Multiple sequence alignment - TraesCS5B01G160700

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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 TraesCS5B01G160700 chr5B 100.000 4799 0 0 1 4799 296379964 296375166 0.000000e+00 8863.0
1 TraesCS5B01G160700 chr5B 88.889 54 4 2 4422 4475 605830515 605830566 1.110000e-06 65.8
2 TraesCS5B01G160700 chr5B 96.970 33 1 0 2815 2847 398349949 398349981 6.710000e-04 56.5
3 TraesCS5B01G160700 chr5A 93.095 2100 88 26 1815 3890 350237271 350235205 0.000000e+00 3022.0
4 TraesCS5B01G160700 chr5A 93.432 1690 78 19 72 1751 350239072 350237406 0.000000e+00 2475.0
5 TraesCS5B01G160700 chr5A 90.338 414 22 6 4391 4790 350234682 350234273 1.180000e-145 527.0
6 TraesCS5B01G160700 chr5A 91.429 280 13 4 4129 4398 350234923 350234645 1.630000e-99 374.0
7 TraesCS5B01G160700 chr5A 96.970 33 1 0 2815 2847 440265579 440265611 6.710000e-04 56.5
8 TraesCS5B01G160700 chr5D 92.736 1597 57 18 125 1697 264020095 264018534 0.000000e+00 2252.0
9 TraesCS5B01G160700 chr5D 93.237 1449 60 19 1769 3198 264018333 264016904 0.000000e+00 2098.0
10 TraesCS5B01G160700 chr5D 92.339 496 22 7 3184 3676 263995706 263995224 0.000000e+00 691.0
11 TraesCS5B01G160700 chr5D 91.772 474 15 7 3944 4406 263994554 263994094 5.240000e-179 638.0
12 TraesCS5B01G160700 chr5D 96.629 178 5 1 3766 3942 263994791 263994614 1.310000e-75 294.0
13 TraesCS5B01G160700 chr5D 90.551 127 6 1 1 127 264020254 264020134 3.840000e-36 163.0
14 TraesCS5B01G160700 chr5D 93.396 106 7 0 3676 3781 263994917 263994812 1.790000e-34 158.0
15 TraesCS5B01G160700 chr5D 96.970 33 1 0 2815 2847 339356061 339356093 6.710000e-04 56.5
16 TraesCS5B01G160700 chr6D 80.376 372 52 17 3315 3672 36256018 36256382 3.680000e-66 263.0
17 TraesCS5B01G160700 chr3B 80.000 365 53 17 3315 3665 60735345 60734987 7.970000e-63 252.0
18 TraesCS5B01G160700 chr2A 79.706 340 48 15 3347 3672 178130072 178130404 4.830000e-55 226.0
19 TraesCS5B01G160700 chr2A 84.932 73 8 3 4391 4461 661705704 661705633 2.400000e-08 71.3
20 TraesCS5B01G160700 chr2A 85.714 56 5 3 4422 4476 113188399 113188452 6.710000e-04 56.5
21 TraesCS5B01G160700 chr1D 82.692 104 10 8 4421 4520 86108591 86108492 8.560000e-13 86.1
22 TraesCS5B01G160700 chr2B 80.374 107 11 9 4405 4504 664460784 664460887 6.660000e-09 73.1
23 TraesCS5B01G160700 chr4B 80.392 102 9 9 4422 4520 86735104 86735197 3.100000e-07 67.6
24 TraesCS5B01G160700 chr4B 91.304 46 3 1 4422 4467 440917812 440917856 1.440000e-05 62.1
25 TraesCS5B01G160700 chr1B 89.583 48 2 3 4422 4467 616763642 616763688 1.870000e-04 58.4


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 TraesCS5B01G160700 chr5B 296375166 296379964 4798 True 8863.000000 8863 100.000000 1 4799 1 chr5B.!!$R1 4798
1 TraesCS5B01G160700 chr5A 350234273 350239072 4799 True 1599.500000 3022 92.073500 72 4790 4 chr5A.!!$R1 4718
2 TraesCS5B01G160700 chr5D 264016904 264020254 3350 True 1504.333333 2252 92.174667 1 3198 3 chr5D.!!$R2 3197
3 TraesCS5B01G160700 chr5D 263994094 263995706 1612 True 445.250000 691 93.534000 3184 4406 4 chr5D.!!$R1 1222

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
789 852 0.179084 TAAGTACAGCCAGGATGCGC 60.179 55.0 4.01 0.0 36.02 6.09 F
2036 2395 0.032130 CTGCCGCACATATACTCGGT 59.968 55.0 9.48 0.0 43.45 4.69 F
3129 3506 0.316841 TGCTGTATGACGCACAGACA 59.683 50.0 6.67 9.9 46.40 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2710 3081 0.537188 CACCTCGTCCTTGCACCTAT 59.463 55.0 0.00 0.0 0.00 2.57 R
3306 3687 0.179032 ACGCATGGTTCAGTTGTGGA 60.179 50.0 0.00 0.0 0.00 4.02 R
4373 5193 0.108424 CGGCCAGGAGACTCTGAAAG 60.108 60.0 2.24 0.0 40.21 2.62 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
22 23 2.230660 CTTTGAACTCGCTTTTCCCCT 58.769 47.619 0.00 0.00 0.00 4.79
23 24 2.358322 TTGAACTCGCTTTTCCCCTT 57.642 45.000 0.00 0.00 0.00 3.95
24 25 1.892209 TGAACTCGCTTTTCCCCTTC 58.108 50.000 0.00 0.00 0.00 3.46
25 26 1.166129 GAACTCGCTTTTCCCCTTCC 58.834 55.000 0.00 0.00 0.00 3.46
26 27 0.251209 AACTCGCTTTTCCCCTTCCC 60.251 55.000 0.00 0.00 0.00 3.97
27 28 1.378646 CTCGCTTTTCCCCTTCCCC 60.379 63.158 0.00 0.00 0.00 4.81
28 29 1.850755 TCGCTTTTCCCCTTCCCCT 60.851 57.895 0.00 0.00 0.00 4.79
33 34 0.490017 TTTTCCCCTTCCCCTTTCCC 59.510 55.000 0.00 0.00 0.00 3.97
35 36 0.481607 TTCCCCTTCCCCTTTCCCAT 60.482 55.000 0.00 0.00 0.00 4.00
168 210 5.324409 ACTGGGCTAAAATGTGAAATCAGA 58.676 37.500 0.00 0.00 0.00 3.27
190 236 8.481314 TCAGAGAGCTACAATGTGAATATCTTT 58.519 33.333 0.00 0.00 0.00 2.52
330 387 1.843368 AACCGAATACTGACCCTCGA 58.157 50.000 0.00 0.00 33.13 4.04
331 388 2.068834 ACCGAATACTGACCCTCGAT 57.931 50.000 0.00 0.00 33.13 3.59
332 389 1.955080 ACCGAATACTGACCCTCGATC 59.045 52.381 0.00 0.00 33.13 3.69
333 390 1.069159 CCGAATACTGACCCTCGATCG 60.069 57.143 9.36 9.36 33.13 3.69
344 401 1.189752 CCTCGATCGATGATCCCCAT 58.810 55.000 19.78 0.00 35.83 4.00
363 420 5.407387 CCCCATATAAAGCACATGTACGTAC 59.593 44.000 18.90 18.90 0.00 3.67
548 611 1.945394 GGCTGGTTATGAGCATGACAG 59.055 52.381 0.00 6.98 38.27 3.51
549 612 2.420547 GGCTGGTTATGAGCATGACAGA 60.421 50.000 0.00 0.00 38.27 3.41
581 644 4.929808 TCTCCGTTAAACAAATGAGCTCTC 59.070 41.667 16.19 0.00 0.00 3.20
782 845 3.553922 GCTGCCTCTATAAGTACAGCCAG 60.554 52.174 0.00 0.00 42.91 4.85
789 852 0.179084 TAAGTACAGCCAGGATGCGC 60.179 55.000 4.01 0.00 36.02 6.09
793 856 1.326951 TACAGCCAGGATGCGCAGTA 61.327 55.000 18.32 7.03 34.84 2.74
917 980 1.531149 CAGCGTACTTTTGGACCTGTG 59.469 52.381 0.00 0.00 0.00 3.66
936 999 1.132500 GGATACCTTGCTAGGCACCT 58.868 55.000 14.60 0.00 46.22 4.00
983 1046 1.659098 CGTGTCAATCCGGAAGTAAGC 59.341 52.381 9.01 0.00 0.00 3.09
1122 1185 2.685380 CGCCTCCTCCAGAAGGGT 60.685 66.667 0.00 0.00 46.23 4.34
1134 1197 1.005867 GAAGGGTTACACCGTGCGA 60.006 57.895 0.00 0.00 39.83 5.10
1246 1316 3.767900 CGATCGTTCGCATGACTTG 57.232 52.632 7.03 0.00 38.75 3.16
1269 1339 3.209410 GGCAGTTGATCCGAAGAATGAT 58.791 45.455 0.00 0.00 0.00 2.45
1275 1345 4.327982 TGATCCGAAGAATGATCACCTC 57.672 45.455 0.00 0.00 0.00 3.85
1287 1357 1.686052 GATCACCTCAGAGCCTTCGAT 59.314 52.381 0.00 0.00 0.00 3.59
1434 1504 0.305617 CCATTGATGCCACACGATCG 59.694 55.000 14.88 14.88 0.00 3.69
1706 1960 7.972623 AATTGTTTTGTTTTGTTCATGCATG 57.027 28.000 21.07 21.07 0.00 4.06
1751 2006 5.701290 ACTATCCTTTCAAACTCAGAAACCG 59.299 40.000 0.00 0.00 32.09 4.44
1753 2008 2.287608 CCTTTCAAACTCAGAAACCGGC 60.288 50.000 0.00 0.00 32.09 6.13
1754 2009 1.314730 TTCAAACTCAGAAACCGGCC 58.685 50.000 0.00 0.00 0.00 6.13
1755 2010 0.882927 TCAAACTCAGAAACCGGCCG 60.883 55.000 21.04 21.04 0.00 6.13
1756 2011 1.599797 AAACTCAGAAACCGGCCGG 60.600 57.895 42.17 42.17 42.03 6.13
1758 2116 4.778143 CTCAGAAACCGGCCGGGG 62.778 72.222 44.99 28.08 41.60 5.73
1760 2118 4.338710 CAGAAACCGGCCGGGGAA 62.339 66.667 44.99 0.00 41.60 3.97
1765 2123 1.003928 GAAACCGGCCGGGGAATATAT 59.996 52.381 44.99 21.70 41.60 0.86
1767 2125 1.451387 CCGGCCGGGGAATATATGC 60.451 63.158 37.42 0.00 0.00 3.14
1771 2129 0.740737 GCCGGGGAATATATGCATGC 59.259 55.000 11.82 11.82 0.00 4.06
1793 2151 4.336433 GCTTACTGCCAATGATTTGCTAGA 59.664 41.667 2.85 0.00 35.15 2.43
1867 2226 3.019564 GTGGATGCAAAGCTGGAATACT 58.980 45.455 0.00 0.00 0.00 2.12
1876 2235 8.574251 TGCAAAGCTGGAATACTTATAGAAAA 57.426 30.769 0.00 0.00 0.00 2.29
1915 2274 1.338337 CCTACTGAGGCGTATGAGGTG 59.662 57.143 0.00 0.00 35.54 4.00
2036 2395 0.032130 CTGCCGCACATATACTCGGT 59.968 55.000 9.48 0.00 43.45 4.69
2579 2947 4.492160 CGCGTCCTCGGCAAGCTA 62.492 66.667 0.00 0.00 37.56 3.32
2585 2953 0.691078 TCCTCGGCAAGCTATTCCCT 60.691 55.000 0.00 0.00 0.00 4.20
2609 2977 1.194121 ACCCCGTACCCACCAAGTAC 61.194 60.000 0.00 0.00 37.35 2.73
2632 3000 1.690283 CGTCGCATGCAGACTGGAAG 61.690 60.000 27.65 15.51 42.29 3.46
2636 3004 1.329906 CGCATGCAGACTGGAAGAATC 59.670 52.381 19.57 0.00 37.43 2.52
2637 3005 2.362736 GCATGCAGACTGGAAGAATCA 58.637 47.619 14.21 0.00 37.43 2.57
2638 3006 2.097142 GCATGCAGACTGGAAGAATCAC 59.903 50.000 14.21 0.00 37.43 3.06
2639 3007 2.479566 TGCAGACTGGAAGAATCACC 57.520 50.000 4.26 0.00 37.43 4.02
2640 3008 1.980765 TGCAGACTGGAAGAATCACCT 59.019 47.619 4.26 0.00 37.43 4.00
2641 3009 2.027745 TGCAGACTGGAAGAATCACCTC 60.028 50.000 4.26 0.00 37.43 3.85
2642 3010 2.027745 GCAGACTGGAAGAATCACCTCA 60.028 50.000 4.26 0.00 37.43 3.86
2644 3012 2.569404 AGACTGGAAGAATCACCTCACC 59.431 50.000 0.00 0.00 37.43 4.02
2657 3028 1.218316 CTCACCGCTGGTTCTACCC 59.782 63.158 0.00 0.00 37.50 3.69
2674 3045 7.147966 GGTTCTACCCAGTATATTTTTGGTTGG 60.148 40.741 0.00 0.00 30.04 3.77
2677 3048 8.613034 TCTACCCAGTATATTTTTGGTTGGTTA 58.387 33.333 0.00 0.00 0.00 2.85
2678 3049 9.416284 CTACCCAGTATATTTTTGGTTGGTTAT 57.584 33.333 0.00 0.00 0.00 1.89
2679 3050 8.673456 ACCCAGTATATTTTTGGTTGGTTATT 57.327 30.769 0.00 0.00 0.00 1.40
2680 3051 8.755028 ACCCAGTATATTTTTGGTTGGTTATTC 58.245 33.333 0.00 0.00 0.00 1.75
2681 3052 7.918562 CCCAGTATATTTTTGGTTGGTTATTCG 59.081 37.037 0.00 0.00 0.00 3.34
2684 3055 8.392612 AGTATATTTTTGGTTGGTTATTCGACG 58.607 33.333 0.00 0.00 0.00 5.12
2686 3057 5.692613 TTTTTGGTTGGTTATTCGACGAT 57.307 34.783 0.00 0.00 0.00 3.73
2687 3058 5.692613 TTTTGGTTGGTTATTCGACGATT 57.307 34.783 0.00 0.00 0.00 3.34
2688 3059 6.798315 TTTTGGTTGGTTATTCGACGATTA 57.202 33.333 0.00 0.00 0.00 1.75
2695 3066 6.971527 TGGTTATTCGACGATTAACATGTT 57.028 33.333 29.32 16.68 33.03 2.71
2708 3079 2.842208 ACATGTTCGTTTGGTGTGTG 57.158 45.000 0.00 0.00 0.00 3.82
2709 3080 2.088423 ACATGTTCGTTTGGTGTGTGT 58.912 42.857 0.00 0.00 0.00 3.72
2710 3081 3.271729 ACATGTTCGTTTGGTGTGTGTA 58.728 40.909 0.00 0.00 0.00 2.90
2711 3082 3.880490 ACATGTTCGTTTGGTGTGTGTAT 59.120 39.130 0.00 0.00 0.00 2.29
2777 3148 0.622665 CCAACCAGAGGCTCAAGGAT 59.377 55.000 26.52 15.75 0.00 3.24
2783 3154 1.148048 GAGGCTCAAGGATCTGGGC 59.852 63.158 10.25 0.00 42.48 5.36
2810 3181 4.996434 GTGCCGGTGCTGCAGAGT 62.996 66.667 20.43 0.00 39.87 3.24
3028 3401 5.300969 TCGGTCTTATATATGCGTACACC 57.699 43.478 0.00 0.00 0.00 4.16
3029 3402 4.093514 CGGTCTTATATATGCGTACACCG 58.906 47.826 9.82 9.82 38.43 4.94
3030 3403 4.418392 GGTCTTATATATGCGTACACCGG 58.582 47.826 0.00 0.00 36.94 5.28
3031 3404 4.082571 GGTCTTATATATGCGTACACCGGT 60.083 45.833 0.00 0.00 36.94 5.28
3032 3405 5.123820 GGTCTTATATATGCGTACACCGGTA 59.876 44.000 6.87 0.00 36.94 4.02
3033 3406 6.024049 GTCTTATATATGCGTACACCGGTAC 58.976 44.000 6.87 0.93 45.18 3.34
3096 3469 1.602323 TGGGTTGGTTGGCGATCAC 60.602 57.895 0.00 0.00 0.00 3.06
3100 3473 1.400494 GGTTGGTTGGCGATCACATAC 59.600 52.381 0.00 0.00 0.00 2.39
3102 3475 2.682856 GTTGGTTGGCGATCACATACAT 59.317 45.455 0.00 0.00 0.00 2.29
3128 3505 3.122150 TGCTGTATGACGCACAGAC 57.878 52.632 6.67 6.22 45.10 3.51
3129 3506 0.316841 TGCTGTATGACGCACAGACA 59.683 50.000 6.67 9.90 46.40 3.41
3130 3507 0.716108 GCTGTATGACGCACAGACAC 59.284 55.000 6.67 4.08 44.24 3.67
3131 3508 1.934849 GCTGTATGACGCACAGACACA 60.935 52.381 6.67 4.07 44.24 3.72
3147 3524 7.017055 CACAGACACACACACAATGTTATATG 58.983 38.462 0.00 0.00 40.64 1.78
3237 3618 0.810648 CATACCCGTGCATTGCAACT 59.189 50.000 13.94 0.00 41.47 3.16
3240 3621 2.431260 CCGTGCATTGCAACTGGC 60.431 61.111 13.94 6.98 41.47 4.85
3306 3687 1.824852 TCTCAGCCATCACACGTACAT 59.175 47.619 0.00 0.00 0.00 2.29
3313 3694 2.415168 CCATCACACGTACATCCACAAC 59.585 50.000 0.00 0.00 0.00 3.32
3343 3724 1.398451 CGTCGCAAGTGAATGTCCAAC 60.398 52.381 0.00 0.00 39.48 3.77
3362 3743 9.179909 TGTCCAACAGTTTTAAAAGTAATCTCA 57.820 29.630 7.95 2.44 0.00 3.27
3372 3753 5.344743 AAAAGTAATCTCATCGAGCTGGA 57.655 39.130 0.00 0.00 0.00 3.86
3377 3758 4.620589 AATCTCATCGAGCTGGAATGAT 57.379 40.909 1.37 4.31 0.00 2.45
3381 3762 4.586421 TCTCATCGAGCTGGAATGATTACT 59.414 41.667 1.37 0.00 0.00 2.24
3614 3998 9.157104 TGAAATGTTTTTAAGAAAAGGGTGAAC 57.843 29.630 0.00 0.00 35.53 3.18
3688 4379 9.554724 AAAACAACACATATAGTCTAAAATGCG 57.445 29.630 5.78 0.87 0.00 4.73
3709 4400 4.663091 GCGCATACGGTTTAGAAAAATACG 59.337 41.667 0.30 0.00 40.57 3.06
3863 4590 3.881937 AGCCATGCATTCCTTCTTTTC 57.118 42.857 0.00 0.00 0.00 2.29
3975 4785 2.736670 CCTTTCCCTCCCAAGGTATG 57.263 55.000 0.00 0.00 41.59 2.39
4252 5067 0.698238 AGGCAAGCCCATAAGTGTGA 59.302 50.000 7.62 0.00 36.58 3.58
4255 5070 1.808411 CAAGCCCATAAGTGTGACGT 58.192 50.000 0.00 0.00 0.00 4.34
4284 5100 1.210413 GAAGACAGTCTGCTCGCGA 59.790 57.895 9.26 9.26 0.00 5.87
4285 5101 0.179150 GAAGACAGTCTGCTCGCGAT 60.179 55.000 10.36 0.00 0.00 4.58
4313 5133 3.241530 ACAGGGGTCAAGCGAGCA 61.242 61.111 0.00 0.00 41.62 4.26
4354 5174 7.322699 CGACCAATTTGTACAACTCAAACATAC 59.677 37.037 8.07 0.00 37.56 2.39
4355 5175 8.232913 ACCAATTTGTACAACTCAAACATACT 57.767 30.769 8.07 0.00 37.56 2.12
4356 5176 8.134895 ACCAATTTGTACAACTCAAACATACTG 58.865 33.333 8.07 0.00 37.56 2.74
4357 5177 7.594758 CCAATTTGTACAACTCAAACATACTGG 59.405 37.037 8.07 0.76 37.56 4.00
4358 5178 8.349245 CAATTTGTACAACTCAAACATACTGGA 58.651 33.333 8.07 0.00 37.56 3.86
4359 5179 6.854496 TTGTACAACTCAAACATACTGGAC 57.146 37.500 3.59 0.00 0.00 4.02
4360 5180 5.302360 TGTACAACTCAAACATACTGGACC 58.698 41.667 0.00 0.00 0.00 4.46
4361 5181 3.399330 ACAACTCAAACATACTGGACCG 58.601 45.455 0.00 0.00 0.00 4.79
4362 5182 2.742053 CAACTCAAACATACTGGACCGG 59.258 50.000 0.00 0.00 0.00 5.28
4363 5183 1.975680 ACTCAAACATACTGGACCGGT 59.024 47.619 6.92 6.92 0.00 5.28
4364 5184 2.370849 ACTCAAACATACTGGACCGGTT 59.629 45.455 12.24 0.00 0.00 4.44
4365 5185 3.181448 ACTCAAACATACTGGACCGGTTT 60.181 43.478 12.24 0.00 32.33 3.27
4366 5186 3.818773 CTCAAACATACTGGACCGGTTTT 59.181 43.478 12.24 3.43 29.89 2.43
4367 5187 4.208746 TCAAACATACTGGACCGGTTTTT 58.791 39.130 12.24 6.43 29.89 1.94
4368 5188 4.036971 TCAAACATACTGGACCGGTTTTTG 59.963 41.667 12.24 17.15 29.89 2.44
4369 5189 3.495434 ACATACTGGACCGGTTTTTGA 57.505 42.857 12.24 0.00 0.00 2.69
4370 5190 3.822940 ACATACTGGACCGGTTTTTGAA 58.177 40.909 12.24 0.00 0.00 2.69
4371 5191 4.208746 ACATACTGGACCGGTTTTTGAAA 58.791 39.130 12.24 0.00 0.00 2.69
4372 5192 4.037089 ACATACTGGACCGGTTTTTGAAAC 59.963 41.667 12.24 0.00 0.00 2.78
4373 5193 1.752498 ACTGGACCGGTTTTTGAAACC 59.248 47.619 9.42 11.61 36.96 3.27
4374 5194 2.028876 CTGGACCGGTTTTTGAAACCT 58.971 47.619 9.42 3.17 38.15 3.50
4375 5195 2.429250 CTGGACCGGTTTTTGAAACCTT 59.571 45.455 9.42 7.03 38.15 3.50
4376 5196 2.832733 TGGACCGGTTTTTGAAACCTTT 59.167 40.909 9.42 6.73 38.15 3.11
4377 5197 3.119065 TGGACCGGTTTTTGAAACCTTTC 60.119 43.478 9.42 13.39 38.15 2.62
4378 5198 3.119065 GGACCGGTTTTTGAAACCTTTCA 60.119 43.478 9.42 0.00 44.78 2.69
4379 5199 4.109766 GACCGGTTTTTGAAACCTTTCAG 58.890 43.478 9.42 4.77 46.68 3.02
4380 5200 3.764972 ACCGGTTTTTGAAACCTTTCAGA 59.235 39.130 17.62 0.00 46.68 3.27
4383 5203 5.034797 CGGTTTTTGAAACCTTTCAGAGTC 58.965 41.667 17.62 0.00 46.68 3.36
4385 5205 6.266323 GGTTTTTGAAACCTTTCAGAGTCTC 58.734 40.000 13.83 0.00 46.68 3.36
4390 5210 0.980423 ACCTTTCAGAGTCTCCTGGC 59.020 55.000 0.00 0.00 34.99 4.85
4392 5212 0.108424 CTTTCAGAGTCTCCTGGCCG 60.108 60.000 0.00 0.00 34.99 6.13
4394 5214 2.681778 CAGAGTCTCCTGGCCGGT 60.682 66.667 11.58 0.00 0.00 5.28
4399 5219 0.537371 AGTCTCCTGGCCGGTTTTTG 60.537 55.000 11.58 0.00 0.00 2.44
4400 5220 0.536460 GTCTCCTGGCCGGTTTTTGA 60.536 55.000 11.58 0.00 0.00 2.69
4404 5225 0.750249 CCTGGCCGGTTTTTGAAACT 59.250 50.000 11.58 0.00 0.00 2.66
4638 5459 8.801715 TGTTCATGCTTTTCTATCTTCAAAAC 57.198 30.769 0.00 0.00 0.00 2.43
4739 5573 9.277783 TGTTCTTCTTTTCCAAAAATTGTTCAA 57.722 25.926 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.294675 CCAAAACCAGCAAGAGATACATGAAA 60.295 38.462 0.00 0.00 0.00 2.69
213 259 4.448210 ACGATGCCATACTCCGTATTTTT 58.552 39.130 0.00 0.00 0.00 1.94
236 282 3.512219 TCAAGCCCATCATGCATATGA 57.488 42.857 6.97 0.00 46.67 2.15
330 387 5.045651 TGTGCTTTATATGGGGATCATCGAT 60.046 40.000 0.00 0.00 37.30 3.59
331 388 4.285775 TGTGCTTTATATGGGGATCATCGA 59.714 41.667 0.00 0.00 37.30 3.59
332 389 4.578871 TGTGCTTTATATGGGGATCATCG 58.421 43.478 0.00 0.00 37.30 3.84
333 390 5.948162 ACATGTGCTTTATATGGGGATCATC 59.052 40.000 0.00 0.00 37.30 2.92
344 401 8.272436 CGTATTGTACGTACATGTGCTTTATA 57.728 34.615 27.82 16.61 46.41 0.98
363 420 5.813157 TGTGGGTTGTCATATGTACGTATTG 59.187 40.000 4.78 2.31 0.00 1.90
383 440 1.129998 CTACGGTGTACTCGTCTGTGG 59.870 57.143 15.72 4.25 41.38 4.17
548 611 6.963049 TTGTTTAACGGAGATTAAGCTCTC 57.037 37.500 19.47 8.90 40.83 3.20
549 612 7.606456 TCATTTGTTTAACGGAGATTAAGCTCT 59.394 33.333 19.47 3.62 35.26 4.09
581 644 2.109463 CAGTAGTACTACATGCGTGCG 58.891 52.381 29.87 8.11 38.48 5.34
782 845 0.969894 AGATAGGGTACTGCGCATCC 59.030 55.000 12.24 14.11 0.00 3.51
789 852 7.122048 TGGATATGAGATGAGATAGGGTACTG 58.878 42.308 0.00 0.00 0.00 2.74
793 856 4.961730 GCTGGATATGAGATGAGATAGGGT 59.038 45.833 0.00 0.00 0.00 4.34
917 980 1.132500 AGGTGCCTAGCAAGGTATCC 58.868 55.000 0.00 0.00 45.64 2.59
967 1030 1.136305 CTCGGCTTACTTCCGGATTGA 59.864 52.381 4.15 0.00 46.43 2.57
983 1046 1.608590 GCATCTCTCTCTTCCTCTCGG 59.391 57.143 0.00 0.00 0.00 4.63
1152 1215 2.125673 GCGATGCCACACGTACCT 60.126 61.111 0.00 0.00 0.00 3.08
1246 1316 1.808411 TTCTTCGGATCAACTGCCAC 58.192 50.000 0.00 0.00 0.00 5.01
1269 1339 0.820226 CATCGAAGGCTCTGAGGTGA 59.180 55.000 6.83 0.00 0.00 4.02
1510 1580 1.549170 GTGATCACGTACTTGGTCCCT 59.451 52.381 10.69 0.00 0.00 4.20
1685 1755 4.334759 CCCATGCATGAACAAAACAAAACA 59.665 37.500 28.31 0.00 0.00 2.83
1686 1756 4.574013 TCCCATGCATGAACAAAACAAAAC 59.426 37.500 28.31 0.00 0.00 2.43
1702 1956 6.576185 AGAAATTGATTATTGTGTCCCATGC 58.424 36.000 0.00 0.00 0.00 4.06
1703 1957 8.906867 AGTAGAAATTGATTATTGTGTCCCATG 58.093 33.333 0.00 0.00 0.00 3.66
1724 1979 8.095169 GGTTTCTGAGTTTGAAAGGATAGTAGA 58.905 37.037 0.00 0.00 34.58 2.59
1730 1985 3.821033 CCGGTTTCTGAGTTTGAAAGGAT 59.179 43.478 0.00 0.00 34.58 3.24
1731 1986 3.211045 CCGGTTTCTGAGTTTGAAAGGA 58.789 45.455 0.00 0.00 34.58 3.36
1732 1987 2.287608 GCCGGTTTCTGAGTTTGAAAGG 60.288 50.000 1.90 0.00 34.58 3.11
1737 1992 1.574428 CGGCCGGTTTCTGAGTTTG 59.426 57.895 20.10 0.00 0.00 2.93
1744 1999 1.350310 ATATTCCCCGGCCGGTTTCT 61.350 55.000 40.52 24.71 0.00 2.52
1751 2006 1.392589 CATGCATATATTCCCCGGCC 58.607 55.000 0.00 0.00 0.00 6.13
1753 2008 2.425143 AGCATGCATATATTCCCCGG 57.575 50.000 21.98 0.00 0.00 5.73
1754 2009 4.333649 CAGTAAGCATGCATATATTCCCCG 59.666 45.833 21.98 0.00 0.00 5.73
1755 2010 4.096984 GCAGTAAGCATGCATATATTCCCC 59.903 45.833 21.98 0.00 43.31 4.81
1756 2011 5.240713 GCAGTAAGCATGCATATATTCCC 57.759 43.478 21.98 0.00 43.31 3.97
1771 2129 6.261118 GTTCTAGCAAATCATTGGCAGTAAG 58.739 40.000 0.00 0.00 37.02 2.34
1793 2151 9.068008 CCATCAAAAATTAATTAAGCGTACGTT 57.932 29.630 17.90 8.23 0.00 3.99
1867 2226 6.592607 AGAAATCAACGTCGCCTTTTCTATAA 59.407 34.615 9.81 0.00 33.08 0.98
1876 2235 2.028385 AGGTAAGAAATCAACGTCGCCT 60.028 45.455 0.00 0.00 0.00 5.52
1906 2265 2.488153 GCCAAGGAACAACACCTCATAC 59.512 50.000 0.00 0.00 36.67 2.39
1907 2266 2.554344 GGCCAAGGAACAACACCTCATA 60.554 50.000 0.00 0.00 36.67 2.15
1915 2274 1.363807 GCACTGGCCAAGGAACAAC 59.636 57.895 7.01 0.00 0.00 3.32
2369 2737 2.429571 GTGCTCGCGTTCACCGTA 60.430 61.111 17.98 0.00 39.32 4.02
2579 2947 1.690527 GGTACGGGGTACTCAGGGAAT 60.691 57.143 0.00 0.00 38.85 3.01
2585 2953 1.305213 GGTGGGTACGGGGTACTCA 60.305 63.158 4.44 4.44 45.76 3.41
2609 2977 3.545481 GTCTGCATGCGACGGACG 61.545 66.667 21.00 0.00 45.66 4.79
2637 3005 1.542187 GGTAGAACCAGCGGTGAGGT 61.542 60.000 17.83 2.96 38.42 3.85
2638 3006 1.218316 GGTAGAACCAGCGGTGAGG 59.782 63.158 17.83 2.18 38.42 3.86
2639 3007 1.218316 GGGTAGAACCAGCGGTGAG 59.782 63.158 17.83 8.87 41.02 3.51
2640 3008 1.534476 TGGGTAGAACCAGCGGTGA 60.534 57.895 17.83 0.00 41.02 4.02
2641 3009 3.065306 TGGGTAGAACCAGCGGTG 58.935 61.111 7.86 7.86 41.02 4.94
2657 3028 9.498307 GTCGAATAACCAACCAAAAATATACTG 57.502 33.333 0.00 0.00 0.00 2.74
2660 3031 8.489990 TCGTCGAATAACCAACCAAAAATATA 57.510 30.769 0.00 0.00 0.00 0.86
2661 3032 7.380431 TCGTCGAATAACCAACCAAAAATAT 57.620 32.000 0.00 0.00 0.00 1.28
2674 3045 6.689547 ACGAACATGTTAATCGTCGAATAAC 58.310 36.000 21.16 21.16 45.84 1.89
2684 3055 5.398122 CACACACCAAACGAACATGTTAATC 59.602 40.000 11.95 0.00 0.00 1.75
2686 3057 4.156190 ACACACACCAAACGAACATGTTAA 59.844 37.500 11.95 0.00 0.00 2.01
2687 3058 3.690139 ACACACACCAAACGAACATGTTA 59.310 39.130 11.95 0.00 0.00 2.41
2688 3059 2.490115 ACACACACCAAACGAACATGTT 59.510 40.909 11.78 11.78 0.00 2.71
2695 3066 3.655486 CACCTATACACACACCAAACGA 58.345 45.455 0.00 0.00 0.00 3.85
2708 3079 1.755380 ACCTCGTCCTTGCACCTATAC 59.245 52.381 0.00 0.00 0.00 1.47
2709 3080 1.754803 CACCTCGTCCTTGCACCTATA 59.245 52.381 0.00 0.00 0.00 1.31
2710 3081 0.537188 CACCTCGTCCTTGCACCTAT 59.463 55.000 0.00 0.00 0.00 2.57
2711 3082 0.541063 TCACCTCGTCCTTGCACCTA 60.541 55.000 0.00 0.00 0.00 3.08
2759 3130 1.558756 AGATCCTTGAGCCTCTGGTTG 59.441 52.381 0.00 0.00 0.00 3.77
2777 3148 1.296392 CACGAACTCCATGCCCAGA 59.704 57.895 0.00 0.00 0.00 3.86
2810 3181 3.750130 GGCTCTTCACCGTCTCGTATATA 59.250 47.826 0.00 0.00 0.00 0.86
2877 3248 0.994247 TCATGCAGGTTGTCTGGGAT 59.006 50.000 0.00 0.00 43.54 3.85
2881 3252 2.936928 TGCTCATGCAGGTTGTCTG 58.063 52.632 0.00 0.00 45.31 3.51
3028 3401 4.907188 TTAAAAGTGCATACGTGTACCG 57.093 40.909 0.00 2.71 41.28 4.02
3029 3402 6.025280 CCAATTAAAAGTGCATACGTGTACC 58.975 40.000 0.00 0.00 41.28 3.34
3030 3403 6.521821 CACCAATTAAAAGTGCATACGTGTAC 59.478 38.462 0.00 0.00 40.75 2.90
3031 3404 6.604012 CACCAATTAAAAGTGCATACGTGTA 58.396 36.000 0.00 0.00 0.00 2.90
3032 3405 5.457140 CACCAATTAAAAGTGCATACGTGT 58.543 37.500 0.00 0.00 0.00 4.49
3033 3406 5.990745 CACCAATTAAAAGTGCATACGTG 57.009 39.130 0.00 0.00 0.00 4.49
3096 3469 5.857822 CATACAGCACTGATCCATGTATG 57.142 43.478 4.31 8.69 44.05 2.39
3100 3473 2.798847 CGTCATACAGCACTGATCCATG 59.201 50.000 4.31 2.98 0.00 3.66
3102 3475 1.471501 GCGTCATACAGCACTGATCCA 60.472 52.381 4.31 0.00 0.00 3.41
3126 3503 5.937187 TGCATATAACATTGTGTGTGTGTC 58.063 37.500 0.00 0.00 41.14 3.67
3128 3505 7.641020 CACTATGCATATAACATTGTGTGTGTG 59.359 37.037 6.92 3.00 42.49 3.82
3129 3506 7.552330 TCACTATGCATATAACATTGTGTGTGT 59.448 33.333 21.55 0.00 45.43 3.72
3130 3507 7.918643 TCACTATGCATATAACATTGTGTGTG 58.081 34.615 21.55 7.34 45.43 3.82
3131 3508 8.681486 ATCACTATGCATATAACATTGTGTGT 57.319 30.769 21.55 14.40 45.43 3.72
3147 3524 6.398918 AGTCCGTGGATTTATATCACTATGC 58.601 40.000 0.00 0.00 32.09 3.14
3210 3591 2.186532 TGCACGGGTATGTTTGCTAA 57.813 45.000 0.00 0.00 35.91 3.09
3255 3636 7.121759 CACCTTTGAGATAGACCACATTTGAAT 59.878 37.037 0.00 0.00 0.00 2.57
3306 3687 0.179032 ACGCATGGTTCAGTTGTGGA 60.179 50.000 0.00 0.00 0.00 4.02
3313 3694 1.133253 CTTGCGACGCATGGTTCAG 59.867 57.895 25.09 13.01 38.76 3.02
3343 3724 8.660373 AGCTCGATGAGATTACTTTTAAAACTG 58.340 33.333 0.00 0.00 0.00 3.16
3362 3743 3.397482 GCAGTAATCATTCCAGCTCGAT 58.603 45.455 0.00 0.00 0.00 3.59
3372 3753 3.635591 CTTGGGAAGGGCAGTAATCATT 58.364 45.455 0.00 0.00 0.00 2.57
3377 3758 1.280998 GTAGCTTGGGAAGGGCAGTAA 59.719 52.381 0.00 0.00 0.00 2.24
3381 3762 2.668632 CGTAGCTTGGGAAGGGCA 59.331 61.111 0.00 0.00 0.00 5.36
3564 3947 2.010145 ATTCTATGTGTTCACGCGCT 57.990 45.000 5.73 0.00 0.00 5.92
3565 3948 2.430956 CAATTCTATGTGTTCACGCGC 58.569 47.619 5.73 0.00 0.00 6.86
3566 3949 2.159720 TGCAATTCTATGTGTTCACGCG 60.160 45.455 3.53 3.53 0.00 6.01
3567 3950 3.469899 TGCAATTCTATGTGTTCACGC 57.530 42.857 0.00 0.00 0.00 5.34
3568 3951 5.220557 TCATGCAATTCTATGTGTTCACG 57.779 39.130 0.00 0.00 0.00 4.35
3709 4400 8.279800 GTGTTGGTGCCTTTTGAAAAATATTAC 58.720 33.333 0.00 0.00 0.00 1.89
3777 4504 5.464069 TGCTACACTCCCAATCCTATTAGA 58.536 41.667 0.00 0.00 0.00 2.10
3863 4590 1.526575 AAACTCCGCTGTGCCCATTG 61.527 55.000 0.00 0.00 0.00 2.82
3942 4693 8.279361 TGGGAGGGAAAGGTATTAAAAAGATAG 58.721 37.037 0.00 0.00 0.00 2.08
3946 4755 6.154534 CCTTGGGAGGGAAAGGTATTAAAAAG 59.845 42.308 0.00 0.00 39.55 2.27
3975 4785 6.024552 TGTGCCAATGAAAAGAAGGAATAC 57.975 37.500 0.00 0.00 0.00 1.89
4038 4848 8.371571 AGAAATTGGAAGAAGGAATAAATGCT 57.628 30.769 0.00 0.00 0.00 3.79
4111 4926 5.650266 TCAAATTAATAAGCCGCCTCAAGAA 59.350 36.000 0.00 0.00 0.00 2.52
4252 5067 1.208535 TGTCTTCCACTTCCACAACGT 59.791 47.619 0.00 0.00 0.00 3.99
4255 5070 2.771943 AGACTGTCTTCCACTTCCACAA 59.228 45.455 4.06 0.00 0.00 3.33
4313 5133 0.956902 GGTCGGCCCATAACACGTTT 60.957 55.000 0.00 0.00 0.00 3.60
4354 5174 2.028876 AGGTTTCAAAAACCGGTCCAG 58.971 47.619 8.04 0.00 44.82 3.86
4355 5175 2.146920 AGGTTTCAAAAACCGGTCCA 57.853 45.000 8.04 0.00 44.82 4.02
4356 5176 3.119065 TGAAAGGTTTCAAAAACCGGTCC 60.119 43.478 8.04 1.09 43.62 4.46
4357 5177 4.109766 CTGAAAGGTTTCAAAAACCGGTC 58.890 43.478 8.04 14.75 45.61 4.79
4358 5178 3.764972 TCTGAAAGGTTTCAAAAACCGGT 59.235 39.130 0.00 0.00 45.61 5.28
4359 5179 4.142249 ACTCTGAAAGGTTTCAAAAACCGG 60.142 41.667 14.21 0.00 45.61 5.28
4360 5180 4.993905 ACTCTGAAAGGTTTCAAAAACCG 58.006 39.130 14.21 2.50 45.61 4.44
4361 5181 6.208988 AGACTCTGAAAGGTTTCAAAAACC 57.791 37.500 12.64 12.64 45.61 3.27
4362 5182 6.095580 AGGAGACTCTGAAAGGTTTCAAAAAC 59.904 38.462 6.61 0.00 45.61 2.43
4363 5183 6.095440 CAGGAGACTCTGAAAGGTTTCAAAAA 59.905 38.462 6.61 0.00 42.46 1.94
4364 5184 5.590259 CAGGAGACTCTGAAAGGTTTCAAAA 59.410 40.000 6.61 0.00 42.46 2.44
4365 5185 5.126067 CAGGAGACTCTGAAAGGTTTCAAA 58.874 41.667 6.61 0.00 42.46 2.69
4366 5186 4.444876 CCAGGAGACTCTGAAAGGTTTCAA 60.445 45.833 6.61 0.00 42.46 2.69
4367 5187 3.071602 CCAGGAGACTCTGAAAGGTTTCA 59.928 47.826 1.74 5.09 41.41 2.69
4368 5188 3.669536 CCAGGAGACTCTGAAAGGTTTC 58.330 50.000 1.74 0.00 40.21 2.78
4369 5189 2.224646 GCCAGGAGACTCTGAAAGGTTT 60.225 50.000 1.74 0.00 40.21 3.27
4370 5190 1.349357 GCCAGGAGACTCTGAAAGGTT 59.651 52.381 1.74 0.00 40.21 3.50
4371 5191 0.980423 GCCAGGAGACTCTGAAAGGT 59.020 55.000 1.74 0.00 40.21 3.50
4372 5192 0.251634 GGCCAGGAGACTCTGAAAGG 59.748 60.000 0.00 0.00 40.21 3.11
4373 5193 0.108424 CGGCCAGGAGACTCTGAAAG 60.108 60.000 2.24 0.00 40.21 2.62
4374 5194 1.544825 CCGGCCAGGAGACTCTGAAA 61.545 60.000 2.24 0.00 45.00 2.69
4375 5195 1.984570 CCGGCCAGGAGACTCTGAA 60.985 63.158 2.24 0.00 45.00 3.02
4376 5196 2.363018 CCGGCCAGGAGACTCTGA 60.363 66.667 2.24 0.00 45.00 3.27
4377 5197 1.831652 AAACCGGCCAGGAGACTCTG 61.832 60.000 18.74 0.00 45.00 3.35
4378 5198 1.128188 AAAACCGGCCAGGAGACTCT 61.128 55.000 18.74 0.00 45.00 3.24
4379 5199 0.250770 AAAAACCGGCCAGGAGACTC 60.251 55.000 18.74 0.00 45.00 3.36
4380 5200 0.537371 CAAAAACCGGCCAGGAGACT 60.537 55.000 18.74 0.00 45.00 3.24
4383 5203 1.036707 TTTCAAAAACCGGCCAGGAG 58.963 50.000 18.74 0.00 45.00 3.69
4385 5205 5.736671 GAAAAGTTTCAAAAACCGGCCAGG 61.737 45.833 0.00 7.94 40.48 4.45
4390 5210 5.407502 ACTCTGAAAAGTTTCAAAAACCGG 58.592 37.500 0.00 0.00 45.61 5.28
4404 5225 1.604604 CGGCCAGGAAACTCTGAAAA 58.395 50.000 2.24 0.00 40.21 2.29


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

AutoCloner maintained by Alex Coulton.