Multiple sequence alignment - TraesCS5B01G516200

Loading Multiple Alignment...

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 TraesCS5B01G516200 chr5B 100.000 3050 0 0 1 3050 680579331 680582380 0.000000e+00 5633.0
1 TraesCS5B01G516200 chr5B 80.440 455 71 14 1196 1643 491994863 491994420 6.300000e-87 331.0
2 TraesCS5B01G516200 chr4A 92.314 2368 90 36 162 2481 629488191 629485868 0.000000e+00 3280.0
3 TraesCS5B01G516200 chr4A 89.803 559 39 11 2508 3050 629485774 629485218 0.000000e+00 701.0
4 TraesCS5B01G516200 chr4A 91.743 109 3 2 1 109 657316818 657316716 2.450000e-31 147.0
5 TraesCS5B01G516200 chr5D 91.212 2401 74 30 149 2478 539013469 539015803 0.000000e+00 3138.0
6 TraesCS5B01G516200 chr5D 89.825 570 35 14 2496 3050 539015889 539016450 0.000000e+00 710.0
7 TraesCS5B01G516200 chr5D 79.955 449 69 16 1196 1643 410241859 410241431 8.210000e-81 311.0
8 TraesCS5B01G516200 chr2D 93.450 458 16 7 995 1450 520537212 520536767 0.000000e+00 667.0
9 TraesCS5B01G516200 chr4B 88.604 351 34 5 2703 3050 584072887 584073234 3.640000e-114 422.0
10 TraesCS5B01G516200 chr4B 91.743 109 3 3 1 109 374366288 374366186 2.450000e-31 147.0
11 TraesCS5B01G516200 chr5A 81.500 400 57 13 1196 1588 521744636 521744247 2.280000e-81 313.0
12 TraesCS5B01G516200 chr1B 88.360 189 21 1 1457 1644 460487613 460487425 3.060000e-55 226.0
13 TraesCS5B01G516200 chr1B 91.743 109 3 2 1 109 274463536 274463638 2.450000e-31 147.0
14 TraesCS5B01G516200 chr1B 94.737 38 1 1 101 138 133242929 133242965 1.180000e-04 58.4
15 TraesCS5B01G516200 chr3B 93.578 109 5 2 1 109 253793932 253794038 8.750000e-36 161.0
16 TraesCS5B01G516200 chr3B 93.269 104 2 1 1 104 617861301 617861399 6.810000e-32 148.0
17 TraesCS5B01G516200 chr7B 93.269 104 2 1 1 104 109057968 109058066 6.810000e-32 148.0
18 TraesCS5B01G516200 chr6B 93.269 104 2 1 1 104 639482500 639482402 6.810000e-32 148.0
19 TraesCS5B01G516200 chr2B 93.269 104 2 2 1 104 498922855 498922757 6.810000e-32 148.0
20 TraesCS5B01G516200 chr2B 90.826 109 4 2 1 109 449722083 449722185 1.140000e-29 141.0
21 TraesCS5B01G516200 chr2B 94.444 36 1 1 101 136 719555778 719555812 2.000000e-03 54.7
22 TraesCS5B01G516200 chr1A 92.105 38 2 1 101 137 338611375 338611412 5.000000e-03 52.8


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 TraesCS5B01G516200 chr5B 680579331 680582380 3049 False 5633.0 5633 100.0000 1 3050 1 chr5B.!!$F1 3049
1 TraesCS5B01G516200 chr4A 629485218 629488191 2973 True 1990.5 3280 91.0585 162 3050 2 chr4A.!!$R2 2888
2 TraesCS5B01G516200 chr5D 539013469 539016450 2981 False 1924.0 3138 90.5185 149 3050 2 chr5D.!!$F1 2901

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
51 52 0.108567 GACTTGAGCGAAGACCTCCC 60.109 60.0 5.62 0.0 35.42 4.30 F
460 481 0.179153 GCCTTTTCATTCCAGCGAGC 60.179 55.0 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1873 1.817099 GGCGAGGTTGATGAGCTGG 60.817 63.158 0.0 0.0 35.91 4.85 R
2285 2367 3.432782 GAAATCATCGGCAAAGCTCAAG 58.567 45.455 0.0 0.0 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
22 23 5.551760 GATGAGTTTGTGATGGGTACTTG 57.448 43.478 0.00 0.00 0.00 3.16
23 24 3.750371 TGAGTTTGTGATGGGTACTTGG 58.250 45.455 0.00 0.00 0.00 3.61
24 25 3.137544 TGAGTTTGTGATGGGTACTTGGT 59.862 43.478 0.00 0.00 0.00 3.67
25 26 4.348461 TGAGTTTGTGATGGGTACTTGGTA 59.652 41.667 0.00 0.00 0.00 3.25
26 27 5.013704 TGAGTTTGTGATGGGTACTTGGTAT 59.986 40.000 0.00 0.00 0.00 2.73
27 28 5.253330 AGTTTGTGATGGGTACTTGGTATG 58.747 41.667 0.00 0.00 0.00 2.39
28 29 4.919774 TTGTGATGGGTACTTGGTATGT 57.080 40.909 0.00 0.00 0.00 2.29
29 30 4.481368 TGTGATGGGTACTTGGTATGTC 57.519 45.455 0.00 0.00 0.00 3.06
30 31 4.101114 TGTGATGGGTACTTGGTATGTCT 58.899 43.478 0.00 0.00 0.00 3.41
31 32 4.534500 TGTGATGGGTACTTGGTATGTCTT 59.466 41.667 0.00 0.00 0.00 3.01
32 33 4.876107 GTGATGGGTACTTGGTATGTCTTG 59.124 45.833 0.00 0.00 0.00 3.02
33 34 4.780554 TGATGGGTACTTGGTATGTCTTGA 59.219 41.667 0.00 0.00 0.00 3.02
34 35 4.546829 TGGGTACTTGGTATGTCTTGAC 57.453 45.455 0.00 0.00 0.00 3.18
35 36 4.164981 TGGGTACTTGGTATGTCTTGACT 58.835 43.478 2.35 0.00 0.00 3.41
36 37 4.595781 TGGGTACTTGGTATGTCTTGACTT 59.404 41.667 2.35 0.00 0.00 3.01
37 38 4.935808 GGGTACTTGGTATGTCTTGACTTG 59.064 45.833 2.35 0.00 0.00 3.16
38 39 5.279809 GGGTACTTGGTATGTCTTGACTTGA 60.280 44.000 2.35 0.00 0.00 3.02
39 40 5.869888 GGTACTTGGTATGTCTTGACTTGAG 59.130 44.000 2.35 0.00 0.00 3.02
40 41 4.319177 ACTTGGTATGTCTTGACTTGAGC 58.681 43.478 2.35 0.00 0.00 4.26
41 42 2.959516 TGGTATGTCTTGACTTGAGCG 58.040 47.619 2.35 0.00 0.00 5.03
42 43 2.560981 TGGTATGTCTTGACTTGAGCGA 59.439 45.455 2.35 0.00 0.00 4.93
43 44 3.006430 TGGTATGTCTTGACTTGAGCGAA 59.994 43.478 2.35 0.00 0.00 4.70
44 45 3.614616 GGTATGTCTTGACTTGAGCGAAG 59.385 47.826 2.35 0.00 37.73 3.79
45 46 3.667497 ATGTCTTGACTTGAGCGAAGA 57.333 42.857 5.62 0.00 35.42 2.87
46 47 2.743938 TGTCTTGACTTGAGCGAAGAC 58.256 47.619 12.47 12.47 43.05 3.01
47 48 2.062519 GTCTTGACTTGAGCGAAGACC 58.937 52.381 5.62 0.00 38.83 3.85
48 49 1.964223 TCTTGACTTGAGCGAAGACCT 59.036 47.619 5.62 0.00 35.42 3.85
49 50 2.029828 TCTTGACTTGAGCGAAGACCTC 60.030 50.000 5.62 0.00 35.42 3.85
50 51 0.603569 TGACTTGAGCGAAGACCTCC 59.396 55.000 5.62 0.00 35.42 4.30
51 52 0.108567 GACTTGAGCGAAGACCTCCC 60.109 60.000 5.62 0.00 35.42 4.30
52 53 1.153745 CTTGAGCGAAGACCTCCCG 60.154 63.158 0.00 0.00 32.82 5.14
56 57 4.516195 GCGAAGACCTCCCGCTCC 62.516 72.222 0.00 0.00 44.83 4.70
57 58 3.839432 CGAAGACCTCCCGCTCCC 61.839 72.222 0.00 0.00 0.00 4.30
58 59 3.839432 GAAGACCTCCCGCTCCCG 61.839 72.222 0.00 0.00 0.00 5.14
76 77 4.745549 GCAACGACGCCAGAAATC 57.254 55.556 0.00 0.00 0.00 2.17
77 78 1.134694 GCAACGACGCCAGAAATCC 59.865 57.895 0.00 0.00 0.00 3.01
78 79 1.298859 GCAACGACGCCAGAAATCCT 61.299 55.000 0.00 0.00 0.00 3.24
79 80 1.156736 CAACGACGCCAGAAATCCTT 58.843 50.000 0.00 0.00 0.00 3.36
80 81 1.128692 CAACGACGCCAGAAATCCTTC 59.871 52.381 0.00 0.00 0.00 3.46
81 82 0.608640 ACGACGCCAGAAATCCTTCT 59.391 50.000 0.00 0.00 42.96 2.85
82 83 1.002087 ACGACGCCAGAAATCCTTCTT 59.998 47.619 0.00 0.00 40.05 2.52
83 84 1.394917 CGACGCCAGAAATCCTTCTTG 59.605 52.381 0.00 0.00 40.05 3.02
84 85 2.699954 GACGCCAGAAATCCTTCTTGA 58.300 47.619 0.00 0.00 40.05 3.02
85 86 3.274288 GACGCCAGAAATCCTTCTTGAT 58.726 45.455 0.00 0.00 40.05 2.57
86 87 4.442706 GACGCCAGAAATCCTTCTTGATA 58.557 43.478 0.00 0.00 40.05 2.15
87 88 4.192317 ACGCCAGAAATCCTTCTTGATAC 58.808 43.478 0.00 0.00 40.05 2.24
88 89 4.191544 CGCCAGAAATCCTTCTTGATACA 58.808 43.478 0.00 0.00 40.05 2.29
89 90 4.818546 CGCCAGAAATCCTTCTTGATACAT 59.181 41.667 0.00 0.00 40.05 2.29
90 91 5.049818 CGCCAGAAATCCTTCTTGATACATC 60.050 44.000 0.00 0.00 40.05 3.06
91 92 6.060788 GCCAGAAATCCTTCTTGATACATCT 58.939 40.000 0.00 0.00 40.05 2.90
92 93 6.545298 GCCAGAAATCCTTCTTGATACATCTT 59.455 38.462 0.00 0.00 40.05 2.40
93 94 7.716998 GCCAGAAATCCTTCTTGATACATCTTA 59.283 37.037 0.00 0.00 40.05 2.10
94 95 9.618890 CCAGAAATCCTTCTTGATACATCTTAA 57.381 33.333 0.00 0.00 40.05 1.85
96 97 9.336171 AGAAATCCTTCTTGATACATCTTAAGC 57.664 33.333 0.00 0.00 38.89 3.09
97 98 9.336171 GAAATCCTTCTTGATACATCTTAAGCT 57.664 33.333 0.00 0.00 0.00 3.74
98 99 9.692325 AAATCCTTCTTGATACATCTTAAGCTT 57.308 29.630 3.48 3.48 0.00 3.74
99 100 8.674263 ATCCTTCTTGATACATCTTAAGCTTG 57.326 34.615 9.86 0.00 0.00 4.01
100 101 6.540189 TCCTTCTTGATACATCTTAAGCTTGC 59.460 38.462 9.86 0.00 0.00 4.01
101 102 5.973651 TCTTGATACATCTTAAGCTTGCG 57.026 39.130 9.86 0.00 0.00 4.85
102 103 5.419542 TCTTGATACATCTTAAGCTTGCGT 58.580 37.500 9.86 1.42 0.00 5.24
103 104 5.874810 TCTTGATACATCTTAAGCTTGCGTT 59.125 36.000 9.86 0.00 0.00 4.84
104 105 7.039270 TCTTGATACATCTTAAGCTTGCGTTA 58.961 34.615 9.86 0.00 0.00 3.18
105 106 7.547722 TCTTGATACATCTTAAGCTTGCGTTAA 59.452 33.333 9.86 0.00 0.00 2.01
106 107 7.234187 TGATACATCTTAAGCTTGCGTTAAG 57.766 36.000 9.86 4.30 38.38 1.85
107 108 6.816640 TGATACATCTTAAGCTTGCGTTAAGT 59.183 34.615 9.86 1.89 38.25 2.24
108 109 5.941948 ACATCTTAAGCTTGCGTTAAGTT 57.058 34.783 9.86 0.00 38.25 2.66
109 110 8.712285 ATACATCTTAAGCTTGCGTTAAGTTA 57.288 30.769 9.86 0.00 38.25 2.24
110 111 7.611213 ACATCTTAAGCTTGCGTTAAGTTAT 57.389 32.000 9.86 0.00 38.25 1.89
111 112 8.712285 ACATCTTAAGCTTGCGTTAAGTTATA 57.288 30.769 9.86 0.00 38.25 0.98
112 113 9.158233 ACATCTTAAGCTTGCGTTAAGTTATAA 57.842 29.630 9.86 0.00 38.25 0.98
113 114 9.982291 CATCTTAAGCTTGCGTTAAGTTATAAA 57.018 29.630 9.86 0.00 38.25 1.40
115 116 8.173130 TCTTAAGCTTGCGTTAAGTTATAAAGC 58.827 33.333 9.86 9.58 38.25 3.51
117 118 6.496338 AGCTTGCGTTAAGTTATAAAGCTT 57.504 33.333 12.51 0.00 44.73 3.74
118 119 6.909909 AGCTTGCGTTAAGTTATAAAGCTTT 58.090 32.000 17.30 17.30 44.73 3.51
119 120 6.801862 AGCTTGCGTTAAGTTATAAAGCTTTG 59.198 34.615 22.02 1.80 44.73 2.77
120 121 6.452480 GCTTGCGTTAAGTTATAAAGCTTTGC 60.452 38.462 22.02 12.23 38.70 3.68
121 122 6.249035 TGCGTTAAGTTATAAAGCTTTGCT 57.751 33.333 22.02 11.18 42.56 3.91
138 139 6.650807 AGCTTTGCTTTTCCTTAATAAAAGGC 59.349 34.615 17.94 13.66 41.91 4.35
139 140 6.426633 GCTTTGCTTTTCCTTAATAAAAGGCA 59.573 34.615 17.94 15.37 41.91 4.75
140 141 7.041440 GCTTTGCTTTTCCTTAATAAAAGGCAA 60.041 33.333 19.43 19.43 41.91 4.52
141 142 8.738645 TTTGCTTTTCCTTAATAAAAGGCAAA 57.261 26.923 24.90 24.90 41.91 3.68
142 143 7.722795 TGCTTTTCCTTAATAAAAGGCAAAC 57.277 32.000 17.94 7.48 41.91 2.93
143 144 7.275920 TGCTTTTCCTTAATAAAAGGCAAACA 58.724 30.769 17.94 9.15 41.91 2.83
144 145 7.770897 TGCTTTTCCTTAATAAAAGGCAAACAA 59.229 29.630 17.94 0.48 41.91 2.83
145 146 8.067784 GCTTTTCCTTAATAAAAGGCAAACAAC 58.932 33.333 17.94 3.33 41.91 3.32
146 147 9.325198 CTTTTCCTTAATAAAAGGCAAACAACT 57.675 29.630 12.27 0.00 39.29 3.16
147 148 8.655651 TTTCCTTAATAAAAGGCAAACAACTG 57.344 30.769 0.00 0.00 37.34 3.16
153 154 6.655078 ATAAAAGGCAAACAACTGACTGAT 57.345 33.333 0.00 0.00 33.83 2.90
172 173 4.200874 TGATGTTCGCCCCGTATAATTTT 58.799 39.130 0.00 0.00 0.00 1.82
173 174 4.641094 TGATGTTCGCCCCGTATAATTTTT 59.359 37.500 0.00 0.00 0.00 1.94
181 182 6.095720 TCGCCCCGTATAATTTTTGAGAAAAT 59.904 34.615 0.00 0.00 45.06 1.82
196 197 9.607988 TTTTGAGAAAATAAAGAAAAACTCCCC 57.392 29.630 0.00 0.00 0.00 4.81
197 198 7.297936 TGAGAAAATAAAGAAAAACTCCCCC 57.702 36.000 0.00 0.00 0.00 5.40
198 199 6.841755 TGAGAAAATAAAGAAAAACTCCCCCA 59.158 34.615 0.00 0.00 0.00 4.96
199 200 7.512402 TGAGAAAATAAAGAAAAACTCCCCCAT 59.488 33.333 0.00 0.00 0.00 4.00
200 201 7.907389 AGAAAATAAAGAAAAACTCCCCCATC 58.093 34.615 0.00 0.00 0.00 3.51
201 202 5.914898 AATAAAGAAAAACTCCCCCATCG 57.085 39.130 0.00 0.00 0.00 3.84
202 203 1.545841 AAGAAAAACTCCCCCATCGC 58.454 50.000 0.00 0.00 0.00 4.58
460 481 0.179153 GCCTTTTCATTCCAGCGAGC 60.179 55.000 0.00 0.00 0.00 5.03
552 579 2.090999 GCCCCCATTAAACCCTAATCCA 60.091 50.000 0.00 0.00 0.00 3.41
555 582 4.326610 CCCCCATTAAACCCTAATCCAACT 60.327 45.833 0.00 0.00 0.00 3.16
589 616 1.574134 ATCACGCGTTAATTACCCCG 58.426 50.000 10.22 0.00 0.00 5.73
600 627 5.220643 CGTTAATTACCCCGTTTTATTCGCT 60.221 40.000 0.00 0.00 0.00 4.93
611 638 4.201685 CGTTTTATTCGCTCGGATTTGACT 60.202 41.667 0.00 0.00 0.00 3.41
662 689 3.897122 TGGGGCCAGCGGTTTCTT 61.897 61.111 4.39 0.00 0.00 2.52
663 690 2.600470 GGGGCCAGCGGTTTCTTT 60.600 61.111 4.39 0.00 0.00 2.52
664 691 2.650778 GGGCCAGCGGTTTCTTTG 59.349 61.111 4.39 0.00 0.00 2.77
665 692 2.650778 GGCCAGCGGTTTCTTTGG 59.349 61.111 0.00 0.00 0.00 3.28
666 693 1.901464 GGCCAGCGGTTTCTTTGGA 60.901 57.895 0.00 0.00 32.34 3.53
667 694 1.285950 GCCAGCGGTTTCTTTGGAC 59.714 57.895 0.00 0.00 32.34 4.02
668 695 1.172812 GCCAGCGGTTTCTTTGGACT 61.173 55.000 0.00 0.00 32.34 3.85
1014 1081 3.917760 CGGATGGAGTCGGAGGGC 61.918 72.222 0.00 0.00 0.00 5.19
1022 1089 3.083997 GTCGGAGGGCCAGGACAT 61.084 66.667 6.18 0.00 0.00 3.06
1157 1224 3.787001 GGTGGAGCTCTTCGGGGG 61.787 72.222 14.64 0.00 0.00 5.40
1435 1502 4.019513 TCCGGATCCCCACCCAGT 62.020 66.667 6.06 0.00 0.00 4.00
1436 1503 3.480133 CCGGATCCCCACCCAGTC 61.480 72.222 6.06 0.00 0.00 3.51
1437 1504 3.480133 CGGATCCCCACCCAGTCC 61.480 72.222 6.06 0.00 0.00 3.85
1438 1505 2.042930 GGATCCCCACCCAGTCCT 59.957 66.667 0.00 0.00 0.00 3.85
1439 1506 2.073101 GGATCCCCACCCAGTCCTC 61.073 68.421 0.00 0.00 0.00 3.71
1440 1507 2.042930 ATCCCCACCCAGTCCTCC 59.957 66.667 0.00 0.00 0.00 4.30
1441 1508 2.553438 GATCCCCACCCAGTCCTCCT 62.553 65.000 0.00 0.00 0.00 3.69
1442 1509 2.553438 ATCCCCACCCAGTCCTCCTC 62.553 65.000 0.00 0.00 0.00 3.71
1443 1510 2.689034 CCCACCCAGTCCTCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
1857 1933 1.227853 AGCTGTGTTCCCCAACGTC 60.228 57.895 0.00 0.00 34.95 4.34
2091 2173 3.349006 CACTCCACTGCACGCACC 61.349 66.667 0.00 0.00 0.00 5.01
2092 2174 3.550431 ACTCCACTGCACGCACCT 61.550 61.111 0.00 0.00 0.00 4.00
2195 2277 2.270858 TGATACCACTGTTGCCCCTAA 58.729 47.619 0.00 0.00 0.00 2.69
2196 2278 2.849943 TGATACCACTGTTGCCCCTAAT 59.150 45.455 0.00 0.00 0.00 1.73
2285 2367 5.578776 AGAACACGAAACATGGAGAAAAAC 58.421 37.500 0.00 0.00 0.00 2.43
2296 2378 4.045636 TGGAGAAAAACTTGAGCTTTGC 57.954 40.909 0.00 0.00 0.00 3.68
2297 2379 3.181476 TGGAGAAAAACTTGAGCTTTGCC 60.181 43.478 0.00 0.00 0.00 4.52
2362 2444 5.391577 ACTTTTGGTTGGTTCCCTAACTA 57.608 39.130 0.00 0.00 35.81 2.24
2438 2531 5.351740 GGTGCTACATTCTGTTAACTCTTCC 59.648 44.000 7.22 0.00 0.00 3.46
2484 2577 9.890352 GAAGGAAATTGATCTTCATAATACTGC 57.110 33.333 9.45 0.00 37.44 4.40
2579 2752 6.927294 AACAAGTTCTGAAGTAACTTCCTG 57.073 37.500 3.11 0.00 43.52 3.86
2629 2802 2.422597 TCCACTATTTTCACAGCCACG 58.577 47.619 0.00 0.00 0.00 4.94
2644 2817 1.464997 GCCACGCCAGAACTCTTTAAG 59.535 52.381 0.00 0.00 0.00 1.85
2658 2831 6.473397 ACTCTTTAAGTCTTCATGCTTTCG 57.527 37.500 0.00 0.00 30.02 3.46
2660 2833 6.146347 ACTCTTTAAGTCTTCATGCTTTCGTC 59.854 38.462 0.00 0.00 30.02 4.20
2690 2863 5.992217 ACAAAGTCAGTTTTCTGCTACTAGG 59.008 40.000 0.00 0.00 46.59 3.02
2769 2942 3.129287 CAGGAATTTACAGTGCCATGACC 59.871 47.826 0.00 0.00 0.00 4.02
2774 2947 6.127479 GGAATTTACAGTGCCATGACCAAATA 60.127 38.462 0.00 0.00 0.00 1.40
2780 2953 4.403432 CAGTGCCATGACCAAATATTTCCT 59.597 41.667 0.00 0.00 0.00 3.36
2781 2954 5.593909 CAGTGCCATGACCAAATATTTCCTA 59.406 40.000 0.00 0.00 0.00 2.94
2815 2989 5.016831 TCTCATCTTGTTGCTACAGTCCTA 58.983 41.667 0.37 0.00 35.28 2.94
2816 2990 5.073311 TCATCTTGTTGCTACAGTCCTAC 57.927 43.478 0.37 0.00 35.28 3.18
2817 2991 4.526650 TCATCTTGTTGCTACAGTCCTACA 59.473 41.667 0.37 0.00 35.28 2.74
2818 2992 4.948341 TCTTGTTGCTACAGTCCTACAA 57.052 40.909 0.37 0.00 35.28 2.41
2821 2995 5.246203 TCTTGTTGCTACAGTCCTACAATCT 59.754 40.000 0.37 0.00 35.28 2.40
2822 2996 4.820897 TGTTGCTACAGTCCTACAATCTG 58.179 43.478 0.00 0.00 35.60 2.90
2823 2997 3.526931 TGCTACAGTCCTACAATCTGC 57.473 47.619 0.00 0.00 33.12 4.26
2825 2999 3.260632 TGCTACAGTCCTACAATCTGCAA 59.739 43.478 0.00 0.00 33.12 4.08
2826 3000 4.253685 GCTACAGTCCTACAATCTGCAAA 58.746 43.478 0.00 0.00 33.12 3.68
2827 3001 4.878397 GCTACAGTCCTACAATCTGCAAAT 59.122 41.667 0.00 0.00 33.12 2.32
2828 3002 5.220739 GCTACAGTCCTACAATCTGCAAATG 60.221 44.000 0.00 0.00 33.12 2.32
2830 3004 4.940046 ACAGTCCTACAATCTGCAAATGAG 59.060 41.667 0.00 0.00 33.12 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.396166 CCAAGTACCCATCACAAACTCATC 59.604 45.833 0.00 0.00 0.00 2.92
1 2 4.202567 ACCAAGTACCCATCACAAACTCAT 60.203 41.667 0.00 0.00 0.00 2.90
2 3 3.137544 ACCAAGTACCCATCACAAACTCA 59.862 43.478 0.00 0.00 0.00 3.41
3 4 3.751518 ACCAAGTACCCATCACAAACTC 58.248 45.455 0.00 0.00 0.00 3.01
4 5 3.876309 ACCAAGTACCCATCACAAACT 57.124 42.857 0.00 0.00 0.00 2.66
5 6 5.007682 ACATACCAAGTACCCATCACAAAC 58.992 41.667 0.00 0.00 0.00 2.93
6 7 5.013704 AGACATACCAAGTACCCATCACAAA 59.986 40.000 0.00 0.00 0.00 2.83
7 8 4.534500 AGACATACCAAGTACCCATCACAA 59.466 41.667 0.00 0.00 0.00 3.33
8 9 4.101114 AGACATACCAAGTACCCATCACA 58.899 43.478 0.00 0.00 0.00 3.58
9 10 4.755266 AGACATACCAAGTACCCATCAC 57.245 45.455 0.00 0.00 0.00 3.06
10 11 4.780554 TCAAGACATACCAAGTACCCATCA 59.219 41.667 0.00 0.00 0.00 3.07
11 12 5.104900 AGTCAAGACATACCAAGTACCCATC 60.105 44.000 2.72 0.00 0.00 3.51
12 13 4.783227 AGTCAAGACATACCAAGTACCCAT 59.217 41.667 2.72 0.00 0.00 4.00
13 14 4.164981 AGTCAAGACATACCAAGTACCCA 58.835 43.478 2.72 0.00 0.00 4.51
14 15 4.820894 AGTCAAGACATACCAAGTACCC 57.179 45.455 2.72 0.00 0.00 3.69
15 16 5.790593 TCAAGTCAAGACATACCAAGTACC 58.209 41.667 2.72 0.00 0.00 3.34
16 17 5.348997 GCTCAAGTCAAGACATACCAAGTAC 59.651 44.000 2.72 0.00 0.00 2.73
17 18 5.479306 GCTCAAGTCAAGACATACCAAGTA 58.521 41.667 2.72 0.00 0.00 2.24
18 19 4.319177 GCTCAAGTCAAGACATACCAAGT 58.681 43.478 2.72 0.00 0.00 3.16
19 20 3.369147 CGCTCAAGTCAAGACATACCAAG 59.631 47.826 2.72 0.00 0.00 3.61
20 21 3.006430 TCGCTCAAGTCAAGACATACCAA 59.994 43.478 2.72 0.00 0.00 3.67
21 22 2.560981 TCGCTCAAGTCAAGACATACCA 59.439 45.455 2.72 0.00 0.00 3.25
22 23 3.232213 TCGCTCAAGTCAAGACATACC 57.768 47.619 2.72 0.00 0.00 2.73
23 24 4.324936 GTCTTCGCTCAAGTCAAGACATAC 59.675 45.833 13.82 0.00 42.87 2.39
24 25 4.486090 GTCTTCGCTCAAGTCAAGACATA 58.514 43.478 13.82 0.00 42.87 2.29
25 26 3.321497 GTCTTCGCTCAAGTCAAGACAT 58.679 45.455 13.82 0.00 42.87 3.06
26 27 2.545952 GGTCTTCGCTCAAGTCAAGACA 60.546 50.000 17.61 0.00 44.43 3.41
27 28 2.062519 GGTCTTCGCTCAAGTCAAGAC 58.937 52.381 11.71 11.71 42.70 3.01
28 29 1.964223 AGGTCTTCGCTCAAGTCAAGA 59.036 47.619 0.00 0.00 33.27 3.02
29 30 2.333014 GAGGTCTTCGCTCAAGTCAAG 58.667 52.381 0.00 0.00 33.27 3.02
30 31 1.000955 GGAGGTCTTCGCTCAAGTCAA 59.999 52.381 0.00 0.00 33.27 3.18
31 32 0.603569 GGAGGTCTTCGCTCAAGTCA 59.396 55.000 0.00 0.00 33.27 3.41
32 33 0.108567 GGGAGGTCTTCGCTCAAGTC 60.109 60.000 0.00 0.00 35.94 3.01
33 34 1.878656 CGGGAGGTCTTCGCTCAAGT 61.879 60.000 0.00 0.00 36.65 3.16
34 35 1.153745 CGGGAGGTCTTCGCTCAAG 60.154 63.158 0.00 0.00 36.65 3.02
35 36 2.970639 CGGGAGGTCTTCGCTCAA 59.029 61.111 0.00 0.00 36.65 3.02
36 37 3.760035 GCGGGAGGTCTTCGCTCA 61.760 66.667 10.63 0.00 45.16 4.26
59 60 1.134694 GGATTTCTGGCGTCGTTGC 59.865 57.895 0.00 0.00 0.00 4.17
60 61 1.128692 GAAGGATTTCTGGCGTCGTTG 59.871 52.381 0.00 0.00 0.00 4.10
61 62 1.002087 AGAAGGATTTCTGGCGTCGTT 59.998 47.619 0.00 0.00 42.04 3.85
62 63 0.608640 AGAAGGATTTCTGGCGTCGT 59.391 50.000 0.00 0.00 42.04 4.34
63 64 1.394917 CAAGAAGGATTTCTGGCGTCG 59.605 52.381 0.00 0.00 42.80 5.12
64 65 2.699954 TCAAGAAGGATTTCTGGCGTC 58.300 47.619 0.00 0.00 42.80 5.19
65 66 2.859165 TCAAGAAGGATTTCTGGCGT 57.141 45.000 0.00 0.00 42.80 5.68
66 67 4.191544 TGTATCAAGAAGGATTTCTGGCG 58.808 43.478 0.00 0.00 42.80 5.69
67 68 6.060788 AGATGTATCAAGAAGGATTTCTGGC 58.939 40.000 0.00 0.00 42.80 4.85
68 69 9.618890 TTAAGATGTATCAAGAAGGATTTCTGG 57.381 33.333 0.00 0.00 42.80 3.86
70 71 9.336171 GCTTAAGATGTATCAAGAAGGATTTCT 57.664 33.333 6.67 0.00 45.51 2.52
71 72 9.336171 AGCTTAAGATGTATCAAGAAGGATTTC 57.664 33.333 6.67 0.00 0.00 2.17
72 73 9.692325 AAGCTTAAGATGTATCAAGAAGGATTT 57.308 29.630 6.67 0.00 0.00 2.17
73 74 9.118300 CAAGCTTAAGATGTATCAAGAAGGATT 57.882 33.333 6.67 0.00 0.00 3.01
74 75 7.228308 GCAAGCTTAAGATGTATCAAGAAGGAT 59.772 37.037 6.67 0.00 0.00 3.24
75 76 6.540189 GCAAGCTTAAGATGTATCAAGAAGGA 59.460 38.462 6.67 0.00 0.00 3.36
76 77 6.510799 CGCAAGCTTAAGATGTATCAAGAAGG 60.511 42.308 6.67 0.00 0.00 3.46
77 78 6.036517 ACGCAAGCTTAAGATGTATCAAGAAG 59.963 38.462 6.67 0.00 45.62 2.85
78 79 5.874810 ACGCAAGCTTAAGATGTATCAAGAA 59.125 36.000 6.67 0.00 45.62 2.52
79 80 5.419542 ACGCAAGCTTAAGATGTATCAAGA 58.580 37.500 6.67 0.00 45.62 3.02
80 81 5.725110 ACGCAAGCTTAAGATGTATCAAG 57.275 39.130 6.67 0.00 45.62 3.02
81 82 7.333423 ACTTAACGCAAGCTTAAGATGTATCAA 59.667 33.333 20.48 0.00 40.31 2.57
82 83 6.816640 ACTTAACGCAAGCTTAAGATGTATCA 59.183 34.615 20.48 0.00 40.31 2.15
83 84 7.235430 ACTTAACGCAAGCTTAAGATGTATC 57.765 36.000 20.48 0.00 40.31 2.24
84 85 7.611213 AACTTAACGCAAGCTTAAGATGTAT 57.389 32.000 20.48 0.00 40.31 2.29
85 86 8.712285 ATAACTTAACGCAAGCTTAAGATGTA 57.288 30.769 20.48 13.59 40.31 2.29
86 87 5.941948 AACTTAACGCAAGCTTAAGATGT 57.058 34.783 20.48 0.00 40.31 3.06
87 88 9.982291 TTTATAACTTAACGCAAGCTTAAGATG 57.018 29.630 20.48 5.51 40.31 2.90
89 90 8.173130 GCTTTATAACTTAACGCAAGCTTAAGA 58.827 33.333 20.48 8.29 40.31 2.10
90 91 8.175716 AGCTTTATAACTTAACGCAAGCTTAAG 58.824 33.333 0.00 15.79 42.14 1.85
91 92 8.036273 AGCTTTATAACTTAACGCAAGCTTAA 57.964 30.769 0.00 0.00 42.14 1.85
92 93 7.605410 AGCTTTATAACTTAACGCAAGCTTA 57.395 32.000 0.00 0.00 42.14 3.09
93 94 6.496338 AGCTTTATAACTTAACGCAAGCTT 57.504 33.333 0.00 0.00 42.14 3.74
94 95 6.496338 AAGCTTTATAACTTAACGCAAGCT 57.504 33.333 0.00 0.00 45.73 3.74
95 96 6.452480 GCAAAGCTTTATAACTTAACGCAAGC 60.452 38.462 12.25 1.29 45.62 4.01
96 97 6.801862 AGCAAAGCTTTATAACTTAACGCAAG 59.198 34.615 12.25 0.00 33.89 4.01
97 98 6.674066 AGCAAAGCTTTATAACTTAACGCAA 58.326 32.000 12.25 0.00 33.89 4.85
98 99 6.249035 AGCAAAGCTTTATAACTTAACGCA 57.751 33.333 12.25 0.00 33.89 5.24
112 113 7.173218 GCCTTTTATTAAGGAAAAGCAAAGCTT 59.827 33.333 15.28 0.00 44.42 3.74
113 114 6.650807 GCCTTTTATTAAGGAAAAGCAAAGCT 59.349 34.615 15.28 0.00 40.86 3.74
114 115 6.426633 TGCCTTTTATTAAGGAAAAGCAAAGC 59.573 34.615 15.28 13.74 40.86 3.51
115 116 7.961325 TGCCTTTTATTAAGGAAAAGCAAAG 57.039 32.000 15.28 7.13 40.86 2.77
116 117 8.616942 GTTTGCCTTTTATTAAGGAAAAGCAAA 58.383 29.630 23.04 23.04 43.69 3.68
117 118 7.770897 TGTTTGCCTTTTATTAAGGAAAAGCAA 59.229 29.630 9.46 17.10 43.69 3.91
118 119 7.275920 TGTTTGCCTTTTATTAAGGAAAAGCA 58.724 30.769 9.46 13.96 43.69 3.91
119 120 7.722795 TGTTTGCCTTTTATTAAGGAAAAGC 57.277 32.000 9.46 12.37 43.69 3.51
120 121 9.325198 AGTTGTTTGCCTTTTATTAAGGAAAAG 57.675 29.630 9.46 14.33 43.69 2.27
121 122 9.103861 CAGTTGTTTGCCTTTTATTAAGGAAAA 57.896 29.630 7.71 6.67 41.49 2.29
122 123 8.478877 TCAGTTGTTTGCCTTTTATTAAGGAAA 58.521 29.630 7.71 0.26 39.81 3.13
123 124 7.923878 GTCAGTTGTTTGCCTTTTATTAAGGAA 59.076 33.333 7.71 0.00 39.81 3.36
124 125 7.286775 AGTCAGTTGTTTGCCTTTTATTAAGGA 59.713 33.333 7.71 0.00 39.81 3.36
125 126 7.382218 CAGTCAGTTGTTTGCCTTTTATTAAGG 59.618 37.037 0.00 0.00 40.39 2.69
126 127 8.134895 TCAGTCAGTTGTTTGCCTTTTATTAAG 58.865 33.333 0.00 0.00 0.00 1.85
127 128 8.001881 TCAGTCAGTTGTTTGCCTTTTATTAA 57.998 30.769 0.00 0.00 0.00 1.40
128 129 7.575414 TCAGTCAGTTGTTTGCCTTTTATTA 57.425 32.000 0.00 0.00 0.00 0.98
129 130 6.463995 TCAGTCAGTTGTTTGCCTTTTATT 57.536 33.333 0.00 0.00 0.00 1.40
130 131 6.040842 ACATCAGTCAGTTGTTTGCCTTTTAT 59.959 34.615 0.00 0.00 0.00 1.40
131 132 5.359576 ACATCAGTCAGTTGTTTGCCTTTTA 59.640 36.000 0.00 0.00 0.00 1.52
132 133 4.160252 ACATCAGTCAGTTGTTTGCCTTTT 59.840 37.500 0.00 0.00 0.00 2.27
133 134 3.701040 ACATCAGTCAGTTGTTTGCCTTT 59.299 39.130 0.00 0.00 0.00 3.11
134 135 3.290710 ACATCAGTCAGTTGTTTGCCTT 58.709 40.909 0.00 0.00 0.00 4.35
135 136 2.936202 ACATCAGTCAGTTGTTTGCCT 58.064 42.857 0.00 0.00 0.00 4.75
136 137 3.632189 GAACATCAGTCAGTTGTTTGCC 58.368 45.455 0.00 0.00 39.58 4.52
137 138 3.291585 CGAACATCAGTCAGTTGTTTGC 58.708 45.455 0.00 0.00 39.58 3.68
138 139 3.291585 GCGAACATCAGTCAGTTGTTTG 58.708 45.455 0.00 0.00 39.58 2.93
139 140 2.290641 GGCGAACATCAGTCAGTTGTTT 59.709 45.455 0.00 0.00 39.58 2.83
140 141 1.873591 GGCGAACATCAGTCAGTTGTT 59.126 47.619 0.00 0.00 41.57 2.83
141 142 1.512926 GGCGAACATCAGTCAGTTGT 58.487 50.000 0.00 0.00 0.00 3.32
142 143 0.798776 GGGCGAACATCAGTCAGTTG 59.201 55.000 0.00 0.00 0.00 3.16
143 144 0.321653 GGGGCGAACATCAGTCAGTT 60.322 55.000 0.00 0.00 0.00 3.16
144 145 1.296715 GGGGCGAACATCAGTCAGT 59.703 57.895 0.00 0.00 0.00 3.41
145 146 1.811266 CGGGGCGAACATCAGTCAG 60.811 63.158 0.00 0.00 0.00 3.51
146 147 1.252215 TACGGGGCGAACATCAGTCA 61.252 55.000 0.00 0.00 0.00 3.41
147 148 0.104304 ATACGGGGCGAACATCAGTC 59.896 55.000 0.00 0.00 0.00 3.51
153 154 4.008330 TCAAAAATTATACGGGGCGAACA 58.992 39.130 0.00 0.00 0.00 3.18
172 173 7.345914 TGGGGGAGTTTTTCTTTATTTTCTCAA 59.654 33.333 0.00 0.00 0.00 3.02
173 174 6.841755 TGGGGGAGTTTTTCTTTATTTTCTCA 59.158 34.615 0.00 0.00 0.00 3.27
181 182 3.086282 GCGATGGGGGAGTTTTTCTTTA 58.914 45.455 0.00 0.00 0.00 1.85
185 186 1.320344 GGGCGATGGGGGAGTTTTTC 61.320 60.000 0.00 0.00 0.00 2.29
187 188 2.359011 GGGCGATGGGGGAGTTTT 59.641 61.111 0.00 0.00 0.00 2.43
188 189 2.938798 TGGGCGATGGGGGAGTTT 60.939 61.111 0.00 0.00 0.00 2.66
189 190 3.411517 CTGGGCGATGGGGGAGTT 61.412 66.667 0.00 0.00 0.00 3.01
190 191 4.741239 ACTGGGCGATGGGGGAGT 62.741 66.667 0.00 0.00 0.00 3.85
191 192 4.181010 CACTGGGCGATGGGGGAG 62.181 72.222 0.00 0.00 0.00 4.30
460 481 0.110419 TTCGAAACCGAAATGCAGCG 60.110 50.000 0.00 0.00 42.32 5.18
470 491 4.439472 CCGCGCCTTTCGAAACCG 62.439 66.667 17.28 17.28 41.67 4.44
552 579 1.205460 ATTACGAGGTGGGCCCAGTT 61.205 55.000 29.55 17.44 34.66 3.16
555 582 1.613928 TGATTACGAGGTGGGCCCA 60.614 57.895 24.45 24.45 34.66 5.36
589 616 5.217895 AGTCAAATCCGAGCGAATAAAAC 57.782 39.130 0.00 0.00 0.00 2.43
600 627 0.522626 TGCGTACGAGTCAAATCCGA 59.477 50.000 21.65 0.00 0.00 4.55
662 689 1.747367 CCGCGCCCATTAAGTCCAA 60.747 57.895 0.00 0.00 0.00 3.53
663 690 2.124901 CCGCGCCCATTAAGTCCA 60.125 61.111 0.00 0.00 0.00 4.02
664 691 2.124860 ACCGCGCCCATTAAGTCC 60.125 61.111 0.00 0.00 0.00 3.85
665 692 2.469516 CCACCGCGCCCATTAAGTC 61.470 63.158 0.00 0.00 0.00 3.01
666 693 2.437716 CCACCGCGCCCATTAAGT 60.438 61.111 0.00 0.00 0.00 2.24
667 694 3.209097 CCCACCGCGCCCATTAAG 61.209 66.667 0.00 0.00 0.00 1.85
693 720 4.899239 GGCCAGCCAGTCGGATCG 62.899 72.222 3.12 0.00 35.81 3.69
771 831 3.849951 CGCTGTAGATGGGCCCGT 61.850 66.667 19.20 19.20 0.00 5.28
931 992 3.420482 GAGATGGTGGGGGTGGGG 61.420 72.222 0.00 0.00 0.00 4.96
1435 1502 4.144727 GGAGGCGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1436 1503 4.150454 AGGAGGCGGAGGAGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1437 1504 2.520741 GAGGAGGCGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1438 1505 4.144727 GGAGGAGGCGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1543 1619 4.281947 GGAGTAGTAGGCGGCGGC 62.282 72.222 27.24 27.24 38.90 6.53
1695 1771 2.472059 CGGGATCATGTGGTTGCCG 61.472 63.158 0.00 0.00 0.00 5.69
1797 1873 1.817099 GGCGAGGTTGATGAGCTGG 60.817 63.158 0.00 0.00 35.91 4.85
1857 1933 3.709880 TTGATGGTAGTCGGCGGCG 62.710 63.158 27.15 27.15 0.00 6.46
2091 2173 4.279169 TCTTTGGATTGACTTTTGGCTGAG 59.721 41.667 0.00 0.00 0.00 3.35
2092 2174 4.214310 TCTTTGGATTGACTTTTGGCTGA 58.786 39.130 0.00 0.00 0.00 4.26
2285 2367 3.432782 GAAATCATCGGCAAAGCTCAAG 58.567 45.455 0.00 0.00 0.00 3.02
2362 2444 8.067751 TGTAGTTCAGTATAGTGCTTCATTCT 57.932 34.615 2.40 0.00 0.00 2.40
2395 2488 4.439289 GCACCATTTTCAAGCTGATACTCC 60.439 45.833 0.00 0.00 0.00 3.85
2502 2663 9.387123 CTAGCGATATAAAAATCAAAAGGAAGC 57.613 33.333 0.00 0.00 0.00 3.86
2506 2667 8.958043 GCAACTAGCGATATAAAAATCAAAAGG 58.042 33.333 0.00 0.00 0.00 3.11
2574 2736 4.090761 ACAGAAGCAGAAATGACAGGAA 57.909 40.909 0.00 0.00 0.00 3.36
2579 2752 7.467623 CCACTATTTACAGAAGCAGAAATGAC 58.532 38.462 0.00 0.00 0.00 3.06
2629 2802 5.391416 GCATGAAGACTTAAAGAGTTCTGGC 60.391 44.000 0.00 0.00 39.19 4.85
2644 2817 5.405571 TGTTCTAAGACGAAAGCATGAAGAC 59.594 40.000 0.00 0.00 0.00 3.01
2658 2831 6.907748 GCAGAAAACTGACTTTGTTCTAAGAC 59.092 38.462 0.00 0.00 0.00 3.01
2660 2833 7.020914 AGCAGAAAACTGACTTTGTTCTAAG 57.979 36.000 0.00 0.00 0.00 2.18
2701 2874 0.317603 GCTCTGCAACAGCAAGTGTG 60.318 55.000 11.62 0.00 40.26 3.82
2731 2904 9.423061 GTAAATTCCTGATTGTGCAGTAAATTT 57.577 29.630 2.57 2.57 39.70 1.82
2790 2964 4.322349 GGACTGTAGCAACAAGATGAGACT 60.322 45.833 0.00 0.00 34.49 3.24


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

AutoCloner maintained by Alex Coulton.