Multiple sequence alignment - TraesCS6B01G340200

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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 TraesCS6B01G340200 chr6B 100.000 4044 0 0 1 4044 599670221 599674264 0 7468
1 TraesCS6B01G340200 chr6B 94.592 4068 161 21 1 4044 718737670 718733638 0 6239
2 TraesCS6B01G340200 chr6B 93.682 4068 181 38 1 4044 67270814 67266799 0 6019
3 TraesCS6B01G340200 chr6B 92.613 4075 210 43 1 4044 200025690 200021676 0 5773
4 TraesCS6B01G340200 chr6B 92.502 4068 209 45 14 4044 665436346 665432338 0 5734
5 TraesCS6B01G340200 chr6B 93.674 2292 93 15 1458 3729 94642517 94644776 0 3382
6 TraesCS6B01G340200 chr1B 96.714 4048 126 5 1 4044 492781072 492777028 0 6732
7 TraesCS6B01G340200 chr7B 95.876 4049 152 9 1 4044 130595124 130591086 0 6538
8 TraesCS6B01G340200 chr7B 94.443 4067 166 20 1 4044 201428560 201424531 0 6204
9 TraesCS6B01G340200 chr2B 94.676 4095 162 13 1 4044 67261075 67265164 0 6303
10 TraesCS6B01G340200 chr2B 91.879 3177 147 40 895 4042 626144995 626148089 0 4335
11 TraesCS6B01G340200 chr4B 94.222 4067 179 23 1 4044 382409414 382413447 0 6157
12 TraesCS6B01G340200 chr4B 96.606 1473 49 1 2572 4044 187384594 187386065 0 2442
13 TraesCS6B01G340200 chr4B 94.044 1276 65 9 753 2025 539956433 539957700 0 1925
14 TraesCS6B01G340200 chr4A 93.547 2340 102 13 1727 4044 740394894 740397206 0 3439
15 TraesCS6B01G340200 chr1D 95.581 2014 80 7 1 2009 10795887 10797896 0 3217
16 TraesCS6B01G340200 chr1D 93.146 1605 65 17 2480 4044 58471147 58472746 0 2313
17 TraesCS6B01G340200 chr4D 95.380 2013 86 5 1 2009 65868075 65870084 0 3195
18 TraesCS6B01G340200 chr7D 95.233 2014 82 11 1 2009 30320590 30318586 0 3175
19 TraesCS6B01G340200 chr7D 93.662 2067 94 21 2005 4044 34186295 34188351 0 3057
20 TraesCS6B01G340200 chr5D 93.162 2062 111 17 2005 4044 424143319 424141266 0 3000


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 TraesCS6B01G340200 chr6B 599670221 599674264 4043 False 7468 7468 100.000 1 4044 1 chr6B.!!$F2 4043
1 TraesCS6B01G340200 chr6B 718733638 718737670 4032 True 6239 6239 94.592 1 4044 1 chr6B.!!$R4 4043
2 TraesCS6B01G340200 chr6B 67266799 67270814 4015 True 6019 6019 93.682 1 4044 1 chr6B.!!$R1 4043
3 TraesCS6B01G340200 chr6B 200021676 200025690 4014 True 5773 5773 92.613 1 4044 1 chr6B.!!$R2 4043
4 TraesCS6B01G340200 chr6B 665432338 665436346 4008 True 5734 5734 92.502 14 4044 1 chr6B.!!$R3 4030
5 TraesCS6B01G340200 chr6B 94642517 94644776 2259 False 3382 3382 93.674 1458 3729 1 chr6B.!!$F1 2271
6 TraesCS6B01G340200 chr1B 492777028 492781072 4044 True 6732 6732 96.714 1 4044 1 chr1B.!!$R1 4043
7 TraesCS6B01G340200 chr7B 130591086 130595124 4038 True 6538 6538 95.876 1 4044 1 chr7B.!!$R1 4043
8 TraesCS6B01G340200 chr7B 201424531 201428560 4029 True 6204 6204 94.443 1 4044 1 chr7B.!!$R2 4043
9 TraesCS6B01G340200 chr2B 67261075 67265164 4089 False 6303 6303 94.676 1 4044 1 chr2B.!!$F1 4043
10 TraesCS6B01G340200 chr2B 626144995 626148089 3094 False 4335 4335 91.879 895 4042 1 chr2B.!!$F2 3147
11 TraesCS6B01G340200 chr4B 382409414 382413447 4033 False 6157 6157 94.222 1 4044 1 chr4B.!!$F2 4043
12 TraesCS6B01G340200 chr4B 187384594 187386065 1471 False 2442 2442 96.606 2572 4044 1 chr4B.!!$F1 1472
13 TraesCS6B01G340200 chr4B 539956433 539957700 1267 False 1925 1925 94.044 753 2025 1 chr4B.!!$F3 1272
14 TraesCS6B01G340200 chr4A 740394894 740397206 2312 False 3439 3439 93.547 1727 4044 1 chr4A.!!$F1 2317
15 TraesCS6B01G340200 chr1D 10795887 10797896 2009 False 3217 3217 95.581 1 2009 1 chr1D.!!$F1 2008
16 TraesCS6B01G340200 chr1D 58471147 58472746 1599 False 2313 2313 93.146 2480 4044 1 chr1D.!!$F2 1564
17 TraesCS6B01G340200 chr4D 65868075 65870084 2009 False 3195 3195 95.380 1 2009 1 chr4D.!!$F1 2008
18 TraesCS6B01G340200 chr7D 30318586 30320590 2004 True 3175 3175 95.233 1 2009 1 chr7D.!!$R1 2008
19 TraesCS6B01G340200 chr7D 34186295 34188351 2056 False 3057 3057 93.662 2005 4044 1 chr7D.!!$F1 2039
20 TraesCS6B01G340200 chr5D 424141266 424143319 2053 True 3000 3000 93.162 2005 4044 1 chr5D.!!$R1 2039

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
882 886 1.118838 TGCCAAACACAAAAGGAGGG 58.881 50.0 0.00 0.00 0.00 4.30 F
1263 1270 0.610232 AATTGGACCCAGCAGCTGTC 60.610 55.0 21.26 12.62 0.00 3.51 F
2902 3058 0.878523 TGTTCGCACTGCTTAACGCT 60.879 50.0 0.00 0.00 40.11 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1726 0.033504 TCGAAGGGTCACAGAAGCAC 59.966 55.000 0.00 0.0 0.00 4.40 R
2969 3125 1.064758 GGTGACCCAGTCATATGCCAA 60.065 52.381 0.05 0.0 44.63 4.52 R
3857 4048 1.153524 ATCCTGCCCAGTTGCACAA 59.846 52.632 0.00 0.0 36.04 3.33 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
148 149 4.082125 CCTTTCCTGTGCCAGATTTTAGT 58.918 43.478 4.00 0.00 32.44 2.24
338 341 1.473257 CGGCAAGAGTAAGGCAGCATA 60.473 52.381 0.00 0.00 0.00 3.14
367 370 1.472662 CCCTCACGTGGTCCAGAAGT 61.473 60.000 17.00 0.00 0.00 3.01
454 457 5.333645 GCAGATGCTGAAGTAAATATGGTCG 60.334 44.000 0.00 0.00 38.21 4.79
605 609 1.963515 GATTGTCAAGTTTGCCAGGGT 59.036 47.619 0.00 0.00 0.00 4.34
619 623 1.203050 CCAGGGTCACAAAGGTGGAAT 60.203 52.381 0.00 0.00 45.32 3.01
683 687 1.601419 GCCACAGCCATTGATGCAGT 61.601 55.000 0.00 0.00 0.00 4.40
751 755 2.224523 CCAACCACAGATACCAGTGTGT 60.225 50.000 2.10 0.00 42.17 3.72
882 886 1.118838 TGCCAAACACAAAAGGAGGG 58.881 50.000 0.00 0.00 0.00 4.30
917 921 4.344865 GCCGTCCCCAAGAGCCAA 62.345 66.667 0.00 0.00 0.00 4.52
920 924 1.228124 CGTCCCCAAGAGCCAACAA 60.228 57.895 0.00 0.00 0.00 2.83
922 926 1.632589 GTCCCCAAGAGCCAACAAAT 58.367 50.000 0.00 0.00 0.00 2.32
1218 1225 1.608283 GCAGTAGAAACAGCGGAAGGT 60.608 52.381 0.00 0.00 46.81 3.50
1245 1252 7.549134 GGTGTGATTAGTATTGATGAGTGTGAA 59.451 37.037 0.00 0.00 0.00 3.18
1263 1270 0.610232 AATTGGACCCAGCAGCTGTC 60.610 55.000 21.26 12.62 0.00 3.51
1355 1362 2.504032 CCACACCCCGATATGCGT 59.496 61.111 0.00 0.00 38.67 5.24
1408 1415 2.420129 GGACCACCTATTGCACGAAGAT 60.420 50.000 0.00 0.00 0.00 2.40
1562 1572 4.880120 TGAAGGAGCAAATGATGAAGCTAG 59.120 41.667 0.00 0.00 37.48 3.42
1585 1595 3.326880 CAGGTAAACTAACTCCCCACAGT 59.673 47.826 0.00 0.00 0.00 3.55
1711 1724 9.073368 TGTTTTTCAATTTCATGCACATTTTTG 57.927 25.926 0.00 0.00 0.00 2.44
1713 1726 8.616377 TTTTCAATTTCATGCACATTTTTGTG 57.384 26.923 0.00 1.80 42.32 3.33
1743 1756 2.367567 TGACCCTTCGAGCTAACTTGTT 59.632 45.455 0.00 0.00 0.00 2.83
2270 2302 6.457528 GCTTTTTCTTAGCTACAGCCTGTATG 60.458 42.308 4.77 1.37 43.38 2.39
2297 2330 3.625313 TCTGAAATCGTTCACACTTGCAA 59.375 39.130 0.00 0.00 38.88 4.08
2417 2477 4.090761 AGTTCTTGATTCAAGCAGGACA 57.909 40.909 19.53 0.85 40.84 4.02
2669 2731 5.478679 AGACACAGTACTAGTCTGCAATCTT 59.521 40.000 22.45 3.69 40.83 2.40
2738 2844 1.203052 GTGGCACATAAGCAGTTGCAT 59.797 47.619 13.86 0.00 44.52 3.96
2784 2934 2.083774 GGCACATAAGCAGTTGCACTA 58.916 47.619 6.90 0.00 45.16 2.74
2902 3058 0.878523 TGTTCGCACTGCTTAACGCT 60.879 50.000 0.00 0.00 40.11 5.07
2969 3125 6.426646 AAGTACTCAACATCAGGAAGAAGT 57.573 37.500 0.00 0.00 0.00 3.01
3374 3563 7.137490 TGTCTCAAAGCTACAAATGATGAAG 57.863 36.000 0.00 0.00 0.00 3.02
3857 4048 0.523072 CGCAACTAGGCAGCATGTTT 59.477 50.000 0.00 0.00 39.31 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.140325 TCGGCAAATCCTTGTCTTTCT 57.860 42.857 0.00 0.00 34.84 2.52
148 149 6.155049 TGATCTTCTCACACATATCTTGGTCA 59.845 38.462 0.00 0.00 0.00 4.02
317 320 1.079127 GCTGCCTTACTCTTGCCGA 60.079 57.895 0.00 0.00 0.00 5.54
338 341 1.150536 ACGTGAGGGTTTGCCATGT 59.849 52.632 0.00 0.00 36.17 3.21
367 370 7.566760 TCTTCTTCATTGAAACTGCTTTACA 57.433 32.000 0.01 0.00 0.00 2.41
474 477 4.408182 ACTCACTACAGTTGGCATATCC 57.592 45.455 0.00 0.00 0.00 2.59
605 609 1.707989 TGGCCTATTCCACCTTTGTGA 59.292 47.619 3.32 0.00 45.76 3.58
619 623 1.710816 CCCAAACCTTTTGTGGCCTA 58.289 50.000 3.32 0.00 0.00 3.93
683 687 0.036732 CCTAGCAGAAGTTGGCACCA 59.963 55.000 0.00 0.00 0.00 4.17
692 696 0.321919 TGGCAGCAACCTAGCAGAAG 60.322 55.000 0.00 0.00 36.85 2.85
882 886 1.683385 GGCAATTTGGTAGCAGGATCC 59.317 52.381 2.48 2.48 0.00 3.36
917 921 1.067354 GCTTGCTTGGCTGCTATTTGT 60.067 47.619 0.00 0.00 0.00 2.83
920 924 0.324091 AGGCTTGCTTGGCTGCTATT 60.324 50.000 0.00 0.00 41.44 1.73
922 926 2.759114 AGGCTTGCTTGGCTGCTA 59.241 55.556 0.00 0.00 41.44 3.49
1202 1209 1.053424 ACCACCTTCCGCTGTTTCTA 58.947 50.000 0.00 0.00 0.00 2.10
1218 1225 6.818142 CACACTCATCAATACTAATCACACCA 59.182 38.462 0.00 0.00 0.00 4.17
1245 1252 1.001641 GACAGCTGCTGGGTCCAAT 60.002 57.895 31.00 10.38 35.51 3.16
1263 1270 0.248498 CAGCAGCGCATCCTTCATTG 60.248 55.000 11.47 0.00 0.00 2.82
1373 1380 1.070758 GTGGTCCTGAAGAACTGCTCA 59.929 52.381 0.00 0.00 31.28 4.26
1408 1415 2.492196 CGGGCCTTATTACCCTCCTCTA 60.492 54.545 0.84 0.00 44.63 2.43
1562 1572 2.039348 TGTGGGGAGTTAGTTTACCTGC 59.961 50.000 0.00 0.00 0.00 4.85
1585 1595 9.665719 TGCAACTGAAAAAGATATGTATGTAGA 57.334 29.630 0.00 0.00 0.00 2.59
1711 1724 1.230324 GAAGGGTCACAGAAGCACAC 58.770 55.000 0.00 0.00 0.00 3.82
1713 1726 0.033504 TCGAAGGGTCACAGAAGCAC 59.966 55.000 0.00 0.00 0.00 4.40
1761 1781 9.547279 ACCTGATTATCTTAGGGTTGAATTTTT 57.453 29.630 4.03 0.00 35.89 1.94
1764 1784 9.799106 CATACCTGATTATCTTAGGGTTGAATT 57.201 33.333 4.03 0.00 35.89 2.17
1770 1791 6.390504 TCACCATACCTGATTATCTTAGGGT 58.609 40.000 4.03 2.69 35.89 4.34
2417 2477 6.070596 TGGTCATCAACTCAATGTCATCTAGT 60.071 38.462 0.00 0.00 0.00 2.57
2738 2844 2.083774 GCAACTGCTTATGTGCCACTA 58.916 47.619 0.00 0.00 38.21 2.74
2784 2934 6.600822 ACTCTGTGCAAATGCTTATGTTCTAT 59.399 34.615 6.97 0.00 42.66 1.98
2969 3125 1.064758 GGTGACCCAGTCATATGCCAA 60.065 52.381 0.05 0.00 44.63 4.52
3065 3222 1.340017 GCAACTACCTCCATGGAGCAA 60.340 52.381 32.97 21.83 40.69 3.91
3360 3549 9.376075 ACTGTGATTCTACTTCATCATTTGTAG 57.624 33.333 0.00 0.00 32.07 2.74
3374 3563 4.440802 CCACTCAGGCTACTGTGATTCTAC 60.441 50.000 13.04 0.00 45.14 2.59
3657 3847 2.620115 CTGTGTGGTTGCAGAGAACATT 59.380 45.455 0.00 0.00 34.87 2.71
3857 4048 1.153524 ATCCTGCCCAGTTGCACAA 59.846 52.632 0.00 0.00 36.04 3.33


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

AutoCloner maintained by Alex Coulton.