Multiple sequence alignment - TraesCS3B01G399900

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 TraesCS3B01G399900 chr3B 100.000 3653 0 0 1 3653 631047244 631050896 0.000000e+00 6746
1 TraesCS3B01G399900 chr3B 84.615 130 19 1 73 202 448791118 448790990 1.060000e-25 128
2 TraesCS3B01G399900 chr3A 96.060 2843 90 11 24 2851 617072387 617075222 0.000000e+00 4610
3 TraesCS3B01G399900 chr3A 91.667 216 9 4 2852 3063 25765225 25765015 1.280000e-74 291
4 TraesCS3B01G399900 chr3A 82.308 130 22 1 73 202 468016033 468015905 1.070000e-20 111
5 TraesCS3B01G399900 chr3D 95.352 2603 65 21 275 2851 474653946 474656518 0.000000e+00 4085
6 TraesCS3B01G399900 chr3D 90.805 261 21 2 6 266 474651910 474652167 2.700000e-91 346
7 TraesCS3B01G399900 chr3D 81.633 147 22 5 1 146 524216892 524217034 2.300000e-22 117
8 TraesCS3B01G399900 chr3D 80.556 144 23 5 4 146 524006187 524006048 4.990000e-19 106
9 TraesCS3B01G399900 chr1B 96.774 806 19 5 2852 3653 162777685 162778487 0.000000e+00 1338
10 TraesCS3B01G399900 chr1B 94.570 221 3 4 2848 3063 7517414 7517630 2.100000e-87 333
11 TraesCS3B01G399900 chr6B 96.715 761 17 5 2897 3653 184365144 184365900 0.000000e+00 1260
12 TraesCS3B01G399900 chr6B 78.583 621 109 22 1085 1696 505683150 505682545 4.420000e-104 388
13 TraesCS3B01G399900 chr7D 97.931 580 12 0 3073 3652 376953170 376952591 0.000000e+00 1005
14 TraesCS3B01G399900 chrUn 97.603 584 14 0 3070 3653 91453864 91454447 0.000000e+00 1002
15 TraesCS3B01G399900 chr5A 97.432 584 15 0 3070 3653 226950468 226951051 0.000000e+00 996
16 TraesCS3B01G399900 chr4A 97.432 584 15 0 3070 3653 699093558 699094141 0.000000e+00 996
17 TraesCS3B01G399900 chr5B 97.418 581 15 0 3073 3653 613628765 613628185 0.000000e+00 990
18 TraesCS3B01G399900 chr5B 97.235 217 2 2 2849 3061 661283742 661283526 7.450000e-97 364
19 TraesCS3B01G399900 chr5B 95.890 219 3 3 2849 3063 661280249 661280033 2.090000e-92 350
20 TraesCS3B01G399900 chr5B 92.130 216 10 6 2853 3063 61657957 61658170 7.670000e-77 298
21 TraesCS3B01G399900 chr4D 97.423 582 14 1 3073 3653 471413050 471412469 0.000000e+00 990
22 TraesCS3B01G399900 chr1A 97.260 584 16 0 3070 3653 27386435 27387018 0.000000e+00 990
23 TraesCS3B01G399900 chr2A 79.393 626 111 16 1928 2544 663145884 663145268 3.370000e-115 425
24 TraesCS3B01G399900 chr2A 77.364 698 120 32 1085 1766 663146733 663146058 2.660000e-101 379
25 TraesCS3B01G399900 chr2D 79.073 626 113 18 1928 2544 518970139 518970755 7.300000e-112 414
26 TraesCS3B01G399900 chr2D 77.000 700 119 34 1085 1766 518969290 518969965 2.680000e-96 363
27 TraesCS3B01G399900 chr2B 78.275 626 118 18 1928 2544 611193117 611193733 1.590000e-103 387
28 TraesCS3B01G399900 chr2B 77.031 714 132 26 1066 1766 611192240 611192934 7.400000e-102 381
29 TraesCS3B01G399900 chr6D 76.768 693 133 26 1085 1766 318453749 318454424 2.680000e-96 363
30 TraesCS3B01G399900 chr6A 76.734 692 135 24 1085 1766 456011608 456012283 2.680000e-96 363
31 TraesCS3B01G399900 chr7A 93.607 219 4 9 2852 3061 627234007 627233790 5.890000e-83 318
32 TraesCS3B01G399900 chr7B 92.523 214 7 3 2852 3061 655043529 655043321 7.670000e-77 298


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 TraesCS3B01G399900 chr3B 631047244 631050896 3652 False 6746.0 6746 100.0000 1 3653 1 chr3B.!!$F1 3652
1 TraesCS3B01G399900 chr3A 617072387 617075222 2835 False 4610.0 4610 96.0600 24 2851 1 chr3A.!!$F1 2827
2 TraesCS3B01G399900 chr3D 474651910 474656518 4608 False 2215.5 4085 93.0785 6 2851 2 chr3D.!!$F2 2845
3 TraesCS3B01G399900 chr1B 162777685 162778487 802 False 1338.0 1338 96.7740 2852 3653 1 chr1B.!!$F2 801
4 TraesCS3B01G399900 chr6B 184365144 184365900 756 False 1260.0 1260 96.7150 2897 3653 1 chr6B.!!$F1 756
5 TraesCS3B01G399900 chr6B 505682545 505683150 605 True 388.0 388 78.5830 1085 1696 1 chr6B.!!$R1 611
6 TraesCS3B01G399900 chr7D 376952591 376953170 579 True 1005.0 1005 97.9310 3073 3652 1 chr7D.!!$R1 579
7 TraesCS3B01G399900 chrUn 91453864 91454447 583 False 1002.0 1002 97.6030 3070 3653 1 chrUn.!!$F1 583
8 TraesCS3B01G399900 chr5A 226950468 226951051 583 False 996.0 996 97.4320 3070 3653 1 chr5A.!!$F1 583
9 TraesCS3B01G399900 chr4A 699093558 699094141 583 False 996.0 996 97.4320 3070 3653 1 chr4A.!!$F1 583
10 TraesCS3B01G399900 chr5B 613628185 613628765 580 True 990.0 990 97.4180 3073 3653 1 chr5B.!!$R1 580
11 TraesCS3B01G399900 chr5B 661280033 661283742 3709 True 357.0 364 96.5625 2849 3063 2 chr5B.!!$R2 214
12 TraesCS3B01G399900 chr4D 471412469 471413050 581 True 990.0 990 97.4230 3073 3653 1 chr4D.!!$R1 580
13 TraesCS3B01G399900 chr1A 27386435 27387018 583 False 990.0 990 97.2600 3070 3653 1 chr1A.!!$F1 583
14 TraesCS3B01G399900 chr2A 663145268 663146733 1465 True 402.0 425 78.3785 1085 2544 2 chr2A.!!$R1 1459
15 TraesCS3B01G399900 chr2D 518969290 518970755 1465 False 388.5 414 78.0365 1085 2544 2 chr2D.!!$F1 1459
16 TraesCS3B01G399900 chr2B 611192240 611193733 1493 False 384.0 387 77.6530 1066 2544 2 chr2B.!!$F1 1478
17 TraesCS3B01G399900 chr6D 318453749 318454424 675 False 363.0 363 76.7680 1085 1766 1 chr6D.!!$F1 681
18 TraesCS3B01G399900 chr6A 456011608 456012283 675 False 363.0 363 76.7340 1085 1766 1 chr6A.!!$F1 681

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
589 2382 0.596341 ATGGCAAACGAACAAACGCC 60.596 50.0 0.00 0.0 40.02 5.68 F
1019 2828 0.106769 ATGGCCACGGCAATGTATGA 60.107 50.0 8.16 0.0 42.43 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 3546 0.975556 TGATCCGCCACAGGAAGCTA 60.976 55.000 0.0 0.0 44.5 3.32 R
2779 4641 1.407618 TGACGATCCACCAATACCTCG 59.592 52.381 0.0 0.0 0.0 4.63 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
39 40 1.544246 ACGGTGTGATGATCAGTTCGA 59.456 47.619 14.84 0.00 0.00 3.71
45 46 6.640907 CGGTGTGATGATCAGTTCGATTTATA 59.359 38.462 0.09 0.00 33.17 0.98
181 182 5.517411 GGTTCTTTGGTTTTCGGTGTAAAAG 59.483 40.000 0.00 0.00 0.00 2.27
197 198 3.857157 AAAAGTGCTCACCTCTAACCA 57.143 42.857 0.00 0.00 0.00 3.67
353 2146 5.050490 GCATACACTTGTCCTGTATACCAG 58.950 45.833 0.00 0.00 41.15 4.00
397 2190 3.694072 TCTTTCTGGTTCAGTTGGTTGTG 59.306 43.478 0.00 0.00 32.61 3.33
453 2246 2.544685 CTACTGCTATCGCTTGCAAGT 58.455 47.619 26.55 10.62 38.81 3.16
472 2265 0.960364 TTCGTTGCATTGCCTCCTCC 60.960 55.000 6.12 0.00 0.00 4.30
532 2325 0.984995 ACTGTGGGCTACCTTTCTCC 59.015 55.000 0.00 0.00 37.76 3.71
536 2329 0.984230 TGGGCTACCTTTCTCCAGTG 59.016 55.000 0.00 0.00 37.76 3.66
556 2349 1.069636 GTGCGCAAACAAGAGAGGAAG 60.070 52.381 14.00 0.00 0.00 3.46
571 2364 0.736053 GGAAGACGAGAGCAGTCGAT 59.264 55.000 13.97 0.51 42.85 3.59
587 2380 1.041726 CGATGGCAAACGAACAAACG 58.958 50.000 11.00 0.00 39.31 3.60
589 2382 0.596341 ATGGCAAACGAACAAACGCC 60.596 50.000 0.00 0.00 40.02 5.68
600 2393 3.550030 CGAACAAACGCCCTGAATTTTCT 60.550 43.478 0.00 0.00 0.00 2.52
919 2725 2.203139 CCCAACTCACCACGCACA 60.203 61.111 0.00 0.00 0.00 4.57
1017 2826 2.417978 CATGGCCACGGCAATGTAT 58.582 52.632 16.16 0.00 45.03 2.29
1019 2828 0.106769 ATGGCCACGGCAATGTATGA 60.107 50.000 8.16 0.00 42.43 2.15
1021 2830 1.029408 GGCCACGGCAATGTATGACA 61.029 55.000 10.83 0.00 44.11 3.58
1027 2836 0.248215 GGCAATGTATGACAGCGTGC 60.248 55.000 4.84 4.84 36.87 5.34
1028 2837 0.729116 GCAATGTATGACAGCGTGCT 59.271 50.000 0.00 0.00 33.89 4.40
1642 3463 3.692406 GCAAGGACCCCGAGACGT 61.692 66.667 0.00 0.00 0.00 4.34
1993 3850 0.318441 CAGCTGGTTCTTCTGGACGA 59.682 55.000 5.57 0.00 0.00 4.20
2706 4567 7.176165 TCTGAATTCTGATGCTTGTTCATTCTT 59.824 33.333 10.68 0.00 0.00 2.52
2779 4641 5.857517 TGTTTTTCGGTTGTGTACTTTTGAC 59.142 36.000 0.00 0.00 0.00 3.18
3083 4951 2.497138 CAGATCGCTGCCATGGATTTA 58.503 47.619 18.40 0.00 34.95 1.40
3459 5449 4.154195 TCGCTGGTTGAAGCTTTCTTATTC 59.846 41.667 0.00 0.00 41.24 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.124238 CCGTATACACCGAAATGGACATT 58.876 43.478 3.32 0.00 42.00 2.71
1 2 3.133362 ACCGTATACACCGAAATGGACAT 59.867 43.478 3.32 0.00 42.00 3.06
2 3 2.496871 ACCGTATACACCGAAATGGACA 59.503 45.455 3.32 0.00 42.00 4.02
3 4 2.861935 CACCGTATACACCGAAATGGAC 59.138 50.000 3.32 0.00 42.00 4.02
4 5 2.496871 ACACCGTATACACCGAAATGGA 59.503 45.455 3.32 0.00 42.00 3.41
11 12 2.855660 TCATCACACCGTATACACCG 57.144 50.000 3.32 0.00 0.00 4.94
19 20 1.544246 TCGAACTGATCATCACACCGT 59.456 47.619 0.00 0.00 0.00 4.83
20 21 2.278026 TCGAACTGATCATCACACCG 57.722 50.000 0.00 0.00 0.00 4.94
49 50 8.805175 TGTTTGGATGTATCATCAGTTTTCATT 58.195 29.630 11.08 0.00 0.00 2.57
61 62 5.596361 AGTTGTTTGGTGTTTGGATGTATCA 59.404 36.000 0.00 0.00 0.00 2.15
128 129 7.551617 ACCGAATTAAGTTGGTCGATATTCTTT 59.448 33.333 9.09 0.00 35.54 2.52
131 132 6.839820 ACCGAATTAAGTTGGTCGATATTC 57.160 37.500 9.09 0.00 35.54 1.75
140 141 5.447624 AGAACCAAACCGAATTAAGTTGG 57.552 39.130 7.67 7.67 0.00 3.77
146 147 5.855740 AACCAAAGAACCAAACCGAATTA 57.144 34.783 0.00 0.00 0.00 1.40
181 182 4.576463 CCAATTATGGTTAGAGGTGAGCAC 59.424 45.833 0.00 0.00 42.18 4.40
232 241 2.604174 CGCGCTGTTCCTCGGTTTT 61.604 57.895 5.56 0.00 0.00 2.43
233 242 3.041940 CGCGCTGTTCCTCGGTTT 61.042 61.111 5.56 0.00 0.00 3.27
353 2146 8.709386 AAGAAACATATCAGACACATGTAGAC 57.291 34.615 0.00 0.00 32.70 2.59
397 2190 0.991920 TCTCCCCTTCCAACCATCAC 59.008 55.000 0.00 0.00 0.00 3.06
453 2246 0.960364 GGAGGAGGCAATGCAACGAA 60.960 55.000 7.79 0.00 0.00 3.85
472 2265 2.594654 CGTGCTTGAGTTACTAGAAGCG 59.405 50.000 18.04 6.61 43.10 4.68
532 2325 0.657312 TCTCTTGTTTGCGCACACTG 59.343 50.000 25.53 18.09 0.00 3.66
536 2329 0.944386 TTCCTCTCTTGTTTGCGCAC 59.056 50.000 11.12 0.00 0.00 5.34
556 2349 1.587613 GCCATCGACTGCTCTCGTC 60.588 63.158 0.00 0.00 35.10 4.20
571 2364 1.226717 GGCGTTTGTTCGTTTGCCA 60.227 52.632 0.00 0.00 42.03 4.92
587 2380 0.604578 TGCTGCAGAAAATTCAGGGC 59.395 50.000 20.43 0.00 0.00 5.19
589 2382 3.054878 GTTGTGCTGCAGAAAATTCAGG 58.945 45.455 20.43 0.00 0.00 3.86
600 2393 2.203337 GGAGGGTGTTGTGCTGCA 60.203 61.111 0.00 0.00 0.00 4.41
708 2513 0.244721 TGGTGATGTCGCTCACTCTG 59.755 55.000 10.89 0.00 44.05 3.35
919 2725 2.080693 TCGTGATTAACAAATGGCGCT 58.919 42.857 7.64 0.00 0.00 5.92
1015 2824 0.320683 AAGTGCAGCACGCTGTCATA 60.321 50.000 19.96 2.67 45.24 2.15
1017 2826 2.203056 AAGTGCAGCACGCTGTCA 60.203 55.556 19.96 14.71 45.24 3.58
1019 2828 3.957535 GCAAGTGCAGCACGCTGT 61.958 61.111 23.71 9.53 45.24 4.40
1725 3546 0.975556 TGATCCGCCACAGGAAGCTA 60.976 55.000 0.00 0.00 44.50 3.32
1993 3850 2.507944 GTCCGGCCTCTGCATGAT 59.492 61.111 0.00 0.00 40.13 2.45
2706 4567 3.140325 AGAAGAACAAATTCAGCGGGA 57.860 42.857 0.00 0.00 37.29 5.14
2779 4641 1.407618 TGACGATCCACCAATACCTCG 59.592 52.381 0.00 0.00 0.00 4.63
2842 4706 2.041216 CCTAGTGGTGCCCTTTACCTTT 59.959 50.000 0.00 0.00 39.01 3.11
2925 4789 1.923356 TTTTGCTCCAGATCCAACCC 58.077 50.000 0.00 0.00 0.00 4.11
3083 4951 2.762234 CGTAACGGAGCTCGAGCCT 61.762 63.158 32.94 20.30 43.38 4.58
3459 5449 7.767261 AGAAAGCTACAACTAGACACTATGAG 58.233 38.462 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.