Multiple sequence alignment - TraesCS7D01G493100

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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 TraesCS7D01G493100 chr7D 100.000 2597 0 0 1 2597 601362225 601359629 0.000000e+00 4796
1 TraesCS7D01G493100 chr7D 97.238 1629 41 4 1 1628 478769265 478767640 0.000000e+00 2756
2 TraesCS7D01G493100 chr7D 95.828 1630 65 3 1 1629 104229420 104227793 0.000000e+00 2630
3 TraesCS7D01G493100 chr7D 90.032 311 30 1 1973 2283 104668491 104668182 4.030000e-108 401
4 TraesCS7D01G493100 chr7D 89.711 311 30 2 1973 2283 28407994 28407686 1.870000e-106 396
5 TraesCS7D01G493100 chr2D 97.360 1629 40 3 1 1628 57200728 57199102 0.000000e+00 2767
6 TraesCS7D01G493100 chr5D 97.304 1632 35 7 1 1627 276557853 276556226 0.000000e+00 2761
7 TraesCS7D01G493100 chr5D 89.677 310 31 1 1974 2283 433196855 433196547 6.740000e-106 394
8 TraesCS7D01G493100 chr1D 96.069 1628 62 2 1 1627 22301055 22302681 0.000000e+00 2651
9 TraesCS7D01G493100 chr1D 95.895 1632 61 6 1 1630 494854607 494852980 0.000000e+00 2638
10 TraesCS7D01G493100 chr1D 89.776 313 29 2 1973 2283 102828871 102828560 5.210000e-107 398
11 TraesCS7D01G493100 chr5B 95.188 1621 72 5 1 1616 690657824 690656205 0.000000e+00 2556
12 TraesCS7D01G493100 chr5B 94.843 1629 80 4 1 1627 707136749 707138375 0.000000e+00 2540
13 TraesCS7D01G493100 chr1A 94.911 1631 81 2 1 1629 561946444 561944814 0.000000e+00 2551
14 TraesCS7D01G493100 chr7A 93.252 978 41 13 1627 2597 693014618 693013659 0.000000e+00 1417
15 TraesCS7D01G493100 chr7A 92.536 978 52 10 1627 2597 693109772 693108809 0.000000e+00 1382
16 TraesCS7D01G493100 chr6B 91.318 311 27 0 1973 2283 79325744 79325434 2.390000e-115 425
17 TraesCS7D01G493100 chr6B 89.490 314 30 3 1973 2283 538736084 538736397 6.740000e-106 394
18 TraesCS7D01G493100 chr7B 90.654 321 22 4 2282 2597 680341015 680340698 1.110000e-113 420
19 TraesCS7D01G493100 chr1B 90.735 313 27 2 1973 2283 8616436 8616748 1.440000e-112 416


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 TraesCS7D01G493100 chr7D 601359629 601362225 2596 True 4796 4796 100.000 1 2597 1 chr7D.!!$R5 2596
1 TraesCS7D01G493100 chr7D 478767640 478769265 1625 True 2756 2756 97.238 1 1628 1 chr7D.!!$R4 1627
2 TraesCS7D01G493100 chr7D 104227793 104229420 1627 True 2630 2630 95.828 1 1629 1 chr7D.!!$R2 1628
3 TraesCS7D01G493100 chr2D 57199102 57200728 1626 True 2767 2767 97.360 1 1628 1 chr2D.!!$R1 1627
4 TraesCS7D01G493100 chr5D 276556226 276557853 1627 True 2761 2761 97.304 1 1627 1 chr5D.!!$R1 1626
5 TraesCS7D01G493100 chr1D 22301055 22302681 1626 False 2651 2651 96.069 1 1627 1 chr1D.!!$F1 1626
6 TraesCS7D01G493100 chr1D 494852980 494854607 1627 True 2638 2638 95.895 1 1630 1 chr1D.!!$R2 1629
7 TraesCS7D01G493100 chr5B 690656205 690657824 1619 True 2556 2556 95.188 1 1616 1 chr5B.!!$R1 1615
8 TraesCS7D01G493100 chr5B 707136749 707138375 1626 False 2540 2540 94.843 1 1627 1 chr5B.!!$F1 1626
9 TraesCS7D01G493100 chr1A 561944814 561946444 1630 True 2551 2551 94.911 1 1629 1 chr1A.!!$R1 1628
10 TraesCS7D01G493100 chr7A 693013659 693014618 959 True 1417 1417 93.252 1627 2597 1 chr7A.!!$R1 970
11 TraesCS7D01G493100 chr7A 693108809 693109772 963 True 1382 1382 92.536 1627 2597 1 chr7A.!!$R2 970

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
948 955 1.115467 CTGGATTGGTCGAGCTACCT 58.885 55.0 16.64 0.0 40.44 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2272 1.086696 CACTATTCAAGGCGGTGTGG 58.913 55.0 0.0 0.0 0.0 4.17 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
759 764 2.172505 TGTCCCAATGCCCATACTGTAG 59.827 50.000 0.00 0.00 0.00 2.74
948 955 1.115467 CTGGATTGGTCGAGCTACCT 58.885 55.000 16.64 0.00 40.44 3.08
1000 1007 3.295093 TGGTGGCAAAGAAGACAATTCA 58.705 40.909 0.00 0.00 0.00 2.57
1006 1013 4.229096 GCAAAGAAGACAATTCATGCGAA 58.771 39.130 0.00 0.00 35.05 4.70
1106 1113 5.923204 AGCTAAATCTACACCCAAGATCAG 58.077 41.667 0.00 0.00 32.48 2.90
1122 1129 4.250305 AGCAGGTGGCCGACGTTT 62.250 61.111 0.00 0.00 46.50 3.60
1175 1182 2.028420 TCATTCACAGAGGGCGATTG 57.972 50.000 0.00 0.00 0.00 2.67
1201 1208 1.543208 GGTCTTGTGGTGCTGTCATCA 60.543 52.381 0.00 0.00 0.00 3.07
1210 1217 2.354503 GGTGCTGTCATCAGTGATCACT 60.355 50.000 22.89 22.89 43.05 3.41
1360 1367 5.007682 TGAGATCGGATAATATCACGGTGA 58.992 41.667 14.01 14.01 0.00 4.02
1528 1537 2.158871 TGGGGACGTGCTAATAATCCAC 60.159 50.000 7.11 0.00 33.13 4.02
1570 1584 4.005650 GCCTGATTTCATTGTGAGTCTGA 58.994 43.478 0.00 0.00 0.00 3.27
1675 1694 6.403636 GCGATTGAAGTGTAAATCAGAATGGT 60.404 38.462 0.00 0.00 36.16 3.55
1801 1824 1.674441 CTACACATGCCAATCAGCCAG 59.326 52.381 0.00 0.00 0.00 4.85
1813 1836 0.396435 TCAGCCAGTAACACACCTGG 59.604 55.000 1.31 1.31 39.79 4.45
1862 1885 1.203050 CCAATTTGTCACCCTCCACCT 60.203 52.381 0.00 0.00 0.00 4.00
1914 1937 4.142160 GGGGCAGCAGTAAATAAAAAGAGG 60.142 45.833 0.00 0.00 0.00 3.69
1971 1995 1.603172 GGATAGTCGTTCCCGCAGATG 60.603 57.143 0.00 0.00 0.00 2.90
2045 2070 2.751259 ACAAAACATGATGAGCATCGCT 59.249 40.909 0.00 0.00 43.88 4.93
2055 2080 4.521062 GCATCGCTCGGCCTCTGT 62.521 66.667 0.00 0.00 0.00 3.41
2068 2093 5.138276 TCGGCCTCTGTATAACTAAGATGT 58.862 41.667 0.00 0.00 0.00 3.06
2076 2101 7.415229 TCTGTATAACTAAGATGTACACAGCG 58.585 38.462 0.00 0.00 37.34 5.18
2148 2175 5.516059 AGTAGGATCATATAGGACCGACA 57.484 43.478 15.68 1.06 0.00 4.35
2206 2233 1.496001 AGATTATGCTGCCACCCATGA 59.504 47.619 0.00 0.00 0.00 3.07
2368 2395 3.321497 ACATGAGAGCGACAAAAGAGAC 58.679 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
336 337 4.103013 TGGTTCCCCCTTACTGTTAAAC 57.897 45.455 0.00 0.00 0.00 2.01
759 764 0.105039 CTAAGTCCCCGCACCATCTC 59.895 60.000 0.00 0.00 0.00 2.75
1000 1007 6.038714 GGAGTCAATATTTCTTCCTTTCGCAT 59.961 38.462 0.00 0.00 0.00 4.73
1006 1013 6.595716 CGTTCTGGAGTCAATATTTCTTCCTT 59.404 38.462 9.22 0.00 0.00 3.36
1106 1113 2.775032 TAGAAACGTCGGCCACCTGC 62.775 60.000 2.24 0.00 40.16 4.85
1175 1182 2.555547 GCACCACAAGACCCTGCAC 61.556 63.158 0.00 0.00 0.00 4.57
1201 1208 3.184628 TGAAAGATCCCCAGTGATCACT 58.815 45.455 22.89 22.89 42.95 3.41
1210 1217 0.107214 GCCGACATGAAAGATCCCCA 60.107 55.000 0.00 0.00 0.00 4.96
1360 1367 7.093201 ACCTTCATTGAATTTAAGTGCATCCAT 60.093 33.333 0.00 0.00 0.00 3.41
1444 1452 6.067217 ACAATGCTCAATAGTAAACCTCCT 57.933 37.500 0.00 0.00 0.00 3.69
1528 1537 1.668419 GGGTCATCAATCCAACGAGG 58.332 55.000 0.00 0.00 39.47 4.63
1675 1694 4.780554 TGGTATGTGTCCTTCTTCCATACA 59.219 41.667 0.00 0.00 39.57 2.29
1774 1797 3.564027 GGCATGTGTAGCGTCGCC 61.564 66.667 14.86 0.00 0.00 5.54
1801 1824 2.993899 CTGTTCGATCCAGGTGTGTTAC 59.006 50.000 5.02 0.00 0.00 2.50
1813 1836 4.051922 CAATAGGTACTGGCTGTTCGATC 58.948 47.826 1.31 0.00 41.52 3.69
2021 2046 5.066893 AGCGATGCTCATCATGTTTTGTATT 59.933 36.000 10.13 0.00 37.69 1.89
2045 2070 5.138276 ACATCTTAGTTATACAGAGGCCGA 58.862 41.667 0.00 0.00 0.00 5.54
2055 2080 8.245491 TGTTTCGCTGTGTACATCTTAGTTATA 58.755 33.333 0.00 0.00 0.00 0.98
2068 2093 5.343593 CAGTTTGTTTTTGTTTCGCTGTGTA 59.656 36.000 0.00 0.00 0.00 2.90
2171 2198 2.257409 AATCTCCGGATTGGCGCACT 62.257 55.000 10.83 0.00 40.30 4.40
2211 2238 3.003173 TGGCCAGGGAGGTCTTCG 61.003 66.667 0.00 0.00 44.59 3.79
2245 2272 1.086696 CACTATTCAAGGCGGTGTGG 58.913 55.000 0.00 0.00 0.00 4.17
2350 2377 2.864097 GCAGTCTCTTTTGTCGCTCTCA 60.864 50.000 0.00 0.00 0.00 3.27
2441 2471 3.290308 TCTTGTCTCACTCGCTTCTTC 57.710 47.619 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.