Multiple sequence alignment - TraesCS7A01G146800

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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 TraesCS7A01G146800 chr7A 100.000 2219 0 0 1 2219 99143541 99141323 0.000000e+00 4098
1 TraesCS7A01G146800 chr7D 93.762 1507 92 2 1 1507 95148796 95147292 0.000000e+00 2261
2 TraesCS7A01G146800 chr7D 87.260 1405 154 13 3 1402 95834858 95833474 0.000000e+00 1580
3 TraesCS7A01G146800 chr7D 87.136 1407 143 18 3 1402 95990249 95988874 0.000000e+00 1561
4 TraesCS7A01G146800 chr7D 86.709 1407 167 9 3 1402 96017117 96015724 0.000000e+00 1544
5 TraesCS7A01G146800 chr7D 87.069 1392 146 18 16 1402 95970296 95968934 0.000000e+00 1543
6 TraesCS7A01G146800 chr7D 86.861 1408 140 25 1 1396 96031666 96030292 0.000000e+00 1533
7 TraesCS7A01G146800 chr7D 85.977 1412 166 15 3 1402 95964237 95962846 0.000000e+00 1482
8 TraesCS7A01G146800 chr7D 85.926 1350 149 15 133 1471 95976277 95974958 0.000000e+00 1402
9 TraesCS7A01G146800 chr7D 87.118 621 43 18 1627 2219 95147293 95146682 0.000000e+00 669
10 TraesCS7A01G146800 chr7D 85.122 699 54 20 1351 2034 96079888 96079225 0.000000e+00 669
11 TraesCS7A01G146800 chr7D 89.954 219 17 3 1648 1862 96081146 96080929 6.030000e-71 278
12 TraesCS7A01G146800 chr7B 89.542 1310 124 4 1 1310 49361689 49362985 0.000000e+00 1648
13 TraesCS7A01G146800 chr7B 88.406 1311 140 3 1 1310 49587808 49589107 0.000000e+00 1568
14 TraesCS7A01G146800 chr7B 87.796 1311 147 4 1 1310 49612482 49611184 0.000000e+00 1522
15 TraesCS7A01G146800 chr7B 82.612 1432 157 41 694 2103 50363793 50362432 0.000000e+00 1181
16 TraesCS7A01G146800 chr7B 86.076 711 88 6 694 1402 50680647 50679946 0.000000e+00 754
17 TraesCS7A01G146800 chr7B 85.091 711 93 9 694 1402 50626524 50625825 0.000000e+00 713
18 TraesCS7A01G146800 chr7B 82.797 715 91 18 694 1402 50629643 50628955 5.240000e-171 610
19 TraesCS7A01G146800 chr7B 87.945 506 59 2 743 1247 50635378 50634874 1.470000e-166 595
20 TraesCS7A01G146800 chr7B 77.857 560 68 28 1422 1965 49549392 49548873 1.670000e-76 296
21 TraesCS7A01G146800 chr7B 78.423 482 61 21 1488 1965 49607637 49608079 7.810000e-70 274
22 TraesCS7A01G146800 chr7B 82.927 246 25 13 1688 1928 49610879 49610646 2.890000e-49 206


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 TraesCS7A01G146800 chr7A 99141323 99143541 2218 True 4098.0 4098 100.0000 1 2219 1 chr7A.!!$R1 2218
1 TraesCS7A01G146800 chr7D 95833474 95834858 1384 True 1580.0 1580 87.2600 3 1402 1 chr7D.!!$R1 1399
2 TraesCS7A01G146800 chr7D 95988874 95990249 1375 True 1561.0 1561 87.1360 3 1402 1 chr7D.!!$R5 1399
3 TraesCS7A01G146800 chr7D 96015724 96017117 1393 True 1544.0 1544 86.7090 3 1402 1 chr7D.!!$R6 1399
4 TraesCS7A01G146800 chr7D 95968934 95970296 1362 True 1543.0 1543 87.0690 16 1402 1 chr7D.!!$R3 1386
5 TraesCS7A01G146800 chr7D 96030292 96031666 1374 True 1533.0 1533 86.8610 1 1396 1 chr7D.!!$R7 1395
6 TraesCS7A01G146800 chr7D 95962846 95964237 1391 True 1482.0 1482 85.9770 3 1402 1 chr7D.!!$R2 1399
7 TraesCS7A01G146800 chr7D 95146682 95148796 2114 True 1465.0 2261 90.4400 1 2219 2 chr7D.!!$R8 2218
8 TraesCS7A01G146800 chr7D 95974958 95976277 1319 True 1402.0 1402 85.9260 133 1471 1 chr7D.!!$R4 1338
9 TraesCS7A01G146800 chr7D 96079225 96081146 1921 True 473.5 669 87.5380 1351 2034 2 chr7D.!!$R9 683
10 TraesCS7A01G146800 chr7B 49361689 49362985 1296 False 1648.0 1648 89.5420 1 1310 1 chr7B.!!$F1 1309
11 TraesCS7A01G146800 chr7B 49587808 49589107 1299 False 1568.0 1568 88.4060 1 1310 1 chr7B.!!$F2 1309
12 TraesCS7A01G146800 chr7B 50362432 50363793 1361 True 1181.0 1181 82.6120 694 2103 1 chr7B.!!$R2 1409
13 TraesCS7A01G146800 chr7B 49610646 49612482 1836 True 864.0 1522 85.3615 1 1928 2 chr7B.!!$R5 1927
14 TraesCS7A01G146800 chr7B 50679946 50680647 701 True 754.0 754 86.0760 694 1402 1 chr7B.!!$R4 708
15 TraesCS7A01G146800 chr7B 50625825 50629643 3818 True 661.5 713 83.9440 694 1402 2 chr7B.!!$R6 708
16 TraesCS7A01G146800 chr7B 50634874 50635378 504 True 595.0 595 87.9450 743 1247 1 chr7B.!!$R3 504
17 TraesCS7A01G146800 chr7B 49548873 49549392 519 True 296.0 296 77.8570 1422 1965 1 chr7B.!!$R1 543

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
156 157 0.036952 CCATCGACAAGGTGTGCTCT 60.037 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1234 0.910513 CTCGCGAGAACAGAACATCG 59.089 55.0 32.06 0.0 41.32 3.84 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
51 52 2.330372 CCTCCTCGTCCACGTCGAA 61.330 63.158 0.00 0.00 40.80 3.71
100 101 1.384989 GGAGAGCGTCGGGATGAAGA 61.385 60.000 0.00 0.00 0.00 2.87
156 157 0.036952 CCATCGACAAGGTGTGCTCT 60.037 55.000 0.00 0.00 0.00 4.09
240 241 2.094906 CGACTTGGACGACACCATAGAA 60.095 50.000 0.00 0.00 39.82 2.10
255 256 0.958876 TAGAACGCTGCCTCGTCTCA 60.959 55.000 0.82 0.00 42.46 3.27
337 338 3.630013 ACGCCTTCAGCCTGCTCA 61.630 61.111 0.00 0.00 38.78 4.26
833 839 3.144506 CTCTTGCCATGTTCACAGAAGT 58.855 45.455 0.00 0.00 0.00 3.01
950 958 5.957798 TCCTCAATTTGTTTCAGATGATGC 58.042 37.500 0.00 0.00 0.00 3.91
982 990 3.306917 TTCTGACATTGCTGGCAATTG 57.693 42.857 16.82 14.28 40.83 2.32
983 991 2.241160 TCTGACATTGCTGGCAATTGT 58.759 42.857 16.82 16.77 40.83 2.71
986 995 4.109766 CTGACATTGCTGGCAATTGTATG 58.890 43.478 16.82 10.37 40.83 2.39
997 1006 6.561737 TGGCAATTGTATGTTCTTCGTTTA 57.438 33.333 7.40 0.00 0.00 2.01
1219 1234 4.094887 TCTGCAAACAAGACAAGAACTGAC 59.905 41.667 0.00 0.00 0.00 3.51
1243 1258 2.159421 TGTTCTGTTCTCGCGAGGATAC 60.159 50.000 33.98 26.83 0.00 2.24
1310 1332 4.516652 AGATCCTGCTCCTGCTATTTTT 57.483 40.909 0.00 0.00 40.48 1.94
1311 1333 5.636903 AGATCCTGCTCCTGCTATTTTTA 57.363 39.130 0.00 0.00 40.48 1.52
1312 1334 6.006275 AGATCCTGCTCCTGCTATTTTTAA 57.994 37.500 0.00 0.00 40.48 1.52
1313 1335 5.825151 AGATCCTGCTCCTGCTATTTTTAAC 59.175 40.000 0.00 0.00 40.48 2.01
1315 1337 6.308015 TCCTGCTCCTGCTATTTTTAACTA 57.692 37.500 0.00 0.00 40.48 2.24
1316 1338 6.113411 TCCTGCTCCTGCTATTTTTAACTAC 58.887 40.000 0.00 0.00 40.48 2.73
1318 1340 6.037610 CCTGCTCCTGCTATTTTTAACTACTG 59.962 42.308 0.00 0.00 40.48 2.74
1319 1341 5.354234 TGCTCCTGCTATTTTTAACTACTGC 59.646 40.000 0.00 0.00 40.48 4.40
1332 1364 4.785511 AACTACTGCTGTAGGTAGTGTG 57.214 45.455 27.98 7.94 44.21 3.82
1381 1416 4.391830 CGAGCAGAAGGTTAAGCAATAACA 59.608 41.667 7.52 0.00 44.77 2.41
1471 4637 9.261318 GTGATTGCTTTTTCTGTTTAAACAAAC 57.739 29.630 20.89 3.37 38.66 2.93
1473 4639 6.396459 TGCTTTTTCTGTTTAAACAAACGG 57.604 33.333 20.89 10.21 38.66 4.44
1519 4687 6.956299 AAATCATTCAAAGCAGAAATTCCG 57.044 33.333 0.00 0.00 0.00 4.30
1524 4692 7.028962 TCATTCAAAGCAGAAATTCCGTATTG 58.971 34.615 0.00 0.00 0.00 1.90
1541 4709 5.472137 CCGTATTGGATCCCGAAATACAAAT 59.528 40.000 23.26 11.70 42.00 2.32
1604 4772 1.071699 ACCGCCACACACATAGAAGTT 59.928 47.619 0.00 0.00 0.00 2.66
2054 5276 9.158364 CATACACGCATTTCTATTTTGTATGTC 57.842 33.333 9.62 0.00 39.77 3.06
2157 5380 3.032609 CCGATCATCGCGCTGACC 61.033 66.667 15.73 4.13 38.82 4.02
2194 5417 3.728474 GTCTGCATGAGGCCATCG 58.272 61.111 5.01 0.00 43.89 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.144727 AGGATCCGGCGGGTCTCT 62.145 66.667 35.52 27.22 33.83 3.10
255 256 3.511779 TGGCTGGCCATCTCCTTT 58.488 55.556 5.51 0.00 41.89 3.11
531 536 1.374190 CTGGAGGAGCTTGTGCAGT 59.626 57.895 8.97 0.00 42.74 4.40
833 839 1.964373 GGCAAGGCGTTCCGAAGAA 60.964 57.895 0.00 0.00 37.47 2.52
950 958 8.961092 CCAGCAATGTCAGAAATTATTAAATCG 58.039 33.333 0.00 0.00 0.00 3.34
997 1006 1.683943 CCATTCATCACCGGCATCTT 58.316 50.000 0.00 0.00 0.00 2.40
1219 1234 0.910513 CTCGCGAGAACAGAACATCG 59.089 55.000 32.06 0.00 41.32 3.84
1310 1332 4.703575 CCACACTACCTACAGCAGTAGTTA 59.296 45.833 14.41 4.64 45.30 2.24
1311 1333 3.510360 CCACACTACCTACAGCAGTAGTT 59.490 47.826 14.41 3.65 45.30 2.24
1313 1335 3.090037 ACCACACTACCTACAGCAGTAG 58.910 50.000 9.22 9.22 45.90 2.57
1315 1337 1.893801 GACCACACTACCTACAGCAGT 59.106 52.381 0.00 0.00 0.00 4.40
1316 1338 1.893137 TGACCACACTACCTACAGCAG 59.107 52.381 0.00 0.00 0.00 4.24
1318 1340 3.611766 ATTGACCACACTACCTACAGC 57.388 47.619 0.00 0.00 0.00 4.40
1319 1341 5.417894 TGTCTATTGACCACACTACCTACAG 59.582 44.000 4.82 0.00 42.28 2.74
1332 1364 3.929610 GCTGAGTTGTCTGTCTATTGACC 59.070 47.826 4.82 0.00 42.28 4.02
1381 1416 8.042515 AGAATTACAATGTAATTTTGGCATGCT 58.957 29.630 26.23 15.89 31.22 3.79
1471 4637 2.465860 TGTAATTCTGTGACCACCCG 57.534 50.000 0.00 0.00 0.00 5.28
1524 4692 7.595130 GCTCATTTAATTTGTATTTCGGGATCC 59.405 37.037 1.92 1.92 0.00 3.36
1541 4709 6.252599 ACTATGTGATGGGAGCTCATTTAA 57.747 37.500 17.19 0.00 0.00 1.52
1576 4744 1.599518 TGTGTGGCGGTCACCATTC 60.600 57.895 10.66 0.00 45.48 2.67
1714 4890 8.294954 AGGAGAGAGACATACGAATTAAGAAA 57.705 34.615 0.00 0.00 0.00 2.52
1717 4893 8.410141 AGAAAGGAGAGAGACATACGAATTAAG 58.590 37.037 0.00 0.00 0.00 1.85
2034 5256 6.474364 TGTCGACATACAAAATAGAAATGCG 58.526 36.000 15.76 0.00 0.00 4.73
2110 5333 0.931005 CCATAGCGGCTTTCTTCGTC 59.069 55.000 8.26 0.00 0.00 4.20
2132 5355 3.088941 GCGATGATCGGGGTGTGGA 62.089 63.158 17.27 0.00 40.84 4.02
2167 5390 2.680352 ATGCAGACCCTCGTCCGT 60.680 61.111 0.00 0.00 40.12 4.69
2184 5407 2.586245 CCAGCTTCGATGGCCTCA 59.414 61.111 3.32 0.00 0.00 3.86
2191 5414 1.207791 AGAACCATCCCAGCTTCGAT 58.792 50.000 0.00 0.00 0.00 3.59
2194 5417 2.087646 GTGAAGAACCATCCCAGCTTC 58.912 52.381 0.00 0.00 36.42 3.86


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

AutoCloner maintained by Alex Coulton.