Multiple sequence alignment - TraesCS6A01G128900

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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 TraesCS6A01G128900 chr6A 100.000 2249 0 0 1 2249 100767446 100765198 0.000000e+00 4154.0
1 TraesCS6A01G128900 chr6A 90.202 1235 89 24 995 2206 100813193 100811968 0.000000e+00 1581.0
2 TraesCS6A01G128900 chr6A 89.223 1030 83 10 1214 2236 100179987 100180995 0.000000e+00 1262.0
3 TraesCS6A01G128900 chr6A 91.501 906 64 6 1 904 100905597 100904703 0.000000e+00 1234.0
4 TraesCS6A01G128900 chr6A 88.776 588 57 7 1 582 100814265 100813681 0.000000e+00 712.0
5 TraesCS6A01G128900 chr6A 88.272 162 14 2 660 816 100813688 100813527 2.950000e-44 189.0
6 TraesCS6A01G128900 chr6B 88.514 1628 100 27 657 2206 159409194 159407576 0.000000e+00 1890.0
7 TraesCS6A01G128900 chr6B 91.176 1326 87 16 904 2206 159600475 159599157 0.000000e+00 1773.0
8 TraesCS6A01G128900 chr6B 91.658 1007 71 5 1212 2206 158144411 158145416 0.000000e+00 1382.0
9 TraesCS6A01G128900 chr6B 89.753 566 50 4 1 563 159602176 159601616 0.000000e+00 717.0
10 TraesCS6A01G128900 chr6B 88.194 576 53 10 1 563 159409779 159409206 0.000000e+00 673.0
11 TraesCS6A01G128900 chr6B 88.953 344 35 3 251 592 159601082 159600740 2.670000e-114 422.0
12 TraesCS6A01G128900 chr6B 92.520 254 15 2 651 904 159600766 159600517 5.900000e-96 361.0
13 TraesCS6A01G128900 chr6B 88.532 218 17 4 678 894 159601588 159601378 7.970000e-65 257.0
14 TraesCS6A01G128900 chr6D 87.068 1214 100 22 1013 2206 83551576 83550400 0.000000e+00 1319.0
15 TraesCS6A01G128900 chr6D 84.960 1250 106 28 1010 2206 83101176 83102396 0.000000e+00 1192.0
16 TraesCS6A01G128900 chr6D 90.000 780 58 7 1488 2249 84031816 84031039 0.000000e+00 990.0
17 TraesCS6A01G128900 chr6D 89.863 582 50 5 1 578 83553549 83552973 0.000000e+00 739.0
18 TraesCS6A01G128900 chr6D 88.496 565 48 6 1 563 84066375 84065826 0.000000e+00 667.0
19 TraesCS6A01G128900 chr6D 86.792 530 32 12 957 1480 84032284 84031787 7.020000e-155 556.0
20 TraesCS6A01G128900 chr6D 91.768 328 25 2 252 578 84065292 84064966 2.630000e-124 455.0
21 TraesCS6A01G128900 chr6D 88.547 358 22 3 254 592 83552455 83552098 1.240000e-112 416.0
22 TraesCS6A01G128900 chr6D 92.208 231 14 2 651 881 84064978 84064752 7.750000e-85 324.0
23 TraesCS6A01G128900 chr6D 90.323 217 12 4 678 894 83552962 83552755 2.200000e-70 276.0
24 TraesCS6A01G128900 chr6D 89.401 217 16 3 678 894 84065798 84065589 1.320000e-67 267.0
25 TraesCS6A01G128900 chr6D 91.566 166 14 0 651 816 83552124 83551959 1.740000e-56 230.0
26 TraesCS6A01G128900 chr6D 97.368 38 1 0 904 941 84032364 84032327 5.180000e-07 65.8
27 TraesCS6A01G128900 chr6D 94.444 36 0 2 871 904 84032440 84032405 1.000000e-03 54.7
28 TraesCS6A01G128900 chr5B 87.425 334 38 4 251 582 48846874 48846543 4.530000e-102 381.0
29 TraesCS6A01G128900 chr7B 84.967 153 21 2 1 153 670276661 670276511 1.080000e-33 154.0
30 TraesCS6A01G128900 chr7B 92.000 75 2 4 582 653 72284851 72284778 3.950000e-18 102.0
31 TraesCS6A01G128900 chr7B 91.026 78 4 3 582 656 72286084 72286007 3.950000e-18 102.0
32 TraesCS6A01G128900 chr7B 92.958 71 1 4 582 648 178736684 178736614 1.420000e-17 100.0
33 TraesCS6A01G128900 chr7B 90.909 66 3 3 582 644 72285881 72285816 3.980000e-13 86.1
34 TraesCS6A01G128900 chr5A 80.952 168 29 3 6 171 666476622 666476788 1.810000e-26 130.0
35 TraesCS6A01G128900 chr7A 81.290 155 27 2 1 153 683498795 683498949 8.430000e-25 124.0
36 TraesCS6A01G128900 chr2D 93.243 74 1 3 583 653 650993067 650992995 3.050000e-19 106.0
37 TraesCS6A01G128900 chr2D 90.789 76 2 5 582 653 390709709 390709635 1.840000e-16 97.1
38 TraesCS6A01G128900 chr1B 90.141 71 3 3 583 649 676610488 676610558 3.080000e-14 89.8
39 TraesCS6A01G128900 chr1B 88.889 72 3 3 583 649 676566396 676566467 1.430000e-12 84.2


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 TraesCS6A01G128900 chr6A 100765198 100767446 2248 True 4154.000000 4154 100.000000 1 2249 1 chr6A.!!$R1 2248
1 TraesCS6A01G128900 chr6A 100179987 100180995 1008 False 1262.000000 1262 89.223000 1214 2236 1 chr6A.!!$F1 1022
2 TraesCS6A01G128900 chr6A 100904703 100905597 894 True 1234.000000 1234 91.501000 1 904 1 chr6A.!!$R2 903
3 TraesCS6A01G128900 chr6A 100811968 100814265 2297 True 827.333333 1581 89.083333 1 2206 3 chr6A.!!$R3 2205
4 TraesCS6A01G128900 chr6B 158144411 158145416 1005 False 1382.000000 1382 91.658000 1212 2206 1 chr6B.!!$F1 994
5 TraesCS6A01G128900 chr6B 159407576 159409779 2203 True 1281.500000 1890 88.354000 1 2206 2 chr6B.!!$R1 2205
6 TraesCS6A01G128900 chr6B 159599157 159602176 3019 True 706.000000 1773 90.186800 1 2206 5 chr6B.!!$R2 2205
7 TraesCS6A01G128900 chr6D 83101176 83102396 1220 False 1192.000000 1192 84.960000 1010 2206 1 chr6D.!!$F1 1196
8 TraesCS6A01G128900 chr6D 83550400 83553549 3149 True 596.000000 1319 89.473400 1 2206 5 chr6D.!!$R1 2205
9 TraesCS6A01G128900 chr6D 84064752 84066375 1623 True 428.250000 667 90.468250 1 894 4 chr6D.!!$R3 893
10 TraesCS6A01G128900 chr6D 84031039 84032440 1401 True 416.625000 990 92.151000 871 2249 4 chr6D.!!$R2 1378

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
997 2181 0.592247 CAAGCGCAACAACTGACCAC 60.592 55.0 11.47 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 3402 0.251209 TGTCACCACCGAGTCTAGCT 60.251 55.0 0.0 0.0 0.0 3.32 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
74 75 4.537751 ACATCTTCGAGAGGGTCTGAATA 58.462 43.478 0.00 0.00 28.79 1.75
79 80 1.001406 CGAGAGGGTCTGAATATGGGC 59.999 57.143 0.00 0.00 0.00 5.36
103 106 2.833151 ATCGTGTCCCCCTTGCCCTA 62.833 60.000 0.00 0.00 0.00 3.53
112 115 1.780309 CCCCTTGCCCTATTACCATCA 59.220 52.381 0.00 0.00 0.00 3.07
130 133 2.764269 TCATCCTAAGGCTACCAGCTT 58.236 47.619 0.00 0.00 41.99 3.74
145 148 2.459710 CTTGGGACCCCCTACCCT 59.540 66.667 8.45 0.00 45.70 4.34
155 158 1.503784 CCCCCTACCCTAGATCTGTCA 59.496 57.143 5.18 0.00 0.00 3.58
160 163 4.717280 CCCTACCCTAGATCTGTCAAGTTT 59.283 45.833 5.18 0.00 0.00 2.66
281 284 0.617413 CCAGGAGAAGGTGCTGTCAT 59.383 55.000 0.00 0.00 43.03 3.06
311 314 3.181507 CCCGATGTAGTTGCACAATTCAG 60.182 47.826 0.00 0.00 30.84 3.02
324 327 4.142227 GCACAATTCAGCCTTGATGAGATT 60.142 41.667 0.00 0.00 32.27 2.40
335 338 3.204306 TGATGAGATTGGCAGTGATCC 57.796 47.619 0.00 0.00 0.00 3.36
340 351 2.300152 GAGATTGGCAGTGATCCCGATA 59.700 50.000 0.00 0.00 0.00 2.92
427 440 4.017591 TCATGAATTGGGTAAGACATGGGT 60.018 41.667 0.00 0.00 35.71 4.51
564 1446 8.791675 TGTATGAGCATTGTATTGACTTTTTCA 58.208 29.630 0.00 0.00 0.00 2.69
578 1460 8.485976 TTGACTTTTTCATTTCGAACCATTTT 57.514 26.923 0.00 0.00 32.84 1.82
580 1462 9.243637 TGACTTTTTCATTTCGAACCATTTTAG 57.756 29.630 0.00 0.00 31.73 1.85
649 1531 3.675775 GCAGAAAAGCAACCAGTCACAAA 60.676 43.478 0.00 0.00 0.00 2.83
654 1536 4.734398 AAGCAACCAGTCACAAATTTCA 57.266 36.364 0.00 0.00 0.00 2.69
655 1537 4.734398 AGCAACCAGTCACAAATTTCAA 57.266 36.364 0.00 0.00 0.00 2.69
707 1589 3.141398 CCGCCAAGTTACATATGCATCT 58.859 45.455 0.19 0.00 0.00 2.90
816 1705 4.253685 GCCAGCTTATTTGTCAGTGTAGA 58.746 43.478 0.00 0.00 0.00 2.59
818 1707 5.482908 CCAGCTTATTTGTCAGTGTAGACT 58.517 41.667 0.00 0.00 39.27 3.24
820 1709 6.428159 CCAGCTTATTTGTCAGTGTAGACTTT 59.572 38.462 0.00 0.00 39.27 2.66
821 1710 7.602644 CCAGCTTATTTGTCAGTGTAGACTTTA 59.397 37.037 0.00 0.00 39.27 1.85
822 1711 8.651588 CAGCTTATTTGTCAGTGTAGACTTTAG 58.348 37.037 0.00 0.00 39.27 1.85
824 1713 8.648968 GCTTATTTGTCAGTGTAGACTTTAGTC 58.351 37.037 1.59 1.59 45.08 2.59
828 1893 8.418597 TTTGTCAGTGTAGACTTTAGTCCTAT 57.581 34.615 6.28 0.00 45.85 2.57
910 2033 6.978659 TCGCTCTATTAACATTGAACTACTGG 59.021 38.462 0.00 0.00 0.00 4.00
955 2111 4.554036 GGACCGGGCATCCTGCTC 62.554 72.222 11.00 0.00 44.28 4.26
997 2181 0.592247 CAAGCGCAACAACTGACCAC 60.592 55.000 11.47 0.00 0.00 4.16
1045 2244 1.968540 AGCGCAGGAGGAAAGCAAC 60.969 57.895 11.47 0.00 0.00 4.17
1123 2351 0.108138 ACTCATGCGGGTAACAGAGC 60.108 55.000 0.00 0.00 39.74 4.09
1247 2512 3.551863 CGAAGAGGAGGAAAGATCGGATG 60.552 52.174 0.00 0.00 0.00 3.51
1248 2513 3.320610 AGAGGAGGAAAGATCGGATGA 57.679 47.619 0.00 0.00 0.00 2.92
1535 2855 4.367450 CTCTTTCTTCTCCGGTCATCATC 58.633 47.826 0.00 0.00 0.00 2.92
2077 3402 1.649321 AAGCCTGTGACTGAGATGGA 58.351 50.000 0.00 0.00 0.00 3.41
2079 3404 0.461693 GCCTGTGACTGAGATGGAGC 60.462 60.000 0.00 0.00 0.00 4.70
2106 3431 0.321653 GGTGGTGACATCCTTCGCTT 60.322 55.000 0.00 0.00 46.14 4.68
2112 3437 0.678048 GACATCCTTCGCTTGCCCTT 60.678 55.000 0.00 0.00 0.00 3.95
2129 3454 0.733729 CTTCTCCGTCGATCGACCTT 59.266 55.000 35.48 0.00 41.76 3.50
2173 3501 1.608717 GAGATGGTGGCAGACTCGGT 61.609 60.000 0.00 0.00 0.00 4.69
2219 3562 1.585006 GTCGGAGAAGAAGGCGACA 59.415 57.895 0.00 0.00 39.69 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 0.965363 GGGACACGATGTTTGCCCAT 60.965 55.000 0.00 0.00 33.13 4.00
79 80 0.881118 CAAGGGGGACACGATGTTTG 59.119 55.000 0.00 0.00 0.00 2.93
103 106 5.162637 TGGTAGCCTTAGGATGATGGTAAT 58.837 41.667 0.69 0.00 0.00 1.89
112 115 1.771255 CCAAGCTGGTAGCCTTAGGAT 59.229 52.381 0.69 0.00 43.77 3.24
155 158 2.146342 CGCTGTGATGGAGTCAAACTT 58.854 47.619 0.00 0.00 38.90 2.66
160 163 0.247460 CTTCCGCTGTGATGGAGTCA 59.753 55.000 0.00 0.00 35.26 3.41
281 284 0.916086 AACTACATCGGGGATTGCCA 59.084 50.000 0.00 0.00 35.15 4.92
311 314 1.404391 CACTGCCAATCTCATCAAGGC 59.596 52.381 0.00 0.00 45.41 4.35
324 327 1.040646 GACTATCGGGATCACTGCCA 58.959 55.000 0.00 0.00 31.98 4.92
335 338 2.353607 GCCGCTGTCGACTATCGG 60.354 66.667 27.14 27.14 40.88 4.18
340 351 4.363990 CAGGTGCCGCTGTCGACT 62.364 66.667 17.92 0.00 38.10 4.18
600 1482 0.046552 TATAAAGTGGGGCAGGGGGA 59.953 55.000 0.00 0.00 0.00 4.81
707 1589 7.093596 TGGTGTGCATTTGTTAATTCCATGATA 60.094 33.333 0.00 0.00 0.00 2.15
798 1687 8.535690 ACTAAAGTCTACACTGACAAATAAGC 57.464 34.615 0.00 0.00 39.27 3.09
845 1910 3.994392 ACGAGTTCACCATGTGTAATCAC 59.006 43.478 0.00 0.00 44.08 3.06
910 2033 4.494350 TCAATTTGAGCAGAAGCAACTC 57.506 40.909 0.00 0.00 45.49 3.01
997 2181 3.626996 TTCCACGCTGCTCCATGGG 62.627 63.158 13.02 3.69 32.73 4.00
1011 2210 1.022982 CGCTGATTGCTGCTCTTCCA 61.023 55.000 0.00 0.00 40.11 3.53
1045 2244 4.431131 AGATGCTGGCCGGGGTTG 62.431 66.667 15.02 0.00 0.00 3.77
1535 2855 4.171005 ACAATTGCGATGCTGAAATTCAG 58.829 39.130 18.02 18.02 46.90 3.02
1997 3322 0.811219 CGGAGATTGATGCCTGCGAA 60.811 55.000 0.00 0.00 45.08 4.70
2047 3372 2.550180 GTCACAGGCTTTGTCTTCTTCC 59.450 50.000 0.00 0.00 38.16 3.46
2077 3402 0.251209 TGTCACCACCGAGTCTAGCT 60.251 55.000 0.00 0.00 0.00 3.32
2079 3404 1.405821 GGATGTCACCACCGAGTCTAG 59.594 57.143 0.00 0.00 0.00 2.43
2106 3431 2.771639 CGATCGACGGAGAAGGGCA 61.772 63.158 10.26 0.00 38.46 5.36
2112 3437 0.731417 GAAAGGTCGATCGACGGAGA 59.269 55.000 34.69 4.96 45.41 3.71
2129 3454 2.982130 GGCTCTGCCTTCTCCGAA 59.018 61.111 0.73 0.00 46.69 4.30
2224 3567 1.153429 GATGCCTCCACCACGGTAC 60.153 63.158 0.00 0.00 35.57 3.34


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

AutoCloner maintained by Alex Coulton.