Multiple sequence alignment - TraesCS6A01G229700

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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 TraesCS6A01G229700 chr6A 100.000 2363 0 0 1 2363 432305183 432307545 0.000000e+00 4364.0
1 TraesCS6A01G229700 chr6A 80.634 1389 261 8 2 1385 534645225 534643840 0.000000e+00 1068.0
2 TraesCS6A01G229700 chr6B 92.033 1707 105 16 1 1691 452147700 452146009 0.000000e+00 2370.0
3 TraesCS6A01G229700 chr6B 93.796 677 41 1 1686 2361 452067861 452067185 0.000000e+00 1016.0
4 TraesCS6A01G229700 chr6D 93.449 1206 66 4 1165 2361 291225657 291224456 0.000000e+00 1777.0
5 TraesCS6A01G229700 chr6D 93.499 1169 69 7 1 1162 291227252 291226084 0.000000e+00 1731.0
6 TraesCS6A01G229700 chr5D 82.013 1351 226 17 2 1342 384794058 384795401 0.000000e+00 1133.0
7 TraesCS6A01G229700 chr5D 80.932 1395 257 9 2 1390 505417711 505416320 0.000000e+00 1094.0
8 TraesCS6A01G229700 chr7A 80.863 1390 257 9 2 1385 11263845 11265231 0.000000e+00 1085.0
9 TraesCS6A01G229700 chr3D 80.756 1403 258 11 2 1395 40759142 40757743 0.000000e+00 1085.0
10 TraesCS6A01G229700 chr1D 80.717 1395 259 10 2 1389 253189646 253191037 0.000000e+00 1077.0
11 TraesCS6A01G229700 chr7D 80.617 1393 260 10 2 1388 164403057 164401669 0.000000e+00 1068.0
12 TraesCS6A01G229700 chr4B 80.587 1396 262 9 2 1392 581208310 581209701 0.000000e+00 1068.0
13 TraesCS6A01G229700 chr7B 88.158 76 9 0 2286 2361 557179457 557179382 8.990000e-15 91.6


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 TraesCS6A01G229700 chr6A 432305183 432307545 2362 False 4364 4364 100.000 1 2363 1 chr6A.!!$F1 2362
1 TraesCS6A01G229700 chr6A 534643840 534645225 1385 True 1068 1068 80.634 2 1385 1 chr6A.!!$R1 1383
2 TraesCS6A01G229700 chr6B 452146009 452147700 1691 True 2370 2370 92.033 1 1691 1 chr6B.!!$R2 1690
3 TraesCS6A01G229700 chr6B 452067185 452067861 676 True 1016 1016 93.796 1686 2361 1 chr6B.!!$R1 675
4 TraesCS6A01G229700 chr6D 291224456 291227252 2796 True 1754 1777 93.474 1 2361 2 chr6D.!!$R1 2360
5 TraesCS6A01G229700 chr5D 384794058 384795401 1343 False 1133 1133 82.013 2 1342 1 chr5D.!!$F1 1340
6 TraesCS6A01G229700 chr5D 505416320 505417711 1391 True 1094 1094 80.932 2 1390 1 chr5D.!!$R1 1388
7 TraesCS6A01G229700 chr7A 11263845 11265231 1386 False 1085 1085 80.863 2 1385 1 chr7A.!!$F1 1383
8 TraesCS6A01G229700 chr3D 40757743 40759142 1399 True 1085 1085 80.756 2 1395 1 chr3D.!!$R1 1393
9 TraesCS6A01G229700 chr1D 253189646 253191037 1391 False 1077 1077 80.717 2 1389 1 chr1D.!!$F1 1387
10 TraesCS6A01G229700 chr7D 164401669 164403057 1388 True 1068 1068 80.617 2 1388 1 chr7D.!!$R1 1386
11 TraesCS6A01G229700 chr4B 581208310 581209701 1391 False 1068 1068 80.587 2 1392 1 chr4B.!!$F1 1390

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
70 72 0.683412 TGGAGAGATGCATGGATCCG 59.317 55.0 22.14 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2496 0.034896 GTCTGGTCTTCGCTTTGGGA 59.965 55.0 0.0 0.0 0.0 4.37 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
30 32 5.832539 ATGGTTATATCTGAGAGTTGGGG 57.167 43.478 0.00 0.00 0.00 4.96
70 72 0.683412 TGGAGAGATGCATGGATCCG 59.317 55.000 22.14 0.00 0.00 4.18
149 152 4.819105 TGTTGATCTTATCGACCCAGTT 57.181 40.909 5.11 0.00 41.97 3.16
254 258 9.264719 CTATGCATAACATGACAGACTTCATTA 57.735 33.333 8.00 0.00 40.06 1.90
272 276 9.167311 ACTTCATTACTTGGAGCTATACAAAAG 57.833 33.333 0.00 0.00 33.77 2.27
296 301 6.432783 AGATGGATTGTTTATGGTTCGTTCAA 59.567 34.615 0.00 0.00 0.00 2.69
406 411 6.323739 GGGGTAAGATTTGGCAATTATCTTGA 59.676 38.462 26.30 14.03 38.64 3.02
504 523 7.450074 AGACATATGAAAGTTTCGCCCATATA 58.550 34.615 10.38 2.89 31.47 0.86
511 530 2.073816 GTTTCGCCCATATACCCATCG 58.926 52.381 0.00 0.00 0.00 3.84
651 670 1.611936 GGGAGAGGCAGTTTTGGAGTC 60.612 57.143 0.00 0.00 0.00 3.36
726 745 3.257375 TGTGAACTGACCGCTATAACAGT 59.743 43.478 0.00 0.00 43.92 3.55
741 760 9.263538 CGCTATAACAGTTTGGTATTTATGGTA 57.736 33.333 0.00 0.00 31.72 3.25
761 780 4.654724 GGTAGGATAGAGGTAAGCTGGTTT 59.345 45.833 0.00 0.00 0.00 3.27
782 801 8.602424 TGGTTTATGAAGGAAAGTCTCAAGATA 58.398 33.333 0.00 0.00 0.00 1.98
786 805 9.605275 TTATGAAGGAAAGTCTCAAGATACATG 57.395 33.333 0.00 0.00 0.00 3.21
809 828 1.497309 AACTTCCATGGGAGCCCGAA 61.497 55.000 20.95 0.00 39.42 4.30
881 901 7.082972 AGAATAGAGGTATGGGAAATACCACT 58.917 38.462 15.65 15.65 44.72 4.00
882 902 6.688073 ATAGAGGTATGGGAAATACCACTG 57.312 41.667 18.86 0.00 44.72 3.66
886 906 4.788617 AGGTATGGGAAATACCACTGAAGT 59.211 41.667 15.13 0.00 44.72 3.01
930 950 5.713389 TGATGCTTCTTTTGATCATGACCTT 59.287 36.000 0.00 0.00 0.00 3.50
1028 1050 2.358898 GGTGTGCAGATGTTTTGACAGT 59.641 45.455 0.00 0.00 0.00 3.55
1102 1124 7.048629 TGCAATCATCTTTTTGTTAACTCCA 57.951 32.000 7.22 0.00 0.00 3.86
1157 1179 2.610859 ACATTCAGCGGGAGGGGT 60.611 61.111 0.00 0.00 0.00 4.95
1171 1617 2.431683 GGGTGGCTGCAGTCTTCA 59.568 61.111 20.86 8.36 0.00 3.02
1178 1624 3.691118 GTGGCTGCAGTCTTCAATGATTA 59.309 43.478 20.86 0.00 0.00 1.75
1482 1929 6.309737 GGATGATTTCATTTCTTGACACTTGC 59.690 38.462 0.00 0.00 36.57 4.01
1488 1935 5.108517 TCATTTCTTGACACTTGCCAAAAC 58.891 37.500 0.00 0.00 0.00 2.43
1505 1952 0.942252 AACCTGCGTCTTTTTCGGTC 59.058 50.000 0.00 0.00 0.00 4.79
1512 1959 3.065510 TGCGTCTTTTTCGGTCAAATCAA 59.934 39.130 0.00 0.00 0.00 2.57
1620 2067 3.252554 AGTTTGGAAATTACCCAGCCA 57.747 42.857 0.57 0.00 34.77 4.75
1695 2150 5.625197 GCAGAATAACCTTGGCACATGAAAT 60.625 40.000 0.00 0.00 39.30 2.17
1727 2182 0.471780 TTCCTGCCTGTGAGGACTGA 60.472 55.000 0.00 0.00 39.44 3.41
1756 2212 6.942576 ACAGTTAAAACATGCTATTCCTCTGT 59.057 34.615 0.00 0.00 0.00 3.41
1758 2214 9.113838 CAGTTAAAACATGCTATTCCTCTGTAT 57.886 33.333 0.00 0.00 0.00 2.29
1807 2263 3.659195 TGGGATTGGGAGATATCATTGCT 59.341 43.478 5.32 0.00 0.00 3.91
1808 2264 4.106825 TGGGATTGGGAGATATCATTGCTT 59.893 41.667 5.32 0.00 0.00 3.91
1822 2278 1.655885 TGCTTGTGCATGCACTGTC 59.344 52.632 41.43 30.52 45.31 3.51
1823 2279 1.102222 TGCTTGTGCATGCACTGTCA 61.102 50.000 41.43 32.24 45.31 3.58
1828 2284 2.164338 TGTGCATGCACTGTCAATCAT 58.836 42.857 41.43 0.00 46.30 2.45
1909 2365 2.363683 GGCAAGAAAGATCAGACCTGG 58.636 52.381 0.00 0.00 0.00 4.45
1977 2433 7.564793 AGCTAGTACATAATGAACATGTCCAA 58.435 34.615 0.00 0.00 37.74 3.53
2040 2496 2.476199 AGCTCCTTGACTGCCTCTATT 58.524 47.619 0.00 0.00 0.00 1.73
2264 2720 2.084546 GCTTTCGGCTAAATCTGGTGT 58.915 47.619 0.00 0.00 38.06 4.16
2354 2810 0.178967 TGGACAATTTGCAGGCCTGA 60.179 50.000 37.21 16.68 0.00 3.86
2355 2811 1.188863 GGACAATTTGCAGGCCTGAT 58.811 50.000 37.21 18.37 0.00 2.90
2361 2817 1.186917 TTTGCAGGCCTGATGGTTGG 61.187 55.000 37.21 7.61 35.27 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 5.358298 AACTTTCCTATTCGCACAGTTTC 57.642 39.130 0.00 0.00 0.00 2.78
254 258 6.313519 TCCATCTTTTGTATAGCTCCAAGT 57.686 37.500 0.00 0.00 0.00 3.16
272 276 6.189677 TGAACGAACCATAAACAATCCATC 57.810 37.500 0.00 0.00 0.00 3.51
296 301 6.553100 TGTTTGTTCCATTCCTCCAAATAAGT 59.447 34.615 0.00 0.00 0.00 2.24
406 411 5.096443 TGAAAATTTTCACCTTTGCTGGT 57.904 34.783 26.01 0.00 41.88 4.00
504 523 0.680921 CCCATTCAAGCACGATGGGT 60.681 55.000 15.45 0.00 45.20 4.51
511 530 0.529378 CTTCTGGCCCATTCAAGCAC 59.471 55.000 0.00 0.00 0.00 4.40
556 575 2.222027 CAAACCTCTTTCGCCTTCTGT 58.778 47.619 0.00 0.00 0.00 3.41
651 670 2.435805 TGCTCTGGCATAAGAAGTAGGG 59.564 50.000 1.53 0.00 44.28 3.53
726 745 8.808240 ACCTCTATCCTACCATAAATACCAAA 57.192 34.615 0.00 0.00 0.00 3.28
741 760 6.143915 TCATAAACCAGCTTACCTCTATCCT 58.856 40.000 0.00 0.00 0.00 3.24
761 780 7.712639 GCATGTATCTTGAGACTTTCCTTCATA 59.287 37.037 0.00 0.00 0.00 2.15
782 801 1.203162 TCCCATGGAAGTTTGGCATGT 60.203 47.619 15.22 0.00 0.00 3.21
786 805 1.607801 GGCTCCCATGGAAGTTTGGC 61.608 60.000 15.22 6.18 0.00 4.52
875 895 5.250200 ACTTCACAAAACACTTCAGTGGTA 58.750 37.500 11.62 0.00 46.84 3.25
881 901 6.686630 ACATTCAACTTCACAAAACACTTCA 58.313 32.000 0.00 0.00 0.00 3.02
882 902 7.328249 TCAACATTCAACTTCACAAAACACTTC 59.672 33.333 0.00 0.00 0.00 3.01
886 906 6.035866 GCATCAACATTCAACTTCACAAAACA 59.964 34.615 0.00 0.00 0.00 2.83
930 950 1.497309 CCCCAGTTGTGCCCCTAAGA 61.497 60.000 0.00 0.00 0.00 2.10
1157 1179 2.502142 ATCATTGAAGACTGCAGCCA 57.498 45.000 15.27 4.03 0.00 4.75
1211 1657 8.642935 TGATTCCCTGTTACAATGTTCAAATA 57.357 30.769 0.00 0.00 0.00 1.40
1234 1680 6.591062 GCAATTTCATGAGCAACCTTATTTGA 59.409 34.615 0.00 0.00 0.00 2.69
1279 1725 5.152623 TCCTCAAACCAATCACTAGTCAG 57.847 43.478 0.00 0.00 0.00 3.51
1482 1929 2.116366 CGAAAAAGACGCAGGTTTTGG 58.884 47.619 0.00 0.00 30.06 3.28
1488 1935 0.941542 TTGACCGAAAAAGACGCAGG 59.058 50.000 0.00 0.00 0.00 4.85
1505 1952 9.212641 CTCCACACTATATGATAGGTTGATTTG 57.787 37.037 0.00 0.00 0.00 2.32
1695 2150 5.814705 CACAGGCAGGAAATTTTGTGTTAAA 59.185 36.000 9.34 0.00 33.21 1.52
1727 2182 7.398024 AGGAATAGCATGTTTTAACTGTCTCT 58.602 34.615 0.00 0.00 0.00 3.10
1756 2212 3.118408 ACCATACTTGCTTCGCCTTCATA 60.118 43.478 0.00 0.00 0.00 2.15
1758 2214 1.003118 ACCATACTTGCTTCGCCTTCA 59.997 47.619 0.00 0.00 0.00 3.02
1822 2278 4.936411 AGAACTGCTTCTCTGACATGATTG 59.064 41.667 0.00 0.00 30.11 2.67
1823 2279 5.163281 AGAACTGCTTCTCTGACATGATT 57.837 39.130 0.00 0.00 30.11 2.57
1828 2284 3.161067 AGCTAGAACTGCTTCTCTGACA 58.839 45.455 0.00 0.00 37.87 3.58
1909 2365 3.944087 ACCAAGAAGTGATAGCCAAGAC 58.056 45.455 0.00 0.00 0.00 3.01
1977 2433 4.373156 AGCCACTATTTCCTTGACTTGT 57.627 40.909 0.00 0.00 0.00 3.16
2021 2477 2.484594 GGAATAGAGGCAGTCAAGGAGC 60.485 54.545 0.00 0.00 0.00 4.70
2040 2496 0.034896 GTCTGGTCTTCGCTTTGGGA 59.965 55.000 0.00 0.00 0.00 4.37
2305 2761 6.475596 TGCATTGACTTGATCAGATCTCTA 57.524 37.500 11.83 0.00 38.99 2.43


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

AutoCloner maintained by Alex Coulton.