Multiple sequence alignment - TraesCS6B01G373500

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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 TraesCS6B01G373500 chr6B 100.000 3627 0 0 1 3627 646639668 646636042 0.000000e+00 6698.0
1 TraesCS6B01G373500 chr6B 96.667 1860 48 3 1782 3627 164818184 164820043 0.000000e+00 3079.0
2 TraesCS6B01G373500 chr6B 89.286 1008 46 19 427 1397 164816637 164817619 0.000000e+00 1206.0
3 TraesCS6B01G373500 chr6B 96.000 225 6 3 1559 1783 164817801 164818022 2.660000e-96 363.0
4 TraesCS6B01G373500 chr6B 97.333 150 4 0 129 278 646639465 646639316 4.650000e-64 255.0
5 TraesCS6B01G373500 chr6B 97.333 150 4 0 204 353 646639540 646639391 4.650000e-64 255.0
6 TraesCS6B01G373500 chr6B 97.333 75 2 0 129 203 646639390 646639316 1.060000e-25 128.0
7 TraesCS6B01G373500 chr6B 97.333 75 2 0 279 353 646639540 646639466 1.060000e-25 128.0
8 TraesCS6B01G373500 chr6B 100.000 60 0 0 1501 1560 164817618 164817677 1.060000e-20 111.0
9 TraesCS6B01G373500 chr4A 99.065 3207 24 1 427 3627 467313325 467310119 0.000000e+00 5751.0
10 TraesCS6B01G373500 chr4A 89.831 177 15 2 2915 3089 300286304 300286129 1.310000e-54 224.0
11 TraesCS6B01G373500 chr4A 82.192 73 7 3 221 288 553075344 553075273 1.410000e-04 58.4
12 TraesCS6B01G373500 chr5A 98.780 2050 25 0 1578 3627 675530269 675528220 0.000000e+00 3648.0
13 TraesCS6B01G373500 chr5A 97.455 1847 43 3 1782 3627 243809600 243807757 0.000000e+00 3147.0
14 TraesCS6B01G373500 chr5A 95.267 972 30 3 428 1397 675531338 675530381 0.000000e+00 1526.0
15 TraesCS6B01G373500 chr5A 90.702 1011 48 23 428 1397 243811172 243810167 0.000000e+00 1304.0
16 TraesCS6B01G373500 chr5A 82.883 555 66 10 3089 3627 345568416 345567875 4.240000e-129 472.0
17 TraesCS6B01G373500 chr5A 96.035 227 8 1 1557 1783 243809987 243809762 5.720000e-98 368.0
18 TraesCS6B01G373500 chr5A 99.200 125 0 1 1501 1625 675530382 675530259 1.310000e-54 224.0
19 TraesCS6B01G373500 chr5A 99.091 110 1 0 1393 1502 95823079 95823188 7.940000e-47 198.0
20 TraesCS6B01G373500 chr5A 100.000 60 0 0 1501 1560 243810168 243810109 1.060000e-20 111.0
21 TraesCS6B01G373500 chr5A 92.857 70 3 2 288 357 520438312 520438245 2.300000e-17 100.0
22 TraesCS6B01G373500 chr6D 94.786 2129 84 13 1501 3627 60310549 60308446 0.000000e+00 3291.0
23 TraesCS6B01G373500 chr6D 92.220 527 36 2 873 1397 60311071 60310548 0.000000e+00 741.0
24 TraesCS6B01G373500 chr6D 91.638 287 17 2 432 711 60311526 60311240 1.220000e-104 390.0
25 TraesCS6B01G373500 chr6D 99.099 111 1 0 3089 3199 60309080 60308970 2.210000e-47 200.0
26 TraesCS6B01G373500 chr6D 95.000 120 5 1 280 399 429341499 429341381 1.720000e-43 187.0
27 TraesCS6B01G373500 chr6D 80.916 131 16 8 301 428 430993292 430993416 1.070000e-15 95.3
28 TraesCS6B01G373500 chr4D 95.387 1951 51 5 1501 3451 363569075 363570986 0.000000e+00 3068.0
29 TraesCS6B01G373500 chr4D 87.602 984 56 27 427 1397 363568146 363569076 0.000000e+00 1081.0
30 TraesCS6B01G373500 chr4D 96.875 96 3 0 3468 3563 363571029 363571124 1.040000e-35 161.0
31 TraesCS6B01G373500 chr4D 83.660 153 11 5 697 844 363568431 363568574 8.170000e-27 132.0
32 TraesCS6B01G373500 chr3B 97.217 1689 46 1 1782 3470 796470642 796468955 0.000000e+00 2857.0
33 TraesCS6B01G373500 chr3B 90.585 1009 55 13 427 1397 796472215 796471209 0.000000e+00 1301.0
34 TraesCS6B01G373500 chr3B 96.476 227 7 1 1557 1783 796471029 796470804 1.230000e-99 374.0
35 TraesCS6B01G373500 chr3B 98.857 175 1 1 3454 3627 796468933 796468759 9.780000e-81 311.0
36 TraesCS6B01G373500 chr3B 98.333 60 1 0 1501 1560 796471210 796471151 4.950000e-19 106.0
37 TraesCS6B01G373500 chr3A 94.359 1755 97 2 1501 3255 356923615 356925367 0.000000e+00 2691.0
38 TraesCS6B01G373500 chr3A 87.910 579 59 6 819 1397 356923049 356923616 0.000000e+00 671.0
39 TraesCS6B01G373500 chr3A 95.349 172 8 0 3454 3625 356925442 356925613 1.280000e-69 274.0
40 TraesCS6B01G373500 chr3A 98.214 112 2 0 1391 1502 152176490 152176379 2.860000e-46 196.0
41 TraesCS6B01G373500 chr3A 98.214 112 1 1 1391 1502 308676030 308675920 1.030000e-45 195.0
42 TraesCS6B01G373500 chr2D 86.889 839 71 23 1560 2365 127782056 127781224 0.000000e+00 904.0
43 TraesCS6B01G373500 chr2D 84.259 540 54 10 3089 3612 612421069 612420545 6.990000e-137 497.0
44 TraesCS6B01G373500 chr2D 89.706 68 6 1 206 273 530145122 530145056 6.450000e-13 86.1
45 TraesCS6B01G373500 chr2D 89.706 68 6 1 131 198 530145122 530145056 6.450000e-13 86.1
46 TraesCS6B01G373500 chrUn 100.000 386 0 0 1089 1474 480647683 480648068 0.000000e+00 713.0
47 TraesCS6B01G373500 chr1A 84.018 438 41 20 1560 1978 100017111 100016684 9.440000e-106 394.0
48 TraesCS6B01G373500 chr1A 82.331 266 35 7 427 685 315272128 315271868 1.700000e-53 220.0
49 TraesCS6B01G373500 chr1A 99.091 110 1 0 1396 1505 493213052 493212943 7.940000e-47 198.0
50 TraesCS6B01G373500 chr1A 96.522 115 3 1 1393 1506 11269024 11269138 4.780000e-44 189.0
51 TraesCS6B01G373500 chr4B 91.418 268 21 2 890 1155 203204109 203204376 2.060000e-97 366.0
52 TraesCS6B01G373500 chr4B 82.482 411 54 7 2367 2774 508522060 508521665 9.640000e-91 344.0
53 TraesCS6B01G373500 chr4B 82.264 265 37 5 427 685 167920907 167920647 1.700000e-53 220.0
54 TraesCS6B01G373500 chr4B 77.826 230 34 12 206 428 390833441 390833222 3.800000e-25 126.0
55 TraesCS6B01G373500 chr4B 77.093 227 36 13 206 425 25450030 25450247 2.290000e-22 117.0
56 TraesCS6B01G373500 chr4B 78.767 146 22 8 131 273 390833441 390833302 4.990000e-14 89.8
57 TraesCS6B01G373500 chr4B 89.706 68 6 1 131 198 25450030 25450096 6.450000e-13 86.1
58 TraesCS6B01G373500 chr7A 80.065 306 45 12 390 685 305711990 305711691 2.840000e-51 213.0
59 TraesCS6B01G373500 chr7A 99.091 110 1 0 1393 1502 609518899 609519008 7.940000e-47 198.0
60 TraesCS6B01G373500 chr7D 94.355 124 5 2 1382 1505 568753355 568753476 4.780000e-44 189.0
61 TraesCS6B01G373500 chr6A 81.757 148 20 5 281 428 36853148 36853008 2.290000e-22 117.0
62 TraesCS6B01G373500 chr6A 90.769 65 3 2 131 193 36853148 36853085 2.320000e-12 84.2
63 TraesCS6B01G373500 chr1B 76.522 230 38 13 206 428 669884673 669884453 1.060000e-20 111.0
64 TraesCS6B01G373500 chr1B 89.706 68 6 1 131 198 669884673 669884607 6.450000e-13 86.1
65 TraesCS6B01G373500 chr1B 91.071 56 4 1 704 759 153424625 153424571 1.400000e-09 75.0
66 TraesCS6B01G373500 chr2B 78.010 191 29 12 206 390 415378693 415378510 1.380000e-19 108.0
67 TraesCS6B01G373500 chr2B 79.054 148 22 7 281 426 691264700 691264840 3.860000e-15 93.5
68 TraesCS6B01G373500 chr2B 88.235 68 7 1 131 198 415378693 415378627 3.000000e-11 80.5
69 TraesCS6B01G373500 chr5B 86.667 90 8 4 185 273 40482267 40482353 2.980000e-16 97.1
70 TraesCS6B01G373500 chr5B 88.235 68 7 1 131 198 40482287 40482353 3.000000e-11 80.5


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 TraesCS6B01G373500 chr6B 646636042 646639668 3626 True 1492.800000 6698 97.866400 1 3627 5 chr6B.!!$R1 3626
1 TraesCS6B01G373500 chr6B 164816637 164820043 3406 False 1189.750000 3079 95.488250 427 3627 4 chr6B.!!$F1 3200
2 TraesCS6B01G373500 chr4A 467310119 467313325 3206 True 5751.000000 5751 99.065000 427 3627 1 chr4A.!!$R2 3200
3 TraesCS6B01G373500 chr5A 675528220 675531338 3118 True 1799.333333 3648 97.749000 428 3627 3 chr5A.!!$R4 3199
4 TraesCS6B01G373500 chr5A 243807757 243811172 3415 True 1232.500000 3147 96.048000 428 3627 4 chr5A.!!$R3 3199
5 TraesCS6B01G373500 chr5A 345567875 345568416 541 True 472.000000 472 82.883000 3089 3627 1 chr5A.!!$R1 538
6 TraesCS6B01G373500 chr6D 60308446 60311526 3080 True 1155.500000 3291 94.435750 432 3627 4 chr6D.!!$R2 3195
7 TraesCS6B01G373500 chr4D 363568146 363571124 2978 False 1110.500000 3068 90.881000 427 3563 4 chr4D.!!$F1 3136
8 TraesCS6B01G373500 chr3B 796468759 796472215 3456 True 989.800000 2857 96.293600 427 3627 5 chr3B.!!$R1 3200
9 TraesCS6B01G373500 chr3A 356923049 356925613 2564 False 1212.000000 2691 92.539333 819 3625 3 chr3A.!!$F1 2806
10 TraesCS6B01G373500 chr2D 127781224 127782056 832 True 904.000000 904 86.889000 1560 2365 1 chr2D.!!$R1 805
11 TraesCS6B01G373500 chr2D 612420545 612421069 524 True 497.000000 497 84.259000 3089 3612 1 chr2D.!!$R2 523

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
470 472 0.241749 ATTGCTTCGGTCGTACGTCA 59.758 50.0 16.05 0.0 34.94 4.35 F
491 493 1.230324 GGCAGTCTCGCAGAAAAGTT 58.770 50.0 0.00 0.0 34.09 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 3195 1.065418 CAGCGGTAGGGAATTGGAGTT 60.065 52.381 0.00 0.0 0.00 3.01 R
2737 3488 3.294794 GAAATCTGATTTTGGCGGCACG 61.295 50.000 12.92 0.0 44.29 5.34 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
17 18 3.604629 ACTGTCGTAGCATCGCCT 58.395 55.556 0.00 0.00 0.00 5.52
18 19 1.139734 ACTGTCGTAGCATCGCCTG 59.860 57.895 0.00 0.00 0.00 4.85
26 27 3.567797 GCATCGCCTGCGTCCTTC 61.568 66.667 11.68 0.00 41.97 3.46
27 28 2.892425 CATCGCCTGCGTCCTTCC 60.892 66.667 11.68 0.00 40.74 3.46
28 29 3.390521 ATCGCCTGCGTCCTTCCA 61.391 61.111 11.68 0.00 40.74 3.53
29 30 2.735772 ATCGCCTGCGTCCTTCCAT 61.736 57.895 11.68 0.00 40.74 3.41
30 31 2.650813 ATCGCCTGCGTCCTTCCATC 62.651 60.000 11.68 0.00 40.74 3.51
31 32 2.268920 GCCTGCGTCCTTCCATCA 59.731 61.111 0.00 0.00 0.00 3.07
32 33 2.109126 GCCTGCGTCCTTCCATCAC 61.109 63.158 0.00 0.00 0.00 3.06
33 34 1.450312 CCTGCGTCCTTCCATCACC 60.450 63.158 0.00 0.00 0.00 4.02
34 35 1.811266 CTGCGTCCTTCCATCACCG 60.811 63.158 0.00 0.00 0.00 4.94
35 36 2.264794 GCGTCCTTCCATCACCGT 59.735 61.111 0.00 0.00 0.00 4.83
36 37 2.100631 GCGTCCTTCCATCACCGTG 61.101 63.158 0.00 0.00 0.00 4.94
37 38 2.100631 CGTCCTTCCATCACCGTGC 61.101 63.158 0.00 0.00 0.00 5.34
38 39 1.745489 GTCCTTCCATCACCGTGCC 60.745 63.158 0.00 0.00 0.00 5.01
39 40 2.438434 CCTTCCATCACCGTGCCC 60.438 66.667 0.00 0.00 0.00 5.36
40 41 2.819595 CTTCCATCACCGTGCCCG 60.820 66.667 0.00 0.00 0.00 6.13
92 93 4.827087 CCGCGAGCCACTCATGCT 62.827 66.667 8.23 0.00 43.03 3.79
97 98 2.581354 AGCCACTCATGCTCCGTC 59.419 61.111 0.00 0.00 32.41 4.79
98 99 2.512515 GCCACTCATGCTCCGTCC 60.513 66.667 0.00 0.00 0.00 4.79
99 100 2.202797 CCACTCATGCTCCGTCCG 60.203 66.667 0.00 0.00 0.00 4.79
100 101 2.887568 CACTCATGCTCCGTCCGC 60.888 66.667 0.00 0.00 0.00 5.54
101 102 3.381983 ACTCATGCTCCGTCCGCA 61.382 61.111 0.00 0.00 42.25 5.69
102 103 2.887568 CTCATGCTCCGTCCGCAC 60.888 66.667 0.00 0.00 40.65 5.34
103 104 4.451150 TCATGCTCCGTCCGCACC 62.451 66.667 0.00 0.00 40.65 5.01
136 137 3.908081 CGCGCCCCGGTAGTGTAT 61.908 66.667 0.00 0.00 0.00 2.29
137 138 2.554636 CGCGCCCCGGTAGTGTATA 61.555 63.158 0.00 0.00 0.00 1.47
138 139 1.870055 CGCGCCCCGGTAGTGTATAT 61.870 60.000 0.00 0.00 0.00 0.86
139 140 0.319405 GCGCCCCGGTAGTGTATATT 59.681 55.000 0.00 0.00 0.00 1.28
140 141 1.938016 GCGCCCCGGTAGTGTATATTG 60.938 57.143 0.00 0.00 0.00 1.90
141 142 1.804601 GCCCCGGTAGTGTATATTGC 58.195 55.000 0.00 0.00 0.00 3.56
142 143 1.071071 GCCCCGGTAGTGTATATTGCA 59.929 52.381 0.00 0.00 0.00 4.08
143 144 2.485835 GCCCCGGTAGTGTATATTGCAA 60.486 50.000 0.00 0.00 0.00 4.08
144 145 3.399330 CCCCGGTAGTGTATATTGCAAG 58.601 50.000 4.94 0.00 0.00 4.01
145 146 3.181458 CCCCGGTAGTGTATATTGCAAGT 60.181 47.826 4.94 0.00 0.00 3.16
146 147 3.807622 CCCGGTAGTGTATATTGCAAGTG 59.192 47.826 4.94 0.00 0.00 3.16
147 148 4.442332 CCCGGTAGTGTATATTGCAAGTGA 60.442 45.833 4.94 0.00 0.00 3.41
148 149 5.113383 CCGGTAGTGTATATTGCAAGTGAA 58.887 41.667 4.94 0.00 0.00 3.18
149 150 5.583061 CCGGTAGTGTATATTGCAAGTGAAA 59.417 40.000 4.94 0.00 0.00 2.69
150 151 6.260050 CCGGTAGTGTATATTGCAAGTGAAAT 59.740 38.462 4.94 0.00 0.00 2.17
151 152 7.125755 CGGTAGTGTATATTGCAAGTGAAATG 58.874 38.462 4.94 0.00 0.00 2.32
152 153 7.417612 GGTAGTGTATATTGCAAGTGAAATGG 58.582 38.462 4.94 0.00 0.00 3.16
153 154 7.282224 GGTAGTGTATATTGCAAGTGAAATGGA 59.718 37.037 4.94 0.00 0.00 3.41
154 155 7.886629 AGTGTATATTGCAAGTGAAATGGAT 57.113 32.000 4.94 0.00 0.00 3.41
155 156 8.297470 AGTGTATATTGCAAGTGAAATGGATT 57.703 30.769 4.94 0.00 0.00 3.01
156 157 8.752187 AGTGTATATTGCAAGTGAAATGGATTT 58.248 29.630 4.94 0.00 0.00 2.17
157 158 9.023967 GTGTATATTGCAAGTGAAATGGATTTC 57.976 33.333 4.94 5.32 44.83 2.17
177 178 9.476761 GGATTTCAATTATTTTTCGATTGTTGC 57.523 29.630 0.00 0.00 33.60 4.17
180 181 7.579589 TCAATTATTTTTCGATTGTTGCAGG 57.420 32.000 0.00 0.00 33.60 4.85
181 182 6.090628 TCAATTATTTTTCGATTGTTGCAGGC 59.909 34.615 0.00 0.00 33.60 4.85
182 183 3.665745 ATTTTTCGATTGTTGCAGGCT 57.334 38.095 0.00 0.00 0.00 4.58
183 184 4.782019 ATTTTTCGATTGTTGCAGGCTA 57.218 36.364 0.00 0.00 0.00 3.93
184 185 4.782019 TTTTTCGATTGTTGCAGGCTAT 57.218 36.364 0.00 0.00 0.00 2.97
185 186 4.355543 TTTTCGATTGTTGCAGGCTATC 57.644 40.909 0.00 0.00 0.00 2.08
186 187 2.988010 TCGATTGTTGCAGGCTATCT 57.012 45.000 10.89 0.00 0.00 1.98
187 188 3.266510 TCGATTGTTGCAGGCTATCTT 57.733 42.857 10.89 0.00 0.00 2.40
188 189 3.198068 TCGATTGTTGCAGGCTATCTTC 58.802 45.455 10.89 0.00 0.00 2.87
189 190 3.118629 TCGATTGTTGCAGGCTATCTTCT 60.119 43.478 10.89 0.00 0.00 2.85
190 191 3.624861 CGATTGTTGCAGGCTATCTTCTT 59.375 43.478 10.89 0.00 0.00 2.52
191 192 4.095483 CGATTGTTGCAGGCTATCTTCTTT 59.905 41.667 10.89 0.00 0.00 2.52
192 193 5.294306 CGATTGTTGCAGGCTATCTTCTTTA 59.706 40.000 10.89 0.00 0.00 1.85
193 194 6.017605 CGATTGTTGCAGGCTATCTTCTTTAT 60.018 38.462 10.89 0.00 0.00 1.40
194 195 7.171508 CGATTGTTGCAGGCTATCTTCTTTATA 59.828 37.037 10.89 0.00 0.00 0.98
195 196 7.553881 TTGTTGCAGGCTATCTTCTTTATAC 57.446 36.000 0.00 0.00 0.00 1.47
196 197 6.649155 TGTTGCAGGCTATCTTCTTTATACA 58.351 36.000 0.00 0.00 0.00 2.29
197 198 7.282585 TGTTGCAGGCTATCTTCTTTATACAT 58.717 34.615 0.00 0.00 0.00 2.29
198 199 7.775093 TGTTGCAGGCTATCTTCTTTATACATT 59.225 33.333 0.00 0.00 0.00 2.71
199 200 8.624776 GTTGCAGGCTATCTTCTTTATACATTT 58.375 33.333 0.00 0.00 0.00 2.32
200 201 8.158169 TGCAGGCTATCTTCTTTATACATTTG 57.842 34.615 0.00 0.00 0.00 2.32
201 202 7.992608 TGCAGGCTATCTTCTTTATACATTTGA 59.007 33.333 0.00 0.00 0.00 2.69
202 203 8.840321 GCAGGCTATCTTCTTTATACATTTGAA 58.160 33.333 0.00 0.00 0.00 2.69
220 221 9.231297 ACATTTGAAGTAGTGTATATTGCAAGT 57.769 29.630 4.94 0.00 0.00 3.16
221 222 9.494479 CATTTGAAGTAGTGTATATTGCAAGTG 57.506 33.333 4.94 0.00 0.00 3.16
222 223 8.840833 TTTGAAGTAGTGTATATTGCAAGTGA 57.159 30.769 4.94 0.00 0.00 3.41
223 224 8.840833 TTGAAGTAGTGTATATTGCAAGTGAA 57.159 30.769 4.94 0.00 0.00 3.18
224 225 8.840833 TGAAGTAGTGTATATTGCAAGTGAAA 57.159 30.769 4.94 0.00 0.00 2.69
225 226 9.448438 TGAAGTAGTGTATATTGCAAGTGAAAT 57.552 29.630 4.94 0.00 0.00 2.17
226 227 9.708222 GAAGTAGTGTATATTGCAAGTGAAATG 57.292 33.333 4.94 0.00 0.00 2.32
227 228 9.448438 AAGTAGTGTATATTGCAAGTGAAATGA 57.552 29.630 4.94 0.00 0.00 2.57
228 229 9.448438 AGTAGTGTATATTGCAAGTGAAATGAA 57.552 29.630 4.94 0.00 0.00 2.57
255 256 7.579589 TCAATTATTTTTCGATTGTTGCAGG 57.420 32.000 0.00 0.00 33.60 4.85
256 257 6.090628 TCAATTATTTTTCGATTGTTGCAGGC 59.909 34.615 0.00 0.00 33.60 4.85
257 258 3.665745 ATTTTTCGATTGTTGCAGGCT 57.334 38.095 0.00 0.00 0.00 4.58
258 259 4.782019 ATTTTTCGATTGTTGCAGGCTA 57.218 36.364 0.00 0.00 0.00 3.93
259 260 4.782019 TTTTTCGATTGTTGCAGGCTAT 57.218 36.364 0.00 0.00 0.00 2.97
260 261 4.355543 TTTTCGATTGTTGCAGGCTATC 57.644 40.909 0.00 0.00 0.00 2.08
261 262 2.988010 TCGATTGTTGCAGGCTATCT 57.012 45.000 10.89 0.00 0.00 1.98
262 263 3.266510 TCGATTGTTGCAGGCTATCTT 57.733 42.857 10.89 0.00 0.00 2.40
263 264 3.609853 TCGATTGTTGCAGGCTATCTTT 58.390 40.909 10.89 0.00 0.00 2.52
264 265 4.009675 TCGATTGTTGCAGGCTATCTTTT 58.990 39.130 10.89 0.00 0.00 2.27
265 266 4.458989 TCGATTGTTGCAGGCTATCTTTTT 59.541 37.500 10.89 0.00 0.00 1.94
295 296 9.231297 ACATTTGAAGTAGTGTATATTGCAAGT 57.769 29.630 4.94 0.00 0.00 3.16
296 297 9.494479 CATTTGAAGTAGTGTATATTGCAAGTG 57.506 33.333 4.94 0.00 0.00 3.16
297 298 8.840833 TTTGAAGTAGTGTATATTGCAAGTGA 57.159 30.769 4.94 0.00 0.00 3.41
298 299 8.840833 TTGAAGTAGTGTATATTGCAAGTGAA 57.159 30.769 4.94 0.00 0.00 3.18
299 300 8.840833 TGAAGTAGTGTATATTGCAAGTGAAA 57.159 30.769 4.94 0.00 0.00 2.69
300 301 9.448438 TGAAGTAGTGTATATTGCAAGTGAAAT 57.552 29.630 4.94 0.00 0.00 2.17
301 302 9.708222 GAAGTAGTGTATATTGCAAGTGAAATG 57.292 33.333 4.94 0.00 0.00 2.32
302 303 8.213518 AGTAGTGTATATTGCAAGTGAAATGG 57.786 34.615 4.94 0.00 0.00 3.16
303 304 8.046708 AGTAGTGTATATTGCAAGTGAAATGGA 58.953 33.333 4.94 0.00 0.00 3.41
304 305 7.886629 AGTGTATATTGCAAGTGAAATGGAT 57.113 32.000 4.94 0.00 0.00 3.41
305 306 8.297470 AGTGTATATTGCAAGTGAAATGGATT 57.703 30.769 4.94 0.00 0.00 3.01
306 307 8.752187 AGTGTATATTGCAAGTGAAATGGATTT 58.248 29.630 4.94 0.00 0.00 2.17
307 308 9.023967 GTGTATATTGCAAGTGAAATGGATTTC 57.976 33.333 4.94 5.32 44.83 2.17
330 331 9.947669 TTTCAATTATTTTTCAATTGTTGCAGG 57.052 25.926 5.13 0.00 41.83 4.85
331 332 7.583230 TCAATTATTTTTCAATTGTTGCAGGC 58.417 30.769 5.13 0.00 41.83 4.85
332 333 7.444792 TCAATTATTTTTCAATTGTTGCAGGCT 59.555 29.630 5.13 0.00 41.83 4.58
333 334 8.719648 CAATTATTTTTCAATTGTTGCAGGCTA 58.280 29.630 5.13 0.00 38.17 3.93
334 335 9.452287 AATTATTTTTCAATTGTTGCAGGCTAT 57.548 25.926 5.13 0.00 0.00 2.97
335 336 6.973229 ATTTTTCAATTGTTGCAGGCTATC 57.027 33.333 5.13 0.00 0.00 2.08
336 337 5.726980 TTTTCAATTGTTGCAGGCTATCT 57.273 34.783 5.13 0.00 0.00 1.98
337 338 5.726980 TTTCAATTGTTGCAGGCTATCTT 57.273 34.783 5.13 0.00 0.00 2.40
338 339 5.726980 TTCAATTGTTGCAGGCTATCTTT 57.273 34.783 5.13 0.00 0.00 2.52
339 340 5.726980 TCAATTGTTGCAGGCTATCTTTT 57.273 34.783 5.13 0.00 0.00 2.27
340 341 6.100404 TCAATTGTTGCAGGCTATCTTTTT 57.900 33.333 5.13 0.00 0.00 1.94
470 472 0.241749 ATTGCTTCGGTCGTACGTCA 59.758 50.000 16.05 0.00 34.94 4.35
491 493 1.230324 GGCAGTCTCGCAGAAAAGTT 58.770 50.000 0.00 0.00 34.09 2.66
503 505 4.500477 CGCAGAAAAGTTCCTGAGTTTTTG 59.500 41.667 8.83 0.00 40.19 2.44
576 578 7.334171 AGCCATTTTGCAAATAAATCCTTACAC 59.666 33.333 13.65 0.00 0.00 2.90
1474 1616 9.664332 AATACATCTAGATACATCCATTTCTGC 57.336 33.333 4.54 0.00 0.00 4.26
2737 3488 0.882042 CCACCACTCTATGCGCATCC 60.882 60.000 29.11 0.00 0.00 3.51
3240 4006 5.125578 CCAAGTTCCTTTTACTATTCTGGCC 59.874 44.000 0.00 0.00 0.00 5.36
3511 4361 4.357918 ACAGTATTGTGGCTGACTTCTT 57.642 40.909 0.00 0.00 35.83 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.139734 CAGGCGATGCTACGACAGT 59.860 57.895 10.99 0.00 44.44 3.55
1 2 4.003534 CAGGCGATGCTACGACAG 57.996 61.111 10.99 0.00 44.44 3.51
10 11 2.892425 GGAAGGACGCAGGCGATG 60.892 66.667 21.62 0.00 42.83 3.84
11 12 2.650813 GATGGAAGGACGCAGGCGAT 62.651 60.000 21.62 4.52 42.83 4.58
12 13 3.371097 GATGGAAGGACGCAGGCGA 62.371 63.158 21.62 0.00 42.83 5.54
13 14 2.892425 GATGGAAGGACGCAGGCG 60.892 66.667 12.71 12.71 46.03 5.52
14 15 2.109126 GTGATGGAAGGACGCAGGC 61.109 63.158 0.00 0.00 0.00 4.85
15 16 1.450312 GGTGATGGAAGGACGCAGG 60.450 63.158 0.00 0.00 0.00 4.85
16 17 1.811266 CGGTGATGGAAGGACGCAG 60.811 63.158 0.00 0.00 0.00 5.18
17 18 2.264480 CGGTGATGGAAGGACGCA 59.736 61.111 0.00 0.00 0.00 5.24
18 19 2.100631 CACGGTGATGGAAGGACGC 61.101 63.158 0.74 0.00 0.00 5.19
19 20 2.100631 GCACGGTGATGGAAGGACG 61.101 63.158 13.29 0.00 0.00 4.79
20 21 1.745489 GGCACGGTGATGGAAGGAC 60.745 63.158 13.29 0.00 0.00 3.85
21 22 2.668632 GGCACGGTGATGGAAGGA 59.331 61.111 13.29 0.00 0.00 3.36
22 23 2.438434 GGGCACGGTGATGGAAGG 60.438 66.667 13.29 0.00 0.00 3.46
23 24 2.819595 CGGGCACGGTGATGGAAG 60.820 66.667 13.29 0.00 36.18 3.46
75 76 4.827087 AGCATGAGTGGCTCGCGG 62.827 66.667 6.13 0.00 36.81 6.46
80 81 2.581354 GACGGAGCATGAGTGGCT 59.419 61.111 0.00 0.00 46.07 4.75
81 82 2.512515 GGACGGAGCATGAGTGGC 60.513 66.667 0.00 0.00 0.00 5.01
82 83 2.202797 CGGACGGAGCATGAGTGG 60.203 66.667 0.00 0.00 0.00 4.00
83 84 2.887568 GCGGACGGAGCATGAGTG 60.888 66.667 0.00 0.00 34.19 3.51
84 85 3.381983 TGCGGACGGAGCATGAGT 61.382 61.111 0.00 0.00 40.01 3.41
85 86 2.887568 GTGCGGACGGAGCATGAG 60.888 66.667 0.00 0.00 46.96 2.90
86 87 4.451150 GGTGCGGACGGAGCATGA 62.451 66.667 10.43 0.00 46.96 3.07
119 120 1.870055 ATATACACTACCGGGGCGCG 61.870 60.000 17.81 17.81 0.00 6.86
120 121 0.319405 AATATACACTACCGGGGCGC 59.681 55.000 6.32 0.00 0.00 6.53
121 122 1.938016 GCAATATACACTACCGGGGCG 60.938 57.143 6.32 0.00 0.00 6.13
122 123 1.071071 TGCAATATACACTACCGGGGC 59.929 52.381 6.32 0.00 0.00 5.80
123 124 3.181458 ACTTGCAATATACACTACCGGGG 60.181 47.826 6.32 0.00 0.00 5.73
124 125 3.807622 CACTTGCAATATACACTACCGGG 59.192 47.826 6.32 0.00 0.00 5.73
125 126 4.689071 TCACTTGCAATATACACTACCGG 58.311 43.478 0.00 0.00 0.00 5.28
126 127 6.656314 TTTCACTTGCAATATACACTACCG 57.344 37.500 0.00 0.00 0.00 4.02
127 128 7.282224 TCCATTTCACTTGCAATATACACTACC 59.718 37.037 0.00 0.00 0.00 3.18
128 129 8.208718 TCCATTTCACTTGCAATATACACTAC 57.791 34.615 0.00 0.00 0.00 2.73
129 130 8.978874 ATCCATTTCACTTGCAATATACACTA 57.021 30.769 0.00 0.00 0.00 2.74
130 131 7.886629 ATCCATTTCACTTGCAATATACACT 57.113 32.000 0.00 0.00 0.00 3.55
131 132 8.931385 AAATCCATTTCACTTGCAATATACAC 57.069 30.769 0.00 0.00 0.00 2.90
151 152 9.476761 GCAACAATCGAAAAATAATTGAAATCC 57.523 29.630 0.00 0.00 35.03 3.01
154 155 8.494347 CCTGCAACAATCGAAAAATAATTGAAA 58.506 29.630 0.00 0.00 35.03 2.69
155 156 7.359933 GCCTGCAACAATCGAAAAATAATTGAA 60.360 33.333 0.00 0.00 35.03 2.69
156 157 6.090628 GCCTGCAACAATCGAAAAATAATTGA 59.909 34.615 0.00 0.00 35.03 2.57
157 158 6.091169 AGCCTGCAACAATCGAAAAATAATTG 59.909 34.615 0.00 0.00 36.64 2.32
158 159 6.165577 AGCCTGCAACAATCGAAAAATAATT 58.834 32.000 0.00 0.00 0.00 1.40
159 160 5.723295 AGCCTGCAACAATCGAAAAATAAT 58.277 33.333 0.00 0.00 0.00 1.28
160 161 5.132897 AGCCTGCAACAATCGAAAAATAA 57.867 34.783 0.00 0.00 0.00 1.40
161 162 4.782019 AGCCTGCAACAATCGAAAAATA 57.218 36.364 0.00 0.00 0.00 1.40
162 163 3.665745 AGCCTGCAACAATCGAAAAAT 57.334 38.095 0.00 0.00 0.00 1.82
163 164 4.458989 AGATAGCCTGCAACAATCGAAAAA 59.541 37.500 0.00 0.00 0.00 1.94
164 165 4.009675 AGATAGCCTGCAACAATCGAAAA 58.990 39.130 0.00 0.00 0.00 2.29
165 166 3.609853 AGATAGCCTGCAACAATCGAAA 58.390 40.909 0.00 0.00 0.00 3.46
166 167 3.266510 AGATAGCCTGCAACAATCGAA 57.733 42.857 0.00 0.00 0.00 3.71
167 168 2.988010 AGATAGCCTGCAACAATCGA 57.012 45.000 0.00 0.00 0.00 3.59
168 169 3.201290 AGAAGATAGCCTGCAACAATCG 58.799 45.455 0.00 0.00 0.00 3.34
169 170 5.573337 AAAGAAGATAGCCTGCAACAATC 57.427 39.130 0.00 0.00 0.00 2.67
170 171 7.775093 TGTATAAAGAAGATAGCCTGCAACAAT 59.225 33.333 0.00 0.00 0.00 2.71
171 172 7.109501 TGTATAAAGAAGATAGCCTGCAACAA 58.890 34.615 0.00 0.00 0.00 2.83
172 173 6.649155 TGTATAAAGAAGATAGCCTGCAACA 58.351 36.000 0.00 0.00 0.00 3.33
173 174 7.736447 ATGTATAAAGAAGATAGCCTGCAAC 57.264 36.000 0.00 0.00 0.00 4.17
174 175 8.623903 CAAATGTATAAAGAAGATAGCCTGCAA 58.376 33.333 0.00 0.00 0.00 4.08
175 176 7.992608 TCAAATGTATAAAGAAGATAGCCTGCA 59.007 33.333 0.00 0.00 0.00 4.41
176 177 8.383318 TCAAATGTATAAAGAAGATAGCCTGC 57.617 34.615 0.00 0.00 0.00 4.85
194 195 9.231297 ACTTGCAATATACACTACTTCAAATGT 57.769 29.630 0.00 0.00 0.00 2.71
195 196 9.494479 CACTTGCAATATACACTACTTCAAATG 57.506 33.333 0.00 0.00 0.00 2.32
196 197 9.448438 TCACTTGCAATATACACTACTTCAAAT 57.552 29.630 0.00 0.00 0.00 2.32
197 198 8.840833 TCACTTGCAATATACACTACTTCAAA 57.159 30.769 0.00 0.00 0.00 2.69
198 199 8.840833 TTCACTTGCAATATACACTACTTCAA 57.159 30.769 0.00 0.00 0.00 2.69
199 200 8.840833 TTTCACTTGCAATATACACTACTTCA 57.159 30.769 0.00 0.00 0.00 3.02
200 201 9.708222 CATTTCACTTGCAATATACACTACTTC 57.292 33.333 0.00 0.00 0.00 3.01
201 202 9.448438 TCATTTCACTTGCAATATACACTACTT 57.552 29.630 0.00 0.00 0.00 2.24
202 203 9.448438 TTCATTTCACTTGCAATATACACTACT 57.552 29.630 0.00 0.00 0.00 2.57
229 230 8.494347 CCTGCAACAATCGAAAAATAATTGAAA 58.506 29.630 0.00 0.00 35.03 2.69
230 231 7.359933 GCCTGCAACAATCGAAAAATAATTGAA 60.360 33.333 0.00 0.00 35.03 2.69
231 232 6.090628 GCCTGCAACAATCGAAAAATAATTGA 59.909 34.615 0.00 0.00 35.03 2.57
232 233 6.091169 AGCCTGCAACAATCGAAAAATAATTG 59.909 34.615 0.00 0.00 36.64 2.32
233 234 6.165577 AGCCTGCAACAATCGAAAAATAATT 58.834 32.000 0.00 0.00 0.00 1.40
234 235 5.723295 AGCCTGCAACAATCGAAAAATAAT 58.277 33.333 0.00 0.00 0.00 1.28
235 236 5.132897 AGCCTGCAACAATCGAAAAATAA 57.867 34.783 0.00 0.00 0.00 1.40
236 237 4.782019 AGCCTGCAACAATCGAAAAATA 57.218 36.364 0.00 0.00 0.00 1.40
237 238 3.665745 AGCCTGCAACAATCGAAAAAT 57.334 38.095 0.00 0.00 0.00 1.82
238 239 4.458989 AGATAGCCTGCAACAATCGAAAAA 59.541 37.500 0.00 0.00 0.00 1.94
239 240 4.009675 AGATAGCCTGCAACAATCGAAAA 58.990 39.130 0.00 0.00 0.00 2.29
240 241 3.609853 AGATAGCCTGCAACAATCGAAA 58.390 40.909 0.00 0.00 0.00 3.46
241 242 3.266510 AGATAGCCTGCAACAATCGAA 57.733 42.857 0.00 0.00 0.00 3.71
242 243 2.988010 AGATAGCCTGCAACAATCGA 57.012 45.000 0.00 0.00 0.00 3.59
243 244 4.361451 AAAAGATAGCCTGCAACAATCG 57.639 40.909 0.00 0.00 0.00 3.34
269 270 9.231297 ACTTGCAATATACACTACTTCAAATGT 57.769 29.630 0.00 0.00 0.00 2.71
270 271 9.494479 CACTTGCAATATACACTACTTCAAATG 57.506 33.333 0.00 0.00 0.00 2.32
271 272 9.448438 TCACTTGCAATATACACTACTTCAAAT 57.552 29.630 0.00 0.00 0.00 2.32
272 273 8.840833 TCACTTGCAATATACACTACTTCAAA 57.159 30.769 0.00 0.00 0.00 2.69
273 274 8.840833 TTCACTTGCAATATACACTACTTCAA 57.159 30.769 0.00 0.00 0.00 2.69
274 275 8.840833 TTTCACTTGCAATATACACTACTTCA 57.159 30.769 0.00 0.00 0.00 3.02
275 276 9.708222 CATTTCACTTGCAATATACACTACTTC 57.292 33.333 0.00 0.00 0.00 3.01
276 277 8.677300 CCATTTCACTTGCAATATACACTACTT 58.323 33.333 0.00 0.00 0.00 2.24
277 278 8.046708 TCCATTTCACTTGCAATATACACTACT 58.953 33.333 0.00 0.00 0.00 2.57
278 279 8.208718 TCCATTTCACTTGCAATATACACTAC 57.791 34.615 0.00 0.00 0.00 2.73
279 280 8.978874 ATCCATTTCACTTGCAATATACACTA 57.021 30.769 0.00 0.00 0.00 2.74
280 281 7.886629 ATCCATTTCACTTGCAATATACACT 57.113 32.000 0.00 0.00 0.00 3.55
281 282 8.931385 AAATCCATTTCACTTGCAATATACAC 57.069 30.769 0.00 0.00 0.00 2.90
304 305 9.947669 CCTGCAACAATTGAAAAATAATTGAAA 57.052 25.926 13.59 0.00 44.37 2.69
305 306 8.074972 GCCTGCAACAATTGAAAAATAATTGAA 58.925 29.630 13.59 0.00 44.37 2.69
306 307 7.444792 AGCCTGCAACAATTGAAAAATAATTGA 59.555 29.630 13.59 0.00 44.37 2.57
307 308 7.586747 AGCCTGCAACAATTGAAAAATAATTG 58.413 30.769 13.59 4.68 46.06 2.32
308 309 7.748691 AGCCTGCAACAATTGAAAAATAATT 57.251 28.000 13.59 0.00 0.00 1.40
309 310 9.101655 GATAGCCTGCAACAATTGAAAAATAAT 57.898 29.630 13.59 0.00 0.00 1.28
310 311 8.313292 AGATAGCCTGCAACAATTGAAAAATAA 58.687 29.630 13.59 0.00 0.00 1.40
311 312 7.839907 AGATAGCCTGCAACAATTGAAAAATA 58.160 30.769 13.59 0.00 0.00 1.40
312 313 6.704310 AGATAGCCTGCAACAATTGAAAAAT 58.296 32.000 13.59 0.00 0.00 1.82
313 314 6.100404 AGATAGCCTGCAACAATTGAAAAA 57.900 33.333 13.59 0.00 0.00 1.94
314 315 5.726980 AGATAGCCTGCAACAATTGAAAA 57.273 34.783 13.59 0.00 0.00 2.29
315 316 5.726980 AAGATAGCCTGCAACAATTGAAA 57.273 34.783 13.59 0.00 0.00 2.69
316 317 5.726980 AAAGATAGCCTGCAACAATTGAA 57.273 34.783 13.59 0.00 0.00 2.69
317 318 5.726980 AAAAGATAGCCTGCAACAATTGA 57.273 34.783 13.59 0.00 0.00 2.57
358 359 9.973661 TGGTTGCACCTATAAATATATGCTTAT 57.026 29.630 6.83 0.00 39.58 1.73
359 360 9.448438 CTGGTTGCACCTATAAATATATGCTTA 57.552 33.333 6.83 0.00 39.58 3.09
360 361 8.163408 TCTGGTTGCACCTATAAATATATGCTT 58.837 33.333 6.83 0.00 39.58 3.91
361 362 7.689299 TCTGGTTGCACCTATAAATATATGCT 58.311 34.615 6.83 0.00 39.58 3.79
362 363 7.921786 TCTGGTTGCACCTATAAATATATGC 57.078 36.000 6.83 0.00 39.58 3.14
368 369 9.646522 AGATATTTTCTGGTTGCACCTATAAAT 57.353 29.630 6.83 10.06 39.58 1.40
423 424 8.921205 GGTGGTTTATTAGTAGGTAGAGATGAA 58.079 37.037 0.00 0.00 0.00 2.57
424 425 7.230108 CGGTGGTTTATTAGTAGGTAGAGATGA 59.770 40.741 0.00 0.00 0.00 2.92
425 426 7.230108 TCGGTGGTTTATTAGTAGGTAGAGATG 59.770 40.741 0.00 0.00 0.00 2.90
470 472 1.271054 ACTTTTCTGCGAGACTGCCAT 60.271 47.619 0.00 0.00 0.00 4.40
491 493 5.768164 GGGTTGAATACTCAAAAACTCAGGA 59.232 40.000 0.00 0.00 43.18 3.86
503 505 1.207329 AGGACTGCGGGTTGAATACTC 59.793 52.381 0.00 0.00 0.00 2.59
1087 1226 5.958955 ACAGAATGAAGGAAATAAGCAAGC 58.041 37.500 0.00 0.00 39.69 4.01
1474 1616 3.612860 CCTCCGTTCAGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
2295 3046 1.075536 GGAACCACCATGAACCTCCTT 59.924 52.381 0.00 0.00 38.79 3.36
2444 3195 1.065418 CAGCGGTAGGGAATTGGAGTT 60.065 52.381 0.00 0.00 0.00 3.01
2737 3488 3.294794 GAAATCTGATTTTGGCGGCACG 61.295 50.000 12.92 0.00 44.29 5.34
3511 4361 4.522789 GGATTTAGGACCAAACTTTCTGCA 59.477 41.667 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.