Multiple sequence alignment - TraesCS7D01G552000

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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 TraesCS7D01G552000 chr7D 100.000 3319 0 0 1 3319 634979597 634982915 0.000000e+00 6130
1 TraesCS7D01G552000 chr7D 92.545 3340 214 23 1 3319 634881872 634878547 0.000000e+00 4756
2 TraesCS7D01G552000 chr7D 96.373 2785 94 7 1 2781 634987009 634989790 0.000000e+00 4577
3 TraesCS7D01G552000 chr7D 94.417 2651 125 8 678 3319 635434665 635437301 0.000000e+00 4054
4 TraesCS7D01G552000 chr7D 91.243 2969 216 26 1 2938 634958707 634961662 0.000000e+00 4002
5 TraesCS7D01G552000 chr7D 92.013 2692 183 15 271 2938 635417423 635420106 0.000000e+00 3751
6 TraesCS7D01G552000 chr7D 93.236 1508 80 9 1815 3319 634868206 634866718 0.000000e+00 2200
7 TraesCS7D01G552000 chr7B 94.217 3320 174 12 1 3310 740849915 740846604 0.000000e+00 5051
8 TraesCS7D01G552000 chr7B 93.767 3321 161 16 1 3310 740813466 740810181 0.000000e+00 4944
9 TraesCS7D01G552000 chr7B 93.746 3326 156 19 1 3310 740887705 740884416 0.000000e+00 4942
10 TraesCS7D01G552000 chr7B 90.555 2975 221 30 1 2944 741233295 741230350 0.000000e+00 3882
11 TraesCS7D01G552000 chr7A 91.169 2763 207 23 1 2738 730702917 730700167 0.000000e+00 3716
12 TraesCS7D01G552000 chr7A 91.327 1568 120 12 1 1558 730669609 730668048 0.000000e+00 2128
13 TraesCS7D01G552000 chr7A 89.109 505 49 5 1 500 730690970 730690467 1.010000e-174 623
14 TraesCS7D01G552000 chr7A 90.000 90 6 3 58 146 730702766 730702679 2.710000e-21 113


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 TraesCS7D01G552000 chr7D 634979597 634982915 3318 False 6130.0 6130 100.0000 1 3319 1 chr7D.!!$F2 3318
1 TraesCS7D01G552000 chr7D 634878547 634881872 3325 True 4756.0 4756 92.5450 1 3319 1 chr7D.!!$R2 3318
2 TraesCS7D01G552000 chr7D 634987009 634989790 2781 False 4577.0 4577 96.3730 1 2781 1 chr7D.!!$F3 2780
3 TraesCS7D01G552000 chr7D 635434665 635437301 2636 False 4054.0 4054 94.4170 678 3319 1 chr7D.!!$F5 2641
4 TraesCS7D01G552000 chr7D 634958707 634961662 2955 False 4002.0 4002 91.2430 1 2938 1 chr7D.!!$F1 2937
5 TraesCS7D01G552000 chr7D 635417423 635420106 2683 False 3751.0 3751 92.0130 271 2938 1 chr7D.!!$F4 2667
6 TraesCS7D01G552000 chr7D 634866718 634868206 1488 True 2200.0 2200 93.2360 1815 3319 1 chr7D.!!$R1 1504
7 TraesCS7D01G552000 chr7B 740846604 740849915 3311 True 5051.0 5051 94.2170 1 3310 1 chr7B.!!$R2 3309
8 TraesCS7D01G552000 chr7B 740810181 740813466 3285 True 4944.0 4944 93.7670 1 3310 1 chr7B.!!$R1 3309
9 TraesCS7D01G552000 chr7B 740884416 740887705 3289 True 4942.0 4942 93.7460 1 3310 1 chr7B.!!$R3 3309
10 TraesCS7D01G552000 chr7B 741230350 741233295 2945 True 3882.0 3882 90.5550 1 2944 1 chr7B.!!$R4 2943
11 TraesCS7D01G552000 chr7A 730668048 730669609 1561 True 2128.0 2128 91.3270 1 1558 1 chr7A.!!$R1 1557
12 TraesCS7D01G552000 chr7A 730700167 730702917 2750 True 1914.5 3716 90.5845 1 2738 2 chr7A.!!$R3 2737
13 TraesCS7D01G552000 chr7A 730690467 730690970 503 True 623.0 623 89.1090 1 500 1 chr7A.!!$R2 499

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
361 377 2.511600 CGCGGGAACTGGGCTTAG 60.512 66.667 0.0 0.0 41.75 2.18 F
1698 1726 0.519077 GCTCTGCAACTACCAAGTGC 59.481 55.000 0.0 0.0 35.62 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1772 0.320771 AGTGATTGTGAGGCCACGAC 60.321 55.0 5.01 0.0 46.06 4.34 R
2838 2904 0.757188 AGAGCCCTAGATCCACGGTG 60.757 60.0 0.00 0.0 0.00 4.94 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
361 377 2.511600 CGCGGGAACTGGGCTTAG 60.512 66.667 0.00 0.00 41.75 2.18
421 437 8.736244 GTGTTATACCATGACTTACCAAATGTT 58.264 33.333 0.00 0.00 0.00 2.71
444 460 9.424319 TGTTCTAGTATTTTCTAGTTGCTCTTG 57.576 33.333 0.00 0.00 38.66 3.02
1575 1603 6.455360 AGATCTCAGTCTTGAAGATCTGAC 57.545 41.667 17.49 0.00 41.49 3.51
1621 1649 5.414454 TCGGGTCCAAAAAGACATTAGATTG 59.586 40.000 0.00 0.00 38.59 2.67
1698 1726 0.519077 GCTCTGCAACTACCAAGTGC 59.481 55.000 0.00 0.00 35.62 4.40
1701 1735 1.416030 TCTGCAACTACCAAGTGCTGA 59.584 47.619 0.00 0.00 36.43 4.26
1738 1772 5.344066 ACTACTCATTCACTTATGCAGTCG 58.656 41.667 0.00 0.00 30.92 4.18
1755 1789 1.374125 CGTCGTGGCCTCACAATCA 60.374 57.895 3.32 0.00 43.79 2.57
1818 1852 0.030235 GAACAAACTTCGGCACCACC 59.970 55.000 0.00 0.00 0.00 4.61
2013 2048 5.008980 TGATGCAAACCATGACTCAACATA 58.991 37.500 0.00 0.00 33.29 2.29
2079 2114 5.292589 GTGGCAATGCTTTTTCTATTGATGG 59.707 40.000 4.82 0.00 34.55 3.51
2121 2156 4.756564 TGGGGTTATGCTCTATCAGATCT 58.243 43.478 0.00 0.00 0.00 2.75
2171 2206 3.322254 GGATGCTTACTTAGGCTCTAGCA 59.678 47.826 4.07 10.07 44.36 3.49
2172 2207 4.202264 GGATGCTTACTTAGGCTCTAGCAA 60.202 45.833 4.07 0.00 41.38 3.91
2209 2244 2.427095 GTCTTCCATGGTAAATGGTGGC 59.573 50.000 12.58 0.00 40.06 5.01
2522 2575 8.405531 ACATGTATTTACAACAATGCACCTATC 58.594 33.333 0.00 0.00 39.99 2.08
2764 2828 9.693739 TGCCTTATCAAGAAATTAGAACCATAA 57.306 29.630 0.00 0.00 0.00 1.90
2838 2904 5.236047 TGCACCATTAACAACATTGAAAAGC 59.764 36.000 0.00 0.00 0.00 3.51
2852 2918 2.280628 GAAAAGCACCGTGGATCTAGG 58.719 52.381 0.00 0.00 0.00 3.02
2957 3023 7.374272 ACATAATGACCATCTCATAGAAGACG 58.626 38.462 0.00 0.00 38.82 4.18
2996 3062 9.113838 CACATGTAGCCACTTTTATAGAAGAAT 57.886 33.333 9.85 0.00 0.00 2.40
3056 3122 8.893563 AAATACTATTCTTTTTGGTGGATGGA 57.106 30.769 0.00 0.00 0.00 3.41
3070 3136 3.101437 TGGATGGAATGCATGAGCTTTT 58.899 40.909 0.00 0.00 40.85 2.27
3146 3212 9.073475 AGTTAAAACAACATGTATCTGGCTAAA 57.927 29.630 0.00 0.00 0.00 1.85
3152 3218 7.315142 ACAACATGTATCTGGCTAAAAACATG 58.685 34.615 0.00 15.56 46.01 3.21
3179 3245 7.971183 AAAGAAACACCTAATCTCAGACTTC 57.029 36.000 0.00 0.00 0.00 3.01
3191 3257 3.067320 TCTCAGACTTCCGCATGTCATAG 59.933 47.826 0.00 0.00 35.81 2.23
3311 3378 8.521176 ACATCGTACTTAAGAAGACATACACTT 58.479 33.333 10.09 0.00 0.00 3.16
3312 3379 9.011407 CATCGTACTTAAGAAGACATACACTTC 57.989 37.037 10.09 0.00 42.53 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 58 6.475076 TCAAAAATCAAAAACATCCGACTGTG 59.525 34.615 0.00 0.00 0.00 3.66
248 263 4.394797 AAGGCTTTTTCTGGAAGGATCT 57.605 40.909 0.00 0.00 0.00 2.75
361 377 2.020131 CATCGACATGCCTCCTTGC 58.980 57.895 0.00 0.00 0.00 4.01
421 437 8.035394 CACCAAGAGCAACTAGAAAATACTAGA 58.965 37.037 9.28 0.00 41.42 2.43
444 460 7.069578 TGAGATACCAACTAGGAAAGATACACC 59.930 40.741 0.00 0.00 41.22 4.16
531 547 4.579753 ACTACCTAATCTAGAAGTGGTCGC 59.420 45.833 14.52 0.00 0.00 5.19
833 859 1.270550 CATCCTTCTTTGCAACCGCTT 59.729 47.619 0.00 0.00 39.64 4.68
836 862 1.068333 CCACATCCTTCTTTGCAACCG 60.068 52.381 0.00 0.00 0.00 4.44
1402 1429 3.119849 CGTTTTGTAGGCTTCCAATCCTG 60.120 47.826 0.00 0.00 34.02 3.86
1621 1649 1.526917 ATGCAATGGAGGTAGCCGC 60.527 57.895 0.00 0.00 0.00 6.53
1653 1681 2.281414 CACATGTGCCACCGGTCA 60.281 61.111 13.94 0.00 0.00 4.02
1680 1708 1.802960 CAGCACTTGGTAGTTGCAGAG 59.197 52.381 0.00 0.00 33.57 3.35
1698 1726 5.363868 TGAGTAGTACCCAAATGATCCTCAG 59.636 44.000 0.00 0.00 0.00 3.35
1701 1735 6.386927 TGAATGAGTAGTACCCAAATGATCCT 59.613 38.462 0.00 0.00 0.00 3.24
1738 1772 0.320771 AGTGATTGTGAGGCCACGAC 60.321 55.000 5.01 0.00 46.06 4.34
1755 1789 2.016905 AGGTAGCTGGAGTTGTGAGT 57.983 50.000 0.00 0.00 0.00 3.41
2013 2048 0.620030 GGCCTCCAAATTTTGCCCAT 59.380 50.000 3.50 0.00 36.07 4.00
2079 2114 4.244862 CCATTGTTCAGTGTTAAATGGGC 58.755 43.478 18.08 0.00 42.28 5.36
2121 2156 4.530710 AGGAAACTATTGTAGCACGACA 57.469 40.909 0.00 0.00 40.61 4.35
2171 2206 4.828387 GGAAGACTGTCCTAGATCCGTATT 59.172 45.833 3.76 0.00 34.56 1.89
2172 2207 4.141228 TGGAAGACTGTCCTAGATCCGTAT 60.141 45.833 3.76 0.00 38.62 3.06
2209 2244 3.443045 GGCGGCACATCAACCCAG 61.443 66.667 3.07 0.00 0.00 4.45
2522 2575 6.694411 GCTAATGTTTGCCTCACAATATTCTG 59.306 38.462 0.00 0.00 38.31 3.02
2598 2652 4.887071 TGTGTTGAAGTTTGGACTATGCTT 59.113 37.500 0.00 0.00 34.21 3.91
2603 2659 4.407621 TCTCCTGTGTTGAAGTTTGGACTA 59.592 41.667 0.00 0.00 34.21 2.59
2764 2828 4.444022 GCCACCATCTCTTCACATGTCTAT 60.444 45.833 0.00 0.00 0.00 1.98
2838 2904 0.757188 AGAGCCCTAGATCCACGGTG 60.757 60.000 0.00 0.00 0.00 4.94
2927 2993 8.267620 TCTATGAGATGGTCATTATGTCCTTT 57.732 34.615 9.63 0.00 44.05 3.11
2938 3004 4.270008 TGACGTCTTCTATGAGATGGTCA 58.730 43.478 17.92 7.30 38.50 4.02
2957 3023 5.411361 TGGCTACATGTGTTGATTAACTGAC 59.589 40.000 9.11 0.00 37.68 3.51
3034 3100 7.147915 GCATTCCATCCACCAAAAAGAATAGTA 60.148 37.037 0.00 0.00 0.00 1.82
3037 3103 5.483231 TGCATTCCATCCACCAAAAAGAATA 59.517 36.000 0.00 0.00 0.00 1.75
3138 3204 8.116136 GTGTTTCTTTTTCATGTTTTTAGCCAG 58.884 33.333 0.00 0.00 0.00 4.85
3146 3212 9.750125 GAGATTAGGTGTTTCTTTTTCATGTTT 57.250 29.630 0.00 0.00 0.00 2.83
3152 3218 8.384607 AGTCTGAGATTAGGTGTTTCTTTTTC 57.615 34.615 0.00 0.00 0.00 2.29
3179 3245 4.880886 TCATTGAAACTATGACATGCGG 57.119 40.909 0.00 0.00 0.00 5.69
3275 3342 7.096884 TCTTAAGTACGATGTGCATCTAGTT 57.903 36.000 10.05 11.31 35.72 2.24


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

AutoCloner maintained by Alex Coulton.