Multiple sequence alignment - TraesCS3D01G163300

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 TraesCS3D01G163300 chr3D 100.000 4159 0 0 338 4496 134637619 134641777 0.000000e+00 7681
1 TraesCS3D01G163300 chr3D 83.195 601 71 11 663 1241 49966479 49965887 1.430000e-144 523
2 TraesCS3D01G163300 chr3D 94.118 85 4 1 3594 3677 55373795 55373879 1.310000e-25 128
3 TraesCS3D01G163300 chr3D 100.000 58 0 0 1 58 134637282 134637339 1.710000e-19 108
4 TraesCS3D01G163300 chr1B 93.717 3199 164 18 501 3671 414554677 414557866 0.000000e+00 4759
5 TraesCS3D01G163300 chr1B 93.829 3079 147 10 514 3550 494557074 494553997 0.000000e+00 4593
6 TraesCS3D01G163300 chr6B 93.036 3231 168 20 503 3681 132660572 132657347 0.000000e+00 4667
7 TraesCS3D01G163300 chr5A 93.075 3220 162 21 501 3675 651583622 651580419 0.000000e+00 4654
8 TraesCS3D01G163300 chr5A 93.142 2333 155 2 1241 3568 697888108 697890440 0.000000e+00 3417
9 TraesCS3D01G163300 chr4B 92.837 3225 173 25 501 3675 502274289 502277505 0.000000e+00 4623
10 TraesCS3D01G163300 chr4A 93.889 3093 144 12 501 3550 718010628 718007538 0.000000e+00 4623
11 TraesCS3D01G163300 chr4A 88.040 301 20 11 3380 3675 709875349 709875060 4.310000e-90 342
12 TraesCS3D01G163300 chr2B 93.579 3115 151 14 501 3572 138739940 138736832 0.000000e+00 4599
13 TraesCS3D01G163300 chr2B 88.012 976 71 10 503 1435 235598929 235597957 0.000000e+00 1112
14 TraesCS3D01G163300 chr2B 86.946 429 42 12 3251 3675 227897560 227897142 1.890000e-128 470
15 TraesCS3D01G163300 chr5B 92.974 3117 147 24 501 3576 607480365 607483450 0.000000e+00 4477
16 TraesCS3D01G163300 chr5B 91.536 827 64 5 3676 4496 180585685 180584859 0.000000e+00 1134
17 TraesCS3D01G163300 chr5B 81.742 597 78 14 663 1243 178915772 178915191 1.890000e-128 470
18 TraesCS3D01G163300 chr5B 78.764 259 31 8 748 997 333738283 333738040 7.790000e-33 152
19 TraesCS3D01G163300 chr2D 93.469 2511 135 12 1179 3675 573648345 573650840 0.000000e+00 3701
20 TraesCS3D01G163300 chr2D 92.019 827 59 7 3676 4496 539199081 539199906 0.000000e+00 1155
21 TraesCS3D01G163300 chr2D 88.873 692 63 6 501 1182 573646497 573647184 0.000000e+00 839
22 TraesCS3D01G163300 chr5D 91.176 1870 125 16 573 2431 403889447 403891287 0.000000e+00 2503
23 TraesCS3D01G163300 chr5D 86.236 356 33 2 948 1287 292765466 292765111 5.490000e-99 372
24 TraesCS3D01G163300 chr3B 87.954 1129 100 18 2552 3675 775176785 775175688 0.000000e+00 1299
25 TraesCS3D01G163300 chr3B 91.019 824 64 8 3676 4492 529427611 529426791 0.000000e+00 1103
26 TraesCS3D01G163300 chr3B 87.923 828 93 7 3676 4496 31624691 31623864 0.000000e+00 968
27 TraesCS3D01G163300 chr3B 87.468 790 77 14 2887 3675 769385940 769385172 0.000000e+00 891
28 TraesCS3D01G163300 chr1D 91.778 827 59 8 3676 4496 453159032 453158209 0.000000e+00 1142
29 TraesCS3D01G163300 chr1D 91.041 759 62 6 3676 4429 394233923 394233166 0.000000e+00 1020
30 TraesCS3D01G163300 chr7D 91.165 781 64 5 3676 4452 54165283 54164504 0.000000e+00 1055
31 TraesCS3D01G163300 chr7A 89.722 827 79 6 3676 4496 23776024 23775198 0.000000e+00 1051
32 TraesCS3D01G163300 chr7A 87.908 827 94 6 3676 4496 24659201 24660027 0.000000e+00 968
33 TraesCS3D01G163300 chr7A 84.238 755 75 25 2963 3677 712073921 712074671 0.000000e+00 695
34 TraesCS3D01G163300 chr7A 84.238 755 73 26 2963 3675 706403393 706402643 0.000000e+00 693
35 TraesCS3D01G163300 chr1A 82.432 592 77 14 666 1241 571865867 571865287 4.040000e-135 492


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 TraesCS3D01G163300 chr3D 134637282 134641777 4495 False 3894.5 7681 100.000 1 4496 2 chr3D.!!$F2 4495
1 TraesCS3D01G163300 chr3D 49965887 49966479 592 True 523.0 523 83.195 663 1241 1 chr3D.!!$R1 578
2 TraesCS3D01G163300 chr1B 414554677 414557866 3189 False 4759.0 4759 93.717 501 3671 1 chr1B.!!$F1 3170
3 TraesCS3D01G163300 chr1B 494553997 494557074 3077 True 4593.0 4593 93.829 514 3550 1 chr1B.!!$R1 3036
4 TraesCS3D01G163300 chr6B 132657347 132660572 3225 True 4667.0 4667 93.036 503 3681 1 chr6B.!!$R1 3178
5 TraesCS3D01G163300 chr5A 651580419 651583622 3203 True 4654.0 4654 93.075 501 3675 1 chr5A.!!$R1 3174
6 TraesCS3D01G163300 chr5A 697888108 697890440 2332 False 3417.0 3417 93.142 1241 3568 1 chr5A.!!$F1 2327
7 TraesCS3D01G163300 chr4B 502274289 502277505 3216 False 4623.0 4623 92.837 501 3675 1 chr4B.!!$F1 3174
8 TraesCS3D01G163300 chr4A 718007538 718010628 3090 True 4623.0 4623 93.889 501 3550 1 chr4A.!!$R2 3049
9 TraesCS3D01G163300 chr2B 138736832 138739940 3108 True 4599.0 4599 93.579 501 3572 1 chr2B.!!$R1 3071
10 TraesCS3D01G163300 chr2B 235597957 235598929 972 True 1112.0 1112 88.012 503 1435 1 chr2B.!!$R3 932
11 TraesCS3D01G163300 chr5B 607480365 607483450 3085 False 4477.0 4477 92.974 501 3576 1 chr5B.!!$F1 3075
12 TraesCS3D01G163300 chr5B 180584859 180585685 826 True 1134.0 1134 91.536 3676 4496 1 chr5B.!!$R2 820
13 TraesCS3D01G163300 chr5B 178915191 178915772 581 True 470.0 470 81.742 663 1243 1 chr5B.!!$R1 580
14 TraesCS3D01G163300 chr2D 573646497 573650840 4343 False 2270.0 3701 91.171 501 3675 2 chr2D.!!$F2 3174
15 TraesCS3D01G163300 chr2D 539199081 539199906 825 False 1155.0 1155 92.019 3676 4496 1 chr2D.!!$F1 820
16 TraesCS3D01G163300 chr5D 403889447 403891287 1840 False 2503.0 2503 91.176 573 2431 1 chr5D.!!$F1 1858
17 TraesCS3D01G163300 chr3B 775175688 775176785 1097 True 1299.0 1299 87.954 2552 3675 1 chr3B.!!$R4 1123
18 TraesCS3D01G163300 chr3B 529426791 529427611 820 True 1103.0 1103 91.019 3676 4492 1 chr3B.!!$R2 816
19 TraesCS3D01G163300 chr3B 31623864 31624691 827 True 968.0 968 87.923 3676 4496 1 chr3B.!!$R1 820
20 TraesCS3D01G163300 chr3B 769385172 769385940 768 True 891.0 891 87.468 2887 3675 1 chr3B.!!$R3 788
21 TraesCS3D01G163300 chr1D 453158209 453159032 823 True 1142.0 1142 91.778 3676 4496 1 chr1D.!!$R2 820
22 TraesCS3D01G163300 chr1D 394233166 394233923 757 True 1020.0 1020 91.041 3676 4429 1 chr1D.!!$R1 753
23 TraesCS3D01G163300 chr7D 54164504 54165283 779 True 1055.0 1055 91.165 3676 4452 1 chr7D.!!$R1 776
24 TraesCS3D01G163300 chr7A 23775198 23776024 826 True 1051.0 1051 89.722 3676 4496 1 chr7A.!!$R1 820
25 TraesCS3D01G163300 chr7A 24659201 24660027 826 False 968.0 968 87.908 3676 4496 1 chr7A.!!$F1 820
26 TraesCS3D01G163300 chr7A 712073921 712074671 750 False 695.0 695 84.238 2963 3677 1 chr7A.!!$F2 714
27 TraesCS3D01G163300 chr7A 706402643 706403393 750 True 693.0 693 84.238 2963 3675 1 chr7A.!!$R2 712
28 TraesCS3D01G163300 chr1A 571865287 571865867 580 True 492.0 492 82.432 666 1241 1 chr1A.!!$R1 575

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
459 460 0.032130 GCGGCCAGTGATCGATTAGA 59.968 55.000 2.24 0.0 0.0 2.10 F
1132 1190 0.167908 TGATGCGTTGGCGATTGTTC 59.832 50.000 0.00 0.0 44.1 3.18 F
2451 3687 2.158682 TGCTGGCTCTACAAAAAGGTGA 60.159 45.455 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 2965 2.418368 AACAGAACTTGCCTGACACA 57.582 45.000 0.0 0.0 35.69 3.72 R
2635 3871 0.877071 AAGCGACCAAGTGCATCAAG 59.123 50.000 0.0 0.0 0.00 3.02 R
3653 4968 1.602237 GGCCGGTCCTGAGATTTCA 59.398 57.895 1.9 0.0 0.00 2.69 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
23 24 2.514458 ATTGTTCCTAACAGGCAGGG 57.486 50.000 0.00 0.00 43.27 4.45
24 25 0.251165 TTGTTCCTAACAGGCAGGGC 60.251 55.000 0.00 0.00 43.27 5.19
361 362 4.577246 GCCGAGCGCCAGGAGTAG 62.577 72.222 21.19 0.00 0.00 2.57
362 363 3.905678 CCGAGCGCCAGGAGTAGG 61.906 72.222 12.90 0.00 0.00 3.18
363 364 2.829003 CGAGCGCCAGGAGTAGGA 60.829 66.667 2.29 0.00 0.00 2.94
364 365 2.840066 CGAGCGCCAGGAGTAGGAG 61.840 68.421 2.29 0.00 0.00 3.69
365 366 2.443016 AGCGCCAGGAGTAGGAGG 60.443 66.667 2.29 0.00 0.00 4.30
366 367 4.228567 GCGCCAGGAGTAGGAGGC 62.229 72.222 0.00 0.00 43.61 4.70
367 368 3.541713 CGCCAGGAGTAGGAGGCC 61.542 72.222 0.00 0.00 44.18 5.19
368 369 3.164977 GCCAGGAGTAGGAGGCCC 61.165 72.222 0.00 0.00 41.25 5.80
369 370 2.840102 CCAGGAGTAGGAGGCCCG 60.840 72.222 0.00 0.00 37.58 6.13
370 371 2.279073 CAGGAGTAGGAGGCCCGA 59.721 66.667 0.00 0.00 37.58 5.14
371 372 1.152440 CAGGAGTAGGAGGCCCGAT 60.152 63.158 0.00 0.00 37.58 4.18
372 373 1.154221 AGGAGTAGGAGGCCCGATC 59.846 63.158 0.00 0.00 37.58 3.69
373 374 1.152525 GGAGTAGGAGGCCCGATCA 60.153 63.158 0.00 0.00 37.58 2.92
374 375 1.182385 GGAGTAGGAGGCCCGATCAG 61.182 65.000 0.00 0.00 37.58 2.90
375 376 1.811645 GAGTAGGAGGCCCGATCAGC 61.812 65.000 0.00 0.00 37.58 4.26
376 377 2.134287 GTAGGAGGCCCGATCAGCA 61.134 63.158 0.00 0.00 37.58 4.41
377 378 1.382557 TAGGAGGCCCGATCAGCAA 60.383 57.895 0.00 0.00 37.58 3.91
378 379 0.980754 TAGGAGGCCCGATCAGCAAA 60.981 55.000 0.00 0.00 37.58 3.68
379 380 1.378514 GGAGGCCCGATCAGCAAAA 60.379 57.895 0.00 0.00 0.00 2.44
380 381 0.965363 GGAGGCCCGATCAGCAAAAA 60.965 55.000 0.00 0.00 0.00 1.94
404 405 3.660501 AAAAAGAAACCAAGCCCGATC 57.339 42.857 0.00 0.00 0.00 3.69
405 406 1.165270 AAAGAAACCAAGCCCGATCG 58.835 50.000 8.51 8.51 0.00 3.69
406 407 0.676782 AAGAAACCAAGCCCGATCGG 60.677 55.000 27.65 27.65 0.00 4.18
428 429 3.067985 TGGCAACAGCGATCAGGA 58.932 55.556 0.00 0.00 46.17 3.86
429 430 1.374568 TGGCAACAGCGATCAGGAA 59.625 52.632 0.00 0.00 46.17 3.36
430 431 0.250684 TGGCAACAGCGATCAGGAAA 60.251 50.000 0.00 0.00 46.17 3.13
431 432 0.449388 GGCAACAGCGATCAGGAAAG 59.551 55.000 0.00 0.00 0.00 2.62
432 433 1.442769 GCAACAGCGATCAGGAAAGA 58.557 50.000 0.00 0.00 0.00 2.52
433 434 2.012673 GCAACAGCGATCAGGAAAGAT 58.987 47.619 0.00 0.00 0.00 2.40
434 435 3.198068 GCAACAGCGATCAGGAAAGATA 58.802 45.455 0.00 0.00 0.00 1.98
435 436 3.812053 GCAACAGCGATCAGGAAAGATAT 59.188 43.478 0.00 0.00 0.00 1.63
436 437 4.084118 GCAACAGCGATCAGGAAAGATATC 60.084 45.833 0.00 0.00 0.00 1.63
437 438 4.264460 ACAGCGATCAGGAAAGATATCC 57.736 45.455 0.00 0.00 39.96 2.59
438 439 3.007398 ACAGCGATCAGGAAAGATATCCC 59.993 47.826 0.00 0.00 40.59 3.85
439 440 3.007290 CAGCGATCAGGAAAGATATCCCA 59.993 47.826 0.00 0.00 40.59 4.37
440 441 3.260380 AGCGATCAGGAAAGATATCCCAG 59.740 47.826 0.00 0.00 40.59 4.45
441 442 3.594134 CGATCAGGAAAGATATCCCAGC 58.406 50.000 0.00 0.00 40.59 4.85
442 443 3.594134 GATCAGGAAAGATATCCCAGCG 58.406 50.000 0.00 0.00 40.59 5.18
443 444 1.694150 TCAGGAAAGATATCCCAGCGG 59.306 52.381 0.00 0.00 40.59 5.52
444 445 0.398318 AGGAAAGATATCCCAGCGGC 59.602 55.000 0.00 0.00 40.59 6.53
445 446 0.606673 GGAAAGATATCCCAGCGGCC 60.607 60.000 0.00 0.00 33.05 6.13
446 447 0.108585 GAAAGATATCCCAGCGGCCA 59.891 55.000 2.24 0.00 0.00 5.36
447 448 0.109342 AAAGATATCCCAGCGGCCAG 59.891 55.000 2.24 0.00 0.00 4.85
448 449 1.056700 AAGATATCCCAGCGGCCAGT 61.057 55.000 2.24 0.00 0.00 4.00
449 450 1.302033 GATATCCCAGCGGCCAGTG 60.302 63.158 2.24 0.00 0.00 3.66
450 451 1.758440 GATATCCCAGCGGCCAGTGA 61.758 60.000 2.24 0.00 0.00 3.41
451 452 1.130054 ATATCCCAGCGGCCAGTGAT 61.130 55.000 2.24 0.00 0.00 3.06
452 453 1.758440 TATCCCAGCGGCCAGTGATC 61.758 60.000 2.24 0.00 0.00 2.92
454 455 4.147449 CCAGCGGCCAGTGATCGA 62.147 66.667 2.24 0.00 0.00 3.59
455 456 2.107750 CAGCGGCCAGTGATCGAT 59.892 61.111 2.24 0.00 0.00 3.59
456 457 1.522355 CAGCGGCCAGTGATCGATT 60.522 57.895 2.24 0.00 0.00 3.34
457 458 0.249447 CAGCGGCCAGTGATCGATTA 60.249 55.000 2.24 0.00 0.00 1.75
458 459 0.032678 AGCGGCCAGTGATCGATTAG 59.967 55.000 2.24 0.00 0.00 1.73
459 460 0.032130 GCGGCCAGTGATCGATTAGA 59.968 55.000 2.24 0.00 0.00 2.10
460 461 1.337260 GCGGCCAGTGATCGATTAGAT 60.337 52.381 2.24 0.00 43.51 1.98
475 476 7.112452 TCGATTAGATCATTCTCAGGAAACA 57.888 36.000 0.00 0.00 34.90 2.83
476 477 7.730084 TCGATTAGATCATTCTCAGGAAACAT 58.270 34.615 0.00 0.00 34.90 2.71
477 478 8.206867 TCGATTAGATCATTCTCAGGAAACATT 58.793 33.333 0.00 0.00 34.90 2.71
478 479 8.281194 CGATTAGATCATTCTCAGGAAACATTG 58.719 37.037 0.00 0.00 34.90 2.82
479 480 5.831702 AGATCATTCTCAGGAAACATTGC 57.168 39.130 0.00 0.00 34.90 3.56
480 481 5.258841 AGATCATTCTCAGGAAACATTGCA 58.741 37.500 0.00 0.00 34.90 4.08
481 482 5.713389 AGATCATTCTCAGGAAACATTGCAA 59.287 36.000 0.00 0.00 34.90 4.08
482 483 5.125100 TCATTCTCAGGAAACATTGCAAC 57.875 39.130 0.00 0.00 34.90 4.17
483 484 4.583907 TCATTCTCAGGAAACATTGCAACA 59.416 37.500 0.00 0.00 34.90 3.33
484 485 4.998671 TTCTCAGGAAACATTGCAACAA 57.001 36.364 0.00 0.00 0.00 2.83
485 486 5.534207 TTCTCAGGAAACATTGCAACAAT 57.466 34.783 0.00 0.00 0.00 2.71
486 487 5.534207 TCTCAGGAAACATTGCAACAATT 57.466 34.783 0.00 0.00 0.00 2.32
487 488 5.916318 TCTCAGGAAACATTGCAACAATTT 58.084 33.333 0.00 2.39 0.00 1.82
488 489 5.984926 TCTCAGGAAACATTGCAACAATTTC 59.015 36.000 17.50 17.50 0.00 2.17
489 490 5.916318 TCAGGAAACATTGCAACAATTTCT 58.084 33.333 21.78 11.37 31.40 2.52
490 491 5.984926 TCAGGAAACATTGCAACAATTTCTC 59.015 36.000 21.78 15.50 31.40 2.87
491 492 5.754406 CAGGAAACATTGCAACAATTTCTCA 59.246 36.000 21.78 0.00 31.40 3.27
492 493 6.258287 CAGGAAACATTGCAACAATTTCTCAA 59.742 34.615 21.78 0.00 31.40 3.02
493 494 6.822676 AGGAAACATTGCAACAATTTCTCAAA 59.177 30.769 21.78 0.00 31.40 2.69
494 495 7.499895 AGGAAACATTGCAACAATTTCTCAAAT 59.500 29.630 21.78 8.63 31.40 2.32
495 496 8.772705 GGAAACATTGCAACAATTTCTCAAATA 58.227 29.630 21.78 0.00 31.40 1.40
525 527 3.278668 ACATTGCAAGAGATCCTCTGG 57.721 47.619 4.94 0.00 40.28 3.86
526 528 2.842496 ACATTGCAAGAGATCCTCTGGA 59.158 45.455 4.94 0.00 40.28 3.86
621 625 4.757149 CCTTTCTTCCATCACGAAGAGTTT 59.243 41.667 0.00 0.00 46.70 2.66
713 725 5.833667 CCCCTGGTAATTTCCTTCCTAATTC 59.166 44.000 2.53 0.00 0.00 2.17
778 816 1.553706 CTCCTTTGGCCTTTGCTCAT 58.446 50.000 3.32 0.00 37.74 2.90
789 827 2.824341 CCTTTGCTCATTTGCTCTCCTT 59.176 45.455 0.00 0.00 0.00 3.36
793 831 2.029649 TGCTCATTTGCTCTCCTTTTGC 60.030 45.455 0.00 0.00 0.00 3.68
882 925 9.998106 AGGTATTGAGGTATATTATTCACACAC 57.002 33.333 0.00 0.00 0.00 3.82
1047 1105 6.372659 AGAATAAATTGATGAAGTCACAGCGT 59.627 34.615 0.00 0.00 36.32 5.07
1132 1190 0.167908 TGATGCGTTGGCGATTGTTC 59.832 50.000 0.00 0.00 44.10 3.18
1135 1193 2.332654 GCGTTGGCGATTGTTCCCT 61.333 57.895 0.00 0.00 41.33 4.20
1187 2409 5.105392 ACTCAGACTCTGATAAGCAAGAAGG 60.105 44.000 9.26 0.00 39.92 3.46
1366 2600 4.409247 TCTTAGTTGAGAAAGGGCCTATCC 59.591 45.833 6.41 0.00 0.00 2.59
1419 2654 7.186021 TGAAGAAGGAAGACATTTTTCGTAC 57.814 36.000 0.00 0.00 34.96 3.67
1657 2893 9.906660 TTAATAACATGAACAAGTGGAATGAAC 57.093 29.630 0.00 0.00 0.00 3.18
1678 2914 7.957002 TGAACTGAGAGTTAGACTGAGAAAAT 58.043 34.615 0.00 0.00 38.80 1.82
1889 3125 5.808540 CAGAATTTGACATGGTAATGCAAGG 59.191 40.000 0.00 0.00 37.29 3.61
1937 3173 9.736414 CAAGGAAATCCATTATCACTATCTCAT 57.264 33.333 1.67 0.00 38.89 2.90
2252 3488 4.489737 AGGGGTCAAGGATATGATAACGA 58.510 43.478 0.00 0.00 0.00 3.85
2253 3489 4.905456 AGGGGTCAAGGATATGATAACGAA 59.095 41.667 0.00 0.00 0.00 3.85
2451 3687 2.158682 TGCTGGCTCTACAAAAAGGTGA 60.159 45.455 0.00 0.00 0.00 4.02
2538 3774 6.366332 AGAGTAGAATCAAAAGTGTTACAGCG 59.634 38.462 0.00 0.00 0.00 5.18
2596 3832 4.447724 TGTTTGAGTTACGTCATGCTTCTC 59.552 41.667 0.00 0.00 0.00 2.87
2608 3844 3.118847 TCATGCTTCTCACACTGATCCTC 60.119 47.826 0.00 0.00 0.00 3.71
2617 3853 7.429374 TCTCACACTGATCCTCAAGATAAAT 57.571 36.000 0.00 0.00 34.42 1.40
2663 3899 1.947456 ACTTGGTCGCTTTGAGTTTCC 59.053 47.619 0.00 0.00 0.00 3.13
2752 3988 1.887854 CAACCATGTGCATTGACTCCA 59.112 47.619 0.00 0.00 0.00 3.86
2890 4127 0.874175 TCCAGTGAAACGTCGTGCTG 60.874 55.000 0.00 5.67 45.86 4.41
2904 4141 1.160137 GTGCTGCGAGGAAGAAACAT 58.840 50.000 0.00 0.00 0.00 2.71
3110 4351 6.518493 ACAATGAACTTGAAGAATGTTGCAT 58.482 32.000 0.00 0.00 38.29 3.96
3420 4691 2.618241 GGCCACATTATGCATCGAGAAA 59.382 45.455 0.19 0.00 0.00 2.52
3787 5102 6.315393 TGTTTCCTGTTGTCTTACTGAGAAAC 59.685 38.462 0.00 0.00 37.47 2.78
3858 5173 0.670854 GAAGCGGACAGTCCTTGGTC 60.671 60.000 17.95 5.94 33.30 4.02
3883 5199 3.678056 AGGTTAAAGATGCACTCGACA 57.322 42.857 0.00 0.00 0.00 4.35
3940 5257 3.738982 TGTATAATGAATCTGGCCGTGG 58.261 45.455 0.00 0.00 0.00 4.94
3987 5304 4.602340 CCTAATCAGTAGGGTACGCATT 57.398 45.455 12.95 5.32 45.30 3.56
4002 5319 8.161425 AGGGTACGCATTTTAATAGATGGTATT 58.839 33.333 12.95 0.00 0.00 1.89
4038 5355 2.930040 CAATGTTGTATCGGCGACTCTT 59.070 45.455 13.76 0.00 0.00 2.85
4062 5379 2.876091 CGTTGACCGCTTGATAGAAGA 58.124 47.619 0.00 0.00 0.00 2.87
4063 5380 3.448686 CGTTGACCGCTTGATAGAAGAT 58.551 45.455 0.00 0.00 0.00 2.40
4194 5512 9.217278 TGCAAAAATAACAATAGACATGCAAAT 57.783 25.926 0.00 0.00 37.16 2.32
4234 5555 9.396022 ACAGTAGCTAACACTAATGCAAATATT 57.604 29.630 0.00 0.00 40.88 1.28
4407 5730 2.754946 ACTGTTAGAAATTCGCCCGA 57.245 45.000 0.00 0.00 0.00 5.14
4422 5745 3.866910 TCGCCCGATTGTCTTATTAACAC 59.133 43.478 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.536765 CCCTGCCTGTTAGGAACAATTAT 58.463 43.478 0.00 0.00 41.61 1.28
2 3 3.876156 GCCCTGCCTGTTAGGAACAATTA 60.876 47.826 0.00 0.00 41.61 1.40
5 6 0.251165 GCCCTGCCTGTTAGGAACAA 60.251 55.000 0.00 0.00 41.61 2.83
6 7 1.378762 GCCCTGCCTGTTAGGAACA 59.621 57.895 0.00 0.00 37.67 3.18
7 8 1.378646 GGCCCTGCCTGTTAGGAAC 60.379 63.158 0.00 0.00 46.69 3.62
8 9 3.087065 GGCCCTGCCTGTTAGGAA 58.913 61.111 0.00 0.00 46.69 3.36
344 345 4.577246 CTACTCCTGGCGCTCGGC 62.577 72.222 7.64 8.96 42.51 5.54
345 346 3.905678 CCTACTCCTGGCGCTCGG 61.906 72.222 7.64 8.40 0.00 4.63
346 347 2.829003 TCCTACTCCTGGCGCTCG 60.829 66.667 7.64 0.00 0.00 5.03
347 348 2.494530 CCTCCTACTCCTGGCGCTC 61.495 68.421 7.64 0.00 0.00 5.03
348 349 2.443016 CCTCCTACTCCTGGCGCT 60.443 66.667 7.64 0.00 0.00 5.92
349 350 4.228567 GCCTCCTACTCCTGGCGC 62.229 72.222 0.00 0.00 35.79 6.53
350 351 3.541713 GGCCTCCTACTCCTGGCG 61.542 72.222 0.00 0.00 45.75 5.69
351 352 3.164977 GGGCCTCCTACTCCTGGC 61.165 72.222 0.84 0.00 44.22 4.85
352 353 2.664835 ATCGGGCCTCCTACTCCTGG 62.665 65.000 0.84 0.00 0.00 4.45
353 354 1.152440 ATCGGGCCTCCTACTCCTG 60.152 63.158 0.84 0.00 0.00 3.86
354 355 1.154221 GATCGGGCCTCCTACTCCT 59.846 63.158 0.84 0.00 0.00 3.69
355 356 1.152525 TGATCGGGCCTCCTACTCC 60.153 63.158 0.84 0.00 0.00 3.85
356 357 1.811645 GCTGATCGGGCCTCCTACTC 61.812 65.000 0.84 0.00 0.00 2.59
357 358 1.834822 GCTGATCGGGCCTCCTACT 60.835 63.158 0.84 0.00 0.00 2.57
358 359 1.686325 TTGCTGATCGGGCCTCCTAC 61.686 60.000 0.84 0.00 0.00 3.18
359 360 0.980754 TTTGCTGATCGGGCCTCCTA 60.981 55.000 0.84 0.00 0.00 2.94
360 361 1.852157 TTTTGCTGATCGGGCCTCCT 61.852 55.000 0.84 0.00 0.00 3.69
361 362 0.965363 TTTTTGCTGATCGGGCCTCC 60.965 55.000 0.84 0.00 0.00 4.30
362 363 2.566824 TTTTTGCTGATCGGGCCTC 58.433 52.632 0.84 0.00 0.00 4.70
363 364 4.841441 TTTTTGCTGATCGGGCCT 57.159 50.000 0.84 0.00 0.00 5.19
384 385 2.030274 CGATCGGGCTTGGTTTCTTTTT 60.030 45.455 7.38 0.00 0.00 1.94
385 386 1.539827 CGATCGGGCTTGGTTTCTTTT 59.460 47.619 7.38 0.00 0.00 2.27
386 387 1.165270 CGATCGGGCTTGGTTTCTTT 58.835 50.000 7.38 0.00 0.00 2.52
387 388 0.676782 CCGATCGGGCTTGGTTTCTT 60.677 55.000 26.95 0.00 0.00 2.52
388 389 1.078426 CCGATCGGGCTTGGTTTCT 60.078 57.895 26.95 0.00 0.00 2.52
389 390 3.497879 CCGATCGGGCTTGGTTTC 58.502 61.111 26.95 0.00 0.00 2.78
398 399 4.776322 TGCCAGTTGCCGATCGGG 62.776 66.667 33.98 17.89 40.16 5.14
399 400 2.745884 TTGCCAGTTGCCGATCGG 60.746 61.111 30.03 30.03 40.16 4.18
400 401 2.244436 CTGTTGCCAGTTGCCGATCG 62.244 60.000 8.51 8.51 40.16 3.69
401 402 1.503542 CTGTTGCCAGTTGCCGATC 59.496 57.895 0.00 0.00 40.16 3.69
402 403 2.629656 GCTGTTGCCAGTTGCCGAT 61.630 57.895 0.00 0.00 41.02 4.18
403 404 3.286751 GCTGTTGCCAGTTGCCGA 61.287 61.111 0.00 0.00 41.02 5.54
404 405 4.688419 CGCTGTTGCCAGTTGCCG 62.688 66.667 0.00 0.00 41.02 5.69
405 406 2.533391 GATCGCTGTTGCCAGTTGCC 62.533 60.000 0.00 0.00 41.02 4.52
406 407 1.154150 GATCGCTGTTGCCAGTTGC 60.154 57.895 0.00 0.00 41.02 4.17
407 408 0.167470 CTGATCGCTGTTGCCAGTTG 59.833 55.000 0.00 0.00 41.02 3.16
408 409 0.957395 CCTGATCGCTGTTGCCAGTT 60.957 55.000 0.00 0.00 41.02 3.16
409 410 1.376424 CCTGATCGCTGTTGCCAGT 60.376 57.895 0.00 0.00 41.02 4.00
410 411 0.674581 TTCCTGATCGCTGTTGCCAG 60.675 55.000 0.00 0.00 41.91 4.85
411 412 0.250684 TTTCCTGATCGCTGTTGCCA 60.251 50.000 0.00 0.00 35.36 4.92
412 413 0.449388 CTTTCCTGATCGCTGTTGCC 59.551 55.000 0.00 0.00 35.36 4.52
413 414 1.442769 TCTTTCCTGATCGCTGTTGC 58.557 50.000 0.00 0.00 0.00 4.17
414 415 4.450419 GGATATCTTTCCTGATCGCTGTTG 59.550 45.833 2.05 0.00 32.68 3.33
415 416 4.503991 GGGATATCTTTCCTGATCGCTGTT 60.504 45.833 2.05 0.00 35.97 3.16
416 417 3.007398 GGGATATCTTTCCTGATCGCTGT 59.993 47.826 2.05 0.00 35.97 4.40
417 418 3.007290 TGGGATATCTTTCCTGATCGCTG 59.993 47.826 2.05 0.00 35.97 5.18
418 419 3.242867 TGGGATATCTTTCCTGATCGCT 58.757 45.455 2.05 0.00 35.97 4.93
419 420 3.594134 CTGGGATATCTTTCCTGATCGC 58.406 50.000 2.05 0.00 35.97 4.58
420 421 3.594134 GCTGGGATATCTTTCCTGATCG 58.406 50.000 2.05 0.00 35.97 3.69
421 422 3.594134 CGCTGGGATATCTTTCCTGATC 58.406 50.000 2.05 0.00 35.97 2.92
422 423 2.304180 CCGCTGGGATATCTTTCCTGAT 59.696 50.000 2.05 0.00 35.97 2.90
423 424 1.694150 CCGCTGGGATATCTTTCCTGA 59.306 52.381 2.05 0.00 35.97 3.86
424 425 1.879796 GCCGCTGGGATATCTTTCCTG 60.880 57.143 2.05 1.28 35.97 3.86
425 426 0.398318 GCCGCTGGGATATCTTTCCT 59.602 55.000 2.05 0.00 35.97 3.36
426 427 0.606673 GGCCGCTGGGATATCTTTCC 60.607 60.000 2.05 0.00 34.06 3.13
427 428 0.108585 TGGCCGCTGGGATATCTTTC 59.891 55.000 2.05 0.00 34.06 2.62
428 429 0.109342 CTGGCCGCTGGGATATCTTT 59.891 55.000 2.05 0.00 34.06 2.52
429 430 1.056700 ACTGGCCGCTGGGATATCTT 61.057 55.000 2.05 0.00 34.06 2.40
430 431 1.460305 ACTGGCCGCTGGGATATCT 60.460 57.895 2.05 0.00 34.06 1.98
431 432 1.302033 CACTGGCCGCTGGGATATC 60.302 63.158 0.00 0.00 34.06 1.63
432 433 1.130054 ATCACTGGCCGCTGGGATAT 61.130 55.000 6.22 0.00 34.06 1.63
433 434 1.758440 GATCACTGGCCGCTGGGATA 61.758 60.000 7.77 0.00 34.06 2.59
434 435 3.092511 ATCACTGGCCGCTGGGAT 61.093 61.111 0.00 0.00 34.06 3.85
435 436 3.785859 GATCACTGGCCGCTGGGA 61.786 66.667 0.00 0.00 34.06 4.37
437 438 2.930385 AATCGATCACTGGCCGCTGG 62.930 60.000 0.00 0.00 0.00 4.85
438 439 0.249447 TAATCGATCACTGGCCGCTG 60.249 55.000 0.00 0.00 0.00 5.18
439 440 0.032678 CTAATCGATCACTGGCCGCT 59.967 55.000 0.00 0.00 0.00 5.52
440 441 0.032130 TCTAATCGATCACTGGCCGC 59.968 55.000 0.00 0.00 0.00 6.53
441 442 2.600731 GATCTAATCGATCACTGGCCG 58.399 52.381 0.00 0.00 46.35 6.13
450 451 7.730084 TGTTTCCTGAGAATGATCTAATCGAT 58.270 34.615 0.00 0.00 35.54 3.59
451 452 7.112452 TGTTTCCTGAGAATGATCTAATCGA 57.888 36.000 0.00 0.00 35.54 3.59
452 453 7.959689 ATGTTTCCTGAGAATGATCTAATCG 57.040 36.000 0.00 0.00 35.54 3.34
453 454 8.074972 GCAATGTTTCCTGAGAATGATCTAATC 58.925 37.037 0.00 0.00 35.54 1.75
454 455 7.558807 TGCAATGTTTCCTGAGAATGATCTAAT 59.441 33.333 0.00 0.00 35.54 1.73
455 456 6.885918 TGCAATGTTTCCTGAGAATGATCTAA 59.114 34.615 0.00 0.00 35.54 2.10
456 457 6.417258 TGCAATGTTTCCTGAGAATGATCTA 58.583 36.000 0.00 0.00 35.54 1.98
457 458 5.258841 TGCAATGTTTCCTGAGAATGATCT 58.741 37.500 0.00 0.00 39.10 2.75
458 459 5.571784 TGCAATGTTTCCTGAGAATGATC 57.428 39.130 0.00 0.00 0.00 2.92
459 460 5.244402 TGTTGCAATGTTTCCTGAGAATGAT 59.756 36.000 0.59 0.00 0.00 2.45
460 461 4.583907 TGTTGCAATGTTTCCTGAGAATGA 59.416 37.500 0.59 0.00 0.00 2.57
461 462 4.873817 TGTTGCAATGTTTCCTGAGAATG 58.126 39.130 0.59 0.00 0.00 2.67
462 463 5.534207 TTGTTGCAATGTTTCCTGAGAAT 57.466 34.783 0.59 0.00 0.00 2.40
463 464 4.998671 TTGTTGCAATGTTTCCTGAGAA 57.001 36.364 0.59 0.00 0.00 2.87
464 465 5.534207 AATTGTTGCAATGTTTCCTGAGA 57.466 34.783 0.59 0.00 0.00 3.27
465 466 5.987347 AGAAATTGTTGCAATGTTTCCTGAG 59.013 36.000 20.80 0.00 31.02 3.35
466 467 5.916318 AGAAATTGTTGCAATGTTTCCTGA 58.084 33.333 20.80 0.00 31.02 3.86
467 468 5.754406 TGAGAAATTGTTGCAATGTTTCCTG 59.246 36.000 20.80 0.00 31.02 3.86
468 469 5.916318 TGAGAAATTGTTGCAATGTTTCCT 58.084 33.333 20.80 13.27 31.02 3.36
469 470 6.601741 TTGAGAAATTGTTGCAATGTTTCC 57.398 33.333 20.80 15.71 31.02 3.13
496 497 6.042437 AGGATCTCTTGCAATGTTTCCTTTTT 59.958 34.615 12.77 0.00 0.00 1.94
497 498 5.541484 AGGATCTCTTGCAATGTTTCCTTTT 59.459 36.000 12.77 0.00 0.00 2.27
498 499 5.082425 AGGATCTCTTGCAATGTTTCCTTT 58.918 37.500 12.77 0.00 0.00 3.11
499 500 4.670765 AGGATCTCTTGCAATGTTTCCTT 58.329 39.130 12.77 2.14 0.00 3.36
500 501 4.268359 GAGGATCTCTTGCAATGTTTCCT 58.732 43.478 16.59 16.59 35.12 3.36
501 502 4.629251 GAGGATCTCTTGCAATGTTTCC 57.371 45.455 0.00 5.09 0.00 3.13
621 625 2.040606 GTAGGGCTGGGACCTGGA 59.959 66.667 0.00 0.00 43.53 3.86
713 725 1.003851 AACGGCGACCAACATAATCG 58.996 50.000 16.62 0.00 38.87 3.34
778 816 3.759581 AGATGAGCAAAAGGAGAGCAAA 58.240 40.909 0.00 0.00 0.00 3.68
789 827 5.946377 TGTCTAGAGTCTGTAGATGAGCAAA 59.054 40.000 9.77 0.00 0.00 3.68
793 831 7.713073 TGTATGTGTCTAGAGTCTGTAGATGAG 59.287 40.741 9.77 0.00 0.00 2.90
843 886 4.080919 CCTCAATACCTGATGTCCTGAACA 60.081 45.833 0.00 0.00 43.51 3.18
844 887 4.080863 ACCTCAATACCTGATGTCCTGAAC 60.081 45.833 0.00 0.00 32.14 3.18
897 940 2.236395 ACGGTGCTAGCTCTAAACCAAT 59.764 45.455 17.23 2.90 0.00 3.16
946 995 3.126858 GCGCCATGAGAACAAACAGAATA 59.873 43.478 0.00 0.00 0.00 1.75
950 999 0.109597 GGCGCCATGAGAACAAACAG 60.110 55.000 24.80 0.00 0.00 3.16
988 1037 0.323629 TCCTTTTGTGGCTACCCGAG 59.676 55.000 0.00 0.00 0.00 4.63
1035 1093 0.601558 TACCTCCACGCTGTGACTTC 59.398 55.000 9.75 0.00 35.23 3.01
1047 1105 4.584874 TGAGAAATTTGCGAATACCTCCA 58.415 39.130 18.32 9.25 0.00 3.86
1088 1146 2.290960 GGGTCTGGCAAAGTAGTGGAAT 60.291 50.000 0.00 0.00 0.00 3.01
1132 1190 1.691196 TGTTGCTCTTCCACAAAGGG 58.309 50.000 0.00 0.00 38.62 3.95
1135 1193 5.906113 TTAGTTTGTTGCTCTTCCACAAA 57.094 34.783 0.00 0.00 0.00 2.83
1177 2399 6.248433 TGGAGTTGATATTTCCTTCTTGCTT 58.752 36.000 0.00 0.00 32.12 3.91
1187 2409 4.552767 CGCCGATGTTGGAGTTGATATTTC 60.553 45.833 0.00 0.00 0.00 2.17
1400 2635 4.062991 AGCGTACGAAAAATGTCTTCCTT 58.937 39.130 21.65 0.00 0.00 3.36
1419 2654 9.882996 TTGCTTAATTTTCTATGATAATGAGCG 57.117 29.630 0.00 0.00 32.04 5.03
1657 2893 8.287439 TCCTATTTTCTCAGTCTAACTCTCAG 57.713 38.462 0.00 0.00 0.00 3.35
1678 2914 5.885912 GCCATTCCTTGTCAATAGTTTCCTA 59.114 40.000 0.00 0.00 0.00 2.94
1700 2936 5.596845 TCTCCTTTGTTGTTTTATGTTGCC 58.403 37.500 0.00 0.00 0.00 4.52
1708 2944 7.386059 ACACATTCTTTCTCCTTTGTTGTTTT 58.614 30.769 0.00 0.00 0.00 2.43
1712 2948 6.135290 TGACACATTCTTTCTCCTTTGTTG 57.865 37.500 0.00 0.00 0.00 3.33
1729 2965 2.418368 AACAGAACTTGCCTGACACA 57.582 45.000 0.00 0.00 35.69 3.72
1889 3125 3.637998 TCTCAACACGTCTAAGGTGAC 57.362 47.619 6.77 0.00 37.42 3.67
2012 3248 4.511826 GGATAACAGAGAAATACTTGGCCG 59.488 45.833 0.00 0.00 0.00 6.13
2253 3489 9.726438 CCTCGGTATTTTCCTTTCATATTAGAT 57.274 33.333 0.00 0.00 0.00 1.98
2538 3774 4.815269 ACTCAGCGGCTTGATATCTTATC 58.185 43.478 0.00 0.00 0.00 1.75
2576 3812 3.987868 GTGAGAAGCATGACGTAACTCAA 59.012 43.478 0.00 0.00 35.29 3.02
2617 3853 6.147492 GCATCAAGTAAATTTTTGGCATCACA 59.853 34.615 0.00 0.00 0.00 3.58
2635 3871 0.877071 AAGCGACCAAGTGCATCAAG 59.123 50.000 0.00 0.00 0.00 3.02
2663 3899 8.843885 ATCATGTCAGATAATCATACCAACTG 57.156 34.615 0.00 0.00 0.00 3.16
2796 4033 5.548056 ACTTGAAGAAAACCCCTCATCTCTA 59.452 40.000 0.00 0.00 0.00 2.43
2890 4127 5.991328 TCATCATAATGTTTCTTCCTCGC 57.009 39.130 0.00 0.00 34.32 5.03
2904 4141 9.506018 TCTTCTTGACAATCACTTTCATCATAA 57.494 29.630 0.00 0.00 0.00 1.90
3051 4292 1.137872 AGAGTGCCCGAGCTCAATAAG 59.862 52.381 15.40 0.00 40.80 1.73
3234 4504 1.699083 TCAACTTCTCTGACATGCCCA 59.301 47.619 0.00 0.00 0.00 5.36
3366 4637 5.965033 ACCTATCTTGAGTCATGGTTGAT 57.035 39.130 6.21 3.21 33.56 2.57
3420 4691 9.123902 TCGATGTCAATCTCATCCAATAATTTT 57.876 29.630 0.00 0.00 38.60 1.82
3653 4968 1.602237 GGCCGGTCCTGAGATTTCA 59.398 57.895 1.90 0.00 0.00 2.69
3858 5173 4.098044 TCGAGTGCATCTTTAACCTAGAGG 59.902 45.833 0.00 0.00 42.17 3.69
3862 5177 4.794278 TGTCGAGTGCATCTTTAACCTA 57.206 40.909 0.00 0.00 0.00 3.08
3883 5199 2.750637 ACTCTCGGTGCGGTCGAT 60.751 61.111 0.00 0.00 36.01 3.59
3940 5257 2.627699 TGGTTGAGAATTTTGAGGCCAC 59.372 45.455 5.01 0.00 0.00 5.01
3987 5304 9.135189 AGCATGCTTCAAATACCATCTATTAAA 57.865 29.630 16.30 0.00 0.00 1.52
4053 5370 6.094048 GGTGCAAGCTTGTTAATCTTCTATCA 59.906 38.462 26.55 9.12 0.00 2.15
4060 5377 5.473066 AAATGGTGCAAGCTTGTTAATCT 57.527 34.783 26.55 6.37 33.76 2.40
4061 5378 6.202570 TGAAAAATGGTGCAAGCTTGTTAATC 59.797 34.615 26.55 13.96 33.76 1.75
4062 5379 6.054295 TGAAAAATGGTGCAAGCTTGTTAAT 58.946 32.000 26.55 13.02 33.76 1.40
4063 5380 5.423015 TGAAAAATGGTGCAAGCTTGTTAA 58.577 33.333 26.55 11.00 33.76 2.01
4092 5409 5.295292 CGAGCTGAATGGAGAAATTGTATGT 59.705 40.000 0.00 0.00 0.00 2.29
4155 5472 6.580791 TGTTATTTTTGCATTAGTGTTCGCTC 59.419 34.615 0.00 0.00 0.00 5.03
4203 5522 6.878923 TGCATTAGTGTTAGCTACTGTCAATT 59.121 34.615 0.00 0.00 0.00 2.32
4204 5523 6.406370 TGCATTAGTGTTAGCTACTGTCAAT 58.594 36.000 0.00 0.00 0.00 2.57
4234 5555 4.525100 TGCGGTATACATGGTGCTAGATTA 59.475 41.667 5.01 0.00 0.00 1.75
4237 5558 2.312390 TGCGGTATACATGGTGCTAGA 58.688 47.619 5.01 0.00 0.00 2.43
4403 5726 4.033587 CACCGTGTTAATAAGACAATCGGG 59.966 45.833 9.90 0.00 39.54 5.14
4407 5730 7.499321 TTTGTCACCGTGTTAATAAGACAAT 57.501 32.000 0.00 0.00 42.08 2.71
4422 5745 6.603237 TTATAGCTGATCAATTTGTCACCG 57.397 37.500 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.