Multiple sequence alignment - TraesCS7A01G452000

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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 TraesCS7A01G452000 chr7A 100.000 2753 0 0 1 2753 644784219 644786971 0.000000e+00 5084
1 TraesCS7A01G452000 chr7A 89.230 1272 89 28 676 1915 644734799 644736054 0.000000e+00 1546
2 TraesCS7A01G452000 chr7A 86.071 1321 125 32 676 1965 644721728 644723020 0.000000e+00 1365
3 TraesCS7A01G452000 chr7A 88.143 894 96 9 879 1772 644710470 644711353 0.000000e+00 1055
4 TraesCS7A01G452000 chr7A 83.065 248 32 5 2375 2620 644720727 644720966 1.660000e-52 217
5 TraesCS7A01G452000 chr7B 90.126 2147 136 30 676 2753 608414805 608416944 0.000000e+00 2721
6 TraesCS7A01G452000 chr7B 86.662 1327 119 33 676 1965 608391981 608393286 0.000000e+00 1417
7 TraesCS7A01G452000 chr7B 84.771 1287 127 41 709 1965 608405052 608406299 0.000000e+00 1227
8 TraesCS7A01G452000 chr7B 85.998 1107 119 27 879 1963 608379924 608381016 0.000000e+00 1153
9 TraesCS7A01G452000 chr7B 85.069 288 41 1 2375 2662 608410213 608410498 2.680000e-75 292
10 TraesCS7A01G452000 chr7D 95.381 1364 53 8 676 2032 560701629 560702989 0.000000e+00 2161
11 TraesCS7A01G452000 chr7D 95.224 1361 52 10 676 2026 560682664 560684021 0.000000e+00 2141
12 TraesCS7A01G452000 chr7D 87.975 1289 100 31 676 1930 560596944 560598211 0.000000e+00 1471
13 TraesCS7A01G452000 chr7D 85.108 1296 131 38 676 1928 560602825 560604101 0.000000e+00 1267
14 TraesCS7A01G452000 chr7D 87.169 717 50 10 2065 2753 560703306 560704008 0.000000e+00 776
15 TraesCS7A01G452000 chr5A 98.818 677 8 0 1 677 323359073 323359749 0.000000e+00 1206
16 TraesCS7A01G452000 chr5A 97.630 675 16 0 1 675 69038524 69039198 0.000000e+00 1158
17 TraesCS7A01G452000 chr4A 98.817 676 8 0 1 676 284802104 284801429 0.000000e+00 1205
18 TraesCS7A01G452000 chr4A 98.667 675 9 0 1 675 284806892 284806218 0.000000e+00 1197
19 TraesCS7A01G452000 chr4A 98.667 675 9 0 1 675 284811671 284810997 0.000000e+00 1197
20 TraesCS7A01G452000 chr4A 98.363 672 11 0 4 675 359949282 359948611 0.000000e+00 1181
21 TraesCS7A01G452000 chr4A 98.077 676 13 0 1 676 361551542 361552217 0.000000e+00 1177
22 TraesCS7A01G452000 chr1A 97.661 684 11 1 1 679 252099873 252100556 0.000000e+00 1170
23 TraesCS7A01G452000 chr6D 92.939 609 36 6 1 607 441764306 441764909 0.000000e+00 880


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 TraesCS7A01G452000 chr7A 644784219 644786971 2752 False 5084.0 5084 100.000 1 2753 1 chr7A.!!$F3 2752
1 TraesCS7A01G452000 chr7A 644734799 644736054 1255 False 1546.0 1546 89.230 676 1915 1 chr7A.!!$F2 1239
2 TraesCS7A01G452000 chr7A 644710470 644711353 883 False 1055.0 1055 88.143 879 1772 1 chr7A.!!$F1 893
3 TraesCS7A01G452000 chr7A 644720727 644723020 2293 False 791.0 1365 84.568 676 2620 2 chr7A.!!$F4 1944
4 TraesCS7A01G452000 chr7B 608414805 608416944 2139 False 2721.0 2721 90.126 676 2753 1 chr7B.!!$F3 2077
5 TraesCS7A01G452000 chr7B 608391981 608393286 1305 False 1417.0 1417 86.662 676 1965 1 chr7B.!!$F2 1289
6 TraesCS7A01G452000 chr7B 608379924 608381016 1092 False 1153.0 1153 85.998 879 1963 1 chr7B.!!$F1 1084
7 TraesCS7A01G452000 chr7B 608405052 608410498 5446 False 759.5 1227 84.920 709 2662 2 chr7B.!!$F4 1953
8 TraesCS7A01G452000 chr7D 560682664 560684021 1357 False 2141.0 2141 95.224 676 2026 1 chr7D.!!$F3 1350
9 TraesCS7A01G452000 chr7D 560596944 560598211 1267 False 1471.0 1471 87.975 676 1930 1 chr7D.!!$F1 1254
10 TraesCS7A01G452000 chr7D 560701629 560704008 2379 False 1468.5 2161 91.275 676 2753 2 chr7D.!!$F4 2077
11 TraesCS7A01G452000 chr7D 560602825 560604101 1276 False 1267.0 1267 85.108 676 1928 1 chr7D.!!$F2 1252
12 TraesCS7A01G452000 chr5A 323359073 323359749 676 False 1206.0 1206 98.818 1 677 1 chr5A.!!$F2 676
13 TraesCS7A01G452000 chr5A 69038524 69039198 674 False 1158.0 1158 97.630 1 675 1 chr5A.!!$F1 674
14 TraesCS7A01G452000 chr4A 284801429 284802104 675 True 1205.0 1205 98.817 1 676 1 chr4A.!!$R1 675
15 TraesCS7A01G452000 chr4A 284806218 284806892 674 True 1197.0 1197 98.667 1 675 1 chr4A.!!$R2 674
16 TraesCS7A01G452000 chr4A 284810997 284811671 674 True 1197.0 1197 98.667 1 675 1 chr4A.!!$R3 674
17 TraesCS7A01G452000 chr4A 359948611 359949282 671 True 1181.0 1181 98.363 4 675 1 chr4A.!!$R4 671
18 TraesCS7A01G452000 chr4A 361551542 361552217 675 False 1177.0 1177 98.077 1 676 1 chr4A.!!$F1 675
19 TraesCS7A01G452000 chr1A 252099873 252100556 683 False 1170.0 1170 97.661 1 679 1 chr1A.!!$F1 678
20 TraesCS7A01G452000 chr6D 441764306 441764909 603 False 880.0 880 92.939 1 607 1 chr6D.!!$F1 606

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
957 1340 2.318908 AGCAACCAATTCCAAAGCTCA 58.681 42.857 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 6336 2.194271 CGGTAGCGAATCTCAAGGTTC 58.806 52.381 9.07 0.0 0.0 3.62 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
302 303 5.403512 CAGACTAGGATTTAGGGGGTGATA 58.596 45.833 0.00 0.00 0.00 2.15
373 374 6.737254 TTCGTCAGTTTCAGTCTTTTCTTT 57.263 33.333 0.00 0.00 0.00 2.52
464 465 3.838271 GCCCTCACCGATCGCTCA 61.838 66.667 10.32 0.00 0.00 4.26
532 533 4.449391 CGACCCCGTTTCTGTTGT 57.551 55.556 0.00 0.00 0.00 3.32
909 1283 9.084533 CCTATAAATACTAGCCTTCTTCACTCT 57.915 37.037 0.00 0.00 0.00 3.24
928 1303 6.019881 TCACTCTATAAACATCGCACAATTCG 60.020 38.462 0.00 0.00 0.00 3.34
957 1340 2.318908 AGCAACCAATTCCAAAGCTCA 58.681 42.857 0.00 0.00 0.00 4.26
1095 1478 0.107312 CCAGCCATCTCCAGGACTTG 60.107 60.000 0.00 0.00 0.00 3.16
1107 1490 1.954146 GGACTTGTGCGTCGCTGAA 60.954 57.895 19.50 9.79 34.75 3.02
1422 1816 2.203938 TTCGGCCTCAACCCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
1452 1846 0.108615 CGCGTTCCACTGAGATCCTT 60.109 55.000 0.00 0.00 0.00 3.36
1730 2124 2.266055 GGAGAAGAGCACGGTGGG 59.734 66.667 10.60 0.00 0.00 4.61
1733 2127 0.670854 GAGAAGAGCACGGTGGGTTC 60.671 60.000 10.60 0.00 0.00 3.62
1814 2232 7.918562 GGTACTGCTTTGTGTTTAGATTCAAAA 59.081 33.333 0.00 0.00 31.07 2.44
1877 2299 1.317613 TTGTGTCCTCATTGGTGTGC 58.682 50.000 0.00 0.00 37.07 4.57
2033 2498 6.432783 TGAAGGGTTATCTTGTGTAATGTTGG 59.567 38.462 0.00 0.00 0.00 3.77
2125 6160 4.772100 CCCACACATCCTTCCAAAATAAGT 59.228 41.667 0.00 0.00 0.00 2.24
2177 6218 8.392372 ACAAAATCCTAGTGATGATGATGATG 57.608 34.615 10.65 0.00 32.68 3.07
2221 6263 9.436957 ACCTTATATGTGCTAAAAATAGGATCG 57.563 33.333 0.00 0.00 0.00 3.69
2287 6329 6.202937 TGCAAAAGTTGTTAGAATAACCACG 58.797 36.000 0.00 0.00 31.28 4.94
2294 6336 8.084590 AGTTGTTAGAATAACCACGAGAAAAG 57.915 34.615 0.00 0.00 31.28 2.27
2349 6423 2.094757 TTGCGAGCTCACCGGAGAAA 62.095 55.000 15.40 0.00 44.26 2.52
2459 6539 6.550108 TCCCAAGTAGATACTGAAGTCCATAC 59.450 42.308 0.00 0.00 36.50 2.39
2469 6549 5.072741 ACTGAAGTCCATACTGCACATTTT 58.927 37.500 0.00 0.00 36.26 1.82
2473 6553 4.517285 AGTCCATACTGCACATTTTCGAT 58.483 39.130 0.00 0.00 33.57 3.59
2517 6597 6.727231 TCTCCCTTGTGTACCTTGTTTAGATA 59.273 38.462 0.00 0.00 0.00 1.98
2551 6631 5.708948 TGCATAACACAAAATTAGTGCTCC 58.291 37.500 10.03 0.00 40.59 4.70
2565 6645 8.757982 AATTAGTGCTCCTATTCATTGAACAT 57.242 30.769 0.15 0.00 0.00 2.71
2609 6690 6.701841 CGGCCCTTACATACACATATATCATC 59.298 42.308 0.00 0.00 0.00 2.92
2647 6728 5.380043 AGTCTTGATGATGGACAAGTTGTT 58.620 37.500 10.45 0.00 42.50 2.83
2657 6738 6.549364 TGATGGACAAGTTGTTACCAAAGATT 59.451 34.615 17.63 4.07 34.28 2.40
2663 6744 5.924475 AGTTGTTACCAAAGATTCTCACG 57.076 39.130 0.00 0.00 30.94 4.35
2681 6762 6.455647 TCTCACGTTCTATTTGTCACTCATT 58.544 36.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
302 303 4.469657 TGCAGACTTGGGTTTATTCAACT 58.530 39.130 0.00 0.00 35.46 3.16
373 374 3.825014 ACCTGAAGCTACTGACGAAACTA 59.175 43.478 0.00 0.00 0.00 2.24
464 465 1.301244 GATGCTCGTGCCATCCGAT 60.301 57.895 7.05 0.00 38.71 4.18
532 533 9.702253 ATTCCTCTCTACTTATTCAGAGTACAA 57.298 33.333 0.00 0.00 39.48 2.41
909 1283 4.568760 TGCTCGAATTGTGCGATGTTTATA 59.431 37.500 0.00 0.00 39.94 0.98
928 1303 2.223665 GGAATTGGTTGCTATGCTGCTC 60.224 50.000 0.00 0.00 0.00 4.26
957 1340 7.265673 TCGCTAGAGTAAAATATCAAGCAGTT 58.734 34.615 0.00 0.00 0.00 3.16
966 1349 8.475639 TGTTTTCTCCTCGCTAGAGTAAAATAT 58.524 33.333 0.00 0.00 42.86 1.28
969 1352 6.092955 TGTTTTCTCCTCGCTAGAGTAAAA 57.907 37.500 0.00 0.00 42.86 1.52
1095 1478 0.512952 ATGTCTTTTCAGCGACGCAC 59.487 50.000 23.70 9.92 32.93 5.34
1107 1490 4.974645 TGTTGTACCTGGAGATGTCTTT 57.025 40.909 0.00 0.00 0.00 2.52
1155 1546 8.792830 TTGAGTGATTGCTTAAGCTTAACTAT 57.207 30.769 26.90 13.13 42.66 2.12
1422 1816 2.028484 GAACGCGGGTGAGTGTGA 59.972 61.111 12.47 0.00 34.76 3.58
1452 1846 0.902531 GGCAACCCTCTAGCACAGTA 59.097 55.000 0.00 0.00 0.00 2.74
1730 2124 1.079503 GAACTGTGCCTGGATCGAAC 58.920 55.000 0.00 0.00 0.00 3.95
1733 2127 2.093973 ACTTAGAACTGTGCCTGGATCG 60.094 50.000 0.00 0.00 0.00 3.69
2006 2445 7.687941 ACATTACACAAGATAACCCTTCAAG 57.312 36.000 0.00 0.00 0.00 3.02
2009 2448 6.433093 ACCAACATTACACAAGATAACCCTTC 59.567 38.462 0.00 0.00 0.00 3.46
2011 2450 5.710099 CACCAACATTACACAAGATAACCCT 59.290 40.000 0.00 0.00 0.00 4.34
2014 2453 6.966021 ACACACCAACATTACACAAGATAAC 58.034 36.000 0.00 0.00 0.00 1.89
2033 2498 3.767630 AAGGTGCCCCACGACACAC 62.768 63.158 0.00 0.00 38.57 3.82
2177 6218 5.707242 AAGGTTGCATCATCATCATCATC 57.293 39.130 0.00 0.00 0.00 2.92
2252 6294 9.685828 TCTAACAACTTTTGCATTTTGGTATAC 57.314 29.630 0.00 0.00 0.00 1.47
2287 6329 4.693095 AGCGAATCTCAAGGTTCTTTTCTC 59.307 41.667 1.81 0.00 0.00 2.87
2294 6336 2.194271 CGGTAGCGAATCTCAAGGTTC 58.806 52.381 9.07 0.00 0.00 3.62
2349 6423 6.775629 TGGCTTCAAACACTTAGATTAGGTTT 59.224 34.615 0.00 0.00 32.33 3.27
2459 6539 6.317088 AGAACAATGTATCGAAAATGTGCAG 58.683 36.000 0.00 0.00 0.00 4.41
2469 6549 5.977635 AGACCATGAAGAACAATGTATCGA 58.022 37.500 0.00 0.00 0.00 3.59
2473 6553 5.338381 GGGAGAGACCATGAAGAACAATGTA 60.338 44.000 0.00 0.00 41.20 2.29
2517 6597 4.983671 TGTGTTATGCATCTCTACGAGT 57.016 40.909 0.19 0.00 0.00 4.18
2539 6619 8.579850 TGTTCAATGAATAGGAGCACTAATTT 57.420 30.769 0.00 0.00 34.79 1.82
2565 6645 5.336134 GGGCCGATTAAAGTTTTTCAGCTAA 60.336 40.000 0.00 0.00 0.00 3.09
2609 6690 8.707938 TCATCAAGACTAGTTATCATGTTGTG 57.292 34.615 0.00 0.00 0.00 3.33
2647 6728 7.876068 ACAAATAGAACGTGAGAATCTTTGGTA 59.124 33.333 0.00 0.00 34.92 3.25
2657 6738 5.447624 TGAGTGACAAATAGAACGTGAGA 57.552 39.130 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.