Multiple sequence alignment - TraesCS6D01G142000

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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 TraesCS6D01G142000 chr6D 100.000 3998 0 0 1 3998 111442893 111438896 0.000000e+00 7384.0
1 TraesCS6D01G142000 chr6B 96.978 3177 68 17 839 3998 200317059 200313894 0.000000e+00 5310.0
2 TraesCS6D01G142000 chr6B 94.444 36 2 0 3088 3123 200314840 200314805 5.580000e-04 56.5
3 TraesCS6D01G142000 chr6A 95.081 2155 81 19 841 2982 136947058 136949200 0.000000e+00 3369.0
4 TraesCS6D01G142000 chr6A 93.848 699 38 3 3300 3998 136991005 136991698 0.000000e+00 1048.0
5 TraesCS6D01G142000 chr6A 82.406 665 82 29 198 844 583552334 583551687 7.550000e-152 547.0
6 TraesCS6D01G142000 chr3D 89.151 848 61 7 1 840 523848975 523848151 0.000000e+00 1027.0
7 TraesCS6D01G142000 chr7B 88.639 845 77 16 1 839 643480985 643481816 0.000000e+00 1011.0
8 TraesCS6D01G142000 chr7B 87.515 841 93 12 2 840 25581698 25582528 0.000000e+00 961.0
9 TraesCS6D01G142000 chr7B 100.000 35 0 0 3255 3289 703561718 703561752 9.270000e-07 65.8
10 TraesCS6D01G142000 chr5A 87.873 569 52 12 144 701 17971178 17970616 0.000000e+00 652.0
11 TraesCS6D01G142000 chr5A 83.115 610 67 28 256 840 477327396 477327994 1.270000e-144 523.0
12 TraesCS6D01G142000 chr1D 84.219 659 71 22 205 840 364124940 364124292 9.500000e-171 610.0
13 TraesCS6D01G142000 chr7A 81.601 712 89 21 142 839 403199876 403200559 5.840000e-153 551.0
14 TraesCS6D01G142000 chr2A 83.502 594 87 10 2 589 762187249 762186661 9.770000e-151 544.0
15 TraesCS6D01G142000 chr5B 82.521 595 74 26 256 840 389176617 389176043 2.780000e-136 496.0
16 TraesCS6D01G142000 chr5B 100.000 35 0 0 3255 3289 280589008 280589042 9.270000e-07 65.8
17 TraesCS6D01G142000 chr2B 85.470 468 61 6 1 466 702720844 702721306 7.770000e-132 481.0
18 TraesCS6D01G142000 chr2B 85.941 441 56 4 1 440 247950678 247951113 2.180000e-127 466.0
19 TraesCS6D01G142000 chr7D 88.845 251 26 2 1 251 213517858 213518106 1.400000e-79 307.0
20 TraesCS6D01G142000 chr7D 100.000 35 0 0 3255 3289 381895332 381895366 9.270000e-07 65.8
21 TraesCS6D01G142000 chrUn 100.000 35 0 0 3255 3289 237093949 237093983 9.270000e-07 65.8
22 TraesCS6D01G142000 chr5D 100.000 35 0 0 3255 3289 464527878 464527912 9.270000e-07 65.8
23 TraesCS6D01G142000 chr4D 100.000 35 0 0 3255 3289 123476904 123476870 9.270000e-07 65.8
24 TraesCS6D01G142000 chr4D 100.000 35 0 0 3255 3289 450990591 450990625 9.270000e-07 65.8
25 TraesCS6D01G142000 chr4D 100.000 35 0 0 3255 3289 451011303 451011269 9.270000e-07 65.8


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 TraesCS6D01G142000 chr6D 111438896 111442893 3997 True 7384.00 7384 100.000 1 3998 1 chr6D.!!$R1 3997
1 TraesCS6D01G142000 chr6B 200313894 200317059 3165 True 2683.25 5310 95.711 839 3998 2 chr6B.!!$R1 3159
2 TraesCS6D01G142000 chr6A 136947058 136949200 2142 False 3369.00 3369 95.081 841 2982 1 chr6A.!!$F1 2141
3 TraesCS6D01G142000 chr6A 136991005 136991698 693 False 1048.00 1048 93.848 3300 3998 1 chr6A.!!$F2 698
4 TraesCS6D01G142000 chr6A 583551687 583552334 647 True 547.00 547 82.406 198 844 1 chr6A.!!$R1 646
5 TraesCS6D01G142000 chr3D 523848151 523848975 824 True 1027.00 1027 89.151 1 840 1 chr3D.!!$R1 839
6 TraesCS6D01G142000 chr7B 643480985 643481816 831 False 1011.00 1011 88.639 1 839 1 chr7B.!!$F2 838
7 TraesCS6D01G142000 chr7B 25581698 25582528 830 False 961.00 961 87.515 2 840 1 chr7B.!!$F1 838
8 TraesCS6D01G142000 chr5A 17970616 17971178 562 True 652.00 652 87.873 144 701 1 chr5A.!!$R1 557
9 TraesCS6D01G142000 chr5A 477327396 477327994 598 False 523.00 523 83.115 256 840 1 chr5A.!!$F1 584
10 TraesCS6D01G142000 chr1D 364124292 364124940 648 True 610.00 610 84.219 205 840 1 chr1D.!!$R1 635
11 TraesCS6D01G142000 chr7A 403199876 403200559 683 False 551.00 551 81.601 142 839 1 chr7A.!!$F1 697
12 TraesCS6D01G142000 chr2A 762186661 762187249 588 True 544.00 544 83.502 2 589 1 chr2A.!!$R1 587
13 TraesCS6D01G142000 chr5B 389176043 389176617 574 True 496.00 496 82.521 256 840 1 chr5B.!!$R1 584

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
713 799 0.389025 CAAAACCAGCCAGGAACCAC 59.611 55.0 0.00 0.0 41.22 4.16 F
972 1068 0.594540 ACGCACGCGCCGTATAAATA 60.595 50.0 21.39 0.0 44.19 1.40 F
2418 2531 0.600557 TGCTTGGGCGTTTGTAATGG 59.399 50.0 0.00 0.0 42.25 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1877 0.891373 CTTGGAGCTCGTTGGAGAGA 59.109 55.000 7.83 0.0 43.27 3.10 R
2844 2958 1.401552 GACTGCTGACTTGCACACAAA 59.598 47.619 0.00 0.0 38.12 2.83 R
3591 3709 0.338814 ACCCTCCGTTCCTACCTCAT 59.661 55.000 0.00 0.0 0.00 2.90 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
113 114 6.884295 AGATCCGGTACATTTTCTGAATTTCA 59.116 34.615 0.00 0.00 0.00 2.69
535 590 7.623060 CGCGAACGAAATTCAAAATTTTCTATG 59.377 33.333 0.00 0.00 43.93 2.23
713 799 0.389025 CAAAACCAGCCAGGAACCAC 59.611 55.000 0.00 0.00 41.22 4.16
972 1068 0.594540 ACGCACGCGCCGTATAAATA 60.595 50.000 21.39 0.00 44.19 1.40
986 1082 1.658994 TAAATAAGCGCCAACCTCCG 58.341 50.000 2.29 0.00 0.00 4.63
1008 1108 3.769844 GTCACTGATCCTTAACCCTCTCA 59.230 47.826 0.00 0.00 0.00 3.27
1009 1109 4.026744 TCACTGATCCTTAACCCTCTCAG 58.973 47.826 0.00 0.00 36.92 3.35
1010 1110 3.772025 CACTGATCCTTAACCCTCTCAGT 59.228 47.826 0.00 0.00 42.90 3.41
1011 1111 4.027437 ACTGATCCTTAACCCTCTCAGTC 58.973 47.826 0.00 0.00 39.14 3.51
1012 1112 4.264623 ACTGATCCTTAACCCTCTCAGTCT 60.265 45.833 0.00 0.00 39.14 3.24
1013 1113 4.282496 TGATCCTTAACCCTCTCAGTCTC 58.718 47.826 0.00 0.00 0.00 3.36
1014 1114 3.827817 TCCTTAACCCTCTCAGTCTCA 57.172 47.619 0.00 0.00 0.00 3.27
1015 1115 3.432378 TCCTTAACCCTCTCAGTCTCAC 58.568 50.000 0.00 0.00 0.00 3.51
1027 1127 2.367844 GTCTCACTGCATGCGAGAC 58.632 57.895 27.38 27.38 44.37 3.36
1168 1281 2.428890 GACATCGTCAAGATCCTGTCCT 59.571 50.000 0.00 0.00 37.52 3.85
1552 1665 1.304547 CTCCTCAGGGTCGTCACCT 60.305 63.158 0.00 0.00 43.22 4.00
1764 1877 3.276846 GCCGTCAACAACACCGCT 61.277 61.111 0.00 0.00 0.00 5.52
2418 2531 0.600557 TGCTTGGGCGTTTGTAATGG 59.399 50.000 0.00 0.00 42.25 3.16
2599 2713 3.380471 TGATCCATTTTGTACCAGGGG 57.620 47.619 0.00 0.00 0.00 4.79
2784 2898 7.917505 ACATTTTCTTGTTTGCTACTTCTTCTG 59.082 33.333 0.00 0.00 0.00 3.02
2997 3112 2.011222 GGCATTGTCGGTCGGATTAAA 58.989 47.619 0.00 0.00 0.00 1.52
3034 3149 1.209383 CGAGGCAACGACGAGAGAA 59.791 57.895 0.00 0.00 46.39 2.87
3060 3175 1.303317 GCGGCTGGAGGAGGAAAAA 60.303 57.895 0.00 0.00 0.00 1.94
3090 3206 8.759641 GTTCTTATATAGTCGACTTACACGAGA 58.240 37.037 25.44 16.37 40.37 4.04
3174 3292 1.351017 CAACCTCTTAGGCCCTGTTCA 59.649 52.381 0.00 0.00 39.63 3.18
3244 3362 3.121019 CCGTTTTGTTTCCGGCCA 58.879 55.556 2.24 0.00 34.62 5.36
3285 3403 6.042143 AGGTGCAAATAAGCCATTTTATTCG 58.958 36.000 0.00 0.00 34.49 3.34
3591 3709 8.429237 AAATGATATACCTCAAACCAAACCAA 57.571 30.769 0.00 0.00 0.00 3.67
3642 3760 5.163416 GCATATAGTTTCCAAAACCAGGCAT 60.163 40.000 0.00 0.00 0.00 4.40
3660 3778 3.558418 GGCATGCCAAAATAGAATTGCTG 59.442 43.478 32.08 0.00 35.81 4.41
3740 3858 4.918810 AACTGAAAAATCTGGTCACCAC 57.081 40.909 0.00 0.00 0.00 4.16
3798 3916 2.837498 TCGTACATCCTGCATCAATGG 58.163 47.619 7.69 0.00 0.00 3.16
3820 3938 2.632996 AGAGACAACATCTGAAACGGGA 59.367 45.455 0.00 0.00 38.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 7.083875 TGAAATTCAGAAAATGTACCGGATC 57.916 36.000 9.46 0.13 0.00 3.36
504 557 0.706184 TGAATTTCGTTCGCGTCTCG 59.294 50.000 5.77 9.91 39.80 4.04
972 1068 3.936203 TGACGGAGGTTGGCGCTT 61.936 61.111 7.64 0.00 0.00 4.68
976 1072 0.741221 GATCAGTGACGGAGGTTGGC 60.741 60.000 0.00 0.00 0.00 4.52
986 1082 3.769844 TGAGAGGGTTAAGGATCAGTGAC 59.230 47.826 0.00 0.00 0.00 3.67
1012 1112 0.179127 GCTAGTCTCGCATGCAGTGA 60.179 55.000 19.57 13.38 35.04 3.41
1013 1113 1.150567 GGCTAGTCTCGCATGCAGTG 61.151 60.000 19.57 11.31 0.00 3.66
1014 1114 1.142748 GGCTAGTCTCGCATGCAGT 59.857 57.895 19.57 3.65 0.00 4.40
1015 1115 0.875040 CTGGCTAGTCTCGCATGCAG 60.875 60.000 19.57 14.00 0.00 4.41
1027 1127 1.070445 CTTGGGATCGGCTGGCTAG 59.930 63.158 0.00 0.00 0.00 3.42
1168 1281 2.347490 GCTGAACTCGGGGAAGCA 59.653 61.111 1.67 0.00 34.01 3.91
1352 1465 3.069318 GCTTCTCCGGGTCGAGGT 61.069 66.667 0.00 0.00 0.00 3.85
1530 1643 3.063084 ACGACCCTGAGGAGCGTC 61.063 66.667 11.77 4.80 41.46 5.19
1764 1877 0.891373 CTTGGAGCTCGTTGGAGAGA 59.109 55.000 7.83 0.00 43.27 3.10
1987 2100 3.195698 GGAGAACGTGATGCGGCC 61.196 66.667 0.00 0.00 46.52 6.13
2599 2713 2.300437 AGTCCACTCAGACCTAGCAAAC 59.700 50.000 0.00 0.00 37.49 2.93
2813 2927 3.206964 GCAGCTTGTTAATAGTCCCTCC 58.793 50.000 0.00 0.00 0.00 4.30
2844 2958 1.401552 GACTGCTGACTTGCACACAAA 59.598 47.619 0.00 0.00 38.12 2.83
2938 3052 4.836825 TCCTCTCTGCAAAATCAAGGTAG 58.163 43.478 0.00 0.00 0.00 3.18
2939 3053 4.908601 TCCTCTCTGCAAAATCAAGGTA 57.091 40.909 0.00 0.00 0.00 3.08
3017 3132 1.721926 CTTTTCTCTCGTCGTTGCCTC 59.278 52.381 0.00 0.00 0.00 4.70
3034 3149 2.282462 CTCCAGCCGCCCAACTTT 60.282 61.111 0.00 0.00 0.00 2.66
3060 3175 8.628280 GTGTAAGTCGACTATATAAGAACCCTT 58.372 37.037 20.39 0.00 36.43 3.95
3061 3176 7.041508 CGTGTAAGTCGACTATATAAGAACCCT 60.042 40.741 20.39 0.17 0.00 4.34
3064 3179 8.759641 TCTCGTGTAAGTCGACTATATAAGAAC 58.240 37.037 20.39 8.01 33.71 3.01
3066 3181 8.877808 TTCTCGTGTAAGTCGACTATATAAGA 57.122 34.615 20.39 14.24 33.71 2.10
3067 3182 9.926751 TTTTCTCGTGTAAGTCGACTATATAAG 57.073 33.333 20.39 12.21 33.71 1.73
3090 3206 9.993454 GTCGACTATATATAAGAACCCCTTTTT 57.007 33.333 8.70 0.00 36.34 1.94
3111 3227 7.422746 CGATAAATTCTTTTAGTGCAAGTCGAC 59.577 37.037 7.70 7.70 31.07 4.20
3174 3292 7.942990 TGTATTTAAAACGAAAATGGTGACCT 58.057 30.769 2.11 0.00 0.00 3.85
3244 3362 4.099881 TGCACCTTTCTTTGAGCAATTCTT 59.900 37.500 0.00 0.00 0.00 2.52
3591 3709 0.338814 ACCCTCCGTTCCTACCTCAT 59.661 55.000 0.00 0.00 0.00 2.90
3642 3760 5.981088 TCTTCAGCAATTCTATTTTGGCA 57.019 34.783 0.00 0.00 0.00 4.92
3660 3778 9.477484 TGAGTGTTAGAAGTACTGAATTTCTTC 57.523 33.333 0.00 0.00 37.24 2.87
3740 3858 7.254898 CCATGCTATCTACATGTTTGGTTGTAG 60.255 40.741 2.30 4.16 44.28 2.74
3798 3916 2.996621 CCCGTTTCAGATGTTGTCTCTC 59.003 50.000 0.00 0.00 34.00 3.20
3820 3938 3.262420 GACATGAACGTGCCAATCTAGT 58.738 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.