Multiple sequence alignment - TraesCS5A01G124300

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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 TraesCS5A01G124300 chr5A 100.000 1995 0 0 741 2735 272133537 272131543 0.000000e+00 3685.0
1 TraesCS5A01G124300 chr5A 100.000 450 0 0 3066 3515 272131212 272130763 0.000000e+00 832.0
2 TraesCS5A01G124300 chr5A 100.000 254 0 0 1 254 272134277 272134024 1.480000e-128 470.0
3 TraesCS5A01G124300 chr5B 97.797 1997 37 4 741 2733 223985436 223983443 0.000000e+00 3437.0
4 TraesCS5A01G124300 chr5B 97.253 364 9 1 3153 3515 223983072 223982709 1.790000e-172 616.0
5 TraesCS5A01G124300 chr5B 95.276 254 12 0 1 254 223985778 223985525 1.520000e-108 403.0
6 TraesCS5A01G124300 chr5D 97.453 1924 32 7 741 2651 210376286 210374367 0.000000e+00 3265.0
7 TraesCS5A01G124300 chr5D 95.796 452 17 2 3066 3515 210374248 210373797 0.000000e+00 728.0
8 TraesCS5A01G124300 chr5D 95.276 254 12 0 1 254 210376628 210376375 1.520000e-108 403.0
9 TraesCS5A01G124300 chr5D 82.586 379 66 0 1234 1612 389377 388999 5.620000e-88 335.0
10 TraesCS5A01G124300 chr5D 96.923 65 2 0 2669 2733 210374373 210374309 3.710000e-20 110.0
11 TraesCS5A01G124300 chr1D 86.378 624 83 2 1706 2328 8713585 8714207 0.000000e+00 680.0
12 TraesCS5A01G124300 chr1D 84.142 618 98 0 1711 2328 252528696 252528079 1.810000e-167 599.0
13 TraesCS5A01G124300 chr1D 81.273 550 87 14 1095 1632 8712802 8713347 6.970000e-117 431.0
14 TraesCS5A01G124300 chr1B 85.875 623 88 0 1706 2328 11859020 11859642 0.000000e+00 664.0
15 TraesCS5A01G124300 chr1B 85.113 618 92 0 1711 2328 360808768 360809385 1.780000e-177 632.0
16 TraesCS5A01G124300 chr1B 81.455 550 86 13 1095 1632 11858235 11858780 1.500000e-118 436.0
17 TraesCS5A01G124300 chr1B 93.750 64 4 0 1095 1158 360808078 360808141 2.890000e-16 97.1
18 TraesCS5A01G124300 chr1A 85.875 623 88 0 1706 2328 10068025 10068647 0.000000e+00 664.0
19 TraesCS5A01G124300 chr1A 83.657 618 101 0 1711 2328 323643083 323642466 1.820000e-162 582.0
20 TraesCS5A01G124300 chr1A 85.464 399 58 0 1234 1632 10067343 10067741 1.950000e-112 416.0
21 TraesCS5A01G124300 chr1A 95.312 64 3 0 1095 1158 10067167 10067230 6.210000e-18 102.0
22 TraesCS5A01G124300 chr1A 93.750 64 4 0 1095 1158 323643773 323643710 2.890000e-16 97.1
23 TraesCS5A01G124300 chr4B 83.520 625 101 2 1710 2333 39121251 39121874 1.820000e-162 582.0
24 TraesCS5A01G124300 chr4B 84.962 399 60 0 1233 1631 39120608 39121006 4.220000e-109 405.0
25 TraesCS5A01G124300 chr4D 84.461 399 62 0 1233 1631 26668446 26668844 9.150000e-106 394.0
26 TraesCS5A01G124300 chr4A 84.461 399 62 0 1233 1631 576703436 576703038 9.150000e-106 394.0
27 TraesCS5A01G124300 chr3B 82.000 400 68 4 1230 1627 647078352 647078749 1.560000e-88 337.0
28 TraesCS5A01G124300 chr3D 82.713 376 61 4 1233 1606 484287523 484287896 7.270000e-87 331.0


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 TraesCS5A01G124300 chr5A 272130763 272134277 3514 True 1662.333333 3685 100.000000 1 3515 3 chr5A.!!$R1 3514
1 TraesCS5A01G124300 chr5B 223982709 223985778 3069 True 1485.333333 3437 96.775333 1 3515 3 chr5B.!!$R1 3514
2 TraesCS5A01G124300 chr5D 210373797 210376628 2831 True 1126.500000 3265 96.362000 1 3515 4 chr5D.!!$R2 3514
3 TraesCS5A01G124300 chr1D 252528079 252528696 617 True 599.000000 599 84.142000 1711 2328 1 chr1D.!!$R1 617
4 TraesCS5A01G124300 chr1D 8712802 8714207 1405 False 555.500000 680 83.825500 1095 2328 2 chr1D.!!$F1 1233
5 TraesCS5A01G124300 chr1B 11858235 11859642 1407 False 550.000000 664 83.665000 1095 2328 2 chr1B.!!$F1 1233
6 TraesCS5A01G124300 chr1B 360808078 360809385 1307 False 364.550000 632 89.431500 1095 2328 2 chr1B.!!$F2 1233
7 TraesCS5A01G124300 chr1A 10067167 10068647 1480 False 394.000000 664 88.883667 1095 2328 3 chr1A.!!$F1 1233
8 TraesCS5A01G124300 chr1A 323642466 323643773 1307 True 339.550000 582 88.703500 1095 2328 2 chr1A.!!$R1 1233
9 TraesCS5A01G124300 chr4B 39120608 39121874 1266 False 493.500000 582 84.241000 1233 2333 2 chr4B.!!$F1 1100

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
936 937 0.391661 AGGCAGAGTTACGGCATGTG 60.392 55.0 0.0 0.0 41.24 3.21 F
1363 1430 0.608035 GTGACGAGGCCCAATCCAAA 60.608 55.0 0.0 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2475 2908 0.803768 CAATCGCTGGACCTGACTCG 60.804 60.0 1.91 0.0 0.0 4.18 R
3074 3507 0.953960 ATGGGACTCGCACGGAAAAC 60.954 55.0 0.00 0.0 0.0 2.43 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
81 82 0.978146 CATCTCGGTGGGAGGTCCTT 60.978 60.000 0.00 0.00 43.34 3.36
160 161 4.822350 AGTTTCCTTTCTTCTTTTCCGGAG 59.178 41.667 3.34 0.00 0.00 4.63
230 231 1.680522 CTGGGGCGTGCTAGATCTGT 61.681 60.000 5.18 0.00 0.00 3.41
242 243 3.495001 GCTAGATCTGTTGAATTACCCGC 59.505 47.826 5.18 0.00 0.00 6.13
921 922 5.628797 AAAATGGGAGAAAAGAAAAGGCA 57.371 34.783 0.00 0.00 0.00 4.75
936 937 0.391661 AGGCAGAGTTACGGCATGTG 60.392 55.000 0.00 0.00 41.24 3.21
964 969 6.126940 ACTCAGATGATGTTGTAGGTGCTAAT 60.127 38.462 0.00 0.00 0.00 1.73
985 990 7.095607 GCTAATATTCTTGCTGCAACGTAGTAT 60.096 37.037 11.69 3.86 45.00 2.12
1025 1033 5.205565 GGTGAATTTTCTTCTGTTCGTGTC 58.794 41.667 0.00 0.00 0.00 3.67
1069 1078 8.276252 TGGTAATAATAGCCTTCTTGTCAAAC 57.724 34.615 0.00 0.00 0.00 2.93
1363 1430 0.608035 GTGACGAGGCCCAATCCAAA 60.608 55.000 0.00 0.00 0.00 3.28
1402 1469 1.664965 GTACCCGATCGAGCATGGC 60.665 63.158 18.66 0.00 0.00 4.40
2413 2846 8.610035 GTTACAGTAAATACACTCCCTATTTGC 58.390 37.037 0.00 0.00 0.00 3.68
2575 3008 2.494059 TCTTTTCTCAAGTCCTTGCCG 58.506 47.619 2.09 0.00 40.24 5.69
2733 3166 0.882474 CCGCATGTTCCGGGTTTTTA 59.118 50.000 0.00 0.00 41.99 1.52
3106 3539 5.163248 TGCGAGTCCCATAATCATTTCCTTA 60.163 40.000 0.00 0.00 0.00 2.69
3129 3562 3.679502 TGTACATTCACTTCTGCGATGTG 59.320 43.478 14.16 14.16 38.51 3.21
3167 3600 5.188163 TGCCAATTTGATTCATGATTCCTGT 59.812 36.000 13.60 0.00 0.00 4.00
3177 3610 9.246670 TGATTCATGATTCCTGTTTCTAATGTT 57.753 29.630 13.60 0.00 0.00 2.71
3505 3941 2.588027 TTTTCGCCGCCTTTTTCTTT 57.412 40.000 0.00 0.00 0.00 2.52
3507 3943 1.846541 TTCGCCGCCTTTTTCTTTTG 58.153 45.000 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 0.250338 AAGGAAACTGGTGCGAGGAC 60.250 55.000 0.00 0.00 42.68 3.85
160 161 3.319122 CAGGCCAAAATTAGCAGGGATAC 59.681 47.826 5.01 0.00 0.00 2.24
230 231 2.078392 GTCCTTTCGCGGGTAATTCAA 58.922 47.619 6.13 0.00 0.00 2.69
921 922 1.623811 AGTTCCACATGCCGTAACTCT 59.376 47.619 0.00 0.00 0.00 3.24
936 937 4.872691 CACCTACAACATCATCTGAGTTCC 59.127 45.833 0.00 0.00 0.00 3.62
964 969 5.656480 TGATACTACGTTGCAGCAAGAATA 58.344 37.500 8.49 0.45 0.00 1.75
1069 1078 2.938451 TGAGTGACTCTGTTGCACAAAG 59.062 45.455 14.42 0.00 35.08 2.77
1402 1469 2.460330 GTCCCAGTTGCTGACGATG 58.540 57.895 0.00 0.00 32.44 3.84
2154 2587 2.740055 GAGCCACCACTGAGCACG 60.740 66.667 0.00 0.00 0.00 5.34
2400 2833 5.116882 GGTTAGTACAGCAAATAGGGAGTG 58.883 45.833 0.00 0.00 0.00 3.51
2413 2846 7.672983 AAATCAGAACACATGGTTAGTACAG 57.327 36.000 0.00 0.00 40.63 2.74
2475 2908 0.803768 CAATCGCTGGACCTGACTCG 60.804 60.000 1.91 0.00 0.00 4.18
2575 3008 7.278868 AGCAATCTCAAACATAGTAGCTTACAC 59.721 37.037 0.00 0.00 0.00 2.90
3074 3507 0.953960 ATGGGACTCGCACGGAAAAC 60.954 55.000 0.00 0.00 0.00 2.43
3106 3539 4.507710 ACATCGCAGAAGTGAATGTACAT 58.492 39.130 1.41 1.41 43.58 2.29
3167 3600 1.431243 ACTGGGGGCCAACATTAGAAA 59.569 47.619 4.39 0.00 30.80 2.52
3321 3755 4.089839 CCAGTAATGGCCCCCTCT 57.910 61.111 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.