Multiple sequence alignment - TraesCS5A01G147200

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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 TraesCS5A01G147200 chr5A 100.000 2535 0 0 1 2535 324699658 324702192 0.000000e+00 4682.0
1 TraesCS5A01G147200 chr1A 96.685 2534 77 3 4 2535 409667228 409664700 0.000000e+00 4207.0
2 TraesCS5A01G147200 chr1A 90.909 253 21 2 1290 1541 14377869 14378120 3.120000e-89 339.0
3 TraesCS5A01G147200 chr4B 95.128 1642 75 4 896 2535 223338369 223340007 0.000000e+00 2584.0
4 TraesCS5A01G147200 chr4B 92.754 897 55 6 1 895 223337445 223338333 0.000000e+00 1288.0
5 TraesCS5A01G147200 chr7B 96.886 1381 42 1 4 1383 729411063 729409683 0.000000e+00 2311.0
6 TraesCS5A01G147200 chr7B 95.726 468 8 5 1339 1801 729409763 729409303 0.000000e+00 743.0
7 TraesCS5A01G147200 chr1B 96.814 1381 43 1 4 1383 665092497 665091117 0.000000e+00 2305.0
8 TraesCS5A01G147200 chr1B 97.386 880 14 4 1339 2213 665091197 665090322 0.000000e+00 1489.0
9 TraesCS5A01G147200 chr1B 90.000 890 75 5 8 895 573522575 573523452 0.000000e+00 1138.0
10 TraesCS5A01G147200 chr1B 94.166 737 42 1 1799 2535 573554385 573555120 0.000000e+00 1122.0
11 TraesCS5A01G147200 chr1B 93.237 695 37 7 1215 1905 340743038 340742350 0.000000e+00 1014.0
12 TraesCS5A01G147200 chr1B 98.466 326 5 0 2210 2535 665088893 665088568 2.190000e-160 575.0
13 TraesCS5A01G147200 chr4A 98.601 929 10 3 1609 2535 296351449 296350522 0.000000e+00 1640.0
14 TraesCS5A01G147200 chr4A 98.062 929 15 3 1609 2535 319667472 319668399 0.000000e+00 1613.0
15 TraesCS5A01G147200 chr4A 98.060 928 15 3 1609 2534 293292736 293291810 0.000000e+00 1611.0
16 TraesCS5A01G147200 chr2D 91.332 946 51 14 985 1905 356110946 356111885 0.000000e+00 1264.0
17 TraesCS5A01G147200 chr2D 91.888 641 46 4 1898 2534 356111913 356112551 0.000000e+00 891.0
18 TraesCS5A01G147200 chr2D 86.883 648 70 7 253 895 278863772 278864409 0.000000e+00 712.0
19 TraesCS5A01G147200 chr7D 89.827 924 61 15 986 1905 157295645 157294751 0.000000e+00 1155.0
20 TraesCS5A01G147200 chr7D 93.333 645 34 5 1898 2535 20669040 20669682 0.000000e+00 944.0
21 TraesCS5A01G147200 chr7D 90.231 563 30 5 985 1524 20668332 20668892 0.000000e+00 712.0
22 TraesCS5A01G147200 chr7D 97.222 36 1 0 1179 1214 207185724 207185689 7.570000e-06 62.1
23 TraesCS5A01G147200 chr2A 88.627 721 75 5 179 895 279489233 279488516 0.000000e+00 870.0
24 TraesCS5A01G147200 chr2A 87.603 726 77 5 179 895 191893342 191894063 0.000000e+00 830.0
25 TraesCS5A01G147200 chr2A 89.850 266 26 1 894 1158 191894097 191894362 8.690000e-90 340.0
26 TraesCS5A01G147200 chr2A 89.474 266 25 2 894 1158 279488482 279488219 1.450000e-87 333.0
27 TraesCS5A01G147200 chr3D 83.910 578 55 10 1169 1719 465957302 465957868 3.740000e-143 518.0
28 TraesCS5A01G147200 chr6B 87.941 340 23 8 1215 1541 705328139 705328473 3.960000e-103 385.0


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 TraesCS5A01G147200 chr5A 324699658 324702192 2534 False 4682.000000 4682 100.000000 1 2535 1 chr5A.!!$F1 2534
1 TraesCS5A01G147200 chr1A 409664700 409667228 2528 True 4207.000000 4207 96.685000 4 2535 1 chr1A.!!$R1 2531
2 TraesCS5A01G147200 chr4B 223337445 223340007 2562 False 1936.000000 2584 93.941000 1 2535 2 chr4B.!!$F1 2534
3 TraesCS5A01G147200 chr7B 729409303 729411063 1760 True 1527.000000 2311 96.306000 4 1801 2 chr7B.!!$R1 1797
4 TraesCS5A01G147200 chr1B 665088568 665092497 3929 True 1456.333333 2305 97.555333 4 2535 3 chr1B.!!$R2 2531
5 TraesCS5A01G147200 chr1B 573522575 573523452 877 False 1138.000000 1138 90.000000 8 895 1 chr1B.!!$F1 887
6 TraesCS5A01G147200 chr1B 573554385 573555120 735 False 1122.000000 1122 94.166000 1799 2535 1 chr1B.!!$F2 736
7 TraesCS5A01G147200 chr1B 340742350 340743038 688 True 1014.000000 1014 93.237000 1215 1905 1 chr1B.!!$R1 690
8 TraesCS5A01G147200 chr4A 296350522 296351449 927 True 1640.000000 1640 98.601000 1609 2535 1 chr4A.!!$R2 926
9 TraesCS5A01G147200 chr4A 319667472 319668399 927 False 1613.000000 1613 98.062000 1609 2535 1 chr4A.!!$F1 926
10 TraesCS5A01G147200 chr4A 293291810 293292736 926 True 1611.000000 1611 98.060000 1609 2534 1 chr4A.!!$R1 925
11 TraesCS5A01G147200 chr2D 356110946 356112551 1605 False 1077.500000 1264 91.610000 985 2534 2 chr2D.!!$F2 1549
12 TraesCS5A01G147200 chr2D 278863772 278864409 637 False 712.000000 712 86.883000 253 895 1 chr2D.!!$F1 642
13 TraesCS5A01G147200 chr7D 157294751 157295645 894 True 1155.000000 1155 89.827000 986 1905 1 chr7D.!!$R1 919
14 TraesCS5A01G147200 chr7D 20668332 20669682 1350 False 828.000000 944 91.782000 985 2535 2 chr7D.!!$F1 1550
15 TraesCS5A01G147200 chr2A 279488219 279489233 1014 True 601.500000 870 89.050500 179 1158 2 chr2A.!!$R1 979
16 TraesCS5A01G147200 chr2A 191893342 191894362 1020 False 585.000000 830 88.726500 179 1158 2 chr2A.!!$F1 979
17 TraesCS5A01G147200 chr3D 465957302 465957868 566 False 518.000000 518 83.910000 1169 1719 1 chr3D.!!$F1 550

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
464 467 0.040514 TGTTTTGTTGCTGCCGATCG 60.041 50.000 8.51 8.51 0.00 3.69 F
1281 1328 4.446857 TCGCAAGTTCTAAAGACAAACG 57.553 40.909 0.00 0.00 39.48 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1378 1.005394 GTCTTCCCGCGAAGTTGGA 60.005 57.895 8.23 1.19 45.02 3.53 R
2436 4058 3.861840 TGATTAGAGGAAACTTGGAGCG 58.138 45.455 0.00 0.00 44.43 5.03 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
44 45 3.053291 GATCAACGCCGCCACCAA 61.053 61.111 0.00 0.00 0.00 3.67
158 161 4.729918 CGCTTGGCCTCCCTTGCT 62.730 66.667 3.32 0.00 0.00 3.91
373 376 1.081277 GGAGAGGGAAGGTCCAGGT 59.919 63.158 0.00 0.00 38.64 4.00
464 467 0.040514 TGTTTTGTTGCTGCCGATCG 60.041 50.000 8.51 8.51 0.00 3.69
1281 1328 4.446857 TCGCAAGTTCTAAAGACAAACG 57.553 40.909 0.00 0.00 39.48 3.60
1298 1378 2.990479 GGTCCAATGTCGCCTCCT 59.010 61.111 0.00 0.00 0.00 3.69
1324 1404 2.124695 GCGGGAAGACCATCCACC 60.125 66.667 0.00 0.00 41.55 4.61
1325 1405 2.186903 CGGGAAGACCATCCACCG 59.813 66.667 0.00 0.00 41.55 4.94
1342 1422 1.068741 ACCGTTGTCTCTGTGGACTTC 59.931 52.381 0.00 0.00 37.16 3.01
1344 1424 1.140816 GTTGTCTCTGTGGACTTCGC 58.859 55.000 0.00 0.00 37.16 4.70
1357 1437 0.674895 ACTTCGCTGCAAGACCATCC 60.675 55.000 15.41 0.00 34.07 3.51
2004 2189 2.031624 GCTCTGAGATGGTGGCTCCTA 61.032 57.143 9.28 0.00 37.07 2.94
2436 4058 9.585099 TCATATGTGAAATTTTGCTTAATGGAC 57.415 29.630 1.90 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
373 376 2.514582 ACCTTCTTCCTCCTCTCCGATA 59.485 50.000 0.00 0.00 0.00 2.92
464 467 5.997746 ACATATTGTGGGCACTATGATACAC 59.002 40.000 10.49 0.00 39.28 2.90
1063 1110 4.458989 TCAGTTCCCATTCATGCACTTTAC 59.541 41.667 0.00 0.00 0.00 2.01
1281 1328 1.153349 GAGGAGGCGACATTGGACC 60.153 63.158 0.00 0.00 0.00 4.46
1298 1378 1.005394 GTCTTCCCGCGAAGTTGGA 60.005 57.895 8.23 1.19 45.02 3.53
1324 1404 1.409412 CGAAGTCCACAGAGACAACG 58.591 55.000 0.00 0.00 39.34 4.10
1325 1405 1.140816 GCGAAGTCCACAGAGACAAC 58.859 55.000 0.00 0.00 39.34 3.32
1342 1422 3.869272 GCGGATGGTCTTGCAGCG 61.869 66.667 0.00 0.00 0.00 5.18
1344 1424 3.197790 CGGCGGATGGTCTTGCAG 61.198 66.667 0.00 0.00 0.00 4.41
1613 1755 2.597455 TCCTCACATGTGACTGTCTCA 58.403 47.619 24.56 14.13 35.46 3.27
1772 1916 9.684448 TTAAAGATAGATACTTTCTCGCATCAG 57.316 33.333 0.00 0.00 38.34 2.90
2004 2189 6.105397 ACAAGGATGTGCTGAATCATTTTT 57.895 33.333 0.00 0.00 38.69 1.94
2436 4058 3.861840 TGATTAGAGGAAACTTGGAGCG 58.138 45.455 0.00 0.00 44.43 5.03


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

AutoCloner maintained by Alex Coulton.