.520 38.462 0.00 0.00 0.00 3.49
2585 6902 3.256383 TGAGTTTGGTTGCTTGATGATGG 59.744 43.478 0.00 0.00 0.00 3.51
2613 6930 4.022935 TCGCTCTCAATTTTGATTTGTGCT 60.023 37.500 0.00 0.00 36.46 4.40
2682 7008 6.559810 CACTTATGTTGTGTTTCAGTTTGGA 58.440 36.000 0.00 0.00 0.00 3.53
2721 7047 1.202989 TGGTGCAGCTACCCATTTTGA 60.203 47.619 18.08 0.00 40.09 2.69
2729 7055 5.128919 CAGCTACCCATTTTGAGCTAGAAT 58.871 41.667 0.00 0.00 43.34 2.40
2806 7132 5.964958 AGGAACATTGTTGTCACATAAGG 57.035 39.130 6.80 0.00 34.06 2.69
2807 7133 4.766891 AGGAACATTGTTGTCACATAAGGG 59.233 41.667 6.80 0.00 34.06 3.95
2808 7134 4.522789 GGAACATTGTTGTCACATAAGGGT 59.477 41.667 6.80 0.00 34.06 4.34
2809 7135 5.452078 AACATTGTTGTCACATAAGGGTG 57.548 39.130 0.15 0.00 40.16 4.61
2810 7136 4.469657 ACATTGTTGTCACATAAGGGTGT 58.530 39.130 0.00 0.00 39.76 4.16
2819 7145 3.976169 CACATAAGGGTGTGTTTGGTTG 58.024 45.455 0.00 0.00 43.43 3.77
2820 7146 2.364002 ACATAAGGGTGTGTTTGGTTGC 59.636 45.455 0.00 0.00 0.00 4.17
2821 7147 2.145397 TAAGGGTGTGTTTGGTTGCA 57.855 45.000 0.00 0.00 0.00 4.08
2822 7148 0.823460 AAGGGTGTGTTTGGTTGCAG 59.177 50.000 0.00 0.00 0.00 4.41
2823 7149 0.324275 AGGGTGTGTTTGGTTGCAGT 60.324 50.000 0.00 0.00 0.00 4.40
2824 7150 1.064314 AGGGTGTGTTTGGTTGCAGTA 60.064 47.619 0.00 0.00 0.00 2.74
2825 7151 1.751924 GGGTGTGTTTGGTTGCAGTAA 59.248 47.619 0.00 0.00 0.00 2.24
2826 7152 2.480587 GGGTGTGTTTGGTTGCAGTAAC 60.481 50.000 0.00 0.00 38.60 2.50
2842 7168 3.323243 AGTAACCGACTGGAATTTCACG 58.677 45.455 0.00 0.00 36.87 4.35
2843 7169 1.519408 AACCGACTGGAATTTCACGG 58.481 50.000 12.95 12.95 44.77 4.94
2844 7170 0.321298 ACCGACTGGAATTTCACGGG 60.321 55.000 17.49 6.17 43.76 5.28
2845 7171 0.321298 CCGACTGGAATTTCACGGGT 60.321 55.000 7.72 0.00 37.49 5.28
2846 7172 1.076332 CGACTGGAATTTCACGGGTC 58.924 55.000 0.00 0.00 0.00 4.46
2847 7173 1.450025 GACTGGAATTTCACGGGTCC 58.550 55.000 0.00 0.00 0.00 4.46
2848 7174 0.768622 ACTGGAATTTCACGGGTCCA 59.231 50.000 0.00 0.00 37.83 4.02
2849 7175 1.144093 ACTGGAATTTCACGGGTCCAA 59.856 47.619 0.00 0.00 39.62 3.53
2850 7176 1.539827 CTGGAATTTCACGGGTCCAAC 59.460 52.381 0.00 0.00 39.62 3.77
2851 7177 0.885879 GGAATTTCACGGGTCCAACC 59.114 55.000 0.00 0.00 37.60 3.77
2860 7186 2.033602 GGTCCAACCCGTTCCTGG 59.966 66.667 0.00 0.00 30.04 4.45
2861 7187 2.522367 GGTCCAACCCGTTCCTGGA 61.522 63.158 0.00 0.00 36.89 3.86
2862 7188 3.153825 TCCAACCCGTTCCTGGAC 58.846 61.111 0.00 0.00 34.26 4.02
2863 7189 2.033602 CCAACCCGTTCCTGGACC 59.966 66.667 0.00 0.00 31.38 4.46
2864 7190 2.824880 CCAACCCGTTCCTGGACCA 61.825 63.158 0.00 0.00 31.38 4.02
2865 7191 1.599797 CAACCCGTTCCTGGACCAC 60.600 63.158 0.00 0.00 0.00 4.16
2866 7192 3.173167 AACCCGTTCCTGGACCACG 62.173 63.158 12.78 12.78 0.00 4.94
2867 7193 3.622826 CCCGTTCCTGGACCACGT 61.623 66.667 17.05 0.00 31.83 4.49
2868 7194 2.424302 CCGTTCCTGGACCACGTT 59.576 61.111 17.05 0.00 31.83 3.99
2869 7195 1.666872 CCGTTCCTGGACCACGTTC 60.667 63.158 17.05 0.00 31.83 3.95
2870 7196 1.366366 CGTTCCTGGACCACGTTCT 59.634 57.895 11.77 0.00 0.00 3.01
2871 7197 0.666577 CGTTCCTGGACCACGTTCTC 60.667 60.000 11.77 0.00 0.00 2.87
2872 7198 0.666577 GTTCCTGGACCACGTTCTCG 60.667 60.000 0.00 0.00 43.34 4.04
2873 7199 2.430382 TTCCTGGACCACGTTCTCGC 62.430 60.000 0.00 0.00 41.18 5.03
2874 7200 2.805353 CTGGACCACGTTCTCGCG 60.805 66.667 0.00 0.00 41.18 5.87
2875 7201 3.553437 CTGGACCACGTTCTCGCGT 62.553 63.158 5.77 0.00 46.88 6.01
2876 7202 2.355481 GGACCACGTTCTCGCGTT 60.355 61.111 5.77 0.00 43.83 4.84
2877 7203 1.952635 GGACCACGTTCTCGCGTTT 60.953 57.895 5.77 0.00 43.83 3.60
2878 7204 0.664166 GGACCACGTTCTCGCGTTTA 60.664 55.000 5.77 0.00 43.83 2.01
2879 7205 0.706729 GACCACGTTCTCGCGTTTAG 59.293 55.000 5.77 0.00 43.83 1.85
2880 7206 0.031178 ACCACGTTCTCGCGTTTAGT 59.969 50.000 5.77 0.00 43.83 2.24
2881 7207 1.134226 CCACGTTCTCGCGTTTAGTT 58.866 50.000 5.77 0.00 43.83 2.24
2882 7208 1.123756 CCACGTTCTCGCGTTTAGTTC 59.876 52.381 5.77 0.00 43.83 3.01
2883 7209 1.782569 CACGTTCTCGCGTTTAGTTCA 59.217 47.619 5.77 0.00 43.83 3.18
2884 7210 2.049228 ACGTTCTCGCGTTTAGTTCAG 58.951 47.619 5.77 0.00 43.04 3.02
2885 7211 1.201672 CGTTCTCGCGTTTAGTTCAGC 60.202 52.381 5.77 0.00 0.00 4.26
2890 7216 3.877801 GCGTTTAGTTCAGCGATGG 57.122 52.632 0.00 0.00 0.00 3.51
2891 7217 1.355971 GCGTTTAGTTCAGCGATGGA 58.644 50.000 0.00 0.00 0.00 3.41
2892 7218 1.730064 GCGTTTAGTTCAGCGATGGAA 59.270 47.619 0.00 0.00 0.00 3.53
2893 7219 2.474032 GCGTTTAGTTCAGCGATGGAAC 60.474 50.000 0.00 4.37 43.82 3.62
2894 7220 2.093783 CGTTTAGTTCAGCGATGGAACC 59.906 50.000 0.00 0.00 44.40 3.62
2895 7221 2.004583 TTAGTTCAGCGATGGAACCG 57.995 50.000 0.00 0.00 44.40 4.44
2896 7222 0.174845 TAGTTCAGCGATGGAACCGG 59.825 55.000 0.00 0.00 44.40 5.28
2897 7223 1.079405 GTTCAGCGATGGAACCGGA 60.079 57.895 9.46 0.00 38.92 5.14
2898 7224 0.672401 GTTCAGCGATGGAACCGGAA 60.672 55.000 9.46 0.00 38.92 4.30
2899 7225 0.672401 TTCAGCGATGGAACCGGAAC 60.672 55.000 9.46 0.32 0.00 3.62
2900 7226 2.106683 CAGCGATGGAACCGGAACC 61.107 63.158 9.46 11.87 0.00 3.62
2901 7227 2.822701 GCGATGGAACCGGAACCC 60.823 66.667 9.46 6.51 0.00 4.11
2902 7228 2.666207 CGATGGAACCGGAACCCA 59.334 61.111 9.46 12.80 0.00 4.51
2903 7229 1.743995 CGATGGAACCGGAACCCAC 60.744 63.158 9.46 6.78 32.07 4.61
2904 7230 1.683441 GATGGAACCGGAACCCACT 59.317 57.895 9.46 2.64 32.07 4.00
2905 7231 0.676782 GATGGAACCGGAACCCACTG 60.677 60.000 9.46 0.00 32.07 3.66
2906 7232 1.131303 ATGGAACCGGAACCCACTGA 61.131 55.000 9.46 0.00 32.07 3.41
2907 7233 1.131303 TGGAACCGGAACCCACTGAT 61.131 55.000 9.46 0.00 0.00 2.90
2908 7234 0.037734 GGAACCGGAACCCACTGATT 59.962 55.000 9.46 0.00 0.00 2.57
2909 7235 1.450025 GAACCGGAACCCACTGATTC 58.550 55.000 9.46 0.00 0.00 2.52
2910 7236 1.003233 GAACCGGAACCCACTGATTCT 59.997 52.381 9.46 0.00 0.00 2.40
2911 7237 0.613777 ACCGGAACCCACTGATTCTC 59.386 55.000 9.46 0.00 0.00 2.87
2912 7238 0.460284 CCGGAACCCACTGATTCTCG 60.460 60.000 0.00 0.00 0.00 4.04
2913 7239 0.460284 CGGAACCCACTGATTCTCGG 60.460 60.000 0.00 0.00 0.00 4.63
2914 7240 0.107654 GGAACCCACTGATTCTCGGG 60.108 60.000 0.00 0.00 44.88 5.14
2915 7241 0.902531 GAACCCACTGATTCTCGGGA 59.097 55.000 11.21 0.00 41.62 5.14
2916 7242 0.905357 AACCCACTGATTCTCGGGAG 59.095 55.000 11.21 0.00 41.62 4.30
2917 7243 1.144936 CCCACTGATTCTCGGGAGC 59.855 63.158 0.00 0.00 41.62 4.70
2918 7244 1.227089 CCACTGATTCTCGGGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
2919 7245 1.227089 CACTGATTCTCGGGAGCGG 60.227 63.158 0.00 0.00 0.00 5.52
2920 7246 2.279784 CTGATTCTCGGGAGCGGC 60.280 66.667 0.00 0.00 0.00 6.53
2921 7247 3.074369 TGATTCTCGGGAGCGGCA 61.074 61.111 1.45 0.00 0.00 5.69
2922 7248 2.374830 CTGATTCTCGGGAGCGGCAT 62.375 60.000 1.45 0.00 0.00 4.40
2923 7249 1.112916 TGATTCTCGGGAGCGGCATA 61.113 55.000 1.45 0.00 0.00 3.14
2924 7250 0.247736 GATTCTCGGGAGCGGCATAT 59.752 55.000 1.45 0.00 0.00 1.78
2925 7251 0.687354 ATTCTCGGGAGCGGCATATT 59.313 50.000 1.45 0.00 0.00 1.28
2926 7252 0.033504 TTCTCGGGAGCGGCATATTC 59.966 55.000 1.45 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 4127 9.485206 TGTTTACTGATAAGAAAAGGTGACTAC 57.515 33.333 0.00 0.00 42.68 2.73
77 4169 7.724305 TTCACCTTAGAGTACATGTGTTTTC 57.276 36.000 9.11 0.74 0.00 2.29
82 4174 7.765819 TCATTCATTCACCTTAGAGTACATGTG 59.234 37.037 9.11 0.00 0.00 3.21
84 4176 8.722480 TTCATTCATTCACCTTAGAGTACATG 57.278 34.615 0.00 0.00 0.00 3.21
85 4177 7.989741 CCTTCATTCATTCACCTTAGAGTACAT 59.010 37.037 0.00 0.00 0.00 2.29
86 4178 7.331026 CCTTCATTCATTCACCTTAGAGTACA 58.669 38.462 0.00 0.00 0.00 2.90
87 4179 6.763610 CCCTTCATTCATTCACCTTAGAGTAC 59.236 42.308 0.00 0.00 0.00 2.73
88 4180 6.443849 ACCCTTCATTCATTCACCTTAGAGTA 59.556 38.462 0.00 0.00 0.00 2.59
89 4181 5.251700 ACCCTTCATTCATTCACCTTAGAGT 59.748 40.000 0.00 0.00 0.00 3.24
90 4182 5.587844 CACCCTTCATTCATTCACCTTAGAG 59.412 44.000 0.00 0.00 0.00 2.43
91 4183 5.014123 ACACCCTTCATTCATTCACCTTAGA 59.986 40.000 0.00 0.00 0.00 2.10
92 4184 5.256474 ACACCCTTCATTCATTCACCTTAG 58.744 41.667 0.00 0.00 0.00 2.18
93 4185 5.255397 ACACCCTTCATTCATTCACCTTA 57.745 39.130 0.00 0.00 0.00 2.69
94 4186 4.118168 ACACCCTTCATTCATTCACCTT 57.882 40.909 0.00 0.00 0.00 3.50
95 4187 3.814504 ACACCCTTCATTCATTCACCT 57.185 42.857 0.00 0.00 0.00 4.00
96 4188 3.614870 GCAACACCCTTCATTCATTCACC 60.615 47.826 0.00 0.00 0.00 4.02
97 4189 3.256631 AGCAACACCCTTCATTCATTCAC 59.743 43.478 0.00 0.00 0.00 3.18
98 4190 3.499338 AGCAACACCCTTCATTCATTCA 58.501 40.909 0.00 0.00 0.00 2.57
99 4191 5.357878 TGATAGCAACACCCTTCATTCATTC 59.642 40.000 0.00 0.00 0.00 2.67
100 4192 5.263599 TGATAGCAACACCCTTCATTCATT 58.736 37.500 0.00 0.00 0.00 2.57
101 4193 4.858850 TGATAGCAACACCCTTCATTCAT 58.141 39.130 0.00 0.00 0.00 2.57
102 4194 4.299586 TGATAGCAACACCCTTCATTCA 57.700 40.909 0.00 0.00 0.00 2.57
103 4195 4.024556 CGATGATAGCAACACCCTTCATTC 60.025 45.833 0.00 0.00 0.00 2.67
104 4196 3.879295 CGATGATAGCAACACCCTTCATT 59.121 43.478 0.00 0.00 0.00 2.57
105 4197 3.134623 TCGATGATAGCAACACCCTTCAT 59.865 43.478 0.00 0.00 0.00 2.57
106 4198 2.499693 TCGATGATAGCAACACCCTTCA 59.500 45.455 0.00 0.00 0.00 3.02
107 4199 3.179443 TCGATGATAGCAACACCCTTC 57.821 47.619 0.00 0.00 0.00 3.46
108 4200 3.627395 TTCGATGATAGCAACACCCTT 57.373 42.857 0.00 0.00 0.00 3.95
109 4201 3.627395 TTTCGATGATAGCAACACCCT 57.373 42.857 0.00 0.00 0.00 4.34
110 4202 3.689649 ACTTTTCGATGATAGCAACACCC 59.310 43.478 0.00 0.00 0.00 4.61
111 4203 4.946784 ACTTTTCGATGATAGCAACACC 57.053 40.909 0.00 0.00 0.00 4.16
112 4204 6.887376 TCTACTTTTCGATGATAGCAACAC 57.113 37.500 0.00 0.00 0.00 3.32
179 4271 5.064198 TGAAACAGTGCAAGTTGTACTACAC 59.936 40.000 23.77 13.15 41.37 2.90
270 4364 6.293135 GGCTAGCTGCAGTTATAAATTGACTC 60.293 42.308 16.64 0.00 45.15 3.36
346 4440 0.669619 CACACAAATGGCAGTGCTCA 59.330 50.000 16.11 11.78 39.30 4.26
347 4441 0.670162 ACACACAAATGGCAGTGCTC 59.330 50.000 16.11 5.84 39.30 4.26
352 4446 1.321474 ACCTCACACACAAATGGCAG 58.679 50.000 0.00 0.00 0.00 4.85
390 4484 6.951971 AGCTTTGTATCTTACCTCAATGTCT 58.048 36.000 0.00 0.00 0.00 3.41
500 4594 2.361438 CTCCTCACCATACTTCCCGTAC 59.639 54.545 0.00 0.00 0.00 3.67
595 4689 0.376152 GCAGCAACATGTCTCGATGG 59.624 55.000 0.00 0.00 0.00 3.51
680 4779 8.964476 ATATCTTTTGCTTCGAGGAATCTTAA 57.036 30.769 0.00 0.00 0.00 1.85
681 4780 7.382488 CGATATCTTTTGCTTCGAGGAATCTTA 59.618 37.037 0.00 0.00 31.74 2.10
684 4783 5.613577 GCGATATCTTTTGCTTCGAGGAATC 60.614 44.000 0.00 0.00 31.74 2.52
690 4790 2.866156 CTGGCGATATCTTTTGCTTCGA 59.134 45.455 0.34 0.00 31.74 3.71
773 4873 4.602259 GCTAGCCCGGCGTGCATA 62.602 66.667 18.08 5.33 33.60 3.14
1042 5142 0.456312 GCGATGAAGAAGACGACGGT 60.456 55.000 0.00 0.00 0.00 4.83
1049 5149 2.202743 CGGCGGCGATGAAGAAGA 60.203 61.111 29.19 0.00 0.00 2.87
1570 5733 4.498520 CGCCGTCTCCATCAGCGT 62.499 66.667 0.00 0.00 41.78 5.07
1938 6115 2.788750 CGATCGTGTGTTTCCATGCATG 60.789 50.000 20.19 20.19 0.00 4.06
1941 6118 1.075542 TCGATCGTGTGTTTCCATGC 58.924 50.000 15.94 0.00 0.00 4.06
1957 6134 0.668535 AGCTAGCATGCATACGTCGA 59.331 50.000 21.98 0.00 34.99 4.20
1958 6135 2.331809 TAGCTAGCATGCATACGTCG 57.668 50.000 21.98 0.00 34.99 5.12
1959 6136 2.346847 GCATAGCTAGCATGCATACGTC 59.653 50.000 30.49 11.98 46.47 4.34
1960 6137 2.341257 GCATAGCTAGCATGCATACGT 58.659 47.619 30.49 9.21 46.47 3.57
1966 6143 2.352034 CAGCATAGCATAGCTAGCATGC 59.648 50.000 29.32 29.32 44.66 4.06
1967 6144 2.352034 GCAGCATAGCATAGCTAGCATG 59.648 50.000 18.83 18.08 44.66 4.06
1989 6166 0.739813 GAGTCCATTAACCAGCGCGT 60.740 55.000 8.43 0.00 0.00 6.01
1992 6169 2.972625 TCAAGAGTCCATTAACCAGCG 58.027 47.619 0.00 0.00 0.00 5.18
1997 6174 7.308435 CCTTCACAAATCAAGAGTCCATTAAC 58.692 38.462 0.00 0.00 0.00 2.01
2027 6208 2.124320 AGCACACCACACCACACC 60.124 61.111 0.00 0.00 0.00 4.16
2028 6209 0.462937 TACAGCACACCACACCACAC 60.463 55.000 0.00 0.00 0.00 3.82
2029 6210 0.472044 ATACAGCACACCACACCACA 59.528 50.000 0.00 0.00 0.00 4.17
2030 6211 0.874390 CATACAGCACACCACACCAC 59.126 55.000 0.00 0.00 0.00 4.16
2031 6212 0.888736 GCATACAGCACACCACACCA 60.889 55.000 0.00 0.00 44.79 4.17
2077 6258 5.520288 CCTCAAACCTTGATCACATAGTACG 59.480 44.000 0.00 0.00 39.30 3.67
2078 6259 6.640518 TCCTCAAACCTTGATCACATAGTAC 58.359 40.000 0.00 0.00 39.30 2.73
2137 6320 2.533391 GATCAACCTGCTTGCCGTGC 62.533 60.000 0.00 0.00 0.00 5.34
2210 6393 6.098124 TGAAGACATTTTCCAACACAAGGAAT 59.902 34.615 0.00 0.00 44.14 3.01
2214 6397 7.331687 AGTTTTGAAGACATTTTCCAACACAAG 59.668 33.333 0.00 0.00 0.00 3.16
2248 6431 1.065926 TCATGCACCACTCCAGTCATC 60.066 52.381 0.00 0.00 0.00 2.92
2263 6481 5.159209 CCACAGAAAAGAAAGATGTCATGC 58.841 41.667 0.00 0.00 0.00 4.06
2291 6509 6.918022 GGCATTTTATAGAAGATCAAAACGGG 59.082 38.462 0.00 0.00 0.00 5.28
2336 6618 7.969536 TGAAAATCTGGAATGCTATAGCTAC 57.030 36.000 24.61 15.00 42.66 3.58
2338 6620 7.504911 ACAATGAAAATCTGGAATGCTATAGCT 59.495 33.333 24.61 6.22 42.66 3.32
2358 6640 6.826668 TCTTCTCCTTCAGTAAACACAATGA 58.173 36.000 0.00 0.00 0.00 2.57
2375 6657 5.639931 GTCAACTAATGTGGACTTCTTCTCC 59.360 44.000 0.00 0.00 42.42 3.71
2399 6681 1.265095 CATGCGATCTTTCCCATTCCG 59.735 52.381 0.00 0.00 0.00 4.30
2459 6741 7.331687 GGCAAACTAACAATGCATCTATGTTTT 59.668 33.333 17.83 7.07 41.80 2.43
2460 6742 6.813152 GGCAAACTAACAATGCATCTATGTTT 59.187 34.615 17.83 13.56 41.80 2.83
2484 6766 0.747255 ATCCTCGATGTCGGTGAAGG 59.253 55.000 2.25 2.38 40.29 3.46
2556 6838 6.500684 TCAAGCAACCAAACTCAATATCTC 57.499 37.500 0.00 0.00 0.00 2.75
2585 6902 5.803020 AATCAAAATTGAGAGCGACCTAC 57.197 39.130 1.98 0.00 41.08 3.18
2613 6930 1.746991 TGTTGCACACGAACCAGCA 60.747 52.632 0.00 0.00 34.79 4.41
2654 6980 5.762045 ACTGAAACACAACATAAGTGCATC 58.238 37.500 0.00 0.00 40.59 3.91
2721 7047 6.166279 TCATTCGTGAAGAACAATTCTAGCT 58.834 36.000 0.00 0.00 42.39 3.32
2729 7055 4.152938 CAGCTCATCATTCGTGAAGAACAA 59.847 41.667 0.00 0.00 42.39 2.83
2806 7132 2.804647 GTTACTGCAACCAAACACACC 58.195 47.619 0.00 0.00 0.00 4.16
2821 7147 3.323243 CGTGAAATTCCAGTCGGTTACT 58.677 45.455 0.00 0.00 39.81 2.24
2822 7148 2.414138 CCGTGAAATTCCAGTCGGTTAC 59.586 50.000 0.00 0.00 34.38 2.50
2823 7149 2.613474 CCCGTGAAATTCCAGTCGGTTA 60.613 50.000 12.13 0.00 36.84 2.85
2824 7150 1.519408 CCGTGAAATTCCAGTCGGTT 58.481 50.000 0.00 0.00 34.38 4.44
2825 7151 0.321298 CCCGTGAAATTCCAGTCGGT 60.321 55.000 12.13 0.00 36.84 4.69
2826 7152 0.321298 ACCCGTGAAATTCCAGTCGG 60.321 55.000 8.27 8.27 38.05 4.79
2827 7153 1.076332 GACCCGTGAAATTCCAGTCG 58.924 55.000 0.00 0.00 0.00 4.18
2828 7154 1.271163 TGGACCCGTGAAATTCCAGTC 60.271 52.381 0.00 0.00 33.02 3.51
2829 7155 0.768622 TGGACCCGTGAAATTCCAGT 59.231 50.000 0.00 0.00 33.02 4.00
2830 7156 1.539827 GTTGGACCCGTGAAATTCCAG 59.460 52.381 0.00 0.00 39.32 3.86
2831 7157 1.611519 GTTGGACCCGTGAAATTCCA 58.388 50.000 0.00 0.00 36.31 3.53
2832 7158 0.885879 GGTTGGACCCGTGAAATTCC 59.114 55.000 0.00 0.00 30.04 3.01
2843 7169 2.033602 CCAGGAACGGGTTGGACC 59.966 66.667 0.00 0.00 39.39 4.46
2844 7170 3.153825 TCCAGGAACGGGTTGGAC 58.846 61.111 0.00 0.00 46.16 4.02
2845 7171 2.522367 GGTCCAGGAACGGGTTGGA 61.522 63.158 0.00 0.00 46.16 3.53
2846 7172 2.033602 GGTCCAGGAACGGGTTGG 59.966 66.667 0.00 0.00 46.16 3.77
2847 7173 1.599797 GTGGTCCAGGAACGGGTTG 60.600 63.158 0.00 0.00 46.16 3.77
2848 7174 2.833957 GTGGTCCAGGAACGGGTT 59.166 61.111 0.00 0.00 46.16 4.11
2849 7175 3.622826 CGTGGTCCAGGAACGGGT 61.623 66.667 5.60 0.00 46.16 5.28
2851 7177 1.666872 GAACGTGGTCCAGGAACGG 60.667 63.158 18.37 6.26 41.50 4.44
2852 7178 0.666577 GAGAACGTGGTCCAGGAACG 60.667 60.000 18.37 11.51 42.82 3.95
2853 7179 0.666577 CGAGAACGTGGTCCAGGAAC 60.667 60.000 18.37 0.00 34.56 3.62
2854 7180 1.663739 CGAGAACGTGGTCCAGGAA 59.336 57.895 18.37 0.00 34.56 3.36
2855 7181 2.927580 GCGAGAACGTGGTCCAGGA 61.928 63.158 18.37 0.00 41.98 3.86
2856 7182 2.432628 GCGAGAACGTGGTCCAGG 60.433 66.667 10.08 10.08 41.98 4.45
2857 7183 2.805353 CGCGAGAACGTGGTCCAG 60.805 66.667 0.00 0.00 44.76 3.86
2865 7191 1.201672 GCTGAACTAAACGCGAGAACG 60.202 52.381 15.93 0.00 42.93 3.95
2866 7192 2.489051 GCTGAACTAAACGCGAGAAC 57.511 50.000 15.93 0.43 0.00 3.01
2871 7197 0.025001 CCATCGCTGAACTAAACGCG 59.975 55.000 3.53 3.53 46.28 6.01
2872 7198 1.355971 TCCATCGCTGAACTAAACGC 58.644 50.000 0.00 0.00 0.00 4.84
2873 7199 2.093783 GGTTCCATCGCTGAACTAAACG 59.906 50.000 10.09 0.00 41.42 3.60
2874 7200 2.093783 CGGTTCCATCGCTGAACTAAAC 59.906 50.000 10.09 0.00 41.42 2.01
2875 7201 2.343101 CGGTTCCATCGCTGAACTAAA 58.657 47.619 10.09 0.00 41.42 1.85
2876 7202 1.404986 CCGGTTCCATCGCTGAACTAA 60.405 52.381 0.00 0.00 41.42 2.24
2877 7203 0.174845 CCGGTTCCATCGCTGAACTA 59.825 55.000 0.00 0.00 41.42 2.24
2878 7204 1.079127 CCGGTTCCATCGCTGAACT 60.079 57.895 0.00 0.00 41.42 3.01
2879 7205 0.672401 TTCCGGTTCCATCGCTGAAC 60.672 55.000 0.00 0.00 41.05 3.18
2880 7206 0.672401 GTTCCGGTTCCATCGCTGAA 60.672 55.000 0.00 0.00 0.00 3.02
2881 7207 1.079405 GTTCCGGTTCCATCGCTGA 60.079 57.895 0.00 0.00 0.00 4.26
2882 7208 2.106683 GGTTCCGGTTCCATCGCTG 61.107 63.158 0.00 0.00 0.00 5.18
2883 7209 2.267961 GGTTCCGGTTCCATCGCT 59.732 61.111 0.00 0.00 0.00 4.93
2884 7210 2.822701 GGGTTCCGGTTCCATCGC 60.823 66.667 16.61 0.00 0.00 4.58
2885 7211 1.743995 GTGGGTTCCGGTTCCATCG 60.744 63.158 16.61 0.00 32.71 3.84
2886 7212 0.676782 CAGTGGGTTCCGGTTCCATC 60.677 60.000 16.61 10.51 32.71 3.51
2887 7213 1.131303 TCAGTGGGTTCCGGTTCCAT 61.131 55.000 16.61 5.34 32.71 3.41
2888 7214 1.131303 ATCAGTGGGTTCCGGTTCCA 61.131 55.000 16.61 12.81 0.00 3.53
2889 7215 0.037734 AATCAGTGGGTTCCGGTTCC 59.962 55.000 0.00 5.14 0.00 3.62
2890 7216 1.003233 AGAATCAGTGGGTTCCGGTTC 59.997 52.381 0.00 0.00 0.00 3.62
2891 7217 1.003233 GAGAATCAGTGGGTTCCGGTT 59.997 52.381 0.00 0.00 33.17 4.44
2892 7218 0.613777 GAGAATCAGTGGGTTCCGGT 59.386 55.000 0.00 0.00 33.17 5.28
2893 7219 0.460284 CGAGAATCAGTGGGTTCCGG 60.460 60.000 0.00 0.00 33.17 5.14
2894 7220 0.460284 CCGAGAATCAGTGGGTTCCG 60.460 60.000 5.81 8.36 33.17 4.30
2895 7221 0.107654 CCCGAGAATCAGTGGGTTCC 60.108 60.000 5.81 0.00 36.86 3.62
2896 7222 0.902531 TCCCGAGAATCAGTGGGTTC 59.097 55.000 4.74 0.00 42.54 3.62
2897 7223 0.905357 CTCCCGAGAATCAGTGGGTT 59.095 55.000 4.74 0.00 42.54 4.11
2898 7224 1.617947 GCTCCCGAGAATCAGTGGGT 61.618 60.000 0.00 0.00 42.54 4.51
2899 7225 1.144936 GCTCCCGAGAATCAGTGGG 59.855 63.158 0.00 0.00 43.36 4.61
2900 7226 1.227089 CGCTCCCGAGAATCAGTGG 60.227 63.158 0.00 0.00 36.29 4.00
2901 7227 1.227089 CCGCTCCCGAGAATCAGTG 60.227 63.158 0.00 0.00 36.29 3.66
2902 7228 3.082579 GCCGCTCCCGAGAATCAGT 62.083 63.158 0.00 0.00 36.29 3.41
2903 7229 2.279784 GCCGCTCCCGAGAATCAG 60.280 66.667 0.00 0.00 36.29 2.90
2904 7230 1.112916 TATGCCGCTCCCGAGAATCA 61.113 55.000 0.00 0.00 36.29 2.57
2905 7231 0.247736 ATATGCCGCTCCCGAGAATC 59.752 55.000 0.00 0.00 36.29 2.52
2906 7232 0.687354 AATATGCCGCTCCCGAGAAT 59.313 50.000 0.00 0.00 36.29 2.40
2907 7233 0.033504 GAATATGCCGCTCCCGAGAA 59.966 55.000 0.00 0.00 36.29 2.87
2908 7234 1.666011 GAATATGCCGCTCCCGAGA 59.334 57.895 0.00 0.00 36.29 4.04
2909 7235 4.268687 GAATATGCCGCTCCCGAG 57.731 61.111 0.00 0.00 36.29 4.63


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

AutoCloner maintained by Alex Coulton.