Multiple sequence alignment - TraesCS5A01G140700

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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 TraesCS5A01G140700 chr5A 100.000 4137 0 0 1 4137 312920041 312915905 0.000000e+00 7640
1 TraesCS5A01G140700 chr5A 86.755 302 27 9 3622 3919 669912879 669913171 1.430000e-84 324
2 TraesCS5A01G140700 chr5A 91.228 171 13 2 3905 4073 669922215 669922385 8.940000e-57 231
3 TraesCS5A01G140700 chr5D 95.371 4126 138 27 3 4099 240849760 240853861 0.000000e+00 6512
4 TraesCS5A01G140700 chr5B 95.489 4101 118 28 1 4078 262822971 262818915 0.000000e+00 6486


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 TraesCS5A01G140700 chr5A 312915905 312920041 4136 True 7640 7640 100.000 1 4137 1 chr5A.!!$R1 4136
1 TraesCS5A01G140700 chr5D 240849760 240853861 4101 False 6512 6512 95.371 3 4099 1 chr5D.!!$F1 4096
2 TraesCS5A01G140700 chr5B 262818915 262822971 4056 True 6486 6486 95.489 1 4078 1 chr5B.!!$R1 4077

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
162 172 0.885196 GGCTCGGCAATTAACCAACA 59.115 50.000 0.0 0.0 0.00 3.33 F
947 957 1.452108 CCGGCATTTCCTCCCACTC 60.452 63.158 0.0 0.0 0.00 3.51 F
1036 1048 1.579932 GACCTGCTGACGAAGACGA 59.420 57.895 0.0 0.0 42.66 4.20 F
1119 1131 2.039348 AGTACTCTCTCGATCCCTAGCC 59.961 54.545 0.0 0.0 0.00 3.93 F
1680 1694 2.239654 CTGCCCTACCTTTTCATCTGGA 59.760 50.000 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1036 1048 1.068352 AGCCCCTTCACCAGTTTCCT 61.068 55.000 0.00 0.0 0.00 3.36 R
1808 1825 1.074889 ACAATACGGCCAAGGAAACCT 59.925 47.619 2.24 0.0 33.87 3.50 R
2371 2389 1.209504 CCCTCCGTTCAGAAATAGGCA 59.790 52.381 2.37 0.0 0.00 4.75 R
3103 3122 0.180642 CTGATCCACCTGATGCTGCT 59.819 55.000 0.00 0.0 32.41 4.24 R
3655 3681 0.179004 ACGGAAGGAAACATGCCACA 60.179 50.000 0.00 0.0 0.00 4.17 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
29 30 7.020010 CAGCATGTTTAACATTCAGACTCTTC 58.980 38.462 7.97 0.00 36.53 2.87
33 34 9.390795 CATGTTTAACATTCAGACTCTTCTTTG 57.609 33.333 7.97 0.00 36.53 2.77
77 86 7.038729 ACTGATCTAGTTCCTGAAGAATTGTGA 60.039 37.037 0.00 0.00 35.67 3.58
91 100 7.121168 TGAAGAATTGTGAGGTAATCATTCACC 59.879 37.037 1.87 0.00 40.92 4.02
162 172 0.885196 GGCTCGGCAATTAACCAACA 59.115 50.000 0.00 0.00 0.00 3.33
387 397 3.231734 TGAAGCATCAGAACCCACG 57.768 52.632 0.00 0.00 0.00 4.94
493 503 3.381333 CTCCAGATGCTGCTGCGGA 62.381 63.158 13.72 9.99 43.34 5.54
791 801 6.069381 AGAGGGGCAGTGAAAGAATAAACTAT 60.069 38.462 0.00 0.00 0.00 2.12
793 803 7.639378 AGGGGCAGTGAAAGAATAAACTATAA 58.361 34.615 0.00 0.00 0.00 0.98
794 804 7.775561 AGGGGCAGTGAAAGAATAAACTATAAG 59.224 37.037 0.00 0.00 0.00 1.73
795 805 7.773690 GGGGCAGTGAAAGAATAAACTATAAGA 59.226 37.037 0.00 0.00 0.00 2.10
947 957 1.452108 CCGGCATTTCCTCCCACTC 60.452 63.158 0.00 0.00 0.00 3.51
952 962 2.291043 ATTTCCTCCCACTCGCGGT 61.291 57.895 6.13 0.00 0.00 5.68
957 967 4.680237 TCCCACTCGCGGTTGCAG 62.680 66.667 6.13 0.00 42.97 4.41
1036 1048 1.579932 GACCTGCTGACGAAGACGA 59.420 57.895 0.00 0.00 42.66 4.20
1119 1131 2.039348 AGTACTCTCTCGATCCCTAGCC 59.961 54.545 0.00 0.00 0.00 3.93
1280 1292 8.520351 AGTTGGTAAAACTAGATTTGGTATTGC 58.480 33.333 8.15 0.00 0.00 3.56
1423 1435 9.734620 TGCAGAATTATTGTAAATCAATGTAGC 57.265 29.630 3.73 0.00 45.14 3.58
1546 1558 3.059352 TCCTAGGCAAGCTTCAAACTC 57.941 47.619 2.96 0.00 0.00 3.01
1680 1694 2.239654 CTGCCCTACCTTTTCATCTGGA 59.760 50.000 0.00 0.00 0.00 3.86
1782 1799 4.608445 GCGTTATTTATCGATGTGCTCCAC 60.608 45.833 8.54 0.00 34.56 4.02
1783 1800 4.745125 CGTTATTTATCGATGTGCTCCACT 59.255 41.667 8.54 0.00 35.11 4.00
1808 1825 7.398829 TGCTCCATTTAATAGTTAGGTGAACA 58.601 34.615 0.00 0.00 40.86 3.18
2371 2389 3.058224 GCAATTTGAACTAAGACCACGCT 60.058 43.478 0.00 0.00 0.00 5.07
2372 2390 4.466828 CAATTTGAACTAAGACCACGCTG 58.533 43.478 0.00 0.00 0.00 5.18
3103 3122 6.705302 ACAGATGTTTCTTCAAGATAGAGCA 58.295 36.000 0.00 0.00 0.00 4.26
3117 3136 2.045242 AGCAGCAGCATCAGGTGG 60.045 61.111 3.17 0.00 45.49 4.61
3356 3382 5.012239 TCCTCAAACTTTTCATCTCCCATG 58.988 41.667 0.00 0.00 0.00 3.66
3391 3417 7.885399 ACCTTAATGCTGTATGAAAGTTTCTCT 59.115 33.333 16.33 6.80 0.00 3.10
3394 3420 7.750229 AATGCTGTATGAAAGTTTCTCTGAA 57.250 32.000 16.33 6.61 0.00 3.02
3454 3480 5.030147 ACATGTAGTTTCCATCTGTCCCTA 58.970 41.667 0.00 0.00 0.00 3.53
3511 3537 0.537653 GGTGCTCCCTCTTCAGTACC 59.462 60.000 0.00 0.00 38.10 3.34
3544 3570 2.431997 TGAAGGGGCCAATAGATCCAT 58.568 47.619 4.39 0.00 0.00 3.41
3619 3645 2.428171 TGTTGCTTGCTCTTTCTTTGCT 59.572 40.909 0.00 0.00 0.00 3.91
3772 3798 9.301153 ACATTGTTTCTTTGTCACAACTTATTC 57.699 29.630 0.00 0.00 33.33 1.75
3774 3800 6.801575 TGTTTCTTTGTCACAACTTATTCCC 58.198 36.000 0.00 0.00 0.00 3.97
3785 3811 9.232473 GTCACAACTTATTCCCTTATTTTCTCT 57.768 33.333 0.00 0.00 0.00 3.10
3786 3812 9.231297 TCACAACTTATTCCCTTATTTTCTCTG 57.769 33.333 0.00 0.00 0.00 3.35
3787 3813 9.014297 CACAACTTATTCCCTTATTTTCTCTGT 57.986 33.333 0.00 0.00 0.00 3.41
3848 3884 3.802866 TGCTGGGTTTCCAAACAATTTC 58.197 40.909 4.63 0.00 43.51 2.17
3925 3962 7.201911 CCACTTTTCTCTCCTTATTTGTGGTTT 60.202 37.037 0.00 0.00 37.17 3.27
3931 3968 6.934645 TCTCTCCTTATTTGTGGTTTGTGTAG 59.065 38.462 0.00 0.00 0.00 2.74
4084 4121 4.343239 TCTGAGTGACATGATGGATACTGG 59.657 45.833 0.00 0.00 37.61 4.00
4092 4129 5.909477 ACATGATGGATACTGGCATTTTTG 58.091 37.500 0.00 0.00 37.61 2.44
4093 4130 4.389890 TGATGGATACTGGCATTTTTGC 57.610 40.909 0.00 0.00 37.61 3.68
4099 4136 5.244851 TGGATACTGGCATTTTTGCTTGTTA 59.755 36.000 0.00 0.00 37.61 2.41
4100 4137 5.576774 GGATACTGGCATTTTTGCTTGTTAC 59.423 40.000 0.00 0.00 34.73 2.50
4101 4138 3.727726 ACTGGCATTTTTGCTTGTTACC 58.272 40.909 0.00 0.00 34.73 2.85
4102 4139 3.066380 CTGGCATTTTTGCTTGTTACCC 58.934 45.455 0.00 0.00 34.73 3.69
4103 4140 2.065512 GGCATTTTTGCTTGTTACCCG 58.934 47.619 0.00 0.00 34.73 5.28
4104 4141 2.547007 GGCATTTTTGCTTGTTACCCGT 60.547 45.455 0.00 0.00 34.73 5.28
4105 4142 3.127589 GCATTTTTGCTTGTTACCCGTT 58.872 40.909 0.00 0.00 0.00 4.44
4106 4143 3.558006 GCATTTTTGCTTGTTACCCGTTT 59.442 39.130 0.00 0.00 0.00 3.60
4107 4144 4.034626 GCATTTTTGCTTGTTACCCGTTTT 59.965 37.500 0.00 0.00 0.00 2.43
4108 4145 5.447954 GCATTTTTGCTTGTTACCCGTTTTT 60.448 36.000 0.00 0.00 0.00 1.94
4136 4173 9.930693 TTAAACTGATTTTTGTTTGTTACCAGT 57.069 25.926 0.00 0.00 37.06 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.022550 TCAGTCAATGTAATATTGCACACAAAG 58.977 33.333 8.50 0.00 39.77 2.77
33 34 7.923888 AGATCAGTCAATGTAATATTGCACAC 58.076 34.615 8.50 6.25 0.00 3.82
77 86 6.543831 GCTTCTTGTATGGTGAATGATTACCT 59.456 38.462 0.00 0.00 37.84 3.08
91 100 5.471456 AGTTCTGTTTGGAGCTTCTTGTATG 59.529 40.000 0.00 0.00 0.00 2.39
162 172 1.884928 GCATGGGTTCGGTAGTGGTTT 60.885 52.381 0.00 0.00 0.00 3.27
334 344 0.397675 TGGGTGTGTTGAAATGGCCA 60.398 50.000 8.56 8.56 0.00 5.36
493 503 4.711949 CCTGCTGCAACTCCGCCT 62.712 66.667 3.02 0.00 0.00 5.52
656 666 4.444081 CTCCTCCTCGTCCCCCGT 62.444 72.222 0.00 0.00 37.94 5.28
691 701 0.883814 CTCATCCTCTTCCATGGCGC 60.884 60.000 6.96 0.00 0.00 6.53
791 801 1.340991 GCCCAAATGAGCCCAGTCTTA 60.341 52.381 0.00 0.00 0.00 2.10
793 803 1.000396 GCCCAAATGAGCCCAGTCT 60.000 57.895 0.00 0.00 0.00 3.24
794 804 2.054453 GGCCCAAATGAGCCCAGTC 61.054 63.158 0.00 0.00 43.76 3.51
795 805 2.037847 GGCCCAAATGAGCCCAGT 59.962 61.111 0.00 0.00 43.76 4.00
987 999 0.109086 ACGACATCTCGCCTTCACAG 60.109 55.000 0.00 0.00 44.33 3.66
992 1004 1.802880 GCATGTACGACATCTCGCCTT 60.803 52.381 0.00 0.00 44.33 4.35
1036 1048 1.068352 AGCCCCTTCACCAGTTTCCT 61.068 55.000 0.00 0.00 0.00 3.36
1119 1131 4.148825 CGGAAGTGGAGAGGCGGG 62.149 72.222 0.00 0.00 0.00 6.13
1280 1292 1.339055 ACCGACAGATGATGTTGTGGG 60.339 52.381 4.44 4.44 44.17 4.61
1423 1435 2.939103 CAGTTCGCTCTAGAAAATGGGG 59.061 50.000 0.00 0.00 0.00 4.96
1546 1558 6.511416 TGACAGATTTAACATTTTGGTGTGG 58.489 36.000 0.00 0.00 31.49 4.17
1575 1589 6.949352 ATTTGGATCGAGCATAACTGAAAT 57.051 33.333 1.84 0.00 0.00 2.17
1782 1799 7.552687 TGTTCACCTAACTATTAAATGGAGCAG 59.447 37.037 0.00 0.00 38.99 4.24
1783 1800 7.398829 TGTTCACCTAACTATTAAATGGAGCA 58.601 34.615 0.00 0.00 38.99 4.26
1808 1825 1.074889 ACAATACGGCCAAGGAAACCT 59.925 47.619 2.24 0.00 33.87 3.50
2245 2262 5.066117 CACATTCACATCCTCAATTCTGGAG 59.934 44.000 2.85 0.00 35.63 3.86
2343 2361 5.048083 TGGTCTTAGTTCAAATTGCATGGTC 60.048 40.000 0.00 0.00 0.00 4.02
2371 2389 1.209504 CCCTCCGTTCAGAAATAGGCA 59.790 52.381 2.37 0.00 0.00 4.75
2372 2390 1.485066 TCCCTCCGTTCAGAAATAGGC 59.515 52.381 2.37 0.00 0.00 3.93
2850 2869 4.321899 GCCAAAGGATGTTAGTCATGCAAA 60.322 41.667 0.00 0.00 45.37 3.68
3103 3122 0.180642 CTGATCCACCTGATGCTGCT 59.819 55.000 0.00 0.00 32.41 4.24
3117 3136 4.499183 CAGTTACTGTCCTTCACCTGATC 58.501 47.826 3.88 0.00 0.00 2.92
3266 3285 5.278758 CCAAACATGTTTCGAACCCTTACAT 60.279 40.000 20.85 1.50 0.00 2.29
3356 3382 7.822658 TCATACAGCATTAAGGTTAAACCAAC 58.177 34.615 0.00 0.00 41.95 3.77
3391 3417 4.587584 TCAATCAAGCTGCACAATTTCA 57.412 36.364 1.02 0.00 0.00 2.69
3394 3420 6.927416 TCTATTTCAATCAAGCTGCACAATT 58.073 32.000 1.02 0.00 0.00 2.32
3454 3480 6.201806 GCTCAGATTACTAAAATGCTCGTCAT 59.798 38.462 0.00 0.00 36.87 3.06
3511 3537 0.607489 CCCTTCAACCTCACAGCAGG 60.607 60.000 0.00 0.00 39.80 4.85
3544 3570 4.817318 TGCCATATCTCAACAGTGTACA 57.183 40.909 0.00 0.00 0.00 2.90
3619 3645 6.362248 AGGAAAACAGTAAAGAGGTGCTAAA 58.638 36.000 0.00 0.00 0.00 1.85
3654 3680 0.958091 CGGAAGGAAACATGCCACAA 59.042 50.000 0.00 0.00 0.00 3.33
3655 3681 0.179004 ACGGAAGGAAACATGCCACA 60.179 50.000 0.00 0.00 0.00 4.17
3656 3682 0.958822 AACGGAAGGAAACATGCCAC 59.041 50.000 0.00 0.00 0.00 5.01
3662 3688 2.294074 CAACTCCAACGGAAGGAAACA 58.706 47.619 0.00 0.00 34.08 2.83
3751 3777 7.039313 AGGGAATAAGTTGTGACAAAGAAAC 57.961 36.000 0.00 0.00 0.00 2.78
3772 3798 9.014297 ACTCAATAACAACAGAGAAAATAAGGG 57.986 33.333 0.00 0.00 32.59 3.95
3807 3836 7.397221 CCAGCATTAAGGATATAGGAACATGA 58.603 38.462 0.00 0.00 0.00 3.07
3893 3929 9.018582 CAAATAAGGAGAGAAAAGTGGAGAAAT 57.981 33.333 0.00 0.00 0.00 2.17
3925 3962 3.007940 CAGGGACAGATGGAAACTACACA 59.992 47.826 0.00 0.00 0.00 3.72
3931 3968 2.859165 TCACAGGGACAGATGGAAAC 57.141 50.000 0.00 0.00 0.00 2.78
3982 4019 1.527433 GGCTGAAAGGGAGCACCAAC 61.527 60.000 1.58 0.00 43.89 3.77
4032 4069 1.775039 CTCAACAGTGCACGTGTGGG 61.775 60.000 18.38 11.26 0.00 4.61
4084 4121 2.749776 ACGGGTAACAAGCAAAAATGC 58.250 42.857 0.00 0.00 39.74 3.56


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

AutoCloner maintained by Alex Coulton.