Multiple sequence alignment - TraesCS6D01G015400

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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 TraesCS6D01G015400 chr6D 100.000 3302 0 0 1 3302 6345132 6341831 0.000000e+00 6098
1 TraesCS6D01G015400 chr6D 90.319 1694 110 21 169 1811 6366718 6365028 0.000000e+00 2170
2 TraesCS6D01G015400 chr6D 86.957 667 65 11 1898 2563 6359950 6359305 0.000000e+00 730
3 TraesCS6D01G015400 chr6D 98.204 167 3 0 1 167 6367731 6367565 3.220000e-75 292
4 TraesCS6D01G015400 chr6D 92.661 109 8 0 1794 1902 6364999 6364891 1.230000e-34 158
5 TraesCS6D01G015400 chr6D 90.217 92 7 1 3211 3302 48402801 48402712 5.790000e-23 119
6 TraesCS6D01G015400 chr6B 91.121 2444 157 27 172 2563 11587143 11584708 0.000000e+00 3256
7 TraesCS6D01G015400 chr6B 94.177 498 26 3 2562 3057 40078207 40078703 0.000000e+00 756
8 TraesCS6D01G015400 chr6B 95.210 167 8 0 1 167 11588183 11588017 7.030000e-67 265
9 TraesCS6D01G015400 chr6B 97.059 136 4 0 1 136 11590323 11590188 2.560000e-56 230
10 TraesCS6D01G015400 chr6A 91.166 1166 79 4 911 2074 5874412 5873269 0.000000e+00 1561
11 TraesCS6D01G015400 chr6A 96.154 546 20 1 2564 3108 583986357 583985812 0.000000e+00 891
12 TraesCS6D01G015400 chr6A 89.213 686 33 17 172 819 5876252 5875570 0.000000e+00 819
13 TraesCS6D01G015400 chr6A 89.004 482 50 2 2085 2565 5873155 5872676 7.890000e-166 593
14 TraesCS6D01G015400 chr6A 94.611 167 9 0 1 167 5880023 5879857 3.270000e-65 259
15 TraesCS6D01G015400 chr6A 93.413 167 11 0 1 167 5877292 5877126 7.080000e-62 248
16 TraesCS6D01G015400 chr6A 95.690 116 5 0 3121 3236 583985320 583985205 1.560000e-43 187
17 TraesCS6D01G015400 chr7D 82.092 1128 137 44 1243 2324 44521378 44520270 0.000000e+00 904
18 TraesCS6D01G015400 chr7D 91.636 550 39 3 2562 3108 186434266 186434811 0.000000e+00 754
19 TraesCS6D01G015400 chr7D 89.873 553 49 3 2562 3108 388021600 388021049 0.000000e+00 704
20 TraesCS6D01G015400 chr7D 90.756 119 11 0 3118 3236 186435300 186435418 3.410000e-35 159
21 TraesCS6D01G015400 chr7D 100.000 69 0 0 3234 3302 445005875 445005807 9.620000e-26 128
22 TraesCS6D01G015400 chr7D 93.258 89 1 5 3217 3302 378386944 378386858 3.460000e-25 126
23 TraesCS6D01G015400 chr2A 95.446 549 23 2 2562 3108 385357237 385357785 0.000000e+00 874
24 TraesCS6D01G015400 chr2A 94.958 119 6 0 3118 3236 385358261 385358379 1.560000e-43 187
25 TraesCS6D01G015400 chr2D 80.840 1143 160 38 1281 2395 620311608 620310497 0.000000e+00 843
26 TraesCS6D01G015400 chr2D 87.578 161 20 0 1046 1206 620312199 620312039 1.560000e-43 187
27 TraesCS6D01G015400 chr2D 92.784 97 3 4 3209 3302 81679695 81679600 1.600000e-28 137
28 TraesCS6D01G015400 chr3B 80.556 1152 162 39 1281 2407 2507902 2509016 0.000000e+00 830
29 TraesCS6D01G015400 chr3B 81.041 1076 148 34 1281 2321 2417377 2416323 0.000000e+00 806
30 TraesCS6D01G015400 chr3B 81.622 370 40 10 951 1293 2507426 2507794 6.980000e-72 281
31 TraesCS6D01G015400 chr1A 92.754 552 38 2 2558 3108 514636750 514637300 0.000000e+00 797
32 TraesCS6D01G015400 chr1A 93.966 116 7 0 3118 3233 514637789 514637904 3.390000e-40 176
33 TraesCS6D01G015400 chr1A 98.630 73 1 0 3230 3302 206606462 206606534 2.670000e-26 130
34 TraesCS6D01G015400 chr1A 94.048 84 3 2 3220 3302 175078753 175078835 3.460000e-25 126
35 TraesCS6D01G015400 chr3D 90.876 548 43 5 2562 3108 105144916 105145457 0.000000e+00 728
36 TraesCS6D01G015400 chr3D 92.381 105 8 0 3125 3229 105145953 105146057 2.050000e-32 150
37 TraesCS6D01G015400 chr3D 98.630 73 1 0 3230 3302 594343417 594343345 2.670000e-26 130
38 TraesCS6D01G015400 chrUn 81.630 920 114 26 1156 2042 417299021 417298124 0.000000e+00 712
39 TraesCS6D01G015400 chr3A 81.522 920 114 27 1156 2042 49079 49975 0.000000e+00 706
40 TraesCS6D01G015400 chr3A 87.226 548 52 7 2562 3108 684661453 684660923 2.820000e-170 608
41 TraesCS6D01G015400 chr3A 81.958 521 61 13 926 1413 507249 507769 8.530000e-111 411
42 TraesCS6D01G015400 chr3A 92.035 113 8 1 3120 3231 477329115 477329227 1.230000e-34 158
43 TraesCS6D01G015400 chr3A 88.235 102 11 1 3202 3302 550386331 550386230 1.610000e-23 121
44 TraesCS6D01G015400 chr2B 89.734 526 49 4 2588 3108 313562336 313561811 0.000000e+00 667
45 TraesCS6D01G015400 chr2B 93.043 115 8 0 3121 3235 313561320 313561206 5.670000e-38 169
46 TraesCS6D01G015400 chr2B 96.970 66 2 0 3170 3235 313560580 313560515 9.690000e-21 111
47 TraesCS6D01G015400 chr7A 83.669 447 60 8 1243 1680 46965128 46964686 3.070000e-110 409
48 TraesCS6D01G015400 chr7A 82.407 216 25 9 2121 2324 46964685 46964471 3.390000e-40 176
49 TraesCS6D01G015400 chr4A 100.000 72 0 0 3231 3302 21894247 21894176 2.070000e-27 134


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 TraesCS6D01G015400 chr6D 6341831 6345132 3301 True 6098.000000 6098 100.000000 1 3302 1 chr6D.!!$R1 3301
1 TraesCS6D01G015400 chr6D 6364891 6367731 2840 True 873.333333 2170 93.728000 1 1902 3 chr6D.!!$R4 1901
2 TraesCS6D01G015400 chr6D 6359305 6359950 645 True 730.000000 730 86.957000 1898 2563 1 chr6D.!!$R2 665
3 TraesCS6D01G015400 chr6B 11584708 11590323 5615 True 1250.333333 3256 94.463333 1 2563 3 chr6B.!!$R1 2562
4 TraesCS6D01G015400 chr6A 5872676 5880023 7347 True 696.000000 1561 91.481400 1 2565 5 chr6A.!!$R1 2564
5 TraesCS6D01G015400 chr6A 583985205 583986357 1152 True 539.000000 891 95.922000 2564 3236 2 chr6A.!!$R2 672
6 TraesCS6D01G015400 chr7D 44520270 44521378 1108 True 904.000000 904 82.092000 1243 2324 1 chr7D.!!$R1 1081
7 TraesCS6D01G015400 chr7D 388021049 388021600 551 True 704.000000 704 89.873000 2562 3108 1 chr7D.!!$R3 546
8 TraesCS6D01G015400 chr7D 186434266 186435418 1152 False 456.500000 754 91.196000 2562 3236 2 chr7D.!!$F1 674
9 TraesCS6D01G015400 chr2A 385357237 385358379 1142 False 530.500000 874 95.202000 2562 3236 2 chr2A.!!$F1 674
10 TraesCS6D01G015400 chr2D 620310497 620312199 1702 True 515.000000 843 84.209000 1046 2395 2 chr2D.!!$R2 1349
11 TraesCS6D01G015400 chr3B 2416323 2417377 1054 True 806.000000 806 81.041000 1281 2321 1 chr3B.!!$R1 1040
12 TraesCS6D01G015400 chr3B 2507426 2509016 1590 False 555.500000 830 81.089000 951 2407 2 chr3B.!!$F1 1456
13 TraesCS6D01G015400 chr1A 514636750 514637904 1154 False 486.500000 797 93.360000 2558 3233 2 chr1A.!!$F3 675
14 TraesCS6D01G015400 chr3D 105144916 105146057 1141 False 439.000000 728 91.628500 2562 3229 2 chr3D.!!$F1 667
15 TraesCS6D01G015400 chrUn 417298124 417299021 897 True 712.000000 712 81.630000 1156 2042 1 chrUn.!!$R1 886
16 TraesCS6D01G015400 chr3A 49079 49975 896 False 706.000000 706 81.522000 1156 2042 1 chr3A.!!$F1 886
17 TraesCS6D01G015400 chr3A 684660923 684661453 530 True 608.000000 608 87.226000 2562 3108 1 chr3A.!!$R2 546
18 TraesCS6D01G015400 chr3A 507249 507769 520 False 411.000000 411 81.958000 926 1413 1 chr3A.!!$F2 487
19 TraesCS6D01G015400 chr2B 313560515 313562336 1821 True 315.666667 667 93.249000 2588 3235 3 chr2B.!!$R1 647
20 TraesCS6D01G015400 chr7A 46964471 46965128 657 True 292.500000 409 83.038000 1243 2324 2 chr7A.!!$R1 1081

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
778 5253 0.323633 TTGTGATGTCCATGGGCAGG 60.324 55.0 25.65 0.0 0.00 4.85 F
1339 7377 0.239347 AAAGGGTGTAGACGTCGTCG 59.761 55.0 19.11 0.0 37.67 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 7753 0.245539 GGACGGTGATCTTGTCGGAA 59.754 55.0 0.00 0.0 33.45 4.30 R
3249 10744 0.108329 ATGGTAAACCGGTCGCTCTG 60.108 55.0 8.04 0.0 39.43 3.35 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
31 32 5.528870 AGAATCATTTGGTTTTTGTCCGAC 58.471 37.500 0.00 0.00 0.00 4.79
296 4724 5.695816 TGATTTTTATGCTGTTTTGCTGGAC 59.304 36.000 0.00 0.00 0.00 4.02
468 4920 4.293415 CCGTATATCCCGTTGTGTACTTC 58.707 47.826 0.00 0.00 0.00 3.01
474 4926 2.028476 TCCCGTTGTGTACTTCTGATGG 60.028 50.000 0.00 0.00 0.00 3.51
499 4951 3.892284 ACATAAATATGGTTCCCGTGCA 58.108 40.909 5.48 0.00 38.00 4.57
557 5010 6.699575 TCTGCTTTAGGAGGAAAATTATGC 57.300 37.500 0.00 0.00 34.00 3.14
688 5157 9.331282 CATTGAGGTTAAATAAGGACTAGAAGG 57.669 37.037 0.00 0.00 0.00 3.46
689 5158 6.885922 TGAGGTTAAATAAGGACTAGAAGGC 58.114 40.000 0.00 0.00 0.00 4.35
709 5178 5.934781 AGGCCAGTTTAGGATGATTTCTAG 58.065 41.667 5.01 0.00 0.00 2.43
778 5253 0.323633 TTGTGATGTCCATGGGCAGG 60.324 55.000 25.65 0.00 0.00 4.85
892 6455 6.002704 AGGAATTGTCAGCTTCATCATATCC 58.997 40.000 0.00 0.00 0.00 2.59
896 6459 3.062763 GTCAGCTTCATCATATCCCACG 58.937 50.000 0.00 0.00 0.00 4.94
989 6563 4.436317 GCTAGTAGAGCGTTCGATATCTGG 60.436 50.000 0.00 0.00 42.62 3.86
998 6575 4.619394 GCGTTCGATATCTGGATCAGGAAT 60.619 45.833 0.34 0.00 31.51 3.01
1064 6647 0.391661 ACAGGTCACATAGGCAAGCG 60.392 55.000 0.00 0.00 0.00 4.68
1140 6723 4.521062 GCGCCGTCTGATCCAGCT 62.521 66.667 0.00 0.00 0.00 4.24
1238 7132 4.623932 TGTCTGCCTTTCAACTACTCAT 57.376 40.909 0.00 0.00 0.00 2.90
1240 7134 5.376625 TGTCTGCCTTTCAACTACTCATTT 58.623 37.500 0.00 0.00 0.00 2.32
1328 7366 3.945285 CTCGTAAATGCCATAAAGGGTGT 59.055 43.478 0.00 0.00 38.09 4.16
1339 7377 0.239347 AAAGGGTGTAGACGTCGTCG 59.761 55.000 19.11 0.00 37.67 5.12
1368 7407 4.803426 GGGCCTCGTCAGCTCGTG 62.803 72.222 0.84 0.00 0.00 4.35
1422 7466 1.503542 CGGCAATGTGAAGGTCAGC 59.496 57.895 0.00 0.00 0.00 4.26
1425 7473 1.068055 GGCAATGTGAAGGTCAGCTTG 60.068 52.381 0.00 0.00 0.00 4.01
1482 7537 5.865085 TGCAGATTGACCACTTAGTTAGTT 58.135 37.500 0.00 0.00 33.85 2.24
1501 7556 7.392393 AGTTAGTTGTTGTTGTACAGAGGTTTT 59.608 33.333 0.00 0.00 0.00 2.43
1756 7819 2.270850 GTAAGCACGCCCATCCCA 59.729 61.111 0.00 0.00 0.00 4.37
1860 7994 4.097892 GTGTTTGTGGTGGAAGAAGACATT 59.902 41.667 0.00 0.00 0.00 2.71
1864 7998 1.144708 TGGTGGAAGAAGACATTGCCA 59.855 47.619 0.00 0.00 0.00 4.92
1902 8036 1.094073 TCGACGATCCGAGAACCCTC 61.094 60.000 0.00 0.00 34.19 4.30
1926 8060 2.171237 CAAGATCCTGTACATGAGGCCA 59.829 50.000 5.01 0.00 0.00 5.36
2064 8218 0.395686 CCATCATCGATCCTGTGCCT 59.604 55.000 0.00 0.00 0.00 4.75
2095 8354 0.759959 TGGTGTCCGTACATGGTTGT 59.240 50.000 0.00 0.00 38.08 3.32
2111 8370 1.047801 TTGTAGCTGCACCTCTGACA 58.952 50.000 3.11 0.00 0.00 3.58
2142 8424 0.533755 GTAATGATGCAGAGGCGGCT 60.534 55.000 13.09 13.09 45.35 5.52
2172 8454 0.179045 ACATATTGCTGTCCCTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
2272 8565 3.091545 CCCGACCTAAAGTACACCACTA 58.908 50.000 0.00 0.00 36.04 2.74
2305 8609 1.446966 GACCGCCTTCTCTGACAGC 60.447 63.158 0.00 0.00 0.00 4.40
2352 8659 1.131126 CCACAGTCGGCATCAACAATC 59.869 52.381 0.00 0.00 0.00 2.67
2392 8700 3.691020 GCCCCTCCAAATCCAATGATGTA 60.691 47.826 0.00 0.00 0.00 2.29
2403 8711 2.859538 CCAATGATGTATGCGGTTTTGC 59.140 45.455 0.00 0.00 0.00 3.68
2411 8719 0.948678 ATGCGGTTTTGCGTGTAACT 59.051 45.000 0.00 0.00 37.81 2.24
2425 8733 5.294799 TGCGTGTAACTTGTGTAAATTCACT 59.705 36.000 0.00 0.00 35.37 3.41
2729 9044 6.353082 CCACCATCCTCTACTTCAAAACCTAT 60.353 42.308 0.00 0.00 0.00 2.57
2730 9045 7.112779 CACCATCCTCTACTTCAAAACCTATT 58.887 38.462 0.00 0.00 0.00 1.73
2737 9052 6.966021 TCTACTTCAAAACCTATTGTGTTGC 58.034 36.000 0.00 0.00 41.27 4.17
2804 9125 3.130516 TCCTAAGTAATGTCGCAGTGAGG 59.869 47.826 0.00 0.00 0.00 3.86
2833 9154 5.506649 GGACAACACCATTAAACACGATGTT 60.507 40.000 0.00 0.00 43.41 2.71
2962 9283 0.035056 CCATCTTGGGGCTCGAAGTT 60.035 55.000 8.31 0.00 32.67 2.66
3065 9390 1.202510 TCATGTTGGTTGCAAAGTGGC 60.203 47.619 0.00 0.00 0.00 5.01
3074 9399 0.183492 TGCAAAGTGGCCAAGAGTCT 59.817 50.000 7.24 0.00 0.00 3.24
3110 9435 4.760047 CGAGCCAACCGGTCCTGG 62.760 72.222 19.37 19.37 35.44 4.45
3111 9436 3.637273 GAGCCAACCGGTCCTGGT 61.637 66.667 23.26 13.63 46.67 4.00
3112 9437 3.901797 GAGCCAACCGGTCCTGGTG 62.902 68.421 23.26 11.28 42.89 4.17
3113 9438 3.948719 GCCAACCGGTCCTGGTGA 61.949 66.667 23.26 0.00 42.89 4.02
3114 9439 2.347490 CCAACCGGTCCTGGTGAG 59.653 66.667 16.05 0.00 42.89 3.51
3115 9440 2.347490 CAACCGGTCCTGGTGAGG 59.653 66.667 8.04 0.00 42.89 3.86
3119 9923 1.305046 CCGGTCCTGGTGAGGTAGT 60.305 63.158 0.00 0.00 40.76 2.73
3157 9961 2.359850 CCCGTTGCAGCCAAGCTA 60.360 61.111 0.00 0.00 36.40 3.32
3236 10731 0.810648 CATTTGGGCGTGCATACTGT 59.189 50.000 0.00 0.00 0.00 3.55
3237 10732 0.810648 ATTTGGGCGTGCATACTGTG 59.189 50.000 0.00 0.00 0.00 3.66
3238 10733 1.240641 TTTGGGCGTGCATACTGTGG 61.241 55.000 0.00 0.00 0.00 4.17
3239 10734 3.508840 GGGCGTGCATACTGTGGC 61.509 66.667 0.00 0.00 0.00 5.01
3240 10735 2.745884 GGCGTGCATACTGTGGCA 60.746 61.111 5.08 5.08 37.77 4.92
3244 10739 2.354729 TGCATACTGTGGCACCCC 59.645 61.111 16.26 0.00 34.58 4.95
3245 10740 2.824041 GCATACTGTGGCACCCCG 60.824 66.667 16.26 6.16 0.00 5.73
3246 10741 2.124736 CATACTGTGGCACCCCGG 60.125 66.667 16.26 0.00 0.00 5.73
3247 10742 4.109675 ATACTGTGGCACCCCGGC 62.110 66.667 16.26 0.00 41.67 6.13
3262 10757 4.070552 GGCTCAGAGCGACCGGTT 62.071 66.667 16.47 0.00 43.62 4.44
3263 10758 2.048127 GCTCAGAGCGACCGGTTT 60.048 61.111 9.42 0.00 0.00 3.27
3264 10759 1.214589 GCTCAGAGCGACCGGTTTA 59.785 57.895 9.42 0.00 0.00 2.01
3265 10760 1.077089 GCTCAGAGCGACCGGTTTAC 61.077 60.000 9.42 0.55 0.00 2.01
3266 10761 0.458025 CTCAGAGCGACCGGTTTACC 60.458 60.000 9.42 0.00 0.00 2.85
3267 10762 1.180456 TCAGAGCGACCGGTTTACCA 61.180 55.000 9.42 0.00 35.14 3.25
3268 10763 0.108329 CAGAGCGACCGGTTTACCAT 60.108 55.000 9.42 0.00 35.14 3.55
3269 10764 0.108329 AGAGCGACCGGTTTACCATG 60.108 55.000 9.42 0.00 35.14 3.66
3270 10765 1.702491 GAGCGACCGGTTTACCATGC 61.702 60.000 9.42 4.75 35.14 4.06
3271 10766 2.036006 GCGACCGGTTTACCATGCA 61.036 57.895 9.42 0.00 35.14 3.96
3272 10767 1.373590 GCGACCGGTTTACCATGCAT 61.374 55.000 9.42 0.00 35.14 3.96
3273 10768 1.091537 CGACCGGTTTACCATGCATT 58.908 50.000 9.42 0.00 35.14 3.56
3274 10769 1.202132 CGACCGGTTTACCATGCATTG 60.202 52.381 9.42 0.00 35.14 2.82
3275 10770 0.530288 ACCGGTTTACCATGCATTGC 59.470 50.000 0.00 0.46 35.14 3.56
3276 10771 0.179113 CCGGTTTACCATGCATTGCC 60.179 55.000 6.12 0.00 35.14 4.52
3277 10772 0.529833 CGGTTTACCATGCATTGCCA 59.470 50.000 6.12 0.00 35.14 4.92
3278 10773 1.469595 CGGTTTACCATGCATTGCCAG 60.470 52.381 6.12 0.00 35.14 4.85
3279 10774 1.643880 GTTTACCATGCATTGCCAGC 58.356 50.000 6.12 0.00 0.00 4.85
3280 10775 0.536260 TTTACCATGCATTGCCAGCC 59.464 50.000 6.12 0.00 0.00 4.85
3281 10776 1.329171 TTACCATGCATTGCCAGCCC 61.329 55.000 6.12 0.00 0.00 5.19
3282 10777 2.511457 TACCATGCATTGCCAGCCCA 62.511 55.000 6.12 0.00 0.00 5.36
3283 10778 2.499205 CATGCATTGCCAGCCCAG 59.501 61.111 6.12 0.00 0.00 4.45
3284 10779 2.055633 CATGCATTGCCAGCCCAGA 61.056 57.895 6.12 0.00 0.00 3.86
3285 10780 1.756950 ATGCATTGCCAGCCCAGAG 60.757 57.895 6.12 0.00 0.00 3.35
3286 10781 2.044650 GCATTGCCAGCCCAGAGA 60.045 61.111 0.00 0.00 0.00 3.10
3287 10782 2.413142 GCATTGCCAGCCCAGAGAC 61.413 63.158 0.00 0.00 0.00 3.36
3288 10783 1.751927 CATTGCCAGCCCAGAGACC 60.752 63.158 0.00 0.00 0.00 3.85
3289 10784 2.233566 ATTGCCAGCCCAGAGACCA 61.234 57.895 0.00 0.00 0.00 4.02
3290 10785 1.578215 ATTGCCAGCCCAGAGACCAT 61.578 55.000 0.00 0.00 0.00 3.55
3291 10786 2.124403 GCCAGCCCAGAGACCATG 60.124 66.667 0.00 0.00 0.00 3.66
3292 10787 2.976490 GCCAGCCCAGAGACCATGT 61.976 63.158 0.00 0.00 0.00 3.21
3293 10788 1.222936 CCAGCCCAGAGACCATGTC 59.777 63.158 0.00 0.00 0.00 3.06
3294 10789 1.270414 CCAGCCCAGAGACCATGTCT 61.270 60.000 0.00 0.00 46.42 3.41
3295 10790 0.617413 CAGCCCAGAGACCATGTCTT 59.383 55.000 0.00 0.00 43.53 3.01
3296 10791 0.908198 AGCCCAGAGACCATGTCTTC 59.092 55.000 0.00 0.00 43.53 2.87
3297 10792 0.908198 GCCCAGAGACCATGTCTTCT 59.092 55.000 0.00 0.00 43.53 2.85
3298 10793 1.406614 GCCCAGAGACCATGTCTTCTG 60.407 57.143 9.44 9.44 43.53 3.02
3299 10794 1.209019 CCCAGAGACCATGTCTTCTGG 59.791 57.143 21.13 21.13 45.85 3.86
3300 10795 1.406614 CCAGAGACCATGTCTTCTGGC 60.407 57.143 18.14 2.36 43.53 4.85
3301 10796 1.277273 CAGAGACCATGTCTTCTGGCA 59.723 52.381 0.00 0.00 43.53 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.546395 AGCTGTCAAATATTTCGCAAGTTAG 58.454 36.000 0.00 0.00 39.48 2.34
147 3703 7.675270 GCATAAAAATGCTGTTATGAGACTG 57.325 36.000 7.43 0.00 43.79 3.51
167 3723 8.984764 ACTCGATGCGTTATTAATTTAAGCATA 58.015 29.630 17.25 7.81 42.87 3.14
282 4710 4.418392 CATTCTATGTCCAGCAAAACAGC 58.582 43.478 0.00 0.00 0.00 4.40
296 4724 3.785486 TCTCTTCACGTGGCATTCTATG 58.215 45.455 17.00 0.00 0.00 2.23
448 4879 6.140303 TCAGAAGTACACAACGGGATATAC 57.860 41.667 0.00 0.00 0.00 1.47
557 5010 6.019801 GTCACAGCAGATTAAGTTATGTACGG 60.020 42.308 0.00 0.00 0.00 4.02
573 5026 9.740239 AAATATTTGCAATAATAGTCACAGCAG 57.260 29.630 0.00 0.00 0.00 4.24
648 5117 5.395682 ACCTCAATGATTGTGATTTGTGG 57.604 39.130 8.66 0.00 38.22 4.17
688 5157 6.458888 GCAACTAGAAATCATCCTAAACTGGC 60.459 42.308 0.00 0.00 0.00 4.85
689 5158 6.599244 TGCAACTAGAAATCATCCTAAACTGG 59.401 38.462 0.00 0.00 0.00 4.00
778 5253 1.242076 AAGAGCACACAATGTCTGCC 58.758 50.000 9.94 2.54 0.00 4.85
989 6563 3.817647 GTCCAGCACCATAATTCCTGATC 59.182 47.826 0.00 0.00 0.00 2.92
998 6575 2.237143 CTCTCCTTGTCCAGCACCATAA 59.763 50.000 0.00 0.00 0.00 1.90
1064 6647 3.017314 CACTCGCCGCGACGATAC 61.017 66.667 19.79 0.00 42.02 2.24
1119 6702 3.554692 GGATCAGACGGCGCAACG 61.555 66.667 10.83 7.21 40.31 4.10
1140 6723 3.815856 CTCTTGAGGAGCTGCATCTTA 57.184 47.619 8.35 0.00 35.08 2.10
1367 7406 0.532573 GACAATCCTCGACTGCTCCA 59.467 55.000 0.00 0.00 0.00 3.86
1368 7407 0.532573 TGACAATCCTCGACTGCTCC 59.467 55.000 0.00 0.00 0.00 4.70
1375 7414 2.564771 GATTGCCATGACAATCCTCGA 58.435 47.619 20.56 0.00 46.71 4.04
1422 7466 6.321717 TCAAGTAAAAACACAAGCTGACAAG 58.678 36.000 0.00 0.00 0.00 3.16
1425 7473 5.687285 CCATCAAGTAAAAACACAAGCTGAC 59.313 40.000 0.00 0.00 0.00 3.51
1482 7537 4.381079 GGCAAAAACCTCTGTACAACAACA 60.381 41.667 0.00 0.00 0.00 3.33
1698 7753 0.245539 GGACGGTGATCTTGTCGGAA 59.754 55.000 0.00 0.00 33.45 4.30
1902 8036 3.624861 GCCTCATGTACAGGATCTTGTTG 59.375 47.826 16.35 8.66 31.91 3.33
1926 8060 1.964373 GGACACAATGTTCGCCGGT 60.964 57.895 1.90 0.00 0.00 5.28
2018 8155 3.008485 ACCCTTGATCAACTTGAGGAGAC 59.992 47.826 11.32 0.00 0.00 3.36
2082 8236 1.006832 GCAGCTACAACCATGTACGG 58.993 55.000 0.00 0.00 41.05 4.02
2095 8354 1.753649 GAGATGTCAGAGGTGCAGCTA 59.246 52.381 20.22 2.56 30.06 3.32
2111 8370 6.589135 TCTGCATCATTACATGTCAAGAGAT 58.411 36.000 0.00 0.00 0.00 2.75
2142 8424 4.922206 ACAGCAATATGTTCAGAGGGAAA 58.078 39.130 0.00 0.00 37.23 3.13
2172 8454 0.683973 CCCCGATGAAGATGGAGAGG 59.316 60.000 0.00 0.00 0.00 3.69
2305 8609 0.248289 CCATTCCAGCCAGCCAAAAG 59.752 55.000 0.00 0.00 0.00 2.27
2346 8653 6.684686 CCACTTGTTCATCATCTTGATTGTT 58.315 36.000 0.00 0.00 34.28 2.83
2352 8659 2.165030 GGGCCACTTGTTCATCATCTTG 59.835 50.000 4.39 0.00 0.00 3.02
2392 8700 0.948678 AGTTACACGCAAAACCGCAT 59.051 45.000 0.00 0.00 0.00 4.73
2403 8711 8.705134 TCATAGTGAATTTACACAAGTTACACG 58.295 33.333 2.93 0.00 42.45 4.49
2425 8733 6.317140 CAGCAAAGCAGAGGTTCTTATTCATA 59.683 38.462 0.00 0.00 0.00 2.15
2457 8766 5.450453 TCAACTTTTACACTGAAATCCCCA 58.550 37.500 0.00 0.00 0.00 4.96
2489 8798 6.326323 TGCTGGACAATGATCAGGTATAACTA 59.674 38.462 0.09 0.00 0.00 2.24
2503 8812 2.422479 CCAAGATCAGTGCTGGACAATG 59.578 50.000 1.24 0.00 45.71 2.82
2729 9044 2.297701 GGTCTCTTGAAGGCAACACAA 58.702 47.619 0.00 0.00 41.41 3.33
2730 9045 1.211703 TGGTCTCTTGAAGGCAACACA 59.788 47.619 0.00 0.00 41.41 3.72
2737 9052 1.573108 TAGGGCTGGTCTCTTGAAGG 58.427 55.000 0.00 0.00 0.00 3.46
2804 9125 3.829601 TGTTTAATGGTGTTGTCCCATCC 59.170 43.478 0.00 0.00 41.87 3.51
2833 9154 5.417266 TGGATTATTTGGAAGCATCGAAACA 59.583 36.000 1.10 0.00 36.31 2.83
2962 9283 2.252072 GAACATCACGGGCAGGCCTA 62.252 60.000 3.98 0.00 36.10 3.93
3065 9390 2.900546 ACTACCTCACCAAGACTCTTGG 59.099 50.000 29.33 29.33 44.91 3.61
3074 9399 1.823169 GCCGTGGACTACCTCACCAA 61.823 60.000 0.00 0.00 35.40 3.67
3108 9433 1.271840 GGCCATGGACTACCTCACCA 61.272 60.000 18.40 0.00 38.09 4.17
3109 9434 1.527370 GGCCATGGACTACCTCACC 59.473 63.158 18.40 0.00 37.04 4.02
3110 9435 1.144057 CGGCCATGGACTACCTCAC 59.856 63.158 18.40 0.00 37.04 3.51
3111 9436 2.063979 CCGGCCATGGACTACCTCA 61.064 63.158 18.40 0.00 37.04 3.86
3112 9437 2.808206 CCCGGCCATGGACTACCTC 61.808 68.421 18.40 0.00 37.04 3.85
3113 9438 2.621672 ATCCCGGCCATGGACTACCT 62.622 60.000 18.40 0.00 33.94 3.08
3114 9439 2.113243 GATCCCGGCCATGGACTACC 62.113 65.000 18.40 5.92 33.94 3.18
3115 9440 1.122019 AGATCCCGGCCATGGACTAC 61.122 60.000 18.40 8.14 33.94 2.73
3119 9923 2.366837 ACAGATCCCGGCCATGGA 60.367 61.111 18.40 13.13 36.05 3.41
3156 9960 2.505982 GCCCTGCGAGCCAGATTA 59.494 61.111 0.00 0.00 44.64 1.75
3245 10740 2.221906 TAAACCGGTCGCTCTGAGCC 62.222 60.000 22.97 10.44 42.19 4.70
3246 10741 1.077089 GTAAACCGGTCGCTCTGAGC 61.077 60.000 19.53 19.53 41.76 4.26
3247 10742 0.458025 GGTAAACCGGTCGCTCTGAG 60.458 60.000 8.04 0.00 0.00 3.35
3248 10743 1.180456 TGGTAAACCGGTCGCTCTGA 61.180 55.000 8.04 0.00 39.43 3.27
3249 10744 0.108329 ATGGTAAACCGGTCGCTCTG 60.108 55.000 8.04 0.00 39.43 3.35
3250 10745 0.108329 CATGGTAAACCGGTCGCTCT 60.108 55.000 8.04 0.00 39.43 4.09
3251 10746 1.702491 GCATGGTAAACCGGTCGCTC 61.702 60.000 8.04 0.00 39.43 5.03
3252 10747 1.743995 GCATGGTAAACCGGTCGCT 60.744 57.895 8.04 0.00 39.43 4.93
3253 10748 1.373590 ATGCATGGTAAACCGGTCGC 61.374 55.000 8.04 0.18 39.43 5.19
3254 10749 1.091537 AATGCATGGTAAACCGGTCG 58.908 50.000 8.04 0.00 39.43 4.79
3255 10750 1.469079 GCAATGCATGGTAAACCGGTC 60.469 52.381 8.04 0.00 39.43 4.79
3256 10751 0.530288 GCAATGCATGGTAAACCGGT 59.470 50.000 0.00 0.00 39.43 5.28
3257 10752 0.179113 GGCAATGCATGGTAAACCGG 60.179 55.000 7.79 0.00 39.43 5.28
3258 10753 0.529833 TGGCAATGCATGGTAAACCG 59.470 50.000 7.79 0.00 39.43 4.44
3259 10754 1.740043 GCTGGCAATGCATGGTAAACC 60.740 52.381 7.79 0.00 0.00 3.27
3260 10755 1.643880 GCTGGCAATGCATGGTAAAC 58.356 50.000 7.79 0.00 0.00 2.01
3261 10756 0.536260 GGCTGGCAATGCATGGTAAA 59.464 50.000 7.79 0.00 0.00 2.01
3262 10757 1.329171 GGGCTGGCAATGCATGGTAA 61.329 55.000 7.79 0.00 0.00 2.85
3263 10758 1.757731 GGGCTGGCAATGCATGGTA 60.758 57.895 7.79 0.00 0.00 3.25
3264 10759 3.078836 GGGCTGGCAATGCATGGT 61.079 61.111 7.79 0.00 0.00 3.55
3265 10760 3.078196 TGGGCTGGCAATGCATGG 61.078 61.111 7.79 0.00 0.00 3.66
3266 10761 2.016393 CTCTGGGCTGGCAATGCATG 62.016 60.000 7.79 0.00 0.00 4.06
3267 10762 1.756950 CTCTGGGCTGGCAATGCAT 60.757 57.895 7.79 0.00 0.00 3.96
3268 10763 2.361992 CTCTGGGCTGGCAATGCA 60.362 61.111 7.79 0.00 0.00 3.96
3269 10764 2.044650 TCTCTGGGCTGGCAATGC 60.045 61.111 2.88 0.00 0.00 3.56
3270 10765 1.751927 GGTCTCTGGGCTGGCAATG 60.752 63.158 2.88 0.00 0.00 2.82
3271 10766 1.578215 ATGGTCTCTGGGCTGGCAAT 61.578 55.000 2.88 0.00 0.00 3.56
3272 10767 2.233566 ATGGTCTCTGGGCTGGCAA 61.234 57.895 2.88 0.00 0.00 4.52
3273 10768 2.611800 ATGGTCTCTGGGCTGGCA 60.612 61.111 2.88 0.00 0.00 4.92
3274 10769 2.124403 CATGGTCTCTGGGCTGGC 60.124 66.667 0.00 0.00 0.00 4.85
3275 10770 1.222936 GACATGGTCTCTGGGCTGG 59.777 63.158 0.00 0.00 0.00 4.85
3276 10771 0.617413 AAGACATGGTCTCTGGGCTG 59.383 55.000 0.00 0.00 42.59 4.85
3277 10772 0.908198 GAAGACATGGTCTCTGGGCT 59.092 55.000 0.00 0.00 42.59 5.19
3278 10773 0.908198 AGAAGACATGGTCTCTGGGC 59.092 55.000 0.00 0.00 42.59 5.36
3279 10774 1.209019 CCAGAAGACATGGTCTCTGGG 59.791 57.143 22.40 12.74 44.46 4.45
3280 10775 2.687700 CCAGAAGACATGGTCTCTGG 57.312 55.000 19.01 19.01 42.59 3.86
3281 10776 1.277273 TGCCAGAAGACATGGTCTCTG 59.723 52.381 11.32 11.32 42.59 3.35
3282 10777 1.649321 TGCCAGAAGACATGGTCTCT 58.351 50.000 0.00 0.00 42.59 3.10


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

AutoCloner maintained by Alex Coulton.