Multiple sequence alignment - TraesCS7A01G482900

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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 TraesCS7A01G482900 chr7A 100.000 2402 0 0 1 2402 674797820 674795419 0.000000e+00 4436.0
1 TraesCS7A01G482900 chr7A 94.916 1790 70 9 395 2181 674609065 674607294 0.000000e+00 2782.0
2 TraesCS7A01G482900 chr7A 88.920 1426 106 19 883 2294 674521234 674519847 0.000000e+00 1711.0
3 TraesCS7A01G482900 chr7A 89.478 1245 111 12 408 1647 674803095 674801866 0.000000e+00 1555.0
4 TraesCS7A01G482900 chr7A 90.746 670 45 8 1629 2298 674751444 674750792 0.000000e+00 878.0
5 TraesCS7A01G482900 chr7A 90.299 670 46 9 1629 2298 674736709 674736059 0.000000e+00 859.0
6 TraesCS7A01G482900 chr7A 95.082 305 9 4 102 403 674613628 674613327 2.160000e-130 475.0
7 TraesCS7A01G482900 chr7A 85.981 214 20 8 62 267 195199884 195200095 1.120000e-53 220.0
8 TraesCS7A01G482900 chr7A 96.667 120 2 2 2177 2294 674556224 674556105 5.240000e-47 198.0
9 TraesCS7A01G482900 chr7A 94.545 110 3 3 262 371 693838006 693838112 1.480000e-37 167.0
10 TraesCS7A01G482900 chr7A 89.189 74 3 4 1845 1917 86390789 86390720 1.180000e-13 87.9
11 TraesCS7A01G482900 chr7A 80.488 82 3 3 1 69 674613716 674613635 1.600000e-02 51.0
12 TraesCS7A01G482900 chr7D 88.524 1856 150 36 458 2290 582748408 582746593 0.000000e+00 2189.0
13 TraesCS7A01G482900 chr7D 87.004 1739 142 44 408 2126 582662731 582661057 0.000000e+00 1882.0
14 TraesCS7A01G482900 chr7D 86.552 1740 148 45 408 2126 582557556 582555882 0.000000e+00 1838.0
15 TraesCS7A01G482900 chr7D 92.157 612 42 5 1519 2126 583037884 583037275 0.000000e+00 859.0
16 TraesCS7A01G482900 chr7D 91.818 220 16 1 400 619 582562063 582561846 3.000000e-79 305.0
17 TraesCS7A01G482900 chr7D 91.818 220 16 1 400 619 582667389 582667172 3.000000e-79 305.0
18 TraesCS7A01G482900 chr7D 98.630 73 1 0 2219 2291 583037277 583037205 1.940000e-26 130.0
19 TraesCS7A01G482900 chr7D 93.506 77 4 1 2219 2294 582555884 582555808 1.950000e-21 113.0
20 TraesCS7A01G482900 chr7D 93.506 77 4 1 2219 2294 582661059 582660983 1.950000e-21 113.0
21 TraesCS7A01G482900 chr7D 96.875 32 0 1 1 32 502478719 502478689 4.000000e-03 52.8
22 TraesCS7A01G482900 chr7B 89.764 1231 109 8 428 1654 650551174 650549957 0.000000e+00 1559.0
23 TraesCS7A01G482900 chr7B 89.358 1231 110 9 428 1654 650585480 650584267 0.000000e+00 1528.0
24 TraesCS7A01G482900 chr7B 89.115 1231 117 8 428 1654 650540624 650539407 0.000000e+00 1515.0
25 TraesCS7A01G482900 chr7B 88.871 1231 107 9 428 1654 650562699 650561495 0.000000e+00 1487.0
26 TraesCS7A01G482900 chr7B 88.933 1003 98 5 655 1654 650574329 650573337 0.000000e+00 1225.0
27 TraesCS7A01G482900 chr7B 92.857 322 18 4 428 747 650551881 650551563 1.680000e-126 462.0
28 TraesCS7A01G482900 chr7B 87.054 224 10 8 55 267 585546719 585546934 3.990000e-58 235.0
29 TraesCS7A01G482900 chr7B 91.813 171 3 3 102 261 633239090 633239260 6.680000e-56 228.0
30 TraesCS7A01G482900 chr7B 93.878 98 6 0 2124 2221 705887485 705887388 5.350000e-32 148.0
31 TraesCS7A01G482900 chrUn 82.656 369 47 12 1152 1507 189558046 189557682 6.450000e-81 311.0
32 TraesCS7A01G482900 chrUn 82.114 369 49 12 1152 1507 154546336 154546700 1.400000e-77 300.0
33 TraesCS7A01G482900 chrUn 82.738 336 43 10 1152 1474 363525201 363524868 3.910000e-73 285.0
34 TraesCS7A01G482900 chrUn 82.738 336 43 10 1152 1474 363556862 363557195 3.910000e-73 285.0
35 TraesCS7A01G482900 chrUn 93.229 192 12 1 1452 1642 388900209 388900400 5.060000e-72 281.0
36 TraesCS7A01G482900 chrUn 93.229 192 12 1 1452 1642 388901873 388902064 5.060000e-72 281.0
37 TraesCS7A01G482900 chr4B 82.544 338 50 6 1152 1480 654751846 654751509 3.020000e-74 289.0
38 TraesCS7A01G482900 chr4B 82.249 338 51 6 1152 1480 654762085 654761748 1.410000e-72 283.0
39 TraesCS7A01G482900 chr4B 81.953 338 52 7 1152 1480 654774291 654773954 6.540000e-71 278.0
40 TraesCS7A01G482900 chr6D 85.357 280 18 12 102 369 445581610 445581342 3.940000e-68 268.0
41 TraesCS7A01G482900 chr6D 96.774 124 2 2 2281 2402 278944519 278944396 3.130000e-49 206.0
42 TraesCS7A01G482900 chr6D 80.455 220 17 15 51 267 281043040 281043236 6.920000e-31 145.0
43 TraesCS7A01G482900 chr2B 87.665 227 13 7 55 267 661330687 661330912 1.430000e-62 250.0
44 TraesCS7A01G482900 chr2B 92.661 109 5 2 264 372 771215241 771215136 1.150000e-33 154.0
45 TraesCS7A01G482900 chr2B 89.062 64 2 1 3 61 9033285 9033348 9.210000e-10 75.0
46 TraesCS7A01G482900 chr3B 82.927 287 25 13 102 374 797014460 797014184 1.110000e-58 237.0
47 TraesCS7A01G482900 chr3B 80.930 215 19 11 55 267 666176121 666175927 1.490000e-32 150.0
48 TraesCS7A01G482900 chr3B 90.090 111 8 3 2112 2221 738697161 738697269 8.950000e-30 141.0
49 TraesCS7A01G482900 chr3A 88.421 190 14 4 96 277 737540861 737541050 3.110000e-54 222.0
50 TraesCS7A01G482900 chr2D 91.071 168 10 4 102 267 47055519 47055355 3.110000e-54 222.0
51 TraesCS7A01G482900 chr2D 91.150 113 8 1 261 373 101884138 101884248 4.140000e-33 152.0
52 TraesCS7A01G482900 chr2D 92.929 99 7 0 2123 2221 206682657 206682755 6.920000e-31 145.0
53 TraesCS7A01G482900 chr2D 87.838 74 8 1 36 109 512693647 512693719 4.250000e-13 86.1
54 TraesCS7A01G482900 chr4A 89.503 181 8 6 102 273 712846728 712846550 4.020000e-53 219.0
55 TraesCS7A01G482900 chr4A 92.793 111 5 2 262 371 619148340 619148448 8.890000e-35 158.0
56 TraesCS7A01G482900 chr4A 94.595 37 1 1 1 36 711243772 711243736 3.340000e-04 56.5
57 TraesCS7A01G482900 chr6A 94.203 138 4 4 2268 2402 519561441 519561305 8.700000e-50 207.0
58 TraesCS7A01G482900 chr6A 92.661 109 6 1 265 373 145188722 145188616 3.200000e-34 156.0
59 TraesCS7A01G482900 chr6A 92.661 109 5 2 265 373 109973845 109973950 1.150000e-33 154.0
60 TraesCS7A01G482900 chr6A 90.000 110 8 3 2112 2220 517665439 517665546 3.220000e-29 139.0
61 TraesCS7A01G482900 chr5D 97.541 122 2 1 2281 2402 36088980 36088860 8.700000e-50 207.0
62 TraesCS7A01G482900 chr5D 96.748 123 3 1 2281 2402 488037421 488037299 1.130000e-48 204.0
63 TraesCS7A01G482900 chr5D 94.615 130 5 2 2274 2402 353704821 353704693 1.460000e-47 200.0
64 TraesCS7A01G482900 chr5D 98.214 112 2 0 2291 2402 382415453 382415342 1.880000e-46 196.0
65 TraesCS7A01G482900 chr5D 89.655 58 4 2 1849 1906 120881399 120881344 3.310000e-09 73.1
66 TraesCS7A01G482900 chr3D 97.521 121 2 1 2282 2402 2756279 2756398 3.130000e-49 206.0
67 TraesCS7A01G482900 chr3D 85.211 142 15 6 1710 1848 93586164 93586302 8.950000e-30 141.0
68 TraesCS7A01G482900 chr1D 96.721 122 4 0 2281 2402 44399564 44399443 1.130000e-48 204.0
69 TraesCS7A01G482900 chr1D 80.460 174 25 8 1676 1846 314831480 314831313 9.020000e-25 124.0
70 TraesCS7A01G482900 chr1D 81.879 149 20 7 2250 2395 445335280 445335424 4.190000e-23 119.0
71 TraesCS7A01G482900 chr1D 82.051 78 8 6 1845 1920 161567265 161567192 7.170000e-06 62.1
72 TraesCS7A01G482900 chr1A 92.806 139 7 3 2267 2402 486015778 486015916 5.240000e-47 198.0
73 TraesCS7A01G482900 chr1A 77.928 222 21 15 55 272 585655806 585656003 1.950000e-21 113.0
74 TraesCS7A01G482900 chr1B 90.909 110 10 0 2112 2221 600973410 600973519 5.350000e-32 148.0
75 TraesCS7A01G482900 chr5B 91.346 104 9 0 2124 2227 625959462 625959565 2.490000e-30 143.0
76 TraesCS7A01G482900 chr5B 93.333 60 2 2 1849 1908 712011902 712011845 1.180000e-13 87.9
77 TraesCS7A01G482900 chr5A 96.610 59 1 1 56 113 616368553 616368611 1.970000e-16 97.1


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 TraesCS7A01G482900 chr7A 674795419 674797820 2401 True 4436.0 4436 100.0000 1 2402 1 chr7A.!!$R7 2401
1 TraesCS7A01G482900 chr7A 674607294 674609065 1771 True 2782.0 2782 94.9160 395 2181 1 chr7A.!!$R4 1786
2 TraesCS7A01G482900 chr7A 674519847 674521234 1387 True 1711.0 1711 88.9200 883 2294 1 chr7A.!!$R2 1411
3 TraesCS7A01G482900 chr7A 674801866 674803095 1229 True 1555.0 1555 89.4780 408 1647 1 chr7A.!!$R8 1239
4 TraesCS7A01G482900 chr7A 674750792 674751444 652 True 878.0 878 90.7460 1629 2298 1 chr7A.!!$R6 669
5 TraesCS7A01G482900 chr7A 674736059 674736709 650 True 859.0 859 90.2990 1629 2298 1 chr7A.!!$R5 669
6 TraesCS7A01G482900 chr7D 582746593 582748408 1815 True 2189.0 2189 88.5240 458 2290 1 chr7D.!!$R4 1832
7 TraesCS7A01G482900 chr7D 582660983 582662731 1748 True 997.5 1882 90.2550 408 2294 2 chr7D.!!$R6 1886
8 TraesCS7A01G482900 chr7D 582555808 582557556 1748 True 975.5 1838 90.0290 408 2294 2 chr7D.!!$R5 1886
9 TraesCS7A01G482900 chr7D 583037205 583037884 679 True 494.5 859 95.3935 1519 2291 2 chr7D.!!$R7 772
10 TraesCS7A01G482900 chr7B 650584267 650585480 1213 True 1528.0 1528 89.3580 428 1654 1 chr7B.!!$R4 1226
11 TraesCS7A01G482900 chr7B 650539407 650540624 1217 True 1515.0 1515 89.1150 428 1654 1 chr7B.!!$R1 1226
12 TraesCS7A01G482900 chr7B 650561495 650562699 1204 True 1487.0 1487 88.8710 428 1654 1 chr7B.!!$R2 1226
13 TraesCS7A01G482900 chr7B 650573337 650574329 992 True 1225.0 1225 88.9330 655 1654 1 chr7B.!!$R3 999
14 TraesCS7A01G482900 chr7B 650549957 650551881 1924 True 1010.5 1559 91.3105 428 1654 2 chr7B.!!$R6 1226
15 TraesCS7A01G482900 chrUn 388900209 388902064 1855 False 281.0 281 93.2290 1452 1642 2 chrUn.!!$F3 190

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
81 82 2.043115 TGGGTCTGTCTAGGACACATCT 59.957 50.000 0.0 0.0 41.46 2.90 F
223 224 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.0 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1759 1.608717 GAAGAGGGCGAGCTTGGAGA 61.609 60.0 2.37 0.0 0.00 3.71 R
1507 2264 2.158900 ACACCTGACATATAGTGCCTGC 60.159 50.0 0.00 0.0 33.46 4.85 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
39 40 5.011090 TGTGACATACATCTAAGCTCCAC 57.989 43.478 0.00 0.00 33.42 4.02
40 41 4.711846 TGTGACATACATCTAAGCTCCACT 59.288 41.667 0.00 0.00 33.42 4.00
41 42 5.163509 TGTGACATACATCTAAGCTCCACTC 60.164 44.000 0.00 0.00 33.42 3.51
42 43 5.068460 GTGACATACATCTAAGCTCCACTCT 59.932 44.000 0.00 0.00 0.00 3.24
43 44 5.068329 TGACATACATCTAAGCTCCACTCTG 59.932 44.000 0.00 0.00 0.00 3.35
44 45 4.959210 ACATACATCTAAGCTCCACTCTGT 59.041 41.667 0.00 0.00 0.00 3.41
45 46 5.423610 ACATACATCTAAGCTCCACTCTGTT 59.576 40.000 0.00 0.00 0.00 3.16
46 47 4.899352 ACATCTAAGCTCCACTCTGTTT 57.101 40.909 0.00 0.00 0.00 2.83
47 48 7.124298 ACATACATCTAAGCTCCACTCTGTTTA 59.876 37.037 0.00 0.00 0.00 2.01
48 49 6.552445 ACATCTAAGCTCCACTCTGTTTAT 57.448 37.500 0.00 0.00 0.00 1.40
49 50 6.344500 ACATCTAAGCTCCACTCTGTTTATG 58.656 40.000 0.00 0.00 0.00 1.90
50 51 5.344743 TCTAAGCTCCACTCTGTTTATGG 57.655 43.478 0.00 0.00 34.58 2.74
51 52 4.777896 TCTAAGCTCCACTCTGTTTATGGT 59.222 41.667 0.00 0.00 34.89 3.55
52 53 3.618690 AGCTCCACTCTGTTTATGGTC 57.381 47.619 0.00 0.00 34.89 4.02
53 54 3.177228 AGCTCCACTCTGTTTATGGTCT 58.823 45.455 0.00 0.00 34.89 3.85
54 55 4.353777 AGCTCCACTCTGTTTATGGTCTA 58.646 43.478 0.00 0.00 34.89 2.59
55 56 4.965532 AGCTCCACTCTGTTTATGGTCTAT 59.034 41.667 0.00 0.00 34.89 1.98
56 57 5.426833 AGCTCCACTCTGTTTATGGTCTATT 59.573 40.000 0.00 0.00 34.89 1.73
57 58 6.069963 AGCTCCACTCTGTTTATGGTCTATTT 60.070 38.462 0.00 0.00 34.89 1.40
58 59 6.599638 GCTCCACTCTGTTTATGGTCTATTTT 59.400 38.462 0.00 0.00 34.89 1.82
59 60 7.121315 GCTCCACTCTGTTTATGGTCTATTTTT 59.879 37.037 0.00 0.00 34.89 1.94
77 78 3.764237 TTTTGGGTCTGTCTAGGACAC 57.236 47.619 0.00 0.00 37.67 3.67
78 79 2.391926 TTGGGTCTGTCTAGGACACA 57.608 50.000 0.00 0.00 44.14 3.72
79 80 2.623418 TGGGTCTGTCTAGGACACAT 57.377 50.000 0.00 0.00 41.46 3.21
80 81 2.457598 TGGGTCTGTCTAGGACACATC 58.542 52.381 0.00 0.00 41.46 3.06
81 82 2.043115 TGGGTCTGTCTAGGACACATCT 59.957 50.000 0.00 0.00 41.46 2.90
82 83 3.268595 TGGGTCTGTCTAGGACACATCTA 59.731 47.826 0.00 0.00 41.46 1.98
83 84 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
84 85 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
85 86 5.381757 GGTCTGTCTAGGACACATCTAGAT 58.618 45.833 0.00 0.00 43.25 1.98
86 87 5.240623 GGTCTGTCTAGGACACATCTAGATG 59.759 48.000 27.63 27.63 43.25 2.90
140 141 8.011844 ACATACTTATGTCACATCTAAGCTGA 57.988 34.615 0.00 0.00 42.96 4.26
141 142 8.646004 ACATACTTATGTCACATCTAAGCTGAT 58.354 33.333 0.00 0.00 42.96 2.90
142 143 8.923683 CATACTTATGTCACATCTAAGCTGATG 58.076 37.037 11.48 11.48 46.61 3.07
151 152 5.926214 CATCTAAGCTGATGTCCATTCTG 57.074 43.478 5.99 0.00 39.05 3.02
152 153 5.366460 CATCTAAGCTGATGTCCATTCTGT 58.634 41.667 5.99 0.00 39.05 3.41
153 154 5.426689 TCTAAGCTGATGTCCATTCTGTT 57.573 39.130 0.00 0.00 0.00 3.16
154 155 5.809001 TCTAAGCTGATGTCCATTCTGTTT 58.191 37.500 0.00 0.00 0.00 2.83
155 156 4.778534 AAGCTGATGTCCATTCTGTTTG 57.221 40.909 0.00 0.00 0.00 2.93
156 157 3.759581 AGCTGATGTCCATTCTGTTTGT 58.240 40.909 0.00 0.00 0.00 2.83
157 158 3.504906 AGCTGATGTCCATTCTGTTTGTG 59.495 43.478 0.00 0.00 0.00 3.33
158 159 3.366679 GCTGATGTCCATTCTGTTTGTGG 60.367 47.826 0.00 0.00 0.00 4.17
159 160 3.822735 CTGATGTCCATTCTGTTTGTGGT 59.177 43.478 0.00 0.00 34.61 4.16
160 161 4.214310 TGATGTCCATTCTGTTTGTGGTT 58.786 39.130 0.00 0.00 34.61 3.67
161 162 4.648762 TGATGTCCATTCTGTTTGTGGTTT 59.351 37.500 0.00 0.00 34.61 3.27
162 163 5.128499 TGATGTCCATTCTGTTTGTGGTTTT 59.872 36.000 0.00 0.00 34.61 2.43
163 164 5.413309 TGTCCATTCTGTTTGTGGTTTTT 57.587 34.783 0.00 0.00 34.61 1.94
211 212 9.613428 TGCTGTATTATATATATTTGTGGGAGC 57.387 33.333 0.00 2.17 0.00 4.70
212 213 9.838339 GCTGTATTATATATATTTGTGGGAGCT 57.162 33.333 0.00 0.00 0.00 4.09
220 221 9.896645 ATATATATTTGTGGGAGCTTAGATGTG 57.103 33.333 0.00 0.00 0.00 3.21
221 222 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
222 223 3.334583 TTGTGGGAGCTTAGATGTGAC 57.665 47.619 0.00 0.00 0.00 3.67
223 224 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
224 225 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
225 226 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
226 227 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
227 228 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
228 229 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
229 230 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
230 231 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
231 232 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
232 233 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
233 234 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
261 262 9.376075 CATCTAGATGTGAATTAGACAAACTGT 57.624 33.333 22.42 0.00 34.23 3.55
303 304 5.876612 TTTTTGTTTCTTGTTGCTGCATT 57.123 30.435 1.84 0.00 0.00 3.56
304 305 6.974932 TTTTTGTTTCTTGTTGCTGCATTA 57.025 29.167 1.84 0.00 0.00 1.90
305 306 7.551035 TTTTTGTTTCTTGTTGCTGCATTAT 57.449 28.000 1.84 0.00 0.00 1.28
306 307 8.654230 TTTTTGTTTCTTGTTGCTGCATTATA 57.346 26.923 1.84 0.00 0.00 0.98
307 308 8.830201 TTTTGTTTCTTGTTGCTGCATTATAT 57.170 26.923 1.84 0.00 0.00 0.86
308 309 9.920133 TTTTGTTTCTTGTTGCTGCATTATATA 57.080 25.926 1.84 0.00 0.00 0.86
314 315 9.518906 TTCTTGTTGCTGCATTATATATTTGTG 57.481 29.630 1.84 0.00 0.00 3.33
315 316 8.901793 TCTTGTTGCTGCATTATATATTTGTGA 58.098 29.630 1.84 0.00 0.00 3.58
316 317 9.177304 CTTGTTGCTGCATTATATATTTGTGAG 57.823 33.333 1.84 0.00 0.00 3.51
317 318 8.449251 TGTTGCTGCATTATATATTTGTGAGA 57.551 30.769 1.84 0.00 0.00 3.27
318 319 8.562052 TGTTGCTGCATTATATATTTGTGAGAG 58.438 33.333 1.84 0.00 0.00 3.20
319 320 7.137490 TGCTGCATTATATATTTGTGAGAGC 57.863 36.000 0.00 0.00 0.00 4.09
320 321 6.938596 TGCTGCATTATATATTTGTGAGAGCT 59.061 34.615 0.00 0.00 0.00 4.09
321 322 7.446319 TGCTGCATTATATATTTGTGAGAGCTT 59.554 33.333 0.00 0.00 0.00 3.74
322 323 8.939929 GCTGCATTATATATTTGTGAGAGCTTA 58.060 33.333 0.00 0.00 0.00 3.09
334 335 8.654230 TTTGTGAGAGCTTAGATATGACATTC 57.346 34.615 0.00 0.00 0.00 2.67
335 336 7.594351 TGTGAGAGCTTAGATATGACATTCT 57.406 36.000 0.00 0.00 0.00 2.40
336 337 8.016301 TGTGAGAGCTTAGATATGACATTCTT 57.984 34.615 0.00 0.00 0.00 2.52
337 338 9.136323 TGTGAGAGCTTAGATATGACATTCTTA 57.864 33.333 0.00 0.00 0.00 2.10
338 339 9.973450 GTGAGAGCTTAGATATGACATTCTTAA 57.027 33.333 0.00 0.00 0.00 1.85
378 379 9.959749 ATGTGAATTAAACAAACTGTTATTCGT 57.040 25.926 0.00 0.00 40.14 3.85
379 380 9.440784 TGTGAATTAAACAAACTGTTATTCGTC 57.559 29.630 0.00 0.00 40.14 4.20
380 381 9.440784 GTGAATTAAACAAACTGTTATTCGTCA 57.559 29.630 0.00 2.01 40.14 4.35
383 384 9.790389 AATTAAACAAACTGTTATTCGTCAACA 57.210 25.926 0.00 0.00 40.14 3.33
384 385 9.959749 ATTAAACAAACTGTTATTCGTCAACAT 57.040 25.926 0.00 0.00 40.14 2.71
387 388 8.776680 AACAAACTGTTATTCGTCAACATAAC 57.223 30.769 0.00 0.00 39.09 1.89
388 389 7.357303 ACAAACTGTTATTCGTCAACATAACC 58.643 34.615 0.00 0.00 35.72 2.85
389 390 7.012515 ACAAACTGTTATTCGTCAACATAACCA 59.987 33.333 0.00 0.00 35.72 3.67
390 391 7.499321 AACTGTTATTCGTCAACATAACCAA 57.501 32.000 0.00 0.00 35.72 3.67
391 392 7.681939 ACTGTTATTCGTCAACATAACCAAT 57.318 32.000 0.00 0.00 35.72 3.16
392 393 7.526608 ACTGTTATTCGTCAACATAACCAATG 58.473 34.615 0.00 0.00 41.74 2.82
393 394 6.847400 TGTTATTCGTCAACATAACCAATGG 58.153 36.000 0.00 0.00 40.16 3.16
833 1549 5.695818 ACGGTTGCACATAATCTTTACAAC 58.304 37.500 0.00 0.00 36.16 3.32
1395 2148 2.203788 TCCGACTTCACCTGCCCT 60.204 61.111 0.00 0.00 0.00 5.19
1408 2161 1.206610 CCTGCCCTATCTGATCCATCG 59.793 57.143 0.00 0.00 0.00 3.84
1410 2163 2.166050 CTGCCCTATCTGATCCATCGAG 59.834 54.545 0.00 0.00 0.00 4.04
1483 2239 1.586578 CATGTCATACGTACGCACCAC 59.413 52.381 16.72 8.07 0.00 4.16
1507 2264 8.328146 CACACGTATATTTTCTATGTTCCAGTG 58.672 37.037 0.00 0.00 0.00 3.66
1512 2269 2.113860 TTCTATGTTCCAGTGCAGGC 57.886 50.000 0.00 0.00 0.00 4.85
1533 2290 3.242413 GCACTATATGTCAGGTGTTTGCG 60.242 47.826 0.00 0.00 32.90 4.85
1658 2562 9.431887 GTACAAGGATATACAAAGTTGTCTTGA 57.568 33.333 20.57 8.68 38.90 3.02
1675 2579 8.609176 GTTGTCTTGACAGTACATGAAGTTAAA 58.391 33.333 0.00 0.00 0.00 1.52
1961 3249 7.325725 TCATGATCACATTTCATAGGGAGAT 57.674 36.000 0.00 0.00 34.15 2.75
1963 3251 9.054580 TCATGATCACATTTCATAGGGAGATAT 57.945 33.333 0.00 0.00 34.15 1.63
2071 3362 9.665719 TTGATTCAGTTATACATGTTAAGAGCA 57.334 29.630 2.30 0.00 0.00 4.26
2148 3560 5.203528 CTCCCTCCATTCCAAAATATGTGT 58.796 41.667 0.00 0.00 0.00 3.72
2172 3584 9.090692 TGTCTCAACTTTGTACTAACTTTGTAC 57.909 33.333 6.58 6.58 40.27 2.90
2307 4051 8.823220 ATAGGTATAATGTTGGAAATATGCCC 57.177 34.615 0.00 0.00 32.76 5.36
2308 4052 6.863322 AGGTATAATGTTGGAAATATGCCCT 58.137 36.000 0.00 0.00 32.76 5.19
2309 4053 7.995663 AGGTATAATGTTGGAAATATGCCCTA 58.004 34.615 0.00 0.00 32.76 3.53
2311 4055 8.107095 GGTATAATGTTGGAAATATGCCCTAGA 58.893 37.037 0.00 0.00 0.00 2.43
2312 4056 9.167311 GTATAATGTTGGAAATATGCCCTAGAG 57.833 37.037 0.00 0.00 0.00 2.43
2313 4057 4.437682 TGTTGGAAATATGCCCTAGAGG 57.562 45.455 0.00 0.00 39.47 3.69
2330 4074 8.934023 CCCTAGAGGCAATAATAAAATGGTTA 57.066 34.615 0.00 0.00 0.00 2.85
2331 4075 9.533831 CCCTAGAGGCAATAATAAAATGGTTAT 57.466 33.333 0.00 0.00 0.00 1.89
2373 4117 9.955208 TTCATGATAATTGTCTATTGTTCATGC 57.045 29.630 18.84 0.00 41.74 4.06
2374 4118 9.346005 TCATGATAATTGTCTATTGTTCATGCT 57.654 29.630 18.84 0.00 41.74 3.79
2384 4128 9.394767 TGTCTATTGTTCATGCTATAATTGTGT 57.605 29.630 0.00 0.00 0.00 3.72
2390 4134 7.860613 TGTTCATGCTATAATTGTGTTATCCG 58.139 34.615 0.00 0.00 0.00 4.18
2392 4136 6.764379 TCATGCTATAATTGTGTTATCCGGA 58.236 36.000 6.61 6.61 0.00 5.14
2393 4137 7.220740 TCATGCTATAATTGTGTTATCCGGAA 58.779 34.615 9.01 0.00 0.00 4.30
2394 4138 7.717436 TCATGCTATAATTGTGTTATCCGGAAA 59.283 33.333 9.01 0.99 0.00 3.13
2395 4139 8.514594 CATGCTATAATTGTGTTATCCGGAAAT 58.485 33.333 9.01 0.00 0.00 2.17
2396 4140 8.094798 TGCTATAATTGTGTTATCCGGAAATC 57.905 34.615 9.01 1.80 0.00 2.17
2397 4141 7.095397 TGCTATAATTGTGTTATCCGGAAATCG 60.095 37.037 9.01 0.00 38.88 3.34
2399 4143 9.414295 CTATAATTGTGTTATCCGGAAATCGTA 57.586 33.333 9.01 0.00 37.11 3.43
2400 4144 6.988622 AATTGTGTTATCCGGAAATCGTAA 57.011 33.333 9.01 0.00 37.11 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.711846 AGTGGAGCTTAGATGTATGTCACA 59.288 41.667 0.00 0.00 42.69 3.58
18 19 5.068460 AGAGTGGAGCTTAGATGTATGTCAC 59.932 44.000 0.00 0.00 0.00 3.67
19 20 5.068329 CAGAGTGGAGCTTAGATGTATGTCA 59.932 44.000 0.00 0.00 0.00 3.58
20 21 5.068460 ACAGAGTGGAGCTTAGATGTATGTC 59.932 44.000 0.00 0.00 0.00 3.06
21 22 4.959210 ACAGAGTGGAGCTTAGATGTATGT 59.041 41.667 0.00 0.00 0.00 2.29
22 23 5.528043 ACAGAGTGGAGCTTAGATGTATG 57.472 43.478 0.00 0.00 0.00 2.39
23 24 6.552445 AAACAGAGTGGAGCTTAGATGTAT 57.448 37.500 0.00 0.00 0.00 2.29
24 25 7.417911 CCATAAACAGAGTGGAGCTTAGATGTA 60.418 40.741 0.00 0.00 34.94 2.29
25 26 4.899352 AAACAGAGTGGAGCTTAGATGT 57.101 40.909 0.00 0.00 0.00 3.06
26 27 5.757320 CCATAAACAGAGTGGAGCTTAGATG 59.243 44.000 0.00 0.00 34.94 2.90
27 28 5.426833 ACCATAAACAGAGTGGAGCTTAGAT 59.573 40.000 0.00 0.00 36.82 1.98
28 29 4.777896 ACCATAAACAGAGTGGAGCTTAGA 59.222 41.667 0.00 0.00 36.82 2.10
29 30 5.091261 ACCATAAACAGAGTGGAGCTTAG 57.909 43.478 0.00 0.00 36.82 2.18
30 31 4.777896 AGACCATAAACAGAGTGGAGCTTA 59.222 41.667 0.00 0.00 36.82 3.09
31 32 3.584848 AGACCATAAACAGAGTGGAGCTT 59.415 43.478 0.00 0.00 36.82 3.74
32 33 3.177228 AGACCATAAACAGAGTGGAGCT 58.823 45.455 0.00 0.00 36.82 4.09
33 34 3.618690 AGACCATAAACAGAGTGGAGC 57.381 47.619 0.00 0.00 36.82 4.70
34 35 8.567285 AAAAATAGACCATAAACAGAGTGGAG 57.433 34.615 0.00 0.00 36.82 3.86
56 57 3.456644 TGTGTCCTAGACAGACCCAAAAA 59.543 43.478 0.00 0.00 43.57 1.94
57 58 3.042682 TGTGTCCTAGACAGACCCAAAA 58.957 45.455 0.00 0.00 43.57 2.44
58 59 2.684943 TGTGTCCTAGACAGACCCAAA 58.315 47.619 0.00 0.00 43.57 3.28
59 60 2.391926 TGTGTCCTAGACAGACCCAA 57.608 50.000 0.00 0.00 43.57 4.12
60 61 2.043115 AGATGTGTCCTAGACAGACCCA 59.957 50.000 0.00 0.00 43.57 4.51
61 62 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
62 63 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
63 64 6.312399 CATCTAGATGTGTCCTAGACAGAC 57.688 45.833 22.42 0.00 43.57 3.51
116 117 8.923683 CATCAGCTTAGATGTGACATAAGTATG 58.076 37.037 0.00 4.03 40.35 2.39
129 130 5.366460 ACAGAATGGACATCAGCTTAGATG 58.634 41.667 11.48 11.48 45.61 2.90
130 131 5.627182 ACAGAATGGACATCAGCTTAGAT 57.373 39.130 0.00 0.00 43.62 1.98
131 132 5.426689 AACAGAATGGACATCAGCTTAGA 57.573 39.130 0.00 0.00 43.62 2.10
132 133 5.413833 ACAAACAGAATGGACATCAGCTTAG 59.586 40.000 0.00 0.00 43.62 2.18
133 134 5.181811 CACAAACAGAATGGACATCAGCTTA 59.818 40.000 0.00 0.00 43.62 3.09
134 135 4.022589 CACAAACAGAATGGACATCAGCTT 60.023 41.667 0.00 0.00 43.62 3.74
135 136 3.504906 CACAAACAGAATGGACATCAGCT 59.495 43.478 0.00 0.00 43.62 4.24
136 137 3.366679 CCACAAACAGAATGGACATCAGC 60.367 47.826 0.00 0.00 43.62 4.26
137 138 3.822735 ACCACAAACAGAATGGACATCAG 59.177 43.478 0.00 0.00 43.62 2.90
138 139 3.831323 ACCACAAACAGAATGGACATCA 58.169 40.909 0.00 0.00 43.62 3.07
139 140 4.853924 AACCACAAACAGAATGGACATC 57.146 40.909 0.00 0.00 43.62 3.06
140 141 5.612725 AAAACCACAAACAGAATGGACAT 57.387 34.783 0.00 0.00 43.62 3.06
141 142 5.413309 AAAAACCACAAACAGAATGGACA 57.587 34.783 0.00 0.00 43.62 4.02
185 186 9.613428 GCTCCCACAAATATATATAATACAGCA 57.387 33.333 0.00 0.00 0.00 4.41
186 187 9.838339 AGCTCCCACAAATATATATAATACAGC 57.162 33.333 0.00 0.00 0.00 4.40
194 195 9.896645 CACATCTAAGCTCCCACAAATATATAT 57.103 33.333 0.00 0.00 0.00 0.86
195 196 9.100197 TCACATCTAAGCTCCCACAAATATATA 57.900 33.333 0.00 0.00 0.00 0.86
196 197 7.880195 GTCACATCTAAGCTCCCACAAATATAT 59.120 37.037 0.00 0.00 0.00 0.86
197 198 7.147567 TGTCACATCTAAGCTCCCACAAATATA 60.148 37.037 0.00 0.00 0.00 0.86
198 199 6.058183 GTCACATCTAAGCTCCCACAAATAT 58.942 40.000 0.00 0.00 0.00 1.28
199 200 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
200 201 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
201 202 3.072330 TGTCACATCTAAGCTCCCACAAA 59.928 43.478 0.00 0.00 0.00 2.83
202 203 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
203 204 2.256306 TGTCACATCTAAGCTCCCACA 58.744 47.619 0.00 0.00 0.00 4.17
204 205 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
205 206 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
206 207 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
207 208 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
208 209 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
235 236 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
281 282 5.876612 AATGCAGCAACAAGAAACAAAAA 57.123 30.435 0.00 0.00 0.00 1.94
282 283 8.830201 ATATAATGCAGCAACAAGAAACAAAA 57.170 26.923 0.00 0.00 0.00 2.44
288 289 9.518906 CACAAATATATAATGCAGCAACAAGAA 57.481 29.630 0.00 0.00 0.00 2.52
289 290 8.901793 TCACAAATATATAATGCAGCAACAAGA 58.098 29.630 0.00 0.00 0.00 3.02
290 291 9.177304 CTCACAAATATATAATGCAGCAACAAG 57.823 33.333 0.00 0.00 0.00 3.16
291 292 8.901793 TCTCACAAATATATAATGCAGCAACAA 58.098 29.630 0.00 0.00 0.00 2.83
292 293 8.449251 TCTCACAAATATATAATGCAGCAACA 57.551 30.769 0.00 0.00 0.00 3.33
293 294 7.536622 GCTCTCACAAATATATAATGCAGCAAC 59.463 37.037 0.00 0.00 0.00 4.17
294 295 7.446319 AGCTCTCACAAATATATAATGCAGCAA 59.554 33.333 0.00 0.00 0.00 3.91
295 296 6.938596 AGCTCTCACAAATATATAATGCAGCA 59.061 34.615 0.00 0.00 0.00 4.41
296 297 7.375106 AGCTCTCACAAATATATAATGCAGC 57.625 36.000 0.00 0.00 0.00 5.25
308 309 9.270640 GAATGTCATATCTAAGCTCTCACAAAT 57.729 33.333 0.00 0.00 0.00 2.32
309 310 8.481314 AGAATGTCATATCTAAGCTCTCACAAA 58.519 33.333 0.00 0.00 0.00 2.83
310 311 8.016301 AGAATGTCATATCTAAGCTCTCACAA 57.984 34.615 0.00 0.00 0.00 3.33
311 312 7.594351 AGAATGTCATATCTAAGCTCTCACA 57.406 36.000 0.00 0.00 0.00 3.58
312 313 9.973450 TTAAGAATGTCATATCTAAGCTCTCAC 57.027 33.333 0.00 0.00 0.00 3.51
352 353 9.959749 ACGAATAACAGTTTGTTTAATTCACAT 57.040 25.926 13.56 2.02 41.45 3.21
353 354 9.440784 GACGAATAACAGTTTGTTTAATTCACA 57.559 29.630 13.56 0.00 41.45 3.58
354 355 9.440784 TGACGAATAACAGTTTGTTTAATTCAC 57.559 29.630 13.56 9.33 41.45 3.18
357 358 9.790389 TGTTGACGAATAACAGTTTGTTTAATT 57.210 25.926 0.00 0.00 41.45 1.40
358 359 9.959749 ATGTTGACGAATAACAGTTTGTTTAAT 57.040 25.926 0.00 0.00 41.45 1.40
361 362 9.228636 GTTATGTTGACGAATAACAGTTTGTTT 57.771 29.630 0.00 0.00 41.45 2.83
362 363 7.858879 GGTTATGTTGACGAATAACAGTTTGTT 59.141 33.333 7.59 0.00 43.88 2.83
363 364 7.012515 TGGTTATGTTGACGAATAACAGTTTGT 59.987 33.333 7.59 0.00 40.92 2.83
364 365 7.356540 TGGTTATGTTGACGAATAACAGTTTG 58.643 34.615 7.59 0.00 40.92 2.93
365 366 7.499321 TGGTTATGTTGACGAATAACAGTTT 57.501 32.000 7.59 0.00 40.92 2.66
366 367 7.499321 TTGGTTATGTTGACGAATAACAGTT 57.501 32.000 7.59 0.00 40.92 3.16
367 368 7.361713 CCATTGGTTATGTTGACGAATAACAGT 60.362 37.037 7.59 0.00 40.92 3.55
368 369 6.966632 CCATTGGTTATGTTGACGAATAACAG 59.033 38.462 7.59 0.00 40.92 3.16
369 370 6.655425 TCCATTGGTTATGTTGACGAATAACA 59.345 34.615 1.86 0.00 39.82 2.41
370 371 7.079182 TCCATTGGTTATGTTGACGAATAAC 57.921 36.000 1.86 0.00 38.15 1.89
371 372 7.873719 ATCCATTGGTTATGTTGACGAATAA 57.126 32.000 1.86 0.00 31.99 1.40
372 373 7.988028 TGTATCCATTGGTTATGTTGACGAATA 59.012 33.333 1.86 0.00 31.99 1.75
373 374 6.826231 TGTATCCATTGGTTATGTTGACGAAT 59.174 34.615 1.86 0.00 31.99 3.34
374 375 6.174049 TGTATCCATTGGTTATGTTGACGAA 58.826 36.000 1.86 0.00 31.99 3.85
375 376 5.735766 TGTATCCATTGGTTATGTTGACGA 58.264 37.500 1.86 0.00 31.99 4.20
376 377 5.815222 TCTGTATCCATTGGTTATGTTGACG 59.185 40.000 1.86 0.00 31.99 4.35
377 378 7.807977 ATCTGTATCCATTGGTTATGTTGAC 57.192 36.000 1.86 0.00 31.99 3.18
378 379 8.821686 AAATCTGTATCCATTGGTTATGTTGA 57.178 30.769 1.86 0.00 31.99 3.18
379 380 9.950680 GTAAATCTGTATCCATTGGTTATGTTG 57.049 33.333 1.86 0.00 31.99 3.33
380 381 9.920946 AGTAAATCTGTATCCATTGGTTATGTT 57.079 29.630 1.86 0.00 31.99 2.71
1007 1759 1.608717 GAAGAGGGCGAGCTTGGAGA 61.609 60.000 2.37 0.00 0.00 3.71
1434 2187 7.978982 ACTAGTTACGAGTACAACGATTATGT 58.021 34.615 16.81 7.36 34.81 2.29
1483 2239 7.011016 TGCACTGGAACATAGAAAATATACGTG 59.989 37.037 0.00 0.00 38.20 4.49
1507 2264 2.158900 ACACCTGACATATAGTGCCTGC 60.159 50.000 0.00 0.00 33.46 4.85
1512 2269 3.932710 ACGCAAACACCTGACATATAGTG 59.067 43.478 0.00 0.00 36.30 2.74
1568 2325 6.657966 ACACTGATCATTGATCAATCACAAGT 59.342 34.615 25.29 16.64 46.51 3.16
1635 2393 8.322906 TGTCAAGACAACTTTGTATATCCTTG 57.677 34.615 11.52 11.52 42.43 3.61
1961 3249 6.283544 ACAAATTCATGACCAATGTGCATA 57.716 33.333 0.00 0.00 37.56 3.14
1963 3251 4.603989 ACAAATTCATGACCAATGTGCA 57.396 36.364 0.00 0.00 37.56 4.57
2148 3560 8.190122 TCGTACAAAGTTAGTACAAAGTTGAGA 58.810 33.333 0.00 0.00 41.40 3.27
2172 3584 9.408069 AGTGACTCAACTTTATACTAACTTTCG 57.592 33.333 0.00 0.00 0.00 3.46
2291 4035 4.990526 CCTCTAGGGCATATTTCCAACAT 58.009 43.478 0.00 0.00 0.00 2.71
2305 4049 7.839680 AACCATTTTATTATTGCCTCTAGGG 57.160 36.000 0.00 0.00 35.18 3.53
2348 4092 9.346005 AGCATGAACAATAGACAATTATCATGA 57.654 29.630 19.46 0.00 44.39 3.07
2364 4108 8.341903 CGGATAACACAATTATAGCATGAACAA 58.658 33.333 0.00 0.00 0.00 2.83
2366 4110 7.172532 TCCGGATAACACAATTATAGCATGAAC 59.827 37.037 0.00 0.00 0.00 3.18
2367 4111 7.220740 TCCGGATAACACAATTATAGCATGAA 58.779 34.615 0.00 0.00 0.00 2.57
2368 4112 6.764379 TCCGGATAACACAATTATAGCATGA 58.236 36.000 0.00 0.00 0.00 3.07
2369 4113 7.433708 TTCCGGATAACACAATTATAGCATG 57.566 36.000 4.15 0.00 0.00 4.06
2370 4114 8.635765 ATTTCCGGATAACACAATTATAGCAT 57.364 30.769 4.15 0.00 0.00 3.79
2373 4117 8.306680 ACGATTTCCGGATAACACAATTATAG 57.693 34.615 4.15 0.00 43.93 1.31
2374 4118 9.761504 TTACGATTTCCGGATAACACAATTATA 57.238 29.630 4.15 0.00 43.93 0.98
2377 4121 6.988622 TTACGATTTCCGGATAACACAATT 57.011 33.333 4.15 0.00 43.93 2.32


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

AutoCloner maintained by Alex Coulton.