Multiple sequence alignment - TraesCS7B01G162800

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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 TraesCS7B01G162800 chr7B 100.000 4569 0 0 1 4569 223667228 223662660 0.000000e+00 8438
1 TraesCS7B01G162800 chr7B 98.840 862 9 1 1654 2514 358414566 358413705 0.000000e+00 1535
2 TraesCS7B01G162800 chr7B 81.273 1100 184 12 2516 3599 216675626 216676719 0.000000e+00 870
3 TraesCS7B01G162800 chr7D 99.592 1224 5 0 2516 3739 394386875 394385652 0.000000e+00 2233
4 TraesCS7B01G162800 chr7D 99.125 800 7 0 828 1627 394387671 394386872 0.000000e+00 1439
5 TraesCS7B01G162800 chr7D 96.552 841 20 6 1 836 394398361 394397525 0.000000e+00 1384
6 TraesCS7B01G162800 chr7D 81.182 1100 185 12 2516 3599 241092236 241093329 0.000000e+00 865
7 TraesCS7B01G162800 chr1A 98.611 1224 14 2 2567 3789 143283616 143282395 0.000000e+00 2163
8 TraesCS7B01G162800 chr1A 96.997 899 11 4 1619 2514 382097158 382098043 0.000000e+00 1496
9 TraesCS7B01G162800 chr1A 96.220 873 29 4 1 870 143322784 143321913 0.000000e+00 1426
10 TraesCS7B01G162800 chr1A 97.789 769 17 0 859 1627 143320526 143319758 0.000000e+00 1327
11 TraesCS7B01G162800 chr2B 94.760 897 36 10 1622 2512 175414026 175414917 0.000000e+00 1386
12 TraesCS7B01G162800 chr2B 96.296 783 28 1 3787 4569 202504600 202505381 0.000000e+00 1284
13 TraesCS7B01G162800 chr2B 92.618 867 53 10 1652 2512 42189775 42188914 0.000000e+00 1236
14 TraesCS7B01G162800 chr2B 82.759 319 42 11 3 313 458125745 458125432 5.820000e-69 272
15 TraesCS7B01G162800 chr4B 94.837 891 35 10 1629 2514 468249105 468248221 0.000000e+00 1380
16 TraesCS7B01G162800 chr4B 90.022 902 68 14 1625 2514 519821408 519820517 0.000000e+00 1147
17 TraesCS7B01G162800 chr4B 86.805 773 71 19 1760 2514 610530109 610529350 0.000000e+00 833
18 TraesCS7B01G162800 chr6B 94.822 869 36 9 1651 2514 685082103 685081239 0.000000e+00 1347
19 TraesCS7B01G162800 chr6B 93.468 888 38 7 1629 2514 701624186 701623317 0.000000e+00 1301
20 TraesCS7B01G162800 chr6B 80.343 1109 178 20 2516 3587 232740808 232739703 0.000000e+00 804
21 TraesCS7B01G162800 chr6B 76.398 1127 215 25 2516 3599 232870082 232868964 1.110000e-155 560
22 TraesCS7B01G162800 chr3B 96.547 782 27 0 3788 4569 257845943 257845162 0.000000e+00 1295
23 TraesCS7B01G162800 chr3B 95.658 783 33 1 3787 4569 198546085 198545304 0.000000e+00 1256
24 TraesCS7B01G162800 chr3B 95.658 783 32 2 3788 4569 773751945 773752726 0.000000e+00 1256
25 TraesCS7B01G162800 chr5B 96.296 783 28 1 3787 4569 629889967 629890748 0.000000e+00 1284
26 TraesCS7B01G162800 chr5B 95.530 783 34 1 3787 4569 107927915 107928696 0.000000e+00 1251
27 TraesCS7B01G162800 chr5B 91.203 898 59 12 1630 2514 8938873 8937983 0.000000e+00 1203
28 TraesCS7B01G162800 chr5B 80.343 1109 173 24 2516 3587 380322281 380323381 0.000000e+00 798
29 TraesCS7B01G162800 chr5B 77.342 1121 210 29 2516 3598 380652069 380653183 1.400000e-174 623
30 TraesCS7B01G162800 chr1B 96.296 783 28 1 3787 4569 524268581 524269362 0.000000e+00 1284
31 TraesCS7B01G162800 chr1B 96.178 785 26 4 3788 4569 26839807 26840590 0.000000e+00 1280
32 TraesCS7B01G162800 chr1B 95.918 784 30 2 3788 4569 328144891 328145674 0.000000e+00 1269
33 TraesCS7B01G162800 chr7A 81.182 1100 185 12 2516 3599 257363444 257362351 0.000000e+00 865
34 TraesCS7B01G162800 chr2D 82.759 319 43 9 3 313 386822341 386822027 1.620000e-69 274


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 TraesCS7B01G162800 chr7B 223662660 223667228 4568 True 8438.0 8438 100.0000 1 4569 1 chr7B.!!$R1 4568
1 TraesCS7B01G162800 chr7B 358413705 358414566 861 True 1535.0 1535 98.8400 1654 2514 1 chr7B.!!$R2 860
2 TraesCS7B01G162800 chr7B 216675626 216676719 1093 False 870.0 870 81.2730 2516 3599 1 chr7B.!!$F1 1083
3 TraesCS7B01G162800 chr7D 394385652 394387671 2019 True 1836.0 2233 99.3585 828 3739 2 chr7D.!!$R2 2911
4 TraesCS7B01G162800 chr7D 394397525 394398361 836 True 1384.0 1384 96.5520 1 836 1 chr7D.!!$R1 835
5 TraesCS7B01G162800 chr7D 241092236 241093329 1093 False 865.0 865 81.1820 2516 3599 1 chr7D.!!$F1 1083
6 TraesCS7B01G162800 chr1A 143282395 143283616 1221 True 2163.0 2163 98.6110 2567 3789 1 chr1A.!!$R1 1222
7 TraesCS7B01G162800 chr1A 382097158 382098043 885 False 1496.0 1496 96.9970 1619 2514 1 chr1A.!!$F1 895
8 TraesCS7B01G162800 chr1A 143319758 143322784 3026 True 1376.5 1426 97.0045 1 1627 2 chr1A.!!$R2 1626
9 TraesCS7B01G162800 chr2B 175414026 175414917 891 False 1386.0 1386 94.7600 1622 2512 1 chr2B.!!$F1 890
10 TraesCS7B01G162800 chr2B 202504600 202505381 781 False 1284.0 1284 96.2960 3787 4569 1 chr2B.!!$F2 782
11 TraesCS7B01G162800 chr2B 42188914 42189775 861 True 1236.0 1236 92.6180 1652 2512 1 chr2B.!!$R1 860
12 TraesCS7B01G162800 chr4B 468248221 468249105 884 True 1380.0 1380 94.8370 1629 2514 1 chr4B.!!$R1 885
13 TraesCS7B01G162800 chr4B 519820517 519821408 891 True 1147.0 1147 90.0220 1625 2514 1 chr4B.!!$R2 889
14 TraesCS7B01G162800 chr4B 610529350 610530109 759 True 833.0 833 86.8050 1760 2514 1 chr4B.!!$R3 754
15 TraesCS7B01G162800 chr6B 685081239 685082103 864 True 1347.0 1347 94.8220 1651 2514 1 chr6B.!!$R3 863
16 TraesCS7B01G162800 chr6B 701623317 701624186 869 True 1301.0 1301 93.4680 1629 2514 1 chr6B.!!$R4 885
17 TraesCS7B01G162800 chr6B 232739703 232740808 1105 True 804.0 804 80.3430 2516 3587 1 chr6B.!!$R1 1071
18 TraesCS7B01G162800 chr6B 232868964 232870082 1118 True 560.0 560 76.3980 2516 3599 1 chr6B.!!$R2 1083
19 TraesCS7B01G162800 chr3B 257845162 257845943 781 True 1295.0 1295 96.5470 3788 4569 1 chr3B.!!$R2 781
20 TraesCS7B01G162800 chr3B 198545304 198546085 781 True 1256.0 1256 95.6580 3787 4569 1 chr3B.!!$R1 782
21 TraesCS7B01G162800 chr3B 773751945 773752726 781 False 1256.0 1256 95.6580 3788 4569 1 chr3B.!!$F1 781
22 TraesCS7B01G162800 chr5B 629889967 629890748 781 False 1284.0 1284 96.2960 3787 4569 1 chr5B.!!$F4 782
23 TraesCS7B01G162800 chr5B 107927915 107928696 781 False 1251.0 1251 95.5300 3787 4569 1 chr5B.!!$F1 782
24 TraesCS7B01G162800 chr5B 8937983 8938873 890 True 1203.0 1203 91.2030 1630 2514 1 chr5B.!!$R1 884
25 TraesCS7B01G162800 chr5B 380322281 380323381 1100 False 798.0 798 80.3430 2516 3587 1 chr5B.!!$F2 1071
26 TraesCS7B01G162800 chr5B 380652069 380653183 1114 False 623.0 623 77.3420 2516 3598 1 chr5B.!!$F3 1082
27 TraesCS7B01G162800 chr1B 524268581 524269362 781 False 1284.0 1284 96.2960 3787 4569 1 chr1B.!!$F3 782
28 TraesCS7B01G162800 chr1B 26839807 26840590 783 False 1280.0 1280 96.1780 3788 4569 1 chr1B.!!$F1 781
29 TraesCS7B01G162800 chr1B 328144891 328145674 783 False 1269.0 1269 95.9180 3788 4569 1 chr1B.!!$F2 781
30 TraesCS7B01G162800 chr7A 257362351 257363444 1093 True 865.0 865 81.1820 2516 3599 1 chr7A.!!$R1 1083

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
273 274 0.108329 ATCGTACGTTTGCTCCCCTG 60.108 55.000 16.05 0.00 0.00 4.45 F
488 489 0.661552 CGAGATTCGGTAGCGGAGAA 59.338 55.000 15.23 1.62 36.00 2.87 F
600 605 0.811281 GATTTTTCCTGCTCACCGGG 59.189 55.000 6.32 0.00 41.74 5.73 F
1614 3021 1.065854 CAAGCCCGATTTCTCCTCTGT 60.066 52.381 0.00 0.00 0.00 3.41 F
2514 3975 0.958091 GCATGCTACCAAACACACCA 59.042 50.000 11.37 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 3030 0.591170 CCCTACCAAACACACGCTTG 59.409 55.000 0.00 0.0 0.00 4.01 R
1627 3034 0.816018 TGCACCCTACCAAACACACG 60.816 55.000 0.00 0.0 0.00 4.49 R
2514 3975 3.125607 TCGTGAGCGACCACTTGT 58.874 55.556 6.15 0.0 42.81 3.16 R
3218 4697 2.289694 ACTTAGCAGCTTCAATCCGTGT 60.290 45.455 0.00 0.0 0.00 4.49 R
4406 5911 0.176680 AGTAGCCTTGCAGACGATGG 59.823 55.000 0.00 0.0 0.00 3.51 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
85 86 2.686816 CCGAACGCACAATCCACCC 61.687 63.158 0.00 0.00 0.00 4.61
112 113 2.158415 CCCCATAGCCATCATCAACCTT 60.158 50.000 0.00 0.00 0.00 3.50
125 126 2.542907 AACCTTGTGCCAAGTCGCG 61.543 57.895 0.00 0.00 0.00 5.87
178 179 1.497286 TCAAACAAGCAGGGGTAGGTT 59.503 47.619 0.00 0.00 0.00 3.50
215 216 1.340697 GGCCGAACCTGGGTAAATCTT 60.341 52.381 0.00 0.00 34.51 2.40
273 274 0.108329 ATCGTACGTTTGCTCCCCTG 60.108 55.000 16.05 0.00 0.00 4.45
338 339 3.929948 GAGCTTTGCGCCGGATCG 61.930 66.667 5.05 0.00 40.39 3.69
408 409 2.301009 AGGTACGAAACGAGGTGGAAAT 59.699 45.455 0.00 0.00 0.00 2.17
488 489 0.661552 CGAGATTCGGTAGCGGAGAA 59.338 55.000 15.23 1.62 36.00 2.87
600 605 0.811281 GATTTTTCCTGCTCACCGGG 59.189 55.000 6.32 0.00 41.74 5.73
801 808 5.941647 CGTAACAGATTTCCCTTTCCCTTAA 59.058 40.000 0.00 0.00 0.00 1.85
805 812 7.303182 ACAGATTTCCCTTTCCCTTAAAAAG 57.697 36.000 0.00 0.00 34.25 2.27
1614 3021 1.065854 CAAGCCCGATTTCTCCTCTGT 60.066 52.381 0.00 0.00 0.00 3.41
1623 3030 2.125350 CTCCTCTGTTGCGCCTCC 60.125 66.667 4.18 0.00 0.00 4.30
1627 3034 2.669569 TCTGTTGCGCCTCCAAGC 60.670 61.111 4.18 0.00 0.00 4.01
2514 3975 0.958091 GCATGCTACCAAACACACCA 59.042 50.000 11.37 0.00 0.00 4.17
2760 4221 1.614317 CCTTCAGTTAAGTGCCCCCAG 60.614 57.143 5.35 0.00 32.89 4.45
3218 4697 3.529341 TTGCAGAAGCGGAGGCGAA 62.529 57.895 0.00 0.00 46.23 4.70
3393 4894 6.538021 AGACGAAATGAAAAGGATCATCTGAG 59.462 38.462 0.00 0.00 39.08 3.35
3760 5262 2.747396 TTTACTATGTTCACCGCCGT 57.253 45.000 0.00 0.00 0.00 5.68
3761 5263 1.999048 TTACTATGTTCACCGCCGTG 58.001 50.000 0.00 0.00 41.72 4.94
3841 5343 4.783667 AAAAACGGCCTAGTCGCA 57.216 50.000 0.00 0.00 32.11 5.10
3851 5353 1.762460 CTAGTCGCACCCCCAGGAT 60.762 63.158 0.00 0.00 36.73 3.24
3853 5355 2.815684 TAGTCGCACCCCCAGGATGT 62.816 60.000 0.00 0.00 36.73 3.06
4078 5581 1.611148 CGGCCTACTCCGCTAGATAGT 60.611 57.143 0.00 0.00 43.18 2.12
4104 5607 0.742990 CCGCCGGAAAATAGCAGTGA 60.743 55.000 5.05 0.00 0.00 3.41
4406 5911 0.318699 GGGTGAAAGCAAAGAACCGC 60.319 55.000 0.00 0.00 34.77 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 2.030027 TGATGGCTATGGGGGACTAG 57.970 55.000 0.00 0.00 0.00 2.57
112 113 2.355837 GAGACGCGACTTGGCACA 60.356 61.111 15.93 0.00 0.00 4.57
125 126 3.804873 GGAGATGATTACAAAGGCGAGAC 59.195 47.826 0.00 0.00 0.00 3.36
215 216 0.842030 ATCAGGCAAGACAGGGACCA 60.842 55.000 0.00 0.00 0.00 4.02
273 274 6.477360 GCTTGAGTAGCTAGGATTTTCTGTAC 59.523 42.308 0.00 0.00 46.77 2.90
488 489 1.145119 AGTTCTTCTTTTCCCCGCCTT 59.855 47.619 0.00 0.00 0.00 4.35
552 554 1.962807 TGCCCCATCTGTTCAGTTTTG 59.037 47.619 0.00 0.00 0.00 2.44
801 808 6.613679 TGGGGAATCTGTTAGGTTTTTCTTTT 59.386 34.615 0.00 0.00 0.00 2.27
805 812 7.898014 ATATGGGGAATCTGTTAGGTTTTTC 57.102 36.000 0.00 0.00 0.00 2.29
1623 3030 0.591170 CCCTACCAAACACACGCTTG 59.409 55.000 0.00 0.00 0.00 4.01
1627 3034 0.816018 TGCACCCTACCAAACACACG 60.816 55.000 0.00 0.00 0.00 4.49
2514 3975 3.125607 TCGTGAGCGACCACTTGT 58.874 55.556 6.15 0.00 42.81 3.16
2786 4247 3.991051 CGACTGGCCGGACTGTGT 61.991 66.667 26.31 12.96 0.00 3.72
3218 4697 2.289694 ACTTAGCAGCTTCAATCCGTGT 60.290 45.455 0.00 0.00 0.00 4.49
3393 4894 3.311048 GTCCGGAGCATTTGAAATCTCTC 59.689 47.826 3.06 10.66 0.00 3.20
3760 5262 6.557253 AGGCACTATGGTAGGATAAATACACA 59.443 38.462 0.00 0.00 36.02 3.72
3761 5263 7.005709 AGGCACTATGGTAGGATAAATACAC 57.994 40.000 0.00 0.00 36.02 2.90
3834 5336 2.063979 CATCCTGGGGGTGCGACTA 61.064 63.158 0.00 0.00 0.00 2.59
3841 5343 0.999712 ATTTTCGACATCCTGGGGGT 59.000 50.000 0.00 0.00 0.00 4.95
3853 5355 2.095847 CCGAACCGGCGATTTTCGA 61.096 57.895 27.84 0.00 43.83 3.71
4211 5716 1.407979 ACCGAGTCAGTCAAAACGTCT 59.592 47.619 0.00 0.00 0.00 4.18
4406 5911 0.176680 AGTAGCCTTGCAGACGATGG 59.823 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.