Multiple sequence alignment - TraesCS7B01G459100

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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 TraesCS7B01G459100 chr7B 100.000 2609 0 0 1 2609 717053684 717056292 0.000000e+00 4819.0
1 TraesCS7B01G459100 chr7D 95.097 2590 88 21 46 2609 12336441 12333865 0.000000e+00 4043.0
2 TraesCS7B01G459100 chr7D 90.769 1170 80 14 52 1202 12313508 12312348 0.000000e+00 1537.0
3 TraesCS7B01G459100 chr7D 86.408 103 10 2 2054 2152 49269786 49269684 2.750000e-20 110.0
4 TraesCS7B01G459100 chr7A 94.840 2597 89 18 46 2609 11907311 11904727 0.000000e+00 4012.0
5 TraesCS7B01G459100 chr7A 94.804 2598 92 18 46 2609 11960642 11958054 0.000000e+00 4010.0
6 TraesCS7B01G459100 chr7A 94.650 2598 93 18 46 2609 11861406 11858821 0.000000e+00 3986.0
7 TraesCS7B01G459100 chr7A 92.354 1491 83 16 1084 2559 11814579 11813105 0.000000e+00 2093.0
8 TraesCS7B01G459100 chr7A 92.220 1491 85 16 1084 2559 11780473 11778999 0.000000e+00 2082.0
9 TraesCS7B01G459100 chr7A 90.129 1165 80 19 62 1202 11762675 11761522 0.000000e+00 1482.0
10 TraesCS7B01G459100 chr7A 94.529 859 28 11 1765 2609 11974639 11973786 0.000000e+00 1308.0
11 TraesCS7B01G459100 chr7A 91.019 913 59 8 135 1027 11784828 11783919 0.000000e+00 1210.0
12 TraesCS7B01G459100 chr7A 90.909 913 59 8 135 1027 11818877 11817969 0.000000e+00 1205.0
13 TraesCS7B01G459100 chr7A 96.058 685 24 1 1084 1765 11976614 11975930 0.000000e+00 1112.0
14 TraesCS7B01G459100 chr7A 94.609 575 16 4 517 1078 11978871 11978299 0.000000e+00 876.0
15 TraesCS7B01G459100 chr7A 97.115 104 2 1 2507 2609 11779003 11778900 9.600000e-40 174.0
16 TraesCS7B01G459100 chr7A 97.115 104 2 1 2507 2609 11813109 11813006 9.600000e-40 174.0
17 TraesCS7B01G459100 chr7A 100.000 55 0 0 1024 1078 11782208 11782154 4.590000e-18 102.0
18 TraesCS7B01G459100 chr7A 98.113 53 1 0 1 53 11866001 11865949 2.760000e-15 93.5
19 TraesCS7B01G459100 chr7A 98.113 53 1 0 1 53 11911909 11911857 2.760000e-15 93.5
20 TraesCS7B01G459100 chr4A 92.063 1890 95 14 532 2399 725856631 725858487 0.000000e+00 2608.0
21 TraesCS7B01G459100 chr4A 87.847 288 25 3 76 354 725843183 725843469 1.940000e-86 329.0
22 TraesCS7B01G459100 chrUn 98.113 53 1 0 1 53 477703338 477703286 2.760000e-15 93.5


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 TraesCS7B01G459100 chr7B 717053684 717056292 2608 False 4819.000000 4819 100.000000 1 2609 1 chr7B.!!$F1 2608
1 TraesCS7B01G459100 chr7D 12333865 12336441 2576 True 4043.000000 4043 95.097000 46 2609 1 chr7D.!!$R2 2563
2 TraesCS7B01G459100 chr7D 12312348 12313508 1160 True 1537.000000 1537 90.769000 52 1202 1 chr7D.!!$R1 1150
3 TraesCS7B01G459100 chr7A 11904727 11907311 2584 True 4012.000000 4012 94.840000 46 2609 1 chr7A.!!$R4 2563
4 TraesCS7B01G459100 chr7A 11958054 11960642 2588 True 4010.000000 4010 94.804000 46 2609 1 chr7A.!!$R6 2563
5 TraesCS7B01G459100 chr7A 11858821 11861406 2585 True 3986.000000 3986 94.650000 46 2609 1 chr7A.!!$R2 2563
6 TraesCS7B01G459100 chr7A 11761522 11762675 1153 True 1482.000000 1482 90.129000 62 1202 1 chr7A.!!$R1 1140
7 TraesCS7B01G459100 chr7A 11813006 11818877 5871 True 1157.333333 2093 93.459333 135 2609 3 chr7A.!!$R8 2474
8 TraesCS7B01G459100 chr7A 11973786 11978871 5085 True 1098.666667 1308 95.065333 517 2609 3 chr7A.!!$R9 2092
9 TraesCS7B01G459100 chr7A 11778900 11784828 5928 True 892.000000 2082 95.088500 135 2609 4 chr7A.!!$R7 2474
10 TraesCS7B01G459100 chr4A 725856631 725858487 1856 False 2608.000000 2608 92.063000 532 2399 1 chr4A.!!$F2 1867

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
222 237 1.353022 TGATTTTCTTAGGCGGTGGGT 59.647 47.619 0.0 0.0 0.00 4.51 F
1078 4515 0.670706 CGCTCATGCTAGTGGCTCTA 59.329 55.000 0.0 0.0 42.39 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 4653 1.473278 CACTAAGTCACGGAGGTCCTC 59.527 57.143 10.78 10.78 0.00 3.71 R
2024 6771 1.484240 AGATGGACTCTTGCCACTAGC 59.516 52.381 0.00 0.00 38.44 3.42 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
92 93 6.925718 GTGCGCATCATGTACCTATGATATAT 59.074 38.462 15.91 0.00 43.93 0.86
123 129 4.384247 CCTTATGATCGCTAGCTCTTTTCG 59.616 45.833 13.93 0.00 0.00 3.46
169 175 4.124238 TCGAAACCGAATCAACCCATATC 58.876 43.478 0.00 0.00 32.51 1.63
172 178 3.553828 ACCGAATCAACCCATATCGTT 57.446 42.857 0.00 0.00 0.00 3.85
191 201 4.683781 TCGTTACGTGTTGGTATTGGTAAC 59.316 41.667 4.24 0.00 37.45 2.50
192 202 4.685628 CGTTACGTGTTGGTATTGGTAACT 59.314 41.667 0.00 0.00 38.21 2.24
222 237 1.353022 TGATTTTCTTAGGCGGTGGGT 59.647 47.619 0.00 0.00 0.00 4.51
234 249 1.375551 CGGTGGGTAGTAAACATGCC 58.624 55.000 0.00 0.00 0.00 4.40
321 342 6.435904 TGTGATTTTTAACTGGGGGAATACAG 59.564 38.462 0.00 0.00 40.48 2.74
343 364 4.649218 AGCTGTTGTAAAAGTCAACCCATT 59.351 37.500 6.38 0.00 42.82 3.16
480 504 7.901874 TTTGTAACTACTCGAAAATGCAAAC 57.098 32.000 0.00 0.00 0.00 2.93
486 510 8.419076 AACTACTCGAAAATGCAAACAAAAAT 57.581 26.923 0.00 0.00 0.00 1.82
737 761 9.355916 ACTACAACAAGATCTATAGTGAGCATA 57.644 33.333 0.00 0.00 0.00 3.14
834 858 5.831525 ACCGATAGTACACATATTCTGGACA 59.168 40.000 0.00 0.00 0.00 4.02
940 968 3.273434 TCTCTGCAATACACATGCTTCC 58.727 45.455 0.00 0.00 44.14 3.46
1078 4515 0.670706 CGCTCATGCTAGTGGCTCTA 59.329 55.000 0.00 0.00 42.39 2.43
1111 4548 2.042831 AAGGCGACCAAGCTCATGC 61.043 57.895 0.00 0.00 37.29 4.06
1216 4653 1.448540 AATCGAAGTGCCGAGGCTG 60.449 57.895 15.75 0.72 42.21 4.85
1240 4677 0.888619 CCTCCGTGACTTAGTGCTCA 59.111 55.000 0.00 0.00 0.00 4.26
1372 4809 3.118629 TGAGGTGGAGTATGAAGATGTGC 60.119 47.826 0.00 0.00 0.00 4.57
1809 6547 8.299570 GGATAATTGGAAATATGATTGTCGCTT 58.700 33.333 0.00 0.00 0.00 4.68
1843 6581 3.153919 TGCTTCAAGGGGATACAACAAC 58.846 45.455 0.00 0.00 39.74 3.32
1860 6598 2.738521 CGCCACTGGTTCACTCCG 60.739 66.667 0.00 0.00 0.00 4.63
2024 6771 3.062639 GTGTCAAGCGTGGATCAATACTG 59.937 47.826 0.00 0.00 0.00 2.74
2424 7187 1.195448 CACAGACGCTCACCATGAAAC 59.805 52.381 0.00 0.00 0.00 2.78
2591 7409 6.115446 TGGACATTTGATCTAGGATGTTGAC 58.885 40.000 0.00 0.00 33.21 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 8.722394 CGTACACGCCAGATATGATATATAGAT 58.278 37.037 0.00 0.00 0.00 1.98
42 43 7.713942 ACGTACACGCCAGATATGATATATAGA 59.286 37.037 0.85 0.00 44.43 1.98
43 44 7.798982 CACGTACACGCCAGATATGATATATAG 59.201 40.741 0.85 0.00 44.43 1.31
44 45 7.636326 CACGTACACGCCAGATATGATATATA 58.364 38.462 0.85 0.00 44.43 0.86
45 46 6.495706 CACGTACACGCCAGATATGATATAT 58.504 40.000 0.85 0.00 44.43 0.86
46 47 5.675323 GCACGTACACGCCAGATATGATATA 60.675 44.000 0.85 0.00 44.43 0.86
47 48 4.733850 CACGTACACGCCAGATATGATAT 58.266 43.478 0.85 0.00 44.43 1.63
48 49 3.610821 GCACGTACACGCCAGATATGATA 60.611 47.826 0.85 0.00 44.43 2.15
49 50 2.862530 GCACGTACACGCCAGATATGAT 60.863 50.000 0.85 0.00 44.43 2.45
50 51 1.535226 GCACGTACACGCCAGATATGA 60.535 52.381 0.85 0.00 44.43 2.15
51 52 0.852777 GCACGTACACGCCAGATATG 59.147 55.000 0.85 0.00 44.43 1.78
92 93 4.022242 GCTAGCGATCATAAGGAGGTAACA 60.022 45.833 0.00 0.00 41.41 2.41
169 175 4.685628 AGTTACCAATACCAACACGTAACG 59.314 41.667 0.00 0.00 40.13 3.18
172 178 7.565323 AAAAAGTTACCAATACCAACACGTA 57.435 32.000 0.00 0.00 0.00 3.57
222 237 3.751175 GCACTGTCAAGGCATGTTTACTA 59.249 43.478 0.00 0.00 0.00 1.82
234 249 2.959516 TCATTCGTAGGCACTGTCAAG 58.040 47.619 0.00 0.00 41.52 3.02
321 342 4.584327 ATGGGTTGACTTTTACAACAGC 57.416 40.909 0.00 0.00 46.16 4.40
343 364 9.878667 TTGTATTTCCAAGTCGATTATTGTCTA 57.121 29.630 0.00 0.00 0.00 2.59
480 504 8.975410 TCAAGTCTATGATTGCTCAATTTTTG 57.025 30.769 0.00 0.00 34.37 2.44
486 510 6.053650 CCTCATCAAGTCTATGATTGCTCAA 58.946 40.000 0.00 0.00 37.96 3.02
737 761 7.851228 TCTCTCTATGTTCCACAAATACACAT 58.149 34.615 0.00 0.00 32.80 3.21
940 968 1.830477 CTGAGAGGGAGGTGGAGAAAG 59.170 57.143 0.00 0.00 0.00 2.62
1078 4515 1.833934 CCTTGGGCTTGCCACTGTT 60.834 57.895 14.04 0.00 0.00 3.16
1111 4548 2.019984 GGCCTTCTTACATGCTTCCAG 58.980 52.381 0.00 0.00 0.00 3.86
1122 4559 3.596214 GTTGTTGATCGAGGCCTTCTTA 58.404 45.455 6.77 0.00 0.00 2.10
1216 4653 1.473278 CACTAAGTCACGGAGGTCCTC 59.527 57.143 10.78 10.78 0.00 3.71
1240 4677 5.105752 GCTCTTAAAGATGTCGACAGTGAT 58.894 41.667 24.41 6.76 0.00 3.06
1452 4889 6.823689 GGTTGTAATTCATATCCACACAGTCT 59.176 38.462 0.00 0.00 0.00 3.24
1654 5091 6.151985 TCCGAGTAAATTTATGCCACAACAAT 59.848 34.615 0.31 0.00 0.00 2.71
1774 6512 3.297134 TTCCAATTATCCAGCTGGTCC 57.703 47.619 31.58 0.00 36.34 4.46
1809 6547 2.916702 TGAAGCAGAGAAGACAAGCA 57.083 45.000 0.00 0.00 0.00 3.91
1843 6581 2.738521 CGGAGTGAACCAGTGGCG 60.739 66.667 9.78 0.00 0.00 5.69
1860 6598 9.758651 AACCCAAATTAAAGTTAGATTTCACAC 57.241 29.630 0.00 0.00 0.00 3.82
2024 6771 1.484240 AGATGGACTCTTGCCACTAGC 59.516 52.381 0.00 0.00 38.44 3.42
2273 7027 5.878116 GTGTATGAATACTTGCAACAGGGTA 59.122 40.000 0.00 0.00 34.41 3.69
2358 7121 9.132521 GTTTTTCATCTTGTGATCGAATCAAAT 57.867 29.630 0.00 0.00 41.69 2.32
2452 7217 3.365265 CCTGCCTGCCACCGTTTC 61.365 66.667 0.00 0.00 0.00 2.78
2503 7270 5.689514 CCGCATTTTCAAATCACAAACAGTA 59.310 36.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.