Multiple sequence alignment - TraesCS5B01G254700

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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 TraesCS5B01G254700 chr5B 100.000 3038 0 0 1 3038 437539070 437536033 0.000000e+00 5611.0
1 TraesCS5B01G254700 chr5B 91.860 3022 166 29 3 2993 437306549 437303577 0.000000e+00 4145.0
2 TraesCS5B01G254700 chr5B 94.442 2213 98 9 3 2196 437369082 437366876 0.000000e+00 3382.0
3 TraesCS5B01G254700 chr5B 96.366 1596 46 5 1404 2994 437462535 437460947 0.000000e+00 2615.0
4 TraesCS5B01G254700 chr5B 92.883 1658 88 20 977 2612 437572025 437573674 0.000000e+00 2381.0
5 TraesCS5B01G254700 chr5B 91.461 1663 111 18 977 2617 437601302 437602955 0.000000e+00 2255.0
6 TraesCS5B01G254700 chr5B 93.697 1428 67 8 3 1411 437464965 437463542 0.000000e+00 2117.0
7 TraesCS5B01G254700 chr5B 86.078 2040 152 63 714 2682 437807164 437809142 0.000000e+00 2073.0
8 TraesCS5B01G254700 chr5B 80.101 397 47 17 4 398 437517437 437517071 1.800000e-67 267.0
9 TraesCS5B01G254700 chr5B 79.500 400 46 16 2 398 437344665 437344299 5.030000e-63 252.0
10 TraesCS5B01G254700 chr5B 78.750 400 49 16 2 398 437439979 437439613 5.060000e-58 235.0
11 TraesCS5B01G254700 chr5D 91.877 2216 125 14 103 2299 369062406 369060227 0.000000e+00 3044.0
12 TraesCS5B01G254700 chr5D 90.998 611 30 11 2393 2993 369057863 369057268 0.000000e+00 800.0
13 TraesCS5B01G254700 chr5D 95.806 310 12 1 2046 2354 369058168 369057859 1.630000e-137 499.0
14 TraesCS5B01G254700 chr5D 87.151 358 29 10 2425 2767 369058621 369058266 1.020000e-104 390.0
15 TraesCS5B01G254700 chr5A 88.610 1554 111 38 740 2266 470667514 470669028 0.000000e+00 1829.0
16 TraesCS5B01G254700 chr5A 91.179 1349 85 24 759 2092 471511303 471512632 0.000000e+00 1801.0
17 TraesCS5B01G254700 chr5A 81.387 591 67 14 2431 2983 471507253 471507838 2.780000e-120 442.0
18 TraesCS5B01G254700 chr3A 81.970 599 74 14 103 697 456434329 456434897 7.620000e-131 477.0
19 TraesCS5B01G254700 chr1B 81.313 594 80 17 103 692 394413092 394412526 1.280000e-123 453.0
20 TraesCS5B01G254700 chr1D 78.897 526 78 18 1 523 19756204 19756699 2.920000e-85 326.0
21 TraesCS5B01G254700 chr1D 80.541 185 27 6 514 696 19756644 19756821 1.900000e-27 134.0
22 TraesCS5B01G254700 chr1A 77.912 249 43 10 239 483 516453601 516453841 8.780000e-31 145.0
23 TraesCS5B01G254700 chr6D 98.000 50 1 0 2989 3038 384768652 384768603 1.500000e-13 87.9


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 TraesCS5B01G254700 chr5B 437536033 437539070 3037 True 5611.00 5611 100.0000 1 3038 1 chr5B.!!$R6 3037
1 TraesCS5B01G254700 chr5B 437303577 437306549 2972 True 4145.00 4145 91.8600 3 2993 1 chr5B.!!$R1 2990
2 TraesCS5B01G254700 chr5B 437366876 437369082 2206 True 3382.00 3382 94.4420 3 2196 1 chr5B.!!$R3 2193
3 TraesCS5B01G254700 chr5B 437572025 437573674 1649 False 2381.00 2381 92.8830 977 2612 1 chr5B.!!$F1 1635
4 TraesCS5B01G254700 chr5B 437460947 437464965 4018 True 2366.00 2615 95.0315 3 2994 2 chr5B.!!$R7 2991
5 TraesCS5B01G254700 chr5B 437601302 437602955 1653 False 2255.00 2255 91.4610 977 2617 1 chr5B.!!$F2 1640
6 TraesCS5B01G254700 chr5B 437807164 437809142 1978 False 2073.00 2073 86.0780 714 2682 1 chr5B.!!$F3 1968
7 TraesCS5B01G254700 chr5D 369057268 369062406 5138 True 1183.25 3044 91.4580 103 2993 4 chr5D.!!$R1 2890
8 TraesCS5B01G254700 chr5A 470667514 470669028 1514 False 1829.00 1829 88.6100 740 2266 1 chr5A.!!$F1 1526
9 TraesCS5B01G254700 chr5A 471507253 471512632 5379 False 1121.50 1801 86.2830 759 2983 2 chr5A.!!$F2 2224
10 TraesCS5B01G254700 chr3A 456434329 456434897 568 False 477.00 477 81.9700 103 697 1 chr3A.!!$F1 594
11 TraesCS5B01G254700 chr1B 394412526 394413092 566 True 453.00 453 81.3130 103 692 1 chr1B.!!$R1 589
12 TraesCS5B01G254700 chr1D 19756204 19756821 617 False 230.00 326 79.7190 1 696 2 chr1D.!!$F1 695

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
183 199 0.959553 AGTTGTGACCTCGTGACGAT 59.040 50.0 8.60 0.0 34.61 3.73 F
324 369 1.695893 CGTCGACGCAATTCCATGCT 61.696 55.0 26.59 0.0 44.21 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 6225 0.908198 GTCCTCTGGGAAGTGCTGAT 59.092 55.000 0.0 0.0 44.15 2.90 R
2180 8860 8.879759 GTCGGTTTTCAGTCAAAGATATATTCA 58.120 33.333 0.0 0.0 0.00 2.57 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
48 50 1.001815 CTTGAACCGGTGTCGCAAAAT 60.002 47.619 8.52 0.00 34.56 1.82
166 182 1.202580 GCTACATCCATCAAGCGGAGT 60.203 52.381 0.00 0.00 35.56 3.85
169 185 1.003580 ACATCCATCAAGCGGAGTTGT 59.996 47.619 0.00 0.00 35.56 3.32
183 199 0.959553 AGTTGTGACCTCGTGACGAT 59.040 50.000 8.60 0.00 34.61 3.73
324 369 1.695893 CGTCGACGCAATTCCATGCT 61.696 55.000 26.59 0.00 44.21 3.79
398 443 4.697592 CTGCTGAGAGCTGCAACT 57.302 55.556 1.02 0.09 46.28 3.16
472 517 4.754667 GGACCGGCGACAAGGACC 62.755 72.222 9.30 0.00 35.43 4.46
511 556 3.461773 CGATGAGGACGGCCACCT 61.462 66.667 11.69 17.02 40.80 4.00
537 582 1.987855 CAGGCCAACGAGGGGTAGA 60.988 63.158 5.01 0.00 38.09 2.59
697 752 2.419324 ACGCGTATGGCCGAAATTTTTA 59.581 40.909 11.67 0.00 38.94 1.52
885 4181 2.681778 CCAGGGACCACTCGAGCT 60.682 66.667 13.61 0.00 0.00 4.09
927 4223 7.548097 AGCATCCCAACTTCTATATATACGTG 58.452 38.462 0.00 0.00 0.00 4.49
1005 4320 4.891727 CCTCCGTTCCCGATGGCG 62.892 72.222 0.00 0.00 35.63 5.69
1523 5859 2.244117 ATCCACCGCGACATCAAGCT 62.244 55.000 8.23 0.00 0.00 3.74
1889 6225 0.539438 ATTTCCCGCAACAAGCTCCA 60.539 50.000 0.00 0.00 42.61 3.86
2180 8860 8.284945 AGTGTGCATGAGATTGTATGTTAATT 57.715 30.769 0.00 0.00 0.00 1.40
2622 9379 6.859508 CCTACAAGTTTGTACCGAAAAATTCC 59.140 38.462 0.73 0.00 42.35 3.01
2893 9658 5.192927 GTGGGGTTGTCATTCATATTCTGA 58.807 41.667 0.00 0.00 0.00 3.27
2924 9689 4.265073 AGCCCTTACTTCACATTAGCAAG 58.735 43.478 0.00 0.00 0.00 4.01
3004 9769 9.933723 TTAGTGAAGTACTTATTGTTAGGGAAC 57.066 33.333 8.42 0.00 40.89 3.62
3005 9770 7.095270 AGTGAAGTACTTATTGTTAGGGAACG 58.905 38.462 8.42 0.00 35.64 3.95
3006 9771 6.870439 GTGAAGTACTTATTGTTAGGGAACGT 59.130 38.462 8.42 0.00 38.51 3.99
3007 9772 8.028938 GTGAAGTACTTATTGTTAGGGAACGTA 58.971 37.037 8.42 0.00 38.51 3.57
3008 9773 8.246180 TGAAGTACTTATTGTTAGGGAACGTAG 58.754 37.037 8.42 0.00 38.51 3.51
3010 9775 8.807948 AGTACTTATTGTTAGGGAACGTAGTA 57.192 34.615 0.00 0.00 45.00 1.82
3011 9776 9.243105 AGTACTTATTGTTAGGGAACGTAGTAA 57.757 33.333 0.00 0.00 45.00 2.24
3014 9779 9.948964 ACTTATTGTTAGGGAACGTAGTAATTT 57.051 29.630 0.00 0.00 45.00 1.82
3016 9781 9.941325 TTATTGTTAGGGAACGTAGTAATTTCA 57.059 29.630 0.00 0.00 45.00 2.69
3017 9782 8.851541 ATTGTTAGGGAACGTAGTAATTTCAA 57.148 30.769 0.00 0.00 45.00 2.69
3018 9783 8.674263 TTGTTAGGGAACGTAGTAATTTCAAA 57.326 30.769 0.00 0.00 45.00 2.69
3019 9784 8.674263 TGTTAGGGAACGTAGTAATTTCAAAA 57.326 30.769 0.00 0.00 45.00 2.44
3020 9785 9.118300 TGTTAGGGAACGTAGTAATTTCAAAAA 57.882 29.630 0.00 0.00 45.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.456280 GTTCAAGCTTTCATTGTGGCAA 58.544 40.909 0.00 0.00 0.00 4.52
48 50 5.504994 GCTTTTTGTGATGTCGGTTGAAGTA 60.505 40.000 0.00 0.00 0.00 2.24
110 125 5.587443 GCCGTTAGTACCAAAATCCAACTAT 59.413 40.000 0.00 0.00 0.00 2.12
166 182 0.038618 CCATCGTCACGAGGTCACAA 60.039 55.000 11.45 0.00 39.91 3.33
169 185 2.571757 GCCATCGTCACGAGGTCA 59.428 61.111 11.45 0.00 39.91 4.02
183 199 0.109179 GCAGCAAATCATTGTCGCCA 60.109 50.000 0.00 0.00 38.85 5.69
324 369 0.394192 CCTCGCCATTGATGCTCCTA 59.606 55.000 0.00 0.00 0.00 2.94
511 556 4.263572 CGTTGGCCTGTCCCCACA 62.264 66.667 3.32 0.00 30.65 4.17
525 570 0.679321 GTCGGTCTCTACCCCTCGTT 60.679 60.000 0.00 0.00 43.54 3.85
537 582 1.593296 GCCGTCCTAGTTGTCGGTCT 61.593 60.000 11.60 0.00 44.07 3.85
543 588 2.939261 CGGTGGCCGTCCTAGTTGT 61.939 63.158 13.68 0.00 42.73 3.32
927 4223 1.452145 ATTGTGGTTGTGGTGGTCGC 61.452 55.000 0.00 0.00 0.00 5.19
1005 4320 2.174319 GGGGAAGACGCGCTTGATC 61.174 63.158 18.16 3.11 36.83 2.92
1523 5859 2.355986 CCGACGAGGATGTTCCCCA 61.356 63.158 0.00 0.00 45.00 4.96
1633 5969 2.172483 ATCTCCGGCGCCATGTATCC 62.172 60.000 28.98 0.00 0.00 2.59
1889 6225 0.908198 GTCCTCTGGGAAGTGCTGAT 59.092 55.000 0.00 0.00 44.15 2.90
2180 8860 8.879759 GTCGGTTTTCAGTCAAAGATATATTCA 58.120 33.333 0.00 0.00 0.00 2.57
2924 9689 4.986260 AAACACGTGTTCGCAAAGTTTGC 61.986 43.478 32.36 27.23 44.52 3.68
2994 9759 8.674263 TTTTGAAATTACTACGTTCCCTAACA 57.326 30.769 0.00 0.00 35.16 2.41


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

AutoCloner maintained by Alex Coulton.