Multiple sequence alignment - TraesCS7D01G517600

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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 TraesCS7D01G517600 chr7D 100.000 2330 0 0 1 2330 616459446 616457117 0.000000e+00 4303.0
1 TraesCS7D01G517600 chr7D 88.546 681 70 6 1655 2330 463028595 463029272 0.000000e+00 819.0
2 TraesCS7D01G517600 chr1A 91.275 2361 168 12 1 2330 545474041 545476394 0.000000e+00 3184.0
3 TraesCS7D01G517600 chr1A 88.935 1672 137 16 1 1649 528297326 528295680 0.000000e+00 2019.0
4 TraesCS7D01G517600 chr1A 87.925 265 28 3 83 344 545473703 545473966 2.250000e-80 309.0
5 TraesCS7D01G517600 chr1B 88.151 1671 160 18 4 1654 617087717 617089369 0.000000e+00 1954.0
6 TraesCS7D01G517600 chr1B 91.509 318 24 2 1 316 617283881 617284197 3.560000e-118 435.0
7 TraesCS7D01G517600 chr1B 88.806 268 26 3 82 346 617087375 617087641 2.230000e-85 326.0
8 TraesCS7D01G517600 chr1B 88.571 245 21 4 362 600 617284185 617284428 8.140000e-75 291.0
9 TraesCS7D01G517600 chr1B 89.498 219 22 1 546 764 617284442 617284659 2.280000e-70 276.0
10 TraesCS7D01G517600 chr1B 85.821 268 26 4 82 346 617283550 617283808 8.200000e-70 274.0
11 TraesCS7D01G517600 chr1B 92.929 99 7 0 1555 1653 617284673 617284771 6.710000e-31 145.0
12 TraesCS7D01G517600 chr1D 91.262 618 46 7 1 614 450203297 450203910 0.000000e+00 835.0
13 TraesCS7D01G517600 chr1D 87.776 679 74 7 1655 2330 292109229 292109901 0.000000e+00 785.0
14 TraesCS7D01G517600 chr1D 88.060 268 24 4 82 346 450202962 450203224 6.250000e-81 311.0
15 TraesCS7D01G517600 chr4B 87.500 680 77 7 1655 2330 411627769 411627094 0.000000e+00 778.0
16 TraesCS7D01G517600 chr2B 87.500 680 77 6 1657 2330 154646238 154645561 0.000000e+00 778.0
17 TraesCS7D01G517600 chr2D 87.281 684 75 10 1655 2330 323069432 323070111 0.000000e+00 771.0
18 TraesCS7D01G517600 chr6D 87.206 680 80 6 1655 2330 109481658 109480982 0.000000e+00 767.0
19 TraesCS7D01G517600 chr4D 87.135 684 76 9 1655 2330 145490638 145489959 0.000000e+00 765.0
20 TraesCS7D01G517600 chrUn 86.912 680 81 7 1655 2330 56351390 56350715 0.000000e+00 756.0
21 TraesCS7D01G517600 chr4A 94.872 39 2 0 10 48 725589044 725589006 6.950000e-06 62.1


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 TraesCS7D01G517600 chr7D 616457117 616459446 2329 True 4303.0 4303 100.0000 1 2330 1 chr7D.!!$R1 2329
1 TraesCS7D01G517600 chr7D 463028595 463029272 677 False 819.0 819 88.5460 1655 2330 1 chr7D.!!$F1 675
2 TraesCS7D01G517600 chr1A 528295680 528297326 1646 True 2019.0 2019 88.9350 1 1649 1 chr1A.!!$R1 1648
3 TraesCS7D01G517600 chr1A 545473703 545476394 2691 False 1746.5 3184 89.6000 1 2330 2 chr1A.!!$F1 2329
4 TraesCS7D01G517600 chr1B 617087375 617089369 1994 False 1140.0 1954 88.4785 4 1654 2 chr1B.!!$F1 1650
5 TraesCS7D01G517600 chr1B 617283550 617284771 1221 False 284.2 435 89.6656 1 1653 5 chr1B.!!$F2 1652
6 TraesCS7D01G517600 chr1D 292109229 292109901 672 False 785.0 785 87.7760 1655 2330 1 chr1D.!!$F1 675
7 TraesCS7D01G517600 chr1D 450202962 450203910 948 False 573.0 835 89.6610 1 614 2 chr1D.!!$F2 613
8 TraesCS7D01G517600 chr4B 411627094 411627769 675 True 778.0 778 87.5000 1655 2330 1 chr4B.!!$R1 675
9 TraesCS7D01G517600 chr2B 154645561 154646238 677 True 778.0 778 87.5000 1657 2330 1 chr2B.!!$R1 673
10 TraesCS7D01G517600 chr2D 323069432 323070111 679 False 771.0 771 87.2810 1655 2330 1 chr2D.!!$F1 675
11 TraesCS7D01G517600 chr6D 109480982 109481658 676 True 767.0 767 87.2060 1655 2330 1 chr6D.!!$R1 675
12 TraesCS7D01G517600 chr4D 145489959 145490638 679 True 765.0 765 87.1350 1655 2330 1 chr4D.!!$R1 675
13 TraesCS7D01G517600 chrUn 56350715 56351390 675 True 756.0 756 86.9120 1655 2330 1 chrUn.!!$R1 675

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
785 1203 0.257328 TTTCCTCAACCACCACTGCA 59.743 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 2056 1.064389 ACTAGCTTTTGAGATGGCCCC 60.064 52.381 0.0 0.0 0.0 5.8 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
49 389 2.080693 CACCGCCAAACTGCATACTAA 58.919 47.619 0.00 0.00 0.00 2.24
65 405 8.815565 TGCATACTAAATTTATGAAGTCCCAA 57.184 30.769 0.00 0.00 0.00 4.12
131 471 4.577693 AGTTCTTGCATCGACGTACCTATA 59.422 41.667 0.00 0.00 0.00 1.31
364 709 6.511767 GCATCGAGGTATTTATGAACAACCAG 60.512 42.308 0.00 1.57 32.43 4.00
407 752 9.859427 TTGAACATCAATCTTTTTGATATCCAC 57.141 29.630 0.00 0.00 37.06 4.02
411 756 6.344572 TCAATCTTTTTGATATCCACGACG 57.655 37.500 0.00 0.00 34.45 5.12
541 890 7.342581 TCATTTGTATATCCACTGCCAAACTA 58.657 34.615 0.00 0.00 0.00 2.24
543 892 4.689071 TGTATATCCACTGCCAAACTACG 58.311 43.478 0.00 0.00 0.00 3.51
557 907 8.360325 TGCCAAACTACGTATACATTTATGAG 57.640 34.615 3.32 0.00 0.00 2.90
564 982 6.681729 ACGTATACATTTATGAGGTCCCAT 57.318 37.500 3.32 0.00 0.00 4.00
665 1083 7.416213 CGTTTCATATACAATTGTCCCCAACAT 60.416 37.037 15.85 3.63 37.82 2.71
669 1087 7.502226 TCATATACAATTGTCCCCAACATTCTC 59.498 37.037 15.85 0.00 37.82 2.87
708 1126 2.154462 GGCTTCTAGTTGAGCTTGCAA 58.846 47.619 0.00 0.00 0.00 4.08
774 1192 7.013942 CCATAATCATCATGCTCTTTTCCTCAA 59.986 37.037 0.00 0.00 0.00 3.02
785 1203 0.257328 TTTCCTCAACCACCACTGCA 59.743 50.000 0.00 0.00 0.00 4.41
850 1288 7.500227 CCATAAATGCTTCAATCAACTCCTCTA 59.500 37.037 0.00 0.00 0.00 2.43
867 1305 6.174720 TCCTCTAAATACCATCACATCACC 57.825 41.667 0.00 0.00 0.00 4.02
906 1344 4.069232 CTCCGGCAGGACAAGCGA 62.069 66.667 0.00 0.00 42.75 4.93
958 1396 2.874457 GCCCTCGTTGGTGTAGACATTT 60.874 50.000 0.00 0.00 0.00 2.32
960 1398 3.188460 CCCTCGTTGGTGTAGACATTTTG 59.812 47.826 0.00 0.00 0.00 2.44
1013 1451 4.211794 GGTCAAAGAAATGTTGCACAATGG 59.788 41.667 0.00 0.00 0.00 3.16
1097 1535 0.330604 ACCAGCCTCAATGTCTGCAT 59.669 50.000 0.00 0.00 36.80 3.96
1099 1537 0.656259 CAGCCTCAATGTCTGCATCG 59.344 55.000 0.00 0.00 33.50 3.84
1317 1755 3.642377 TGATGGCACCATATTGGGATTTG 59.358 43.478 1.19 0.00 43.37 2.32
1418 1856 9.219603 GCCTTATTATGATAGTTTCTGTATGCA 57.780 33.333 0.00 0.00 0.00 3.96
1500 1938 1.004277 ACGTTTCCACATGGCACCTAT 59.996 47.619 0.00 0.00 34.44 2.57
1560 1998 0.616395 TCTGACGTGGCCCCATTAGA 60.616 55.000 0.00 0.00 0.00 2.10
1618 2056 9.715121 ATTTTGGCCATTTAGCTCAATATATTG 57.285 29.630 17.82 17.82 39.10 1.90
1701 2149 2.304761 GGGGTGATTTGACTACCTGACA 59.695 50.000 0.00 0.00 34.87 3.58
1712 2160 8.844441 TTTGACTACCTGACAAAATAAAAACG 57.156 30.769 0.00 0.00 37.37 3.60
1771 2221 5.468746 GCAATTCTACCAAGTCAAGTACACA 59.531 40.000 0.00 0.00 0.00 3.72
1803 2253 3.256879 CAGGTCTAAGAGTTGAGCAGTGA 59.743 47.826 0.00 0.00 33.63 3.41
1836 2286 9.515226 AAGACTTTGCATATGTAAGTAAAGGAA 57.485 29.630 18.98 0.00 40.35 3.36
1843 2293 8.405531 TGCATATGTAAGTAAAGGAAAGATTGC 58.594 33.333 4.29 0.00 0.00 3.56
1850 2300 9.346725 GTAAGTAAAGGAAAGATTGCAGATTTG 57.653 33.333 0.00 0.00 0.00 2.32
1954 2405 1.125711 ACGGAGGGTAAGGTTGCACT 61.126 55.000 0.00 0.00 0.00 4.40
1957 2408 1.407025 GGAGGGTAAGGTTGCACTAGC 60.407 57.143 0.00 0.00 42.57 3.42
2080 2532 7.453393 TCTTCATGAAGTAGGTGATCTGTTTT 58.547 34.615 29.80 0.00 39.38 2.43
2146 2601 5.339200 CCCAAGTGACACCTAACCAATCTAT 60.339 44.000 0.84 0.00 0.00 1.98
2147 2602 6.126883 CCCAAGTGACACCTAACCAATCTATA 60.127 42.308 0.84 0.00 0.00 1.31
2158 2613 5.878406 AACCAATCTATAGGAGACACCAG 57.122 43.478 0.00 0.00 42.04 4.00
2160 2615 4.651503 ACCAATCTATAGGAGACACCAGTG 59.348 45.833 0.00 0.00 42.04 3.66
2162 2617 5.129485 CCAATCTATAGGAGACACCAGTGTT 59.871 44.000 4.68 0.00 45.05 3.32
2226 2681 5.122869 GCTCTTGTGCTTCAAATGATAGTCA 59.877 40.000 0.00 0.00 35.48 3.41
2252 2707 3.085443 ACACTCAAACACTCTCTCACG 57.915 47.619 0.00 0.00 0.00 4.35
2259 2714 5.123227 TCAAACACTCTCTCACGGATTTTT 58.877 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 460 8.186821 ACACATCTAACTTTGTATAGGTACGTC 58.813 37.037 0.00 0.00 33.36 4.34
190 532 4.750952 TCCTCGTATTAATGCTCTCTCG 57.249 45.455 0.00 0.00 0.00 4.04
331 676 2.622064 ATACCTCGATGCCCACTTTC 57.378 50.000 0.00 0.00 0.00 2.62
407 752 6.346598 CCCATTAATGTAACATAGCTTCGTCG 60.347 42.308 14.25 0.00 0.00 5.12
411 756 5.770162 AGGCCCATTAATGTAACATAGCTTC 59.230 40.000 14.25 0.00 0.00 3.86
496 845 4.598022 TGATTAATGTCCACTCCATGCAA 58.402 39.130 0.00 0.00 0.00 4.08
541 890 6.681729 ATGGGACCTCATAAATGTATACGT 57.318 37.500 0.00 0.00 0.00 3.57
543 892 9.959721 ATACAATGGGACCTCATAAATGTATAC 57.040 33.333 12.45 0.00 31.86 1.47
600 1018 0.928505 ATGGATGGTTGGATGGCTCA 59.071 50.000 0.00 0.00 0.00 4.26
665 1083 7.231317 AGCCTTGAATTGTATTGAAACTGAGAA 59.769 33.333 0.00 0.00 0.00 2.87
669 1087 7.373493 AGAAGCCTTGAATTGTATTGAAACTG 58.627 34.615 0.00 0.00 0.00 3.16
708 1126 1.094785 GTCCGTGCTATTGCCATTGT 58.905 50.000 0.00 0.00 38.71 2.71
774 1192 1.920734 TTGGTCTGTGCAGTGGTGGT 61.921 55.000 0.00 0.00 0.00 4.16
785 1203 1.946768 CCAATGTCGTTGTTGGTCTGT 59.053 47.619 4.13 0.00 39.97 3.41
850 1288 5.097742 TCTTCGGTGATGTGATGGTATTT 57.902 39.130 0.00 0.00 0.00 1.40
867 1305 1.579808 GTCGAGACGCAGAATTCTTCG 59.420 52.381 23.11 23.11 38.53 3.79
906 1344 1.707427 AGGTCCTTTGCCTCATCACTT 59.293 47.619 0.00 0.00 0.00 3.16
958 1396 6.000246 TGCAGTAATGATATGTCCCTTCAA 58.000 37.500 0.00 0.00 0.00 2.69
960 1398 6.017605 CACTTGCAGTAATGATATGTCCCTTC 60.018 42.308 0.00 0.00 0.00 3.46
1013 1451 2.602878 CTGTTGATGTGCCATTCTTGC 58.397 47.619 0.00 0.00 0.00 4.01
1082 1520 1.354506 GCGATGCAGACATTGAGGC 59.645 57.895 0.00 0.00 39.73 4.70
1097 1535 0.175760 GTAGTCCTTGAGCATGGCGA 59.824 55.000 0.00 0.00 0.00 5.54
1099 1537 0.253044 TGGTAGTCCTTGAGCATGGC 59.747 55.000 0.00 0.00 34.23 4.40
1357 1795 9.859427 AGTAAAATGGATATCACAACAACATTG 57.141 29.630 4.83 0.00 0.00 2.82
1412 1850 2.684374 TCTTCACACCATGCATGCATAC 59.316 45.455 31.73 0.00 34.91 2.39
1418 1856 2.372264 GGACATCTTCACACCATGCAT 58.628 47.619 0.00 0.00 0.00 3.96
1560 1998 2.158667 CGGCCCATCTAAACTACCCATT 60.159 50.000 0.00 0.00 0.00 3.16
1618 2056 1.064389 ACTAGCTTTTGAGATGGCCCC 60.064 52.381 0.00 0.00 0.00 5.80
1689 2137 7.556733 ACGTTTTTATTTTGTCAGGTAGTCA 57.443 32.000 0.00 0.00 0.00 3.41
1734 2183 6.245408 TGGTAGAATTGCTAAACTTGACCAT 58.755 36.000 0.00 0.00 0.00 3.55
1738 2187 6.995686 TGACTTGGTAGAATTGCTAAACTTGA 59.004 34.615 0.00 0.00 0.00 3.02
1771 2221 4.090090 ACTCTTAGACCTGCATGTGTAGT 58.910 43.478 0.00 0.00 0.00 2.73
1836 2286 9.932207 TTCATTACATTTCAAATCTGCAATCTT 57.068 25.926 0.00 0.00 0.00 2.40
1843 2293 8.229811 TCGTGTCTTCATTACATTTCAAATCTG 58.770 33.333 0.00 0.00 0.00 2.90
1850 2300 9.559958 AAAATCATCGTGTCTTCATTACATTTC 57.440 29.630 0.00 0.00 0.00 2.17
2080 2532 3.460340 TGAACCAAGGAGTTTGTAAGGGA 59.540 43.478 0.00 0.00 34.87 4.20
2118 2573 1.071699 GTTAGGTGTCACTTGGGAGCA 59.928 52.381 2.35 0.00 0.00 4.26
2146 2601 4.444306 CCTTTTGAACACTGGTGTCTCCTA 60.444 45.833 6.84 0.00 44.13 2.94
2147 2602 3.545703 CTTTTGAACACTGGTGTCTCCT 58.454 45.455 6.84 0.00 44.13 3.69
2158 2613 5.467735 ACACCGTCTATTACCTTTTGAACAC 59.532 40.000 0.00 0.00 0.00 3.32
2160 2615 6.368213 CAACACCGTCTATTACCTTTTGAAC 58.632 40.000 0.00 0.00 0.00 3.18
2162 2617 4.453136 GCAACACCGTCTATTACCTTTTGA 59.547 41.667 0.00 0.00 0.00 2.69
2226 2681 1.564348 AGAGTGTTTGAGTGTTGGGGT 59.436 47.619 0.00 0.00 0.00 4.95
2252 2707 4.950475 CCCTCTCCTACCAAAGAAAAATCC 59.050 45.833 0.00 0.00 0.00 3.01
2259 2714 3.115390 CAATCCCCTCTCCTACCAAAGA 58.885 50.000 0.00 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.