Multiple sequence alignment - TraesCS7B01G486000

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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 TraesCS7B01G486000 chr7B 100.000 2595 0 0 1 2595 742245692 742243098 0.000000e+00 4793
1 TraesCS7B01G486000 chrUn 88.943 2071 106 56 106 2096 108695406 108693379 0.000000e+00 2442
2 TraesCS7B01G486000 chrUn 93.533 433 25 3 2114 2545 108665278 108664848 2.180000e-180 641
3 TraesCS7B01G486000 chrUn 91.228 114 10 0 1 114 108695883 108695770 3.460000e-34 156
4 TraesCS7B01G486000 chr4B 88.634 1874 104 46 599 2438 665453099 665451301 0.000000e+00 2180
5 TraesCS7B01G486000 chr4B 89.246 1246 76 26 644 1879 665344466 665345663 0.000000e+00 1506
6 TraesCS7B01G486000 chr4B 94.231 624 19 6 1 609 665454016 665453395 0.000000e+00 937
7 TraesCS7B01G486000 chr4B 88.688 442 32 9 156 580 665343373 665343813 8.230000e-145 523
8 TraesCS7B01G486000 chr4B 97.656 256 5 1 2341 2595 665346169 665346424 3.070000e-119 438
9 TraesCS7B01G486000 chr4B 98.765 162 1 1 2435 2595 665449477 665449316 1.180000e-73 287
10 TraesCS7B01G486000 chr4B 96.000 150 5 1 1947 2096 665345698 665345846 2.580000e-60 243
11 TraesCS7B01G486000 chr4B 90.000 170 12 1 2100 2269 665345973 665346137 5.620000e-52 215
12 TraesCS7B01G486000 chr4B 82.895 152 19 3 1 150 665342944 665343090 2.100000e-26 130
13 TraesCS7B01G486000 chr5A 87.121 924 70 21 498 1407 705304216 705305104 0.000000e+00 1002
14 TraesCS7B01G486000 chr5A 83.012 518 53 20 16 513 705303509 705304011 1.100000e-118 436
15 TraesCS7B01G486000 chr5A 87.619 315 37 2 2282 2595 705306081 705306394 5.280000e-97 364
16 TraesCS7B01G486000 chr5A 84.091 264 34 7 1434 1694 705305101 705305359 5.550000e-62 248


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 TraesCS7B01G486000 chr7B 742243098 742245692 2594 True 4793.000000 4793 100.000000 1 2595 1 chr7B.!!$R1 2594
1 TraesCS7B01G486000 chrUn 108693379 108695883 2504 True 1299.000000 2442 90.085500 1 2096 2 chrUn.!!$R2 2095
2 TraesCS7B01G486000 chr4B 665449316 665454016 4700 True 1134.666667 2180 93.876667 1 2595 3 chr4B.!!$R1 2594
3 TraesCS7B01G486000 chr4B 665342944 665346424 3480 False 509.166667 1506 90.747500 1 2595 6 chr4B.!!$F1 2594
4 TraesCS7B01G486000 chr5A 705303509 705306394 2885 False 512.500000 1002 85.460750 16 2595 4 chr5A.!!$F1 2579

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
330 1003 0.399454 CCTATGGCCTCTGTCATGGG 59.601 60.0 3.32 0.0 46.92 4.0 F
880 2719 0.953471 GAACATGGGCAGCACGTACA 60.953 55.0 0.00 0.0 0.00 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 3124 1.576421 GGACTGCTTTGCGACCTTG 59.424 57.895 0.00 0.0 0.00 3.61 R
2193 4218 2.198336 TCTCGGAGGAGAAGTAGACCT 58.802 52.381 4.96 0.0 46.11 3.85 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
138 511 4.343239 ACACTCGTCATTTACCCCTATACC 59.657 45.833 0.00 0.00 0.00 2.73
261 917 4.116238 GCTTAGATGGATATAAGCCGAGC 58.884 47.826 12.93 0.00 46.42 5.03
330 1003 0.399454 CCTATGGCCTCTGTCATGGG 59.601 60.000 3.32 0.00 46.92 4.00
377 1054 5.718649 AAACATCTAATCGGACGTGATTG 57.281 39.130 10.50 0.00 38.92 2.67
392 1071 7.152645 GGACGTGATTGGTATATCAGTAACAT 58.847 38.462 0.00 0.00 35.32 2.71
420 1099 1.864565 TATTGATCATGGACGCGGTG 58.135 50.000 12.47 3.73 0.00 4.94
445 1124 6.987386 AGCACTTATATCTCGCTTATGAACT 58.013 36.000 0.00 0.00 0.00 3.01
455 1134 4.765273 TCGCTTATGAACTGGCTTATCAA 58.235 39.130 0.00 0.00 0.00 2.57
700 2519 2.688477 CCTGCCTTCTCCTAATCTCCT 58.312 52.381 0.00 0.00 0.00 3.69
880 2719 0.953471 GAACATGGGCAGCACGTACA 60.953 55.000 0.00 0.00 0.00 2.90
900 2739 1.009829 CTCCAGCTCATTACGTTGGC 58.990 55.000 0.00 0.00 0.00 4.52
942 2781 1.846124 AAGCCGGAGACCCCTTTCA 60.846 57.895 5.05 0.00 0.00 2.69
955 2794 2.025981 CCCCTTTCATCATCACACCTCA 60.026 50.000 0.00 0.00 0.00 3.86
1004 2847 4.993584 ACACTAATCAAGATCGATCATGGC 59.006 41.667 25.60 2.01 0.00 4.40
1281 3124 1.880340 CGGAATCGCTGAGGCTCAC 60.880 63.158 14.43 9.86 36.09 3.51
1380 3226 1.599797 CTGCGACCCCGAAAAACCT 60.600 57.895 0.00 0.00 38.22 3.50
1528 3374 2.633967 ACAAAGCATTGGAAATGGAGCA 59.366 40.909 6.62 0.00 41.01 4.26
1608 3456 0.981183 ATGTAAACCGAGTGCTGGGA 59.019 50.000 7.25 0.00 32.36 4.37
1609 3457 0.320374 TGTAAACCGAGTGCTGGGAG 59.680 55.000 7.25 0.00 32.36 4.30
1617 3465 1.386485 AGTGCTGGGAGGGGCATAT 60.386 57.895 0.00 0.00 40.66 1.78
1717 3566 4.180057 GGTGCAATCAATAAAAATCGGCA 58.820 39.130 0.00 0.00 0.00 5.69
1831 3722 8.264347 ACAAAAGAAAGAAAAAGGAGGCATTTA 58.736 29.630 0.00 0.00 0.00 1.40
1833 3724 9.679661 AAAAGAAAGAAAAAGGAGGCATTTAAA 57.320 25.926 0.00 0.00 0.00 1.52
1834 3725 9.851686 AAAGAAAGAAAAAGGAGGCATTTAAAT 57.148 25.926 0.00 0.00 0.00 1.40
1835 3726 9.851686 AAGAAAGAAAAAGGAGGCATTTAAATT 57.148 25.926 0.00 0.00 0.00 1.82
1836 3727 9.851686 AGAAAGAAAAAGGAGGCATTTAAATTT 57.148 25.926 0.00 0.00 0.00 1.82
1895 3795 7.806014 TGTTCAAATATTTACTGGAGCGTTTTC 59.194 33.333 0.00 0.00 0.00 2.29
1920 3820 5.047802 CCATACCACAAGAAGAAATGTTGCT 60.048 40.000 0.00 0.00 35.77 3.91
1940 3840 8.575589 TGTTGCTCTGTACAAATGAAATATTGT 58.424 29.630 0.00 0.00 42.16 2.71
2120 4145 6.799926 ATGTGTTTGTTTATTTCAATGGGC 57.200 33.333 0.00 0.00 0.00 5.36
2418 4808 7.065803 ACGTGAACTTTAAGTAAGCATGCATAT 59.934 33.333 21.98 8.21 37.37 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 511 9.750125 AAAAGCACTCTTATTTTAAAACTCAGG 57.250 29.630 1.97 0.00 31.02 3.86
261 917 1.006832 CCAGAGTTTTACATCGGCCG 58.993 55.000 22.12 22.12 0.00 6.13
330 1003 8.654230 TTCTTAGTGAAGATCTGCATACATTC 57.346 34.615 6.69 0.00 41.40 2.67
392 1071 5.700832 GCGTCCATGATCAATAATTCTGGTA 59.299 40.000 0.00 0.00 0.00 3.25
420 1099 7.061673 CAGTTCATAAGCGAGATATAAGTGCTC 59.938 40.741 0.00 0.00 34.19 4.26
455 1134 5.534207 TGATGGTCAGCAGATTTGTTTTT 57.466 34.783 0.00 0.00 0.00 1.94
580 1505 7.096271 GCATACAACTCAGAGAATGATACGAAG 60.096 40.741 3.79 0.00 37.28 3.79
684 2503 6.054860 TGAAACAAGGAGATTAGGAGAAGG 57.945 41.667 0.00 0.00 0.00 3.46
700 2519 5.942236 CAGATCCTTTCTCTCCATGAAACAA 59.058 40.000 0.00 0.00 29.93 2.83
736 2565 7.756272 TGCTGATCATGTTTATTGCTACTTTTG 59.244 33.333 0.00 0.00 0.00 2.44
773 2606 4.155280 TGAGATGTTGACTTGCATGTCATG 59.845 41.667 29.48 8.56 45.03 3.07
774 2607 4.329392 TGAGATGTTGACTTGCATGTCAT 58.671 39.130 29.48 18.52 45.03 3.06
775 2608 3.742385 TGAGATGTTGACTTGCATGTCA 58.258 40.909 26.52 26.52 44.17 3.58
776 2609 4.438336 CCATGAGATGTTGACTTGCATGTC 60.438 45.833 22.34 22.34 36.37 3.06
777 2610 3.442625 CCATGAGATGTTGACTTGCATGT 59.557 43.478 4.68 4.68 32.09 3.21
880 2719 1.676014 GCCAACGTAATGAGCTGGAGT 60.676 52.381 4.38 0.00 0.00 3.85
942 2781 3.449018 GTGAGGTACTGAGGTGTGATGAT 59.551 47.826 0.00 0.00 41.55 2.45
1004 2847 2.274232 TAATCGGCGGACGTGGTGAG 62.274 60.000 7.21 0.00 44.69 3.51
1281 3124 1.576421 GGACTGCTTTGCGACCTTG 59.424 57.895 0.00 0.00 0.00 3.61
1380 3226 3.726557 AGGAATGCATCTTTCTGACCA 57.273 42.857 0.00 0.00 0.00 4.02
1680 3529 5.476254 TGATTGCACCATGAGTCAAACATAA 59.524 36.000 0.00 0.00 0.00 1.90
1806 3694 7.558161 AAATGCCTCCTTTTTCTTTCTTTTG 57.442 32.000 0.00 0.00 0.00 2.44
1859 3750 4.470334 AATATTTGAACACACCCATGCC 57.530 40.909 0.00 0.00 0.00 4.40
1895 3795 5.713025 CAACATTTCTTCTTGTGGTATGGG 58.287 41.667 0.00 0.00 0.00 4.00
1920 3820 7.975058 CCATGCACAATATTTCATTTGTACAGA 59.025 33.333 0.00 0.00 33.80 3.41
1940 3840 4.099113 TCGCATCAATTAAAATCCCATGCA 59.901 37.500 0.00 0.00 35.87 3.96
2096 3998 6.073331 CGCCCATTGAAATAAACAAACACATT 60.073 34.615 0.00 0.00 0.00 2.71
2115 4140 3.011517 AGCCAGAGGTTCGCCCAT 61.012 61.111 0.00 0.00 38.27 4.00
2120 4145 2.289002 GCATTAATCAGCCAGAGGTTCG 59.711 50.000 0.00 0.00 0.00 3.95
2159 4184 2.835764 TGTATCCCCGTAGAAAAGCACT 59.164 45.455 0.00 0.00 0.00 4.40
2188 4213 4.131596 CGGAGGAGAAGTAGACCTAGAAG 58.868 52.174 0.00 0.00 33.89 2.85
2191 4216 3.388676 TCTCGGAGGAGAAGTAGACCTAG 59.611 52.174 4.96 0.00 46.11 3.02
2193 4218 2.198336 TCTCGGAGGAGAAGTAGACCT 58.802 52.381 4.96 0.00 46.11 3.85


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

AutoCloner maintained by Alex Coulton.