Multiple sequence alignment - TraesCS7D01G386300

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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 TraesCS7D01G386300 chr7D 100.000 4521 0 0 1 4521 500771586 500776106 0.000000e+00 8349
1 TraesCS7D01G386300 chr7D 93.799 1645 93 6 1812 3450 113581187 113582828 0.000000e+00 2464
2 TraesCS7D01G386300 chr7D 88.034 1404 148 15 2164 3552 523057027 523055629 0.000000e+00 1644
3 TraesCS7D01G386300 chr7D 86.689 1480 173 18 2051 3515 523133927 523132457 0.000000e+00 1620
4 TraesCS7D01G386300 chr7D 87.322 1404 160 14 2109 3502 523128208 523126813 0.000000e+00 1591
5 TraesCS7D01G386300 chr7D 93.775 996 48 6 1 983 113579081 113580075 0.000000e+00 1483
6 TraesCS7D01G386300 chr7D 88.023 693 47 19 1020 1692 113580076 113580752 0.000000e+00 787
7 TraesCS7D01G386300 chr7D 95.349 129 3 1 4396 4521 113582861 113582989 7.670000e-48 202
8 TraesCS7D01G386300 chr7D 84.426 122 12 2 1692 1813 113580817 113580931 3.700000e-21 113
9 TraesCS7D01G386300 chr7B 94.536 3093 126 14 754 3818 528870227 528873304 0.000000e+00 4735
10 TraesCS7D01G386300 chr7B 91.053 2090 113 22 1812 3875 73173848 73175889 0.000000e+00 2756
11 TraesCS7D01G386300 chr7B 87.440 1465 159 10 2109 3552 557491665 557490205 0.000000e+00 1663
12 TraesCS7D01G386300 chr7B 86.414 1450 175 14 2113 3548 557257487 557256046 0.000000e+00 1567
13 TraesCS7D01G386300 chr7B 85.504 1428 188 16 2083 3502 557460718 557459302 0.000000e+00 1472
14 TraesCS7D01G386300 chr7B 98.529 748 8 2 1 747 528868935 528869680 0.000000e+00 1317
15 TraesCS7D01G386300 chr7B 87.410 691 54 13 1020 1692 73172840 73173515 0.000000e+00 763
16 TraesCS7D01G386300 chr7B 91.698 530 17 2 1 530 73171629 73172131 0.000000e+00 710
17 TraesCS7D01G386300 chr7B 92.540 496 26 6 4032 4521 73175889 73176379 0.000000e+00 701
18 TraesCS7D01G386300 chr7B 92.553 470 10 9 4034 4503 528873308 528873752 0.000000e+00 651
19 TraesCS7D01G386300 chr7B 89.487 409 32 3 586 983 73172431 73172839 1.450000e-139 507
20 TraesCS7D01G386300 chr7B 77.088 419 36 25 4053 4432 664399451 664399054 2.150000e-43 187
21 TraesCS7D01G386300 chr7B 85.246 122 11 3 1692 1813 73173573 73173687 7.940000e-23 119
22 TraesCS7D01G386300 chr7A 93.428 2176 119 8 1716 3873 566787791 566789960 0.000000e+00 3205
23 TraesCS7D01G386300 chr7A 87.526 1427 160 12 2140 3552 603331692 603330270 0.000000e+00 1633
24 TraesCS7D01G386300 chr7A 92.629 1004 43 8 1 983 566786061 566787054 0.000000e+00 1415
25 TraesCS7D01G386300 chr7A 87.977 682 58 17 1020 1692 566787055 566787721 0.000000e+00 784
26 TraesCS7D01G386300 chr7A 89.184 490 26 8 4032 4521 566789961 566790423 1.810000e-163 586
27 TraesCS7D01G386300 chr7A 93.785 177 8 2 3866 4040 494786821 494786996 3.470000e-66 263
28 TraesCS7D01G386300 chr7A 77.207 487 50 35 4051 4521 566909830 566910271 1.270000e-55 228
29 TraesCS7D01G386300 chr3D 88.029 969 80 10 1896 2843 603682150 603683103 0.000000e+00 1114
30 TraesCS7D01G386300 chr3D 77.816 293 17 24 4059 4325 598726670 598726400 2.190000e-28 137
31 TraesCS7D01G386300 chrUn 82.427 478 38 21 4051 4521 86611602 86612040 4.270000e-100 375
32 TraesCS7D01G386300 chr2D 97.714 175 3 1 3864 4037 387193687 387193861 2.640000e-77 300
33 TraesCS7D01G386300 chr2D 96.951 164 5 0 3872 4035 50239884 50240047 4.460000e-70 276
34 TraesCS7D01G386300 chr4D 96.491 171 5 1 3871 4041 49508592 49508761 9.580000e-72 281
35 TraesCS7D01G386300 chr4D 94.152 171 10 0 3866 4036 43645043 43644873 1.250000e-65 261
36 TraesCS7D01G386300 chr5D 96.386 166 6 0 3872 4037 384145774 384145609 1.600000e-69 274
37 TraesCS7D01G386300 chr5A 95.294 170 7 1 3872 4041 320214405 320214237 7.450000e-68 268
38 TraesCS7D01G386300 chr1D 95.238 168 8 0 3872 4039 463382066 463381899 2.680000e-67 267
39 TraesCS7D01G386300 chr1D 93.258 178 10 2 3871 4048 324412227 324412402 1.250000e-65 261
40 TraesCS7D01G386300 chr3B 80.488 287 23 21 4099 4376 810195314 810195052 5.970000e-44 189
41 TraesCS7D01G386300 chr3B 77.899 276 18 21 4071 4325 805977922 805977669 1.020000e-26 132
42 TraesCS7D01G386300 chr3B 78.390 236 20 16 4064 4290 805812441 805812228 1.710000e-24 124
43 TraesCS7D01G386300 chr3B 83.200 125 6 2 3754 3874 810195452 810195339 2.880000e-17 100
44 TraesCS7D01G386300 chr3A 80.916 262 18 16 4099 4352 732405069 732404832 1.290000e-40 178


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 TraesCS7D01G386300 chr7D 500771586 500776106 4520 False 8349.000000 8349 100.000000 1 4521 1 chr7D.!!$F1 4520
1 TraesCS7D01G386300 chr7D 523055629 523057027 1398 True 1644.000000 1644 88.034000 2164 3552 1 chr7D.!!$R1 1388
2 TraesCS7D01G386300 chr7D 523132457 523133927 1470 True 1620.000000 1620 86.689000 2051 3515 1 chr7D.!!$R3 1464
3 TraesCS7D01G386300 chr7D 523126813 523128208 1395 True 1591.000000 1591 87.322000 2109 3502 1 chr7D.!!$R2 1393
4 TraesCS7D01G386300 chr7D 113579081 113582989 3908 False 1009.800000 2464 91.074400 1 4521 5 chr7D.!!$F2 4520
5 TraesCS7D01G386300 chr7B 528868935 528873752 4817 False 2234.333333 4735 95.206000 1 4503 3 chr7B.!!$F2 4502
6 TraesCS7D01G386300 chr7B 557490205 557491665 1460 True 1663.000000 1663 87.440000 2109 3552 1 chr7B.!!$R3 1443
7 TraesCS7D01G386300 chr7B 557256046 557257487 1441 True 1567.000000 1567 86.414000 2113 3548 1 chr7B.!!$R1 1435
8 TraesCS7D01G386300 chr7B 557459302 557460718 1416 True 1472.000000 1472 85.504000 2083 3502 1 chr7B.!!$R2 1419
9 TraesCS7D01G386300 chr7B 73171629 73176379 4750 False 926.000000 2756 89.572333 1 4521 6 chr7B.!!$F1 4520
10 TraesCS7D01G386300 chr7A 603330270 603331692 1422 True 1633.000000 1633 87.526000 2140 3552 1 chr7A.!!$R1 1412
11 TraesCS7D01G386300 chr7A 566786061 566790423 4362 False 1497.500000 3205 90.804500 1 4521 4 chr7A.!!$F3 4520
12 TraesCS7D01G386300 chr3D 603682150 603683103 953 False 1114.000000 1114 88.029000 1896 2843 1 chr3D.!!$F1 947

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
209 210 4.232091 ACCTAGTTCTTCCTCAGTTTCCA 58.768 43.478 0.00 0.0 0.00 3.53 F
1759 2663 1.152756 GGTTGTCACCAAGGCCACT 60.153 57.895 5.01 0.0 43.61 4.00 F
2592 3818 0.179062 GCACTCCTGTCTATGCCCAG 60.179 60.000 0.00 0.0 31.71 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 3125 0.533951 GGTTGGTCCTACCTGGTACG 59.466 60.0 14.64 0.0 39.58 3.67 R
2998 4228 0.318762 GGAACTCGGTGAACTGCTCT 59.681 55.0 0.00 0.0 0.00 4.09 R
3537 4790 1.118838 ATGAGAGGCTGTGCTAGTCC 58.881 55.0 0.00 0.0 0.00 3.85 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
61 62 6.808008 ATGTTAGTTGAATGTGTCAGGAAG 57.192 37.500 0.00 0.00 37.61 3.46
209 210 4.232091 ACCTAGTTCTTCCTCAGTTTCCA 58.768 43.478 0.00 0.00 0.00 3.53
828 1627 9.936759 GTTCATTAGCTAGCCTCTTCTATTTAT 57.063 33.333 12.13 0.00 0.00 1.40
972 1778 4.827692 TGTATGTGTTAGTGTGATGACCC 58.172 43.478 0.00 0.00 0.00 4.46
1429 2247 4.803452 TGGTTTCATCTCCAAAGAACCTT 58.197 39.130 0.00 0.00 34.49 3.50
1679 2518 3.084039 TGGAGTGCATTTGAATCTGGTC 58.916 45.455 0.00 0.00 0.00 4.02
1696 2600 4.962995 TCTGGTCAGTTTTAGCTATAGCCT 59.037 41.667 21.17 7.83 43.38 4.58
1759 2663 1.152756 GGTTGTCACCAAGGCCACT 60.153 57.895 5.01 0.00 43.61 4.00
1961 3125 2.467566 ACCACACGGTACCTCAAATC 57.532 50.000 10.90 0.00 46.71 2.17
1964 3128 2.094597 CCACACGGTACCTCAAATCGTA 60.095 50.000 10.90 0.00 32.56 3.43
1965 3129 2.919229 CACACGGTACCTCAAATCGTAC 59.081 50.000 10.90 0.00 35.20 3.67
2554 3776 4.139420 CTCGCTTTCGCCACGCAG 62.139 66.667 0.00 0.00 35.26 5.18
2592 3818 0.179062 GCACTCCTGTCTATGCCCAG 60.179 60.000 0.00 0.00 31.71 4.45
2644 3870 4.295119 GACGACCTGGTGTGCGGT 62.295 66.667 2.82 0.00 35.90 5.68
2835 4063 3.422303 GGCTCACATTGCGTCGCA 61.422 61.111 17.58 17.58 36.47 5.10
3143 4373 2.505557 GCAGCAAGGCGCACATTC 60.506 61.111 10.83 0.00 46.13 2.67
3145 4375 1.582968 CAGCAAGGCGCACATTCTT 59.417 52.632 10.83 0.00 46.13 2.52
3211 4441 4.980805 TTCCTGACACACGCCGGC 62.981 66.667 19.07 19.07 0.00 6.13
3223 4453 4.373116 GCCGGCTGGAACTCGACA 62.373 66.667 22.15 0.00 37.49 4.35
3274 4504 1.130054 TGTGCTGGCCCTTCTTCTCT 61.130 55.000 0.00 0.00 0.00 3.10
3298 4531 0.607489 AGCAGATCAACAGCCGCTTT 60.607 50.000 0.00 0.00 0.00 3.51
3336 4569 2.276740 GGGGCTGGACATGAAGGG 59.723 66.667 0.00 0.00 0.00 3.95
3392 4632 2.927856 AGGCCATGGTGTCCGACA 60.928 61.111 14.67 0.00 0.00 4.35
3531 4784 0.110486 TCCTGTTGAAGCCCAGAACC 59.890 55.000 0.00 0.00 0.00 3.62
3537 4790 2.205022 TGAAGCCCAGAACCAATGAG 57.795 50.000 0.00 0.00 0.00 2.90
3609 4872 6.177610 ACTTATTCTAGCATTTCCCGAACAA 58.822 36.000 0.00 0.00 0.00 2.83
3620 4883 7.069331 AGCATTTCCCGAACAAATATATGGAAA 59.931 33.333 11.48 11.48 42.60 3.13
3621 4884 7.382218 GCATTTCCCGAACAAATATATGGAAAG 59.618 37.037 13.51 8.86 41.95 2.62
3622 4885 8.629158 CATTTCCCGAACAAATATATGGAAAGA 58.371 33.333 13.51 0.00 41.95 2.52
3623 4886 8.760980 TTTCCCGAACAAATATATGGAAAGAT 57.239 30.769 6.95 0.00 35.95 2.40
3624 4887 7.744087 TCCCGAACAAATATATGGAAAGATG 57.256 36.000 0.00 0.00 0.00 2.90
3625 4888 7.513856 TCCCGAACAAATATATGGAAAGATGA 58.486 34.615 0.00 0.00 0.00 2.92
3627 4890 7.094634 CCCGAACAAATATATGGAAAGATGAGG 60.095 40.741 0.00 0.00 0.00 3.86
3644 4907 9.539194 AAAGATGAGGAAATGTAAGAGGAATTT 57.461 29.630 0.00 0.00 0.00 1.82
3735 5000 5.848406 TGTGCCAATTTTTACTTTGGTAGG 58.152 37.500 3.85 0.00 43.54 3.18
3746 5011 2.174854 ACTTTGGTAGGCACTTGGTTCT 59.825 45.455 0.00 0.00 41.75 3.01
3747 5012 3.393278 ACTTTGGTAGGCACTTGGTTCTA 59.607 43.478 0.00 0.00 41.75 2.10
3748 5013 4.042934 ACTTTGGTAGGCACTTGGTTCTAT 59.957 41.667 0.00 0.00 41.75 1.98
3749 5014 4.650972 TTGGTAGGCACTTGGTTCTATT 57.349 40.909 0.00 0.00 41.75 1.73
3874 5139 9.305555 TGACTGGTTAAGTACTTATGTTCTACT 57.694 33.333 15.92 0.00 40.07 2.57
3875 5140 9.786105 GACTGGTTAAGTACTTATGTTCTACTC 57.214 37.037 15.92 5.61 40.07 2.59
3876 5141 8.747471 ACTGGTTAAGTACTTATGTTCTACTCC 58.253 37.037 15.92 8.17 37.36 3.85
3877 5142 8.071177 TGGTTAAGTACTTATGTTCTACTCCC 57.929 38.462 15.92 0.00 0.00 4.30
3878 5143 7.897565 TGGTTAAGTACTTATGTTCTACTCCCT 59.102 37.037 15.92 0.00 0.00 4.20
3879 5144 8.412456 GGTTAAGTACTTATGTTCTACTCCCTC 58.588 40.741 15.92 0.00 0.00 4.30
3880 5145 8.412456 GTTAAGTACTTATGTTCTACTCCCTCC 58.588 40.741 15.92 0.00 0.00 4.30
3881 5146 5.131784 AGTACTTATGTTCTACTCCCTCCG 58.868 45.833 0.00 0.00 0.00 4.63
3882 5147 3.978610 ACTTATGTTCTACTCCCTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
3883 5148 4.351127 ACTTATGTTCTACTCCCTCCGTT 58.649 43.478 0.00 0.00 0.00 4.44
3884 5149 4.401837 ACTTATGTTCTACTCCCTCCGTTC 59.598 45.833 0.00 0.00 0.00 3.95
3885 5150 1.553706 TGTTCTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
3886 5151 1.203087 TGTTCTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
3887 5152 1.897802 GTTCTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 0.00 3.53
3888 5153 2.301009 GTTCTACTCCCTCCGTTCCAAA 59.699 50.000 0.00 0.00 0.00 3.28
3889 5154 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
3890 5155 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
3891 5156 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
3892 5157 4.966805 TCTACTCCCTCCGTTCCAAAATAT 59.033 41.667 0.00 0.00 0.00 1.28
3893 5158 6.138263 TCTACTCCCTCCGTTCCAAAATATA 58.862 40.000 0.00 0.00 0.00 0.86
3894 5159 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
3895 5160 5.681639 ACTCCCTCCGTTCCAAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
3896 5161 5.191124 ACTCCCTCCGTTCCAAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
3897 5162 5.677567 TCCCTCCGTTCCAAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
3898 5163 5.427481 TCCCTCCGTTCCAAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
3899 5164 6.069847 TCCCTCCGTTCCAAAATATAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
3900 5165 6.602009 CCCTCCGTTCCAAAATATAAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
3901 5166 7.122204 CCCTCCGTTCCAAAATATAAGTCTTTT 59.878 37.037 0.00 0.00 0.00 2.27
3902 5167 8.520351 CCTCCGTTCCAAAATATAAGTCTTTTT 58.480 33.333 0.00 0.00 0.00 1.94
3920 5185 9.660180 AGTCTTTTTAGAGATTTCACTATGGAC 57.340 33.333 0.00 0.00 0.00 4.02
3921 5186 9.660180 GTCTTTTTAGAGATTTCACTATGGACT 57.340 33.333 0.00 0.00 0.00 3.85
3928 5193 7.877003 AGAGATTTCACTATGGACTACATACG 58.123 38.462 0.00 0.00 41.03 3.06
3929 5194 6.982852 AGATTTCACTATGGACTACATACGG 58.017 40.000 0.00 0.00 41.03 4.02
3930 5195 6.776116 AGATTTCACTATGGACTACATACGGA 59.224 38.462 0.00 0.00 41.03 4.69
3931 5196 6.971726 TTTCACTATGGACTACATACGGAT 57.028 37.500 0.00 0.00 41.03 4.18
3932 5197 5.959618 TCACTATGGACTACATACGGATG 57.040 43.478 5.94 5.94 41.03 3.51
3934 5199 6.536447 TCACTATGGACTACATACGGATGTA 58.464 40.000 19.32 19.32 44.77 2.29
3935 5200 7.173032 TCACTATGGACTACATACGGATGTAT 58.827 38.462 20.64 9.39 45.42 2.29
3936 5201 8.323567 TCACTATGGACTACATACGGATGTATA 58.676 37.037 20.64 10.04 45.42 1.47
3937 5202 9.121658 CACTATGGACTACATACGGATGTATAT 57.878 37.037 20.64 12.15 45.42 0.86
3941 5206 8.728337 TGGACTACATACGGATGTATATAGAC 57.272 38.462 20.64 10.95 45.42 2.59
3942 5207 8.323567 TGGACTACATACGGATGTATATAGACA 58.676 37.037 20.64 12.12 45.42 3.41
3943 5208 9.339850 GGACTACATACGGATGTATATAGACAT 57.660 37.037 20.64 12.70 45.42 3.06
3974 5239 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3975 5240 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3976 5241 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3977 5242 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3978 5243 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3979 5244 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3980 5245 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3981 5246 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3982 5247 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3983 5248 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3984 5249 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3985 5250 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3986 5251 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
3987 5252 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
3988 5253 1.466856 TTGCTCCGTATGTAGTCCGT 58.533 50.000 0.00 0.00 0.00 4.69
3989 5254 2.330440 TGCTCCGTATGTAGTCCGTA 57.670 50.000 0.00 0.00 0.00 4.02
3990 5255 2.216046 TGCTCCGTATGTAGTCCGTAG 58.784 52.381 0.00 0.00 0.00 3.51
3991 5256 2.216898 GCTCCGTATGTAGTCCGTAGT 58.783 52.381 0.00 0.00 0.00 2.73
3992 5257 2.032204 GCTCCGTATGTAGTCCGTAGTG 60.032 54.545 0.00 0.00 0.00 2.74
3993 5258 2.547211 CTCCGTATGTAGTCCGTAGTGG 59.453 54.545 0.00 0.00 40.09 4.00
4007 5272 6.845758 TCCGTAGTGGAATCTCTAAAAAGA 57.154 37.500 0.00 0.00 46.38 2.52
4008 5273 6.628185 TCCGTAGTGGAATCTCTAAAAAGAC 58.372 40.000 0.00 0.00 46.38 3.01
4009 5274 6.436532 TCCGTAGTGGAATCTCTAAAAAGACT 59.563 38.462 0.00 0.00 46.38 3.24
4010 5275 7.039223 TCCGTAGTGGAATCTCTAAAAAGACTT 60.039 37.037 0.00 0.00 46.38 3.01
4011 5276 8.248945 CCGTAGTGGAATCTCTAAAAAGACTTA 58.751 37.037 0.00 0.00 42.00 2.24
4012 5277 9.804758 CGTAGTGGAATCTCTAAAAAGACTTAT 57.195 33.333 0.00 0.00 0.00 1.73
4027 5292 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
4028 5293 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4029 5294 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4030 5295 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4296 5561 4.404098 GTTGACGGCGGGGTGGAT 62.404 66.667 13.24 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 210 3.181482 CCATACGTCAGAGCTTCATCAGT 60.181 47.826 0.00 0.00 0.00 3.41
828 1627 8.972127 ACTGTTAATAGCAGTAGAGATTCTTCA 58.028 33.333 8.01 0.00 44.41 3.02
972 1778 1.661112 GATGGCCGAAGAGAAGTTTCG 59.339 52.381 0.00 0.74 45.12 3.46
1429 2247 6.324512 AGCTAATATTGTTTGCAATCATCCCA 59.675 34.615 10.87 0.00 43.61 4.37
1648 2487 2.401583 ATGCACTCCAGCGACATAAA 57.598 45.000 0.00 0.00 37.31 1.40
1679 2518 5.402867 GTCGCTAAGGCTATAGCTAAAACTG 59.597 44.000 23.53 9.29 44.89 3.16
1696 2600 1.601903 CAGCTTTGTGTTGGTCGCTAA 59.398 47.619 0.00 0.00 0.00 3.09
1701 2605 0.675633 ATGGCAGCTTTGTGTTGGTC 59.324 50.000 0.00 0.00 0.00 4.02
1759 2663 4.886247 AACACGTTTTGCAGTTAGCTAA 57.114 36.364 0.86 0.86 45.94 3.09
1803 2707 7.935755 CAGATCCAGGTGACATCTAATTTATGT 59.064 37.037 5.96 5.96 40.23 2.29
1961 3125 0.533951 GGTTGGTCCTACCTGGTACG 59.466 60.000 14.64 0.00 39.58 3.67
1964 3128 1.152183 ACGGTTGGTCCTACCTGGT 60.152 57.895 18.79 4.05 39.58 4.00
1965 3129 1.295423 CACGGTTGGTCCTACCTGG 59.705 63.158 18.79 8.12 39.58 4.45
1968 3132 0.601841 CACACACGGTTGGTCCTACC 60.602 60.000 12.16 12.16 39.22 3.18
2368 3555 4.436998 CTGCGAGGGTGGTCGTCC 62.437 72.222 0.00 0.00 42.17 4.79
2500 3722 3.773262 CTCGGCGATGTCGATGGCA 62.773 63.158 11.27 0.00 39.46 4.92
2542 3764 3.345808 GCACTCTGCGTGGCGAAA 61.346 61.111 0.00 0.00 43.97 3.46
2554 3776 2.097038 CAGGTAGCTGCACGCACTC 61.097 63.158 9.34 1.54 42.61 3.51
2624 3850 4.295119 GCACACCAGGTCGTCCGT 62.295 66.667 0.00 0.00 39.05 4.69
2644 3870 2.690881 CCCTCCATCCCCGGAACA 60.691 66.667 0.73 0.00 33.65 3.18
2818 4046 3.422303 TGCGACGCAATGTGAGCC 61.422 61.111 22.24 0.00 34.76 4.70
2835 4063 3.917870 CGAAGACGTCGCTTGTGT 58.082 55.556 10.46 0.00 44.14 3.72
2998 4228 0.318762 GGAACTCGGTGAACTGCTCT 59.681 55.000 0.00 0.00 0.00 4.09
3140 4370 1.558756 CTGAGGAGCCCACTCAAGAAT 59.441 52.381 4.46 0.00 45.42 2.40
3143 4373 1.078567 GCTGAGGAGCCCACTCAAG 60.079 63.158 4.46 1.42 45.42 3.02
3145 4375 3.385384 CGCTGAGGAGCCCACTCA 61.385 66.667 3.07 3.07 45.42 3.41
3211 4441 0.962489 ACTCCAGTGTCGAGTTCCAG 59.038 55.000 0.00 0.00 37.28 3.86
3223 4453 3.241530 TCCAAGGCGCACTCCAGT 61.242 61.111 10.83 0.00 0.00 4.00
3274 4504 0.321919 GGCTGTTGATCTGCTGGTCA 60.322 55.000 1.88 1.88 40.19 4.02
3531 4784 1.209019 AGGCTGTGCTAGTCCTCATTG 59.791 52.381 0.00 0.00 30.23 2.82
3537 4790 1.118838 ATGAGAGGCTGTGCTAGTCC 58.881 55.000 0.00 0.00 0.00 3.85
3620 4883 7.559170 CCAAATTCCTCTTACATTTCCTCATCT 59.441 37.037 0.00 0.00 0.00 2.90
3621 4884 7.340487 ACCAAATTCCTCTTACATTTCCTCATC 59.660 37.037 0.00 0.00 0.00 2.92
3622 4885 7.184862 ACCAAATTCCTCTTACATTTCCTCAT 58.815 34.615 0.00 0.00 0.00 2.90
3623 4886 6.552008 ACCAAATTCCTCTTACATTTCCTCA 58.448 36.000 0.00 0.00 0.00 3.86
3624 4887 6.887002 AGACCAAATTCCTCTTACATTTCCTC 59.113 38.462 0.00 0.00 0.00 3.71
3625 4888 6.660949 CAGACCAAATTCCTCTTACATTTCCT 59.339 38.462 0.00 0.00 0.00 3.36
3627 4890 7.454260 ACAGACCAAATTCCTCTTACATTTC 57.546 36.000 0.00 0.00 0.00 2.17
3630 4893 6.431234 GTCAACAGACCAAATTCCTCTTACAT 59.569 38.462 0.00 0.00 0.00 2.29
3644 4907 1.557371 TGGTGTCAAGTCAACAGACCA 59.443 47.619 0.00 0.00 32.62 4.02
3704 4968 9.421806 CAAAGTAAAAATTGGCACATCTGAATA 57.578 29.630 0.00 0.00 39.30 1.75
3735 5000 8.780249 TCTTACAAAGTAAATAGAACCAAGTGC 58.220 33.333 0.00 0.00 0.00 4.40
3787 5052 4.284490 AGCTGTGTTTCTCATGAGGACTTA 59.716 41.667 22.42 12.52 0.00 2.24
3874 5139 5.427481 AGACTTATATTTTGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3875 5140 5.681639 AGACTTATATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3876 5141 7.625828 AAAGACTTATATTTTGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3894 5159 9.660180 GTCCATAGTGAAATCTCTAAAAAGACT 57.340 33.333 0.00 0.00 0.00 3.24
3895 5160 9.660180 AGTCCATAGTGAAATCTCTAAAAAGAC 57.340 33.333 0.00 0.00 0.00 3.01
3902 5167 9.000486 CGTATGTAGTCCATAGTGAAATCTCTA 58.000 37.037 0.00 0.00 36.71 2.43
3903 5168 7.040340 CCGTATGTAGTCCATAGTGAAATCTCT 60.040 40.741 0.00 0.00 36.71 3.10
3904 5169 7.040617 TCCGTATGTAGTCCATAGTGAAATCTC 60.041 40.741 0.00 0.00 36.71 2.75
3905 5170 6.776116 TCCGTATGTAGTCCATAGTGAAATCT 59.224 38.462 0.00 0.00 36.71 2.40
3906 5171 6.978338 TCCGTATGTAGTCCATAGTGAAATC 58.022 40.000 0.00 0.00 36.71 2.17
3907 5172 6.971726 TCCGTATGTAGTCCATAGTGAAAT 57.028 37.500 0.00 0.00 36.71 2.17
3908 5173 6.322969 ACATCCGTATGTAGTCCATAGTGAAA 59.677 38.462 0.00 0.00 44.66 2.69
3909 5174 5.831525 ACATCCGTATGTAGTCCATAGTGAA 59.168 40.000 0.00 0.00 44.66 3.18
3910 5175 5.382616 ACATCCGTATGTAGTCCATAGTGA 58.617 41.667 0.00 0.00 44.66 3.41
3911 5176 5.707242 ACATCCGTATGTAGTCCATAGTG 57.293 43.478 0.00 0.00 44.66 2.74
3938 5203 9.469097 AGTGAATCTACACTCTAAAGTATGTCT 57.531 33.333 0.00 0.00 46.36 3.41
3952 5217 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3953 5218 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3954 5219 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3955 5220 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3956 5221 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3957 5222 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3958 5223 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3959 5224 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3960 5225 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3961 5226 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3962 5227 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3963 5228 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
3964 5229 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
3965 5230 3.245284 CGGACTACATACGGAGCAAAATG 59.755 47.826 0.00 0.00 0.00 2.32
3966 5231 3.118884 ACGGACTACATACGGAGCAAAAT 60.119 43.478 0.00 0.00 0.00 1.82
3967 5232 2.231964 ACGGACTACATACGGAGCAAAA 59.768 45.455 0.00 0.00 0.00 2.44
3968 5233 1.820519 ACGGACTACATACGGAGCAAA 59.179 47.619 0.00 0.00 0.00 3.68
3969 5234 1.466856 ACGGACTACATACGGAGCAA 58.533 50.000 0.00 0.00 0.00 3.91
3970 5235 2.216046 CTACGGACTACATACGGAGCA 58.784 52.381 0.00 0.00 31.15 4.26
3971 5236 2.032204 CACTACGGACTACATACGGAGC 60.032 54.545 0.00 0.00 42.12 4.70
3972 5237 2.547211 CCACTACGGACTACATACGGAG 59.453 54.545 0.00 0.00 43.89 4.63
3973 5238 2.170397 TCCACTACGGACTACATACGGA 59.830 50.000 0.00 0.00 39.64 4.69
3974 5239 2.564771 TCCACTACGGACTACATACGG 58.435 52.381 0.00 0.00 39.64 4.02
3975 5240 4.514441 AGATTCCACTACGGACTACATACG 59.486 45.833 0.00 0.00 46.36 3.06
3976 5241 5.764192 AGAGATTCCACTACGGACTACATAC 59.236 44.000 0.00 0.00 46.36 2.39
3977 5242 5.938279 AGAGATTCCACTACGGACTACATA 58.062 41.667 0.00 0.00 46.36 2.29
3978 5243 4.794334 AGAGATTCCACTACGGACTACAT 58.206 43.478 0.00 0.00 46.36 2.29
3979 5244 4.232188 AGAGATTCCACTACGGACTACA 57.768 45.455 0.00 0.00 46.36 2.74
3980 5245 6.690194 TTTAGAGATTCCACTACGGACTAC 57.310 41.667 0.00 0.00 46.36 2.73
3981 5246 7.613022 TCTTTTTAGAGATTCCACTACGGACTA 59.387 37.037 0.00 0.00 46.36 2.59
3982 5247 6.436532 TCTTTTTAGAGATTCCACTACGGACT 59.563 38.462 0.00 0.00 46.36 3.85
3983 5248 6.530887 GTCTTTTTAGAGATTCCACTACGGAC 59.469 42.308 0.00 0.00 46.36 4.79
3984 5249 6.436532 AGTCTTTTTAGAGATTCCACTACGGA 59.563 38.462 0.00 0.00 44.40 4.69
3985 5250 6.631962 AGTCTTTTTAGAGATTCCACTACGG 58.368 40.000 0.00 0.00 0.00 4.02
3986 5251 9.804758 ATAAGTCTTTTTAGAGATTCCACTACG 57.195 33.333 0.00 0.00 0.00 3.51
4001 5266 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
4002 5267 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4003 5268 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4004 5269 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4005 5270 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4006 5271 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4007 5272 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4008 5273 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4011 5276 9.643735 CTATATACTCCCTCCGTTCCTAAATAT 57.356 37.037 0.00 0.00 0.00 1.28
4012 5277 8.618385 ACTATATACTCCCTCCGTTCCTAAATA 58.382 37.037 0.00 0.00 0.00 1.40
4013 5278 7.477008 ACTATATACTCCCTCCGTTCCTAAAT 58.523 38.462 0.00 0.00 0.00 1.40
4014 5279 6.856757 ACTATATACTCCCTCCGTTCCTAAA 58.143 40.000 0.00 0.00 0.00 1.85
4015 5280 6.460103 ACTATATACTCCCTCCGTTCCTAA 57.540 41.667 0.00 0.00 0.00 2.69
4016 5281 6.460103 AACTATATACTCCCTCCGTTCCTA 57.540 41.667 0.00 0.00 0.00 2.94
4017 5282 5.336491 AACTATATACTCCCTCCGTTCCT 57.664 43.478 0.00 0.00 0.00 3.36
4018 5283 6.479884 TCTAACTATATACTCCCTCCGTTCC 58.520 44.000 0.00 0.00 0.00 3.62
4019 5284 6.598850 CCTCTAACTATATACTCCCTCCGTTC 59.401 46.154 0.00 0.00 0.00 3.95
4020 5285 6.483405 CCTCTAACTATATACTCCCTCCGTT 58.517 44.000 0.00 0.00 0.00 4.44
4021 5286 5.573296 GCCTCTAACTATATACTCCCTCCGT 60.573 48.000 0.00 0.00 0.00 4.69
4022 5287 4.883006 GCCTCTAACTATATACTCCCTCCG 59.117 50.000 0.00 0.00 0.00 4.63
4023 5288 6.082228 AGCCTCTAACTATATACTCCCTCC 57.918 45.833 0.00 0.00 0.00 4.30
4024 5289 8.550585 TCTAAGCCTCTAACTATATACTCCCTC 58.449 40.741 0.00 0.00 0.00 4.30
4025 5290 8.465798 TCTAAGCCTCTAACTATATACTCCCT 57.534 38.462 0.00 0.00 0.00 4.20
4026 5291 7.283807 GCTCTAAGCCTCTAACTATATACTCCC 59.716 44.444 0.00 0.00 34.48 4.30
4027 5292 7.830201 TGCTCTAAGCCTCTAACTATATACTCC 59.170 40.741 0.00 0.00 41.51 3.85
4028 5293 8.795842 TGCTCTAAGCCTCTAACTATATACTC 57.204 38.462 0.00 0.00 41.51 2.59
4280 5545 4.402528 CATCCACCCCGCCGTCAA 62.403 66.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.