Multiple sequence alignment - TraesCS5D01G469500

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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 TraesCS5D01G469500 chr5D 100.000 2466 0 0 1 2466 510493445 510490980 0.000000e+00 4554.0
1 TraesCS5D01G469500 chr5D 85.732 2397 254 47 1 2386 510627298 510624979 0.000000e+00 2451.0
2 TraesCS5D01G469500 chr5D 85.299 2408 275 34 1 2386 510390021 510387671 0.000000e+00 2412.0
3 TraesCS5D01G469500 chr5D 84.513 975 120 11 997 1962 510353960 510353008 0.000000e+00 935.0
4 TraesCS5D01G469500 chr5D 100.000 313 0 0 2936 3248 510490510 510490198 2.170000e-161 579.0
5 TraesCS5D01G469500 chr5D 76.632 1164 194 44 1014 2162 510904586 510905686 3.640000e-159 571.0
6 TraesCS5D01G469500 chr5D 96.815 314 9 1 2936 3248 473047741 473048054 1.030000e-144 523.0
7 TraesCS5D01G469500 chr5D 89.500 400 39 1 997 1393 510440172 510439773 1.350000e-138 503.0
8 TraesCS5D01G469500 chr5D 73.971 1118 214 47 998 2100 510599630 510598575 6.580000e-102 381.0
9 TraesCS5D01G469500 chr5D 87.958 191 22 1 1790 1980 510619531 510619342 1.170000e-54 224.0
10 TraesCS5D01G469500 chr5D 81.448 221 26 8 2166 2386 510654740 510654535 2.000000e-37 167.0
11 TraesCS5D01G469500 chr5D 89.600 125 12 1 721 845 510903716 510903839 1.210000e-34 158.0
12 TraesCS5D01G469500 chr5D 77.679 224 34 13 2166 2386 510603076 510602866 4.400000e-24 122.0
13 TraesCS5D01G469500 chr5A 97.260 2445 64 3 1 2445 638764186 638761745 0.000000e+00 4141.0
14 TraesCS5D01G469500 chr5A 76.395 1165 195 47 1014 2162 639098444 639099544 3.660000e-154 555.0
15 TraesCS5D01G469500 chr5A 75.149 1175 219 34 999 2162 638812425 638811313 4.870000e-133 484.0
16 TraesCS5D01G469500 chr5A 90.400 125 11 1 721 845 639097596 639097719 2.590000e-36 163.0
17 TraesCS5D01G469500 chr5A 80.000 215 29 7 2174 2386 638814220 638814018 2.610000e-31 147.0
18 TraesCS5D01G469500 chr5B 83.945 1881 234 32 527 2386 641402154 641400321 0.000000e+00 1738.0
19 TraesCS5D01G469500 chr5B 94.787 422 21 1 1 422 641402601 641402181 0.000000e+00 656.0
20 TraesCS5D01G469500 chr5B 86.308 577 70 8 998 1570 641161450 641160879 1.280000e-173 619.0
21 TraesCS5D01G469500 chr5B 76.632 1164 194 46 1014 2162 641805368 641806468 3.640000e-159 571.0
22 TraesCS5D01G469500 chr5B 75.635 1182 214 45 997 2162 641412979 641411856 1.340000e-143 520.0
23 TraesCS5D01G469500 chr5B 74.300 1179 229 36 997 2162 641428270 641427153 6.440000e-117 431.0
24 TraesCS5D01G469500 chr5B 95.556 45 2 0 721 765 641804511 641804555 4.500000e-09 73.1
25 TraesCS5D01G469500 chr7D 97.106 311 9 0 2936 3246 602279464 602279774 2.870000e-145 525.0
26 TraesCS5D01G469500 chr7D 97.106 311 9 0 2936 3246 602283735 602284045 2.870000e-145 525.0
27 TraesCS5D01G469500 chr7D 96.805 313 10 0 2936 3248 48276699 48276387 1.030000e-144 523.0
28 TraesCS5D01G469500 chr4D 96.805 313 10 0 2936 3248 468417385 468417073 1.030000e-144 523.0
29 TraesCS5D01G469500 chr1D 96.805 313 10 0 2936 3248 438586664 438586352 1.030000e-144 523.0
30 TraesCS5D01G469500 chr2A 90.169 295 8 10 2954 3248 109602297 109602024 6.620000e-97 364.0
31 TraesCS5D01G469500 chr1B 85.938 320 17 10 2936 3248 510812863 510813161 1.880000e-82 316.0
32 TraesCS5D01G469500 chr2B 83.125 320 27 9 2936 3248 657718525 657718226 1.920000e-67 267.0


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 TraesCS5D01G469500 chr5D 510490198 510493445 3247 True 2566.50 4554 100.0000 1 3248 2 chr5D.!!$R7 3247
1 TraesCS5D01G469500 chr5D 510624979 510627298 2319 True 2451.00 2451 85.7320 1 2386 1 chr5D.!!$R5 2385
2 TraesCS5D01G469500 chr5D 510387671 510390021 2350 True 2412.00 2412 85.2990 1 2386 1 chr5D.!!$R2 2385
3 TraesCS5D01G469500 chr5D 510353008 510353960 952 True 935.00 935 84.5130 997 1962 1 chr5D.!!$R1 965
4 TraesCS5D01G469500 chr5D 510903716 510905686 1970 False 364.50 571 83.1160 721 2162 2 chr5D.!!$F2 1441
5 TraesCS5D01G469500 chr5D 510598575 510603076 4501 True 251.50 381 75.8250 998 2386 2 chr5D.!!$R8 1388
6 TraesCS5D01G469500 chr5A 638761745 638764186 2441 True 4141.00 4141 97.2600 1 2445 1 chr5A.!!$R1 2444
7 TraesCS5D01G469500 chr5A 639097596 639099544 1948 False 359.00 555 83.3975 721 2162 2 chr5A.!!$F1 1441
8 TraesCS5D01G469500 chr5A 638811313 638814220 2907 True 315.50 484 77.5745 999 2386 2 chr5A.!!$R2 1387
9 TraesCS5D01G469500 chr5B 641400321 641402601 2280 True 1197.00 1738 89.3660 1 2386 2 chr5B.!!$R4 2385
10 TraesCS5D01G469500 chr5B 641160879 641161450 571 True 619.00 619 86.3080 998 1570 1 chr5B.!!$R1 572
11 TraesCS5D01G469500 chr5B 641411856 641412979 1123 True 520.00 520 75.6350 997 2162 1 chr5B.!!$R2 1165
12 TraesCS5D01G469500 chr5B 641427153 641428270 1117 True 431.00 431 74.3000 997 2162 1 chr5B.!!$R3 1165
13 TraesCS5D01G469500 chr5B 641804511 641806468 1957 False 322.05 571 86.0940 721 2162 2 chr5B.!!$F1 1441
14 TraesCS5D01G469500 chr7D 602279464 602284045 4581 False 525.00 525 97.1060 2936 3246 2 chr7D.!!$F1 310

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
623 636 0.66102 CCCTGTGTCAACCAAACGAC 59.339 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 4972 2.058798 GCATTGCTATTAGCGACGCTA 58.941 47.619 25.04 25.04 46.26 4.26 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
165 166 2.555199 GTCGCAGATGCAACCTAGATT 58.445 47.619 5.55 0.00 40.67 2.40
256 257 1.071542 TCGTGATGCCAAAGGAAGTCA 59.928 47.619 0.00 0.00 0.00 3.41
465 466 8.421249 TCCCTTTTTATCAGATCACATTGTTT 57.579 30.769 0.00 0.00 0.00 2.83
466 467 8.869109 TCCCTTTTTATCAGATCACATTGTTTT 58.131 29.630 0.00 0.00 0.00 2.43
467 468 9.492973 CCCTTTTTATCAGATCACATTGTTTTT 57.507 29.630 0.00 0.00 0.00 1.94
472 473 9.695526 TTTATCAGATCACATTGTTTTTCAAGG 57.304 29.630 0.00 0.00 42.57 3.61
512 525 5.709631 TGTGTATTATGTTGTCACCATTGCT 59.290 36.000 0.00 0.00 0.00 3.91
623 636 0.661020 CCCTGTGTCAACCAAACGAC 59.339 55.000 0.00 0.00 0.00 4.34
815 828 2.795329 AGGCCCACTTGTTGACTAATG 58.205 47.619 0.00 0.00 0.00 1.90
1057 3589 1.679305 ATCCTGTCTCGACTGCCGT 60.679 57.895 0.00 0.00 39.75 5.68
1086 3618 0.743688 TGTGCCGCTTCAAATGTGTT 59.256 45.000 0.00 0.00 0.00 3.32
1122 3654 5.803795 GCTTGCCTTCTCATCTCATCCATAT 60.804 44.000 0.00 0.00 0.00 1.78
1263 3797 6.377146 ACAAGGAAATTGACACAACACTTAGT 59.623 34.615 0.00 0.00 41.83 2.24
1514 4054 4.415332 GTCGAGCGCGGTCCTGAA 62.415 66.667 30.42 12.37 38.28 3.02
1530 4070 5.316987 GTCCTGAACCCTCATATAATTGGG 58.683 45.833 0.00 0.00 44.89 4.12
1591 4131 1.798813 CGTGGTCTAGTTGTCTTTGGC 59.201 52.381 0.00 0.00 0.00 4.52
1803 4346 8.109634 ACTTTCTGTTCTAATGGATGTATTGGT 58.890 33.333 0.00 0.00 0.00 3.67
1954 4497 2.808543 GACATTTTTCTCCGCACTGACT 59.191 45.455 0.00 0.00 0.00 3.41
2090 4636 1.507141 AAACGCTCGCAGTCCCAAAG 61.507 55.000 0.00 0.00 0.00 2.77
2219 4766 8.706492 ATGTTTTACAATTTATGGCATCAGTG 57.294 30.769 1.65 4.28 0.00 3.66
2236 4795 5.499139 TCAGTGCTGTACTTTCCTTTTTG 57.501 39.130 0.00 0.00 37.60 2.44
2427 4988 2.664698 CGTCATAGCGTCGCTAATAGCA 60.665 50.000 29.13 9.37 44.62 3.49
2445 5006 2.609459 AGCAATGCTATAGCGTGTTGAC 59.391 45.455 27.52 21.06 45.83 3.18
2446 5007 2.351418 GCAATGCTATAGCGTGTTGACA 59.649 45.455 27.52 9.66 45.83 3.58
2447 5008 3.544834 GCAATGCTATAGCGTGTTGACAG 60.545 47.826 27.52 12.94 45.83 3.51
2448 5009 2.293677 TGCTATAGCGTGTTGACAGG 57.706 50.000 19.55 0.00 45.83 4.00
2449 5010 1.134818 TGCTATAGCGTGTTGACAGGG 60.135 52.381 19.55 0.00 45.83 4.45
2450 5011 1.571919 CTATAGCGTGTTGACAGGGC 58.428 55.000 6.04 3.07 32.80 5.19
2451 5012 0.177141 TATAGCGTGTTGACAGGGCC 59.823 55.000 0.00 0.00 32.80 5.80
2452 5013 2.852495 ATAGCGTGTTGACAGGGCCG 62.852 60.000 0.00 0.00 32.80 6.13
3017 9849 2.760385 GGACTAGACGGCTGGGCT 60.760 66.667 7.70 0.00 30.02 5.19
3035 9867 0.674581 CTTCAGGCAGCACGATGGAA 60.675 55.000 0.00 0.00 0.00 3.53
3075 9907 2.154462 CATATTTGCCGCTAGGAAGGG 58.846 52.381 0.00 0.00 41.02 3.95
3117 9949 3.166657 GTTCCTAGTTACTACGTGCACG 58.833 50.000 35.99 35.99 46.33 5.34
3183 10015 5.696260 TTAGTTCGTGCATGTCGATAAAG 57.304 39.130 13.76 0.00 37.18 1.85
3198 10030 6.590292 TGTCGATAAAGAAGGAACAGATTGAC 59.410 38.462 0.00 0.00 0.00 3.18
3246 10078 1.268234 CGCAGCGATTCCCAATTTCTC 60.268 52.381 9.98 0.00 0.00 2.87
3247 10079 1.745087 GCAGCGATTCCCAATTTCTCA 59.255 47.619 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 166 1.863491 CGAAACGGATGGCGTTGAA 59.137 52.632 0.00 0.00 0.00 2.69
256 257 5.717178 AGATCATGTATATGCTCCTAACCGT 59.283 40.000 0.00 0.00 31.38 4.83
465 466 8.458052 CACATGTTGCTATAATACACCTTGAAA 58.542 33.333 0.00 0.00 0.00 2.69
466 467 7.609918 ACACATGTTGCTATAATACACCTTGAA 59.390 33.333 0.00 0.00 0.00 2.69
467 468 7.109501 ACACATGTTGCTATAATACACCTTGA 58.890 34.615 0.00 0.00 0.00 3.02
468 469 7.320443 ACACATGTTGCTATAATACACCTTG 57.680 36.000 0.00 0.00 0.00 3.61
469 470 9.627123 AATACACATGTTGCTATAATACACCTT 57.373 29.630 0.00 0.00 0.00 3.50
512 525 4.009675 GCCATCCATTTCACAACTAGTCA 58.990 43.478 0.00 0.00 0.00 3.41
569 582 9.890629 ATCTAGTAGTTATGTGCAAGATCAAAA 57.109 29.630 0.00 0.00 0.00 2.44
573 586 8.300286 TGCTATCTAGTAGTTATGTGCAAGATC 58.700 37.037 0.00 0.00 32.72 2.75
623 636 0.108138 GAGTGGGTCACAGGGATTCG 60.108 60.000 0.78 0.00 36.74 3.34
808 821 4.873827 TCCCGTTCAATGCTTACATTAGTC 59.126 41.667 0.00 0.00 44.83 2.59
815 828 1.816074 TGGTCCCGTTCAATGCTTAC 58.184 50.000 0.00 0.00 0.00 2.34
871 884 9.489393 CCAAAAATTAAAACTCAAGCAAAGTTC 57.511 29.630 0.00 0.00 35.96 3.01
1057 3589 0.465460 AAGCGGCACAAGGACTTCAA 60.465 50.000 1.45 0.00 0.00 2.69
1122 3654 4.153673 TCTTGGGAACTTTTGTCGGTAA 57.846 40.909 0.00 0.00 0.00 2.85
1434 3974 6.072112 TCAAAACACAACTTGAGATTAGCC 57.928 37.500 0.00 0.00 0.00 3.93
1514 4054 3.916989 GGAGGTCCCAATTATATGAGGGT 59.083 47.826 0.00 0.00 42.12 4.34
1530 4070 5.678955 ATACCTTAACTTCAGTGGAGGTC 57.321 43.478 14.64 0.00 40.82 3.85
1591 4131 3.396260 TTCCCAAAGACAACTAGACCG 57.604 47.619 0.00 0.00 0.00 4.79
1803 4346 2.094182 GCATAAGACACCCGAAGACTGA 60.094 50.000 0.00 0.00 0.00 3.41
1954 4497 3.007506 TCGAAAAGCCAGTATCCTTCACA 59.992 43.478 0.00 0.00 0.00 3.58
2090 4636 2.095461 GGGTGAAGCTTCTTGGAATCC 58.905 52.381 26.09 12.22 0.00 3.01
2152 4698 4.263949 ACCCTTAACTGCTAAAGCTGGAAT 60.264 41.667 12.64 2.62 43.15 3.01
2219 4766 5.067283 TCCAACTCAAAAAGGAAAGTACAGC 59.933 40.000 0.00 0.00 0.00 4.40
2236 4795 7.023575 CACATAACAACAGCTTAATCCAACTC 58.976 38.462 0.00 0.00 0.00 3.01
2408 4969 3.636282 TTGCTATTAGCGACGCTATGA 57.364 42.857 28.67 16.40 46.26 2.15
2409 4970 3.482598 GCATTGCTATTAGCGACGCTATG 60.483 47.826 28.67 22.61 46.26 2.23
2411 4972 2.058798 GCATTGCTATTAGCGACGCTA 58.941 47.619 25.04 25.04 46.26 4.26
2427 4988 3.198068 CCTGTCAACACGCTATAGCATT 58.802 45.455 23.99 12.05 42.21 3.56
2942 5503 6.759272 ACCATAGCTAACATGTGTATACCTG 58.241 40.000 0.00 0.00 0.00 4.00
2998 9830 2.656069 GCCCAGCCGTCTAGTCCAA 61.656 63.158 0.00 0.00 0.00 3.53
3017 9849 0.955428 GTTCCATCGTGCTGCCTGAA 60.955 55.000 0.00 0.00 0.00 3.02
3075 9907 3.531829 CGAATCGATCGCTGGCTC 58.468 61.111 11.09 1.24 45.89 4.70
3127 9959 3.873910 TCGGAAAGGATCAATCAGTTCC 58.126 45.455 11.30 11.30 37.65 3.62
3183 10015 3.009584 AGAAGGGGTCAATCTGTTCCTTC 59.990 47.826 10.84 10.84 46.22 3.46
3198 10030 0.462759 GTGCGAGATGGAAGAAGGGG 60.463 60.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.