Multiple sequence alignment - TraesCS4D01G092300

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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 TraesCS4D01G092300 chr4D 100.000 2552 0 0 1 2552 67276021 67273470 0.000000e+00 4713
1 TraesCS4D01G092300 chr4D 88.921 686 58 12 875 1549 67244832 67244154 0.000000e+00 830
2 TraesCS4D01G092300 chr4B 89.134 1675 75 41 371 1999 99266454 99264841 0.000000e+00 1986
3 TraesCS4D01G092300 chr4B 89.949 587 40 10 988 1566 99082143 99081568 0.000000e+00 739
4 TraesCS4D01G092300 chr4B 90.667 300 23 1 44 343 99266734 99266440 6.620000e-106 394
5 TraesCS4D01G092300 chr4B 80.374 428 69 11 2138 2552 592185388 592185813 6.860000e-81 311
6 TraesCS4D01G092300 chr4A 92.157 1428 61 15 371 1776 516370709 516369311 0.000000e+00 1969
7 TraesCS4D01G092300 chr4A 89.067 686 56 13 875 1548 516355530 516354852 0.000000e+00 833
8 TraesCS4D01G092300 chr4A 85.227 440 56 6 2114 2552 516368430 516367999 6.480000e-121 444
9 TraesCS4D01G092300 chr4A 83.389 301 41 7 2132 2424 686533754 686533455 1.160000e-68 270
10 TraesCS4D01G092300 chr4A 82.803 157 13 6 1870 2012 516368640 516368484 7.410000e-26 128
11 TraesCS4D01G092300 chr4A 90.426 94 4 1 193 286 516370811 516370723 4.460000e-23 119
12 TraesCS4D01G092300 chr1D 83.488 430 54 9 2138 2552 288837814 288838241 3.980000e-103 385
13 TraesCS4D01G092300 chr2D 83.218 435 51 13 2138 2552 625195733 625195301 1.850000e-101 379
14 TraesCS4D01G092300 chr5D 83.005 406 59 7 2138 2535 373954635 373954232 2.410000e-95 359
15 TraesCS4D01G092300 chr5D 83.283 329 43 8 2138 2455 384210246 384210573 2.480000e-75 292
16 TraesCS4D01G092300 chr5D 84.333 300 36 8 2138 2428 470050042 470050339 1.490000e-72 283
17 TraesCS4D01G092300 chr5D 83.710 221 24 8 2342 2552 360753052 360752834 5.570000e-47 198
18 TraesCS4D01G092300 chr3D 82.326 430 61 9 2138 2552 91383974 91383545 2.410000e-95 359
19 TraesCS4D01G092300 chr3D 81.900 442 52 15 2138 2552 300932613 300932173 5.230000e-92 348
20 TraesCS4D01G092300 chrUn 80.742 431 58 14 2138 2552 74563147 74562726 1.910000e-81 313
21 TraesCS4D01G092300 chr2A 77.934 426 71 16 2139 2552 691179682 691180096 7.050000e-61 244
22 TraesCS4D01G092300 chr7B 78.701 385 51 15 2196 2552 455996666 455997047 7.100000e-56 228


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 TraesCS4D01G092300 chr4D 67273470 67276021 2551 True 4713 4713 100.00000 1 2552 1 chr4D.!!$R2 2551
1 TraesCS4D01G092300 chr4D 67244154 67244832 678 True 830 830 88.92100 875 1549 1 chr4D.!!$R1 674
2 TraesCS4D01G092300 chr4B 99264841 99266734 1893 True 1190 1986 89.90050 44 1999 2 chr4B.!!$R2 1955
3 TraesCS4D01G092300 chr4B 99081568 99082143 575 True 739 739 89.94900 988 1566 1 chr4B.!!$R1 578
4 TraesCS4D01G092300 chr4A 516354852 516355530 678 True 833 833 89.06700 875 1548 1 chr4A.!!$R1 673
5 TraesCS4D01G092300 chr4A 516367999 516370811 2812 True 665 1969 87.65325 193 2552 4 chr4A.!!$R3 2359

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
352 353 0.033228 CCTTGCAATCCCACGCAAAA 59.967 50.0 0.0 0.0 46.73 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2698 0.107654 GGAGGTGATTTGAGGGTCCG 60.108 60.0 0.0 0.0 0.0 4.79 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
62 63 2.270352 TACAACCAGGAGCCAAAGTG 57.730 50.000 0.00 0.00 0.00 3.16
64 65 0.954452 CAACCAGGAGCCAAAGTGTC 59.046 55.000 0.00 0.00 0.00 3.67
66 67 0.398318 ACCAGGAGCCAAAGTGTCTC 59.602 55.000 0.00 0.00 0.00 3.36
67 68 0.322008 CCAGGAGCCAAAGTGTCTCC 60.322 60.000 0.00 0.00 45.11 3.71
119 120 7.154656 AGAAATGTGCCAAGATTAGTTTTTCC 58.845 34.615 0.00 0.00 0.00 3.13
131 132 8.797266 AGATTAGTTTTTCCGTTCACAAAATC 57.203 30.769 0.00 0.00 0.00 2.17
142 143 6.432783 TCCGTTCACAAAATCCATCTACAAAT 59.567 34.615 0.00 0.00 0.00 2.32
174 175 2.945315 GTGATAGCACACGGACGAG 58.055 57.895 6.17 0.00 44.51 4.18
176 177 1.313091 TGATAGCACACGGACGAGCT 61.313 55.000 13.20 13.20 40.92 4.09
191 192 4.496673 GGACGAGCTATCAACTCAGTACTG 60.497 50.000 17.17 17.17 33.58 2.74
248 249 0.108138 CCGTTGGGGTTGCTCTAGAG 60.108 60.000 15.85 15.85 0.00 2.43
260 261 1.377536 CTCTAGAGCAAAGGCAAGGC 58.622 55.000 6.86 0.00 44.61 4.35
261 262 0.692476 TCTAGAGCAAAGGCAAGGCA 59.308 50.000 0.00 0.00 44.61 4.75
275 276 0.605589 AAGGCAAGGAACGGTACTGC 60.606 55.000 0.23 0.00 0.00 4.40
320 321 1.806623 GCATAGACAGCAGGTTACCGG 60.807 57.143 0.00 0.00 0.00 5.28
331 332 0.323999 GGTTACCGGCCCTTCCAAAT 60.324 55.000 0.00 0.00 34.01 2.32
342 343 2.624636 CCTTCCAAATGCCTTGCAATC 58.375 47.619 0.00 0.00 43.62 2.67
343 344 2.624636 CTTCCAAATGCCTTGCAATCC 58.375 47.619 0.00 0.00 43.62 3.01
344 345 0.903942 TCCAAATGCCTTGCAATCCC 59.096 50.000 0.00 0.00 43.62 3.85
345 346 0.614294 CCAAATGCCTTGCAATCCCA 59.386 50.000 0.00 0.00 43.62 4.37
346 347 1.676615 CCAAATGCCTTGCAATCCCAC 60.677 52.381 0.00 0.00 43.62 4.61
347 348 0.247185 AAATGCCTTGCAATCCCACG 59.753 50.000 0.00 0.00 43.62 4.94
348 349 2.229690 AATGCCTTGCAATCCCACGC 62.230 55.000 0.00 0.00 43.62 5.34
349 350 3.372730 GCCTTGCAATCCCACGCA 61.373 61.111 0.00 0.00 36.05 5.24
350 351 2.929903 GCCTTGCAATCCCACGCAA 61.930 57.895 0.00 0.00 45.45 4.85
351 352 1.664873 CCTTGCAATCCCACGCAAA 59.335 52.632 0.00 0.00 46.73 3.68
352 353 0.033228 CCTTGCAATCCCACGCAAAA 59.967 50.000 0.00 0.00 46.73 2.44
353 354 1.539929 CCTTGCAATCCCACGCAAAAA 60.540 47.619 0.00 0.00 46.73 1.94
354 355 2.415776 CTTGCAATCCCACGCAAAAAT 58.584 42.857 0.00 0.00 46.73 1.82
355 356 3.583806 CTTGCAATCCCACGCAAAAATA 58.416 40.909 0.00 0.00 46.73 1.40
356 357 3.667497 TGCAATCCCACGCAAAAATAA 57.333 38.095 0.00 0.00 34.59 1.40
357 358 3.995199 TGCAATCCCACGCAAAAATAAA 58.005 36.364 0.00 0.00 34.59 1.40
358 359 4.380531 TGCAATCCCACGCAAAAATAAAA 58.619 34.783 0.00 0.00 34.59 1.52
359 360 4.999950 TGCAATCCCACGCAAAAATAAAAT 59.000 33.333 0.00 0.00 34.59 1.82
360 361 6.166279 TGCAATCCCACGCAAAAATAAAATA 58.834 32.000 0.00 0.00 34.59 1.40
361 362 6.650807 TGCAATCCCACGCAAAAATAAAATAA 59.349 30.769 0.00 0.00 34.59 1.40
362 363 7.173218 TGCAATCCCACGCAAAAATAAAATAAA 59.827 29.630 0.00 0.00 34.59 1.40
363 364 8.017946 GCAATCCCACGCAAAAATAAAATAAAA 58.982 29.630 0.00 0.00 0.00 1.52
433 434 4.308458 GCCCCAACCCAAAACCGC 62.308 66.667 0.00 0.00 0.00 5.68
435 436 2.733945 CCCAACCCAAAACCGCAG 59.266 61.111 0.00 0.00 0.00 5.18
507 508 0.465460 TTGTTGCCTGTCCTGTCACC 60.465 55.000 0.00 0.00 0.00 4.02
508 509 1.344953 TGTTGCCTGTCCTGTCACCT 61.345 55.000 0.00 0.00 0.00 4.00
513 514 1.271597 GCCTGTCCTGTCACCTTCAAT 60.272 52.381 0.00 0.00 0.00 2.57
545 546 6.196724 CGGTCTCGTTCAGTTTATCAGTTATC 59.803 42.308 0.00 0.00 0.00 1.75
569 570 2.569404 ACCATCTCTTTCACCAGTCTCC 59.431 50.000 0.00 0.00 0.00 3.71
570 571 2.836981 CCATCTCTTTCACCAGTCTCCT 59.163 50.000 0.00 0.00 0.00 3.69
628 629 4.378770 CCAGAGAATTGATGGTTCGTGTTG 60.379 45.833 0.00 0.00 0.00 3.33
629 630 4.452114 CAGAGAATTGATGGTTCGTGTTGA 59.548 41.667 0.00 0.00 0.00 3.18
630 631 4.692625 AGAGAATTGATGGTTCGTGTTGAG 59.307 41.667 0.00 0.00 0.00 3.02
788 811 4.505922 TGCAATGCAAAGAAAAAGTTACCG 59.494 37.500 5.01 0.00 34.76 4.02
838 865 4.758251 CCCACATGCGCACCGAGA 62.758 66.667 14.90 0.00 0.00 4.04
843 870 4.063967 ATGCGCACCGAGACCGAA 62.064 61.111 14.90 0.00 38.22 4.30
844 871 3.371097 ATGCGCACCGAGACCGAAT 62.371 57.895 14.90 0.00 38.22 3.34
845 872 3.255379 GCGCACCGAGACCGAATC 61.255 66.667 0.30 0.00 38.22 2.52
846 873 2.949678 CGCACCGAGACCGAATCG 60.950 66.667 0.00 0.00 39.86 3.34
847 874 2.488355 GCACCGAGACCGAATCGA 59.512 61.111 3.36 0.00 42.76 3.59
963 991 3.799755 CGCTCCCCTTTTTCGCCG 61.800 66.667 0.00 0.00 0.00 6.46
1659 1694 1.190763 CAGATTTGCTGCGTTTGTTGC 59.809 47.619 0.00 0.00 37.90 4.17
1737 1772 0.105964 TGCTAACTGGTGCGTCAACT 59.894 50.000 0.00 0.00 0.00 3.16
1806 2441 4.771590 GATTGCTGAAATCAGTCAACCA 57.228 40.909 16.76 3.90 45.45 3.67
1807 2442 3.988379 TTGCTGAAATCAGTCAACCAC 57.012 42.857 11.77 0.00 45.45 4.16
1808 2443 2.929641 TGCTGAAATCAGTCAACCACA 58.070 42.857 11.77 0.00 45.45 4.17
1833 2468 3.278574 TGTGTGAGAAAAAGGGTCAGTG 58.721 45.455 0.00 0.00 0.00 3.66
1836 2471 3.138283 TGTGAGAAAAAGGGTCAGTGGAT 59.862 43.478 0.00 0.00 0.00 3.41
1847 2482 4.105697 AGGGTCAGTGGATAAAGGTTCAAA 59.894 41.667 0.00 0.00 0.00 2.69
1962 2634 2.591715 GCGTTGTGTCACTGGGCT 60.592 61.111 4.27 0.00 0.00 5.19
2006 2698 3.723348 GTGACGGCTTCCCAACGC 61.723 66.667 0.00 0.00 0.00 4.84
2024 2716 0.744771 GCGGACCCTCAAATCACCTC 60.745 60.000 0.00 0.00 0.00 3.85
2025 2717 0.107654 CGGACCCTCAAATCACCTCC 60.108 60.000 0.00 0.00 0.00 4.30
2032 2724 2.076863 CTCAAATCACCTCCAACCGTC 58.923 52.381 0.00 0.00 0.00 4.79
2035 2727 1.189524 AATCACCTCCAACCGTCCGA 61.190 55.000 0.00 0.00 0.00 4.55
2036 2728 0.976073 ATCACCTCCAACCGTCCGAT 60.976 55.000 0.00 0.00 0.00 4.18
2040 2732 1.516386 CTCCAACCGTCCGATCGTG 60.516 63.158 15.09 5.81 0.00 4.35
2042 2734 2.092291 CCAACCGTCCGATCGTGTG 61.092 63.158 15.09 2.52 0.00 3.82
2043 2735 2.092291 CAACCGTCCGATCGTGTGG 61.092 63.158 15.09 14.05 0.00 4.17
2044 2736 2.567497 AACCGTCCGATCGTGTGGT 61.567 57.895 15.09 14.70 0.00 4.16
2045 2737 1.243342 AACCGTCCGATCGTGTGGTA 61.243 55.000 18.81 0.00 0.00 3.25
2046 2738 1.226491 CCGTCCGATCGTGTGGTAC 60.226 63.158 15.09 1.62 0.00 3.34
2059 2751 4.119442 GTGTGGTACGGACATATTCTGT 57.881 45.455 0.00 5.20 46.38 3.41
2071 2763 4.454678 ACATATTCTGTCATCCAATGCGT 58.545 39.130 0.00 0.00 29.94 5.24
2072 2764 5.610398 ACATATTCTGTCATCCAATGCGTA 58.390 37.500 0.00 0.00 29.94 4.42
2073 2765 6.233434 ACATATTCTGTCATCCAATGCGTAT 58.767 36.000 0.00 0.00 29.94 3.06
2074 2766 6.712095 ACATATTCTGTCATCCAATGCGTATT 59.288 34.615 0.00 0.00 29.94 1.89
2075 2767 7.229306 ACATATTCTGTCATCCAATGCGTATTT 59.771 33.333 0.00 0.00 29.94 1.40
2076 2768 4.880886 TCTGTCATCCAATGCGTATTTG 57.119 40.909 0.00 0.00 0.00 2.32
2077 2769 4.260985 TCTGTCATCCAATGCGTATTTGT 58.739 39.130 0.00 0.00 0.00 2.83
2078 2770 5.423886 TCTGTCATCCAATGCGTATTTGTA 58.576 37.500 0.00 0.00 0.00 2.41
2079 2771 6.054941 TCTGTCATCCAATGCGTATTTGTAT 58.945 36.000 0.00 0.00 0.00 2.29
2080 2772 6.542005 TCTGTCATCCAATGCGTATTTGTATT 59.458 34.615 0.00 0.00 0.00 1.89
2081 2773 6.493978 TGTCATCCAATGCGTATTTGTATTG 58.506 36.000 0.00 0.00 40.36 1.90
2087 2779 4.552166 ATGCGTATTTGTATTGGTCTGC 57.448 40.909 0.00 0.00 0.00 4.26
2088 2780 3.605634 TGCGTATTTGTATTGGTCTGCT 58.394 40.909 0.00 0.00 0.00 4.24
2089 2781 3.621268 TGCGTATTTGTATTGGTCTGCTC 59.379 43.478 0.00 0.00 0.00 4.26
2090 2782 3.302480 GCGTATTTGTATTGGTCTGCTCG 60.302 47.826 0.00 0.00 0.00 5.03
2091 2783 4.109766 CGTATTTGTATTGGTCTGCTCGA 58.890 43.478 0.00 0.00 0.00 4.04
2092 2784 4.026804 CGTATTTGTATTGGTCTGCTCGAC 60.027 45.833 0.00 0.00 42.07 4.20
2093 2785 1.990799 TTGTATTGGTCTGCTCGACG 58.009 50.000 0.00 0.00 43.79 5.12
2094 2786 0.172578 TGTATTGGTCTGCTCGACGG 59.827 55.000 0.00 0.00 43.79 4.79
2095 2787 0.172803 GTATTGGTCTGCTCGACGGT 59.827 55.000 0.00 0.00 43.79 4.83
2096 2788 0.454600 TATTGGTCTGCTCGACGGTC 59.545 55.000 0.00 0.00 43.79 4.79
2097 2789 2.227089 ATTGGTCTGCTCGACGGTCC 62.227 60.000 1.91 0.00 43.79 4.46
2098 2790 3.371063 GGTCTGCTCGACGGTCCA 61.371 66.667 1.91 0.00 43.79 4.02
2099 2791 2.179517 GTCTGCTCGACGGTCCAG 59.820 66.667 1.91 0.00 32.04 3.86
2100 2792 2.033602 TCTGCTCGACGGTCCAGA 59.966 61.111 6.96 8.91 32.35 3.86
2101 2793 1.378646 TCTGCTCGACGGTCCAGAT 60.379 57.895 6.96 0.00 30.00 2.90
2102 2794 1.226802 CTGCTCGACGGTCCAGATG 60.227 63.158 6.96 0.00 0.00 2.90
2103 2795 2.583593 GCTCGACGGTCCAGATGC 60.584 66.667 6.96 0.00 0.00 3.91
2104 2796 2.885113 CTCGACGGTCCAGATGCA 59.115 61.111 1.91 0.00 0.00 3.96
2105 2797 1.439228 CTCGACGGTCCAGATGCAT 59.561 57.895 0.00 0.00 0.00 3.96
2106 2798 0.179100 CTCGACGGTCCAGATGCATT 60.179 55.000 0.00 0.00 0.00 3.56
2107 2799 0.249120 TCGACGGTCCAGATGCATTT 59.751 50.000 0.00 0.00 0.00 2.32
2108 2800 1.086696 CGACGGTCCAGATGCATTTT 58.913 50.000 0.00 0.00 0.00 1.82
2109 2801 1.468520 CGACGGTCCAGATGCATTTTT 59.531 47.619 0.00 0.00 0.00 1.94
2152 2844 6.534475 ACTATAAACATCTACAACCGGACA 57.466 37.500 9.46 0.00 0.00 4.02
2153 2845 6.335777 ACTATAAACATCTACAACCGGACAC 58.664 40.000 9.46 0.00 0.00 3.67
2154 2846 2.467566 AACATCTACAACCGGACACC 57.532 50.000 9.46 0.00 0.00 4.16
2155 2847 1.640917 ACATCTACAACCGGACACCT 58.359 50.000 9.46 0.00 0.00 4.00
2156 2848 1.549170 ACATCTACAACCGGACACCTC 59.451 52.381 9.46 0.00 0.00 3.85
2157 2849 1.548719 CATCTACAACCGGACACCTCA 59.451 52.381 9.46 0.00 0.00 3.86
2158 2850 1.707106 TCTACAACCGGACACCTCAA 58.293 50.000 9.46 0.00 0.00 3.02
2159 2851 2.040939 TCTACAACCGGACACCTCAAA 58.959 47.619 9.46 0.00 0.00 2.69
2160 2852 2.140717 CTACAACCGGACACCTCAAAC 58.859 52.381 9.46 0.00 0.00 2.93
2161 2853 0.464916 ACAACCGGACACCTCAAACC 60.465 55.000 9.46 0.00 0.00 3.27
2162 2854 1.149854 AACCGGACACCTCAAACCC 59.850 57.895 9.46 0.00 0.00 4.11
2163 2855 1.350310 AACCGGACACCTCAAACCCT 61.350 55.000 9.46 0.00 0.00 4.34
2171 2863 2.230660 CACCTCAAACCCTCCTCAAAC 58.769 52.381 0.00 0.00 0.00 2.93
2201 2897 0.814010 GCCGCTTATTGTCCGGTCAT 60.814 55.000 1.21 0.00 43.70 3.06
2224 2920 0.608035 TTTTGACCCAGATGGACGCC 60.608 55.000 0.00 0.00 37.39 5.68
2242 2938 1.083015 CTCAAACGGGCGTCAAACG 60.083 57.895 0.00 0.00 45.88 3.60
2273 2969 2.109181 GCACCCCTCGTATCCAGC 59.891 66.667 0.00 0.00 0.00 4.85
2295 2991 2.446435 CAAATATGGGGCGGATAAGGG 58.554 52.381 0.00 0.00 0.00 3.95
2304 3001 2.841044 GGATAAGGGGCGTCCGGA 60.841 66.667 0.00 0.00 41.52 5.14
2356 3053 2.076184 CCCACCCGACCCCACATAT 61.076 63.158 0.00 0.00 0.00 1.78
2374 3071 0.608640 ATATTCGTCCCCATCCGCTC 59.391 55.000 0.00 0.00 0.00 5.03
2408 3105 2.564947 CCTAGCCACTTCACTTCACTCT 59.435 50.000 0.00 0.00 0.00 3.24
2409 3106 2.829741 AGCCACTTCACTTCACTCTC 57.170 50.000 0.00 0.00 0.00 3.20
2422 3119 1.127343 CACTCTCCTCCATTCCCCTC 58.873 60.000 0.00 0.00 0.00 4.30
2423 3120 0.030603 ACTCTCCTCCATTCCCCTCC 60.031 60.000 0.00 0.00 0.00 4.30
2425 3122 2.768344 TCCTCCATTCCCCTCCGC 60.768 66.667 0.00 0.00 0.00 5.54
2432 3129 0.611896 CATTCCCCTCCGCCAGTTTT 60.612 55.000 0.00 0.00 0.00 2.43
2455 3152 4.802051 TTCTCCGGCATGGCAGGC 62.802 66.667 17.03 17.03 43.33 4.85
2467 3164 4.615815 GCAGGCAGCGGATCGGAT 62.616 66.667 4.16 0.00 0.00 4.18
2470 3167 2.136878 AGGCAGCGGATCGGATTCT 61.137 57.895 4.16 0.00 0.00 2.40
2480 3177 2.202932 CGGATTCTGGCCAGTCCG 60.203 66.667 36.41 36.41 46.26 4.79
2481 3178 2.190578 GGATTCTGGCCAGTCCGG 59.809 66.667 31.58 7.72 42.90 5.14
2486 3183 4.227134 CTGGCCAGTCCGGATCCG 62.227 72.222 27.65 27.65 44.37 4.18
2491 3188 2.194212 CCAGTCCGGATCCGTCGAT 61.194 63.158 31.22 12.53 36.56 3.59
2493 3190 0.595053 CAGTCCGGATCCGTCGATTG 60.595 60.000 31.22 23.26 37.81 2.67
2504 3201 0.750850 CGTCGATTGGGGTGTATCCT 59.249 55.000 0.00 0.00 36.25 3.24
2527 3224 0.482446 TGGGTTTGAGGAGGCAATGT 59.518 50.000 0.00 0.00 0.00 2.71
2533 3230 0.615331 TGAGGAGGCAATGTCAGTCC 59.385 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.955660 CACTTTGGCTCCTGGTTGTAAA 59.044 45.455 0.00 0.00 0.00 2.01
42 43 2.092103 ACACTTTGGCTCCTGGTTGTAA 60.092 45.455 0.00 0.00 0.00 2.41
48 49 3.239861 GAGACACTTTGGCTCCTGG 57.760 57.895 0.00 0.00 46.78 4.45
67 68 2.715763 TAGGGCTTCTATGTAGGGGG 57.284 55.000 0.00 0.00 0.00 5.40
78 79 7.094592 GGCACATTTCTAGATTATTAGGGCTTC 60.095 40.741 0.00 0.00 0.00 3.86
81 82 6.003950 TGGCACATTTCTAGATTATTAGGGC 58.996 40.000 0.00 0.00 0.00 5.19
113 114 6.155475 AGATGGATTTTGTGAACGGAAAAA 57.845 33.333 0.00 0.00 0.00 1.94
119 120 9.225201 CATATTTGTAGATGGATTTTGTGAACG 57.775 33.333 0.00 0.00 0.00 3.95
142 143 4.511454 GTGCTATCACGAGGCAAATTCATA 59.489 41.667 0.00 0.00 37.73 2.15
148 149 1.438651 GTGTGCTATCACGAGGCAAA 58.561 50.000 0.00 0.00 46.01 3.68
174 175 3.526931 TGGCAGTACTGAGTTGATAGC 57.473 47.619 27.08 7.27 0.00 2.97
176 177 5.604565 CATGATGGCAGTACTGAGTTGATA 58.395 41.667 27.08 6.15 0.00 2.15
191 192 1.069432 CAGCTCATAACGCATGATGGC 60.069 52.381 0.00 3.08 42.82 4.40
248 249 0.601046 GTTCCTTGCCTTGCCTTTGC 60.601 55.000 0.00 0.00 38.26 3.68
257 258 1.003718 GCAGTACCGTTCCTTGCCT 60.004 57.895 0.00 0.00 0.00 4.75
258 259 1.298859 CTGCAGTACCGTTCCTTGCC 61.299 60.000 5.25 0.00 33.98 4.52
259 260 1.912371 GCTGCAGTACCGTTCCTTGC 61.912 60.000 16.64 0.00 35.42 4.01
260 261 0.602638 TGCTGCAGTACCGTTCCTTG 60.603 55.000 16.64 0.00 0.00 3.61
261 262 0.320771 CTGCTGCAGTACCGTTCCTT 60.321 55.000 21.21 0.00 0.00 3.36
275 276 2.558286 CCAACCACACCTGCTGCTG 61.558 63.158 0.00 0.00 0.00 4.41
320 321 1.078918 GCAAGGCATTTGGAAGGGC 60.079 57.895 2.86 0.00 37.26 5.19
331 332 3.372730 GCGTGGGATTGCAAGGCA 61.373 61.111 4.94 0.00 36.47 4.75
359 360 9.646427 ACGATTGCAAGGCTTTATTTTATTTTA 57.354 25.926 4.94 0.00 0.00 1.52
360 361 8.442384 CACGATTGCAAGGCTTTATTTTATTTT 58.558 29.630 4.94 0.00 0.00 1.82
361 362 7.602265 ACACGATTGCAAGGCTTTATTTTATTT 59.398 29.630 4.94 0.00 0.00 1.40
362 363 7.096551 ACACGATTGCAAGGCTTTATTTTATT 58.903 30.769 4.94 0.00 0.00 1.40
363 364 6.630071 ACACGATTGCAAGGCTTTATTTTAT 58.370 32.000 4.94 0.00 0.00 1.40
364 365 6.019779 ACACGATTGCAAGGCTTTATTTTA 57.980 33.333 4.94 0.00 0.00 1.52
365 366 4.881920 ACACGATTGCAAGGCTTTATTTT 58.118 34.783 4.94 0.00 0.00 1.82
366 367 4.519540 ACACGATTGCAAGGCTTTATTT 57.480 36.364 4.94 0.00 0.00 1.40
367 368 4.438744 GCTACACGATTGCAAGGCTTTATT 60.439 41.667 4.94 0.00 0.00 1.40
368 369 3.065371 GCTACACGATTGCAAGGCTTTAT 59.935 43.478 4.94 0.00 0.00 1.40
369 370 2.418628 GCTACACGATTGCAAGGCTTTA 59.581 45.455 4.94 0.00 0.00 1.85
370 371 1.200020 GCTACACGATTGCAAGGCTTT 59.800 47.619 4.94 0.00 0.00 3.51
371 372 0.804989 GCTACACGATTGCAAGGCTT 59.195 50.000 4.94 0.00 0.00 4.35
372 373 0.036010 AGCTACACGATTGCAAGGCT 60.036 50.000 4.94 3.09 0.00 4.58
373 374 0.097674 CAGCTACACGATTGCAAGGC 59.902 55.000 4.94 0.00 0.00 4.35
374 375 1.725641 TCAGCTACACGATTGCAAGG 58.274 50.000 4.94 1.62 0.00 3.61
375 376 3.371898 TGATTCAGCTACACGATTGCAAG 59.628 43.478 4.94 0.00 0.00 4.01
376 377 3.333804 TGATTCAGCTACACGATTGCAA 58.666 40.909 0.00 0.00 0.00 4.08
377 378 2.971307 TGATTCAGCTACACGATTGCA 58.029 42.857 0.00 0.00 0.00 4.08
378 379 3.806521 AGATGATTCAGCTACACGATTGC 59.193 43.478 1.83 0.00 0.00 3.56
379 380 4.210746 CCAGATGATTCAGCTACACGATTG 59.789 45.833 3.75 0.00 0.00 2.67
380 381 4.141846 ACCAGATGATTCAGCTACACGATT 60.142 41.667 3.75 0.00 0.00 3.34
381 382 3.386078 ACCAGATGATTCAGCTACACGAT 59.614 43.478 3.75 0.00 0.00 3.73
382 383 2.760650 ACCAGATGATTCAGCTACACGA 59.239 45.455 3.75 0.00 0.00 4.35
433 434 1.670406 GGTGAGCTGCTGTGTCCTG 60.670 63.158 7.01 0.00 0.00 3.86
435 436 0.390472 GTAGGTGAGCTGCTGTGTCC 60.390 60.000 7.01 3.91 0.00 4.02
507 508 2.263077 CGAGACCGACTTGGATTGAAG 58.737 52.381 0.00 0.00 42.00 3.02
508 509 1.616865 ACGAGACCGACTTGGATTGAA 59.383 47.619 0.00 0.00 42.00 2.69
513 514 0.596577 CTGAACGAGACCGACTTGGA 59.403 55.000 0.00 0.00 42.00 3.53
545 546 3.070018 GACTGGTGAAAGAGATGGTGTG 58.930 50.000 0.00 0.00 0.00 3.82
622 623 0.992072 CACGCATACTCCTCAACACG 59.008 55.000 0.00 0.00 0.00 4.49
628 629 1.068250 GAGGCCACGCATACTCCTC 59.932 63.158 5.01 0.00 36.86 3.71
629 630 1.685765 TGAGGCCACGCATACTCCT 60.686 57.895 5.01 0.00 0.00 3.69
630 631 1.521681 GTGAGGCCACGCATACTCC 60.522 63.158 5.01 0.00 33.10 3.85
676 694 1.962092 GCGGTGCGAGCAAAACGATA 61.962 55.000 17.69 0.00 34.19 2.92
680 698 2.725815 GTGCGGTGCGAGCAAAAC 60.726 61.111 0.00 0.00 46.97 2.43
717 735 7.504574 CCTCCTTTCTCTTTGGGTTTAGTTAAA 59.495 37.037 0.00 0.00 0.00 1.52
718 736 7.002276 CCTCCTTTCTCTTTGGGTTTAGTTAA 58.998 38.462 0.00 0.00 0.00 2.01
788 811 3.531207 GGTCGGCCCGGTAGGTAC 61.531 72.222 1.90 0.00 38.26 3.34
808 835 3.782443 GTGGGGCAGGTACCTCCG 61.782 72.222 12.84 2.66 41.99 4.63
837 864 1.810030 GTGGCCACTCGATTCGGTC 60.810 63.158 29.12 0.00 0.00 4.79
838 865 2.264794 GTGGCCACTCGATTCGGT 59.735 61.111 29.12 0.33 0.00 4.69
841 868 1.519455 CTCGGTGGCCACTCGATTC 60.519 63.158 34.38 19.69 34.98 2.52
843 870 2.362503 TCTCGGTGGCCACTCGAT 60.363 61.111 34.38 0.00 34.98 3.59
844 871 3.062466 CTCTCGGTGGCCACTCGA 61.062 66.667 33.01 33.01 34.56 4.04
845 872 3.057547 CTCTCTCGGTGGCCACTCG 62.058 68.421 33.91 31.49 0.00 4.18
846 873 1.040339 ATCTCTCTCGGTGGCCACTC 61.040 60.000 33.91 22.61 0.00 3.51
847 874 0.259065 TATCTCTCTCGGTGGCCACT 59.741 55.000 33.91 14.42 0.00 4.00
914 941 3.181475 GGCGTATTTGAGGAGATGTCAGA 60.181 47.826 0.00 0.00 0.00 3.27
963 991 2.125106 CTGCGAGCCCTGGGTAAC 60.125 66.667 15.56 5.31 0.00 2.50
986 1015 1.826921 GCCATGGCTGGTGGATCTG 60.827 63.158 29.98 0.00 45.10 2.90
1658 1693 1.149174 ACCCATCATCCATCACGGC 59.851 57.895 0.00 0.00 33.14 5.68
1659 1694 0.181114 ACACCCATCATCCATCACGG 59.819 55.000 0.00 0.00 0.00 4.94
1737 1772 5.420421 TCGATGCAAATTATCCTCCCAAAAA 59.580 36.000 0.00 0.00 0.00 1.94
1772 1808 7.924947 TGATTTCAGCAATCACAACAATTAACA 59.075 29.630 0.00 0.00 45.45 2.41
1773 1809 8.296799 TGATTTCAGCAATCACAACAATTAAC 57.703 30.769 0.00 0.00 45.45 2.01
1774 1810 8.143193 ACTGATTTCAGCAATCACAACAATTAA 58.857 29.630 7.48 0.00 45.45 1.40
1775 1811 7.660112 ACTGATTTCAGCAATCACAACAATTA 58.340 30.769 7.48 0.00 45.45 1.40
1776 1812 6.518493 ACTGATTTCAGCAATCACAACAATT 58.482 32.000 7.48 0.00 45.45 2.32
1777 1813 6.092955 ACTGATTTCAGCAATCACAACAAT 57.907 33.333 7.48 0.00 45.45 2.71
1778 1814 5.067544 TGACTGATTTCAGCAATCACAACAA 59.932 36.000 7.48 0.00 45.45 2.83
1808 2443 4.277476 TGACCCTTTTTCTCACACAATGT 58.723 39.130 0.00 0.00 0.00 2.71
1825 2460 3.713826 TGAACCTTTATCCACTGACCC 57.286 47.619 0.00 0.00 0.00 4.46
1833 2468 4.081917 TCGCCCATTTTTGAACCTTTATCC 60.082 41.667 0.00 0.00 0.00 2.59
1836 2471 3.637229 TGTCGCCCATTTTTGAACCTTTA 59.363 39.130 0.00 0.00 0.00 1.85
1847 2482 2.625823 CCGCTTGTGTCGCCCATTT 61.626 57.895 0.00 0.00 0.00 2.32
1879 2531 1.904865 AACGGTGTCCTCTACGGCA 60.905 57.895 0.00 0.00 0.00 5.69
1881 2533 0.170561 CTCAACGGTGTCCTCTACGG 59.829 60.000 0.00 0.00 0.00 4.02
2006 2698 0.107654 GGAGGTGATTTGAGGGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
2024 2716 2.092291 CACACGATCGGACGGTTGG 61.092 63.158 20.98 0.85 37.61 3.77
2025 2717 2.092291 CCACACGATCGGACGGTTG 61.092 63.158 20.98 9.80 37.61 3.77
2035 2727 6.896819 ACAGAATATGTCCGTACCACACGAT 61.897 44.000 0.00 0.00 46.61 3.73
2036 2728 5.641330 ACAGAATATGTCCGTACCACACGA 61.641 45.833 0.00 0.00 46.61 4.35
2050 2742 6.732531 ATACGCATTGGATGACAGAATATG 57.267 37.500 0.00 0.00 0.00 1.78
2051 2743 7.229306 ACAAATACGCATTGGATGACAGAATAT 59.771 33.333 0.00 0.00 32.02 1.28
2052 2744 6.542005 ACAAATACGCATTGGATGACAGAATA 59.458 34.615 0.00 0.00 32.02 1.75
2053 2745 5.357878 ACAAATACGCATTGGATGACAGAAT 59.642 36.000 0.00 0.00 32.02 2.40
2054 2746 4.699735 ACAAATACGCATTGGATGACAGAA 59.300 37.500 0.00 0.00 32.02 3.02
2055 2747 4.260985 ACAAATACGCATTGGATGACAGA 58.739 39.130 0.00 0.00 32.02 3.41
2056 2748 4.621068 ACAAATACGCATTGGATGACAG 57.379 40.909 0.00 0.00 32.02 3.51
2057 2749 6.459435 CCAATACAAATACGCATTGGATGACA 60.459 38.462 6.37 0.00 46.87 3.58
2058 2750 5.914635 CCAATACAAATACGCATTGGATGAC 59.085 40.000 6.37 0.00 46.87 3.06
2059 2751 5.592282 ACCAATACAAATACGCATTGGATGA 59.408 36.000 16.81 0.00 46.87 2.92
2060 2752 5.830912 ACCAATACAAATACGCATTGGATG 58.169 37.500 16.81 0.00 46.87 3.51
2061 2753 5.827797 AGACCAATACAAATACGCATTGGAT 59.172 36.000 16.81 4.59 46.87 3.41
2062 2754 5.065859 CAGACCAATACAAATACGCATTGGA 59.934 40.000 16.81 0.00 46.87 3.53
2064 2756 4.734854 GCAGACCAATACAAATACGCATTG 59.265 41.667 0.00 0.00 0.00 2.82
2065 2757 4.640201 AGCAGACCAATACAAATACGCATT 59.360 37.500 0.00 0.00 0.00 3.56
2066 2758 4.199310 AGCAGACCAATACAAATACGCAT 58.801 39.130 0.00 0.00 0.00 4.73
2067 2759 3.605634 AGCAGACCAATACAAATACGCA 58.394 40.909 0.00 0.00 0.00 5.24
2068 2760 3.302480 CGAGCAGACCAATACAAATACGC 60.302 47.826 0.00 0.00 0.00 4.42
2069 2761 4.026804 GTCGAGCAGACCAATACAAATACG 60.027 45.833 1.39 0.00 43.95 3.06
2070 2762 4.026804 CGTCGAGCAGACCAATACAAATAC 60.027 45.833 6.74 0.00 46.92 1.89
2071 2763 4.109766 CGTCGAGCAGACCAATACAAATA 58.890 43.478 6.74 0.00 46.92 1.40
2072 2764 2.930040 CGTCGAGCAGACCAATACAAAT 59.070 45.455 6.74 0.00 46.92 2.32
2073 2765 2.333926 CGTCGAGCAGACCAATACAAA 58.666 47.619 6.74 0.00 46.92 2.83
2074 2766 1.403647 CCGTCGAGCAGACCAATACAA 60.404 52.381 6.74 0.00 46.92 2.41
2075 2767 0.172578 CCGTCGAGCAGACCAATACA 59.827 55.000 6.74 0.00 46.92 2.29
2076 2768 0.172803 ACCGTCGAGCAGACCAATAC 59.827 55.000 6.74 0.00 46.92 1.89
2077 2769 0.454600 GACCGTCGAGCAGACCAATA 59.545 55.000 6.74 0.00 46.92 1.90
2078 2770 1.215647 GACCGTCGAGCAGACCAAT 59.784 57.895 6.74 0.00 46.92 3.16
2079 2771 2.649034 GACCGTCGAGCAGACCAA 59.351 61.111 6.74 0.00 46.92 3.67
2080 2772 3.371063 GGACCGTCGAGCAGACCA 61.371 66.667 6.74 0.00 46.92 4.02
2081 2773 3.343788 CTGGACCGTCGAGCAGACC 62.344 68.421 6.74 0.00 46.92 3.85
2082 2774 1.658686 ATCTGGACCGTCGAGCAGAC 61.659 60.000 5.71 2.66 46.16 3.51
2083 2775 1.378646 ATCTGGACCGTCGAGCAGA 60.379 57.895 5.71 6.99 0.00 4.26
2084 2776 1.226802 CATCTGGACCGTCGAGCAG 60.227 63.158 5.71 1.85 0.00 4.24
2085 2777 2.885113 CATCTGGACCGTCGAGCA 59.115 61.111 5.71 0.00 0.00 4.26
2086 2778 2.583593 GCATCTGGACCGTCGAGC 60.584 66.667 5.71 0.00 0.00 5.03
2087 2779 0.179100 AATGCATCTGGACCGTCGAG 60.179 55.000 0.00 4.24 0.00 4.04
2088 2780 0.249120 AAATGCATCTGGACCGTCGA 59.751 50.000 0.00 0.00 0.00 4.20
2089 2781 1.086696 AAAATGCATCTGGACCGTCG 58.913 50.000 0.00 0.00 0.00 5.12
2126 2818 8.139350 TGTCCGGTTGTAGATGTTTATAGTATG 58.861 37.037 0.00 0.00 0.00 2.39
2133 2825 3.579586 AGGTGTCCGGTTGTAGATGTTTA 59.420 43.478 0.00 0.00 0.00 2.01
2134 2826 2.370849 AGGTGTCCGGTTGTAGATGTTT 59.629 45.455 0.00 0.00 0.00 2.83
2136 2828 1.549170 GAGGTGTCCGGTTGTAGATGT 59.451 52.381 0.00 0.00 0.00 3.06
2143 2835 1.170290 GGGTTTGAGGTGTCCGGTTG 61.170 60.000 0.00 0.00 0.00 3.77
2152 2844 1.202770 CGTTTGAGGAGGGTTTGAGGT 60.203 52.381 0.00 0.00 0.00 3.85
2153 2845 1.523758 CGTTTGAGGAGGGTTTGAGG 58.476 55.000 0.00 0.00 0.00 3.86
2154 2846 0.875059 GCGTTTGAGGAGGGTTTGAG 59.125 55.000 0.00 0.00 0.00 3.02
2155 2847 0.472471 AGCGTTTGAGGAGGGTTTGA 59.528 50.000 0.00 0.00 0.00 2.69
2156 2848 0.875059 GAGCGTTTGAGGAGGGTTTG 59.125 55.000 0.00 0.00 0.00 2.93
2157 2849 0.602905 CGAGCGTTTGAGGAGGGTTT 60.603 55.000 0.00 0.00 0.00 3.27
2158 2850 1.004918 CGAGCGTTTGAGGAGGGTT 60.005 57.895 0.00 0.00 0.00 4.11
2159 2851 1.878656 CTCGAGCGTTTGAGGAGGGT 61.879 60.000 8.58 0.00 32.06 4.34
2160 2852 1.153745 CTCGAGCGTTTGAGGAGGG 60.154 63.158 8.58 0.00 32.06 4.30
2161 2853 1.807573 GCTCGAGCGTTTGAGGAGG 60.808 63.158 23.61 0.00 35.66 4.30
2162 2854 3.773974 GCTCGAGCGTTTGAGGAG 58.226 61.111 23.61 3.03 35.66 3.69
2180 2872 2.900337 CCGGACAATAAGCGGCCC 60.900 66.667 0.00 0.00 0.00 5.80
2181 2873 2.124860 ACCGGACAATAAGCGGCC 60.125 61.111 9.46 0.00 0.00 6.13
2209 2905 1.899437 TTGAGGCGTCCATCTGGGTC 61.899 60.000 3.56 0.00 38.11 4.46
2213 2909 1.361668 CCGTTTGAGGCGTCCATCTG 61.362 60.000 3.56 0.00 0.00 2.90
2224 2920 1.083015 CGTTTGACGCCCGTTTGAG 60.083 57.895 0.00 0.00 33.65 3.02
2329 3026 4.358841 TCGGGTGGGCCAACATGG 62.359 66.667 25.48 12.11 41.55 3.66
2339 3036 1.358152 ATATATGTGGGGTCGGGTGG 58.642 55.000 0.00 0.00 0.00 4.61
2356 3053 1.802337 CGAGCGGATGGGGACGAATA 61.802 60.000 0.00 0.00 0.00 1.75
2374 3071 1.810030 GCTAGGGTTTGCTCCGACG 60.810 63.158 0.00 0.00 0.00 5.12
2376 3073 1.916273 TGGCTAGGGTTTGCTCCGA 60.916 57.895 0.00 0.00 0.00 4.55
2408 3105 2.768344 GCGGAGGGGAATGGAGGA 60.768 66.667 0.00 0.00 0.00 3.71
2409 3106 3.878667 GGCGGAGGGGAATGGAGG 61.879 72.222 0.00 0.00 0.00 4.30
2425 3122 2.556286 GGAGAAGGCCGAAAACTGG 58.444 57.895 0.00 0.00 0.00 4.00
2455 3152 1.958205 GCCAGAATCCGATCCGCTG 60.958 63.158 0.00 0.00 0.00 5.18
2459 3156 0.250081 GACTGGCCAGAATCCGATCC 60.250 60.000 39.19 11.53 0.00 3.36
2460 3157 0.250081 GGACTGGCCAGAATCCGATC 60.250 60.000 39.19 22.70 36.34 3.69
2467 3164 2.367202 GGATCCGGACTGGCCAGAA 61.367 63.158 39.19 17.86 37.80 3.02
2480 3177 1.227556 CACCCCAATCGACGGATCC 60.228 63.158 0.00 0.00 30.81 3.36
2481 3178 0.748450 TACACCCCAATCGACGGATC 59.252 55.000 4.25 0.00 30.81 3.36
2484 3181 0.249741 GGATACACCCCAATCGACGG 60.250 60.000 0.00 0.00 0.00 4.79
2486 3183 1.485066 ACAGGATACACCCCAATCGAC 59.515 52.381 0.00 0.00 40.05 4.20
2491 3188 0.695924 CCACACAGGATACACCCCAA 59.304 55.000 0.00 0.00 41.22 4.12
2493 3190 1.205460 ACCCACACAGGATACACCCC 61.205 60.000 0.00 0.00 41.22 4.95
2504 3201 1.150536 GCCTCCTCAAACCCACACA 59.849 57.895 0.00 0.00 0.00 3.72
2527 3224 2.359850 GGGTGCAATGCGGACTGA 60.360 61.111 0.00 0.00 35.96 3.41


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

AutoCloner maintained by Alex Coulton.