Multiple sequence alignment - TraesCS7A01G237900

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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 TraesCS7A01G237900 chr7A 100.000 3059 0 0 1 3059 211345618 211342560 0 5650
1 TraesCS7A01G237900 chr2A 97.523 2059 32 5 1 2041 755521031 755518974 0 3502
2 TraesCS7A01G237900 chr2A 97.570 1029 25 0 2031 3059 673251886 673252914 0 1762
3 TraesCS7A01G237900 chrUn 97.426 2059 34 5 1 2041 223715532 223717589 0 3491
4 TraesCS7A01G237900 chrUn 97.237 1665 28 3 1 1647 257855590 257853926 0 2804
5 TraesCS7A01G237900 chrUn 97.376 1029 27 0 2031 3059 264056117 264057145 0 1751
6 TraesCS7A01G237900 chrUn 97.279 1029 28 0 2031 3059 86512460 86513488 0 1746
7 TraesCS7A01G237900 chrUn 97.279 1029 28 0 2031 3059 189400862 189399834 0 1746
8 TraesCS7A01G237900 chrUn 97.279 1029 28 0 2031 3059 266526047 266527075 0 1746
9 TraesCS7A01G237900 chr7D 97.376 2058 35 6 1 2041 381882024 381879969 0 3483
10 TraesCS7A01G237900 chr7D 96.986 2057 40 6 1 2041 203530186 203528136 0 3435
11 TraesCS7A01G237900 chr7D 97.376 1029 27 0 2031 3059 203508372 203507344 0 1751
12 TraesCS7A01G237900 chr7D 97.376 1029 27 0 2031 3059 381932379 381931351 0 1751
13 TraesCS7A01G237900 chr4D 97.374 2056 38 5 1 2041 123731212 123729158 0 3483
14 TraesCS7A01G237900 chr4D 96.738 2054 52 5 1 2041 134969062 134971113 0 3408
15 TraesCS7A01G237900 chr3B 97.458 2046 42 7 1 2041 201605905 201603865 0 3482
16 TraesCS7A01G237900 chr5B 97.230 2058 38 6 1 2041 127798287 127796232 0 3467
17 TraesCS7A01G237900 chr2D 97.182 2058 39 6 1 2041 635019091 635021146 0 3461
18 TraesCS7A01G237900 chr3D 97.260 2044 49 6 1 2041 501892025 501894064 0 3458
19 TraesCS7A01G237900 chr1B 97.129 2055 41 11 1 2039 638719583 638717531 0 3452
20 TraesCS7A01G237900 chr7B 97.570 1029 25 0 2031 3059 644454833 644453805 0 1762
21 TraesCS7A01G237900 chr6D 97.376 1029 27 0 2031 3059 124525904 124524876 0 1751


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 TraesCS7A01G237900 chr7A 211342560 211345618 3058 True 5650 5650 100.000 1 3059 1 chr7A.!!$R1 3058
1 TraesCS7A01G237900 chr2A 755518974 755521031 2057 True 3502 3502 97.523 1 2041 1 chr2A.!!$R1 2040
2 TraesCS7A01G237900 chr2A 673251886 673252914 1028 False 1762 1762 97.570 2031 3059 1 chr2A.!!$F1 1028
3 TraesCS7A01G237900 chrUn 223715532 223717589 2057 False 3491 3491 97.426 1 2041 1 chrUn.!!$F2 2040
4 TraesCS7A01G237900 chrUn 257853926 257855590 1664 True 2804 2804 97.237 1 1647 1 chrUn.!!$R2 1646
5 TraesCS7A01G237900 chrUn 264056117 264057145 1028 False 1751 1751 97.376 2031 3059 1 chrUn.!!$F3 1028
6 TraesCS7A01G237900 chrUn 86512460 86513488 1028 False 1746 1746 97.279 2031 3059 1 chrUn.!!$F1 1028
7 TraesCS7A01G237900 chrUn 189399834 189400862 1028 True 1746 1746 97.279 2031 3059 1 chrUn.!!$R1 1028
8 TraesCS7A01G237900 chrUn 266526047 266527075 1028 False 1746 1746 97.279 2031 3059 1 chrUn.!!$F4 1028
9 TraesCS7A01G237900 chr7D 381879969 381882024 2055 True 3483 3483 97.376 1 2041 1 chr7D.!!$R3 2040
10 TraesCS7A01G237900 chr7D 203528136 203530186 2050 True 3435 3435 96.986 1 2041 1 chr7D.!!$R2 2040
11 TraesCS7A01G237900 chr7D 203507344 203508372 1028 True 1751 1751 97.376 2031 3059 1 chr7D.!!$R1 1028
12 TraesCS7A01G237900 chr7D 381931351 381932379 1028 True 1751 1751 97.376 2031 3059 1 chr7D.!!$R4 1028
13 TraesCS7A01G237900 chr4D 123729158 123731212 2054 True 3483 3483 97.374 1 2041 1 chr4D.!!$R1 2040
14 TraesCS7A01G237900 chr4D 134969062 134971113 2051 False 3408 3408 96.738 1 2041 1 chr4D.!!$F1 2040
15 TraesCS7A01G237900 chr3B 201603865 201605905 2040 True 3482 3482 97.458 1 2041 1 chr3B.!!$R1 2040
16 TraesCS7A01G237900 chr5B 127796232 127798287 2055 True 3467 3467 97.230 1 2041 1 chr5B.!!$R1 2040
17 TraesCS7A01G237900 chr2D 635019091 635021146 2055 False 3461 3461 97.182 1 2041 1 chr2D.!!$F1 2040
18 TraesCS7A01G237900 chr3D 501892025 501894064 2039 False 3458 3458 97.260 1 2041 1 chr3D.!!$F1 2040
19 TraesCS7A01G237900 chr1B 638717531 638719583 2052 True 3452 3452 97.129 1 2039 1 chr1B.!!$R1 2038
20 TraesCS7A01G237900 chr7B 644453805 644454833 1028 True 1762 1762 97.570 2031 3059 1 chr7B.!!$R1 1028
21 TraesCS7A01G237900 chr6D 124524876 124525904 1028 True 1751 1751 97.376 2031 3059 1 chr6D.!!$R1 1028

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
74 75 1.876156 CTCAATAGGAATCGGCAAGCC 59.124 52.381 0.00 0.0 0.0 4.35 F
1375 1407 0.536687 TCGGTGTCTCGGAGTTGTCT 60.537 55.000 4.69 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1633 1.816961 GCAATCCGGCCAGATGAAGAT 60.817 52.381 1.14 0.0 0.00 2.40 R
2400 2437 0.109913 ATCATGGATCAGCATGCCGT 59.890 50.000 15.66 0.0 34.76 5.68 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
56 57 6.556212 TCTCATTTGTCACTCTCGTATTCTC 58.444 40.000 0.00 0.00 0.00 2.87
74 75 1.876156 CTCAATAGGAATCGGCAAGCC 59.124 52.381 0.00 0.00 0.00 4.35
142 144 2.581216 ACGAAGTCAGGTCCAGTAGA 57.419 50.000 0.00 0.00 29.74 2.59
387 389 7.412672 GGGTTTCTATCAGTTAGTAACAAAGCG 60.413 40.741 15.28 1.37 38.98 4.68
537 539 7.576477 CGCCAATATCATATTGACTCTCTCTCA 60.576 40.741 17.68 0.00 0.00 3.27
760 762 5.012893 AGACTTGGATTTCATGGGTTTCTC 58.987 41.667 0.00 0.00 0.00 2.87
930 962 2.418368 TTGATTATTCAGGGCGCAGT 57.582 45.000 10.83 0.00 32.27 4.40
975 1007 3.069005 GGGGGTAAATAAGGGGGAAGAT 58.931 50.000 0.00 0.00 0.00 2.40
1114 1146 3.917629 TCTTAGTTATTGGTGGGGGTTCA 59.082 43.478 0.00 0.00 0.00 3.18
1375 1407 0.536687 TCGGTGTCTCGGAGTTGTCT 60.537 55.000 4.69 0.00 0.00 3.41
1452 1484 1.172180 TGAGCTTTTGGGGAGCAACG 61.172 55.000 0.00 0.00 42.56 4.10
1481 1513 3.896317 GCTTAGCTAGCGCCATACT 57.104 52.632 9.55 0.00 40.71 2.12
1601 1633 4.439057 CTTATTTTAGTAGGCGCCAGTCA 58.561 43.478 31.54 8.11 0.00 3.41
1616 1648 0.467384 AGTCATCTTCATCTGGCCGG 59.533 55.000 4.71 4.71 0.00 6.13
1774 1807 2.230130 TGCTCCTAATGTTTTGGGGG 57.770 50.000 0.00 0.00 37.03 5.40
1965 2002 6.980051 AAAGAAATGTATGTCCGTAGTTCC 57.020 37.500 0.00 0.00 0.00 3.62
2106 2143 8.313292 TGATTGATAAACAAGAAGGAAAATGGG 58.687 33.333 0.00 0.00 42.02 4.00
2116 2153 7.014326 ACAAGAAGGAAAATGGGAAAGTAGAAC 59.986 37.037 0.00 0.00 0.00 3.01
2360 2397 1.614850 GCGAAACCAATTCCCAGGGTA 60.615 52.381 5.01 0.00 34.34 3.69
2372 2409 2.129146 CAGGGTATGACGGGCGGTA 61.129 63.158 0.00 0.00 0.00 4.02
2384 2421 2.440817 GGCGGTATGTACAGGGCCT 61.441 63.158 17.23 0.00 36.37 5.19
2400 2437 1.493022 GGCCTGGGTACATATTCACCA 59.507 52.381 0.00 0.00 36.48 4.17
2415 2452 2.124612 CCACGGCATGCTGATCCA 60.125 61.111 32.80 0.00 0.00 3.41
2471 2508 3.953712 TGCAGAGAACAATCCGAACTA 57.046 42.857 0.00 0.00 0.00 2.24
2753 2790 3.182972 CGTCGTCGTAACCAATTTCAACT 59.817 43.478 0.00 0.00 0.00 3.16
2801 2838 4.408270 TGACGTCACTATAGGTAGGTCTCT 59.592 45.833 15.76 0.00 31.96 3.10
2817 2854 0.178992 CTCTGTGGGTCTTGGGCAAA 60.179 55.000 0.00 0.00 0.00 3.68
2856 2893 2.030805 GTGAAAGTGCTTCGAAAGGCAT 60.031 45.455 14.28 0.13 40.66 4.40
2923 2960 3.260632 TGGCACTCAATCAAGTAGTAGCA 59.739 43.478 0.00 0.00 0.00 3.49
2943 2980 2.171209 CTGGCACATCACTCGGTGGA 62.171 60.000 4.52 0.00 38.20 4.02
2980 3017 3.645884 GCATGTCTCAGCAACACAAAAT 58.354 40.909 0.00 0.00 0.00 1.82
2993 3030 2.693074 ACACAAAATGAGGGTTTCGCTT 59.307 40.909 0.00 0.00 0.00 4.68
2994 3031 3.132111 ACACAAAATGAGGGTTTCGCTTT 59.868 39.130 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.588252 CGGCTTGCCGATTCCTATTG 59.412 55.000 27.61 0.00 34.88 1.90
74 75 2.872245 CAATGGCCTAGTGGTTGTATCG 59.128 50.000 3.32 0.00 35.27 2.92
164 166 0.908198 GACCACCAGCAGGAAGATCT 59.092 55.000 0.35 0.00 38.69 2.75
537 539 9.041354 AGTAACTCTCAGAAACTCTTATTGGAT 57.959 33.333 0.00 0.00 0.00 3.41
760 762 5.570262 TTCAAACGAACGACTAGTCATTG 57.430 39.130 22.37 15.56 0.00 2.82
930 962 2.234414 GCCTTGATGGAAATTGGCTTCA 59.766 45.455 0.00 0.00 38.35 3.02
975 1007 9.706691 ATTTCTCTTTTCTATCGTTACAACTCA 57.293 29.630 0.00 0.00 0.00 3.41
1114 1146 8.863872 ACTAAACAAATACCTGCTAATGAACT 57.136 30.769 0.00 0.00 0.00 3.01
1253 1285 4.612401 TGCCCCATTAGCATGCATATAAT 58.388 39.130 21.98 12.34 34.69 1.28
1481 1513 8.739108 AGTCACTATGGTATCTCCTACTACTA 57.261 38.462 0.00 0.00 37.07 1.82
1601 1633 1.816961 GCAATCCGGCCAGATGAAGAT 60.817 52.381 1.14 0.00 0.00 2.40
1774 1807 4.332819 GCAGGTATATAATTGTCGGGATGC 59.667 45.833 0.00 0.00 0.00 3.91
1956 1993 3.022607 AGTCGAAAACTGGAACTACGG 57.977 47.619 0.00 0.00 36.65 4.02
2116 2153 6.984474 ACCTCAACGGTATAAACATGTAGATG 59.016 38.462 0.00 0.00 46.73 2.90
2360 2397 0.387929 CTGTACATACCGCCCGTCAT 59.612 55.000 0.00 0.00 0.00 3.06
2372 2409 0.252974 TGTACCCAGGCCCTGTACAT 60.253 55.000 20.06 0.00 39.75 2.29
2384 2421 1.134340 GCCGTGGTGAATATGTACCCA 60.134 52.381 6.27 0.00 36.10 4.51
2400 2437 0.109913 ATCATGGATCAGCATGCCGT 59.890 50.000 15.66 0.00 34.76 5.68
2415 2452 8.554528 CATGAAGTTGAAATCGCTAGTAATCAT 58.445 33.333 0.00 0.00 0.00 2.45
2471 2508 2.424956 GCGAATCTGGAAAGATTGCCTT 59.575 45.455 5.72 0.00 38.50 4.35
2753 2790 1.985159 ACCAGTGAGCATGGAGGTTTA 59.015 47.619 0.00 0.00 40.51 2.01
2801 2838 1.388065 CGTTTTGCCCAAGACCCACA 61.388 55.000 0.00 0.00 0.00 4.17
2817 2854 0.179129 ACGTGTGAACCGAAGTCGTT 60.179 50.000 0.00 0.00 37.74 3.85
2856 2893 0.331278 ATTTCACCATTGGGAGCCGA 59.669 50.000 7.78 0.00 38.05 5.54
2923 2960 1.004560 CACCGAGTGATGTGCCAGT 60.005 57.895 0.00 0.00 35.23 4.00
2943 2980 3.356290 ACATGCGCCTAAGGAGAAATTT 58.644 40.909 4.18 0.00 0.00 1.82
2980 3017 4.939439 GTCCTATAAAAAGCGAAACCCTCA 59.061 41.667 0.00 0.00 0.00 3.86
2993 3030 8.160765 TGAGATGTTTGGTCAAGTCCTATAAAA 58.839 33.333 0.00 0.00 0.00 1.52
2994 3031 7.606456 GTGAGATGTTTGGTCAAGTCCTATAAA 59.394 37.037 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.