Multiple sequence alignment - TraesCS3A01G466800

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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 TraesCS3A01G466800 chr3A 100.000 2423 0 0 1 2423 700567860 700570282 0.000000e+00 4475.0
1 TraesCS3A01G466800 chr3A 94.625 2437 97 15 1 2423 701856291 701858707 0.000000e+00 3744.0
2 TraesCS3A01G466800 chr3A 74.068 1234 235 59 772 1960 699251507 699250314 6.190000e-116 427.0
3 TraesCS3A01G466800 chr3A 73.260 819 175 28 768 1557 699540769 699541572 2.390000e-65 259.0
4 TraesCS3A01G466800 chr3A 79.535 215 35 8 261 473 697585522 697585315 6.980000e-31 145.0
5 TraesCS3A01G466800 chr3A 95.238 42 2 0 2382 2423 700575133 700575174 1.550000e-07 67.6
6 TraesCS3A01G466800 chr3D 94.381 2438 92 17 1 2423 567224388 567221981 0.000000e+00 3701.0
7 TraesCS3A01G466800 chr3D 73.709 1046 225 38 520 1545 567109042 567110057 1.770000e-96 363.0
8 TraesCS3A01G466800 chr3D 76.347 334 55 16 771 1096 569578571 569578254 8.970000e-35 158.0
9 TraesCS3A01G466800 chr3D 86.667 75 8 2 320 393 565982602 565982675 5.550000e-12 82.4
10 TraesCS3A01G466800 chr3D 97.619 42 1 0 2382 2423 567217168 567217127 3.340000e-09 73.1
11 TraesCS3A01G466800 chr3D 95.238 42 2 0 2382 2423 569546189 569546230 1.550000e-07 67.6
12 TraesCS3A01G466800 chrUn 93.742 2445 106 20 4 2423 41111227 41108805 0.000000e+00 3624.0
13 TraesCS3A01G466800 chrUn 85.027 187 22 2 2075 2256 41102086 41101901 4.110000e-43 185.0
14 TraesCS3A01G466800 chrUn 81.944 72 8 4 61 128 177130250 177130180 3.370000e-04 56.5
15 TraesCS3A01G466800 chr3B 93.211 2445 105 21 1 2423 754981396 754983801 0.000000e+00 3539.0
16 TraesCS3A01G466800 chr3B 75.276 995 198 36 950 1907 752122268 752121285 4.790000e-117 431.0
17 TraesCS3A01G466800 chr3B 75.777 611 128 16 962 1565 756185904 756185307 8.470000e-75 291.0
18 TraesCS3A01G466800 chr3B 72.970 899 198 32 696 1567 752966881 752966001 3.070000e-69 272.0
19 TraesCS3A01G466800 chr3B 77.725 211 39 7 261 470 749685597 749685394 3.270000e-24 122.0
20 TraesCS3A01G466800 chr3B 81.538 130 18 5 320 446 754502548 754502674 4.260000e-18 102.0
21 TraesCS3A01G466800 chr3B 100.000 41 0 0 2383 2423 755041867 755041907 2.580000e-10 76.8
22 TraesCS3A01G466800 chr5D 72.763 760 168 32 1035 1771 547932581 547931838 1.130000e-53 220.0
23 TraesCS3A01G466800 chr6A 80.083 241 38 7 1338 1571 598382579 598382816 1.150000e-38 171.0
24 TraesCS3A01G466800 chr5B 95.122 41 2 0 2382 2422 619014504 619014544 5.590000e-07 65.8
25 TraesCS3A01G466800 chr2B 81.944 72 8 4 61 128 1319116 1319046 3.370000e-04 56.5


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 TraesCS3A01G466800 chr3A 700567860 700570282 2422 False 4475 4475 100.000 1 2423 1 chr3A.!!$F2 2422
1 TraesCS3A01G466800 chr3A 701856291 701858707 2416 False 3744 3744 94.625 1 2423 1 chr3A.!!$F4 2422
2 TraesCS3A01G466800 chr3A 699250314 699251507 1193 True 427 427 74.068 772 1960 1 chr3A.!!$R2 1188
3 TraesCS3A01G466800 chr3A 699540769 699541572 803 False 259 259 73.260 768 1557 1 chr3A.!!$F1 789
4 TraesCS3A01G466800 chr3D 567221981 567224388 2407 True 3701 3701 94.381 1 2423 1 chr3D.!!$R2 2422
5 TraesCS3A01G466800 chr3D 567109042 567110057 1015 False 363 363 73.709 520 1545 1 chr3D.!!$F2 1025
6 TraesCS3A01G466800 chrUn 41108805 41111227 2422 True 3624 3624 93.742 4 2423 1 chrUn.!!$R2 2419
7 TraesCS3A01G466800 chr3B 754981396 754983801 2405 False 3539 3539 93.211 1 2423 1 chr3B.!!$F2 2422
8 TraesCS3A01G466800 chr3B 752121285 752122268 983 True 431 431 75.276 950 1907 1 chr3B.!!$R2 957
9 TraesCS3A01G466800 chr3B 756185307 756185904 597 True 291 291 75.777 962 1565 1 chr3B.!!$R4 603
10 TraesCS3A01G466800 chr3B 752966001 752966881 880 True 272 272 72.970 696 1567 1 chr3B.!!$R3 871
11 TraesCS3A01G466800 chr5D 547931838 547932581 743 True 220 220 72.763 1035 1771 1 chr5D.!!$R1 736

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
590 595 0.169672 CTGCGATGGCCTTCTTGTTG 59.83 55.0 16.03 2.06 38.85 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2481 1.497286 AGCACACCAACCCTTTTCCTA 59.503 47.619 0.0 0.0 0.0 2.94 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
196 199 2.352032 CGTCTCCTCCGCTCCCTTT 61.352 63.158 0.00 0.00 0.00 3.11
266 270 0.950836 CAACAACCAAGATGCCGACA 59.049 50.000 0.00 0.00 0.00 4.35
315 319 4.717629 CGCCTCTTCGCCACGACA 62.718 66.667 0.00 0.00 34.89 4.35
374 378 1.550130 TTCGCCTCGACCCCAAATCT 61.550 55.000 0.00 0.00 34.89 2.40
499 504 6.458478 CGTTAGACGAAGAATACATCCTCACT 60.458 42.308 0.00 0.00 46.05 3.41
586 591 0.393537 CTTCCTGCGATGGCCTTCTT 60.394 55.000 16.03 0.00 38.85 2.52
589 594 0.962356 CCTGCGATGGCCTTCTTGTT 60.962 55.000 16.03 0.00 38.85 2.83
590 595 0.169672 CTGCGATGGCCTTCTTGTTG 59.830 55.000 16.03 2.06 38.85 3.33
629 640 5.375773 TGACTGACACCATTGATTTCTCAA 58.624 37.500 0.00 0.00 45.15 3.02
701 712 2.423064 GGCTTGCGGTTATTGGGGG 61.423 63.158 0.00 0.00 0.00 5.40
761 786 8.033038 TGTTACTTGAACTCGATAGCTACAATT 58.967 33.333 0.00 0.00 38.98 2.32
898 923 3.097877 TGCGATAGTCTGCATTGGTAG 57.902 47.619 0.00 0.00 35.90 3.18
899 924 2.430694 TGCGATAGTCTGCATTGGTAGT 59.569 45.455 0.00 0.00 35.90 2.73
900 925 3.118775 TGCGATAGTCTGCATTGGTAGTT 60.119 43.478 0.00 0.00 35.90 2.24
901 926 3.871594 GCGATAGTCTGCATTGGTAGTTT 59.128 43.478 0.00 0.00 39.35 2.66
912 943 4.566070 GCATTGGTAGTTTGGTACCCAGTA 60.566 45.833 10.07 0.34 41.79 2.74
1038 1078 3.281727 TCCACCAACTCATATGCCTTC 57.718 47.619 0.00 0.00 0.00 3.46
1224 1297 2.363306 ATGTGGAGGTTGTTTCAGCA 57.637 45.000 0.00 0.00 0.00 4.41
1228 1301 1.239347 GGAGGTTGTTTCAGCAGACC 58.761 55.000 0.00 0.00 0.00 3.85
1229 1302 1.476833 GGAGGTTGTTTCAGCAGACCA 60.477 52.381 0.00 0.00 32.81 4.02
1429 1508 6.257411 CACTTCACCATTCATCTGATGTCTAC 59.743 42.308 16.66 0.00 0.00 2.59
1434 1513 4.989797 CCATTCATCTGATGTCTACTGAGC 59.010 45.833 16.66 0.00 0.00 4.26
1720 1870 6.061022 TGTGTCTATTTTCTTGGGCTGATA 57.939 37.500 0.00 0.00 0.00 2.15
1984 2134 5.625251 CAGCTTGAGCACTACACATTAAAG 58.375 41.667 5.70 0.00 45.16 1.85
2020 2170 8.893727 GCATAAGAGTAGTTGACACCATTTATT 58.106 33.333 0.00 0.00 0.00 1.40
2027 2177 9.959721 AGTAGTTGACACCATTTATTTATGACT 57.040 29.630 0.00 0.00 0.00 3.41
2065 2216 6.402222 ACCTCTGTTCACTATGACTCATTTC 58.598 40.000 0.00 0.00 0.00 2.17
2123 2278 6.973474 AGTTAATATCTACTCGACAGTGCAAC 59.027 38.462 0.00 0.00 33.62 4.17
2124 2279 2.656560 ATCTACTCGACAGTGCAACC 57.343 50.000 0.00 0.00 37.80 3.77
2128 2288 0.039437 ACTCGACAGTGCAACCGTAG 60.039 55.000 0.00 0.00 37.80 3.51
2167 2327 7.011950 TGGCACCGAAAATATAGAACATAGTTG 59.988 37.037 0.00 0.00 0.00 3.16
2195 2355 8.954950 TTAAATTATTGGGCCAACAATGTATG 57.045 30.769 22.62 0.00 40.97 2.39
2302 2462 3.926616 ACCCACTCACTAGAACATTTCG 58.073 45.455 0.00 0.00 34.02 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.037222 CCTTATTGGCCCCCTAAACAAAT 58.963 43.478 0.00 0.00 0.00 2.32
107 108 4.288398 TCTGCAGGAGATGAGAGAATTCT 58.712 43.478 15.13 7.95 36.01 2.40
466 470 0.179145 CTTCGTCTAACGCGATGGGT 60.179 55.000 15.93 0.00 42.21 4.51
518 523 2.872388 CGACAGTGTGGAGCTGGGT 61.872 63.158 0.00 0.00 38.22 4.51
589 594 3.006859 CAGTCATGTTGTACCTGGAGACA 59.993 47.826 0.00 0.89 39.59 3.41
590 595 3.258372 TCAGTCATGTTGTACCTGGAGAC 59.742 47.826 0.00 0.00 0.00 3.36
629 640 2.747446 GACGAGTGGCCATGTTACAAAT 59.253 45.455 9.72 0.00 0.00 2.32
638 649 0.527565 GCAAATTGACGAGTGGCCAT 59.472 50.000 9.72 0.00 0.00 4.40
701 712 2.537401 GGTAGGTTGATGCGAGTACAC 58.463 52.381 0.00 0.00 0.00 2.90
747 758 4.743151 CAGGCGTTTAATTGTAGCTATCGA 59.257 41.667 0.00 0.00 0.00 3.59
761 786 2.875933 CAAGTTGGTCTTCAGGCGTTTA 59.124 45.455 0.00 0.00 33.63 2.01
912 943 6.422100 CGTAGCTGCTTTCACTCACATAATAT 59.578 38.462 7.79 0.00 0.00 1.28
1038 1078 2.669670 GCCGAGTGTATCATCCATCTCG 60.670 54.545 0.00 0.00 42.51 4.04
1228 1301 1.923204 GACTAGCAAGAGCACGTCATG 59.077 52.381 0.00 0.00 45.49 3.07
1229 1302 1.546029 TGACTAGCAAGAGCACGTCAT 59.454 47.619 7.45 0.00 42.92 3.06
1429 1508 1.739562 GAAGCACCACCTCGCTCAG 60.740 63.158 0.00 0.00 37.54 3.35
1914 2064 7.267128 TGCACATCAAGAAACAGAAAAATCTT 58.733 30.769 0.00 0.00 32.55 2.40
1984 2134 8.175716 GTCAACTACTCTTATGCAACCATTTAC 58.824 37.037 0.00 0.00 32.85 2.01
2020 2170 7.016858 AGAGGTTTGGTTGGTAGTTAGTCATAA 59.983 37.037 0.00 0.00 0.00 1.90
2025 2175 4.411212 ACAGAGGTTTGGTTGGTAGTTAGT 59.589 41.667 0.00 0.00 0.00 2.24
2027 2177 5.104444 TGAACAGAGGTTTGGTTGGTAGTTA 60.104 40.000 0.00 0.00 37.36 2.24
2033 2183 2.654863 AGTGAACAGAGGTTTGGTTGG 58.345 47.619 0.00 0.00 37.36 3.77
2065 2216 5.697633 CACAAAATTCAGTGAAAGGAATGGG 59.302 40.000 10.14 2.86 37.97 4.00
2123 2278 4.569564 GTGCCAAAACCTAAGATACTACGG 59.430 45.833 0.00 0.00 0.00 4.02
2124 2279 4.569564 GGTGCCAAAACCTAAGATACTACG 59.430 45.833 0.00 0.00 37.24 3.51
2128 2288 3.602483 TCGGTGCCAAAACCTAAGATAC 58.398 45.455 0.00 0.00 38.14 2.24
2167 2327 8.105097 ACATTGTTGGCCCAATAATTTAAAAC 57.895 30.769 15.00 0.00 33.99 2.43
2321 2481 1.497286 AGCACACCAACCCTTTTCCTA 59.503 47.619 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.