Multiple sequence alignment - TraesCS7A01G324000

Loading Multiple Alignment...

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 TraesCS7A01G324000 chr7A 100.000 2378 0 0 1 2378 471264407 471262030 0.000000e+00 4392.0
1 TraesCS7A01G324000 chr7A 92.843 517 34 3 2 517 274476402 274476916 0.000000e+00 747.0
2 TraesCS7A01G324000 chr7A 92.650 517 36 2 2 517 271349303 271349818 0.000000e+00 743.0
3 TraesCS7A01G324000 chr6A 93.405 1865 113 6 518 2378 144491473 144493331 0.000000e+00 2754.0
4 TraesCS7A01G324000 chr6A 89.221 1874 134 31 518 2378 596355514 596357332 0.000000e+00 2279.0
5 TraesCS7A01G324000 chr2D 93.043 1883 108 8 517 2378 520043084 520044964 0.000000e+00 2730.0
6 TraesCS7A01G324000 chr2D 89.730 1889 130 18 522 2375 451467953 451469812 0.000000e+00 2355.0
7 TraesCS7A01G324000 chr2D 89.134 1905 158 21 516 2378 260867189 260865292 0.000000e+00 2326.0
8 TraesCS7A01G324000 chr2D 89.359 1889 136 25 518 2378 241269968 241271819 0.000000e+00 2314.0
9 TraesCS7A01G324000 chr2D 89.812 1649 120 14 507 2145 35331909 35330299 0.000000e+00 2071.0
10 TraesCS7A01G324000 chr2D 92.507 1428 105 2 515 1940 613419780 613421207 0.000000e+00 2043.0
11 TraesCS7A01G324000 chr2D 93.037 517 33 3 2 517 582729164 582728650 0.000000e+00 752.0
12 TraesCS7A01G324000 chr2D 92.471 518 34 4 2 517 36651663 36651149 0.000000e+00 736.0
13 TraesCS7A01G324000 chr2D 91.246 297 17 4 2086 2378 613421282 613421573 1.710000e-106 396.0
14 TraesCS7A01G324000 chr2D 92.017 238 15 2 2144 2378 35330344 35330108 4.900000e-87 331.0
15 TraesCS7A01G324000 chr2D 93.023 43 3 0 2144 2186 241271537 241271579 1.970000e-06 63.9
16 TraesCS7A01G324000 chr7D 90.148 1888 130 28 522 2378 151511976 151513838 0.000000e+00 2405.0
17 TraesCS7A01G324000 chr7D 92.471 518 34 4 1 517 169341892 169342405 0.000000e+00 736.0
18 TraesCS7A01G324000 chr6B 89.061 1874 160 18 515 2375 494076432 494078273 0.000000e+00 2283.0
19 TraesCS7A01G324000 chr6B 92.823 209 12 1 2171 2376 28119099 28119307 1.380000e-77 300.0
20 TraesCS7A01G324000 chr5D 89.768 1769 145 15 640 2378 26959808 26958046 0.000000e+00 2231.0
21 TraesCS7A01G324000 chr5D 92.471 518 36 3 1 517 532578595 532579110 0.000000e+00 737.0
22 TraesCS7A01G324000 chr3A 88.568 1872 146 29 519 2378 478913597 478915412 0.000000e+00 2209.0
23 TraesCS7A01G324000 chr3A 92.486 519 36 3 1 517 401570557 401571074 0.000000e+00 739.0
24 TraesCS7A01G324000 chr5B 91.387 1428 117 5 517 1940 260234931 260236356 0.000000e+00 1951.0
25 TraesCS7A01G324000 chr6D 91.374 1426 119 3 518 1940 114017560 114016136 0.000000e+00 1949.0
26 TraesCS7A01G324000 chr6D 92.471 518 36 3 1 517 88535669 88536184 0.000000e+00 737.0
27 TraesCS7A01G324000 chr2A 93.037 517 33 3 2 517 580494696 580495210 0.000000e+00 752.0


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 TraesCS7A01G324000 chr7A 471262030 471264407 2377 True 4392.00 4392 100.0000 1 2378 1 chr7A.!!$R1 2377
1 TraesCS7A01G324000 chr7A 274476402 274476916 514 False 747.00 747 92.8430 2 517 1 chr7A.!!$F2 515
2 TraesCS7A01G324000 chr7A 271349303 271349818 515 False 743.00 743 92.6500 2 517 1 chr7A.!!$F1 515
3 TraesCS7A01G324000 chr6A 144491473 144493331 1858 False 2754.00 2754 93.4050 518 2378 1 chr6A.!!$F1 1860
4 TraesCS7A01G324000 chr6A 596355514 596357332 1818 False 2279.00 2279 89.2210 518 2378 1 chr6A.!!$F2 1860
5 TraesCS7A01G324000 chr2D 520043084 520044964 1880 False 2730.00 2730 93.0430 517 2378 1 chr2D.!!$F2 1861
6 TraesCS7A01G324000 chr2D 451467953 451469812 1859 False 2355.00 2355 89.7300 522 2375 1 chr2D.!!$F1 1853
7 TraesCS7A01G324000 chr2D 260865292 260867189 1897 True 2326.00 2326 89.1340 516 2378 1 chr2D.!!$R2 1862
8 TraesCS7A01G324000 chr2D 613419780 613421573 1793 False 1219.50 2043 91.8765 515 2378 2 chr2D.!!$F4 1863
9 TraesCS7A01G324000 chr2D 35330108 35331909 1801 True 1201.00 2071 90.9145 507 2378 2 chr2D.!!$R4 1871
10 TraesCS7A01G324000 chr2D 241269968 241271819 1851 False 1188.95 2314 91.1910 518 2378 2 chr2D.!!$F3 1860
11 TraesCS7A01G324000 chr2D 582728650 582729164 514 True 752.00 752 93.0370 2 517 1 chr2D.!!$R3 515
12 TraesCS7A01G324000 chr2D 36651149 36651663 514 True 736.00 736 92.4710 2 517 1 chr2D.!!$R1 515
13 TraesCS7A01G324000 chr7D 151511976 151513838 1862 False 2405.00 2405 90.1480 522 2378 1 chr7D.!!$F1 1856
14 TraesCS7A01G324000 chr7D 169341892 169342405 513 False 736.00 736 92.4710 1 517 1 chr7D.!!$F2 516
15 TraesCS7A01G324000 chr6B 494076432 494078273 1841 False 2283.00 2283 89.0610 515 2375 1 chr6B.!!$F2 1860
16 TraesCS7A01G324000 chr5D 26958046 26959808 1762 True 2231.00 2231 89.7680 640 2378 1 chr5D.!!$R1 1738
17 TraesCS7A01G324000 chr5D 532578595 532579110 515 False 737.00 737 92.4710 1 517 1 chr5D.!!$F1 516
18 TraesCS7A01G324000 chr3A 478913597 478915412 1815 False 2209.00 2209 88.5680 519 2378 1 chr3A.!!$F2 1859
19 TraesCS7A01G324000 chr3A 401570557 401571074 517 False 739.00 739 92.4860 1 517 1 chr3A.!!$F1 516
20 TraesCS7A01G324000 chr5B 260234931 260236356 1425 False 1951.00 1951 91.3870 517 1940 1 chr5B.!!$F1 1423
21 TraesCS7A01G324000 chr6D 114016136 114017560 1424 True 1949.00 1949 91.3740 518 1940 1 chr6D.!!$R1 1422
22 TraesCS7A01G324000 chr6D 88535669 88536184 515 False 737.00 737 92.4710 1 517 1 chr6D.!!$F1 516
23 TraesCS7A01G324000 chr2A 580494696 580495210 514 False 752.00 752 93.0370 2 517 1 chr2A.!!$F1 515

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
429 437 0.100325 TGGCGTGAGTTGCAAAACTG 59.900 50.0 0.0 0.0 32.22 3.16 F
778 812 0.409484 CCCCACTTCCCAGTCCAAAT 59.591 55.0 0.0 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1285 0.028770 TTCTGCACCAACGCGAAAAG 59.971 50.0 15.93 0.03 33.35 2.27 R
1726 1763 1.033746 CCGTCAATCTTGCCCAGCAT 61.034 55.0 0.00 0.00 38.76 3.79 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
68 72 7.895759 TCTTAGCAACAAATTATCTTGCCTTT 58.104 30.769 9.78 0.00 41.05 3.11
69 73 8.028938 TCTTAGCAACAAATTATCTTGCCTTTC 58.971 33.333 9.78 0.00 41.05 2.62
191 196 1.173043 TAAGCATCGCAACCCCAAAG 58.827 50.000 0.00 0.00 0.00 2.77
205 210 5.700722 ACCCCAAAGTTTAAGAAACGATC 57.299 39.130 0.00 0.00 45.88 3.69
209 214 5.080068 CCAAAGTTTAAGAAACGATCGCTC 58.920 41.667 16.60 12.32 45.88 5.03
237 242 6.554334 TTCTTGCTAAACCACACTTCATAC 57.446 37.500 0.00 0.00 0.00 2.39
398 405 1.794222 GGACACACCATTACGCTGC 59.206 57.895 0.00 0.00 38.79 5.25
429 437 0.100325 TGGCGTGAGTTGCAAAACTG 59.900 50.000 0.00 0.00 32.22 3.16
493 501 7.809880 AATATTCTCCTCCATGATCAGATCA 57.190 36.000 15.69 15.69 44.55 2.92
586 594 3.726859 ACCCCCTGATCTATATTTTGGCA 59.273 43.478 0.00 0.00 0.00 4.92
633 653 1.452801 GGACAAAACACCTCCCGGA 59.547 57.895 0.73 0.00 0.00 5.14
635 655 1.279846 GGACAAAACACCTCCCGGATA 59.720 52.381 0.73 0.00 0.00 2.59
776 810 2.160171 CCCCCACTTCCCAGTCCAA 61.160 63.158 0.00 0.00 0.00 3.53
777 811 1.725169 CCCCCACTTCCCAGTCCAAA 61.725 60.000 0.00 0.00 0.00 3.28
778 812 0.409484 CCCCACTTCCCAGTCCAAAT 59.591 55.000 0.00 0.00 0.00 2.32
779 813 1.616994 CCCCACTTCCCAGTCCAAATC 60.617 57.143 0.00 0.00 0.00 2.17
780 814 1.616994 CCCACTTCCCAGTCCAAATCC 60.617 57.143 0.00 0.00 0.00 3.01
781 815 1.616994 CCACTTCCCAGTCCAAATCCC 60.617 57.143 0.00 0.00 0.00 3.85
782 816 1.355720 CACTTCCCAGTCCAAATCCCT 59.644 52.381 0.00 0.00 0.00 4.20
783 817 2.576191 CACTTCCCAGTCCAAATCCCTA 59.424 50.000 0.00 0.00 0.00 3.53
784 818 3.010138 CACTTCCCAGTCCAAATCCCTAA 59.990 47.826 0.00 0.00 0.00 2.69
785 819 3.660669 ACTTCCCAGTCCAAATCCCTAAA 59.339 43.478 0.00 0.00 0.00 1.85
786 820 3.732048 TCCCAGTCCAAATCCCTAAAC 57.268 47.619 0.00 0.00 0.00 2.01
787 821 2.310647 TCCCAGTCCAAATCCCTAAACC 59.689 50.000 0.00 0.00 0.00 3.27
788 822 2.311841 CCCAGTCCAAATCCCTAAACCT 59.688 50.000 0.00 0.00 0.00 3.50
789 823 3.526019 CCCAGTCCAAATCCCTAAACCTA 59.474 47.826 0.00 0.00 0.00 3.08
801 835 3.980698 CCCTAAACCTATTCTCCATGGGA 59.019 47.826 13.02 5.29 36.97 4.37
849 883 4.379243 CCGGACGCCTTGAGCACT 62.379 66.667 0.00 0.00 44.04 4.40
1007 1041 2.591753 CACTCCGGCCATGGATGT 59.408 61.111 18.40 2.74 37.41 3.06
1051 1085 1.604755 ACGTGCTTTTGGTAATTGCGA 59.395 42.857 0.00 0.00 0.00 5.10
1059 1093 2.971660 TGGTAATTGCGATCGGAGAA 57.028 45.000 18.30 0.00 43.58 2.87
1167 1201 2.524640 TGCCCACCACACGACCTA 60.525 61.111 0.00 0.00 0.00 3.08
1191 1225 1.827969 CTGACCTTCTCAACGGAGGAT 59.172 52.381 0.00 0.00 41.69 3.24
1251 1285 0.110373 GTTGTCGGCGTTGGATTCAC 60.110 55.000 6.85 0.00 0.00 3.18
1375 1409 4.058817 GTCCGTGAAAGATGTTCTCAAGT 58.941 43.478 0.00 0.00 0.00 3.16
1378 1412 4.627467 CCGTGAAAGATGTTCTCAAGTAGG 59.373 45.833 0.00 0.00 0.00 3.18
1452 1486 0.107897 TAATGGCGTGGCTTCGTGAT 60.108 50.000 0.00 0.00 0.00 3.06
1462 1496 1.131315 GGCTTCGTGATCCTTGCTTTC 59.869 52.381 0.00 0.00 0.00 2.62
1478 1512 2.031120 CTTTCTTGGCAAGGTGGTGAA 58.969 47.619 25.92 10.05 0.00 3.18
1579 1615 0.674581 TGACTACGGACCATCGTCGT 60.675 55.000 0.00 0.00 42.82 4.34
1596 1632 3.576648 GTCGTCGAGGAAGAAGAACAAT 58.423 45.455 9.78 0.00 31.00 2.71
1601 1637 5.163982 CGTCGAGGAAGAAGAACAATTTACC 60.164 44.000 0.00 0.00 0.00 2.85
1639 1675 3.118775 CCACATGAAGGAGGTTGTCGATA 60.119 47.826 0.00 0.00 0.00 2.92
1648 1684 2.496470 GAGGTTGTCGATAGTGGTCCTT 59.504 50.000 0.00 0.00 37.40 3.36
1710 1746 1.367471 CAAGGACCTGACTCGCACA 59.633 57.895 0.00 0.00 0.00 4.57
1726 1763 5.125578 ACTCGCACACATATCTTCAAGACTA 59.874 40.000 0.00 0.00 0.00 2.59
1740 1777 3.054139 TCAAGACTATGCTGGGCAAGATT 60.054 43.478 0.00 0.00 43.62 2.40
1811 1866 3.333804 CACTTTGGCACTTGGTTTGTTT 58.666 40.909 0.00 0.00 0.00 2.83
1936 2005 6.922247 TGTGCCAAAATTATGCCAAATATG 57.078 33.333 0.00 0.00 0.00 1.78
1964 2093 8.995220 GTTGGTACTATGTTGTCTTGTGAAATA 58.005 33.333 0.00 0.00 0.00 1.40
2121 2266 6.082338 CACAAATTCTGCAGCTTAACAGTAG 58.918 40.000 9.47 0.00 35.37 2.57
2122 2267 5.182001 ACAAATTCTGCAGCTTAACAGTAGG 59.818 40.000 9.47 0.00 35.37 3.18
2123 2268 4.826274 ATTCTGCAGCTTAACAGTAGGA 57.174 40.909 9.47 0.00 35.37 2.94
2124 2269 4.617253 TTCTGCAGCTTAACAGTAGGAA 57.383 40.909 9.47 0.00 35.37 3.36
2134 2293 5.969435 GCTTAACAGTAGGAAACAAACACAC 59.031 40.000 0.00 0.00 0.00 3.82
2147 2306 4.799678 ACAAACACACGTTCATCAAACAA 58.200 34.783 0.00 0.00 37.77 2.83
2293 2468 5.193099 ACATGCTAACCCTGGTAGATTTT 57.807 39.130 0.00 0.00 0.00 1.82
2311 2486 9.131791 GTAGATTTTCTCCTTCTCTGACTAGAT 57.868 37.037 0.00 0.00 31.21 1.98
2337 2515 1.750778 ACCAGGTGTTCTGTTTGCTTG 59.249 47.619 0.00 0.00 41.83 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 61 8.581253 TCTATCATAGATCGAAAGGCAAGATA 57.419 34.615 0.00 0.00 0.00 1.98
58 62 7.473735 TCTATCATAGATCGAAAGGCAAGAT 57.526 36.000 0.00 0.00 0.00 2.40
59 63 6.901081 TCTATCATAGATCGAAAGGCAAGA 57.099 37.500 0.00 0.00 0.00 3.02
68 72 5.944599 GGGTACACCTTCTATCATAGATCGA 59.055 44.000 0.00 0.00 34.22 3.59
69 73 5.710567 TGGGTACACCTTCTATCATAGATCG 59.289 44.000 0.00 0.00 41.11 3.69
183 188 4.214758 CGATCGTTTCTTAAACTTTGGGGT 59.785 41.667 7.03 0.00 39.23 4.95
191 196 3.678548 ACCTGAGCGATCGTTTCTTAAAC 59.321 43.478 17.81 0.00 38.02 2.01
205 210 3.188895 GTTTAGCAAGAAACCTGAGCG 57.811 47.619 0.00 0.00 33.93 5.03
302 307 5.622770 ATTTGTCACTATCGTTTTGGGTC 57.377 39.130 0.00 0.00 0.00 4.46
320 327 8.706936 CAATCTATGATGTCTCTTACCGATTTG 58.293 37.037 0.00 0.00 0.00 2.32
398 405 1.736645 CACGCCACCTAGAACACCG 60.737 63.158 0.00 0.00 0.00 4.94
429 437 4.981674 TCTTCATTTGAAACAATGCGGAAC 59.018 37.500 0.00 0.00 33.07 3.62
586 594 3.673543 TTTGTTTGGGGTGTAGAAGGT 57.326 42.857 0.00 0.00 0.00 3.50
716 736 3.961408 ACAGGGAACGACAGCTCTATAAT 59.039 43.478 0.00 0.00 0.00 1.28
776 810 5.075067 CCCATGGAGAATAGGTTTAGGGATT 59.925 44.000 15.22 0.00 34.49 3.01
777 811 4.603610 CCCATGGAGAATAGGTTTAGGGAT 59.396 45.833 15.22 0.00 34.49 3.85
778 812 3.980698 CCCATGGAGAATAGGTTTAGGGA 59.019 47.826 15.22 0.00 34.49 4.20
779 813 3.980698 TCCCATGGAGAATAGGTTTAGGG 59.019 47.826 15.22 0.00 0.00 3.53
926 960 4.351054 CCAGCCACCACACCTCCC 62.351 72.222 0.00 0.00 0.00 4.30
1024 1058 2.255172 CCAAAAGCACGTACCGCCA 61.255 57.895 0.00 0.00 0.00 5.69
1039 1073 2.971660 TCTCCGATCGCAATTACCAA 57.028 45.000 10.32 0.00 0.00 3.67
1043 1077 1.865865 GCCTTCTCCGATCGCAATTA 58.134 50.000 10.32 0.00 0.00 1.40
1046 1080 2.202743 CGCCTTCTCCGATCGCAA 60.203 61.111 10.32 0.80 0.00 4.85
1051 1085 1.754621 TCTGCTCGCCTTCTCCGAT 60.755 57.895 0.00 0.00 33.83 4.18
1059 1093 2.653702 GTCACTGTCTGCTCGCCT 59.346 61.111 0.00 0.00 0.00 5.52
1167 1201 0.036010 CCGTTGAGAAGGTCAGCCAT 60.036 55.000 0.00 0.00 36.21 4.40
1191 1225 0.898320 GGAGCACCTCAGAGCACTTA 59.102 55.000 0.00 0.00 31.08 2.24
1251 1285 0.028770 TTCTGCACCAACGCGAAAAG 59.971 50.000 15.93 0.03 33.35 2.27
1375 1409 3.390521 CAGCTCGCCACCCACCTA 61.391 66.667 0.00 0.00 0.00 3.08
1378 1412 2.512515 GATCAGCTCGCCACCCAC 60.513 66.667 0.00 0.00 0.00 4.61
1462 1496 1.067516 CACTTTCACCACCTTGCCAAG 59.932 52.381 0.00 0.00 0.00 3.61
1478 1512 4.098196 GCTTCGACTTAGGTATCTCCACTT 59.902 45.833 0.00 0.00 39.02 3.16
1579 1615 5.860611 TGGTAAATTGTTCTTCTTCCTCGA 58.139 37.500 0.00 0.00 0.00 4.04
1596 1632 7.293828 TGTGGCAAATGATAGGATATGGTAAA 58.706 34.615 0.00 0.00 0.00 2.01
1601 1637 7.362660 CCTTCATGTGGCAAATGATAGGATATG 60.363 40.741 27.56 8.52 36.00 1.78
1639 1675 2.435372 TCAACAAGCAAAGGACCACT 57.565 45.000 0.00 0.00 0.00 4.00
1648 1684 3.857157 AGGTAGTCCTTCAACAAGCAA 57.143 42.857 0.00 0.00 42.12 3.91
1669 1705 1.203441 TCTCCTGGCAGCCACTCATT 61.203 55.000 11.22 0.00 0.00 2.57
1710 1746 5.744300 GCCCAGCATAGTCTTGAAGATATGT 60.744 44.000 17.66 8.59 0.00 2.29
1726 1763 1.033746 CCGTCAATCTTGCCCAGCAT 61.034 55.000 0.00 0.00 38.76 3.79
1936 2005 5.756347 TCACAAGACAACATAGTACCAACAC 59.244 40.000 0.00 0.00 0.00 3.32
1964 2093 5.220710 ACAGAGAAGCTCACAATTGTACT 57.779 39.130 11.53 6.45 32.06 2.73
2121 2266 4.022464 TGATGAACGTGTGTTTGTTTCC 57.978 40.909 0.00 0.00 38.78 3.13
2122 2267 5.343593 TGTTTGATGAACGTGTGTTTGTTTC 59.656 36.000 0.00 0.00 41.29 2.78
2123 2268 5.223382 TGTTTGATGAACGTGTGTTTGTTT 58.777 33.333 0.00 0.00 41.29 2.83
2124 2269 4.799678 TGTTTGATGAACGTGTGTTTGTT 58.200 34.783 0.00 0.00 41.29 2.83
2134 2293 5.214417 TGCAGAATCTTTGTTTGATGAACG 58.786 37.500 0.00 0.00 41.29 3.95
2147 2306 5.997746 TGTTACTGTTAAGCTGCAGAATCTT 59.002 36.000 20.43 13.88 36.62 2.40
2203 2377 6.068670 AGCCTTCAAATTGTTAGTAGGTTGT 58.931 36.000 0.00 0.00 0.00 3.32
2293 2468 5.368230 TGCTAGATCTAGTCAGAGAAGGAGA 59.632 44.000 26.73 1.90 35.65 3.71
2311 2486 2.438021 AAACAGAACACCTGGTGCTAGA 59.562 45.455 26.20 0.00 43.32 2.43


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

AutoCloner maintained by Alex Coulton.