Multiple sequence alignment - TraesCS3B01G564700

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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 TraesCS3B01G564700 chr3B 100.000 2594 0 0 1 2594 797592970 797590377 0 4791
1 TraesCS3B01G564700 chr5A 97.657 2603 51 4 1 2594 19248880 19246279 0 4460
2 TraesCS3B01G564700 chr5A 97.116 2601 67 4 1 2594 238822843 238820244 0 4381
3 TraesCS3B01G564700 chr7D 97.540 2602 55 4 1 2594 381923965 381926565 0 4442
4 TraesCS3B01G564700 chr7D 97.502 2602 56 4 1 2594 203499963 203502563 0 4436
5 TraesCS3B01G564700 chr7D 97.426 2603 57 4 1 2594 382050042 382052643 0 4427
6 TraesCS3B01G564700 chr7A 97.536 2597 60 3 1 2594 60279277 60281872 0 4438
7 TraesCS3B01G564700 chr1A 97.536 2597 60 3 1 2594 498691263 498688668 0 4438
8 TraesCS3B01G564700 chr7B 97.497 2597 60 4 1 2594 716878816 716876222 0 4431
9 TraesCS3B01G564700 chr7B 97.420 2597 63 3 1 2594 742989410 742992005 0 4421


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 TraesCS3B01G564700 chr3B 797590377 797592970 2593 True 4791 4791 100.000 1 2594 1 chr3B.!!$R1 2593
1 TraesCS3B01G564700 chr5A 19246279 19248880 2601 True 4460 4460 97.657 1 2594 1 chr5A.!!$R1 2593
2 TraesCS3B01G564700 chr5A 238820244 238822843 2599 True 4381 4381 97.116 1 2594 1 chr5A.!!$R2 2593
3 TraesCS3B01G564700 chr7D 381923965 381926565 2600 False 4442 4442 97.540 1 2594 1 chr7D.!!$F2 2593
4 TraesCS3B01G564700 chr7D 203499963 203502563 2600 False 4436 4436 97.502 1 2594 1 chr7D.!!$F1 2593
5 TraesCS3B01G564700 chr7D 382050042 382052643 2601 False 4427 4427 97.426 1 2594 1 chr7D.!!$F3 2593
6 TraesCS3B01G564700 chr7A 60279277 60281872 2595 False 4438 4438 97.536 1 2594 1 chr7A.!!$F1 2593
7 TraesCS3B01G564700 chr1A 498688668 498691263 2595 True 4438 4438 97.536 1 2594 1 chr1A.!!$R1 2593
8 TraesCS3B01G564700 chr7B 716876222 716878816 2594 True 4431 4431 97.497 1 2594 1 chr7B.!!$R1 2593
9 TraesCS3B01G564700 chr7B 742989410 742992005 2595 False 4421 4421 97.420 1 2594 1 chr7B.!!$F1 2593

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
551 556 1.068264 CAAAAAGGAAGAAGGCCGAGC 60.068 52.381 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 2445 1.361543 ACTGGACAGGGGTAAGCTCTA 59.638 52.381 4.14 0.0 0.0 2.43 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
52 53 1.854939 AGCCCTGAATGGATTGGATCA 59.145 47.619 0.00 0.00 38.35 2.92
64 65 6.005066 TGGATTGGATCATTTCTGCTTCTA 57.995 37.500 0.00 0.00 0.00 2.10
74 75 5.529430 TCATTTCTGCTTCTACCAACGAAAA 59.471 36.000 0.00 0.00 0.00 2.29
307 308 1.289160 TGTAATCCCTGCAGCTTCCT 58.711 50.000 8.66 0.00 0.00 3.36
496 501 6.362248 GGATATTAGCTGGGTAAGGAAAACA 58.638 40.000 0.00 0.00 0.00 2.83
532 537 7.200778 TGAGATGTCGATTTGTTTTTCATCA 57.799 32.000 8.87 0.00 34.55 3.07
551 556 1.068264 CAAAAAGGAAGAAGGCCGAGC 60.068 52.381 0.00 0.00 0.00 5.03
660 665 1.282157 GAAAGGGGTCCATGTAGCTGT 59.718 52.381 0.00 0.00 0.00 4.40
693 698 1.153369 GAGCAGCAGGTTCGGCATA 60.153 57.895 0.00 0.00 0.00 3.14
702 707 4.040461 AGCAGGTTCGGCATATACTACAAT 59.960 41.667 0.00 0.00 0.00 2.71
777 782 1.587547 GAGAGCGGACCAAATGGATC 58.412 55.000 6.42 0.30 38.94 3.36
813 818 2.957006 AGAGTGGAGTTACGTGAACAGT 59.043 45.455 0.00 0.00 40.86 3.55
819 824 3.187227 GGAGTTACGTGAACAGTCGTCTA 59.813 47.826 0.00 0.00 40.86 2.59
831 836 6.485313 TGAACAGTCGTCTAATGGAAAACAAT 59.515 34.615 0.00 0.00 0.00 2.71
832 837 6.241207 ACAGTCGTCTAATGGAAAACAATG 57.759 37.500 0.00 0.00 0.00 2.82
980 986 1.324005 CCCTCTCCCTCGGACTCAAC 61.324 65.000 0.00 0.00 0.00 3.18
1132 1138 5.632902 GCTTCCTATGGGGGTACATTACAAA 60.633 44.000 0.00 0.00 35.33 2.83
1455 1461 4.506288 TCCATTACAATGTTCTCATACGCG 59.494 41.667 3.53 3.53 34.60 6.01
1517 1523 1.338655 GTTCTTTGCCGCTTTGGGTTA 59.661 47.619 0.00 0.00 38.63 2.85
1568 1574 5.678583 AGTAGTGACTAGCGTTATAGGTCA 58.321 41.667 0.00 0.00 32.65 4.02
1574 1580 3.965347 ACTAGCGTTATAGGTCATTGGGT 59.035 43.478 0.00 0.00 0.00 4.51
1832 1838 0.179233 CTGCGCGCGATCGTATACTA 60.179 55.000 37.18 2.45 38.14 1.82
1858 1864 1.302993 CCCCGTCGGTTGTTGGAAT 60.303 57.895 11.06 0.00 0.00 3.01
2091 2097 0.811281 GGAAGGGGCACGAAGAAATG 59.189 55.000 0.00 0.00 0.00 2.32
2342 2348 1.141657 GCTGTAATGGATGGCAGAGGA 59.858 52.381 0.00 0.00 0.00 3.71
2434 2445 4.943705 CCACACTTGGCTCTACACATTTAT 59.056 41.667 0.00 0.00 35.56 1.40
2504 2515 2.361438 GTCGACTCGTTATCCCCATCTT 59.639 50.000 8.70 0.00 0.00 2.40
2555 2566 1.413808 GGGGAGAGAGTGGAGCCTATT 60.414 57.143 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.205821 AGCAGAAATGATCCAATCCATTCA 58.794 37.500 0.00 0.00 32.36 2.57
52 53 5.763204 TCTTTTCGTTGGTAGAAGCAGAAAT 59.237 36.000 0.00 0.00 0.00 2.17
64 65 1.605753 GAGGCCTTCTTTTCGTTGGT 58.394 50.000 6.77 0.00 0.00 3.67
204 205 2.124507 CTTTCTTCCTCCCGTGCCCA 62.125 60.000 0.00 0.00 0.00 5.36
209 210 2.288886 CGACTTTCTTTCTTCCTCCCGT 60.289 50.000 0.00 0.00 0.00 5.28
344 349 1.381867 AACATGATTGGAGGGGTCCA 58.618 50.000 0.00 0.00 38.14 4.02
496 501 3.444034 TCGACATCTCAATCTCCGAAAGT 59.556 43.478 0.00 0.00 0.00 2.66
532 537 1.248486 GCTCGGCCTTCTTCCTTTTT 58.752 50.000 0.00 0.00 0.00 1.94
551 556 0.598680 CGAAGGAAGGCTGCTATCCG 60.599 60.000 15.21 4.21 38.31 4.18
585 590 4.272748 AGCCGGAATTCTTTATTAGAACGC 59.727 41.667 5.05 0.00 45.33 4.84
623 628 4.039124 CCCTTTCTTTATGTTGTTGCCAGT 59.961 41.667 0.00 0.00 0.00 4.00
660 665 4.641645 CTCAGTGGGCGGGCACAA 62.642 66.667 0.00 0.00 0.00 3.33
693 698 9.647918 TGAAGTGGATTCTCTCTATTGTAGTAT 57.352 33.333 0.00 0.00 38.83 2.12
702 707 7.068839 GTGGTTATCTGAAGTGGATTCTCTCTA 59.931 40.741 0.00 0.00 38.83 2.43
777 782 3.574396 TCCACTCTCGGCTTGGATTATAG 59.426 47.826 0.00 0.00 34.35 1.31
813 818 6.869315 TGAACATTGTTTTCCATTAGACGA 57.131 33.333 3.08 0.00 0.00 4.20
819 824 5.695816 CCGAACATGAACATTGTTTTCCATT 59.304 36.000 0.00 0.00 0.00 3.16
831 836 3.653344 CTCTCTGAACCGAACATGAACA 58.347 45.455 0.00 0.00 0.00 3.18
832 837 2.413453 GCTCTCTGAACCGAACATGAAC 59.587 50.000 0.00 0.00 0.00 3.18
980 986 8.310382 CCCACATATATAGAGTCAAAAGAGAGG 58.690 40.741 0.00 0.00 0.00 3.69
1036 1042 1.347707 AGAAAGGAATGCTGTCACCGA 59.652 47.619 0.00 0.00 0.00 4.69
1132 1138 7.186021 CAATGCTGCAGAAAAAGAAGATTTT 57.814 32.000 20.43 0.00 35.29 1.82
1503 1509 1.680651 CCCATAACCCAAAGCGGCA 60.681 57.895 1.45 0.00 0.00 5.69
1537 1543 2.613133 CGCTAGTCACTACTCCCACTAC 59.387 54.545 0.00 0.00 37.15 2.73
1568 1574 2.380571 AAACCTTCCGGCCACCCAAT 62.381 55.000 2.24 0.00 0.00 3.16
1970 1976 2.158445 TCCCAACGAAAATGGAAAGGGA 60.158 45.455 0.00 0.00 40.56 4.20
2091 2097 1.611936 GCTTCTCCCCCACACTTCTTC 60.612 57.143 0.00 0.00 0.00 2.87
2252 2258 7.656412 TCAAAGGTTTCATGAAATCGAAATCA 58.344 30.769 23.05 6.04 36.56 2.57
2302 2308 1.741770 GAGCCGTTTCATGAGCGGT 60.742 57.895 29.00 20.47 46.41 5.68
2326 2332 2.705148 TGGATCCTCTGCCATCCATTA 58.295 47.619 14.23 0.00 43.11 1.90
2342 2348 2.365617 CAGTGCTTCGGGTACTATGGAT 59.634 50.000 0.00 0.00 38.80 3.41
2434 2445 1.361543 ACTGGACAGGGGTAAGCTCTA 59.638 52.381 4.14 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.