Multiple sequence alignment - TraesCS5B01G037800

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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 TraesCS5B01G037800 chr5B 100.000 1644 0 0 1569 3212 42178619 42180262 0.000000e+00 3037
1 TraesCS5B01G037800 chr5B 100.000 1531 0 0 1 1531 42177051 42178581 0.000000e+00 2828
2 TraesCS5B01G037800 chr5B 86.537 1441 160 29 1783 3211 79788388 79786970 0.000000e+00 1555
3 TraesCS5B01G037800 chr5B 78.151 595 120 8 922 1511 79789299 79788710 1.410000e-98 370
4 TraesCS5B01G037800 chr5B 82.407 324 48 9 501 820 79790572 79790254 1.140000e-69 274
5 TraesCS5B01G037800 chr1A 99.331 1645 7 2 1569 3212 21636015 21634374 0.000000e+00 2974
6 TraesCS5B01G037800 chr1A 99.271 1645 11 1 1569 3212 573952906 573954550 0.000000e+00 2970
7 TraesCS5B01G037800 chr1A 98.933 1031 11 0 501 1531 573951815 573952845 0.000000e+00 1844
8 TraesCS5B01G037800 chr1A 98.789 991 12 0 499 1489 21637233 21636243 0.000000e+00 1764
9 TraesCS5B01G037800 chr1A 86.648 1438 163 24 1783 3211 95836775 95838192 0.000000e+00 1565
10 TraesCS5B01G037800 chr1A 78.873 639 124 9 879 1511 95835820 95836453 3.830000e-114 422
11 TraesCS5B01G037800 chr2D 96.292 1645 54 4 1569 3212 471445730 471444092 0.000000e+00 2693
12 TraesCS5B01G037800 chr2D 94.203 1035 42 10 502 1531 471446804 471445783 0.000000e+00 1563
13 TraesCS5B01G037800 chr2D 85.345 1433 187 13 1796 3212 534514796 534513371 0.000000e+00 1461
14 TraesCS5B01G037800 chr2D 76.125 578 97 34 501 1050 14262375 14262939 6.830000e-67 265
15 TraesCS5B01G037800 chr4B 86.806 1440 157 28 1783 3211 633916831 633918248 0.000000e+00 1576
16 TraesCS5B01G037800 chr4B 78.717 639 125 9 879 1511 633915876 633916509 1.780000e-112 416
17 TraesCS5B01G037800 chr4B 83.591 323 46 7 501 820 633915555 633915873 2.420000e-76 296
18 TraesCS5B01G037800 chr1D 85.131 1446 190 16 1784 3212 78384339 78385776 0.000000e+00 1456
19 TraesCS5B01G037800 chr1D 97.006 501 14 1 1 500 209989997 209990497 0.000000e+00 841
20 TraesCS5B01G037800 chr2A 83.826 1422 196 25 1813 3211 718367764 718366354 0.000000e+00 1321
21 TraesCS5B01G037800 chr2A 96.400 500 17 1 1 500 650095914 650096412 0.000000e+00 822
22 TraesCS5B01G037800 chr2A 79.468 940 163 22 501 1419 718369070 718368140 9.720000e-180 640
23 TraesCS5B01G037800 chr3D 86.221 987 118 11 2240 3212 561029074 561028092 0.000000e+00 1053
24 TraesCS5B01G037800 chr3D 84.314 408 62 2 1796 2203 561029478 561029073 6.460000e-107 398
25 TraesCS5B01G037800 chr3D 76.748 572 100 19 896 1460 422761104 422760559 4.050000e-74 289
26 TraesCS5B01G037800 chr3D 78.505 321 59 10 501 818 422761463 422761150 5.430000e-48 202
27 TraesCS5B01G037800 chr3A 99.600 500 2 0 1 500 739820580 739821079 0.000000e+00 913
28 TraesCS5B01G037800 chr7A 99.400 500 3 0 1 500 53218661 53218162 0.000000e+00 907
29 TraesCS5B01G037800 chr6A 99.400 500 3 0 1 500 567085362 567084863 0.000000e+00 907
30 TraesCS5B01G037800 chr6A 96.600 500 16 1 1 500 447894465 447894963 0.000000e+00 828
31 TraesCS5B01G037800 chr4A 99.400 500 3 0 1 500 16837033 16836534 0.000000e+00 907
32 TraesCS5B01G037800 chr4A 96.800 500 16 0 1 500 593676461 593675962 0.000000e+00 835
33 TraesCS5B01G037800 chr3B 95.808 501 20 1 1 500 490053716 490054216 0.000000e+00 808
34 TraesCS5B01G037800 chr4D 76.239 585 106 25 501 1064 105892928 105892356 2.440000e-71 279
35 TraesCS5B01G037800 chr6D 74.286 455 84 27 501 934 4274224 4273782 9.220000e-36 161
36 TraesCS5B01G037800 chr7B 81.295 139 26 0 1282 1420 676864286 676864424 2.620000e-21 113


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 TraesCS5B01G037800 chr5B 42177051 42180262 3211 False 2932.500000 3037 100.0000 1 3212 2 chr5B.!!$F1 3211
1 TraesCS5B01G037800 chr5B 79786970 79790572 3602 True 733.000000 1555 82.3650 501 3211 3 chr5B.!!$R1 2710
2 TraesCS5B01G037800 chr1A 573951815 573954550 2735 False 2407.000000 2970 99.1020 501 3212 2 chr1A.!!$F2 2711
3 TraesCS5B01G037800 chr1A 21634374 21637233 2859 True 2369.000000 2974 99.0600 499 3212 2 chr1A.!!$R1 2713
4 TraesCS5B01G037800 chr1A 95835820 95838192 2372 False 993.500000 1565 82.7605 879 3211 2 chr1A.!!$F1 2332
5 TraesCS5B01G037800 chr2D 471444092 471446804 2712 True 2128.000000 2693 95.2475 502 3212 2 chr2D.!!$R2 2710
6 TraesCS5B01G037800 chr2D 534513371 534514796 1425 True 1461.000000 1461 85.3450 1796 3212 1 chr2D.!!$R1 1416
7 TraesCS5B01G037800 chr2D 14262375 14262939 564 False 265.000000 265 76.1250 501 1050 1 chr2D.!!$F1 549
8 TraesCS5B01G037800 chr4B 633915555 633918248 2693 False 762.666667 1576 83.0380 501 3211 3 chr4B.!!$F1 2710
9 TraesCS5B01G037800 chr1D 78384339 78385776 1437 False 1456.000000 1456 85.1310 1784 3212 1 chr1D.!!$F1 1428
10 TraesCS5B01G037800 chr1D 209989997 209990497 500 False 841.000000 841 97.0060 1 500 1 chr1D.!!$F2 499
11 TraesCS5B01G037800 chr2A 718366354 718369070 2716 True 980.500000 1321 81.6470 501 3211 2 chr2A.!!$R1 2710
12 TraesCS5B01G037800 chr3D 561028092 561029478 1386 True 725.500000 1053 85.2675 1796 3212 2 chr3D.!!$R2 1416
13 TraesCS5B01G037800 chr3D 422760559 422761463 904 True 245.500000 289 77.6265 501 1460 2 chr3D.!!$R1 959
14 TraesCS5B01G037800 chr3B 490053716 490054216 500 False 808.000000 808 95.8080 1 500 1 chr3B.!!$F1 499
15 TraesCS5B01G037800 chr4D 105892356 105892928 572 True 279.000000 279 76.2390 501 1064 1 chr4D.!!$R1 563

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
267 269 1.00990 GGCGAGGTAGATGTCGTCG 60.010 63.158 0.0 0.0 43.09 5.12 F
1211 2165 1.06319 ACCACATAGATCCAGTCCCGA 60.063 52.381 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 3123 1.078214 CAGGGCGCTCATCCTTGAA 60.078 57.895 11.40 0.00 33.01 2.69 R
2828 4097 3.233578 GCGAATGAATTCTGAAAACGCA 58.766 40.909 18.99 5.05 42.39 5.24 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
56 57 5.241728 AGGAAATAAGCTTGTGGTGACTTTC 59.758 40.000 9.86 1.17 0.00 2.62
58 59 6.430000 GGAAATAAGCTTGTGGTGACTTTCTA 59.570 38.462 9.86 0.00 0.00 2.10
113 114 1.112916 GGCAGAGAGCTAGAGACCCC 61.113 65.000 0.00 0.00 44.79 4.95
240 242 3.896479 GCCTTGACAGTGGCTAGC 58.104 61.111 6.04 6.04 45.26 3.42
247 249 1.229336 ACAGTGGCTAGCTGGGAGT 60.229 57.895 15.72 4.70 38.22 3.85
267 269 1.009900 GGCGAGGTAGATGTCGTCG 60.010 63.158 0.00 0.00 43.09 5.12
580 588 3.075134 AGTCTTGGGATTTGGAGAAAGCT 59.925 43.478 0.00 0.00 0.00 3.74
642 650 4.766375 ACCTCCAAATACAGTATGGAACG 58.234 43.478 4.73 1.53 42.41 3.95
706 714 2.727392 CGGGTAGTCGGAATGGGCA 61.727 63.158 0.00 0.00 0.00 5.36
735 743 2.000447 GGAACGTGCAATCCTGAGTAC 59.000 52.381 0.00 0.00 32.75 2.73
1059 2012 1.671054 CAGGTTCGTTCCCGTGCAT 60.671 57.895 0.00 0.00 35.01 3.96
1211 2165 1.063190 ACCACATAGATCCAGTCCCGA 60.063 52.381 0.00 0.00 0.00 5.14
1857 3123 3.626924 GACCGTGTGCCCTGTCCT 61.627 66.667 0.00 0.00 0.00 3.85
2386 3655 7.028926 ACACATAGACGTCTATACCAAAGAG 57.971 40.000 32.06 21.02 37.07 2.85
2830 4099 1.663135 GAAGAGAGCTTCGAATGGTGC 59.337 52.381 0.00 0.00 40.96 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.591643 TCTTTCGATTCAAAAGAACTCCG 57.408 39.130 0.00 0.00 39.22 4.63
18 19 7.050377 AGCTTATTTCCTGATCTTTCGATTCA 58.950 34.615 0.00 0.00 0.00 2.57
56 57 2.159572 CGGTCCAATGCGAAAACCTTAG 60.160 50.000 0.00 0.00 0.00 2.18
58 59 0.596082 CGGTCCAATGCGAAAACCTT 59.404 50.000 0.00 0.00 0.00 3.50
113 114 1.081892 CAACATCCTTCAGAGCACCG 58.918 55.000 0.00 0.00 0.00 4.94
237 239 2.359169 CCTCGCCAACTCCCAGCTA 61.359 63.158 0.00 0.00 0.00 3.32
240 242 0.970937 TCTACCTCGCCAACTCCCAG 60.971 60.000 0.00 0.00 0.00 4.45
247 249 0.454600 GACGACATCTACCTCGCCAA 59.545 55.000 0.00 0.00 32.98 4.52
267 269 2.737376 GTCACGGCCCTTGTCGAC 60.737 66.667 9.11 9.11 43.95 4.20
580 588 2.959484 GCACAGGACAGGCCAGCTA 61.959 63.158 5.01 0.00 40.02 3.32
626 634 3.687698 GTGCACCGTTCCATACTGTATTT 59.312 43.478 5.22 0.00 0.00 1.40
642 650 2.359478 CCCCACTTACGGTGCACC 60.359 66.667 26.78 26.78 44.08 5.01
706 714 1.978455 TTGCACGTTCCTGGTCCACT 61.978 55.000 0.00 0.00 0.00 4.00
1059 2012 4.404715 CCTAGGAGAAAAACGGACCAGATA 59.595 45.833 1.05 0.00 0.00 1.98
1211 2165 5.014544 CCCCATTATCCAGAAGGTACATCAT 59.985 44.000 0.00 0.00 35.89 2.45
1568 2653 5.124776 CACACCCGTACCATCAATTTTACAT 59.875 40.000 0.00 0.00 0.00 2.29
1570 2655 4.696402 TCACACCCGTACCATCAATTTTAC 59.304 41.667 0.00 0.00 0.00 2.01
1857 3123 1.078214 CAGGGCGCTCATCCTTGAA 60.078 57.895 11.40 0.00 33.01 2.69
2386 3655 5.099042 TCTCCCTCAACTGCCTTATTAAC 57.901 43.478 0.00 0.00 0.00 2.01
2828 4097 3.233578 GCGAATGAATTCTGAAAACGCA 58.766 40.909 18.99 5.05 42.39 5.24
2830 4099 5.088068 TCATGCGAATGAATTCTGAAAACG 58.912 37.500 2.71 5.55 34.69 3.60


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

AutoCloner maintained by Alex Coulton.