Multiple sequence alignment - TraesCS4B01G354100

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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 TraesCS4B01G354100 chr4B 100.000 2549 0 0 1 2549 645968364 645965816 0 4708
1 TraesCS4B01G354100 chr4B 94.180 567 31 2 2 567 516413528 516412963 0 863
2 TraesCS4B01G354100 chr4B 93.122 567 37 2 2 567 489505366 489504801 0 830
3 TraesCS4B01G354100 chr4B 92.416 567 41 2 2 567 284234766 284235331 0 808
4 TraesCS4B01G354100 chr2D 95.390 1974 84 5 569 2538 64508698 64510668 0 3134
5 TraesCS4B01G354100 chr3B 94.523 1972 106 2 569 2538 687040066 687042037 0 3042
6 TraesCS4B01G354100 chr3B 94.368 1971 102 4 569 2538 804661032 804662994 0 3016
7 TraesCS4B01G354100 chr3B 94.174 1974 103 8 569 2538 53523443 53525408 0 2998
8 TraesCS4B01G354100 chr1B 94.388 1978 105 5 564 2538 542264936 542266910 0 3033
9 TraesCS4B01G354100 chr1B 92.945 567 37 3 2 567 341415670 341415106 0 822
10 TraesCS4B01G354100 chr1B 92.593 567 40 2 2 567 221632158 221631593 0 813
11 TraesCS4B01G354100 chr5B 94.307 1985 103 7 558 2538 26059389 26057411 0 3031
12 TraesCS4B01G354100 chr5B 92.606 568 37 4 2 567 390856564 390856000 0 811
13 TraesCS4B01G354100 chrUn 94.186 1978 104 7 569 2538 60558711 60560685 0 3005
14 TraesCS4B01G354100 chrUn 94.070 1973 108 6 570 2538 37355777 37353810 0 2987
15 TraesCS4B01G354100 chrUn 94.070 1973 108 6 570 2538 287431304 287429337 0 2987
16 TraesCS4B01G354100 chr7B 92.593 567 39 3 2 567 210600514 210601078 0 811
17 TraesCS4B01G354100 chr3D 92.593 567 39 3 2 567 50256387 50255823 0 811
18 TraesCS4B01G354100 chr6B 92.430 568 39 4 2 567 362191628 362191063 0 808


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 TraesCS4B01G354100 chr4B 645965816 645968364 2548 True 4708 4708 100.000 1 2549 1 chr4B.!!$R3 2548
1 TraesCS4B01G354100 chr4B 516412963 516413528 565 True 863 863 94.180 2 567 1 chr4B.!!$R2 565
2 TraesCS4B01G354100 chr4B 489504801 489505366 565 True 830 830 93.122 2 567 1 chr4B.!!$R1 565
3 TraesCS4B01G354100 chr4B 284234766 284235331 565 False 808 808 92.416 2 567 1 chr4B.!!$F1 565
4 TraesCS4B01G354100 chr2D 64508698 64510668 1970 False 3134 3134 95.390 569 2538 1 chr2D.!!$F1 1969
5 TraesCS4B01G354100 chr3B 687040066 687042037 1971 False 3042 3042 94.523 569 2538 1 chr3B.!!$F2 1969
6 TraesCS4B01G354100 chr3B 804661032 804662994 1962 False 3016 3016 94.368 569 2538 1 chr3B.!!$F3 1969
7 TraesCS4B01G354100 chr3B 53523443 53525408 1965 False 2998 2998 94.174 569 2538 1 chr3B.!!$F1 1969
8 TraesCS4B01G354100 chr1B 542264936 542266910 1974 False 3033 3033 94.388 564 2538 1 chr1B.!!$F1 1974
9 TraesCS4B01G354100 chr1B 341415106 341415670 564 True 822 822 92.945 2 567 1 chr1B.!!$R2 565
10 TraesCS4B01G354100 chr1B 221631593 221632158 565 True 813 813 92.593 2 567 1 chr1B.!!$R1 565
11 TraesCS4B01G354100 chr5B 26057411 26059389 1978 True 3031 3031 94.307 558 2538 1 chr5B.!!$R1 1980
12 TraesCS4B01G354100 chr5B 390856000 390856564 564 True 811 811 92.606 2 567 1 chr5B.!!$R2 565
13 TraesCS4B01G354100 chrUn 60558711 60560685 1974 False 3005 3005 94.186 569 2538 1 chrUn.!!$F1 1969
14 TraesCS4B01G354100 chrUn 37353810 37355777 1967 True 2987 2987 94.070 570 2538 1 chrUn.!!$R1 1968
15 TraesCS4B01G354100 chrUn 287429337 287431304 1967 True 2987 2987 94.070 570 2538 1 chrUn.!!$R2 1968
16 TraesCS4B01G354100 chr7B 210600514 210601078 564 False 811 811 92.593 2 567 1 chr7B.!!$F1 565
17 TraesCS4B01G354100 chr3D 50255823 50256387 564 True 811 811 92.593 2 567 1 chr3D.!!$R1 565
18 TraesCS4B01G354100 chr6B 362191063 362191628 565 True 808 808 92.430 2 567 1 chr6B.!!$R1 565

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
90 91 0.392193 CTGAATGGAGCGCAGGAGTT 60.392 55.0 11.47 0.0 0.0 3.01 F
510 516 0.461870 CAATCCTCGCGAATCCCACA 60.462 55.0 11.33 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1112 1120 0.321653 ATTCTGGTTCCTCGGTGTGC 60.322 55.0 0.00 0.00 0.00 4.57 R
2220 2247 0.040781 CTAACCAAAACCACGTGGCG 60.041 55.0 34.26 19.27 38.58 5.69 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
66 67 1.070957 GGCTATAGGGGACGTTGCC 59.929 63.158 1.04 0.00 35.54 4.52
90 91 0.392193 CTGAATGGAGCGCAGGAGTT 60.392 55.000 11.47 0.00 0.00 3.01
142 143 7.741785 TCCCTAAGTCTCTATCTCTACTCTTG 58.258 42.308 0.00 0.00 0.00 3.02
423 427 1.370064 GTTAGTGGTCAGCCGGTGT 59.630 57.895 1.90 0.00 37.67 4.16
428 432 0.604578 GTGGTCAGCCGGTGTAAGTA 59.395 55.000 1.90 0.00 37.67 2.24
510 516 0.461870 CAATCCTCGCGAATCCCACA 60.462 55.000 11.33 0.00 0.00 4.17
567 573 9.906660 TGTTTTTAAGCCATAGTATTTGACAAG 57.093 29.630 0.00 0.00 0.00 3.16
590 596 4.542697 GGGTTCATTATCCTTTTGCCCTA 58.457 43.478 0.00 0.00 0.00 3.53
702 708 1.006571 GCGTCTCCGTCAGGTCAAA 60.007 57.895 0.00 0.00 39.05 2.69
704 710 1.137513 CGTCTCCGTCAGGTCAAAAC 58.862 55.000 0.00 0.00 39.05 2.43
923 929 1.451936 GATGGCGGTGGGAAGCTAT 59.548 57.895 0.00 0.00 37.27 2.97
992 998 1.469335 TTGAGTTCCCGTTCGGCTCT 61.469 55.000 14.65 8.85 0.00 4.09
1073 1081 2.025155 GGAGATGCCTGTCTTCGTCTA 58.975 52.381 0.00 0.00 0.00 2.59
1083 1091 1.002684 GTCTTCGTCTATCCGCGATGT 60.003 52.381 8.23 0.00 36.97 3.06
1149 1157 3.252701 AGAATCGTCTGTTCTACGTGTGT 59.747 43.478 0.00 0.00 41.08 3.72
1153 1161 2.350102 CGTCTGTTCTACGTGTGTAGCA 60.350 50.000 0.00 0.00 46.33 3.49
1162 1170 1.346395 ACGTGTGTAGCAAGAATGGGA 59.654 47.619 0.00 0.00 0.00 4.37
1218 1226 3.631250 GGGATCTTTGAGCAATGGGTTA 58.369 45.455 0.00 0.00 0.00 2.85
1296 1304 6.070251 TGGCCAAGACTCTGATAAATGAACTA 60.070 38.462 0.61 0.00 0.00 2.24
1321 1329 4.660168 AGAAGAGCATGAAGAATGGTTGT 58.340 39.130 0.00 0.00 46.95 3.32
1332 1340 1.189524 AATGGTTGTGCATGCTGCCT 61.190 50.000 20.33 3.55 44.23 4.75
1434 1442 6.715280 TGAGCTTAGGATGTTGAAGAAGAAT 58.285 36.000 0.00 0.00 0.00 2.40
1859 1880 1.811965 TGTCATGGAAAATGTGCCTCG 59.188 47.619 0.00 0.00 0.00 4.63
1902 1923 7.151308 CACCTAGTGCCAAAATAAATGAACAA 58.849 34.615 0.00 0.00 0.00 2.83
2029 2052 2.028876 GTTTGTGGTGTTTAGGGCTGT 58.971 47.619 0.00 0.00 0.00 4.40
2031 2054 0.840617 TGTGGTGTTTAGGGCTGTGA 59.159 50.000 0.00 0.00 0.00 3.58
2033 2056 2.640332 TGTGGTGTTTAGGGCTGTGATA 59.360 45.455 0.00 0.00 0.00 2.15
2088 2111 4.209154 TGGGTAGGGAAGGAAGGTATAG 57.791 50.000 0.00 0.00 0.00 1.31
2116 2139 7.601856 AGTGAGACTGTGAAATTTGTCAAAAA 58.398 30.769 1.31 0.00 32.41 1.94
2117 2140 8.253113 AGTGAGACTGTGAAATTTGTCAAAAAT 58.747 29.630 1.31 0.00 32.41 1.82
2358 2394 3.787001 GCTTCTCACCCCCTCCGG 61.787 72.222 0.00 0.00 0.00 5.14
2432 2468 6.127196 GGGAAGAAATTATATGTTTGGGCACA 60.127 38.462 0.00 0.00 0.00 4.57
2538 2577 1.138069 ACAGTTCACGGACACATGACA 59.862 47.619 0.00 0.00 0.00 3.58
2539 2578 2.224281 ACAGTTCACGGACACATGACAT 60.224 45.455 0.00 0.00 0.00 3.06
2540 2579 2.158254 CAGTTCACGGACACATGACATG 59.842 50.000 14.02 14.02 0.00 3.21
2541 2580 2.037121 AGTTCACGGACACATGACATGA 59.963 45.455 22.19 0.00 0.00 3.07
2542 2581 2.078849 TCACGGACACATGACATGAC 57.921 50.000 22.19 11.80 0.00 3.06
2543 2582 1.342819 TCACGGACACATGACATGACA 59.657 47.619 22.19 0.00 0.00 3.58
2544 2583 1.460743 CACGGACACATGACATGACAC 59.539 52.381 22.19 11.17 0.00 3.67
2545 2584 0.715551 CGGACACATGACATGACACG 59.284 55.000 22.19 15.11 0.00 4.49
2546 2585 1.668628 CGGACACATGACATGACACGA 60.669 52.381 22.19 0.00 0.00 4.35
2547 2586 1.726791 GGACACATGACATGACACGAC 59.273 52.381 22.19 7.43 0.00 4.34
2548 2587 2.403259 GACACATGACATGACACGACA 58.597 47.619 22.19 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.289010 GCACTGTTGAAATTTGGGGAGG 60.289 50.000 0.00 0.00 0.00 4.30
37 38 1.551329 CCCTATAGCCACTCCCTCCTC 60.551 61.905 0.00 0.00 0.00 3.71
90 91 1.672737 CCATCTACTGCTTCGTGTGCA 60.673 52.381 0.00 0.00 38.81 4.57
142 143 9.609346 ACAAAGAAGACTAGTAGAGATAGAGAC 57.391 37.037 3.59 0.00 0.00 3.36
174 176 8.705134 CGACACAGTACTATTCAATTTGTTGTA 58.295 33.333 0.00 0.00 0.00 2.41
175 177 7.225931 ACGACACAGTACTATTCAATTTGTTGT 59.774 33.333 0.00 0.00 0.00 3.32
176 178 7.572759 ACGACACAGTACTATTCAATTTGTTG 58.427 34.615 0.00 0.00 0.00 3.33
288 291 1.477553 GGCACACCATCATCACCAAT 58.522 50.000 0.00 0.00 35.26 3.16
340 344 7.493320 GTCTACGTGGTGTTTGGAATTATATGA 59.507 37.037 0.00 0.00 0.00 2.15
423 427 5.910355 AAAATACCCGGGGCTATTACTTA 57.090 39.130 27.92 4.56 0.00 2.24
428 432 3.464456 AGGTTAAAATACCCGGGGCTATT 59.536 43.478 27.92 17.69 39.08 1.73
510 516 5.295152 GTCGGATGGAAATCTAACGGTTAT 58.705 41.667 0.29 0.00 0.00 1.89
567 573 2.434336 GGGCAAAAGGATAATGAACCCC 59.566 50.000 0.00 0.00 0.00 4.95
590 596 1.002888 CTGAGCAGATGGACACCACTT 59.997 52.381 0.00 0.00 35.80 3.16
702 708 3.991367 CTGTAAGGGACGAGTCAAAGTT 58.009 45.455 5.55 0.00 0.00 2.66
970 976 1.300388 CCGAACGGGAACTCAACGT 60.300 57.895 5.25 0.00 43.43 3.99
978 984 2.970639 CTCAGAGCCGAACGGGAA 59.029 61.111 15.01 0.00 38.47 3.97
992 998 1.219124 GCGGAAGACATGGAGCTCA 59.781 57.895 17.19 1.87 0.00 4.26
1086 1094 2.293627 CCTCGGATAAACGCTCGCG 61.294 63.158 10.06 10.06 46.03 5.87
1112 1120 0.321653 ATTCTGGTTCCTCGGTGTGC 60.322 55.000 0.00 0.00 0.00 4.57
1149 1157 6.070656 CCCAATTCTTATCCCATTCTTGCTA 58.929 40.000 0.00 0.00 0.00 3.49
1153 1161 4.226384 GCCCCAATTCTTATCCCATTCTT 58.774 43.478 0.00 0.00 0.00 2.52
1162 1170 3.118298 GGTGCAATTGCCCCAATTCTTAT 60.118 43.478 24.97 0.00 41.40 1.73
1218 1226 2.485426 CTGCATGAACACGGAACAGATT 59.515 45.455 0.00 0.00 0.00 2.40
1296 1304 4.660168 ACCATTCTTCATGCTCTTCTTGT 58.340 39.130 0.00 0.00 0.00 3.16
1638 1655 9.912634 ACATATTTAAATGTTGGTCACTTCTTG 57.087 29.630 11.05 0.00 36.71 3.02
1691 1712 7.171848 TGCATTTCATTGATCAAAAGTTTCTGG 59.828 33.333 13.09 0.00 0.00 3.86
1859 1880 2.093606 GGTGTAAACCTCTACCAGAGCC 60.094 54.545 0.00 0.00 40.98 4.70
2029 2052 4.160642 TCTGTCCTAGCGGTTACTATCA 57.839 45.455 0.00 0.00 0.00 2.15
2031 2054 3.827302 CCATCTGTCCTAGCGGTTACTAT 59.173 47.826 0.00 0.00 0.00 2.12
2033 2056 2.032620 CCATCTGTCCTAGCGGTTACT 58.967 52.381 0.00 0.00 0.00 2.24
2088 2111 7.658179 TGACAAATTTCACAGTCTCACTATC 57.342 36.000 7.62 0.00 32.41 2.08
2116 2139 8.408601 GCAAACATTCATGGTCTCACTATTTAT 58.591 33.333 0.00 0.00 0.00 1.40
2117 2140 7.392953 TGCAAACATTCATGGTCTCACTATTTA 59.607 33.333 0.00 0.00 0.00 1.40
2218 2245 4.639171 CCAAAACCACGTGGCGGC 62.639 66.667 34.26 0.00 39.32 6.53
2220 2247 0.040781 CTAACCAAAACCACGTGGCG 60.041 55.000 34.26 19.27 38.58 5.69


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

AutoCloner maintained by Alex Coulton.