Multiple sequence alignment - TraesCS2A01G521700

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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 TraesCS2A01G521700 chr2A 100.000 3377 0 0 1 3377 744451072 744447696 0.000000e+00 6237.0
1 TraesCS2A01G521700 chr2A 84.868 304 34 10 2 297 127727862 127727563 2.550000e-76 296.0
2 TraesCS2A01G521700 chr2B 94.281 3392 146 22 1 3377 747182876 747179518 0.000000e+00 5145.0
3 TraesCS2A01G521700 chr2D 95.053 3093 124 15 305 3377 612345824 612342741 0.000000e+00 4837.0
4 TraesCS2A01G521700 chr7D 83.820 377 35 13 2250 2624 618084818 618084466 5.400000e-88 335.0
5 TraesCS2A01G521700 chr7A 84.691 307 37 10 2 301 207923178 207923481 7.080000e-77 298.0
6 TraesCS2A01G521700 chr7A 84.667 300 39 7 3 297 426642056 426641759 3.300000e-75 292.0
7 TraesCS2A01G521700 chr7A 80.892 314 26 20 2320 2631 711814462 711814181 2.040000e-52 217.0
8 TraesCS2A01G521700 chr6A 84.768 302 38 8 2 297 386665812 386666111 2.550000e-76 296.0
9 TraesCS2A01G521700 chr6A 84.718 301 40 6 2 297 522884213 522884512 2.550000e-76 296.0
10 TraesCS2A01G521700 chr4A 84.818 303 36 10 2 297 43384924 43385223 2.550000e-76 296.0
11 TraesCS2A01G521700 chr4A 84.365 307 39 9 2 301 333911572 333911268 3.300000e-75 292.0
12 TraesCS2A01G521700 chr1A 84.718 301 38 8 2 297 106014278 106013981 9.160000e-76 294.0
13 TraesCS2A01G521700 chr3A 75.351 499 75 32 1900 2371 587878227 587878704 2.660000e-46 196.0
14 TraesCS2A01G521700 chr3D 87.097 155 14 5 1896 2046 446064953 446065105 1.610000e-38 171.0
15 TraesCS2A01G521700 chr5B 90.909 55 2 2 1624 1676 382332998 382332945 1.680000e-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 TraesCS2A01G521700 chr2A 744447696 744451072 3376 True 6237 6237 100.000 1 3377 1 chr2A.!!$R2 3376
1 TraesCS2A01G521700 chr2B 747179518 747182876 3358 True 5145 5145 94.281 1 3377 1 chr2B.!!$R1 3376
2 TraesCS2A01G521700 chr2D 612342741 612345824 3083 True 4837 4837 95.053 305 3377 1 chr2D.!!$R1 3072

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
494 501 1.199327 GCTCGTCCCTTGCCTAAAAAC 59.801 52.381 0.0 0.0 0.00 2.43 F
1719 1731 1.201429 AACCTGGGTCGCAGAAGGAT 61.201 55.000 18.0 0.0 39.69 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 1846 0.752009 TTGCTCGTCCTCCGCTCTAT 60.752 55.0 0.0 0.0 36.19 1.98 R
2671 2704 0.327924 TGTTGAGGCCGACATTCCAT 59.672 50.0 0.0 0.0 31.92 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
25 26 3.832490 GGCCTCCTTTGGTTTGTAGAAAT 59.168 43.478 0.00 0.00 0.00 2.17
39 40 9.974980 GGTTTGTAGAAATTTTGTAGGAATTCA 57.025 29.630 7.93 0.00 0.00 2.57
208 209 7.615039 ATGTATCAAATGACATCTCTCTCCT 57.385 36.000 0.00 0.00 30.32 3.69
210 211 6.608808 TGTATCAAATGACATCTCTCTCCTCA 59.391 38.462 0.00 0.00 0.00 3.86
216 217 4.724399 TGACATCTCTCTCCTCATAGGAC 58.276 47.826 0.00 0.00 40.06 3.85
247 248 8.147058 GGTACATGTCATCTCACTTTCTATGAT 58.853 37.037 0.00 0.00 31.49 2.45
387 388 9.965824 ATCGTTGAAAACTTCTTTCAAATATGT 57.034 25.926 12.79 0.00 46.99 2.29
388 389 9.796120 TCGTTGAAAACTTCTTTCAAATATGTT 57.204 25.926 12.79 0.00 46.99 2.71
447 454 2.268920 GCAGCTCGGTTCATCCCA 59.731 61.111 0.00 0.00 0.00 4.37
451 458 1.745489 GCTCGGTTCATCCCACCAC 60.745 63.158 0.00 0.00 33.36 4.16
478 485 9.079833 ACTTATCAATCATTTCAAATTTGCTCG 57.920 29.630 13.54 2.31 0.00 5.03
481 488 5.863397 TCAATCATTTCAAATTTGCTCGTCC 59.137 36.000 13.54 0.00 0.00 4.79
493 500 1.202830 TGCTCGTCCCTTGCCTAAAAA 60.203 47.619 0.00 0.00 0.00 1.94
494 501 1.199327 GCTCGTCCCTTGCCTAAAAAC 59.801 52.381 0.00 0.00 0.00 2.43
513 520 3.708563 ACAACACCACATTTGTGCTAC 57.291 42.857 5.15 0.00 44.34 3.58
523 530 5.106712 CCACATTTGTGCTACGTTATTGTCT 60.107 40.000 5.15 0.00 44.34 3.41
557 564 2.456577 GTTTGCACCCCCAACTCATAT 58.543 47.619 0.00 0.00 0.00 1.78
687 695 6.519761 CGGTCTCTTAAATTTGTCAATCAACG 59.480 38.462 0.00 0.00 35.61 4.10
754 762 2.472059 ATTCGTGCGCGCCATCATT 61.472 52.632 30.77 6.14 38.14 2.57
814 822 4.437682 TCATGGGGACTAATTAAGCCAG 57.562 45.455 0.00 0.00 0.00 4.85
845 854 2.951229 AACTGTTGGATCCGTTTCCT 57.049 45.000 7.39 0.00 36.68 3.36
1233 1245 4.499183 AGATCATGGTGAAGTTCGAGAAC 58.501 43.478 7.83 7.83 41.45 3.01
1719 1731 1.201429 AACCTGGGTCGCAGAAGGAT 61.201 55.000 18.00 0.00 39.69 3.24
1831 1846 2.489971 ACGCGTTCCAAGAAAAGATCA 58.510 42.857 5.58 0.00 0.00 2.92
1832 1847 3.074412 ACGCGTTCCAAGAAAAGATCAT 58.926 40.909 5.58 0.00 0.00 2.45
2095 2110 3.966026 CTCCCTCGCGTGTTCGTCC 62.966 68.421 5.77 0.00 39.49 4.79
2133 2148 4.043200 GCCAAGGACGTGCAAGCC 62.043 66.667 10.52 2.19 0.00 4.35
2209 2224 3.818787 GCAAGCTCGGGTGCATGG 61.819 66.667 3.21 0.00 40.58 3.66
2301 2316 1.131126 GTCCATTACGAGGACGACGAA 59.869 52.381 0.00 0.00 45.35 3.85
2386 2401 1.166129 CTGCTGCTGATGCTCTGTTT 58.834 50.000 0.00 0.00 40.48 2.83
2428 2444 1.981495 AGGCTAAAGTTCTCCTGCTGT 59.019 47.619 0.00 0.00 0.00 4.40
2663 2696 5.157067 GTTCAGAATTTTACCTGAAGCTGC 58.843 41.667 7.38 0.00 46.33 5.25
2664 2697 3.436704 TCAGAATTTTACCTGAAGCTGCG 59.563 43.478 0.00 0.00 36.58 5.18
2665 2698 3.189287 CAGAATTTTACCTGAAGCTGCGT 59.811 43.478 0.00 0.00 32.37 5.24
2666 2699 3.437049 AGAATTTTACCTGAAGCTGCGTC 59.563 43.478 8.69 8.69 0.00 5.19
2667 2700 2.248280 TTTTACCTGAAGCTGCGTCA 57.752 45.000 16.99 16.99 0.00 4.35
2668 2701 1.795768 TTTACCTGAAGCTGCGTCAG 58.204 50.000 30.39 30.39 41.87 3.51
2669 2702 0.966179 TTACCTGAAGCTGCGTCAGA 59.034 50.000 36.02 20.85 44.44 3.27
2670 2703 0.528017 TACCTGAAGCTGCGTCAGAG 59.472 55.000 36.02 28.43 44.44 3.35
2671 2704 1.181741 ACCTGAAGCTGCGTCAGAGA 61.182 55.000 36.02 9.67 44.44 3.10
2672 2705 0.175302 CCTGAAGCTGCGTCAGAGAT 59.825 55.000 36.02 0.00 44.44 2.75
2673 2706 1.279152 CTGAAGCTGCGTCAGAGATG 58.721 55.000 32.66 12.49 44.44 2.90
2674 2707 0.108472 TGAAGCTGCGTCAGAGATGG 60.108 55.000 14.20 0.00 32.44 3.51
2748 2781 4.860907 ACACGTCGACACTAAAATGGATAC 59.139 41.667 17.16 0.00 0.00 2.24
2769 2802 5.847670 ACTGAACTCGAATAAACAAGAGC 57.152 39.130 0.00 0.00 34.31 4.09
3024 3060 6.215495 ACGGGGTGTTTATTTCCATTAATG 57.785 37.500 8.58 8.58 0.00 1.90
3085 3121 3.522731 CGGGTGAGAGCCTCGGAG 61.523 72.222 0.00 0.00 32.48 4.63
3103 3139 0.760567 AGACCATCATAGCTCCCGCA 60.761 55.000 0.00 0.00 39.10 5.69
3157 3193 1.490490 ACCTTGACTGCTGTTCTTCCA 59.510 47.619 0.00 0.00 0.00 3.53
3168 3204 2.448582 TTCTTCCAGTGGCGGTGGT 61.449 57.895 3.51 0.00 36.37 4.16
3194 3230 1.267806 TCTTGGTCGTCTCGGTAACAC 59.732 52.381 0.00 0.00 0.00 3.32
3205 3241 2.421073 CTCGGTAACACGGTATGTCTCA 59.579 50.000 0.00 0.00 42.31 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 2.705127 ACCAAAGGCACCAAATGAATGT 59.295 40.909 0.00 0.00 0.00 2.71
63 64 3.405823 ACCAAAGGCACCAAATGAATG 57.594 42.857 0.00 0.00 0.00 2.67
64 65 4.136051 CAAACCAAAGGCACCAAATGAAT 58.864 39.130 0.00 0.00 0.00 2.57
65 66 3.054802 ACAAACCAAAGGCACCAAATGAA 60.055 39.130 0.00 0.00 0.00 2.57
187 188 7.852550 ATGAGGAGAGAGATGTCATTTGATA 57.147 36.000 0.00 0.00 0.00 2.15
208 209 4.780554 TGACATGTACCTTTGGTCCTATGA 59.219 41.667 0.00 0.00 37.09 2.15
210 211 5.667626 AGATGACATGTACCTTTGGTCCTAT 59.332 40.000 0.00 0.00 37.09 2.57
216 217 4.836825 AGTGAGATGACATGTACCTTTGG 58.163 43.478 0.00 0.00 0.00 3.28
269 270 7.817418 TGGCTTCATTTGGTTAATAGGATAC 57.183 36.000 0.00 0.00 0.00 2.24
286 287 5.127031 GGTTAGGCTCAAAATTATGGCTTCA 59.873 40.000 0.00 0.00 36.69 3.02
340 341 8.437360 ACGATATATTTTTCTGAGATGCAACA 57.563 30.769 0.00 0.00 0.00 3.33
409 410 3.120338 GCCGCTTGCGCTATATATTTTCA 60.120 43.478 9.73 0.00 0.00 2.69
441 448 4.525996 TGATTGATAAGTGTGGTGGGATG 58.474 43.478 0.00 0.00 0.00 3.51
442 449 4.860802 TGATTGATAAGTGTGGTGGGAT 57.139 40.909 0.00 0.00 0.00 3.85
478 485 3.491964 GGTGTTGTTTTTAGGCAAGGGAC 60.492 47.826 0.00 0.00 0.00 4.46
481 488 3.118956 TGTGGTGTTGTTTTTAGGCAAGG 60.119 43.478 0.00 0.00 0.00 3.61
513 520 1.209128 CGGGCTAGCAGACAATAACG 58.791 55.000 18.24 2.70 0.00 3.18
523 530 3.702048 AAACGGAGCGGGCTAGCA 61.702 61.111 18.24 0.00 40.15 3.49
663 671 7.360361 ACGTTGATTGACAAATTTAAGAGACC 58.640 34.615 0.00 0.00 40.36 3.85
687 695 0.036388 TTCGATGGAACTGGCCAGAC 60.036 55.000 39.19 28.28 42.15 3.51
754 762 5.826643 AGGCAAAAATAGGAGTGATAACCA 58.173 37.500 0.00 0.00 0.00 3.67
814 822 1.228154 AACAGTTTCCTCCACGGCC 60.228 57.895 0.00 0.00 0.00 6.13
845 854 1.813753 GCGATGCGGCTTTGTAGGA 60.814 57.895 0.00 0.00 0.00 2.94
958 967 1.394618 CGGTGCTAGCTAGTTCCTCT 58.605 55.000 21.62 0.00 0.00 3.69
1706 1718 1.536284 CGTCCTTATCCTTCTGCGACC 60.536 57.143 0.00 0.00 0.00 4.79
1831 1846 0.752009 TTGCTCGTCCTCCGCTCTAT 60.752 55.000 0.00 0.00 36.19 1.98
1832 1847 1.378119 TTGCTCGTCCTCCGCTCTA 60.378 57.895 0.00 0.00 36.19 2.43
1957 1972 4.465512 CAGGATGTTGCGCACGGC 62.466 66.667 11.12 3.89 43.96 5.68
2119 2134 2.281761 CAGGGCTTGCACGTCCTT 60.282 61.111 14.68 0.00 36.73 3.36
2301 2316 2.979197 CTGGAACTCGCCGTCGTCT 61.979 63.158 0.00 0.00 36.96 4.18
2386 2401 4.320608 ACGGTAGACTGTAACGGAAAAA 57.679 40.909 0.00 0.00 32.82 1.94
2428 2444 8.609176 CACTGTACAAAGTAGAAGCAACTAAAA 58.391 33.333 0.00 0.00 0.00 1.52
2509 2526 8.661345 GGAGGGAGAAAATTATTACTGTAGGAT 58.339 37.037 0.00 0.00 0.00 3.24
2605 2626 2.540383 TCAACACAGGCTGAGTCCTAT 58.460 47.619 23.66 0.77 33.95 2.57
2609 2630 2.289320 ACAGATCAACACAGGCTGAGTC 60.289 50.000 23.66 7.44 0.00 3.36
2663 2696 1.845266 CCGACATTCCATCTCTGACG 58.155 55.000 0.00 0.00 0.00 4.35
2664 2697 1.576356 GCCGACATTCCATCTCTGAC 58.424 55.000 0.00 0.00 0.00 3.51
2665 2698 0.465705 GGCCGACATTCCATCTCTGA 59.534 55.000 0.00 0.00 0.00 3.27
2666 2699 0.467384 AGGCCGACATTCCATCTCTG 59.533 55.000 0.00 0.00 0.00 3.35
2667 2700 0.755686 GAGGCCGACATTCCATCTCT 59.244 55.000 0.00 0.00 0.00 3.10
2668 2701 0.465705 TGAGGCCGACATTCCATCTC 59.534 55.000 0.00 0.00 0.00 2.75
2669 2702 0.911769 TTGAGGCCGACATTCCATCT 59.088 50.000 0.00 0.00 0.00 2.90
2670 2703 1.017387 GTTGAGGCCGACATTCCATC 58.983 55.000 0.00 0.00 0.00 3.51
2671 2704 0.327924 TGTTGAGGCCGACATTCCAT 59.672 50.000 0.00 0.00 31.92 3.41
2672 2705 0.327924 ATGTTGAGGCCGACATTCCA 59.672 50.000 14.28 8.86 43.17 3.53
2673 2706 3.175133 ATGTTGAGGCCGACATTCC 57.825 52.632 14.28 4.52 43.17 3.01
2727 2760 5.100259 CAGTATCCATTTTAGTGTCGACGT 58.900 41.667 11.62 3.06 0.00 4.34
2732 2765 7.033791 TCGAGTTCAGTATCCATTTTAGTGTC 58.966 38.462 0.00 0.00 0.00 3.67
2748 2781 5.845985 TGCTCTTGTTTATTCGAGTTCAG 57.154 39.130 0.00 0.00 0.00 3.02
2769 2802 6.406093 GTCATGTCTCTGACTTTTCTGATG 57.594 41.667 0.00 0.00 41.87 3.07
3103 3139 1.548269 GTGACCAGCAGCTACTTCTCT 59.452 52.381 0.00 0.00 0.00 3.10
3194 3230 3.571828 AGATCAGTGGATGAGACATACCG 59.428 47.826 0.00 0.00 42.53 4.02
3205 3241 1.590932 GCGCAATCAGATCAGTGGAT 58.409 50.000 0.30 0.00 36.13 3.41


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

AutoCloner maintained by Alex Coulton.