Multiple sequence alignment - TraesCS5A01G111100

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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 TraesCS5A01G111100 chr5A 100.000 2411 0 0 1 2411 213233846 213231436 0.000000e+00 4453
1 TraesCS5A01G111100 chr5A 96.232 2415 85 6 2 2411 210234341 210231928 0.000000e+00 3951
2 TraesCS5A01G111100 chr5A 94.619 2416 123 7 1 2411 147590625 147593038 0.000000e+00 3735
3 TraesCS5A01G111100 chr5A 84.580 441 54 6 68 495 35913222 35913661 2.220000e-115 425
4 TraesCS5A01G111100 chr1A 96.056 2409 91 4 7 2411 147728731 147726323 0.000000e+00 3919
5 TraesCS5A01G111100 chr6A 93.686 2423 126 12 9 2410 206133921 206136337 0.000000e+00 3602
6 TraesCS5A01G111100 chr6A 80.078 256 26 11 256 486 547318766 547318511 1.480000e-37 167
7 TraesCS5A01G111100 chr4D 92.508 1842 113 9 9 1830 215033701 215035537 0.000000e+00 2614
8 TraesCS5A01G111100 chr4D 94.186 1032 51 8 1389 2411 313783419 313782388 0.000000e+00 1565
9 TraesCS5A01G111100 chr4D 85.851 940 89 26 490 1391 15874836 15873903 0.000000e+00 959
10 TraesCS5A01G111100 chr4D 92.953 596 30 6 1820 2411 215046728 215047315 0.000000e+00 857
11 TraesCS5A01G111100 chr4D 88.501 487 46 4 9 495 313784377 313783901 4.470000e-162 580
12 TraesCS5A01G111100 chr2A 91.351 1029 78 10 1389 2411 402113211 402114234 0.000000e+00 1397
13 TraesCS5A01G111100 chr2A 91.254 1029 79 10 1389 2411 404058329 404059352 0.000000e+00 1391
14 TraesCS5A01G111100 chr2A 81.106 434 48 12 94 495 404057436 404057867 1.390000e-82 316
15 TraesCS5A01G111100 chr2A 80.645 434 50 12 94 495 402112318 402112749 3.010000e-79 305
16 TraesCS5A01G111100 chr7A 91.068 1030 81 9 1389 2411 195277216 195276191 0.000000e+00 1382
17 TraesCS5A01G111100 chr4B 84.942 943 90 26 490 1391 27398917 27397986 0.000000e+00 907
18 TraesCS5A01G111100 chr4A 90.123 486 42 4 910 1391 584697312 584696829 5.660000e-176 627
19 TraesCS5A01G111100 chr3B 76.587 709 114 28 662 1354 822552226 822552898 2.300000e-90 342
20 TraesCS5A01G111100 chr3B 76.356 719 119 29 690 1391 824261330 824260646 2.970000e-89 339
21 TraesCS5A01G111100 chr1B 80.093 432 56 13 94 495 604623224 604622793 6.520000e-76 294
22 TraesCS5A01G111100 chr3D 84.211 323 28 6 21 343 604116827 604116528 2.340000e-75 292


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 TraesCS5A01G111100 chr5A 213231436 213233846 2410 True 4453.0 4453 100.0000 1 2411 1 chr5A.!!$R2 2410
1 TraesCS5A01G111100 chr5A 210231928 210234341 2413 True 3951.0 3951 96.2320 2 2411 1 chr5A.!!$R1 2409
2 TraesCS5A01G111100 chr5A 147590625 147593038 2413 False 3735.0 3735 94.6190 1 2411 1 chr5A.!!$F2 2410
3 TraesCS5A01G111100 chr1A 147726323 147728731 2408 True 3919.0 3919 96.0560 7 2411 1 chr1A.!!$R1 2404
4 TraesCS5A01G111100 chr6A 206133921 206136337 2416 False 3602.0 3602 93.6860 9 2410 1 chr6A.!!$F1 2401
5 TraesCS5A01G111100 chr4D 215033701 215035537 1836 False 2614.0 2614 92.5080 9 1830 1 chr4D.!!$F1 1821
6 TraesCS5A01G111100 chr4D 313782388 313784377 1989 True 1072.5 1565 91.3435 9 2411 2 chr4D.!!$R2 2402
7 TraesCS5A01G111100 chr4D 15873903 15874836 933 True 959.0 959 85.8510 490 1391 1 chr4D.!!$R1 901
8 TraesCS5A01G111100 chr4D 215046728 215047315 587 False 857.0 857 92.9530 1820 2411 1 chr4D.!!$F2 591
9 TraesCS5A01G111100 chr2A 404057436 404059352 1916 False 853.5 1391 86.1800 94 2411 2 chr2A.!!$F2 2317
10 TraesCS5A01G111100 chr2A 402112318 402114234 1916 False 851.0 1397 85.9980 94 2411 2 chr2A.!!$F1 2317
11 TraesCS5A01G111100 chr7A 195276191 195277216 1025 True 1382.0 1382 91.0680 1389 2411 1 chr7A.!!$R1 1022
12 TraesCS5A01G111100 chr4B 27397986 27398917 931 True 907.0 907 84.9420 490 1391 1 chr4B.!!$R1 901
13 TraesCS5A01G111100 chr3B 822552226 822552898 672 False 342.0 342 76.5870 662 1354 1 chr3B.!!$F1 692
14 TraesCS5A01G111100 chr3B 824260646 824261330 684 True 339.0 339 76.3560 690 1391 1 chr3B.!!$R1 701

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
132 133 0.600255 ACCACGCCTTGTCTTCTTCG 60.6 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 2086 0.598065 GACGCCCAGAGTTGCAATTT 59.402 50.0 0.59 0.0 0.0 1.82 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
121 122 2.665000 CACTCCATCACCACGCCT 59.335 61.111 0.00 0.00 0.00 5.52
132 133 0.600255 ACCACGCCTTGTCTTCTTCG 60.600 55.000 0.00 0.00 0.00 3.79
184 186 1.375523 GTCGTGATGCCCCGAACTT 60.376 57.895 0.00 0.00 34.47 2.66
220 234 0.886490 CGCTGCTGGTTGACCTTCTT 60.886 55.000 1.34 0.00 36.82 2.52
226 240 2.036346 GCTGGTTGACCTTCTTGCAAAT 59.964 45.455 0.00 0.00 36.82 2.32
404 438 2.478894 TGAAGTCGACGCCTTGATTTTC 59.521 45.455 10.46 5.73 0.00 2.29
487 521 2.187685 CCATGGAGTGCTGCGCTA 59.812 61.111 16.70 1.38 0.00 4.26
650 1059 1.566231 GGACAAGAATCACCCATCCCT 59.434 52.381 0.00 0.00 0.00 4.20
724 1138 6.350629 AGCAAGATGCCAACTTTTCTATTT 57.649 33.333 0.00 0.00 46.52 1.40
869 1306 6.722590 TCTCACAGGTTAATTGGTAGTAGTCA 59.277 38.462 0.00 0.00 0.00 3.41
977 1418 7.648142 TGTCACTTCATTTTCTCGCTATTTTT 58.352 30.769 0.00 0.00 0.00 1.94
1088 1530 0.113776 AAGTACGAGGAGTGGGACCA 59.886 55.000 0.00 0.00 0.00 4.02
1120 1562 5.239744 CGCTATGACTACTACAATGACCTCT 59.760 44.000 0.00 0.00 0.00 3.69
1145 1593 2.908015 GGACAAGGGCTATCCGCA 59.092 61.111 0.00 0.00 41.67 5.69
1165 1613 2.738521 CGGTTCTCAGTGGCACCG 60.739 66.667 15.27 3.74 45.75 4.94
1217 1665 1.476845 GGCCGACCCCCAACAAAAAT 61.477 55.000 0.00 0.00 0.00 1.82
1318 1771 2.495669 GGGGATTTGATCTTTTCGCCAA 59.504 45.455 15.55 0.00 40.05 4.52
1372 1825 0.105039 GATACAGGAGGCCCTCAACG 59.895 60.000 13.90 2.30 42.02 4.10
1419 1872 2.758423 TGCATCTTCCTAGTTGCTACGA 59.242 45.455 8.99 0.00 44.07 3.43
1573 2028 5.410067 CATTTTACCCATTTAGCCAGTGTG 58.590 41.667 0.00 0.00 0.00 3.82
1666 2121 3.124636 GGGCGTCTGTGTAATGTTTGTAG 59.875 47.826 0.00 0.00 0.00 2.74
1751 2206 9.626045 AAACTTTTGAAACAAAGAGTGAGTAAG 57.374 29.630 0.25 0.00 0.00 2.34
1873 2337 8.029642 ACTATGGTATTTTCACACGAAGAAAG 57.970 34.615 0.00 0.00 36.45 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.733647 AGAGGAAGGGATTAACAGGATTTCT 59.266 40.000 0.00 0.00 0.00 2.52
16 17 5.042979 AGAGAAGGAGAAGAGGAAGGGATTA 60.043 44.000 0.00 0.00 0.00 1.75
73 74 0.327924 TTCCGATGCCTGGTGTTGAT 59.672 50.000 0.00 0.00 0.00 2.57
121 122 3.244105 GCAGCGCGAAGAAGACAA 58.756 55.556 12.10 0.00 0.00 3.18
184 186 1.228124 CGGTTGGGGAAAGCAGACA 60.228 57.895 0.00 0.00 35.96 3.41
220 234 2.334946 GGTCGAGCTGGCATTTGCA 61.335 57.895 7.51 0.00 44.36 4.08
226 240 1.471829 TTGAGAAGGTCGAGCTGGCA 61.472 55.000 19.39 13.44 0.00 4.92
404 438 4.774124 TCCTCTGTTCTTGCTTATCCATG 58.226 43.478 0.00 0.00 0.00 3.66
482 516 0.032267 GTCAGTAGGGATGGTAGCGC 59.968 60.000 0.00 0.00 0.00 5.92
487 521 2.930109 ACTCAGTCAGTAGGGATGGT 57.070 50.000 0.00 0.00 31.37 3.55
576 975 3.324993 ACACCTGCAACTTGTTGTTTTG 58.675 40.909 13.97 9.17 36.63 2.44
650 1059 1.401539 CGAGAGATTCGGATATGCGCA 60.402 52.381 14.96 14.96 45.54 6.09
679 1089 9.451002 TTGCTATAAGATCTAACGACTAGCTAT 57.549 33.333 0.00 0.00 33.30 2.97
869 1306 2.827921 GGTGCTCTGGGATTGAAAACAT 59.172 45.455 0.00 0.00 0.00 2.71
977 1418 1.354031 TGCTGGGCAAATAGGTCTGAA 59.646 47.619 0.00 0.00 34.76 3.02
1061 1503 3.497262 CCACTCCTCGTACTTTTTGGTTC 59.503 47.826 0.00 0.00 0.00 3.62
1088 1530 5.128205 TGTAGTAGTCATAGCGGTACACAT 58.872 41.667 0.00 0.00 0.00 3.21
1120 1562 4.329545 GCCCTTGTCCGGCTCACA 62.330 66.667 0.00 0.00 43.48 3.58
1145 1593 3.241530 TGCCACTGAGAACCGGCT 61.242 61.111 0.00 0.00 45.13 5.52
1156 1604 1.371558 GGAGTTCTTCGGTGCCACT 59.628 57.895 0.00 0.00 0.00 4.00
1158 1606 2.747686 GGGAGTTCTTCGGTGCCA 59.252 61.111 0.00 0.00 0.00 4.92
1165 1613 1.049402 CGGGGATAGGGGAGTTCTTC 58.951 60.000 0.00 0.00 0.00 2.87
1217 1665 0.969149 CACTGCACTGGACTCACCTA 59.031 55.000 0.00 0.00 39.86 3.08
1318 1771 3.121929 TCTGCTCTCCAATCTAGGGTT 57.878 47.619 0.00 0.00 0.00 4.11
1372 1825 2.094659 CATCACGCGGGACAGTGAC 61.095 63.158 16.24 0.00 45.38 3.67
1627 2082 3.068873 ACGCCCAGAGTTGCAATTTTAAA 59.931 39.130 0.59 0.00 0.00 1.52
1631 2086 0.598065 GACGCCCAGAGTTGCAATTT 59.402 50.000 0.59 0.00 0.00 1.82
1666 2121 7.862873 CCTGAACTTCCATTTTCTTTACAAGTC 59.137 37.037 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.