Multiple sequence alignment - TraesCS1B01G360200

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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 TraesCS1B01G360200 chr1B 100.000 5161 0 0 1 5161 588797300 588802460 0.000000e+00 9531.0
1 TraesCS1B01G360200 chr1B 86.301 73 9 1 4775 4847 588801944 588802015 1.540000e-10 78.7
2 TraesCS1B01G360200 chr1B 86.301 73 9 1 4645 4716 588802074 588802146 1.540000e-10 78.7
3 TraesCS1B01G360200 chr1B 93.750 48 1 2 1 46 299982231 299982278 2.580000e-08 71.3
4 TraesCS1B01G360200 chr1D 98.105 3694 58 7 924 4611 435465363 435469050 0.000000e+00 6423.0
5 TraesCS1B01G360200 chr1D 95.871 557 12 1 4613 5158 435469298 435469854 0.000000e+00 891.0
6 TraesCS1B01G360200 chr1D 87.671 73 8 1 4775 4847 435469330 435469401 3.310000e-12 84.2
7 TraesCS1B01G360200 chr1D 86.301 73 9 1 4645 4716 435469471 435469543 1.540000e-10 78.7
8 TraesCS1B01G360200 chr1A 96.382 3593 112 11 913 4494 532929731 532933316 0.000000e+00 5899.0
9 TraesCS1B01G360200 chr1A 96.344 547 19 1 4613 5158 532934019 532934565 0.000000e+00 898.0
10 TraesCS1B01G360200 chr1A 98.851 87 1 0 4525 4611 532933685 532933771 6.920000e-34 156.0
11 TraesCS1B01G360200 chr1A 87.671 73 8 1 4775 4847 532934051 532934122 3.310000e-12 84.2
12 TraesCS1B01G360200 chr5B 98.567 907 10 1 1 907 18066859 18065956 0.000000e+00 1600.0
13 TraesCS1B01G360200 chr4B 91.067 862 48 13 47 908 438353642 438352810 0.000000e+00 1138.0
14 TraesCS1B01G360200 chr7A 91.858 565 31 8 46 605 719024585 719024031 0.000000e+00 774.0
15 TraesCS1B01G360200 chr7A 91.504 565 33 8 46 605 719300188 719299634 0.000000e+00 763.0
16 TraesCS1B01G360200 chr7A 92.500 280 20 1 625 904 719024036 719023758 2.900000e-107 399.0
17 TraesCS1B01G360200 chr7A 91.071 280 24 1 625 904 719299639 719299361 1.360000e-100 377.0
18 TraesCS1B01G360200 chr7A 93.750 48 1 2 1 46 150086631 150086584 2.580000e-08 71.3
19 TraesCS1B01G360200 chr7A 88.525 61 4 3 1 58 612974498 612974558 2.580000e-08 71.3
20 TraesCS1B01G360200 chr5A 93.750 48 1 2 1 46 546715170 546715123 2.580000e-08 71.3
21 TraesCS1B01G360200 chr7D 87.302 63 3 5 2 61 499063877 499063817 3.340000e-07 67.6
22 TraesCS1B01G360200 chr6A 87.931 58 5 2 1 56 216075558 216075501 3.340000e-07 67.6
23 TraesCS1B01G360200 chr2A 88.333 60 2 4 1 56 41589555 41589613 3.340000e-07 67.6
24 TraesCS1B01G360200 chr2A 85.714 63 6 3 6 67 693541190 693541130 4.310000e-06 63.9
25 TraesCS1B01G360200 chr4A 87.931 58 4 3 4452 4507 125398478 125398422 1.200000e-06 65.8
26 TraesCS1B01G360200 chr4A 100.000 28 0 0 1555 1582 614102663 614102636 9.000000e-03 52.8


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 TraesCS1B01G360200 chr1B 588797300 588802460 5160 False 3229.466667 9531 90.867333 1 5161 3 chr1B.!!$F2 5160
1 TraesCS1B01G360200 chr1D 435465363 435469854 4491 False 1869.225000 6423 91.987000 924 5158 4 chr1D.!!$F1 4234
2 TraesCS1B01G360200 chr1A 532929731 532934565 4834 False 1759.300000 5899 94.812000 913 5158 4 chr1A.!!$F1 4245
3 TraesCS1B01G360200 chr5B 18065956 18066859 903 True 1600.000000 1600 98.567000 1 907 1 chr5B.!!$R1 906
4 TraesCS1B01G360200 chr4B 438352810 438353642 832 True 1138.000000 1138 91.067000 47 908 1 chr4B.!!$R1 861
5 TraesCS1B01G360200 chr7A 719023758 719024585 827 True 586.500000 774 92.179000 46 904 2 chr7A.!!$R2 858
6 TraesCS1B01G360200 chr7A 719299361 719300188 827 True 570.000000 763 91.287500 46 904 2 chr7A.!!$R3 858

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
962 970 1.761198 AGACGGGTAATGAGTAAGCCC 59.239 52.381 0.0 0.0 36.08 5.19 F
1803 1815 1.581934 CAGACCAGTCAAACTTCGCA 58.418 50.000 0.0 0.0 0.00 5.10 F
1840 1852 0.535797 GACGGGTCTTCGGGATCTTT 59.464 55.000 0.0 0.0 0.00 2.52 F
3229 3241 0.322098 TGGGCGAACTGGTAATGTGG 60.322 55.000 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1852 1.471119 CGTAGGCCCTCTAGAACACA 58.529 55.000 0.00 0.0 0.00 3.72 R
3192 3204 2.158564 CCCAAGTAGATCCACCATGCAT 60.159 50.000 0.00 0.0 0.00 3.96 R
3594 3606 3.813443 CACATAGCCTGCAGTCCTTAAT 58.187 45.455 13.81 0.0 0.00 1.40 R
4505 4522 0.836400 GCCATAGGATTCCCTCCCGA 60.836 60.000 0.00 0.0 46.27 5.14 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
386 387 1.899814 AGTATGTGGCCTGAGAAACGA 59.100 47.619 3.32 0.00 0.00 3.85
399 400 3.772853 AAACGACAGCAGCTGGCCA 62.773 57.895 26.38 4.71 46.50 5.36
798 804 7.092979 TGCCAAATTATTCCCAAAGATTGATCA 60.093 33.333 0.00 0.00 0.00 2.92
802 808 8.843308 AATTATTCCCAAAGATTGATCAGGAA 57.157 30.769 11.47 11.47 0.00 3.36
962 970 1.761198 AGACGGGTAATGAGTAAGCCC 59.239 52.381 0.00 0.00 36.08 5.19
1010 1018 1.982958 AGTTCCCATCTTAACGGGTGT 59.017 47.619 0.00 0.00 43.57 4.16
1038 1046 1.604604 CCAACTTCCCGTGACATGTT 58.395 50.000 0.00 0.00 0.00 2.71
1095 1104 1.879380 TCCGGTTTTCTGATGCTGTTG 59.121 47.619 0.00 0.00 0.00 3.33
1756 1768 1.620323 GCAAGGCTTGGGACATCTTTT 59.380 47.619 27.25 0.00 39.30 2.27
1803 1815 1.581934 CAGACCAGTCAAACTTCGCA 58.418 50.000 0.00 0.00 0.00 5.10
1840 1852 0.535797 GACGGGTCTTCGGGATCTTT 59.464 55.000 0.00 0.00 0.00 2.52
1881 1893 2.844348 CCCTTTAGCCCTTAAGACAGGA 59.156 50.000 3.36 0.00 35.71 3.86
2014 2026 6.381133 TGAGTACACATGGTCAACTATGATCT 59.619 38.462 12.72 5.68 37.58 2.75
2589 2601 3.111853 GACACTGTGTCATGGAACTCA 57.888 47.619 30.43 0.00 46.22 3.41
3192 3204 1.065926 CCTCTGCTGGAACACTATGCA 60.066 52.381 0.00 0.00 0.00 3.96
3229 3241 0.322098 TGGGCGAACTGGTAATGTGG 60.322 55.000 0.00 0.00 0.00 4.17
3348 3360 0.902984 TCGGTAGAAGGGCTGCTGAA 60.903 55.000 0.00 0.00 40.98 3.02
3503 3515 0.532417 GGCTGTAGCTGGATGCAGAG 60.532 60.000 19.59 7.35 45.94 3.35
3594 3606 3.009033 CCCTCCAGGATTTGTACACTTCA 59.991 47.826 0.00 0.00 38.24 3.02
3831 3843 7.515514 ACCAAGAGAGATATTGACATTAGGGAT 59.484 37.037 0.00 0.00 0.00 3.85
3986 3999 6.454795 GGTTGCCATTCAGAAGATTTTGTTA 58.545 36.000 0.00 0.00 0.00 2.41
4028 4041 5.588648 GCAGAGAAGAGTATACTGACTGACT 59.411 44.000 10.90 5.82 0.00 3.41
4029 4042 6.764085 GCAGAGAAGAGTATACTGACTGACTA 59.236 42.308 10.90 0.00 0.00 2.59
4030 4043 7.254658 GCAGAGAAGAGTATACTGACTGACTAC 60.255 44.444 10.90 0.00 0.00 2.73
4031 4044 7.766738 CAGAGAAGAGTATACTGACTGACTACA 59.233 40.741 10.90 0.00 0.00 2.74
4054 4067 0.617935 TGTTGCTATGCTGTGGCCTA 59.382 50.000 3.32 0.00 37.74 3.93
4056 4069 0.617935 TTGCTATGCTGTGGCCTACA 59.382 50.000 3.32 6.05 37.74 2.74
4060 4073 0.899019 TATGCTGTGGCCTACAACGA 59.101 50.000 3.32 0.00 39.20 3.85
4101 4114 6.109156 TGAGATAGTCAACAGCCTGTTAAA 57.891 37.500 10.26 0.00 38.77 1.52
4131 4145 1.140852 CGCCTGGATTGGAATCTGGTA 59.859 52.381 0.00 0.00 35.73 3.25
4233 4247 5.070770 CCATTTTGCATGGTAGCTTAACA 57.929 39.130 0.00 0.00 34.56 2.41
4234 4248 5.477510 CCATTTTGCATGGTAGCTTAACAA 58.522 37.500 0.00 0.00 34.56 2.83
4235 4249 5.577945 CCATTTTGCATGGTAGCTTAACAAG 59.422 40.000 0.00 0.00 34.56 3.16
4285 4302 4.735338 GCAGCTGAAAGACTTAAACAACAC 59.265 41.667 20.43 0.00 34.07 3.32
4505 4522 2.094752 ACGCAAAGCTTTTGTGTGTTCT 60.095 40.909 19.89 3.23 41.07 3.01
4611 4966 4.943705 TGCTCTCTACCAAATGAAACCATC 59.056 41.667 0.00 0.00 0.00 3.51
4708 5309 4.617959 TGTCTAAATTAGGCTCGAATCCG 58.382 43.478 6.17 0.00 37.07 4.18
4782 5394 5.057149 GGTGGAACTCGAGCATATTGTAAT 58.943 41.667 13.61 0.00 36.74 1.89
5058 5671 2.441410 TGATGAGTTCGACTCTGCTCT 58.559 47.619 13.65 0.00 45.27 4.09
5132 5745 5.641209 GTCTGTTTCTCTCAGCAACATGTAT 59.359 40.000 0.00 0.00 33.48 2.29
5159 5772 8.893219 TTGTTTAAACAATGATGTGGCATTAA 57.107 26.923 26.05 2.32 43.45 1.40
5160 5773 8.893219 TGTTTAAACAATGATGTGGCATTAAA 57.107 26.923 18.54 0.00 40.46 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 2.015736 ACCATCTGTTCTGCGATCAC 57.984 50.000 0.00 0.00 0.00 3.06
386 387 2.816601 GATGACTGGCCAGCTGCTGT 62.817 60.000 33.06 13.27 40.92 4.40
399 400 1.986757 ACGCCCTCTGCAGATGACT 60.987 57.895 18.63 0.00 41.33 3.41
802 808 1.747444 TTTCTTTCCTCCCAGGCTCT 58.253 50.000 0.00 0.00 34.61 4.09
962 970 3.912496 TGTCATGGATAACAGGGACAG 57.088 47.619 0.00 0.00 40.35 3.51
1084 1093 3.281240 GGTGGGCAACAGCATCAG 58.719 61.111 0.00 0.00 46.64 2.90
1236 1248 2.543802 CGCGAGCTCCTGGATACGA 61.544 63.158 8.47 0.00 42.51 3.43
1803 1815 2.738846 CGTCACAGCTAAAAGCACAGAT 59.261 45.455 1.22 0.00 45.56 2.90
1840 1852 1.471119 CGTAGGCCCTCTAGAACACA 58.529 55.000 0.00 0.00 0.00 3.72
1881 1893 4.703575 CCAATGACCACATCACTCTCAAAT 59.296 41.667 0.00 0.00 41.24 2.32
2014 2026 2.432146 GACCACCATGAGATAGTGCAGA 59.568 50.000 0.00 0.00 0.00 4.26
2463 2475 2.584835 AGCTATTGAACTGGCAACCA 57.415 45.000 0.00 0.00 0.00 3.67
3192 3204 2.158564 CCCAAGTAGATCCACCATGCAT 60.159 50.000 0.00 0.00 0.00 3.96
3503 3515 7.225931 TGACAAATGAGTACACTTTGTTCCTAC 59.774 37.037 16.55 8.27 37.59 3.18
3594 3606 3.813443 CACATAGCCTGCAGTCCTTAAT 58.187 45.455 13.81 0.00 0.00 1.40
3831 3843 6.661377 TCCTAAAATGATGAAACCGATTTCCA 59.339 34.615 0.00 0.00 43.18 3.53
3915 3928 6.483640 CAGAATGTATCTACTTTGGGGCTTAC 59.516 42.308 0.00 0.00 36.32 2.34
3986 3999 6.759272 TCTCTGCTTTGTGTGTTATAACTCT 58.241 36.000 16.33 0.00 0.00 3.24
4028 4041 4.441792 CCACAGCATAGCAACATACTGTA 58.558 43.478 0.00 0.00 36.28 2.74
4029 4042 3.273434 CCACAGCATAGCAACATACTGT 58.727 45.455 0.00 0.00 38.84 3.55
4030 4043 2.032550 GCCACAGCATAGCAACATACTG 59.967 50.000 0.00 0.00 39.53 2.74
4031 4044 2.292267 GCCACAGCATAGCAACATACT 58.708 47.619 0.00 0.00 39.53 2.12
4032 4045 1.334869 GGCCACAGCATAGCAACATAC 59.665 52.381 0.00 0.00 42.56 2.39
4060 4073 4.769688 TCTCAATATTGCATCCACGAACT 58.230 39.130 10.76 0.00 0.00 3.01
4093 4106 2.007608 GCGCTTCTAGGGTTTAACAGG 58.992 52.381 0.00 0.00 0.00 4.00
4101 4114 0.983378 AATCCAGGCGCTTCTAGGGT 60.983 55.000 7.64 0.00 0.00 4.34
4228 4242 5.068591 GCTTCCCTTTGTTTCCTCTTGTTAA 59.931 40.000 0.00 0.00 0.00 2.01
4229 4243 4.583073 GCTTCCCTTTGTTTCCTCTTGTTA 59.417 41.667 0.00 0.00 0.00 2.41
4232 4246 3.005155 CAGCTTCCCTTTGTTTCCTCTTG 59.995 47.826 0.00 0.00 0.00 3.02
4233 4247 3.225940 CAGCTTCCCTTTGTTTCCTCTT 58.774 45.455 0.00 0.00 0.00 2.85
4234 4248 2.489802 CCAGCTTCCCTTTGTTTCCTCT 60.490 50.000 0.00 0.00 0.00 3.69
4235 4249 1.889170 CCAGCTTCCCTTTGTTTCCTC 59.111 52.381 0.00 0.00 0.00 3.71
4505 4522 0.836400 GCCATAGGATTCCCTCCCGA 60.836 60.000 0.00 0.00 46.27 5.14
4611 4966 2.033801 CAGAACACTTTTGACAGCCCTG 59.966 50.000 0.00 0.00 0.00 4.45
5058 5671 1.626356 CCAGGGCTGCCAACTAGCTA 61.626 60.000 22.05 0.00 40.92 3.32


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

AutoCloner maintained by Alex Coulton.