Multiple sequence alignment - TraesCS1D01G333600

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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 TraesCS1D01G333600 chr1D 100.000 2345 0 0 1 2345 423734776 423732432 0.000000e+00 4331.0
1 TraesCS1D01G333600 chr1D 93.618 1661 90 10 690 2345 423659803 423661452 0.000000e+00 2466.0
2 TraesCS1D01G333600 chr1D 81.572 814 132 16 693 1497 423656157 423656961 0.000000e+00 656.0
3 TraesCS1D01G333600 chr1D 92.893 394 26 1 1 394 423658831 423659222 2.610000e-159 571.0
4 TraesCS1D01G333600 chr1D 98.658 298 3 1 394 690 423659475 423659772 5.740000e-146 527.0
5 TraesCS1D01G333600 chr1D 84.173 139 18 3 130 267 193841396 193841261 5.260000e-27 132.0
6 TraesCS1D01G333600 chr1D 85.714 105 11 3 130 233 231683085 231682984 8.860000e-20 108.0
7 TraesCS1D01G333600 chr1B 94.093 1659 90 4 690 2345 573144757 573143104 0.000000e+00 2514.0
8 TraesCS1D01G333600 chr1B 88.525 1098 106 10 694 1781 573054393 573055480 0.000000e+00 1312.0
9 TraesCS1D01G333600 chr1B 85.561 935 111 16 713 1629 573046594 573047522 0.000000e+00 957.0
10 TraesCS1D01G333600 chr1B 91.436 397 28 4 1 394 573145731 573145338 7.370000e-150 540.0
11 TraesCS1D01G333600 chr1B 95.973 298 11 1 394 690 573145085 573144788 1.260000e-132 483.0
12 TraesCS1D01G333600 chr1B 91.946 298 22 2 394 690 573179211 573178915 1.300000e-112 416.0
13 TraesCS1D01G333600 chr1B 92.776 263 17 1 132 394 573045716 573045976 1.700000e-101 379.0
14 TraesCS1D01G333600 chr1B 78.495 558 92 20 703 1255 572946015 572946549 8.030000e-90 340.0
15 TraesCS1D01G333600 chr1B 85.430 302 39 2 394 690 573054059 573054360 2.260000e-80 309.0
16 TraesCS1D01G333600 chr1B 83.162 291 37 5 398 677 573046231 573046520 2.990000e-64 255.0
17 TraesCS1D01G333600 chr1B 92.308 39 2 1 509 546 637712943 637712981 1.000000e-03 54.7
18 TraesCS1D01G333600 chr1B 100.000 28 0 0 1655 1682 573050940 573050967 4.000000e-03 52.8
19 TraesCS1D01G333600 chr1A 95.297 893 39 2 690 1580 520003840 520002949 0.000000e+00 1413.0
20 TraesCS1D01G333600 chr1A 86.627 1002 95 17 1328 2315 519855206 519856182 0.000000e+00 1072.0
21 TraesCS1D01G333600 chr1A 93.434 396 22 2 1 394 520004814 520004421 3.360000e-163 584.0
22 TraesCS1D01G333600 chr1A 94.966 298 14 1 394 690 520004168 520003871 1.270000e-127 466.0
23 TraesCS1D01G333600 chr1A 87.595 395 45 3 1 394 519852487 519852878 2.750000e-124 455.0
24 TraesCS1D01G333600 chr1A 91.228 285 5 5 2063 2345 520002493 520002227 1.020000e-98 370.0
25 TraesCS1D01G333600 chr1A 96.341 82 3 0 2216 2297 520002955 520002874 4.060000e-28 135.0
26 TraesCS1D01G333600 chr1A 80.357 168 28 2 1257 1419 519851075 519851242 3.160000e-24 122.0
27 TraesCS1D01G333600 chr2B 82.014 139 21 3 130 267 241470011 241470146 5.300000e-22 115.0
28 TraesCS1D01G333600 chr2B 88.000 50 3 2 509 557 709099457 709099504 3.260000e-04 56.5
29 TraesCS1D01G333600 chr2B 92.308 39 2 1 509 546 749507677 749507715 1.000000e-03 54.7
30 TraesCS1D01G333600 chr4D 80.576 139 23 3 130 267 209017292 209017427 1.150000e-18 104.0
31 TraesCS1D01G333600 chr4D 95.122 41 2 0 1028 1068 466473740 466473700 5.410000e-07 65.8
32 TraesCS1D01G333600 chr7D 95.455 44 2 0 1025 1068 512431762 512431805 1.160000e-08 71.3
33 TraesCS1D01G333600 chr5B 73.958 192 35 11 718 898 90076943 90076756 1.950000e-06 63.9
34 TraesCS1D01G333600 chr5D 94.737 38 2 0 835 872 81735741 81735704 2.520000e-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 TraesCS1D01G333600 chr1D 423732432 423734776 2344 True 4331.000000 4331 100.000000 1 2345 1 chr1D.!!$R3 2344
1 TraesCS1D01G333600 chr1D 423656157 423661452 5295 False 1055.000000 2466 91.685250 1 2345 4 chr1D.!!$F1 2344
2 TraesCS1D01G333600 chr1B 573143104 573145731 2627 True 1179.000000 2514 93.834000 1 2345 3 chr1B.!!$R2 2344
3 TraesCS1D01G333600 chr1B 573045716 573055480 9764 False 544.133333 1312 89.242333 132 1781 6 chr1B.!!$F3 1649
4 TraesCS1D01G333600 chr1B 572946015 572946549 534 False 340.000000 340 78.495000 703 1255 1 chr1B.!!$F1 552
5 TraesCS1D01G333600 chr1A 520002227 520004814 2587 True 593.600000 1413 94.253200 1 2345 5 chr1A.!!$R1 2344
6 TraesCS1D01G333600 chr1A 519851075 519856182 5107 False 549.666667 1072 84.859667 1 2315 3 chr1A.!!$F1 2314

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
86 2972 2.33862 GCCACCGGAAAAAGGCAC 59.661 61.111 9.46 0.0 46.26 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 11100 0.892755 TAGCAACGGTACAGACAGGG 59.107 55.0 0.0 0.0 0.0 4.45 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
86 2972 2.338620 GCCACCGGAAAAAGGCAC 59.661 61.111 9.46 0.0 46.26 5.01
456 8409 6.434596 CAATTTTAACGTTCATGGTGTCAGA 58.565 36.000 2.82 0.0 0.00 3.27
660 8627 4.378774 CAAAATCATGTTTGGCTCCACAA 58.621 39.130 0.00 0.0 35.29 3.33
803 8810 6.155475 ACTGTCAAGATCTTAGCTATCCAC 57.845 41.667 7.86 0.0 0.00 4.02
992 9005 8.868522 TTCCTGTCTATTCAGATTCACAAAAT 57.131 30.769 0.00 0.0 37.61 1.82
1158 9171 5.129980 TGCAAGATCACTAGAGTCCATTCAT 59.870 40.000 0.00 0.0 0.00 2.57
1350 10452 6.238731 CCTTTGCTTGTAGATGTTGAAAGTGA 60.239 38.462 0.00 0.0 0.00 3.41
1383 10485 5.829924 CCTGGTGGAGTTATTCTTGCATATT 59.170 40.000 0.00 0.0 34.57 1.28
1628 10809 4.298626 AGCTGGGACTATTGAGGTGATTA 58.701 43.478 0.00 0.0 0.00 1.75
1629 10810 4.910304 AGCTGGGACTATTGAGGTGATTAT 59.090 41.667 0.00 0.0 0.00 1.28
1685 10866 0.885196 TAGGGCGTTTTGAACCATGC 59.115 50.000 0.00 0.0 0.00 4.06
1693 10874 4.222886 CGTTTTGAACCATGCGTTTGATA 58.777 39.130 1.80 0.0 33.74 2.15
1694 10875 4.320690 CGTTTTGAACCATGCGTTTGATAG 59.679 41.667 1.80 0.0 33.74 2.08
1700 10881 3.937814 ACCATGCGTTTGATAGACAAGA 58.062 40.909 0.00 0.0 39.77 3.02
1706 10887 8.773645 CCATGCGTTTGATAGACAAGATAAATA 58.226 33.333 0.00 0.0 39.77 1.40
1781 11021 0.179161 GTCTGACCGTGGATGTCGAG 60.179 60.000 0.00 0.0 35.46 4.04
1801 11041 4.379082 CGAGTAACTGGGTTTGGTAATTGC 60.379 45.833 0.00 0.0 0.00 3.56
1851 11091 3.372954 TGCGTTTTCCCAAATTAACACG 58.627 40.909 0.00 0.0 0.00 4.49
1860 11100 3.377172 CCCAAATTAACACGATCAGTCCC 59.623 47.826 0.00 0.0 0.00 4.46
1862 11102 3.277142 AATTAACACGATCAGTCCCCC 57.723 47.619 0.00 0.0 0.00 5.40
1936 11176 5.127845 TGTTAAAACAGGCAATTTGTGGAGA 59.872 36.000 0.00 0.0 34.30 3.71
1975 11215 4.346127 TGGTAGCAGCTATGATCAGATTGT 59.654 41.667 5.14 0.0 0.00 2.71
1984 11224 2.981898 TGATCAGATTGTGGTGCTCAG 58.018 47.619 0.00 0.0 0.00 3.35
1995 11236 4.513442 TGTGGTGCTCAGTATTATGTTCC 58.487 43.478 0.00 0.0 0.00 3.62
2197 11450 5.556915 TGGTTTGGGAGAACACAACTATAG 58.443 41.667 0.00 0.0 39.28 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.355837 GTTCGCTGCGTGGTCTCA 60.356 61.111 22.48 0.00 0.00 3.27
49 2935 1.431488 CGGCTCCATGTTCATGGTCG 61.431 60.000 25.06 22.00 42.28 4.79
85 2971 2.522436 TCCGGACGGTGGTTCTGT 60.522 61.111 10.90 0.00 38.51 3.41
86 2972 2.261671 CTCCGGACGGTGGTTCTG 59.738 66.667 10.90 0.00 36.47 3.02
456 8409 5.315109 ACTTTTAAGGGTAGGGGAGTTGATT 59.685 40.000 0.00 0.00 0.00 2.57
521 8475 3.753787 CCTTTCAAGTGAAGGGGCT 57.246 52.632 13.09 0.00 44.67 5.19
660 8627 3.441101 TGGGCATAGCTACCTCGATAAT 58.559 45.455 0.00 0.00 0.00 1.28
803 8810 6.216801 ACCATGTCCAGATTTGAATTCATG 57.783 37.500 9.40 4.36 33.57 3.07
992 9005 4.776837 AGCAATTTGTTCCCATTGGTGATA 59.223 37.500 1.20 0.00 39.16 2.15
1001 9014 1.112315 ACGCCAGCAATTTGTTCCCA 61.112 50.000 0.00 0.00 0.00 4.37
1158 9171 3.874383 TTCCTGGAATCAACCACAAGA 57.126 42.857 4.68 0.00 35.91 3.02
1295 9308 5.007332 GCCAAATCCAAATCATTGAGATTGC 59.993 40.000 8.67 2.85 46.09 3.56
1350 10452 4.270153 TCCACCAGGGGCCAGACT 62.270 66.667 4.39 0.00 37.22 3.24
1383 10485 7.126726 CAAGTTTGGACAAAAACACAATGAA 57.873 32.000 0.00 0.00 41.56 2.57
1412 10517 9.607988 TTAGAAAGTGTACAGATGTGAGAAAAA 57.392 29.630 0.00 0.00 0.00 1.94
1522 10630 5.974158 CCAATATAGACACTGAGAAGACACG 59.026 44.000 0.00 0.00 0.00 4.49
1638 10819 6.183360 GGGTCAAATATGAAGTTGTGAGCTAC 60.183 42.308 0.00 0.00 37.30 3.58
1728 10968 3.262420 ACATGCTCGATAGGTTCAACAC 58.738 45.455 0.00 0.00 0.00 3.32
1736 10976 3.987547 ACATCTGAACATGCTCGATAGG 58.012 45.455 0.00 0.00 0.00 2.57
1737 10977 5.277202 CCAAACATCTGAACATGCTCGATAG 60.277 44.000 0.00 0.00 0.00 2.08
1781 11021 3.366577 CCGCAATTACCAAACCCAGTTAC 60.367 47.826 0.00 0.00 0.00 2.50
1801 11041 2.636830 AGGCAAGAATGATCAACTCCG 58.363 47.619 0.00 0.00 0.00 4.63
1860 11100 0.892755 TAGCAACGGTACAGACAGGG 59.107 55.000 0.00 0.00 0.00 4.45
1862 11102 1.736032 GCCTAGCAACGGTACAGACAG 60.736 57.143 0.00 0.00 0.00 3.51
1975 11215 3.196901 ACGGAACATAATACTGAGCACCA 59.803 43.478 0.00 0.00 0.00 4.17
1984 11224 4.377021 TGATGCTCCACGGAACATAATAC 58.623 43.478 1.97 0.00 31.90 1.89
1995 11236 4.336433 ACCTAAATTGAATGATGCTCCACG 59.664 41.667 0.00 0.00 0.00 4.94
2125 11376 2.361483 TGCCGCTCAGGTACCGTA 60.361 61.111 6.18 0.00 43.70 4.02


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

AutoCloner maintained by Alex Coulton.