Multiple sequence alignment - TraesCS7B01G380400

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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 TraesCS7B01G380400 chr7B 100.000 2333 0 0 1 2333 645258659 645256327 0.000000e+00 4309
1 TraesCS7B01G380400 chr1D 94.455 1569 70 6 1 1553 469033151 469034718 0.000000e+00 2399
2 TraesCS7B01G380400 chr2A 91.111 1575 104 7 1 1540 360449843 360451416 0.000000e+00 2100
3 TraesCS7B01G380400 chr4A 90.869 1588 109 12 1 1553 236931273 236932859 0.000000e+00 2097
4 TraesCS7B01G380400 chr4A 90.955 1570 109 9 1 1549 494014635 494013078 0.000000e+00 2082
5 TraesCS7B01G380400 chr4A 90.564 975 62 3 601 1546 552205894 552204921 0.000000e+00 1264
6 TraesCS7B01G380400 chr4A 92.170 613 43 3 1 608 552212931 552212319 0.000000e+00 861
7 TraesCS7B01G380400 chr4A 86.207 145 15 5 821 964 721011761 721011901 4.020000e-33 152
8 TraesCS7B01G380400 chr3D 90.406 1626 74 18 1 1555 550035751 550037365 0.000000e+00 2063
9 TraesCS7B01G380400 chr6D 90.130 1621 78 18 1 1550 138815894 138817503 0.000000e+00 2032
10 TraesCS7B01G380400 chr6A 89.133 1592 98 21 1 1527 49119295 49117714 0.000000e+00 1912
11 TraesCS7B01G380400 chr1B 91.589 1391 76 12 1 1360 672697201 672698581 0.000000e+00 1882
12 TraesCS7B01G380400 chr7D 90.775 1290 73 15 306 1552 28800455 28799169 0.000000e+00 1681
13 TraesCS7B01G380400 chr7D 93.214 781 41 8 1557 2333 579535322 579536094 0.000000e+00 1138
14 TraesCS7B01G380400 chr7A 93.365 633 31 7 1702 2332 671218893 671219516 0.000000e+00 926
15 TraesCS7B01G380400 chr2D 90.097 414 21 7 836 1231 618898343 618897932 9.550000e-144 520
16 TraesCS7B01G380400 chr2D 90.937 331 19 2 1227 1546 618889183 618888853 3.560000e-118 435
17 TraesCS7B01G380400 chr2B 75.778 739 116 43 841 1547 790816741 790816034 4.840000e-82 315


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 TraesCS7B01G380400 chr7B 645256327 645258659 2332 True 4309 4309 100.000 1 2333 1 chr7B.!!$R1 2332
1 TraesCS7B01G380400 chr1D 469033151 469034718 1567 False 2399 2399 94.455 1 1553 1 chr1D.!!$F1 1552
2 TraesCS7B01G380400 chr2A 360449843 360451416 1573 False 2100 2100 91.111 1 1540 1 chr2A.!!$F1 1539
3 TraesCS7B01G380400 chr4A 236931273 236932859 1586 False 2097 2097 90.869 1 1553 1 chr4A.!!$F1 1552
4 TraesCS7B01G380400 chr4A 494013078 494014635 1557 True 2082 2082 90.955 1 1549 1 chr4A.!!$R1 1548
5 TraesCS7B01G380400 chr4A 552204921 552205894 973 True 1264 1264 90.564 601 1546 1 chr4A.!!$R2 945
6 TraesCS7B01G380400 chr4A 552212319 552212931 612 True 861 861 92.170 1 608 1 chr4A.!!$R3 607
7 TraesCS7B01G380400 chr3D 550035751 550037365 1614 False 2063 2063 90.406 1 1555 1 chr3D.!!$F1 1554
8 TraesCS7B01G380400 chr6D 138815894 138817503 1609 False 2032 2032 90.130 1 1550 1 chr6D.!!$F1 1549
9 TraesCS7B01G380400 chr6A 49117714 49119295 1581 True 1912 1912 89.133 1 1527 1 chr6A.!!$R1 1526
10 TraesCS7B01G380400 chr1B 672697201 672698581 1380 False 1882 1882 91.589 1 1360 1 chr1B.!!$F1 1359
11 TraesCS7B01G380400 chr7D 28799169 28800455 1286 True 1681 1681 90.775 306 1552 1 chr7D.!!$R1 1246
12 TraesCS7B01G380400 chr7D 579535322 579536094 772 False 1138 1138 93.214 1557 2333 1 chr7D.!!$F1 776
13 TraesCS7B01G380400 chr7A 671218893 671219516 623 False 926 926 93.365 1702 2332 1 chr7A.!!$F1 630
14 TraesCS7B01G380400 chr2B 790816034 790816741 707 True 315 315 75.778 841 1547 1 chr2B.!!$R1 706

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
228 229 0.462047 GAACCGGCACTATCTGGTGG 60.462 60.0 0.0 0.0 44.63 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1752 0.226984 GCGCGCACTTGTTTCTTTTG 59.773 50.0 29.1 0.0 0.0 2.44 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
29 30 9.562408 TGTTAATTAGGTACAAGACAACATGAA 57.438 29.630 0.00 0.00 0.00 2.57
53 54 6.866480 ACAACAGTGTTTTGTCAATCAGATT 58.134 32.000 5.57 0.00 32.58 2.40
56 57 9.467258 CAACAGTGTTTTGTCAATCAGATTTAT 57.533 29.630 5.57 0.00 0.00 1.40
228 229 0.462047 GAACCGGCACTATCTGGTGG 60.462 60.000 0.00 0.00 44.63 4.61
259 267 2.189594 TTGGAGCATGAAGTGGAGTG 57.810 50.000 0.00 0.00 0.00 3.51
265 273 2.012673 GCATGAAGTGGAGTGTGATCC 58.987 52.381 0.00 0.00 40.03 3.36
290 298 8.324306 CCCTCATTATCATATCAACAGGTATGT 58.676 37.037 0.00 0.00 43.15 2.29
376 384 0.670546 AGAACACATGACCTTCCGCG 60.671 55.000 0.00 0.00 0.00 6.46
457 479 5.803461 GTCAAAACCTGTCCAAAACACTTAC 59.197 40.000 0.00 0.00 33.24 2.34
514 547 4.724399 TGAGAAAATGAAGTAACCAGGCA 58.276 39.130 0.00 0.00 0.00 4.75
548 581 3.198872 GTGGCTTAGATAGAGTGTTGGC 58.801 50.000 0.00 0.00 0.00 4.52
592 625 2.948315 GCTTTCTTAGATCCCTTGCCTG 59.052 50.000 0.00 0.00 0.00 4.85
603 636 1.747355 CCCTTGCCTGCTGTCTTAATG 59.253 52.381 0.00 0.00 0.00 1.90
653 687 3.838903 TCCCTTTCCCTCTGTCTCTTTAC 59.161 47.826 0.00 0.00 0.00 2.01
697 737 5.046663 TGACCTGCGAGGCAATGATATATTA 60.047 40.000 2.50 0.00 39.63 0.98
735 775 8.858003 ATTGAAGTATGTAAGAGTACGTGATG 57.142 34.615 0.00 0.00 32.40 3.07
906 954 8.457261 ACAGATTGTCAGATTAAAAGAGCAATC 58.543 33.333 13.08 13.08 40.40 2.67
1120 1223 2.683933 GGCGAGGAGAGGTTGGGA 60.684 66.667 0.00 0.00 0.00 4.37
1359 1538 1.305802 AGGTGTCATCGTGGGGCTA 60.306 57.895 0.00 0.00 0.00 3.93
1562 1752 6.927936 AGTGTAGATGTAGATGCATCATTCAC 59.072 38.462 27.81 20.54 45.58 3.18
1586 1776 3.404141 AAACAAGTGCGCGCGGTTT 62.404 52.632 33.06 28.70 0.00 3.27
1595 1785 2.003443 CGCGCGGTTTCACAACTTG 61.003 57.895 24.84 0.00 32.90 3.16
1648 1838 4.875536 CCATGAAGGTCGACAAATCATGTA 59.124 41.667 32.42 12.42 44.12 2.29
1725 1915 2.125106 GTCTAGTTGGCTGGCGGG 60.125 66.667 0.00 0.00 0.00 6.13
1866 2056 3.291101 CTTCCCCGCGTCGAGGAAA 62.291 63.158 17.36 9.29 39.14 3.13
1914 2104 2.422479 CTCCATCCAGAACATGTTGCAG 59.578 50.000 17.58 5.20 0.00 4.41
1935 2125 3.398353 GACGGCGAGGTCGAGGAAG 62.398 68.421 16.62 0.00 43.02 3.46
2115 2305 1.278413 TGCAGAGCAGAGCAAGAAGAT 59.722 47.619 0.00 0.00 37.90 2.40
2132 2322 0.738975 GATGAGATCGACCGACACCA 59.261 55.000 0.00 0.00 0.00 4.17
2134 2324 1.182667 TGAGATCGACCGACACCATT 58.817 50.000 0.00 0.00 0.00 3.16
2138 2328 2.758979 AGATCGACCGACACCATTACTT 59.241 45.455 0.00 0.00 0.00 2.24
2140 2330 2.165167 TCGACCGACACCATTACTTCT 58.835 47.619 0.00 0.00 0.00 2.85
2141 2331 2.163010 TCGACCGACACCATTACTTCTC 59.837 50.000 0.00 0.00 0.00 2.87
2142 2332 2.163815 CGACCGACACCATTACTTCTCT 59.836 50.000 0.00 0.00 0.00 3.10
2143 2333 3.376234 CGACCGACACCATTACTTCTCTA 59.624 47.826 0.00 0.00 0.00 2.43
2144 2334 4.496010 CGACCGACACCATTACTTCTCTAG 60.496 50.000 0.00 0.00 0.00 2.43
2146 2336 3.130516 CCGACACCATTACTTCTCTAGCA 59.869 47.826 0.00 0.00 0.00 3.49
2147 2337 4.106197 CGACACCATTACTTCTCTAGCAC 58.894 47.826 0.00 0.00 0.00 4.40
2158 2352 5.858381 ACTTCTCTAGCACTCACATTTCAA 58.142 37.500 0.00 0.00 0.00 2.69
2166 2360 3.004106 GCACTCACATTTCAAAGCAGAGT 59.996 43.478 0.00 0.00 35.44 3.24
2167 2361 4.781071 CACTCACATTTCAAAGCAGAGTC 58.219 43.478 0.00 0.00 33.01 3.36
2170 2364 2.807967 CACATTTCAAAGCAGAGTCGGA 59.192 45.455 0.00 0.00 0.00 4.55
2171 2365 3.070018 ACATTTCAAAGCAGAGTCGGAG 58.930 45.455 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.895636 TCTGATTGACAAAACACTGTTGT 57.104 34.783 0.00 0.00 41.84 3.32
228 229 7.487189 CACTTCATGCTCCAAATTCATTAAGAC 59.513 37.037 5.48 0.00 30.32 3.01
259 267 7.551974 CCTGTTGATATGATAATGAGGGATCAC 59.448 40.741 0.00 0.00 34.98 3.06
265 273 9.376075 GACATACCTGTTGATATGATAATGAGG 57.624 37.037 0.00 0.00 35.14 3.86
376 384 2.978010 CAACGACACACCCCAGCC 60.978 66.667 0.00 0.00 0.00 4.85
457 479 7.847487 TGAATCACAAGTAAAGTCGTGTTAAG 58.153 34.615 0.00 0.00 0.00 1.85
502 535 1.256812 GCCATGTTGCCTGGTTACTT 58.743 50.000 0.00 0.00 36.10 2.24
548 581 5.631512 GCTACGTCTGCTATTCTAAATGGAG 59.368 44.000 0.00 0.00 0.00 3.86
592 625 9.226345 GATGCAATACTAAAACATTAAGACAGC 57.774 33.333 0.00 0.00 0.00 4.40
603 636 7.122204 AGGTAAACAGGGATGCAATACTAAAAC 59.878 37.037 0.00 0.00 0.00 2.43
735 775 6.613755 ACGGCAATTCAGGTAAATACATAC 57.386 37.500 0.00 0.00 0.00 2.39
791 831 1.690893 GGCATCCTCTGAGCATAGTGA 59.309 52.381 0.00 0.00 0.00 3.41
879 919 7.750229 TGCTCTTTTAATCTGACAATCTGTT 57.250 32.000 0.00 0.00 0.00 3.16
906 954 3.131709 TCAGGCAGAAGACAAAAGGAG 57.868 47.619 0.00 0.00 0.00 3.69
972 1020 7.036220 CGAGGACATATGACTACTTTTTGACT 58.964 38.462 10.38 0.00 0.00 3.41
977 1025 7.429633 CATCTCGAGGACATATGACTACTTTT 58.570 38.462 13.56 0.00 0.00 2.27
1120 1223 4.394712 CCTCGACCCGCCTTGCTT 62.395 66.667 0.00 0.00 0.00 3.91
1216 1320 4.101448 CCGCCTTGCTGCCCTACT 62.101 66.667 0.00 0.00 0.00 2.57
1297 1432 3.075005 ATCTACGCCGCCACCACT 61.075 61.111 0.00 0.00 0.00 4.00
1371 1550 0.390472 GTCGGCAGACTCCCTCTTTG 60.390 60.000 9.95 0.00 43.80 2.77
1374 1553 2.143575 TCTGTCGGCAGACTCCCTCT 62.144 60.000 17.42 0.00 45.94 3.69
1376 1555 2.441051 TCTGTCGGCAGACTCCCT 59.559 61.111 17.42 0.00 45.94 4.20
1555 1745 4.797868 CGCACTTGTTTCTTTTGTGAATGA 59.202 37.500 0.00 0.00 0.00 2.57
1562 1752 0.226984 GCGCGCACTTGTTTCTTTTG 59.773 50.000 29.10 0.00 0.00 2.44
1586 1776 3.329386 GCAGTGCTATCTCAAGTTGTGA 58.671 45.455 8.18 9.88 34.17 3.58
1595 1785 2.527100 ACGTTTACGCAGTGCTATCTC 58.473 47.619 14.33 0.23 45.73 2.75
1648 1838 5.527582 GTGATGTAATAAAGCCGTGAAGGAT 59.472 40.000 0.00 0.00 45.00 3.24
1689 1879 4.515361 AGACTGGCTTCTTCTTCATGATG 58.485 43.478 0.00 0.00 0.00 3.07
1690 1880 4.840716 AGACTGGCTTCTTCTTCATGAT 57.159 40.909 0.00 0.00 0.00 2.45
1691 1881 4.774726 ACTAGACTGGCTTCTTCTTCATGA 59.225 41.667 0.00 0.00 0.00 3.07
1866 2056 1.079819 CAGGATGTTCGGCGTGACT 60.080 57.895 6.85 0.00 0.00 3.41
2115 2305 1.182667 AATGGTGTCGGTCGATCTCA 58.817 50.000 0.00 0.00 0.00 3.27
2132 2322 7.615403 TGAAATGTGAGTGCTAGAGAAGTAAT 58.385 34.615 0.00 0.00 0.00 1.89
2134 2324 6.590234 TGAAATGTGAGTGCTAGAGAAGTA 57.410 37.500 0.00 0.00 0.00 2.24
2138 2328 4.692625 GCTTTGAAATGTGAGTGCTAGAGA 59.307 41.667 0.00 0.00 0.00 3.10
2140 2330 4.388485 TGCTTTGAAATGTGAGTGCTAGA 58.612 39.130 0.00 0.00 0.00 2.43
2141 2331 4.453478 TCTGCTTTGAAATGTGAGTGCTAG 59.547 41.667 0.00 0.00 0.00 3.42
2142 2332 4.388485 TCTGCTTTGAAATGTGAGTGCTA 58.612 39.130 0.00 0.00 0.00 3.49
2143 2333 3.216800 TCTGCTTTGAAATGTGAGTGCT 58.783 40.909 0.00 0.00 0.00 4.40
2144 2334 3.004106 ACTCTGCTTTGAAATGTGAGTGC 59.996 43.478 6.21 0.00 32.90 4.40
2146 2336 3.496130 CGACTCTGCTTTGAAATGTGAGT 59.504 43.478 6.57 6.57 36.22 3.41
2147 2337 3.120408 CCGACTCTGCTTTGAAATGTGAG 60.120 47.826 0.00 0.00 0.00 3.51
2158 2352 1.416401 TGTTTTCCTCCGACTCTGCTT 59.584 47.619 0.00 0.00 0.00 3.91
2166 2360 1.483004 TCTGTGTGTGTTTTCCTCCGA 59.517 47.619 0.00 0.00 0.00 4.55
2167 2361 1.867233 CTCTGTGTGTGTTTTCCTCCG 59.133 52.381 0.00 0.00 0.00 4.63
2170 2364 3.197766 TGTCTCTCTGTGTGTGTTTTCCT 59.802 43.478 0.00 0.00 0.00 3.36
2171 2365 3.309954 GTGTCTCTCTGTGTGTGTTTTCC 59.690 47.826 0.00 0.00 0.00 3.13
2288 2486 4.520618 GTGCAGTACGTCGACGAA 57.479 55.556 41.52 17.51 43.02 3.85


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

AutoCloner maintained by Alex Coulton.