Multiple sequence alignment - TraesCS6B01G155700

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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 TraesCS6B01G155700 chr6B 100.000 3221 0 0 1 3221 158194140 158190920 0.000000e+00 5949
1 TraesCS6B01G155700 chr6B 79.717 1982 377 20 116 2087 157109323 157107357 0.000000e+00 1410
2 TraesCS6B01G155700 chr6B 76.533 2250 475 42 116 2340 157765873 157763652 0.000000e+00 1181
3 TraesCS6B01G155700 chr6B 81.032 601 107 4 120 718 125052187 125051592 3.760000e-129 472
4 TraesCS6B01G155700 chr6A 93.873 2987 133 26 52 3032 100368183 100365241 0.000000e+00 4457
5 TraesCS6B01G155700 chr6A 79.223 1983 385 20 116 2087 98888042 98886076 0.000000e+00 1354
6 TraesCS6B01G155700 chr6A 78.934 1989 382 29 116 2088 99016116 99014149 0.000000e+00 1317
7 TraesCS6B01G155700 chr6A 78.539 1985 400 22 116 2088 98982310 98980340 0.000000e+00 1282
8 TraesCS6B01G155700 chr6A 75.197 2282 502 50 149 2397 100363366 100361116 0.000000e+00 1020
9 TraesCS6B01G155700 chr6A 86.765 680 78 8 1391 2069 100736478 100737146 0.000000e+00 747
10 TraesCS6B01G155700 chr6A 73.539 2139 474 71 116 2220 100087860 100085780 0.000000e+00 730
11 TraesCS6B01G155700 chr6A 95.302 149 6 1 3024 3171 100364563 100364415 5.370000e-58 235
12 TraesCS6B01G155700 chr6D 96.489 2079 38 11 687 2763 83210510 83208465 0.000000e+00 3402
13 TraesCS6B01G155700 chr6D 87.867 1533 159 12 722 2250 46902105 46903614 0.000000e+00 1775
14 TraesCS6B01G155700 chr6D 79.910 2215 421 17 116 2323 83108477 83106280 0.000000e+00 1604
15 TraesCS6B01G155700 chr6D 80.514 1986 354 27 116 2087 82203919 82201953 0.000000e+00 1493
16 TraesCS6B01G155700 chr6D 79.829 1983 376 20 116 2088 82220430 82218462 0.000000e+00 1424
17 TraesCS6B01G155700 chr6D 95.087 692 27 2 2 691 83213029 83212343 0.000000e+00 1083
18 TraesCS6B01G155700 chr6D 75.357 2244 511 35 116 2340 82958120 82955900 0.000000e+00 1042
19 TraesCS6B01G155700 chr6D 98.726 471 6 0 2751 3221 83206716 83206246 0.000000e+00 837
20 TraesCS6B01G155700 chr6D 76.611 962 202 17 1364 2316 81919056 81918109 2.870000e-140 508


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 TraesCS6B01G155700 chr6B 158190920 158194140 3220 True 5949 5949 100.000000 1 3221 1 chr6B.!!$R4 3220
1 TraesCS6B01G155700 chr6B 157107357 157109323 1966 True 1410 1410 79.717000 116 2087 1 chr6B.!!$R2 1971
2 TraesCS6B01G155700 chr6B 157763652 157765873 2221 True 1181 1181 76.533000 116 2340 1 chr6B.!!$R3 2224
3 TraesCS6B01G155700 chr6B 125051592 125052187 595 True 472 472 81.032000 120 718 1 chr6B.!!$R1 598
4 TraesCS6B01G155700 chr6A 100361116 100368183 7067 True 1904 4457 88.124000 52 3171 3 chr6A.!!$R5 3119
5 TraesCS6B01G155700 chr6A 98886076 98888042 1966 True 1354 1354 79.223000 116 2087 1 chr6A.!!$R1 1971
6 TraesCS6B01G155700 chr6A 99014149 99016116 1967 True 1317 1317 78.934000 116 2088 1 chr6A.!!$R3 1972
7 TraesCS6B01G155700 chr6A 98980340 98982310 1970 True 1282 1282 78.539000 116 2088 1 chr6A.!!$R2 1972
8 TraesCS6B01G155700 chr6A 100736478 100737146 668 False 747 747 86.765000 1391 2069 1 chr6A.!!$F1 678
9 TraesCS6B01G155700 chr6A 100085780 100087860 2080 True 730 730 73.539000 116 2220 1 chr6A.!!$R4 2104
10 TraesCS6B01G155700 chr6D 46902105 46903614 1509 False 1775 1775 87.867000 722 2250 1 chr6D.!!$F1 1528
11 TraesCS6B01G155700 chr6D 83206246 83213029 6783 True 1774 3402 96.767333 2 3221 3 chr6D.!!$R6 3219
12 TraesCS6B01G155700 chr6D 83106280 83108477 2197 True 1604 1604 79.910000 116 2323 1 chr6D.!!$R5 2207
13 TraesCS6B01G155700 chr6D 82201953 82203919 1966 True 1493 1493 80.514000 116 2087 1 chr6D.!!$R2 1971
14 TraesCS6B01G155700 chr6D 82218462 82220430 1968 True 1424 1424 79.829000 116 2088 1 chr6D.!!$R3 1972
15 TraesCS6B01G155700 chr6D 82955900 82958120 2220 True 1042 1042 75.357000 116 2340 1 chr6D.!!$R4 2224
16 TraesCS6B01G155700 chr6D 81918109 81919056 947 True 508 508 76.611000 1364 2316 1 chr6D.!!$R1 952

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
43 44 0.820891 CTGGTGCCCATATGCCAGTC 60.821 60.000 15.37 4.42 42.47 3.51 F
806 2651 1.407258 GGACTCTCCCAGATGAACTCG 59.593 57.143 0.00 0.00 0.00 4.18 F
1379 3224 2.346803 GCGTAACTTCAGGCATGAGAA 58.653 47.619 0.00 0.00 36.61 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 3224 0.254178 GGTGTCATCCTCTGGCATGT 59.746 55.000 0.00 0.00 42.55 3.21 R
1872 3721 0.975040 AGTCTAGGACCTGCAGGCTG 60.975 60.000 33.06 17.22 39.32 4.85 R
2804 11150 6.754675 GGTGTGCAGTTACAAGTTATTTTTGT 59.245 34.615 0.00 0.00 41.36 2.83 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
39 40 2.649831 CATCTGGTGCCCATATGCC 58.350 57.895 0.00 0.00 32.78 4.40
43 44 0.820891 CTGGTGCCCATATGCCAGTC 60.821 60.000 15.37 4.42 42.47 3.51
50 51 3.244665 TGCCCATATGCCAGTCTCATAAG 60.245 47.826 0.00 0.00 31.08 1.73
51 52 3.008375 GCCCATATGCCAGTCTCATAAGA 59.992 47.826 0.00 0.00 31.08 2.10
52 53 4.505566 GCCCATATGCCAGTCTCATAAGAA 60.506 45.833 0.00 0.00 31.93 2.52
53 54 5.624159 CCCATATGCCAGTCTCATAAGAAA 58.376 41.667 0.00 0.00 31.93 2.52
54 55 6.243900 CCCATATGCCAGTCTCATAAGAAAT 58.756 40.000 0.00 0.00 31.93 2.17
129 130 3.016736 CGATAAGTTCCCTTGGCATTGT 58.983 45.455 0.00 0.00 31.89 2.71
134 135 2.893489 AGTTCCCTTGGCATTGTTCTTC 59.107 45.455 0.00 0.00 0.00 2.87
322 325 2.924290 GACGGTTACTGATGTCTTGCTC 59.076 50.000 0.00 0.00 0.00 4.26
806 2651 1.407258 GGACTCTCCCAGATGAACTCG 59.593 57.143 0.00 0.00 0.00 4.18
1204 3049 4.497006 GCAGAAATCTAATTGCACTGCGAT 60.497 41.667 0.00 0.00 36.17 4.58
1379 3224 2.346803 GCGTAACTTCAGGCATGAGAA 58.653 47.619 0.00 0.00 36.61 2.87
1872 3721 2.821969 AGAATCAACATGCAACCTCACC 59.178 45.455 0.00 0.00 0.00 4.02
2049 8619 4.933400 TCTAGCTTTGACGGGAATACAAAC 59.067 41.667 0.00 0.00 31.67 2.93
2064 8634 7.016268 GGGAATACAAACCTCTGTGGATCTATA 59.984 40.741 2.23 0.00 39.71 1.31
2237 8808 4.637534 TGGCTAGTACTACTCCAGTTTACG 59.362 45.833 12.77 0.00 38.80 3.18
2238 8809 4.637977 GGCTAGTACTACTCCAGTTTACGT 59.362 45.833 0.00 0.00 38.80 3.57
2239 8810 5.817816 GGCTAGTACTACTCCAGTTTACGTA 59.182 44.000 0.00 0.00 38.80 3.57
2240 8811 6.238239 GGCTAGTACTACTCCAGTTTACGTAC 60.238 46.154 0.00 0.00 38.80 3.67
2241 8812 6.536941 GCTAGTACTACTCCAGTTTACGTACT 59.463 42.308 0.00 0.00 38.80 2.73
2397 8980 8.988060 TCCATTTCAAGGAGATGTACAAGTATA 58.012 33.333 0.00 0.00 0.00 1.47
2398 8981 9.784531 CCATTTCAAGGAGATGTACAAGTATAT 57.215 33.333 0.00 0.00 0.00 0.86
2804 11150 4.943705 GCATCCCAATCTTTTGAGTACTCA 59.056 41.667 21.74 21.74 37.91 3.41
2923 11269 0.469917 CCTAGCATCATTCCACCGGT 59.530 55.000 0.00 0.00 0.00 5.28
2946 11292 1.005630 GCAGTGCACTCCGAACTCT 60.006 57.895 18.64 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.897509 TCTTATGAGACTGGCATATGGG 57.102 45.455 4.56 0.00 0.00 4.00
39 40 7.487189 GCATGGTTTTCATTTCTTATGAGACTG 59.513 37.037 0.00 0.00 32.92 3.51
43 44 6.255020 GCTGCATGGTTTTCATTTCTTATGAG 59.745 38.462 0.00 0.00 32.92 2.90
50 51 2.738314 GTGGCTGCATGGTTTTCATTTC 59.262 45.455 0.50 0.00 32.92 2.17
51 52 2.369532 AGTGGCTGCATGGTTTTCATTT 59.630 40.909 0.50 0.00 32.92 2.32
52 53 1.972795 AGTGGCTGCATGGTTTTCATT 59.027 42.857 0.50 0.00 32.92 2.57
53 54 1.547372 GAGTGGCTGCATGGTTTTCAT 59.453 47.619 0.50 0.00 36.31 2.57
54 55 0.961019 GAGTGGCTGCATGGTTTTCA 59.039 50.000 0.50 0.00 0.00 2.69
266 267 0.541863 GTGATCCCTTCCCACGTGAT 59.458 55.000 19.30 0.00 0.00 3.06
267 268 1.550130 GGTGATCCCTTCCCACGTGA 61.550 60.000 19.30 0.00 0.00 4.35
322 325 0.674895 CCTGAAGACCCTTGGAAGCG 60.675 60.000 0.00 0.00 0.00 4.68
355 358 3.123620 GCGAGGCTGCCAAGAGTG 61.124 66.667 22.65 4.54 0.00 3.51
599 605 1.915614 GCATTGAGTGCGACCAGGTG 61.916 60.000 0.00 0.00 45.23 4.00
806 2651 3.858247 ACTCCAACGAGGTAGCATTAAC 58.142 45.455 0.00 0.00 40.77 2.01
985 2830 8.040002 TCCCCATACATGATATTACTGTTCAA 57.960 34.615 0.00 0.00 0.00 2.69
986 2831 7.625498 TCCCCATACATGATATTACTGTTCA 57.375 36.000 0.00 0.00 0.00 3.18
1204 3049 4.879545 GCCGTGGAACTTATTGGAAGATAA 59.120 41.667 0.00 0.00 31.75 1.75
1379 3224 0.254178 GGTGTCATCCTCTGGCATGT 59.746 55.000 0.00 0.00 42.55 3.21
1872 3721 0.975040 AGTCTAGGACCTGCAGGCTG 60.975 60.000 33.06 17.22 39.32 4.85
2049 8619 6.907853 TGAATGAGTATAGATCCACAGAGG 57.092 41.667 0.00 0.00 39.47 3.69
2064 8634 5.121811 GCTGAACCACATCTATGAATGAGT 58.878 41.667 0.00 0.00 0.00 3.41
2239 8810 9.444600 AACGAAATTGACCTAAACATATACAGT 57.555 29.630 0.00 0.00 0.00 3.55
2240 8811 9.916397 GAACGAAATTGACCTAAACATATACAG 57.084 33.333 0.00 0.00 0.00 2.74
2241 8812 9.438228 TGAACGAAATTGACCTAAACATATACA 57.562 29.630 0.00 0.00 0.00 2.29
2397 8980 7.927788 TGCCCCACATTATTACATATACAGAT 58.072 34.615 0.00 0.00 0.00 2.90
2398 8981 7.017155 ACTGCCCCACATTATTACATATACAGA 59.983 37.037 0.00 0.00 0.00 3.41
2399 8982 7.168219 ACTGCCCCACATTATTACATATACAG 58.832 38.462 0.00 0.00 0.00 2.74
2400 8983 7.085476 ACTGCCCCACATTATTACATATACA 57.915 36.000 0.00 0.00 0.00 2.29
2804 11150 6.754675 GGTGTGCAGTTACAAGTTATTTTTGT 59.245 34.615 0.00 0.00 41.36 2.83
3132 11478 8.024145 ACCCAAAAGTTATGGTTTTGTGATAA 57.976 30.769 7.35 0.00 41.40 1.75


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

AutoCloner maintained by Alex Coulton.