Multiple sequence alignment - TraesCS5A01G139400

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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 TraesCS5A01G139400 chr5A 100.000 2300 0 0 1 2300 311673483 311675782 0.000000e+00 4248.0
1 TraesCS5A01G139400 chr5D 97.338 1803 31 5 499 2300 241844247 241846033 0.000000e+00 3048.0
2 TraesCS5A01G139400 chr5D 99.000 400 4 0 1 400 241843680 241844079 0.000000e+00 717.0
3 TraesCS5A01G139400 chr5D 100.000 43 0 0 399 441 241844203 241844245 1.890000e-11 80.5
4 TraesCS5A01G139400 chr5B 92.706 1796 92 15 533 2300 256614139 256615923 0.000000e+00 2555.0
5 TraesCS5A01G139400 chr5B 88.372 430 19 9 1 430 256613695 256614093 2.660000e-134 488.0
6 TraesCS5A01G139400 chr5B 87.368 95 7 2 427 517 45538356 45538263 1.120000e-18 104.0
7 TraesCS5A01G139400 chr7B 89.524 105 9 1 423 527 566634958 566635060 5.160000e-27 132.0
8 TraesCS5A01G139400 chr6B 90.909 88 6 1 429 514 51735060 51734973 1.440000e-22 117.0
9 TraesCS5A01G139400 chr6B 90.000 90 5 1 425 510 609385996 609386085 1.870000e-21 113.0
10 TraesCS5A01G139400 chr2D 88.421 95 5 2 428 517 382456025 382455932 2.420000e-20 110.0
11 TraesCS5A01G139400 chr2D 87.500 96 7 1 416 506 619480889 619480794 3.130000e-19 106.0
12 TraesCS5A01G139400 chr3B 86.869 99 8 1 422 515 70273586 70273684 3.130000e-19 106.0
13 TraesCS5A01G139400 chr3B 86.869 99 5 3 428 519 450376643 450376546 1.120000e-18 104.0
14 TraesCS5A01G139400 chr1B 83.784 111 10 3 425 529 675980643 675980535 5.230000e-17 99.0


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 TraesCS5A01G139400 chr5A 311673483 311675782 2299 False 4248.000000 4248 100.000000 1 2300 1 chr5A.!!$F1 2299
1 TraesCS5A01G139400 chr5D 241843680 241846033 2353 False 1281.833333 3048 98.779333 1 2300 3 chr5D.!!$F1 2299
2 TraesCS5A01G139400 chr5B 256613695 256615923 2228 False 1521.500000 2555 90.539000 1 2300 2 chr5B.!!$F1 2299

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
230 231 1.667724 CGACCAGTGGCATTGATTCTC 59.332 52.381 9.78 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1753 1.064017 TGTGAGTTTCCTGCCTTGGTT 60.064 47.619 0.0 0.0 0.0 3.67 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
230 231 1.667724 CGACCAGTGGCATTGATTCTC 59.332 52.381 9.78 0.00 0.00 2.87
441 567 6.488769 TTTTGTGAAGTACTCCCTCTGTAA 57.511 37.500 0.00 0.00 0.00 2.41
442 568 6.488769 TTTGTGAAGTACTCCCTCTGTAAA 57.511 37.500 0.00 0.00 0.00 2.01
443 569 5.723672 TGTGAAGTACTCCCTCTGTAAAG 57.276 43.478 0.00 0.00 0.00 1.85
444 570 5.391256 TGTGAAGTACTCCCTCTGTAAAGA 58.609 41.667 0.00 0.00 0.00 2.52
445 571 5.836898 TGTGAAGTACTCCCTCTGTAAAGAA 59.163 40.000 0.00 0.00 0.00 2.52
446 572 6.325545 TGTGAAGTACTCCCTCTGTAAAGAAA 59.674 38.462 0.00 0.00 0.00 2.52
447 573 7.016268 TGTGAAGTACTCCCTCTGTAAAGAAAT 59.984 37.037 0.00 0.00 0.00 2.17
448 574 8.529476 GTGAAGTACTCCCTCTGTAAAGAAATA 58.471 37.037 0.00 0.00 0.00 1.40
449 575 9.268282 TGAAGTACTCCCTCTGTAAAGAAATAT 57.732 33.333 0.00 0.00 0.00 1.28
455 581 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
456 582 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
457 583 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
458 584 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
625 770 8.777578 TGCCTTAGAGTTAGGAACATCTAATA 57.222 34.615 0.00 2.41 34.14 0.98
626 771 9.209048 TGCCTTAGAGTTAGGAACATCTAATAA 57.791 33.333 0.00 0.00 34.14 1.40
683 828 6.942976 TCGGTTCATTACACTCCTTAAATCT 58.057 36.000 0.00 0.00 0.00 2.40
713 858 6.163476 TGACGTAATTGAATAGTCTTGCACT 58.837 36.000 0.00 0.00 39.41 4.40
899 1044 7.869937 ACTATTTCATCCTCAGATATCGTGTTG 59.130 37.037 0.00 0.00 0.00 3.33
1205 1350 4.069304 TCTTTTCCCTTGTATTGGTCACG 58.931 43.478 0.00 0.00 0.00 4.35
1407 1552 5.673337 TGTCTGCAGAATTTGTAGTTGAC 57.327 39.130 20.19 2.23 40.11 3.18
1478 1623 4.764308 TGCATTGCAATTAACTCCTACACA 59.236 37.500 9.83 0.00 34.76 3.72
1515 1660 5.007385 ACAATCCACTCACGTCCTTATAC 57.993 43.478 0.00 0.00 0.00 1.47
1588 1753 7.485418 TTTTCACGCTGTTTCTACTTAATCA 57.515 32.000 0.00 0.00 0.00 2.57
1622 1787 3.146104 ACTCACATTTTCCTGTCCCTG 57.854 47.619 0.00 0.00 0.00 4.45
1626 1791 2.564062 CACATTTTCCTGTCCCTGCATT 59.436 45.455 0.00 0.00 0.00 3.56
1659 1824 5.047188 GGAGCAGCTAGTTCAAGAGATTAC 58.953 45.833 0.00 0.00 0.00 1.89
2059 2225 0.971386 CCAACTGCAATTGAGGCCTT 59.029 50.000 9.94 0.00 0.00 4.35
2060 2226 1.337447 CCAACTGCAATTGAGGCCTTG 60.337 52.381 9.94 1.17 0.00 3.61
2116 2282 6.591935 AGTTCAGGACTTAGTTCACAAATCA 58.408 36.000 0.00 0.00 33.92 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.280654 TCATTTCATCAGATCGATCCACA 57.719 39.130 21.66 6.4 29.21 4.17
230 231 6.348540 GGAACAAGGTAGTACAAAGCATCAAG 60.349 42.308 2.06 0.0 0.00 3.02
474 600 9.956720 CCCACAAAGAAATATAAGAGCATTTAG 57.043 33.333 0.00 0.0 0.00 1.85
475 601 8.912988 CCCCACAAAGAAATATAAGAGCATTTA 58.087 33.333 0.00 0.0 0.00 1.40
476 602 7.147672 CCCCCACAAAGAAATATAAGAGCATTT 60.148 37.037 0.00 0.0 0.00 2.32
477 603 6.324770 CCCCCACAAAGAAATATAAGAGCATT 59.675 38.462 0.00 0.0 0.00 3.56
478 604 5.835280 CCCCCACAAAGAAATATAAGAGCAT 59.165 40.000 0.00 0.0 0.00 3.79
479 605 5.200483 CCCCCACAAAGAAATATAAGAGCA 58.800 41.667 0.00 0.0 0.00 4.26
480 606 5.774498 CCCCCACAAAGAAATATAAGAGC 57.226 43.478 0.00 0.0 0.00 4.09
660 805 7.611213 AAGATTTAAGGAGTGTAATGAACCG 57.389 36.000 0.00 0.0 0.00 4.44
683 828 7.667043 AGACTATTCAATTACGTCAGCAAAA 57.333 32.000 0.00 0.0 0.00 2.44
899 1044 1.927895 CACGGACATCTACAGAAGCC 58.072 55.000 0.00 0.0 0.00 4.35
1205 1350 5.048846 ACACTCCATATATTGGGTTGGAC 57.951 43.478 4.69 0.0 46.45 4.02
1478 1623 6.299141 AGTGGATTGTTTGTGATGTCTAGTT 58.701 36.000 0.00 0.0 0.00 2.24
1515 1660 4.814294 GCAGAGCCGTACCCACCG 62.814 72.222 0.00 0.0 0.00 4.94
1588 1753 1.064017 TGTGAGTTTCCTGCCTTGGTT 60.064 47.619 0.00 0.0 0.00 3.67
1622 1787 4.521146 AGCTGCTCCATATACCATAATGC 58.479 43.478 0.00 0.0 0.00 3.56
1626 1791 6.016555 TGAACTAGCTGCTCCATATACCATA 58.983 40.000 4.91 0.0 0.00 2.74
1659 1824 7.997482 AGTACACTACACAATACTCATAGGTG 58.003 38.462 0.00 0.0 35.66 4.00
1746 1911 9.303116 TCAGGTAAAATTTAGGTCATTTTGCTA 57.697 29.630 0.00 0.0 36.79 3.49
2059 2225 6.901300 ACCTATATCCCACTAGTTGACTTTCA 59.099 38.462 0.00 0.0 0.00 2.69
2060 2226 7.362802 ACCTATATCCCACTAGTTGACTTTC 57.637 40.000 0.00 0.0 0.00 2.62
2116 2282 2.927028 AGGTTACCGAACAAGCAAACT 58.073 42.857 0.00 0.0 37.29 2.66
2229 2395 4.530710 TGGGCTTGTAACAGTACTACAG 57.469 45.455 0.00 0.0 31.17 2.74


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

AutoCloner maintained by Alex Coulton.