Multiple sequence alignment - TraesCS7B01G326800

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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 TraesCS7B01G326800 chr7B 100.000 2291 0 0 1 2291 580877361 580875071 0.000000e+00 4231.0
1 TraesCS7B01G326800 chr7B 85.577 416 43 11 1565 1966 181407885 181408297 9.790000e-114 420.0
2 TraesCS7B01G326800 chr7B 97.500 40 1 0 1503 1542 581349326 581349365 4.080000e-08 69.4
3 TraesCS7B01G326800 chr6B 98.188 1380 23 2 1 1379 159146927 159148305 0.000000e+00 2409.0
4 TraesCS7B01G326800 chr6B 87.545 1381 169 3 1 1379 412284212 412282833 0.000000e+00 1594.0
5 TraesCS7B01G326800 chr6B 87.148 1385 172 4 1 1379 708043398 708042014 0.000000e+00 1567.0
6 TraesCS7B01G326800 chr1B 97.536 1380 33 1 1 1379 321687303 321688682 0.000000e+00 2359.0
7 TraesCS7B01G326800 chr1B 87.355 1384 170 5 1 1381 550680009 550681390 0.000000e+00 1581.0
8 TraesCS7B01G326800 chr3D 96.159 1380 50 3 1 1379 433508730 433510107 0.000000e+00 2252.0
9 TraesCS7B01G326800 chr3D 86.563 387 35 11 1592 1965 418216323 418215941 5.890000e-111 411.0
10 TraesCS7B01G326800 chr3D 83.171 410 55 10 1564 1964 115034938 115034534 1.670000e-96 363.0
11 TraesCS7B01G326800 chr4A 91.151 1390 118 3 1 1387 67263559 67262172 0.000000e+00 1881.0
12 TraesCS7B01G326800 chr2A 90.416 1273 121 1 91 1362 554506905 554508177 0.000000e+00 1674.0
13 TraesCS7B01G326800 chr2B 87.328 1381 173 2 1 1379 383360205 383361585 0.000000e+00 1580.0
14 TraesCS7B01G326800 chr2B 82.381 420 62 10 1561 1968 43229141 43228722 2.800000e-94 355.0
15 TraesCS7B01G326800 chr2B 82.169 415 60 11 1564 1965 419553596 419554009 6.060000e-91 344.0
16 TraesCS7B01G326800 chr7D 92.208 924 52 13 1380 2291 538138608 538137693 0.000000e+00 1290.0
17 TraesCS7B01G326800 chr7D 85.075 67 10 0 1476 1542 538666486 538666552 4.080000e-08 69.4
18 TraesCS7B01G326800 chr7A 91.587 523 37 6 1775 2291 619257805 619257284 0.000000e+00 715.0
19 TraesCS7B01G326800 chr7A 94.276 297 12 4 1380 1671 619289898 619289602 1.250000e-122 449.0
20 TraesCS7B01G326800 chr7A 93.617 282 17 1 1966 2246 619164211 619163930 9.790000e-114 420.0
21 TraesCS7B01G326800 chr7A 93.220 177 9 3 2006 2180 619574261 619574086 8.120000e-65 257.0
22 TraesCS7B01G326800 chr7A 89.617 183 14 2 1380 1559 619574445 619574265 6.370000e-56 228.0
23 TraesCS7B01G326800 chr7A 86.667 195 15 4 1380 1563 619164396 619164202 2.980000e-49 206.0
24 TraesCS7B01G326800 chr7A 89.147 129 10 3 2167 2291 619573801 619573673 8.470000e-35 158.0
25 TraesCS7B01G326800 chr7A 97.500 40 1 0 1503 1542 620174350 620174389 4.080000e-08 69.4
26 TraesCS7B01G326800 chr3B 84.615 416 47 12 1564 1965 544546257 544545845 4.590000e-107 398.0
27 TraesCS7B01G326800 chr5D 84.300 414 49 14 1564 1965 509542677 509543086 7.670000e-105 390.0
28 TraesCS7B01G326800 chr2D 82.767 412 53 11 1564 1963 56323916 56324321 3.620000e-93 351.0


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 TraesCS7B01G326800 chr7B 580875071 580877361 2290 True 4231.000000 4231 100.000000 1 2291 1 chr7B.!!$R1 2290
1 TraesCS7B01G326800 chr6B 159146927 159148305 1378 False 2409.000000 2409 98.188000 1 1379 1 chr6B.!!$F1 1378
2 TraesCS7B01G326800 chr6B 412282833 412284212 1379 True 1594.000000 1594 87.545000 1 1379 1 chr6B.!!$R1 1378
3 TraesCS7B01G326800 chr6B 708042014 708043398 1384 True 1567.000000 1567 87.148000 1 1379 1 chr6B.!!$R2 1378
4 TraesCS7B01G326800 chr1B 321687303 321688682 1379 False 2359.000000 2359 97.536000 1 1379 1 chr1B.!!$F1 1378
5 TraesCS7B01G326800 chr1B 550680009 550681390 1381 False 1581.000000 1581 87.355000 1 1381 1 chr1B.!!$F2 1380
6 TraesCS7B01G326800 chr3D 433508730 433510107 1377 False 2252.000000 2252 96.159000 1 1379 1 chr3D.!!$F1 1378
7 TraesCS7B01G326800 chr4A 67262172 67263559 1387 True 1881.000000 1881 91.151000 1 1387 1 chr4A.!!$R1 1386
8 TraesCS7B01G326800 chr2A 554506905 554508177 1272 False 1674.000000 1674 90.416000 91 1362 1 chr2A.!!$F1 1271
9 TraesCS7B01G326800 chr2B 383360205 383361585 1380 False 1580.000000 1580 87.328000 1 1379 1 chr2B.!!$F1 1378
10 TraesCS7B01G326800 chr7D 538137693 538138608 915 True 1290.000000 1290 92.208000 1380 2291 1 chr7D.!!$R1 911
11 TraesCS7B01G326800 chr7A 619257284 619257805 521 True 715.000000 715 91.587000 1775 2291 1 chr7A.!!$R1 516
12 TraesCS7B01G326800 chr7A 619573673 619574445 772 True 214.333333 257 90.661333 1380 2291 3 chr7A.!!$R4 911

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
58 59 0.338814 ACTACCAACCCCTCGAGGAT 59.661 55.0 33.39 17.57 38.24 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1849 0.251916 TCTCCCATGCGAAATTCCGT 59.748 50.0 0.0 0.0 0.0 4.69 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
46 47 6.043243 AGAGGTTGAAGAGAATTCACTACCAA 59.957 38.462 19.35 16.11 33.80 3.67
58 59 0.338814 ACTACCAACCCCTCGAGGAT 59.661 55.000 33.39 17.57 38.24 3.24
537 545 1.686115 CCCAAAGACATGGCCCCTAAG 60.686 57.143 0.00 0.00 39.26 2.18
1069 1078 0.879400 TGCCGCGACTTCCGTTAAAA 60.879 50.000 8.23 0.00 41.15 1.52
1132 1141 2.373169 AGACCACTTGCTTCCTTGATGA 59.627 45.455 0.00 0.00 0.00 2.92
1190 1199 4.142337 TGCACGGATCTTTCGTAATACTGA 60.142 41.667 0.00 0.00 38.94 3.41
1297 1306 0.233332 GCCGCGAGAGTGATTATTGC 59.767 55.000 8.23 0.00 46.66 3.56
1424 1433 5.241285 ACCGTTAAAACCAATACAAACCGAT 59.759 36.000 0.00 0.00 0.00 4.18
1451 1461 9.793252 CAGGAGATGATACAAACAATAAAAAGG 57.207 33.333 0.00 0.00 0.00 3.11
1500 1513 7.278203 GCCTTATGAGTACTTCTTAACAAGGAC 59.722 40.741 15.61 0.00 37.48 3.85
1501 1514 7.488471 CCTTATGAGTACTTCTTAACAAGGACG 59.512 40.741 0.00 0.00 41.57 4.79
1588 1601 2.306715 TATACAGGAGCTCCCGGGCA 62.307 60.000 29.54 13.97 40.87 5.36
1607 1620 1.681793 CACTCCACACCCCTATACGAG 59.318 57.143 0.00 0.00 0.00 4.18
1610 1623 2.883386 CTCCACACCCCTATACGAGTAC 59.117 54.545 0.00 0.00 0.00 2.73
1667 1683 7.605410 AATGAAATTAGGCAAATCAAAGCTG 57.395 32.000 0.00 0.00 32.46 4.24
1668 1684 6.100404 TGAAATTAGGCAAATCAAAGCTGT 57.900 33.333 0.00 0.00 0.00 4.40
1671 1687 4.935352 TTAGGCAAATCAAAGCTGTGTT 57.065 36.364 3.21 0.00 0.00 3.32
1682 1698 5.610398 TCAAAGCTGTGTTCTCAATCTACA 58.390 37.500 3.21 0.00 0.00 2.74
1683 1699 5.466728 TCAAAGCTGTGTTCTCAATCTACAC 59.533 40.000 3.21 0.00 41.85 2.90
1737 1758 2.104281 AGGTATGCGTGGGGAAATACTC 59.896 50.000 0.00 0.00 0.00 2.59
1740 1761 0.174845 TGCGTGGGGAAATACTCTCG 59.825 55.000 0.00 0.00 0.00 4.04
1846 1869 0.251916 ACGGAATTTCGCATGGGAGA 59.748 50.000 12.66 9.06 0.00 3.71
1859 1882 2.534042 TGGGAGAAGATCGAGAACCT 57.466 50.000 0.00 0.00 0.00 3.50
1880 1906 7.554959 ACCTAGGTTCGATATCCACAAATAT 57.445 36.000 9.21 0.00 0.00 1.28
1980 2008 4.039973 CCGCTTCCAGGTCCATTATTACTA 59.960 45.833 0.00 0.00 0.00 1.82
2035 2063 2.230992 GCATGACACTATTGTTGGCCAA 59.769 45.455 16.05 16.05 35.47 4.52
2041 2071 2.489329 CACTATTGTTGGCCAACCTCTG 59.511 50.000 38.90 28.39 40.46 3.35
2096 2126 2.548875 ACACATGTTGTTTTGCGCAAT 58.451 38.095 25.64 3.58 33.09 3.56
2112 2142 2.159198 CGCAATCCATGAAGGGGAAAAG 60.159 50.000 0.00 0.00 38.09 2.27
2121 2151 3.091545 TGAAGGGGAAAAGCATCATGAC 58.908 45.455 0.00 0.00 0.00 3.06
2240 2569 8.996271 ACTAAGGTAAATAAGTTGTGTACTTGC 58.004 33.333 0.57 0.00 46.46 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.694696 GCAATCTTATCCTCGAGGGGT 59.305 52.381 30.80 21.31 35.41 4.95
58 59 0.901827 TGAGCTGACCCGCAATCTTA 59.098 50.000 0.00 0.00 0.00 2.10
113 114 2.391724 GACTTGACCAAGACCGCCCA 62.392 60.000 15.84 0.00 40.79 5.36
537 545 9.737427 TTCTTCTTCTTCGACAACTCATATATC 57.263 33.333 0.00 0.00 0.00 1.63
1132 1141 5.488919 TCCACAACTCCCAAGAGATAAGAAT 59.511 40.000 0.00 0.00 43.39 2.40
1190 1199 0.991920 AATGACTCCAACCGGGACAT 59.008 50.000 6.32 0.00 42.15 3.06
1451 1461 6.183360 GGCACTACCAACAGATGAATTAGTTC 60.183 42.308 0.00 0.00 38.86 3.01
1500 1513 2.535984 GAGAACATTCTGTGATACGGCG 59.464 50.000 4.80 4.80 37.73 6.46
1501 1514 2.535984 CGAGAACATTCTGTGATACGGC 59.464 50.000 0.00 0.00 37.73 5.68
1588 1601 1.287146 ACTCGTATAGGGGTGTGGAGT 59.713 52.381 0.00 0.00 0.00 3.85
1591 1604 2.941480 AGTACTCGTATAGGGGTGTGG 58.059 52.381 8.22 0.00 0.00 4.17
1645 1658 5.927689 CACAGCTTTGATTTGCCTAATTTCA 59.072 36.000 0.00 0.00 0.00 2.69
1646 1659 5.928264 ACACAGCTTTGATTTGCCTAATTTC 59.072 36.000 6.92 0.00 0.00 2.17
1649 1665 5.244626 AGAACACAGCTTTGATTTGCCTAAT 59.755 36.000 6.92 0.00 0.00 1.73
1652 1668 2.961062 AGAACACAGCTTTGATTTGCCT 59.039 40.909 6.92 0.00 0.00 4.75
1664 1680 3.003480 GGGTGTAGATTGAGAACACAGC 58.997 50.000 7.10 0.00 44.18 4.40
1667 1683 2.993899 CACGGGTGTAGATTGAGAACAC 59.006 50.000 0.00 0.00 42.17 3.32
1668 1684 2.631062 ACACGGGTGTAGATTGAGAACA 59.369 45.455 1.96 0.00 42.90 3.18
1671 1687 2.521126 TCACACGGGTGTAGATTGAGA 58.479 47.619 19.06 0.00 45.45 3.27
1682 1698 1.956297 TCACGAAATTTCACACGGGT 58.044 45.000 17.99 3.90 0.00 5.28
1683 1699 3.341857 TTTCACGAAATTTCACACGGG 57.658 42.857 17.99 5.99 0.00 5.28
1707 1723 2.432444 CCACGCATACCTTTTCTGGAA 58.568 47.619 0.00 0.00 0.00 3.53
1714 1731 2.525105 ATTTCCCCACGCATACCTTT 57.475 45.000 0.00 0.00 0.00 3.11
1717 1734 2.104281 AGAGTATTTCCCCACGCATACC 59.896 50.000 0.00 0.00 0.00 2.73
1718 1735 3.391049 GAGAGTATTTCCCCACGCATAC 58.609 50.000 0.00 0.00 0.00 2.39
1737 1758 4.782019 TTGGATGGATTTTTGTTCCGAG 57.218 40.909 0.00 0.00 35.94 4.63
1740 1761 5.610398 ACTGTTTGGATGGATTTTTGTTCC 58.390 37.500 0.00 0.00 0.00 3.62
1826 1848 0.378257 CTCCCATGCGAAATTCCGTG 59.622 55.000 0.00 0.00 0.00 4.94
1827 1849 0.251916 TCTCCCATGCGAAATTCCGT 59.748 50.000 0.00 0.00 0.00 4.69
1828 1850 1.331756 CTTCTCCCATGCGAAATTCCG 59.668 52.381 0.00 0.00 0.00 4.30
1829 1851 2.643551 TCTTCTCCCATGCGAAATTCC 58.356 47.619 0.00 0.00 0.00 3.01
1837 1860 2.478831 GTTCTCGATCTTCTCCCATGC 58.521 52.381 0.00 0.00 0.00 4.06
1840 1863 2.534042 AGGTTCTCGATCTTCTCCCA 57.466 50.000 0.00 0.00 0.00 4.37
1980 2008 6.952773 TGCAAGTGTAGGAAACAATAAGTT 57.047 33.333 0.00 0.00 40.63 2.66
2014 2042 1.818060 TGGCCAACAATAGTGTCATGC 59.182 47.619 0.61 0.00 36.80 4.06
2035 2063 4.461781 CAGCAATCTTTTGATTCCAGAGGT 59.538 41.667 0.00 0.00 46.51 3.85
2041 2071 3.766051 AGGACCAGCAATCTTTTGATTCC 59.234 43.478 0.00 0.00 46.51 3.01
2096 2126 2.042842 TGATGCTTTTCCCCTTCATGGA 59.957 45.455 0.00 0.00 38.35 3.41
2112 2142 4.788840 GCTTTGTGATAGCAGTCATGATGC 60.789 45.833 17.30 17.30 44.18 3.91
2121 2151 0.729116 CGGTGGCTTTGTGATAGCAG 59.271 55.000 0.00 0.00 40.42 4.24
2240 2569 7.759433 GTGGGACATAAATAATCACAACCTTTG 59.241 37.037 0.00 0.00 44.52 2.77
2260 2589 7.882179 ACAACTCAAAAAGTAATATGTGGGAC 58.118 34.615 0.00 0.00 37.17 4.46


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

AutoCloner maintained by Alex Coulton.