Multiple sequence alignment - TraesCS7A01G029300

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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 TraesCS7A01G029300 chr7A 100.000 2600 0 0 1 2600 11960658 11958059 0.000000e+00 4802
1 TraesCS7A01G029300 chr7A 98.462 2601 34 6 1 2600 11907327 11904732 0.000000e+00 4577
2 TraesCS7A01G029300 chr7A 98.194 2602 40 7 1 2600 11861422 11858826 0.000000e+00 4538
3 TraesCS7A01G029300 chr7A 91.139 1501 99 15 1066 2553 11814588 11813109 0.000000e+00 2004
4 TraesCS7A01G029300 chr7A 91.006 1501 101 15 1066 2553 11780482 11779003 0.000000e+00 1993
5 TraesCS7A01G029300 chr7A 90.684 1170 85 14 32 1193 11762675 11761522 0.000000e+00 1535
6 TraesCS7A01G029300 chr7A 92.544 912 64 4 109 1018 11784828 11783919 0.000000e+00 1304
7 TraesCS7A01G029300 chr7A 92.527 910 67 1 109 1018 11818877 11817969 0.000000e+00 1303
8 TraesCS7A01G029300 chr7A 94.373 853 33 8 1759 2600 11974639 11973791 0.000000e+00 1295
9 TraesCS7A01G029300 chr7A 95.101 694 34 0 1066 1759 11976623 11975930 0.000000e+00 1094
10 TraesCS7A01G029300 chr7A 95.960 99 3 1 2503 2600 11779003 11778905 2.680000e-35 159
11 TraesCS7A01G029300 chr7A 95.960 99 3 1 2503 2600 11813109 11813011 2.680000e-35 159
12 TraesCS7A01G029300 chr7A 100.000 56 0 0 1015 1070 11782208 11782153 1.270000e-18 104
13 TraesCS7A01G029300 chr7A 88.043 92 6 2 17 107 11786759 11786672 1.270000e-18 104
14 TraesCS7A01G029300 chr7A 100.000 56 0 0 1015 1070 11816313 11816258 1.270000e-18 104
15 TraesCS7A01G029300 chr7A 88.043 92 6 2 17 107 11820805 11820718 1.270000e-18 104
16 TraesCS7A01G029300 chr7D 95.710 2611 78 18 1 2600 12336457 12333870 0.000000e+00 4170
17 TraesCS7A01G029300 chr7D 91.681 1166 78 12 32 1193 12313498 12312348 0.000000e+00 1598
18 TraesCS7A01G029300 chr7D 85.149 101 11 2 2047 2143 49269784 49269684 1.650000e-17 100
19 TraesCS7A01G029300 chr7B 94.794 2593 92 18 17 2600 717053729 717056287 0.000000e+00 4000
20 TraesCS7A01G029300 chr4A 91.456 1896 113 20 510 2395 725856631 725858487 0.000000e+00 2558
21 TraesCS7A01G029300 chr4A 90.068 292 19 4 46 332 725843183 725843469 1.140000e-98 370
22 TraesCS7A01G029300 chr4A 88.601 193 17 4 320 512 725844037 725844224 2.010000e-56 230


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 TraesCS7A01G029300 chr7A 11958059 11960658 2599 True 4802.0 4802 100.0000 1 2600 1 chr7A.!!$R4 2599
1 TraesCS7A01G029300 chr7A 11904732 11907327 2595 True 4577.0 4577 98.4620 1 2600 1 chr7A.!!$R3 2599
2 TraesCS7A01G029300 chr7A 11858826 11861422 2596 True 4538.0 4538 98.1940 1 2600 1 chr7A.!!$R2 2599
3 TraesCS7A01G029300 chr7A 11761522 11762675 1153 True 1535.0 1535 90.6840 32 1193 1 chr7A.!!$R1 1161
4 TraesCS7A01G029300 chr7A 11973791 11976623 2832 True 1194.5 1295 94.7370 1066 2600 2 chr7A.!!$R7 1534
5 TraesCS7A01G029300 chr7A 11813011 11820805 7794 True 734.8 2004 93.5338 17 2600 5 chr7A.!!$R6 2583
6 TraesCS7A01G029300 chr7A 11778905 11786759 7854 True 732.8 1993 93.5106 17 2600 5 chr7A.!!$R5 2583
7 TraesCS7A01G029300 chr7D 12333870 12336457 2587 True 4170.0 4170 95.7100 1 2600 1 chr7D.!!$R2 2599
8 TraesCS7A01G029300 chr7D 12312348 12313498 1150 True 1598.0 1598 91.6810 32 1193 1 chr7D.!!$R1 1161
9 TraesCS7A01G029300 chr7B 717053729 717056287 2558 False 4000.0 4000 94.7940 17 2600 1 chr7B.!!$F1 2583
10 TraesCS7A01G029300 chr4A 725856631 725858487 1856 False 2558.0 2558 91.4560 510 2395 1 chr4A.!!$F1 1885
11 TraesCS7A01G029300 chr4A 725843183 725844224 1041 False 300.0 370 89.3345 46 512 2 chr4A.!!$F2 466

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
230 2087 3.955771 TTTTTGACAGTGCCTACGAAC 57.044 42.857 0.00 0.00 0.00 3.95 F
1167 7011 5.415415 AATCTATCACGCAAGAATTCTGC 57.585 39.130 9.17 13.31 43.62 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 6952 0.254178 ATCGAGGCCTTCTTGCATGT 59.746 50.000 6.77 0.00 0.00 3.21 R
2183 9345 1.521010 CTGATCGCTCCTGCAGGTG 60.521 63.158 31.58 29.16 39.64 4.00 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
170 2027 6.918569 TGACGTGTTGGTATTGGTAATTTTTG 59.081 34.615 0.00 0.00 0.00 2.44
230 2087 3.955771 TTTTTGACAGTGCCTACGAAC 57.044 42.857 0.00 0.00 0.00 3.95
1167 7011 5.415415 AATCTATCACGCAAGAATTCTGC 57.585 39.130 9.17 13.31 43.62 4.26
1200 7044 0.603569 AGTCGGACAATCGAAGTGCT 59.396 50.000 11.27 0.00 41.05 4.40
1273 7117 1.801913 CGTGTCACTGCCGCTAGTC 60.802 63.158 0.65 0.00 0.00 2.59
1326 7170 0.251922 AGGGAACAGTGGCAATGCAT 60.252 50.000 15.76 3.98 0.00 3.96
1526 7370 4.519437 TGCGGAGGCGCTCATCAG 62.519 66.667 7.64 5.48 44.10 2.90
1567 7411 3.490439 TGCTTCTCATCCTCAACAACA 57.510 42.857 0.00 0.00 0.00 3.33
1781 8926 4.074970 ACTTGTAAAAGACCAGCTGGATG 58.925 43.478 39.19 17.41 38.94 3.51
1806 8951 2.948979 GGAAATATGATTGTCGCACCCA 59.051 45.455 0.00 0.00 0.00 4.51
1839 8984 3.763897 GCTTCAAGGGGATACAACAATGT 59.236 43.478 0.00 0.00 43.74 2.71
2128 9290 4.625028 TGAAGTCTCACTTGACACTCATG 58.375 43.478 0.00 0.00 38.80 3.07
2183 9345 7.873505 ACAGACCTAAGAGAAACATGTACTTTC 59.126 37.037 0.00 0.00 0.00 2.62
2416 9582 1.218047 GGCACAGACGCTCACCATA 59.782 57.895 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 2027 4.234574 CCACCGCCTAAGAAAATCAAAAC 58.765 43.478 0.00 0.00 0.00 2.43
230 2087 0.317603 CCAGCCGGACTAACGTATCG 60.318 60.000 5.05 0.00 0.00 2.92
698 3142 5.369685 ACACAGATGCTCACTATAGATCG 57.630 43.478 6.78 0.00 0.00 3.69
755 3199 3.055240 TGTTGAATGCCCATTTTGGATCC 60.055 43.478 4.20 4.20 40.96 3.36
1108 6952 0.254178 ATCGAGGCCTTCTTGCATGT 59.746 50.000 6.77 0.00 0.00 3.21
1167 7011 0.320771 CCGACTGAAGGGTGGACAAG 60.321 60.000 0.00 0.00 0.00 3.16
1326 7170 4.346709 TCCACCTCACAATAACTGAGAACA 59.653 41.667 0.00 0.00 37.90 3.18
1526 7370 4.143094 GCATGTACAACTCCTCGTTTTCTC 60.143 45.833 0.00 0.00 32.27 2.87
1567 7411 9.256228 ACGGACATCATATGATATTAGTAAGGT 57.744 33.333 17.77 8.35 32.63 3.50
1648 7492 6.861065 ATCCGAGTAAATTTATGCGACAAT 57.139 33.333 18.41 9.78 0.00 2.71
1653 7497 6.745450 ACACAAAATCCGAGTAAATTTATGCG 59.255 34.615 0.31 8.18 0.00 4.73
1781 8926 5.215160 GGTGCGACAATCATATTTCCAATC 58.785 41.667 0.00 0.00 0.00 2.67
1806 8951 2.026449 CCCCTTGAAGCAGAGAAGACAT 60.026 50.000 0.00 0.00 0.00 3.06
2128 9290 2.278332 AGGCCTTGAACAGTTCCTTC 57.722 50.000 10.93 0.00 0.00 3.46
2183 9345 1.521010 CTGATCGCTCCTGCAGGTG 60.521 63.158 31.58 29.16 39.64 4.00


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

AutoCloner maintained by Alex Coulton.