Multiple sequence alignment - TraesCS6B01G155600

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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 TraesCS6B01G155600 chr6B 100.000 4148 0 0 1 4148 158190915 158186768 0.000000e+00 7661.0
1 TraesCS6B01G155600 chr6B 84.100 2761 316 59 740 3474 159390215 159392878 0.000000e+00 2553.0
2 TraesCS6B01G155600 chr6B 83.704 1976 309 10 1039 3006 156740946 156738976 0.000000e+00 1853.0
3 TraesCS6B01G155600 chr6B 83.434 1986 306 18 1039 3014 157027356 157025384 0.000000e+00 1823.0
4 TraesCS6B01G155600 chr6B 77.723 2249 446 50 1043 3264 157765875 157763655 0.000000e+00 1327.0
5 TraesCS6B01G155600 chr6B 75.114 1969 435 48 1031 2977 159395978 159397913 0.000000e+00 870.0
6 TraesCS6B01G155600 chr6B 88.344 652 52 11 10 642 159377027 159377673 0.000000e+00 761.0
7 TraesCS6B01G155600 chr6D 97.833 4153 71 10 1 4148 83206241 83202103 0.000000e+00 7153.0
8 TraesCS6B01G155600 chr6D 81.241 2095 373 13 1062 3149 83020766 83018685 0.000000e+00 1674.0
9 TraesCS6B01G155600 chr6D 75.997 2333 503 46 1078 3385 83108444 83106144 0.000000e+00 1153.0
10 TraesCS6B01G155600 chr6D 94.767 172 7 1 3490 3659 206560445 206560274 2.460000e-67 267.0
11 TraesCS6B01G155600 chr6D 81.875 160 23 5 811 970 83524863 83525016 3.370000e-26 130.0
12 TraesCS6B01G155600 chr6A 87.859 3138 340 28 357 3474 100364091 100360975 0.000000e+00 3646.0
13 TraesCS6B01G155600 chr6A 85.285 2759 336 39 752 3480 100357519 100354801 0.000000e+00 2782.0
14 TraesCS6B01G155600 chr6A 87.218 1815 194 25 740 2537 100742921 100744714 0.000000e+00 2032.0
15 TraesCS6B01G155600 chr6A 81.970 1980 348 7 1039 3012 98256385 98254409 0.000000e+00 1670.0
16 TraesCS6B01G155600 chr6A 74.589 2310 503 61 727 2992 100229192 100226923 0.000000e+00 937.0
17 TraesCS6B01G155600 chr6A 89.141 396 35 6 250 642 100737539 100737929 1.730000e-133 486.0
18 TraesCS6B01G155600 chr6A 95.495 111 5 0 4038 4148 100354194 100354084 1.180000e-40 178.0
19 TraesCS6B01G155600 chr6A 81.250 160 24 5 811 970 100755003 100755156 1.570000e-24 124.0
20 TraesCS6B01G155600 chr6A 94.118 68 1 1 4084 4148 100360732 100360665 2.640000e-17 100.0
21 TraesCS6B01G155600 chr6A 93.548 62 4 0 3983 4044 100354272 100354211 4.420000e-15 93.5
22 TraesCS6B01G155600 chr2A 96.970 165 5 0 3497 3661 310407936 310408100 1.140000e-70 278.0
23 TraesCS6B01G155600 chr2A 92.021 188 8 5 3474 3659 744795916 744796098 1.480000e-64 257.0
24 TraesCS6B01G155600 chr5B 96.970 165 3 1 3497 3659 521152512 521152676 4.080000e-70 276.0
25 TraesCS6B01G155600 chr4A 95.322 171 6 1 3496 3664 362068076 362067906 1.900000e-68 270.0
26 TraesCS6B01G155600 chr1D 95.833 168 5 1 3494 3659 178466303 178466470 1.900000e-68 270.0
27 TraesCS6B01G155600 chr3A 92.857 182 10 2 3494 3672 671642911 671642730 1.140000e-65 261.0
28 TraesCS6B01G155600 chr3D 92.391 184 11 2 3497 3678 4171281 4171099 4.110000e-65 259.0
29 TraesCS6B01G155600 chrUn 86.076 158 19 3 3824 3980 262705553 262705398 2.560000e-37 167.0
30 TraesCS6B01G155600 chr4D 85.443 158 20 3 3824 3980 197922289 197922134 1.190000e-35 161.0
31 TraesCS6B01G155600 chr2B 85.065 154 21 2 3824 3976 600089739 600089891 5.550000e-34 156.0
32 TraesCS6B01G155600 chr2B 83.234 167 26 2 3824 3989 795598329 795598494 7.180000e-33 152.0
33 TraesCS6B01G155600 chr7D 84.277 159 23 2 3824 3981 23526222 23526379 2.000000e-33 154.0
34 TraesCS6B01G155600 chr7D 84.177 158 20 5 3824 3978 92227931 92227776 9.290000e-32 148.0
35 TraesCS6B01G155600 chr7A 84.416 154 22 2 3824 3976 134553768 134553920 2.580000e-32 150.0
36 TraesCS6B01G155600 chr5A 84.076 157 19 5 3824 3977 46367413 46367566 3.340000e-31 147.0


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 TraesCS6B01G155600 chr6B 158186768 158190915 4147 True 7661.0 7661 100.000 1 4148 1 chr6B.!!$R4 4147
1 TraesCS6B01G155600 chr6B 156738976 156740946 1970 True 1853.0 1853 83.704 1039 3006 1 chr6B.!!$R1 1967
2 TraesCS6B01G155600 chr6B 157025384 157027356 1972 True 1823.0 1823 83.434 1039 3014 1 chr6B.!!$R2 1975
3 TraesCS6B01G155600 chr6B 159390215 159397913 7698 False 1711.5 2553 79.607 740 3474 2 chr6B.!!$F2 2734
4 TraesCS6B01G155600 chr6B 157763655 157765875 2220 True 1327.0 1327 77.723 1043 3264 1 chr6B.!!$R3 2221
5 TraesCS6B01G155600 chr6B 159377027 159377673 646 False 761.0 761 88.344 10 642 1 chr6B.!!$F1 632
6 TraesCS6B01G155600 chr6D 83202103 83206241 4138 True 7153.0 7153 97.833 1 4148 1 chr6D.!!$R3 4147
7 TraesCS6B01G155600 chr6D 83018685 83020766 2081 True 1674.0 1674 81.241 1062 3149 1 chr6D.!!$R1 2087
8 TraesCS6B01G155600 chr6D 83106144 83108444 2300 True 1153.0 1153 75.997 1078 3385 1 chr6D.!!$R2 2307
9 TraesCS6B01G155600 chr6A 100742921 100744714 1793 False 2032.0 2032 87.218 740 2537 1 chr6A.!!$F2 1797
10 TraesCS6B01G155600 chr6A 98254409 98256385 1976 True 1670.0 1670 81.970 1039 3012 1 chr6A.!!$R1 1973
11 TraesCS6B01G155600 chr6A 100354084 100364091 10007 True 1359.9 3646 91.261 357 4148 5 chr6A.!!$R3 3791
12 TraesCS6B01G155600 chr6A 100226923 100229192 2269 True 937.0 937 74.589 727 2992 1 chr6A.!!$R2 2265

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
474 498 2.224042 GCTTTTTGTTCAGTCTTGGGGG 60.224 50.000 0.0 0.0 0.00 5.40 F
1020 1072 1.083806 TGCAGCCGCTTAGTCATTCG 61.084 55.000 0.0 0.0 39.64 3.34 F
2797 9044 1.611673 CCCAGTCGATTTGCAACCTCT 60.612 52.381 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1653 2.759985 ACCGTGAAGGATGGTGAGT 58.240 52.632 0.0 0.0 42.98 3.41 R
2797 9044 0.394938 TCTAGCACCCGCAACTTTGA 59.605 50.000 0.0 0.0 42.27 2.69 R
3829 10394 2.968675 AGCGTATTTTAAGAGCCACGT 58.031 42.857 0.0 0.0 0.00 4.49 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
48 49 5.660864 TCCCAAAAGAAAAATTGACCACTCT 59.339 36.000 0.00 0.00 0.00 3.24
79 80 7.719193 TGATCAATGACAGAAACAACTAGGAAA 59.281 33.333 0.00 0.00 0.00 3.13
147 157 3.251487 GCTGGCATGAAATTGCAGTTTTT 59.749 39.130 8.72 0.00 44.59 1.94
149 159 5.122711 GCTGGCATGAAATTGCAGTTTTTAT 59.877 36.000 8.72 4.42 44.59 1.40
186 204 3.557595 GCAAGTCTAGAATCCCACGAATG 59.442 47.826 0.00 0.00 0.00 2.67
193 211 3.274288 AGAATCCCACGAATGAAAGAGC 58.726 45.455 0.00 0.00 0.00 4.09
200 218 4.253685 CCACGAATGAAAGAGCTCCTTAA 58.746 43.478 10.93 0.00 34.00 1.85
234 252 3.648545 GGCCCTATAGAGGTTCTGTTGAT 59.351 47.826 2.04 0.00 41.95 2.57
474 498 2.224042 GCTTTTTGTTCAGTCTTGGGGG 60.224 50.000 0.00 0.00 0.00 5.40
515 539 4.043750 CACCACTTGTTTGTTATGCACAG 58.956 43.478 0.00 0.00 36.48 3.66
528 552 6.234920 TGTTATGCACAGTTAGGTAACATGT 58.765 36.000 0.00 0.00 38.62 3.21
531 555 4.709250 TGCACAGTTAGGTAACATGTCAA 58.291 39.130 0.00 0.00 38.62 3.18
1020 1072 1.083806 TGCAGCCGCTTAGTCATTCG 61.084 55.000 0.00 0.00 39.64 3.34
2797 9044 1.611673 CCCAGTCGATTTGCAACCTCT 60.612 52.381 0.00 0.00 0.00 3.69
3096 9343 4.614993 GCAATTGCCTTTAGTGCGTTCTTA 60.615 41.667 20.06 0.00 34.31 2.10
3151 9405 4.297299 TCGAGGTATTTTGGCTAGTACG 57.703 45.455 0.00 0.00 0.00 3.67
3152 9406 3.696051 TCGAGGTATTTTGGCTAGTACGT 59.304 43.478 0.00 0.00 0.00 3.57
3153 9407 4.881273 TCGAGGTATTTTGGCTAGTACGTA 59.119 41.667 0.00 0.00 0.00 3.57
3154 9408 4.972440 CGAGGTATTTTGGCTAGTACGTAC 59.028 45.833 18.10 18.10 0.00 3.67
3163 9417 6.910536 TTGGCTAGTACGTACTACTCTAAC 57.089 41.667 27.51 15.41 36.95 2.34
3487 9764 9.625747 TGCTGAACATTGAATAATATTACCTCA 57.374 29.630 0.00 1.50 0.00 3.86
3615 10176 7.330946 TCATTTTTCTCCGTATGTAGTCACTTG 59.669 37.037 0.00 0.00 0.00 3.16
3622 10183 5.693104 TCCGTATGTAGTCACTTGTTGAAAC 59.307 40.000 0.00 0.00 35.39 2.78
3692 10253 4.957684 ATTTCTAGATACAACGGAGGGG 57.042 45.455 0.00 0.00 0.00 4.79
3752 10317 4.299155 ACGAGTAACACTTGAGTCATGTG 58.701 43.478 28.41 28.41 42.61 3.21
3850 10415 3.332034 ACGTGGCTCTTAAAATACGCTT 58.668 40.909 0.00 0.00 35.17 4.68
3870 10435 7.143340 ACGCTTATTAGTGTGCTATAAATCGA 58.857 34.615 0.00 0.00 43.27 3.59
3931 10496 5.627499 TTTAGCGAGACATTGCTCAAAAT 57.373 34.783 0.00 0.00 43.03 1.82
3976 10541 3.428870 GCTATAGCGCGCTATTTCTTTCA 59.571 43.478 46.76 30.62 39.65 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.935828 GGAACTGTCCTAGACATTTGAGC 59.064 47.826 5.21 0.00 41.94 4.26
48 49 6.992123 AGTTGTTTCTGTCATTGATCAGTGTA 59.008 34.615 16.80 7.68 33.89 2.90
79 80 6.976934 ACCTATGTTTTCATGTGGACTTTT 57.023 33.333 0.00 0.00 41.09 2.27
84 85 5.505780 CCCTTACCTATGTTTTCATGTGGA 58.494 41.667 0.00 0.00 41.09 4.02
186 204 6.560253 TGAACACAATTAAGGAGCTCTTTC 57.440 37.500 15.17 0.00 36.93 2.62
193 211 4.381932 GGGCCAATGAACACAATTAAGGAG 60.382 45.833 4.39 0.00 0.00 3.69
200 218 5.380043 CTCTATAGGGCCAATGAACACAAT 58.620 41.667 6.18 0.00 0.00 2.71
1571 1629 8.903820 AGTTATTGCAGAAATAAGTTGGTATCC 58.096 33.333 0.00 0.00 40.14 2.59
1595 1653 2.759985 ACCGTGAAGGATGGTGAGT 58.240 52.632 0.00 0.00 42.98 3.41
2797 9044 0.394938 TCTAGCACCCGCAACTTTGA 59.605 50.000 0.00 0.00 42.27 2.69
3096 9343 1.204146 CATACAGCACCCCTACACCT 58.796 55.000 0.00 0.00 0.00 4.00
3163 9417 7.246674 AGTTGGCAATAAACAGATATGTACG 57.753 36.000 1.92 0.00 0.00 3.67
3395 9671 8.050778 TGTTCTGAAAAGATTTACACACAGTT 57.949 30.769 0.00 0.00 0.00 3.16
3487 9764 5.607171 AGGAACGGAGGGAGTAATTCATTAT 59.393 40.000 0.00 0.00 0.00 1.28
3488 9765 4.966805 AGGAACGGAGGGAGTAATTCATTA 59.033 41.667 0.00 0.00 0.00 1.90
3491 9768 2.829023 AGGAACGGAGGGAGTAATTCA 58.171 47.619 0.00 0.00 0.00 2.57
3596 10157 4.763279 TCAACAAGTGACTACATACGGAGA 59.237 41.667 0.00 0.00 0.00 3.71
3692 10253 3.206150 CATGGCTCCAGTGTTATGTACC 58.794 50.000 0.00 0.00 0.00 3.34
3829 10394 2.968675 AGCGTATTTTAAGAGCCACGT 58.031 42.857 0.00 0.00 0.00 4.49
3846 10411 7.562640 TCGATTTATAGCACACTAATAAGCG 57.437 36.000 0.00 0.00 36.65 4.68
3931 10496 3.733988 GCCGCTAATAGCACGATATAGCA 60.734 47.826 13.15 0.00 42.58 3.49
3976 10541 5.528043 TTGTGTGATGTATTTTTGGCAGT 57.472 34.783 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.