Multiple sequence alignment - TraesCS5A01G142300

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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 TraesCS5A01G142300 chr5A 100.000 2309 0 0 1 2309 315535476 315537784 0.000000e+00 4265
1 TraesCS5A01G142300 chr2D 96.574 1547 52 1 1 1546 355482239 355483785 0.000000e+00 2562
2 TraesCS5A01G142300 chr3B 95.602 1546 63 4 1 1544 782022538 782024080 0.000000e+00 2473
3 TraesCS5A01G142300 chr2A 94.774 1550 74 6 1 1546 755357970 755356424 0.000000e+00 2407
4 TraesCS5A01G142300 chr2A 96.148 1246 45 3 303 1546 377108675 377109919 0.000000e+00 2032
5 TraesCS5A01G142300 chr7D 88.462 1560 163 14 3 1555 23563084 23564633 0.000000e+00 1868
6 TraesCS5A01G142300 chr7D 88.387 1550 165 12 3 1546 135769095 135770635 0.000000e+00 1851
7 TraesCS5A01G142300 chr7D 88.372 1548 164 13 3 1544 400291674 400290137 0.000000e+00 1847
8 TraesCS5A01G142300 chr7D 89.724 1450 137 9 3 1449 135763960 135762520 0.000000e+00 1842
9 TraesCS5A01G142300 chr7D 93.185 763 52 0 1547 2309 536722493 536721731 0.000000e+00 1122
10 TraesCS5A01G142300 chr7D 93.176 762 52 0 1547 2308 279642995 279642234 0.000000e+00 1120
11 TraesCS5A01G142300 chr7D 92.950 766 54 0 1544 2309 157467888 157468653 0.000000e+00 1116
12 TraesCS5A01G142300 chr6B 87.943 1551 171 13 3 1546 96339365 96340906 0.000000e+00 1814
13 TraesCS5A01G142300 chr6D 93.570 762 48 1 1548 2309 378725492 378726252 0.000000e+00 1134
14 TraesCS5A01G142300 chr6D 92.960 767 50 4 1544 2309 406616417 406617180 0.000000e+00 1114
15 TraesCS5A01G142300 chr5D 93.194 764 51 1 1547 2309 416383550 416382787 0.000000e+00 1122
16 TraesCS5A01G142300 chr5D 93.054 763 53 0 1547 2309 309145998 309145236 0.000000e+00 1116
17 TraesCS5A01G142300 chr5D 90.987 466 31 4 1083 1546 450667817 450667361 3.260000e-173 617
18 TraesCS5A01G142300 chr1D 93.263 757 51 0 1553 2309 125942898 125942142 0.000000e+00 1116
19 TraesCS5A01G142300 chr1D 92.950 766 54 0 1544 2309 439003502 439004267 0.000000e+00 1116
20 TraesCS5A01G142300 chr4D 90.558 466 32 5 1083 1546 483639168 483638713 7.060000e-170 606


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 TraesCS5A01G142300 chr5A 315535476 315537784 2308 False 4265 4265 100.000 1 2309 1 chr5A.!!$F1 2308
1 TraesCS5A01G142300 chr2D 355482239 355483785 1546 False 2562 2562 96.574 1 1546 1 chr2D.!!$F1 1545
2 TraesCS5A01G142300 chr3B 782022538 782024080 1542 False 2473 2473 95.602 1 1544 1 chr3B.!!$F1 1543
3 TraesCS5A01G142300 chr2A 755356424 755357970 1546 True 2407 2407 94.774 1 1546 1 chr2A.!!$R1 1545
4 TraesCS5A01G142300 chr2A 377108675 377109919 1244 False 2032 2032 96.148 303 1546 1 chr2A.!!$F1 1243
5 TraesCS5A01G142300 chr7D 23563084 23564633 1549 False 1868 1868 88.462 3 1555 1 chr7D.!!$F1 1552
6 TraesCS5A01G142300 chr7D 135769095 135770635 1540 False 1851 1851 88.387 3 1546 1 chr7D.!!$F2 1543
7 TraesCS5A01G142300 chr7D 400290137 400291674 1537 True 1847 1847 88.372 3 1544 1 chr7D.!!$R3 1541
8 TraesCS5A01G142300 chr7D 135762520 135763960 1440 True 1842 1842 89.724 3 1449 1 chr7D.!!$R1 1446
9 TraesCS5A01G142300 chr7D 536721731 536722493 762 True 1122 1122 93.185 1547 2309 1 chr7D.!!$R4 762
10 TraesCS5A01G142300 chr7D 279642234 279642995 761 True 1120 1120 93.176 1547 2308 1 chr7D.!!$R2 761
11 TraesCS5A01G142300 chr7D 157467888 157468653 765 False 1116 1116 92.950 1544 2309 1 chr7D.!!$F3 765
12 TraesCS5A01G142300 chr6B 96339365 96340906 1541 False 1814 1814 87.943 3 1546 1 chr6B.!!$F1 1543
13 TraesCS5A01G142300 chr6D 378725492 378726252 760 False 1134 1134 93.570 1548 2309 1 chr6D.!!$F1 761
14 TraesCS5A01G142300 chr6D 406616417 406617180 763 False 1114 1114 92.960 1544 2309 1 chr6D.!!$F2 765
15 TraesCS5A01G142300 chr5D 416382787 416383550 763 True 1122 1122 93.194 1547 2309 1 chr5D.!!$R2 762
16 TraesCS5A01G142300 chr5D 309145236 309145998 762 True 1116 1116 93.054 1547 2309 1 chr5D.!!$R1 762
17 TraesCS5A01G142300 chr1D 125942142 125942898 756 True 1116 1116 93.263 1553 2309 1 chr1D.!!$R1 756
18 TraesCS5A01G142300 chr1D 439003502 439004267 765 False 1116 1116 92.950 1544 2309 1 chr1D.!!$F1 765

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
68 69 0.766674 AAGGGGAAAAACCAAGGGGC 60.767 55.0 0.0 0.0 41.2 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1501 0.187117 TGAACTTCACCAATGGGCCA 59.813 50.0 9.61 9.61 37.9 5.36 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
43 44 2.682856 CAAGGGTATGACAATGGTTCGG 59.317 50.000 0.00 0.00 0.00 4.30
68 69 0.766674 AAGGGGAAAAACCAAGGGGC 60.767 55.000 0.00 0.00 41.20 5.80
150 151 6.039616 CAGCCTGAATCTTACTCTTAGTGAC 58.960 44.000 0.00 0.00 0.00 3.67
316 318 5.238868 CGATGGGAGAGTCGAATAAAGAGTA 59.761 44.000 0.00 0.00 40.11 2.59
511 514 8.458573 TGTAAACATGGTGAGTAAGAAATTGT 57.541 30.769 0.00 0.00 0.00 2.71
520 523 9.706691 TGGTGAGTAAGAAATTGTAGTCTAAAG 57.293 33.333 0.00 0.00 0.00 1.85
794 797 4.978083 ACTTTCTGGTGATGATTGATGC 57.022 40.909 0.00 0.00 0.00 3.91
829 832 7.411486 TCCTTGACTAGTAGATTTGAGGAAG 57.589 40.000 3.59 0.00 0.00 3.46
930 933 8.819974 AGAAAATGTTGCACTAATTTTGTCAAG 58.180 29.630 14.59 0.00 34.51 3.02
935 938 6.972328 TGTTGCACTAATTTTGTCAAGACTTC 59.028 34.615 1.53 0.00 0.00 3.01
1059 1062 6.881065 AGATATTTGAGTTTGTTAGAGCTGCA 59.119 34.615 1.02 0.00 0.00 4.41
1060 1063 5.772825 ATTTGAGTTTGTTAGAGCTGCAA 57.227 34.783 1.02 0.00 0.00 4.08
1109 1114 6.238676 GCTTATCGTATCCTCTTGACTGTACA 60.239 42.308 0.00 0.00 0.00 2.90
1115 1120 5.946942 ATCCTCTTGACTGTACATGTCAT 57.053 39.130 21.13 8.91 42.95 3.06
1127 1132 4.761227 TGTACATGTCATTGTTGCATCAGT 59.239 37.500 0.00 0.00 0.00 3.41
1246 1251 9.261180 TCGAGAAGAATATGTTGGACAATATTC 57.739 33.333 9.03 9.03 33.64 1.75
1337 1342 4.821805 GGAGGTTTGCTAGCATGCTATTTA 59.178 41.667 27.03 13.70 0.00 1.40
1511 1520 0.187117 TGGCCCATTGGTGAAGTTCA 59.813 50.000 0.08 0.08 0.00 3.18
1539 1548 1.950484 GCCTTCGAAATCCTTGAGCCA 60.950 52.381 0.00 0.00 0.00 4.75
1668 1677 4.446385 TGTTTGAGTAGATCCGTTTTGTCG 59.554 41.667 0.00 0.00 0.00 4.35
1674 1683 1.202604 AGATCCGTTTTGTCGTGTGGT 60.203 47.619 0.00 0.00 0.00 4.16
1683 1692 4.455917 TTTGTCGTGTGGTTTAATCGTC 57.544 40.909 0.00 0.00 0.00 4.20
1695 1704 4.698304 GGTTTAATCGTCATCTTGGTTGGA 59.302 41.667 0.00 0.00 0.00 3.53
1699 1708 3.417069 TCGTCATCTTGGTTGGAATGT 57.583 42.857 0.00 0.00 0.00 2.71
1706 1715 6.808212 GTCATCTTGGTTGGAATGTTTGTATG 59.192 38.462 0.00 0.00 0.00 2.39
1761 1772 3.055719 CGCGCAAACATGAGGGGT 61.056 61.111 8.75 0.00 0.00 4.95
1774 1785 2.525877 GGGGTCCCCGCTATAGCA 60.526 66.667 23.99 1.75 42.21 3.49
1809 1820 3.298619 TCATGATTTGCTTATGGTGGGG 58.701 45.455 0.00 0.00 0.00 4.96
1812 1823 2.225242 TGATTTGCTTATGGTGGGGTGT 60.225 45.455 0.00 0.00 0.00 4.16
1844 1855 4.159135 CAGAAGCTTAAACCCGAGTAGGTA 59.841 45.833 0.00 0.00 40.05 3.08
1854 1865 1.405121 CCGAGTAGGTAGGTTGTTGCC 60.405 57.143 0.00 0.00 34.51 4.52
1902 1915 2.666272 TGCTATGGTTGGGTTTCACA 57.334 45.000 0.00 0.00 0.00 3.58
1904 1917 3.300388 TGCTATGGTTGGGTTTCACAAA 58.700 40.909 0.00 0.00 0.00 2.83
1948 1961 0.034089 ATGCTTGCTAGGGGTCCAAC 60.034 55.000 0.00 0.00 0.00 3.77
1965 1978 6.237901 GGTCCAACCATAAGTGCATATGATA 58.762 40.000 6.97 0.00 38.42 2.15
1969 1982 7.228507 TCCAACCATAAGTGCATATGATACAAC 59.771 37.037 6.97 0.00 35.69 3.32
2032 2045 8.218338 AGAATTGCAAGAATGATTACTGGTAG 57.782 34.615 4.94 0.00 0.00 3.18
2058 2071 1.717194 TCGATTGCGTAGGGACAAAC 58.283 50.000 0.00 0.00 38.98 2.93
2294 2307 8.475639 ACACTCTTATTTATCGAAGAAGGCTAA 58.524 33.333 0.00 0.00 43.58 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.006859 CCTTGGTTTTTCCCCTTCATGTC 59.993 47.826 0.00 0.00 34.77 3.06
218 219 4.637977 GCTGCCATCTTTTAGTAGAGCTTT 59.362 41.667 0.00 0.00 0.00 3.51
316 318 6.598457 GGTGCTTGATATCTGATAGCATGAAT 59.402 38.462 24.36 0.65 43.01 2.57
386 388 1.668919 CGCTCTTAGTCTTGGCGTCAA 60.669 52.381 0.91 0.91 40.78 3.18
453 455 0.467474 CATGCCAGATGACCATGCCT 60.467 55.000 0.00 0.00 31.16 4.75
511 514 7.823665 ACATCAATACACACGACTTTAGACTA 58.176 34.615 0.00 0.00 0.00 2.59
520 523 6.946229 AAGAGTAACATCAATACACACGAC 57.054 37.500 0.00 0.00 0.00 4.34
794 797 3.755378 ACTAGTCAAGGAAGCAATTGCAG 59.245 43.478 30.89 17.43 45.16 4.41
829 832 5.841957 AATATGCTCCCAAATGACTTCAC 57.158 39.130 0.00 0.00 0.00 3.18
1059 1062 8.938906 GCAATTGAGACATTTGGATAACAATTT 58.061 29.630 10.34 0.00 39.21 1.82
1060 1063 8.316214 AGCAATTGAGACATTTGGATAACAATT 58.684 29.630 10.34 0.00 39.21 2.32
1109 1114 5.456548 TTCAACTGATGCAACAATGACAT 57.543 34.783 10.45 0.00 0.00 3.06
1115 1120 3.953612 ACTCCTTTCAACTGATGCAACAA 59.046 39.130 0.00 0.00 0.00 2.83
1168 1173 2.566833 TGGGACATTGTTGACCTCAG 57.433 50.000 0.00 0.00 37.75 3.35
1254 1259 6.850555 TGACGCAAAATCATCAATGACAATA 58.149 32.000 0.00 0.00 40.03 1.90
1292 1297 4.448395 CCAGAATTCATGAGAAGCGAGATC 59.552 45.833 8.44 0.00 37.14 2.75
1345 1350 9.956720 GTATCATAGAAGCTACAATGCAAAAAT 57.043 29.630 0.00 0.00 34.99 1.82
1492 1501 0.187117 TGAACTTCACCAATGGGCCA 59.813 50.000 9.61 9.61 37.90 5.36
1511 1520 2.211468 GATTTCGAAGGCCCTGGGGT 62.211 60.000 16.03 0.00 37.65 4.95
1539 1548 1.705002 TTACACCACTGCACAGGGCT 61.705 55.000 0.00 0.00 45.15 5.19
1581 1590 6.476378 AGTTGAGCACCATGTTTAAGTAGAT 58.524 36.000 0.00 0.00 0.00 1.98
1668 1677 4.454504 ACCAAGATGACGATTAAACCACAC 59.545 41.667 0.00 0.00 0.00 3.82
1674 1683 6.432783 ACATTCCAACCAAGATGACGATTAAA 59.567 34.615 0.00 0.00 0.00 1.52
1683 1692 6.690530 ACATACAAACATTCCAACCAAGATG 58.309 36.000 0.00 0.00 0.00 2.90
1706 1715 8.789762 ACTGTAGGACAACACCATAAATAAAAC 58.210 33.333 0.00 0.00 0.00 2.43
1761 1772 0.250295 GCAACATGCTATAGCGGGGA 60.250 55.000 19.55 2.47 45.83 4.81
1766 1777 4.732285 ACGTATTGCAACATGCTATAGC 57.268 40.909 18.18 18.18 45.31 2.97
1767 1778 6.285790 TGAACGTATTGCAACATGCTATAG 57.714 37.500 0.00 0.00 45.31 1.31
1770 1781 4.633565 TCATGAACGTATTGCAACATGCTA 59.366 37.500 16.54 0.00 45.31 3.49
1771 1782 3.439825 TCATGAACGTATTGCAACATGCT 59.560 39.130 16.54 0.00 45.31 3.79
1773 1784 6.688601 CAAATCATGAACGTATTGCAACATG 58.311 36.000 15.64 15.64 37.18 3.21
1774 1785 5.289193 GCAAATCATGAACGTATTGCAACAT 59.711 36.000 19.63 0.00 41.93 2.71
1809 1820 2.810439 AGCTTCTGTCACTCTCACAC 57.190 50.000 0.00 0.00 0.00 3.82
1812 1823 4.503296 GGGTTTAAGCTTCTGTCACTCTCA 60.503 45.833 0.00 0.00 0.00 3.27
1844 1855 4.229582 TCTTTATCCCATAGGCAACAACCT 59.770 41.667 0.00 0.00 44.31 3.50
1854 1865 8.429237 AGTATCAAGTCCTCTTTATCCCATAG 57.571 38.462 0.00 0.00 0.00 2.23
1902 1915 9.431887 TCGCAACTACTAAAGATCATTAAGTTT 57.568 29.630 5.46 0.00 0.00 2.66
1904 1917 8.997621 TTCGCAACTACTAAAGATCATTAAGT 57.002 30.769 0.00 0.00 0.00 2.24
1948 1961 9.363763 CTCTAGTTGTATCATATGCACTTATGG 57.636 37.037 7.33 0.00 31.71 2.74
1969 1982 8.584157 AGGCATGAGATAACATACTTTCTCTAG 58.416 37.037 0.00 0.00 36.43 2.43
2027 2040 3.852286 ACGCAATCGATAACAACTACCA 58.148 40.909 0.00 0.00 39.41 3.25
2032 2045 3.244579 GTCCCTACGCAATCGATAACAAC 59.755 47.826 0.00 0.00 39.41 3.32
2058 2071 4.662145 AGCTTTTGTCAACAAGAAAGTCG 58.338 39.130 10.05 0.00 37.15 4.18


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

AutoCloner maintained by Alex Coulton.