Multiple sequence alignment - TraesCS6D01G137600

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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 TraesCS6D01G137600 chr6D 100.000 2654 0 0 1 2654 106078908 106081561 0.000000e+00 4902.0
1 TraesCS6D01G137600 chr6D 95.082 61 0 3 1781 1840 106080646 106080704 2.810000e-15 93.5
2 TraesCS6D01G137600 chr6D 95.082 61 0 3 1739 1797 106080688 106080747 2.810000e-15 93.5
3 TraesCS6D01G137600 chr6A 95.925 1546 41 8 710 2246 129340589 129342121 0.000000e+00 2486.0
4 TraesCS6D01G137600 chr6A 93.833 227 14 0 2414 2640 129342766 129342992 2.530000e-90 342.0
5 TraesCS6D01G137600 chr6A 83.191 351 21 11 220 557 129337978 129338303 1.200000e-73 287.0
6 TraesCS6D01G137600 chr6A 88.987 227 13 8 3 223 129337722 129337942 1.210000e-68 270.0
7 TraesCS6D01G137600 chr6A 87.179 117 13 2 569 685 129338345 129338459 5.960000e-27 132.0
8 TraesCS6D01G137600 chr6B 96.270 992 24 5 716 1705 192925922 192926902 0.000000e+00 1615.0
9 TraesCS6D01G137600 chr6B 89.513 534 28 15 1720 2238 192931262 192931782 0.000000e+00 651.0
10 TraesCS6D01G137600 chr6B 87.525 505 35 8 217 709 192925213 192925701 2.310000e-155 558.0
11 TraesCS6D01G137600 chr6B 92.793 222 9 2 3 223 192924965 192925180 5.510000e-82 315.0
12 TraesCS6D01G137600 chr6B 85.567 97 11 3 1897 1993 26227640 26227547 6.050000e-17 99.0
13 TraesCS6D01G137600 chr7B 83.634 886 107 23 817 1686 212419368 212418505 0.000000e+00 798.0
14 TraesCS6D01G137600 chr7A 87.029 717 78 9 978 1686 251254153 251253444 0.000000e+00 795.0
15 TraesCS6D01G137600 chr7A 84.906 106 15 1 1889 1994 168896017 168895913 3.610000e-19 106.0
16 TraesCS6D01G137600 chr7D 86.034 716 87 7 978 1686 236010780 236010071 0.000000e+00 756.0
17 TraesCS6D01G137600 chr7D 94.186 86 5 0 11 96 537251026 537251111 5.960000e-27 132.0
18 TraesCS6D01G137600 chr7D 84.043 94 14 1 3 96 48842256 48842348 3.640000e-14 89.8
19 TraesCS6D01G137600 chr5A 75.195 512 106 15 1166 1656 321328886 321328375 3.440000e-54 222.0
20 TraesCS6D01G137600 chr5A 94.505 91 4 1 6 96 380178577 380178488 3.560000e-29 139.0
21 TraesCS6D01G137600 chr5A 86.364 88 11 1 1889 1976 389131228 389131314 7.820000e-16 95.3
22 TraesCS6D01G137600 chr5D 92.308 91 6 1 6 96 287796023 287795934 7.710000e-26 128.0
23 TraesCS6D01G137600 chr4D 92.045 88 5 2 15 101 487470418 487470332 3.590000e-24 122.0
24 TraesCS6D01G137600 chr4D 88.235 51 5 1 47 97 494843187 494843138 2.850000e-05 60.2
25 TraesCS6D01G137600 chr2D 84.677 124 17 2 1889 2011 542126542 542126664 3.590000e-24 122.0
26 TraesCS6D01G137600 chr4B 90.323 93 6 3 1882 1973 33175225 33175135 4.640000e-23 119.0
27 TraesCS6D01G137600 chr3A 83.200 125 19 2 1888 2011 647468347 647468224 2.160000e-21 113.0
28 TraesCS6D01G137600 chr2B 81.481 108 16 4 1889 1994 52340704 52340809 4.710000e-13 86.1


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 TraesCS6D01G137600 chr6D 106078908 106081561 2653 False 1696.333333 4902 96.721333 1 2654 3 chr6D.!!$F1 2653
1 TraesCS6D01G137600 chr6A 129337722 129342992 5270 False 703.400000 2486 89.823000 3 2640 5 chr6A.!!$F1 2637
2 TraesCS6D01G137600 chr6B 192924965 192926902 1937 False 829.333333 1615 92.196000 3 1705 3 chr6B.!!$F2 1702
3 TraesCS6D01G137600 chr6B 192931262 192931782 520 False 651.000000 651 89.513000 1720 2238 1 chr6B.!!$F1 518
4 TraesCS6D01G137600 chr7B 212418505 212419368 863 True 798.000000 798 83.634000 817 1686 1 chr7B.!!$R1 869
5 TraesCS6D01G137600 chr7A 251253444 251254153 709 True 795.000000 795 87.029000 978 1686 1 chr7A.!!$R2 708
6 TraesCS6D01G137600 chr7D 236010071 236010780 709 True 756.000000 756 86.034000 978 1686 1 chr7D.!!$R1 708
7 TraesCS6D01G137600 chr5A 321328375 321328886 511 True 222.000000 222 75.195000 1166 1656 1 chr5A.!!$R1 490

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
497 556 1.196911 TCGATCCCCCACAAACGTAT 58.803 50.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 4270 2.416162 GCTTCGTGGTGGTTTTCAAACA 60.416 45.455 4.85 0.0 40.63 2.83 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
286 332 6.428465 TGTGCTCATATTCAAAACGGAAAGTA 59.572 34.615 0.00 0.0 0.00 2.24
303 349 2.208619 TACCGCTTGTTCCACCGGA 61.209 57.895 9.46 0.0 43.20 5.14
336 382 7.733046 ATTTTGTTTTCATTTTTGTTTCCGC 57.267 28.000 0.00 0.0 0.00 5.54
339 385 7.539712 TTGTTTTCATTTTTGTTTCCGCATA 57.460 28.000 0.00 0.0 0.00 3.14
469 527 2.513204 CGCAGGATGGTGCTCTGG 60.513 66.667 0.00 0.0 41.62 3.86
476 535 1.641577 GATGGTGCTCTGGTCGTTAC 58.358 55.000 0.00 0.0 0.00 2.50
497 556 1.196911 TCGATCCCCCACAAACGTAT 58.803 50.000 0.00 0.0 0.00 3.06
502 561 5.070180 TCGATCCCCCACAAACGTATTATTA 59.930 40.000 0.00 0.0 0.00 0.98
507 566 8.363761 TCCCCCACAAACGTATTATTATTTTT 57.636 30.769 0.00 0.0 0.00 1.94
587 676 7.687941 TTTTTCCAACAACTATTTTTGCCAA 57.312 28.000 0.00 0.0 0.00 4.52
934 3319 2.671177 CCCTCGCTCACTTTGCACG 61.671 63.158 0.00 0.0 0.00 5.34
1007 3396 0.591170 CGAACGTTCACAATGGCCTT 59.409 50.000 26.71 0.0 0.00 4.35
1491 3910 1.411977 CTGATCAAGGACATCGAGGCT 59.588 52.381 0.00 0.0 0.00 4.58
1707 4126 2.083774 GAGCGTGATCAATGGTTTGGA 58.916 47.619 0.00 0.0 33.44 3.53
1715 4134 6.332630 GTGATCAATGGTTTGGAAGTTATGG 58.667 40.000 0.00 0.0 33.44 2.74
1743 4162 9.601217 AGTTCTCTATAGCGTTGATTAATTGTT 57.399 29.630 0.00 0.0 0.00 2.83
1770 4189 5.907866 TGTCTTGGTCTCATCGTATACAA 57.092 39.130 3.32 0.0 0.00 2.41
1807 4226 5.907866 TGTTATGTCTTGGTCTCATCGTA 57.092 39.130 0.00 0.0 0.00 3.43
1816 4235 7.033791 GTCTTGGTCTCATCGTATACAAAAGA 58.966 38.462 3.32 0.0 0.00 2.52
1817 4236 7.544566 GTCTTGGTCTCATCGTATACAAAAGAA 59.455 37.037 3.32 0.0 0.00 2.52
1818 4237 8.092068 TCTTGGTCTCATCGTATACAAAAGAAA 58.908 33.333 3.32 0.0 0.00 2.52
1819 4238 8.610248 TTGGTCTCATCGTATACAAAAGAAAA 57.390 30.769 3.32 0.0 0.00 2.29
1820 4239 8.610248 TGGTCTCATCGTATACAAAAGAAAAA 57.390 30.769 3.32 0.0 0.00 1.94
1821 4240 8.717821 TGGTCTCATCGTATACAAAAGAAAAAG 58.282 33.333 3.32 0.0 0.00 2.27
1822 4241 8.932791 GGTCTCATCGTATACAAAAGAAAAAGA 58.067 33.333 3.32 0.0 0.00 2.52
1851 4270 9.730420 GTTGTATCATGTTTGTTAAAGTCAAGT 57.270 29.630 0.00 0.0 0.00 3.16
1867 4286 3.924073 GTCAAGTGTTTGAAAACCACCAC 59.076 43.478 3.59 0.0 44.49 4.16
1876 4300 2.428890 TGAAAACCACCACGAAGCAATT 59.571 40.909 0.00 0.0 0.00 2.32
1880 4304 2.820330 ACCACCACGAAGCAATTTTTG 58.180 42.857 0.00 0.0 0.00 2.44
1887 4311 5.040635 CCACGAAGCAATTTTTGTACAACT 58.959 37.500 8.07 0.0 0.00 3.16
2021 4445 2.647299 TGTTGGATCTTGTACACCCCAT 59.353 45.455 0.00 0.0 0.00 4.00
2061 4485 2.487762 ACTAACATGACGCAAATGGTGG 59.512 45.455 0.00 0.0 30.16 4.61
2312 5059 9.961265 GAAAGCACTTTTTGTTAATACTAGGTT 57.039 29.630 0.00 0.0 32.11 3.50
2315 5062 8.565416 AGCACTTTTTGTTAATACTAGGTTGTC 58.435 33.333 0.00 0.0 0.00 3.18
2326 5073 7.982371 AATACTAGGTTGTCGTAGATTTTCG 57.018 36.000 0.00 0.0 40.67 3.46
2363 5111 0.608035 GGCTTCCCATTGACGTTGGA 60.608 55.000 6.32 0.0 36.26 3.53
2376 5124 0.893270 CGTTGGATGGGCAGAACCAA 60.893 55.000 0.00 0.0 45.13 3.67
2504 5415 6.820656 CAGCCAGACACTATCTAGACAAAAAT 59.179 38.462 0.00 0.0 35.15 1.82
2516 5427 4.006780 AGACAAAAATCATTGGCCCAAC 57.993 40.909 0.00 0.0 39.23 3.77
2531 5442 2.769893 CCCAACTGGCCTTTTCAAATG 58.230 47.619 3.32 0.0 0.00 2.32
2549 5460 7.230849 TCAAATGTCCTCTATTTGTTTGCAT 57.769 32.000 9.46 0.0 42.94 3.96
2562 5473 4.652131 TGCATGGCCGGACCGTTT 62.652 61.111 13.94 0.0 43.94 3.60
2616 5527 2.440599 GACATGTTGGCCCCACCT 59.559 61.111 0.00 0.0 40.22 4.00
2621 5532 1.006813 ATGTTGGCCCCACCTAATCA 58.993 50.000 0.00 0.0 40.22 2.57
2631 5542 3.605634 CCCACCTAATCACACGAAATCA 58.394 45.455 0.00 0.0 0.00 2.57
2640 5551 3.750371 TCACACGAAATCAACATTCCCT 58.250 40.909 0.00 0.0 0.00 4.20
2641 5552 3.501828 TCACACGAAATCAACATTCCCTG 59.498 43.478 0.00 0.0 0.00 4.45
2642 5553 3.501828 CACACGAAATCAACATTCCCTGA 59.498 43.478 0.00 0.0 0.00 3.86
2643 5554 4.156556 CACACGAAATCAACATTCCCTGAT 59.843 41.667 0.00 0.0 33.66 2.90
2644 5555 4.766891 ACACGAAATCAACATTCCCTGATT 59.233 37.500 0.00 0.0 42.67 2.57
2650 5561 7.543359 AAATCAACATTCCCTGATTTCTTCA 57.457 32.000 4.59 0.0 44.94 3.02
2651 5562 7.729124 AATCAACATTCCCTGATTTCTTCAT 57.271 32.000 0.00 0.0 38.79 2.57
2652 5563 6.764308 TCAACATTCCCTGATTTCTTCATC 57.236 37.500 0.00 0.0 32.72 2.92
2653 5564 6.247676 TCAACATTCCCTGATTTCTTCATCA 58.752 36.000 0.00 0.0 32.72 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
311 357 7.809806 TGCGGAAACAAAAATGAAAACAAAATT 59.190 25.926 0.00 0.00 0.00 1.82
336 382 8.885494 TGGAAGTGGAAACAAAATTTTCTATG 57.115 30.769 0.00 0.00 46.06 2.23
339 385 8.806429 AAATGGAAGTGGAAACAAAATTTTCT 57.194 26.923 0.00 0.00 46.06 2.52
456 514 0.535335 TAACGACCAGAGCACCATCC 59.465 55.000 0.00 0.00 0.00 3.51
469 527 0.819582 TGGGGGATCGAAGTAACGAC 59.180 55.000 0.00 0.00 44.84 4.34
476 535 0.321298 ACGTTTGTGGGGGATCGAAG 60.321 55.000 0.00 0.00 0.00 3.79
507 566 5.596772 GGGCCAGGCTTTCTACAATAATTAA 59.403 40.000 12.43 0.00 0.00 1.40
508 567 5.137551 GGGCCAGGCTTTCTACAATAATTA 58.862 41.667 12.43 0.00 0.00 1.40
897 3282 3.053917 AGGGCGGGACAAACTATAACATT 60.054 43.478 0.00 0.00 0.00 2.71
934 3319 3.567478 AATGATCTACTCCAGTTGGCC 57.433 47.619 0.00 0.00 34.44 5.36
1707 4126 5.834204 ACGCTATAGAGAACTCCCATAACTT 59.166 40.000 10.73 0.00 0.00 2.66
1715 4134 8.704234 CAATTAATCAACGCTATAGAGAACTCC 58.296 37.037 10.73 0.00 0.00 3.85
1743 4162 4.801330 ACGATGAGACCAAGACATAACA 57.199 40.909 0.00 0.00 0.00 2.41
1824 4243 9.729023 CTTGACTTTAACAAACATGATACAACA 57.271 29.630 0.00 0.00 0.00 3.33
1825 4244 9.730420 ACTTGACTTTAACAAACATGATACAAC 57.270 29.630 0.00 0.00 0.00 3.32
1826 4245 9.729023 CACTTGACTTTAACAAACATGATACAA 57.271 29.630 0.00 0.00 0.00 2.41
1827 4246 8.898761 ACACTTGACTTTAACAAACATGATACA 58.101 29.630 0.00 0.00 0.00 2.29
1828 4247 9.730420 AACACTTGACTTTAACAAACATGATAC 57.270 29.630 0.00 0.00 0.00 2.24
1851 4270 2.416162 GCTTCGTGGTGGTTTTCAAACA 60.416 45.455 4.85 0.00 40.63 2.83
1867 4286 7.672351 TTGTAGTTGTACAAAAATTGCTTCG 57.328 32.000 10.51 0.00 44.53 3.79
1910 4334 7.374272 TCGACTTATCCAAATTGCAAATTCAA 58.626 30.769 1.71 0.00 0.00 2.69
2021 4445 3.472652 AGTGCTGGACGTTTTCATAACA 58.527 40.909 0.00 0.00 0.00 2.41
2266 5013 9.880157 TGCTTTCTTCGTAAACTAATATAAGGT 57.120 29.630 0.00 0.00 0.00 3.50
2277 5024 6.864560 ACAAAAAGTGCTTTCTTCGTAAAC 57.135 33.333 0.00 0.00 31.45 2.01
2282 5029 8.782533 AGTATTAACAAAAAGTGCTTTCTTCG 57.217 30.769 0.00 0.00 31.45 3.79
2287 5034 9.744468 CAACCTAGTATTAACAAAAAGTGCTTT 57.256 29.630 0.00 0.00 0.00 3.51
2326 5073 3.786635 AGCCATCATGACGTAGAGAAAC 58.213 45.455 0.00 0.00 0.00 2.78
2363 5111 7.919385 AATATTTTATCTTGGTTCTGCCCAT 57.081 32.000 0.00 0.00 33.60 4.00
2376 5124 7.717875 TGGTGCTAGCCGTTTAATATTTTATCT 59.282 33.333 13.29 0.00 0.00 1.98
2397 5145 9.489084 TTTCTTATGTATATATGTCACTGGTGC 57.511 33.333 0.00 0.00 0.00 5.01
2429 5340 4.272489 TGTTGAAGATGCCCTAATCAAGG 58.728 43.478 0.00 0.00 46.09 3.61
2516 5427 3.160269 AGAGGACATTTGAAAAGGCCAG 58.840 45.455 7.87 0.00 0.00 4.85
2530 5441 3.193267 GCCATGCAAACAAATAGAGGACA 59.807 43.478 0.00 0.00 0.00 4.02
2531 5442 3.429410 GGCCATGCAAACAAATAGAGGAC 60.429 47.826 0.00 0.00 0.00 3.85
2549 5460 2.188161 GTTTGAAACGGTCCGGCCA 61.188 57.895 17.28 7.31 36.97 5.36
2562 5473 1.142060 ACATGTCCGAACAGGGTTTGA 59.858 47.619 0.00 0.00 41.44 2.69
2585 5496 1.378514 ATGTCGGGTCCAACATGGC 60.379 57.895 8.03 0.00 37.47 4.40
2604 5515 0.039035 TGTGATTAGGTGGGGCCAAC 59.961 55.000 4.39 3.29 40.61 3.77
2605 5516 0.039035 GTGTGATTAGGTGGGGCCAA 59.961 55.000 4.39 0.00 40.61 4.52
2606 5517 1.688811 GTGTGATTAGGTGGGGCCA 59.311 57.895 4.39 0.00 40.61 5.36
2616 5527 5.943416 AGGGAATGTTGATTTCGTGTGATTA 59.057 36.000 0.00 0.00 0.00 1.75
2621 5532 3.750371 TCAGGGAATGTTGATTTCGTGT 58.250 40.909 0.00 0.00 35.33 4.49


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

AutoCloner maintained by Alex Coulton.