Multiple sequence alignment - TraesCS1A01G026800

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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 TraesCS1A01G026800 chr1A 100.000 2225 0 0 1 2225 12699445 12697221 0.000000e+00 4109
1 TraesCS1A01G026800 chr1A 94.618 1059 56 1 607 1665 22634220 22633163 0.000000e+00 1639
2 TraesCS1A01G026800 chr1A 96.869 543 17 0 1683 2225 582630413 582630955 0.000000e+00 909
3 TraesCS1A01G026800 chr1A 96.501 543 19 0 1683 2225 6704133 6703591 0.000000e+00 898
4 TraesCS1A01G026800 chr1D 94.002 1067 55 3 607 1665 11123622 11124687 0.000000e+00 1607
5 TraesCS1A01G026800 chr1D 93.160 614 29 7 1 608 43146873 43146267 0.000000e+00 889
6 TraesCS1A01G026800 chr1D 92.480 625 29 9 1 613 33439716 33439098 0.000000e+00 878
7 TraesCS1A01G026800 chr1D 92.939 609 32 7 1 608 469472783 469472185 0.000000e+00 876
8 TraesCS1A01G026800 chr1D 94.977 219 4 1 607 818 11040947 11041165 9.840000e-89 337
9 TraesCS1A01G026800 chr1D 94.977 219 4 1 607 818 11089658 11089876 9.840000e-89 337
10 TraesCS1A01G026800 chr1B 93.025 1061 70 4 607 1665 16692982 16694040 0.000000e+00 1546
11 TraesCS1A01G026800 chr1B 91.722 1063 80 8 607 1665 16478263 16479321 0.000000e+00 1469
12 TraesCS1A01G026800 chr1B 91.931 756 57 2 910 1665 16645423 16646174 0.000000e+00 1055
13 TraesCS1A01G026800 chr6A 97.238 543 15 0 1683 2225 516448366 516448908 0.000000e+00 920
14 TraesCS1A01G026800 chr6A 96.501 543 19 0 1683 2225 127393554 127394096 0.000000e+00 898
15 TraesCS1A01G026800 chr2A 96.869 543 17 0 1683 2225 734828351 734827809 0.000000e+00 909
16 TraesCS1A01G026800 chr2A 96.685 543 18 0 1683 2225 94305437 94305979 0.000000e+00 904
17 TraesCS1A01G026800 chr7A 96.685 543 17 1 1683 2225 679328444 679328985 0.000000e+00 902
18 TraesCS1A01G026800 chr4A 96.501 543 19 0 1683 2225 179662317 179662859 0.000000e+00 898
19 TraesCS1A01G026800 chr4A 96.501 543 19 0 1683 2225 579644179 579643637 0.000000e+00 898
20 TraesCS1A01G026800 chr3D 92.071 618 33 8 1 612 541663680 541664287 0.000000e+00 856
21 TraesCS1A01G026800 chr2B 91.948 621 33 12 2 608 655887353 655887970 0.000000e+00 854
22 TraesCS1A01G026800 chr6D 92.182 614 30 8 1 608 428500361 428500962 0.000000e+00 852
23 TraesCS1A01G026800 chr2D 92.282 609 33 8 1 608 606230936 606230341 0.000000e+00 852
24 TraesCS1A01G026800 chr2D 92.118 609 36 6 1 609 627006048 627006644 0.000000e+00 848
25 TraesCS1A01G026800 chr7D 92.144 611 34 6 1 608 16066275 16065676 0.000000e+00 850


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 TraesCS1A01G026800 chr1A 12697221 12699445 2224 True 4109 4109 100.000 1 2225 1 chr1A.!!$R2 2224
1 TraesCS1A01G026800 chr1A 22633163 22634220 1057 True 1639 1639 94.618 607 1665 1 chr1A.!!$R3 1058
2 TraesCS1A01G026800 chr1A 582630413 582630955 542 False 909 909 96.869 1683 2225 1 chr1A.!!$F1 542
3 TraesCS1A01G026800 chr1A 6703591 6704133 542 True 898 898 96.501 1683 2225 1 chr1A.!!$R1 542
4 TraesCS1A01G026800 chr1D 11123622 11124687 1065 False 1607 1607 94.002 607 1665 1 chr1D.!!$F3 1058
5 TraesCS1A01G026800 chr1D 43146267 43146873 606 True 889 889 93.160 1 608 1 chr1D.!!$R2 607
6 TraesCS1A01G026800 chr1D 33439098 33439716 618 True 878 878 92.480 1 613 1 chr1D.!!$R1 612
7 TraesCS1A01G026800 chr1D 469472185 469472783 598 True 876 876 92.939 1 608 1 chr1D.!!$R3 607
8 TraesCS1A01G026800 chr1B 16692982 16694040 1058 False 1546 1546 93.025 607 1665 1 chr1B.!!$F3 1058
9 TraesCS1A01G026800 chr1B 16478263 16479321 1058 False 1469 1469 91.722 607 1665 1 chr1B.!!$F1 1058
10 TraesCS1A01G026800 chr1B 16645423 16646174 751 False 1055 1055 91.931 910 1665 1 chr1B.!!$F2 755
11 TraesCS1A01G026800 chr6A 516448366 516448908 542 False 920 920 97.238 1683 2225 1 chr6A.!!$F2 542
12 TraesCS1A01G026800 chr6A 127393554 127394096 542 False 898 898 96.501 1683 2225 1 chr6A.!!$F1 542
13 TraesCS1A01G026800 chr2A 734827809 734828351 542 True 909 909 96.869 1683 2225 1 chr2A.!!$R1 542
14 TraesCS1A01G026800 chr2A 94305437 94305979 542 False 904 904 96.685 1683 2225 1 chr2A.!!$F1 542
15 TraesCS1A01G026800 chr7A 679328444 679328985 541 False 902 902 96.685 1683 2225 1 chr7A.!!$F1 542
16 TraesCS1A01G026800 chr4A 179662317 179662859 542 False 898 898 96.501 1683 2225 1 chr4A.!!$F1 542
17 TraesCS1A01G026800 chr4A 579643637 579644179 542 True 898 898 96.501 1683 2225 1 chr4A.!!$R1 542
18 TraesCS1A01G026800 chr3D 541663680 541664287 607 False 856 856 92.071 1 612 1 chr3D.!!$F1 611
19 TraesCS1A01G026800 chr2B 655887353 655887970 617 False 854 854 91.948 2 608 1 chr2B.!!$F1 606
20 TraesCS1A01G026800 chr6D 428500361 428500962 601 False 852 852 92.182 1 608 1 chr6D.!!$F1 607
21 TraesCS1A01G026800 chr2D 606230341 606230936 595 True 852 852 92.282 1 608 1 chr2D.!!$R1 607
22 TraesCS1A01G026800 chr2D 627006048 627006644 596 False 848 848 92.118 1 609 1 chr2D.!!$F1 608
23 TraesCS1A01G026800 chr7D 16065676 16066275 599 True 850 850 92.144 1 608 1 chr7D.!!$R1 607

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
581 608 1.205417 CTAAAGGCCCTTACGAACCGA 59.795 52.381 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 1953 1.174783 AGCGGCGTCTAAGAGAGAAA 58.825 50.0 9.37 0.0 35.37 2.52 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
61 62 4.489679 GAGATTTTTGCTCGACCAAGTT 57.510 40.909 0.00 0.00 0.00 2.66
76 77 5.377478 GACCAAGTTATAGATCCCAAAGGG 58.623 45.833 0.00 0.00 46.11 3.95
215 224 2.306847 GGTGGTGGTTGTGAGACATTT 58.693 47.619 0.00 0.00 0.00 2.32
226 235 9.631257 TGGTTGTGAGACATTTGATGATATATT 57.369 29.630 0.00 0.00 0.00 1.28
483 505 1.825090 CCATGTGCTGGCACTTTAGA 58.175 50.000 23.30 6.26 46.30 2.10
581 608 1.205417 CTAAAGGCCCTTACGAACCGA 59.795 52.381 0.00 0.00 0.00 4.69
592 619 1.445582 CGAACCGACGCTAAAGCCT 60.446 57.895 0.00 0.00 37.91 4.58
778 816 6.855763 TCCATATTTCCATTTCCATATGCC 57.144 37.500 0.00 0.00 30.99 4.40
780 818 6.664816 TCCATATTTCCATTTCCATATGCCTC 59.335 38.462 0.00 0.00 30.99 4.70
849 887 7.015877 CGGAGTTATCCTTCTTTTCGAAAAAG 58.984 38.462 22.67 17.55 44.22 2.27
886 924 7.775729 GCATTAGCGTTATTTTTATGCGTAT 57.224 32.000 0.00 0.00 32.81 3.06
927 966 5.989477 AGACGATTTGATGACCTATTTGGA 58.011 37.500 0.00 0.00 39.71 3.53
934 973 4.843728 TGATGACCTATTTGGACCAACTC 58.156 43.478 6.36 0.00 39.71 3.01
1041 1080 2.840102 CCCGCCGGAGAGGAGAAT 60.840 66.667 5.05 0.00 43.02 2.40
1351 1390 6.876789 TGTGTCGATGTACTTATGGTTCAATT 59.123 34.615 0.00 0.00 0.00 2.32
1392 1431 9.632807 TTTTTAATTTATGAGATGTCGGTTTGG 57.367 29.630 0.00 0.00 0.00 3.28
1399 1438 2.218603 AGATGTCGGTTTGGTGTTCAC 58.781 47.619 0.00 0.00 0.00 3.18
1413 1452 5.867166 TGGTGTTCACGTGTTTACTAAAAC 58.133 37.500 16.51 10.24 44.40 2.43
1431 1470 7.483307 ACTAAAACGCTCATGAAATATGCATT 58.517 30.769 3.54 0.00 0.00 3.56
1543 1582 1.139853 GAAGAACTCGAGCCCCATGAT 59.860 52.381 13.61 0.00 0.00 2.45
1611 1650 8.883731 AGATGAGAATTAGTTTTATTGTGACCG 58.116 33.333 0.00 0.00 0.00 4.79
1621 1661 1.089481 ATTGTGACCGCGTGCCTATG 61.089 55.000 4.92 0.00 0.00 2.23
1661 1701 3.181470 GGCTTAACCTTTTGCTCAAACCA 60.181 43.478 0.00 0.00 34.51 3.67
1665 1705 6.038161 GCTTAACCTTTTGCTCAAACCATTTT 59.962 34.615 0.00 0.00 0.00 1.82
1666 1706 5.816449 AACCTTTTGCTCAAACCATTTTG 57.184 34.783 0.00 0.00 43.17 2.44
1667 1707 3.627123 ACCTTTTGCTCAAACCATTTTGC 59.373 39.130 0.00 0.00 41.78 3.68
1668 1708 3.878699 CCTTTTGCTCAAACCATTTTGCT 59.121 39.130 0.00 0.00 41.78 3.91
1669 1709 5.055812 CCTTTTGCTCAAACCATTTTGCTA 58.944 37.500 0.00 0.00 41.78 3.49
1670 1710 5.702209 CCTTTTGCTCAAACCATTTTGCTAT 59.298 36.000 0.00 0.00 41.78 2.97
1671 1711 6.128472 CCTTTTGCTCAAACCATTTTGCTATC 60.128 38.462 0.00 0.00 41.78 2.08
1672 1712 5.465532 TTGCTCAAACCATTTTGCTATCA 57.534 34.783 0.00 0.00 41.78 2.15
1673 1713 5.465532 TGCTCAAACCATTTTGCTATCAA 57.534 34.783 0.00 0.00 41.78 2.57
1674 1714 5.229423 TGCTCAAACCATTTTGCTATCAAC 58.771 37.500 0.00 0.00 41.78 3.18
1675 1715 5.221402 TGCTCAAACCATTTTGCTATCAACA 60.221 36.000 0.00 0.00 41.78 3.33
1676 1716 5.870978 GCTCAAACCATTTTGCTATCAACAT 59.129 36.000 0.00 0.00 41.78 2.71
1677 1717 6.369615 GCTCAAACCATTTTGCTATCAACATT 59.630 34.615 0.00 0.00 41.78 2.71
1678 1718 7.545265 GCTCAAACCATTTTGCTATCAACATTA 59.455 33.333 0.00 0.00 41.78 1.90
1679 1719 9.590451 CTCAAACCATTTTGCTATCAACATTAT 57.410 29.630 0.00 0.00 41.78 1.28
1680 1720 9.941325 TCAAACCATTTTGCTATCAACATTATT 57.059 25.926 0.00 0.00 41.78 1.40
1789 1830 2.227388 CCGAACGAAGGTGTAGTGTAGT 59.773 50.000 0.00 0.00 0.00 2.73
1912 1953 0.623723 AAACCGGGTATGCCACATCT 59.376 50.000 6.32 0.00 36.17 2.90
1947 1988 2.489722 GCCGCTTCTCCAAAGAAAGAAT 59.510 45.455 0.00 0.00 40.95 2.40
2088 2129 1.798735 CACGGATCGTACTCGGTGT 59.201 57.895 12.14 0.00 38.32 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 3.674410 GCGGTAGCGGGTAATACTATTCC 60.674 52.174 17.08 0.00 0.00 3.01
581 608 1.275291 TGCAGAACTAGGCTTTAGCGT 59.725 47.619 0.00 2.29 43.26 5.07
592 619 4.380973 GCATGAGACACTAGTGCAGAACTA 60.381 45.833 22.90 3.73 40.56 2.24
778 816 4.583871 ACAGAGAAACTTATTGGCAGGAG 58.416 43.478 0.00 0.00 0.00 3.69
780 818 5.220931 GCATACAGAGAAACTTATTGGCAGG 60.221 44.000 0.00 0.00 0.00 4.85
849 887 9.751542 AATAACGCTAATGCTAGTCATATATCC 57.248 33.333 0.00 0.00 34.33 2.59
918 957 6.884295 TCACAATAAGAGTTGGTCCAAATAGG 59.116 38.462 5.69 0.00 34.25 2.57
927 966 8.157476 AGACTACAAATCACAATAAGAGTTGGT 58.843 33.333 8.02 0.00 43.21 3.67
934 973 9.208022 TCAGTTCAGACTACAAATCACAATAAG 57.792 33.333 0.00 0.00 33.90 1.73
1041 1080 1.672854 CCTCCGGCCATGACGTCTTA 61.673 60.000 17.92 0.00 28.54 2.10
1138 1177 2.892425 GGTCATCGCCGAGCCAAG 60.892 66.667 0.00 0.00 0.00 3.61
1315 1354 1.298157 ATCGACACACGCCATTGGTG 61.298 55.000 14.72 14.72 42.26 4.17
1388 1427 6.492007 TTTAGTAAACACGTGAACACCAAA 57.508 33.333 25.01 13.73 0.00 3.28
1392 1431 4.431070 GCGTTTTAGTAAACACGTGAACAC 59.569 41.667 25.01 15.42 43.05 3.32
1399 1438 5.258685 TCATGAGCGTTTTAGTAAACACG 57.741 39.130 18.09 18.09 43.05 4.49
1413 1452 4.849926 GCAGTAATGCATATTTCATGAGCG 59.150 41.667 10.86 0.00 34.41 5.03
1431 1470 2.039974 CAGCAACATGCCCGCAGTA 61.040 57.895 0.00 0.00 46.52 2.74
1436 1475 1.321474 ATAATCCAGCAACATGCCCG 58.679 50.000 0.00 0.00 46.52 6.13
1509 1548 8.780249 GCTCGAGTTCTTCTCTAAGTAGATTAT 58.220 37.037 15.13 0.00 40.75 1.28
1565 1604 4.269183 TCTCAGAAGTTTGTCCAAAGCAA 58.731 39.130 0.00 0.00 0.00 3.91
1603 1642 1.739929 CATAGGCACGCGGTCACAA 60.740 57.895 12.47 0.00 0.00 3.33
1611 1650 4.552166 ACAATAATGTTCATAGGCACGC 57.448 40.909 0.00 0.00 35.91 5.34
1621 1661 7.702348 GGTTAAGCCTCATCAACAATAATGTTC 59.298 37.037 0.00 0.00 46.78 3.18
1665 1705 6.667370 CGTGCCAATAATAATGTTGATAGCA 58.333 36.000 0.00 0.00 29.82 3.49
1666 1706 5.569059 GCGTGCCAATAATAATGTTGATAGC 59.431 40.000 0.00 0.00 29.82 2.97
1667 1707 6.667370 TGCGTGCCAATAATAATGTTGATAG 58.333 36.000 0.00 0.00 29.82 2.08
1668 1708 6.625873 TGCGTGCCAATAATAATGTTGATA 57.374 33.333 0.00 0.00 29.82 2.15
1669 1709 5.512753 TGCGTGCCAATAATAATGTTGAT 57.487 34.783 0.00 0.00 29.82 2.57
1670 1710 4.972514 TGCGTGCCAATAATAATGTTGA 57.027 36.364 0.00 0.00 29.82 3.18
1671 1711 5.042593 ACATGCGTGCCAATAATAATGTTG 58.957 37.500 5.64 0.00 0.00 3.33
1672 1712 5.261209 ACATGCGTGCCAATAATAATGTT 57.739 34.783 5.64 0.00 0.00 2.71
1673 1713 4.916983 ACATGCGTGCCAATAATAATGT 57.083 36.364 5.64 0.00 0.00 2.71
1674 1714 6.239908 TCTACATGCGTGCCAATAATAATG 57.760 37.500 5.64 0.00 0.00 1.90
1675 1715 6.072508 CCTTCTACATGCGTGCCAATAATAAT 60.073 38.462 5.64 0.00 0.00 1.28
1676 1716 5.238432 CCTTCTACATGCGTGCCAATAATAA 59.762 40.000 5.64 0.00 0.00 1.40
1677 1717 4.754618 CCTTCTACATGCGTGCCAATAATA 59.245 41.667 5.64 0.00 0.00 0.98
1678 1718 3.565482 CCTTCTACATGCGTGCCAATAAT 59.435 43.478 5.64 0.00 0.00 1.28
1679 1719 2.942376 CCTTCTACATGCGTGCCAATAA 59.058 45.455 5.64 0.00 0.00 1.40
1680 1720 2.560504 CCTTCTACATGCGTGCCAATA 58.439 47.619 5.64 0.00 0.00 1.90
1681 1721 1.382522 CCTTCTACATGCGTGCCAAT 58.617 50.000 5.64 0.00 0.00 3.16
1789 1830 6.945435 TCTTTGCTATGTTTAACCTTCATCCA 59.055 34.615 0.00 0.00 0.00 3.41
1912 1953 1.174783 AGCGGCGTCTAAGAGAGAAA 58.825 50.000 9.37 0.00 35.37 2.52
2088 2129 4.519437 CTGATGCGAGCCAGCCGA 62.519 66.667 4.97 0.00 36.02 5.54
2102 2143 2.423577 GAAGACTAAAAAGGGCGCTGA 58.576 47.619 7.64 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.