Multiple sequence alignment - TraesCS3A01G213500

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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 TraesCS3A01G213500 chr3A 100.000 2571 0 0 1 2571 385525353 385522783 0.000000e+00 4748
1 TraesCS3A01G213500 chr3A 92.564 780 52 4 1790 2566 389051573 389052349 0.000000e+00 1114
2 TraesCS3A01G213500 chr3A 92.159 778 57 2 1792 2566 386883567 386882791 0.000000e+00 1096
3 TraesCS3A01G213500 chr3A 91.260 778 65 1 1792 2566 388614681 388613904 0.000000e+00 1057
4 TraesCS3A01G213500 chr3A 91.001 789 58 7 1791 2570 341232302 341231518 0.000000e+00 1051
5 TraesCS3A01G213500 chr3D 96.212 1663 43 8 1 1646 292372998 292374657 0.000000e+00 2704
6 TraesCS3A01G213500 chr3D 90.818 795 59 9 1786 2571 4191109 4190320 0.000000e+00 1051
7 TraesCS3A01G213500 chr3B 93.231 916 36 13 765 1656 386375765 386374852 0.000000e+00 1325
8 TraesCS3A01G213500 chr3B 95.686 765 25 4 1 762 386376764 386376005 0.000000e+00 1223
9 TraesCS3A01G213500 chr3B 96.226 106 4 0 1683 1788 386374857 386374752 9.460000e-40 174
10 TraesCS3A01G213500 chr4A 91.720 785 54 7 1791 2566 477292287 477293069 0.000000e+00 1079
11 TraesCS3A01G213500 chr7A 91.233 787 57 9 1795 2571 492380390 492381174 0.000000e+00 1061
12 TraesCS3A01G213500 chr2D 91.105 787 60 5 1786 2565 538596243 538595460 0.000000e+00 1057
13 TraesCS3A01G213500 chr1A 90.818 795 58 7 1785 2567 49143904 49144695 0.000000e+00 1050


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 TraesCS3A01G213500 chr3A 385522783 385525353 2570 True 4748.000000 4748 100.000000 1 2571 1 chr3A.!!$R2 2570
1 TraesCS3A01G213500 chr3A 389051573 389052349 776 False 1114.000000 1114 92.564000 1790 2566 1 chr3A.!!$F1 776
2 TraesCS3A01G213500 chr3A 386882791 386883567 776 True 1096.000000 1096 92.159000 1792 2566 1 chr3A.!!$R3 774
3 TraesCS3A01G213500 chr3A 388613904 388614681 777 True 1057.000000 1057 91.260000 1792 2566 1 chr3A.!!$R4 774
4 TraesCS3A01G213500 chr3A 341231518 341232302 784 True 1051.000000 1051 91.001000 1791 2570 1 chr3A.!!$R1 779
5 TraesCS3A01G213500 chr3D 292372998 292374657 1659 False 2704.000000 2704 96.212000 1 1646 1 chr3D.!!$F1 1645
6 TraesCS3A01G213500 chr3D 4190320 4191109 789 True 1051.000000 1051 90.818000 1786 2571 1 chr3D.!!$R1 785
7 TraesCS3A01G213500 chr3B 386374752 386376764 2012 True 907.333333 1325 95.047667 1 1788 3 chr3B.!!$R1 1787
8 TraesCS3A01G213500 chr4A 477292287 477293069 782 False 1079.000000 1079 91.720000 1791 2566 1 chr4A.!!$F1 775
9 TraesCS3A01G213500 chr7A 492380390 492381174 784 False 1061.000000 1061 91.233000 1795 2571 1 chr7A.!!$F1 776
10 TraesCS3A01G213500 chr2D 538595460 538596243 783 True 1057.000000 1057 91.105000 1786 2565 1 chr2D.!!$R1 779
11 TraesCS3A01G213500 chr1A 49143904 49144695 791 False 1050.000000 1050 90.818000 1785 2567 1 chr1A.!!$F1 782

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
212 213 0.036732 TTCTATCCCCCGCATGCATC 59.963 55.000 19.57 0.0 0.00 3.91 F
504 505 1.142667 TGTTGGTGGCATCTGAAGACA 59.857 47.619 0.00 0.0 0.00 3.41 F
1217 1478 1.536284 GGTAAGCTAGCGCGTGATTCT 60.536 52.381 9.55 0.0 42.32 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1217 1478 0.671251 AATTTCCGCTTGCGTTTCCA 59.329 45.0 13.97 0.0 0.00 3.53 R
1369 1640 0.968901 ACTGATCGCCTACCGTGGAA 60.969 55.0 0.00 0.0 38.35 3.53 R
2531 2818 0.730265 TCGCTCGCTTTCTCTCTCTC 59.270 55.0 0.00 0.0 0.00 3.20 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
177 178 2.095461 GATGTTCCCCCTTTTCTCTGC 58.905 52.381 0.00 0.00 0.00 4.26
188 189 4.217334 CCCTTTTCTCTGCTTTTCTCCTTC 59.783 45.833 0.00 0.00 0.00 3.46
212 213 0.036732 TTCTATCCCCCGCATGCATC 59.963 55.000 19.57 0.00 0.00 3.91
242 243 5.653769 CCAATCATGTAAATCCTGACTTGGT 59.346 40.000 0.00 0.00 32.33 3.67
244 245 5.241403 TCATGTAAATCCTGACTTGGTGT 57.759 39.130 0.00 0.00 0.00 4.16
326 327 3.136626 GCTGTAGTTATCTGATGGGGGTT 59.863 47.826 0.00 0.00 0.00 4.11
480 481 2.948979 TGTTGCTTGGTCGAAATGTCTT 59.051 40.909 0.00 0.00 0.00 3.01
504 505 1.142667 TGTTGGTGGCATCTGAAGACA 59.857 47.619 0.00 0.00 0.00 3.41
617 618 5.165911 TCGAGTTTATGTCGGTATGAGTC 57.834 43.478 0.00 0.00 38.02 3.36
618 619 4.637091 TCGAGTTTATGTCGGTATGAGTCA 59.363 41.667 0.00 0.00 38.02 3.41
721 725 2.290896 TGTGGGAATGTGGGTGAGATTC 60.291 50.000 0.00 0.00 34.27 2.52
905 1146 6.472686 TGCTAAGGATCTTTTCTCTAGGTC 57.527 41.667 0.00 0.00 0.00 3.85
930 1174 5.048507 GTGGTTGATCTTCGTATCCCTAAC 58.951 45.833 0.00 0.00 0.00 2.34
1010 1271 2.642311 TCCCAGTAGACATGGCTTCAAA 59.358 45.455 6.27 0.00 36.43 2.69
1217 1478 1.536284 GGTAAGCTAGCGCGTGATTCT 60.536 52.381 9.55 0.00 42.32 2.40
1369 1640 2.165437 GTCGAGAAGCAGATCTCCAAGT 59.835 50.000 0.00 0.00 42.34 3.16
1392 1664 1.133598 CACGGTAGGCGATCAGTGTAA 59.866 52.381 0.00 0.00 0.00 2.41
1458 1730 1.142667 TGCAGGAGTTGTGTCCATCAA 59.857 47.619 0.00 0.00 39.34 2.57
1646 1918 2.604046 TGAGCGCTATCCCTCTTTTC 57.396 50.000 11.50 0.00 0.00 2.29
1649 1921 1.414550 AGCGCTATCCCTCTTTTCTCC 59.585 52.381 8.99 0.00 0.00 3.71
1651 1923 2.043227 CGCTATCCCTCTTTTCTCCCT 58.957 52.381 0.00 0.00 0.00 4.20
1652 1924 2.436173 CGCTATCCCTCTTTTCTCCCTT 59.564 50.000 0.00 0.00 0.00 3.95
1653 1925 3.493524 CGCTATCCCTCTTTTCTCCCTTC 60.494 52.174 0.00 0.00 0.00 3.46
1654 1926 3.714280 GCTATCCCTCTTTTCTCCCTTCT 59.286 47.826 0.00 0.00 0.00 2.85
1655 1927 4.165180 GCTATCCCTCTTTTCTCCCTTCTT 59.835 45.833 0.00 0.00 0.00 2.52
1656 1928 4.853468 ATCCCTCTTTTCTCCCTTCTTC 57.147 45.455 0.00 0.00 0.00 2.87
1657 1929 3.875571 TCCCTCTTTTCTCCCTTCTTCT 58.124 45.455 0.00 0.00 0.00 2.85
1658 1930 4.243643 TCCCTCTTTTCTCCCTTCTTCTT 58.756 43.478 0.00 0.00 0.00 2.52
1659 1931 4.665483 TCCCTCTTTTCTCCCTTCTTCTTT 59.335 41.667 0.00 0.00 0.00 2.52
1660 1932 5.134509 TCCCTCTTTTCTCCCTTCTTCTTTT 59.865 40.000 0.00 0.00 0.00 2.27
1661 1933 5.835819 CCCTCTTTTCTCCCTTCTTCTTTTT 59.164 40.000 0.00 0.00 0.00 1.94
1708 1980 3.386768 TTAGCGCTCAATCTGTATCCC 57.613 47.619 16.34 0.00 0.00 3.85
1741 2013 9.976511 AGAAAATCATATGTAGATTGCCATTTG 57.023 29.630 1.90 0.00 35.96 2.32
1779 2051 1.686325 GGGCTCCTGGCAACTCGATA 61.686 60.000 0.00 0.00 44.01 2.92
1848 2120 6.370433 TTCGTCTGTCATGACATTTTTCAA 57.630 33.333 28.00 13.44 41.01 2.69
1852 2124 7.920151 TCGTCTGTCATGACATTTTTCAAAAAT 59.080 29.630 28.00 1.98 41.01 1.82
1983 2257 5.080969 TCCGGATTTAAGTCACACCTAAG 57.919 43.478 0.00 0.00 0.00 2.18
2007 2282 8.751302 AGCCGTTATTTTACATTTTTCGAAAT 57.249 26.923 12.12 0.00 0.00 2.17
2011 2286 9.349145 CGTTATTTTACATTTTTCGAAATCCCT 57.651 29.630 12.12 0.00 0.00 4.20
2122 2397 9.778741 ACTCCGATTTGAACATGTTATATATGT 57.221 29.630 11.95 0.46 40.30 2.29
2512 2799 1.923356 ATCGCAGGGGAAAACAACAT 58.077 45.000 0.00 0.00 0.00 2.71
2567 2854 1.412710 GCGAGAGAGAGAGAGAGAGGA 59.587 57.143 0.00 0.00 0.00 3.71
2570 2857 3.493350 CGAGAGAGAGAGAGAGAGGAAGG 60.493 56.522 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 0.902531 GGGAACATCTCGGAGGAACA 59.097 55.000 4.96 0.00 0.00 3.18
177 178 5.432645 GGATAGAAGGGTGAAGGAGAAAAG 58.567 45.833 0.00 0.00 0.00 2.27
188 189 1.418908 ATGCGGGGGATAGAAGGGTG 61.419 60.000 0.00 0.00 0.00 4.61
212 213 6.206243 GTCAGGATTTACATGATTGGGAGATG 59.794 42.308 0.00 0.00 41.30 2.90
242 243 6.215841 TCATAGTTAACCCAGGTATCCAAACA 59.784 38.462 0.88 0.00 0.00 2.83
244 245 6.894735 TCATAGTTAACCCAGGTATCCAAA 57.105 37.500 0.88 0.00 0.00 3.28
326 327 1.302271 CCTGCTCTGCTGTGAAGCA 60.302 57.895 0.00 0.00 43.22 3.91
451 452 2.614983 TCGACCAAGCAACACCTAAAAC 59.385 45.455 0.00 0.00 0.00 2.43
480 481 4.458989 GTCTTCAGATGCCACCAACAAATA 59.541 41.667 0.00 0.00 0.00 1.40
504 505 2.613977 CCTCTCTTCAACAACCGCTCAT 60.614 50.000 0.00 0.00 0.00 2.90
617 618 8.498575 TGGAGGATAGATAGATAGGTACATCTG 58.501 40.741 6.07 0.00 35.99 2.90
618 619 8.645902 TGGAGGATAGATAGATAGGTACATCT 57.354 38.462 0.00 0.00 38.76 2.90
721 725 3.058016 ACTCATCAGGCACAAAATTGACG 60.058 43.478 0.00 0.00 0.00 4.35
905 1146 2.470821 GGATACGAAGATCAACCACCG 58.529 52.381 0.00 0.00 0.00 4.94
960 1204 9.807921 TGAATGTCACTCACATATATAGAGGTA 57.192 33.333 15.13 4.19 45.77 3.08
1010 1271 4.077822 CAGAGCTTTCTTCAAACCCATCT 58.922 43.478 0.00 0.00 0.00 2.90
1217 1478 0.671251 AATTTCCGCTTGCGTTTCCA 59.329 45.000 13.97 0.00 0.00 3.53
1308 1579 0.969149 AGTGCATCGACACCTTCAGA 59.031 50.000 2.76 0.00 41.67 3.27
1369 1640 0.968901 ACTGATCGCCTACCGTGGAA 60.969 55.000 0.00 0.00 38.35 3.53
1458 1730 3.181461 CGTCTTCATCCCCAGCTCTATTT 60.181 47.826 0.00 0.00 0.00 1.40
1603 1875 5.645624 TCGTTTTCATCAAAGAAAAGTGCA 58.354 33.333 2.43 0.00 45.21 4.57
1666 1938 8.144478 GCTAAAAGAAGAAGGGAGAAAATGTTT 58.856 33.333 0.00 0.00 0.00 2.83
1667 1939 7.522236 CGCTAAAAGAAGAAGGGAGAAAATGTT 60.522 37.037 0.00 0.00 0.00 2.71
1668 1940 6.072452 CGCTAAAAGAAGAAGGGAGAAAATGT 60.072 38.462 0.00 0.00 0.00 2.71
1669 1941 6.317857 CGCTAAAAGAAGAAGGGAGAAAATG 58.682 40.000 0.00 0.00 0.00 2.32
1670 1942 5.106118 GCGCTAAAAGAAGAAGGGAGAAAAT 60.106 40.000 0.00 0.00 0.00 1.82
1671 1943 4.215613 GCGCTAAAAGAAGAAGGGAGAAAA 59.784 41.667 0.00 0.00 0.00 2.29
1672 1944 3.751698 GCGCTAAAAGAAGAAGGGAGAAA 59.248 43.478 0.00 0.00 0.00 2.52
1673 1945 3.008049 AGCGCTAAAAGAAGAAGGGAGAA 59.992 43.478 8.99 0.00 0.00 2.87
1674 1946 2.567615 AGCGCTAAAAGAAGAAGGGAGA 59.432 45.455 8.99 0.00 0.00 3.71
1675 1947 2.933260 GAGCGCTAAAAGAAGAAGGGAG 59.067 50.000 11.50 0.00 0.00 4.30
1676 1948 2.301870 TGAGCGCTAAAAGAAGAAGGGA 59.698 45.455 11.50 0.00 0.00 4.20
1677 1949 2.699954 TGAGCGCTAAAAGAAGAAGGG 58.300 47.619 11.50 0.00 0.00 3.95
1678 1950 4.633565 AGATTGAGCGCTAAAAGAAGAAGG 59.366 41.667 11.50 0.00 0.00 3.46
1679 1951 5.121454 ACAGATTGAGCGCTAAAAGAAGAAG 59.879 40.000 11.50 0.00 0.00 2.85
1680 1952 4.997395 ACAGATTGAGCGCTAAAAGAAGAA 59.003 37.500 11.50 0.00 0.00 2.52
1681 1953 4.569943 ACAGATTGAGCGCTAAAAGAAGA 58.430 39.130 11.50 0.00 0.00 2.87
1735 2007 1.750399 CGGGTGGCTCCTCAAATGG 60.750 63.158 5.46 0.00 36.25 3.16
1741 2013 4.083862 GGACACGGGTGGCTCCTC 62.084 72.222 0.00 0.00 39.02 3.71
1933 2207 6.514376 GCGGGTTGATTTTAAGAAAAGACAGA 60.514 38.462 0.00 0.00 33.22 3.41
1946 2220 1.319614 CCGGATGGCGGGTTGATTTT 61.320 55.000 0.00 0.00 0.00 1.82
1983 2257 8.105742 GGATTTCGAAAAATGTAAAATAACGGC 58.894 33.333 15.66 0.00 35.21 5.68
2007 2282 6.216662 TGAATTACCTAAAACATCAGGAGGGA 59.783 38.462 0.00 0.00 35.76 4.20
2089 2364 5.354234 ACATGTTCAAATCGGAGTTATGGTC 59.646 40.000 0.00 0.00 0.00 4.02
2392 2672 6.104146 TCCGGATCATCATCGGTATAAAAA 57.896 37.500 0.00 0.00 43.75 1.94
2397 2677 3.679917 GCAATCCGGATCATCATCGGTAT 60.680 47.826 19.43 0.00 43.75 2.73
2399 2679 1.609061 GCAATCCGGATCATCATCGGT 60.609 52.381 19.43 0.00 43.75 4.69
2402 2682 4.778534 ATTTGCAATCCGGATCATCATC 57.221 40.909 19.43 4.18 0.00 2.92
2403 2683 6.040729 TGTTTATTTGCAATCCGGATCATCAT 59.959 34.615 19.43 9.89 0.00 2.45
2404 2684 5.359292 TGTTTATTTGCAATCCGGATCATCA 59.641 36.000 19.43 12.89 0.00 3.07
2512 2799 5.358160 TCTCTCACTCTTGCGATGAGAAATA 59.642 40.000 7.09 0.00 46.17 1.40
2531 2818 0.730265 TCGCTCGCTTTCTCTCTCTC 59.270 55.000 0.00 0.00 0.00 3.20
2532 2819 0.732571 CTCGCTCGCTTTCTCTCTCT 59.267 55.000 0.00 0.00 0.00 3.10
2533 2820 0.730265 TCTCGCTCGCTTTCTCTCTC 59.270 55.000 0.00 0.00 0.00 3.20
2534 2821 0.732571 CTCTCGCTCGCTTTCTCTCT 59.267 55.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.