Multiple sequence alignment - TraesCS3D01G221600

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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 TraesCS3D01G221600 chr3D 100.000 4800 0 0 1 4800 301894853 301890054 0.000000e+00 8865.0
1 TraesCS3D01G221600 chr3B 95.050 2182 75 17 684 2844 419056193 419058362 0.000000e+00 3400.0
2 TraesCS3D01G221600 chr3B 91.466 1160 52 16 3080 4229 419058599 419059721 0.000000e+00 1550.0
3 TraesCS3D01G221600 chr3B 91.557 533 40 4 4271 4800 419059864 419060394 0.000000e+00 730.0
4 TraesCS3D01G221600 chr3B 91.703 229 10 4 2842 3064 419058390 419058615 4.670000e-80 309.0
5 TraesCS3D01G221600 chr3B 85.171 263 33 6 4540 4800 419060402 419060660 1.020000e-66 265.0
6 TraesCS3D01G221600 chr3B 90.566 53 4 1 4178 4229 55395233 55395285 8.620000e-08 69.4
7 TraesCS3D01G221600 chr3A 93.837 1363 51 11 1495 2844 433329004 433330346 0.000000e+00 2021.0
8 TraesCS3D01G221600 chr3A 90.305 1506 111 17 1 1487 433325689 433327178 0.000000e+00 1940.0
9 TraesCS3D01G221600 chr3A 93.035 1163 54 6 3080 4229 433330573 433331721 0.000000e+00 1674.0
10 TraesCS3D01G221600 chr3A 91.176 578 44 5 4228 4800 433331847 433332422 0.000000e+00 778.0
11 TraesCS3D01G221600 chr3A 86.667 570 68 8 4236 4800 746183950 746184516 4.080000e-175 625.0
12 TraesCS3D01G221600 chr3A 82.700 237 17 11 2836 3064 433330369 433330589 6.340000e-44 189.0
13 TraesCS3D01G221600 chr3A 75.874 286 56 12 48 327 58997864 58997586 3.010000e-27 134.0
14 TraesCS3D01G221600 chr3A 78.363 171 27 10 4340 4503 655785173 655785006 8.500000e-18 102.0
15 TraesCS3D01G221600 chr4D 85.192 574 62 18 4235 4800 74098487 74097929 6.970000e-158 568.0
16 TraesCS3D01G221600 chr6A 88.356 292 27 5 4260 4546 578696604 578696315 1.280000e-90 344.0
17 TraesCS3D01G221600 chr6A 83.333 276 40 4 4530 4800 578696150 578695876 2.870000e-62 250.0
18 TraesCS3D01G221600 chr4A 87.319 276 32 3 4392 4666 513976543 513976816 3.610000e-81 313.0
19 TraesCS3D01G221600 chr4A 86.447 273 30 6 4529 4798 513996898 513997166 4.700000e-75 292.0
20 TraesCS3D01G221600 chr7A 85.911 291 32 8 4260 4544 151346096 151345809 7.810000e-78 302.0
21 TraesCS3D01G221600 chr7B 84.074 270 38 5 4533 4800 113504844 113504578 6.160000e-64 255.0
22 TraesCS3D01G221600 chr7B 82.295 305 36 13 4260 4560 113557902 113557612 1.030000e-61 248.0
23 TraesCS3D01G221600 chr2D 78.806 335 58 6 1 322 561326854 561326520 3.760000e-51 213.0
24 TraesCS3D01G221600 chr2D 83.607 122 14 5 241 358 309083721 309083602 5.080000e-20 110.0
25 TraesCS3D01G221600 chr1B 80.513 195 38 0 1 195 561767038 561767232 2.990000e-32 150.0
26 TraesCS3D01G221600 chr1A 75.617 324 58 16 1 306 496484756 496484436 1.800000e-29 141.0
27 TraesCS3D01G221600 chr2B 85.981 107 10 4 241 343 359112938 359113043 5.080000e-20 110.0
28 TraesCS3D01G221600 chr1D 78.571 168 28 7 4340 4503 479335122 479334959 2.360000e-18 104.0
29 TraesCS3D01G221600 chr5B 77.372 137 27 4 1 135 292183695 292183829 1.430000e-10 78.7


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 TraesCS3D01G221600 chr3D 301890054 301894853 4799 True 8865.0 8865 100.0000 1 4800 1 chr3D.!!$R1 4799
1 TraesCS3D01G221600 chr3B 419056193 419060660 4467 False 1250.8 3400 90.9894 684 4800 5 chr3B.!!$F2 4116
2 TraesCS3D01G221600 chr3A 433325689 433332422 6733 False 1320.4 2021 90.2106 1 4800 5 chr3A.!!$F2 4799
3 TraesCS3D01G221600 chr3A 746183950 746184516 566 False 625.0 625 86.6670 4236 4800 1 chr3A.!!$F1 564
4 TraesCS3D01G221600 chr4D 74097929 74098487 558 True 568.0 568 85.1920 4235 4800 1 chr4D.!!$R1 565
5 TraesCS3D01G221600 chr6A 578695876 578696604 728 True 297.0 344 85.8445 4260 4800 2 chr6A.!!$R1 540

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
659 661 0.107508 ATCACCATCACCTTGCCGAG 60.108 55.0 0.00 0.0 0.00 4.63 F
1209 1216 0.174845 CGTCTATGAAAGTGCCCGGA 59.825 55.0 0.73 0.0 0.00 5.14 F
2366 4221 0.478072 TCACACCAGGGAAACAGCAT 59.522 50.0 0.00 0.0 0.00 3.79 F
3607 5523 0.602905 GCTGTAGCCTCACGGTGTTT 60.603 55.0 8.17 0.0 34.31 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 3699 0.169672 GGTCATCGACGAAGGACGAA 59.830 55.0 20.06 0.0 45.77 3.85 R
3075 4978 0.035056 AGGCACTTGACATACAGCCC 60.035 55.0 0.00 0.0 37.86 5.19 R
3754 5670 0.395311 TCCGATCGTAGCCTTGTCCT 60.395 55.0 15.09 0.0 0.00 3.85 R
4626 6891 4.405358 TCCACTGGCTTGTTTCAAAAAGAT 59.595 37.5 0.00 0.0 0.00 2.40 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 6.377712 TGCACAACATGATTATGAAGGATGAA 59.622 34.615 4.20 0.00 37.73 2.57
74 75 5.298777 GGTCTGGAATTTGAGAAGATGGATG 59.701 44.000 0.00 0.00 0.00 3.51
78 79 6.665695 TGGAATTTGAGAAGATGGATGATCA 58.334 36.000 0.00 0.00 32.86 2.92
95 96 6.312426 GGATGATCATATCGAACTTCCACATC 59.688 42.308 8.54 0.00 39.33 3.06
108 109 0.173255 CCACATCAAAATCCGGCCAC 59.827 55.000 2.24 0.00 0.00 5.01
137 138 4.630111 GGAGTTTGTCCAAATGCATCAAA 58.370 39.130 0.00 2.81 46.10 2.69
139 140 5.178067 GGAGTTTGTCCAAATGCATCAAAAG 59.822 40.000 10.94 0.00 46.10 2.27
147 148 4.083110 CCAAATGCATCAAAAGACTCGACT 60.083 41.667 0.00 0.00 0.00 4.18
149 150 4.935885 ATGCATCAAAAGACTCGACTTC 57.064 40.909 0.00 0.00 0.00 3.01
172 173 2.041620 AGGAACTCATGGGCAGCTTAAA 59.958 45.455 0.00 0.00 0.00 1.52
181 182 5.130975 TCATGGGCAGCTTAAAGAAGATCTA 59.869 40.000 0.00 0.00 34.25 1.98
185 186 7.573710 TGGGCAGCTTAAAGAAGATCTAATTA 58.426 34.615 0.00 0.00 34.25 1.40
199 200 9.547753 GAAGATCTAATTAAACATCTGTAGGCA 57.452 33.333 0.00 0.00 0.00 4.75
214 215 2.849294 AGGCACTTGAAGAGGAGAAC 57.151 50.000 0.00 0.00 27.25 3.01
221 222 4.524714 CACTTGAAGAGGAGAACTAGACCA 59.475 45.833 0.00 0.00 0.00 4.02
229 230 4.290093 AGGAGAACTAGACCATATGTGCA 58.710 43.478 0.00 0.00 0.00 4.57
232 233 3.389329 AGAACTAGACCATATGTGCAGGG 59.611 47.826 0.00 0.00 0.00 4.45
235 236 2.425143 AGACCATATGTGCAGGGTTG 57.575 50.000 1.24 0.00 32.77 3.77
236 237 1.915489 AGACCATATGTGCAGGGTTGA 59.085 47.619 1.24 0.00 32.77 3.18
308 310 9.730420 ATTACTGTCGCATTTGATTATTTTACC 57.270 29.630 0.00 0.00 0.00 2.85
310 312 5.897050 TGTCGCATTTGATTATTTTACCCC 58.103 37.500 0.00 0.00 0.00 4.95
315 317 7.038659 CGCATTTGATTATTTTACCCCTCAAA 58.961 34.615 0.00 0.00 37.12 2.69
332 334 9.660544 ACCCCTCAAAGATTTTATGCTATTATT 57.339 29.630 0.00 0.00 0.00 1.40
340 342 9.546428 AAGATTTTATGCTATTATTTTGGGTGC 57.454 29.630 0.00 0.00 0.00 5.01
358 360 6.113411 TGGGTGCTATAGACTTAAGAAAAGC 58.887 40.000 10.09 10.54 0.00 3.51
362 364 6.258947 GTGCTATAGACTTAAGAAAAGCAGGG 59.741 42.308 10.09 0.00 39.22 4.45
368 370 2.467566 TAAGAAAAGCAGGGACGGAC 57.532 50.000 0.00 0.00 0.00 4.79
376 378 0.803117 GCAGGGACGGACTTTTAAGC 59.197 55.000 0.00 0.00 0.00 3.09
378 380 0.672711 AGGGACGGACTTTTAAGCGC 60.673 55.000 0.00 0.00 0.00 5.92
382 384 0.802494 ACGGACTTTTAAGCGCCATG 59.198 50.000 2.29 0.00 0.00 3.66
401 403 4.445305 CCATGATTAGATGGCCACTTCTCA 60.445 45.833 8.16 13.41 36.69 3.27
408 410 0.758734 TGGCCACTTCTCATATCCGG 59.241 55.000 0.00 0.00 0.00 5.14
413 415 3.499918 GCCACTTCTCATATCCGGATTTG 59.500 47.826 24.71 24.45 0.00 2.32
415 417 4.129380 CACTTCTCATATCCGGATTTGCA 58.871 43.478 24.71 11.79 0.00 4.08
416 418 4.576053 CACTTCTCATATCCGGATTTGCAA 59.424 41.667 24.71 17.86 0.00 4.08
418 420 5.066505 ACTTCTCATATCCGGATTTGCAAAC 59.933 40.000 24.71 8.51 0.00 2.93
424 426 0.168128 CCGGATTTGCAAACGAGTCC 59.832 55.000 20.10 18.22 33.60 3.85
436 438 1.765230 ACGAGTCCAGAGACATACCC 58.235 55.000 0.00 0.00 46.15 3.69
441 443 3.890147 GAGTCCAGAGACATACCCGTAAT 59.110 47.826 0.00 0.00 46.15 1.89
445 447 4.280929 TCCAGAGACATACCCGTAATCATG 59.719 45.833 0.00 0.00 0.00 3.07
446 448 4.560128 CAGAGACATACCCGTAATCATGG 58.440 47.826 0.00 0.00 0.00 3.66
448 450 4.524714 AGAGACATACCCGTAATCATGGAG 59.475 45.833 0.00 0.00 31.77 3.86
456 458 8.668353 CATACCCGTAATCATGGAGAAATATTG 58.332 37.037 0.00 0.00 31.77 1.90
461 463 5.443185 AATCATGGAGAAATATTGTGCCG 57.557 39.130 0.00 0.00 0.00 5.69
466 468 6.375736 TCATGGAGAAATATTGTGCCGTTTTA 59.624 34.615 0.00 0.00 0.00 1.52
467 469 6.576662 TGGAGAAATATTGTGCCGTTTTAA 57.423 33.333 0.00 0.00 0.00 1.52
472 474 4.976224 ATATTGTGCCGTTTTAAGGGTC 57.024 40.909 3.45 0.00 36.36 4.46
473 475 1.320507 TTGTGCCGTTTTAAGGGTCC 58.679 50.000 3.45 0.00 36.36 4.46
476 478 0.885596 TGCCGTTTTAAGGGTCCGTG 60.886 55.000 3.45 0.00 36.36 4.94
480 482 2.211806 CGTTTTAAGGGTCCGTGTTGA 58.788 47.619 0.00 0.00 0.00 3.18
486 488 0.321653 AGGGTCCGTGTTGAAGATGC 60.322 55.000 0.00 0.00 0.00 3.91
487 489 0.321653 GGGTCCGTGTTGAAGATGCT 60.322 55.000 0.00 0.00 0.00 3.79
497 499 5.006165 CGTGTTGAAGATGCTCTTAGAATCC 59.994 44.000 0.00 0.00 36.73 3.01
503 505 3.135530 AGATGCTCTTAGAATCCCCACAC 59.864 47.826 0.00 0.00 30.08 3.82
539 541 6.304356 TCTTAGAATGTTTCAAGTGCACTG 57.696 37.500 22.49 14.60 0.00 3.66
540 542 3.360249 AGAATGTTTCAAGTGCACTGC 57.640 42.857 22.49 9.18 0.00 4.40
541 543 2.689471 AGAATGTTTCAAGTGCACTGCA 59.311 40.909 22.49 14.44 35.60 4.41
547 549 1.713597 TCAAGTGCACTGCATAGTCG 58.286 50.000 22.49 2.02 41.91 4.18
604 606 2.410262 GCTAATACGTGTGCGCATCATC 60.410 50.000 15.91 0.00 42.83 2.92
609 611 1.266718 ACGTGTGCGCATCATCTTTTT 59.733 42.857 15.91 0.00 42.83 1.94
649 651 5.675684 TGACTTTGCTAGTATCACCATCA 57.324 39.130 0.00 0.00 37.17 3.07
656 658 2.717639 AGTATCACCATCACCTTGCC 57.282 50.000 0.00 0.00 0.00 4.52
659 661 0.107508 ATCACCATCACCTTGCCGAG 60.108 55.000 0.00 0.00 0.00 4.63
661 663 1.021390 CACCATCACCTTGCCGAGAC 61.021 60.000 0.00 0.00 0.00 3.36
664 666 1.207089 CCATCACCTTGCCGAGACTTA 59.793 52.381 0.00 0.00 0.00 2.24
665 667 2.271800 CATCACCTTGCCGAGACTTAC 58.728 52.381 0.00 0.00 0.00 2.34
666 668 1.334160 TCACCTTGCCGAGACTTACA 58.666 50.000 0.00 0.00 0.00 2.41
672 674 3.325870 CTTGCCGAGACTTACAACATGA 58.674 45.455 0.00 0.00 0.00 3.07
755 757 2.953020 ACAGATCAAACTCGAGCAGTC 58.047 47.619 13.61 4.14 32.30 3.51
805 808 9.804758 ATTCGGTTAATTAATTAATTTTCCGCA 57.195 25.926 32.85 28.82 42.76 5.69
806 809 8.844441 TCGGTTAATTAATTAATTTTCCGCAG 57.156 30.769 32.85 21.40 42.76 5.18
852 859 0.535102 GATACAACTCCGGCCCCATG 60.535 60.000 0.00 0.00 0.00 3.66
909 916 1.155889 TTAACACGGCAGCATGTGAG 58.844 50.000 20.45 0.00 39.38 3.51
982 989 2.228138 AGAACACCACGCGAAGTTTA 57.772 45.000 15.93 0.00 0.00 2.01
983 990 2.553086 AGAACACCACGCGAAGTTTAA 58.447 42.857 15.93 0.00 0.00 1.52
998 1005 5.178809 CGAAGTTTAACAGGAACGAGGAAAT 59.821 40.000 0.00 0.00 32.38 2.17
1209 1216 0.174845 CGTCTATGAAAGTGCCCGGA 59.825 55.000 0.73 0.00 0.00 5.14
1493 3332 4.539509 TTGGCGTGCTTATTAATTACCG 57.460 40.909 0.00 0.00 0.00 4.02
1509 3348 0.833287 ACCGCCACAGAGCAGAATAT 59.167 50.000 0.00 0.00 0.00 1.28
1729 3572 2.358267 GACCAGGAGTCGATGAACGTAT 59.642 50.000 0.00 0.00 43.13 3.06
1736 3582 7.273598 CCAGGAGTCGATGAACGTATTATTATG 59.726 40.741 0.00 0.00 43.13 1.90
1793 3639 2.047274 TGGCCGGAGAAAAGAGCG 60.047 61.111 5.05 0.00 0.00 5.03
1797 3643 1.805945 CCGGAGAAAAGAGCGGACG 60.806 63.158 0.00 0.00 0.00 4.79
1839 3685 1.538876 TACCAGGGCCTTCTGCAGT 60.539 57.895 14.67 0.00 43.89 4.40
1841 3687 1.975407 CCAGGGCCTTCTGCAGTTG 60.975 63.158 14.67 7.64 43.89 3.16
1853 3699 2.574006 TGCAGTTGGAGAAGCAGATT 57.426 45.000 0.00 0.00 32.48 2.40
1957 3803 3.178046 TGTCTCATGGCTGGGTAACTTA 58.822 45.455 0.00 0.00 0.00 2.24
2065 3919 1.194781 AAGATAGGGATGCCGCCGAT 61.195 55.000 0.00 0.00 0.00 4.18
2215 4070 0.531200 GGTGCGTACCTAAGCTGACT 59.469 55.000 16.23 0.00 43.97 3.41
2241 4096 1.005557 GTCTGAATTCTCGCATGCGTC 60.006 52.381 36.50 26.57 40.74 5.19
2366 4221 0.478072 TCACACCAGGGAAACAGCAT 59.522 50.000 0.00 0.00 0.00 3.79
2495 4350 7.963532 TGATACATAGGATGGTTTTAGGTCTC 58.036 38.462 0.00 0.00 33.60 3.36
2497 4352 6.487299 ACATAGGATGGTTTTAGGTCTCTC 57.513 41.667 0.00 0.00 33.60 3.20
2646 4502 2.303163 AACAGCGTGTACAGTGTCAA 57.697 45.000 0.00 0.00 0.00 3.18
2822 4687 6.009115 ACTATTCCACACGAAAATTTCACC 57.991 37.500 6.53 0.00 33.08 4.02
2953 4850 2.814097 GCCTTAAAGCTGTGGACCAGAA 60.814 50.000 0.00 0.00 44.49 3.02
3023 4926 3.364889 TGGATACGGATAAACTCAGCG 57.635 47.619 0.00 0.00 42.51 5.18
3045 4948 3.632145 GGAAGACTGTTCAATTGGTGTGT 59.368 43.478 5.42 0.41 0.00 3.72
3046 4949 4.498009 GGAAGACTGTTCAATTGGTGTGTG 60.498 45.833 5.42 0.00 0.00 3.82
3047 4950 3.620488 AGACTGTTCAATTGGTGTGTGT 58.380 40.909 5.42 0.00 0.00 3.72
3048 4951 3.378112 AGACTGTTCAATTGGTGTGTGTG 59.622 43.478 5.42 0.00 0.00 3.82
3049 4952 3.088532 ACTGTTCAATTGGTGTGTGTGT 58.911 40.909 5.42 0.00 0.00 3.72
3050 4953 4.265893 ACTGTTCAATTGGTGTGTGTGTA 58.734 39.130 5.42 0.00 0.00 2.90
3051 4954 4.887071 ACTGTTCAATTGGTGTGTGTGTAT 59.113 37.500 5.42 0.00 0.00 2.29
3052 4955 5.180367 TGTTCAATTGGTGTGTGTGTATG 57.820 39.130 5.42 0.00 0.00 2.39
3053 4956 4.642437 TGTTCAATTGGTGTGTGTGTATGT 59.358 37.500 5.42 0.00 0.00 2.29
3054 4957 5.212194 GTTCAATTGGTGTGTGTGTATGTC 58.788 41.667 5.42 0.00 0.00 3.06
3055 4958 4.455606 TCAATTGGTGTGTGTGTATGTCA 58.544 39.130 5.42 0.00 0.00 3.58
3056 4959 4.884164 TCAATTGGTGTGTGTGTATGTCAA 59.116 37.500 5.42 0.00 0.00 3.18
3057 4960 5.008514 TCAATTGGTGTGTGTGTATGTCAAG 59.991 40.000 5.42 0.00 0.00 3.02
3058 4961 3.552132 TGGTGTGTGTGTATGTCAAGT 57.448 42.857 0.00 0.00 0.00 3.16
3059 4962 3.202097 TGGTGTGTGTGTATGTCAAGTG 58.798 45.455 0.00 0.00 0.00 3.16
3060 4963 3.202906 GGTGTGTGTGTATGTCAAGTGT 58.797 45.455 0.00 0.00 0.00 3.55
3061 4964 3.247648 GGTGTGTGTGTATGTCAAGTGTC 59.752 47.826 0.00 0.00 0.00 3.67
3062 4965 4.119862 GTGTGTGTGTATGTCAAGTGTCT 58.880 43.478 0.00 0.00 0.00 3.41
3063 4966 4.570772 GTGTGTGTGTATGTCAAGTGTCTT 59.429 41.667 0.00 0.00 0.00 3.01
3064 4967 5.064707 GTGTGTGTGTATGTCAAGTGTCTTT 59.935 40.000 0.00 0.00 0.00 2.52
3065 4968 5.645929 TGTGTGTGTATGTCAAGTGTCTTTT 59.354 36.000 0.00 0.00 0.00 2.27
3066 4969 6.150307 TGTGTGTGTATGTCAAGTGTCTTTTT 59.850 34.615 0.00 0.00 0.00 1.94
3092 4995 1.369091 CGGGGCTGTATGTCAAGTGC 61.369 60.000 0.00 0.00 0.00 4.40
3125 5028 2.475200 AGCAACGAAAGCTTGTGTTC 57.525 45.000 12.28 8.61 39.87 3.18
3159 5062 4.760047 GTGCTCATCGGTGCCGGT 62.760 66.667 10.94 0.00 40.25 5.28
3200 5103 2.347490 CCTTACACGCTGGCCTGT 59.653 61.111 11.69 6.03 0.00 4.00
3406 5313 3.499737 GTCCAGCCATCCAACGCG 61.500 66.667 3.53 3.53 0.00 6.01
3424 5331 1.731093 GCAGCTCCTCGTCTACCTC 59.269 63.158 0.00 0.00 0.00 3.85
3607 5523 0.602905 GCTGTAGCCTCACGGTGTTT 60.603 55.000 8.17 0.00 34.31 2.83
3682 5598 4.157120 ACGCATCGGGTGGGCTAC 62.157 66.667 5.09 0.00 44.09 3.58
3840 5756 2.246993 CTTGCCGCGCATTCCGTTTA 62.247 55.000 8.75 0.00 38.76 2.01
3865 5781 6.985645 AGTTTGGATACGTTTTACACACTGTA 59.014 34.615 0.00 0.00 42.51 2.74
4057 5981 0.461693 GCCACTGATGCAGGAGACTC 60.462 60.000 0.00 0.00 40.21 3.36
4144 6068 1.226974 CCTGCCGGTACATCTCACG 60.227 63.158 1.90 0.00 0.00 4.35
4184 6109 0.099968 TCGTGCTATGGCGTACAGAC 59.900 55.000 0.00 0.00 42.25 3.51
4214 6139 5.858381 TCCCTCAGTATCATAATGCAAGAC 58.142 41.667 0.00 0.00 0.00 3.01
4273 6344 9.744468 TTGCTTTCTTACTTTCTGGTATTTTTC 57.256 29.630 0.00 0.00 0.00 2.29
4312 6387 8.313944 TGATGGCTCCATACTACTAGTTTTTA 57.686 34.615 0.00 0.00 36.70 1.52
4362 6442 4.592942 TCTCTCTCCCAAACAAATCCATG 58.407 43.478 0.00 0.00 0.00 3.66
4790 7327 7.575414 TTGTGAAATAAGCCAGTGAAAAGTA 57.425 32.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.712639 GCAGTATCTTCACTTTCATCCTTCATA 59.287 37.037 0.00 0.00 0.00 2.15
20 21 6.541641 GCAGTATCTTCACTTTCATCCTTCAT 59.458 38.462 0.00 0.00 0.00 2.57
23 24 5.189180 GGCAGTATCTTCACTTTCATCCTT 58.811 41.667 0.00 0.00 0.00 3.36
31 32 3.177228 ACCTCTGGCAGTATCTTCACTT 58.823 45.455 15.27 0.00 0.00 3.16
74 75 7.482654 TTTGATGTGGAAGTTCGATATGATC 57.517 36.000 1.89 0.00 0.00 2.92
78 79 6.017934 CGGATTTTGATGTGGAAGTTCGATAT 60.018 38.462 0.00 0.00 0.00 1.63
95 96 0.312416 TCAAACGTGGCCGGATTTTG 59.688 50.000 5.05 6.49 38.78 2.44
108 109 4.290155 CATTTGGACAAACTCCTCAAACG 58.710 43.478 0.00 0.00 40.26 3.60
147 148 0.250234 CTGCCCATGAGTTCCTCGAA 59.750 55.000 0.00 0.00 32.35 3.71
149 150 1.817099 GCTGCCCATGAGTTCCTCG 60.817 63.158 0.00 0.00 32.35 4.63
172 173 9.771534 GCCTACAGATGTTTAATTAGATCTTCT 57.228 33.333 0.00 0.00 0.00 2.85
181 182 7.665559 TCTTCAAGTGCCTACAGATGTTTAATT 59.334 33.333 0.00 0.00 0.00 1.40
185 186 4.973168 TCTTCAAGTGCCTACAGATGTTT 58.027 39.130 0.00 0.00 0.00 2.83
192 193 2.889512 TCTCCTCTTCAAGTGCCTACA 58.110 47.619 0.00 0.00 0.00 2.74
195 196 2.334023 AGTTCTCCTCTTCAAGTGCCT 58.666 47.619 0.00 0.00 0.00 4.75
199 200 4.742012 TGGTCTAGTTCTCCTCTTCAAGT 58.258 43.478 0.00 0.00 0.00 3.16
214 215 3.134623 TCAACCCTGCACATATGGTCTAG 59.865 47.826 7.80 0.09 0.00 2.43
275 277 7.745022 ATCAAATGCGACAGTAATTCAAATG 57.255 32.000 0.00 0.00 0.00 2.32
286 288 5.977129 GGGGTAAAATAATCAAATGCGACAG 59.023 40.000 0.00 0.00 0.00 3.51
290 292 6.142818 TGAGGGGTAAAATAATCAAATGCG 57.857 37.500 0.00 0.00 0.00 4.73
315 317 8.927411 AGCACCCAAAATAATAGCATAAAATCT 58.073 29.630 0.00 0.00 0.00 2.40
330 332 9.528489 TTTTCTTAAGTCTATAGCACCCAAAAT 57.472 29.630 1.63 0.00 0.00 1.82
331 333 8.927675 TTTTCTTAAGTCTATAGCACCCAAAA 57.072 30.769 1.63 0.00 0.00 2.44
332 334 7.120726 GCTTTTCTTAAGTCTATAGCACCCAAA 59.879 37.037 1.63 0.00 0.00 3.28
333 335 6.598064 GCTTTTCTTAAGTCTATAGCACCCAA 59.402 38.462 1.63 0.00 0.00 4.12
334 336 6.113411 GCTTTTCTTAAGTCTATAGCACCCA 58.887 40.000 1.63 0.00 0.00 4.51
340 342 6.697892 CGTCCCTGCTTTTCTTAAGTCTATAG 59.302 42.308 1.63 0.00 0.00 1.31
343 345 4.322499 CCGTCCCTGCTTTTCTTAAGTCTA 60.322 45.833 1.63 0.00 0.00 2.59
344 346 3.557264 CCGTCCCTGCTTTTCTTAAGTCT 60.557 47.826 1.63 0.00 0.00 3.24
353 355 2.067365 AAAAGTCCGTCCCTGCTTTT 57.933 45.000 0.00 0.00 36.64 2.27
358 360 1.076332 CGCTTAAAAGTCCGTCCCTG 58.924 55.000 0.00 0.00 0.00 4.45
362 364 1.084289 ATGGCGCTTAAAAGTCCGTC 58.916 50.000 7.64 0.00 0.00 4.79
368 370 5.455392 CCATCTAATCATGGCGCTTAAAAG 58.545 41.667 7.64 0.00 37.12 2.27
378 380 4.070716 GAGAAGTGGCCATCTAATCATGG 58.929 47.826 9.72 0.00 45.70 3.66
382 384 6.112058 GGATATGAGAAGTGGCCATCTAATC 58.888 44.000 9.72 12.03 0.00 1.75
395 397 5.514279 GTTTGCAAATCCGGATATGAGAAG 58.486 41.667 19.48 3.99 0.00 2.85
401 403 3.541632 ACTCGTTTGCAAATCCGGATAT 58.458 40.909 19.48 5.29 0.00 1.63
408 410 3.067106 TCTCTGGACTCGTTTGCAAATC 58.933 45.455 16.21 8.54 0.00 2.17
413 415 2.086054 ATGTCTCTGGACTCGTTTGC 57.914 50.000 0.00 0.00 42.54 3.68
415 417 2.496470 GGGTATGTCTCTGGACTCGTTT 59.504 50.000 0.00 0.00 42.54 3.60
416 418 2.100989 GGGTATGTCTCTGGACTCGTT 58.899 52.381 0.00 0.00 42.54 3.85
418 420 0.663688 CGGGTATGTCTCTGGACTCG 59.336 60.000 0.00 0.00 42.54 4.18
424 426 4.280929 TCCATGATTACGGGTATGTCTCTG 59.719 45.833 0.00 0.00 0.00 3.35
436 438 6.373779 GGCACAATATTTCTCCATGATTACG 58.626 40.000 0.00 0.00 0.00 3.18
441 443 3.884895 ACGGCACAATATTTCTCCATGA 58.115 40.909 0.00 0.00 0.00 3.07
445 447 6.033966 CCTTAAAACGGCACAATATTTCTCC 58.966 40.000 0.00 0.00 0.00 3.71
446 448 6.033966 CCCTTAAAACGGCACAATATTTCTC 58.966 40.000 0.00 0.00 0.00 2.87
448 450 5.716094 ACCCTTAAAACGGCACAATATTTC 58.284 37.500 0.00 0.00 0.00 2.17
456 458 0.886043 ACGGACCCTTAAAACGGCAC 60.886 55.000 0.00 0.00 0.00 5.01
461 463 3.878699 TCTTCAACACGGACCCTTAAAAC 59.121 43.478 0.00 0.00 0.00 2.43
466 468 1.882352 GCATCTTCAACACGGACCCTT 60.882 52.381 0.00 0.00 0.00 3.95
467 469 0.321653 GCATCTTCAACACGGACCCT 60.322 55.000 0.00 0.00 0.00 4.34
486 488 3.887621 TTCGTGTGGGGATTCTAAGAG 57.112 47.619 0.00 0.00 0.00 2.85
487 489 4.627284 TTTTCGTGTGGGGATTCTAAGA 57.373 40.909 0.00 0.00 0.00 2.10
512 514 5.299028 TGCACTTGAAACATTCTAAGAGCAA 59.701 36.000 16.44 0.00 39.13 3.91
529 531 0.723414 CCGACTATGCAGTGCACTTG 59.277 55.000 22.44 15.43 43.04 3.16
609 611 8.800031 GCAAAGTCAACGAAACAATTAGTAAAA 58.200 29.630 0.00 0.00 0.00 1.52
610 612 8.185505 AGCAAAGTCAACGAAACAATTAGTAAA 58.814 29.630 0.00 0.00 0.00 2.01
611 613 7.699566 AGCAAAGTCAACGAAACAATTAGTAA 58.300 30.769 0.00 0.00 0.00 2.24
649 651 1.414919 TGTTGTAAGTCTCGGCAAGGT 59.585 47.619 0.00 0.00 0.00 3.50
656 658 8.110612 GTGATGTTAATCATGTTGTAAGTCTCG 58.889 37.037 0.00 0.00 44.54 4.04
661 663 9.844790 ACAATGTGATGTTAATCATGTTGTAAG 57.155 29.630 14.59 0.00 43.69 2.34
664 666 9.624697 GTTACAATGTGATGTTAATCATGTTGT 57.375 29.630 17.72 17.72 44.54 3.32
665 667 9.844790 AGTTACAATGTGATGTTAATCATGTTG 57.155 29.630 0.00 11.34 44.54 3.33
666 668 9.844790 CAGTTACAATGTGATGTTAATCATGTT 57.155 29.630 0.00 0.00 44.54 2.71
672 674 9.944376 AGTAGACAGTTACAATGTGATGTTAAT 57.056 29.630 0.00 0.00 34.75 1.40
909 916 2.682494 TCACCCTCACCCTACCGC 60.682 66.667 0.00 0.00 0.00 5.68
982 989 3.009033 TCCATCATTTCCTCGTTCCTGTT 59.991 43.478 0.00 0.00 0.00 3.16
983 990 2.571653 TCCATCATTTCCTCGTTCCTGT 59.428 45.455 0.00 0.00 0.00 4.00
998 1005 2.586245 CAAGCCGCTCCTCCATCA 59.414 61.111 0.00 0.00 0.00 3.07
1186 1193 1.348594 GCACTTTCATAGACGGCGC 59.651 57.895 6.90 0.00 0.00 6.53
1380 1387 2.192263 GGGGAGTTCTTGGTGATCTCT 58.808 52.381 0.00 0.00 39.95 3.10
1474 1495 2.912366 GCGGTAATTAATAAGCACGCC 58.088 47.619 10.08 0.00 39.88 5.68
1493 3332 7.678947 ACAATTATATATTCTGCTCTGTGGC 57.321 36.000 0.00 0.00 0.00 5.01
1509 3348 3.182341 ACAACGCCGGCTACAATTATA 57.818 42.857 26.68 0.00 0.00 0.98
1570 3413 3.644399 GACCTCGGCGACCAAGGTC 62.644 68.421 24.26 24.26 46.47 3.85
1705 3548 2.338500 GTTCATCGACTCCTGGTCAAC 58.662 52.381 0.00 0.00 44.70 3.18
1714 3557 7.798486 AGCATAATAATACGTTCATCGACTC 57.202 36.000 0.00 0.00 42.86 3.36
1729 3572 6.422333 TGTTCATCCACCTGAAGCATAATAA 58.578 36.000 0.00 0.00 35.88 1.40
1736 3582 1.200948 GCTTGTTCATCCACCTGAAGC 59.799 52.381 0.00 0.00 35.88 3.86
1839 3685 2.303022 AGGACGAAATCTGCTTCTCCAA 59.697 45.455 0.00 0.00 30.87 3.53
1841 3687 2.682155 AGGACGAAATCTGCTTCTCC 57.318 50.000 0.00 0.00 0.00 3.71
1853 3699 0.169672 GGTCATCGACGAAGGACGAA 59.830 55.000 20.06 0.00 45.77 3.85
2065 3919 5.332707 CGTGAGATGAGATTGTTCTTCGTA 58.667 41.667 0.00 0.00 30.30 3.43
2123 3977 2.225491 TCACAATTAAACCTGCGTCTGC 59.775 45.455 0.00 0.00 43.20 4.26
2215 4070 4.025730 GCATGCGAGAATTCAGACGATAAA 60.026 41.667 18.58 5.94 0.00 1.40
2241 4096 1.325640 CCTGCGAGAAATCACATCACG 59.674 52.381 0.00 0.00 34.63 4.35
2366 4221 4.188462 TGCTCTTTCAGACGTTTGAAGAA 58.812 39.130 19.37 11.81 38.25 2.52
2646 4502 4.580580 AGAGATGTTGGAAGCGAAAAACTT 59.419 37.500 0.00 0.00 0.00 2.66
2740 4605 7.830217 TTGTAATCTTTCGAATCAAACAACG 57.170 32.000 0.00 0.00 0.00 4.10
2822 4687 7.408756 TTCAGGATTATTCACAAAGATTGGG 57.591 36.000 0.00 0.00 34.65 4.12
2915 4812 1.379642 GGCCCCTTTGATTCGCAGAG 61.380 60.000 0.00 0.00 38.43 3.35
3023 4926 3.632145 ACACACCAATTGAACAGTCTTCC 59.368 43.478 7.12 0.00 0.00 3.46
3067 4970 0.885196 GACATACAGCCCCGCAAAAA 59.115 50.000 0.00 0.00 0.00 1.94
3068 4971 0.250945 TGACATACAGCCCCGCAAAA 60.251 50.000 0.00 0.00 0.00 2.44
3069 4972 0.250945 TTGACATACAGCCCCGCAAA 60.251 50.000 0.00 0.00 0.00 3.68
3070 4973 0.676466 CTTGACATACAGCCCCGCAA 60.676 55.000 0.00 0.00 0.00 4.85
3071 4974 1.078497 CTTGACATACAGCCCCGCA 60.078 57.895 0.00 0.00 0.00 5.69
3072 4975 1.078426 ACTTGACATACAGCCCCGC 60.078 57.895 0.00 0.00 0.00 6.13
3073 4976 1.369091 GCACTTGACATACAGCCCCG 61.369 60.000 0.00 0.00 0.00 5.73
3074 4977 1.032114 GGCACTTGACATACAGCCCC 61.032 60.000 0.00 0.00 33.14 5.80
3075 4978 0.035056 AGGCACTTGACATACAGCCC 60.035 55.000 0.00 0.00 37.86 5.19
3076 4979 3.558674 AGGCACTTGACATACAGCC 57.441 52.632 0.00 0.00 37.54 4.85
3406 5313 1.731093 GAGGTAGACGAGGAGCTGC 59.269 63.158 0.00 0.00 0.00 5.25
3550 5466 2.202756 GAGACGATGGCCACGACC 60.203 66.667 27.07 19.10 34.70 4.79
3665 5581 4.157120 GTAGCCCACCCGATGCGT 62.157 66.667 0.00 0.00 0.00 5.24
3751 5667 1.802880 CGATCGTAGCCTTGTCCTTGG 60.803 57.143 7.03 0.00 0.00 3.61
3754 5670 0.395311 TCCGATCGTAGCCTTGTCCT 60.395 55.000 15.09 0.00 0.00 3.85
3763 5679 1.663445 GCGTCCTTCATCCGATCGTAG 60.663 57.143 15.09 3.33 0.00 3.51
3840 5756 5.818857 ACAGTGTGTAAAACGTATCCAAACT 59.181 36.000 0.00 0.00 0.00 2.66
3865 5781 6.894339 AATCGAACCAGTTCCAACTAAAAT 57.106 33.333 4.99 0.00 37.08 1.82
3918 5834 2.223180 GGCGACTTCTCACAAAAACGTT 60.223 45.455 0.00 0.00 0.00 3.99
3926 5842 1.299850 CACACGGCGACTTCTCACA 60.300 57.895 16.62 0.00 0.00 3.58
4057 5981 2.094752 CCTTTTTATTCACCACGGCCAG 60.095 50.000 2.24 0.00 0.00 4.85
4144 6068 1.591327 CACGGCAAAAACCAGTGGC 60.591 57.895 9.78 0.00 33.45 5.01
4184 6109 6.815641 GCATTATGATACTGAGGGAGTACATG 59.184 42.308 0.00 0.00 40.09 3.21
4197 6122 6.747280 GCAAAAACGTCTTGCATTATGATACT 59.253 34.615 23.29 0.00 46.78 2.12
4278 6349 9.105844 AGTAGTATGGAGCCATCAAACTAATAT 57.894 33.333 5.06 0.00 37.82 1.28
4282 6355 7.067421 ACTAGTAGTATGGAGCCATCAAACTA 58.933 38.462 5.06 5.97 37.82 2.24
4312 6387 7.329471 GTGATGTCGCATGTATACTACATTCAT 59.671 37.037 4.17 3.21 46.69 2.57
4452 6535 4.448210 TCTTGTTCTAAAGGTCTTTGCGT 58.552 39.130 6.24 0.00 34.23 5.24
4626 6891 4.405358 TCCACTGGCTTGTTTCAAAAAGAT 59.595 37.500 0.00 0.00 0.00 2.40
4745 7282 9.065798 TCACAAAAGTCACATCTATTTCAATCA 57.934 29.630 0.00 0.00 0.00 2.57
4746 7283 9.897744 TTCACAAAAGTCACATCTATTTCAATC 57.102 29.630 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.