Multiple sequence alignment - TraesCS7B01G479300

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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 TraesCS7B01G479300 chr7B 100.000 5834 0 0 1 5834 733859344 733865177 0.000000e+00 10774.0
1 TraesCS7B01G479300 chr7B 93.298 5237 316 16 1 5228 733924206 733929416 0.000000e+00 7694.0
2 TraesCS7B01G479300 chr7B 99.575 2120 9 0 3715 5834 733887659 733889778 0.000000e+00 3866.0
3 TraesCS7B01G479300 chr7B 99.653 2018 7 0 1668 3685 733885649 733887666 0.000000e+00 3688.0
4 TraesCS7B01G479300 chr7B 99.045 1676 16 0 1 1676 733883849 733885524 0.000000e+00 3007.0
5 TraesCS7B01G479300 chr7B 78.187 2416 452 50 997 3373 733811142 733813521 0.000000e+00 1472.0
6 TraesCS7B01G479300 chr7B 74.872 1958 410 60 995 2901 733759177 733761103 0.000000e+00 815.0
7 TraesCS7B01G479300 chr7B 71.014 1687 373 75 1749 3342 890353 888690 3.420000e-77 300.0
8 TraesCS7B01G479300 chr7A 91.777 5424 355 34 452 5834 727228147 727233520 0.000000e+00 7461.0
9 TraesCS7B01G479300 chr7A 76.524 2411 479 54 992 3372 726770315 726767962 0.000000e+00 1236.0
10 TraesCS7B01G479300 chr7A 73.837 2450 522 79 988 3372 726686234 726683839 0.000000e+00 863.0
11 TraesCS7B01G479300 chr7A 74.864 1659 342 56 1748 3372 726814162 726812545 0.000000e+00 684.0
12 TraesCS7B01G479300 chr7A 72.373 1180 259 47 1010 2151 727215337 727214187 1.580000e-80 311.0
13 TraesCS7B01G479300 chr7A 96.429 112 4 0 345 456 685837730 685837619 9.980000e-43 185.0
14 TraesCS7B01G479300 chr7D 77.984 2421 448 57 997 3373 631424352 631426731 0.000000e+00 1439.0
15 TraesCS7B01G479300 chr7D 91.558 154 12 1 77 230 632637691 632637843 1.650000e-50 211.0
16 TraesCS7B01G479300 chr6D 73.279 1714 355 68 1664 3312 469051271 469052946 3.090000e-147 532.0
17 TraesCS7B01G479300 chr6D 72.918 1717 364 69 1663 3312 468941584 468943266 8.730000e-138 501.0
18 TraesCS7B01G479300 chr6D 75.048 521 99 21 1626 2123 468255404 468254892 4.580000e-51 213.0
19 TraesCS7B01G479300 chr6D 89.937 159 13 3 77 235 8343888 8343733 9.910000e-48 202.0
20 TraesCS7B01G479300 chr6D 92.063 126 7 2 330 454 307291461 307291338 2.160000e-39 174.0
21 TraesCS7B01G479300 chr4B 90.000 160 16 0 77 236 652990489 652990330 2.130000e-49 207.0
22 TraesCS7B01G479300 chr3B 89.937 159 14 2 82 240 5607144 5606988 2.760000e-48 204.0
23 TraesCS7B01G479300 chr3B 90.260 154 14 1 77 230 471474158 471474310 3.570000e-47 200.0
24 TraesCS7B01G479300 chr6B 88.957 163 16 2 77 237 260601154 260601316 3.570000e-47 200.0
25 TraesCS7B01G479300 chr5B 88.889 162 17 1 77 238 276825470 276825630 1.280000e-46 198.0
26 TraesCS7B01G479300 chr5B 90.141 71 7 0 4 74 488950336 488950266 6.220000e-15 93.5
27 TraesCS7B01G479300 chr5A 98.148 108 2 0 346 453 134983942 134984049 7.720000e-44 189.0
28 TraesCS7B01G479300 chr5A 92.969 128 6 2 334 461 582384411 582384287 3.590000e-42 183.0
29 TraesCS7B01G479300 chr5A 92.000 125 9 1 345 469 346203973 346203850 2.160000e-39 174.0
30 TraesCS7B01G479300 chr2D 96.364 110 4 0 346 455 326217584 326217475 1.290000e-41 182.0
31 TraesCS7B01G479300 chr2A 93.443 122 8 0 340 461 647957925 647958046 1.290000e-41 182.0
32 TraesCS7B01G479300 chrUn 91.549 71 6 0 4 74 71742611 71742541 1.340000e-16 99.0
33 TraesCS7B01G479300 chrUn 89.189 74 8 0 1 74 378829530 378829603 6.220000e-15 93.5
34 TraesCS7B01G479300 chr1B 90.541 74 7 0 1 74 647543637 647543710 1.340000e-16 99.0
35 TraesCS7B01G479300 chr3D 90.141 71 7 0 4 74 559447120 559447050 6.220000e-15 93.5
36 TraesCS7B01G479300 chr3D 90.141 71 7 0 4 74 559473780 559473710 6.220000e-15 93.5
37 TraesCS7B01G479300 chr6A 88.889 72 7 1 4 75 29120299 29120229 2.900000e-13 87.9


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 TraesCS7B01G479300 chr7B 733859344 733865177 5833 False 10774.000000 10774 100.000000 1 5834 1 chr7B.!!$F3 5833
1 TraesCS7B01G479300 chr7B 733924206 733929416 5210 False 7694.000000 7694 93.298000 1 5228 1 chr7B.!!$F4 5227
2 TraesCS7B01G479300 chr7B 733883849 733889778 5929 False 3520.333333 3866 99.424333 1 5834 3 chr7B.!!$F5 5833
3 TraesCS7B01G479300 chr7B 733811142 733813521 2379 False 1472.000000 1472 78.187000 997 3373 1 chr7B.!!$F2 2376
4 TraesCS7B01G479300 chr7B 733759177 733761103 1926 False 815.000000 815 74.872000 995 2901 1 chr7B.!!$F1 1906
5 TraesCS7B01G479300 chr7B 888690 890353 1663 True 300.000000 300 71.014000 1749 3342 1 chr7B.!!$R1 1593
6 TraesCS7B01G479300 chr7A 727228147 727233520 5373 False 7461.000000 7461 91.777000 452 5834 1 chr7A.!!$F1 5382
7 TraesCS7B01G479300 chr7A 726767962 726770315 2353 True 1236.000000 1236 76.524000 992 3372 1 chr7A.!!$R3 2380
8 TraesCS7B01G479300 chr7A 726683839 726686234 2395 True 863.000000 863 73.837000 988 3372 1 chr7A.!!$R2 2384
9 TraesCS7B01G479300 chr7A 726812545 726814162 1617 True 684.000000 684 74.864000 1748 3372 1 chr7A.!!$R4 1624
10 TraesCS7B01G479300 chr7A 727214187 727215337 1150 True 311.000000 311 72.373000 1010 2151 1 chr7A.!!$R5 1141
11 TraesCS7B01G479300 chr7D 631424352 631426731 2379 False 1439.000000 1439 77.984000 997 3373 1 chr7D.!!$F1 2376
12 TraesCS7B01G479300 chr6D 469051271 469052946 1675 False 532.000000 532 73.279000 1664 3312 1 chr6D.!!$F2 1648
13 TraesCS7B01G479300 chr6D 468941584 468943266 1682 False 501.000000 501 72.918000 1663 3312 1 chr6D.!!$F1 1649
14 TraesCS7B01G479300 chr6D 468254892 468255404 512 True 213.000000 213 75.048000 1626 2123 1 chr6D.!!$R3 497

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
511 518 2.092968 TGAATGAAGGGGGTCGATTGAG 60.093 50.000 0.00 0.00 0.00 3.02 F
1204 1237 1.763770 CCCAGTTTGGAGGAGCTGT 59.236 57.895 0.00 0.00 40.96 4.40 F
1264 1297 4.834911 TGGACGAGCTCCAGTACA 57.165 55.556 8.47 5.28 44.99 2.90 F
2730 3010 5.011533 TGTCCCAAAATCCATTCGTCATTTT 59.988 36.000 0.00 0.00 31.30 1.82 F
3353 3651 5.415221 TGTGTCAAAAGGTGATTTGGAAAC 58.585 37.500 0.48 0.00 38.94 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2730 3010 6.128035 CGTATTTGTCTTTCATGGTGATGGAA 60.128 38.462 0.00 0.0 0.00 3.53 R
3353 3651 0.466555 TCCCCAAACCAACCTCAACG 60.467 55.000 0.00 0.0 0.00 4.10 R
3693 3991 8.463930 TCTGAACAAGACTGGAAATGTTAATT 57.536 30.769 0.00 0.0 36.22 1.40 R
3880 4178 1.941377 TCCTGCAGGAATGGCAATTT 58.059 45.000 33.41 0.0 42.18 1.82 R
5491 5789 1.451072 GTGGTTGGACCCGGTGTTA 59.549 57.895 0.00 0.0 37.50 2.41 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
299 300 3.011517 ATGCCTCCACTTCCCGCT 61.012 61.111 0.00 0.00 0.00 5.52
396 397 7.667219 ACCTTGAAGACATTTCAGACAATGTAT 59.333 33.333 9.58 5.75 45.55 2.29
511 518 2.092968 TGAATGAAGGGGGTCGATTGAG 60.093 50.000 0.00 0.00 0.00 3.02
1204 1237 1.763770 CCCAGTTTGGAGGAGCTGT 59.236 57.895 0.00 0.00 40.96 4.40
1264 1297 4.834911 TGGACGAGCTCCAGTACA 57.165 55.556 8.47 5.28 44.99 2.90
2730 3010 5.011533 TGTCCCAAAATCCATTCGTCATTTT 59.988 36.000 0.00 0.00 31.30 1.82
3353 3651 5.415221 TGTGTCAAAAGGTGATTTGGAAAC 58.585 37.500 0.48 0.00 38.94 2.78
3689 3987 6.537660 CAGTTATTGCATCTCAGATCACTCAA 59.462 38.462 0.00 0.00 0.00 3.02
3693 3991 9.617523 TTATTGCATCTCAGATCACTCAAATTA 57.382 29.630 0.00 0.00 0.00 1.40
3697 3995 9.617523 TGCATCTCAGATCACTCAAATTAATTA 57.382 29.630 0.01 0.00 0.00 1.40
4951 5249 5.598416 AGCACAGCTATGTACTATGTCAA 57.402 39.130 0.00 0.00 37.65 3.18
4973 5271 3.817647 AGCTTTCAAATTTCGAGCTCTGT 59.182 39.130 12.85 0.00 39.32 3.41
5491 5789 4.033709 ACTGAATACTGCTAGGACCATGT 58.966 43.478 0.00 0.00 0.00 3.21
5646 5944 2.301577 GCTTCTCATAAGCAGTCGGT 57.698 50.000 4.91 0.00 42.56 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
299 300 1.048601 AGCGAGGAGACTTTGGTTGA 58.951 50.000 0.00 0.00 44.43 3.18
396 397 5.362430 AGACAACTCAAATTGGGCTGTTTTA 59.638 36.000 3.21 0.00 33.63 1.52
1204 1237 0.682532 TTGGTGTGGAGCTTGTGCAA 60.683 50.000 0.00 0.00 42.74 4.08
1264 1297 1.698532 GAGCTGGTCCTGGATGATGAT 59.301 52.381 0.00 0.00 0.00 2.45
2730 3010 6.128035 CGTATTTGTCTTTCATGGTGATGGAA 60.128 38.462 0.00 0.00 0.00 3.53
3353 3651 0.466555 TCCCCAAACCAACCTCAACG 60.467 55.000 0.00 0.00 0.00 4.10
3693 3991 8.463930 TCTGAACAAGACTGGAAATGTTAATT 57.536 30.769 0.00 0.00 36.22 1.40
3697 3995 6.064060 TGATCTGAACAAGACTGGAAATGTT 58.936 36.000 0.00 0.00 37.88 2.71
3705 4003 4.214971 CCTGGTTTGATCTGAACAAGACTG 59.785 45.833 14.74 3.15 37.88 3.51
3707 4005 3.503748 CCCTGGTTTGATCTGAACAAGAC 59.496 47.826 14.74 3.40 37.88 3.01
3708 4006 3.498481 CCCCTGGTTTGATCTGAACAAGA 60.498 47.826 14.74 0.00 39.94 3.02
3880 4178 1.941377 TCCTGCAGGAATGGCAATTT 58.059 45.000 33.41 0.00 42.18 1.82
3881 4179 3.695803 TCCTGCAGGAATGGCAATT 57.304 47.368 33.41 0.00 42.18 2.32
4951 5249 3.817647 ACAGAGCTCGAAATTTGAAAGCT 59.182 39.130 14.97 14.97 45.54 3.74
4973 5271 8.567104 GGATTCACAATATATGTACACATTGCA 58.433 33.333 19.23 9.22 41.46 4.08
5491 5789 1.451072 GTGGTTGGACCCGGTGTTA 59.549 57.895 0.00 0.00 37.50 2.41


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

AutoCloner maintained by Alex Coulton.