Multiple sequence alignment - TraesCS3B01G004000

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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 TraesCS3B01G004000 chr3B 100.000 3500 0 0 1 3500 2425221 2428720 0.000000e+00 6464
1 TraesCS3B01G004000 chr3B 96.176 523 8 4 2990 3500 591476063 591476585 0.000000e+00 845
2 TraesCS3B01G004000 chr6B 98.356 2980 36 5 533 3500 18577834 18574856 0.000000e+00 5219
3 TraesCS3B01G004000 chr6B 96.243 2981 60 12 532 3500 56431921 56434861 0.000000e+00 4837
4 TraesCS3B01G004000 chr6B 98.211 2571 44 2 532 3102 195191936 195194504 0.000000e+00 4492
5 TraesCS3B01G004000 chr6B 98.944 663 7 0 1 663 56431334 56431996 0.000000e+00 1186
6 TraesCS3B01G004000 chr6B 97.888 663 14 0 1 663 195191377 195192039 0.000000e+00 1147
7 TraesCS3B01G004000 chr6B 97.738 663 10 1 1 663 18578445 18577788 0.000000e+00 1136
8 TraesCS3B01G004000 chr6B 96.176 523 8 4 2990 3500 57424938 57424416 0.000000e+00 845
9 TraesCS3B01G004000 chr6B 96.176 523 8 4 2990 3500 195194353 195194875 0.000000e+00 845
10 TraesCS3B01G004000 chr5B 97.218 3091 57 3 1 3063 264917806 264920895 0.000000e+00 5204
11 TraesCS3B01G004000 chr5B 98.212 2572 43 3 532 3102 371296093 371298662 0.000000e+00 4492
12 TraesCS3B01G004000 chr5B 98.039 663 13 0 1 663 371295506 371296168 0.000000e+00 1153
13 TraesCS3B01G004000 chr5B 95.035 564 14 5 2951 3500 162879194 162879757 0.000000e+00 874
14 TraesCS3B01G004000 chr5B 96.558 523 6 4 2990 3500 371298511 371299033 0.000000e+00 856
15 TraesCS3B01G004000 chr5A 96.931 3095 62 4 1 3063 613971493 613974586 0.000000e+00 5158
16 TraesCS3B01G004000 chr5A 96.901 484 3 3 3029 3500 613974474 613974957 0.000000e+00 800
17 TraesCS3B01G004000 chr4A 96.585 3104 64 6 1 3063 674544844 674541742 0.000000e+00 5107
18 TraesCS3B01G004000 chr3A 98.289 2571 43 1 532 3102 684725233 684722664 0.000000e+00 4503
19 TraesCS3B01G004000 chr3A 98.492 663 10 0 1 663 684725820 684725158 0.000000e+00 1170
20 TraesCS3B01G004000 chr6A 99.002 2504 24 1 560 3063 53128067 53125565 0.000000e+00 4484
21 TraesCS3B01G004000 chr6A 96.488 484 5 3 3029 3500 53125677 53125194 0.000000e+00 789
22 TraesCS3B01G004000 chr6A 92.812 320 11 3 3193 3500 356980825 356980506 1.480000e-123 453
23 TraesCS3B01G004000 chr6A 91.875 320 14 3 3193 3500 16611373 16611692 1.490000e-118 436
24 TraesCS3B01G004000 chr6A 91.022 323 14 4 3193 3500 444680677 444680355 4.180000e-114 422
25 TraesCS3B01G004000 chr6A 92.414 290 10 3 3223 3500 41592231 41591942 1.510000e-108 403
26 TraesCS3B01G004000 chr1B 95.303 1767 70 4 1452 3205 637322446 637324212 0.000000e+00 2791
27 TraesCS3B01G004000 chr1B 96.750 523 5 4 2990 3500 7060770 7060248 0.000000e+00 861
28 TraesCS3B01G004000 chr2A 96.805 1659 22 3 1 1630 61498617 61500273 0.000000e+00 2741
29 TraesCS3B01G004000 chr4B 95.985 523 9 4 2990 3500 644580757 644581279 0.000000e+00 839
30 TraesCS3B01G004000 chr6D 92.188 320 13 3 3193 3500 323703777 323703458 3.210000e-120 442
31 TraesCS3B01G004000 chr1A 92.414 290 10 4 3223 3500 265700228 265700517 1.510000e-108 403
32 TraesCS3B01G004000 chr1D 88.438 320 25 2 3193 3500 27471422 27471741 3.300000e-100 375


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 TraesCS3B01G004000 chr3B 2425221 2428720 3499 False 6464.000000 6464 100.0000 1 3500 1 chr3B.!!$F1 3499
1 TraesCS3B01G004000 chr3B 591476063 591476585 522 False 845.000000 845 96.1760 2990 3500 1 chr3B.!!$F2 510
2 TraesCS3B01G004000 chr6B 18574856 18578445 3589 True 3177.500000 5219 98.0470 1 3500 2 chr6B.!!$R2 3499
3 TraesCS3B01G004000 chr6B 56431334 56434861 3527 False 3011.500000 4837 97.5935 1 3500 2 chr6B.!!$F1 3499
4 TraesCS3B01G004000 chr6B 195191377 195194875 3498 False 2161.333333 4492 97.4250 1 3500 3 chr6B.!!$F2 3499
5 TraesCS3B01G004000 chr6B 57424416 57424938 522 True 845.000000 845 96.1760 2990 3500 1 chr6B.!!$R1 510
6 TraesCS3B01G004000 chr5B 264917806 264920895 3089 False 5204.000000 5204 97.2180 1 3063 1 chr5B.!!$F2 3062
7 TraesCS3B01G004000 chr5B 371295506 371299033 3527 False 2167.000000 4492 97.6030 1 3500 3 chr5B.!!$F3 3499
8 TraesCS3B01G004000 chr5B 162879194 162879757 563 False 874.000000 874 95.0350 2951 3500 1 chr5B.!!$F1 549
9 TraesCS3B01G004000 chr5A 613971493 613974957 3464 False 2979.000000 5158 96.9160 1 3500 2 chr5A.!!$F1 3499
10 TraesCS3B01G004000 chr4A 674541742 674544844 3102 True 5107.000000 5107 96.5850 1 3063 1 chr4A.!!$R1 3062
11 TraesCS3B01G004000 chr3A 684722664 684725820 3156 True 2836.500000 4503 98.3905 1 3102 2 chr3A.!!$R1 3101
12 TraesCS3B01G004000 chr6A 53125194 53128067 2873 True 2636.500000 4484 97.7450 560 3500 2 chr6A.!!$R4 2940
13 TraesCS3B01G004000 chr1B 637322446 637324212 1766 False 2791.000000 2791 95.3030 1452 3205 1 chr1B.!!$F1 1753
14 TraesCS3B01G004000 chr1B 7060248 7060770 522 True 861.000000 861 96.7500 2990 3500 1 chr1B.!!$R1 510
15 TraesCS3B01G004000 chr2A 61498617 61500273 1656 False 2741.000000 2741 96.8050 1 1630 1 chr2A.!!$F1 1629
16 TraesCS3B01G004000 chr4B 644580757 644581279 522 False 839.000000 839 95.9850 2990 3500 1 chr4B.!!$F1 510

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
344 345 1.003580 CGGCTTATGGGCATAGGATGT 59.996 52.381 0.0 0.0 40.9 3.06 F
1241 1414 1.073025 AAACAGCGATGCAGACCCA 59.927 52.632 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2276 1.601903 TCACATCGAACACCAACTTGC 59.398 47.619 0.00 0.0 0.00 4.01 R
2996 3340 0.689080 CAGGAAGAGCTCCCTGGCTA 60.689 60.000 24.17 0.0 46.81 3.93 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
25 26 3.066064 GTGAGTGTACATGCAACAAACCA 59.934 43.478 0.00 0.61 0.00 3.67
213 214 4.391155 GACGGTGAGAGAGTATACATCCT 58.609 47.826 5.50 0.00 0.00 3.24
344 345 1.003580 CGGCTTATGGGCATAGGATGT 59.996 52.381 0.00 0.00 40.90 3.06
408 409 2.100631 GTGCTTCCACATCGACGGG 61.101 63.158 0.00 0.00 41.67 5.28
1031 1204 3.127895 GTGAACCAGTGCAGTTACACAAA 59.872 43.478 0.00 0.00 43.23 2.83
1216 1389 3.207777 AGGTCCCTTAGAGGCAGAATCTA 59.792 47.826 0.00 0.00 32.73 1.98
1241 1414 1.073025 AAACAGCGATGCAGACCCA 59.927 52.632 0.00 0.00 0.00 4.51
1344 1518 1.812571 GTAACCATCACAGGCCACTTG 59.187 52.381 5.01 0.00 0.00 3.16
2408 2582 3.591527 ACAAATATCTGGGGTGAGGTTCA 59.408 43.478 0.00 0.00 0.00 3.18
2414 2588 1.615424 GGGGTGAGGTTCAGGCCTA 60.615 63.158 3.98 0.00 39.34 3.93
2680 2868 4.841246 ACTCTTCATCTACAGGGTGACTTT 59.159 41.667 0.00 0.00 0.00 2.66
2882 3070 0.249398 GCCACGTCCCTCTGTACAAT 59.751 55.000 0.00 0.00 0.00 2.71
2947 3135 1.507141 CTGTGCACCGTGAAGAACCC 61.507 60.000 15.69 0.00 0.00 4.11
2996 3340 0.106819 GCATGAGCCACCTCCTTCAT 60.107 55.000 0.00 0.00 37.29 2.57
3407 3831 2.338620 CCGACGCAGGAGACACAA 59.661 61.111 0.00 0.00 0.00 3.33
3440 3864 2.424601 CGAGGTTAACTATGGTCGTGGA 59.575 50.000 5.42 0.00 0.00 4.02
3441 3865 3.119388 CGAGGTTAACTATGGTCGTGGAA 60.119 47.826 5.42 0.00 0.00 3.53
3442 3866 4.430908 GAGGTTAACTATGGTCGTGGAAG 58.569 47.826 5.42 0.00 0.00 3.46
3443 3867 4.091549 AGGTTAACTATGGTCGTGGAAGA 58.908 43.478 5.42 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.100749 GCAAGGTAGGTGCAACAACTTT 59.899 45.455 3.64 0.00 41.80 2.66
344 345 5.423704 TTGTTCAGGTCGGGACAATATTA 57.576 39.130 0.75 0.00 0.00 0.98
408 409 0.937304 TCTTGCTCTTGTTGTCGCAC 59.063 50.000 0.00 0.00 31.24 5.34
1031 1204 2.872858 GAGAAACGTTTCACTTGCCTCT 59.127 45.455 35.29 16.82 39.61 3.69
1216 1389 2.629656 GCATCGCTGTTTGCCACCT 61.630 57.895 0.00 0.00 38.78 4.00
1617 1791 2.189833 CAGGCCTCTGTACGTAGCA 58.810 57.895 0.00 0.00 36.30 3.49
2102 2276 1.601903 TCACATCGAACACCAACTTGC 59.398 47.619 0.00 0.00 0.00 4.01
2408 2582 4.686122 CGAACATTTCCCAGTTATAGGCCT 60.686 45.833 11.78 11.78 0.00 5.19
2414 2588 3.732048 ACCCGAACATTTCCCAGTTAT 57.268 42.857 0.00 0.00 0.00 1.89
2497 2671 1.693627 GTGAGAGGGGCTTCGATCTA 58.306 55.000 0.00 0.00 0.00 1.98
2680 2868 1.374343 CCTCTCGCGCCTGTACTGTA 61.374 60.000 0.00 0.00 0.00 2.74
2882 3070 2.496070 CAGAGGGTCGTGGTTCTGAATA 59.504 50.000 0.00 0.00 39.46 1.75
2947 3135 1.077212 CCCTGGCTGTGAAGGATGG 60.077 63.158 0.00 0.00 35.40 3.51
2996 3340 0.689080 CAGGAAGAGCTCCCTGGCTA 60.689 60.000 24.17 0.00 46.81 3.93


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

AutoCloner maintained by Alex Coulton.