Multiple sequence alignment - TraesCS5B01G514200

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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 TraesCS5B01G514200 chr5B 100.000 2897 0 0 1 2897 679324505 679327401 0.000000e+00 5350
1 TraesCS5B01G514200 chr5B 88.787 767 60 18 483 1240 62950955 62950206 0.000000e+00 917
2 TraesCS5B01G514200 chr4A 91.282 1904 101 32 49 1914 631579388 631577512 0.000000e+00 2536
3 TraesCS5B01G514200 chr4A 87.400 1000 73 16 1948 2897 598145688 598144692 0.000000e+00 1099
4 TraesCS5B01G514200 chr4A 83.832 1002 95 21 1944 2897 609939363 609940345 0.000000e+00 891
5 TraesCS5B01G514200 chr5D 93.516 1604 58 19 345 1914 538343977 538345568 0.000000e+00 2344
6 TraesCS5B01G514200 chr5D 87.100 1000 75 15 1948 2897 130173336 130174331 0.000000e+00 1083
7 TraesCS5B01G514200 chr5D 80.135 297 34 16 124 402 538341028 538341317 6.330000e-47 198
8 TraesCS5B01G514200 chr3D 86.331 1390 158 16 497 1870 603015495 603014122 0.000000e+00 1485
9 TraesCS5B01G514200 chr3D 77.057 632 105 28 1261 1869 130942580 130943194 7.740000e-86 327
10 TraesCS5B01G514200 chr1D 82.235 1396 219 17 481 1869 237323785 237322412 0.000000e+00 1177
11 TraesCS5B01G514200 chr7A 89.297 953 70 13 1966 2891 686115249 686116196 0.000000e+00 1166
12 TraesCS5B01G514200 chr1A 89.051 959 72 11 1966 2897 57751580 57750628 0.000000e+00 1158
13 TraesCS5B01G514200 chr1A 81.818 1397 218 22 481 1869 308381099 308382467 0.000000e+00 1140
14 TraesCS5B01G514200 chr1A 87.614 985 74 11 1958 2897 285429631 285430612 0.000000e+00 1099
15 TraesCS5B01G514200 chr1A 85.196 1020 77 29 1949 2897 543488262 543489278 0.000000e+00 979
16 TraesCS5B01G514200 chr3A 88.819 957 79 8 1966 2897 67576355 67577308 0.000000e+00 1149
17 TraesCS5B01G514200 chr3A 86.940 804 58 18 2137 2897 9811365 9810566 0.000000e+00 859
18 TraesCS5B01G514200 chr3A 84.715 772 96 13 793 1552 732934999 732934238 0.000000e+00 752
19 TraesCS5B01G514200 chr3A 89.121 478 44 7 1422 1897 732922201 732921730 3.220000e-164 588
20 TraesCS5B01G514200 chr3A 87.898 471 43 12 481 951 732923194 732922738 2.540000e-150 542
21 TraesCS5B01G514200 chr4B 85.323 1131 132 13 486 1601 98053957 98052846 0.000000e+00 1138
22 TraesCS5B01G514200 chr5A 88.100 958 80 14 1966 2897 623558644 623557695 0.000000e+00 1107
23 TraesCS5B01G514200 chr5A 87.398 976 76 10 1966 2897 620405164 620404192 0.000000e+00 1077
24 TraesCS5B01G514200 chr5A 85.567 970 85 17 1977 2897 4213035 4212072 0.000000e+00 965
25 TraesCS5B01G514200 chr5A 78.179 692 108 22 2243 2897 400415287 400415972 4.500000e-108 401
26 TraesCS5B01G514200 chr1B 81.232 1396 233 17 481 1869 369204980 369206353 0.000000e+00 1099
27 TraesCS5B01G514200 chr2A 87.001 977 79 11 1966 2897 584070627 584069654 0.000000e+00 1057
28 TraesCS5B01G514200 chr2A 79.854 958 155 24 1966 2895 74059677 74060624 0.000000e+00 665
29 TraesCS5B01G514200 chr6A 86.554 1004 80 21 1945 2897 610950399 610951398 0.000000e+00 1055
30 TraesCS5B01G514200 chr6A 86.312 789 62 17 2152 2897 54484438 54483653 0.000000e+00 817
31 TraesCS5B01G514200 chr3B 83.555 979 99 24 1966 2897 38457299 38456336 0.000000e+00 859
32 TraesCS5B01G514200 chr3B 83.514 740 94 13 817 1538 810654386 810653657 0.000000e+00 665
33 TraesCS5B01G514200 chr2B 78.526 475 54 18 2468 2897 684809387 684808916 4.760000e-68 268


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 TraesCS5B01G514200 chr5B 679324505 679327401 2896 False 5350 5350 100.0000 1 2897 1 chr5B.!!$F1 2896
1 TraesCS5B01G514200 chr5B 62950206 62950955 749 True 917 917 88.7870 483 1240 1 chr5B.!!$R1 757
2 TraesCS5B01G514200 chr4A 631577512 631579388 1876 True 2536 2536 91.2820 49 1914 1 chr4A.!!$R2 1865
3 TraesCS5B01G514200 chr4A 598144692 598145688 996 True 1099 1099 87.4000 1948 2897 1 chr4A.!!$R1 949
4 TraesCS5B01G514200 chr4A 609939363 609940345 982 False 891 891 83.8320 1944 2897 1 chr4A.!!$F1 953
5 TraesCS5B01G514200 chr5D 538341028 538345568 4540 False 1271 2344 86.8255 124 1914 2 chr5D.!!$F2 1790
6 TraesCS5B01G514200 chr5D 130173336 130174331 995 False 1083 1083 87.1000 1948 2897 1 chr5D.!!$F1 949
7 TraesCS5B01G514200 chr3D 603014122 603015495 1373 True 1485 1485 86.3310 497 1870 1 chr3D.!!$R1 1373
8 TraesCS5B01G514200 chr3D 130942580 130943194 614 False 327 327 77.0570 1261 1869 1 chr3D.!!$F1 608
9 TraesCS5B01G514200 chr1D 237322412 237323785 1373 True 1177 1177 82.2350 481 1869 1 chr1D.!!$R1 1388
10 TraesCS5B01G514200 chr7A 686115249 686116196 947 False 1166 1166 89.2970 1966 2891 1 chr7A.!!$F1 925
11 TraesCS5B01G514200 chr1A 57750628 57751580 952 True 1158 1158 89.0510 1966 2897 1 chr1A.!!$R1 931
12 TraesCS5B01G514200 chr1A 308381099 308382467 1368 False 1140 1140 81.8180 481 1869 1 chr1A.!!$F2 1388
13 TraesCS5B01G514200 chr1A 285429631 285430612 981 False 1099 1099 87.6140 1958 2897 1 chr1A.!!$F1 939
14 TraesCS5B01G514200 chr1A 543488262 543489278 1016 False 979 979 85.1960 1949 2897 1 chr1A.!!$F3 948
15 TraesCS5B01G514200 chr3A 67576355 67577308 953 False 1149 1149 88.8190 1966 2897 1 chr3A.!!$F1 931
16 TraesCS5B01G514200 chr3A 9810566 9811365 799 True 859 859 86.9400 2137 2897 1 chr3A.!!$R1 760
17 TraesCS5B01G514200 chr3A 732934238 732934999 761 True 752 752 84.7150 793 1552 1 chr3A.!!$R2 759
18 TraesCS5B01G514200 chr3A 732921730 732923194 1464 True 565 588 88.5095 481 1897 2 chr3A.!!$R3 1416
19 TraesCS5B01G514200 chr4B 98052846 98053957 1111 True 1138 1138 85.3230 486 1601 1 chr4B.!!$R1 1115
20 TraesCS5B01G514200 chr5A 623557695 623558644 949 True 1107 1107 88.1000 1966 2897 1 chr5A.!!$R3 931
21 TraesCS5B01G514200 chr5A 620404192 620405164 972 True 1077 1077 87.3980 1966 2897 1 chr5A.!!$R2 931
22 TraesCS5B01G514200 chr5A 4212072 4213035 963 True 965 965 85.5670 1977 2897 1 chr5A.!!$R1 920
23 TraesCS5B01G514200 chr5A 400415287 400415972 685 False 401 401 78.1790 2243 2897 1 chr5A.!!$F1 654
24 TraesCS5B01G514200 chr1B 369204980 369206353 1373 False 1099 1099 81.2320 481 1869 1 chr1B.!!$F1 1388
25 TraesCS5B01G514200 chr2A 584069654 584070627 973 True 1057 1057 87.0010 1966 2897 1 chr2A.!!$R1 931
26 TraesCS5B01G514200 chr2A 74059677 74060624 947 False 665 665 79.8540 1966 2895 1 chr2A.!!$F1 929
27 TraesCS5B01G514200 chr6A 610950399 610951398 999 False 1055 1055 86.5540 1945 2897 1 chr6A.!!$F1 952
28 TraesCS5B01G514200 chr6A 54483653 54484438 785 True 817 817 86.3120 2152 2897 1 chr6A.!!$R1 745
29 TraesCS5B01G514200 chr3B 38456336 38457299 963 True 859 859 83.5550 1966 2897 1 chr3B.!!$R1 931
30 TraesCS5B01G514200 chr3B 810653657 810654386 729 True 665 665 83.5140 817 1538 1 chr3B.!!$R2 721

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
314 3088 0.179094 GTCATGTGGCAATGCATGGG 60.179 55.000 7.79 0.00 41.83 4.00 F
318 3092 1.153509 GTGGCAATGCATGGGCTTC 60.154 57.895 26.42 16.21 41.91 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 4863 1.200716 CAACGCCATCCATATCCATGC 59.799 52.381 0.0 0.0 0.00 4.06 R
2035 5033 2.558359 GGGATGAACCTTGTCCAGTTTG 59.442 50.000 0.0 0.0 38.98 2.93 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
27 28 9.004717 TGAAATTAACGAGGATGAATTTGTACA 57.995 29.630 0.00 0.00 32.94 2.90
42 43 9.134734 TGAATTTGTACATTTTATTTCTTCGGC 57.865 29.630 0.00 0.00 0.00 5.54
43 44 7.734538 ATTTGTACATTTTATTTCTTCGGCG 57.265 32.000 0.00 0.00 0.00 6.46
44 45 5.224562 TGTACATTTTATTTCTTCGGCGG 57.775 39.130 7.21 0.00 0.00 6.13
45 46 3.145212 ACATTTTATTTCTTCGGCGGC 57.855 42.857 7.21 0.00 0.00 6.53
46 47 2.159296 ACATTTTATTTCTTCGGCGGCC 60.159 45.455 9.54 9.54 0.00 6.13
47 48 1.535833 TTTTATTTCTTCGGCGGCCA 58.464 45.000 20.71 3.24 0.00 5.36
48 49 0.806241 TTTATTTCTTCGGCGGCCAC 59.194 50.000 20.71 0.00 0.00 5.01
49 50 1.363145 TTATTTCTTCGGCGGCCACG 61.363 55.000 20.71 10.37 44.63 4.94
50 51 2.228389 TATTTCTTCGGCGGCCACGA 62.228 55.000 20.71 14.80 44.60 4.35
51 52 4.735132 TTCTTCGGCGGCCACGAG 62.735 66.667 20.71 12.87 44.60 4.18
53 54 4.735132 CTTCGGCGGCCACGAGAA 62.735 66.667 20.71 12.85 44.60 2.87
54 55 4.077184 TTCGGCGGCCACGAGAAT 62.077 61.111 20.71 0.00 44.60 2.40
55 56 2.622903 CTTCGGCGGCCACGAGAATA 62.623 60.000 20.71 4.56 44.60 1.75
56 57 2.202824 CGGCGGCCACGAGAATAA 60.203 61.111 20.71 0.00 44.60 1.40
57 58 1.594293 CGGCGGCCACGAGAATAAT 60.594 57.895 20.71 0.00 44.60 1.28
58 59 1.157870 CGGCGGCCACGAGAATAATT 61.158 55.000 20.71 0.00 44.60 1.40
59 60 1.021968 GGCGGCCACGAGAATAATTT 58.978 50.000 15.62 0.00 44.60 1.82
60 61 1.404035 GGCGGCCACGAGAATAATTTT 59.596 47.619 15.62 0.00 44.60 1.82
61 62 2.159296 GGCGGCCACGAGAATAATTTTT 60.159 45.455 15.62 0.00 44.60 1.94
79 80 4.935352 TTTTTGTTTGTGGATGGAGGAG 57.065 40.909 0.00 0.00 0.00 3.69
80 81 3.593442 TTTGTTTGTGGATGGAGGAGT 57.407 42.857 0.00 0.00 0.00 3.85
81 82 4.715534 TTTGTTTGTGGATGGAGGAGTA 57.284 40.909 0.00 0.00 0.00 2.59
82 83 4.715534 TTGTTTGTGGATGGAGGAGTAA 57.284 40.909 0.00 0.00 0.00 2.24
83 84 4.715534 TGTTTGTGGATGGAGGAGTAAA 57.284 40.909 0.00 0.00 0.00 2.01
84 85 4.394729 TGTTTGTGGATGGAGGAGTAAAC 58.605 43.478 0.00 0.00 0.00 2.01
85 86 4.141367 TGTTTGTGGATGGAGGAGTAAACA 60.141 41.667 0.00 0.00 35.27 2.83
86 87 4.927267 TTGTGGATGGAGGAGTAAACAT 57.073 40.909 0.00 0.00 0.00 2.71
87 88 4.220693 TGTGGATGGAGGAGTAAACATG 57.779 45.455 0.00 0.00 0.00 3.21
88 89 3.054434 TGTGGATGGAGGAGTAAACATGG 60.054 47.826 0.00 0.00 0.00 3.66
89 90 2.509548 TGGATGGAGGAGTAAACATGGG 59.490 50.000 0.00 0.00 0.00 4.00
90 91 2.158608 GGATGGAGGAGTAAACATGGGG 60.159 54.545 0.00 0.00 0.00 4.96
91 92 0.623723 TGGAGGAGTAAACATGGGGC 59.376 55.000 0.00 0.00 0.00 5.80
92 93 0.919710 GGAGGAGTAAACATGGGGCT 59.080 55.000 0.00 0.00 0.00 5.19
93 94 2.124411 GGAGGAGTAAACATGGGGCTA 58.876 52.381 0.00 0.00 0.00 3.93
94 95 2.104963 GGAGGAGTAAACATGGGGCTAG 59.895 54.545 0.00 0.00 0.00 3.42
95 96 3.039011 GAGGAGTAAACATGGGGCTAGA 58.961 50.000 0.00 0.00 0.00 2.43
96 97 3.041946 AGGAGTAAACATGGGGCTAGAG 58.958 50.000 0.00 0.00 0.00 2.43
97 98 2.104963 GGAGTAAACATGGGGCTAGAGG 59.895 54.545 0.00 0.00 0.00 3.69
98 99 2.104963 GAGTAAACATGGGGCTAGAGGG 59.895 54.545 0.00 0.00 0.00 4.30
99 100 2.124411 GTAAACATGGGGCTAGAGGGA 58.876 52.381 0.00 0.00 0.00 4.20
100 101 1.681229 AAACATGGGGCTAGAGGGAA 58.319 50.000 0.00 0.00 0.00 3.97
101 102 1.216990 AACATGGGGCTAGAGGGAAG 58.783 55.000 0.00 0.00 0.00 3.46
102 103 0.343372 ACATGGGGCTAGAGGGAAGA 59.657 55.000 0.00 0.00 0.00 2.87
103 104 1.274416 ACATGGGGCTAGAGGGAAGAA 60.274 52.381 0.00 0.00 0.00 2.52
104 105 1.846439 CATGGGGCTAGAGGGAAGAAA 59.154 52.381 0.00 0.00 0.00 2.52
105 106 2.053747 TGGGGCTAGAGGGAAGAAAA 57.946 50.000 0.00 0.00 0.00 2.29
106 107 1.633945 TGGGGCTAGAGGGAAGAAAAC 59.366 52.381 0.00 0.00 0.00 2.43
107 108 1.064611 GGGGCTAGAGGGAAGAAAACC 60.065 57.143 0.00 0.00 0.00 3.27
108 109 1.633945 GGGCTAGAGGGAAGAAAACCA 59.366 52.381 0.00 0.00 0.00 3.67
109 110 2.356227 GGGCTAGAGGGAAGAAAACCAG 60.356 54.545 0.00 0.00 0.00 4.00
110 111 2.356227 GGCTAGAGGGAAGAAAACCAGG 60.356 54.545 0.00 0.00 0.00 4.45
111 112 2.356227 GCTAGAGGGAAGAAAACCAGGG 60.356 54.545 0.00 0.00 0.00 4.45
112 113 1.834540 AGAGGGAAGAAAACCAGGGT 58.165 50.000 0.00 0.00 0.00 4.34
113 114 2.999928 AGAGGGAAGAAAACCAGGGTA 58.000 47.619 0.00 0.00 0.00 3.69
114 115 3.542604 AGAGGGAAGAAAACCAGGGTAT 58.457 45.455 0.00 0.00 0.00 2.73
115 116 3.267031 AGAGGGAAGAAAACCAGGGTATG 59.733 47.826 0.00 0.00 0.00 2.39
146 147 5.838531 AAACAACATGTTCGGTTAAAGGA 57.161 34.783 8.48 0.00 40.14 3.36
180 2947 4.336993 GGTGTGTAGGTTGACAACAATTCA 59.663 41.667 19.58 8.88 38.32 2.57
182 2949 5.914635 GTGTGTAGGTTGACAACAATTCATG 59.085 40.000 19.58 0.00 38.32 3.07
183 2950 4.917415 GTGTAGGTTGACAACAATTCATGC 59.083 41.667 19.58 0.17 38.32 4.06
186 2953 2.030363 GGTTGACAACAATTCATGCGGA 60.030 45.455 19.58 0.00 38.32 5.54
219 2988 6.795144 AATTGATGTGATGGCTGGAAATAA 57.205 33.333 0.00 0.00 0.00 1.40
223 2992 3.088532 TGTGATGGCTGGAAATAACACC 58.911 45.455 0.00 0.00 0.00 4.16
240 3009 2.620115 ACACCTTCACTTGTGCTCAATG 59.380 45.455 0.99 3.64 35.90 2.82
285 3059 8.988064 TGTGTAGAGAATATCTTTTGAGTGTC 57.012 34.615 0.00 0.00 39.64 3.67
291 3065 1.148310 ATCTTTTGAGTGTCGCCGTG 58.852 50.000 0.00 0.00 0.00 4.94
293 3067 0.655733 CTTTTGAGTGTCGCCGTGTT 59.344 50.000 0.00 0.00 0.00 3.32
299 3073 0.531974 AGTGTCGCCGTGTTTGTCAT 60.532 50.000 0.00 0.00 0.00 3.06
306 3080 0.383590 CCGTGTTTGTCATGTGGCAA 59.616 50.000 0.00 0.00 37.94 4.52
307 3081 1.000385 CCGTGTTTGTCATGTGGCAAT 60.000 47.619 0.35 0.00 39.61 3.56
311 3085 2.037381 TGTTTGTCATGTGGCAATGCAT 59.963 40.909 7.79 0.00 39.61 3.96
312 3086 2.371910 TTGTCATGTGGCAATGCATG 57.628 45.000 7.79 9.60 42.62 4.06
314 3088 0.179094 GTCATGTGGCAATGCATGGG 60.179 55.000 7.79 0.00 41.83 4.00
315 3089 1.522806 CATGTGGCAATGCATGGGC 60.523 57.895 20.51 20.51 38.90 5.36
316 3090 1.687840 ATGTGGCAATGCATGGGCT 60.688 52.632 26.42 5.63 41.91 5.19
317 3091 1.268992 ATGTGGCAATGCATGGGCTT 61.269 50.000 26.42 10.29 41.91 4.35
318 3092 1.153509 GTGGCAATGCATGGGCTTC 60.154 57.895 26.42 16.21 41.91 3.86
320 3094 2.105528 GCAATGCATGGGCTTCGG 59.894 61.111 14.52 0.00 41.91 4.30
321 3095 2.809706 CAATGCATGGGCTTCGGG 59.190 61.111 0.00 0.00 41.91 5.14
330 3110 1.767759 TGGGCTTCGGGTAGTACTAC 58.232 55.000 22.53 22.53 35.40 2.73
344 3124 2.498885 AGTACTACCGGTTAAGCTTGGG 59.501 50.000 15.04 7.63 0.00 4.12
345 3125 1.355112 ACTACCGGTTAAGCTTGGGT 58.645 50.000 15.04 13.07 34.81 4.51
346 3126 2.539302 ACTACCGGTTAAGCTTGGGTA 58.461 47.619 15.04 13.49 32.29 3.69
347 3127 2.234661 ACTACCGGTTAAGCTTGGGTAC 59.765 50.000 15.04 1.89 32.29 3.34
395 3179 1.608590 AGAAATGGTTGTTGAGCCGTG 59.391 47.619 0.00 0.00 0.00 4.94
1914 4906 2.027751 GCTAGGATCGACGGTGCC 59.972 66.667 0.00 0.00 0.00 5.01
1915 4907 2.331805 CTAGGATCGACGGTGCCG 59.668 66.667 9.29 9.29 46.03 5.69
1916 4908 3.195591 CTAGGATCGACGGTGCCGG 62.196 68.421 15.44 0.00 44.69 6.13
1919 4911 4.137872 GATCGACGGTGCCGGGAA 62.138 66.667 15.44 0.00 44.69 3.97
1920 4912 3.652539 GATCGACGGTGCCGGGAAA 62.653 63.158 15.44 0.00 44.69 3.13
1921 4913 2.918230 GATCGACGGTGCCGGGAAAT 62.918 60.000 15.44 3.06 44.69 2.17
1922 4914 1.678598 ATCGACGGTGCCGGGAAATA 61.679 55.000 15.44 0.00 44.69 1.40
1923 4915 2.169146 CGACGGTGCCGGGAAATAC 61.169 63.158 15.44 0.00 44.69 1.89
1924 4916 1.078988 GACGGTGCCGGGAAATACA 60.079 57.895 15.44 0.00 44.69 2.29
1925 4917 1.363885 GACGGTGCCGGGAAATACAC 61.364 60.000 15.44 0.55 44.69 2.90
1926 4918 1.078708 CGGTGCCGGGAAATACACT 60.079 57.895 2.18 0.00 35.56 3.55
1927 4919 0.675522 CGGTGCCGGGAAATACACTT 60.676 55.000 2.18 0.00 35.56 3.16
1928 4920 1.541379 GGTGCCGGGAAATACACTTT 58.459 50.000 2.18 0.00 33.53 2.66
1929 4921 1.201414 GGTGCCGGGAAATACACTTTG 59.799 52.381 2.18 0.00 33.53 2.77
1930 4922 1.201414 GTGCCGGGAAATACACTTTGG 59.799 52.381 2.18 0.00 0.00 3.28
1931 4923 1.074084 TGCCGGGAAATACACTTTGGA 59.926 47.619 2.18 0.00 0.00 3.53
1932 4924 2.291282 TGCCGGGAAATACACTTTGGAT 60.291 45.455 2.18 0.00 0.00 3.41
1933 4925 2.099098 GCCGGGAAATACACTTTGGATG 59.901 50.000 2.18 0.00 0.00 3.51
1934 4926 3.352648 CCGGGAAATACACTTTGGATGT 58.647 45.455 0.00 0.00 0.00 3.06
1935 4927 3.761752 CCGGGAAATACACTTTGGATGTT 59.238 43.478 0.00 0.00 0.00 2.71
1936 4928 4.219725 CCGGGAAATACACTTTGGATGTTT 59.780 41.667 0.00 0.00 0.00 2.83
1937 4929 5.160641 CGGGAAATACACTTTGGATGTTTG 58.839 41.667 0.00 0.00 0.00 2.93
1938 4930 4.929211 GGGAAATACACTTTGGATGTTTGC 59.071 41.667 0.00 0.00 0.00 3.68
1939 4931 5.279456 GGGAAATACACTTTGGATGTTTGCT 60.279 40.000 0.00 0.00 0.00 3.91
1940 4932 6.223120 GGAAATACACTTTGGATGTTTGCTT 58.777 36.000 0.00 0.00 0.00 3.91
1941 4933 6.705825 GGAAATACACTTTGGATGTTTGCTTT 59.294 34.615 0.00 0.00 0.00 3.51
1942 4934 7.307337 GGAAATACACTTTGGATGTTTGCTTTG 60.307 37.037 0.00 0.00 0.00 2.77
1946 4938 5.810074 ACACTTTGGATGTTTGCTTTGTAAC 59.190 36.000 0.00 0.00 0.00 2.50
1983 4980 4.402056 TTTCTCAACTCTCGGTGAAGTT 57.598 40.909 0.00 0.00 0.00 2.66
1986 4983 5.723672 TCTCAACTCTCGGTGAAGTTTAT 57.276 39.130 0.00 0.00 0.00 1.40
1987 4984 6.097915 TCTCAACTCTCGGTGAAGTTTATT 57.902 37.500 0.00 0.00 0.00 1.40
2018 5015 2.546368 TCAACTCCAAAATCGGACAACG 59.454 45.455 0.00 0.00 46.11 4.10
2035 5033 1.852633 ACGTACACCCCTAACTACCC 58.147 55.000 0.00 0.00 0.00 3.69
2129 5128 5.468072 CCATGCTCACTCATATTCCTGTAAC 59.532 44.000 0.00 0.00 0.00 2.50
2170 5190 8.134895 TGAACTTTTTGAAATCCACATACACTC 58.865 33.333 0.00 0.00 0.00 3.51
2176 5196 8.408043 TTTGAAATCCACATACACTCTTCAAT 57.592 30.769 0.00 0.00 33.09 2.57
2209 5229 4.657075 TTTTCAAGGTCGCGTATTTCTC 57.343 40.909 5.77 0.00 0.00 2.87
2376 5412 9.434420 TTTTCAAAGTCATGAACTGTTTTTGAT 57.566 25.926 13.47 0.00 38.95 2.57
2388 5424 8.175069 TGAACTGTTTTTGATATTCGCATACTC 58.825 33.333 0.00 0.00 0.00 2.59
2551 5602 4.924305 AGTCCATATCCGCGTACTTTTA 57.076 40.909 4.92 0.00 0.00 1.52
2552 5603 5.266733 AGTCCATATCCGCGTACTTTTAA 57.733 39.130 4.92 0.00 0.00 1.52
2707 5842 8.347729 ACTTGGAAAAAGTACGCAAAATTTAG 57.652 30.769 0.00 0.00 0.00 1.85
2721 5856 7.593644 ACGCAAAATTTAGAAAGGTTCACATAC 59.406 33.333 0.00 0.00 0.00 2.39
2822 5959 2.124109 TGGGACAGCGCCAAAACA 60.124 55.556 2.29 0.00 0.00 2.83
2854 5991 3.690460 GTGACCAGGGATGAATCTTGTT 58.310 45.455 0.00 0.00 0.00 2.83
2855 5992 4.622933 CGTGACCAGGGATGAATCTTGTTA 60.623 45.833 0.00 0.00 0.00 2.41
2859 5996 5.036916 ACCAGGGATGAATCTTGTTAGGTA 58.963 41.667 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.004717 TGTACAAATTCATCCTCGTTAATTTCA 57.995 29.630 0.00 0.00 31.05 2.69
16 17 9.134734 GCCGAAGAAATAAAATGTACAAATTCA 57.865 29.630 0.00 0.00 0.00 2.57
17 18 8.311120 CGCCGAAGAAATAAAATGTACAAATTC 58.689 33.333 0.00 0.00 0.00 2.17
18 19 7.274686 CCGCCGAAGAAATAAAATGTACAAATT 59.725 33.333 0.00 0.33 0.00 1.82
19 20 6.750039 CCGCCGAAGAAATAAAATGTACAAAT 59.250 34.615 0.00 0.00 0.00 2.32
20 21 6.087522 CCGCCGAAGAAATAAAATGTACAAA 58.912 36.000 0.00 0.00 0.00 2.83
21 22 5.632959 CCGCCGAAGAAATAAAATGTACAA 58.367 37.500 0.00 0.00 0.00 2.41
22 23 4.437659 GCCGCCGAAGAAATAAAATGTACA 60.438 41.667 0.00 0.00 0.00 2.90
23 24 4.033019 GCCGCCGAAGAAATAAAATGTAC 58.967 43.478 0.00 0.00 0.00 2.90
24 25 3.065648 GGCCGCCGAAGAAATAAAATGTA 59.934 43.478 0.00 0.00 0.00 2.29
25 26 2.159296 GGCCGCCGAAGAAATAAAATGT 60.159 45.455 0.00 0.00 0.00 2.71
26 27 2.159310 TGGCCGCCGAAGAAATAAAATG 60.159 45.455 4.58 0.00 0.00 2.32
27 28 2.096248 TGGCCGCCGAAGAAATAAAAT 58.904 42.857 4.58 0.00 0.00 1.82
28 29 1.200484 GTGGCCGCCGAAGAAATAAAA 59.800 47.619 4.45 0.00 0.00 1.52
29 30 0.806241 GTGGCCGCCGAAGAAATAAA 59.194 50.000 4.45 0.00 0.00 1.40
30 31 1.363145 CGTGGCCGCCGAAGAAATAA 61.363 55.000 11.56 0.00 0.00 1.40
31 32 1.812093 CGTGGCCGCCGAAGAAATA 60.812 57.895 11.56 0.00 0.00 1.40
32 33 3.124921 CGTGGCCGCCGAAGAAAT 61.125 61.111 11.56 0.00 0.00 2.17
33 34 4.302509 TCGTGGCCGCCGAAGAAA 62.303 61.111 11.56 0.00 0.00 2.52
34 35 4.735132 CTCGTGGCCGCCGAAGAA 62.735 66.667 16.82 0.00 33.34 2.52
36 37 2.622903 TATTCTCGTGGCCGCCGAAG 62.623 60.000 16.82 9.67 33.34 3.79
37 38 2.228389 TTATTCTCGTGGCCGCCGAA 62.228 55.000 16.82 16.14 33.34 4.30
38 39 2.023414 ATTATTCTCGTGGCCGCCGA 62.023 55.000 11.56 13.89 0.00 5.54
39 40 1.157870 AATTATTCTCGTGGCCGCCG 61.158 55.000 11.56 9.72 0.00 6.46
40 41 1.021968 AAATTATTCTCGTGGCCGCC 58.978 50.000 11.56 1.04 0.00 6.13
41 42 2.844122 AAAATTATTCTCGTGGCCGC 57.156 45.000 6.11 6.11 0.00 6.53
58 59 4.285863 ACTCCTCCATCCACAAACAAAAA 58.714 39.130 0.00 0.00 0.00 1.94
59 60 3.909732 ACTCCTCCATCCACAAACAAAA 58.090 40.909 0.00 0.00 0.00 2.44
60 61 3.593442 ACTCCTCCATCCACAAACAAA 57.407 42.857 0.00 0.00 0.00 2.83
61 62 4.715534 TTACTCCTCCATCCACAAACAA 57.284 40.909 0.00 0.00 0.00 2.83
62 63 4.141367 TGTTTACTCCTCCATCCACAAACA 60.141 41.667 0.00 0.00 33.57 2.83
63 64 4.394729 TGTTTACTCCTCCATCCACAAAC 58.605 43.478 0.00 0.00 0.00 2.93
64 65 4.715534 TGTTTACTCCTCCATCCACAAA 57.284 40.909 0.00 0.00 0.00 2.83
65 66 4.567537 CCATGTTTACTCCTCCATCCACAA 60.568 45.833 0.00 0.00 0.00 3.33
66 67 3.054434 CCATGTTTACTCCTCCATCCACA 60.054 47.826 0.00 0.00 0.00 4.17
67 68 3.545703 CCATGTTTACTCCTCCATCCAC 58.454 50.000 0.00 0.00 0.00 4.02
68 69 2.509548 CCCATGTTTACTCCTCCATCCA 59.490 50.000 0.00 0.00 0.00 3.41
69 70 2.158608 CCCCATGTTTACTCCTCCATCC 60.159 54.545 0.00 0.00 0.00 3.51
70 71 2.749800 GCCCCATGTTTACTCCTCCATC 60.750 54.545 0.00 0.00 0.00 3.51
71 72 1.215423 GCCCCATGTTTACTCCTCCAT 59.785 52.381 0.00 0.00 0.00 3.41
72 73 0.623723 GCCCCATGTTTACTCCTCCA 59.376 55.000 0.00 0.00 0.00 3.86
73 74 0.919710 AGCCCCATGTTTACTCCTCC 59.080 55.000 0.00 0.00 0.00 4.30
74 75 3.039011 TCTAGCCCCATGTTTACTCCTC 58.961 50.000 0.00 0.00 0.00 3.71
75 76 3.041946 CTCTAGCCCCATGTTTACTCCT 58.958 50.000 0.00 0.00 0.00 3.69
76 77 2.104963 CCTCTAGCCCCATGTTTACTCC 59.895 54.545 0.00 0.00 0.00 3.85
77 78 2.104963 CCCTCTAGCCCCATGTTTACTC 59.895 54.545 0.00 0.00 0.00 2.59
78 79 2.127708 CCCTCTAGCCCCATGTTTACT 58.872 52.381 0.00 0.00 0.00 2.24
79 80 2.124411 TCCCTCTAGCCCCATGTTTAC 58.876 52.381 0.00 0.00 0.00 2.01
80 81 2.579624 TCCCTCTAGCCCCATGTTTA 57.420 50.000 0.00 0.00 0.00 2.01
81 82 1.566231 CTTCCCTCTAGCCCCATGTTT 59.434 52.381 0.00 0.00 0.00 2.83
82 83 1.216990 CTTCCCTCTAGCCCCATGTT 58.783 55.000 0.00 0.00 0.00 2.71
83 84 0.343372 TCTTCCCTCTAGCCCCATGT 59.657 55.000 0.00 0.00 0.00 3.21
84 85 1.511613 TTCTTCCCTCTAGCCCCATG 58.488 55.000 0.00 0.00 0.00 3.66
85 86 2.242452 GTTTTCTTCCCTCTAGCCCCAT 59.758 50.000 0.00 0.00 0.00 4.00
86 87 1.633945 GTTTTCTTCCCTCTAGCCCCA 59.366 52.381 0.00 0.00 0.00 4.96
87 88 1.064611 GGTTTTCTTCCCTCTAGCCCC 60.065 57.143 0.00 0.00 0.00 5.80
88 89 1.633945 TGGTTTTCTTCCCTCTAGCCC 59.366 52.381 0.00 0.00 0.00 5.19
89 90 2.356227 CCTGGTTTTCTTCCCTCTAGCC 60.356 54.545 0.00 0.00 0.00 3.93
90 91 2.356227 CCCTGGTTTTCTTCCCTCTAGC 60.356 54.545 0.00 0.00 0.00 3.42
91 92 2.913617 ACCCTGGTTTTCTTCCCTCTAG 59.086 50.000 0.00 0.00 0.00 2.43
92 93 2.999928 ACCCTGGTTTTCTTCCCTCTA 58.000 47.619 0.00 0.00 0.00 2.43
93 94 1.834540 ACCCTGGTTTTCTTCCCTCT 58.165 50.000 0.00 0.00 0.00 3.69
94 95 3.621558 CATACCCTGGTTTTCTTCCCTC 58.378 50.000 0.00 0.00 0.00 4.30
95 96 2.311841 CCATACCCTGGTTTTCTTCCCT 59.688 50.000 0.00 0.00 40.49 4.20
96 97 2.623239 CCCATACCCTGGTTTTCTTCCC 60.623 54.545 0.00 0.00 44.30 3.97
97 98 2.623239 CCCCATACCCTGGTTTTCTTCC 60.623 54.545 0.00 0.00 44.30 3.46
98 99 2.623239 CCCCCATACCCTGGTTTTCTTC 60.623 54.545 0.00 0.00 44.30 2.87
99 100 1.361197 CCCCCATACCCTGGTTTTCTT 59.639 52.381 0.00 0.00 44.30 2.52
100 101 1.007607 CCCCCATACCCTGGTTTTCT 58.992 55.000 0.00 0.00 44.30 2.52
101 102 0.708209 ACCCCCATACCCTGGTTTTC 59.292 55.000 0.00 0.00 44.30 2.29
102 103 1.172508 AACCCCCATACCCTGGTTTT 58.827 50.000 0.00 0.00 44.30 2.43
103 104 0.411848 CAACCCCCATACCCTGGTTT 59.588 55.000 0.00 0.00 44.30 3.27
104 105 0.478789 TCAACCCCCATACCCTGGTT 60.479 55.000 0.00 0.00 44.30 3.67
105 106 0.478789 TTCAACCCCCATACCCTGGT 60.479 55.000 0.00 0.00 44.30 4.00
106 107 0.707616 TTTCAACCCCCATACCCTGG 59.292 55.000 0.00 0.00 45.51 4.45
107 108 2.176045 GTTTTCAACCCCCATACCCTG 58.824 52.381 0.00 0.00 0.00 4.45
108 109 1.790157 TGTTTTCAACCCCCATACCCT 59.210 47.619 0.00 0.00 0.00 4.34
109 110 2.312424 TGTTTTCAACCCCCATACCC 57.688 50.000 0.00 0.00 0.00 3.69
120 121 6.531948 CCTTTAACCGAACATGTTGTTTTCAA 59.468 34.615 17.58 3.90 41.28 2.69
121 122 6.037098 CCTTTAACCGAACATGTTGTTTTCA 58.963 36.000 17.58 0.00 41.28 2.69
122 123 6.267070 TCCTTTAACCGAACATGTTGTTTTC 58.733 36.000 17.58 0.00 41.28 2.29
141 142 4.086457 ACACACCACAGTTTTCTTCCTTT 58.914 39.130 0.00 0.00 0.00 3.11
146 147 4.230745 ACCTACACACCACAGTTTTCTT 57.769 40.909 0.00 0.00 0.00 2.52
180 2947 3.955471 TCAATTTTCTTCCTCTCCGCAT 58.045 40.909 0.00 0.00 0.00 4.73
182 2949 3.691609 ACATCAATTTTCTTCCTCTCCGC 59.308 43.478 0.00 0.00 0.00 5.54
183 2950 4.937620 TCACATCAATTTTCTTCCTCTCCG 59.062 41.667 0.00 0.00 0.00 4.63
186 2953 5.126707 GCCATCACATCAATTTTCTTCCTCT 59.873 40.000 0.00 0.00 0.00 3.69
219 2988 2.418368 TTGAGCACAAGTGAAGGTGT 57.582 45.000 4.04 0.00 37.35 4.16
223 2992 3.976793 ACACATTGAGCACAAGTGAAG 57.023 42.857 22.75 13.00 39.46 3.02
240 3009 4.267452 CACAAACACAAAAGGCACATACAC 59.733 41.667 0.00 0.00 0.00 2.90
285 3059 1.082169 CCACATGACAAACACGGCG 60.082 57.895 4.80 4.80 0.00 6.46
291 3065 2.151881 TGCATTGCCACATGACAAAC 57.848 45.000 6.12 0.00 0.00 2.93
293 3067 1.066787 CCATGCATTGCCACATGACAA 60.067 47.619 6.12 1.03 45.23 3.18
299 3073 1.890625 GAAGCCCATGCATTGCCACA 61.891 55.000 13.06 0.00 41.13 4.17
306 3080 1.149174 CTACCCGAAGCCCATGCAT 59.851 57.895 0.00 0.00 41.13 3.96
307 3081 0.978667 TACTACCCGAAGCCCATGCA 60.979 55.000 0.00 0.00 41.13 3.96
311 3085 1.767759 GTAGTACTACCCGAAGCCCA 58.232 55.000 20.47 0.00 0.00 5.36
321 3095 4.440663 CCCAAGCTTAACCGGTAGTACTAC 60.441 50.000 22.53 22.53 35.40 2.73
330 3110 1.445871 GTGTACCCAAGCTTAACCGG 58.554 55.000 0.00 0.00 0.00 5.28
344 3124 2.349297 AGCTAGCTTGTGTCGTGTAC 57.651 50.000 12.68 0.00 0.00 2.90
345 3125 3.340928 TCTAGCTAGCTTGTGTCGTGTA 58.659 45.455 24.88 0.00 0.00 2.90
346 3126 2.160205 TCTAGCTAGCTTGTGTCGTGT 58.840 47.619 24.88 0.00 0.00 4.49
347 3127 2.921634 TCTAGCTAGCTTGTGTCGTG 57.078 50.000 24.88 3.77 0.00 4.35
418 3202 1.153745 CGACAAGGAAGGCGAGGAG 60.154 63.158 0.00 0.00 0.00 3.69
902 3716 2.202570 CCGCGTTGGAGTAGACGG 60.203 66.667 4.92 0.00 42.00 4.79
1799 4791 2.233654 CCGTACAGCTCGCTCATGC 61.234 63.158 0.00 0.00 0.00 4.06
1871 4863 1.200716 CAACGCCATCCATATCCATGC 59.799 52.381 0.00 0.00 0.00 4.06
1914 4906 5.160641 CAAACATCCAAAGTGTATTTCCCG 58.839 41.667 0.00 0.00 0.00 5.14
1915 4907 4.929211 GCAAACATCCAAAGTGTATTTCCC 59.071 41.667 0.00 0.00 0.00 3.97
1916 4908 5.783111 AGCAAACATCCAAAGTGTATTTCC 58.217 37.500 0.00 0.00 0.00 3.13
1917 4909 7.224557 ACAAAGCAAACATCCAAAGTGTATTTC 59.775 33.333 0.00 0.00 0.00 2.17
1918 4910 7.047271 ACAAAGCAAACATCCAAAGTGTATTT 58.953 30.769 0.00 0.00 0.00 1.40
1919 4911 6.581712 ACAAAGCAAACATCCAAAGTGTATT 58.418 32.000 0.00 0.00 0.00 1.89
1920 4912 6.160576 ACAAAGCAAACATCCAAAGTGTAT 57.839 33.333 0.00 0.00 0.00 2.29
1921 4913 5.590530 ACAAAGCAAACATCCAAAGTGTA 57.409 34.783 0.00 0.00 0.00 2.90
1922 4914 4.470334 ACAAAGCAAACATCCAAAGTGT 57.530 36.364 0.00 0.00 0.00 3.55
1923 4915 5.809562 TGTTACAAAGCAAACATCCAAAGTG 59.190 36.000 0.00 0.00 30.88 3.16
1924 4916 5.971763 TGTTACAAAGCAAACATCCAAAGT 58.028 33.333 0.00 0.00 30.88 2.66
1925 4917 6.272318 TCTGTTACAAAGCAAACATCCAAAG 58.728 36.000 0.00 0.00 35.21 2.77
1926 4918 6.096141 TCTCTGTTACAAAGCAAACATCCAAA 59.904 34.615 0.00 0.00 35.21 3.28
1927 4919 5.592282 TCTCTGTTACAAAGCAAACATCCAA 59.408 36.000 0.00 0.00 35.21 3.53
1928 4920 5.129634 TCTCTGTTACAAAGCAAACATCCA 58.870 37.500 0.00 0.00 35.21 3.41
1929 4921 5.689383 TCTCTGTTACAAAGCAAACATCC 57.311 39.130 0.00 0.00 35.21 3.51
1930 4922 7.702348 ACTTTTCTCTGTTACAAAGCAAACATC 59.298 33.333 0.00 0.00 35.21 3.06
1931 4923 7.547227 ACTTTTCTCTGTTACAAAGCAAACAT 58.453 30.769 0.00 0.00 35.21 2.71
1932 4924 6.919721 ACTTTTCTCTGTTACAAAGCAAACA 58.080 32.000 0.00 0.00 34.57 2.83
1933 4925 7.812309 AACTTTTCTCTGTTACAAAGCAAAC 57.188 32.000 0.00 0.00 30.63 2.93
1934 4926 8.825667 AAAACTTTTCTCTGTTACAAAGCAAA 57.174 26.923 0.00 0.00 30.63 3.68
1935 4927 8.825667 AAAAACTTTTCTCTGTTACAAAGCAA 57.174 26.923 0.00 0.00 30.63 3.91
1961 4958 4.402056 ACTTCACCGAGAGTTGAGAAAA 57.598 40.909 0.00 0.00 0.00 2.29
1983 4980 5.068215 TGGAGTTGAGGGACCAAAAATAA 57.932 39.130 0.00 0.00 0.00 1.40
1986 4983 3.390175 TTGGAGTTGAGGGACCAAAAA 57.610 42.857 0.00 0.00 39.07 1.94
1987 4984 3.390175 TTTGGAGTTGAGGGACCAAAA 57.610 42.857 0.00 0.00 45.35 2.44
2018 5015 3.584406 AGTTTGGGTAGTTAGGGGTGTAC 59.416 47.826 0.00 0.00 0.00 2.90
2035 5033 2.558359 GGGATGAACCTTGTCCAGTTTG 59.442 50.000 0.00 0.00 38.98 2.93
2209 5229 9.340695 TCGCTGATTTGAGTATGTTTATTTTTG 57.659 29.630 0.00 0.00 0.00 2.44
2359 5393 6.907741 TGCGAATATCAAAAACAGTTCATGA 58.092 32.000 0.00 0.00 0.00 3.07
2376 5412 7.281999 TGTGGATTTGAAATGAGTATGCGAATA 59.718 33.333 0.00 0.00 0.00 1.75
2388 5424 6.788684 TGAAAAGCATGTGGATTTGAAATG 57.211 33.333 0.00 0.00 34.82 2.32
2466 5507 8.024285 TCAACTTGAAACAAGTACGTGAATTTT 58.976 29.630 16.00 5.75 0.00 1.82
2552 5603 9.862585 GAATTTCAAAATTTTATGCGAACTTGT 57.137 25.926 2.44 0.00 38.64 3.16
2814 5951 1.134936 ACGGTTTTGACCTGTTTTGGC 60.135 47.619 0.00 0.00 0.00 4.52
2854 5991 5.027460 TGCACCCTTAACTTCTGATACCTA 58.973 41.667 0.00 0.00 0.00 3.08
2855 5992 3.844211 TGCACCCTTAACTTCTGATACCT 59.156 43.478 0.00 0.00 0.00 3.08
2859 5996 4.373156 ACTTGCACCCTTAACTTCTGAT 57.627 40.909 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.