Multiple sequence alignment - TraesCS7A01G006700

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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 TraesCS7A01G006700 chr7A 100.000 3027 0 0 1 3027 3209446 3206420 0 5590
1 TraesCS7A01G006700 chr7A 91.052 3051 225 18 1 3027 1997937 1994911 0 4078
2 TraesCS7A01G006700 chr7A 89.926 1618 158 4 1413 3027 3312631 3314246 0 2080
3 TraesCS7A01G006700 chr7A 93.739 1150 67 3 1 1149 3311142 3312287 0 1720
4 TraesCS7A01G006700 chr7A 91.522 1156 95 3 1 1155 2118994 2117841 0 1589
5 TraesCS7A01G006700 chr7D 92.262 3063 200 13 1 3027 3634644 3631583 0 4309
6 TraesCS7A01G006700 chr7D 91.218 3063 215 13 1 3027 2359133 2356089 0 4117
7 TraesCS7A01G006700 chr7D 94.102 2221 89 14 1 2200 3905528 3907727 0 3338
8 TraesCS7A01G006700 chr7D 91.038 1618 141 3 1413 3027 3786994 3785378 0 2182
9 TraesCS7A01G006700 chr7D 93.772 1156 69 3 1 1155 3788437 3787284 0 1733
10 TraesCS7A01G006700 chr7D 93.080 1156 77 3 1 1155 2567616 2566463 0 1688
11 TraesCS7A01G006700 chr4A 91.578 1603 133 1 1427 3027 739867599 739869201 0 2211
12 TraesCS7A01G006700 chr4A 90.813 1611 146 1 1413 3021 739652040 739653650 0 2154
13 TraesCS7A01G006700 chr4A 90.813 1611 146 1 1413 3021 742057319 742058929 0 2154
14 TraesCS7A01G006700 chr4A 90.840 1572 140 3 1459 3027 740019075 740017505 0 2102
15 TraesCS7A01G006700 chr4A 90.229 1617 149 6 1413 3021 740579035 740580650 0 2102
16 TraesCS7A01G006700 chr4A 94.185 1135 62 3 1 1134 739866132 739867263 0 1727


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 TraesCS7A01G006700 chr7A 3206420 3209446 3026 True 5590.0 5590 100.0000 1 3027 1 chr7A.!!$R3 3026
1 TraesCS7A01G006700 chr7A 1994911 1997937 3026 True 4078.0 4078 91.0520 1 3027 1 chr7A.!!$R1 3026
2 TraesCS7A01G006700 chr7A 3311142 3314246 3104 False 1900.0 2080 91.8325 1 3027 2 chr7A.!!$F1 3026
3 TraesCS7A01G006700 chr7A 2117841 2118994 1153 True 1589.0 1589 91.5220 1 1155 1 chr7A.!!$R2 1154
4 TraesCS7A01G006700 chr7D 3631583 3634644 3061 True 4309.0 4309 92.2620 1 3027 1 chr7D.!!$R3 3026
5 TraesCS7A01G006700 chr7D 2356089 2359133 3044 True 4117.0 4117 91.2180 1 3027 1 chr7D.!!$R1 3026
6 TraesCS7A01G006700 chr7D 3905528 3907727 2199 False 3338.0 3338 94.1020 1 2200 1 chr7D.!!$F1 2199
7 TraesCS7A01G006700 chr7D 3785378 3788437 3059 True 1957.5 2182 92.4050 1 3027 2 chr7D.!!$R4 3026
8 TraesCS7A01G006700 chr7D 2566463 2567616 1153 True 1688.0 1688 93.0800 1 1155 1 chr7D.!!$R2 1154
9 TraesCS7A01G006700 chr4A 739652040 739653650 1610 False 2154.0 2154 90.8130 1413 3021 1 chr4A.!!$F1 1608
10 TraesCS7A01G006700 chr4A 742057319 742058929 1610 False 2154.0 2154 90.8130 1413 3021 1 chr4A.!!$F3 1608
11 TraesCS7A01G006700 chr4A 740017505 740019075 1570 True 2102.0 2102 90.8400 1459 3027 1 chr4A.!!$R1 1568
12 TraesCS7A01G006700 chr4A 740579035 740580650 1615 False 2102.0 2102 90.2290 1413 3021 1 chr4A.!!$F2 1608
13 TraesCS7A01G006700 chr4A 739866132 739869201 3069 False 1969.0 2211 92.8815 1 3027 2 chr4A.!!$F4 3026

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
979 982 0.673644 CCATTGTCGGGCTTTCGTCT 60.674 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2875 3033 0.119155 TCTCTGGAGATGGTGGGGTT 59.881 55.0 0.0 0.0 31.41 4.11 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
212 214 3.660177 AGGTAGAGGCAGAGAGATGGATA 59.340 47.826 0.00 0.00 0.00 2.59
468 470 3.523606 TTGCATTGACAACTTTGTGCT 57.476 38.095 11.00 0.00 42.43 4.40
558 560 5.948162 AGTGGCAGAAACAGATTGAATATGT 59.052 36.000 0.00 0.00 36.02 2.29
865 867 1.241990 ACTCTCTGGCTAACGACGCA 61.242 55.000 0.00 0.00 0.00 5.24
979 982 0.673644 CCATTGTCGGGCTTTCGTCT 60.674 55.000 0.00 0.00 0.00 4.18
1130 1133 4.575885 TGTCTACATGGCAAAAGGTACTC 58.424 43.478 0.00 0.00 38.49 2.59
1585 1740 7.426929 AACAACTACACAGATTGAAGATGTC 57.573 36.000 0.00 0.00 0.00 3.06
1648 1803 5.649395 TGAGATGAAACCTTTGGATGATGAC 59.351 40.000 0.00 0.00 0.00 3.06
1751 1906 7.257722 CCAAATTGTAGAAATATGTGGTGGTC 58.742 38.462 0.00 0.00 0.00 4.02
1934 2089 3.118261 TCCTCATTACCTCAAGACATGCC 60.118 47.826 0.00 0.00 0.00 4.40
1936 2091 4.521146 CTCATTACCTCAAGACATGCCTT 58.479 43.478 0.00 0.00 0.00 4.35
1980 2135 3.545703 AGGGCTCCATAATCTTCAAACG 58.454 45.455 0.00 0.00 0.00 3.60
1991 2146 1.760613 TCTTCAAACGTGACCTGGTCT 59.239 47.619 26.03 4.80 31.90 3.85
1992 2147 2.169769 TCTTCAAACGTGACCTGGTCTT 59.830 45.455 26.03 10.84 31.90 3.01
2019 2175 0.961753 GTGGCTGAAGGGTTTCTTGG 59.038 55.000 0.00 0.00 35.50 3.61
2063 2221 5.185828 GGAGGAAGTTGCAGGAATGTATTTT 59.814 40.000 0.00 0.00 0.00 1.82
2169 2327 4.881273 TGGTACATGATCTTATTGCACACC 59.119 41.667 0.00 0.00 0.00 4.16
2188 2346 4.202357 ACACCAGTGTGCTGAAGAGAATTA 60.202 41.667 1.88 0.00 46.86 1.40
2255 2413 2.713863 AGGTCCGTCGACTATCTCTT 57.286 50.000 14.70 0.00 39.15 2.85
2372 2530 1.268625 TGCATTGCAGAGTTCAAGCTG 59.731 47.619 7.38 0.00 33.32 4.24
2430 2588 2.047179 GCGACCAAGACCTGTCCC 60.047 66.667 0.00 0.00 0.00 4.46
2495 2653 6.939622 TCTGAAGATTGTATGTGATGTCTGT 58.060 36.000 0.00 0.00 0.00 3.41
2507 2665 4.819630 TGTGATGTCTGTGTAAAACTTCCC 59.180 41.667 0.00 0.00 0.00 3.97
2630 2788 2.465813 CACCTCAGTCTTCCTCCTCAT 58.534 52.381 0.00 0.00 0.00 2.90
2714 2872 4.701651 CAGGATCTTTGCATTTCTACACCA 59.298 41.667 0.00 0.00 0.00 4.17
2726 2884 5.623956 TTTCTACACCACCTTCTTCAGAA 57.376 39.130 0.00 0.00 0.00 3.02
2759 2917 5.422012 TCTGTACAGAAACATGGATGCTCTA 59.578 40.000 23.24 0.00 33.91 2.43
2772 2930 8.954350 ACATGGATGCTCTAGATTATTTAATGC 58.046 33.333 0.00 0.00 0.00 3.56
2875 3033 8.017418 AGAGTTTTGTGGATTTTGGATAAACA 57.983 30.769 0.00 0.00 0.00 2.83
2911 3069 0.108615 AGATTTGAGGTCTCACCGCG 60.109 55.000 0.00 0.00 44.90 6.46
2937 3095 4.502962 CCCCGTCATATTTTGCAAAATGT 58.497 39.130 36.30 30.25 38.90 2.71
2940 3098 7.429633 CCCCGTCATATTTTGCAAAATGTATA 58.570 34.615 36.30 22.73 38.90 1.47
2949 3107 5.913137 TTGCAAAATGTATAAGTGGGAGG 57.087 39.130 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 214 2.037772 CCAGAGAAACACTGCTACTGGT 59.962 50.000 0.00 0.00 38.67 4.00
468 470 1.077169 TGTAGCCAAGAGACTCAGGGA 59.923 52.381 14.66 0.00 0.00 4.20
865 867 0.252479 CCACCTTCAGCTGCTGATCT 59.748 55.000 30.80 14.52 40.39 2.75
979 982 0.260230 TCAGGCTTTTTGGACACCCA 59.740 50.000 0.00 0.00 41.64 4.51
1130 1133 7.944061 TCATGCTATTTGGATGTGGAAAATAG 58.056 34.615 9.11 9.11 43.72 1.73
1344 1415 0.659957 GCCATTGAATCGACAGGCTC 59.340 55.000 8.16 0.00 39.02 4.70
1648 1803 4.397417 CCAAAGAATAGCTTCCTTGAGTGG 59.603 45.833 0.00 0.00 35.64 4.00
1861 2016 5.043903 TGTCTCGTTCTTTCTGAAGTTGAG 58.956 41.667 0.00 0.00 35.01 3.02
1934 2089 5.989477 TGGATACATACCAAGTTGGAGAAG 58.011 41.667 28.80 16.01 46.17 2.85
1980 2135 0.883833 CCATTGCAAGACCAGGTCAC 59.116 55.000 22.31 10.98 34.60 3.67
1991 2146 1.186917 CCTTCAGCCACCCATTGCAA 61.187 55.000 0.00 0.00 0.00 4.08
1992 2147 1.607178 CCTTCAGCCACCCATTGCA 60.607 57.895 0.00 0.00 0.00 4.08
2019 2175 3.572255 TCCATGTTTTGCCCTTCACTTAC 59.428 43.478 0.00 0.00 0.00 2.34
2063 2221 6.767423 TGAATCTTCTGTCAACAAGTTCATCA 59.233 34.615 0.00 0.00 0.00 3.07
2169 2327 3.990469 ACGTAATTCTCTTCAGCACACTG 59.010 43.478 0.00 0.00 45.95 3.66
2173 2331 4.377431 CCACAACGTAATTCTCTTCAGCAC 60.377 45.833 0.00 0.00 0.00 4.40
2188 2346 4.859304 TTGTGATCTACTACCACAACGT 57.141 40.909 0.00 0.00 43.34 3.99
2289 2447 7.870826 TGTACTTGTGACTTTATGATGTTTGG 58.129 34.615 0.00 0.00 0.00 3.28
2495 2653 4.970711 TCATACGGTTGGGAAGTTTTACA 58.029 39.130 0.00 0.00 0.00 2.41
2507 2665 0.811616 GCAGCCCTCTCATACGGTTG 60.812 60.000 0.00 0.00 0.00 3.77
2630 2788 4.263462 ACAGACCAATCCAGCAGATTTGTA 60.263 41.667 6.29 0.00 42.86 2.41
2714 2872 4.712337 AGATGGTCGTATTCTGAAGAAGGT 59.288 41.667 0.00 0.00 37.48 3.50
2726 2884 5.654603 TGTTTCTGTACAGATGGTCGTAT 57.345 39.130 25.68 0.00 37.29 3.06
2759 2917 9.961265 CTGTCATGTTCATGCATTAAATAATCT 57.039 29.630 0.00 0.00 0.00 2.40
2772 2930 4.232221 GTTTTCAGGCTGTCATGTTCATG 58.768 43.478 15.27 6.46 0.00 3.07
2875 3033 0.119155 TCTCTGGAGATGGTGGGGTT 59.881 55.000 0.00 0.00 31.41 4.11
2911 3069 0.249031 GCAAAATATGACGGGGCTGC 60.249 55.000 0.00 0.00 0.00 5.25
2937 3095 4.566907 GCCAAGTTGTTCCTCCCACTTATA 60.567 45.833 1.45 0.00 0.00 0.98
2940 3098 1.754201 GCCAAGTTGTTCCTCCCACTT 60.754 52.381 1.45 0.00 0.00 3.16
2949 3107 2.946564 GCATAGGTTGCCAAGTTGTTC 58.053 47.619 1.45 0.00 46.15 3.18


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

AutoCloner maintained by Alex Coulton.