Multiple sequence alignment - TraesCS4D01G116900

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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 TraesCS4D01G116900 chr4D 100.000 3238 0 0 1 3238 97719741 97722978 0.000000e+00 5980.0
1 TraesCS4D01G116900 chr4D 98.658 2161 28 1 1078 3238 97766056 97763897 0.000000e+00 3829.0
2 TraesCS4D01G116900 chr4D 95.981 1493 54 2 1751 3238 43451553 43450062 0.000000e+00 2420.0
3 TraesCS4D01G116900 chr4D 95.582 1494 57 5 1749 3234 273919366 273917874 0.000000e+00 2385.0
4 TraesCS4D01G116900 chr4D 93.185 763 25 8 821 1561 97605188 97605945 0.000000e+00 1096.0
5 TraesCS4D01G116900 chr4D 92.535 710 26 8 874 1561 97508603 97509307 0.000000e+00 992.0
6 TraesCS4D01G116900 chr4D 88.604 702 49 14 874 1560 97957915 97958600 0.000000e+00 824.0
7 TraesCS4D01G116900 chr4D 98.361 61 1 0 821 881 97508512 97508572 1.230000e-19 108.0
8 TraesCS4D01G116900 chr3D 97.587 1492 33 3 1749 3238 579700175 579701665 0.000000e+00 2553.0
9 TraesCS4D01G116900 chr3D 96.445 1491 47 2 1754 3238 481537502 481538992 0.000000e+00 2455.0
10 TraesCS4D01G116900 chr3D 95.497 1488 50 6 1757 3238 89895382 89893906 0.000000e+00 2361.0
11 TraesCS4D01G116900 chr5D 97.312 1488 33 6 1755 3238 84191543 84193027 0.000000e+00 2519.0
12 TraesCS4D01G116900 chr5D 95.906 1490 50 4 1755 3238 105608880 105610364 0.000000e+00 2403.0
13 TraesCS4D01G116900 chr5D 99.148 822 5 2 1 821 332219927 332219107 0.000000e+00 1478.0
14 TraesCS4D01G116900 chr5D 84.685 111 17 0 1606 1716 59607856 59607966 9.500000e-21 111.0
15 TraesCS4D01G116900 chr1D 95.576 1492 60 2 1753 3238 48872393 48870902 0.000000e+00 2385.0
16 TraesCS4D01G116900 chr6D 99.391 821 4 1 1 820 453935871 453935051 0.000000e+00 1487.0
17 TraesCS4D01G116900 chr6D 84.426 122 12 4 1638 1754 260861819 260861700 2.640000e-21 113.0
18 TraesCS4D01G116900 chr1B 97.451 824 19 2 1 823 17703994 17703172 0.000000e+00 1404.0
19 TraesCS4D01G116900 chr7D 96.093 819 31 1 1 818 113749519 113748701 0.000000e+00 1334.0
20 TraesCS4D01G116900 chr7D 84.071 113 18 0 1603 1715 407258824 407258712 3.420000e-20 110.0
21 TraesCS4D01G116900 chr7B 95.981 821 32 1 1 820 532151318 532152138 0.000000e+00 1332.0
22 TraesCS4D01G116900 chr7B 95.859 821 33 1 1 820 69987584 69986764 0.000000e+00 1327.0
23 TraesCS4D01G116900 chr7A 95.869 823 32 2 1 821 137843478 137844300 0.000000e+00 1330.0
24 TraesCS4D01G116900 chr7A 84.685 111 17 0 1606 1716 621764505 621764615 9.500000e-21 111.0
25 TraesCS4D01G116900 chr3B 95.981 821 30 3 1 820 736664272 736665090 0.000000e+00 1330.0
26 TraesCS4D01G116900 chr3B 84.667 150 23 0 1605 1754 252610592 252610741 2.010000e-32 150.0
27 TraesCS4D01G116900 chr5A 95.250 821 38 1 1 820 387355150 387355970 0.000000e+00 1299.0
28 TraesCS4D01G116900 chr5A 79.885 348 64 5 944 1289 326058235 326057892 1.930000e-62 250.0
29 TraesCS4D01G116900 chr4A 93.875 702 23 6 874 1561 478302748 478302053 0.000000e+00 1040.0
30 TraesCS4D01G116900 chr4A 93.534 696 29 4 874 1557 478340051 478339360 0.000000e+00 1022.0
31 TraesCS4D01G116900 chr4B 90.883 691 37 18 874 1561 139472266 139472933 0.000000e+00 904.0
32 TraesCS4D01G116900 chr4B 90.883 691 37 18 874 1561 139510714 139511381 0.000000e+00 904.0
33 TraesCS4D01G116900 chr4B 90.647 695 36 18 874 1561 139399117 139399789 0.000000e+00 896.0
34 TraesCS4D01G116900 chr4B 93.478 368 22 2 1388 1754 139531505 139531871 2.200000e-151 545.0
35 TraesCS4D01G116900 chr4B 96.154 52 2 0 821 872 139399021 139399072 5.760000e-13 86.1
36 TraesCS4D01G116900 chr5B 85.294 136 19 1 1618 1752 248029963 248030098 4.360000e-29 139.0
37 TraesCS4D01G116900 chr5B 85.294 136 19 1 1618 1752 248265385 248265520 4.360000e-29 139.0
38 TraesCS4D01G116900 chr2B 85.714 105 15 0 1610 1714 692525258 692525154 9.500000e-21 111.0


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 TraesCS4D01G116900 chr4D 97719741 97722978 3237 False 5980.00 5980 100.0000 1 3238 1 chr4D.!!$F2 3237
1 TraesCS4D01G116900 chr4D 97763897 97766056 2159 True 3829.00 3829 98.6580 1078 3238 1 chr4D.!!$R2 2160
2 TraesCS4D01G116900 chr4D 43450062 43451553 1491 True 2420.00 2420 95.9810 1751 3238 1 chr4D.!!$R1 1487
3 TraesCS4D01G116900 chr4D 273917874 273919366 1492 True 2385.00 2385 95.5820 1749 3234 1 chr4D.!!$R3 1485
4 TraesCS4D01G116900 chr4D 97605188 97605945 757 False 1096.00 1096 93.1850 821 1561 1 chr4D.!!$F1 740
5 TraesCS4D01G116900 chr4D 97957915 97958600 685 False 824.00 824 88.6040 874 1560 1 chr4D.!!$F3 686
6 TraesCS4D01G116900 chr4D 97508512 97509307 795 False 550.00 992 95.4480 821 1561 2 chr4D.!!$F4 740
7 TraesCS4D01G116900 chr3D 579700175 579701665 1490 False 2553.00 2553 97.5870 1749 3238 1 chr3D.!!$F2 1489
8 TraesCS4D01G116900 chr3D 481537502 481538992 1490 False 2455.00 2455 96.4450 1754 3238 1 chr3D.!!$F1 1484
9 TraesCS4D01G116900 chr3D 89893906 89895382 1476 True 2361.00 2361 95.4970 1757 3238 1 chr3D.!!$R1 1481
10 TraesCS4D01G116900 chr5D 84191543 84193027 1484 False 2519.00 2519 97.3120 1755 3238 1 chr5D.!!$F2 1483
11 TraesCS4D01G116900 chr5D 105608880 105610364 1484 False 2403.00 2403 95.9060 1755 3238 1 chr5D.!!$F3 1483
12 TraesCS4D01G116900 chr5D 332219107 332219927 820 True 1478.00 1478 99.1480 1 821 1 chr5D.!!$R1 820
13 TraesCS4D01G116900 chr1D 48870902 48872393 1491 True 2385.00 2385 95.5760 1753 3238 1 chr1D.!!$R1 1485
14 TraesCS4D01G116900 chr6D 453935051 453935871 820 True 1487.00 1487 99.3910 1 820 1 chr6D.!!$R2 819
15 TraesCS4D01G116900 chr1B 17703172 17703994 822 True 1404.00 1404 97.4510 1 823 1 chr1B.!!$R1 822
16 TraesCS4D01G116900 chr7D 113748701 113749519 818 True 1334.00 1334 96.0930 1 818 1 chr7D.!!$R1 817
17 TraesCS4D01G116900 chr7B 532151318 532152138 820 False 1332.00 1332 95.9810 1 820 1 chr7B.!!$F1 819
18 TraesCS4D01G116900 chr7B 69986764 69987584 820 True 1327.00 1327 95.8590 1 820 1 chr7B.!!$R1 819
19 TraesCS4D01G116900 chr7A 137843478 137844300 822 False 1330.00 1330 95.8690 1 821 1 chr7A.!!$F1 820
20 TraesCS4D01G116900 chr3B 736664272 736665090 818 False 1330.00 1330 95.9810 1 820 1 chr3B.!!$F2 819
21 TraesCS4D01G116900 chr5A 387355150 387355970 820 False 1299.00 1299 95.2500 1 820 1 chr5A.!!$F1 819
22 TraesCS4D01G116900 chr4A 478302053 478302748 695 True 1040.00 1040 93.8750 874 1561 1 chr4A.!!$R1 687
23 TraesCS4D01G116900 chr4A 478339360 478340051 691 True 1022.00 1022 93.5340 874 1557 1 chr4A.!!$R2 683
24 TraesCS4D01G116900 chr4B 139472266 139472933 667 False 904.00 904 90.8830 874 1561 1 chr4B.!!$F1 687
25 TraesCS4D01G116900 chr4B 139510714 139511381 667 False 904.00 904 90.8830 874 1561 1 chr4B.!!$F2 687
26 TraesCS4D01G116900 chr4B 139399021 139399789 768 False 491.05 896 93.4005 821 1561 2 chr4B.!!$F4 740

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
917 970 0.175302 CATTGCTGTCCTCTCGCTCT 59.825 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2805 2902 7.775397 AACATACAAACGTTACAGTGTTAGT 57.225 32.0 15.77 9.68 0.0 2.24 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
198 200 3.592059 GTTTACCGGCTCATCACACTTA 58.408 45.455 0.00 0.0 0.00 2.24
832 835 1.681666 CCACTGCTCCACCACATCT 59.318 57.895 0.00 0.0 0.00 2.90
917 970 0.175302 CATTGCTGTCCTCTCGCTCT 59.825 55.000 0.00 0.0 0.00 4.09
931 984 2.262915 CTCTTCCTCGCGCTGGTT 59.737 61.111 5.56 0.0 0.00 3.67
1601 1682 7.835822 TCTAAACCAACATAATTTGTCATGGG 58.164 34.615 12.27 0.0 39.57 4.00
1938 2030 1.383109 ATCTGGATCAGACGGGGCA 60.383 57.895 0.00 0.0 43.63 5.36
2249 2343 2.041755 GGTTGGTTGAGATTCCTTCCCT 59.958 50.000 0.00 0.0 0.00 4.20
2805 2902 9.575783 GGTGAAATAAGTGTTTTGTTTAGTCAA 57.424 29.630 0.00 0.0 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 200 1.873591 CGCTACTGGCAAAGTCAAAGT 59.126 47.619 0.00 0.00 40.56 2.66
327 329 7.877097 GTCATCAGTTCCAGCAAATATATCTCT 59.123 37.037 0.00 0.00 0.00 3.10
832 835 3.668447 CCTTGAGAGAGCTTGTTTGCTA 58.332 45.455 0.00 0.00 44.17 3.49
964 1017 0.667453 GAGTAGAATCCCGACGACCC 59.333 60.000 0.00 0.00 0.00 4.46
965 1018 0.667453 GGAGTAGAATCCCGACGACC 59.333 60.000 0.00 0.00 32.79 4.79
1601 1682 1.472188 AGGACCGAGGTACTACTTGC 58.528 55.000 4.95 0.00 41.55 4.01
2805 2902 7.775397 AACATACAAACGTTACAGTGTTAGT 57.225 32.000 15.77 9.68 0.00 2.24


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

AutoCloner maintained by Alex Coulton.