Multiple sequence alignment - TraesCS7D01G440900

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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 TraesCS7D01G440900 chr7D 100.000 2753 0 0 1 2753 560681995 560684747 0.000000e+00 5084.0
1 TraesCS7D01G440900 chr7D 99.456 2207 5 6 1 2204 560700960 560703162 0.000000e+00 4002.0
2 TraesCS7D01G440900 chr7D 87.315 1348 112 34 615 1928 560596889 560598211 0.000000e+00 1487.0
3 TraesCS7D01G440900 chr7D 85.651 1352 126 42 619 1926 560602774 560604101 0.000000e+00 1360.0
4 TraesCS7D01G440900 chr7D 96.805 626 14 1 2134 2753 560674318 560674943 0.000000e+00 1040.0
5 TraesCS7D01G440900 chr7D 86.875 640 60 16 1306 1926 560590253 560590887 0.000000e+00 695.0
6 TraesCS7D01G440900 chr7D 100.000 152 0 0 2602 2753 560710548 560710699 5.800000e-72 281.0
7 TraesCS7D01G440900 chr7D 78.697 399 70 9 142 530 560596423 560596816 4.550000e-63 252.0
8 TraesCS7D01G440900 chr7B 93.574 1494 77 12 615 2102 608414750 608416230 0.000000e+00 2209.0
9 TraesCS7D01G440900 chr7B 83.494 1969 217 60 19 1926 608391322 608393243 0.000000e+00 1736.0
10 TraesCS7D01G440900 chr7B 84.765 1385 129 48 619 1966 608404960 608406299 0.000000e+00 1314.0
11 TraesCS7D01G440900 chr7B 87.407 1072 98 21 873 1926 608379924 608380976 0.000000e+00 1197.0
12 TraesCS7D01G440900 chr7B 93.617 564 27 3 2198 2753 608475028 608475590 0.000000e+00 833.0
13 TraesCS7D01G440900 chr7B 85.000 420 49 10 150 563 608410655 608411066 5.490000e-112 414.0
14 TraesCS7D01G440900 chr7B 97.368 38 1 0 577 614 608414697 608414734 6.360000e-07 65.8
15 TraesCS7D01G440900 chr7A 95.224 1361 52 10 670 2027 644784894 644786244 0.000000e+00 2141.0
16 TraesCS7D01G440900 chr7A 84.263 1989 199 61 1 1926 644721041 644722978 0.000000e+00 1834.0
17 TraesCS7D01G440900 chr7A 88.253 1311 100 27 635 1912 644734764 644736053 0.000000e+00 1519.0
18 TraesCS7D01G440900 chr7A 85.322 1349 131 39 619 1926 644768291 644769613 0.000000e+00 1332.0
19 TraesCS7D01G440900 chr7A 84.734 1166 109 34 619 1776 644710253 644711357 0.000000e+00 1103.0
20 TraesCS7D01G440900 chr7A 94.830 677 29 5 2 674 644779029 644779703 0.000000e+00 1051.0
21 TraesCS7D01G440900 chr7A 88.235 459 35 10 2198 2647 644854875 644855323 5.220000e-147 531.0
22 TraesCS7D01G440900 chr7A 82.324 611 75 19 17 614 644727209 644727799 1.470000e-137 499.0
23 TraesCS7D01G440900 chr7A 94.949 99 4 1 2109 2207 419932559 419932462 1.320000e-33 154.0
24 TraesCS7D01G440900 chr6A 82.410 415 48 19 2356 2753 39148198 39148604 3.400000e-89 339.0
25 TraesCS7D01G440900 chr6A 90.000 110 9 2 2098 2207 78477071 78477178 1.030000e-29 141.0
26 TraesCS7D01G440900 chr4D 90.179 112 9 2 2096 2207 426842881 426842772 7.950000e-31 145.0
27 TraesCS7D01G440900 chr2D 93.000 100 6 1 2108 2207 106145485 106145583 7.950000e-31 145.0
28 TraesCS7D01G440900 chr2D 89.474 114 7 4 2097 2207 114647849 114647960 3.700000e-29 139.0
29 TraesCS7D01G440900 chr1D 89.286 112 10 2 2097 2207 318585939 318585829 3.700000e-29 139.0
30 TraesCS7D01G440900 chr5D 88.696 115 9 3 2096 2207 497870839 497870952 1.330000e-28 137.0


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 TraesCS7D01G440900 chr7D 560681995 560684747 2752 False 5084.000000 5084 100.000000 1 2753 1 chr7D.!!$F4 2752
1 TraesCS7D01G440900 chr7D 560700960 560703162 2202 False 4002.000000 4002 99.456000 1 2204 1 chr7D.!!$F5 2203
2 TraesCS7D01G440900 chr7D 560602774 560604101 1327 False 1360.000000 1360 85.651000 619 1926 1 chr7D.!!$F2 1307
3 TraesCS7D01G440900 chr7D 560674318 560674943 625 False 1040.000000 1040 96.805000 2134 2753 1 chr7D.!!$F3 619
4 TraesCS7D01G440900 chr7D 560596423 560598211 1788 False 869.500000 1487 83.006000 142 1928 2 chr7D.!!$F7 1786
5 TraesCS7D01G440900 chr7D 560590253 560590887 634 False 695.000000 695 86.875000 1306 1926 1 chr7D.!!$F1 620
6 TraesCS7D01G440900 chr7B 608391322 608393243 1921 False 1736.000000 1736 83.494000 19 1926 1 chr7B.!!$F2 1907
7 TraesCS7D01G440900 chr7B 608404960 608406299 1339 False 1314.000000 1314 84.765000 619 1966 1 chr7B.!!$F3 1347
8 TraesCS7D01G440900 chr7B 608379924 608380976 1052 False 1197.000000 1197 87.407000 873 1926 1 chr7B.!!$F1 1053
9 TraesCS7D01G440900 chr7B 608410655 608416230 5575 False 896.266667 2209 91.980667 150 2102 3 chr7B.!!$F5 1952
10 TraesCS7D01G440900 chr7B 608475028 608475590 562 False 833.000000 833 93.617000 2198 2753 1 chr7B.!!$F4 555
11 TraesCS7D01G440900 chr7A 644784894 644786244 1350 False 2141.000000 2141 95.224000 670 2027 1 chr7A.!!$F7 1357
12 TraesCS7D01G440900 chr7A 644721041 644722978 1937 False 1834.000000 1834 84.263000 1 1926 1 chr7A.!!$F2 1925
13 TraesCS7D01G440900 chr7A 644734764 644736053 1289 False 1519.000000 1519 88.253000 635 1912 1 chr7A.!!$F4 1277
14 TraesCS7D01G440900 chr7A 644768291 644769613 1322 False 1332.000000 1332 85.322000 619 1926 1 chr7A.!!$F5 1307
15 TraesCS7D01G440900 chr7A 644710253 644711357 1104 False 1103.000000 1103 84.734000 619 1776 1 chr7A.!!$F1 1157
16 TraesCS7D01G440900 chr7A 644779029 644779703 674 False 1051.000000 1051 94.830000 2 674 1 chr7A.!!$F6 672
17 TraesCS7D01G440900 chr7A 644727209 644727799 590 False 499.000000 499 82.324000 17 614 1 chr7A.!!$F3 597

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
1428 5205 2.34749 CTCAACCCTCCCCACACG 59.653 66.667 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 6375 4.389077 ACAGAAGAAATTAAGCGAACCTCG 59.611 41.667 0.0 0.0 43.89 4.63 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
1428 5205 2.347490 CTCAACCCTCCCCACACG 59.653 66.667 0.00 0.00 0.0 4.49
2030 5837 7.595819 TTTTGAAGGGTTATCTTGTGTGATT 57.404 32.000 0.00 0.00 0.0 2.57
2151 5959 3.301274 GGTTAGAGGGACAGTGCTATCT 58.699 50.000 5.83 5.83 0.0 1.98
2215 6023 9.532494 TTCCTGGATTATTTTTCAATTCAGAGA 57.468 29.630 0.00 0.00 40.2 3.10
2449 6265 4.992951 AGCAAGCTTTGGAATCAAAATCAC 59.007 37.500 0.00 0.00 41.7 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2172 5980 1.334869 GGAATAATGCGAGCAACAGGG 59.665 52.381 0.57 0.00 0.00 4.45
2215 6023 1.955778 CCGATGAGATCTGAGCTCTGT 59.044 52.381 21.98 11.85 33.57 3.41
2449 6265 7.678218 GCACATAAGCTTTCTATGAACTTCCAG 60.678 40.741 13.42 0.00 0.00 3.86
2559 6375 4.389077 ACAGAAGAAATTAAGCGAACCTCG 59.611 41.667 0.00 0.00 43.89 4.63


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

AutoCloner maintained by Alex Coulton.