Multiple sequence alignment - TraesCS3B01G531200

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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 TraesCS3B01G531200 chr3B 100.000 3281 0 0 1 3281 772254139 772250859 0.000000e+00 6059
1 TraesCS3B01G531200 chr3B 94.432 2784 115 19 509 3281 772182838 772180084 0.000000e+00 4246
2 TraesCS3B01G531200 chr3B 98.240 1591 23 2 1 1590 772168605 772167019 0.000000e+00 2778
3 TraesCS3B01G531200 chr3B 90.281 1883 133 22 582 2441 771841918 771840063 0.000000e+00 2418
4 TraesCS3B01G531200 chr3B 98.293 1347 23 0 1582 2928 772161881 772160535 0.000000e+00 2361
5 TraesCS3B01G531200 chr3B 89.432 1883 140 21 582 2441 772224925 772223079 0.000000e+00 2320
6 TraesCS3B01G531200 chr3B 88.736 435 39 2 2550 2982 771840063 771839637 1.040000e-144 523
7 TraesCS3B01G531200 chr3B 88.453 433 40 2 2552 2982 772223077 772222653 6.280000e-142 514
8 TraesCS3B01G531200 chr3B 93.171 205 14 0 3043 3247 772146636 772146432 5.320000e-78 302
9 TraesCS3B01G531200 chr3B 97.895 95 2 0 2954 3048 772160536 772160442 7.280000e-37 165
10 TraesCS3B01G531200 chr3D 94.941 2787 104 15 509 3281 578523261 578526024 0.000000e+00 4331
11 TraesCS3B01G531200 chr3D 89.857 1883 141 19 582 2441 578566704 578568559 0.000000e+00 2374
12 TraesCS3B01G531200 chr3D 87.834 1085 97 18 582 1648 578549635 578550702 0.000000e+00 1240
13 TraesCS3B01G531200 chr3D 87.727 440 41 3 2547 2982 578568556 578568986 4.890000e-138 501
14 TraesCS3B01G531200 chr3D 87.225 227 9 6 1 207 578522927 578523153 1.180000e-59 241
15 TraesCS3B01G531200 chr3D 97.895 95 2 0 113 207 578523164 578523258 7.280000e-37 165
16 TraesCS3B01G531200 chr3D 92.500 80 5 1 509 587 578534435 578534514 2.680000e-21 113
17 TraesCS3B01G531200 chr3A 95.076 2051 80 10 509 2543 714108188 714106143 0.000000e+00 3208
18 TraesCS3B01G531200 chr3A 89.580 1881 136 22 582 2441 714026639 714024798 0.000000e+00 2333
19 TraesCS3B01G531200 chr3A 86.826 1670 148 33 585 2221 714086864 714085234 0.000000e+00 1799
20 TraesCS3B01G531200 chr3A 95.898 512 21 0 2769 3280 714093562 714093051 0.000000e+00 830
21 TraesCS3B01G531200 chr3A 87.075 441 41 4 2550 2982 714024798 714024366 4.920000e-133 484
22 TraesCS3B01G531200 chr3A 91.618 346 22 5 2255 2599 714085237 714084898 3.830000e-129 472
23 TraesCS3B01G531200 chr3A 95.528 246 11 0 2507 2752 714106096 714105851 8.530000e-106 394
24 TraesCS3B01G531200 chr3A 94.175 206 11 1 1 206 714108976 714108772 2.460000e-81 313
25 TraesCS3B01G531200 chr3A 90.000 200 19 1 3 202 714087971 714087773 1.170000e-64 257
26 TraesCS3B01G531200 chr3A 89.571 163 15 2 45 207 628653473 628653633 4.290000e-49 206
27 TraesCS3B01G531200 chr3A 81.538 195 23 5 3095 3281 714024177 714023988 7.340000e-32 148
28 TraesCS3B01G531200 chr3A 93.750 80 4 1 509 587 714087767 714087688 5.750000e-23 119
29 TraesCS3B01G531200 chr2B 92.628 312 21 2 204 513 607947840 607947529 6.460000e-122 448
30 TraesCS3B01G531200 chr2D 91.558 308 23 3 206 511 391993985 391993679 3.910000e-114 422
31 TraesCS3B01G531200 chr5A 91.026 312 25 3 204 513 706828524 706828214 5.060000e-113 418
32 TraesCS3B01G531200 chr5A 90.415 313 28 2 203 513 203679169 203678857 8.470000e-111 411
33 TraesCS3B01G531200 chr5D 91.205 307 23 4 206 510 155834811 155835115 6.550000e-112 414
34 TraesCS3B01G531200 chr5D 88.406 345 26 13 185 520 393904737 393904398 1.420000e-108 403
35 TraesCS3B01G531200 chr7D 90.675 311 25 4 203 510 181709552 181709243 8.470000e-111 411
36 TraesCS3B01G531200 chr4D 90.031 321 25 7 197 514 46878386 46878702 3.050000e-110 409


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 TraesCS3B01G531200 chr3B 772250859 772254139 3280 True 6059.000000 6059 100.000000 1 3281 1 chr3B.!!$R4 3280
1 TraesCS3B01G531200 chr3B 772180084 772182838 2754 True 4246.000000 4246 94.432000 509 3281 1 chr3B.!!$R3 2772
2 TraesCS3B01G531200 chr3B 772167019 772168605 1586 True 2778.000000 2778 98.240000 1 1590 1 chr3B.!!$R2 1589
3 TraesCS3B01G531200 chr3B 771839637 771841918 2281 True 1470.500000 2418 89.508500 582 2982 2 chr3B.!!$R5 2400
4 TraesCS3B01G531200 chr3B 772222653 772224925 2272 True 1417.000000 2320 88.942500 582 2982 2 chr3B.!!$R7 2400
5 TraesCS3B01G531200 chr3B 772160442 772161881 1439 True 1263.000000 2361 98.094000 1582 3048 2 chr3B.!!$R6 1466
6 TraesCS3B01G531200 chr3D 578522927 578526024 3097 False 1579.000000 4331 93.353667 1 3281 3 chr3D.!!$F3 3280
7 TraesCS3B01G531200 chr3D 578566704 578568986 2282 False 1437.500000 2374 88.792000 582 2982 2 chr3D.!!$F4 2400
8 TraesCS3B01G531200 chr3D 578549635 578550702 1067 False 1240.000000 1240 87.834000 582 1648 1 chr3D.!!$F2 1066
9 TraesCS3B01G531200 chr3A 714105851 714108976 3125 True 1305.000000 3208 94.926333 1 2752 3 chr3A.!!$R4 2751
10 TraesCS3B01G531200 chr3A 714023988 714026639 2651 True 988.333333 2333 86.064333 582 3281 3 chr3A.!!$R2 2699
11 TraesCS3B01G531200 chr3A 714093051 714093562 511 True 830.000000 830 95.898000 2769 3280 1 chr3A.!!$R1 511
12 TraesCS3B01G531200 chr3A 714084898 714087971 3073 True 661.750000 1799 90.548500 3 2599 4 chr3A.!!$R3 2596

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
489 1196 2.531522 ATTTGAGTTTGTGGCCTTGC 57.468 45.0 3.32 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 4221 4.503296 GCCACTGAAACTTCTCCTTGACTA 60.503 45.833 0.0 0.0 0.0 2.59 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
285 991 4.833390 AGGCCACTAATTATAATCGAGGC 58.167 43.478 19.13 19.13 38.84 4.70
321 1028 9.472361 TGATGTTTTCTAGTAGTACAACTGTTC 57.528 33.333 2.52 0.00 0.00 3.18
467 1174 8.387813 AGTCATTAAATTTCACCTTGGTACCTA 58.612 33.333 14.36 4.36 0.00 3.08
468 1175 8.456471 GTCATTAAATTTCACCTTGGTACCTAC 58.544 37.037 14.36 0.00 0.00 3.18
488 1195 3.795877 ACAATTTGAGTTTGTGGCCTTG 58.204 40.909 3.32 0.00 36.02 3.61
489 1196 2.531522 ATTTGAGTTTGTGGCCTTGC 57.468 45.000 3.32 0.00 0.00 4.01
505 1212 2.590821 CTTGCATAAGGGAATGGAGGG 58.409 52.381 0.00 0.00 0.00 4.30
593 2126 7.406104 AGACCACCTAGCATTAAAGAGAAATT 58.594 34.615 0.00 0.00 0.00 1.82
1827 3406 7.309438 GCTGAAAAACCTATCCATTATGATCCC 60.309 40.741 0.00 0.00 0.00 3.85
1906 3487 0.110486 TCCCCAGCAAAGTGGAAGTC 59.890 55.000 0.00 0.00 40.44 3.01
2531 4204 6.516478 AAGATTGTCGATGATATGTTGTCG 57.484 37.500 0.00 0.00 35.55 4.35
2730 4514 5.281727 GCATGTGATCGAGTATAACTGTCA 58.718 41.667 0.00 0.00 0.00 3.58
2909 4699 9.627123 TTAGGAGTAATTTATGATGGTTTCAGG 57.373 33.333 0.00 0.00 37.89 3.86
3174 5048 4.447389 GCGTTGCCAAAATATCTGTTTGTT 59.553 37.500 0.00 0.00 34.75 2.83
3215 5097 1.185618 TAGAGCGTGACCTTGCCAGT 61.186 55.000 0.00 0.00 0.00 4.00
3241 5123 4.279671 TGTGCCGACATGGTTTTATTTCTT 59.720 37.500 0.00 0.00 41.21 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 971 6.554334 TTTGCCTCGATTATAATTAGTGGC 57.446 37.500 25.16 25.16 38.42 5.01
390 1097 3.390135 ACTGGCATCATTAATACGTCCG 58.610 45.455 0.00 0.00 0.00 4.79
400 1107 5.957842 TCTTTTCGTTTACTGGCATCATT 57.042 34.783 0.00 0.00 0.00 2.57
467 1174 3.795877 CAAGGCCACAAACTCAAATTGT 58.204 40.909 5.01 0.00 41.50 2.71
468 1175 2.545106 GCAAGGCCACAAACTCAAATTG 59.455 45.455 5.01 0.00 0.00 2.32
488 1195 1.777272 ACTCCCTCCATTCCCTTATGC 59.223 52.381 0.00 0.00 0.00 3.14
489 1196 5.850046 AATACTCCCTCCATTCCCTTATG 57.150 43.478 0.00 0.00 0.00 1.90
505 1212 7.094118 GGGACCTGACAGATCTATGTAATACTC 60.094 44.444 3.32 0.00 32.25 2.59
624 2157 2.393271 TGATGACACACACACACACA 57.607 45.000 0.00 0.00 0.00 3.72
625 2158 3.133691 AGATGATGACACACACACACAC 58.866 45.455 0.00 0.00 0.00 3.82
626 2159 3.070015 AGAGATGATGACACACACACACA 59.930 43.478 0.00 0.00 0.00 3.72
627 2160 3.657634 AGAGATGATGACACACACACAC 58.342 45.455 0.00 0.00 0.00 3.82
2548 4221 4.503296 GCCACTGAAACTTCTCCTTGACTA 60.503 45.833 0.00 0.00 0.00 2.59
2909 4699 7.552458 ACCCAAACAAAATTTGATCTTTGTC 57.448 32.000 13.19 0.00 43.25 3.18
3215 5097 2.264005 AAAACCATGTCGGCACAGTA 57.736 45.000 0.00 0.00 39.03 2.74


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

AutoCloner maintained by Alex Coulton.