Multiple sequence alignment - TraesCS2D01G530800

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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 TraesCS2D01G530800 chr2D 100.000 2423 0 0 1 2423 617075601 617073179 0.000000e+00 4475
1 TraesCS2D01G530800 chr2B 95.608 2436 76 12 1 2423 752832604 752830187 0.000000e+00 3877
2 TraesCS2D01G530800 chr2A 95.065 1925 83 7 504 2423 747145981 747144064 0.000000e+00 3018
3 TraesCS2D01G530800 chr2A 88.962 1223 115 13 380 1588 746979091 746977875 0.000000e+00 1493
4 TraesCS2D01G530800 chr2A 85.817 557 69 3 1703 2252 746977660 746977107 1.250000e-162 582
5 TraesCS2D01G530800 chr2A 91.111 135 8 4 805 937 746980190 746980322 1.910000e-41 180
6 TraesCS2D01G530800 chr5B 82.784 1214 159 26 386 1557 570933260 570934465 0.000000e+00 1038
7 TraesCS2D01G530800 chr5B 81.282 577 76 18 1052 1598 571122031 571122605 2.860000e-119 438
8 TraesCS2D01G530800 chr5B 78.187 706 119 16 1721 2411 570934758 570935443 3.730000e-113 418
9 TraesCS2D01G530800 chr5A 82.220 1198 157 23 386 1536 584490566 584491754 0.000000e+00 981
10 TraesCS2D01G530800 chr5A 79.831 709 113 18 1721 2418 584507059 584507748 7.780000e-135 490
11 TraesCS2D01G530800 chr3B 84.814 698 100 2 1726 2423 671747470 671746779 0.000000e+00 697
12 TraesCS2D01G530800 chr3B 81.897 232 38 3 1865 2094 13965227 13965456 2.460000e-45 193
13 TraesCS2D01G530800 chr5D 81.818 770 93 27 874 1598 464076394 464077161 9.580000e-169 603
14 TraesCS2D01G530800 chr5D 85.743 491 67 1 385 872 464075869 464076359 1.280000e-142 516
15 TraesCS2D01G530800 chr5D 79.580 666 111 10 1751 2411 464077349 464077994 1.020000e-123 453


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 TraesCS2D01G530800 chr2D 617073179 617075601 2422 True 4475.0 4475 100.000000 1 2423 1 chr2D.!!$R1 2422
1 TraesCS2D01G530800 chr2B 752830187 752832604 2417 True 3877.0 3877 95.608000 1 2423 1 chr2B.!!$R1 2422
2 TraesCS2D01G530800 chr2A 747144064 747145981 1917 True 3018.0 3018 95.065000 504 2423 1 chr2A.!!$R1 1919
3 TraesCS2D01G530800 chr2A 746977107 746979091 1984 True 1037.5 1493 87.389500 380 2252 2 chr2A.!!$R2 1872
4 TraesCS2D01G530800 chr5B 570933260 570935443 2183 False 728.0 1038 80.485500 386 2411 2 chr5B.!!$F2 2025
5 TraesCS2D01G530800 chr5B 571122031 571122605 574 False 438.0 438 81.282000 1052 1598 1 chr5B.!!$F1 546
6 TraesCS2D01G530800 chr5A 584490566 584491754 1188 False 981.0 981 82.220000 386 1536 1 chr5A.!!$F1 1150
7 TraesCS2D01G530800 chr5A 584507059 584507748 689 False 490.0 490 79.831000 1721 2418 1 chr5A.!!$F2 697
8 TraesCS2D01G530800 chr3B 671746779 671747470 691 True 697.0 697 84.814000 1726 2423 1 chr3B.!!$R1 697
9 TraesCS2D01G530800 chr5D 464075869 464077994 2125 False 524.0 603 82.380333 385 2411 3 chr5D.!!$F1 2026

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
799 805 0.179 CTGAGTAATCCCGCTTGGCT 59.821 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2121 0.320683 CGACCATGAAGTGCACCAGA 60.321 55.0 14.63 0.0 0.0 3.86 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
24 25 6.981762 AGAGATTGCTTGTGTTTATCTCAG 57.018 37.500 11.61 0.00 42.21 3.35
39 40 9.554395 TGTTTATCTCAGATGTGTTTTTGTCTA 57.446 29.630 0.00 0.00 0.00 2.59
43 44 7.895975 TCTCAGATGTGTTTTTGTCTATCTG 57.104 36.000 0.00 0.00 41.59 2.90
48 49 8.618677 CAGATGTGTTTTTGTCTATCTGCATAT 58.381 33.333 0.00 0.00 36.32 1.78
112 113 2.936919 ATAAGAGATGGCCATTCGCA 57.063 45.000 21.84 12.02 40.31 5.10
179 180 6.109359 ACTACTTAACAATGGAGCTGCTTAG 58.891 40.000 6.82 0.00 0.00 2.18
185 186 4.874970 ACAATGGAGCTGCTTAGTTTTTG 58.125 39.130 6.82 5.54 0.00 2.44
266 267 8.992073 CCCATTTTTGTTTCCTAATTTCAGAAG 58.008 33.333 0.00 0.00 0.00 2.85
267 268 9.762933 CCATTTTTGTTTCCTAATTTCAGAAGA 57.237 29.630 0.00 0.00 0.00 2.87
273 274 9.573166 TTGTTTCCTAATTTCAGAAGATTCAGA 57.427 29.630 0.00 0.00 0.00 3.27
274 275 9.745018 TGTTTCCTAATTTCAGAAGATTCAGAT 57.255 29.630 0.00 0.00 0.00 2.90
276 277 9.964354 TTTCCTAATTTCAGAAGATTCAGATGA 57.036 29.630 0.00 0.00 0.00 2.92
277 278 9.610705 TTCCTAATTTCAGAAGATTCAGATGAG 57.389 33.333 0.00 0.00 0.00 2.90
278 279 8.985922 TCCTAATTTCAGAAGATTCAGATGAGA 58.014 33.333 0.00 0.00 0.00 3.27
279 280 9.610705 CCTAATTTCAGAAGATTCAGATGAGAA 57.389 33.333 0.00 0.00 0.00 2.87
320 321 5.554070 TGTTTTTACTCAAGCTACCTACCC 58.446 41.667 0.00 0.00 0.00 3.69
321 322 5.072058 TGTTTTTACTCAAGCTACCTACCCA 59.928 40.000 0.00 0.00 0.00 4.51
344 345 7.545265 CCCAAATGGTTTGTCATACTGTTTATG 59.455 37.037 0.00 0.00 38.98 1.90
720 726 4.113815 CAGGAGATTGGGCCGGCA 62.114 66.667 30.85 8.42 0.00 5.69
799 805 0.179000 CTGAGTAATCCCGCTTGGCT 59.821 55.000 0.00 0.00 0.00 4.75
872 911 2.072487 AGTGGTGGCCAGTGTCAGT 61.072 57.895 5.11 2.49 35.61 3.41
908 947 7.651304 ACTTGTCGATATGAGATTCTGAATCAC 59.349 37.037 27.06 22.23 40.42 3.06
918 957 0.249826 TCTGAATCACTGTGCACGCA 60.250 50.000 13.13 0.00 0.00 5.24
1068 1129 4.248058 CGCAGGATGATGATGTATTGCTA 58.752 43.478 0.00 0.00 39.69 3.49
1169 1236 1.078214 CATCCCAAGCTGCCGAAGA 60.078 57.895 0.00 0.00 0.00 2.87
1388 1483 4.760204 ACCTCCTGTATGTTGTTTTGTAGC 59.240 41.667 0.00 0.00 0.00 3.58
1742 2077 4.500375 GCAACAAAGCCAGAACAAGAGATT 60.500 41.667 0.00 0.00 0.00 2.40
1778 2121 0.680921 CGATGCCTCCATGGTGGTTT 60.681 55.000 29.03 18.82 39.03 3.27
1967 2322 0.898320 AGCTGACTTGCACCGATAGT 59.102 50.000 0.00 0.00 34.99 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.308014 ACACATCTGAGATAAACACAAGCA 58.692 37.500 0.00 0.00 0.00 3.91
24 25 9.793252 AAATATGCAGATAGACAAAAACACATC 57.207 29.630 0.00 0.00 0.00 3.06
93 94 2.936919 TGCGAATGGCCATCTCTTAT 57.063 45.000 21.08 0.73 42.61 1.73
95 96 1.838112 TTTGCGAATGGCCATCTCTT 58.162 45.000 21.08 3.20 42.61 2.85
156 157 6.109359 ACTAAGCAGCTCCATTGTTAAGTAG 58.891 40.000 0.00 0.00 0.00 2.57
166 167 3.160269 AGCAAAAACTAAGCAGCTCCAT 58.840 40.909 0.00 0.00 0.00 3.41
185 186 6.468543 TGGGTGGTCCAAAATTAAATTAAGC 58.531 36.000 0.00 0.00 43.84 3.09
250 251 9.964354 TCATCTGAATCTTCTGAAATTAGGAAA 57.036 29.630 4.00 0.00 38.39 3.13
266 267 8.380743 AGCTCATGTAAATTCTCATCTGAATC 57.619 34.615 0.00 0.00 35.82 2.52
267 268 8.749026 AAGCTCATGTAAATTCTCATCTGAAT 57.251 30.769 0.00 0.00 38.19 2.57
268 269 9.842775 ATAAGCTCATGTAAATTCTCATCTGAA 57.157 29.630 0.00 0.00 0.00 3.02
300 301 5.829062 TTGGGTAGGTAGCTTGAGTAAAA 57.171 39.130 0.00 0.00 0.00 1.52
320 321 7.598118 TGCATAAACAGTATGACAAACCATTTG 59.402 33.333 0.00 0.00 42.76 2.32
321 322 7.665690 TGCATAAACAGTATGACAAACCATTT 58.334 30.769 0.00 0.00 39.69 2.32
367 369 8.888579 AATTTCTACTGTACGATATTTCCAGG 57.111 34.615 0.00 0.00 0.00 4.45
467 470 3.318839 TGAGTGCCAAAAATGTGAGAAGG 59.681 43.478 0.00 0.00 0.00 3.46
720 726 1.001406 GCCTCAGCTGCCGATACTATT 59.999 52.381 9.47 0.00 35.50 1.73
799 805 0.250901 GGCTGCTCAAGGGAGTTCAA 60.251 55.000 0.00 0.00 43.37 2.69
872 911 0.677288 ATCGACAAGTTCACCACCGA 59.323 50.000 0.00 0.00 0.00 4.69
908 947 1.630244 GCTTACCTCTGCGTGCACAG 61.630 60.000 18.64 7.88 39.12 3.66
918 957 0.617820 ACATCACCCCGCTTACCTCT 60.618 55.000 0.00 0.00 0.00 3.69
1068 1129 0.909610 TCCCACTCCGGCTTGATTCT 60.910 55.000 0.00 0.00 0.00 2.40
1189 1256 2.360475 GGTCTGCCTTGTCAGCCC 60.360 66.667 0.00 0.00 34.19 5.19
1251 1318 4.299978 GCTTACCTTCATCCATCTCGTAC 58.700 47.826 0.00 0.00 0.00 3.67
1388 1483 1.995484 CTACAACGATGCAGTCACCTG 59.005 52.381 0.00 0.00 41.91 4.00
1778 2121 0.320683 CGACCATGAAGTGCACCAGA 60.321 55.000 14.63 0.00 0.00 3.86
1967 2322 7.066163 CCTGTGTTGATCTGAATTGTAGCATTA 59.934 37.037 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.