Multiple sequence alignment - TraesCS5B01G483100

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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 TraesCS5B01G483100 chr5B 100.000 3180 0 0 1 3180 655128261 655131440 0.000000e+00 5873.0
1 TraesCS5B01G483100 chr4B 97.101 2380 55 7 34 2403 467801702 467804077 0.000000e+00 4000.0
2 TraesCS5B01G483100 chr4B 97.992 996 20 0 2185 3180 467804009 467805004 0.000000e+00 1729.0
3 TraesCS5B01G483100 chr4B 97.569 946 23 0 2235 3180 530202646 530201701 0.000000e+00 1620.0
4 TraesCS5B01G483100 chr4B 87.868 577 48 9 880 1437 530203596 530203023 0.000000e+00 658.0
5 TraesCS5B01G483100 chr4B 95.181 83 3 1 462 544 467802220 467802301 2.570000e-26 130.0
6 TraesCS5B01G483100 chr2A 95.627 2378 69 12 36 2391 596260878 596258514 0.000000e+00 3783.0
7 TraesCS5B01G483100 chr2A 95.772 946 18 3 2235 3180 596258713 596257790 0.000000e+00 1506.0
8 TraesCS5B01G483100 chr2A 94.048 84 4 1 462 545 596260363 596260281 3.330000e-25 126.0
9 TraesCS5B01G483100 chr2A 97.143 35 1 0 4 38 96151158 96151192 3.430000e-05 60.2
10 TraesCS5B01G483100 chr2A 97.059 34 1 0 3 36 19913362 19913395 1.230000e-04 58.4
11 TraesCS5B01G483100 chr7B 93.866 1402 58 11 880 2258 3900646 3899250 0.000000e+00 2087.0
12 TraesCS5B01G483100 chr7B 90.835 1233 74 8 191 1417 12728930 12727731 0.000000e+00 1615.0
13 TraesCS5B01G483100 chr7B 97.754 846 17 2 2335 3180 3899250 3898407 0.000000e+00 1456.0
14 TraesCS5B01G483100 chr7B 90.129 233 9 5 36 257 598172706 598172477 1.120000e-74 291.0
15 TraesCS5B01G483100 chr5A 94.931 1302 57 6 1099 2397 352406532 352405237 0.000000e+00 2030.0
16 TraesCS5B01G483100 chr5A 92.140 1425 90 16 974 2397 559463184 559461781 0.000000e+00 1991.0
17 TraesCS5B01G483100 chr5A 97.149 947 25 2 2235 3180 352405443 352404498 0.000000e+00 1598.0
18 TraesCS5B01G483100 chr5A 97.149 947 25 2 2235 3180 559461987 559461042 0.000000e+00 1598.0
19 TraesCS5B01G483100 chr5A 94.737 38 2 0 1 38 433565901 433565864 3.430000e-05 60.2
20 TraesCS5B01G483100 chr6B 92.118 1421 91 15 979 2397 184670490 184669089 0.000000e+00 1984.0
21 TraesCS5B01G483100 chr6B 96.085 945 35 2 2235 3178 184669295 184668352 0.000000e+00 1539.0
22 TraesCS5B01G483100 chr3B 92.151 1427 79 11 955 2353 252334001 252335422 0.000000e+00 1984.0
23 TraesCS5B01G483100 chr2B 96.763 1143 35 2 2039 3180 464453345 464454486 0.000000e+00 1905.0
24 TraesCS5B01G483100 chr2B 91.264 1076 77 12 971 2043 464443552 464444613 0.000000e+00 1450.0
25 TraesCS5B01G483100 chr2B 84.058 276 33 7 880 1150 7781955 7782224 4.070000e-64 255.0
26 TraesCS5B01G483100 chr7D 91.987 1248 57 9 191 1417 70157828 70156603 0.000000e+00 1711.0
27 TraesCS5B01G483100 chr7D 91.740 1247 61 9 191 1417 70044490 70045714 0.000000e+00 1694.0
28 TraesCS5B01G483100 chr3D 95.378 952 37 5 2235 3180 92510188 92511138 0.000000e+00 1507.0
29 TraesCS5B01G483100 chr7A 89.960 757 67 7 1601 2353 164104942 164104191 0.000000e+00 968.0
30 TraesCS5B01G483100 chr7A 90.591 457 32 8 1092 1541 164105394 164104942 2.110000e-166 595.0
31 TraesCS5B01G483100 chr7A 94.737 38 2 0 1 38 194057737 194057774 3.430000e-05 60.2
32 TraesCS5B01G483100 chr6D 97.222 36 1 0 3 38 337847427 337847392 9.520000e-06 62.1
33 TraesCS5B01G483100 chr1D 97.222 36 1 0 3 38 285439754 285439719 9.520000e-06 62.1
34 TraesCS5B01G483100 chr1D 100.000 32 0 0 7 38 448378195 448378164 3.430000e-05 60.2
35 TraesCS5B01G483100 chr2D 100.000 32 0 0 7 38 541070396 541070427 3.430000e-05 60.2
36 TraesCS5B01G483100 chr1B 97.143 35 1 0 4 38 562893904 562893938 3.430000e-05 60.2


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 TraesCS5B01G483100 chr5B 655128261 655131440 3179 False 5873.0 5873 100.0000 1 3180 1 chr5B.!!$F1 3179
1 TraesCS5B01G483100 chr4B 467801702 467805004 3302 False 1953.0 4000 96.7580 34 3180 3 chr4B.!!$F1 3146
2 TraesCS5B01G483100 chr4B 530201701 530203596 1895 True 1139.0 1620 92.7185 880 3180 2 chr4B.!!$R1 2300
3 TraesCS5B01G483100 chr2A 596257790 596260878 3088 True 1805.0 3783 95.1490 36 3180 3 chr2A.!!$R1 3144
4 TraesCS5B01G483100 chr7B 3898407 3900646 2239 True 1771.5 2087 95.8100 880 3180 2 chr7B.!!$R3 2300
5 TraesCS5B01G483100 chr7B 12727731 12728930 1199 True 1615.0 1615 90.8350 191 1417 1 chr7B.!!$R1 1226
6 TraesCS5B01G483100 chr5A 352404498 352406532 2034 True 1814.0 2030 96.0400 1099 3180 2 chr5A.!!$R2 2081
7 TraesCS5B01G483100 chr5A 559461042 559463184 2142 True 1794.5 1991 94.6445 974 3180 2 chr5A.!!$R3 2206
8 TraesCS5B01G483100 chr6B 184668352 184670490 2138 True 1761.5 1984 94.1015 979 3178 2 chr6B.!!$R1 2199
9 TraesCS5B01G483100 chr3B 252334001 252335422 1421 False 1984.0 1984 92.1510 955 2353 1 chr3B.!!$F1 1398
10 TraesCS5B01G483100 chr2B 464453345 464454486 1141 False 1905.0 1905 96.7630 2039 3180 1 chr2B.!!$F3 1141
11 TraesCS5B01G483100 chr2B 464443552 464444613 1061 False 1450.0 1450 91.2640 971 2043 1 chr2B.!!$F2 1072
12 TraesCS5B01G483100 chr7D 70156603 70157828 1225 True 1711.0 1711 91.9870 191 1417 1 chr7D.!!$R1 1226
13 TraesCS5B01G483100 chr7D 70044490 70045714 1224 False 1694.0 1694 91.7400 191 1417 1 chr7D.!!$F1 1226
14 TraesCS5B01G483100 chr3D 92510188 92511138 950 False 1507.0 1507 95.3780 2235 3180 1 chr3D.!!$F1 945
15 TraesCS5B01G483100 chr7A 164104191 164105394 1203 True 781.5 968 90.2755 1092 2353 2 chr7A.!!$R1 1261

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
677 691 0.908198 GAGAGACAGGGTTGGATGCT 59.092 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 2665 3.152341 AGTCAGCCAAATGTTTCAGAGG 58.848 45.455 0.0 0.0 0.0 3.69 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
20 21 3.632420 ATATAGTCCCTCCGGTCCTTT 57.368 47.619 0.00 0.0 0.00 3.11
21 22 2.265526 ATAGTCCCTCCGGTCCTTTT 57.734 50.000 0.00 0.0 0.00 2.27
22 23 2.034436 TAGTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.0 0.00 1.94
23 24 2.034436 AGTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.0 0.00 1.52
24 25 1.627329 AGTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.0 0.00 2.01
25 26 1.627329 GTCCCTCCGGTCCTTTTTACT 59.373 52.381 0.00 0.0 0.00 2.24
26 27 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.0 0.00 2.59
27 28 1.065636 CCCTCCGGTCCTTTTTACTCC 60.066 57.143 0.00 0.0 0.00 3.85
28 29 1.405121 CCTCCGGTCCTTTTTACTCCG 60.405 57.143 0.00 0.0 40.72 4.63
29 30 1.274447 CTCCGGTCCTTTTTACTCCGT 59.726 52.381 0.00 0.0 39.62 4.69
30 31 1.001181 TCCGGTCCTTTTTACTCCGTG 59.999 52.381 0.00 0.0 39.62 4.94
31 32 1.270465 CCGGTCCTTTTTACTCCGTGT 60.270 52.381 0.00 0.0 39.62 4.49
32 33 2.029110 CCGGTCCTTTTTACTCCGTGTA 60.029 50.000 0.00 0.0 39.62 2.90
159 167 1.414158 CCCAAATCGCCCTCTCTCTA 58.586 55.000 0.00 0.0 0.00 2.43
183 191 2.548904 CTCTATCTAGGGGAACGACACG 59.451 54.545 0.00 0.0 0.00 4.49
187 196 1.228521 TAGGGGAACGACACGTCCA 60.229 57.895 0.00 0.0 39.99 4.02
200 209 2.041819 GTCCACGATCCCCTCCCT 60.042 66.667 0.00 0.0 0.00 4.20
342 351 3.692772 GCAAATCTAGGGAGGGAGAGAGA 60.693 52.174 0.00 0.0 0.00 3.10
677 691 0.908198 GAGAGACAGGGTTGGATGCT 59.092 55.000 0.00 0.0 0.00 3.79
685 699 1.074775 GGTTGGATGCTGGTGTGGA 59.925 57.895 0.00 0.0 0.00 4.02
823 837 9.066892 ACAGAGATGTGAGAAAGAGAGATATAC 57.933 37.037 0.00 0.0 0.00 1.47
824 838 9.288576 CAGAGATGTGAGAAAGAGAGATATACT 57.711 37.037 0.00 0.0 0.00 2.12
825 839 9.507329 AGAGATGTGAGAAAGAGAGATATACTC 57.493 37.037 0.00 0.0 45.22 2.59
1483 1533 2.507407 TAGGAACCAAAGTGGGATGC 57.493 50.000 0.00 0.0 43.37 3.91
1486 1536 1.560505 GAACCAAAGTGGGATGCCAT 58.439 50.000 10.01 0.0 43.37 4.40
1548 1599 7.920151 CCTGTTTTGTTCATATCTTTGTTGTGA 59.080 33.333 0.00 0.0 0.00 3.58
1583 1634 8.936070 TGTATTAATGTAGCTATGTCAAACGT 57.064 30.769 0.00 0.0 0.00 3.99
1864 1916 6.183360 CCAGTACAGGTAATAGTAGTGCCATT 60.183 42.308 7.49 0.0 39.29 3.16
1949 2001 4.583907 TGATTGCAATGGACAAACAGAGAA 59.416 37.500 18.59 0.0 0.00 2.87
1978 2030 8.850007 AAGATAGGTTGGTAGAAGAAAGAAAC 57.150 34.615 0.00 0.0 0.00 2.78
2155 2211 4.792513 AAGGAAGAGCCAGATCATCAAT 57.207 40.909 0.00 0.0 40.02 2.57
2253 2309 9.419297 TGAAATGTGTCTTGTAATCTGTACTAC 57.581 33.333 0.00 0.0 0.00 2.73
2293 2351 7.031372 CCATTTGGATGAAATGTGTCTTGTAG 58.969 38.462 0.00 0.0 46.70 2.74
2688 2948 1.030488 CGCCTCTCGGTGAGAAGGTA 61.030 60.000 8.57 0.0 45.39 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.274447 ACGGAGTAAAAAGGACCGGAG 59.726 52.381 9.46 0.00 46.45 4.63
10 11 1.001181 CACGGAGTAAAAAGGACCGGA 59.999 52.381 9.46 0.00 46.45 5.14
11 12 1.270465 ACACGGAGTAAAAAGGACCGG 60.270 52.381 0.00 0.00 46.45 5.28
12 13 2.159327 ACACGGAGTAAAAAGGACCG 57.841 50.000 0.00 0.00 41.61 4.79
13 14 6.633856 TCTAATACACGGAGTAAAAAGGACC 58.366 40.000 0.00 0.00 41.61 4.46
14 15 6.255237 GCTCTAATACACGGAGTAAAAAGGAC 59.745 42.308 0.00 0.00 41.61 3.85
15 16 6.071221 TGCTCTAATACACGGAGTAAAAAGGA 60.071 38.462 0.00 0.00 41.61 3.36
16 17 6.103997 TGCTCTAATACACGGAGTAAAAAGG 58.896 40.000 0.00 0.00 41.61 3.11
17 18 7.331193 ACTTGCTCTAATACACGGAGTAAAAAG 59.669 37.037 0.00 0.00 41.61 2.27
18 19 7.156673 ACTTGCTCTAATACACGGAGTAAAAA 58.843 34.615 0.00 0.00 41.61 1.94
19 20 6.694447 ACTTGCTCTAATACACGGAGTAAAA 58.306 36.000 0.00 0.00 41.61 1.52
20 21 6.276832 ACTTGCTCTAATACACGGAGTAAA 57.723 37.500 0.00 0.00 41.61 2.01
21 22 5.163581 GGACTTGCTCTAATACACGGAGTAA 60.164 44.000 0.00 0.00 41.61 2.24
22 23 4.337555 GGACTTGCTCTAATACACGGAGTA 59.662 45.833 0.00 0.00 41.61 2.59
24 25 3.130516 TGGACTTGCTCTAATACACGGAG 59.869 47.826 0.00 0.00 0.00 4.63
25 26 3.093814 TGGACTTGCTCTAATACACGGA 58.906 45.455 0.00 0.00 0.00 4.69
26 27 3.448686 CTGGACTTGCTCTAATACACGG 58.551 50.000 0.00 0.00 0.00 4.94
27 28 2.860735 GCTGGACTTGCTCTAATACACG 59.139 50.000 0.00 0.00 0.00 4.49
28 29 3.861840 TGCTGGACTTGCTCTAATACAC 58.138 45.455 0.00 0.00 0.00 2.90
29 30 3.679917 GCTGCTGGACTTGCTCTAATACA 60.680 47.826 0.00 0.00 0.00 2.29
30 31 2.869192 GCTGCTGGACTTGCTCTAATAC 59.131 50.000 0.00 0.00 0.00 1.89
31 32 2.481969 CGCTGCTGGACTTGCTCTAATA 60.482 50.000 0.00 0.00 0.00 0.98
32 33 1.741732 CGCTGCTGGACTTGCTCTAAT 60.742 52.381 0.00 0.00 0.00 1.73
181 189 2.758737 GGAGGGGATCGTGGACGT 60.759 66.667 0.00 0.00 40.80 4.34
182 190 3.537874 GGGAGGGGATCGTGGACG 61.538 72.222 0.00 0.00 41.45 4.79
183 191 2.041819 AGGGAGGGGATCGTGGAC 60.042 66.667 0.00 0.00 0.00 4.02
187 196 1.075896 GAGTCAGGGAGGGGATCGT 60.076 63.158 0.00 0.00 0.00 3.73
200 209 3.695606 GCCTCCACCAGCGAGTCA 61.696 66.667 0.00 0.00 0.00 3.41
278 287 7.095481 TGAGAGAAAATCAGTGAATGAACGAAG 60.095 37.037 0.00 0.00 42.53 3.79
602 614 0.121197 TCCCTTCAATCCCCTCCAGT 59.879 55.000 0.00 0.00 0.00 4.00
677 691 1.480212 CCACTAGCCAGTCCACACCA 61.480 60.000 0.00 0.00 30.46 4.17
685 699 1.543429 GCAACAACTCCACTAGCCAGT 60.543 52.381 0.00 0.00 34.42 4.00
914 928 6.525976 CAGTAGCAAAAATTTCTAGCAAGCTC 59.474 38.462 0.00 0.00 0.00 4.09
1580 1631 3.440173 CCATTGGCATAGAGAACAAACGT 59.560 43.478 0.00 0.00 0.00 3.99
1583 1634 4.943705 GTCTCCATTGGCATAGAGAACAAA 59.056 41.667 11.72 0.00 37.14 2.83
1864 1916 4.231658 TCCAAGATACCCCCAAATGATTCA 59.768 41.667 0.00 0.00 0.00 2.57
1949 2001 8.881262 TCTTTCTTCTACCAACCTATCTTCTTT 58.119 33.333 0.00 0.00 0.00 2.52
2002 2056 9.036671 CGTATCTTTTCTTCTTCTAATTCCCTC 57.963 37.037 0.00 0.00 0.00 4.30
2003 2057 8.759782 TCGTATCTTTTCTTCTTCTAATTCCCT 58.240 33.333 0.00 0.00 0.00 4.20
2004 2058 8.943909 TCGTATCTTTTCTTCTTCTAATTCCC 57.056 34.615 0.00 0.00 0.00 3.97
2060 2116 5.481473 TCATTATTTTGCTTTCTTCAGCCCT 59.519 36.000 0.00 0.00 39.25 5.19
2225 2281 9.507329 AGTACAGATTACAAGACACATTTCATT 57.493 29.630 0.00 0.00 0.00 2.57
2227 2283 9.419297 GTAGTACAGATTACAAGACACATTTCA 57.581 33.333 0.00 0.00 0.00 2.69
2228 2284 9.640963 AGTAGTACAGATTACAAGACACATTTC 57.359 33.333 2.52 0.00 0.00 2.17
2229 2285 9.998106 AAGTAGTACAGATTACAAGACACATTT 57.002 29.630 2.52 0.00 0.00 2.32
2253 2309 9.056005 TCATCCAAATGGTTCGAAGATAATAAG 57.944 33.333 0.00 0.00 32.10 1.73
2293 2351 9.662545 GGTTCGAAGATAATAAGTAGTACAGAC 57.337 37.037 0.00 0.00 35.04 3.51
2405 2665 3.152341 AGTCAGCCAAATGTTTCAGAGG 58.848 45.455 0.00 0.00 0.00 3.69
2688 2948 5.598830 ACGATAACATGGGAGAACTAGTGAT 59.401 40.000 0.00 0.00 0.00 3.06
3031 3292 0.610232 AGTTGAAGGGCATGCTCCAC 60.610 55.000 15.67 9.39 0.00 4.02


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

AutoCloner maintained by Alex Coulton.