Multiple sequence alignment - TraesCS7A01G252600

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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 TraesCS7A01G252600 chr7A 100.000 2534 0 0 1 2534 237515955 237518488 0.000000e+00 4680.0
1 TraesCS7A01G252600 chr7D 94.941 2451 85 15 1 2444 224059130 224056712 0.000000e+00 3803.0
2 TraesCS7A01G252600 chr7D 93.878 98 0 1 2443 2534 224056552 224056455 2.630000e-30 143.0
3 TraesCS7A01G252600 chr7D 84.762 105 10 1 3 107 616218808 616218906 1.600000e-17 100.0
4 TraesCS7A01G252600 chr7D 83.019 106 10 4 3 107 616258545 616258447 3.470000e-14 89.8
5 TraesCS7A01G252600 chr7B 93.730 2552 111 19 1 2534 173868523 173866003 0.000000e+00 3781.0


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 TraesCS7A01G252600 chr7A 237515955 237518488 2533 False 4680 4680 100.0000 1 2534 1 chr7A.!!$F1 2533
1 TraesCS7A01G252600 chr7D 224056455 224059130 2675 True 1973 3803 94.4095 1 2534 2 chr7D.!!$R2 2533
2 TraesCS7A01G252600 chr7B 173866003 173868523 2520 True 3781 3781 93.7300 1 2534 1 chr7B.!!$R1 2533

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
874 875 1.515954 GATGAGGACGGAGGCGAAA 59.484 57.895 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2140 0.240411 GCTTTGCTTCAGCTCCAGTG 59.76 55.0 0.0 0.0 42.66 3.66 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
558 559 3.775654 GTGGCACGGGAGAGGGAG 61.776 72.222 0.00 0.00 0.00 4.30
867 868 3.515286 GACGGCGATGAGGACGGA 61.515 66.667 16.62 0.00 44.54 4.69
874 875 1.515954 GATGAGGACGGAGGCGAAA 59.484 57.895 0.00 0.00 0.00 3.46
1068 1069 1.141881 GAAGCTGATCGGCGAGGAA 59.858 57.895 20.62 1.98 37.29 3.36
1442 1443 4.933064 CGAGGAGATGGGCGACGC 62.933 72.222 12.43 12.43 0.00 5.19
1521 1522 1.021968 GCGGCAATATCGAAGGGTTT 58.978 50.000 0.00 0.00 0.00 3.27
1583 1584 1.680735 TGGATTGCCACACAGTCAAAC 59.319 47.619 0.00 0.00 39.92 2.93
1617 1622 9.956640 TGGAATAATATTTTTGCATGAAGGTTT 57.043 25.926 8.39 0.00 0.00 3.27
1625 1630 7.913674 TTTTTGCATGAAGGTTTTTGTTACT 57.086 28.000 0.00 0.00 0.00 2.24
1626 1631 9.606631 ATTTTTGCATGAAGGTTTTTGTTACTA 57.393 25.926 0.00 0.00 0.00 1.82
1670 1676 5.876460 GCAATAAATCACAGGCCATTTTCTT 59.124 36.000 5.01 0.00 0.00 2.52
1675 1681 4.038271 TCACAGGCCATTTTCTTCTCAT 57.962 40.909 5.01 0.00 0.00 2.90
1684 1690 6.040878 GCCATTTTCTTCTCATTCAATCCAG 58.959 40.000 0.00 0.00 0.00 3.86
1798 1806 2.158534 ACATACAAGCCAAACCACTGGA 60.159 45.455 0.71 0.00 38.96 3.86
1831 1839 0.320073 TGCACACGGCTACCAACTAC 60.320 55.000 0.00 0.00 45.15 2.73
1832 1840 0.037605 GCACACGGCTACCAACTACT 60.038 55.000 0.00 0.00 40.25 2.57
1833 1841 1.203052 GCACACGGCTACCAACTACTA 59.797 52.381 0.00 0.00 40.25 1.82
1938 1946 1.482593 CACCTCCCTACACTGCCTAAG 59.517 57.143 0.00 0.00 0.00 2.18
2019 2028 1.303091 ACCGCGGTTCCAAGTTATGC 61.303 55.000 28.70 0.00 0.00 3.14
2043 2052 5.395682 TTCTTCCTTGCTGATGAATTTGG 57.604 39.130 0.00 0.00 0.00 3.28
2048 2057 1.321805 TGCTGATGAATTTGGCGGGG 61.322 55.000 0.00 0.00 0.00 5.73
2064 2073 4.344865 GGGTTGAGGCGCCTCCAA 62.345 66.667 44.85 35.07 42.09 3.53
2065 2074 2.044946 GGTTGAGGCGCCTCCAAT 60.045 61.111 44.85 19.99 42.09 3.16
2071 2080 2.592861 GGCGCCTCCAATGCCTAG 60.593 66.667 22.15 0.00 45.40 3.02
2153 2162 0.179009 TGGAGCTGAAGCAAAGCACT 60.179 50.000 4.90 0.00 43.37 4.40
2161 2170 2.165998 GAAGCAAAGCACTGGGAAGAT 58.834 47.619 0.00 0.00 0.00 2.40
2162 2171 2.299326 AGCAAAGCACTGGGAAGATT 57.701 45.000 0.00 0.00 0.00 2.40
2163 2172 3.439857 AGCAAAGCACTGGGAAGATTA 57.560 42.857 0.00 0.00 0.00 1.75
2177 2190 5.817296 TGGGAAGATTAACTGATTCATCGTG 59.183 40.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
525 526 2.431942 ACCGCGTCGAACATGTCC 60.432 61.111 4.92 0.00 0.00 4.02
848 849 4.175489 CGTCCTCATCGCCGTCGT 62.175 66.667 0.00 0.00 36.96 4.34
1008 1009 4.621460 GTGCGCATGTATATGTACCAGTAG 59.379 45.833 15.91 0.00 36.65 2.57
1068 1069 3.395702 TACCGCCGCTTCATGGGT 61.396 61.111 0.00 0.00 34.81 4.51
1539 1540 0.669318 GTGCGTGCTGTAGGCTGTAA 60.669 55.000 11.45 0.00 40.72 2.41
1542 1543 3.481903 CGTGCGTGCTGTAGGCTG 61.482 66.667 11.45 1.22 40.72 4.85
1574 1575 1.134521 TCCACGCTGAAGTTTGACTGT 60.135 47.619 0.00 0.00 0.00 3.55
1577 1578 4.742438 TTATTCCACGCTGAAGTTTGAC 57.258 40.909 0.00 0.00 0.00 3.18
1580 1581 9.139174 CAAAAATATTATTCCACGCTGAAGTTT 57.861 29.630 0.00 0.00 0.00 2.66
1583 1584 6.751425 TGCAAAAATATTATTCCACGCTGAAG 59.249 34.615 0.00 0.00 0.00 3.02
1624 1629 8.942338 TTGCAGATTACAGTAATTGGTAGTAG 57.058 34.615 7.26 0.00 0.00 2.57
1626 1631 9.899661 TTATTGCAGATTACAGTAATTGGTAGT 57.100 29.630 7.26 2.87 0.00 2.73
1684 1690 6.092748 GTGTGGTAAAACATCATCCATTCAC 58.907 40.000 0.00 0.00 31.49 3.18
1693 1699 4.527944 TCCAGTTGTGTGGTAAAACATCA 58.472 39.130 0.00 0.00 38.88 3.07
1798 1806 5.588648 AGCCGTGTGCAAAATATGTATAGTT 59.411 36.000 0.00 0.00 44.83 2.24
1831 1839 5.324784 TGTGCTTATCCACACTGTACTAG 57.675 43.478 0.00 0.00 40.55 2.57
1938 1946 5.779806 AGATTGTACATACGTGACTTTGC 57.220 39.130 0.00 0.00 0.00 3.68
1948 1956 5.428253 TCCAGCAAGGAAGATTGTACATAC 58.572 41.667 0.00 0.00 45.65 2.39
1978 1987 4.862018 GTGCTTCAAAGTGCTAACAAAACA 59.138 37.500 0.00 0.00 0.00 2.83
2019 2028 5.867716 CCAAATTCATCAGCAAGGAAGAAAG 59.132 40.000 0.00 0.00 29.52 2.62
2060 2069 0.975556 TGCGACTCCTAGGCATTGGA 60.976 55.000 2.96 0.79 0.00 3.53
2063 2072 0.461961 GAGTGCGACTCCTAGGCATT 59.538 55.000 2.96 0.00 39.28 3.56
2064 2073 1.729470 CGAGTGCGACTCCTAGGCAT 61.729 60.000 2.96 0.00 42.12 4.40
2065 2074 2.407428 CGAGTGCGACTCCTAGGCA 61.407 63.158 2.96 0.00 42.12 4.75
2068 2077 1.729470 ATGCCGAGTGCGACTCCTAG 61.729 60.000 9.71 0.00 42.12 3.02
2071 2080 2.583593 GATGCCGAGTGCGACTCC 60.584 66.667 9.71 0.34 42.12 3.85
2111 2120 9.179909 TCCAGTGTTTTGAAGTGTCTTAATTAA 57.820 29.630 0.00 0.00 0.00 1.40
2112 2121 8.740123 TCCAGTGTTTTGAAGTGTCTTAATTA 57.260 30.769 0.00 0.00 0.00 1.40
2113 2122 7.639113 TCCAGTGTTTTGAAGTGTCTTAATT 57.361 32.000 0.00 0.00 0.00 1.40
2114 2123 6.238759 GCTCCAGTGTTTTGAAGTGTCTTAAT 60.239 38.462 0.00 0.00 0.00 1.40
2115 2124 5.065988 GCTCCAGTGTTTTGAAGTGTCTTAA 59.934 40.000 0.00 0.00 0.00 1.85
2116 2125 4.574828 GCTCCAGTGTTTTGAAGTGTCTTA 59.425 41.667 0.00 0.00 0.00 2.10
2129 2138 1.952296 CTTTGCTTCAGCTCCAGTGTT 59.048 47.619 0.00 0.00 42.66 3.32
2131 2140 0.240411 GCTTTGCTTCAGCTCCAGTG 59.760 55.000 0.00 0.00 42.66 3.66
2153 2162 5.817296 CACGATGAATCAGTTAATCTTCCCA 59.183 40.000 0.00 0.00 0.00 4.37
2161 2170 6.198403 GCGATACTTCACGATGAATCAGTTAA 59.802 38.462 0.00 0.00 35.59 2.01
2162 2171 5.685954 GCGATACTTCACGATGAATCAGTTA 59.314 40.000 0.00 0.00 35.59 2.24
2163 2172 4.504461 GCGATACTTCACGATGAATCAGTT 59.496 41.667 0.00 0.00 35.59 3.16
2177 2190 4.045783 GCCTCTTGAACTAGCGATACTTC 58.954 47.826 0.00 0.00 0.00 3.01
2236 2249 5.296035 GGAAGTACACCTATGGCAAACATAC 59.704 44.000 0.00 0.00 41.03 2.39


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

AutoCloner maintained by Alex Coulton.