Multiple sequence alignment - TraesCS1D01G299300

Loading Multiple Alignment...

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 TraesCS1D01G299300 chr1D 100.000 5065 0 0 1 5065 397234735 397239799 0 9354
1 TraesCS1D01G299300 chr1D 96.431 5071 130 12 1 5039 92135907 92140958 0 8314
2 TraesCS1D01G299300 chr1D 96.024 5055 155 10 1 5023 489137294 489142334 0 8179
3 TraesCS1D01G299300 chr1D 95.158 4564 158 21 534 5065 467757284 467761816 0 7145
4 TraesCS1D01G299300 chr1D 95.092 3851 137 15 1 3825 477584890 477581066 0 6017
5 TraesCS1D01G299300 chr1D 96.231 3449 107 10 1477 4906 434394320 434397764 0 5627
6 TraesCS1D01G299300 chr1D 97.944 2675 45 3 2399 5064 487232302 487234975 0 4626
7 TraesCS1D01G299300 chr3D 96.961 5101 117 9 1 5065 68959214 68964312 0 8527
8 TraesCS1D01G299300 chr3D 96.026 4077 138 9 1008 5065 520482852 520478781 0 6610
9 TraesCS1D01G299300 chr3D 97.159 2675 57 3 2399 5065 80441863 80444526 0 4501
10 TraesCS1D01G299300 chr6D 96.979 5097 109 8 1 5065 449939375 449944458 0 8517
11 TraesCS1D01G299300 chr6D 94.697 4790 195 18 1 4770 18223312 18218562 0 7384
12 TraesCS1D01G299300 chr6D 97.869 2675 47 3 2399 5065 85930922 85933594 0 4615
13 TraesCS1D01G299300 chr6D 97.524 2666 51 5 2408 5065 462586608 462583950 0 4543
14 TraesCS1D01G299300 chr6D 95.521 2679 98 13 1 2667 448279692 448277024 0 4263
15 TraesCS1D01G299300 chr6D 95.331 2163 66 11 1 2142 462588761 462586613 0 3402
16 TraesCS1D01G299300 chr7D 96.725 5099 127 9 1 5063 580151813 580146719 0 8455
17 TraesCS1D01G299300 chr2D 97.608 2676 54 3 2399 5065 88035799 88033125 0 4578
18 TraesCS1D01G299300 chr2D 97.064 1090 24 1 3984 5065 481518587 481519676 0 1829
19 TraesCS1D01G299300 chr5D 97.495 2675 57 3 2399 5065 449453373 449456045 0 4560
20 TraesCS1D01G299300 chrUn 95.104 2165 66 9 1 2142 294090138 294087991 0 3374
21 TraesCS1D01G299300 chrUn 93.645 2093 70 14 1 2057 110729125 110727060 0 3070
22 TraesCS1D01G299300 chrUn 97.500 840 20 1 1 839 188360037 188360876 0 1434


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 TraesCS1D01G299300 chr1D 397234735 397239799 5064 False 9354.0 9354 100.0000 1 5065 1 chr1D.!!$F2 5064
1 TraesCS1D01G299300 chr1D 92135907 92140958 5051 False 8314.0 8314 96.4310 1 5039 1 chr1D.!!$F1 5038
2 TraesCS1D01G299300 chr1D 489137294 489142334 5040 False 8179.0 8179 96.0240 1 5023 1 chr1D.!!$F6 5022
3 TraesCS1D01G299300 chr1D 467757284 467761816 4532 False 7145.0 7145 95.1580 534 5065 1 chr1D.!!$F4 4531
4 TraesCS1D01G299300 chr1D 477581066 477584890 3824 True 6017.0 6017 95.0920 1 3825 1 chr1D.!!$R1 3824
5 TraesCS1D01G299300 chr1D 434394320 434397764 3444 False 5627.0 5627 96.2310 1477 4906 1 chr1D.!!$F3 3429
6 TraesCS1D01G299300 chr1D 487232302 487234975 2673 False 4626.0 4626 97.9440 2399 5064 1 chr1D.!!$F5 2665
7 TraesCS1D01G299300 chr3D 68959214 68964312 5098 False 8527.0 8527 96.9610 1 5065 1 chr3D.!!$F1 5064
8 TraesCS1D01G299300 chr3D 520478781 520482852 4071 True 6610.0 6610 96.0260 1008 5065 1 chr3D.!!$R1 4057
9 TraesCS1D01G299300 chr3D 80441863 80444526 2663 False 4501.0 4501 97.1590 2399 5065 1 chr3D.!!$F2 2666
10 TraesCS1D01G299300 chr6D 449939375 449944458 5083 False 8517.0 8517 96.9790 1 5065 1 chr6D.!!$F2 5064
11 TraesCS1D01G299300 chr6D 18218562 18223312 4750 True 7384.0 7384 94.6970 1 4770 1 chr6D.!!$R1 4769
12 TraesCS1D01G299300 chr6D 85930922 85933594 2672 False 4615.0 4615 97.8690 2399 5065 1 chr6D.!!$F1 2666
13 TraesCS1D01G299300 chr6D 448277024 448279692 2668 True 4263.0 4263 95.5210 1 2667 1 chr6D.!!$R2 2666
14 TraesCS1D01G299300 chr6D 462583950 462588761 4811 True 3972.5 4543 96.4275 1 5065 2 chr6D.!!$R3 5064
15 TraesCS1D01G299300 chr7D 580146719 580151813 5094 True 8455.0 8455 96.7250 1 5063 1 chr7D.!!$R1 5062
16 TraesCS1D01G299300 chr2D 88033125 88035799 2674 True 4578.0 4578 97.6080 2399 5065 1 chr2D.!!$R1 2666
17 TraesCS1D01G299300 chr2D 481518587 481519676 1089 False 1829.0 1829 97.0640 3984 5065 1 chr2D.!!$F1 1081
18 TraesCS1D01G299300 chr5D 449453373 449456045 2672 False 4560.0 4560 97.4950 2399 5065 1 chr5D.!!$F1 2666
19 TraesCS1D01G299300 chrUn 294087991 294090138 2147 True 3374.0 3374 95.1040 1 2142 1 chrUn.!!$R2 2141
20 TraesCS1D01G299300 chrUn 110727060 110729125 2065 True 3070.0 3070 93.6450 1 2057 1 chrUn.!!$R1 2056
21 TraesCS1D01G299300 chrUn 188360037 188360876 839 False 1434.0 1434 97.5000 1 839 1 chrUn.!!$F1 838

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
924 980 3.573967 TGCTTTTCTTCCCCAAATCAGAC 59.426 43.478 0.0 0.0 0.00 3.51 F
1218 1275 0.325296 AGGAGGTGGCGGTTGATCTA 60.325 55.000 0.0 0.0 0.00 1.98 F
1995 2070 1.349688 AGCCAATCTAACGGTGGACAA 59.650 47.619 0.0 0.0 34.05 3.18 F
2130 2209 1.885887 GCACAACCAACCTCATAGCAA 59.114 47.619 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2058 2.953284 TTCCCATTTGTCCACCGTTA 57.047 45.000 0.00 0.0 0.00 3.18 R
2602 2687 5.528043 TGTTTGTTGTTAATGGCAGACAT 57.472 34.783 0.00 0.0 43.07 3.06 R
3951 4059 0.460635 GCATGTTTAGCCCGGACGTA 60.461 55.000 0.73 0.0 0.00 3.57 R
4115 4232 2.418746 GGGCAGAAGTATCACACGACAT 60.419 50.000 0.00 0.0 0.00 3.06 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
523 527 8.200792 ACCTATTTGTAAATTTTGCACAGTTCA 58.799 29.630 0.00 0.00 0.00 3.18
924 980 3.573967 TGCTTTTCTTCCCCAAATCAGAC 59.426 43.478 0.00 0.00 0.00 3.51
1050 1107 1.038130 AGAAGGACGCAGCGGTAGAT 61.038 55.000 21.15 0.00 0.00 1.98
1081 1138 1.181098 GCCTGTTGTGGTCATTGCCT 61.181 55.000 0.00 0.00 0.00 4.75
1149 1206 0.604511 CACCATCTGCTGTGACTGCA 60.605 55.000 16.20 16.20 36.88 4.41
1212 1269 3.003763 GAGGAGGAGGTGGCGGTT 61.004 66.667 0.00 0.00 0.00 4.44
1218 1275 0.325296 AGGAGGTGGCGGTTGATCTA 60.325 55.000 0.00 0.00 0.00 1.98
1454 1523 2.351726 GCAGCACGGATTAGATTTCGTT 59.648 45.455 0.00 0.00 33.31 3.85
1483 1552 6.627087 AGGTTATGTTTCTTGATCTCTCCA 57.373 37.500 0.00 0.00 0.00 3.86
1639 1708 4.214545 TGCTGTAGAAAACGGTGTATTTGG 59.785 41.667 0.00 0.00 36.77 3.28
1647 1716 7.850193 AGAAAACGGTGTATTTGGTAGGTATA 58.150 34.615 0.00 0.00 0.00 1.47
1921 1996 5.505173 TTGCTTGAGCTTCTATAAATGGC 57.495 39.130 4.44 0.00 42.66 4.40
1995 2070 1.349688 AGCCAATCTAACGGTGGACAA 59.650 47.619 0.00 0.00 34.05 3.18
2130 2209 1.885887 GCACAACCAACCTCATAGCAA 59.114 47.619 0.00 0.00 0.00 3.91
2188 2267 3.070429 ACAGCGCAAACTCTTTTCTTG 57.930 42.857 11.47 0.00 0.00 3.02
2378 2463 2.351060 CGTGTGTCTCGCTAGTACCAAA 60.351 50.000 0.00 0.00 0.00 3.28
2585 2670 2.290197 TGGTCAGTACTGATGCATGCAA 60.290 45.455 27.54 8.38 42.18 4.08
2602 2687 4.521130 TGCAATAACAATTTACGGCCAA 57.479 36.364 2.24 0.00 0.00 4.52
2716 2805 5.643777 AGTCCATGCAACAGTACATTTCTAC 59.356 40.000 0.00 0.00 0.00 2.59
2723 2812 5.912955 GCAACAGTACATTTCTACCAACAAC 59.087 40.000 0.00 0.00 0.00 3.32
3685 3791 9.453572 ACTCTTATGAAATGCTACATTTTCTGA 57.546 29.630 6.97 2.57 33.87 3.27
3700 3806 7.978982 ACATTTTCTGAATTCCTAATCTGACG 58.021 34.615 2.27 0.00 0.00 4.35
3951 4059 4.035102 GGAGGAACCGCAAGCCCT 62.035 66.667 0.00 0.00 33.80 5.19
4051 4159 3.358076 CTCCTCGTCCGGCCAAGAC 62.358 68.421 12.03 12.03 0.00 3.01
4214 4343 6.648879 ACATGCTATGTTTAAGTGTTTGGT 57.351 33.333 0.00 0.00 41.63 3.67
4215 4344 7.753309 ACATGCTATGTTTAAGTGTTTGGTA 57.247 32.000 0.00 0.00 41.63 3.25
4216 4345 7.816640 ACATGCTATGTTTAAGTGTTTGGTAG 58.183 34.615 0.00 0.00 41.63 3.18
4217 4346 7.447238 ACATGCTATGTTTAAGTGTTTGGTAGT 59.553 33.333 0.00 0.00 41.63 2.73
4231 4360 7.014230 AGTGTTTGGTAGTACATTGCTCATTTT 59.986 33.333 2.06 0.00 0.00 1.82
4323 4452 3.861886 GCAGCAGTGCCAATTTGTACATT 60.862 43.478 12.58 0.00 44.72 2.71
4438 4567 2.290387 TGCGGTCAACCTTGCCTAATAA 60.290 45.455 0.00 0.00 0.00 1.40
4451 4586 5.968676 TGCCTAATAACTCCACTATGGTT 57.031 39.130 0.00 0.00 39.03 3.67
4664 4803 6.680874 TTTGAAGCAAAACAAATGAGCATT 57.319 29.167 0.00 0.00 32.26 3.56
4739 4878 3.197265 GCCACTTTTTGACATGCACTTT 58.803 40.909 0.00 0.00 0.00 2.66
4883 5022 5.106712 CGTGATTGCCAAAAGTATGTACTGT 60.107 40.000 0.00 0.00 36.50 3.55
4942 5082 7.397192 TCATACCCTACTTTTTACGGTCTTAGT 59.603 37.037 0.00 0.00 0.00 2.24
4966 5106 3.445096 GGTGTTAGCAAGCCATCTTTCAT 59.555 43.478 0.00 0.00 0.00 2.57
5048 5188 7.933215 TCATAACTAGTGCTAACTACAGTGA 57.067 36.000 0.00 0.00 37.88 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
563 569 5.116882 ACAAGTGAGTCCAGTTTGTAAGTC 58.883 41.667 0.00 0.00 33.87 3.01
784 793 2.365293 ACACCCCAACTGCTTTCATTTC 59.635 45.455 0.00 0.00 0.00 2.17
924 980 1.981495 AGGTGAGAGGAGAGGGTTTTG 59.019 52.381 0.00 0.00 0.00 2.44
1050 1107 0.535780 CAACAGGCTTCTCCACTGCA 60.536 55.000 0.00 0.00 37.29 4.41
1212 1269 1.993956 GCCTCTGCTCCTCTAGATCA 58.006 55.000 0.00 0.00 33.53 2.92
1454 1523 9.206690 AGAGATCAAGAAACATAACCTATCTGA 57.793 33.333 0.00 0.00 0.00 3.27
1483 1552 9.948747 ACAACTAGTACTAATCCTAACCCTAAT 57.051 33.333 3.76 0.00 0.00 1.73
1647 1716 6.884295 TGGAAATCGTATGAATCAAAGAGGTT 59.116 34.615 0.00 0.00 0.00 3.50
1661 1730 3.340034 TCCTGCGTTTTGGAAATCGTAT 58.660 40.909 4.91 0.00 34.54 3.06
1921 1996 9.796120 TTTCCAGAGTACATGTTTTAAAAGTTG 57.204 29.630 2.30 4.85 0.00 3.16
1983 2058 2.953284 TTCCCATTTGTCCACCGTTA 57.047 45.000 0.00 0.00 0.00 3.18
2052 2128 5.950883 TCTATATAGTACGCATGCTTGGAC 58.049 41.667 17.13 8.04 0.00 4.02
2116 2195 6.016777 GGAGAAACATATTGCTATGAGGTTGG 60.017 42.308 0.29 0.00 38.49 3.77
2188 2267 9.143631 AGTTCAAAGCATTAGCAATTCATTTAC 57.856 29.630 0.00 0.00 45.49 2.01
2249 2328 9.781834 TGTGTGTGTTTTCTTTAATAAAGTGAG 57.218 29.630 11.97 0.00 39.52 3.51
2300 2385 8.522830 CAATTATTTCAGGTCCACTTACATTGT 58.477 33.333 0.00 0.00 0.00 2.71
2363 2448 6.376299 TGATACTCTTTTTGGTACTAGCGAGA 59.624 38.462 0.00 0.00 0.00 4.04
2585 2670 5.678616 GCAGACATTGGCCGTAAATTGTTAT 60.679 40.000 0.00 0.00 0.00 1.89
2602 2687 5.528043 TGTTTGTTGTTAATGGCAGACAT 57.472 34.783 0.00 0.00 43.07 3.06
3681 3787 5.594725 AGCTACGTCAGATTAGGAATTCAGA 59.405 40.000 7.93 0.00 0.00 3.27
3685 3791 5.593010 GACAGCTACGTCAGATTAGGAATT 58.407 41.667 0.00 0.00 35.88 2.17
3700 3806 4.323868 GTGTGTTAGTTGATCGACAGCTAC 59.676 45.833 15.59 9.15 40.86 3.58
3819 3926 1.745115 GCCTGTTGTATCCGCTGCA 60.745 57.895 0.00 0.00 0.00 4.41
3951 4059 0.460635 GCATGTTTAGCCCGGACGTA 60.461 55.000 0.73 0.00 0.00 3.57
4051 4159 2.732468 CGCATCAGATCCTCGGCG 60.732 66.667 0.00 0.00 38.45 6.46
4115 4232 2.418746 GGGCAGAAGTATCACACGACAT 60.419 50.000 0.00 0.00 0.00 3.06
4208 4337 7.116233 CCAAAAATGAGCAATGTACTACCAAAC 59.884 37.037 0.00 0.00 0.00 2.93
4209 4338 7.151308 CCAAAAATGAGCAATGTACTACCAAA 58.849 34.615 0.00 0.00 0.00 3.28
4210 4339 6.266558 ACCAAAAATGAGCAATGTACTACCAA 59.733 34.615 0.00 0.00 0.00 3.67
4211 4340 5.772672 ACCAAAAATGAGCAATGTACTACCA 59.227 36.000 0.00 0.00 0.00 3.25
4212 4341 6.267496 ACCAAAAATGAGCAATGTACTACC 57.733 37.500 0.00 0.00 0.00 3.18
4213 4342 9.289303 CATTACCAAAAATGAGCAATGTACTAC 57.711 33.333 0.00 0.00 38.84 2.73
4214 4343 8.465999 CCATTACCAAAAATGAGCAATGTACTA 58.534 33.333 0.00 0.00 38.84 1.82
4215 4344 7.322664 CCATTACCAAAAATGAGCAATGTACT 58.677 34.615 0.00 0.00 38.84 2.73
4216 4345 6.035975 GCCATTACCAAAAATGAGCAATGTAC 59.964 38.462 0.00 0.00 38.84 2.90
4217 4346 6.105333 GCCATTACCAAAAATGAGCAATGTA 58.895 36.000 0.00 0.00 38.84 2.29
4380 4509 9.169592 GGTAGGTGCTAACAAGATAAACAATAA 57.830 33.333 0.00 0.00 0.00 1.40
4438 4567 9.784376 ATGTACCATATATAACCATAGTGGAGT 57.216 33.333 2.45 0.00 40.96 3.85
4664 4803 7.555914 TGCTACATTTCTGGCAATTACTAATGA 59.444 33.333 0.00 0.00 0.00 2.57
4739 4878 9.688091 TTTTGGCAATATCTTATAGTACAACCA 57.312 29.630 0.00 0.00 0.00 3.67
4942 5082 2.584835 AGATGGCTTGCTAACACCAA 57.415 45.000 0.00 0.00 35.41 3.67
5030 5170 5.593095 TGGGTATCACTGTAGTTAGCACTAG 59.407 44.000 0.00 0.00 36.09 2.57


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

AutoCloner maintained by Alex Coulton.