Multiple sequence alignment - TraesCS3D01G092200

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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 TraesCS3D01G092200 chr3D 100.000 2858 0 0 1 2858 46485388 46488245 0.000000e+00 5278.0
1 TraesCS3D01G092200 chr3D 90.724 2404 167 36 37 2419 46524617 46526985 0.000000e+00 3153.0
2 TraesCS3D01G092200 chr3B 94.331 2752 78 21 1 2736 72715072 72717761 0.000000e+00 4146.0
3 TraesCS3D01G092200 chr3B 89.139 1556 121 28 887 2419 72923088 72924618 0.000000e+00 1893.0
4 TraesCS3D01G092200 chr3B 91.208 853 45 14 38 890 72922106 72922928 0.000000e+00 1133.0
5 TraesCS3D01G092200 chr3B 97.710 131 3 0 2728 2858 72718307 72718437 2.870000e-55 226.0
6 TraesCS3D01G092200 chr3B 89.855 69 7 0 2574 2642 72925713 72925781 3.920000e-14 89.8
7 TraesCS3D01G092200 chr3A 94.479 1920 83 10 1 1919 57904330 57906227 0.000000e+00 2937.0
8 TraesCS3D01G092200 chr3A 91.882 1047 80 5 798 1841 57981158 57980114 0.000000e+00 1458.0
9 TraesCS3D01G092200 chr3A 90.950 895 48 9 1992 2858 57906262 57907151 0.000000e+00 1173.0
10 TraesCS3D01G092200 chr3A 85.901 383 38 7 2047 2419 57968394 57968018 7.420000e-106 394.0
11 TraesCS3D01G092200 chr3A 85.874 269 27 5 37 305 57915956 57916213 2.800000e-70 276.0
12 TraesCS3D01G092200 chr3A 91.379 116 5 2 1849 1960 57975401 57975287 1.370000e-33 154.0
13 TraesCS3D01G092200 chr5A 75.815 1472 321 30 316 1774 143659792 143658343 0.000000e+00 713.0
14 TraesCS3D01G092200 chr5B 75.747 1472 321 32 316 1774 141149021 141147573 0.000000e+00 708.0
15 TraesCS3D01G092200 chr5D 76.003 1396 300 30 392 1774 128643430 128642057 0.000000e+00 689.0
16 TraesCS3D01G092200 chr6D 75.855 1375 292 30 401 1750 53175718 53174359 0.000000e+00 664.0
17 TraesCS3D01G092200 chr7A 75.839 1370 281 34 401 1743 631984736 631986082 0.000000e+00 651.0
18 TraesCS3D01G092200 chr7B 75.802 1372 278 37 401 1743 591461942 591463288 0.000000e+00 645.0
19 TraesCS3D01G092200 chr6B 75.447 1397 303 28 401 1772 120132595 120131214 0.000000e+00 643.0
20 TraesCS3D01G092200 chr7D 75.729 1372 279 36 401 1743 548231394 548232740 8.630000e-180 640.0
21 TraesCS3D01G092200 chr1B 75.175 1430 311 33 401 1804 4597252 4595841 4.020000e-178 634.0
22 TraesCS3D01G092200 chr1B 75.254 1378 285 42 402 1743 46830010 46828653 3.150000e-169 604.0


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 TraesCS3D01G092200 chr3D 46485388 46488245 2857 False 5278.0 5278 100.000000 1 2858 1 chr3D.!!$F1 2857
1 TraesCS3D01G092200 chr3D 46524617 46526985 2368 False 3153.0 3153 90.724000 37 2419 1 chr3D.!!$F2 2382
2 TraesCS3D01G092200 chr3B 72715072 72718437 3365 False 2186.0 4146 96.020500 1 2858 2 chr3B.!!$F1 2857
3 TraesCS3D01G092200 chr3B 72922106 72925781 3675 False 1038.6 1893 90.067333 38 2642 3 chr3B.!!$F2 2604
4 TraesCS3D01G092200 chr3A 57904330 57907151 2821 False 2055.0 2937 92.714500 1 2858 2 chr3A.!!$F2 2857
5 TraesCS3D01G092200 chr3A 57980114 57981158 1044 True 1458.0 1458 91.882000 798 1841 1 chr3A.!!$R3 1043
6 TraesCS3D01G092200 chr5A 143658343 143659792 1449 True 713.0 713 75.815000 316 1774 1 chr5A.!!$R1 1458
7 TraesCS3D01G092200 chr5B 141147573 141149021 1448 True 708.0 708 75.747000 316 1774 1 chr5B.!!$R1 1458
8 TraesCS3D01G092200 chr5D 128642057 128643430 1373 True 689.0 689 76.003000 392 1774 1 chr5D.!!$R1 1382
9 TraesCS3D01G092200 chr6D 53174359 53175718 1359 True 664.0 664 75.855000 401 1750 1 chr6D.!!$R1 1349
10 TraesCS3D01G092200 chr7A 631984736 631986082 1346 False 651.0 651 75.839000 401 1743 1 chr7A.!!$F1 1342
11 TraesCS3D01G092200 chr7B 591461942 591463288 1346 False 645.0 645 75.802000 401 1743 1 chr7B.!!$F1 1342
12 TraesCS3D01G092200 chr6B 120131214 120132595 1381 True 643.0 643 75.447000 401 1772 1 chr6B.!!$R1 1371
13 TraesCS3D01G092200 chr7D 548231394 548232740 1346 False 640.0 640 75.729000 401 1743 1 chr7D.!!$F1 1342
14 TraesCS3D01G092200 chr1B 4595841 4597252 1411 True 634.0 634 75.175000 401 1804 1 chr1B.!!$R1 1403
15 TraesCS3D01G092200 chr1B 46828653 46830010 1357 True 604.0 604 75.254000 402 1743 1 chr1B.!!$R2 1341

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
851 860 0.31179 CGTGGCTGTTCATTGCAAGT 59.688 50.0 4.94 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 2582 3.096092 AGGCCAACAAAACTCTGACAAA 58.904 40.909 5.01 0.0 0.0 2.83 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
25 26 5.957771 AATGTCCAAAGGAGTATGCTAGA 57.042 39.130 0.00 0.00 33.13 2.43
27 28 5.957771 TGTCCAAAGGAGTATGCTAGAAT 57.042 39.130 0.00 0.00 33.13 2.40
28 29 6.313519 TGTCCAAAGGAGTATGCTAGAATT 57.686 37.500 0.00 0.00 33.13 2.17
29 30 6.721318 TGTCCAAAGGAGTATGCTAGAATTT 58.279 36.000 0.00 0.00 33.13 1.82
30 31 7.175104 TGTCCAAAGGAGTATGCTAGAATTTT 58.825 34.615 0.00 0.00 33.13 1.82
31 32 7.669722 TGTCCAAAGGAGTATGCTAGAATTTTT 59.330 33.333 0.00 0.00 33.13 1.94
78 79 2.303022 CAACTTCCTCAGGAGCACCTAA 59.697 50.000 1.02 0.00 45.94 2.69
92 93 2.763448 GCACCTAAGTCTCAGTCCTCAT 59.237 50.000 0.00 0.00 0.00 2.90
170 171 5.710513 TTCTGATTGGTTGTTTCTGGATG 57.289 39.130 0.00 0.00 0.00 3.51
172 173 3.499338 TGATTGGTTGTTTCTGGATGCT 58.501 40.909 0.00 0.00 0.00 3.79
173 174 3.256383 TGATTGGTTGTTTCTGGATGCTG 59.744 43.478 0.00 0.00 0.00 4.41
215 216 4.943705 GCAGTTTCAGATACTTGGGATGAA 59.056 41.667 0.00 0.00 0.00 2.57
247 255 9.367444 CTTCGATGTTGTTCCTTATTAGTAACT 57.633 33.333 0.00 0.00 0.00 2.24
267 275 8.495949 AGTAACTCATGAATTTTCACAAGTACG 58.504 33.333 0.00 0.00 40.49 3.67
270 278 8.771920 ACTCATGAATTTTCACAAGTACGATA 57.228 30.769 0.00 0.00 40.49 2.92
271 279 8.656849 ACTCATGAATTTTCACAAGTACGATAC 58.343 33.333 0.00 0.00 40.49 2.24
337 345 6.927936 TGCTATGCTTAACTCTGATTCTCATC 59.072 38.462 0.00 0.00 0.00 2.92
479 487 4.634883 CCAGGACAAGTGATCTGAATTCTG 59.365 45.833 7.05 6.50 0.00 3.02
661 669 0.896923 GCCATGGCAATCAGTTGGAA 59.103 50.000 32.08 0.00 41.49 3.53
671 679 2.151502 TCAGTTGGAAAACCAAGGCA 57.848 45.000 1.75 0.00 0.00 4.75
766 774 2.170607 TGGTCTTGGTTATCTAGCCTGC 59.829 50.000 0.00 0.00 0.00 4.85
790 798 2.217510 AGAAACTAGCGTCCCTCAGA 57.782 50.000 0.00 0.00 0.00 3.27
794 802 1.115467 ACTAGCGTCCCTCAGATTGG 58.885 55.000 0.00 0.00 0.00 3.16
851 860 0.311790 CGTGGCTGTTCATTGCAAGT 59.688 50.000 4.94 0.00 0.00 3.16
938 1110 3.718434 TGGCTCTGTAGGATCATTGGAAT 59.282 43.478 0.00 0.00 0.00 3.01
1589 1790 1.174783 TTACTGGAGACACTCGAGCC 58.825 55.000 13.61 5.65 39.41 4.70
1590 1791 0.037734 TACTGGAGACACTCGAGCCA 59.962 55.000 13.61 10.42 39.41 4.75
1591 1792 0.613292 ACTGGAGACACTCGAGCCAT 60.613 55.000 13.61 0.00 39.41 4.40
1661 1862 3.830755 GCCCCATGCTTGATTAATCTCAT 59.169 43.478 16.24 12.89 36.87 2.90
1965 2177 0.895530 TCCCTGACATCAACTCCGTC 59.104 55.000 0.00 0.00 0.00 4.79
1966 2178 0.898320 CCCTGACATCAACTCCGTCT 59.102 55.000 0.00 0.00 0.00 4.18
1967 2179 1.134965 CCCTGACATCAACTCCGTCTC 60.135 57.143 0.00 0.00 0.00 3.36
1968 2180 1.546029 CCTGACATCAACTCCGTCTCA 59.454 52.381 0.00 0.00 0.00 3.27
1970 2182 3.443037 CTGACATCAACTCCGTCTCATC 58.557 50.000 0.00 0.00 0.00 2.92
1971 2183 3.092301 TGACATCAACTCCGTCTCATCT 58.908 45.455 0.00 0.00 0.00 2.90
1972 2184 3.119352 TGACATCAACTCCGTCTCATCTG 60.119 47.826 0.00 0.00 0.00 2.90
1973 2185 2.200067 CATCAACTCCGTCTCATCTGC 58.800 52.381 0.00 0.00 0.00 4.26
1974 2186 1.550327 TCAACTCCGTCTCATCTGCT 58.450 50.000 0.00 0.00 0.00 4.24
1975 2187 1.474478 TCAACTCCGTCTCATCTGCTC 59.526 52.381 0.00 0.00 0.00 4.26
1976 2188 0.820871 AACTCCGTCTCATCTGCTCC 59.179 55.000 0.00 0.00 0.00 4.70
1977 2189 0.323816 ACTCCGTCTCATCTGCTCCA 60.324 55.000 0.00 0.00 0.00 3.86
1978 2190 0.385029 CTCCGTCTCATCTGCTCCAG 59.615 60.000 0.00 0.00 0.00 3.86
1979 2191 0.034089 TCCGTCTCATCTGCTCCAGA 60.034 55.000 0.00 0.00 44.99 3.86
1981 2193 1.000385 CCGTCTCATCTGCTCCAGATC 60.000 57.143 4.82 0.00 46.83 2.75
1982 2194 1.680207 CGTCTCATCTGCTCCAGATCA 59.320 52.381 4.82 0.00 46.83 2.92
1983 2195 2.287728 CGTCTCATCTGCTCCAGATCAG 60.288 54.545 4.82 2.52 46.83 2.90
2253 2477 7.303261 AGCGTAAAAATAAGTAGTTTTGGAGC 58.697 34.615 6.73 8.51 34.79 4.70
2357 2582 5.688621 GCACATAAATCGACATTGCATTGAT 59.311 36.000 15.20 0.00 0.00 2.57
2466 2729 4.081309 CCGTCACTTATTCAGGAAACCCTA 60.081 45.833 0.00 0.00 31.47 3.53
2500 2776 4.441087 GTCGTTTGATTGAAGGAAAAGCAC 59.559 41.667 0.00 0.00 0.00 4.40
2668 3843 9.652114 AGAAAGATGCCCAAGATAGAAATAAAT 57.348 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 2.503765 TCGCATGAAAACCTCCTCCATA 59.496 45.455 0.00 0.00 0.00 2.74
126 127 9.952188 CAGAAATATGAGTCTACGAGATAACAA 57.048 33.333 0.00 0.00 0.00 2.83
247 255 8.541133 TGTATCGTACTTGTGAAAATTCATGA 57.459 30.769 0.00 0.00 39.73 3.07
337 345 2.095364 GCAGAGCACTGGACAGAAATTG 60.095 50.000 13.26 0.00 43.62 2.32
479 487 0.234884 CGCTTCGACACAAGGGAAAC 59.765 55.000 0.00 0.00 38.33 2.78
661 669 2.664402 ACACAGAGATGCCTTGGTTT 57.336 45.000 0.00 0.00 0.00 3.27
671 679 5.453057 GGCAGTGAGATGATAACACAGAGAT 60.453 44.000 0.00 0.00 37.05 2.75
766 774 1.079503 GGGACGCTAGTTTCTTGCAG 58.920 55.000 0.00 0.71 32.19 4.41
790 798 0.105760 TGTTTGGTGTGGAGGCCAAT 60.106 50.000 5.01 0.00 43.38 3.16
794 802 2.514803 AGTTATGTTTGGTGTGGAGGC 58.485 47.619 0.00 0.00 0.00 4.70
851 860 3.777106 AATGTGGAGAGCAGAAAGACA 57.223 42.857 0.00 0.00 0.00 3.41
938 1110 5.381174 TCGCACTTCTTTACTACAAGCTA 57.619 39.130 0.00 0.00 0.00 3.32
1589 1790 3.133362 ACTTATGGCCTTGCAATCCAATG 59.867 43.478 20.16 15.58 33.04 2.82
1590 1791 3.377573 ACTTATGGCCTTGCAATCCAAT 58.622 40.909 20.16 13.01 33.04 3.16
1591 1792 2.818921 ACTTATGGCCTTGCAATCCAA 58.181 42.857 20.16 7.93 33.04 3.53
1661 1862 3.695606 GGTCACAGAGCCGGAGCA 61.696 66.667 5.05 0.00 43.56 4.26
1977 2189 4.032310 AGGAGAAGATGCAGAACTGATCT 58.968 43.478 5.97 8.07 39.68 2.75
1978 2190 4.405116 AGGAGAAGATGCAGAACTGATC 57.595 45.455 5.97 6.18 0.00 2.92
1979 2191 4.840716 AAGGAGAAGATGCAGAACTGAT 57.159 40.909 5.97 0.00 0.00 2.90
1980 2192 5.660417 AGATAAGGAGAAGATGCAGAACTGA 59.340 40.000 5.97 0.00 0.00 3.41
1981 2193 5.916318 AGATAAGGAGAAGATGCAGAACTG 58.084 41.667 0.00 0.00 0.00 3.16
1982 2194 5.898972 AGAGATAAGGAGAAGATGCAGAACT 59.101 40.000 0.00 0.00 0.00 3.01
1983 2195 6.040842 AGAGAGATAAGGAGAAGATGCAGAAC 59.959 42.308 0.00 0.00 0.00 3.01
2357 2582 3.096092 AGGCCAACAAAACTCTGACAAA 58.904 40.909 5.01 0.00 0.00 2.83
2466 2729 9.855021 CCTTCAATCAAACGACCTTTATATTTT 57.145 29.630 0.00 0.00 0.00 1.82
2500 2776 7.693969 ACTTCTATCACTCAAATCTTTTGGG 57.306 36.000 0.00 0.00 0.00 4.12
2769 4498 4.837093 ATTTGAGGGAGAACGTTGGATA 57.163 40.909 5.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.