Multiple sequence alignment - TraesCS3B01G223100

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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 TraesCS3B01G223100 chr3B 100.000 2841 0 0 1 2841 289834808 289837648 0.000000e+00 5247
1 TraesCS3B01G223100 chr3B 90.785 1606 127 19 1 1593 533671880 533670283 0.000000e+00 2126
2 TraesCS3B01G223100 chr3B 90.050 1588 141 13 1 1578 453572008 453570428 0.000000e+00 2041
3 TraesCS3B01G223100 chr3B 89.409 1558 155 9 26 1576 81049924 81051478 0.000000e+00 1954
4 TraesCS3B01G223100 chr3B 88.311 1249 107 24 1630 2841 284885577 284884331 0.000000e+00 1461
5 TraesCS3B01G223100 chr4B 93.640 2846 155 23 12 2841 207928244 207925409 0.000000e+00 4229
6 TraesCS3B01G223100 chr4B 89.407 2851 239 43 39 2841 486848462 486845627 0.000000e+00 3533
7 TraesCS3B01G223100 chr4B 83.997 2662 347 62 34 2644 154113666 154111033 0.000000e+00 2483
8 TraesCS3B01G223100 chr1B 94.001 2684 118 23 198 2841 534467428 534470108 0.000000e+00 4024
9 TraesCS3B01G223100 chr1B 89.461 2875 228 45 27 2841 475662759 475665618 0.000000e+00 3561
10 TraesCS3B01G223100 chr7B 91.794 2815 210 19 39 2841 182947006 182944201 0.000000e+00 3899
11 TraesCS3B01G223100 chr7B 86.047 2924 308 60 1 2841 518290322 518287416 0.000000e+00 3048
12 TraesCS3B01G223100 chr7B 86.031 1353 131 36 1539 2841 360406475 360405131 0.000000e+00 1399
13 TraesCS3B01G223100 chr7B 85.344 1351 139 40 1539 2841 594476100 594474761 0.000000e+00 1343
14 TraesCS3B01G223100 chr7B 85.344 1351 139 40 1539 2841 594480487 594479148 0.000000e+00 1343
15 TraesCS3B01G223100 chr2B 90.157 2794 226 33 80 2841 575350886 575353662 0.000000e+00 3591
16 TraesCS3B01G223100 chr2B 90.018 2805 208 43 96 2841 405161439 405164230 0.000000e+00 3563
17 TraesCS3B01G223100 chr2B 94.801 1981 71 20 891 2841 279188892 279186914 0.000000e+00 3059
18 TraesCS3B01G223100 chr2B 85.000 240 31 5 1 237 272995398 272995161 3.660000e-59 239
19 TraesCS3B01G223100 chr2B 79.348 184 26 11 1 177 279185183 279185005 4.970000e-23 119


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 TraesCS3B01G223100 chr3B 289834808 289837648 2840 False 5247 5247 100.0000 1 2841 1 chr3B.!!$F2 2840
1 TraesCS3B01G223100 chr3B 533670283 533671880 1597 True 2126 2126 90.7850 1 1593 1 chr3B.!!$R3 1592
2 TraesCS3B01G223100 chr3B 453570428 453572008 1580 True 2041 2041 90.0500 1 1578 1 chr3B.!!$R2 1577
3 TraesCS3B01G223100 chr3B 81049924 81051478 1554 False 1954 1954 89.4090 26 1576 1 chr3B.!!$F1 1550
4 TraesCS3B01G223100 chr3B 284884331 284885577 1246 True 1461 1461 88.3110 1630 2841 1 chr3B.!!$R1 1211
5 TraesCS3B01G223100 chr4B 207925409 207928244 2835 True 4229 4229 93.6400 12 2841 1 chr4B.!!$R2 2829
6 TraesCS3B01G223100 chr4B 486845627 486848462 2835 True 3533 3533 89.4070 39 2841 1 chr4B.!!$R3 2802
7 TraesCS3B01G223100 chr4B 154111033 154113666 2633 True 2483 2483 83.9970 34 2644 1 chr4B.!!$R1 2610
8 TraesCS3B01G223100 chr1B 534467428 534470108 2680 False 4024 4024 94.0010 198 2841 1 chr1B.!!$F2 2643
9 TraesCS3B01G223100 chr1B 475662759 475665618 2859 False 3561 3561 89.4610 27 2841 1 chr1B.!!$F1 2814
10 TraesCS3B01G223100 chr7B 182944201 182947006 2805 True 3899 3899 91.7940 39 2841 1 chr7B.!!$R1 2802
11 TraesCS3B01G223100 chr7B 518287416 518290322 2906 True 3048 3048 86.0470 1 2841 1 chr7B.!!$R3 2840
12 TraesCS3B01G223100 chr7B 360405131 360406475 1344 True 1399 1399 86.0310 1539 2841 1 chr7B.!!$R2 1302
13 TraesCS3B01G223100 chr7B 594474761 594480487 5726 True 1343 1343 85.3440 1539 2841 2 chr7B.!!$R4 1302
14 TraesCS3B01G223100 chr2B 575350886 575353662 2776 False 3591 3591 90.1570 80 2841 1 chr2B.!!$F2 2761
15 TraesCS3B01G223100 chr2B 405161439 405164230 2791 False 3563 3563 90.0180 96 2841 1 chr2B.!!$F1 2745
16 TraesCS3B01G223100 chr2B 279185005 279188892 3887 True 1589 3059 87.0745 1 2841 2 chr2B.!!$R2 2840

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
162 171 0.323087 GGGCGTAAAATCCCACTGGT 60.323 55.000 0.00 0.0 42.18 4.00 F
684 697 2.269978 CACATGGGTGGCCTGAAAG 58.730 57.895 3.32 0.0 41.45 2.62 F
1287 1325 3.041946 AGATCCAATGTCTACCACTCCC 58.958 50.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1166 2.616376 TGAATGTGAAGGTGTTGGAACG 59.384 45.455 0.00 0.0 0.0 3.95 R
1825 4680 4.033009 TCCAGCTTCACTCTTCCATATGA 58.967 43.478 3.65 0.0 0.0 2.15 R
2315 5202 4.133078 GGAATCATCACTTCTCCATGTCC 58.867 47.826 0.00 0.0 0.0 4.02 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
93 98 1.203994 TGTCACCTAGCTTTAGCCGAC 59.796 52.381 0.00 0.00 43.38 4.79
124 131 1.682684 CGCCTAGTCCCTGTGGAGT 60.683 63.158 0.00 0.00 46.43 3.85
128 135 2.816411 CCTAGTCCCTGTGGAGTACAA 58.184 52.381 0.00 0.00 42.80 2.41
162 171 0.323087 GGGCGTAAAATCCCACTGGT 60.323 55.000 0.00 0.00 42.18 4.00
184 193 6.014755 TGGTCTTACAATTGATCATTTTGGCA 60.015 34.615 13.59 7.29 0.00 4.92
638 651 2.517875 GCATGAGCTTCGCCCCAT 60.518 61.111 0.00 0.00 37.91 4.00
684 697 2.269978 CACATGGGTGGCCTGAAAG 58.730 57.895 3.32 0.00 41.45 2.62
774 787 6.638953 AGGGATTTAGGTATGAAGAGGAGAT 58.361 40.000 0.00 0.00 0.00 2.75
1046 1081 4.098807 GGAGCTAGTGGAAGAAGTAAGGAG 59.901 50.000 0.00 0.00 0.00 3.69
1131 1166 7.064371 GCTGAGATATCCATTGATACATGTGAC 59.936 40.741 9.11 2.81 36.32 3.67
1287 1325 3.041946 AGATCCAATGTCTACCACTCCC 58.958 50.000 0.00 0.00 0.00 4.30
1384 1422 6.700081 GCGTGATGTGTCAGGTTTATCTAATA 59.300 38.462 0.91 0.00 41.20 0.98
1825 4680 1.000396 GGAGAAGCAATGGGGCACT 60.000 57.895 0.00 0.00 35.83 4.40
2753 5684 5.858581 GGCACAGTCATCATTTAAACTTGTC 59.141 40.000 0.00 0.00 0.00 3.18
2802 5733 9.297037 AGTTTAAAATGGTCATGCTTACTAGTT 57.703 29.630 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 131 2.479837 CCAAACTGCGAGTGTCTTGTA 58.520 47.619 0.00 0.00 0.00 2.41
128 135 1.598130 GCCCAAACTGCGAGTGTCT 60.598 57.895 0.00 0.00 0.00 3.41
162 171 6.397272 GGTGCCAAAATGATCAATTGTAAGA 58.603 36.000 18.10 0.00 0.00 2.10
274 285 6.070136 GGAACAAGGGTTAGGAGTTAGAGATT 60.070 42.308 0.00 0.00 37.36 2.40
638 651 5.429681 TTGTTTTGGTATGAGCTAGGCTA 57.570 39.130 0.00 0.00 39.88 3.93
684 697 5.982356 TGCTCCTATATGACATATTCTGGC 58.018 41.667 13.09 12.56 0.00 4.85
774 787 2.105649 TGTTGTGGAGCATAGTTGTGGA 59.894 45.455 0.00 0.00 0.00 4.02
1046 1081 5.106396 CCAGTGTTGATGTTCTTCTCAATCC 60.106 44.000 0.00 0.00 34.18 3.01
1131 1166 2.616376 TGAATGTGAAGGTGTTGGAACG 59.384 45.455 0.00 0.00 0.00 3.95
1287 1325 9.193133 TCTACAACATCTTCTTTTACTTCTTCG 57.807 33.333 0.00 0.00 0.00 3.79
1825 4680 4.033009 TCCAGCTTCACTCTTCCATATGA 58.967 43.478 3.65 0.00 0.00 2.15
2315 5202 4.133078 GGAATCATCACTTCTCCATGTCC 58.867 47.826 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.