Multiple sequence alignment - TraesCS7A01G438900

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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 TraesCS7A01G438900 chr7A 100.000 4740 0 0 1 4740 633040714 633035975 0.000000e+00 8717
1 TraesCS7A01G438900 chr7A 99.355 2480 12 2 1 2480 632911971 632909496 0.000000e+00 4488
2 TraesCS7A01G438900 chr7A 96.656 2691 62 16 363 3034 632590949 632588268 0.000000e+00 4464
3 TraesCS7A01G438900 chr7A 98.950 2476 19 1 1 2469 632974434 632971959 0.000000e+00 4421
4 TraesCS7A01G438900 chr7A 99.112 2253 11 1 2497 4740 632971777 632969525 0.000000e+00 4043
5 TraesCS7A01G438900 chr7A 99.315 2190 15 0 2551 4740 632909170 632906981 0.000000e+00 3962
6 TraesCS7A01G438900 chr7A 93.519 1296 53 12 3042 4330 632588145 632586874 0.000000e+00 1899
7 TraesCS7A01G438900 chr7A 97.078 1061 29 2 3680 4740 632712321 632711263 0.000000e+00 1786
8 TraesCS7A01G438900 chr7A 96.890 1061 32 1 3680 4740 633096635 633095576 0.000000e+00 1775
9 TraesCS7A01G438900 chr7A 87.538 987 108 7 2905 3878 630389933 630390917 0.000000e+00 1127
10 TraesCS7A01G438900 chr7A 86.355 1004 102 22 1508 2486 631964009 631963016 0.000000e+00 1062
11 TraesCS7A01G438900 chr7A 87.070 959 91 22 1505 2440 630388346 630389294 0.000000e+00 1053
12 TraesCS7A01G438900 chr7A 87.053 811 90 11 3068 3863 631961123 631960313 0.000000e+00 902
13 TraesCS7A01G438900 chr7A 85.185 810 92 11 3110 3909 630035649 630036440 0.000000e+00 806
14 TraesCS7A01G438900 chr7A 84.512 523 70 7 2064 2580 630034536 630035053 1.510000e-144 523
15 TraesCS7A01G438900 chr7A 92.625 339 22 2 2530 2868 630389605 630389940 7.130000e-133 484
16 TraesCS7A01G438900 chr7A 90.617 373 7 2 4368 4740 632586875 632586531 2.000000e-128 470
17 TraesCS7A01G438900 chr7A 89.835 364 28 5 1 361 435003222 435003579 4.320000e-125 459
18 TraesCS7A01G438900 chr7A 95.023 221 11 0 1 221 632593510 632593290 9.760000e-92 348
19 TraesCS7A01G438900 chr7A 87.255 306 33 2 409 714 630032731 630033030 1.260000e-90 344
20 TraesCS7A01G438900 chr7A 87.213 305 17 8 2564 2868 631961642 631961360 1.270000e-85 327
21 TraesCS7A01G438900 chr7A 85.430 302 40 1 448 749 631965199 631965496 1.280000e-80 311
22 TraesCS7A01G438900 chr7A 81.793 368 50 12 1061 1422 630033382 630033738 4.640000e-75 292
23 TraesCS7A01G438900 chr7A 92.462 199 10 2 2905 3100 631961367 631961171 3.610000e-71 279
24 TraesCS7A01G438900 chr7A 80.267 375 64 4 976 1342 630387922 630388294 1.680000e-69 274
25 TraesCS7A01G438900 chr7A 85.795 176 19 5 803 976 630033093 630033264 1.050000e-41 182
26 TraesCS7A01G438900 chr7B 94.391 4386 177 29 414 4740 592364549 592360174 0.000000e+00 6691
27 TraesCS7A01G438900 chr7B 88.742 151 12 2 4590 4740 592417078 592416933 3.770000e-41 180
28 TraesCS7A01G438900 chr7D 94.571 2247 89 9 2503 4740 548805740 548803518 0.000000e+00 3443
29 TraesCS7A01G438900 chr7D 87.874 1336 115 27 1553 2857 548132996 548131677 0.000000e+00 1544
30 TraesCS7A01G438900 chr7D 96.009 927 23 8 1515 2431 548806668 548805746 0.000000e+00 1495
31 TraesCS7A01G438900 chr7D 92.697 1027 47 15 414 1413 548807694 548806669 0.000000e+00 1456
32 TraesCS7A01G438900 chr7D 85.200 750 96 5 3110 3849 546754399 546755143 0.000000e+00 756
33 TraesCS7A01G438900 chr7D 90.934 364 24 4 1 361 15396692 15397049 9.230000e-132 481
34 TraesCS7A01G438900 chr7D 85.126 437 48 14 2590 3016 546753961 546754390 9.420000e-117 431
35 TraesCS7A01G438900 chr7D 87.539 321 34 3 444 764 546751694 546752008 2.700000e-97 366
36 TraesCS7A01G438900 chr7D 89.328 253 24 2 3032 3283 548130257 548130007 9.900000e-82 315
37 TraesCS7A01G438900 chr7D 85.000 320 26 5 3628 3940 548129988 548129684 5.960000e-79 305
38 TraesCS7A01G438900 chr7D 92.763 152 9 2 4590 4740 548811063 548810913 7.990000e-53 219
39 TraesCS7A01G438900 chr7D 89.933 149 8 4 2903 3044 548131675 548131527 8.100000e-43 185
40 TraesCS7A01G438900 chr7D 84.076 157 14 6 4590 4740 83600428 83600277 1.780000e-29 141
41 TraesCS7A01G438900 chr3A 90.659 364 25 4 1 361 143228080 143228437 4.290000e-130 475
42 TraesCS7A01G438900 chr3D 90.411 365 25 5 1 361 551894593 551894951 5.550000e-129 472
43 TraesCS7A01G438900 chr5A 90.358 363 27 4 1 361 576738279 576738635 2.000000e-128 470
44 TraesCS7A01G438900 chr2A 86.863 373 34 10 11 372 236540709 236541077 2.050000e-108 403
45 TraesCS7A01G438900 chr2A 85.317 252 32 3 3999 4250 764900878 764901124 6.090000e-64 255
46 TraesCS7A01G438900 chr1A 83.889 360 45 8 4009 4366 500838142 500837794 9.830000e-87 331
47 TraesCS7A01G438900 chr6D 82.873 362 33 4 1 334 19961635 19961995 9.970000e-77 298
48 TraesCS7A01G438900 chr1D 83.648 318 45 4 3998 4311 445557863 445558177 4.640000e-75 292
49 TraesCS7A01G438900 chr5B 88.000 100 6 5 3010 3106 13704400 13704496 3.880000e-21 113
50 TraesCS7A01G438900 chr4D 88.764 89 6 2 3015 3103 432765544 432765460 6.490000e-19 106
51 TraesCS7A01G438900 chr1B 86.598 97 5 4 3012 3104 259512275 259512183 3.020000e-17 100


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 TraesCS7A01G438900 chr7A 633035975 633040714 4739 True 8717.000000 8717 100.00000 1 4740 1 chr7A.!!$R2 4739
1 TraesCS7A01G438900 chr7A 632969525 632974434 4909 True 4232.000000 4421 99.03100 1 4740 2 chr7A.!!$R7 4739
2 TraesCS7A01G438900 chr7A 632906981 632911971 4990 True 4225.000000 4488 99.33500 1 4740 2 chr7A.!!$R6 4739
3 TraesCS7A01G438900 chr7A 632586531 632593510 6979 True 1795.250000 4464 93.95375 1 4740 4 chr7A.!!$R5 4739
4 TraesCS7A01G438900 chr7A 632711263 632712321 1058 True 1786.000000 1786 97.07800 3680 4740 1 chr7A.!!$R1 1060
5 TraesCS7A01G438900 chr7A 633095576 633096635 1059 True 1775.000000 1775 96.89000 3680 4740 1 chr7A.!!$R3 1060
6 TraesCS7A01G438900 chr7A 630387922 630390917 2995 False 734.500000 1127 86.87500 976 3878 4 chr7A.!!$F4 2902
7 TraesCS7A01G438900 chr7A 631960313 631964009 3696 True 642.500000 1062 88.27075 1508 3863 4 chr7A.!!$R4 2355
8 TraesCS7A01G438900 chr7A 630032731 630036440 3709 False 429.400000 806 84.90800 409 3909 5 chr7A.!!$F3 3500
9 TraesCS7A01G438900 chr7B 592360174 592364549 4375 True 6691.000000 6691 94.39100 414 4740 1 chr7B.!!$R1 4326
10 TraesCS7A01G438900 chr7D 548803518 548811063 7545 True 1653.250000 3443 94.01000 414 4740 4 chr7D.!!$R3 4326
11 TraesCS7A01G438900 chr7D 548129684 548132996 3312 True 587.250000 1544 88.03375 1553 3940 4 chr7D.!!$R2 2387
12 TraesCS7A01G438900 chr7D 546751694 546755143 3449 False 517.666667 756 85.95500 444 3849 3 chr7D.!!$F2 3405

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
352 2240 0.179200 CTTGAAACGCACGGGCATAC 60.179 55.000 11.77 0.00 41.24 2.39 F
2300 5797 2.165167 CCATCATTGTGAAGCAGGTGT 58.835 47.619 0.00 0.00 0.00 4.16 F
3162 9776 9.382244 GAGCTACTAAACAGTAACAAATTTGTG 57.618 33.333 23.93 13.81 41.31 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 5797 4.955811 ATCGCAGGTAAGTATGGATTCA 57.044 40.909 0.0 0.0 0.0 2.57 R
3162 9776 1.202580 CCATGTCGATGAGAGAACCCC 60.203 57.143 0.0 0.0 0.0 4.95 R
4458 11100 7.284034 GGGACTTCATCAAATTCATACTGACAT 59.716 37.037 0.0 0.0 0.0 3.06 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
234 235 0.325933 CATGTCCAGTGAGAAGGCCA 59.674 55.000 5.01 0.00 0.00 5.36
328 2216 9.262358 GCTTGTCGTAAATAAAATATCTCTCCT 57.738 33.333 0.00 0.00 0.00 3.69
352 2240 0.179200 CTTGAAACGCACGGGCATAC 60.179 55.000 11.77 0.00 41.24 2.39
2300 5797 2.165167 CCATCATTGTGAAGCAGGTGT 58.835 47.619 0.00 0.00 0.00 4.16
3162 9776 9.382244 GAGCTACTAAACAGTAACAAATTTGTG 57.618 33.333 23.93 13.81 41.31 3.33
3308 9922 3.120095 TGGTGTAACAGACATAGACGACG 60.120 47.826 0.00 0.00 41.14 5.12
3797 10430 0.173708 CCCGGTCAACAGTCTAGAGC 59.826 60.000 0.00 0.00 0.00 4.09
4033 10673 7.209475 AGAACCACCAAACTTTGTTATTCATG 58.791 34.615 0.88 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 235 0.037790 GCGAGAGAGCAAGGAGTTGT 60.038 55.000 0.00 0.00 35.92 3.32
328 2216 1.063327 CCGTGCGTTTCAAGCAACA 59.937 52.632 0.00 0.00 46.97 3.33
352 2240 7.589395 ACTCTCTTATATCAGAATAGCACACG 58.411 38.462 0.00 0.00 0.00 4.49
550 3508 2.124653 GAGGAGAGGTCGCGAGGA 60.125 66.667 10.24 0.00 0.00 3.71
2300 5797 4.955811 ATCGCAGGTAAGTATGGATTCA 57.044 40.909 0.00 0.00 0.00 2.57
3162 9776 1.202580 CCATGTCGATGAGAGAACCCC 60.203 57.143 0.00 0.00 0.00 4.95
3308 9922 2.120909 CACGATTCCATGGGCCCAC 61.121 63.158 31.51 12.88 0.00 4.61
3797 10430 1.268896 ACAGTGTCCACGTACAACTCG 60.269 52.381 0.00 0.00 36.20 4.18
3950 10590 3.058914 CCAAGTAGTCAAAAAGCGACTGG 60.059 47.826 3.13 0.00 43.50 4.00
4033 10673 7.497579 ACATTTATTTTCCCAGTTTTGTGAACC 59.502 33.333 0.00 0.00 0.00 3.62
4458 11100 7.284034 GGGACTTCATCAAATTCATACTGACAT 59.716 37.037 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.