Multiple sequence alignment - TraesCS7B01G469300

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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 TraesCS7B01G469300 chr7B 100.000 3221 0 0 1 3221 726107301 726104081 0.000000e+00 5949.0
1 TraesCS7B01G469300 chr5B 98.792 3145 30 6 81 3221 509688272 509685132 0.000000e+00 5590.0
2 TraesCS7B01G469300 chr6B 93.467 2939 137 24 164 3085 547718593 547721493 0.000000e+00 4313.0
3 TraesCS7B01G469300 chr6B 88.160 549 40 15 1518 2048 520330888 520331429 5.860000e-177 630.0
4 TraesCS7B01G469300 chr6B 90.859 361 26 7 2428 2782 90027745 90027386 8.080000e-131 477.0
5 TraesCS7B01G469300 chr6B 82.528 269 36 6 2086 2344 266860333 266860600 3.230000e-55 226.0
6 TraesCS7B01G469300 chr6B 91.216 148 6 1 3081 3221 547722184 547722331 9.120000e-46 195.0
7 TraesCS7B01G469300 chr6B 97.248 109 3 0 82 190 547718461 547718569 5.490000e-43 185.0
8 TraesCS7B01G469300 chr7D 94.485 1795 89 9 187 1975 53682268 53680478 0.000000e+00 2758.0
9 TraesCS7B01G469300 chr7D 87.500 496 37 8 2309 2782 54495716 54495224 1.690000e-152 549.0
10 TraesCS7B01G469300 chr7D 94.595 111 6 0 80 190 53682432 53682322 4.270000e-39 172.0
11 TraesCS7B01G469300 chr7D 90.756 119 4 1 3110 3221 53680481 53680363 5.570000e-33 152.0
12 TraesCS7B01G469300 chr3D 92.340 1423 83 18 1519 2922 505789051 505787636 0.000000e+00 2001.0
13 TraesCS7B01G469300 chr3D 91.489 376 28 4 2411 2782 45525665 45526040 6.160000e-142 514.0
14 TraesCS7B01G469300 chr3D 91.289 287 17 2 2943 3221 505787642 505787356 5.040000e-103 385.0
15 TraesCS7B01G469300 chr2A 89.047 913 56 22 1646 2520 306138645 306139551 0.000000e+00 1092.0
16 TraesCS7B01G469300 chr2A 91.337 404 28 4 2311 2709 376798021 376798422 2.190000e-151 545.0
17 TraesCS7B01G469300 chr2A 91.521 401 25 4 2523 2922 306139622 306140014 7.860000e-151 544.0
18 TraesCS7B01G469300 chr2A 92.308 286 15 1 2943 3221 306140008 306140293 1.800000e-107 399.0
19 TraesCS7B01G469300 chr2A 95.699 93 4 0 1518 1610 306138195 306138287 2.000000e-32 150.0
20 TraesCS7B01G469300 chr2A 93.333 60 4 0 1518 1577 256199724 256199783 4.430000e-14 89.8
21 TraesCS7B01G469300 chr2D 91.627 633 46 6 2154 2782 484037031 484037660 0.000000e+00 869.0
22 TraesCS7B01G469300 chr1D 84.777 808 66 21 736 1516 371661290 371660513 0.000000e+00 758.0
23 TraesCS7B01G469300 chr1D 97.872 47 1 0 1 47 276250057 276250103 7.410000e-12 82.4
24 TraesCS7B01G469300 chr1B 84.653 808 67 21 736 1516 496098836 496098059 0.000000e+00 752.0
25 TraesCS7B01G469300 chr1A 86.377 668 57 17 857 1516 471324052 471323411 0.000000e+00 699.0
26 TraesCS7B01G469300 chr2B 85.370 622 50 21 1646 2228 357169719 357170338 9.880000e-170 606.0
27 TraesCS7B01G469300 chr2B 89.027 401 26 6 2523 2922 357170938 357171321 6.250000e-132 481.0
28 TraesCS7B01G469300 chr2B 92.278 259 16 3 2266 2524 357170570 357170824 6.570000e-97 364.0
29 TraesCS7B01G469300 chr2B 90.210 286 18 4 2943 3221 357171315 357171597 6.570000e-97 364.0
30 TraesCS7B01G469300 chr2B 95.699 93 4 0 1518 1610 357169266 357169358 2.000000e-32 150.0
31 TraesCS7B01G469300 chr4A 89.383 405 33 8 2311 2707 443843824 443843422 4.800000e-138 501.0
32 TraesCS7B01G469300 chr4B 89.521 334 32 2 2154 2487 545866437 545866107 1.380000e-113 420.0
33 TraesCS7B01G469300 chr3B 85.377 212 31 0 2133 2344 810247281 810247492 1.500000e-53 220.0
34 TraesCS7B01G469300 chr5A 81.413 269 40 5 2086 2344 572508517 572508249 9.050000e-51 211.0
35 TraesCS7B01G469300 chr5A 93.333 60 4 0 1518 1577 139483915 139483856 4.430000e-14 89.8
36 TraesCS7B01G469300 chr7A 97.872 47 1 0 1 47 75224091 75224045 7.410000e-12 82.4


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 TraesCS7B01G469300 chr7B 726104081 726107301 3220 True 5949.000000 5949 100.000000 1 3221 1 chr7B.!!$R1 3220
1 TraesCS7B01G469300 chr5B 509685132 509688272 3140 True 5590.000000 5590 98.792000 81 3221 1 chr5B.!!$R1 3140
2 TraesCS7B01G469300 chr6B 547718461 547722331 3870 False 1564.333333 4313 93.977000 82 3221 3 chr6B.!!$F3 3139
3 TraesCS7B01G469300 chr6B 520330888 520331429 541 False 630.000000 630 88.160000 1518 2048 1 chr6B.!!$F2 530
4 TraesCS7B01G469300 chr7D 53680363 53682432 2069 True 1027.333333 2758 93.278667 80 3221 3 chr7D.!!$R2 3141
5 TraesCS7B01G469300 chr3D 505787356 505789051 1695 True 1193.000000 2001 91.814500 1519 3221 2 chr3D.!!$R1 1702
6 TraesCS7B01G469300 chr2A 306138195 306140293 2098 False 546.250000 1092 92.143750 1518 3221 4 chr2A.!!$F3 1703
7 TraesCS7B01G469300 chr2D 484037031 484037660 629 False 869.000000 869 91.627000 2154 2782 1 chr2D.!!$F1 628
8 TraesCS7B01G469300 chr1D 371660513 371661290 777 True 758.000000 758 84.777000 736 1516 1 chr1D.!!$R1 780
9 TraesCS7B01G469300 chr1B 496098059 496098836 777 True 752.000000 752 84.653000 736 1516 1 chr1B.!!$R1 780
10 TraesCS7B01G469300 chr1A 471323411 471324052 641 True 699.000000 699 86.377000 857 1516 1 chr1A.!!$R1 659
11 TraesCS7B01G469300 chr2B 357169266 357171597 2331 False 393.000000 606 90.516800 1518 3221 5 chr2B.!!$F1 1703

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
24 25 0.103937 GAGATGGACAGGGAAGCGAG 59.896 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3093 4618 1.139058 GTAGTCATCCGCCAATCCAGT 59.861 52.381 0.0 0.0 0.0 4.0 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
17 18 3.978164 GGAGGGAGATGGACAGGG 58.022 66.667 0.00 0.0 0.00 4.45
18 19 1.314867 GGAGGGAGATGGACAGGGA 59.685 63.158 0.00 0.0 0.00 4.20
19 20 0.326618 GGAGGGAGATGGACAGGGAA 60.327 60.000 0.00 0.0 0.00 3.97
20 21 1.127343 GAGGGAGATGGACAGGGAAG 58.873 60.000 0.00 0.0 0.00 3.46
21 22 0.985490 AGGGAGATGGACAGGGAAGC 60.985 60.000 0.00 0.0 0.00 3.86
22 23 1.144936 GGAGATGGACAGGGAAGCG 59.855 63.158 0.00 0.0 0.00 4.68
23 24 1.330655 GGAGATGGACAGGGAAGCGA 61.331 60.000 0.00 0.0 0.00 4.93
24 25 0.103937 GAGATGGACAGGGAAGCGAG 59.896 60.000 0.00 0.0 0.00 5.03
25 26 0.616111 AGATGGACAGGGAAGCGAGT 60.616 55.000 0.00 0.0 0.00 4.18
26 27 0.460987 GATGGACAGGGAAGCGAGTG 60.461 60.000 0.00 0.0 0.00 3.51
27 28 0.904865 ATGGACAGGGAAGCGAGTGA 60.905 55.000 0.00 0.0 0.00 3.41
28 29 1.118965 TGGACAGGGAAGCGAGTGAA 61.119 55.000 0.00 0.0 0.00 3.18
29 30 0.250513 GGACAGGGAAGCGAGTGAAT 59.749 55.000 0.00 0.0 0.00 2.57
30 31 1.646189 GACAGGGAAGCGAGTGAATC 58.354 55.000 0.00 0.0 0.00 2.52
31 32 0.250513 ACAGGGAAGCGAGTGAATCC 59.749 55.000 0.00 0.0 0.00 3.01
32 33 0.539051 CAGGGAAGCGAGTGAATCCT 59.461 55.000 0.00 0.0 32.41 3.24
33 34 0.827368 AGGGAAGCGAGTGAATCCTC 59.173 55.000 0.00 0.0 32.41 3.71
34 35 0.179070 GGGAAGCGAGTGAATCCTCC 60.179 60.000 0.00 0.0 32.41 4.30
35 36 0.528684 GGAAGCGAGTGAATCCTCCG 60.529 60.000 0.00 0.0 0.00 4.63
36 37 1.148759 GAAGCGAGTGAATCCTCCGC 61.149 60.000 0.00 0.0 33.88 5.54
37 38 2.579684 AAGCGAGTGAATCCTCCGCC 62.580 60.000 0.00 0.0 34.05 6.13
38 39 2.278857 CGAGTGAATCCTCCGCCG 60.279 66.667 0.00 0.0 0.00 6.46
39 40 2.771639 CGAGTGAATCCTCCGCCGA 61.772 63.158 0.00 0.0 0.00 5.54
40 41 1.066587 GAGTGAATCCTCCGCCGAG 59.933 63.158 0.00 0.0 35.72 4.63
41 42 2.586357 GTGAATCCTCCGCCGAGC 60.586 66.667 0.00 0.0 34.49 5.03
42 43 3.074369 TGAATCCTCCGCCGAGCA 61.074 61.111 0.00 0.0 34.49 4.26
43 44 2.586357 GAATCCTCCGCCGAGCAC 60.586 66.667 0.00 0.0 34.49 4.40
44 45 4.162690 AATCCTCCGCCGAGCACC 62.163 66.667 0.00 0.0 34.49 5.01
55 56 4.874977 GAGCACCGCCCGCTAGTC 62.875 72.222 0.00 0.0 40.63 2.59
62 63 4.893601 GCCCGCTAGTCGCCCTTC 62.894 72.222 0.00 0.0 36.73 3.46
63 64 3.458163 CCCGCTAGTCGCCCTTCA 61.458 66.667 0.00 0.0 36.73 3.02
64 65 2.202756 CCGCTAGTCGCCCTTCAC 60.203 66.667 0.00 0.0 36.73 3.18
65 66 2.571757 CGCTAGTCGCCCTTCACA 59.428 61.111 0.00 0.0 34.21 3.58
66 67 1.517257 CGCTAGTCGCCCTTCACAG 60.517 63.158 0.00 0.0 34.21 3.66
67 68 1.592223 GCTAGTCGCCCTTCACAGT 59.408 57.895 0.00 0.0 0.00 3.55
68 69 0.458716 GCTAGTCGCCCTTCACAGTC 60.459 60.000 0.00 0.0 0.00 3.51
69 70 0.179161 CTAGTCGCCCTTCACAGTCG 60.179 60.000 0.00 0.0 0.00 4.18
70 71 0.607217 TAGTCGCCCTTCACAGTCGA 60.607 55.000 0.00 0.0 0.00 4.20
71 72 1.006571 GTCGCCCTTCACAGTCGAA 60.007 57.895 0.00 0.0 0.00 3.71
72 73 0.599204 GTCGCCCTTCACAGTCGAAA 60.599 55.000 0.00 0.0 0.00 3.46
73 74 0.599204 TCGCCCTTCACAGTCGAAAC 60.599 55.000 0.00 0.0 0.00 2.78
74 75 1.566018 CGCCCTTCACAGTCGAAACC 61.566 60.000 0.00 0.0 0.00 3.27
75 76 1.566018 GCCCTTCACAGTCGAAACCG 61.566 60.000 0.00 0.0 0.00 4.44
76 77 0.249741 CCCTTCACAGTCGAAACCGT 60.250 55.000 0.00 0.0 0.00 4.83
77 78 1.578583 CCTTCACAGTCGAAACCGTT 58.421 50.000 0.00 0.0 0.00 4.44
78 79 1.525619 CCTTCACAGTCGAAACCGTTC 59.474 52.381 0.00 0.0 0.00 3.95
394 452 1.171308 CAGAAACCCTAGTCGTCCGA 58.829 55.000 0.00 0.0 0.00 4.55
399 457 0.750911 ACCCTAGTCGTCCGACCATC 60.751 60.000 15.60 0.0 45.59 3.51
405 463 1.673337 TCGTCCGACCATCGTGACT 60.673 57.895 13.89 0.0 38.40 3.41
459 517 5.574970 ATGTTATCAATCCCTTCTCTCCC 57.425 43.478 0.00 0.0 0.00 4.30
620 687 3.327172 AGGATAAGCAGCAGTAGCATGAT 59.673 43.478 0.00 0.0 45.49 2.45
1250 1338 4.350245 TCTGTAAGCCTTCAAGCTACCTA 58.650 43.478 0.00 0.0 44.11 3.08
2855 3638 7.535139 TGCAACTTTACTCATAATACCTTTGC 58.465 34.615 0.00 0.0 35.99 3.68
3093 4618 1.267574 GGAGGAGGATGACAGTGCCA 61.268 60.000 0.00 0.0 0.00 4.92
3118 4643 3.321111 GGATTGGCGGATGACTACTTCTA 59.679 47.826 0.00 0.0 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.326618 TTCCCTGTCCATCTCCCTCC 60.327 60.000 0.00 0.00 0.00 4.30
1 2 1.127343 CTTCCCTGTCCATCTCCCTC 58.873 60.000 0.00 0.00 0.00 4.30
2 3 0.985490 GCTTCCCTGTCCATCTCCCT 60.985 60.000 0.00 0.00 0.00 4.20
3 4 1.529309 GCTTCCCTGTCCATCTCCC 59.471 63.158 0.00 0.00 0.00 4.30
4 5 1.144936 CGCTTCCCTGTCCATCTCC 59.855 63.158 0.00 0.00 0.00 3.71
5 6 0.103937 CTCGCTTCCCTGTCCATCTC 59.896 60.000 0.00 0.00 0.00 2.75
6 7 0.616111 ACTCGCTTCCCTGTCCATCT 60.616 55.000 0.00 0.00 0.00 2.90
7 8 0.460987 CACTCGCTTCCCTGTCCATC 60.461 60.000 0.00 0.00 0.00 3.51
8 9 0.904865 TCACTCGCTTCCCTGTCCAT 60.905 55.000 0.00 0.00 0.00 3.41
9 10 1.118965 TTCACTCGCTTCCCTGTCCA 61.119 55.000 0.00 0.00 0.00 4.02
10 11 0.250513 ATTCACTCGCTTCCCTGTCC 59.749 55.000 0.00 0.00 0.00 4.02
11 12 1.646189 GATTCACTCGCTTCCCTGTC 58.354 55.000 0.00 0.00 0.00 3.51
12 13 0.250513 GGATTCACTCGCTTCCCTGT 59.749 55.000 0.00 0.00 0.00 4.00
13 14 0.539051 AGGATTCACTCGCTTCCCTG 59.461 55.000 0.00 0.00 0.00 4.45
14 15 0.827368 GAGGATTCACTCGCTTCCCT 59.173 55.000 0.00 0.00 0.00 4.20
15 16 0.179070 GGAGGATTCACTCGCTTCCC 60.179 60.000 0.00 0.00 38.39 3.97
16 17 0.528684 CGGAGGATTCACTCGCTTCC 60.529 60.000 0.00 0.00 38.39 3.46
17 18 1.148759 GCGGAGGATTCACTCGCTTC 61.149 60.000 0.00 0.00 38.39 3.86
18 19 1.153549 GCGGAGGATTCACTCGCTT 60.154 57.895 0.00 0.00 38.39 4.68
19 20 2.496817 GCGGAGGATTCACTCGCT 59.503 61.111 0.00 0.00 38.39 4.93
20 21 2.586357 GGCGGAGGATTCACTCGC 60.586 66.667 0.00 0.00 38.39 5.03
21 22 2.278857 CGGCGGAGGATTCACTCG 60.279 66.667 0.00 0.00 38.39 4.18
22 23 1.066587 CTCGGCGGAGGATTCACTC 59.933 63.158 13.25 0.00 36.61 3.51
23 24 3.082579 GCTCGGCGGAGGATTCACT 62.083 63.158 21.36 0.00 40.80 3.41
24 25 2.586357 GCTCGGCGGAGGATTCAC 60.586 66.667 21.36 1.43 40.80 3.18
25 26 3.074369 TGCTCGGCGGAGGATTCA 61.074 61.111 21.36 8.97 40.80 2.57
26 27 2.586357 GTGCTCGGCGGAGGATTC 60.586 66.667 21.36 5.63 42.93 2.52
27 28 4.162690 GGTGCTCGGCGGAGGATT 62.163 66.667 21.36 0.00 42.93 3.01
38 39 4.874977 GACTAGCGGGCGGTGCTC 62.875 72.222 0.62 0.00 42.85 4.26
50 51 0.179161 CGACTGTGAAGGGCGACTAG 60.179 60.000 0.00 0.00 0.00 2.57
51 52 0.607217 TCGACTGTGAAGGGCGACTA 60.607 55.000 0.00 0.00 0.00 2.59
52 53 1.461091 TTCGACTGTGAAGGGCGACT 61.461 55.000 0.00 0.00 0.00 4.18
53 54 0.599204 TTTCGACTGTGAAGGGCGAC 60.599 55.000 0.00 0.00 0.00 5.19
54 55 0.599204 GTTTCGACTGTGAAGGGCGA 60.599 55.000 0.00 0.00 0.00 5.54
55 56 1.566018 GGTTTCGACTGTGAAGGGCG 61.566 60.000 0.00 0.00 0.00 6.13
56 57 1.566018 CGGTTTCGACTGTGAAGGGC 61.566 60.000 0.00 0.00 39.00 5.19
57 58 0.249741 ACGGTTTCGACTGTGAAGGG 60.250 55.000 0.00 0.00 40.11 3.95
58 59 1.525619 GAACGGTTTCGACTGTGAAGG 59.474 52.381 0.00 0.00 40.11 3.46
59 60 2.924432 GAACGGTTTCGACTGTGAAG 57.076 50.000 0.00 0.00 40.11 3.02
69 70 3.619729 TGTGTTTAATGCGAACGGTTTC 58.380 40.909 0.00 0.00 0.00 2.78
70 71 3.694535 TGTGTTTAATGCGAACGGTTT 57.305 38.095 0.00 0.00 0.00 3.27
71 72 3.907894 ATGTGTTTAATGCGAACGGTT 57.092 38.095 0.00 0.00 0.00 4.44
72 73 3.251245 TGAATGTGTTTAATGCGAACGGT 59.749 39.130 0.00 0.00 0.00 4.83
73 74 3.816091 TGAATGTGTTTAATGCGAACGG 58.184 40.909 0.00 0.00 0.00 4.44
74 75 3.297979 GCTGAATGTGTTTAATGCGAACG 59.702 43.478 0.00 0.00 0.00 3.95
75 76 4.321745 CAGCTGAATGTGTTTAATGCGAAC 59.678 41.667 8.42 0.00 0.00 3.95
76 77 4.475028 CAGCTGAATGTGTTTAATGCGAA 58.525 39.130 8.42 0.00 0.00 4.70
77 78 3.670359 GCAGCTGAATGTGTTTAATGCGA 60.670 43.478 20.43 0.00 0.00 5.10
78 79 2.595536 GCAGCTGAATGTGTTTAATGCG 59.404 45.455 20.43 0.00 0.00 4.73
201 259 0.693049 GAAACAGGAGAGAGGGGCAA 59.307 55.000 0.00 0.00 0.00 4.52
394 452 2.261671 GCGGTCAGTCACGATGGT 59.738 61.111 0.00 0.00 0.00 3.55
399 457 4.662961 TGCCTGCGGTCAGTCACG 62.663 66.667 0.00 0.00 38.66 4.35
405 463 2.238847 GAGGTATGTGCCTGCGGTCA 62.239 60.000 0.00 0.00 39.34 4.02
459 517 1.199615 GAGGGTGAGAAGAAGGAGGG 58.800 60.000 0.00 0.00 0.00 4.30
620 687 1.353358 TCAAGAGAGAGGGTCGTACCA 59.647 52.381 6.41 0.00 41.02 3.25
3093 4618 1.139058 GTAGTCATCCGCCAATCCAGT 59.861 52.381 0.00 0.00 0.00 4.00
3118 4643 1.327690 ACGACATCCATACGCCACCT 61.328 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.