Multiple sequence alignment - TraesCS3B01G453900

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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 TraesCS3B01G453900 chr3B 100.000 2900 0 0 1 2900 694806864 694803965 0 5356
1 TraesCS3B01G453900 chr3B 90.062 2918 246 27 5 2900 657695659 657692764 0 3742
2 TraesCS3B01G453900 chr3B 96.450 2197 73 3 1 2194 103311885 103309691 0 3620
3 TraesCS3B01G453900 chr3B 91.332 2561 195 20 348 2897 797909565 797912109 0 3474
4 TraesCS3B01G453900 chr3B 89.013 1338 127 12 1562 2897 692070290 692071609 0 1639
5 TraesCS3B01G453900 chr3B 88.560 1285 123 15 1619 2900 36749919 36748656 0 1537
6 TraesCS3B01G453900 chr4B 90.909 2904 231 29 5 2900 99428961 99426083 0 3869
7 TraesCS3B01G453900 chr4B 92.296 2557 179 14 348 2900 553948353 553945811 0 3615
8 TraesCS3B01G453900 chr7B 90.245 2901 247 30 8 2900 556728871 556725999 0 3757
9 TraesCS3B01G453900 chr2B 96.263 2194 77 3 1 2194 747121791 747119603 0 3592
10 TraesCS3B01G453900 chr6B 90.966 2557 206 20 347 2897 420671211 420673748 0 3419
11 TraesCS3B01G453900 chr1B 90.802 2555 207 22 349 2897 50150842 50148310 0 3391


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 TraesCS3B01G453900 chr3B 694803965 694806864 2899 True 5356 5356 100.000 1 2900 1 chr3B.!!$R4 2899
1 TraesCS3B01G453900 chr3B 657692764 657695659 2895 True 3742 3742 90.062 5 2900 1 chr3B.!!$R3 2895
2 TraesCS3B01G453900 chr3B 103309691 103311885 2194 True 3620 3620 96.450 1 2194 1 chr3B.!!$R2 2193
3 TraesCS3B01G453900 chr3B 797909565 797912109 2544 False 3474 3474 91.332 348 2897 1 chr3B.!!$F2 2549
4 TraesCS3B01G453900 chr3B 692070290 692071609 1319 False 1639 1639 89.013 1562 2897 1 chr3B.!!$F1 1335
5 TraesCS3B01G453900 chr3B 36748656 36749919 1263 True 1537 1537 88.560 1619 2900 1 chr3B.!!$R1 1281
6 TraesCS3B01G453900 chr4B 99426083 99428961 2878 True 3869 3869 90.909 5 2900 1 chr4B.!!$R1 2895
7 TraesCS3B01G453900 chr4B 553945811 553948353 2542 True 3615 3615 92.296 348 2900 1 chr4B.!!$R2 2552
8 TraesCS3B01G453900 chr7B 556725999 556728871 2872 True 3757 3757 90.245 8 2900 1 chr7B.!!$R1 2892
9 TraesCS3B01G453900 chr2B 747119603 747121791 2188 True 3592 3592 96.263 1 2194 1 chr2B.!!$R1 2193
10 TraesCS3B01G453900 chr6B 420671211 420673748 2537 False 3419 3419 90.966 347 2897 1 chr6B.!!$F1 2550
11 TraesCS3B01G453900 chr1B 50148310 50150842 2532 True 3391 3391 90.802 349 2897 1 chr1B.!!$R1 2548

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
29 30 1.893544 CATCCTGGCCAAGCTGATAG 58.106 55.000 7.01 0.0 0.0 2.08 F
637 740 4.923281 GTGTCCCAATTATGTGCAGAAAAC 59.077 41.667 0.00 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1240 1.255667 TAGGGCTTCCACCACGACTC 61.256 60.0 0.0 0.0 0.00 3.36 R
2177 2303 0.588252 AGTTGCACGAATGAGCACAC 59.412 50.0 0.0 0.0 41.52 3.82 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
29 30 1.893544 CATCCTGGCCAAGCTGATAG 58.106 55.000 7.01 0.00 0.00 2.08
455 558 5.754782 TGCTTGTCCCACACATATATTCTT 58.245 37.500 0.00 0.00 33.90 2.52
637 740 4.923281 GTGTCCCAATTATGTGCAGAAAAC 59.077 41.667 0.00 0.00 0.00 2.43
1101 1216 5.602145 ACAAGGAAATTGGTCAGAAAATGGA 59.398 36.000 0.00 0.00 43.68 3.41
1102 1217 6.099557 ACAAGGAAATTGGTCAGAAAATGGAA 59.900 34.615 0.00 0.00 43.68 3.53
1125 1240 4.991056 AGATATGTTTACTACATGCAGGCG 59.009 41.667 0.00 0.00 46.81 5.52
1213 1328 2.418368 AGTGGTGTCTTTGCAGTCAA 57.582 45.000 0.00 0.00 0.00 3.18
1331 1446 4.016666 AGAAGAAGAAGGAGAGGATGAGGA 60.017 45.833 0.00 0.00 0.00 3.71
1438 1553 4.770795 ACGGATGGTTTTCTCTATCAAGG 58.229 43.478 0.00 0.00 0.00 3.61
1496 1611 8.816144 TGAATTGATAAAACAACAGTTTTGCTC 58.184 29.630 14.57 11.63 43.29 4.26
1561 1676 1.992277 CCTCCTGTCCTGGACCCTG 60.992 68.421 23.42 13.26 31.94 4.45
1653 1768 7.190501 AGGAGGTTGGTACTAGTAAGAAGAAT 58.809 38.462 3.61 0.00 0.00 2.40
1741 1865 3.771160 GGCGATGGGAGGTGACGT 61.771 66.667 0.00 0.00 0.00 4.34
1950 2074 6.049955 AGTGTGCAACTGTTATGGTACTAT 57.950 37.500 0.00 0.00 37.88 2.12
2110 2236 6.717540 AGTGCAAAAGGGTTTTTAAAAAGGTT 59.282 30.769 13.58 5.19 34.81 3.50
2117 2243 7.612065 AGGGTTTTTAAAAAGGTTCAGCTAT 57.388 32.000 13.58 0.00 0.00 2.97
2177 2303 1.486310 TCCTATTACTGTGCAGCTGGG 59.514 52.381 17.12 3.82 0.00 4.45
2183 2309 4.193893 TGTGCAGCTGGGTGTGCT 62.194 61.111 17.12 0.00 40.54 4.40
2286 2413 1.069668 TGGATCTGAGATGATGGTGCG 59.930 52.381 0.00 0.00 0.00 5.34
2314 2441 5.306678 TGGACCAAAGGCAATAACAAATCTT 59.693 36.000 0.00 0.00 0.00 2.40
2353 2480 2.915604 AGATGACACAAAGGAGGGTGAT 59.084 45.455 0.00 0.00 38.38 3.06
2354 2481 3.331889 AGATGACACAAAGGAGGGTGATT 59.668 43.478 0.00 0.00 38.38 2.57
2381 2508 1.055338 GACAATTGCGCACTTCAAGC 58.945 50.000 11.12 0.00 0.00 4.01
2419 2546 7.446013 ACCGATCTAGACTTCTTCTATAAGGTG 59.554 40.741 0.00 0.00 36.17 4.00
2524 2651 5.277011 CGATTGCATATCGTTTGACATGACT 60.277 40.000 17.58 0.00 30.26 3.41
2556 2683 6.597672 ACCAACATGTACAATATGTCATTCGT 59.402 34.615 0.00 0.00 37.77 3.85
2566 2693 3.558931 ATGTCATTCGTGCCCTTCATA 57.441 42.857 0.00 0.00 0.00 2.15
2650 2777 4.202050 GCATCGAGCTTTGATTGGGTATTT 60.202 41.667 0.01 0.00 41.15 1.40
2651 2778 4.963276 TCGAGCTTTGATTGGGTATTTG 57.037 40.909 0.00 0.00 0.00 2.32
2698 2825 3.057946 GCAAACCTCCTGACAACTTCATC 60.058 47.826 0.00 0.00 32.17 2.92
2728 2855 1.028330 ATGGTGCAATGAGGCAGTCG 61.028 55.000 0.00 0.00 45.96 4.18
2758 2886 1.098712 TCTTTCCAACCACCGTGCAC 61.099 55.000 6.82 6.82 0.00 4.57
2777 2905 2.476051 GCTGTTGTCGATGGCACG 59.524 61.111 0.00 0.00 0.00 5.34
2829 2959 1.416401 GCTATTGTCCGGAATCCAGGA 59.584 52.381 5.23 8.43 0.00 3.86
2848 2978 5.485620 CAGGACTCTCTGATGATTTCAACA 58.514 41.667 0.00 0.00 36.93 3.33
2849 2979 5.581479 CAGGACTCTCTGATGATTTCAACAG 59.419 44.000 10.60 10.60 44.86 3.16
2850 2980 4.874966 GGACTCTCTGATGATTTCAACAGG 59.125 45.833 15.24 8.29 44.01 4.00
2870 3000 2.880890 GGTGTGTTGACTTCAGCTTCAT 59.119 45.455 0.00 0.00 0.00 2.57
2873 3003 3.947196 TGTGTTGACTTCAGCTTCATTGT 59.053 39.130 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.202137 AGATGTTTGATTTTTCATGGATCCATC 58.798 33.333 24.93 12.98 33.90 3.51
455 558 2.487762 GCTTTGCAATAGGTGTGCTACA 59.512 45.455 0.00 0.00 42.69 2.74
523 626 8.301720 ACTATAGATATATGTTTTTCGTCGCCA 58.698 33.333 6.78 0.00 0.00 5.69
637 740 5.450137 CCATTTGCAAGGAGCTTATTCAGAG 60.450 44.000 0.00 0.00 45.94 3.35
1125 1240 1.255667 TAGGGCTTCCACCACGACTC 61.256 60.000 0.00 0.00 0.00 3.36
1424 1539 7.453393 AGATGTGTTCACCTTGATAGAGAAAA 58.547 34.615 0.37 0.00 0.00 2.29
1438 1553 3.243336 GTGTCCGTCTAGATGTGTTCAC 58.757 50.000 11.03 9.74 0.00 3.18
1496 1611 6.325596 GCTTTGGGCTTCTTGAACTTATTAG 58.674 40.000 0.00 0.00 38.06 1.73
1653 1768 4.316205 TGTCTCACGTTTGCTCTTCTTA 57.684 40.909 0.00 0.00 0.00 2.10
1741 1865 4.443621 TGATTGTGGTCACGAACAAAGTA 58.556 39.130 0.00 0.00 39.57 2.24
1950 2074 6.127758 ACAGTTAAGTCATTTCAGTTGCACAA 60.128 34.615 0.00 0.00 0.00 3.33
2095 2221 7.709182 ACACATAGCTGAACCTTTTTAAAAACC 59.291 33.333 9.31 1.10 0.00 3.27
2110 2236 3.264193 ACAGGAAATGGACACATAGCTGA 59.736 43.478 0.00 0.00 35.94 4.26
2117 2243 6.065976 AGATAATCACAGGAAATGGACACA 57.934 37.500 0.00 0.00 0.00 3.72
2177 2303 0.588252 AGTTGCACGAATGAGCACAC 59.412 50.000 0.00 0.00 41.52 3.82
2212 2339 8.161610 CGTCCTGCATAATACAAAAACAAAATG 58.838 33.333 0.00 0.00 0.00 2.32
2286 2413 5.146010 TGTTATTGCCTTTGGTCCAAATC 57.854 39.130 17.43 12.47 32.70 2.17
2314 2441 7.117236 GTGTCATCTCTACGGAAATTTGTACAA 59.883 37.037 3.59 3.59 0.00 2.41
2322 2449 5.046591 TCCTTTGTGTCATCTCTACGGAAAT 60.047 40.000 0.00 0.00 0.00 2.17
2353 2480 3.004629 AGTGCGCAATTGTCTCAATCAAA 59.995 39.130 14.00 0.00 0.00 2.69
2354 2481 2.553602 AGTGCGCAATTGTCTCAATCAA 59.446 40.909 14.00 0.00 0.00 2.57
2419 2546 7.768120 ACAACTCTGTCCTCTTCATCATATTTC 59.232 37.037 0.00 0.00 0.00 2.17
2488 2615 1.153628 GCAATCGTGGTACGCCTCT 60.154 57.895 0.00 0.00 42.21 3.69
2551 2678 3.864789 ATTCCTATGAAGGGCACGAAT 57.135 42.857 0.00 0.00 43.84 3.34
2556 2683 3.456644 TCGGTTTATTCCTATGAAGGGCA 59.543 43.478 0.00 0.00 43.84 5.36
2566 2693 1.283613 TGGCCATGTCGGTTTATTCCT 59.716 47.619 0.00 0.00 36.97 3.36
2650 2777 2.775490 TAGCCTCTAGGAATGCTCCA 57.225 50.000 0.00 0.00 45.24 3.86
2651 2778 2.235898 CCATAGCCTCTAGGAATGCTCC 59.764 54.545 0.00 0.00 42.81 4.70
2728 2855 4.333926 GTGGTTGGAAAGATGCTCTGTATC 59.666 45.833 0.00 0.00 0.00 2.24
2758 2886 2.741985 TGCCATCGACAACAGCGG 60.742 61.111 0.00 0.00 0.00 5.52
2777 2905 4.853924 TTTCCTGAGCCTTTTTCATGAC 57.146 40.909 0.00 0.00 0.00 3.06
2829 2959 5.221803 ACACCTGTTGAAATCATCAGAGAGT 60.222 40.000 18.56 12.27 43.06 3.24
2848 2978 2.092968 TGAAGCTGAAGTCAACACACCT 60.093 45.455 0.00 0.00 0.00 4.00
2849 2979 2.288666 TGAAGCTGAAGTCAACACACC 58.711 47.619 0.00 0.00 0.00 4.16
2850 2980 4.201950 ACAATGAAGCTGAAGTCAACACAC 60.202 41.667 0.00 0.00 0.00 3.82
2870 3000 4.316205 TTCTGCTCAAACTCGTCTACAA 57.684 40.909 0.00 0.00 0.00 2.41
2873 3003 4.245660 CCAATTCTGCTCAAACTCGTCTA 58.754 43.478 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.