Multiple sequence alignment - TraesCS5B01G557900

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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 TraesCS5B01G557900 chr5B 100.000 2639 0 0 1 2639 705517665 705520303 0.000000e+00 4874.0
1 TraesCS5B01G557900 chr5B 99.269 684 5 0 1956 2639 303237599 303238282 0.000000e+00 1236.0
2 TraesCS5B01G557900 chr5B 96.591 352 10 1 54 403 711065458 711065107 1.360000e-162 582.0
3 TraesCS5B01G557900 chr5B 97.436 78 0 1 1823 1898 711058628 711058551 5.930000e-27 132.0
4 TraesCS5B01G557900 chr5B 97.436 78 0 1 1823 1898 711064612 711064689 5.930000e-27 132.0
5 TraesCS5B01G557900 chr5B 95.652 46 1 1 1893 1937 711058520 711058475 3.640000e-09 73.1
6 TraesCS5B01G557900 chr5B 95.652 46 1 1 1893 1937 711064720 711064765 3.640000e-09 73.1
7 TraesCS5B01G557900 chr5D 90.805 1490 75 23 438 1897 563120806 563122263 0.000000e+00 1936.0
8 TraesCS5B01G557900 chr5D 93.724 239 15 0 151 389 563120567 563120805 2.500000e-95 359.0
9 TraesCS5B01G557900 chr5D 95.302 149 6 1 1 149 563104516 563104663 4.390000e-58 235.0
10 TraesCS5B01G557900 chr5D 87.975 158 15 3 151 305 467857864 467858020 1.610000e-42 183.0
11 TraesCS5B01G557900 chr4A 90.476 1428 78 28 497 1897 609183848 609182452 0.000000e+00 1831.0
12 TraesCS5B01G557900 chr4A 84.746 236 25 4 151 377 609185566 609185333 2.640000e-55 226.0
13 TraesCS5B01G557900 chr4A 91.946 149 12 0 1 149 592008559 592008411 2.660000e-50 209.0
14 TraesCS5B01G557900 chr4A 97.059 68 2 0 398 465 609184216 609184149 5.970000e-22 115.0
15 TraesCS5B01G557900 chr4A 93.750 48 1 2 357 403 609185035 609184989 1.310000e-08 71.3
16 TraesCS5B01G557900 chr3A 99.706 680 2 0 1960 2639 457934606 457933927 0.000000e+00 1245.0
17 TraesCS5B01G557900 chr3A 91.333 150 12 1 1 149 703348812 703348961 1.240000e-48 204.0
18 TraesCS5B01G557900 chrUn 99.705 678 2 0 1962 2639 464388389 464389066 0.000000e+00 1242.0
19 TraesCS5B01G557900 chrUn 88.333 60 4 3 1927 1985 165321660 165321717 4.710000e-08 69.4
20 TraesCS5B01G557900 chrUn 96.875 32 0 1 1906 1936 77427988 77427957 5.000000e-03 52.8
21 TraesCS5B01G557900 chr7A 99.559 681 3 0 1959 2639 84756785 84756105 0.000000e+00 1242.0
22 TraesCS5B01G557900 chr7A 99.558 678 3 0 1962 2639 332823278 332823955 0.000000e+00 1236.0
23 TraesCS5B01G557900 chr7A 98.844 692 7 1 1948 2639 220124089 220123399 0.000000e+00 1232.0
24 TraesCS5B01G557900 chr7A 98.698 691 7 2 1949 2639 672066404 672067092 0.000000e+00 1225.0
25 TraesCS5B01G557900 chr7A 88.312 154 14 3 151 300 703759101 703759254 5.800000e-42 182.0
26 TraesCS5B01G557900 chr7A 87.342 158 15 4 151 304 703810318 703810474 2.700000e-40 176.0
27 TraesCS5B01G557900 chr6B 99.558 679 3 0 1961 2639 640912125 640911447 0.000000e+00 1238.0
28 TraesCS5B01G557900 chr6B 91.946 149 10 2 1 149 42410242 42410096 9.570000e-50 207.0
29 TraesCS5B01G557900 chr6B 97.143 35 1 0 1928 1962 512551396 512551430 2.840000e-05 60.2
30 TraesCS5B01G557900 chr6B 94.118 34 2 0 1929 1962 58851860 58851893 5.000000e-03 52.8
31 TraesCS5B01G557900 chr2A 99.558 678 3 0 1962 2639 125629645 125630322 0.000000e+00 1236.0
32 TraesCS5B01G557900 chr6D 92.617 149 11 0 1 149 174296666 174296518 5.720000e-52 215.0
33 TraesCS5B01G557900 chr6D 91.946 149 9 3 1 149 140104219 140104074 3.440000e-49 206.0
34 TraesCS5B01G557900 chr6D 87.342 158 17 2 151 305 174296198 174296041 7.510000e-41 178.0
35 TraesCS5B01G557900 chr4D 91.333 150 12 1 1 149 427612425 427612276 1.240000e-48 204.0
36 TraesCS5B01G557900 chr3D 91.275 149 13 0 1 149 396430705 396430853 1.240000e-48 204.0
37 TraesCS5B01G557900 chr3D 96.970 33 1 0 1930 1962 85763878 85763910 3.670000e-04 56.5
38 TraesCS5B01G557900 chr2D 87.421 159 15 4 151 305 537510585 537510428 7.510000e-41 178.0
39 TraesCS5B01G557900 chr7D 87.097 155 17 2 154 305 111425322 111425168 3.490000e-39 172.0
40 TraesCS5B01G557900 chr7B 86.875 160 14 5 151 305 218862043 218861886 3.490000e-39 172.0
41 TraesCS5B01G557900 chr7B 94.286 35 1 1 1928 1962 702179689 702179722 5.000000e-03 52.8
42 TraesCS5B01G557900 chr1A 94.737 38 0 2 1927 1962 540380680 540380643 1.020000e-04 58.4
43 TraesCS5B01G557900 chr5A 100.000 29 0 0 1934 1962 681491167 681491195 1.000000e-03 54.7
44 TraesCS5B01G557900 chr1B 100.000 29 0 0 1934 1962 18391061 18391089 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G557900 chr5B 705517665 705520303 2638 False 4874.000 4874 100.00000 1 2639 1 chr5B.!!$F2 2638
1 TraesCS5B01G557900 chr5B 303237599 303238282 683 False 1236.000 1236 99.26900 1956 2639 1 chr5B.!!$F1 683
2 TraesCS5B01G557900 chr5D 563120567 563122263 1696 False 1147.500 1936 92.26450 151 1897 2 chr5D.!!$F3 1746
3 TraesCS5B01G557900 chr4A 609182452 609185566 3114 True 560.825 1831 91.50775 151 1897 4 chr4A.!!$R2 1746
4 TraesCS5B01G557900 chr3A 457933927 457934606 679 True 1245.000 1245 99.70600 1960 2639 1 chr3A.!!$R1 679
5 TraesCS5B01G557900 chrUn 464388389 464389066 677 False 1242.000 1242 99.70500 1962 2639 1 chrUn.!!$F2 677
6 TraesCS5B01G557900 chr7A 84756105 84756785 680 True 1242.000 1242 99.55900 1959 2639 1 chr7A.!!$R1 680
7 TraesCS5B01G557900 chr7A 332823278 332823955 677 False 1236.000 1236 99.55800 1962 2639 1 chr7A.!!$F1 677
8 TraesCS5B01G557900 chr7A 220123399 220124089 690 True 1232.000 1232 98.84400 1948 2639 1 chr7A.!!$R2 691
9 TraesCS5B01G557900 chr7A 672066404 672067092 688 False 1225.000 1225 98.69800 1949 2639 1 chr7A.!!$F2 690
10 TraesCS5B01G557900 chr6B 640911447 640912125 678 True 1238.000 1238 99.55800 1961 2639 1 chr6B.!!$R2 678
11 TraesCS5B01G557900 chr2A 125629645 125630322 677 False 1236.000 1236 99.55800 1962 2639 1 chr2A.!!$F1 677

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
855 2250 0.186386 ATCCCTCCACTCCGACCTAG 59.814 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 3162 2.837591 TGCAGCCTATACACAAGGAGAA 59.162 45.455 0.0 0.0 36.08 2.87 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
34 35 7.851508 AGATTCCATGTTAATATGTTTCGACG 58.148 34.615 10.82 0.00 0.00 5.12
35 36 7.709182 AGATTCCATGTTAATATGTTTCGACGA 59.291 33.333 10.82 0.00 0.00 4.20
36 37 7.598189 TTCCATGTTAATATGTTTCGACGAA 57.402 32.000 6.10 6.10 0.00 3.85
37 38 7.780008 TCCATGTTAATATGTTTCGACGAAT 57.220 32.000 11.71 0.00 0.00 3.34
38 39 8.203937 TCCATGTTAATATGTTTCGACGAATT 57.796 30.769 11.71 4.91 0.00 2.17
39 40 8.670135 TCCATGTTAATATGTTTCGACGAATTT 58.330 29.630 11.71 2.15 0.00 1.82
40 41 9.284594 CCATGTTAATATGTTTCGACGAATTTT 57.715 29.630 11.71 1.28 0.00 1.82
58 59 2.797177 TTTTTGGGCCAAAAGTTGCT 57.203 40.000 35.25 0.00 42.91 3.91
59 60 3.914426 TTTTTGGGCCAAAAGTTGCTA 57.086 38.095 35.25 22.01 42.91 3.49
60 61 4.429854 TTTTTGGGCCAAAAGTTGCTAT 57.570 36.364 35.25 0.00 42.91 2.97
61 62 3.399440 TTTGGGCCAAAAGTTGCTATG 57.601 42.857 28.69 0.00 29.89 2.23
62 63 2.300956 TGGGCCAAAAGTTGCTATGA 57.699 45.000 2.13 0.00 0.00 2.15
63 64 2.818921 TGGGCCAAAAGTTGCTATGAT 58.181 42.857 2.13 0.00 0.00 2.45
64 65 2.496871 TGGGCCAAAAGTTGCTATGATG 59.503 45.455 2.13 0.00 0.00 3.07
65 66 2.497273 GGGCCAAAAGTTGCTATGATGT 59.503 45.455 4.39 0.00 0.00 3.06
66 67 3.055891 GGGCCAAAAGTTGCTATGATGTT 60.056 43.478 4.39 0.00 0.00 2.71
67 68 4.563374 GGGCCAAAAGTTGCTATGATGTTT 60.563 41.667 4.39 0.00 0.00 2.83
68 69 5.337169 GGGCCAAAAGTTGCTATGATGTTTA 60.337 40.000 4.39 0.00 0.00 2.01
69 70 5.576774 GGCCAAAAGTTGCTATGATGTTTAC 59.423 40.000 0.00 0.00 0.00 2.01
70 71 6.155827 GCCAAAAGTTGCTATGATGTTTACA 58.844 36.000 0.00 0.00 0.00 2.41
71 72 6.089417 GCCAAAAGTTGCTATGATGTTTACAC 59.911 38.462 0.00 0.00 0.00 2.90
72 73 7.370383 CCAAAAGTTGCTATGATGTTTACACT 58.630 34.615 0.00 0.00 0.00 3.55
73 74 7.326789 CCAAAAGTTGCTATGATGTTTACACTG 59.673 37.037 0.00 0.00 0.00 3.66
74 75 7.510549 AAAGTTGCTATGATGTTTACACTGT 57.489 32.000 0.00 0.00 0.00 3.55
75 76 8.615878 AAAGTTGCTATGATGTTTACACTGTA 57.384 30.769 0.00 0.00 0.00 2.74
76 77 8.792830 AAGTTGCTATGATGTTTACACTGTAT 57.207 30.769 0.00 0.00 0.00 2.29
77 78 8.792830 AGTTGCTATGATGTTTACACTGTATT 57.207 30.769 0.00 0.00 0.00 1.89
78 79 9.231297 AGTTGCTATGATGTTTACACTGTATTT 57.769 29.630 0.00 0.00 0.00 1.40
79 80 9.277565 GTTGCTATGATGTTTACACTGTATTTG 57.722 33.333 0.00 0.00 0.00 2.32
80 81 7.471721 TGCTATGATGTTTACACTGTATTTGC 58.528 34.615 0.00 0.00 0.00 3.68
81 82 6.628856 GCTATGATGTTTACACTGTATTTGCG 59.371 38.462 0.00 0.00 0.00 4.85
82 83 6.735678 ATGATGTTTACACTGTATTTGCGA 57.264 33.333 0.00 0.00 0.00 5.10
83 84 6.735678 TGATGTTTACACTGTATTTGCGAT 57.264 33.333 0.00 0.00 0.00 4.58
84 85 7.835634 TGATGTTTACACTGTATTTGCGATA 57.164 32.000 0.00 0.00 0.00 2.92
85 86 7.905126 TGATGTTTACACTGTATTTGCGATAG 58.095 34.615 0.00 0.00 0.00 2.08
86 87 7.547722 TGATGTTTACACTGTATTTGCGATAGT 59.452 33.333 0.00 0.00 39.35 2.12
87 88 7.056002 TGTTTACACTGTATTTGCGATAGTG 57.944 36.000 0.00 0.00 43.20 2.74
89 90 7.171848 TGTTTACACTGTATTTGCGATAGTGTT 59.828 33.333 12.74 0.00 46.96 3.32
90 91 7.661127 TTACACTGTATTTGCGATAGTGTTT 57.339 32.000 12.74 0.00 46.96 2.83
91 92 8.760103 TTACACTGTATTTGCGATAGTGTTTA 57.240 30.769 12.74 1.19 46.96 2.01
92 93 7.057149 ACACTGTATTTGCGATAGTGTTTAC 57.943 36.000 0.00 0.00 46.96 2.01
93 94 6.647481 ACACTGTATTTGCGATAGTGTTTACA 59.353 34.615 0.00 0.00 46.96 2.41
94 95 6.953743 CACTGTATTTGCGATAGTGTTTACAC 59.046 38.462 4.87 4.87 46.77 2.90
108 109 5.827666 GTGTTTACACTAAAGTTGCCATGT 58.172 37.500 5.78 0.00 43.25 3.21
109 110 5.685511 GTGTTTACACTAAAGTTGCCATGTG 59.314 40.000 5.78 0.00 43.25 3.21
110 111 5.219633 GTTTACACTAAAGTTGCCATGTGG 58.780 41.667 0.00 0.00 38.53 4.17
127 128 7.099266 CCATGTGGCAATTTCAGTTTATAGA 57.901 36.000 0.00 0.00 0.00 1.98
128 129 7.719483 CCATGTGGCAATTTCAGTTTATAGAT 58.281 34.615 0.00 0.00 0.00 1.98
129 130 7.864379 CCATGTGGCAATTTCAGTTTATAGATC 59.136 37.037 0.00 0.00 0.00 2.75
130 131 7.936496 TGTGGCAATTTCAGTTTATAGATCA 57.064 32.000 0.00 0.00 0.00 2.92
131 132 8.523915 TGTGGCAATTTCAGTTTATAGATCAT 57.476 30.769 0.00 0.00 0.00 2.45
132 133 8.407832 TGTGGCAATTTCAGTTTATAGATCATG 58.592 33.333 0.00 0.00 0.00 3.07
133 134 7.380602 GTGGCAATTTCAGTTTATAGATCATGC 59.619 37.037 0.00 0.00 0.00 4.06
134 135 6.865205 GGCAATTTCAGTTTATAGATCATGCC 59.135 38.462 0.00 0.00 0.00 4.40
135 136 7.428020 GCAATTTCAGTTTATAGATCATGCCA 58.572 34.615 0.00 0.00 0.00 4.92
136 137 7.922278 GCAATTTCAGTTTATAGATCATGCCAA 59.078 33.333 0.00 0.00 0.00 4.52
137 138 9.976511 CAATTTCAGTTTATAGATCATGCCAAT 57.023 29.630 0.00 0.00 0.00 3.16
231 232 9.977762 GAAATTCAAAAAGATTTCCATATGCAC 57.022 29.630 0.00 0.00 0.00 4.57
268 269 3.278574 GCAATCTGTGTGTTATAGGGCA 58.721 45.455 0.00 0.00 0.00 5.36
403 729 6.580788 ACTACGATCAAGACTGCTAGTACTA 58.419 40.000 1.89 1.89 0.00 1.82
404 730 5.994887 ACGATCAAGACTGCTAGTACTAG 57.005 43.478 23.25 23.25 36.29 2.57
465 1569 5.864474 CGGATTCCTTTCCTTCGATACATAG 59.136 44.000 0.30 0.00 33.30 2.23
466 1570 6.516860 CGGATTCCTTTCCTTCGATACATAGT 60.517 42.308 0.30 0.00 33.30 2.12
468 1572 7.715686 GGATTCCTTTCCTTCGATACATAGTTT 59.284 37.037 0.00 0.00 32.68 2.66
469 1573 8.664211 ATTCCTTTCCTTCGATACATAGTTTC 57.336 34.615 0.00 0.00 0.00 2.78
470 1574 6.579865 TCCTTTCCTTCGATACATAGTTTCC 58.420 40.000 0.00 0.00 0.00 3.13
471 1575 6.383147 TCCTTTCCTTCGATACATAGTTTCCT 59.617 38.462 0.00 0.00 0.00 3.36
472 1576 7.048512 CCTTTCCTTCGATACATAGTTTCCTT 58.951 38.462 0.00 0.00 0.00 3.36
473 1577 8.202137 CCTTTCCTTCGATACATAGTTTCCTTA 58.798 37.037 0.00 0.00 0.00 2.69
474 1578 9.250624 CTTTCCTTCGATACATAGTTTCCTTAG 57.749 37.037 0.00 0.00 0.00 2.18
598 1969 0.657368 CAAGGAAAAGTGCGTGCGTC 60.657 55.000 0.00 0.00 0.00 5.19
621 1992 1.867233 CCAGCAAATTAGATCGTCCCG 59.133 52.381 0.00 0.00 0.00 5.14
637 2008 1.084289 CCCGTTCCTTGTTTCCGATC 58.916 55.000 0.00 0.00 0.00 3.69
638 2009 1.084289 CCGTTCCTTGTTTCCGATCC 58.916 55.000 0.00 0.00 0.00 3.36
639 2010 0.719465 CGTTCCTTGTTTCCGATCCG 59.281 55.000 0.00 0.00 0.00 4.18
674 2045 4.631813 GCCAGCAAGCTATATATGTGTACC 59.368 45.833 0.00 0.00 0.00 3.34
702 2073 1.135228 GTGAGTCTTCGCTCCTTCTCC 60.135 57.143 0.00 0.00 34.74 3.71
713 2084 1.754226 CTCCTTCTCCTTCTCCCGAAG 59.246 57.143 0.00 0.00 45.00 3.79
756 2134 3.484649 CGTTAGTTTCCGATCCATACACG 59.515 47.826 0.00 0.00 0.00 4.49
855 2250 0.186386 ATCCCTCCACTCCGACCTAG 59.814 60.000 0.00 0.00 0.00 3.02
957 2352 0.903454 ACACCCCGACCGAATCTCTT 60.903 55.000 0.00 0.00 0.00 2.85
1146 2541 2.579787 CTCGACATCGACACGGGC 60.580 66.667 0.00 0.00 44.22 6.13
1257 2652 1.339610 CTGATCCTACTCTCCTTGGCG 59.660 57.143 0.00 0.00 0.00 5.69
1258 2653 1.342076 TGATCCTACTCTCCTTGGCGT 60.342 52.381 0.00 0.00 0.00 5.68
1353 2748 3.894427 TCTACTTCATCTCCTCCATGCTC 59.106 47.826 0.00 0.00 0.00 4.26
1396 2791 2.809010 GCGACCTCAGCCTCTACC 59.191 66.667 0.00 0.00 0.00 3.18
1398 2793 1.749638 CGACCTCAGCCTCTACCGT 60.750 63.158 0.00 0.00 0.00 4.83
1421 2816 1.365633 CCAGCCTGCTCGGATACTC 59.634 63.158 0.00 0.00 33.16 2.59
1425 2820 0.037790 GCCTGCTCGGATACTCCATC 60.038 60.000 0.00 0.00 35.91 3.51
1426 2821 1.332195 CCTGCTCGGATACTCCATCA 58.668 55.000 0.00 0.00 35.91 3.07
1428 2823 2.353505 CCTGCTCGGATACTCCATCATG 60.354 54.545 0.00 0.00 35.91 3.07
1452 2847 0.681887 TGACCATCTTCTCGGCGGTA 60.682 55.000 7.21 0.00 0.00 4.02
1518 2913 2.426023 GGGTTCGTGCTGTGGTCT 59.574 61.111 0.00 0.00 0.00 3.85
1521 2916 0.032952 GGTTCGTGCTGTGGTCTACA 59.967 55.000 0.00 0.00 37.78 2.74
1582 2977 3.612247 GATGGGCATCGGGGGATCG 62.612 68.421 0.00 0.00 0.00 3.69
1678 3073 7.141363 GGTTGGTATTATGCAAGAACATCATC 58.859 38.462 0.00 0.00 0.00 2.92
1681 3076 8.467963 TGGTATTATGCAAGAACATCATCATT 57.532 30.769 0.00 0.00 0.00 2.57
1741 3142 7.331193 GTCAGATATTCGTTGTTCTTTAGGTGT 59.669 37.037 0.00 0.00 0.00 4.16
1761 3162 6.725834 AGGTGTCCATTATTCATTTTGTTCCT 59.274 34.615 0.00 0.00 0.00 3.36
1897 3301 2.426024 TGATCTACTCCGCTGGTTGTAC 59.574 50.000 0.00 0.00 0.00 2.90
1898 3302 0.806868 TCTACTCCGCTGGTTGTACG 59.193 55.000 0.00 0.00 0.00 3.67
1900 3304 2.216750 TACTCCGCTGGTTGTACGGC 62.217 60.000 0.00 0.00 46.49 5.68
1901 3305 3.583276 CTCCGCTGGTTGTACGGCA 62.583 63.158 0.00 0.00 46.49 5.69
1902 3306 3.419759 CCGCTGGTTGTACGGCAC 61.420 66.667 0.00 0.00 42.90 5.01
1903 3307 2.357034 CGCTGGTTGTACGGCACT 60.357 61.111 0.00 0.00 42.90 4.40
1904 3308 2.667318 CGCTGGTTGTACGGCACTG 61.667 63.158 0.00 0.00 42.90 3.66
1905 3309 1.597027 GCTGGTTGTACGGCACTGT 60.597 57.895 0.00 0.00 42.32 3.55
1906 3310 0.320073 GCTGGTTGTACGGCACTGTA 60.320 55.000 0.00 0.00 42.32 2.74
1907 3311 1.674817 GCTGGTTGTACGGCACTGTAT 60.675 52.381 0.00 0.00 42.32 2.29
1908 3312 2.417651 GCTGGTTGTACGGCACTGTATA 60.418 50.000 0.00 0.00 42.32 1.47
1909 3313 3.740141 GCTGGTTGTACGGCACTGTATAT 60.740 47.826 0.00 0.00 42.32 0.86
1910 3314 4.049186 CTGGTTGTACGGCACTGTATATC 58.951 47.826 0.00 0.00 0.00 1.63
1911 3315 3.702548 TGGTTGTACGGCACTGTATATCT 59.297 43.478 0.00 0.00 0.00 1.98
1912 3316 4.160814 TGGTTGTACGGCACTGTATATCTT 59.839 41.667 0.00 0.00 0.00 2.40
1913 3317 5.114081 GGTTGTACGGCACTGTATATCTTT 58.886 41.667 0.00 0.00 0.00 2.52
1914 3318 6.127394 TGGTTGTACGGCACTGTATATCTTTA 60.127 38.462 0.00 0.00 0.00 1.85
1915 3319 6.927381 GGTTGTACGGCACTGTATATCTTTAT 59.073 38.462 0.00 0.00 0.00 1.40
1916 3320 7.115947 GGTTGTACGGCACTGTATATCTTTATC 59.884 40.741 0.00 0.00 0.00 1.75
1917 3321 7.520451 TGTACGGCACTGTATATCTTTATCT 57.480 36.000 0.00 0.00 0.00 1.98
1918 3322 7.948357 TGTACGGCACTGTATATCTTTATCTT 58.052 34.615 0.00 0.00 0.00 2.40
1919 3323 8.418662 TGTACGGCACTGTATATCTTTATCTTT 58.581 33.333 0.00 0.00 0.00 2.52
1920 3324 9.257651 GTACGGCACTGTATATCTTTATCTTTT 57.742 33.333 0.00 0.00 0.00 2.27
1921 3325 8.732746 ACGGCACTGTATATCTTTATCTTTTT 57.267 30.769 0.00 0.00 0.00 1.94
1922 3326 9.826574 ACGGCACTGTATATCTTTATCTTTTTA 57.173 29.630 0.00 0.00 0.00 1.52
2083 3487 8.291191 TGATATCTCATGGTCATGATCTAGTC 57.709 38.462 13.26 9.22 45.74 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.709182 TCGTCGAAACATATTAACATGGAATCT 59.291 33.333 0.00 0.00 0.00 2.40
10 11 7.847487 TCGTCGAAACATATTAACATGGAATC 58.153 34.615 0.00 0.00 0.00 2.52
11 12 7.780008 TCGTCGAAACATATTAACATGGAAT 57.220 32.000 0.00 0.00 0.00 3.01
12 13 7.598189 TTCGTCGAAACATATTAACATGGAA 57.402 32.000 4.91 0.00 0.00 3.53
13 14 7.780008 ATTCGTCGAAACATATTAACATGGA 57.220 32.000 12.40 0.00 0.00 3.41
14 15 8.835467 AAATTCGTCGAAACATATTAACATGG 57.165 30.769 12.40 0.00 0.00 3.66
39 40 2.797177 AGCAACTTTTGGCCCAAAAA 57.203 40.000 21.34 6.95 41.77 1.94
40 41 3.389329 TCATAGCAACTTTTGGCCCAAAA 59.611 39.130 20.00 20.00 40.41 2.44
41 42 2.968574 TCATAGCAACTTTTGGCCCAAA 59.031 40.909 4.38 4.38 0.00 3.28
42 43 2.603021 TCATAGCAACTTTTGGCCCAA 58.397 42.857 0.00 0.00 0.00 4.12
43 44 2.300956 TCATAGCAACTTTTGGCCCA 57.699 45.000 0.00 0.00 0.00 5.36
44 45 2.497273 ACATCATAGCAACTTTTGGCCC 59.503 45.455 0.00 0.00 0.00 5.80
45 46 3.874392 ACATCATAGCAACTTTTGGCC 57.126 42.857 0.00 0.00 0.00 5.36
46 47 6.089417 GTGTAAACATCATAGCAACTTTTGGC 59.911 38.462 0.00 0.00 0.00 4.52
47 48 7.326789 CAGTGTAAACATCATAGCAACTTTTGG 59.673 37.037 0.00 0.00 0.00 3.28
48 49 7.862372 ACAGTGTAAACATCATAGCAACTTTTG 59.138 33.333 0.00 0.00 0.00 2.44
49 50 7.940850 ACAGTGTAAACATCATAGCAACTTTT 58.059 30.769 0.00 0.00 0.00 2.27
50 51 7.510549 ACAGTGTAAACATCATAGCAACTTT 57.489 32.000 0.00 0.00 0.00 2.66
51 52 8.792830 ATACAGTGTAAACATCATAGCAACTT 57.207 30.769 7.16 0.00 0.00 2.66
52 53 8.792830 AATACAGTGTAAACATCATAGCAACT 57.207 30.769 7.16 0.00 0.00 3.16
53 54 9.277565 CAAATACAGTGTAAACATCATAGCAAC 57.722 33.333 7.16 0.00 0.00 4.17
54 55 7.967854 GCAAATACAGTGTAAACATCATAGCAA 59.032 33.333 7.16 0.00 0.00 3.91
55 56 7.471721 GCAAATACAGTGTAAACATCATAGCA 58.528 34.615 7.16 0.00 0.00 3.49
56 57 6.628856 CGCAAATACAGTGTAAACATCATAGC 59.371 38.462 7.16 1.58 0.00 2.97
57 58 7.905126 TCGCAAATACAGTGTAAACATCATAG 58.095 34.615 7.16 0.00 0.00 2.23
58 59 7.835634 TCGCAAATACAGTGTAAACATCATA 57.164 32.000 7.16 0.00 0.00 2.15
59 60 6.735678 TCGCAAATACAGTGTAAACATCAT 57.264 33.333 7.16 0.00 0.00 2.45
60 61 6.735678 ATCGCAAATACAGTGTAAACATCA 57.264 33.333 7.16 0.00 0.00 3.07
61 62 7.846107 CACTATCGCAAATACAGTGTAAACATC 59.154 37.037 7.16 0.00 33.53 3.06
62 63 7.333423 ACACTATCGCAAATACAGTGTAAACAT 59.667 33.333 7.16 0.00 45.90 2.71
63 64 6.647481 ACACTATCGCAAATACAGTGTAAACA 59.353 34.615 7.16 0.00 45.90 2.83
64 65 7.057149 ACACTATCGCAAATACAGTGTAAAC 57.943 36.000 7.16 0.00 45.90 2.01
65 66 7.661127 AACACTATCGCAAATACAGTGTAAA 57.339 32.000 7.16 0.00 46.76 2.01
66 67 7.661127 AAACACTATCGCAAATACAGTGTAA 57.339 32.000 7.16 0.00 46.76 2.41
67 68 7.813627 TGTAAACACTATCGCAAATACAGTGTA 59.186 33.333 5.24 5.24 46.76 2.90
69 70 6.953743 GTGTAAACACTATCGCAAATACAGTG 59.046 38.462 5.99 0.00 43.25 3.66
70 71 7.057149 GTGTAAACACTATCGCAAATACAGT 57.943 36.000 5.99 0.00 43.25 3.55
85 86 5.685511 CACATGGCAACTTTAGTGTAAACAC 59.314 40.000 5.07 5.07 42.11 3.32
86 87 5.221145 CCACATGGCAACTTTAGTGTAAACA 60.221 40.000 0.00 0.00 37.61 2.83
87 88 5.219633 CCACATGGCAACTTTAGTGTAAAC 58.780 41.667 0.00 0.00 37.61 2.01
88 89 5.446143 CCACATGGCAACTTTAGTGTAAA 57.554 39.130 0.00 0.00 37.61 2.01
103 104 7.099266 TCTATAAACTGAAATTGCCACATGG 57.901 36.000 0.00 0.00 38.53 3.66
104 105 8.407832 TGATCTATAAACTGAAATTGCCACATG 58.592 33.333 0.00 0.00 0.00 3.21
105 106 8.523915 TGATCTATAAACTGAAATTGCCACAT 57.476 30.769 0.00 0.00 0.00 3.21
106 107 7.936496 TGATCTATAAACTGAAATTGCCACA 57.064 32.000 0.00 0.00 0.00 4.17
107 108 7.380602 GCATGATCTATAAACTGAAATTGCCAC 59.619 37.037 0.00 0.00 0.00 5.01
108 109 7.428020 GCATGATCTATAAACTGAAATTGCCA 58.572 34.615 0.00 0.00 0.00 4.92
109 110 6.865205 GGCATGATCTATAAACTGAAATTGCC 59.135 38.462 0.00 0.00 0.00 4.52
110 111 7.428020 TGGCATGATCTATAAACTGAAATTGC 58.572 34.615 0.00 0.00 0.00 3.56
111 112 9.976511 ATTGGCATGATCTATAAACTGAAATTG 57.023 29.630 0.00 0.00 0.00 2.32
131 132 9.760077 TCCGTTTTAAAAATACTAAAATTGGCA 57.240 25.926 1.31 0.00 32.45 4.92
204 205 9.947433 TGCATATGGAAATCTTTTTGAATTTCT 57.053 25.926 4.56 0.00 34.47 2.52
210 211 6.092092 CACGTGCATATGGAAATCTTTTTGA 58.908 36.000 0.82 0.00 0.00 2.69
225 226 1.079474 ATGTCACCGCACGTGCATA 60.079 52.632 37.03 18.40 42.69 3.14
242 243 1.819928 TAACACACAGATTGCGCCAT 58.180 45.000 4.18 0.00 0.00 4.40
268 269 0.887933 GGAAACAACATCGGCCACAT 59.112 50.000 2.24 0.00 0.00 3.21
404 730 3.127425 ACAAAGGAGTCCTTGTACTGC 57.873 47.619 25.25 0.00 43.92 4.40
531 1902 1.000052 GAGGGTTCCGAGATTCGATCC 60.000 57.143 0.00 0.05 43.74 3.36
598 1969 3.499918 GGGACGATCTAATTTGCTGGATG 59.500 47.826 0.00 0.00 0.00 3.51
645 2016 7.173907 ACACATATATAGCTTGCTGGCTAAAAG 59.826 37.037 13.36 6.72 46.06 2.27
674 2045 2.432628 GAAGACTCACACGCGGGG 60.433 66.667 15.46 5.78 0.00 5.73
731 2109 4.400251 TGTATGGATCGGAAACTAACGAGT 59.600 41.667 0.00 0.00 42.89 4.18
756 2134 2.884207 GTTCCGGTCGATCGTGGC 60.884 66.667 18.13 6.76 0.00 5.01
824 2219 0.256177 GGAGGGATTGAAGACCACCC 59.744 60.000 0.00 0.00 40.71 4.61
837 2232 1.613610 CTAGGTCGGAGTGGAGGGA 59.386 63.158 0.00 0.00 0.00 4.20
1094 2489 0.456142 CGGCTCATCGTCGAAGTTGA 60.456 55.000 10.92 10.92 45.36 3.18
1146 2541 2.203126 GCCTTCCGCCAGATGAGG 60.203 66.667 0.00 0.00 0.00 3.86
1235 2630 1.339610 CCAAGGAGAGTAGGATCAGCG 59.660 57.143 0.00 0.00 0.00 5.18
1323 2718 5.445964 GAGGAGATGAAGTAGAGGAAGACT 58.554 45.833 0.00 0.00 0.00 3.24
1324 2719 4.583073 GGAGGAGATGAAGTAGAGGAAGAC 59.417 50.000 0.00 0.00 0.00 3.01
1425 2820 3.129109 CGAGAAGATGGTCATGGACATG 58.871 50.000 5.95 5.95 40.09 3.21
1426 2821 2.103771 CCGAGAAGATGGTCATGGACAT 59.896 50.000 3.20 3.20 33.68 3.06
1428 2823 1.808133 GCCGAGAAGATGGTCATGGAC 60.808 57.143 0.00 0.00 0.00 4.02
1452 2847 3.854669 CGCGGCAGGAAGAGGGAT 61.855 66.667 0.00 0.00 0.00 3.85
1518 2913 1.679311 CCTGCTGCAGACCCTTGTA 59.321 57.895 30.10 0.00 32.44 2.41
1521 2916 3.255397 AGCCTGCTGCAGACCCTT 61.255 61.111 30.10 8.17 44.83 3.95
1568 2963 2.591715 CAACGATCCCCCGATGCC 60.592 66.667 0.00 0.00 0.00 4.40
1579 2974 2.125269 GCACGGGTAGGCAACGAT 60.125 61.111 0.00 0.00 46.39 3.73
1582 2977 2.038837 GGAAGCACGGGTAGGCAAC 61.039 63.158 0.00 0.00 0.00 4.17
1712 3113 8.883731 CCTAAAGAACAACGAATATCTGACAAT 58.116 33.333 0.00 0.00 0.00 2.71
1713 3114 7.876068 ACCTAAAGAACAACGAATATCTGACAA 59.124 33.333 0.00 0.00 0.00 3.18
1714 3115 7.330946 CACCTAAAGAACAACGAATATCTGACA 59.669 37.037 0.00 0.00 0.00 3.58
1715 3116 7.331193 ACACCTAAAGAACAACGAATATCTGAC 59.669 37.037 0.00 0.00 0.00 3.51
1716 3117 7.383687 ACACCTAAAGAACAACGAATATCTGA 58.616 34.615 0.00 0.00 0.00 3.27
1717 3118 7.201530 GGACACCTAAAGAACAACGAATATCTG 60.202 40.741 0.00 0.00 0.00 2.90
1725 3126 6.737254 ATAATGGACACCTAAAGAACAACG 57.263 37.500 0.00 0.00 0.00 4.10
1741 3142 7.895429 AGGAGAAGGAACAAAATGAATAATGGA 59.105 33.333 0.00 0.00 0.00 3.41
1761 3162 2.837591 TGCAGCCTATACACAAGGAGAA 59.162 45.455 0.00 0.00 36.08 2.87
1947 3351 9.697990 ACACTTAGCTAGTTAGTAGGTAAAGAT 57.302 33.333 16.38 6.00 46.32 2.40
1948 3352 9.171877 GACACTTAGCTAGTTAGTAGGTAAAGA 57.828 37.037 16.38 0.00 46.32 2.52
1949 3353 8.404765 GGACACTTAGCTAGTTAGTAGGTAAAG 58.595 40.741 16.38 14.24 46.32 1.85
1950 3354 7.066284 CGGACACTTAGCTAGTTAGTAGGTAAA 59.934 40.741 16.38 4.87 46.32 2.01
1951 3355 6.540189 CGGACACTTAGCTAGTTAGTAGGTAA 59.460 42.308 15.27 15.27 45.40 2.85
1952 3356 6.051717 CGGACACTTAGCTAGTTAGTAGGTA 58.948 44.000 2.24 2.24 40.15 3.08
1953 3357 4.880696 CGGACACTTAGCTAGTTAGTAGGT 59.119 45.833 4.17 4.17 42.35 3.08
1954 3358 4.880696 ACGGACACTTAGCTAGTTAGTAGG 59.119 45.833 0.00 0.00 33.85 3.18
1955 3359 5.730010 GCACGGACACTTAGCTAGTTAGTAG 60.730 48.000 0.00 0.00 33.85 2.57
1956 3360 4.095483 GCACGGACACTTAGCTAGTTAGTA 59.905 45.833 0.00 0.00 33.85 1.82
1957 3361 3.119566 GCACGGACACTTAGCTAGTTAGT 60.120 47.826 0.00 0.00 33.85 2.24
2083 3487 7.936950 AGACAATGACAAGATGTATGTATCG 57.063 36.000 0.00 0.00 32.33 2.92


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

AutoCloner maintained by Alex Coulton.