Multiple sequence alignment - TraesCS6A01G366300

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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 TraesCS6A01G366300 chr6A 100.000 2920 0 0 1 2920 594075660 594072741 0.000000e+00 5393
1 TraesCS6A01G366300 chr1A 95.103 2920 127 5 1 2920 118167984 118170887 0.000000e+00 4586
2 TraesCS6A01G366300 chr1A 94.619 2676 127 8 246 2920 363572874 363575533 0.000000e+00 4128
3 TraesCS6A01G366300 chr1A 92.830 1046 75 0 1 1046 446458082 446457037 0.000000e+00 1517
4 TraesCS6A01G366300 chr1A 93.122 945 63 1 102 1046 548110698 548109756 0.000000e+00 1384
5 TraesCS6A01G366300 chr2A 95.068 2920 128 5 1 2920 53545004 53547907 0.000000e+00 4580
6 TraesCS6A01G366300 chr2A 93.588 577 21 4 2344 2920 697179164 697178604 0.000000e+00 846
7 TraesCS6A01G366300 chr2A 94.872 234 12 0 1 234 591209312 591209545 1.650000e-97 366
8 TraesCS6A01G366300 chr1D 90.268 2497 164 18 465 2920 366398865 366401323 0.000000e+00 3192
9 TraesCS6A01G366300 chr1D 93.471 1884 96 11 1043 2920 100563035 100561173 0.000000e+00 2772
10 TraesCS6A01G366300 chr5A 94.462 1878 88 5 1043 2920 689814312 689816173 0.000000e+00 2878
11 TraesCS6A01G366300 chr5A 94.073 1046 61 1 1 1046 689813231 689814275 0.000000e+00 1587
12 TraesCS6A01G366300 chr7A 94.089 1878 94 6 1043 2920 499988487 499986627 0.000000e+00 2837
13 TraesCS6A01G366300 chr7A 93.358 1882 97 16 1043 2920 536411109 536409252 0.000000e+00 2758
14 TraesCS6A01G366300 chr7A 94.229 953 55 0 94 1046 499989476 499988524 0.000000e+00 1456
15 TraesCS6A01G366300 chr6D 93.404 1880 104 9 1043 2920 437028554 437026693 0.000000e+00 2767
16 TraesCS6A01G366300 chr4D 93.351 1880 103 11 1043 2920 482640949 482642808 0.000000e+00 2760
17 TraesCS6A01G366300 chr4D 91.010 1891 129 11 1045 2920 490745726 490743862 0.000000e+00 2512
18 TraesCS6A01G366300 chr4D 90.189 581 51 4 465 1044 482640335 482640910 0.000000e+00 752
19 TraesCS6A01G366300 chr4D 94.872 234 12 0 1 234 482639305 482639538 1.650000e-97 366
20 TraesCS6A01G366300 chr3A 92.543 1046 76 2 1 1046 617206456 617207499 0.000000e+00 1498
21 TraesCS6A01G366300 chr3A 92.105 494 19 5 2427 2920 617208865 617209338 0.000000e+00 678
22 TraesCS6A01G366300 chr7D 95.238 231 10 1 239 468 518155029 518154799 5.950000e-97 364


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 TraesCS6A01G366300 chr6A 594072741 594075660 2919 True 5393.000000 5393 100.0000 1 2920 1 chr6A.!!$R1 2919
1 TraesCS6A01G366300 chr1A 118167984 118170887 2903 False 4586.000000 4586 95.1030 1 2920 1 chr1A.!!$F1 2919
2 TraesCS6A01G366300 chr1A 363572874 363575533 2659 False 4128.000000 4128 94.6190 246 2920 1 chr1A.!!$F2 2674
3 TraesCS6A01G366300 chr1A 446457037 446458082 1045 True 1517.000000 1517 92.8300 1 1046 1 chr1A.!!$R1 1045
4 TraesCS6A01G366300 chr1A 548109756 548110698 942 True 1384.000000 1384 93.1220 102 1046 1 chr1A.!!$R2 944
5 TraesCS6A01G366300 chr2A 53545004 53547907 2903 False 4580.000000 4580 95.0680 1 2920 1 chr2A.!!$F1 2919
6 TraesCS6A01G366300 chr2A 697178604 697179164 560 True 846.000000 846 93.5880 2344 2920 1 chr2A.!!$R1 576
7 TraesCS6A01G366300 chr1D 366398865 366401323 2458 False 3192.000000 3192 90.2680 465 2920 1 chr1D.!!$F1 2455
8 TraesCS6A01G366300 chr1D 100561173 100563035 1862 True 2772.000000 2772 93.4710 1043 2920 1 chr1D.!!$R1 1877
9 TraesCS6A01G366300 chr5A 689813231 689816173 2942 False 2232.500000 2878 94.2675 1 2920 2 chr5A.!!$F1 2919
10 TraesCS6A01G366300 chr7A 536409252 536411109 1857 True 2758.000000 2758 93.3580 1043 2920 1 chr7A.!!$R1 1877
11 TraesCS6A01G366300 chr7A 499986627 499989476 2849 True 2146.500000 2837 94.1590 94 2920 2 chr7A.!!$R2 2826
12 TraesCS6A01G366300 chr6D 437026693 437028554 1861 True 2767.000000 2767 93.4040 1043 2920 1 chr6D.!!$R1 1877
13 TraesCS6A01G366300 chr4D 490743862 490745726 1864 True 2512.000000 2512 91.0100 1045 2920 1 chr4D.!!$R1 1875
14 TraesCS6A01G366300 chr4D 482639305 482642808 3503 False 1292.666667 2760 92.8040 1 2920 3 chr4D.!!$F1 2919
15 TraesCS6A01G366300 chr3A 617206456 617209338 2882 False 1088.000000 1498 92.3240 1 2920 2 chr3A.!!$F1 2919

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
135 136 0.398522 TACGCCCATGACCCTCAGAT 60.399 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2706 0.106719 CGCATGGTCCCCTTGGTATT 60.107 55.0 0.0 0.0 0.0 1.89 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
84 85 9.626045 GAAAAACATTTTGAATACAGAGGTAGG 57.374 33.333 0.00 0.00 31.88 3.18
135 136 0.398522 TACGCCCATGACCCTCAGAT 60.399 55.000 0.00 0.00 0.00 2.90
145 146 4.808414 TGACCCTCAGATAAGAACACTG 57.192 45.455 0.00 0.00 0.00 3.66
172 173 2.739913 ACACGGTTGTCCATCAATAACG 59.260 45.455 0.00 0.00 38.38 3.18
224 226 2.513026 CTTCGGTGCCTCCACTCCTG 62.513 65.000 0.00 0.00 41.75 3.86
250 518 1.444724 CGCATGTTACGTCGACCCA 60.445 57.895 10.58 2.12 0.00 4.51
533 1101 4.150627 CACATAGCACCATAGCACGAATAC 59.849 45.833 0.00 0.00 36.85 1.89
584 1152 1.517276 GTGCATCACGTAGCATCGTAC 59.483 52.381 11.83 0.00 43.44 3.67
585 1153 1.133407 TGCATCACGTAGCATCGTACA 59.867 47.619 5.52 1.31 42.27 2.90
590 1158 2.162809 TCACGTAGCATCGTACATGTGT 59.837 45.455 9.11 0.00 42.27 3.72
748 1316 0.461961 ACTGCTCCTACCAGCGATTC 59.538 55.000 0.00 0.00 42.92 2.52
793 1361 2.370349 CCAATAAATGTACCACGCCCA 58.630 47.619 0.00 0.00 0.00 5.36
820 1388 4.005650 TCTGAGAGTTAAAGCTGCCATTG 58.994 43.478 0.00 0.00 0.00 2.82
875 1453 6.183361 TGCCTCTACAATACATACTACCCCTA 60.183 42.308 0.00 0.00 0.00 3.53
927 1509 5.804692 TTTGACAGCAAACTACGAAAGAA 57.195 34.783 0.00 0.00 38.99 2.52
1024 1607 2.200373 AAGAAAACCCACGATCCAGG 57.800 50.000 0.00 0.00 0.00 4.45
1033 1616 2.348888 ACGATCCAGGACCCACGAC 61.349 63.158 12.18 0.00 0.00 4.34
1066 1708 4.595986 GCCCTTAAATTTAGACTCCCACA 58.404 43.478 0.00 0.00 0.00 4.17
1166 1808 1.598130 GACCAACTGCTCCAAGCGT 60.598 57.895 0.00 0.00 46.26 5.07
1261 1903 4.988598 CACAAGGCGGCGACCACT 62.989 66.667 10.28 0.00 0.00 4.00
1280 1922 2.099921 ACTATTGAGCAGTTCGAGCGAT 59.900 45.455 0.00 0.00 37.01 4.58
1351 1993 0.249120 ACGACCATGGCGAAGATCAA 59.751 50.000 27.68 0.00 0.00 2.57
1399 2041 0.106708 GCAAGGATCATCCGGTGCTA 59.893 55.000 22.05 0.00 44.14 3.49
1404 2046 1.271102 GGATCATCCGGTGCTACTCTC 59.729 57.143 0.00 0.00 0.00 3.20
1411 2053 1.471119 CGGTGCTACTCTCCCAACTA 58.529 55.000 0.00 0.00 0.00 2.24
1437 2079 1.237285 GCCGACAAGAACTGCACCAT 61.237 55.000 0.00 0.00 0.00 3.55
1517 2159 2.203082 ATAGAGATGCTCGGCCGCA 61.203 57.895 23.51 15.00 45.10 5.69
1689 2331 0.250858 CACCTGTCCATGAGGCACAA 60.251 55.000 0.00 0.00 33.39 3.33
1690 2332 0.700564 ACCTGTCCATGAGGCACAAT 59.299 50.000 0.00 0.00 33.39 2.71
1802 2445 1.669115 GAGCAGACCAGAAAGCGCA 60.669 57.895 11.47 0.00 0.00 6.09
1967 2634 5.883673 ACAGTTAACCTTGTAGTTTGCTTGA 59.116 36.000 0.88 0.00 0.00 3.02
1979 2646 7.767261 TGTAGTTTGCTTGAAGTTTACATGTT 58.233 30.769 2.30 0.00 0.00 2.71
2039 2706 6.161855 CACTTATGTGCCTATGTTCCTCTA 57.838 41.667 0.00 0.00 37.38 2.43
2183 2855 1.798626 TGGAGCTCATAGTCCATGCT 58.201 50.000 17.19 0.00 37.96 3.79
2565 3237 0.547471 TGCTCCATCCTTCACCTCCA 60.547 55.000 0.00 0.00 0.00 3.86
2677 3349 1.736365 TACGTGACTGTGCCCGTTCA 61.736 55.000 0.00 0.00 34.95 3.18
2682 3354 2.029073 CTGTGCCCGTTCAGTCGT 59.971 61.111 0.00 0.00 0.00 4.34
2738 3410 3.694072 GCCTCTGCCACACAACATATAAA 59.306 43.478 0.00 0.00 0.00 1.40
2739 3411 4.157656 GCCTCTGCCACACAACATATAAAA 59.842 41.667 0.00 0.00 0.00 1.52
2740 3412 5.640732 CCTCTGCCACACAACATATAAAAC 58.359 41.667 0.00 0.00 0.00 2.43
2741 3413 5.393027 CCTCTGCCACACAACATATAAAACC 60.393 44.000 0.00 0.00 0.00 3.27
2743 3415 5.714333 TCTGCCACACAACATATAAAACCAT 59.286 36.000 0.00 0.00 0.00 3.55
2744 3416 6.887002 TCTGCCACACAACATATAAAACCATA 59.113 34.615 0.00 0.00 0.00 2.74
2745 3417 7.559533 TCTGCCACACAACATATAAAACCATAT 59.440 33.333 0.00 0.00 0.00 1.78
2746 3418 7.487484 TGCCACACAACATATAAAACCATATG 58.513 34.615 0.00 0.00 42.29 1.78
2747 3419 6.420604 GCCACACAACATATAAAACCATATGC 59.579 38.462 0.00 0.00 40.91 3.14
2748 3420 7.487484 CCACACAACATATAAAACCATATGCA 58.513 34.615 0.00 0.00 40.91 3.96
2749 3421 7.978414 CCACACAACATATAAAACCATATGCAA 59.022 33.333 0.00 0.00 40.91 4.08
2750 3422 9.022915 CACACAACATATAAAACCATATGCAAG 57.977 33.333 0.00 0.00 40.91 4.01
2751 3423 8.965819 ACACAACATATAAAACCATATGCAAGA 58.034 29.630 0.00 0.00 40.91 3.02
2752 3424 9.970395 CACAACATATAAAACCATATGCAAGAT 57.030 29.630 0.00 0.00 40.91 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 7.229907 TGTTTTCCAAGGAGAATAAACACCTAC 59.770 37.037 11.02 0.00 30.79 3.18
135 136 2.288213 CCGTGTCTCTGCAGTGTTCTTA 60.288 50.000 14.67 0.00 0.00 2.10
224 226 0.389426 ACGTAACATGCGGTCTCCAC 60.389 55.000 0.00 0.00 0.00 4.02
250 518 5.114081 GGTAACGTCATATTTAGTGCCAGT 58.886 41.667 0.00 0.00 0.00 4.00
468 1036 2.037641 AGCTGTGCACTGAAGTACATGA 59.962 45.455 25.94 0.00 33.68 3.07
584 1152 2.146342 AGGCGAAACAAGAGACACATG 58.854 47.619 0.00 0.00 0.00 3.21
585 1153 2.037772 AGAGGCGAAACAAGAGACACAT 59.962 45.455 0.00 0.00 0.00 3.21
590 1158 2.656560 GCTAGAGGCGAAACAAGAGA 57.343 50.000 0.00 0.00 0.00 3.10
648 1216 1.194772 CGGAAAGAACGAGAAGCAACC 59.805 52.381 0.00 0.00 0.00 3.77
748 1316 6.017400 AGTGGCAATTGTTTTCAGTGATAG 57.983 37.500 7.40 0.00 0.00 2.08
793 1361 3.999663 GCAGCTTTAACTCTCAGACACAT 59.000 43.478 0.00 0.00 0.00 3.21
875 1453 3.610040 TTACAATCTCGTGAGGCATGT 57.390 42.857 0.00 3.32 0.00 3.21
927 1509 4.836825 ACAAGTCATGGAGATGATCGTTT 58.163 39.130 0.00 0.00 40.78 3.60
1024 1607 2.586635 TTGTGCACGTCGTGGGTC 60.587 61.111 25.70 10.65 33.64 4.46
1033 1616 1.787057 TTTAAGGGCGGTTGTGCACG 61.787 55.000 13.13 0.46 45.07 5.34
1066 1708 2.031163 GTGTGTGAGAAGGCCGCT 59.969 61.111 0.00 0.00 0.00 5.52
1166 1808 4.606476 TGAATTCCCTCATGAATCCCAA 57.394 40.909 2.27 0.00 33.91 4.12
1176 1818 1.064463 GCACCTCCATGAATTCCCTCA 60.064 52.381 2.27 0.00 0.00 3.86
1177 1819 1.064463 TGCACCTCCATGAATTCCCTC 60.064 52.381 2.27 0.00 0.00 4.30
1261 1903 2.871182 ATCGCTCGAACTGCTCAATA 57.129 45.000 0.00 0.00 0.00 1.90
1280 1922 2.707849 GGCGCTCGAACTGGAGGTA 61.708 63.158 7.64 0.00 34.56 3.08
1351 1993 3.261677 TGGGCTAGGGCGGGTTTT 61.262 61.111 0.00 0.00 39.81 2.43
1399 2041 1.215647 CGCGCTTAGTTGGGAGAGT 59.784 57.895 5.56 0.00 0.00 3.24
1411 2053 4.980805 TTCTTGTCGGCCGCGCTT 62.981 61.111 23.51 0.00 0.00 4.68
1437 2079 0.937699 CGCGAGGAAGTTGTCGAACA 60.938 55.000 0.00 0.00 38.50 3.18
1517 2159 2.203771 GGGCGATCTCCAGTCCGAT 61.204 63.158 3.71 0.00 0.00 4.18
1561 2203 2.241281 TGGTAGCTGTAGGCACCTTA 57.759 50.000 0.00 0.00 44.79 2.69
1563 2205 0.905357 CTTGGTAGCTGTAGGCACCT 59.095 55.000 0.00 0.00 44.79 4.00
1671 2313 0.700564 ATTGTGCCTCATGGACAGGT 59.299 50.000 1.25 0.00 32.98 4.00
1689 2331 0.739813 GTCCTTTGCCGCGTACTCAT 60.740 55.000 4.92 0.00 0.00 2.90
1690 2332 1.373748 GTCCTTTGCCGCGTACTCA 60.374 57.895 4.92 0.00 0.00 3.41
1802 2445 0.330604 TAGTCGCCACAGGACCTAGT 59.669 55.000 0.00 0.00 34.97 2.57
1979 2646 6.183360 GCACTGGAAATAAACTTGTGCAAAAA 60.183 34.615 9.82 0.00 45.64 1.94
2033 2700 2.319747 TGGTCCCCTTGGTATTAGAGGA 59.680 50.000 0.00 0.00 32.11 3.71
2039 2706 0.106719 CGCATGGTCCCCTTGGTATT 60.107 55.000 0.00 0.00 0.00 1.89
2183 2855 3.320541 GTGACACATTTTCATTGTGGGGA 59.679 43.478 0.00 0.00 46.89 4.81
2565 3237 1.148310 CGTCGTTCTTGTTGAGGCAT 58.852 50.000 0.00 0.00 0.00 4.40
2677 3349 1.552337 AGAGGCATGAATGTGACGACT 59.448 47.619 0.00 0.00 30.43 4.18
2682 3354 3.421919 TTGTGAGAGGCATGAATGTGA 57.578 42.857 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.