Multiple sequence alignment - TraesCS6D01G323100

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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 TraesCS6D01G323100 chr6D 100.000 3380 0 0 1 3380 429896383 429893004 0.000000e+00 6242.0
1 TraesCS6D01G323100 chr6D 94.180 2440 103 14 943 3380 429946164 429943762 0.000000e+00 3683.0
2 TraesCS6D01G323100 chr6D 95.737 1431 60 1 933 2363 430365657 430364228 0.000000e+00 2303.0
3 TraesCS6D01G323100 chr6D 95.497 955 37 3 2429 3380 430364221 430363270 0.000000e+00 1520.0
4 TraesCS6D01G323100 chr6D 95.793 927 36 3 1 925 460305885 460306810 0.000000e+00 1493.0
5 TraesCS6D01G323100 chr6D 91.234 308 24 3 2753 3059 430369886 430369581 1.880000e-112 416.0
6 TraesCS6D01G323100 chr6D 93.522 247 16 0 1986 2232 430245022 430245268 5.330000e-98 368.0
7 TraesCS6D01G323100 chr6D 96.429 56 2 0 3091 3146 297302297 297302242 3.590000e-15 93.5
8 TraesCS6D01G323100 chr6B 92.947 2155 128 10 944 3091 648258222 648256085 0.000000e+00 3116.0
9 TraesCS6D01G323100 chr6B 87.324 213 23 2 3172 3380 695148719 695148507 1.210000e-59 241.0
10 TraesCS6D01G323100 chr6B 87.081 209 23 2 3176 3380 523014279 523014487 2.030000e-57 233.0
11 TraesCS6D01G323100 chr5B 88.099 1773 147 31 952 2692 609845674 609843934 0.000000e+00 2047.0
12 TraesCS6D01G323100 chr5B 79.143 537 97 10 1659 2189 489313170 489312643 1.150000e-94 357.0
13 TraesCS6D01G323100 chr5B 93.333 60 2 1 3095 3154 450383793 450383736 1.670000e-13 87.9
14 TraesCS6D01G323100 chr2D 95.905 928 33 5 1 925 486303808 486304733 0.000000e+00 1498.0
15 TraesCS6D01G323100 chr2D 95.685 927 37 3 1 925 70390998 70391923 0.000000e+00 1487.0
16 TraesCS6D01G323100 chr2D 95.038 927 40 5 1 925 623949395 623950317 0.000000e+00 1452.0
17 TraesCS6D01G323100 chr2D 96.429 56 2 0 3092 3147 404040033 404040088 3.590000e-15 93.5
18 TraesCS6D01G323100 chr1D 95.587 929 37 3 1 925 426586244 426585316 0.000000e+00 1485.0
19 TraesCS6D01G323100 chr1D 86.603 209 24 3 3176 3380 408537529 408537737 9.430000e-56 228.0
20 TraesCS6D01G323100 chr7D 95.264 929 38 6 1 925 114467390 114468316 0.000000e+00 1467.0
21 TraesCS6D01G323100 chr7D 86.124 209 25 2 3176 3380 45706930 45707138 4.390000e-54 222.0
22 TraesCS6D01G323100 chr7D 96.364 55 2 0 3092 3146 254906992 254907046 1.290000e-14 91.6
23 TraesCS6D01G323100 chr3D 95.269 930 36 8 1 925 214958781 214959707 0.000000e+00 1467.0
24 TraesCS6D01G323100 chr3D 95.043 928 42 4 1 925 460502718 460501792 0.000000e+00 1456.0
25 TraesCS6D01G323100 chr3D 94.962 933 37 9 1 925 191558535 191557605 0.000000e+00 1454.0
26 TraesCS6D01G323100 chr5A 79.182 538 95 12 1659 2189 513869855 513869328 1.150000e-94 357.0
27 TraesCS6D01G323100 chr5D 78.439 538 99 11 1659 2189 407988379 407987852 5.400000e-88 335.0
28 TraesCS6D01G323100 chr5D 89.474 209 18 3 3176 3380 520857861 520857653 9.300000e-66 261.0
29 TraesCS6D01G323100 chr5D 94.828 58 3 0 3095 3152 29498158 29498215 1.290000e-14 91.6
30 TraesCS6D01G323100 chr5D 92.063 63 4 1 3091 3153 242626974 242627035 1.670000e-13 87.9
31 TraesCS6D01G323100 chr2A 88.152 211 19 3 3174 3380 744426004 744425796 2.600000e-61 246.0
32 TraesCS6D01G323100 chr2A 96.429 56 2 0 3092 3147 542385050 542385105 3.590000e-15 93.5
33 TraesCS6D01G323100 chr4B 87.560 209 22 3 3176 3380 438599662 438599870 4.360000e-59 239.0


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 TraesCS6D01G323100 chr6D 429893004 429896383 3379 True 6242 6242 100.000 1 3380 1 chr6D.!!$R2 3379
1 TraesCS6D01G323100 chr6D 429943762 429946164 2402 True 3683 3683 94.180 943 3380 1 chr6D.!!$R3 2437
2 TraesCS6D01G323100 chr6D 460305885 460306810 925 False 1493 1493 95.793 1 925 1 chr6D.!!$F2 924
3 TraesCS6D01G323100 chr6D 430363270 430369886 6616 True 1413 2303 94.156 933 3380 3 chr6D.!!$R4 2447
4 TraesCS6D01G323100 chr6B 648256085 648258222 2137 True 3116 3116 92.947 944 3091 1 chr6B.!!$R1 2147
5 TraesCS6D01G323100 chr5B 609843934 609845674 1740 True 2047 2047 88.099 952 2692 1 chr5B.!!$R3 1740
6 TraesCS6D01G323100 chr5B 489312643 489313170 527 True 357 357 79.143 1659 2189 1 chr5B.!!$R2 530
7 TraesCS6D01G323100 chr2D 486303808 486304733 925 False 1498 1498 95.905 1 925 1 chr2D.!!$F3 924
8 TraesCS6D01G323100 chr2D 70390998 70391923 925 False 1487 1487 95.685 1 925 1 chr2D.!!$F1 924
9 TraesCS6D01G323100 chr2D 623949395 623950317 922 False 1452 1452 95.038 1 925 1 chr2D.!!$F4 924
10 TraesCS6D01G323100 chr1D 426585316 426586244 928 True 1485 1485 95.587 1 925 1 chr1D.!!$R1 924
11 TraesCS6D01G323100 chr7D 114467390 114468316 926 False 1467 1467 95.264 1 925 1 chr7D.!!$F2 924
12 TraesCS6D01G323100 chr3D 214958781 214959707 926 False 1467 1467 95.269 1 925 1 chr3D.!!$F1 924
13 TraesCS6D01G323100 chr3D 460501792 460502718 926 True 1456 1456 95.043 1 925 1 chr3D.!!$R2 924
14 TraesCS6D01G323100 chr3D 191557605 191558535 930 True 1454 1454 94.962 1 925 1 chr3D.!!$R1 924
15 TraesCS6D01G323100 chr5A 513869328 513869855 527 True 357 357 79.182 1659 2189 1 chr5A.!!$R1 530
16 TraesCS6D01G323100 chr5D 407987852 407988379 527 True 335 335 78.439 1659 2189 1 chr5D.!!$R1 530

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
656 670 0.534877 TTCAGCGACATGGCAACTGT 60.535 50.000 16.12 0.0 34.64 3.55 F
926 943 1.523032 GATCCCTTAACGCCCACGG 60.523 63.158 0.00 0.0 46.04 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 4761 0.464870 TTGTCGACGGGGAGTTTCAA 59.535 50.0 11.62 0.0 0.0 2.69 R
2564 5920 1.021202 CTTCGAAGCCCAACAACACA 58.979 50.0 13.09 0.0 0.0 3.72 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
197 200 2.500714 CCAAGCTGCCAGTTGCCAA 61.501 57.895 0.00 0.00 40.16 4.52
299 308 6.432472 TGTCAGTTGCCATATGTTTTGTATGA 59.568 34.615 1.24 0.00 32.52 2.15
499 512 6.420903 GGCAACTCCTAAAGTTTTGAAATCAC 59.579 38.462 0.00 0.00 46.26 3.06
656 670 0.534877 TTCAGCGACATGGCAACTGT 60.535 50.000 16.12 0.00 34.64 3.55
770 785 4.347453 GACGTACCGGGCGTGTGT 62.347 66.667 26.63 7.33 43.04 3.72
869 886 2.337170 CCCACACACAGACGCGTA 59.663 61.111 13.97 0.00 0.00 4.42
926 943 1.523032 GATCCCTTAACGCCCACGG 60.523 63.158 0.00 0.00 46.04 4.94
927 944 3.692370 ATCCCTTAACGCCCACGGC 62.692 63.158 0.00 0.00 46.75 5.68
1163 4465 2.819595 CAACTCCGGCGGACCATG 60.820 66.667 27.46 19.42 34.57 3.66
1167 4469 4.077184 TCCGGCGGACCATGTCAC 62.077 66.667 27.46 0.00 33.68 3.67
1491 4793 3.119096 GACAAGGAGAACGCGCCC 61.119 66.667 5.73 2.14 34.01 6.13
1980 5294 0.896940 AGGGCTTCGTCGACAAGGTA 60.897 55.000 17.16 0.00 0.00 3.08
1983 5297 1.458445 GGCTTCGTCGACAAGGTAAAC 59.542 52.381 17.16 5.36 0.00 2.01
1984 5298 1.123756 GCTTCGTCGACAAGGTAAACG 59.876 52.381 17.16 0.00 34.80 3.60
2291 5608 1.677966 CTGCAAGCTGGAGCCACAT 60.678 57.895 0.00 0.00 43.38 3.21
2314 5631 1.734465 CGAAGAAGGCCATGAGTGAAC 59.266 52.381 5.01 0.00 0.00 3.18
2388 5707 5.389778 TCAGCGCATAATTAAACACTTGTG 58.610 37.500 11.47 0.00 0.00 3.33
2389 5708 5.049060 TCAGCGCATAATTAAACACTTGTGT 60.049 36.000 11.47 0.00 0.00 3.72
2405 5724 7.334090 ACACTTGTGTCATGAATAATCTAGCT 58.666 34.615 0.00 0.00 0.00 3.32
2406 5725 8.478066 ACACTTGTGTCATGAATAATCTAGCTA 58.522 33.333 0.00 0.00 0.00 3.32
2432 5779 6.039941 GCTAGCTAGTTTCCATTGTCTCTAGA 59.960 42.308 21.62 0.00 0.00 2.43
2463 5813 7.224557 GTGTTTTCTTCTTTTGTGTGCCATATT 59.775 33.333 0.00 0.00 0.00 1.28
2658 6014 2.472909 CCCGCGGAGGCTTGATTTC 61.473 63.158 30.73 0.00 39.21 2.17
2661 6017 1.709147 CGCGGAGGCTTGATTTCCTG 61.709 60.000 0.00 0.00 36.88 3.86
2705 6061 7.226720 CACATAACTAAGACACTTCACTTGGTT 59.773 37.037 0.00 0.00 44.98 3.67
2720 6090 3.181418 ACTTGGTTCCCAACAATCATCCT 60.181 43.478 0.00 0.00 38.75 3.24
2725 6095 5.431731 TGGTTCCCAACAATCATCCTAGTAT 59.568 40.000 0.00 0.00 0.00 2.12
2967 6337 0.606401 CACAACCTCCCGACATTGCT 60.606 55.000 0.00 0.00 0.00 3.91
2984 6354 1.004277 GCTGACGTGAGGTGTTCGAG 61.004 60.000 3.66 0.00 0.00 4.04
3135 6507 7.287696 ACAAAGTTGAGTCACTTATTTTGGGAT 59.712 33.333 12.94 0.00 35.87 3.85
3142 6514 5.044179 AGTCACTTATTTTGGGATGGATGGA 60.044 40.000 0.00 0.00 0.00 3.41
3212 6584 3.102515 CGCTATATAAGTGCCGCGT 57.897 52.632 4.92 0.00 36.28 6.01
3234 6606 4.555747 GTCGCAAATATGTGGTTTTTACCG 59.444 41.667 0.00 0.00 37.65 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.389106 GAACTGCTAAACGCCTACACG 59.611 52.381 0.00 0.00 38.05 4.49
197 200 1.806542 CCATCTACACTGCAAAACGCT 59.193 47.619 0.00 0.00 43.06 5.07
499 512 1.005037 TGGTCTACTGCAGTTGCCG 60.005 57.895 27.06 11.40 41.18 5.69
620 634 3.792401 CTGAACTACGGTTGCCATATCA 58.208 45.455 0.00 0.00 35.58 2.15
623 637 1.737696 CGCTGAACTACGGTTGCCATA 60.738 52.381 0.00 0.00 35.58 2.74
656 670 4.487948 CCTCGTCCATGTTCGTTTAAGTA 58.512 43.478 6.65 0.00 0.00 2.24
925 942 8.287503 CGGTTGTACTAATAAATTTAGGATGCC 58.712 37.037 3.94 0.00 0.00 4.40
926 943 8.833493 ACGGTTGTACTAATAAATTTAGGATGC 58.167 33.333 3.94 0.00 0.00 3.91
1242 4544 4.988598 AGCCGTGCCAGGAACGTG 62.989 66.667 19.34 11.27 39.38 4.49
1245 4547 4.373116 TCGAGCCGTGCCAGGAAC 62.373 66.667 0.00 0.00 0.00 3.62
1335 4637 2.084681 CAGGAACGCGTCGTACACC 61.085 63.158 14.44 9.66 39.99 4.16
1459 4761 0.464870 TTGTCGACGGGGAGTTTCAA 59.535 50.000 11.62 0.00 0.00 2.69
2370 5689 8.741101 TTCATGACACAAGTGTTTAATTATGC 57.259 30.769 7.35 0.00 45.05 3.14
2388 5707 7.985634 GCTAGCTAGCTAGATTATTCATGAC 57.014 40.000 42.59 23.01 46.56 3.06
2405 5724 5.894393 AGAGACAATGGAAACTAGCTAGCTA 59.106 40.000 22.85 22.85 0.00 3.32
2406 5725 4.714308 AGAGACAATGGAAACTAGCTAGCT 59.286 41.667 23.12 23.12 0.00 3.32
2432 5779 7.297391 GCACACAAAAGAAGAAAACACAAATT 58.703 30.769 0.00 0.00 0.00 1.82
2548 5901 6.985188 ACAACACAGTGTCCATGATATAAC 57.015 37.500 6.67 0.00 0.00 1.89
2564 5920 1.021202 CTTCGAAGCCCAACAACACA 58.979 50.000 13.09 0.00 0.00 3.72
2658 6014 2.357009 GCAAGTACTGATCATTGGCAGG 59.643 50.000 0.00 0.00 36.47 4.85
2661 6017 2.749076 TGTGCAAGTACTGATCATTGGC 59.251 45.455 0.00 2.91 0.00 4.52
2705 6061 4.350816 CCCATACTAGGATGATTGTTGGGA 59.649 45.833 17.12 0.00 43.21 4.37
2720 6090 5.361857 GCTAGTAAGGTTGACACCCATACTA 59.638 44.000 12.05 12.05 45.63 1.82
2725 6095 1.626825 GGCTAGTAAGGTTGACACCCA 59.373 52.381 0.00 0.00 45.63 4.51
2875 6245 7.415229 GTTGTTAAGTTATGGATTTCGATCCC 58.585 38.462 2.62 0.00 39.99 3.85
2918 6288 3.422796 GGTCAAGAGACAGTGACTAGGA 58.577 50.000 0.00 0.00 46.80 2.94
2967 6337 1.026584 TTCTCGAACACCTCACGTCA 58.973 50.000 0.00 0.00 0.00 4.35
2984 6354 2.415776 CAACCATGCACCATTGGTTTC 58.584 47.619 17.80 1.69 42.12 2.78
3099 6471 9.880157 AAGTGACTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
3135 6507 5.211973 GCCAGATATATCCTACTCCATCCA 58.788 45.833 9.18 0.00 0.00 3.41
3142 6514 8.884323 TCTCAAATTTGCCAGATATATCCTACT 58.116 33.333 13.54 0.00 0.00 2.57
3212 6584 4.724303 CGGTAAAAACCACATATTTGCGA 58.276 39.130 0.00 0.00 0.00 5.10
3283 6655 0.525761 TTGCGCTGAACCCTTTATGC 59.474 50.000 9.73 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.