Multiple sequence alignment - TraesCS4A01G212600

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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 TraesCS4A01G212600 chr4A 100.000 2501 0 0 1 2501 508495603 508493103 0.000000e+00 4619.0
1 TraesCS4A01G212600 chr4A 95.367 2504 81 6 1 2501 508359245 508356774 0.000000e+00 3949.0
2 TraesCS4A01G212600 chr4A 95.069 1156 53 2 516 1668 508274990 508273836 0.000000e+00 1816.0
3 TraesCS4A01G212600 chr4A 98.102 843 16 0 1659 2501 508245121 508244279 0.000000e+00 1469.0
4 TraesCS4A01G212600 chr4A 97.679 517 12 0 1 517 508369261 508368745 0.000000e+00 889.0
5 TraesCS4A01G212600 chr4A 95.810 525 19 3 1 524 680013329 680012807 0.000000e+00 845.0
6 TraesCS4A01G212600 chr4A 83.333 96 14 2 1419 1513 596166829 596166735 1.230000e-13 87.9
7 TraesCS4A01G212600 chr4B 89.780 773 69 5 876 1641 109222275 109223044 0.000000e+00 981.0
8 TraesCS4A01G212600 chr4B 92.384 302 16 5 2203 2501 108764739 108764442 8.270000e-115 424.0
9 TraesCS4A01G212600 chr4B 89.720 107 11 0 725 831 109222157 109222263 1.210000e-28 137.0
10 TraesCS4A01G212600 chr5A 96.712 517 17 0 1 517 228379773 228380289 0.000000e+00 861.0
11 TraesCS4A01G212600 chr5A 96.304 514 19 0 1 514 228389576 228390089 0.000000e+00 845.0
12 TraesCS4A01G212600 chr5A 83.716 479 66 11 1066 1537 617204543 617205016 2.280000e-120 442.0
13 TraesCS4A01G212600 chr5A 80.168 358 51 16 1007 1354 617187450 617187797 1.490000e-62 250.0
14 TraesCS4A01G212600 chr5A 75.252 497 87 18 1001 1472 617206721 617207206 1.170000e-48 204.0
15 TraesCS4A01G212600 chr3A 96.190 525 16 4 1 524 600221985 600221464 0.000000e+00 856.0
16 TraesCS4A01G212600 chr2A 96.008 526 17 4 1 524 382300668 382300145 0.000000e+00 852.0
17 TraesCS4A01G212600 chr7A 96.161 521 17 3 5 524 332484933 332484415 0.000000e+00 848.0
18 TraesCS4A01G212600 chr6A 96.139 518 18 2 1 517 447923651 447924167 0.000000e+00 845.0
19 TraesCS4A01G212600 chr1A 96.139 518 19 1 1 517 211042347 211042864 0.000000e+00 845.0
20 TraesCS4A01G212600 chr2D 95.168 476 22 1 1732 2206 631167900 631167425 0.000000e+00 750.0
21 TraesCS4A01G212600 chr2D 83.108 296 49 1 2203 2497 474995884 474995589 4.100000e-68 268.0
22 TraesCS4A01G212600 chr6D 92.827 474 34 0 1732 2205 81160500 81160973 0.000000e+00 688.0
23 TraesCS4A01G212600 chr3D 91.314 449 38 1 1758 2205 549527130 549527578 1.640000e-171 612.0
24 TraesCS4A01G212600 chr7D 90.302 464 44 1 1743 2205 588177570 588177107 7.650000e-170 606.0
25 TraesCS4A01G212600 chr5D 83.597 506 70 12 1039 1537 494189106 494189605 1.750000e-126 462.0
26 TraesCS4A01G212600 chr5D 91.469 211 15 2 516 724 81157931 81157722 1.130000e-73 287.0
27 TraesCS4A01G212600 chr5D 90.826 218 15 3 517 730 424283566 424283350 1.130000e-73 287.0
28 TraesCS4A01G212600 chr5D 77.644 331 63 8 1146 1474 494215755 494216076 9.130000e-45 191.0
29 TraesCS4A01G212600 chr5B 82.937 504 74 12 1039 1537 610301050 610301546 6.350000e-121 444.0
30 TraesCS4A01G212600 chr5B 77.644 331 63 8 1146 1474 610499610 610499931 9.130000e-45 191.0
31 TraesCS4A01G212600 chr5B 76.946 334 60 13 1146 1474 610305554 610305875 9.200000e-40 174.0
32 TraesCS4A01G212600 chr1D 91.818 220 13 3 512 727 261072853 261072635 4.040000e-78 302.0
33 TraesCS4A01G212600 chr1D 91.743 218 14 2 513 726 436852128 436852345 1.450000e-77 300.0
34 TraesCS4A01G212600 chr1D 92.019 213 15 1 513 723 454849796 454850008 5.230000e-77 298.0
35 TraesCS4A01G212600 chr1D 91.163 215 16 2 513 724 1074734 1074520 3.150000e-74 289.0
36 TraesCS4A01G212600 chr1D 90.411 219 15 4 516 730 31064395 31064179 1.460000e-72 283.0
37 TraesCS4A01G212600 chr4D 82.292 96 15 2 1419 1513 7420259 7420353 5.730000e-12 82.4


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 TraesCS4A01G212600 chr4A 508493103 508495603 2500 True 4619 4619 100.000 1 2501 1 chr4A.!!$R5 2500
1 TraesCS4A01G212600 chr4A 508356774 508359245 2471 True 3949 3949 95.367 1 2501 1 chr4A.!!$R3 2500
2 TraesCS4A01G212600 chr4A 508273836 508274990 1154 True 1816 1816 95.069 516 1668 1 chr4A.!!$R2 1152
3 TraesCS4A01G212600 chr4A 508244279 508245121 842 True 1469 1469 98.102 1659 2501 1 chr4A.!!$R1 842
4 TraesCS4A01G212600 chr4A 508368745 508369261 516 True 889 889 97.679 1 517 1 chr4A.!!$R4 516
5 TraesCS4A01G212600 chr4A 680012807 680013329 522 True 845 845 95.810 1 524 1 chr4A.!!$R7 523
6 TraesCS4A01G212600 chr4B 109222157 109223044 887 False 559 981 89.750 725 1641 2 chr4B.!!$F1 916
7 TraesCS4A01G212600 chr5A 228379773 228380289 516 False 861 861 96.712 1 517 1 chr5A.!!$F1 516
8 TraesCS4A01G212600 chr5A 228389576 228390089 513 False 845 845 96.304 1 514 1 chr5A.!!$F2 513
9 TraesCS4A01G212600 chr5A 617204543 617207206 2663 False 323 442 79.484 1001 1537 2 chr5A.!!$F4 536
10 TraesCS4A01G212600 chr3A 600221464 600221985 521 True 856 856 96.190 1 524 1 chr3A.!!$R1 523
11 TraesCS4A01G212600 chr2A 382300145 382300668 523 True 852 852 96.008 1 524 1 chr2A.!!$R1 523
12 TraesCS4A01G212600 chr7A 332484415 332484933 518 True 848 848 96.161 5 524 1 chr7A.!!$R1 519
13 TraesCS4A01G212600 chr6A 447923651 447924167 516 False 845 845 96.139 1 517 1 chr6A.!!$F1 516
14 TraesCS4A01G212600 chr1A 211042347 211042864 517 False 845 845 96.139 1 517 1 chr1A.!!$F1 516

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
894 903 1.067565 CGCAGTGCTCTTGGAGTCTTA 60.068 52.381 14.33 0.0 31.39 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2299 3.185246 ACCCGATAACTGATGAAGCAG 57.815 47.619 0.0 0.0 41.63 4.24 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
137 141 7.147655 ACAGATTACTATTACACCAGATGCAGT 60.148 37.037 0.00 0.00 0.00 4.40
241 245 2.169144 CCTGATGATCAGTAGTGGTGCA 59.831 50.000 20.06 0.00 42.80 4.57
327 332 2.480759 GCCATGAGTGTTTGGATGATGC 60.481 50.000 0.00 0.00 34.81 3.91
526 532 3.966218 GTGTTACAAGTTGCGTGAATGAC 59.034 43.478 1.81 0.00 0.00 3.06
552 558 2.521126 TCGACAGGTCTTACATGGTCA 58.479 47.619 0.00 0.00 33.62 4.02
688 697 3.745163 GCGGGGATAAAAATACCCTTCGA 60.745 47.826 4.17 0.00 42.90 3.71
734 743 1.357079 AGCAGGGCTCTTTTTCCTCAT 59.643 47.619 0.00 0.00 30.62 2.90
840 849 5.219633 GGTACACATCACAAATTCACAACC 58.780 41.667 0.00 0.00 0.00 3.77
894 903 1.067565 CGCAGTGCTCTTGGAGTCTTA 60.068 52.381 14.33 0.00 31.39 2.10
915 924 2.577059 GATCCGGCGACCAGTTCA 59.423 61.111 9.30 0.00 0.00 3.18
950 966 5.428496 TCGTTGGACCACTAACTATATCG 57.572 43.478 0.00 0.00 35.76 2.92
1053 1069 1.079819 CGTGCGAGATGTGACCCTT 60.080 57.895 0.00 0.00 0.00 3.95
1059 1075 1.613630 AGATGTGACCCTTCGGCCT 60.614 57.895 0.00 0.00 0.00 5.19
1142 1158 0.326238 ATGACGTGGGACCCCTACAT 60.326 55.000 8.45 5.96 36.94 2.29
1249 1268 3.680786 CCGTCAGCTCGGTGTCCA 61.681 66.667 5.70 0.00 44.77 4.02
1415 1434 1.663388 CTAGTGGACGTGCGCAACA 60.663 57.895 22.85 6.44 0.00 3.33
1700 2022 8.809468 TTCTCTATTCTTCTCTACACTTAGCA 57.191 34.615 0.00 0.00 0.00 3.49
1715 2037 6.231211 ACACTTAGCATGCAAAAGTACTACT 58.769 36.000 27.82 10.38 32.35 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 141 1.146930 GGAGCGGAATCATCAGGCA 59.853 57.895 0.00 0.0 0.00 4.75
241 245 2.602676 CCCGATCACCCCCAACTGT 61.603 63.158 0.00 0.0 0.00 3.55
327 332 8.525876 CGTCAATCAAGTGCATAAATAACATTG 58.474 33.333 0.00 0.0 0.00 2.82
526 532 3.868757 TGTAAGACCTGTCGAATCCAG 57.131 47.619 0.00 0.0 34.09 3.86
552 558 2.286365 AAAACATCACACGACCCCAT 57.714 45.000 0.00 0.0 0.00 4.00
575 581 1.259609 CGTACAGTACCCTGGTCCAA 58.740 55.000 5.07 0.0 43.36 3.53
576 582 0.112995 ACGTACAGTACCCTGGTCCA 59.887 55.000 5.07 0.0 43.36 4.02
688 697 3.263681 GTGCTCCTCCCTAACCTAGTTTT 59.736 47.826 0.00 0.0 0.00 2.43
734 743 2.828095 AGCACGCAACAACCAGCA 60.828 55.556 0.00 0.0 0.00 4.41
778 787 2.273370 TTGTCGCGGTCAGTAGATTC 57.727 50.000 6.13 0.0 0.00 2.52
877 886 4.873010 TCCTATAAGACTCCAAGAGCACT 58.127 43.478 0.00 0.0 32.04 4.40
894 903 0.759436 AACTGGTCGCCGGATCCTAT 60.759 55.000 5.05 0.0 33.36 2.57
915 924 4.020573 TGGTCCAACGAATCAATAGTCTGT 60.021 41.667 0.00 0.0 0.00 3.41
950 966 1.269831 ACACGGTCACTTGAGAAGCTC 60.270 52.381 0.00 0.0 0.00 4.09
1237 1256 2.573869 CGACATGGACACCGAGCT 59.426 61.111 0.00 0.0 0.00 4.09
1356 1375 0.320771 CCTCCACCTCCTTGAACACG 60.321 60.000 0.00 0.0 0.00 4.49
1363 1382 2.612115 CAGCCCCTCCACCTCCTT 60.612 66.667 0.00 0.0 0.00 3.36
1395 1414 4.735132 TGCGCACGTCCACTAGCC 62.735 66.667 5.66 0.0 0.00 3.93
1399 1418 2.280797 ATGTTGCGCACGTCCACT 60.281 55.556 11.12 0.0 0.00 4.00
1715 2037 6.975772 GCAAGAAAAACACACCAAATAGTACA 59.024 34.615 0.00 0.0 0.00 2.90
1787 2109 9.388506 CTTGTGAGAGGTTATTGATCTTTGTAT 57.611 33.333 0.00 0.0 0.00 2.29
1919 2241 3.679389 TCAAGCATTTGAGGAGTCTTCC 58.321 45.455 0.00 0.0 38.37 3.46
1977 2299 3.185246 ACCCGATAACTGATGAAGCAG 57.815 47.619 0.00 0.0 41.63 4.24


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

AutoCloner maintained by Alex Coulton.