Multiple sequence alignment - TraesCS7A01G558000

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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 TraesCS7A01G558000 chr7A 100.000 3056 0 0 1 3056 730702773 730699718 0.000000e+00 5644.0
1 TraesCS7A01G558000 chr7A 96.790 2710 82 4 350 3056 730680111 730677404 0.000000e+00 4518.0
2 TraesCS7A01G558000 chr7A 91.358 2592 204 14 25 2607 730591786 730589206 0.000000e+00 3528.0
3 TraesCS7A01G558000 chr7D 95.218 2614 116 8 1 2607 634958851 634961462 0.000000e+00 4126.0
4 TraesCS7A01G558000 chr7D 94.648 2616 121 13 1 2607 634881725 634879120 0.000000e+00 4037.0
5 TraesCS7A01G558000 chr7D 95.731 2483 99 5 131 2607 635417425 635419906 0.000000e+00 3991.0
6 TraesCS7A01G558000 chr7D 91.552 2616 192 18 1 2607 634979739 634982334 0.000000e+00 3579.0
7 TraesCS7A01G558000 chr7D 91.269 2600 199 17 16 2607 634987168 634989747 0.000000e+00 3518.0
8 TraesCS7A01G558000 chr7D 89.301 458 33 6 2608 3054 634887137 634886685 7.400000e-156 560.0
9 TraesCS7A01G558000 chr7D 87.747 253 24 3 2809 3054 511648431 511648179 3.860000e-74 289.0
10 TraesCS7A01G558000 chr7D 87.352 253 25 3 2809 3054 566127609 566127357 1.790000e-72 283.0
11 TraesCS7A01G558000 chr7D 95.960 99 4 0 2645 2743 635403015 635403113 8.770000e-36 161.0
12 TraesCS7A01G558000 chr7D 92.308 52 4 0 2760 2811 635403111 635403162 1.180000e-09 75.0
13 TraesCS7A01G558000 chr7D 100.000 36 0 0 2643 2678 634974627 634974662 1.970000e-07 67.6
14 TraesCS7A01G558000 chr7B 94.106 2613 136 10 1 2607 741233158 741230558 0.000000e+00 3956.0
15 TraesCS7A01G558000 chr7B 94.433 2497 124 10 1 2487 741275441 741277932 0.000000e+00 3827.0
16 TraesCS7A01G558000 chr7B 93.137 204 14 0 2608 2811 740907075 740906872 1.780000e-77 300.0
17 TraesCS7A01G558000 chr2A 88.142 253 23 4 2809 3054 598630495 598630747 8.290000e-76 294.0
18 TraesCS7A01G558000 chr2D 88.306 248 22 3 2809 3049 372702583 372702830 1.070000e-74 291.0
19 TraesCS7A01G558000 chr4A 87.843 255 20 5 2809 3054 648472743 648472995 3.860000e-74 289.0
20 TraesCS7A01G558000 chr4B 87.649 251 23 4 2811 3054 483507636 483507885 4.990000e-73 285.0
21 TraesCS7A01G558000 chr6D 87.402 254 23 5 2809 3054 10715226 10714974 1.790000e-72 283.0


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 TraesCS7A01G558000 chr7A 730699718 730702773 3055 True 5644 5644 100.000 1 3056 1 chr7A.!!$R3 3055
1 TraesCS7A01G558000 chr7A 730677404 730680111 2707 True 4518 4518 96.790 350 3056 1 chr7A.!!$R2 2706
2 TraesCS7A01G558000 chr7A 730589206 730591786 2580 True 3528 3528 91.358 25 2607 1 chr7A.!!$R1 2582
3 TraesCS7A01G558000 chr7D 634958851 634961462 2611 False 4126 4126 95.218 1 2607 1 chr7D.!!$F1 2606
4 TraesCS7A01G558000 chr7D 634879120 634881725 2605 True 4037 4037 94.648 1 2607 1 chr7D.!!$R3 2606
5 TraesCS7A01G558000 chr7D 635417425 635419906 2481 False 3991 3991 95.731 131 2607 1 chr7D.!!$F5 2476
6 TraesCS7A01G558000 chr7D 634979739 634982334 2595 False 3579 3579 91.552 1 2607 1 chr7D.!!$F3 2606
7 TraesCS7A01G558000 chr7D 634987168 634989747 2579 False 3518 3518 91.269 16 2607 1 chr7D.!!$F4 2591
8 TraesCS7A01G558000 chr7B 741230558 741233158 2600 True 3956 3956 94.106 1 2607 1 chr7B.!!$R2 2606
9 TraesCS7A01G558000 chr7B 741275441 741277932 2491 False 3827 3827 94.433 1 2487 1 chr7B.!!$F1 2486

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
915 921 4.280819 ACACCAATATGCTGTTAGCCAAT 58.719 39.13 0.00 0.0 41.51 3.16 F
1119 1126 0.534412 CGTCTGACATCTCTGCCCTT 59.466 55.00 8.73 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1918 0.249120 CATTGCCACTCGAGTACCCA 59.751 55.0 19.57 12.44 0.00 4.51 R
2978 3002 0.884704 TCCGTGAAGACAGCAAAGGC 60.885 55.0 0.00 0.00 41.61 4.35 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
452 455 8.213679 AGGATATGGATGTAATAAATGGGATCG 58.786 37.037 0.00 0.00 0.00 3.69
453 456 7.993183 GGATATGGATGTAATAAATGGGATCGT 59.007 37.037 0.00 0.00 0.00 3.73
915 921 4.280819 ACACCAATATGCTGTTAGCCAAT 58.719 39.130 0.00 0.00 41.51 3.16
1015 1022 4.649674 ACAATAGTATGCCGAGGAAAGAGA 59.350 41.667 0.00 0.00 0.00 3.10
1102 1109 1.164041 CGGTTTGTTCAAGAGGGCGT 61.164 55.000 0.00 0.00 0.00 5.68
1119 1126 0.534412 CGTCTGACATCTCTGCCCTT 59.466 55.000 8.73 0.00 0.00 3.95
1155 1162 2.229062 TGCAGTCGTCCTAGAGACAAAG 59.771 50.000 12.97 6.04 46.69 2.77
1332 1339 0.601558 TGACCGAGGAAGACCGAAAG 59.398 55.000 0.00 0.00 41.83 2.62
1485 1492 4.156008 GTCCAAAAAGACATTAGATGCCGT 59.844 41.667 0.00 0.00 36.73 5.68
1602 1609 6.099701 TGGGTACTACTCATTCACTAATGCAT 59.900 38.462 0.00 0.00 41.96 3.96
1625 1632 0.976641 TCGTGGCCTCACAATCTCTT 59.023 50.000 3.32 0.00 43.79 2.85
1679 1686 2.422127 CACAACCAGAACAAACTTCGGT 59.578 45.455 0.00 0.00 0.00 4.69
1881 1888 1.282817 CAAACCACGACTCAACGTCA 58.717 50.000 0.00 0.00 44.76 4.35
1887 1894 1.079819 CGACTCAACGTCAGGGCAT 60.080 57.895 0.00 0.00 42.98 4.40
2043 2050 2.732844 ACTTAGGCTCTAGCGGTACT 57.267 50.000 0.00 0.00 43.26 2.73
2053 2060 4.839121 CTCTAGCGGTACTGATCTAGGAT 58.161 47.826 5.68 0.00 31.80 3.24
2100 2107 1.841302 TTGATGTGCCGCCCTCTTCT 61.841 55.000 0.00 0.00 0.00 2.85
2377 2392 7.362056 CGAATGAAGGAAGTGGAACATGTATTT 60.362 37.037 0.00 0.00 44.52 1.40
2391 2406 6.100404 ACATGTATTTCAACAATGCACCTT 57.900 33.333 0.00 0.00 32.02 3.50
2616 2640 0.997196 GACGTGAATAGACCGTTGGC 59.003 55.000 0.00 0.00 34.51 4.52
2633 2657 3.822192 CCAGCGACGGTGATCGGA 61.822 66.667 27.42 0.00 42.49 4.55
2653 2677 6.237901 TCGGAGATATTTATGGTTGGGATTG 58.762 40.000 0.00 0.00 0.00 2.67
2690 2714 6.483307 GCACCTTTCCAAAAGAGCTAAAAATT 59.517 34.615 1.06 0.00 0.00 1.82
2754 2778 3.275617 TCTATTGTTGGGAATGGGACG 57.724 47.619 0.00 0.00 0.00 4.79
2758 2782 0.250989 TGTTGGGAATGGGACGTTCC 60.251 55.000 5.70 5.70 43.52 3.62
2770 2794 1.392510 GGACGTTCCGTTAACAGCATC 59.607 52.381 6.39 0.00 41.37 3.91
2775 2799 3.303495 CGTTCCGTTAACAGCATCTACAG 59.697 47.826 6.39 0.00 38.03 2.74
2870 2894 0.999406 GCAACTACGTCGATGCACAT 59.001 50.000 15.90 0.00 38.63 3.21
2903 2927 6.096987 CCAACTACTCCATCACACTACACTAT 59.903 42.308 0.00 0.00 0.00 2.12
2940 2964 6.567050 ACTAGCAAAATTTGGCATGTCTATG 58.433 36.000 19.63 0.00 37.36 2.23
2978 3002 4.778143 CCCTTGCCCTTCCCGACG 62.778 72.222 0.00 0.00 0.00 5.12
2983 3007 4.717313 GCCCTTCCCGACGCCTTT 62.717 66.667 0.00 0.00 0.00 3.11
2990 3014 2.357517 CCGACGCCTTTGCTGTCT 60.358 61.111 0.00 0.00 38.22 3.41
2993 3017 1.221466 CGACGCCTTTGCTGTCTTCA 61.221 55.000 0.00 0.00 38.22 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.017440 CCTCAAAACTAAAAACATCCGACTGA 60.017 38.462 0.00 0.00 0.00 3.41
467 470 6.841119 TCCTTTGTTGATCACATTGATTACG 58.159 36.000 0.00 0.00 37.20 3.18
1102 1109 3.107402 AGTAAGGGCAGAGATGTCAGA 57.893 47.619 0.00 0.00 0.00 3.27
1119 1126 1.007963 ACTGCAACCCTAGCCCTAGTA 59.992 52.381 1.99 0.00 0.00 1.82
1155 1162 5.107133 CCAAATGAGTGCATCTTTCCATTC 58.893 41.667 0.00 0.00 32.35 2.67
1332 1339 6.737254 TTCATACGAAGGATGGAAAGTTTC 57.263 37.500 7.09 7.09 0.00 2.78
1602 1609 0.107703 GATTGTGAGGCCACGATGGA 60.108 55.000 5.01 0.00 45.12 3.41
1625 1632 1.374947 GCAGGTGGCTGGAGTTGTA 59.625 57.895 0.00 0.00 40.25 2.41
1797 1804 2.084610 TCTGAACATGCAACTCCTCG 57.915 50.000 0.00 0.00 0.00 4.63
1881 1888 0.936691 AGGCCTCCAAATTATGCCCT 59.063 50.000 0.00 0.00 43.18 5.19
1911 1918 0.249120 CATTGCCACTCGAGTACCCA 59.751 55.000 19.57 12.44 0.00 4.51
2043 2050 5.970289 ACCATGGAAGACTATCCTAGATCA 58.030 41.667 21.47 0.00 40.35 2.92
2053 2060 4.785914 TCCACCATTTACCATGGAAGACTA 59.214 41.667 21.47 0.00 41.64 2.59
2100 2107 7.437713 AAGACCATCAATATCTTGTCCAGTA 57.562 36.000 0.00 0.00 31.47 2.74
2249 2257 5.979517 GGAACACTTAGCATGCATATTTTCC 59.020 40.000 21.98 18.49 0.00 3.13
2250 2258 6.563422 TGGAACACTTAGCATGCATATTTTC 58.437 36.000 21.98 13.80 0.00 2.29
2616 2640 3.758088 CTCCGATCACCGTCGCTGG 62.758 68.421 0.00 0.00 40.17 4.85
2633 2657 9.143155 GGTAAACAATCCCAACCATAAATATCT 57.857 33.333 0.00 0.00 0.00 1.98
2653 2677 2.544277 GGAAAGGTGCCAAACGGTAAAC 60.544 50.000 0.00 0.00 0.00 2.01
2738 2762 1.611519 GAACGTCCCATTCCCAACAA 58.388 50.000 0.00 0.00 0.00 2.83
2754 2778 3.062234 GCTGTAGATGCTGTTAACGGAAC 59.938 47.826 18.81 8.01 38.65 3.62
2758 2782 1.588404 CGGCTGTAGATGCTGTTAACG 59.412 52.381 0.26 0.00 32.57 3.18
2770 2794 2.125106 GCCAAGTCCCGGCTGTAG 60.125 66.667 0.00 0.00 46.56 2.74
2870 2894 4.097437 GTGATGGAGTAGTTGGACGATGTA 59.903 45.833 0.00 0.00 0.00 2.29
2880 2904 7.832685 TGTATAGTGTAGTGTGATGGAGTAGTT 59.167 37.037 0.00 0.00 0.00 2.24
2903 2927 1.408969 TGCTAGTCCGATGGCATGTA 58.591 50.000 3.81 0.00 31.01 2.29
2955 2979 2.747855 GAAGGGCAAGGGCAGTCG 60.748 66.667 0.00 0.00 43.71 4.18
2978 3002 0.884704 TCCGTGAAGACAGCAAAGGC 60.885 55.000 0.00 0.00 41.61 4.35
2983 3007 1.000506 GGTACTTCCGTGAAGACAGCA 59.999 52.381 17.18 0.00 41.71 4.41
3011 3035 2.417924 CCAGCTCGATCTGTACTGCTTT 60.418 50.000 14.70 0.00 32.32 3.51


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

AutoCloner maintained by Alex Coulton.