Multiple sequence alignment - TraesCS3B01G223400

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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 TraesCS3B01G223400 chr3B 100.000 2696 0 0 1 2696 292164226 292161531 0.000000e+00 4979
1 TraesCS3B01G223400 chr3B 87.049 471 38 12 91 546 235858027 235857565 6.660000e-141 510
2 TraesCS3B01G223400 chr7A 98.480 2697 39 2 1 2696 468299666 468302361 0.000000e+00 4752
3 TraesCS3B01G223400 chr7A 93.981 1761 94 5 938 2696 537035383 537037133 0.000000e+00 2654
4 TraesCS3B01G223400 chr7A 92.398 1881 114 9 819 2696 668181213 668183067 0.000000e+00 2654
5 TraesCS3B01G223400 chr2A 92.181 1880 113 12 819 2696 629533071 629534918 0.000000e+00 2627
6 TraesCS3B01G223400 chr2A 88.677 1519 136 14 1178 2696 5903178 5904660 0.000000e+00 1820
7 TraesCS3B01G223400 chr5B 94.322 1638 87 4 1062 2696 652564023 652565657 0.000000e+00 2505
8 TraesCS3B01G223400 chr5B 89.157 1531 133 20 1180 2696 63985454 63983943 0.000000e+00 1877
9 TraesCS3B01G223400 chr5B 95.550 809 36 0 6 814 534307970 534308778 0.000000e+00 1295
10 TraesCS3B01G223400 chr5B 97.849 186 4 0 819 1004 652563835 652564020 3.350000e-84 322
11 TraesCS3B01G223400 chr3A 94.581 1587 72 5 819 2401 672321198 672322774 0.000000e+00 2442
12 TraesCS3B01G223400 chr3A 88.512 1532 128 19 1178 2696 732712057 732710561 0.000000e+00 1810
13 TraesCS3B01G223400 chr3A 93.333 810 37 8 9 818 686550680 686549888 0.000000e+00 1181
14 TraesCS3B01G223400 chr3A 85.629 668 89 5 1126 1791 34975147 34975809 0.000000e+00 695
15 TraesCS3B01G223400 chr3A 93.987 449 21 2 370 818 11684699 11684257 0.000000e+00 675
16 TraesCS3B01G223400 chr3A 93.750 432 21 2 387 818 11710064 11709639 0.000000e+00 643
17 TraesCS3B01G223400 chr3A 90.311 289 17 6 9 297 11685329 11685052 4.240000e-98 368
18 TraesCS3B01G223400 chr4A 88.120 1532 133 20 1178 2696 208835994 208834499 0.000000e+00 1775
19 TraesCS3B01G223400 chr4A 91.646 814 42 7 9 822 614874394 614873607 0.000000e+00 1103
20 TraesCS3B01G223400 chr4A 83.761 702 104 6 1126 1822 730335116 730334420 0.000000e+00 656
21 TraesCS3B01G223400 chr6A 97.680 819 18 1 1 818 29294864 29294046 0.000000e+00 1406
22 TraesCS3B01G223400 chr6A 91.411 326 17 3 9 334 100302829 100302515 1.150000e-118 436
23 TraesCS3B01G223400 chr7B 95.337 815 32 4 6 818 728657345 728658155 0.000000e+00 1290
24 TraesCS3B01G223400 chr7B 94.565 828 40 5 6 829 29703042 29703868 0.000000e+00 1275
25 TraesCS3B01G223400 chr7B 85.629 668 89 3 1126 1791 705031703 705032365 0.000000e+00 695
26 TraesCS3B01G223400 chr7B 89.098 532 51 5 87 611 680641293 680641824 0.000000e+00 654
27 TraesCS3B01G223400 chr7B 88.740 524 52 5 95 611 680634013 680634536 3.790000e-178 634
28 TraesCS3B01G223400 chr7B 87.429 525 58 6 95 611 680627234 680627758 4.970000e-167 597
29 TraesCS3B01G223400 chr7D 83.295 1293 165 26 1386 2659 123837194 123835934 0.000000e+00 1144
30 TraesCS3B01G223400 chr4B 90.672 536 32 6 91 611 251666333 251666865 0.000000e+00 697
31 TraesCS3B01G223400 chr5D 84.167 720 100 8 1126 1842 441693461 441692753 0.000000e+00 686
32 TraesCS3B01G223400 chr6D 82.143 336 37 15 820 1137 464449774 464449444 1.590000e-67 267
33 TraesCS3B01G223400 chr3D 81.982 333 37 16 820 1134 48065219 48065546 7.400000e-66 261
34 TraesCS3B01G223400 chr3D 81.845 336 38 16 820 1137 48086495 48086165 7.400000e-66 261
35 TraesCS3B01G223400 chr3D 81.737 334 38 15 820 1134 593594744 593594415 9.580000e-65 257


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 TraesCS3B01G223400 chr3B 292161531 292164226 2695 True 4979.0 4979 100.0000 1 2696 1 chr3B.!!$R2 2695
1 TraesCS3B01G223400 chr7A 468299666 468302361 2695 False 4752.0 4752 98.4800 1 2696 1 chr7A.!!$F1 2695
2 TraesCS3B01G223400 chr7A 537035383 537037133 1750 False 2654.0 2654 93.9810 938 2696 1 chr7A.!!$F2 1758
3 TraesCS3B01G223400 chr7A 668181213 668183067 1854 False 2654.0 2654 92.3980 819 2696 1 chr7A.!!$F3 1877
4 TraesCS3B01G223400 chr2A 629533071 629534918 1847 False 2627.0 2627 92.1810 819 2696 1 chr2A.!!$F2 1877
5 TraesCS3B01G223400 chr2A 5903178 5904660 1482 False 1820.0 1820 88.6770 1178 2696 1 chr2A.!!$F1 1518
6 TraesCS3B01G223400 chr5B 63983943 63985454 1511 True 1877.0 1877 89.1570 1180 2696 1 chr5B.!!$R1 1516
7 TraesCS3B01G223400 chr5B 652563835 652565657 1822 False 1413.5 2505 96.0855 819 2696 2 chr5B.!!$F2 1877
8 TraesCS3B01G223400 chr5B 534307970 534308778 808 False 1295.0 1295 95.5500 6 814 1 chr5B.!!$F1 808
9 TraesCS3B01G223400 chr3A 672321198 672322774 1576 False 2442.0 2442 94.5810 819 2401 1 chr3A.!!$F2 1582
10 TraesCS3B01G223400 chr3A 732710561 732712057 1496 True 1810.0 1810 88.5120 1178 2696 1 chr3A.!!$R3 1518
11 TraesCS3B01G223400 chr3A 686549888 686550680 792 True 1181.0 1181 93.3330 9 818 1 chr3A.!!$R2 809
12 TraesCS3B01G223400 chr3A 34975147 34975809 662 False 695.0 695 85.6290 1126 1791 1 chr3A.!!$F1 665
13 TraesCS3B01G223400 chr3A 11684257 11685329 1072 True 521.5 675 92.1490 9 818 2 chr3A.!!$R4 809
14 TraesCS3B01G223400 chr4A 208834499 208835994 1495 True 1775.0 1775 88.1200 1178 2696 1 chr4A.!!$R1 1518
15 TraesCS3B01G223400 chr4A 614873607 614874394 787 True 1103.0 1103 91.6460 9 822 1 chr4A.!!$R2 813
16 TraesCS3B01G223400 chr4A 730334420 730335116 696 True 656.0 656 83.7610 1126 1822 1 chr4A.!!$R3 696
17 TraesCS3B01G223400 chr6A 29294046 29294864 818 True 1406.0 1406 97.6800 1 818 1 chr6A.!!$R1 817
18 TraesCS3B01G223400 chr7B 728657345 728658155 810 False 1290.0 1290 95.3370 6 818 1 chr7B.!!$F6 812
19 TraesCS3B01G223400 chr7B 29703042 29703868 826 False 1275.0 1275 94.5650 6 829 1 chr7B.!!$F1 823
20 TraesCS3B01G223400 chr7B 705031703 705032365 662 False 695.0 695 85.6290 1126 1791 1 chr7B.!!$F5 665
21 TraesCS3B01G223400 chr7B 680641293 680641824 531 False 654.0 654 89.0980 87 611 1 chr7B.!!$F4 524
22 TraesCS3B01G223400 chr7B 680634013 680634536 523 False 634.0 634 88.7400 95 611 1 chr7B.!!$F3 516
23 TraesCS3B01G223400 chr7B 680627234 680627758 524 False 597.0 597 87.4290 95 611 1 chr7B.!!$F2 516
24 TraesCS3B01G223400 chr7D 123835934 123837194 1260 True 1144.0 1144 83.2950 1386 2659 1 chr7D.!!$R1 1273
25 TraesCS3B01G223400 chr4B 251666333 251666865 532 False 697.0 697 90.6720 91 611 1 chr4B.!!$F1 520
26 TraesCS3B01G223400 chr5D 441692753 441693461 708 True 686.0 686 84.1670 1126 1842 1 chr5D.!!$R1 716

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
553 863 1.809547 GAGAAGAAGCCTTTGTGGAGC 59.190 52.381 0.0 0.0 38.35 4.70 F
1099 1416 1.748493 TGCTTGACTTGTTTGACCCAC 59.252 47.619 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1854 7.619965 TCTGATTGTGTTTCCCTTTTCTTTTT 58.380 30.769 0.0 0.0 0.00 1.94 R
2066 2420 9.865321 CAAATCAACAAATCATACTGGATTTCT 57.135 29.630 0.0 0.0 43.66 2.52 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
166 169 6.097554 GTCTCCAACTCTCCATAAATCTCAGA 59.902 42.308 0.00 0.00 0.00 3.27
309 326 4.535781 TCTCCCTCTCTTTCTCTGATCTG 58.464 47.826 0.00 0.00 0.00 2.90
483 793 2.247699 TGTAGTGGAGGTAGCATGGT 57.752 50.000 1.62 1.62 0.00 3.55
553 863 1.809547 GAGAAGAAGCCTTTGTGGAGC 59.190 52.381 0.00 0.00 38.35 4.70
1099 1416 1.748493 TGCTTGACTTGTTTGACCCAC 59.252 47.619 0.00 0.00 0.00 4.61
2066 2420 8.333235 AGGTTGTAATGTATGGTTTCTAATCCA 58.667 33.333 0.00 0.00 38.14 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.715070 TCAGTTTTCCACGTCAAACAAATT 58.285 33.333 14.03 0.0 35.66 1.82
11 12 3.375922 GGAGTTTTCAGTTTTCCACGTCA 59.624 43.478 0.00 0.0 0.00 4.35
18 19 4.154375 GGGATCGAGGAGTTTTCAGTTTTC 59.846 45.833 0.00 0.0 0.00 2.29
166 169 0.560688 GGGAGAGGAGAGGACTGGAT 59.439 60.000 0.00 0.0 0.00 3.41
269 286 3.964031 GGAGATGAGAACATACCTCCTGT 59.036 47.826 0.00 0.0 36.82 4.00
309 326 4.277476 TCAGAGAAGGAGATGGAGAAGAC 58.723 47.826 0.00 0.0 0.00 3.01
1016 1333 3.068024 CACTAGTTCAAAAAGGCAGGCAA 59.932 43.478 0.00 0.0 0.00 4.52
1534 1854 7.619965 TCTGATTGTGTTTCCCTTTTCTTTTT 58.380 30.769 0.00 0.0 0.00 1.94
2066 2420 9.865321 CAAATCAACAAATCATACTGGATTTCT 57.135 29.630 0.00 0.0 43.66 2.52


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

AutoCloner maintained by Alex Coulton.