Multiple sequence alignment - TraesCS7A01G505100

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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 TraesCS7A01G505100 chr7A 100.000 2222 0 0 1 2222 692939676 692941897 0.000000e+00 4104.0
1 TraesCS7A01G505100 chr7B 93.733 1500 57 18 745 2222 680273091 680274575 0.000000e+00 2215.0
2 TraesCS7A01G505100 chr7B 99.865 743 1 0 1 743 674015952 674015210 0.000000e+00 1367.0
3 TraesCS7A01G505100 chr1B 100.000 742 0 0 1 742 673986962 673986221 0.000000e+00 1371.0
4 TraesCS7A01G505100 chr1B 98.003 751 8 1 1 751 11925139 11924396 0.000000e+00 1297.0
5 TraesCS7A01G505100 chr1B 78.947 152 24 7 167 311 676077251 676077101 1.820000e-16 97.1
6 TraesCS7A01G505100 chr4B 99.596 743 3 0 1 743 298685193 298684451 0.000000e+00 1356.0
7 TraesCS7A01G505100 chr2B 99.462 743 4 0 1 743 732555826 732555084 0.000000e+00 1351.0
8 TraesCS7A01G505100 chr1A 99.461 742 4 0 1 742 30577517 30576776 0.000000e+00 1349.0
9 TraesCS7A01G505100 chr2A 98.789 743 9 0 1 743 245703015 245702273 0.000000e+00 1323.0
10 TraesCS7A01G505100 chr7D 91.035 792 40 20 793 1568 601230590 601229814 0.000000e+00 1040.0
11 TraesCS7A01G505100 chr7D 86.515 571 44 16 1684 2222 601229134 601228565 4.080000e-167 597.0
12 TraesCS7A01G505100 chr7D 94.000 150 7 2 595 742 282160123 282160272 2.220000e-55 226.0
13 TraesCS7A01G505100 chr3A 93.377 604 28 6 150 744 156075275 156074675 0.000000e+00 883.0
14 TraesCS7A01G505100 chr6B 78.462 325 41 17 165 483 383771739 383771438 3.770000e-43 185.0
15 TraesCS7A01G505100 chr3B 100.000 38 0 0 1 38 237623095 237623132 1.100000e-08 71.3


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 TraesCS7A01G505100 chr7A 692939676 692941897 2221 False 4104.0 4104 100.000 1 2222 1 chr7A.!!$F1 2221
1 TraesCS7A01G505100 chr7B 680273091 680274575 1484 False 2215.0 2215 93.733 745 2222 1 chr7B.!!$F1 1477
2 TraesCS7A01G505100 chr7B 674015210 674015952 742 True 1367.0 1367 99.865 1 743 1 chr7B.!!$R1 742
3 TraesCS7A01G505100 chr1B 673986221 673986962 741 True 1371.0 1371 100.000 1 742 1 chr1B.!!$R2 741
4 TraesCS7A01G505100 chr1B 11924396 11925139 743 True 1297.0 1297 98.003 1 751 1 chr1B.!!$R1 750
5 TraesCS7A01G505100 chr4B 298684451 298685193 742 True 1356.0 1356 99.596 1 743 1 chr4B.!!$R1 742
6 TraesCS7A01G505100 chr2B 732555084 732555826 742 True 1351.0 1351 99.462 1 743 1 chr2B.!!$R1 742
7 TraesCS7A01G505100 chr1A 30576776 30577517 741 True 1349.0 1349 99.461 1 742 1 chr1A.!!$R1 741
8 TraesCS7A01G505100 chr2A 245702273 245703015 742 True 1323.0 1323 98.789 1 743 1 chr2A.!!$R1 742
9 TraesCS7A01G505100 chr7D 601228565 601230590 2025 True 818.5 1040 88.775 793 2222 2 chr7D.!!$R1 1429
10 TraesCS7A01G505100 chr3A 156074675 156075275 600 True 883.0 883 93.377 150 744 1 chr3A.!!$R1 594

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
768 778 0.822164 AAGTAGCAACGCCCGAGTAT 59.178 50.0 0.0 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 2317 0.824109 TCGAAAGGACGATGCTGGAT 59.176 50.0 0.0 0.0 37.37 3.41 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
745 755 4.082571 TCACGTGTAAGCTTACTAGTTCCC 60.083 45.833 31.14 8.55 34.77 3.97
746 756 4.082354 CACGTGTAAGCTTACTAGTTCCCT 60.082 45.833 31.14 10.74 34.77 4.20
751 761 7.275123 CGTGTAAGCTTACTAGTTCCCTTAAAG 59.725 40.741 31.14 10.03 34.77 1.85
768 778 0.822164 AAGTAGCAACGCCCGAGTAT 59.178 50.000 0.00 0.00 0.00 2.12
856 882 3.197116 CCACGTTACTCCCAATACTCCTT 59.803 47.826 0.00 0.00 0.00 3.36
857 883 4.430908 CACGTTACTCCCAATACTCCTTC 58.569 47.826 0.00 0.00 0.00 3.46
861 887 1.141185 CTCCCAATACTCCTTCCCCC 58.859 60.000 0.00 0.00 0.00 5.40
877 903 1.693640 CCCCCAGTCTGCCATTTCT 59.306 57.895 0.00 0.00 0.00 2.52
892 918 3.696548 CCATTTCTGTTTTCTCCCTAGCC 59.303 47.826 0.00 0.00 0.00 3.93
896 922 1.451567 GTTTTCTCCCTAGCCGGCC 60.452 63.158 26.15 5.07 0.00 6.13
1263 1294 2.412770 TCGATTTTCGGAAGGTAAACGC 59.587 45.455 0.00 0.00 40.88 4.84
1267 1298 0.249826 TTCGGAAGGTAAACGCCGTT 60.250 50.000 0.00 0.00 40.95 4.44
1300 1334 2.030335 TCGTGTATGATTGATTGCGCAC 59.970 45.455 11.12 0.00 0.00 5.34
1313 1347 1.369689 GCGCACAATCGATCCATGC 60.370 57.895 15.08 15.08 0.00 4.06
1330 1365 4.592351 TCCATGCATTCAAAGAAAGGGAAA 59.408 37.500 0.00 0.00 0.00 3.13
1342 1377 7.231519 TCAAAGAAAGGGAAAGAGAAAAGATCC 59.768 37.037 0.00 0.00 0.00 3.36
1461 1498 3.257127 CGGGGTTGTTAATCCACATGTTT 59.743 43.478 0.00 0.00 0.00 2.83
1462 1499 4.617298 CGGGGTTGTTAATCCACATGTTTC 60.617 45.833 0.00 0.00 0.00 2.78
1495 1532 5.835113 ATTCATAAGTGGATTTGGGTTCG 57.165 39.130 0.00 0.00 0.00 3.95
1498 1535 2.899303 AAGTGGATTTGGGTTCGGAT 57.101 45.000 0.00 0.00 0.00 4.18
1499 1536 2.128771 AGTGGATTTGGGTTCGGATG 57.871 50.000 0.00 0.00 0.00 3.51
1500 1537 0.455815 GTGGATTTGGGTTCGGATGC 59.544 55.000 0.00 0.00 0.00 3.91
1501 1538 0.038890 TGGATTTGGGTTCGGATGCA 59.961 50.000 0.00 0.00 0.00 3.96
1502 1539 1.181786 GGATTTGGGTTCGGATGCAA 58.818 50.000 0.00 0.00 0.00 4.08
1503 1540 1.135112 GGATTTGGGTTCGGATGCAAC 60.135 52.381 0.00 0.00 0.00 4.17
1504 1541 1.818674 GATTTGGGTTCGGATGCAACT 59.181 47.619 0.00 0.00 0.00 3.16
1528 1565 7.927629 ACTTGCAAGTGTTTTGATCAATGTTAT 59.072 29.630 30.66 0.00 37.98 1.89
1546 1583 8.635124 CAATGTTATGATCCGTTTGTTTTGTAC 58.365 33.333 0.00 0.00 0.00 2.90
1635 1990 7.172703 ACCTCGTCGATTTTCATTAAAGAAACT 59.827 33.333 5.40 0.87 37.24 2.66
1660 2015 6.337356 ACCAATGTTTTACAAAGAACCACAG 58.663 36.000 0.00 0.00 0.00 3.66
1667 2022 7.600752 TGTTTTACAAAGAACCACAGAAAAAGG 59.399 33.333 0.00 0.00 0.00 3.11
1681 2041 5.212934 CAGAAAAAGGAACTCGCTAAAACC 58.787 41.667 0.00 0.00 38.49 3.27
1711 2317 3.812262 CCCATGTGCTCTGTTCATGATA 58.188 45.455 0.00 0.00 40.64 2.15
1721 2327 4.563061 TCTGTTCATGATATCCAGCATCG 58.437 43.478 0.00 0.00 0.00 3.84
1736 2342 1.518929 GCATCGTCCTTTCGATCTTCG 59.481 52.381 0.00 0.00 46.64 3.79
1907 2540 5.432645 TCACAGACAACTTAACCAATCACA 58.567 37.500 0.00 0.00 0.00 3.58
2009 2643 3.256383 TGACATTTGCATCTGGAACCTTG 59.744 43.478 0.00 0.00 0.00 3.61
2105 2742 3.571401 CCAGCAGGTTGAACTTGATCTTT 59.429 43.478 11.86 0.00 0.00 2.52
2114 2751 8.477256 AGGTTGAACTTGATCTTTCAAAATTCA 58.523 29.630 15.08 9.37 42.02 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
745 755 1.659098 CTCGGGCGTTGCTACTTTAAG 59.341 52.381 0.00 0.00 0.00 1.85
746 756 1.001181 ACTCGGGCGTTGCTACTTTAA 59.999 47.619 0.00 0.00 0.00 1.52
751 761 0.596859 GGATACTCGGGCGTTGCTAC 60.597 60.000 0.00 0.00 0.00 3.58
861 887 1.915141 AACAGAAATGGCAGACTGGG 58.085 50.000 17.77 0.00 35.08 4.45
877 903 1.298667 GCCGGCTAGGGAGAAAACA 59.701 57.895 22.15 0.00 41.48 2.83
896 922 2.281070 CCGGGATTGGCGATGGAG 60.281 66.667 0.00 0.00 0.00 3.86
993 1019 1.743623 CGGTAGTGCCATGGCGAAA 60.744 57.895 30.87 15.94 45.51 3.46
1236 1262 2.348140 CTTCCGAAAATCGAGCCGCG 62.348 60.000 0.00 0.00 43.74 6.46
1263 1294 3.782046 ACACGATCCAAGAATAGAACGG 58.218 45.455 0.00 0.00 33.16 4.44
1267 1298 7.951591 TCAATCATACACGATCCAAGAATAGA 58.048 34.615 0.00 0.00 0.00 1.98
1300 1334 5.177725 TCTTTGAATGCATGGATCGATTG 57.822 39.130 0.00 0.00 0.00 2.67
1313 1347 8.416329 TCTTTTCTCTTTCCCTTTCTTTGAATG 58.584 33.333 0.00 0.00 0.00 2.67
1330 1365 3.328931 TGCAACCTCTGGATCTTTTCTCT 59.671 43.478 0.00 0.00 0.00 3.10
1342 1377 2.868583 CGGATGTAATCTGCAACCTCTG 59.131 50.000 0.00 0.00 43.82 3.35
1374 1409 0.907486 AATGCAGTCTGCTAGCCTCA 59.093 50.000 24.76 3.79 45.31 3.86
1499 1536 3.864583 TGATCAAAACACTTGCAAGTTGC 59.135 39.130 29.23 21.17 45.29 4.17
1500 1537 6.036300 ACATTGATCAAAACACTTGCAAGTTG 59.964 34.615 29.23 23.29 37.08 3.16
1501 1538 6.108015 ACATTGATCAAAACACTTGCAAGTT 58.892 32.000 29.23 17.28 37.08 2.66
1502 1539 5.663456 ACATTGATCAAAACACTTGCAAGT 58.337 33.333 26.36 26.36 40.60 3.16
1503 1540 6.592798 AACATTGATCAAAACACTTGCAAG 57.407 33.333 24.84 24.84 0.00 4.01
1504 1541 7.924947 TCATAACATTGATCAAAACACTTGCAA 59.075 29.630 13.09 0.00 0.00 4.08
1528 1565 9.607988 ATGATATAGTACAAAACAAACGGATCA 57.392 29.630 0.00 0.00 0.00 2.92
1592 1947 5.585500 CGAGGTGTGATCGTTCTTTAAAA 57.415 39.130 0.00 0.00 35.48 1.52
1635 1990 7.339721 TCTGTGGTTCTTTGTAAAACATTGGTA 59.660 33.333 0.00 0.00 0.00 3.25
1660 2015 5.177725 TGGTTTTAGCGAGTTCCTTTTTC 57.822 39.130 0.00 0.00 0.00 2.29
1667 2022 2.937149 GGATCCTGGTTTTAGCGAGTTC 59.063 50.000 3.84 0.00 0.00 3.01
1681 2041 2.903855 GCACATGGGCGGATCCTG 60.904 66.667 3.02 3.07 34.39 3.86
1711 2317 0.824109 TCGAAAGGACGATGCTGGAT 59.176 50.000 0.00 0.00 37.37 3.41
1721 2327 0.915227 GTCGCGAAGATCGAAAGGAC 59.085 55.000 12.06 0.00 43.74 3.85
1736 2342 1.596477 GCATGGATGAGGGAGTCGC 60.596 63.158 0.00 0.00 0.00 5.19
1907 2540 8.732746 AAATATTAGCAAACATACTCGGTCTT 57.267 30.769 0.00 0.00 0.00 3.01
1943 2577 6.908870 TGTCTGCTAAATGTGTGCTATAAG 57.091 37.500 0.00 0.00 0.00 1.73
2070 2704 5.104402 TCAACCTGCTGGATCTTATCAATGA 60.104 40.000 17.64 0.00 37.04 2.57
2165 2803 6.825610 ACATTTTTGTGGCTATCTTTGGAAA 58.174 32.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.