Multiple sequence alignment - TraesCS6A01G217900

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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 TraesCS6A01G217900 chr6A 100.000 2806 0 0 1 2806 401496467 401499272 0 5182
1 TraesCS6A01G217900 chr6A 93.123 1265 84 3 1543 2806 178093438 178094700 0 1851
2 TraesCS6A01G217900 chr5A 91.002 2823 186 25 1 2806 232665047 232662276 0 3744
3 TraesCS6A01G217900 chr5A 90.371 2129 180 18 695 2806 398742432 398744552 0 2772
4 TraesCS6A01G217900 chr7A 89.525 2778 234 31 45 2806 16193060 16195796 0 3465
5 TraesCS6A01G217900 chr4D 90.981 2018 148 6 5 2016 170243649 170241660 0 2687
6 TraesCS6A01G217900 chr4D 87.351 2174 235 33 647 2806 179920118 179917971 0 2455
7 TraesCS6A01G217900 chr1D 90.567 2046 159 8 1 2016 344094822 344092781 0 2678
8 TraesCS6A01G217900 chr1D 90.423 898 63 6 1 898 110918259 110917385 0 1160
9 TraesCS6A01G217900 chr5D 89.932 2046 167 10 5 2016 551045352 551043312 0 2601
10 TraesCS6A01G217900 chr5D 87.856 2174 222 33 647 2806 188380317 188378172 0 2514
11 TraesCS6A01G217900 chr5D 92.238 1778 123 9 1 1770 196186350 196184580 0 2505
12 TraesCS6A01G217900 chr5D 89.639 1940 166 23 875 2806 464313209 464311297 0 2436
13 TraesCS6A01G217900 chr4A 92.056 1800 130 8 1 1793 279463644 279461851 0 2519
14 TraesCS6A01G217900 chr7D 87.305 2182 225 40 647 2806 122697124 122699275 0 2447
15 TraesCS6A01G217900 chr7D 87.783 884 95 10 1 874 557863420 557862540 0 1022
16 TraesCS6A01G217900 chr2B 85.859 2178 264 37 647 2806 366587893 366590044 0 2276
17 TraesCS6A01G217900 chr4B 86.674 908 108 11 1 897 131328550 131329455 0 994


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 TraesCS6A01G217900 chr6A 401496467 401499272 2805 False 5182 5182 100.000 1 2806 1 chr6A.!!$F2 2805
1 TraesCS6A01G217900 chr6A 178093438 178094700 1262 False 1851 1851 93.123 1543 2806 1 chr6A.!!$F1 1263
2 TraesCS6A01G217900 chr5A 232662276 232665047 2771 True 3744 3744 91.002 1 2806 1 chr5A.!!$R1 2805
3 TraesCS6A01G217900 chr5A 398742432 398744552 2120 False 2772 2772 90.371 695 2806 1 chr5A.!!$F1 2111
4 TraesCS6A01G217900 chr7A 16193060 16195796 2736 False 3465 3465 89.525 45 2806 1 chr7A.!!$F1 2761
5 TraesCS6A01G217900 chr4D 170241660 170243649 1989 True 2687 2687 90.981 5 2016 1 chr4D.!!$R1 2011
6 TraesCS6A01G217900 chr4D 179917971 179920118 2147 True 2455 2455 87.351 647 2806 1 chr4D.!!$R2 2159
7 TraesCS6A01G217900 chr1D 344092781 344094822 2041 True 2678 2678 90.567 1 2016 1 chr1D.!!$R2 2015
8 TraesCS6A01G217900 chr1D 110917385 110918259 874 True 1160 1160 90.423 1 898 1 chr1D.!!$R1 897
9 TraesCS6A01G217900 chr5D 551043312 551045352 2040 True 2601 2601 89.932 5 2016 1 chr5D.!!$R4 2011
10 TraesCS6A01G217900 chr5D 188378172 188380317 2145 True 2514 2514 87.856 647 2806 1 chr5D.!!$R1 2159
11 TraesCS6A01G217900 chr5D 196184580 196186350 1770 True 2505 2505 92.238 1 1770 1 chr5D.!!$R2 1769
12 TraesCS6A01G217900 chr5D 464311297 464313209 1912 True 2436 2436 89.639 875 2806 1 chr5D.!!$R3 1931
13 TraesCS6A01G217900 chr4A 279461851 279463644 1793 True 2519 2519 92.056 1 1793 1 chr4A.!!$R1 1792
14 TraesCS6A01G217900 chr7D 122697124 122699275 2151 False 2447 2447 87.305 647 2806 1 chr7D.!!$F1 2159
15 TraesCS6A01G217900 chr7D 557862540 557863420 880 True 1022 1022 87.783 1 874 1 chr7D.!!$R1 873
16 TraesCS6A01G217900 chr2B 366587893 366590044 2151 False 2276 2276 85.859 647 2806 1 chr2B.!!$F1 2159
17 TraesCS6A01G217900 chr4B 131328550 131329455 905 False 994 994 86.674 1 897 1 chr4B.!!$F1 896

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
449 452 0.166814 CACGCTCAAGCAGCCTAAAC 59.833 55.000 2.5 0.0 46.74 2.01 F
937 1132 1.338389 GCCTTTCCTACGTTACAGCCA 60.338 52.381 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1482 0.321653 GTCAGCGTCCCAAGTCCATT 60.322 55.0 0.0 0.0 0.0 3.16 R
2499 2768 0.325272 TGCACGCCCACCTTACATTA 59.675 50.0 0.0 0.0 0.0 1.90 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 2.114411 GGGTCTTCCCGTTGGCAA 59.886 61.111 0.00 0.00 44.74 4.52
85 86 0.394488 CTGAGGAGACGCTAGGACCA 60.394 60.000 0.00 0.00 0.00 4.02
108 109 2.731691 TTTGCTGACCGTCCAGAGCC 62.732 60.000 6.83 0.00 36.29 4.70
148 149 0.890542 GCATGGACCACAGCTTGACA 60.891 55.000 12.35 0.00 0.00 3.58
189 190 4.737578 AGCTGGATGGCTATGATTGAAAT 58.262 39.130 0.00 0.00 41.16 2.17
191 192 5.944599 AGCTGGATGGCTATGATTGAAATAG 59.055 40.000 0.00 0.00 41.16 1.73
205 206 9.690913 ATGATTGAAATAGATCAAGTCCAAGAA 57.309 29.630 0.00 0.00 42.21 2.52
218 219 4.137543 AGTCCAAGAAAATGAGACGCTTT 58.862 39.130 0.00 0.00 32.70 3.51
266 267 1.078426 GTGCCGGCCTACTTCATGT 60.078 57.895 26.77 0.00 0.00 3.21
291 292 2.422832 GCTTCTTCCCATTTCTGCAGAG 59.577 50.000 17.43 5.44 0.00 3.35
387 388 4.056097 GCAATACACGGCTTTGCG 57.944 55.556 0.00 0.00 36.72 4.85
449 452 0.166814 CACGCTCAAGCAGCCTAAAC 59.833 55.000 2.50 0.00 46.74 2.01
483 486 1.918262 ACCAATGGAGAGGCAGATGAA 59.082 47.619 6.16 0.00 0.00 2.57
539 547 6.930667 AAGTTGTGTTACGGACTTATTTGT 57.069 33.333 0.00 0.00 29.31 2.83
541 549 7.647907 AGTTGTGTTACGGACTTATTTGTAG 57.352 36.000 0.00 0.00 0.00 2.74
760 800 7.466746 ACTGTAGTTGCCATGTTTAATGAAT 57.533 32.000 0.00 0.00 0.00 2.57
937 1132 1.338389 GCCTTTCCTACGTTACAGCCA 60.338 52.381 0.00 0.00 0.00 4.75
960 1155 6.127647 CCAACATCAACATAAGGTGCTACAAT 60.128 38.462 0.00 0.00 0.00 2.71
1022 1227 5.698832 CACATTCCACGAAGAAATAAAGCA 58.301 37.500 0.00 0.00 0.00 3.91
1023 1228 5.796935 CACATTCCACGAAGAAATAAAGCAG 59.203 40.000 0.00 0.00 0.00 4.24
1024 1229 5.473504 ACATTCCACGAAGAAATAAAGCAGT 59.526 36.000 0.00 0.00 0.00 4.40
1193 1398 2.674954 CCGATGCTGCAAATTTGAACA 58.325 42.857 22.31 15.09 0.00 3.18
1277 1482 2.477176 GCCATTTCATACGGCGGCA 61.477 57.895 13.24 0.00 39.38 5.69
1331 1537 4.318974 GCCACAAACATCAAATGCAGTTTC 60.319 41.667 0.00 0.00 32.34 2.78
1363 1569 2.685106 TGAGAGACCAGAGTCAACCT 57.315 50.000 0.00 0.00 46.15 3.50
1396 1602 2.101249 AGGCACATTGTGTTGACAAAGG 59.899 45.455 17.64 0.00 45.23 3.11
1398 1604 3.243839 GGCACATTGTGTTGACAAAGGAT 60.244 43.478 17.64 0.00 45.23 3.24
1399 1605 4.022416 GGCACATTGTGTTGACAAAGGATA 60.022 41.667 17.64 0.00 45.23 2.59
1461 1667 1.000274 GCGAGGGTTGCAGAAAAACAT 60.000 47.619 0.00 0.00 0.00 2.71
1529 1735 2.167487 CTGAGGAAGCCTTAGACAGGTC 59.833 54.545 0.00 0.00 46.07 3.85
1567 1773 4.760047 CTTCGTCCACGGGGCCAG 62.760 72.222 4.39 3.10 40.29 4.85
1675 1881 7.180748 GCGTCCAAAAGAGATAAGATACAAAC 58.819 38.462 0.00 0.00 0.00 2.93
1709 1915 7.254218 GGAGATTCAAGCAAAACACAAGAAAAG 60.254 37.037 0.00 0.00 0.00 2.27
1758 1965 3.864789 ACATTGGAGGACTGTGACTTT 57.135 42.857 0.00 0.00 0.00 2.66
1777 1986 6.146837 TGACTTTGTTGTTGGTGACATTTTTG 59.853 34.615 0.00 0.00 42.32 2.44
1793 2002 7.175990 TGACATTTTTGGTAAGGTAGATGTTCC 59.824 37.037 0.00 0.00 0.00 3.62
1901 2116 3.894427 TGTGTGGTACTGAATTTGCCATT 59.106 39.130 0.00 0.00 0.00 3.16
1913 2128 7.669722 ACTGAATTTGCCATTCCTTTTCTACTA 59.330 33.333 3.84 0.00 0.00 1.82
1926 2141 5.221126 CCTTTTCTACTAAATCTGCCATGCC 60.221 44.000 0.00 0.00 0.00 4.40
1957 2172 6.040166 CACTAAATCTGCCATGCCTTTTCTAT 59.960 38.462 0.00 0.00 0.00 1.98
2031 2293 1.129326 CCATCGCGTAGATTTCCGTC 58.871 55.000 5.77 0.00 37.52 4.79
2097 2360 6.293135 GCAAACTGTGGAAAACAAGTTGAAAA 60.293 34.615 10.54 0.00 38.67 2.29
2115 2378 5.793675 TGAAAACAATCATGTGCAAAAACG 58.206 33.333 0.00 0.00 40.46 3.60
2116 2379 5.578336 TGAAAACAATCATGTGCAAAAACGA 59.422 32.000 0.00 0.00 40.46 3.85
2125 2388 2.355132 TGTGCAAAAACGACACGGTTAT 59.645 40.909 0.00 0.00 34.97 1.89
2135 2398 0.738412 ACACGGTTATGGCTGCGTAC 60.738 55.000 0.00 0.00 0.00 3.67
2152 2415 3.733077 GCGTACGAACTACCATGCTAACT 60.733 47.826 21.65 0.00 0.00 2.24
2444 2713 6.075984 ACGGGGAGATGTAGTCATAACTTAT 58.924 40.000 0.00 0.00 36.92 1.73
2499 2768 2.026262 ACCTTACATTCCTCGGCAACAT 60.026 45.455 0.00 0.00 0.00 2.71
2547 2817 1.719246 CACCACGTGATCACTTGTACG 59.281 52.381 25.46 15.57 41.86 3.67
2557 2827 3.804786 TCACTTGTACGTCTTGTTGGA 57.195 42.857 0.00 0.00 0.00 3.53
2582 2852 5.946942 TCTTGACAGCTTCCTCTATGAAT 57.053 39.130 0.00 0.00 0.00 2.57
2607 2877 0.033642 TGCGTTGGACCGTATGTTGA 59.966 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.259204 CTGTGCATTGCCAACGGG 59.741 61.111 6.12 0.00 37.18 5.28
85 86 1.347707 TCTGGACGGTCAGCAAAGAAT 59.652 47.619 10.76 0.00 34.91 2.40
108 109 2.099062 GCTCGAATGCCTTGTGCG 59.901 61.111 0.00 0.00 45.60 5.34
148 149 1.344763 CTCCGTTCAAACTCCTCCACT 59.655 52.381 0.00 0.00 0.00 4.00
189 190 6.813649 CGTCTCATTTTCTTGGACTTGATCTA 59.186 38.462 0.00 0.00 0.00 1.98
191 192 5.672321 GCGTCTCATTTTCTTGGACTTGATC 60.672 44.000 0.00 0.00 0.00 2.92
218 219 1.323271 CGCTTCTCCCACAGGCTAGA 61.323 60.000 0.00 0.00 0.00 2.43
266 267 3.244875 TGCAGAAATGGGAAGAAGCACTA 60.245 43.478 0.00 0.00 0.00 2.74
309 310 4.586001 ACCACTTCAGAACAGCATTGAAAT 59.414 37.500 0.00 0.00 31.11 2.17
310 311 3.953612 ACCACTTCAGAACAGCATTGAAA 59.046 39.130 0.00 0.00 31.11 2.69
400 402 1.759445 TCTTGCTGTAGCTCAGATCCC 59.241 52.381 14.86 1.25 46.27 3.85
449 452 8.840321 CCTCTCCATTGGTAAATATGTTAACAG 58.160 37.037 14.65 0.00 0.00 3.16
528 536 6.599638 ACCTTCATGCTTCTACAAATAAGTCC 59.400 38.462 0.00 0.00 0.00 3.85
530 538 8.322091 ACTACCTTCATGCTTCTACAAATAAGT 58.678 33.333 0.00 0.00 0.00 2.24
539 547 4.099573 GCACCTACTACCTTCATGCTTCTA 59.900 45.833 0.00 0.00 0.00 2.10
541 549 3.198872 GCACCTACTACCTTCATGCTTC 58.801 50.000 0.00 0.00 0.00 3.86
602 615 9.358406 ACTCAATGGATGCTTTCAATATATCAA 57.642 29.630 0.00 0.00 0.00 2.57
617 631 6.433847 TGGTTACCCTATACTCAATGGATG 57.566 41.667 0.00 0.00 0.00 3.51
619 633 6.147473 TCATGGTTACCCTATACTCAATGGA 58.853 40.000 0.00 0.00 0.00 3.41
630 644 6.239772 GGCAACTACATATCATGGTTACCCTA 60.240 42.308 0.00 0.00 33.60 3.53
760 800 5.301551 AGTTGATTTCACATGGCAACTACAA 59.698 36.000 0.00 0.00 45.04 2.41
937 1132 7.609918 TGTATTGTAGCACCTTATGTTGATGTT 59.390 33.333 0.00 0.00 0.00 2.71
1001 1203 5.796935 CACTGCTTTATTTCTTCGTGGAATG 59.203 40.000 0.00 0.00 0.00 2.67
1022 1227 0.950555 CGTGTACATGCTGGCACACT 60.951 55.000 1.29 0.00 36.15 3.55
1023 1228 1.497278 CGTGTACATGCTGGCACAC 59.503 57.895 1.29 0.97 35.45 3.82
1024 1229 1.670730 CCGTGTACATGCTGGCACA 60.671 57.895 9.72 0.00 31.18 4.57
1175 1380 3.916761 TCCTGTTCAAATTTGCAGCATC 58.083 40.909 13.54 0.00 0.00 3.91
1193 1398 0.700564 ACAGCACACAATCCCATCCT 59.299 50.000 0.00 0.00 0.00 3.24
1217 1422 6.248631 GCGTTCATGTCCATTACTTTTAGTC 58.751 40.000 0.00 0.00 0.00 2.59
1277 1482 0.321653 GTCAGCGTCCCAAGTCCATT 60.322 55.000 0.00 0.00 0.00 3.16
1331 1537 2.335752 GTCTCTCATCATGCATAGCCG 58.664 52.381 0.00 0.00 0.00 5.52
1381 1587 6.209192 TCAGCATTATCCTTTGTCAACACAAT 59.791 34.615 0.00 0.00 42.28 2.71
1396 1602 8.379161 CGCTTCATCTATTAGTTCAGCATTATC 58.621 37.037 0.00 0.00 0.00 1.75
1398 1604 7.169813 CACGCTTCATCTATTAGTTCAGCATTA 59.830 37.037 0.00 0.00 0.00 1.90
1399 1605 6.018425 CACGCTTCATCTATTAGTTCAGCATT 60.018 38.462 0.00 0.00 0.00 3.56
1461 1667 2.840651 CTCTCTTTTCAGGGCCTTCCTA 59.159 50.000 1.32 0.00 46.12 2.94
1567 1773 3.619038 CCTACCTTCGAGTTTTCAGATGC 59.381 47.826 0.00 0.00 0.00 3.91
1675 1881 3.008835 TGCTTGAATCTCCAATCCCAG 57.991 47.619 0.00 0.00 0.00 4.45
1709 1915 1.472878 GATTGCCCGACCCTTTCTTTC 59.527 52.381 0.00 0.00 0.00 2.62
1758 1965 4.543590 ACCAAAAATGTCACCAACAACA 57.456 36.364 0.00 0.00 42.37 3.33
1901 2116 5.590259 GCATGGCAGATTTAGTAGAAAAGGA 59.410 40.000 0.00 0.00 0.00 3.36
1913 2128 1.188863 GGAACAGGCATGGCAGATTT 58.811 50.000 22.64 8.13 0.00 2.17
1926 2141 3.181493 GCATGGCAGATTTAGTGGAACAG 60.181 47.826 0.00 0.00 41.80 3.16
1957 2172 6.595326 CAGTAGAACTAACATGGCAGATTCAA 59.405 38.462 0.00 0.00 0.00 2.69
2031 2293 4.213270 TGGACTAAAATGCGTTGACTGAAG 59.787 41.667 0.00 0.00 0.00 3.02
2097 2360 3.796178 GTGTCGTTTTTGCACATGATTGT 59.204 39.130 0.00 0.00 36.15 2.71
2115 2378 0.458889 TACGCAGCCATAACCGTGTC 60.459 55.000 0.00 0.00 35.36 3.67
2116 2379 0.738412 GTACGCAGCCATAACCGTGT 60.738 55.000 0.00 0.00 35.36 4.49
2125 2388 1.213537 GGTAGTTCGTACGCAGCCA 59.786 57.895 11.24 0.00 31.59 4.75
2135 2398 7.594714 ACTATATCAGTTAGCATGGTAGTTCG 58.405 38.462 4.57 0.00 31.59 3.95
2444 2713 9.168451 TGTTCTTTCAAAACTATGTCTGTGTAA 57.832 29.630 0.00 0.00 0.00 2.41
2499 2768 0.325272 TGCACGCCCACCTTACATTA 59.675 50.000 0.00 0.00 0.00 1.90
2547 2817 4.276926 AGCTGTCAAGAAATCCAACAAGAC 59.723 41.667 0.00 0.00 0.00 3.01
2557 2827 6.305272 TCATAGAGGAAGCTGTCAAGAAAT 57.695 37.500 0.00 0.00 0.00 2.17
2582 2852 1.794151 TACGGTCCAACGCACGAGAA 61.794 55.000 0.00 0.00 37.37 2.87
2607 2877 8.377034 TGGAATTGGTTGATGATTGAAGATTTT 58.623 29.630 0.00 0.00 0.00 1.82
2647 2917 0.955428 GCAATGGTCGTTGAGCTCCA 60.955 55.000 12.15 0.87 0.00 3.86
2684 2954 2.292785 AAAGTGGGAAGGCCAACGGT 62.293 55.000 5.01 0.00 43.42 4.83
2689 2959 1.075674 TTGCAAAGTGGGAAGGCCA 60.076 52.632 5.01 0.00 35.15 5.36
2754 3033 7.630242 TTTTCTGTGTTCTCTTGAGTTGAAT 57.370 32.000 0.00 0.00 0.00 2.57
2755 3034 7.336679 TGATTTTCTGTGTTCTCTTGAGTTGAA 59.663 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.