Multiple sequence alignment - TraesCS4A01G427600

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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 TraesCS4A01G427600 chr4A 100.000 3637 0 0 1 3637 698490676 698494312 0.000000e+00 6717
1 TraesCS4A01G427600 chr4A 93.240 3698 161 33 3 3637 698309625 698313296 0.000000e+00 5361
2 TraesCS4A01G427600 chr4A 94.388 1764 91 5 1874 3637 698669121 698670876 0.000000e+00 2702
3 TraesCS4A01G427600 chr4A 91.985 786 33 8 915 1677 698668346 698669124 0.000000e+00 1075
4 TraesCS4A01G427600 chr4A 85.930 597 69 8 1099 1683 531105157 531104564 1.110000e-174 623
5 TraesCS4A01G427600 chr4A 86.290 248 30 3 79 324 698662545 698662790 2.150000e-67 267
6 TraesCS4A01G427600 chr4A 91.667 120 9 1 801 920 698662892 698663010 8.080000e-37 165
7 TraesCS4A01G427600 chr7D 94.257 2960 91 26 1 2891 30394226 30397175 0.000000e+00 4451
8 TraesCS4A01G427600 chr7D 87.725 334 35 3 3133 3465 30397390 30397718 5.700000e-103 385
9 TraesCS4A01G427600 chr7D 94.286 175 9 1 3 177 30388765 30388938 2.150000e-67 267
10 TraesCS4A01G427600 chr7D 88.202 178 15 4 2892 3067 30397208 30397381 1.320000e-49 207
11 TraesCS4A01G427600 chr7A 91.867 1205 51 15 931 2088 30876121 30877325 0.000000e+00 1639
12 TraesCS4A01G427600 chr7A 91.304 805 46 7 2084 2886 30878600 30879382 0.000000e+00 1077
13 TraesCS4A01G427600 chr7A 90.091 656 43 8 176 826 30875219 30875857 0.000000e+00 832
14 TraesCS4A01G427600 chr7A 87.879 165 17 2 14 176 30872583 30872746 1.330000e-44 191
15 TraesCS4A01G427600 chr7A 94.915 118 5 1 3476 3593 30888314 30888430 2.230000e-42 183
16 TraesCS4A01G427600 chr2D 86.981 699 76 8 2034 2728 114538703 114538016 0.000000e+00 773
17 TraesCS4A01G427600 chr2D 84.129 649 86 15 1040 1683 114539706 114539070 2.400000e-171 612
18 TraesCS4A01G427600 chr2D 82.353 238 34 6 1759 1992 114539005 114538772 2.210000e-47 200
19 TraesCS4A01G427600 chr2A 83.885 695 91 11 2034 2728 115786957 115786284 0.000000e+00 643
20 TraesCS4A01G427600 chr2A 82.550 596 93 4 1099 1683 115787922 115787327 6.960000e-142 514
21 TraesCS4A01G427600 chr4B 85.452 598 70 9 1099 1683 95710160 95709567 1.120000e-169 606
22 TraesCS4A01G427600 chr5D 83.661 661 85 15 1039 1683 506210179 506210832 5.200000e-168 601
23 TraesCS4A01G427600 chr5D 81.997 661 92 18 1041 1683 506167336 506167987 1.490000e-148 536
24 TraesCS4A01G427600 chr5D 89.157 415 40 4 323 734 510564270 510563858 2.500000e-141 512
25 TraesCS4A01G427600 chr5D 81.849 584 90 12 2126 2700 506168032 506168608 9.140000e-131 477
26 TraesCS4A01G427600 chr5D 81.993 572 89 11 2122 2685 506210960 506211525 1.180000e-129 473
27 TraesCS4A01G427600 chr2B 85.316 538 76 1 2034 2571 165068331 165067797 1.480000e-153 553
28 TraesCS4A01G427600 chr5B 83.752 597 82 5 1099 1683 636929095 636929688 5.310000e-153 551
29 TraesCS4A01G427600 chr5B 83.154 279 41 5 2169 2444 654091878 654091603 2.170000e-62 250
30 TraesCS4A01G427600 chr7B 90.120 415 32 7 324 733 551947401 551947811 6.910000e-147 531
31 TraesCS4A01G427600 chr1A 90.024 411 33 7 324 730 481926151 481926557 3.220000e-145 525
32 TraesCS4A01G427600 chr6A 89.372 414 38 5 324 733 74975751 74975340 1.940000e-142 516
33 TraesCS4A01G427600 chr6A 88.810 420 38 7 324 737 185636273 185636689 1.170000e-139 507
34 TraesCS4A01G427600 chr3B 82.190 612 96 11 2036 2639 755207724 755208330 6.960000e-142 514
35 TraesCS4A01G427600 chr1D 89.294 411 35 8 317 723 386895586 386895991 1.170000e-139 507


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 TraesCS4A01G427600 chr4A 698490676 698494312 3636 False 6717.000000 6717 100.000000 1 3637 1 chr4A.!!$F2 3636
1 TraesCS4A01G427600 chr4A 698309625 698313296 3671 False 5361.000000 5361 93.240000 3 3637 1 chr4A.!!$F1 3634
2 TraesCS4A01G427600 chr4A 698668346 698670876 2530 False 1888.500000 2702 93.186500 915 3637 2 chr4A.!!$F4 2722
3 TraesCS4A01G427600 chr4A 531104564 531105157 593 True 623.000000 623 85.930000 1099 1683 1 chr4A.!!$R1 584
4 TraesCS4A01G427600 chr7D 30394226 30397718 3492 False 1681.000000 4451 90.061333 1 3465 3 chr7D.!!$F2 3464
5 TraesCS4A01G427600 chr7A 30872583 30879382 6799 False 934.750000 1639 90.285250 14 2886 4 chr7A.!!$F2 2872
6 TraesCS4A01G427600 chr2D 114538016 114539706 1690 True 528.333333 773 84.487667 1040 2728 3 chr2D.!!$R1 1688
7 TraesCS4A01G427600 chr2A 115786284 115787922 1638 True 578.500000 643 83.217500 1099 2728 2 chr2A.!!$R1 1629
8 TraesCS4A01G427600 chr4B 95709567 95710160 593 True 606.000000 606 85.452000 1099 1683 1 chr4B.!!$R1 584
9 TraesCS4A01G427600 chr5D 506210179 506211525 1346 False 537.000000 601 82.827000 1039 2685 2 chr5D.!!$F2 1646
10 TraesCS4A01G427600 chr5D 506167336 506168608 1272 False 506.500000 536 81.923000 1041 2700 2 chr5D.!!$F1 1659
11 TraesCS4A01G427600 chr2B 165067797 165068331 534 True 553.000000 553 85.316000 2034 2571 1 chr2B.!!$R1 537
12 TraesCS4A01G427600 chr5B 636929095 636929688 593 False 551.000000 551 83.752000 1099 1683 1 chr5B.!!$F1 584
13 TraesCS4A01G427600 chr3B 755207724 755208330 606 False 514.000000 514 82.190000 2036 2639 1 chr3B.!!$F1 603

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
580 3060 0.321564 CTTCGACCCAGGATGCAACA 60.322 55.000 0.0 0.0 31.97 3.33 F
1389 4073 1.518572 CGAGGCGAGCACCGTTAAT 60.519 57.895 0.0 0.0 41.15 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 4382 1.048724 TAAGGAGGAGGATGTGCCGG 61.049 60.0 0.0 0.0 43.43 6.13 R
3307 7425 0.950836 CGACCCATGTGCAAGTTCAA 59.049 50.0 0.0 0.0 0.00 2.69 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
72 75 3.181487 GCGATGTTTGGTATGCTGGAAAT 60.181 43.478 0.00 0.00 0.00 2.17
83 87 8.532186 TGGTATGCTGGAAATAATGTTACATT 57.468 30.769 15.22 15.22 0.00 2.71
145 149 7.213216 TGAATTTCAATGAAAGTTGGATCGA 57.787 32.000 14.10 0.00 34.92 3.59
580 3060 0.321564 CTTCGACCCAGGATGCAACA 60.322 55.000 0.00 0.00 31.97 3.33
742 3231 3.546002 TCGTATTTTCCGGCAAAGTTG 57.454 42.857 5.32 0.00 0.00 3.16
805 3299 1.896220 TAGCTGGGCAACTCAAACTG 58.104 50.000 0.00 0.00 0.00 3.16
889 3383 4.210537 CGAAGCATATAACCGAACCGAATT 59.789 41.667 0.00 0.00 0.00 2.17
1265 3948 3.449227 CGCGCTCCAGGACAGGTA 61.449 66.667 5.56 0.00 0.00 3.08
1389 4073 1.518572 CGAGGCGAGCACCGTTAAT 60.519 57.895 0.00 0.00 41.15 1.40
1684 4380 3.742882 GGTACTCAAACTCCGGTACAAAC 59.257 47.826 0.00 0.00 37.03 2.93
1686 4382 3.725490 ACTCAAACTCCGGTACAAACTC 58.275 45.455 0.00 0.00 0.00 3.01
1687 4383 3.064931 CTCAAACTCCGGTACAAACTCC 58.935 50.000 0.00 0.00 0.00 3.85
1713 4443 5.342017 CACATCCTCCTCCTTATATGGGTA 58.658 45.833 4.90 0.00 0.00 3.69
1763 4506 1.604438 CGTGTTGATCAGTCCGGTGAA 60.604 52.381 0.00 0.00 0.00 3.18
1779 4522 4.235762 AATATGGCGGCCGCGACT 62.236 61.111 41.05 29.39 43.06 4.18
1930 4676 2.490217 CACCTCTCCGTACGCCTG 59.510 66.667 10.49 1.80 0.00 4.85
1962 4708 2.969821 TCCTAATGGTGCACTTGGTT 57.030 45.000 17.98 8.99 34.23 3.67
2030 4788 2.108362 GGTCGGAATGGCTACCCG 59.892 66.667 6.42 6.42 44.22 5.28
2238 6305 0.830444 TAGGTTCCTGCACGACCACT 60.830 55.000 10.15 1.27 35.89 4.00
2289 6356 1.073125 TCCGGATGCCAAAGTTCAAGA 59.927 47.619 0.00 0.00 0.00 3.02
2941 7056 8.674607 CACTCGCTTGACAGTGGTATATATATA 58.325 37.037 0.00 0.00 37.04 0.86
3039 7156 9.905713 AAATATAAGATTTGTTAGACTCTGGCA 57.094 29.630 0.00 0.00 0.00 4.92
3047 7164 6.599356 TTGTTAGACTCTGGCAGTGTATAA 57.401 37.500 24.69 24.69 34.41 0.98
3129 7246 4.310022 AAAATTCCATCGAGGGTTACCA 57.690 40.909 16.92 0.00 40.13 3.25
3190 7307 2.821366 GAGAGCATGCACCCCGTG 60.821 66.667 21.98 0.00 36.51 4.94
3252 7369 1.626654 CGGCGCGTGACTTCATCTTT 61.627 55.000 8.43 0.00 0.00 2.52
3304 7422 8.856153 TTTTTCTACATATTCAGTAGTTGGCA 57.144 30.769 0.00 0.00 39.86 4.92
3318 7436 4.178545 AGTTGGCATATTGAACTTGCAC 57.821 40.909 3.97 0.00 38.12 4.57
3319 7437 3.573538 AGTTGGCATATTGAACTTGCACA 59.426 39.130 3.97 0.00 38.12 4.57
3353 7471 2.052690 GGTAGAGCGAGGTGAGGCA 61.053 63.158 0.00 0.00 0.00 4.75
3372 7490 2.711542 CACTCGCCCTACCTTGATTTT 58.288 47.619 0.00 0.00 0.00 1.82
3377 7495 2.446435 GCCCTACCTTGATTTTGAGCA 58.554 47.619 0.00 0.00 0.00 4.26
3381 7504 5.654497 CCCTACCTTGATTTTGAGCAATTC 58.346 41.667 0.00 0.00 0.00 2.17
3382 7505 5.394553 CCCTACCTTGATTTTGAGCAATTCC 60.395 44.000 0.00 0.00 0.00 3.01
3383 7506 5.420104 CCTACCTTGATTTTGAGCAATTCCT 59.580 40.000 0.00 0.00 0.00 3.36
3384 7507 5.813513 ACCTTGATTTTGAGCAATTCCTT 57.186 34.783 0.00 0.00 0.00 3.36
3385 7508 6.178607 ACCTTGATTTTGAGCAATTCCTTT 57.821 33.333 0.00 0.00 0.00 3.11
3426 7549 6.910536 ATAAGTCACAGATCGATGGAAAAC 57.089 37.500 0.54 0.00 0.00 2.43
3498 7621 2.727647 GCTCGAATCGCGCGATCT 60.728 61.111 41.66 30.58 40.61 2.75
3532 7655 0.653636 CGTCGCTCTAGTCTCCAGAC 59.346 60.000 0.00 0.00 45.08 3.51
3616 7739 2.972505 CGGCCAACAAGAGCACGT 60.973 61.111 2.24 0.00 0.00 4.49
3617 7740 2.639286 GGCCAACAAGAGCACGTG 59.361 61.111 12.28 12.28 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 149 0.698818 GTCCACCTCCCTTCACCATT 59.301 55.000 0.00 0.00 0.00 3.16
274 2752 4.511527 CGCGTCTCCCTTCCTATACTATA 58.488 47.826 0.00 0.00 0.00 1.31
552 3032 1.533625 CTGGGTCGAAGATTTGGCAA 58.466 50.000 0.00 0.00 40.67 4.52
553 3033 0.322456 CCTGGGTCGAAGATTTGGCA 60.322 55.000 0.00 0.00 40.67 4.92
625 3105 9.990360 AAATCTTTTTCGGTACCAAACATAATT 57.010 25.926 13.54 1.20 0.00 1.40
689 3171 0.544223 TACCAGCGCACCCAATATGT 59.456 50.000 11.47 0.00 0.00 2.29
742 3231 9.699703 CTCTCATAGCTTTCCTTTTATAGTACC 57.300 37.037 0.00 0.00 0.00 3.34
763 3254 2.068821 GGCCTCCCTGCATCTCTCA 61.069 63.158 0.00 0.00 0.00 3.27
794 3288 5.066505 GGCTAATATGGACCAGTTTGAGTTG 59.933 44.000 0.00 0.00 0.00 3.16
805 3299 3.067106 CACGTGATGGCTAATATGGACC 58.933 50.000 10.90 0.00 0.00 4.46
850 3344 5.821516 TGCTTCGTTCTTTCCTTTTGTTA 57.178 34.783 0.00 0.00 0.00 2.41
889 3383 4.276678 GCATCCGATCTGATTTGGATTTGA 59.723 41.667 17.70 0.00 39.16 2.69
1362 4045 2.105128 CTCGCCTCGGCCTTGTAG 59.895 66.667 0.00 0.00 37.98 2.74
1684 4380 2.801631 GGAGGAGGATGTGCCGGAG 61.802 68.421 5.05 0.00 43.43 4.63
1686 4382 1.048724 TAAGGAGGAGGATGTGCCGG 61.049 60.000 0.00 0.00 43.43 6.13
1687 4383 1.051812 ATAAGGAGGAGGATGTGCCG 58.948 55.000 0.00 0.00 43.43 5.69
1763 4506 2.646175 ATAGTCGCGGCCGCCATAT 61.646 57.895 42.07 31.38 37.98 1.78
1779 4522 2.138179 GGGCGTAGGGAGCACCATA 61.138 63.158 1.58 0.00 43.89 2.74
1930 4676 2.025887 CCATTAGGATATGGCCTGGGAC 60.026 54.545 3.32 0.00 38.75 4.46
1974 4720 3.259876 GCGATATATGGTGGGTTAGGTGA 59.740 47.826 0.00 0.00 0.00 4.02
2289 6356 2.549563 CGATGCTGCTATGGAAGGACAT 60.550 50.000 0.00 0.00 34.90 3.06
2941 7056 5.107133 CAGAACCCGTCTAACAATTCGTAT 58.893 41.667 0.00 0.00 33.56 3.06
2989 7105 5.815233 TCATTGGTGAAAATTGCCCTTTA 57.185 34.783 0.00 0.00 0.00 1.85
3039 7156 4.142026 TGCGCCAGAGTTATGTTATACACT 60.142 41.667 4.18 0.00 0.00 3.55
3047 7164 1.447838 CCGTGCGCCAGAGTTATGT 60.448 57.895 4.18 0.00 0.00 2.29
3129 7246 7.500227 CACTTCCATAACCACTGATAATGACAT 59.500 37.037 0.00 0.00 0.00 3.06
3190 7307 2.511600 CCTTGGCGACGGGATGTC 60.512 66.667 0.00 0.00 44.53 3.06
3212 7329 2.350895 CAATGGTGAGGACCGGCA 59.649 61.111 0.00 0.00 46.62 5.69
3217 7334 1.718757 GCCGATGCAATGGTGAGGAC 61.719 60.000 9.12 0.00 37.47 3.85
3252 7369 3.010027 TGGCCAACTCTGGATGTTATCAA 59.990 43.478 0.61 0.00 46.92 2.57
3304 7422 3.378112 CGACCCATGTGCAAGTTCAATAT 59.622 43.478 0.00 0.00 0.00 1.28
3307 7425 0.950836 CGACCCATGTGCAAGTTCAA 59.049 50.000 0.00 0.00 0.00 2.69
3318 7436 2.124983 CCACAGCTCCGACCCATG 60.125 66.667 0.00 0.00 0.00 3.66
3319 7437 2.815684 TACCCACAGCTCCGACCCAT 62.816 60.000 0.00 0.00 0.00 4.00
3353 7471 2.304761 TCAAAATCAAGGTAGGGCGAGT 59.695 45.455 0.00 0.00 0.00 4.18
3446 7569 2.613691 GGACGACGATTTTCTTAGCCA 58.386 47.619 0.00 0.00 0.00 4.75
3492 7615 3.545633 GAACAACACAACTGAAGATCGC 58.454 45.455 0.00 0.00 0.00 4.58
3498 7621 1.061421 GCGACGAACAACACAACTGAA 59.939 47.619 0.00 0.00 0.00 3.02
3532 7655 0.528470 GTCAGAGGAAGGTCTGGTCG 59.472 60.000 1.20 0.00 43.69 4.79
3591 7714 2.909965 TTGTTGGCCGCTGGGAAC 60.910 61.111 0.00 0.00 34.06 3.62


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

AutoCloner maintained by Alex Coulton.