Multiple sequence alignment - TraesCS3D01G058800

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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 TraesCS3D01G058800 chr3D 100.000 4453 0 0 1 4453 25517994 25522446 0.000000e+00 8224.0
1 TraesCS3D01G058800 chr7D 97.418 4260 61 13 1 4253 37669208 37664991 0.000000e+00 7212.0
2 TraesCS3D01G058800 chr7D 80.303 528 71 17 1340 1835 48133217 48132691 7.040000e-98 368.0
3 TraesCS3D01G058800 chr7D 100.000 157 0 0 4297 4453 37664246 37664090 1.570000e-74 291.0
4 TraesCS3D01G058800 chr4A 89.431 3444 184 63 122 3457 687311348 687314719 0.000000e+00 4178.0
5 TraesCS3D01G058800 chr4A 99.187 123 1 0 4331 4453 687316015 687316137 5.800000e-54 222.0
6 TraesCS3D01G058800 chr4A 82.000 250 30 8 3548 3789 687314808 687315050 9.770000e-47 198.0
7 TraesCS3D01G058800 chr2A 93.204 2840 119 21 738 3531 720379342 720382153 0.000000e+00 4108.0
8 TraesCS3D01G058800 chr2A 95.425 153 3 4 4302 4451 720383330 720383481 1.600000e-59 241.0
9 TraesCS3D01G058800 chr2A 77.437 359 44 21 381 703 720378621 720378978 3.540000e-41 180.0
10 TraesCS3D01G058800 chr3A 82.342 521 64 17 1342 1835 242902387 242901868 1.140000e-115 427.0
11 TraesCS3D01G058800 chr3A 95.833 120 5 0 4333 4452 301803641 301803522 1.260000e-45 195.0
12 TraesCS3D01G058800 chr2B 81.712 514 67 15 1341 1828 65242799 65243311 1.930000e-108 403.0
13 TraesCS3D01G058800 chr6A 81.285 529 69 17 1340 1839 120275837 120275310 6.940000e-108 401.0
14 TraesCS3D01G058800 chr6A 80.989 526 70 17 1340 1836 120355135 120355659 1.500000e-104 390.0
15 TraesCS3D01G058800 chr5B 81.553 515 66 18 1342 1828 517822121 517822634 8.970000e-107 398.0
16 TraesCS3D01G058800 chr5B 81.546 401 51 9 1578 1956 35283714 35284113 4.330000e-80 309.0
17 TraesCS3D01G058800 chr5B 95.000 120 6 0 4332 4451 35288863 35288982 5.880000e-44 189.0
18 TraesCS3D01G058800 chr5B 95.000 40 2 0 3618 3657 35285786 35285825 3.720000e-06 63.9
19 TraesCS3D01G058800 chr5D 80.880 523 71 18 1341 1835 25853101 25852580 6.990000e-103 385.0
20 TraesCS3D01G058800 chr5D 81.313 396 56 11 1578 1956 41292160 41292554 5.600000e-79 305.0
21 TraesCS3D01G058800 chr5D 93.277 119 8 0 4333 4451 41297069 41297187 4.580000e-40 176.0
22 TraesCS3D01G058800 chr5D 92.437 119 9 0 4333 4451 35180876 35180758 2.130000e-38 171.0
23 TraesCS3D01G058800 chr5A 93.277 119 8 0 4333 4451 29626825 29626943 4.580000e-40 176.0
24 TraesCS3D01G058800 chr5A 92.437 119 9 0 4333 4451 23853138 23853020 2.130000e-38 171.0
25 TraesCS3D01G058800 chr7A 94.286 105 6 0 960 1064 37085018 37084914 1.280000e-35 161.0
26 TraesCS3D01G058800 chr7A 87.879 66 6 2 639 703 37085220 37085156 4.780000e-10 76.8


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 TraesCS3D01G058800 chr3D 25517994 25522446 4452 False 8224.000000 8224 100.000000 1 4453 1 chr3D.!!$F1 4452
1 TraesCS3D01G058800 chr7D 37664090 37669208 5118 True 3751.500000 7212 98.709000 1 4453 2 chr7D.!!$R2 4452
2 TraesCS3D01G058800 chr7D 48132691 48133217 526 True 368.000000 368 80.303000 1340 1835 1 chr7D.!!$R1 495
3 TraesCS3D01G058800 chr4A 687311348 687316137 4789 False 1532.666667 4178 90.206000 122 4453 3 chr4A.!!$F1 4331
4 TraesCS3D01G058800 chr2A 720378621 720383481 4860 False 1509.666667 4108 88.688667 381 4451 3 chr2A.!!$F1 4070
5 TraesCS3D01G058800 chr3A 242901868 242902387 519 True 427.000000 427 82.342000 1342 1835 1 chr3A.!!$R1 493
6 TraesCS3D01G058800 chr2B 65242799 65243311 512 False 403.000000 403 81.712000 1341 1828 1 chr2B.!!$F1 487
7 TraesCS3D01G058800 chr6A 120275310 120275837 527 True 401.000000 401 81.285000 1340 1839 1 chr6A.!!$R1 499
8 TraesCS3D01G058800 chr6A 120355135 120355659 524 False 390.000000 390 80.989000 1340 1836 1 chr6A.!!$F1 496
9 TraesCS3D01G058800 chr5B 517822121 517822634 513 False 398.000000 398 81.553000 1342 1828 1 chr5B.!!$F1 486
10 TraesCS3D01G058800 chr5D 25852580 25853101 521 True 385.000000 385 80.880000 1341 1835 1 chr5D.!!$R1 494

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
88 89 0.035056 CAGGATTTGTTCCCCTCGCT 60.035 55.000 0.00 0.00 46.81 4.93 F
89 90 0.253327 AGGATTTGTTCCCCTCGCTC 59.747 55.000 0.00 0.00 46.81 5.03 F
1081 1507 0.252927 CTCCTTCCCCTCAACCCTCT 60.253 60.000 0.00 0.00 0.00 3.69 F
1269 1695 3.905678 CTCGGCCGCCTCCTGTAG 61.906 72.222 23.51 5.96 0.00 2.74 F
2203 2665 1.001641 CCTGGTCTGGCTTCCTTGG 60.002 63.158 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 1507 0.547471 TTCATGGTGAGAGGGAGGCA 60.547 55.000 0.0 0.0 0.00 4.75 R
2060 2522 6.700520 CAGGAAAACTACCACCGAGATTATAC 59.299 42.308 0.0 0.0 0.00 1.47 R
2203 2665 2.802816 GCTGTATGCCTGTATAGCACAC 59.197 50.000 0.0 0.0 44.40 3.82 R
3154 3682 1.162698 GAAGGCAAACCGTTAGTCCC 58.837 55.000 0.0 0.0 42.76 4.46 R
3865 4536 0.243636 AGCAAAAACATAGGTGCCGC 59.756 50.000 0.0 0.0 37.73 6.53 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
82 83 1.212751 GCACGCAGGATTTGTTCCC 59.787 57.895 0.00 0.00 46.81 3.97
83 84 1.883021 CACGCAGGATTTGTTCCCC 59.117 57.895 0.00 0.00 46.81 4.81
84 85 0.609131 CACGCAGGATTTGTTCCCCT 60.609 55.000 0.00 0.00 46.81 4.79
85 86 0.322546 ACGCAGGATTTGTTCCCCTC 60.323 55.000 0.00 0.00 46.81 4.30
86 87 1.369091 CGCAGGATTTGTTCCCCTCG 61.369 60.000 0.00 0.00 46.81 4.63
87 88 1.657751 GCAGGATTTGTTCCCCTCGC 61.658 60.000 0.00 0.00 46.81 5.03
88 89 0.035056 CAGGATTTGTTCCCCTCGCT 60.035 55.000 0.00 0.00 46.81 4.93
89 90 0.253327 AGGATTTGTTCCCCTCGCTC 59.747 55.000 0.00 0.00 46.81 5.03
90 91 0.748367 GGATTTGTTCCCCTCGCTCC 60.748 60.000 0.00 0.00 38.75 4.70
91 92 1.078426 ATTTGTTCCCCTCGCTCCG 60.078 57.895 0.00 0.00 0.00 4.63
92 93 1.838073 ATTTGTTCCCCTCGCTCCGT 61.838 55.000 0.00 0.00 0.00 4.69
93 94 2.444700 TTTGTTCCCCTCGCTCCGTC 62.445 60.000 0.00 0.00 0.00 4.79
94 95 3.069318 GTTCCCCTCGCTCCGTCT 61.069 66.667 0.00 0.00 0.00 4.18
95 96 2.754658 TTCCCCTCGCTCCGTCTC 60.755 66.667 0.00 0.00 0.00 3.36
96 97 3.283812 TTCCCCTCGCTCCGTCTCT 62.284 63.158 0.00 0.00 0.00 3.10
97 98 3.213402 CCCCTCGCTCCGTCTCTC 61.213 72.222 0.00 0.00 0.00 3.20
98 99 3.213402 CCCTCGCTCCGTCTCTCC 61.213 72.222 0.00 0.00 0.00 3.71
99 100 3.213402 CCTCGCTCCGTCTCTCCC 61.213 72.222 0.00 0.00 0.00 4.30
100 101 2.438614 CTCGCTCCGTCTCTCCCA 60.439 66.667 0.00 0.00 0.00 4.37
520 593 1.633945 CCTAGGGTAGTTTTGCCTGGT 59.366 52.381 0.00 0.00 0.00 4.00
556 633 5.900339 TTACTAGTTTCTGAACAGCAACG 57.100 39.130 0.00 2.58 39.10 4.10
613 705 1.003839 CCTAACCGCTGTCTTGCCA 60.004 57.895 0.00 0.00 0.00 4.92
621 713 1.596260 CGCTGTCTTGCCATCTGTATG 59.404 52.381 0.00 0.00 0.00 2.39
1081 1507 0.252927 CTCCTTCCCCTCAACCCTCT 60.253 60.000 0.00 0.00 0.00 3.69
1269 1695 3.905678 CTCGGCCGCCTCCTGTAG 61.906 72.222 23.51 5.96 0.00 2.74
1688 2140 6.110033 TGAACTTGTTGTGAGTTGTAAGCTA 58.890 36.000 0.00 0.00 37.46 3.32
2060 2522 8.239681 TCGAGATGTGAATGTTTTTACAGTAG 57.760 34.615 0.00 0.00 35.14 2.57
2203 2665 1.001641 CCTGGTCTGGCTTCCTTGG 60.002 63.158 0.00 0.00 0.00 3.61
3154 3682 2.034687 CCACCCCTGCCTTGTCAG 59.965 66.667 0.00 0.00 0.00 3.51
3885 4556 1.981254 CGGCACCTATGTTTTTGCTG 58.019 50.000 0.00 0.00 35.24 4.41
4273 5042 1.523095 GCGAATGGAGTTCATACGCTC 59.477 52.381 0.00 0.00 41.07 5.03
4280 5049 2.924290 GGAGTTCATACGCTCACTCAAC 59.076 50.000 0.00 0.00 37.92 3.18
4281 5050 2.924290 GAGTTCATACGCTCACTCAACC 59.076 50.000 0.00 0.00 36.46 3.77
4283 5052 3.762288 AGTTCATACGCTCACTCAACCTA 59.238 43.478 0.00 0.00 0.00 3.08
4285 5054 4.569761 TCATACGCTCACTCAACCTATC 57.430 45.455 0.00 0.00 0.00 2.08
4286 5055 4.207955 TCATACGCTCACTCAACCTATCT 58.792 43.478 0.00 0.00 0.00 1.98
4288 5057 2.447443 ACGCTCACTCAACCTATCTGA 58.553 47.619 0.00 0.00 0.00 3.27
4290 5059 2.792890 CGCTCACTCAACCTATCTGACG 60.793 54.545 0.00 0.00 0.00 4.35
4291 5060 2.803451 CTCACTCAACCTATCTGACGC 58.197 52.381 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.747976 GTGCCCGAGCCGCAATTT 61.748 61.111 0.00 0.00 38.13 1.82
82 83 3.213402 GGGAGAGACGGAGCGAGG 61.213 72.222 0.00 0.00 0.00 4.63
83 84 2.438614 TGGGAGAGACGGAGCGAG 60.439 66.667 0.00 0.00 0.00 5.03
84 85 2.750637 GTGGGAGAGACGGAGCGA 60.751 66.667 0.00 0.00 0.00 4.93
85 86 2.343163 GATGTGGGAGAGACGGAGCG 62.343 65.000 0.00 0.00 0.00 5.03
86 87 1.439644 GATGTGGGAGAGACGGAGC 59.560 63.158 0.00 0.00 0.00 4.70
87 88 1.730487 CGATGTGGGAGAGACGGAG 59.270 63.158 0.00 0.00 0.00 4.63
88 89 2.415608 GCGATGTGGGAGAGACGGA 61.416 63.158 0.00 0.00 0.00 4.69
89 90 2.021068 ATGCGATGTGGGAGAGACGG 62.021 60.000 0.00 0.00 0.00 4.79
90 91 0.596083 GATGCGATGTGGGAGAGACG 60.596 60.000 0.00 0.00 0.00 4.18
91 92 0.749649 AGATGCGATGTGGGAGAGAC 59.250 55.000 0.00 0.00 0.00 3.36
92 93 1.035923 GAGATGCGATGTGGGAGAGA 58.964 55.000 0.00 0.00 0.00 3.10
93 94 0.033228 GGAGATGCGATGTGGGAGAG 59.967 60.000 0.00 0.00 0.00 3.20
94 95 1.402896 GGGAGATGCGATGTGGGAGA 61.403 60.000 0.00 0.00 0.00 3.71
95 96 1.070445 GGGAGATGCGATGTGGGAG 59.930 63.158 0.00 0.00 0.00 4.30
96 97 2.796193 CGGGAGATGCGATGTGGGA 61.796 63.158 0.00 0.00 0.00 4.37
97 98 2.280389 CGGGAGATGCGATGTGGG 60.280 66.667 0.00 0.00 0.00 4.61
98 99 2.969238 GCGGGAGATGCGATGTGG 60.969 66.667 0.00 0.00 0.00 4.17
99 100 1.953138 GAGCGGGAGATGCGATGTG 60.953 63.158 0.00 0.00 37.44 3.21
100 101 2.419198 GAGCGGGAGATGCGATGT 59.581 61.111 0.00 0.00 37.44 3.06
556 633 4.507710 TGTTGAGAGCATATGAGAACCAC 58.492 43.478 6.97 0.00 0.00 4.16
613 705 1.906574 ACGTGGGTTGGACATACAGAT 59.093 47.619 0.00 0.00 0.00 2.90
621 713 3.041940 CGCTCACGTGGGTTGGAC 61.042 66.667 18.43 0.00 33.53 4.02
1081 1507 0.547471 TTCATGGTGAGAGGGAGGCA 60.547 55.000 0.00 0.00 0.00 4.75
2060 2522 6.700520 CAGGAAAACTACCACCGAGATTATAC 59.299 42.308 0.00 0.00 0.00 1.47
2203 2665 2.802816 GCTGTATGCCTGTATAGCACAC 59.197 50.000 0.00 0.00 44.40 3.82
3043 3571 2.814805 ACAGCAATAACTGGGAGCAT 57.185 45.000 0.00 0.00 42.21 3.79
3154 3682 1.162698 GAAGGCAAACCGTTAGTCCC 58.837 55.000 0.00 0.00 42.76 4.46
3863 4534 1.070471 CAAAAACATAGGTGCCGCGC 61.070 55.000 0.00 0.00 0.00 6.86
3864 4535 1.070471 GCAAAAACATAGGTGCCGCG 61.070 55.000 0.00 0.00 0.00 6.46
3865 4536 0.243636 AGCAAAAACATAGGTGCCGC 59.756 50.000 0.00 0.00 37.73 6.53
3866 4537 1.981254 CAGCAAAAACATAGGTGCCG 58.019 50.000 0.00 0.00 37.73 5.69
3869 4540 3.665745 AAGGCAGCAAAAACATAGGTG 57.334 42.857 0.00 0.00 0.00 4.00
3870 4541 4.687901 AAAAGGCAGCAAAAACATAGGT 57.312 36.364 0.00 0.00 0.00 3.08
3871 4542 4.319694 GCAAAAAGGCAGCAAAAACATAGG 60.320 41.667 0.00 0.00 0.00 2.57
3872 4543 4.512571 AGCAAAAAGGCAGCAAAAACATAG 59.487 37.500 0.00 0.00 35.83 2.23
3873 4544 4.450053 AGCAAAAAGGCAGCAAAAACATA 58.550 34.783 0.00 0.00 35.83 2.29
3874 4545 3.281158 AGCAAAAAGGCAGCAAAAACAT 58.719 36.364 0.00 0.00 35.83 2.71
3875 4546 2.709213 AGCAAAAAGGCAGCAAAAACA 58.291 38.095 0.00 0.00 35.83 2.83
3876 4547 3.428163 CAAGCAAAAAGGCAGCAAAAAC 58.572 40.909 0.00 0.00 35.83 2.43
3885 4556 0.605083 CCTCCTCCAAGCAAAAAGGC 59.395 55.000 0.00 0.00 0.00 4.35
3921 4639 2.822561 ACTGCTCGACTCTGAATTCTGA 59.177 45.455 13.64 13.64 0.00 3.27
4273 5042 1.135373 ACGCGTCAGATAGGTTGAGTG 60.135 52.381 5.58 0.00 0.00 3.51
4280 5049 0.458543 AAGCACACGCGTCAGATAGG 60.459 55.000 9.86 0.00 45.49 2.57
4281 5050 1.059692 CAAAGCACACGCGTCAGATAG 59.940 52.381 9.86 0.00 45.49 2.08
4283 5052 0.880278 ACAAAGCACACGCGTCAGAT 60.880 50.000 9.86 0.00 45.49 2.90
4285 5054 1.368019 CACAAAGCACACGCGTCAG 60.368 57.895 9.86 5.82 45.49 3.51
4286 5055 2.706432 CACAAAGCACACGCGTCA 59.294 55.556 9.86 0.00 45.49 4.35
4288 5057 4.589700 CGCACAAAGCACACGCGT 62.590 61.111 5.58 5.58 46.13 6.01
4290 5059 2.722188 GACGCACAAAGCACACGC 60.722 61.111 0.00 0.00 46.13 5.34
4291 5060 1.083401 GAGACGCACAAAGCACACG 60.083 57.895 0.00 0.00 46.13 4.49


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

AutoCloner maintained by Alex Coulton.