Multiple sequence alignment - TraesCS3A01G238900

Loading Multiple Alignment...

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 TraesCS3A01G238900 chr3A 100.000 3542 0 0 1 3542 447278399 447274858 0.000000e+00 6541
1 TraesCS3A01G238900 chr3A 98.220 2640 22 5 905 3542 408949508 408946892 0.000000e+00 4591
2 TraesCS3A01G238900 chr3A 94.389 909 47 3 1 909 408950716 408949812 0.000000e+00 1393
3 TraesCS3A01G238900 chr3A 91.818 660 51 3 1 659 447287270 447286613 0.000000e+00 917
4 TraesCS3A01G238900 chr3A 91.667 660 51 4 1 659 430932936 430932280 0.000000e+00 911
5 TraesCS3A01G238900 chr3A 82.386 176 29 2 660 835 589544406 589544233 6.120000e-33 152
6 TraesCS3A01G238900 chr3D 95.135 2179 68 13 833 2992 317550882 317553041 0.000000e+00 3402
7 TraesCS3A01G238900 chr3D 97.236 398 8 1 3040 3437 317553039 317553433 0.000000e+00 671
8 TraesCS3A01G238900 chr3B 94.667 2119 66 15 834 2931 401413836 401411744 0.000000e+00 3243
9 TraesCS3A01G238900 chr3B 96.605 324 8 1 2922 3245 401411473 401411153 5.200000e-148 534
10 TraesCS3A01G238900 chr3B 98.485 198 3 0 3240 3437 401411043 401410846 2.020000e-92 350
11 TraesCS3A01G238900 chr3B 94.340 106 4 2 3434 3538 12406770 12406666 1.020000e-35 161
12 TraesCS3A01G238900 chr3B 93.519 108 5 2 3429 3535 220754733 220754839 3.660000e-35 159
13 TraesCS3A01G238900 chr3B 92.593 108 6 2 3429 3535 219440235 219440341 1.700000e-33 154
14 TraesCS3A01G238900 chr7A 92.868 659 45 2 1 659 251159707 251159051 0.000000e+00 955
15 TraesCS3A01G238900 chr7A 91.047 659 55 3 1 659 388684435 388683781 0.000000e+00 887
16 TraesCS3A01G238900 chr7A 90.512 664 56 5 1 659 208610163 208609502 0.000000e+00 870
17 TraesCS3A01G238900 chr2A 90.909 660 57 3 1 659 223500798 223501455 0.000000e+00 883
18 TraesCS3A01G238900 chr1A 90.526 665 57 2 1 660 230571446 230572109 0.000000e+00 874
19 TraesCS3A01G238900 chr4A 90.469 661 59 4 1 659 524824047 524824705 0.000000e+00 869
20 TraesCS3A01G238900 chr4B 85.321 436 52 8 1005 1430 825924 825491 1.170000e-119 440
21 TraesCS3A01G238900 chr4B 75.296 846 183 20 1551 2383 825411 824579 7.180000e-102 381
22 TraesCS3A01G238900 chr4D 85.417 432 48 9 1005 1429 1197805 1198228 5.430000e-118 435
23 TraesCS3A01G238900 chr4D 75.750 833 178 20 1545 2365 1198323 1199143 7.120000e-107 398
24 TraesCS3A01G238900 chr4D 94.175 103 5 1 3433 3534 213702959 213702857 4.730000e-34 156
25 TraesCS3A01G238900 chr1D 95.098 102 4 1 3433 3533 12070095 12070196 3.660000e-35 159
26 TraesCS3A01G238900 chr6B 95.050 101 4 1 3436 3535 633054114 633054014 1.320000e-34 158
27 TraesCS3A01G238900 chr6B 94.175 103 5 1 3435 3536 475446752 475446854 4.730000e-34 156
28 TraesCS3A01G238900 chr2B 93.458 107 5 2 3430 3535 683271070 683270965 1.320000e-34 158


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 TraesCS3A01G238900 chr3A 447274858 447278399 3541 True 6541.000000 6541 100.000000 1 3542 1 chr3A.!!$R2 3541
1 TraesCS3A01G238900 chr3A 408946892 408950716 3824 True 2992.000000 4591 96.304500 1 3542 2 chr3A.!!$R5 3541
2 TraesCS3A01G238900 chr3A 447286613 447287270 657 True 917.000000 917 91.818000 1 659 1 chr3A.!!$R3 658
3 TraesCS3A01G238900 chr3A 430932280 430932936 656 True 911.000000 911 91.667000 1 659 1 chr3A.!!$R1 658
4 TraesCS3A01G238900 chr3D 317550882 317553433 2551 False 2036.500000 3402 96.185500 833 3437 2 chr3D.!!$F1 2604
5 TraesCS3A01G238900 chr3B 401410846 401413836 2990 True 1375.666667 3243 96.585667 834 3437 3 chr3B.!!$R2 2603
6 TraesCS3A01G238900 chr7A 251159051 251159707 656 True 955.000000 955 92.868000 1 659 1 chr7A.!!$R2 658
7 TraesCS3A01G238900 chr7A 388683781 388684435 654 True 887.000000 887 91.047000 1 659 1 chr7A.!!$R3 658
8 TraesCS3A01G238900 chr7A 208609502 208610163 661 True 870.000000 870 90.512000 1 659 1 chr7A.!!$R1 658
9 TraesCS3A01G238900 chr2A 223500798 223501455 657 False 883.000000 883 90.909000 1 659 1 chr2A.!!$F1 658
10 TraesCS3A01G238900 chr1A 230571446 230572109 663 False 874.000000 874 90.526000 1 660 1 chr1A.!!$F1 659
11 TraesCS3A01G238900 chr4A 524824047 524824705 658 False 869.000000 869 90.469000 1 659 1 chr4A.!!$F1 658
12 TraesCS3A01G238900 chr4B 824579 825924 1345 True 410.500000 440 80.308500 1005 2383 2 chr4B.!!$R1 1378
13 TraesCS3A01G238900 chr4D 1197805 1199143 1338 False 416.500000 435 80.583500 1005 2365 2 chr4D.!!$F1 1360

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
743 754 0.398522 TGAGTGGTGTGTGTCCCTCT 60.399 55.0 0.00 0.00 0.00 3.69 F
1130 1449 0.248134 GTCTCGGTCGACTTCATCCG 60.248 60.0 16.46 9.63 43.65 4.18 F
2289 2647 0.522626 TCGTTGCGTCGGTGATCTAA 59.477 50.0 0.00 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 2597 0.858583 TCGTTGAGCGTGAACACATG 59.141 50.0 5.80 0.00 42.13 3.21 R
2372 2730 2.000429 CAAAGCATACTTGGCAAGCC 58.000 50.0 26.45 12.53 35.85 4.35 R
3520 4273 4.676799 CCTGGTCTATATACTCCCTCCA 57.323 50.0 0.00 0.00 0.00 3.86 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
76 77 5.003804 GCAGTATCCTTGTTTCCTCTTTGA 58.996 41.667 0.00 0.00 0.00 2.69
152 154 1.896220 ATCAGTGCAACACGACCAAT 58.104 45.000 0.00 0.00 41.43 3.16
211 213 3.296709 GACGGCGTCACCACCAGAT 62.297 63.158 33.07 0.00 39.03 2.90
237 239 1.519408 GCAGGCGAAGACCACTTTTA 58.481 50.000 0.00 0.00 31.70 1.52
242 244 2.613691 GCGAAGACCACTTTTATCCGA 58.386 47.619 0.00 0.00 36.39 4.55
318 321 4.392940 CGCTCAATATTTGGGAAGAGGAT 58.607 43.478 0.00 0.00 30.85 3.24
427 437 1.374758 CCTCGCGAGGCTGTTCTTT 60.375 57.895 39.83 0.00 42.44 2.52
571 582 2.957006 GAGTTAGGCCCTGAGATCGTAA 59.043 50.000 0.00 0.00 0.00 3.18
687 698 1.405821 CGGTGTCGGAGCTTTAGATCT 59.594 52.381 0.00 0.00 0.00 2.75
696 707 6.020520 GTCGGAGCTTTAGATCTTTTTACGAG 60.021 42.308 0.00 0.00 0.00 4.18
698 709 6.697892 CGGAGCTTTAGATCTTTTTACGAGAT 59.302 38.462 0.00 0.00 36.60 2.75
736 747 8.633561 TCTTCTAAGATATATGAGTGGTGTGTG 58.366 37.037 0.00 0.00 0.00 3.82
743 754 0.398522 TGAGTGGTGTGTGTCCCTCT 60.399 55.000 0.00 0.00 0.00 3.69
747 758 0.686789 TGGTGTGTGTCCCTCTGATG 59.313 55.000 0.00 0.00 0.00 3.07
757 768 5.705441 TGTGTCCCTCTGATGTTTTATTCAC 59.295 40.000 0.00 0.00 0.00 3.18
792 803 6.327279 ACTTTTGTACATAAACTTCTGCCC 57.673 37.500 0.00 0.00 0.00 5.36
798 809 6.582636 TGTACATAAACTTCTGCCCTCTATG 58.417 40.000 0.00 0.00 0.00 2.23
806 817 2.972625 TCTGCCCTCTATGAAACAACG 58.027 47.619 0.00 0.00 0.00 4.10
812 823 4.766375 CCCTCTATGAAACAACGGTATGT 58.234 43.478 0.00 0.00 34.24 2.29
827 838 4.114073 CGGTATGTCATTGGCGTACTTAA 58.886 43.478 17.64 0.00 0.00 1.85
828 839 4.567558 CGGTATGTCATTGGCGTACTTAAA 59.432 41.667 17.64 0.00 0.00 1.52
1130 1449 0.248134 GTCTCGGTCGACTTCATCCG 60.248 60.000 16.46 9.63 43.65 4.18
1384 1712 2.849646 AGCTTATCCCCCGCCCTC 60.850 66.667 0.00 0.00 0.00 4.30
1484 1833 7.282585 TCGATCCAATCCAACATAAGAGAAAT 58.717 34.615 0.00 0.00 0.00 2.17
1563 1918 4.718858 TTTGTAGGTCACGAAATTCACG 57.281 40.909 0.00 3.96 0.00 4.35
2289 2647 0.522626 TCGTTGCGTCGGTGATCTAA 59.477 50.000 0.00 0.00 0.00 2.10
2385 2743 1.449601 CGACGGGCTTGCCAAGTAT 60.450 57.895 14.04 0.00 0.00 2.12
2390 2748 0.897621 GGGCTTGCCAAGTATGCTTT 59.102 50.000 14.04 0.00 31.49 3.51
2651 3009 4.812626 GGGCAATTCCATTCATGATTTCAC 59.187 41.667 0.00 0.00 36.21 3.18
3520 4273 8.193953 ACAAATTGAGTCACTTATTTTGGGAT 57.806 30.769 16.81 0.00 30.25 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.418083 GCGCTTGCCCCTTTAGCAT 61.418 57.895 0.00 0.00 40.59 3.79
152 154 0.601558 GTCTTGTCGTCCTGCTGGTA 59.398 55.000 9.73 0.00 34.23 3.25
179 181 4.436998 CGTCCTGGGCTCCACGAC 62.437 72.222 0.00 10.97 36.62 4.34
211 213 2.927856 TCTTCGCCTGCCAAGGGA 60.928 61.111 0.00 0.00 44.67 4.20
237 239 6.321690 AGACAACTAGTACAAGCTATTCGGAT 59.678 38.462 0.00 0.00 0.00 4.18
242 244 5.958987 AGGGAGACAACTAGTACAAGCTATT 59.041 40.000 0.00 0.00 0.00 1.73
318 321 5.405063 AGTTCTACTTATAGAGGCCCTGA 57.595 43.478 0.00 0.00 38.69 3.86
427 437 2.557056 CTGAGGACGAACAGTACAAGGA 59.443 50.000 0.00 0.00 35.65 3.36
571 582 1.431440 CTCTCTAGCTCGCGCACTT 59.569 57.895 8.75 0.00 39.10 3.16
591 602 1.315981 TGCGCACGAAGATCTCTCCT 61.316 55.000 5.66 0.00 0.00 3.69
666 677 0.179108 ATCTAAAGCTCCGACACCGC 60.179 55.000 0.00 0.00 0.00 5.68
687 698 8.517062 AGACTTAGCCTACTATCTCGTAAAAA 57.483 34.615 0.00 0.00 0.00 1.94
721 732 2.501723 GAGGGACACACACCACTCATAT 59.498 50.000 0.00 0.00 0.00 1.78
724 735 0.398522 AGAGGGACACACACCACTCA 60.399 55.000 0.00 0.00 31.75 3.41
747 758 8.782533 AAGTTCGAACAAGATGTGAATAAAAC 57.217 30.769 28.78 0.00 0.00 2.43
757 768 9.658475 TTTATGTACAAAAGTTCGAACAAGATG 57.342 29.630 28.78 21.76 0.00 2.90
768 779 6.549736 AGGGCAGAAGTTTATGTACAAAAGTT 59.450 34.615 16.60 16.60 33.30 2.66
792 803 7.401860 CAATGACATACCGTTGTTTCATAGAG 58.598 38.462 0.00 0.00 0.00 2.43
798 809 3.498082 GCCAATGACATACCGTTGTTTC 58.502 45.455 0.00 0.00 32.61 2.78
806 817 6.425577 TTTTAAGTACGCCAATGACATACC 57.574 37.500 0.00 0.00 0.00 2.73
972 1291 0.614697 GGGTTGGTGGGGGAAATCAG 60.615 60.000 0.00 0.00 0.00 2.90
1484 1833 1.642037 CGTCGCTCGTCTGGGTCTTA 61.642 60.000 0.00 0.00 34.52 2.10
1662 2017 3.797353 ACTGATGGCGCCGGGAAT 61.797 61.111 23.90 9.73 0.00 3.01
1845 2200 4.353437 ACCGCGTCGAAGGTGGAC 62.353 66.667 20.57 0.00 39.66 4.02
2095 2453 2.701951 AGTCCGTGAACCTCACCTTAAA 59.298 45.455 1.34 0.00 44.20 1.52
2239 2597 0.858583 TCGTTGAGCGTGAACACATG 59.141 50.000 5.80 0.00 42.13 3.21
2372 2730 2.000429 CAAAGCATACTTGGCAAGCC 58.000 50.000 26.45 12.53 35.85 4.35
3153 3791 8.954350 GCAGGATAATGCTATCAACAGATTATT 58.046 33.333 0.00 0.00 43.07 1.40
3154 3792 7.555554 GGCAGGATAATGCTATCAACAGATTAT 59.444 37.037 0.00 0.00 45.75 1.28
3520 4273 4.676799 CCTGGTCTATATACTCCCTCCA 57.323 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.