Multiple sequence alignment - TraesCS7B01G454200

Loading Multiple Alignment...

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 TraesCS7B01G454200 chr7B 100.000 2997 0 0 1 2997 714901438 714898442 0.000000e+00 5535.0
1 TraesCS7B01G454200 chr7B 96.971 3037 44 6 1 2997 715155814 715152786 0.000000e+00 5055.0
2 TraesCS7B01G454200 chr7B 96.905 3037 47 5 1 2997 715123134 715120105 0.000000e+00 5044.0
3 TraesCS7B01G454200 chr7B 96.801 3032 50 11 1 2997 715083737 715080718 0.000000e+00 5018.0
4 TraesCS7B01G454200 chr7B 95.775 1799 27 13 1236 2997 714947476 714945690 0.000000e+00 2856.0
5 TraesCS7B01G454200 chr7B 86.957 1794 155 34 235 1998 715322453 715320709 0.000000e+00 1943.0
6 TraesCS7B01G454200 chr7B 96.098 1179 35 5 67 1238 714950521 714949347 0.000000e+00 1912.0
7 TraesCS7B01G454200 chr7B 89.440 625 53 11 1771 2394 714845000 714844388 0.000000e+00 776.0
8 TraesCS7B01G454200 chr7B 91.086 359 11 1 2458 2795 714844385 714844027 1.630000e-127 466.0
9 TraesCS7B01G454200 chr7B 90.547 201 1 2 2797 2997 714843991 714843809 1.780000e-62 250.0
10 TraesCS7B01G454200 chr4A 94.120 2211 87 12 67 2272 700430228 700428056 0.000000e+00 3323.0
11 TraesCS7B01G454200 chr7D 86.978 1843 167 43 192 1995 619581941 619583749 0.000000e+00 2006.0
12 TraesCS7B01G454200 chr7D 86.341 1845 164 54 192 1995 620583009 620584806 0.000000e+00 1930.0
13 TraesCS7B01G454200 chr7D 92.795 458 25 5 507 964 619359201 619358752 0.000000e+00 656.0
14 TraesCS7B01G454200 chr7D 89.587 509 20 8 2311 2795 495333934 495333435 1.530000e-172 616.0
15 TraesCS7B01G454200 chr7D 91.686 433 23 9 153 583 619359590 619359169 3.330000e-164 588.0
16 TraesCS7B01G454200 chr7D 94.608 204 7 2 2798 2997 495333398 495333195 2.240000e-81 313.0
17 TraesCS7B01G454200 chr7D 94.118 68 4 0 1 68 580807989 580808056 1.470000e-18 104.0
18 TraesCS7B01G454200 chr7D 92.754 69 5 0 1 69 601931638 601931570 1.900000e-17 100.0
19 TraesCS7B01G454200 chr7A 86.865 1850 173 35 192 1995 713833345 713835170 0.000000e+00 2006.0
20 TraesCS7B01G454200 chrUn 87.222 1393 116 35 157 1519 93249919 93248559 0.000000e+00 1530.0
21 TraesCS7B01G454200 chr3B 94.372 231 13 0 2565 2795 284637012 284637242 3.670000e-94 355.0
22 TraesCS7B01G454200 chr3B 97.000 200 6 0 2798 2997 284637279 284637478 1.330000e-88 337.0
23 TraesCS7B01G454200 chr3B 93.953 215 9 3 2308 2522 284636687 284636897 3.730000e-84 322.0
24 TraesCS7B01G454200 chr3B 95.833 48 2 0 2523 2570 284636949 284636996 8.910000e-11 78.7
25 TraesCS7B01G454200 chr6D 95.312 64 3 0 1 64 11489793 11489856 5.290000e-18 102.0
26 TraesCS7B01G454200 chr2D 94.030 67 4 0 2 68 492997056 492997122 5.290000e-18 102.0
27 TraesCS7B01G454200 chr1B 95.312 64 3 0 1 64 571832518 571832455 5.290000e-18 102.0
28 TraesCS7B01G454200 chr1A 92.754 69 4 1 1 69 557194891 557194824 6.840000e-17 99.0


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 TraesCS7B01G454200 chr7B 714898442 714901438 2996 True 5535.000000 5535 100.000000 1 2997 1 chr7B.!!$R1 2996
1 TraesCS7B01G454200 chr7B 715152786 715155814 3028 True 5055.000000 5055 96.971000 1 2997 1 chr7B.!!$R4 2996
2 TraesCS7B01G454200 chr7B 715120105 715123134 3029 True 5044.000000 5044 96.905000 1 2997 1 chr7B.!!$R3 2996
3 TraesCS7B01G454200 chr7B 715080718 715083737 3019 True 5018.000000 5018 96.801000 1 2997 1 chr7B.!!$R2 2996
4 TraesCS7B01G454200 chr7B 714945690 714950521 4831 True 2384.000000 2856 95.936500 67 2997 2 chr7B.!!$R7 2930
5 TraesCS7B01G454200 chr7B 715320709 715322453 1744 True 1943.000000 1943 86.957000 235 1998 1 chr7B.!!$R5 1763
6 TraesCS7B01G454200 chr7B 714843809 714845000 1191 True 497.333333 776 90.357667 1771 2997 3 chr7B.!!$R6 1226
7 TraesCS7B01G454200 chr4A 700428056 700430228 2172 True 3323.000000 3323 94.120000 67 2272 1 chr4A.!!$R1 2205
8 TraesCS7B01G454200 chr7D 619581941 619583749 1808 False 2006.000000 2006 86.978000 192 1995 1 chr7D.!!$F2 1803
9 TraesCS7B01G454200 chr7D 620583009 620584806 1797 False 1930.000000 1930 86.341000 192 1995 1 chr7D.!!$F3 1803
10 TraesCS7B01G454200 chr7D 619358752 619359590 838 True 622.000000 656 92.240500 153 964 2 chr7D.!!$R3 811
11 TraesCS7B01G454200 chr7D 495333195 495333934 739 True 464.500000 616 92.097500 2311 2997 2 chr7D.!!$R2 686
12 TraesCS7B01G454200 chr7A 713833345 713835170 1825 False 2006.000000 2006 86.865000 192 1995 1 chr7A.!!$F1 1803
13 TraesCS7B01G454200 chrUn 93248559 93249919 1360 True 1530.000000 1530 87.222000 157 1519 1 chrUn.!!$R1 1362
14 TraesCS7B01G454200 chr3B 284636687 284637478 791 False 273.175000 355 95.289500 2308 2997 4 chr3B.!!$F1 689

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
719 793 2.135933 CTTCAAAGCGGTCGAAGAACT 58.864 47.619 17.35 0.0 45.87 3.01 F
839 913 2.180276 ACGGCTCCTATCTCAACACTT 58.820 47.619 0.00 0.0 0.00 3.16 F
1637 3616 1.277557 ACTCAGCCTTCACTGACATCC 59.722 52.381 0.00 0.0 41.72 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 3616 0.251916 TTACCAGGGGCGTGATTGAG 59.748 55.000 0.0 0.0 0.00 3.02 R
1774 3762 1.009078 TCAGCTTGCCATCGAAATCG 58.991 50.000 0.0 0.0 41.45 3.34 R
2480 4520 5.581126 ACTTCAGCAAATTCAAACAGTGA 57.419 34.783 0.0 0.0 0.00 3.41 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 4.689062 TGGAGAGTTGAGGATAAGAGGTT 58.311 43.478 0.00 0.00 0.00 3.50
34 35 5.094387 TGGAGAGTTGAGGATAAGAGGTTT 58.906 41.667 0.00 0.00 0.00 3.27
347 360 3.161450 ACCACGATCCCATCCCCG 61.161 66.667 0.00 0.00 0.00 5.73
719 793 2.135933 CTTCAAAGCGGTCGAAGAACT 58.864 47.619 17.35 0.00 45.87 3.01
839 913 2.180276 ACGGCTCCTATCTCAACACTT 58.820 47.619 0.00 0.00 0.00 3.16
985 1084 9.614792 AAATAATCGTTTCTATCTACTGCCTTT 57.385 29.630 0.00 0.00 0.00 3.11
1637 3616 1.277557 ACTCAGCCTTCACTGACATCC 59.722 52.381 0.00 0.00 41.72 3.51
1774 3762 1.069358 GGAGGATCGGATCAGTCCAAC 59.931 57.143 23.74 6.83 45.37 3.77
1813 3801 1.680522 CCCCATGCTGCGAGAGTACT 61.681 60.000 0.00 0.00 0.00 2.73
2040 4028 5.236478 GCTAGTTGGCGCAATATCTTTTAGA 59.764 40.000 10.83 0.00 0.00 2.10
2274 4289 8.577296 TGATAACTCTAATCAGTAGGCATGTAC 58.423 37.037 0.00 0.00 0.00 2.90
2275 4290 8.713708 ATAACTCTAATCAGTAGGCATGTACT 57.286 34.615 0.00 0.00 33.25 2.73
2276 4291 6.642707 ACTCTAATCAGTAGGCATGTACTC 57.357 41.667 0.00 0.00 30.40 2.59
2277 4292 5.239744 ACTCTAATCAGTAGGCATGTACTCG 59.760 44.000 0.00 0.00 30.40 4.18
2278 4293 5.131067 TCTAATCAGTAGGCATGTACTCGT 58.869 41.667 0.00 0.00 30.40 4.18
2279 4294 6.293698 TCTAATCAGTAGGCATGTACTCGTA 58.706 40.000 0.00 0.00 30.40 3.43
2297 4312 5.309020 ACTCGTATATGACTAGAGGGGTACA 59.691 44.000 0.00 0.00 33.58 2.90
2413 4452 3.054361 AGTTGTCTCAACCTGGAAGTTGT 60.054 43.478 0.00 0.00 45.90 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.640967 CCTCTTATCCTCAACTCTCCAGG 59.359 52.174 0.00 0.0 0.00 4.45
16 17 6.380079 ACATGAAACCTCTTATCCTCAACT 57.620 37.500 0.00 0.0 0.00 3.16
347 360 1.460497 GAGGGAGGGAGATGGGGAC 60.460 68.421 0.00 0.0 0.00 4.46
719 793 4.032960 AGACAAACATGCTGGACCATTA 57.967 40.909 0.00 0.0 0.00 1.90
839 913 6.046593 CCAAAACAGGAGACGTAGCATAATA 58.953 40.000 0.00 0.0 0.00 0.98
1637 3616 0.251916 TTACCAGGGGCGTGATTGAG 59.748 55.000 0.00 0.0 0.00 3.02
1774 3762 1.009078 TCAGCTTGCCATCGAAATCG 58.991 50.000 0.00 0.0 41.45 3.34
1813 3801 1.279496 CACAGAACCCTCCCTCATCA 58.721 55.000 0.00 0.0 0.00 3.07
2040 4028 8.314751 ACTCGCATCCTATTTATAACAGCTAAT 58.685 33.333 0.00 0.0 0.00 1.73
2138 4146 8.836413 ACACCCGTTCATGTTTAATCTATAATG 58.164 33.333 0.00 0.0 0.00 1.90
2274 4289 5.642919 GTGTACCCCTCTAGTCATATACGAG 59.357 48.000 0.00 0.0 32.48 4.18
2275 4290 5.555017 GTGTACCCCTCTAGTCATATACGA 58.445 45.833 0.00 0.0 0.00 3.43
2276 4291 4.391216 CGTGTACCCCTCTAGTCATATACG 59.609 50.000 0.00 0.0 0.00 3.06
2277 4292 4.155644 GCGTGTACCCCTCTAGTCATATAC 59.844 50.000 0.00 0.0 0.00 1.47
2278 4293 4.330250 GCGTGTACCCCTCTAGTCATATA 58.670 47.826 0.00 0.0 0.00 0.86
2279 4294 3.155501 GCGTGTACCCCTCTAGTCATAT 58.844 50.000 0.00 0.0 0.00 1.78
2326 4360 6.296202 GGCAACCCCACCTTTTTCTTTTATAT 60.296 38.462 0.00 0.0 0.00 0.86
2327 4361 5.012251 GGCAACCCCACCTTTTTCTTTTATA 59.988 40.000 0.00 0.0 0.00 0.98
2413 4452 7.086376 GCAAATTCAGCAACTCTTGAATAGAA 58.914 34.615 0.67 0.0 31.61 2.10
2480 4520 5.581126 ACTTCAGCAAATTCAAACAGTGA 57.419 34.783 0.00 0.0 0.00 3.41
2712 4824 6.359804 ACATTACAGTGGATCAATGCAGTAT 58.640 36.000 0.00 0.0 32.35 2.12


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

AutoCloner maintained by Alex Coulton.