Multiple sequence alignment - TraesCS4D01G286700

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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 TraesCS4D01G286700 chr4D 100.000 3064 0 0 1 3064 458383021 458386084 0.000000e+00 5659
1 TraesCS4D01G286700 chr4B 95.731 3022 66 21 55 3043 572552476 572555467 0.000000e+00 4807
2 TraesCS4D01G286700 chr4B 94.466 524 11 3 2537 3043 276890751 276890229 0.000000e+00 791
3 TraesCS4D01G286700 chr4B 94.275 524 12 3 2537 3043 101490878 101490356 0.000000e+00 785
4 TraesCS4D01G286700 chr4B 94.275 524 12 3 2537 3043 463531860 463532382 0.000000e+00 785
5 TraesCS4D01G286700 chr4B 93.893 524 14 3 2537 3043 528244831 528244309 0.000000e+00 774
6 TraesCS4D01G286700 chr4A 94.261 2509 77 25 594 3064 10638774 10636295 0.000000e+00 3773
7 TraesCS4D01G286700 chr4A 86.190 840 114 2 1266 2104 742138955 742138117 0.000000e+00 907
8 TraesCS4D01G286700 chr4A 78.150 1103 195 31 1035 2110 740939990 740941073 0.000000e+00 660
9 TraesCS4D01G286700 chr4A 77.357 1082 193 36 1040 2089 740581399 740582460 7.310000e-166 593
10 TraesCS4D01G286700 chr4A 77.692 1031 183 33 1062 2064 740016737 740015726 1.220000e-163 586
11 TraesCS4D01G286700 chr7A 83.563 1089 172 6 1021 2104 2604734 2603648 0.000000e+00 1013
12 TraesCS4D01G286700 chr7A 83.424 1098 166 9 1021 2104 2751376 2752471 0.000000e+00 1005
13 TraesCS4D01G286700 chr7A 77.015 1092 203 32 1035 2089 2115266 2114186 1.580000e-162 582
14 TraesCS4D01G286700 chr3A 97.436 507 12 1 2537 3043 181115602 181115097 0.000000e+00 863
15 TraesCS4D01G286700 chr3A 96.869 511 10 3 2537 3043 180540190 180540698 0.000000e+00 850
16 TraesCS4D01G286700 chr6A 97.431 506 12 1 2537 3042 41460120 41459616 0.000000e+00 861
17 TraesCS4D01G286700 chr6A 96.844 507 15 1 2537 3043 75096649 75096144 0.000000e+00 846
18 TraesCS4D01G286700 chr2B 97.041 507 14 1 2537 3043 1114639 1115144 0.000000e+00 852
19 TraesCS4D01G286700 chr6B 96.844 507 15 1 2537 3043 635524579 635524074 0.000000e+00 846
20 TraesCS4D01G286700 chr7D 80.666 1081 178 11 1047 2104 9923683 9924755 0.000000e+00 809
21 TraesCS4D01G286700 chr7D 80.961 541 77 18 1541 2065 3245749 3245219 3.680000e-109 405
22 TraesCS4D01G286700 chr1B 94.466 524 11 3 2537 3043 320368463 320367941 0.000000e+00 791
23 TraesCS4D01G286700 chr6D 94.030 67 4 0 2044 2110 370897157 370897223 5.400000e-18 102


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 TraesCS4D01G286700 chr4D 458383021 458386084 3063 False 5659 5659 100.000 1 3064 1 chr4D.!!$F1 3063
1 TraesCS4D01G286700 chr4B 572552476 572555467 2991 False 4807 4807 95.731 55 3043 1 chr4B.!!$F2 2988
2 TraesCS4D01G286700 chr4B 276890229 276890751 522 True 791 791 94.466 2537 3043 1 chr4B.!!$R2 506
3 TraesCS4D01G286700 chr4B 101490356 101490878 522 True 785 785 94.275 2537 3043 1 chr4B.!!$R1 506
4 TraesCS4D01G286700 chr4B 463531860 463532382 522 False 785 785 94.275 2537 3043 1 chr4B.!!$F1 506
5 TraesCS4D01G286700 chr4B 528244309 528244831 522 True 774 774 93.893 2537 3043 1 chr4B.!!$R3 506
6 TraesCS4D01G286700 chr4A 10636295 10638774 2479 True 3773 3773 94.261 594 3064 1 chr4A.!!$R1 2470
7 TraesCS4D01G286700 chr4A 742138117 742138955 838 True 907 907 86.190 1266 2104 1 chr4A.!!$R3 838
8 TraesCS4D01G286700 chr4A 740939990 740941073 1083 False 660 660 78.150 1035 2110 1 chr4A.!!$F2 1075
9 TraesCS4D01G286700 chr4A 740581399 740582460 1061 False 593 593 77.357 1040 2089 1 chr4A.!!$F1 1049
10 TraesCS4D01G286700 chr4A 740015726 740016737 1011 True 586 586 77.692 1062 2064 1 chr4A.!!$R2 1002
11 TraesCS4D01G286700 chr7A 2603648 2604734 1086 True 1013 1013 83.563 1021 2104 1 chr7A.!!$R2 1083
12 TraesCS4D01G286700 chr7A 2751376 2752471 1095 False 1005 1005 83.424 1021 2104 1 chr7A.!!$F1 1083
13 TraesCS4D01G286700 chr7A 2114186 2115266 1080 True 582 582 77.015 1035 2089 1 chr7A.!!$R1 1054
14 TraesCS4D01G286700 chr3A 181115097 181115602 505 True 863 863 97.436 2537 3043 1 chr3A.!!$R1 506
15 TraesCS4D01G286700 chr3A 180540190 180540698 508 False 850 850 96.869 2537 3043 1 chr3A.!!$F1 506
16 TraesCS4D01G286700 chr6A 41459616 41460120 504 True 861 861 97.431 2537 3042 1 chr6A.!!$R1 505
17 TraesCS4D01G286700 chr6A 75096144 75096649 505 True 846 846 96.844 2537 3043 1 chr6A.!!$R2 506
18 TraesCS4D01G286700 chr2B 1114639 1115144 505 False 852 852 97.041 2537 3043 1 chr2B.!!$F1 506
19 TraesCS4D01G286700 chr6B 635524074 635524579 505 True 846 846 96.844 2537 3043 1 chr6B.!!$R1 506
20 TraesCS4D01G286700 chr7D 9923683 9924755 1072 False 809 809 80.666 1047 2104 1 chr7D.!!$F1 1057
21 TraesCS4D01G286700 chr7D 3245219 3245749 530 True 405 405 80.961 1541 2065 1 chr7D.!!$R1 524
22 TraesCS4D01G286700 chr1B 320367941 320368463 522 True 791 791 94.466 2537 3043 1 chr1B.!!$R1 506

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
46 47 0.106819 AGCAGGGGCAGAAGCATTAG 60.107 55.0 0.0 0.0 44.61 1.73 F
47 48 0.107017 GCAGGGGCAGAAGCATTAGA 60.107 55.0 0.0 0.0 44.61 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2036 0.976073 TAGAAGTCCTTGGGCCTCCG 60.976 60.000 4.53 0.0 35.24 4.63 R
2401 2516 4.114058 TGCAGCCAAAGATAAATCAAGC 57.886 40.909 0.00 0.0 0.00 4.01 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
33 34 4.798344 CAGAGGGCTGCAGCAGGG 62.798 72.222 37.63 18.99 44.36 4.45
43 44 2.044252 CAGCAGGGGCAGAAGCAT 60.044 61.111 0.00 0.00 44.61 3.79
44 45 1.681327 CAGCAGGGGCAGAAGCATT 60.681 57.895 0.00 0.00 44.61 3.56
45 46 0.394762 CAGCAGGGGCAGAAGCATTA 60.395 55.000 0.00 0.00 44.61 1.90
46 47 0.106819 AGCAGGGGCAGAAGCATTAG 60.107 55.000 0.00 0.00 44.61 1.73
47 48 0.107017 GCAGGGGCAGAAGCATTAGA 60.107 55.000 0.00 0.00 44.61 2.10
48 49 1.683011 GCAGGGGCAGAAGCATTAGAA 60.683 52.381 0.00 0.00 44.61 2.10
49 50 2.295885 CAGGGGCAGAAGCATTAGAAG 58.704 52.381 0.00 0.00 44.61 2.85
50 51 1.213926 AGGGGCAGAAGCATTAGAAGG 59.786 52.381 0.00 0.00 44.61 3.46
51 52 1.685148 GGGCAGAAGCATTAGAAGGG 58.315 55.000 0.00 0.00 44.61 3.95
52 53 1.685148 GGCAGAAGCATTAGAAGGGG 58.315 55.000 0.00 0.00 44.61 4.79
53 54 1.028130 GCAGAAGCATTAGAAGGGGC 58.972 55.000 0.00 0.00 41.58 5.80
121 122 8.927675 TCTCTCTCTACAGGTATAAATCCTTC 57.072 38.462 0.00 0.00 32.37 3.46
124 125 8.290277 TCTCTCTACAGGTATAAATCCTTCCTT 58.710 37.037 0.00 0.00 32.37 3.36
128 129 5.685728 ACAGGTATAAATCCTTCCTTGCTC 58.314 41.667 0.00 0.00 32.37 4.26
129 130 4.752101 CAGGTATAAATCCTTCCTTGCTCG 59.248 45.833 0.00 0.00 32.37 5.03
132 133 2.206576 AAATCCTTCCTTGCTCGCTT 57.793 45.000 0.00 0.00 0.00 4.68
151 161 3.117171 CTTGCTTGCTCGCTCGCT 61.117 61.111 0.00 0.00 0.00 4.93
152 162 3.081159 CTTGCTTGCTCGCTCGCTC 62.081 63.158 0.00 0.00 0.00 5.03
313 340 1.271934 TGCCATGGGTTCGATTTGTTG 59.728 47.619 15.13 0.00 0.00 3.33
314 341 1.994916 CCATGGGTTCGATTTGTTGC 58.005 50.000 2.85 0.00 0.00 4.17
359 386 0.883833 CCTGCGCATGTTCTTCCTTT 59.116 50.000 12.24 0.00 0.00 3.11
365 392 3.070018 CGCATGTTCTTCCTTTCTCTGT 58.930 45.455 0.00 0.00 0.00 3.41
366 393 3.499918 CGCATGTTCTTCCTTTCTCTGTT 59.500 43.478 0.00 0.00 0.00 3.16
367 394 4.612259 CGCATGTTCTTCCTTTCTCTGTTG 60.612 45.833 0.00 0.00 0.00 3.33
368 395 4.320788 GCATGTTCTTCCTTTCTCTGTTGG 60.321 45.833 0.00 0.00 0.00 3.77
369 396 4.771114 TGTTCTTCCTTTCTCTGTTGGA 57.229 40.909 0.00 0.00 0.00 3.53
483 510 1.002502 GGTTTGGTTCTCGGGGGAG 60.003 63.158 0.00 0.00 0.00 4.30
590 617 1.918262 TCAGATCTCAAATGCCCCTGT 59.082 47.619 0.00 0.00 0.00 4.00
1520 1612 2.169352 TGGAAAGATACTGAGCTCTGCC 59.831 50.000 19.49 11.39 0.00 4.85
1532 1624 2.230992 GAGCTCTGCCGAGATGTATGAT 59.769 50.000 9.60 0.00 39.74 2.45
1574 1666 1.776667 CCCCTTCCCAGCATGAATAGA 59.223 52.381 0.00 0.00 39.69 1.98
1925 2036 1.009829 GTGACCGGCTGATTGTCATC 58.990 55.000 0.00 0.00 40.75 2.92
2401 2516 5.771469 TGATGAACAACCTGTTAAGCAATG 58.229 37.500 0.00 0.00 41.28 2.82
2543 2658 7.096551 GGTAATGATATGTTGTTTTGCTGGTT 58.903 34.615 0.00 0.00 0.00 3.67
2639 2754 7.771361 TGTTTGACTCAGGTGTTTTAGTTCATA 59.229 33.333 0.00 0.00 0.00 2.15
2818 2993 4.124851 TGTTGCTAGCCTAGAAGTAAGC 57.875 45.455 13.29 0.00 0.00 3.09
2854 3029 9.136323 GTTTTACTGGATCATTGAATTATCCCT 57.864 33.333 14.11 4.14 38.76 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.798344 CCCTGCTGCAGCCCTCTG 62.798 72.222 34.64 18.55 43.16 3.35
26 27 0.394762 TAATGCTTCTGCCCCTGCTG 60.395 55.000 0.00 0.00 38.71 4.41
27 28 0.106819 CTAATGCTTCTGCCCCTGCT 60.107 55.000 0.00 0.00 38.71 4.24
28 29 0.107017 TCTAATGCTTCTGCCCCTGC 60.107 55.000 0.00 0.00 38.71 4.85
29 30 2.295885 CTTCTAATGCTTCTGCCCCTG 58.704 52.381 0.00 0.00 38.71 4.45
30 31 1.213926 CCTTCTAATGCTTCTGCCCCT 59.786 52.381 0.00 0.00 38.71 4.79
31 32 1.685148 CCTTCTAATGCTTCTGCCCC 58.315 55.000 0.00 0.00 38.71 5.80
32 33 1.685148 CCCTTCTAATGCTTCTGCCC 58.315 55.000 0.00 0.00 38.71 5.36
33 34 1.685148 CCCCTTCTAATGCTTCTGCC 58.315 55.000 0.00 0.00 38.71 4.85
34 35 1.028130 GCCCCTTCTAATGCTTCTGC 58.972 55.000 0.00 0.00 40.20 4.26
35 36 2.295885 CTGCCCCTTCTAATGCTTCTG 58.704 52.381 0.00 0.00 0.00 3.02
36 37 1.918957 ACTGCCCCTTCTAATGCTTCT 59.081 47.619 0.00 0.00 0.00 2.85
37 38 2.424956 CAACTGCCCCTTCTAATGCTTC 59.575 50.000 0.00 0.00 0.00 3.86
38 39 2.225117 ACAACTGCCCCTTCTAATGCTT 60.225 45.455 0.00 0.00 0.00 3.91
39 40 1.355720 ACAACTGCCCCTTCTAATGCT 59.644 47.619 0.00 0.00 0.00 3.79
40 41 1.839424 ACAACTGCCCCTTCTAATGC 58.161 50.000 0.00 0.00 0.00 3.56
41 42 3.694566 GGTTACAACTGCCCCTTCTAATG 59.305 47.826 0.00 0.00 0.00 1.90
42 43 3.332485 TGGTTACAACTGCCCCTTCTAAT 59.668 43.478 0.00 0.00 0.00 1.73
43 44 2.712087 TGGTTACAACTGCCCCTTCTAA 59.288 45.455 0.00 0.00 0.00 2.10
44 45 2.340731 TGGTTACAACTGCCCCTTCTA 58.659 47.619 0.00 0.00 0.00 2.10
45 46 1.145571 TGGTTACAACTGCCCCTTCT 58.854 50.000 0.00 0.00 0.00 2.85
46 47 1.886542 CTTGGTTACAACTGCCCCTTC 59.113 52.381 0.00 0.00 32.14 3.46
47 48 1.216930 ACTTGGTTACAACTGCCCCTT 59.783 47.619 0.00 0.00 32.14 3.95
48 49 0.850784 ACTTGGTTACAACTGCCCCT 59.149 50.000 0.00 0.00 32.14 4.79
49 50 0.958822 CACTTGGTTACAACTGCCCC 59.041 55.000 0.00 0.00 32.14 5.80
50 51 0.958822 CCACTTGGTTACAACTGCCC 59.041 55.000 0.00 0.00 32.14 5.36
51 52 0.313987 GCCACTTGGTTACAACTGCC 59.686 55.000 0.00 0.00 37.57 4.85
52 53 1.001378 CTGCCACTTGGTTACAACTGC 60.001 52.381 0.00 0.00 37.57 4.40
53 54 1.001378 GCTGCCACTTGGTTACAACTG 60.001 52.381 0.00 0.00 37.57 3.16
121 122 2.126580 GCAAGCAAGCGAGCAAGG 60.127 61.111 6.21 0.00 36.85 3.61
124 125 2.640989 CAAGCAAGCAAGCGAGCA 59.359 55.556 12.73 0.00 40.15 4.26
128 129 2.501222 CGAGCAAGCAAGCAAGCG 60.501 61.111 3.19 0.55 40.15 4.68
129 130 2.804090 GCGAGCAAGCAAGCAAGC 60.804 61.111 3.19 4.16 36.85 4.01
132 133 3.417224 CGAGCGAGCAAGCAAGCA 61.417 61.111 12.73 0.00 40.15 3.91
151 161 2.805546 GTCCTACCAGATGCGCGA 59.194 61.111 12.10 0.00 0.00 5.87
152 162 2.655364 CGTCCTACCAGATGCGCG 60.655 66.667 0.00 0.00 0.00 6.86
153 163 2.279517 CCGTCCTACCAGATGCGC 60.280 66.667 0.00 0.00 0.00 6.09
154 164 1.360551 CTCCGTCCTACCAGATGCG 59.639 63.158 0.00 0.00 0.00 4.73
254 281 2.943199 GCCCAAGGAAATCTGGACTGAG 60.943 54.545 0.00 0.00 0.00 3.35
283 310 2.711311 CCATGGCAAGATCACGCG 59.289 61.111 3.53 3.53 0.00 6.01
313 340 4.379918 GGCAAGAAAGAATCACCTAACAGC 60.380 45.833 0.00 0.00 0.00 4.40
314 341 4.156739 GGGCAAGAAAGAATCACCTAACAG 59.843 45.833 0.00 0.00 0.00 3.16
359 386 4.868172 ATCCAATCCAATCCAACAGAGA 57.132 40.909 0.00 0.00 0.00 3.10
365 392 4.409574 CCAATCCAATCCAATCCAATCCAA 59.590 41.667 0.00 0.00 0.00 3.53
366 393 3.968649 CCAATCCAATCCAATCCAATCCA 59.031 43.478 0.00 0.00 0.00 3.41
367 394 4.225573 TCCAATCCAATCCAATCCAATCC 58.774 43.478 0.00 0.00 0.00 3.01
368 395 5.279809 CCATCCAATCCAATCCAATCCAATC 60.280 44.000 0.00 0.00 0.00 2.67
369 396 4.595781 CCATCCAATCCAATCCAATCCAAT 59.404 41.667 0.00 0.00 0.00 3.16
448 475 2.058001 CCAAATCTTTCCCCCGCCC 61.058 63.158 0.00 0.00 0.00 6.13
451 478 1.275010 CCAAACCAAATCTTTCCCCCG 59.725 52.381 0.00 0.00 0.00 5.73
455 482 4.546570 CGAGAACCAAACCAAATCTTTCC 58.453 43.478 0.00 0.00 0.00 3.13
457 484 3.320826 CCCGAGAACCAAACCAAATCTTT 59.679 43.478 0.00 0.00 0.00 2.52
483 510 2.440247 CTCCCACCCCCAAATCGC 60.440 66.667 0.00 0.00 0.00 4.58
590 617 2.674177 GCGAGAAGAAACGGATCAGGAA 60.674 50.000 0.00 0.00 0.00 3.36
731 768 2.069273 CCCGCTCGGCTTATTATCTTG 58.931 52.381 2.18 0.00 0.00 3.02
882 941 3.257561 CTCCATGTCTTCCGCGCG 61.258 66.667 25.67 25.67 0.00 6.86
1520 1612 5.230936 GTGTGTCACAGAATCATACATCTCG 59.769 44.000 5.74 0.00 34.08 4.04
1532 1624 2.027653 TGTCCAAGTGTGTGTCACAGAA 60.028 45.455 5.74 0.00 45.43 3.02
1574 1666 3.055530 CACCAGAACACATCTTCCTAGCT 60.056 47.826 0.00 0.00 35.73 3.32
1925 2036 0.976073 TAGAAGTCCTTGGGCCTCCG 60.976 60.000 4.53 0.00 35.24 4.63
2401 2516 4.114058 TGCAGCCAAAGATAAATCAAGC 57.886 40.909 0.00 0.00 0.00 4.01
2543 2658 8.344831 GCATCTAATAGCACATACAAATTCACA 58.655 33.333 0.00 0.00 0.00 3.58
2818 2993 4.080356 TGATCCAGTAAAACCATGAGGAGG 60.080 45.833 0.00 0.00 38.69 4.30
2854 3029 1.608590 CTTTTTGCCCTTTCGCTCTCA 59.391 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.