Multiple sequence alignment - TraesCS1A01G124900

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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 TraesCS1A01G124900 chr1A 100.000 3474 0 0 1 3474 147729849 147726376 0.000000e+00 6416
1 TraesCS1A01G124900 chr1A 90.390 718 59 7 1 715 206963255 206963965 0.000000e+00 935
2 TraesCS1A01G124900 chr5A 95.890 2847 112 5 629 3474 213234331 213231489 0.000000e+00 4604
3 TraesCS1A01G124900 chr5A 96.801 2626 81 3 851 3474 210234605 210231981 0.000000e+00 4381
4 TraesCS1A01G124900 chr5A 95.339 2510 110 7 968 3474 147590480 147592985 0.000000e+00 3980
5 TraesCS1A01G124900 chr5A 95.772 615 25 1 1 615 380244343 380244956 0.000000e+00 990
6 TraesCS1A01G124900 chr5A 85.202 446 43 13 1180 1608 35913222 35913661 1.480000e-118 436
7 TraesCS1A01G124900 chr5A 96.429 224 6 2 627 850 210235060 210234839 5.480000e-98 368
8 TraesCS1A01G124900 chr6A 94.245 2502 119 9 991 3474 206133791 206136285 0.000000e+00 3799
9 TraesCS1A01G124900 chr4D 92.477 2313 135 14 664 2945 215033233 215035537 0.000000e+00 3271
10 TraesCS1A01G124900 chr4D 94.371 977 50 4 2503 3474 313783419 313782443 0.000000e+00 1495
11 TraesCS1A01G124900 chr4D 89.254 912 68 15 705 1608 313784790 313783901 0.000000e+00 1114
12 TraesCS1A01G124900 chr4D 87.021 940 79 24 1603 2505 15874836 15873903 0.000000e+00 1020
13 TraesCS1A01G124900 chr4D 92.989 542 28 4 2935 3474 215046728 215047261 0.000000e+00 782
14 TraesCS1A01G124900 chr4D 81.752 137 19 6 607 741 508395394 508395526 3.670000e-20 110
15 TraesCS1A01G124900 chr2A 91.992 974 71 6 2503 3473 404058329 404059298 0.000000e+00 1360
16 TraesCS1A01G124900 chr2A 91.786 974 73 6 2503 3473 402113211 402114180 0.000000e+00 1349
17 TraesCS1A01G124900 chr2A 95.617 616 26 1 1 616 412385875 412386489 0.000000e+00 987
18 TraesCS1A01G124900 chr2A 89.937 318 24 3 803 1113 416909218 416908902 1.500000e-108 403
19 TraesCS1A01G124900 chr2A 87.385 325 35 5 793 1113 513538376 513538054 5.480000e-98 368
20 TraesCS1A01G124900 chr2A 82.529 435 41 13 1206 1608 404057436 404057867 1.980000e-92 350
21 TraesCS1A01G124900 chr2A 82.069 435 43 13 1206 1608 402112318 402112749 4.290000e-89 339
22 TraesCS1A01G124900 chr7A 91.718 978 69 10 2503 3474 195277216 195276245 0.000000e+00 1347
23 TraesCS1A01G124900 chr7A 96.423 615 20 2 1 615 81712607 81711995 0.000000e+00 1013
24 TraesCS1A01G124900 chr7A 95.935 615 24 1 1 615 261121628 261122241 0.000000e+00 996
25 TraesCS1A01G124900 chr7A 91.172 725 57 7 1 721 582968445 582969166 0.000000e+00 977
26 TraesCS1A01G124900 chr7A 89.198 324 30 4 794 1113 373883207 373882885 1.940000e-107 399
27 TraesCS1A01G124900 chr4A 96.260 615 22 1 1 615 83862882 83863495 0.000000e+00 1007
28 TraesCS1A01G124900 chr4A 95.772 615 25 1 1 615 269194803 269194190 0.000000e+00 990
29 TraesCS1A01G124900 chr4A 90.041 723 65 6 1 720 347849052 347848334 0.000000e+00 929
30 TraesCS1A01G124900 chr4A 82.818 937 97 35 1603 2505 584697735 584696829 0.000000e+00 780
31 TraesCS1A01G124900 chr4B 85.684 943 84 24 1603 2505 27398917 27397986 0.000000e+00 946
32 TraesCS1A01G124900 chr3A 87.906 678 63 10 946 1608 281209451 281208778 0.000000e+00 780
33 TraesCS1A01G124900 chr3D 87.425 668 54 13 791 1456 604117167 604116528 0.000000e+00 741
34 TraesCS1A01G124900 chr7B 88.889 324 32 3 793 1113 209869032 209869354 2.510000e-106 396
35 TraesCS1A01G124900 chr3B 77.542 708 110 28 1775 2468 822552226 822552898 7.040000e-102 381
36 TraesCS1A01G124900 chr3B 77.266 717 115 26 1804 2505 824261329 824260646 9.100000e-101 377
37 TraesCS1A01G124900 chr7D 85.000 120 12 6 606 722 527213142 527213258 2.190000e-22 117
38 TraesCS1A01G124900 chr5B 85.345 116 12 4 609 722 454603233 454603345 7.880000e-22 115


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 TraesCS1A01G124900 chr1A 147726376 147729849 3473 True 6416.0 6416 100.0000 1 3474 1 chr1A.!!$R1 3473
1 TraesCS1A01G124900 chr1A 206963255 206963965 710 False 935.0 935 90.3900 1 715 1 chr1A.!!$F1 714
2 TraesCS1A01G124900 chr5A 213231489 213234331 2842 True 4604.0 4604 95.8900 629 3474 1 chr5A.!!$R1 2845
3 TraesCS1A01G124900 chr5A 147590480 147592985 2505 False 3980.0 3980 95.3390 968 3474 1 chr5A.!!$F2 2506
4 TraesCS1A01G124900 chr5A 210231981 210235060 3079 True 2374.5 4381 96.6150 627 3474 2 chr5A.!!$R2 2847
5 TraesCS1A01G124900 chr5A 380244343 380244956 613 False 990.0 990 95.7720 1 615 1 chr5A.!!$F3 614
6 TraesCS1A01G124900 chr6A 206133791 206136285 2494 False 3799.0 3799 94.2450 991 3474 1 chr6A.!!$F1 2483
7 TraesCS1A01G124900 chr4D 215033233 215035537 2304 False 3271.0 3271 92.4770 664 2945 1 chr4D.!!$F1 2281
8 TraesCS1A01G124900 chr4D 313782443 313784790 2347 True 1304.5 1495 91.8125 705 3474 2 chr4D.!!$R2 2769
9 TraesCS1A01G124900 chr4D 15873903 15874836 933 True 1020.0 1020 87.0210 1603 2505 1 chr4D.!!$R1 902
10 TraesCS1A01G124900 chr4D 215046728 215047261 533 False 782.0 782 92.9890 2935 3474 1 chr4D.!!$F2 539
11 TraesCS1A01G124900 chr2A 412385875 412386489 614 False 987.0 987 95.6170 1 616 1 chr2A.!!$F1 615
12 TraesCS1A01G124900 chr2A 404057436 404059298 1862 False 855.0 1360 87.2605 1206 3473 2 chr2A.!!$F3 2267
13 TraesCS1A01G124900 chr2A 402112318 402114180 1862 False 844.0 1349 86.9275 1206 3473 2 chr2A.!!$F2 2267
14 TraesCS1A01G124900 chr7A 195276245 195277216 971 True 1347.0 1347 91.7180 2503 3474 1 chr7A.!!$R2 971
15 TraesCS1A01G124900 chr7A 81711995 81712607 612 True 1013.0 1013 96.4230 1 615 1 chr7A.!!$R1 614
16 TraesCS1A01G124900 chr7A 261121628 261122241 613 False 996.0 996 95.9350 1 615 1 chr7A.!!$F1 614
17 TraesCS1A01G124900 chr7A 582968445 582969166 721 False 977.0 977 91.1720 1 721 1 chr7A.!!$F2 720
18 TraesCS1A01G124900 chr4A 83862882 83863495 613 False 1007.0 1007 96.2600 1 615 1 chr4A.!!$F1 614
19 TraesCS1A01G124900 chr4A 269194190 269194803 613 True 990.0 990 95.7720 1 615 1 chr4A.!!$R1 614
20 TraesCS1A01G124900 chr4A 347848334 347849052 718 True 929.0 929 90.0410 1 720 1 chr4A.!!$R2 719
21 TraesCS1A01G124900 chr4A 584696829 584697735 906 True 780.0 780 82.8180 1603 2505 1 chr4A.!!$R3 902
22 TraesCS1A01G124900 chr4B 27397986 27398917 931 True 946.0 946 85.6840 1603 2505 1 chr4B.!!$R1 902
23 TraesCS1A01G124900 chr3A 281208778 281209451 673 True 780.0 780 87.9060 946 1608 1 chr3A.!!$R1 662
24 TraesCS1A01G124900 chr3D 604116528 604117167 639 True 741.0 741 87.4250 791 1456 1 chr3D.!!$R1 665
25 TraesCS1A01G124900 chr3B 822552226 822552898 672 False 381.0 381 77.5420 1775 2468 1 chr3B.!!$F1 693
26 TraesCS1A01G124900 chr3B 824260646 824261329 683 True 377.0 377 77.2660 1804 2505 1 chr3B.!!$R1 701

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
321 322 1.160137 CTGTGCCAGCCTTCTAACAC 58.840 55.0 0.00 0.0 0.00 3.32 F
1114 1367 0.538057 CAGTCCCTTTCTTGCTGCCA 60.538 55.0 0.00 0.0 0.00 4.92 F
1265 1518 0.107993 GCTACAGCTGCTCCACATCA 60.108 55.0 15.27 0.0 38.21 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1498 0.107993 GATGTGGAGCAGCTGTAGCA 60.108 55.000 16.64 8.17 45.16 3.49 R
2241 2896 2.908015 GCGGATAGCCCTTGTCCA 59.092 61.111 0.00 0.00 40.81 4.02 R
2785 3454 5.278758 CGCCCTGAACTTCCATTTTCTTTAA 60.279 40.000 0.00 0.00 0.00 1.52 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
227 228 3.499737 CTTCGCGGCGCTTCCATT 61.500 61.111 30.54 0.00 34.01 3.16
321 322 1.160137 CTGTGCCAGCCTTCTAACAC 58.840 55.000 0.00 0.00 0.00 3.32
494 496 4.383861 CGCTGCTGACCTCTGCCA 62.384 66.667 0.00 0.00 39.65 4.92
814 829 2.664652 AAACCACCCCACCCTACCCT 62.665 60.000 0.00 0.00 0.00 4.34
1114 1367 0.538057 CAGTCCCTTTCTTGCTGCCA 60.538 55.000 0.00 0.00 0.00 4.92
1130 1383 1.648467 GCCAGCGGAAATCCTGTCAC 61.648 60.000 0.00 0.00 0.00 3.67
1148 1401 2.107366 CACTCCCTTCCTCTTCTCCTC 58.893 57.143 0.00 0.00 0.00 3.71
1154 1407 3.449918 CCTTCCTCTTCTCCTCCTCTTT 58.550 50.000 0.00 0.00 0.00 2.52
1245 1498 1.374758 CGCGCCCTGTCTTCTTCTT 60.375 57.895 0.00 0.00 0.00 2.52
1265 1518 0.107993 GCTACAGCTGCTCCACATCA 60.108 55.000 15.27 0.00 38.21 3.07
1569 1855 5.068329 CAGAGCATGAGTAGAACATGGACTA 59.932 44.000 0.00 0.00 43.39 2.59
1579 1865 1.153842 CATGGACTACTCGCACGCA 60.154 57.895 0.00 0.00 0.00 5.24
1663 2272 5.463392 CACAGATATAATGGACTGGTTCGTG 59.537 44.000 0.00 0.00 35.08 4.35
1772 2392 1.916273 ACCCATCCCCGCGCATATA 60.916 57.895 8.75 0.00 0.00 0.86
2067 2718 9.495572 TCTCACAGGTTTTGTTTTGTTTATTTT 57.504 25.926 0.00 0.00 38.16 1.82
2645 3314 1.915489 TGTGGTGGTGAATAGCTCCAT 59.085 47.619 0.00 0.00 46.06 3.41
2647 3316 2.092968 GTGGTGGTGAATAGCTCCATCA 60.093 50.000 0.27 0.27 46.19 3.07
2785 3454 6.689669 GCGTCTGTGTAATGTTTGTAAACTTT 59.310 34.615 8.74 10.36 39.59 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.687354 GCCTGGAGTCTGGAAGTTCA 59.313 55.000 5.01 0.00 34.32 3.18
129 130 3.744155 CCTCTTGGAAGGGGGCCC 61.744 72.222 15.76 15.76 43.29 5.80
227 228 1.520600 TAGTGCGGTGCTCTTCGTCA 61.521 55.000 0.00 0.00 34.22 4.35
494 496 2.920645 CGACCTCCGCAGTCAGTGT 61.921 63.158 0.00 0.00 33.70 3.55
617 619 6.425114 CAGAATAGTGCTACTCTCTCTCTCTC 59.575 46.154 0.00 0.00 0.00 3.20
619 621 6.288294 TCAGAATAGTGCTACTCTCTCTCTC 58.712 44.000 0.00 0.00 0.00 3.20
621 623 6.149474 GGATCAGAATAGTGCTACTCTCTCTC 59.851 46.154 0.00 0.00 0.00 3.20
623 625 5.183140 GGGATCAGAATAGTGCTACTCTCTC 59.817 48.000 0.00 0.00 0.00 3.20
809 824 2.122989 GGATCGGGGCAGAGGGTA 60.123 66.667 0.00 0.00 0.00 3.69
870 1118 4.691820 GCGGCGAGATCGAGCGAT 62.692 66.667 12.98 4.89 43.02 4.58
1114 1367 0.250513 GGAGTGACAGGATTTCCGCT 59.749 55.000 0.00 0.00 42.08 5.52
1130 1383 1.290732 AGGAGGAGAAGAGGAAGGGAG 59.709 57.143 0.00 0.00 0.00 4.30
1148 1401 3.688673 GCAAAGATCACTGGAGAAAGAGG 59.311 47.826 0.00 0.00 0.00 3.69
1245 1498 0.107993 GATGTGGAGCAGCTGTAGCA 60.108 55.000 16.64 8.17 45.16 3.49
1265 1518 3.052082 ACGACGATGGACGGACGT 61.052 61.111 0.00 0.00 46.39 4.34
1322 1588 1.869690 GCCTTTGCGAGAAGGTCAC 59.130 57.895 15.82 0.20 46.43 3.67
1579 1865 4.101448 GGAGCAGTCCATGGCGGT 62.101 66.667 6.96 3.21 43.31 5.68
2241 2896 2.908015 GCGGATAGCCCTTGTCCA 59.092 61.111 0.00 0.00 40.81 4.02
2785 3454 5.278758 CGCCCTGAACTTCCATTTTCTTTAA 60.279 40.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.