Multiple sequence alignment - TraesCS5A01G106700

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 TraesCS5A01G106700 chr5A 100.000 2366 0 0 1 2366 176943789 176941424 0.000000e+00 4370
1 TraesCS5A01G106700 chr5A 88.761 694 64 12 1 688 131342926 131342241 0.000000e+00 837
2 TraesCS5A01G106700 chr6A 96.326 2368 78 5 1 2365 266026589 266028950 0.000000e+00 3882
3 TraesCS5A01G106700 chr6A 96.284 2368 78 5 1 2365 266018711 266021071 0.000000e+00 3877
4 TraesCS5A01G106700 chr6A 87.361 1345 141 23 1 1328 259362607 259361275 0.000000e+00 1515
5 TraesCS5A01G106700 chr6A 85.329 1261 154 27 1 1237 430717059 430715806 0.000000e+00 1275
6 TraesCS5A01G106700 chr6A 93.032 775 49 5 1294 2065 259361195 259360423 0.000000e+00 1127
7 TraesCS5A01G106700 chr6A 89.847 522 49 4 1845 2364 312689354 312689873 0.000000e+00 667
8 TraesCS5A01G106700 chr3A 95.564 2367 95 7 3 2364 347832932 347830571 0.000000e+00 3781
9 TraesCS5A01G106700 chr3A 89.665 687 63 7 1 683 293307468 293308150 0.000000e+00 869
10 TraesCS5A01G106700 chr3A 95.882 170 7 0 1399 1568 94336544 94336375 2.320000e-70 276
11 TraesCS5A01G106700 chr4A 93.969 2371 132 10 1 2364 197215288 197212922 0.000000e+00 3576
12 TraesCS5A01G106700 chr4A 86.672 1343 148 27 3 1328 205932280 205933608 0.000000e+00 1459
13 TraesCS5A01G106700 chr4A 86.076 1343 150 27 3 1328 205924354 205925676 0.000000e+00 1410
14 TraesCS5A01G106700 chr4A 92.699 767 41 5 1298 2062 205925761 205926514 0.000000e+00 1092
15 TraesCS5A01G106700 chr4A 92.183 742 44 4 1323 2062 205933716 205934445 0.000000e+00 1037
16 TraesCS5A01G106700 chr7A 95.517 1740 71 5 626 2364 420702004 420703737 0.000000e+00 2774
17 TraesCS5A01G106700 chr7A 96.355 631 22 1 4 633 420701353 420701983 0.000000e+00 1037
18 TraesCS5A01G106700 chr7A 90.306 392 28 10 1498 1886 324976859 324977243 2.710000e-139 505
19 TraesCS5A01G106700 chr7A 90.253 277 21 6 1295 1570 324967844 324968115 8.040000e-95 357
20 TraesCS5A01G106700 chr7A 92.683 82 5 1 1248 1328 324967678 324967759 1.490000e-22 117
21 TraesCS5A01G106700 chr2A 88.970 689 66 10 3 688 305113653 305114334 0.000000e+00 843
22 TraesCS5A01G106700 chr2A 88.841 690 67 10 3 688 305105800 305106483 0.000000e+00 839
23 TraesCS5A01G106700 chr1A 92.514 521 37 2 1845 2364 326543230 326542711 0.000000e+00 745
24 TraesCS5A01G106700 chr1A 92.322 521 38 2 1845 2364 385002421 385002940 0.000000e+00 739
25 TraesCS5A01G106700 chr1A 91.731 520 41 2 1846 2364 326535656 326535138 0.000000e+00 721


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 TraesCS5A01G106700 chr5A 176941424 176943789 2365 True 4370.0 4370 100.0000 1 2366 1 chr5A.!!$R2 2365
1 TraesCS5A01G106700 chr5A 131342241 131342926 685 True 837.0 837 88.7610 1 688 1 chr5A.!!$R1 687
2 TraesCS5A01G106700 chr6A 266026589 266028950 2361 False 3882.0 3882 96.3260 1 2365 1 chr6A.!!$F2 2364
3 TraesCS5A01G106700 chr6A 266018711 266021071 2360 False 3877.0 3877 96.2840 1 2365 1 chr6A.!!$F1 2364
4 TraesCS5A01G106700 chr6A 259360423 259362607 2184 True 1321.0 1515 90.1965 1 2065 2 chr6A.!!$R2 2064
5 TraesCS5A01G106700 chr6A 430715806 430717059 1253 True 1275.0 1275 85.3290 1 1237 1 chr6A.!!$R1 1236
6 TraesCS5A01G106700 chr6A 312689354 312689873 519 False 667.0 667 89.8470 1845 2364 1 chr6A.!!$F3 519
7 TraesCS5A01G106700 chr3A 347830571 347832932 2361 True 3781.0 3781 95.5640 3 2364 1 chr3A.!!$R2 2361
8 TraesCS5A01G106700 chr3A 293307468 293308150 682 False 869.0 869 89.6650 1 683 1 chr3A.!!$F1 682
9 TraesCS5A01G106700 chr4A 197212922 197215288 2366 True 3576.0 3576 93.9690 1 2364 1 chr4A.!!$R1 2363
10 TraesCS5A01G106700 chr4A 205924354 205926514 2160 False 1251.0 1410 89.3875 3 2062 2 chr4A.!!$F1 2059
11 TraesCS5A01G106700 chr4A 205932280 205934445 2165 False 1248.0 1459 89.4275 3 2062 2 chr4A.!!$F2 2059
12 TraesCS5A01G106700 chr7A 420701353 420703737 2384 False 1905.5 2774 95.9360 4 2364 2 chr7A.!!$F3 2360
13 TraesCS5A01G106700 chr2A 305113653 305114334 681 False 843.0 843 88.9700 3 688 1 chr2A.!!$F2 685
14 TraesCS5A01G106700 chr2A 305105800 305106483 683 False 839.0 839 88.8410 3 688 1 chr2A.!!$F1 685
15 TraesCS5A01G106700 chr1A 326542711 326543230 519 True 745.0 745 92.5140 1845 2364 1 chr1A.!!$R2 519
16 TraesCS5A01G106700 chr1A 385002421 385002940 519 False 739.0 739 92.3220 1845 2364 1 chr1A.!!$F1 519
17 TraesCS5A01G106700 chr1A 326535138 326535656 518 True 721.0 721 91.7310 1846 2364 1 chr1A.!!$R1 518

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
773 838 0.107945 GCGAAGAGGCTTGTGGATCT 60.108 55.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2330 0.234625 GTGCGCGTCTGAAATTGTCA 59.765 50.0 8.43 0.0 34.17 3.58 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
633 678 9.212641 TCTATAAATATGCAATGCTCTGAGAAC 57.787 33.333 9.28 0.00 0.00 3.01
656 705 5.356751 ACATTAATAATTCGCTGCCAACTGA 59.643 36.000 0.00 0.00 0.00 3.41
657 706 5.888691 TTAATAATTCGCTGCCAACTGAA 57.111 34.783 0.00 0.00 0.00 3.02
748 813 2.270874 CTTACCCATGGGCTTCGGCT 62.271 60.000 31.73 12.05 41.44 5.52
757 822 2.637025 GCTTCGGCTTGTTTGCGA 59.363 55.556 0.00 0.00 38.08 5.10
773 838 0.107945 GCGAAGAGGCTTGTGGATCT 60.108 55.000 0.00 0.00 0.00 2.75
1407 1701 1.525077 GAAACTGCCGGTGGTGACA 60.525 57.895 1.90 0.00 38.70 3.58
1458 1752 0.465705 GAACTCGAGGCCATCCATGA 59.534 55.000 18.41 0.00 33.74 3.07
1478 1772 1.122019 AGTCGGGTGCTCTCCTGTTT 61.122 55.000 0.00 0.00 35.51 2.83
1686 1980 0.687354 CTGGTTGGTGCAGACTAGGT 59.313 55.000 0.00 0.00 0.00 3.08
1710 2004 0.485099 ATCGAGAGGTGGAGGGCTAT 59.515 55.000 0.00 0.00 0.00 2.97
1723 2017 0.683179 GGGCTATGGTTTGGGTGGAC 60.683 60.000 0.00 0.00 0.00 4.02
1724 2018 0.331616 GGCTATGGTTTGGGTGGACT 59.668 55.000 0.00 0.00 0.00 3.85
1757 2051 2.242926 CGATAGAGAAGGGATCTGGCA 58.757 52.381 0.00 0.00 38.96 4.92
1795 2089 1.594331 GAACAACAAGGAAGAGCGGT 58.406 50.000 0.00 0.00 0.00 5.68
2043 2341 0.393448 TCGGGTCCGTGACAATTTCA 59.607 50.000 9.36 0.00 40.74 2.69
2084 2382 2.745492 GCACTGTGCAGAGAGGGC 60.745 66.667 26.70 13.72 44.26 5.19
2116 2414 1.080093 GTCGCATCGGACAACTCCA 60.080 57.895 0.00 0.00 36.12 3.86
2174 2472 4.200283 GCGAGACTGCGAGGGGAG 62.200 72.222 0.00 0.00 37.67 4.30
2175 2473 2.438614 CGAGACTGCGAGGGGAGA 60.439 66.667 0.00 0.00 35.29 3.71
2365 2670 4.080356 TCATCCCATTCCGAGAACATTTCT 60.080 41.667 0.00 0.00 44.21 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 194 5.187772 AGTTTTCTTTTGCTTCACCCTCTTT 59.812 36.000 0.00 0.0 0.00 2.52
598 615 3.073209 TGCATATTTATAGAACGGCCCCA 59.927 43.478 0.00 0.0 0.00 4.96
633 678 5.820131 TCAGTTGGCAGCGAATTATTAATG 58.180 37.500 0.00 0.0 0.00 1.90
731 796 2.305607 AAGCCGAAGCCCATGGGTA 61.306 57.895 31.58 0.0 41.25 3.69
748 813 1.065401 CACAAGCCTCTTCGCAAACAA 59.935 47.619 0.00 0.0 0.00 2.83
757 822 0.034670 GCCAGATCCACAAGCCTCTT 60.035 55.000 0.00 0.0 0.00 2.85
963 1031 4.809496 CCATGCTTCCCTGCCGCT 62.809 66.667 0.00 0.0 0.00 5.52
1112 1180 1.903877 CTCCCCTGCATCCTGTTCGT 61.904 60.000 0.00 0.0 0.00 3.85
1181 1249 1.837439 TGTCCCCTGCTATGTTCGATT 59.163 47.619 0.00 0.0 0.00 3.34
1329 1623 3.023949 GCCATCTCCAGCCTCGTGT 62.024 63.158 0.00 0.0 0.00 4.49
1407 1701 3.048602 CCGTCTCAACCACCTCGT 58.951 61.111 0.00 0.0 0.00 4.18
1458 1752 1.122019 AACAGGAGAGCACCCGACTT 61.122 55.000 0.00 0.0 0.00 3.01
1478 1772 1.352017 TCCGTCTCTGTACCAGGTACA 59.648 52.381 27.70 27.7 45.20 2.90
1686 1980 1.422024 CCCTCCACCTCTCGATCTCTA 59.578 57.143 0.00 0.0 0.00 2.43
1710 2004 0.764890 CTCTCAGTCCACCCAAACCA 59.235 55.000 0.00 0.0 0.00 3.67
1723 2017 4.905429 TCTCTATCGGGATCTTCTCTCAG 58.095 47.826 0.00 0.0 0.00 3.35
1724 2018 4.984146 TCTCTATCGGGATCTTCTCTCA 57.016 45.455 0.00 0.0 0.00 3.27
1924 2220 4.003648 CTCGCCTATTTTTCTTGACCACT 58.996 43.478 0.00 0.0 0.00 4.00
2033 2330 0.234625 GTGCGCGTCTGAAATTGTCA 59.765 50.000 8.43 0.0 34.17 3.58
2116 2414 0.252284 TCCTTCCCCTCTTCGCTTCT 60.252 55.000 0.00 0.0 0.00 2.85
2173 2471 0.261696 GGGCCCTCTCTCTCTCTTCT 59.738 60.000 17.04 0.0 0.00 2.85
2174 2472 1.106944 CGGGCCCTCTCTCTCTCTTC 61.107 65.000 22.43 0.0 0.00 2.87
2175 2473 1.076339 CGGGCCCTCTCTCTCTCTT 60.076 63.158 22.43 0.0 0.00 2.85
2221 2526 1.599542 GTATAGCCGGTCTAACGTCGT 59.400 52.381 1.90 0.0 0.00 4.34
2250 2555 3.602483 TGATAGCCCAACCGTTAAACTC 58.398 45.455 0.00 0.0 0.00 3.01
2283 2588 2.677836 GCCTGTCAAGTTTCATCGCATA 59.322 45.455 0.00 0.0 0.00 3.14


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

AutoCloner maintained by Alex Coulton.