Multiple sequence alignment - TraesCS5A01G221100

Loading Multiple Alignment...

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 TraesCS5A01G221100 chr5A 100.000 4734 0 0 3194 7927 437223959 437219226 0.000000e+00 8743.0
1 TraesCS5A01G221100 chr5A 100.000 2885 0 0 1 2885 437227152 437224268 0.000000e+00 5328.0
2 TraesCS5A01G221100 chr5B 95.971 2656 75 24 3222 5860 394022912 394020272 0.000000e+00 4283.0
3 TraesCS5A01G221100 chr5B 89.158 1365 70 36 561 1917 394025443 394024149 0.000000e+00 1629.0
4 TraesCS5A01G221100 chr5B 96.865 925 24 2 6234 7158 394020036 394019117 0.000000e+00 1543.0
5 TraesCS5A01G221100 chr5B 95.530 962 33 5 1914 2871 394024109 394023154 0.000000e+00 1530.0
6 TraesCS5A01G221100 chr5B 91.799 378 16 10 7164 7527 394019084 394018708 5.490000e-141 512.0
7 TraesCS5A01G221100 chr5B 93.519 324 20 1 7604 7927 394018684 394018362 1.550000e-131 481.0
8 TraesCS5A01G221100 chr5B 93.023 215 15 0 5937 6151 394020250 394020036 1.660000e-81 315.0
9 TraesCS5A01G221100 chr5B 94.048 84 4 1 158 240 394025451 394025368 8.350000e-25 126.0
10 TraesCS5A01G221100 chr5D 98.490 2318 24 5 5614 7927 336060328 336058018 0.000000e+00 4076.0
11 TraesCS5A01G221100 chr5D 96.584 1405 27 10 4173 5563 336062107 336060710 0.000000e+00 2309.0
12 TraesCS5A01G221100 chr5D 94.996 1119 48 3 799 1917 336065138 336064028 0.000000e+00 1749.0
13 TraesCS5A01G221100 chr5D 96.457 875 29 2 1996 2869 336063973 336063100 0.000000e+00 1443.0
14 TraesCS5A01G221100 chr5D 95.780 782 27 3 3226 4001 336062889 336062108 0.000000e+00 1256.0
15 TraesCS5A01G221100 chr5D 92.045 528 26 7 298 813 336065681 336065158 0.000000e+00 728.0
16 TraesCS5A01G221100 chr5D 94.949 297 11 2 1 297 336065930 336065638 5.600000e-126 462.0
17 TraesCS5A01G221100 chr5D 84.615 182 18 7 4003 4181 502027248 502027074 1.060000e-38 172.0
18 TraesCS5A01G221100 chr5D 82.099 162 21 8 3960 4115 213216785 213216944 1.790000e-26 132.0
19 TraesCS5A01G221100 chr5D 89.062 64 3 4 4114 4176 359051201 359051261 8.530000e-10 76.8
20 TraesCS5A01G221100 chr2A 90.210 143 13 1 3991 4133 184561144 184561285 1.360000e-42 185.0
21 TraesCS5A01G221100 chr1D 91.852 135 7 4 3997 4129 387944777 387944909 1.360000e-42 185.0
22 TraesCS5A01G221100 chr1D 98.000 50 1 0 684 733 348065954 348065905 3.940000e-13 87.9
23 TraesCS5A01G221100 chr7D 86.188 181 11 9 4003 4183 154185909 154186075 4.890000e-42 183.0
24 TraesCS5A01G221100 chr7D 85.143 175 18 6 4009 4177 421459123 421458951 1.060000e-38 172.0
25 TraesCS5A01G221100 chr3B 91.176 136 11 1 3998 4133 492351000 492351134 4.890000e-42 183.0
26 TraesCS5A01G221100 chr3A 85.556 180 18 6 3999 4176 663433454 663433627 1.760000e-41 182.0
27 TraesCS5A01G221100 chr1B 85.714 175 18 5 4003 4176 364115946 364116114 2.270000e-40 178.0
28 TraesCS5A01G221100 chr3D 85.465 172 18 5 4006 4176 595302938 595302773 1.060000e-38 172.0
29 TraesCS5A01G221100 chr3D 91.837 49 2 1 672 720 1382623 1382669 5.130000e-07 67.6
30 TraesCS5A01G221100 chr6B 98.039 51 1 0 685 735 46068939 46068989 1.100000e-13 89.8
31 TraesCS5A01G221100 chr6B 87.719 57 6 1 678 733 40609953 40610009 1.850000e-06 65.8
32 TraesCS5A01G221100 chr1A 95.918 49 2 0 684 732 448929349 448929301 6.590000e-11 80.5
33 TraesCS5A01G221100 chr2B 89.062 64 3 3 4114 4176 331238693 331238753 8.530000e-10 76.8
34 TraesCS5A01G221100 chr6D 97.561 41 1 0 681 721 13167761 13167721 3.970000e-08 71.3
35 TraesCS5A01G221100 chr6D 88.136 59 4 2 678 733 24617344 24617286 5.130000e-07 67.6


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 TraesCS5A01G221100 chr5A 437219226 437227152 7926 True 7035.500000 8743 100.000000 1 7927 2 chr5A.!!$R1 7926
1 TraesCS5A01G221100 chr5B 394018362 394025451 7089 True 1302.375000 4283 93.739125 158 7927 8 chr5B.!!$R1 7769
2 TraesCS5A01G221100 chr5D 336058018 336065930 7912 True 1717.571429 4076 95.614429 1 7927 7 chr5D.!!$R2 7926

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
29 30 0.110192 GTTAGAAGCGTGTTGGCAGC 60.110 55.000 0.00 0.00 34.64 5.25 F
1309 1374 0.464554 GCAACTACCTCAGCATCCCC 60.465 60.000 0.00 0.00 0.00 4.81 F
1683 1748 0.036732 TGAGTGCCTGAATGGTGGTC 59.963 55.000 0.00 0.00 38.35 4.02 F
1843 1908 0.721718 GATGCTTCTTTGGACGACGG 59.278 55.000 0.00 0.00 0.00 4.79 F
2884 2996 1.448985 TGGCGTTTGAATACTGCTCC 58.551 50.000 0.00 0.00 0.00 4.70 F
3942 4060 2.626785 TCAGACCACCCATTCAGGTTA 58.373 47.619 0.00 0.00 38.39 2.85 F
4566 4694 2.026915 TGCATAGTGGAAGCTGTCACAT 60.027 45.455 18.16 9.34 36.43 3.21 F
5335 5469 2.279935 AGATCCCTACCTAGTCAGCG 57.720 55.000 0.00 0.00 0.00 5.18 F
6576 7081 4.051237 GTTCTTTTGGTGCAACATTCCTC 58.949 43.478 4.62 0.00 39.98 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1710 0.036732 ACAGCACACATACCCACAGG 59.963 55.000 0.00 0.0 40.04 4.00 R
2663 2775 2.507058 AGGCATGCCTGTAGAAATGAGA 59.493 45.455 38.23 0.0 46.22 3.27 R
3564 3679 1.892474 TGGGTCAAGGCAGCATAAAAC 59.108 47.619 0.00 0.0 0.00 2.43 R
3772 3887 3.683802 AGAAGAATGGCCAGAGAAACAG 58.316 45.455 13.05 0.0 0.00 3.16 R
3997 4115 4.968971 TTTAGAAACGGAGGGAGAAGTT 57.031 40.909 0.00 0.0 0.00 2.66 R
5119 5251 1.080298 GCTGCTTTCCATGGTGCAC 60.080 57.895 19.95 8.8 0.00 4.57 R
5883 6388 4.823989 ACAGCAGTGCTAAGTTCAAAGAAT 59.176 37.500 19.26 0.0 36.40 2.40 R
6795 7300 1.818674 ACTGCCCTAAAAATCAAGCCG 59.181 47.619 0.00 0.0 0.00 5.52 R
7746 8294 3.369892 CCTTCAGGTCTTGTAGGTCATGG 60.370 52.174 0.00 0.0 39.00 3.66 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
27 28 0.887387 GGGTTAGAAGCGTGTTGGCA 60.887 55.000 0.00 0.00 34.64 4.92
28 29 0.517316 GGTTAGAAGCGTGTTGGCAG 59.483 55.000 0.00 0.00 34.64 4.85
29 30 0.110192 GTTAGAAGCGTGTTGGCAGC 60.110 55.000 0.00 0.00 34.64 5.25
110 111 7.612633 GGTATACTACACCCTCATTTGGAAAAA 59.387 37.037 2.25 0.00 0.00 1.94
197 198 4.291540 TCAAATGTTCGAGCATATTGCC 57.708 40.909 15.51 0.00 46.52 4.52
272 279 4.093115 TGTGCACTTTGAGCATTGTTTTTG 59.907 37.500 19.41 0.00 44.79 2.44
273 280 4.093261 GTGCACTTTGAGCATTGTTTTTGT 59.907 37.500 10.32 0.00 44.79 2.83
274 281 4.694509 TGCACTTTGAGCATTGTTTTTGTT 59.305 33.333 0.00 0.00 37.02 2.83
275 282 5.180868 TGCACTTTGAGCATTGTTTTTGTTT 59.819 32.000 0.00 0.00 37.02 2.83
276 283 6.085573 GCACTTTGAGCATTGTTTTTGTTTT 58.914 32.000 0.00 0.00 0.00 2.43
277 284 6.581919 GCACTTTGAGCATTGTTTTTGTTTTT 59.418 30.769 0.00 0.00 0.00 1.94
301 308 2.949451 CGAGAGCTCCACATACACTT 57.051 50.000 10.93 0.00 0.00 3.16
302 309 3.238108 CGAGAGCTCCACATACACTTT 57.762 47.619 10.93 0.00 0.00 2.66
303 310 2.926200 CGAGAGCTCCACATACACTTTG 59.074 50.000 10.93 0.00 0.00 2.77
304 311 3.367395 CGAGAGCTCCACATACACTTTGA 60.367 47.826 10.93 0.00 0.00 2.69
305 312 4.180057 GAGAGCTCCACATACACTTTGAG 58.820 47.826 10.93 0.00 0.00 3.02
306 313 2.675348 GAGCTCCACATACACTTTGAGC 59.325 50.000 0.87 0.00 44.17 4.26
307 314 2.038952 AGCTCCACATACACTTTGAGCA 59.961 45.455 11.38 0.00 45.76 4.26
308 315 3.012518 GCTCCACATACACTTTGAGCAT 58.987 45.455 0.00 0.00 43.50 3.79
309 316 3.441572 GCTCCACATACACTTTGAGCATT 59.558 43.478 0.00 0.00 43.50 3.56
310 317 4.673580 GCTCCACATACACTTTGAGCATTG 60.674 45.833 0.00 0.00 43.50 2.82
311 318 4.397420 TCCACATACACTTTGAGCATTGT 58.603 39.130 0.00 0.00 0.00 2.71
312 319 4.826733 TCCACATACACTTTGAGCATTGTT 59.173 37.500 0.00 0.00 0.00 2.83
313 320 5.301551 TCCACATACACTTTGAGCATTGTTT 59.698 36.000 0.00 0.00 0.00 2.83
314 321 5.984926 CCACATACACTTTGAGCATTGTTTT 59.015 36.000 0.00 0.00 0.00 2.43
315 322 6.479660 CCACATACACTTTGAGCATTGTTTTT 59.520 34.615 0.00 0.00 0.00 1.94
316 323 7.339207 CACATACACTTTGAGCATTGTTTTTG 58.661 34.615 0.00 0.00 0.00 2.44
317 324 7.010367 CACATACACTTTGAGCATTGTTTTTGT 59.990 33.333 0.00 0.00 0.00 2.83
354 361 6.322201 AGAGCTCCACATATGTTATTTTTGGG 59.678 38.462 10.93 1.83 0.00 4.12
393 400 7.011482 AGGAGCTCGAACATTTGATGTATTAAC 59.989 37.037 7.83 0.00 44.07 2.01
472 489 3.306166 GCAGTGGCTACGTTACATTACAG 59.694 47.826 0.00 0.00 36.96 2.74
480 497 3.499048 ACGTTACATTACAGCGAGAGTG 58.501 45.455 0.00 0.00 0.00 3.51
495 512 3.674682 CGAGAGTGAAGGAAAGTAGCCAG 60.675 52.174 0.00 0.00 0.00 4.85
513 530 3.057033 GCCAGTACTCTCGAGTTTGGTAA 60.057 47.826 21.26 0.00 42.28 2.85
595 612 3.549299 AATGTTCGAGCTTCTTGCAAG 57.451 42.857 20.81 20.81 45.94 4.01
610 627 5.184711 TCTTGCAAGTTTTCAGCCAAAAAT 58.815 33.333 25.19 0.00 35.68 1.82
613 630 7.498570 TCTTGCAAGTTTTCAGCCAAAAATAAT 59.501 29.630 25.19 0.00 35.68 1.28
615 632 8.845413 TGCAAGTTTTCAGCCAAAAATAATAT 57.155 26.923 0.00 0.00 35.68 1.28
616 633 8.719648 TGCAAGTTTTCAGCCAAAAATAATATG 58.280 29.630 0.00 0.00 35.68 1.78
618 635 8.719648 CAAGTTTTCAGCCAAAAATAATATGCA 58.280 29.630 0.00 0.00 35.68 3.96
671 689 9.820725 AAATCATCAATGTTCAAAAAGTTCAGA 57.179 25.926 0.00 0.00 0.00 3.27
674 692 9.820725 TCATCAATGTTCAAAAAGTTCAGATTT 57.179 25.926 0.00 0.00 0.00 2.17
681 699 9.487790 TGTTCAAAAAGTTCAGATTTTTCACTT 57.512 25.926 0.00 0.00 37.67 3.16
910 964 2.943653 GTCACTTTTCACCGCCCG 59.056 61.111 0.00 0.00 0.00 6.13
933 987 1.587043 GAAAACCAGCCTTCTCCCGC 61.587 60.000 0.00 0.00 0.00 6.13
934 988 3.569200 AAACCAGCCTTCTCCCGCC 62.569 63.158 0.00 0.00 0.00 6.13
958 1016 0.901827 TTATTGGCTCGCTGTCTCCA 59.098 50.000 0.00 0.00 0.00 3.86
961 1019 3.695606 GGCTCGCTGTCTCCACCA 61.696 66.667 0.00 0.00 0.00 4.17
1204 1269 0.471211 TTGTTCCAGGTCTCCGAGGT 60.471 55.000 0.00 0.00 0.00 3.85
1309 1374 0.464554 GCAACTACCTCAGCATCCCC 60.465 60.000 0.00 0.00 0.00 4.81
1401 1466 3.614870 GCCCCTGTCTTGTTGCTTTATTG 60.615 47.826 0.00 0.00 0.00 1.90
1408 1473 7.867403 CCTGTCTTGTTGCTTTATTGTAATGTT 59.133 33.333 0.00 0.00 0.00 2.71
1545 1610 1.874345 CGCACTACTCCGACCACCTT 61.874 60.000 0.00 0.00 0.00 3.50
1611 1676 0.821711 TTTGGCTGTTCCCGGTTCTG 60.822 55.000 0.00 0.00 0.00 3.02
1615 1680 0.539986 GCTGTTCCCGGTTCTGGATA 59.460 55.000 0.00 0.00 0.00 2.59
1631 1696 9.120538 GGTTCTGGATAGTCTTTTTATTGCATA 57.879 33.333 0.00 0.00 0.00 3.14
1645 1710 4.644103 ATTGCATAGCTTGATTGGTGAC 57.356 40.909 0.00 0.00 0.00 3.67
1649 1714 3.614092 CATAGCTTGATTGGTGACCTGT 58.386 45.455 2.11 0.00 0.00 4.00
1683 1748 0.036732 TGAGTGCCTGAATGGTGGTC 59.963 55.000 0.00 0.00 38.35 4.02
1726 1791 2.568956 TCCAGAGAGTTGCTTGCAGTAT 59.431 45.455 0.00 0.00 0.00 2.12
1738 1803 2.561733 TGCAGTATGACTACGACAGC 57.438 50.000 0.00 0.00 39.69 4.40
1804 1869 4.586001 TGCCTTCTGAAGCTTGATTTCTTT 59.414 37.500 2.10 0.00 0.00 2.52
1816 1881 7.824672 AGCTTGATTTCTTTGGTTCTATTGAG 58.175 34.615 0.00 0.00 0.00 3.02
1825 1890 1.416401 GGTTCTATTGAGCCCGATGGA 59.584 52.381 0.00 0.00 37.58 3.41
1838 1903 1.672881 CCGATGGATGCTTCTTTGGAC 59.327 52.381 0.00 0.00 0.00 4.02
1843 1908 0.721718 GATGCTTCTTTGGACGACGG 59.278 55.000 0.00 0.00 0.00 4.79
1910 1975 9.216117 GTAAAATGTAGGTTCTCACTAATGTGT 57.784 33.333 0.00 0.00 44.14 3.72
1942 2050 2.626785 TGGACATTGGGTCTAGTGGAA 58.373 47.619 0.00 0.00 46.16 3.53
1963 2071 5.358160 GGAACTTTAATGGTGCTGCTAGAAT 59.642 40.000 0.00 0.00 0.00 2.40
1964 2072 5.824904 ACTTTAATGGTGCTGCTAGAATG 57.175 39.130 0.00 0.00 0.00 2.67
1974 2082 7.282585 TGGTGCTGCTAGAATGTTAAGAATAT 58.717 34.615 0.00 0.00 0.00 1.28
1998 2106 7.395190 TGATTCTCCACCACTATTCATTTTG 57.605 36.000 0.00 0.00 0.00 2.44
2005 2113 6.038356 CCACCACTATTCATTTTGCTGATTC 58.962 40.000 0.00 0.00 0.00 2.52
2078 2186 4.069304 TCCTGGTGTTGGAAAATCTTACG 58.931 43.478 0.00 0.00 0.00 3.18
2105 2213 3.311322 TGTTTGTTGACCAGCTAAGTTCG 59.689 43.478 0.00 0.00 0.00 3.95
2222 2330 5.817296 GGTAATTTTGAATTGATCCAAGCCC 59.183 40.000 0.00 0.00 0.00 5.19
2223 2331 5.767277 AATTTTGAATTGATCCAAGCCCT 57.233 34.783 0.00 0.00 0.00 5.19
2305 2414 4.627611 TCAGTAGTCGTTACACATAGCC 57.372 45.455 3.43 0.00 34.56 3.93
2319 2428 4.466370 ACACATAGCCTGAGTTAAGTAGCA 59.534 41.667 0.00 0.00 0.00 3.49
2320 2429 4.806247 CACATAGCCTGAGTTAAGTAGCAC 59.194 45.833 0.00 0.00 0.00 4.40
2321 2430 4.466370 ACATAGCCTGAGTTAAGTAGCACA 59.534 41.667 0.00 0.00 0.00 4.57
2328 2437 4.116961 TGAGTTAAGTAGCACACACACAC 58.883 43.478 0.00 0.00 0.00 3.82
2379 2488 5.836821 TCACTGGTCAGTACACATATCTC 57.163 43.478 3.06 0.00 40.20 2.75
2428 2539 4.580167 TCCCATGTAGTTAATGCTTGATGC 59.420 41.667 0.00 0.00 43.25 3.91
2511 2623 5.160607 TCTCGTTGGGAAGATAATTGTGT 57.839 39.130 0.00 0.00 0.00 3.72
2520 2632 8.224389 TGGGAAGATAATTGTGTATGTCATTG 57.776 34.615 0.00 0.00 0.00 2.82
2573 2685 2.505819 CCACAGTAATCTGCCCTAGGTT 59.494 50.000 8.29 0.00 44.77 3.50
2620 2732 4.510711 CCTGCACTCAGTTATAGCTTCATG 59.489 45.833 0.00 0.00 38.66 3.07
2871 2983 2.923121 ACTGCATCTGATTATGGCGTT 58.077 42.857 0.00 0.00 0.00 4.84
2872 2984 3.282021 ACTGCATCTGATTATGGCGTTT 58.718 40.909 0.00 0.00 0.00 3.60
2873 2985 3.065786 ACTGCATCTGATTATGGCGTTTG 59.934 43.478 0.00 0.00 0.00 2.93
2874 2986 3.277715 TGCATCTGATTATGGCGTTTGA 58.722 40.909 0.00 0.00 0.00 2.69
2875 2987 3.693578 TGCATCTGATTATGGCGTTTGAA 59.306 39.130 0.00 0.00 0.00 2.69
2876 2988 4.338964 TGCATCTGATTATGGCGTTTGAAT 59.661 37.500 0.00 0.00 0.00 2.57
2877 2989 5.530543 TGCATCTGATTATGGCGTTTGAATA 59.469 36.000 0.00 0.00 0.00 1.75
2878 2990 5.853282 GCATCTGATTATGGCGTTTGAATAC 59.147 40.000 0.00 0.00 0.00 1.89
2879 2991 6.293626 GCATCTGATTATGGCGTTTGAATACT 60.294 38.462 0.00 0.00 0.00 2.12
2880 2992 6.603237 TCTGATTATGGCGTTTGAATACTG 57.397 37.500 0.00 0.00 0.00 2.74
2881 2993 5.007626 TCTGATTATGGCGTTTGAATACTGC 59.992 40.000 0.00 0.00 0.00 4.40
2882 2994 4.881273 TGATTATGGCGTTTGAATACTGCT 59.119 37.500 0.00 0.00 0.00 4.24
2883 2995 4.875544 TTATGGCGTTTGAATACTGCTC 57.124 40.909 0.00 0.00 0.00 4.26
2884 2996 1.448985 TGGCGTTTGAATACTGCTCC 58.551 50.000 0.00 0.00 0.00 4.70
3220 3332 8.896320 TGTAGCTAAAATCTTGTTCACTAACA 57.104 30.769 0.00 0.00 43.85 2.41
3413 3527 5.506708 ACCAACTCACCTTTCTACTTTGTT 58.493 37.500 0.00 0.00 0.00 2.83
3501 3616 9.420118 TCTCCATGCATAGTTTACCATTAAAAT 57.580 29.630 0.00 0.00 30.78 1.82
3942 4060 2.626785 TCAGACCACCCATTCAGGTTA 58.373 47.619 0.00 0.00 38.39 2.85
4006 4124 4.287766 TCCTTAGCAAAGAACTTCTCCC 57.712 45.455 0.00 0.00 34.37 4.30
4048 4166 8.608844 AGTCTTTTTAGAGATTTCAACGTGAT 57.391 30.769 0.00 0.00 0.00 3.06
4057 4175 6.913132 AGAGATTTCAACGTGATCTACATACG 59.087 38.462 0.00 1.37 42.98 3.06
4566 4694 2.026915 TGCATAGTGGAAGCTGTCACAT 60.027 45.455 18.16 9.34 36.43 3.21
4574 4702 4.937620 GTGGAAGCTGTCACATGATTTAGA 59.062 41.667 12.98 0.00 34.32 2.10
5186 5318 3.841372 GCAACTTGTTCGTCAACTCTTCG 60.841 47.826 0.00 0.00 33.17 3.79
5296 5430 7.233389 TCTAGCTATGAAAGGGCTATTGTAG 57.767 40.000 0.00 0.00 37.82 2.74
5335 5469 2.279935 AGATCCCTACCTAGTCAGCG 57.720 55.000 0.00 0.00 0.00 5.18
5883 6388 7.567458 TGTGATGTCCTCTAATTCATCATCAA 58.433 34.615 8.09 0.00 44.98 2.57
5889 6394 9.690913 TGTCCTCTAATTCATCATCAATTCTTT 57.309 29.630 0.00 0.00 0.00 2.52
5890 6395 9.947669 GTCCTCTAATTCATCATCAATTCTTTG 57.052 33.333 0.00 0.00 0.00 2.77
6576 7081 4.051237 GTTCTTTTGGTGCAACATTCCTC 58.949 43.478 4.62 0.00 39.98 3.71
6648 7153 4.701765 CAGATATCTACACCAGCAAGCTT 58.298 43.478 4.54 0.00 0.00 3.74
6808 7313 6.487331 TGTTTAGAGAACCGGCTTGATTTTTA 59.513 34.615 0.00 0.00 0.00 1.52
6999 7504 0.755686 TTTGTTTGTGGCCATGGGAC 59.244 50.000 9.72 6.64 0.00 4.46
7746 8294 3.572584 CATTTCCAGTTCTTGCTGCTTC 58.427 45.455 0.00 0.00 35.28 3.86
7830 8378 1.638529 ACTGCTACAGCTGGAGTCTT 58.361 50.000 26.79 8.57 43.15 3.01
7849 8397 6.205101 GTCTTAAGACTCTTATCCGTTCCA 57.795 41.667 25.30 0.00 41.65 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.540830 AAGAGAGTGTCCGTCCTGCT 60.541 55.000 0.00 0.00 0.00 4.24
28 29 0.318762 AAAGAGAGTGTCCGTCCTGC 59.681 55.000 0.00 0.00 0.00 4.85
29 30 2.408050 CAAAAGAGAGTGTCCGTCCTG 58.592 52.381 0.00 0.00 0.00 3.86
197 198 5.299148 TCCTCAAATGTTGGCTGAAATTTG 58.701 37.500 0.00 9.44 40.00 2.32
281 288 0.457851 AGTGTATGTGGAGCTCTCGC 59.542 55.000 14.64 10.92 0.00 5.03
282 289 2.926200 CAAAGTGTATGTGGAGCTCTCG 59.074 50.000 14.64 0.00 0.00 4.04
283 290 4.180057 CTCAAAGTGTATGTGGAGCTCTC 58.820 47.826 14.64 8.02 0.00 3.20
284 291 3.618507 GCTCAAAGTGTATGTGGAGCTCT 60.619 47.826 14.64 0.00 43.21 4.09
285 292 2.675348 GCTCAAAGTGTATGTGGAGCTC 59.325 50.000 4.71 4.71 43.21 4.09
286 293 2.038952 TGCTCAAAGTGTATGTGGAGCT 59.961 45.455 12.03 0.00 45.87 4.09
287 294 2.426522 TGCTCAAAGTGTATGTGGAGC 58.573 47.619 0.00 0.00 45.89 4.70
288 295 4.456911 ACAATGCTCAAAGTGTATGTGGAG 59.543 41.667 0.00 0.00 0.00 3.86
289 296 4.397420 ACAATGCTCAAAGTGTATGTGGA 58.603 39.130 0.00 0.00 0.00 4.02
290 297 4.771590 ACAATGCTCAAAGTGTATGTGG 57.228 40.909 0.00 0.00 0.00 4.17
291 298 7.010367 ACAAAAACAATGCTCAAAGTGTATGTG 59.990 33.333 0.00 0.00 0.00 3.21
292 299 7.041107 ACAAAAACAATGCTCAAAGTGTATGT 58.959 30.769 0.00 0.00 0.00 2.29
293 300 7.467557 ACAAAAACAATGCTCAAAGTGTATG 57.532 32.000 0.00 0.00 0.00 2.39
294 301 8.491331 AAACAAAAACAATGCTCAAAGTGTAT 57.509 26.923 0.00 0.00 0.00 2.29
295 302 7.897575 AAACAAAAACAATGCTCAAAGTGTA 57.102 28.000 0.00 0.00 0.00 2.90
296 303 6.799926 AAACAAAAACAATGCTCAAAGTGT 57.200 29.167 0.00 0.00 0.00 3.55
328 335 7.420800 CCAAAAATAACATATGTGGAGCTCTC 58.579 38.462 14.64 8.02 0.00 3.20
354 361 5.607119 TCGAGCTCCTTGTAATTTTTCAC 57.393 39.130 8.47 0.00 0.00 3.18
365 372 3.438087 ACATCAAATGTTCGAGCTCCTTG 59.562 43.478 8.47 2.96 41.63 3.61
366 373 3.679389 ACATCAAATGTTCGAGCTCCTT 58.321 40.909 8.47 0.00 41.63 3.36
465 482 3.510388 TCCTTCACTCTCGCTGTAATG 57.490 47.619 0.00 0.00 0.00 1.90
472 489 2.263945 GCTACTTTCCTTCACTCTCGC 58.736 52.381 0.00 0.00 0.00 5.03
480 497 4.439016 CGAGAGTACTGGCTACTTTCCTTC 60.439 50.000 0.00 0.00 35.66 3.46
567 584 6.253746 CAAGAAGCTCGAACATTTGATAAGG 58.746 40.000 0.00 0.00 0.00 2.69
595 612 8.177013 CCTTGCATATTATTTTTGGCTGAAAAC 58.823 33.333 0.00 0.00 33.09 2.43
610 627 6.731292 TTAGTGAGAGCTCCTTGCATATTA 57.269 37.500 10.93 0.00 45.94 0.98
613 630 5.420725 TTTTAGTGAGAGCTCCTTGCATA 57.579 39.130 10.93 0.00 45.94 3.14
615 632 3.668447 CTTTTAGTGAGAGCTCCTTGCA 58.332 45.455 10.93 0.78 45.94 4.08
616 633 2.418280 GCTTTTAGTGAGAGCTCCTTGC 59.582 50.000 10.93 0.00 43.29 4.01
618 635 4.357918 TTGCTTTTAGTGAGAGCTCCTT 57.642 40.909 10.93 0.00 37.32 3.36
689 707 2.680577 GTGTACTACACCCGAGTTTGG 58.319 52.381 7.99 0.00 43.05 3.28
958 1016 2.360980 CGAGGGGAGAGGAGTGGT 59.639 66.667 0.00 0.00 0.00 4.16
961 1019 4.824515 CGGCGAGGGGAGAGGAGT 62.825 72.222 0.00 0.00 0.00 3.85
1109 1171 3.121030 CGAACGGGCTGAAGGCAG 61.121 66.667 0.00 4.32 45.13 4.85
1154 1216 1.477195 CCCAGTCACCGGGTTGTAAAA 60.477 52.381 6.32 0.00 39.05 1.52
1204 1269 2.402572 CGAGGAGAGCGTGCTCAGA 61.403 63.158 22.70 0.00 43.80 3.27
1309 1374 2.514592 ATGTCCTTGATGGCGGCG 60.515 61.111 0.51 0.51 35.26 6.46
1353 1418 4.493747 GTCGGGAGGAGCGAACGG 62.494 72.222 0.00 0.00 0.00 4.44
1408 1473 8.592809 ACCAGCAAATTCAGTATCCATTTTAAA 58.407 29.630 0.00 0.00 0.00 1.52
1418 1483 3.778265 ACCCAACCAGCAAATTCAGTAT 58.222 40.909 0.00 0.00 0.00 2.12
1425 1490 1.665442 GCGAACCCAACCAGCAAAT 59.335 52.632 0.00 0.00 0.00 2.32
1545 1610 4.558296 GCGAGATCATAGATCAAGCACTGA 60.558 45.833 16.28 0.00 38.81 3.41
1611 1676 8.840321 TCAAGCTATGCAATAAAAAGACTATCC 58.160 33.333 0.00 0.00 0.00 2.59
1615 1680 7.977853 CCAATCAAGCTATGCAATAAAAAGACT 59.022 33.333 0.00 0.00 0.00 3.24
1631 1696 1.546323 CCACAGGTCACCAATCAAGCT 60.546 52.381 0.00 0.00 0.00 3.74
1645 1710 0.036732 ACAGCACACATACCCACAGG 59.963 55.000 0.00 0.00 40.04 4.00
1649 1714 1.055849 ACTCACAGCACACATACCCA 58.944 50.000 0.00 0.00 0.00 4.51
1683 1748 2.424557 ACTTCAGCTGCACAGAGAATG 58.575 47.619 9.47 0.00 0.00 2.67
1726 1791 1.336887 GGAAAGCTGCTGTCGTAGTCA 60.337 52.381 13.43 0.00 0.00 3.41
1738 1803 1.676967 GCCCCTGACAGGAAAGCTG 60.677 63.158 23.77 4.62 37.67 4.24
1804 1869 1.140852 CCATCGGGCTCAATAGAACCA 59.859 52.381 0.00 0.00 31.35 3.67
1816 1881 0.383231 CAAAGAAGCATCCATCGGGC 59.617 55.000 0.00 0.00 0.00 6.13
1825 1890 0.320374 TCCGTCGTCCAAAGAAGCAT 59.680 50.000 0.00 0.00 0.00 3.79
1838 1903 0.109226 GAACTCCTCACCTTCCGTCG 60.109 60.000 0.00 0.00 0.00 5.12
1875 1940 8.729756 TGAGAACCTACATTTTACATGTGAATG 58.270 33.333 23.97 23.97 36.95 2.67
1910 1975 2.827322 CCAATGTCCAAGCTTGAATGGA 59.173 45.455 28.05 14.60 43.32 3.41
1942 2050 5.256474 ACATTCTAGCAGCACCATTAAAGT 58.744 37.500 0.00 0.00 0.00 2.66
1963 2071 7.861629 AGTGGTGGAGAATCATATTCTTAACA 58.138 34.615 3.80 3.39 36.25 2.41
1974 2082 6.127647 GCAAAATGAATAGTGGTGGAGAATCA 60.128 38.462 0.00 0.00 36.25 2.57
1998 2106 6.026513 GTCTGCATTTAACTTCAGAATCAGC 58.973 40.000 0.00 0.00 37.33 4.26
2005 2113 7.648908 TGTTCATTTGTCTGCATTTAACTTCAG 59.351 33.333 0.00 0.00 0.00 3.02
2051 2159 2.649531 TTTCCAACACCAGGACGAAT 57.350 45.000 0.00 0.00 34.19 3.34
2078 2186 0.102300 GCTGGTCAACAAACACCCAC 59.898 55.000 0.00 0.00 0.00 4.61
2105 2213 5.744819 GCCGTAGAGTTCTTTTATCTCAGTC 59.255 44.000 0.00 0.00 0.00 3.51
2222 2330 9.985318 GAAGTGAACAAAATGAATATGAGAGAG 57.015 33.333 0.00 0.00 0.00 3.20
2223 2331 9.730705 AGAAGTGAACAAAATGAATATGAGAGA 57.269 29.630 0.00 0.00 0.00 3.10
2264 2373 9.509855 CTACTGATAGTGCTTTACTACTTCAAG 57.490 37.037 0.00 0.00 44.30 3.02
2305 2414 4.209288 GTGTGTGTGTGCTACTTAACTCAG 59.791 45.833 0.00 0.00 0.00 3.35
2319 2428 6.704493 AGTTCAAAAGTATATCGTGTGTGTGT 59.296 34.615 0.00 0.00 0.00 3.72
2320 2429 7.117241 AGTTCAAAAGTATATCGTGTGTGTG 57.883 36.000 0.00 0.00 0.00 3.82
2321 2430 7.063074 GCTAGTTCAAAAGTATATCGTGTGTGT 59.937 37.037 0.00 0.00 0.00 3.72
2328 2437 7.636359 GTGCTTTGCTAGTTCAAAAGTATATCG 59.364 37.037 0.00 0.00 35.75 2.92
2379 2488 3.007979 TGTGTGTGCACTACTTAGTCG 57.992 47.619 19.41 0.00 45.44 4.18
2473 2585 6.045318 CCAACGAGAATTATCAGACACATCT 58.955 40.000 0.35 0.00 34.57 2.90
2559 2671 7.672239 TGTTTTATAAACAACCTAGGGCAGATT 59.328 33.333 14.81 5.98 0.00 2.40
2620 2732 7.772332 ACAGTTATTAAGCTGTGCATAGTAC 57.228 36.000 12.41 0.00 43.45 2.73
2663 2775 2.507058 AGGCATGCCTGTAGAAATGAGA 59.493 45.455 38.23 0.00 46.22 3.27
3194 3306 9.332502 TGTTAGTGAACAAGATTTTAGCTACAA 57.667 29.630 0.00 0.00 42.66 2.41
3195 3307 8.770828 GTGTTAGTGAACAAGATTTTAGCTACA 58.229 33.333 0.00 0.00 46.99 2.74
3196 3308 8.989980 AGTGTTAGTGAACAAGATTTTAGCTAC 58.010 33.333 0.00 0.00 46.99 3.58
3197 3309 9.555727 AAGTGTTAGTGAACAAGATTTTAGCTA 57.444 29.630 0.00 0.00 46.99 3.32
3198 3310 8.451908 AAGTGTTAGTGAACAAGATTTTAGCT 57.548 30.769 0.00 0.00 46.99 3.32
3202 3314 9.797556 GGTTAAAGTGTTAGTGAACAAGATTTT 57.202 29.630 0.00 0.00 46.99 1.82
3203 3315 9.185680 AGGTTAAAGTGTTAGTGAACAAGATTT 57.814 29.630 0.00 0.00 46.99 2.17
3204 3316 8.621286 CAGGTTAAAGTGTTAGTGAACAAGATT 58.379 33.333 0.00 0.00 46.99 2.40
3205 3317 7.990886 TCAGGTTAAAGTGTTAGTGAACAAGAT 59.009 33.333 0.00 0.00 46.99 2.40
3206 3318 7.332557 TCAGGTTAAAGTGTTAGTGAACAAGA 58.667 34.615 0.00 0.00 46.99 3.02
3207 3319 7.548196 TCAGGTTAAAGTGTTAGTGAACAAG 57.452 36.000 0.00 0.00 46.99 3.16
3208 3320 9.048446 GTATCAGGTTAAAGTGTTAGTGAACAA 57.952 33.333 0.00 0.00 46.99 2.83
3209 3321 8.426489 AGTATCAGGTTAAAGTGTTAGTGAACA 58.574 33.333 0.00 0.00 43.41 3.18
3210 3322 8.709646 CAGTATCAGGTTAAAGTGTTAGTGAAC 58.290 37.037 5.83 0.00 36.00 3.18
3211 3323 8.426489 ACAGTATCAGGTTAAAGTGTTAGTGAA 58.574 33.333 13.38 0.00 0.00 3.18
3212 3324 7.959175 ACAGTATCAGGTTAAAGTGTTAGTGA 58.041 34.615 13.38 0.00 0.00 3.41
3213 3325 8.603242 AACAGTATCAGGTTAAAGTGTTAGTG 57.397 34.615 0.00 8.44 34.56 2.74
3214 3326 9.269453 GAAACAGTATCAGGTTAAAGTGTTAGT 57.731 33.333 0.00 0.00 35.10 2.24
3215 3327 9.490379 AGAAACAGTATCAGGTTAAAGTGTTAG 57.510 33.333 0.00 0.00 35.10 2.34
3216 3328 9.485206 GAGAAACAGTATCAGGTTAAAGTGTTA 57.515 33.333 0.00 0.00 35.10 2.41
3217 3329 7.170998 CGAGAAACAGTATCAGGTTAAAGTGTT 59.829 37.037 0.00 0.00 37.15 3.32
3218 3330 6.645415 CGAGAAACAGTATCAGGTTAAAGTGT 59.355 38.462 0.00 0.00 0.00 3.55
3219 3331 6.645415 ACGAGAAACAGTATCAGGTTAAAGTG 59.355 38.462 0.00 0.00 0.00 3.16
3220 3332 6.756221 ACGAGAAACAGTATCAGGTTAAAGT 58.244 36.000 0.00 0.00 0.00 2.66
3281 3393 6.135400 GCAATGGTTTTAAAGTTGCATTGAC 58.865 36.000 17.35 0.00 43.33 3.18
3413 3527 8.010697 TCTAGTAAATAACTCATCCCTCCATCA 58.989 37.037 0.00 0.00 39.80 3.07
3564 3679 1.892474 TGGGTCAAGGCAGCATAAAAC 59.108 47.619 0.00 0.00 0.00 2.43
3698 3813 5.296813 ACGAGAATGGCAGAACAAAATAC 57.703 39.130 0.00 0.00 0.00 1.89
3772 3887 3.683802 AGAAGAATGGCCAGAGAAACAG 58.316 45.455 13.05 0.00 0.00 3.16
3942 4060 7.004555 TCAGTAGTGTAGAAATGTTCCACAT 57.995 36.000 0.00 0.00 41.31 3.21
3997 4115 4.968971 TTTAGAAACGGAGGGAGAAGTT 57.031 40.909 0.00 0.00 0.00 2.66
4154 4272 8.062536 AGACCTACTCACTCTGTTCCTAAATAT 58.937 37.037 0.00 0.00 0.00 1.28
5119 5251 1.080298 GCTGCTTTCCATGGTGCAC 60.080 57.895 19.95 8.80 0.00 4.57
5282 5416 3.606687 CCAACGACTACAATAGCCCTTT 58.393 45.455 0.00 0.00 0.00 3.11
5296 5430 1.378531 TCATGCCTAATGCCAACGAC 58.621 50.000 0.00 0.00 40.16 4.34
5335 5469 5.362430 AGGAGAAAGATGACACTATGGACTC 59.638 44.000 0.00 0.00 0.00 3.36
5583 5722 9.415544 CCTTCAAAATACATTTTTCTTGAGGAG 57.584 33.333 0.00 0.00 37.86 3.69
5883 6388 4.823989 ACAGCAGTGCTAAGTTCAAAGAAT 59.176 37.500 19.26 0.00 36.40 2.40
5889 6394 7.102993 TGATAATAACAGCAGTGCTAAGTTCA 58.897 34.615 19.26 9.70 36.40 3.18
5890 6395 7.539712 TGATAATAACAGCAGTGCTAAGTTC 57.460 36.000 19.26 7.23 36.40 3.01
5970 6475 6.030548 TGTCTTCTTAGTTCTGATGACAGG 57.969 41.667 0.00 0.00 43.60 4.00
5974 6479 9.645059 CATTAGTTGTCTTCTTAGTTCTGATGA 57.355 33.333 0.00 0.00 0.00 2.92
6576 7081 3.743521 TGATTCCTTTCCTGTGTCTGTG 58.256 45.455 0.00 0.00 0.00 3.66
6648 7153 4.517285 GGGCATATGACAAGAAGTTCTCA 58.483 43.478 11.56 0.53 0.00 3.27
6791 7296 2.416836 GCCCTAAAAATCAAGCCGGTTC 60.417 50.000 1.90 0.00 0.00 3.62
6795 7300 1.818674 ACTGCCCTAAAAATCAAGCCG 59.181 47.619 0.00 0.00 0.00 5.52
6808 7313 8.592809 TCAAAATAAATGAAATGTAACTGCCCT 58.407 29.630 0.00 0.00 0.00 5.19
6972 7477 2.276201 GGCCACAAACAAAAACCACTC 58.724 47.619 0.00 0.00 0.00 3.51
6999 7504 2.862536 CGAATGCAGTGACAGTATGGAG 59.137 50.000 0.00 0.00 43.62 3.86
7746 8294 3.369892 CCTTCAGGTCTTGTAGGTCATGG 60.370 52.174 0.00 0.00 39.00 3.66
7830 8378 7.148306 GCATTTTTGGAACGGATAAGAGTCTTA 60.148 37.037 14.87 14.87 0.00 2.10


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

AutoCloner maintained by Alex Coulton.