Multiple sequence alignment - TraesCS7B01G501400

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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 TraesCS7B01G501400 chr7B 100.000 1850 0 0 629 2478 750371700 750369851 0.000000e+00 3417.0
1 TraesCS7B01G501400 chr7B 100.000 272 0 0 1 272 750372328 750372057 1.020000e-138 503.0
2 TraesCS7B01G501400 chr5B 94.816 1852 77 5 629 2478 629217632 629215798 0.000000e+00 2870.0
3 TraesCS7B01G501400 chr5B 87.500 272 13 2 1 272 629218191 629217941 6.700000e-76 294.0
4 TraesCS7B01G501400 chr5B 95.745 47 2 0 226 272 141778338 141778292 2.640000e-10 76.8
5 TraesCS7B01G501400 chr7A 93.301 1851 90 5 629 2478 104383416 104381599 0.000000e+00 2700.0
6 TraesCS7B01G501400 chr7A 90.761 1169 65 4 629 1796 358383188 358384314 0.000000e+00 1520.0
7 TraesCS7B01G501400 chr7A 90.358 1172 64 6 629 1799 676810372 676809249 0.000000e+00 1493.0
8 TraesCS7B01G501400 chr7A 90.017 1172 70 7 629 1799 676837191 676836066 0.000000e+00 1472.0
9 TraesCS7B01G501400 chr7A 89.505 1172 79 5 629 1799 676724368 676723240 0.000000e+00 1443.0
10 TraesCS7B01G501400 chr7A 98.675 151 2 0 1 151 104384057 104383907 4.060000e-68 268.0
11 TraesCS7B01G501400 chr7A 88.095 210 17 5 9 212 658773133 658773340 2.460000e-60 243.0
12 TraesCS7B01G501400 chr7A 88.350 206 16 6 9 208 704400179 704399976 8.860000e-60 241.0
13 TraesCS7B01G501400 chr1D 93.946 1784 101 2 696 2478 24353535 24351758 0.000000e+00 2689.0
14 TraesCS7B01G501400 chr1D 96.575 876 30 0 1603 2478 262485267 262486142 0.000000e+00 1452.0
15 TraesCS7B01G501400 chr1D 95.185 270 12 1 1 270 262483780 262484048 2.280000e-115 425.0
16 TraesCS7B01G501400 chr2A 92.869 1851 98 15 629 2478 547863084 547864901 0.000000e+00 2656.0
17 TraesCS7B01G501400 chr2A 87.543 289 12 2 4 268 663567040 663566752 1.850000e-81 313.0
18 TraesCS7B01G501400 chr2A 89.706 204 13 6 9 206 481103304 481103103 1.140000e-63 254.0
19 TraesCS7B01G501400 chr1A 90.358 1172 70 10 629 1799 579141378 579140249 0.000000e+00 1498.0
20 TraesCS7B01G501400 chr5A 90.273 1172 72 3 629 1799 75980196 75979066 0.000000e+00 1495.0
21 TraesCS7B01G501400 chr5A 95.847 915 38 0 1564 2478 543656530 543657444 0.000000e+00 1480.0
22 TraesCS7B01G501400 chr5A 85.616 438 36 16 629 1066 543641571 543641981 3.780000e-118 435.0
23 TraesCS7B01G501400 chr5A 93.015 272 13 1 1 272 543640877 543641142 2.310000e-105 392.0
24 TraesCS7B01G501400 chr6A 90.163 1169 72 12 629 1796 82806792 82805666 0.000000e+00 1482.0
25 TraesCS7B01G501400 chr6A 100.000 33 0 0 240 272 217307886 217307918 7.400000e-06 62.1
26 TraesCS7B01G501400 chr3D 97.136 873 24 1 1606 2478 558028406 558027535 0.000000e+00 1472.0
27 TraesCS7B01G501400 chr3D 96.461 876 30 1 1603 2478 114342369 114343243 0.000000e+00 1445.0
28 TraesCS7B01G501400 chr3D 96.604 265 9 0 8 272 114340790 114341054 8.130000e-120 440.0
29 TraesCS7B01G501400 chr3D 87.671 73 8 1 710 782 605102789 605102718 1.580000e-12 84.2
30 TraesCS7B01G501400 chr3A 89.846 1172 77 9 629 1799 644406816 644405686 0.000000e+00 1467.0
31 TraesCS7B01G501400 chr3A 86.667 210 20 5 9 212 667987239 667987446 2.480000e-55 226.0
32 TraesCS7B01G501400 chr5D 96.465 877 30 1 1603 2478 462629114 462629990 0.000000e+00 1447.0
33 TraesCS7B01G501400 chr5D 95.652 69 3 0 629 697 462628290 462628358 7.240000e-21 111.0
34 TraesCS7B01G501400 chr4D 90.256 1016 83 7 977 1990 407023980 407022979 0.000000e+00 1314.0
35 TraesCS7B01G501400 chr4A 92.704 233 17 0 11 243 355345598 355345366 1.100000e-88 337.0
36 TraesCS7B01G501400 chr2B 96.000 50 0 2 223 272 467356848 467356801 2.040000e-11 80.5


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 TraesCS7B01G501400 chr7B 750369851 750372328 2477 True 1960.0 3417 100.0000 1 2478 2 chr7B.!!$R1 2477
1 TraesCS7B01G501400 chr5B 629215798 629218191 2393 True 1582.0 2870 91.1580 1 2478 2 chr5B.!!$R2 2477
2 TraesCS7B01G501400 chr7A 358383188 358384314 1126 False 1520.0 1520 90.7610 629 1796 1 chr7A.!!$F1 1167
3 TraesCS7B01G501400 chr7A 676809249 676810372 1123 True 1493.0 1493 90.3580 629 1799 1 chr7A.!!$R2 1170
4 TraesCS7B01G501400 chr7A 104381599 104384057 2458 True 1484.0 2700 95.9880 1 2478 2 chr7A.!!$R5 2477
5 TraesCS7B01G501400 chr7A 676836066 676837191 1125 True 1472.0 1472 90.0170 629 1799 1 chr7A.!!$R3 1170
6 TraesCS7B01G501400 chr7A 676723240 676724368 1128 True 1443.0 1443 89.5050 629 1799 1 chr7A.!!$R1 1170
7 TraesCS7B01G501400 chr1D 24351758 24353535 1777 True 2689.0 2689 93.9460 696 2478 1 chr1D.!!$R1 1782
8 TraesCS7B01G501400 chr1D 262483780 262486142 2362 False 938.5 1452 95.8800 1 2478 2 chr1D.!!$F1 2477
9 TraesCS7B01G501400 chr2A 547863084 547864901 1817 False 2656.0 2656 92.8690 629 2478 1 chr2A.!!$F1 1849
10 TraesCS7B01G501400 chr1A 579140249 579141378 1129 True 1498.0 1498 90.3580 629 1799 1 chr1A.!!$R1 1170
11 TraesCS7B01G501400 chr5A 75979066 75980196 1130 True 1495.0 1495 90.2730 629 1799 1 chr5A.!!$R1 1170
12 TraesCS7B01G501400 chr5A 543656530 543657444 914 False 1480.0 1480 95.8470 1564 2478 1 chr5A.!!$F1 914
13 TraesCS7B01G501400 chr5A 543640877 543641981 1104 False 413.5 435 89.3155 1 1066 2 chr5A.!!$F2 1065
14 TraesCS7B01G501400 chr6A 82805666 82806792 1126 True 1482.0 1482 90.1630 629 1796 1 chr6A.!!$R1 1167
15 TraesCS7B01G501400 chr3D 558027535 558028406 871 True 1472.0 1472 97.1360 1606 2478 1 chr3D.!!$R1 872
16 TraesCS7B01G501400 chr3D 114340790 114343243 2453 False 942.5 1445 96.5325 8 2478 2 chr3D.!!$F1 2470
17 TraesCS7B01G501400 chr3A 644405686 644406816 1130 True 1467.0 1467 89.8460 629 1799 1 chr3A.!!$R1 1170
18 TraesCS7B01G501400 chr5D 462628290 462629990 1700 False 779.0 1447 96.0585 629 2478 2 chr5D.!!$F1 1849
19 TraesCS7B01G501400 chr4D 407022979 407023980 1001 True 1314.0 1314 90.2560 977 1990 1 chr4D.!!$R1 1013

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
943 1606 1.231928 GGGGTCTTGGGTTTGGTGT 59.768 57.895 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 3008 1.299926 GGCTGTGTCGTCTTCGTGT 60.3 57.895 0.0 0.0 38.33 4.49 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
152 153 4.415150 CCACACTCCGCTGCCCAT 62.415 66.667 0.00 0.00 0.00 4.00
687 1282 4.194720 GGCGCTCTCCATCGACGT 62.195 66.667 7.64 0.00 0.00 4.34
867 1482 2.363795 CCTCCCTCTACACGCCCA 60.364 66.667 0.00 0.00 0.00 5.36
895 1558 2.043248 GTACGCCTCCCTCTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
943 1606 1.231928 GGGGTCTTGGGTTTGGTGT 59.768 57.895 0.00 0.00 0.00 4.16
1230 1962 0.106708 GTGAGTGCCTCTGTTGACCA 59.893 55.000 4.21 0.00 0.00 4.02
1291 2024 2.017049 GTGCTGACCTATCGCCATTTT 58.983 47.619 0.00 0.00 0.00 1.82
1338 2071 0.839853 AAGTGCCAGAGGGAGAAGCT 60.840 55.000 0.00 0.00 35.59 3.74
1360 2093 4.421058 TCAAGACCATTAACATCGACGAG 58.579 43.478 3.01 0.00 0.00 4.18
1397 2130 0.723981 CACGCTAGGCTTTCAAGAGC 59.276 55.000 0.00 0.00 41.96 4.09
1499 2233 6.980577 TGAACTAATTGGGGATGGATTAGTT 58.019 36.000 16.28 16.28 45.28 2.24
1566 2301 3.815401 TGTAGCCTGAAAAGCTCTGTTTC 59.185 43.478 2.93 2.93 41.83 2.78
1601 2678 6.009115 AGTCCTAGTTGGCAAATTTAAACG 57.991 37.500 5.17 0.00 35.26 3.60
1630 2707 2.233186 TCAGCTTGGTGACTGATGAGAG 59.767 50.000 0.00 0.00 37.99 3.20
1639 2716 2.103373 GACTGATGAGAGCCCACACTA 58.897 52.381 0.00 0.00 0.00 2.74
1855 2932 7.976135 ACATGTGCTTGGAAGATATATTCTC 57.024 36.000 9.80 1.65 31.78 2.87
1930 3008 2.473768 TGGTCTGGCCAAGATCCAA 58.526 52.632 7.01 0.00 45.94 3.53
1967 3045 3.193691 AGCCATGTGTCTACACTAGTGAC 59.806 47.826 29.30 16.94 46.55 3.67
2005 3083 2.145397 AGTCAGGTAGATCTGCCGAA 57.855 50.000 22.38 12.76 40.50 4.30
2058 3136 9.961265 CATGCAACAGAGATATCATAACATTTT 57.039 29.630 5.32 0.00 0.00 1.82
2110 3188 0.447801 CAGCTGTTTACATGGCGGAC 59.552 55.000 5.25 0.00 0.00 4.79
2406 3485 5.999205 AACATAAATGGCTTGTTGATCCA 57.001 34.783 0.00 0.00 32.61 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 1.377987 GGTTTGCGTCCTATGGGCA 60.378 57.895 0.00 0.0 34.35 5.36
157 187 1.078708 CGTGGGGTTTGCGTCCTAT 60.079 57.895 0.00 0.0 0.00 2.57
206 236 2.037620 GCGAGTGAGGCATCAGGGAT 62.038 60.000 0.00 0.0 35.66 3.85
235 265 3.862991 GAGGGGAGTTAGGGCGGC 61.863 72.222 0.00 0.0 0.00 6.53
687 1282 4.666253 GCTCACCTGCCCAAGCCA 62.666 66.667 0.00 0.0 38.69 4.75
700 1295 2.874648 AATCCGCTGCGATTGGCTCA 62.875 55.000 25.45 0.0 44.05 4.26
765 1380 3.368571 GCCTCTGCAGCGCCTTTT 61.369 61.111 9.47 0.0 37.47 2.27
895 1558 2.835431 CGCGGGGAGAGAGGTGAT 60.835 66.667 0.00 0.0 0.00 3.06
932 1595 4.130554 ACCGGCACACCAAACCCA 62.131 61.111 0.00 0.0 34.57 4.51
1091 1822 1.651240 GCTGCTGATGTTGGCGATGT 61.651 55.000 0.00 0.0 0.00 3.06
1139 1870 0.749454 GGCATCCTTGGCGATCTTGT 60.749 55.000 0.00 0.0 38.79 3.16
1230 1962 0.466922 AGGCAAAACAGAGCAGCAGT 60.467 50.000 0.00 0.0 0.00 4.40
1291 2024 2.230508 CGCCCTACAGTACAGACAAGAA 59.769 50.000 0.00 0.0 0.00 2.52
1338 2071 4.421058 CTCGTCGATGTTAATGGTCTTGA 58.579 43.478 4.21 0.0 0.00 3.02
1499 2233 5.006896 TGGACCTACCTAACTCTCAAAGA 57.993 43.478 0.00 0.0 39.86 2.52
1566 2301 3.314541 ACTAGGACTAACCAAAGTGCG 57.685 47.619 0.00 0.0 42.17 5.34
1601 2678 1.198637 GTCACCAAGCTGAACATGAGC 59.801 52.381 0.00 0.0 36.65 4.26
1630 2707 2.359975 GTGCCAGGTAGTGTGGGC 60.360 66.667 0.00 0.0 46.58 5.36
1639 2716 3.956199 CAATAAGATGATTGGTGCCAGGT 59.044 43.478 0.00 0.0 33.86 4.00
1749 2826 9.415544 GACAATTCTTAGTGCTTCAAATCATTT 57.584 29.630 0.00 0.0 0.00 2.32
1855 2932 3.256558 TCACGCTCTGAGATGAACATTG 58.743 45.455 9.28 0.0 0.00 2.82
1930 3008 1.299926 GGCTGTGTCGTCTTCGTGT 60.300 57.895 0.00 0.0 38.33 4.49
1962 3040 2.580601 CCCGAAAGTCCCCGTCACT 61.581 63.158 0.00 0.0 0.00 3.41
1967 3045 2.182537 CGTACCCGAAAGTCCCCG 59.817 66.667 0.00 0.0 35.63 5.73
2110 3188 2.185004 AGAAAACATCTGTGGACCGG 57.815 50.000 0.00 0.0 36.88 5.28


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

AutoCloner maintained by Alex Coulton.