Multiple sequence alignment - TraesCS6D01G124800

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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 TraesCS6D01G124800 chr6D 100.000 4424 0 0 1 4424 89160337 89164760 0.000000e+00 8170.0
1 TraesCS6D01G124800 chr6D 83.359 649 107 1 2759 3406 89066700 89067348 2.280000e-167 599.0
2 TraesCS6D01G124800 chr6D 76.482 995 208 20 1695 2676 89065663 89066644 6.560000e-143 518.0
3 TraesCS6D01G124800 chr6D 77.387 597 119 14 2814 3402 89306055 89306643 1.520000e-89 340.0
4 TraesCS6D01G124800 chr6D 77.955 440 89 6 2910 3345 89302921 89303356 7.290000e-68 268.0
5 TraesCS6D01G124800 chr6D 77.955 440 89 6 2910 3345 89304501 89304936 7.290000e-68 268.0
6 TraesCS6D01G124800 chr6A 96.041 2450 71 6 1 2429 107247101 107249545 0.000000e+00 3964.0
7 TraesCS6D01G124800 chr6A 94.524 767 15 6 2418 3177 107250752 107251498 0.000000e+00 1158.0
8 TraesCS6D01G124800 chr6A 95.878 655 15 6 3167 3818 107252704 107253349 0.000000e+00 1050.0
9 TraesCS6D01G124800 chr6A 83.821 649 103 2 2759 3406 107212596 107213243 2.260000e-172 616.0
10 TraesCS6D01G124800 chr6A 89.254 456 36 4 3905 4350 107267228 107267680 3.860000e-155 558.0
11 TraesCS6D01G124800 chr6A 76.281 995 213 19 1695 2676 107211556 107212540 3.950000e-140 508.0
12 TraesCS6D01G124800 chr6A 74.003 627 131 22 2754 3373 107271623 107272224 4.450000e-55 226.0
13 TraesCS6D01G124800 chr6A 89.103 156 16 1 3216 3371 107273265 107273419 4.520000e-45 193.0
14 TraesCS6D01G124800 chr6A 94.048 84 5 0 4341 4424 107267706 107267789 1.290000e-25 128.0
15 TraesCS6D01G124800 chr6B 94.194 1688 57 11 1 1654 171186765 171188445 0.000000e+00 2536.0
16 TraesCS6D01G124800 chr6B 97.806 1094 23 1 1637 2729 171189840 171190933 0.000000e+00 1886.0
17 TraesCS6D01G124800 chr6B 95.258 717 17 6 3715 4424 171200518 171201224 0.000000e+00 1120.0
18 TraesCS6D01G124800 chr6B 97.671 644 15 0 2758 3401 171198150 171198793 0.000000e+00 1107.0
19 TraesCS6D01G124800 chr6B 96.491 342 8 3 3388 3728 171199142 171199480 2.990000e-156 562.0
20 TraesCS6D01G124800 chr6B 90.909 55 5 0 3683 3737 70745752 70745806 1.710000e-09 75.0
21 TraesCS6D01G124800 chr6B 95.122 41 2 0 3683 3723 661073236 661073196 1.030000e-06 65.8
22 TraesCS6D01G124800 chr7D 86.478 318 31 4 3957 4262 218390794 218390477 5.480000e-89 339.0
23 TraesCS6D01G124800 chr5B 86.076 316 34 4 3957 4262 9654928 9654613 9.170000e-87 331.0
24 TraesCS6D01G124800 chr5B 84.345 313 41 5 3957 4262 702897646 702897957 2.590000e-77 300.0
25 TraesCS6D01G124800 chr5A 85.804 317 34 3 3957 4262 40085650 40085334 4.270000e-85 326.0
26 TraesCS6D01G124800 chr5A 85.804 317 34 3 3957 4262 484812306 484812622 4.270000e-85 326.0
27 TraesCS6D01G124800 chr1B 85.804 317 34 3 3957 4262 320783082 320782766 4.270000e-85 326.0
28 TraesCS6D01G124800 chr1B 84.326 319 37 6 3957 4262 365470550 365470232 2.590000e-77 300.0
29 TraesCS6D01G124800 chr1B 72.340 846 206 24 1816 2647 660466141 660466972 1.590000e-59 241.0
30 TraesCS6D01G124800 chr4B 84.858 317 37 3 3957 4262 43674746 43675062 4.300000e-80 309.0
31 TraesCS6D01G124800 chrUn 77.955 440 89 6 2910 3345 325919287 325918852 7.290000e-68 268.0
32 TraesCS6D01G124800 chr2B 100.000 38 0 0 3685 3722 29050832 29050795 2.210000e-08 71.3
33 TraesCS6D01G124800 chr2B 91.837 49 3 1 3683 3730 474544357 474544309 2.860000e-07 67.6
34 TraesCS6D01G124800 chr7A 90.000 50 5 0 3679 3728 63382141 63382190 1.030000e-06 65.8
35 TraesCS6D01G124800 chr2A 95.122 41 1 1 3685 3724 66844931 66844891 3.690000e-06 63.9
36 TraesCS6D01G124800 chr2D 100.000 32 0 0 3692 3723 476797481 476797450 4.780000e-05 60.2


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 TraesCS6D01G124800 chr6D 89160337 89164760 4423 False 8170.000000 8170 100.000000 1 4424 1 chr6D.!!$F1 4423
1 TraesCS6D01G124800 chr6D 89065663 89067348 1685 False 558.500000 599 79.920500 1695 3406 2 chr6D.!!$F2 1711
2 TraesCS6D01G124800 chr6D 89302921 89306643 3722 False 292.000000 340 77.765667 2814 3402 3 chr6D.!!$F3 588
3 TraesCS6D01G124800 chr6A 107247101 107253349 6248 False 2057.333333 3964 95.481000 1 3818 3 chr6A.!!$F2 3817
4 TraesCS6D01G124800 chr6A 107211556 107213243 1687 False 562.000000 616 80.051000 1695 3406 2 chr6A.!!$F1 1711
5 TraesCS6D01G124800 chr6A 107267228 107273419 6191 False 276.250000 558 86.602000 2754 4424 4 chr6A.!!$F3 1670
6 TraesCS6D01G124800 chr6B 171186765 171190933 4168 False 2211.000000 2536 96.000000 1 2729 2 chr6B.!!$F2 2728
7 TraesCS6D01G124800 chr6B 171198150 171201224 3074 False 929.666667 1120 96.473333 2758 4424 3 chr6B.!!$F3 1666
8 TraesCS6D01G124800 chr1B 660466141 660466972 831 False 241.000000 241 72.340000 1816 2647 1 chr1B.!!$F1 831

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
573 578 0.475048 TCCTCGGGGGAAAAAGGAGT 60.475 55.000 0.0 0.0 41.91 3.85 F
1209 1248 1.693083 GCCATGTTACCGCACTCGAC 61.693 60.000 0.0 0.0 38.10 4.20 F
1221 1260 2.029623 GCACTCGACCTATCCTGGTTA 58.970 52.381 0.0 0.0 41.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2648 5329 1.863454 CTGGCGTTGTCTCTATCATGC 59.137 52.381 0.00 0.0 0.0 4.06 R
3165 6422 4.168922 TGCAGAACTTGAATCATGCTTG 57.831 40.909 7.21 0.0 34.8 4.01 R
3480 9493 6.598753 TCCGCTGCATATAAAGTAAAAGTC 57.401 37.500 0.00 0.0 0.0 3.01 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
169 171 9.299963 CTAATTCCTATATGCTTCTTCATCTCG 57.700 37.037 0.00 0.00 0.00 4.04
294 299 4.396166 ACAGCGCTGTTGCTTAATTAAGAT 59.604 37.500 36.44 8.78 44.46 2.40
333 338 4.279659 CGACTTTTTGGAAGTTCCTTTCG 58.720 43.478 22.41 15.39 37.46 3.46
506 511 1.296715 GCGGTCACTCCCATTGACT 59.703 57.895 2.73 0.00 42.63 3.41
573 578 0.475048 TCCTCGGGGGAAAAAGGAGT 60.475 55.000 0.00 0.00 41.91 3.85
578 583 2.109304 TCGGGGGAAAAAGGAGTTTCAT 59.891 45.455 0.61 0.00 38.93 2.57
656 661 3.630312 GGTGACTTGGCTTTCTGTTAACA 59.370 43.478 8.28 8.28 0.00 2.41
689 694 6.704050 TCATTCACCACAACCACATATATACG 59.296 38.462 0.00 0.00 0.00 3.06
698 703 2.230508 CCACATATATACGTGGCCGTCT 59.769 50.000 14.61 0.00 46.28 4.18
859 883 5.380043 CTGACCCATTCTACTATTGCCAAT 58.620 41.667 0.00 0.00 0.00 3.16
1158 1197 3.017323 CATGCCGAATCGACCTGC 58.983 61.111 3.36 0.00 0.00 4.85
1159 1198 1.815003 CATGCCGAATCGACCTGCA 60.815 57.895 3.36 5.40 36.23 4.41
1181 1220 3.041940 GTTCGGCGTCACCTGTGG 61.042 66.667 6.85 0.00 35.61 4.17
1209 1248 1.693083 GCCATGTTACCGCACTCGAC 61.693 60.000 0.00 0.00 38.10 4.20
1221 1260 2.029623 GCACTCGACCTATCCTGGTTA 58.970 52.381 0.00 0.00 41.00 2.85
1260 1299 2.818274 GCCTTGTACTTCCCGGCG 60.818 66.667 0.00 0.00 0.00 6.46
2784 5472 2.484889 GACATAATCTGGAAGGGACGC 58.515 52.381 0.00 0.00 0.00 5.19
2843 6100 5.316167 TGGTATTGATCTGTCAAGCAACTT 58.684 37.500 0.00 0.00 46.75 2.66
3499 9514 9.490663 CTTTTCCGACTTTTACTTTATATGCAG 57.509 33.333 0.00 0.00 0.00 4.41
3959 11027 3.960102 TCATTGCAGACTTTTGGAGGTTT 59.040 39.130 0.00 0.00 0.00 3.27
3961 11029 4.817318 TTGCAGACTTTTGGAGGTTTTT 57.183 36.364 0.00 0.00 0.00 1.94
4028 11100 7.665145 TCTTCAAGTCAATGAACACCATATGAA 59.335 33.333 3.65 0.00 35.55 2.57
4029 11101 7.381766 TCAAGTCAATGAACACCATATGAAG 57.618 36.000 3.65 0.00 34.45 3.02
4030 11102 6.375174 TCAAGTCAATGAACACCATATGAAGG 59.625 38.462 3.65 0.00 34.45 3.46
4031 11103 4.641989 AGTCAATGAACACCATATGAAGGC 59.358 41.667 3.65 0.00 34.45 4.35
4050 11122 4.040755 AGGCCCTTCTTTTGCTCTCTATA 58.959 43.478 0.00 0.00 0.00 1.31
4051 11123 4.662650 AGGCCCTTCTTTTGCTCTCTATAT 59.337 41.667 0.00 0.00 0.00 0.86
4099 11171 0.108992 TGACTTACATGGTCGACCGC 60.109 55.000 28.70 7.51 39.43 5.68
4150 11222 7.857734 TGTCACACTTGTCATTCTTCTTAAA 57.142 32.000 0.00 0.00 0.00 1.52
4162 11234 6.876789 TCATTCTTCTTAAACGGTGCTCAATA 59.123 34.615 0.00 0.00 0.00 1.90
4171 11243 2.166664 ACGGTGCTCAATAACTCTCTCC 59.833 50.000 0.00 0.00 0.00 3.71
4172 11244 2.482142 CGGTGCTCAATAACTCTCTCCC 60.482 54.545 0.00 0.00 0.00 4.30
4173 11245 2.158885 GGTGCTCAATAACTCTCTCCCC 60.159 54.545 0.00 0.00 0.00 4.81
4174 11246 2.119495 TGCTCAATAACTCTCTCCCCC 58.881 52.381 0.00 0.00 0.00 5.40
4177 11249 2.103941 CTCAATAACTCTCTCCCCCAGC 59.896 54.545 0.00 0.00 0.00 4.85
4183 11255 1.211456 CTCTCTCCCCCAGCTTCATT 58.789 55.000 0.00 0.00 0.00 2.57
4209 11281 5.001237 TGGCTCATCAACTTAATTGCATG 57.999 39.130 0.00 0.00 38.29 4.06
4267 11339 9.950496 AAGATTGGTATTAATATACTCAGCCAG 57.050 33.333 0.00 0.00 37.39 4.85
4339 11411 6.267699 TCTGAGACCTCTTCACAACTTAATGA 59.732 38.462 0.00 0.00 0.00 2.57
4382 11456 1.743321 CTCAGACTCCTGGATCCGCC 61.743 65.000 7.39 0.00 40.76 6.13
4383 11457 1.760086 CAGACTCCTGGATCCGCCT 60.760 63.158 7.39 0.00 36.77 5.52
4417 11491 6.959871 GCATGCTAGTATCATCAAATGAATCG 59.040 38.462 11.37 0.00 43.50 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 171 2.464157 ACCTGCTGTGCTTCTAGAAC 57.536 50.000 0.00 0.00 0.00 3.01
294 299 6.385649 AAAGTCGCAAAGGAAAGTGATAAA 57.614 33.333 0.00 0.00 0.00 1.40
333 338 3.611766 AAGTAGTATCACAGGCCACAC 57.388 47.619 5.01 0.00 0.00 3.82
506 511 3.793797 TGTGTCACGAAAGAGAAGTCA 57.206 42.857 0.00 0.00 31.00 3.41
573 578 2.259917 TCTGGGAGCTGACTGATGAAA 58.740 47.619 0.00 0.00 0.00 2.69
578 583 3.386078 GTCAATATCTGGGAGCTGACTGA 59.614 47.826 0.00 0.00 32.36 3.41
656 661 3.495100 GGTTGTGGTGAATGAGACTGTCT 60.495 47.826 10.66 10.66 0.00 3.41
689 694 0.037326 TGAATGAGACAGACGGCCAC 60.037 55.000 2.24 0.00 0.00 5.01
698 703 4.206477 CAGTATGGTGGTGAATGAGACA 57.794 45.455 0.00 0.00 0.00 3.41
859 883 5.770663 GGAGGTCATTAGTCAGCAGTATAGA 59.229 44.000 0.00 0.00 0.00 1.98
1158 1197 1.209127 GGTGACGCCGAACCAATTG 59.791 57.895 8.49 0.00 36.41 2.32
1159 1198 1.072505 AGGTGACGCCGAACCAATT 59.927 52.632 14.36 0.00 43.70 2.32
1183 1222 2.833533 CGGTAACATGGCCGGCATG 61.834 63.158 30.85 28.31 43.85 4.06
1209 1248 4.392940 CATTGAGGCTTAACCAGGATAGG 58.607 47.826 0.00 0.00 43.14 2.57
1260 1299 0.872388 GTGTGGTGATGTTCCGGAAC 59.128 55.000 35.49 35.49 41.50 3.62
2648 5329 1.863454 CTGGCGTTGTCTCTATCATGC 59.137 52.381 0.00 0.00 0.00 4.06
2739 5427 7.555195 TCCATCTGACCATCATATGAATAATGC 59.445 37.037 9.99 0.00 34.15 3.56
2946 6203 6.625873 AGAGACTCCACATTTTTCAAACTC 57.374 37.500 0.00 0.00 0.00 3.01
3165 6422 4.168922 TGCAGAACTTGAATCATGCTTG 57.831 40.909 7.21 0.00 34.80 4.01
3480 9493 6.598753 TCCGCTGCATATAAAGTAAAAGTC 57.401 37.500 0.00 0.00 0.00 3.01
3499 9514 6.238211 GCCATGAACAATACATCTATATCCGC 60.238 42.308 0.00 0.00 0.00 5.54
3959 11027 2.229792 GTCATGTGGTGAGCCTTGAAA 58.770 47.619 0.00 0.00 37.56 2.69
3961 11029 0.764271 TGTCATGTGGTGAGCCTTGA 59.236 50.000 0.00 0.00 37.56 3.02
4028 11100 1.071434 AGAGAGCAAAAGAAGGGCCT 58.929 50.000 0.00 0.00 0.00 5.19
4029 11101 2.789409 TAGAGAGCAAAAGAAGGGCC 57.211 50.000 0.00 0.00 0.00 5.80
4030 11102 5.863965 AGATATAGAGAGCAAAAGAAGGGC 58.136 41.667 0.00 0.00 0.00 5.19
4031 11103 7.301868 AGAGATATAGAGAGCAAAAGAAGGG 57.698 40.000 0.00 0.00 0.00 3.95
4050 11122 6.161855 TGATACGGCAACTTATGAAGAGAT 57.838 37.500 0.00 0.00 29.94 2.75
4051 11123 5.592104 TGATACGGCAACTTATGAAGAGA 57.408 39.130 0.00 0.00 29.94 3.10
4132 11204 5.277828 GCACCGTTTAAGAAGAATGACAAGT 60.278 40.000 0.00 0.00 0.00 3.16
4150 11222 2.166664 GGAGAGAGTTATTGAGCACCGT 59.833 50.000 0.00 0.00 0.00 4.83
4162 11234 0.178891 TGAAGCTGGGGGAGAGAGTT 60.179 55.000 0.00 0.00 0.00 3.01
4171 11243 1.035139 GCCATACAATGAAGCTGGGG 58.965 55.000 0.00 0.00 0.00 4.96
4172 11244 1.952296 GAGCCATACAATGAAGCTGGG 59.048 52.381 0.00 0.00 32.97 4.45
4173 11245 2.646930 TGAGCCATACAATGAAGCTGG 58.353 47.619 0.00 0.00 32.97 4.85
4174 11246 3.881089 TGATGAGCCATACAATGAAGCTG 59.119 43.478 0.00 0.00 32.97 4.24
4177 11249 6.446781 AAGTTGATGAGCCATACAATGAAG 57.553 37.500 0.00 0.00 0.00 3.02
4183 11255 5.651576 TGCAATTAAGTTGATGAGCCATACA 59.348 36.000 0.00 0.00 40.37 2.29
4223 11295 7.041107 CCAATCTTCAAGAACAAGGTTCAAAA 58.959 34.615 11.28 2.42 0.00 2.44
4271 11343 9.923143 GGCTACTAAACTTTTCAACCATATTTT 57.077 29.630 0.00 0.00 0.00 1.82
4339 11411 4.591072 GTCAGAGAGGCCCTAATTGTATCT 59.409 45.833 0.00 0.00 0.00 1.98
4382 11456 4.329801 TGATACTAGCATGCGTTTTGTGAG 59.670 41.667 13.01 3.55 0.00 3.51
4383 11457 4.249661 TGATACTAGCATGCGTTTTGTGA 58.750 39.130 13.01 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.