Multiple sequence alignment - TraesCS5A01G506300

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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 TraesCS5A01G506300 chr5A 100.000 2026 0 0 514 2539 671203004 671200979 0.000000e+00 3742.0
1 TraesCS5A01G506300 chr5A 100.000 49 0 0 1 49 671203517 671203469 9.670000e-15 91.6
2 TraesCS5A01G506300 chr4A 95.125 882 35 3 1660 2539 685311957 685312832 0.000000e+00 1384.0
3 TraesCS5A01G506300 chr3B 94.938 889 36 4 1660 2539 670194914 670194026 0.000000e+00 1384.0
4 TraesCS5A01G506300 chr3B 92.958 355 9 5 611 952 790347566 790347917 1.050000e-138 503.0
5 TraesCS5A01G506300 chr7A 94.388 891 38 7 1656 2539 579597383 579596498 0.000000e+00 1358.0
6 TraesCS5A01G506300 chr7A 98.670 376 5 0 581 956 101800423 101800048 0.000000e+00 667.0
7 TraesCS5A01G506300 chr7A 100.000 49 0 0 1 49 101801122 101801074 9.670000e-15 91.6
8 TraesCS5A01G506300 chr7B 94.482 888 35 8 1660 2539 424536588 424535707 0.000000e+00 1356.0
9 TraesCS5A01G506300 chr7B 93.966 895 35 12 1657 2539 693326378 693327265 0.000000e+00 1336.0
10 TraesCS5A01G506300 chr7B 98.413 315 5 0 642 956 26023390 26023704 2.850000e-154 555.0
11 TraesCS5A01G506300 chr7B 91.643 347 14 7 623 956 717785085 717785429 1.380000e-127 466.0
12 TraesCS5A01G506300 chr7B 100.000 49 0 0 1 49 26022989 26023037 9.670000e-15 91.6
13 TraesCS5A01G506300 chr6B 93.898 885 48 6 1658 2539 648264620 648263739 0.000000e+00 1330.0
14 TraesCS5A01G506300 chr2A 93.919 888 39 5 1658 2539 750532867 750533745 0.000000e+00 1327.0
15 TraesCS5A01G506300 chr6A 93.596 890 46 7 1656 2539 106843397 106842513 0.000000e+00 1317.0
16 TraesCS5A01G506300 chr6A 99.261 406 3 0 550 955 560200507 560200912 0.000000e+00 734.0
17 TraesCS5A01G506300 chr6A 92.758 359 11 5 611 956 525014375 525014019 2.920000e-139 505.0
18 TraesCS5A01G506300 chr6A 100.000 49 0 0 1 49 560200001 560200049 9.670000e-15 91.6
19 TraesCS5A01G506300 chr2B 93.371 890 50 5 1656 2539 418659997 418660883 0.000000e+00 1308.0
20 TraesCS5A01G506300 chr4D 88.211 721 38 17 953 1660 489753876 489753190 0.000000e+00 817.0
21 TraesCS5A01G506300 chr4B 90.956 586 31 7 965 1538 628972478 628971903 0.000000e+00 769.0
22 TraesCS5A01G506300 chr4B 99.292 424 3 0 529 952 180196328 180195905 0.000000e+00 767.0
23 TraesCS5A01G506300 chr4B 89.577 614 41 11 942 1538 629048482 629047875 0.000000e+00 758.0
24 TraesCS5A01G506300 chr4B 90.444 586 34 7 965 1538 629009341 629008766 0.000000e+00 752.0
25 TraesCS5A01G506300 chr4B 84.058 759 69 21 928 1660 628947099 628946367 0.000000e+00 684.0
26 TraesCS5A01G506300 chr4B 100.000 49 0 0 1 49 180196553 180196505 9.670000e-15 91.6
27 TraesCS5A01G506300 chr1A 98.133 375 4 3 584 956 38701045 38701418 0.000000e+00 651.0
28 TraesCS5A01G506300 chr1A 92.479 359 11 5 611 956 58360407 58360762 1.360000e-137 499.0
29 TraesCS5A01G506300 chr1A 100.000 49 0 0 1 49 38700471 38700519 9.670000e-15 91.6
30 TraesCS5A01G506300 chr2D 86.455 347 41 6 611 952 34886563 34886218 2.380000e-100 375.0


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 TraesCS5A01G506300 chr5A 671200979 671203517 2538 True 1916.8 3742 100.0000 1 2539 2 chr5A.!!$R1 2538
1 TraesCS5A01G506300 chr4A 685311957 685312832 875 False 1384.0 1384 95.1250 1660 2539 1 chr4A.!!$F1 879
2 TraesCS5A01G506300 chr3B 670194026 670194914 888 True 1384.0 1384 94.9380 1660 2539 1 chr3B.!!$R1 879
3 TraesCS5A01G506300 chr7A 579596498 579597383 885 True 1358.0 1358 94.3880 1656 2539 1 chr7A.!!$R1 883
4 TraesCS5A01G506300 chr7A 101800048 101801122 1074 True 379.3 667 99.3350 1 956 2 chr7A.!!$R2 955
5 TraesCS5A01G506300 chr7B 424535707 424536588 881 True 1356.0 1356 94.4820 1660 2539 1 chr7B.!!$R1 879
6 TraesCS5A01G506300 chr7B 693326378 693327265 887 False 1336.0 1336 93.9660 1657 2539 1 chr7B.!!$F1 882
7 TraesCS5A01G506300 chr7B 26022989 26023704 715 False 323.3 555 99.2065 1 956 2 chr7B.!!$F3 955
8 TraesCS5A01G506300 chr6B 648263739 648264620 881 True 1330.0 1330 93.8980 1658 2539 1 chr6B.!!$R1 881
9 TraesCS5A01G506300 chr2A 750532867 750533745 878 False 1327.0 1327 93.9190 1658 2539 1 chr2A.!!$F1 881
10 TraesCS5A01G506300 chr6A 106842513 106843397 884 True 1317.0 1317 93.5960 1656 2539 1 chr6A.!!$R1 883
11 TraesCS5A01G506300 chr6A 560200001 560200912 911 False 412.8 734 99.6305 1 955 2 chr6A.!!$F1 954
12 TraesCS5A01G506300 chr2B 418659997 418660883 886 False 1308.0 1308 93.3710 1656 2539 1 chr2B.!!$F1 883
13 TraesCS5A01G506300 chr4D 489753190 489753876 686 True 817.0 817 88.2110 953 1660 1 chr4D.!!$R1 707
14 TraesCS5A01G506300 chr4B 628971903 628972478 575 True 769.0 769 90.9560 965 1538 1 chr4B.!!$R2 573
15 TraesCS5A01G506300 chr4B 629047875 629048482 607 True 758.0 758 89.5770 942 1538 1 chr4B.!!$R4 596
16 TraesCS5A01G506300 chr4B 629008766 629009341 575 True 752.0 752 90.4440 965 1538 1 chr4B.!!$R3 573
17 TraesCS5A01G506300 chr4B 628946367 628947099 732 True 684.0 684 84.0580 928 1660 1 chr4B.!!$R1 732
18 TraesCS5A01G506300 chr4B 180195905 180196553 648 True 429.3 767 99.6460 1 952 2 chr4B.!!$R5 951
19 TraesCS5A01G506300 chr1A 38700471 38701418 947 False 371.3 651 99.0665 1 956 2 chr1A.!!$F2 955

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
687 807 3.126225 GAGAGGAGACGCGACGGT 61.126 66.667 15.93 0.0 34.13 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1729 0.108992 AACGGATGCACACGTACGAT 60.109 50.0 24.41 6.62 42.05 3.73 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
687 807 3.126225 GAGAGGAGACGCGACGGT 61.126 66.667 15.93 0.00 34.13 4.83
1027 1150 1.886777 GCATCGCTCTGCTCCTTCC 60.887 63.158 0.53 0.00 39.12 3.46
1036 1159 2.104451 CTCTGCTCCTTCCTATGCACAT 59.896 50.000 0.00 0.00 0.00 3.21
1041 1164 3.464907 CTCCTTCCTATGCACATCACAG 58.535 50.000 0.00 0.00 0.00 3.66
1042 1165 3.106827 TCCTTCCTATGCACATCACAGA 58.893 45.455 0.00 0.00 0.00 3.41
1043 1166 3.713248 TCCTTCCTATGCACATCACAGAT 59.287 43.478 0.00 0.00 0.00 2.90
1044 1167 4.063689 CCTTCCTATGCACATCACAGATC 58.936 47.826 0.00 0.00 0.00 2.75
1045 1168 4.443881 CCTTCCTATGCACATCACAGATCA 60.444 45.833 0.00 0.00 0.00 2.92
1046 1169 4.063998 TCCTATGCACATCACAGATCAC 57.936 45.455 0.00 0.00 0.00 3.06
1047 1170 3.451902 TCCTATGCACATCACAGATCACA 59.548 43.478 0.00 0.00 0.00 3.58
1058 1183 3.831911 TCACAGATCACACCACATAGTCA 59.168 43.478 0.00 0.00 0.00 3.41
1163 1292 4.864334 CCTCGCCATGCTGGTCCC 62.864 72.222 4.45 0.00 40.46 4.46
1286 1427 2.512301 GCATCTCGACGTGCAGAGC 61.512 63.158 11.33 0.00 40.94 4.09
1341 1482 4.406173 CCGAGCTGCGACGAGTGT 62.406 66.667 19.62 0.00 44.57 3.55
1364 1505 4.409588 CGCCGCGTTCGACAAGTG 62.410 66.667 11.80 0.00 38.10 3.16
1365 1506 4.719616 GCCGCGTTCGACAAGTGC 62.720 66.667 4.92 0.00 38.10 4.40
1366 1507 3.334751 CCGCGTTCGACAAGTGCA 61.335 61.111 4.92 0.00 38.10 4.57
1374 1515 3.368571 GACAAGTGCAGCAGGGCC 61.369 66.667 0.00 0.00 0.00 5.80
1543 1705 2.224281 ACCTGCGTGTGAAGAGAATCAA 60.224 45.455 0.00 0.00 37.82 2.57
1556 1718 3.522750 AGAGAATCAAGAGAGGGCAACAT 59.477 43.478 0.00 0.00 37.82 2.71
1567 1729 4.178861 GCAACATGCCGTCGTCTA 57.821 55.556 0.00 0.00 37.42 2.59
1568 1730 2.677971 GCAACATGCCGTCGTCTAT 58.322 52.632 0.00 0.00 37.42 1.98
1583 1745 2.382519 GTCTATCGTACGTGTGCATCC 58.617 52.381 16.05 0.00 0.00 3.51
1596 1758 0.533085 TGCATCCGTTTCGTGGTTCA 60.533 50.000 0.00 0.00 0.00 3.18
1613 1775 3.367025 GGTTCAATCGTTTCTAGTCGTGG 59.633 47.826 0.00 0.00 0.00 4.94
1650 1825 1.136169 GGTCGTTGGTTGTCATAACGC 60.136 52.381 0.00 0.00 44.76 4.84
1720 1896 1.069090 GTCCTGTGAAGACGCACCA 59.931 57.895 0.00 0.00 37.99 4.17
1823 2000 7.458038 AAAACGACTCAAATTTAACGCAAAT 57.542 28.000 0.00 0.00 38.54 2.32
1839 2016 3.952535 GCAAATATCGGCGAGTTCATTT 58.047 40.909 17.22 14.37 0.00 2.32
1964 2150 1.660560 GGAGGCTGTAGAACCGCGTA 61.661 60.000 4.92 0.00 0.00 4.42
1978 2164 2.354305 CGTATAGTCACCGCCGCC 60.354 66.667 0.00 0.00 0.00 6.13
1979 2165 2.354305 GTATAGTCACCGCCGCCG 60.354 66.667 0.00 0.00 0.00 6.46
1980 2166 4.274700 TATAGTCACCGCCGCCGC 62.275 66.667 0.00 0.00 0.00 6.53
2099 2312 4.707840 GCGTCGTCGTCGTCGTCA 62.708 66.667 19.72 0.00 46.29 4.35
2264 2477 1.177256 GCCGGGCTATCTCCTCGTAA 61.177 60.000 12.87 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
526 527 4.925861 GGAGATGCAGGGGCGAGC 62.926 72.222 0.00 0.00 45.35 5.03
527 528 4.247380 GGGAGATGCAGGGGCGAG 62.247 72.222 0.00 0.00 45.35 5.03
962 1085 1.807142 GTCCTGACACTTGGCTAAAGC 59.193 52.381 0.00 0.00 39.76 3.51
1027 1150 3.558829 GGTGTGATCTGTGATGTGCATAG 59.441 47.826 0.00 0.00 37.10 2.23
1036 1159 3.831911 TGACTATGTGGTGTGATCTGTGA 59.168 43.478 0.00 0.00 0.00 3.58
1041 1164 5.528043 AGATCTGACTATGTGGTGTGATC 57.472 43.478 0.00 0.00 0.00 2.92
1042 1165 5.423290 TGAAGATCTGACTATGTGGTGTGAT 59.577 40.000 0.00 0.00 0.00 3.06
1043 1166 4.772100 TGAAGATCTGACTATGTGGTGTGA 59.228 41.667 0.00 0.00 0.00 3.58
1044 1167 4.867047 GTGAAGATCTGACTATGTGGTGTG 59.133 45.833 0.00 0.00 0.00 3.82
1045 1168 4.528206 TGTGAAGATCTGACTATGTGGTGT 59.472 41.667 0.00 0.00 0.00 4.16
1046 1169 5.077134 TGTGAAGATCTGACTATGTGGTG 57.923 43.478 0.00 0.00 0.00 4.17
1047 1170 5.423290 TGATGTGAAGATCTGACTATGTGGT 59.577 40.000 0.00 0.00 0.00 4.16
1058 1183 8.076910 AGTAGAAGAATGTGATGTGAAGATCT 57.923 34.615 0.00 0.00 0.00 2.75
1530 1692 3.055530 TGCCCTCTCTTGATTCTCTTCAC 60.056 47.826 0.00 0.00 0.00 3.18
1556 1718 1.083806 ACGTACGATAGACGACGGCA 61.084 55.000 24.41 0.00 45.77 5.69
1563 1725 2.382519 GGATGCACACGTACGATAGAC 58.617 52.381 24.41 7.64 41.38 2.59
1565 1727 1.268386 ACGGATGCACACGTACGATAG 60.268 52.381 24.41 13.48 42.05 2.08
1566 1728 0.734309 ACGGATGCACACGTACGATA 59.266 50.000 24.41 3.25 42.05 2.92
1567 1729 0.108992 AACGGATGCACACGTACGAT 60.109 50.000 24.41 6.62 42.05 3.73
1568 1730 0.318869 AAACGGATGCACACGTACGA 60.319 50.000 24.41 0.00 42.05 3.43
1583 1745 2.656192 AACGATTGAACCACGAAACG 57.344 45.000 0.00 0.00 0.00 3.60
1596 1758 2.416972 GCCTCCACGACTAGAAACGATT 60.417 50.000 13.28 0.00 0.00 3.34
1650 1825 2.366916 CTGGAGATGCCCTAAGGTAGTG 59.633 54.545 0.00 0.00 34.97 2.74
1703 1878 1.367471 CTGGTGCGTCTTCACAGGA 59.633 57.895 0.00 0.00 38.66 3.86
1823 2000 7.830940 TTAAGTTTAAATGAACTCGCCGATA 57.169 32.000 0.00 0.00 38.86 2.92
2174 2387 2.577059 GACGAGATGGTCCGGCAA 59.423 61.111 0.00 0.00 33.27 4.52
2289 2502 4.477975 CGTCCTCGTCGAGCCCAC 62.478 72.222 17.02 11.14 0.00 4.61


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

AutoCloner maintained by Alex Coulton.