Multiple sequence alignment - TraesCS6B01G166900

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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 TraesCS6B01G166900 chr6B 100.000 3573 0 0 1 3573 174952312 174955884 0.000000e+00 6599.0
1 TraesCS6B01G166900 chr6B 94.618 3623 145 11 1 3573 671090889 671087267 0.000000e+00 5565.0
2 TraesCS6B01G166900 chr6B 94.569 2799 98 13 1 2746 635286992 635284195 0.000000e+00 4277.0
3 TraesCS6B01G166900 chr3B 95.739 3614 113 13 1 3573 478634070 478637683 0.000000e+00 5782.0
4 TraesCS6B01G166900 chr3B 95.334 3622 117 16 1 3573 259907600 259903982 0.000000e+00 5705.0
5 TraesCS6B01G166900 chr3B 94.826 3614 143 6 1 3573 532661310 532657700 0.000000e+00 5598.0
6 TraesCS6B01G166900 chr3B 94.621 2863 100 13 1 2816 499184242 499181387 0.000000e+00 4385.0
7 TraesCS6B01G166900 chr3B 93.774 1799 74 10 1801 3573 37294501 37296287 0.000000e+00 2667.0
8 TraesCS6B01G166900 chr3B 77.570 321 39 17 2583 2900 453197076 453197366 2.850000e-36 163.0
9 TraesCS6B01G166900 chr3B 97.222 36 1 0 2605 2640 85115409 85115374 1.070000e-05 62.1
10 TraesCS6B01G166900 chr1B 95.133 3616 130 16 1 3573 631847717 631844105 0.000000e+00 5661.0
11 TraesCS6B01G166900 chr1B 94.454 3318 130 11 297 3573 507392423 507389119 0.000000e+00 5059.0
12 TraesCS6B01G166900 chr1B 94.336 3178 109 24 1 3130 551874155 551877309 0.000000e+00 4806.0
13 TraesCS6B01G166900 chr1B 93.980 3173 121 17 1 3126 670668994 670665845 0.000000e+00 4737.0
14 TraesCS6B01G166900 chr7B 95.030 3622 125 9 1 3573 708528169 708524554 0.000000e+00 5640.0
15 TraesCS6B01G166900 chr7B 94.353 3170 110 22 1 3123 33886907 33890054 0.000000e+00 4798.0
16 TraesCS6B01G166900 chr4B 94.992 3614 136 14 1 3573 638687826 638691435 0.000000e+00 5629.0
17 TraesCS6B01G166900 chr4B 94.632 3614 147 15 1 3573 414230124 414233731 0.000000e+00 5555.0
18 TraesCS6B01G166900 chr4B 95.882 510 18 1 1 507 648180164 648180673 0.000000e+00 822.0
19 TraesCS6B01G166900 chr4A 94.776 3618 140 18 1 3573 740137219 740140832 0.000000e+00 5589.0
20 TraesCS6B01G166900 chr2B 94.369 3623 153 9 1 3573 56031031 56027410 0.000000e+00 5513.0
21 TraesCS6B01G166900 chr2B 94.303 3177 111 24 1 3130 9223250 9226403 0.000000e+00 4800.0
22 TraesCS6B01G166900 chr2B 94.822 2897 103 11 1 2850 166038652 166035756 0.000000e+00 4475.0
23 TraesCS6B01G166900 chr5B 95.455 2926 92 6 1 2885 520578579 520575654 0.000000e+00 4628.0
24 TraesCS6B01G166900 chr5B 94.118 663 19 7 1 643 516273633 516274295 0.000000e+00 990.0


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 TraesCS6B01G166900 chr6B 174952312 174955884 3572 False 6599 6599 100.000 1 3573 1 chr6B.!!$F1 3572
1 TraesCS6B01G166900 chr6B 671087267 671090889 3622 True 5565 5565 94.618 1 3573 1 chr6B.!!$R2 3572
2 TraesCS6B01G166900 chr6B 635284195 635286992 2797 True 4277 4277 94.569 1 2746 1 chr6B.!!$R1 2745
3 TraesCS6B01G166900 chr3B 478634070 478637683 3613 False 5782 5782 95.739 1 3573 1 chr3B.!!$F3 3572
4 TraesCS6B01G166900 chr3B 259903982 259907600 3618 True 5705 5705 95.334 1 3573 1 chr3B.!!$R2 3572
5 TraesCS6B01G166900 chr3B 532657700 532661310 3610 True 5598 5598 94.826 1 3573 1 chr3B.!!$R4 3572
6 TraesCS6B01G166900 chr3B 499181387 499184242 2855 True 4385 4385 94.621 1 2816 1 chr3B.!!$R3 2815
7 TraesCS6B01G166900 chr3B 37294501 37296287 1786 False 2667 2667 93.774 1801 3573 1 chr3B.!!$F1 1772
8 TraesCS6B01G166900 chr1B 631844105 631847717 3612 True 5661 5661 95.133 1 3573 1 chr1B.!!$R2 3572
9 TraesCS6B01G166900 chr1B 507389119 507392423 3304 True 5059 5059 94.454 297 3573 1 chr1B.!!$R1 3276
10 TraesCS6B01G166900 chr1B 551874155 551877309 3154 False 4806 4806 94.336 1 3130 1 chr1B.!!$F1 3129
11 TraesCS6B01G166900 chr1B 670665845 670668994 3149 True 4737 4737 93.980 1 3126 1 chr1B.!!$R3 3125
12 TraesCS6B01G166900 chr7B 708524554 708528169 3615 True 5640 5640 95.030 1 3573 1 chr7B.!!$R1 3572
13 TraesCS6B01G166900 chr7B 33886907 33890054 3147 False 4798 4798 94.353 1 3123 1 chr7B.!!$F1 3122
14 TraesCS6B01G166900 chr4B 638687826 638691435 3609 False 5629 5629 94.992 1 3573 1 chr4B.!!$F2 3572
15 TraesCS6B01G166900 chr4B 414230124 414233731 3607 False 5555 5555 94.632 1 3573 1 chr4B.!!$F1 3572
16 TraesCS6B01G166900 chr4B 648180164 648180673 509 False 822 822 95.882 1 507 1 chr4B.!!$F3 506
17 TraesCS6B01G166900 chr4A 740137219 740140832 3613 False 5589 5589 94.776 1 3573 1 chr4A.!!$F1 3572
18 TraesCS6B01G166900 chr2B 56027410 56031031 3621 True 5513 5513 94.369 1 3573 1 chr2B.!!$R1 3572
19 TraesCS6B01G166900 chr2B 9223250 9226403 3153 False 4800 4800 94.303 1 3130 1 chr2B.!!$F1 3129
20 TraesCS6B01G166900 chr2B 166035756 166038652 2896 True 4475 4475 94.822 1 2850 1 chr2B.!!$R2 2849
21 TraesCS6B01G166900 chr5B 520575654 520578579 2925 True 4628 4628 95.455 1 2885 1 chr5B.!!$R1 2884
22 TraesCS6B01G166900 chr5B 516273633 516274295 662 False 990 990 94.118 1 643 1 chr5B.!!$F1 642

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
227 229 1.019278 CCCGTGGATTCTGTTGGTCG 61.019 60.0 0.0 0.0 0.0 4.79 F
1226 1250 0.606401 CCTCAACCCGATGTGCTTGT 60.606 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2045 0.899019 TGGCCTGACGCTGTAACATA 59.101 50.000 3.32 0.0 37.74 2.29 R
2869 2986 1.079405 TACAGTGCAGCGCCTAACC 60.079 57.895 2.29 0.0 0.00 2.85 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
80 82 6.162777 GCCTTTAGTTGAAATTTACATGCCA 58.837 36.000 0.00 0.00 0.00 4.92
166 168 1.609239 TGGTCCTGCCATGCCTTAG 59.391 57.895 0.00 0.00 43.61 2.18
195 197 1.985334 TACACACCGTACATCAAGCG 58.015 50.000 0.00 0.00 0.00 4.68
227 229 1.019278 CCCGTGGATTCTGTTGGTCG 61.019 60.000 0.00 0.00 0.00 4.79
230 232 1.375396 TGGATTCTGTTGGTCGGCG 60.375 57.895 0.00 0.00 0.00 6.46
288 290 1.833630 TCTTGTTGATCGATGGAGGCT 59.166 47.619 0.54 0.00 0.00 4.58
315 317 2.359900 GCACAGTTTCCATCTTCGGAT 58.640 47.619 0.00 0.00 34.19 4.18
372 374 1.067212 GATCACCGGTCTTGCTATCGT 59.933 52.381 2.59 0.00 0.00 3.73
394 396 1.412361 GGGAGGCCTCTCTGTATGAGT 60.412 57.143 31.36 0.00 43.13 3.41
612 634 3.181514 CGTTGTGTCGAGGACTTTGTTTT 60.182 43.478 0.00 0.00 33.15 2.43
673 695 1.621107 GCGTTGACCGTCTTCGATAA 58.379 50.000 15.95 0.00 39.71 1.75
691 713 1.341080 AACAAATGGAGCTGGGGTTG 58.659 50.000 0.00 0.00 0.00 3.77
769 791 7.094075 ACTCATTTCTTCATTAGCAATGCAAGA 60.094 33.333 8.35 4.34 37.40 3.02
815 839 4.322080 TCTTTCATATGTAGCTGGACGG 57.678 45.455 1.90 0.00 0.00 4.79
859 883 1.550072 GTGCAGGCATTGGTGGTAATT 59.450 47.619 0.00 0.00 0.00 1.40
1084 1108 4.298626 TGAGCAGGTAAGGAGGTCATTAT 58.701 43.478 0.00 0.00 35.15 1.28
1189 1213 3.706373 GCGGGTGAGAGCTTGGGA 61.706 66.667 0.00 0.00 0.00 4.37
1226 1250 0.606401 CCTCAACCCGATGTGCTTGT 60.606 55.000 0.00 0.00 0.00 3.16
1275 1299 1.064463 CCCACTGATATGCAACTGGGT 60.064 52.381 0.00 0.00 38.75 4.51
1554 1578 1.364626 GCAAGCTCGTAGCACTGCAT 61.365 55.000 19.30 0.00 45.73 3.96
1618 1642 6.576185 ACTACGTACGATGGTTTATTGGAAT 58.424 36.000 24.41 0.00 0.00 3.01
1665 1689 7.217200 GCCGGCATATAATGAGGATATTCTTA 58.783 38.462 24.80 0.00 33.32 2.10
1809 1834 3.698539 TCCCGTTGACCGTATTACACATA 59.301 43.478 0.00 0.00 33.66 2.29
1818 1843 8.950208 TGACCGTATTACACATATTTGAATGA 57.050 30.769 0.00 0.00 0.00 2.57
2350 2380 3.457234 CGCATATGTGTTCAAGCCTAGA 58.543 45.455 8.16 0.00 0.00 2.43
2495 2543 2.266055 CGGAGGAGGAAGTGCACC 59.734 66.667 14.63 0.00 0.00 5.01
2976 3132 7.040478 GGCTTGCATCACATCCATAATACTTAA 60.040 37.037 0.00 0.00 0.00 1.85
3071 3227 8.780846 ATTCAAACATTACTACGACATGGTTA 57.219 30.769 0.00 0.00 0.00 2.85
3108 3264 3.181463 ACAAATGACAAATGGCAGCTTGT 60.181 39.130 15.36 15.36 37.88 3.16
3159 3315 1.878102 GCCCTCACAACTTCACGACAT 60.878 52.381 0.00 0.00 0.00 3.06
3369 3525 1.479573 CCGCTCCATCCTCTCCTTCTA 60.480 57.143 0.00 0.00 0.00 2.10
3390 3546 1.293498 GACGCTCTTCCTCCAAGCA 59.707 57.895 0.00 0.00 35.76 3.91
3447 3603 4.876107 CCTAAGACAATCTGCGTATTGGTT 59.124 41.667 13.52 9.50 40.48 3.67
3516 3672 1.982660 CATAGAGGAGGCGGTGACTA 58.017 55.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 110 3.409026 TCTTCAGAGGTTCAAGCTTCC 57.591 47.619 0.00 0.00 0.00 3.46
166 168 2.126189 GGTGTGTACCGCTCGTCC 60.126 66.667 0.00 0.00 37.19 4.79
230 232 2.511600 CAGATTCGGCGTGGACCC 60.512 66.667 6.85 0.00 0.00 4.46
288 290 0.396435 ATGGAAACTGTGCGTCTCCA 59.604 50.000 0.00 0.00 0.00 3.86
315 317 1.884075 CGTCACGGTCATCTCCCCAA 61.884 60.000 0.00 0.00 0.00 4.12
372 374 0.468214 CATACAGAGAGGCCTCCCGA 60.468 60.000 29.54 10.88 40.30 5.14
394 396 2.631062 ACGCCACCCATTAGAATCGATA 59.369 45.455 0.00 0.00 0.00 2.92
612 634 1.070758 GTTCTTGCCAGTGGAGTCAGA 59.929 52.381 15.20 4.63 0.00 3.27
673 695 0.482446 TCAACCCCAGCTCCATTTGT 59.518 50.000 0.00 0.00 0.00 2.83
691 713 1.067495 ACAAGTAGGCAAGAGTCGCTC 60.067 52.381 0.00 0.00 0.00 5.03
769 791 8.491331 AAAAACAATGTTAACTTGACAGCAAT 57.509 26.923 18.56 0.00 32.68 3.56
815 839 1.265095 CTGTGATCCTGCAACACACAC 59.735 52.381 10.22 7.38 39.17 3.82
859 883 5.046304 AGCTCCATACAGAAAGTAGAAGCAA 60.046 40.000 0.00 0.00 37.64 3.91
1084 1108 3.254166 GCAAGCATGAGAAAGGACTGAAA 59.746 43.478 0.00 0.00 0.00 2.69
1189 1213 1.673808 GGCGGAACTCCTCGGTGTAT 61.674 60.000 0.00 0.00 0.00 2.29
1226 1250 2.803285 AGCCAGAGATCCTTATCCCA 57.197 50.000 0.00 0.00 31.98 4.37
1275 1299 1.269517 GCGGCAAATGAAACTCAACCA 60.270 47.619 0.00 0.00 0.00 3.67
1618 1642 4.607955 CGGCAATATCTCAACTCGAGTAA 58.392 43.478 20.39 9.45 42.88 2.24
1665 1689 7.168905 AGATCCTCAAAGTTTACGGATTCTTT 58.831 34.615 15.28 0.00 34.77 2.52
1671 1695 4.464951 TGCTAGATCCTCAAAGTTTACGGA 59.535 41.667 7.32 7.32 0.00 4.69
1818 1843 6.992063 ATGAGAAAGAATGAATGCGTTAGT 57.008 33.333 0.00 0.00 0.00 2.24
2015 2045 0.899019 TGGCCTGACGCTGTAACATA 59.101 50.000 3.32 0.00 37.74 2.29
2071 2101 7.829706 CAGATGGTTCATCATATTCAGGATCAT 59.170 37.037 10.08 0.00 42.72 2.45
2495 2543 1.153667 GAGCACGAGCCTCCTCTTG 60.154 63.158 0.00 0.00 43.56 3.02
2547 2598 4.287781 TTCCGCGCGTGTTCCTGA 62.288 61.111 29.95 14.00 0.00 3.86
2869 2986 1.079405 TACAGTGCAGCGCCTAACC 60.079 57.895 2.29 0.00 0.00 2.85
2976 3132 1.201647 GCTGTGATGCTGCAGTCATTT 59.798 47.619 16.64 0.00 41.05 2.32
3071 3227 6.964908 TGTCATTTGTAATGAATGTGTCGTT 58.035 32.000 3.83 0.00 38.98 3.85
3108 3264 6.897966 AGATGTTGGTGAACTATCTTCTAGGA 59.102 38.462 0.00 0.00 31.42 2.94
3159 3315 8.833493 TCGTCGTCAACTATCTTCTAATGAATA 58.167 33.333 0.00 0.00 0.00 1.75
3369 3525 0.038159 CTTGGAGGAAGAGCGTCGTT 60.038 55.000 0.00 0.00 32.82 3.85
3412 3568 1.980232 TCTTAGGAGGCAACGGCGA 60.980 57.895 16.62 0.00 46.39 5.54
3447 3603 4.464008 AGTGCCAGAAGATGTGAAAAAGA 58.536 39.130 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.