Multiple sequence alignment - TraesCS7B01G450500

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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 TraesCS7B01G450500 chr7B 100.000 3843 0 0 1 3843 712607259 712611101 0.000000e+00 7097
1 TraesCS7B01G450500 chr7B 92.820 3677 182 47 1 3646 733218508 733214883 0.000000e+00 5252
2 TraesCS7B01G450500 chr7B 91.086 1234 60 32 2616 3842 733215907 733214717 0.000000e+00 1624
3 TraesCS7B01G450500 chr4B 96.213 3855 116 25 1 3842 638494144 638490307 0.000000e+00 6283
4 TraesCS7B01G450500 chr1B 92.357 3873 183 61 1 3842 621587228 621583438 0.000000e+00 5408
5 TraesCS7B01G450500 chr3B 94.074 2413 112 22 1 2392 18008499 18006097 0.000000e+00 3635
6 TraesCS7B01G450500 chr7D 86.323 2910 285 74 969 3842 21681054 21678222 0.000000e+00 3064
7 TraesCS7B01G450500 chr7D 86.170 2914 290 72 969 3842 108301252 108298412 0.000000e+00 3044
8 TraesCS7B01G450500 chr7D 86.008 2916 296 74 969 3842 108264327 108261482 0.000000e+00 3022
9 TraesCS7B01G450500 chr7D 87.097 372 39 8 546 913 21681528 21681162 2.760000e-111 412
10 TraesCS7B01G450500 chr7D 87.591 274 25 7 31 297 21681880 21681609 3.730000e-80 309
11 TraesCS7B01G450500 chr5D 86.219 2917 290 76 969 3842 30633327 30630480 0.000000e+00 3057
12 TraesCS7B01G450500 chr5D 85.575 2052 208 58 1827 3842 420308643 420306644 0.000000e+00 2069
13 TraesCS7B01G450500 chr5D 86.828 372 41 7 546 913 30633802 30633435 3.570000e-110 409
14 TraesCS7B01G450500 chr5D 87.956 274 24 7 31 297 420310355 420310084 8.010000e-82 315
15 TraesCS7B01G450500 chr2D 85.704 2917 302 80 969 3842 343142486 343139642 0.000000e+00 2970
16 TraesCS7B01G450500 chr6A 85.930 2516 266 66 976 3455 615412320 615409857 0.000000e+00 2604
17 TraesCS7B01G450500 chr6A 82.807 570 80 15 358 913 615412999 615412434 9.590000e-136 494
18 TraesCS7B01G450500 chr1D 86.301 2314 235 57 969 3258 66199556 66197301 0.000000e+00 2442
19 TraesCS7B01G450500 chr1D 87.366 372 40 7 546 913 66200035 66199667 1.650000e-113 420
20 TraesCS7B01G450500 chr3A 85.438 1394 165 27 976 2355 735465571 735466940 0.000000e+00 1415
21 TraesCS7B01G450500 chr3A 88.184 1041 89 25 2420 3447 735466926 735467945 0.000000e+00 1210
22 TraesCS7B01G450500 chr3A 81.771 576 76 17 358 908 735464881 735465452 4.530000e-124 455
23 TraesCS7B01G450500 chr3A 85.953 299 25 14 31 321 735464588 735464877 1.730000e-78 303


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 TraesCS7B01G450500 chr7B 712607259 712611101 3842 False 7097.000000 7097 100.000000 1 3843 1 chr7B.!!$F1 3842
1 TraesCS7B01G450500 chr7B 733214717 733218508 3791 True 3438.000000 5252 91.953000 1 3842 2 chr7B.!!$R1 3841
2 TraesCS7B01G450500 chr4B 638490307 638494144 3837 True 6283.000000 6283 96.213000 1 3842 1 chr4B.!!$R1 3841
3 TraesCS7B01G450500 chr1B 621583438 621587228 3790 True 5408.000000 5408 92.357000 1 3842 1 chr1B.!!$R1 3841
4 TraesCS7B01G450500 chr3B 18006097 18008499 2402 True 3635.000000 3635 94.074000 1 2392 1 chr3B.!!$R1 2391
5 TraesCS7B01G450500 chr7D 108298412 108301252 2840 True 3044.000000 3044 86.170000 969 3842 1 chr7D.!!$R2 2873
6 TraesCS7B01G450500 chr7D 108261482 108264327 2845 True 3022.000000 3022 86.008000 969 3842 1 chr7D.!!$R1 2873
7 TraesCS7B01G450500 chr7D 21678222 21681880 3658 True 1261.666667 3064 87.003667 31 3842 3 chr7D.!!$R3 3811
8 TraesCS7B01G450500 chr5D 30630480 30633802 3322 True 1733.000000 3057 86.523500 546 3842 2 chr5D.!!$R1 3296
9 TraesCS7B01G450500 chr5D 420306644 420310355 3711 True 1192.000000 2069 86.765500 31 3842 2 chr5D.!!$R2 3811
10 TraesCS7B01G450500 chr2D 343139642 343142486 2844 True 2970.000000 2970 85.704000 969 3842 1 chr2D.!!$R1 2873
11 TraesCS7B01G450500 chr6A 615409857 615412999 3142 True 1549.000000 2604 84.368500 358 3455 2 chr6A.!!$R1 3097
12 TraesCS7B01G450500 chr1D 66197301 66200035 2734 True 1431.000000 2442 86.833500 546 3258 2 chr1D.!!$R1 2712
13 TraesCS7B01G450500 chr3A 735464588 735467945 3357 False 845.750000 1415 85.336500 31 3447 4 chr3A.!!$F1 3416

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
582 609 1.762957 CAGGGAGGTTCGTCCATACAT 59.237 52.381 12.54 0.0 38.52 2.29 F
1212 1307 1.165270 CCCCTTCCTTTTGTGTAGCG 58.835 55.000 0.00 0.0 0.00 4.26 F
1595 1704 2.494073 TGGCCGTGATTTTATGGTTTCC 59.506 45.455 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2348 0.678950 TGCTCACCATGAACTGACGA 59.321 50.00 0.00 0.0 0.00 4.20 R
2705 2881 1.699656 CGCTGCAGAGGATTTCGTGG 61.700 60.00 20.43 0.0 0.00 4.94 R
3464 3679 4.618635 TGCATTAAAGAAATGATGGGGGA 58.381 39.13 2.01 0.0 46.81 4.81 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
93 94 4.924305 ACAACACATTCAAGAGTTGCAT 57.076 36.364 0.00 0.00 41.71 3.96
343 349 6.656632 TTTTGCATACACACCATTTTCCTA 57.343 33.333 0.00 0.00 0.00 2.94
350 356 4.917385 ACACACCATTTTCCTATGCTACA 58.083 39.130 0.00 0.00 0.00 2.74
510 534 8.752005 AATTTGCTGTAATAAATCTCCTGCTA 57.248 30.769 0.00 0.00 0.00 3.49
582 609 1.762957 CAGGGAGGTTCGTCCATACAT 59.237 52.381 12.54 0.00 38.52 2.29
666 693 7.820872 CAGTTTAAAGAAAAGGATGGCATCATT 59.179 33.333 27.39 24.11 34.32 2.57
1051 1146 5.374071 TGCAGAGATATTCAGCAACATCAT 58.626 37.500 0.00 0.00 44.20 2.45
1212 1307 1.165270 CCCCTTCCTTTTGTGTAGCG 58.835 55.000 0.00 0.00 0.00 4.26
1218 1313 3.678056 TCCTTTTGTGTAGCGTCATCT 57.322 42.857 0.00 0.00 0.00 2.90
1389 1493 7.628234 AGCTTTCTTTAGGATCTTCATCAAGA 58.372 34.615 0.00 0.00 43.06 3.02
1595 1704 2.494073 TGGCCGTGATTTTATGGTTTCC 59.506 45.455 0.00 0.00 0.00 3.13
1643 1755 7.284820 ACAATACTAGTTGTTAAACCACCTGT 58.715 34.615 0.00 0.00 39.15 4.00
1931 2079 7.095229 GGGTGGAAGCTCAACAATTAAATTTTC 60.095 37.037 0.00 0.00 0.00 2.29
1993 2142 2.499693 CTCTGAAGAAGGAAGGAGGGAC 59.500 54.545 0.00 0.00 0.00 4.46
2011 2160 3.006247 GGACATGAGGAGAAAAGCACTC 58.994 50.000 0.00 0.00 0.00 3.51
2050 2199 3.698040 CTGGAAAAGCATTGCCTCTACAT 59.302 43.478 4.70 0.00 0.00 2.29
2219 2377 4.299586 TCATGGTGAGCATTGGTTCTTA 57.700 40.909 0.00 0.00 0.00 2.10
2223 2381 4.661222 TGGTGAGCATTGGTTCTTATTCA 58.339 39.130 0.00 0.00 0.00 2.57
2705 2881 0.244721 GTGGATGCAAACTTGGGCTC 59.755 55.000 0.00 0.00 0.00 4.70
2778 2954 2.030805 GGGTCAGATTTGCTGTTGACAC 60.031 50.000 5.91 0.00 45.14 3.67
3176 3371 6.096141 AGTTTAACAACATCACACAACATCCA 59.904 34.615 0.00 0.00 35.05 3.41
3293 3497 7.282916 CAATTCGGATTGTGTCATTTTGTTTC 58.717 34.615 8.37 0.00 38.25 2.78
3299 3503 6.930722 GGATTGTGTCATTTTGTTTCCAGATT 59.069 34.615 0.00 0.00 0.00 2.40
3464 3679 9.492973 CCCTTGTTCATTTGTTTCTATCATTTT 57.507 29.630 0.00 0.00 0.00 1.82
3481 3696 7.993349 ATCATTTTCCCCCATCATTTCTTTA 57.007 32.000 0.00 0.00 0.00 1.85
3598 3813 1.633945 GGTCAGTGTTCCTACCCCAAT 59.366 52.381 0.00 0.00 0.00 3.16
3669 3898 9.610705 TTATAATGTATGCATTTGCCAAAACAT 57.389 25.926 14.47 12.07 42.19 2.71
3828 4059 0.110486 TCTTGAACTTCCAGCACCCC 59.890 55.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.343814 TGTTGCTTATCGTCTATCCCATCA 59.656 41.667 0.00 0.00 0.00 3.07
93 94 3.081061 GTCTAATGGGTGCAATGTGTCA 58.919 45.455 0.00 0.00 0.00 3.58
221 222 3.104512 TCCGAGTTCATCTGTAATGGGT 58.895 45.455 0.00 0.00 0.00 4.51
315 319 7.173047 GGAAAATGGTGTGTATGCAAAAAGAAT 59.827 33.333 0.00 0.00 0.00 2.40
343 349 5.806654 AAGTGGGTGAATTTTTGTAGCAT 57.193 34.783 0.00 0.00 0.00 3.79
440 449 2.524306 TGGCAAAAAGATGGTACCTGG 58.476 47.619 14.36 0.00 0.00 4.45
569 596 2.482336 TGTGCACAATGTATGGACGAAC 59.518 45.455 19.28 0.00 40.97 3.95
582 609 1.065491 ACAGGTTGTCTCTGTGCACAA 60.065 47.619 21.98 10.91 43.07 3.33
609 636 2.162408 GTCTCTGTACTTGCAAATGCCC 59.838 50.000 0.00 0.00 41.18 5.36
666 693 5.055265 TGGGAAAAAGACATACCAAGTCA 57.945 39.130 0.00 0.00 38.46 3.41
764 798 7.920151 TCTGAATGAAAGTTTTGTTGTGTATGG 59.080 33.333 0.00 0.00 0.00 2.74
956 1035 6.076981 ACGAAGCACAAATTTTGAGAGAAT 57.923 33.333 15.81 0.00 0.00 2.40
1003 1096 4.020307 AGGCACAAATAATGTTGAAAGGGG 60.020 41.667 0.00 0.00 41.46 4.79
1389 1493 4.657814 TGGAGGCAAATTCTCTTTACCT 57.342 40.909 0.00 0.00 0.00 3.08
1626 1738 3.117813 TGGCTACAGGTGGTTTAACAACT 60.118 43.478 2.40 0.00 39.45 3.16
1643 1755 4.642437 TCAATCAACACAACAACTTGGCTA 59.358 37.500 0.00 0.00 0.00 3.93
1938 2086 8.093927 TCCCAAGAAAATAATCATGGTTTTGTC 58.906 33.333 0.00 0.00 36.64 3.18
1948 2097 7.181569 GGACCAATTCCCAAGAAAATAATCA 57.818 36.000 0.00 0.00 38.70 2.57
1993 2142 3.935315 TCTGAGTGCTTTTCTCCTCATG 58.065 45.455 0.00 0.00 33.77 3.07
2011 2160 1.743958 CCAGCTCCATTGAAGCTTCTG 59.256 52.381 26.09 16.91 36.69 3.02
2050 2199 4.443621 TCAACCATACACGTTCACTTTCA 58.556 39.130 0.00 0.00 0.00 2.69
2190 2348 0.678950 TGCTCACCATGAACTGACGA 59.321 50.000 0.00 0.00 0.00 4.20
2219 2377 8.437360 TTCTTGCTATAATGTCGACAATGAAT 57.563 30.769 24.13 15.04 0.00 2.57
2352 2522 7.708051 TGTGTGTGTTAGCAGCTTAATTTAAA 58.292 30.769 0.00 0.00 0.00 1.52
2370 2540 5.177881 CACAAAAATGGAATGGATGTGTGTG 59.822 40.000 0.00 0.00 32.43 3.82
2705 2881 1.699656 CGCTGCAGAGGATTTCGTGG 61.700 60.000 20.43 0.00 0.00 4.94
2778 2954 9.307121 CCTCTGTGTTGTGAATACTAAATAGAG 57.693 37.037 0.00 0.00 36.01 2.43
3141 3336 9.429359 TGTGATGTTGTTAAACTTTTGTGATTT 57.571 25.926 0.00 0.00 37.19 2.17
3176 3371 6.560003 TCATATTGTTCCTCCATGTACACT 57.440 37.500 0.00 0.00 0.00 3.55
3293 3497 9.869844 GAACTGATGTTTTCGATATTAATCTGG 57.130 33.333 0.00 0.00 36.39 3.86
3464 3679 4.618635 TGCATTAAAGAAATGATGGGGGA 58.381 39.130 2.01 0.00 46.81 4.81
3649 3878 5.549347 AGAATGTTTTGGCAAATGCATACA 58.451 33.333 22.19 18.80 44.36 2.29
3650 3879 6.484818 AAGAATGTTTTGGCAAATGCATAC 57.515 33.333 22.19 14.79 44.36 2.39
3689 3918 8.215736 ACTATGAATGTTCATGGATGATCTTGA 58.784 33.333 21.17 0.00 45.63 3.02
3691 3920 8.991783 AACTATGAATGTTCATGGATGATCTT 57.008 30.769 21.17 5.65 45.63 2.40
3693 3922 7.664731 AGGAACTATGAATGTTCATGGATGATC 59.335 37.037 21.17 13.93 45.63 2.92


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

AutoCloner maintained by Alex Coulton.