Multiple sequence alignment - TraesCS7A01G228800

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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 TraesCS7A01G228800 chr7A 100.000 4964 0 0 1 4964 199149590 199144627 0.000000e+00 9167
1 TraesCS7A01G228800 chr7A 96.376 4967 168 11 3 4964 405966512 405971471 0.000000e+00 8165
2 TraesCS7A01G228800 chr6B 97.220 4964 111 9 3 4964 641688889 641693827 0.000000e+00 8377
3 TraesCS7A01G228800 chr6B 97.995 4739 83 5 3 4738 655034552 655039281 0.000000e+00 8215
4 TraesCS7A01G228800 chr2A 98.312 4739 76 4 3 4738 509596833 509592096 0.000000e+00 8305
5 TraesCS7A01G228800 chr2A 90.994 322 24 5 4646 4964 629396826 629396507 3.550000e-116 429
6 TraesCS7A01G228800 chr1B 98.270 4739 79 3 3 4738 259400791 259405529 0.000000e+00 8294
7 TraesCS7A01G228800 chr1B 98.228 4740 76 6 3 4738 245469158 245464423 0.000000e+00 8281
8 TraesCS7A01G228800 chr1B 98.017 4740 87 7 3 4738 630412147 630416883 0.000000e+00 8226
9 TraesCS7A01G228800 chr1B 97.807 228 5 0 4737 4964 245464342 245464115 1.300000e-105 394
10 TraesCS7A01G228800 chr5B 98.079 4738 86 5 5 4738 349334447 349329711 0.000000e+00 8240
11 TraesCS7A01G228800 chr5A 98.038 4739 90 3 3 4738 99056359 99051621 0.000000e+00 8233
12 TraesCS7A01G228800 chr4B 96.058 4972 176 12 3 4964 604572820 604567859 0.000000e+00 8078
13 TraesCS7A01G228800 chr4B 95.455 1254 35 7 3712 4964 77631853 77633085 0.000000e+00 1980
14 TraesCS7A01G228800 chr3A 92.811 1697 91 16 3275 4964 471751750 471750078 0.000000e+00 2429
15 TraesCS7A01G228800 chr6A 97.807 228 5 0 4737 4964 188490273 188490500 1.300000e-105 394
16 TraesCS7A01G228800 chr4A 97.807 228 5 0 4737 4964 673308674 673308901 1.300000e-105 394


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 TraesCS7A01G228800 chr7A 199144627 199149590 4963 True 9167.0 9167 100.0000 1 4964 1 chr7A.!!$R1 4963
1 TraesCS7A01G228800 chr7A 405966512 405971471 4959 False 8165.0 8165 96.3760 3 4964 1 chr7A.!!$F1 4961
2 TraesCS7A01G228800 chr6B 641688889 641693827 4938 False 8377.0 8377 97.2200 3 4964 1 chr6B.!!$F1 4961
3 TraesCS7A01G228800 chr6B 655034552 655039281 4729 False 8215.0 8215 97.9950 3 4738 1 chr6B.!!$F2 4735
4 TraesCS7A01G228800 chr2A 509592096 509596833 4737 True 8305.0 8305 98.3120 3 4738 1 chr2A.!!$R1 4735
5 TraesCS7A01G228800 chr1B 259400791 259405529 4738 False 8294.0 8294 98.2700 3 4738 1 chr1B.!!$F1 4735
6 TraesCS7A01G228800 chr1B 630412147 630416883 4736 False 8226.0 8226 98.0170 3 4738 1 chr1B.!!$F2 4735
7 TraesCS7A01G228800 chr1B 245464115 245469158 5043 True 4337.5 8281 98.0175 3 4964 2 chr1B.!!$R1 4961
8 TraesCS7A01G228800 chr5B 349329711 349334447 4736 True 8240.0 8240 98.0790 5 4738 1 chr5B.!!$R1 4733
9 TraesCS7A01G228800 chr5A 99051621 99056359 4738 True 8233.0 8233 98.0380 3 4738 1 chr5A.!!$R1 4735
10 TraesCS7A01G228800 chr4B 604567859 604572820 4961 True 8078.0 8078 96.0580 3 4964 1 chr4B.!!$R1 4961
11 TraesCS7A01G228800 chr4B 77631853 77633085 1232 False 1980.0 1980 95.4550 3712 4964 1 chr4B.!!$F1 1252
12 TraesCS7A01G228800 chr3A 471750078 471751750 1672 True 2429.0 2429 92.8110 3275 4964 1 chr3A.!!$R1 1689

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
569 579 0.321919 GCATCTGTGGACTCTTGCCA 60.322 55.000 0.00 0.0 0.00 4.92 F
1792 1802 0.250234 CCAGCTCCCTGATGACGAAA 59.750 55.000 0.00 0.0 41.77 3.46 F
2279 2294 1.604185 CCTTTGCCAAAATTTCGCCGA 60.604 47.619 7.52 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 1893 3.612472 TTAAAATATTACCGCTGGCGC 57.388 42.857 9.63 0.0 38.24 6.53 R
3774 3794 0.034756 CGTCAGTTCATCCACCACCA 59.965 55.000 0.00 0.0 0.00 4.17 R
4166 4188 0.324943 CCACAGGATCAAAGTCGGGT 59.675 55.000 0.00 0.0 0.00 5.28 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
569 579 0.321919 GCATCTGTGGACTCTTGCCA 60.322 55.000 0.00 0.0 0.00 4.92
621 631 1.587547 CTATTTCTCCTCCAAGCGCC 58.412 55.000 2.29 0.0 0.00 6.53
796 806 1.004628 TGCTTCTGATGCTTAGGCCAA 59.995 47.619 5.01 0.0 37.74 4.52
809 819 1.699730 AGGCCAAGCGGTTTAACTTT 58.300 45.000 5.01 0.0 33.28 2.66
961 971 3.829601 TCAACACCTTTTTATCCGGCATT 59.170 39.130 0.00 0.0 0.00 3.56
1585 1595 2.558359 CACCCTTTTCCACAAAGGCTAG 59.442 50.000 7.72 0.0 44.17 3.42
1588 1598 2.238521 CTTTTCCACAAAGGCTAGGCA 58.761 47.619 19.70 0.0 37.29 4.75
1792 1802 0.250234 CCAGCTCCCTGATGACGAAA 59.750 55.000 0.00 0.0 41.77 3.46
1879 1893 2.034558 CCTTACTGCACCACCAACAAAG 59.965 50.000 0.00 0.0 0.00 2.77
2279 2294 1.604185 CCTTTGCCAAAATTTCGCCGA 60.604 47.619 7.52 0.0 0.00 5.54
3239 3254 3.989787 CCAAGGGCCGGTTTGTGC 61.990 66.667 1.90 0.0 0.00 4.57
3264 3279 2.711009 TGGTCAAACCAGGACTTGATCT 59.289 45.455 15.90 0.0 44.79 2.75
3489 3507 4.289672 CCCCCAAGTATCAGGCATATAACT 59.710 45.833 0.00 0.0 0.00 2.24
3545 3565 5.933187 TCGTCTGTGCAAAGCTTAAAATA 57.067 34.783 0.00 0.0 0.00 1.40
3609 3629 3.204827 CGATTTGCAGGAGGCCCG 61.205 66.667 0.00 0.0 43.89 6.13
3774 3794 0.960861 GCTGAAGCGGCCCTTAAACT 60.961 55.000 0.00 0.0 32.78 2.66
4056 4078 1.146263 CCGGCGCCCTCTTTAATCT 59.854 57.895 23.46 0.0 0.00 2.40
4107 4129 2.507944 CCCGGATTGAGGAGCTGG 59.492 66.667 0.73 0.0 40.03 4.85
4140 4162 2.780595 CGAACCGGAGCCATCAATT 58.219 52.632 9.46 0.0 0.00 2.32
4166 4188 2.044451 CGGGCAAAGGCATGGGTA 60.044 61.111 0.00 0.0 43.71 3.69
4189 4211 2.289694 CCGACTTTGATCCTGTGGAAGT 60.290 50.000 0.00 0.0 34.34 3.01
4512 4534 0.911769 CCAGCCAATGGGTAGAGACA 59.088 55.000 2.68 0.0 46.36 3.41
4587 4609 3.696051 TGAAGAGCTATTTGCAACATCCC 59.304 43.478 0.00 0.0 45.94 3.85
4762 4869 4.365723 CATGTTTGATCATAAAGCTGGCC 58.634 43.478 0.00 0.0 0.00 5.36
4836 4944 2.361483 TAGCGCCCGTACAGACCA 60.361 61.111 2.29 0.0 0.00 4.02
4894 5003 7.519032 TGATGTTAACAGGGAAAAGGTAAAG 57.481 36.000 14.65 0.0 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 4.619760 GCCGGTTTACAGCAACTAAAAATC 59.380 41.667 1.90 0.00 0.00 2.17
621 631 2.098280 CGGATATGTGCGGGAGATCTAG 59.902 54.545 0.00 0.00 35.34 2.43
796 806 6.290294 TCTCTATGGTAAAGTTAAACCGCT 57.710 37.500 3.56 0.00 38.70 5.52
961 971 4.837093 ATAAGTGATCCGGTTCAAGGAA 57.163 40.909 16.70 4.03 41.69 3.36
1585 1595 5.007724 CGTATTTAATTCTCTCCTTGGTGCC 59.992 44.000 0.00 0.00 0.00 5.01
1588 1598 5.990668 AGCGTATTTAATTCTCTCCTTGGT 58.009 37.500 0.00 0.00 0.00 3.67
1879 1893 3.612472 TTAAAATATTACCGCTGGCGC 57.388 42.857 9.63 0.00 38.24 6.53
2279 2294 6.578944 AGAAAATTTAACTTTCCGGTTTGCT 58.421 32.000 0.00 0.00 34.00 3.91
2667 2682 2.876892 GCTTGGTTTCGGTTTAGCCCTA 60.877 50.000 0.00 0.00 0.00 3.53
2970 2985 1.004745 GCAGGATTCCCAGGTTCAGAA 59.995 52.381 0.00 0.00 33.88 3.02
3134 3149 1.999648 TTTGACCAAGCCAGCTTCAT 58.000 45.000 0.90 0.00 33.42 2.57
3253 3268 7.587037 TCAAAAATGTTCAAGATCAAGTCCT 57.413 32.000 0.00 0.00 0.00 3.85
3264 3279 5.051374 GCCGACGAATTTCAAAAATGTTCAA 60.051 36.000 0.00 0.00 0.00 2.69
3281 3296 1.721664 CTCGAGGGTTATGCCGACGA 61.722 60.000 3.91 0.00 40.80 4.20
3489 3507 7.825331 TGGAAGTATCAACCACATAACAAAA 57.175 32.000 0.00 0.00 0.00 2.44
3609 3629 0.250901 TTCAGCCTGCTGGGTCTTTC 60.251 55.000 18.38 0.00 43.07 2.62
3774 3794 0.034756 CGTCAGTTCATCCACCACCA 59.965 55.000 0.00 0.00 0.00 4.17
4056 4078 3.165875 ACAGCTTGCTAAGAGTGTCCTA 58.834 45.455 0.00 0.00 0.00 2.94
4107 4129 0.456142 GTTCGGGCAGCGGATTTTTC 60.456 55.000 0.00 0.00 0.00 2.29
4140 4162 0.395173 GCCTTTGCCCGGATTAAGGA 60.395 55.000 24.06 0.00 39.60 3.36
4166 4188 0.324943 CCACAGGATCAAAGTCGGGT 59.675 55.000 0.00 0.00 0.00 5.28
4351 4373 0.679640 CGCTTCAATAGTTGGGGCCA 60.680 55.000 4.39 0.00 0.00 5.36
4512 4534 1.673665 CTGCCGCTTCAGCTTCCTT 60.674 57.895 0.00 0.00 39.32 3.36
4529 4551 0.326427 AAGCCTGCTCCTCATCCTCT 60.326 55.000 0.00 0.00 0.00 3.69
4616 4639 1.765904 TCCTATTACAAGGCGGCATGA 59.234 47.619 21.63 0.00 36.51 3.07
4649 4673 3.470709 CACGAAGGCATATTCCAGACAT 58.529 45.455 0.00 0.00 0.00 3.06
4681 4705 8.722480 ATTAAAGTTTTTCAAGCAAAAGCTCT 57.278 26.923 0.00 0.00 42.83 4.09
4762 4869 1.372087 CCGCTTCAGGCTTGGCTAAG 61.372 60.000 5.28 5.28 39.13 2.18
4836 4944 3.577415 GGGGGCTCGTATTAAGTCAGTAT 59.423 47.826 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.