Multiple sequence alignment - TraesCS7B01G091300

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 TraesCS7B01G091300 chr7B 100.000 2237 0 0 1 2237 105238616 105236380 0.000000e+00 4132
1 TraesCS7B01G091300 chr7B 96.609 1563 50 3 1 1560 622431954 622430392 0.000000e+00 2590
2 TraesCS7B01G091300 chr7B 96.481 1563 52 3 1 1560 662732928 662734490 0.000000e+00 2579
3 TraesCS7B01G091300 chr2A 96.673 1563 49 3 1 1560 543187675 543189237 0.000000e+00 2595
4 TraesCS7B01G091300 chr2A 95.029 1569 57 7 1 1560 394048781 394050337 0.000000e+00 2446
5 TraesCS7B01G091300 chr6B 96.545 1563 49 4 1 1560 515380557 515378997 0.000000e+00 2582
6 TraesCS7B01G091300 chr3B 96.417 1563 52 4 1 1560 201549316 201550877 0.000000e+00 2573
7 TraesCS7B01G091300 chr3B 96.289 1563 55 3 1 1560 201565367 201563805 0.000000e+00 2562
8 TraesCS7B01G091300 chr3B 95.259 675 17 6 1569 2234 101914321 101914989 0.000000e+00 1055
9 TraesCS7B01G091300 chr1D 96.159 1562 58 2 1 1560 254531612 254533173 0.000000e+00 2551
10 TraesCS7B01G091300 chr1B 96.161 1563 56 4 1 1560 633733456 633731895 0.000000e+00 2551
11 TraesCS7B01G091300 chr3A 95.905 1563 61 3 1 1560 695636414 695637976 0.000000e+00 2529
12 TraesCS7B01G091300 chr3A 94.978 677 20 6 1569 2237 66014479 66013809 0.000000e+00 1050
13 TraesCS7B01G091300 chr3A 97.436 195 5 0 1366 1560 65997940 65998134 1.280000e-87 333
14 TraesCS7B01G091300 chr3A 98.726 157 2 0 1304 1460 435412836 435412680 1.690000e-71 279
15 TraesCS7B01G091300 chr4A 93.150 1562 79 14 1 1560 219344418 219342883 0.000000e+00 2266
16 TraesCS7B01G091300 chr4A 92.503 867 49 9 698 1559 310777141 310776286 0.000000e+00 1227
17 TraesCS7B01G091300 chr4A 93.322 569 23 9 1569 2129 309522053 309522614 0.000000e+00 826
18 TraesCS7B01G091300 chr5B 92.976 1566 83 13 1 1560 432872163 432873707 0.000000e+00 2257
19 TraesCS7B01G091300 chr1A 95.252 674 18 5 1569 2234 554515394 554516061 0.000000e+00 1055
20 TraesCS7B01G091300 chr2B 95.104 674 19 5 1569 2234 474911587 474912254 0.000000e+00 1050
21 TraesCS7B01G091300 chr6D 94.963 675 19 7 1569 2234 168260811 168261479 0.000000e+00 1044
22 TraesCS7B01G091300 chr5D 94.963 675 19 6 1569 2234 503221361 503222029 0.000000e+00 1044
23 TraesCS7B01G091300 chr5D 94.519 675 22 6 1569 2234 6192081 6192749 0.000000e+00 1027
24 TraesCS7B01G091300 chr5D 93.953 678 27 8 1569 2237 432400678 432400006 0.000000e+00 1013
25 TraesCS7B01G091300 chr5D 93.862 668 27 8 1569 2234 432425781 432426436 0.000000e+00 994
26 TraesCS7B01G091300 chr3D 94.838 678 20 7 1569 2237 589273814 589273143 0.000000e+00 1044
27 TraesCS7B01G091300 chr7D 95.793 523 14 4 1714 2234 231575500 231576016 0.000000e+00 837
28 TraesCS7B01G091300 chrUn 95.918 490 13 3 1746 2234 441244155 441244638 0.000000e+00 787
29 TraesCS7B01G091300 chrUn 94.311 457 11 6 1568 2015 412653703 412653253 0.000000e+00 686


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 TraesCS7B01G091300 chr7B 105236380 105238616 2236 True 4132 4132 100.000 1 2237 1 chr7B.!!$R1 2236
1 TraesCS7B01G091300 chr7B 622430392 622431954 1562 True 2590 2590 96.609 1 1560 1 chr7B.!!$R2 1559
2 TraesCS7B01G091300 chr7B 662732928 662734490 1562 False 2579 2579 96.481 1 1560 1 chr7B.!!$F1 1559
3 TraesCS7B01G091300 chr2A 543187675 543189237 1562 False 2595 2595 96.673 1 1560 1 chr2A.!!$F2 1559
4 TraesCS7B01G091300 chr2A 394048781 394050337 1556 False 2446 2446 95.029 1 1560 1 chr2A.!!$F1 1559
5 TraesCS7B01G091300 chr6B 515378997 515380557 1560 True 2582 2582 96.545 1 1560 1 chr6B.!!$R1 1559
6 TraesCS7B01G091300 chr3B 201549316 201550877 1561 False 2573 2573 96.417 1 1560 1 chr3B.!!$F2 1559
7 TraesCS7B01G091300 chr3B 201563805 201565367 1562 True 2562 2562 96.289 1 1560 1 chr3B.!!$R1 1559
8 TraesCS7B01G091300 chr3B 101914321 101914989 668 False 1055 1055 95.259 1569 2234 1 chr3B.!!$F1 665
9 TraesCS7B01G091300 chr1D 254531612 254533173 1561 False 2551 2551 96.159 1 1560 1 chr1D.!!$F1 1559
10 TraesCS7B01G091300 chr1B 633731895 633733456 1561 True 2551 2551 96.161 1 1560 1 chr1B.!!$R1 1559
11 TraesCS7B01G091300 chr3A 695636414 695637976 1562 False 2529 2529 95.905 1 1560 1 chr3A.!!$F2 1559
12 TraesCS7B01G091300 chr3A 66013809 66014479 670 True 1050 1050 94.978 1569 2237 1 chr3A.!!$R1 668
13 TraesCS7B01G091300 chr4A 219342883 219344418 1535 True 2266 2266 93.150 1 1560 1 chr4A.!!$R1 1559
14 TraesCS7B01G091300 chr4A 310776286 310777141 855 True 1227 1227 92.503 698 1559 1 chr4A.!!$R2 861
15 TraesCS7B01G091300 chr4A 309522053 309522614 561 False 826 826 93.322 1569 2129 1 chr4A.!!$F1 560
16 TraesCS7B01G091300 chr5B 432872163 432873707 1544 False 2257 2257 92.976 1 1560 1 chr5B.!!$F1 1559
17 TraesCS7B01G091300 chr1A 554515394 554516061 667 False 1055 1055 95.252 1569 2234 1 chr1A.!!$F1 665
18 TraesCS7B01G091300 chr2B 474911587 474912254 667 False 1050 1050 95.104 1569 2234 1 chr2B.!!$F1 665
19 TraesCS7B01G091300 chr6D 168260811 168261479 668 False 1044 1044 94.963 1569 2234 1 chr6D.!!$F1 665
20 TraesCS7B01G091300 chr5D 503221361 503222029 668 False 1044 1044 94.963 1569 2234 1 chr5D.!!$F3 665
21 TraesCS7B01G091300 chr5D 6192081 6192749 668 False 1027 1027 94.519 1569 2234 1 chr5D.!!$F1 665
22 TraesCS7B01G091300 chr5D 432400006 432400678 672 True 1013 1013 93.953 1569 2237 1 chr5D.!!$R1 668
23 TraesCS7B01G091300 chr5D 432425781 432426436 655 False 994 994 93.862 1569 2234 1 chr5D.!!$F2 665
24 TraesCS7B01G091300 chr3D 589273143 589273814 671 True 1044 1044 94.838 1569 2237 1 chr3D.!!$R1 668
25 TraesCS7B01G091300 chr7D 231575500 231576016 516 False 837 837 95.793 1714 2234 1 chr7D.!!$F1 520

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
157 158 3.372822 GGTGGAATAGCGATTTTCGAACA 59.627 43.478 0.0 0.0 43.74 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 1976 1.035139 ATTCAATGAGCATTCCCCGC 58.965 50.0 0.0 0.0 0.0 6.13 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
32 33 9.449719 TTCTTTCTTAGCTAAATAGGTGAAAGG 57.550 33.333 26.80 16.70 40.46 3.11
75 76 4.795970 ATATCATGGACTCGAAAAACGC 57.204 40.909 0.00 0.00 42.26 4.84
157 158 3.372822 GGTGGAATAGCGATTTTCGAACA 59.627 43.478 0.00 0.00 43.74 3.18
286 287 6.404184 CGCGGAATGATAGTGAATAGAGAGAT 60.404 42.308 0.00 0.00 0.00 2.75
368 369 6.687604 TCATGTCTTTCAATTCTCGTACTCA 58.312 36.000 0.00 0.00 0.00 3.41
423 424 8.763356 TCATTTTGCAATGAAAACAACAGATAC 58.237 29.630 0.00 0.00 44.89 2.24
510 515 5.103728 TGGCCCACCATTGATTAGAAGATTA 60.104 40.000 0.00 0.00 42.67 1.75
512 517 6.323739 GGCCCACCATTGATTAGAAGATTAAA 59.676 38.462 0.00 0.00 35.26 1.52
1047 1058 6.840780 AATAGGGGTTCTGTTGAATTTCAG 57.159 37.500 0.00 0.00 34.40 3.02
1157 1175 2.610833 GACTTTTGGGAAAACGTCGACT 59.389 45.455 14.70 0.00 0.00 4.18
1228 1246 3.880047 TCGGTCAGTTGAATATTCGGT 57.120 42.857 10.80 0.00 0.00 4.69
1229 1247 4.196626 TCGGTCAGTTGAATATTCGGTT 57.803 40.909 10.80 0.00 0.00 4.44
1240 1258 8.303876 AGTTGAATATTCGGTTGCAGTAATTTT 58.696 29.630 10.80 0.00 0.00 1.82
1453 1475 1.477553 ACACCCATCAATGCATGGTC 58.522 50.000 0.00 0.00 41.84 4.02
1499 1521 8.493607 TCTTGATGGTGAGGATGTTATTGATTA 58.506 33.333 0.00 0.00 0.00 1.75
1560 1583 3.757745 ATTGCGGAAAACCGAACTATG 57.242 42.857 12.85 0.00 34.88 2.23
1561 1584 2.172851 TGCGGAAAACCGAACTATGT 57.827 45.000 12.85 0.00 34.88 2.29
1562 1585 2.496111 TGCGGAAAACCGAACTATGTT 58.504 42.857 12.85 0.00 34.88 2.71
1563 1586 2.879646 TGCGGAAAACCGAACTATGTTT 59.120 40.909 12.85 0.00 36.29 2.83
1564 1587 4.063689 TGCGGAAAACCGAACTATGTTTA 58.936 39.130 12.85 0.00 33.76 2.01
1565 1588 4.083908 TGCGGAAAACCGAACTATGTTTAC 60.084 41.667 12.85 0.00 33.76 2.01
1566 1589 4.631036 CGGAAAACCGAACTATGTTTACG 58.369 43.478 2.30 0.00 33.76 3.18
1567 1590 4.385447 CGGAAAACCGAACTATGTTTACGA 59.615 41.667 2.30 0.00 37.24 3.43
1624 1652 3.081061 TGCGCTCAAAGGATACAAACAT 58.919 40.909 9.73 0.00 41.41 2.71
1747 1779 4.074970 TGAGCAACCTCTTTTGGATTCTC 58.925 43.478 0.00 0.00 38.93 2.87
1826 1860 3.883489 GGGATTTTTAGGATCGTTCAGGG 59.117 47.826 0.00 0.00 0.00 4.45
1905 1939 7.726738 GGTTAAGGACCTCAGAAGATAGAGTAT 59.273 40.741 0.00 0.00 45.55 2.12
1906 1940 8.789762 GTTAAGGACCTCAGAAGATAGAGTATC 58.210 40.741 0.00 0.00 35.41 2.24
1907 1941 5.887754 AGGACCTCAGAAGATAGAGTATCC 58.112 45.833 0.00 0.00 36.34 2.59
1908 1942 5.615261 AGGACCTCAGAAGATAGAGTATCCT 59.385 44.000 0.00 0.00 39.17 3.24
1910 1944 7.464265 AGGACCTCAGAAGATAGAGTATCCTAT 59.536 40.741 9.49 0.00 40.77 2.57
1911 1945 7.556275 GGACCTCAGAAGATAGAGTATCCTATG 59.444 44.444 0.00 0.00 34.66 2.23
1912 1946 8.225863 ACCTCAGAAGATAGAGTATCCTATGA 57.774 38.462 0.00 0.00 35.79 2.15
1913 1947 8.328758 ACCTCAGAAGATAGAGTATCCTATGAG 58.671 40.741 9.02 9.02 37.66 2.90
1914 1948 7.283127 CCTCAGAAGATAGAGTATCCTATGAGC 59.717 44.444 10.00 0.00 37.17 4.26
1918 1952 5.445069 AGATAGAGTATCCTATGAGCGCAT 58.555 41.667 11.47 8.35 35.79 4.73
1942 1976 4.130118 CCCAGATTTCCGGAATACTTCTG 58.870 47.826 25.27 25.27 35.78 3.02
2051 2085 1.899814 TCGCCTGTCTACCATTTCACT 59.100 47.619 0.00 0.00 0.00 3.41
2150 2184 4.168101 AGGTGGAGTCTTGGAGTATTTCA 58.832 43.478 0.00 0.00 0.00 2.69
2196 2230 5.347342 AGTCAGACATCAAATAGCTTCGAG 58.653 41.667 2.66 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.011981 ACCAAATTGGATAGACCTTTCACCTA 60.012 38.462 20.25 0.00 40.96 3.08
75 76 7.022979 TCGTGCATTTCAGTCAAATTTAGATG 58.977 34.615 0.00 0.00 31.79 2.90
157 158 9.942526 ATGGAAACCATTCTCTTATAGGAAATT 57.057 29.630 0.00 0.00 42.23 1.82
242 243 3.961240 CGCGTCTTCGACTTCTATTAGTC 59.039 47.826 0.00 0.00 40.90 2.59
368 369 6.887002 GTCTCCTTCCAGAACTTTCCAATTAT 59.113 38.462 0.00 0.00 0.00 1.28
419 420 6.721571 TTCGAAATTGTCCAGAGTTGTATC 57.278 37.500 0.00 0.00 0.00 2.24
423 424 6.000891 TGATTTCGAAATTGTCCAGAGTTG 57.999 37.500 23.49 0.00 0.00 3.16
510 515 7.391148 AACCAATAGCGATTCATACAAGTTT 57.609 32.000 0.00 0.00 0.00 2.66
512 517 6.597672 TCAAACCAATAGCGATTCATACAAGT 59.402 34.615 0.00 0.00 0.00 3.16
1026 1037 4.105697 ACCTGAAATTCAACAGAACCCCTA 59.894 41.667 0.00 0.00 36.38 3.53
1047 1058 8.548721 CGTATCTTATTGGTGAAACTGAATACC 58.451 37.037 0.00 0.00 36.74 2.73
1157 1175 3.482156 TTGCCAAATAAGCCAGCAAAA 57.518 38.095 0.00 0.00 40.26 2.44
1499 1521 8.444783 TGTGTAAATAGCCTAATATGGGTTCAT 58.555 33.333 0.00 0.00 38.86 2.57
1566 1589 5.049818 AGCGATCAAGGAAATCGATCAAATC 60.050 40.000 9.48 0.00 46.89 2.17
1567 1590 4.818546 AGCGATCAAGGAAATCGATCAAAT 59.181 37.500 9.48 0.00 46.89 2.32
1624 1652 4.033709 TCCCCTTTTTGTTTGTGAATCCA 58.966 39.130 0.00 0.00 0.00 3.41
1747 1779 1.611673 CCTACTGCAAGGGTGGTCTTG 60.612 57.143 0.00 0.00 44.97 3.02
1850 1884 7.974504 TCCCTGAGAAAAGTAGACAGTAAAAT 58.025 34.615 0.00 0.00 0.00 1.82
1905 1939 2.427320 GGGCATGCGCTCATAGGA 59.573 61.111 26.07 0.00 39.07 2.94
1906 1940 2.111669 TGGGCATGCGCTCATAGG 59.888 61.111 31.56 0.00 46.28 2.57
1911 1945 1.358046 GAAATCTGGGCATGCGCTC 59.642 57.895 31.56 18.55 40.02 5.03
1912 1946 2.123428 GGAAATCTGGGCATGCGCT 61.123 57.895 31.56 14.24 38.60 5.92
1913 1947 2.414594 GGAAATCTGGGCATGCGC 59.585 61.111 26.55 26.55 37.44 6.09
1914 1948 2.717485 CGGAAATCTGGGCATGCG 59.283 61.111 12.44 0.00 0.00 4.73
1918 1952 1.843851 AGTATTCCGGAAATCTGGGCA 59.156 47.619 23.08 0.00 42.72 5.36
1942 1976 1.035139 ATTCAATGAGCATTCCCCGC 58.965 50.000 0.00 0.00 0.00 6.13
2035 2069 5.525378 GCCTTGATAGTGAAATGGTAGACAG 59.475 44.000 0.00 0.00 0.00 3.51
2120 2154 2.816087 CCAAGACTCCACCTTTGTCATG 59.184 50.000 0.00 0.00 33.56 3.07
2150 2184 3.131223 CAGGCCTATATGACCGATCGATT 59.869 47.826 18.66 2.17 0.00 3.34
2196 2230 2.870411 GGTGTCCTACGGATAATGCAAC 59.130 50.000 0.00 0.00 32.73 4.17


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

AutoCloner maintained by Alex Coulton.