Multiple sequence alignment - TraesCS4A01G489100

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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 TraesCS4A01G489100 chr4A 100.000 3643 0 0 1 3643 740268315 740271957 0.000000e+00 6728.0
1 TraesCS4A01G489100 chr4A 99.342 3645 19 3 1 3643 740302468 740306109 0.000000e+00 6593.0
2 TraesCS4A01G489100 chr4A 99.589 3407 13 1 1 3406 740345720 740349126 0.000000e+00 6213.0
3 TraesCS4A01G489100 chr4A 86.683 2478 223 44 1227 3641 741795946 741793513 0.000000e+00 2649.0
4 TraesCS4A01G489100 chr4A 90.226 1197 98 10 1227 2406 740022146 740020952 0.000000e+00 1544.0
5 TraesCS4A01G489100 chr4A 87.055 1375 114 26 1243 2560 739866238 739867605 0.000000e+00 1495.0
6 TraesCS4A01G489100 chr4A 91.698 1072 85 3 1227 2294 741589009 741590080 0.000000e+00 1483.0
7 TraesCS4A01G489100 chr4A 86.963 1258 128 16 2401 3641 740455595 740454357 0.000000e+00 1382.0
8 TraesCS4A01G489100 chr4A 90.568 1039 94 4 2596 3632 739652056 739653092 0.000000e+00 1373.0
9 TraesCS4A01G489100 chr4A 90.680 1030 96 0 2603 3632 739867608 739868637 0.000000e+00 1371.0
10 TraesCS4A01G489100 chr4A 90.472 1039 95 4 2596 3632 742057335 742058371 0.000000e+00 1367.0
11 TraesCS4A01G489100 chr4A 86.848 1247 127 22 2406 3632 740578863 740580092 0.000000e+00 1360.0
12 TraesCS4A01G489100 chr4A 94.991 559 25 2 547 1102 740926793 740927351 0.000000e+00 874.0
13 TraesCS4A01G489100 chr4A 91.320 553 44 2 548 1096 741588187 741588739 0.000000e+00 752.0
14 TraesCS4A01G489100 chr4A 90.353 539 48 4 550 1086 740022763 740022227 0.000000e+00 704.0
15 TraesCS4A01G489100 chr4A 89.781 548 47 6 548 1086 741491253 741490706 0.000000e+00 693.0
16 TraesCS4A01G489100 chr4A 92.233 103 7 1 2325 2426 740455705 740455603 1.050000e-30 145.0
17 TraesCS4A01G489100 chr4A 100.000 48 0 0 1086 1133 741588906 741588953 5.010000e-14 89.8
18 TraesCS4A01G489100 chr7D 88.898 2423 210 37 1243 3635 3788331 3785938 0.000000e+00 2929.0
19 TraesCS4A01G489100 chr7D 87.609 1719 172 25 602 2296 2611920 2610219 0.000000e+00 1956.0
20 TraesCS4A01G489100 chr7D 92.155 1058 74 8 1243 2296 2359027 2357975 0.000000e+00 1485.0
21 TraesCS4A01G489100 chr7D 92.148 1057 76 5 1243 2296 3634538 3633486 0.000000e+00 1485.0
22 TraesCS4A01G489100 chr7D 90.512 1054 98 2 2589 3641 3633190 3632138 0.000000e+00 1391.0
23 TraesCS4A01G489100 chr7D 83.752 1274 136 40 2401 3641 2566281 2565046 0.000000e+00 1140.0
24 TraesCS4A01G489100 chr7D 86.531 542 71 2 4 543 3641072 3640531 2.420000e-166 595.0
25 TraesCS4A01G489100 chr7D 75.100 498 78 25 4 472 2360392 2359912 1.340000e-44 191.0
26 TraesCS4A01G489100 chr7D 95.146 103 4 1 2325 2426 2566391 2566289 1.050000e-35 161.0
27 TraesCS4A01G489100 chr7D 86.154 130 12 5 86 210 17177090 17177218 6.350000e-28 135.0
28 TraesCS4A01G489100 chr7A 90.850 1071 95 3 2572 3641 3631636 3630568 0.000000e+00 1432.0
29 TraesCS4A01G489100 chr7A 89.554 1053 108 1 2589 3641 3208025 3206975 0.000000e+00 1334.0
30 TraesCS4A01G489100 chr7A 92.473 558 36 3 550 1102 2002628 2002072 0.000000e+00 793.0
31 TraesCS4A01G489100 chr7A 89.761 586 53 3 548 1133 3285285 3285863 0.000000e+00 743.0
32 TraesCS4A01G489100 chr7A 90.179 560 43 5 553 1101 3634750 3634192 0.000000e+00 719.0
33 TraesCS4A01G489100 chr7A 78.704 216 37 6 9 215 200237132 200236917 6.350000e-28 135.0
34 TraesCS4A01G489100 chr7A 74.251 334 64 15 4 318 736574543 736574213 1.780000e-23 121.0
35 TraesCS4A01G489100 chr3D 77.116 319 58 13 7 317 350664593 350664282 1.740000e-38 171.0
36 TraesCS4A01G489100 chr1A 80.952 126 22 1 87 210 492274156 492274281 8.330000e-17 99.0


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 TraesCS4A01G489100 chr4A 740268315 740271957 3642 False 6728.000000 6728 100.000000 1 3643 1 chr4A.!!$F2 3642
1 TraesCS4A01G489100 chr4A 740302468 740306109 3641 False 6593.000000 6593 99.342000 1 3643 1 chr4A.!!$F3 3642
2 TraesCS4A01G489100 chr4A 740345720 740349126 3406 False 6213.000000 6213 99.589000 1 3406 1 chr4A.!!$F4 3405
3 TraesCS4A01G489100 chr4A 741793513 741795946 2433 True 2649.000000 2649 86.683000 1227 3641 1 chr4A.!!$R2 2414
4 TraesCS4A01G489100 chr4A 739866238 739868637 2399 False 1433.000000 1495 88.867500 1243 3632 2 chr4A.!!$F8 2389
5 TraesCS4A01G489100 chr4A 739652056 739653092 1036 False 1373.000000 1373 90.568000 2596 3632 1 chr4A.!!$F1 1036
6 TraesCS4A01G489100 chr4A 742057335 742058371 1036 False 1367.000000 1367 90.472000 2596 3632 1 chr4A.!!$F7 1036
7 TraesCS4A01G489100 chr4A 740578863 740580092 1229 False 1360.000000 1360 86.848000 2406 3632 1 chr4A.!!$F5 1226
8 TraesCS4A01G489100 chr4A 740020952 740022763 1811 True 1124.000000 1544 90.289500 550 2406 2 chr4A.!!$R3 1856
9 TraesCS4A01G489100 chr4A 740926793 740927351 558 False 874.000000 874 94.991000 547 1102 1 chr4A.!!$F6 555
10 TraesCS4A01G489100 chr4A 741588187 741590080 1893 False 774.933333 1483 94.339333 548 2294 3 chr4A.!!$F9 1746
11 TraesCS4A01G489100 chr4A 740454357 740455705 1348 True 763.500000 1382 89.598000 2325 3641 2 chr4A.!!$R4 1316
12 TraesCS4A01G489100 chr4A 741490706 741491253 547 True 693.000000 693 89.781000 548 1086 1 chr4A.!!$R1 538
13 TraesCS4A01G489100 chr7D 3785938 3788331 2393 True 2929.000000 2929 88.898000 1243 3635 1 chr7D.!!$R3 2392
14 TraesCS4A01G489100 chr7D 2610219 2611920 1701 True 1956.000000 1956 87.609000 602 2296 1 chr7D.!!$R1 1694
15 TraesCS4A01G489100 chr7D 3632138 3634538 2400 True 1438.000000 1485 91.330000 1243 3641 2 chr7D.!!$R6 2398
16 TraesCS4A01G489100 chr7D 2357975 2360392 2417 True 838.000000 1485 83.627500 4 2296 2 chr7D.!!$R4 2292
17 TraesCS4A01G489100 chr7D 2565046 2566391 1345 True 650.500000 1140 89.449000 2325 3641 2 chr7D.!!$R5 1316
18 TraesCS4A01G489100 chr7D 3640531 3641072 541 True 595.000000 595 86.531000 4 543 1 chr7D.!!$R2 539
19 TraesCS4A01G489100 chr7A 3206975 3208025 1050 True 1334.000000 1334 89.554000 2589 3641 1 chr7A.!!$R2 1052
20 TraesCS4A01G489100 chr7A 3630568 3634750 4182 True 1075.500000 1432 90.514500 553 3641 2 chr7A.!!$R5 3088
21 TraesCS4A01G489100 chr7A 2002072 2002628 556 True 793.000000 793 92.473000 550 1102 1 chr7A.!!$R1 552
22 TraesCS4A01G489100 chr7A 3285285 3285863 578 False 743.000000 743 89.761000 548 1133 1 chr7A.!!$F1 585

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
1347 2745 3.141083 AGGTAGAGGCAGAGACATGGATA 59.859 47.826 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2768 4346 0.670546 ACTTGTTCTGGGTCATCGCG 60.671 55.0 0.0 0.0 0.0 5.87 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
1347 2745 3.141083 AGGTAGAGGCAGAGACATGGATA 59.859 47.826 0.0 0.0 0.00 2.59
1948 3346 4.674362 GCCTTGTGAGAAAACTTGTTTCGT 60.674 41.667 0.0 0.0 33.86 3.85
1968 3366 3.552273 CGTCCTAGTAATTGATGGTCGGG 60.552 52.174 0.0 0.0 0.00 5.14
2035 3436 4.623886 GCTCAAGGTGGTGTCTATTCATGA 60.624 45.833 0.0 0.0 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1347 2745 4.796618 GCCTAGAGAAACACTGAAACTCGT 60.797 45.833 0.0 0.0 33.53 4.18
1948 3346 3.386726 CACCCGACCATCAATTACTAGGA 59.613 47.826 0.0 0.0 0.00 2.94
1968 3366 6.478588 CCATCGAGTTAATAAACTTGCTCAC 58.521 40.000 0.0 0.0 46.09 3.51
2035 3436 7.661027 CCATTGTTTTACCAAGACATCCAAATT 59.339 33.333 0.0 0.0 0.00 1.82
2768 4346 0.670546 ACTTGTTCTGGGTCATCGCG 60.671 55.000 0.0 0.0 0.00 5.87
3451 5045 4.460263 ACTTTCTGATGTTTGCTGGTGTA 58.540 39.130 0.0 0.0 0.00 2.90


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

AutoCloner maintained by Alex Coulton.