Multiple sequence alignment - TraesCS2B01G177300

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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 TraesCS2B01G177300 chr2B 100.000 3830 0 0 1 3830 152471323 152475152 0.000000e+00 7073.0
1 TraesCS2B01G177300 chr2B 87.425 1169 133 9 1669 2830 152609752 152608591 0.000000e+00 1332.0
2 TraesCS2B01G177300 chr2B 91.073 941 79 4 2025 2964 152569896 152568960 0.000000e+00 1267.0
3 TraesCS2B01G177300 chr2B 98.510 537 7 1 3294 3830 490855690 490855155 0.000000e+00 946.0
4 TraesCS2B01G177300 chr2B 98.155 542 9 1 3290 3830 152495326 152495867 0.000000e+00 944.0
5 TraesCS2B01G177300 chr2B 92.624 583 41 2 1000 1580 152610676 152610094 0.000000e+00 837.0
6 TraesCS2B01G177300 chr2B 91.582 594 36 7 1340 1919 152570483 152569890 0.000000e+00 808.0
7 TraesCS2B01G177300 chr2B 85.077 583 38 18 732 1277 152571139 152570569 2.010000e-152 549.0
8 TraesCS2B01G177300 chr2B 84.211 190 20 4 515 702 152571315 152571134 3.930000e-40 176.0
9 TraesCS2B01G177300 chr2B 88.034 117 10 1 371 487 152571503 152571391 6.670000e-28 135.0
10 TraesCS2B01G177300 chr2A 95.000 2340 91 14 837 3165 100538207 100540531 0.000000e+00 3650.0
11 TraesCS2B01G177300 chr2A 87.537 2704 215 55 336 2968 100633830 100631178 0.000000e+00 3014.0
12 TraesCS2B01G177300 chr2A 90.801 1174 105 1 1657 2830 100651175 100650005 0.000000e+00 1567.0
13 TraesCS2B01G177300 chr2A 91.832 857 66 4 2315 3169 100631171 100630317 0.000000e+00 1192.0
14 TraesCS2B01G177300 chr2A 90.909 594 42 4 1000 1581 100656979 100656386 0.000000e+00 787.0
15 TraesCS2B01G177300 chr2A 92.281 285 9 3 376 647 100537808 100538092 3.590000e-105 392.0
16 TraesCS2B01G177300 chr2A 92.216 167 12 1 1 166 100531668 100531834 6.400000e-58 235.0
17 TraesCS2B01G177300 chr2A 96.386 83 3 0 303 385 100537549 100537631 1.860000e-28 137.0
18 TraesCS2B01G177300 chr2A 88.776 98 8 1 247 344 100640154 100640060 2.420000e-22 117.0
19 TraesCS2B01G177300 chr2D 90.562 2543 149 53 542 3047 101365556 101363068 0.000000e+00 3282.0
20 TraesCS2B01G177300 chr2D 88.830 2283 188 40 935 3169 100955057 100952794 0.000000e+00 2741.0
21 TraesCS2B01G177300 chr2D 88.039 2366 193 49 865 3169 100784417 100782081 0.000000e+00 2719.0
22 TraesCS2B01G177300 chr2D 94.566 1417 75 2 1608 3022 100420960 100422376 0.000000e+00 2189.0
23 TraesCS2B01G177300 chr2D 87.105 1171 133 11 1669 2830 101379045 101377884 0.000000e+00 1310.0
24 TraesCS2B01G177300 chr2D 96.528 576 20 0 1000 1575 100420386 100420961 0.000000e+00 953.0
25 TraesCS2B01G177300 chr2D 87.954 606 43 10 1000 1582 101380217 101379619 0.000000e+00 688.0
26 TraesCS2B01G177300 chr2D 84.464 457 27 18 491 930 100419924 100420353 9.900000e-111 411.0
27 TraesCS2B01G177300 chr2D 94.141 256 13 2 245 500 100417539 100417792 4.640000e-104 388.0
28 TraesCS2B01G177300 chr2D 87.547 265 23 5 253 514 101366087 101365830 8.040000e-77 298.0
29 TraesCS2B01G177300 chr2D 93.976 166 10 0 1 166 100417379 100417544 6.350000e-63 252.0
30 TraesCS2B01G177300 chr2D 88.439 173 15 4 540 710 100957562 100957393 1.800000e-48 204.0
31 TraesCS2B01G177300 chr2D 86.260 131 13 5 3042 3169 101308515 101308387 1.860000e-28 137.0
32 TraesCS2B01G177300 chr5D 79.848 1970 313 67 988 2921 529525402 529527323 0.000000e+00 1362.0
33 TraesCS2B01G177300 chr5D 94.186 86 5 0 163 248 338666290 338666205 8.630000e-27 132.0
34 TraesCS2B01G177300 chr5D 87.778 90 11 0 163 252 253048861 253048772 5.230000e-19 106.0
35 TraesCS2B01G177300 chr5B 79.724 1884 303 57 1076 2917 668461351 668463197 0.000000e+00 1290.0
36 TraesCS2B01G177300 chr5B 97.952 537 11 0 3294 3830 13316375 13315839 0.000000e+00 931.0
37 TraesCS2B01G177300 chr3B 98.155 542 9 1 3290 3830 444600410 444599869 0.000000e+00 944.0
38 TraesCS2B01G177300 chr3B 91.304 92 7 1 163 254 460106296 460106386 1.440000e-24 124.0
39 TraesCS2B01G177300 chr1B 98.138 537 10 0 3294 3830 14221059 14221595 0.000000e+00 937.0
40 TraesCS2B01G177300 chr1B 98.138 537 10 0 3294 3830 638801989 638802525 0.000000e+00 937.0
41 TraesCS2B01G177300 chr1B 97.786 542 10 2 3290 3830 14234033 14234573 0.000000e+00 933.0
42 TraesCS2B01G177300 chr1B 97.786 542 10 2 3290 3830 670462521 670463061 0.000000e+00 933.0
43 TraesCS2B01G177300 chr1B 92.157 102 6 2 163 263 286320573 286320473 3.990000e-30 143.0
44 TraesCS2B01G177300 chr1B 85.385 130 16 1 3167 3296 516116408 516116534 8.630000e-27 132.0
45 TraesCS2B01G177300 chr1B 94.118 68 3 1 3217 3284 648098095 648098029 6.770000e-18 102.0
46 TraesCS2B01G177300 chr4B 97.091 550 15 1 3282 3830 412103548 412102999 0.000000e+00 926.0
47 TraesCS2B01G177300 chr4B 87.368 95 12 0 158 252 647126753 647126847 4.050000e-20 110.0
48 TraesCS2B01G177300 chr5A 81.599 538 72 20 1064 1578 657537610 657538143 1.650000e-113 420.0
49 TraesCS2B01G177300 chr5A 90.698 129 12 0 3167 3295 3192340 3192468 5.090000e-39 172.0
50 TraesCS2B01G177300 chr5A 90.217 92 8 1 159 249 608401471 608401380 6.720000e-23 119.0
51 TraesCS2B01G177300 chr5A 90.000 90 9 0 163 252 623008732 623008643 2.420000e-22 117.0
52 TraesCS2B01G177300 chr4A 80.144 554 83 16 1023 1569 714270704 714271237 4.640000e-104 388.0
53 TraesCS2B01G177300 chr4A 89.922 129 13 0 3167 3295 274758651 274758523 2.370000e-37 167.0
54 TraesCS2B01G177300 chr4A 91.860 86 7 0 163 248 737382335 737382250 1.870000e-23 121.0
55 TraesCS2B01G177300 chr7B 88.462 130 13 2 3167 3295 637690031 637689903 5.120000e-34 156.0
56 TraesCS2B01G177300 chr7B 93.617 94 6 0 163 256 443310956 443310863 1.430000e-29 141.0
57 TraesCS2B01G177300 chr7B 90.323 93 9 0 163 255 157808014 157808106 5.200000e-24 122.0
58 TraesCS2B01G177300 chr7D 88.372 129 14 1 3167 3295 606509108 606508981 1.840000e-33 154.0
59 TraesCS2B01G177300 chr7D 91.209 91 8 0 163 253 540714224 540714314 1.440000e-24 124.0
60 TraesCS2B01G177300 chr7A 94.186 86 5 0 163 248 68752154 68752069 8.630000e-27 132.0
61 TraesCS2B01G177300 chr1A 91.667 96 6 2 158 252 568115704 568115610 8.630000e-27 132.0
62 TraesCS2B01G177300 chr1A 93.103 87 6 0 162 248 344497750 344497664 1.120000e-25 128.0
63 TraesCS2B01G177300 chr1A 90.805 87 8 0 162 248 467183762 467183676 2.420000e-22 117.0
64 TraesCS2B01G177300 chrUn 94.118 85 5 0 3211 3295 37406555 37406471 3.110000e-26 130.0
65 TraesCS2B01G177300 chrUn 90.476 84 8 0 165 248 95562533 95562450 1.120000e-20 111.0
66 TraesCS2B01G177300 chrUn 82.075 106 8 6 158 252 56557339 56557234 3.170000e-11 80.5
67 TraesCS2B01G177300 chr6B 93.182 88 6 0 162 249 1952137 1952050 3.110000e-26 130.0
68 TraesCS2B01G177300 chr6B 92.045 88 7 0 161 248 217682261 217682348 1.440000e-24 124.0
69 TraesCS2B01G177300 chr3D 89.247 93 9 1 160 251 305742795 305742703 8.690000e-22 115.0
70 TraesCS2B01G177300 chr3D 87.500 96 12 0 163 258 339850269 339850174 1.120000e-20 111.0
71 TraesCS2B01G177300 chr1D 90.698 86 8 0 163 248 318847056 318847141 8.690000e-22 115.0
72 TraesCS2B01G177300 chr1D 90.698 86 8 0 163 248 318847141 318847056 8.690000e-22 115.0
73 TraesCS2B01G177300 chr1D 88.506 87 10 0 162 248 472333355 472333269 5.230000e-19 106.0
74 TraesCS2B01G177300 chr1D 86.585 82 8 1 3217 3295 468747077 468746996 1.900000e-13 87.9
75 TraesCS2B01G177300 chr1D 89.552 67 5 2 191 256 447257684 447257619 2.450000e-12 84.2
76 TraesCS2B01G177300 chr1D 91.667 60 4 1 3236 3295 468747351 468747293 8.820000e-12 82.4
77 TraesCS2B01G177300 chr6D 88.506 87 9 1 163 248 304689886 304689800 1.880000e-18 104.0
78 TraesCS2B01G177300 chr6D 89.333 75 6 2 191 264 100387834 100387761 4.070000e-15 93.5
79 TraesCS2B01G177300 chr6D 94.915 59 3 0 190 248 447247841 447247899 4.070000e-15 93.5
80 TraesCS2B01G177300 chr6D 91.045 67 4 2 190 255 392856482 392856547 5.270000e-14 89.8
81 TraesCS2B01G177300 chr6D 84.536 97 7 4 163 251 453814007 453814103 5.270000e-14 89.8
82 TraesCS2B01G177300 chr6D 94.872 39 2 0 210 248 2244827 2244789 1.150000e-05 62.1
83 TraesCS2B01G177300 chr6D 100.000 28 0 0 222 249 295320649 295320622 7.000000e-03 52.8
84 TraesCS2B01G177300 chr4D 95.082 61 3 0 191 251 15859622 15859562 3.150000e-16 97.1
85 TraesCS2B01G177300 chr4D 84.694 98 13 2 153 249 430817112 430817016 3.150000e-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 TraesCS2B01G177300 chr2B 152471323 152475152 3829 False 7073.0 7073 100.000000 1 3830 1 chr2B.!!$F1 3829
1 TraesCS2B01G177300 chr2B 152608591 152610676 2085 True 1084.5 1332 90.024500 1000 2830 2 chr2B.!!$R3 1830
2 TraesCS2B01G177300 chr2B 490855155 490855690 535 True 946.0 946 98.510000 3294 3830 1 chr2B.!!$R1 536
3 TraesCS2B01G177300 chr2B 152495326 152495867 541 False 944.0 944 98.155000 3290 3830 1 chr2B.!!$F2 540
4 TraesCS2B01G177300 chr2B 152568960 152571503 2543 True 587.0 1267 87.995400 371 2964 5 chr2B.!!$R2 2593
5 TraesCS2B01G177300 chr2A 100630317 100633830 3513 True 2103.0 3014 89.684500 336 3169 2 chr2A.!!$R4 2833
6 TraesCS2B01G177300 chr2A 100650005 100651175 1170 True 1567.0 1567 90.801000 1657 2830 1 chr2A.!!$R2 1173
7 TraesCS2B01G177300 chr2A 100537549 100540531 2982 False 1393.0 3650 94.555667 303 3165 3 chr2A.!!$F2 2862
8 TraesCS2B01G177300 chr2A 100656386 100656979 593 True 787.0 787 90.909000 1000 1581 1 chr2A.!!$R3 581
9 TraesCS2B01G177300 chr2D 100782081 100784417 2336 True 2719.0 2719 88.039000 865 3169 1 chr2D.!!$R1 2304
10 TraesCS2B01G177300 chr2D 101363068 101366087 3019 True 1790.0 3282 89.054500 253 3047 2 chr2D.!!$R4 2794
11 TraesCS2B01G177300 chr2D 100952794 100957562 4768 True 1472.5 2741 88.634500 540 3169 2 chr2D.!!$R3 2629
12 TraesCS2B01G177300 chr2D 101377884 101380217 2333 True 999.0 1310 87.529500 1000 2830 2 chr2D.!!$R5 1830
13 TraesCS2B01G177300 chr2D 100417379 100422376 4997 False 838.6 2189 92.735000 1 3022 5 chr2D.!!$F1 3021
14 TraesCS2B01G177300 chr5D 529525402 529527323 1921 False 1362.0 1362 79.848000 988 2921 1 chr5D.!!$F1 1933
15 TraesCS2B01G177300 chr5B 668461351 668463197 1846 False 1290.0 1290 79.724000 1076 2917 1 chr5B.!!$F1 1841
16 TraesCS2B01G177300 chr5B 13315839 13316375 536 True 931.0 931 97.952000 3294 3830 1 chr5B.!!$R1 536
17 TraesCS2B01G177300 chr3B 444599869 444600410 541 True 944.0 944 98.155000 3290 3830 1 chr3B.!!$R1 540
18 TraesCS2B01G177300 chr1B 14221059 14221595 536 False 937.0 937 98.138000 3294 3830 1 chr1B.!!$F1 536
19 TraesCS2B01G177300 chr1B 638801989 638802525 536 False 937.0 937 98.138000 3294 3830 1 chr1B.!!$F4 536
20 TraesCS2B01G177300 chr1B 14234033 14234573 540 False 933.0 933 97.786000 3290 3830 1 chr1B.!!$F2 540
21 TraesCS2B01G177300 chr1B 670462521 670463061 540 False 933.0 933 97.786000 3290 3830 1 chr1B.!!$F5 540
22 TraesCS2B01G177300 chr4B 412102999 412103548 549 True 926.0 926 97.091000 3282 3830 1 chr4B.!!$R1 548
23 TraesCS2B01G177300 chr5A 657537610 657538143 533 False 420.0 420 81.599000 1064 1578 1 chr5A.!!$F2 514
24 TraesCS2B01G177300 chr4A 714270704 714271237 533 False 388.0 388 80.144000 1023 1569 1 chr4A.!!$F1 546

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
841 5585 0.174845 CCGTCGACCAGAAAGCCATA 59.825 55.000 10.58 0.0 0.00 2.74 F
1015 5800 1.229209 ACCATGGGTCTCGTCTGGT 60.229 57.895 18.09 0.0 35.41 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 8819 2.125326 CCCTATGCACGACCTCGGA 61.125 63.158 0.0 0.0 44.95 4.55 R
2999 9176 1.638589 TGGGGAGATAAAGGTGGTTGG 59.361 52.381 0.0 0.0 0.00 3.77 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
86 87 7.010697 TGTGTAGTTGTGATATTAATTGCGG 57.989 36.000 0.00 0.00 0.00 5.69
95 96 6.909895 TGTGATATTAATTGCGGAATGAAACG 59.090 34.615 1.80 0.00 0.00 3.60
162 163 9.924650 ACTTATCGTGATTTTAGTTTGAGTAGT 57.075 29.630 0.00 0.00 0.00 2.73
166 167 8.961294 TCGTGATTTTAGTTTGAGTAGTACTC 57.039 34.615 21.35 21.35 45.26 2.59
167 168 8.025445 TCGTGATTTTAGTTTGAGTAGTACTCC 58.975 37.037 24.32 11.44 44.44 3.85
168 169 7.275123 CGTGATTTTAGTTTGAGTAGTACTCCC 59.725 40.741 24.32 13.74 44.44 4.30
169 170 8.312564 GTGATTTTAGTTTGAGTAGTACTCCCT 58.687 37.037 24.32 18.93 44.44 4.20
170 171 8.311836 TGATTTTAGTTTGAGTAGTACTCCCTG 58.688 37.037 24.32 0.00 44.44 4.45
171 172 5.656213 TTAGTTTGAGTAGTACTCCCTGC 57.344 43.478 24.32 13.33 44.44 4.85
172 173 2.492484 AGTTTGAGTAGTACTCCCTGCG 59.508 50.000 24.32 0.00 44.44 5.18
173 174 2.211250 TTGAGTAGTACTCCCTGCGT 57.789 50.000 24.32 0.00 44.44 5.24
174 175 2.211250 TGAGTAGTACTCCCTGCGTT 57.789 50.000 24.32 0.00 44.44 4.84
175 176 2.089980 TGAGTAGTACTCCCTGCGTTC 58.910 52.381 24.32 1.22 44.44 3.95
176 177 2.290768 TGAGTAGTACTCCCTGCGTTCT 60.291 50.000 24.32 0.00 44.44 3.01
177 178 3.054875 TGAGTAGTACTCCCTGCGTTCTA 60.055 47.826 24.32 2.20 44.44 2.10
178 179 3.944015 GAGTAGTACTCCCTGCGTTCTAA 59.056 47.826 18.10 0.00 39.28 2.10
179 180 4.338879 AGTAGTACTCCCTGCGTTCTAAA 58.661 43.478 0.00 0.00 0.00 1.85
180 181 4.768968 AGTAGTACTCCCTGCGTTCTAAAA 59.231 41.667 0.00 0.00 0.00 1.52
181 182 4.820894 AGTACTCCCTGCGTTCTAAAAT 57.179 40.909 0.00 0.00 0.00 1.82
182 183 5.927281 AGTACTCCCTGCGTTCTAAAATA 57.073 39.130 0.00 0.00 0.00 1.40
183 184 5.903810 AGTACTCCCTGCGTTCTAAAATAG 58.096 41.667 0.00 0.00 0.00 1.73
184 185 5.655532 AGTACTCCCTGCGTTCTAAAATAGA 59.344 40.000 0.00 0.00 0.00 1.98
185 186 5.615925 ACTCCCTGCGTTCTAAAATAGAT 57.384 39.130 0.00 0.00 34.22 1.98
186 187 5.360591 ACTCCCTGCGTTCTAAAATAGATG 58.639 41.667 0.00 0.00 34.22 2.90
187 188 5.128827 ACTCCCTGCGTTCTAAAATAGATGA 59.871 40.000 0.00 0.00 34.22 2.92
188 189 5.357257 TCCCTGCGTTCTAAAATAGATGAC 58.643 41.667 0.00 0.00 34.22 3.06
189 190 5.128827 TCCCTGCGTTCTAAAATAGATGACT 59.871 40.000 0.00 0.00 34.22 3.41
190 191 5.817816 CCCTGCGTTCTAAAATAGATGACTT 59.182 40.000 0.00 0.00 34.22 3.01
191 192 6.984474 CCCTGCGTTCTAAAATAGATGACTTA 59.016 38.462 0.00 0.00 34.22 2.24
192 193 7.494625 CCCTGCGTTCTAAAATAGATGACTTAA 59.505 37.037 0.00 0.00 34.22 1.85
193 194 8.328864 CCTGCGTTCTAAAATAGATGACTTAAC 58.671 37.037 0.00 0.00 34.22 2.01
194 195 8.997621 TGCGTTCTAAAATAGATGACTTAACT 57.002 30.769 0.00 0.00 34.22 2.24
195 196 9.431887 TGCGTTCTAAAATAGATGACTTAACTT 57.568 29.630 0.00 0.00 34.22 2.66
239 240 9.855021 AAAATTGAGTTATCTATTTTGGAACGG 57.145 29.630 8.79 0.00 44.08 4.44
240 241 8.801882 AATTGAGTTATCTATTTTGGAACGGA 57.198 30.769 0.00 0.00 28.12 4.69
241 242 7.843490 TTGAGTTATCTATTTTGGAACGGAG 57.157 36.000 0.00 0.00 0.00 4.63
242 243 6.346096 TGAGTTATCTATTTTGGAACGGAGG 58.654 40.000 0.00 0.00 0.00 4.30
243 244 5.681639 AGTTATCTATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
284 285 3.584834 CAAGGAATTAAAAGTTGCGGGG 58.415 45.455 0.00 0.00 0.00 5.73
301 302 3.058155 GCGGGGAAAGAAGAAGAAGAAAC 60.058 47.826 0.00 0.00 0.00 2.78
408 595 7.925483 CCATGTTTGTTTGACAAGGAAATAGAA 59.075 33.333 0.00 0.00 39.53 2.10
435 622 2.159366 GCGAGGAAGAGAAGTCAATCGA 60.159 50.000 0.00 0.00 31.21 3.59
445 632 9.307121 GAAGAGAAGTCAATCGAGATAAATCAA 57.693 33.333 0.00 0.00 0.00 2.57
685 3296 2.693864 AGCTGGGGTCCATCCTGG 60.694 66.667 0.00 0.00 39.43 4.45
716 3327 3.138798 GTCCGAGGCTGGCTCGTA 61.139 66.667 39.23 28.87 42.15 3.43
717 3328 3.138798 TCCGAGGCTGGCTCGTAC 61.139 66.667 39.23 14.02 42.15 3.67
718 3329 3.141488 CCGAGGCTGGCTCGTACT 61.141 66.667 39.23 5.49 42.15 2.73
719 3330 2.711922 CCGAGGCTGGCTCGTACTT 61.712 63.158 39.23 4.74 42.15 2.24
721 3332 1.153549 GAGGCTGGCTCGTACTTGG 60.154 63.158 15.80 0.00 0.00 3.61
754 5478 3.461773 ACGGCTGATCTCACCCGG 61.462 66.667 16.11 0.00 46.40 5.73
779 5503 1.071567 CGACGAAACGCCTCTCTTCC 61.072 60.000 0.00 0.00 0.00 3.46
787 5511 1.153469 GCCTCTCTTCCGCCTTCTG 60.153 63.158 0.00 0.00 0.00 3.02
841 5585 0.174845 CCGTCGACCAGAAAGCCATA 59.825 55.000 10.58 0.00 0.00 2.74
944 5728 3.060602 GTCTCAAACTCACAGTACAGGC 58.939 50.000 0.00 0.00 0.00 4.85
948 5732 2.125512 CTCACAGTACAGGCCGCC 60.126 66.667 0.00 0.00 0.00 6.13
968 5753 3.315470 GCCGATATTTTCTCCTTGTTCCC 59.685 47.826 0.00 0.00 0.00 3.97
1015 5800 1.229209 ACCATGGGTCTCGTCTGGT 60.229 57.895 18.09 0.00 35.41 4.00
2177 7684 1.406539 GCTTATGTTGGAGGCATGTGG 59.593 52.381 0.00 0.00 0.00 4.17
2178 7685 1.406539 CTTATGTTGGAGGCATGTGGC 59.593 52.381 0.00 0.00 43.74 5.01
2353 7863 3.622630 GAGGAGGTGCTAAGAGAGTGTA 58.377 50.000 0.00 0.00 0.00 2.90
2652 8819 4.807643 GCCTTATTGTCTTTCTCCAGTGGT 60.808 45.833 9.54 0.00 0.00 4.16
2999 9176 8.593492 AATAAGTTCTTGATTTTTCTTGCCAC 57.407 30.769 0.00 0.00 0.00 5.01
3013 9190 1.917872 TGCCACCAACCACCTTTATC 58.082 50.000 0.00 0.00 0.00 1.75
3166 9346 7.714377 TCAAATTGCACACAAGGAATAAATGTT 59.286 29.630 0.00 0.00 39.69 2.71
3167 9347 8.986847 CAAATTGCACACAAGGAATAAATGTTA 58.013 29.630 0.00 0.00 39.69 2.41
3168 9348 8.532977 AATTGCACACAAGGAATAAATGTTAC 57.467 30.769 0.00 0.00 39.69 2.50
3169 9349 6.892658 TGCACACAAGGAATAAATGTTACT 57.107 33.333 0.00 0.00 0.00 2.24
3170 9350 6.908825 TGCACACAAGGAATAAATGTTACTC 58.091 36.000 0.00 0.00 0.00 2.59
3171 9351 6.072175 TGCACACAAGGAATAAATGTTACTCC 60.072 38.462 0.00 0.00 0.00 3.85
3172 9352 6.625081 GCACACAAGGAATAAATGTTACTCCC 60.625 42.308 0.00 0.00 0.00 4.30
3173 9353 6.659242 CACACAAGGAATAAATGTTACTCCCT 59.341 38.462 0.00 0.00 0.00 4.20
3174 9354 6.884836 ACACAAGGAATAAATGTTACTCCCTC 59.115 38.462 0.00 0.00 0.00 4.30
3175 9355 6.318900 CACAAGGAATAAATGTTACTCCCTCC 59.681 42.308 0.00 0.00 0.00 4.30
3176 9356 5.291905 AGGAATAAATGTTACTCCCTCCG 57.708 43.478 0.00 0.00 0.00 4.63
3177 9357 4.720273 AGGAATAAATGTTACTCCCTCCGT 59.280 41.667 0.00 0.00 0.00 4.69
3178 9358 5.055144 GGAATAAATGTTACTCCCTCCGTC 58.945 45.833 0.00 0.00 0.00 4.79
3179 9359 5.163332 GGAATAAATGTTACTCCCTCCGTCT 60.163 44.000 0.00 0.00 0.00 4.18
3180 9360 3.889520 AAATGTTACTCCCTCCGTCTC 57.110 47.619 0.00 0.00 0.00 3.36
3181 9361 1.390565 ATGTTACTCCCTCCGTCTCG 58.609 55.000 0.00 0.00 0.00 4.04
3191 9371 4.420143 CCGTCTCGGTGCATTAGG 57.580 61.111 0.00 0.00 42.73 2.69
3192 9372 1.883084 CCGTCTCGGTGCATTAGGC 60.883 63.158 0.00 0.00 42.73 3.93
3193 9373 2.572095 CCGTCTCGGTGCATTAGGCA 62.572 60.000 0.00 0.00 44.59 4.75
3207 9387 6.486253 GCATTAGGCATCTATCGAAAATCA 57.514 37.500 0.00 0.00 43.97 2.57
3208 9388 6.902341 GCATTAGGCATCTATCGAAAATCAA 58.098 36.000 0.00 0.00 43.97 2.57
3209 9389 7.362662 GCATTAGGCATCTATCGAAAATCAAA 58.637 34.615 0.00 0.00 43.97 2.69
3210 9390 8.025445 GCATTAGGCATCTATCGAAAATCAAAT 58.975 33.333 0.00 0.00 43.97 2.32
3216 9396 9.346725 GGCATCTATCGAAAATCAAATAATTCC 57.653 33.333 0.00 0.00 0.00 3.01
3217 9397 9.897744 GCATCTATCGAAAATCAAATAATTCCA 57.102 29.630 0.00 0.00 0.00 3.53
3224 9404 9.434420 TCGAAAATCAAATAATTCCAAAATGCT 57.566 25.926 0.00 0.00 0.00 3.79
3229 9409 8.667076 ATCAAATAATTCCAAAATGCTAAGGC 57.333 30.769 0.00 0.00 39.26 4.35
3242 9422 4.730949 TGCTAAGGCACGAAATAGTAGT 57.269 40.909 0.00 0.00 44.28 2.73
3243 9423 5.840243 TGCTAAGGCACGAAATAGTAGTA 57.160 39.130 0.00 0.00 44.28 1.82
3244 9424 5.585390 TGCTAAGGCACGAAATAGTAGTAC 58.415 41.667 0.00 0.00 44.28 2.73
3245 9425 5.359009 TGCTAAGGCACGAAATAGTAGTACT 59.641 40.000 8.14 8.14 44.28 2.73
3246 9426 6.543465 TGCTAAGGCACGAAATAGTAGTACTA 59.457 38.462 12.38 12.38 44.28 1.82
3247 9427 7.076983 GCTAAGGCACGAAATAGTAGTACTAG 58.923 42.308 15.08 4.76 34.68 2.57
3248 9428 7.041508 GCTAAGGCACGAAATAGTAGTACTAGA 60.042 40.741 15.08 0.00 34.68 2.43
3249 9429 7.820578 AAGGCACGAAATAGTAGTACTAGAT 57.179 36.000 15.08 6.74 33.66 1.98
3250 9430 7.204496 AGGCACGAAATAGTAGTACTAGATG 57.796 40.000 15.08 9.45 33.66 2.90
3251 9431 5.857517 GGCACGAAATAGTAGTACTAGATGC 59.142 44.000 15.08 16.49 33.66 3.91
3252 9432 6.436261 GCACGAAATAGTAGTACTAGATGCA 58.564 40.000 15.08 0.00 33.66 3.96
3253 9433 7.085116 GCACGAAATAGTAGTACTAGATGCAT 58.915 38.462 15.08 0.00 33.66 3.96
3254 9434 7.061210 GCACGAAATAGTAGTACTAGATGCATG 59.939 40.741 15.08 9.90 33.66 4.06
3255 9435 7.061210 CACGAAATAGTAGTACTAGATGCATGC 59.939 40.741 11.82 11.82 33.66 4.06
3256 9436 7.084486 CGAAATAGTAGTACTAGATGCATGCA 58.916 38.462 25.04 25.04 33.66 3.96
3257 9437 7.757173 CGAAATAGTAGTACTAGATGCATGCAT 59.243 37.037 32.66 32.66 33.66 3.96
3271 9451 8.503458 AGATGCATGCATATTAATTAGACTCC 57.497 34.615 32.27 14.66 36.70 3.85
3272 9452 8.105197 AGATGCATGCATATTAATTAGACTCCA 58.895 33.333 32.27 0.00 36.70 3.86
3273 9453 8.818622 ATGCATGCATATTAATTAGACTCCAT 57.181 30.769 31.35 1.24 34.49 3.41
3274 9454 8.272545 TGCATGCATATTAATTAGACTCCATC 57.727 34.615 18.46 0.00 0.00 3.51
3275 9455 8.105197 TGCATGCATATTAATTAGACTCCATCT 58.895 33.333 18.46 0.00 41.95 2.90
3276 9456 9.605275 GCATGCATATTAATTAGACTCCATCTA 57.395 33.333 14.21 0.00 39.04 1.98
3493 9673 0.035739 GGTGCGAACCCTTCTACCAA 59.964 55.000 0.00 0.00 35.74 3.67
3503 9683 1.596496 CTTCTACCAATGGAGGGGGT 58.404 55.000 6.16 0.00 38.70 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.589908 ACTTGTAAGATCCAATGACCCAC 58.410 43.478 0.00 0.00 0.00 4.61
25 26 9.255304 GAGAAGATACTTGTAAGATCCAATGAC 57.745 37.037 0.00 0.00 0.00 3.06
62 63 6.819146 TCCGCAATTAATATCACAACTACACA 59.181 34.615 0.00 0.00 0.00 3.72
67 68 7.566760 TCATTCCGCAATTAATATCACAACT 57.433 32.000 0.00 0.00 0.00 3.16
68 69 8.531530 GTTTCATTCCGCAATTAATATCACAAC 58.468 33.333 0.00 0.00 0.00 3.32
140 141 9.570488 GAGTACTACTCAAACTAAAATCACGAT 57.430 33.333 10.85 0.00 44.45 3.73
160 161 4.820894 ATTTTAGAACGCAGGGAGTACT 57.179 40.909 0.00 0.00 0.00 2.73
161 162 5.899299 TCTATTTTAGAACGCAGGGAGTAC 58.101 41.667 0.00 0.00 0.00 2.73
162 163 6.322969 TCATCTATTTTAGAACGCAGGGAGTA 59.677 38.462 0.00 0.00 38.50 2.59
163 164 5.128827 TCATCTATTTTAGAACGCAGGGAGT 59.871 40.000 0.00 0.00 38.50 3.85
164 165 5.463724 GTCATCTATTTTAGAACGCAGGGAG 59.536 44.000 0.00 0.00 38.50 4.30
165 166 5.128827 AGTCATCTATTTTAGAACGCAGGGA 59.871 40.000 0.00 0.00 38.50 4.20
166 167 5.360591 AGTCATCTATTTTAGAACGCAGGG 58.639 41.667 0.00 0.00 38.50 4.45
167 168 6.910536 AAGTCATCTATTTTAGAACGCAGG 57.089 37.500 0.00 0.00 38.50 4.85
168 169 9.088512 AGTTAAGTCATCTATTTTAGAACGCAG 57.911 33.333 0.00 0.00 38.50 5.18
169 170 8.997621 AGTTAAGTCATCTATTTTAGAACGCA 57.002 30.769 0.00 0.00 38.50 5.24
213 214 9.855021 CCGTTCCAAAATAGATAACTCAATTTT 57.145 29.630 0.00 0.00 33.07 1.82
214 215 9.238368 TCCGTTCCAAAATAGATAACTCAATTT 57.762 29.630 0.00 0.00 0.00 1.82
215 216 8.801882 TCCGTTCCAAAATAGATAACTCAATT 57.198 30.769 0.00 0.00 0.00 2.32
216 217 7.499232 CCTCCGTTCCAAAATAGATAACTCAAT 59.501 37.037 0.00 0.00 0.00 2.57
217 218 6.821665 CCTCCGTTCCAAAATAGATAACTCAA 59.178 38.462 0.00 0.00 0.00 3.02
218 219 6.346096 CCTCCGTTCCAAAATAGATAACTCA 58.654 40.000 0.00 0.00 0.00 3.41
219 220 5.758784 CCCTCCGTTCCAAAATAGATAACTC 59.241 44.000 0.00 0.00 0.00 3.01
220 221 5.427481 TCCCTCCGTTCCAAAATAGATAACT 59.573 40.000 0.00 0.00 0.00 2.24
221 222 5.677567 TCCCTCCGTTCCAAAATAGATAAC 58.322 41.667 0.00 0.00 0.00 1.89
222 223 5.427481 ACTCCCTCCGTTCCAAAATAGATAA 59.573 40.000 0.00 0.00 0.00 1.75
223 224 4.966805 ACTCCCTCCGTTCCAAAATAGATA 59.033 41.667 0.00 0.00 0.00 1.98
224 225 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
225 226 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
226 227 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
227 228 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
228 229 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
229 230 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
230 231 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
231 232 2.019807 AAGTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
232 233 2.905415 TAAGTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
233 234 7.178097 ACATATAATAAGTACTCCCTCCGTTCC 59.822 40.741 0.00 0.00 0.00 3.62
234 235 8.120140 ACATATAATAAGTACTCCCTCCGTTC 57.880 38.462 0.00 0.00 0.00 3.95
235 236 8.488308 AACATATAATAAGTACTCCCTCCGTT 57.512 34.615 0.00 0.00 0.00 4.44
236 237 8.365647 CAAACATATAATAAGTACTCCCTCCGT 58.634 37.037 0.00 0.00 0.00 4.69
237 238 7.331193 GCAAACATATAATAAGTACTCCCTCCG 59.669 40.741 0.00 0.00 0.00 4.63
238 239 8.154856 TGCAAACATATAATAAGTACTCCCTCC 58.845 37.037 0.00 0.00 0.00 4.30
239 240 9.555727 TTGCAAACATATAATAAGTACTCCCTC 57.444 33.333 0.00 0.00 0.00 4.30
240 241 9.561069 CTTGCAAACATATAATAAGTACTCCCT 57.439 33.333 0.00 0.00 0.00 4.20
241 242 8.784043 CCTTGCAAACATATAATAAGTACTCCC 58.216 37.037 0.00 0.00 0.00 4.30
242 243 9.555727 TCCTTGCAAACATATAATAAGTACTCC 57.444 33.333 0.00 0.00 0.00 3.85
284 285 5.050023 CGTGAGGGTTTCTTCTTCTTCTTTC 60.050 44.000 0.00 0.00 0.00 2.62
301 302 0.795735 CGTAACTGCGTACGTGAGGG 60.796 60.000 17.90 5.46 41.51 4.30
408 595 2.167487 GACTTCTCTTCCTCGCCAAGAT 59.833 50.000 0.00 0.00 0.00 2.40
435 622 5.407995 GCTAGATTGAGCGCTTGATTTATCT 59.592 40.000 13.26 15.04 31.57 1.98
445 632 0.467384 ACATGGCTAGATTGAGCGCT 59.533 50.000 11.27 11.27 43.83 5.92
618 3219 1.065764 CGTACGCATGGAGCTGCTA 59.934 57.895 6.82 0.00 42.61 3.49
685 3296 3.488090 GGACGCGCACCAACTAGC 61.488 66.667 5.73 0.00 0.00 3.42
715 3326 0.034198 TGCGTGCAAGTAGCCAAGTA 59.966 50.000 0.59 0.00 44.83 2.24
716 3327 0.606401 ATGCGTGCAAGTAGCCAAGT 60.606 50.000 0.00 0.00 44.83 3.16
717 3328 0.097674 GATGCGTGCAAGTAGCCAAG 59.902 55.000 0.00 0.00 44.83 3.61
718 3329 0.605050 TGATGCGTGCAAGTAGCCAA 60.605 50.000 3.38 0.00 44.83 4.52
719 3330 1.003959 TGATGCGTGCAAGTAGCCA 60.004 52.632 3.38 0.00 44.83 4.75
721 3332 1.059369 CGTGATGCGTGCAAGTAGC 59.941 57.895 0.00 0.00 45.96 3.58
779 5503 3.387947 ACCGGGGTACAGAAGGCG 61.388 66.667 6.32 0.00 0.00 5.52
895 5644 3.917329 TGTGTTTGTTTCCGTTGTGAA 57.083 38.095 0.00 0.00 0.00 3.18
944 5728 2.561569 ACAAGGAGAAAATATCGGCGG 58.438 47.619 7.21 0.00 0.00 6.13
948 5732 4.439057 TCGGGAACAAGGAGAAAATATCG 58.561 43.478 0.00 0.00 0.00 2.92
968 5753 0.458543 CGGTGGTCACTCAGGATTCG 60.459 60.000 0.93 0.00 0.00 3.34
1137 5922 1.186917 TCCCGGCGAAGAACCTGTAA 61.187 55.000 9.30 0.00 0.00 2.41
1449 6343 4.542075 GGGTTCCCGATGCTCTTC 57.458 61.111 0.00 0.00 0.00 2.87
1593 6524 4.918129 ACACGTCAACGCGCGTCT 62.918 61.111 37.77 22.85 44.43 4.18
1597 6528 3.816474 GACACACACGTCAACGCGC 62.816 63.158 5.73 0.00 44.43 6.86
2652 8819 2.125326 CCCTATGCACGACCTCGGA 61.125 63.158 0.00 0.00 44.95 4.55
2995 9172 2.092323 GAGATAAAGGTGGTTGGTGGC 58.908 52.381 0.00 0.00 0.00 5.01
2999 9176 1.638589 TGGGGAGATAAAGGTGGTTGG 59.361 52.381 0.00 0.00 0.00 3.77
3013 9190 4.346418 AGATAGTGACTATGCTTTGGGGAG 59.654 45.833 10.29 0.00 0.00 4.30
3175 9355 3.706140 GCCTAATGCACCGAGACG 58.294 61.111 0.00 0.00 40.77 4.18
3198 9378 9.434420 AGCATTTTGGAATTATTTGATTTTCGA 57.566 25.926 0.00 0.00 0.00 3.71
3203 9383 9.112725 GCCTTAGCATTTTGGAATTATTTGATT 57.887 29.630 0.00 0.00 39.53 2.57
3204 9384 8.266473 TGCCTTAGCATTTTGGAATTATTTGAT 58.734 29.630 0.00 0.00 46.52 2.57
3205 9385 7.619050 TGCCTTAGCATTTTGGAATTATTTGA 58.381 30.769 0.00 0.00 46.52 2.69
3206 9386 7.846644 TGCCTTAGCATTTTGGAATTATTTG 57.153 32.000 0.00 0.00 46.52 2.32
3221 9401 7.255035 CTAGTACTACTATTTCGTGCCTTAGCA 60.255 40.741 0.00 0.00 37.01 3.49
3222 9402 5.829829 AGTACTACTATTTCGTGCCTTAGC 58.170 41.667 0.00 0.00 40.48 3.09
3223 9403 8.375608 TCTAGTACTACTATTTCGTGCCTTAG 57.624 38.462 0.00 0.00 29.08 2.18
3224 9404 8.781196 CATCTAGTACTACTATTTCGTGCCTTA 58.219 37.037 0.00 0.00 29.08 2.69
3225 9405 7.649973 CATCTAGTACTACTATTTCGTGCCTT 58.350 38.462 0.00 0.00 29.08 4.35
3226 9406 6.294065 GCATCTAGTACTACTATTTCGTGCCT 60.294 42.308 0.00 0.00 29.08 4.75
3227 9407 5.857517 GCATCTAGTACTACTATTTCGTGCC 59.142 44.000 0.00 0.00 29.08 5.01
3228 9408 6.436261 TGCATCTAGTACTACTATTTCGTGC 58.564 40.000 0.00 2.22 29.08 5.34
3229 9409 7.061210 GCATGCATCTAGTACTACTATTTCGTG 59.939 40.741 14.21 3.85 29.08 4.35
3230 9410 7.085116 GCATGCATCTAGTACTACTATTTCGT 58.915 38.462 14.21 0.00 29.08 3.85
3231 9411 7.084486 TGCATGCATCTAGTACTACTATTTCG 58.916 38.462 18.46 0.00 29.08 3.46
3232 9412 8.994429 ATGCATGCATCTAGTACTACTATTTC 57.006 34.615 27.46 0.00 29.08 2.17
3245 9425 9.605275 GGAGTCTAATTAATATGCATGCATCTA 57.395 33.333 35.35 23.86 37.82 1.98
3246 9426 8.105197 TGGAGTCTAATTAATATGCATGCATCT 58.895 33.333 35.35 23.86 37.82 2.90
3247 9427 8.272545 TGGAGTCTAATTAATATGCATGCATC 57.727 34.615 35.35 17.36 37.82 3.91
3248 9428 8.818622 ATGGAGTCTAATTAATATGCATGCAT 57.181 30.769 33.92 33.92 40.19 3.96
3249 9429 8.105197 AGATGGAGTCTAATTAATATGCATGCA 58.895 33.333 25.04 25.04 34.69 3.96
3250 9430 8.503458 AGATGGAGTCTAATTAATATGCATGC 57.497 34.615 11.82 11.82 34.69 4.06
3282 9462 1.676968 CCACGACATTGGTCCTCCA 59.323 57.895 0.00 0.00 41.13 3.86
3283 9463 4.617875 CCACGACATTGGTCCTCC 57.382 61.111 0.00 0.00 41.13 4.30
3289 9469 3.679980 CAGACTTAGAACCACGACATTGG 59.320 47.826 0.00 0.00 43.04 3.16
3290 9470 4.386049 GTCAGACTTAGAACCACGACATTG 59.614 45.833 0.00 0.00 0.00 2.82
3291 9471 4.038763 TGTCAGACTTAGAACCACGACATT 59.961 41.667 1.31 0.00 0.00 2.71
3292 9472 3.572682 TGTCAGACTTAGAACCACGACAT 59.427 43.478 1.31 0.00 0.00 3.06
3493 9673 2.222461 TATAAGCCAACCCCCTCCAT 57.778 50.000 0.00 0.00 0.00 3.41
3503 9683 3.955650 GGCGTCCTCTATATAAGCCAA 57.044 47.619 0.00 0.00 42.37 4.52


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

AutoCloner maintained by Alex Coulton.