Multiple sequence alignment - TraesCS7B01G430600

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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 TraesCS7B01G430600 chr7B 100.000 5051 0 0 1 5051 699143635 699138585 0.000000e+00 9328
1 TraesCS7B01G430600 chr7B 91.488 2937 173 27 2156 5047 698654870 698651966 0.000000e+00 3967
2 TraesCS7B01G430600 chr7B 90.912 2751 151 30 2157 4857 694364218 694361517 0.000000e+00 3603
3 TraesCS7B01G430600 chr7B 93.444 2410 106 18 2156 4538 699182400 699180016 0.000000e+00 3528
4 TraesCS7B01G430600 chr7B 91.751 2473 141 21 2156 4590 699145180 699142733 0.000000e+00 3378
5 TraesCS7B01G430600 chr7B 92.287 2191 116 23 2065 4217 696145225 696143050 0.000000e+00 3061
6 TraesCS7B01G430600 chr7B 87.356 1993 146 42 3111 5047 693621424 693619482 0.000000e+00 2187
7 TraesCS7B01G430600 chr7B 100.000 903 0 0 1 903 698653325 698652423 0.000000e+00 1668
8 TraesCS7B01G430600 chr7B 98.786 906 6 2 1 902 694362675 694361771 0.000000e+00 1607
9 TraesCS7B01G430600 chr7B 98.238 908 11 2 1 903 693620832 693619925 0.000000e+00 1583
10 TraesCS7B01G430600 chr7B 92.779 914 42 4 6 903 699139951 699139046 0.000000e+00 1301
11 TraesCS7B01G430600 chr7B 92.503 867 40 7 6 851 699180878 699180016 0.000000e+00 1218
12 TraesCS7B01G430600 chr7B 92.052 541 35 4 7 546 696143583 696143050 0.000000e+00 754
13 TraesCS7B01G430600 chr7B 85.624 473 44 13 979 1448 694189267 694189718 4.580000e-130 475
14 TraesCS7B01G430600 chr7B 85.854 410 36 15 1038 1439 699183216 699182821 2.810000e-112 416
15 TraesCS7B01G430600 chr7B 85.677 384 36 12 998 1377 696145855 696145487 2.210000e-103 387
16 TraesCS7B01G430600 chr7B 85.526 380 39 12 998 1376 685289173 685288809 2.850000e-102 383
17 TraesCS7B01G430600 chr7B 90.288 278 17 5 4768 5042 699179743 699179473 6.220000e-94 355
18 TraesCS7B01G430600 chr7B 91.489 188 14 1 4866 5051 696142310 696142123 1.800000e-64 257
19 TraesCS7B01G430600 chr7B 84.865 185 16 9 1267 1447 697358625 697358801 5.200000e-40 176
20 TraesCS7B01G430600 chr7B 85.600 125 9 3 1253 1377 697024502 697024617 6.870000e-24 122
21 TraesCS7B01G430600 chr7B 87.000 100 13 0 1792 1891 699182814 699182715 4.130000e-21 113
22 TraesCS7B01G430600 chr7D 89.830 2409 158 37 2163 4525 608199114 608196747 0.000000e+00 3011
23 TraesCS7B01G430600 chr7D 91.195 1431 89 13 2734 4135 514748944 514747522 0.000000e+00 1910
24 TraesCS7B01G430600 chr7D 88.738 1323 119 17 1927 3228 600232753 600234066 0.000000e+00 1591
25 TraesCS7B01G430600 chr7D 88.634 1091 93 18 2035 3102 610532265 610533347 0.000000e+00 1299
26 TraesCS7B01G430600 chr7D 86.763 1035 87 23 3223 4217 610533556 610534580 0.000000e+00 1107
27 TraesCS7B01G430600 chr7D 90.270 853 54 14 6 838 608197590 608196747 0.000000e+00 1088
28 TraesCS7B01G430600 chr7D 93.204 515 29 5 4133 4641 514747037 514746523 0.000000e+00 752
29 TraesCS7B01G430600 chr7D 89.233 613 30 17 4213 4821 610534742 610535322 0.000000e+00 734
30 TraesCS7B01G430600 chr7D 87.958 573 49 12 2044 2601 514749623 514749056 0.000000e+00 658
31 TraesCS7B01G430600 chr7D 88.913 460 33 6 462 903 514747037 514746578 7.390000e-153 551
32 TraesCS7B01G430600 chr7D 88.791 455 30 10 997 1448 610531533 610531969 5.750000e-149 538
33 TraesCS7B01G430600 chr7D 83.571 560 57 22 913 1451 514750388 514749843 4.540000e-135 492
34 TraesCS7B01G430600 chr7D 85.011 447 48 14 4525 4967 609668780 609669211 2.160000e-118 436
35 TraesCS7B01G430600 chr7D 84.389 442 46 13 936 1377 608199907 608199489 3.640000e-111 412
36 TraesCS7B01G430600 chr7D 89.490 314 15 3 542 838 610534742 610535054 1.030000e-101 381
37 TraesCS7B01G430600 chr7D 91.270 252 16 3 4573 4821 600235585 600235833 6.260000e-89 339
38 TraesCS7B01G430600 chr7D 93.085 188 11 1 4863 5048 610535324 610535511 1.790000e-69 274
39 TraesCS7B01G430600 chr7D 90.957 188 11 2 4866 5051 514746379 514746196 1.090000e-61 248
40 TraesCS7B01G430600 chr7A 86.805 2175 171 55 2717 4821 700504954 700507082 0.000000e+00 2320
41 TraesCS7B01G430600 chr7A 89.020 1867 135 37 3241 5051 700208104 700206252 0.000000e+00 2248
42 TraesCS7B01G430600 chr7A 90.543 920 60 9 3 903 700207624 700206713 0.000000e+00 1192
43 TraesCS7B01G430600 chr7A 89.987 779 51 11 1 775 700505943 700506698 0.000000e+00 981
44 TraesCS7B01G430600 chr7A 85.021 701 75 16 1927 2606 700209383 700208692 0.000000e+00 686
45 TraesCS7B01G430600 chr7A 84.137 498 42 24 998 1485 700503670 700504140 9.980000e-122 448
46 TraesCS7B01G430600 chr7A 83.766 154 17 7 1489 1636 700209678 700209527 6.820000e-29 139
47 TraesCS7B01G430600 chr4A 94.795 1095 44 6 2915 3998 661823500 661822408 0.000000e+00 1694
48 TraesCS7B01G430600 chr4A 89.286 1008 62 18 4050 5051 661822411 661821444 0.000000e+00 1221
49 TraesCS7B01G430600 chr4A 91.062 772 52 7 2157 2917 661825963 661825198 0.000000e+00 1027
50 TraesCS7B01G430600 chr4A 84.472 322 35 9 936 1254 661826365 661826056 2.280000e-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 TraesCS7B01G430600 chr7B 699138585 699143635 5050 True 9328.000000 9328 100.000000 1 5051 1 chr7B.!!$R2 5050
1 TraesCS7B01G430600 chr7B 698651966 698654870 2904 True 2817.500000 3967 95.744000 1 5047 2 chr7B.!!$R6 5046
2 TraesCS7B01G430600 chr7B 694361517 694364218 2701 True 2605.000000 3603 94.849000 1 4857 2 chr7B.!!$R4 4856
3 TraesCS7B01G430600 chr7B 699139046 699145180 6134 True 2339.500000 3378 92.265000 6 4590 2 chr7B.!!$R7 4584
4 TraesCS7B01G430600 chr7B 693619482 693621424 1942 True 1885.000000 2187 92.797000 1 5047 2 chr7B.!!$R3 5046
5 TraesCS7B01G430600 chr7B 699179473 699183216 3743 True 1126.000000 3528 89.817800 6 5042 5 chr7B.!!$R8 5036
6 TraesCS7B01G430600 chr7B 696142123 696145855 3732 True 1114.750000 3061 90.376250 7 5051 4 chr7B.!!$R5 5044
7 TraesCS7B01G430600 chr7D 608196747 608199907 3160 True 1503.666667 3011 88.163000 6 4525 3 chr7D.!!$R2 4519
8 TraesCS7B01G430600 chr7D 600232753 600235833 3080 False 965.000000 1591 90.004000 1927 4821 2 chr7D.!!$F2 2894
9 TraesCS7B01G430600 chr7D 514746196 514750388 4192 True 768.500000 1910 89.299667 462 5051 6 chr7D.!!$R1 4589
10 TraesCS7B01G430600 chr7D 610531533 610535511 3978 False 722.166667 1299 89.332667 542 5048 6 chr7D.!!$F3 4506
11 TraesCS7B01G430600 chr7A 700503670 700507082 3412 False 1249.666667 2320 86.976333 1 4821 3 chr7A.!!$F1 4820
12 TraesCS7B01G430600 chr7A 700206252 700209678 3426 True 1066.250000 2248 87.087500 3 5051 4 chr7A.!!$R1 5048
13 TraesCS7B01G430600 chr4A 661821444 661826365 4921 True 1061.250000 1694 89.903750 936 5051 4 chr4A.!!$R1 4115

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
2294 4106 7.725251 TCAATTGGTTGGATTAGGATTTATGC 58.275 34.615 5.42 0.0 35.99 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4600 9063 1.769026 CCAGCAGGCTGAGTACTAGA 58.231 55.0 20.86 0.0 46.3 2.43 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
2294 4106 7.725251 TCAATTGGTTGGATTAGGATTTATGC 58.275 34.615 5.42 0.0 35.99 3.14
2300 4112 8.257306 TGGTTGGATTAGGATTTATGCTTTTTC 58.743 33.333 0.00 0.0 0.00 2.29
4600 9063 6.541641 CAGCAGCAAGAAAGAAACTATCCTAT 59.458 38.462 0.00 0.0 0.00 2.57
4604 9067 9.474920 CAGCAAGAAAGAAACTATCCTATCTAG 57.525 37.037 0.00 0.0 0.00 2.43
4660 9127 2.100631 CATTCCGGCACCTCACGAC 61.101 63.158 0.00 0.0 0.00 4.34
4785 9372 1.344438 TGCATTATTCCTCGAGCGGAT 59.656 47.619 6.99 3.4 32.02 4.18
4793 9380 0.387202 CCTCGAGCGGATTGAGTGAT 59.613 55.000 6.99 0.0 37.70 3.06
4797 9384 3.473625 TCGAGCGGATTGAGTGATACTA 58.526 45.455 0.00 0.0 0.00 1.82
4801 9388 5.049612 CGAGCGGATTGAGTGATACTACTTA 60.050 44.000 0.00 0.0 0.00 2.24
4802 9389 6.512903 CGAGCGGATTGAGTGATACTACTTAA 60.513 42.308 0.00 0.0 31.85 1.85
4803 9390 7.291411 AGCGGATTGAGTGATACTACTTAAT 57.709 36.000 0.00 0.0 38.93 1.40
4985 9573 2.606519 ACGGGGCAGTTAGGCAGA 60.607 61.111 0.00 0.0 46.44 4.26
5007 9595 3.044156 AGATAGAAGCTGCTCCATCCAA 58.956 45.455 0.00 0.0 0.00 3.53
5034 9624 5.276963 GGTTCAATCTACTCTACTCTCGACG 60.277 48.000 0.00 0.0 0.00 5.12
5048 9638 3.961182 TCTCGACGCACTTAATATGACC 58.039 45.455 0.00 0.0 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.426738 TCTGGTTTTCAAACAGCAGTGG 59.573 45.455 4.85 0.00 40.63 4.00
7 8 3.781079 TCTGGTTTTCAAACAGCAGTG 57.219 42.857 4.85 0.00 40.63 3.66
9 10 4.217118 AGCTATCTGGTTTTCAAACAGCAG 59.783 41.667 11.91 7.86 40.63 4.24
2159 3966 1.080298 GGCATGCAAACACCTCAGC 60.080 57.895 21.36 0.00 0.00 4.26
2294 4106 2.159627 ACATGCGTAGAAGCCGAAAAAG 59.840 45.455 0.00 0.00 36.02 2.27
2300 4112 1.883084 GGGACATGCGTAGAAGCCG 60.883 63.158 0.00 0.00 36.02 5.52
4600 9063 1.769026 CCAGCAGGCTGAGTACTAGA 58.231 55.000 20.86 0.00 46.30 2.43
4624 9091 1.055849 TGGCTGCTTGTACCTTGAGA 58.944 50.000 0.00 0.00 0.00 3.27
4660 9127 0.037326 TCTGCTTGTACCTTGAGCGG 60.037 55.000 9.09 9.09 42.70 5.52
4758 9229 4.319333 GCTCGAGGAATAATGCAGTTGATG 60.319 45.833 15.58 0.00 0.00 3.07
4797 9384 8.846211 ACATTTACACACACTGCTTTATTAAGT 58.154 29.630 0.00 0.00 33.74 2.24
4801 9388 5.920273 GCACATTTACACACACTGCTTTATT 59.080 36.000 0.00 0.00 0.00 1.40
4802 9389 5.009510 TGCACATTTACACACACTGCTTTAT 59.990 36.000 0.00 0.00 0.00 1.40
4803 9390 4.336713 TGCACATTTACACACACTGCTTTA 59.663 37.500 0.00 0.00 0.00 1.85
4985 9573 3.044156 TGGATGGAGCAGCTTCTATCTT 58.956 45.455 1.29 0.00 35.91 2.40
5007 9595 6.829298 TCGAGAGTAGAGTAGATTGAACCATT 59.171 38.462 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.