Multiple sequence alignment - TraesCS5A01G080800

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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 TraesCS5A01G080800 chr5A 100.000 2234 0 0 1 2234 103568104 103570337 0.000000e+00 4126.0
1 TraesCS5A01G080800 chr5A 90.551 127 9 1 1065 1191 103901734 103901857 4.940000e-37 165.0
2 TraesCS5A01G080800 chr5A 93.878 49 3 0 1187 1235 103902126 103902174 8.560000e-10 75.0
3 TraesCS5A01G080800 chr5D 90.603 2288 128 45 1 2234 99419762 99417508 0.000000e+00 2953.0
4 TraesCS5A01G080800 chr5D 95.455 44 2 0 1192 1235 99350859 99350816 1.110000e-08 71.3
5 TraesCS5A01G080800 chr5B 93.600 1250 67 7 567 1816 108551815 108550579 0.000000e+00 1853.0
6 TraesCS5A01G080800 chr5B 93.504 585 19 7 3 568 108552506 108551922 0.000000e+00 852.0
7 TraesCS5A01G080800 chr5B 89.433 388 36 5 1848 2234 108550580 108550197 3.340000e-133 484.0
8 TraesCS5A01G080800 chr2A 84.277 318 46 4 1685 2001 367684663 367684977 7.750000e-80 307.0
9 TraesCS5A01G080800 chr1D 81.860 215 34 5 1781 1993 471920299 471920510 2.280000e-40 176.0
10 TraesCS5A01G080800 chr7D 81.604 212 32 6 1807 2018 235394524 235394320 3.820000e-38 169.0
11 TraesCS5A01G080800 chr1B 80.631 222 38 5 1781 2000 656054637 656054855 1.370000e-37 167.0
12 TraesCS5A01G080800 chr1B 82.090 201 30 6 1802 2000 656057015 656057211 1.370000e-37 167.0
13 TraesCS5A01G080800 chr1B 80.543 221 39 4 1781 2000 656060623 656060840 1.370000e-37 167.0
14 TraesCS5A01G080800 chr1B 80.660 212 36 5 1785 1995 656063023 656063230 2.300000e-35 159.0
15 TraesCS5A01G080800 chr4B 86.301 73 10 0 1160 1232 445240823 445240895 1.840000e-11 80.5
16 TraesCS5A01G080800 chr3D 100.000 30 0 0 1015 1044 608512067 608512038 3.100000e-04 56.5
17 TraesCS5A01G080800 chr3B 100.000 30 0 0 1015 1044 818926808 818926779 3.100000e-04 56.5
18 TraesCS5A01G080800 chr3A 100.000 30 0 0 1015 1044 741625240 741625211 3.100000e-04 56.5


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 TraesCS5A01G080800 chr5A 103568104 103570337 2233 False 4126 4126 100.000 1 2234 1 chr5A.!!$F1 2233
1 TraesCS5A01G080800 chr5D 99417508 99419762 2254 True 2953 2953 90.603 1 2234 1 chr5D.!!$R2 2233
2 TraesCS5A01G080800 chr5B 108550197 108552506 2309 True 1063 1853 92.179 3 2234 3 chr5B.!!$R1 2231

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
942 1107 0.250513 ATCCTCAACGACCAGAAGCC 59.749 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 1999 1.06643 GGAACTTGGTATGAGCGACCA 60.066 52.381 0.0 0.0 45.38 4.02 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
26 27 8.351414 TGGATATAGGGTGTTGGATATGAGATA 58.649 37.037 0.00 0.00 0.00 1.98
34 35 3.942130 TGGATATGAGATACGTGGCTG 57.058 47.619 0.00 0.00 0.00 4.85
40 41 0.460284 GAGATACGTGGCTGTGTGGG 60.460 60.000 0.00 0.00 0.00 4.61
57 58 4.695928 GTGTGGGTGAGAATTTAAGGTCTC 59.304 45.833 9.48 9.48 40.64 3.36
72 73 0.674534 GTCTCACCGGTCACTGTCTT 59.325 55.000 2.59 0.00 0.00 3.01
82 91 2.610374 GGTCACTGTCTTTGCAAACGTA 59.390 45.455 8.05 0.00 0.00 3.57
130 149 7.872993 TGGTTATAGATGCTATTAGTGTCTTGC 59.127 37.037 5.64 0.00 0.00 4.01
153 172 1.017387 GAACGATGGATGAGGTTGGC 58.983 55.000 0.00 0.00 0.00 4.52
260 309 2.786495 CGGTCGCTAGGAGCCATGT 61.786 63.158 0.00 0.00 40.06 3.21
261 310 1.227380 GGTCGCTAGGAGCCATGTG 60.227 63.158 0.00 0.00 38.18 3.21
262 311 1.227380 GTCGCTAGGAGCCATGTGG 60.227 63.158 0.00 0.00 38.18 4.17
263 312 2.109799 CGCTAGGAGCCATGTGGG 59.890 66.667 0.54 0.00 38.18 4.61
273 322 1.005867 CCATGTGGGCTTTGTGTGC 60.006 57.895 0.00 0.00 0.00 4.57
391 440 2.022129 CGGTGACTTGTCGTGCTCC 61.022 63.158 0.00 0.00 0.00 4.70
505 562 1.055338 CGTTAACTCCCACGAACGTC 58.945 55.000 3.71 0.00 39.74 4.34
679 844 2.488153 GTCCTAAGAAAATTGCACCGCT 59.512 45.455 0.00 0.00 0.00 5.52
716 881 0.464373 GCCGAAAGAGATGGCCATCA 60.464 55.000 40.05 6.04 43.06 3.07
719 884 1.685148 GAAAGAGATGGCCATCACCC 58.315 55.000 40.05 28.88 40.22 4.61
748 913 6.459670 GGACACGGTCCCATAAATTATTTT 57.540 37.500 10.92 0.00 46.19 1.82
875 1040 0.457035 CCACCTTGGATTGGCATTCG 59.543 55.000 3.53 0.00 40.96 3.34
877 1042 1.322538 ACCTTGGATTGGCATTCGGC 61.323 55.000 3.53 0.00 43.74 5.54
913 1078 0.736325 CAAGTTACCCGGCTCTCACG 60.736 60.000 0.00 0.00 0.00 4.35
937 1102 1.270839 ACAACCATCCTCAACGACCAG 60.271 52.381 0.00 0.00 0.00 4.00
942 1107 0.250513 ATCCTCAACGACCAGAAGCC 59.749 55.000 0.00 0.00 0.00 4.35
1103 1268 4.308458 CAGTCCGGTGGGCGTCAA 62.308 66.667 0.00 0.00 0.00 3.18
1104 1269 4.003788 AGTCCGGTGGGCGTCAAG 62.004 66.667 0.00 0.00 0.00 3.02
1412 1583 1.002366 GTCACTTCCATAGCACTGCG 58.998 55.000 0.00 0.00 0.00 5.18
1573 1767 3.746492 ACGAGATTCGGGTTCAGAAAAAG 59.254 43.478 3.37 0.00 45.59 2.27
1593 1788 8.871686 AAAAAGTGAACATGTTATTCTGGTTC 57.128 30.769 11.95 0.00 38.59 3.62
1612 1807 1.611491 TCAGAAAACGGTTTGCATCCC 59.389 47.619 13.86 0.00 0.00 3.85
1618 1813 0.753479 ACGGTTTGCATCCCACAACA 60.753 50.000 0.00 0.00 0.00 3.33
1619 1814 0.602562 CGGTTTGCATCCCACAACAT 59.397 50.000 0.00 0.00 0.00 2.71
1632 1827 5.524284 TCCCACAACATAAAATTGTTCGTG 58.476 37.500 10.32 10.32 38.22 4.35
1644 1842 6.642707 AAATTGTTCGTGGTTCAATTAGGA 57.357 33.333 0.00 0.00 39.72 2.94
1645 1843 6.834168 AATTGTTCGTGGTTCAATTAGGAT 57.166 33.333 0.00 0.00 39.13 3.24
1646 1844 6.834168 ATTGTTCGTGGTTCAATTAGGATT 57.166 33.333 0.00 0.00 0.00 3.01
1647 1845 6.642707 TTGTTCGTGGTTCAATTAGGATTT 57.357 33.333 0.00 0.00 0.00 2.17
1648 1846 6.642707 TGTTCGTGGTTCAATTAGGATTTT 57.357 33.333 0.00 0.00 0.00 1.82
1651 1849 9.451002 TGTTCGTGGTTCAATTAGGATTTTATA 57.549 29.630 0.00 0.00 0.00 0.98
1704 1902 4.812626 AGAACTTACGTTTTTGTCGGTCAT 59.187 37.500 0.00 0.00 32.39 3.06
1712 1910 4.925054 CGTTTTTGTCGGTCATAGGTTCTA 59.075 41.667 0.00 0.00 0.00 2.10
1717 1915 5.471556 TGTCGGTCATAGGTTCTAAAACA 57.528 39.130 0.00 0.00 37.10 2.83
1777 1976 6.446318 AGTTGAAATATTTTGTCACACGCAT 58.554 32.000 1.43 0.00 0.00 4.73
1781 1980 7.089538 TGAAATATTTTGTCACACGCATGATT 58.910 30.769 1.43 0.00 0.00 2.57
1803 2002 9.829507 TGATTTGAAACTCATTATTTTGTTGGT 57.170 25.926 0.00 0.00 0.00 3.67
1833 2032 5.738619 ACCAAGTTCCAAAAGTTGAAACT 57.261 34.783 7.18 0.00 45.03 2.66
1881 2080 4.939509 AACGTAATCAAAATGGGTCTCG 57.060 40.909 0.00 0.00 0.00 4.04
1894 2093 1.605753 GGTCTCGTTTGAAAGCCCTT 58.394 50.000 0.00 0.00 0.00 3.95
1921 2120 6.932400 TCACCAGAAACACGAATATGTAAACT 59.068 34.615 0.00 0.00 30.75 2.66
2041 2240 1.452108 CCTCTTCCATGGGAACGGC 60.452 63.158 13.02 0.00 36.71 5.68
2042 2241 1.299648 CTCTTCCATGGGAACGGCA 59.700 57.895 13.02 0.00 36.71 5.69
2057 2256 0.383231 CGGCAGGGAATTTGCATCTC 59.617 55.000 3.19 0.00 43.28 2.75
2077 2280 2.308570 TCACATGCTAGTCCCCACATTT 59.691 45.455 0.00 0.00 0.00 2.32
2078 2281 2.424601 CACATGCTAGTCCCCACATTTG 59.575 50.000 0.00 0.00 0.00 2.32
2079 2282 1.406539 CATGCTAGTCCCCACATTTGC 59.593 52.381 0.00 0.00 0.00 3.68
2080 2283 0.676466 TGCTAGTCCCCACATTTGCG 60.676 55.000 0.00 0.00 0.00 4.85
2081 2284 0.392461 GCTAGTCCCCACATTTGCGA 60.392 55.000 0.00 0.00 0.00 5.10
2098 2301 1.730064 GCGAACCATTGTAAGCGAAGA 59.270 47.619 0.00 0.00 0.00 2.87
2111 2314 6.499172 TGTAAGCGAAGAGAGATTGTCTATG 58.501 40.000 0.00 0.00 34.71 2.23
2170 2373 2.369532 AGCCACAAAAACATGCCTTGAT 59.630 40.909 8.53 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.641436 ACAGCCACGTATCTCATATCCAA 59.359 43.478 0.00 0.00 0.00 3.53
26 27 3.460672 CTCACCCACACAGCCACGT 62.461 63.158 0.00 0.00 0.00 4.49
34 35 4.652822 AGACCTTAAATTCTCACCCACAC 58.347 43.478 0.00 0.00 0.00 3.82
57 58 0.813610 TGCAAAGACAGTGACCGGTG 60.814 55.000 14.63 0.00 0.00 4.94
72 73 0.745128 CCGGCCCTATACGTTTGCAA 60.745 55.000 0.00 0.00 0.00 4.08
82 91 2.290071 CGATTACCAAATCCGGCCCTAT 60.290 50.000 0.00 0.00 38.66 2.57
130 149 3.127548 CCAACCTCATCCATCGTTCAAAG 59.872 47.826 0.00 0.00 0.00 2.77
153 172 5.992217 GGTTTGATAGGTATCCAGCACTTAG 59.008 44.000 0.00 0.00 31.71 2.18
263 312 1.588082 CCTCATGGGCACACAAAGC 59.412 57.895 0.00 0.00 0.00 3.51
391 440 2.279851 TCTCCAACACACGCCACG 60.280 61.111 0.00 0.00 0.00 4.94
505 562 0.388649 ACTTTGTAGGCGCGTCAGAG 60.389 55.000 15.58 11.47 0.00 3.35
679 844 1.509463 CGCCCACGCTCAAGTAGTA 59.491 57.895 0.00 0.00 0.00 1.82
748 913 2.742053 GTTTGGTAGCGCATCTCTTTCA 59.258 45.455 11.47 0.00 0.00 2.69
877 1042 4.755266 ACTTGGGTGCTACTTATAGTGG 57.245 45.455 0.00 0.00 0.00 4.00
913 1078 0.240945 CGTTGAGGATGGTTGTTGGC 59.759 55.000 0.00 0.00 0.00 4.52
937 1102 4.636249 TCTCTTCTCTCTGTTTTGGCTTC 58.364 43.478 0.00 0.00 0.00 3.86
942 1107 4.375272 TGTGCTCTCTTCTCTCTGTTTTG 58.625 43.478 0.00 0.00 0.00 2.44
1412 1583 1.867233 CGGTACATACATTCCTGCAGC 59.133 52.381 8.66 0.00 0.00 5.25
1485 1656 8.200792 ACTAGTCAACAAACATCATAGATCTCC 58.799 37.037 0.00 0.00 0.00 3.71
1573 1767 6.801539 TCTGAACCAGAATAACATGTTCAC 57.198 37.500 15.85 7.83 40.06 3.18
1585 1780 3.428316 GCAAACCGTTTTCTGAACCAGAA 60.428 43.478 5.38 5.38 46.93 3.02
1593 1788 1.339610 TGGGATGCAAACCGTTTTCTG 59.660 47.619 0.00 0.00 0.00 3.02
1612 1807 6.473778 TGAACCACGAACAATTTTATGTTGTG 59.526 34.615 0.00 6.59 43.31 3.33
1618 1813 8.798402 TCCTAATTGAACCACGAACAATTTTAT 58.202 29.630 0.00 0.00 41.97 1.40
1619 1814 8.167605 TCCTAATTGAACCACGAACAATTTTA 57.832 30.769 0.00 0.00 41.97 1.52
1690 1888 6.790285 TTAGAACCTATGACCGACAAAAAC 57.210 37.500 0.00 0.00 0.00 2.43
1749 1947 7.357532 GCGTGTGACAAAATATTTCAACTTCTG 60.358 37.037 0.10 0.00 0.00 3.02
1771 1970 7.745022 AATAATGAGTTTCAAATCATGCGTG 57.255 32.000 3.38 0.00 42.25 5.34
1777 1976 9.829507 ACCAACAAAATAATGAGTTTCAAATCA 57.170 25.926 0.00 0.00 37.42 2.57
1781 1980 6.419413 GCGACCAACAAAATAATGAGTTTCAA 59.581 34.615 0.00 0.00 0.00 2.69
1800 1999 1.066430 GGAACTTGGTATGAGCGACCA 60.066 52.381 0.00 0.00 45.38 4.02
1803 2002 3.410631 TTTGGAACTTGGTATGAGCGA 57.589 42.857 0.00 0.00 0.00 4.93
1881 2080 4.079253 TCTGGTGATAAGGGCTTTCAAAC 58.921 43.478 0.00 0.00 0.00 2.93
1894 2093 8.875803 GTTTACATATTCGTGTTTCTGGTGATA 58.124 33.333 0.00 0.00 33.62 2.15
2041 2240 3.737047 GCATGTGAGATGCAAATTCCCTG 60.737 47.826 9.90 0.00 44.00 4.45
2042 2241 2.429610 GCATGTGAGATGCAAATTCCCT 59.570 45.455 9.90 0.00 44.00 4.20
2057 2256 2.424601 CAAATGTGGGGACTAGCATGTG 59.575 50.000 0.00 0.00 0.00 3.21
2077 2280 1.463056 CTTCGCTTACAATGGTTCGCA 59.537 47.619 0.00 0.00 0.00 5.10
2078 2281 1.730064 TCTTCGCTTACAATGGTTCGC 59.270 47.619 0.00 0.00 0.00 4.70
2079 2282 3.250744 TCTCTTCGCTTACAATGGTTCG 58.749 45.455 0.00 0.00 0.00 3.95
2080 2283 4.495422 TCTCTCTTCGCTTACAATGGTTC 58.505 43.478 0.00 0.00 0.00 3.62
2081 2284 4.537135 TCTCTCTTCGCTTACAATGGTT 57.463 40.909 0.00 0.00 0.00 3.67
2098 2301 5.649265 TGAGGATAGCCATAGACAATCTCT 58.351 41.667 0.00 0.00 36.29 3.10


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

AutoCloner maintained by Alex Coulton.