Multiple sequence alignment - TraesCS5D01G088200

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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 TraesCS5D01G088200 chr5D 100.000 4121 0 0 1 4121 94051426 94055546 0.000000e+00 7611.0
1 TraesCS5D01G088200 chr5D 81.901 3387 490 56 778 4121 266166607 266163301 0.000000e+00 2745.0
2 TraesCS5D01G088200 chr5D 93.197 588 20 5 3554 4121 78358886 78358299 0.000000e+00 846.0
3 TraesCS5D01G088200 chr5D 83.212 137 10 4 568 703 266172279 266172155 3.370000e-21 113.0
4 TraesCS5D01G088200 chr3D 97.711 3495 56 10 648 4121 372520430 372516939 0.000000e+00 5989.0
5 TraesCS5D01G088200 chr2A 89.183 3587 320 27 567 4121 192012302 192008752 0.000000e+00 4412.0
6 TraesCS5D01G088200 chr6A 89.130 3505 328 21 653 4119 259407522 259411011 0.000000e+00 4313.0
7 TraesCS5D01G088200 chr1D 93.062 2508 141 11 1645 4121 202183711 202181206 0.000000e+00 3637.0
8 TraesCS5D01G088200 chr6D 93.087 2271 114 12 1885 4121 459273168 459275429 0.000000e+00 3284.0
9 TraesCS5D01G088200 chr6B 88.918 2283 205 14 1873 4121 673590693 673592961 0.000000e+00 2771.0
10 TraesCS5D01G088200 chr6B 84.560 2662 361 28 552 3188 275242500 275245136 0.000000e+00 2593.0
11 TraesCS5D01G088200 chr6B 92.727 880 63 1 997 1875 673549987 673550866 0.000000e+00 1269.0
12 TraesCS5D01G088200 chr4A 81.713 3013 465 56 681 3667 522292140 522289188 0.000000e+00 2433.0
13 TraesCS5D01G088200 chr4A 84.035 451 70 2 3672 4121 522279128 522278679 2.280000e-117 433.0
14 TraesCS5D01G088200 chr5B 78.981 3573 643 65 617 4121 174901695 174905227 0.000000e+00 2338.0
15 TraesCS5D01G088200 chr5B 82.504 2292 348 33 1862 4118 234104647 234102374 0.000000e+00 1962.0
16 TraesCS5D01G088200 chr5B 97.276 514 14 0 1 514 101408467 101408980 0.000000e+00 872.0
17 TraesCS5D01G088200 chr5B 75.729 1714 341 50 555 2251 453272046 453273701 0.000000e+00 791.0
18 TraesCS5D01G088200 chr7A 90.724 1671 141 4 559 2226 286226026 286227685 0.000000e+00 2215.0
19 TraesCS5D01G088200 chr7A 87.656 1928 187 19 2221 4119 286231494 286233399 0.000000e+00 2194.0
20 TraesCS5D01G088200 chr7D 90.855 1006 54 14 3137 4121 245520035 245519047 0.000000e+00 1314.0
21 TraesCS5D01G088200 chr5A 96.693 514 17 0 1 514 87982714 87983227 0.000000e+00 856.0
22 TraesCS5D01G088200 chr3B 74.581 1373 272 54 577 1913 250267997 250266666 7.840000e-147 531.0
23 TraesCS5D01G088200 chr1B 93.333 45 3 0 566 610 115447732 115447688 2.660000e-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 TraesCS5D01G088200 chr5D 94051426 94055546 4120 False 7611.0 7611 100.000 1 4121 1 chr5D.!!$F1 4120
1 TraesCS5D01G088200 chr5D 266163301 266166607 3306 True 2745.0 2745 81.901 778 4121 1 chr5D.!!$R2 3343
2 TraesCS5D01G088200 chr5D 78358299 78358886 587 True 846.0 846 93.197 3554 4121 1 chr5D.!!$R1 567
3 TraesCS5D01G088200 chr3D 372516939 372520430 3491 True 5989.0 5989 97.711 648 4121 1 chr3D.!!$R1 3473
4 TraesCS5D01G088200 chr2A 192008752 192012302 3550 True 4412.0 4412 89.183 567 4121 1 chr2A.!!$R1 3554
5 TraesCS5D01G088200 chr6A 259407522 259411011 3489 False 4313.0 4313 89.130 653 4119 1 chr6A.!!$F1 3466
6 TraesCS5D01G088200 chr1D 202181206 202183711 2505 True 3637.0 3637 93.062 1645 4121 1 chr1D.!!$R1 2476
7 TraesCS5D01G088200 chr6D 459273168 459275429 2261 False 3284.0 3284 93.087 1885 4121 1 chr6D.!!$F1 2236
8 TraesCS5D01G088200 chr6B 673590693 673592961 2268 False 2771.0 2771 88.918 1873 4121 1 chr6B.!!$F3 2248
9 TraesCS5D01G088200 chr6B 275242500 275245136 2636 False 2593.0 2593 84.560 552 3188 1 chr6B.!!$F1 2636
10 TraesCS5D01G088200 chr6B 673549987 673550866 879 False 1269.0 1269 92.727 997 1875 1 chr6B.!!$F2 878
11 TraesCS5D01G088200 chr4A 522289188 522292140 2952 True 2433.0 2433 81.713 681 3667 1 chr4A.!!$R2 2986
12 TraesCS5D01G088200 chr5B 174901695 174905227 3532 False 2338.0 2338 78.981 617 4121 1 chr5B.!!$F2 3504
13 TraesCS5D01G088200 chr5B 234102374 234104647 2273 True 1962.0 1962 82.504 1862 4118 1 chr5B.!!$R1 2256
14 TraesCS5D01G088200 chr5B 101408467 101408980 513 False 872.0 872 97.276 1 514 1 chr5B.!!$F1 513
15 TraesCS5D01G088200 chr5B 453272046 453273701 1655 False 791.0 791 75.729 555 2251 1 chr5B.!!$F3 1696
16 TraesCS5D01G088200 chr7A 286226026 286233399 7373 False 2204.5 2215 89.190 559 4119 2 chr7A.!!$F1 3560
17 TraesCS5D01G088200 chr7D 245519047 245520035 988 True 1314.0 1314 90.855 3137 4121 1 chr7D.!!$R1 984
18 TraesCS5D01G088200 chr5A 87982714 87983227 513 False 856.0 856 96.693 1 514 1 chr5A.!!$F1 513
19 TraesCS5D01G088200 chr3B 250266666 250267997 1331 True 531.0 531 74.581 577 1913 1 chr3B.!!$R1 1336

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
534 535 0.030908 GGGTCCGAGCAATACGAGAG 59.969 60.0 0.0 0.0 0.00 3.20 F
540 541 0.179108 GAGCAATACGAGAGCGGGTT 60.179 55.0 0.0 0.0 43.17 4.11 F
541 542 0.249398 AGCAATACGAGAGCGGGTTT 59.751 50.0 0.0 0.0 43.17 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1838 1.401552 CCGGTCGATGATGCATTTGTT 59.598 47.619 0.0 0.0 0.00 2.83 R
3018 6950 0.032540 TGGCGATGATGGAGATGTCG 59.967 55.000 0.0 0.0 35.56 4.35 R
3229 7161 2.605823 CCTCGACGCCTAATTCTAGCAG 60.606 54.545 0.0 0.0 0.00 4.24 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
43 44 1.301677 GAGGGCCTTCACTTTGCTCG 61.302 60.000 7.89 0.00 0.00 5.03
150 151 0.741221 GATGCCTCAGGACGACAACC 60.741 60.000 0.00 0.00 0.00 3.77
191 192 4.521639 TGAATCTTTTGATGCAGCAGAAGT 59.478 37.500 27.94 14.76 39.49 3.01
263 264 2.167487 TGTTGCCGTCATCTGTAGCATA 59.833 45.455 0.00 0.00 32.67 3.14
318 319 4.765088 GTTGTCAGAGTTGCTGCCAAGC 62.765 54.545 0.00 0.00 42.52 4.01
371 372 1.871408 GCGAGGCGACTTCATGATGAT 60.871 52.381 15.03 0.19 44.43 2.45
374 375 1.134310 AGGCGACTTCATGATGATGCA 60.134 47.619 21.59 0.00 37.44 3.96
519 520 9.863845 TTATTTGAAAAGAAATATTTCGGGGTC 57.136 29.630 19.86 15.93 41.92 4.46
520 521 5.907866 TGAAAAGAAATATTTCGGGGTCC 57.092 39.130 19.86 10.50 41.92 4.46
531 532 3.213264 GGGGTCCGAGCAATACGA 58.787 61.111 0.00 0.00 0.00 3.43
532 533 1.067582 GGGGTCCGAGCAATACGAG 59.932 63.158 0.00 0.00 0.00 4.18
533 534 1.389609 GGGGTCCGAGCAATACGAGA 61.390 60.000 0.00 0.00 0.00 4.04
534 535 0.030908 GGGTCCGAGCAATACGAGAG 59.969 60.000 0.00 0.00 0.00 3.20
535 536 0.595310 GGTCCGAGCAATACGAGAGC 60.595 60.000 0.00 0.00 0.00 4.09
536 537 0.930742 GTCCGAGCAATACGAGAGCG 60.931 60.000 0.00 0.00 44.79 5.03
537 538 1.658717 CCGAGCAATACGAGAGCGG 60.659 63.158 0.00 0.00 43.17 5.52
538 539 1.658717 CGAGCAATACGAGAGCGGG 60.659 63.158 0.00 0.00 43.17 6.13
539 540 1.437986 GAGCAATACGAGAGCGGGT 59.562 57.895 0.00 0.00 43.17 5.28
540 541 0.179108 GAGCAATACGAGAGCGGGTT 60.179 55.000 0.00 0.00 43.17 4.11
541 542 0.249398 AGCAATACGAGAGCGGGTTT 59.751 50.000 0.00 0.00 43.17 3.27
542 543 1.084289 GCAATACGAGAGCGGGTTTT 58.916 50.000 0.00 0.00 43.17 2.43
543 544 1.202031 GCAATACGAGAGCGGGTTTTG 60.202 52.381 0.00 0.00 43.17 2.44
544 545 2.343101 CAATACGAGAGCGGGTTTTGA 58.657 47.619 0.00 0.00 43.17 2.69
545 546 2.005971 ATACGAGAGCGGGTTTTGAC 57.994 50.000 0.00 0.00 43.17 3.18
546 547 0.963962 TACGAGAGCGGGTTTTGACT 59.036 50.000 0.00 0.00 43.17 3.41
547 548 0.600255 ACGAGAGCGGGTTTTGACTG 60.600 55.000 0.00 0.00 43.17 3.51
548 549 1.291877 CGAGAGCGGGTTTTGACTGG 61.292 60.000 0.00 0.00 0.00 4.00
549 550 0.250338 GAGAGCGGGTTTTGACTGGT 60.250 55.000 0.00 0.00 0.00 4.00
550 551 0.535102 AGAGCGGGTTTTGACTGGTG 60.535 55.000 0.00 0.00 0.00 4.17
553 554 0.534203 GCGGGTTTTGACTGGTGAGA 60.534 55.000 0.00 0.00 0.00 3.27
559 560 1.722034 TTTGACTGGTGAGAGCTCCT 58.278 50.000 10.93 0.00 0.00 3.69
564 565 2.039624 GGTGAGAGCTCCTCCCCA 59.960 66.667 10.93 0.00 39.02 4.96
570 571 4.523282 AGCTCCTCCCCATCCCCC 62.523 72.222 0.00 0.00 0.00 5.40
571 572 4.843331 GCTCCTCCCCATCCCCCA 62.843 72.222 0.00 0.00 0.00 4.96
921 939 5.172205 GGATATTAGCAGGGATCGACTTTC 58.828 45.833 0.00 0.00 0.00 2.62
1202 1227 4.917998 CGTTGATTGTAGAGATCCCATACG 59.082 45.833 0.00 0.00 0.00 3.06
2642 6555 3.702048 CGAGTTCGCCCCAGGGAA 61.702 66.667 7.25 0.00 42.18 3.97
3018 6950 0.244994 ATGAGCCACTGACTGACGAC 59.755 55.000 0.00 0.00 0.00 4.34
3225 7157 5.342866 AGTTAGGACCCATGTTAGTTCTCT 58.657 41.667 0.00 0.00 0.00 3.10
3229 7161 4.020128 AGGACCCATGTTAGTTCTCTGTTC 60.020 45.833 0.00 0.00 0.00 3.18
3328 7260 2.867109 AAGCTGGCAGTGTATCTGTT 57.133 45.000 17.16 0.00 45.23 3.16
3667 7604 0.895530 TGTGGGTGTCTTCTCGATCC 59.104 55.000 0.00 0.00 0.00 3.36
3668 7605 0.179134 GTGGGTGTCTTCTCGATCCG 60.179 60.000 0.00 0.00 0.00 4.18
3669 7606 1.320344 TGGGTGTCTTCTCGATCCGG 61.320 60.000 0.00 0.00 0.00 5.14
3670 7607 1.321074 GGGTGTCTTCTCGATCCGGT 61.321 60.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.705997 AAGTGAAGGCCCTCGTTGGT 61.706 55.000 0.00 0.00 0.00 3.67
191 192 6.707440 TCACCAAGAACAATGAAGCTAAAA 57.293 33.333 0.00 0.00 0.00 1.52
234 235 1.266718 GATGACGGCAACAGAAGCAAA 59.733 47.619 0.00 0.00 0.00 3.68
263 264 0.987294 AGTACAGTTCAGGCCTGCAT 59.013 50.000 28.91 13.05 33.09 3.96
318 319 2.620112 CCGTGGCAAGGTGCTGAAG 61.620 63.158 11.63 0.00 44.28 3.02
371 372 2.124612 CATCCACGCCCTCATGCA 60.125 61.111 0.00 0.00 0.00 3.96
374 375 2.050144 AGATAACATCCACGCCCTCAT 58.950 47.619 0.00 0.00 0.00 2.90
514 515 1.067582 CTCGTATTGCTCGGACCCC 59.932 63.158 0.00 0.00 0.00 4.95
515 516 0.030908 CTCTCGTATTGCTCGGACCC 59.969 60.000 0.00 0.00 0.00 4.46
516 517 0.595310 GCTCTCGTATTGCTCGGACC 60.595 60.000 0.00 0.00 0.00 4.46
517 518 0.930742 CGCTCTCGTATTGCTCGGAC 60.931 60.000 0.00 0.00 0.00 4.79
518 519 1.355563 CGCTCTCGTATTGCTCGGA 59.644 57.895 0.00 0.00 0.00 4.55
519 520 1.658717 CCGCTCTCGTATTGCTCGG 60.659 63.158 0.00 0.00 0.00 4.63
520 521 1.658717 CCCGCTCTCGTATTGCTCG 60.659 63.158 0.00 0.00 0.00 5.03
521 522 0.179108 AACCCGCTCTCGTATTGCTC 60.179 55.000 0.00 0.00 0.00 4.26
522 523 0.249398 AAACCCGCTCTCGTATTGCT 59.751 50.000 0.00 0.00 0.00 3.91
523 524 1.084289 AAAACCCGCTCTCGTATTGC 58.916 50.000 0.00 0.00 0.00 3.56
524 525 2.093783 GTCAAAACCCGCTCTCGTATTG 59.906 50.000 0.00 0.00 0.00 1.90
525 526 2.028385 AGTCAAAACCCGCTCTCGTATT 60.028 45.455 0.00 0.00 0.00 1.89
526 527 1.549170 AGTCAAAACCCGCTCTCGTAT 59.451 47.619 0.00 0.00 0.00 3.06
527 528 0.963962 AGTCAAAACCCGCTCTCGTA 59.036 50.000 0.00 0.00 0.00 3.43
528 529 0.600255 CAGTCAAAACCCGCTCTCGT 60.600 55.000 0.00 0.00 0.00 4.18
529 530 1.291877 CCAGTCAAAACCCGCTCTCG 61.292 60.000 0.00 0.00 0.00 4.04
530 531 0.250338 ACCAGTCAAAACCCGCTCTC 60.250 55.000 0.00 0.00 0.00 3.20
531 532 0.535102 CACCAGTCAAAACCCGCTCT 60.535 55.000 0.00 0.00 0.00 4.09
532 533 0.534203 TCACCAGTCAAAACCCGCTC 60.534 55.000 0.00 0.00 0.00 5.03
533 534 0.535102 CTCACCAGTCAAAACCCGCT 60.535 55.000 0.00 0.00 0.00 5.52
534 535 0.534203 TCTCACCAGTCAAAACCCGC 60.534 55.000 0.00 0.00 0.00 6.13
535 536 1.512926 CTCTCACCAGTCAAAACCCG 58.487 55.000 0.00 0.00 0.00 5.28
536 537 1.202818 AGCTCTCACCAGTCAAAACCC 60.203 52.381 0.00 0.00 0.00 4.11
537 538 2.147150 GAGCTCTCACCAGTCAAAACC 58.853 52.381 6.43 0.00 0.00 3.27
538 539 2.147150 GGAGCTCTCACCAGTCAAAAC 58.853 52.381 14.64 0.00 0.00 2.43
539 540 2.037772 GAGGAGCTCTCACCAGTCAAAA 59.962 50.000 14.64 0.00 42.02 2.44
540 541 1.620819 GAGGAGCTCTCACCAGTCAAA 59.379 52.381 14.64 0.00 42.02 2.69
541 542 1.261480 GAGGAGCTCTCACCAGTCAA 58.739 55.000 14.64 0.00 42.02 3.18
542 543 0.613292 GGAGGAGCTCTCACCAGTCA 60.613 60.000 14.64 0.00 44.19 3.41
543 544 1.326951 GGGAGGAGCTCTCACCAGTC 61.327 65.000 14.64 0.00 44.19 3.51
544 545 1.305718 GGGAGGAGCTCTCACCAGT 60.306 63.158 14.64 0.00 44.19 4.00
545 546 3.627690 GGGAGGAGCTCTCACCAG 58.372 66.667 14.64 0.00 44.19 4.00
548 549 1.406860 GGATGGGGAGGAGCTCTCAC 61.407 65.000 14.64 10.08 45.09 3.51
549 550 1.074926 GGATGGGGAGGAGCTCTCA 60.075 63.158 14.64 5.32 44.19 3.27
550 551 1.841103 GGGATGGGGAGGAGCTCTC 60.841 68.421 14.64 9.01 41.71 3.20
553 554 4.523282 GGGGGATGGGGAGGAGCT 62.523 72.222 0.00 0.00 0.00 4.09
559 560 4.549741 GGGGATGGGGGATGGGGA 62.550 72.222 0.00 0.00 0.00 4.81
618 619 4.821589 GCCAGCGACGGAAGAGGG 62.822 72.222 0.00 0.00 0.00 4.30
1792 1838 1.401552 CCGGTCGATGATGCATTTGTT 59.598 47.619 0.00 0.00 0.00 2.83
3018 6950 0.032540 TGGCGATGATGGAGATGTCG 59.967 55.000 0.00 0.00 35.56 4.35
3225 7157 3.733988 CGACGCCTAATTCTAGCAGAACA 60.734 47.826 1.44 0.00 37.00 3.18
3229 7161 2.605823 CCTCGACGCCTAATTCTAGCAG 60.606 54.545 0.00 0.00 0.00 4.24
3328 7260 7.227116 TCACAATTCTATTGATGATCATGCGAA 59.773 33.333 14.30 8.29 0.00 4.70
3483 7415 2.551270 TCCTGTAGGCAGAGAATTGGT 58.449 47.619 0.00 0.00 45.28 3.67
3667 7604 2.751166 AAGAGGATGAACACTGACCG 57.249 50.000 0.00 0.00 0.00 4.79
3668 7605 3.999663 CAGAAAGAGGATGAACACTGACC 59.000 47.826 0.00 0.00 0.00 4.02
3669 7606 3.999663 CCAGAAAGAGGATGAACACTGAC 59.000 47.826 0.00 0.00 0.00 3.51
3670 7607 3.557898 GCCAGAAAGAGGATGAACACTGA 60.558 47.826 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.