Multiple sequence alignment - TraesCS2A01G335500

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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 TraesCS2A01G335500 chr2A 100.000 7654 0 0 1 7654 569300533 569292880 0.000000e+00 14135
1 TraesCS2A01G335500 chr2A 92.832 6306 362 40 611 6858 736729717 736735990 0.000000e+00 9058
2 TraesCS2A01G335500 chr1A 97.233 7662 191 9 1 7654 302028664 302021016 0.000000e+00 12955
3 TraesCS2A01G335500 chr1A 92.296 3401 218 32 1036 4407 58251746 58248361 0.000000e+00 4789
4 TraesCS2A01G335500 chr1A 94.107 2291 120 5 511 2800 555682841 555680565 0.000000e+00 3469
5 TraesCS2A01G335500 chr1A 94.073 1569 89 4 6087 7654 555670673 555669108 0.000000e+00 2379
6 TraesCS2A01G335500 chr1A 89.039 1113 108 9 6545 7654 58237268 58236167 0.000000e+00 1367
7 TraesCS2A01G335500 chr1B 95.789 7695 260 21 1 7654 442214971 442207300 0.000000e+00 12357
8 TraesCS2A01G335500 chr1B 90.670 418 38 1 1 417 626073726 626073309 8.680000e-154 555
9 TraesCS2A01G335500 chr7B 94.704 7100 299 27 611 7654 99490955 99498033 0.000000e+00 10957
10 TraesCS2A01G335500 chr7B 95.729 1475 59 2 1 1471 586935497 586936971 0.000000e+00 2372
11 TraesCS2A01G335500 chr3A 94.569 7015 345 22 418 7418 55062577 55055585 0.000000e+00 10811
12 TraesCS2A01G335500 chr3A 84.348 345 39 5 1 344 727404768 727405098 2.660000e-84 324
13 TraesCS2A01G335500 chr6A 91.013 6554 503 44 1140 7654 447685058 447678552 0.000000e+00 8761
14 TraesCS2A01G335500 chr6A 92.420 5462 358 31 1036 6453 107622391 107616942 0.000000e+00 7742
15 TraesCS2A01G335500 chr6A 89.559 1111 101 9 6547 7654 107616940 107615842 0.000000e+00 1395
16 TraesCS2A01G335500 chr2B 92.696 5641 381 19 1135 6760 140591816 140586192 0.000000e+00 8106
17 TraesCS2A01G335500 chr2B 91.343 901 70 7 6756 7654 140554480 140553586 0.000000e+00 1225
18 TraesCS2A01G335500 chr2B 95.511 646 25 2 1 642 697696722 697696077 0.000000e+00 1029
19 TraesCS2A01G335500 chr2B 92.340 718 53 2 418 1135 140630733 140630018 0.000000e+00 1020
20 TraesCS2A01G335500 chrUn 94.027 4169 202 17 2964 7113 286328946 286324806 0.000000e+00 6276
21 TraesCS2A01G335500 chr4D 96.563 2968 96 6 4689 7654 6935425 6932462 0.000000e+00 4911
22 TraesCS2A01G335500 chr4D 94.918 1771 83 3 502 2272 6951542 6949779 0.000000e+00 2765
23 TraesCS2A01G335500 chr4D 93.881 523 22 6 1 516 6952018 6951499 0.000000e+00 780
24 TraesCS2A01G335500 chr5B 88.291 3775 387 33 1140 4874 703940687 703936928 0.000000e+00 4471
25 TraesCS2A01G335500 chr5B 94.161 1627 81 4 6032 7654 703933448 703931832 0.000000e+00 2466
26 TraesCS2A01G335500 chr5B 80.114 176 28 5 132 306 359144311 359144480 2.900000e-24 124
27 TraesCS2A01G335500 chr7A 91.963 1854 137 7 418 2267 571254535 571252690 0.000000e+00 2588
28 TraesCS2A01G335500 chr7A 86.427 722 64 18 6941 7654 501091673 501092368 0.000000e+00 760
29 TraesCS2A01G335500 chr4A 81.356 177 31 2 132 306 352589197 352589373 8.010000e-30 143


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 TraesCS2A01G335500 chr2A 569292880 569300533 7653 True 14135.0 14135 100.0000 1 7654 1 chr2A.!!$R1 7653
1 TraesCS2A01G335500 chr2A 736729717 736735990 6273 False 9058.0 9058 92.8320 611 6858 1 chr2A.!!$F1 6247
2 TraesCS2A01G335500 chr1A 302021016 302028664 7648 True 12955.0 12955 97.2330 1 7654 1 chr1A.!!$R3 7653
3 TraesCS2A01G335500 chr1A 58248361 58251746 3385 True 4789.0 4789 92.2960 1036 4407 1 chr1A.!!$R2 3371
4 TraesCS2A01G335500 chr1A 555680565 555682841 2276 True 3469.0 3469 94.1070 511 2800 1 chr1A.!!$R5 2289
5 TraesCS2A01G335500 chr1A 555669108 555670673 1565 True 2379.0 2379 94.0730 6087 7654 1 chr1A.!!$R4 1567
6 TraesCS2A01G335500 chr1A 58236167 58237268 1101 True 1367.0 1367 89.0390 6545 7654 1 chr1A.!!$R1 1109
7 TraesCS2A01G335500 chr1B 442207300 442214971 7671 True 12357.0 12357 95.7890 1 7654 1 chr1B.!!$R1 7653
8 TraesCS2A01G335500 chr7B 99490955 99498033 7078 False 10957.0 10957 94.7040 611 7654 1 chr7B.!!$F1 7043
9 TraesCS2A01G335500 chr7B 586935497 586936971 1474 False 2372.0 2372 95.7290 1 1471 1 chr7B.!!$F2 1470
10 TraesCS2A01G335500 chr3A 55055585 55062577 6992 True 10811.0 10811 94.5690 418 7418 1 chr3A.!!$R1 7000
11 TraesCS2A01G335500 chr6A 447678552 447685058 6506 True 8761.0 8761 91.0130 1140 7654 1 chr6A.!!$R1 6514
12 TraesCS2A01G335500 chr6A 107615842 107622391 6549 True 4568.5 7742 90.9895 1036 7654 2 chr6A.!!$R2 6618
13 TraesCS2A01G335500 chr2B 140586192 140591816 5624 True 8106.0 8106 92.6960 1135 6760 1 chr2B.!!$R2 5625
14 TraesCS2A01G335500 chr2B 140553586 140554480 894 True 1225.0 1225 91.3430 6756 7654 1 chr2B.!!$R1 898
15 TraesCS2A01G335500 chr2B 697696077 697696722 645 True 1029.0 1029 95.5110 1 642 1 chr2B.!!$R4 641
16 TraesCS2A01G335500 chr2B 140630018 140630733 715 True 1020.0 1020 92.3400 418 1135 1 chr2B.!!$R3 717
17 TraesCS2A01G335500 chrUn 286324806 286328946 4140 True 6276.0 6276 94.0270 2964 7113 1 chrUn.!!$R1 4149
18 TraesCS2A01G335500 chr4D 6932462 6935425 2963 True 4911.0 4911 96.5630 4689 7654 1 chr4D.!!$R1 2965
19 TraesCS2A01G335500 chr4D 6949779 6952018 2239 True 1772.5 2765 94.3995 1 2272 2 chr4D.!!$R2 2271
20 TraesCS2A01G335500 chr5B 703931832 703940687 8855 True 3468.5 4471 91.2260 1140 7654 2 chr5B.!!$R1 6514
21 TraesCS2A01G335500 chr7A 571252690 571254535 1845 True 2588.0 2588 91.9630 418 2267 1 chr7A.!!$R1 1849
22 TraesCS2A01G335500 chr7A 501091673 501092368 695 False 760.0 760 86.4270 6941 7654 1 chr7A.!!$F1 713

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
723 731 1.077930 AGTTGCGGCTCATGCTCAT 60.078 52.632 0.00 0.00 39.59 2.90 F
2056 2139 0.173481 CCGTGAGCTCCTTCGATTCA 59.827 55.000 12.15 0.00 0.00 2.57 F
2817 2912 2.141011 CTGGGGGTGGTGATGCTTCA 62.141 60.000 0.00 0.00 0.00 3.02 F
3505 3618 1.045911 GTCTGGCAGAGAGGGGGTAG 61.046 65.000 19.38 0.00 0.00 3.18 F
5002 7085 0.704076 ATGTGCTTTCCTTAGGGGCA 59.296 50.000 0.00 4.47 34.39 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 2683 0.314935 CTGCTGCAAACCGTTGGAAT 59.685 50.000 3.02 0.00 34.32 3.01 R
3192 3289 0.615331 GTGATCTCAGGCCACTTGGA 59.385 55.000 5.01 0.00 37.39 3.53 R
3739 3852 1.930908 GACCCTTCGACCGTCGTCAT 61.931 60.000 19.89 3.61 41.35 3.06 R
5499 7584 1.299939 ACTTCCCTTCCCCAAGATCC 58.700 55.000 0.00 0.00 0.00 3.36 R
6739 9222 1.202830 ACAAACAACATAGGGCACGGA 60.203 47.619 0.00 0.00 0.00 4.69 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
133 134 9.927668 CATTTGGTTTTAGGTCTGTATGATTTT 57.072 29.630 0.00 0.00 0.00 1.82
657 663 7.945134 ACATGTTTCTTGCTTCTTATTTGTCT 58.055 30.769 0.00 0.00 0.00 3.41
690 698 5.360999 TGTATGATGTTGTTGGGTTGTTGAA 59.639 36.000 0.00 0.00 0.00 2.69
723 731 1.077930 AGTTGCGGCTCATGCTCAT 60.078 52.632 0.00 0.00 39.59 2.90
836 844 3.830755 GGAGGTTCTAATATAGGGCGTGA 59.169 47.826 0.00 0.00 0.00 4.35
1091 1147 1.451504 CTGCTGTTGTCCCTGGTCA 59.548 57.895 0.00 0.00 0.00 4.02
1333 1402 4.057428 GAGCTCGACCGTGGCTGT 62.057 66.667 14.28 0.00 36.37 4.40
1351 1420 3.058224 GCTGTGGTAAATCGCAGAAAACT 60.058 43.478 7.96 0.00 45.25 2.66
1415 1484 4.207019 GCATGAAAGTTCTTCGTTTGTTGG 59.793 41.667 0.00 0.00 0.00 3.77
2056 2139 0.173481 CCGTGAGCTCCTTCGATTCA 59.827 55.000 12.15 0.00 0.00 2.57
2594 2683 3.190327 CGGGATATTGTTGTTTGCAGTCA 59.810 43.478 0.00 0.00 0.00 3.41
2599 2688 4.669206 ATTGTTGTTTGCAGTCATTCCA 57.331 36.364 0.00 0.00 0.00 3.53
2817 2912 2.141011 CTGGGGGTGGTGATGCTTCA 62.141 60.000 0.00 0.00 0.00 3.02
3192 3289 8.367156 ACATATTTACCACTTTCACTTGCAATT 58.633 29.630 0.00 0.00 0.00 2.32
3505 3618 1.045911 GTCTGGCAGAGAGGGGGTAG 61.046 65.000 19.38 0.00 0.00 3.18
3739 3852 3.450578 GGTTTGCCTTATATCGACGTCA 58.549 45.455 17.16 3.13 0.00 4.35
3888 4015 8.341173 CACAGGTGATGAAATATCTCTTTAAGC 58.659 37.037 0.00 0.00 0.00 3.09
4036 4164 1.475682 TGCATTGTGGCGCATATTTGA 59.524 42.857 10.83 0.00 36.28 2.69
4305 4435 1.428912 TGGAGGTGAAAAGATTGGCCT 59.571 47.619 3.32 0.00 0.00 5.19
4679 4811 4.144297 TGTTGTTCCTCCTGAAAGATTGG 58.856 43.478 0.00 0.00 34.07 3.16
4765 4897 2.989253 TTGCCGTCTCGCTCTGGA 60.989 61.111 0.00 0.00 0.00 3.86
5002 7085 0.704076 ATGTGCTTTCCTTAGGGGCA 59.296 50.000 0.00 4.47 34.39 5.36
5058 7141 4.683334 GCGTCGCTGTTGTTGCCC 62.683 66.667 10.68 0.00 0.00 5.36
5249 7332 2.550830 ACTTTGCGTGATGTCCTCTT 57.449 45.000 0.00 0.00 0.00 2.85
5597 7682 4.248691 ACCTCTTGGTTTGTACGTCTAC 57.751 45.455 0.00 0.00 46.05 2.59
5627 7712 6.317140 CCAATAGCTGCTATTGTTTCTTCTGA 59.683 38.462 39.29 10.70 46.83 3.27
5884 7971 3.881688 CCCAAATCATAGGCTGACTCTTG 59.118 47.826 0.00 0.00 36.48 3.02
5910 7997 5.353123 GGTTGGTGTTTCGATTATGCTTCTA 59.647 40.000 0.00 0.00 0.00 2.10
5939 8026 0.681175 AGCCAGGCAAATGGTTTGTC 59.319 50.000 15.80 0.00 45.31 3.18
6116 8577 1.343142 TCCTGTTCGTGTGTGCTATGT 59.657 47.619 0.00 0.00 0.00 2.29
6118 8579 1.386748 CTGTTCGTGTGTGCTATGTCG 59.613 52.381 0.00 0.00 0.00 4.35
6136 8601 7.169982 GCTATGTCGTGACAATTAATAAGAGCT 59.830 37.037 6.80 0.00 45.41 4.09
6182 8647 8.014263 TGTTGGTATATATCTTAAGGGTCCTGA 58.986 37.037 1.85 0.00 0.00 3.86
6309 8774 5.319043 AGAACATTGTTTTCCCTGAGGTA 57.681 39.130 3.08 0.00 0.00 3.08
6694 9176 7.500227 CACTGATAATGGTCCTATCAAACACAT 59.500 37.037 3.20 0.00 35.79 3.21
6739 9222 3.957497 CAGGTACATGGCTTCTCTAGACT 59.043 47.826 0.00 0.00 30.89 3.24
6837 9324 5.931146 GTCTAACATCTATGCTGAGATTGGG 59.069 44.000 0.00 0.00 33.75 4.12
6898 9385 2.079170 TGTTGTTTCTTGGCATGGGA 57.921 45.000 0.00 0.00 0.00 4.37
7201 9699 3.858135 CTCCTGGGCTCCTTTATAGGTA 58.142 50.000 0.00 0.00 42.60 3.08
7312 9829 5.357032 ACTCAAGTTTGAACTGACCGATTTT 59.643 36.000 0.00 0.00 39.66 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
657 663 3.920446 ACAACATCATACACACACGCTA 58.080 40.909 0.00 0.00 0.00 4.26
690 698 2.840753 AACTGGACCACGGGCCATT 61.841 57.895 12.19 2.22 30.92 3.16
836 844 5.248640 CAGTGACATGATTAGAAACAGGGT 58.751 41.667 0.00 0.00 0.00 4.34
847 855 0.806868 CGGCAAGCAGTGACATGATT 59.193 50.000 0.00 0.00 33.13 2.57
1091 1147 1.229658 AACCTAGGACCAGCAGCCT 60.230 57.895 17.98 0.00 38.31 4.58
1333 1402 5.759506 TTTCAGTTTTCTGCGATTTACCA 57.240 34.783 0.00 0.00 46.59 3.25
1351 1420 3.358775 CGAAACTCAACGCACATTTTCA 58.641 40.909 0.00 0.00 0.00 2.69
1415 1484 1.402613 ACGGCCAACAACAACAACTAC 59.597 47.619 2.24 0.00 0.00 2.73
1514 1584 4.069304 CCTCCAAACTCACATAAACCGAA 58.931 43.478 0.00 0.00 0.00 4.30
1979 2061 2.073816 GCTTAGCGCCTTTACAACAGA 58.926 47.619 2.29 0.00 0.00 3.41
2010 2093 1.716028 CCGGGGGATCCTTAAAGGGG 61.716 65.000 12.58 0.16 35.59 4.79
2594 2683 0.314935 CTGCTGCAAACCGTTGGAAT 59.685 50.000 3.02 0.00 34.32 3.01
2599 2688 2.991250 AGATATCTGCTGCAAACCGTT 58.009 42.857 3.89 0.00 0.00 4.44
2817 2912 6.126883 TGGTCATCCTATTCCGACTATTTGTT 60.127 38.462 0.00 0.00 34.23 2.83
3192 3289 0.615331 GTGATCTCAGGCCACTTGGA 59.385 55.000 5.01 0.00 37.39 3.53
3474 3587 2.430694 TCTGCCAGACAAGTATATGCGT 59.569 45.455 0.00 0.00 0.00 5.24
3505 3618 1.234821 TTCAACACCAATCTCACCGC 58.765 50.000 0.00 0.00 0.00 5.68
3739 3852 1.930908 GACCCTTCGACCGTCGTCAT 61.931 60.000 19.89 3.61 41.35 3.06
4036 4164 7.923878 ACGGCATTTTAAAGTGTATTTCAAACT 59.076 29.630 11.77 0.00 0.00 2.66
4188 4318 4.125703 AGCATCTTCGAACATCTCATTCC 58.874 43.478 0.00 0.00 0.00 3.01
4305 4435 9.546428 CACTCAAAGGATGTACATAATACATGA 57.454 33.333 8.71 8.08 38.18 3.07
4679 4811 6.501781 CCAACTCATCAAGAAGCATATTTCC 58.498 40.000 0.00 0.00 0.00 3.13
4765 4897 2.533916 TCATCAGACTGCTCACCTTCT 58.466 47.619 0.00 0.00 0.00 2.85
5002 7085 6.402222 CAACAGTAAGCACTATCTTCCTCTT 58.598 40.000 0.00 0.00 32.21 2.85
5058 7141 1.903877 AATGAGCAGTCCTCCCACCG 61.904 60.000 0.00 0.00 39.98 4.94
5249 7332 3.054139 AGCAAGATCTGGATTAGCCACAA 60.054 43.478 0.00 0.00 43.33 3.33
5499 7584 1.299939 ACTTCCCTTCCCCAAGATCC 58.700 55.000 0.00 0.00 0.00 3.36
5884 7971 3.689649 AGCATAATCGAAACACCAACCTC 59.310 43.478 0.00 0.00 0.00 3.85
6116 8577 6.462487 CCCCTAGCTCTTATTAATTGTCACGA 60.462 42.308 0.00 0.00 0.00 4.35
6118 8579 5.470437 GCCCCTAGCTCTTATTAATTGTCAC 59.530 44.000 0.00 0.00 38.99 3.67
6182 8647 2.858745 ACAACTGCCCGTGAGTAAAAT 58.141 42.857 0.00 0.00 0.00 1.82
6694 9176 3.573538 CACATCCAAAAGGACCATGTCAA 59.426 43.478 0.00 0.00 33.68 3.18
6739 9222 1.202830 ACAAACAACATAGGGCACGGA 60.203 47.619 0.00 0.00 0.00 4.69
6837 9324 3.266636 GAACTTAGGCAAGAGCTTCTCC 58.733 50.000 0.00 0.00 41.70 3.71
6898 9385 6.263842 CACCAATATCAGCATAGATGTGGTTT 59.736 38.462 15.21 1.57 41.75 3.27
7312 9829 7.615365 ACCCTCATAACAATTGAATGCTAGAAA 59.385 33.333 13.59 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.