Multiple sequence alignment - TraesCS7A01G511200

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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 TraesCS7A01G511200 chr7A 100.000 2468 0 0 1 2468 698821623 698824090 0.000000e+00 4558
1 TraesCS7A01G511200 chr7A 97.691 2469 54 3 2 2468 698953927 698956394 0.000000e+00 4241
2 TraesCS7A01G511200 chr7A 95.683 1135 45 3 920 2052 698744929 698746061 0.000000e+00 1821
3 TraesCS7A01G511200 chr7A 87.370 673 74 7 932 1602 698730033 698730696 0.000000e+00 761
4 TraesCS7A01G511200 chr7A 94.789 403 15 3 2052 2454 698747110 698747506 7.490000e-175 623
5 TraesCS7A01G511200 chr7A 87.671 292 25 4 1597 1881 698731062 698731349 1.830000e-86 329
6 TraesCS7A01G511200 chr7A 79.093 397 82 1 270 665 676432722 676432326 3.130000e-69 272
7 TraesCS7A01G511200 chr7A 82.323 198 20 8 2271 2465 698731835 698732020 9.140000e-35 158
8 TraesCS7A01G511200 chr7D 95.815 1553 53 6 920 2468 606684798 606686342 0.000000e+00 2497
9 TraesCS7A01G511200 chr7D 90.695 935 70 5 1 919 55788427 55787494 0.000000e+00 1229
10 TraesCS7A01G511200 chr7D 89.530 936 82 4 1 920 590452929 590451994 0.000000e+00 1171
11 TraesCS7A01G511200 chr7D 85.124 968 104 17 920 1884 606658001 606658931 0.000000e+00 953
12 TraesCS7A01G511200 chr7D 82.972 922 135 6 1 900 587951283 587950362 0.000000e+00 813
13 TraesCS7A01G511200 chr7D 83.419 585 97 0 79 663 38348972 38348388 6.000000e-151 544
14 TraesCS7A01G511200 chr7D 88.542 96 8 2 2271 2366 606659513 606659605 2.010000e-21 113
15 TraesCS7A01G511200 chr1A 91.892 925 59 5 1 909 576081328 576082252 0.000000e+00 1279
16 TraesCS7A01G511200 chr1A 88.676 680 61 2 1 664 576081232 576081911 0.000000e+00 815
17 TraesCS7A01G511200 chr6D 89.733 935 80 8 1 919 55164333 55165267 0.000000e+00 1181
18 TraesCS7A01G511200 chr6D 88.840 681 60 5 1 665 55164141 55164821 0.000000e+00 822
19 TraesCS7A01G511200 chr6D 88.399 681 63 5 1 665 55164237 55164917 0.000000e+00 806
20 TraesCS7A01G511200 chr2D 89.541 937 82 4 1 921 401166195 401165259 0.000000e+00 1173
21 TraesCS7A01G511200 chr2D 89.010 919 88 4 1 919 95730055 95729150 0.000000e+00 1125
22 TraesCS7A01G511200 chr2D 89.605 683 55 4 253 919 21833964 21833282 0.000000e+00 854
23 TraesCS7A01G511200 chr2D 73.519 287 67 7 1071 1353 621670719 621670438 1.560000e-17 100
24 TraesCS7A01G511200 chr5D 87.974 923 107 3 1 920 301214854 301215775 0.000000e+00 1086
25 TraesCS7A01G511200 chr1D 87.500 912 80 8 24 919 495325515 495324622 0.000000e+00 1022
26 TraesCS7A01G511200 chr7B 85.419 967 97 17 912 1868 690905009 690905941 0.000000e+00 965
27 TraesCS7A01G511200 chr7B 79.303 459 61 13 2019 2466 690906246 690906681 8.630000e-75 291
28 TraesCS7A01G511200 chr6B 85.204 196 22 3 1616 1811 322068251 322068439 6.960000e-46 195
29 TraesCS7A01G511200 chr6A 77.181 298 60 5 930 1225 616989705 616989414 1.520000e-37 167
30 TraesCS7A01G511200 chr2A 72.449 392 95 11 967 1353 753433698 753433315 2.010000e-21 113
31 TraesCS7A01G511200 chr2B 73.333 285 69 5 1071 1353 763492642 763492363 5.620000e-17 99


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 TraesCS7A01G511200 chr7A 698821623 698824090 2467 False 4558.000000 4558 100.000000 1 2468 1 chr7A.!!$F1 2467
1 TraesCS7A01G511200 chr7A 698953927 698956394 2467 False 4241.000000 4241 97.691000 2 2468 1 chr7A.!!$F2 2466
2 TraesCS7A01G511200 chr7A 698744929 698747506 2577 False 1222.000000 1821 95.236000 920 2454 2 chr7A.!!$F4 1534
3 TraesCS7A01G511200 chr7A 698730033 698732020 1987 False 416.000000 761 85.788000 932 2465 3 chr7A.!!$F3 1533
4 TraesCS7A01G511200 chr7D 606684798 606686342 1544 False 2497.000000 2497 95.815000 920 2468 1 chr7D.!!$F1 1548
5 TraesCS7A01G511200 chr7D 55787494 55788427 933 True 1229.000000 1229 90.695000 1 919 1 chr7D.!!$R2 918
6 TraesCS7A01G511200 chr7D 590451994 590452929 935 True 1171.000000 1171 89.530000 1 920 1 chr7D.!!$R4 919
7 TraesCS7A01G511200 chr7D 587950362 587951283 921 True 813.000000 813 82.972000 1 900 1 chr7D.!!$R3 899
8 TraesCS7A01G511200 chr7D 38348388 38348972 584 True 544.000000 544 83.419000 79 663 1 chr7D.!!$R1 584
9 TraesCS7A01G511200 chr7D 606658001 606659605 1604 False 533.000000 953 86.833000 920 2366 2 chr7D.!!$F2 1446
10 TraesCS7A01G511200 chr1A 576081232 576082252 1020 False 1047.000000 1279 90.284000 1 909 2 chr1A.!!$F1 908
11 TraesCS7A01G511200 chr6D 55164141 55165267 1126 False 936.333333 1181 88.990667 1 919 3 chr6D.!!$F1 918
12 TraesCS7A01G511200 chr2D 401165259 401166195 936 True 1173.000000 1173 89.541000 1 921 1 chr2D.!!$R3 920
13 TraesCS7A01G511200 chr2D 95729150 95730055 905 True 1125.000000 1125 89.010000 1 919 1 chr2D.!!$R2 918
14 TraesCS7A01G511200 chr2D 21833282 21833964 682 True 854.000000 854 89.605000 253 919 1 chr2D.!!$R1 666
15 TraesCS7A01G511200 chr5D 301214854 301215775 921 False 1086.000000 1086 87.974000 1 920 1 chr5D.!!$F1 919
16 TraesCS7A01G511200 chr1D 495324622 495325515 893 True 1022.000000 1022 87.500000 24 919 1 chr1D.!!$R1 895
17 TraesCS7A01G511200 chr7B 690905009 690906681 1672 False 628.000000 965 82.361000 912 2466 2 chr7B.!!$F1 1554

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
224 321 0.034896 CTAGGCCTGTTGTCGTGGTT 59.965 55.0 17.99 0.0 0.00 3.67 F
560 785 0.106708 TTTGCCGAGTGTTGCTCTCT 59.893 50.0 0.00 0.0 41.98 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1685 1.078759 CGGCACTTAGAACCTCGCAG 61.079 60.000 0.0 0.0 0.0 5.18 R
1708 2552 3.998341 CTGCTTTGGGAAATGAAATGTGG 59.002 43.478 0.0 0.0 0.0 4.17 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
178 275 1.630878 CTCCTACTGGTTCCCTTTGCT 59.369 52.381 0.00 0.00 34.23 3.91
184 281 1.072965 CTGGTTCCCTTTGCTGAGAGT 59.927 52.381 0.00 0.00 0.00 3.24
207 304 1.275291 CTCTCGTCAAAGTTGGCCCTA 59.725 52.381 0.00 0.00 0.00 3.53
224 321 0.034896 CTAGGCCTGTTGTCGTGGTT 59.965 55.000 17.99 0.00 0.00 3.67
240 337 0.678048 GGTTCCACATGTCAGGAGGC 60.678 60.000 0.00 0.00 34.91 4.70
444 541 2.261671 GGAGGCGACACGTGTCAT 59.738 61.111 39.14 27.62 44.99 3.06
471 568 1.270358 ACTGGTTCTCTTTGCCGAGAC 60.270 52.381 0.00 0.00 39.62 3.36
560 785 0.106708 TTTGCCGAGTGTTGCTCTCT 59.893 50.000 0.00 0.00 41.98 3.10
667 1085 2.489938 TGGCTCTCGGCAAAGTTTAT 57.510 45.000 0.00 0.00 43.40 1.40
812 1252 0.390124 TTTGCCGAAGAGGTGTACGT 59.610 50.000 0.00 0.00 43.70 3.57
1047 1487 3.265995 AGTTTTACGGTCCAATGAGGGAT 59.734 43.478 0.00 0.00 39.62 3.85
1056 1496 3.091545 TCCAATGAGGGATGAACAAAGC 58.908 45.455 0.00 0.00 38.24 3.51
1170 1610 7.203910 ACCTGAATAATGACGAGTATGAAGAC 58.796 38.462 0.00 0.00 0.00 3.01
1762 2606 7.015680 ACTATCTTCCATGACCACATCTATCT 58.984 38.462 0.00 0.00 34.15 1.98
2184 4334 7.138692 AGATGCTTAGTTCTTTCAATGTGAC 57.861 36.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 247 1.834263 GAACCAGTAGGAGGCTGACAT 59.166 52.381 0.00 0.00 38.69 3.06
184 281 0.884704 GCCAACTTTGACGAGAGCCA 60.885 55.000 0.00 0.00 0.00 4.75
207 304 1.227853 GAACCACGACAACAGGCCT 60.228 57.895 0.00 0.00 0.00 5.19
224 321 1.609210 TCGCCTCCTGACATGTGGA 60.609 57.895 1.15 3.53 0.00 4.02
444 541 3.554337 GGCAAAGAGAACCAGTACGAGAA 60.554 47.826 0.00 0.00 0.00 2.87
560 785 1.302993 GCCAAGGGCCGACTTTACA 60.303 57.895 0.00 0.00 44.06 2.41
600 1018 3.916392 GACACGTGTCGCCTCCTGG 62.916 68.421 31.03 0.00 35.12 4.45
812 1252 1.152860 TTCAGCAAAAGCCACCCGA 60.153 52.632 0.00 0.00 0.00 5.14
1047 1487 3.065233 CAGTTACACTGCAGCTTTGTTCA 59.935 43.478 15.27 0.00 39.62 3.18
1170 1610 4.100529 CGACAAGCAAATGCCTAAGAATG 58.899 43.478 0.94 0.00 43.38 2.67
1245 1685 1.078759 CGGCACTTAGAACCTCGCAG 61.079 60.000 0.00 0.00 0.00 5.18
1695 2538 8.421249 AAATGAAATGTGGACATAGAAGGAAA 57.579 30.769 0.00 0.00 35.10 3.13
1708 2552 3.998341 CTGCTTTGGGAAATGAAATGTGG 59.002 43.478 0.00 0.00 0.00 4.17
1762 2606 7.566760 TTGCTGAAGTTTTAACTCATCTCAA 57.433 32.000 0.00 0.00 38.57 3.02
1828 2672 8.956533 TCTCCATCATATAAAAATTCGACACA 57.043 30.769 0.00 0.00 0.00 3.72
2075 4142 8.150945 ACTCAACTAGTCTAGCTTTCATTTTCA 58.849 33.333 6.81 0.00 30.33 2.69
2184 4334 4.156556 AGTGTGTGCTATGCCAAGTAAATG 59.843 41.667 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.