Multiple sequence alignment - TraesCS2B01G469000

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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 TraesCS2B01G469000 chr2B 100.000 4079 0 0 1 4079 664932026 664936104 0.000000e+00 7533.0
1 TraesCS2B01G469000 chr2D 87.571 4216 237 127 1 4073 557257012 557261083 0.000000e+00 4617.0
2 TraesCS2B01G469000 chr2A 87.551 4177 261 124 1 4018 697288198 697292274 0.000000e+00 4593.0
3 TraesCS2B01G469000 chr6A 92.377 223 17 0 1867 2089 488062703 488062481 6.580000e-83 318.0
4 TraesCS2B01G469000 chr6A 87.923 207 23 2 1374 1578 488063009 488062803 4.070000e-60 243.0
5 TraesCS2B01G469000 chr6A 81.022 274 37 11 2235 2499 488062396 488062129 1.920000e-48 204.0
6 TraesCS2B01G469000 chr6B 87.793 213 22 4 1368 1578 524064817 524064607 3.150000e-61 246.0
7 TraesCS2B01G469000 chr6B 84.685 222 24 6 2283 2496 524064120 524063901 3.190000e-51 213.0
8 TraesCS2B01G469000 chr6D 87.383 214 23 3 1369 1578 354223193 354223406 4.070000e-60 243.0
9 TraesCS2B01G469000 chr7A 81.328 241 40 5 1867 2105 573097002 573096765 1.500000e-44 191.0
10 TraesCS2B01G469000 chr7A 76.423 246 35 15 1867 2090 303102172 303101928 1.200000e-20 111.0
11 TraesCS2B01G469000 chr7D 81.778 225 39 2 1867 2090 505603597 505603374 1.940000e-43 187.0
12 TraesCS2B01G469000 chr7B 81.858 226 37 4 1867 2090 533570540 533570317 1.940000e-43 187.0
13 TraesCS2B01G469000 chr7B 76.829 246 34 15 1867 2090 268454509 268454753 2.580000e-22 117.0
14 TraesCS2B01G469000 chr1A 82.353 102 12 5 2384 2485 348399217 348399122 2.610000e-12 84.2
15 TraesCS2B01G469000 chr1D 81.373 102 13 5 2384 2485 275942635 275942540 1.220000e-10 78.7
16 TraesCS2B01G469000 chr1B 81.188 101 13 5 2385 2485 375257129 375257035 4.370000e-10 76.8


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 TraesCS2B01G469000 chr2B 664932026 664936104 4078 False 7533.0 7533 100.000000 1 4079 1 chr2B.!!$F1 4078
1 TraesCS2B01G469000 chr2D 557257012 557261083 4071 False 4617.0 4617 87.571000 1 4073 1 chr2D.!!$F1 4072
2 TraesCS2B01G469000 chr2A 697288198 697292274 4076 False 4593.0 4593 87.551000 1 4018 1 chr2A.!!$F1 4017
3 TraesCS2B01G469000 chr6A 488062129 488063009 880 True 255.0 318 87.107333 1374 2499 3 chr6A.!!$R1 1125
4 TraesCS2B01G469000 chr6B 524063901 524064817 916 True 229.5 246 86.239000 1368 2496 2 chr6B.!!$R1 1128

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
987 1039 0.106619 TTTACCACCACCACCACCAC 60.107 55.0 0.0 0.0 0.00 4.16 F
2517 2674 0.313043 GCAAGAGCAAAGCAGAGCAA 59.687 50.0 0.0 0.0 41.58 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 2826 0.100503 GCAATGGCGGCTCGTTATTT 59.899 50.0 11.43 0.0 0.0 1.4 R
3823 4091 0.745845 GCCATGATTCGACCAGCACT 60.746 55.0 0.00 0.0 0.0 4.4 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.974300 GCATGATGCAATGATGATGAAAAC 58.026 37.500 13.36 0.00 40.64 2.43
81 87 2.198827 TCCTGGGCTGTTACAACATG 57.801 50.000 0.00 0.00 38.41 3.21
82 88 1.423541 TCCTGGGCTGTTACAACATGT 59.576 47.619 0.00 0.00 38.41 3.21
91 97 4.212213 TGTTACAACATGTTTACACGCC 57.788 40.909 8.77 0.00 33.17 5.68
115 121 6.256757 CCCACGTTTAAATTGTTCACAATGTT 59.743 34.615 5.94 5.86 45.06 2.71
118 124 7.221838 CACGTTTAAATTGTTCACAATGTTCCT 59.778 33.333 5.94 0.00 45.06 3.36
144 152 6.436890 TCTTTTCTTAAAGTTTGAGGGGGAA 58.563 36.000 7.48 0.00 41.25 3.97
154 162 4.835056 AGTTTGAGGGGGAAGAGAATTTTG 59.165 41.667 0.00 0.00 0.00 2.44
173 181 1.745489 CGCTCCTTTTCTTCCGGGG 60.745 63.158 0.00 0.00 0.00 5.73
344 357 3.723348 GGTTCAACGCACCGGAGC 61.723 66.667 14.54 14.54 0.00 4.70
345 358 2.970324 GTTCAACGCACCGGAGCA 60.970 61.111 23.87 0.59 0.00 4.26
347 360 4.680237 TCAACGCACCGGAGCAGG 62.680 66.667 23.87 10.78 37.30 4.85
374 387 5.072872 CCATGGTGATTATCTTTCCTCCTCT 59.927 44.000 2.57 0.00 0.00 3.69
377 390 6.418101 TGGTGATTATCTTTCCTCCTCTTTG 58.582 40.000 0.00 0.00 0.00 2.77
378 391 6.215431 TGGTGATTATCTTTCCTCCTCTTTGA 59.785 38.462 0.00 0.00 0.00 2.69
379 392 6.540551 GGTGATTATCTTTCCTCCTCTTTGAC 59.459 42.308 0.00 0.00 0.00 3.18
383 399 4.457834 TCTTTCCTCCTCTTTGACGATC 57.542 45.455 0.00 0.00 0.00 3.69
411 427 1.738030 GCTAATCGCGTGGTTAGTGGT 60.738 52.381 25.48 0.00 31.98 4.16
431 447 2.281208 TGTGGCGTGGTTAGTGGC 60.281 61.111 0.00 0.00 0.00 5.01
504 520 3.854669 CCACTCCCCTAGCAGCCG 61.855 72.222 0.00 0.00 0.00 5.52
510 526 1.001406 CTCCCCTAGCAGCCGAAATAG 59.999 57.143 0.00 0.00 0.00 1.73
605 626 4.085312 CGCATAAACAAAAACAAACCGAGG 60.085 41.667 0.00 0.00 0.00 4.63
606 627 4.210328 GCATAAACAAAAACAAACCGAGGG 59.790 41.667 0.00 0.00 0.00 4.30
607 628 5.593010 CATAAACAAAAACAAACCGAGGGA 58.407 37.500 0.00 0.00 0.00 4.20
608 629 3.793797 AACAAAAACAAACCGAGGGAG 57.206 42.857 0.00 0.00 0.00 4.30
609 630 1.407618 ACAAAAACAAACCGAGGGAGC 59.592 47.619 0.00 0.00 0.00 4.70
617 638 1.841302 AACCGAGGGAGCAGCATCAA 61.841 55.000 0.00 0.00 0.00 2.57
642 663 1.031571 ACACGTAGTCGGCCGGATTA 61.032 55.000 27.83 12.59 41.61 1.75
705 731 3.190849 CGTCAGTGCTGATGCCGG 61.191 66.667 8.28 0.00 42.18 6.13
706 732 3.503363 GTCAGTGCTGATGCCGGC 61.503 66.667 22.73 22.73 42.18 6.13
707 733 4.783621 TCAGTGCTGATGCCGGCC 62.784 66.667 26.77 10.34 44.00 6.13
893 930 4.832608 GATGGCACGGACCCGGAC 62.833 72.222 13.43 4.75 44.69 4.79
970 1021 0.469892 CTCCCCTGCTGGTTTGGTTT 60.470 55.000 9.00 0.00 0.00 3.27
987 1039 0.106619 TTTACCACCACCACCACCAC 60.107 55.000 0.00 0.00 0.00 4.16
1024 1076 2.156051 GACACTCGCGACCTTTCCCT 62.156 60.000 3.71 0.00 0.00 4.20
1137 1189 2.300967 AAATCCTCTGCGCTCCCCA 61.301 57.895 9.73 0.00 0.00 4.96
1149 1201 2.203938 TCCCCACGCCTCCTTCTT 60.204 61.111 0.00 0.00 0.00 2.52
1175 1227 3.959975 GCCGCTTGCCGTGTTTGA 61.960 61.111 0.00 0.00 34.38 2.69
1281 1333 1.661463 ATCTCTGCTTCCCCTGTTCA 58.339 50.000 0.00 0.00 0.00 3.18
1290 1342 3.566351 CTTCCCCTGTTCACCTTTTCTT 58.434 45.455 0.00 0.00 0.00 2.52
1299 1351 5.496556 TGTTCACCTTTTCTTTCTCTGTGA 58.503 37.500 0.00 0.00 0.00 3.58
1330 1382 4.226761 GCTCTGTTCGTTGGTTTTATTGG 58.773 43.478 0.00 0.00 0.00 3.16
1331 1383 4.794169 CTCTGTTCGTTGGTTTTATTGGG 58.206 43.478 0.00 0.00 0.00 4.12
1527 1579 4.166011 GACTGCATCAACGGCGCC 62.166 66.667 19.07 19.07 0.00 6.53
1581 1633 2.665089 CCACGCCATCCAGGTACCA 61.665 63.158 15.94 0.00 40.61 3.25
1582 1634 1.526887 CACGCCATCCAGGTACCAT 59.473 57.895 15.94 0.00 40.61 3.55
1603 1660 5.721480 CCATACCATTTCTTCCCTTTCCTTT 59.279 40.000 0.00 0.00 0.00 3.11
1605 1662 5.079998 ACCATTTCTTCCCTTTCCTTTCT 57.920 39.130 0.00 0.00 0.00 2.52
1607 1664 4.464244 CCATTTCTTCCCTTTCCTTTCTCC 59.536 45.833 0.00 0.00 0.00 3.71
1625 1682 2.292569 CTCCCTTCGCATTGGATTCATG 59.707 50.000 0.00 0.00 0.00 3.07
1727 1820 4.014569 TGCTAGATTTGCAGTTGGTGTA 57.985 40.909 0.00 0.00 35.31 2.90
1737 1830 1.556911 CAGTTGGTGTATCCTCCAGCT 59.443 52.381 0.00 0.00 43.80 4.24
1802 1896 3.704800 ACTAACTTCCTTCCTTGAGCC 57.295 47.619 0.00 0.00 0.00 4.70
1823 1918 0.475906 CCCCCTGTTCCATCTCATCC 59.524 60.000 0.00 0.00 0.00 3.51
1827 1922 3.254960 CCCTGTTCCATCTCATCCCTAT 58.745 50.000 0.00 0.00 0.00 2.57
1828 1923 4.429505 CCCTGTTCCATCTCATCCCTATA 58.570 47.826 0.00 0.00 0.00 1.31
1838 1940 5.249780 TCTCATCCCTATACTCTCTGACC 57.750 47.826 0.00 0.00 0.00 4.02
2094 2226 2.223971 CCTCGGATGCAAGGTACGTATT 60.224 50.000 0.00 0.00 0.00 1.89
2095 2227 2.794910 CTCGGATGCAAGGTACGTATTG 59.205 50.000 0.00 1.15 0.00 1.90
2097 2229 3.380954 TCGGATGCAAGGTACGTATTGTA 59.619 43.478 9.90 6.49 0.00 2.41
2098 2230 3.734231 CGGATGCAAGGTACGTATTGTAG 59.266 47.826 9.90 0.00 32.51 2.74
2142 2281 2.432628 GGTCGGTCAACGCCTCTG 60.433 66.667 0.00 0.00 43.86 3.35
2150 2289 1.929836 GTCAACGCCTCTGCTAGATTG 59.070 52.381 0.00 0.00 34.43 2.67
2157 2296 2.211806 CCTCTGCTAGATTGCTTCAGC 58.788 52.381 0.00 0.00 42.50 4.26
2224 2363 5.700373 GGCATTGTGATTTGGTTGTTTATGT 59.300 36.000 0.00 0.00 0.00 2.29
2242 2383 2.809601 GTGGACGCGCAGATCGTT 60.810 61.111 5.73 0.00 40.59 3.85
2245 2386 3.554692 GACGCGCAGATCGTTGGG 61.555 66.667 5.73 0.00 40.59 4.12
2435 2588 2.982130 CCAACAGCTACCGCTCCT 59.018 61.111 0.00 0.00 45.15 3.69
2485 2641 4.743018 CCCTTCGGCAACCTCATT 57.257 55.556 0.00 0.00 0.00 2.57
2496 2652 2.227388 GCAACCTCATTGTGGAGTTCTG 59.773 50.000 11.60 2.64 40.77 3.02
2507 2664 1.417517 TGGAGTTCTGAGCAAGAGCAA 59.582 47.619 6.15 0.00 45.49 3.91
2508 2665 2.158769 TGGAGTTCTGAGCAAGAGCAAA 60.159 45.455 6.15 0.00 45.49 3.68
2512 2669 1.520494 TCTGAGCAAGAGCAAAGCAG 58.480 50.000 0.00 0.00 45.49 4.24
2513 2670 1.071228 TCTGAGCAAGAGCAAAGCAGA 59.929 47.619 0.00 0.00 45.49 4.26
2516 2673 0.536687 AGCAAGAGCAAAGCAGAGCA 60.537 50.000 0.00 0.00 45.49 4.26
2517 2674 0.313043 GCAAGAGCAAAGCAGAGCAA 59.687 50.000 0.00 0.00 41.58 3.91
2518 2675 1.929482 GCAAGAGCAAAGCAGAGCAAC 60.929 52.381 0.00 0.00 41.58 4.17
2519 2676 0.590195 AAGAGCAAAGCAGAGCAACG 59.410 50.000 0.00 0.00 0.00 4.10
2573 2731 4.898320 TGTAGCATACACATCCATCCATC 58.102 43.478 0.00 0.00 46.14 3.51
2575 2733 2.712627 AGCATACACATCCATCCATCCA 59.287 45.455 0.00 0.00 0.00 3.41
2578 2736 5.193124 AGCATACACATCCATCCATCCATAT 59.807 40.000 0.00 0.00 0.00 1.78
2597 2760 8.480133 TCCATATCTACCTCTAGAGTTTTTCC 57.520 38.462 18.42 0.00 32.24 3.13
2632 2812 6.070767 TGTTCTATACACCAAGGAGAAGGAAG 60.071 42.308 0.00 0.00 0.00 3.46
2633 2813 4.962995 TCTATACACCAAGGAGAAGGAAGG 59.037 45.833 0.00 0.00 0.00 3.46
2634 2814 2.118403 ACACCAAGGAGAAGGAAGGA 57.882 50.000 0.00 0.00 0.00 3.36
2635 2815 1.981495 ACACCAAGGAGAAGGAAGGAG 59.019 52.381 0.00 0.00 0.00 3.69
2636 2816 0.988063 ACCAAGGAGAAGGAAGGAGC 59.012 55.000 0.00 0.00 0.00 4.70
2637 2817 1.284313 CCAAGGAGAAGGAAGGAGCT 58.716 55.000 0.00 0.00 0.00 4.09
2638 2818 1.632920 CCAAGGAGAAGGAAGGAGCTT 59.367 52.381 0.00 0.00 0.00 3.74
2639 2819 2.840651 CCAAGGAGAAGGAAGGAGCTTA 59.159 50.000 0.00 0.00 0.00 3.09
2640 2820 3.264450 CCAAGGAGAAGGAAGGAGCTTAA 59.736 47.826 0.00 0.00 0.00 1.85
2641 2821 4.512484 CAAGGAGAAGGAAGGAGCTTAAG 58.488 47.826 0.00 0.00 0.00 1.85
2642 2822 2.503765 AGGAGAAGGAAGGAGCTTAAGC 59.496 50.000 20.09 20.09 42.49 3.09
2643 2823 2.237392 GGAGAAGGAAGGAGCTTAAGCA 59.763 50.000 28.39 0.00 45.16 3.91
2644 2824 3.307762 GGAGAAGGAAGGAGCTTAAGCAA 60.308 47.826 28.39 0.00 45.16 3.91
2645 2825 4.327680 GAGAAGGAAGGAGCTTAAGCAAA 58.672 43.478 28.39 0.00 45.16 3.68
2646 2826 4.729868 AGAAGGAAGGAGCTTAAGCAAAA 58.270 39.130 28.39 0.00 45.16 2.44
2716 2896 2.203337 GCAGGGCAATGCGGGATA 60.203 61.111 0.00 0.00 36.28 2.59
2717 2897 2.263741 GCAGGGCAATGCGGGATAG 61.264 63.158 0.00 0.00 36.28 2.08
2719 2899 0.886490 CAGGGCAATGCGGGATAGTC 60.886 60.000 0.00 0.00 0.00 2.59
2731 2911 3.021695 CGGGATAGTCACCACTACTTCA 58.978 50.000 0.00 0.00 37.97 3.02
2739 2923 6.859112 AGTCACCACTACTTCATCATAGTT 57.141 37.500 0.00 0.00 28.91 2.24
2783 2975 2.381752 AACAGGAAGGAAGGGTTTGG 57.618 50.000 0.00 0.00 0.00 3.28
2788 2980 1.328279 GAAGGAAGGGTTTGGGTGTG 58.672 55.000 0.00 0.00 0.00 3.82
2789 2981 0.634465 AAGGAAGGGTTTGGGTGTGT 59.366 50.000 0.00 0.00 0.00 3.72
2791 2983 1.037493 GGAAGGGTTTGGGTGTGTTC 58.963 55.000 0.00 0.00 0.00 3.18
2818 3010 2.183555 GAACGGCGGGAGGTAGTG 59.816 66.667 13.24 0.00 0.00 2.74
2820 3012 4.691359 ACGGCGGGAGGTAGTGGT 62.691 66.667 13.24 0.00 0.00 4.16
2827 3019 1.134401 CGGGAGGTAGTGGTCGTAGTA 60.134 57.143 0.00 0.00 0.00 1.82
2828 3020 2.570135 GGGAGGTAGTGGTCGTAGTAG 58.430 57.143 0.00 0.00 0.00 2.57
2829 3021 2.171448 GGGAGGTAGTGGTCGTAGTAGA 59.829 54.545 0.00 0.00 0.00 2.59
2830 3022 3.370953 GGGAGGTAGTGGTCGTAGTAGAA 60.371 52.174 0.00 0.00 0.00 2.10
2831 3023 3.876320 GGAGGTAGTGGTCGTAGTAGAAG 59.124 52.174 0.00 0.00 0.00 2.85
2832 3024 4.512484 GAGGTAGTGGTCGTAGTAGAAGT 58.488 47.826 0.00 0.00 0.00 3.01
2834 3026 5.320277 AGGTAGTGGTCGTAGTAGAAGTTT 58.680 41.667 0.00 0.00 0.00 2.66
2836 3028 6.266330 AGGTAGTGGTCGTAGTAGAAGTTTTT 59.734 38.462 0.00 0.00 0.00 1.94
2837 3029 7.448469 AGGTAGTGGTCGTAGTAGAAGTTTTTA 59.552 37.037 0.00 0.00 0.00 1.52
2838 3030 7.539022 GGTAGTGGTCGTAGTAGAAGTTTTTAC 59.461 40.741 0.00 0.00 0.00 2.01
2839 3031 7.282332 AGTGGTCGTAGTAGAAGTTTTTACT 57.718 36.000 6.34 6.34 34.64 2.24
2840 3032 7.366513 AGTGGTCGTAGTAGAAGTTTTTACTC 58.633 38.462 4.76 0.00 32.64 2.59
2841 3033 6.584184 GTGGTCGTAGTAGAAGTTTTTACTCC 59.416 42.308 4.76 2.44 32.64 3.85
2842 3034 5.797434 GGTCGTAGTAGAAGTTTTTACTCCG 59.203 44.000 4.76 5.95 32.59 4.63
2843 3035 6.374578 GTCGTAGTAGAAGTTTTTACTCCGT 58.625 40.000 10.83 0.00 32.97 4.69
2844 3036 6.304208 GTCGTAGTAGAAGTTTTTACTCCGTG 59.696 42.308 10.83 1.37 32.97 4.94
2845 3037 6.204688 TCGTAGTAGAAGTTTTTACTCCGTGA 59.795 38.462 10.83 2.94 32.97 4.35
2874 3072 6.036191 GGTAGCTAGCTACTAAGTTTTGCAAG 59.964 42.308 39.86 0.00 45.88 4.01
2886 3084 8.745590 ACTAAGTTTTGCAAGTTTCTTTCCTTA 58.254 29.630 0.00 0.00 0.00 2.69
2893 3091 4.395231 GCAAGTTTCTTTCCTTATAGGCGT 59.605 41.667 0.00 0.00 34.61 5.68
3001 3199 6.441274 TGATATTCGTCGTCCTGTAATAACC 58.559 40.000 0.00 0.00 0.00 2.85
3002 3200 4.996788 ATTCGTCGTCCTGTAATAACCT 57.003 40.909 0.00 0.00 0.00 3.50
3044 3242 1.072331 ACGGCCTTCTTCAATGTCACT 59.928 47.619 0.00 0.00 0.00 3.41
3045 3243 1.466167 CGGCCTTCTTCAATGTCACTG 59.534 52.381 0.00 0.00 0.00 3.66
3067 3271 5.177326 TGTGCTTGTTTTTGCTTGAATTCT 58.823 33.333 7.05 0.00 0.00 2.40
3143 3380 1.707989 AGACCTGTGAGTCTGAGAGGA 59.292 52.381 9.59 0.00 45.41 3.71
3145 3382 3.525609 AGACCTGTGAGTCTGAGAGGATA 59.474 47.826 9.59 0.00 45.41 2.59
3158 3395 2.109181 GGATACTCTGCCGGTGCC 59.891 66.667 1.90 0.00 36.33 5.01
3180 3417 4.156556 CCAGAAAAATCTCTGCGGATTTGA 59.843 41.667 0.00 0.00 42.77 2.69
3198 3435 3.881019 AAGGAGACGGTGGCGAGGA 62.881 63.158 0.00 0.00 0.00 3.71
3225 3462 3.860605 ACTGTGGCACCGTCAGCA 61.861 61.111 16.26 0.00 33.12 4.41
3291 3532 2.774799 ATTCATGAAAGCGGCCGGC 61.775 57.895 29.38 21.18 44.05 6.13
3422 3664 4.814041 AGGCCTGCCTCCCCTCTC 62.814 72.222 3.11 0.00 44.43 3.20
3463 3706 5.390251 GCAGTAGCAATGAATACGATGGATG 60.390 44.000 0.00 0.00 41.58 3.51
3464 3707 5.121298 CAGTAGCAATGAATACGATGGATGG 59.879 44.000 0.00 0.00 0.00 3.51
3465 3708 4.356405 AGCAATGAATACGATGGATGGA 57.644 40.909 0.00 0.00 0.00 3.41
3466 3709 4.914983 AGCAATGAATACGATGGATGGAT 58.085 39.130 0.00 0.00 0.00 3.41
3526 3769 3.306973 CCAATGATGCTGTACTACGTGTG 59.693 47.826 0.00 0.00 0.00 3.82
3527 3770 1.990799 TGATGCTGTACTACGTGTGC 58.009 50.000 0.00 0.00 0.00 4.57
3528 3771 1.544246 TGATGCTGTACTACGTGTGCT 59.456 47.619 0.00 0.00 32.31 4.40
3529 3772 1.920574 GATGCTGTACTACGTGTGCTG 59.079 52.381 0.00 3.74 34.41 4.41
3530 3773 2.070861 GCTGTACTACGTGTGCTGC 58.929 57.895 16.42 16.42 45.05 5.25
3531 3774 1.352156 GCTGTACTACGTGTGCTGCC 61.352 60.000 18.74 8.20 45.31 4.85
3570 3818 1.807742 GTGGAGCGAGCTCGTAGATAT 59.192 52.381 34.46 15.41 43.59 1.63
3574 3822 3.181514 GGAGCGAGCTCGTAGATATCTTC 60.182 52.174 34.46 17.58 43.59 2.87
3613 3861 0.460311 CGCATCTAGGGAAAGGTCGT 59.540 55.000 0.00 0.00 0.00 4.34
3675 3926 0.108041 CCATTTCCCTTGGCATGTGC 60.108 55.000 0.00 0.00 41.14 4.57
3746 4014 1.170919 TGGATCTAGCTCCCGTACGC 61.171 60.000 10.49 0.00 34.12 4.42
3806 4074 1.528586 CGCTCTTGTTTCTCCACTGTG 59.471 52.381 0.00 0.00 0.00 3.66
3812 4080 1.742831 TGTTTCTCCACTGTGCACAAC 59.257 47.619 21.98 13.62 0.00 3.32
3814 4082 3.202906 GTTTCTCCACTGTGCACAACTA 58.797 45.455 21.98 5.86 0.00 2.24
3819 4087 2.963101 TCCACTGTGCACAACTAGTACT 59.037 45.455 21.98 0.00 0.00 2.73
3821 4089 4.022589 TCCACTGTGCACAACTAGTACTAC 60.023 45.833 21.98 0.00 0.00 2.73
3822 4090 4.261867 CCACTGTGCACAACTAGTACTACA 60.262 45.833 21.98 0.00 0.00 2.74
3823 4091 5.286438 CACTGTGCACAACTAGTACTACAA 58.714 41.667 21.98 0.00 0.00 2.41
3824 4092 5.402568 CACTGTGCACAACTAGTACTACAAG 59.597 44.000 21.98 6.21 0.00 3.16
3827 4095 4.905412 GCACAACTAGTACTACAAGTGC 57.095 45.455 22.54 22.54 43.27 4.40
3847 4119 1.595382 GGTCGAATCATGGCCGGAG 60.595 63.158 5.05 0.00 0.00 4.63
3925 4210 4.057432 ACGCCTGGAAAATTGAAAATGTG 58.943 39.130 0.00 0.00 0.00 3.21
3963 4248 3.951332 CGTGACTGACGTTGCCAT 58.049 55.556 0.00 0.00 43.50 4.40
3966 4258 2.316867 TGACTGACGTTGCCATGCG 61.317 57.895 0.00 0.00 0.00 4.73
3968 4260 4.799473 CTGACGTTGCCATGCGCG 62.799 66.667 0.00 0.00 42.08 6.86
4025 4317 3.422303 CACACGCACGGACATGGG 61.422 66.667 0.00 0.00 38.44 4.00
4049 4355 2.056223 GCACCATTGCCATCTGCCT 61.056 57.895 0.00 0.00 43.66 4.75
4056 4362 2.280052 GCCATCTGCCTCTCTCGC 60.280 66.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 66 3.265737 ACATGTTGTAACAGCCCAGGATA 59.734 43.478 3.66 0.00 43.04 2.59
62 68 1.423541 ACATGTTGTAACAGCCCAGGA 59.576 47.619 3.66 0.00 43.04 3.86
91 97 6.820470 ACATTGTGAACAATTTAAACGTGG 57.180 33.333 5.94 0.00 43.48 4.94
100 106 9.696917 GAAAAGATAGGAACATTGTGAACAATT 57.303 29.630 5.94 0.00 43.48 2.32
115 121 7.888546 CCCCTCAAACTTTAAGAAAAGATAGGA 59.111 37.037 0.00 0.00 44.14 2.94
118 124 7.761608 TCCCCCTCAAACTTTAAGAAAAGATA 58.238 34.615 0.00 0.00 44.14 1.98
132 138 4.561530 GCAAAATTCTCTTCCCCCTCAAAC 60.562 45.833 0.00 0.00 0.00 2.93
144 152 3.823304 AGAAAAGGAGCGCAAAATTCTCT 59.177 39.130 11.47 0.00 0.00 3.10
154 162 2.399356 CCCGGAAGAAAAGGAGCGC 61.399 63.158 0.73 0.00 0.00 5.92
173 181 2.026822 TCATGGCTGAGTTTTCTCCTCC 60.027 50.000 0.00 0.00 45.63 4.30
232 240 8.499162 ACTGTTGCGAATATAATAAAGATGCTC 58.501 33.333 0.00 0.00 0.00 4.26
344 357 0.877071 GATAATCACCATGGCGCCTG 59.123 55.000 29.70 21.88 0.00 4.85
345 358 0.767375 AGATAATCACCATGGCGCCT 59.233 50.000 29.70 10.60 0.00 5.52
347 360 2.030805 GGAAAGATAATCACCATGGCGC 60.031 50.000 13.04 0.00 0.00 6.53
374 387 0.599991 AGCACAGCACGATCGTCAAA 60.600 50.000 19.84 0.00 0.00 2.69
377 390 1.518929 GATTAGCACAGCACGATCGTC 59.481 52.381 19.84 13.27 0.00 4.20
378 391 1.560923 GATTAGCACAGCACGATCGT 58.439 50.000 16.60 16.60 0.00 3.73
379 392 0.500178 CGATTAGCACAGCACGATCG 59.500 55.000 14.88 14.88 33.52 3.69
411 427 0.319083 CCACTAACCACGCCACACTA 59.681 55.000 0.00 0.00 0.00 2.74
504 520 2.546162 GCTCTACGGGAGTGCCTATTTC 60.546 54.545 2.83 0.00 46.80 2.17
534 550 1.664649 CGTCACTCGCTTTGCTCCA 60.665 57.895 0.00 0.00 0.00 3.86
605 626 1.086634 GTCCTCGTTGATGCTGCTCC 61.087 60.000 0.00 0.00 0.00 4.70
606 627 0.390340 TGTCCTCGTTGATGCTGCTC 60.390 55.000 0.00 0.00 0.00 4.26
607 628 0.671781 GTGTCCTCGTTGATGCTGCT 60.672 55.000 0.00 0.00 0.00 4.24
608 629 1.790387 GTGTCCTCGTTGATGCTGC 59.210 57.895 0.00 0.00 0.00 5.25
609 630 0.667487 ACGTGTCCTCGTTGATGCTG 60.667 55.000 0.00 0.00 41.37 4.41
617 638 2.684843 GCCGACTACGTGTCCTCGT 61.685 63.158 0.00 0.00 45.97 4.18
642 663 0.249699 TCGCGTTGCCATCCGATAAT 60.250 50.000 5.77 0.00 0.00 1.28
780 806 0.959553 GTGTTGTCCTGTCGAGAGGA 59.040 55.000 26.46 26.46 40.03 3.71
926 976 1.668101 TTTCAGGGGCGCGTTTGTTT 61.668 50.000 8.43 0.00 0.00 2.83
970 1021 1.384783 AGTGGTGGTGGTGGTGGTA 60.385 57.895 0.00 0.00 0.00 3.25
987 1039 0.969149 TCACAGCACTGGGTAGACAG 59.031 55.000 0.00 0.00 44.03 3.51
1137 1189 0.899019 GAGGAAGAAGAAGGAGGCGT 59.101 55.000 0.00 0.00 0.00 5.68
1146 1198 0.036952 CAAGCGGCAGAGGAAGAAGA 60.037 55.000 1.45 0.00 0.00 2.87
1149 1201 2.046892 GCAAGCGGCAGAGGAAGA 60.047 61.111 1.45 0.00 43.97 2.87
1281 1333 8.980481 TTTAATCTCACAGAGAAAGAAAAGGT 57.020 30.769 0.29 0.00 42.27 3.50
1290 1342 6.705302 ACAGAGCATTTAATCTCACAGAGAA 58.295 36.000 0.29 0.00 42.27 2.87
1299 1351 5.003804 ACCAACGAACAGAGCATTTAATCT 58.996 37.500 0.00 0.00 0.00 2.40
1330 1382 2.019156 GCCATTAGCCAGAGAACCACC 61.019 57.143 0.00 0.00 34.35 4.61
1331 1383 1.383523 GCCATTAGCCAGAGAACCAC 58.616 55.000 0.00 0.00 34.35 4.16
1527 1579 3.007920 AGGCACTGGGAGCAGAGG 61.008 66.667 0.00 0.00 37.18 3.69
1581 1633 6.805150 AGAAAGGAAAGGGAAGAAATGGTAT 58.195 36.000 0.00 0.00 0.00 2.73
1582 1634 6.214177 AGAAAGGAAAGGGAAGAAATGGTA 57.786 37.500 0.00 0.00 0.00 3.25
1586 1638 4.358310 AGGGAGAAAGGAAAGGGAAGAAAT 59.642 41.667 0.00 0.00 0.00 2.17
1587 1639 3.727391 AGGGAGAAAGGAAAGGGAAGAAA 59.273 43.478 0.00 0.00 0.00 2.52
1588 1640 3.336676 AGGGAGAAAGGAAAGGGAAGAA 58.663 45.455 0.00 0.00 0.00 2.52
1589 1641 3.005529 AGGGAGAAAGGAAAGGGAAGA 57.994 47.619 0.00 0.00 0.00 2.87
1590 1642 3.691575 GAAGGGAGAAAGGAAAGGGAAG 58.308 50.000 0.00 0.00 0.00 3.46
1591 1643 2.039879 CGAAGGGAGAAAGGAAAGGGAA 59.960 50.000 0.00 0.00 0.00 3.97
1592 1644 1.628846 CGAAGGGAGAAAGGAAAGGGA 59.371 52.381 0.00 0.00 0.00 4.20
1593 1645 1.950954 GCGAAGGGAGAAAGGAAAGGG 60.951 57.143 0.00 0.00 0.00 3.95
1603 1660 1.559219 TGAATCCAATGCGAAGGGAGA 59.441 47.619 0.00 0.00 33.47 3.71
1605 1662 2.300433 CATGAATCCAATGCGAAGGGA 58.700 47.619 0.00 0.00 34.70 4.20
1607 1664 3.129113 TGAACATGAATCCAATGCGAAGG 59.871 43.478 0.00 0.00 0.00 3.46
1644 1701 2.797177 AACAGGGAGCATCTTCTTCC 57.203 50.000 0.00 0.00 33.73 3.46
1727 1820 2.370445 CCGTTGGGAGCTGGAGGAT 61.370 63.158 0.00 0.00 34.06 3.24
1737 1830 2.291043 GGAAGAGAGGCCGTTGGGA 61.291 63.158 0.00 0.00 34.06 4.37
1823 1918 4.580995 ACGAACATGGTCAGAGAGTATAGG 59.419 45.833 12.13 0.00 0.00 2.57
1827 1922 3.056821 CCAACGAACATGGTCAGAGAGTA 60.057 47.826 12.13 0.00 33.08 2.59
1828 1923 2.289072 CCAACGAACATGGTCAGAGAGT 60.289 50.000 12.13 0.00 33.08 3.24
1838 1940 2.098280 TGGAACACAACCAACGAACATG 59.902 45.455 0.00 0.00 34.25 3.21
1884 2016 1.585521 GCGGATCACGTCGTGGTAG 60.586 63.158 24.33 15.86 46.52 3.18
1932 2064 3.307906 TAGGTCTGCACGCCGGTT 61.308 61.111 1.90 0.00 0.00 4.44
2142 2281 1.598601 GCTGAGCTGAAGCAATCTAGC 59.401 52.381 12.14 3.30 45.16 3.42
2150 2289 1.077915 GAACTGAGCTGAGCTGAAGC 58.922 55.000 13.71 9.53 39.88 3.86
2224 2363 3.567478 AACGATCTGCGCGTCCACA 62.567 57.895 8.43 0.00 46.04 4.17
2478 2634 2.289945 GCTCAGAACTCCACAATGAGGT 60.290 50.000 0.00 0.00 38.24 3.85
2485 2641 1.270518 GCTCTTGCTCAGAACTCCACA 60.271 52.381 0.00 0.00 36.03 4.17
2496 2652 0.168568 GCTCTGCTTTGCTCTTGCTC 59.831 55.000 0.00 0.00 40.48 4.26
2573 2731 7.014422 ACGGAAAAACTCTAGAGGTAGATATGG 59.986 40.741 23.50 7.09 34.63 2.74
2575 2733 8.536340 AACGGAAAAACTCTAGAGGTAGATAT 57.464 34.615 23.50 0.00 34.63 1.63
2578 2736 5.184671 GGAACGGAAAAACTCTAGAGGTAGA 59.815 44.000 23.50 0.00 33.96 2.59
2644 2824 2.874849 CAATGGCGGCTCGTTATTTTT 58.125 42.857 11.43 0.00 0.00 1.94
2645 2825 1.469079 GCAATGGCGGCTCGTTATTTT 60.469 47.619 11.43 0.00 0.00 1.82
2646 2826 0.100503 GCAATGGCGGCTCGTTATTT 59.899 50.000 11.43 0.00 0.00 1.40
2702 2882 1.148273 TGACTATCCCGCATTGCCC 59.852 57.895 2.41 0.00 0.00 5.36
2703 2883 1.166531 GGTGACTATCCCGCATTGCC 61.167 60.000 2.41 0.00 0.00 4.52
2713 2893 8.172352 ACTATGATGAAGTAGTGGTGACTATC 57.828 38.462 0.00 0.00 37.03 2.08
2716 2896 6.859112 AACTATGATGAAGTAGTGGTGACT 57.141 37.500 0.00 0.00 36.07 3.41
2717 2897 7.773149 AGTAACTATGATGAAGTAGTGGTGAC 58.227 38.462 0.00 0.00 31.83 3.67
2719 2899 8.683615 TGTAGTAACTATGATGAAGTAGTGGTG 58.316 37.037 0.00 0.00 31.83 4.17
2739 2923 5.163385 ACCAGCACAGTAACTGTTTGTAGTA 60.163 40.000 0.00 0.00 42.59 1.82
2783 2975 2.048503 CGGGGAGACGAACACACC 60.049 66.667 0.00 0.00 35.47 4.16
2788 2980 2.126189 CGTTCCGGGGAGACGAAC 60.126 66.667 0.00 0.00 38.99 3.95
2789 2981 3.376078 CCGTTCCGGGGAGACGAA 61.376 66.667 17.73 0.00 44.15 3.85
2827 3019 4.755123 CCACATCACGGAGTAAAAACTTCT 59.245 41.667 0.00 0.00 41.61 2.85
2828 3020 4.514066 ACCACATCACGGAGTAAAAACTTC 59.486 41.667 0.00 0.00 41.61 3.01
2829 3021 4.457466 ACCACATCACGGAGTAAAAACTT 58.543 39.130 0.00 0.00 41.61 2.66
2830 3022 4.081322 ACCACATCACGGAGTAAAAACT 57.919 40.909 0.00 0.00 41.61 2.66
2831 3023 4.142966 GCTACCACATCACGGAGTAAAAAC 60.143 45.833 0.00 0.00 41.61 2.43
2832 3024 3.998341 GCTACCACATCACGGAGTAAAAA 59.002 43.478 0.00 0.00 41.61 1.94
2834 3026 2.829720 AGCTACCACATCACGGAGTAAA 59.170 45.455 0.00 0.00 41.61 2.01
2836 3028 2.139323 AGCTACCACATCACGGAGTA 57.861 50.000 0.00 0.00 41.61 2.59
2838 3030 1.269309 GCTAGCTACCACATCACGGAG 60.269 57.143 7.70 0.00 0.00 4.63
2839 3031 0.744874 GCTAGCTACCACATCACGGA 59.255 55.000 7.70 0.00 0.00 4.69
2840 3032 0.747255 AGCTAGCTACCACATCACGG 59.253 55.000 17.69 0.00 0.00 4.94
2841 3033 3.001395 GTAGCTAGCTACCACATCACG 57.999 52.381 35.21 0.00 42.11 4.35
2874 3072 4.698780 ACCAACGCCTATAAGGAAAGAAAC 59.301 41.667 0.00 0.00 37.67 2.78
2886 3084 3.008704 ACCTAAGAACAACCAACGCCTAT 59.991 43.478 0.00 0.00 0.00 2.57
2893 3091 5.010933 TCAAACACACCTAAGAACAACCAA 58.989 37.500 0.00 0.00 0.00 3.67
3044 3242 5.177326 AGAATTCAAGCAAAAACAAGCACA 58.823 33.333 8.44 0.00 0.00 4.57
3045 3243 5.723492 AGAATTCAAGCAAAAACAAGCAC 57.277 34.783 8.44 0.00 0.00 4.40
3067 3271 4.386711 GAAACGGGGAAGAAGAAGAAGAA 58.613 43.478 0.00 0.00 0.00 2.52
3134 3371 1.477740 CCGGCAGAGTATCCTCTCAGA 60.478 57.143 0.00 0.00 45.08 3.27
3158 3395 5.300969 TCAAATCCGCAGAGATTTTTCTG 57.699 39.130 4.15 0.00 42.46 3.02
3180 3417 3.382832 CCTCGCCACCGTCTCCTT 61.383 66.667 0.00 0.00 35.54 3.36
3340 3582 1.207329 GTTCCTGGCTCTTCCGTATGT 59.793 52.381 0.00 0.00 37.80 2.29
3414 3656 3.615811 AGGGGCACAGAGAGGGGA 61.616 66.667 0.00 0.00 0.00 4.81
3416 3658 2.608988 ACAGGGGCACAGAGAGGG 60.609 66.667 0.00 0.00 0.00 4.30
3422 3664 2.033141 CCACAGACAGGGGCACAG 59.967 66.667 0.00 0.00 30.89 3.66
3465 3708 2.158652 TCTCAACCCTAGATCGGTCGAT 60.159 50.000 5.49 5.49 37.59 3.59
3466 3709 1.211212 TCTCAACCCTAGATCGGTCGA 59.789 52.381 0.00 0.00 31.48 4.20
3570 3818 1.410517 GCATGGGAGACGAGATGAAGA 59.589 52.381 0.00 0.00 0.00 2.87
3574 3822 2.681706 GTATGCATGGGAGACGAGATG 58.318 52.381 10.16 0.00 0.00 2.90
3717 3968 1.953686 AGCTAGATCCAGAGCGAACTC 59.046 52.381 0.00 0.00 43.72 3.01
3718 3969 1.953686 GAGCTAGATCCAGAGCGAACT 59.046 52.381 0.00 0.00 43.72 3.01
3720 3971 1.323412 GGAGCTAGATCCAGAGCGAA 58.677 55.000 22.23 0.00 43.72 4.70
3806 4074 4.386049 CAGCACTTGTAGTACTAGTTGTGC 59.614 45.833 28.32 28.32 46.55 4.57
3812 4080 3.688185 TCGACCAGCACTTGTAGTACTAG 59.312 47.826 1.87 9.81 0.00 2.57
3814 4082 2.511659 TCGACCAGCACTTGTAGTACT 58.488 47.619 0.00 0.00 0.00 2.73
3819 4087 3.261580 CATGATTCGACCAGCACTTGTA 58.738 45.455 0.00 0.00 0.00 2.41
3821 4089 1.399440 CCATGATTCGACCAGCACTTG 59.601 52.381 0.00 0.00 0.00 3.16
3822 4090 1.742761 CCATGATTCGACCAGCACTT 58.257 50.000 0.00 0.00 0.00 3.16
3823 4091 0.745845 GCCATGATTCGACCAGCACT 60.746 55.000 0.00 0.00 0.00 4.40
3824 4092 1.718757 GGCCATGATTCGACCAGCAC 61.719 60.000 0.00 0.00 0.00 4.40
3827 4095 1.889105 CCGGCCATGATTCGACCAG 60.889 63.158 2.24 0.00 0.00 4.00
3831 4103 1.760480 TCCTCCGGCCATGATTCGA 60.760 57.895 2.24 0.00 0.00 3.71
3911 4196 3.066380 GCTCGCCCACATTTTCAATTTT 58.934 40.909 0.00 0.00 0.00 1.82
3995 4287 4.927782 GTGTGTGCGTGAGGGGCA 62.928 66.667 0.00 0.00 38.25 5.36
4041 4347 1.363443 GAGGCGAGAGAGGCAGATG 59.637 63.158 0.00 0.00 39.37 2.90
4042 4348 2.192861 CGAGGCGAGAGAGGCAGAT 61.193 63.158 0.00 0.00 39.37 2.90


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

AutoCloner maintained by Alex Coulton.