Multiple sequence alignment - TraesCS1B01G329900

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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 TraesCS1B01G329900 chr1B 100.000 3112 0 0 1 3112 555910909 555907798 0 5747
1 TraesCS1B01G329900 chr5D 95.080 3130 129 15 1 3112 378825357 378822235 0 4903
2 TraesCS1B01G329900 chr3B 94.187 3131 160 17 1 3112 402661749 402664876 0 4754
3 TraesCS1B01G329900 chr3B 93.558 3120 188 13 1 3112 246995882 246992768 0 4636
4 TraesCS1B01G329900 chr3B 93.528 3121 183 13 6 3112 355967255 355964140 0 4626
5 TraesCS1B01G329900 chr5B 93.950 3124 170 15 3 3112 453089981 453086863 0 4704
6 TraesCS1B01G329900 chr4B 93.694 3124 183 9 1 3112 379338795 379335674 0 4665
7 TraesCS1B01G329900 chr2B 93.704 3129 169 19 1 3112 352032945 352036062 0 4662
8 TraesCS1B01G329900 chr2B 93.436 3123 191 12 1 3112 315008234 315011353 0 4619
9 TraesCS1B01G329900 chr6B 93.532 3123 180 12 1 3112 628277131 628274020 0 4628


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 TraesCS1B01G329900 chr1B 555907798 555910909 3111 True 5747 5747 100.000 1 3112 1 chr1B.!!$R1 3111
1 TraesCS1B01G329900 chr5D 378822235 378825357 3122 True 4903 4903 95.080 1 3112 1 chr5D.!!$R1 3111
2 TraesCS1B01G329900 chr3B 402661749 402664876 3127 False 4754 4754 94.187 1 3112 1 chr3B.!!$F1 3111
3 TraesCS1B01G329900 chr3B 246992768 246995882 3114 True 4636 4636 93.558 1 3112 1 chr3B.!!$R1 3111
4 TraesCS1B01G329900 chr3B 355964140 355967255 3115 True 4626 4626 93.528 6 3112 1 chr3B.!!$R2 3106
5 TraesCS1B01G329900 chr5B 453086863 453089981 3118 True 4704 4704 93.950 3 3112 1 chr5B.!!$R1 3109
6 TraesCS1B01G329900 chr4B 379335674 379338795 3121 True 4665 4665 93.694 1 3112 1 chr4B.!!$R1 3111
7 TraesCS1B01G329900 chr2B 352032945 352036062 3117 False 4662 4662 93.704 1 3112 1 chr2B.!!$F2 3111
8 TraesCS1B01G329900 chr2B 315008234 315011353 3119 False 4619 4619 93.436 1 3112 1 chr2B.!!$F1 3111
9 TraesCS1B01G329900 chr6B 628274020 628277131 3111 True 4628 4628 93.532 1 3112 1 chr6B.!!$R1 3111

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
93 99 0.173708 GTCTACTTCTGCCAGTCCCG 59.826 60.0 0.0 0.0 0.0 5.14 F
859 870 0.250467 GGACAAGAGCAGCAACCTCA 60.250 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1035 1.138036 CAACGCCGACGATCCTACA 59.862 57.895 0.0 0.0 43.93 2.74 R
2174 2187 0.876342 CCTCCCGCTCTTTCGCATAC 60.876 60.000 0.0 0.0 0.00 2.39 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
49 54 0.945813 CACCCGTGAACGCCTAAAAA 59.054 50.000 0.00 0.00 38.18 1.94
93 99 0.173708 GTCTACTTCTGCCAGTCCCG 59.826 60.000 0.00 0.00 0.00 5.14
164 170 9.587772 AATGCGAATATAATACATCCTGTACTC 57.412 33.333 0.00 0.00 35.42 2.59
310 318 8.730680 GGTACATTCAATTACACTTCAATCACT 58.269 33.333 0.00 0.00 0.00 3.41
353 361 3.390639 GGAGTTCAGACCTCCATCATCAT 59.609 47.826 9.16 0.00 37.24 2.45
398 406 5.233988 GGATAAGCAGCTGATAAGTACAGG 58.766 45.833 20.43 0.00 36.09 4.00
419 427 4.165950 AGGTTGACTATATGAATGGGTGCA 59.834 41.667 0.00 0.00 0.00 4.57
445 453 2.234896 AAATGCCATCATCACCACCA 57.765 45.000 0.00 0.00 31.27 4.17
472 480 1.745087 CGTGCAAGTGGGATTTAGCAT 59.255 47.619 0.00 0.00 34.24 3.79
477 485 3.428045 GCAAGTGGGATTTAGCATGTCAC 60.428 47.826 0.00 0.00 0.00 3.67
509 517 4.400529 TGACAAGACTAGTCAGTGCAAA 57.599 40.909 24.44 8.51 40.80 3.68
619 627 3.632080 CCCCACGCCACTACACCA 61.632 66.667 0.00 0.00 0.00 4.17
635 643 2.740826 CAACTACACCCACGCCCG 60.741 66.667 0.00 0.00 0.00 6.13
859 870 0.250467 GGACAAGAGCAGCAACCTCA 60.250 55.000 0.00 0.00 0.00 3.86
861 872 2.355108 GGACAAGAGCAGCAACCTCATA 60.355 50.000 0.00 0.00 0.00 2.15
885 896 4.367023 CACGTCCCCGGCGAGAAA 62.367 66.667 9.30 0.00 38.78 2.52
903 914 3.654178 ACGCGAGTACACAACAACT 57.346 47.368 15.93 0.00 46.88 3.16
908 919 3.120792 GCGAGTACACAACAACTCTCAA 58.879 45.455 0.00 0.00 40.00 3.02
945 956 0.737715 GCAACGAGACGCTGGAGATT 60.738 55.000 0.00 0.00 0.00 2.40
999 1010 2.952978 GGTGATCTCGAGGCTCTAGAAA 59.047 50.000 20.90 10.88 0.00 2.52
1001 1012 4.038642 GGTGATCTCGAGGCTCTAGAAAAT 59.961 45.833 20.90 6.59 0.00 1.82
1238 1249 6.222038 TCATCAGACTTGTATCCCAACTAC 57.778 41.667 0.00 0.00 0.00 2.73
1298 1309 9.539825 CTACTGCATTTTCTCAAGTAGATACAT 57.460 33.333 2.68 0.00 33.05 2.29
1302 1313 9.665719 TGCATTTTCTCAAGTAGATACATTGTA 57.334 29.630 0.00 0.00 33.05 2.41
1403 1415 7.952671 ACTAGTGTAGTTTCTGAAGTTGATCA 58.047 34.615 0.00 0.00 34.86 2.92
1848 1861 1.703438 GCTGCAGCATGAGAAGTCGG 61.703 60.000 33.36 0.00 39.69 4.79
1905 1918 1.968493 AGAAGCTGAAGTTGTCCGGTA 59.032 47.619 0.00 0.00 0.00 4.02
1988 2001 5.163683 CGGAAAAGAGTACGACTCCTTGATA 60.164 44.000 10.24 0.00 46.18 2.15
2002 2015 2.357009 CCTTGATAGATGTTGCAGCCAC 59.643 50.000 0.00 0.00 0.00 5.01
2048 2061 4.456911 GGCATGAAGAAGAAGATCAACACA 59.543 41.667 0.00 0.00 0.00 3.72
2109 2122 1.476891 ACAACCTCATCGAGTACGCAT 59.523 47.619 0.00 0.00 39.58 4.73
2145 2158 1.724623 CCACGTACAAGTCATGGTTCG 59.275 52.381 0.00 0.00 0.00 3.95
2174 2187 5.506483 CGACTACATCACAGATGGTTAGGAG 60.506 48.000 11.29 2.31 0.00 3.69
2222 2236 2.283388 TACGACCGCCCCTTCTGT 60.283 61.111 0.00 0.00 0.00 3.41
2304 2318 8.729805 TTGCCTTTTATCTTGTTGTTTCAAAT 57.270 26.923 0.00 0.00 0.00 2.32
2305 2319 8.729805 TGCCTTTTATCTTGTTGTTTCAAATT 57.270 26.923 0.00 0.00 0.00 1.82
2306 2320 9.823647 TGCCTTTTATCTTGTTGTTTCAAATTA 57.176 25.926 0.00 0.00 0.00 1.40
2480 2499 8.691661 TTCAAAAGTAGCTTCTAAATGGAACT 57.308 30.769 0.00 0.00 0.00 3.01
2587 2606 9.825972 ATAGAAAACATAACGTTGAGAACAATG 57.174 29.630 11.99 7.23 45.35 2.82
2786 2807 7.094075 ACAGTAATAGTACACTTGATCGGACAA 60.094 37.037 2.81 0.00 32.12 3.18
2795 2816 6.273825 ACACTTGATCGGACAATACATACTC 58.726 40.000 0.00 0.00 0.00 2.59
2813 2834 7.739295 ACATACTCACTACAATAAAAAGCACG 58.261 34.615 0.00 0.00 0.00 5.34
2825 2846 4.510038 AAAAAGCACGAAGAAGCATCAT 57.490 36.364 0.00 0.00 34.91 2.45
2855 2876 4.219507 AGCGCTACTATGAATGCACTATCT 59.780 41.667 8.99 0.00 0.00 1.98
2873 2894 7.415765 GCACTATCTGTACAACTCAGTCTACAT 60.416 40.741 0.00 0.00 34.86 2.29
2909 2932 4.687901 TCTGAAATGACACCAGAAGACA 57.312 40.909 0.00 0.00 34.38 3.41
2950 2975 5.861222 AACAAACACAAAAAGAAGGCAAG 57.139 34.783 0.00 0.00 0.00 4.01
3026 3051 7.228706 ACAAAAAGTATCAGTCCAAGTTACTGG 59.771 37.037 6.05 0.00 43.69 4.00
3089 3141 0.038744 ATTGACTGCCCAAGGTCAGG 59.961 55.000 1.92 0.00 42.31 3.86
3096 3148 4.335647 CCAAGGTCAGGCGCAGGT 62.336 66.667 10.83 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 99 5.344743 TGTACTGATGGTCCTTCTGAATC 57.655 43.478 15.86 0.00 0.00 2.52
130 136 8.746922 ATGTATTATATTCGCATTTTGCTTGG 57.253 30.769 0.00 0.00 42.25 3.61
258 266 4.207891 ACCAGTGAGAATATGTGTGGTC 57.792 45.455 0.00 0.00 30.94 4.02
269 277 6.774673 TGAATGTACCAAATACCAGTGAGAA 58.225 36.000 0.00 0.00 32.16 2.87
310 318 4.290459 TCCTCTACTGTGGTACTTGGACTA 59.710 45.833 0.00 0.00 0.00 2.59
353 361 2.693250 CTTGCACGTGTCAGGGTCGA 62.693 60.000 18.38 0.00 0.00 4.20
398 406 5.356751 TGTTGCACCCATTCATATAGTCAAC 59.643 40.000 0.00 0.00 0.00 3.18
413 421 1.342819 TGGCATTTTACTGTTGCACCC 59.657 47.619 4.76 0.00 38.12 4.61
414 422 2.810439 TGGCATTTTACTGTTGCACC 57.190 45.000 4.76 0.00 38.12 5.01
419 427 4.771577 TGGTGATGATGGCATTTTACTGTT 59.228 37.500 0.00 0.00 34.11 3.16
445 453 1.069765 CCCACTTGCACGTCTCTGT 59.930 57.895 0.00 0.00 0.00 3.41
509 517 7.147863 ACCGTCCAAGTTAAATGGTTTTTACTT 60.148 33.333 8.08 0.00 42.41 2.24
560 568 3.953775 AACCGCTCAGTGGGTGGG 61.954 66.667 26.23 13.60 37.55 4.61
619 627 4.692475 GCGGGCGTGGGTGTAGTT 62.692 66.667 0.00 0.00 0.00 2.24
635 643 3.998672 TGGGAGGTGGTTCGTCGC 61.999 66.667 0.00 0.00 41.87 5.19
885 896 1.066605 AGAGTTGTTGTGTACTCGCGT 59.933 47.619 5.77 0.00 44.26 6.01
908 919 2.750350 CGTGGAGCTCAACCCCTT 59.250 61.111 15.83 0.00 0.00 3.95
945 956 2.342279 GGTACGCTGGTGCAGACA 59.658 61.111 0.00 0.00 39.64 3.41
987 998 2.357323 GCCAAGCATTTTCTAGAGCCTC 59.643 50.000 0.00 0.00 0.00 4.70
999 1010 1.589716 GACTCTTGCCGCCAAGCATT 61.590 55.000 0.24 0.00 46.38 3.56
1001 1012 2.669569 GACTCTTGCCGCCAAGCA 60.670 61.111 0.24 0.00 46.38 3.91
1024 1035 1.138036 CAACGCCGACGATCCTACA 59.862 57.895 0.00 0.00 43.93 2.74
1205 1216 8.950210 GGATACAAGTCTGATGAAATTTTCAGA 58.050 33.333 15.52 15.52 44.55 3.27
1228 1239 5.128827 CCACACTAGTACATGTAGTTGGGAT 59.871 44.000 25.10 10.92 31.66 3.85
1238 1249 6.612247 TTTCACAAACCACACTAGTACATG 57.388 37.500 0.00 0.00 0.00 3.21
1302 1313 7.933033 AGTGCATCAGGTTCAAAAATACATTTT 59.067 29.630 0.00 0.00 41.93 1.82
1403 1415 6.694877 TCGAGTGCATAGACTACACTATTT 57.305 37.500 5.89 0.00 44.40 1.40
1577 1589 5.706833 TCAGTCAATGTTGTATGTTCTGCAT 59.293 36.000 0.00 0.00 41.42 3.96
1846 1859 1.740585 TGAAACCGGCAAATATGACCG 59.259 47.619 0.00 4.72 42.26 4.79
1848 1861 4.167554 TGTTGAAACCGGCAAATATGAC 57.832 40.909 0.00 0.00 0.00 3.06
1988 2001 1.672356 GACGGTGGCTGCAACATCT 60.672 57.895 9.76 0.00 0.00 2.90
2002 2015 1.484653 TGTAGAATGGGTGGATGACGG 59.515 52.381 0.00 0.00 0.00 4.79
2048 2061 3.181454 CCCACAGTTTGTAGTCTTCCTGT 60.181 47.826 0.00 0.00 33.68 4.00
2084 2097 1.633774 ACTCGATGAGGTTGTCCTGT 58.366 50.000 0.00 0.00 45.24 4.00
2086 2099 1.743958 CGTACTCGATGAGGTTGTCCT 59.256 52.381 0.00 0.00 42.58 3.85
2145 2158 5.833082 ACCATCTGTGATGTAGTCGATTAC 58.167 41.667 10.90 10.90 0.00 1.89
2174 2187 0.876342 CCTCCCGCTCTTTCGCATAC 60.876 60.000 0.00 0.00 0.00 2.39
2304 2318 5.043737 ACCCAACAAGAGCAAACTACTAA 57.956 39.130 0.00 0.00 0.00 2.24
2305 2319 4.699925 ACCCAACAAGAGCAAACTACTA 57.300 40.909 0.00 0.00 0.00 1.82
2306 2320 3.577805 ACCCAACAAGAGCAAACTACT 57.422 42.857 0.00 0.00 0.00 2.57
2307 2321 3.630312 TCAACCCAACAAGAGCAAACTAC 59.370 43.478 0.00 0.00 0.00 2.73
2359 2377 9.944663 TTGATGACATAACTAAACTTGTTCAAC 57.055 29.630 0.00 0.00 0.00 3.18
2471 2490 2.036346 GAGCAGCCACAAAGTTCCATTT 59.964 45.455 0.00 0.00 0.00 2.32
2480 2499 4.351874 AGTACTTTAGAGCAGCCACAAA 57.648 40.909 0.00 0.00 0.00 2.83
2587 2606 5.280945 TGTTAAGCAACTCAAATTGTGCTC 58.719 37.500 9.50 0.30 35.56 4.26
2622 2641 8.832521 TGAAGTACTAAGAATTTTCGCTTCAAA 58.167 29.630 0.00 0.00 37.46 2.69
2723 2744 1.871039 GCGACCAACATAAGTGTGTGT 59.129 47.619 0.00 0.00 38.92 3.72
2795 2816 6.303259 GCTTCTTCGTGCTTTTTATTGTAGTG 59.697 38.462 0.00 0.00 0.00 2.74
2810 2831 5.739752 TTATGGAATGATGCTTCTTCGTG 57.260 39.130 0.88 0.00 0.00 4.35
2813 2834 4.781071 CGCTTATGGAATGATGCTTCTTC 58.219 43.478 0.88 2.99 0.00 2.87
2825 2846 4.690748 GCATTCATAGTAGCGCTTATGGAA 59.309 41.667 18.68 14.07 0.00 3.53
2855 2876 4.864704 TGCATGTAGACTGAGTTGTACA 57.135 40.909 10.11 10.11 0.00 2.90
2873 2894 6.371548 GTCATTTCAGAACTATGGTACTTGCA 59.628 38.462 0.00 0.00 0.00 4.08
2909 2932 9.868277 TGTTTGTTTTTGTGATTATTCTCAAGT 57.132 25.926 3.26 0.00 36.87 3.16
3026 3051 7.152645 TGTTTGAATCTAGTACTTGACTCCAC 58.847 38.462 12.15 9.67 39.81 4.02
3089 3141 3.044059 GCATTGTCAGGACCTGCGC 62.044 63.158 17.33 12.17 32.16 6.09


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

AutoCloner maintained by Alex Coulton.