Multiple sequence alignment - TraesCS3B01G288600

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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 TraesCS3B01G288600 chr3B 100.000 8802 0 0 1 8802 463122683 463113882 0.000000e+00 16255.0
1 TraesCS3B01G288600 chr3B 94.737 38 2 0 887 924 463121689 463121726 9.540000e-05 60.2
2 TraesCS3B01G288600 chr3B 97.143 35 1 0 958 992 463121760 463121794 9.540000e-05 60.2
3 TraesCS3B01G288600 chr3A 99.443 8802 44 5 1 8802 477599838 477591042 0.000000e+00 15978.0
4 TraesCS3B01G288600 chr3A 74.373 558 105 22 3712 4250 733999065 733999603 4.170000e-48 204.0
5 TraesCS3B01G288600 chr3A 94.737 38 2 0 887 924 477598844 477598881 9.540000e-05 60.2
6 TraesCS3B01G288600 chr3A 97.143 35 1 0 958 992 477598915 477598949 9.540000e-05 60.2
7 TraesCS3B01G288600 chr3D 97.828 967 8 2 1 955 355417225 355418190 0.000000e+00 1657.0
8 TraesCS3B01G288600 chr3D 98.472 916 14 0 1006 1921 355419733 355420648 0.000000e+00 1615.0
9 TraesCS3B01G288600 chr3D 81.741 471 86 0 16 486 604354546 604355016 2.300000e-105 394.0
10 TraesCS3B01G288600 chr3D 94.737 38 2 0 958 995 355418159 355418122 9.540000e-05 60.2
11 TraesCS3B01G288600 chr1B 84.958 472 67 4 17 486 15174110 15173641 8.000000e-130 475.0
12 TraesCS3B01G288600 chr1B 84.017 463 51 16 5024 5469 15168553 15168097 2.940000e-114 424.0
13 TraesCS3B01G288600 chr1B 81.235 405 61 10 3694 4086 15169729 15169328 6.630000e-81 313.0
14 TraesCS3B01G288600 chr1D 84.664 476 68 5 17 490 10265801 10265329 3.720000e-128 470.0
15 TraesCS3B01G288600 chr1D 83.333 462 56 13 5024 5469 10259967 10259511 2.960000e-109 407.0
16 TraesCS3B01G288600 chr1D 79.487 585 90 24 3694 4250 10261126 10260544 1.070000e-103 388.0
17 TraesCS3B01G288600 chr1A 84.091 484 71 6 7 486 11942874 11942393 6.230000e-126 462.0
18 TraesCS3B01G288600 chr1A 83.297 455 58 16 5024 5469 11936563 11936118 3.830000e-108 403.0
19 TraesCS3B01G288600 chr1A 79.412 578 94 16 3694 4250 11938181 11937608 1.390000e-102 385.0
20 TraesCS3B01G288600 chr1A 92.929 99 7 0 2821 2919 11938476 11938378 2.560000e-30 145.0
21 TraesCS3B01G288600 chrUn 81.741 471 86 0 16 486 42199642 42199172 2.300000e-105 394.0
22 TraesCS3B01G288600 chrUn 74.373 558 101 28 3712 4250 42195469 42194935 5.390000e-47 200.0
23 TraesCS3B01G288600 chr5D 87.879 99 12 0 2821 2919 369026928 369027026 5.580000e-22 117.0


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 TraesCS3B01G288600 chr3B 463113882 463122683 8801 True 16255.00 16255 100.000000 1 8802 1 chr3B.!!$R1 8801
1 TraesCS3B01G288600 chr3A 477591042 477599838 8796 True 15978.00 15978 99.443000 1 8802 1 chr3A.!!$R1 8801
2 TraesCS3B01G288600 chr3A 733999065 733999603 538 False 204.00 204 74.373000 3712 4250 1 chr3A.!!$F1 538
3 TraesCS3B01G288600 chr3D 355417225 355420648 3423 False 1636.00 1657 98.150000 1 1921 2 chr3D.!!$F2 1920
4 TraesCS3B01G288600 chr1B 15168097 15174110 6013 True 404.00 475 83.403333 17 5469 3 chr1B.!!$R1 5452
5 TraesCS3B01G288600 chr1D 10259511 10261126 1615 True 397.50 407 81.410000 3694 5469 2 chr1D.!!$R2 1775
6 TraesCS3B01G288600 chr1A 11936118 11942874 6756 True 348.75 462 84.932250 7 5469 4 chr1A.!!$R1 5462
7 TraesCS3B01G288600 chrUn 42194935 42199642 4707 True 297.00 394 78.057000 16 4250 2 chrUn.!!$R1 4234

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
2040 4920 0.471617 AGATCGGATGAAGCCCCTTG 59.528 55.000 0.00 0.0 0.00 3.61 F
3190 6177 2.359230 GGTGTGCCTCACAGAGCC 60.359 66.667 10.47 0.0 45.43 4.70 F
4571 7670 1.600023 TGCTTTCCGTACCTTGTTGG 58.400 50.000 0.00 0.0 42.93 3.77 F
5839 9479 1.529226 TATGGTTGAACTTGCCACCG 58.471 50.000 0.00 0.0 34.84 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4017 7025 1.501582 AAGTCAGGGGATACTGCTCC 58.498 55.000 0.00 0.0 38.36 4.70 R
4718 7817 3.903876 CATGGCTACACGCAATGTC 57.096 52.632 0.00 0.0 43.74 3.06 R
6538 10178 3.614092 AGCTTCTGTGATGGTGTTATGG 58.386 45.455 0.00 0.0 0.00 2.74 R
7801 11441 0.105593 CGCTCAGGTATGGCATCACT 59.894 55.000 1.65 0.0 0.00 3.41 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
2040 4920 0.471617 AGATCGGATGAAGCCCCTTG 59.528 55.000 0.00 0.00 0.00 3.61
2938 5923 6.016777 AGGTATCTTCTCAAGCAAAAACACAG 60.017 38.462 0.00 0.00 0.00 3.66
3190 6177 2.359230 GGTGTGCCTCACAGAGCC 60.359 66.667 10.47 0.00 45.43 4.70
3358 6352 4.023707 AGTTGTGCCTTCTCGAAAATTCAG 60.024 41.667 0.00 0.00 0.00 3.02
4017 7025 1.607467 CTGGGTTTGGGCTTCCTGG 60.607 63.158 0.00 0.00 0.00 4.45
4372 7471 8.978874 TGTGAAGTGCAATGATAGGTAAATAT 57.021 30.769 0.00 0.00 0.00 1.28
4401 7500 4.637534 TGTTGAATGATAGCTGGCTTCTTC 59.362 41.667 0.00 0.85 0.00 2.87
4571 7670 1.600023 TGCTTTCCGTACCTTGTTGG 58.400 50.000 0.00 0.00 42.93 3.77
4718 7817 5.760253 CCCAGACAGTGTGGCTTATTTATAG 59.240 44.000 11.47 0.00 29.42 1.31
5839 9479 1.529226 TATGGTTGAACTTGCCACCG 58.471 50.000 0.00 0.00 34.84 4.94
6605 10245 4.717279 TGTAGTACAAGGGAAAAGCCTT 57.283 40.909 0.00 0.00 36.66 4.35
6606 10246 4.648651 TGTAGTACAAGGGAAAAGCCTTC 58.351 43.478 0.00 0.00 36.66 3.46
6643 10283 8.674263 ATGCGATCTTCATTATTTTCTTCTCT 57.326 30.769 0.00 0.00 0.00 3.10
6745 10385 1.745653 GCTTAGAGATTTGTGGCCCAC 59.254 52.381 7.01 7.01 34.56 4.61
7196 10836 3.474798 AGATGTTCTGTCACTAGGGGA 57.525 47.619 0.00 0.00 0.00 4.81
7213 10853 1.478654 GGGAACAACAGAAGCTTGGGA 60.479 52.381 2.10 0.00 0.00 4.37
7250 10890 3.244044 TGGCAAGCCACCTTTATTTGTTC 60.244 43.478 10.24 0.00 41.89 3.18
7284 10924 7.995289 TGTATGTTGTTGAGTTCATTGAAAGT 58.005 30.769 0.00 0.00 0.00 2.66
7396 11036 5.820423 TCACGATTTTCTTTTGACTTCTCCA 59.180 36.000 0.00 0.00 0.00 3.86
7398 11038 6.972328 CACGATTTTCTTTTGACTTCTCCAAA 59.028 34.615 0.00 0.00 0.00 3.28
7399 11039 7.487829 CACGATTTTCTTTTGACTTCTCCAAAA 59.512 33.333 0.00 0.00 40.09 2.44
7400 11040 8.032451 ACGATTTTCTTTTGACTTCTCCAAAAA 58.968 29.630 0.00 0.00 41.28 1.94
7588 11228 9.202273 TGACAACACAAAATTTCTTATATTGGC 57.798 29.630 0.00 0.00 0.00 4.52
7607 11247 4.391155 TGGCGAACTGTTAATGTTTAGGT 58.609 39.130 0.00 0.00 0.00 3.08
7801 11441 1.067060 CTATGTTCGATCCGCCAGTGA 59.933 52.381 0.00 0.00 0.00 3.41
8015 11655 6.013293 AGTTTAGCTTACATCAAGGAGAAGGT 60.013 38.462 0.00 0.00 34.56 3.50
8089 11729 1.798813 GTGTTTCCGAGTTGCAGTAGG 59.201 52.381 0.00 0.00 0.00 3.18
8208 11848 9.918630 GCTATCACAGGCAAATCAATAAATAAT 57.081 29.630 0.00 0.00 0.00 1.28
8581 12221 5.173131 GCTCAAATTTTGGTACGACAAGTTG 59.827 40.000 9.71 9.71 0.00 3.16
8679 12319 2.430332 CCCAACAGCTCCAGTTCAAAAA 59.570 45.455 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 207 3.244561 CCAACAAGAGCCTCAAACCTCTA 60.245 47.826 0.00 0.00 37.44 2.43
2040 4920 9.505995 CGAGAATAAAGTTCCTAGAACTAGTTC 57.494 37.037 25.24 25.24 39.78 3.01
2142 5033 1.737816 CAACAGCAAGCAACTGCCT 59.262 52.632 0.00 0.00 43.73 4.75
2938 5923 9.476202 AAGGAAACTAAAGCAATAATGTGTTTC 57.524 29.630 0.00 0.00 42.68 2.78
3190 6177 7.676104 GCCCATAATTAAAATTTCAAACAGCGG 60.676 37.037 0.00 0.00 0.00 5.52
4017 7025 1.501582 AAGTCAGGGGATACTGCTCC 58.498 55.000 0.00 0.00 38.36 4.70
4137 7150 6.120905 AGCTCATCAGATTAGCACTTCAATT 58.879 36.000 17.21 0.00 38.75 2.32
4303 7336 9.206870 CAAACAAGCATTTAATTAACTGATGGT 57.793 29.630 17.14 12.48 0.00 3.55
4304 7337 9.421806 TCAAACAAGCATTTAATTAACTGATGG 57.578 29.630 17.14 11.91 0.00 3.51
4372 7471 4.098349 GCCAGCTATCATTCAACAATCCAA 59.902 41.667 0.00 0.00 0.00 3.53
4718 7817 3.903876 CATGGCTACACGCAATGTC 57.096 52.632 0.00 0.00 43.74 3.06
6538 10178 3.614092 AGCTTCTGTGATGGTGTTATGG 58.386 45.455 0.00 0.00 0.00 2.74
6605 10245 3.291584 AGATCGCATACCAGTCAGAAGA 58.708 45.455 0.00 0.00 0.00 2.87
6606 10246 3.724508 AGATCGCATACCAGTCAGAAG 57.275 47.619 0.00 0.00 0.00 2.85
6745 10385 4.442753 GCTTGATAACTCTCCCAGAGAAGG 60.443 50.000 7.55 0.00 45.07 3.46
7196 10836 2.242043 CCATCCCAAGCTTCTGTTGTT 58.758 47.619 0.00 0.00 0.00 2.83
7250 10890 9.299963 TGAACTCAACAACATACAAAATGAAAG 57.700 29.630 0.00 0.00 0.00 2.62
7284 10924 6.127310 GGCCTAGAACAAAGATGAGAGAGTTA 60.127 42.308 0.00 0.00 0.00 2.24
7432 11072 7.607607 GCAATCAAGGAAAATTTTAGGAACCAT 59.392 33.333 2.75 0.00 0.00 3.55
7540 11180 5.070446 TCACAGGGATTATCGAAGCACTTAT 59.930 40.000 0.00 0.00 30.31 1.73
7801 11441 0.105593 CGCTCAGGTATGGCATCACT 59.894 55.000 1.65 0.00 0.00 3.41
8015 11655 2.492881 GTGGATCACAATCATGCACCAA 59.507 45.455 0.00 0.00 36.78 3.67
8089 11729 2.289320 ACATGTCTCTTCTGCTGTCCAC 60.289 50.000 0.00 0.00 0.00 4.02
8208 11848 2.857575 CTAGCCGTGCAGCATCCACA 62.858 60.000 0.00 0.00 32.85 4.17
8581 12221 4.615912 GCACATCTGTTTTATGGGTGTCAC 60.616 45.833 0.00 0.00 30.08 3.67


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

AutoCloner maintained by Alex Coulton.