Multiple sequence alignment - TraesCS4B01G203500

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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 TraesCS4B01G203500 chr4B 100.000 3407 0 0 1 3407 434971518 434974924 0 6292
1 TraesCS4B01G203500 chr7B 95.957 3438 99 7 1 3402 300041531 300044964 0 5542
2 TraesCS4B01G203500 chr7B 93.603 1907 80 7 1 1871 19762830 19764730 0 2808
3 TraesCS4B01G203500 chr7B 93.449 1908 78 17 1 1871 19805139 19807036 0 2787
4 TraesCS4B01G203500 chr6B 95.898 3437 99 6 1 3402 85662840 85666269 0 5528
5 TraesCS4B01G203500 chr6B 95.309 1876 57 3 1558 3402 42182353 42180478 0 2948
6 TraesCS4B01G203500 chr6B 95.312 1877 54 4 1558 3402 536421859 536419985 0 2948
7 TraesCS4B01G203500 chr6B 94.272 1414 60 9 1 1404 42183844 42182442 0 2143
8 TraesCS4B01G203500 chr6B 93.564 1414 67 9 1 1404 536423347 536421948 0 2085
9 TraesCS4B01G203500 chr2B 95.870 3438 97 9 1 3402 317055748 317052320 0 5520
10 TraesCS4B01G203500 chr2B 95.442 1843 73 7 1564 3402 293244289 293246124 0 2928
11 TraesCS4B01G203500 chr3B 95.029 3440 128 16 1 3402 151826088 151822654 0 5365
12 TraesCS4B01G203500 chr3B 94.914 3441 123 20 1 3402 545972556 545969129 0 5337
13 TraesCS4B01G203500 chr3B 94.435 2839 113 11 599 3402 151821927 151819099 0 4325
14 TraesCS4B01G203500 chr3B 96.047 1872 47 2 1558 3402 664731837 664729966 0 3022
15 TraesCS4B01G203500 chr3B 95.200 1875 60 4 1558 3402 649104069 649102195 0 2937
16 TraesCS4B01G203500 chr5A 94.309 3444 138 16 1 3402 141902096 141905523 0 5221
17 TraesCS4B01G203500 chr5A 94.333 2682 100 16 207 2848 142251480 142248811 0 4063
18 TraesCS4B01G203500 chr1B 95.652 1840 71 6 1567 3402 84524087 84522253 0 2946
19 TraesCS4B01G203500 chr1B 94.130 1414 60 13 1 1404 84525611 84524211 0 2130
20 TraesCS4B01G203500 chr1B 94.411 823 31 7 1 811 575090018 575089199 0 1251


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 TraesCS4B01G203500 chr4B 434971518 434974924 3406 False 6292.0 6292 100.0000 1 3407 1 chr4B.!!$F1 3406
1 TraesCS4B01G203500 chr7B 300041531 300044964 3433 False 5542.0 5542 95.9570 1 3402 1 chr7B.!!$F3 3401
2 TraesCS4B01G203500 chr7B 19762830 19764730 1900 False 2808.0 2808 93.6030 1 1871 1 chr7B.!!$F1 1870
3 TraesCS4B01G203500 chr7B 19805139 19807036 1897 False 2787.0 2787 93.4490 1 1871 1 chr7B.!!$F2 1870
4 TraesCS4B01G203500 chr6B 85662840 85666269 3429 False 5528.0 5528 95.8980 1 3402 1 chr6B.!!$F1 3401
5 TraesCS4B01G203500 chr6B 42180478 42183844 3366 True 2545.5 2948 94.7905 1 3402 2 chr6B.!!$R1 3401
6 TraesCS4B01G203500 chr6B 536419985 536423347 3362 True 2516.5 2948 94.4380 1 3402 2 chr6B.!!$R2 3401
7 TraesCS4B01G203500 chr2B 317052320 317055748 3428 True 5520.0 5520 95.8700 1 3402 1 chr2B.!!$R1 3401
8 TraesCS4B01G203500 chr2B 293244289 293246124 1835 False 2928.0 2928 95.4420 1564 3402 1 chr2B.!!$F1 1838
9 TraesCS4B01G203500 chr3B 545969129 545972556 3427 True 5337.0 5337 94.9140 1 3402 1 chr3B.!!$R1 3401
10 TraesCS4B01G203500 chr3B 151819099 151826088 6989 True 4845.0 5365 94.7320 1 3402 2 chr3B.!!$R4 3401
11 TraesCS4B01G203500 chr3B 664729966 664731837 1871 True 3022.0 3022 96.0470 1558 3402 1 chr3B.!!$R3 1844
12 TraesCS4B01G203500 chr3B 649102195 649104069 1874 True 2937.0 2937 95.2000 1558 3402 1 chr3B.!!$R2 1844
13 TraesCS4B01G203500 chr5A 141902096 141905523 3427 False 5221.0 5221 94.3090 1 3402 1 chr5A.!!$F1 3401
14 TraesCS4B01G203500 chr5A 142248811 142251480 2669 True 4063.0 4063 94.3330 207 2848 1 chr5A.!!$R1 2641
15 TraesCS4B01G203500 chr1B 84522253 84525611 3358 True 2538.0 2946 94.8910 1 3402 2 chr1B.!!$R2 3401
16 TraesCS4B01G203500 chr1B 575089199 575090018 819 True 1251.0 1251 94.4110 1 811 1 chr1B.!!$R1 810

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
673 676 1.300931 GCAGAGACGTGCAAGTGGA 60.301 57.895 10.87 0.0 43.41 4.02 F
960 974 1.418637 TCCACTACACACAAACCTCCC 59.581 52.381 0.00 0.0 0.00 4.30 F
1215 1229 1.449246 CTGGAGGAAGCTTGGCGAG 60.449 63.158 2.10 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2118 1.952990 TCGCTTTCAATGCTGAAACCA 59.047 42.857 0.00 0.0 44.76 3.67 R
2110 2194 2.758736 ACTCTCCACATGAGCTGAAC 57.241 50.000 0.00 0.0 41.18 3.18 R
3066 6714 2.159226 CGGGCTCGAGTTCAAGTATCTT 60.159 50.000 15.13 0.0 39.00 2.40 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
120 121 8.552083 TTGATATATCTGATGCAAAACGCTAT 57.448 30.769 13.79 0.00 43.06 2.97
138 139 4.688879 CGCTATTGTGAACCAGTAACTCAA 59.311 41.667 0.00 0.00 0.00 3.02
376 377 8.520351 CGAATATAATACATCCTGTACTGGTGA 58.480 37.037 17.42 0.84 35.42 4.02
522 525 6.038825 ACGTTCAATTACACTTCAATCACCAA 59.961 34.615 0.00 0.00 0.00 3.67
529 532 3.007940 ACACTTCAATCACCAATCCGAGA 59.992 43.478 0.00 0.00 0.00 4.04
547 550 3.188873 CGAGAACGACAGTAGAGGAGTTT 59.811 47.826 0.00 0.00 42.66 2.66
673 676 1.300931 GCAGAGACGTGCAAGTGGA 60.301 57.895 10.87 0.00 43.41 4.02
862 876 4.033776 CCGCCTCCCACACACCAT 62.034 66.667 0.00 0.00 0.00 3.55
868 882 1.873270 CTCCCACACACCATCGTCGA 61.873 60.000 0.00 0.00 0.00 4.20
908 922 4.105377 CCCATTGTATTCCATCTCTCCCTT 59.895 45.833 0.00 0.00 0.00 3.95
960 974 1.418637 TCCACTACACACAAACCTCCC 59.581 52.381 0.00 0.00 0.00 4.30
1082 1096 1.894466 TGTCGACATTAAAGTCCCCGA 59.106 47.619 15.76 0.00 35.07 5.14
1215 1229 1.449246 CTGGAGGAAGCTTGGCGAG 60.449 63.158 2.10 0.00 0.00 5.03
1270 1284 3.208747 ACACCAACGAAGATGAACCTT 57.791 42.857 0.00 0.00 29.10 3.50
1462 1476 6.482308 AGATGTACTAGTGTGGTTTGTGAAAC 59.518 38.462 5.39 0.00 40.65 2.78
1546 1561 7.531857 TGCACTGGATTACTATTTGGAAAAA 57.468 32.000 0.00 0.00 0.00 1.94
1577 1631 8.668353 CGGAAGATTAAATTCTGAAGTTGATCA 58.332 33.333 26.28 0.00 34.96 2.92
1781 1861 7.588854 CAGAACATACAACATTGACTGAAACTG 59.411 37.037 0.00 0.00 0.00 3.16
2034 2118 4.717233 TGACAAGTTGTTCACATTTGCT 57.283 36.364 10.45 0.00 0.00 3.91
2110 2194 0.796312 CCCCAACAAGTTCATCGACG 59.204 55.000 0.00 0.00 0.00 5.12
2117 2201 2.061773 CAAGTTCATCGACGTTCAGCT 58.938 47.619 0.00 0.00 0.00 4.24
2120 2204 2.094494 AGTTCATCGACGTTCAGCTCAT 60.094 45.455 0.00 0.00 0.00 2.90
2685 6330 4.730657 TGTCGTTGCTCTAAAGTACTAGC 58.269 43.478 8.20 8.20 35.51 3.42
3017 6664 7.093727 TGGAGGAGTCAAGTACTAGATTCAAAG 60.094 40.741 0.00 0.00 39.07 2.77
3066 6714 2.677524 GCAGGCCCTGACAATGCA 60.678 61.111 16.85 0.00 36.88 3.96
3153 6801 1.376553 GCCCACAGGTCAAGAGAGC 60.377 63.158 0.00 0.00 42.53 4.09
3364 7018 3.813166 CCTACATCGTCAACAAAACACCT 59.187 43.478 0.00 0.00 0.00 4.00
3365 7019 3.691049 ACATCGTCAACAAAACACCTG 57.309 42.857 0.00 0.00 0.00 4.00
3383 7040 2.094675 CTGACCAAATAAGCCCAGGTG 58.905 52.381 0.00 0.00 31.57 4.00
3402 7059 1.844289 TACAAACCAGAGGGCGGGT 60.844 57.895 0.00 0.00 44.92 5.28
3403 7060 2.119484 TACAAACCAGAGGGCGGGTG 62.119 60.000 0.00 0.00 42.02 4.61
3404 7061 2.852075 AAACCAGAGGGCGGGTGA 60.852 61.111 0.00 0.00 42.02 4.02
3405 7062 2.895424 AAACCAGAGGGCGGGTGAG 61.895 63.158 0.00 0.00 42.02 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 6.576662 TTTTGTTGAGTTACTGGTTCACAA 57.423 33.333 0.00 0.00 0.00 3.33
522 525 2.093075 TCCTCTACTGTCGTTCTCGGAT 60.093 50.000 0.00 0.00 37.69 4.18
529 532 4.458642 GGTCTAAACTCCTCTACTGTCGTT 59.541 45.833 0.00 0.00 0.00 3.85
547 550 0.178955 TCGGTGTTGGTGGAGGTCTA 60.179 55.000 0.00 0.00 0.00 2.59
673 676 5.711976 AGCTGTACTTATGACCTGCAAAATT 59.288 36.000 0.00 0.00 0.00 1.82
908 922 1.759445 CAATGGTGGTTTGTGGGAACA 59.241 47.619 0.00 0.00 38.70 3.18
960 974 1.807573 GGCTTTGGAGAGAGACGCG 60.808 63.158 3.53 3.53 0.00 6.01
1041 1055 2.264455 AGGTTGCTCCTCTTGTCTGAT 58.736 47.619 0.00 0.00 44.42 2.90
1062 1076 1.894466 TCGGGGACTTTAATGTCGACA 59.106 47.619 22.48 22.48 37.81 4.35
1082 1096 0.666577 GGTGTAGTTGCGCTTCTCGT 60.667 55.000 9.73 0.00 41.07 4.18
1143 1157 1.515020 GCTGGTGCAGACGATCTCT 59.485 57.895 0.00 0.00 39.41 3.10
1215 1229 1.268437 CCGACGATCCTACGAAACCTC 60.268 57.143 0.00 0.00 37.03 3.85
1270 1284 3.785859 GACTGCCGCCATCTGGGA 61.786 66.667 0.00 0.00 40.01 4.37
1353 1367 2.225467 GCAGGGCAAATGAGTAGGATC 58.775 52.381 0.00 0.00 0.00 3.36
1546 1561 6.431234 ACTTCAGAATTTAATCTTCCGCAAGT 59.569 34.615 0.00 0.00 0.00 3.16
1830 1910 8.818622 ACCTCAAAAACTAGTAAAGGAAGTTT 57.181 30.769 13.02 0.00 43.43 2.66
1836 1916 9.280174 TGAATGTACCTCAAAAACTAGTAAAGG 57.720 33.333 0.00 1.76 0.00 3.11
1853 1933 7.823745 AGGATAAACAATGGATGAATGTACC 57.176 36.000 0.00 0.00 0.00 3.34
2034 2118 1.952990 TCGCTTTCAATGCTGAAACCA 59.047 42.857 0.00 0.00 44.76 3.67
2110 2194 2.758736 ACTCTCCACATGAGCTGAAC 57.241 50.000 0.00 0.00 41.18 3.18
2685 6330 6.183360 ACGTTGTGTGATTAGTTGCATCATAG 60.183 38.462 0.00 0.00 33.22 2.23
3066 6714 2.159226 CGGGCTCGAGTTCAAGTATCTT 60.159 50.000 15.13 0.00 39.00 2.40
3153 6801 2.976881 TTATACACGGCGCTCGCTCG 62.977 60.000 16.48 16.57 43.89 5.03
3364 7018 1.427368 ACACCTGGGCTTATTTGGTCA 59.573 47.619 0.00 0.00 0.00 4.02
3365 7019 2.215942 ACACCTGGGCTTATTTGGTC 57.784 50.000 0.00 0.00 0.00 4.02
3383 7040 1.376812 CCCGCCCTCTGGTTTGTAC 60.377 63.158 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.