Multiple sequence alignment - TraesCS3D01G262400

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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 TraesCS3D01G262400 chr3D 100.000 2315 0 0 2620 4934 363870579 363868265 0.000000e+00 4276.0
1 TraesCS3D01G262400 chr3D 100.000 2245 0 0 1 2245 363873198 363870954 0.000000e+00 4146.0
2 TraesCS3D01G262400 chr3B 93.902 2296 113 13 2654 4934 474030426 474028143 0.000000e+00 3439.0
3 TraesCS3D01G262400 chr3B 94.333 600 19 2 800 1390 474031887 474031294 0.000000e+00 905.0
4 TraesCS3D01G262400 chr3B 89.286 616 24 15 1 591 474032814 474032216 0.000000e+00 734.0
5 TraesCS3D01G262400 chr3B 89.270 466 31 7 1793 2245 474030975 474030516 2.580000e-157 566.0
6 TraesCS3D01G262400 chr3B 92.887 239 5 4 585 811 474032157 474031919 2.200000e-88 337.0
7 TraesCS3D01G262400 chr3A 92.791 1623 80 13 3338 4934 485012949 485011338 0.000000e+00 2314.0
8 TraesCS3D01G262400 chr3A 89.900 1604 70 28 687 2245 485015251 485013695 0.000000e+00 1980.0
9 TraesCS3D01G262400 chr3A 95.087 631 22 4 2654 3275 485013604 485012974 0.000000e+00 985.0
10 TraesCS3D01G262400 chr3A 86.438 612 37 25 1 591 485015975 485015389 3.240000e-176 628.0
11 TraesCS3D01G262400 chr3A 90.667 75 3 4 585 656 485015326 485015253 4.070000e-16 97.1
12 TraesCS3D01G262400 chr7A 85.600 125 14 4 1232 1354 567456875 567456753 1.440000e-25 128.0
13 TraesCS3D01G262400 chr6D 91.111 90 8 0 1267 1356 441899540 441899451 6.710000e-24 122.0
14 TraesCS3D01G262400 chr6D 91.011 89 6 2 1267 1354 138904817 138904904 8.680000e-23 119.0
15 TraesCS3D01G262400 chr6B 84.921 126 13 6 1232 1354 238168052 238168174 6.710000e-24 122.0
16 TraesCS3D01G262400 chr6B 91.111 90 8 0 1267 1356 667899833 667899744 6.710000e-24 122.0
17 TraesCS3D01G262400 chr6A 91.111 90 8 0 1267 1356 591267546 591267457 6.710000e-24 122.0
18 TraesCS3D01G262400 chr6A 91.011 89 6 2 1267 1354 181563851 181563938 8.680000e-23 119.0
19 TraesCS3D01G262400 chr1D 90.217 92 9 0 4842 4933 457074694 457074603 2.410000e-23 121.0
20 TraesCS3D01G262400 chr1A 91.111 90 7 1 4845 4933 549712735 549712646 2.410000e-23 121.0


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 TraesCS3D01G262400 chr3D 363868265 363873198 4933 True 4211.00 4276 100.0000 1 4934 2 chr3D.!!$R1 4933
1 TraesCS3D01G262400 chr3B 474028143 474032814 4671 True 1196.20 3439 91.9356 1 4934 5 chr3B.!!$R1 4933
2 TraesCS3D01G262400 chr3A 485011338 485015975 4637 True 1200.82 2314 90.9766 1 4934 5 chr3A.!!$R1 4933

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
397 421 0.254178 GCAGCCAGAGGGAAAGATGA 59.746 55.0 0.00 0.00 35.59 2.92 F
1401 1588 0.238289 CCGCACTTCGCTTCATTGTT 59.762 50.0 0.00 0.00 39.08 2.83 F
1674 1868 0.720027 CACTGCTGCAGATCGTCTTG 59.280 55.0 34.28 16.97 35.18 3.02 F
2642 2851 0.111639 ACACGTTATGGGTTGCCCTT 59.888 50.0 5.73 1.88 45.70 3.95 F
3543 3769 0.108804 ACTTATGACAGGGCACGTCG 60.109 55.0 6.48 0.00 36.11 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1962 0.107268 ACGGGGAAACGTAGCAACTT 59.893 50.0 0.00 0.00 46.58 2.66 R
2620 2829 0.239879 GGCAACCCATAACGTGTGTG 59.760 55.0 0.00 0.00 0.00 3.82 R
3432 3650 0.400213 ATCACCCCAGCAACTTCGAA 59.600 50.0 0.00 0.00 0.00 3.71 R
3798 4024 0.179097 GGGAGATCTGTCGGCACTTC 60.179 60.0 0.00 0.00 0.00 3.01 R
4424 4667 0.543277 TGTCTATTCTGCAGCCCCAG 59.457 55.0 9.47 3.51 0.00 4.45 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
53 54 1.251251 GCCACATCTCCTGTTTGCTT 58.749 50.000 0.00 0.00 35.29 3.91
164 171 1.675641 CAACCGGCAGGAGGGAAAG 60.676 63.158 10.86 0.00 41.02 2.62
168 175 1.153086 CGGCAGGAGGGAAAGGATG 60.153 63.158 0.00 0.00 0.00 3.51
281 296 1.344942 CGTGCCTGCTCGTTCTGTAC 61.345 60.000 5.51 0.00 0.00 2.90
298 315 9.309516 CGTTCTGTACATGTGTAGGTTTATTAT 57.690 33.333 9.11 0.00 0.00 1.28
322 339 1.645034 TTGCTCGAGCTGTGCTAATC 58.355 50.000 35.27 5.71 39.88 1.75
369 387 0.963856 TCGAGTACATGACCCGCACT 60.964 55.000 0.00 0.00 0.00 4.40
371 389 0.460284 GAGTACATGACCCGCACTGG 60.460 60.000 0.00 0.00 37.55 4.00
372 390 2.106683 GTACATGACCCGCACTGGC 61.107 63.158 0.00 0.00 35.87 4.85
395 419 1.222936 CGCAGCCAGAGGGAAAGAT 59.777 57.895 0.00 0.00 35.59 2.40
396 420 1.094073 CGCAGCCAGAGGGAAAGATG 61.094 60.000 0.00 0.00 35.59 2.90
397 421 0.254178 GCAGCCAGAGGGAAAGATGA 59.746 55.000 0.00 0.00 35.59 2.92
401 425 1.066143 GCCAGAGGGAAAGATGAACGA 60.066 52.381 0.00 0.00 35.59 3.85
486 510 4.764143 CCCCCATCCCAAAGACAC 57.236 61.111 0.00 0.00 0.00 3.67
545 570 0.734253 CGCCACGTTCTCTCCTTCAG 60.734 60.000 0.00 0.00 0.00 3.02
661 776 1.955080 CCACCATAGACCGACTAGTCC 59.045 57.143 17.23 3.45 37.49 3.85
664 779 2.025605 ACCATAGACCGACTAGTCCACA 60.026 50.000 17.23 0.00 37.49 4.17
681 799 1.007336 ACAACGACGACCGCAGAATC 61.007 55.000 0.00 0.00 43.32 2.52
719 837 4.451150 TCAGCCGATCCGCCACAC 62.451 66.667 2.19 0.00 0.00 3.82
724 842 4.873129 CGATCCGCCACACTCCGG 62.873 72.222 0.00 0.00 45.64 5.14
855 1025 2.039624 TGAGCTCCCACCTCCCTC 59.960 66.667 12.15 0.00 0.00 4.30
856 1026 2.766229 GAGCTCCCACCTCCCTCC 60.766 72.222 0.87 0.00 0.00 4.30
857 1027 4.423209 AGCTCCCACCTCCCTCCC 62.423 72.222 0.00 0.00 0.00 4.30
859 1029 3.700350 CTCCCACCTCCCTCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
860 1030 3.695825 TCCCACCTCCCTCCCCTC 61.696 72.222 0.00 0.00 0.00 4.30
883 1053 1.610673 TCCTCTCTGCTCCCACCAC 60.611 63.158 0.00 0.00 0.00 4.16
895 1065 4.866224 CACCACGCCACCACCACA 62.866 66.667 0.00 0.00 0.00 4.17
896 1066 4.116585 ACCACGCCACCACCACAA 62.117 61.111 0.00 0.00 0.00 3.33
924 1094 1.527370 CCTCCGATCCAAACCCTCC 59.473 63.158 0.00 0.00 0.00 4.30
925 1095 0.983378 CCTCCGATCCAAACCCTCCT 60.983 60.000 0.00 0.00 0.00 3.69
930 1100 1.290134 GATCCAAACCCTCCTCCACT 58.710 55.000 0.00 0.00 0.00 4.00
1369 1556 3.168193 GTCAACATTTTCGGGTAATGCG 58.832 45.455 0.00 0.00 36.65 4.73
1370 1557 3.075148 TCAACATTTTCGGGTAATGCGA 58.925 40.909 0.00 0.00 36.65 5.10
1399 1586 1.512734 GCCGCACTTCGCTTCATTG 60.513 57.895 0.00 0.00 39.08 2.82
1401 1588 0.238289 CCGCACTTCGCTTCATTGTT 59.762 50.000 0.00 0.00 39.08 2.83
1402 1589 1.321016 CGCACTTCGCTTCATTGTTG 58.679 50.000 0.00 0.00 39.08 3.33
1403 1590 1.055338 GCACTTCGCTTCATTGTTGC 58.945 50.000 0.00 0.00 37.77 4.17
1404 1591 1.335324 GCACTTCGCTTCATTGTTGCT 60.335 47.619 0.00 0.00 37.77 3.91
1405 1592 2.313234 CACTTCGCTTCATTGTTGCTG 58.687 47.619 0.00 0.00 0.00 4.41
1406 1593 1.334054 CTTCGCTTCATTGTTGCTGC 58.666 50.000 0.00 0.00 0.00 5.25
1407 1594 0.953727 TTCGCTTCATTGTTGCTGCT 59.046 45.000 0.00 0.00 0.00 4.24
1408 1595 1.807139 TCGCTTCATTGTTGCTGCTA 58.193 45.000 0.00 0.00 0.00 3.49
1409 1596 1.464608 TCGCTTCATTGTTGCTGCTAC 59.535 47.619 7.29 7.29 0.00 3.58
1419 1606 4.873746 TGTTGCTGCTACTACTTCTTCT 57.126 40.909 14.81 0.00 0.00 2.85
1430 1617 4.853007 ACTACTTCTTCTAAGCCGGACTA 58.147 43.478 5.05 0.00 0.00 2.59
1433 1620 1.022735 TCTTCTAAGCCGGACTAGCG 58.977 55.000 5.05 0.00 34.64 4.26
1456 1643 2.084546 CGGGTGAGAAGGTTTCCATTC 58.915 52.381 0.00 0.00 0.00 2.67
1483 1670 2.798148 CTTCCGGGAGACGTTTGGGG 62.798 65.000 2.45 0.00 42.24 4.96
1487 1674 1.759236 GGGAGACGTTTGGGGAAGT 59.241 57.895 0.00 0.00 0.00 3.01
1505 1692 2.097825 AGTTGCGTACTGGGTAGTAGG 58.902 52.381 0.00 0.00 44.27 3.18
1520 1712 9.716556 CTGGGTAGTAGGAGTAATATGGATATT 57.283 37.037 0.00 0.00 36.89 1.28
1648 1841 8.861086 AGCGAAAGATCATCTTATTTAGGTAGA 58.139 33.333 0.00 0.00 35.27 2.59
1649 1842 9.134734 GCGAAAGATCATCTTATTTAGGTAGAG 57.865 37.037 0.00 0.00 35.27 2.43
1669 1863 1.923204 GTACTTCACTGCTGCAGATCG 59.077 52.381 34.28 21.15 35.18 3.69
1674 1868 0.720027 CACTGCTGCAGATCGTCTTG 59.280 55.000 34.28 16.97 35.18 3.02
1723 1917 9.286170 ACAAGATAAGGAAAAAGAACCTAGTTC 57.714 33.333 0.00 0.00 42.25 3.01
1841 2035 5.508567 TCTGTCCAGCCATGAAAATTATCA 58.491 37.500 0.00 0.00 0.00 2.15
1860 2054 7.643569 TTATCATTGTATTGCTGTCCAACAT 57.356 32.000 0.00 0.00 35.99 2.71
1866 2060 1.514678 TTGCTGTCCAACATGGCGAC 61.515 55.000 0.00 0.00 37.47 5.19
1904 2098 5.606348 TTGGTTCTTGCTTTTGGTGTTAT 57.394 34.783 0.00 0.00 0.00 1.89
1905 2099 6.716934 TTGGTTCTTGCTTTTGGTGTTATA 57.283 33.333 0.00 0.00 0.00 0.98
1934 2128 7.418597 GGACACACCATATCAGTCCATTAGTTA 60.419 40.741 0.00 0.00 46.15 2.24
1950 2144 6.092259 CCATTAGTTAAGAAAACCTCGACCTG 59.908 42.308 0.00 0.00 0.00 4.00
1978 2172 8.789767 TTCTAGGATTAGATGGATTTCAGAGT 57.210 34.615 0.00 0.00 35.88 3.24
1982 2176 8.503428 AGGATTAGATGGATTTCAGAGTACAT 57.497 34.615 0.00 0.00 0.00 2.29
1983 2177 8.373981 AGGATTAGATGGATTTCAGAGTACATG 58.626 37.037 0.00 0.00 0.00 3.21
1984 2178 8.370940 GGATTAGATGGATTTCAGAGTACATGA 58.629 37.037 0.00 0.00 0.00 3.07
2000 2194 0.753262 ATGAGCGGTTGCCTAGTAGG 59.247 55.000 12.27 12.27 44.31 3.18
2069 2271 4.123506 GTTCCAGGCTATCTCTTGTTAGC 58.876 47.826 0.00 0.00 39.51 3.09
2076 2278 6.209589 CAGGCTATCTCTTGTTAGCTATACCA 59.790 42.308 0.00 0.00 39.90 3.25
2084 2286 8.242053 TCTCTTGTTAGCTATACCATTATACGC 58.758 37.037 0.00 0.00 0.00 4.42
2100 2302 1.136828 ACGCTAAGAATGGGGCCATA 58.863 50.000 4.39 0.00 35.31 2.74
2108 2310 2.439507 AGAATGGGGCCATAGTACTGTG 59.560 50.000 12.39 12.39 35.31 3.66
2126 2328 3.124921 CCCGACATTGTGGGCGTC 61.125 66.667 12.04 0.00 38.90 5.19
2129 2331 2.390599 CGACATTGTGGGCGTCCTG 61.391 63.158 7.97 0.00 0.00 3.86
2221 2430 5.760253 AGGATGTTGTATTTCGAGGCATAAG 59.240 40.000 0.00 0.00 0.00 1.73
2236 2445 3.430929 GGCATAAGTAGTGGGTCTGTCTG 60.431 52.174 0.00 0.00 0.00 3.51
2237 2446 3.786635 CATAAGTAGTGGGTCTGTCTGC 58.213 50.000 0.00 0.00 0.00 4.26
2638 2847 0.948678 ACACACACGTTATGGGTTGC 59.051 50.000 0.00 0.00 45.28 4.17
2639 2848 0.239879 CACACACGTTATGGGTTGCC 59.760 55.000 1.87 0.00 45.28 4.52
2640 2849 0.891904 ACACACGTTATGGGTTGCCC 60.892 55.000 0.00 0.00 45.28 5.36
2641 2850 0.608035 CACACGTTATGGGTTGCCCT 60.608 55.000 5.73 0.00 45.70 5.19
2642 2851 0.111639 ACACGTTATGGGTTGCCCTT 59.888 50.000 5.73 1.88 45.70 3.95
2643 2852 1.253100 CACGTTATGGGTTGCCCTTT 58.747 50.000 5.73 0.00 45.70 3.11
2644 2853 2.224818 ACACGTTATGGGTTGCCCTTTA 60.225 45.455 5.73 0.00 45.70 1.85
2645 2854 2.162809 CACGTTATGGGTTGCCCTTTAC 59.837 50.000 5.73 2.93 45.70 2.01
2646 2855 1.399089 CGTTATGGGTTGCCCTTTACG 59.601 52.381 14.10 14.10 45.70 3.18
2647 2856 1.133598 GTTATGGGTTGCCCTTTACGC 59.866 52.381 5.73 0.00 45.70 4.42
2648 2857 0.621609 TATGGGTTGCCCTTTACGCT 59.378 50.000 5.73 0.00 45.70 5.07
2649 2858 0.679960 ATGGGTTGCCCTTTACGCTC 60.680 55.000 5.73 0.00 45.70 5.03
2650 2859 2.396157 GGGTTGCCCTTTACGCTCG 61.396 63.158 0.00 0.00 41.34 5.03
2651 2860 1.670083 GGTTGCCCTTTACGCTCGT 60.670 57.895 0.00 0.00 0.00 4.18
2652 2861 1.495951 GTTGCCCTTTACGCTCGTG 59.504 57.895 5.05 0.00 0.00 4.35
2668 2877 3.181502 GCTCGTGAGTTAGTACCCTACAC 60.182 52.174 0.00 0.00 0.00 2.90
2669 2878 3.002791 TCGTGAGTTAGTACCCTACACG 58.997 50.000 17.55 17.55 46.61 4.49
2681 2890 7.179076 AGTACCCTACACGAGAATATGTTTT 57.821 36.000 0.00 0.00 0.00 2.43
2684 2893 5.189145 ACCCTACACGAGAATATGTTTTCCT 59.811 40.000 0.00 0.00 0.00 3.36
2690 2899 6.051717 CACGAGAATATGTTTTCCTCCTGAT 58.948 40.000 0.00 0.00 0.00 2.90
2710 2919 6.183360 CCTGATATCCATCTTAATAGACCCCG 60.183 46.154 0.00 0.00 31.99 5.73
2744 2955 6.475504 CAGGTATGATTATGCTGGTTATGGA 58.524 40.000 0.00 0.00 0.00 3.41
3132 3349 1.002868 CCTGCTCCCCAGAGTTGTG 60.003 63.158 0.00 0.00 44.64 3.33
3134 3351 2.360475 GCTCCCCAGAGTTGTGGC 60.360 66.667 0.00 0.00 42.59 5.01
3203 3421 5.184892 AGATCAGCTTGGTAAATTGTCCT 57.815 39.130 0.00 0.00 0.00 3.85
3263 3481 5.966742 ACCCTCTTCTTTTTCAATACTGC 57.033 39.130 0.00 0.00 0.00 4.40
3276 3494 1.500474 ATACTGCCTGCCTCTTGCTA 58.500 50.000 0.00 0.00 42.00 3.49
3294 3512 3.389002 TGCTATCTTGCATTGCCTCTCTA 59.611 43.478 6.12 0.00 38.12 2.43
3304 3522 4.444876 GCATTGCCTCTCTAGTGGGATAAA 60.445 45.833 0.00 0.00 0.00 1.40
3317 3535 7.953493 TCTAGTGGGATAAAGGGATTTGTTTTT 59.047 33.333 0.00 0.00 0.00 1.94
3318 3536 9.250246 CTAGTGGGATAAAGGGATTTGTTTTTA 57.750 33.333 0.00 0.00 0.00 1.52
3352 3570 4.999950 ACCACTACATTGAGAAGCTGAAAG 59.000 41.667 0.00 0.00 0.00 2.62
3396 3614 5.185454 TGATCACCAAGCCAAGTATGTAAG 58.815 41.667 0.00 0.00 0.00 2.34
3405 3623 7.696453 CCAAGCCAAGTATGTAAGAATTAAACG 59.304 37.037 0.00 0.00 28.70 3.60
3459 3677 4.718961 AGTTGCTGGGGTGATATAACATC 58.281 43.478 0.00 0.00 0.00 3.06
3460 3678 3.788227 TGCTGGGGTGATATAACATCC 57.212 47.619 3.69 3.69 40.05 3.51
3488 3706 6.868339 CACCCCAGTTTTTACATCAGAATTTC 59.132 38.462 0.00 0.00 0.00 2.17
3543 3769 0.108804 ACTTATGACAGGGCACGTCG 60.109 55.000 6.48 0.00 36.11 5.12
3642 3868 3.297620 GGTGGGCACTGCAACCTG 61.298 66.667 14.91 0.00 35.06 4.00
3681 3907 3.817647 ACATCAGGCACTTGAAGAAGTTC 59.182 43.478 0.00 0.00 40.68 3.01
3687 3913 2.607635 GCACTTGAAGAAGTTCGTGTCA 59.392 45.455 0.00 0.00 40.68 3.58
3693 3919 2.156343 AGAAGTTCGTGTCAAGCCTC 57.844 50.000 0.00 0.00 0.00 4.70
3756 3982 2.681706 ACAGAAGACACATCTCGCAAG 58.318 47.619 0.00 0.00 32.34 4.01
3798 4024 1.286880 CAAACCCCAAGAAGCTGCG 59.713 57.895 0.00 0.00 0.00 5.18
3816 4042 0.526524 CGAAGTGCCGACAGATCTCC 60.527 60.000 0.00 0.00 0.00 3.71
4090 4318 7.890127 TGTTAAATGTGGGAGAAGAAGAATCAT 59.110 33.333 0.00 0.00 0.00 2.45
4119 4347 7.254761 CGCTGGTGAATAAGCTGTTATTTATCA 60.255 37.037 0.00 0.00 38.70 2.15
4250 4488 4.018050 AGGGACAAGGATAGAACATTTGCT 60.018 41.667 0.00 0.00 0.00 3.91
4319 4557 8.427902 AGCAACATATTCTAGTCTGGATATGA 57.572 34.615 15.81 0.00 0.00 2.15
4424 4667 7.976734 ACTGTATGTTACTTAGAATCTGACTGC 59.023 37.037 0.00 0.00 0.00 4.40
4539 4782 3.266636 CCACTCCAATGTACGTATGCAA 58.733 45.455 0.00 0.00 0.00 4.08
4602 4845 7.345691 ACCAATCACATATTTACATCACCTGA 58.654 34.615 0.00 0.00 0.00 3.86
4633 4878 0.030908 AAGAATCGTCGGATCGCTCC 59.969 55.000 0.00 0.00 38.29 4.70
4670 4915 5.411977 AGCAAATCTCTCAACAGTGATGAAG 59.588 40.000 4.52 5.64 33.89 3.02
4685 4931 0.393820 TGAAGTAAAACTCGGCCGGT 59.606 50.000 27.83 19.40 0.00 5.28
4698 4944 2.935955 CCGGTCGCAAACACTGAC 59.064 61.111 0.00 0.00 0.00 3.51
4704 4953 3.592059 GGTCGCAAACACTGACCTAATA 58.408 45.455 3.46 0.00 46.86 0.98
4705 4954 3.370061 GGTCGCAAACACTGACCTAATAC 59.630 47.826 3.46 0.00 46.86 1.89
4706 4955 4.243270 GTCGCAAACACTGACCTAATACT 58.757 43.478 0.00 0.00 0.00 2.12
4707 4956 5.404946 GTCGCAAACACTGACCTAATACTA 58.595 41.667 0.00 0.00 0.00 1.82
4739 4988 1.004200 GTGTTAGGGGTGGTGGTCG 60.004 63.158 0.00 0.00 0.00 4.79
4831 5080 0.606401 CGTCTTTGTGACCCAGGCAT 60.606 55.000 0.00 0.00 42.49 4.40
4834 5083 0.523072 CTTTGTGACCCAGGCATTCG 59.477 55.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.618487 TTTGATCCATGTGCACAGCA 58.382 45.000 25.84 14.19 35.60 4.41
128 135 1.918800 GGATAGGGATCGGTGGGGG 60.919 68.421 0.00 0.00 32.28 5.40
164 171 1.714899 CCGGACGCAACAATCCATCC 61.715 60.000 0.00 0.00 34.35 3.51
168 175 4.160635 CGCCGGACGCAACAATCC 62.161 66.667 5.05 0.00 37.30 3.01
298 315 1.148310 GCACAGCTCGAGCAAAAGTA 58.852 50.000 36.87 0.00 45.16 2.24
299 316 0.533755 AGCACAGCTCGAGCAAAAGT 60.534 50.000 36.87 25.35 45.16 2.66
383 401 3.601443 ACTCGTTCATCTTTCCCTCTG 57.399 47.619 0.00 0.00 0.00 3.35
395 419 6.259387 GGTTCCTTTTCTAAAGAACTCGTTCA 59.741 38.462 11.90 0.00 41.84 3.18
396 420 6.259387 TGGTTCCTTTTCTAAAGAACTCGTTC 59.741 38.462 1.62 1.62 38.87 3.95
397 421 6.117488 TGGTTCCTTTTCTAAAGAACTCGTT 58.883 36.000 0.89 0.00 38.87 3.85
401 425 7.175119 GCTGTATGGTTCCTTTTCTAAAGAACT 59.825 37.037 0.89 0.00 38.87 3.01
478 502 6.149633 CCGATAAAAGAAAAGGGTGTCTTTG 58.850 40.000 0.00 0.00 44.30 2.77
486 510 5.977489 AGTTTCCCGATAAAAGAAAAGGG 57.023 39.130 0.00 0.00 40.16 3.95
545 570 3.829601 ACTAGGAGTCCAGCTATGTATGC 59.170 47.826 12.86 0.00 0.00 3.14
661 776 1.282248 ATTCTGCGGTCGTCGTTGTG 61.282 55.000 0.00 0.00 41.72 3.33
664 779 1.800315 CGATTCTGCGGTCGTCGTT 60.800 57.895 0.00 0.00 41.72 3.85
724 842 0.245813 GTTGGACTCACCCGGACTAC 59.754 60.000 0.73 0.00 38.00 2.73
855 1025 3.039526 AGAGAGGAGGGGGAGGGG 61.040 72.222 0.00 0.00 0.00 4.79
856 1026 2.285180 CAGAGAGGAGGGGGAGGG 59.715 72.222 0.00 0.00 0.00 4.30
857 1027 2.445654 GCAGAGAGGAGGGGGAGG 60.446 72.222 0.00 0.00 0.00 4.30
858 1028 1.457455 GAGCAGAGAGGAGGGGGAG 60.457 68.421 0.00 0.00 0.00 4.30
859 1029 2.693017 GAGCAGAGAGGAGGGGGA 59.307 66.667 0.00 0.00 0.00 4.81
860 1030 2.445654 GGAGCAGAGAGGAGGGGG 60.446 72.222 0.00 0.00 0.00 5.40
883 1053 3.591835 GTGGTTGTGGTGGTGGCG 61.592 66.667 0.00 0.00 0.00 5.69
895 1065 0.037734 GATCGGAGGGTTTGGTGGTT 59.962 55.000 0.00 0.00 0.00 3.67
896 1066 1.683441 GATCGGAGGGTTTGGTGGT 59.317 57.895 0.00 0.00 0.00 4.16
924 1094 3.869272 GCGGCATGCGAAGTGGAG 61.869 66.667 12.44 0.00 0.00 3.86
1384 1571 1.055338 GCAACAATGAAGCGAAGTGC 58.945 50.000 0.00 0.00 46.98 4.40
1399 1586 5.289917 GCTTAGAAGAAGTAGTAGCAGCAAC 59.710 44.000 0.00 0.00 0.00 4.17
1401 1588 4.142138 GGCTTAGAAGAAGTAGTAGCAGCA 60.142 45.833 0.00 0.00 0.00 4.41
1402 1589 4.364860 GGCTTAGAAGAAGTAGTAGCAGC 58.635 47.826 0.00 0.00 0.00 5.25
1403 1590 4.498345 CCGGCTTAGAAGAAGTAGTAGCAG 60.498 50.000 0.00 0.00 0.00 4.24
1404 1591 3.380637 CCGGCTTAGAAGAAGTAGTAGCA 59.619 47.826 0.00 0.00 0.00 3.49
1405 1592 3.631227 TCCGGCTTAGAAGAAGTAGTAGC 59.369 47.826 0.00 0.00 0.00 3.58
1406 1593 4.883006 AGTCCGGCTTAGAAGAAGTAGTAG 59.117 45.833 0.00 0.00 0.00 2.57
1407 1594 4.853007 AGTCCGGCTTAGAAGAAGTAGTA 58.147 43.478 0.00 0.00 0.00 1.82
1408 1595 3.699413 AGTCCGGCTTAGAAGAAGTAGT 58.301 45.455 0.00 0.00 0.00 2.73
1409 1596 4.261280 GCTAGTCCGGCTTAGAAGAAGTAG 60.261 50.000 14.12 4.39 0.00 2.57
1419 1606 2.493030 GCACGCTAGTCCGGCTTA 59.507 61.111 0.00 0.00 0.00 3.09
1430 1617 4.379243 CCTTCTCACCCGCACGCT 62.379 66.667 0.00 0.00 0.00 5.07
1433 1620 1.235281 GGAAACCTTCTCACCCGCAC 61.235 60.000 0.00 0.00 0.00 5.34
1439 1626 2.084546 CCCGAATGGAAACCTTCTCAC 58.915 52.381 0.00 0.00 37.49 3.51
1456 1643 2.267961 CTCCCGGAAGTTTCCCCG 59.732 66.667 0.73 0.00 44.67 5.73
1483 1670 2.738013 ACTACCCAGTACGCAACTTC 57.262 50.000 0.00 0.00 35.76 3.01
1487 1674 2.291153 ACTCCTACTACCCAGTACGCAA 60.291 50.000 0.00 0.00 36.14 4.85
1505 1692 7.744087 TGCACACCAAATATCCATATTACTC 57.256 36.000 0.00 0.00 32.91 2.59
1610 1803 5.412640 TGATCTTTCGCTAATTTACCACGA 58.587 37.500 0.00 0.00 0.00 4.35
1611 1804 5.712217 TGATCTTTCGCTAATTTACCACG 57.288 39.130 0.00 0.00 0.00 4.94
1613 1806 9.778741 ATAAGATGATCTTTCGCTAATTTACCA 57.221 29.630 13.54 0.00 37.89 3.25
1622 1815 8.861086 TCTACCTAAATAAGATGATCTTTCGCT 58.139 33.333 13.54 0.00 37.89 4.93
1648 1841 2.416566 CGATCTGCAGCAGTGAAGTACT 60.417 50.000 22.10 0.00 41.36 2.73
1649 1842 1.923204 CGATCTGCAGCAGTGAAGTAC 59.077 52.381 22.10 6.29 30.06 2.73
1669 1863 7.011295 TGCAATTCAAAAATTTGAGTCCAAGAC 59.989 33.333 8.44 0.00 46.68 3.01
1674 1868 6.036953 TGTGTGCAATTCAAAAATTTGAGTCC 59.963 34.615 8.44 3.02 46.68 3.85
1723 1917 4.521130 TTCATCCGCAGCTAATACTAGG 57.479 45.455 0.00 0.00 0.00 3.02
1766 1960 0.240145 GGGGAAACGTAGCAACTTGC 59.760 55.000 5.55 5.55 45.46 4.01
1767 1961 0.515564 CGGGGAAACGTAGCAACTTG 59.484 55.000 0.00 0.00 0.00 3.16
1768 1962 0.107268 ACGGGGAAACGTAGCAACTT 59.893 50.000 0.00 0.00 46.58 2.66
1769 1963 1.750297 ACGGGGAAACGTAGCAACT 59.250 52.632 0.00 0.00 46.58 3.16
1770 1964 4.366603 ACGGGGAAACGTAGCAAC 57.633 55.556 0.00 0.00 46.58 4.17
1814 2008 8.716674 ATAATTTTCATGGCTGGACAGATTAT 57.283 30.769 3.00 0.00 0.00 1.28
1841 2035 3.119029 GCCATGTTGGACAGCAATACAAT 60.119 43.478 0.00 0.00 40.96 2.71
1875 2069 5.820423 ACCAAAAGCAAGAACCAAATAAACC 59.180 36.000 0.00 0.00 0.00 3.27
1878 2072 5.983540 ACACCAAAAGCAAGAACCAAATAA 58.016 33.333 0.00 0.00 0.00 1.40
1904 2098 3.709653 GGACTGATATGGTGTGTCCCTTA 59.290 47.826 0.00 0.00 40.74 2.69
1905 2099 2.505819 GGACTGATATGGTGTGTCCCTT 59.494 50.000 0.00 0.00 40.74 3.95
1934 2128 4.974399 AGAAATCAGGTCGAGGTTTTCTT 58.026 39.130 9.95 0.00 31.30 2.52
1977 2171 1.134788 ACTAGGCAACCGCTCATGTAC 60.135 52.381 0.00 0.00 38.60 2.90
1978 2172 1.191535 ACTAGGCAACCGCTCATGTA 58.808 50.000 0.00 0.00 38.60 2.29
1982 2176 0.613853 ACCTACTAGGCAACCGCTCA 60.614 55.000 1.55 0.00 39.63 4.26
1983 2177 0.179108 CACCTACTAGGCAACCGCTC 60.179 60.000 1.55 0.00 39.63 5.03
1984 2178 0.903454 ACACCTACTAGGCAACCGCT 60.903 55.000 1.55 0.00 39.63 5.52
2069 2271 7.926555 CCCCATTCTTAGCGTATAATGGTATAG 59.073 40.741 17.18 6.89 44.51 1.31
2076 2278 3.329520 TGGCCCCATTCTTAGCGTATAAT 59.670 43.478 0.00 0.00 0.00 1.28
2084 2286 4.348168 ACAGTACTATGGCCCCATTCTTAG 59.652 45.833 4.94 0.00 37.82 2.18
2100 2302 0.685097 ACAATGTCGGGCACAGTACT 59.315 50.000 0.00 0.00 38.85 2.73
2221 2430 0.247736 CCAGCAGACAGACCCACTAC 59.752 60.000 0.00 0.00 0.00 2.73
2619 2828 0.948678 GCAACCCATAACGTGTGTGT 59.051 50.000 0.00 0.00 0.00 3.72
2620 2829 0.239879 GGCAACCCATAACGTGTGTG 59.760 55.000 0.00 0.00 0.00 3.82
2621 2830 2.636299 GGCAACCCATAACGTGTGT 58.364 52.632 0.00 0.00 0.00 3.72
2634 2843 0.947180 TCACGAGCGTAAAGGGCAAC 60.947 55.000 0.00 0.00 0.00 4.17
2635 2844 0.669318 CTCACGAGCGTAAAGGGCAA 60.669 55.000 0.00 0.00 0.00 4.52
2636 2845 1.080093 CTCACGAGCGTAAAGGGCA 60.080 57.895 0.00 0.00 0.00 5.36
2637 2846 0.669625 AACTCACGAGCGTAAAGGGC 60.670 55.000 0.00 0.00 0.00 5.19
2638 2847 2.094854 ACTAACTCACGAGCGTAAAGGG 60.095 50.000 0.00 0.00 0.00 3.95
2639 2848 3.213249 ACTAACTCACGAGCGTAAAGG 57.787 47.619 0.00 0.00 0.00 3.11
2640 2849 4.094212 GGTACTAACTCACGAGCGTAAAG 58.906 47.826 0.00 0.00 0.00 1.85
2641 2850 3.119849 GGGTACTAACTCACGAGCGTAAA 60.120 47.826 0.00 0.00 0.00 2.01
2642 2851 2.420022 GGGTACTAACTCACGAGCGTAA 59.580 50.000 0.00 0.00 0.00 3.18
2643 2852 2.009774 GGGTACTAACTCACGAGCGTA 58.990 52.381 0.00 0.00 0.00 4.42
2644 2853 0.807496 GGGTACTAACTCACGAGCGT 59.193 55.000 0.00 0.00 0.00 5.07
2645 2854 1.093159 AGGGTACTAACTCACGAGCG 58.907 55.000 0.00 0.00 0.00 5.03
2646 2855 3.012518 TGTAGGGTACTAACTCACGAGC 58.987 50.000 0.00 0.00 0.00 5.03
2647 2856 3.063180 CGTGTAGGGTACTAACTCACGAG 59.937 52.174 18.19 0.00 46.10 4.18
2648 2857 3.002791 CGTGTAGGGTACTAACTCACGA 58.997 50.000 18.19 0.00 46.10 4.35
2649 2858 3.002791 TCGTGTAGGGTACTAACTCACG 58.997 50.000 17.48 17.48 45.10 4.35
2650 2859 4.256920 TCTCGTGTAGGGTACTAACTCAC 58.743 47.826 0.00 0.00 0.00 3.51
2651 2860 4.558226 TCTCGTGTAGGGTACTAACTCA 57.442 45.455 0.00 0.00 0.00 3.41
2652 2861 7.228308 ACATATTCTCGTGTAGGGTACTAACTC 59.772 40.741 0.00 0.00 0.00 3.01
2668 2877 7.547370 GGATATCAGGAGGAAAACATATTCTCG 59.453 40.741 4.83 0.00 0.00 4.04
2669 2878 8.378565 TGGATATCAGGAGGAAAACATATTCTC 58.621 37.037 4.83 0.00 0.00 2.87
2681 2890 7.841729 GGTCTATTAAGATGGATATCAGGAGGA 59.158 40.741 4.83 0.00 35.70 3.71
2684 2893 6.903534 GGGGTCTATTAAGATGGATATCAGGA 59.096 42.308 4.83 0.00 35.70 3.86
2690 2899 5.649395 CGTACGGGGTCTATTAAGATGGATA 59.351 44.000 7.57 0.00 33.30 2.59
2710 2919 5.558273 GCATAATCATACCTGCAACACGTAC 60.558 44.000 0.00 0.00 34.77 3.67
2744 2955 6.677076 ACAAATATACCTTCCCTGTAGACCTT 59.323 38.462 0.00 0.00 0.00 3.50
3110 3321 4.748798 CTCTGGGGAGCAGGGGGT 62.749 72.222 0.00 0.00 32.43 4.95
3132 3349 8.193438 GGAAAATATATCAGCCATTTATCAGCC 58.807 37.037 0.00 0.00 0.00 4.85
3161 3379 8.322906 TGATCTTGTCGACATTCTACAAAATT 57.677 30.769 20.80 0.00 32.74 1.82
3203 3421 9.725019 ATAGAACTTACATGAATGACAAGAACA 57.275 29.630 0.00 0.00 32.08 3.18
3276 3494 3.433314 CCACTAGAGAGGCAATGCAAGAT 60.433 47.826 7.79 0.00 0.00 2.40
3294 3512 7.953493 TCTAAAAACAAATCCCTTTATCCCACT 59.047 33.333 0.00 0.00 0.00 4.00
3370 3588 5.754782 ACATACTTGGCTTGGTGATCATTA 58.245 37.500 0.00 0.00 0.00 1.90
3375 3593 5.435686 TCTTACATACTTGGCTTGGTGAT 57.564 39.130 0.00 0.00 0.00 3.06
3432 3650 0.400213 ATCACCCCAGCAACTTCGAA 59.600 50.000 0.00 0.00 0.00 3.71
3459 3677 4.085733 TGATGTAAAAACTGGGGTGATGG 58.914 43.478 0.00 0.00 0.00 3.51
3460 3678 5.009631 TCTGATGTAAAAACTGGGGTGATG 58.990 41.667 0.00 0.00 0.00 3.07
3467 3685 6.582295 CACCGAAATTCTGATGTAAAAACTGG 59.418 38.462 0.00 0.00 0.00 4.00
3488 3706 3.067106 AGTTATGACAACTGAAGCACCG 58.933 45.455 0.00 0.00 0.00 4.94
3543 3769 1.193874 GACCAATCAACAACGTCGTCC 59.806 52.381 0.00 0.00 0.00 4.79
3642 3868 3.891977 TGATGTAGTCAGGATACAGCTCC 59.108 47.826 3.43 0.00 39.63 4.70
3681 3907 1.781025 TTTTGCCGAGGCTTGACACG 61.781 55.000 15.75 0.00 42.51 4.49
3798 4024 0.179097 GGGAGATCTGTCGGCACTTC 60.179 60.000 0.00 0.00 0.00 3.01
3816 4042 5.310451 ACTCTACTATCTAAGCTCTTCCGG 58.690 45.833 0.00 0.00 0.00 5.14
3863 4089 2.417933 CTCATTCGTGGCTTTTCAGGAG 59.582 50.000 0.00 0.00 33.83 3.69
3992 4218 4.450976 ACACTATGACACAGTTGCTTGAA 58.549 39.130 0.00 0.00 0.00 2.69
4032 4258 0.888619 CTCTACTGCGGGAACTGTCA 59.111 55.000 0.00 0.00 36.83 3.58
4090 4318 1.001974 ACAGCTTATTCACCAGCGTCA 59.998 47.619 0.00 0.00 41.24 4.35
4119 4347 4.315803 CATGTTGAGACGTACCCTCTTTT 58.684 43.478 10.22 0.00 0.00 2.27
4424 4667 0.543277 TGTCTATTCTGCAGCCCCAG 59.457 55.000 9.47 3.51 0.00 4.45
4582 4825 6.828273 CCCTTTCAGGTGATGTAAATATGTGA 59.172 38.462 0.00 0.00 31.93 3.58
4633 4878 2.679837 AGATTTGCTTGCCGTGTATGAG 59.320 45.455 0.00 0.00 0.00 2.90
4670 4915 2.733671 GCGACCGGCCGAGTTTTAC 61.734 63.158 30.73 9.70 34.80 2.01
4685 4931 4.530710 AGTATTAGGTCAGTGTTTGCGA 57.469 40.909 0.00 0.00 0.00 5.10
4698 4944 6.207025 CACCAGCCAGTAGTAGTAGTATTAGG 59.793 46.154 0.00 0.00 0.00 2.69
4704 4953 3.453059 ACACCAGCCAGTAGTAGTAGT 57.547 47.619 0.00 0.00 0.00 2.73
4705 4954 4.338682 CCTAACACCAGCCAGTAGTAGTAG 59.661 50.000 0.00 0.00 0.00 2.57
4706 4955 4.275810 CCTAACACCAGCCAGTAGTAGTA 58.724 47.826 0.00 0.00 0.00 1.82
4707 4956 3.097614 CCTAACACCAGCCAGTAGTAGT 58.902 50.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.