Multiple sequence alignment - TraesCS3A01G194500

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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 TraesCS3A01G194500 chr3A 100.000 2636 0 0 1 2636 271615977 271618612 0.000000e+00 4868.0
1 TraesCS3A01G194500 chr3A 95.118 1946 64 8 721 2636 271624586 271626530 0.000000e+00 3038.0
2 TraesCS3A01G194500 chr3A 92.844 1076 67 7 1566 2636 607071650 607072720 0.000000e+00 1552.0
3 TraesCS3A01G194500 chr3A 89.677 155 13 2 696 847 368696773 368696619 7.440000e-46 195.0
4 TraesCS3A01G194500 chr2A 94.572 1953 99 6 691 2636 604503381 604501429 0.000000e+00 3013.0
5 TraesCS3A01G194500 chr2A 94.157 1951 91 6 690 2636 604495494 604493563 0.000000e+00 2950.0
6 TraesCS3A01G194500 chr2A 87.385 1308 124 28 1358 2636 225185810 225187105 0.000000e+00 1463.0
7 TraesCS3A01G194500 chr2A 86.757 1329 115 35 1360 2636 184230022 184228703 0.000000e+00 1423.0
8 TraesCS3A01G194500 chr2A 87.745 1175 122 19 1477 2636 327302904 327304071 0.000000e+00 1352.0
9 TraesCS3A01G194500 chr2A 95.665 692 29 1 2 692 194880827 194880136 0.000000e+00 1110.0
10 TraesCS3A01G194500 chr2A 95.507 690 30 1 2 690 649975004 649975693 0.000000e+00 1101.0
11 TraesCS3A01G194500 chr2A 89.683 378 39 0 984 1361 454947567 454947944 1.420000e-132 483.0
12 TraesCS3A01G194500 chr2A 79.688 192 17 11 1238 1427 220344162 220343991 4.610000e-23 119.0
13 TraesCS3A01G194500 chr7A 92.844 1076 67 7 1566 2636 514731221 514730151 0.000000e+00 1552.0
14 TraesCS3A01G194500 chr7A 90.892 1076 85 11 1570 2636 396966085 396965014 0.000000e+00 1432.0
15 TraesCS3A01G194500 chr7A 90.680 1073 89 9 1572 2636 396973963 396972894 0.000000e+00 1417.0
16 TraesCS3A01G194500 chr7A 89.723 253 26 0 1118 1370 511395878 511395626 9.100000e-85 324.0
17 TraesCS3A01G194500 chr7A 91.613 155 9 2 696 847 307981325 307981172 7.390000e-51 211.0
18 TraesCS3A01G194500 chr7A 91.275 149 9 3 696 841 182522396 182522543 1.600000e-47 200.0
19 TraesCS3A01G194500 chr7A 85.714 112 11 4 849 957 374453718 374453827 2.140000e-21 113.0
20 TraesCS3A01G194500 chr6A 92.379 1076 72 7 1566 2636 112351379 112350309 0.000000e+00 1524.0
21 TraesCS3A01G194500 chr6A 94.356 691 37 2 2 691 326372632 326371943 0.000000e+00 1059.0
22 TraesCS3A01G194500 chr6A 92.328 378 29 0 984 1361 157320816 157320439 2.990000e-149 538.0
23 TraesCS3A01G194500 chr6A 88.441 372 35 5 849 1215 206269755 206269387 2.410000e-120 442.0
24 TraesCS3A01G194500 chr6A 85.950 363 45 5 857 1215 248634279 248633919 1.480000e-102 383.0
25 TraesCS3A01G194500 chr6A 91.613 155 9 3 690 841 378279719 378279872 7.390000e-51 211.0
26 TraesCS3A01G194500 chr1A 92.255 1020 70 8 1623 2636 132156325 132155309 0.000000e+00 1437.0
27 TraesCS3A01G194500 chr1A 94.645 691 35 2 4 692 548637970 548638660 0.000000e+00 1070.0
28 TraesCS3A01G194500 chr1A 85.744 484 54 2 893 1361 164740180 164740663 5.070000e-137 497.0
29 TraesCS3A01G194500 chr1A 86.528 193 17 7 696 884 203770552 203770365 1.240000e-48 204.0
30 TraesCS3A01G194500 chr1A 85.492 193 19 7 696 884 203716473 203716286 2.680000e-45 193.0
31 TraesCS3A01G194500 chr5A 95.080 691 31 2 2 691 146513345 146514033 0.000000e+00 1085.0
32 TraesCS3A01G194500 chr5A 90.514 253 24 0 1118 1370 479311384 479311132 4.200000e-88 335.0
33 TraesCS3A01G194500 chr7D 94.798 692 35 1 2 692 51438589 51437898 0.000000e+00 1077.0
34 TraesCS3A01G194500 chr1D 94.220 692 38 2 2 692 70228203 70228893 0.000000e+00 1055.0
35 TraesCS3A01G194500 chr2B 94.075 692 40 1 2 692 171038652 171037961 0.000000e+00 1050.0
36 TraesCS3A01G194500 chr2B 94.075 692 40 1 2 692 537318456 537317765 0.000000e+00 1050.0
37 TraesCS3A01G194500 chr2B 85.714 77 10 1 886 961 101915610 101915534 2.170000e-11 80.5
38 TraesCS3A01G194500 chr4A 87.438 605 55 11 787 1370 389312798 389312194 0.000000e+00 676.0
39 TraesCS3A01G194500 chr4A 89.677 155 12 3 690 841 259615651 259615804 7.440000e-46 195.0


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 TraesCS3A01G194500 chr3A 271615977 271618612 2635 False 4868 4868 100.000 1 2636 1 chr3A.!!$F1 2635
1 TraesCS3A01G194500 chr3A 271624586 271626530 1944 False 3038 3038 95.118 721 2636 1 chr3A.!!$F2 1915
2 TraesCS3A01G194500 chr3A 607071650 607072720 1070 False 1552 1552 92.844 1566 2636 1 chr3A.!!$F3 1070
3 TraesCS3A01G194500 chr2A 604501429 604503381 1952 True 3013 3013 94.572 691 2636 1 chr2A.!!$R5 1945
4 TraesCS3A01G194500 chr2A 604493563 604495494 1931 True 2950 2950 94.157 690 2636 1 chr2A.!!$R4 1946
5 TraesCS3A01G194500 chr2A 225185810 225187105 1295 False 1463 1463 87.385 1358 2636 1 chr2A.!!$F1 1278
6 TraesCS3A01G194500 chr2A 184228703 184230022 1319 True 1423 1423 86.757 1360 2636 1 chr2A.!!$R1 1276
7 TraesCS3A01G194500 chr2A 327302904 327304071 1167 False 1352 1352 87.745 1477 2636 1 chr2A.!!$F2 1159
8 TraesCS3A01G194500 chr2A 194880136 194880827 691 True 1110 1110 95.665 2 692 1 chr2A.!!$R2 690
9 TraesCS3A01G194500 chr2A 649975004 649975693 689 False 1101 1101 95.507 2 690 1 chr2A.!!$F4 688
10 TraesCS3A01G194500 chr7A 514730151 514731221 1070 True 1552 1552 92.844 1566 2636 1 chr7A.!!$R5 1070
11 TraesCS3A01G194500 chr7A 396965014 396966085 1071 True 1432 1432 90.892 1570 2636 1 chr7A.!!$R2 1066
12 TraesCS3A01G194500 chr7A 396972894 396973963 1069 True 1417 1417 90.680 1572 2636 1 chr7A.!!$R3 1064
13 TraesCS3A01G194500 chr6A 112350309 112351379 1070 True 1524 1524 92.379 1566 2636 1 chr6A.!!$R1 1070
14 TraesCS3A01G194500 chr6A 326371943 326372632 689 True 1059 1059 94.356 2 691 1 chr6A.!!$R5 689
15 TraesCS3A01G194500 chr1A 132155309 132156325 1016 True 1437 1437 92.255 1623 2636 1 chr1A.!!$R1 1013
16 TraesCS3A01G194500 chr1A 548637970 548638660 690 False 1070 1070 94.645 4 692 1 chr1A.!!$F2 688
17 TraesCS3A01G194500 chr5A 146513345 146514033 688 False 1085 1085 95.080 2 691 1 chr5A.!!$F1 689
18 TraesCS3A01G194500 chr7D 51437898 51438589 691 True 1077 1077 94.798 2 692 1 chr7D.!!$R1 690
19 TraesCS3A01G194500 chr1D 70228203 70228893 690 False 1055 1055 94.220 2 692 1 chr1D.!!$F1 690
20 TraesCS3A01G194500 chr2B 171037961 171038652 691 True 1050 1050 94.075 2 692 1 chr2B.!!$R2 690
21 TraesCS3A01G194500 chr2B 537317765 537318456 691 True 1050 1050 94.075 2 692 1 chr2B.!!$R3 690
22 TraesCS3A01G194500 chr4A 389312194 389312798 604 True 676 676 87.438 787 1370 1 chr4A.!!$R1 583

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
845 886 0.030705 CCTCCTTCCTCATCCCCTCA 60.031 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2481 0.806102 CGGATCCTCACAAACGCGAT 60.806 55.0 15.93 0.0 0.0 4.58 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
109 110 1.276989 TCTACCGCGTCAAAAGGGATT 59.723 47.619 4.92 0.00 0.00 3.01
155 156 7.997223 AGATATGATCTCAAATGAAAAGGAGCA 59.003 33.333 0.00 0.00 33.42 4.26
244 245 3.550437 AGAAGTTGAGAGTGCACAAGT 57.450 42.857 21.04 4.36 30.90 3.16
372 374 6.713762 TTGAAAAGAGAAACATGTCATGGT 57.286 33.333 17.08 7.75 33.60 3.55
443 445 1.452145 GGAGTGCGGCAAAGGTGAAA 61.452 55.000 3.23 0.00 0.00 2.69
451 453 3.727726 CGGCAAAGGTGAAAAAGGAAAT 58.272 40.909 0.00 0.00 0.00 2.17
604 606 6.670695 ATGGGCTTATTTTAATCCATGGAC 57.329 37.500 18.99 0.00 34.16 4.02
708 711 0.037447 GCCTCTTTGCTGTTCCCTCT 59.963 55.000 0.00 0.00 0.00 3.69
837 864 3.393970 CCGCAGCCTCCTTCCTCA 61.394 66.667 0.00 0.00 0.00 3.86
841 868 1.835693 CAGCCTCCTTCCTCATCCC 59.164 63.158 0.00 0.00 0.00 3.85
845 886 0.030705 CCTCCTTCCTCATCCCCTCA 60.031 60.000 0.00 0.00 0.00 3.86
847 888 0.417437 TCCTTCCTCATCCCCTCACA 59.583 55.000 0.00 0.00 0.00 3.58
876 918 4.182433 GCCTCTACCCCTGCTGCC 62.182 72.222 0.00 0.00 0.00 4.85
1036 1081 2.988839 GCCTCCTCCCTGTGGCATT 61.989 63.158 0.00 0.00 44.34 3.56
1143 1188 2.359230 GCTGCTGTTCCGCCTTCT 60.359 61.111 0.00 0.00 0.00 2.85
1151 1196 0.903236 GTTCCGCCTTCTACCTCCTT 59.097 55.000 0.00 0.00 0.00 3.36
1217 1262 1.893544 TCTCTCTCAAGGTCGAACGT 58.106 50.000 0.00 0.00 0.00 3.99
1294 1339 4.688879 TCGACAAGTTTGATGACGCTATTT 59.311 37.500 0.00 0.00 36.24 1.40
1507 1553 5.403166 CGAAAACATTGTACGAGTACTTCCA 59.597 40.000 13.67 0.00 37.00 3.53
1555 1601 1.028330 CGCCCTGTACGACTACCTCA 61.028 60.000 0.00 0.00 0.00 3.86
1564 1610 6.039493 CCTGTACGACTACCTCAACTATGAAT 59.961 42.308 0.00 0.00 34.49 2.57
1697 1750 1.181098 GGTGCACCCTTTGTCTGCAT 61.181 55.000 26.31 0.00 42.65 3.96
1870 1964 1.784115 CGTTTTCGTTATCGTTGCCGG 60.784 52.381 0.00 0.00 38.65 6.13
2180 2285 6.035368 CCAAATAATTGATGTGGTGTTCCA 57.965 37.500 0.00 0.00 38.08 3.53
2347 2455 3.765026 TGTTTGCTTCTTTTCGGTGTTC 58.235 40.909 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.630242 ATTGAAACGGTCTTGAACATATGAT 57.370 32.000 10.38 0.00 0.00 2.45
109 110 1.684450 TGAAGTGGCACTCTTACGACA 59.316 47.619 22.31 9.61 42.60 4.35
155 156 5.473066 AGCCAATGTCAGCACTTTAATTT 57.527 34.783 0.00 0.00 0.00 1.82
244 245 9.823647 TTGAAGTAATGGCAATTCTTGTTTTAA 57.176 25.926 0.00 0.00 0.00 1.52
398 400 7.695480 TGTAAAGGAAGCTTGCACATAATTA 57.305 32.000 20.82 6.51 0.00 1.40
443 445 8.579863 CCTTCATAGTTTTCACTCATTTCCTTT 58.420 33.333 0.00 0.00 34.06 3.11
451 453 5.560722 TGGTCCTTCATAGTTTTCACTCA 57.439 39.130 0.00 0.00 34.06 3.41
487 489 6.041523 TGGATAATGTGTGGATCGAAGATGTA 59.958 38.462 0.00 0.00 45.12 2.29
497 499 7.959658 TGAAGAAAATGGATAATGTGTGGAT 57.040 32.000 0.00 0.00 0.00 3.41
663 666 9.474920 CCATTTAGATTAGCAACAAAAGTGAAA 57.525 29.630 0.00 0.00 0.00 2.69
837 864 2.586792 GCGAGCTTGTGAGGGGAT 59.413 61.111 2.14 0.00 0.00 3.85
841 868 2.125350 GGAGGCGAGCTTGTGAGG 60.125 66.667 2.14 0.00 0.00 3.86
1143 1188 2.488347 GGTCCTGCAACAAAAGGAGGTA 60.488 50.000 0.00 0.00 43.27 3.08
1151 1196 1.152830 GGGAGGGTCCTGCAACAAA 59.847 57.895 10.60 0.00 36.57 2.83
1217 1262 1.233950 TGTCTCGTGTAACCGGCGTA 61.234 55.000 6.01 0.00 0.00 4.42
1507 1553 1.985662 TACACGGGTCTTCGGCCAT 60.986 57.895 2.24 0.00 0.00 4.40
1555 1601 4.819105 TGTTCTCGGGACATTCATAGTT 57.181 40.909 0.00 0.00 0.00 2.24
1564 1610 2.758979 GGAAGTAGATGTTCTCGGGACA 59.241 50.000 0.00 0.00 0.00 4.02
1697 1750 3.629438 TGAGTGACAATACGAACACGA 57.371 42.857 0.00 0.00 38.15 4.35
1849 1943 1.244352 GGCAACGATAACGAAAACGC 58.756 50.000 0.00 0.00 42.66 4.84
1870 1964 2.273179 GGAAACGAAAGGGGTGCCC 61.273 63.158 0.00 0.00 45.90 5.36
1883 1978 1.096416 TTTGTCACCGTGGTGGAAAC 58.904 50.000 18.47 10.29 45.43 2.78
1998 2099 9.117145 CATATGCCTTAGTAATTTATTGCAACG 57.883 33.333 0.00 0.00 0.00 4.10
2372 2481 0.806102 CGGATCCTCACAAACGCGAT 60.806 55.000 15.93 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.