Multiple sequence alignment - TraesCS1D01G097300

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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 TraesCS1D01G097300 chr1D 100.000 2201 0 0 1 2201 83914582 83916782 0.000000e+00 4065.0
1 TraesCS1D01G097300 chr1D 82.258 372 55 8 1562 1929 195998386 195998750 5.900000e-81 311.0
2 TraesCS1D01G097300 chr1B 95.153 1568 39 12 1 1546 136926695 136928247 0.000000e+00 2440.0
3 TraesCS1D01G097300 chr1B 86.325 468 54 8 1560 2023 540713039 540713500 3.260000e-138 501.0
4 TraesCS1D01G097300 chr1A 94.017 1571 57 15 1 1547 100417771 100419328 0.000000e+00 2346.0
5 TraesCS1D01G097300 chr1A 87.500 344 36 5 1562 1899 118556203 118556545 7.370000e-105 390.0
6 TraesCS1D01G097300 chr7B 84.722 504 58 10 1565 2052 678095156 678094656 9.130000e-134 486.0
7 TraesCS1D01G097300 chr7B 89.781 137 14 0 2065 2201 678094671 678094535 2.250000e-40 176.0
8 TraesCS1D01G097300 chr4D 90.000 340 28 5 1565 1899 51300401 51300739 3.360000e-118 435.0
9 TraesCS1D01G097300 chr4D 91.241 137 11 1 2065 2201 51300904 51301039 3.730000e-43 185.0
10 TraesCS1D01G097300 chr7A 88.235 340 33 5 1566 1899 722767472 722767134 1.220000e-107 399.0
11 TraesCS1D01G097300 chr7A 90.511 137 12 1 2065 2201 722766970 722766835 1.740000e-41 180.0
12 TraesCS1D01G097300 chr2B 86.471 340 43 3 1562 1899 512489368 512489030 9.600000e-99 370.0
13 TraesCS1D01G097300 chr2B 91.971 137 10 1 2065 2201 512488868 512488733 8.020000e-45 191.0
14 TraesCS1D01G097300 chr2B 100.000 28 0 0 886 913 103794715 103794742 4.000000e-03 52.8
15 TraesCS1D01G097300 chr3D 83.514 370 54 7 1566 1929 483003763 483004131 2.710000e-89 339.0
16 TraesCS1D01G097300 chr3D 89.781 137 13 1 2065 2201 395522180 395522315 8.080000e-40 174.0
17 TraesCS1D01G097300 chr5D 82.888 374 57 7 1560 1929 84681996 84682366 1.630000e-86 329.0
18 TraesCS1D01G097300 chr5A 89.595 173 15 3 1881 2052 487747547 487747377 1.320000e-52 217.0
19 TraesCS1D01G097300 chr5A 91.852 135 10 1 2067 2201 487747390 487747257 1.040000e-43 187.0
20 TraesCS1D01G097300 chr7D 90.511 137 12 1 2065 2201 604991413 604991278 1.740000e-41 180.0
21 TraesCS1D01G097300 chr6D 90.511 137 12 1 2065 2201 278629529 278629394 1.740000e-41 180.0
22 TraesCS1D01G097300 chr2D 89.781 137 13 1 2065 2201 592377418 592377283 8.080000e-40 174.0
23 TraesCS1D01G097300 chr2D 100.000 28 0 0 886 913 67443219 67443192 4.000000e-03 52.8
24 TraesCS1D01G097300 chr2D 100.000 28 0 0 886 913 67445849 67445822 4.000000e-03 52.8
25 TraesCS1D01G097300 chr2A 100.000 28 0 0 886 913 66914715 66914742 4.000000e-03 52.8


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 TraesCS1D01G097300 chr1D 83914582 83916782 2200 False 4065.0 4065 100.0000 1 2201 1 chr1D.!!$F1 2200
1 TraesCS1D01G097300 chr1B 136926695 136928247 1552 False 2440.0 2440 95.1530 1 1546 1 chr1B.!!$F1 1545
2 TraesCS1D01G097300 chr1A 100417771 100419328 1557 False 2346.0 2346 94.0170 1 1547 1 chr1A.!!$F1 1546
3 TraesCS1D01G097300 chr7B 678094535 678095156 621 True 331.0 486 87.2515 1565 2201 2 chr7B.!!$R1 636
4 TraesCS1D01G097300 chr4D 51300401 51301039 638 False 310.0 435 90.6205 1565 2201 2 chr4D.!!$F1 636
5 TraesCS1D01G097300 chr7A 722766835 722767472 637 True 289.5 399 89.3730 1566 2201 2 chr7A.!!$R1 635
6 TraesCS1D01G097300 chr2B 512488733 512489368 635 True 280.5 370 89.2210 1562 2201 2 chr2B.!!$R1 639

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
110 118 0.031585 CGAACGAGATTGCCGGGATA 59.968 55.0 2.18 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1732 0.526954 CGTATCCAAGCGCGGTTAGT 60.527 55.0 24.58 14.37 0.0 2.24 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
28 30 7.067496 AGAGTCCTGATAAAACTGACTTCAA 57.933 36.000 0.00 0.00 0.00 2.69
41 43 6.515272 ACTGACTTCAACAGTTCAACATTT 57.485 33.333 0.00 0.00 44.69 2.32
110 118 0.031585 CGAACGAGATTGCCGGGATA 59.968 55.000 2.18 0.00 0.00 2.59
243 262 5.874093 TCTCTGAGGAGCAAAAGAAAATCT 58.126 37.500 4.59 0.00 39.31 2.40
254 286 1.154488 GAAAATCTCAACGCGCGCA 60.154 52.632 32.58 13.54 0.00 6.09
284 316 2.300152 AGTTGGTCTGATGCTTCGAAGA 59.700 45.455 28.95 13.86 0.00 2.87
312 344 0.467844 AGCACTGTGATTGGCCAACA 60.468 50.000 23.27 17.83 0.00 3.33
1106 1147 1.016130 ACGCGCATCTTGGAGAACAG 61.016 55.000 5.73 0.00 0.00 3.16
1224 1265 3.000322 CACTCTGTCGATATTTCGGTTGC 60.000 47.826 5.72 0.00 45.53 4.17
1257 1298 2.993899 ACGATGATTTGTGGAAGACGAC 59.006 45.455 0.00 0.00 0.00 4.34
1258 1299 2.028045 CGATGATTTGTGGAAGACGACG 59.972 50.000 0.00 0.00 0.00 5.12
1259 1300 2.804697 TGATTTGTGGAAGACGACGA 57.195 45.000 0.00 0.00 0.00 4.20
1304 1345 7.174599 AGCTATGAATGATTCTCAATGGTAAGC 59.825 37.037 6.73 0.00 0.00 3.09
1343 1384 1.135094 TGATCCAAGGGAGATGGCTC 58.865 55.000 0.00 0.00 40.54 4.70
1376 1417 3.075884 GGTCGTAGGGTTGCAATGTTTA 58.924 45.455 0.59 0.00 0.00 2.01
1384 1425 3.320826 GGGTTGCAATGTTTAGTCTGGTT 59.679 43.478 0.59 0.00 0.00 3.67
1439 1480 3.532641 AGGGTCTTTTTGCTGGAAGAT 57.467 42.857 0.00 0.00 34.68 2.40
1473 1514 5.348451 GCATGGGTTGTGTTAATTTAAGCTG 59.652 40.000 0.00 0.00 0.00 4.24
1517 1558 4.328983 CGTTCATGTCGGTAGCTTAACAAT 59.671 41.667 0.00 0.00 0.00 2.71
1585 1626 3.167485 AGAGTCAATTACACCGGTGGTA 58.833 45.455 36.47 24.26 32.11 3.25
1609 1650 1.598601 GAACTTGGCGTAAACGGTCAA 59.401 47.619 4.49 0.00 40.23 3.18
1617 1658 2.287129 GCGTAAACGGTCAATTTGGTGT 60.287 45.455 4.49 0.00 40.23 4.16
1630 1671 5.654650 TCAATTTGGTGTTAGAACTTGTGGT 59.345 36.000 0.00 0.00 0.00 4.16
1634 1675 9.528489 AATTTGGTGTTAGAACTTGTGGTATAT 57.472 29.630 0.00 0.00 0.00 0.86
1678 1732 2.933492 GCTCGGGTGTGCAAATACAGTA 60.933 50.000 0.00 0.00 34.77 2.74
1687 1741 2.924926 TGCAAATACAGTACTAACCGCG 59.075 45.455 0.00 0.00 0.00 6.46
1705 1759 2.032894 CGCGCTTGGATACGAAATCAAT 60.033 45.455 5.56 0.00 42.51 2.57
1715 1769 5.294306 GGATACGAAATCAATGCTGACTTGA 59.706 40.000 0.00 0.00 37.06 3.02
1723 1777 0.399454 ATGCTGACTTGACTGCCAGT 59.601 50.000 0.00 0.00 34.63 4.00
1746 1800 4.416738 GTGGGGCCCTCTGTCAGC 62.417 72.222 25.93 1.93 0.00 4.26
1762 1816 1.954382 TCAGCGACTAGAAGTGTGTGT 59.046 47.619 0.00 0.00 0.00 3.72
1766 1821 2.486982 GCGACTAGAAGTGTGTGTCCTA 59.513 50.000 0.00 0.00 0.00 2.94
1920 2010 2.628657 AGACTCCTACACTCCAACACAC 59.371 50.000 0.00 0.00 0.00 3.82
1925 2015 1.340248 CTACACTCCAACACACGACCT 59.660 52.381 0.00 0.00 0.00 3.85
1926 2016 1.405872 ACACTCCAACACACGACCTA 58.594 50.000 0.00 0.00 0.00 3.08
1927 2017 1.068127 ACACTCCAACACACGACCTAC 59.932 52.381 0.00 0.00 0.00 3.18
1967 2059 2.718073 CGCGGCCTACTGTTAGGGT 61.718 63.158 0.00 0.00 44.91 4.34
1975 2067 1.808531 TACTGTTAGGGTGCACGCGT 61.809 55.000 25.95 19.44 0.00 6.01
2002 2094 2.230992 GCCACTGCACCAATTACATTCA 59.769 45.455 0.00 0.00 37.47 2.57
2018 2110 8.723942 ATTACATTCAGATGTCTAACAAGGAC 57.276 34.615 0.00 0.00 42.83 3.85
2024 2116 5.070446 TCAGATGTCTAACAAGGACAACAGT 59.930 40.000 0.72 0.00 45.09 3.55
2102 2194 0.460811 GGGCTTAAATTGGCTGCAGC 60.461 55.000 30.88 30.88 41.14 5.25
2123 2215 3.229501 TGCGGCCCATTTTGCACA 61.230 55.556 0.00 0.00 31.31 4.57
2124 2216 2.265424 GCGGCCCATTTTGCACAT 59.735 55.556 0.00 0.00 0.00 3.21
2141 2233 4.553323 GCACATGCAAGTTCTCTTTGAAT 58.447 39.130 0.00 0.00 41.59 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.515272 AAATGTTGAACTGTTGAAGTCAGT 57.485 33.333 0.00 0.00 46.30 3.41
28 30 5.721876 TCGTTTACGAAATGTTGAACTGT 57.278 34.783 1.95 0.00 46.30 3.55
110 118 2.123428 GCTTCATTGCCATCCGCCT 61.123 57.895 0.00 0.00 36.24 5.52
254 286 1.311859 TCAGACCAACTCGTACGTGT 58.688 50.000 16.65 16.65 0.00 4.49
259 291 2.415491 CGAAGCATCAGACCAACTCGTA 60.415 50.000 0.00 0.00 0.00 3.43
284 316 0.822811 ATCACAGTGCTGCTCGATCT 59.177 50.000 0.00 0.00 0.00 2.75
312 344 4.201891 CGGCTCACTTAGAACACGTAGTAT 60.202 45.833 0.00 0.00 41.61 2.12
1183 1224 2.803155 GATCACAACGGGCTCCTGCA 62.803 60.000 0.00 0.00 41.91 4.41
1257 1298 1.662608 CTCCTCCATCCGTCCATCG 59.337 63.158 0.00 0.00 39.52 3.84
1258 1299 1.369321 GCTCCTCCATCCGTCCATC 59.631 63.158 0.00 0.00 0.00 3.51
1259 1300 0.982852 TTGCTCCTCCATCCGTCCAT 60.983 55.000 0.00 0.00 0.00 3.41
1304 1345 3.068732 TCATTCGTAGCCTCCAAGATCTG 59.931 47.826 0.00 0.00 0.00 2.90
1343 1384 1.005294 CTACGACCCAAACCGTCACG 61.005 60.000 0.00 0.00 39.86 4.35
1376 1417 4.411212 ACCCACTAAACTAACAACCAGACT 59.589 41.667 0.00 0.00 0.00 3.24
1384 1425 7.068348 TGCACAAAATTACCCACTAAACTAACA 59.932 33.333 0.00 0.00 0.00 2.41
1439 1480 9.860650 ATTAACACAACCCATGCTATTATTAGA 57.139 29.630 0.00 0.00 0.00 2.10
1473 1514 2.030274 GGGTCACCACACAATTAGCAAC 60.030 50.000 0.00 0.00 36.50 4.17
1517 1558 5.941555 AACTTGGACCAAAAACACCAATA 57.058 34.783 8.59 0.00 40.78 1.90
1547 1588 9.449719 AATTGACTCTAAAAAGGTGTAATCGAT 57.550 29.630 0.00 0.00 0.00 3.59
1548 1589 8.842358 AATTGACTCTAAAAAGGTGTAATCGA 57.158 30.769 0.00 0.00 0.00 3.59
1549 1590 9.968743 GTAATTGACTCTAAAAAGGTGTAATCG 57.031 33.333 0.00 0.00 0.00 3.34
1552 1593 9.059260 GGTGTAATTGACTCTAAAAAGGTGTAA 57.941 33.333 0.00 0.00 0.00 2.41
1553 1594 7.385752 CGGTGTAATTGACTCTAAAAAGGTGTA 59.614 37.037 0.00 0.00 0.00 2.90
1554 1595 6.204108 CGGTGTAATTGACTCTAAAAAGGTGT 59.796 38.462 0.00 0.00 0.00 4.16
1555 1596 6.348213 CCGGTGTAATTGACTCTAAAAAGGTG 60.348 42.308 0.00 0.00 0.00 4.00
1556 1597 5.704053 CCGGTGTAATTGACTCTAAAAAGGT 59.296 40.000 0.00 0.00 0.00 3.50
1557 1598 5.704053 ACCGGTGTAATTGACTCTAAAAAGG 59.296 40.000 6.12 0.00 0.00 3.11
1558 1599 6.348213 CCACCGGTGTAATTGACTCTAAAAAG 60.348 42.308 31.80 7.10 0.00 2.27
1559 1600 5.470777 CCACCGGTGTAATTGACTCTAAAAA 59.529 40.000 31.80 0.00 0.00 1.94
1560 1601 4.998672 CCACCGGTGTAATTGACTCTAAAA 59.001 41.667 31.80 0.00 0.00 1.52
1585 1626 1.600485 CCGTTTACGCCAAGTTCAAGT 59.400 47.619 0.00 0.00 38.18 3.16
1634 1675 5.336372 GCCAAGTTATTGCACCAGTTCAATA 60.336 40.000 0.00 0.00 34.95 1.90
1678 1732 0.526954 CGTATCCAAGCGCGGTTAGT 60.527 55.000 24.58 14.37 0.00 2.24
1687 1741 4.035558 TCAGCATTGATTTCGTATCCAAGC 59.964 41.667 0.00 0.00 0.00 4.01
1705 1759 0.533531 CACTGGCAGTCAAGTCAGCA 60.534 55.000 19.13 0.00 44.91 4.41
1739 1793 2.030717 ACACACTTCTAGTCGCTGACAG 60.031 50.000 10.52 0.00 34.60 3.51
1746 1800 4.966965 ATAGGACACACACTTCTAGTCG 57.033 45.455 0.00 0.00 0.00 4.18
1851 1911 2.690497 CGGGACTCATCTGTCATACAGT 59.310 50.000 6.93 0.00 46.03 3.55
1863 1923 2.762535 ATTTTCACGTCGGGACTCAT 57.237 45.000 0.00 0.00 0.00 2.90
1953 2045 0.739813 CGTGCACCCTAACAGTAGGC 60.740 60.000 12.15 0.00 45.16 3.93
1967 2059 2.047750 TGGCTATGAACGCGTGCA 60.048 55.556 24.73 24.73 0.00 4.57
1975 2067 2.512692 ATTGGTGCAGTGGCTATGAA 57.487 45.000 0.00 0.00 41.91 2.57
2002 2094 5.542779 GACTGTTGTCCTTGTTAGACATCT 58.457 41.667 0.00 0.00 43.46 2.90
2018 2110 9.745880 ATCCTTATACTACATTAACGACTGTTG 57.254 33.333 0.00 0.00 39.12 3.33
2057 2149 9.288576 CCACATGTATCATCCTTATATTGTGTT 57.711 33.333 0.00 0.00 31.05 3.32
2058 2150 7.884877 CCCACATGTATCATCCTTATATTGTGT 59.115 37.037 0.00 0.00 31.05 3.72
2059 2151 7.337689 CCCCACATGTATCATCCTTATATTGTG 59.662 40.741 0.00 0.00 31.87 3.33
2060 2152 7.405292 CCCCACATGTATCATCCTTATATTGT 58.595 38.462 0.00 0.00 0.00 2.71
2061 2153 6.319658 GCCCCACATGTATCATCCTTATATTG 59.680 42.308 0.00 0.00 0.00 1.90
2062 2154 6.218315 AGCCCCACATGTATCATCCTTATATT 59.782 38.462 0.00 0.00 0.00 1.28
2063 2155 5.733154 AGCCCCACATGTATCATCCTTATAT 59.267 40.000 0.00 0.00 0.00 0.86
2064 2156 5.100811 AGCCCCACATGTATCATCCTTATA 58.899 41.667 0.00 0.00 0.00 0.98
2065 2157 3.918912 AGCCCCACATGTATCATCCTTAT 59.081 43.478 0.00 0.00 0.00 1.73
2066 2158 3.326521 AGCCCCACATGTATCATCCTTA 58.673 45.455 0.00 0.00 0.00 2.69
2067 2159 2.138542 AGCCCCACATGTATCATCCTT 58.861 47.619 0.00 0.00 0.00 3.36
2068 2160 1.825105 AGCCCCACATGTATCATCCT 58.175 50.000 0.00 0.00 0.00 3.24
2069 2161 2.664402 AAGCCCCACATGTATCATCC 57.336 50.000 0.00 0.00 0.00 3.51
2070 2162 6.449698 CAATTTAAGCCCCACATGTATCATC 58.550 40.000 0.00 0.00 0.00 2.92
2071 2163 5.305128 CCAATTTAAGCCCCACATGTATCAT 59.695 40.000 0.00 0.00 0.00 2.45
2072 2164 4.648762 CCAATTTAAGCCCCACATGTATCA 59.351 41.667 0.00 0.00 0.00 2.15
2073 2165 4.501400 GCCAATTTAAGCCCCACATGTATC 60.501 45.833 0.00 0.00 0.00 2.24
2074 2166 3.387699 GCCAATTTAAGCCCCACATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
2075 2167 2.763448 GCCAATTTAAGCCCCACATGTA 59.237 45.455 0.00 0.00 0.00 2.29
2076 2168 1.554617 GCCAATTTAAGCCCCACATGT 59.445 47.619 0.00 0.00 0.00 3.21
2077 2169 1.832998 AGCCAATTTAAGCCCCACATG 59.167 47.619 0.00 0.00 0.00 3.21
2078 2170 1.832998 CAGCCAATTTAAGCCCCACAT 59.167 47.619 0.00 0.00 0.00 3.21
2079 2171 1.265236 CAGCCAATTTAAGCCCCACA 58.735 50.000 0.00 0.00 0.00 4.17
2102 2194 1.139520 GCAAAATGGGCCGCACTAG 59.860 57.895 0.00 0.00 0.00 2.57
2109 2201 3.893572 GCATGTGCAAAATGGGCC 58.106 55.556 11.50 0.00 41.59 5.80
2123 2215 9.199982 CACAAATAATTCAAAGAGAACTTGCAT 57.800 29.630 0.00 0.00 39.49 3.96
2124 2216 8.412456 TCACAAATAATTCAAAGAGAACTTGCA 58.588 29.630 0.00 0.00 39.49 4.08


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

AutoCloner maintained by Alex Coulton.