Multiple sequence alignment - TraesCS4A01G193500

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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 TraesCS4A01G193500 chr4A 100.000 2922 0 0 1 2922 475388649 475391570 0.000000e+00 5397
1 TraesCS4A01G193500 chr4A 77.337 706 118 24 823 1491 695909057 695908357 2.130000e-101 379
2 TraesCS4A01G193500 chr5A 99.898 1959 2 0 1 1959 473244970 473243012 0.000000e+00 3607
3 TraesCS4A01G193500 chr5A 97.802 1956 20 7 1 1954 685965588 685967522 0.000000e+00 3352
4 TraesCS4A01G193500 chr6A 99.282 1950 12 2 1 1950 434546213 434548160 0.000000e+00 3522
5 TraesCS4A01G193500 chr1A 99.082 1960 15 3 1 1959 457823931 457821974 0.000000e+00 3517
6 TraesCS4A01G193500 chr2D 94.246 1738 85 6 2 1732 634829436 634831165 0.000000e+00 2641
7 TraesCS4A01G193500 chr2D 85.547 1370 187 8 589 1952 386814280 386815644 0.000000e+00 1423
8 TraesCS4A01G193500 chr7B 99.628 1076 3 1 885 1960 586051083 586052157 0.000000e+00 1964
9 TraesCS4A01G193500 chr5D 99.887 882 1 0 1 882 487562531 487561650 0.000000e+00 1624
10 TraesCS4A01G193500 chr2B 80.073 1907 361 18 59 1955 135778619 135780516 0.000000e+00 1399
11 TraesCS4A01G193500 chr4D 91.170 974 66 10 1953 2918 100820420 100819459 0.000000e+00 1304
12 TraesCS4A01G193500 chr4B 88.132 851 77 16 1953 2788 143320294 143319453 0.000000e+00 990
13 TraesCS4A01G193500 chr3B 93.182 264 17 1 1666 1928 663414908 663415171 1.270000e-103 387
14 TraesCS4A01G193500 chrUn 100.000 135 0 0 1 135 328339472 328339606 1.740000e-62 250


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 TraesCS4A01G193500 chr4A 475388649 475391570 2921 False 5397 5397 100.000 1 2922 1 chr4A.!!$F1 2921
1 TraesCS4A01G193500 chr4A 695908357 695909057 700 True 379 379 77.337 823 1491 1 chr4A.!!$R1 668
2 TraesCS4A01G193500 chr5A 473243012 473244970 1958 True 3607 3607 99.898 1 1959 1 chr5A.!!$R1 1958
3 TraesCS4A01G193500 chr5A 685965588 685967522 1934 False 3352 3352 97.802 1 1954 1 chr5A.!!$F1 1953
4 TraesCS4A01G193500 chr6A 434546213 434548160 1947 False 3522 3522 99.282 1 1950 1 chr6A.!!$F1 1949
5 TraesCS4A01G193500 chr1A 457821974 457823931 1957 True 3517 3517 99.082 1 1959 1 chr1A.!!$R1 1958
6 TraesCS4A01G193500 chr2D 634829436 634831165 1729 False 2641 2641 94.246 2 1732 1 chr2D.!!$F2 1730
7 TraesCS4A01G193500 chr2D 386814280 386815644 1364 False 1423 1423 85.547 589 1952 1 chr2D.!!$F1 1363
8 TraesCS4A01G193500 chr7B 586051083 586052157 1074 False 1964 1964 99.628 885 1960 1 chr7B.!!$F1 1075
9 TraesCS4A01G193500 chr5D 487561650 487562531 881 True 1624 1624 99.887 1 882 1 chr5D.!!$R1 881
10 TraesCS4A01G193500 chr2B 135778619 135780516 1897 False 1399 1399 80.073 59 1955 1 chr2B.!!$F1 1896
11 TraesCS4A01G193500 chr4D 100819459 100820420 961 True 1304 1304 91.170 1953 2918 1 chr4D.!!$R1 965
12 TraesCS4A01G193500 chr4B 143319453 143320294 841 True 990 990 88.132 1953 2788 1 chr4B.!!$R1 835

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
1894 1939 2.697431 TTGTAAATGACGCTGTTGCC 57.303 45.0 0.0 0.0 35.36 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2749 2819 0.191064 TGACCCTGGTCTCTTGGACT 59.809 55.0 16.81 0.0 44.8 3.85 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
1894 1939 2.697431 TTGTAAATGACGCTGTTGCC 57.303 45.000 0.00 0.00 35.36 4.52
2025 2071 1.144057 CCACCGGCACAGATAGGAC 59.856 63.158 0.00 0.00 0.00 3.85
2070 2116 3.816994 TCGTTCTTCTCCTGGATCGATA 58.183 45.455 0.00 0.00 31.58 2.92
2090 2136 5.674148 CGATAAAGAGTGATCAATTTGCACG 59.326 40.000 0.00 4.23 37.60 5.34
2318 2367 2.033424 TGTCGATGCTGAGAACTATCGG 59.967 50.000 0.00 0.00 41.82 4.18
2398 2448 4.637534 GTCACACAAATCCATAGCATCTGT 59.362 41.667 0.00 0.00 0.00 3.41
2481 2540 8.766151 TGGATTTTTACAATTTTACTTTTCGGC 58.234 29.630 0.00 0.00 0.00 5.54
2499 2558 3.749665 GGCTGATGCTGAGAACTATCT 57.250 47.619 0.00 0.00 37.77 1.98
2580 2650 5.312895 ACCAATACAAACAGAGCATGTGTA 58.687 37.500 0.00 0.00 44.43 2.90
2633 2703 4.352009 ACCTGACAAATATTCCCAATGCA 58.648 39.130 0.00 0.00 0.00 3.96
2649 2719 4.309099 CAATGCACACCAATAACAAAGCT 58.691 39.130 0.00 0.00 0.00 3.74
2650 2720 4.605640 ATGCACACCAATAACAAAGCTT 57.394 36.364 0.00 0.00 0.00 3.74
2677 2747 4.466726 AGCTCTACATCGTAAAGGAACCTT 59.533 41.667 0.00 0.00 37.98 3.50
2678 2748 4.804665 GCTCTACATCGTAAAGGAACCTTC 59.195 45.833 6.56 0.00 34.84 3.46
2708 2778 1.001706 CACCTCGACTGAAGACAACGA 60.002 52.381 0.00 0.00 35.24 3.85
2724 2794 5.710099 AGACAACGAACATTACCAAATCCAT 59.290 36.000 0.00 0.00 0.00 3.41
2730 2800 7.054124 ACGAACATTACCAAATCCATAGTGAT 58.946 34.615 0.00 0.00 0.00 3.06
2749 2819 4.947388 GTGATAAGCCAAACCACAAGGATA 59.053 41.667 0.00 0.00 38.69 2.59
2781 2852 1.492176 CAGGGTCATCCATTAGGCAGT 59.508 52.381 0.00 0.00 38.24 4.40
2795 2866 2.665000 CAGTCATGGAGGGCACGT 59.335 61.111 0.00 0.00 0.00 4.49
2832 2903 4.821589 CCTGGTCGCCTTCCTCGC 62.822 72.222 0.00 0.00 0.00 5.03
2867 2938 4.744795 ATCGACTTGCCAGATTTAGAGT 57.255 40.909 0.00 0.00 0.00 3.24
2875 2946 2.484889 CCAGATTTAGAGTTAGCCGCC 58.515 52.381 0.00 0.00 0.00 6.13
2880 2951 1.112113 TTAGAGTTAGCCGCCTCCAG 58.888 55.000 0.00 0.00 0.00 3.86
2882 2953 2.284699 AGTTAGCCGCCTCCAGGT 60.285 61.111 0.00 0.00 37.57 4.00
2909 2980 6.814076 CGATCAAGTCGTAAAGCTATTTCT 57.186 37.500 0.00 0.00 45.19 2.52
2918 2989 7.982354 AGTCGTAAAGCTATTTCTCAATTAGCT 59.018 33.333 6.79 6.79 44.95 3.32
2919 2990 8.058915 GTCGTAAAGCTATTTCTCAATTAGCTG 58.941 37.037 11.52 2.88 42.57 4.24
2920 2991 7.764443 TCGTAAAGCTATTTCTCAATTAGCTGT 59.236 33.333 11.52 9.51 42.57 4.40
2921 2992 8.058915 CGTAAAGCTATTTCTCAATTAGCTGTC 58.941 37.037 11.52 6.50 42.57 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1894 1939 2.034879 AATGCTGGACAAGTCGCCG 61.035 57.895 0.00 0.00 0.00 6.46
2020 2066 8.493607 TGTCCATCATTAATCTTGATTGTCCTA 58.506 33.333 6.15 0.00 31.50 2.94
2025 2071 8.228464 CGATCTGTCCATCATTAATCTTGATTG 58.772 37.037 6.15 0.00 31.50 2.67
2070 2116 3.254166 AGCGTGCAAATTGATCACTCTTT 59.746 39.130 0.00 0.00 0.00 2.52
2090 2136 0.110192 GTAGCTGCGTTGTTCCAAGC 60.110 55.000 0.00 0.00 0.00 4.01
2245 2294 7.603404 CCATTCAATTGAGATTTAGCAAAACCA 59.397 33.333 8.41 0.00 0.00 3.67
2318 2367 9.612620 CTGTTGAAGGTAAAAATAATGTGAGAC 57.387 33.333 0.00 0.00 0.00 3.36
2334 2383 2.050144 TCTTCTGCCTCTGTTGAAGGT 58.950 47.619 0.00 0.00 37.21 3.50
2398 2448 9.944376 AACTCTCTGAACAAAATTATACTAGCA 57.056 29.630 0.00 0.00 0.00 3.49
2481 2540 7.451501 TGAGATAGATAGTTCTCAGCATCAG 57.548 40.000 0.00 0.00 42.52 2.90
2508 2567 8.710835 TCTTTTGCTTCCGTTTAAGAATTTTT 57.289 26.923 0.00 0.00 0.00 1.94
2509 2568 8.887036 ATCTTTTGCTTCCGTTTAAGAATTTT 57.113 26.923 0.00 0.00 0.00 1.82
2510 2569 8.887036 AATCTTTTGCTTCCGTTTAAGAATTT 57.113 26.923 0.00 0.00 0.00 1.82
2511 2570 8.764287 CAAATCTTTTGCTTCCGTTTAAGAATT 58.236 29.630 0.00 0.00 0.00 2.17
2512 2571 7.926018 ACAAATCTTTTGCTTCCGTTTAAGAAT 59.074 29.630 0.06 0.00 0.00 2.40
2525 2585 9.476202 GTTAATTAAGTGGACAAATCTTTTGCT 57.524 29.630 0.00 0.00 0.00 3.91
2572 2642 5.122239 TGCTTTATGAGTTGTCTACACATGC 59.878 40.000 7.41 4.05 38.33 4.06
2606 2676 6.773976 TTGGGAATATTTGTCAGGTCAATC 57.226 37.500 0.00 0.00 0.00 2.67
2611 2681 4.160252 GTGCATTGGGAATATTTGTCAGGT 59.840 41.667 0.00 0.00 0.00 4.00
2612 2682 4.160065 TGTGCATTGGGAATATTTGTCAGG 59.840 41.667 0.00 0.00 0.00 3.86
2614 2684 4.081752 GGTGTGCATTGGGAATATTTGTCA 60.082 41.667 0.00 0.00 0.00 3.58
2633 2703 4.499696 GCTGTGAAGCTTTGTTATTGGTGT 60.500 41.667 0.00 0.00 0.00 4.16
2649 2719 4.461431 TCCTTTACGATGTAGAGCTGTGAA 59.539 41.667 0.00 0.00 0.00 3.18
2650 2720 4.014406 TCCTTTACGATGTAGAGCTGTGA 58.986 43.478 0.00 0.00 0.00 3.58
2677 2747 1.760613 AGTCGAGGTGTTCTTGTTGGA 59.239 47.619 0.00 0.00 0.00 3.53
2678 2748 1.867233 CAGTCGAGGTGTTCTTGTTGG 59.133 52.381 0.00 0.00 0.00 3.77
2683 2753 2.693591 TGTCTTCAGTCGAGGTGTTCTT 59.306 45.455 0.00 0.00 0.00 2.52
2708 2778 8.850156 GCTTATCACTATGGATTTGGTAATGTT 58.150 33.333 0.00 0.00 0.00 2.71
2724 2794 4.042311 TCCTTGTGGTTTGGCTTATCACTA 59.958 41.667 4.84 0.00 34.23 2.74
2730 2800 4.566907 GGACTATCCTTGTGGTTTGGCTTA 60.567 45.833 0.00 0.00 32.53 3.09
2749 2819 0.191064 TGACCCTGGTCTCTTGGACT 59.809 55.000 16.81 0.00 44.80 3.85
2795 2866 1.552254 GGGCAAATTCAAGAAGGGGGA 60.552 52.381 0.00 0.00 0.00 4.81
2798 2869 1.551883 CAGGGGCAAATTCAAGAAGGG 59.448 52.381 0.00 0.00 0.00 3.95
2832 2903 1.078214 TCGATTGCTTGCCTCCTGG 60.078 57.895 0.00 0.00 0.00 4.45
2862 2933 0.755698 CCTGGAGGCGGCTAACTCTA 60.756 60.000 13.24 0.00 34.22 2.43
2867 2938 3.458163 CGACCTGGAGGCGGCTAA 61.458 66.667 13.24 1.94 39.32 3.09
2875 2946 1.227089 CTTGATCGCCGACCTGGAG 60.227 63.158 0.00 0.00 42.00 3.86
2887 2958 7.757097 TGAGAAATAGCTTTACGACTTGATC 57.243 36.000 0.00 0.00 0.00 2.92
2889 2960 8.547967 AATTGAGAAATAGCTTTACGACTTGA 57.452 30.769 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.