Multiple sequence alignment - TraesCS1D01G060100

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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 TraesCS1D01G060100 chr1D 100.000 3005 0 0 1 3005 40227592 40230596 0.000000e+00 5550.0
1 TraesCS1D01G060100 chr1D 98.328 2033 25 5 1 2030 40432271 40434297 0.000000e+00 3557.0
2 TraesCS1D01G060100 chr1D 98.946 1138 9 1 1243 2380 40315788 40316922 0.000000e+00 2032.0
3 TraesCS1D01G060100 chr1D 88.545 1615 110 40 788 2380 40201967 40203528 0.000000e+00 1888.0
4 TraesCS1D01G060100 chr1D 87.183 1615 97 44 606 2180 40488761 40490305 0.000000e+00 1735.0
5 TraesCS1D01G060100 chr1D 87.834 1496 101 48 702 2163 40325377 40326825 0.000000e+00 1679.0
6 TraesCS1D01G060100 chr1D 87.508 1497 105 50 702 2163 40244038 40245487 0.000000e+00 1653.0
7 TraesCS1D01G060100 chr1D 87.284 1502 101 50 702 2163 40380381 40381832 0.000000e+00 1633.0
8 TraesCS1D01G060100 chr1D 97.756 713 14 1 33 743 40315003 40315715 0.000000e+00 1227.0
9 TraesCS1D01G060100 chr1D 88.525 366 23 3 2028 2380 40470604 40470963 2.770000e-115 425.0
10 TraesCS1D01G060100 chr1D 82.103 447 42 19 420 845 40173750 40174179 6.170000e-92 348.0
11 TraesCS1D01G060100 chr1D 93.617 188 12 0 2432 2619 40236135 40235948 6.340000e-72 281.0
12 TraesCS1D01G060100 chr1D 81.776 214 17 11 598 802 40175223 40175423 3.100000e-35 159.0
13 TraesCS1D01G060100 chr1D 97.260 73 2 0 1 73 7635983 7635911 1.130000e-24 124.0
14 TraesCS1D01G060100 chr1D 96.053 76 3 0 1 76 79143806 79143731 1.130000e-24 124.0
15 TraesCS1D01G060100 chr1D 83.846 130 19 2 2381 2509 180131003 180130875 4.070000e-24 122.0
16 TraesCS1D01G060100 chr1B 88.151 1612 101 27 648 2202 59912382 59913960 0.000000e+00 1836.0
17 TraesCS1D01G060100 chr1B 87.965 1612 104 27 648 2202 59854913 59856491 0.000000e+00 1820.0
18 TraesCS1D01G060100 chr1B 87.229 1613 86 57 607 2164 60534962 60533415 0.000000e+00 1727.0
19 TraesCS1D01G060100 chr1B 87.532 1187 81 31 1023 2186 59926923 59928065 0.000000e+00 1310.0
20 TraesCS1D01G060100 chr1B 86.872 1135 86 22 1232 2310 59918450 59919577 0.000000e+00 1212.0
21 TraesCS1D01G060100 chr1B 87.037 486 21 15 777 1242 59917523 59917986 7.430000e-141 510.0
22 TraesCS1D01G060100 chr1B 82.175 331 51 4 76 406 59916004 59916326 8.200000e-71 278.0
23 TraesCS1D01G060100 chr1B 83.682 239 24 8 717 950 59960994 59961222 8.440000e-51 211.0
24 TraesCS1D01G060100 chr1B 83.682 239 24 8 717 950 60047430 60047658 8.440000e-51 211.0
25 TraesCS1D01G060100 chr1B 87.640 89 4 1 2251 2332 59943420 59943508 2.470000e-16 97.1
26 TraesCS1D01G060100 chr1B 87.640 89 4 1 2251 2332 60036587 60036675 2.470000e-16 97.1
27 TraesCS1D01G060100 chrUn 86.455 1388 97 45 831 2186 335951176 335949848 0.000000e+00 1437.0
28 TraesCS1D01G060100 chrUn 94.872 78 4 0 1 78 97824148 97824225 4.070000e-24 122.0
29 TraesCS1D01G060100 chrUn 86.957 92 5 1 2251 2335 329121749 329121658 2.470000e-16 97.1
30 TraesCS1D01G060100 chrUn 87.640 89 4 1 2251 2332 398422883 398422971 2.470000e-16 97.1
31 TraesCS1D01G060100 chrUn 87.640 89 4 1 2251 2332 430510818 430510906 2.470000e-16 97.1
32 TraesCS1D01G060100 chr1A 89.098 1064 50 30 1151 2180 39832218 39833249 0.000000e+00 1262.0
33 TraesCS1D01G060100 chr1A 88.287 794 57 14 730 1514 39757517 39758283 0.000000e+00 918.0
34 TraesCS1D01G060100 chr1A 81.488 1156 132 42 74 1170 39831141 39832273 0.000000e+00 874.0
35 TraesCS1D01G060100 chr1A 84.962 665 53 19 1359 2008 31945902 31946534 5.470000e-177 630.0
36 TraesCS1D01G060100 chr1A 83.600 500 28 28 1918 2380 39823976 39824458 1.290000e-113 420.0
37 TraesCS1D01G060100 chr3D 97.192 641 8 2 2374 3005 29932489 29933128 0.000000e+00 1075.0
38 TraesCS1D01G060100 chr3D 93.724 239 15 0 2381 2619 29938734 29938496 2.850000e-95 359.0
39 TraesCS1D01G060100 chr3D 97.297 74 2 0 1 74 598507622 598507549 3.140000e-25 126.0
40 TraesCS1D01G060100 chr6D 96.057 634 16 1 2381 3005 262420208 262420841 0.000000e+00 1024.0
41 TraesCS1D01G060100 chr6D 93.277 238 16 0 2382 2619 262426471 262426234 4.770000e-93 351.0
42 TraesCS1D01G060100 chr6D 83.077 130 20 2 2381 2509 121361425 121361553 1.890000e-22 117.0
43 TraesCS1D01G060100 chr5D 92.955 440 24 2 2381 2814 479132662 479133100 4.230000e-178 634.0
44 TraesCS1D01G060100 chr5D 93.841 276 17 0 2381 2656 479153918 479153643 1.670000e-112 416.0
45 TraesCS1D01G060100 chr5D 96.053 76 3 0 1 76 43104524 43104449 1.130000e-24 124.0
46 TraesCS1D01G060100 chr5D 97.260 73 2 0 1 73 339027493 339027565 1.130000e-24 124.0
47 TraesCS1D01G060100 chr5B 83.136 338 35 5 2672 3005 530257651 530257332 3.790000e-74 289.0
48 TraesCS1D01G060100 chr5B 80.476 210 23 6 2382 2588 530260923 530260729 8.680000e-31 145.0
49 TraesCS1D01G060100 chr7D 97.297 74 2 0 1 74 55132798 55132725 3.140000e-25 126.0


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 TraesCS1D01G060100 chr1D 40227592 40230596 3004 False 5550.0 5550 100.00000 1 3005 1 chr1D.!!$F2 3004
1 TraesCS1D01G060100 chr1D 40432271 40434297 2026 False 3557.0 3557 98.32800 1 2030 1 chr1D.!!$F6 2029
2 TraesCS1D01G060100 chr1D 40201967 40203528 1561 False 1888.0 1888 88.54500 788 2380 1 chr1D.!!$F1 1592
3 TraesCS1D01G060100 chr1D 40488761 40490305 1544 False 1735.0 1735 87.18300 606 2180 1 chr1D.!!$F8 1574
4 TraesCS1D01G060100 chr1D 40325377 40326825 1448 False 1679.0 1679 87.83400 702 2163 1 chr1D.!!$F4 1461
5 TraesCS1D01G060100 chr1D 40244038 40245487 1449 False 1653.0 1653 87.50800 702 2163 1 chr1D.!!$F3 1461
6 TraesCS1D01G060100 chr1D 40380381 40381832 1451 False 1633.0 1633 87.28400 702 2163 1 chr1D.!!$F5 1461
7 TraesCS1D01G060100 chr1D 40315003 40316922 1919 False 1629.5 2032 98.35100 33 2380 2 chr1D.!!$F10 2347
8 TraesCS1D01G060100 chr1D 40173750 40175423 1673 False 253.5 348 81.93950 420 845 2 chr1D.!!$F9 425
9 TraesCS1D01G060100 chr1B 59854913 59856491 1578 False 1820.0 1820 87.96500 648 2202 1 chr1B.!!$F1 1554
10 TraesCS1D01G060100 chr1B 60533415 60534962 1547 True 1727.0 1727 87.22900 607 2164 1 chr1B.!!$R1 1557
11 TraesCS1D01G060100 chr1B 59926923 59928065 1142 False 1310.0 1310 87.53200 1023 2186 1 chr1B.!!$F2 1163
12 TraesCS1D01G060100 chr1B 59912382 59919577 7195 False 959.0 1836 86.05875 76 2310 4 chr1B.!!$F7 2234
13 TraesCS1D01G060100 chrUn 335949848 335951176 1328 True 1437.0 1437 86.45500 831 2186 1 chrUn.!!$R2 1355
14 TraesCS1D01G060100 chr1A 39831141 39833249 2108 False 1068.0 1262 85.29300 74 2180 2 chr1A.!!$F4 2106
15 TraesCS1D01G060100 chr1A 39757517 39758283 766 False 918.0 918 88.28700 730 1514 1 chr1A.!!$F2 784
16 TraesCS1D01G060100 chr1A 31945902 31946534 632 False 630.0 630 84.96200 1359 2008 1 chr1A.!!$F1 649
17 TraesCS1D01G060100 chr3D 29932489 29933128 639 False 1075.0 1075 97.19200 2374 3005 1 chr3D.!!$F1 631
18 TraesCS1D01G060100 chr6D 262420208 262420841 633 False 1024.0 1024 96.05700 2381 3005 1 chr6D.!!$F2 624
19 TraesCS1D01G060100 chr5B 530257332 530260923 3591 True 217.0 289 81.80600 2382 3005 2 chr5B.!!$R1 623

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
58 59 1.676968 CAACCGGGACAGATGACCA 59.323 57.895 6.32 0.0 0.00 4.02 F
227 228 1.678635 GCTGGCATGGGCTGTAACA 60.679 57.895 0.00 0.0 40.87 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 2759 1.576421 GGGCTTCTTGTGCAAGTCG 59.424 57.895 11.17 5.63 39.38 4.18 R
2064 8638 4.519540 TTAAGCTGCAGAAAAATGACCC 57.480 40.909 20.43 0.00 0.00 4.46 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
58 59 1.676968 CAACCGGGACAGATGACCA 59.323 57.895 6.32 0.0 0.00 4.02
143 144 6.674694 AGAATGATGAGAAATGAAAGACGG 57.325 37.500 0.00 0.0 0.00 4.79
194 195 2.325082 ACCATTGCCGTCTTCGTGC 61.325 57.895 0.00 0.0 35.18 5.34
227 228 1.678635 GCTGGCATGGGCTGTAACA 60.679 57.895 0.00 0.0 40.87 2.41
1051 2039 2.490115 GCTATCGATCGTCATCTCCCTT 59.510 50.000 15.94 0.0 0.00 3.95
2415 9031 3.305813 CGTGAGTGCCTAAACTTGTCCTA 60.306 47.826 0.00 0.0 0.00 2.94
2482 9098 1.720694 CGCAACTTGTCCCGTGGTTT 61.721 55.000 0.00 0.0 0.00 3.27
2792 12429 3.736433 CGAGCAGTTGAATGAGAGTAGGG 60.736 52.174 0.00 0.0 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.885879 GTAAGGGCCTTTTGTTCCGG 59.114 55.000 26.29 0.00 0.00 5.14
24 25 2.043992 GGTTGGTAAGGGCCTTTTGTT 58.956 47.619 26.29 1.03 0.00 2.83
58 59 7.456902 TCCCCTACTTGACACTAGTAGAAAAAT 59.543 37.037 13.65 0.00 45.06 1.82
194 195 1.202818 GCCAGCCTCATTACCTAAGGG 60.203 57.143 0.00 0.00 38.88 3.95
1705 2759 1.576421 GGGCTTCTTGTGCAAGTCG 59.424 57.895 11.17 5.63 39.38 4.18
1990 3082 8.749499 CGAGATGAATGAAATGAAATAAAAGGC 58.251 33.333 0.00 0.00 0.00 4.35
2064 8638 4.519540 TTAAGCTGCAGAAAAATGACCC 57.480 40.909 20.43 0.00 0.00 4.46
2393 9009 1.798813 GGACAAGTTTAGGCACTCACG 59.201 52.381 0.00 0.00 41.75 4.35
2415 9031 0.324943 AGGCACTAAACTGACCGCAT 59.675 50.000 0.00 0.00 36.02 4.73
2482 9098 2.829720 ACGTCTGGAGGCACTGTATTTA 59.170 45.455 0.00 0.00 41.55 1.40
2669 12297 0.551396 GGGGATTTGGGGATCGAGTT 59.449 55.000 0.00 0.00 0.00 3.01
2892 12529 2.814183 ATTCCTCGTCGTCGCGCTTT 62.814 55.000 5.56 0.00 36.96 3.51


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

AutoCloner maintained by Alex Coulton.