Multiple sequence alignment - TraesCS3A01G226900

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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 TraesCS3A01G226900 chr3A 100.000 2708 0 0 1 2708 424249430 424252137 0.000000e+00 5001.0
1 TraesCS3A01G226900 chr3A 98.643 737 9 1 1972 2708 424254412 424253677 0.000000e+00 1304.0
2 TraesCS3A01G226900 chr3B 94.429 1400 57 7 583 1971 415644917 415643528 0.000000e+00 2134.0
3 TraesCS3A01G226900 chr3B 90.547 603 37 11 3 590 415645740 415645143 0.000000e+00 780.0
4 TraesCS3A01G226900 chr3B 90.778 553 22 7 1971 2503 528644182 528644725 0.000000e+00 712.0
5 TraesCS3A01G226900 chr3B 95.276 254 9 3 1972 2224 8479989 8479738 1.510000e-107 399.0
6 TraesCS3A01G226900 chr3B 88.485 165 14 3 1971 2135 528647046 528646887 7.650000e-46 195.0
7 TraesCS3A01G226900 chr3B 84.793 217 6 5 2502 2708 8477576 8477377 2.750000e-45 193.0
8 TraesCS3A01G226900 chr3D 94.118 1224 43 12 758 1971 306016679 306017883 0.000000e+00 1834.0
9 TraesCS3A01G226900 chr3D 91.813 342 23 3 146 485 306016090 306016428 3.160000e-129 472.0
10 TraesCS3A01G226900 chr3D 90.964 166 8 4 514 672 306016429 306016594 1.630000e-52 217.0
11 TraesCS3A01G226900 chr3D 89.610 77 7 1 2401 2477 142730479 142730404 2.220000e-16 97.1
12 TraesCS3A01G226900 chrUn 100.000 300 0 0 2409 2708 453081169 453081468 3.050000e-154 555.0
13 TraesCS3A01G226900 chr2B 92.982 57 4 0 1972 2028 173571257 173571313 1.730000e-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 TraesCS3A01G226900 chr3A 424249430 424252137 2707 False 5001 5001 100.000000 1 2708 1 chr3A.!!$F1 2707
1 TraesCS3A01G226900 chr3A 424253677 424254412 735 True 1304 1304 98.643000 1972 2708 1 chr3A.!!$R1 736
2 TraesCS3A01G226900 chr3B 415643528 415645740 2212 True 1457 2134 92.488000 3 1971 2 chr3B.!!$R3 1968
3 TraesCS3A01G226900 chr3B 528644182 528644725 543 False 712 712 90.778000 1971 2503 1 chr3B.!!$F1 532
4 TraesCS3A01G226900 chr3B 8477377 8479989 2612 True 296 399 90.034500 1972 2708 2 chr3B.!!$R2 736
5 TraesCS3A01G226900 chr3D 306016090 306017883 1793 False 841 1834 92.298333 146 1971 3 chr3D.!!$F1 1825

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
892 1145 1.964344 GCCCACACTCTCTCCTCTCAT 60.964 57.143 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2200 2.189521 GGGCCGACACCATGTAGG 59.81 66.667 0.0 3.93 44.6 3.18 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
60 61 4.818534 TGTTTGTCTTCTGATTGTGAGC 57.181 40.909 0.00 0.0 0.00 4.26
103 115 3.006430 ACCTTGGCCCGAACAATAAAAAG 59.994 43.478 0.00 0.0 0.00 2.27
105 117 2.877866 TGGCCCGAACAATAAAAAGGA 58.122 42.857 0.00 0.0 0.00 3.36
120 132 5.343307 AAAAAGGAAAGCTTTTGAGAGCA 57.657 34.783 14.05 0.0 45.12 4.26
126 138 5.948162 AGGAAAGCTTTTGAGAGCATTGATA 59.052 36.000 14.05 0.0 45.12 2.15
278 290 3.309954 GCGAAGTCGAGCTCCATTTTTAT 59.690 43.478 8.47 0.0 43.02 1.40
430 444 3.033185 CGTTTTTCTTAAGCACACACCG 58.967 45.455 0.00 0.0 0.00 4.94
444 458 4.925054 GCACACACCGTAGAACAATAGTTA 59.075 41.667 0.00 0.0 38.30 2.24
517 531 8.641498 AAAGGATGAAGCTAAAAAGAAGATCA 57.359 30.769 0.00 0.0 0.00 2.92
595 845 4.099573 TGCAGTTAGAAGGTAGTATGAGCC 59.900 45.833 0.00 0.0 0.00 4.70
697 947 2.028203 CCCAAAGTTTACTGCCCATTGG 60.028 50.000 0.00 0.0 36.46 3.16
720 970 4.612259 GCGCTGCCTATAATCACATCAAAG 60.612 45.833 0.00 0.0 0.00 2.77
723 973 6.433766 GCTGCCTATAATCACATCAAAGAAC 58.566 40.000 0.00 0.0 0.00 3.01
726 976 9.499479 CTGCCTATAATCACATCAAAGAACTAT 57.501 33.333 0.00 0.0 0.00 2.12
771 1021 5.767665 ACACTACATGCCAAACACTTGAATA 59.232 36.000 0.00 0.0 34.14 1.75
825 1077 4.966965 ATATACTCCTGATACTTCCGCG 57.033 45.455 0.00 0.0 0.00 6.46
892 1145 1.964344 GCCCACACTCTCTCCTCTCAT 60.964 57.143 0.00 0.0 0.00 2.90
963 1216 3.272364 ATCCAAAGAGCCGCTGCCA 62.272 57.895 0.00 0.0 38.69 4.92
1035 1291 2.418910 CGATGCCGGAGAGTGGTCT 61.419 63.158 5.05 0.0 34.86 3.85
1096 1352 2.443016 CGGAGCTCCTAGCCCTGT 60.443 66.667 29.73 0.0 43.77 4.00
1121 1377 2.042435 CCTCTCCCGCTCCTTCCT 60.042 66.667 0.00 0.0 0.00 3.36
1124 1380 2.364317 CTCCCGCTCCTTCCTCCA 60.364 66.667 0.00 0.0 0.00 3.86
1326 1582 4.980805 TTCACCGCCACACCGCTC 62.981 66.667 0.00 0.0 0.00 5.03
1503 1759 1.364171 GCCTGATATGCGTCGGTCT 59.636 57.895 0.00 0.0 0.00 3.85
1518 1774 0.806492 GGTCTGATTCGGAGAACGGC 60.806 60.000 0.00 0.0 45.90 5.68
1520 1776 1.218047 CTGATTCGGAGAACGGCCA 59.782 57.895 2.24 0.0 45.90 5.36
1719 1981 0.033504 TGAAGTGACGAGGGAGTTGC 59.966 55.000 0.00 0.0 0.00 4.17
1839 2101 4.934001 TGCTTCTTGTCTTTCTAGCATCTG 59.066 41.667 0.00 0.0 34.05 2.90
1936 2198 7.541122 AGATTACTCAATTTTAGACCTTCGC 57.459 36.000 0.00 0.0 0.00 4.70
1938 2200 3.344515 ACTCAATTTTAGACCTTCGCCC 58.655 45.455 0.00 0.0 0.00 6.13
1942 2204 3.555527 ATTTTAGACCTTCGCCCCTAC 57.444 47.619 0.00 0.0 0.00 3.18
2183 2446 4.405680 ACTGACCTATGTTTCCATCGATCA 59.594 41.667 0.00 0.0 32.29 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.300034 TGCTCACAATCAGAAGACAAACAAT 59.700 36.000 0.00 0.00 0.00 2.71
38 39 4.639755 TGCTCACAATCAGAAGACAAACAA 59.360 37.500 0.00 0.00 0.00 2.83
40 41 4.818534 TGCTCACAATCAGAAGACAAAC 57.181 40.909 0.00 0.00 0.00 2.93
42 43 4.823442 ACATTGCTCACAATCAGAAGACAA 59.177 37.500 0.00 0.00 44.83 3.18
80 92 3.436577 TTTATTGTTCGGGCCAAGGTA 57.563 42.857 4.39 0.00 0.00 3.08
82 94 3.584834 CTTTTTATTGTTCGGGCCAAGG 58.415 45.455 4.39 0.00 0.00 3.61
103 115 4.510038 TCAATGCTCTCAAAAGCTTTCC 57.490 40.909 13.10 0.00 42.94 3.13
240 252 4.626042 ACTTCGCATGATCTTAGATGGAC 58.374 43.478 0.00 0.00 0.00 4.02
247 259 2.359214 AGCTCGACTTCGCATGATCTTA 59.641 45.455 0.00 0.00 39.60 2.10
248 260 1.135915 AGCTCGACTTCGCATGATCTT 59.864 47.619 0.00 0.00 39.60 2.40
252 264 1.139734 GGAGCTCGACTTCGCATGA 59.860 57.895 7.83 0.00 39.60 3.07
278 290 5.687166 ACACTCCCTATTTTGTCGGATAA 57.313 39.130 0.00 0.00 0.00 1.75
402 416 3.417645 GTGCTTAAGAAAAACGAACGCAG 59.582 43.478 6.67 0.00 0.00 5.18
491 505 8.734386 TGATCTTCTTTTTAGCTTCATCCTTTC 58.266 33.333 0.00 0.00 0.00 2.62
517 531 9.920946 TGGATAAGCTATTTCTTCCTTTTGTAT 57.079 29.630 0.00 0.00 0.00 2.29
574 591 5.737635 GCTGGCTCATACTACCTTCTAACTG 60.738 48.000 0.00 0.00 0.00 3.16
595 845 2.555325 TGCAGAATTCAAGTCTTGGCTG 59.445 45.455 12.66 14.30 0.00 4.85
697 947 2.416747 TGATGTGATTATAGGCAGCGC 58.583 47.619 0.00 0.00 0.00 5.92
799 1051 6.660800 CGGAAGTATCAGGAGTATATAGGGA 58.339 44.000 0.00 0.00 0.00 4.20
800 1052 5.299782 GCGGAAGTATCAGGAGTATATAGGG 59.700 48.000 0.00 0.00 0.00 3.53
801 1053 5.007823 CGCGGAAGTATCAGGAGTATATAGG 59.992 48.000 0.00 0.00 0.00 2.57
802 1054 5.007823 CCGCGGAAGTATCAGGAGTATATAG 59.992 48.000 24.07 0.00 0.00 1.31
803 1055 4.880120 CCGCGGAAGTATCAGGAGTATATA 59.120 45.833 24.07 0.00 0.00 0.86
872 1125 0.613292 TGAGAGGAGAGAGTGTGGGC 60.613 60.000 0.00 0.00 0.00 5.36
892 1145 0.399233 CAGGGGTTTGGGTTGGGAAA 60.399 55.000 0.00 0.00 0.00 3.13
963 1216 2.651361 CGAAGAGAGTGCGTGGGT 59.349 61.111 0.00 0.00 0.00 4.51
1488 1744 2.604614 CGAATCAGACCGACGCATATCA 60.605 50.000 0.00 0.00 0.00 2.15
1491 1747 0.030235 CCGAATCAGACCGACGCATA 59.970 55.000 0.00 0.00 0.00 3.14
1503 1759 1.218047 CTGGCCGTTCTCCGAATCA 59.782 57.895 0.00 0.00 39.56 2.57
1548 1804 2.268920 GCACCGCATTCCTCTGGA 59.731 61.111 0.00 0.00 0.00 3.86
1647 1903 2.332654 GCCGGCGACCAAGACAAAT 61.333 57.895 12.58 0.00 0.00 2.32
1667 1929 2.415010 CCTGAGCATCGTCTCCGG 59.585 66.667 0.00 0.00 38.61 5.14
1839 2101 7.597386 AGCAAGTGGAGAAAAGAAACATATTC 58.403 34.615 0.00 0.00 0.00 1.75
1938 2200 2.189521 GGGCCGACACCATGTAGG 59.810 66.667 0.00 3.93 44.60 3.18
1942 2204 4.386951 TCGTGGGCCGACACCATG 62.387 66.667 18.72 5.27 44.58 3.66
2396 4412 5.895534 AGCATTCACATCATGGGAACTTTAT 59.104 36.000 3.86 0.00 43.35 1.40


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

AutoCloner maintained by Alex Coulton.