Multiple sequence alignment - TraesCS5D01G082400

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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 TraesCS5D01G082400 chr5D 100.000 9019 0 0 1 9019 84324370 84315352 0.000000e+00 16656.0
1 TraesCS5D01G082400 chr5D 83.333 828 94 21 7719 8519 87525314 87524504 0.000000e+00 725.0
2 TraesCS5D01G082400 chr5D 83.192 827 92 25 7719 8519 84199782 84198977 0.000000e+00 713.0
3 TraesCS5D01G082400 chr5D 82.830 827 98 24 7719 8519 122046951 122046143 0.000000e+00 701.0
4 TraesCS5D01G082400 chr5D 93.056 216 8 4 6032 6242 84318138 84317925 8.790000e-80 309.0
5 TraesCS5D01G082400 chr5D 93.056 216 8 4 6233 6446 84318339 84318129 8.790000e-80 309.0
6 TraesCS5D01G082400 chr5D 83.929 280 23 14 5034 5299 84318805 84318534 1.940000e-61 248.0
7 TraesCS5D01G082400 chr5D 83.929 280 23 14 5566 5837 84319337 84319072 1.940000e-61 248.0
8 TraesCS5D01G082400 chr5D 89.286 168 16 2 5202 5367 84319003 84318836 9.180000e-50 209.0
9 TraesCS5D01G082400 chr5D 89.286 168 16 2 5368 5535 84319169 84319004 9.180000e-50 209.0
10 TraesCS5D01G082400 chr5D 76.887 212 33 13 5493 5698 84318456 84318255 1.240000e-18 106.0
11 TraesCS5D01G082400 chr5D 76.887 212 33 13 5915 6116 84318878 84318673 1.240000e-18 106.0
12 TraesCS5D01G082400 chr5A 95.017 6101 173 43 1 6014 78970530 78964474 0.000000e+00 9461.0
13 TraesCS5D01G082400 chr5A 94.275 1799 59 8 7058 8852 78962741 78960983 0.000000e+00 2712.0
14 TraesCS5D01G082400 chr5A 95.378 952 39 3 6129 7075 78964048 78963097 0.000000e+00 1509.0
15 TraesCS5D01G082400 chr5A 92.093 215 12 2 6032 6241 78963944 78963730 1.900000e-76 298.0
16 TraesCS5D01G082400 chr5A 91.163 215 16 2 8797 9011 78961001 78960790 1.150000e-73 289.0
17 TraesCS5D01G082400 chr5A 85.830 247 21 10 5594 5837 78965420 78965185 5.410000e-62 250.0
18 TraesCS5D01G082400 chr5A 86.344 227 21 6 5368 5594 78965281 78965065 1.170000e-58 239.0
19 TraesCS5D01G082400 chr5A 88.060 201 21 3 5170 5367 78965159 78964959 1.510000e-57 235.0
20 TraesCS5D01G082400 chr5A 84.490 245 25 9 5065 5299 78964891 78964650 7.040000e-56 230.0
21 TraesCS5D01G082400 chr5A 95.690 116 4 1 6332 6446 78964050 78963935 1.550000e-42 185.0
22 TraesCS5D01G082400 chr5A 87.023 131 17 0 5303 5433 78965588 78965718 2.030000e-31 148.0
23 TraesCS5D01G082400 chr5A 80.142 141 21 5 5980 6116 78964926 78964789 2.070000e-16 99.0
24 TraesCS5D01G082400 chr5B 95.775 3834 89 25 1 3794 91200148 91196348 0.000000e+00 6115.0
25 TraesCS5D01G082400 chr5B 96.039 1868 52 11 6421 8270 91193091 91191228 0.000000e+00 3020.0
26 TraesCS5D01G082400 chr5B 93.535 1191 44 15 5019 6180 91194933 91193747 0.000000e+00 1742.0
27 TraesCS5D01G082400 chr5B 93.611 1127 41 11 3840 4942 91196049 91194930 0.000000e+00 1653.0
28 TraesCS5D01G082400 chr5B 91.954 696 42 7 8265 8951 91188099 91187409 0.000000e+00 963.0
29 TraesCS5D01G082400 chr5B 94.512 492 21 6 6232 6718 91193745 91193255 0.000000e+00 754.0
30 TraesCS5D01G082400 chr5B 89.157 249 21 5 5594 5837 91194889 91194642 1.140000e-78 305.0
31 TraesCS5D01G082400 chr5B 92.823 209 10 2 6038 6241 91193739 91193531 1.900000e-76 298.0
32 TraesCS5D01G082400 chr5B 82.562 281 26 14 5034 5299 91194374 91194102 9.110000e-55 226.0
33 TraesCS5D01G082400 chr5B 84.979 233 22 10 5202 5429 91194573 91194349 3.280000e-54 224.0
34 TraesCS5D01G082400 chr5B 92.857 154 10 1 6233 6385 91193900 91193747 1.180000e-53 222.0
35 TraesCS5D01G082400 chr5B 84.746 236 19 6 5368 5594 91194739 91194512 4.240000e-53 220.0
36 TraesCS5D01G082400 chr5B 89.888 89 6 2 4937 5022 440023835 440023747 2.660000e-20 111.0
37 TraesCS5D01G082400 chr5B 93.243 74 4 1 8946 9019 91185485 91185413 3.440000e-19 108.0
38 TraesCS5D01G082400 chr5B 83.471 121 15 3 5635 5752 91194098 91193980 3.440000e-19 108.0
39 TraesCS5D01G082400 chr5B 81.356 118 16 5 5845 5956 91194304 91194187 3.470000e-14 91.6
40 TraesCS5D01G082400 chr5B 87.879 66 8 0 5632 5697 91193724 91193659 2.700000e-10 78.7
41 TraesCS5D01G082400 chr5B 94.737 38 2 0 5800 5837 91194456 91194419 9.780000e-05 60.2
42 TraesCS5D01G082400 chr3B 87.871 404 42 6 868 1269 136499693 136500091 1.370000e-127 468.0
43 TraesCS5D01G082400 chrUn 90.426 94 5 4 4932 5022 110238063 110238155 4.420000e-23 121.0
44 TraesCS5D01G082400 chrUn 90.426 94 5 4 4932 5022 187694385 187694477 4.420000e-23 121.0
45 TraesCS5D01G082400 chrUn 90.426 94 5 4 4932 5022 254193328 254193420 4.420000e-23 121.0
46 TraesCS5D01G082400 chr2A 92.045 88 4 2 4938 5022 539325665 539325578 4.420000e-23 121.0
47 TraesCS5D01G082400 chr1D 87.500 104 10 3 4933 5035 489727979 489727878 5.720000e-22 117.0
48 TraesCS5D01G082400 chr3D 88.660 97 7 3 4937 5029 124616845 124616749 2.060000e-21 115.0
49 TraesCS5D01G082400 chr2B 89.362 94 7 2 4936 5026 483453042 483452949 2.060000e-21 115.0


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 TraesCS5D01G082400 chr5D 84315352 84324370 9018 True 16656.000000 16656 100.000000 1 9019 1 chr5D.!!$R2 9018
1 TraesCS5D01G082400 chr5D 87524504 87525314 810 True 725.000000 725 83.333000 7719 8519 1 chr5D.!!$R3 800
2 TraesCS5D01G082400 chr5D 84198977 84199782 805 True 713.000000 713 83.192000 7719 8519 1 chr5D.!!$R1 800
3 TraesCS5D01G082400 chr5D 122046143 122046951 808 True 701.000000 701 82.830000 7719 8519 1 chr5D.!!$R4 800
4 TraesCS5D01G082400 chr5D 84317925 84319337 1412 True 218.000000 309 85.789500 5034 6446 8 chr5D.!!$R5 1412
5 TraesCS5D01G082400 chr5A 78960790 78970530 9740 True 2409.000000 9461 93.936000 1 9011 6 chr5A.!!$R1 9010
6 TraesCS5D01G082400 chr5A 78964650 78965420 770 True 210.600000 250 84.973200 5065 6116 5 chr5A.!!$R2 1051
7 TraesCS5D01G082400 chr5B 91185413 91200148 14735 True 952.264706 6115 90.190353 1 9019 17 chr5B.!!$R2 9018

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
915 966 1.003580 TGTGAAGACCCAAGAGCATCC 59.996 52.381 0.00 0.0 33.66 3.51 F
1892 1958 0.537188 ACCTAGTGATGTTGGGCTCG 59.463 55.000 0.00 0.0 0.00 5.03 F
3143 3212 3.199727 TGCACCATGGTATAGCTCTTGAA 59.800 43.478 19.28 0.0 0.00 2.69 F
3834 3911 1.887242 TGCGGCACAGTCACAAGTC 60.887 57.895 0.00 0.0 0.00 3.01 F
3836 3913 1.934463 CGGCACAGTCACAAGTCAC 59.066 57.895 0.00 0.0 0.00 3.67 F
4707 5051 2.024273 TCTACCCTCCTCCAATCGACTT 60.024 50.000 0.00 0.0 0.00 3.01 F
6579 7279 0.445436 GACAGCCAAGTGAATCAGCG 59.555 55.000 0.00 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2119 0.248843 GAGCCTTCTCACCCTGTCAG 59.751 60.000 0.0 0.0 39.16 3.51 R
3679 3748 1.428448 CAGAAGAATCCGCACACGAA 58.572 50.000 0.0 0.0 43.93 3.85 R
4183 4520 0.250338 GCGAAAGAGTTGGGAGTGGT 60.250 55.000 0.0 0.0 0.00 4.16 R
5012 5365 3.252215 CACTATTCTCTGCTACTCCCTCG 59.748 52.174 0.0 0.0 0.00 4.63 R
6449 7148 6.918022 CCACACACAAAGAGAAATTAGGTTTC 59.082 38.462 0.0 0.0 45.31 2.78 R
6593 7293 0.611714 AGCCGAAACATTCTACCCGT 59.388 50.000 0.0 0.0 0.00 5.28 R
8300 13002 0.249120 CATCACTGCCTCGGTAACCA 59.751 55.000 0.0 0.0 0.00 3.67 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
129 133 5.046663 GGCCATAGAAAGGAGATAAGGAGAG 60.047 48.000 0.00 0.00 0.00 3.20
290 302 3.717707 TCGGTGAGTGAGTTCTTTCTTG 58.282 45.455 0.00 0.00 0.00 3.02
342 356 4.853924 ATTTGGTTTGATTCGCTTCTGT 57.146 36.364 0.00 0.00 0.00 3.41
377 391 1.614903 TGCTGATGTGAGGCCTTTTTG 59.385 47.619 6.77 0.00 0.00 2.44
378 392 1.615392 GCTGATGTGAGGCCTTTTTGT 59.385 47.619 6.77 0.00 0.00 2.83
390 404 4.641396 GGCCTTTTTGTTGCCTTTTCTAT 58.359 39.130 0.00 0.00 42.01 1.98
543 557 7.008941 TCCTCCCAACTGTAGGATAATACTAC 58.991 42.308 0.43 0.00 40.87 2.73
547 561 8.505246 TCCCAACTGTAGGATAATACTACTACA 58.495 37.037 7.67 0.00 42.32 2.74
548 562 8.574737 CCCAACTGTAGGATAATACTACTACAC 58.425 40.741 7.67 0.00 40.40 2.90
771 821 2.817665 GAGTGTAGTTACTCCCACCCT 58.182 52.381 10.26 0.00 40.92 4.34
775 825 2.158127 TGTAGTTACTCCCACCCTCCAA 60.158 50.000 0.00 0.00 0.00 3.53
779 829 1.591768 TACTCCCACCCTCCAATTCC 58.408 55.000 0.00 0.00 0.00 3.01
825 875 7.547370 TGATTAAATGCCCTAAATTCCGTTTTG 59.453 33.333 0.00 0.00 0.00 2.44
915 966 1.003580 TGTGAAGACCCAAGAGCATCC 59.996 52.381 0.00 0.00 33.66 3.51
987 1039 3.987220 GAGAGAGTGTTCTTGCTTGAGTC 59.013 47.826 0.00 0.00 32.53 3.36
1194 1247 1.284841 CCAATCCTGGCTCCCCTCTT 61.285 60.000 0.00 0.00 35.39 2.85
1202 1255 0.547075 GGCTCCCCTCTTTAACTCCC 59.453 60.000 0.00 0.00 0.00 4.30
1231 1284 5.281727 CGCTTTTACTTTCTTTTGCTTCCT 58.718 37.500 0.00 0.00 0.00 3.36
1233 1286 5.399596 GCTTTTACTTTCTTTTGCTTCCTCG 59.600 40.000 0.00 0.00 0.00 4.63
1255 1308 1.193650 GTACAGTTCGATTGTGCGCAA 59.806 47.619 14.00 16.21 39.16 4.85
1265 1318 1.163420 TTGTGCGCAAACAGGACGAT 61.163 50.000 14.00 0.00 32.37 3.73
1269 1322 0.793861 GCGCAAACAGGACGATGTAA 59.206 50.000 0.30 0.00 31.70 2.41
1270 1323 1.396996 GCGCAAACAGGACGATGTAAT 59.603 47.619 0.30 0.00 31.70 1.89
1271 1324 2.536928 GCGCAAACAGGACGATGTAATC 60.537 50.000 0.30 0.00 40.89 1.75
1272 1325 2.930040 CGCAAACAGGACGATGTAATCT 59.070 45.455 0.00 0.00 42.58 2.40
1273 1326 3.000322 CGCAAACAGGACGATGTAATCTC 60.000 47.826 0.00 0.00 42.58 2.75
1274 1327 3.932710 GCAAACAGGACGATGTAATCTCA 59.067 43.478 0.00 0.00 42.58 3.27
1402 1459 5.164158 GCGTTCAATAATGCTCTGTTTTGTG 60.164 40.000 0.00 0.00 43.13 3.33
1412 1469 3.490348 CTCTGTTTTGTGAAGTCCCCAT 58.510 45.455 0.00 0.00 0.00 4.00
1414 1471 4.394729 TCTGTTTTGTGAAGTCCCCATAC 58.605 43.478 0.00 0.00 0.00 2.39
1430 1487 6.369065 GTCCCCATACATAATCGACTTCATTC 59.631 42.308 0.00 0.00 0.00 2.67
1444 1501 9.726232 ATCGACTTCATTCATGTATTGATTTTG 57.274 29.630 0.00 0.00 33.34 2.44
1504 1561 8.022550 TGTTATTGCATACTTTGTTGATCTGTG 58.977 33.333 0.00 0.00 0.00 3.66
1525 1582 3.635373 TGAAGGGCTGTACCTACTATTCG 59.365 47.826 0.00 0.00 40.87 3.34
1657 1715 7.604164 TCTGCCACTTTGAAGTATAGAAAAGAG 59.396 37.037 0.00 0.00 37.08 2.85
1752 1810 9.214957 TCCTTTGCATATATTTAGGTATGAACG 57.785 33.333 0.00 0.00 31.48 3.95
1829 1895 6.823689 ACTTGCACTTACCCTGTTCTATTATG 59.176 38.462 0.00 0.00 0.00 1.90
1892 1958 0.537188 ACCTAGTGATGTTGGGCTCG 59.463 55.000 0.00 0.00 0.00 5.03
2010 2076 7.416817 TGTTATGCATCGATGTAATTTCCTTG 58.583 34.615 25.47 0.00 0.00 3.61
2011 2077 7.281999 TGTTATGCATCGATGTAATTTCCTTGA 59.718 33.333 25.47 0.00 0.00 3.02
2019 2087 9.627123 ATCGATGTAATTTCCTTGAGGATTTAA 57.373 29.630 0.00 0.00 44.98 1.52
2051 2119 4.044426 CCTGCTGCTTTTGTTGTTCTTAC 58.956 43.478 0.00 0.00 0.00 2.34
2055 2123 4.735338 GCTGCTTTTGTTGTTCTTACTGAC 59.265 41.667 0.00 0.00 0.00 3.51
2302 2370 5.391312 AATGTTTAACCATGCTCCTTGTC 57.609 39.130 0.00 0.00 0.00 3.18
2303 2371 4.098914 TGTTTAACCATGCTCCTTGTCT 57.901 40.909 0.00 0.00 0.00 3.41
2702 2771 9.770097 TGATTTCTATATTTTAGCAGAGGACTG 57.230 33.333 0.00 0.00 45.91 3.51
3143 3212 3.199727 TGCACCATGGTATAGCTCTTGAA 59.800 43.478 19.28 0.00 0.00 2.69
3331 3400 7.491048 GTGCTTGTTTCATCTTTTGAGGTTAAA 59.509 33.333 0.00 0.00 35.27 1.52
3348 3417 8.390921 TGAGGTTAAAGACTAATTGGATTTCCT 58.609 33.333 0.00 0.98 36.82 3.36
3679 3748 4.832266 TGGTTGTGCCATACTTTCTTTGAT 59.168 37.500 0.00 0.00 43.61 2.57
3682 3751 5.295431 TGTGCCATACTTTCTTTGATTCG 57.705 39.130 0.00 0.00 0.00 3.34
3806 3875 4.252493 GGGAACAACTCCTCCCCT 57.748 61.111 0.00 0.00 45.03 4.79
3830 3907 4.214327 TCGTGCGGCACAGTCACA 62.214 61.111 30.23 5.93 33.40 3.58
3831 3908 3.268603 CGTGCGGCACAGTCACAA 61.269 61.111 30.23 0.00 33.40 3.33
3832 3909 2.633657 GTGCGGCACAGTCACAAG 59.366 61.111 27.10 0.00 34.08 3.16
3833 3910 2.180204 GTGCGGCACAGTCACAAGT 61.180 57.895 27.10 0.00 34.08 3.16
3834 3911 1.887242 TGCGGCACAGTCACAAGTC 60.887 57.895 0.00 0.00 0.00 3.01
3835 3912 1.887242 GCGGCACAGTCACAAGTCA 60.887 57.895 0.00 0.00 0.00 3.41
3836 3913 1.934463 CGGCACAGTCACAAGTCAC 59.066 57.895 0.00 0.00 0.00 3.67
3852 4174 4.677673 AGTCACGTGTAGGGTTTTACTT 57.322 40.909 16.51 0.00 0.00 2.24
4435 4779 4.541705 TCAAATCCAAAAGTTCCACCTCA 58.458 39.130 0.00 0.00 0.00 3.86
4453 4797 6.767423 CCACCTCAAAAATCAACTTTGGAATT 59.233 34.615 0.00 0.00 35.03 2.17
4556 4900 2.371841 TGGGACAATGACACTTAGCACT 59.628 45.455 0.00 0.00 31.92 4.40
4707 5051 2.024273 TCTACCCTCCTCCAATCGACTT 60.024 50.000 0.00 0.00 0.00 3.01
4878 5228 6.767902 TCTTGTTGCTTTGTTCTAGATCAAGT 59.232 34.615 14.30 0.00 33.03 3.16
4925 5275 2.503546 GTAGCAGCAGGAGGAGGC 59.496 66.667 0.00 0.00 0.00 4.70
4958 5308 8.896722 AGAATAGTACTCCCTCTGTAAAGAAA 57.103 34.615 0.00 0.00 0.00 2.52
4968 5318 9.892130 CTCCCTCTGTAAAGAAATATAAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
5000 5353 9.593134 ACTAAAGTAGTGATCTAAATGCTCTTG 57.407 33.333 0.00 0.00 37.69 3.02
6446 7145 3.717294 GCGGCTCAAGGAGGGGAA 61.717 66.667 0.00 0.00 0.00 3.97
6449 7148 1.228510 GGCTCAAGGAGGGGAATGG 59.771 63.158 0.00 0.00 0.00 3.16
6579 7279 0.445436 GACAGCCAAGTGAATCAGCG 59.555 55.000 0.00 0.00 0.00 5.18
6593 7293 1.080093 CAGCGACGGCAAGGAAGTA 60.080 57.895 0.00 0.00 43.41 2.24
6594 7294 1.080025 AGCGACGGCAAGGAAGTAC 60.080 57.895 0.00 0.00 43.41 2.73
6610 7310 3.515330 AGTACGGGTAGAATGTTTCGG 57.485 47.619 0.00 0.00 34.02 4.30
6625 7325 2.201436 TTCGGCTCGACTGCTGTCTC 62.201 60.000 19.86 9.73 40.86 3.36
6635 7335 1.613925 ACTGCTGTCTCGTGCTTCTAA 59.386 47.619 0.00 0.00 0.00 2.10
6797 7961 2.558359 GGCTGCTTGACTTACCATTTGT 59.442 45.455 0.00 0.00 0.00 2.83
6828 7992 1.451028 GCTCCAGTTAGCAGCCCTG 60.451 63.158 0.00 0.00 42.30 4.45
7029 8197 5.116882 CCGGGGATTTCTAGTTAGAACTTG 58.883 45.833 0.00 0.00 41.64 3.16
7031 8199 5.437946 GGGGATTTCTAGTTAGAACTTGGG 58.562 45.833 0.00 0.00 41.64 4.12
7050 8218 8.964533 ACTTGGGAATACTATACTGATGATCT 57.035 34.615 0.00 0.00 0.00 2.75
7082 8623 7.172190 CACATCACATCTGAATATAACCCAGTC 59.828 40.741 0.00 0.00 0.00 3.51
7106 8647 9.788960 GTCTATTGTTTCTCAAGACAAAGTTTT 57.211 29.630 0.00 0.00 39.03 2.43
7138 8679 7.941238 AGAACTATTTATGCTATGCCTTGTCAT 59.059 33.333 0.00 0.00 0.00 3.06
7145 8686 2.424601 GCTATGCCTTGTCATCTGCAAA 59.575 45.455 0.00 0.00 37.27 3.68
7396 8937 2.331893 CCCGTTGCCAATCTTCGCA 61.332 57.895 0.00 0.00 0.00 5.10
7585 9126 6.876257 GGAACATCTACATCATTGGACTATCC 59.124 42.308 0.00 0.00 36.96 2.59
7621 9162 3.320826 TCTCGATCCCTCAATATTTCGCA 59.679 43.478 1.05 0.00 0.00 5.10
7677 9218 3.381272 CGAACAAATGCAGGATGGGTATT 59.619 43.478 0.00 0.00 35.86 1.89
7715 9264 9.241317 CCTTTGCATCATTGTTTAGTTATCATC 57.759 33.333 0.00 0.00 0.00 2.92
7982 9534 3.137913 AGGAGTTCTACAGCTACCCGATA 59.862 47.826 0.00 0.00 0.00 2.92
8385 13092 3.507622 GCAAGTAAACTGGCCTGATCTTT 59.492 43.478 17.64 9.08 36.93 2.52
8529 13260 1.153667 GAGCAGCCTGAAGAGACGG 60.154 63.158 0.00 0.00 0.00 4.79
8532 13263 2.284258 AGCCTGAAGAGACGGCCT 60.284 61.111 0.00 0.00 44.84 5.19
8536 13267 0.249657 CCTGAAGAGACGGCCTATGC 60.250 60.000 0.00 0.00 0.00 3.14
8551 13282 1.062587 CTATGCCAGGAAAACGAAGCG 59.937 52.381 0.00 0.00 0.00 4.68
8563 13294 1.787056 CGAAGCGCGGTTTTCGTTC 60.787 57.895 25.80 10.22 40.79 3.95
8613 13345 2.286294 GCTATTGTGAGATTGTGAGGCG 59.714 50.000 0.00 0.00 0.00 5.52
8630 13362 1.071699 GGCGTTGGGAATATGGAGCTA 59.928 52.381 0.00 0.00 0.00 3.32
8632 13364 3.412386 GCGTTGGGAATATGGAGCTATT 58.588 45.455 0.00 0.00 0.00 1.73
8637 13369 4.973168 TGGGAATATGGAGCTATTGTGTC 58.027 43.478 0.00 0.00 0.00 3.67
8664 13396 1.210931 CACAGCGCTTTCATGTGGG 59.789 57.895 7.50 0.00 40.47 4.61
8680 13412 1.067060 GTGGGAAGAAACGCTTTGCTT 59.933 47.619 0.00 0.00 36.83 3.91
8742 13474 0.679960 CCACCCGGGAAGTTGAATCC 60.680 60.000 32.02 0.00 40.01 3.01
8814 13546 6.753107 TTTGTAGCCTATAGTGCCTTTTTC 57.247 37.500 8.94 0.00 0.00 2.29
8875 13638 0.037139 TGAATGTCCCGTTACACCCG 60.037 55.000 0.00 0.00 30.75 5.28
8895 13658 0.539901 TATGCGAGGCTCCTAGACCC 60.540 60.000 9.32 0.00 0.00 4.46
8905 13668 2.092321 GCTCCTAGACCCAGTCTCAGTA 60.092 54.545 0.00 0.00 42.40 2.74
8920 13683 7.138081 CAGTCTCAGTATTGTGCATACTCTAG 58.862 42.308 0.00 0.00 44.32 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 150 4.808414 AAAGCCTCCAGCCTTTATTTTC 57.192 40.909 0.00 0.00 45.47 2.29
290 302 3.752339 CGAAAAGCAGCAGGGGGC 61.752 66.667 0.00 0.00 45.30 5.80
342 356 6.889177 TCACATCAGCACATTAAAATAAGGGA 59.111 34.615 0.00 0.00 0.00 4.20
377 391 5.578336 GGATGCAAGAAATAGAAAAGGCAAC 59.422 40.000 0.00 0.00 33.33 4.17
378 392 5.481473 AGGATGCAAGAAATAGAAAAGGCAA 59.519 36.000 0.00 0.00 33.33 4.52
390 404 3.384146 TGCAGTGAAAAGGATGCAAGAAA 59.616 39.130 0.00 0.00 45.09 2.52
554 586 3.744940 AAGATGCAAATCTTGAGGGGA 57.255 42.857 1.73 0.00 39.26 4.81
775 825 2.644798 AGAGTAAACCAGTGCCAGGAAT 59.355 45.455 0.00 0.00 0.00 3.01
779 829 3.258372 TCAGTAGAGTAAACCAGTGCCAG 59.742 47.826 0.00 0.00 0.00 4.85
915 966 3.897505 ACAGGAAGGAAAAACAATCAGGG 59.102 43.478 0.00 0.00 0.00 4.45
987 1039 1.809207 GCCCATTGGATCAACACCG 59.191 57.895 3.62 0.00 0.00 4.94
1194 1247 1.785353 AAAGCGGGCAGGGGAGTTAA 61.785 55.000 0.00 0.00 0.00 2.01
1202 1255 1.534729 AGAAAGTAAAAGCGGGCAGG 58.465 50.000 0.00 0.00 0.00 4.85
1231 1284 2.055838 GCACAATCGAACTGTACACGA 58.944 47.619 9.18 9.18 40.18 4.35
1233 1286 1.461888 GCGCACAATCGAACTGTACAC 60.462 52.381 0.30 0.00 0.00 2.90
1255 1308 5.860941 ATCTGAGATTACATCGTCCTGTT 57.139 39.130 0.00 0.00 0.00 3.16
1269 1322 9.787435 CTGTAGGTAGTACTAGAAATCTGAGAT 57.213 37.037 1.87 0.00 32.19 2.75
1270 1323 8.990203 TCTGTAGGTAGTACTAGAAATCTGAGA 58.010 37.037 1.87 0.00 32.19 3.27
1271 1324 9.787435 ATCTGTAGGTAGTACTAGAAATCTGAG 57.213 37.037 1.87 0.00 32.19 3.35
1402 1459 5.470047 AGTCGATTATGTATGGGGACTTC 57.530 43.478 0.00 0.00 29.61 3.01
1430 1487 9.297586 CAGGAGATTCAACAAAATCAATACATG 57.702 33.333 0.00 0.00 37.98 3.21
1444 1501 7.856145 ATTCTACATGAACAGGAGATTCAAC 57.144 36.000 0.00 0.00 39.43 3.18
1504 1561 3.635836 ACGAATAGTAGGTACAGCCCTTC 59.364 47.826 0.00 0.00 38.26 3.46
1525 1582 4.264253 TGAACATCCCAGATTCACATCAC 58.736 43.478 0.00 0.00 0.00 3.06
1683 1741 6.944862 AGGAGATATGCAGACAAAGACTTTTT 59.055 34.615 0.00 0.00 0.00 1.94
1752 1810 4.332828 AGTAAACCAATTCCAGCAGTACC 58.667 43.478 0.00 0.00 0.00 3.34
1829 1895 3.550437 ACCTGAACTGTAGATGATGGC 57.450 47.619 0.00 0.00 0.00 4.40
1892 1958 4.494350 AATTGACACAAGCATGACAGTC 57.506 40.909 0.00 1.71 0.00 3.51
2010 2076 5.595952 AGCAGGGAATCAACATTAAATCCTC 59.404 40.000 0.00 0.00 0.00 3.71
2011 2077 5.361857 CAGCAGGGAATCAACATTAAATCCT 59.638 40.000 0.00 0.00 0.00 3.24
2019 2087 2.226962 AAGCAGCAGGGAATCAACAT 57.773 45.000 0.00 0.00 0.00 2.71
2051 2119 0.248843 GAGCCTTCTCACCCTGTCAG 59.751 60.000 0.00 0.00 39.16 3.51
2055 2123 1.079543 CACGAGCCTTCTCACCCTG 60.080 63.158 0.00 0.00 39.30 4.45
2302 2370 5.694006 TCCAAATAACATTTGCCAAAACGAG 59.306 36.000 6.17 0.00 0.00 4.18
2303 2371 5.601662 TCCAAATAACATTTGCCAAAACGA 58.398 33.333 6.17 0.00 0.00 3.85
2702 2771 8.972349 GTTTCCATTCTTTCTTTCTCAATGTTC 58.028 33.333 0.00 0.00 0.00 3.18
3331 3400 8.712228 AGAACAAAAGGAAATCCAATTAGTCT 57.288 30.769 1.67 0.66 38.89 3.24
3348 3417 6.612247 TGCACGAAAGAAGATAGAACAAAA 57.388 33.333 0.00 0.00 0.00 2.44
3632 3701 8.554528 CCAATCATCACATCACATAGAAAGTAC 58.445 37.037 0.00 0.00 0.00 2.73
3679 3748 1.428448 CAGAAGAATCCGCACACGAA 58.572 50.000 0.00 0.00 43.93 3.85
3682 3751 1.648467 GCCCAGAAGAATCCGCACAC 61.648 60.000 0.00 0.00 0.00 3.82
3818 3895 1.821241 CGTGACTTGTGACTGTGCCG 61.821 60.000 0.00 0.00 0.00 5.69
3830 3907 4.677673 AGTAAAACCCTACACGTGACTT 57.322 40.909 25.01 1.74 0.00 3.01
3831 3908 4.677673 AAGTAAAACCCTACACGTGACT 57.322 40.909 25.01 8.81 0.00 3.41
3832 3909 5.739752 AAAAGTAAAACCCTACACGTGAC 57.260 39.130 25.01 6.33 0.00 3.67
3833 3910 8.584157 TCTATAAAAGTAAAACCCTACACGTGA 58.416 33.333 25.01 4.97 0.00 4.35
3834 3911 8.761575 TCTATAAAAGTAAAACCCTACACGTG 57.238 34.615 15.48 15.48 0.00 4.49
3835 3912 9.948964 ATTCTATAAAAGTAAAACCCTACACGT 57.051 29.630 0.00 0.00 0.00 4.49
3852 4174 9.177304 CATTTACGCGTGAGACTATTCTATAAA 57.823 33.333 24.59 9.29 29.47 1.40
4183 4520 0.250338 GCGAAAGAGTTGGGAGTGGT 60.250 55.000 0.00 0.00 0.00 4.16
4211 4548 4.519540 TTCAAGTCATCGTCATCACTCA 57.480 40.909 0.00 0.00 0.00 3.41
4556 4900 1.139256 TGTGCGTCTGGTGTTCCTAAA 59.861 47.619 0.00 0.00 34.23 1.85
4707 5051 4.026744 CCTTGATCTAGGAGACAAGACCA 58.973 47.826 17.33 0.00 36.43 4.02
4756 5106 8.530804 AGTAAACTAGATACCAATAAGACCGT 57.469 34.615 0.00 0.00 0.00 4.83
4925 5275 4.630111 AGGGAGTACTATTCTACTCGTCG 58.370 47.826 0.00 0.00 42.54 5.12
5000 5353 6.752168 TGCTACTCCCTCGGTAAATAAATAC 58.248 40.000 0.00 0.00 0.00 1.89
5012 5365 3.252215 CACTATTCTCTGCTACTCCCTCG 59.748 52.174 0.00 0.00 0.00 4.63
6446 7145 7.287696 ACACACAAAGAGAAATTAGGTTTCCAT 59.712 33.333 0.00 0.00 45.96 3.41
6449 7148 6.918022 CCACACACAAAGAGAAATTAGGTTTC 59.082 38.462 0.00 0.00 45.31 2.78
6527 7226 2.656069 GCCCAACTAGCCCAGACGA 61.656 63.158 0.00 0.00 0.00 4.20
6529 7228 2.272471 GGCCCAACTAGCCCAGAC 59.728 66.667 0.00 0.00 45.16 3.51
6579 7279 1.447314 CCCGTACTTCCTTGCCGTC 60.447 63.158 0.00 0.00 0.00 4.79
6593 7293 0.611714 AGCCGAAACATTCTACCCGT 59.388 50.000 0.00 0.00 0.00 5.28
6594 7294 1.287425 GAGCCGAAACATTCTACCCG 58.713 55.000 0.00 0.00 0.00 5.28
6625 7325 3.725010 GCGAAGGAAATGTTAGAAGCACG 60.725 47.826 0.00 0.00 0.00 5.34
6635 7335 1.705337 CGGCATCGCGAAGGAAATGT 61.705 55.000 15.24 0.00 0.00 2.71
6819 7983 1.302285 CCAGTCATTCAGGGCTGCT 59.698 57.895 0.00 0.00 0.00 4.24
6828 7992 3.696051 TGCATTTAGCTTCCCAGTCATTC 59.304 43.478 0.00 0.00 45.94 2.67
6939 8103 2.165641 CCACCGTCAGATTGCACTACTA 59.834 50.000 0.00 0.00 0.00 1.82
7082 8623 9.237846 GGAAAACTTTGTCTTGAGAAACAATAG 57.762 33.333 0.00 0.00 37.88 1.73
7106 8647 8.660435 AGGCATAGCATAAATAGTTCTAAAGGA 58.340 33.333 0.00 0.00 0.00 3.36
7138 8679 6.211584 AGGAAGATAAGTCTAGTGTTTGCAGA 59.788 38.462 0.00 0.00 33.30 4.26
7396 8937 5.221501 ACCAAACAAGATGCAGTAAATTGCT 60.222 36.000 0.00 0.00 44.38 3.91
7585 9126 2.099141 TCGAGATGCCAAGGAACAAG 57.901 50.000 0.00 0.00 0.00 3.16
8300 13002 0.249120 CATCACTGCCTCGGTAACCA 59.751 55.000 0.00 0.00 0.00 3.67
8385 13092 6.270156 TGAGCATCTTGTGATAAAATGCAA 57.730 33.333 3.14 0.00 43.96 4.08
8529 13260 1.401905 CTTCGTTTTCCTGGCATAGGC 59.598 52.381 0.00 0.00 46.87 3.93
8532 13263 1.083489 CGCTTCGTTTTCCTGGCATA 58.917 50.000 0.00 0.00 0.00 3.14
8536 13267 2.173382 CGCGCTTCGTTTTCCTGG 59.827 61.111 5.56 0.00 0.00 4.45
8551 13282 1.203313 CTCCACGAACGAAAACCGC 59.797 57.895 0.14 0.00 43.32 5.68
8585 13316 4.802039 CACAATCTCACAATAGCAAATGCC 59.198 41.667 0.94 0.00 43.38 4.40
8613 13345 5.133221 ACACAATAGCTCCATATTCCCAAC 58.867 41.667 0.00 0.00 0.00 3.77
8630 13362 3.965258 TGGGCAGGGCGACACAAT 61.965 61.111 0.00 0.00 0.00 2.71
8652 13384 2.922335 GCGTTTCTTCCCACATGAAAGC 60.922 50.000 0.00 0.00 30.73 3.51
8656 13388 2.270352 AAGCGTTTCTTCCCACATGA 57.730 45.000 0.00 0.00 0.00 3.07
8664 13396 4.083271 ACCATAGAAGCAAAGCGTTTCTTC 60.083 41.667 14.82 14.82 41.96 2.87
8680 13412 2.041922 AGCTGCCCCGACCATAGA 60.042 61.111 0.00 0.00 0.00 1.98
8875 13638 0.599060 GGTCTAGGAGCCTCGCATAC 59.401 60.000 0.00 0.00 0.00 2.39
8905 13668 6.500589 AATGGGTACTAGAGTATGCACAAT 57.499 37.500 0.00 0.00 32.54 2.71
8920 13683 3.146066 TCACAACTCTGCAAATGGGTAC 58.854 45.455 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.