Multiple sequence alignment - TraesCS5B01G129100

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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 TraesCS5B01G129100 chr5B 100.000 2394 0 0 1 2394 237158857 237156464 0 4421
1 TraesCS5B01G129100 chr6B 93.369 1493 96 3 8 1498 68900873 68902364 0 2206
2 TraesCS5B01G129100 chr3B 92.968 1479 100 4 22 1498 125892123 125893599 0 2152
3 TraesCS5B01G129100 chr7A 92.642 1495 105 5 6 1497 270771078 270772570 0 2146
4 TraesCS5B01G129100 chr7A 95.136 884 41 2 1511 2394 485864196 485863315 0 1393
5 TraesCS5B01G129100 chr7A 94.910 884 44 1 1511 2394 502894032 502894914 0 1382
6 TraesCS5B01G129100 chr7A 94.910 884 44 1 1511 2394 505170012 505169130 0 1382
7 TraesCS5B01G129100 chr7A 94.683 884 46 1 1511 2394 496596385 496595503 0 1371
8 TraesCS5B01G129100 chr7A 94.570 884 47 1 1511 2394 486291951 486291069 0 1365
9 TraesCS5B01G129100 chr7D 90.381 1497 133 10 8 1498 7795923 7797414 0 1956
10 TraesCS5B01G129100 chr4B 89.891 1474 141 7 3 1471 422027796 422029266 0 1890
11 TraesCS5B01G129100 chr4B 89.365 1495 147 9 6 1498 144340454 144338970 0 1869
12 TraesCS5B01G129100 chr4B 92.986 884 61 1 1511 2394 88284351 88285233 0 1288
13 TraesCS5B01G129100 chr5A 88.621 1494 167 3 6 1498 622529037 622527546 0 1814
14 TraesCS5B01G129100 chr7B 88.294 1495 166 9 11 1501 592906886 592908375 0 1783
15 TraesCS5B01G129100 chr2D 86.922 1491 188 7 11 1498 642787456 642785970 0 1666
16 TraesCS5B01G129100 chr1D 94.052 891 43 4 1511 2394 244868216 244867329 0 1343
17 TraesCS5B01G129100 chr1B 93.715 891 46 4 1511 2394 187726545 187727432 0 1327
18 TraesCS5B01G129100 chr2B 93.490 891 48 4 1511 2394 339911942 339911055 0 1315


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 TraesCS5B01G129100 chr5B 237156464 237158857 2393 True 4421 4421 100.000 1 2394 1 chr5B.!!$R1 2393
1 TraesCS5B01G129100 chr6B 68900873 68902364 1491 False 2206 2206 93.369 8 1498 1 chr6B.!!$F1 1490
2 TraesCS5B01G129100 chr3B 125892123 125893599 1476 False 2152 2152 92.968 22 1498 1 chr3B.!!$F1 1476
3 TraesCS5B01G129100 chr7A 270771078 270772570 1492 False 2146 2146 92.642 6 1497 1 chr7A.!!$F1 1491
4 TraesCS5B01G129100 chr7A 485863315 485864196 881 True 1393 1393 95.136 1511 2394 1 chr7A.!!$R1 883
5 TraesCS5B01G129100 chr7A 502894032 502894914 882 False 1382 1382 94.910 1511 2394 1 chr7A.!!$F2 883
6 TraesCS5B01G129100 chr7A 505169130 505170012 882 True 1382 1382 94.910 1511 2394 1 chr7A.!!$R4 883
7 TraesCS5B01G129100 chr7A 496595503 496596385 882 True 1371 1371 94.683 1511 2394 1 chr7A.!!$R3 883
8 TraesCS5B01G129100 chr7A 486291069 486291951 882 True 1365 1365 94.570 1511 2394 1 chr7A.!!$R2 883
9 TraesCS5B01G129100 chr7D 7795923 7797414 1491 False 1956 1956 90.381 8 1498 1 chr7D.!!$F1 1490
10 TraesCS5B01G129100 chr4B 422027796 422029266 1470 False 1890 1890 89.891 3 1471 1 chr4B.!!$F2 1468
11 TraesCS5B01G129100 chr4B 144338970 144340454 1484 True 1869 1869 89.365 6 1498 1 chr4B.!!$R1 1492
12 TraesCS5B01G129100 chr4B 88284351 88285233 882 False 1288 1288 92.986 1511 2394 1 chr4B.!!$F1 883
13 TraesCS5B01G129100 chr5A 622527546 622529037 1491 True 1814 1814 88.621 6 1498 1 chr5A.!!$R1 1492
14 TraesCS5B01G129100 chr7B 592906886 592908375 1489 False 1783 1783 88.294 11 1501 1 chr7B.!!$F1 1490
15 TraesCS5B01G129100 chr2D 642785970 642787456 1486 True 1666 1666 86.922 11 1498 1 chr2D.!!$R1 1487
16 TraesCS5B01G129100 chr1D 244867329 244868216 887 True 1343 1343 94.052 1511 2394 1 chr1D.!!$R1 883
17 TraesCS5B01G129100 chr1B 187726545 187727432 887 False 1327 1327 93.715 1511 2394 1 chr1B.!!$F1 883
18 TraesCS5B01G129100 chr2B 339911055 339911942 887 True 1315 1315 93.490 1511 2394 1 chr2B.!!$R1 883

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
343 346 1.079819 GGTGCGAGCTGCTTAGTCA 60.08 57.895 2.53 1.88 46.63 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1512 0.940126 GGGCTGCAGATGTACATTCG 59.06 55.0 20.43 5.49 0.0 3.34 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
34 35 2.294233 ACTCAAAACAACATCGCTGCAT 59.706 40.909 0.00 0.00 0.00 3.96
166 169 1.597027 CTCTTCGGTTGGGTTGCGT 60.597 57.895 0.00 0.00 0.00 5.24
256 259 1.968493 TGTCAGTCTTTCGCCTACCTT 59.032 47.619 0.00 0.00 0.00 3.50
343 346 1.079819 GGTGCGAGCTGCTTAGTCA 60.080 57.895 2.53 1.88 46.63 3.41
365 369 3.061429 ACGTGGAAAAACATTTGCAAACG 59.939 39.130 15.41 9.25 34.13 3.60
387 391 3.263425 GGAAAGACATTGGTGGTCTAGGA 59.737 47.826 0.00 0.00 44.50 2.94
714 718 5.043737 AGGTTTTAGTGGCTACAGTTTGA 57.956 39.130 2.02 0.00 0.00 2.69
722 726 4.644685 AGTGGCTACAGTTTGACAAAACAT 59.355 37.500 2.02 0.00 46.80 2.71
867 871 2.567615 ACTACCGTTCTCTGCCAAGAAT 59.432 45.455 1.68 0.00 37.59 2.40
897 901 3.760151 CCTCCATTGTTGCTGAAGATTCA 59.240 43.478 0.00 0.00 35.57 2.57
901 905 4.158949 CCATTGTTGCTGAAGATTCATCCA 59.841 41.667 0.00 0.00 36.46 3.41
909 913 4.789807 CTGAAGATTCATCCAACCCTCAT 58.210 43.478 0.00 0.00 36.46 2.90
938 942 1.151810 TCTGGGCCTCCAAGGTTCT 60.152 57.895 4.53 0.00 43.51 3.01
948 952 3.245052 CCTCCAAGGTTCTGATCAAGGTT 60.245 47.826 0.00 0.00 0.00 3.50
1030 1034 1.016627 GCACATTGCTCAATCGGCTA 58.983 50.000 7.40 0.00 40.96 3.93
1142 1146 1.481056 CCGTCTCCAACCTCCCTTGT 61.481 60.000 0.00 0.00 0.00 3.16
1384 1388 3.266636 GCTTAACTTCCTCTCTTCAGCC 58.733 50.000 0.00 0.00 0.00 4.85
1392 1397 1.134159 CCTCTCTTCAGCCATTCCCTG 60.134 57.143 0.00 0.00 0.00 4.45
1437 1444 4.461431 TGCTGTTGTAATTCTCGACTCCTA 59.539 41.667 0.00 0.00 0.00 2.94
1774 1783 6.426937 GGATATGTACGCACACATTATTTCCT 59.573 38.462 5.57 0.00 39.77 3.36
1775 1784 7.041372 GGATATGTACGCACACATTATTTCCTT 60.041 37.037 5.57 0.00 39.77 3.36
1795 1804 4.329801 CCTTGTTGGAGAAAAAGCAAACAC 59.670 41.667 0.00 0.00 38.35 3.32
1822 1831 3.195661 AGAGTTCCTTTGTGTTGACGTC 58.804 45.455 9.11 9.11 0.00 4.34
1875 1884 4.865905 ACCCAACAATGCCATGATTACTA 58.134 39.130 0.00 0.00 0.00 1.82
1879 1888 6.545666 CCCAACAATGCCATGATTACTACTAA 59.454 38.462 0.00 0.00 0.00 2.24
1910 1919 5.906113 ACCAATTATTTCACACGCCATTA 57.094 34.783 0.00 0.00 0.00 1.90
1920 1929 7.392494 TTTCACACGCCATTATATTTAACCA 57.608 32.000 0.00 0.00 0.00 3.67
1960 1969 5.533528 AGGGCGTTGAAATTTAGTAGTTGTT 59.466 36.000 0.00 0.00 0.00 2.83
2051 2067 6.448852 TCAATGCTTTAGTAGTTGTCACGTA 58.551 36.000 0.00 0.00 0.00 3.57
2078 2094 3.118261 TGCTTTTACAAACCAATTGCCCA 60.118 39.130 0.00 0.00 43.13 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.119536 TGTTGTTTTGAGTGGATGAGTTAGT 58.880 36.000 0.00 0.00 0.00 2.24
2 3 6.618287 TGTTGTTTTGAGTGGATGAGTTAG 57.382 37.500 0.00 0.00 0.00 2.34
34 35 7.937700 AGGAGGATAAAGAACATCCAATAGA 57.062 36.000 0.00 0.00 43.85 1.98
166 169 3.233980 ACCACGTGAGAGCAGGCA 61.234 61.111 19.30 0.00 33.32 4.75
256 259 5.501413 CGTCAAGTTTAGCTACGATCGACTA 60.501 44.000 24.34 16.41 32.52 2.59
288 291 0.543410 TGGACCAGAAGAACGCCCTA 60.543 55.000 0.00 0.00 0.00 3.53
343 346 3.061429 CGTTTGCAAATGTTTTTCCACGT 59.939 39.130 21.00 0.00 0.00 4.49
365 369 3.263425 TCCTAGACCACCAATGTCTTTCC 59.737 47.826 0.00 0.00 42.78 3.13
387 391 9.893305 CGGTTGTGAACTTCTAGATTTTTAATT 57.107 29.630 0.00 0.00 0.00 1.40
714 718 4.522789 AGGTTCGCCAATAAGATGTTTTGT 59.477 37.500 0.00 0.00 40.60 2.83
722 726 2.762360 CGCAGGTTCGCCAATAAGA 58.238 52.632 0.00 0.00 40.60 2.10
867 871 1.340017 GCAACAATGGAGGAGTAGGCA 60.340 52.381 0.00 0.00 0.00 4.75
897 901 4.264083 ACAAAGTCATGATGAGGGTTGGAT 60.264 41.667 13.81 0.00 0.00 3.41
901 905 4.330250 CAGACAAAGTCATGATGAGGGTT 58.670 43.478 0.00 0.00 34.60 4.11
909 913 1.003580 GAGGCCCAGACAAAGTCATGA 59.996 52.381 0.00 0.00 34.60 3.07
938 942 5.084818 TGCGAAGATCTTAACCTTGATCA 57.915 39.130 8.25 0.00 40.92 2.92
948 952 3.493350 GGAGAAGCCATGCGAAGATCTTA 60.493 47.826 8.25 0.00 36.34 2.10
1030 1034 2.548067 GGTCTTGACAACGAGGACATGT 60.548 50.000 0.00 0.00 0.00 3.21
1142 1146 0.840617 TGGGTGTTGGTGTAGAGCAA 59.159 50.000 0.00 0.00 37.24 3.91
1206 1210 2.113860 TAGCTTCCATGCAACAGTCC 57.886 50.000 0.00 0.00 34.99 3.85
1333 1337 7.234371 TGCCTAGCATAGATATTGTCTTCTTCT 59.766 37.037 0.00 0.00 42.77 2.85
1334 1338 7.382110 TGCCTAGCATAGATATTGTCTTCTTC 58.618 38.462 0.00 0.00 42.77 2.87
1350 1354 3.303351 AGTTAAGCCATTGCCTAGCAT 57.697 42.857 0.00 0.00 38.76 3.79
1384 1388 6.207417 AGTTACAACATCAACTTCAGGGAATG 59.793 38.462 0.00 0.00 30.89 2.67
1392 1397 5.909610 GCAGTTCAGTTACAACATCAACTTC 59.090 40.000 0.00 0.00 32.72 3.01
1457 1464 3.827752 GGAGAGCTTCCCCACCTT 58.172 61.111 0.00 0.00 40.37 3.50
1498 1507 4.151335 GGCTGCAGATGTACATTCGATTAG 59.849 45.833 20.43 5.76 0.00 1.73
1499 1508 4.058124 GGCTGCAGATGTACATTCGATTA 58.942 43.478 20.43 0.00 0.00 1.75
1500 1509 2.874701 GGCTGCAGATGTACATTCGATT 59.125 45.455 20.43 0.00 0.00 3.34
1501 1510 2.487934 GGCTGCAGATGTACATTCGAT 58.512 47.619 20.43 0.00 0.00 3.59
1502 1511 1.473257 GGGCTGCAGATGTACATTCGA 60.473 52.381 20.43 0.00 0.00 3.71
1503 1512 0.940126 GGGCTGCAGATGTACATTCG 59.060 55.000 20.43 5.49 0.00 3.34
1504 1513 2.042686 TGGGCTGCAGATGTACATTC 57.957 50.000 20.43 3.64 0.00 2.67
1505 1514 2.304092 CATGGGCTGCAGATGTACATT 58.696 47.619 20.43 0.00 0.00 2.71
1506 1515 1.977056 CATGGGCTGCAGATGTACAT 58.023 50.000 20.43 8.43 0.00 2.29
1507 1516 3.482147 CATGGGCTGCAGATGTACA 57.518 52.632 20.43 8.27 0.00 2.90
1650 1659 2.624838 CTCACAACTTCCCAGCAAATGT 59.375 45.455 0.00 0.00 0.00 2.71
1774 1783 4.887748 TGTGTTTGCTTTTTCTCCAACAA 58.112 34.783 0.00 0.00 0.00 2.83
1775 1784 4.527509 TGTGTTTGCTTTTTCTCCAACA 57.472 36.364 0.00 0.00 0.00 3.33
1784 1793 4.989279 ACTCTCACATGTGTTTGCTTTT 57.011 36.364 24.63 0.90 0.00 2.27
1795 1804 4.576053 TCAACACAAAGGAACTCTCACATG 59.424 41.667 0.00 0.00 38.49 3.21
1822 1831 8.867112 AGCAGTTATTCTTTGCATTGATATTG 57.133 30.769 0.00 0.00 40.22 1.90
1879 1888 7.915397 GCGTGTGAAATAATTGGTTCTATCAAT 59.085 33.333 0.00 0.00 36.50 2.57
1887 1896 4.799564 ATGGCGTGTGAAATAATTGGTT 57.200 36.364 0.00 0.00 0.00 3.67
2051 2067 5.008514 GCAATTGGTTTGTAAAAGCAATGGT 59.991 36.000 23.28 11.44 44.57 3.55


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

AutoCloner maintained by Alex Coulton.