Multiple sequence alignment - TraesCS2B01G437000

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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 TraesCS2B01G437000 chr2B 100.000 2354 0 0 1 2354 628806467 628804114 0.000000e+00 4348
1 TraesCS2B01G437000 chr2D 91.700 2024 65 41 1 1971 529178963 529176990 0.000000e+00 2712
2 TraesCS2B01G437000 chr2D 96.834 379 12 0 1976 2354 529176962 529176584 3.300000e-178 634
3 TraesCS2B01G437000 chr2A 87.879 2013 127 54 1 1970 674000665 674002603 0.000000e+00 2257
4 TraesCS2B01G437000 chr2A 90.909 396 16 9 1976 2354 674002633 674003025 4.490000e-142 514


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 TraesCS2B01G437000 chr2B 628804114 628806467 2353 True 4348.0 4348 100.000 1 2354 1 chr2B.!!$R1 2353
1 TraesCS2B01G437000 chr2D 529176584 529178963 2379 True 1673.0 2712 94.267 1 2354 2 chr2D.!!$R1 2353
2 TraesCS2B01G437000 chr2A 674000665 674003025 2360 False 1385.5 2257 89.394 1 2354 2 chr2A.!!$F1 2353

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
725 787 0.379669 CGTGGTCCTATTCGTACGCT 59.62 55.0 11.24 2.7 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1907 0.179089 ATCATCTGGACTGCGTCTGC 60.179 55.0 8.26 0.0 43.2 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
31 32 2.819154 TGTGTCGGCCATGCGATG 60.819 61.111 2.24 0.00 0.00 3.84
65 66 3.860605 TCCGCACACTGCACCACT 61.861 61.111 0.00 0.00 45.36 4.00
124 142 2.980233 AACGCACTGCAGCTTCCC 60.980 61.111 15.27 0.00 0.00 3.97
553 598 3.005554 GGAAAAGACGGGTAGTAAAGCC 58.994 50.000 0.00 0.00 42.76 4.35
725 787 0.379669 CGTGGTCCTATTCGTACGCT 59.620 55.000 11.24 2.70 0.00 5.07
792 854 3.357079 GGCTGTCAGCGTTGGTGG 61.357 66.667 18.44 0.00 43.62 4.61
994 1073 3.749064 GCTCCGAGCCGTGTGAGA 61.749 66.667 9.42 0.00 34.48 3.27
1239 1334 3.060020 GCAGGAGTACGGCTACGCA 62.060 63.158 0.00 0.00 46.04 5.24
1355 1450 2.648102 CGCCGTCGTCGTCTGATC 60.648 66.667 0.71 0.00 35.01 2.92
1356 1451 2.483745 GCCGTCGTCGTCTGATCA 59.516 61.111 0.71 0.00 35.01 2.92
1359 1454 0.654760 CCGTCGTCGTCTGATCATCG 60.655 60.000 12.28 12.28 35.01 3.84
1360 1455 0.300789 CGTCGTCGTCTGATCATCGA 59.699 55.000 15.72 15.72 0.00 3.59
1368 1463 2.980586 GTCTGATCATCGACGAGTGAG 58.019 52.381 3.01 0.00 0.00 3.51
1369 1464 1.332065 TCTGATCATCGACGAGTGAGC 59.668 52.381 14.48 14.48 0.00 4.26
1370 1465 0.028110 TGATCATCGACGAGTGAGCG 59.972 55.000 15.57 0.00 33.68 5.03
1371 1466 0.305009 GATCATCGACGAGTGAGCGA 59.695 55.000 3.01 0.00 38.51 4.93
1372 1467 0.306228 ATCATCGACGAGTGAGCGAG 59.694 55.000 3.01 0.00 37.48 5.03
1373 1468 1.297967 CATCGACGAGTGAGCGAGG 60.298 63.158 3.01 0.00 37.48 4.63
1374 1469 1.449778 ATCGACGAGTGAGCGAGGA 60.450 57.895 3.01 0.00 37.48 3.71
1395 1502 3.507009 GAGCGACCTCGTAGCCGT 61.507 66.667 0.00 0.00 42.22 5.68
1396 1503 2.124983 AGCGACCTCGTAGCCGTA 60.125 61.111 0.00 0.00 42.22 4.02
1491 1600 2.331451 GCTGTTCGGTGGTTGTGC 59.669 61.111 0.00 0.00 0.00 4.57
1492 1601 2.186826 GCTGTTCGGTGGTTGTGCT 61.187 57.895 0.00 0.00 0.00 4.40
1493 1602 1.724582 GCTGTTCGGTGGTTGTGCTT 61.725 55.000 0.00 0.00 0.00 3.91
1494 1603 0.029300 CTGTTCGGTGGTTGTGCTTG 59.971 55.000 0.00 0.00 0.00 4.01
1496 1605 0.028902 GTTCGGTGGTTGTGCTTGTC 59.971 55.000 0.00 0.00 0.00 3.18
1497 1606 0.107410 TTCGGTGGTTGTGCTTGTCT 60.107 50.000 0.00 0.00 0.00 3.41
1500 1609 1.230324 GGTGGTTGTGCTTGTCTCTC 58.770 55.000 0.00 0.00 0.00 3.20
1501 1610 0.861837 GTGGTTGTGCTTGTCTCTCG 59.138 55.000 0.00 0.00 0.00 4.04
1502 1611 0.750249 TGGTTGTGCTTGTCTCTCGA 59.250 50.000 0.00 0.00 0.00 4.04
1505 1614 0.318699 TTGTGCTTGTCTCTCGACGG 60.319 55.000 0.00 0.00 43.21 4.79
1526 1637 1.048160 AGGGCTGAGGCTTCTAGCTC 61.048 60.000 15.90 13.45 41.99 4.09
1544 1655 0.530744 TCGACTCCATTTGGGACTCG 59.469 55.000 6.19 6.19 46.90 4.18
1673 1786 3.740115 AGTACGTGCAAATCTTCACCTT 58.260 40.909 6.38 0.00 0.00 3.50
1747 1860 7.217200 TCTTCATGCGGCTATAACTAATTTCT 58.783 34.615 0.00 0.00 0.00 2.52
1767 1880 6.823678 TTCTTCGTGTTAGTTGAGAACTTC 57.176 37.500 0.00 0.00 42.81 3.01
1789 1902 9.001542 ACTTCTACACCGATACATACTTAGATC 57.998 37.037 0.00 0.00 0.00 2.75
1790 1903 8.913487 TTCTACACCGATACATACTTAGATCA 57.087 34.615 0.00 0.00 0.00 2.92
1791 1904 8.549338 TCTACACCGATACATACTTAGATCAG 57.451 38.462 0.00 0.00 0.00 2.90
1792 1905 8.373220 TCTACACCGATACATACTTAGATCAGA 58.627 37.037 0.00 0.00 0.00 3.27
1793 1906 7.204496 ACACCGATACATACTTAGATCAGAC 57.796 40.000 0.00 0.00 0.00 3.51
1794 1907 6.073167 ACACCGATACATACTTAGATCAGACG 60.073 42.308 0.00 0.00 0.00 4.18
1835 1948 1.284491 TGCATGGCCCAAAGATGTCTA 59.716 47.619 0.00 0.00 0.00 2.59
1836 1949 1.678101 GCATGGCCCAAAGATGTCTAC 59.322 52.381 0.00 0.00 0.00 2.59
1837 1950 2.684927 GCATGGCCCAAAGATGTCTACT 60.685 50.000 0.00 0.00 0.00 2.57
1838 1951 3.209410 CATGGCCCAAAGATGTCTACTC 58.791 50.000 0.00 0.00 0.00 2.59
1839 1952 2.551270 TGGCCCAAAGATGTCTACTCT 58.449 47.619 0.00 0.00 0.00 3.24
1858 1971 2.764010 TCTAACCCTTCGCTTATCTGCA 59.236 45.455 0.00 0.00 0.00 4.41
1920 2034 4.156556 GGCCTCGATAACCGTATACATACA 59.843 45.833 3.32 0.00 39.75 2.29
1921 2035 5.163581 GGCCTCGATAACCGTATACATACAT 60.164 44.000 3.32 0.00 39.75 2.29
1922 2036 6.038603 GGCCTCGATAACCGTATACATACATA 59.961 42.308 3.32 0.00 39.75 2.29
1923 2037 6.909357 GCCTCGATAACCGTATACATACATAC 59.091 42.308 3.32 0.00 39.75 2.39
1973 2087 5.233225 CCATCACAGAATGCGTATCTATGT 58.767 41.667 0.00 0.00 42.53 2.29
1974 2088 5.698089 CCATCACAGAATGCGTATCTATGTT 59.302 40.000 0.00 0.00 42.53 2.71
2072 2219 0.807667 CCGTGCATGTAGCTCAGTCC 60.808 60.000 4.96 0.00 45.94 3.85
2096 2247 5.414454 CAGTCTAGCTAGTCTCAACAACTCT 59.586 44.000 20.10 0.00 0.00 3.24
2208 2359 2.093235 GCCTCTGCTTTCTGATGGTACT 60.093 50.000 0.00 0.00 33.53 2.73
2216 2367 4.574013 GCTTTCTGATGGTACTGGAGAATG 59.426 45.833 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.094675 GGCGGGTACAGTAACAGTAGA 58.905 52.381 0.00 0.00 0.00 2.59
106 107 2.253452 GGAAGCTGCAGTGCGTTG 59.747 61.111 16.64 4.43 38.13 4.10
110 111 2.749441 GAGGGGAAGCTGCAGTGC 60.749 66.667 16.64 8.58 0.00 4.40
112 113 3.334054 GGGAGGGGAAGCTGCAGT 61.334 66.667 16.64 0.00 0.00 4.40
113 114 4.120755 GGGGAGGGGAAGCTGCAG 62.121 72.222 10.11 10.11 0.00 4.41
379 419 2.426023 GTCCGCCACTCCACTTGT 59.574 61.111 0.00 0.00 0.00 3.16
553 598 0.793478 CTCGACACGTCAAGCCTACG 60.793 60.000 0.00 1.95 45.64 3.51
561 606 0.249699 AACCATTGCTCGACACGTCA 60.250 50.000 0.00 0.00 0.00 4.35
1140 1235 4.824515 CGCTCCGTCTCCTCCCCT 62.825 72.222 0.00 0.00 0.00 4.79
1354 1449 1.706287 CCTCGCTCACTCGTCGATGA 61.706 60.000 7.21 7.21 0.00 2.92
1355 1450 1.297967 CCTCGCTCACTCGTCGATG 60.298 63.158 0.00 0.00 0.00 3.84
1356 1451 1.025113 TTCCTCGCTCACTCGTCGAT 61.025 55.000 0.00 0.00 0.00 3.59
1359 1454 1.515304 GCTTCCTCGCTCACTCGTC 60.515 63.158 0.00 0.00 0.00 4.20
1360 1455 2.569134 GCTTCCTCGCTCACTCGT 59.431 61.111 0.00 0.00 0.00 4.18
1364 1459 2.883253 GCTCGCTTCCTCGCTCAC 60.883 66.667 0.00 0.00 0.00 3.51
1365 1460 4.482684 CGCTCGCTTCCTCGCTCA 62.483 66.667 0.00 0.00 0.00 4.26
1366 1461 4.180946 TCGCTCGCTTCCTCGCTC 62.181 66.667 0.00 0.00 0.00 5.03
1367 1462 4.484258 GTCGCTCGCTTCCTCGCT 62.484 66.667 0.00 0.00 0.00 4.93
1369 1464 3.743091 GAGGTCGCTCGCTTCCTCG 62.743 68.421 11.33 0.00 37.35 4.63
1370 1465 2.103340 GAGGTCGCTCGCTTCCTC 59.897 66.667 11.33 11.33 39.41 3.71
1371 1466 3.816524 CGAGGTCGCTCGCTTCCT 61.817 66.667 0.00 2.37 40.05 3.36
1396 1503 8.893727 ACAAGATCACGCTAAAATTAAGCTATT 58.106 29.630 10.12 0.00 37.85 1.73
1496 1605 3.522731 CAGCCCTCCCGTCGAGAG 61.523 72.222 0.00 0.00 41.63 3.20
1497 1606 3.997400 CTCAGCCCTCCCGTCGAGA 62.997 68.421 0.00 0.00 41.63 4.04
1505 1614 2.038814 GCTAGAAGCCTCAGCCCTCC 62.039 65.000 0.00 0.00 41.25 4.30
1544 1655 5.612351 AGTACCAAGAACTGAAGAAGAACC 58.388 41.667 0.00 0.00 0.00 3.62
1673 1786 3.637229 AGAAAGAGACTGAACGAACAGGA 59.363 43.478 15.14 0.00 41.59 3.86
1747 1860 6.694411 GTGTAGAAGTTCTCAACTAACACGAA 59.306 38.462 9.12 0.00 41.91 3.85
1767 1880 8.444715 GTCTGATCTAAGTATGTATCGGTGTAG 58.555 40.741 0.00 0.00 0.00 2.74
1794 1907 0.179089 ATCATCTGGACTGCGTCTGC 60.179 55.000 8.26 0.00 43.20 4.26
1835 1948 3.181474 GCAGATAAGCGAAGGGTTAGAGT 60.181 47.826 0.00 0.00 39.29 3.24
1836 1949 3.181475 TGCAGATAAGCGAAGGGTTAGAG 60.181 47.826 0.00 0.00 39.29 2.43
1837 1950 2.764010 TGCAGATAAGCGAAGGGTTAGA 59.236 45.455 0.00 0.00 39.29 2.10
1838 1951 3.179443 TGCAGATAAGCGAAGGGTTAG 57.821 47.619 0.00 0.00 39.29 2.34
1839 1952 3.055385 AGTTGCAGATAAGCGAAGGGTTA 60.055 43.478 0.00 0.00 40.13 2.85
1858 1971 2.825532 AGTTGGCACACAAGACAAAGTT 59.174 40.909 0.00 0.00 40.38 2.66
2072 2219 5.414454 AGAGTTGTTGAGACTAGCTAGACTG 59.586 44.000 26.87 3.34 0.00 3.51
2096 2247 2.221299 CGTCCTTGGACCTTGGGGA 61.221 63.158 13.53 0.00 36.25 4.81


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

AutoCloner maintained by Alex Coulton.