Multiple sequence alignment - TraesCS7D01G080800

Loading Multiple Alignment...

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 TraesCS7D01G080800 chr7D 100.000 2473 0 0 1 2473 47515438 47517910 0.000000e+00 4567.0
1 TraesCS7D01G080800 chr7D 81.853 788 119 13 780 1557 48257335 48258108 2.070000e-180 641.0
2 TraesCS7D01G080800 chr7D 86.050 595 71 9 933 1516 10750967 10751560 1.610000e-176 628.0
3 TraesCS7D01G080800 chr7D 85.274 584 68 12 929 1495 22340505 22339923 9.850000e-164 586.0
4 TraesCS7D01G080800 chr7D 91.597 119 8 2 2356 2473 472257701 472257818 1.970000e-36 163.0
5 TraesCS7D01G080800 chr7D 81.283 187 15 12 763 949 22414599 22414433 1.540000e-27 134.0
6 TraesCS7D01G080800 chr7D 79.703 202 19 14 745 946 22340700 22340521 2.580000e-25 126.0
7 TraesCS7D01G080800 chr7D 79.703 202 18 14 745 946 10750769 10750947 9.290000e-25 124.0
8 TraesCS7D01G080800 chrUn 94.430 1975 81 9 501 2473 234382479 234384426 0.000000e+00 3011.0
9 TraesCS7D01G080800 chrUn 94.329 1975 83 8 501 2473 82331222 82329275 0.000000e+00 3000.0
10 TraesCS7D01G080800 chrUn 94.803 1424 70 4 1 1421 363503070 363504492 0.000000e+00 2217.0
11 TraesCS7D01G080800 chrUn 94.663 1424 72 4 4 1424 82325721 82324299 0.000000e+00 2206.0
12 TraesCS7D01G080800 chr4A 89.153 968 69 6 745 1693 662519448 662520398 0.000000e+00 1173.0
13 TraesCS7D01G080800 chr4B 89.096 752 74 6 1 749 107462570 107461824 0.000000e+00 928.0
14 TraesCS7D01G080800 chr4B 88.830 752 71 11 1 749 33642681 33641940 0.000000e+00 911.0
15 TraesCS7D01G080800 chr4B 91.111 45 2 2 2352 2395 158276517 158276474 2.660000e-05 60.2
16 TraesCS7D01G080800 chr6D 88.682 751 79 4 1 749 312676444 312677190 0.000000e+00 911.0
17 TraesCS7D01G080800 chr6D 88.579 753 78 7 1 749 132575341 132574593 0.000000e+00 907.0
18 TraesCS7D01G080800 chr4D 88.492 756 80 5 1 753 109383962 109384713 0.000000e+00 907.0
19 TraesCS7D01G080800 chr1D 88.564 752 80 4 1 749 273584936 273584188 0.000000e+00 907.0
20 TraesCS7D01G080800 chr2D 88.755 747 73 7 1 742 465930329 465929589 0.000000e+00 904.0
21 TraesCS7D01G080800 chr7A 84.639 638 80 11 933 1552 9976756 9977393 9.720000e-174 619.0
22 TraesCS7D01G080800 chr5D 89.431 123 10 3 2352 2473 495965068 495965188 4.260000e-33 152.0
23 TraesCS7D01G080800 chr1A 93.478 46 3 0 2352 2397 497941696 497941741 4.410000e-08 69.4


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 TraesCS7D01G080800 chr7D 47515438 47517910 2472 False 4567 4567 100.0000 1 2473 1 chr7D.!!$F1 2472
1 TraesCS7D01G080800 chr7D 48257335 48258108 773 False 641 641 81.8530 780 1557 1 chr7D.!!$F2 777
2 TraesCS7D01G080800 chr7D 10750769 10751560 791 False 376 628 82.8765 745 1516 2 chr7D.!!$F4 771
3 TraesCS7D01G080800 chr7D 22339923 22340700 777 True 356 586 82.4885 745 1495 2 chr7D.!!$R2 750
4 TraesCS7D01G080800 chrUn 234382479 234384426 1947 False 3011 3011 94.4300 501 2473 1 chrUn.!!$F1 1972
5 TraesCS7D01G080800 chrUn 82324299 82331222 6923 True 2603 3000 94.4960 4 2473 2 chrUn.!!$R1 2469
6 TraesCS7D01G080800 chrUn 363503070 363504492 1422 False 2217 2217 94.8030 1 1421 1 chrUn.!!$F2 1420
7 TraesCS7D01G080800 chr4A 662519448 662520398 950 False 1173 1173 89.1530 745 1693 1 chr4A.!!$F1 948
8 TraesCS7D01G080800 chr4B 107461824 107462570 746 True 928 928 89.0960 1 749 1 chr4B.!!$R2 748
9 TraesCS7D01G080800 chr4B 33641940 33642681 741 True 911 911 88.8300 1 749 1 chr4B.!!$R1 748
10 TraesCS7D01G080800 chr6D 312676444 312677190 746 False 911 911 88.6820 1 749 1 chr6D.!!$F1 748
11 TraesCS7D01G080800 chr6D 132574593 132575341 748 True 907 907 88.5790 1 749 1 chr6D.!!$R1 748
12 TraesCS7D01G080800 chr4D 109383962 109384713 751 False 907 907 88.4920 1 753 1 chr4D.!!$F1 752
13 TraesCS7D01G080800 chr1D 273584188 273584936 748 True 907 907 88.5640 1 749 1 chr1D.!!$R1 748
14 TraesCS7D01G080800 chr2D 465929589 465930329 740 True 904 904 88.7550 1 742 1 chr2D.!!$R1 741
15 TraesCS7D01G080800 chr7A 9976756 9977393 637 False 619 619 84.6390 933 1552 1 chr7A.!!$F1 619

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
615 6128 1.327303 TGCGTTTGCCTTCTCCAAAT 58.673 45.0 0.0 0.0 41.78 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 7497 0.104855 ACGCAGCATATCGGTCACAT 59.895 50.0 0.0 0.0 0.0 3.21 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
116 5618 9.902684 ACTCATATGTTGAAATCAAGAGATTCT 57.097 29.630 13.23 0.00 43.52 2.40
159 5661 5.530176 AATTTCTAGCCTTCCCCAAGTTA 57.470 39.130 0.00 0.00 0.00 2.24
258 5766 6.712241 TGAAGCATAAGAGAAAAGACTTCG 57.288 37.500 0.00 0.00 36.04 3.79
296 5804 6.473758 GTCTATTACCTTTTGGAGAGTGGTT 58.526 40.000 0.00 0.00 44.07 3.67
297 5805 6.594547 GTCTATTACCTTTTGGAGAGTGGTTC 59.405 42.308 0.00 0.00 44.07 3.62
301 5809 2.373502 CCTTTTGGAGAGTGGTTCCTCT 59.626 50.000 0.00 0.00 44.44 3.69
319 5827 5.338632 TCCTCTTAGATTGGTTAGGTGTCA 58.661 41.667 0.00 0.00 0.00 3.58
518 6028 2.276201 CGCAACCGTTATCCTTCATCA 58.724 47.619 0.00 0.00 0.00 3.07
558 6070 2.104170 TGGATGTACGATAGCACCACA 58.896 47.619 0.00 0.00 42.67 4.17
559 6071 2.159156 TGGATGTACGATAGCACCACAC 60.159 50.000 0.00 0.00 42.67 3.82
588 6100 4.764823 AGAACCACGCCAAAAATCTTCATA 59.235 37.500 0.00 0.00 0.00 2.15
615 6128 1.327303 TGCGTTTGCCTTCTCCAAAT 58.673 45.000 0.00 0.00 41.78 2.32
622 6135 2.562296 TGCCTTCTCCAAATCCTACCT 58.438 47.619 0.00 0.00 0.00 3.08
699 6213 4.021719 TGTGTAGGGTGTTACTTGACTAGC 60.022 45.833 0.00 0.00 0.00 3.42
779 6294 1.623359 GTAGTGCTTGTCTCGCTCAG 58.377 55.000 0.00 0.00 0.00 3.35
942 6458 5.705441 TGTGACATTTGGAGTCCAACTATTC 59.295 40.000 24.52 17.28 43.82 1.75
1127 6711 6.147164 TCTCGTGTTAACTTCTTGCCATTAAG 59.853 38.462 7.22 0.00 0.00 1.85
1380 6977 1.064654 GCTACTGCTGCCACAATAAGC 59.935 52.381 0.00 0.00 37.46 3.09
1502 7102 5.228579 TGCTCGAATAAATTTTGCATCGA 57.771 34.783 0.00 6.57 37.68 3.59
1613 7214 0.523072 CCGCATGTTTTCTGTGGAGG 59.477 55.000 0.00 0.00 45.25 4.30
1703 7304 1.098712 TTCTTTGGCCGTCGTGCTTT 61.099 50.000 0.00 0.00 0.00 3.51
1780 7381 2.481969 GCACGCATTGGTCTATCTCTCA 60.482 50.000 0.00 0.00 0.00 3.27
1824 7425 2.034507 CGTTCAGCTTTATCGCTAGTGC 60.035 50.000 0.00 0.00 38.41 4.40
1826 7427 2.814269 TCAGCTTTATCGCTAGTGCTG 58.186 47.619 13.04 13.04 46.21 4.41
1835 7436 0.435008 CGCTAGTGCTGTTGTTCGTC 59.565 55.000 0.00 0.00 36.97 4.20
1851 7452 1.752198 GTCATGGGCCGGCATACTA 59.248 57.895 30.85 9.56 0.00 1.82
1896 7497 0.610509 TGCCTATTTTTCCGCTGGCA 60.611 50.000 0.00 0.00 46.59 4.92
2040 7641 4.259810 CGTGCCATTAAGTAGTTCACATCG 60.260 45.833 0.00 0.00 0.00 3.84
2084 7685 9.606631 ATCTTCAGAGTTTAATGTTAGCCTTAG 57.393 33.333 0.00 0.00 0.00 2.18
2085 7686 7.549488 TCTTCAGAGTTTAATGTTAGCCTTAGC 59.451 37.037 0.00 0.00 40.32 3.09
2086 7687 6.707290 TCAGAGTTTAATGTTAGCCTTAGCA 58.293 36.000 0.00 0.00 43.56 3.49
2087 7688 7.338710 TCAGAGTTTAATGTTAGCCTTAGCAT 58.661 34.615 0.00 0.00 43.56 3.79
2088 7689 7.829211 TCAGAGTTTAATGTTAGCCTTAGCATT 59.171 33.333 1.67 1.67 41.63 3.56
2089 7690 8.462016 CAGAGTTTAATGTTAGCCTTAGCATTT 58.538 33.333 1.37 0.00 40.07 2.32
2090 7691 9.025041 AGAGTTTAATGTTAGCCTTAGCATTTT 57.975 29.630 1.37 0.00 40.07 1.82
2102 7703 7.484140 AGCCTTAGCATTTTATTTAGTTGCTC 58.516 34.615 0.00 0.00 42.34 4.26
2162 7763 8.936864 CATTCAACTTCTAACCGAATCTTAACT 58.063 33.333 0.00 0.00 0.00 2.24
2191 7792 6.391227 ACCTTGCCCATAATTTTCTTATCG 57.609 37.500 0.00 0.00 0.00 2.92
2289 7890 4.892934 TGTATGGAAAGTGGAGCTGTTTTT 59.107 37.500 0.00 0.00 0.00 1.94
2306 7907 1.893544 TTTGTAACGGGCGGATGAAA 58.106 45.000 0.00 0.00 0.00 2.69
2312 7913 0.036306 ACGGGCGGATGAAAGAAGTT 59.964 50.000 0.00 0.00 0.00 2.66
2314 7915 1.135689 CGGGCGGATGAAAGAAGTTTG 60.136 52.381 0.00 0.00 0.00 2.93
2369 7970 5.493809 ACATTACTAGTTAAATGCCCGTGT 58.506 37.500 15.36 0.00 36.72 4.49
2378 7979 1.573829 AATGCCCGTGTGTTGCTACG 61.574 55.000 0.00 0.00 39.83 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.108425 GGAAAAGAAGGGGTGGAGAAGT 59.892 50.000 0.00 0.00 0.00 3.01
6 7 2.108250 TGGAAAAGAAGGGGTGGAGAAG 59.892 50.000 0.00 0.00 0.00 2.85
8 9 1.827792 TGGAAAAGAAGGGGTGGAGA 58.172 50.000 0.00 0.00 0.00 3.71
10 11 4.355588 TCTTTATGGAAAAGAAGGGGTGGA 59.644 41.667 0.00 0.00 33.72 4.02
12 13 5.570320 TCTCTTTATGGAAAAGAAGGGGTG 58.430 41.667 2.20 0.00 36.01 4.61
13 14 5.860648 TCTCTTTATGGAAAAGAAGGGGT 57.139 39.130 2.20 0.00 36.01 4.95
116 5618 8.485578 AAATTAAGGTTCAAATGGTAGGAACA 57.514 30.769 0.00 0.00 41.98 3.18
117 5619 8.803235 AGAAATTAAGGTTCAAATGGTAGGAAC 58.197 33.333 0.00 0.00 40.04 3.62
159 5661 5.073428 GGAAGAAGGATTTGAGTGGAAAGT 58.927 41.667 0.00 0.00 0.00 2.66
258 5766 4.565564 GGTAATAGACGGTGTGTTGATGAC 59.434 45.833 0.00 0.00 0.00 3.06
296 5804 5.187186 GTGACACCTAACCAATCTAAGAGGA 59.813 44.000 0.00 0.00 0.00 3.71
297 5805 5.187967 AGTGACACCTAACCAATCTAAGAGG 59.812 44.000 0.84 0.00 0.00 3.69
301 5809 5.308497 TCCAAGTGACACCTAACCAATCTAA 59.692 40.000 0.84 0.00 0.00 2.10
319 5827 0.036010 CATGTCGGAGGCTTCCAAGT 60.036 55.000 16.07 0.00 44.26 3.16
518 6028 4.039973 TCCACGTTAATGGAGACTTCAACT 59.960 41.667 0.00 0.00 44.14 3.16
558 6070 0.981183 TTGGCGTGGTTCTGATAGGT 59.019 50.000 0.00 0.00 0.00 3.08
559 6071 2.107950 TTTGGCGTGGTTCTGATAGG 57.892 50.000 0.00 0.00 0.00 2.57
588 6100 1.474077 GAAGGCAAACGCAATGGAGAT 59.526 47.619 0.00 0.00 0.00 2.75
615 6128 6.116711 TGCACATGTAAGTAAAAGGTAGGA 57.883 37.500 0.00 0.00 0.00 2.94
622 6135 8.841300 TGTAGAACATTGCACATGTAAGTAAAA 58.159 29.630 12.78 0.00 0.00 1.52
699 6213 7.581213 TGTGGGTAGATTTTAGCAATTATGG 57.419 36.000 0.00 0.00 0.00 2.74
758 6272 0.243907 GAGCGAGACAAGCACTACCA 59.756 55.000 0.00 0.00 37.01 3.25
942 6458 7.229581 AGTCTAGTGTAAAGTTCCACTAAGG 57.770 40.000 13.39 6.34 42.04 2.69
1282 6879 0.809241 GGTGATCTTGCTCTCGCCTG 60.809 60.000 0.00 0.00 38.69 4.85
1502 7102 9.092876 CAAACCAAATAACGTGCCATTTATTAT 57.907 29.630 0.00 0.00 29.58 1.28
1613 7214 4.751098 TCATCAAATTTTGCCTTGCTGAAC 59.249 37.500 4.19 0.00 27.83 3.18
1703 7304 4.080919 AGAGCATAGTAGACAATTGTGCCA 60.081 41.667 17.58 0.00 0.00 4.92
1744 7345 4.408821 TGCCGCCACCCTCATGAC 62.409 66.667 0.00 0.00 0.00 3.06
1770 7371 5.641209 GCTGAAAAGCAAAGTGAGAGATAGA 59.359 40.000 0.00 0.00 34.41 1.98
1780 7381 1.959282 CCTGGAGCTGAAAAGCAAAGT 59.041 47.619 0.00 0.00 37.25 2.66
1824 7425 1.875963 GGCCCATGACGAACAACAG 59.124 57.895 0.00 0.00 0.00 3.16
1826 7427 2.686816 CCGGCCCATGACGAACAAC 61.687 63.158 0.00 0.00 0.00 3.32
1835 7436 0.108585 AAGTAGTATGCCGGCCCATG 59.891 55.000 26.77 0.00 0.00 3.66
1846 7447 5.368989 GCAAATGGTAGGAGCAAGTAGTAT 58.631 41.667 0.00 0.00 0.00 2.12
1851 7452 1.453155 CGCAAATGGTAGGAGCAAGT 58.547 50.000 0.00 0.00 0.00 3.16
1896 7497 0.104855 ACGCAGCATATCGGTCACAT 59.895 50.000 0.00 0.00 0.00 3.21
1978 7579 6.593382 GCAAAATGCAAATATTACCACTCCAA 59.407 34.615 0.00 0.00 44.26 3.53
2064 7665 8.581253 AAATGCTAAGGCTAACATTAAACTCT 57.419 30.769 9.21 0.00 39.59 3.24
2074 7675 9.020813 GCAACTAAATAAAATGCTAAGGCTAAC 57.979 33.333 0.00 0.00 39.59 2.34
2075 7676 8.966868 AGCAACTAAATAAAATGCTAAGGCTAA 58.033 29.630 0.00 0.00 44.92 3.09
2076 7677 8.519799 AGCAACTAAATAAAATGCTAAGGCTA 57.480 30.769 0.00 0.00 44.92 3.93
2077 7678 7.410120 AGCAACTAAATAAAATGCTAAGGCT 57.590 32.000 0.00 0.00 44.92 4.58
2078 7679 6.697455 GGAGCAACTAAATAAAATGCTAAGGC 59.303 38.462 0.00 0.00 46.58 4.35
2079 7680 8.000780 AGGAGCAACTAAATAAAATGCTAAGG 57.999 34.615 0.00 0.00 46.58 2.69
2080 7681 9.860898 AAAGGAGCAACTAAATAAAATGCTAAG 57.139 29.630 0.00 0.00 46.58 2.18
2102 7703 9.249457 GGAGAAGTTGAAGTTGAAATTTAAAGG 57.751 33.333 0.00 0.00 0.00 3.11
2162 7763 5.309282 AGAAAATTATGGGCAAGGTTTGGAA 59.691 36.000 0.00 0.00 0.00 3.53
2191 7792 0.833949 TTGGTGGGGTTTGGAAAAGC 59.166 50.000 0.00 0.00 0.00 3.51
2240 7841 2.749621 GGGTTTGAACTAGAGGCATGTG 59.250 50.000 0.00 0.00 0.00 3.21
2241 7842 2.290960 GGGGTTTGAACTAGAGGCATGT 60.291 50.000 0.00 0.00 0.00 3.21
2289 7890 0.609151 TCTTTCATCCGCCCGTTACA 59.391 50.000 0.00 0.00 0.00 2.41
2306 7907 6.544928 AAGTTTCAACCCATTCAAACTTCT 57.455 33.333 3.38 0.00 42.66 2.85
2312 7913 7.432869 CACATAGAAAGTTTCAACCCATTCAA 58.567 34.615 17.65 0.00 0.00 2.69
2314 7915 6.389906 CCACATAGAAAGTTTCAACCCATTC 58.610 40.000 17.65 0.00 0.00 2.67
2347 7948 5.353123 ACACACGGGCATTTAACTAGTAATG 59.647 40.000 12.27 12.27 35.39 1.90
2404 8005 6.721208 TCTCAGTGCTAAATGGGATTTTTCTT 59.279 34.615 0.00 0.00 33.82 2.52
2405 8006 6.248433 TCTCAGTGCTAAATGGGATTTTTCT 58.752 36.000 0.00 0.00 33.82 2.52
2406 8007 6.515272 TCTCAGTGCTAAATGGGATTTTTC 57.485 37.500 0.00 0.00 33.82 2.29


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

AutoCloner maintained by Alex Coulton.