Multiple sequence alignment - TraesCS3B01G350600

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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 TraesCS3B01G350600 chr3B 100.000 2957 0 0 1 2957 560874917 560871961 0.000000e+00 5461.0
1 TraesCS3B01G350600 chr3D 98.265 2593 28 4 1 2588 428895640 428893060 0.000000e+00 4523.0
2 TraesCS3B01G350600 chr3D 94.638 373 7 2 2585 2957 428893032 428892673 1.540000e-157 566.0
3 TraesCS3B01G350600 chr2A 91.048 2223 126 20 415 2588 773283980 773281782 0.000000e+00 2935.0
4 TraesCS3B01G350600 chr2A 91.935 372 28 2 2585 2955 773281754 773281384 1.210000e-143 520.0
5 TraesCS3B01G350600 chr2A 84.977 426 25 10 1 420 773284428 773284036 2.140000e-106 396.0
6 TraesCS3B01G350600 chr2D 89.840 876 69 11 1718 2588 646216347 646215487 0.000000e+00 1107.0
7 TraesCS3B01G350600 chr2D 86.280 758 63 15 416 1164 646353324 646354049 0.000000e+00 785.0
8 TraesCS3B01G350600 chr2D 88.993 427 25 14 1 420 646352856 646353267 2.630000e-140 508.0
9 TraesCS3B01G350600 chr2D 79.720 715 70 29 1008 1684 646217427 646216750 5.810000e-122 448.0
10 TraesCS3B01G350600 chr2D 83.646 373 43 13 2585 2955 646361355 646361711 4.720000e-88 335.0
11 TraesCS3B01G350600 chr2D 84.615 273 13 6 2255 2520 646354153 646354403 8.190000e-61 244.0
12 TraesCS3B01G350600 chr3A 96.022 553 20 1 2038 2588 556989747 556990299 0.000000e+00 898.0
13 TraesCS3B01G350600 chr3A 94.118 289 16 1 2585 2872 556990327 556990615 3.500000e-119 438.0
14 TraesCS3B01G350600 chr3A 95.614 114 2 1 71 181 556989620 556989733 2.340000e-41 180.0
15 TraesCS3B01G350600 chr3A 95.960 99 4 0 2859 2957 556992143 556992241 8.480000e-36 161.0
16 TraesCS3B01G350600 chr2B 83.060 183 23 3 2664 2841 357379315 357379494 3.050000e-35 159.0
17 TraesCS3B01G350600 chr2B 96.154 52 2 0 517 568 5086355 5086406 5.250000e-13 86.1
18 TraesCS3B01G350600 chr7D 85.437 103 12 2 875 977 618235748 618235649 1.450000e-18 104.0
19 TraesCS3B01G350600 chr7D 89.583 48 5 0 2664 2711 120307848 120307801 8.850000e-06 62.1
20 TraesCS3B01G350600 chr6B 85.859 99 12 2 879 977 239367842 239367938 1.450000e-18 104.0


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 TraesCS3B01G350600 chr3B 560871961 560874917 2956 True 5461.000000 5461 100.000000 1 2957 1 chr3B.!!$R1 2956
1 TraesCS3B01G350600 chr3D 428892673 428895640 2967 True 2544.500000 4523 96.451500 1 2957 2 chr3D.!!$R1 2956
2 TraesCS3B01G350600 chr2A 773281384 773284428 3044 True 1283.666667 2935 89.320000 1 2955 3 chr2A.!!$R1 2954
3 TraesCS3B01G350600 chr2D 646215487 646217427 1940 True 777.500000 1107 84.780000 1008 2588 2 chr2D.!!$R1 1580
4 TraesCS3B01G350600 chr2D 646352856 646354403 1547 False 512.333333 785 86.629333 1 2520 3 chr2D.!!$F2 2519
5 TraesCS3B01G350600 chr3A 556989620 556992241 2621 False 419.250000 898 95.428500 71 2957 4 chr3A.!!$F1 2886

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
380 405 2.097685 GCGATCGATCTTGACAACGATG 60.098 50.0 21.57 4.23 43.72 3.84 F
1553 1720 0.033208 TTGGCCTGCCTAAAGGATGG 60.033 55.0 9.97 1.94 40.02 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 2452 1.339151 GCACTGGTCCTCCTAACTTGG 60.339 57.143 0.00 0.0 34.23 3.61 R
2723 3304 1.466856 CATTGGTACCAGCAGCATGT 58.533 50.000 15.65 0.0 39.31 3.21 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
248 271 5.300792 TCATCAGTTCCCCTTGTTGTTAAAC 59.699 40.000 0.00 0.00 36.78 2.01
262 285 3.404899 TGTTAAACCAATCCGTCTCACC 58.595 45.455 0.00 0.00 0.00 4.02
380 405 2.097685 GCGATCGATCTTGACAACGATG 60.098 50.000 21.57 4.23 43.72 3.84
1235 1380 4.444056 GGTTGTGTTGAATCAATGAAACGG 59.556 41.667 0.00 0.00 0.00 4.44
1330 1481 1.705186 ACATTACAACTCCAGCCACCT 59.295 47.619 0.00 0.00 0.00 4.00
1553 1720 0.033208 TTGGCCTGCCTAAAGGATGG 60.033 55.000 9.97 1.94 40.02 3.51
1916 2452 1.474879 GGAGATGCTAGCGATACCCTC 59.525 57.143 10.77 9.27 0.00 4.30
2423 2973 0.322456 TCTCGCCTCCAAACCCATTG 60.322 55.000 0.00 0.00 38.84 2.82
2437 2987 2.644299 ACCCATTGTGACATTCTCCTCA 59.356 45.455 0.00 0.00 0.00 3.86
2611 3192 2.338785 GGCCAGACAAAGCTCCTGC 61.339 63.158 0.00 0.00 40.05 4.85
2752 3333 2.228822 CTGGTACCAATGGCAACTTGAC 59.771 50.000 17.11 0.00 37.61 3.18
2799 3380 6.414732 TCAGACCAATTCCCATACTGTAAAG 58.585 40.000 0.00 0.00 0.00 1.85
2917 5041 7.270579 GCTCTATGATTTCGTTTTGTTTACACC 59.729 37.037 0.00 0.00 0.00 4.16
2918 5042 8.155821 TCTATGATTTCGTTTTGTTTACACCA 57.844 30.769 0.00 0.00 0.00 4.17
2931 5055 4.591498 TGTTTACACCAGTGAGTGACCTAT 59.409 41.667 15.85 0.00 40.34 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 271 0.176680 CTCCTGGTGAGACGGATTGG 59.823 60.000 0.00 0.00 44.42 3.16
262 285 5.468072 CCTAATCGGATGATTGTTTCTCCTG 59.532 44.000 0.93 0.00 44.46 3.86
634 731 7.743116 AAAGGGAAGGAAACTAAAGGAAAAA 57.257 32.000 0.00 0.00 42.68 1.94
1001 1117 2.031012 CTGCCTTCCTGTGCGTCA 59.969 61.111 0.00 0.00 0.00 4.35
1235 1380 6.152379 GTCATCAAACAGAAAAATCAGGGAC 58.848 40.000 0.00 0.00 0.00 4.46
1309 1460 2.108250 AGGTGGCTGGAGTTGTAATGTT 59.892 45.455 0.00 0.00 0.00 2.71
1330 1481 1.903860 ACACTAGCCGGAATTGTACCA 59.096 47.619 5.05 0.00 0.00 3.25
1916 2452 1.339151 GCACTGGTCCTCCTAACTTGG 60.339 57.143 0.00 0.00 34.23 3.61
2082 2621 2.489722 CTCACAGATTCACTCGTGGAGA 59.510 50.000 0.00 0.00 33.32 3.71
2197 2736 2.739293 GCGCAAAGCTTGTATAGTCC 57.261 50.000 0.30 0.00 44.04 3.85
2437 2987 4.514066 GGTCACGGAAGTTTTGTAAGACAT 59.486 41.667 0.00 0.00 46.40 3.06
2723 3304 1.466856 CATTGGTACCAGCAGCATGT 58.533 50.000 15.65 0.00 39.31 3.21
2752 3333 3.160679 AGTCCCTCCAATTTGAAGTGG 57.839 47.619 3.92 3.92 45.10 4.00
2818 3401 2.430694 GGCCTTTTCACACAAAACCTCT 59.569 45.455 0.00 0.00 0.00 3.69
2917 5041 4.023980 TGGAAGGTATAGGTCACTCACTG 58.976 47.826 0.00 0.00 0.00 3.66
2918 5042 4.332683 TGGAAGGTATAGGTCACTCACT 57.667 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.