Multiple sequence alignment - TraesCS4D01G109700

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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 TraesCS4D01G109700 chr4D 100.000 4360 0 0 1 4360 89418521 89422880 0 8052
1 TraesCS4D01G109700 chr4A 95.523 3440 112 17 869 4297 501958934 501962342 0 5461
2 TraesCS4D01G109700 chr4A 84.279 846 103 13 3 828 501958097 501958932 0 798
3 TraesCS4D01G109700 chr4B 94.055 3482 110 38 886 4360 126319782 126323173 0 5193
4 TraesCS4D01G109700 chr4B 93.953 893 53 1 3 894 126317649 126318541 0 1349


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 TraesCS4D01G109700 chr4D 89418521 89422880 4359 False 8052.0 8052 100.000 1 4360 1 chr4D.!!$F1 4359
1 TraesCS4D01G109700 chr4A 501958097 501962342 4245 False 3129.5 5461 89.901 3 4297 2 chr4A.!!$F1 4294
2 TraesCS4D01G109700 chr4B 126317649 126323173 5524 False 3271.0 5193 94.004 3 4360 2 chr4B.!!$F1 4357

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
21 22 0.035458 AAGGACTTGGACCAAGAGCG 59.965 55.0 35.69 14.64 43.42 5.03 F
82 83 0.105760 AACACCAATTCCCACTGGCA 60.106 50.0 0.00 0.00 36.03 4.92 F
479 486 0.179121 CGGAGCACGTGTTATGCCTA 60.179 55.0 18.38 0.00 44.53 3.93 F
1796 3075 0.033796 ACCCCGATTCCGTGAGTAGA 60.034 55.0 0.00 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 2829 0.322975 TCCACTGAAGCTGCTCCTTC 59.677 55.0 1.0 9.18 41.21 3.46 R
1772 3051 0.688487 TCACGGAATCGGGGTTTTCT 59.312 50.0 0.0 0.00 40.80 2.52 R
2276 3556 0.613777 AGCCCTTGTCCGAGGTAAAG 59.386 55.0 0.0 0.00 34.88 1.85 R
3560 4844 0.331278 TCACCCAGCCCTACCAATTG 59.669 55.0 0.0 0.00 0.00 2.32 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
21 22 0.035458 AAGGACTTGGACCAAGAGCG 59.965 55.000 35.69 14.64 43.42 5.03
82 83 0.105760 AACACCAATTCCCACTGGCA 60.106 50.000 0.00 0.00 36.03 4.92
101 102 2.095059 GCACTATGGAACTTGTTGGCTG 60.095 50.000 0.00 0.00 0.00 4.85
238 241 1.122019 AACCCCTCTGAAGTCGTGCT 61.122 55.000 0.00 0.00 0.00 4.40
257 261 3.060602 GCTCCCGCATCAAGTACTATTC 58.939 50.000 0.00 0.00 35.78 1.75
263 267 3.391049 GCATCAAGTACTATTCGGGGAC 58.609 50.000 0.00 0.00 0.00 4.46
288 292 1.336887 CGTCATGAAACGTGTCCTCCT 60.337 52.381 2.58 0.00 37.86 3.69
289 293 2.338500 GTCATGAAACGTGTCCTCCTC 58.662 52.381 2.58 0.00 0.00 3.71
290 294 1.275291 TCATGAAACGTGTCCTCCTCC 59.725 52.381 2.58 0.00 0.00 4.30
343 350 1.541310 CCAAGACCTAGGTGACGCCA 61.541 60.000 22.10 0.00 40.61 5.69
380 387 2.187946 CCATGCTCACGGAGACCC 59.812 66.667 5.24 0.00 0.00 4.46
467 474 1.154188 GACTGTCGAGTCGGAGCAC 60.154 63.158 13.54 3.80 39.44 4.40
469 476 2.967473 CTGTCGAGTCGGAGCACGT 61.967 63.158 13.54 0.00 44.69 4.49
479 486 0.179121 CGGAGCACGTGTTATGCCTA 60.179 55.000 18.38 0.00 44.53 3.93
482 489 3.724374 GGAGCACGTGTTATGCCTAATA 58.276 45.455 18.38 0.00 44.53 0.98
586 593 4.133820 CCTTCCATAATTGGTGCGACATA 58.866 43.478 0.00 0.00 44.06 2.29
605 612 4.142337 ACATATACAATGACGACGGTGACA 60.142 41.667 0.00 0.00 0.00 3.58
717 738 1.258982 GAAGCTGGTGCGATGAATACG 59.741 52.381 0.00 0.00 45.42 3.06
722 743 2.656897 CTGGTGCGATGAATACGTATCG 59.343 50.000 8.86 11.19 46.51 2.92
836 860 4.612264 TGTTAAGGGACTGGTGTCTAAC 57.388 45.455 0.00 0.00 40.86 2.34
848 872 2.620115 GGTGTCTAACCGATCATCCGTA 59.380 50.000 0.00 0.00 39.81 4.02
856 880 2.034685 ACCGATCATCCGTAGACATGTG 59.965 50.000 1.15 0.00 0.00 3.21
1269 2547 1.592223 CTTTTCCTCCGTCGAGCCT 59.408 57.895 0.00 0.00 34.49 4.58
1338 2616 3.387397 GCCTCCAATTGATTATGCTTGC 58.613 45.455 7.12 0.00 0.00 4.01
1496 2774 2.071540 CAAGTCGCAGAAATCTCAGCA 58.928 47.619 0.00 0.00 39.69 4.41
1560 2838 7.875971 ACTAAGTACAAAATTTGAAGGAGCAG 58.124 34.615 13.19 3.49 0.00 4.24
1575 2854 0.471617 AGCAGCTTCAGTGGAGTGTT 59.528 50.000 0.00 0.00 0.00 3.32
1607 2886 9.878667 TGATATAAATAAGAAACCTCGTGACAA 57.121 29.630 0.00 0.00 0.00 3.18
1663 2942 3.673484 CCGGCAAAGCACACTGGG 61.673 66.667 0.00 0.00 0.00 4.45
1743 3022 0.531200 AAGTAGTGCCCGAGCTGTAC 59.469 55.000 0.00 0.00 40.80 2.90
1796 3075 0.033796 ACCCCGATTCCGTGAGTAGA 60.034 55.000 0.00 0.00 0.00 2.59
1798 3077 1.687123 CCCCGATTCCGTGAGTAGAAT 59.313 52.381 0.00 0.00 35.43 2.40
1811 3090 5.277202 CGTGAGTAGAATGAGCCATTTCATG 60.277 44.000 2.53 0.00 37.83 3.07
1812 3091 5.587844 GTGAGTAGAATGAGCCATTTCATGT 59.412 40.000 0.00 0.00 37.83 3.21
1820 3099 3.896888 TGAGCCATTTCATGTTCCTGTTT 59.103 39.130 0.00 0.00 0.00 2.83
1822 3101 5.163322 TGAGCCATTTCATGTTCCTGTTTTT 60.163 36.000 0.00 0.00 0.00 1.94
1865 3145 3.266636 TCATTGTATCGCGTCATTTGGT 58.733 40.909 5.77 0.00 0.00 3.67
2276 3556 4.397417 AGCTCATACACAATCCTTTCAAGC 59.603 41.667 0.00 0.00 0.00 4.01
2308 3588 4.446311 GGACAAGGGCTATATGGTGAATGT 60.446 45.833 0.00 0.00 0.00 2.71
2448 3728 7.336679 TCTTTAGCACAAGCATGTAATATGTGT 59.663 33.333 14.96 8.31 45.49 3.72
2473 3753 4.225942 TCCAGGAGTGCTCTCACATTAATT 59.774 41.667 17.04 0.00 45.49 1.40
2600 3881 4.932200 ACCTCATAGTTTCTCGCTTGAAAG 59.068 41.667 1.98 0.00 36.72 2.62
2625 3906 9.193806 AGCAATGATTAACCTCATAGTTCAAAT 57.806 29.630 0.00 0.00 34.79 2.32
2679 3960 6.452494 AAGAGCATTCTTTGATTCTCATGG 57.548 37.500 0.00 0.00 40.79 3.66
2743 4024 1.208776 GGGCATTAACGTACCCAGTCT 59.791 52.381 0.00 0.00 42.33 3.24
3021 4303 2.158769 AGTTTCAGAGCACATGGACACA 60.159 45.455 0.00 0.00 0.00 3.72
3063 4345 5.659426 CGTTGTTTCAGTGATTTTTCATGC 58.341 37.500 0.00 0.00 0.00 4.06
3130 4412 2.146342 CAACGTGGACTGCTGAAGATT 58.854 47.619 0.00 0.00 0.00 2.40
3183 4465 1.220206 CAGAGATCGCCAAGGTGCT 59.780 57.895 0.00 0.00 0.00 4.40
3499 4782 2.571653 TGAATGGAGTGGGAACGATCTT 59.428 45.455 0.00 0.00 0.00 2.40
3523 4807 3.347216 GCAAGATGGTTAAGCCTGAAGA 58.653 45.455 1.51 0.00 38.35 2.87
3587 4871 1.973812 GGGCTGGGTGAAGAAGCAC 60.974 63.158 0.00 0.00 38.73 4.40
3739 5024 3.332919 GCCATCATCTAGTGCATACCAG 58.667 50.000 0.00 0.00 0.00 4.00
3757 5042 5.821516 ACCAGAAACGTGTTGATGTTAAA 57.178 34.783 0.00 0.00 30.69 1.52
3868 5154 5.577164 GTGCTAACTTGATATCACGAGTGTT 59.423 40.000 15.55 12.27 35.06 3.32
3869 5155 5.576774 TGCTAACTTGATATCACGAGTGTTG 59.423 40.000 15.55 7.84 35.06 3.33
3870 5156 4.928661 AACTTGATATCACGAGTGTTGC 57.071 40.909 15.55 0.00 35.06 4.17
3871 5157 4.193826 ACTTGATATCACGAGTGTTGCT 57.806 40.909 15.55 0.00 33.77 3.91
3872 5158 3.928992 ACTTGATATCACGAGTGTTGCTG 59.071 43.478 15.55 0.00 33.77 4.41
3873 5159 2.270923 TGATATCACGAGTGTTGCTGC 58.729 47.619 0.00 0.00 0.00 5.25
3874 5160 2.094026 TGATATCACGAGTGTTGCTGCT 60.094 45.455 0.00 0.00 0.00 4.24
3875 5161 1.713597 TATCACGAGTGTTGCTGCTG 58.286 50.000 0.00 0.00 0.00 4.41
3876 5162 1.572085 ATCACGAGTGTTGCTGCTGC 61.572 55.000 8.89 8.89 40.20 5.25
4060 5355 2.669391 GCTTGTTGGCTTGCTGTATGAC 60.669 50.000 0.00 0.00 0.00 3.06
4309 5604 5.106673 CCGTTTCCATTTGTAAGAGGAGAAC 60.107 44.000 0.00 0.00 0.00 3.01
4319 5614 3.778954 AAGAGGAGAACTTGACCCTTG 57.221 47.619 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.675317 CGCTCTTGGTCCAAGTCCTTAG 60.675 54.545 27.29 18.87 41.66 2.18
1 2 1.275291 CGCTCTTGGTCCAAGTCCTTA 59.725 52.381 27.29 10.13 41.66 2.69
21 22 1.219522 CGTCGTGGGTTGGAGTTGTC 61.220 60.000 0.00 0.00 0.00 3.18
66 67 1.072266 TAGTGCCAGTGGGAATTGGT 58.928 50.000 9.49 0.00 36.81 3.67
82 83 3.412386 GTCAGCCAACAAGTTCCATAGT 58.588 45.455 0.00 0.00 0.00 2.12
116 117 3.751246 CGACGGGGACAACGCCTA 61.751 66.667 0.00 0.00 45.32 3.93
166 169 1.589716 GGTGGTGAGCATTGGAGCAC 61.590 60.000 0.00 0.00 37.37 4.40
167 170 1.303561 GGTGGTGAGCATTGGAGCA 60.304 57.895 0.00 0.00 36.85 4.26
238 241 2.035449 CCGAATAGTACTTGATGCGGGA 59.965 50.000 15.03 0.00 40.14 5.14
279 283 0.898789 TCCAACGAGGAGGAGGACAC 60.899 60.000 0.00 0.00 43.07 3.67
290 294 2.105128 CGCTAGCCCTCCAACGAG 59.895 66.667 9.66 0.00 35.72 4.18
343 350 0.889186 GGTTTGCGAGGATGTGTGGT 60.889 55.000 0.00 0.00 0.00 4.16
479 486 4.513442 TGCATTAACTCGCCTCAGTTATT 58.487 39.130 0.00 0.00 38.40 1.40
482 489 2.472695 TGCATTAACTCGCCTCAGTT 57.527 45.000 0.00 0.00 39.94 3.16
495 502 2.239654 CCTCCTCCTCAACCTTGCATTA 59.760 50.000 0.00 0.00 0.00 1.90
586 593 3.306917 TTGTCACCGTCGTCATTGTAT 57.693 42.857 0.00 0.00 0.00 2.29
605 612 2.820330 CCACCAAACGCTTTTGTCATT 58.180 42.857 13.89 0.00 40.61 2.57
722 743 8.800031 TGCAAACTAACAAAATTTAACGAGTTC 58.200 29.630 8.20 1.19 0.00 3.01
836 860 2.666026 CACATGTCTACGGATGATCGG 58.334 52.381 0.00 0.00 0.00 4.18
848 872 6.332630 GCAAACCTTAAATATGCACATGTCT 58.667 36.000 0.00 0.00 37.00 3.41
856 880 3.862845 CCAACGGCAAACCTTAAATATGC 59.137 43.478 0.00 0.00 36.31 3.14
1338 2616 1.283793 CAAGCCAGTGCGAAACAGG 59.716 57.895 0.00 0.00 44.33 4.00
1496 2774 5.649831 AGAAGAAACTTCAGTTGCAGACTTT 59.350 36.000 12.86 0.00 38.44 2.66
1539 2817 4.829492 AGCTGCTCCTTCAAATTTTGTACT 59.171 37.500 8.89 0.00 0.00 2.73
1540 2818 5.126396 AGCTGCTCCTTCAAATTTTGTAC 57.874 39.130 8.89 0.00 0.00 2.90
1541 2819 5.301551 TGAAGCTGCTCCTTCAAATTTTGTA 59.698 36.000 14.47 0.00 45.88 2.41
1542 2820 4.099881 TGAAGCTGCTCCTTCAAATTTTGT 59.900 37.500 14.47 0.00 45.88 2.83
1543 2821 4.624015 TGAAGCTGCTCCTTCAAATTTTG 58.376 39.130 14.47 2.59 45.88 2.44
1544 2822 4.942761 TGAAGCTGCTCCTTCAAATTTT 57.057 36.364 14.47 0.00 45.88 1.82
1551 2829 0.322975 TCCACTGAAGCTGCTCCTTC 59.677 55.000 1.00 9.18 41.21 3.46
1560 2838 1.024271 TGCAAACACTCCACTGAAGC 58.976 50.000 0.00 0.00 0.00 3.86
1575 2854 8.826710 CGAGGTTTCTTATTTATATCAGTGCAA 58.173 33.333 0.00 0.00 0.00 4.08
1772 3051 0.688487 TCACGGAATCGGGGTTTTCT 59.312 50.000 0.00 0.00 40.80 2.52
1830 3109 6.202762 GCGATACAATGAACAGGAACATATCA 59.797 38.462 0.00 0.00 0.00 2.15
2276 3556 0.613777 AGCCCTTGTCCGAGGTAAAG 59.386 55.000 0.00 0.00 34.88 1.85
2308 3588 7.587629 CAAGAGCATCATTTTCACTTACAAGA 58.412 34.615 0.00 0.00 37.82 3.02
2448 3728 2.532250 TGTGAGAGCACTCCTGGATA 57.468 50.000 8.77 0.00 45.36 2.59
2600 3881 9.455847 GATTTGAACTATGAGGTTAATCATTGC 57.544 33.333 0.00 0.00 40.40 3.56
2625 3906 5.664294 ATAAGTTTGCATCAAATGGCTGA 57.336 34.783 0.00 0.00 35.74 4.26
2627 3908 7.011669 GCATAAATAAGTTTGCATCAAATGGCT 59.988 33.333 0.00 0.00 35.74 4.75
2679 3960 2.393271 ATACTGCAGGCAGACAAGTC 57.607 50.000 26.63 0.00 46.30 3.01
2732 4013 2.719426 AACTTTCGAGACTGGGTACG 57.281 50.000 0.00 0.00 0.00 3.67
2734 4015 4.884668 ATCAAACTTTCGAGACTGGGTA 57.115 40.909 0.00 0.00 0.00 3.69
2743 4024 9.817809 AACTAATATCTGCTATCAAACTTTCGA 57.182 29.630 0.00 0.00 0.00 3.71
2968 4250 1.193323 TTGTACCTTAATCCGGCGGA 58.807 50.000 33.10 33.10 35.55 5.54
2969 4251 1.667212 GTTTGTACCTTAATCCGGCGG 59.333 52.381 22.51 22.51 0.00 6.13
3021 4303 3.211045 ACGCTAACCACACACAATTTCT 58.789 40.909 0.00 0.00 0.00 2.52
3063 4345 2.559998 ACCAAGTGAAACAAAGCGTG 57.440 45.000 0.00 0.00 41.43 5.34
3130 4412 4.623932 ATTGTCTGTAGTCCTCAAGCAA 57.376 40.909 0.00 0.00 0.00 3.91
3183 4465 9.052759 GGTTTACAGAGACAATAAGAGAAACAA 57.947 33.333 0.00 0.00 0.00 2.83
3499 4782 0.704076 AGGCTTAACCATCTTGCCCA 59.296 50.000 0.00 0.00 44.19 5.36
3523 4807 6.238566 CCGCATCAACATCTGATCTTAAACAT 60.239 38.462 0.00 0.00 43.28 2.71
3560 4844 0.331278 TCACCCAGCCCTACCAATTG 59.669 55.000 0.00 0.00 0.00 2.32
3587 4871 2.699809 GCTGCTTGCGATCGTCTG 59.300 61.111 17.81 7.90 0.00 3.51
3696 4980 5.231357 GGCCTTTTGTAATTATGCTAAACGC 59.769 40.000 0.00 0.00 39.77 4.84
3739 5024 8.109843 TGTCATTTTTAACATCAACACGTTTC 57.890 30.769 0.00 0.00 0.00 2.78
3849 5135 4.389992 CAGCAACACTCGTGATATCAAGTT 59.610 41.667 16.71 9.74 0.00 2.66
3873 5159 2.979197 GACCAAGCAGCAGCAGCAG 61.979 63.158 12.92 3.98 45.49 4.24
3874 5160 2.981909 GACCAAGCAGCAGCAGCA 60.982 61.111 12.92 0.00 45.49 4.41
3875 5161 4.099170 CGACCAAGCAGCAGCAGC 62.099 66.667 3.17 0.46 45.49 5.25
3876 5162 1.909141 CTTCGACCAAGCAGCAGCAG 61.909 60.000 3.17 0.00 45.49 4.24
4026 5321 2.487986 CCAACAAGCAAGAAGAGACCCT 60.488 50.000 0.00 0.00 0.00 4.34
4060 5355 4.156556 TGCTGAATTTTCCGAGGATGAAAG 59.843 41.667 0.00 0.00 33.58 2.62


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

AutoCloner maintained by Alex Coulton.