Multiple sequence alignment - TraesCS5A01G104700

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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 TraesCS5A01G104700 chr5A 100.000 3394 0 0 1 3394 169183892 169180499 0 6268
1 TraesCS5A01G104700 chr5A 93.802 3453 148 21 1 3394 33905150 33908595 0 5131
2 TraesCS5A01G104700 chr5A 95.285 509 21 3 1 508 524675838 524676344 0 804
3 TraesCS5A01G104700 chr7A 94.172 3449 139 12 1 3394 675357175 675353734 0 5199
4 TraesCS5A01G104700 chr7A 94.384 3401 123 9 59 3394 299349069 299352466 0 5160
5 TraesCS5A01G104700 chr7A 96.654 508 16 1 1 508 701357926 701357420 0 843
6 TraesCS5A01G104700 chr6A 94.029 3450 143 12 1 3394 531051939 531055381 0 5171
7 TraesCS5A01G104700 chr6A 94.579 2527 108 9 892 3394 87945940 87943419 0 3880
8 TraesCS5A01G104700 chr6A 94.134 2148 79 6 1289 3394 184604852 184602710 0 3225
9 TraesCS5A01G104700 chr3A 93.859 3436 159 25 1 3394 450957039 450960464 0 5129
10 TraesCS5A01G104700 chr3A 96.443 506 17 1 1 506 32205281 32205785 0 833
11 TraesCS5A01G104700 chr2A 93.716 3453 148 22 1 3394 733070552 733073994 0 5110
12 TraesCS5A01G104700 chr2A 93.368 3453 152 25 1 3393 58510449 58507014 0 5036
13 TraesCS5A01G104700 chr2A 95.669 508 21 1 1 508 614204138 614204644 0 815
14 TraesCS5A01G104700 chr2A 95.079 508 24 1 1 508 619881425 619880919 0 798
15 TraesCS5A01G104700 chr1A 93.457 3454 160 19 1 3394 365631521 365634968 0 5066
16 TraesCS5A01G104700 chr1A 93.256 3455 163 23 1 3394 21073585 21070140 0 5025
17 TraesCS5A01G104700 chr1A 95.088 509 23 2 1 508 10682098 10682605 0 800
18 TraesCS5A01G104700 chr3D 95.122 2911 109 13 507 3394 175421712 175418812 0 4558
19 TraesCS5A01G104700 chr7D 94.919 2913 112 15 507 3394 30313315 30316216 0 4527
20 TraesCS5A01G104700 chr1D 94.540 2912 123 17 507 3394 58485006 58482107 0 4464
21 TraesCS5A01G104700 chr1D 94.420 2921 119 18 507 3394 10803743 10800834 0 4451
22 TraesCS5A01G104700 chr5D 94.538 2911 123 15 507 3394 526633760 526636657 0 4462
23 TraesCS5A01G104700 chr2D 94.194 2911 116 15 507 3394 536209054 536211934 0 4390
24 TraesCS5A01G104700 chr7B 94.541 2528 109 9 891 3394 666521722 666524244 0 3877


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 TraesCS5A01G104700 chr5A 169180499 169183892 3393 True 6268 6268 100.000 1 3394 1 chr5A.!!$R1 3393
1 TraesCS5A01G104700 chr5A 33905150 33908595 3445 False 5131 5131 93.802 1 3394 1 chr5A.!!$F1 3393
2 TraesCS5A01G104700 chr5A 524675838 524676344 506 False 804 804 95.285 1 508 1 chr5A.!!$F2 507
3 TraesCS5A01G104700 chr7A 675353734 675357175 3441 True 5199 5199 94.172 1 3394 1 chr7A.!!$R1 3393
4 TraesCS5A01G104700 chr7A 299349069 299352466 3397 False 5160 5160 94.384 59 3394 1 chr7A.!!$F1 3335
5 TraesCS5A01G104700 chr7A 701357420 701357926 506 True 843 843 96.654 1 508 1 chr7A.!!$R2 507
6 TraesCS5A01G104700 chr6A 531051939 531055381 3442 False 5171 5171 94.029 1 3394 1 chr6A.!!$F1 3393
7 TraesCS5A01G104700 chr6A 87943419 87945940 2521 True 3880 3880 94.579 892 3394 1 chr6A.!!$R1 2502
8 TraesCS5A01G104700 chr6A 184602710 184604852 2142 True 3225 3225 94.134 1289 3394 1 chr6A.!!$R2 2105
9 TraesCS5A01G104700 chr3A 450957039 450960464 3425 False 5129 5129 93.859 1 3394 1 chr3A.!!$F2 3393
10 TraesCS5A01G104700 chr3A 32205281 32205785 504 False 833 833 96.443 1 506 1 chr3A.!!$F1 505
11 TraesCS5A01G104700 chr2A 733070552 733073994 3442 False 5110 5110 93.716 1 3394 1 chr2A.!!$F2 3393
12 TraesCS5A01G104700 chr2A 58507014 58510449 3435 True 5036 5036 93.368 1 3393 1 chr2A.!!$R1 3392
13 TraesCS5A01G104700 chr2A 614204138 614204644 506 False 815 815 95.669 1 508 1 chr2A.!!$F1 507
14 TraesCS5A01G104700 chr2A 619880919 619881425 506 True 798 798 95.079 1 508 1 chr2A.!!$R2 507
15 TraesCS5A01G104700 chr1A 365631521 365634968 3447 False 5066 5066 93.457 1 3394 1 chr1A.!!$F2 3393
16 TraesCS5A01G104700 chr1A 21070140 21073585 3445 True 5025 5025 93.256 1 3394 1 chr1A.!!$R1 3393
17 TraesCS5A01G104700 chr1A 10682098 10682605 507 False 800 800 95.088 1 508 1 chr1A.!!$F1 507
18 TraesCS5A01G104700 chr3D 175418812 175421712 2900 True 4558 4558 95.122 507 3394 1 chr3D.!!$R1 2887
19 TraesCS5A01G104700 chr7D 30313315 30316216 2901 False 4527 4527 94.919 507 3394 1 chr7D.!!$F1 2887
20 TraesCS5A01G104700 chr1D 58482107 58485006 2899 True 4464 4464 94.540 507 3394 1 chr1D.!!$R2 2887
21 TraesCS5A01G104700 chr1D 10800834 10803743 2909 True 4451 4451 94.420 507 3394 1 chr1D.!!$R1 2887
22 TraesCS5A01G104700 chr5D 526633760 526636657 2897 False 4462 4462 94.538 507 3394 1 chr5D.!!$F1 2887
23 TraesCS5A01G104700 chr2D 536209054 536211934 2880 False 4390 4390 94.194 507 3394 1 chr2D.!!$F1 2887
24 TraesCS5A01G104700 chr7B 666521722 666524244 2522 False 3877 3877 94.541 891 3394 1 chr7B.!!$F1 2503

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
167 171 3.143211 ACATGCATGTTGGCCAAAAAT 57.857 38.095 26.61 14.48 37.90 1.82 F
346 353 4.955450 ACTGAAATATGTATGCTGGCCAAA 59.045 37.500 7.01 0.00 0.00 3.28 F
1190 1265 1.076118 CATTAGCCCATGGTGCCCA 60.076 57.895 18.29 8.45 38.19 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1159 1234 0.466922 GCTAATGACTGGCCTGCCAT 60.467 55.000 11.98 7.66 46.15 4.40 R
1754 1836 1.293924 GAGCGGATGATTGTGGTCAG 58.706 55.000 0.00 0.00 0.00 3.51 R
2679 2813 1.069668 CTCATCGCACCATCCTGATCA 59.930 52.381 0.00 0.00 0.00 2.92 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
39 40 4.741321 ATCCTGGCCAATTAAACATGTG 57.259 40.909 7.01 0.00 0.00 3.21
99 101 7.072177 TGTTTGTGAGTGAACACTTTAGAAG 57.928 36.000 8.87 0.00 42.66 2.85
167 171 3.143211 ACATGCATGTTGGCCAAAAAT 57.857 38.095 26.61 14.48 37.90 1.82
207 214 5.425217 TGGCCAACTGAGACATCTATTCTAA 59.575 40.000 0.61 0.00 0.00 2.10
328 335 8.474025 ACTAAAAACATTGAATGTCCAACTGAA 58.526 29.630 11.70 0.00 44.07 3.02
346 353 4.955450 ACTGAAATATGTATGCTGGCCAAA 59.045 37.500 7.01 0.00 0.00 3.28
920 989 8.406297 AGGTTGTTTGAAATACTCTTTTCTGTC 58.594 33.333 0.00 0.00 36.71 3.51
1059 1133 5.308759 TGAGCTTCCTCATGATATGGATCAA 59.691 40.000 3.19 0.00 42.98 2.57
1159 1234 2.394632 ACCCTACGAGCCATGACAATA 58.605 47.619 0.00 0.00 0.00 1.90
1190 1265 1.076118 CATTAGCCCATGGTGCCCA 60.076 57.895 18.29 8.45 38.19 5.36
1238 1313 2.159099 GCCATACTCTTGATGACACGGA 60.159 50.000 0.00 0.00 0.00 4.69
1255 1330 2.812358 GGAAACCGAGGCAAATGTTT 57.188 45.000 0.00 0.00 33.87 2.83
1422 1497 3.383505 ACAACAGCTATGCACTACGGATA 59.616 43.478 0.00 0.00 0.00 2.59
1558 1633 2.716017 GCTCCTCCTGTCCTGGACG 61.716 68.421 21.15 15.25 34.95 4.79
1659 1738 7.971722 GCTGGTACTAGTAAGAAGAAGAAGAAG 59.028 40.741 3.61 0.00 0.00 2.85
1660 1739 9.233649 CTGGTACTAGTAAGAAGAAGAAGAAGA 57.766 37.037 3.61 0.00 0.00 2.87
1661 1740 9.584008 TGGTACTAGTAAGAAGAAGAAGAAGAA 57.416 33.333 3.61 0.00 0.00 2.52
1669 1751 4.759183 AGAAGAAGAAGAAGAAGCGCAAAT 59.241 37.500 11.47 0.00 0.00 2.32
1754 1836 1.947456 GGAGGTGACACACTTTGTTCC 59.053 52.381 8.08 0.00 39.17 3.62
1933 2017 1.305886 TCCCTCTAGGCAGTCCAGTA 58.694 55.000 0.00 0.00 34.51 2.74
2248 2382 6.252599 TGTAATGGCAGAGTTCTATGGATT 57.747 37.500 0.00 0.00 0.00 3.01
2348 2482 4.397103 GGTGATCTGATTGAGACAATTGCA 59.603 41.667 5.05 0.00 31.75 4.08
2354 2488 5.300034 TCTGATTGAGACAATTGCACACTTT 59.700 36.000 5.05 0.00 0.00 2.66
2616 2750 0.107945 AGGAGTTGGCATCGAGCTTC 60.108 55.000 6.78 1.81 44.79 3.86
2641 2775 2.647299 TGGGTCTTTGGAGCATTCCTAA 59.353 45.455 0.00 0.00 44.36 2.69
2679 2813 4.696479 ACCTCTTGACAACTTCATCACT 57.304 40.909 0.00 0.00 32.84 3.41
2719 2853 3.689347 AGGCAGTCAATACAAAGCATCA 58.311 40.909 0.00 0.00 0.00 3.07
2953 3102 3.751175 CGAATACATGTCAACTTGGGTGT 59.249 43.478 0.00 0.00 0.00 4.16
2972 3121 3.062909 GTGTCGTGCTACTTCAAACACAA 59.937 43.478 0.00 0.00 36.10 3.33
3104 3254 6.923199 AAAAATCCAGAATCACATCCTTGT 57.077 33.333 0.00 0.00 36.15 3.16
3198 3348 6.374613 AGAAGCAAGCTTACAAAACCTATACC 59.625 38.462 7.37 0.00 36.26 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.625790 GTTGGCCAGGACACATGTTTAA 59.374 45.455 5.11 0.00 0.00 1.52
39 40 2.514803 ACATGTTTAGTTGGCCAGGAC 58.485 47.619 5.11 1.52 0.00 3.85
167 171 4.314522 TGGCCAGGATACATTTTCTCAA 57.685 40.909 0.00 0.00 41.41 3.02
207 214 4.218417 GGACAGTTAATGCATTCAGTTGGT 59.782 41.667 16.86 8.05 0.00 3.67
328 335 4.482030 TCCATTTGGCCAGCATACATATT 58.518 39.130 5.11 0.00 34.44 1.28
346 353 2.189676 TGCCAGGATGCATTTTTCCAT 58.810 42.857 0.00 0.00 36.04 3.41
372 379 6.561614 TCTGATTTTCGCTAGAATAGACGTT 58.438 36.000 0.00 0.00 42.77 3.99
647 702 2.264005 TTCCGTTTTGCAAGGAGCTA 57.736 45.000 0.00 0.00 45.94 3.32
830 896 9.508567 GATATTCTTAGTTCCAAAAGCAACATC 57.491 33.333 0.00 0.00 0.00 3.06
920 989 5.801350 ATTGATGTCATCAGTTGGTAACG 57.199 39.130 14.98 0.00 40.94 3.18
953 1022 3.181451 CCACACACTCCCTGCACATATAT 60.181 47.826 0.00 0.00 0.00 0.86
999 1073 4.497674 GGCAACTCATTGAGATCAAGCATC 60.498 45.833 20.33 2.21 39.47 3.91
1059 1133 1.247567 GTTGTATGCTGGGTTGCTGT 58.752 50.000 0.00 0.00 0.00 4.40
1159 1234 0.466922 GCTAATGACTGGCCTGCCAT 60.467 55.000 11.98 7.66 46.15 4.40
1190 1265 3.492102 ACTGCAAAGACACCACTACAT 57.508 42.857 0.00 0.00 0.00 2.29
1238 1313 2.035832 CCAGAAACATTTGCCTCGGTTT 59.964 45.455 0.00 0.00 36.27 3.27
1422 1497 6.214412 AGGTGTTCATCTTGATAGAGAAACCT 59.786 38.462 0.00 0.00 32.95 3.50
1669 1751 2.995939 CAGTCTGCTTTATTGTCTCGCA 59.004 45.455 0.00 0.00 0.00 5.10
1754 1836 1.293924 GAGCGGATGATTGTGGTCAG 58.706 55.000 0.00 0.00 0.00 3.51
1933 2017 5.874810 CACAGTAGTACCATAACAGTTGCAT 59.125 40.000 0.00 0.00 0.00 3.96
2248 2382 1.737838 GAACGGCACCATCATCTCAA 58.262 50.000 0.00 0.00 0.00 3.02
2400 2534 5.971763 ACAACTCTGTCCTCTTCATCATAC 58.028 41.667 0.00 0.00 0.00 2.39
2481 2615 2.095853 GGTGGTGTCAAACGATATGCAG 59.904 50.000 0.00 0.00 0.00 4.41
2616 2750 1.755179 ATGCTCCAAAGACCCAATCG 58.245 50.000 0.00 0.00 0.00 3.34
2641 2775 1.288932 AGGTTTGCCATCCATAGCCTT 59.711 47.619 0.00 0.00 37.19 4.35
2679 2813 1.069668 CTCATCGCACCATCCTGATCA 59.930 52.381 0.00 0.00 0.00 2.92
2719 2853 1.901464 GGTGCACGGTGGTTGGAAT 60.901 57.895 11.45 0.00 0.00 3.01
2953 3102 3.527533 ACTTGTGTTTGAAGTAGCACGA 58.472 40.909 0.00 0.00 31.72 4.35
2972 3121 3.338519 AGACTAGAGGAAGGGGAAGAACT 59.661 47.826 0.00 0.00 0.00 3.01
3104 3254 2.519771 ATCATTGCAGCCTTCCTTGA 57.480 45.000 0.00 0.00 0.00 3.02
3198 3348 0.036306 ACTTGCGGTAAAGGTCCCTG 59.964 55.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.